Multiple sequence alignment - TraesCS6A01G092800

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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 TraesCS6A01G092800 chr6A 100.000 2309 0 0 1 2309 60715740 60718048 0.000000e+00 4265.0
1 TraesCS6A01G092800 chr6A 79.641 835 107 34 595 1379 60492464 60493285 2.020000e-150 542.0
2 TraesCS6A01G092800 chr6B 89.145 1474 100 28 5 1439 116351166 116352618 0.000000e+00 1781.0
3 TraesCS6A01G092800 chr6B 78.860 842 112 38 595 1384 116106841 116107668 2.050000e-140 508.0
4 TraesCS6A01G092800 chr6B 89.512 410 19 5 1914 2309 116353143 116353542 4.430000e-137 497.0
5 TraesCS6A01G092800 chr6B 91.736 121 6 3 1565 1685 116352615 116352731 5.100000e-37 165.0
6 TraesCS6A01G092800 chr6D 81.265 822 87 36 595 1379 46860977 46861768 9.130000e-169 603.0
7 TraesCS6A01G092800 chr1B 82.282 333 56 1 984 1313 330991680 330992012 3.750000e-73 285.0
8 TraesCS6A01G092800 chr1A 81.982 333 57 1 984 1313 300577201 300577533 1.750000e-71 279.0
9 TraesCS6A01G092800 chr1A 79.027 329 66 1 984 1309 300672840 300673168 2.990000e-54 222.0
10 TraesCS6A01G092800 chr1D 80.909 330 60 1 987 1313 247123139 247122810 8.190000e-65 257.0
11 TraesCS6A01G092800 chr1D 79.939 329 63 1 984 1309 246970454 246970126 2.960000e-59 239.0
12 TraesCS6A01G092800 chrUn 93.846 130 3 3 1441 1568 259012 258886 8.420000e-45 191.0
13 TraesCS6A01G092800 chr2B 91.096 146 6 5 1430 1571 567903237 567903379 8.420000e-45 191.0
14 TraesCS6A01G092800 chr2B 81.897 116 13 7 1692 1804 793493358 793493248 8.790000e-15 91.6
15 TraesCS6A01G092800 chr2A 92.593 135 6 3 1435 1568 508731438 508731569 8.420000e-45 191.0
16 TraesCS6A01G092800 chr2A 92.647 136 5 3 1441 1574 604991511 604991643 8.420000e-45 191.0
17 TraesCS6A01G092800 chr5A 92.537 134 5 3 1437 1568 688512350 688512220 1.090000e-43 187.0
18 TraesCS6A01G092800 chr3D 91.429 140 7 3 1431 1568 464998586 464998722 1.090000e-43 187.0
19 TraesCS6A01G092800 chr3B 91.367 139 6 4 1436 1572 125525673 125525807 3.920000e-43 185.0
20 TraesCS6A01G092800 chr3B 91.304 138 6 4 1434 1568 656597566 656597700 1.410000e-42 183.0
21 TraesCS6A01G092800 chr5B 90.780 141 8 3 1433 1571 82212308 82212171 1.410000e-42 183.0
22 TraesCS6A01G092800 chr5D 84.615 143 14 7 1692 1832 411224893 411224757 4.000000e-28 135.0
23 TraesCS6A01G092800 chr4A 82.550 149 21 5 1695 1841 64953737 64953592 2.410000e-25 126.0
24 TraesCS6A01G092800 chr7B 78.626 131 18 6 1692 1820 666322639 666322761 6.840000e-11 78.7


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 TraesCS6A01G092800 chr6A 60715740 60718048 2308 False 4265.000000 4265 100.000 1 2309 1 chr6A.!!$F2 2308
1 TraesCS6A01G092800 chr6A 60492464 60493285 821 False 542.000000 542 79.641 595 1379 1 chr6A.!!$F1 784
2 TraesCS6A01G092800 chr6B 116351166 116353542 2376 False 814.333333 1781 90.131 5 2309 3 chr6B.!!$F2 2304
3 TraesCS6A01G092800 chr6B 116106841 116107668 827 False 508.000000 508 78.860 595 1384 1 chr6B.!!$F1 789
4 TraesCS6A01G092800 chr6D 46860977 46861768 791 False 603.000000 603 81.265 595 1379 1 chr6D.!!$F1 784

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
217 218 0.1078 AGCTCAGTCGTAGCCTCGTA 60.108 55.0 0.0 0.0 41.02 3.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1774 1888 0.03601 CAGCCCATCCGAGTTCAAGT 60.036 55.0 0.0 0.0 0.0 3.16 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
39 40 2.680370 GGAGGCCAAGGACCGGATT 61.680 63.158 9.46 0.00 0.00 3.01
46 47 0.322456 CAAGGACCGGATTTGGCAGA 60.322 55.000 9.46 0.00 0.00 4.26
62 63 2.565841 GCAGATTAACACCAGCTAGGG 58.434 52.381 7.06 0.00 43.89 3.53
147 148 4.935495 CGGGATGCATGACGGGGG 62.935 72.222 2.46 0.00 0.00 5.40
153 154 2.903855 GCATGACGGGGGATGCAG 60.904 66.667 0.00 0.00 43.75 4.41
163 164 0.179034 GGGGATGCAGTCACAGATCC 60.179 60.000 0.00 0.00 34.67 3.36
165 166 0.531532 GGATGCAGTCACAGATCCGG 60.532 60.000 0.00 0.00 0.00 5.14
166 167 0.176680 GATGCAGTCACAGATCCGGT 59.823 55.000 0.00 0.00 0.00 5.28
167 168 1.409064 GATGCAGTCACAGATCCGGTA 59.591 52.381 0.00 0.00 0.00 4.02
172 173 2.294791 CAGTCACAGATCCGGTATCTCC 59.705 54.545 11.94 3.69 43.42 3.71
202 203 3.895232 TGAATCCTAGTCAACCAGCTC 57.105 47.619 0.00 0.00 0.00 4.09
205 206 2.310779 TCCTAGTCAACCAGCTCAGT 57.689 50.000 0.00 0.00 0.00 3.41
206 207 2.171840 TCCTAGTCAACCAGCTCAGTC 58.828 52.381 0.00 0.00 0.00 3.51
207 208 1.135257 CCTAGTCAACCAGCTCAGTCG 60.135 57.143 0.00 0.00 0.00 4.18
208 209 1.542030 CTAGTCAACCAGCTCAGTCGT 59.458 52.381 0.00 0.00 0.00 4.34
210 211 1.542030 AGTCAACCAGCTCAGTCGTAG 59.458 52.381 0.00 0.00 0.00 3.51
211 212 0.243907 TCAACCAGCTCAGTCGTAGC 59.756 55.000 0.00 0.00 40.40 3.58
212 213 0.737715 CAACCAGCTCAGTCGTAGCC 60.738 60.000 0.00 0.00 41.02 3.93
213 214 0.900647 AACCAGCTCAGTCGTAGCCT 60.901 55.000 0.00 0.00 41.02 4.58
214 215 1.316706 ACCAGCTCAGTCGTAGCCTC 61.317 60.000 0.00 0.00 41.02 4.70
215 216 1.063327 CAGCTCAGTCGTAGCCTCG 59.937 63.158 0.00 0.00 41.02 4.63
216 217 1.377463 AGCTCAGTCGTAGCCTCGT 60.377 57.895 0.00 0.00 41.02 4.18
217 218 0.107800 AGCTCAGTCGTAGCCTCGTA 60.108 55.000 0.00 0.00 41.02 3.43
218 219 0.305313 GCTCAGTCGTAGCCTCGTAG 59.695 60.000 0.00 0.00 33.73 3.51
219 220 0.938713 CTCAGTCGTAGCCTCGTAGG 59.061 60.000 0.00 0.00 38.80 3.18
240 241 3.702623 GGGGGTCCAGGGTAGGGA 61.703 72.222 0.00 0.00 0.00 4.20
248 249 2.064581 CAGGGTAGGGACGGGAAGG 61.065 68.421 0.00 0.00 0.00 3.46
253 254 3.691297 TAGGGACGGGAAGGAGGGC 62.691 68.421 0.00 0.00 0.00 5.19
261 262 4.593864 GAAGGAGGGCGGCGCTAG 62.594 72.222 32.30 2.71 0.00 3.42
292 293 4.462280 GTAACGGGGGCGGTGGAG 62.462 72.222 0.00 0.00 0.00 3.86
307 332 2.670148 GGAGCGGGGACTGAATGGT 61.670 63.158 0.00 0.00 36.31 3.55
308 333 1.450312 GAGCGGGGACTGAATGGTG 60.450 63.158 0.00 0.00 36.31 4.17
311 336 1.377202 CGGGGACTGAATGGTGGTG 60.377 63.158 0.00 0.00 36.31 4.17
313 338 2.040544 GGGACTGAATGGTGGTGCG 61.041 63.158 0.00 0.00 0.00 5.34
314 339 1.302511 GGACTGAATGGTGGTGCGT 60.303 57.895 0.00 0.00 0.00 5.24
320 345 2.187599 GAATGGTGGTGCGTGCTGAC 62.188 60.000 0.00 0.00 0.00 3.51
361 386 5.535753 AAAAGAAACTGAGGTGGGAAATG 57.464 39.130 0.00 0.00 0.00 2.32
401 427 7.331089 AGGTGGTAAATTAACCTCTTTCTCT 57.669 36.000 0.00 0.00 40.34 3.10
445 471 7.206981 TCCTACATTTTGCTCAGAAAAGAAG 57.793 36.000 0.00 0.00 0.00 2.85
458 484 6.096036 TCAGAAAAGAAGAGCATTCTAGACG 58.904 40.000 4.79 0.00 31.96 4.18
459 485 5.290643 CAGAAAAGAAGAGCATTCTAGACGG 59.709 44.000 4.79 0.00 31.96 4.79
465 491 3.673594 AAGAGCATTCTAGACGGTTCACG 60.674 47.826 0.00 0.00 40.03 4.35
479 505 4.208355 CGGTTCACGTGATTAAACAACTG 58.792 43.478 20.80 13.49 37.93 3.16
533 559 3.429043 GCATTGGGCACATCAACAG 57.571 52.632 0.00 0.00 43.97 3.16
537 563 1.533625 TTGGGCACATCAACAGCTAC 58.466 50.000 0.00 0.00 0.00 3.58
547 573 6.598525 CACATCAACAGCTACGATACAAAAA 58.401 36.000 0.00 0.00 0.00 1.94
551 577 5.703592 TCAACAGCTACGATACAAAAATGGT 59.296 36.000 0.00 0.00 0.00 3.55
556 582 6.742718 CAGCTACGATACAAAAATGGTTCTTG 59.257 38.462 0.00 0.00 0.00 3.02
565 591 0.323725 AATGGTTCTTGCTCGCCCAT 60.324 50.000 0.00 0.00 37.51 4.00
566 592 0.323725 ATGGTTCTTGCTCGCCCATT 60.324 50.000 0.00 0.00 31.99 3.16
567 593 0.960364 TGGTTCTTGCTCGCCCATTC 60.960 55.000 0.00 0.00 0.00 2.67
568 594 1.425428 GTTCTTGCTCGCCCATTCG 59.575 57.895 0.00 0.00 0.00 3.34
569 595 1.019278 GTTCTTGCTCGCCCATTCGA 61.019 55.000 0.00 0.00 36.94 3.71
652 680 7.562088 TCCTTGTTTGGAGTAGTAAAAATTGGT 59.438 33.333 0.00 0.00 0.00 3.67
653 681 7.651704 CCTTGTTTGGAGTAGTAAAAATTGGTG 59.348 37.037 0.00 0.00 0.00 4.17
672 706 1.416813 GCCACATCGTCTCTGCGAAG 61.417 60.000 0.00 0.00 44.38 3.79
687 721 1.482278 CGAAGAGCGACCTGATAAGC 58.518 55.000 0.00 0.00 44.57 3.09
697 731 4.459685 GCGACCTGATAAGCTCTATCCTTA 59.540 45.833 11.15 0.00 0.00 2.69
716 751 7.822161 TCCTTAGTTATTACCGCTGTACATA 57.178 36.000 0.00 0.00 0.00 2.29
719 754 7.597743 CCTTAGTTATTACCGCTGTACATAAGG 59.402 40.741 0.00 2.70 0.00 2.69
741 776 4.466015 GGGACACCATGTAATCCAAACAAT 59.534 41.667 8.23 0.00 36.50 2.71
744 783 6.404734 GGACACCATGTAATCCAAACAATCTC 60.405 42.308 0.00 0.00 0.00 2.75
745 784 5.418840 ACACCATGTAATCCAAACAATCTCC 59.581 40.000 0.00 0.00 0.00 3.71
746 785 5.418524 CACCATGTAATCCAAACAATCTCCA 59.581 40.000 0.00 0.00 0.00 3.86
747 786 5.418840 ACCATGTAATCCAAACAATCTCCAC 59.581 40.000 0.00 0.00 0.00 4.02
757 796 4.762289 AACAATCTCCACCATCTCTACC 57.238 45.455 0.00 0.00 0.00 3.18
772 811 2.436173 CTCTACCATTCAGTTCCCCTCC 59.564 54.545 0.00 0.00 0.00 4.30
804 849 2.463589 TTTGGGGCTGTACCGAGCAG 62.464 60.000 7.43 0.00 41.08 4.24
874 934 2.645838 ACAAGCCACAACTCATCAGT 57.354 45.000 0.00 0.00 0.00 3.41
963 1062 3.186047 GCGTCCACGTTATGCGCT 61.186 61.111 9.73 0.00 46.11 5.92
1035 1137 1.826054 CCAGAGAGGCGAGGACGAT 60.826 63.158 0.00 0.00 42.66 3.73
1072 1174 2.809601 GCAGGTACCACAGCGACG 60.810 66.667 15.94 0.00 0.00 5.12
1092 1194 2.742372 GACATGGTCGCGGCACTT 60.742 61.111 14.93 0.00 0.00 3.16
1111 1213 4.111016 CCACGCGCTGGTACGAGA 62.111 66.667 5.73 0.00 36.63 4.04
1204 1306 1.286260 GACGAGTGCGACTCCAAGT 59.714 57.895 9.71 3.87 42.12 3.16
1232 1334 2.426522 CAAGGACAACATCGTGGTCAT 58.573 47.619 4.15 0.00 38.17 3.06
1244 1346 4.593864 GGTCATCTCCCTCGCCGC 62.594 72.222 0.00 0.00 0.00 6.53
1384 1498 4.357947 GACGGCAGTGCTCACGGA 62.358 66.667 16.11 0.00 36.20 4.69
1392 1506 0.246635 AGTGCTCACGGAAGCGTATT 59.753 50.000 6.78 0.00 45.54 1.89
1404 1518 4.143597 CGGAAGCGTATTGTGTTATCGATC 60.144 45.833 0.00 0.00 0.00 3.69
1416 1530 3.046390 GTTATCGATCGAGTCAAGGCAG 58.954 50.000 23.84 0.00 0.00 4.85
1421 1535 0.247736 ATCGAGTCAAGGCAGGTGTC 59.752 55.000 0.00 0.00 0.00 3.67
1435 1549 1.411246 AGGTGTCACTGTCGTTGCTAA 59.589 47.619 2.35 0.00 0.00 3.09
1436 1550 1.792949 GGTGTCACTGTCGTTGCTAAG 59.207 52.381 2.35 0.00 0.00 2.18
1437 1551 2.470821 GTGTCACTGTCGTTGCTAAGT 58.529 47.619 0.00 0.00 0.00 2.24
1438 1552 3.551454 GGTGTCACTGTCGTTGCTAAGTA 60.551 47.826 2.35 0.00 0.00 2.24
1439 1553 3.669122 GTGTCACTGTCGTTGCTAAGTAG 59.331 47.826 0.00 0.00 0.00 2.57
1440 1554 3.317149 TGTCACTGTCGTTGCTAAGTAGT 59.683 43.478 0.00 0.00 0.00 2.73
1441 1555 4.516321 TGTCACTGTCGTTGCTAAGTAGTA 59.484 41.667 0.00 0.00 0.00 1.82
1442 1556 4.850470 GTCACTGTCGTTGCTAAGTAGTAC 59.150 45.833 0.00 0.00 0.00 2.73
1443 1557 4.758674 TCACTGTCGTTGCTAAGTAGTACT 59.241 41.667 0.00 0.00 0.00 2.73
1444 1558 5.087397 CACTGTCGTTGCTAAGTAGTACTC 58.913 45.833 2.58 0.00 0.00 2.59
1445 1559 4.155644 ACTGTCGTTGCTAAGTAGTACTCC 59.844 45.833 2.58 0.00 0.00 3.85
1446 1560 3.441572 TGTCGTTGCTAAGTAGTACTCCC 59.558 47.826 2.58 0.00 0.00 4.30
1447 1561 3.693578 GTCGTTGCTAAGTAGTACTCCCT 59.306 47.826 2.58 0.00 0.00 4.20
1448 1562 4.157472 GTCGTTGCTAAGTAGTACTCCCTT 59.843 45.833 2.58 5.80 0.00 3.95
1449 1563 4.397417 TCGTTGCTAAGTAGTACTCCCTTC 59.603 45.833 2.58 0.00 0.00 3.46
1450 1564 4.157289 CGTTGCTAAGTAGTACTCCCTTCA 59.843 45.833 2.58 0.00 0.00 3.02
1451 1565 5.163540 CGTTGCTAAGTAGTACTCCCTTCAT 60.164 44.000 2.58 0.00 0.00 2.57
1452 1566 6.627508 CGTTGCTAAGTAGTACTCCCTTCATT 60.628 42.308 2.58 0.00 0.00 2.57
1453 1567 6.466885 TGCTAAGTAGTACTCCCTTCATTC 57.533 41.667 2.58 0.00 0.00 2.67
1454 1568 5.363005 TGCTAAGTAGTACTCCCTTCATTCC 59.637 44.000 2.58 0.00 0.00 3.01
1455 1569 5.507650 GCTAAGTAGTACTCCCTTCATTCCG 60.508 48.000 2.58 0.00 0.00 4.30
1456 1570 4.246712 AGTAGTACTCCCTTCATTCCGA 57.753 45.455 0.00 0.00 0.00 4.55
1457 1571 4.607239 AGTAGTACTCCCTTCATTCCGAA 58.393 43.478 0.00 0.00 0.00 4.30
1458 1572 5.209659 AGTAGTACTCCCTTCATTCCGAAT 58.790 41.667 0.00 0.00 31.69 3.34
1459 1573 5.661759 AGTAGTACTCCCTTCATTCCGAATT 59.338 40.000 0.00 0.00 31.69 2.17
1460 1574 6.837568 AGTAGTACTCCCTTCATTCCGAATTA 59.162 38.462 0.00 0.00 31.69 1.40
1461 1575 6.749036 AGTACTCCCTTCATTCCGAATTAT 57.251 37.500 0.00 0.00 31.69 1.28
1462 1576 6.525629 AGTACTCCCTTCATTCCGAATTATG 58.474 40.000 0.00 0.00 31.69 1.90
1463 1577 5.373812 ACTCCCTTCATTCCGAATTATGT 57.626 39.130 0.00 0.00 31.69 2.29
1464 1578 5.368989 ACTCCCTTCATTCCGAATTATGTC 58.631 41.667 0.00 0.00 31.69 3.06
1465 1579 5.131142 ACTCCCTTCATTCCGAATTATGTCT 59.869 40.000 0.00 0.00 31.69 3.41
1466 1580 6.001449 TCCCTTCATTCCGAATTATGTCTT 57.999 37.500 0.00 0.00 31.69 3.01
1467 1581 7.131907 TCCCTTCATTCCGAATTATGTCTTA 57.868 36.000 0.00 0.00 31.69 2.10
1468 1582 7.217200 TCCCTTCATTCCGAATTATGTCTTAG 58.783 38.462 0.00 0.00 31.69 2.18
1469 1583 7.070696 TCCCTTCATTCCGAATTATGTCTTAGA 59.929 37.037 0.00 0.00 31.69 2.10
1470 1584 7.880195 CCCTTCATTCCGAATTATGTCTTAGAT 59.120 37.037 0.00 0.00 31.69 1.98
1471 1585 9.277783 CCTTCATTCCGAATTATGTCTTAGATT 57.722 33.333 0.00 0.00 31.69 2.40
1474 1588 9.613428 TCATTCCGAATTATGTCTTAGATTTGT 57.387 29.630 0.00 0.00 0.00 2.83
1475 1589 9.869844 CATTCCGAATTATGTCTTAGATTTGTC 57.130 33.333 0.00 0.00 0.00 3.18
1476 1590 9.838339 ATTCCGAATTATGTCTTAGATTTGTCT 57.162 29.630 0.00 0.00 0.00 3.41
1478 1592 9.967346 TCCGAATTATGTCTTAGATTTGTCTAG 57.033 33.333 0.00 0.00 0.00 2.43
1479 1593 9.967346 CCGAATTATGTCTTAGATTTGTCTAGA 57.033 33.333 0.00 0.00 0.00 2.43
1485 1599 8.693120 ATGTCTTAGATTTGTCTAGATACGGA 57.307 34.615 0.00 0.00 0.00 4.69
1486 1600 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
1487 1601 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
1488 1602 7.539366 GTCTTAGATTTGTCTAGATACGGATGC 59.461 40.741 0.00 0.00 0.00 3.91
1489 1603 4.799678 AGATTTGTCTAGATACGGATGCG 58.200 43.478 4.58 4.58 0.00 4.73
1490 1604 4.278669 AGATTTGTCTAGATACGGATGCGT 59.721 41.667 18.47 18.47 0.00 5.24
1491 1605 5.472478 AGATTTGTCTAGATACGGATGCGTA 59.528 40.000 21.95 21.95 0.00 4.42
1492 1606 5.700722 TTTGTCTAGATACGGATGCGTAT 57.299 39.130 29.12 29.12 37.72 3.06
1493 1607 4.941325 TGTCTAGATACGGATGCGTATC 57.059 45.455 37.67 37.67 46.42 2.24
1500 1614 5.146482 GATACGGATGCGTATCTAGACTC 57.854 47.826 37.37 20.78 44.14 3.36
1501 1615 2.847441 ACGGATGCGTATCTAGACTCA 58.153 47.619 11.73 0.00 33.68 3.41
1502 1616 3.413327 ACGGATGCGTATCTAGACTCAT 58.587 45.455 11.73 0.00 33.68 2.90
1503 1617 3.821600 ACGGATGCGTATCTAGACTCATT 59.178 43.478 11.73 0.00 33.68 2.57
1504 1618 4.278669 ACGGATGCGTATCTAGACTCATTT 59.721 41.667 11.73 0.00 33.68 2.32
1505 1619 5.221263 ACGGATGCGTATCTAGACTCATTTT 60.221 40.000 11.73 0.00 33.68 1.82
1506 1620 6.016527 ACGGATGCGTATCTAGACTCATTTTA 60.017 38.462 11.73 0.00 33.68 1.52
1507 1621 6.524933 CGGATGCGTATCTAGACTCATTTTAG 59.475 42.308 13.38 0.00 33.68 1.85
1508 1622 7.371936 GGATGCGTATCTAGACTCATTTTAGT 58.628 38.462 13.38 0.00 33.68 2.24
1509 1623 7.327275 GGATGCGTATCTAGACTCATTTTAGTG 59.673 40.741 13.38 0.00 33.68 2.74
1510 1624 5.977725 TGCGTATCTAGACTCATTTTAGTGC 59.022 40.000 0.00 0.00 0.00 4.40
1511 1625 6.183360 TGCGTATCTAGACTCATTTTAGTGCT 60.183 38.462 0.00 0.00 0.00 4.40
1512 1626 7.012989 TGCGTATCTAGACTCATTTTAGTGCTA 59.987 37.037 0.00 0.00 0.00 3.49
1513 1627 7.535940 GCGTATCTAGACTCATTTTAGTGCTAG 59.464 40.741 0.00 0.00 33.34 3.42
1514 1628 8.775527 CGTATCTAGACTCATTTTAGTGCTAGA 58.224 37.037 0.00 0.00 38.76 2.43
1518 1632 9.069082 TCTAGACTCATTTTAGTGCTAGATACC 57.931 37.037 0.00 0.00 34.69 2.73
1519 1633 7.906199 AGACTCATTTTAGTGCTAGATACCT 57.094 36.000 0.00 0.00 0.00 3.08
1520 1634 8.312669 AGACTCATTTTAGTGCTAGATACCTT 57.687 34.615 0.00 0.00 0.00 3.50
1521 1635 8.763601 AGACTCATTTTAGTGCTAGATACCTTT 58.236 33.333 0.00 0.00 0.00 3.11
1522 1636 8.723942 ACTCATTTTAGTGCTAGATACCTTTG 57.276 34.615 0.00 0.00 0.00 2.77
1523 1637 8.322091 ACTCATTTTAGTGCTAGATACCTTTGT 58.678 33.333 0.00 0.00 0.00 2.83
1524 1638 9.817809 CTCATTTTAGTGCTAGATACCTTTGTA 57.182 33.333 0.00 0.00 0.00 2.41
1554 1668 8.480643 AGACAAATCTAAGACAAGTAATTCGG 57.519 34.615 0.00 0.00 31.46 4.30
1555 1669 8.311836 AGACAAATCTAAGACAAGTAATTCGGA 58.688 33.333 0.00 0.00 31.46 4.55
1556 1670 8.842358 ACAAATCTAAGACAAGTAATTCGGAA 57.158 30.769 0.00 0.00 0.00 4.30
1557 1671 8.718734 ACAAATCTAAGACAAGTAATTCGGAAC 58.281 33.333 0.00 0.00 0.00 3.62
1589 1703 2.160721 TCTCGATGGGTAGGAGCTTT 57.839 50.000 0.00 0.00 0.00 3.51
1644 1758 4.260172 CGGATTTGCCAAAACTGTTTTCAC 60.260 41.667 15.17 10.80 35.94 3.18
1645 1759 4.875536 GGATTTGCCAAAACTGTTTTCACT 59.124 37.500 15.17 2.98 36.34 3.41
1646 1760 5.353956 GGATTTGCCAAAACTGTTTTCACTT 59.646 36.000 15.17 2.83 36.34 3.16
1647 1761 6.536941 GGATTTGCCAAAACTGTTTTCACTTA 59.463 34.615 15.17 2.99 36.34 2.24
1648 1762 7.065204 GGATTTGCCAAAACTGTTTTCACTTAA 59.935 33.333 15.17 7.34 36.34 1.85
1677 1791 9.661954 AGATGAGGATTAATAAAGTCTGGTCTA 57.338 33.333 0.00 0.00 0.00 2.59
1709 1823 6.715347 ACATTATAAGACCAATTCAAGGGC 57.285 37.500 0.00 0.00 0.00 5.19
1711 1825 7.582719 ACATTATAAGACCAATTCAAGGGCTA 58.417 34.615 0.00 0.00 46.21 3.93
1712 1826 8.058847 ACATTATAAGACCAATTCAAGGGCTAA 58.941 33.333 0.00 0.00 46.21 3.09
1713 1827 9.082313 CATTATAAGACCAATTCAAGGGCTAAT 57.918 33.333 0.00 0.00 46.21 1.73
1714 1828 8.691661 TTATAAGACCAATTCAAGGGCTAATC 57.308 34.615 0.00 0.00 46.21 1.75
1715 1829 4.870021 AGACCAATTCAAGGGCTAATCT 57.130 40.909 0.00 0.00 44.68 2.40
1716 1830 5.198602 AGACCAATTCAAGGGCTAATCTT 57.801 39.130 0.00 0.00 44.68 2.40
1717 1831 5.583932 AGACCAATTCAAGGGCTAATCTTT 58.416 37.500 0.00 0.00 44.68 2.52
1718 1832 5.420104 AGACCAATTCAAGGGCTAATCTTTG 59.580 40.000 0.00 0.00 44.68 2.77
1719 1833 5.086621 ACCAATTCAAGGGCTAATCTTTGT 58.913 37.500 0.00 0.00 0.00 2.83
1720 1834 5.543790 ACCAATTCAAGGGCTAATCTTTGTT 59.456 36.000 0.00 0.00 0.00 2.83
1721 1835 5.870978 CCAATTCAAGGGCTAATCTTTGTTG 59.129 40.000 0.00 0.00 0.00 3.33
1722 1836 5.665916 ATTCAAGGGCTAATCTTTGTTGG 57.334 39.130 0.00 0.00 0.00 3.77
1723 1837 2.825532 TCAAGGGCTAATCTTTGTTGGC 59.174 45.455 0.00 0.00 35.15 4.52
1724 1838 2.562298 CAAGGGCTAATCTTTGTTGGCA 59.438 45.455 0.00 0.00 37.32 4.92
1725 1839 3.105959 AGGGCTAATCTTTGTTGGCAT 57.894 42.857 0.00 0.00 37.32 4.40
1726 1840 3.444029 AGGGCTAATCTTTGTTGGCATT 58.556 40.909 0.00 0.00 37.32 3.56
1727 1841 3.840078 AGGGCTAATCTTTGTTGGCATTT 59.160 39.130 0.00 0.00 37.32 2.32
1728 1842 4.286808 AGGGCTAATCTTTGTTGGCATTTT 59.713 37.500 0.00 0.00 37.32 1.82
1729 1843 5.003160 GGGCTAATCTTTGTTGGCATTTTT 58.997 37.500 0.00 0.00 37.32 1.94
1754 1868 9.547753 TTTCTATATAGAAGAAACACCATGAGC 57.452 33.333 21.40 0.00 42.66 4.26
1755 1869 8.250143 TCTATATAGAAGAAACACCATGAGCA 57.750 34.615 10.11 0.00 0.00 4.26
1756 1870 8.874156 TCTATATAGAAGAAACACCATGAGCAT 58.126 33.333 10.11 0.00 0.00 3.79
1757 1871 7.976135 ATATAGAAGAAACACCATGAGCATC 57.024 36.000 0.00 0.00 0.00 3.91
1771 1885 3.839654 GCATCATGCATCCAAGTCG 57.160 52.632 4.20 0.00 44.26 4.18
1772 1886 0.309922 GCATCATGCATCCAAGTCGG 59.690 55.000 4.20 0.00 44.26 4.79
1773 1887 0.949397 CATCATGCATCCAAGTCGGG 59.051 55.000 0.00 0.00 34.36 5.14
1774 1888 0.839277 ATCATGCATCCAAGTCGGGA 59.161 50.000 0.00 0.00 42.21 5.14
1775 1889 0.107703 TCATGCATCCAAGTCGGGAC 60.108 55.000 0.00 0.00 40.44 4.46
1776 1890 0.107508 CATGCATCCAAGTCGGGACT 60.108 55.000 0.00 0.00 44.94 3.85
1785 1899 1.965219 AGTCGGGACTTGAACTCGG 59.035 57.895 0.00 0.00 38.83 4.63
1786 1900 0.538977 AGTCGGGACTTGAACTCGGA 60.539 55.000 0.00 0.00 38.83 4.55
1787 1901 0.531200 GTCGGGACTTGAACTCGGAT 59.469 55.000 0.00 0.00 0.00 4.18
1788 1902 0.530744 TCGGGACTTGAACTCGGATG 59.469 55.000 0.00 0.00 0.00 3.51
1789 1903 0.460284 CGGGACTTGAACTCGGATGG 60.460 60.000 0.00 0.00 0.00 3.51
1790 1904 0.107654 GGGACTTGAACTCGGATGGG 60.108 60.000 0.00 0.00 0.00 4.00
1791 1905 0.744771 GGACTTGAACTCGGATGGGC 60.745 60.000 0.00 0.00 0.00 5.36
1792 1906 0.250513 GACTTGAACTCGGATGGGCT 59.749 55.000 0.00 0.00 0.00 5.19
1793 1907 0.036010 ACTTGAACTCGGATGGGCTG 60.036 55.000 0.00 0.00 0.00 4.85
1794 1908 0.745845 CTTGAACTCGGATGGGCTGG 60.746 60.000 0.00 0.00 0.00 4.85
1795 1909 2.514824 GAACTCGGATGGGCTGGC 60.515 66.667 0.00 0.00 0.00 4.85
1796 1910 3.329542 GAACTCGGATGGGCTGGCA 62.330 63.158 2.88 0.00 0.00 4.92
1797 1911 2.819984 GAACTCGGATGGGCTGGCAA 62.820 60.000 2.88 0.00 0.00 4.52
1798 1912 2.825836 CTCGGATGGGCTGGCAAC 60.826 66.667 2.88 0.00 0.00 4.17
1810 1924 2.647297 GGCAACAACCTCAGCTGC 59.353 61.111 9.47 0.00 0.00 5.25
1811 1925 2.647297 GCAACAACCTCAGCTGCC 59.353 61.111 9.47 0.00 0.00 4.85
1812 1926 2.924105 GCAACAACCTCAGCTGCCC 61.924 63.158 9.47 0.00 0.00 5.36
1813 1927 1.529010 CAACAACCTCAGCTGCCCA 60.529 57.895 9.47 0.00 0.00 5.36
1814 1928 1.108727 CAACAACCTCAGCTGCCCAA 61.109 55.000 9.47 0.00 0.00 4.12
1815 1929 1.109323 AACAACCTCAGCTGCCCAAC 61.109 55.000 9.47 0.00 0.00 3.77
1816 1930 2.116125 AACCTCAGCTGCCCAACC 59.884 61.111 9.47 0.00 0.00 3.77
1817 1931 2.766925 AACCTCAGCTGCCCAACCA 61.767 57.895 9.47 0.00 0.00 3.67
1818 1932 2.115910 CCTCAGCTGCCCAACCAA 59.884 61.111 9.47 0.00 0.00 3.67
1819 1933 2.270986 CCTCAGCTGCCCAACCAAC 61.271 63.158 9.47 0.00 0.00 3.77
1820 1934 2.203480 TCAGCTGCCCAACCAACC 60.203 61.111 9.47 0.00 0.00 3.77
1821 1935 3.673484 CAGCTGCCCAACCAACCG 61.673 66.667 0.00 0.00 0.00 4.44
1822 1936 4.974721 AGCTGCCCAACCAACCGG 62.975 66.667 0.00 0.00 38.77 5.28
1831 1945 3.982241 ACCAACCGGTCGACGTCC 61.982 66.667 8.04 0.59 44.71 4.79
1857 1971 8.703336 CGACCTATATTGTGAACACTGATATTG 58.297 37.037 14.29 12.87 0.00 1.90
1860 1974 7.445096 CCTATATTGTGAACACTGATATTGGCA 59.555 37.037 17.96 0.00 32.87 4.92
1873 1987 2.611974 ATTGGCATGACGTTCGAAAC 57.388 45.000 0.00 0.00 0.00 2.78
2114 2564 7.977789 TGGCAAAAGAAAGAGAAAAAGTTTT 57.022 28.000 0.00 0.00 0.00 2.43
2141 2591 6.090763 GCCATGGCAAAAATGTAGAGTAAAAC 59.909 38.462 32.08 0.00 41.49 2.43
2179 2629 2.485835 CCAGGGGTACACGACAAAGAAA 60.486 50.000 0.00 0.00 0.00 2.52
2242 2704 4.126208 TGCCATTGTAATTTCCATGCAG 57.874 40.909 0.00 0.00 0.00 4.41
2301 2764 6.558771 AAAAAGGAATTAAACTTGCCATGC 57.441 33.333 0.00 0.00 0.00 4.06
2304 2767 5.582689 AGGAATTAAACTTGCCATGCTAC 57.417 39.130 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.124983 CAGCCACCCATCGGTCAG 60.125 66.667 0.00 0.00 42.04 3.51
2 3 4.489771 CCCAGCCACCCATCGGTC 62.490 72.222 0.00 0.00 42.04 4.79
7 8 2.693864 CTCCTCCCAGCCACCCAT 60.694 66.667 0.00 0.00 0.00 4.00
15 16 2.285668 TCCTTGGCCTCCTCCCAG 60.286 66.667 3.32 0.00 33.13 4.45
39 40 2.584835 AGCTGGTGTTAATCTGCCAA 57.415 45.000 0.00 0.00 0.00 4.52
46 47 0.180406 CCGCCCTAGCTGGTGTTAAT 59.820 55.000 0.00 0.00 36.60 1.40
62 63 4.489771 CCTGGATGACCCCACCGC 62.490 72.222 0.00 0.00 34.81 5.68
69 70 0.819666 GCCGGATTTCCTGGATGACC 60.820 60.000 5.05 0.38 33.48 4.02
70 71 1.160329 CGCCGGATTTCCTGGATGAC 61.160 60.000 5.05 0.00 33.48 3.06
147 148 0.176680 ACCGGATCTGTGACTGCATC 59.823 55.000 9.46 0.00 0.00 3.91
153 154 2.307768 TGGAGATACCGGATCTGTGAC 58.692 52.381 9.46 0.43 45.48 3.67
163 164 1.135660 CATCCGTCGATGGAGATACCG 60.136 57.143 29.15 11.05 42.45 4.02
165 166 3.917329 TTCATCCGTCGATGGAGATAC 57.083 47.619 29.15 0.00 45.20 2.24
166 167 3.444034 GGATTCATCCGTCGATGGAGATA 59.556 47.826 29.15 17.33 45.20 1.98
167 168 2.232452 GGATTCATCCGTCGATGGAGAT 59.768 50.000 29.15 21.78 45.20 2.75
185 186 2.763448 GACTGAGCTGGTTGACTAGGAT 59.237 50.000 0.00 0.00 0.00 3.24
189 190 1.617322 ACGACTGAGCTGGTTGACTA 58.383 50.000 9.80 0.00 0.00 2.59
190 191 1.542030 CTACGACTGAGCTGGTTGACT 59.458 52.381 9.80 0.00 0.00 3.41
223 224 3.702623 TCCCTACCCTGGACCCCC 61.703 72.222 0.00 0.00 0.00 5.40
231 232 2.239680 CTCCTTCCCGTCCCTACCCT 62.240 65.000 0.00 0.00 0.00 4.34
235 236 2.694305 CCCTCCTTCCCGTCCCTA 59.306 66.667 0.00 0.00 0.00 3.53
291 292 2.671070 CACCATTCAGTCCCCGCT 59.329 61.111 0.00 0.00 0.00 5.52
292 293 2.438434 CCACCATTCAGTCCCCGC 60.438 66.667 0.00 0.00 0.00 6.13
293 294 1.377202 CACCACCATTCAGTCCCCG 60.377 63.158 0.00 0.00 0.00 5.73
294 295 1.678970 GCACCACCATTCAGTCCCC 60.679 63.158 0.00 0.00 0.00 4.81
298 323 2.260869 GCACGCACCACCATTCAGT 61.261 57.895 0.00 0.00 0.00 3.41
313 338 3.689649 AGGATTATTTTCCACGTCAGCAC 59.310 43.478 0.00 0.00 38.32 4.40
314 339 3.938963 GAGGATTATTTTCCACGTCAGCA 59.061 43.478 0.00 0.00 38.32 4.41
401 427 2.747446 GAGCTCTGCCGTCCATTAAAAA 59.253 45.455 6.43 0.00 0.00 1.94
412 438 1.667724 CAAAATGTAGGAGCTCTGCCG 59.332 52.381 14.64 0.00 0.00 5.69
445 471 2.186076 CGTGAACCGTCTAGAATGCTC 58.814 52.381 0.00 0.00 0.00 4.26
458 484 5.164606 ACAGTTGTTTAATCACGTGAACC 57.835 39.130 24.13 9.11 0.00 3.62
459 485 7.372396 CAGTAACAGTTGTTTAATCACGTGAAC 59.628 37.037 24.13 16.41 39.31 3.18
465 491 6.970043 TGTTGCAGTAACAGTTGTTTAATCAC 59.030 34.615 0.00 0.00 44.07 3.06
479 505 6.241207 ACATCATGTAGTTGTTGCAGTAAC 57.759 37.500 6.96 6.96 39.80 2.50
533 559 5.511729 GCAAGAACCATTTTTGTATCGTAGC 59.488 40.000 0.00 0.00 0.00 3.58
537 563 4.788100 CGAGCAAGAACCATTTTTGTATCG 59.212 41.667 0.00 6.97 31.86 2.92
547 573 0.323725 AATGGGCGAGCAAGAACCAT 60.324 50.000 0.00 0.00 43.39 3.55
551 577 0.107703 ATCGAATGGGCGAGCAAGAA 60.108 50.000 0.00 0.00 44.26 2.52
556 582 1.929836 GATATGATCGAATGGGCGAGC 59.070 52.381 0.00 0.00 45.95 5.03
568 594 5.602458 TCGTGTGGTACTACGATATGATC 57.398 43.478 13.64 0.00 41.69 2.92
652 680 2.125952 CGCAGAGACGATGTGGCA 60.126 61.111 0.00 0.00 34.06 4.92
653 681 1.416813 CTTCGCAGAGACGATGTGGC 61.417 60.000 0.00 0.00 42.54 5.01
682 716 8.468399 GCGGTAATAACTAAGGATAGAGCTTAT 58.532 37.037 0.00 0.00 33.15 1.73
684 718 6.494146 AGCGGTAATAACTAAGGATAGAGCTT 59.506 38.462 0.00 0.00 33.15 3.74
687 721 7.216973 ACAGCGGTAATAACTAAGGATAGAG 57.783 40.000 0.00 0.00 33.15 2.43
697 731 5.599656 TCCCTTATGTACAGCGGTAATAACT 59.400 40.000 0.33 0.00 0.00 2.24
716 751 4.086457 GTTTGGATTACATGGTGTCCCTT 58.914 43.478 0.00 0.00 0.00 3.95
719 754 5.418840 AGATTGTTTGGATTACATGGTGTCC 59.581 40.000 0.00 1.50 0.00 4.02
741 776 3.963374 CTGAATGGTAGAGATGGTGGAGA 59.037 47.826 0.00 0.00 0.00 3.71
744 783 4.446371 GAACTGAATGGTAGAGATGGTGG 58.554 47.826 0.00 0.00 0.00 4.61
745 784 4.446371 GGAACTGAATGGTAGAGATGGTG 58.554 47.826 0.00 0.00 0.00 4.17
746 785 3.456277 GGGAACTGAATGGTAGAGATGGT 59.544 47.826 0.00 0.00 0.00 3.55
747 786 3.181450 GGGGAACTGAATGGTAGAGATGG 60.181 52.174 0.00 0.00 0.00 3.51
757 796 1.453155 CGTTGGAGGGGAACTGAATG 58.547 55.000 0.00 0.00 0.00 2.67
772 811 1.373246 CCCAAACATGGCTGCGTTG 60.373 57.895 0.00 0.00 0.00 4.10
804 849 4.839668 ACATAACGATGCTCTCTAGGTC 57.160 45.455 0.00 0.00 36.43 3.85
874 934 2.410322 CTTGCTGTGGCCTGTGGGTA 62.410 60.000 3.32 0.00 37.74 3.69
904 987 2.340809 CACCACCGCGAGTTGGTA 59.659 61.111 21.70 0.00 37.72 3.25
997 1099 2.550978 GTACCCGTTCCATGTCATGAG 58.449 52.381 14.67 4.83 0.00 2.90
1005 1107 1.486211 CTCTCTGGTACCCGTTCCAT 58.514 55.000 10.07 0.00 33.01 3.41
1121 1223 0.179062 GCGGATCATCCTCTTGCACT 60.179 55.000 1.10 0.00 33.30 4.40
1204 1306 1.004277 GATGTTGTCCTTGCACCCCTA 59.996 52.381 0.00 0.00 0.00 3.53
1384 1498 4.603985 TCGATCGATAACACAATACGCTT 58.396 39.130 15.15 0.00 0.00 4.68
1392 1506 3.733988 GCCTTGACTCGATCGATAACACA 60.734 47.826 19.78 11.27 0.00 3.72
1404 1518 0.946221 GTGACACCTGCCTTGACTCG 60.946 60.000 0.00 0.00 0.00 4.18
1416 1530 1.792949 CTTAGCAACGACAGTGACACC 59.207 52.381 0.84 0.00 0.00 4.16
1421 1535 5.044428 AGTACTACTTAGCAACGACAGTG 57.956 43.478 0.00 0.00 0.00 3.66
1435 1549 4.246712 TCGGAATGAAGGGAGTACTACT 57.753 45.455 4.77 0.00 0.00 2.57
1436 1550 4.996788 TTCGGAATGAAGGGAGTACTAC 57.003 45.455 0.00 0.00 31.44 2.73
1437 1551 7.289317 ACATAATTCGGAATGAAGGGAGTACTA 59.711 37.037 3.59 0.00 40.65 1.82
1438 1552 6.099845 ACATAATTCGGAATGAAGGGAGTACT 59.900 38.462 3.59 0.00 40.65 2.73
1439 1553 6.289064 ACATAATTCGGAATGAAGGGAGTAC 58.711 40.000 3.59 0.00 40.65 2.73
1440 1554 6.326583 AGACATAATTCGGAATGAAGGGAGTA 59.673 38.462 3.59 0.00 40.65 2.59
1441 1555 5.131142 AGACATAATTCGGAATGAAGGGAGT 59.869 40.000 3.59 0.00 40.65 3.85
1442 1556 5.615289 AGACATAATTCGGAATGAAGGGAG 58.385 41.667 3.59 0.00 40.65 4.30
1443 1557 5.630415 AGACATAATTCGGAATGAAGGGA 57.370 39.130 3.59 0.00 40.65 4.20
1444 1558 7.217200 TCTAAGACATAATTCGGAATGAAGGG 58.783 38.462 3.59 0.00 40.65 3.95
1445 1559 8.839310 ATCTAAGACATAATTCGGAATGAAGG 57.161 34.615 3.59 0.63 40.65 3.46
1448 1562 9.613428 ACAAATCTAAGACATAATTCGGAATGA 57.387 29.630 3.59 0.00 0.00 2.57
1449 1563 9.869844 GACAAATCTAAGACATAATTCGGAATG 57.130 33.333 3.59 0.00 0.00 2.67
1450 1564 9.838339 AGACAAATCTAAGACATAATTCGGAAT 57.162 29.630 0.00 0.00 31.46 3.01
1452 1566 9.967346 CTAGACAAATCTAAGACATAATTCGGA 57.033 33.333 0.00 0.00 36.98 4.55
1453 1567 9.967346 TCTAGACAAATCTAAGACATAATTCGG 57.033 33.333 0.00 0.00 36.98 4.30
1459 1573 9.788889 TCCGTATCTAGACAAATCTAAGACATA 57.211 33.333 0.00 0.00 36.98 2.29
1460 1574 8.693120 TCCGTATCTAGACAAATCTAAGACAT 57.307 34.615 0.00 0.00 36.98 3.06
1461 1575 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
1462 1576 7.539366 GCATCCGTATCTAGACAAATCTAAGAC 59.461 40.741 0.00 0.00 36.98 3.01
1463 1577 7.573283 CGCATCCGTATCTAGACAAATCTAAGA 60.573 40.741 0.00 0.00 36.98 2.10
1464 1578 6.524933 CGCATCCGTATCTAGACAAATCTAAG 59.475 42.308 0.00 0.00 36.98 2.18
1465 1579 6.379386 CGCATCCGTATCTAGACAAATCTAA 58.621 40.000 0.00 0.00 36.98 2.10
1466 1580 5.939457 CGCATCCGTATCTAGACAAATCTA 58.061 41.667 0.00 0.00 36.29 1.98
1467 1581 4.799678 CGCATCCGTATCTAGACAAATCT 58.200 43.478 0.00 0.00 39.15 2.40
1482 1596 4.427096 AATGAGTCTAGATACGCATCCG 57.573 45.455 0.00 0.00 38.70 4.18
1483 1597 7.327275 CACTAAAATGAGTCTAGATACGCATCC 59.673 40.741 0.00 0.00 38.70 3.51
1484 1598 7.148885 GCACTAAAATGAGTCTAGATACGCATC 60.149 40.741 0.00 0.00 38.70 3.91
1485 1599 6.642950 GCACTAAAATGAGTCTAGATACGCAT 59.357 38.462 0.00 0.00 40.96 4.73
1486 1600 5.977725 GCACTAAAATGAGTCTAGATACGCA 59.022 40.000 0.00 0.00 33.60 5.24
1487 1601 6.210078 AGCACTAAAATGAGTCTAGATACGC 58.790 40.000 0.00 0.00 0.00 4.42
1488 1602 8.775527 TCTAGCACTAAAATGAGTCTAGATACG 58.224 37.037 0.00 0.00 34.65 3.06
1492 1606 9.069082 GGTATCTAGCACTAAAATGAGTCTAGA 57.931 37.037 11.59 11.59 38.76 2.43
1493 1607 9.073475 AGGTATCTAGCACTAAAATGAGTCTAG 57.927 37.037 0.00 0.00 33.29 2.43
1494 1608 8.998277 AGGTATCTAGCACTAAAATGAGTCTA 57.002 34.615 0.00 0.00 0.00 2.59
1495 1609 7.906199 AGGTATCTAGCACTAAAATGAGTCT 57.094 36.000 0.00 0.00 0.00 3.24
1496 1610 8.821894 CAAAGGTATCTAGCACTAAAATGAGTC 58.178 37.037 0.00 0.00 0.00 3.36
1497 1611 8.322091 ACAAAGGTATCTAGCACTAAAATGAGT 58.678 33.333 0.00 0.00 0.00 3.41
1498 1612 8.723942 ACAAAGGTATCTAGCACTAAAATGAG 57.276 34.615 0.00 0.00 0.00 2.90
1528 1642 8.936864 CCGAATTACTTGTCTTAGATTTGTCTT 58.063 33.333 0.00 0.00 0.00 3.01
1529 1643 8.311836 TCCGAATTACTTGTCTTAGATTTGTCT 58.688 33.333 0.00 0.00 0.00 3.41
1530 1644 8.475331 TCCGAATTACTTGTCTTAGATTTGTC 57.525 34.615 0.00 0.00 0.00 3.18
1531 1645 8.718734 GTTCCGAATTACTTGTCTTAGATTTGT 58.281 33.333 0.00 0.00 0.00 2.83
1532 1646 7.898309 CGTTCCGAATTACTTGTCTTAGATTTG 59.102 37.037 0.00 0.00 0.00 2.32
1533 1647 7.064253 CCGTTCCGAATTACTTGTCTTAGATTT 59.936 37.037 0.00 0.00 0.00 2.17
1534 1648 6.534079 CCGTTCCGAATTACTTGTCTTAGATT 59.466 38.462 0.00 0.00 0.00 2.40
1535 1649 6.040878 CCGTTCCGAATTACTTGTCTTAGAT 58.959 40.000 0.00 0.00 0.00 1.98
1536 1650 5.183713 TCCGTTCCGAATTACTTGTCTTAGA 59.816 40.000 0.00 0.00 0.00 2.10
1537 1651 5.404946 TCCGTTCCGAATTACTTGTCTTAG 58.595 41.667 0.00 0.00 0.00 2.18
1538 1652 5.389859 TCCGTTCCGAATTACTTGTCTTA 57.610 39.130 0.00 0.00 0.00 2.10
1539 1653 4.243270 CTCCGTTCCGAATTACTTGTCTT 58.757 43.478 0.00 0.00 0.00 3.01
1540 1654 3.368116 CCTCCGTTCCGAATTACTTGTCT 60.368 47.826 0.00 0.00 0.00 3.41
1541 1655 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
1542 1656 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
1543 1657 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
1544 1658 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
1545 1659 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
1546 1660 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
1547 1661 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
1548 1662 1.856629 TACTCCCTCCGTTCCGAATT 58.143 50.000 0.00 0.00 0.00 2.17
1549 1663 1.856629 TTACTCCCTCCGTTCCGAAT 58.143 50.000 0.00 0.00 0.00 3.34
1550 1664 1.856629 ATTACTCCCTCCGTTCCGAA 58.143 50.000 0.00 0.00 0.00 4.30
1551 1665 1.753073 GAATTACTCCCTCCGTTCCGA 59.247 52.381 0.00 0.00 0.00 4.55
1552 1666 1.755380 AGAATTACTCCCTCCGTTCCG 59.245 52.381 0.00 0.00 0.00 4.30
1553 1667 2.223758 CGAGAATTACTCCCTCCGTTCC 60.224 54.545 0.00 0.00 42.18 3.62
1554 1668 2.686915 TCGAGAATTACTCCCTCCGTTC 59.313 50.000 0.00 0.00 42.18 3.95
1555 1669 2.731572 TCGAGAATTACTCCCTCCGTT 58.268 47.619 0.00 0.00 42.18 4.44
1556 1670 2.431954 TCGAGAATTACTCCCTCCGT 57.568 50.000 0.00 0.00 42.18 4.69
1557 1671 2.029828 CCATCGAGAATTACTCCCTCCG 60.030 54.545 0.00 0.00 42.18 4.63
1558 1672 2.300437 CCCATCGAGAATTACTCCCTCC 59.700 54.545 0.00 0.00 42.18 4.30
1559 1673 2.966516 ACCCATCGAGAATTACTCCCTC 59.033 50.000 0.00 0.00 42.18 4.30
1560 1674 3.047695 ACCCATCGAGAATTACTCCCT 57.952 47.619 0.00 0.00 42.18 4.20
1561 1675 3.258622 CCTACCCATCGAGAATTACTCCC 59.741 52.174 0.00 0.00 42.18 4.30
1562 1676 4.150359 TCCTACCCATCGAGAATTACTCC 58.850 47.826 0.00 0.00 42.18 3.85
1563 1677 4.321378 GCTCCTACCCATCGAGAATTACTC 60.321 50.000 0.00 0.00 41.79 2.59
1589 1703 1.275505 CTACGTACTCGAGCTCGACA 58.724 55.000 33.84 21.51 44.22 4.35
1656 1770 9.268282 TGAGTTAGACCAGACTTTATTAATCCT 57.732 33.333 0.00 0.00 0.00 3.24
1685 1799 7.582719 AGCCCTTGAATTGGTCTTATAATGTA 58.417 34.615 0.00 0.00 0.00 2.29
1688 1802 9.301897 GATTAGCCCTTGAATTGGTCTTATAAT 57.698 33.333 0.00 0.00 0.00 1.28
1689 1803 8.502738 AGATTAGCCCTTGAATTGGTCTTATAA 58.497 33.333 0.00 0.00 0.00 0.98
1690 1804 8.045720 AGATTAGCCCTTGAATTGGTCTTATA 57.954 34.615 0.00 0.00 0.00 0.98
1691 1805 6.915786 AGATTAGCCCTTGAATTGGTCTTAT 58.084 36.000 0.00 0.00 0.00 1.73
1692 1806 6.327386 AGATTAGCCCTTGAATTGGTCTTA 57.673 37.500 0.00 0.00 0.00 2.10
1693 1807 5.198602 AGATTAGCCCTTGAATTGGTCTT 57.801 39.130 0.00 0.00 0.00 3.01
1694 1808 4.870021 AGATTAGCCCTTGAATTGGTCT 57.130 40.909 0.00 0.00 0.00 3.85
1695 1809 5.185828 ACAAAGATTAGCCCTTGAATTGGTC 59.814 40.000 0.00 0.00 0.00 4.02
1696 1810 5.086621 ACAAAGATTAGCCCTTGAATTGGT 58.913 37.500 0.00 0.00 0.00 3.67
1697 1811 5.665916 ACAAAGATTAGCCCTTGAATTGG 57.334 39.130 0.00 0.00 0.00 3.16
1698 1812 5.870978 CCAACAAAGATTAGCCCTTGAATTG 59.129 40.000 0.00 0.00 0.00 2.32
1699 1813 5.569428 GCCAACAAAGATTAGCCCTTGAATT 60.569 40.000 0.00 0.00 0.00 2.17
1700 1814 4.081476 GCCAACAAAGATTAGCCCTTGAAT 60.081 41.667 0.00 0.00 0.00 2.57
1701 1815 3.258123 GCCAACAAAGATTAGCCCTTGAA 59.742 43.478 0.00 0.00 0.00 2.69
1702 1816 2.825532 GCCAACAAAGATTAGCCCTTGA 59.174 45.455 0.00 0.00 0.00 3.02
1703 1817 2.562298 TGCCAACAAAGATTAGCCCTTG 59.438 45.455 0.00 0.00 0.00 3.61
1704 1818 2.888212 TGCCAACAAAGATTAGCCCTT 58.112 42.857 0.00 0.00 0.00 3.95
1705 1819 2.603075 TGCCAACAAAGATTAGCCCT 57.397 45.000 0.00 0.00 0.00 5.19
1706 1820 3.893326 AATGCCAACAAAGATTAGCCC 57.107 42.857 0.00 0.00 0.00 5.19
1728 1842 9.547753 GCTCATGGTGTTTCTTCTATATAGAAA 57.452 33.333 22.42 10.15 41.37 2.52
1729 1843 8.704668 TGCTCATGGTGTTTCTTCTATATAGAA 58.295 33.333 21.24 21.24 39.82 2.10
1730 1844 8.250143 TGCTCATGGTGTTTCTTCTATATAGA 57.750 34.615 8.44 8.44 0.00 1.98
1731 1845 9.149225 GATGCTCATGGTGTTTCTTCTATATAG 57.851 37.037 3.10 3.10 0.00 1.31
1732 1846 8.650490 TGATGCTCATGGTGTTTCTTCTATATA 58.350 33.333 0.00 0.00 0.00 0.86
1733 1847 7.512130 TGATGCTCATGGTGTTTCTTCTATAT 58.488 34.615 0.00 0.00 0.00 0.86
1734 1848 6.888105 TGATGCTCATGGTGTTTCTTCTATA 58.112 36.000 0.00 0.00 0.00 1.31
1735 1849 5.748402 TGATGCTCATGGTGTTTCTTCTAT 58.252 37.500 0.00 0.00 0.00 1.98
1736 1850 5.164620 TGATGCTCATGGTGTTTCTTCTA 57.835 39.130 0.00 0.00 0.00 2.10
1737 1851 4.025040 TGATGCTCATGGTGTTTCTTCT 57.975 40.909 0.00 0.00 0.00 2.85
1738 1852 4.978083 ATGATGCTCATGGTGTTTCTTC 57.022 40.909 0.00 0.00 35.43 2.87
1749 1863 2.885266 GACTTGGATGCATGATGCTCAT 59.115 45.455 19.19 4.32 45.31 2.90
1750 1864 2.294979 GACTTGGATGCATGATGCTCA 58.705 47.619 19.19 11.18 45.31 4.26
1751 1865 1.263484 CGACTTGGATGCATGATGCTC 59.737 52.381 19.19 12.73 45.31 4.26
1752 1866 1.306148 CGACTTGGATGCATGATGCT 58.694 50.000 19.19 3.99 45.31 3.79
1753 1867 0.309922 CCGACTTGGATGCATGATGC 59.690 55.000 11.12 11.12 42.07 3.91
1754 1868 0.949397 CCCGACTTGGATGCATGATG 59.051 55.000 2.46 0.00 42.00 3.07
1755 1869 0.839277 TCCCGACTTGGATGCATGAT 59.161 50.000 2.46 0.00 42.00 2.45
1756 1870 0.107703 GTCCCGACTTGGATGCATGA 60.108 55.000 2.46 0.00 42.00 3.07
1757 1871 0.107508 AGTCCCGACTTGGATGCATG 60.108 55.000 2.46 0.00 42.00 4.06
1758 1872 2.300996 AGTCCCGACTTGGATGCAT 58.699 52.632 0.00 0.00 42.00 3.96
1759 1873 3.805928 AGTCCCGACTTGGATGCA 58.194 55.556 0.00 0.00 42.00 3.96
1767 1881 0.538977 TCCGAGTTCAAGTCCCGACT 60.539 55.000 0.00 0.00 44.94 4.18
1768 1882 0.531200 ATCCGAGTTCAAGTCCCGAC 59.469 55.000 0.00 0.00 0.00 4.79
1769 1883 0.530744 CATCCGAGTTCAAGTCCCGA 59.469 55.000 0.00 0.00 0.00 5.14
1770 1884 0.460284 CCATCCGAGTTCAAGTCCCG 60.460 60.000 0.00 0.00 0.00 5.14
1771 1885 0.107654 CCCATCCGAGTTCAAGTCCC 60.108 60.000 0.00 0.00 0.00 4.46
1772 1886 0.744771 GCCCATCCGAGTTCAAGTCC 60.745 60.000 0.00 0.00 0.00 3.85
1773 1887 0.250513 AGCCCATCCGAGTTCAAGTC 59.749 55.000 0.00 0.00 0.00 3.01
1774 1888 0.036010 CAGCCCATCCGAGTTCAAGT 60.036 55.000 0.00 0.00 0.00 3.16
1775 1889 0.745845 CCAGCCCATCCGAGTTCAAG 60.746 60.000 0.00 0.00 0.00 3.02
1776 1890 1.299648 CCAGCCCATCCGAGTTCAA 59.700 57.895 0.00 0.00 0.00 2.69
1777 1891 2.989639 CCAGCCCATCCGAGTTCA 59.010 61.111 0.00 0.00 0.00 3.18
1778 1892 2.514824 GCCAGCCCATCCGAGTTC 60.515 66.667 0.00 0.00 0.00 3.01
1779 1893 2.905996 TTGCCAGCCCATCCGAGTT 61.906 57.895 0.00 0.00 0.00 3.01
1780 1894 3.329889 TTGCCAGCCCATCCGAGT 61.330 61.111 0.00 0.00 0.00 4.18
1781 1895 2.825836 GTTGCCAGCCCATCCGAG 60.826 66.667 0.00 0.00 0.00 4.63
1782 1896 3.203086 TTGTTGCCAGCCCATCCGA 62.203 57.895 0.00 0.00 0.00 4.55
1783 1897 2.676121 TTGTTGCCAGCCCATCCG 60.676 61.111 0.00 0.00 0.00 4.18
1784 1898 2.649129 GGTTGTTGCCAGCCCATCC 61.649 63.158 0.00 0.00 36.03 3.51
1785 1899 1.598701 GAGGTTGTTGCCAGCCCATC 61.599 60.000 0.00 0.00 42.60 3.51
1786 1900 1.607467 GAGGTTGTTGCCAGCCCAT 60.607 57.895 0.00 0.00 42.60 4.00
1787 1901 2.203480 GAGGTTGTTGCCAGCCCA 60.203 61.111 0.00 0.00 42.60 5.36
1788 1902 2.203480 TGAGGTTGTTGCCAGCCC 60.203 61.111 0.00 0.00 42.60 5.19
1789 1903 2.924105 GCTGAGGTTGTTGCCAGCC 61.924 63.158 0.00 0.00 44.39 4.85
1790 1904 2.647297 GCTGAGGTTGTTGCCAGC 59.353 61.111 0.00 0.00 44.00 4.85
1791 1905 1.954528 CAGCTGAGGTTGTTGCCAG 59.045 57.895 8.42 0.00 0.00 4.85
1792 1906 2.195567 GCAGCTGAGGTTGTTGCCA 61.196 57.895 20.43 0.00 35.99 4.92
1793 1907 2.647297 GCAGCTGAGGTTGTTGCC 59.353 61.111 20.43 0.00 35.99 4.52
1794 1908 2.647297 GGCAGCTGAGGTTGTTGC 59.353 61.111 20.43 0.00 40.18 4.17
1795 1909 1.108727 TTGGGCAGCTGAGGTTGTTG 61.109 55.000 20.43 0.00 0.00 3.33
1796 1910 1.109323 GTTGGGCAGCTGAGGTTGTT 61.109 55.000 20.43 0.00 0.00 2.83
1797 1911 1.529244 GTTGGGCAGCTGAGGTTGT 60.529 57.895 20.43 0.00 0.00 3.32
1798 1912 2.270986 GGTTGGGCAGCTGAGGTTG 61.271 63.158 20.43 0.00 0.00 3.77
1799 1913 2.116125 GGTTGGGCAGCTGAGGTT 59.884 61.111 20.43 0.00 0.00 3.50
1800 1914 2.766925 TTGGTTGGGCAGCTGAGGT 61.767 57.895 20.43 0.00 0.00 3.85
1801 1915 2.115910 TTGGTTGGGCAGCTGAGG 59.884 61.111 20.43 0.00 0.00 3.86
1802 1916 2.270986 GGTTGGTTGGGCAGCTGAG 61.271 63.158 20.43 0.00 0.00 3.35
1803 1917 2.203480 GGTTGGTTGGGCAGCTGA 60.203 61.111 20.43 0.00 0.00 4.26
1804 1918 3.673484 CGGTTGGTTGGGCAGCTG 61.673 66.667 10.11 10.11 0.00 4.24
1805 1919 4.974721 CCGGTTGGTTGGGCAGCT 62.975 66.667 0.00 0.00 0.00 4.24
1823 1937 2.288729 CACAATATAGGTCGGACGTCGA 59.711 50.000 9.92 7.72 46.77 4.20
1824 1938 2.288729 TCACAATATAGGTCGGACGTCG 59.711 50.000 9.92 5.26 40.90 5.12
1825 1939 3.976793 TCACAATATAGGTCGGACGTC 57.023 47.619 7.13 7.13 0.00 4.34
1826 1940 3.444742 TGTTCACAATATAGGTCGGACGT 59.555 43.478 8.53 8.53 0.00 4.34
1827 1941 3.795101 GTGTTCACAATATAGGTCGGACG 59.205 47.826 1.43 0.00 0.00 4.79
1828 1942 4.804139 CAGTGTTCACAATATAGGTCGGAC 59.196 45.833 0.00 0.00 0.00 4.79
1829 1943 4.707934 TCAGTGTTCACAATATAGGTCGGA 59.292 41.667 5.74 0.00 0.00 4.55
1830 1944 5.006153 TCAGTGTTCACAATATAGGTCGG 57.994 43.478 5.74 0.00 0.00 4.79
1831 1945 8.703336 CAATATCAGTGTTCACAATATAGGTCG 58.297 37.037 5.74 0.00 0.00 4.79
1832 1946 8.993121 CCAATATCAGTGTTCACAATATAGGTC 58.007 37.037 5.74 0.00 0.00 3.85
1833 1947 7.445402 GCCAATATCAGTGTTCACAATATAGGT 59.555 37.037 5.74 0.00 0.00 3.08
1834 1948 7.445096 TGCCAATATCAGTGTTCACAATATAGG 59.555 37.037 5.74 1.07 0.00 2.57
1835 1949 8.382030 TGCCAATATCAGTGTTCACAATATAG 57.618 34.615 5.74 5.40 0.00 1.31
1836 1950 8.785946 CATGCCAATATCAGTGTTCACAATATA 58.214 33.333 5.74 1.28 0.00 0.86
1837 1951 7.503230 TCATGCCAATATCAGTGTTCACAATAT 59.497 33.333 5.74 5.65 0.00 1.28
1838 1952 6.827762 TCATGCCAATATCAGTGTTCACAATA 59.172 34.615 5.74 3.76 0.00 1.90
1839 1953 5.653330 TCATGCCAATATCAGTGTTCACAAT 59.347 36.000 5.74 1.79 0.00 2.71
1840 1954 5.008980 TCATGCCAATATCAGTGTTCACAA 58.991 37.500 5.74 0.00 0.00 3.33
1857 1971 0.865769 ACTGTTTCGAACGTCATGCC 59.134 50.000 0.00 0.00 0.00 4.40
1991 2441 6.919662 ACTGCAAATTTACTTTCACAGACATG 59.080 34.615 0.00 0.00 34.40 3.21
1996 2446 5.830912 TCCACTGCAAATTTACTTTCACAG 58.169 37.500 0.00 0.00 35.54 3.66
2001 2451 8.253113 CCATATTCTCCACTGCAAATTTACTTT 58.747 33.333 0.00 0.00 0.00 2.66
2083 2533 6.409524 TTCTCTTTCTTTTGCCATGACATT 57.590 33.333 0.00 0.00 0.00 2.71
2084 2534 6.409524 TTTCTCTTTCTTTTGCCATGACAT 57.590 33.333 0.00 0.00 0.00 3.06
2087 2537 6.877236 ACTTTTTCTCTTTCTTTTGCCATGA 58.123 32.000 0.00 0.00 0.00 3.07
2090 2540 7.977789 AAAACTTTTTCTCTTTCTTTTGCCA 57.022 28.000 0.00 0.00 0.00 4.92
2141 2591 0.686224 TGGCTTTTCCCTGGCAAATG 59.314 50.000 0.00 0.00 35.82 2.32
2208 2670 8.449251 AATTACAATGGCATCAACAAAAGTTT 57.551 26.923 0.00 0.00 0.00 2.66
2282 2745 5.016173 TGTAGCATGGCAAGTTTAATTCCT 58.984 37.500 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.