Multiple sequence alignment - TraesCS5A01G505700

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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 TraesCS5A01G505700 chr5A 100.000 4866 0 0 1 4866 671157829 671162694 0.000000e+00 8986.0
1 TraesCS5A01G505700 chr4B 94.961 1528 61 9 1702 3228 627939901 627941413 0.000000e+00 2381.0
2 TraesCS5A01G505700 chr4B 90.962 1029 60 16 3302 4325 627941440 627942440 0.000000e+00 1354.0
3 TraesCS5A01G505700 chr4B 83.068 1193 146 35 532 1702 627938775 627939933 0.000000e+00 1033.0
4 TraesCS5A01G505700 chr4B 85.139 323 22 10 4494 4790 627942590 627942912 1.700000e-79 307.0
5 TraesCS5A01G505700 chr4D 94.627 1005 34 10 1702 2700 489709066 489710056 0.000000e+00 1539.0
6 TraesCS5A01G505700 chr4D 94.124 1004 49 4 3302 4305 489710644 489711637 0.000000e+00 1519.0
7 TraesCS5A01G505700 chr4D 87.636 1197 99 19 532 1702 489707925 489709098 0.000000e+00 1345.0
8 TraesCS5A01G505700 chr4D 96.667 540 18 0 2689 3228 489710078 489710617 0.000000e+00 898.0
9 TraesCS5A01G505700 chr4D 82.979 470 27 26 4439 4866 489711718 489712176 4.600000e-100 375.0
10 TraesCS5A01G505700 chr2A 95.930 516 9 3 1 504 177964461 177963946 0.000000e+00 826.0
11 TraesCS5A01G505700 chr2A 90.291 103 8 2 402 503 132616506 132616607 3.060000e-27 134.0
12 TraesCS5A01G505700 chr1B 95.257 506 11 4 1 493 633781164 633781669 0.000000e+00 789.0
13 TraesCS5A01G505700 chr1B 90.476 105 10 0 402 506 89460232 89460128 6.570000e-29 139.0
14 TraesCS5A01G505700 chr3A 92.131 521 22 4 1 502 235835621 235835101 0.000000e+00 717.0
15 TraesCS5A01G505700 chr3A 90.297 505 35 4 1 491 214468271 214468775 0.000000e+00 649.0
16 TraesCS5A01G505700 chr3A 87.156 109 13 1 404 511 585737348 585737240 6.610000e-24 122.0
17 TraesCS5A01G505700 chr3A 84.252 127 14 5 403 527 111806977 111807099 8.560000e-23 119.0
18 TraesCS5A01G505700 chr6A 82.019 317 39 9 198 502 244169393 244169083 2.250000e-63 254.0
19 TraesCS5A01G505700 chr7A 80.997 321 38 13 198 502 32597169 32597482 2.930000e-57 233.0
20 TraesCS5A01G505700 chr7A 85.833 120 14 3 394 512 217760163 217760280 1.840000e-24 124.0
21 TraesCS5A01G505700 chr1A 80.685 321 37 13 198 502 275054370 275054059 4.900000e-55 226.0
22 TraesCS5A01G505700 chr6B 90.090 111 9 2 392 501 271487656 271487547 5.080000e-30 143.0
23 TraesCS5A01G505700 chr6B 86.957 115 12 3 392 504 511341744 511341857 5.110000e-25 126.0
24 TraesCS5A01G505700 chr2B 88.496 113 11 2 394 505 76014769 76014658 8.500000e-28 135.0
25 TraesCS5A01G505700 chr3B 84.783 138 15 3 309 440 769474502 769474639 3.060000e-27 134.0
26 TraesCS5A01G505700 chr7B 89.109 101 11 0 404 504 606348787 606348687 5.110000e-25 126.0
27 TraesCS5A01G505700 chr1D 83.133 83 7 5 263 344 261459723 261459799 8.740000e-08 69.4


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 TraesCS5A01G505700 chr5A 671157829 671162694 4865 False 8986.00 8986 100.0000 1 4866 1 chr5A.!!$F1 4865
1 TraesCS5A01G505700 chr4B 627938775 627942912 4137 False 1268.75 2381 88.5325 532 4790 4 chr4B.!!$F1 4258
2 TraesCS5A01G505700 chr4D 489707925 489712176 4251 False 1135.20 1539 91.2066 532 4866 5 chr4D.!!$F1 4334
3 TraesCS5A01G505700 chr2A 177963946 177964461 515 True 826.00 826 95.9300 1 504 1 chr2A.!!$R1 503
4 TraesCS5A01G505700 chr1B 633781164 633781669 505 False 789.00 789 95.2570 1 493 1 chr1B.!!$F1 492
5 TraesCS5A01G505700 chr3A 235835101 235835621 520 True 717.00 717 92.1310 1 502 1 chr3A.!!$R1 501
6 TraesCS5A01G505700 chr3A 214468271 214468775 504 False 649.00 649 90.2970 1 491 1 chr3A.!!$F2 490

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
867 920 0.250081 GATCTCCACGATTCCTGGGC 60.250 60.0 0.00 0.0 30.84 5.36 F
1510 1574 0.249911 GACTGTTCTGCGGAGTGGTT 60.250 55.0 3.10 0.0 0.00 3.67 F
1532 1596 0.462581 TGGACCGCTGATTGCTCATC 60.463 55.0 0.00 0.0 40.11 2.92 F
3321 3425 0.662619 TCAGGTTGCGCTGAAGTTTG 59.337 50.0 9.73 0.0 0.00 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2570 2642 1.531149 ACTTCATCAAAAGTGACCGCG 59.469 47.619 0.0 0.0 38.06 6.46 R
3374 3478 0.245539 GCACTCTACGGGTGTTGCTA 59.754 55.000 0.0 0.0 37.07 3.49 R
3379 3483 0.973632 TCAATGCACTCTACGGGTGT 59.026 50.000 0.0 0.0 37.07 4.16 R
4488 4629 0.173255 GGAACCCATGATTTGCCACG 59.827 55.000 0.0 0.0 0.00 4.94 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
64 65 1.999634 AAGTGGAGCTGGTGCAAGGT 62.000 55.000 1.75 0.00 42.74 3.50
171 172 4.332543 TGCGGAAGGAGGGGAGGT 62.333 66.667 0.00 0.00 0.00 3.85
504 527 9.706691 CGTGCTTTATTATTAGGGAGAGATTAA 57.293 33.333 0.00 0.00 0.00 1.40
514 537 7.873699 TTAGGGAGAGATTAATTAAGGAGGG 57.126 40.000 3.94 0.00 0.00 4.30
515 538 6.056997 AGGGAGAGATTAATTAAGGAGGGA 57.943 41.667 3.94 0.00 0.00 4.20
516 539 6.648856 AGGGAGAGATTAATTAAGGAGGGAT 58.351 40.000 3.94 0.00 0.00 3.85
517 540 7.092223 AGGGAGAGATTAATTAAGGAGGGATT 58.908 38.462 3.94 0.00 0.00 3.01
518 541 8.249490 AGGGAGAGATTAATTAAGGAGGGATTA 58.751 37.037 3.94 0.00 0.00 1.75
519 542 8.544622 GGGAGAGATTAATTAAGGAGGGATTAG 58.455 40.741 3.94 0.00 0.00 1.73
520 543 8.544622 GGAGAGATTAATTAAGGAGGGATTAGG 58.455 40.741 3.94 0.00 0.00 2.69
521 544 8.456221 AGAGATTAATTAAGGAGGGATTAGGG 57.544 38.462 3.94 0.00 0.00 3.53
522 545 8.249490 AGAGATTAATTAAGGAGGGATTAGGGA 58.751 37.037 3.94 0.00 0.00 4.20
523 546 9.063484 GAGATTAATTAAGGAGGGATTAGGGAT 57.937 37.037 3.94 0.00 0.00 3.85
527 550 9.923348 TTAATTAAGGAGGGATTAGGGATAGAA 57.077 33.333 0.00 0.00 0.00 2.10
528 551 8.830084 AATTAAGGAGGGATTAGGGATAGAAA 57.170 34.615 0.00 0.00 0.00 2.52
529 552 9.424906 AATTAAGGAGGGATTAGGGATAGAAAT 57.575 33.333 0.00 0.00 0.00 2.17
606 629 1.289800 GGACTCCTCGCCGTTGTTTC 61.290 60.000 0.00 0.00 0.00 2.78
611 634 0.666374 CCTCGCCGTTGTTTCCTTTT 59.334 50.000 0.00 0.00 0.00 2.27
829 882 2.469516 CGAGGTATTTGCACCCGCC 61.470 63.158 0.00 0.00 39.62 6.13
867 920 0.250081 GATCTCCACGATTCCTGGGC 60.250 60.000 0.00 0.00 30.84 5.36
935 988 1.571460 GGGCGTCGATTGATCATGC 59.429 57.895 0.00 0.00 0.00 4.06
949 1002 2.159327 TCATGCTGCTGATATGGTCG 57.841 50.000 0.00 0.00 0.00 4.79
954 1007 2.693074 TGCTGCTGATATGGTCGAGTTA 59.307 45.455 0.00 0.00 0.00 2.24
969 1022 7.822658 TGGTCGAGTTATTTCCTTTAAATTGG 58.177 34.615 0.00 0.00 38.71 3.16
970 1023 6.750501 GGTCGAGTTATTTCCTTTAAATTGGC 59.249 38.462 0.00 0.00 38.71 4.52
981 1037 2.806945 TAAATTGGCAGGACCTGAGG 57.193 50.000 26.25 0.00 40.22 3.86
1055 1111 2.095212 GGAAGAAAGCAAAAGGTAGGCG 60.095 50.000 0.00 0.00 0.00 5.52
1081 1137 1.751924 CTTCCTCTTCCCTGGTACTCG 59.248 57.143 0.00 0.00 0.00 4.18
1111 1167 6.979817 TCAAACATCATGCTAATTTATGCACC 59.020 34.615 0.00 0.00 42.26 5.01
1140 1199 3.187022 GTGCCTTGGTGATTCAATTTTGC 59.813 43.478 0.00 0.00 0.00 3.68
1204 1263 8.688151 TCTTTTAGATAGAGCTAACTTGAGACC 58.312 37.037 0.00 0.00 30.53 3.85
1227 1290 4.201753 CGACAGAAGCATATGTTCCAACAG 60.202 45.833 4.29 0.00 43.04 3.16
1231 1294 5.647658 CAGAAGCATATGTTCCAACAGGTTA 59.352 40.000 4.29 0.00 43.04 2.85
1241 1304 2.916934 TCCAACAGGTTACATAGGGCTT 59.083 45.455 0.00 0.00 0.00 4.35
1314 1377 6.092259 AGCTGTATGATAGTTTTTGAACGGAC 59.908 38.462 0.00 0.00 0.00 4.79
1367 1430 9.691362 TTCCTTTTTCAGTTACTGCATTAATTC 57.309 29.630 7.61 0.00 0.00 2.17
1399 1463 3.587061 TCCCATATATACCTGCCAACTGG 59.413 47.826 0.00 0.00 40.61 4.00
1430 1494 1.140652 TGCATTCCTATGATCGGCACA 59.859 47.619 0.00 0.00 33.37 4.57
1431 1495 2.224597 TGCATTCCTATGATCGGCACAT 60.225 45.455 0.00 0.00 33.37 3.21
1494 1558 3.967987 GGAACCCTGTATATGACCTGACT 59.032 47.826 0.00 0.00 0.00 3.41
1498 1562 4.406003 ACCCTGTATATGACCTGACTGTTC 59.594 45.833 0.00 0.00 0.00 3.18
1505 1569 0.389166 GACCTGACTGTTCTGCGGAG 60.389 60.000 0.00 0.00 0.00 4.63
1509 1573 1.367840 GACTGTTCTGCGGAGTGGT 59.632 57.895 3.10 0.00 0.00 4.16
1510 1574 0.249911 GACTGTTCTGCGGAGTGGTT 60.250 55.000 3.10 0.00 0.00 3.67
1512 1576 0.868406 CTGTTCTGCGGAGTGGTTTC 59.132 55.000 3.10 0.00 0.00 2.78
1517 1581 0.951040 CTGCGGAGTGGTTTCTGGAC 60.951 60.000 0.00 0.00 0.00 4.02
1518 1582 1.671379 GCGGAGTGGTTTCTGGACC 60.671 63.158 0.00 0.00 40.23 4.46
1532 1596 0.462581 TGGACCGCTGATTGCTCATC 60.463 55.000 0.00 0.00 40.11 2.92
1538 1602 2.477357 CCGCTGATTGCTCATCTTGTTG 60.477 50.000 0.00 0.00 40.11 3.33
1557 1623 9.701098 TCTTGTTGTAGTATCTCGTTGTTTTAT 57.299 29.630 0.00 0.00 0.00 1.40
1588 1654 4.582869 AGTTTGAGTAATAACCGTTCCCC 58.417 43.478 0.00 0.00 0.00 4.81
1589 1655 4.041938 AGTTTGAGTAATAACCGTTCCCCA 59.958 41.667 0.00 0.00 0.00 4.96
1606 1672 3.591527 TCCCCACCTTTATCTGATGTTGT 59.408 43.478 0.00 0.00 0.00 3.32
1610 1676 4.637534 CCACCTTTATCTGATGTTGTCTGG 59.362 45.833 0.00 0.00 0.00 3.86
1611 1677 5.248640 CACCTTTATCTGATGTTGTCTGGT 58.751 41.667 0.00 0.00 0.00 4.00
1620 1686 6.406370 TCTGATGTTGTCTGGTAAATACAGG 58.594 40.000 0.00 0.00 36.62 4.00
1626 1692 8.927675 TGTTGTCTGGTAAATACAGGTTAATT 57.072 30.769 0.00 0.00 36.62 1.40
1627 1693 9.357161 TGTTGTCTGGTAAATACAGGTTAATTT 57.643 29.630 0.00 0.00 36.62 1.82
1633 1699 8.184304 TGGTAAATACAGGTTAATTTTGTGCT 57.816 30.769 0.00 0.00 0.00 4.40
1635 1701 8.921670 GGTAAATACAGGTTAATTTTGTGCTTG 58.078 33.333 0.00 0.00 0.00 4.01
1636 1702 7.961325 AAATACAGGTTAATTTTGTGCTTGG 57.039 32.000 0.00 0.00 0.00 3.61
1639 1705 5.739959 ACAGGTTAATTTTGTGCTTGGTTT 58.260 33.333 0.00 0.00 0.00 3.27
1640 1706 5.584251 ACAGGTTAATTTTGTGCTTGGTTTG 59.416 36.000 0.00 0.00 0.00 2.93
1641 1707 5.584251 CAGGTTAATTTTGTGCTTGGTTTGT 59.416 36.000 0.00 0.00 0.00 2.83
1644 1710 7.175816 AGGTTAATTTTGTGCTTGGTTTGTTTT 59.824 29.630 0.00 0.00 0.00 2.43
1645 1711 8.451748 GGTTAATTTTGTGCTTGGTTTGTTTTA 58.548 29.630 0.00 0.00 0.00 1.52
1646 1712 9.484326 GTTAATTTTGTGCTTGGTTTGTTTTAG 57.516 29.630 0.00 0.00 0.00 1.85
1650 1716 7.497925 TTTGTGCTTGGTTTGTTTTAGTTTT 57.502 28.000 0.00 0.00 0.00 2.43
1651 1717 6.713792 TGTGCTTGGTTTGTTTTAGTTTTC 57.286 33.333 0.00 0.00 0.00 2.29
1652 1718 6.223852 TGTGCTTGGTTTGTTTTAGTTTTCA 58.776 32.000 0.00 0.00 0.00 2.69
1653 1719 6.367422 TGTGCTTGGTTTGTTTTAGTTTTCAG 59.633 34.615 0.00 0.00 0.00 3.02
1654 1720 5.350091 TGCTTGGTTTGTTTTAGTTTTCAGC 59.650 36.000 0.00 0.00 0.00 4.26
1657 1723 4.109766 GGTTTGTTTTAGTTTTCAGCGCT 58.890 39.130 2.64 2.64 0.00 5.92
1660 1726 6.401688 GGTTTGTTTTAGTTTTCAGCGCTTTT 60.402 34.615 7.50 0.00 0.00 2.27
1685 1751 2.104281 AGCCTTCGTCTGGTTGTACTTT 59.896 45.455 0.00 0.00 0.00 2.66
1686 1752 3.322828 AGCCTTCGTCTGGTTGTACTTTA 59.677 43.478 0.00 0.00 0.00 1.85
1687 1753 4.020485 AGCCTTCGTCTGGTTGTACTTTAT 60.020 41.667 0.00 0.00 0.00 1.40
1688 1754 4.694037 GCCTTCGTCTGGTTGTACTTTATT 59.306 41.667 0.00 0.00 0.00 1.40
1689 1755 5.390567 GCCTTCGTCTGGTTGTACTTTATTG 60.391 44.000 0.00 0.00 0.00 1.90
1690 1756 5.699458 CCTTCGTCTGGTTGTACTTTATTGT 59.301 40.000 0.00 0.00 0.00 2.71
1691 1757 6.128634 CCTTCGTCTGGTTGTACTTTATTGTC 60.129 42.308 0.00 0.00 0.00 3.18
1692 1758 5.845103 TCGTCTGGTTGTACTTTATTGTCA 58.155 37.500 0.00 0.00 0.00 3.58
1693 1759 6.460781 TCGTCTGGTTGTACTTTATTGTCAT 58.539 36.000 0.00 0.00 0.00 3.06
1694 1760 6.588756 TCGTCTGGTTGTACTTTATTGTCATC 59.411 38.462 0.00 0.00 0.00 2.92
1695 1761 6.590292 CGTCTGGTTGTACTTTATTGTCATCT 59.410 38.462 0.00 0.00 0.00 2.90
1696 1762 7.411912 CGTCTGGTTGTACTTTATTGTCATCTG 60.412 40.741 0.00 0.00 0.00 2.90
1697 1763 7.602644 GTCTGGTTGTACTTTATTGTCATCTGA 59.397 37.037 0.00 0.00 0.00 3.27
1698 1764 8.154203 TCTGGTTGTACTTTATTGTCATCTGAA 58.846 33.333 0.00 0.00 0.00 3.02
1699 1765 8.862325 TGGTTGTACTTTATTGTCATCTGAAT 57.138 30.769 0.00 0.00 0.00 2.57
1700 1766 8.946085 TGGTTGTACTTTATTGTCATCTGAATC 58.054 33.333 0.00 0.00 0.00 2.52
1701 1767 9.167311 GGTTGTACTTTATTGTCATCTGAATCT 57.833 33.333 0.00 0.00 0.00 2.40
1704 1770 9.087424 TGTACTTTATTGTCATCTGAATCTTCG 57.913 33.333 0.00 0.00 0.00 3.79
1705 1771 9.088512 GTACTTTATTGTCATCTGAATCTTCGT 57.911 33.333 0.00 0.00 0.00 3.85
1706 1772 8.190888 ACTTTATTGTCATCTGAATCTTCGTC 57.809 34.615 0.00 0.00 0.00 4.20
1707 1773 8.037758 ACTTTATTGTCATCTGAATCTTCGTCT 58.962 33.333 0.00 0.00 0.00 4.18
1708 1774 7.761651 TTATTGTCATCTGAATCTTCGTCTG 57.238 36.000 0.00 0.00 0.00 3.51
1709 1775 4.115401 TGTCATCTGAATCTTCGTCTGG 57.885 45.455 0.00 0.00 0.00 3.86
1710 1776 3.511540 TGTCATCTGAATCTTCGTCTGGT 59.488 43.478 0.00 0.00 0.00 4.00
1711 1777 4.021104 TGTCATCTGAATCTTCGTCTGGTT 60.021 41.667 0.00 0.00 0.00 3.67
1712 1778 4.328440 GTCATCTGAATCTTCGTCTGGTTG 59.672 45.833 0.00 0.00 0.00 3.77
1713 1779 4.021104 TCATCTGAATCTTCGTCTGGTTGT 60.021 41.667 0.00 0.00 0.00 3.32
1714 1780 5.185056 TCATCTGAATCTTCGTCTGGTTGTA 59.815 40.000 0.00 0.00 0.00 2.41
1715 1781 4.806330 TCTGAATCTTCGTCTGGTTGTAC 58.194 43.478 0.00 0.00 0.00 2.90
1716 1782 4.523173 TCTGAATCTTCGTCTGGTTGTACT 59.477 41.667 0.00 0.00 0.00 2.73
1717 1783 5.010719 TCTGAATCTTCGTCTGGTTGTACTT 59.989 40.000 0.00 0.00 0.00 2.24
1718 1784 5.607477 TGAATCTTCGTCTGGTTGTACTTT 58.393 37.500 0.00 0.00 0.00 2.66
1719 1785 6.053005 TGAATCTTCGTCTGGTTGTACTTTT 58.947 36.000 0.00 0.00 0.00 2.27
1746 1812 5.741510 GTCATCTGAATCTACGAGTGTCTTG 59.258 44.000 0.00 0.00 0.00 3.02
1749 1815 4.158579 TCTGAATCTACGAGTGTCTTGCAT 59.841 41.667 0.00 0.00 0.00 3.96
1754 1820 5.386958 TCTACGAGTGTCTTGCATTAACT 57.613 39.130 0.00 0.00 0.00 2.24
1755 1821 5.779922 TCTACGAGTGTCTTGCATTAACTT 58.220 37.500 0.00 0.00 0.00 2.66
1756 1822 6.916440 TCTACGAGTGTCTTGCATTAACTTA 58.084 36.000 0.00 0.00 0.00 2.24
1763 1829 8.430801 AGTGTCTTGCATTAACTTATCTCATC 57.569 34.615 0.00 0.00 0.00 2.92
1860 1931 1.414919 TCTGGTTTGGTAAGCACTCGT 59.585 47.619 0.00 0.00 36.88 4.18
1867 1938 5.390567 GGTTTGGTAAGCACTCGTCATTTAG 60.391 44.000 0.00 0.00 0.00 1.85
1868 1939 3.259064 TGGTAAGCACTCGTCATTTAGC 58.741 45.455 0.00 0.00 0.00 3.09
1869 1940 2.608090 GGTAAGCACTCGTCATTTAGCC 59.392 50.000 0.00 0.00 0.00 3.93
1885 1956 1.301637 GCCGCCCATTGCAGTTTTT 60.302 52.632 0.00 0.00 41.33 1.94
1914 1986 8.251721 GTGTGTGAAGATAATGTCCTAACTACT 58.748 37.037 0.00 0.00 0.00 2.57
1953 2025 9.942850 AGCTAAAAACACATTGCCTTTATTATT 57.057 25.926 0.00 0.00 0.00 1.40
1954 2026 9.971744 GCTAAAAACACATTGCCTTTATTATTG 57.028 29.630 0.00 0.00 0.00 1.90
2098 2170 8.617290 TCCAAAGTAAGATCCTTGTAAAGTTC 57.383 34.615 0.00 0.00 44.25 3.01
2200 2272 3.016736 GCTGCTAGTTTGGCCTCATTAA 58.983 45.455 3.32 0.00 0.00 1.40
2213 2285 5.776744 GGCCTCATTAAAGCCTCATAAATG 58.223 41.667 0.00 0.00 43.62 2.32
2214 2286 5.302823 GGCCTCATTAAAGCCTCATAAATGT 59.697 40.000 0.00 0.00 43.62 2.71
2215 2287 6.490040 GGCCTCATTAAAGCCTCATAAATGTA 59.510 38.462 0.00 0.00 43.62 2.29
2216 2288 7.363431 GCCTCATTAAAGCCTCATAAATGTAC 58.637 38.462 0.00 0.00 0.00 2.90
2448 2520 1.731160 GCAGCTGTGTTCTTAGCTCAG 59.269 52.381 16.64 0.00 46.76 3.35
2450 2522 2.735663 CAGCTGTGTTCTTAGCTCAGTG 59.264 50.000 5.25 0.00 46.76 3.66
2456 2528 5.368145 TGTGTTCTTAGCTCAGTGTTTCAT 58.632 37.500 0.00 0.00 0.00 2.57
2513 2585 5.282055 TCCTAACTTATGGCATGTCAGAG 57.718 43.478 10.98 8.98 0.00 3.35
2570 2642 2.680974 TGCTCCTGCAGGTGTCAACC 62.681 60.000 31.58 16.09 45.31 3.77
2710 2814 4.518970 TGAAAACATAGGAAGTTGGTGCTC 59.481 41.667 0.00 0.00 0.00 4.26
2769 2873 5.776744 AGCTGGATTTGAATCTTTTGTCAC 58.223 37.500 3.94 0.00 35.73 3.67
2823 2927 2.470057 AACCAACATTCAACCCCACT 57.530 45.000 0.00 0.00 0.00 4.00
2824 2928 1.703411 ACCAACATTCAACCCCACTG 58.297 50.000 0.00 0.00 0.00 3.66
2843 2947 5.824624 CCACTGCTTCTCCATATTGTGTTAT 59.175 40.000 0.00 0.00 0.00 1.89
2911 3015 3.561310 GCAATACCTTCATGATCGCTTCA 59.439 43.478 0.00 0.00 39.12 3.02
3015 3119 0.804989 CCGAGGTTGGATTTGACAGC 59.195 55.000 0.00 0.00 0.00 4.40
3048 3152 4.039973 TCTGTTACCAAGTACAACTCAGGG 59.960 45.833 0.00 0.00 30.32 4.45
3107 3211 8.850454 TTACAAATGTAAGTCTTTGCAAGTTC 57.150 30.769 0.00 0.00 35.75 3.01
3123 3227 3.018423 AGTTCCTGCTTTGTTCAAGGT 57.982 42.857 0.00 0.00 32.37 3.50
3166 3270 1.197492 TGTGACACATTGCTCGAATGC 59.803 47.619 3.56 0.00 44.85 3.56
3218 3322 2.004733 GCCCACATAGTTGTTCGGTAC 58.995 52.381 0.00 0.00 32.34 3.34
3228 3332 5.148651 AGTTGTTCGGTACTGCTTTAGAT 57.851 39.130 0.00 0.00 0.00 1.98
3231 3335 6.812160 AGTTGTTCGGTACTGCTTTAGATTAG 59.188 38.462 0.00 0.00 0.00 1.73
3232 3336 5.657474 TGTTCGGTACTGCTTTAGATTAGG 58.343 41.667 0.00 0.00 0.00 2.69
3233 3337 5.419788 TGTTCGGTACTGCTTTAGATTAGGA 59.580 40.000 0.00 0.00 0.00 2.94
3234 3338 5.769484 TCGGTACTGCTTTAGATTAGGAG 57.231 43.478 0.00 0.00 37.14 3.69
3235 3339 5.198965 TCGGTACTGCTTTAGATTAGGAGT 58.801 41.667 0.00 0.00 44.89 3.85
3236 3340 6.359804 TCGGTACTGCTTTAGATTAGGAGTA 58.640 40.000 0.00 0.00 41.69 2.59
3237 3341 6.485984 TCGGTACTGCTTTAGATTAGGAGTAG 59.514 42.308 4.76 0.00 44.01 2.57
3238 3342 6.262720 CGGTACTGCTTTAGATTAGGAGTAGT 59.737 42.308 4.76 0.00 44.01 2.73
3239 3343 7.443575 CGGTACTGCTTTAGATTAGGAGTAGTA 59.556 40.741 4.76 0.00 44.01 1.82
3240 3344 9.129532 GGTACTGCTTTAGATTAGGAGTAGTAA 57.870 37.037 4.76 0.00 44.01 2.24
3257 3361 9.018582 GGAGTAGTAAGTAGTAACAAGGAAGAA 57.981 37.037 0.00 0.00 0.00 2.52
3275 3379 9.628500 AAGGAAGAACTTGACTAGTTAAATTGT 57.372 29.630 0.00 0.00 47.00 2.71
3276 3380 9.057089 AGGAAGAACTTGACTAGTTAAATTGTG 57.943 33.333 0.00 0.00 47.00 3.33
3277 3381 7.803659 GGAAGAACTTGACTAGTTAAATTGTGC 59.196 37.037 0.00 0.00 47.00 4.57
3278 3382 7.801716 AGAACTTGACTAGTTAAATTGTGCA 57.198 32.000 0.00 0.00 47.00 4.57
3279 3383 7.865707 AGAACTTGACTAGTTAAATTGTGCAG 58.134 34.615 0.00 0.00 47.00 4.41
3280 3384 6.002062 ACTTGACTAGTTAAATTGTGCAGC 57.998 37.500 0.00 0.00 31.29 5.25
3281 3385 5.765182 ACTTGACTAGTTAAATTGTGCAGCT 59.235 36.000 0.00 0.00 31.29 4.24
3282 3386 6.934645 ACTTGACTAGTTAAATTGTGCAGCTA 59.065 34.615 0.00 0.00 31.29 3.32
3283 3387 7.444183 ACTTGACTAGTTAAATTGTGCAGCTAA 59.556 33.333 0.00 0.00 31.29 3.09
3284 3388 7.921786 TGACTAGTTAAATTGTGCAGCTAAT 57.078 32.000 0.00 0.00 0.00 1.73
3285 3389 8.335532 TGACTAGTTAAATTGTGCAGCTAATT 57.664 30.769 0.00 0.00 0.00 1.40
3286 3390 8.236586 TGACTAGTTAAATTGTGCAGCTAATTG 58.763 33.333 0.00 0.49 0.00 2.32
3287 3391 8.110860 ACTAGTTAAATTGTGCAGCTAATTGT 57.889 30.769 8.40 0.95 0.00 2.71
3288 3392 8.237267 ACTAGTTAAATTGTGCAGCTAATTGTC 58.763 33.333 8.40 4.23 0.00 3.18
3289 3393 7.219484 AGTTAAATTGTGCAGCTAATTGTCT 57.781 32.000 8.40 5.80 0.00 3.41
3290 3394 8.335532 AGTTAAATTGTGCAGCTAATTGTCTA 57.664 30.769 8.40 0.00 0.00 2.59
3291 3395 8.792633 AGTTAAATTGTGCAGCTAATTGTCTAA 58.207 29.630 8.40 3.20 0.00 2.10
3292 3396 9.405587 GTTAAATTGTGCAGCTAATTGTCTAAA 57.594 29.630 8.40 0.00 0.00 1.85
3293 3397 9.624697 TTAAATTGTGCAGCTAATTGTCTAAAG 57.375 29.630 8.40 0.00 0.00 1.85
3294 3398 4.685169 TGTGCAGCTAATTGTCTAAAGC 57.315 40.909 0.00 0.00 35.16 3.51
3295 3399 3.125146 TGTGCAGCTAATTGTCTAAAGCG 59.875 43.478 0.00 0.00 39.94 4.68
3296 3400 2.677836 TGCAGCTAATTGTCTAAAGCGG 59.322 45.455 0.00 0.00 39.94 5.52
3297 3401 2.936498 GCAGCTAATTGTCTAAAGCGGA 59.064 45.455 0.73 0.00 39.94 5.54
3298 3402 3.374058 GCAGCTAATTGTCTAAAGCGGAA 59.626 43.478 0.73 0.00 39.94 4.30
3299 3403 4.494855 GCAGCTAATTGTCTAAAGCGGAAG 60.495 45.833 0.73 0.00 39.94 3.46
3321 3425 0.662619 TCAGGTTGCGCTGAAGTTTG 59.337 50.000 9.73 0.00 0.00 2.93
3374 3478 8.634188 AGGATAATACTGGTAACTTTTAGGGT 57.366 34.615 0.00 0.00 37.61 4.34
3379 3483 5.571791 ACTGGTAACTTTTAGGGTAGCAA 57.428 39.130 0.00 0.00 37.61 3.91
3411 3515 2.935201 GTGCATTGAGATGTCTGTCTCC 59.065 50.000 0.00 0.00 43.17 3.71
3454 3560 7.124750 TCTCTTGACAAACTCCATCTGATATGA 59.875 37.037 0.00 0.00 0.00 2.15
3458 3564 7.044181 TGACAAACTCCATCTGATATGACTTC 58.956 38.462 0.00 0.00 0.00 3.01
3484 3590 7.768120 CCCTATATTGGATATCTTCTGCAAGTC 59.232 40.741 4.60 0.00 33.76 3.01
3509 3615 2.752354 TGACCGGATGCATTTTGGTTAG 59.248 45.455 9.46 0.00 31.86 2.34
3618 3724 2.185310 ATCCACCTGTTCAGCCCGAC 62.185 60.000 0.00 0.00 0.00 4.79
3872 3978 3.083349 TCAGCCCCTGATCACCCG 61.083 66.667 0.00 0.00 35.39 5.28
3873 3979 4.864334 CAGCCCCTGATCACCCGC 62.864 72.222 0.00 0.00 32.44 6.13
3981 4088 6.105333 CGATGATTCTTTTTGGTCTCTCTCT 58.895 40.000 0.00 0.00 0.00 3.10
3982 4089 6.255453 CGATGATTCTTTTTGGTCTCTCTCTC 59.745 42.308 0.00 0.00 0.00 3.20
3992 4099 3.716872 TGGTCTCTCTCTCTTTTTGGGTT 59.283 43.478 0.00 0.00 0.00 4.11
4074 4181 0.691078 TTCCTCCGATTAGCCTGCCT 60.691 55.000 0.00 0.00 0.00 4.75
4127 4234 8.788325 ACTGGAAATATACAGAGGTTTTGTAC 57.212 34.615 8.47 0.00 38.09 2.90
4128 4235 8.603304 ACTGGAAATATACAGAGGTTTTGTACT 58.397 33.333 8.47 0.00 38.09 2.73
4138 4245 8.086143 ACAGAGGTTTTGTACTATTAGGCATA 57.914 34.615 0.00 0.00 0.00 3.14
4151 4259 2.046285 GGCATACGCTTTGGCCACT 61.046 57.895 3.88 0.00 45.70 4.00
4167 4275 1.402968 CCACTCCAGGCGATGAAATTG 59.597 52.381 0.00 0.00 0.00 2.32
4179 4287 3.365666 CGATGAAATTGCTGACTTGCTGT 60.366 43.478 0.00 0.00 0.00 4.40
4180 4288 3.631145 TGAAATTGCTGACTTGCTGTC 57.369 42.857 3.95 3.95 45.54 3.51
4200 4308 0.793104 CGGGTTTGCTCGAAAATCGC 60.793 55.000 0.00 0.00 42.12 4.58
4212 4320 3.620300 AAATCGCCGCGTCGACTGA 62.620 57.895 16.73 0.00 41.62 3.41
4213 4321 4.538283 ATCGCCGCGTCGACTGAG 62.538 66.667 16.73 8.88 41.62 3.35
4220 4328 2.675423 CGTCGACTGAGGGGGTCA 60.675 66.667 14.70 0.00 33.73 4.02
4248 4356 5.707298 CAGGGTGAGTGATTGTTAGTTTGAT 59.293 40.000 0.00 0.00 0.00 2.57
4254 4362 8.110612 GTGAGTGATTGTTAGTTTGATATCGTG 58.889 37.037 0.00 0.00 0.00 4.35
4255 4363 7.277760 TGAGTGATTGTTAGTTTGATATCGTGG 59.722 37.037 0.00 0.00 0.00 4.94
4256 4364 7.327975 AGTGATTGTTAGTTTGATATCGTGGA 58.672 34.615 0.00 0.00 0.00 4.02
4258 4366 8.612619 GTGATTGTTAGTTTGATATCGTGGATT 58.387 33.333 0.00 0.00 0.00 3.01
4286 4394 1.273048 TGCATTTCCCTGATGTGTTGC 59.727 47.619 0.00 0.00 0.00 4.17
4298 4406 1.229975 TGTGTTGCTGTCATGGCTCG 61.230 55.000 0.00 0.00 0.00 5.03
4304 4412 1.160137 GCTGTCATGGCTCGTCTTTT 58.840 50.000 0.00 0.00 0.00 2.27
4305 4413 1.129437 GCTGTCATGGCTCGTCTTTTC 59.871 52.381 0.00 0.00 0.00 2.29
4318 4426 2.030457 CGTCTTTTCGCTGAAAGTGTGT 59.970 45.455 8.07 0.00 46.69 3.72
4325 4433 3.466836 TCGCTGAAAGTGTGTTGAGATT 58.533 40.909 0.00 0.00 46.69 2.40
4326 4434 3.876914 TCGCTGAAAGTGTGTTGAGATTT 59.123 39.130 0.00 0.00 46.69 2.17
4327 4435 4.335315 TCGCTGAAAGTGTGTTGAGATTTT 59.665 37.500 0.00 0.00 46.69 1.82
4328 4436 4.438797 CGCTGAAAGTGTGTTGAGATTTTG 59.561 41.667 0.00 0.00 40.27 2.44
4329 4437 4.741676 GCTGAAAGTGTGTTGAGATTTTGG 59.258 41.667 0.00 0.00 35.30 3.28
4330 4438 5.261209 TGAAAGTGTGTTGAGATTTTGGG 57.739 39.130 0.00 0.00 0.00 4.12
4337 4476 3.559655 GTGTTGAGATTTTGGGTTTTGCC 59.440 43.478 0.00 0.00 0.00 4.52
4357 4496 1.983691 CATGTCCTGGATGGCCTATCT 59.016 52.381 3.32 0.00 36.03 1.98
4371 4510 5.132502 TGGCCTATCTACCAATGATTTGTG 58.867 41.667 3.32 0.00 31.46 3.33
4372 4511 5.133221 GGCCTATCTACCAATGATTTGTGT 58.867 41.667 0.00 0.00 0.00 3.72
4373 4512 5.009010 GGCCTATCTACCAATGATTTGTGTG 59.991 44.000 0.00 0.00 0.00 3.82
4380 4519 1.275856 CAATGATTTGTGTGGGGGTGG 59.724 52.381 0.00 0.00 0.00 4.61
4381 4520 0.252193 ATGATTTGTGTGGGGGTGGG 60.252 55.000 0.00 0.00 0.00 4.61
4382 4521 1.609210 GATTTGTGTGGGGGTGGGG 60.609 63.158 0.00 0.00 0.00 4.96
4383 4522 2.087857 GATTTGTGTGGGGGTGGGGA 62.088 60.000 0.00 0.00 0.00 4.81
4384 4523 1.451372 ATTTGTGTGGGGGTGGGGAT 61.451 55.000 0.00 0.00 0.00 3.85
4385 4524 2.379120 TTTGTGTGGGGGTGGGGATG 62.379 60.000 0.00 0.00 0.00 3.51
4386 4525 4.759205 GTGTGGGGGTGGGGATGC 62.759 72.222 0.00 0.00 0.00 3.91
4394 4533 4.101448 GTGGGGATGCCTGCGTCT 62.101 66.667 2.19 0.00 32.85 4.18
4395 4534 4.100084 TGGGGATGCCTGCGTCTG 62.100 66.667 2.19 0.00 32.85 3.51
4397 4536 4.479993 GGGATGCCTGCGTCTGCT 62.480 66.667 10.89 0.00 43.34 4.24
4398 4537 2.437359 GGATGCCTGCGTCTGCTT 60.437 61.111 10.89 0.00 43.34 3.91
4401 4540 2.249557 GATGCCTGCGTCTGCTTGTG 62.250 60.000 4.11 0.00 43.34 3.33
4404 4543 3.730761 CTGCGTCTGCTTGTGGGC 61.731 66.667 0.00 0.00 43.34 5.36
4425 4566 2.359975 GGCACCGTTCTCTTGGGG 60.360 66.667 0.00 0.00 0.00 4.96
4434 4575 4.052518 CTCTTGGGGCTGGGTGGG 62.053 72.222 0.00 0.00 0.00 4.61
4443 4584 2.364579 CTGGGTGGGCATTGGCAT 60.365 61.111 12.70 0.00 43.71 4.40
4444 4585 1.991167 CTGGGTGGGCATTGGCATT 60.991 57.895 12.70 0.00 43.71 3.56
4445 4586 2.246761 CTGGGTGGGCATTGGCATTG 62.247 60.000 12.70 5.04 43.71 2.82
4446 4587 1.988956 GGGTGGGCATTGGCATTGA 60.989 57.895 13.23 0.00 43.71 2.57
4447 4588 1.518774 GGTGGGCATTGGCATTGAG 59.481 57.895 13.23 0.00 43.71 3.02
4488 4629 2.621526 GAGGACGAGATCTCTCTTTCCC 59.378 54.545 20.26 11.24 40.75 3.97
4545 4686 2.895404 GTGTCACCTCACCTACTACCAA 59.105 50.000 0.00 0.00 32.81 3.67
4548 4689 1.831736 CACCTCACCTACTACCAAGGG 59.168 57.143 0.00 0.00 38.54 3.95
4549 4690 1.435959 ACCTCACCTACTACCAAGGGT 59.564 52.381 0.00 0.00 38.54 4.34
4640 4803 1.424638 CCCAACTCTATCCGACCCAT 58.575 55.000 0.00 0.00 0.00 4.00
4665 4829 1.144298 ACCCACTGACTAAAACCCCAC 59.856 52.381 0.00 0.00 0.00 4.61
4668 4832 2.422235 CCACTGACTAAAACCCCACACA 60.422 50.000 0.00 0.00 0.00 3.72
4669 4833 2.616842 CACTGACTAAAACCCCACACAC 59.383 50.000 0.00 0.00 0.00 3.82
4670 4834 2.508300 ACTGACTAAAACCCCACACACT 59.492 45.455 0.00 0.00 0.00 3.55
4673 4837 3.054287 TGACTAAAACCCCACACACTTCA 60.054 43.478 0.00 0.00 0.00 3.02
4674 4838 3.949113 GACTAAAACCCCACACACTTCAA 59.051 43.478 0.00 0.00 0.00 2.69
4693 4860 0.886490 AAGGTTTCAGCAGCACGAGG 60.886 55.000 0.00 0.00 0.00 4.63
4695 4862 0.884704 GGTTTCAGCAGCACGAGGAA 60.885 55.000 0.00 0.00 0.00 3.36
4708 4878 3.406595 GAGGAAGGTGATGGGGGCG 62.407 68.421 0.00 0.00 0.00 6.13
4830 5018 1.597854 CCACGGCTGCTGAAACTCA 60.598 57.895 16.72 0.00 0.00 3.41
4839 5030 1.218047 CTGAAACTCATCCGCGGGA 59.782 57.895 27.83 15.01 35.55 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 2.365105 CCGTGGGCCTCCTCCTTA 60.365 66.667 4.53 0.00 0.00 2.69
390 399 1.544759 CCCGCAGTCCCTGTTTTAGTT 60.545 52.381 0.00 0.00 33.43 2.24
523 546 9.796120 CCGAAGCAAACCAAATTTATATTTCTA 57.204 29.630 0.00 0.00 31.63 2.10
524 547 7.763985 CCCGAAGCAAACCAAATTTATATTTCT 59.236 33.333 0.00 0.00 31.63 2.52
525 548 7.547722 ACCCGAAGCAAACCAAATTTATATTTC 59.452 33.333 0.00 0.00 31.63 2.17
526 549 7.333174 CACCCGAAGCAAACCAAATTTATATTT 59.667 33.333 0.00 0.00 34.29 1.40
527 550 6.816140 CACCCGAAGCAAACCAAATTTATATT 59.184 34.615 0.00 0.00 0.00 1.28
528 551 6.337356 CACCCGAAGCAAACCAAATTTATAT 58.663 36.000 0.00 0.00 0.00 0.86
529 552 5.715070 CACCCGAAGCAAACCAAATTTATA 58.285 37.500 0.00 0.00 0.00 0.98
530 553 4.565022 CACCCGAAGCAAACCAAATTTAT 58.435 39.130 0.00 0.00 0.00 1.40
587 610 1.289800 GAAACAACGGCGAGGAGTCC 61.290 60.000 16.62 0.00 0.00 3.85
763 790 4.508128 GGCGGAGATGAACGGCGA 62.508 66.667 16.62 0.00 45.38 5.54
766 793 4.891727 CGGGGCGGAGATGAACGG 62.892 72.222 0.00 0.00 0.00 4.44
769 796 3.467226 GGACGGGGCGGAGATGAA 61.467 66.667 0.00 0.00 0.00 2.57
808 852 0.725117 CGGGTGCAAATACCTCGAAC 59.275 55.000 0.00 0.00 40.66 3.95
809 853 1.022451 GCGGGTGCAAATACCTCGAA 61.022 55.000 0.00 0.00 40.66 3.71
829 882 1.003118 TCAGTGGGGTTTGGAGAATCG 59.997 52.381 0.00 0.00 34.37 3.34
917 970 0.882042 AGCATGATCAATCGACGCCC 60.882 55.000 0.00 0.00 0.00 6.13
935 988 5.406780 GGAAATAACTCGACCATATCAGCAG 59.593 44.000 0.00 0.00 0.00 4.24
949 1002 7.759886 GTCCTGCCAATTTAAAGGAAATAACTC 59.240 37.037 2.12 0.00 40.45 3.01
954 1007 5.046376 CAGGTCCTGCCAATTTAAAGGAAAT 60.046 40.000 5.79 0.00 40.45 2.17
966 1019 3.160585 CACCTCAGGTCCTGCCAA 58.839 61.111 14.64 0.00 40.61 4.52
969 1022 1.376553 GAAGCACCTCAGGTCCTGC 60.377 63.158 14.64 2.74 31.02 4.85
970 1023 1.480137 CTAGAAGCACCTCAGGTCCTG 59.520 57.143 13.21 13.21 31.02 3.86
981 1037 0.905357 TCCTTCCCAGCTAGAAGCAC 59.095 55.000 16.66 0.00 45.56 4.40
1055 1111 0.182299 CAGGGAAGAGGAAGATGCCC 59.818 60.000 0.00 0.00 35.79 5.36
1111 1167 1.321474 ATCACCAAGGCACACAACAG 58.679 50.000 0.00 0.00 0.00 3.16
1140 1199 0.617413 ATTCTCAGGACCAGCCACAG 59.383 55.000 0.00 0.00 40.02 3.66
1199 1258 3.444703 ACATATGCTTCTGTCGGTCTC 57.555 47.619 1.58 0.00 0.00 3.36
1204 1263 3.684305 TGTTGGAACATATGCTTCTGTCG 59.316 43.478 1.58 0.00 39.30 4.35
1227 1290 3.352648 TCAAAGCAAGCCCTATGTAACC 58.647 45.455 0.00 0.00 0.00 2.85
1231 1294 3.026694 GGATTCAAAGCAAGCCCTATGT 58.973 45.455 0.00 0.00 0.00 2.29
1241 1304 1.985473 AGTGCAGTGGATTCAAAGCA 58.015 45.000 0.00 0.00 34.15 3.91
1367 1430 6.680625 GCAGGTATATATGGGACTACACATCG 60.681 46.154 0.00 0.00 40.87 3.84
1399 1463 2.793278 AGGAATGCAACAACGGTTTC 57.207 45.000 0.00 0.00 34.21 2.78
1490 1554 1.367471 CCACTCCGCAGAACAGTCA 59.633 57.895 0.00 0.00 0.00 3.41
1491 1555 0.249911 AACCACTCCGCAGAACAGTC 60.250 55.000 0.00 0.00 0.00 3.51
1494 1558 0.468226 AGAAACCACTCCGCAGAACA 59.532 50.000 0.00 0.00 0.00 3.18
1498 1562 0.951040 GTCCAGAAACCACTCCGCAG 60.951 60.000 0.00 0.00 0.00 5.18
1505 1569 0.321653 ATCAGCGGTCCAGAAACCAC 60.322 55.000 0.00 0.00 39.43 4.16
1509 1573 2.555123 GCAATCAGCGGTCCAGAAA 58.445 52.632 0.00 0.00 0.00 2.52
1510 1574 4.301505 GCAATCAGCGGTCCAGAA 57.698 55.556 0.00 0.00 0.00 3.02
1561 1627 8.034804 GGGAACGGTTATTACTCAAACTAGTTA 58.965 37.037 8.92 0.00 31.69 2.24
1562 1628 6.875726 GGGAACGGTTATTACTCAAACTAGTT 59.124 38.462 1.12 1.12 33.03 2.24
1563 1629 6.401394 GGGAACGGTTATTACTCAAACTAGT 58.599 40.000 0.00 0.00 0.00 2.57
1564 1630 5.814188 GGGGAACGGTTATTACTCAAACTAG 59.186 44.000 0.00 0.00 0.00 2.57
1568 1634 4.325972 GTGGGGAACGGTTATTACTCAAA 58.674 43.478 0.00 0.00 0.00 2.69
1574 1640 5.429435 AGATAAAGGTGGGGAACGGTTATTA 59.571 40.000 0.00 0.00 0.00 0.98
1585 1651 3.947834 GACAACATCAGATAAAGGTGGGG 59.052 47.826 0.00 0.00 0.00 4.96
1588 1654 5.248640 ACCAGACAACATCAGATAAAGGTG 58.751 41.667 0.00 0.00 0.00 4.00
1589 1655 5.505181 ACCAGACAACATCAGATAAAGGT 57.495 39.130 0.00 0.00 0.00 3.50
1606 1672 8.301002 GCACAAAATTAACCTGTATTTACCAGA 58.699 33.333 0.00 0.00 0.00 3.86
1610 1676 8.921670 CCAAGCACAAAATTAACCTGTATTTAC 58.078 33.333 0.00 0.00 0.00 2.01
1611 1677 8.643324 ACCAAGCACAAAATTAACCTGTATTTA 58.357 29.630 0.00 0.00 0.00 1.40
1620 1686 9.484326 CTAAAACAAACCAAGCACAAAATTAAC 57.516 29.630 0.00 0.00 0.00 2.01
1626 1692 7.226720 TGAAAACTAAAACAAACCAAGCACAAA 59.773 29.630 0.00 0.00 0.00 2.83
1627 1693 6.706270 TGAAAACTAAAACAAACCAAGCACAA 59.294 30.769 0.00 0.00 0.00 3.33
1633 1699 4.327627 GCGCTGAAAACTAAAACAAACCAA 59.672 37.500 0.00 0.00 0.00 3.67
1635 1701 4.109766 AGCGCTGAAAACTAAAACAAACC 58.890 39.130 10.39 0.00 0.00 3.27
1636 1702 5.696260 AAGCGCTGAAAACTAAAACAAAC 57.304 34.783 12.58 0.00 0.00 2.93
1660 1726 3.202829 ACAACCAGACGAAGGCTTAAA 57.797 42.857 0.00 0.00 0.00 1.52
1667 1733 6.422701 TGACAATAAAGTACAACCAGACGAAG 59.577 38.462 0.00 0.00 0.00 3.79
1685 1751 6.127338 ACCAGACGAAGATTCAGATGACAATA 60.127 38.462 0.00 0.00 0.00 1.90
1686 1752 5.114780 CCAGACGAAGATTCAGATGACAAT 58.885 41.667 0.00 0.00 0.00 2.71
1687 1753 4.021104 ACCAGACGAAGATTCAGATGACAA 60.021 41.667 0.00 0.00 0.00 3.18
1688 1754 3.511540 ACCAGACGAAGATTCAGATGACA 59.488 43.478 0.00 0.00 0.00 3.58
1689 1755 4.116747 ACCAGACGAAGATTCAGATGAC 57.883 45.455 0.00 0.00 0.00 3.06
1690 1756 4.021104 ACAACCAGACGAAGATTCAGATGA 60.021 41.667 0.00 0.00 0.00 2.92
1691 1757 4.248859 ACAACCAGACGAAGATTCAGATG 58.751 43.478 0.00 0.00 0.00 2.90
1692 1758 4.543590 ACAACCAGACGAAGATTCAGAT 57.456 40.909 0.00 0.00 0.00 2.90
1693 1759 4.523173 AGTACAACCAGACGAAGATTCAGA 59.477 41.667 0.00 0.00 0.00 3.27
1694 1760 4.810790 AGTACAACCAGACGAAGATTCAG 58.189 43.478 0.00 0.00 0.00 3.02
1695 1761 4.866508 AGTACAACCAGACGAAGATTCA 57.133 40.909 0.00 0.00 0.00 2.57
1696 1762 6.541111 AAAAGTACAACCAGACGAAGATTC 57.459 37.500 0.00 0.00 0.00 2.52
1697 1763 6.937436 AAAAAGTACAACCAGACGAAGATT 57.063 33.333 0.00 0.00 0.00 2.40
1717 1783 6.929049 ACACTCGTAGATTCAGATGACAAAAA 59.071 34.615 0.00 0.00 33.89 1.94
1718 1784 6.455647 ACACTCGTAGATTCAGATGACAAAA 58.544 36.000 0.00 0.00 33.89 2.44
1719 1785 6.025749 ACACTCGTAGATTCAGATGACAAA 57.974 37.500 0.00 0.00 33.89 2.83
1736 1802 6.531594 TGAGATAAGTTAATGCAAGACACTCG 59.468 38.462 0.00 0.00 0.00 4.18
1860 1931 2.114638 GCAATGGGCGGCTAAATGA 58.885 52.632 9.56 0.00 0.00 2.57
1885 1956 7.936847 AGTTAGGACATTATCTTCACACACAAA 59.063 33.333 0.00 0.00 0.00 2.83
1914 1986 5.518487 GTGTTTTTAGCTAACAAGCAAGCAA 59.482 36.000 5.45 0.00 41.32 3.91
1953 2025 6.878923 GCTGTGATACCCTGCAATATAATACA 59.121 38.462 0.00 0.00 0.00 2.29
1954 2026 6.316390 GGCTGTGATACCCTGCAATATAATAC 59.684 42.308 0.00 0.00 0.00 1.89
1955 2027 6.215431 AGGCTGTGATACCCTGCAATATAATA 59.785 38.462 0.00 0.00 0.00 0.98
2003 2075 2.985896 ACCCGTATGTCACCAATGAAG 58.014 47.619 0.00 0.00 36.31 3.02
2098 2170 6.092122 TGCATGTAAACAAGAATAGAGAACCG 59.908 38.462 0.00 0.00 0.00 4.44
2131 2203 9.146984 GCAATAATACACTGTAGTCTTTGTACA 57.853 33.333 0.00 0.00 0.00 2.90
2346 2418 9.383519 TCAGTACATTCTTTATAGCCTCAAAAG 57.616 33.333 0.00 0.00 0.00 2.27
2423 2495 3.196469 AGCTAAGAACACAGCTGCATAGA 59.804 43.478 15.27 0.00 46.21 1.98
2486 2558 4.781934 ACATGCCATAAGTTAGGAAGGTC 58.218 43.478 0.00 0.00 0.00 3.85
2488 2560 4.780815 TGACATGCCATAAGTTAGGAAGG 58.219 43.478 0.00 0.00 0.00 3.46
2570 2642 1.531149 ACTTCATCAAAAGTGACCGCG 59.469 47.619 0.00 0.00 38.06 6.46
2710 2814 6.560433 CGCTGAATGCATTACTCGTTTACTAG 60.560 42.308 12.97 0.00 43.06 2.57
2823 2927 6.889177 TGGAAATAACACAATATGGAGAAGCA 59.111 34.615 0.00 0.00 0.00 3.91
2824 2928 7.333528 TGGAAATAACACAATATGGAGAAGC 57.666 36.000 0.00 0.00 0.00 3.86
2911 3015 3.233507 AGCCAATGGTTGAATTCAGTGT 58.766 40.909 8.41 0.00 0.00 3.55
3048 3152 4.899352 ATCATCCTTGGTATAGCTGACC 57.101 45.455 11.74 11.74 37.49 4.02
3107 3211 3.799281 TGAAACCTTGAACAAAGCAGG 57.201 42.857 0.00 0.00 34.24 4.85
3123 3227 3.860641 TGCAGATCTCGTATGCTTGAAA 58.139 40.909 0.00 0.00 45.21 2.69
3166 3270 4.978083 AGCAGAAAGATGTAATTGGCTG 57.022 40.909 0.00 0.00 0.00 4.85
3231 3335 8.572855 TCTTCCTTGTTACTACTTACTACTCC 57.427 38.462 0.00 0.00 0.00 3.85
3232 3336 9.838975 GTTCTTCCTTGTTACTACTTACTACTC 57.161 37.037 0.00 0.00 0.00 2.59
3233 3337 9.585369 AGTTCTTCCTTGTTACTACTTACTACT 57.415 33.333 0.00 0.00 0.00 2.57
3236 3340 8.921205 TCAAGTTCTTCCTTGTTACTACTTACT 58.079 33.333 0.00 0.00 42.01 2.24
3237 3341 8.976471 GTCAAGTTCTTCCTTGTTACTACTTAC 58.024 37.037 0.00 0.00 42.01 2.34
3238 3342 8.921205 AGTCAAGTTCTTCCTTGTTACTACTTA 58.079 33.333 0.00 0.00 42.01 2.24
3239 3343 7.793036 AGTCAAGTTCTTCCTTGTTACTACTT 58.207 34.615 0.00 0.00 42.01 2.24
3240 3344 7.362802 AGTCAAGTTCTTCCTTGTTACTACT 57.637 36.000 0.00 0.00 42.01 2.57
3241 3345 8.358895 ACTAGTCAAGTTCTTCCTTGTTACTAC 58.641 37.037 0.00 0.00 42.01 2.73
3257 3361 5.765182 AGCTGCACAATTTAACTAGTCAAGT 59.235 36.000 1.02 0.00 41.49 3.16
3265 3369 7.219484 AGACAATTAGCTGCACAATTTAACT 57.781 32.000 1.02 4.03 0.00 2.24
3266 3370 8.964420 TTAGACAATTAGCTGCACAATTTAAC 57.036 30.769 1.02 2.06 0.00 2.01
3267 3371 9.624697 CTTTAGACAATTAGCTGCACAATTTAA 57.375 29.630 1.02 1.34 0.00 1.52
3268 3372 7.754924 GCTTTAGACAATTAGCTGCACAATTTA 59.245 33.333 1.02 0.00 0.00 1.40
3269 3373 6.587608 GCTTTAGACAATTAGCTGCACAATTT 59.412 34.615 1.02 0.00 0.00 1.82
3270 3374 6.095377 GCTTTAGACAATTAGCTGCACAATT 58.905 36.000 1.02 4.44 0.00 2.32
3271 3375 5.644644 GCTTTAGACAATTAGCTGCACAAT 58.355 37.500 1.02 0.00 0.00 2.71
3272 3376 4.378356 CGCTTTAGACAATTAGCTGCACAA 60.378 41.667 1.02 0.00 0.00 3.33
3273 3377 3.125146 CGCTTTAGACAATTAGCTGCACA 59.875 43.478 1.02 0.00 0.00 4.57
3274 3378 3.485877 CCGCTTTAGACAATTAGCTGCAC 60.486 47.826 1.02 0.00 0.00 4.57
3275 3379 2.677836 CCGCTTTAGACAATTAGCTGCA 59.322 45.455 1.02 0.00 0.00 4.41
3276 3380 2.936498 TCCGCTTTAGACAATTAGCTGC 59.064 45.455 0.00 0.00 0.00 5.25
3277 3381 4.494855 GCTTCCGCTTTAGACAATTAGCTG 60.495 45.833 0.00 0.00 0.00 4.24
3278 3382 3.623510 GCTTCCGCTTTAGACAATTAGCT 59.376 43.478 0.00 0.00 0.00 3.32
3279 3383 3.623510 AGCTTCCGCTTTAGACAATTAGC 59.376 43.478 0.00 0.00 46.47 3.09
3293 3397 2.563427 GCAACCTGAAGCTTCCGC 59.437 61.111 23.42 13.73 0.00 5.54
3294 3398 2.863153 CGCAACCTGAAGCTTCCG 59.137 61.111 23.42 16.98 0.00 4.30
3295 3399 1.968540 AGCGCAACCTGAAGCTTCC 60.969 57.895 23.42 6.06 36.41 3.46
3296 3400 1.208614 CAGCGCAACCTGAAGCTTC 59.791 57.895 19.89 19.89 37.94 3.86
3297 3401 0.819259 TTCAGCGCAACCTGAAGCTT 60.819 50.000 11.47 0.00 44.49 3.74
3298 3402 1.227943 TTCAGCGCAACCTGAAGCT 60.228 52.632 11.47 0.00 44.49 3.74
3299 3403 3.343972 TTCAGCGCAACCTGAAGC 58.656 55.556 11.47 0.00 44.49 3.86
3310 3414 1.459592 CTACGGGTTCAAACTTCAGCG 59.540 52.381 0.00 0.00 0.00 5.18
3321 3425 7.724305 TGATATTTTAATCAGCTACGGGTTC 57.276 36.000 0.00 0.00 32.18 3.62
3374 3478 0.245539 GCACTCTACGGGTGTTGCTA 59.754 55.000 0.00 0.00 37.07 3.49
3379 3483 0.973632 TCAATGCACTCTACGGGTGT 59.026 50.000 0.00 0.00 37.07 4.16
3385 3489 4.753233 ACAGACATCTCAATGCACTCTAC 58.247 43.478 0.00 0.00 36.26 2.59
3388 3492 3.859443 AGACAGACATCTCAATGCACTC 58.141 45.455 0.00 0.00 36.26 3.51
3411 3515 7.388776 TGTCAAGAGAAAATGTCTGTAATCCTG 59.611 37.037 0.00 0.00 36.41 3.86
3454 3560 7.459125 TGCAGAAGATATCCAATATAGGGAAGT 59.541 37.037 0.00 0.00 38.09 3.01
3458 3564 7.628234 ACTTGCAGAAGATATCCAATATAGGG 58.372 38.462 0.00 0.00 32.98 3.53
3484 3590 2.223641 CCAAAATGCATCCGGTCATCAG 60.224 50.000 0.00 0.00 0.00 2.90
3703 3809 2.081212 CGTCTTGAGCGTCGTGGAC 61.081 63.158 0.00 0.00 0.00 4.02
3981 4088 6.608002 ACCAATACTGTTGTAACCCAAAAAGA 59.392 34.615 0.00 0.00 34.07 2.52
3982 4089 6.811954 ACCAATACTGTTGTAACCCAAAAAG 58.188 36.000 0.00 0.00 34.07 2.27
3992 4099 4.018324 TGGGCCAATACCAATACTGTTGTA 60.018 41.667 2.13 0.00 34.44 2.41
4090 4197 4.995058 TCCAGTTCCCGGCCCCTT 62.995 66.667 0.00 0.00 0.00 3.95
4092 4199 1.928714 TATTTCCAGTTCCCGGCCCC 61.929 60.000 0.00 0.00 0.00 5.80
4127 4234 2.484264 GGCCAAAGCGTATGCCTAATAG 59.516 50.000 2.51 0.00 44.31 1.73
4128 4235 2.158740 TGGCCAAAGCGTATGCCTAATA 60.159 45.455 0.61 0.00 44.32 0.98
4129 4236 1.318576 GGCCAAAGCGTATGCCTAAT 58.681 50.000 2.51 0.00 44.31 1.73
4151 4259 1.097232 CAGCAATTTCATCGCCTGGA 58.903 50.000 0.00 0.00 0.00 3.86
4155 4263 2.523015 CAAGTCAGCAATTTCATCGCC 58.477 47.619 0.00 0.00 0.00 5.54
4176 4284 0.882927 TTTCGAGCAAACCCGGACAG 60.883 55.000 0.73 0.00 0.00 3.51
4179 4287 1.161843 GATTTTCGAGCAAACCCGGA 58.838 50.000 0.73 0.00 0.00 5.14
4180 4288 0.179200 CGATTTTCGAGCAAACCCGG 60.179 55.000 0.00 0.00 43.74 5.73
4212 4320 1.307343 CACCCTGAGATGACCCCCT 60.307 63.158 0.00 0.00 0.00 4.79
4213 4321 1.306997 TCACCCTGAGATGACCCCC 60.307 63.158 0.00 0.00 0.00 5.40
4214 4322 4.480480 TCACCCTGAGATGACCCC 57.520 61.111 0.00 0.00 0.00 4.95
4248 4356 3.879998 TGCAGGCTTAAAATCCACGATA 58.120 40.909 0.00 0.00 0.00 2.92
4254 4362 3.452264 AGGGAAATGCAGGCTTAAAATCC 59.548 43.478 0.00 0.00 0.00 3.01
4255 4363 4.160252 TCAGGGAAATGCAGGCTTAAAATC 59.840 41.667 0.00 0.00 0.00 2.17
4256 4364 4.095946 TCAGGGAAATGCAGGCTTAAAAT 58.904 39.130 0.00 0.00 0.00 1.82
4258 4366 3.168035 TCAGGGAAATGCAGGCTTAAA 57.832 42.857 0.00 0.00 0.00 1.52
4286 4394 1.391485 CGAAAAGACGAGCCATGACAG 59.609 52.381 0.00 0.00 35.09 3.51
4298 4406 3.675467 ACACACTTTCAGCGAAAAGAC 57.325 42.857 17.35 0.00 38.30 3.01
4304 4412 2.595124 TCTCAACACACTTTCAGCGA 57.405 45.000 0.00 0.00 0.00 4.93
4305 4413 3.885484 AATCTCAACACACTTTCAGCG 57.115 42.857 0.00 0.00 0.00 5.18
4318 4426 4.141528 ACATGGCAAAACCCAAAATCTCAA 60.142 37.500 0.00 0.00 38.61 3.02
4325 4433 1.415659 CAGGACATGGCAAAACCCAAA 59.584 47.619 0.00 0.00 38.61 3.28
4326 4434 1.047002 CAGGACATGGCAAAACCCAA 58.953 50.000 0.00 0.00 38.61 4.12
4327 4435 0.831288 CCAGGACATGGCAAAACCCA 60.831 55.000 0.00 0.00 43.83 4.51
4328 4436 1.974543 CCAGGACATGGCAAAACCC 59.025 57.895 0.00 0.00 43.83 4.11
4357 4496 2.110899 ACCCCCACACAAATCATTGGTA 59.889 45.455 0.00 0.00 41.01 3.25
4380 4519 3.984193 AAGCAGACGCAGGCATCCC 62.984 63.158 0.00 0.00 42.27 3.85
4381 4520 2.437359 AAGCAGACGCAGGCATCC 60.437 61.111 0.00 0.00 42.27 3.51
4382 4521 2.037136 ACAAGCAGACGCAGGCATC 61.037 57.895 0.00 0.00 42.27 3.91
4383 4522 2.033141 ACAAGCAGACGCAGGCAT 59.967 55.556 0.00 0.00 42.27 4.40
4384 4523 2.974148 CACAAGCAGACGCAGGCA 60.974 61.111 0.00 0.00 42.27 4.75
4385 4524 3.730761 CCACAAGCAGACGCAGGC 61.731 66.667 0.00 0.00 42.27 4.85
4386 4525 3.052082 CCCACAAGCAGACGCAGG 61.052 66.667 0.00 0.00 42.27 4.85
4387 4526 3.730761 GCCCACAAGCAGACGCAG 61.731 66.667 0.00 0.00 42.27 5.18
4388 4527 4.560743 TGCCCACAAGCAGACGCA 62.561 61.111 0.00 0.00 42.27 5.24
4395 4534 4.073200 GTGCCCATGCCCACAAGC 62.073 66.667 8.55 0.00 36.33 4.01
4396 4535 3.384532 GGTGCCCATGCCCACAAG 61.385 66.667 13.66 0.00 36.33 3.16
4401 4540 4.740822 AGAACGGTGCCCATGCCC 62.741 66.667 0.00 0.00 36.33 5.36
4404 4543 1.308069 CCAAGAGAACGGTGCCCATG 61.308 60.000 0.00 0.00 0.00 3.66
4414 4553 1.303643 CACCCAGCCCCAAGAGAAC 60.304 63.158 0.00 0.00 0.00 3.01
4434 4575 0.528924 TCACTGCTCAATGCCAATGC 59.471 50.000 0.00 0.00 42.00 3.56
4438 4579 1.625315 ACTAGTCACTGCTCAATGCCA 59.375 47.619 0.00 0.00 42.00 4.92
4441 4582 3.519579 CCTCACTAGTCACTGCTCAATG 58.480 50.000 0.00 0.00 0.00 2.82
4442 4583 2.499289 CCCTCACTAGTCACTGCTCAAT 59.501 50.000 0.00 0.00 0.00 2.57
4443 4584 1.895798 CCCTCACTAGTCACTGCTCAA 59.104 52.381 0.00 0.00 0.00 3.02
4444 4585 1.075536 TCCCTCACTAGTCACTGCTCA 59.924 52.381 0.00 0.00 0.00 4.26
4445 4586 1.474879 GTCCCTCACTAGTCACTGCTC 59.525 57.143 0.00 0.00 0.00 4.26
4446 4587 1.551452 GTCCCTCACTAGTCACTGCT 58.449 55.000 0.00 0.00 0.00 4.24
4447 4588 0.533032 GGTCCCTCACTAGTCACTGC 59.467 60.000 0.00 0.00 0.00 4.40
4488 4629 0.173255 GGAACCCATGATTTGCCACG 59.827 55.000 0.00 0.00 0.00 4.94
4554 4695 3.542676 AAGTGACGACGCACCCCA 61.543 61.111 15.56 0.00 39.59 4.96
4555 4696 3.041940 CAAGTGACGACGCACCCC 61.042 66.667 15.56 0.00 39.59 4.95
4559 4700 4.980805 GGGCCAAGTGACGACGCA 62.981 66.667 4.39 0.00 0.00 5.24
4640 4803 3.244770 GGGTTTTAGTCAGTGGGTGATGA 60.245 47.826 0.00 0.00 37.56 2.92
4665 4829 3.699067 CTGCTGAAACCTTTGAAGTGTG 58.301 45.455 0.00 0.00 0.00 3.82
4668 4832 2.099756 GTGCTGCTGAAACCTTTGAAGT 59.900 45.455 0.00 0.00 0.00 3.01
4669 4833 2.735823 GTGCTGCTGAAACCTTTGAAG 58.264 47.619 0.00 0.00 0.00 3.02
4670 4834 1.065401 CGTGCTGCTGAAACCTTTGAA 59.935 47.619 0.00 0.00 0.00 2.69
4673 4837 0.947244 CTCGTGCTGCTGAAACCTTT 59.053 50.000 0.00 0.00 0.00 3.11
4674 4838 0.886490 CCTCGTGCTGCTGAAACCTT 60.886 55.000 0.00 0.00 0.00 3.50
4693 4860 3.728373 ACCGCCCCCATCACCTTC 61.728 66.667 0.00 0.00 0.00 3.46
4708 4878 3.044059 GCTGCTCGCCATTGTCACC 62.044 63.158 0.00 0.00 0.00 4.02
4809 4997 4.577677 TTTCAGCAGCCGTGGCCA 62.578 61.111 0.00 0.00 43.17 5.36
4814 5002 0.674895 GGATGAGTTTCAGCAGCCGT 60.675 55.000 0.00 0.00 33.81 5.68


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

AutoCloner maintained by Alex Coulton.