Multiple sequence alignment - TraesCS4A01G357000

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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 TraesCS4A01G357000 chr4A 100.000 2246 0 0 1 2246 630614319 630612074 0.000000e+00 4148
1 TraesCS4A01G357000 chr4A 97.240 1377 35 3 261 1634 587723613 587724989 0.000000e+00 2329
2 TraesCS4A01G357000 chr4A 97.421 349 8 1 1753 2101 587724979 587725326 5.340000e-166 593
3 TraesCS4A01G357000 chr4A 95.862 145 6 0 2102 2246 587726762 587726906 3.730000e-58 235
4 TraesCS4A01G357000 chr7A 97.195 1604 38 4 1 1597 106589965 106588362 0.000000e+00 2706
5 TraesCS4A01G357000 chr7A 95.328 1327 54 4 1 1321 647417606 647416282 0.000000e+00 2100
6 TraesCS4A01G357000 chr2A 95.820 1603 61 3 1 1597 88834928 88836530 0.000000e+00 2584
7 TraesCS4A01G357000 chr2A 95.633 1603 62 5 1 1597 708688400 708690000 0.000000e+00 2566
8 TraesCS4A01G357000 chr3A 95.446 1603 63 6 1 1597 743242947 743241349 0.000000e+00 2547
9 TraesCS4A01G357000 chr3A 95.435 1599 52 4 1 1597 41657049 41658628 0.000000e+00 2529
10 TraesCS4A01G357000 chr1A 94.558 1323 54 5 1 1321 287039089 287040395 0.000000e+00 2028
11 TraesCS4A01G357000 chr1A 98.812 505 6 0 1597 2101 537533554 537534058 0.000000e+00 900
12 TraesCS4A01G357000 chr1A 97.241 145 4 0 2102 2246 537536150 537536294 1.720000e-61 246
13 TraesCS4A01G357000 chr5A 94.273 1327 49 6 1 1321 388937754 388936449 0.000000e+00 2004
14 TraesCS4A01G357000 chr3B 93.586 764 38 3 1 754 782861906 782861144 0.000000e+00 1129
15 TraesCS4A01G357000 chr6B 99.283 279 2 0 1319 1597 673370236 673370514 2.570000e-139 505
16 TraesCS4A01G357000 chr4B 98.925 279 3 0 1319 1597 559905701 559905423 1.200000e-137 499
17 TraesCS4A01G357000 chr1B 85.714 133 14 2 2113 2244 645050717 645050845 3.890000e-28 135


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 TraesCS4A01G357000 chr4A 630612074 630614319 2245 True 4148.000000 4148 100.0000 1 2246 1 chr4A.!!$R1 2245
1 TraesCS4A01G357000 chr4A 587723613 587726906 3293 False 1052.333333 2329 96.8410 261 2246 3 chr4A.!!$F1 1985
2 TraesCS4A01G357000 chr7A 106588362 106589965 1603 True 2706.000000 2706 97.1950 1 1597 1 chr7A.!!$R1 1596
3 TraesCS4A01G357000 chr7A 647416282 647417606 1324 True 2100.000000 2100 95.3280 1 1321 1 chr7A.!!$R2 1320
4 TraesCS4A01G357000 chr2A 88834928 88836530 1602 False 2584.000000 2584 95.8200 1 1597 1 chr2A.!!$F1 1596
5 TraesCS4A01G357000 chr2A 708688400 708690000 1600 False 2566.000000 2566 95.6330 1 1597 1 chr2A.!!$F2 1596
6 TraesCS4A01G357000 chr3A 743241349 743242947 1598 True 2547.000000 2547 95.4460 1 1597 1 chr3A.!!$R1 1596
7 TraesCS4A01G357000 chr3A 41657049 41658628 1579 False 2529.000000 2529 95.4350 1 1597 1 chr3A.!!$F1 1596
8 TraesCS4A01G357000 chr1A 287039089 287040395 1306 False 2028.000000 2028 94.5580 1 1321 1 chr1A.!!$F1 1320
9 TraesCS4A01G357000 chr1A 537533554 537536294 2740 False 573.000000 900 98.0265 1597 2246 2 chr1A.!!$F2 649
10 TraesCS4A01G357000 chr5A 388936449 388937754 1305 True 2004.000000 2004 94.2730 1 1321 1 chr5A.!!$R1 1320
11 TraesCS4A01G357000 chr3B 782861144 782861906 762 True 1129.000000 1129 93.5860 1 754 1 chr3B.!!$R1 753

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
419 433 1.067295 ACTTCTTGGAGCCCATGACA 58.933 50.0 8.65 0.0 37.41 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1673 1693 0.03601 AAGTGAGTTGATCCAGCCCG 60.036 55.0 0.0 0.0 0.0 6.13 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
56 57 2.316237 GCCTTTTGTTTTTGGGCCG 58.684 52.632 0.00 0.00 37.12 6.13
139 144 4.878397 CCAATAGTCAGATGGGTTTGAGTC 59.122 45.833 0.00 0.00 0.00 3.36
312 326 8.684386 TCAAACATACTTCACATCAGGTTTAA 57.316 30.769 0.00 0.00 0.00 1.52
419 433 1.067295 ACTTCTTGGAGCCCATGACA 58.933 50.000 8.65 0.00 37.41 3.58
519 535 6.675486 GCACATTAACTTGTAGGCAGTATGTG 60.675 42.308 11.42 11.42 39.31 3.21
520 536 6.371548 CACATTAACTTGTAGGCAGTATGTGT 59.628 38.462 0.00 0.00 39.31 3.72
561 577 9.895138 AAATAAGCAAAATGAGGCATAGAAATT 57.105 25.926 0.00 0.00 0.00 1.82
978 997 4.827835 CGATCATTAACTAGAGACCTCCCA 59.172 45.833 0.00 0.00 0.00 4.37
1059 1078 1.686110 CTACCTCTCAGGGGCCGTT 60.686 63.158 0.00 0.00 40.58 4.44
1108 1127 2.915659 TCGAACAGCACCGACCCT 60.916 61.111 0.00 0.00 0.00 4.34
1110 1129 1.597027 CGAACAGCACCGACCCTTT 60.597 57.895 0.00 0.00 0.00 3.11
1316 1335 7.501559 AGCAAACAGTATTCAGAGCATCATTAT 59.498 33.333 0.00 0.00 37.82 1.28
1414 1433 2.564771 GGATCGAACCTTGATGATGCA 58.435 47.619 4.14 0.00 0.00 3.96
1480 1499 1.173444 GGGAAGCTCCGCTCGATCTA 61.173 60.000 0.00 0.00 38.25 1.98
1633 1653 4.898320 TGATACAGCCCATCACATGATAC 58.102 43.478 0.00 0.00 32.63 2.24
1634 1654 2.245159 ACAGCCCATCACATGATACG 57.755 50.000 0.00 0.00 32.63 3.06
1635 1655 0.870393 CAGCCCATCACATGATACGC 59.130 55.000 0.00 0.00 32.63 4.42
1636 1656 0.761187 AGCCCATCACATGATACGCT 59.239 50.000 0.00 8.39 34.90 5.07
1637 1657 0.870393 GCCCATCACATGATACGCTG 59.130 55.000 0.00 0.00 32.63 5.18
1638 1658 0.870393 CCCATCACATGATACGCTGC 59.130 55.000 0.00 0.00 32.63 5.25
1639 1659 1.541889 CCCATCACATGATACGCTGCT 60.542 52.381 0.00 0.00 32.63 4.24
1640 1660 2.289010 CCCATCACATGATACGCTGCTA 60.289 50.000 0.00 0.00 32.63 3.49
1641 1661 2.733552 CCATCACATGATACGCTGCTAC 59.266 50.000 0.00 0.00 32.63 3.58
1642 1662 3.553715 CCATCACATGATACGCTGCTACT 60.554 47.826 0.00 0.00 32.63 2.57
1643 1663 3.084070 TCACATGATACGCTGCTACTG 57.916 47.619 0.00 0.00 0.00 2.74
1644 1664 2.130395 CACATGATACGCTGCTACTGG 58.870 52.381 0.00 0.00 0.00 4.00
1645 1665 2.031870 ACATGATACGCTGCTACTGGA 58.968 47.619 0.00 0.00 0.00 3.86
1646 1666 2.223829 ACATGATACGCTGCTACTGGAC 60.224 50.000 0.00 0.00 0.00 4.02
1647 1667 0.744874 TGATACGCTGCTACTGGACC 59.255 55.000 0.00 0.00 0.00 4.46
1648 1668 0.744874 GATACGCTGCTACTGGACCA 59.255 55.000 0.00 0.00 0.00 4.02
1649 1669 0.460311 ATACGCTGCTACTGGACCAC 59.540 55.000 0.00 0.00 0.00 4.16
1650 1670 1.601419 TACGCTGCTACTGGACCACC 61.601 60.000 0.00 0.00 0.00 4.61
1651 1671 2.650116 CGCTGCTACTGGACCACCT 61.650 63.158 0.00 0.00 37.04 4.00
1652 1672 1.320344 CGCTGCTACTGGACCACCTA 61.320 60.000 0.00 0.00 37.04 3.08
1653 1673 0.461961 GCTGCTACTGGACCACCTAG 59.538 60.000 0.00 0.00 37.04 3.02
1654 1674 1.853963 CTGCTACTGGACCACCTAGT 58.146 55.000 0.00 0.00 37.04 2.57
1655 1675 1.478510 CTGCTACTGGACCACCTAGTG 59.521 57.143 0.00 0.00 37.04 2.74
1656 1676 1.203137 TGCTACTGGACCACCTAGTGT 60.203 52.381 0.00 0.00 37.04 3.55
1657 1677 1.204941 GCTACTGGACCACCTAGTGTG 59.795 57.143 0.00 4.81 45.01 3.82
1658 1678 2.526432 CTACTGGACCACCTAGTGTGT 58.474 52.381 9.57 0.00 43.85 3.72
1659 1679 1.802553 ACTGGACCACCTAGTGTGTT 58.197 50.000 9.57 0.00 43.85 3.32
1660 1680 2.124411 ACTGGACCACCTAGTGTGTTT 58.876 47.619 9.57 0.00 43.85 2.83
1661 1681 2.158813 ACTGGACCACCTAGTGTGTTTG 60.159 50.000 9.57 0.00 43.85 2.93
1662 1682 2.104111 CTGGACCACCTAGTGTGTTTGA 59.896 50.000 9.57 0.00 43.85 2.69
1663 1683 2.708861 TGGACCACCTAGTGTGTTTGAT 59.291 45.455 9.57 0.00 43.85 2.57
1664 1684 3.244422 TGGACCACCTAGTGTGTTTGATC 60.244 47.826 9.57 0.00 43.85 2.92
1665 1685 3.008049 GGACCACCTAGTGTGTTTGATCT 59.992 47.826 9.57 0.00 43.85 2.75
1666 1686 3.997021 GACCACCTAGTGTGTTTGATCTG 59.003 47.826 9.57 0.00 43.85 2.90
1667 1687 3.244561 ACCACCTAGTGTGTTTGATCTGG 60.245 47.826 9.57 0.00 43.85 3.86
1668 1688 3.338249 CACCTAGTGTGTTTGATCTGGG 58.662 50.000 0.00 0.00 40.26 4.45
1669 1689 2.979678 ACCTAGTGTGTTTGATCTGGGT 59.020 45.455 0.00 0.00 37.05 4.51
1670 1690 3.244561 ACCTAGTGTGTTTGATCTGGGTG 60.245 47.826 0.00 0.00 39.60 4.61
1671 1691 2.276732 AGTGTGTTTGATCTGGGTGG 57.723 50.000 0.00 0.00 0.00 4.61
1672 1692 1.774254 AGTGTGTTTGATCTGGGTGGA 59.226 47.619 0.00 0.00 0.00 4.02
1673 1693 1.880027 GTGTGTTTGATCTGGGTGGAC 59.120 52.381 0.00 0.00 0.00 4.02
1674 1694 1.156736 GTGTTTGATCTGGGTGGACG 58.843 55.000 0.00 0.00 0.00 4.79
1675 1695 0.036164 TGTTTGATCTGGGTGGACGG 59.964 55.000 0.00 0.00 0.00 4.79
1676 1696 0.676782 GTTTGATCTGGGTGGACGGG 60.677 60.000 0.00 0.00 0.00 5.28
1677 1697 2.478335 TTTGATCTGGGTGGACGGGC 62.478 60.000 0.00 0.00 0.00 6.13
1678 1698 3.083997 GATCTGGGTGGACGGGCT 61.084 66.667 0.00 0.00 0.00 5.19
1679 1699 3.391665 GATCTGGGTGGACGGGCTG 62.392 68.421 0.00 0.00 0.00 4.85
1683 1703 4.176752 GGGTGGACGGGCTGGATC 62.177 72.222 0.00 0.00 0.00 3.36
1684 1704 3.399181 GGTGGACGGGCTGGATCA 61.399 66.667 0.00 0.00 0.00 2.92
1685 1705 2.668632 GTGGACGGGCTGGATCAA 59.331 61.111 0.00 0.00 0.00 2.57
1686 1706 1.745489 GTGGACGGGCTGGATCAAC 60.745 63.158 0.00 0.00 0.00 3.18
1687 1707 1.918293 TGGACGGGCTGGATCAACT 60.918 57.895 0.00 0.00 0.00 3.16
1688 1708 1.153349 GGACGGGCTGGATCAACTC 60.153 63.158 0.00 0.00 0.00 3.01
1689 1709 1.596934 GACGGGCTGGATCAACTCA 59.403 57.895 0.00 0.00 0.00 3.41
1690 1710 0.741221 GACGGGCTGGATCAACTCAC 60.741 60.000 0.00 0.00 0.00 3.51
1691 1711 1.194781 ACGGGCTGGATCAACTCACT 61.195 55.000 0.00 0.00 0.00 3.41
1692 1712 0.036010 CGGGCTGGATCAACTCACTT 60.036 55.000 0.00 0.00 0.00 3.16
1693 1713 1.743996 GGGCTGGATCAACTCACTTC 58.256 55.000 0.00 0.00 0.00 3.01
1694 1714 1.680249 GGGCTGGATCAACTCACTTCC 60.680 57.143 0.00 0.00 0.00 3.46
1695 1715 1.003580 GGCTGGATCAACTCACTTCCA 59.996 52.381 0.00 0.00 36.81 3.53
1696 1716 2.079925 GCTGGATCAACTCACTTCCAC 58.920 52.381 0.00 0.00 34.62 4.02
1697 1717 2.550855 GCTGGATCAACTCACTTCCACA 60.551 50.000 0.00 0.00 34.62 4.17
1698 1718 3.871463 GCTGGATCAACTCACTTCCACAT 60.871 47.826 0.00 0.00 34.62 3.21
1699 1719 4.330250 CTGGATCAACTCACTTCCACATT 58.670 43.478 0.00 0.00 34.62 2.71
1700 1720 4.728772 TGGATCAACTCACTTCCACATTT 58.271 39.130 0.00 0.00 33.40 2.32
1701 1721 5.875224 TGGATCAACTCACTTCCACATTTA 58.125 37.500 0.00 0.00 33.40 1.40
1702 1722 5.705441 TGGATCAACTCACTTCCACATTTAC 59.295 40.000 0.00 0.00 33.40 2.01
1703 1723 5.705441 GGATCAACTCACTTCCACATTTACA 59.295 40.000 0.00 0.00 0.00 2.41
1704 1724 6.375455 GGATCAACTCACTTCCACATTTACAT 59.625 38.462 0.00 0.00 0.00 2.29
1705 1725 7.552687 GGATCAACTCACTTCCACATTTACATA 59.447 37.037 0.00 0.00 0.00 2.29
1706 1726 9.113838 GATCAACTCACTTCCACATTTACATAT 57.886 33.333 0.00 0.00 0.00 1.78
1707 1727 8.267620 TCAACTCACTTCCACATTTACATATG 57.732 34.615 0.00 0.00 0.00 1.78
1708 1728 6.683974 ACTCACTTCCACATTTACATATGC 57.316 37.500 1.58 0.00 0.00 3.14
1709 1729 5.590259 ACTCACTTCCACATTTACATATGCC 59.410 40.000 1.58 0.00 0.00 4.40
1710 1730 4.887071 TCACTTCCACATTTACATATGCCC 59.113 41.667 1.58 0.00 0.00 5.36
1711 1731 4.037923 CACTTCCACATTTACATATGCCCC 59.962 45.833 1.58 0.00 0.00 5.80
1712 1732 3.237268 TCCACATTTACATATGCCCCC 57.763 47.619 1.58 0.00 0.00 5.40
1713 1733 2.788807 TCCACATTTACATATGCCCCCT 59.211 45.455 1.58 0.00 0.00 4.79
1714 1734 3.206412 TCCACATTTACATATGCCCCCTT 59.794 43.478 1.58 0.00 0.00 3.95
1715 1735 3.321682 CCACATTTACATATGCCCCCTTG 59.678 47.826 1.58 0.00 0.00 3.61
1716 1736 3.960102 CACATTTACATATGCCCCCTTGT 59.040 43.478 1.58 0.00 0.00 3.16
1717 1737 5.136828 CACATTTACATATGCCCCCTTGTA 58.863 41.667 1.58 0.00 0.00 2.41
1718 1738 5.009610 CACATTTACATATGCCCCCTTGTAC 59.990 44.000 1.58 0.00 0.00 2.90
1719 1739 4.864483 TTTACATATGCCCCCTTGTACA 57.136 40.909 1.58 0.00 0.00 2.90
1720 1740 5.396057 TTTACATATGCCCCCTTGTACAT 57.604 39.130 1.58 0.00 0.00 2.29
1721 1741 3.971468 ACATATGCCCCCTTGTACATT 57.029 42.857 1.58 0.00 0.00 2.71
1722 1742 4.264373 ACATATGCCCCCTTGTACATTT 57.736 40.909 1.58 0.00 0.00 2.32
1723 1743 5.396057 ACATATGCCCCCTTGTACATTTA 57.604 39.130 1.58 0.00 0.00 1.40
1724 1744 5.137551 ACATATGCCCCCTTGTACATTTAC 58.862 41.667 1.58 0.00 0.00 2.01
1725 1745 2.116827 TGCCCCCTTGTACATTTACG 57.883 50.000 0.00 0.00 0.00 3.18
1726 1746 1.351683 TGCCCCCTTGTACATTTACGT 59.648 47.619 0.00 0.00 0.00 3.57
1727 1747 2.011947 GCCCCCTTGTACATTTACGTC 58.988 52.381 0.00 0.00 0.00 4.34
1728 1748 2.355412 GCCCCCTTGTACATTTACGTCT 60.355 50.000 0.00 0.00 0.00 4.18
1729 1749 3.871074 GCCCCCTTGTACATTTACGTCTT 60.871 47.826 0.00 0.00 0.00 3.01
1730 1750 3.687698 CCCCCTTGTACATTTACGTCTTG 59.312 47.826 0.00 0.00 0.00 3.02
1731 1751 3.687698 CCCCTTGTACATTTACGTCTTGG 59.312 47.826 0.00 0.00 0.00 3.61
1732 1752 3.126343 CCCTTGTACATTTACGTCTTGGC 59.874 47.826 0.00 0.00 0.00 4.52
1733 1753 3.126343 CCTTGTACATTTACGTCTTGGCC 59.874 47.826 0.00 0.00 0.00 5.36
1734 1754 2.702261 TGTACATTTACGTCTTGGCCC 58.298 47.619 0.00 0.00 0.00 5.80
1735 1755 2.011947 GTACATTTACGTCTTGGCCCC 58.988 52.381 0.00 0.00 0.00 5.80
1736 1756 0.696501 ACATTTACGTCTTGGCCCCT 59.303 50.000 0.00 0.00 0.00 4.79
1737 1757 1.910671 ACATTTACGTCTTGGCCCCTA 59.089 47.619 0.00 0.00 0.00 3.53
1738 1758 2.306512 ACATTTACGTCTTGGCCCCTAA 59.693 45.455 0.00 0.00 0.00 2.69
1739 1759 3.244981 ACATTTACGTCTTGGCCCCTAAA 60.245 43.478 0.00 0.00 0.00 1.85
1740 1760 3.505480 TTTACGTCTTGGCCCCTAAAA 57.495 42.857 0.00 0.00 0.00 1.52
1741 1761 3.505480 TTACGTCTTGGCCCCTAAAAA 57.495 42.857 0.00 0.00 0.00 1.94
2101 2251 4.582869 ACTGAAAGCATGAGCACTATGAA 58.417 39.130 0.00 0.00 45.49 2.57
2102 2252 5.191426 ACTGAAAGCATGAGCACTATGAAT 58.809 37.500 0.00 0.00 45.49 2.57
2158 4399 5.895636 TTTGTTCTACCATGCATCGAATT 57.104 34.783 0.00 0.00 0.00 2.17
2169 4410 0.748005 CATCGAATTGAAGGGGCGGT 60.748 55.000 0.00 0.00 0.00 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 2.427095 ACTGTTGAGTCAAAAAGGCCAC 59.573 45.455 7.25 0.00 0.00 5.01
139 144 0.108138 GACTCTGACCATTGGGACCG 60.108 60.000 7.78 0.00 38.05 4.79
254 268 6.205853 TGTGGTGTATGTTTGATTGTAAGGTC 59.794 38.462 0.00 0.00 0.00 3.85
289 303 8.082242 GCTTTAAACCTGATGTGAAGTATGTTT 58.918 33.333 0.00 0.00 0.00 2.83
312 326 2.143876 AGTTGTGTTCTTGGTGGCTT 57.856 45.000 0.00 0.00 0.00 4.35
419 433 5.470098 AGATGCTGTACTTCATTCGTGTTTT 59.530 36.000 0.00 0.00 0.00 2.43
538 554 9.189156 ACTAATTTCTATGCCTCATTTTGCTTA 57.811 29.630 0.00 0.00 0.00 3.09
561 577 9.064706 GCTGATAGTAACTACTTGTATCCACTA 57.935 37.037 0.00 0.00 37.73 2.74
703 719 6.853720 TGTTGTTCAAACGGTTAAATTCTGA 58.146 32.000 0.00 0.00 0.00 3.27
978 997 0.329596 CTGTTAGGGCTTTGGCTCCT 59.670 55.000 0.00 0.00 40.45 3.69
1038 1057 1.001760 GGCCCCTGAGAGGTAGTCA 59.998 63.158 0.00 0.00 31.93 3.41
1059 1078 1.995066 AGGGTCATCACCGCCATCA 60.995 57.895 0.00 0.00 44.91 3.07
1108 1127 2.247358 GACATTTTCTCCAGGGCCAAA 58.753 47.619 6.18 0.00 0.00 3.28
1110 1129 0.322456 CGACATTTTCTCCAGGGCCA 60.322 55.000 6.18 0.00 0.00 5.36
1316 1335 1.946984 ACCCGTGATTAACCTCTGGA 58.053 50.000 0.00 0.00 0.00 3.86
1414 1433 2.522185 AGGACAAGCAGCAACATCATT 58.478 42.857 0.00 0.00 0.00 2.57
1632 1652 2.657237 GTGGTCCAGTAGCAGCGT 59.343 61.111 0.00 0.00 35.94 5.07
1633 1653 2.125512 GGTGGTCCAGTAGCAGCG 60.126 66.667 0.00 0.00 43.43 5.18
1635 1655 1.478510 CACTAGGTGGTCCAGTAGCAG 59.521 57.143 7.78 0.00 35.94 4.24
1636 1656 1.203137 ACACTAGGTGGTCCAGTAGCA 60.203 52.381 7.78 0.00 37.94 3.49
1637 1657 1.204941 CACACTAGGTGGTCCAGTAGC 59.795 57.143 7.78 0.00 44.04 3.58
1648 1668 2.979678 ACCCAGATCAAACACACTAGGT 59.020 45.455 0.00 0.00 0.00 3.08
1649 1669 3.338249 CACCCAGATCAAACACACTAGG 58.662 50.000 0.00 0.00 0.00 3.02
1650 1670 3.007940 TCCACCCAGATCAAACACACTAG 59.992 47.826 0.00 0.00 0.00 2.57
1651 1671 2.976185 TCCACCCAGATCAAACACACTA 59.024 45.455 0.00 0.00 0.00 2.74
1652 1672 1.774254 TCCACCCAGATCAAACACACT 59.226 47.619 0.00 0.00 0.00 3.55
1653 1673 1.880027 GTCCACCCAGATCAAACACAC 59.120 52.381 0.00 0.00 0.00 3.82
1654 1674 1.542328 CGTCCACCCAGATCAAACACA 60.542 52.381 0.00 0.00 0.00 3.72
1655 1675 1.156736 CGTCCACCCAGATCAAACAC 58.843 55.000 0.00 0.00 0.00 3.32
1656 1676 0.036164 CCGTCCACCCAGATCAAACA 59.964 55.000 0.00 0.00 0.00 2.83
1657 1677 0.676782 CCCGTCCACCCAGATCAAAC 60.677 60.000 0.00 0.00 0.00 2.93
1658 1678 1.682849 CCCGTCCACCCAGATCAAA 59.317 57.895 0.00 0.00 0.00 2.69
1659 1679 2.966732 GCCCGTCCACCCAGATCAA 61.967 63.158 0.00 0.00 0.00 2.57
1660 1680 3.399181 GCCCGTCCACCCAGATCA 61.399 66.667 0.00 0.00 0.00 2.92
1661 1681 3.083997 AGCCCGTCCACCCAGATC 61.084 66.667 0.00 0.00 0.00 2.75
1662 1682 3.402681 CAGCCCGTCCACCCAGAT 61.403 66.667 0.00 0.00 0.00 2.90
1666 1686 4.176752 GATCCAGCCCGTCCACCC 62.177 72.222 0.00 0.00 0.00 4.61
1667 1687 2.966732 TTGATCCAGCCCGTCCACC 61.967 63.158 0.00 0.00 0.00 4.61
1668 1688 1.745489 GTTGATCCAGCCCGTCCAC 60.745 63.158 0.00 0.00 0.00 4.02
1669 1689 1.899437 GAGTTGATCCAGCCCGTCCA 61.899 60.000 0.00 0.00 0.00 4.02
1670 1690 1.153349 GAGTTGATCCAGCCCGTCC 60.153 63.158 0.00 0.00 0.00 4.79
1671 1691 0.741221 GTGAGTTGATCCAGCCCGTC 60.741 60.000 0.00 0.00 0.00 4.79
1672 1692 1.194781 AGTGAGTTGATCCAGCCCGT 61.195 55.000 0.00 0.00 0.00 5.28
1673 1693 0.036010 AAGTGAGTTGATCCAGCCCG 60.036 55.000 0.00 0.00 0.00 6.13
1674 1694 1.680249 GGAAGTGAGTTGATCCAGCCC 60.680 57.143 0.00 0.00 32.08 5.19
1675 1695 1.003580 TGGAAGTGAGTTGATCCAGCC 59.996 52.381 0.00 0.00 37.05 4.85
1676 1696 2.079925 GTGGAAGTGAGTTGATCCAGC 58.920 52.381 0.00 0.00 42.35 4.85
1677 1697 3.407424 TGTGGAAGTGAGTTGATCCAG 57.593 47.619 0.00 0.00 42.35 3.86
1678 1698 4.371624 AATGTGGAAGTGAGTTGATCCA 57.628 40.909 0.00 0.00 39.57 3.41
1679 1699 5.705441 TGTAAATGTGGAAGTGAGTTGATCC 59.295 40.000 0.00 0.00 0.00 3.36
1680 1700 6.801539 TGTAAATGTGGAAGTGAGTTGATC 57.198 37.500 0.00 0.00 0.00 2.92
1681 1701 8.896744 CATATGTAAATGTGGAAGTGAGTTGAT 58.103 33.333 0.00 0.00 0.00 2.57
1682 1702 7.148255 GCATATGTAAATGTGGAAGTGAGTTGA 60.148 37.037 4.29 0.00 0.00 3.18
1683 1703 6.968904 GCATATGTAAATGTGGAAGTGAGTTG 59.031 38.462 4.29 0.00 0.00 3.16
1684 1704 6.095440 GGCATATGTAAATGTGGAAGTGAGTT 59.905 38.462 4.29 0.00 0.00 3.01
1685 1705 5.590259 GGCATATGTAAATGTGGAAGTGAGT 59.410 40.000 4.29 0.00 0.00 3.41
1686 1706 5.009010 GGGCATATGTAAATGTGGAAGTGAG 59.991 44.000 4.29 0.00 0.00 3.51
1687 1707 4.887071 GGGCATATGTAAATGTGGAAGTGA 59.113 41.667 4.29 0.00 0.00 3.41
1688 1708 4.037923 GGGGCATATGTAAATGTGGAAGTG 59.962 45.833 4.29 0.00 0.00 3.16
1689 1709 4.215109 GGGGCATATGTAAATGTGGAAGT 58.785 43.478 4.29 0.00 0.00 3.01
1690 1710 3.573967 GGGGGCATATGTAAATGTGGAAG 59.426 47.826 4.29 0.00 0.00 3.46
1691 1711 3.206412 AGGGGGCATATGTAAATGTGGAA 59.794 43.478 4.29 0.00 0.00 3.53
1692 1712 2.788807 AGGGGGCATATGTAAATGTGGA 59.211 45.455 4.29 0.00 0.00 4.02
1693 1713 3.243359 AGGGGGCATATGTAAATGTGG 57.757 47.619 4.29 0.00 0.00 4.17
1694 1714 3.960102 ACAAGGGGGCATATGTAAATGTG 59.040 43.478 4.29 0.00 0.00 3.21
1695 1715 4.264373 ACAAGGGGGCATATGTAAATGT 57.736 40.909 4.29 0.54 0.00 2.71
1696 1716 5.136828 TGTACAAGGGGGCATATGTAAATG 58.863 41.667 4.29 0.00 30.71 2.32
1697 1717 5.396057 TGTACAAGGGGGCATATGTAAAT 57.604 39.130 4.29 0.00 30.71 1.40
1698 1718 4.864483 TGTACAAGGGGGCATATGTAAA 57.136 40.909 4.29 0.00 30.71 2.01
1699 1719 5.396057 AATGTACAAGGGGGCATATGTAA 57.604 39.130 0.00 0.00 30.71 2.41
1700 1720 5.396057 AAATGTACAAGGGGGCATATGTA 57.604 39.130 0.00 0.00 0.00 2.29
1701 1721 3.971468 AATGTACAAGGGGGCATATGT 57.029 42.857 0.00 0.00 0.00 2.29
1702 1722 4.215399 CGTAAATGTACAAGGGGGCATATG 59.785 45.833 0.00 0.00 0.00 1.78
1703 1723 4.141344 ACGTAAATGTACAAGGGGGCATAT 60.141 41.667 0.00 0.00 0.00 1.78
1704 1724 3.200385 ACGTAAATGTACAAGGGGGCATA 59.800 43.478 0.00 0.00 0.00 3.14
1705 1725 2.025699 ACGTAAATGTACAAGGGGGCAT 60.026 45.455 0.00 0.00 0.00 4.40
1706 1726 1.351683 ACGTAAATGTACAAGGGGGCA 59.648 47.619 0.00 0.00 0.00 5.36
1707 1727 2.011947 GACGTAAATGTACAAGGGGGC 58.988 52.381 0.00 0.00 0.00 5.80
1708 1728 3.622166 AGACGTAAATGTACAAGGGGG 57.378 47.619 0.00 0.00 0.00 5.40
1709 1729 3.687698 CCAAGACGTAAATGTACAAGGGG 59.312 47.826 0.00 0.00 0.00 4.79
1710 1730 3.126343 GCCAAGACGTAAATGTACAAGGG 59.874 47.826 0.00 0.00 0.00 3.95
1711 1731 3.126343 GGCCAAGACGTAAATGTACAAGG 59.874 47.826 0.00 0.00 0.00 3.61
1712 1732 3.126343 GGGCCAAGACGTAAATGTACAAG 59.874 47.826 4.39 0.00 0.00 3.16
1713 1733 3.075884 GGGCCAAGACGTAAATGTACAA 58.924 45.455 4.39 0.00 0.00 2.41
1714 1734 2.616001 GGGGCCAAGACGTAAATGTACA 60.616 50.000 4.39 0.00 0.00 2.90
1715 1735 2.011947 GGGGCCAAGACGTAAATGTAC 58.988 52.381 4.39 0.00 0.00 2.90
1716 1736 1.910671 AGGGGCCAAGACGTAAATGTA 59.089 47.619 4.39 0.00 0.00 2.29
1717 1737 0.696501 AGGGGCCAAGACGTAAATGT 59.303 50.000 4.39 0.00 0.00 2.71
1718 1738 2.702592 TAGGGGCCAAGACGTAAATG 57.297 50.000 4.39 0.00 0.00 2.32
1719 1739 3.724732 TTTAGGGGCCAAGACGTAAAT 57.275 42.857 4.39 0.00 0.00 1.40
1720 1740 3.505480 TTTTAGGGGCCAAGACGTAAA 57.495 42.857 4.39 2.74 0.00 2.01
1721 1741 3.505480 TTTTTAGGGGCCAAGACGTAA 57.495 42.857 4.39 0.00 0.00 3.18
1744 1764 9.817809 GTCTATAGTGATTTTGTGAGGACATAA 57.182 33.333 0.00 0.00 30.13 1.90
1745 1765 8.421784 GGTCTATAGTGATTTTGTGAGGACATA 58.578 37.037 0.00 0.00 30.13 2.29
1746 1766 7.126421 AGGTCTATAGTGATTTTGTGAGGACAT 59.874 37.037 0.00 0.00 30.13 3.06
1747 1767 6.440647 AGGTCTATAGTGATTTTGTGAGGACA 59.559 38.462 0.00 0.00 0.00 4.02
1748 1768 6.879400 AGGTCTATAGTGATTTTGTGAGGAC 58.121 40.000 0.00 0.00 0.00 3.85
1749 1769 7.180229 TGAAGGTCTATAGTGATTTTGTGAGGA 59.820 37.037 0.00 0.00 0.00 3.71
1750 1770 7.278868 GTGAAGGTCTATAGTGATTTTGTGAGG 59.721 40.741 0.00 0.00 0.00 3.86
1751 1771 7.278868 GGTGAAGGTCTATAGTGATTTTGTGAG 59.721 40.741 0.00 0.00 0.00 3.51
1752 1772 7.038302 AGGTGAAGGTCTATAGTGATTTTGTGA 60.038 37.037 0.00 0.00 0.00 3.58
1753 1773 7.106239 AGGTGAAGGTCTATAGTGATTTTGTG 58.894 38.462 0.00 0.00 0.00 3.33
1754 1774 7.181125 AGAGGTGAAGGTCTATAGTGATTTTGT 59.819 37.037 0.00 0.00 0.00 2.83
1755 1775 7.560368 AGAGGTGAAGGTCTATAGTGATTTTG 58.440 38.462 0.00 0.00 0.00 2.44
1756 1776 7.621683 AGAGAGGTGAAGGTCTATAGTGATTTT 59.378 37.037 0.00 0.00 0.00 1.82
1757 1777 7.129425 AGAGAGGTGAAGGTCTATAGTGATTT 58.871 38.462 0.00 0.00 0.00 2.17
1758 1778 6.678547 AGAGAGGTGAAGGTCTATAGTGATT 58.321 40.000 0.00 0.00 0.00 2.57
1759 1779 6.274322 AGAGAGGTGAAGGTCTATAGTGAT 57.726 41.667 0.00 0.00 0.00 3.06
1760 1780 5.398126 GGAGAGAGGTGAAGGTCTATAGTGA 60.398 48.000 0.00 0.00 0.00 3.41
1761 1781 4.825085 GGAGAGAGGTGAAGGTCTATAGTG 59.175 50.000 0.00 0.00 0.00 2.74
1973 2123 4.019950 TGTCTGCATTCCATCTCTCTTTCA 60.020 41.667 0.00 0.00 0.00 2.69
2158 4399 2.925706 TGTGCTACCGCCCCTTCA 60.926 61.111 0.00 0.00 34.43 3.02
2169 4410 3.133542 CAGATCCATCCTCTTGTGTGCTA 59.866 47.826 0.00 0.00 0.00 3.49


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

AutoCloner maintained by Alex Coulton.