Multiple sequence alignment - TraesCS4A01G310500

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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 TraesCS4A01G310500 chr4A 100.000 2222 0 0 1 2222 603339065 603341286 0.000000e+00 4104
1 TraesCS4A01G310500 chr4A 94.347 1539 70 8 1 1537 553534071 553535594 0.000000e+00 2344
2 TraesCS4A01G310500 chr5B 95.844 1540 59 4 1 1537 492816933 492815396 0.000000e+00 2484
3 TraesCS4A01G310500 chr5B 79.696 527 78 18 1664 2187 478479137 478479637 9.760000e-94 353
4 TraesCS4A01G310500 chr1A 95.839 1538 61 3 1 1536 22341220 22342756 0.000000e+00 2483
5 TraesCS4A01G310500 chr1A 96.429 364 13 0 1 364 446243449 446243812 3.160000e-168 601
6 TraesCS4A01G310500 chr6A 95.218 1401 62 3 1 1398 224099762 224098364 0.000000e+00 2211
7 TraesCS4A01G310500 chr6A 96.429 364 12 1 1 364 472969196 472969558 1.140000e-167 599
8 TraesCS4A01G310500 chr6A 96.154 364 13 1 1 364 595511812 595511450 5.280000e-166 593
9 TraesCS4A01G310500 chr3A 95.428 1181 50 3 360 1536 11598672 11597492 0.000000e+00 1879
10 TraesCS4A01G310500 chr3A 95.428 1181 50 3 360 1536 11605560 11604380 0.000000e+00 1879
11 TraesCS4A01G310500 chr3A 95.254 1180 54 1 360 1537 684744299 684745478 0.000000e+00 1868
12 TraesCS4A01G310500 chr3A 95.169 1180 55 1 360 1537 459622888 459621709 0.000000e+00 1862
13 TraesCS4A01G310500 chr4B 95.339 1180 53 1 360 1537 604143343 604144522 0.000000e+00 1873
14 TraesCS4A01G310500 chr4B 81.333 300 43 10 1890 2187 2210128 2209840 4.770000e-57 231
15 TraesCS4A01G310500 chr4B 81.333 300 43 10 1890 2187 2240118 2239830 4.770000e-57 231
16 TraesCS4A01G310500 chr4B 82.775 209 27 5 1629 1836 643023047 643023247 6.300000e-41 178
17 TraesCS4A01G310500 chr7A 95.008 1182 56 3 360 1538 677974754 677975935 0.000000e+00 1853
18 TraesCS4A01G310500 chr7A 96.154 364 14 0 1 364 609346615 609346978 1.470000e-166 595
19 TraesCS4A01G310500 chr2A 95.035 564 25 1 1 564 38289420 38289980 0.000000e+00 883
20 TraesCS4A01G310500 chr5D 80.455 527 76 14 1664 2187 398527901 398528403 5.790000e-101 377
21 TraesCS4A01G310500 chr5A 80.192 520 76 14 1671 2187 503520952 503521447 4.510000e-97 364
22 TraesCS4A01G310500 chr4D 83.260 227 29 6 1611 1836 1652823 1652605 1.350000e-47 200
23 TraesCS4A01G310500 chr4D 83.810 210 24 6 1629 1836 499903190 499902989 8.100000e-45 191


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 TraesCS4A01G310500 chr4A 603339065 603341286 2221 False 4104 4104 100.000 1 2222 1 chr4A.!!$F2 2221
1 TraesCS4A01G310500 chr4A 553534071 553535594 1523 False 2344 2344 94.347 1 1537 1 chr4A.!!$F1 1536
2 TraesCS4A01G310500 chr5B 492815396 492816933 1537 True 2484 2484 95.844 1 1537 1 chr5B.!!$R1 1536
3 TraesCS4A01G310500 chr5B 478479137 478479637 500 False 353 353 79.696 1664 2187 1 chr5B.!!$F1 523
4 TraesCS4A01G310500 chr1A 22341220 22342756 1536 False 2483 2483 95.839 1 1536 1 chr1A.!!$F1 1535
5 TraesCS4A01G310500 chr6A 224098364 224099762 1398 True 2211 2211 95.218 1 1398 1 chr6A.!!$R1 1397
6 TraesCS4A01G310500 chr3A 11597492 11598672 1180 True 1879 1879 95.428 360 1536 1 chr3A.!!$R1 1176
7 TraesCS4A01G310500 chr3A 11604380 11605560 1180 True 1879 1879 95.428 360 1536 1 chr3A.!!$R2 1176
8 TraesCS4A01G310500 chr3A 684744299 684745478 1179 False 1868 1868 95.254 360 1537 1 chr3A.!!$F1 1177
9 TraesCS4A01G310500 chr3A 459621709 459622888 1179 True 1862 1862 95.169 360 1537 1 chr3A.!!$R3 1177
10 TraesCS4A01G310500 chr4B 604143343 604144522 1179 False 1873 1873 95.339 360 1537 1 chr4B.!!$F1 1177
11 TraesCS4A01G310500 chr7A 677974754 677975935 1181 False 1853 1853 95.008 360 1538 1 chr7A.!!$F2 1178
12 TraesCS4A01G310500 chr2A 38289420 38289980 560 False 883 883 95.035 1 564 1 chr2A.!!$F1 563
13 TraesCS4A01G310500 chr5D 398527901 398528403 502 False 377 377 80.455 1664 2187 1 chr5D.!!$F1 523

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
498 502 2.540931 TGACGCGTGTAAAGTTTTCTCC 59.459 45.455 20.7 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1931 1940 0.032403 TGTTTGCTTGGCACATCTGC 59.968 50.0 0.0 0.0 38.71 4.26 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
27 28 7.970061 TGTAAGACGCTTTGTACGTATAGAAAT 59.030 33.333 0.00 0.00 45.24 2.17
128 129 8.103305 AGATTTCAGGTCAGCTTCTAAATTACA 58.897 33.333 0.00 0.00 0.00 2.41
276 277 5.653330 TGTAACTGTGTAATACCTGATCCGA 59.347 40.000 0.00 0.00 0.00 4.55
314 318 9.300681 CATTATTATTATTGGAGGAAAGAGGCA 57.699 33.333 0.00 0.00 0.00 4.75
498 502 2.540931 TGACGCGTGTAAAGTTTTCTCC 59.459 45.455 20.70 0.00 0.00 3.71
629 633 8.239314 CACACTGATCAAATAGCACAAATAAGT 58.761 33.333 0.00 0.00 0.00 2.24
731 735 3.272574 AGCCGACATGAACATGAGAAT 57.727 42.857 19.56 0.00 41.20 2.40
822 826 6.600822 ACAAGATTGCTGCATTCTTATGTACT 59.399 34.615 28.87 11.46 33.94 2.73
1029 1034 3.550431 GCCGGAGAGCATGCCCTA 61.550 66.667 15.66 0.00 0.00 3.53
1157 1162 1.146263 CTTCCCCCATCGTGGCTAC 59.854 63.158 0.00 0.00 35.79 3.58
1158 1163 1.306654 TTCCCCCATCGTGGCTACT 60.307 57.895 0.00 0.00 35.79 2.57
1167 1172 0.108662 TCGTGGCTACTGTGCATGAG 60.109 55.000 0.00 0.00 34.04 2.90
1170 1175 1.200760 TGGCTACTGTGCATGAGGGT 61.201 55.000 0.00 0.00 34.04 4.34
1209 1214 7.201920 GCGATTAGCTTCCTAATAGGATGGATA 60.202 40.741 19.76 12.04 42.76 2.59
1363 1370 6.730447 TGGAGTTTCATATTTTCCTCCATGA 58.270 36.000 0.00 0.00 42.54 3.07
1547 1556 7.993349 ATAGTAGTATAGATACTCCCTCCGT 57.007 40.000 5.46 0.00 42.31 4.69
1548 1557 6.298441 AGTAGTATAGATACTCCCTCCGTC 57.702 45.833 5.46 0.00 42.31 4.79
1549 1558 4.573021 AGTATAGATACTCCCTCCGTCC 57.427 50.000 0.00 0.00 39.27 4.79
1550 1559 3.915073 AGTATAGATACTCCCTCCGTCCA 59.085 47.826 0.00 0.00 39.27 4.02
1551 1560 3.897657 ATAGATACTCCCTCCGTCCAA 57.102 47.619 0.00 0.00 0.00 3.53
1552 1561 2.544844 AGATACTCCCTCCGTCCAAA 57.455 50.000 0.00 0.00 0.00 3.28
1553 1562 2.829023 AGATACTCCCTCCGTCCAAAA 58.171 47.619 0.00 0.00 0.00 2.44
1554 1563 3.178865 AGATACTCCCTCCGTCCAAAAA 58.821 45.455 0.00 0.00 0.00 1.94
1576 1585 7.898014 AAAAACTTGTCCCAAACTTATCTCT 57.102 32.000 0.00 0.00 0.00 3.10
1577 1586 7.511959 AAAACTTGTCCCAAACTTATCTCTC 57.488 36.000 0.00 0.00 0.00 3.20
1578 1587 6.441088 AACTTGTCCCAAACTTATCTCTCT 57.559 37.500 0.00 0.00 0.00 3.10
1579 1588 5.799213 ACTTGTCCCAAACTTATCTCTCTG 58.201 41.667 0.00 0.00 0.00 3.35
1580 1589 5.544176 ACTTGTCCCAAACTTATCTCTCTGA 59.456 40.000 0.00 0.00 0.00 3.27
1581 1590 6.214412 ACTTGTCCCAAACTTATCTCTCTGAT 59.786 38.462 0.00 0.00 39.11 2.90
1582 1591 5.982356 TGTCCCAAACTTATCTCTCTGATG 58.018 41.667 0.00 0.00 36.65 3.07
1583 1592 4.813697 GTCCCAAACTTATCTCTCTGATGC 59.186 45.833 0.00 0.00 36.65 3.91
1584 1593 4.718774 TCCCAAACTTATCTCTCTGATGCT 59.281 41.667 0.00 0.00 36.65 3.79
1585 1594 5.899547 TCCCAAACTTATCTCTCTGATGCTA 59.100 40.000 0.00 0.00 36.65 3.49
1586 1595 6.041409 TCCCAAACTTATCTCTCTGATGCTAG 59.959 42.308 0.00 0.00 36.65 3.42
1587 1596 6.041409 CCCAAACTTATCTCTCTGATGCTAGA 59.959 42.308 0.00 0.00 36.65 2.43
1588 1597 7.256261 CCCAAACTTATCTCTCTGATGCTAGAT 60.256 40.741 0.00 0.00 36.65 1.98
1589 1598 8.801299 CCAAACTTATCTCTCTGATGCTAGATA 58.199 37.037 0.00 0.00 36.65 1.98
1590 1599 9.624697 CAAACTTATCTCTCTGATGCTAGATAC 57.375 37.037 0.00 0.00 36.65 2.24
1591 1600 8.932434 AACTTATCTCTCTGATGCTAGATACA 57.068 34.615 0.00 0.00 36.65 2.29
1592 1601 9.532494 AACTTATCTCTCTGATGCTAGATACAT 57.468 33.333 0.00 0.00 36.65 2.29
1593 1602 9.532494 ACTTATCTCTCTGATGCTAGATACATT 57.468 33.333 0.00 0.00 36.65 2.71
1595 1604 9.525826 TTATCTCTCTGATGCTAGATACATTCA 57.474 33.333 0.00 0.00 36.65 2.57
1596 1605 8.598202 ATCTCTCTGATGCTAGATACATTCAT 57.402 34.615 0.00 0.00 33.43 2.57
1597 1606 8.419922 TCTCTCTGATGCTAGATACATTCATT 57.580 34.615 0.00 0.00 0.00 2.57
1598 1607 8.868103 TCTCTCTGATGCTAGATACATTCATTT 58.132 33.333 0.00 0.00 0.00 2.32
1599 1608 8.828688 TCTCTGATGCTAGATACATTCATTTG 57.171 34.615 0.00 0.00 0.00 2.32
1600 1609 7.876582 TCTCTGATGCTAGATACATTCATTTGG 59.123 37.037 0.00 0.00 0.00 3.28
1601 1610 6.938596 TCTGATGCTAGATACATTCATTTGGG 59.061 38.462 0.00 0.00 0.00 4.12
1602 1611 6.005823 TGATGCTAGATACATTCATTTGGGG 58.994 40.000 0.00 0.00 0.00 4.96
1603 1612 4.728772 TGCTAGATACATTCATTTGGGGG 58.271 43.478 0.00 0.00 0.00 5.40
1618 1627 3.298320 GGGGGCAAGCTATTTTGGA 57.702 52.632 0.00 0.00 0.00 3.53
1619 1628 0.824109 GGGGGCAAGCTATTTTGGAC 59.176 55.000 0.00 0.00 0.00 4.02
1620 1629 0.455815 GGGGCAAGCTATTTTGGACG 59.544 55.000 0.00 0.00 0.00 4.79
1621 1630 0.455815 GGGCAAGCTATTTTGGACGG 59.544 55.000 0.00 0.00 0.00 4.79
1622 1631 1.459450 GGCAAGCTATTTTGGACGGA 58.541 50.000 0.00 0.00 0.00 4.69
1623 1632 1.401905 GGCAAGCTATTTTGGACGGAG 59.598 52.381 0.00 0.00 0.00 4.63
1624 1633 2.356135 GCAAGCTATTTTGGACGGAGA 58.644 47.619 0.00 0.00 0.00 3.71
1625 1634 2.352960 GCAAGCTATTTTGGACGGAGAG 59.647 50.000 0.00 0.00 0.00 3.20
1626 1635 3.861840 CAAGCTATTTTGGACGGAGAGA 58.138 45.455 0.00 0.00 0.00 3.10
1627 1636 3.810310 AGCTATTTTGGACGGAGAGAG 57.190 47.619 0.00 0.00 0.00 3.20
1628 1637 3.100671 AGCTATTTTGGACGGAGAGAGT 58.899 45.455 0.00 0.00 0.00 3.24
1629 1638 4.279145 AGCTATTTTGGACGGAGAGAGTA 58.721 43.478 0.00 0.00 0.00 2.59
1630 1639 4.339814 AGCTATTTTGGACGGAGAGAGTAG 59.660 45.833 0.00 0.00 0.00 2.57
1631 1640 3.528597 ATTTTGGACGGAGAGAGTAGC 57.471 47.619 0.00 0.00 0.00 3.58
1632 1641 1.919240 TTTGGACGGAGAGAGTAGCA 58.081 50.000 0.00 0.00 0.00 3.49
1633 1642 2.145397 TTGGACGGAGAGAGTAGCAT 57.855 50.000 0.00 0.00 0.00 3.79
1634 1643 2.145397 TGGACGGAGAGAGTAGCATT 57.855 50.000 0.00 0.00 0.00 3.56
1635 1644 2.457598 TGGACGGAGAGAGTAGCATTT 58.542 47.619 0.00 0.00 0.00 2.32
1636 1645 3.628008 TGGACGGAGAGAGTAGCATTTA 58.372 45.455 0.00 0.00 0.00 1.40
1637 1646 4.215908 TGGACGGAGAGAGTAGCATTTAT 58.784 43.478 0.00 0.00 0.00 1.40
1638 1647 5.382616 TGGACGGAGAGAGTAGCATTTATA 58.617 41.667 0.00 0.00 0.00 0.98
1639 1648 6.010850 TGGACGGAGAGAGTAGCATTTATAT 58.989 40.000 0.00 0.00 0.00 0.86
1640 1649 6.493802 TGGACGGAGAGAGTAGCATTTATATT 59.506 38.462 0.00 0.00 0.00 1.28
1641 1650 7.030768 GGACGGAGAGAGTAGCATTTATATTC 58.969 42.308 0.00 0.00 0.00 1.75
1642 1651 6.926313 ACGGAGAGAGTAGCATTTATATTCC 58.074 40.000 0.00 0.00 0.00 3.01
1643 1652 6.493802 ACGGAGAGAGTAGCATTTATATTCCA 59.506 38.462 0.00 0.00 0.00 3.53
1644 1653 7.179338 ACGGAGAGAGTAGCATTTATATTCCAT 59.821 37.037 0.00 0.00 0.00 3.41
1645 1654 7.490725 CGGAGAGAGTAGCATTTATATTCCATG 59.509 40.741 0.00 0.00 0.00 3.66
1646 1655 7.768120 GGAGAGAGTAGCATTTATATTCCATGG 59.232 40.741 4.97 4.97 0.00 3.66
1647 1656 8.212259 AGAGAGTAGCATTTATATTCCATGGT 57.788 34.615 12.58 0.00 33.35 3.55
1648 1657 8.099537 AGAGAGTAGCATTTATATTCCATGGTG 58.900 37.037 12.58 0.54 31.29 4.17
1649 1658 6.656693 AGAGTAGCATTTATATTCCATGGTGC 59.343 38.462 12.58 11.54 32.94 5.01
1650 1659 6.306199 AGTAGCATTTATATTCCATGGTGCA 58.694 36.000 18.56 3.43 34.58 4.57
1651 1660 6.950041 AGTAGCATTTATATTCCATGGTGCAT 59.050 34.615 18.56 9.85 34.58 3.96
1652 1661 6.276832 AGCATTTATATTCCATGGTGCATC 57.723 37.500 18.56 0.00 34.01 3.91
1653 1662 6.014647 AGCATTTATATTCCATGGTGCATCT 58.985 36.000 18.56 4.21 34.01 2.90
1654 1663 6.071560 AGCATTTATATTCCATGGTGCATCTG 60.072 38.462 18.56 7.67 34.01 2.90
1655 1664 6.294899 GCATTTATATTCCATGGTGCATCTGT 60.295 38.462 12.58 0.00 0.00 3.41
1656 1665 6.882610 TTTATATTCCATGGTGCATCTGTC 57.117 37.500 12.58 0.00 0.00 3.51
1657 1666 4.719026 ATATTCCATGGTGCATCTGTCT 57.281 40.909 12.58 0.00 0.00 3.41
1658 1667 2.408271 TTCCATGGTGCATCTGTCTC 57.592 50.000 12.58 0.00 0.00 3.36
1659 1668 1.576577 TCCATGGTGCATCTGTCTCT 58.423 50.000 12.58 0.00 0.00 3.10
1660 1669 1.483827 TCCATGGTGCATCTGTCTCTC 59.516 52.381 12.58 0.00 0.00 3.20
1661 1670 1.208776 CCATGGTGCATCTGTCTCTCA 59.791 52.381 2.57 0.00 0.00 3.27
1662 1671 2.552031 CATGGTGCATCTGTCTCTCAG 58.448 52.381 0.00 0.00 44.85 3.35
1663 1672 1.637338 TGGTGCATCTGTCTCTCAGT 58.363 50.000 0.00 0.00 43.97 3.41
1664 1673 1.547820 TGGTGCATCTGTCTCTCAGTC 59.452 52.381 0.00 0.00 43.97 3.51
1665 1674 1.824230 GGTGCATCTGTCTCTCAGTCT 59.176 52.381 0.00 0.00 43.97 3.24
1666 1675 2.159254 GGTGCATCTGTCTCTCAGTCTC 60.159 54.545 0.00 0.00 43.97 3.36
1667 1676 2.491298 GTGCATCTGTCTCTCAGTCTCA 59.509 50.000 0.00 0.00 43.97 3.27
1668 1677 2.754002 TGCATCTGTCTCTCAGTCTCAG 59.246 50.000 0.00 0.00 43.97 3.35
1669 1678 2.480073 GCATCTGTCTCTCAGTCTCAGC 60.480 54.545 0.00 0.00 43.97 4.26
1674 1683 4.009675 CTGTCTCTCAGTCTCAGCTAAGT 58.990 47.826 0.00 0.00 39.17 2.24
1684 1693 5.176590 CAGTCTCAGCTAAGTGAACTGTTTC 59.823 44.000 0.00 0.00 34.41 2.78
1697 1706 3.996150 ACTGTTTCCTTGCAGTTCATG 57.004 42.857 0.00 0.00 42.61 3.07
1708 1717 0.321564 CAGTTCATGGCACGGGAGAA 60.322 55.000 0.00 0.00 0.00 2.87
1710 1719 0.734889 GTTCATGGCACGGGAGAATG 59.265 55.000 0.00 0.00 0.00 2.67
1745 1754 3.453059 AAAACGGAGGTAGAGGAGAGA 57.547 47.619 0.00 0.00 0.00 3.10
1748 1757 1.210967 ACGGAGGTAGAGGAGAGACTG 59.789 57.143 0.00 0.00 0.00 3.51
1749 1758 1.476110 CGGAGGTAGAGGAGAGACTGG 60.476 61.905 0.00 0.00 0.00 4.00
1750 1759 1.133606 GGAGGTAGAGGAGAGACTGGG 60.134 61.905 0.00 0.00 0.00 4.45
1751 1760 0.260523 AGGTAGAGGAGAGACTGGGC 59.739 60.000 0.00 0.00 0.00 5.36
1761 1770 2.564947 GAGAGACTGGGCAGAGAAAAGA 59.435 50.000 0.00 0.00 0.00 2.52
1765 1774 1.072965 ACTGGGCAGAGAAAAGACTGG 59.927 52.381 0.00 0.00 35.05 4.00
1766 1775 1.349026 CTGGGCAGAGAAAAGACTGGA 59.651 52.381 0.00 0.00 35.05 3.86
1769 1778 2.614229 GGGCAGAGAAAAGACTGGACTC 60.614 54.545 0.00 0.00 35.05 3.36
1770 1779 2.614229 GGCAGAGAAAAGACTGGACTCC 60.614 54.545 0.00 0.00 35.05 3.85
1771 1780 2.928731 GCAGAGAAAAGACTGGACTCCG 60.929 54.545 0.00 0.00 35.05 4.63
1772 1781 1.896465 AGAGAAAAGACTGGACTCCGG 59.104 52.381 1.90 1.90 35.68 5.14
1775 1784 2.300437 AGAAAAGACTGGACTCCGGAAG 59.700 50.000 11.20 1.72 33.36 3.46
1826 1835 3.240069 CAAGGCAAATGAGAAAAGAGCG 58.760 45.455 0.00 0.00 0.00 5.03
1829 1838 2.159462 GGCAAATGAGAAAAGAGCGGAG 60.159 50.000 0.00 0.00 0.00 4.63
1863 1872 7.772757 AGATGCTTCTCCAGAAAAATTACCTAG 59.227 37.037 0.00 0.00 33.07 3.02
1867 1876 5.497474 TCTCCAGAAAAATTACCTAGTGGC 58.503 41.667 0.00 0.00 36.63 5.01
1875 1884 1.103803 TTACCTAGTGGCAGAGCTCG 58.896 55.000 8.37 4.60 36.63 5.03
1877 1886 1.034838 ACCTAGTGGCAGAGCTCGAG 61.035 60.000 8.45 8.45 36.63 4.04
1882 1891 2.202730 GGCAGAGCTCGAGCAGTC 60.203 66.667 36.87 26.40 45.16 3.51
1888 1897 3.184683 GCTCGAGCAGTCGCAAGG 61.185 66.667 31.91 0.00 46.39 3.61
1898 1907 1.669115 GTCGCAAGGAGAGCTGCAA 60.669 57.895 1.02 0.00 38.52 4.08
1915 1924 1.148310 CAACGCGAGAAAGACCATGT 58.852 50.000 15.93 0.00 0.00 3.21
1916 1925 1.126846 CAACGCGAGAAAGACCATGTC 59.873 52.381 15.93 0.00 0.00 3.06
1917 1926 0.317160 ACGCGAGAAAGACCATGTCA 59.683 50.000 15.93 0.00 34.60 3.58
1918 1927 0.716108 CGCGAGAAAGACCATGTCAC 59.284 55.000 0.00 0.00 34.60 3.67
1919 1928 1.795768 GCGAGAAAGACCATGTCACA 58.204 50.000 0.00 0.00 34.60 3.58
1922 1931 3.364366 GCGAGAAAGACCATGTCACAAAG 60.364 47.826 0.00 0.00 34.60 2.77
1923 1932 3.364366 CGAGAAAGACCATGTCACAAAGC 60.364 47.826 0.00 0.00 34.60 3.51
1927 1936 2.936202 AGACCATGTCACAAAGCAAGT 58.064 42.857 0.00 0.00 34.60 3.16
1931 1940 3.067180 ACCATGTCACAAAGCAAGTTGAG 59.933 43.478 7.16 0.00 32.59 3.02
1932 1941 2.849880 TGTCACAAAGCAAGTTGAGC 57.150 45.000 7.16 0.00 32.59 4.26
1934 1943 2.097954 TGTCACAAAGCAAGTTGAGCAG 59.902 45.455 7.16 0.00 32.59 4.24
1938 1947 2.954318 ACAAAGCAAGTTGAGCAGATGT 59.046 40.909 7.16 0.00 32.59 3.06
1949 1958 2.818350 GCAGATGTGCCAAGCAAAC 58.182 52.632 2.79 0.00 44.72 2.93
1950 1959 0.032403 GCAGATGTGCCAAGCAAACA 59.968 50.000 2.79 0.00 44.72 2.83
1954 1963 2.816087 AGATGTGCCAAGCAAACAGTAG 59.184 45.455 0.00 0.00 41.47 2.57
1958 1967 0.387750 GCCAAGCAAACAGTAGCAGC 60.388 55.000 1.19 0.00 0.00 5.25
1959 1968 0.110056 CCAAGCAAACAGTAGCAGCG 60.110 55.000 1.19 0.00 0.00 5.18
1960 1969 0.588252 CAAGCAAACAGTAGCAGCGT 59.412 50.000 1.19 0.00 0.00 5.07
1961 1970 0.868406 AAGCAAACAGTAGCAGCGTC 59.132 50.000 1.19 0.00 0.00 5.19
1962 1971 0.034059 AGCAAACAGTAGCAGCGTCT 59.966 50.000 1.19 0.00 0.00 4.18
1963 1972 0.868406 GCAAACAGTAGCAGCGTCTT 59.132 50.000 0.00 0.00 0.00 3.01
1977 1986 2.744202 AGCGTCTTTGTATTTGGCTCTG 59.256 45.455 0.00 0.00 0.00 3.35
1978 1987 2.729156 GCGTCTTTGTATTTGGCTCTGC 60.729 50.000 0.00 0.00 0.00 4.26
1988 1997 4.042251 GGCTCTGCCTCTACCACT 57.958 61.111 0.73 0.00 46.69 4.00
1989 1998 3.209091 GGCTCTGCCTCTACCACTA 57.791 57.895 0.73 0.00 46.69 2.74
1990 1999 0.747852 GGCTCTGCCTCTACCACTAC 59.252 60.000 0.73 0.00 46.69 2.73
1991 2000 1.686741 GGCTCTGCCTCTACCACTACT 60.687 57.143 0.73 0.00 46.69 2.57
2000 2009 4.136051 CCTCTACCACTACTACTAGTGCC 58.864 52.174 5.39 0.00 46.12 5.01
2001 2010 4.384978 CCTCTACCACTACTACTAGTGCCA 60.385 50.000 5.39 0.00 46.12 4.92
2004 2013 5.826737 TCTACCACTACTACTAGTGCCATTC 59.173 44.000 5.39 0.00 46.12 2.67
2006 2015 3.704566 CCACTACTACTAGTGCCATTCCA 59.295 47.826 5.39 0.00 46.12 3.53
2007 2016 4.345257 CCACTACTACTAGTGCCATTCCAT 59.655 45.833 5.39 0.00 46.12 3.41
2013 2022 6.717289 ACTACTAGTGCCATTCCATTAACAA 58.283 36.000 5.39 0.00 0.00 2.83
2015 2024 6.515272 ACTAGTGCCATTCCATTAACAAAG 57.485 37.500 0.00 0.00 0.00 2.77
2022 2031 5.170748 CCATTCCATTAACAAAGTTCAGCC 58.829 41.667 0.00 0.00 0.00 4.85
2026 2035 4.832266 TCCATTAACAAAGTTCAGCCACAT 59.168 37.500 0.00 0.00 0.00 3.21
2027 2036 4.925054 CCATTAACAAAGTTCAGCCACATG 59.075 41.667 0.00 0.00 0.00 3.21
2034 2043 4.574674 AAGTTCAGCCACATGGAGATAA 57.425 40.909 0.87 0.00 37.39 1.75
2045 2054 4.631377 CACATGGAGATAAAAGAAGCGACA 59.369 41.667 0.00 0.00 0.00 4.35
2047 2056 3.262420 TGGAGATAAAAGAAGCGACAGC 58.738 45.455 0.00 0.00 45.58 4.40
2064 2073 1.466167 CAGCCAACTTTGATGACTCCG 59.534 52.381 0.00 0.00 0.00 4.63
2072 2081 6.310197 CAACTTTGATGACTCCGAAAAGATC 58.690 40.000 0.00 0.00 33.19 2.75
2130 2139 0.236711 CCGTCATACTACCGTAGCCG 59.763 60.000 5.42 1.35 0.00 5.52
2137 2146 4.512944 TCATACTACCGTAGCCGTAAAGAG 59.487 45.833 5.42 0.00 0.00 2.85
2141 2150 3.160777 ACCGTAGCCGTAAAGAGATTG 57.839 47.619 0.00 0.00 0.00 2.67
2187 2196 8.012957 AGATAAAGAGTTCAATGACGAGGTAT 57.987 34.615 0.00 0.00 0.00 2.73
2188 2197 7.923344 AGATAAAGAGTTCAATGACGAGGTATG 59.077 37.037 0.00 0.00 0.00 2.39
2189 2198 5.407407 AAGAGTTCAATGACGAGGTATGT 57.593 39.130 0.00 0.00 0.00 2.29
2190 2199 6.525578 AAGAGTTCAATGACGAGGTATGTA 57.474 37.500 0.00 0.00 0.00 2.29
2191 2200 6.525578 AGAGTTCAATGACGAGGTATGTAA 57.474 37.500 0.00 0.00 0.00 2.41
2192 2201 7.113658 AGAGTTCAATGACGAGGTATGTAAT 57.886 36.000 0.00 0.00 0.00 1.89
2193 2202 7.556844 AGAGTTCAATGACGAGGTATGTAATT 58.443 34.615 0.00 0.00 0.00 1.40
2194 2203 8.041323 AGAGTTCAATGACGAGGTATGTAATTT 58.959 33.333 0.00 0.00 0.00 1.82
2195 2204 9.309516 GAGTTCAATGACGAGGTATGTAATTTA 57.690 33.333 0.00 0.00 0.00 1.40
2196 2205 9.661563 AGTTCAATGACGAGGTATGTAATTTAA 57.338 29.630 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
150 151 5.288804 TGCAAATTGTTGGCTCTTTCTTAC 58.711 37.500 0.00 0.00 35.10 2.34
314 318 3.080319 GCCTCTCTTTCTTTGTCTGCAT 58.920 45.455 0.00 0.00 0.00 3.96
517 521 5.252863 TCTCCAGGGATAGGTTGAAAATCAA 59.747 40.000 0.00 0.00 33.32 2.57
629 633 4.473444 GCCATCCCCTTGATTAGAATTGA 58.527 43.478 0.00 0.00 0.00 2.57
731 735 9.486497 GATGCAGAGTCTATTTCTCATGATTAA 57.514 33.333 0.00 0.00 34.73 1.40
1029 1034 0.741326 CGACGACTCCATCCATGTCT 59.259 55.000 0.00 0.00 0.00 3.41
1157 1162 2.034532 TGCCACCCTCATGCACAG 59.965 61.111 0.00 0.00 0.00 3.66
1158 1163 2.034532 CTGCCACCCTCATGCACA 59.965 61.111 0.00 0.00 0.00 4.57
1233 1239 8.950210 GGAAACTAATCTCAGACAAATTCATCA 58.050 33.333 0.00 0.00 0.00 3.07
1363 1370 6.560003 TTACATTGACTGACCATACTCCAT 57.440 37.500 0.00 0.00 0.00 3.41
1371 1378 6.714810 ACTTAGCAATTTACATTGACTGACCA 59.285 34.615 5.78 0.00 42.35 4.02
1430 1437 8.782137 ATTAGGCCCACTAAAATCAATGTAAT 57.218 30.769 0.00 0.00 44.39 1.89
1434 1441 5.299279 ACGATTAGGCCCACTAAAATCAATG 59.701 40.000 0.00 0.00 44.39 2.82
1555 1564 7.256835 ATCAGAGAGATAAGTTTGGGACAAGTT 60.257 37.037 0.00 0.00 38.48 2.66
1556 1565 6.214412 ATCAGAGAGATAAGTTTGGGACAAGT 59.786 38.462 0.00 0.00 38.48 3.16
1557 1566 6.538021 CATCAGAGAGATAAGTTTGGGACAAG 59.462 42.308 0.00 0.00 38.48 3.16
1558 1567 6.409704 CATCAGAGAGATAAGTTTGGGACAA 58.590 40.000 0.00 0.00 38.48 3.18
1559 1568 5.627735 GCATCAGAGAGATAAGTTTGGGACA 60.628 44.000 0.00 0.00 34.43 4.02
1560 1569 4.813697 GCATCAGAGAGATAAGTTTGGGAC 59.186 45.833 0.00 0.00 34.43 4.46
1561 1570 4.718774 AGCATCAGAGAGATAAGTTTGGGA 59.281 41.667 0.00 0.00 34.43 4.37
1562 1571 5.033589 AGCATCAGAGAGATAAGTTTGGG 57.966 43.478 0.00 0.00 34.43 4.12
1563 1572 7.048629 TCTAGCATCAGAGAGATAAGTTTGG 57.951 40.000 0.00 0.00 34.43 3.28
1564 1573 9.624697 GTATCTAGCATCAGAGAGATAAGTTTG 57.375 37.037 0.00 0.00 33.75 2.93
1565 1574 9.360901 TGTATCTAGCATCAGAGAGATAAGTTT 57.639 33.333 0.00 0.00 33.75 2.66
1566 1575 8.932434 TGTATCTAGCATCAGAGAGATAAGTT 57.068 34.615 0.00 0.00 33.75 2.66
1567 1576 9.532494 AATGTATCTAGCATCAGAGAGATAAGT 57.468 33.333 0.00 0.00 33.75 2.24
1569 1578 9.525826 TGAATGTATCTAGCATCAGAGAGATAA 57.474 33.333 0.00 0.00 33.75 1.75
1570 1579 9.697990 ATGAATGTATCTAGCATCAGAGAGATA 57.302 33.333 0.00 0.00 34.43 1.98
1571 1580 8.598202 ATGAATGTATCTAGCATCAGAGAGAT 57.402 34.615 0.00 0.00 37.48 2.75
1572 1581 8.419922 AATGAATGTATCTAGCATCAGAGAGA 57.580 34.615 0.00 0.00 0.00 3.10
1573 1582 8.927721 CAAATGAATGTATCTAGCATCAGAGAG 58.072 37.037 0.00 0.00 0.00 3.20
1574 1583 7.876582 CCAAATGAATGTATCTAGCATCAGAGA 59.123 37.037 0.00 0.00 0.00 3.10
1575 1584 7.119407 CCCAAATGAATGTATCTAGCATCAGAG 59.881 40.741 0.00 0.00 0.00 3.35
1576 1585 6.938596 CCCAAATGAATGTATCTAGCATCAGA 59.061 38.462 0.00 0.00 0.00 3.27
1577 1586 6.150641 CCCCAAATGAATGTATCTAGCATCAG 59.849 42.308 0.00 0.00 0.00 2.90
1578 1587 6.005823 CCCCAAATGAATGTATCTAGCATCA 58.994 40.000 0.00 0.00 0.00 3.07
1579 1588 5.416952 CCCCCAAATGAATGTATCTAGCATC 59.583 44.000 0.00 0.00 0.00 3.91
1580 1589 5.327732 CCCCCAAATGAATGTATCTAGCAT 58.672 41.667 0.00 0.00 0.00 3.79
1581 1590 4.728772 CCCCCAAATGAATGTATCTAGCA 58.271 43.478 0.00 0.00 0.00 3.49
1600 1609 0.824109 GTCCAAAATAGCTTGCCCCC 59.176 55.000 0.00 0.00 0.00 5.40
1601 1610 0.455815 CGTCCAAAATAGCTTGCCCC 59.544 55.000 0.00 0.00 0.00 5.80
1602 1611 0.455815 CCGTCCAAAATAGCTTGCCC 59.544 55.000 0.00 0.00 0.00 5.36
1603 1612 1.401905 CTCCGTCCAAAATAGCTTGCC 59.598 52.381 0.00 0.00 0.00 4.52
1604 1613 2.352960 CTCTCCGTCCAAAATAGCTTGC 59.647 50.000 0.00 0.00 0.00 4.01
1605 1614 3.861840 TCTCTCCGTCCAAAATAGCTTG 58.138 45.455 0.00 0.00 0.00 4.01
1606 1615 3.515901 ACTCTCTCCGTCCAAAATAGCTT 59.484 43.478 0.00 0.00 0.00 3.74
1607 1616 3.100671 ACTCTCTCCGTCCAAAATAGCT 58.899 45.455 0.00 0.00 0.00 3.32
1608 1617 3.528597 ACTCTCTCCGTCCAAAATAGC 57.471 47.619 0.00 0.00 0.00 2.97
1609 1618 4.098044 TGCTACTCTCTCCGTCCAAAATAG 59.902 45.833 0.00 0.00 0.00 1.73
1610 1619 4.021229 TGCTACTCTCTCCGTCCAAAATA 58.979 43.478 0.00 0.00 0.00 1.40
1611 1620 2.832129 TGCTACTCTCTCCGTCCAAAAT 59.168 45.455 0.00 0.00 0.00 1.82
1612 1621 2.244695 TGCTACTCTCTCCGTCCAAAA 58.755 47.619 0.00 0.00 0.00 2.44
1613 1622 1.919240 TGCTACTCTCTCCGTCCAAA 58.081 50.000 0.00 0.00 0.00 3.28
1614 1623 2.145397 ATGCTACTCTCTCCGTCCAA 57.855 50.000 0.00 0.00 0.00 3.53
1615 1624 2.145397 AATGCTACTCTCTCCGTCCA 57.855 50.000 0.00 0.00 0.00 4.02
1616 1625 4.857509 ATAAATGCTACTCTCTCCGTCC 57.142 45.455 0.00 0.00 0.00 4.79
1617 1626 7.030768 GGAATATAAATGCTACTCTCTCCGTC 58.969 42.308 0.00 0.00 0.00 4.79
1618 1627 6.493802 TGGAATATAAATGCTACTCTCTCCGT 59.506 38.462 0.00 0.00 0.00 4.69
1619 1628 6.925211 TGGAATATAAATGCTACTCTCTCCG 58.075 40.000 0.00 0.00 0.00 4.63
1620 1629 7.768120 CCATGGAATATAAATGCTACTCTCTCC 59.232 40.741 5.56 0.00 0.00 3.71
1621 1630 8.317679 ACCATGGAATATAAATGCTACTCTCTC 58.682 37.037 21.47 0.00 0.00 3.20
1622 1631 8.099537 CACCATGGAATATAAATGCTACTCTCT 58.900 37.037 21.47 0.00 0.00 3.10
1623 1632 7.148340 GCACCATGGAATATAAATGCTACTCTC 60.148 40.741 21.47 0.00 0.00 3.20
1624 1633 6.656693 GCACCATGGAATATAAATGCTACTCT 59.343 38.462 21.47 0.00 0.00 3.24
1625 1634 6.430925 TGCACCATGGAATATAAATGCTACTC 59.569 38.462 21.47 0.00 33.03 2.59
1626 1635 6.306199 TGCACCATGGAATATAAATGCTACT 58.694 36.000 21.47 0.00 33.03 2.57
1627 1636 6.573664 TGCACCATGGAATATAAATGCTAC 57.426 37.500 21.47 0.00 33.03 3.58
1628 1637 7.121611 CAGATGCACCATGGAATATAAATGCTA 59.878 37.037 21.47 6.53 33.03 3.49
1629 1638 6.014647 AGATGCACCATGGAATATAAATGCT 58.985 36.000 21.47 5.18 33.03 3.79
1630 1639 6.097356 CAGATGCACCATGGAATATAAATGC 58.903 40.000 21.47 15.59 0.00 3.56
1631 1640 7.176165 AGACAGATGCACCATGGAATATAAATG 59.824 37.037 21.47 4.35 0.00 2.32
1632 1641 7.236529 AGACAGATGCACCATGGAATATAAAT 58.763 34.615 21.47 1.64 0.00 1.40
1633 1642 6.604171 AGACAGATGCACCATGGAATATAAA 58.396 36.000 21.47 0.00 0.00 1.40
1634 1643 6.043590 AGAGACAGATGCACCATGGAATATAA 59.956 38.462 21.47 0.00 0.00 0.98
1635 1644 5.545335 AGAGACAGATGCACCATGGAATATA 59.455 40.000 21.47 0.00 0.00 0.86
1636 1645 4.350225 AGAGACAGATGCACCATGGAATAT 59.650 41.667 21.47 8.92 0.00 1.28
1637 1646 3.713248 AGAGACAGATGCACCATGGAATA 59.287 43.478 21.47 3.70 0.00 1.75
1638 1647 2.508716 AGAGACAGATGCACCATGGAAT 59.491 45.455 21.47 8.95 0.00 3.01
1639 1648 1.911357 AGAGACAGATGCACCATGGAA 59.089 47.619 21.47 3.61 0.00 3.53
1640 1649 1.483827 GAGAGACAGATGCACCATGGA 59.516 52.381 21.47 0.00 0.00 3.41
1641 1650 1.208776 TGAGAGACAGATGCACCATGG 59.791 52.381 11.19 11.19 0.00 3.66
1642 1651 2.685850 TGAGAGACAGATGCACCATG 57.314 50.000 0.00 0.00 0.00 3.66
1653 1662 3.755905 CACTTAGCTGAGACTGAGAGACA 59.244 47.826 13.21 0.00 0.00 3.41
1654 1663 4.006989 TCACTTAGCTGAGACTGAGAGAC 58.993 47.826 13.21 0.00 0.00 3.36
1655 1664 4.293662 TCACTTAGCTGAGACTGAGAGA 57.706 45.455 13.21 0.00 0.00 3.10
1656 1665 4.458989 AGTTCACTTAGCTGAGACTGAGAG 59.541 45.833 13.21 0.00 0.00 3.20
1657 1666 4.217334 CAGTTCACTTAGCTGAGACTGAGA 59.783 45.833 16.46 3.60 38.64 3.27
1658 1667 4.022416 ACAGTTCACTTAGCTGAGACTGAG 60.022 45.833 24.06 9.00 38.64 3.35
1659 1668 3.891977 ACAGTTCACTTAGCTGAGACTGA 59.108 43.478 24.06 12.17 38.64 3.41
1660 1669 4.250116 ACAGTTCACTTAGCTGAGACTG 57.750 45.455 18.64 18.64 38.64 3.51
1661 1670 4.946478 AACAGTTCACTTAGCTGAGACT 57.054 40.909 13.21 2.43 38.64 3.24
1662 1671 4.449405 GGAAACAGTTCACTTAGCTGAGAC 59.551 45.833 13.21 0.00 38.64 3.36
1663 1672 4.345257 AGGAAACAGTTCACTTAGCTGAGA 59.655 41.667 13.21 0.00 38.64 3.27
1664 1673 4.636249 AGGAAACAGTTCACTTAGCTGAG 58.364 43.478 3.53 3.53 38.64 3.35
1665 1674 4.689612 AGGAAACAGTTCACTTAGCTGA 57.310 40.909 0.00 0.00 38.64 4.26
1666 1675 4.555511 GCAAGGAAACAGTTCACTTAGCTG 60.556 45.833 0.00 0.00 41.87 4.24
1667 1676 3.565902 GCAAGGAAACAGTTCACTTAGCT 59.434 43.478 0.00 0.00 35.25 3.32
1668 1677 3.315191 TGCAAGGAAACAGTTCACTTAGC 59.685 43.478 2.96 8.63 35.25 3.09
1669 1678 4.576463 ACTGCAAGGAAACAGTTCACTTAG 59.424 41.667 2.96 1.94 44.59 2.18
1684 1693 1.210931 CGTGCCATGAACTGCAAGG 59.789 57.895 0.00 0.00 39.57 3.61
1696 1705 2.359850 GTGCATTCTCCCGTGCCA 60.360 61.111 0.00 0.00 40.56 4.92
1697 1706 2.045926 AGTGCATTCTCCCGTGCC 60.046 61.111 0.00 0.00 40.56 5.01
1729 1738 1.476110 CCAGTCTCTCCTCTACCTCCG 60.476 61.905 0.00 0.00 0.00 4.63
1742 1751 2.301583 AGTCTTTTCTCTGCCCAGTCTC 59.698 50.000 0.00 0.00 0.00 3.36
1745 1754 1.072965 CCAGTCTTTTCTCTGCCCAGT 59.927 52.381 0.00 0.00 0.00 4.00
1748 1757 1.349357 AGTCCAGTCTTTTCTCTGCCC 59.651 52.381 0.00 0.00 0.00 5.36
1749 1758 2.614229 GGAGTCCAGTCTTTTCTCTGCC 60.614 54.545 3.60 0.00 0.00 4.85
1750 1759 2.694213 GGAGTCCAGTCTTTTCTCTGC 58.306 52.381 3.60 0.00 0.00 4.26
1751 1760 2.353208 CCGGAGTCCAGTCTTTTCTCTG 60.353 54.545 10.49 0.00 0.00 3.35
1782 1791 2.540361 GCAGCTCGTTGCATATTTGGAG 60.540 50.000 0.70 0.00 45.94 3.86
1805 1814 3.240069 CGCTCTTTTCTCATTTGCCTTG 58.760 45.455 0.00 0.00 0.00 3.61
1818 1827 1.194781 TCCTCCAGCTCCGCTCTTTT 61.195 55.000 0.00 0.00 36.40 2.27
1826 1835 0.106521 GAAGCATCTCCTCCAGCTCC 59.893 60.000 0.00 0.00 36.07 4.70
1829 1838 3.684693 GAGAAGCATCTCCTCCAGC 57.315 57.895 7.75 0.00 45.35 4.85
1837 1846 6.488715 AGGTAATTTTTCTGGAGAAGCATCT 58.511 36.000 0.00 0.00 39.10 2.90
1838 1847 6.765915 AGGTAATTTTTCTGGAGAAGCATC 57.234 37.500 0.00 0.00 35.21 3.91
1840 1849 6.655003 CACTAGGTAATTTTTCTGGAGAAGCA 59.345 38.462 0.00 0.00 35.21 3.91
1852 1861 4.518249 GAGCTCTGCCACTAGGTAATTTT 58.482 43.478 6.43 0.00 37.19 1.82
1857 1866 0.255033 TCGAGCTCTGCCACTAGGTA 59.745 55.000 12.85 0.00 37.19 3.08
1858 1867 1.000771 TCGAGCTCTGCCACTAGGT 60.001 57.895 12.85 0.00 37.19 3.08
1863 1872 2.508887 CTGCTCGAGCTCTGCCAC 60.509 66.667 35.27 7.21 42.66 5.01
1867 1876 2.579249 GCGACTGCTCGAGCTCTG 60.579 66.667 35.27 26.04 43.06 3.35
1875 1884 1.809209 GCTCTCCTTGCGACTGCTC 60.809 63.158 0.00 0.00 43.34 4.26
1877 1886 2.099431 CAGCTCTCCTTGCGACTGC 61.099 63.158 0.00 0.00 43.20 4.40
1882 1891 2.866028 GTTGCAGCTCTCCTTGCG 59.134 61.111 0.00 0.00 35.28 4.85
1888 1897 1.284982 TTTCTCGCGTTGCAGCTCTC 61.285 55.000 5.77 0.00 34.40 3.20
1898 1907 0.317160 TGACATGGTCTTTCTCGCGT 59.683 50.000 5.77 0.00 33.15 6.01
1915 1924 2.642427 TCTGCTCAACTTGCTTTGTGA 58.358 42.857 0.00 0.00 0.00 3.58
1916 1925 3.243301 ACATCTGCTCAACTTGCTTTGTG 60.243 43.478 0.00 0.00 0.00 3.33
1917 1926 2.954318 ACATCTGCTCAACTTGCTTTGT 59.046 40.909 0.00 0.00 0.00 2.83
1918 1927 3.305964 CACATCTGCTCAACTTGCTTTG 58.694 45.455 0.00 0.00 0.00 2.77
1919 1928 2.288030 GCACATCTGCTCAACTTGCTTT 60.288 45.455 0.00 0.00 40.63 3.51
1922 1931 0.109412 GGCACATCTGCTCAACTTGC 60.109 55.000 0.00 0.00 43.66 4.01
1923 1932 1.241165 TGGCACATCTGCTCAACTTG 58.759 50.000 0.00 0.00 43.66 3.16
1927 1936 0.537828 TGCTTGGCACATCTGCTCAA 60.538 50.000 0.00 0.00 43.66 3.02
1931 1940 0.032403 TGTTTGCTTGGCACATCTGC 59.968 50.000 0.00 0.00 38.71 4.26
1932 1941 1.338973 ACTGTTTGCTTGGCACATCTG 59.661 47.619 0.00 0.00 38.71 2.90
1934 1943 2.669391 GCTACTGTTTGCTTGGCACATC 60.669 50.000 0.00 0.00 38.71 3.06
1938 1947 0.953727 CTGCTACTGTTTGCTTGGCA 59.046 50.000 6.94 0.00 36.47 4.92
1944 1953 0.868406 AAGACGCTGCTACTGTTTGC 59.132 50.000 0.00 0.00 0.00 3.68
1949 1958 4.436050 CCAAATACAAAGACGCTGCTACTG 60.436 45.833 0.00 0.00 0.00 2.74
1950 1959 3.684788 CCAAATACAAAGACGCTGCTACT 59.315 43.478 0.00 0.00 0.00 2.57
1954 1963 1.200020 AGCCAAATACAAAGACGCTGC 59.800 47.619 0.00 0.00 0.00 5.25
1958 1967 3.122937 GCAGAGCCAAATACAAAGACG 57.877 47.619 0.00 0.00 0.00 4.18
1986 1995 7.125204 TGTTAATGGAATGGCACTAGTAGTAGT 59.875 37.037 1.57 4.29 40.38 2.73
1987 1996 7.497595 TGTTAATGGAATGGCACTAGTAGTAG 58.502 38.462 1.57 2.87 0.00 2.57
1988 1997 7.426606 TGTTAATGGAATGGCACTAGTAGTA 57.573 36.000 1.57 0.00 0.00 1.82
1989 1998 6.308015 TGTTAATGGAATGGCACTAGTAGT 57.692 37.500 0.00 0.00 0.00 2.73
1990 1999 7.336931 ACTTTGTTAATGGAATGGCACTAGTAG 59.663 37.037 0.00 0.00 0.00 2.57
1991 2000 7.172342 ACTTTGTTAATGGAATGGCACTAGTA 58.828 34.615 0.00 0.00 0.00 1.82
2000 2009 5.634859 GTGGCTGAACTTTGTTAATGGAATG 59.365 40.000 0.00 0.00 0.00 2.67
2001 2010 5.304101 TGTGGCTGAACTTTGTTAATGGAAT 59.696 36.000 0.00 0.00 0.00 3.01
2004 2013 4.582701 TGTGGCTGAACTTTGTTAATGG 57.417 40.909 0.00 0.00 0.00 3.16
2006 2015 4.832266 TCCATGTGGCTGAACTTTGTTAAT 59.168 37.500 0.00 0.00 34.44 1.40
2007 2016 4.211125 TCCATGTGGCTGAACTTTGTTAA 58.789 39.130 0.00 0.00 34.44 2.01
2013 2022 4.574674 TTATCTCCATGTGGCTGAACTT 57.425 40.909 0.00 0.00 34.44 2.66
2015 2024 4.943705 TCTTTTATCTCCATGTGGCTGAAC 59.056 41.667 0.00 0.00 34.44 3.18
2022 2031 4.631377 TGTCGCTTCTTTTATCTCCATGTG 59.369 41.667 0.00 0.00 0.00 3.21
2026 2035 3.262420 GCTGTCGCTTCTTTTATCTCCA 58.738 45.455 0.00 0.00 0.00 3.86
2027 2036 2.609916 GGCTGTCGCTTCTTTTATCTCC 59.390 50.000 0.00 0.00 36.09 3.71
2034 2043 1.680338 AAGTTGGCTGTCGCTTCTTT 58.320 45.000 0.00 0.00 36.09 2.52
2045 2054 1.347707 TCGGAGTCATCAAAGTTGGCT 59.652 47.619 0.00 0.00 0.00 4.75
2047 2056 4.515191 TCTTTTCGGAGTCATCAAAGTTGG 59.485 41.667 0.00 0.00 0.00 3.77
2064 2073 0.811281 CCACCTTGCCCGATCTTTTC 59.189 55.000 0.00 0.00 0.00 2.29
2075 2084 2.200337 GGTTCCACACCCACCTTGC 61.200 63.158 0.00 0.00 40.19 4.01
2076 2085 1.896660 CGGTTCCACACCCACCTTG 60.897 63.158 0.00 0.00 43.83 3.61
2077 2086 2.333701 GACGGTTCCACACCCACCTT 62.334 60.000 0.00 0.00 43.83 3.50
2078 2087 2.770904 ACGGTTCCACACCCACCT 60.771 61.111 0.00 0.00 43.83 4.00
2130 2139 4.142881 GCCTTCACGGTTCAATCTCTTTAC 60.143 45.833 0.00 0.00 34.25 2.01
2137 2146 1.234821 TGTGCCTTCACGGTTCAATC 58.765 50.000 0.00 0.00 46.01 2.67
2141 2150 0.307760 CTGTTGTGCCTTCACGGTTC 59.692 55.000 0.00 0.00 46.01 3.62


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

AutoCloner maintained by Alex Coulton.