Multiple sequence alignment - TraesCS4A01G175100

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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 TraesCS4A01G175100 chr4A 100.000 4904 0 0 1 4904 446467938 446472841 0.000000e+00 9057
1 TraesCS4A01G175100 chr4A 98.865 705 7 1 4201 4904 537234299 537233595 0.000000e+00 1256
2 TraesCS4A01G175100 chr4A 98.723 705 8 1 4201 4904 72014896 72015600 0.000000e+00 1251
3 TraesCS4A01G175100 chr4A 96.178 314 11 1 3885 4198 377591787 377592099 3.390000e-141 512
4 TraesCS4A01G175100 chr4A 94.545 330 16 2 3885 4213 537234667 537234339 4.380000e-140 508
5 TraesCS4A01G175100 chr4A 88.496 226 25 1 1001 1225 109423738 109423963 6.250000e-69 272
6 TraesCS4A01G175100 chr4B 92.978 1780 76 20 2124 3884 188194544 188192795 0.000000e+00 2549
7 TraesCS4A01G175100 chr4B 88.657 1578 102 32 2 1543 188198357 188196821 0.000000e+00 1851
8 TraesCS4A01G175100 chr4B 94.065 337 17 3 3879 4213 489025278 489024943 4.380000e-140 508
9 TraesCS4A01G175100 chr4B 80.851 517 62 22 1599 2093 188196801 188196300 5.990000e-99 372
10 TraesCS4A01G175100 chr4D 94.418 1666 78 7 2223 3884 124261825 124260171 0.000000e+00 2547
11 TraesCS4A01G175100 chr4D 88.265 1568 125 26 2 1543 124264129 124262595 0.000000e+00 1821
12 TraesCS4A01G175100 chr4D 88.496 226 25 1 1001 1225 355860561 355860336 6.250000e-69 272
13 TraesCS4A01G175100 chr5B 88.897 1441 155 3 2446 3882 112266203 112264764 0.000000e+00 1770
14 TraesCS4A01G175100 chr5A 88.850 1444 156 3 2443 3882 95567277 95568719 0.000000e+00 1770
15 TraesCS4A01G175100 chr5A 98.723 705 8 1 4201 4904 488265386 488266090 0.000000e+00 1251
16 TraesCS4A01G175100 chr6A 88.448 1463 163 4 2424 3882 571031988 571030528 0.000000e+00 1760
17 TraesCS4A01G175100 chr6A 89.140 221 22 2 1001 1220 571033767 571033548 1.740000e-69 274
18 TraesCS4A01G175100 chr6A 82.121 330 47 7 232 553 608656317 608655992 6.250000e-69 272
19 TraesCS4A01G175100 chr6A 79.620 368 65 6 191 551 374426488 374426124 6.300000e-64 255
20 TraesCS4A01G175100 chr6A 81.731 312 51 5 244 551 497996608 497996299 6.300000e-64 255
21 TraesCS4A01G175100 chr5D 88.611 1440 161 1 2446 3882 103215125 103213686 0.000000e+00 1748
22 TraesCS4A01G175100 chr2B 88.427 1443 164 1 2443 3882 534841113 534842555 0.000000e+00 1736
23 TraesCS4A01G175100 chr2B 97.134 314 9 0 3885 4198 461096750 461097063 9.350000e-147 531
24 TraesCS4A01G175100 chr2B 96.815 314 10 0 3885 4198 39425062 39425375 4.350000e-145 525
25 TraesCS4A01G175100 chr2B 89.140 221 22 2 1001 1220 534839209 534839428 1.740000e-69 274
26 TraesCS4A01G175100 chr6D 87.910 1464 170 4 2424 3882 426116965 426115504 0.000000e+00 1716
27 TraesCS4A01G175100 chr6D 88.235 221 24 2 1001 1220 426118839 426118620 3.760000e-66 263
28 TraesCS4A01G175100 chr6B 88.125 1440 168 1 2446 3882 641410983 641409544 0.000000e+00 1709
29 TraesCS4A01G175100 chr6B 99.149 705 5 1 4201 4904 660355125 660354421 0.000000e+00 1267
30 TraesCS4A01G175100 chr6B 98.582 705 9 1 4201 4904 669342543 669343247 0.000000e+00 1245
31 TraesCS4A01G175100 chr6B 96.178 314 12 0 3885 4198 669342175 669342488 9.410000e-142 514
32 TraesCS4A01G175100 chr6B 89.140 221 22 2 1001 1220 641412893 641412674 1.740000e-69 274
33 TraesCS4A01G175100 chr1A 99.007 705 6 1 4201 4904 449181146 449181850 0.000000e+00 1262
34 TraesCS4A01G175100 chr1A 96.815 314 10 0 3885 4198 58178564 58178877 4.350000e-145 525
35 TraesCS4A01G175100 chr1A 95.860 314 12 1 3885 4198 449180779 449181091 1.580000e-139 507
36 TraesCS4A01G175100 chr7A 98.723 705 8 1 4201 4904 121045597 121046301 0.000000e+00 1251
37 TraesCS4A01G175100 chr7A 98.723 705 8 1 4201 4904 333071107 333071811 0.000000e+00 1251
38 TraesCS4A01G175100 chr7A 80.902 377 61 6 194 561 641454391 641454017 2.230000e-73 287
39 TraesCS4A01G175100 chr1B 98.582 705 9 1 4201 4904 439510648 439509944 0.000000e+00 1245
40 TraesCS4A01G175100 chr1B 95.455 330 13 2 3885 4213 439511016 439510688 4.350000e-145 525
41 TraesCS4A01G175100 chr1B 89.904 208 21 0 1009 1216 512175825 512175618 8.090000e-68 268
42 TraesCS4A01G175100 chr2A 95.152 330 14 2 3885 4213 145437860 145437532 2.020000e-143 520
43 TraesCS4A01G175100 chr2A 81.731 312 51 3 244 551 2742057 2741748 6.300000e-64 255
44 TraesCS4A01G175100 chr1D 82.524 309 48 5 246 550 487025341 487025647 2.910000e-67 267
45 TraesCS4A01G175100 chr7B 80.702 342 56 7 218 551 117633831 117633492 1.750000e-64 257


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 TraesCS4A01G175100 chr4A 446467938 446472841 4903 False 9057.000000 9057 100.000000 1 4904 1 chr4A.!!$F4 4903
1 TraesCS4A01G175100 chr4A 72014896 72015600 704 False 1251.000000 1251 98.723000 4201 4904 1 chr4A.!!$F1 703
2 TraesCS4A01G175100 chr4A 537233595 537234667 1072 True 882.000000 1256 96.705000 3885 4904 2 chr4A.!!$R1 1019
3 TraesCS4A01G175100 chr4B 188192795 188198357 5562 True 1590.666667 2549 87.495333 2 3884 3 chr4B.!!$R2 3882
4 TraesCS4A01G175100 chr4D 124260171 124264129 3958 True 2184.000000 2547 91.341500 2 3884 2 chr4D.!!$R2 3882
5 TraesCS4A01G175100 chr5B 112264764 112266203 1439 True 1770.000000 1770 88.897000 2446 3882 1 chr5B.!!$R1 1436
6 TraesCS4A01G175100 chr5A 95567277 95568719 1442 False 1770.000000 1770 88.850000 2443 3882 1 chr5A.!!$F1 1439
7 TraesCS4A01G175100 chr5A 488265386 488266090 704 False 1251.000000 1251 98.723000 4201 4904 1 chr5A.!!$F2 703
8 TraesCS4A01G175100 chr6A 571030528 571033767 3239 True 1017.000000 1760 88.794000 1001 3882 2 chr6A.!!$R4 2881
9 TraesCS4A01G175100 chr5D 103213686 103215125 1439 True 1748.000000 1748 88.611000 2446 3882 1 chr5D.!!$R1 1436
10 TraesCS4A01G175100 chr2B 534839209 534842555 3346 False 1005.000000 1736 88.783500 1001 3882 2 chr2B.!!$F3 2881
11 TraesCS4A01G175100 chr6D 426115504 426118839 3335 True 989.500000 1716 88.072500 1001 3882 2 chr6D.!!$R1 2881
12 TraesCS4A01G175100 chr6B 660354421 660355125 704 True 1267.000000 1267 99.149000 4201 4904 1 chr6B.!!$R1 703
13 TraesCS4A01G175100 chr6B 641409544 641412893 3349 True 991.500000 1709 88.632500 1001 3882 2 chr6B.!!$R2 2881
14 TraesCS4A01G175100 chr6B 669342175 669343247 1072 False 879.500000 1245 97.380000 3885 4904 2 chr6B.!!$F1 1019
15 TraesCS4A01G175100 chr1A 449180779 449181850 1071 False 884.500000 1262 97.433500 3885 4904 2 chr1A.!!$F2 1019
16 TraesCS4A01G175100 chr7A 121045597 121046301 704 False 1251.000000 1251 98.723000 4201 4904 1 chr7A.!!$F1 703
17 TraesCS4A01G175100 chr7A 333071107 333071811 704 False 1251.000000 1251 98.723000 4201 4904 1 chr7A.!!$F2 703
18 TraesCS4A01G175100 chr1B 439509944 439511016 1072 True 885.000000 1245 97.018500 3885 4904 2 chr1B.!!$R2 1019

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
924 952 0.249398 CGTTTCACCCCCTCTACCAG 59.751 60.000 0.00 0.00 0.00 4.00 F
1604 1875 0.188342 AGGGGAAAACATGGCACTGT 59.812 50.000 0.00 0.00 0.00 3.55 F
2742 5378 1.001764 TGGAGTGATTGCAGGCCTG 60.002 57.895 29.34 29.34 0.00 4.85 F
2871 5507 1.000843 GGTGGCACCTTTGATGTTTCC 59.999 52.381 29.22 0.00 34.73 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2666 5302 0.465460 GGCAGGGACAGTGACAACAA 60.465 55.000 0.00 0.00 0.00 2.83 R
2799 5435 1.202879 CCAACACTGGTGGCCTTCTTA 60.203 52.381 3.32 0.00 38.00 2.10 R
3759 6395 0.112995 TCAGCCTGCCCTTGTCATTT 59.887 50.000 0.00 0.00 0.00 2.32 R
4741 7431 1.667236 CTCATCGTAAGGCATGGCAA 58.333 50.000 22.64 6.11 38.47 4.52 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
167 182 0.256752 TGCATGCTGCTAGGGTCATT 59.743 50.000 20.33 0.00 45.31 2.57
181 196 2.034066 CATTGGAGGGCGTGTGGT 59.966 61.111 0.00 0.00 0.00 4.16
188 203 4.404098 GGGCGTGTGGTGGGGTAG 62.404 72.222 0.00 0.00 0.00 3.18
189 204 3.633116 GGCGTGTGGTGGGGTAGT 61.633 66.667 0.00 0.00 0.00 2.73
192 207 2.055299 CGTGTGGTGGGGTAGTTCT 58.945 57.895 0.00 0.00 0.00 3.01
207 225 0.809385 GTTCTGTCGGATCTCACGGA 59.191 55.000 0.00 0.00 0.00 4.69
212 230 1.822371 TGTCGGATCTCACGGAATTCA 59.178 47.619 7.93 0.00 0.00 2.57
213 231 2.232696 TGTCGGATCTCACGGAATTCAA 59.767 45.455 7.93 0.00 0.00 2.69
215 233 3.246226 GTCGGATCTCACGGAATTCAATG 59.754 47.826 7.93 4.86 0.00 2.82
216 234 2.032549 CGGATCTCACGGAATTCAATGC 60.033 50.000 7.93 0.00 0.00 3.56
250 268 4.690184 GGTGGATCCGTTAATTCGTTTT 57.310 40.909 7.39 0.00 0.00 2.43
251 269 4.655027 GGTGGATCCGTTAATTCGTTTTC 58.345 43.478 7.39 0.00 0.00 2.29
252 270 4.154556 GGTGGATCCGTTAATTCGTTTTCA 59.845 41.667 7.39 0.00 0.00 2.69
323 345 1.401318 ATGGTTGCTGCTTTGGTGCA 61.401 50.000 0.00 0.00 41.05 4.57
339 361 1.248785 TGCACTGGTCCTACGGAGTC 61.249 60.000 0.00 0.00 43.93 3.36
346 368 1.677052 GGTCCTACGGAGTCTTAGCAG 59.323 57.143 0.00 0.00 43.93 4.24
365 387 0.873054 GGACGACTTCTCGACTGTCA 59.127 55.000 8.73 0.00 43.06 3.58
408 430 3.017581 AGCAAGGGAGGGCCGATT 61.018 61.111 0.00 0.00 33.83 3.34
413 435 4.256180 GGGAGGGCCGATTGCGAT 62.256 66.667 0.00 0.00 42.61 4.58
449 471 1.893137 TCCAGTGCTTGTAGTCATCGT 59.107 47.619 0.00 0.00 0.00 3.73
466 488 2.283388 TTAGGTGGTCCGCGGACT 60.283 61.111 46.25 33.48 44.04 3.85
469 491 3.998672 GGTGGTCCGCGGACTTGA 61.999 66.667 46.25 31.76 44.04 3.02
475 497 1.472728 GGTCCGCGGACTTGATTGTAT 60.473 52.381 46.25 0.00 44.04 2.29
506 528 7.786046 TTACCTCTGGTGTTCTTTATACTGA 57.214 36.000 0.00 0.00 36.19 3.41
510 532 7.399191 ACCTCTGGTGTTCTTTATACTGACATA 59.601 37.037 0.00 0.00 32.98 2.29
587 611 2.362077 GCTCTCTTCAAAAAGCCAACCA 59.638 45.455 0.00 0.00 32.18 3.67
593 617 4.339247 TCTTCAAAAAGCCAACCAAGAGAG 59.661 41.667 0.00 0.00 32.18 3.20
601 625 2.744494 GCCAACCAAGAGAGATAGCCAG 60.744 54.545 0.00 0.00 0.00 4.85
602 626 2.768527 CCAACCAAGAGAGATAGCCAGA 59.231 50.000 0.00 0.00 0.00 3.86
768 795 6.254281 AGGAAAGAAACACGACCAATATTG 57.746 37.500 8.58 8.58 0.00 1.90
911 939 4.367023 CCGTCCGCCTCCGTTTCA 62.367 66.667 0.00 0.00 0.00 2.69
920 948 0.616679 CCTCCGTTTCACCCCCTCTA 60.617 60.000 0.00 0.00 0.00 2.43
924 952 0.249398 CGTTTCACCCCCTCTACCAG 59.751 60.000 0.00 0.00 0.00 4.00
979 1010 3.116531 GCACCACCGCCGTACTTC 61.117 66.667 0.00 0.00 0.00 3.01
1251 1295 6.425721 CCACCTTTCGTCATTACTCTTGTTTA 59.574 38.462 0.00 0.00 0.00 2.01
1253 1297 8.169268 CACCTTTCGTCATTACTCTTGTTTATC 58.831 37.037 0.00 0.00 0.00 1.75
1272 1316 3.627732 TCCGCTTTAGATCTGTCGATC 57.372 47.619 5.18 0.00 45.18 3.69
1289 1333 1.395826 ATCGGGGCTCTGTCTAGTGC 61.396 60.000 0.00 0.00 41.49 4.40
1312 1356 2.677902 CGGATTGAGCTTAGTTCAGCCA 60.678 50.000 15.78 0.00 41.12 4.75
1313 1357 2.680339 GGATTGAGCTTAGTTCAGCCAC 59.320 50.000 12.51 2.11 41.12 5.01
1342 1386 5.980698 TCGATTTTGTACGGTTTGTTACA 57.019 34.783 0.00 0.00 0.00 2.41
1354 1418 4.973663 CGGTTTGTTACAGTTTAGCCTTTG 59.026 41.667 0.00 0.00 0.00 2.77
1355 1419 4.743151 GGTTTGTTACAGTTTAGCCTTTGC 59.257 41.667 0.00 0.00 37.95 3.68
1359 1423 6.885952 TGTTACAGTTTAGCCTTTGCAATA 57.114 33.333 0.00 0.00 41.13 1.90
1375 1439 2.223112 GCAATATGTTCTGGTGTCAGCG 60.223 50.000 0.00 0.00 40.69 5.18
1397 1461 3.163594 CGTGCTTCGGTTGATTTGATTC 58.836 45.455 0.00 0.00 35.71 2.52
1430 1504 1.377202 CCTGCGCCAGGTTACATGT 60.377 57.895 4.18 2.69 45.82 3.21
1431 1505 1.647545 CCTGCGCCAGGTTACATGTG 61.648 60.000 9.11 0.00 45.82 3.21
1432 1506 1.647545 CTGCGCCAGGTTACATGTGG 61.648 60.000 9.11 1.21 0.00 4.17
1458 1532 5.475564 TGGTTGCTTAGTTTAATCTGTTCCC 59.524 40.000 0.00 0.00 0.00 3.97
1474 1696 1.624336 TCCCGCCGTAGCTGTATTAT 58.376 50.000 0.00 0.00 36.60 1.28
1475 1697 2.794103 TCCCGCCGTAGCTGTATTATA 58.206 47.619 0.00 0.00 36.60 0.98
1477 1699 4.525996 TCCCGCCGTAGCTGTATTATATA 58.474 43.478 0.00 0.00 36.60 0.86
1481 1703 7.040892 TCCCGCCGTAGCTGTATTATATAATAG 60.041 40.741 14.26 7.88 36.60 1.73
1535 1757 1.340502 TGGATACTTTTGCATGCGGGA 60.341 47.619 14.09 0.00 37.61 5.14
1550 1772 0.804989 CGGGAGCTTGGTTCAATCAC 59.195 55.000 0.00 0.00 0.00 3.06
1556 1778 0.950836 CTTGGTTCAATCACGGTGCA 59.049 50.000 2.51 0.00 0.00 4.57
1568 1839 6.364706 TCAATCACGGTGCAATTATTTGTTTC 59.635 34.615 2.51 0.00 35.17 2.78
1569 1840 5.446143 TCACGGTGCAATTATTTGTTTCT 57.554 34.783 2.51 0.00 35.17 2.52
1570 1841 5.218885 TCACGGTGCAATTATTTGTTTCTG 58.781 37.500 2.51 0.00 35.17 3.02
1572 1843 3.367630 CGGTGCAATTATTTGTTTCTGCC 59.632 43.478 0.00 0.00 35.17 4.85
1573 1844 3.684305 GGTGCAATTATTTGTTTCTGCCC 59.316 43.478 0.00 0.00 35.17 5.36
1575 1846 5.337169 GGTGCAATTATTTGTTTCTGCCCTA 60.337 40.000 0.00 0.00 35.17 3.53
1577 1848 6.476706 GTGCAATTATTTGTTTCTGCCCTATC 59.523 38.462 0.00 0.00 35.17 2.08
1578 1849 5.985530 GCAATTATTTGTTTCTGCCCTATCC 59.014 40.000 0.00 0.00 35.17 2.59
1579 1850 6.515832 CAATTATTTGTTTCTGCCCTATCCC 58.484 40.000 0.00 0.00 0.00 3.85
1580 1851 5.466127 TTATTTGTTTCTGCCCTATCCCT 57.534 39.130 0.00 0.00 0.00 4.20
1581 1852 3.366052 TTTGTTTCTGCCCTATCCCTC 57.634 47.619 0.00 0.00 0.00 4.30
1582 1853 2.270434 TGTTTCTGCCCTATCCCTCT 57.730 50.000 0.00 0.00 0.00 3.69
1583 1854 3.414759 TGTTTCTGCCCTATCCCTCTA 57.585 47.619 0.00 0.00 0.00 2.43
1584 1855 3.941629 TGTTTCTGCCCTATCCCTCTAT 58.058 45.455 0.00 0.00 0.00 1.98
1585 1856 5.087923 TGTTTCTGCCCTATCCCTCTATA 57.912 43.478 0.00 0.00 0.00 1.31
1586 1857 5.087323 TGTTTCTGCCCTATCCCTCTATAG 58.913 45.833 0.00 0.00 0.00 1.31
1587 1858 4.338795 TTCTGCCCTATCCCTCTATAGG 57.661 50.000 0.00 3.37 45.61 2.57
1601 1872 4.137543 CTCTATAGGGGAAAACATGGCAC 58.862 47.826 0.00 0.00 0.00 5.01
1604 1875 0.188342 AGGGGAAAACATGGCACTGT 59.812 50.000 0.00 0.00 0.00 3.55
1620 1891 3.315191 GCACTGTCAAAGCCAGTAAGAAA 59.685 43.478 0.00 0.00 41.10 2.52
1621 1892 4.202010 GCACTGTCAAAGCCAGTAAGAAAA 60.202 41.667 0.00 0.00 41.10 2.29
1622 1893 5.678616 GCACTGTCAAAGCCAGTAAGAAAAA 60.679 40.000 0.00 0.00 41.10 1.94
1646 1917 5.419155 AGAATCGAAAGTAGATGTGGACTCA 59.581 40.000 0.00 0.00 0.00 3.41
1732 2138 3.503363 TGTGCCATCTAGCTTGAACAAAG 59.497 43.478 0.99 0.00 39.07 2.77
1749 2580 4.084287 ACAAAGTGGATGATGCATCACTT 58.916 39.130 30.92 24.70 42.13 3.16
1753 2584 7.557358 ACAAAGTGGATGATGCATCACTTAATA 59.443 33.333 30.92 11.87 42.13 0.98
1754 2585 8.573885 CAAAGTGGATGATGCATCACTTAATAT 58.426 33.333 30.92 13.89 42.13 1.28
1788 2619 2.684001 TGGAATACCAAGCACTACCG 57.316 50.000 0.00 0.00 43.91 4.02
1795 2626 2.453521 ACCAAGCACTACCGTCTGATA 58.546 47.619 0.00 0.00 0.00 2.15
1797 2628 4.212716 ACCAAGCACTACCGTCTGATATA 58.787 43.478 0.00 0.00 0.00 0.86
1899 2740 7.011482 GGAGTTAGCACCTGTGATGTAAATTAG 59.989 40.741 0.51 0.00 0.00 1.73
1908 2749 6.127366 CCTGTGATGTAAATTAGCCCATTTGT 60.127 38.462 1.72 0.00 0.00 2.83
1910 2751 7.319646 TGTGATGTAAATTAGCCCATTTGTTC 58.680 34.615 1.72 0.00 0.00 3.18
1953 2812 4.853924 AAATCACTGGTTGCTAACTTGG 57.146 40.909 0.00 0.00 0.00 3.61
1955 2814 4.634012 ATCACTGGTTGCTAACTTGGTA 57.366 40.909 0.00 0.00 0.00 3.25
1959 2818 5.830991 TCACTGGTTGCTAACTTGGTAAAAT 59.169 36.000 0.00 0.00 0.00 1.82
1966 2825 8.354426 GGTTGCTAACTTGGTAAAATTCTGTAA 58.646 33.333 0.00 0.00 0.00 2.41
1967 2826 9.908152 GTTGCTAACTTGGTAAAATTCTGTAAT 57.092 29.630 0.00 0.00 0.00 1.89
1968 2827 9.906660 TTGCTAACTTGGTAAAATTCTGTAATG 57.093 29.630 0.00 0.00 0.00 1.90
1969 2828 9.073475 TGCTAACTTGGTAAAATTCTGTAATGT 57.927 29.630 0.00 0.00 0.00 2.71
2034 2902 2.509166 TCTGGTATCTGACACGGTCT 57.491 50.000 5.77 0.00 33.15 3.85
2051 2920 3.676172 CGGTCTTATTTTGTGTCTACGCA 59.324 43.478 0.00 0.00 34.11 5.24
2053 2922 5.163893 CGGTCTTATTTTGTGTCTACGCATT 60.164 40.000 0.00 0.00 36.14 3.56
2057 2926 7.589954 GTCTTATTTTGTGTCTACGCATTTTGT 59.410 33.333 0.00 0.00 36.14 2.83
2068 2937 6.578545 GTCTACGCATTTTGTAATATGGCATG 59.421 38.462 10.98 0.00 0.00 4.06
2082 2954 3.306472 TGGCATGTAATAAGGGGGAAC 57.694 47.619 0.00 0.00 0.00 3.62
2093 2966 2.671963 GGGGAACGGACCTTGTGC 60.672 66.667 0.00 0.00 0.00 4.57
2167 4768 8.689061 AGCATCTTGATTATTGACTTTTATGCA 58.311 29.630 0.00 0.00 37.79 3.96
2188 4800 5.861251 TGCATCAATGTTTGTTATTCCGTTC 59.139 36.000 0.00 0.00 0.00 3.95
2191 4803 7.410728 GCATCAATGTTTGTTATTCCGTTCAAG 60.411 37.037 0.00 0.00 0.00 3.02
2193 4805 4.839668 TGTTTGTTATTCCGTTCAAGGG 57.160 40.909 0.00 0.00 0.00 3.95
2209 4821 2.453242 GGGTCCACCTTGTCTCTGT 58.547 57.895 0.00 0.00 35.85 3.41
2210 4822 1.640917 GGGTCCACCTTGTCTCTGTA 58.359 55.000 0.00 0.00 35.85 2.74
2211 4823 1.275573 GGGTCCACCTTGTCTCTGTAC 59.724 57.143 0.00 0.00 35.85 2.90
2212 4824 2.249139 GGTCCACCTTGTCTCTGTACT 58.751 52.381 0.00 0.00 0.00 2.73
2213 4825 3.428532 GGTCCACCTTGTCTCTGTACTA 58.571 50.000 0.00 0.00 0.00 1.82
2214 4826 3.444388 GGTCCACCTTGTCTCTGTACTAG 59.556 52.174 0.00 0.00 0.00 2.57
2215 4827 3.444388 GTCCACCTTGTCTCTGTACTAGG 59.556 52.174 0.00 10.11 44.80 3.02
2216 4828 2.166664 CCACCTTGTCTCTGTACTAGGC 59.833 54.545 11.08 0.00 43.59 3.93
2217 4829 2.826128 CACCTTGTCTCTGTACTAGGCA 59.174 50.000 11.08 0.00 43.59 4.75
2218 4830 3.258372 CACCTTGTCTCTGTACTAGGCAA 59.742 47.826 13.02 13.02 43.59 4.52
2220 4832 4.792521 CTTGTCTCTGTACTAGGCAAGT 57.207 45.455 23.75 0.00 46.68 3.16
2221 4833 5.140747 CTTGTCTCTGTACTAGGCAAGTT 57.859 43.478 23.75 0.00 46.68 2.66
2230 4842 6.152323 TCTGTACTAGGCAAGTTTACCAGTAG 59.848 42.308 0.00 0.00 39.80 2.57
2234 4846 5.720041 ACTAGGCAAGTTTACCAGTAGATCA 59.280 40.000 0.00 0.00 33.35 2.92
2238 4850 5.758784 GGCAAGTTTACCAGTAGATCATACC 59.241 44.000 0.00 0.00 0.00 2.73
2255 4867 5.968254 TCATACCGTGCTTTGTTCTGTATA 58.032 37.500 0.00 0.00 0.00 1.47
2256 4868 6.399743 TCATACCGTGCTTTGTTCTGTATAA 58.600 36.000 0.00 0.00 0.00 0.98
2258 4870 3.435671 ACCGTGCTTTGTTCTGTATAAGC 59.564 43.478 0.00 0.00 42.46 3.09
2289 4901 8.749499 GCATGTTTTCTGATGATTAATTACTGC 58.251 33.333 0.00 0.00 0.00 4.40
2328 4959 8.690203 TCCTGAACTGATTTCAAGTTTGATTA 57.310 30.769 0.00 0.00 43.90 1.75
2422 5053 9.787532 ATTGTGATAAATTGGTATTTCAAGTCG 57.212 29.630 0.00 0.00 35.61 4.18
2432 5065 4.572389 GGTATTTCAAGTCGCTGACATGAT 59.428 41.667 14.17 6.44 39.44 2.45
2433 5066 5.753438 GGTATTTCAAGTCGCTGACATGATA 59.247 40.000 14.17 11.22 39.44 2.15
2434 5067 6.257849 GGTATTTCAAGTCGCTGACATGATAA 59.742 38.462 14.17 12.01 39.44 1.75
2444 5077 4.034858 CGCTGACATGATAATTTGCTCTGT 59.965 41.667 0.00 0.00 0.00 3.41
2508 5141 2.369860 TGTCCAGAGTGACATGAAGCTT 59.630 45.455 0.00 0.00 40.22 3.74
2534 5167 2.553904 CCTTCAAGGTCATTGCTGGACT 60.554 50.000 0.00 0.00 38.89 3.85
2666 5302 1.180029 GGCAGCACCATCAAGAATGT 58.820 50.000 0.00 0.00 38.86 2.71
2700 5336 2.503356 CCCTGCCTACTTCAATGACTCT 59.497 50.000 0.00 0.00 0.00 3.24
2742 5378 1.001764 TGGAGTGATTGCAGGCCTG 60.002 57.895 29.34 29.34 0.00 4.85
2757 5393 1.067516 GGCCTGAATGTTATGCGCATT 59.932 47.619 30.42 11.14 39.04 3.56
2772 5408 1.665679 CGCATTATCAACGAGCCAACT 59.334 47.619 0.00 0.00 0.00 3.16
2799 5435 4.518211 GCTGCTATTGCTTATGGTCTTGAT 59.482 41.667 0.00 0.00 40.48 2.57
2868 5504 1.039856 GTGGTGGCACCTTTGATGTT 58.960 50.000 34.69 0.00 39.58 2.71
2871 5507 1.000843 GGTGGCACCTTTGATGTTTCC 59.999 52.381 29.22 0.00 34.73 3.13
2874 5510 1.546029 GGCACCTTTGATGTTTCCCTC 59.454 52.381 0.00 0.00 0.00 4.30
2955 5591 2.503765 TGGTGAGGACTTTGACAACAGA 59.496 45.455 0.00 0.00 0.00 3.41
3006 5642 7.922382 TCAAGAGGAAGAACAAGAAGGATATT 58.078 34.615 0.00 0.00 0.00 1.28
3322 5958 3.416156 GACTTCTTCAATGGCAAGGAGT 58.584 45.455 0.00 0.00 41.68 3.85
3402 6038 1.661463 TCTTGAGTGGAGAGGGCAAT 58.339 50.000 0.00 0.00 0.00 3.56
3542 6178 1.903183 GCAGGTCTTCTCCACCTACTT 59.097 52.381 0.00 0.00 42.85 2.24
3714 6350 2.029838 ATGGCATTCTGAACGTCTCC 57.970 50.000 0.00 0.00 0.00 3.71
3759 6395 4.999311 CAGAAGAACAAGATCACCATCACA 59.001 41.667 0.00 0.00 0.00 3.58
3873 6509 2.519013 GTGGAGTCAAAGAATGCCCTT 58.481 47.619 0.00 0.00 0.00 3.95
3913 6549 2.306805 TCACAGATTTGACCTGAGGCAT 59.693 45.455 0.00 0.00 35.69 4.40
4071 6707 2.281761 CTTGTCCAGTTGCGGCCT 60.282 61.111 0.00 0.00 0.00 5.19
4164 6800 1.738099 CAGTGACTTAAGCGCGGCT 60.738 57.895 8.83 2.05 42.56 5.52
4198 6835 2.500910 CCAGGCAGTTCTTCATCTCTCT 59.499 50.000 0.00 0.00 0.00 3.10
4414 7103 9.962759 CCGTAGTGTTATTTATTAGTTCACAAC 57.037 33.333 0.00 0.00 0.00 3.32
4555 7245 4.919774 TGTAAGGATGGTTTGGCTTCTA 57.080 40.909 0.00 0.00 0.00 2.10
4735 7425 1.411612 GATTCGGTATCACGGGGTCTT 59.588 52.381 0.00 0.00 33.21 3.01
4741 7431 1.553704 GTATCACGGGGTCTTTGGTCT 59.446 52.381 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.097614 AGCGTAGGTTTCACCATACTCT 58.902 45.455 0.00 0.00 41.95 3.24
6 7 2.937873 GCCATTAGCGTAGGTTTCACCA 60.938 50.000 0.00 0.00 41.95 4.17
13 14 2.024590 GACCGGCCATTAGCGTAGGT 62.025 60.000 0.00 0.00 43.96 3.08
41 42 4.087892 CTCCCGGGTCAGGTGCAG 62.088 72.222 22.86 3.33 0.00 4.41
42 43 4.631740 TCTCCCGGGTCAGGTGCA 62.632 66.667 22.86 0.00 0.00 4.57
43 44 3.316573 CTTCTCCCGGGTCAGGTGC 62.317 68.421 22.86 0.00 0.00 5.01
44 45 1.481056 AACTTCTCCCGGGTCAGGTG 61.481 60.000 22.86 10.19 0.00 4.00
45 46 0.115745 TAACTTCTCCCGGGTCAGGT 59.884 55.000 22.86 15.80 0.00 4.00
46 47 1.066358 GTTAACTTCTCCCGGGTCAGG 60.066 57.143 22.86 11.20 0.00 3.86
47 48 1.403780 CGTTAACTTCTCCCGGGTCAG 60.404 57.143 22.86 16.90 0.00 3.51
48 49 0.604578 CGTTAACTTCTCCCGGGTCA 59.395 55.000 22.86 4.99 0.00 4.02
49 50 0.605083 ACGTTAACTTCTCCCGGGTC 59.395 55.000 22.86 0.34 0.00 4.46
50 51 0.605083 GACGTTAACTTCTCCCGGGT 59.395 55.000 22.86 1.40 0.00 5.28
105 120 3.269486 GCAACATGCATGAGAGCTATG 57.731 47.619 32.75 17.79 44.26 2.23
132 147 3.125829 GCATGCACGAGAATCTTCAAAGA 59.874 43.478 14.21 0.00 39.78 2.52
133 148 3.126514 AGCATGCACGAGAATCTTCAAAG 59.873 43.478 21.98 0.00 0.00 2.77
137 152 2.733820 CAGCATGCACGAGAATCTTC 57.266 50.000 21.98 0.00 0.00 2.87
181 196 1.006758 AGATCCGACAGAACTACCCCA 59.993 52.381 0.00 0.00 0.00 4.96
184 199 2.223294 CGTGAGATCCGACAGAACTACC 60.223 54.545 0.00 0.00 0.00 3.18
188 203 0.809385 TCCGTGAGATCCGACAGAAC 59.191 55.000 0.00 0.00 0.00 3.01
189 204 1.541379 TTCCGTGAGATCCGACAGAA 58.459 50.000 0.00 0.00 0.00 3.02
192 207 1.822371 TGAATTCCGTGAGATCCGACA 59.178 47.619 2.27 0.00 0.00 4.35
207 225 3.609175 CGAAGACCAACACGCATTGAATT 60.609 43.478 0.95 0.00 0.00 2.17
212 230 0.534203 ACCGAAGACCAACACGCATT 60.534 50.000 0.00 0.00 0.00 3.56
213 231 1.070786 ACCGAAGACCAACACGCAT 59.929 52.632 0.00 0.00 0.00 4.73
215 233 2.604174 CCACCGAAGACCAACACGC 61.604 63.158 0.00 0.00 0.00 5.34
216 234 0.320421 ATCCACCGAAGACCAACACG 60.320 55.000 0.00 0.00 0.00 4.49
241 259 8.879342 TGTAAACATCCAAATGAAAACGAATT 57.121 26.923 0.00 0.00 36.67 2.17
242 260 7.598493 CCTGTAAACATCCAAATGAAAACGAAT 59.402 33.333 0.00 0.00 36.67 3.34
244 262 6.039941 ACCTGTAAACATCCAAATGAAAACGA 59.960 34.615 0.00 0.00 36.67 3.85
245 263 6.212955 ACCTGTAAACATCCAAATGAAAACG 58.787 36.000 0.00 0.00 36.67 3.60
246 264 8.334632 CAAACCTGTAAACATCCAAATGAAAAC 58.665 33.333 0.00 0.00 36.67 2.43
248 266 7.786030 TCAAACCTGTAAACATCCAAATGAAA 58.214 30.769 0.00 0.00 36.67 2.69
249 267 7.353414 TCAAACCTGTAAACATCCAAATGAA 57.647 32.000 0.00 0.00 36.67 2.57
250 268 6.968263 TCAAACCTGTAAACATCCAAATGA 57.032 33.333 0.00 0.00 36.67 2.57
251 269 6.813152 GGATCAAACCTGTAAACATCCAAATG 59.187 38.462 0.00 0.00 38.93 2.32
252 270 6.725834 AGGATCAAACCTGTAAACATCCAAAT 59.274 34.615 0.00 0.00 39.01 2.32
338 360 1.738350 CGAGAAGTCGTCCTGCTAAGA 59.262 52.381 0.00 0.00 41.57 2.10
339 361 1.738350 TCGAGAAGTCGTCCTGCTAAG 59.262 52.381 0.00 0.00 46.85 2.18
346 368 0.873054 TGACAGTCGAGAAGTCGTCC 59.127 55.000 0.00 0.00 46.85 4.79
383 405 3.393970 CTCCCTTGCTGGAGCCGA 61.394 66.667 4.87 0.00 45.13 5.54
449 471 1.909781 AAGTCCGCGGACCACCTAA 60.910 57.895 45.66 15.08 45.59 2.69
626 653 0.106469 TGGCTGGCCTGTAACACAAA 60.106 50.000 11.69 0.00 36.94 2.83
722 749 8.808092 TCCTTTTTCTCTTTTTCTGTTTTGGTA 58.192 29.630 0.00 0.00 0.00 3.25
723 750 7.676004 TCCTTTTTCTCTTTTTCTGTTTTGGT 58.324 30.769 0.00 0.00 0.00 3.67
724 751 8.546597 TTCCTTTTTCTCTTTTTCTGTTTTGG 57.453 30.769 0.00 0.00 0.00 3.28
726 753 9.996554 TCTTTCCTTTTTCTCTTTTTCTGTTTT 57.003 25.926 0.00 0.00 0.00 2.43
727 754 9.996554 TTCTTTCCTTTTTCTCTTTTTCTGTTT 57.003 25.926 0.00 0.00 0.00 2.83
728 755 9.996554 TTTCTTTCCTTTTTCTCTTTTTCTGTT 57.003 25.926 0.00 0.00 0.00 3.16
729 756 9.424319 GTTTCTTTCCTTTTTCTCTTTTTCTGT 57.576 29.630 0.00 0.00 0.00 3.41
730 757 9.423061 TGTTTCTTTCCTTTTTCTCTTTTTCTG 57.577 29.630 0.00 0.00 0.00 3.02
731 758 9.424319 GTGTTTCTTTCCTTTTTCTCTTTTTCT 57.576 29.630 0.00 0.00 0.00 2.52
732 759 8.373256 CGTGTTTCTTTCCTTTTTCTCTTTTTC 58.627 33.333 0.00 0.00 0.00 2.29
738 765 5.163693 TGGTCGTGTTTCTTTCCTTTTTCTC 60.164 40.000 0.00 0.00 0.00 2.87
774 801 4.559153 GTGGTTTCGTAGTTGTAGGCTTA 58.441 43.478 0.00 0.00 0.00 3.09
776 803 2.608752 CGTGGTTTCGTAGTTGTAGGCT 60.609 50.000 0.00 0.00 0.00 4.58
777 804 1.723003 CGTGGTTTCGTAGTTGTAGGC 59.277 52.381 0.00 0.00 0.00 3.93
778 805 1.723003 GCGTGGTTTCGTAGTTGTAGG 59.277 52.381 0.00 0.00 0.00 3.18
779 806 1.723003 GGCGTGGTTTCGTAGTTGTAG 59.277 52.381 0.00 0.00 0.00 2.74
780 807 1.340889 AGGCGTGGTTTCGTAGTTGTA 59.659 47.619 0.00 0.00 0.00 2.41
781 808 0.105408 AGGCGTGGTTTCGTAGTTGT 59.895 50.000 0.00 0.00 0.00 3.32
782 809 0.788391 GAGGCGTGGTTTCGTAGTTG 59.212 55.000 0.00 0.00 0.00 3.16
783 810 0.665369 CGAGGCGTGGTTTCGTAGTT 60.665 55.000 0.00 0.00 0.00 2.24
784 811 1.080974 CGAGGCGTGGTTTCGTAGT 60.081 57.895 0.00 0.00 0.00 2.73
911 939 1.704704 GAGGACTGGTAGAGGGGGT 59.295 63.158 0.00 0.00 0.00 4.95
920 948 2.529389 GGTGGTGGGAGGACTGGT 60.529 66.667 0.00 0.00 0.00 4.00
924 952 0.826256 GGTTTTGGTGGTGGGAGGAC 60.826 60.000 0.00 0.00 0.00 3.85
979 1010 2.357517 AGCTGTCGCTCGGTTTGG 60.358 61.111 0.00 0.00 45.15 3.28
1272 1316 2.496817 GCACTAGACAGAGCCCCG 59.503 66.667 0.00 0.00 32.75 5.73
1289 1333 1.590238 CTGAACTAAGCTCAATCCGCG 59.410 52.381 0.00 0.00 0.00 6.46
1312 1356 4.817517 ACCGTACAAAATCGATCTGAAGT 58.182 39.130 12.95 4.78 0.00 3.01
1313 1357 5.779806 AACCGTACAAAATCGATCTGAAG 57.220 39.130 12.95 5.15 0.00 3.02
1342 1386 6.350445 CCAGAACATATTGCAAAGGCTAAACT 60.350 38.462 1.71 0.00 41.91 2.66
1354 1418 2.223112 CGCTGACACCAGAACATATTGC 60.223 50.000 0.00 0.00 43.02 3.56
1355 1419 2.223112 GCGCTGACACCAGAACATATTG 60.223 50.000 0.00 0.00 43.02 1.90
1359 1423 2.029288 CGCGCTGACACCAGAACAT 61.029 57.895 5.56 0.00 43.02 2.71
1375 1439 0.237235 TCAAATCAACCGAAGCACGC 59.763 50.000 0.00 0.00 41.07 5.34
1397 1461 1.983605 CGCAGGTACAACTAGTCAACG 59.016 52.381 0.00 0.00 0.00 4.10
1432 1506 5.629079 ACAGATTAAACTAAGCAACCAGC 57.371 39.130 0.00 0.00 46.19 4.85
1474 1696 6.487103 CGCACGCACAGATCTATCTATTATA 58.513 40.000 0.00 0.00 34.85 0.98
1475 1697 5.335935 CGCACGCACAGATCTATCTATTAT 58.664 41.667 0.00 0.00 34.85 1.28
1477 1699 3.569548 CGCACGCACAGATCTATCTATT 58.430 45.455 0.00 0.00 34.85 1.73
1481 1703 1.849306 GCGCACGCACAGATCTATC 59.151 57.895 10.65 0.00 41.49 2.08
1516 1738 1.334869 CTCCCGCATGCAAAAGTATCC 59.665 52.381 19.57 0.00 0.00 2.59
1524 1746 3.063704 CCAAGCTCCCGCATGCAA 61.064 61.111 19.57 1.03 39.10 4.08
1535 1757 1.238439 CACCGTGATTGAACCAAGCT 58.762 50.000 0.00 0.00 30.51 3.74
1538 1760 1.393603 TTGCACCGTGATTGAACCAA 58.606 45.000 1.65 0.00 0.00 3.67
1540 1762 2.723124 AATTGCACCGTGATTGAACC 57.277 45.000 1.65 0.00 0.00 3.62
1541 1763 5.633182 ACAAATAATTGCACCGTGATTGAAC 59.367 36.000 1.65 0.00 40.34 3.18
1543 1765 5.384063 ACAAATAATTGCACCGTGATTGA 57.616 34.783 1.65 0.00 40.34 2.57
1544 1766 6.365789 AGAAACAAATAATTGCACCGTGATTG 59.634 34.615 1.65 0.00 40.34 2.67
1550 1772 3.367630 GGCAGAAACAAATAATTGCACCG 59.632 43.478 0.00 0.00 40.34 4.94
1556 1778 6.443832 AGGGATAGGGCAGAAACAAATAATT 58.556 36.000 0.00 0.00 0.00 1.40
1578 1849 3.138283 TGCCATGTTTTCCCCTATAGAGG 59.862 47.826 0.00 0.00 43.33 3.69
1579 1850 4.137543 GTGCCATGTTTTCCCCTATAGAG 58.862 47.826 0.00 0.00 0.00 2.43
1580 1851 3.785887 AGTGCCATGTTTTCCCCTATAGA 59.214 43.478 0.00 0.00 0.00 1.98
1581 1852 3.885297 CAGTGCCATGTTTTCCCCTATAG 59.115 47.826 0.00 0.00 0.00 1.31
1582 1853 3.268334 ACAGTGCCATGTTTTCCCCTATA 59.732 43.478 0.00 0.00 0.00 1.31
1583 1854 2.042979 ACAGTGCCATGTTTTCCCCTAT 59.957 45.455 0.00 0.00 0.00 2.57
1584 1855 1.427368 ACAGTGCCATGTTTTCCCCTA 59.573 47.619 0.00 0.00 0.00 3.53
1585 1856 0.188342 ACAGTGCCATGTTTTCCCCT 59.812 50.000 0.00 0.00 0.00 4.79
1586 1857 0.603065 GACAGTGCCATGTTTTCCCC 59.397 55.000 0.00 0.00 32.25 4.81
1587 1858 1.327303 TGACAGTGCCATGTTTTCCC 58.673 50.000 0.00 0.00 32.25 3.97
1588 1859 3.383761 CTTTGACAGTGCCATGTTTTCC 58.616 45.455 0.00 0.00 32.25 3.13
1589 1860 2.796593 GCTTTGACAGTGCCATGTTTTC 59.203 45.455 0.00 0.00 32.25 2.29
1590 1861 2.483538 GGCTTTGACAGTGCCATGTTTT 60.484 45.455 13.72 0.00 45.46 2.43
1591 1862 1.069049 GGCTTTGACAGTGCCATGTTT 59.931 47.619 13.72 0.00 45.46 2.83
1592 1863 0.675633 GGCTTTGACAGTGCCATGTT 59.324 50.000 13.72 0.00 45.46 2.71
1593 1864 2.344535 GGCTTTGACAGTGCCATGT 58.655 52.632 13.72 0.00 45.46 3.21
1601 1872 6.377327 TCTTTTTCTTACTGGCTTTGACAG 57.623 37.500 0.00 0.00 45.62 3.51
1604 1875 6.485313 TCGATTCTTTTTCTTACTGGCTTTGA 59.515 34.615 0.00 0.00 0.00 2.69
1620 1891 6.702329 AGTCCACATCTACTTTCGATTCTTT 58.298 36.000 0.00 0.00 0.00 2.52
1621 1892 6.071334 TGAGTCCACATCTACTTTCGATTCTT 60.071 38.462 0.00 0.00 0.00 2.52
1622 1893 5.419155 TGAGTCCACATCTACTTTCGATTCT 59.581 40.000 0.00 0.00 0.00 2.40
1763 2594 4.307032 AGTGCTTGGTATTCCACTGATT 57.693 40.909 0.00 0.00 44.22 2.57
1768 2599 2.277084 CGGTAGTGCTTGGTATTCCAC 58.723 52.381 0.00 0.00 44.22 4.02
1771 2602 3.119245 TCAGACGGTAGTGCTTGGTATTC 60.119 47.826 0.00 0.00 0.00 1.75
1776 2607 3.735237 ATATCAGACGGTAGTGCTTGG 57.265 47.619 0.00 0.00 0.00 3.61
1779 2610 6.940867 TGAAGTATATATCAGACGGTAGTGCT 59.059 38.462 0.00 0.00 0.00 4.40
1899 2740 5.132897 TCACTTATGTTGAACAAATGGGC 57.867 39.130 0.62 0.00 0.00 5.36
1935 2776 4.425180 TTACCAAGTTAGCAACCAGTGA 57.575 40.909 0.00 0.00 0.00 3.41
1938 2779 6.863126 CAGAATTTTACCAAGTTAGCAACCAG 59.137 38.462 0.00 0.00 0.00 4.00
1939 2780 6.322712 ACAGAATTTTACCAAGTTAGCAACCA 59.677 34.615 0.00 0.00 0.00 3.67
2011 2877 4.747580 GACCGTGTCAGATACCAGATGGT 61.748 52.174 9.88 9.88 41.13 3.55
2034 2902 9.900710 ATTACAAAATGCGTAGACACAAAATAA 57.099 25.926 0.00 0.00 0.00 1.40
2048 2917 7.872163 ATTACATGCCATATTACAAAATGCG 57.128 32.000 0.00 0.00 0.00 4.73
2053 2922 7.453126 CCCCCTTATTACATGCCATATTACAAA 59.547 37.037 0.00 0.00 0.00 2.83
2057 2926 6.979018 TCCCCCTTATTACATGCCATATTA 57.021 37.500 0.00 0.00 0.00 0.98
2068 2937 2.121948 AGGTCCGTTCCCCCTTATTAC 58.878 52.381 0.00 0.00 0.00 1.89
2082 2954 2.669569 CCAGTGGCACAAGGTCCG 60.670 66.667 21.41 0.00 44.16 4.79
2093 2966 6.415573 AGGAAATTAGTAAAGTAGCCAGTGG 58.584 40.000 4.20 4.20 0.00 4.00
2107 2980 9.189156 TGCAAAAGCATAGAATAGGAAATTAGT 57.811 29.630 0.00 0.00 0.00 2.24
2109 2982 9.970395 CATGCAAAAGCATAGAATAGGAAATTA 57.030 29.630 2.28 0.00 0.00 1.40
2110 2983 8.480501 ACATGCAAAAGCATAGAATAGGAAATT 58.519 29.630 2.28 0.00 0.00 1.82
2111 2984 7.924412 CACATGCAAAAGCATAGAATAGGAAAT 59.076 33.333 2.28 0.00 0.00 2.17
2112 2985 7.093814 ACACATGCAAAAGCATAGAATAGGAAA 60.094 33.333 2.28 0.00 0.00 3.13
2113 2986 6.377996 ACACATGCAAAAGCATAGAATAGGAA 59.622 34.615 2.28 0.00 0.00 3.36
2142 4743 8.861033 TGCATAAAAGTCAATAATCAAGATGC 57.139 30.769 0.00 0.00 36.27 3.91
2159 4760 8.867935 CGGAATAACAAACATTGATGCATAAAA 58.132 29.630 0.00 0.00 0.00 1.52
2162 4763 7.094508 ACGGAATAACAAACATTGATGCATA 57.905 32.000 0.00 0.00 0.00 3.14
2163 4764 5.964758 ACGGAATAACAAACATTGATGCAT 58.035 33.333 0.00 0.00 0.00 3.96
2164 4765 5.384063 ACGGAATAACAAACATTGATGCA 57.616 34.783 0.00 0.00 0.00 3.96
2165 4766 5.861251 TGAACGGAATAACAAACATTGATGC 59.139 36.000 0.00 0.00 0.00 3.91
2166 4767 7.062138 CCTTGAACGGAATAACAAACATTGATG 59.938 37.037 0.00 0.00 0.00 3.07
2167 4768 7.090173 CCTTGAACGGAATAACAAACATTGAT 58.910 34.615 0.00 0.00 0.00 2.57
2169 4770 5.633182 CCCTTGAACGGAATAACAAACATTG 59.367 40.000 0.00 0.00 0.00 2.82
2170 4771 5.303333 ACCCTTGAACGGAATAACAAACATT 59.697 36.000 0.00 0.00 0.00 2.71
2171 4772 4.830600 ACCCTTGAACGGAATAACAAACAT 59.169 37.500 0.00 0.00 0.00 2.71
2172 4773 4.208746 ACCCTTGAACGGAATAACAAACA 58.791 39.130 0.00 0.00 0.00 2.83
2173 4774 4.320714 GGACCCTTGAACGGAATAACAAAC 60.321 45.833 0.00 0.00 0.00 2.93
2191 4803 1.275573 GTACAGAGACAAGGTGGACCC 59.724 57.143 0.00 0.00 36.42 4.46
2193 4805 3.444388 CCTAGTACAGAGACAAGGTGGAC 59.556 52.174 0.00 0.00 0.00 4.02
2205 4817 4.836736 ACTGGTAAACTTGCCTAGTACAGA 59.163 41.667 0.00 0.00 35.54 3.41
2209 4821 6.893554 TGATCTACTGGTAAACTTGCCTAGTA 59.106 38.462 0.00 4.23 35.54 1.82
2210 4822 5.720041 TGATCTACTGGTAAACTTGCCTAGT 59.280 40.000 0.00 3.40 39.32 2.57
2211 4823 6.222038 TGATCTACTGGTAAACTTGCCTAG 57.778 41.667 0.00 0.00 33.70 3.02
2212 4824 6.808321 ATGATCTACTGGTAAACTTGCCTA 57.192 37.500 0.00 0.00 33.70 3.93
2213 4825 5.700402 ATGATCTACTGGTAAACTTGCCT 57.300 39.130 0.00 0.00 33.70 4.75
2214 4826 5.758784 GGTATGATCTACTGGTAAACTTGCC 59.241 44.000 0.00 0.00 0.00 4.52
2215 4827 5.462398 CGGTATGATCTACTGGTAAACTTGC 59.538 44.000 0.00 0.00 0.00 4.01
2216 4828 6.475727 CACGGTATGATCTACTGGTAAACTTG 59.524 42.308 12.75 1.50 0.00 3.16
2217 4829 6.570692 CACGGTATGATCTACTGGTAAACTT 58.429 40.000 12.75 0.00 0.00 2.66
2218 4830 5.451520 GCACGGTATGATCTACTGGTAAACT 60.452 44.000 12.75 0.00 0.00 2.66
2219 4831 4.743644 GCACGGTATGATCTACTGGTAAAC 59.256 45.833 12.75 0.00 0.00 2.01
2220 4832 4.647853 AGCACGGTATGATCTACTGGTAAA 59.352 41.667 12.75 0.00 0.00 2.01
2221 4833 4.212716 AGCACGGTATGATCTACTGGTAA 58.787 43.478 12.75 0.00 0.00 2.85
2230 4842 3.684788 ACAGAACAAAGCACGGTATGATC 59.315 43.478 0.00 0.00 0.00 2.92
2234 4846 5.293569 GCTTATACAGAACAAAGCACGGTAT 59.706 40.000 1.27 0.00 43.00 2.73
2238 4850 4.928661 AGCTTATACAGAACAAAGCACG 57.071 40.909 8.44 0.00 45.31 5.34
2255 4867 5.603596 TCATCAGAAAACATGCAAAAGCTT 58.396 33.333 0.00 0.00 0.00 3.74
2256 4868 5.204409 TCATCAGAAAACATGCAAAAGCT 57.796 34.783 0.00 0.00 0.00 3.74
2300 4912 8.010733 TCAAACTTGAAATCAGTTCAGGAAAT 57.989 30.769 3.72 0.00 46.85 2.17
2303 4915 7.587037 AATCAAACTTGAAATCAGTTCAGGA 57.413 32.000 3.72 0.00 46.85 3.86
2401 5032 7.640240 GTCAGCGACTTGAAATACCAATTTATC 59.360 37.037 0.00 0.00 35.41 1.75
2413 5044 6.741992 AATTATCATGTCAGCGACTTGAAA 57.258 33.333 21.56 17.87 45.22 2.69
2419 5050 4.272018 AGAGCAAATTATCATGTCAGCGAC 59.728 41.667 0.00 2.32 0.00 5.19
2420 5051 4.271776 CAGAGCAAATTATCATGTCAGCGA 59.728 41.667 0.00 0.00 0.00 4.93
2421 5052 4.034858 ACAGAGCAAATTATCATGTCAGCG 59.965 41.667 0.00 0.00 0.00 5.18
2422 5053 5.496133 ACAGAGCAAATTATCATGTCAGC 57.504 39.130 0.00 0.00 0.00 4.26
2432 5065 4.336433 GCTTGGCATCTACAGAGCAAATTA 59.664 41.667 0.44 0.00 0.00 1.40
2433 5066 3.129988 GCTTGGCATCTACAGAGCAAATT 59.870 43.478 0.44 0.00 0.00 1.82
2434 5067 2.686915 GCTTGGCATCTACAGAGCAAAT 59.313 45.455 0.44 0.00 0.00 2.32
2444 5077 2.554142 CAATGAGACGCTTGGCATCTA 58.446 47.619 0.00 0.00 28.87 1.98
2508 5141 1.631405 CAATGACCTTGAAGGGCCAA 58.369 50.000 15.84 0.00 45.26 4.52
2534 5167 4.574674 ACAATCATAGGCTTGTCTCCAA 57.425 40.909 0.00 0.00 29.85 3.53
2666 5302 0.465460 GGCAGGGACAGTGACAACAA 60.465 55.000 0.00 0.00 0.00 2.83
2700 5336 2.853542 TTGGTGGCCTGCCTCTGA 60.854 61.111 16.05 0.00 36.94 3.27
2742 5378 5.439828 TCGTTGATAATGCGCATAACATTC 58.560 37.500 25.61 15.63 38.62 2.67
2772 5408 1.951602 CCATAAGCAATAGCAGCAGCA 59.048 47.619 3.17 0.00 45.49 4.41
2799 5435 1.202879 CCAACACTGGTGGCCTTCTTA 60.203 52.381 3.32 0.00 38.00 2.10
2868 5504 2.631384 TCTTCAATGGTGAGGAGGGAA 58.369 47.619 0.00 0.00 35.11 3.97
2874 5510 3.713764 AGATACCCTCTTCAATGGTGAGG 59.286 47.826 12.92 12.92 45.02 3.86
3077 5713 1.228094 TCAATGGTGGTCTGCGCAA 60.228 52.632 13.05 0.00 0.00 4.85
3322 5958 1.336440 CGGGTTGATGTTCTTGCACAA 59.664 47.619 0.00 0.00 0.00 3.33
3714 6350 2.432628 GTGGTCTTGTCCTCGGCG 60.433 66.667 0.00 0.00 0.00 6.46
3759 6395 0.112995 TCAGCCTGCCCTTGTCATTT 59.887 50.000 0.00 0.00 0.00 2.32
3873 6509 4.019411 TGTGATTTCTGCCCATAGTTCTCA 60.019 41.667 0.00 0.00 0.00 3.27
3913 6549 7.581213 ACAGGTCAGTTTGTGATTTGATTTA 57.419 32.000 0.00 0.00 37.56 1.40
4005 6641 2.615227 CTAAGGGGAAGGCGCTGCAT 62.615 60.000 7.64 0.00 0.00 3.96
4198 6835 2.466547 TCAGATCTGAGAGGGATGCA 57.533 50.000 21.67 0.00 34.14 3.96
4414 7103 7.605449 AGGGTTTCAACAACAAGAATCATATG 58.395 34.615 0.00 0.00 0.00 1.78
4523 7213 7.171337 CCAAACCATCCTTACAATTTCAAACAG 59.829 37.037 0.00 0.00 0.00 3.16
4735 7425 4.521338 TCGTAAGGCATGGCAAGACCAA 62.521 50.000 22.64 3.42 46.91 3.67
4741 7431 1.667236 CTCATCGTAAGGCATGGCAA 58.333 50.000 22.64 6.11 38.47 4.52


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

AutoCloner maintained by Alex Coulton.