Multiple sequence alignment - TraesCS2D01G328500

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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 TraesCS2D01G328500 chr2D 100.000 3811 0 0 1 3811 421798596 421794786 0.000000e+00 7038.0
1 TraesCS2D01G328500 chr2A 97.168 2083 47 5 1734 3811 568287946 568285871 0.000000e+00 3509.0
2 TraesCS2D01G328500 chr2A 93.966 1508 58 21 10 1502 568289503 568288014 0.000000e+00 2250.0
3 TraesCS2D01G328500 chr2A 100.000 119 0 0 1618 1736 733544682 733544800 1.780000e-53 220.0
4 TraesCS2D01G328500 chr2A 96.212 132 3 2 1617 1747 653424111 653424241 8.290000e-52 215.0
5 TraesCS2D01G328500 chr2B 96.780 2050 42 10 1734 3781 494267549 494265522 0.000000e+00 3398.0
6 TraesCS2D01G328500 chr2B 94.286 1505 69 10 10 1502 494269116 494267617 0.000000e+00 2287.0
7 TraesCS2D01G328500 chr2B 97.656 128 2 1 1610 1736 58667104 58667231 6.410000e-53 219.0
8 TraesCS2D01G328500 chr2B 94.737 38 2 0 1515 1552 758596282 758596245 4.110000e-05 60.2
9 TraesCS2D01G328500 chr2B 90.698 43 3 1 1515 1556 717477926 717477968 5.320000e-04 56.5
10 TraesCS2D01G328500 chr1D 99.206 126 1 0 1613 1738 391969805 391969930 1.070000e-55 228.0
11 TraesCS2D01G328500 chr6B 98.413 126 2 0 1613 1738 200732036 200731911 4.960000e-54 222.0
12 TraesCS2D01G328500 chr6B 94.737 38 2 0 1515 1552 231351275 231351238 4.110000e-05 60.2
13 TraesCS2D01G328500 chr6A 96.970 132 2 2 1612 1742 15623183 15623313 1.780000e-53 220.0
14 TraesCS2D01G328500 chr6A 98.387 124 2 0 1613 1736 116863042 116863165 6.410000e-53 219.0
15 TraesCS2D01G328500 chr6A 98.000 50 1 0 3761 3810 498584378 498584427 1.890000e-13 87.9
16 TraesCS2D01G328500 chr6A 94.737 38 2 0 1515 1552 172114706 172114669 4.110000e-05 60.2
17 TraesCS2D01G328500 chrUn 99.167 120 1 0 1617 1736 266938678 266938797 2.310000e-52 217.0
18 TraesCS2D01G328500 chrUn 98.000 50 1 0 3761 3810 90452954 90453003 1.890000e-13 87.9
19 TraesCS2D01G328500 chr7D 96.212 132 4 1 1615 1746 357383650 357383520 8.290000e-52 215.0
20 TraesCS2D01G328500 chr7D 95.349 43 1 1 1515 1556 45817309 45817267 2.460000e-07 67.6
21 TraesCS2D01G328500 chr7D 94.737 38 2 0 1515 1552 45933438 45933475 4.110000e-05 60.2
22 TraesCS2D01G328500 chr5D 96.552 58 2 0 3752 3809 395735715 395735772 3.130000e-16 97.1
23 TraesCS2D01G328500 chr5B 94.828 58 3 0 3753 3810 155715227 155715170 1.460000e-14 91.6
24 TraesCS2D01G328500 chr4A 96.364 55 1 1 3757 3810 514080007 514080061 5.240000e-14 89.8
25 TraesCS2D01G328500 chr3D 98.039 51 1 0 3760 3810 138078842 138078892 5.240000e-14 89.8
26 TraesCS2D01G328500 chr3B 98.000 50 1 0 3758 3807 507132187 507132236 1.890000e-13 87.9
27 TraesCS2D01G328500 chr3A 96.226 53 2 0 3758 3810 401026582 401026634 1.890000e-13 87.9
28 TraesCS2D01G328500 chr6D 95.000 40 2 0 1513 1552 133209765 133209726 3.180000e-06 63.9
29 TraesCS2D01G328500 chr6D 92.500 40 3 0 1513 1552 133209793 133209832 1.480000e-04 58.4
30 TraesCS2D01G328500 chr4D 93.023 43 1 2 1515 1556 494829633 494829592 1.140000e-05 62.1
31 TraesCS2D01G328500 chr4D 100.000 28 0 0 3063 3090 292300251 292300278 7.000000e-03 52.8
32 TraesCS2D01G328500 chr4B 100.000 29 0 0 3065 3093 156923776 156923804 2.000000e-03 54.7


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 TraesCS2D01G328500 chr2D 421794786 421798596 3810 True 7038.0 7038 100.000 1 3811 1 chr2D.!!$R1 3810
1 TraesCS2D01G328500 chr2A 568285871 568289503 3632 True 2879.5 3509 95.567 10 3811 2 chr2A.!!$R1 3801
2 TraesCS2D01G328500 chr2B 494265522 494269116 3594 True 2842.5 3398 95.533 10 3781 2 chr2B.!!$R2 3771

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
640 647 0.739462 TCGCAACGACCCATTAGCAG 60.739 55.0 0.0 0.0 0.00 4.24 F
1529 1556 0.103390 TCCGTCTGTTTGAGCGTCAA 59.897 50.0 0.0 0.0 34.03 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1683 1710 0.031817 ATTGGAGGGGATTTGCAGGG 60.032 55.0 0.0 0.00 0.00 4.45 R
3063 3095 0.179132 TGTTGTTGTTGCTGCTGCTG 60.179 50.0 17.0 0.77 40.48 4.41 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
50 51 4.718774 ACCTCACATGACATGTCTTATCCT 59.281 41.667 25.55 2.18 42.70 3.24
66 67 6.868339 GTCTTATCCTTTGGAAACCACAATTG 59.132 38.462 3.24 3.24 34.34 2.32
93 94 5.761165 AACCTGCACGTAACTTACAAAAT 57.239 34.783 0.00 0.00 0.00 1.82
162 163 3.819564 AGTGCCGATTGTGCTAAGATA 57.180 42.857 0.00 0.00 0.00 1.98
380 387 2.967201 TGGAAAGAACAGGGAGAACGTA 59.033 45.455 0.00 0.00 0.00 3.57
484 491 8.624776 GTTTTATAGTTTGGCTCATATGAAGCT 58.375 33.333 19.71 10.43 0.00 3.74
640 647 0.739462 TCGCAACGACCCATTAGCAG 60.739 55.000 0.00 0.00 0.00 4.24
965 979 5.460091 GGAACATTCACAGTGAAAGAAAAGC 59.540 40.000 22.35 8.36 40.12 3.51
966 980 4.601019 ACATTCACAGTGAAAGAAAAGCG 58.399 39.130 22.35 6.64 40.12 4.68
968 982 5.009010 ACATTCACAGTGAAAGAAAAGCGAT 59.991 36.000 22.35 0.00 40.12 4.58
1139 1157 1.006832 CGGTGATCATCGGGTTTGTC 58.993 55.000 20.80 0.00 0.00 3.18
1184 1202 4.756642 AGAAGAACACGCAAGATCAAATCA 59.243 37.500 0.00 0.00 43.62 2.57
1219 1237 5.991328 ATTGGTAATATCACAACTCAGCG 57.009 39.130 0.00 0.00 0.00 5.18
1220 1238 3.792401 TGGTAATATCACAACTCAGCGG 58.208 45.455 0.00 0.00 0.00 5.52
1222 1240 4.403113 TGGTAATATCACAACTCAGCGGTA 59.597 41.667 0.00 0.00 0.00 4.02
1223 1241 5.105269 TGGTAATATCACAACTCAGCGGTAA 60.105 40.000 0.00 0.00 0.00 2.85
1241 1259 4.142491 CGGTAAAATTGCAGATGCTGGTAA 60.142 41.667 6.35 0.00 42.66 2.85
1242 1260 5.450412 CGGTAAAATTGCAGATGCTGGTAAT 60.450 40.000 6.35 0.00 42.66 1.89
1251 1270 4.800471 GCAGATGCTGGTAATTTTACTTGC 59.200 41.667 0.00 6.04 38.21 4.01
1257 1276 9.884465 GATGCTGGTAATTTTACTTGCTAATAG 57.116 33.333 14.26 0.00 35.04 1.73
1258 1277 9.627123 ATGCTGGTAATTTTACTTGCTAATAGA 57.373 29.630 14.26 1.29 35.04 1.98
1260 1279 8.560374 GCTGGTAATTTTACTTGCTAATAGAGG 58.440 37.037 0.00 0.00 34.16 3.69
1270 1289 9.627123 TTACTTGCTAATAGAGGTATGCAATTT 57.373 29.630 0.00 0.00 39.24 1.82
1271 1290 7.934457 ACTTGCTAATAGAGGTATGCAATTTG 58.066 34.615 0.00 0.00 39.24 2.32
1272 1291 6.882610 TGCTAATAGAGGTATGCAATTTGG 57.117 37.500 0.00 0.00 0.00 3.28
1299 1318 1.808411 ATGTTGCAGAGGTTGGTACG 58.192 50.000 0.00 0.00 0.00 3.67
1368 1387 4.235939 AGAGATATACGCTGCAACTGAG 57.764 45.455 0.00 0.00 0.00 3.35
1428 1449 5.129650 TGCAGGTACATAACAATACTAGCCA 59.870 40.000 0.00 0.00 0.00 4.75
1432 1453 9.120538 CAGGTACATAACAATACTAGCCAATTT 57.879 33.333 0.00 0.00 0.00 1.82
1433 1454 9.338622 AGGTACATAACAATACTAGCCAATTTC 57.661 33.333 0.00 0.00 0.00 2.17
1434 1455 9.116067 GGTACATAACAATACTAGCCAATTTCA 57.884 33.333 0.00 0.00 0.00 2.69
1437 1458 9.461312 ACATAACAATACTAGCCAATTTCAGAA 57.539 29.630 0.00 0.00 0.00 3.02
1470 1491 8.465201 TCATTATCCATGAATCAGATAGAGACG 58.535 37.037 0.00 0.00 39.11 4.18
1486 1507 0.735632 GACGCAGAGAGCAGAACTGG 60.736 60.000 3.99 0.00 46.13 4.00
1491 1512 2.482839 GCAGAGAGCAGAACTGGGATAC 60.483 54.545 3.99 0.00 44.79 2.24
1499 1526 4.080129 AGCAGAACTGGGATACAACATGAT 60.080 41.667 0.00 0.00 39.74 2.45
1505 1532 8.204836 AGAACTGGGATACAACATGATAAGTAC 58.795 37.037 0.00 0.00 39.74 2.73
1506 1533 7.676683 ACTGGGATACAACATGATAAGTACT 57.323 36.000 0.00 0.00 39.74 2.73
1507 1534 8.090788 ACTGGGATACAACATGATAAGTACTT 57.909 34.615 13.68 13.68 39.74 2.24
1508 1535 8.204836 ACTGGGATACAACATGATAAGTACTTC 58.795 37.037 12.39 0.00 39.74 3.01
1509 1536 7.506114 TGGGATACAACATGATAAGTACTTCC 58.494 38.462 12.39 6.20 39.74 3.46
1511 1538 7.873505 GGGATACAACATGATAAGTACTTCCTC 59.126 40.741 12.39 10.87 39.74 3.71
1512 1539 7.873505 GGATACAACATGATAAGTACTTCCTCC 59.126 40.741 12.39 2.80 0.00 4.30
1513 1540 5.661458 ACAACATGATAAGTACTTCCTCCG 58.339 41.667 12.39 7.13 0.00 4.63
1514 1541 5.187186 ACAACATGATAAGTACTTCCTCCGT 59.813 40.000 12.39 7.69 0.00 4.69
1515 1542 5.517322 ACATGATAAGTACTTCCTCCGTC 57.483 43.478 12.39 3.23 0.00 4.79
1516 1543 5.202004 ACATGATAAGTACTTCCTCCGTCT 58.798 41.667 12.39 0.00 0.00 4.18
1517 1544 5.067936 ACATGATAAGTACTTCCTCCGTCTG 59.932 44.000 12.39 7.99 0.00 3.51
1518 1545 4.597004 TGATAAGTACTTCCTCCGTCTGT 58.403 43.478 12.39 0.00 0.00 3.41
1519 1546 5.014858 TGATAAGTACTTCCTCCGTCTGTT 58.985 41.667 12.39 0.00 0.00 3.16
1520 1547 5.479375 TGATAAGTACTTCCTCCGTCTGTTT 59.521 40.000 12.39 0.00 0.00 2.83
1521 1548 3.662247 AGTACTTCCTCCGTCTGTTTG 57.338 47.619 0.00 0.00 0.00 2.93
1522 1549 3.228453 AGTACTTCCTCCGTCTGTTTGA 58.772 45.455 0.00 0.00 0.00 2.69
1523 1550 2.821991 ACTTCCTCCGTCTGTTTGAG 57.178 50.000 0.00 0.00 0.00 3.02
1524 1551 1.270358 ACTTCCTCCGTCTGTTTGAGC 60.270 52.381 0.00 0.00 0.00 4.26
1525 1552 0.319555 TTCCTCCGTCTGTTTGAGCG 60.320 55.000 0.00 0.00 0.00 5.03
1526 1553 1.006102 CCTCCGTCTGTTTGAGCGT 60.006 57.895 0.00 0.00 0.00 5.07
1527 1554 1.009389 CCTCCGTCTGTTTGAGCGTC 61.009 60.000 0.00 0.00 0.00 5.19
1528 1555 0.318699 CTCCGTCTGTTTGAGCGTCA 60.319 55.000 0.00 0.00 0.00 4.35
1529 1556 0.103390 TCCGTCTGTTTGAGCGTCAA 59.897 50.000 0.00 0.00 34.03 3.18
1530 1557 0.232303 CCGTCTGTTTGAGCGTCAAC 59.768 55.000 0.76 0.00 35.89 3.18
1531 1558 1.209128 CGTCTGTTTGAGCGTCAACT 58.791 50.000 0.76 0.00 35.89 3.16
1532 1559 2.390938 CGTCTGTTTGAGCGTCAACTA 58.609 47.619 0.76 0.00 35.89 2.24
1533 1560 2.792674 CGTCTGTTTGAGCGTCAACTAA 59.207 45.455 0.76 0.00 35.89 2.24
1534 1561 3.428870 CGTCTGTTTGAGCGTCAACTAAT 59.571 43.478 0.76 0.00 35.89 1.73
1535 1562 4.084537 CGTCTGTTTGAGCGTCAACTAATT 60.085 41.667 0.76 0.00 35.89 1.40
1536 1563 5.374898 GTCTGTTTGAGCGTCAACTAATTC 58.625 41.667 0.76 0.00 35.89 2.17
1537 1564 4.451096 TCTGTTTGAGCGTCAACTAATTCC 59.549 41.667 0.76 0.00 35.89 3.01
1538 1565 3.185594 TGTTTGAGCGTCAACTAATTCCG 59.814 43.478 0.76 0.00 35.89 4.30
1539 1566 2.004583 TGAGCGTCAACTAATTCCGG 57.995 50.000 0.00 0.00 0.00 5.14
1540 1567 1.546923 TGAGCGTCAACTAATTCCGGA 59.453 47.619 0.00 0.00 0.00 5.14
1541 1568 1.925185 GAGCGTCAACTAATTCCGGAC 59.075 52.381 1.83 0.00 0.00 4.79
1542 1569 1.274167 AGCGTCAACTAATTCCGGACA 59.726 47.619 1.83 0.00 0.00 4.02
1543 1570 1.659098 GCGTCAACTAATTCCGGACAG 59.341 52.381 1.83 4.27 0.00 3.51
1544 1571 2.673043 GCGTCAACTAATTCCGGACAGA 60.673 50.000 1.83 0.00 0.00 3.41
1545 1572 3.581755 CGTCAACTAATTCCGGACAGAA 58.418 45.455 1.83 0.00 0.00 3.02
1546 1573 3.612860 CGTCAACTAATTCCGGACAGAAG 59.387 47.826 1.83 1.76 0.00 2.85
1547 1574 3.933332 GTCAACTAATTCCGGACAGAAGG 59.067 47.826 1.83 0.00 0.00 3.46
1548 1575 3.835978 TCAACTAATTCCGGACAGAAGGA 59.164 43.478 1.83 0.00 34.19 3.36
1549 1576 4.081642 TCAACTAATTCCGGACAGAAGGAG 60.082 45.833 1.83 0.00 37.88 3.69
1550 1577 3.442076 ACTAATTCCGGACAGAAGGAGT 58.558 45.455 1.83 0.00 37.88 3.85
1551 1578 4.607239 ACTAATTCCGGACAGAAGGAGTA 58.393 43.478 1.83 0.00 37.88 2.59
1552 1579 5.021458 ACTAATTCCGGACAGAAGGAGTAA 58.979 41.667 1.83 0.00 37.88 2.24
1553 1580 4.903045 AATTCCGGACAGAAGGAGTAAA 57.097 40.909 1.83 0.00 37.88 2.01
1554 1581 4.903045 ATTCCGGACAGAAGGAGTAAAA 57.097 40.909 1.83 0.00 37.88 1.52
1555 1582 4.693042 TTCCGGACAGAAGGAGTAAAAA 57.307 40.909 1.83 0.00 37.88 1.94
1556 1583 4.267349 TCCGGACAGAAGGAGTAAAAAG 57.733 45.455 0.00 0.00 31.95 2.27
1557 1584 3.644738 TCCGGACAGAAGGAGTAAAAAGT 59.355 43.478 0.00 0.00 31.95 2.66
1558 1585 4.834496 TCCGGACAGAAGGAGTAAAAAGTA 59.166 41.667 0.00 0.00 31.95 2.24
1559 1586 5.305128 TCCGGACAGAAGGAGTAAAAAGTAA 59.695 40.000 0.00 0.00 31.95 2.24
1560 1587 6.013984 TCCGGACAGAAGGAGTAAAAAGTAAT 60.014 38.462 0.00 0.00 31.95 1.89
1561 1588 6.653740 CCGGACAGAAGGAGTAAAAAGTAATT 59.346 38.462 0.00 0.00 0.00 1.40
1562 1589 7.820872 CCGGACAGAAGGAGTAAAAAGTAATTA 59.179 37.037 0.00 0.00 0.00 1.40
1563 1590 8.870879 CGGACAGAAGGAGTAAAAAGTAATTAG 58.129 37.037 0.00 0.00 0.00 1.73
1564 1591 9.722184 GGACAGAAGGAGTAAAAAGTAATTAGT 57.278 33.333 0.00 0.00 0.00 2.24
1581 1608 2.770164 AGTGACCACATTCAGTAGGC 57.230 50.000 2.78 0.00 0.00 3.93
1603 1630 5.123979 GGCTATTGTTGTTCTAAGAGTTGGG 59.876 44.000 0.00 0.00 0.00 4.12
1612 1639 2.038557 TCTAAGAGTTGGGTGCACCTTC 59.961 50.000 33.91 24.01 41.11 3.46
1613 1640 0.178990 AAGAGTTGGGTGCACCTTCC 60.179 55.000 33.91 20.92 41.11 3.46
1614 1641 1.062488 AGAGTTGGGTGCACCTTCCT 61.062 55.000 33.91 24.88 41.11 3.36
1615 1642 0.890996 GAGTTGGGTGCACCTTCCTG 60.891 60.000 33.91 0.00 41.11 3.86
1616 1643 1.150536 GTTGGGTGCACCTTCCTGA 59.849 57.895 33.91 11.84 41.11 3.86
1617 1644 0.890996 GTTGGGTGCACCTTCCTGAG 60.891 60.000 33.91 0.00 41.11 3.35
1626 1653 3.256281 CCTTCCTGAGGGCTTGTTC 57.744 57.895 0.00 0.00 42.26 3.18
1627 1654 0.674895 CCTTCCTGAGGGCTTGTTCG 60.675 60.000 0.00 0.00 42.26 3.95
1628 1655 0.674895 CTTCCTGAGGGCTTGTTCGG 60.675 60.000 0.00 0.00 0.00 4.30
1629 1656 1.415672 TTCCTGAGGGCTTGTTCGGT 61.416 55.000 0.00 0.00 0.00 4.69
1630 1657 1.073199 CCTGAGGGCTTGTTCGGTT 59.927 57.895 0.00 0.00 0.00 4.44
1631 1658 1.237285 CCTGAGGGCTTGTTCGGTTG 61.237 60.000 0.00 0.00 0.00 3.77
1632 1659 0.250295 CTGAGGGCTTGTTCGGTTGA 60.250 55.000 0.00 0.00 0.00 3.18
1633 1660 0.250295 TGAGGGCTTGTTCGGTTGAG 60.250 55.000 0.00 0.00 0.00 3.02
1634 1661 0.955919 GAGGGCTTGTTCGGTTGAGG 60.956 60.000 0.00 0.00 0.00 3.86
1635 1662 1.228154 GGGCTTGTTCGGTTGAGGT 60.228 57.895 0.00 0.00 0.00 3.85
1636 1663 1.515521 GGGCTTGTTCGGTTGAGGTG 61.516 60.000 0.00 0.00 0.00 4.00
1637 1664 1.515521 GGCTTGTTCGGTTGAGGTGG 61.516 60.000 0.00 0.00 0.00 4.61
1638 1665 0.534203 GCTTGTTCGGTTGAGGTGGA 60.534 55.000 0.00 0.00 0.00 4.02
1639 1666 1.882352 GCTTGTTCGGTTGAGGTGGAT 60.882 52.381 0.00 0.00 0.00 3.41
1640 1667 2.504367 CTTGTTCGGTTGAGGTGGATT 58.496 47.619 0.00 0.00 0.00 3.01
1641 1668 2.649531 TGTTCGGTTGAGGTGGATTT 57.350 45.000 0.00 0.00 0.00 2.17
1642 1669 2.226330 TGTTCGGTTGAGGTGGATTTG 58.774 47.619 0.00 0.00 0.00 2.32
1643 1670 2.158740 TGTTCGGTTGAGGTGGATTTGA 60.159 45.455 0.00 0.00 0.00 2.69
1644 1671 2.882137 GTTCGGTTGAGGTGGATTTGAA 59.118 45.455 0.00 0.00 0.00 2.69
1645 1672 2.778299 TCGGTTGAGGTGGATTTGAAG 58.222 47.619 0.00 0.00 0.00 3.02
1646 1673 1.812571 CGGTTGAGGTGGATTTGAAGG 59.187 52.381 0.00 0.00 0.00 3.46
1647 1674 2.171003 GGTTGAGGTGGATTTGAAGGG 58.829 52.381 0.00 0.00 0.00 3.95
1648 1675 2.171003 GTTGAGGTGGATTTGAAGGGG 58.829 52.381 0.00 0.00 0.00 4.79
1649 1676 1.753903 TGAGGTGGATTTGAAGGGGA 58.246 50.000 0.00 0.00 0.00 4.81
1650 1677 2.287584 TGAGGTGGATTTGAAGGGGAT 58.712 47.619 0.00 0.00 0.00 3.85
1651 1678 2.654385 TGAGGTGGATTTGAAGGGGATT 59.346 45.455 0.00 0.00 0.00 3.01
1652 1679 3.026694 GAGGTGGATTTGAAGGGGATTG 58.973 50.000 0.00 0.00 0.00 2.67
1653 1680 2.654385 AGGTGGATTTGAAGGGGATTGA 59.346 45.455 0.00 0.00 0.00 2.57
1654 1681 3.026694 GGTGGATTTGAAGGGGATTGAG 58.973 50.000 0.00 0.00 0.00 3.02
1655 1682 3.026694 GTGGATTTGAAGGGGATTGAGG 58.973 50.000 0.00 0.00 0.00 3.86
1656 1683 2.925653 TGGATTTGAAGGGGATTGAGGA 59.074 45.455 0.00 0.00 0.00 3.71
1657 1684 3.053395 TGGATTTGAAGGGGATTGAGGAG 60.053 47.826 0.00 0.00 0.00 3.69
1658 1685 3.560105 GATTTGAAGGGGATTGAGGAGG 58.440 50.000 0.00 0.00 0.00 4.30
1659 1686 2.359376 TTGAAGGGGATTGAGGAGGA 57.641 50.000 0.00 0.00 0.00 3.71
1660 1687 2.359376 TGAAGGGGATTGAGGAGGAA 57.641 50.000 0.00 0.00 0.00 3.36
1661 1688 2.863884 TGAAGGGGATTGAGGAGGAAT 58.136 47.619 0.00 0.00 0.00 3.01
1662 1689 3.201363 TGAAGGGGATTGAGGAGGAATT 58.799 45.455 0.00 0.00 0.00 2.17
1663 1690 4.379875 TGAAGGGGATTGAGGAGGAATTA 58.620 43.478 0.00 0.00 0.00 1.40
1664 1691 4.793520 TGAAGGGGATTGAGGAGGAATTAA 59.206 41.667 0.00 0.00 0.00 1.40
1665 1692 5.436374 TGAAGGGGATTGAGGAGGAATTAAT 59.564 40.000 0.00 0.00 0.00 1.40
1666 1693 5.590976 AGGGGATTGAGGAGGAATTAATC 57.409 43.478 0.00 0.00 0.00 1.75
1677 1704 1.688735 GGAATTAATCCCCTGCAAGCC 59.311 52.381 0.00 0.00 43.00 4.35
1678 1705 2.387757 GAATTAATCCCCTGCAAGCCA 58.612 47.619 0.00 0.00 0.00 4.75
1679 1706 2.548464 ATTAATCCCCTGCAAGCCAA 57.452 45.000 0.00 0.00 0.00 4.52
1680 1707 2.317371 TTAATCCCCTGCAAGCCAAA 57.683 45.000 0.00 0.00 0.00 3.28
1681 1708 2.317371 TAATCCCCTGCAAGCCAAAA 57.683 45.000 0.00 0.00 0.00 2.44
1682 1709 1.660242 AATCCCCTGCAAGCCAAAAT 58.340 45.000 0.00 0.00 0.00 1.82
1683 1710 1.197812 ATCCCCTGCAAGCCAAAATC 58.802 50.000 0.00 0.00 0.00 2.17
1684 1711 0.904394 TCCCCTGCAAGCCAAAATCC 60.904 55.000 0.00 0.00 0.00 3.01
1685 1712 1.598517 CCCTGCAAGCCAAAATCCC 59.401 57.895 0.00 0.00 0.00 3.85
1686 1713 0.906282 CCCTGCAAGCCAAAATCCCT 60.906 55.000 0.00 0.00 0.00 4.20
1687 1714 0.248289 CCTGCAAGCCAAAATCCCTG 59.752 55.000 0.00 0.00 0.00 4.45
1688 1715 0.390735 CTGCAAGCCAAAATCCCTGC 60.391 55.000 0.00 0.00 0.00 4.85
1689 1716 1.120184 TGCAAGCCAAAATCCCTGCA 61.120 50.000 0.00 0.00 0.00 4.41
1690 1717 0.035176 GCAAGCCAAAATCCCTGCAA 59.965 50.000 0.00 0.00 0.00 4.08
1691 1718 1.542987 GCAAGCCAAAATCCCTGCAAA 60.543 47.619 0.00 0.00 0.00 3.68
1692 1719 2.876892 GCAAGCCAAAATCCCTGCAAAT 60.877 45.455 0.00 0.00 0.00 2.32
1693 1720 3.004862 CAAGCCAAAATCCCTGCAAATC 58.995 45.455 0.00 0.00 0.00 2.17
1694 1721 1.556451 AGCCAAAATCCCTGCAAATCC 59.444 47.619 0.00 0.00 0.00 3.01
1695 1722 1.407299 GCCAAAATCCCTGCAAATCCC 60.407 52.381 0.00 0.00 0.00 3.85
1696 1723 1.210234 CCAAAATCCCTGCAAATCCCC 59.790 52.381 0.00 0.00 0.00 4.81
1697 1724 2.190538 CAAAATCCCTGCAAATCCCCT 58.809 47.619 0.00 0.00 0.00 4.79
1698 1725 2.165357 AAATCCCTGCAAATCCCCTC 57.835 50.000 0.00 0.00 0.00 4.30
1699 1726 0.262876 AATCCCTGCAAATCCCCTCC 59.737 55.000 0.00 0.00 0.00 4.30
1700 1727 0.925720 ATCCCTGCAAATCCCCTCCA 60.926 55.000 0.00 0.00 0.00 3.86
1701 1728 1.145900 TCCCTGCAAATCCCCTCCAA 61.146 55.000 0.00 0.00 0.00 3.53
1702 1729 0.031817 CCCTGCAAATCCCCTCCAAT 60.032 55.000 0.00 0.00 0.00 3.16
1703 1730 1.406903 CCTGCAAATCCCCTCCAATC 58.593 55.000 0.00 0.00 0.00 2.67
1704 1731 1.406903 CTGCAAATCCCCTCCAATCC 58.593 55.000 0.00 0.00 0.00 3.01
1705 1732 0.709397 TGCAAATCCCCTCCAATCCA 59.291 50.000 0.00 0.00 0.00 3.41
1706 1733 1.114627 GCAAATCCCCTCCAATCCAC 58.885 55.000 0.00 0.00 0.00 4.02
1707 1734 1.780503 CAAATCCCCTCCAATCCACC 58.219 55.000 0.00 0.00 0.00 4.61
1708 1735 1.288932 CAAATCCCCTCCAATCCACCT 59.711 52.381 0.00 0.00 0.00 4.00
1709 1736 0.929244 AATCCCCTCCAATCCACCTG 59.071 55.000 0.00 0.00 0.00 4.00
1710 1737 0.995675 ATCCCCTCCAATCCACCTGG 60.996 60.000 0.00 0.00 35.05 4.45
1711 1738 2.693871 CCCCTCCAATCCACCTGGG 61.694 68.421 0.00 0.00 34.46 4.45
1712 1739 2.693871 CCCTCCAATCCACCTGGGG 61.694 68.421 0.00 0.00 37.22 4.96
1713 1740 1.930656 CCTCCAATCCACCTGGGGT 60.931 63.158 0.00 0.00 31.87 4.95
1714 1741 1.509548 CCTCCAATCCACCTGGGGTT 61.510 60.000 0.00 0.00 42.20 4.11
1717 1744 3.190349 AATCCACCTGGGGTTGGG 58.810 61.111 0.00 0.00 39.05 4.12
1718 1745 1.467190 AATCCACCTGGGGTTGGGA 60.467 57.895 0.00 0.00 39.05 4.37
1719 1746 0.855400 AATCCACCTGGGGTTGGGAT 60.855 55.000 0.00 3.60 39.05 3.85
1720 1747 0.855400 ATCCACCTGGGGTTGGGATT 60.855 55.000 0.00 0.00 35.72 3.01
1721 1748 0.178828 TCCACCTGGGGTTGGGATTA 60.179 55.000 0.00 0.00 37.22 1.75
1722 1749 0.707616 CCACCTGGGGTTGGGATTAA 59.292 55.000 0.00 0.00 31.02 1.40
1723 1750 1.618616 CCACCTGGGGTTGGGATTAAC 60.619 57.143 0.00 0.00 31.02 2.01
1916 1943 1.028868 GTGATGGGCAGGAAGAGTGC 61.029 60.000 0.00 0.00 40.42 4.40
2077 2104 1.189752 GCCTGTCATGGACTCAGAGA 58.810 55.000 3.79 0.00 33.15 3.10
2134 2161 4.290985 TGGTTCCTTCACATATTCCCTGAA 59.709 41.667 0.00 0.00 0.00 3.02
2217 2244 4.484236 CTGCGAATTCAAGTAATGCCAAA 58.516 39.130 6.22 0.00 0.00 3.28
2226 2253 9.754382 AATTCAAGTAATGCCAAATCATACATC 57.246 29.630 0.00 0.00 0.00 3.06
2541 2568 4.609691 ACGAAACGATCAACTGTGTTTT 57.390 36.364 0.00 0.00 34.89 2.43
2580 2609 2.158549 ACCTTTTGCTCTCAGGCTTCTT 60.159 45.455 0.00 0.00 0.00 2.52
2729 2758 1.421268 TCCATGGAGCAAGTTGTGTCT 59.579 47.619 11.44 0.00 0.00 3.41
2886 2916 2.364632 TCCCATGACCATGTTTAAGCG 58.635 47.619 8.93 0.00 37.11 4.68
2928 2958 2.708051 ACAATCTGATGCAGTGGTGAG 58.292 47.619 0.00 0.00 32.61 3.51
3077 3109 3.516981 TTTTTACAGCAGCAGCAACAA 57.483 38.095 3.17 0.00 45.49 2.83
3084 3116 1.067000 AGCAGCAGCAACAACAACAAA 60.067 42.857 3.17 0.00 45.49 2.83
3130 3162 9.393249 CCAACATATTTAGTAACACAACAACAG 57.607 33.333 0.00 0.00 0.00 3.16
3303 3335 4.627035 GCCAAAATGGTATTCTGCAGAAAC 59.373 41.667 31.55 26.25 40.46 2.78
3342 3374 7.500227 ACACCACCATATCAGACATTATCAAAG 59.500 37.037 0.00 0.00 0.00 2.77
3388 3420 8.739039 TCATTGTAATCTTTTTGGTTCATCGAT 58.261 29.630 0.00 0.00 0.00 3.59
3418 3450 0.038166 AGCCATGCGGGAGAAAAAGA 59.962 50.000 0.00 0.00 40.01 2.52
3588 3620 2.740981 CAGTCACTGACTTTCCATGCTC 59.259 50.000 9.11 0.00 41.37 4.26
3631 3663 8.800332 AGATTTTGAACATTTAGAGAAGCACAT 58.200 29.630 0.00 0.00 0.00 3.21
3701 3733 6.254157 CAGTGACATTTTGAAACTCAACTTGG 59.746 38.462 0.00 0.00 35.89 3.61
3784 3816 8.210946 TGTACTCCCTCCATTCACAAATATAAG 58.789 37.037 0.00 0.00 0.00 1.73
3790 3822 8.571336 CCCTCCATTCACAAATATAAGATGTTC 58.429 37.037 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.853924 AACTTGCATAAACCAGTGAAGG 57.146 40.909 0.00 0.00 0.00 3.46
1 2 5.830912 TCAAACTTGCATAAACCAGTGAAG 58.169 37.500 0.00 0.00 0.00 3.02
2 3 5.843673 TCAAACTTGCATAAACCAGTGAA 57.156 34.783 0.00 0.00 0.00 3.18
3 4 5.534278 TCATCAAACTTGCATAAACCAGTGA 59.466 36.000 0.00 0.00 0.00 3.41
4 5 5.630680 GTCATCAAACTTGCATAAACCAGTG 59.369 40.000 0.00 0.00 0.00 3.66
5 6 5.278957 GGTCATCAAACTTGCATAAACCAGT 60.279 40.000 0.00 0.00 0.00 4.00
6 7 5.047802 AGGTCATCAAACTTGCATAAACCAG 60.048 40.000 0.00 0.00 0.00 4.00
7 8 4.832266 AGGTCATCAAACTTGCATAAACCA 59.168 37.500 0.00 0.00 0.00 3.67
8 9 5.048083 TGAGGTCATCAAACTTGCATAAACC 60.048 40.000 0.00 0.00 34.02 3.27
50 51 6.098982 AGGTTACATCAATTGTGGTTTCCAAA 59.901 34.615 5.13 0.00 39.48 3.28
66 67 4.925054 TGTAAGTTACGTGCAGGTTACATC 59.075 41.667 25.10 16.39 0.00 3.06
93 94 5.355910 GGTCCACAAAACAAAGAAGTCACTA 59.644 40.000 0.00 0.00 0.00 2.74
162 163 1.546476 CTCCAAGCTGTAAGAGTCCGT 59.454 52.381 0.00 0.00 34.07 4.69
380 387 6.159046 TGGGGTATAATGCTTGGTAAACTACT 59.841 38.462 0.00 0.00 0.00 2.57
584 591 1.264749 TGGTTCGGGCATAGCAGAGT 61.265 55.000 0.00 0.00 0.00 3.24
714 721 7.271223 CCATTTTGTCATATTCTTGTGACGTTC 59.729 37.037 0.00 0.00 44.44 3.95
965 979 2.996621 GTCTGGGAAGAACACAAGATCG 59.003 50.000 0.00 0.00 0.00 3.69
966 980 2.996621 CGTCTGGGAAGAACACAAGATC 59.003 50.000 0.00 0.00 0.00 2.75
968 982 1.760613 ACGTCTGGGAAGAACACAAGA 59.239 47.619 0.00 0.00 0.00 3.02
1139 1157 2.352651 CCTGATGTGGCAGTAAATGACG 59.647 50.000 0.00 0.00 41.39 4.35
1206 1224 4.615912 GCAATTTTACCGCTGAGTTGTGAT 60.616 41.667 0.00 0.00 0.00 3.06
1218 1236 2.164219 ACCAGCATCTGCAATTTTACCG 59.836 45.455 4.79 0.00 45.16 4.02
1219 1237 3.874392 ACCAGCATCTGCAATTTTACC 57.126 42.857 4.79 0.00 45.16 2.85
1220 1238 7.832503 AAATTACCAGCATCTGCAATTTTAC 57.167 32.000 4.79 0.00 45.16 2.01
1222 1240 8.096414 AGTAAAATTACCAGCATCTGCAATTTT 58.904 29.630 19.05 19.05 41.56 1.82
1223 1241 7.614494 AGTAAAATTACCAGCATCTGCAATTT 58.386 30.769 4.79 5.26 36.78 1.82
1241 1259 9.627123 TTGCATACCTCTATTAGCAAGTAAAAT 57.373 29.630 0.00 0.00 37.10 1.82
1242 1260 9.627123 ATTGCATACCTCTATTAGCAAGTAAAA 57.373 29.630 0.00 0.00 43.99 1.52
1251 1270 6.882610 TGCCAAATTGCATACCTCTATTAG 57.117 37.500 0.00 0.00 36.04 1.73
1270 1289 3.018856 CCTCTGCAACATAAAGATGCCA 58.981 45.455 0.00 0.00 44.63 4.92
1271 1290 3.019564 ACCTCTGCAACATAAAGATGCC 58.980 45.455 0.00 0.00 44.63 4.40
1272 1291 4.418392 CAACCTCTGCAACATAAAGATGC 58.582 43.478 0.00 0.00 45.38 3.91
1282 1301 1.574702 GCCGTACCAACCTCTGCAAC 61.575 60.000 0.00 0.00 0.00 4.17
1299 1318 1.476891 TCCTCATACTCAACAGACGCC 59.523 52.381 0.00 0.00 0.00 5.68
1368 1387 6.797033 CGATGATGTTTGAAAGGTGTAAGTTC 59.203 38.462 0.00 0.00 0.00 3.01
1444 1465 8.465201 CGTCTCTATCTGATTCATGGATAATGA 58.535 37.037 0.00 0.00 43.79 2.57
1445 1466 7.222417 GCGTCTCTATCTGATTCATGGATAATG 59.778 40.741 0.00 0.00 37.66 1.90
1446 1467 7.093596 TGCGTCTCTATCTGATTCATGGATAAT 60.094 37.037 0.00 0.00 0.00 1.28
1451 1472 4.022503 TCTGCGTCTCTATCTGATTCATGG 60.023 45.833 0.00 0.00 0.00 3.66
1458 1479 2.217750 GCTCTCTGCGTCTCTATCTGA 58.782 52.381 0.00 0.00 0.00 3.27
1466 1487 0.243365 CAGTTCTGCTCTCTGCGTCT 59.757 55.000 0.00 0.00 46.63 4.18
1467 1488 0.735632 CCAGTTCTGCTCTCTGCGTC 60.736 60.000 0.00 0.00 46.63 5.19
1468 1489 1.291588 CCAGTTCTGCTCTCTGCGT 59.708 57.895 0.00 0.00 46.63 5.24
1470 1491 0.540923 ATCCCAGTTCTGCTCTCTGC 59.459 55.000 0.00 0.00 43.25 4.26
1486 1507 7.873505 GGAGGAAGTACTTATCATGTTGTATCC 59.126 40.741 8.42 0.51 0.00 2.59
1491 1512 5.661458 ACGGAGGAAGTACTTATCATGTTG 58.339 41.667 8.42 2.26 0.00 3.33
1499 1526 4.828939 TCAAACAGACGGAGGAAGTACTTA 59.171 41.667 8.42 0.00 0.00 2.24
1505 1532 1.433534 GCTCAAACAGACGGAGGAAG 58.566 55.000 0.00 0.00 0.00 3.46
1506 1533 0.319555 CGCTCAAACAGACGGAGGAA 60.320 55.000 0.00 0.00 0.00 3.36
1507 1534 1.289066 CGCTCAAACAGACGGAGGA 59.711 57.895 0.00 0.00 0.00 3.71
1508 1535 1.006102 ACGCTCAAACAGACGGAGG 60.006 57.895 0.00 0.00 0.00 4.30
1509 1536 0.318699 TGACGCTCAAACAGACGGAG 60.319 55.000 0.00 0.00 0.00 4.63
1511 1538 0.232303 GTTGACGCTCAAACAGACGG 59.768 55.000 2.65 0.00 38.22 4.79
1512 1539 1.209128 AGTTGACGCTCAAACAGACG 58.791 50.000 2.65 0.00 38.22 4.18
1513 1540 4.992381 ATTAGTTGACGCTCAAACAGAC 57.008 40.909 2.65 0.00 38.22 3.51
1514 1541 4.451096 GGAATTAGTTGACGCTCAAACAGA 59.549 41.667 2.65 0.00 38.22 3.41
1515 1542 4.666655 CGGAATTAGTTGACGCTCAAACAG 60.667 45.833 2.65 0.00 38.22 3.16
1516 1543 3.185594 CGGAATTAGTTGACGCTCAAACA 59.814 43.478 2.65 0.00 38.22 2.83
1517 1544 3.424433 CCGGAATTAGTTGACGCTCAAAC 60.424 47.826 0.00 0.00 38.22 2.93
1518 1545 2.739913 CCGGAATTAGTTGACGCTCAAA 59.260 45.455 0.00 0.00 38.22 2.69
1519 1546 2.028839 TCCGGAATTAGTTGACGCTCAA 60.029 45.455 0.00 0.00 33.32 3.02
1520 1547 1.546923 TCCGGAATTAGTTGACGCTCA 59.453 47.619 0.00 0.00 0.00 4.26
1521 1548 1.925185 GTCCGGAATTAGTTGACGCTC 59.075 52.381 5.23 0.00 0.00 5.03
1522 1549 1.274167 TGTCCGGAATTAGTTGACGCT 59.726 47.619 5.23 0.00 0.00 5.07
1523 1550 1.659098 CTGTCCGGAATTAGTTGACGC 59.341 52.381 5.23 0.00 0.00 5.19
1524 1551 3.226346 TCTGTCCGGAATTAGTTGACG 57.774 47.619 5.23 0.00 0.00 4.35
1525 1552 3.933332 CCTTCTGTCCGGAATTAGTTGAC 59.067 47.826 5.23 0.00 0.00 3.18
1526 1553 3.835978 TCCTTCTGTCCGGAATTAGTTGA 59.164 43.478 5.23 0.00 0.00 3.18
1527 1554 4.184629 CTCCTTCTGTCCGGAATTAGTTG 58.815 47.826 5.23 3.15 0.00 3.16
1528 1555 3.838903 ACTCCTTCTGTCCGGAATTAGTT 59.161 43.478 5.23 0.00 0.00 2.24
1529 1556 3.442076 ACTCCTTCTGTCCGGAATTAGT 58.558 45.455 5.23 0.01 0.00 2.24
1530 1557 5.593679 TTACTCCTTCTGTCCGGAATTAG 57.406 43.478 5.23 5.41 0.00 1.73
1531 1558 6.363167 TTTTACTCCTTCTGTCCGGAATTA 57.637 37.500 5.23 0.00 0.00 1.40
1532 1559 4.903045 TTTACTCCTTCTGTCCGGAATT 57.097 40.909 5.23 0.00 0.00 2.17
1533 1560 4.903045 TTTTACTCCTTCTGTCCGGAAT 57.097 40.909 5.23 0.00 0.00 3.01
1534 1561 4.102054 ACTTTTTACTCCTTCTGTCCGGAA 59.898 41.667 5.23 0.00 0.00 4.30
1535 1562 3.644738 ACTTTTTACTCCTTCTGTCCGGA 59.355 43.478 0.00 0.00 0.00 5.14
1536 1563 4.004196 ACTTTTTACTCCTTCTGTCCGG 57.996 45.455 0.00 0.00 0.00 5.14
1537 1564 7.668525 AATTACTTTTTACTCCTTCTGTCCG 57.331 36.000 0.00 0.00 0.00 4.79
1538 1565 9.722184 ACTAATTACTTTTTACTCCTTCTGTCC 57.278 33.333 0.00 0.00 0.00 4.02
1542 1569 9.722184 GGTCACTAATTACTTTTTACTCCTTCT 57.278 33.333 0.00 0.00 0.00 2.85
1543 1570 9.498176 TGGTCACTAATTACTTTTTACTCCTTC 57.502 33.333 0.00 0.00 0.00 3.46
1544 1571 9.281371 GTGGTCACTAATTACTTTTTACTCCTT 57.719 33.333 0.00 0.00 0.00 3.36
1545 1572 8.434392 TGTGGTCACTAATTACTTTTTACTCCT 58.566 33.333 2.66 0.00 0.00 3.69
1546 1573 8.611654 TGTGGTCACTAATTACTTTTTACTCC 57.388 34.615 2.66 0.00 0.00 3.85
1551 1578 9.131791 ACTGAATGTGGTCACTAATTACTTTTT 57.868 29.630 2.66 0.00 0.00 1.94
1552 1579 8.691661 ACTGAATGTGGTCACTAATTACTTTT 57.308 30.769 2.66 0.00 0.00 2.27
1553 1580 9.436957 CTACTGAATGTGGTCACTAATTACTTT 57.563 33.333 2.66 0.00 0.00 2.66
1554 1581 8.041323 CCTACTGAATGTGGTCACTAATTACTT 58.959 37.037 2.66 0.00 0.00 2.24
1555 1582 7.556844 CCTACTGAATGTGGTCACTAATTACT 58.443 38.462 2.66 0.00 0.00 2.24
1556 1583 6.258068 GCCTACTGAATGTGGTCACTAATTAC 59.742 42.308 2.66 0.00 0.00 1.89
1557 1584 6.156256 AGCCTACTGAATGTGGTCACTAATTA 59.844 38.462 2.66 0.00 0.00 1.40
1558 1585 5.045578 AGCCTACTGAATGTGGTCACTAATT 60.046 40.000 2.66 0.00 0.00 1.40
1559 1586 4.471386 AGCCTACTGAATGTGGTCACTAAT 59.529 41.667 2.66 0.00 0.00 1.73
1560 1587 3.838317 AGCCTACTGAATGTGGTCACTAA 59.162 43.478 2.66 0.00 0.00 2.24
1561 1588 3.441101 AGCCTACTGAATGTGGTCACTA 58.559 45.455 2.66 0.00 0.00 2.74
1562 1589 2.260822 AGCCTACTGAATGTGGTCACT 58.739 47.619 2.66 0.00 0.00 3.41
1563 1590 2.770164 AGCCTACTGAATGTGGTCAC 57.230 50.000 0.00 0.00 0.00 3.67
1564 1591 4.225042 ACAATAGCCTACTGAATGTGGTCA 59.775 41.667 0.00 0.00 0.00 4.02
1565 1592 4.770795 ACAATAGCCTACTGAATGTGGTC 58.229 43.478 0.00 0.00 0.00 4.02
1581 1608 6.348540 GCACCCAACTCTTAGAACAACAATAG 60.349 42.308 0.00 0.00 0.00 1.73
1603 1630 2.360475 GCCCTCAGGAAGGTGCAC 60.360 66.667 8.80 8.80 44.56 4.57
1612 1639 1.073199 AACCGAACAAGCCCTCAGG 59.927 57.895 0.00 0.00 0.00 3.86
1613 1640 0.250295 TCAACCGAACAAGCCCTCAG 60.250 55.000 0.00 0.00 0.00 3.35
1614 1641 0.250295 CTCAACCGAACAAGCCCTCA 60.250 55.000 0.00 0.00 0.00 3.86
1615 1642 0.955919 CCTCAACCGAACAAGCCCTC 60.956 60.000 0.00 0.00 0.00 4.30
1616 1643 1.073199 CCTCAACCGAACAAGCCCT 59.927 57.895 0.00 0.00 0.00 5.19
1617 1644 1.228154 ACCTCAACCGAACAAGCCC 60.228 57.895 0.00 0.00 0.00 5.19
1618 1645 1.515521 CCACCTCAACCGAACAAGCC 61.516 60.000 0.00 0.00 0.00 4.35
1619 1646 0.534203 TCCACCTCAACCGAACAAGC 60.534 55.000 0.00 0.00 0.00 4.01
1620 1647 2.185004 ATCCACCTCAACCGAACAAG 57.815 50.000 0.00 0.00 0.00 3.16
1621 1648 2.621055 CAAATCCACCTCAACCGAACAA 59.379 45.455 0.00 0.00 0.00 2.83
1622 1649 2.158740 TCAAATCCACCTCAACCGAACA 60.159 45.455 0.00 0.00 0.00 3.18
1623 1650 2.500229 TCAAATCCACCTCAACCGAAC 58.500 47.619 0.00 0.00 0.00 3.95
1624 1651 2.940994 TCAAATCCACCTCAACCGAA 57.059 45.000 0.00 0.00 0.00 4.30
1625 1652 2.552155 CCTTCAAATCCACCTCAACCGA 60.552 50.000 0.00 0.00 0.00 4.69
1626 1653 1.812571 CCTTCAAATCCACCTCAACCG 59.187 52.381 0.00 0.00 0.00 4.44
1627 1654 2.171003 CCCTTCAAATCCACCTCAACC 58.829 52.381 0.00 0.00 0.00 3.77
1628 1655 2.171003 CCCCTTCAAATCCACCTCAAC 58.829 52.381 0.00 0.00 0.00 3.18
1629 1656 2.069775 TCCCCTTCAAATCCACCTCAA 58.930 47.619 0.00 0.00 0.00 3.02
1630 1657 1.753903 TCCCCTTCAAATCCACCTCA 58.246 50.000 0.00 0.00 0.00 3.86
1631 1658 3.026694 CAATCCCCTTCAAATCCACCTC 58.973 50.000 0.00 0.00 0.00 3.85
1632 1659 2.654385 TCAATCCCCTTCAAATCCACCT 59.346 45.455 0.00 0.00 0.00 4.00
1633 1660 3.026694 CTCAATCCCCTTCAAATCCACC 58.973 50.000 0.00 0.00 0.00 4.61
1634 1661 3.026694 CCTCAATCCCCTTCAAATCCAC 58.973 50.000 0.00 0.00 0.00 4.02
1635 1662 2.925653 TCCTCAATCCCCTTCAAATCCA 59.074 45.455 0.00 0.00 0.00 3.41
1636 1663 3.560105 CTCCTCAATCCCCTTCAAATCC 58.440 50.000 0.00 0.00 0.00 3.01
1637 1664 3.203040 TCCTCCTCAATCCCCTTCAAATC 59.797 47.826 0.00 0.00 0.00 2.17
1638 1665 3.201363 TCCTCCTCAATCCCCTTCAAAT 58.799 45.455 0.00 0.00 0.00 2.32
1639 1666 2.642982 TCCTCCTCAATCCCCTTCAAA 58.357 47.619 0.00 0.00 0.00 2.69
1640 1667 2.359376 TCCTCCTCAATCCCCTTCAA 57.641 50.000 0.00 0.00 0.00 2.69
1641 1668 2.359376 TTCCTCCTCAATCCCCTTCA 57.641 50.000 0.00 0.00 0.00 3.02
1642 1669 3.961484 AATTCCTCCTCAATCCCCTTC 57.039 47.619 0.00 0.00 0.00 3.46
1643 1670 5.162936 GGATTAATTCCTCCTCAATCCCCTT 60.163 44.000 3.43 0.00 41.78 3.95
1644 1671 4.355287 GGATTAATTCCTCCTCAATCCCCT 59.645 45.833 3.43 0.00 41.78 4.79
1645 1672 4.667573 GGATTAATTCCTCCTCAATCCCC 58.332 47.826 3.43 0.00 41.78 4.81
1647 1674 4.667573 GGGGATTAATTCCTCCTCAATCC 58.332 47.826 12.74 5.62 44.75 3.01
1655 1682 2.625314 GCTTGCAGGGGATTAATTCCTC 59.375 50.000 12.74 4.42 46.63 3.71
1656 1683 2.670939 GCTTGCAGGGGATTAATTCCT 58.329 47.619 12.74 8.82 44.75 3.36
1657 1684 1.688735 GGCTTGCAGGGGATTAATTCC 59.311 52.381 3.88 3.88 44.62 3.01
1658 1685 2.387757 TGGCTTGCAGGGGATTAATTC 58.612 47.619 0.00 0.00 0.00 2.17
1659 1686 2.548464 TGGCTTGCAGGGGATTAATT 57.452 45.000 0.00 0.00 0.00 1.40
1660 1687 2.548464 TTGGCTTGCAGGGGATTAAT 57.452 45.000 0.00 0.00 0.00 1.40
1661 1688 2.317371 TTTGGCTTGCAGGGGATTAA 57.683 45.000 0.00 0.00 0.00 1.40
1662 1689 2.317371 TTTTGGCTTGCAGGGGATTA 57.683 45.000 0.00 0.00 0.00 1.75
1663 1690 1.556451 GATTTTGGCTTGCAGGGGATT 59.444 47.619 0.00 0.00 0.00 3.01
1664 1691 1.197812 GATTTTGGCTTGCAGGGGAT 58.802 50.000 0.00 0.00 0.00 3.85
1665 1692 0.904394 GGATTTTGGCTTGCAGGGGA 60.904 55.000 0.00 0.00 0.00 4.81
1666 1693 1.598517 GGATTTTGGCTTGCAGGGG 59.401 57.895 0.00 0.00 0.00 4.79
1667 1694 0.906282 AGGGATTTTGGCTTGCAGGG 60.906 55.000 0.00 0.00 0.00 4.45
1668 1695 0.248289 CAGGGATTTTGGCTTGCAGG 59.752 55.000 0.00 0.00 0.00 4.85
1669 1696 0.390735 GCAGGGATTTTGGCTTGCAG 60.391 55.000 0.00 0.00 0.00 4.41
1670 1697 1.120184 TGCAGGGATTTTGGCTTGCA 61.120 50.000 0.00 0.00 39.03 4.08
1671 1698 0.035176 TTGCAGGGATTTTGGCTTGC 59.965 50.000 0.00 0.00 0.00 4.01
1672 1699 2.547299 TTTGCAGGGATTTTGGCTTG 57.453 45.000 0.00 0.00 0.00 4.01
1673 1700 2.026915 GGATTTGCAGGGATTTTGGCTT 60.027 45.455 0.00 0.00 0.00 4.35
1674 1701 1.556451 GGATTTGCAGGGATTTTGGCT 59.444 47.619 0.00 0.00 0.00 4.75
1675 1702 1.407299 GGGATTTGCAGGGATTTTGGC 60.407 52.381 0.00 0.00 0.00 4.52
1676 1703 1.210234 GGGGATTTGCAGGGATTTTGG 59.790 52.381 0.00 0.00 0.00 3.28
1677 1704 2.169144 GAGGGGATTTGCAGGGATTTTG 59.831 50.000 0.00 0.00 0.00 2.44
1678 1705 2.470990 GAGGGGATTTGCAGGGATTTT 58.529 47.619 0.00 0.00 0.00 1.82
1679 1706 1.343377 GGAGGGGATTTGCAGGGATTT 60.343 52.381 0.00 0.00 0.00 2.17
1680 1707 0.262876 GGAGGGGATTTGCAGGGATT 59.737 55.000 0.00 0.00 0.00 3.01
1681 1708 0.925720 TGGAGGGGATTTGCAGGGAT 60.926 55.000 0.00 0.00 0.00 3.85
1682 1709 1.145900 TTGGAGGGGATTTGCAGGGA 61.146 55.000 0.00 0.00 0.00 4.20
1683 1710 0.031817 ATTGGAGGGGATTTGCAGGG 60.032 55.000 0.00 0.00 0.00 4.45
1684 1711 1.406903 GATTGGAGGGGATTTGCAGG 58.593 55.000 0.00 0.00 0.00 4.85
1685 1712 1.342275 TGGATTGGAGGGGATTTGCAG 60.342 52.381 0.00 0.00 0.00 4.41
1686 1713 0.709397 TGGATTGGAGGGGATTTGCA 59.291 50.000 0.00 0.00 0.00 4.08
1687 1714 1.114627 GTGGATTGGAGGGGATTTGC 58.885 55.000 0.00 0.00 0.00 3.68
1688 1715 1.288932 AGGTGGATTGGAGGGGATTTG 59.711 52.381 0.00 0.00 0.00 2.32
1689 1716 1.288932 CAGGTGGATTGGAGGGGATTT 59.711 52.381 0.00 0.00 0.00 2.17
1690 1717 0.929244 CAGGTGGATTGGAGGGGATT 59.071 55.000 0.00 0.00 0.00 3.01
1691 1718 0.995675 CCAGGTGGATTGGAGGGGAT 60.996 60.000 0.00 0.00 37.96 3.85
1692 1719 1.619363 CCAGGTGGATTGGAGGGGA 60.619 63.158 0.00 0.00 37.96 4.81
1693 1720 2.693871 CCCAGGTGGATTGGAGGGG 61.694 68.421 0.00 0.00 37.96 4.79
1694 1721 2.693871 CCCCAGGTGGATTGGAGGG 61.694 68.421 0.00 0.00 37.96 4.30
1695 1722 1.509548 AACCCCAGGTGGATTGGAGG 61.510 60.000 0.00 0.00 37.96 4.30
1696 1723 0.323725 CAACCCCAGGTGGATTGGAG 60.324 60.000 0.00 0.00 37.96 3.86
1697 1724 1.773635 CAACCCCAGGTGGATTGGA 59.226 57.895 0.00 0.00 37.96 3.53
1698 1725 1.305213 CCAACCCCAGGTGGATTGG 60.305 63.158 14.28 14.28 41.57 3.16
1699 1726 1.305213 CCCAACCCCAGGTGGATTG 60.305 63.158 0.00 2.08 35.34 2.67
1700 1727 0.855400 ATCCCAACCCCAGGTGGATT 60.855 55.000 0.00 0.00 35.72 3.01
1701 1728 0.855400 AATCCCAACCCCAGGTGGAT 60.855 55.000 0.00 0.00 39.30 3.41
1702 1729 0.178828 TAATCCCAACCCCAGGTGGA 60.179 55.000 0.00 0.00 35.34 4.02
1703 1730 0.707616 TTAATCCCAACCCCAGGTGG 59.292 55.000 0.00 0.00 35.34 4.61
1704 1731 1.618616 GGTTAATCCCAACCCCAGGTG 60.619 57.143 0.00 0.00 41.89 4.00
1705 1732 0.708209 GGTTAATCCCAACCCCAGGT 59.292 55.000 0.00 0.00 41.89 4.00
1706 1733 0.395173 CGGTTAATCCCAACCCCAGG 60.395 60.000 0.00 0.00 44.37 4.45
1707 1734 0.621609 TCGGTTAATCCCAACCCCAG 59.378 55.000 0.00 0.00 44.37 4.45
1708 1735 1.073931 TTCGGTTAATCCCAACCCCA 58.926 50.000 0.00 0.00 44.37 4.96
1709 1736 1.272037 TGTTCGGTTAATCCCAACCCC 60.272 52.381 0.00 0.00 44.37 4.95
1710 1737 2.203470 TGTTCGGTTAATCCCAACCC 57.797 50.000 0.00 0.00 44.37 4.11
1711 1738 3.613193 GCTTTGTTCGGTTAATCCCAACC 60.613 47.826 0.00 0.00 43.88 3.77
1712 1739 3.571571 GCTTTGTTCGGTTAATCCCAAC 58.428 45.455 0.00 0.00 0.00 3.77
1713 1740 2.559231 GGCTTTGTTCGGTTAATCCCAA 59.441 45.455 0.00 0.00 0.00 4.12
1714 1741 2.164338 GGCTTTGTTCGGTTAATCCCA 58.836 47.619 0.00 0.00 0.00 4.37
1715 1742 2.163613 CAGGCTTTGTTCGGTTAATCCC 59.836 50.000 0.00 0.00 0.00 3.85
1716 1743 3.078837 TCAGGCTTTGTTCGGTTAATCC 58.921 45.455 0.00 0.00 0.00 3.01
1717 1744 4.156008 ACATCAGGCTTTGTTCGGTTAATC 59.844 41.667 0.00 0.00 0.00 1.75
1718 1745 4.079253 ACATCAGGCTTTGTTCGGTTAAT 58.921 39.130 0.00 0.00 0.00 1.40
1719 1746 3.252215 CACATCAGGCTTTGTTCGGTTAA 59.748 43.478 0.00 0.00 0.00 2.01
1720 1747 2.811431 CACATCAGGCTTTGTTCGGTTA 59.189 45.455 0.00 0.00 0.00 2.85
1721 1748 1.608590 CACATCAGGCTTTGTTCGGTT 59.391 47.619 0.00 0.00 0.00 4.44
1722 1749 1.202758 TCACATCAGGCTTTGTTCGGT 60.203 47.619 0.00 0.00 0.00 4.69
1723 1750 1.522668 TCACATCAGGCTTTGTTCGG 58.477 50.000 0.00 0.00 0.00 4.30
1724 1751 3.837213 AATCACATCAGGCTTTGTTCG 57.163 42.857 0.00 0.00 0.00 3.95
1725 1752 3.676646 GCAAATCACATCAGGCTTTGTTC 59.323 43.478 0.00 0.00 0.00 3.18
1726 1753 3.069872 TGCAAATCACATCAGGCTTTGTT 59.930 39.130 0.00 0.00 0.00 2.83
1727 1754 2.629137 TGCAAATCACATCAGGCTTTGT 59.371 40.909 0.00 0.00 0.00 2.83
1728 1755 3.250744 CTGCAAATCACATCAGGCTTTG 58.749 45.455 0.00 0.00 0.00 2.77
1729 1756 2.232941 CCTGCAAATCACATCAGGCTTT 59.767 45.455 0.00 0.00 39.53 3.51
1730 1757 1.822990 CCTGCAAATCACATCAGGCTT 59.177 47.619 0.00 0.00 39.53 4.35
1731 1758 1.471119 CCTGCAAATCACATCAGGCT 58.529 50.000 0.00 0.00 39.53 4.58
1732 1759 0.458669 CCCTGCAAATCACATCAGGC 59.541 55.000 1.79 0.00 43.51 4.85
1916 1943 4.568359 ACGCATAGCTCATACACAAGAAAG 59.432 41.667 0.00 0.00 0.00 2.62
2022 2049 8.792633 TCCCTGTCATCAAATTGTTACTTTTAG 58.207 33.333 0.00 0.00 0.00 1.85
2077 2104 0.035317 TGCCAAGTGCGATCTGAAGT 59.965 50.000 0.00 0.00 45.60 3.01
2134 2161 0.957395 CTCGGTGAACAATGCAGCCT 60.957 55.000 0.00 0.00 0.00 4.58
2217 2244 8.978874 TTGTTGGCTACAATAAGATGTATGAT 57.021 30.769 10.43 0.00 41.73 2.45
2541 2568 9.653287 GCAAAAGGTATGTATGTATATCAGCTA 57.347 33.333 0.00 0.00 0.00 3.32
2580 2609 3.265221 ACATTTCCCTCTCTGATGAGCAA 59.735 43.478 0.00 0.00 40.03 3.91
2750 2779 6.426328 GCTTATCATCGTCTCTCATGGAAATT 59.574 38.462 0.00 0.00 0.00 1.82
2753 2782 4.557496 CGCTTATCATCGTCTCTCATGGAA 60.557 45.833 0.00 0.00 0.00 3.53
2886 2916 2.281345 ACCTCAGCACAGCACAGC 60.281 61.111 0.00 0.00 0.00 4.40
3063 3095 0.179132 TGTTGTTGTTGCTGCTGCTG 60.179 50.000 17.00 0.77 40.48 4.41
3064 3096 0.531657 TTGTTGTTGTTGCTGCTGCT 59.468 45.000 17.00 0.00 40.48 4.24
3065 3097 1.357907 TTTGTTGTTGTTGCTGCTGC 58.642 45.000 8.89 8.89 40.20 5.25
3066 3098 3.186001 TGTTTTTGTTGTTGTTGCTGCTG 59.814 39.130 0.00 0.00 0.00 4.41
3067 3099 3.397482 TGTTTTTGTTGTTGTTGCTGCT 58.603 36.364 0.00 0.00 0.00 4.24
3068 3100 3.802722 TGTTTTTGTTGTTGTTGCTGC 57.197 38.095 0.00 0.00 0.00 5.25
3084 3116 8.780846 TGTTGGTACGACTATCATTATTGTTT 57.219 30.769 0.00 0.00 0.00 2.83
3100 3132 8.710551 TGTTGTGTTACTAAATATGTTGGTACG 58.289 33.333 0.00 0.00 0.00 3.67
3130 3162 3.368236 GTCAGGAAAGTTCAGTACGATGC 59.632 47.826 0.00 0.00 0.00 3.91
3303 3335 1.263217 GGTGGTGTGTTTTGCTACTCG 59.737 52.381 0.00 0.00 0.00 4.18
3388 3420 1.155889 CGCATGGCTTGTGTGTCTTA 58.844 50.000 5.82 0.00 0.00 2.10
3701 3733 6.485648 ACTTTGTTGGTCTATACTTGTTGACC 59.514 38.462 0.00 0.00 46.53 4.02
3749 3781 4.216411 TGGAGGGAGTACAAAGTAATGC 57.784 45.455 0.00 0.00 0.00 3.56
3784 3816 8.734386 GGTCCATATTGAAATATCCAGAACATC 58.266 37.037 0.00 0.00 29.35 3.06


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

AutoCloner maintained by Alex Coulton.