Multiple sequence alignment - TraesCS6A01G289500

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


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

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6A01G289500 chr6A 100.000 4156 0 0 1278 5433 521461974 521457819 0.000000e+00 7675
1 TraesCS6A01G289500 chr6A 100.000 1114 0 0 1 1114 521463251 521462138 0.000000e+00 2058
2 TraesCS6A01G289500 chr6A 92.562 121 7 1 4815 4933 359665290 359665170 7.230000e-39 172
3 TraesCS6A01G289500 chr6B 95.453 3475 109 24 1355 4816 567411081 567407643 0.000000e+00 5496
4 TraesCS6A01G289500 chr6B 88.448 1134 49 37 26 1110 567412287 567411187 0.000000e+00 1293
5 TraesCS6A01G289500 chr6B 94.622 502 27 0 4931 5432 567407645 567407144 0.000000e+00 778
6 TraesCS6A01G289500 chr6B 93.548 124 6 1 4812 4933 355180249 355180126 3.340000e-42 183
7 TraesCS6A01G289500 chr6D 95.034 3484 97 24 1355 4816 379563862 379567291 0.000000e+00 5406
8 TraesCS6A01G289500 chr6D 90.503 1053 38 21 95 1111 379562731 379563757 0.000000e+00 1334
9 TraesCS6A01G289500 chr6D 94.024 502 26 1 4931 5432 379567289 379567786 0.000000e+00 758
10 TraesCS6A01G289500 chr7D 84.663 326 48 2 4109 4433 171306130 171306454 1.890000e-84 324
11 TraesCS6A01G289500 chr7D 90.909 121 8 2 4815 4933 11908530 11908411 5.630000e-35 159
12 TraesCS6A01G289500 chr7B 84.356 326 49 2 4109 4433 137787822 137788146 8.780000e-83 318
13 TraesCS6A01G289500 chr7B 92.437 119 7 1 4815 4931 474900201 474900319 9.360000e-38 169
14 TraesCS6A01G289500 chr7B 94.118 68 2 2 4456 4522 537019939 537019873 9.630000e-18 102
15 TraesCS6A01G289500 chr7A 90.083 121 8 1 4813 4933 286535294 286535410 2.620000e-33 154
16 TraesCS6A01G289500 chr5B 89.916 119 10 2 4815 4933 192178401 192178517 9.430000e-33 152
17 TraesCS6A01G289500 chr4D 88.235 119 14 0 4815 4933 493248617 493248735 5.670000e-30 143
18 TraesCS6A01G289500 chr4D 89.076 119 6 6 4815 4933 474562564 474562675 2.040000e-29 141
19 TraesCS6A01G289500 chr1A 87.603 121 4 9 4815 4933 501028910 501028799 4.420000e-26 130


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 TraesCS6A01G289500 chr6A 521457819 521463251 5432 True 4866.500000 7675 100.000 1 5433 2 chr6A.!!$R2 5432
1 TraesCS6A01G289500 chr6B 567407144 567412287 5143 True 2522.333333 5496 92.841 26 5432 3 chr6B.!!$R2 5406
2 TraesCS6A01G289500 chr6D 379562731 379567786 5055 False 2499.333333 5406 93.187 95 5432 3 chr6D.!!$F1 5337

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
151 153 0.178967 TCCCTTGTCCATTTGCTGCA 60.179 50.0 0.00 0.00 0.00 4.41 F
797 840 0.188587 AGGTGAGTGAGGTGAGGTGA 59.811 55.0 0.00 0.00 0.00 4.02 F
1386 1453 0.040067 GTTTGTTCCTCTTGCGCTGG 60.040 55.0 9.73 5.95 0.00 4.85 F
1607 1674 0.632835 AGGCCATGGTTCCATCACAT 59.367 50.0 14.67 0.00 0.00 3.21 F
2333 2406 0.034059 GTGTACTGCTCTGTGGTGCT 59.966 55.0 0.00 0.00 33.63 4.40 F
2349 2422 0.316522 TGCTCTGCTCACTGTCAGAC 59.683 55.0 6.91 0.00 35.66 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1334 1401 0.249398 CCAGTAGTTCTTGGTCCGGG 59.751 60.000 0.00 0.00 0.00 5.73 R
2332 2405 0.109365 CCGTCTGACAGTGAGCAGAG 60.109 60.000 16.83 12.15 41.42 3.35 R
2333 2406 0.537371 TCCGTCTGACAGTGAGCAGA 60.537 55.000 13.77 13.77 38.72 4.26 R
2608 2683 0.882042 GGCTGTAGGACATCGGCATG 60.882 60.000 0.00 0.00 37.65 4.06 R
4249 4328 1.276421 CTGACCACCTCCGACATCTTT 59.724 52.381 0.00 0.00 0.00 2.52 R
4563 4644 5.418840 TGTACAGTTCATCTGAGATGTGCTA 59.581 40.000 20.82 0.00 46.27 3.49 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
40 41 3.821841 CTTGCGTTGTGTTTATCTTCCC 58.178 45.455 0.00 0.00 0.00 3.97
41 42 1.801771 TGCGTTGTGTTTATCTTCCCG 59.198 47.619 0.00 0.00 0.00 5.14
42 43 2.070783 GCGTTGTGTTTATCTTCCCGA 58.929 47.619 0.00 0.00 0.00 5.14
43 44 2.159747 GCGTTGTGTTTATCTTCCCGAC 60.160 50.000 0.00 0.00 0.00 4.79
63 64 2.289072 ACTGTCACTGGGATTTCACTCG 60.289 50.000 0.00 0.00 0.00 4.18
69 70 3.751175 CACTGGGATTTCACTCGCTTTTA 59.249 43.478 0.00 0.00 0.00 1.52
70 71 3.751698 ACTGGGATTTCACTCGCTTTTAC 59.248 43.478 0.00 0.00 0.00 2.01
71 72 3.078837 TGGGATTTCACTCGCTTTTACC 58.921 45.455 0.00 0.00 0.00 2.85
72 73 3.078837 GGGATTTCACTCGCTTTTACCA 58.921 45.455 0.00 0.00 0.00 3.25
73 74 3.119955 GGGATTTCACTCGCTTTTACCAC 60.120 47.826 0.00 0.00 0.00 4.16
74 75 3.119955 GGATTTCACTCGCTTTTACCACC 60.120 47.826 0.00 0.00 0.00 4.61
99 100 6.368243 CACCTAATCTGATCCTCGATTGATTG 59.632 42.308 10.51 0.00 32.46 2.67
100 101 6.268617 ACCTAATCTGATCCTCGATTGATTGA 59.731 38.462 10.51 0.00 32.46 2.57
102 103 7.823310 CCTAATCTGATCCTCGATTGATTGATT 59.177 37.037 19.01 19.01 32.46 2.57
103 104 7.670009 AATCTGATCCTCGATTGATTGATTC 57.330 36.000 14.34 1.44 30.63 2.52
104 105 6.416631 TCTGATCCTCGATTGATTGATTCT 57.583 37.500 0.00 0.00 0.00 2.40
105 106 6.453943 TCTGATCCTCGATTGATTGATTCTC 58.546 40.000 0.00 0.00 0.00 2.87
148 150 1.147817 AGGTTCCCTTGTCCATTTGCT 59.852 47.619 0.00 0.00 0.00 3.91
151 153 0.178967 TCCCTTGTCCATTTGCTGCA 60.179 50.000 0.00 0.00 0.00 4.41
153 155 0.675083 CCTTGTCCATTTGCTGCACA 59.325 50.000 0.00 0.00 0.00 4.57
199 203 2.435059 GCGCTTCCTCCCTGTCAC 60.435 66.667 0.00 0.00 0.00 3.67
301 305 4.785453 CGAGCCCCTTGTCCAGCC 62.785 72.222 0.00 0.00 0.00 4.85
317 333 1.805539 GCCGCGGAATTCTTTTGCC 60.806 57.895 33.48 1.41 0.00 4.52
402 422 1.592400 TACAACCACGCTCTCCTCCG 61.592 60.000 0.00 0.00 0.00 4.63
480 500 1.271102 GATTAGCCTAGGCCACTCGAG 59.729 57.143 30.42 11.84 43.17 4.04
484 504 0.386113 GCCTAGGCCACTCGAGTTAG 59.614 60.000 24.19 14.62 34.56 2.34
540 569 2.561037 GGTTTTCACACAGGCCCCG 61.561 63.158 0.00 0.00 0.00 5.73
543 572 1.701031 TTTTCACACAGGCCCCGAGA 61.701 55.000 0.00 0.00 0.00 4.04
544 573 2.111999 TTTCACACAGGCCCCGAGAG 62.112 60.000 0.00 0.00 0.00 3.20
545 574 2.997315 CACACAGGCCCCGAGAGA 60.997 66.667 0.00 0.00 0.00 3.10
547 576 2.363018 CACAGGCCCCGAGAGAGA 60.363 66.667 0.00 0.00 0.00 3.10
548 577 1.984570 CACAGGCCCCGAGAGAGAA 60.985 63.158 0.00 0.00 0.00 2.87
587 621 5.241728 AGGGTGGAAAAGAAGAATTTTCTCG 59.758 40.000 10.68 0.00 44.80 4.04
593 627 3.990959 AGAAGAATTTTCTCGCCTCCT 57.009 42.857 0.00 0.00 36.28 3.69
594 628 3.867857 AGAAGAATTTTCTCGCCTCCTC 58.132 45.455 0.00 0.00 36.28 3.71
647 682 6.196918 TCCAATATTCTACTCCTACTCCGA 57.803 41.667 0.00 0.00 0.00 4.55
794 837 0.894141 CAGAGGTGAGTGAGGTGAGG 59.106 60.000 0.00 0.00 0.00 3.86
795 838 0.485099 AGAGGTGAGTGAGGTGAGGT 59.515 55.000 0.00 0.00 0.00 3.85
796 839 0.605589 GAGGTGAGTGAGGTGAGGTG 59.394 60.000 0.00 0.00 0.00 4.00
797 840 0.188587 AGGTGAGTGAGGTGAGGTGA 59.811 55.000 0.00 0.00 0.00 4.02
798 841 0.605589 GGTGAGTGAGGTGAGGTGAG 59.394 60.000 0.00 0.00 0.00 3.51
816 859 3.381049 AGGCATCCCTCCCTCCCT 61.381 66.667 0.00 0.00 36.46 4.20
817 860 2.851588 GGCATCCCTCCCTCCCTC 60.852 72.222 0.00 0.00 0.00 4.30
818 861 2.851588 GCATCCCTCCCTCCCTCC 60.852 72.222 0.00 0.00 0.00 4.30
819 862 2.122189 CATCCCTCCCTCCCTCCC 60.122 72.222 0.00 0.00 0.00 4.30
820 863 2.289979 ATCCCTCCCTCCCTCCCT 60.290 66.667 0.00 0.00 0.00 4.20
821 864 2.416923 ATCCCTCCCTCCCTCCCTC 61.417 68.421 0.00 0.00 0.00 4.30
822 865 4.179599 CCCTCCCTCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
823 866 4.179599 CCTCCCTCCCTCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
889 933 1.738099 GCGAGAAGAAAGGCTGCGA 60.738 57.895 0.00 0.00 0.00 5.10
925 969 4.035102 GCCTCACCCTCGCCCTTT 62.035 66.667 0.00 0.00 0.00 3.11
996 1052 2.242196 AGAGAGAGAGAGACCTTCCCTG 59.758 54.545 0.00 0.00 0.00 4.45
997 1053 1.111277 GAGAGAGAGACCTTCCCTGC 58.889 60.000 0.00 0.00 0.00 4.85
1026 1082 3.060615 GTTCCCCTGCTGCTGCTG 61.061 66.667 17.00 15.58 40.48 4.41
1036 1098 3.318006 CTGCTGCTGCTGCTCCTCT 62.318 63.158 27.67 0.00 40.48 3.69
1322 1389 3.381908 TCGCCACCTTGTTTTGTTTGTAT 59.618 39.130 0.00 0.00 0.00 2.29
1323 1390 4.116238 CGCCACCTTGTTTTGTTTGTATT 58.884 39.130 0.00 0.00 0.00 1.89
1324 1391 4.026145 CGCCACCTTGTTTTGTTTGTATTG 60.026 41.667 0.00 0.00 0.00 1.90
1325 1392 4.272261 GCCACCTTGTTTTGTTTGTATTGG 59.728 41.667 0.00 0.00 0.00 3.16
1326 1393 5.665459 CCACCTTGTTTTGTTTGTATTGGA 58.335 37.500 0.00 0.00 0.00 3.53
1327 1394 6.287525 CCACCTTGTTTTGTTTGTATTGGAT 58.712 36.000 0.00 0.00 0.00 3.41
1328 1395 6.765512 CCACCTTGTTTTGTTTGTATTGGATT 59.234 34.615 0.00 0.00 0.00 3.01
1329 1396 7.042119 CCACCTTGTTTTGTTTGTATTGGATTC 60.042 37.037 0.00 0.00 0.00 2.52
1330 1397 7.710475 CACCTTGTTTTGTTTGTATTGGATTCT 59.290 33.333 0.00 0.00 0.00 2.40
1331 1398 8.264347 ACCTTGTTTTGTTTGTATTGGATTCTT 58.736 29.630 0.00 0.00 0.00 2.52
1332 1399 8.764287 CCTTGTTTTGTTTGTATTGGATTCTTC 58.236 33.333 0.00 0.00 0.00 2.87
1333 1400 9.533253 CTTGTTTTGTTTGTATTGGATTCTTCT 57.467 29.630 0.00 0.00 0.00 2.85
1334 1401 9.528018 TTGTTTTGTTTGTATTGGATTCTTCTC 57.472 29.630 0.00 0.00 0.00 2.87
1335 1402 8.141268 TGTTTTGTTTGTATTGGATTCTTCTCC 58.859 33.333 0.00 0.00 35.74 3.71
1336 1403 6.834168 TTGTTTGTATTGGATTCTTCTCCC 57.166 37.500 0.00 0.00 34.12 4.30
1337 1404 4.941263 TGTTTGTATTGGATTCTTCTCCCG 59.059 41.667 0.00 0.00 34.12 5.14
1338 1405 3.838244 TGTATTGGATTCTTCTCCCGG 57.162 47.619 0.00 0.00 34.12 5.73
1339 1406 3.380393 TGTATTGGATTCTTCTCCCGGA 58.620 45.455 0.73 0.00 34.12 5.14
1340 1407 3.134081 TGTATTGGATTCTTCTCCCGGAC 59.866 47.826 0.73 0.00 34.12 4.79
1341 1408 0.909623 TTGGATTCTTCTCCCGGACC 59.090 55.000 0.73 0.00 34.12 4.46
1342 1409 0.252513 TGGATTCTTCTCCCGGACCA 60.253 55.000 0.73 0.00 34.12 4.02
1343 1410 0.909623 GGATTCTTCTCCCGGACCAA 59.090 55.000 0.73 0.00 0.00 3.67
1344 1411 1.134371 GGATTCTTCTCCCGGACCAAG 60.134 57.143 0.73 0.90 0.00 3.61
1345 1412 1.831736 GATTCTTCTCCCGGACCAAGA 59.168 52.381 0.73 3.71 0.00 3.02
1346 1413 1.724545 TTCTTCTCCCGGACCAAGAA 58.275 50.000 0.73 10.23 33.45 2.52
1347 1414 0.974383 TCTTCTCCCGGACCAAGAAC 59.026 55.000 0.73 0.00 0.00 3.01
1348 1415 0.977395 CTTCTCCCGGACCAAGAACT 59.023 55.000 0.73 0.00 0.00 3.01
1349 1416 2.176889 CTTCTCCCGGACCAAGAACTA 58.823 52.381 0.73 0.00 0.00 2.24
1350 1417 1.553706 TCTCCCGGACCAAGAACTAC 58.446 55.000 0.73 0.00 0.00 2.73
1351 1418 1.076677 TCTCCCGGACCAAGAACTACT 59.923 52.381 0.73 0.00 0.00 2.57
1352 1419 1.204941 CTCCCGGACCAAGAACTACTG 59.795 57.143 0.73 0.00 0.00 2.74
1353 1420 0.249398 CCCGGACCAAGAACTACTGG 59.751 60.000 0.73 0.00 0.00 4.00
1383 1450 2.119457 CTTTGTTTGTTCCTCTTGCGC 58.881 47.619 0.00 0.00 0.00 6.09
1384 1451 1.388547 TTGTTTGTTCCTCTTGCGCT 58.611 45.000 9.73 0.00 0.00 5.92
1385 1452 0.662619 TGTTTGTTCCTCTTGCGCTG 59.337 50.000 9.73 1.08 0.00 5.18
1386 1453 0.040067 GTTTGTTCCTCTTGCGCTGG 60.040 55.000 9.73 5.95 0.00 4.85
1387 1454 1.795170 TTTGTTCCTCTTGCGCTGGC 61.795 55.000 9.73 0.00 40.52 4.85
1388 1455 3.793144 GTTCCTCTTGCGCTGGCG 61.793 66.667 9.73 10.80 44.10 5.69
1389 1456 4.002506 TTCCTCTTGCGCTGGCGA 62.003 61.111 19.31 1.28 44.10 5.54
1426 1493 3.582208 ACTGGCAATCTCTCTTCTGTTCT 59.418 43.478 0.00 0.00 0.00 3.01
1427 1494 4.774726 ACTGGCAATCTCTCTTCTGTTCTA 59.225 41.667 0.00 0.00 0.00 2.10
1428 1495 5.078411 TGGCAATCTCTCTTCTGTTCTAC 57.922 43.478 0.00 0.00 0.00 2.59
1544 1611 1.078143 GACCATGGTCACCTGCTCC 60.078 63.158 35.21 9.26 44.02 4.70
1576 1643 1.154197 GTCACCGGCCTGTAAGTTTC 58.846 55.000 0.00 0.00 0.00 2.78
1607 1674 0.632835 AGGCCATGGTTCCATCACAT 59.367 50.000 14.67 0.00 0.00 3.21
1609 1676 2.158564 AGGCCATGGTTCCATCACATAG 60.159 50.000 14.67 0.00 0.00 2.23
1620 1687 6.211515 GTTCCATCACATAGCAATCATTTCC 58.788 40.000 0.00 0.00 0.00 3.13
1629 1696 1.135689 GCAATCATTTCCGTCGCAAGT 60.136 47.619 0.00 0.00 39.48 3.16
1638 1705 1.332375 TCCGTCGCAAGTTTTCCTTTG 59.668 47.619 0.00 0.00 39.48 2.77
1664 1731 4.712337 TCCTAACCCTTTGTCATCTCTCTC 59.288 45.833 0.00 0.00 0.00 3.20
1665 1732 3.990959 AACCCTTTGTCATCTCTCTCC 57.009 47.619 0.00 0.00 0.00 3.71
1666 1733 2.192263 ACCCTTTGTCATCTCTCTCCC 58.808 52.381 0.00 0.00 0.00 4.30
1820 1887 6.073003 CCACTGTATGTCTGTTCCTTTTTCTC 60.073 42.308 0.00 0.00 0.00 2.87
1842 1915 3.266510 TGAGAACACATGGGAGTATGC 57.733 47.619 0.00 0.00 0.00 3.14
1883 1956 7.847096 AGAGATCTTCCTTACCTTTTCTTCTC 58.153 38.462 0.00 0.00 0.00 2.87
1884 1957 7.678171 AGAGATCTTCCTTACCTTTTCTTCTCT 59.322 37.037 0.00 0.00 32.42 3.10
2101 2174 4.077108 GCCAGCCATGAATGAATGATAGA 58.923 43.478 0.00 0.00 0.00 1.98
2121 2194 5.843019 AGAATACTCTGAAGGTTTCCCAA 57.157 39.130 0.00 0.00 0.00 4.12
2132 2205 1.560505 GTTTCCCAATCATGGCCTGT 58.439 50.000 3.32 0.00 46.09 4.00
2133 2206 1.901833 GTTTCCCAATCATGGCCTGTT 59.098 47.619 3.32 0.00 46.09 3.16
2134 2207 1.559368 TTCCCAATCATGGCCTGTTG 58.441 50.000 3.32 3.68 46.09 3.33
2199 2272 0.894642 TGCATTGTGCTGCCTGCTAA 60.895 50.000 12.53 0.00 45.31 3.09
2222 2295 1.680338 GAGGCTCAACAACAACACCT 58.320 50.000 10.25 0.00 0.00 4.00
2299 2372 4.006319 GAGTATCCTCTGCTTGTTTTGCT 58.994 43.478 0.00 0.00 34.69 3.91
2300 2373 3.755378 AGTATCCTCTGCTTGTTTTGCTG 59.245 43.478 0.00 0.00 0.00 4.41
2301 2374 2.057137 TCCTCTGCTTGTTTTGCTGT 57.943 45.000 0.00 0.00 0.00 4.40
2324 2397 4.062293 TGTTATGTGGTTGTGTACTGCTC 58.938 43.478 0.00 0.00 0.00 4.26
2325 2398 4.202315 TGTTATGTGGTTGTGTACTGCTCT 60.202 41.667 0.00 0.00 0.00 4.09
2326 2399 2.238942 TGTGGTTGTGTACTGCTCTG 57.761 50.000 0.00 0.00 0.00 3.35
2327 2400 1.484653 TGTGGTTGTGTACTGCTCTGT 59.515 47.619 0.00 0.00 0.00 3.41
2328 2401 1.867233 GTGGTTGTGTACTGCTCTGTG 59.133 52.381 0.00 0.00 0.00 3.66
2329 2402 1.202639 TGGTTGTGTACTGCTCTGTGG 60.203 52.381 0.00 0.00 0.00 4.17
2330 2403 1.202651 GGTTGTGTACTGCTCTGTGGT 60.203 52.381 0.00 0.00 0.00 4.16
2331 2404 1.867233 GTTGTGTACTGCTCTGTGGTG 59.133 52.381 0.00 0.00 0.00 4.17
2332 2405 0.249868 TGTGTACTGCTCTGTGGTGC 60.250 55.000 0.00 0.00 0.00 5.01
2333 2406 0.034059 GTGTACTGCTCTGTGGTGCT 59.966 55.000 0.00 0.00 33.63 4.40
2349 2422 0.316522 TGCTCTGCTCACTGTCAGAC 59.683 55.000 6.91 0.00 35.66 3.51
2474 2547 8.573035 TGTCATTTTATCTTTGACCAAAGTACC 58.427 33.333 18.57 3.40 45.88 3.34
2533 2608 8.078060 ACTGACCTTATGGGAAAATTAATTGG 57.922 34.615 0.39 0.00 38.76 3.16
2608 2683 5.170748 CAAGATTGTTATGGAACTTTGCCC 58.829 41.667 0.00 0.00 36.45 5.36
2701 2776 8.854614 ATTAATTTCTACCCTGCACTGATATC 57.145 34.615 0.00 0.00 0.00 1.63
2715 2791 9.747293 CTGCACTGATATCATATAGATGGTAAG 57.253 37.037 5.72 0.00 37.57 2.34
2930 3006 5.411781 AGTCTAAAATTACTCACCGAGCTG 58.588 41.667 0.00 0.00 32.04 4.24
2952 3028 4.467082 TGATAATGGCCAGATGCTTGTTTT 59.533 37.500 13.05 0.00 40.92 2.43
2953 3029 2.754946 ATGGCCAGATGCTTGTTTTG 57.245 45.000 13.05 0.00 40.92 2.44
2957 3033 1.796459 GCCAGATGCTTGTTTTGCTTG 59.204 47.619 0.00 0.00 36.87 4.01
3006 3082 4.168760 GTTATTTTGCAGACCAGCACATC 58.831 43.478 0.00 0.00 45.61 3.06
3015 3091 0.885879 ACCAGCACATCGAGAACGTA 59.114 50.000 0.00 0.00 40.69 3.57
3080 3156 2.615447 CTGCAACAGAGAACTTCAGCAA 59.385 45.455 0.00 0.00 32.44 3.91
3364 3440 5.909621 AACACATCAGAATTTCAGGATGG 57.090 39.130 23.49 17.72 41.03 3.51
3597 3673 4.082125 AGAACAAAGAATCCCACATGACC 58.918 43.478 0.00 0.00 0.00 4.02
3608 3684 8.451245 AGAATCCCACATGACCAGATATTAAAT 58.549 33.333 0.00 0.00 0.00 1.40
4040 4119 9.935241 GTAAGATCATTGTCATACTCATATGGT 57.065 33.333 2.13 2.61 39.04 3.55
4285 4364 0.532573 TCAGGATGCTCGAAGGTGAC 59.467 55.000 0.00 0.00 34.76 3.67
4563 4644 2.936919 TGCATTCTGTCAGGAAGTGT 57.063 45.000 0.00 0.00 0.00 3.55
4708 4789 3.565307 TGAGATGCAAGTTTTGGTCCTT 58.435 40.909 0.00 0.00 0.00 3.36
4821 4920 9.503369 AGTATACTTATTTCCTTTGTACTCCCT 57.497 33.333 0.00 0.00 0.00 4.20
4822 4921 9.761504 GTATACTTATTTCCTTTGTACTCCCTC 57.238 37.037 0.00 0.00 0.00 4.30
4823 4922 6.063496 ACTTATTTCCTTTGTACTCCCTCC 57.937 41.667 0.00 0.00 0.00 4.30
4824 4923 3.629142 ATTTCCTTTGTACTCCCTCCG 57.371 47.619 0.00 0.00 0.00 4.63
4825 4924 2.019807 TTCCTTTGTACTCCCTCCGT 57.980 50.000 0.00 0.00 0.00 4.69
4826 4925 2.019807 TCCTTTGTACTCCCTCCGTT 57.980 50.000 0.00 0.00 0.00 4.44
4827 4926 1.897802 TCCTTTGTACTCCCTCCGTTC 59.102 52.381 0.00 0.00 0.00 3.95
4828 4927 1.066358 CCTTTGTACTCCCTCCGTTCC 60.066 57.143 0.00 0.00 0.00 3.62
4829 4928 1.900486 CTTTGTACTCCCTCCGTTCCT 59.100 52.381 0.00 0.00 0.00 3.36
4830 4929 2.905415 TTGTACTCCCTCCGTTCCTA 57.095 50.000 0.00 0.00 0.00 2.94
4831 4930 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
4832 4931 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
4833 4932 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
4834 4933 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
4835 4934 5.461327 TGTACTCCCTCCGTTCCTAAATAT 58.539 41.667 0.00 0.00 0.00 1.28
4836 4935 5.901276 TGTACTCCCTCCGTTCCTAAATATT 59.099 40.000 0.00 0.00 0.00 1.28
4837 4936 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
4838 4937 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
4839 4938 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
4840 4939 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
4841 4940 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
4842 4941 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
4843 4942 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
4844 4943 7.122204 CCCTCCGTTCCTAAATATTTGTCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
4845 4944 8.520351 CCTCCGTTCCTAAATATTTGTCTTTTT 58.480 33.333 11.05 0.00 0.00 1.94
4862 4961 9.965824 TTGTCTTTTTAGAGATTTCAAATGGAC 57.034 29.630 0.00 0.00 0.00 4.02
4863 4962 9.354673 TGTCTTTTTAGAGATTTCAAATGGACT 57.645 29.630 0.00 0.00 0.00 3.85
4879 4978 3.900971 TGGACTACCACATACGGATGTA 58.099 45.455 14.23 0.00 44.82 2.29
4880 4979 4.476297 TGGACTACCACATACGGATGTAT 58.524 43.478 14.23 7.46 44.82 2.29
4881 4980 5.633117 TGGACTACCACATACGGATGTATA 58.367 41.667 14.23 8.27 44.82 1.47
4882 4981 6.250711 TGGACTACCACATACGGATGTATAT 58.749 40.000 14.23 4.37 44.82 0.86
4883 4982 7.404481 TGGACTACCACATACGGATGTATATA 58.596 38.462 14.23 5.36 44.82 0.86
4884 4983 7.555195 TGGACTACCACATACGGATGTATATAG 59.445 40.741 14.23 16.35 44.82 1.31
4885 4984 7.772292 GGACTACCACATACGGATGTATATAGA 59.228 40.741 22.62 5.04 44.82 1.98
4886 4985 8.503458 ACTACCACATACGGATGTATATAGAC 57.497 38.462 22.62 0.00 44.82 2.59
4887 4986 8.327271 ACTACCACATACGGATGTATATAGACT 58.673 37.037 22.62 7.05 44.82 3.24
4888 4987 9.175312 CTACCACATACGGATGTATATAGACTT 57.825 37.037 14.23 0.00 44.82 3.01
4889 4988 7.827701 ACCACATACGGATGTATATAGACTTG 58.172 38.462 14.23 0.00 44.82 3.16
4890 4989 7.450634 ACCACATACGGATGTATATAGACTTGT 59.549 37.037 14.23 0.00 44.82 3.16
4891 4990 8.304596 CCACATACGGATGTATATAGACTTGTT 58.695 37.037 14.23 0.00 44.82 2.83
4892 4991 9.129209 CACATACGGATGTATATAGACTTGTTG 57.871 37.037 14.23 0.00 44.82 3.33
4893 4992 9.074576 ACATACGGATGTATATAGACTTGTTGA 57.925 33.333 12.79 0.00 44.77 3.18
4894 4993 9.908152 CATACGGATGTATATAGACTTGTTGAA 57.092 33.333 0.00 0.00 39.28 2.69
4897 4996 9.477484 ACGGATGTATATAGACTTGTTGAAATC 57.523 33.333 0.00 0.00 0.00 2.17
4898 4997 9.698309 CGGATGTATATAGACTTGTTGAAATCT 57.302 33.333 0.00 0.00 0.00 2.40
4908 5007 8.825667 AGACTTGTTGAAATCTCTAGAAAGAC 57.174 34.615 0.00 0.00 0.00 3.01
4909 5008 8.424918 AGACTTGTTGAAATCTCTAGAAAGACA 58.575 33.333 0.00 0.00 0.00 3.41
4910 5009 8.964476 ACTTGTTGAAATCTCTAGAAAGACAA 57.036 30.769 0.00 0.00 0.00 3.18
4911 5010 9.396022 ACTTGTTGAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
4924 5023 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
4925 5024 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
4926 5025 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
4927 5026 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
4928 5027 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
4929 5028 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
5089 5188 3.514645 ACAGCAGCAAACAAAAGAACAG 58.485 40.909 0.00 0.00 0.00 3.16
5093 5192 3.460103 CAGCAAACAAAAGAACAGGCAT 58.540 40.909 0.00 0.00 0.00 4.40
5161 5260 2.571202 TCCACCAGCATTGTCAGTGATA 59.429 45.455 0.00 0.00 0.00 2.15
5167 5266 3.379057 CAGCATTGTCAGTGATATTGCCA 59.621 43.478 24.42 4.32 33.00 4.92
5172 5271 4.968812 TGTCAGTGATATTGCCATGTTG 57.031 40.909 0.00 0.00 0.00 3.33
5277 5376 2.422127 GCTCGGGTGCAAGCTATTTTAA 59.578 45.455 0.75 0.00 35.60 1.52
5315 5414 4.329462 TTTGTGGATAGGTTTGGTTTGC 57.671 40.909 0.00 0.00 0.00 3.68
5397 5496 0.107361 GTGGGGCACGGCTAAATAGT 60.107 55.000 0.00 0.00 0.00 2.12
5407 5506 1.339291 GGCTAAATAGTAGTCGCCCGT 59.661 52.381 0.74 0.00 0.00 5.28
5412 5511 4.989279 AAATAGTAGTCGCCCGTTAGAA 57.011 40.909 0.00 0.00 0.00 2.10
5421 5520 1.809684 GCCCGTTAGAAAAGAGCAGT 58.190 50.000 0.00 0.00 0.00 4.40
5432 5531 2.440539 AAGAGCAGTACGGTCACTTG 57.559 50.000 15.63 0.00 44.97 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.196808 AGATAAACACAACGCAAGCCG 59.803 47.619 0.00 0.00 45.62 5.52
17 18 2.989422 AGATAAACACAACGCAAGCC 57.011 45.000 0.00 0.00 45.62 4.35
18 19 3.234386 GGAAGATAAACACAACGCAAGC 58.766 45.455 0.00 0.00 45.62 4.01
20 21 2.224549 CGGGAAGATAAACACAACGCAA 59.775 45.455 0.00 0.00 0.00 4.85
21 22 1.801771 CGGGAAGATAAACACAACGCA 59.198 47.619 0.00 0.00 0.00 5.24
22 23 2.070783 TCGGGAAGATAAACACAACGC 58.929 47.619 0.00 0.00 0.00 4.84
23 24 3.122948 CAGTCGGGAAGATAAACACAACG 59.877 47.826 0.00 0.00 0.00 4.10
24 25 4.062991 ACAGTCGGGAAGATAAACACAAC 58.937 43.478 0.00 0.00 0.00 3.32
40 41 2.069273 GTGAAATCCCAGTGACAGTCG 58.931 52.381 0.00 0.00 0.00 4.18
41 42 3.330267 GAGTGAAATCCCAGTGACAGTC 58.670 50.000 0.00 0.00 0.00 3.51
42 43 2.289072 CGAGTGAAATCCCAGTGACAGT 60.289 50.000 0.00 0.00 0.00 3.55
43 44 2.341257 CGAGTGAAATCCCAGTGACAG 58.659 52.381 0.00 0.00 0.00 3.51
63 64 4.585879 TCAGATTAGGTGGTGGTAAAAGC 58.414 43.478 0.00 0.00 0.00 3.51
69 70 3.041946 GAGGATCAGATTAGGTGGTGGT 58.958 50.000 0.00 0.00 33.17 4.16
70 71 2.036475 CGAGGATCAGATTAGGTGGTGG 59.964 54.545 0.00 0.00 33.17 4.61
71 72 2.959030 TCGAGGATCAGATTAGGTGGTG 59.041 50.000 0.00 0.00 33.17 4.17
72 73 3.314307 TCGAGGATCAGATTAGGTGGT 57.686 47.619 0.00 0.00 33.17 4.16
73 74 4.281941 TCAATCGAGGATCAGATTAGGTGG 59.718 45.833 9.11 0.45 36.65 4.61
74 75 5.459536 TCAATCGAGGATCAGATTAGGTG 57.540 43.478 9.11 1.19 36.65 4.00
99 100 4.675190 CATGCATTACGGATGGAGAATC 57.325 45.455 0.00 0.00 39.61 2.52
148 150 1.526686 CCTGCCTGAAGTGTGTGCA 60.527 57.895 0.00 0.00 0.00 4.57
151 153 2.113986 GGCCTGCCTGAAGTGTGT 59.886 61.111 0.00 0.00 0.00 3.72
153 155 4.335647 CCGGCCTGCCTGAAGTGT 62.336 66.667 6.60 0.00 0.00 3.55
292 296 2.033448 AATTCCGCGGCTGGACAA 59.967 55.556 23.51 9.02 37.89 3.18
301 305 4.056097 CGGCAAAAGAATTCCGCG 57.944 55.556 0.00 0.00 35.20 6.46
317 333 1.470098 CACCTTTGAGGGATTCTTGCG 59.530 52.381 0.00 0.00 40.58 4.85
402 422 5.057149 TCCGAGAAAGGCATTAGCTTTATC 58.943 41.667 0.00 0.00 39.36 1.75
480 500 0.610687 AGTGAGAGTGGGCTGCTAAC 59.389 55.000 0.00 0.00 0.00 2.34
484 504 0.536006 AAACAGTGAGAGTGGGCTGC 60.536 55.000 0.00 0.00 32.65 5.25
540 569 2.907236 GGCCTGGCCTTCTCTCTC 59.093 66.667 30.42 0.00 46.69 3.20
587 621 1.680314 CAAGGCAAAGGGAGGAGGC 60.680 63.158 0.00 0.00 0.00 4.70
593 627 1.852157 ATCGGAGCAAGGCAAAGGGA 61.852 55.000 0.00 0.00 0.00 4.20
594 628 0.107214 TATCGGAGCAAGGCAAAGGG 60.107 55.000 0.00 0.00 0.00 3.95
698 741 2.558359 CAAAGGTACAAAAGCAGGGGAG 59.442 50.000 0.00 0.00 0.00 4.30
794 837 1.383803 AGGGAGGGATGCCTCTCAC 60.384 63.158 32.38 21.56 39.62 3.51
795 838 1.074926 GAGGGAGGGATGCCTCTCA 60.075 63.158 32.38 0.00 39.62 3.27
796 839 1.841103 GGAGGGAGGGATGCCTCTC 60.841 68.421 29.82 27.62 37.57 3.20
797 840 2.288643 GGAGGGAGGGATGCCTCT 59.711 66.667 29.82 13.78 37.05 3.69
798 841 2.851588 GGGAGGGAGGGATGCCTC 60.852 72.222 24.37 24.37 36.20 4.70
818 861 4.748798 AGTGGGCAGGGAGGGAGG 62.749 72.222 0.00 0.00 0.00 4.30
819 862 3.406200 CAGTGGGCAGGGAGGGAG 61.406 72.222 0.00 0.00 0.00 4.30
889 933 2.032681 AAGGAAAGGAAGCGCGCT 59.967 55.556 31.32 31.32 0.00 5.92
925 969 0.828762 AACATGGAAGCAGGCAAGCA 60.829 50.000 0.00 0.00 36.85 3.91
997 1053 2.440247 GGGAACCGCCTCCATTGG 60.440 66.667 0.00 0.00 40.86 3.16
1026 1082 1.685355 GGGAGGAGAAGAGGAGCAGC 61.685 65.000 0.00 0.00 0.00 5.25
1036 1098 2.440430 CGCGAGAGGGGAGGAGAA 60.440 66.667 0.00 0.00 40.85 2.87
1277 1342 3.876320 GCTCCAATGCAAGAAAACCAAAA 59.124 39.130 0.00 0.00 0.00 2.44
1294 1359 2.337879 AAACAAGGTGGCGAGCTCCA 62.338 55.000 8.47 0.00 0.00 3.86
1322 1389 0.909623 GGTCCGGGAGAAGAATCCAA 59.090 55.000 0.00 0.00 41.52 3.53
1323 1390 0.252513 TGGTCCGGGAGAAGAATCCA 60.253 55.000 0.00 0.00 41.52 3.41
1324 1391 0.909623 TTGGTCCGGGAGAAGAATCC 59.090 55.000 0.00 0.00 38.76 3.01
1325 1392 1.831736 TCTTGGTCCGGGAGAAGAATC 59.168 52.381 13.58 0.00 0.00 2.52
1326 1393 1.952621 TCTTGGTCCGGGAGAAGAAT 58.047 50.000 13.58 0.00 0.00 2.40
1327 1394 1.346722 GTTCTTGGTCCGGGAGAAGAA 59.653 52.381 20.02 20.02 30.66 2.52
1328 1395 0.974383 GTTCTTGGTCCGGGAGAAGA 59.026 55.000 12.41 12.41 30.66 2.87
1329 1396 0.977395 AGTTCTTGGTCCGGGAGAAG 59.023 55.000 0.00 3.06 30.66 2.85
1330 1397 1.897802 GTAGTTCTTGGTCCGGGAGAA 59.102 52.381 0.00 4.00 0.00 2.87
1331 1398 1.076677 AGTAGTTCTTGGTCCGGGAGA 59.923 52.381 0.00 0.00 0.00 3.71
1332 1399 1.204941 CAGTAGTTCTTGGTCCGGGAG 59.795 57.143 0.00 0.00 0.00 4.30
1333 1400 1.263356 CAGTAGTTCTTGGTCCGGGA 58.737 55.000 0.00 0.00 0.00 5.14
1334 1401 0.249398 CCAGTAGTTCTTGGTCCGGG 59.751 60.000 0.00 0.00 0.00 5.73
1335 1402 0.391263 GCCAGTAGTTCTTGGTCCGG 60.391 60.000 0.00 0.00 0.00 5.14
1336 1403 0.608640 AGCCAGTAGTTCTTGGTCCG 59.391 55.000 0.00 0.00 0.00 4.79
1337 1404 1.903183 AGAGCCAGTAGTTCTTGGTCC 59.097 52.381 0.00 0.00 37.13 4.46
1338 1405 3.259625 AGAAGAGCCAGTAGTTCTTGGTC 59.740 47.826 0.00 0.00 45.12 4.02
1339 1406 3.243724 AGAAGAGCCAGTAGTTCTTGGT 58.756 45.455 0.00 0.00 45.12 3.67
1340 1407 3.971245 AGAAGAGCCAGTAGTTCTTGG 57.029 47.619 0.00 0.00 45.12 3.61
1341 1408 4.020662 AGGAAGAAGAGCCAGTAGTTCTTG 60.021 45.833 1.07 0.00 45.12 3.02
1343 1410 3.785364 AGGAAGAAGAGCCAGTAGTTCT 58.215 45.455 0.00 0.00 37.72 3.01
1344 1411 4.545208 AAGGAAGAAGAGCCAGTAGTTC 57.455 45.455 0.00 0.00 0.00 3.01
1345 1412 4.103311 ACAAAGGAAGAAGAGCCAGTAGTT 59.897 41.667 0.00 0.00 0.00 2.24
1346 1413 3.648545 ACAAAGGAAGAAGAGCCAGTAGT 59.351 43.478 0.00 0.00 0.00 2.73
1347 1414 4.278975 ACAAAGGAAGAAGAGCCAGTAG 57.721 45.455 0.00 0.00 0.00 2.57
1348 1415 4.706842 AACAAAGGAAGAAGAGCCAGTA 57.293 40.909 0.00 0.00 0.00 2.74
1349 1416 3.584733 AACAAAGGAAGAAGAGCCAGT 57.415 42.857 0.00 0.00 0.00 4.00
1350 1417 3.633986 ACAAACAAAGGAAGAAGAGCCAG 59.366 43.478 0.00 0.00 0.00 4.85
1351 1418 3.631250 ACAAACAAAGGAAGAAGAGCCA 58.369 40.909 0.00 0.00 0.00 4.75
1352 1419 4.499865 GGAACAAACAAAGGAAGAAGAGCC 60.500 45.833 0.00 0.00 0.00 4.70
1353 1420 4.339530 AGGAACAAACAAAGGAAGAAGAGC 59.660 41.667 0.00 0.00 0.00 4.09
1383 1450 1.956170 GTCACACACCAGTCGCCAG 60.956 63.158 0.00 0.00 0.00 4.85
1384 1451 2.108157 GTCACACACCAGTCGCCA 59.892 61.111 0.00 0.00 0.00 5.69
1385 1452 2.108157 TGTCACACACCAGTCGCC 59.892 61.111 0.00 0.00 0.00 5.54
1386 1453 3.319904 GTGTCACACACCAGTCGC 58.680 61.111 2.00 0.00 43.05 5.19
1592 1659 4.581409 TGATTGCTATGTGATGGAACCATG 59.419 41.667 11.27 0.00 36.70 3.66
1607 1674 2.017138 TGCGACGGAAATGATTGCTA 57.983 45.000 0.00 0.00 0.00 3.49
1609 1676 1.135689 ACTTGCGACGGAAATGATTGC 60.136 47.619 2.72 0.00 0.00 3.56
1620 1687 1.332375 TCCAAAGGAAAACTTGCGACG 59.668 47.619 0.00 0.00 39.96 5.12
1629 1696 5.348259 AAGGGTTAGGATCCAAAGGAAAA 57.652 39.130 15.82 0.00 34.34 2.29
1638 1705 4.410555 AGAGATGACAAAGGGTTAGGATCC 59.589 45.833 2.48 2.48 0.00 3.36
1664 1731 4.320494 CCTGAGAGAACAAATTGAAACGGG 60.320 45.833 0.00 0.00 0.00 5.28
1665 1732 4.320494 CCCTGAGAGAACAAATTGAAACGG 60.320 45.833 0.00 0.00 0.00 4.44
1666 1733 4.515191 TCCCTGAGAGAACAAATTGAAACG 59.485 41.667 0.00 0.00 0.00 3.60
1820 1887 3.624861 GCATACTCCCATGTGTTCTCAAG 59.375 47.826 0.00 0.00 0.00 3.02
1842 1915 3.146104 TCTCTTCCAGCCCAAAAGAAG 57.854 47.619 0.00 0.00 37.63 2.85
1883 1956 3.864160 GCTGTGAACAAGAGAAGAGGGAG 60.864 52.174 0.00 0.00 0.00 4.30
1884 1957 2.037772 GCTGTGAACAAGAGAAGAGGGA 59.962 50.000 0.00 0.00 0.00 4.20
2034 2107 2.028930 CACTCACAAGTACTGGAGGTCC 60.029 54.545 18.35 0.00 33.25 4.46
2132 2205 2.874014 TCATGGCTCATGTTGGAACAA 58.126 42.857 12.89 0.00 41.51 2.83
2133 2206 2.583024 TCATGGCTCATGTTGGAACA 57.417 45.000 12.89 0.00 41.98 3.18
2134 2207 3.947196 TGTATCATGGCTCATGTTGGAAC 59.053 43.478 12.89 7.55 41.98 3.62
2199 2272 1.064758 TGTTGTTGTTGAGCCTCCTGT 60.065 47.619 0.00 0.00 0.00 4.00
2222 2295 3.561120 AAGGGAATGCGCCGGACAA 62.561 57.895 5.05 0.00 0.00 3.18
2299 2372 4.035792 GCAGTACACAACCACATAACAACA 59.964 41.667 0.00 0.00 0.00 3.33
2300 2373 4.274950 AGCAGTACACAACCACATAACAAC 59.725 41.667 0.00 0.00 0.00 3.32
2301 2374 4.456535 AGCAGTACACAACCACATAACAA 58.543 39.130 0.00 0.00 0.00 2.83
2324 2397 0.949588 CAGTGAGCAGAGCACCACAG 60.950 60.000 13.89 5.41 37.04 3.66
2325 2398 1.070275 CAGTGAGCAGAGCACCACA 59.930 57.895 13.89 0.00 37.04 4.17
2326 2399 0.948141 GACAGTGAGCAGAGCACCAC 60.948 60.000 0.00 6.48 36.95 4.16
2327 2400 1.368950 GACAGTGAGCAGAGCACCA 59.631 57.895 0.00 0.00 36.95 4.17
2328 2401 0.669932 CTGACAGTGAGCAGAGCACC 60.670 60.000 10.83 0.00 36.95 5.01
2329 2402 0.316522 TCTGACAGTGAGCAGAGCAC 59.683 55.000 13.77 0.00 36.31 4.40
2330 2403 0.316522 GTCTGACAGTGAGCAGAGCA 59.683 55.000 16.83 0.00 41.42 4.26
2331 2404 0.732196 CGTCTGACAGTGAGCAGAGC 60.732 60.000 16.83 12.15 41.42 4.09
2332 2405 0.109365 CCGTCTGACAGTGAGCAGAG 60.109 60.000 16.83 12.15 41.42 3.35
2333 2406 0.537371 TCCGTCTGACAGTGAGCAGA 60.537 55.000 13.77 13.77 38.72 4.26
2349 2422 1.407437 CCCTGAGAATTGGGAAGTCCG 60.407 57.143 0.00 0.00 46.15 4.79
2474 2547 9.689633 ATGGTAAACATGTCTCCACTGGAGATG 62.690 44.444 27.30 23.56 45.07 2.90
2513 2588 9.958180 AGAAAACCAATTAATTTTCCCATAAGG 57.042 29.630 16.87 0.00 43.03 2.69
2533 2608 4.261801 TCCCTACTATGCTGCAAGAAAAC 58.738 43.478 6.36 0.00 34.07 2.43
2608 2683 0.882042 GGCTGTAGGACATCGGCATG 60.882 60.000 0.00 0.00 37.65 4.06
2745 2821 1.285280 TTGCTGGCAGTATGGTACCT 58.715 50.000 17.16 1.08 35.86 3.08
2747 2823 3.947834 AGATTTTGCTGGCAGTATGGTAC 59.052 43.478 17.16 3.17 35.86 3.34
2748 2824 4.235079 AGATTTTGCTGGCAGTATGGTA 57.765 40.909 17.16 0.00 35.86 3.25
2749 2825 3.091633 AGATTTTGCTGGCAGTATGGT 57.908 42.857 17.16 0.00 35.86 3.55
2751 2827 5.505324 GCTCTTAGATTTTGCTGGCAGTATG 60.505 44.000 17.16 1.44 40.87 2.39
2752 2828 4.578105 GCTCTTAGATTTTGCTGGCAGTAT 59.422 41.667 17.16 4.90 0.00 2.12
2930 3006 4.660789 AAACAAGCATCTGGCCATTATC 57.339 40.909 5.51 0.00 46.50 1.75
2952 3028 2.375174 AGTAACTGATTCCACCCAAGCA 59.625 45.455 0.00 0.00 0.00 3.91
2953 3029 2.749621 CAGTAACTGATTCCACCCAAGC 59.250 50.000 0.00 0.00 32.44 4.01
2957 3033 2.633488 GCTCAGTAACTGATTCCACCC 58.367 52.381 0.00 0.00 39.92 4.61
3006 3082 4.271776 AGGTTTTCAAGGTTTACGTTCTCG 59.728 41.667 0.00 0.00 43.34 4.04
3080 3156 4.396166 CGCCTTTTCCTATCATGTTCTTGT 59.604 41.667 0.00 0.00 0.00 3.16
3276 3352 2.445682 AGATCAGTAGCCTCTCGGTT 57.554 50.000 0.00 0.00 0.00 4.44
3351 3427 9.541143 TTTTAAGAAACAACCATCCTGAAATTC 57.459 29.630 0.00 0.00 0.00 2.17
3397 3473 2.187958 TGGTGGCTATGTCACTAGCTT 58.812 47.619 0.00 0.00 43.02 3.74
3552 3628 2.200081 AGCTATGCCCAAAGGAGAAGA 58.800 47.619 0.00 0.00 33.47 2.87
3608 3684 8.723311 CCTGTAATTGGTTATGTAAGAACGAAA 58.277 33.333 0.00 0.00 29.93 3.46
3617 3693 5.044772 TGGCTTCCCTGTAATTGGTTATGTA 60.045 40.000 0.00 0.00 0.00 2.29
4040 4119 5.495640 TCATATGCATGAAACCACACTGTA 58.504 37.500 10.16 0.00 38.25 2.74
4249 4328 1.276421 CTGACCACCTCCGACATCTTT 59.724 52.381 0.00 0.00 0.00 2.52
4563 4644 5.418840 TGTACAGTTCATCTGAGATGTGCTA 59.581 40.000 20.82 0.00 46.27 3.49
4708 4789 6.095580 GCAACAATTTTACAAAAGGGGGAAAA 59.904 34.615 0.00 0.00 0.00 2.29
4748 4846 1.321474 CAACATGACACTGCCAGGTT 58.679 50.000 0.00 0.00 38.81 3.50
4798 4897 7.418712 CGGAGGGAGTACAAAGGAAATAAGTAT 60.419 40.741 0.00 0.00 0.00 2.12
4813 4912 6.416631 AATATTTAGGAACGGAGGGAGTAC 57.583 41.667 0.00 0.00 0.00 2.73
4814 4913 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
4815 4914 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
4816 4915 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
4817 4916 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
4818 4917 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
4819 4918 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
4836 4935 9.965824 GTCCATTTGAAATCTCTAAAAAGACAA 57.034 29.630 0.00 0.00 0.00 3.18
4837 4936 9.354673 AGTCCATTTGAAATCTCTAAAAAGACA 57.645 29.630 0.00 0.00 0.00 3.41
4841 4940 9.581289 TGGTAGTCCATTTGAAATCTCTAAAAA 57.419 29.630 0.00 0.00 39.03 1.94
4842 4941 9.010029 GTGGTAGTCCATTTGAAATCTCTAAAA 57.990 33.333 0.00 0.00 46.20 1.52
4843 4942 8.160765 TGTGGTAGTCCATTTGAAATCTCTAAA 58.839 33.333 0.00 0.00 46.20 1.85
4844 4943 7.685481 TGTGGTAGTCCATTTGAAATCTCTAA 58.315 34.615 0.00 0.00 46.20 2.10
4845 4944 7.252612 TGTGGTAGTCCATTTGAAATCTCTA 57.747 36.000 0.00 0.00 46.20 2.43
4846 4945 6.126863 TGTGGTAGTCCATTTGAAATCTCT 57.873 37.500 0.00 0.00 46.20 3.10
4847 4946 7.254455 CGTATGTGGTAGTCCATTTGAAATCTC 60.254 40.741 0.00 0.00 46.20 2.75
4848 4947 6.538742 CGTATGTGGTAGTCCATTTGAAATCT 59.461 38.462 0.00 0.00 46.20 2.40
4849 4948 6.238374 CCGTATGTGGTAGTCCATTTGAAATC 60.238 42.308 0.00 0.00 46.20 2.17
4850 4949 5.588648 CCGTATGTGGTAGTCCATTTGAAAT 59.411 40.000 0.00 0.00 46.20 2.17
4851 4950 4.938832 CCGTATGTGGTAGTCCATTTGAAA 59.061 41.667 0.00 0.00 46.20 2.69
4852 4951 4.223255 TCCGTATGTGGTAGTCCATTTGAA 59.777 41.667 0.00 0.00 46.20 2.69
4853 4952 3.770388 TCCGTATGTGGTAGTCCATTTGA 59.230 43.478 0.00 0.00 46.20 2.69
4854 4953 4.131649 TCCGTATGTGGTAGTCCATTTG 57.868 45.455 0.00 0.00 46.20 2.32
4855 4954 4.163458 ACATCCGTATGTGGTAGTCCATTT 59.837 41.667 0.00 0.00 44.79 2.32
4856 4955 3.709653 ACATCCGTATGTGGTAGTCCATT 59.290 43.478 0.00 0.00 44.79 3.16
4857 4956 3.305720 ACATCCGTATGTGGTAGTCCAT 58.694 45.455 0.00 0.00 44.79 3.41
4858 4957 2.742348 ACATCCGTATGTGGTAGTCCA 58.258 47.619 0.00 0.00 44.79 4.02
4859 4958 6.770746 ATATACATCCGTATGTGGTAGTCC 57.229 41.667 3.56 0.00 45.99 3.85
4860 4959 8.610896 GTCTATATACATCCGTATGTGGTAGTC 58.389 40.741 3.56 0.00 45.99 2.59
4861 4960 8.327271 AGTCTATATACATCCGTATGTGGTAGT 58.673 37.037 3.56 0.00 45.99 2.73
4862 4961 8.734218 AGTCTATATACATCCGTATGTGGTAG 57.266 38.462 3.56 3.93 45.99 3.18
4863 4962 8.953313 CAAGTCTATATACATCCGTATGTGGTA 58.047 37.037 3.56 0.00 45.99 3.25
4864 4963 7.450634 ACAAGTCTATATACATCCGTATGTGGT 59.549 37.037 3.56 0.00 45.99 4.16
4865 4964 7.827701 ACAAGTCTATATACATCCGTATGTGG 58.172 38.462 3.56 0.00 45.99 4.17
4866 4965 9.129209 CAACAAGTCTATATACATCCGTATGTG 57.871 37.037 3.56 0.00 45.99 3.21
4868 4967 9.908152 TTCAACAAGTCTATATACATCCGTATG 57.092 33.333 0.00 0.00 38.79 2.39
4871 4970 9.477484 GATTTCAACAAGTCTATATACATCCGT 57.523 33.333 0.00 0.00 0.00 4.69
4872 4971 9.698309 AGATTTCAACAAGTCTATATACATCCG 57.302 33.333 0.00 0.00 27.06 4.18
4882 4981 9.915629 GTCTTTCTAGAGATTTCAACAAGTCTA 57.084 33.333 0.00 0.00 28.99 2.59
4883 4982 8.424918 TGTCTTTCTAGAGATTTCAACAAGTCT 58.575 33.333 0.00 0.00 31.44 3.24
4884 4983 8.594881 TGTCTTTCTAGAGATTTCAACAAGTC 57.405 34.615 0.00 0.00 0.00 3.01
4885 4984 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
4898 4997 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
4899 4998 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
4900 4999 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
4901 5000 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
4902 5001 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
4903 5002 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
4904 5003 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
4905 5004 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
4906 5005 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
4907 5006 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
4908 5007 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
4909 5008 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
4910 5009 6.614496 AGTTACTCCCTCCGTTCCTAAATATT 59.386 38.462 0.00 0.00 0.00 1.28
4911 5010 6.141790 AGTTACTCCCTCCGTTCCTAAATAT 58.858 40.000 0.00 0.00 0.00 1.28
4912 5011 5.522641 AGTTACTCCCTCCGTTCCTAAATA 58.477 41.667 0.00 0.00 0.00 1.40
4913 5012 4.359996 AGTTACTCCCTCCGTTCCTAAAT 58.640 43.478 0.00 0.00 0.00 1.40
4914 5013 3.782992 AGTTACTCCCTCCGTTCCTAAA 58.217 45.455 0.00 0.00 0.00 1.85
4915 5014 3.463048 AGTTACTCCCTCCGTTCCTAA 57.537 47.619 0.00 0.00 0.00 2.69
4916 5015 3.463048 AAGTTACTCCCTCCGTTCCTA 57.537 47.619 0.00 0.00 0.00 2.94
4917 5016 2.322339 AAGTTACTCCCTCCGTTCCT 57.678 50.000 0.00 0.00 0.00 3.36
4918 5017 5.859205 TTATAAGTTACTCCCTCCGTTCC 57.141 43.478 0.00 0.00 0.00 3.62
4919 5018 7.287512 AGATTATAAGTTACTCCCTCCGTTC 57.712 40.000 0.00 0.00 0.00 3.95
4920 5019 7.039853 GCTAGATTATAAGTTACTCCCTCCGTT 60.040 40.741 0.00 0.00 0.00 4.44
4921 5020 6.433716 GCTAGATTATAAGTTACTCCCTCCGT 59.566 42.308 0.00 0.00 0.00 4.69
4922 5021 6.433404 TGCTAGATTATAAGTTACTCCCTCCG 59.567 42.308 0.00 0.00 0.00 4.63
4923 5022 7.778185 TGCTAGATTATAAGTTACTCCCTCC 57.222 40.000 0.00 0.00 0.00 4.30
4991 5090 6.175471 AGTTATGATGTCAGTTGCATTGAGA 58.825 36.000 1.96 1.89 0.00 3.27
5089 5188 0.388659 TGCTGTGGTTGTTTCATGCC 59.611 50.000 0.00 0.00 0.00 4.40
5093 5192 2.762887 TCCATTTGCTGTGGTTGTTTCA 59.237 40.909 3.19 0.00 37.96 2.69
5161 5260 3.890756 TGTCAAGAAGTCAACATGGCAAT 59.109 39.130 0.00 0.00 0.00 3.56
5167 5266 5.066505 GTGGAGTTTGTCAAGAAGTCAACAT 59.933 40.000 0.00 0.00 32.82 2.71
5172 5271 4.442706 TCTGTGGAGTTTGTCAAGAAGTC 58.557 43.478 0.00 0.00 0.00 3.01
5277 5376 8.716674 ATCCACAAAATTCCAGCTATATGAAT 57.283 30.769 0.00 0.00 0.00 2.57
5315 5414 1.017701 GGAACGGCCTTCTGGTAACG 61.018 60.000 0.00 0.00 42.51 3.18
5397 5496 2.416431 GCTCTTTTCTAACGGGCGACTA 60.416 50.000 0.00 0.00 0.00 2.59
5407 5506 4.280174 AGTGACCGTACTGCTCTTTTCTAA 59.720 41.667 0.00 0.00 0.00 2.10
5412 5511 2.755650 CAAGTGACCGTACTGCTCTTT 58.244 47.619 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.