Multiple sequence alignment - TraesCS6D01G079100

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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 TraesCS6D01G079100 chr6D 100.000 6764 0 0 1 6764 44501870 44508633 0.000000e+00 12491.0
1 TraesCS6D01G079100 chr6D 97.970 3301 44 13 3483 6764 44735568 44738864 0.000000e+00 5703.0
2 TraesCS6D01G079100 chr6D 94.293 3627 137 25 2788 6379 44861992 44865583 0.000000e+00 5487.0
3 TraesCS6D01G079100 chr6D 97.856 2332 32 7 2519 4834 80295638 80297967 0.000000e+00 4013.0
4 TraesCS6D01G079100 chr6D 97.121 1598 29 7 1 1590 80287967 80289555 0.000000e+00 2680.0
5 TraesCS6D01G079100 chr6D 90.443 1852 154 12 4420 6256 44933969 44935812 0.000000e+00 2418.0
6 TraesCS6D01G079100 chr6D 89.532 1815 158 18 3929 5725 80290265 80292065 0.000000e+00 2270.0
7 TraesCS6D01G079100 chr6D 84.723 1715 215 30 4059 5761 45208859 45210538 0.000000e+00 1672.0
8 TraesCS6D01G079100 chr6D 84.768 1661 212 31 4123 5761 45203512 45205153 0.000000e+00 1628.0
9 TraesCS6D01G079100 chr6D 93.612 908 34 4 2524 3428 44734686 44735572 0.000000e+00 1334.0
10 TraesCS6D01G079100 chr6D 82.609 920 119 26 4272 5182 45479905 45480792 0.000000e+00 774.0
11 TraesCS6D01G079100 chr6D 91.915 470 7 2 1956 2395 100507971 100508439 4.450000e-176 628.0
12 TraesCS6D01G079100 chr6D 86.751 551 63 5 5212 5761 45480794 45481335 7.500000e-169 604.0
13 TraesCS6D01G079100 chr6D 88.454 485 35 11 3929 4411 44933343 44933808 3.540000e-157 566.0
14 TraesCS6D01G079100 chr6D 91.375 371 28 3 986 1355 44862740 44863107 7.830000e-139 505.0
15 TraesCS6D01G079100 chr6D 90.541 370 31 3 986 1355 80296657 80297022 2.840000e-133 486.0
16 TraesCS6D01G079100 chr6D 90.000 370 34 2 986 1355 44735621 44735987 6.140000e-130 475.0
17 TraesCS6D01G079100 chr6D 88.378 370 27 11 3536 3889 80288953 80289322 1.350000e-116 431.0
18 TraesCS6D01G079100 chr6D 86.375 411 31 11 3494 3880 44932774 44933183 6.270000e-115 425.0
19 TraesCS6D01G079100 chr6D 87.838 370 29 12 3536 3889 44502855 44503224 2.920000e-113 420.0
20 TraesCS6D01G079100 chr6D 87.838 370 29 12 986 1355 44505405 44505758 2.920000e-113 420.0
21 TraesCS6D01G079100 chr6D 99.543 219 1 0 1956 2174 409509004 409508786 3.800000e-107 399.0
22 TraesCS6D01G079100 chr6D 83.002 453 49 19 988 1429 44932816 44933251 1.060000e-102 385.0
23 TraesCS6D01G079100 chr6D 98.500 200 2 1 5002 5201 80297964 80298162 1.080000e-92 351.0
24 TraesCS6D01G079100 chr6D 85.758 330 27 8 6446 6763 44867551 44867872 1.410000e-86 331.0
25 TraesCS6D01G079100 chr6D 86.007 293 20 8 2519 2792 398237018 398236728 1.840000e-75 294.0
26 TraesCS6D01G079100 chr6D 86.026 229 17 10 1688 1902 315995181 315995408 1.470000e-56 231.0
27 TraesCS6D01G079100 chr6D 99.194 124 1 0 2389 2512 80289551 80289674 2.450000e-54 224.0
28 TraesCS6D01G079100 chr6D 77.627 295 41 16 2519 2792 395935471 395935181 9.080000e-34 156.0
29 TraesCS6D01G079100 chr6D 89.256 121 10 3 1783 1902 463540128 463540246 1.520000e-31 148.0
30 TraesCS6D01G079100 chr6D 79.894 189 17 9 6442 6615 44936095 44936277 1.190000e-22 119.0
31 TraesCS6D01G079100 chr6D 98.182 55 1 0 1901 1955 463539839 463539893 5.580000e-16 97.1
32 TraesCS6D01G079100 chr6D 98.182 55 1 0 1901 1955 463540279 463540333 5.580000e-16 97.1
33 TraesCS6D01G079100 chr6D 98.148 54 1 0 1901 1954 27144250 27144197 2.010000e-15 95.3
34 TraesCS6D01G079100 chr6D 100.000 51 0 0 1901 1951 38486589 38486639 2.010000e-15 95.3
35 TraesCS6D01G079100 chr6D 100.000 51 0 0 1901 1951 100502360 100502410 2.010000e-15 95.3
36 TraesCS6D01G079100 chr6D 98.039 51 1 0 6405 6455 472799415 472799365 9.340000e-14 89.8
37 TraesCS6D01G079100 chr6D 97.917 48 1 0 6408 6455 108860696 108860649 4.350000e-12 84.2
38 TraesCS6D01G079100 chr6D 97.917 48 1 0 6408 6455 147675639 147675686 4.350000e-12 84.2
39 TraesCS6D01G079100 chr6D 97.917 48 1 0 6408 6455 366701175 366701222 4.350000e-12 84.2
40 TraesCS6D01G079100 chr6D 96.078 51 2 0 6405 6455 379335408 379335358 4.350000e-12 84.2
41 TraesCS6D01G079100 chr6D 90.625 64 1 4 5955 6018 45210736 45210794 5.620000e-11 80.5
42 TraesCS6D01G079100 chr6D 90.000 60 5 1 6397 6455 34522356 34522297 7.270000e-10 76.8
43 TraesCS6D01G079100 chr6A 93.185 2832 136 26 3476 6260 59675531 59678352 0.000000e+00 4108.0
44 TraesCS6D01G079100 chr6A 91.375 2342 165 20 3929 6248 59344400 59346726 0.000000e+00 3171.0
45 TraesCS6D01G079100 chr6A 85.003 1667 206 27 4107 5761 59785738 59787372 0.000000e+00 1653.0
46 TraesCS6D01G079100 chr6A 84.264 1665 221 29 4123 5761 59708795 59710444 0.000000e+00 1585.0
47 TraesCS6D01G079100 chr6A 94.241 764 32 8 835 1590 59342638 59343397 0.000000e+00 1157.0
48 TraesCS6D01G079100 chr6A 93.510 339 19 2 1 337 59341448 59341785 1.010000e-137 501.0
49 TraesCS6D01G079100 chr6A 90.811 370 32 1 986 1355 59675591 59675958 1.690000e-135 494.0
50 TraesCS6D01G079100 chr6A 96.029 277 9 2 6489 6764 59356511 59356786 3.720000e-122 449.0
51 TraesCS6D01G079100 chr6A 92.476 319 17 4 1591 1902 73847353 73847671 3.720000e-122 449.0
52 TraesCS6D01G079100 chr6A 88.679 371 25 12 3536 3889 59342794 59343164 2.900000e-118 436.0
53 TraesCS6D01G079100 chr6A 83.333 294 25 9 2519 2792 404633397 404633108 4.050000e-62 250.0
54 TraesCS6D01G079100 chr6A 87.222 180 10 5 6241 6407 59355766 59355945 6.920000e-45 193.0
55 TraesCS6D01G079100 chr6A 92.063 126 8 2 2389 2512 59343393 59343518 6.970000e-40 176.0
56 TraesCS6D01G079100 chr6A 91.860 86 7 0 3409 3494 606036576 606036491 3.310000e-23 121.0
57 TraesCS6D01G079100 chr6A 79.787 188 19 8 6454 6627 59678685 59678867 1.190000e-22 119.0
58 TraesCS6D01G079100 chr6A 90.698 86 8 0 3409 3494 23402237 23402322 1.540000e-21 115.0
59 TraesCS6D01G079100 chr6A 84.252 127 11 7 5955 6081 59710642 59710759 1.540000e-21 115.0
60 TraesCS6D01G079100 chr6A 90.698 86 8 0 3409 3494 393541446 393541361 1.540000e-21 115.0
61 TraesCS6D01G079100 chr6A 84.375 64 4 5 5955 6018 59787570 59787627 2.630000e-04 58.4
62 TraesCS6D01G079100 chr6B 91.639 2129 154 12 4084 6201 113655924 113658039 0.000000e+00 2924.0
63 TraesCS6D01G079100 chr6B 91.356 1851 137 13 4413 6248 113771080 113772922 0.000000e+00 2510.0
64 TraesCS6D01G079100 chr6B 96.895 612 19 0 979 1590 113649483 113650094 0.000000e+00 1026.0
65 TraesCS6D01G079100 chr6B 88.106 908 39 18 3540 4411 113770079 113770953 0.000000e+00 1014.0
66 TraesCS6D01G079100 chr6B 90.534 581 45 5 1 574 113648542 113649119 0.000000e+00 760.0
67 TraesCS6D01G079100 chr6B 90.608 362 27 5 999 1355 113770085 113770444 2.210000e-129 473.0
68 TraesCS6D01G079100 chr6B 88.378 370 27 11 3536 3889 113649490 113649859 1.350000e-116 431.0
69 TraesCS6D01G079100 chr6B 87.783 221 14 6 6199 6406 113658205 113658425 5.240000e-61 246.0
70 TraesCS6D01G079100 chr6B 83.730 252 21 10 2562 2793 635273835 635273584 3.180000e-53 220.0
71 TraesCS6D01G079100 chr6B 95.161 124 6 0 2389 2512 113650090 113650213 5.350000e-46 196.0
72 TraesCS6D01G079100 chr6B 77.850 307 43 19 5751 6042 114027454 114027750 4.200000e-37 167.0
73 TraesCS6D01G079100 chr6B 93.103 87 6 0 3409 3495 560702903 560702989 1.980000e-25 128.0
74 TraesCS6D01G079100 chr6B 87.500 104 11 1 3515 3616 113843445 113843548 1.190000e-22 119.0
75 TraesCS6D01G079100 chr6B 100.000 53 0 0 6404 6456 530129477 530129529 1.550000e-16 99.0
76 TraesCS6D01G079100 chr6B 100.000 51 0 0 6405 6455 46937367 46937417 2.010000e-15 95.3
77 TraesCS6D01G079100 chr6B 85.417 96 4 7 1868 1954 348659979 348659885 2.600000e-14 91.6
78 TraesCS6D01G079100 chr6B 86.022 93 3 7 1868 1951 348686580 348686671 2.600000e-14 91.6
79 TraesCS6D01G079100 chr3D 87.828 838 47 41 1591 2388 287048019 287047197 0.000000e+00 931.0
80 TraesCS6D01G079100 chr3D 85.507 621 87 2 2790 3409 175536545 175535927 0.000000e+00 645.0
81 TraesCS6D01G079100 chr3D 90.638 470 13 9 1956 2395 527120314 527120782 4.520000e-166 595.0
82 TraesCS6D01G079100 chr3D 91.733 375 12 7 1591 1954 5090027 5089661 2.820000e-138 503.0
83 TraesCS6D01G079100 chr3D 92.690 342 18 4 2057 2395 569501191 569500854 2.840000e-133 486.0
84 TraesCS6D01G079100 chr3D 84.698 281 35 6 2519 2792 80479386 80479665 2.400000e-69 274.0
85 TraesCS6D01G079100 chr3D 91.954 87 7 0 3409 3495 234810731 234810645 9.210000e-24 122.0
86 TraesCS6D01G079100 chr3D 93.506 77 5 0 3418 3494 80479653 80479729 1.540000e-21 115.0
87 TraesCS6D01G079100 chr5D 90.224 624 57 4 2790 3410 353832207 353832829 0.000000e+00 811.0
88 TraesCS6D01G079100 chr5D 92.000 475 6 2 1956 2400 434302293 434301821 7.400000e-179 638.0
89 TraesCS6D01G079100 chr5D 92.191 461 6 1 1958 2388 15536215 15536675 5.760000e-175 625.0
90 TraesCS6D01G079100 chr5D 93.846 325 13 3 1581 1902 184103474 184103794 3.670000e-132 483.0
91 TraesCS6D01G079100 chr5D 90.811 370 19 10 1591 1954 381623895 381623535 1.320000e-131 481.0
92 TraesCS6D01G079100 chr5D 87.339 387 19 18 1591 1955 511808368 511808746 3.770000e-112 416.0
93 TraesCS6D01G079100 chr5D 87.324 284 17 9 2524 2790 418625934 418626215 2.370000e-79 307.0
94 TraesCS6D01G079100 chr5D 98.182 55 1 0 1901 1955 278461687 278461741 5.580000e-16 97.1
95 TraesCS6D01G079100 chr5D 98.039 51 1 0 6405 6455 97387265 97387315 9.340000e-14 89.8
96 TraesCS6D01G079100 chr5D 94.545 55 3 0 6405 6459 74721947 74722001 1.210000e-12 86.1
97 TraesCS6D01G079100 chr1D 93.926 461 5 3 1956 2395 397980465 397980007 0.000000e+00 675.0
98 TraesCS6D01G079100 chr1D 93.609 266 13 3 1912 2174 232147 231883 1.770000e-105 394.0
99 TraesCS6D01G079100 chr1D 84.589 292 24 8 2519 2792 376863612 376863324 3.110000e-68 270.0
100 TraesCS6D01G079100 chr1D 98.039 51 1 0 6405 6455 25454443 25454493 9.340000e-14 89.8
101 TraesCS6D01G079100 chr1D 92.063 63 3 2 6408 6469 7289653 7289714 3.360000e-13 87.9
102 TraesCS6D01G079100 chr3A 94.091 440 25 1 1956 2395 20399714 20400152 0.000000e+00 667.0
103 TraesCS6D01G079100 chr2D 87.392 579 70 3 2832 3409 612468157 612467581 0.000000e+00 662.0
104 TraesCS6D01G079100 chr2D 94.551 312 6 7 1591 1902 379706722 379706422 7.940000e-129 472.0
105 TraesCS6D01G079100 chr2D 93.103 87 6 0 3409 3495 632465583 632465497 1.980000e-25 128.0
106 TraesCS6D01G079100 chr2D 98.113 53 1 0 6405 6457 531675924 531675976 7.220000e-15 93.5
107 TraesCS6D01G079100 chr5A 85.968 620 84 3 2790 3408 532472510 532473127 0.000000e+00 660.0
108 TraesCS6D01G079100 chr1A 85.463 626 87 4 2790 3413 580431272 580431895 0.000000e+00 649.0
109 TraesCS6D01G079100 chr1A 85.000 620 88 3 2790 3408 29976446 29975831 5.760000e-175 625.0
110 TraesCS6D01G079100 chr1A 84.282 369 30 12 1590 1951 497858891 497859238 1.090000e-87 335.0
111 TraesCS6D01G079100 chr1A 84.752 282 33 8 2519 2792 480588955 480588676 2.400000e-69 274.0
112 TraesCS6D01G079100 chr1A 91.429 70 6 0 3425 3494 527097507 527097438 5.580000e-16 97.1
113 TraesCS6D01G079100 chrUn 90.426 470 14 8 1956 2395 27171980 27171512 2.100000e-164 590.0
114 TraesCS6D01G079100 chrUn 94.268 314 13 2 1590 1902 27183408 27183099 6.140000e-130 475.0
115 TraesCS6D01G079100 chrUn 91.843 331 8 11 1591 1902 27172501 27172171 1.730000e-120 444.0
116 TraesCS6D01G079100 chrUn 91.541 331 9 10 1591 1902 27167036 27166706 8.050000e-119 438.0
117 TraesCS6D01G079100 chrUn 99.543 219 1 0 1956 2174 348419482 348419700 3.800000e-107 399.0
118 TraesCS6D01G079100 chrUn 88.024 334 14 15 1591 1902 22462281 22461952 8.280000e-99 372.0
119 TraesCS6D01G079100 chrUn 87.202 336 19 12 1591 1902 64724601 64724266 1.790000e-95 361.0
120 TraesCS6D01G079100 chrUn 87.202 336 19 16 1591 1902 83550312 83550647 1.790000e-95 361.0
121 TraesCS6D01G079100 chrUn 86.510 341 17 16 1591 1902 381498811 381499151 1.400000e-91 348.0
122 TraesCS6D01G079100 chrUn 83.740 246 12 17 1683 1902 171698398 171698155 2.470000e-49 207.0
123 TraesCS6D01G079100 chrUn 98.148 54 1 0 1901 1954 27172138 27172085 2.010000e-15 95.3
124 TraesCS6D01G079100 chrUn 98.148 54 1 0 1901 1954 27177603 27177550 2.010000e-15 95.3
125 TraesCS6D01G079100 chrUn 98.148 54 1 0 1901 1954 171717165 171717112 2.010000e-15 95.3
126 TraesCS6D01G079100 chrUn 100.000 49 0 0 1901 1949 240443740 240443788 2.600000e-14 91.6
127 TraesCS6D01G079100 chrUn 96.429 56 0 2 1901 1955 460328133 460328079 2.600000e-14 91.6
128 TraesCS6D01G079100 chrUn 100.000 48 0 0 1901 1948 6024430 6024477 9.340000e-14 89.8
129 TraesCS6D01G079100 chrUn 96.296 54 2 0 1901 1954 22461919 22461866 9.340000e-14 89.8
130 TraesCS6D01G079100 chrUn 96.296 54 2 0 1901 1954 27166673 27166620 9.340000e-14 89.8
131 TraesCS6D01G079100 chrUn 98.039 51 1 0 1901 1951 96514002 96514052 9.340000e-14 89.8
132 TraesCS6D01G079100 chrUn 96.296 54 2 0 1901 1954 114980837 114980784 9.340000e-14 89.8
133 TraesCS6D01G079100 chrUn 98.039 51 1 0 6405 6455 278783035 278783085 9.340000e-14 89.8
134 TraesCS6D01G079100 chrUn 98.039 51 1 0 6405 6455 317427211 317427161 9.340000e-14 89.8
135 TraesCS6D01G079100 chrUn 96.078 51 2 0 6405 6455 37412795 37412845 4.350000e-12 84.2
136 TraesCS6D01G079100 chrUn 94.118 51 3 0 6405 6455 11850113 11850163 2.020000e-10 78.7
137 TraesCS6D01G079100 chrUn 94.118 51 3 0 6405 6455 70385182 70385232 2.020000e-10 78.7
138 TraesCS6D01G079100 chrUn 95.833 48 2 0 6408 6455 76605136 76605183 2.020000e-10 78.7
139 TraesCS6D01G079100 chrUn 94.118 51 3 0 6405 6455 87827459 87827509 2.020000e-10 78.7
140 TraesCS6D01G079100 chrUn 94.118 51 3 0 6405 6455 309972504 309972554 2.020000e-10 78.7
141 TraesCS6D01G079100 chrUn 95.833 48 2 0 6408 6455 351755239 351755192 2.020000e-10 78.7
142 TraesCS6D01G079100 chrUn 93.333 45 3 0 2748 2792 346144678 346144722 4.380000e-07 67.6
143 TraesCS6D01G079100 chr3B 84.343 594 91 2 2788 3380 13251254 13251846 1.260000e-161 580.0
144 TraesCS6D01G079100 chr3B 85.512 283 31 7 2519 2792 4207502 4207221 3.090000e-73 287.0
145 TraesCS6D01G079100 chr4D 94.212 311 15 2 1589 1898 35619911 35620219 7.940000e-129 472.0
146 TraesCS6D01G079100 chr4D 90.884 362 12 8 1591 1948 70342675 70342331 3.690000e-127 466.0
147 TraesCS6D01G079100 chr4D 93.016 315 15 4 1590 1902 348422007 348422316 2.880000e-123 453.0
148 TraesCS6D01G079100 chr4D 99.543 219 1 0 1956 2174 3855038 3855256 3.800000e-107 399.0
149 TraesCS6D01G079100 chr4D 99.543 219 1 0 1956 2174 46618507 46618289 3.800000e-107 399.0
150 TraesCS6D01G079100 chr4D 82.857 280 37 9 2519 2790 388119290 388119566 2.440000e-59 241.0
151 TraesCS6D01G079100 chr4D 82.653 294 29 10 2519 2792 488687777 488687486 2.440000e-59 241.0
152 TraesCS6D01G079100 chr4D 93.023 86 6 0 3409 3494 506936411 506936496 7.120000e-25 126.0
153 TraesCS6D01G079100 chr4D 93.590 78 5 0 3417 3494 112226246 112226323 4.290000e-22 117.0
154 TraesCS6D01G079100 chr4D 90.588 85 8 0 2708 2792 421810459 421810375 5.540000e-21 113.0
155 TraesCS6D01G079100 chr4D 96.078 51 2 0 6405 6455 12295211 12295261 4.350000e-12 84.2
156 TraesCS6D01G079100 chr4D 94.444 54 3 0 6405 6458 500825102 500825155 4.350000e-12 84.2
157 TraesCS6D01G079100 chr7D 93.291 313 15 3 1591 1902 626954330 626954637 2.220000e-124 457.0
158 TraesCS6D01G079100 chr7D 84.065 433 51 13 1961 2388 93687531 93687112 1.060000e-107 401.0
159 TraesCS6D01G079100 chr7D 83.333 282 36 9 2519 2792 101035781 101036059 4.050000e-62 250.0
160 TraesCS6D01G079100 chr7D 93.023 86 6 0 3409 3494 101036038 101036123 7.120000e-25 126.0
161 TraesCS6D01G079100 chr7D 98.182 55 1 0 1901 1955 90117026 90117080 5.580000e-16 97.1
162 TraesCS6D01G079100 chr7D 98.039 51 1 0 6405 6455 5522243 5522293 9.340000e-14 89.8
163 TraesCS6D01G079100 chr4A 85.959 292 22 6 2520 2792 687327844 687328135 1.840000e-75 294.0
164 TraesCS6D01G079100 chr4A 83.904 292 29 10 2519 2792 687330887 687331178 5.200000e-66 263.0
165 TraesCS6D01G079100 chr4B 83.045 289 28 8 2523 2792 455976448 455976734 6.780000e-60 243.0
166 TraesCS6D01G079100 chr4B 82.182 275 23 14 2544 2792 150420677 150420951 5.310000e-51 213.0
167 TraesCS6D01G079100 chr4B 84.753 223 12 7 2590 2792 615385036 615385256 3.200000e-48 204.0
168 TraesCS6D01G079100 chr4B 98.305 59 1 0 6405 6463 527282585 527282643 3.340000e-18 104.0
169 TraesCS6D01G079100 chr5B 93.548 93 6 0 3403 3495 122447483 122447391 9.150000e-29 139.0
170 TraesCS6D01G079100 chr5B 93.103 87 6 0 3409 3495 122447883 122447797 1.980000e-25 128.0
171 TraesCS6D01G079100 chr5B 100.000 51 0 0 6405 6455 558559023 558559073 2.010000e-15 95.3
172 TraesCS6D01G079100 chr1B 94.186 86 5 0 3409 3494 20692955 20693040 1.530000e-26 132.0
173 TraesCS6D01G079100 chr1B 93.023 86 6 0 3409 3494 408109436 408109521 7.120000e-25 126.0
174 TraesCS6D01G079100 chr1B 100.000 51 0 0 6405 6455 499898255 499898205 2.010000e-15 95.3
175 TraesCS6D01G079100 chr1B 89.552 67 6 1 6405 6471 674876196 674876261 4.350000e-12 84.2
176 TraesCS6D01G079100 chr1B 90.476 63 4 2 6408 6469 9983756 9983695 1.560000e-11 82.4
177 TraesCS6D01G079100 chr7B 89.535 86 9 0 3409 3494 583976059 583976144 7.170000e-20 110.0
178 TraesCS6D01G079100 chr7B 100.000 51 0 0 6405 6455 434925973 434926023 2.010000e-15 95.3
179 TraesCS6D01G079100 chr7B 98.077 52 1 0 6405 6456 78695296 78695347 2.600000e-14 91.6


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 TraesCS6D01G079100 chr6D 44501870 44508633 6763 False 12491.000000 12491 100.000000 1 6764 1 chr6D.!!$F2 6763
1 TraesCS6D01G079100 chr6D 44861992 44865583 3591 False 2996.000000 5487 92.834000 986 6379 2 chr6D.!!$F11 5393
2 TraesCS6D01G079100 chr6D 44734686 44738864 4178 False 2504.000000 5703 93.860667 986 6764 3 chr6D.!!$F10 5778
3 TraesCS6D01G079100 chr6D 80287967 80298162 10195 False 1493.571429 4013 94.446000 1 5725 7 chr6D.!!$F15 5724
4 TraesCS6D01G079100 chr6D 45203512 45210794 7282 False 1126.833333 1672 86.705333 4059 6018 3 chr6D.!!$F13 1959
5 TraesCS6D01G079100 chr6D 44932774 44936277 3503 False 782.600000 2418 85.633600 988 6615 5 chr6D.!!$F12 5627
6 TraesCS6D01G079100 chr6D 45479905 45481335 1430 False 689.000000 774 84.680000 4272 5761 2 chr6D.!!$F14 1489
7 TraesCS6D01G079100 chr6D 44502855 44505758 2903 False 420.000000 420 87.838000 986 3889 2 chr6D.!!$F9 2903
8 TraesCS6D01G079100 chr6A 59675531 59678867 3336 False 1573.666667 4108 87.927667 986 6627 3 chr6A.!!$F5 5641
9 TraesCS6D01G079100 chr6A 59341448 59346726 5278 False 1088.200000 3171 91.973600 1 6248 5 chr6A.!!$F3 6247
10 TraesCS6D01G079100 chr6A 59785738 59787627 1889 False 855.700000 1653 84.689000 4107 6018 2 chr6A.!!$F7 1911
11 TraesCS6D01G079100 chr6A 59708795 59710759 1964 False 850.000000 1585 84.258000 4123 6081 2 chr6A.!!$F6 1958
12 TraesCS6D01G079100 chr6A 59355766 59356786 1020 False 321.000000 449 91.625500 6241 6764 2 chr6A.!!$F4 523
13 TraesCS6D01G079100 chr6B 113655924 113658425 2501 False 1585.000000 2924 89.711000 4084 6406 2 chr6B.!!$F8 2322
14 TraesCS6D01G079100 chr6B 113770079 113772922 2843 False 1332.333333 2510 90.023333 999 6248 3 chr6B.!!$F9 5249
15 TraesCS6D01G079100 chr6B 113648542 113650213 1671 False 603.250000 1026 92.742000 1 3889 4 chr6B.!!$F7 3888
16 TraesCS6D01G079100 chr3D 287047197 287048019 822 True 931.000000 931 87.828000 1591 2388 1 chr3D.!!$R4 797
17 TraesCS6D01G079100 chr3D 175535927 175536545 618 True 645.000000 645 85.507000 2790 3409 1 chr3D.!!$R2 619
18 TraesCS6D01G079100 chr5D 353832207 353832829 622 False 811.000000 811 90.224000 2790 3410 1 chr5D.!!$F6 620
19 TraesCS6D01G079100 chr2D 612467581 612468157 576 True 662.000000 662 87.392000 2832 3409 1 chr2D.!!$R2 577
20 TraesCS6D01G079100 chr5A 532472510 532473127 617 False 660.000000 660 85.968000 2790 3408 1 chr5A.!!$F1 618
21 TraesCS6D01G079100 chr1A 580431272 580431895 623 False 649.000000 649 85.463000 2790 3413 1 chr1A.!!$F2 623
22 TraesCS6D01G079100 chr1A 29975831 29976446 615 True 625.000000 625 85.000000 2790 3408 1 chr1A.!!$R1 618
23 TraesCS6D01G079100 chrUn 27171512 27172501 989 True 376.433333 590 93.472333 1591 2395 3 chrUn.!!$R12 804
24 TraesCS6D01G079100 chr3B 13251254 13251846 592 False 580.000000 580 84.343000 2788 3380 1 chr3B.!!$F1 592
25 TraesCS6D01G079100 chr4A 687327844 687331178 3334 False 278.500000 294 84.931500 2519 2792 2 chr4A.!!$F1 273

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
924 1388 0.396060 GAGGGCCCATCTCATCTCAC 59.604 60.000 27.56 0.00 0.00 3.51 F
3633 11509 4.459089 GCCTCAGGCCCAGTCGAC 62.459 72.222 3.37 7.70 44.06 4.20 F
3702 11578 0.034380 AGGATCTCGAAGGTGTCCGA 60.034 55.000 0.00 0.00 34.19 4.55 F
3793 11669 0.098376 AACAGATCCTCGCGTACGTC 59.902 55.000 17.90 8.33 41.18 4.34 F
3905 11781 0.179140 GCGATTTACCGGTCACCGTA 60.179 55.000 16.87 4.91 46.80 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3605 11481 4.127040 CTGAGGCTGCGCGAGTCT 62.127 66.667 12.10 11.76 40.34 3.24 R
5113 19585 0.523519 GCCTTGCCAAACAGCTCTAC 59.476 55.000 0.00 0.00 0.00 2.59 R
5537 20009 0.865769 CTCCAGTGCCGTGTTAACAC 59.134 55.000 25.73 25.73 43.15 3.32 R
5676 20148 1.696336 AGCTTCTTCAGGCACTCAAGA 59.304 47.619 0.00 0.00 45.78 3.02 R
6449 21186 6.937392 AGAGTGGAAATTAGTCTGTTACTCC 58.063 40.000 0.00 0.00 39.80 3.85 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
147 150 5.014755 TGCCTCCTCCCTTTTTGTAAGAATA 59.985 40.000 0.00 0.00 0.00 1.75
268 271 6.486993 GGAGCGTGGGATTTCTTCTTATTTAT 59.513 38.462 0.00 0.00 0.00 1.40
608 723 7.874940 TCTGTAATTTCTTGTGAACTGATTGG 58.125 34.615 0.00 0.00 31.02 3.16
677 797 3.338250 ACCCCCACCATCGCACAT 61.338 61.111 0.00 0.00 0.00 3.21
924 1388 0.396060 GAGGGCCCATCTCATCTCAC 59.604 60.000 27.56 0.00 0.00 3.51
3633 11509 4.459089 GCCTCAGGCCCAGTCGAC 62.459 72.222 3.37 7.70 44.06 4.20
3634 11510 2.997315 CCTCAGGCCCAGTCGACA 60.997 66.667 19.50 0.00 0.00 4.35
3635 11511 2.575993 CTCAGGCCCAGTCGACAG 59.424 66.667 19.50 10.04 0.00 3.51
3636 11512 2.997315 TCAGGCCCAGTCGACAGG 60.997 66.667 19.47 19.47 0.00 4.00
3637 11513 3.314331 CAGGCCCAGTCGACAGGT 61.314 66.667 23.63 4.57 0.00 4.00
3638 11514 2.526873 AGGCCCAGTCGACAGGTT 60.527 61.111 23.63 11.00 0.00 3.50
3639 11515 2.047179 GGCCCAGTCGACAGGTTC 60.047 66.667 23.63 15.12 0.00 3.62
3640 11516 2.047179 GCCCAGTCGACAGGTTCC 60.047 66.667 23.63 9.49 0.00 3.62
3641 11517 2.261671 CCCAGTCGACAGGTTCCG 59.738 66.667 23.63 6.43 0.00 4.30
3642 11518 2.273179 CCCAGTCGACAGGTTCCGA 61.273 63.158 23.63 0.00 0.00 4.55
3644 11520 1.100510 CCAGTCGACAGGTTCCGATA 58.899 55.000 19.50 0.00 37.14 2.92
3645 11521 1.065701 CCAGTCGACAGGTTCCGATAG 59.934 57.143 19.50 0.00 37.14 2.08
3657 11533 3.788817 CGATAGGCGCGGTTTTGA 58.211 55.556 8.83 0.00 0.00 2.69
3659 11535 1.352056 GATAGGCGCGGTTTTGAGC 59.648 57.895 8.83 0.00 0.00 4.26
3666 11542 2.549282 CGGTTTTGAGCCGTCGTG 59.451 61.111 0.00 0.00 43.84 4.35
3667 11543 2.943653 GGTTTTGAGCCGTCGTGG 59.056 61.111 0.00 0.00 42.50 4.94
3679 11555 3.376078 TCGTGGGTCCCGCTGTAC 61.376 66.667 19.43 2.52 0.00 2.90
3680 11556 3.687102 CGTGGGTCCCGCTGTACA 61.687 66.667 19.43 0.00 0.00 2.90
3682 11558 1.375523 GTGGGTCCCGCTGTACAAG 60.376 63.158 14.73 0.00 0.00 3.16
3684 11560 1.218316 GGGTCCCGCTGTACAAGAG 59.782 63.158 0.00 0.00 0.00 2.85
3685 11561 1.218316 GGTCCCGCTGTACAAGAGG 59.782 63.158 0.00 2.74 45.09 3.69
3702 11578 0.034380 AGGATCTCGAAGGTGTCCGA 60.034 55.000 0.00 0.00 34.19 4.55
3703 11579 0.100861 GGATCTCGAAGGTGTCCGAC 59.899 60.000 0.00 0.00 0.00 4.79
3704 11580 0.248134 GATCTCGAAGGTGTCCGACG 60.248 60.000 0.00 0.00 0.00 5.12
3705 11581 1.654954 ATCTCGAAGGTGTCCGACGG 61.655 60.000 7.84 7.84 0.00 4.79
3706 11582 3.966026 CTCGAAGGTGTCCGACGGC 62.966 68.421 9.66 5.12 0.00 5.68
3707 11583 4.351938 CGAAGGTGTCCGACGGCA 62.352 66.667 9.66 8.02 0.00 5.69
3710 11586 3.222354 AAGGTGTCCGACGGCAGAC 62.222 63.158 9.66 0.00 0.00 3.51
3711 11587 4.736896 GGTGTCCGACGGCAGACC 62.737 72.222 9.66 12.41 31.76 3.85
3722 11598 4.301027 GCAGACCGCCGGGGATAG 62.301 72.222 21.95 5.84 39.97 2.08
3723 11599 2.838225 CAGACCGCCGGGGATAGT 60.838 66.667 21.95 9.55 39.97 2.12
3724 11600 2.838225 AGACCGCCGGGGATAGTG 60.838 66.667 21.95 5.01 39.97 2.74
3725 11601 3.925090 GACCGCCGGGGATAGTGG 61.925 72.222 21.95 4.20 39.97 4.00
3733 11609 4.301027 GGGATAGTGGCGGCGGAG 62.301 72.222 9.78 0.00 0.00 4.63
3734 11610 3.224324 GGATAGTGGCGGCGGAGA 61.224 66.667 9.78 0.00 0.00 3.71
3735 11611 2.574955 GGATAGTGGCGGCGGAGAT 61.575 63.158 9.78 0.00 0.00 2.75
3736 11612 1.373497 GATAGTGGCGGCGGAGATG 60.373 63.158 9.78 0.00 0.00 2.90
3743 11619 2.417516 CGGCGGAGATGGACGAAT 59.582 61.111 0.00 0.00 0.00 3.34
3744 11620 1.951130 CGGCGGAGATGGACGAATG 60.951 63.158 0.00 0.00 0.00 2.67
3745 11621 1.595382 GGCGGAGATGGACGAATGG 60.595 63.158 0.00 0.00 0.00 3.16
3746 11622 2.247437 GCGGAGATGGACGAATGGC 61.247 63.158 0.00 0.00 0.00 4.40
3748 11624 0.598680 CGGAGATGGACGAATGGCTC 60.599 60.000 0.00 0.00 0.00 4.70
3750 11626 0.598680 GAGATGGACGAATGGCTCCG 60.599 60.000 0.00 0.00 0.00 4.63
3751 11627 1.595382 GATGGACGAATGGCTCCGG 60.595 63.158 0.00 0.00 0.00 5.14
3752 11628 3.757248 ATGGACGAATGGCTCCGGC 62.757 63.158 0.00 0.00 37.82 6.13
3758 11634 3.011517 AATGGCTCCGGCAGAGGT 61.012 61.111 0.00 0.00 43.46 3.85
3759 11635 2.932130 GAATGGCTCCGGCAGAGGTC 62.932 65.000 0.00 0.00 43.46 3.85
3768 11644 3.844090 GCAGAGGTCCCGGCTCTC 61.844 72.222 7.08 7.76 0.00 3.20
3769 11645 3.522731 CAGAGGTCCCGGCTCTCG 61.523 72.222 7.08 1.22 38.88 4.04
3782 11658 2.675519 CTCTCGCAGCAACAGATCC 58.324 57.895 0.00 0.00 0.00 3.36
3783 11659 0.175302 CTCTCGCAGCAACAGATCCT 59.825 55.000 0.00 0.00 0.00 3.24
3784 11660 0.174389 TCTCGCAGCAACAGATCCTC 59.826 55.000 0.00 0.00 0.00 3.71
3785 11661 1.144565 CTCGCAGCAACAGATCCTCG 61.145 60.000 0.00 0.00 0.00 4.63
3786 11662 2.806856 CGCAGCAACAGATCCTCGC 61.807 63.158 0.00 0.00 0.00 5.03
3787 11663 2.806856 GCAGCAACAGATCCTCGCG 61.807 63.158 0.00 0.00 0.00 5.87
3788 11664 1.446792 CAGCAACAGATCCTCGCGT 60.447 57.895 5.77 0.00 0.00 6.01
3790 11666 0.179134 AGCAACAGATCCTCGCGTAC 60.179 55.000 5.77 0.00 0.00 3.67
3792 11668 0.179171 CAACAGATCCTCGCGTACGT 60.179 55.000 17.90 0.00 41.18 3.57
3793 11669 0.098376 AACAGATCCTCGCGTACGTC 59.902 55.000 17.90 8.33 41.18 4.34
3794 11670 1.009900 CAGATCCTCGCGTACGTCC 60.010 63.158 17.90 0.00 41.18 4.79
3795 11671 2.052414 GATCCTCGCGTACGTCCG 60.052 66.667 17.90 12.89 41.18 4.79
3802 11678 2.098298 GCGTACGTCCGCGAACTA 59.902 61.111 17.90 0.00 44.69 2.24
3804 11680 1.724046 GCGTACGTCCGCGAACTAAC 61.724 60.000 17.90 0.00 44.69 2.34
3808 11684 1.804326 CGTCCGCGAACTAACCAGG 60.804 63.158 8.23 0.00 41.33 4.45
3809 11685 1.291272 GTCCGCGAACTAACCAGGT 59.709 57.895 8.23 0.00 0.00 4.00
3810 11686 0.320160 GTCCGCGAACTAACCAGGTT 60.320 55.000 8.23 10.50 0.00 3.50
3811 11687 0.393820 TCCGCGAACTAACCAGGTTT 59.606 50.000 11.02 0.00 0.00 3.27
3813 11689 2.036992 TCCGCGAACTAACCAGGTTTAA 59.963 45.455 11.02 0.00 0.00 1.52
3815 11691 3.319755 CGCGAACTAACCAGGTTTAAGA 58.680 45.455 11.02 0.00 0.00 2.10
3816 11692 3.742369 CGCGAACTAACCAGGTTTAAGAA 59.258 43.478 11.02 0.00 0.00 2.52
3817 11693 4.143179 CGCGAACTAACCAGGTTTAAGAAG 60.143 45.833 11.02 3.66 0.00 2.85
3820 11696 6.565435 GCGAACTAACCAGGTTTAAGAAGAAC 60.565 42.308 11.02 1.07 0.00 3.01
3821 11697 6.346359 CGAACTAACCAGGTTTAAGAAGAACG 60.346 42.308 11.02 8.71 0.00 3.95
3822 11698 6.165700 ACTAACCAGGTTTAAGAAGAACGA 57.834 37.500 11.02 0.00 0.00 3.85
3824 11700 4.004196 ACCAGGTTTAAGAAGAACGAGG 57.996 45.455 0.00 0.00 0.00 4.63
3826 11702 2.742589 CAGGTTTAAGAAGAACGAGGGC 59.257 50.000 0.00 0.00 0.00 5.19
3827 11703 1.730612 GGTTTAAGAAGAACGAGGGCG 59.269 52.381 0.00 0.00 44.79 6.13
3828 11704 1.128136 GTTTAAGAAGAACGAGGGCGC 59.872 52.381 0.00 0.00 42.48 6.53
3829 11705 0.734942 TTAAGAAGAACGAGGGCGCG 60.735 55.000 0.00 0.00 42.48 6.86
3847 11723 3.775654 CTCGAGGTGCCACCCCTC 61.776 72.222 11.06 1.15 44.24 4.30
3856 11732 2.689813 CCACCCCTCCCCCAAATC 59.310 66.667 0.00 0.00 0.00 2.17
3858 11734 1.615262 CACCCCTCCCCCAAATCTC 59.385 63.158 0.00 0.00 0.00 2.75
3861 11737 0.553333 CCCCTCCCCCAAATCTCTTC 59.447 60.000 0.00 0.00 0.00 2.87
3862 11738 0.553333 CCCTCCCCCAAATCTCTTCC 59.447 60.000 0.00 0.00 0.00 3.46
3863 11739 1.601248 CCTCCCCCAAATCTCTTCCT 58.399 55.000 0.00 0.00 0.00 3.36
3866 11742 3.245766 CCTCCCCCAAATCTCTTCCTTTT 60.246 47.826 0.00 0.00 0.00 2.27
3867 11743 3.766051 CTCCCCCAAATCTCTTCCTTTTG 59.234 47.826 0.00 0.00 0.00 2.44
3868 11744 3.142028 TCCCCCAAATCTCTTCCTTTTGT 59.858 43.478 0.00 0.00 0.00 2.83
3869 11745 3.903714 CCCCCAAATCTCTTCCTTTTGTT 59.096 43.478 0.00 0.00 0.00 2.83
3870 11746 4.262592 CCCCCAAATCTCTTCCTTTTGTTG 60.263 45.833 0.00 0.00 0.00 3.33
3871 11747 4.344968 CCCCAAATCTCTTCCTTTTGTTGT 59.655 41.667 0.00 0.00 0.00 3.32
3873 11749 5.985530 CCCAAATCTCTTCCTTTTGTTGTTC 59.014 40.000 0.00 0.00 0.00 3.18
3874 11750 5.687285 CCAAATCTCTTCCTTTTGTTGTTCG 59.313 40.000 0.00 0.00 0.00 3.95
3875 11751 6.459573 CCAAATCTCTTCCTTTTGTTGTTCGA 60.460 38.462 0.00 0.00 0.00 3.71
3876 11752 6.884280 AATCTCTTCCTTTTGTTGTTCGAT 57.116 33.333 0.00 0.00 0.00 3.59
3877 11753 5.673337 TCTCTTCCTTTTGTTGTTCGATG 57.327 39.130 0.00 0.00 0.00 3.84
3878 11754 4.024048 TCTCTTCCTTTTGTTGTTCGATGC 60.024 41.667 0.00 0.00 0.00 3.91
3879 11755 3.882888 TCTTCCTTTTGTTGTTCGATGCT 59.117 39.130 0.00 0.00 0.00 3.79
3880 11756 3.624326 TCCTTTTGTTGTTCGATGCTG 57.376 42.857 0.00 0.00 0.00 4.41
3881 11757 2.053627 CCTTTTGTTGTTCGATGCTGC 58.946 47.619 0.00 0.00 0.00 5.25
3882 11758 2.543445 CCTTTTGTTGTTCGATGCTGCA 60.543 45.455 4.13 4.13 0.00 4.41
3884 11760 3.367992 TTTGTTGTTCGATGCTGCATT 57.632 38.095 17.36 0.09 0.00 3.56
3885 11761 4.495911 TTTGTTGTTCGATGCTGCATTA 57.504 36.364 17.36 5.56 0.00 1.90
3886 11762 3.745332 TGTTGTTCGATGCTGCATTAG 57.255 42.857 17.36 13.79 0.00 1.73
3896 11772 2.300623 GCTGCATTAGCGATTTACCG 57.699 50.000 0.00 0.00 46.23 4.02
3898 11774 2.210116 CTGCATTAGCGATTTACCGGT 58.790 47.619 13.98 13.98 46.23 5.28
3899 11775 2.206750 TGCATTAGCGATTTACCGGTC 58.793 47.619 12.40 0.00 46.23 4.79
3900 11776 2.206750 GCATTAGCGATTTACCGGTCA 58.793 47.619 12.40 0.00 40.88 4.02
3901 11777 2.033151 GCATTAGCGATTTACCGGTCAC 60.033 50.000 12.40 0.00 40.88 3.67
3902 11778 2.298411 TTAGCGATTTACCGGTCACC 57.702 50.000 12.40 0.00 40.88 4.02
3905 11781 0.179140 GCGATTTACCGGTCACCGTA 60.179 55.000 16.87 4.91 46.80 4.02
3906 11782 1.536709 GCGATTTACCGGTCACCGTAT 60.537 52.381 16.87 5.37 46.80 3.06
3908 11784 3.189285 CGATTTACCGGTCACCGTATTT 58.811 45.455 16.87 0.00 46.80 1.40
3909 11785 3.618150 CGATTTACCGGTCACCGTATTTT 59.382 43.478 16.87 0.00 46.80 1.82
3910 11786 4.259930 CGATTTACCGGTCACCGTATTTTC 60.260 45.833 16.87 5.60 46.80 2.29
3911 11787 2.276472 TACCGGTCACCGTATTTTCG 57.724 50.000 16.87 0.00 46.80 3.46
3912 11788 0.602562 ACCGGTCACCGTATTTTCGA 59.397 50.000 16.87 0.00 46.80 3.71
3913 11789 1.205417 ACCGGTCACCGTATTTTCGAT 59.795 47.619 16.87 0.00 46.80 3.59
3914 11790 2.426738 ACCGGTCACCGTATTTTCGATA 59.573 45.455 16.87 0.00 46.80 2.92
3916 11792 2.465109 CGGTCACCGTATTTTCGATACG 59.535 50.000 8.54 9.54 42.73 3.06
3917 11793 2.217167 GGTCACCGTATTTTCGATACGC 59.783 50.000 10.77 0.00 44.10 4.42
3959 11835 6.762077 TTTTCCTCCCCAAAAATGATTCTT 57.238 33.333 0.00 0.00 0.00 2.52
3961 11837 4.750941 TCCTCCCCAAAAATGATTCTTGT 58.249 39.130 0.00 0.00 0.00 3.16
3962 11838 4.527816 TCCTCCCCAAAAATGATTCTTGTG 59.472 41.667 0.00 0.00 0.00 3.33
3965 11841 5.083122 TCCCCAAAAATGATTCTTGTGCTA 58.917 37.500 0.00 0.00 0.00 3.49
3966 11842 5.047377 TCCCCAAAAATGATTCTTGTGCTAC 60.047 40.000 0.00 0.00 0.00 3.58
3968 11844 6.152661 CCCCAAAAATGATTCTTGTGCTACTA 59.847 38.462 0.00 0.00 0.00 1.82
3969 11845 7.029563 CCCAAAAATGATTCTTGTGCTACTAC 58.970 38.462 0.00 0.00 0.00 2.73
3970 11846 7.029563 CCAAAAATGATTCTTGTGCTACTACC 58.970 38.462 0.00 0.00 0.00 3.18
3971 11847 7.309133 CCAAAAATGATTCTTGTGCTACTACCA 60.309 37.037 0.00 0.00 0.00 3.25
3973 11849 7.944729 AAATGATTCTTGTGCTACTACCATT 57.055 32.000 0.00 0.00 0.00 3.16
3975 11851 6.741992 TGATTCTTGTGCTACTACCATTTG 57.258 37.500 0.00 0.00 0.00 2.32
3977 11853 4.014569 TCTTGTGCTACTACCATTTGCA 57.985 40.909 0.00 0.00 0.00 4.08
3978 11854 4.393834 TCTTGTGCTACTACCATTTGCAA 58.606 39.130 0.00 0.00 35.34 4.08
3979 11855 5.009631 TCTTGTGCTACTACCATTTGCAAT 58.990 37.500 0.00 0.00 35.34 3.56
3980 11856 4.963276 TGTGCTACTACCATTTGCAATC 57.037 40.909 0.00 0.00 35.34 2.67
3981 11857 4.331108 TGTGCTACTACCATTTGCAATCA 58.669 39.130 0.00 0.00 35.34 2.57
3982 11858 4.395854 TGTGCTACTACCATTTGCAATCAG 59.604 41.667 0.00 0.00 35.34 2.90
3983 11859 4.396166 GTGCTACTACCATTTGCAATCAGT 59.604 41.667 0.00 0.11 35.34 3.41
3984 11860 5.009631 TGCTACTACCATTTGCAATCAGTT 58.990 37.500 0.00 0.00 0.00 3.16
3985 11861 6.093495 GTGCTACTACCATTTGCAATCAGTTA 59.907 38.462 0.00 0.00 35.34 2.24
3986 11862 6.093495 TGCTACTACCATTTGCAATCAGTTAC 59.907 38.462 0.00 0.00 0.00 2.50
3989 11865 4.685169 ACCATTTGCAATCAGTTACGAG 57.315 40.909 0.00 0.00 0.00 4.18
3991 11867 5.242434 ACCATTTGCAATCAGTTACGAGTA 58.758 37.500 0.00 0.00 0.00 2.59
3993 11869 5.351465 CCATTTGCAATCAGTTACGAGTAGT 59.649 40.000 0.00 0.00 0.00 2.73
3994 11870 6.533723 CCATTTGCAATCAGTTACGAGTAGTA 59.466 38.462 0.00 0.00 0.00 1.82
3995 11871 6.939551 TTTGCAATCAGTTACGAGTAGTAC 57.060 37.500 0.00 0.00 34.56 2.73
3996 11872 5.892160 TGCAATCAGTTACGAGTAGTACT 57.108 39.130 1.37 1.37 34.56 2.73
3997 11873 5.877031 TGCAATCAGTTACGAGTAGTACTC 58.123 41.667 18.77 18.77 41.71 2.59
3999 11875 6.072342 TGCAATCAGTTACGAGTAGTACTCAA 60.072 38.462 26.06 13.52 45.30 3.02
4000 11876 6.973474 GCAATCAGTTACGAGTAGTACTCAAT 59.027 38.462 26.06 17.18 45.30 2.57
4001 11877 8.127327 GCAATCAGTTACGAGTAGTACTCAATA 58.873 37.037 26.06 16.29 45.30 1.90
4024 11900 9.685276 AATATTATTGATAATCATGAAGGCCGA 57.315 29.630 0.00 0.00 34.91 5.54
4025 11901 9.857656 ATATTATTGATAATCATGAAGGCCGAT 57.142 29.630 0.00 0.00 34.91 4.18
4026 11902 5.892160 ATTGATAATCATGAAGGCCGATG 57.108 39.130 0.00 1.14 0.00 3.84
4027 11903 3.076621 TGATAATCATGAAGGCCGATGC 58.923 45.455 0.00 0.00 0.00 3.91
4029 11905 2.936919 AATCATGAAGGCCGATGCTA 57.063 45.000 0.00 0.00 37.74 3.49
4033 11909 2.170397 TCATGAAGGCCGATGCTAAAGA 59.830 45.455 0.00 0.00 37.74 2.52
4035 11911 1.831106 TGAAGGCCGATGCTAAAGAGA 59.169 47.619 0.00 0.00 37.74 3.10
4036 11912 2.159043 TGAAGGCCGATGCTAAAGAGAG 60.159 50.000 0.00 0.00 37.74 3.20
4037 11913 1.781786 AGGCCGATGCTAAAGAGAGA 58.218 50.000 0.00 0.00 37.74 3.10
4038 11914 2.111384 AGGCCGATGCTAAAGAGAGAA 58.889 47.619 0.00 0.00 37.74 2.87
4039 11915 2.501723 AGGCCGATGCTAAAGAGAGAAA 59.498 45.455 0.00 0.00 37.74 2.52
4040 11916 3.055094 AGGCCGATGCTAAAGAGAGAAAA 60.055 43.478 0.00 0.00 37.74 2.29
4041 11917 3.689649 GGCCGATGCTAAAGAGAGAAAAA 59.310 43.478 0.00 0.00 37.74 1.94
4572 19042 4.261741 GGTGCAATCTCTTTCTGAGCAAAA 60.262 41.667 0.00 0.00 42.38 2.44
4827 19299 3.356290 GTTGGCATACAAAGGTCTGGAT 58.644 45.455 0.00 0.00 41.58 3.41
4862 19334 7.486407 AGATGAAAGCCAAAAATATGGTTCT 57.514 32.000 0.00 0.00 42.75 3.01
5537 20009 8.970859 ACTGAGTTCTATTTGGATAAATCTGG 57.029 34.615 0.00 0.00 37.64 3.86
5676 20148 3.806941 TGCTGGTGCAGAGTCTTTT 57.193 47.368 0.00 0.00 45.31 2.27
6449 21186 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
147 150 4.042934 ACCAGCAGAATTTACCTACCTGTT 59.957 41.667 0.00 0.00 0.00 3.16
268 271 7.105588 TGAATTCTCGAATCTTGATCTTGGAA 58.894 34.615 7.05 0.00 0.00 3.53
578 693 9.787532 TCAGTTCACAAGAAATTACAGAAAAAG 57.212 29.630 0.00 0.00 35.08 2.27
660 775 3.338250 ATGTGCGATGGTGGGGGT 61.338 61.111 0.00 0.00 0.00 4.95
674 794 2.828549 GGGCCGGCGAAATCATGT 60.829 61.111 22.54 0.00 0.00 3.21
677 797 2.828095 CATGGGCCGGCGAAATCA 60.828 61.111 22.54 13.51 0.00 2.57
778 899 6.836577 TGAAATCCGGAAACAATTTTGAAC 57.163 33.333 9.01 0.00 0.00 3.18
924 1388 1.084370 GGTTCGGCGTGATTCTCCTG 61.084 60.000 6.85 0.00 0.00 3.86
977 1441 2.287849 GGACTGGCTGCTTGAGTTTTTC 60.288 50.000 0.00 0.00 0.00 2.29
3605 11481 4.127040 CTGAGGCTGCGCGAGTCT 62.127 66.667 12.10 11.76 40.34 3.24
3617 11493 2.997315 TGTCGACTGGGCCTGAGG 60.997 66.667 17.92 8.15 0.00 3.86
3618 11494 2.575993 CTGTCGACTGGGCCTGAG 59.424 66.667 17.92 10.45 0.00 3.35
3619 11495 2.997315 CCTGTCGACTGGGCCTGA 60.997 66.667 28.59 0.73 0.00 3.86
3620 11496 2.788191 GAACCTGTCGACTGGGCCTG 62.788 65.000 35.63 17.23 39.04 4.85
3621 11497 2.526873 AACCTGTCGACTGGGCCT 60.527 61.111 35.63 21.58 39.04 5.19
3622 11498 2.047179 GAACCTGTCGACTGGGCC 60.047 66.667 35.63 25.33 39.04 5.80
3623 11499 2.047179 GGAACCTGTCGACTGGGC 60.047 66.667 35.63 27.82 39.04 5.36
3624 11500 1.605058 ATCGGAACCTGTCGACTGGG 61.605 60.000 35.63 28.13 38.25 4.45
3626 11502 1.065701 CCTATCGGAACCTGTCGACTG 59.934 57.143 17.92 16.32 38.25 3.51
3627 11503 1.390565 CCTATCGGAACCTGTCGACT 58.609 55.000 17.92 0.00 38.25 4.18
3628 11504 0.248949 GCCTATCGGAACCTGTCGAC 60.249 60.000 9.11 9.11 38.25 4.20
3629 11505 1.721664 CGCCTATCGGAACCTGTCGA 61.722 60.000 0.00 0.00 39.79 4.20
3630 11506 1.299165 CGCCTATCGGAACCTGTCG 60.299 63.158 0.00 0.00 33.78 4.35
3631 11507 1.591863 GCGCCTATCGGAACCTGTC 60.592 63.158 0.00 0.00 38.94 3.51
3633 11509 2.658593 CGCGCCTATCGGAACCTG 60.659 66.667 0.00 0.00 38.94 4.00
3640 11516 1.636340 CTCAAAACCGCGCCTATCG 59.364 57.895 0.00 0.00 42.12 2.92
3641 11517 1.352056 GCTCAAAACCGCGCCTATC 59.648 57.895 0.00 0.00 0.00 2.08
3642 11518 2.112815 GGCTCAAAACCGCGCCTAT 61.113 57.895 0.00 0.00 39.42 2.57
3651 11527 1.838568 GACCCACGACGGCTCAAAAC 61.839 60.000 0.00 0.00 0.00 2.43
3653 11529 2.029964 GACCCACGACGGCTCAAA 59.970 61.111 0.00 0.00 0.00 2.69
3654 11530 3.998672 GGACCCACGACGGCTCAA 61.999 66.667 0.00 0.00 0.00 3.02
3661 11537 3.376078 TACAGCGGGACCCACGAC 61.376 66.667 12.15 0.00 0.00 4.34
3663 11539 3.229156 TTGTACAGCGGGACCCACG 62.229 63.158 12.15 0.00 0.00 4.94
3665 11541 1.534476 TCTTGTACAGCGGGACCCA 60.534 57.895 12.15 0.00 0.00 4.51
3666 11542 1.218316 CTCTTGTACAGCGGGACCC 59.782 63.158 0.00 0.00 0.00 4.46
3667 11543 1.218316 CCTCTTGTACAGCGGGACC 59.782 63.158 0.00 0.00 0.00 4.46
3669 11545 1.112113 GATCCTCTTGTACAGCGGGA 58.888 55.000 12.79 12.79 0.00 5.14
3670 11546 1.067821 GAGATCCTCTTGTACAGCGGG 59.932 57.143 0.00 0.00 0.00 6.13
3671 11547 1.268794 CGAGATCCTCTTGTACAGCGG 60.269 57.143 0.00 0.00 0.00 5.52
3672 11548 1.671328 TCGAGATCCTCTTGTACAGCG 59.329 52.381 0.00 0.00 0.00 5.18
3673 11549 3.490078 CCTTCGAGATCCTCTTGTACAGC 60.490 52.174 0.00 0.00 0.00 4.40
3675 11551 3.444034 CACCTTCGAGATCCTCTTGTACA 59.556 47.826 0.00 0.00 0.00 2.90
3676 11552 3.444388 ACACCTTCGAGATCCTCTTGTAC 59.556 47.826 0.00 0.00 0.00 2.90
3679 11555 2.159170 GGACACCTTCGAGATCCTCTTG 60.159 54.545 0.00 0.00 0.00 3.02
3680 11556 2.104170 GGACACCTTCGAGATCCTCTT 58.896 52.381 0.00 0.00 0.00 2.85
3682 11558 0.382515 CGGACACCTTCGAGATCCTC 59.617 60.000 0.00 0.00 0.00 3.71
3684 11560 0.100861 GTCGGACACCTTCGAGATCC 59.899 60.000 2.62 0.00 36.00 3.36
3685 11561 0.248134 CGTCGGACACCTTCGAGATC 60.248 60.000 9.10 0.00 36.00 2.75
3686 11562 1.654954 CCGTCGGACACCTTCGAGAT 61.655 60.000 4.91 0.00 36.00 2.75
3688 11564 2.178521 CCGTCGGACACCTTCGAG 59.821 66.667 4.91 0.00 36.00 4.04
3689 11565 4.047059 GCCGTCGGACACCTTCGA 62.047 66.667 17.49 0.00 0.00 3.71
3690 11566 4.351938 TGCCGTCGGACACCTTCG 62.352 66.667 17.49 0.00 0.00 3.79
3692 11568 2.915659 TCTGCCGTCGGACACCTT 60.916 61.111 17.49 0.00 0.00 3.50
3693 11569 3.681835 GTCTGCCGTCGGACACCT 61.682 66.667 17.49 0.00 45.69 4.00
3705 11581 4.301027 CTATCCCCGGCGGTCTGC 62.301 72.222 26.32 0.00 45.38 4.26
3706 11582 2.838225 ACTATCCCCGGCGGTCTG 60.838 66.667 26.32 13.06 0.00 3.51
3707 11583 2.838225 CACTATCCCCGGCGGTCT 60.838 66.667 26.32 11.23 0.00 3.85
3716 11592 4.301027 CTCCGCCGCCACTATCCC 62.301 72.222 0.00 0.00 0.00 3.85
3717 11593 2.574955 ATCTCCGCCGCCACTATCC 61.575 63.158 0.00 0.00 0.00 2.59
3718 11594 1.373497 CATCTCCGCCGCCACTATC 60.373 63.158 0.00 0.00 0.00 2.08
3725 11601 3.792053 ATTCGTCCATCTCCGCCGC 62.792 63.158 0.00 0.00 0.00 6.53
3726 11602 1.951130 CATTCGTCCATCTCCGCCG 60.951 63.158 0.00 0.00 0.00 6.46
3728 11604 2.247437 GCCATTCGTCCATCTCCGC 61.247 63.158 0.00 0.00 0.00 5.54
3729 11605 0.598680 GAGCCATTCGTCCATCTCCG 60.599 60.000 0.00 0.00 0.00 4.63
3730 11606 0.250081 GGAGCCATTCGTCCATCTCC 60.250 60.000 0.00 0.00 34.13 3.71
3731 11607 0.598680 CGGAGCCATTCGTCCATCTC 60.599 60.000 0.00 0.00 32.55 2.75
3733 11609 1.595382 CCGGAGCCATTCGTCCATC 60.595 63.158 0.00 0.00 32.55 3.51
3734 11610 2.505982 CCGGAGCCATTCGTCCAT 59.494 61.111 0.00 0.00 32.55 3.41
3735 11611 4.467084 GCCGGAGCCATTCGTCCA 62.467 66.667 5.05 0.00 32.55 4.02
3736 11612 4.467084 TGCCGGAGCCATTCGTCC 62.467 66.667 5.05 0.00 38.69 4.79
3738 11614 3.376935 CTCTGCCGGAGCCATTCGT 62.377 63.158 5.05 0.00 38.69 3.85
3739 11615 2.587194 CTCTGCCGGAGCCATTCG 60.587 66.667 5.05 0.00 38.69 3.34
3751 11627 3.844090 GAGAGCCGGGACCTCTGC 61.844 72.222 14.03 3.79 39.66 4.26
3752 11628 3.522731 CGAGAGCCGGGACCTCTG 61.523 72.222 14.03 4.33 39.66 3.35
3764 11640 0.175302 AGGATCTGTTGCTGCGAGAG 59.825 55.000 7.70 7.70 0.00 3.20
3765 11641 0.174389 GAGGATCTGTTGCTGCGAGA 59.826 55.000 0.00 0.00 0.00 4.04
3766 11642 1.144565 CGAGGATCTGTTGCTGCGAG 61.145 60.000 0.00 0.00 0.00 5.03
3767 11643 1.153765 CGAGGATCTGTTGCTGCGA 60.154 57.895 0.00 0.00 0.00 5.10
3768 11644 2.806856 GCGAGGATCTGTTGCTGCG 61.807 63.158 0.00 0.00 0.00 5.18
3769 11645 2.806856 CGCGAGGATCTGTTGCTGC 61.807 63.158 0.00 0.00 0.00 5.25
3770 11646 0.179137 TACGCGAGGATCTGTTGCTG 60.179 55.000 15.93 0.00 0.00 4.41
3772 11648 1.472276 CGTACGCGAGGATCTGTTGC 61.472 60.000 15.93 0.00 41.33 4.17
3773 11649 0.179171 ACGTACGCGAGGATCTGTTG 60.179 55.000 15.93 0.00 42.00 3.33
3774 11650 0.098376 GACGTACGCGAGGATCTGTT 59.902 55.000 15.93 0.00 42.00 3.16
3775 11651 1.712977 GGACGTACGCGAGGATCTGT 61.713 60.000 15.93 0.24 42.00 3.41
3776 11652 1.009900 GGACGTACGCGAGGATCTG 60.010 63.158 15.93 0.00 42.00 2.90
3777 11653 2.532256 CGGACGTACGCGAGGATCT 61.532 63.158 15.93 0.00 42.00 2.75
3778 11654 2.052414 CGGACGTACGCGAGGATC 60.052 66.667 15.93 3.80 42.00 3.36
3786 11662 1.128147 GGTTAGTTCGCGGACGTACG 61.128 60.000 17.86 17.86 43.49 3.67
3787 11663 0.109781 TGGTTAGTTCGCGGACGTAC 60.110 55.000 12.82 13.76 39.59 3.67
3788 11664 0.168788 CTGGTTAGTTCGCGGACGTA 59.831 55.000 12.82 0.55 41.18 3.57
3790 11666 1.804326 CCTGGTTAGTTCGCGGACG 60.804 63.158 12.82 0.00 42.01 4.79
3792 11668 0.393820 AAACCTGGTTAGTTCGCGGA 59.606 50.000 13.37 0.00 0.00 5.54
3793 11669 2.083167 TAAACCTGGTTAGTTCGCGG 57.917 50.000 13.37 0.00 0.00 6.46
3794 11670 3.319755 TCTTAAACCTGGTTAGTTCGCG 58.680 45.455 13.37 0.00 0.00 5.87
3795 11671 4.992951 TCTTCTTAAACCTGGTTAGTTCGC 59.007 41.667 13.37 0.00 0.00 4.70
3796 11672 6.346359 CGTTCTTCTTAAACCTGGTTAGTTCG 60.346 42.308 13.37 10.73 0.00 3.95
3797 11673 6.703165 TCGTTCTTCTTAAACCTGGTTAGTTC 59.297 38.462 13.37 3.66 0.00 3.01
3798 11674 6.585416 TCGTTCTTCTTAAACCTGGTTAGTT 58.415 36.000 13.37 0.00 0.00 2.24
3799 11675 6.165700 TCGTTCTTCTTAAACCTGGTTAGT 57.834 37.500 13.37 0.20 0.00 2.24
3800 11676 5.638234 CCTCGTTCTTCTTAAACCTGGTTAG 59.362 44.000 13.37 7.76 0.00 2.34
3801 11677 5.511888 CCCTCGTTCTTCTTAAACCTGGTTA 60.512 44.000 13.37 0.00 0.00 2.85
3802 11678 4.386711 CCTCGTTCTTCTTAAACCTGGTT 58.613 43.478 6.18 6.18 0.00 3.67
3804 11680 3.335579 CCCTCGTTCTTCTTAAACCTGG 58.664 50.000 0.00 0.00 0.00 4.45
3808 11684 1.128136 GCGCCCTCGTTCTTCTTAAAC 59.872 52.381 0.00 0.00 38.14 2.01
3809 11685 1.435577 GCGCCCTCGTTCTTCTTAAA 58.564 50.000 0.00 0.00 38.14 1.52
3810 11686 0.734942 CGCGCCCTCGTTCTTCTTAA 60.735 55.000 0.00 0.00 38.14 1.85
3811 11687 1.153901 CGCGCCCTCGTTCTTCTTA 60.154 57.895 0.00 0.00 38.14 2.10
3838 11714 3.679199 GATTTGGGGGAGGGGTGGC 62.679 68.421 0.00 0.00 0.00 5.01
3839 11715 1.935931 AGATTTGGGGGAGGGGTGG 60.936 63.158 0.00 0.00 0.00 4.61
3840 11716 0.921256 AGAGATTTGGGGGAGGGGTG 60.921 60.000 0.00 0.00 0.00 4.61
3841 11717 0.178801 AAGAGATTTGGGGGAGGGGT 60.179 55.000 0.00 0.00 0.00 4.95
3842 11718 0.553333 GAAGAGATTTGGGGGAGGGG 59.447 60.000 0.00 0.00 0.00 4.79
3844 11720 1.601248 AGGAAGAGATTTGGGGGAGG 58.399 55.000 0.00 0.00 0.00 4.30
3845 11721 3.746792 AAAGGAAGAGATTTGGGGGAG 57.253 47.619 0.00 0.00 0.00 4.30
3846 11722 3.142028 ACAAAAGGAAGAGATTTGGGGGA 59.858 43.478 0.00 0.00 38.14 4.81
3847 11723 3.510459 ACAAAAGGAAGAGATTTGGGGG 58.490 45.455 0.00 0.00 38.14 5.40
3848 11724 4.344968 ACAACAAAAGGAAGAGATTTGGGG 59.655 41.667 0.00 0.00 38.14 4.96
3849 11725 5.535753 ACAACAAAAGGAAGAGATTTGGG 57.464 39.130 0.00 0.00 38.14 4.12
3850 11726 5.687285 CGAACAACAAAAGGAAGAGATTTGG 59.313 40.000 0.00 0.00 38.14 3.28
3851 11727 6.494842 TCGAACAACAAAAGGAAGAGATTTG 58.505 36.000 0.00 0.00 39.38 2.32
3853 11729 6.672147 CATCGAACAACAAAAGGAAGAGATT 58.328 36.000 0.00 0.00 0.00 2.40
3854 11730 5.335191 GCATCGAACAACAAAAGGAAGAGAT 60.335 40.000 0.00 0.00 0.00 2.75
3856 11732 4.023707 AGCATCGAACAACAAAAGGAAGAG 60.024 41.667 0.00 0.00 0.00 2.85
3858 11734 3.976942 CAGCATCGAACAACAAAAGGAAG 59.023 43.478 0.00 0.00 0.00 3.46
3861 11737 2.053627 GCAGCATCGAACAACAAAAGG 58.946 47.619 0.00 0.00 0.00 3.11
3862 11738 2.730069 TGCAGCATCGAACAACAAAAG 58.270 42.857 0.00 0.00 0.00 2.27
3863 11739 2.859526 TGCAGCATCGAACAACAAAA 57.140 40.000 0.00 0.00 0.00 2.44
3866 11742 3.745332 CTAATGCAGCATCGAACAACA 57.255 42.857 8.77 0.00 0.00 3.33
3878 11754 2.210116 ACCGGTAAATCGCTAATGCAG 58.790 47.619 4.49 0.00 39.64 4.41
3879 11755 2.206750 GACCGGTAAATCGCTAATGCA 58.793 47.619 7.34 0.00 39.64 3.96
3880 11756 2.033151 GTGACCGGTAAATCGCTAATGC 60.033 50.000 7.34 0.00 0.00 3.56
3881 11757 2.542595 GGTGACCGGTAAATCGCTAATG 59.457 50.000 7.34 0.00 0.00 1.90
3882 11758 2.800629 CGGTGACCGGTAAATCGCTAAT 60.801 50.000 17.80 0.00 44.15 1.73
3884 11760 0.101040 CGGTGACCGGTAAATCGCTA 59.899 55.000 17.80 0.00 44.15 4.26
3885 11761 1.153706 CGGTGACCGGTAAATCGCT 60.154 57.895 17.80 0.00 44.15 4.93
3886 11762 3.391355 CGGTGACCGGTAAATCGC 58.609 61.111 17.80 0.47 44.15 4.58
3896 11772 2.217167 GCGTATCGAAAATACGGTGACC 59.783 50.000 16.34 0.00 45.17 4.02
3939 11815 4.527816 CACAAGAATCATTTTTGGGGAGGA 59.472 41.667 5.68 0.00 0.00 3.71
3940 11816 4.824289 CACAAGAATCATTTTTGGGGAGG 58.176 43.478 5.68 0.00 0.00 4.30
3941 11817 4.020839 AGCACAAGAATCATTTTTGGGGAG 60.021 41.667 5.12 0.00 0.00 4.30
3943 11819 4.276058 AGCACAAGAATCATTTTTGGGG 57.724 40.909 5.12 0.00 0.00 4.96
3945 11821 7.029563 GGTAGTAGCACAAGAATCATTTTTGG 58.970 38.462 5.68 0.00 0.00 3.28
3947 11823 7.759489 TGGTAGTAGCACAAGAATCATTTTT 57.241 32.000 0.00 0.00 0.00 1.94
3948 11824 7.944729 ATGGTAGTAGCACAAGAATCATTTT 57.055 32.000 3.73 0.00 0.00 1.82
3949 11825 7.944729 AATGGTAGTAGCACAAGAATCATTT 57.055 32.000 3.73 0.00 0.00 2.32
3951 11827 6.183360 GCAAATGGTAGTAGCACAAGAATCAT 60.183 38.462 3.73 0.00 0.00 2.45
3952 11828 5.123820 GCAAATGGTAGTAGCACAAGAATCA 59.876 40.000 3.73 0.00 0.00 2.57
3953 11829 5.123820 TGCAAATGGTAGTAGCACAAGAATC 59.876 40.000 3.73 0.00 0.00 2.52
3954 11830 5.009631 TGCAAATGGTAGTAGCACAAGAAT 58.990 37.500 3.73 0.00 0.00 2.40
3955 11831 4.393834 TGCAAATGGTAGTAGCACAAGAA 58.606 39.130 3.73 0.00 0.00 2.52
3957 11833 4.764679 TTGCAAATGGTAGTAGCACAAG 57.235 40.909 3.73 0.00 34.56 3.16
3959 11835 4.331108 TGATTGCAAATGGTAGTAGCACA 58.669 39.130 1.71 0.00 34.56 4.57
3961 11837 4.588899 ACTGATTGCAAATGGTAGTAGCA 58.411 39.130 1.71 4.19 0.00 3.49
3962 11838 5.567138 AACTGATTGCAAATGGTAGTAGC 57.433 39.130 1.71 0.00 0.00 3.58
3965 11841 5.242434 TCGTAACTGATTGCAAATGGTAGT 58.758 37.500 1.71 0.90 0.00 2.73
3966 11842 5.351465 ACTCGTAACTGATTGCAAATGGTAG 59.649 40.000 1.71 0.25 0.00 3.18
3968 11844 4.072131 ACTCGTAACTGATTGCAAATGGT 58.928 39.130 1.71 0.00 0.00 3.55
3969 11845 4.685169 ACTCGTAACTGATTGCAAATGG 57.315 40.909 1.71 0.00 0.00 3.16
3970 11846 6.408858 ACTACTCGTAACTGATTGCAAATG 57.591 37.500 1.71 0.00 0.00 2.32
3971 11847 7.321153 AGTACTACTCGTAACTGATTGCAAAT 58.679 34.615 1.71 0.00 0.00 2.32
3973 11849 6.263516 AGTACTACTCGTAACTGATTGCAA 57.736 37.500 0.00 0.00 0.00 4.08
3997 11873 9.726232 CGGCCTTCATGATTATCAATAATATTG 57.274 33.333 6.65 6.65 33.37 1.90
3999 11875 9.857656 ATCGGCCTTCATGATTATCAATAATAT 57.142 29.630 0.00 0.00 33.37 1.28
4000 11876 9.112725 CATCGGCCTTCATGATTATCAATAATA 57.887 33.333 0.00 0.00 33.37 0.98
4001 11877 7.415989 GCATCGGCCTTCATGATTATCAATAAT 60.416 37.037 0.00 0.00 35.77 1.28
4002 11878 6.127925 GCATCGGCCTTCATGATTATCAATAA 60.128 38.462 0.00 0.00 0.00 1.40
4003 11879 5.355071 GCATCGGCCTTCATGATTATCAATA 59.645 40.000 0.00 0.00 0.00 1.90
4004 11880 4.157289 GCATCGGCCTTCATGATTATCAAT 59.843 41.667 0.00 0.00 0.00 2.57
4005 11881 3.503363 GCATCGGCCTTCATGATTATCAA 59.497 43.478 0.00 0.00 0.00 2.57
4006 11882 3.076621 GCATCGGCCTTCATGATTATCA 58.923 45.455 0.00 0.00 0.00 2.15
4007 11883 3.341823 AGCATCGGCCTTCATGATTATC 58.658 45.455 0.00 0.00 42.56 1.75
4008 11884 3.430042 AGCATCGGCCTTCATGATTAT 57.570 42.857 0.00 0.00 42.56 1.28
4009 11885 2.936919 AGCATCGGCCTTCATGATTA 57.063 45.000 0.00 0.00 42.56 1.75
4012 11888 2.170397 TCTTTAGCATCGGCCTTCATGA 59.830 45.455 0.00 0.00 42.56 3.07
4013 11889 2.547211 CTCTTTAGCATCGGCCTTCATG 59.453 50.000 0.00 1.12 42.56 3.07
4014 11890 2.435805 TCTCTTTAGCATCGGCCTTCAT 59.564 45.455 0.00 0.00 42.56 2.57
4018 11894 1.781786 TCTCTCTTTAGCATCGGCCT 58.218 50.000 0.00 0.00 42.56 5.19
4020 11896 4.946784 TTTTTCTCTCTTTAGCATCGGC 57.053 40.909 0.00 0.00 41.61 5.54
4050 11926 8.961294 TTCATTGTTCCAACTGAATCATTTTT 57.039 26.923 0.00 0.00 34.90 1.94
4051 11927 8.995220 CATTCATTGTTCCAACTGAATCATTTT 58.005 29.630 4.67 0.00 33.90 1.82
4052 11928 8.152246 ACATTCATTGTTCCAACTGAATCATTT 58.848 29.630 4.67 0.00 33.90 2.32
4053 11929 7.673180 ACATTCATTGTTCCAACTGAATCATT 58.327 30.769 4.67 0.00 33.90 2.57
4054 11930 7.235935 ACATTCATTGTTCCAACTGAATCAT 57.764 32.000 4.67 0.00 33.90 2.45
4055 11931 6.653526 ACATTCATTGTTCCAACTGAATCA 57.346 33.333 4.67 0.00 33.90 2.57
4056 11932 6.925165 ACAACATTCATTGTTCCAACTGAATC 59.075 34.615 4.67 0.00 45.55 2.52
4058 11934 6.041511 CACAACATTCATTGTTCCAACTGAA 58.958 36.000 0.00 0.00 45.55 3.02
4059 11935 5.590145 CACAACATTCATTGTTCCAACTGA 58.410 37.500 0.00 0.00 45.55 3.41
4060 11936 4.209703 GCACAACATTCATTGTTCCAACTG 59.790 41.667 0.00 0.00 45.55 3.16
4061 11937 4.099881 AGCACAACATTCATTGTTCCAACT 59.900 37.500 0.00 0.00 45.55 3.16
4062 11938 4.209703 CAGCACAACATTCATTGTTCCAAC 59.790 41.667 0.00 0.00 45.55 3.77
4827 19299 6.550938 TTGGCTTTCATCTTCTCATAGAGA 57.449 37.500 0.00 0.00 36.86 3.10
5113 19585 0.523519 GCCTTGCCAAACAGCTCTAC 59.476 55.000 0.00 0.00 0.00 2.59
5537 20009 0.865769 CTCCAGTGCCGTGTTAACAC 59.134 55.000 25.73 25.73 43.15 3.32
5622 20094 8.072321 ACTCTTCATAGTGCTTCAGAAATCTA 57.928 34.615 0.00 0.00 0.00 1.98
5676 20148 1.696336 AGCTTCTTCAGGCACTCAAGA 59.304 47.619 0.00 0.00 45.78 3.02
6449 21186 6.937392 AGAGTGGAAATTAGTCTGTTACTCC 58.063 40.000 0.00 0.00 39.80 3.85
6725 21970 4.587684 ACTAAACTATGGATACCACGAGGG 59.412 45.833 3.29 0.00 44.81 4.30


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

AutoCloner maintained by Alex Coulton.