Multiple sequence alignment - TraesCS7A01G237100

Loading Multiple Alignment...

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 TraesCS7A01G237100 chr7A 100.000 5125 0 0 1 5125 211210974 211216098 0.000000e+00 9465.0
1 TraesCS7A01G237100 chr7A 95.768 3899 108 10 1264 5119 582928334 582932218 0.000000e+00 6233.0
2 TraesCS7A01G237100 chr7A 100.000 2517 0 0 5879 8395 211216852 211219368 0.000000e+00 4649.0
3 TraesCS7A01G237100 chr7A 95.204 980 40 5 5879 6854 225214489 225215465 0.000000e+00 1543.0
4 TraesCS7A01G237100 chr7A 95.369 691 27 4 5879 6566 5496714 5497402 0.000000e+00 1094.0
5 TraesCS7A01G237100 chr7A 95.369 691 25 6 5879 6566 59744106 59743420 0.000000e+00 1092.0
6 TraesCS7A01G237100 chr7A 95.231 692 26 5 5879 6566 582932938 582933626 0.000000e+00 1088.0
7 TraesCS7A01G237100 chr7A 96.660 479 15 1 7459 7937 644534930 644534453 0.000000e+00 795.0
8 TraesCS7A01G237100 chr7A 96.288 458 13 1 7938 8395 261401780 261401327 0.000000e+00 749.0
9 TraesCS7A01G237100 chr7A 88.614 606 67 2 6855 7459 211412636 211413240 0.000000e+00 736.0
10 TraesCS7A01G237100 chr7A 96.484 256 8 1 7940 8195 130082064 130082318 1.010000e-113 422.0
11 TraesCS7A01G237100 chr7A 83.750 400 53 9 865 1264 211412252 211412639 1.330000e-97 368.0
12 TraesCS7A01G237100 chr7A 96.552 203 7 0 8193 8395 130085145 130085347 3.750000e-88 337.0
13 TraesCS7A01G237100 chr7A 88.021 192 11 5 8010 8195 316028018 316027833 5.100000e-52 217.0
14 TraesCS7A01G237100 chr7A 90.000 50 5 0 7830 7879 727797013 727797062 1.960000e-06 65.8
15 TraesCS7A01G237100 chr4A 96.104 3901 112 7 1264 5125 51941007 51937108 0.000000e+00 6325.0
16 TraesCS7A01G237100 chr4A 93.394 1862 57 21 1621 3445 247019572 247021404 0.000000e+00 2697.0
17 TraesCS7A01G237100 chr4A 93.789 483 26 1 7459 7937 628879063 628879545 0.000000e+00 723.0
18 TraesCS7A01G237100 chr4A 92.447 331 19 3 6529 6854 51935229 51934900 1.280000e-127 468.0
19 TraesCS7A01G237100 chr4A 91.279 344 20 4 1 340 514742347 514742684 2.140000e-125 460.0
20 TraesCS7A01G237100 chr4A 87.302 378 42 4 6482 6854 391067805 391067429 2.170000e-115 427.0
21 TraesCS7A01G237100 chr4A 90.449 178 16 1 7657 7834 564725419 564725595 5.070000e-57 233.0
22 TraesCS7A01G237100 chr4A 85.128 195 27 2 7459 7653 564723987 564724179 1.850000e-46 198.0
23 TraesCS7A01G237100 chr4A 96.262 107 4 0 7830 7936 629984962 629985068 8.660000e-40 176.0
24 TraesCS7A01G237100 chr4A 85.030 167 16 6 8193 8359 628890138 628890295 2.430000e-35 161.0
25 TraesCS7A01G237100 chr4A 79.355 155 26 5 406 557 10851012 10851163 4.140000e-18 104.0
26 TraesCS7A01G237100 chr5A 96.032 3906 98 11 1263 5125 613091418 613087527 0.000000e+00 6301.0
27 TraesCS7A01G237100 chr5A 95.994 3894 94 12 1264 5115 170898088 170894215 0.000000e+00 6270.0
28 TraesCS7A01G237100 chr5A 93.276 937 50 6 5928 6854 500382202 500381269 0.000000e+00 1369.0
29 TraesCS7A01G237100 chr5A 95.238 693 25 4 5880 6566 323343907 323343217 0.000000e+00 1090.0
30 TraesCS7A01G237100 chr5A 95.108 695 23 7 5879 6566 613086748 613086058 0.000000e+00 1085.0
31 TraesCS7A01G237100 chr5A 94.242 330 15 4 6526 6854 584113630 584113956 1.260000e-137 501.0
32 TraesCS7A01G237100 chr5A 89.710 379 37 1 6482 6858 178111094 178111472 4.560000e-132 483.0
33 TraesCS7A01G237100 chr5A 92.661 327 21 3 6529 6854 613086050 613085726 1.280000e-127 468.0
34 TraesCS7A01G237100 chr5A 88.800 375 37 4 6482 6854 630914245 630914616 9.930000e-124 455.0
35 TraesCS7A01G237100 chr5A 97.266 256 7 0 7940 8195 353159719 353159974 1.290000e-117 435.0
36 TraesCS7A01G237100 chr5A 96.552 203 7 0 8193 8395 353162614 353162816 3.750000e-88 337.0
37 TraesCS7A01G237100 chr5A 87.117 163 11 8 8198 8358 429749474 429749320 8.660000e-40 176.0
38 TraesCS7A01G237100 chr3A 96.114 3886 99 9 1264 5119 526712661 526716524 0.000000e+00 6292.0
39 TraesCS7A01G237100 chr3A 97.861 935 20 0 7461 8395 57476612 57475678 0.000000e+00 1616.0
40 TraesCS7A01G237100 chr3A 94.898 980 42 5 5879 6856 554799354 554798381 0.000000e+00 1526.0
41 TraesCS7A01G237100 chr3A 91.765 340 25 2 1 339 606866745 606867082 3.550000e-128 470.0
42 TraesCS7A01G237100 chr1A 95.794 3899 115 12 1264 5119 356012491 356016383 0.000000e+00 6246.0
43 TraesCS7A01G237100 chr1A 95.619 3880 122 10 1264 5114 411072287 411076147 0.000000e+00 6180.0
44 TraesCS7A01G237100 chr1A 94.326 2397 73 19 1262 3603 26683273 26685661 0.000000e+00 3615.0
45 TraesCS7A01G237100 chr1A 95.507 690 27 3 5879 6566 26688020 26688707 0.000000e+00 1099.0
46 TraesCS7A01G237100 chr1A 95.238 546 23 2 6022 6566 411076892 411077435 0.000000e+00 861.0
47 TraesCS7A01G237100 chr1A 95.029 523 17 4 6046 6566 356017024 356017539 0.000000e+00 813.0
48 TraesCS7A01G237100 chr1A 96.436 477 17 0 7461 7937 74091595 74092071 0.000000e+00 787.0
49 TraesCS7A01G237100 chr1A 96.976 463 12 2 6063 6523 219683230 219683692 0.000000e+00 776.0
50 TraesCS7A01G237100 chr1A 87.454 542 68 0 6855 7396 566689047 566689588 7.150000e-175 625.0
51 TraesCS7A01G237100 chr1A 97.006 334 8 1 6141 6474 20726486 20726155 2.050000e-155 560.0
52 TraesCS7A01G237100 chr1A 97.006 334 8 1 6141 6474 293089415 293089084 2.050000e-155 560.0
53 TraesCS7A01G237100 chr1A 93.485 307 18 2 6549 6854 219684110 219684415 9.930000e-124 455.0
54 TraesCS7A01G237100 chr1A 91.617 334 20 4 6526 6854 356017544 356017874 9.930000e-124 455.0
55 TraesCS7A01G237100 chr1A 87.206 383 41 5 6482 6858 7878935 7879315 6.020000e-116 429.0
56 TraesCS7A01G237100 chr1A 90.090 333 26 6 6526 6857 26688712 26689038 7.790000e-115 425.0
57 TraesCS7A01G237100 chr1A 95.817 263 10 1 5879 6140 44970263 44970525 2.800000e-114 424.0
58 TraesCS7A01G237100 chr1A 90.030 331 28 4 6526 6855 411077440 411077766 2.800000e-114 424.0
59 TraesCS7A01G237100 chr1A 95.437 263 10 2 5879 6139 421097302 421097564 1.300000e-112 418.0
60 TraesCS7A01G237100 chr1A 89.697 330 28 5 6529 6854 20724778 20724451 4.690000e-112 416.0
61 TraesCS7A01G237100 chr1A 94.340 265 12 3 5879 6140 48808199 48808463 3.650000e-108 403.0
62 TraesCS7A01G237100 chr1A 88.889 333 28 6 6526 6853 141984608 141984936 1.310000e-107 401.0
63 TraesCS7A01G237100 chr1A 93.939 264 14 2 5879 6140 441649330 441649593 1.700000e-106 398.0
64 TraesCS7A01G237100 chr1A 93.561 264 14 3 5879 6140 459657201 459656939 2.840000e-104 390.0
65 TraesCS7A01G237100 chr1A 93.536 263 14 3 5879 6140 52663268 52663008 1.020000e-103 388.0
66 TraesCS7A01G237100 chr1A 93.487 261 16 1 5879 6138 108970087 108969827 3.680000e-103 387.0
67 TraesCS7A01G237100 chr1A 93.182 264 15 3 5879 6140 16718765 16719027 1.320000e-102 385.0
68 TraesCS7A01G237100 chr1A 87.725 334 31 5 6526 6854 137051520 137051192 1.710000e-101 381.0
69 TraesCS7A01G237100 chr1A 87.463 335 37 4 6526 6856 185309447 185309780 1.710000e-101 381.0
70 TraesCS7A01G237100 chr1A 92.803 264 16 3 5879 6140 419847039 419846777 6.150000e-101 379.0
71 TraesCS7A01G237100 chr1A 85.629 167 15 6 8193 8359 74094817 74094974 5.210000e-37 167.0
72 TraesCS7A01G237100 chr6A 95.554 3914 111 12 1263 5119 525586941 525590848 0.000000e+00 6205.0
73 TraesCS7A01G237100 chr6A 97.173 2865 77 3 2263 5125 65352951 65350089 0.000000e+00 4839.0
74 TraesCS7A01G237100 chr6A 93.177 982 48 9 5879 6856 528499955 528500921 0.000000e+00 1424.0
75 TraesCS7A01G237100 chr6A 95.658 691 24 5 5879 6566 65349250 65348563 0.000000e+00 1105.0
76 TraesCS7A01G237100 chr6A 94.638 690 31 5 5879 6566 587064786 587064101 0.000000e+00 1064.0
77 TraesCS7A01G237100 chr6A 95.169 621 25 4 5936 6554 525591094 525591711 0.000000e+00 976.0
78 TraesCS7A01G237100 chr6A 94.937 553 24 3 5979 6529 308789073 308789623 0.000000e+00 863.0
79 TraesCS7A01G237100 chr6A 96.544 434 14 1 5982 6414 589734262 589734695 0.000000e+00 717.0
80 TraesCS7A01G237100 chr6A 86.900 542 71 0 6855 7396 61409004 61409545 7.210000e-170 608.0
81 TraesCS7A01G237100 chr6A 86.004 543 76 0 6855 7397 61418880 61419422 4.370000e-162 582.0
82 TraesCS7A01G237100 chr6A 85.820 543 77 0 6855 7397 61422777 61423319 2.030000e-160 577.0
83 TraesCS7A01G237100 chr6A 92.771 332 18 5 6526 6855 308789964 308790291 7.620000e-130 475.0
84 TraesCS7A01G237100 chr6A 89.600 375 35 2 6482 6854 253472999 253472627 2.740000e-129 473.0
85 TraesCS7A01G237100 chr6A 92.401 329 21 3 6529 6856 616527827 616527502 4.590000e-127 466.0
86 TraesCS7A01G237100 chr6A 88.594 377 38 5 6482 6855 583629379 583629005 3.570000e-123 453.0
87 TraesCS7A01G237100 chr6A 92.188 320 21 3 6536 6854 65348174 65347858 4.620000e-122 449.0
88 TraesCS7A01G237100 chr6A 91.718 326 23 3 6530 6854 589743872 589744194 4.620000e-122 449.0
89 TraesCS7A01G237100 chr6A 91.411 326 24 3 6530 6854 589734842 589735164 2.150000e-120 444.0
90 TraesCS7A01G237100 chr6A 84.865 185 23 5 7458 7642 97748729 97748908 1.860000e-41 182.0
91 TraesCS7A01G237100 chr6B 91.663 2219 136 16 1264 3459 716942336 716940144 0.000000e+00 3027.0
92 TraesCS7A01G237100 chr6B 86.716 542 71 1 6855 7396 117772485 117773025 1.210000e-167 601.0
93 TraesCS7A01G237100 chr6B 87.793 213 22 3 7442 7653 695054595 695054804 6.510000e-61 246.0
94 TraesCS7A01G237100 chrUn 92.389 1603 76 10 1263 2821 34718842 34720442 0.000000e+00 2242.0
95 TraesCS7A01G237100 chrUn 90.556 900 57 14 1264 2141 239272865 239271972 0.000000e+00 1166.0
96 TraesCS7A01G237100 chrUn 85.820 543 77 0 6855 7397 381573480 381572938 2.030000e-160 577.0
97 TraesCS7A01G237100 chrUn 97.006 334 8 1 6141 6474 184019853 184019522 2.050000e-155 560.0
98 TraesCS7A01G237100 chrUn 97.006 334 8 1 6141 6474 191259145 191259476 2.050000e-155 560.0
99 TraesCS7A01G237100 chrUn 97.006 334 8 1 6141 6474 242430373 242430704 2.050000e-155 560.0
100 TraesCS7A01G237100 chrUn 97.006 334 8 1 6141 6474 350213681 350213350 2.050000e-155 560.0
101 TraesCS7A01G237100 chrUn 96.997 333 8 1 6142 6474 83699544 83699214 7.360000e-155 558.0
102 TraesCS7A01G237100 chrUn 96.997 333 8 1 6142 6474 389038849 389038519 7.360000e-155 558.0
103 TraesCS7A01G237100 chrUn 96.707 334 9 1 6141 6474 13535889 13536220 9.520000e-154 555.0
104 TraesCS7A01G237100 chrUn 96.707 334 9 1 6141 6474 21743262 21743593 9.520000e-154 555.0
105 TraesCS7A01G237100 chrUn 96.707 334 9 1 6141 6474 224104500 224104831 9.520000e-154 555.0
106 TraesCS7A01G237100 chrUn 96.707 334 9 1 6141 6474 272718886 272719217 9.520000e-154 555.0
107 TraesCS7A01G237100 chrUn 88.427 337 22 8 6526 6854 366903789 366904116 2.840000e-104 390.0
108 TraesCS7A01G237100 chrUn 88.131 337 23 8 6526 6854 302426424 302426097 1.320000e-102 385.0
109 TraesCS7A01G237100 chrUn 87.834 337 24 8 6526 6854 453316376 453316703 6.150000e-101 379.0
110 TraesCS7A01G237100 chrUn 87.387 333 37 4 6526 6855 318386893 318387223 2.210000e-100 377.0
111 TraesCS7A01G237100 chrUn 87.387 333 37 4 6526 6855 318390363 318390693 2.210000e-100 377.0
112 TraesCS7A01G237100 chrUn 87.387 333 37 4 6526 6855 351833368 351833698 2.210000e-100 377.0
113 TraesCS7A01G237100 chrUn 87.316 339 28 7 6526 6855 243129621 243129953 2.860000e-99 374.0
114 TraesCS7A01G237100 chrUn 91.852 270 14 4 5879 6140 319739176 319739445 3.700000e-98 370.0
115 TraesCS7A01G237100 chrUn 89.347 291 26 3 6565 6854 342895399 342895685 2.230000e-95 361.0
116 TraesCS7A01G237100 chrUn 85.423 343 50 0 7055 7397 77434118 77433776 2.880000e-94 357.0
117 TraesCS7A01G237100 chrUn 85.196 331 46 3 6526 6854 272720572 272720901 3.750000e-88 337.0
118 TraesCS7A01G237100 chrUn 85.241 332 43 5 6526 6854 467271648 467271976 3.750000e-88 337.0
119 TraesCS7A01G237100 chrUn 93.953 215 10 3 5879 6090 272716941 272717155 1.050000e-83 322.0
120 TraesCS7A01G237100 chrUn 93.578 218 11 3 5879 6093 463971011 463970794 1.050000e-83 322.0
121 TraesCS7A01G237100 chrUn 93.578 218 11 3 5879 6093 471345753 471345536 1.050000e-83 322.0
122 TraesCS7A01G237100 chrUn 91.703 229 14 4 5879 6103 410701394 410701621 6.330000e-81 313.0
123 TraesCS7A01G237100 chrUn 90.417 240 16 5 5879 6113 471654359 471654122 8.180000e-80 309.0
124 TraesCS7A01G237100 chrUn 94.330 194 8 3 5879 6069 87892375 87892568 2.290000e-75 294.0
125 TraesCS7A01G237100 chrUn 92.683 205 11 3 5879 6079 303419832 303420036 8.240000e-75 292.0
126 TraesCS7A01G237100 chrUn 94.828 174 5 3 5879 6048 77150563 77150736 1.390000e-67 268.0
127 TraesCS7A01G237100 chrUn 94.798 173 6 3 5879 6048 370353726 370353554 5.000000e-67 267.0
128 TraesCS7A01G237100 chrUn 82.143 196 29 4 7459 7653 178687710 178687900 6.740000e-36 163.0
129 TraesCS7A01G237100 chr7D 94.456 938 45 5 334 1264 156454673 156455610 0.000000e+00 1437.0
130 TraesCS7A01G237100 chr7D 92.893 605 43 0 6855 7459 156455607 156456211 0.000000e+00 880.0
131 TraesCS7A01G237100 chr7D 87.624 606 73 2 6855 7459 156525713 156526317 0.000000e+00 702.0
132 TraesCS7A01G237100 chr7D 89.318 337 33 3 2 337 258978146 258977812 3.620000e-113 420.0
133 TraesCS7A01G237100 chr7D 89.053 338 29 6 1 336 16184688 16184357 6.060000e-111 412.0
134 TraesCS7A01G237100 chr7D 83.750 400 44 10 865 1264 156525338 156525716 8.010000e-95 359.0
135 TraesCS7A01G237100 chr7D 87.701 187 20 3 7458 7643 8963574 8963758 1.840000e-51 215.0
136 TraesCS7A01G237100 chr7D 87.629 194 13 4 8007 8195 279734723 279734910 1.840000e-51 215.0
137 TraesCS7A01G237100 chr7D 88.000 50 6 0 7830 7879 54497341 54497390 9.100000e-05 60.2
138 TraesCS7A01G237100 chr3B 93.777 932 49 5 1261 2190 98216860 98217784 0.000000e+00 1391.0
139 TraesCS7A01G237100 chr3B 90.491 957 56 18 1264 2190 171495465 171496416 0.000000e+00 1230.0
140 TraesCS7A01G237100 chr3B 90.635 897 56 14 1264 2138 34591361 34592251 0.000000e+00 1166.0
141 TraesCS7A01G237100 chr3B 88.791 339 32 5 1 338 715154190 715153857 2.180000e-110 411.0
142 TraesCS7A01G237100 chr3B 84.138 145 20 3 406 549 309002449 309002591 4.090000e-28 137.0
143 TraesCS7A01G237100 chr5B 92.431 938 57 8 1263 2190 549290318 549289385 0.000000e+00 1327.0
144 TraesCS7A01G237100 chr5B 80.863 371 46 13 7459 7805 335518555 335518924 1.390000e-67 268.0
145 TraesCS7A01G237100 chr5B 88.272 162 10 7 8198 8358 379448012 379448165 1.440000e-42 185.0
146 TraesCS7A01G237100 chr5B 80.102 196 36 3 7459 7653 100025598 100025405 8.780000e-30 143.0
147 TraesCS7A01G237100 chr2B 91.949 944 56 7 1264 2190 752285443 752286383 0.000000e+00 1304.0
148 TraesCS7A01G237100 chr2B 92.941 850 41 12 1358 2190 714410576 714409729 0.000000e+00 1219.0
149 TraesCS7A01G237100 chr2B 90.206 194 13 3 8007 8195 69351549 69351357 1.810000e-61 248.0
150 TraesCS7A01G237100 chr7B 91.605 953 47 12 334 1264 118820701 118821642 0.000000e+00 1286.0
151 TraesCS7A01G237100 chr7B 92.397 605 46 0 6855 7459 118891675 118892279 0.000000e+00 863.0
152 TraesCS7A01G237100 chr7B 91.074 605 54 0 6855 7459 118821639 118822243 0.000000e+00 819.0
153 TraesCS7A01G237100 chr7B 96.875 480 14 1 7459 7937 640933022 640933501 0.000000e+00 802.0
154 TraesCS7A01G237100 chr7B 96.066 483 15 3 7459 7937 417059551 417059069 0.000000e+00 784.0
155 TraesCS7A01G237100 chr7B 82.750 400 51 11 865 1264 118891297 118891678 2.900000e-89 340.0
156 TraesCS7A01G237100 chr7B 90.769 195 17 1 7459 7653 395761982 395762175 8.360000e-65 259.0
157 TraesCS7A01G237100 chr7B 96.183 131 4 1 8193 8323 638083459 638083588 6.600000e-51 213.0
158 TraesCS7A01G237100 chr7B 94.444 72 4 0 8324 8395 638083825 638083896 2.480000e-20 111.0
159 TraesCS7A01G237100 chr7B 80.132 151 25 5 410 558 678652088 678651941 3.200000e-19 108.0
160 TraesCS7A01G237100 chr1B 96.033 479 18 1 7459 7937 4544466 4544943 0.000000e+00 778.0
161 TraesCS7A01G237100 chr1B 86.900 542 71 0 6855 7396 657506934 657507475 7.210000e-170 608.0
162 TraesCS7A01G237100 chr1B 85.263 190 22 4 7457 7646 66955392 66955209 3.090000e-44 191.0
163 TraesCS7A01G237100 chr1B 85.976 164 15 5 8193 8356 4553051 4553206 1.450000e-37 169.0
164 TraesCS7A01G237100 chr5D 86.556 543 73 0 6855 7397 507772098 507771556 4.340000e-167 599.0
165 TraesCS7A01G237100 chr5D 85.890 163 14 7 8198 8359 326742539 326742693 1.870000e-36 165.0
166 TraesCS7A01G237100 chr6D 86.531 542 73 0 6855 7396 53681068 53680527 1.560000e-166 597.0
167 TraesCS7A01G237100 chr6D 85.634 536 76 1 6861 7396 53762057 53761523 5.690000e-156 562.0
168 TraesCS7A01G237100 chr6D 96.450 338 10 1 6137 6474 226236389 226236724 2.650000e-154 556.0
169 TraesCS7A01G237100 chr6D 82.689 543 80 1 6855 7397 53686499 53685971 3.550000e-128 470.0
170 TraesCS7A01G237100 chr6D 89.021 337 28 6 1 334 10676247 10676577 7.840000e-110 409.0
171 TraesCS7A01G237100 chr1D 86.162 542 75 0 6855 7396 473034418 473034959 3.380000e-163 586.0
172 TraesCS7A01G237100 chr1D 84.815 540 82 0 6859 7398 452264796 452264257 2.060000e-150 544.0
173 TraesCS7A01G237100 chr1D 92.537 335 21 4 1 334 423279376 423279045 2.120000e-130 477.0
174 TraesCS7A01G237100 chr2A 89.737 380 31 4 6481 6857 28166453 28166827 5.890000e-131 479.0
175 TraesCS7A01G237100 chr3D 89.796 343 27 4 1 341 551622067 551621731 4.650000e-117 433.0
176 TraesCS7A01G237100 chr3D 82.014 139 24 1 411 549 82134592 82134729 5.320000e-22 117.0
177 TraesCS7A01G237100 chr3D 80.986 142 24 3 409 549 325622741 325622602 8.910000e-20 110.0
178 TraesCS7A01G237100 chr3D 80.851 141 24 3 409 548 61962563 61962425 3.200000e-19 108.0
179 TraesCS7A01G237100 chr3D 93.617 47 3 0 7459 7505 513859319 513859365 4.200000e-08 71.3
180 TraesCS7A01G237100 chr3D 87.755 49 6 0 7888 7936 172898815 172898767 3.270000e-04 58.4
181 TraesCS7A01G237100 chr2D 89.213 343 27 6 1 342 15680300 15679967 3.620000e-113 420.0
182 TraesCS7A01G237100 chr2D 94.340 265 12 2 5879 6140 647580748 647580484 3.650000e-108 403.0
183 TraesCS7A01G237100 chr2D 83.756 197 28 3 7459 7653 30417613 30417419 5.180000e-42 183.0
184 TraesCS7A01G237100 chr2D 94.393 107 6 0 7830 7936 620788773 620788879 1.870000e-36 165.0
185 TraesCS7A01G237100 chr2D 80.612 196 27 7 7459 7653 467998465 467998280 3.160000e-29 141.0
186 TraesCS7A01G237100 chr2D 82.069 145 25 1 405 549 367824390 367824533 1.140000e-23 122.0
187 TraesCS7A01G237100 chr4B 85.640 383 40 12 7459 7834 606296713 606297087 1.020000e-103 388.0
188 TraesCS7A01G237100 chr4B 96.465 198 7 0 8198 8395 606307562 606307759 2.260000e-85 327.0
189 TraesCS7A01G237100 chr4D 87.778 90 10 1 7459 7548 58398275 58398187 4.140000e-18 104.0


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 TraesCS7A01G237100 chr7A 211210974 211219368 8394 False 7057.000000 9465 100.000000 1 8395 2 chr7A.!!$F5 8394
1 TraesCS7A01G237100 chr7A 582928334 582933626 5292 False 3660.500000 6233 95.499500 1264 6566 2 chr7A.!!$F7 5302
2 TraesCS7A01G237100 chr7A 225214489 225215465 976 False 1543.000000 1543 95.204000 5879 6854 1 chr7A.!!$F2 975
3 TraesCS7A01G237100 chr7A 5496714 5497402 688 False 1094.000000 1094 95.369000 5879 6566 1 chr7A.!!$F1 687
4 TraesCS7A01G237100 chr7A 59743420 59744106 686 True 1092.000000 1092 95.369000 5879 6566 1 chr7A.!!$R1 687
5 TraesCS7A01G237100 chr7A 211412252 211413240 988 False 552.000000 736 86.182000 865 7459 2 chr7A.!!$F6 6594
6 TraesCS7A01G237100 chr7A 130082064 130085347 3283 False 379.500000 422 96.518000 7940 8395 2 chr7A.!!$F4 455
7 TraesCS7A01G237100 chr4A 51934900 51941007 6107 True 3396.500000 6325 94.275500 1264 6854 2 chr4A.!!$R2 5590
8 TraesCS7A01G237100 chr4A 247019572 247021404 1832 False 2697.000000 2697 93.394000 1621 3445 1 chr4A.!!$F2 1824
9 TraesCS7A01G237100 chr4A 564723987 564725595 1608 False 215.500000 233 87.788500 7459 7834 2 chr4A.!!$F7 375
10 TraesCS7A01G237100 chr5A 170894215 170898088 3873 True 6270.000000 6270 95.994000 1264 5115 1 chr5A.!!$R1 3851
11 TraesCS7A01G237100 chr5A 613085726 613091418 5692 True 2618.000000 6301 94.600333 1263 6854 3 chr5A.!!$R5 5591
12 TraesCS7A01G237100 chr5A 500381269 500382202 933 True 1369.000000 1369 93.276000 5928 6854 1 chr5A.!!$R4 926
13 TraesCS7A01G237100 chr5A 323343217 323343907 690 True 1090.000000 1090 95.238000 5880 6566 1 chr5A.!!$R2 686
14 TraesCS7A01G237100 chr5A 353159719 353162816 3097 False 386.000000 435 96.909000 7940 8395 2 chr5A.!!$F4 455
15 TraesCS7A01G237100 chr3A 526712661 526716524 3863 False 6292.000000 6292 96.114000 1264 5119 1 chr3A.!!$F1 3855
16 TraesCS7A01G237100 chr3A 57475678 57476612 934 True 1616.000000 1616 97.861000 7461 8395 1 chr3A.!!$R1 934
17 TraesCS7A01G237100 chr3A 554798381 554799354 973 True 1526.000000 1526 94.898000 5879 6856 1 chr3A.!!$R2 977
18 TraesCS7A01G237100 chr1A 356012491 356017874 5383 False 2504.666667 6246 94.146667 1264 6854 3 chr1A.!!$F13 5590
19 TraesCS7A01G237100 chr1A 411072287 411077766 5479 False 2488.333333 6180 93.629000 1264 6855 3 chr1A.!!$F14 5591
20 TraesCS7A01G237100 chr1A 26683273 26689038 5765 False 1713.000000 3615 93.307667 1262 6857 3 chr1A.!!$F10 5595
21 TraesCS7A01G237100 chr1A 566689047 566689588 541 False 625.000000 625 87.454000 6855 7396 1 chr1A.!!$F9 541
22 TraesCS7A01G237100 chr1A 219683230 219684415 1185 False 615.500000 776 95.230500 6063 6854 2 chr1A.!!$F12 791
23 TraesCS7A01G237100 chr1A 20724451 20726486 2035 True 488.000000 560 93.351500 6141 6854 2 chr1A.!!$R7 713
24 TraesCS7A01G237100 chr1A 74091595 74094974 3379 False 477.000000 787 91.032500 7461 8359 2 chr1A.!!$F11 898
25 TraesCS7A01G237100 chr6A 525586941 525591711 4770 False 3590.500000 6205 95.361500 1263 6554 2 chr6A.!!$F7 5291
26 TraesCS7A01G237100 chr6A 65347858 65352951 5093 True 2131.000000 4839 95.006333 2263 6854 3 chr6A.!!$R5 4591
27 TraesCS7A01G237100 chr6A 528499955 528500921 966 False 1424.000000 1424 93.177000 5879 6856 1 chr6A.!!$F3 977
28 TraesCS7A01G237100 chr6A 587064101 587064786 685 True 1064.000000 1064 94.638000 5879 6566 1 chr6A.!!$R3 687
29 TraesCS7A01G237100 chr6A 308789073 308790291 1218 False 669.000000 863 93.854000 5979 6855 2 chr6A.!!$F6 876
30 TraesCS7A01G237100 chr6A 61409004 61409545 541 False 608.000000 608 86.900000 6855 7396 1 chr6A.!!$F1 541
31 TraesCS7A01G237100 chr6A 589734262 589735164 902 False 580.500000 717 93.977500 5982 6854 2 chr6A.!!$F8 872
32 TraesCS7A01G237100 chr6A 61418880 61423319 4439 False 579.500000 582 85.912000 6855 7397 2 chr6A.!!$F5 542
33 TraesCS7A01G237100 chr6B 716940144 716942336 2192 True 3027.000000 3027 91.663000 1264 3459 1 chr6B.!!$R1 2195
34 TraesCS7A01G237100 chr6B 117772485 117773025 540 False 601.000000 601 86.716000 6855 7396 1 chr6B.!!$F1 541
35 TraesCS7A01G237100 chrUn 34718842 34720442 1600 False 2242.000000 2242 92.389000 1263 2821 1 chrUn.!!$F3 1558
36 TraesCS7A01G237100 chrUn 239271972 239272865 893 True 1166.000000 1166 90.556000 1264 2141 1 chrUn.!!$R4 877
37 TraesCS7A01G237100 chrUn 381572938 381573480 542 True 577.000000 577 85.820000 6855 7397 1 chrUn.!!$R8 542
38 TraesCS7A01G237100 chrUn 272716941 272720901 3960 False 404.666667 555 91.952000 5879 6854 3 chrUn.!!$F19 975
39 TraesCS7A01G237100 chrUn 318386893 318390693 3800 False 377.000000 377 87.387000 6526 6855 2 chrUn.!!$F20 329
40 TraesCS7A01G237100 chr7D 156454673 156456211 1538 False 1158.500000 1437 93.674500 334 7459 2 chr7D.!!$F4 7125
41 TraesCS7A01G237100 chr7D 156525338 156526317 979 False 530.500000 702 85.687000 865 7459 2 chr7D.!!$F5 6594
42 TraesCS7A01G237100 chr3B 98216860 98217784 924 False 1391.000000 1391 93.777000 1261 2190 1 chr3B.!!$F2 929
43 TraesCS7A01G237100 chr3B 171495465 171496416 951 False 1230.000000 1230 90.491000 1264 2190 1 chr3B.!!$F3 926
44 TraesCS7A01G237100 chr3B 34591361 34592251 890 False 1166.000000 1166 90.635000 1264 2138 1 chr3B.!!$F1 874
45 TraesCS7A01G237100 chr5B 549289385 549290318 933 True 1327.000000 1327 92.431000 1263 2190 1 chr5B.!!$R2 927
46 TraesCS7A01G237100 chr2B 752285443 752286383 940 False 1304.000000 1304 91.949000 1264 2190 1 chr2B.!!$F1 926
47 TraesCS7A01G237100 chr2B 714409729 714410576 847 True 1219.000000 1219 92.941000 1358 2190 1 chr2B.!!$R2 832
48 TraesCS7A01G237100 chr7B 118820701 118822243 1542 False 1052.500000 1286 91.339500 334 7459 2 chr7B.!!$F3 7125
49 TraesCS7A01G237100 chr7B 118891297 118892279 982 False 601.500000 863 87.573500 865 7459 2 chr7B.!!$F4 6594
50 TraesCS7A01G237100 chr1B 657506934 657507475 541 False 608.000000 608 86.900000 6855 7396 1 chr1B.!!$F3 541
51 TraesCS7A01G237100 chr5D 507771556 507772098 542 True 599.000000 599 86.556000 6855 7397 1 chr5D.!!$R1 542
52 TraesCS7A01G237100 chr6D 53680527 53681068 541 True 597.000000 597 86.531000 6855 7396 1 chr6D.!!$R1 541
53 TraesCS7A01G237100 chr6D 53761523 53762057 534 True 562.000000 562 85.634000 6861 7396 1 chr6D.!!$R3 535
54 TraesCS7A01G237100 chr6D 53685971 53686499 528 True 470.000000 470 82.689000 6855 7397 1 chr6D.!!$R2 542
55 TraesCS7A01G237100 chr1D 473034418 473034959 541 False 586.000000 586 86.162000 6855 7396 1 chr1D.!!$F1 541
56 TraesCS7A01G237100 chr1D 452264257 452264796 539 True 544.000000 544 84.815000 6859 7398 1 chr1D.!!$R2 539

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
300 301 0.099791 ATGGGAAATTTTACGGCGCG 59.900 50.000 6.90 0.0 0.00 6.86 F
330 331 0.166814 GACACGGCTGTTGAAGATGC 59.833 55.000 0.00 0.0 0.00 3.91 F
1258 1285 0.246086 GGACACAGCTGGACTCTCAG 59.754 60.000 19.93 0.0 37.79 3.35 F
2833 3062 0.393402 CTGCTGCTGCTCCCATTACA 60.393 55.000 17.00 0.0 40.48 2.41 F
3172 3401 0.107214 GGCGGATCTTCACCCATCAA 60.107 55.000 0.00 0.0 0.00 2.57 F
4673 4907 2.226674 GACCCTTCACAGTAGCAAAAGC 59.773 50.000 0.00 0.0 0.00 3.51 F
4883 5117 1.909986 GTGAGTAAGGAAGAGGGGCTT 59.090 52.381 0.00 0.0 40.25 4.35 F
6229 8577 1.645710 TCTTCCCGCTTCTTCTCCTT 58.354 50.000 0.00 0.0 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1290 1317 0.397187 TAGTAGGCAAAACCGGTGCA 59.603 50.000 8.52 0.0 46.52 4.57 R
1399 1427 2.009051 CACTGTCTGATGCGCCATTAA 58.991 47.619 4.18 0.0 0.00 1.40 R
3129 3358 2.254546 AATGTGAAGTTGCGACAGGA 57.745 45.000 6.90 0.0 0.00 3.86 R
4730 4964 0.392336 TGGTTTGCTTGATGGTTGGC 59.608 50.000 0.00 0.0 0.00 4.52 R
4810 5044 2.373169 TGTTCCTCTCTTGTCCATGCTT 59.627 45.455 0.00 0.0 0.00 3.91 R
6229 8577 2.185867 GTTGGCACGCGGATAGGA 59.814 61.111 12.47 0.0 0.00 2.94 R
6872 14771 1.270358 ACCTCTTGCTCACGGTTCTTC 60.270 52.381 0.00 0.0 0.00 2.87 R
7491 20487 0.825840 CCGCCCCAACTTCCTTTGAA 60.826 55.000 0.00 0.0 0.00 2.69 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
17 18 3.528370 CGGCGGTGACTAGAGGGG 61.528 72.222 0.00 0.00 0.00 4.79
18 19 3.155167 GGCGGTGACTAGAGGGGG 61.155 72.222 0.00 0.00 0.00 5.40
19 20 3.851128 GCGGTGACTAGAGGGGGC 61.851 72.222 0.00 0.00 0.00 5.80
20 21 3.528370 CGGTGACTAGAGGGGGCG 61.528 72.222 0.00 0.00 0.00 6.13
21 22 3.155167 GGTGACTAGAGGGGGCGG 61.155 72.222 0.00 0.00 0.00 6.13
22 23 2.043248 GTGACTAGAGGGGGCGGA 60.043 66.667 0.00 0.00 0.00 5.54
23 24 2.128507 GTGACTAGAGGGGGCGGAG 61.129 68.421 0.00 0.00 0.00 4.63
24 25 2.522193 GACTAGAGGGGGCGGAGG 60.522 72.222 0.00 0.00 0.00 4.30
25 26 3.028098 ACTAGAGGGGGCGGAGGA 61.028 66.667 0.00 0.00 0.00 3.71
26 27 2.282446 CTAGAGGGGGCGGAGGAA 59.718 66.667 0.00 0.00 0.00 3.36
27 28 1.834822 CTAGAGGGGGCGGAGGAAG 60.835 68.421 0.00 0.00 0.00 3.46
55 56 4.892291 GTGGGGATAGGCCGGGGA 62.892 72.222 2.18 0.00 37.63 4.81
56 57 4.111094 TGGGGATAGGCCGGGGAA 62.111 66.667 2.18 0.00 37.63 3.97
57 58 3.249961 GGGGATAGGCCGGGGAAG 61.250 72.222 2.18 0.00 37.63 3.46
58 59 3.955044 GGGATAGGCCGGGGAAGC 61.955 72.222 2.18 0.00 37.63 3.86
59 60 4.315941 GGATAGGCCGGGGAAGCG 62.316 72.222 2.18 0.00 0.00 4.68
60 61 4.990553 GATAGGCCGGGGAAGCGC 62.991 72.222 2.18 0.00 0.00 5.92
128 129 4.048470 GGGGGAGGGGTGAGTTGC 62.048 72.222 0.00 0.00 0.00 4.17
129 130 4.410400 GGGGAGGGGTGAGTTGCG 62.410 72.222 0.00 0.00 0.00 4.85
130 131 3.319198 GGGAGGGGTGAGTTGCGA 61.319 66.667 0.00 0.00 0.00 5.10
131 132 2.266055 GGAGGGGTGAGTTGCGAG 59.734 66.667 0.00 0.00 0.00 5.03
132 133 2.435059 GAGGGGTGAGTTGCGAGC 60.435 66.667 0.00 0.00 0.00 5.03
133 134 4.379243 AGGGGTGAGTTGCGAGCG 62.379 66.667 0.00 0.00 0.00 5.03
134 135 4.373116 GGGGTGAGTTGCGAGCGA 62.373 66.667 0.00 0.00 0.00 4.93
135 136 2.811317 GGGTGAGTTGCGAGCGAG 60.811 66.667 0.00 0.00 0.00 5.03
136 137 3.482783 GGTGAGTTGCGAGCGAGC 61.483 66.667 0.00 0.00 37.71 5.03
137 138 3.832171 GTGAGTTGCGAGCGAGCG 61.832 66.667 0.00 0.00 40.67 5.03
149 150 4.516135 CGAGCGCGCGAGAGTACA 62.516 66.667 37.18 0.00 0.00 2.90
150 151 2.649349 GAGCGCGCGAGAGTACAG 60.649 66.667 37.18 0.23 0.00 2.74
151 152 4.838486 AGCGCGCGAGAGTACAGC 62.838 66.667 37.18 12.54 0.00 4.40
183 184 2.951227 GCAGCAAATAAGCGGCGC 60.951 61.111 26.86 26.86 45.03 6.53
184 185 2.648724 CAGCAAATAAGCGGCGCG 60.649 61.111 27.59 12.27 40.15 6.86
198 199 4.851114 CGCGCGATGCAGTTTCGG 62.851 66.667 28.94 2.17 46.97 4.30
200 201 4.520846 CGCGATGCAGTTTCGGCC 62.521 66.667 0.00 0.00 37.10 6.13
201 202 4.179579 GCGATGCAGTTTCGGCCC 62.180 66.667 9.99 0.00 37.10 5.80
202 203 3.864686 CGATGCAGTTTCGGCCCG 61.865 66.667 0.00 0.00 33.05 6.13
203 204 4.179579 GATGCAGTTTCGGCCCGC 62.180 66.667 0.00 0.00 0.00 6.13
216 217 4.492160 CCCGCGCGCTGAACTAGA 62.492 66.667 30.48 0.00 0.00 2.43
217 218 2.278857 CCGCGCGCTGAACTAGAT 60.279 61.111 30.48 0.00 0.00 1.98
218 219 1.008881 CCGCGCGCTGAACTAGATA 60.009 57.895 30.48 0.00 0.00 1.98
219 220 0.387367 CCGCGCGCTGAACTAGATAT 60.387 55.000 30.48 0.00 0.00 1.63
220 221 1.135774 CCGCGCGCTGAACTAGATATA 60.136 52.381 30.48 0.00 0.00 0.86
221 222 1.905687 CGCGCGCTGAACTAGATATAC 59.094 52.381 30.48 0.00 0.00 1.47
222 223 2.251893 GCGCGCTGAACTAGATATACC 58.748 52.381 26.67 0.00 0.00 2.73
223 224 2.506865 CGCGCTGAACTAGATATACCG 58.493 52.381 5.56 0.00 0.00 4.02
224 225 2.251893 GCGCTGAACTAGATATACCGC 58.748 52.381 0.00 0.00 0.00 5.68
225 226 2.506865 CGCTGAACTAGATATACCGCG 58.493 52.381 0.00 0.00 0.00 6.46
226 227 2.251893 GCTGAACTAGATATACCGCGC 58.748 52.381 0.00 0.00 0.00 6.86
227 228 2.351447 GCTGAACTAGATATACCGCGCA 60.351 50.000 8.75 0.00 0.00 6.09
228 229 3.235195 CTGAACTAGATATACCGCGCAC 58.765 50.000 8.75 0.00 0.00 5.34
229 230 2.240040 GAACTAGATATACCGCGCACG 58.760 52.381 8.75 0.00 39.67 5.34
230 231 0.109873 ACTAGATATACCGCGCACGC 60.110 55.000 8.75 4.64 38.22 5.34
261 262 2.426023 CCGCTGGGGCCACTATAC 59.574 66.667 6.53 0.00 34.44 1.47
262 263 2.426023 CGCTGGGGCCACTATACC 59.574 66.667 6.53 0.00 34.44 2.73
263 264 2.426023 GCTGGGGCCACTATACCG 59.574 66.667 6.53 0.00 0.00 4.02
264 265 3.148084 CTGGGGCCACTATACCGG 58.852 66.667 6.53 0.00 0.00 5.28
265 266 1.764854 CTGGGGCCACTATACCGGT 60.765 63.158 13.98 13.98 0.00 5.28
266 267 1.307170 TGGGGCCACTATACCGGTT 60.307 57.895 15.04 3.05 0.00 4.44
267 268 1.147600 GGGGCCACTATACCGGTTG 59.852 63.158 15.04 4.29 0.00 3.77
268 269 1.525306 GGGCCACTATACCGGTTGC 60.525 63.158 15.04 6.38 0.00 4.17
269 270 1.885850 GGCCACTATACCGGTTGCG 60.886 63.158 15.04 3.45 0.00 4.85
270 271 1.153509 GCCACTATACCGGTTGCGT 60.154 57.895 15.04 4.20 0.00 5.24
271 272 1.426041 GCCACTATACCGGTTGCGTG 61.426 60.000 15.04 16.89 0.00 5.34
272 273 1.426041 CCACTATACCGGTTGCGTGC 61.426 60.000 15.04 0.00 0.00 5.34
273 274 1.517694 ACTATACCGGTTGCGTGCG 60.518 57.895 15.04 0.00 0.00 5.34
274 275 1.517694 CTATACCGGTTGCGTGCGT 60.518 57.895 15.04 0.00 0.00 5.24
275 276 1.748647 CTATACCGGTTGCGTGCGTG 61.749 60.000 15.04 0.00 0.00 5.34
279 280 3.707700 CGGTTGCGTGCGTGCTAA 61.708 61.111 1.52 0.00 35.36 3.09
280 281 2.634777 GGTTGCGTGCGTGCTAAA 59.365 55.556 1.52 0.00 35.36 1.85
281 282 1.009449 GGTTGCGTGCGTGCTAAAA 60.009 52.632 1.52 0.00 35.36 1.52
282 283 0.386731 GGTTGCGTGCGTGCTAAAAT 60.387 50.000 1.52 0.00 35.36 1.82
283 284 0.702383 GTTGCGTGCGTGCTAAAATG 59.298 50.000 1.52 0.00 35.36 2.32
284 285 0.386605 TTGCGTGCGTGCTAAAATGG 60.387 50.000 1.52 0.00 35.36 3.16
285 286 1.514014 GCGTGCGTGCTAAAATGGG 60.514 57.895 0.00 0.00 0.00 4.00
286 287 1.917782 GCGTGCGTGCTAAAATGGGA 61.918 55.000 0.00 0.00 0.00 4.37
287 288 0.519519 CGTGCGTGCTAAAATGGGAA 59.480 50.000 0.00 0.00 0.00 3.97
288 289 1.068885 CGTGCGTGCTAAAATGGGAAA 60.069 47.619 0.00 0.00 0.00 3.13
289 290 2.415357 CGTGCGTGCTAAAATGGGAAAT 60.415 45.455 0.00 0.00 0.00 2.17
290 291 3.584834 GTGCGTGCTAAAATGGGAAATT 58.415 40.909 0.00 0.00 0.00 1.82
291 292 3.993736 GTGCGTGCTAAAATGGGAAATTT 59.006 39.130 0.00 0.00 0.00 1.82
292 293 4.450757 GTGCGTGCTAAAATGGGAAATTTT 59.549 37.500 0.00 2.04 35.62 1.82
293 294 5.635700 GTGCGTGCTAAAATGGGAAATTTTA 59.364 36.000 0.00 3.89 33.73 1.52
294 295 5.635700 TGCGTGCTAAAATGGGAAATTTTAC 59.364 36.000 0.00 0.00 33.73 2.01
295 296 5.220135 GCGTGCTAAAATGGGAAATTTTACG 60.220 40.000 10.64 10.64 35.41 3.18
296 297 5.287513 CGTGCTAAAATGGGAAATTTTACGG 59.712 40.000 0.00 0.38 31.91 4.02
297 298 5.062934 GTGCTAAAATGGGAAATTTTACGGC 59.937 40.000 0.00 4.38 33.73 5.68
298 299 4.266739 GCTAAAATGGGAAATTTTACGGCG 59.733 41.667 4.80 4.80 33.73 6.46
299 300 2.287393 AATGGGAAATTTTACGGCGC 57.713 45.000 6.90 0.00 0.00 6.53
300 301 0.099791 ATGGGAAATTTTACGGCGCG 59.900 50.000 6.90 0.00 0.00 6.86
301 302 1.226463 GGGAAATTTTACGGCGCGG 60.226 57.895 14.03 14.03 0.00 6.46
302 303 1.870458 GGAAATTTTACGGCGCGGC 60.870 57.895 24.49 24.49 0.00 6.53
303 304 2.202375 AAATTTTACGGCGCGGCG 60.202 55.556 46.57 46.57 0.00 6.46
314 315 3.109547 CGCGGCGCTAGTTTGACA 61.110 61.111 30.54 0.00 0.00 3.58
315 316 2.474712 GCGGCGCTAGTTTGACAC 59.525 61.111 26.86 0.00 0.00 3.67
316 317 2.769617 CGGCGCTAGTTTGACACG 59.230 61.111 7.64 0.00 0.00 4.49
317 318 2.726691 CGGCGCTAGTTTGACACGG 61.727 63.158 7.64 0.00 0.00 4.94
318 319 2.474712 GCGCTAGTTTGACACGGC 59.525 61.111 0.00 0.00 0.00 5.68
319 320 2.027625 GCGCTAGTTTGACACGGCT 61.028 57.895 0.00 0.00 0.00 5.52
320 321 1.781555 CGCTAGTTTGACACGGCTG 59.218 57.895 0.00 0.00 0.00 4.85
321 322 0.944311 CGCTAGTTTGACACGGCTGT 60.944 55.000 0.00 0.00 0.00 4.40
322 323 1.226746 GCTAGTTTGACACGGCTGTT 58.773 50.000 0.00 0.00 0.00 3.16
323 324 1.069906 GCTAGTTTGACACGGCTGTTG 60.070 52.381 0.00 0.00 0.00 3.33
324 325 2.479837 CTAGTTTGACACGGCTGTTGA 58.520 47.619 0.00 0.00 0.00 3.18
325 326 1.745232 AGTTTGACACGGCTGTTGAA 58.255 45.000 0.00 0.00 0.00 2.69
326 327 1.670811 AGTTTGACACGGCTGTTGAAG 59.329 47.619 0.00 0.00 0.00 3.02
327 328 1.668751 GTTTGACACGGCTGTTGAAGA 59.331 47.619 0.00 0.00 0.00 2.87
328 329 2.254546 TTGACACGGCTGTTGAAGAT 57.745 45.000 0.00 0.00 0.00 2.40
329 330 1.511850 TGACACGGCTGTTGAAGATG 58.488 50.000 0.00 0.00 0.00 2.90
330 331 0.166814 GACACGGCTGTTGAAGATGC 59.833 55.000 0.00 0.00 0.00 3.91
331 332 0.250467 ACACGGCTGTTGAAGATGCT 60.250 50.000 0.00 0.00 0.00 3.79
332 333 0.445436 CACGGCTGTTGAAGATGCTC 59.555 55.000 0.00 0.00 0.00 4.26
433 434 2.805671 GGCACTTTGTTTTTATGGCACC 59.194 45.455 0.00 0.00 35.99 5.01
444 445 6.153000 TGTTTTTATGGCACCGTGGTTTATAT 59.847 34.615 0.00 0.00 0.00 0.86
450 451 5.120399 TGGCACCGTGGTTTATATAAAGAG 58.880 41.667 8.18 1.24 0.00 2.85
485 486 6.624352 TCTGAGAAGTTTTCATGACAAAGG 57.376 37.500 0.00 0.00 0.00 3.11
592 593 2.938451 ACCATGCACATAACATCTGTCG 59.062 45.455 0.00 0.00 0.00 4.35
613 614 5.503376 GTCGCACGTTTGAATTATACACTTG 59.497 40.000 0.00 0.00 0.00 3.16
658 659 9.463902 TTCTTACCCACGGAAATAATTAATCAA 57.536 29.630 0.00 0.00 0.00 2.57
730 733 7.489113 CACTCTTTTTGCACAAATTTGTAGACT 59.511 33.333 22.87 7.88 39.91 3.24
741 744 9.817365 CACAAATTTGTAGACTGATCTTAACTG 57.183 33.333 22.87 1.71 39.91 3.16
828 831 1.273886 GATCCTATTGAGACTCCCGCC 59.726 57.143 0.00 0.00 0.00 6.13
857 860 2.502947 TGGCATCACAGCTACAGATCTT 59.497 45.455 0.00 0.00 34.17 2.40
859 862 3.559242 GGCATCACAGCTACAGATCTTTC 59.441 47.826 0.00 0.00 34.17 2.62
861 864 5.452496 GGCATCACAGCTACAGATCTTTCTA 60.452 44.000 0.00 0.00 34.17 2.10
862 865 5.691305 GCATCACAGCTACAGATCTTTCTAG 59.309 44.000 0.00 0.00 0.00 2.43
946 973 2.302733 TCAAGCCATCTCACACTAAGCA 59.697 45.455 0.00 0.00 0.00 3.91
958 985 3.701542 CACACTAAGCATCTCCCTCACTA 59.298 47.826 0.00 0.00 0.00 2.74
1164 1191 2.420568 ATGGTACGGTGCCGATCGT 61.421 57.895 18.16 4.83 43.01 3.73
1187 1214 1.490910 GCTCTACCTTGGCCCACTATT 59.509 52.381 0.00 0.00 0.00 1.73
1215 1242 3.719214 CCGAGCTATTTGACCGGC 58.281 61.111 0.00 0.00 33.47 6.13
1254 1281 3.471620 TGGGACACAGCTGGACTC 58.528 61.111 19.93 9.22 0.00 3.36
1255 1282 1.152247 TGGGACACAGCTGGACTCT 60.152 57.895 19.93 0.00 0.00 3.24
1256 1283 1.188219 TGGGACACAGCTGGACTCTC 61.188 60.000 19.93 9.44 0.00 3.20
1257 1284 1.188219 GGGACACAGCTGGACTCTCA 61.188 60.000 19.93 0.00 0.00 3.27
1258 1285 0.246086 GGACACAGCTGGACTCTCAG 59.754 60.000 19.93 0.00 37.79 3.35
1272 1299 4.509616 GACTCTCAGCTGACACTACTAGA 58.490 47.826 13.74 5.06 0.00 2.43
1278 1305 6.490381 TCTCAGCTGACACTACTAGAAAAAGA 59.510 38.462 13.74 0.00 0.00 2.52
1290 1317 9.544579 ACTACTAGAAAAAGACCTACTAATGGT 57.455 33.333 0.00 0.00 41.07 3.55
1399 1427 6.605995 TGGTGCGCCATTAGTATCTAGTATAT 59.394 38.462 16.89 0.00 40.46 0.86
1433 1483 3.435327 CAGACAGTGCGCCATTAGTTTTA 59.565 43.478 4.18 0.00 0.00 1.52
1609 1680 8.570488 CATATAACAATCATAGCCAACACACAT 58.430 33.333 0.00 0.00 0.00 3.21
1650 1721 7.878127 ACATACATAGCCAATACATAGTTCCAC 59.122 37.037 0.00 0.00 0.00 4.02
1702 1773 3.454447 TCATCCAACACCGTTATCCATCT 59.546 43.478 0.00 0.00 0.00 2.90
2120 2273 8.507524 ACATAAGTTATTTTGGAGCTAACCTC 57.492 34.615 0.00 0.00 39.98 3.85
2565 2767 0.962356 CACCACCATCTCTTGCCCAC 60.962 60.000 0.00 0.00 0.00 4.61
2726 2955 1.020861 TGTTGTCTATGCTGCTGCCG 61.021 55.000 13.47 1.91 38.71 5.69
2833 3062 0.393402 CTGCTGCTGCTCCCATTACA 60.393 55.000 17.00 0.00 40.48 2.41
3172 3401 0.107214 GGCGGATCTTCACCCATCAA 60.107 55.000 0.00 0.00 0.00 2.57
3409 3639 5.511716 CCATCTCTGATAAGCAGCAGAAGAT 60.512 44.000 0.00 0.00 46.09 2.40
3481 3711 5.528690 GCATCACAAGTAATTCAGAGGCATA 59.471 40.000 6.06 0.00 33.53 3.14
3540 3770 7.170320 TCAATGTACGAACTTGAAAGAACTACC 59.830 37.037 0.00 0.00 0.00 3.18
3626 3856 7.557358 TCACATAGTTTGATAACTTGGATGCAT 59.443 33.333 0.00 0.00 41.85 3.96
3745 3976 7.752239 GCAATATATGACAGAAATGTACATGCC 59.248 37.037 9.63 4.41 0.00 4.40
3787 4018 9.875675 GCTTAGCAGTAATATTCTGAGAAAATG 57.124 33.333 15.05 0.00 35.20 2.32
3820 4052 2.695147 CCTGAACAAGTGGCTTTCCTTT 59.305 45.455 0.00 0.00 0.00 3.11
3821 4053 3.132824 CCTGAACAAGTGGCTTTCCTTTT 59.867 43.478 0.00 0.00 0.00 2.27
3948 4180 3.030291 AGTGCACCAAGTCCAAATTCAA 58.970 40.909 14.63 0.00 0.00 2.69
4029 4261 6.377996 TGTTGCTTTCACTTGCCATAATCTAT 59.622 34.615 0.00 0.00 0.00 1.98
4387 4621 6.264744 AGGCATTGATGTGATTATTTCTCTGG 59.735 38.462 0.00 0.00 0.00 3.86
4673 4907 2.226674 GACCCTTCACAGTAGCAAAAGC 59.773 50.000 0.00 0.00 0.00 3.51
4810 5044 9.070179 CAACATCCATTGATCCATGTAAATAGA 57.930 33.333 6.08 0.00 0.00 1.98
4883 5117 1.909986 GTGAGTAAGGAAGAGGGGCTT 59.090 52.381 0.00 0.00 40.25 4.35
5122 5357 3.966930 GAGGAGAGGAGCGGGTGGT 62.967 68.421 0.00 0.00 0.00 4.16
6229 8577 1.645710 TCTTCCCGCTTCTTCTCCTT 58.354 50.000 0.00 0.00 0.00 3.36
6328 8676 2.559668 AGTACCACACCGATTTTCGAGA 59.440 45.455 0.00 0.00 43.74 4.04
6341 8689 7.997643 CCGATTTTCGAGAAGCTTTCTTCCTT 61.998 42.308 0.00 0.00 43.74 3.36
6387 8737 2.091499 ACCGGACATATGGTAGACTCCA 60.091 50.000 9.46 0.00 42.01 3.86
6607 14495 3.181480 ACAAATTACTGGCGCACTTTGTT 60.181 39.130 10.83 0.00 34.20 2.83
6651 14539 6.211587 TCTAACTACTAATGGCGCACTTTA 57.788 37.500 10.83 6.87 0.00 1.85
6652 14540 6.812998 TCTAACTACTAATGGCGCACTTTAT 58.187 36.000 10.83 0.00 0.00 1.40
6654 14542 5.018539 ACTACTAATGGCGCACTTTATCA 57.981 39.130 10.83 0.00 0.00 2.15
6785 14684 6.465178 CCACCTGGTGTGCCATTAGTATATAA 60.465 42.308 24.32 0.00 45.05 0.98
6857 14756 4.104831 AGCCCTTTTCCTAGTAGTGTGAT 58.895 43.478 0.00 0.00 0.00 3.06
6881 14780 1.372623 GACCTTCGCGAAGAACCGT 60.373 57.895 42.22 32.11 40.79 4.83
6886 14785 2.733218 CGCGAAGAACCGTGAGCA 60.733 61.111 0.00 0.00 42.05 4.26
6887 14786 2.307309 CGCGAAGAACCGTGAGCAA 61.307 57.895 0.00 0.00 42.05 3.91
6907 18703 0.249657 GAGGTGATCCACTGCCGATC 60.250 60.000 0.00 0.00 37.29 3.69
6926 18722 2.044053 GCCATGCTTGGTGCCCTA 60.044 61.111 19.05 0.00 45.57 3.53
7053 18849 4.021925 GCAACCCCAGCCTCGTCT 62.022 66.667 0.00 0.00 0.00 4.18
7104 18900 1.180456 CCAAGTTGTGCTCATGGGCA 61.180 55.000 18.52 18.52 40.15 5.36
7129 18925 3.059386 GGGGTTTCGCATTGCCGA 61.059 61.111 2.41 1.10 35.09 5.54
7223 19019 0.392193 CCGAGGCATTCACAGAGCTT 60.392 55.000 0.00 0.00 0.00 3.74
7345 19141 3.661944 CTGACCATATCACTGATCCTGC 58.338 50.000 0.00 0.00 32.37 4.85
7400 19196 3.578456 CCTGGCAAGTAAGGCACG 58.422 61.111 0.00 0.00 39.34 5.34
7417 19213 3.305199 GGCACGTACTAGAGTTGAGTTGT 60.305 47.826 0.00 0.00 0.00 3.32
7427 19223 0.880278 GTTGAGTTGTGAGCTGGCGA 60.880 55.000 0.00 0.00 0.00 5.54
7432 19228 4.687215 TGTGAGCTGGCGAGGTGC 62.687 66.667 4.75 0.00 45.38 5.01
7685 20716 5.303747 TCGGTCGTTCATTGCAATTTATT 57.696 34.783 9.83 0.00 0.00 1.40
7981 21234 6.978338 AGAGGTTACATAAGCGATTCGATAA 58.022 36.000 10.88 0.00 38.61 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.155167 CCCCCTCTAGTCACCGCC 61.155 72.222 0.00 0.00 0.00 6.13
2 3 3.851128 GCCCCCTCTAGTCACCGC 61.851 72.222 0.00 0.00 0.00 5.68
4 5 3.155167 CCGCCCCCTCTAGTCACC 61.155 72.222 0.00 0.00 0.00 4.02
5 6 2.043248 TCCGCCCCCTCTAGTCAC 60.043 66.667 0.00 0.00 0.00 3.67
6 7 2.279073 CTCCGCCCCCTCTAGTCA 59.721 66.667 0.00 0.00 0.00 3.41
7 8 2.522193 CCTCCGCCCCCTCTAGTC 60.522 72.222 0.00 0.00 0.00 2.59
8 9 2.591193 CTTCCTCCGCCCCCTCTAGT 62.591 65.000 0.00 0.00 0.00 2.57
9 10 1.834822 CTTCCTCCGCCCCCTCTAG 60.835 68.421 0.00 0.00 0.00 2.43
10 11 2.282446 CTTCCTCCGCCCCCTCTA 59.718 66.667 0.00 0.00 0.00 2.43
38 39 4.892291 TCCCCGGCCTATCCCCAC 62.892 72.222 0.00 0.00 0.00 4.61
39 40 4.111094 TTCCCCGGCCTATCCCCA 62.111 66.667 0.00 0.00 0.00 4.96
40 41 3.249961 CTTCCCCGGCCTATCCCC 61.250 72.222 0.00 0.00 0.00 4.81
41 42 3.955044 GCTTCCCCGGCCTATCCC 61.955 72.222 0.00 0.00 0.00 3.85
42 43 4.315941 CGCTTCCCCGGCCTATCC 62.316 72.222 0.00 0.00 0.00 2.59
43 44 4.990553 GCGCTTCCCCGGCCTATC 62.991 72.222 0.00 0.00 0.00 2.08
111 112 4.048470 GCAACTCACCCCTCCCCC 62.048 72.222 0.00 0.00 0.00 5.40
112 113 4.410400 CGCAACTCACCCCTCCCC 62.410 72.222 0.00 0.00 0.00 4.81
113 114 3.316573 CTCGCAACTCACCCCTCCC 62.317 68.421 0.00 0.00 0.00 4.30
114 115 2.266055 CTCGCAACTCACCCCTCC 59.734 66.667 0.00 0.00 0.00 4.30
115 116 2.435059 GCTCGCAACTCACCCCTC 60.435 66.667 0.00 0.00 0.00 4.30
116 117 4.379243 CGCTCGCAACTCACCCCT 62.379 66.667 0.00 0.00 0.00 4.79
117 118 4.373116 TCGCTCGCAACTCACCCC 62.373 66.667 0.00 0.00 0.00 4.95
118 119 2.811317 CTCGCTCGCAACTCACCC 60.811 66.667 0.00 0.00 0.00 4.61
119 120 3.482783 GCTCGCTCGCAACTCACC 61.483 66.667 0.00 0.00 0.00 4.02
120 121 3.832171 CGCTCGCTCGCAACTCAC 61.832 66.667 0.00 0.00 0.00 3.51
132 133 4.516135 TGTACTCTCGCGCGCTCG 62.516 66.667 30.48 14.67 39.07 5.03
133 134 2.649349 CTGTACTCTCGCGCGCTC 60.649 66.667 30.48 11.41 0.00 5.03
134 135 4.838486 GCTGTACTCTCGCGCGCT 62.838 66.667 30.48 12.77 0.00 5.92
158 159 2.652893 CTTATTTGCTGCGCCCGCTC 62.653 60.000 17.83 6.41 42.51 5.03
159 160 2.749839 TTATTTGCTGCGCCCGCT 60.750 55.556 17.83 2.93 42.51 5.52
160 161 2.278142 CTTATTTGCTGCGCCCGC 60.278 61.111 4.18 8.60 42.35 6.13
161 162 2.278142 GCTTATTTGCTGCGCCCG 60.278 61.111 4.18 0.00 0.00 6.13
162 163 2.278142 CGCTTATTTGCTGCGCCC 60.278 61.111 4.18 0.00 43.08 6.13
166 167 2.951227 GCGCCGCTTATTTGCTGC 60.951 61.111 0.00 0.00 39.28 5.25
167 168 2.648724 CGCGCCGCTTATTTGCTG 60.649 61.111 7.78 0.00 0.00 4.41
181 182 4.851114 CCGAAACTGCATCGCGCG 62.851 66.667 26.76 26.76 46.97 6.86
183 184 4.520846 GGCCGAAACTGCATCGCG 62.521 66.667 0.00 0.00 38.93 5.87
184 185 4.179579 GGGCCGAAACTGCATCGC 62.180 66.667 2.64 0.00 38.93 4.58
185 186 3.864686 CGGGCCGAAACTGCATCG 61.865 66.667 24.41 1.17 39.92 3.84
186 187 4.179579 GCGGGCCGAAACTGCATC 62.180 66.667 33.44 4.02 39.96 3.91
199 200 2.402282 TATCTAGTTCAGCGCGCGGG 62.402 60.000 33.06 23.76 0.00 6.13
200 201 0.387367 ATATCTAGTTCAGCGCGCGG 60.387 55.000 33.06 26.50 0.00 6.46
201 202 1.905687 GTATATCTAGTTCAGCGCGCG 59.094 52.381 28.44 28.44 0.00 6.86
202 203 2.251893 GGTATATCTAGTTCAGCGCGC 58.748 52.381 26.66 26.66 0.00 6.86
203 204 2.506865 CGGTATATCTAGTTCAGCGCG 58.493 52.381 0.00 0.00 0.00 6.86
204 205 2.251893 GCGGTATATCTAGTTCAGCGC 58.748 52.381 0.00 0.00 46.70 5.92
205 206 2.506865 CGCGGTATATCTAGTTCAGCG 58.493 52.381 0.00 0.00 39.14 5.18
206 207 2.251893 GCGCGGTATATCTAGTTCAGC 58.748 52.381 8.83 0.00 0.00 4.26
207 208 3.235195 GTGCGCGGTATATCTAGTTCAG 58.765 50.000 8.83 0.00 0.00 3.02
208 209 2.350102 CGTGCGCGGTATATCTAGTTCA 60.350 50.000 12.87 0.00 0.00 3.18
209 210 2.240040 CGTGCGCGGTATATCTAGTTC 58.760 52.381 12.87 0.00 0.00 3.01
210 211 1.665161 GCGTGCGCGGTATATCTAGTT 60.665 52.381 22.73 0.00 38.78 2.24
211 212 0.109873 GCGTGCGCGGTATATCTAGT 60.110 55.000 22.73 0.00 38.78 2.57
212 213 2.638329 GCGTGCGCGGTATATCTAG 58.362 57.895 22.73 0.00 38.78 2.43
213 214 4.853507 GCGTGCGCGGTATATCTA 57.146 55.556 22.73 0.00 38.78 1.98
244 245 2.426023 GTATAGTGGCCCCAGCGG 59.574 66.667 0.00 0.00 41.24 5.52
245 246 2.426023 GGTATAGTGGCCCCAGCG 59.574 66.667 0.00 0.00 41.24 5.18
246 247 2.426023 CGGTATAGTGGCCCCAGC 59.574 66.667 0.00 0.00 38.76 4.85
247 248 1.342672 AACCGGTATAGTGGCCCCAG 61.343 60.000 8.00 0.00 0.00 4.45
248 249 1.307170 AACCGGTATAGTGGCCCCA 60.307 57.895 8.00 0.00 0.00 4.96
249 250 1.147600 CAACCGGTATAGTGGCCCC 59.852 63.158 8.00 0.00 0.00 5.80
250 251 1.525306 GCAACCGGTATAGTGGCCC 60.525 63.158 8.00 0.00 0.00 5.80
251 252 1.885850 CGCAACCGGTATAGTGGCC 60.886 63.158 8.00 0.00 29.76 5.36
252 253 1.153509 ACGCAACCGGTATAGTGGC 60.154 57.895 8.00 4.30 39.22 5.01
253 254 1.426041 GCACGCAACCGGTATAGTGG 61.426 60.000 26.68 14.94 39.22 4.00
254 255 1.748647 CGCACGCAACCGGTATAGTG 61.749 60.000 23.59 23.59 39.22 2.74
255 256 1.517694 CGCACGCAACCGGTATAGT 60.518 57.895 8.00 5.05 39.22 2.12
256 257 1.517694 ACGCACGCAACCGGTATAG 60.518 57.895 8.00 4.29 39.22 1.31
257 258 1.806351 CACGCACGCAACCGGTATA 60.806 57.895 8.00 0.00 39.22 1.47
258 259 3.115892 CACGCACGCAACCGGTAT 61.116 61.111 8.00 0.00 39.22 2.73
262 263 2.703425 TTTTAGCACGCACGCAACCG 62.703 55.000 0.00 0.00 41.14 4.44
263 264 0.386731 ATTTTAGCACGCACGCAACC 60.387 50.000 0.00 0.00 0.00 3.77
264 265 0.702383 CATTTTAGCACGCACGCAAC 59.298 50.000 0.00 0.00 0.00 4.17
265 266 0.386605 CCATTTTAGCACGCACGCAA 60.387 50.000 0.00 0.00 0.00 4.85
266 267 1.208870 CCATTTTAGCACGCACGCA 59.791 52.632 0.00 0.00 0.00 5.24
267 268 1.514014 CCCATTTTAGCACGCACGC 60.514 57.895 0.00 0.00 0.00 5.34
268 269 0.519519 TTCCCATTTTAGCACGCACG 59.480 50.000 0.00 0.00 0.00 5.34
269 270 2.715737 TTTCCCATTTTAGCACGCAC 57.284 45.000 0.00 0.00 0.00 5.34
270 271 3.951775 AATTTCCCATTTTAGCACGCA 57.048 38.095 0.00 0.00 0.00 5.24
271 272 5.220135 CGTAAAATTTCCCATTTTAGCACGC 60.220 40.000 0.00 0.00 35.08 5.34
272 273 5.287513 CCGTAAAATTTCCCATTTTAGCACG 59.712 40.000 0.00 4.25 35.08 5.34
273 274 5.062934 GCCGTAAAATTTCCCATTTTAGCAC 59.937 40.000 0.00 0.00 35.08 4.40
274 275 5.172205 GCCGTAAAATTTCCCATTTTAGCA 58.828 37.500 0.00 0.00 35.08 3.49
275 276 4.266739 CGCCGTAAAATTTCCCATTTTAGC 59.733 41.667 0.00 2.18 35.08 3.09
276 277 4.266739 GCGCCGTAAAATTTCCCATTTTAG 59.733 41.667 0.00 0.00 35.08 1.85
277 278 4.174762 GCGCCGTAAAATTTCCCATTTTA 58.825 39.130 0.00 0.00 33.73 1.52
278 279 2.997303 GCGCCGTAAAATTTCCCATTTT 59.003 40.909 0.00 0.00 35.62 1.82
279 280 2.612604 GCGCCGTAAAATTTCCCATTT 58.387 42.857 0.00 0.00 0.00 2.32
280 281 1.468395 CGCGCCGTAAAATTTCCCATT 60.468 47.619 0.00 0.00 0.00 3.16
281 282 0.099791 CGCGCCGTAAAATTTCCCAT 59.900 50.000 0.00 0.00 0.00 4.00
282 283 1.502640 CGCGCCGTAAAATTTCCCA 59.497 52.632 0.00 0.00 0.00 4.37
283 284 1.226463 CCGCGCCGTAAAATTTCCC 60.226 57.895 0.00 0.00 0.00 3.97
284 285 1.870458 GCCGCGCCGTAAAATTTCC 60.870 57.895 0.00 0.00 0.00 3.13
285 286 2.212330 CGCCGCGCCGTAAAATTTC 61.212 57.895 0.00 0.00 0.00 2.17
286 287 2.202375 CGCCGCGCCGTAAAATTT 60.202 55.556 0.00 0.00 0.00 1.82
297 298 3.109547 TGTCAAACTAGCGCCGCG 61.110 61.111 8.83 8.83 0.00 6.46
298 299 2.474712 GTGTCAAACTAGCGCCGC 59.525 61.111 2.29 0.00 0.00 6.53
299 300 2.726691 CCGTGTCAAACTAGCGCCG 61.727 63.158 2.29 0.00 0.00 6.46
300 301 3.023591 GCCGTGTCAAACTAGCGCC 62.024 63.158 2.29 0.00 0.00 6.53
301 302 2.027625 AGCCGTGTCAAACTAGCGC 61.028 57.895 0.00 0.00 32.52 5.92
302 303 0.944311 ACAGCCGTGTCAAACTAGCG 60.944 55.000 0.00 0.00 32.52 4.26
303 304 1.069906 CAACAGCCGTGTCAAACTAGC 60.070 52.381 0.00 0.00 35.08 3.42
304 305 2.479837 TCAACAGCCGTGTCAAACTAG 58.520 47.619 0.00 0.00 35.08 2.57
305 306 2.605837 TCAACAGCCGTGTCAAACTA 57.394 45.000 0.00 0.00 35.08 2.24
306 307 1.670811 CTTCAACAGCCGTGTCAAACT 59.329 47.619 0.00 0.00 35.08 2.66
307 308 1.668751 TCTTCAACAGCCGTGTCAAAC 59.331 47.619 0.00 0.00 35.08 2.93
308 309 2.031258 TCTTCAACAGCCGTGTCAAA 57.969 45.000 0.00 0.00 35.08 2.69
309 310 1.872952 CATCTTCAACAGCCGTGTCAA 59.127 47.619 0.00 0.00 35.08 3.18
310 311 1.511850 CATCTTCAACAGCCGTGTCA 58.488 50.000 0.00 0.00 35.08 3.58
311 312 0.166814 GCATCTTCAACAGCCGTGTC 59.833 55.000 0.00 0.00 35.08 3.67
312 313 0.250467 AGCATCTTCAACAGCCGTGT 60.250 50.000 0.00 0.00 39.19 4.49
313 314 0.445436 GAGCATCTTCAACAGCCGTG 59.555 55.000 0.00 0.00 0.00 4.94
314 315 2.846371 GAGCATCTTCAACAGCCGT 58.154 52.632 0.00 0.00 0.00 5.68
326 327 6.374565 TCCGACTAACTTACTAAGAGCATC 57.625 41.667 2.65 0.00 0.00 3.91
327 328 6.963083 ATCCGACTAACTTACTAAGAGCAT 57.037 37.500 2.65 0.00 0.00 3.79
328 329 6.770746 AATCCGACTAACTTACTAAGAGCA 57.229 37.500 2.65 0.00 0.00 4.26
329 330 7.701445 TGTAATCCGACTAACTTACTAAGAGC 58.299 38.462 2.65 0.00 0.00 4.09
330 331 9.107177 TCTGTAATCCGACTAACTTACTAAGAG 57.893 37.037 2.65 0.00 0.00 2.85
331 332 9.453572 TTCTGTAATCCGACTAACTTACTAAGA 57.546 33.333 2.65 0.00 0.00 2.10
332 333 9.500864 GTTCTGTAATCCGACTAACTTACTAAG 57.499 37.037 0.00 0.00 0.00 2.18
462 463 6.122277 ACCTTTGTCATGAAAACTTCTCAGA 58.878 36.000 0.00 0.00 0.00 3.27
463 464 6.382869 ACCTTTGTCATGAAAACTTCTCAG 57.617 37.500 0.00 0.00 0.00 3.35
474 475 8.253810 TGAAAACAATGTAAACCTTTGTCATGA 58.746 29.630 0.00 0.00 39.70 3.07
485 486 7.872163 TCATGCTCATGAAAACAATGTAAAC 57.128 32.000 9.88 0.00 44.14 2.01
542 543 2.235016 ACAAAGGAAAGGCGTGCATTA 58.765 42.857 0.00 0.00 0.00 1.90
549 550 2.420022 CTGGACATACAAAGGAAAGGCG 59.580 50.000 0.00 0.00 0.00 5.52
592 593 7.617533 AAACAAGTGTATAATTCAAACGTGC 57.382 32.000 0.00 0.00 0.00 5.34
613 614 2.908688 AAAGGGTGTCATGGCAAAAC 57.091 45.000 0.00 0.00 0.00 2.43
656 657 5.245531 TGTTAACCTGATCCTAAGTGCTTG 58.754 41.667 2.48 0.00 0.00 4.01
658 659 5.700402 ATGTTAACCTGATCCTAAGTGCT 57.300 39.130 2.48 0.00 0.00 4.40
730 733 5.048782 GGTTGTGTTGATGCAGTTAAGATCA 60.049 40.000 0.00 0.00 0.00 2.92
741 744 2.610232 GGTGATTGGGTTGTGTTGATGC 60.610 50.000 0.00 0.00 0.00 3.91
828 831 1.138036 CTGTGATGCCATTGGTGCG 59.862 57.895 4.26 0.00 0.00 5.34
946 973 2.443632 TCTCCGATGTAGTGAGGGAGAT 59.556 50.000 4.06 0.00 46.16 2.75
958 985 2.108970 GTCCCTTAGGTTCTCCGATGT 58.891 52.381 0.00 0.00 39.05 3.06
1014 1041 1.542175 CGGGGAGGAGAGGGACATA 59.458 63.158 0.00 0.00 0.00 2.29
1043 1070 1.238439 CACATTCTTCACCGCCTTGT 58.762 50.000 0.00 0.00 0.00 3.16
1164 1191 1.845664 TGGGCCAAGGTAGAGCACA 60.846 57.895 2.13 0.00 37.66 4.57
1187 1214 2.978298 ATAGCTCGGCGGCTCACCTA 62.978 60.000 22.70 8.74 42.97 3.08
1215 1242 1.137086 CCATAGTCACTGGGGAACTCG 59.863 57.143 0.00 0.00 0.00 4.18
1225 1252 1.276622 GTGTCCCACCCATAGTCACT 58.723 55.000 0.00 0.00 0.00 3.41
1247 1274 1.255882 AGTGTCAGCTGAGAGTCCAG 58.744 55.000 18.89 4.71 37.23 3.86
1248 1275 2.163509 GTAGTGTCAGCTGAGAGTCCA 58.836 52.381 23.37 11.90 0.00 4.02
1249 1276 2.442413 AGTAGTGTCAGCTGAGAGTCC 58.558 52.381 23.37 13.42 0.00 3.85
1250 1277 4.509616 TCTAGTAGTGTCAGCTGAGAGTC 58.490 47.826 23.37 15.01 0.00 3.36
1251 1278 4.561500 TCTAGTAGTGTCAGCTGAGAGT 57.438 45.455 23.24 23.24 0.00 3.24
1252 1279 5.888691 TTTCTAGTAGTGTCAGCTGAGAG 57.111 43.478 18.89 2.67 0.00 3.20
1253 1280 6.490381 TCTTTTTCTAGTAGTGTCAGCTGAGA 59.510 38.462 18.89 14.32 0.00 3.27
1254 1281 6.584563 GTCTTTTTCTAGTAGTGTCAGCTGAG 59.415 42.308 18.89 2.46 0.00 3.35
1255 1282 6.448006 GTCTTTTTCTAGTAGTGTCAGCTGA 58.552 40.000 13.74 13.74 0.00 4.26
1256 1283 5.635700 GGTCTTTTTCTAGTAGTGTCAGCTG 59.364 44.000 7.63 7.63 0.00 4.24
1257 1284 5.540719 AGGTCTTTTTCTAGTAGTGTCAGCT 59.459 40.000 0.00 0.00 0.00 4.24
1258 1285 5.785243 AGGTCTTTTTCTAGTAGTGTCAGC 58.215 41.667 0.00 0.00 0.00 4.26
1259 1286 8.113173 AGTAGGTCTTTTTCTAGTAGTGTCAG 57.887 38.462 0.00 0.00 0.00 3.51
1272 1299 4.765339 GGTGCACCATTAGTAGGTCTTTTT 59.235 41.667 31.23 0.00 37.23 1.94
1278 1305 0.539986 CCGGTGCACCATTAGTAGGT 59.460 55.000 34.16 0.00 40.85 3.08
1290 1317 0.397187 TAGTAGGCAAAACCGGTGCA 59.603 50.000 8.52 0.00 46.52 4.57
1343 1370 7.549842 TGCGCCATTAGTAAAAATTACTAGTGA 59.450 33.333 23.35 0.00 38.94 3.41
1399 1427 2.009051 CACTGTCTGATGCGCCATTAA 58.991 47.619 4.18 0.00 0.00 1.40
1578 1649 7.944000 TGTTGGCTATGATTGTTATATGGATGT 59.056 33.333 0.00 0.00 0.00 3.06
1638 1709 8.911965 TGTAATATGTAACGGTGGAACTATGTA 58.088 33.333 0.00 0.00 36.74 2.29
1650 1721 9.834628 ATGTGAAACTTTTGTAATATGTAACGG 57.165 29.630 0.00 0.00 38.04 4.44
2089 2240 8.525290 AGCTCCAAAATAACTTATGTTAGCAT 57.475 30.769 7.24 0.00 41.33 3.79
2726 2955 3.025866 CGAAAGCAGCAGCAATTCC 57.974 52.632 3.17 0.00 45.49 3.01
2833 3062 3.614630 CGGTCATTGTTGCATTTGGACAT 60.615 43.478 0.00 0.00 0.00 3.06
3129 3358 2.254546 AATGTGAAGTTGCGACAGGA 57.745 45.000 6.90 0.00 0.00 3.86
3139 3368 4.526970 AGATCCGCCAAATAATGTGAAGT 58.473 39.130 0.00 0.00 0.00 3.01
3172 3401 4.826733 TGCCTGACAGTTTTATGAACATGT 59.173 37.500 0.93 0.00 0.00 3.21
3235 3465 9.305555 CCTTCACCCATCTCATTATGATATTTT 57.694 33.333 0.00 0.00 0.00 1.82
3237 3467 7.408543 CCCTTCACCCATCTCATTATGATATT 58.591 38.462 0.00 0.00 0.00 1.28
3409 3639 7.795534 TCTGTTGTAAGGGTACTAATTGGTA 57.204 36.000 0.00 0.00 0.00 3.25
3481 3711 9.868277 TGTTTCACAATTTCTGAATTACTTGTT 57.132 25.926 0.00 0.00 33.78 2.83
3540 3770 1.347817 GAACTGTCGCAGAAGCCTCG 61.348 60.000 12.77 0.00 39.69 4.63
3626 3856 5.366482 TGATACTGCACCAATAGCCTTTA 57.634 39.130 0.00 0.00 0.00 1.85
3787 4018 4.800471 CACTTGTTCAGGCTTCAAGAAAAC 59.200 41.667 22.14 5.37 40.35 2.43
3820 4052 9.284968 TCATGGTTTTGGTTCTGTTTTTAAAAA 57.715 25.926 9.31 9.31 0.00 1.94
3821 4053 8.722394 GTCATGGTTTTGGTTCTGTTTTTAAAA 58.278 29.630 0.00 0.00 0.00 1.52
3948 4180 4.637977 GCAGTAGGAAGAGCTTGCTTTAAT 59.362 41.667 9.52 0.00 41.53 1.40
4387 4621 9.780186 ACCTTGCTAGTTTAGGATACATAATTC 57.220 33.333 12.14 0.00 41.41 2.17
4673 4907 3.717400 ATGGTGCGAGTATGTAGACAG 57.283 47.619 0.00 0.00 0.00 3.51
4730 4964 0.392336 TGGTTTGCTTGATGGTTGGC 59.608 50.000 0.00 0.00 0.00 4.52
4810 5044 2.373169 TGTTCCTCTCTTGTCCATGCTT 59.627 45.455 0.00 0.00 0.00 3.91
6229 8577 2.185867 GTTGGCACGCGGATAGGA 59.814 61.111 12.47 0.00 0.00 2.94
6328 8676 6.710744 TCGATACAAGAAAAGGAAGAAAGCTT 59.289 34.615 0.00 0.00 36.96 3.74
6341 8689 2.602878 GGCGTCACTCGATACAAGAAA 58.397 47.619 0.00 0.00 42.86 2.52
6651 14539 5.474578 ACATACTAATGACGCATCCTGAT 57.525 39.130 0.00 0.00 36.54 2.90
6652 14540 4.937201 ACATACTAATGACGCATCCTGA 57.063 40.909 0.00 0.00 36.54 3.86
6654 14542 5.670485 TCAAACATACTAATGACGCATCCT 58.330 37.500 0.00 0.00 36.54 3.24
6692 14580 2.291190 GGTGCGCCACTAGTAACAAAAA 59.709 45.455 12.58 0.00 34.40 1.94
6770 14669 6.046593 GCGCCACTATTATATACTAATGGCA 58.953 40.000 23.94 0.00 38.50 4.92
6785 14684 2.035193 CAGAGATGTAGTGCGCCACTAT 59.965 50.000 18.30 8.36 46.56 2.12
6872 14771 1.270358 ACCTCTTGCTCACGGTTCTTC 60.270 52.381 0.00 0.00 0.00 2.87
6881 14780 1.277273 CAGTGGATCACCTCTTGCTCA 59.723 52.381 0.00 0.00 37.84 4.26
6886 14785 0.904865 TCGGCAGTGGATCACCTCTT 60.905 55.000 0.00 0.00 37.84 2.85
6887 14786 0.689080 ATCGGCAGTGGATCACCTCT 60.689 55.000 0.00 0.00 40.14 3.69
6926 18722 1.807814 ACTCAGGGAAGACACAACCT 58.192 50.000 0.00 0.00 0.00 3.50
7053 18849 1.151777 GCTAGGATGCTTTGCGCGTA 61.152 55.000 8.43 0.00 43.27 4.42
7104 18900 1.827399 ATGCGAAACCCCTCGACAGT 61.827 55.000 0.00 0.00 41.44 3.55
7223 19019 4.081642 CCGTTCTTGATCTCCTTCACCTTA 60.082 45.833 0.00 0.00 0.00 2.69
7345 19141 1.004679 GCCCAGGCATTGTTGTTGG 60.005 57.895 3.12 0.00 41.49 3.77
7400 19196 5.157781 CAGCTCACAACTCAACTCTAGTAC 58.842 45.833 0.00 0.00 0.00 2.73
7407 19203 0.882042 CGCCAGCTCACAACTCAACT 60.882 55.000 0.00 0.00 0.00 3.16
7427 19223 3.838317 TGGTAGTACAAATCAGAGCACCT 59.162 43.478 2.06 0.00 0.00 4.00
7432 19228 9.599866 TTTACATGATGGTAGTACAAATCAGAG 57.400 33.333 17.78 15.37 32.85 3.35
7491 20487 0.825840 CCGCCCCAACTTCCTTTGAA 60.826 55.000 0.00 0.00 0.00 2.69
7786 20817 4.858680 TGGCCGCCAACAACGACA 62.859 61.111 10.50 0.00 0.00 4.35
7981 21234 5.680619 TGAATAACCTGAGCCATTATCGTT 58.319 37.500 0.00 0.00 0.00 3.85
8092 22793 3.512680 AGCATCGTGTTAGTACTGAAGC 58.487 45.455 5.39 2.44 0.00 3.86


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

AutoCloner maintained by Alex Coulton.