Multiple sequence alignment - TraesCS7A01G203500

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7A01G203500 chr7A 100.000 5267 0 0 1 5267 165521207 165526473 0.000000e+00 9727.0
1 TraesCS7A01G203500 chr7A 100.000 4026 0 0 5363 9388 165526569 165530594 0.000000e+00 7435.0
2 TraesCS7A01G203500 chr7A 85.354 396 51 6 192 584 213099119 213099510 4.080000e-108 403.0
3 TraesCS7A01G203500 chr7A 95.960 198 7 1 1 197 442675057 442674860 4.230000e-83 320.0
4 TraesCS7A01G203500 chr7A 98.305 59 0 1 5209 5267 165526569 165526626 1.670000e-17 102.0
5 TraesCS7A01G203500 chr6B 90.332 3589 208 59 5835 9369 605768944 605765441 0.000000e+00 4577.0
6 TraesCS7A01G203500 chr6B 87.111 931 85 22 191 1100 605770721 605769805 0.000000e+00 1022.0
7 TraesCS7A01G203500 chr6B 87.767 891 69 12 1148 2023 605769804 605768939 0.000000e+00 1005.0
8 TraesCS7A01G203500 chr6B 86.227 864 82 17 7651 8497 499015332 499014489 0.000000e+00 902.0
9 TraesCS7A01G203500 chr6B 98.899 454 1 2 5384 5835 459181606 459182057 0.000000e+00 808.0
10 TraesCS7A01G203500 chr6B 87.592 677 66 9 6425 7091 391682771 391682103 0.000000e+00 769.0
11 TraesCS7A01G203500 chr6B 87.482 679 67 9 6423 7091 494380063 494379393 0.000000e+00 767.0
12 TraesCS7A01G203500 chr6B 87.040 679 70 9 6423 7091 522100849 522100179 0.000000e+00 750.0
13 TraesCS7A01G203500 chr6B 99.658 292 1 0 5544 5835 459169634 459169925 1.390000e-147 534.0
14 TraesCS7A01G203500 chr6B 87.565 386 28 12 7271 7647 499016125 499015751 6.740000e-116 429.0
15 TraesCS7A01G203500 chr6B 81.869 535 47 26 5843 6373 391683261 391682773 1.140000e-108 405.0
16 TraesCS7A01G203500 chr6B 87.156 327 35 7 5512 5835 456267472 456267794 1.930000e-96 364.0
17 TraesCS7A01G203500 chr6B 86.462 325 35 9 5514 5835 409107120 409107438 1.940000e-91 348.0
18 TraesCS7A01G203500 chr6B 87.843 255 20 5 6120 6374 494380305 494380062 1.190000e-73 289.0
19 TraesCS7A01G203500 chr6B 80.000 295 39 11 1161 1440 173818287 173817998 5.750000e-47 200.0
20 TraesCS7A01G203500 chr6B 79.322 295 43 11 1161 1440 474646502 474646793 3.460000e-44 191.0
21 TraesCS7A01G203500 chr6B 90.476 147 11 1 6228 6374 476035249 476035392 3.460000e-44 191.0
22 TraesCS7A01G203500 chr6B 92.800 125 4 4 7083 7207 436204038 436203919 9.690000e-40 176.0
23 TraesCS7A01G203500 chr6B 88.496 113 10 3 4886 4997 207140088 207139978 5.910000e-27 134.0
24 TraesCS7A01G203500 chr6B 97.872 47 1 0 8371 8417 522099320 522099366 2.170000e-11 82.4
25 TraesCS7A01G203500 chr6B 100.000 38 0 0 9351 9388 275313480 275313443 4.700000e-08 71.3
26 TraesCS7A01G203500 chr6B 100.000 37 0 0 9352 9388 520653507 520653543 1.690000e-07 69.4
27 TraesCS7A01G203500 chr6B 100.000 30 0 0 6373 6402 143461956 143461927 1.000000e-03 56.5
28 TraesCS7A01G203500 chr6B 100.000 29 0 0 9319 9347 534189958 534189986 5.000000e-03 54.7
29 TraesCS7A01G203500 chr6B 94.286 35 1 1 6373 6406 417466269 417466235 1.700000e-02 52.8
30 TraesCS7A01G203500 chr6B 94.286 35 1 1 6373 6406 507574981 507574947 1.700000e-02 52.8
31 TraesCS7A01G203500 chr1B 92.989 2881 138 45 2024 4868 343961973 343959121 0.000000e+00 4143.0
32 TraesCS7A01G203500 chr1B 88.218 679 59 11 6423 7091 148509468 148510135 0.000000e+00 791.0
33 TraesCS7A01G203500 chr1B 87.130 676 56 14 6426 7091 358387786 358387132 0.000000e+00 737.0
34 TraesCS7A01G203500 chr1B 87.361 538 51 8 6564 7091 377098715 377099245 1.350000e-167 601.0
35 TraesCS7A01G203500 chr1B 87.175 538 52 8 6564 7091 193412784 193412254 6.280000e-166 595.0
36 TraesCS7A01G203500 chr1B 83.948 542 44 23 5836 6375 358388287 358387787 6.590000e-131 479.0
37 TraesCS7A01G203500 chr1B 82.625 541 51 22 5836 6374 148508970 148509469 1.120000e-118 438.0
38 TraesCS7A01G203500 chr1B 85.207 338 40 10 5508 5842 161300146 161299816 1.170000e-88 339.0
39 TraesCS7A01G203500 chr1B 85.498 331 40 8 5508 5835 161308255 161307930 1.170000e-88 339.0
40 TraesCS7A01G203500 chr1B 84.751 341 42 10 5508 5845 643613167 643612834 5.430000e-87 333.0
41 TraesCS7A01G203500 chr1B 86.711 301 32 8 5538 5835 333552177 333552472 2.530000e-85 327.0
42 TraesCS7A01G203500 chr1B 86.747 166 13 5 7104 7269 304179986 304180142 9.690000e-40 176.0
43 TraesCS7A01G203500 chr1B 92.742 124 4 4 7085 7207 193411724 193411605 3.480000e-39 174.0
44 TraesCS7A01G203500 chr1B 92.000 125 5 3 7083 7207 197790664 197790783 4.510000e-38 171.0
45 TraesCS7A01G203500 chr1B 77.820 266 34 8 9069 9329 453015903 453015658 3.530000e-29 141.0
46 TraesCS7A01G203500 chr1B 88.288 111 8 4 4885 4994 385581499 385581605 2.750000e-25 128.0
47 TraesCS7A01G203500 chr1B 89.000 100 8 3 4899 4997 58005788 58005885 4.600000e-23 121.0
48 TraesCS7A01G203500 chr1B 85.185 81 9 3 9287 9365 267743466 267743387 7.810000e-11 80.5
49 TraesCS7A01G203500 chr1B 95.745 47 2 0 8371 8417 148510981 148510935 1.010000e-09 76.8
50 TraesCS7A01G203500 chr1B 95.745 47 2 0 8371 8417 193411395 193411441 1.010000e-09 76.8
51 TraesCS7A01G203500 chr1B 83.133 83 11 3 9284 9364 191669304 191669385 1.310000e-08 73.1
52 TraesCS7A01G203500 chr1B 86.567 67 7 2 9281 9346 197790158 197790223 1.310000e-08 73.1
53 TraesCS7A01G203500 chr1B 100.000 37 0 0 9352 9388 439065451 439065487 1.690000e-07 69.4
54 TraesCS7A01G203500 chr1B 85.714 63 9 0 9292 9354 223900663 223900725 6.080000e-07 67.6
55 TraesCS7A01G203500 chr1B 97.368 38 1 0 9351 9388 198687139 198687176 2.190000e-06 65.8
56 TraesCS7A01G203500 chr1B 95.000 40 1 1 4870 4909 405096906 405096944 2.830000e-05 62.1
57 TraesCS7A01G203500 chr5A 95.966 2553 74 7 6826 9356 237942914 237940369 0.000000e+00 4117.0
58 TraesCS7A01G203500 chr5A 89.829 1111 76 12 194 1286 237949506 237948415 0.000000e+00 1391.0
59 TraesCS7A01G203500 chr5A 95.142 741 34 2 1284 2023 237943836 237943097 0.000000e+00 1168.0
60 TraesCS7A01G203500 chr5A 93.071 534 22 13 4658 5187 367276211 367276733 0.000000e+00 767.0
61 TraesCS7A01G203500 chr5A 97.356 416 9 2 5421 5835 367277046 367277460 0.000000e+00 706.0
62 TraesCS7A01G203500 chr5A 90.667 150 8 5 7083 7231 131736400 131736544 2.670000e-45 195.0
63 TraesCS7A01G203500 chr5A 100.000 38 0 0 9351 9388 151118697 151118734 4.700000e-08 71.3
64 TraesCS7A01G203500 chr6A 92.289 2892 125 50 2006 4862 108106505 108103677 0.000000e+00 4015.0
65 TraesCS7A01G203500 chr6A 97.445 548 10 3 4514 5058 108103666 108103120 0.000000e+00 931.0
66 TraesCS7A01G203500 chr6A 85.455 880 81 16 7651 8511 461838822 461839673 0.000000e+00 872.0
67 TraesCS7A01G203500 chr6A 98.938 471 2 2 5365 5835 108094613 108094146 0.000000e+00 839.0
68 TraesCS7A01G203500 chr6A 88.802 384 28 11 7268 7647 461838035 461838407 3.090000e-124 457.0
69 TraesCS7A01G203500 chr6A 83.168 404 52 10 193 584 203217552 203217951 1.160000e-93 355.0
70 TraesCS7A01G203500 chr6A 96.491 57 0 1 5211 5267 108094613 108094559 1.000000e-14 93.5
71 TraesCS7A01G203500 chr6A 94.444 54 1 2 8371 8422 380416399 380416346 2.170000e-11 82.4
72 TraesCS7A01G203500 chr6A 100.000 38 0 0 9351 9388 566059208 566059245 4.700000e-08 71.3
73 TraesCS7A01G203500 chr6A 100.000 37 0 0 9352 9388 489102099 489102063 1.690000e-07 69.4
74 TraesCS7A01G203500 chr6A 100.000 37 0 0 9352 9388 565831800 565831836 1.690000e-07 69.4
75 TraesCS7A01G203500 chr3A 95.713 2496 83 5 6884 9356 271638945 271641439 0.000000e+00 3995.0
76 TraesCS7A01G203500 chr3A 93.642 1384 71 9 642 2023 271637312 271638680 0.000000e+00 2052.0
77 TraesCS7A01G203500 chr3A 88.772 1042 80 25 3467 4493 33795490 33794471 0.000000e+00 1242.0
78 TraesCS7A01G203500 chr3A 95.780 545 18 5 4723 5266 392419 391879 0.000000e+00 874.0
79 TraesCS7A01G203500 chr3A 84.886 880 86 19 7651 8511 108921276 108922127 0.000000e+00 845.0
80 TraesCS7A01G203500 chr3A 97.363 455 8 3 5382 5835 606162999 606163450 0.000000e+00 771.0
81 TraesCS7A01G203500 chr3A 92.655 531 24 13 4658 5184 606162001 606162520 0.000000e+00 750.0
82 TraesCS7A01G203500 chr3A 92.936 453 31 1 189 640 271632946 271633398 0.000000e+00 658.0
83 TraesCS7A01G203500 chr3A 89.376 433 34 7 7987 8412 209650924 209651351 1.390000e-147 534.0
84 TraesCS7A01G203500 chr3A 88.802 384 28 11 7268 7647 108920489 108920861 3.090000e-124 457.0
85 TraesCS7A01G203500 chr3A 95.219 251 12 0 5835 6085 271638675 271638925 1.900000e-106 398.0
86 TraesCS7A01G203500 chr3A 86.895 351 33 8 7653 7993 209642677 209643024 1.910000e-101 381.0
87 TraesCS7A01G203500 chr3A 96.907 194 6 0 1 194 441237509 441237702 9.090000e-85 326.0
88 TraesCS7A01G203500 chr3A 95.025 201 8 2 1 199 75060302 75060102 1.970000e-81 315.0
89 TraesCS7A01G203500 chr4B 93.951 2579 132 22 2024 4591 277444992 277447557 0.000000e+00 3877.0
90 TraesCS7A01G203500 chr4B 93.871 2578 136 21 2024 4591 277436863 277439428 0.000000e+00 3866.0
91 TraesCS7A01G203500 chr4B 94.225 2511 110 30 2024 4519 250816517 250819007 0.000000e+00 3801.0
92 TraesCS7A01G203500 chr4B 84.725 910 104 19 1041 1932 204720479 204719587 0.000000e+00 878.0
93 TraesCS7A01G203500 chr4B 87.187 679 69 9 6423 7091 401279555 401280225 0.000000e+00 756.0
94 TraesCS7A01G203500 chr4B 87.040 679 59 12 6423 7091 404623648 404622989 0.000000e+00 739.0
95 TraesCS7A01G203500 chr4B 86.617 538 55 8 6564 7091 125063017 125062487 6.320000e-161 579.0
96 TraesCS7A01G203500 chr4B 86.220 537 59 9 6564 7091 491007451 491006921 1.370000e-157 568.0
97 TraesCS7A01G203500 chr4B 85.140 572 60 15 5837 6399 204719465 204718910 6.370000e-156 562.0
98 TraesCS7A01G203500 chr4B 88.652 423 38 9 7116 7532 204711700 204711282 3.030000e-139 507.0
99 TraesCS7A01G203500 chr4B 84.660 515 70 6 6558 7069 249884782 249885290 1.090000e-138 505.0
100 TraesCS7A01G203500 chr4B 83.794 543 48 23 5836 6374 404624153 404623647 6.590000e-131 479.0
101 TraesCS7A01G203500 chr4B 83.026 542 57 23 5836 6374 401279047 401279556 8.590000e-125 459.0
102 TraesCS7A01G203500 chr4B 89.444 360 34 3 6402 6760 204718867 204718511 1.440000e-122 451.0
103 TraesCS7A01G203500 chr4B 88.498 313 32 4 5524 5835 360307594 360307285 8.900000e-100 375.0
104 TraesCS7A01G203500 chr4B 82.716 405 49 21 5445 5835 278939870 278940267 3.250000e-89 340.0
105 TraesCS7A01G203500 chr4B 82.469 405 51 19 5445 5835 278931737 278932135 4.200000e-88 337.0
106 TraesCS7A01G203500 chr4B 84.894 331 41 9 5508 5835 432674650 432674974 9.090000e-85 326.0
107 TraesCS7A01G203500 chr4B 84.290 331 44 8 5508 5835 432682650 432682975 5.470000e-82 316.0
108 TraesCS7A01G203500 chr4B 84.404 327 40 11 5512 5835 620458092 620458410 2.550000e-80 311.0
109 TraesCS7A01G203500 chr4B 91.146 192 16 1 6423 6614 352167639 352167449 9.350000e-65 259.0
110 TraesCS7A01G203500 chr4B 88.636 176 18 1 6423 6598 204712204 204712031 7.380000e-51 213.0
111 TraesCS7A01G203500 chr4B 90.476 147 11 1 6228 6374 373351934 373352077 3.460000e-44 191.0
112 TraesCS7A01G203500 chr4B 92.063 126 4 5 7083 7207 149995037 149995157 1.250000e-38 172.0
113 TraesCS7A01G203500 chr4B 92.000 125 5 4 7083 7207 175306650 175306531 4.510000e-38 171.0
114 TraesCS7A01G203500 chr4B 91.200 125 6 4 7083 7207 404622468 404622349 2.100000e-36 165.0
115 TraesCS7A01G203500 chr4B 91.803 122 5 3 7083 7204 491006393 491006277 2.100000e-36 165.0
116 TraesCS7A01G203500 chr4B 91.200 125 6 4 7083 7207 609103869 609103750 2.100000e-36 165.0
117 TraesCS7A01G203500 chr4B 90.400 125 7 3 7083 7207 316994808 316994927 9.760000e-35 159.0
118 TraesCS7A01G203500 chr4B 90.598 117 7 2 7091 7207 338502987 338502875 1.630000e-32 152.0
119 TraesCS7A01G203500 chr4B 90.123 81 6 2 4906 4986 432674119 432674197 4.640000e-18 104.0
120 TraesCS7A01G203500 chr4B 94.030 67 4 0 6308 6374 204712269 204712203 1.670000e-17 102.0
121 TraesCS7A01G203500 chr4B 95.833 48 2 0 8370 8417 253905808 253905761 2.810000e-10 78.7
122 TraesCS7A01G203500 chr4B 95.745 47 2 0 8371 8417 316996333 316996287 1.010000e-09 76.8
123 TraesCS7A01G203500 chr4B 95.745 47 2 0 8371 8417 404622214 404622260 1.010000e-09 76.8
124 TraesCS7A01G203500 chr4B 97.619 42 1 0 8371 8412 125061643 125061684 1.310000e-08 73.1
125 TraesCS7A01G203500 chr4B 95.556 45 2 0 8371 8415 149995345 149995301 1.310000e-08 73.1
126 TraesCS7A01G203500 chr4B 95.556 45 2 0 8371 8415 172483243 172483199 1.310000e-08 73.1
127 TraesCS7A01G203500 chr4B 84.416 77 9 3 4910 4986 299740149 299740076 1.310000e-08 73.1
128 TraesCS7A01G203500 chr4B 95.000 40 1 1 9349 9388 588090064 588090026 2.830000e-05 62.1
129 TraesCS7A01G203500 chr4B 94.737 38 1 1 4872 4909 203199775 203199811 3.660000e-04 58.4
130 TraesCS7A01G203500 chr4B 94.286 35 1 1 6373 6406 541857780 541857814 1.700000e-02 52.8
131 TraesCS7A01G203500 chr1A 93.687 2582 119 33 2024 4591 236116436 236113885 0.000000e+00 3825.0
132 TraesCS7A01G203500 chr1A 82.569 545 45 24 5836 6374 244177711 244177211 1.450000e-117 435.0
133 TraesCS7A01G203500 chr1A 96.923 195 6 0 1 195 464168396 464168202 2.530000e-85 327.0
134 TraesCS7A01G203500 chr1A 87.952 83 10 0 9271 9353 93764257 93764175 2.160000e-16 99.0
135 TraesCS7A01G203500 chr1A 86.111 72 8 2 9284 9354 272650926 272650996 1.010000e-09 76.8
136 TraesCS7A01G203500 chr1A 100.000 37 0 0 9352 9388 133964280 133964244 1.690000e-07 69.4
137 TraesCS7A01G203500 chr1A 100.000 37 0 0 9352 9388 557764810 557764846 1.690000e-07 69.4
138 TraesCS7A01G203500 chr1A 82.278 79 12 2 9281 9358 376860650 376860573 6.080000e-07 67.6
139 TraesCS7A01G203500 chr3B 93.498 2584 131 29 2024 4584 111487977 111485408 0.000000e+00 3807.0
140 TraesCS7A01G203500 chr3B 93.344 2584 135 29 2024 4584 111495974 111493405 0.000000e+00 3784.0
141 TraesCS7A01G203500 chr3B 91.253 2195 124 38 2709 4862 543910884 543908717 0.000000e+00 2928.0
142 TraesCS7A01G203500 chr3B 90.627 1675 107 29 3555 5213 368788412 368786772 0.000000e+00 2178.0
143 TraesCS7A01G203500 chr3B 89.957 1633 108 30 3555 5170 368780492 368778899 0.000000e+00 2056.0
144 TraesCS7A01G203500 chr3B 98.739 476 3 1 5363 5838 368778452 368777980 0.000000e+00 843.0
145 TraesCS7A01G203500 chr3B 98.906 457 5 0 5379 5835 368786604 368786148 0.000000e+00 817.0
146 TraesCS7A01G203500 chr3B 84.772 834 83 16 1114 1932 330780960 330780156 0.000000e+00 797.0
147 TraesCS7A01G203500 chr3B 90.149 335 31 2 5835 6167 330780035 330779701 1.450000e-117 435.0
148 TraesCS7A01G203500 chr3B 96.392 194 7 0 1 194 128757987 128758180 4.230000e-83 320.0
149 TraesCS7A01G203500 chr3B 88.333 240 21 7 5836 6072 406615736 406615971 2.000000e-71 281.0
150 TraesCS7A01G203500 chr3B 75.000 608 77 30 663 1231 627897147 627896576 2.660000e-50 211.0
151 TraesCS7A01G203500 chr3B 93.600 125 3 3 7083 7207 371037760 371037641 2.080000e-41 182.0
152 TraesCS7A01G203500 chr3B 80.400 250 34 5 659 908 330781467 330781233 9.690000e-40 176.0
153 TraesCS7A01G203500 chr3B 81.500 200 28 7 9160 9352 262652582 262652385 1.260000e-33 156.0
154 TraesCS7A01G203500 chr3B 94.681 94 5 0 1930 2023 330780123 330780030 7.600000e-31 147.0
155 TraesCS7A01G203500 chr3B 79.897 194 34 5 9164 9352 305807086 305807279 4.570000e-28 137.0
156 TraesCS7A01G203500 chr3B 93.243 74 1 1 5194 5267 368778467 368778398 1.290000e-18 106.0
157 TraesCS7A01G203500 chr3B 97.143 35 0 1 6373 6406 411359062 411359028 3.660000e-04 58.4
158 TraesCS7A01G203500 chr2B 92.698 2602 127 41 2709 5267 488392167 488394748 0.000000e+00 3694.0
159 TraesCS7A01G203500 chr2B 98.745 478 2 3 5365 5842 488394759 488395232 0.000000e+00 846.0
160 TraesCS7A01G203500 chr2B 88.807 679 58 9 6423 7091 546971647 546972317 0.000000e+00 817.0
161 TraesCS7A01G203500 chr2B 80.700 829 96 37 7664 8448 62995151 62994343 3.780000e-163 586.0
162 TraesCS7A01G203500 chr2B 89.873 316 28 4 5522 5835 256766706 256767019 4.080000e-108 403.0
163 TraesCS7A01G203500 chr2B 88.797 241 21 6 5836 6072 546971164 546971402 3.320000e-74 291.0
164 TraesCS7A01G203500 chr2B 79.599 299 41 11 1161 1443 459421458 459421164 7.440000e-46 196.0
165 TraesCS7A01G203500 chr2B 93.600 125 3 4 7083 7207 302986199 302986318 2.080000e-41 182.0
166 TraesCS7A01G203500 chr2B 92.800 125 4 3 7083 7207 371937946 371938065 9.690000e-40 176.0
167 TraesCS7A01G203500 chr2B 86.957 115 12 2 9243 9354 520703775 520703889 9.900000e-25 126.0
168 TraesCS7A01G203500 chr2B 78.788 198 27 8 602 784 480543227 480543030 1.660000e-22 119.0
169 TraesCS7A01G203500 chr2B 98.305 59 0 1 5363 5420 488394690 488394748 1.670000e-17 102.0
170 TraesCS7A01G203500 chr2B 96.491 57 0 1 5211 5267 488394759 488394813 1.000000e-14 93.5
171 TraesCS7A01G203500 chr2B 94.872 39 2 0 6369 6407 458623139 458623177 2.830000e-05 62.1
172 TraesCS7A01G203500 chr2B 100.000 28 0 0 6406 6433 463283936 463283909 1.700000e-02 52.8
173 TraesCS7A01G203500 chrUn 92.560 2594 149 37 2024 4600 277238044 277235478 0.000000e+00 3681.0
174 TraesCS7A01G203500 chrUn 93.323 2501 131 27 2023 4507 188792164 188789684 0.000000e+00 3661.0
175 TraesCS7A01G203500 chrUn 82.516 469 56 12 7949 8405 39276075 39276529 1.140000e-103 388.0
176 TraesCS7A01G203500 chrUn 88.704 301 30 4 5535 5835 23332905 23333201 1.930000e-96 364.0
177 TraesCS7A01G203500 chrUn 88.235 272 29 3 5565 5835 419539688 419539957 1.180000e-83 322.0
178 TraesCS7A01G203500 chrUn 86.713 286 34 4 5552 5835 102619745 102619462 1.970000e-81 315.0
179 TraesCS7A01G203500 chrUn 85.315 286 38 4 5552 5835 102629744 102629461 9.220000e-75 292.0
180 TraesCS7A01G203500 chrUn 83.596 317 46 6 5521 5835 367890034 367890346 9.220000e-75 292.0
181 TraesCS7A01G203500 chrUn 84.039 307 38 9 5537 5835 61718382 61718685 1.540000e-72 285.0
182 TraesCS7A01G203500 chrUn 83.178 321 45 8 5517 5835 84563382 84563695 1.540000e-72 285.0
183 TraesCS7A01G203500 chrUn 84.694 294 36 8 5546 5835 407253190 407253478 1.540000e-72 285.0
184 TraesCS7A01G203500 chrUn 84.694 294 36 8 5546 5835 438649976 438650264 1.540000e-72 285.0
185 TraesCS7A01G203500 chrUn 82.154 325 46 12 5519 5835 102061256 102060936 1.550000e-67 268.0
186 TraesCS7A01G203500 chrUn 79.028 391 59 20 5464 5844 242129694 242129317 7.280000e-61 246.0
187 TraesCS7A01G203500 chrUn 89.796 147 12 1 6228 6374 325926916 325926773 1.610000e-42 185.0
188 TraesCS7A01G203500 chrUn 95.745 47 2 0 8371 8417 322994962 322995008 1.010000e-09 76.8
189 TraesCS7A01G203500 chrUn 97.368 38 1 0 9351 9388 13905513 13905550 2.190000e-06 65.8
190 TraesCS7A01G203500 chrUn 100.000 35 0 0 9354 9388 61700121 61700155 2.190000e-06 65.8
191 TraesCS7A01G203500 chrUn 100.000 35 0 0 9354 9388 65658367 65658401 2.190000e-06 65.8
192 TraesCS7A01G203500 chrUn 100.000 35 0 0 9354 9388 238467546 238467512 2.190000e-06 65.8
193 TraesCS7A01G203500 chrUn 100.000 35 0 0 9354 9388 239389525 239389491 2.190000e-06 65.8
194 TraesCS7A01G203500 chrUn 100.000 35 0 0 9354 9388 306084852 306084818 2.190000e-06 65.8
195 TraesCS7A01G203500 chrUn 100.000 35 0 0 9354 9388 314151090 314151056 2.190000e-06 65.8
196 TraesCS7A01G203500 chrUn 97.297 37 1 0 9352 9388 103703957 103703993 7.870000e-06 63.9
197 TraesCS7A01G203500 chrUn 100.000 32 0 0 9357 9388 6244293 6244262 1.020000e-04 60.2
198 TraesCS7A01G203500 chrUn 97.143 35 1 0 9354 9388 11435904 11435938 1.020000e-04 60.2
199 TraesCS7A01G203500 chr2A 92.699 2575 137 37 2709 5267 118151753 118154292 0.000000e+00 3666.0
200 TraesCS7A01G203500 chr2A 91.680 2548 145 38 2709 5240 118159464 118161960 0.000000e+00 3469.0
201 TraesCS7A01G203500 chr2A 98.646 443 5 1 5394 5835 118162484 118162926 0.000000e+00 784.0
202 TraesCS7A01G203500 chr2A 80.497 523 58 16 7664 8159 40559535 40559030 2.490000e-95 361.0
203 TraesCS7A01G203500 chr2A 97.143 35 0 1 6373 6406 100116437 100116403 3.660000e-04 58.4
204 TraesCS7A01G203500 chr5B 93.441 2485 136 23 2024 4496 310034523 310032054 0.000000e+00 3661.0
205 TraesCS7A01G203500 chr5B 86.212 1233 112 49 3552 4765 241175811 241177004 0.000000e+00 1282.0
206 TraesCS7A01G203500 chr5B 95.114 614 14 14 4658 5267 489599513 489600114 0.000000e+00 953.0
207 TraesCS7A01G203500 chr5B 98.214 504 7 2 4723 5226 489591325 489591826 0.000000e+00 880.0
208 TraesCS7A01G203500 chr5B 85.436 872 69 34 3992 4847 241183312 241184141 0.000000e+00 854.0
209 TraesCS7A01G203500 chr5B 99.151 471 1 2 5365 5835 241185142 241185609 0.000000e+00 845.0
210 TraesCS7A01G203500 chr5B 98.526 475 6 1 5363 5836 489600057 489600531 0.000000e+00 837.0
211 TraesCS7A01G203500 chr5B 85.420 679 68 13 6423 7091 158673093 158673750 0.000000e+00 676.0
212 TraesCS7A01G203500 chr5B 97.799 318 6 1 5519 5835 489592247 489592564 1.780000e-151 547.0
213 TraesCS7A01G203500 chr5B 99.658 292 1 0 5544 5835 241177393 241177684 1.390000e-147 534.0
214 TraesCS7A01G203500 chr5B 100.000 285 0 0 4983 5267 241184375 241184659 2.320000e-145 527.0
215 TraesCS7A01G203500 chr5B 88.535 314 32 4 5523 5835 224134377 224134687 2.470000e-100 377.0
216 TraesCS7A01G203500 chr5B 91.333 150 7 4 7083 7231 112633083 112632939 5.750000e-47 200.0
217 TraesCS7A01G203500 chr5B 98.305 59 0 1 5363 5420 241184601 241184659 1.670000e-17 102.0
218 TraesCS7A01G203500 chr5B 96.491 57 0 1 5211 5267 241185142 241185196 1.000000e-14 93.5
219 TraesCS7A01G203500 chr5B 94.231 52 3 0 8371 8422 112632795 112632846 7.810000e-11 80.5
220 TraesCS7A01G203500 chr5B 92.593 54 3 1 8369 8422 251563148 251563200 1.010000e-09 76.8
221 TraesCS7A01G203500 chr5B 87.692 65 7 1 9291 9355 216504307 216504244 3.640000e-09 75.0
222 TraesCS7A01G203500 chr5B 97.436 39 0 1 9350 9388 19238162 19238125 2.190000e-06 65.8
223 TraesCS7A01G203500 chr5B 100.000 31 0 0 6376 6406 245874847 245874817 3.660000e-04 58.4
224 TraesCS7A01G203500 chr5B 90.909 44 2 2 6364 6405 600518132 600518175 3.660000e-04 58.4
225 TraesCS7A01G203500 chr1D 92.714 2539 114 27 6842 9354 28960539 28958046 0.000000e+00 3598.0
226 TraesCS7A01G203500 chr1D 89.465 1272 99 14 190 1438 28963335 28962076 0.000000e+00 1574.0
227 TraesCS7A01G203500 chr1D 90.837 1004 52 10 5835 6812 28961527 28960538 0.000000e+00 1308.0
228 TraesCS7A01G203500 chr1D 92.035 565 25 8 1472 2023 28962079 28961522 0.000000e+00 776.0
229 TraesCS7A01G203500 chr1D 81.679 393 54 14 5451 5835 241421247 241420865 2.550000e-80 311.0
230 TraesCS7A01G203500 chr1D 85.667 300 37 6 5541 5836 248939740 248939443 2.550000e-80 311.0
231 TraesCS7A01G203500 chr1D 86.525 282 34 4 5560 5839 98146072 98146351 3.290000e-79 307.0
232 TraesCS7A01G203500 chr1D 83.582 335 45 9 5509 5835 241431212 241430880 1.180000e-78 305.0
233 TraesCS7A01G203500 chr1D 84.062 320 36 14 5522 5835 410893786 410893476 2.560000e-75 294.0
234 TraesCS7A01G203500 chr1D 82.596 339 49 9 5509 5840 25326034 25326369 3.320000e-74 291.0
235 TraesCS7A01G203500 chr1D 83.086 337 40 15 5509 5835 234945337 234945666 3.320000e-74 291.0
236 TraesCS7A01G203500 chr1D 80.315 381 57 17 5464 5835 339537619 339537248 1.200000e-68 272.0
237 TraesCS7A01G203500 chr1D 85.470 117 12 4 7129 7244 251794133 251794245 5.960000e-22 117.0
238 TraesCS7A01G203500 chr1D 95.000 40 1 1 9349 9388 456618763 456618801 2.830000e-05 62.1
239 TraesCS7A01G203500 chr7B 88.782 1043 87 13 996 2023 304528825 304527798 0.000000e+00 1251.0
240 TraesCS7A01G203500 chr7B 91.655 719 46 3 6401 7118 304527203 304526498 0.000000e+00 983.0
241 TraesCS7A01G203500 chr7B 88.166 676 62 9 6426 7091 246958108 246957441 0.000000e+00 789.0
242 TraesCS7A01G203500 chr7B 87.334 679 68 9 6423 7091 399237712 399238382 0.000000e+00 761.0
243 TraesCS7A01G203500 chr7B 85.814 719 68 14 192 879 304529540 304528825 0.000000e+00 732.0
244 TraesCS7A01G203500 chr7B 89.948 577 30 9 5835 6402 304527803 304527246 0.000000e+00 719.0
245 TraesCS7A01G203500 chr7B 89.655 464 42 5 1471 1932 490183978 490183519 3.780000e-163 586.0
246 TraesCS7A01G203500 chr7B 86.825 463 36 15 8914 9356 304526523 304526066 2.360000e-135 494.0
247 TraesCS7A01G203500 chr7B 83.673 539 43 22 5839 6374 246958606 246958110 5.130000e-127 466.0
248 TraesCS7A01G203500 chr7B 83.179 541 47 20 5836 6374 399237215 399237713 1.110000e-123 455.0
249 TraesCS7A01G203500 chr7B 82.841 542 50 23 5836 6374 299402850 299402349 6.690000e-121 446.0
250 TraesCS7A01G203500 chr7B 92.000 150 6 4 7083 7231 355907344 355907200 1.240000e-48 206.0
251 TraesCS7A01G203500 chr7B 92.800 125 4 3 7083 7207 305507213 305507332 9.690000e-40 176.0
252 TraesCS7A01G203500 chr7B 93.388 121 3 4 7083 7203 195430099 195430214 3.480000e-39 174.0
253 TraesCS7A01G203500 chr7B 82.540 126 19 2 9243 9365 13708809 13708684 3.580000e-19 108.0
254 TraesCS7A01G203500 chr7B 97.872 47 1 0 8371 8417 490069584 490069630 2.170000e-11 82.4
255 TraesCS7A01G203500 chr7B 92.593 54 4 0 8369 8422 355907063 355907116 2.810000e-10 78.7
256 TraesCS7A01G203500 chr7B 88.136 59 5 2 9287 9344 539329317 539329374 1.690000e-07 69.4
257 TraesCS7A01G203500 chr7B 83.562 73 10 2 9287 9358 146340814 146340743 6.080000e-07 67.6
258 TraesCS7A01G203500 chr7B 97.436 39 0 1 9350 9388 476350187 476350224 2.190000e-06 65.8
259 TraesCS7A01G203500 chr3D 82.559 1055 123 44 3492 4521 3788440 3789458 0.000000e+00 872.0
260 TraesCS7A01G203500 chr3D 85.270 482 52 15 5363 5835 69859787 69859316 6.590000e-131 479.0
261 TraesCS7A01G203500 chr3D 83.193 476 56 16 7952 8405 35669093 35668620 1.890000e-111 414.0
262 TraesCS7A01G203500 chr3D 85.166 391 43 8 7268 7647 35670073 35669687 4.110000e-103 387.0
263 TraesCS7A01G203500 chr6D 85.131 881 90 17 7651 8511 324521824 324522683 0.000000e+00 863.0
264 TraesCS7A01G203500 chr6D 86.620 284 34 4 5560 5841 134956978 134957259 2.550000e-80 311.0
265 TraesCS7A01G203500 chr6D 87.050 278 33 3 5560 5835 470694924 470694648 2.550000e-80 311.0
266 TraesCS7A01G203500 chr6D 86.691 278 34 3 5560 5835 470704673 470704397 1.180000e-78 305.0
267 TraesCS7A01G203500 chr6D 85.664 286 33 7 5552 5835 91654874 91654595 2.560000e-75 294.0
268 TraesCS7A01G203500 chr6D 82.779 331 46 11 5508 5836 363092087 363092408 1.540000e-72 285.0
269 TraesCS7A01G203500 chr6D 82.477 331 48 10 5509 5835 232374231 232374555 2.000000e-71 281.0
270 TraesCS7A01G203500 chr6D 82.759 203 15 7 7449 7647 324521314 324521500 7.540000e-36 163.0
271 TraesCS7A01G203500 chr6D 87.218 133 14 3 5000 5130 351461427 351461558 2.110000e-31 148.0
272 TraesCS7A01G203500 chr6D 90.099 101 7 2 7170 7267 363019283 363019183 2.750000e-25 128.0
273 TraesCS7A01G203500 chr6D 100.000 37 0 0 9352 9388 168430582 168430618 1.690000e-07 69.4
274 TraesCS7A01G203500 chr6D 100.000 37 0 0 9352 9388 441218074 441218038 1.690000e-07 69.4
275 TraesCS7A01G203500 chr6D 100.000 35 0 0 9354 9388 7067498 7067532 2.190000e-06 65.8
276 TraesCS7A01G203500 chr6D 100.000 35 0 0 9354 9388 341479075 341479041 2.190000e-06 65.8
277 TraesCS7A01G203500 chr4A 96.875 448 13 1 4748 5195 576135057 576134611 0.000000e+00 749.0
278 TraesCS7A01G203500 chr4A 96.860 414 5 3 5427 5835 576134175 576133765 0.000000e+00 686.0
279 TraesCS7A01G203500 chr4A 96.509 401 9 2 5439 5836 576125920 576125522 0.000000e+00 658.0
280 TraesCS7A01G203500 chr4A 84.104 541 44 19 5836 6374 311726071 311726571 1.420000e-132 484.0
281 TraesCS7A01G203500 chr4A 97.423 194 5 0 1 194 578032730 578032923 1.950000e-86 331.0
282 TraesCS7A01G203500 chr4A 96.907 194 6 0 1 194 556121698 556121505 9.090000e-85 326.0
283 TraesCS7A01G203500 chr4A 79.271 439 63 15 8940 9356 417633736 417634168 2.000000e-71 281.0
284 TraesCS7A01G203500 chr4A 81.132 318 38 17 4232 4537 723783348 723783041 1.580000e-57 235.0
285 TraesCS7A01G203500 chr4A 92.958 142 5 3 7091 7231 319170080 319169943 1.600000e-47 202.0
286 TraesCS7A01G203500 chr4A 77.816 293 51 11 9060 9348 690263847 690264129 1.620000e-37 169.0
287 TraesCS7A01G203500 chr4A 97.143 35 0 1 6373 6406 645422046 645422012 3.660000e-04 58.4
288 TraesCS7A01G203500 chr7D 85.714 483 50 16 5363 5835 409324075 409324548 8.470000e-135 492.0
289 TraesCS7A01G203500 chr7D 85.965 114 13 3 9243 9353 461653828 461653941 1.660000e-22 119.0
290 TraesCS7A01G203500 chr4D 96.907 194 6 0 1 194 293995429 293995236 9.090000e-85 326.0
291 TraesCS7A01G203500 chr4D 96.392 194 7 0 1 194 244981983 244981790 4.230000e-83 320.0
292 TraesCS7A01G203500 chr4D 84.868 304 40 6 5535 5835 497965548 497965248 1.530000e-77 302.0
293 TraesCS7A01G203500 chr4D 82.571 350 49 12 5509 5851 455208915 455208571 1.980000e-76 298.0
294 TraesCS7A01G203500 chr4D 83.234 334 45 11 5509 5835 455218372 455218043 7.130000e-76 296.0
295 TraesCS7A01G203500 chr4D 83.333 330 39 13 5512 5839 124505230 124505545 3.320000e-74 291.0
296 TraesCS7A01G203500 chr4D 79.602 402 64 15 5439 5835 244971563 244971951 1.200000e-68 272.0
297 TraesCS7A01G203500 chr4D 86.831 243 24 7 193 432 329659968 329660205 2.010000e-66 265.0
298 TraesCS7A01G203500 chr4D 77.629 447 81 18 5397 5835 291320913 291320478 4.350000e-63 254.0
299 TraesCS7A01G203500 chr4D 85.492 193 24 3 8670 8860 131063370 131063180 2.070000e-46 198.0
300 TraesCS7A01G203500 chr4D 94.545 55 2 1 7178 7231 366047532 366047586 6.040000e-12 84.2
301 TraesCS7A01G203500 chr4D 97.368 38 1 0 9351 9388 276929859 276929896 2.190000e-06 65.8
302 TraesCS7A01G203500 chr4D 97.368 38 1 0 9351 9388 449409926 449409889 2.190000e-06 65.8
303 TraesCS7A01G203500 chr4D 92.857 42 2 1 6366 6406 34674759 34674718 1.020000e-04 60.2
304 TraesCS7A01G203500 chr4D 96.970 33 1 0 6374 6406 502033450 502033482 1.000000e-03 56.5
305 TraesCS7A01G203500 chr2D 86.475 244 31 2 193 435 281704229 281704471 5.590000e-67 267.0
306 TraesCS7A01G203500 chr5D 75.439 399 82 13 8953 9345 47671967 47672355 7.490000e-41 180.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G203500 chr7A 165521207 165530594 9387 False 8581.000000 9727 100.000000 1 9388 2 chr7A.!!$F3 9387
1 TraesCS7A01G203500 chr6B 605765441 605770721 5280 True 2201.333333 4577 88.403333 191 9369 3 chr6B.!!$R12 9178
2 TraesCS7A01G203500 chr6B 522100179 522100849 670 True 750.000000 750 87.040000 6423 7091 1 chr6B.!!$R8 668
3 TraesCS7A01G203500 chr6B 499014489 499016125 1636 True 665.500000 902 86.896000 7271 8497 2 chr6B.!!$R11 1226
4 TraesCS7A01G203500 chr6B 391682103 391683261 1158 True 587.000000 769 84.730500 5843 7091 2 chr6B.!!$R9 1248
5 TraesCS7A01G203500 chr6B 494379393 494380305 912 True 528.000000 767 87.662500 6120 7091 2 chr6B.!!$R10 971
6 TraesCS7A01G203500 chr1B 343959121 343961973 2852 True 4143.000000 4143 92.989000 2024 4868 1 chr1B.!!$R5 2844
7 TraesCS7A01G203500 chr1B 148508970 148510135 1165 False 614.500000 791 85.421500 5836 7091 2 chr1B.!!$F12 1255
8 TraesCS7A01G203500 chr1B 358387132 358388287 1155 True 608.000000 737 85.539000 5836 7091 2 chr1B.!!$R9 1255
9 TraesCS7A01G203500 chr1B 377098715 377099245 530 False 601.000000 601 87.361000 6564 7091 1 chr1B.!!$F8 527
10 TraesCS7A01G203500 chr1B 193411605 193412784 1179 True 384.500000 595 89.958500 6564 7207 2 chr1B.!!$R8 643
11 TraesCS7A01G203500 chr5A 237940369 237943836 3467 True 2642.500000 4117 95.554000 1284 9356 2 chr5A.!!$R2 8072
12 TraesCS7A01G203500 chr5A 237948415 237949506 1091 True 1391.000000 1391 89.829000 194 1286 1 chr5A.!!$R1 1092
13 TraesCS7A01G203500 chr5A 367276211 367277460 1249 False 736.500000 767 95.213500 4658 5835 2 chr5A.!!$F3 1177
14 TraesCS7A01G203500 chr6A 108103120 108106505 3385 True 2473.000000 4015 94.867000 2006 5058 2 chr6A.!!$R4 3052
15 TraesCS7A01G203500 chr6A 461838035 461839673 1638 False 664.500000 872 87.128500 7268 8511 2 chr6A.!!$F4 1243
16 TraesCS7A01G203500 chr3A 271632946 271641439 8493 False 1775.750000 3995 94.377500 189 9356 4 chr3A.!!$F5 9167
17 TraesCS7A01G203500 chr3A 33794471 33795490 1019 True 1242.000000 1242 88.772000 3467 4493 1 chr3A.!!$R2 1026
18 TraesCS7A01G203500 chr3A 391879 392419 540 True 874.000000 874 95.780000 4723 5266 1 chr3A.!!$R1 543
19 TraesCS7A01G203500 chr3A 606162001 606163450 1449 False 760.500000 771 95.009000 4658 5835 2 chr3A.!!$F6 1177
20 TraesCS7A01G203500 chr3A 108920489 108922127 1638 False 651.000000 845 86.844000 7268 8511 2 chr3A.!!$F4 1243
21 TraesCS7A01G203500 chr4B 277444992 277447557 2565 False 3877.000000 3877 93.951000 2024 4591 1 chr4B.!!$F7 2567
22 TraesCS7A01G203500 chr4B 277436863 277439428 2565 False 3866.000000 3866 93.871000 2024 4591 1 chr4B.!!$F6 2567
23 TraesCS7A01G203500 chr4B 250816517 250819007 2490 False 3801.000000 3801 94.225000 2024 4519 1 chr4B.!!$F5 2495
24 TraesCS7A01G203500 chr4B 204718511 204720479 1968 True 630.333333 878 86.436333 1041 6760 3 chr4B.!!$R14 5719
25 TraesCS7A01G203500 chr4B 401279047 401280225 1178 False 607.500000 756 85.106500 5836 7091 2 chr4B.!!$F16 1255
26 TraesCS7A01G203500 chr4B 125062487 125063017 530 True 579.000000 579 86.617000 6564 7091 1 chr4B.!!$R1 527
27 TraesCS7A01G203500 chr4B 249884782 249885290 508 False 505.000000 505 84.660000 6558 7069 1 chr4B.!!$F4 511
28 TraesCS7A01G203500 chr4B 404622349 404624153 1804 True 461.000000 739 87.344667 5836 7207 3 chr4B.!!$R15 1371
29 TraesCS7A01G203500 chr4B 491006277 491007451 1174 True 366.500000 568 89.011500 6564 7204 2 chr4B.!!$R16 640
30 TraesCS7A01G203500 chr4B 204711282 204712269 987 True 274.000000 507 90.439333 6308 7532 3 chr4B.!!$R13 1224
31 TraesCS7A01G203500 chr4B 432674119 432674974 855 False 215.000000 326 87.508500 4906 5835 2 chr4B.!!$F17 929
32 TraesCS7A01G203500 chr1A 236113885 236116436 2551 True 3825.000000 3825 93.687000 2024 4591 1 chr1A.!!$R3 2567
33 TraesCS7A01G203500 chr1A 244177211 244177711 500 True 435.000000 435 82.569000 5836 6374 1 chr1A.!!$R4 538
34 TraesCS7A01G203500 chr3B 111485408 111487977 2569 True 3807.000000 3807 93.498000 2024 4584 1 chr3B.!!$R1 2560
35 TraesCS7A01G203500 chr3B 111493405 111495974 2569 True 3784.000000 3784 93.344000 2024 4584 1 chr3B.!!$R2 2560
36 TraesCS7A01G203500 chr3B 543908717 543910884 2167 True 2928.000000 2928 91.253000 2709 4862 1 chr3B.!!$R6 2153
37 TraesCS7A01G203500 chr3B 368786148 368788412 2264 True 1497.500000 2178 94.766500 3555 5835 2 chr3B.!!$R10 2280
38 TraesCS7A01G203500 chr3B 368777980 368780492 2512 True 1001.666667 2056 93.979667 3555 5838 3 chr3B.!!$R9 2283
39 TraesCS7A01G203500 chr3B 330779701 330781467 1766 True 388.750000 797 87.500500 659 6167 4 chr3B.!!$R8 5508
40 TraesCS7A01G203500 chr3B 627896576 627897147 571 True 211.000000 211 75.000000 663 1231 1 chr3B.!!$R7 568
41 TraesCS7A01G203500 chr2B 488392167 488395232 3065 False 1183.875000 3694 96.559750 2709 5842 4 chr2B.!!$F6 3133
42 TraesCS7A01G203500 chr2B 62994343 62995151 808 True 586.000000 586 80.700000 7664 8448 1 chr2B.!!$R1 784
43 TraesCS7A01G203500 chr2B 546971164 546972317 1153 False 554.000000 817 88.802000 5836 7091 2 chr2B.!!$F7 1255
44 TraesCS7A01G203500 chrUn 277235478 277238044 2566 True 3681.000000 3681 92.560000 2024 4600 1 chrUn.!!$R9 2576
45 TraesCS7A01G203500 chrUn 188789684 188792164 2480 True 3661.000000 3661 93.323000 2023 4507 1 chrUn.!!$R5 2484
46 TraesCS7A01G203500 chr2A 118151753 118154292 2539 False 3666.000000 3666 92.699000 2709 5267 1 chr2A.!!$F1 2558
47 TraesCS7A01G203500 chr2A 118159464 118162926 3462 False 2126.500000 3469 95.163000 2709 5835 2 chr2A.!!$F2 3126
48 TraesCS7A01G203500 chr2A 40559030 40559535 505 True 361.000000 361 80.497000 7664 8159 1 chr2A.!!$R1 495
49 TraesCS7A01G203500 chr5B 310032054 310034523 2469 True 3661.000000 3661 93.441000 2024 4496 1 chr5B.!!$R5 2472
50 TraesCS7A01G203500 chr5B 241175811 241177684 1873 False 908.000000 1282 92.935000 3552 5835 2 chr5B.!!$F6 2283
51 TraesCS7A01G203500 chr5B 489599513 489600531 1018 False 895.000000 953 96.820000 4658 5836 2 chr5B.!!$F9 1178
52 TraesCS7A01G203500 chr5B 489591325 489592564 1239 False 713.500000 880 98.006500 4723 5835 2 chr5B.!!$F8 1112
53 TraesCS7A01G203500 chr5B 158673093 158673750 657 False 676.000000 676 85.420000 6423 7091 1 chr5B.!!$F2 668
54 TraesCS7A01G203500 chr5B 241183312 241185609 2297 False 484.300000 854 95.876600 3992 5835 5 chr5B.!!$F7 1843
55 TraesCS7A01G203500 chr1D 28958046 28963335 5289 True 1814.000000 3598 91.262750 190 9354 4 chr1D.!!$R6 9164
56 TraesCS7A01G203500 chr7B 304526066 304529540 3474 True 835.800000 1251 88.604800 192 9356 5 chr7B.!!$R7 9164
57 TraesCS7A01G203500 chr7B 246957441 246958606 1165 True 627.500000 789 85.919500 5839 7091 2 chr7B.!!$R6 1252
58 TraesCS7A01G203500 chr7B 399237215 399238382 1167 False 608.000000 761 85.256500 5836 7091 2 chr7B.!!$F7 1255
59 TraesCS7A01G203500 chr7B 299402349 299402850 501 True 446.000000 446 82.841000 5836 6374 1 chr7B.!!$R3 538
60 TraesCS7A01G203500 chr3D 3788440 3789458 1018 False 872.000000 872 82.559000 3492 4521 1 chr3D.!!$F1 1029
61 TraesCS7A01G203500 chr3D 35668620 35670073 1453 True 400.500000 414 84.179500 7268 8405 2 chr3D.!!$R2 1137
62 TraesCS7A01G203500 chr6D 324521314 324522683 1369 False 513.000000 863 83.945000 7449 8511 2 chr6D.!!$F7 1062
63 TraesCS7A01G203500 chr4A 576133765 576135057 1292 True 717.500000 749 96.867500 4748 5835 2 chr4A.!!$R6 1087
64 TraesCS7A01G203500 chr4A 311726071 311726571 500 False 484.000000 484 84.104000 5836 6374 1 chr4A.!!$F1 538

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
592 597 0.108804 CGCGTGGACTCAGGTTACAT 60.109 55.000 0.00 0.00 0.00 2.29 F
811 4728 0.314498 GCGTCGTTGTTTTCGTTCGT 60.314 50.000 0.00 0.00 33.22 3.85 F
1080 5100 0.625849 AGGAGATCAACCGGGCATTT 59.374 50.000 6.32 0.00 0.00 2.32 F
1232 5285 1.891919 GACAGGCGACCACAAGCAA 60.892 57.895 0.00 0.00 34.54 3.91 F
2725 6891 2.103771 GCATCTCCAAGTAGCATCTCCA 59.896 50.000 0.00 0.00 0.00 3.86 F
3237 7405 0.170339 CAGCTGATACCACGACGTCA 59.830 55.000 17.16 0.00 0.00 4.35 F
4022 8217 0.979187 GTGATACCGGTGAAGGGGGA 60.979 60.000 19.93 0.00 35.02 4.81 F
4160 8364 2.418976 TGAATCGTCTCGTCGTTCTGAT 59.581 45.455 0.00 0.00 0.00 2.90 F
5756 12069 5.621197 ATTGAAACGGTTTCGAATCATCA 57.379 34.783 23.41 5.71 42.55 3.07 F
6261 12618 3.011818 TCCATGTTGTGCTATCTTGCTG 58.988 45.455 0.00 0.00 0.00 4.41 F
6908 13322 0.875908 TGCGATGCATCTTCCTACGC 60.876 55.000 23.73 20.04 43.79 4.42 F
7392 14371 1.499007 GGGTTATGTCCCATGGGTGAT 59.501 52.381 30.28 23.09 46.30 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2400 6535 1.393746 TGGAGTCCAGGAGCCAGAT 59.606 57.895 8.12 0.00 0.00 2.90 R
2721 6887 1.000171 TGCTATGCGATGCTACTGGAG 60.000 52.381 0.00 0.00 0.00 3.86 R
2722 6888 1.039856 TGCTATGCGATGCTACTGGA 58.960 50.000 0.00 0.00 0.00 3.86 R
3198 7366 0.102481 AAGCACTTCGTGACGTCAGT 59.898 50.000 20.73 10.63 35.23 3.41 R
4347 8573 0.037697 CAGTCAATGACGAACGGGGA 60.038 55.000 7.83 0.00 37.67 4.81 R
4348 8574 0.320421 ACAGTCAATGACGAACGGGG 60.320 55.000 7.83 0.00 37.67 5.73 R
5404 11708 0.036306 CCCTAACCGAACAGCCACTT 59.964 55.000 0.00 0.00 0.00 3.16 R
5756 12069 2.608752 CGGTTACTGTTGCTAACCTCGT 60.609 50.000 9.43 2.42 40.72 4.18 R
6666 13079 0.750911 GCAAAGCCATCTCCCTCCTG 60.751 60.000 0.00 0.00 0.00 3.86 R
7323 14301 2.413142 GCAAGCATCCCCAGTGAGC 61.413 63.158 0.00 0.00 0.00 4.26 R
8071 15542 2.649831 TGGACGACCCAGACAGTAC 58.350 57.895 0.34 0.00 40.82 2.73 R
9365 16913 2.241176 AGTTGACACTCTTCCAAACCCA 59.759 45.455 0.00 0.00 0.00 4.51 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 7.516198 AAACTCTCTTAATGTCAATTGTGCT 57.484 32.000 5.13 0.00 0.00 4.40
44 45 8.621532 AAACTCTCTTAATGTCAATTGTGCTA 57.378 30.769 5.13 0.00 0.00 3.49
45 46 8.621532 AACTCTCTTAATGTCAATTGTGCTAA 57.378 30.769 5.13 0.00 0.00 3.09
46 47 8.798859 ACTCTCTTAATGTCAATTGTGCTAAT 57.201 30.769 5.13 0.00 0.00 1.73
47 48 9.890629 ACTCTCTTAATGTCAATTGTGCTAATA 57.109 29.630 5.13 0.00 0.00 0.98
57 58 9.866798 TGTCAATTGTGCTAATAATATGCAAAA 57.133 25.926 5.13 0.00 38.15 2.44
59 60 9.311916 TCAATTGTGCTAATAATATGCAAAACC 57.688 29.630 5.13 0.00 36.85 3.27
60 61 8.550376 CAATTGTGCTAATAATATGCAAAACCC 58.450 33.333 0.00 0.00 36.85 4.11
61 62 7.416964 TTGTGCTAATAATATGCAAAACCCT 57.583 32.000 0.00 0.00 38.50 4.34
62 63 8.526667 TTGTGCTAATAATATGCAAAACCCTA 57.473 30.769 0.00 0.00 38.50 3.53
63 64 8.526667 TGTGCTAATAATATGCAAAACCCTAA 57.473 30.769 0.00 0.00 38.50 2.69
64 65 8.629158 TGTGCTAATAATATGCAAAACCCTAAG 58.371 33.333 0.00 0.00 38.50 2.18
65 66 7.595130 GTGCTAATAATATGCAAAACCCTAAGC 59.405 37.037 0.00 0.00 38.50 3.09
66 67 7.505585 TGCTAATAATATGCAAAACCCTAAGCT 59.494 33.333 0.00 0.00 33.48 3.74
67 68 8.360390 GCTAATAATATGCAAAACCCTAAGCTT 58.640 33.333 3.48 3.48 0.00 3.74
68 69 9.683069 CTAATAATATGCAAAACCCTAAGCTTG 57.317 33.333 9.86 0.00 0.00 4.01
69 70 5.343307 AATATGCAAAACCCTAAGCTTGG 57.657 39.130 9.86 5.91 0.00 3.61
78 79 2.557920 CCTAAGCTTGGGGATGCTAG 57.442 55.000 20.71 0.44 38.75 3.42
79 80 1.771255 CCTAAGCTTGGGGATGCTAGT 59.229 52.381 20.71 0.00 38.75 2.57
80 81 2.173569 CCTAAGCTTGGGGATGCTAGTT 59.826 50.000 20.71 0.00 38.75 2.24
81 82 2.907458 AAGCTTGGGGATGCTAGTTT 57.093 45.000 0.00 0.00 38.75 2.66
82 83 2.907458 AGCTTGGGGATGCTAGTTTT 57.093 45.000 0.00 0.00 37.81 2.43
83 84 2.450476 AGCTTGGGGATGCTAGTTTTG 58.550 47.619 0.00 0.00 37.81 2.44
84 85 1.134995 GCTTGGGGATGCTAGTTTTGC 60.135 52.381 0.00 0.00 0.00 3.68
85 86 2.450476 CTTGGGGATGCTAGTTTTGCT 58.550 47.619 0.00 0.00 0.00 3.91
86 87 3.620488 CTTGGGGATGCTAGTTTTGCTA 58.380 45.455 0.00 0.00 0.00 3.49
87 88 3.951563 TGGGGATGCTAGTTTTGCTAT 57.048 42.857 0.00 0.00 0.00 2.97
88 89 3.554934 TGGGGATGCTAGTTTTGCTATG 58.445 45.455 0.00 0.00 0.00 2.23
89 90 3.053693 TGGGGATGCTAGTTTTGCTATGT 60.054 43.478 0.00 0.00 0.00 2.29
90 91 3.565902 GGGGATGCTAGTTTTGCTATGTC 59.434 47.826 0.00 0.00 0.00 3.06
91 92 3.565902 GGGATGCTAGTTTTGCTATGTCC 59.434 47.826 0.00 0.00 0.00 4.02
92 93 4.455606 GGATGCTAGTTTTGCTATGTCCT 58.544 43.478 0.00 0.00 0.00 3.85
93 94 4.513318 GGATGCTAGTTTTGCTATGTCCTC 59.487 45.833 0.00 0.00 0.00 3.71
94 95 4.826274 TGCTAGTTTTGCTATGTCCTCT 57.174 40.909 0.00 0.00 0.00 3.69
95 96 5.932619 TGCTAGTTTTGCTATGTCCTCTA 57.067 39.130 0.00 0.00 0.00 2.43
96 97 6.485830 TGCTAGTTTTGCTATGTCCTCTAT 57.514 37.500 0.00 0.00 0.00 1.98
97 98 6.889198 TGCTAGTTTTGCTATGTCCTCTATT 58.111 36.000 0.00 0.00 0.00 1.73
98 99 7.338710 TGCTAGTTTTGCTATGTCCTCTATTT 58.661 34.615 0.00 0.00 0.00 1.40
99 100 7.280876 TGCTAGTTTTGCTATGTCCTCTATTTG 59.719 37.037 0.00 0.00 0.00 2.32
100 101 7.281100 GCTAGTTTTGCTATGTCCTCTATTTGT 59.719 37.037 0.00 0.00 0.00 2.83
101 102 9.167311 CTAGTTTTGCTATGTCCTCTATTTGTT 57.833 33.333 0.00 0.00 0.00 2.83
102 103 7.820648 AGTTTTGCTATGTCCTCTATTTGTTG 58.179 34.615 0.00 0.00 0.00 3.33
103 104 5.818136 TTGCTATGTCCTCTATTTGTTGC 57.182 39.130 0.00 0.00 0.00 4.17
104 105 4.842574 TGCTATGTCCTCTATTTGTTGCA 58.157 39.130 0.00 0.00 0.00 4.08
105 106 5.252547 TGCTATGTCCTCTATTTGTTGCAA 58.747 37.500 0.00 0.00 0.00 4.08
106 107 5.887598 TGCTATGTCCTCTATTTGTTGCAAT 59.112 36.000 0.59 0.00 0.00 3.56
107 108 6.183360 TGCTATGTCCTCTATTTGTTGCAATG 60.183 38.462 0.59 0.00 0.00 2.82
108 109 6.038603 GCTATGTCCTCTATTTGTTGCAATGA 59.961 38.462 0.59 0.00 0.00 2.57
109 110 7.255381 GCTATGTCCTCTATTTGTTGCAATGAT 60.255 37.037 0.59 0.00 0.00 2.45
110 111 6.441093 TGTCCTCTATTTGTTGCAATGATC 57.559 37.500 0.59 0.00 0.00 2.92
111 112 5.945191 TGTCCTCTATTTGTTGCAATGATCA 59.055 36.000 0.59 0.00 0.00 2.92
112 113 6.604396 TGTCCTCTATTTGTTGCAATGATCAT 59.396 34.615 0.59 1.18 0.00 2.45
113 114 6.916387 GTCCTCTATTTGTTGCAATGATCATG 59.084 38.462 9.46 4.95 0.00 3.07
114 115 6.829811 TCCTCTATTTGTTGCAATGATCATGA 59.170 34.615 9.46 0.00 0.00 3.07
115 116 7.504574 TCCTCTATTTGTTGCAATGATCATGAT 59.495 33.333 8.25 8.25 0.00 2.45
116 117 8.141909 CCTCTATTTGTTGCAATGATCATGATT 58.858 33.333 9.46 0.00 0.00 2.57
117 118 8.865590 TCTATTTGTTGCAATGATCATGATTG 57.134 30.769 9.46 6.06 34.47 2.67
118 119 6.918892 ATTTGTTGCAATGATCATGATTGG 57.081 33.333 9.46 1.39 32.38 3.16
119 120 4.394439 TGTTGCAATGATCATGATTGGG 57.606 40.909 9.46 1.74 32.38 4.12
120 121 3.133183 TGTTGCAATGATCATGATTGGGG 59.867 43.478 9.46 2.10 32.38 4.96
121 122 3.035055 TGCAATGATCATGATTGGGGT 57.965 42.857 9.46 0.00 32.38 4.95
122 123 2.696187 TGCAATGATCATGATTGGGGTG 59.304 45.455 9.46 2.12 32.38 4.61
123 124 2.960384 GCAATGATCATGATTGGGGTGA 59.040 45.455 9.46 0.00 32.38 4.02
124 125 3.576982 GCAATGATCATGATTGGGGTGAT 59.423 43.478 9.46 0.00 35.42 3.06
125 126 4.768448 GCAATGATCATGATTGGGGTGATA 59.232 41.667 9.46 0.00 33.03 2.15
126 127 5.336213 GCAATGATCATGATTGGGGTGATAC 60.336 44.000 9.46 0.00 33.03 2.24
127 128 5.855338 ATGATCATGATTGGGGTGATACT 57.145 39.130 10.14 0.00 33.03 2.12
128 129 5.651612 TGATCATGATTGGGGTGATACTT 57.348 39.130 10.14 0.00 33.03 2.24
129 130 5.624159 TGATCATGATTGGGGTGATACTTC 58.376 41.667 10.14 0.00 33.03 3.01
130 131 5.370584 TGATCATGATTGGGGTGATACTTCT 59.629 40.000 10.14 0.00 33.03 2.85
131 132 5.715439 TCATGATTGGGGTGATACTTCTT 57.285 39.130 0.00 0.00 0.00 2.52
132 133 6.078456 TCATGATTGGGGTGATACTTCTTT 57.922 37.500 0.00 0.00 0.00 2.52
133 134 6.493166 TCATGATTGGGGTGATACTTCTTTT 58.507 36.000 0.00 0.00 0.00 2.27
134 135 6.377996 TCATGATTGGGGTGATACTTCTTTTG 59.622 38.462 0.00 0.00 0.00 2.44
135 136 5.886609 TGATTGGGGTGATACTTCTTTTGA 58.113 37.500 0.00 0.00 0.00 2.69
136 137 6.493166 TGATTGGGGTGATACTTCTTTTGAT 58.507 36.000 0.00 0.00 0.00 2.57
137 138 6.603201 TGATTGGGGTGATACTTCTTTTGATC 59.397 38.462 0.00 0.00 0.00 2.92
138 139 5.779241 TGGGGTGATACTTCTTTTGATCT 57.221 39.130 0.00 0.00 0.00 2.75
139 140 6.139679 TGGGGTGATACTTCTTTTGATCTT 57.860 37.500 0.00 0.00 0.00 2.40
140 141 5.945784 TGGGGTGATACTTCTTTTGATCTTG 59.054 40.000 0.00 0.00 0.00 3.02
141 142 6.180472 GGGGTGATACTTCTTTTGATCTTGA 58.820 40.000 0.00 0.00 0.00 3.02
142 143 6.659242 GGGGTGATACTTCTTTTGATCTTGAA 59.341 38.462 0.00 0.00 0.00 2.69
143 144 7.176690 GGGGTGATACTTCTTTTGATCTTGAAA 59.823 37.037 0.00 0.00 0.00 2.69
144 145 8.576442 GGGTGATACTTCTTTTGATCTTGAAAA 58.424 33.333 0.00 0.00 0.00 2.29
158 159 9.665719 TTGATCTTGAAAATTTATTTAAGCCCC 57.334 29.630 0.00 0.00 0.00 5.80
159 160 8.820831 TGATCTTGAAAATTTATTTAAGCCCCA 58.179 29.630 0.00 0.00 0.00 4.96
160 161 9.836864 GATCTTGAAAATTTATTTAAGCCCCAT 57.163 29.630 0.00 0.00 0.00 4.00
161 162 9.617523 ATCTTGAAAATTTATTTAAGCCCCATG 57.382 29.630 0.00 0.00 0.00 3.66
162 163 8.820831 TCTTGAAAATTTATTTAAGCCCCATGA 58.179 29.630 0.00 0.00 0.00 3.07
163 164 9.617523 CTTGAAAATTTATTTAAGCCCCATGAT 57.382 29.630 0.00 0.00 0.00 2.45
164 165 8.961294 TGAAAATTTATTTAAGCCCCATGATG 57.039 30.769 0.00 0.00 0.00 3.07
165 166 8.766476 TGAAAATTTATTTAAGCCCCATGATGA 58.234 29.630 0.00 0.00 0.00 2.92
166 167 9.612066 GAAAATTTATTTAAGCCCCATGATGAA 57.388 29.630 0.00 0.00 0.00 2.57
171 172 9.599056 TTTATTTAAGCCCCATGATGAATATGA 57.401 29.630 0.00 0.00 0.00 2.15
172 173 7.713734 ATTTAAGCCCCATGATGAATATGAG 57.286 36.000 0.00 0.00 0.00 2.90
173 174 6.452757 TTAAGCCCCATGATGAATATGAGA 57.547 37.500 0.00 0.00 0.00 3.27
174 175 5.531753 AAGCCCCATGATGAATATGAGAT 57.468 39.130 0.00 0.00 0.00 2.75
175 176 5.531753 AGCCCCATGATGAATATGAGATT 57.468 39.130 0.00 0.00 0.00 2.40
176 177 5.262009 AGCCCCATGATGAATATGAGATTG 58.738 41.667 0.00 0.00 0.00 2.67
177 178 5.014860 AGCCCCATGATGAATATGAGATTGA 59.985 40.000 0.00 0.00 0.00 2.57
178 179 5.892119 GCCCCATGATGAATATGAGATTGAT 59.108 40.000 0.00 0.00 0.00 2.57
179 180 7.058525 GCCCCATGATGAATATGAGATTGATA 58.941 38.462 0.00 0.00 0.00 2.15
180 181 7.558807 GCCCCATGATGAATATGAGATTGATAA 59.441 37.037 0.00 0.00 0.00 1.75
181 182 9.642343 CCCCATGATGAATATGAGATTGATAAT 57.358 33.333 0.00 0.00 0.00 1.28
302 304 2.177394 TCTATTTGCGTTGGCTGACA 57.823 45.000 0.00 0.00 40.82 3.58
411 415 0.521735 GTGAGCCTTTTTAGGGTGCG 59.478 55.000 0.00 0.00 40.15 5.34
414 418 2.329614 GCCTTTTTAGGGTGCGCGA 61.330 57.895 12.10 0.00 0.00 5.87
454 459 2.842462 TGGGTGCGTCCTGAGTGT 60.842 61.111 0.00 0.00 36.25 3.55
577 582 0.803768 TTGCATTTTTGTGTGCGCGT 60.804 45.000 8.43 0.00 44.11 6.01
592 597 0.108804 CGCGTGGACTCAGGTTACAT 60.109 55.000 0.00 0.00 0.00 2.29
716 4633 1.530419 AACCGTCTTTGGCATGCCA 60.530 52.632 35.59 35.59 45.63 4.92
811 4728 0.314498 GCGTCGTTGTTTTCGTTCGT 60.314 50.000 0.00 0.00 33.22 3.85
831 4762 1.964223 TGTCTGGTGTTGGAGAGAGTC 59.036 52.381 0.00 0.00 0.00 3.36
1011 5031 1.037579 TGCCGTCGATGAGATCCAGT 61.038 55.000 6.11 0.00 0.00 4.00
1080 5100 0.625849 AGGAGATCAACCGGGCATTT 59.374 50.000 6.32 0.00 0.00 2.32
1102 5122 1.915983 GGCCGGAGAAGGAGGAAAT 59.084 57.895 5.05 0.00 0.00 2.17
1232 5285 1.891919 GACAGGCGACCACAAGCAA 60.892 57.895 0.00 0.00 34.54 3.91
1258 5311 3.898509 GGCGGCAACAGCAACACA 61.899 61.111 3.07 0.00 37.75 3.72
1347 5428 3.066190 CCCGACGCACAGGAGGTA 61.066 66.667 0.00 0.00 0.00 3.08
1520 5605 5.157940 TCTGAACCATCTCTCTTTTCAGG 57.842 43.478 9.20 0.00 42.25 3.86
1798 5883 5.053811 TCTTGTTATCGCTTGTTCAGTCAA 58.946 37.500 0.00 0.00 0.00 3.18
2020 6152 4.623814 GCTGCACATCAGGTAGCA 57.376 55.556 0.00 0.00 42.58 3.49
2021 6153 3.091318 GCTGCACATCAGGTAGCAT 57.909 52.632 0.00 0.00 42.58 3.79
2121 6253 9.813080 GAAGATATCACAACACAACTCTAAAAC 57.187 33.333 5.32 0.00 0.00 2.43
2122 6254 8.902540 AGATATCACAACACAACTCTAAAACA 57.097 30.769 5.32 0.00 0.00 2.83
2123 6255 9.507329 AGATATCACAACACAACTCTAAAACAT 57.493 29.630 5.32 0.00 0.00 2.71
2655 6795 4.489810 CGCCTTATAGCATGTAGAAGAGG 58.510 47.826 9.73 5.48 0.00 3.69
2720 6886 5.068636 CCAAATAGCATCTCCAAGTAGCAT 58.931 41.667 0.00 0.00 0.00 3.79
2721 6887 5.180868 CCAAATAGCATCTCCAAGTAGCATC 59.819 44.000 0.00 0.00 0.00 3.91
2722 6888 5.822132 AATAGCATCTCCAAGTAGCATCT 57.178 39.130 0.00 0.00 0.00 2.90
2723 6889 3.749665 AGCATCTCCAAGTAGCATCTC 57.250 47.619 0.00 0.00 0.00 2.75
2724 6890 2.368221 AGCATCTCCAAGTAGCATCTCC 59.632 50.000 0.00 0.00 0.00 3.71
2725 6891 2.103771 GCATCTCCAAGTAGCATCTCCA 59.896 50.000 0.00 0.00 0.00 3.86
2726 6892 3.803021 GCATCTCCAAGTAGCATCTCCAG 60.803 52.174 0.00 0.00 0.00 3.86
2727 6893 3.107402 TCTCCAAGTAGCATCTCCAGT 57.893 47.619 0.00 0.00 0.00 4.00
2728 6894 4.251103 TCTCCAAGTAGCATCTCCAGTA 57.749 45.455 0.00 0.00 0.00 2.74
2729 6895 4.211125 TCTCCAAGTAGCATCTCCAGTAG 58.789 47.826 0.00 0.00 0.00 2.57
2730 6896 2.695666 TCCAAGTAGCATCTCCAGTAGC 59.304 50.000 0.00 0.00 0.00 3.58
2731 6897 2.432146 CCAAGTAGCATCTCCAGTAGCA 59.568 50.000 0.00 0.00 0.00 3.49
2732 6898 3.070734 CCAAGTAGCATCTCCAGTAGCAT 59.929 47.826 0.00 0.00 0.00 3.79
2733 6899 4.305769 CAAGTAGCATCTCCAGTAGCATC 58.694 47.826 0.00 0.00 0.00 3.91
2734 6900 2.556189 AGTAGCATCTCCAGTAGCATCG 59.444 50.000 0.00 0.00 0.00 3.84
2745 6911 3.369147 CCAGTAGCATCGCATAGCATAAC 59.631 47.826 0.00 0.00 0.00 1.89
3035 7202 2.584608 CCCCACCTAGGCTCAACG 59.415 66.667 9.30 0.00 35.39 4.10
3237 7405 0.170339 CAGCTGATACCACGACGTCA 59.830 55.000 17.16 0.00 0.00 4.35
3239 7407 2.945315 CTGATACCACGACGTCAGC 58.055 57.895 17.16 0.00 32.62 4.26
3333 7502 4.857588 AGATCTCGTTAAGCGTGTTAAGTG 59.142 41.667 0.00 0.00 42.13 3.16
3417 7586 2.218603 CTCCGCCACAAAGTAACAGTT 58.781 47.619 0.00 0.00 0.00 3.16
3751 7926 5.354234 AGGATTAACGAAAGCAGTAACATGG 59.646 40.000 0.00 0.00 0.00 3.66
4022 8217 0.979187 GTGATACCGGTGAAGGGGGA 60.979 60.000 19.93 0.00 35.02 4.81
4042 8237 4.097437 GGGAAAAACATCCGGGAAAGTATC 59.903 45.833 0.00 3.38 40.62 2.24
4139 8343 2.499685 GAACGGGCTGCGTATCCT 59.500 61.111 0.00 0.00 0.00 3.24
4160 8364 2.418976 TGAATCGTCTCGTCGTTCTGAT 59.581 45.455 0.00 0.00 0.00 2.90
5756 12069 5.621197 ATTGAAACGGTTTCGAATCATCA 57.379 34.783 23.41 5.71 42.55 3.07
6037 12378 4.009675 TGGCACTGGCTTTCTTATTACAG 58.990 43.478 3.97 0.00 40.87 2.74
6061 12402 8.499162 CAGACAAAACTAAATGTGGAGAAGTAG 58.501 37.037 0.00 0.00 0.00 2.57
6100 12450 8.698973 TGGTAACTGAATTGAATTACCTTTGA 57.301 30.769 14.86 0.00 44.61 2.69
6176 12526 9.573166 AAGGATTTTATATTTCCATGTCGATCA 57.427 29.630 0.00 0.00 31.65 2.92
6177 12527 9.573166 AGGATTTTATATTTCCATGTCGATCAA 57.427 29.630 0.00 0.00 31.65 2.57
6178 12528 9.612620 GGATTTTATATTTCCATGTCGATCAAC 57.387 33.333 0.00 0.00 0.00 3.18
6181 12531 7.728847 TTATATTTCCATGTCGATCAACTGG 57.271 36.000 0.00 0.00 0.00 4.00
6182 12532 3.694043 TTTCCATGTCGATCAACTGGA 57.306 42.857 2.06 2.06 34.27 3.86
6261 12618 3.011818 TCCATGTTGTGCTATCTTGCTG 58.988 45.455 0.00 0.00 0.00 4.41
6382 12739 7.829211 CACTGAAGTTAATTTCTATTCCCTCCA 59.171 37.037 11.47 0.00 0.00 3.86
6402 12759 5.253330 TCCATCCCAAAATAAGTGTCTCAC 58.747 41.667 0.00 0.00 34.10 3.51
6434 12836 5.048154 GGACGGAGGGAGTACATTATTAGTC 60.048 48.000 0.00 0.00 0.00 2.59
6666 13079 0.882042 CCGACTGCCACCTATCATGC 60.882 60.000 0.00 0.00 0.00 4.06
6908 13322 0.875908 TGCGATGCATCTTCCTACGC 60.876 55.000 23.73 20.04 43.79 4.42
7100 14074 5.196695 AGCTTATGTGAAGATCCCTTTTCC 58.803 41.667 0.00 0.00 31.62 3.13
7323 14301 4.391405 TCTATATGCAGACAGTGTGGTG 57.609 45.455 0.00 0.00 0.00 4.17
7392 14371 1.499007 GGGTTATGTCCCATGGGTGAT 59.501 52.381 30.28 23.09 46.30 3.06
7796 15230 4.594970 TCAACAAGTGTTCTCCAAAAGGA 58.405 39.130 0.00 0.00 35.83 3.36
8105 15583 5.585047 GGTCGTCCAGTTTTTAGCTATCATT 59.415 40.000 0.00 0.00 0.00 2.57
8111 15592 8.515414 GTCCAGTTTTTAGCTATCATTTGTTCT 58.485 33.333 0.00 0.00 0.00 3.01
8325 15822 9.065798 TGATGAACTGTGATTTTACTTTCATCA 57.934 29.630 20.25 20.25 45.56 3.07
8520 16030 9.726438 AGCATAAAAAGTCTGTAGTCAAACTAT 57.274 29.630 0.00 0.00 32.65 2.12
8792 16309 6.704289 ATACAGCTCAACATGCAAATATGT 57.296 33.333 0.00 0.00 42.82 2.29
8906 16431 8.639761 ACTACTTTTAGTCATTGTACTCTGTGT 58.360 33.333 0.00 0.00 32.67 3.72
9209 16753 6.600822 TCTTGCATTTTATGAGAGCTTAGCTT 59.399 34.615 8.58 0.00 39.88 3.74
9259 16805 9.297037 ACAAAAGGCTAAGTTCTTAACATATGT 57.703 29.630 1.41 1.41 0.00 2.29
9336 16884 1.675641 GGTCTCTGCGCCATTTGGT 60.676 57.895 4.18 0.00 37.57 3.67
9360 16908 5.989168 TGCAACGGGTCATCTAGTATTATTG 59.011 40.000 0.00 0.00 0.00 1.90
9365 16913 8.019656 ACGGGTCATCTAGTATTATTGAAAGT 57.980 34.615 0.00 0.00 0.00 2.66
9368 16916 7.661847 GGGTCATCTAGTATTATTGAAAGTGGG 59.338 40.741 0.00 0.00 0.00 4.61
9369 16917 8.211629 GGTCATCTAGTATTATTGAAAGTGGGT 58.788 37.037 0.00 0.00 0.00 4.51
9370 16918 9.614792 GTCATCTAGTATTATTGAAAGTGGGTT 57.385 33.333 0.00 0.00 0.00 4.11
9373 16921 8.801882 TCTAGTATTATTGAAAGTGGGTTTGG 57.198 34.615 0.00 0.00 0.00 3.28
9374 16922 8.607713 TCTAGTATTATTGAAAGTGGGTTTGGA 58.392 33.333 0.00 0.00 0.00 3.53
9375 16923 9.238368 CTAGTATTATTGAAAGTGGGTTTGGAA 57.762 33.333 0.00 0.00 0.00 3.53
9376 16924 8.122472 AGTATTATTGAAAGTGGGTTTGGAAG 57.878 34.615 0.00 0.00 0.00 3.46
9377 16925 7.947890 AGTATTATTGAAAGTGGGTTTGGAAGA 59.052 33.333 0.00 0.00 0.00 2.87
9378 16926 6.648879 TTATTGAAAGTGGGTTTGGAAGAG 57.351 37.500 0.00 0.00 0.00 2.85
9379 16927 3.662759 TGAAAGTGGGTTTGGAAGAGT 57.337 42.857 0.00 0.00 0.00 3.24
9380 16928 3.287222 TGAAAGTGGGTTTGGAAGAGTG 58.713 45.455 0.00 0.00 0.00 3.51
9381 16929 3.288092 GAAAGTGGGTTTGGAAGAGTGT 58.712 45.455 0.00 0.00 0.00 3.55
9382 16930 2.640316 AGTGGGTTTGGAAGAGTGTC 57.360 50.000 0.00 0.00 0.00 3.67
9383 16931 1.843851 AGTGGGTTTGGAAGAGTGTCA 59.156 47.619 0.00 0.00 0.00 3.58
9384 16932 2.241176 AGTGGGTTTGGAAGAGTGTCAA 59.759 45.455 0.00 0.00 0.00 3.18
9385 16933 2.357952 GTGGGTTTGGAAGAGTGTCAAC 59.642 50.000 0.00 0.00 0.00 3.18
9386 16934 2.241176 TGGGTTTGGAAGAGTGTCAACT 59.759 45.455 0.00 0.00 40.21 3.16
9387 16935 3.288092 GGGTTTGGAAGAGTGTCAACTT 58.712 45.455 0.00 0.00 36.52 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 9.236006 AGCACAATTGACATTAAGAGAGTTTAT 57.764 29.630 13.59 0.00 0.00 1.40
18 19 8.621532 AGCACAATTGACATTAAGAGAGTTTA 57.378 30.769 13.59 0.00 0.00 2.01
19 20 7.516198 AGCACAATTGACATTAAGAGAGTTT 57.484 32.000 13.59 0.00 0.00 2.66
20 21 8.621532 TTAGCACAATTGACATTAAGAGAGTT 57.378 30.769 13.59 0.00 0.00 3.01
21 22 8.798859 ATTAGCACAATTGACATTAAGAGAGT 57.201 30.769 13.59 0.00 0.00 3.24
31 32 9.866798 TTTTGCATATTATTAGCACAATTGACA 57.133 25.926 13.59 0.00 38.11 3.58
33 34 9.311916 GGTTTTGCATATTATTAGCACAATTGA 57.688 29.630 13.59 0.00 38.11 2.57
34 35 8.550376 GGGTTTTGCATATTATTAGCACAATTG 58.450 33.333 3.24 3.24 38.11 2.32
35 36 8.485392 AGGGTTTTGCATATTATTAGCACAATT 58.515 29.630 0.00 0.00 38.11 2.32
36 37 8.021898 AGGGTTTTGCATATTATTAGCACAAT 57.978 30.769 0.00 0.00 38.11 2.71
37 38 7.416964 AGGGTTTTGCATATTATTAGCACAA 57.583 32.000 0.00 0.00 38.11 3.33
38 39 8.526667 TTAGGGTTTTGCATATTATTAGCACA 57.473 30.769 0.00 0.00 38.11 4.57
39 40 7.595130 GCTTAGGGTTTTGCATATTATTAGCAC 59.405 37.037 0.00 0.00 38.11 4.40
40 41 7.505585 AGCTTAGGGTTTTGCATATTATTAGCA 59.494 33.333 0.00 0.00 36.32 3.49
41 42 7.886338 AGCTTAGGGTTTTGCATATTATTAGC 58.114 34.615 0.00 0.00 0.00 3.09
42 43 9.683069 CAAGCTTAGGGTTTTGCATATTATTAG 57.317 33.333 0.00 0.00 0.00 1.73
43 44 8.637986 CCAAGCTTAGGGTTTTGCATATTATTA 58.362 33.333 0.00 0.00 0.00 0.98
44 45 7.418942 CCCAAGCTTAGGGTTTTGCATATTATT 60.419 37.037 20.06 0.00 41.61 1.40
45 46 6.041979 CCCAAGCTTAGGGTTTTGCATATTAT 59.958 38.462 20.06 0.00 41.61 1.28
46 47 5.362430 CCCAAGCTTAGGGTTTTGCATATTA 59.638 40.000 20.06 0.00 41.61 0.98
47 48 4.162131 CCCAAGCTTAGGGTTTTGCATATT 59.838 41.667 20.06 0.00 41.61 1.28
48 49 3.706086 CCCAAGCTTAGGGTTTTGCATAT 59.294 43.478 20.06 0.00 41.61 1.78
49 50 3.096092 CCCAAGCTTAGGGTTTTGCATA 58.904 45.455 20.06 0.00 41.61 3.14
50 51 1.901833 CCCAAGCTTAGGGTTTTGCAT 59.098 47.619 20.06 0.00 41.61 3.96
51 52 1.337118 CCCAAGCTTAGGGTTTTGCA 58.663 50.000 20.06 0.00 41.61 4.08
52 53 0.608130 CCCCAAGCTTAGGGTTTTGC 59.392 55.000 20.89 0.00 45.28 3.68
53 54 2.302587 TCCCCAAGCTTAGGGTTTTG 57.697 50.000 26.72 13.48 45.28 2.44
54 55 2.820178 CATCCCCAAGCTTAGGGTTTT 58.180 47.619 26.72 12.28 45.28 2.43
55 56 1.619704 GCATCCCCAAGCTTAGGGTTT 60.620 52.381 26.72 14.57 45.28 3.27
56 57 0.033109 GCATCCCCAAGCTTAGGGTT 60.033 55.000 26.72 17.59 45.28 4.11
57 58 0.921256 AGCATCCCCAAGCTTAGGGT 60.921 55.000 26.72 11.92 45.28 4.34
58 59 1.072965 CTAGCATCCCCAAGCTTAGGG 59.927 57.143 22.89 22.89 46.36 3.53
59 60 1.771255 ACTAGCATCCCCAAGCTTAGG 59.229 52.381 3.60 3.60 42.05 2.69
60 61 3.567478 AACTAGCATCCCCAAGCTTAG 57.433 47.619 0.00 0.00 42.05 2.18
61 62 4.016444 CAAAACTAGCATCCCCAAGCTTA 58.984 43.478 0.00 0.00 42.05 3.09
62 63 2.827921 CAAAACTAGCATCCCCAAGCTT 59.172 45.455 0.00 0.00 42.05 3.74
63 64 2.450476 CAAAACTAGCATCCCCAAGCT 58.550 47.619 0.00 0.00 44.55 3.74
64 65 1.134995 GCAAAACTAGCATCCCCAAGC 60.135 52.381 0.00 0.00 0.00 4.01
65 66 2.450476 AGCAAAACTAGCATCCCCAAG 58.550 47.619 0.00 0.00 0.00 3.61
66 67 2.603075 AGCAAAACTAGCATCCCCAA 57.397 45.000 0.00 0.00 0.00 4.12
67 68 3.053693 ACATAGCAAAACTAGCATCCCCA 60.054 43.478 0.00 0.00 33.29 4.96
68 69 3.555966 ACATAGCAAAACTAGCATCCCC 58.444 45.455 0.00 0.00 33.29 4.81
69 70 3.565902 GGACATAGCAAAACTAGCATCCC 59.434 47.826 0.00 0.00 33.29 3.85
70 71 4.455606 AGGACATAGCAAAACTAGCATCC 58.544 43.478 0.00 0.00 33.29 3.51
71 72 5.363939 AGAGGACATAGCAAAACTAGCATC 58.636 41.667 0.00 0.00 33.29 3.91
72 73 5.365021 AGAGGACATAGCAAAACTAGCAT 57.635 39.130 0.00 0.00 33.29 3.79
73 74 4.826274 AGAGGACATAGCAAAACTAGCA 57.174 40.909 0.00 0.00 33.29 3.49
74 75 7.281100 ACAAATAGAGGACATAGCAAAACTAGC 59.719 37.037 0.00 0.00 33.29 3.42
75 76 8.723942 ACAAATAGAGGACATAGCAAAACTAG 57.276 34.615 0.00 0.00 33.29 2.57
76 77 8.946085 CAACAAATAGAGGACATAGCAAAACTA 58.054 33.333 0.00 0.00 34.64 2.24
77 78 7.575720 GCAACAAATAGAGGACATAGCAAAACT 60.576 37.037 0.00 0.00 0.00 2.66
78 79 6.528072 GCAACAAATAGAGGACATAGCAAAAC 59.472 38.462 0.00 0.00 0.00 2.43
79 80 6.208402 TGCAACAAATAGAGGACATAGCAAAA 59.792 34.615 0.00 0.00 0.00 2.44
80 81 5.709631 TGCAACAAATAGAGGACATAGCAAA 59.290 36.000 0.00 0.00 0.00 3.68
81 82 5.252547 TGCAACAAATAGAGGACATAGCAA 58.747 37.500 0.00 0.00 0.00 3.91
82 83 4.842574 TGCAACAAATAGAGGACATAGCA 58.157 39.130 0.00 0.00 0.00 3.49
83 84 5.818136 TTGCAACAAATAGAGGACATAGC 57.182 39.130 0.00 0.00 0.00 2.97
84 85 7.558161 TCATTGCAACAAATAGAGGACATAG 57.442 36.000 0.00 0.00 0.00 2.23
85 86 7.774625 TGATCATTGCAACAAATAGAGGACATA 59.225 33.333 0.00 0.00 0.00 2.29
86 87 6.604396 TGATCATTGCAACAAATAGAGGACAT 59.396 34.615 0.00 0.00 0.00 3.06
87 88 5.945191 TGATCATTGCAACAAATAGAGGACA 59.055 36.000 0.00 0.00 0.00 4.02
88 89 6.441093 TGATCATTGCAACAAATAGAGGAC 57.559 37.500 0.00 0.00 0.00 3.85
89 90 6.829811 TCATGATCATTGCAACAAATAGAGGA 59.170 34.615 5.16 0.00 0.00 3.71
90 91 7.034685 TCATGATCATTGCAACAAATAGAGG 57.965 36.000 5.16 0.00 0.00 3.69
91 92 8.968242 CAATCATGATCATTGCAACAAATAGAG 58.032 33.333 9.06 0.00 0.00 2.43
92 93 7.923878 CCAATCATGATCATTGCAACAAATAGA 59.076 33.333 9.06 0.00 30.94 1.98
93 94 7.170828 CCCAATCATGATCATTGCAACAAATAG 59.829 37.037 9.06 0.00 30.94 1.73
94 95 6.987404 CCCAATCATGATCATTGCAACAAATA 59.013 34.615 9.06 0.00 30.94 1.40
95 96 5.820423 CCCAATCATGATCATTGCAACAAAT 59.180 36.000 9.06 0.00 30.94 2.32
96 97 5.179533 CCCAATCATGATCATTGCAACAAA 58.820 37.500 9.06 0.00 30.94 2.83
97 98 4.383226 CCCCAATCATGATCATTGCAACAA 60.383 41.667 9.06 0.00 30.94 2.83
98 99 3.133183 CCCCAATCATGATCATTGCAACA 59.867 43.478 9.06 0.00 30.94 3.33
99 100 3.133362 ACCCCAATCATGATCATTGCAAC 59.867 43.478 9.06 0.00 30.94 4.17
100 101 3.133183 CACCCCAATCATGATCATTGCAA 59.867 43.478 9.06 0.00 30.94 4.08
101 102 2.696187 CACCCCAATCATGATCATTGCA 59.304 45.455 9.06 0.00 30.94 4.08
102 103 2.960384 TCACCCCAATCATGATCATTGC 59.040 45.455 9.06 0.00 30.94 3.56
103 104 6.008331 AGTATCACCCCAATCATGATCATTG 58.992 40.000 9.06 4.58 34.86 2.82
104 105 6.210172 AGTATCACCCCAATCATGATCATT 57.790 37.500 9.06 0.00 34.86 2.57
105 106 5.855338 AGTATCACCCCAATCATGATCAT 57.145 39.130 9.06 1.18 34.86 2.45
106 107 5.370584 AGAAGTATCACCCCAATCATGATCA 59.629 40.000 9.06 0.00 34.86 2.92
107 108 5.874093 AGAAGTATCACCCCAATCATGATC 58.126 41.667 9.06 0.00 34.86 2.92
108 109 5.919348 AGAAGTATCACCCCAATCATGAT 57.081 39.130 1.18 1.18 36.95 2.45
109 110 5.715439 AAGAAGTATCACCCCAATCATGA 57.285 39.130 0.00 0.00 0.00 3.07
110 111 6.377996 TCAAAAGAAGTATCACCCCAATCATG 59.622 38.462 0.00 0.00 0.00 3.07
111 112 6.493166 TCAAAAGAAGTATCACCCCAATCAT 58.507 36.000 0.00 0.00 0.00 2.45
112 113 5.886609 TCAAAAGAAGTATCACCCCAATCA 58.113 37.500 0.00 0.00 0.00 2.57
113 114 6.830838 AGATCAAAAGAAGTATCACCCCAATC 59.169 38.462 0.00 0.00 0.00 2.67
114 115 6.735556 AGATCAAAAGAAGTATCACCCCAAT 58.264 36.000 0.00 0.00 0.00 3.16
115 116 6.139679 AGATCAAAAGAAGTATCACCCCAA 57.860 37.500 0.00 0.00 0.00 4.12
116 117 5.779241 AGATCAAAAGAAGTATCACCCCA 57.221 39.130 0.00 0.00 0.00 4.96
117 118 6.180472 TCAAGATCAAAAGAAGTATCACCCC 58.820 40.000 0.00 0.00 0.00 4.95
118 119 7.687941 TTCAAGATCAAAAGAAGTATCACCC 57.312 36.000 0.00 0.00 0.00 4.61
132 133 9.665719 GGGGCTTAAATAAATTTTCAAGATCAA 57.334 29.630 0.00 0.00 0.00 2.57
133 134 8.820831 TGGGGCTTAAATAAATTTTCAAGATCA 58.179 29.630 0.00 0.00 0.00 2.92
134 135 9.836864 ATGGGGCTTAAATAAATTTTCAAGATC 57.163 29.630 0.00 0.00 0.00 2.75
135 136 9.617523 CATGGGGCTTAAATAAATTTTCAAGAT 57.382 29.630 0.00 0.00 0.00 2.40
136 137 8.820831 TCATGGGGCTTAAATAAATTTTCAAGA 58.179 29.630 0.00 0.00 0.00 3.02
137 138 9.617523 ATCATGGGGCTTAAATAAATTTTCAAG 57.382 29.630 0.00 0.00 0.00 3.02
138 139 9.393512 CATCATGGGGCTTAAATAAATTTTCAA 57.606 29.630 0.00 0.00 0.00 2.69
139 140 8.766476 TCATCATGGGGCTTAAATAAATTTTCA 58.234 29.630 0.00 0.00 0.00 2.69
140 141 9.612066 TTCATCATGGGGCTTAAATAAATTTTC 57.388 29.630 0.00 0.00 0.00 2.29
145 146 9.599056 TCATATTCATCATGGGGCTTAAATAAA 57.401 29.630 0.00 0.00 0.00 1.40
146 147 9.246670 CTCATATTCATCATGGGGCTTAAATAA 57.753 33.333 0.00 0.00 0.00 1.40
147 148 8.613923 TCTCATATTCATCATGGGGCTTAAATA 58.386 33.333 0.00 0.00 0.00 1.40
148 149 7.472741 TCTCATATTCATCATGGGGCTTAAAT 58.527 34.615 0.00 0.00 0.00 1.40
149 150 6.851318 TCTCATATTCATCATGGGGCTTAAA 58.149 36.000 0.00 0.00 0.00 1.52
150 151 6.452757 TCTCATATTCATCATGGGGCTTAA 57.547 37.500 0.00 0.00 0.00 1.85
151 152 6.647461 ATCTCATATTCATCATGGGGCTTA 57.353 37.500 0.00 0.00 0.00 3.09
152 153 5.531753 ATCTCATATTCATCATGGGGCTT 57.468 39.130 0.00 0.00 0.00 4.35
153 154 5.014860 TCAATCTCATATTCATCATGGGGCT 59.985 40.000 0.00 0.00 0.00 5.19
154 155 5.258841 TCAATCTCATATTCATCATGGGGC 58.741 41.667 0.00 0.00 0.00 5.80
155 156 9.642343 ATTATCAATCTCATATTCATCATGGGG 57.358 33.333 0.00 0.00 0.00 4.96
169 170 9.878667 AAATTGCAAACATCATTATCAATCTCA 57.121 25.926 1.71 0.00 0.00 3.27
302 304 3.818773 ACGAAAACCAACGAAGATCCAAT 59.181 39.130 0.00 0.00 0.00 3.16
435 440 2.842462 ACTCAGGACGCACCCACA 60.842 61.111 0.00 0.00 40.05 4.17
454 459 2.551472 GAACCGTAAATCGCGCGCAA 62.551 55.000 32.61 15.11 38.35 4.85
599 604 1.301716 GCCAAGAGCGGTTGACTGA 60.302 57.895 2.91 0.00 0.00 3.41
649 4566 2.600729 CCCCTCTGCAACTGCTCCT 61.601 63.158 2.95 0.00 42.66 3.69
679 4596 2.360350 CAGAAGCCGGGTGCACAT 60.360 61.111 20.43 0.00 44.83 3.21
811 4728 1.964223 GACTCTCTCCAACACCAGACA 59.036 52.381 0.00 0.00 0.00 3.41
924 4862 3.096357 ACCTATGGGTTGGGGCAC 58.904 61.111 0.00 0.00 44.73 5.01
1232 5285 3.825611 GTTGCCGCCGATGCCATT 61.826 61.111 0.00 0.00 0.00 3.16
1286 5367 0.546122 ACGCCATCCTTGAATGCCTA 59.454 50.000 0.00 0.00 0.00 3.93
1334 5415 0.393077 GGCATATACCTCCTGTGCGT 59.607 55.000 0.00 0.00 36.70 5.24
1346 5427 1.289066 GCGTGCTCCGAGGCATATA 59.711 57.895 5.65 0.00 44.34 0.86
1347 5428 2.029666 GCGTGCTCCGAGGCATAT 59.970 61.111 5.65 0.00 44.34 1.78
1673 5758 7.501844 GGCATAGACCTGAAAAGTAGTTATCT 58.498 38.462 0.00 0.00 0.00 1.98
1798 5883 4.222810 GGTGAAAGGGCATAAACCAGAAAT 59.777 41.667 0.00 0.00 0.00 2.17
1964 6096 6.150641 CACAGAACTTCACAAATCATCAGGAT 59.849 38.462 0.00 0.00 38.05 3.24
2019 6151 3.680620 ATCGGGGGCGTCACACATG 62.681 63.158 0.00 0.00 0.00 3.21
2020 6152 2.869503 GAATCGGGGGCGTCACACAT 62.870 60.000 0.00 0.00 0.00 3.21
2021 6153 3.599285 GAATCGGGGGCGTCACACA 62.599 63.158 0.00 0.00 0.00 3.72
2400 6535 1.393746 TGGAGTCCAGGAGCCAGAT 59.606 57.895 8.12 0.00 0.00 2.90
2587 6726 3.309265 CGATAGGACTAGCTATCCCCCTT 60.309 52.174 14.84 3.96 36.86 3.95
2635 6775 6.948886 TCTACCCTCTTCTACATGCTATAAGG 59.051 42.308 0.00 0.00 0.00 2.69
2639 6779 7.013220 TCAATCTACCCTCTTCTACATGCTAT 58.987 38.462 0.00 0.00 0.00 2.97
2655 6795 4.828072 ACTTGGAGGACTTCAATCTACC 57.172 45.455 0.00 0.00 0.00 3.18
2720 6886 1.270826 GCTATGCGATGCTACTGGAGA 59.729 52.381 0.00 0.00 0.00 3.71
2721 6887 1.000171 TGCTATGCGATGCTACTGGAG 60.000 52.381 0.00 0.00 0.00 3.86
2722 6888 1.039856 TGCTATGCGATGCTACTGGA 58.960 50.000 0.00 0.00 0.00 3.86
2723 6889 2.090400 ATGCTATGCGATGCTACTGG 57.910 50.000 0.00 0.00 0.00 4.00
2724 6890 3.369147 GGTTATGCTATGCGATGCTACTG 59.631 47.826 0.00 0.00 0.00 2.74
2725 6891 3.589988 GGTTATGCTATGCGATGCTACT 58.410 45.455 0.00 0.00 0.00 2.57
2726 6892 2.673368 GGGTTATGCTATGCGATGCTAC 59.327 50.000 0.00 0.00 0.00 3.58
2727 6893 2.567169 AGGGTTATGCTATGCGATGCTA 59.433 45.455 0.00 0.00 0.00 3.49
2728 6894 1.349026 AGGGTTATGCTATGCGATGCT 59.651 47.619 0.00 0.00 0.00 3.79
2729 6895 1.813513 AGGGTTATGCTATGCGATGC 58.186 50.000 0.00 0.00 0.00 3.91
2730 6896 3.262420 GGTAGGGTTATGCTATGCGATG 58.738 50.000 0.00 0.00 0.00 3.84
2731 6897 2.236395 GGGTAGGGTTATGCTATGCGAT 59.764 50.000 0.00 0.00 0.00 4.58
2732 6898 1.621814 GGGTAGGGTTATGCTATGCGA 59.378 52.381 0.00 0.00 0.00 5.10
2733 6899 1.671850 CGGGTAGGGTTATGCTATGCG 60.672 57.143 0.00 0.00 0.00 4.73
2734 6900 1.338769 CCGGGTAGGGTTATGCTATGC 60.339 57.143 0.00 0.00 35.97 3.14
2745 6911 3.303928 GAGGATCGCCGGGTAGGG 61.304 72.222 2.18 0.00 41.48 3.53
3198 7366 0.102481 AAGCACTTCGTGACGTCAGT 59.898 50.000 20.73 10.63 35.23 3.41
3219 7387 0.452184 CTGACGTCGTGGTATCAGCT 59.548 55.000 11.62 0.00 32.76 4.24
3237 7405 3.646637 GTGGGAGTAGTTATGGGTATGCT 59.353 47.826 0.00 0.00 0.00 3.79
3239 7407 3.640029 ACGTGGGAGTAGTTATGGGTATG 59.360 47.826 0.00 0.00 0.00 2.39
3566 7737 0.608130 CACTTGGGAGGTGATCACGA 59.392 55.000 19.33 0.00 36.89 4.35
3751 7926 6.910536 ACTGCTTGCATTAGATTAGTGTAC 57.089 37.500 0.00 0.00 0.00 2.90
3759 7934 8.642935 TCTACTCTATACTGCTTGCATTAGAT 57.357 34.615 0.00 0.00 0.00 1.98
4139 8343 1.802365 TCAGAACGACGAGACGATTCA 59.198 47.619 0.00 0.00 37.03 2.57
4347 8573 0.037697 CAGTCAATGACGAACGGGGA 60.038 55.000 7.83 0.00 37.67 4.81
4348 8574 0.320421 ACAGTCAATGACGAACGGGG 60.320 55.000 7.83 0.00 37.67 5.73
4524 8877 8.354426 CCCAGAACGGTTTTATAAAAAGAAAGA 58.646 33.333 12.14 0.00 0.00 2.52
4529 8882 5.165676 GCCCCAGAACGGTTTTATAAAAAG 58.834 41.667 12.14 11.54 0.00 2.27
5363 11282 1.342819 CTTCCCTCCACGATCCAGATC 59.657 57.143 0.00 0.00 34.56 2.75
5404 11708 0.036306 CCCTAACCGAACAGCCACTT 59.964 55.000 0.00 0.00 0.00 3.16
5756 12069 2.608752 CGGTTACTGTTGCTAACCTCGT 60.609 50.000 9.43 2.42 40.72 4.18
6037 12378 8.603242 TCTACTTCTCCACATTTAGTTTTGTC 57.397 34.615 0.00 0.00 0.00 3.18
6086 12436 9.148879 TGGGAGTTTTATTCAAAGGTAATTCAA 57.851 29.630 0.00 0.00 0.00 2.69
6122 12472 3.627395 AATCATTACAGCACCTCCGAA 57.373 42.857 0.00 0.00 0.00 4.30
6171 12521 3.649073 TGTGTAGTTGTCCAGTTGATCG 58.351 45.455 0.00 0.00 0.00 3.69
6175 12525 4.876107 AGAAGTTGTGTAGTTGTCCAGTTG 59.124 41.667 0.00 0.00 0.00 3.16
6176 12526 4.876107 CAGAAGTTGTGTAGTTGTCCAGTT 59.124 41.667 0.00 0.00 0.00 3.16
6177 12527 4.161565 TCAGAAGTTGTGTAGTTGTCCAGT 59.838 41.667 0.00 0.00 0.00 4.00
6178 12528 4.693283 TCAGAAGTTGTGTAGTTGTCCAG 58.307 43.478 0.00 0.00 0.00 3.86
6179 12529 4.746535 TCAGAAGTTGTGTAGTTGTCCA 57.253 40.909 0.00 0.00 0.00 4.02
6180 12530 4.691216 GGATCAGAAGTTGTGTAGTTGTCC 59.309 45.833 0.00 0.00 0.00 4.02
6181 12531 5.542779 AGGATCAGAAGTTGTGTAGTTGTC 58.457 41.667 0.00 0.00 0.00 3.18
6182 12532 5.552870 AGGATCAGAAGTTGTGTAGTTGT 57.447 39.130 0.00 0.00 0.00 3.32
6304 12661 8.250332 AGCAATCAACCACGAATAAAACATTAT 58.750 29.630 0.00 0.00 0.00 1.28
6305 12662 7.598278 AGCAATCAACCACGAATAAAACATTA 58.402 30.769 0.00 0.00 0.00 1.90
6306 12663 6.454795 AGCAATCAACCACGAATAAAACATT 58.545 32.000 0.00 0.00 0.00 2.71
6434 12836 5.388371 GCGCAAAAACTATTTAGCCAACTTG 60.388 40.000 0.30 0.00 0.00 3.16
6568 12971 6.425417 GGACCAGAAAACTGAGAAAAGTAGAG 59.575 42.308 0.00 0.00 0.00 2.43
6578 12981 8.454106 CAAACTAATATGGACCAGAAAACTGAG 58.546 37.037 0.00 0.00 0.00 3.35
6666 13079 0.750911 GCAAAGCCATCTCCCTCCTG 60.751 60.000 0.00 0.00 0.00 3.86
6993 13421 3.995705 CGGCCATGTTGTCATTTCAATTT 59.004 39.130 2.24 0.00 31.15 1.82
7010 13438 2.883122 ACACTTATAAAACCCGGCCA 57.117 45.000 2.24 0.00 0.00 5.36
7154 14128 7.201902 GGACAAAAATATTCCACCATGCATCTA 60.202 37.037 0.00 0.00 0.00 1.98
7323 14301 2.413142 GCAAGCATCCCCAGTGAGC 61.413 63.158 0.00 0.00 0.00 4.26
7686 15114 6.645415 CGTTCATACCACAGAAAAAGAGTACT 59.355 38.462 0.00 0.00 0.00 2.73
7796 15230 4.210331 GTGCCCTTGATATTCACCTTCAT 58.790 43.478 0.00 0.00 0.00 2.57
8071 15542 2.649831 TGGACGACCCAGACAGTAC 58.350 57.895 0.34 0.00 40.82 2.73
8325 15822 9.407380 TGGATGTAAGCTCATGTATAAACAATT 57.593 29.630 0.00 0.00 39.58 2.32
8520 16030 6.170506 GGTGTACACTTCATCCAACTGAATA 58.829 40.000 24.55 0.00 34.76 1.75
8665 16177 6.890979 AAATTAGATTGATGAAGGCTAGCC 57.109 37.500 27.19 27.19 0.00 3.93
8698 16210 7.931407 TGTTATTTGATGAGGCGACATACTTAT 59.069 33.333 0.00 0.00 0.00 1.73
8906 16431 4.835284 ACAAGAAGAAAAGGGCCAAAAA 57.165 36.364 6.18 0.00 0.00 1.94
8984 16509 6.424207 AGAGAAAATGAGTAACCGACAAAGAC 59.576 38.462 0.00 0.00 0.00 3.01
9055 16597 7.546250 TCTCACTCTCCTAGAAAATGAACTT 57.454 36.000 0.00 0.00 0.00 2.66
9148 16691 6.262049 AGAGTACAATTGTATTGTGTGCAACA 59.738 34.615 20.72 0.00 37.40 3.33
9283 16831 6.753279 CCATGTGCTCGTTGAAAATATTTGAT 59.247 34.615 0.39 0.00 0.00 2.57
9336 16884 5.801531 ATAATACTAGATGACCCGTTGCA 57.198 39.130 0.00 0.00 0.00 4.08
9360 16908 3.288092 ACACTCTTCCAAACCCACTTTC 58.712 45.455 0.00 0.00 0.00 2.62
9365 16913 2.241176 AGTTGACACTCTTCCAAACCCA 59.759 45.455 0.00 0.00 0.00 4.51


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.