Multiple sequence alignment - TraesCS7D01G172800

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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 TraesCS7D01G172800 chr7D 100.000 2282 0 0 1 2282 124651647 124649366 0.000000e+00 4215.0
1 TraesCS7D01G172800 chr7D 98.794 995 10 1 1 993 587557289 587556295 0.000000e+00 1770.0
2 TraesCS7D01G172800 chr7D 87.794 467 28 7 994 1431 124830494 124830028 9.340000e-144 520.0
3 TraesCS7D01G172800 chr7D 94.545 330 18 0 994 1323 124833060 124832731 5.620000e-141 510.0
4 TraesCS7D01G172800 chr7D 94.737 304 16 0 994 1297 124644152 124643849 7.380000e-130 473.0
5 TraesCS7D01G172800 chr7D 94.118 289 17 0 994 1282 124594696 124594408 7.480000e-120 440.0
6 TraesCS7D01G172800 chr7D 86.464 362 31 9 1234 1590 124596453 124596105 4.600000e-102 381.0
7 TraesCS7D01G172800 chr7D 90.706 269 23 2 1335 1601 124832666 124832398 7.750000e-95 357.0
8 TraesCS7D01G172800 chr7D 96.000 50 2 0 1341 1390 124643855 124643806 5.220000e-12 82.4
9 TraesCS7D01G172800 chr5D 98.896 996 9 1 1 994 6929401 6930396 0.000000e+00 1777.0
10 TraesCS7D01G172800 chr6D 98.606 1004 12 1 1 1002 54803535 54804538 0.000000e+00 1775.0
11 TraesCS7D01G172800 chr6D 98.794 995 9 2 1 993 61748174 61749167 0.000000e+00 1768.0
12 TraesCS7D01G172800 chr6D 98.593 995 11 2 1 993 1938993 1938000 0.000000e+00 1757.0
13 TraesCS7D01G172800 chr6D 97.421 349 9 0 1934 2282 130425820 130425472 1.510000e-166 595.0
14 TraesCS7D01G172800 chr6D 97.421 349 9 0 1934 2282 276226021 276226369 1.510000e-166 595.0
15 TraesCS7D01G172800 chr6D 97.414 348 9 0 1935 2282 162241598 162241251 5.430000e-166 593.0
16 TraesCS7D01G172800 chr4D 98.894 995 9 1 1 993 508953954 508952960 0.000000e+00 1775.0
17 TraesCS7D01G172800 chr4D 98.593 995 12 1 1 993 488840780 488839786 0.000000e+00 1759.0
18 TraesCS7D01G172800 chr4D 97.989 348 7 0 1935 2282 469926135 469926482 2.510000e-169 604.0
19 TraesCS7D01G172800 chr4D 97.414 348 9 0 1935 2282 416848173 416848520 5.430000e-166 593.0
20 TraesCS7D01G172800 chr3D 98.794 995 10 1 1 993 380519197 380518203 0.000000e+00 1770.0
21 TraesCS7D01G172800 chr3D 97.701 348 8 0 1935 2282 428478438 428478091 1.170000e-167 599.0
22 TraesCS7D01G172800 chr3D 97.688 346 8 0 1937 2282 408231487 408231832 1.510000e-166 595.0
23 TraesCS7D01G172800 chr1D 98.597 998 12 1 1 996 447634310 447633313 0.000000e+00 1764.0
24 TraesCS7D01G172800 chr1D 97.701 348 8 0 1935 2282 128368675 128368328 1.170000e-167 599.0
25 TraesCS7D01G172800 chr7B 90.895 626 41 10 994 1603 86648170 86647545 0.000000e+00 826.0
26 TraesCS7D01G172800 chr7B 87.599 629 59 8 994 1603 86637283 86636655 0.000000e+00 712.0
27 TraesCS7D01G172800 chr7A 87.500 624 52 10 994 1593 127003622 127003001 0.000000e+00 697.0
28 TraesCS7D01G172800 chr7A 87.563 595 44 7 994 1586 127041986 127041420 0.000000e+00 662.0
29 TraesCS7D01G172800 chr7A 94.810 289 15 0 994 1282 127001551 127001263 3.460000e-123 451.0
30 TraesCS7D01G172800 chr7A 88.832 197 9 8 1217 1400 127038717 127038521 1.760000e-56 230.0
31 TraesCS7D01G172800 chr2D 97.701 348 8 0 1935 2282 348527844 348527497 1.170000e-167 599.0


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 TraesCS7D01G172800 chr7D 124649366 124651647 2281 True 4215.000000 4215 100.0000 1 2282 1 chr7D.!!$R1 2281
1 TraesCS7D01G172800 chr7D 587556295 587557289 994 True 1770.000000 1770 98.7940 1 993 1 chr7D.!!$R2 992
2 TraesCS7D01G172800 chr7D 124830028 124833060 3032 True 462.333333 520 91.0150 994 1601 3 chr7D.!!$R5 607
3 TraesCS7D01G172800 chr7D 124594408 124596453 2045 True 410.500000 440 90.2910 994 1590 2 chr7D.!!$R3 596
4 TraesCS7D01G172800 chr5D 6929401 6930396 995 False 1777.000000 1777 98.8960 1 994 1 chr5D.!!$F1 993
5 TraesCS7D01G172800 chr6D 54803535 54804538 1003 False 1775.000000 1775 98.6060 1 1002 1 chr6D.!!$F1 1001
6 TraesCS7D01G172800 chr6D 61748174 61749167 993 False 1768.000000 1768 98.7940 1 993 1 chr6D.!!$F2 992
7 TraesCS7D01G172800 chr6D 1938000 1938993 993 True 1757.000000 1757 98.5930 1 993 1 chr6D.!!$R1 992
8 TraesCS7D01G172800 chr4D 508952960 508953954 994 True 1775.000000 1775 98.8940 1 993 1 chr4D.!!$R2 992
9 TraesCS7D01G172800 chr4D 488839786 488840780 994 True 1759.000000 1759 98.5930 1 993 1 chr4D.!!$R1 992
10 TraesCS7D01G172800 chr3D 380518203 380519197 994 True 1770.000000 1770 98.7940 1 993 1 chr3D.!!$R1 992
11 TraesCS7D01G172800 chr1D 447633313 447634310 997 True 1764.000000 1764 98.5970 1 996 1 chr1D.!!$R2 995
12 TraesCS7D01G172800 chr7B 86647545 86648170 625 True 826.000000 826 90.8950 994 1603 1 chr7B.!!$R2 609
13 TraesCS7D01G172800 chr7B 86636655 86637283 628 True 712.000000 712 87.5990 994 1603 1 chr7B.!!$R1 609
14 TraesCS7D01G172800 chr7A 127001263 127003622 2359 True 574.000000 697 91.1550 994 1593 2 chr7A.!!$R1 599
15 TraesCS7D01G172800 chr7A 127038521 127041986 3465 True 446.000000 662 88.1975 994 1586 2 chr7A.!!$R2 592

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
921 924 0.388907 CTCCCGAACCGCGACTAAAA 60.389 55.0 8.23 0.0 44.57 1.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2106 3836 0.035317 TGTTGCTTCCGCTCACTCAT 59.965 50.0 0.0 0.0 36.97 2.9 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
119 120 5.780282 AGTTGTCATCGATATCATCCCCTTA 59.220 40.000 0.00 0.00 0.00 2.69
277 278 7.498900 CAGCACATGGACAGATAATAAAACCTA 59.501 37.037 0.00 0.00 0.00 3.08
517 518 1.803334 TCAAGTTGCTAACCGCGATT 58.197 45.000 8.23 0.00 43.27 3.34
659 660 2.158608 CCACCACCCCCTTCTGAATATC 60.159 54.545 0.00 0.00 0.00 1.63
733 734 0.392595 CTTTAGTCCCGGTTGGCCTC 60.393 60.000 3.32 0.00 0.00 4.70
921 924 0.388907 CTCCCGAACCGCGACTAAAA 60.389 55.000 8.23 0.00 44.57 1.52
1038 1041 3.636231 CAGGGGGAAGTGACGGCA 61.636 66.667 0.00 0.00 0.00 5.69
1071 1074 2.687200 TGGCTGGGGCAGTACGAT 60.687 61.111 0.00 0.00 40.87 3.73
1146 1149 1.885388 CAACCTGTGGTTCGCGTCA 60.885 57.895 5.77 0.14 43.05 4.35
1162 1165 2.749839 CATGGAAGGCGCGGGAAA 60.750 61.111 8.83 0.00 0.00 3.13
1323 1343 4.335400 TCTGCTGTTGTAACTGTGATGA 57.665 40.909 4.04 0.00 0.00 2.92
1325 1345 6.036577 TCTGCTGTTGTAACTGTGATGATA 57.963 37.500 4.04 0.00 0.00 2.15
1415 1502 4.631131 ACCTTTGCAGTTATTTTCCAAGC 58.369 39.130 0.00 0.00 0.00 4.01
1447 1536 7.042797 ACTTTGTATTTTCAGCACTGTGAAT 57.957 32.000 12.86 4.53 36.34 2.57
1474 1563 4.154918 GTGGAGATTTGCAGAGTTGTTAGG 59.845 45.833 0.00 0.00 0.00 2.69
1489 1580 5.011329 AGTTGTTAGGTGATGGACGTTTCTA 59.989 40.000 0.00 0.00 0.00 2.10
1544 1638 5.432645 TCCAGTTGAGTGTTGACAAATACA 58.567 37.500 6.61 0.00 30.25 2.29
1604 1720 8.687824 CATCCTTTGCACGAATTTTTATTACT 57.312 30.769 0.00 0.00 0.00 2.24
1605 1721 8.798153 CATCCTTTGCACGAATTTTTATTACTC 58.202 33.333 0.00 0.00 0.00 2.59
1606 1722 7.309920 TCCTTTGCACGAATTTTTATTACTCC 58.690 34.615 0.00 0.00 0.00 3.85
1607 1723 7.175990 TCCTTTGCACGAATTTTTATTACTCCT 59.824 33.333 0.00 0.00 0.00 3.69
1608 1724 7.812669 CCTTTGCACGAATTTTTATTACTCCTT 59.187 33.333 0.00 0.00 0.00 3.36
1609 1725 8.736751 TTTGCACGAATTTTTATTACTCCTTC 57.263 30.769 0.00 0.00 0.00 3.46
1610 1726 6.848451 TGCACGAATTTTTATTACTCCTTCC 58.152 36.000 0.00 0.00 0.00 3.46
1611 1727 5.963586 GCACGAATTTTTATTACTCCTTCCG 59.036 40.000 0.00 0.00 0.00 4.30
1612 1728 6.183360 GCACGAATTTTTATTACTCCTTCCGA 60.183 38.462 0.00 0.00 0.00 4.55
1613 1729 7.466860 GCACGAATTTTTATTACTCCTTCCGAT 60.467 37.037 0.00 0.00 0.00 4.18
1614 1730 8.062448 CACGAATTTTTATTACTCCTTCCGATC 58.938 37.037 0.00 0.00 0.00 3.69
1615 1731 7.226128 ACGAATTTTTATTACTCCTTCCGATCC 59.774 37.037 0.00 0.00 0.00 3.36
1616 1732 7.225931 CGAATTTTTATTACTCCTTCCGATCCA 59.774 37.037 0.00 0.00 0.00 3.41
1617 1733 8.817092 AATTTTTATTACTCCTTCCGATCCAA 57.183 30.769 0.00 0.00 0.00 3.53
1618 1734 8.817092 ATTTTTATTACTCCTTCCGATCCAAA 57.183 30.769 0.00 0.00 0.00 3.28
1619 1735 8.638629 TTTTTATTACTCCTTCCGATCCAAAA 57.361 30.769 0.00 0.00 0.00 2.44
1620 1736 8.817092 TTTTATTACTCCTTCCGATCCAAAAT 57.183 30.769 0.00 0.00 0.00 1.82
1621 1737 9.908747 TTTTATTACTCCTTCCGATCCAAAATA 57.091 29.630 0.00 0.00 0.00 1.40
1622 1738 9.908747 TTTATTACTCCTTCCGATCCAAAATAA 57.091 29.630 0.00 0.00 0.00 1.40
1624 1740 8.996651 ATTACTCCTTCCGATCCAAAATAATT 57.003 30.769 0.00 0.00 0.00 1.40
1625 1741 6.699575 ACTCCTTCCGATCCAAAATAATTG 57.300 37.500 0.00 0.00 0.00 2.32
1626 1742 6.423182 ACTCCTTCCGATCCAAAATAATTGA 58.577 36.000 0.00 0.00 0.00 2.57
1627 1743 6.543831 ACTCCTTCCGATCCAAAATAATTGAG 59.456 38.462 0.00 0.00 0.00 3.02
1628 1744 5.299279 TCCTTCCGATCCAAAATAATTGAGC 59.701 40.000 0.00 0.00 0.00 4.26
1629 1745 5.067674 CCTTCCGATCCAAAATAATTGAGCA 59.932 40.000 0.00 0.00 0.00 4.26
1630 1746 6.405731 CCTTCCGATCCAAAATAATTGAGCAA 60.406 38.462 0.00 0.00 0.00 3.91
1631 1747 5.890334 TCCGATCCAAAATAATTGAGCAAC 58.110 37.500 0.00 0.00 0.00 4.17
1632 1748 5.043248 CCGATCCAAAATAATTGAGCAACC 58.957 41.667 0.00 0.00 0.00 3.77
1633 1749 5.394005 CCGATCCAAAATAATTGAGCAACCA 60.394 40.000 0.00 0.00 0.00 3.67
1634 1750 5.516339 CGATCCAAAATAATTGAGCAACCAC 59.484 40.000 0.00 0.00 0.00 4.16
1635 1751 6.610075 ATCCAAAATAATTGAGCAACCACT 57.390 33.333 0.00 0.00 0.00 4.00
1636 1752 7.415095 CGATCCAAAATAATTGAGCAACCACTA 60.415 37.037 0.00 0.00 0.00 2.74
1637 1753 7.716799 TCCAAAATAATTGAGCAACCACTAT 57.283 32.000 0.00 0.00 0.00 2.12
1638 1754 8.815565 TCCAAAATAATTGAGCAACCACTATA 57.184 30.769 0.00 0.00 0.00 1.31
1639 1755 8.682710 TCCAAAATAATTGAGCAACCACTATAC 58.317 33.333 0.00 0.00 0.00 1.47
1640 1756 8.465999 CCAAAATAATTGAGCAACCACTATACA 58.534 33.333 0.00 0.00 0.00 2.29
1641 1757 9.853555 CAAAATAATTGAGCAACCACTATACAA 57.146 29.630 0.00 0.00 0.00 2.41
1642 1758 9.855021 AAAATAATTGAGCAACCACTATACAAC 57.145 29.630 0.00 0.00 0.00 3.32
1643 1759 8.574251 AATAATTGAGCAACCACTATACAACA 57.426 30.769 0.00 0.00 0.00 3.33
1644 1760 8.752005 ATAATTGAGCAACCACTATACAACAT 57.248 30.769 0.00 0.00 0.00 2.71
1645 1761 7.466746 AATTGAGCAACCACTATACAACATT 57.533 32.000 0.00 0.00 0.00 2.71
1646 1762 5.878332 TGAGCAACCACTATACAACATTG 57.122 39.130 0.00 0.00 0.00 2.82
1647 1763 5.312895 TGAGCAACCACTATACAACATTGT 58.687 37.500 2.32 2.32 44.86 2.71
1648 1764 6.468543 TGAGCAACCACTATACAACATTGTA 58.531 36.000 6.92 6.92 46.55 2.41
1659 1775 4.657814 ACAACATTGTATTGGAGGGACT 57.342 40.909 0.00 0.00 40.57 3.85
1660 1776 4.335416 ACAACATTGTATTGGAGGGACTG 58.665 43.478 0.00 0.00 38.34 3.51
1661 1777 5.348627 ACAACATTGTATTGGAGGGACTGC 61.349 45.833 0.00 0.00 43.55 4.40
1670 1786 2.396590 GGAGGGACTGCGTCAATTAA 57.603 50.000 10.14 0.00 41.55 1.40
1671 1787 2.919228 GGAGGGACTGCGTCAATTAAT 58.081 47.619 10.14 0.00 41.55 1.40
1672 1788 3.279434 GGAGGGACTGCGTCAATTAATT 58.721 45.455 10.14 0.00 41.55 1.40
1673 1789 3.694566 GGAGGGACTGCGTCAATTAATTT 59.305 43.478 0.00 0.00 41.55 1.82
1674 1790 4.879545 GGAGGGACTGCGTCAATTAATTTA 59.120 41.667 0.00 0.00 41.55 1.40
1675 1791 5.007724 GGAGGGACTGCGTCAATTAATTTAG 59.992 44.000 0.00 0.00 41.55 1.85
1676 1792 5.741011 AGGGACTGCGTCAATTAATTTAGA 58.259 37.500 0.00 0.00 37.18 2.10
1677 1793 6.357367 AGGGACTGCGTCAATTAATTTAGAT 58.643 36.000 0.00 0.00 37.18 1.98
1678 1794 6.260936 AGGGACTGCGTCAATTAATTTAGATG 59.739 38.462 0.00 1.05 37.18 2.90
1679 1795 6.430451 GGACTGCGTCAATTAATTTAGATGG 58.570 40.000 0.00 0.00 33.68 3.51
1680 1796 6.377327 ACTGCGTCAATTAATTTAGATGGG 57.623 37.500 0.00 0.00 0.00 4.00
1681 1797 6.119536 ACTGCGTCAATTAATTTAGATGGGA 58.880 36.000 0.00 0.00 0.00 4.37
1682 1798 6.260936 ACTGCGTCAATTAATTTAGATGGGAG 59.739 38.462 0.00 4.35 0.00 4.30
1683 1799 5.530915 TGCGTCAATTAATTTAGATGGGAGG 59.469 40.000 0.00 0.00 0.00 4.30
1684 1800 5.048713 GCGTCAATTAATTTAGATGGGAGGG 60.049 44.000 0.00 0.00 0.00 4.30
1685 1801 6.296026 CGTCAATTAATTTAGATGGGAGGGA 58.704 40.000 0.00 0.00 0.00 4.20
1686 1802 6.428159 CGTCAATTAATTTAGATGGGAGGGAG 59.572 42.308 0.00 0.00 0.00 4.30
1687 1803 7.290813 GTCAATTAATTTAGATGGGAGGGAGT 58.709 38.462 0.00 0.00 0.00 3.85
1688 1804 7.780271 GTCAATTAATTTAGATGGGAGGGAGTT 59.220 37.037 0.00 0.00 0.00 3.01
1765 1891 6.267070 TGAATTTTAGAAACCACGACAAACC 58.733 36.000 0.00 0.00 0.00 3.27
1766 1892 5.838531 ATTTTAGAAACCACGACAAACCA 57.161 34.783 0.00 0.00 0.00 3.67
1826 1955 2.074547 TTCTTCCAGTTAACCGAGCG 57.925 50.000 0.88 0.00 0.00 5.03
1838 1967 1.068753 CCGAGCGCTCTTCATCCAT 59.931 57.895 32.88 0.00 0.00 3.41
1839 1968 0.943359 CCGAGCGCTCTTCATCCATC 60.943 60.000 32.88 5.86 0.00 3.51
1840 1969 0.943359 CGAGCGCTCTTCATCCATCC 60.943 60.000 32.88 5.03 0.00 3.51
1841 1970 0.105593 GAGCGCTCTTCATCCATCCA 59.894 55.000 29.88 0.00 0.00 3.41
1842 1971 0.543277 AGCGCTCTTCATCCATCCAA 59.457 50.000 2.64 0.00 0.00 3.53
1843 1972 1.142465 AGCGCTCTTCATCCATCCAAT 59.858 47.619 2.64 0.00 0.00 3.16
1844 1973 1.266175 GCGCTCTTCATCCATCCAATG 59.734 52.381 0.00 0.00 0.00 2.82
1845 1974 2.569059 CGCTCTTCATCCATCCAATGT 58.431 47.619 0.00 0.00 0.00 2.71
1847 1976 3.379372 CGCTCTTCATCCATCCAATGTTT 59.621 43.478 0.00 0.00 0.00 2.83
1849 1978 5.066375 CGCTCTTCATCCATCCAATGTTTTA 59.934 40.000 0.00 0.00 0.00 1.52
1850 1979 6.501781 GCTCTTCATCCATCCAATGTTTTAG 58.498 40.000 0.00 0.00 0.00 1.85
1851 1980 6.096001 GCTCTTCATCCATCCAATGTTTTAGT 59.904 38.462 0.00 0.00 0.00 2.24
1856 1985 8.821686 TCATCCATCCAATGTTTTAGTGTATT 57.178 30.769 0.00 0.00 0.00 1.89
1859 1988 8.746052 TCCATCCAATGTTTTAGTGTATTAGG 57.254 34.615 0.00 0.00 0.00 2.69
1864 1993 7.990886 TCCAATGTTTTAGTGTATTAGGGCTAG 59.009 37.037 0.00 0.00 0.00 3.42
1874 2003 3.975168 ATTAGGGCTAGTGACAACGTT 57.025 42.857 0.00 0.00 0.00 3.99
1886 2472 2.610374 TGACAACGTTTCTAACCTGTGC 59.390 45.455 0.00 0.00 0.00 4.57
1887 2473 1.595794 ACAACGTTTCTAACCTGTGCG 59.404 47.619 0.00 0.00 0.00 5.34
1905 2491 5.136828 TGTGCGGGACCATTGATAATATTT 58.863 37.500 0.00 0.00 0.00 1.40
1926 2512 3.443052 TGACGGGGTAAAATGACTCCTA 58.557 45.455 0.00 0.00 37.89 2.94
1935 2521 6.483640 GGGTAAAATGACTCCTACTAATGCTG 59.516 42.308 0.00 0.00 0.00 4.41
1938 2524 5.939764 AATGACTCCTACTAATGCTGTGA 57.060 39.130 0.00 0.00 0.00 3.58
1940 2526 3.128764 TGACTCCTACTAATGCTGTGACG 59.871 47.826 0.00 0.00 0.00 4.35
1942 2528 1.136305 TCCTACTAATGCTGTGACGCC 59.864 52.381 0.00 0.00 0.00 5.68
1943 2529 1.571919 CTACTAATGCTGTGACGCCC 58.428 55.000 0.00 0.00 0.00 6.13
1944 2530 0.177141 TACTAATGCTGTGACGCCCC 59.823 55.000 0.00 0.00 0.00 5.80
1949 2535 4.778143 GCTGTGACGCCCCCGATT 62.778 66.667 0.00 0.00 38.29 3.34
1950 2536 2.046314 CTGTGACGCCCCCGATTT 60.046 61.111 0.00 0.00 38.29 2.17
1951 2537 2.359354 TGTGACGCCCCCGATTTG 60.359 61.111 0.00 0.00 38.29 2.32
1953 2539 2.046700 TGACGCCCCCGATTTGAC 60.047 61.111 0.00 0.00 38.29 3.18
1954 2540 2.822701 GACGCCCCCGATTTGACC 60.823 66.667 0.00 0.00 38.29 4.02
1956 2542 4.770874 CGCCCCCGATTTGACCGT 62.771 66.667 0.00 0.00 36.29 4.83
1957 2543 2.585698 GCCCCCGATTTGACCGTA 59.414 61.111 0.00 0.00 0.00 4.02
1958 2544 1.816679 GCCCCCGATTTGACCGTAC 60.817 63.158 0.00 0.00 0.00 3.67
1959 2545 1.597989 CCCCCGATTTGACCGTACA 59.402 57.895 0.00 0.00 0.00 2.90
1960 2546 0.741927 CCCCCGATTTGACCGTACAC 60.742 60.000 0.00 0.00 0.00 2.90
1961 2547 0.248289 CCCCGATTTGACCGTACACT 59.752 55.000 0.00 0.00 0.00 3.55
1962 2548 1.477700 CCCCGATTTGACCGTACACTA 59.522 52.381 0.00 0.00 0.00 2.74
1963 2549 2.094078 CCCCGATTTGACCGTACACTAA 60.094 50.000 0.00 0.00 0.00 2.24
1964 2550 3.431207 CCCCGATTTGACCGTACACTAAT 60.431 47.826 0.00 0.00 0.00 1.73
1965 2551 3.800506 CCCGATTTGACCGTACACTAATC 59.199 47.826 0.00 2.04 0.00 1.75
1966 2552 4.426416 CCGATTTGACCGTACACTAATCA 58.574 43.478 13.93 0.90 32.03 2.57
1967 2553 5.047847 CCGATTTGACCGTACACTAATCAT 58.952 41.667 13.93 0.00 32.03 2.45
1969 2555 6.143438 CCGATTTGACCGTACACTAATCATAC 59.857 42.308 13.93 0.00 32.03 2.39
1970 2556 6.693978 CGATTTGACCGTACACTAATCATACA 59.306 38.462 13.93 0.00 32.03 2.29
1971 2557 7.305820 CGATTTGACCGTACACTAATCATACAC 60.306 40.741 13.93 0.00 32.03 2.90
1972 2558 4.912214 TGACCGTACACTAATCATACACG 58.088 43.478 0.00 0.00 0.00 4.49
1973 2559 3.699067 ACCGTACACTAATCATACACGC 58.301 45.455 0.00 0.00 0.00 5.34
1975 2561 4.106909 CCGTACACTAATCATACACGCAA 58.893 43.478 0.00 0.00 0.00 4.85
1976 2562 4.027132 CCGTACACTAATCATACACGCAAC 60.027 45.833 0.00 0.00 0.00 4.17
1977 2563 4.316171 CGTACACTAATCATACACGCAACG 60.316 45.833 0.00 0.00 0.00 4.10
1987 2573 4.948576 ACGCAACGTGTACGATCA 57.051 50.000 11.79 0.00 43.02 2.92
1990 2576 1.333115 CGCAACGTGTACGATCAAGA 58.667 50.000 11.79 0.00 43.02 3.02
1992 2578 2.035674 CGCAACGTGTACGATCAAGATC 60.036 50.000 11.79 0.00 43.02 2.75
1993 2579 2.921121 GCAACGTGTACGATCAAGATCA 59.079 45.455 11.79 0.00 43.02 2.92
1995 2581 3.422417 ACGTGTACGATCAAGATCAGG 57.578 47.619 11.79 0.51 43.02 3.86
1996 2582 2.099263 ACGTGTACGATCAAGATCAGGG 59.901 50.000 11.79 0.00 43.02 4.45
1997 2583 2.357952 CGTGTACGATCAAGATCAGGGA 59.642 50.000 10.39 0.00 43.02 4.20
1998 2584 3.707793 GTGTACGATCAAGATCAGGGAC 58.292 50.000 10.39 2.84 37.69 4.46
1999 2585 3.381908 GTGTACGATCAAGATCAGGGACT 59.618 47.826 10.39 0.00 43.88 3.85
2000 2586 3.632604 TGTACGATCAAGATCAGGGACTC 59.367 47.826 10.39 0.00 34.60 3.36
2001 2587 2.739943 ACGATCAAGATCAGGGACTCA 58.260 47.619 10.39 0.00 34.60 3.41
2002 2588 2.428890 ACGATCAAGATCAGGGACTCAC 59.571 50.000 10.39 0.00 34.60 3.51
2004 2590 1.186200 TCAAGATCAGGGACTCACGG 58.814 55.000 0.00 0.00 34.60 4.94
2005 2591 0.176680 CAAGATCAGGGACTCACGGG 59.823 60.000 0.00 0.00 34.60 5.28
2008 2594 0.461961 GATCAGGGACTCACGGGAAG 59.538 60.000 0.00 0.00 34.60 3.46
2009 2595 0.041238 ATCAGGGACTCACGGGAAGA 59.959 55.000 0.00 0.00 34.60 2.87
2018 2889 4.113354 GACTCACGGGAAGATATCACAAC 58.887 47.826 5.32 0.00 0.00 3.32
2024 2895 4.253685 CGGGAAGATATCACAACACAACT 58.746 43.478 5.32 0.00 0.00 3.16
2026 2897 5.491982 GGGAAGATATCACAACACAACTCT 58.508 41.667 5.32 0.00 0.00 3.24
2027 2898 6.627287 CGGGAAGATATCACAACACAACTCTA 60.627 42.308 5.32 0.00 0.00 2.43
2069 3799 4.581824 ACAAGCATCATAATACAAGCCAGG 59.418 41.667 0.00 0.00 0.00 4.45
2098 3828 0.924090 GGCTCGAATACAAGTGCTCG 59.076 55.000 0.00 0.00 0.00 5.03
2100 3830 2.464865 GCTCGAATACAAGTGCTCGAT 58.535 47.619 8.31 0.00 39.39 3.59
2101 3831 2.469516 GCTCGAATACAAGTGCTCGATC 59.530 50.000 8.31 2.80 39.39 3.69
2102 3832 3.695816 CTCGAATACAAGTGCTCGATCA 58.304 45.455 8.31 0.00 39.39 2.92
2103 3833 4.294232 CTCGAATACAAGTGCTCGATCAT 58.706 43.478 8.31 0.00 39.39 2.45
2104 3834 5.432885 TCGAATACAAGTGCTCGATCATA 57.567 39.130 0.00 0.00 35.52 2.15
2106 3836 5.238650 TCGAATACAAGTGCTCGATCATAGA 59.761 40.000 0.00 0.00 35.52 1.98
2107 3837 6.072452 TCGAATACAAGTGCTCGATCATAGAT 60.072 38.462 0.00 0.00 35.52 1.98
2109 3839 4.926140 ACAAGTGCTCGATCATAGATGA 57.074 40.909 0.00 0.00 41.70 2.92
2112 3842 4.502171 AGTGCTCGATCATAGATGAGTG 57.498 45.455 0.00 0.00 40.64 3.51
2113 3843 4.140536 AGTGCTCGATCATAGATGAGTGA 58.859 43.478 0.00 0.00 40.64 3.41
2114 3844 4.216042 AGTGCTCGATCATAGATGAGTGAG 59.784 45.833 14.79 14.79 41.31 3.51
2117 3847 2.861286 CGATCATAGATGAGTGAGCGG 58.139 52.381 5.25 0.00 46.79 5.52
2118 3848 2.485814 CGATCATAGATGAGTGAGCGGA 59.514 50.000 5.25 0.00 46.79 5.54
2120 3850 3.998099 TCATAGATGAGTGAGCGGAAG 57.002 47.619 0.00 0.00 32.11 3.46
2124 3854 7.904257 TCATAGATGAGTGAGCGGAAGCAAC 62.904 48.000 0.00 0.00 45.66 4.17
2137 3867 5.643339 CGGAAGCAACAATATCTGAGTAC 57.357 43.478 0.00 0.00 0.00 2.73
2139 3869 5.233050 CGGAAGCAACAATATCTGAGTACAG 59.767 44.000 0.00 0.00 44.66 2.74
2157 3887 9.826574 TGAGTACAGACATAAGTTAAACAAGTT 57.173 29.630 0.00 0.00 0.00 2.66
2159 3889 8.557029 AGTACAGACATAAGTTAAACAAGTTGC 58.443 33.333 1.81 0.00 0.00 4.17
2160 3890 6.735130 ACAGACATAAGTTAAACAAGTTGCC 58.265 36.000 1.81 0.00 0.00 4.52
2161 3891 6.320164 ACAGACATAAGTTAAACAAGTTGCCA 59.680 34.615 1.81 0.00 0.00 4.92
2162 3892 7.014230 ACAGACATAAGTTAAACAAGTTGCCAT 59.986 33.333 1.81 0.00 0.00 4.40
2163 3893 8.511321 CAGACATAAGTTAAACAAGTTGCCATA 58.489 33.333 1.81 0.00 0.00 2.74
2165 3895 9.341899 GACATAAGTTAAACAAGTTGCCATAAG 57.658 33.333 1.81 0.00 0.00 1.73
2180 3910 4.558538 CCATAAGATGGCTAGCACAAAC 57.441 45.455 18.24 10.42 44.70 2.93
2181 3911 4.202441 CCATAAGATGGCTAGCACAAACT 58.798 43.478 18.24 12.26 44.70 2.66
2182 3912 4.036027 CCATAAGATGGCTAGCACAAACTG 59.964 45.833 18.24 5.30 44.70 3.16
2183 3913 2.119801 AGATGGCTAGCACAAACTGG 57.880 50.000 18.24 0.00 0.00 4.00
2185 3915 0.698238 ATGGCTAGCACAAACTGGGA 59.302 50.000 18.24 0.00 0.00 4.37
2186 3916 0.698238 TGGCTAGCACAAACTGGGAT 59.302 50.000 18.24 0.00 0.00 3.85
2188 3918 2.289565 GGCTAGCACAAACTGGGATAC 58.710 52.381 18.24 0.00 0.00 2.24
2189 3919 2.355716 GGCTAGCACAAACTGGGATACA 60.356 50.000 18.24 0.00 39.74 2.29
2202 3932 2.365617 TGGGATACAGATCGAAAGAGGC 59.634 50.000 0.00 0.00 41.83 4.70
2204 3934 3.800604 GGGATACAGATCGAAAGAGGCAC 60.801 52.174 0.00 0.00 41.83 5.01
2206 3936 7.963256 GGGATACAGATCGAAAGAGGCACAG 62.963 52.000 0.00 0.00 41.83 3.66
2224 3954 4.432741 GCCTCCTGCCTGGGTTCC 62.433 72.222 0.00 0.00 36.20 3.62
2225 3955 2.612115 CCTCCTGCCTGGGTTCCT 60.612 66.667 0.00 0.00 36.20 3.36
2226 3956 2.674220 CCTCCTGCCTGGGTTCCTC 61.674 68.421 0.00 0.00 36.20 3.71
2227 3957 2.610859 TCCTGCCTGGGTTCCTCC 60.611 66.667 0.00 0.00 36.20 4.30
2230 3960 0.914417 CCTGCCTGGGTTCCTCCTAA 60.914 60.000 0.00 0.00 36.25 2.69
2232 3962 0.178873 TGCCTGGGTTCCTCCTAACT 60.179 55.000 0.00 0.00 36.25 2.24
2234 3964 1.485480 GCCTGGGTTCCTCCTAACTAC 59.515 57.143 0.00 0.00 36.25 2.73
2235 3965 2.893153 GCCTGGGTTCCTCCTAACTACT 60.893 54.545 0.00 0.00 36.25 2.57
2237 3967 3.032459 CTGGGTTCCTCCTAACTACTCC 58.968 54.545 0.00 0.00 36.25 3.85
2238 3968 2.658489 TGGGTTCCTCCTAACTACTCCT 59.342 50.000 0.00 0.00 36.25 3.69
2239 3969 3.032459 GGGTTCCTCCTAACTACTCCTG 58.968 54.545 0.00 0.00 36.25 3.86
2240 3970 3.032459 GGTTCCTCCTAACTACTCCTGG 58.968 54.545 0.00 0.00 0.00 4.45
2241 3971 3.566111 GGTTCCTCCTAACTACTCCTGGT 60.566 52.174 0.00 0.00 0.00 4.00
2242 3972 3.666345 TCCTCCTAACTACTCCTGGTC 57.334 52.381 0.00 0.00 0.00 4.02
2243 3973 2.092538 TCCTCCTAACTACTCCTGGTCG 60.093 54.545 0.00 0.00 0.00 4.79
2244 3974 2.356947 CCTCCTAACTACTCCTGGTCGT 60.357 54.545 0.00 0.00 0.00 4.34
2245 3975 2.944349 CTCCTAACTACTCCTGGTCGTC 59.056 54.545 0.00 0.00 0.00 4.20
2248 3978 1.163554 AACTACTCCTGGTCGTCGTC 58.836 55.000 0.00 0.00 0.00 4.20
2249 3979 0.035881 ACTACTCCTGGTCGTCGTCA 59.964 55.000 0.00 0.00 0.00 4.35
2250 3980 0.727970 CTACTCCTGGTCGTCGTCAG 59.272 60.000 10.03 10.03 0.00 3.51
2253 3983 4.778415 CCTGGTCGTCGTCAGCGG 62.778 72.222 11.08 0.20 38.89 5.52
2275 4005 0.101939 GGCACGTAGTAGTAGGCACC 59.898 60.000 0.00 0.00 41.61 5.01
2276 4006 1.101331 GCACGTAGTAGTAGGCACCT 58.899 55.000 0.00 0.00 41.61 4.00
2277 4007 1.065251 GCACGTAGTAGTAGGCACCTC 59.935 57.143 0.00 0.00 41.61 3.85
2278 4008 1.674962 CACGTAGTAGTAGGCACCTCC 59.325 57.143 0.00 0.00 41.61 4.30
2280 4010 1.316651 GTAGTAGTAGGCACCTCCGG 58.683 60.000 0.00 0.00 40.77 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
119 120 6.161170 AGGGGTTAGAATGGAAGAAGATGAAT 59.839 38.462 0.00 0.00 0.00 2.57
517 518 6.582677 TTTCTCATTTATTTTTCCTCCGCA 57.417 33.333 0.00 0.00 0.00 5.69
659 660 2.057316 CTTCACTCAGCTCACTTCACG 58.943 52.381 0.00 0.00 0.00 4.35
1029 1032 0.540830 AGAACTCCTCTGCCGTCACT 60.541 55.000 0.00 0.00 31.12 3.41
1038 1041 2.286523 CCACGCCCAGAACTCCTCT 61.287 63.158 0.00 0.00 33.23 3.69
1067 1070 3.626680 CTGTCGTGGTCCGCATCGT 62.627 63.158 2.76 0.00 36.19 3.73
1146 1149 2.438434 CTTTCCCGCGCCTTCCAT 60.438 61.111 0.00 0.00 0.00 3.41
1252 1255 1.220206 CGAGCTGGGTGATCTTGCT 59.780 57.895 0.00 0.00 36.63 3.91
1350 1427 6.053632 ACACAAACATCCATCTCATACTCA 57.946 37.500 0.00 0.00 0.00 3.41
1404 1491 6.263617 ACAAAGTAGGAAACGCTTGGAAAATA 59.736 34.615 0.00 0.00 32.86 1.40
1405 1492 5.068591 ACAAAGTAGGAAACGCTTGGAAAAT 59.931 36.000 0.00 0.00 32.86 1.82
1409 1496 3.202829 ACAAAGTAGGAAACGCTTGGA 57.797 42.857 0.00 0.00 32.86 3.53
1415 1502 6.577427 GTGCTGAAAATACAAAGTAGGAAACG 59.423 38.462 0.00 0.00 0.00 3.60
1447 1536 3.777106 ACTCTGCAAATCTCCACAGAA 57.223 42.857 0.00 0.00 38.61 3.02
1474 1563 3.326747 AGCTTGTAGAAACGTCCATCAC 58.673 45.455 0.00 0.00 0.00 3.06
1489 1580 6.336842 AGCAAATTAATCAACAGAGCTTGT 57.663 33.333 0.00 0.00 43.45 3.16
1521 1612 5.432645 TGTATTTGTCAACACTCAACTGGA 58.567 37.500 0.00 0.00 0.00 3.86
1544 1638 6.959639 ATTTTATACAGGAAATGCACCGAT 57.040 33.333 0.00 0.00 0.00 4.18
1590 1706 7.225931 TGGATCGGAAGGAGTAATAAAAATTCG 59.774 37.037 0.00 0.00 0.00 3.34
1603 1719 6.514048 GCTCAATTATTTTGGATCGGAAGGAG 60.514 42.308 0.00 0.00 0.00 3.69
1604 1720 5.299279 GCTCAATTATTTTGGATCGGAAGGA 59.701 40.000 0.00 0.00 0.00 3.36
1605 1721 5.067674 TGCTCAATTATTTTGGATCGGAAGG 59.932 40.000 0.00 0.00 0.00 3.46
1606 1722 6.135290 TGCTCAATTATTTTGGATCGGAAG 57.865 37.500 0.00 0.00 0.00 3.46
1607 1723 6.329496 GTTGCTCAATTATTTTGGATCGGAA 58.671 36.000 0.00 0.00 0.00 4.30
1608 1724 5.163561 GGTTGCTCAATTATTTTGGATCGGA 60.164 40.000 0.00 0.00 0.00 4.55
1609 1725 5.043248 GGTTGCTCAATTATTTTGGATCGG 58.957 41.667 0.00 0.00 0.00 4.18
1610 1726 5.516339 GTGGTTGCTCAATTATTTTGGATCG 59.484 40.000 0.00 0.00 0.00 3.69
1611 1727 6.633856 AGTGGTTGCTCAATTATTTTGGATC 58.366 36.000 0.00 0.00 0.00 3.36
1612 1728 6.610075 AGTGGTTGCTCAATTATTTTGGAT 57.390 33.333 0.00 0.00 0.00 3.41
1613 1729 7.716799 ATAGTGGTTGCTCAATTATTTTGGA 57.283 32.000 0.00 0.00 0.00 3.53
1614 1730 8.465999 TGTATAGTGGTTGCTCAATTATTTTGG 58.534 33.333 0.00 0.00 0.00 3.28
1615 1731 9.853555 TTGTATAGTGGTTGCTCAATTATTTTG 57.146 29.630 0.00 0.00 0.00 2.44
1616 1732 9.855021 GTTGTATAGTGGTTGCTCAATTATTTT 57.145 29.630 0.00 0.00 0.00 1.82
1617 1733 9.019656 TGTTGTATAGTGGTTGCTCAATTATTT 57.980 29.630 0.00 0.00 0.00 1.40
1618 1734 8.574251 TGTTGTATAGTGGTTGCTCAATTATT 57.426 30.769 0.00 0.00 0.00 1.40
1619 1735 8.752005 ATGTTGTATAGTGGTTGCTCAATTAT 57.248 30.769 0.00 0.00 0.00 1.28
1620 1736 8.458052 CAATGTTGTATAGTGGTTGCTCAATTA 58.542 33.333 0.00 0.00 0.00 1.40
1621 1737 7.039784 ACAATGTTGTATAGTGGTTGCTCAATT 60.040 33.333 0.00 0.00 40.16 2.32
1622 1738 6.434028 ACAATGTTGTATAGTGGTTGCTCAAT 59.566 34.615 0.00 0.00 40.16 2.57
1623 1739 5.767665 ACAATGTTGTATAGTGGTTGCTCAA 59.232 36.000 0.00 0.00 40.16 3.02
1624 1740 5.312895 ACAATGTTGTATAGTGGTTGCTCA 58.687 37.500 0.00 0.00 40.16 4.26
1625 1741 5.880054 ACAATGTTGTATAGTGGTTGCTC 57.120 39.130 0.00 0.00 40.16 4.26
1637 1753 5.496556 CAGTCCCTCCAATACAATGTTGTA 58.503 41.667 7.94 7.94 46.55 2.41
1638 1754 4.335416 CAGTCCCTCCAATACAATGTTGT 58.665 43.478 3.64 3.64 44.86 3.32
1639 1755 3.129287 GCAGTCCCTCCAATACAATGTTG 59.871 47.826 0.00 0.00 0.00 3.33
1640 1756 3.356290 GCAGTCCCTCCAATACAATGTT 58.644 45.455 0.00 0.00 0.00 2.71
1641 1757 2.680805 CGCAGTCCCTCCAATACAATGT 60.681 50.000 0.00 0.00 0.00 2.71
1642 1758 1.942657 CGCAGTCCCTCCAATACAATG 59.057 52.381 0.00 0.00 0.00 2.82
1643 1759 1.559682 ACGCAGTCCCTCCAATACAAT 59.440 47.619 0.00 0.00 29.74 2.71
1644 1760 0.981183 ACGCAGTCCCTCCAATACAA 59.019 50.000 0.00 0.00 29.74 2.41
1645 1761 2.678786 ACGCAGTCCCTCCAATACA 58.321 52.632 0.00 0.00 29.74 2.29
1658 1774 6.293626 CCTCCCATCTAAATTAATTGACGCAG 60.294 42.308 0.39 0.00 0.00 5.18
1659 1775 5.530915 CCTCCCATCTAAATTAATTGACGCA 59.469 40.000 0.39 0.00 0.00 5.24
1660 1776 5.048713 CCCTCCCATCTAAATTAATTGACGC 60.049 44.000 0.39 0.00 0.00 5.19
1661 1777 6.296026 TCCCTCCCATCTAAATTAATTGACG 58.704 40.000 0.39 0.00 0.00 4.35
1662 1778 7.290813 ACTCCCTCCCATCTAAATTAATTGAC 58.709 38.462 0.39 0.00 0.00 3.18
1663 1779 7.465900 ACTCCCTCCCATCTAAATTAATTGA 57.534 36.000 0.39 0.00 0.00 2.57
1664 1780 8.539117 AAACTCCCTCCCATCTAAATTAATTG 57.461 34.615 0.39 0.00 0.00 2.32
1665 1781 9.560860 AAAAACTCCCTCCCATCTAAATTAATT 57.439 29.630 0.00 0.00 0.00 1.40
1669 1785 9.560860 AAATAAAAACTCCCTCCCATCTAAATT 57.439 29.630 0.00 0.00 0.00 1.82
1670 1786 9.201989 GAAATAAAAACTCCCTCCCATCTAAAT 57.798 33.333 0.00 0.00 0.00 1.40
1671 1787 8.398743 AGAAATAAAAACTCCCTCCCATCTAAA 58.601 33.333 0.00 0.00 0.00 1.85
1672 1788 7.939781 AGAAATAAAAACTCCCTCCCATCTAA 58.060 34.615 0.00 0.00 0.00 2.10
1673 1789 7.525158 AGAAATAAAAACTCCCTCCCATCTA 57.475 36.000 0.00 0.00 0.00 1.98
1674 1790 6.408770 AGAAATAAAAACTCCCTCCCATCT 57.591 37.500 0.00 0.00 0.00 2.90
1675 1791 8.768501 ATTAGAAATAAAAACTCCCTCCCATC 57.231 34.615 0.00 0.00 0.00 3.51
1737 1856 7.972832 TGTCGTGGTTTCTAAAATTCAGTAT 57.027 32.000 0.00 0.00 0.00 2.12
1738 1857 7.789273 TTGTCGTGGTTTCTAAAATTCAGTA 57.211 32.000 0.00 0.00 0.00 2.74
1745 1871 5.415077 TCTTGGTTTGTCGTGGTTTCTAAAA 59.585 36.000 0.00 0.00 0.00 1.52
1748 1874 4.139859 TCTTGGTTTGTCGTGGTTTCTA 57.860 40.909 0.00 0.00 0.00 2.10
1804 1933 3.120649 CGCTCGGTTAACTGGAAGAAAAG 60.121 47.826 14.44 3.91 37.43 2.27
1805 1934 2.803956 CGCTCGGTTAACTGGAAGAAAA 59.196 45.455 14.44 0.00 37.43 2.29
1806 1935 2.409975 CGCTCGGTTAACTGGAAGAAA 58.590 47.619 14.44 0.00 37.43 2.52
1807 1936 1.938016 GCGCTCGGTTAACTGGAAGAA 60.938 52.381 14.44 0.00 37.43 2.52
1808 1937 0.389426 GCGCTCGGTTAACTGGAAGA 60.389 55.000 14.44 2.17 37.43 2.87
1809 1938 0.389948 AGCGCTCGGTTAACTGGAAG 60.390 55.000 14.44 6.68 42.29 3.46
1810 1939 0.389426 GAGCGCTCGGTTAACTGGAA 60.389 55.000 23.61 0.00 0.00 3.53
1811 1940 1.214589 GAGCGCTCGGTTAACTGGA 59.785 57.895 23.61 7.10 0.00 3.86
1812 1941 0.389948 AAGAGCGCTCGGTTAACTGG 60.390 55.000 30.39 6.57 34.09 4.00
1826 1955 4.996788 AAACATTGGATGGATGAAGAGC 57.003 40.909 0.00 0.00 33.60 4.09
1838 1967 6.727394 AGCCCTAATACACTAAAACATTGGA 58.273 36.000 0.00 0.00 0.00 3.53
1839 1968 7.773690 ACTAGCCCTAATACACTAAAACATTGG 59.226 37.037 0.00 0.00 0.00 3.16
1840 1969 8.612619 CACTAGCCCTAATACACTAAAACATTG 58.387 37.037 0.00 0.00 0.00 2.82
1841 1970 8.545472 TCACTAGCCCTAATACACTAAAACATT 58.455 33.333 0.00 0.00 0.00 2.71
1842 1971 7.985752 GTCACTAGCCCTAATACACTAAAACAT 59.014 37.037 0.00 0.00 0.00 2.71
1843 1972 7.038870 TGTCACTAGCCCTAATACACTAAAACA 60.039 37.037 0.00 0.00 0.00 2.83
1844 1973 7.325694 TGTCACTAGCCCTAATACACTAAAAC 58.674 38.462 0.00 0.00 0.00 2.43
1845 1974 7.484993 TGTCACTAGCCCTAATACACTAAAA 57.515 36.000 0.00 0.00 0.00 1.52
1847 1976 6.405065 CGTTGTCACTAGCCCTAATACACTAA 60.405 42.308 0.00 0.00 0.00 2.24
1849 1978 4.142227 CGTTGTCACTAGCCCTAATACACT 60.142 45.833 0.00 0.00 0.00 3.55
1850 1979 4.110482 CGTTGTCACTAGCCCTAATACAC 58.890 47.826 0.00 0.00 0.00 2.90
1851 1980 3.765511 ACGTTGTCACTAGCCCTAATACA 59.234 43.478 0.00 0.00 0.00 2.29
1856 1985 2.895404 AGAAACGTTGTCACTAGCCCTA 59.105 45.455 0.00 0.00 0.00 3.53
1859 1988 3.431233 GGTTAGAAACGTTGTCACTAGCC 59.569 47.826 0.00 11.03 0.00 3.93
1864 1993 3.545426 GCACAGGTTAGAAACGTTGTCAC 60.545 47.826 0.00 0.00 30.60 3.67
1874 2003 1.122632 TGGTCCCGCACAGGTTAGAA 61.123 55.000 0.00 0.00 38.74 2.10
1886 2472 5.106712 CCGTCAAATATTATCAATGGTCCCG 60.107 44.000 0.00 0.00 0.00 5.14
1887 2473 5.183140 CCCGTCAAATATTATCAATGGTCCC 59.817 44.000 0.00 0.00 0.00 4.46
1905 2491 2.262637 AGGAGTCATTTTACCCCGTCA 58.737 47.619 0.00 0.00 0.00 4.35
1926 2512 1.078426 GGGGCGTCACAGCATTAGT 60.078 57.895 0.00 0.00 39.27 2.24
1935 2521 2.046700 TCAAATCGGGGGCGTCAC 60.047 61.111 0.00 0.00 0.00 3.67
1938 2524 4.770874 CGGTCAAATCGGGGGCGT 62.771 66.667 0.00 0.00 0.00 5.68
1940 2526 1.816679 GTACGGTCAAATCGGGGGC 60.817 63.158 0.00 0.00 0.00 5.80
1942 2528 0.248289 AGTGTACGGTCAAATCGGGG 59.752 55.000 0.00 0.00 0.00 5.73
1943 2529 2.945447 TAGTGTACGGTCAAATCGGG 57.055 50.000 0.00 0.00 0.00 5.14
1944 2530 4.426416 TGATTAGTGTACGGTCAAATCGG 58.574 43.478 0.00 0.00 0.00 4.18
1947 2533 6.474427 CGTGTATGATTAGTGTACGGTCAAAT 59.526 38.462 0.00 0.00 0.00 2.32
1949 2535 5.334319 CGTGTATGATTAGTGTACGGTCAA 58.666 41.667 0.00 0.00 0.00 3.18
1950 2536 4.731483 GCGTGTATGATTAGTGTACGGTCA 60.731 45.833 0.00 0.00 0.00 4.02
1951 2537 3.727723 GCGTGTATGATTAGTGTACGGTC 59.272 47.826 0.00 0.00 0.00 4.79
1953 2539 3.697982 TGCGTGTATGATTAGTGTACGG 58.302 45.455 0.00 0.00 0.00 4.02
1954 2540 4.316171 CGTTGCGTGTATGATTAGTGTACG 60.316 45.833 0.00 0.00 0.00 3.67
1956 2542 4.735985 ACGTTGCGTGTATGATTAGTGTA 58.264 39.130 0.00 0.00 39.18 2.90
1957 2543 3.581755 ACGTTGCGTGTATGATTAGTGT 58.418 40.909 0.00 0.00 39.18 3.55
1970 2556 1.057636 CTTGATCGTACACGTTGCGT 58.942 50.000 1.19 0.00 42.36 5.24
1971 2557 1.333115 TCTTGATCGTACACGTTGCG 58.667 50.000 1.19 0.00 40.80 4.85
1972 2558 2.921121 TGATCTTGATCGTACACGTTGC 59.079 45.455 1.19 0.00 40.80 4.17
1973 2559 3.547868 CCTGATCTTGATCGTACACGTTG 59.452 47.826 1.19 0.00 40.80 4.10
1975 2561 2.099263 CCCTGATCTTGATCGTACACGT 59.901 50.000 1.19 0.00 40.80 4.49
1976 2562 2.357952 TCCCTGATCTTGATCGTACACG 59.642 50.000 6.19 0.00 41.45 4.49
1977 2563 3.381908 AGTCCCTGATCTTGATCGTACAC 59.618 47.826 6.19 1.73 0.00 2.90
1979 2565 3.632604 TGAGTCCCTGATCTTGATCGTAC 59.367 47.826 6.19 2.53 0.00 3.67
1980 2566 3.632604 GTGAGTCCCTGATCTTGATCGTA 59.367 47.826 6.19 0.00 0.00 3.43
1981 2567 2.428890 GTGAGTCCCTGATCTTGATCGT 59.571 50.000 6.19 0.00 0.00 3.73
1982 2568 2.542618 CGTGAGTCCCTGATCTTGATCG 60.543 54.545 6.19 2.03 0.00 3.69
1983 2569 2.223923 CCGTGAGTCCCTGATCTTGATC 60.224 54.545 3.82 3.82 0.00 2.92
1984 2570 1.759445 CCGTGAGTCCCTGATCTTGAT 59.241 52.381 0.00 0.00 0.00 2.57
1985 2571 1.186200 CCGTGAGTCCCTGATCTTGA 58.814 55.000 0.00 0.00 0.00 3.02
1987 2573 0.041238 TCCCGTGAGTCCCTGATCTT 59.959 55.000 0.00 0.00 0.00 2.40
1990 2576 0.041238 TCTTCCCGTGAGTCCCTGAT 59.959 55.000 0.00 0.00 0.00 2.90
1992 2578 1.776662 TATCTTCCCGTGAGTCCCTG 58.223 55.000 0.00 0.00 0.00 4.45
1993 2579 2.091278 TGATATCTTCCCGTGAGTCCCT 60.091 50.000 3.98 0.00 0.00 4.20
1995 2581 2.693591 TGTGATATCTTCCCGTGAGTCC 59.306 50.000 3.98 0.00 0.00 3.85
1996 2582 4.113354 GTTGTGATATCTTCCCGTGAGTC 58.887 47.826 3.98 0.00 0.00 3.36
1997 2583 3.513912 TGTTGTGATATCTTCCCGTGAGT 59.486 43.478 3.98 0.00 0.00 3.41
1998 2584 3.865745 GTGTTGTGATATCTTCCCGTGAG 59.134 47.826 3.98 0.00 0.00 3.51
1999 2585 3.259625 TGTGTTGTGATATCTTCCCGTGA 59.740 43.478 3.98 0.00 0.00 4.35
2000 2586 3.595173 TGTGTTGTGATATCTTCCCGTG 58.405 45.455 3.98 0.00 0.00 4.94
2001 2587 3.973206 TGTGTTGTGATATCTTCCCGT 57.027 42.857 3.98 0.00 0.00 5.28
2002 2588 4.253685 AGTTGTGTTGTGATATCTTCCCG 58.746 43.478 3.98 0.00 0.00 5.14
2004 2590 8.547967 TTTAGAGTTGTGTTGTGATATCTTCC 57.452 34.615 3.98 0.00 0.00 3.46
2039 2910 8.562892 GCTTGTATTATGATGCTTGTATGACTT 58.437 33.333 0.00 0.00 0.00 3.01
2040 2911 7.173907 GGCTTGTATTATGATGCTTGTATGACT 59.826 37.037 0.00 0.00 0.00 3.41
2041 2912 7.041167 TGGCTTGTATTATGATGCTTGTATGAC 60.041 37.037 0.00 0.00 0.00 3.06
2042 2913 6.997476 TGGCTTGTATTATGATGCTTGTATGA 59.003 34.615 0.00 0.00 0.00 2.15
2044 2915 6.432162 CCTGGCTTGTATTATGATGCTTGTAT 59.568 38.462 0.00 0.00 0.00 2.29
2045 2916 5.764686 CCTGGCTTGTATTATGATGCTTGTA 59.235 40.000 0.00 0.00 0.00 2.41
2046 2917 4.581824 CCTGGCTTGTATTATGATGCTTGT 59.418 41.667 0.00 0.00 0.00 3.16
2048 2919 4.147321 CCCTGGCTTGTATTATGATGCTT 58.853 43.478 0.00 0.00 0.00 3.91
2049 2920 3.499202 CCCCTGGCTTGTATTATGATGCT 60.499 47.826 0.00 0.00 0.00 3.79
2050 2921 2.821969 CCCCTGGCTTGTATTATGATGC 59.178 50.000 0.00 0.00 0.00 3.91
2051 2922 2.821969 GCCCCTGGCTTGTATTATGATG 59.178 50.000 0.00 0.00 46.69 3.07
2076 3806 1.134670 AGCACTTGTATTCGAGCCCTC 60.135 52.381 0.00 0.00 0.00 4.30
2079 3809 0.924090 CGAGCACTTGTATTCGAGCC 59.076 55.000 0.00 0.00 35.19 4.70
2082 3812 3.775661 TGATCGAGCACTTGTATTCGA 57.224 42.857 0.00 9.86 44.88 3.71
2088 3818 4.340666 ACTCATCTATGATCGAGCACTTGT 59.659 41.667 5.03 0.00 36.02 3.16
2092 3822 4.475028 CTCACTCATCTATGATCGAGCAC 58.525 47.826 5.03 0.00 36.02 4.40
2093 3823 4.762956 CTCACTCATCTATGATCGAGCA 57.237 45.455 5.53 5.53 36.02 4.26
2098 3828 4.484236 CTTCCGCTCACTCATCTATGATC 58.516 47.826 0.00 0.00 36.02 2.92
2100 3830 2.035193 GCTTCCGCTCACTCATCTATGA 59.965 50.000 0.00 0.00 35.16 2.15
2101 3831 2.223900 TGCTTCCGCTCACTCATCTATG 60.224 50.000 0.00 0.00 36.97 2.23
2102 3832 2.034878 TGCTTCCGCTCACTCATCTAT 58.965 47.619 0.00 0.00 36.97 1.98
2103 3833 1.474330 TGCTTCCGCTCACTCATCTA 58.526 50.000 0.00 0.00 36.97 1.98
2104 3834 0.610174 TTGCTTCCGCTCACTCATCT 59.390 50.000 0.00 0.00 36.97 2.90
2106 3836 0.035317 TGTTGCTTCCGCTCACTCAT 59.965 50.000 0.00 0.00 36.97 2.90
2107 3837 0.179059 TTGTTGCTTCCGCTCACTCA 60.179 50.000 0.00 0.00 36.97 3.41
2109 3839 2.472695 TATTGTTGCTTCCGCTCACT 57.527 45.000 0.00 0.00 36.97 3.41
2112 3842 3.198068 TCAGATATTGTTGCTTCCGCTC 58.802 45.455 0.00 0.00 36.97 5.03
2113 3843 3.201290 CTCAGATATTGTTGCTTCCGCT 58.799 45.455 0.00 0.00 36.97 5.52
2114 3844 2.939103 ACTCAGATATTGTTGCTTCCGC 59.061 45.455 0.00 0.00 0.00 5.54
2115 3845 5.109210 TGTACTCAGATATTGTTGCTTCCG 58.891 41.667 0.00 0.00 0.00 4.30
2116 3846 6.341316 TCTGTACTCAGATATTGTTGCTTCC 58.659 40.000 0.00 0.00 44.58 3.46
2129 3859 9.692749 CTTGTTTAACTTATGTCTGTACTCAGA 57.307 33.333 0.00 0.00 46.85 3.27
2130 3860 9.477484 ACTTGTTTAACTTATGTCTGTACTCAG 57.523 33.333 0.00 0.00 42.54 3.35
2133 3863 8.557029 GCAACTTGTTTAACTTATGTCTGTACT 58.443 33.333 0.00 0.00 0.00 2.73
2134 3864 7.801783 GGCAACTTGTTTAACTTATGTCTGTAC 59.198 37.037 0.00 0.00 0.00 2.90
2135 3865 7.499563 TGGCAACTTGTTTAACTTATGTCTGTA 59.500 33.333 0.00 0.00 37.61 2.74
2136 3866 6.320164 TGGCAACTTGTTTAACTTATGTCTGT 59.680 34.615 0.00 0.00 37.61 3.41
2137 3867 6.734137 TGGCAACTTGTTTAACTTATGTCTG 58.266 36.000 0.00 0.00 37.61 3.51
2139 3869 9.341899 CTTATGGCAACTTGTTTAACTTATGTC 57.658 33.333 0.00 0.00 37.61 3.06
2140 3870 9.073475 TCTTATGGCAACTTGTTTAACTTATGT 57.927 29.630 0.00 0.00 37.61 2.29
2143 3873 8.519526 CCATCTTATGGCAACTTGTTTAACTTA 58.480 33.333 0.00 0.00 44.70 2.24
2144 3874 7.378181 CCATCTTATGGCAACTTGTTTAACTT 58.622 34.615 0.00 0.00 44.70 2.66
2145 3875 6.924111 CCATCTTATGGCAACTTGTTTAACT 58.076 36.000 0.00 0.00 44.70 2.24
2160 3890 4.036027 CCAGTTTGTGCTAGCCATCTTATG 59.964 45.833 13.29 3.21 0.00 1.90
2161 3891 4.202441 CCAGTTTGTGCTAGCCATCTTAT 58.798 43.478 13.29 0.00 0.00 1.73
2162 3892 3.609853 CCAGTTTGTGCTAGCCATCTTA 58.390 45.455 13.29 0.00 0.00 2.10
2163 3893 2.440409 CCAGTTTGTGCTAGCCATCTT 58.560 47.619 13.29 0.00 0.00 2.40
2165 3895 1.098050 CCCAGTTTGTGCTAGCCATC 58.902 55.000 13.29 3.48 0.00 3.51
2167 3897 0.698238 ATCCCAGTTTGTGCTAGCCA 59.302 50.000 13.29 7.05 0.00 4.75
2168 3898 2.289565 GTATCCCAGTTTGTGCTAGCC 58.710 52.381 13.29 4.15 0.00 3.93
2169 3899 2.939103 CTGTATCCCAGTTTGTGCTAGC 59.061 50.000 8.10 8.10 36.37 3.42
2170 3900 4.471904 TCTGTATCCCAGTTTGTGCTAG 57.528 45.455 0.00 0.00 42.19 3.42
2173 3903 2.609459 CGATCTGTATCCCAGTTTGTGC 59.391 50.000 0.00 0.00 42.19 4.57
2177 3907 5.395768 CCTCTTTCGATCTGTATCCCAGTTT 60.396 44.000 0.00 0.00 42.19 2.66
2178 3908 4.100189 CCTCTTTCGATCTGTATCCCAGTT 59.900 45.833 0.00 0.00 42.19 3.16
2179 3909 3.639094 CCTCTTTCGATCTGTATCCCAGT 59.361 47.826 0.00 0.00 42.19 4.00
2180 3910 3.553922 GCCTCTTTCGATCTGTATCCCAG 60.554 52.174 0.00 0.00 42.97 4.45
2181 3911 2.365617 GCCTCTTTCGATCTGTATCCCA 59.634 50.000 0.00 0.00 0.00 4.37
2182 3912 2.365617 TGCCTCTTTCGATCTGTATCCC 59.634 50.000 0.00 0.00 0.00 3.85
2183 3913 3.181475 TGTGCCTCTTTCGATCTGTATCC 60.181 47.826 0.00 0.00 0.00 2.59
2185 3915 3.181471 CCTGTGCCTCTTTCGATCTGTAT 60.181 47.826 0.00 0.00 0.00 2.29
2186 3916 2.166459 CCTGTGCCTCTTTCGATCTGTA 59.834 50.000 0.00 0.00 0.00 2.74
2188 3918 1.649664 CCTGTGCCTCTTTCGATCTG 58.350 55.000 0.00 0.00 0.00 2.90
2189 3919 0.107945 GCCTGTGCCTCTTTCGATCT 60.108 55.000 0.00 0.00 0.00 2.75
2191 3921 4.625800 GCCTGTGCCTCTTTCGAT 57.374 55.556 0.00 0.00 0.00 3.59
2208 3938 2.612115 AGGAACCCAGGCAGGAGG 60.612 66.667 0.00 0.00 41.22 4.30
2209 3939 2.674220 GGAGGAACCCAGGCAGGAG 61.674 68.421 0.00 0.00 41.22 3.69
2211 3941 0.914417 TTAGGAGGAACCCAGGCAGG 60.914 60.000 0.00 0.00 40.05 4.85
2212 3942 0.253327 GTTAGGAGGAACCCAGGCAG 59.747 60.000 0.00 0.00 40.05 4.85
2213 3943 0.178873 AGTTAGGAGGAACCCAGGCA 60.179 55.000 0.00 0.00 40.05 4.75
2216 3946 3.032459 GGAGTAGTTAGGAGGAACCCAG 58.968 54.545 0.00 0.00 40.05 4.45
2218 3948 3.032459 CAGGAGTAGTTAGGAGGAACCC 58.968 54.545 0.00 0.00 40.05 4.11
2219 3949 3.032459 CCAGGAGTAGTTAGGAGGAACC 58.968 54.545 0.00 0.00 39.35 3.62
2220 3950 3.700539 GACCAGGAGTAGTTAGGAGGAAC 59.299 52.174 0.00 0.00 0.00 3.62
2221 3951 3.624205 CGACCAGGAGTAGTTAGGAGGAA 60.624 52.174 0.00 0.00 0.00 3.36
2223 3953 2.299521 CGACCAGGAGTAGTTAGGAGG 58.700 57.143 0.00 0.00 0.00 4.30
2224 3954 2.944349 GACGACCAGGAGTAGTTAGGAG 59.056 54.545 0.00 0.00 34.05 3.69
2225 3955 2.679059 CGACGACCAGGAGTAGTTAGGA 60.679 54.545 0.00 0.00 34.05 2.94
2226 3956 1.669779 CGACGACCAGGAGTAGTTAGG 59.330 57.143 0.00 0.00 34.05 2.69
2227 3957 2.351111 GACGACGACCAGGAGTAGTTAG 59.649 54.545 0.00 0.00 34.05 2.34
2230 3960 0.035881 TGACGACGACCAGGAGTAGT 59.964 55.000 0.00 0.00 36.98 2.73
2232 3962 1.303799 GCTGACGACGACCAGGAGTA 61.304 60.000 18.28 0.00 0.00 2.59
2234 3964 2.179517 GCTGACGACGACCAGGAG 59.820 66.667 18.28 2.21 0.00 3.69
2235 3965 3.733960 CGCTGACGACGACCAGGA 61.734 66.667 18.28 0.00 43.93 3.86
2253 3983 1.358046 CCTACTACTACGTGCCGGC 59.642 63.158 22.73 22.73 0.00 6.13
2254 3984 1.358046 GCCTACTACTACGTGCCGG 59.642 63.158 0.00 0.00 0.00 6.13
2255 3985 0.248377 GTGCCTACTACTACGTGCCG 60.248 60.000 0.00 0.00 0.00 5.69
2256 3986 0.101939 GGTGCCTACTACTACGTGCC 59.898 60.000 0.00 0.00 0.00 5.01
2257 3987 1.065251 GAGGTGCCTACTACTACGTGC 59.935 57.143 0.00 0.00 0.00 5.34
2258 3988 1.674962 GGAGGTGCCTACTACTACGTG 59.325 57.143 0.00 0.00 0.00 4.49
2259 3989 1.745141 CGGAGGTGCCTACTACTACGT 60.745 57.143 0.00 0.00 0.00 3.57
2260 3990 0.942962 CGGAGGTGCCTACTACTACG 59.057 60.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.