Multiple sequence alignment - TraesCS6A01G021000

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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 TraesCS6A01G021000 chr6A 100.000 2492 0 0 1 2492 10064975 10067466 0.000000e+00 4602.0
1 TraesCS6A01G021000 chr6A 89.104 670 54 11 1676 2338 10137515 10136858 0.000000e+00 815.0
2 TraesCS6A01G021000 chr6A 91.652 563 43 2 984 1546 10138140 10137582 0.000000e+00 776.0
3 TraesCS6A01G021000 chr6A 93.617 94 5 1 2356 2449 27631359 27631267 3.340000e-29 139.0
4 TraesCS6A01G021000 chr3A 93.268 921 56 1 1 921 395555762 395556676 0.000000e+00 1352.0
5 TraesCS6A01G021000 chr3A 90.330 910 82 5 1 906 496458348 496459255 0.000000e+00 1188.0
6 TraesCS6A01G021000 chr3A 89.583 96 10 0 2348 2443 688425760 688425855 3.370000e-24 122.0
7 TraesCS6A01G021000 chr6D 93.081 925 39 11 1 921 354544259 354545162 0.000000e+00 1330.0
8 TraesCS6A01G021000 chr6D 92.208 924 48 8 1 921 148077533 148078435 0.000000e+00 1286.0
9 TraesCS6A01G021000 chr6D 94.190 568 26 3 984 1546 9147155 9147720 0.000000e+00 859.0
10 TraesCS6A01G021000 chr6D 91.823 587 34 6 984 1562 9195564 9194984 0.000000e+00 806.0
11 TraesCS6A01G021000 chr6D 87.816 435 35 8 1686 2117 9188546 9188127 6.190000e-136 494.0
12 TraesCS6A01G021000 chr6D 86.588 425 32 14 1676 2092 9147782 9148189 1.760000e-121 446.0
13 TraesCS6A01G021000 chr6D 83.296 449 33 20 1896 2336 9162975 9163389 2.340000e-100 375.0
14 TraesCS6A01G021000 chr6D 92.473 93 6 1 2358 2449 379485064 379485156 5.590000e-27 132.0
15 TraesCS6A01G021000 chr1D 92.199 923 69 3 1 921 362920205 362919284 0.000000e+00 1303.0
16 TraesCS6A01G021000 chr7D 90.486 925 74 6 1 921 487869981 487869067 0.000000e+00 1208.0
17 TraesCS6A01G021000 chr7D 93.478 92 6 0 2358 2449 54792382 54792291 1.200000e-28 137.0
18 TraesCS6A01G021000 chr3D 92.009 851 43 11 2 848 18748998 18748169 0.000000e+00 1171.0
19 TraesCS6A01G021000 chr3D 92.391 92 7 0 2358 2449 604535092 604535001 5.590000e-27 132.0
20 TraesCS6A01G021000 chr6B 90.427 867 76 6 60 921 157649731 157650595 0.000000e+00 1134.0
21 TraesCS6A01G021000 chr6B 92.101 633 34 7 984 1608 16970570 16971194 0.000000e+00 878.0
22 TraesCS6A01G021000 chr6B 92.844 545 32 6 997 1536 17091666 17091124 0.000000e+00 784.0
23 TraesCS6A01G021000 chr6B 86.450 369 27 15 1976 2338 17003131 17003482 1.400000e-102 383.0
24 TraesCS6A01G021000 chr6B 88.435 294 23 8 1838 2127 17086076 17085790 6.600000e-91 344.0
25 TraesCS6A01G021000 chr6B 86.751 317 22 8 1676 1981 17091019 17090712 3.970000e-88 335.0
26 TraesCS6A01G021000 chr6B 87.500 264 12 7 1676 1939 17002883 17003125 4.060000e-73 285.0
27 TraesCS6A01G021000 chr6B 85.845 219 20 7 1733 1941 16971261 16971478 3.230000e-54 222.0
28 TraesCS6A01G021000 chr6B 92.857 42 3 0 1609 1650 96329739 96329780 7.440000e-06 62.1
29 TraesCS6A01G021000 chr6B 90.698 43 4 0 940 982 16970505 16970547 9.630000e-05 58.4
30 TraesCS6A01G021000 chr6B 94.118 34 2 0 1610 1643 566285123 566285090 4.000000e-03 52.8
31 TraesCS6A01G021000 chr2B 88.395 922 83 15 14 921 793040985 793040074 0.000000e+00 1088.0
32 TraesCS6A01G021000 chr2B 93.333 45 3 0 1610 1654 28245518 28245474 1.600000e-07 67.6
33 TraesCS6A01G021000 chr5A 89.123 570 45 13 356 921 279743321 279742765 0.000000e+00 693.0
34 TraesCS6A01G021000 chr5D 86.528 579 57 15 1007 1577 104142955 104142390 3.520000e-173 617.0
35 TraesCS6A01G021000 chr5D 86.564 521 62 4 1005 1523 104113148 104112634 3.600000e-158 568.0
36 TraesCS6A01G021000 chr5D 91.667 96 8 0 2355 2450 433345004 433344909 1.550000e-27 134.0
37 TraesCS6A01G021000 chr5D 90.625 96 8 1 2356 2450 86741026 86741121 2.600000e-25 126.0
38 TraesCS6A01G021000 chr5B 88.155 515 52 6 1007 1519 113456854 113456347 2.740000e-169 604.0
39 TraesCS6A01G021000 chr5B 87.154 506 57 4 1020 1523 113327960 113327461 3.600000e-158 568.0
40 TraesCS6A01G021000 chr7A 91.837 98 5 3 2354 2450 201212259 201212164 1.550000e-27 134.0
41 TraesCS6A01G021000 chr7A 93.617 47 3 0 1610 1656 665770191 665770145 1.240000e-08 71.3
42 TraesCS6A01G021000 chr2D 94.186 86 5 0 2358 2443 73287561 73287476 5.590000e-27 132.0
43 TraesCS6A01G021000 chr2D 89.831 59 3 2 1598 1656 57319094 57319149 3.440000e-09 73.1
44 TraesCS6A01G021000 chr2D 100.000 29 0 0 1647 1675 130807851 130807879 1.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G021000 chr6A 10064975 10067466 2491 False 4602.000000 4602 100.0000 1 2492 1 chr6A.!!$F1 2491
1 TraesCS6A01G021000 chr6A 10136858 10138140 1282 True 795.500000 815 90.3780 984 2338 2 chr6A.!!$R2 1354
2 TraesCS6A01G021000 chr3A 395555762 395556676 914 False 1352.000000 1352 93.2680 1 921 1 chr3A.!!$F1 920
3 TraesCS6A01G021000 chr3A 496458348 496459255 907 False 1188.000000 1188 90.3300 1 906 1 chr3A.!!$F2 905
4 TraesCS6A01G021000 chr6D 354544259 354545162 903 False 1330.000000 1330 93.0810 1 921 1 chr6D.!!$F3 920
5 TraesCS6A01G021000 chr6D 148077533 148078435 902 False 1286.000000 1286 92.2080 1 921 1 chr6D.!!$F2 920
6 TraesCS6A01G021000 chr6D 9194984 9195564 580 True 806.000000 806 91.8230 984 1562 1 chr6D.!!$R2 578
7 TraesCS6A01G021000 chr6D 9147155 9148189 1034 False 652.500000 859 90.3890 984 2092 2 chr6D.!!$F5 1108
8 TraesCS6A01G021000 chr1D 362919284 362920205 921 True 1303.000000 1303 92.1990 1 921 1 chr1D.!!$R1 920
9 TraesCS6A01G021000 chr7D 487869067 487869981 914 True 1208.000000 1208 90.4860 1 921 1 chr7D.!!$R2 920
10 TraesCS6A01G021000 chr3D 18748169 18748998 829 True 1171.000000 1171 92.0090 2 848 1 chr3D.!!$R1 846
11 TraesCS6A01G021000 chr6B 157649731 157650595 864 False 1134.000000 1134 90.4270 60 921 1 chr6B.!!$F2 861
12 TraesCS6A01G021000 chr6B 17090712 17091666 954 True 559.500000 784 89.7975 997 1981 2 chr6B.!!$R3 984
13 TraesCS6A01G021000 chr6B 16970505 16971478 973 False 386.133333 878 89.5480 940 1941 3 chr6B.!!$F3 1001
14 TraesCS6A01G021000 chr6B 17002883 17003482 599 False 334.000000 383 86.9750 1676 2338 2 chr6B.!!$F4 662
15 TraesCS6A01G021000 chr2B 793040074 793040985 911 True 1088.000000 1088 88.3950 14 921 1 chr2B.!!$R2 907
16 TraesCS6A01G021000 chr5A 279742765 279743321 556 True 693.000000 693 89.1230 356 921 1 chr5A.!!$R1 565
17 TraesCS6A01G021000 chr5D 104142390 104142955 565 True 617.000000 617 86.5280 1007 1577 1 chr5D.!!$R2 570
18 TraesCS6A01G021000 chr5D 104112634 104113148 514 True 568.000000 568 86.5640 1005 1523 1 chr5D.!!$R1 518
19 TraesCS6A01G021000 chr5B 113456347 113456854 507 True 604.000000 604 88.1550 1007 1519 1 chr5B.!!$R2 512

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
923 967 1.011574 CCGGCGCGTGCTAAAATAC 60.012 57.895 21.89 0.56 42.25 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2464 2649 0.179073 GACATGACGGTGGGAGATGG 60.179 60.0 0.0 0.0 0.0 3.51 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
23 24 6.650427 ACATCGGTGCAACTAGATAGATAA 57.350 37.500 0.00 0.00 33.80 1.75
65 75 5.909621 AGAACTACGGTGCAACTAGATAA 57.090 39.130 13.15 0.00 36.74 1.75
504 518 1.541310 AAGTTCATCTGCGACCGGGA 61.541 55.000 6.32 0.00 0.00 5.14
659 673 1.226603 CGGTAGCTCGAAGAACCCG 60.227 63.158 0.00 1.04 34.09 5.28
843 885 2.281484 GCGTGCCACTTTCTCCCA 60.281 61.111 0.00 0.00 0.00 4.37
848 892 2.030562 CCACTTTCTCCCACGCGT 59.969 61.111 5.58 5.58 0.00 6.01
891 935 4.257654 TTCCCGCCACCGCTGAAA 62.258 61.111 0.00 0.00 0.00 2.69
921 965 4.174129 GCCGGCGCGTGCTAAAAT 62.174 61.111 21.89 0.00 42.25 1.82
922 966 2.815298 GCCGGCGCGTGCTAAAATA 61.815 57.895 21.89 0.00 42.25 1.40
923 967 1.011574 CCGGCGCGTGCTAAAATAC 60.012 57.895 21.89 0.56 42.25 1.89
924 968 1.011574 CGGCGCGTGCTAAAATACC 60.012 57.895 21.89 0.00 42.25 2.73
925 969 1.354155 GGCGCGTGCTAAAATACCC 59.646 57.895 21.89 0.00 42.25 3.69
926 970 1.354155 GCGCGTGCTAAAATACCCC 59.646 57.895 15.02 0.00 38.39 4.95
927 971 2.019337 CGCGTGCTAAAATACCCCC 58.981 57.895 0.00 0.00 0.00 5.40
947 991 4.693915 CCCCTCCCCCAACCCTGA 62.694 72.222 0.00 0.00 0.00 3.86
948 992 3.017581 CCCTCCCCCAACCCTGAG 61.018 72.222 0.00 0.00 0.00 3.35
949 993 3.017581 CCTCCCCCAACCCTGAGG 61.018 72.222 0.00 0.00 38.56 3.86
950 994 3.732849 CTCCCCCAACCCTGAGGC 61.733 72.222 0.00 0.00 36.11 4.70
951 995 4.608514 TCCCCCAACCCTGAGGCA 62.609 66.667 0.00 0.00 36.11 4.75
952 996 4.052518 CCCCCAACCCTGAGGCAG 62.053 72.222 0.00 0.00 36.11 4.85
982 1026 2.124320 AAACCAGTGCGTGCCAGT 60.124 55.556 0.00 0.00 0.00 4.00
994 1059 1.204146 GTGCCAGTCCCTAATCCTCA 58.796 55.000 0.00 0.00 0.00 3.86
1054 1125 2.917227 TGCTCGTGGCTCTGTCCA 60.917 61.111 5.00 0.00 42.39 4.02
1239 1310 2.101575 GACGTCTGCGCGTGGATA 59.898 61.111 8.70 0.00 45.79 2.59
1251 1322 1.442148 GTGGATAGGGAGCGTGTCC 59.558 63.158 0.00 0.00 46.10 4.02
1350 1421 2.807895 ATGTCCGTCCGCGTTTCG 60.808 61.111 4.92 6.60 36.15 3.46
1515 1589 0.818445 ATGTCGATCGACCGCCTACT 60.818 55.000 37.58 15.64 43.97 2.57
1574 1703 1.021968 TGCAGCTAAGCTCGATCGTA 58.978 50.000 15.94 0.00 36.40 3.43
1577 1706 2.047769 CAGCTAAGCTCGATCGTAAGC 58.952 52.381 18.31 18.31 36.40 3.09
1579 1708 2.099263 AGCTAAGCTCGATCGTAAGCAA 59.901 45.455 25.19 14.60 41.06 3.91
1580 1709 2.858344 GCTAAGCTCGATCGTAAGCAAA 59.142 45.455 25.19 14.32 41.06 3.68
1595 1729 9.758651 ATCGTAAGCAAATATCTATTGTGTGTA 57.241 29.630 0.00 0.00 37.18 2.90
1598 1732 9.027129 GTAAGCAAATATCTATTGTGTGTACGA 57.973 33.333 0.00 0.00 0.00 3.43
1599 1733 7.700322 AGCAAATATCTATTGTGTGTACGAG 57.300 36.000 0.00 0.00 0.00 4.18
1600 1734 6.701841 AGCAAATATCTATTGTGTGTACGAGG 59.298 38.462 0.00 0.00 0.00 4.63
1601 1735 6.479001 GCAAATATCTATTGTGTGTACGAGGT 59.521 38.462 0.00 0.00 0.00 3.85
1602 1736 7.011109 GCAAATATCTATTGTGTGTACGAGGTT 59.989 37.037 0.00 0.00 0.00 3.50
1603 1737 8.328146 CAAATATCTATTGTGTGTACGAGGTTG 58.672 37.037 0.00 0.00 0.00 3.77
1604 1738 4.859304 TCTATTGTGTGTACGAGGTTGT 57.141 40.909 0.00 0.00 0.00 3.32
1605 1739 5.963176 TCTATTGTGTGTACGAGGTTGTA 57.037 39.130 0.00 0.00 0.00 2.41
1606 1740 5.702865 TCTATTGTGTGTACGAGGTTGTAC 58.297 41.667 0.00 1.07 43.95 2.90
1607 1741 2.798976 TGTGTGTACGAGGTTGTACC 57.201 50.000 5.27 0.00 43.22 3.34
1608 1742 1.001487 TGTGTGTACGAGGTTGTACCG 60.001 52.381 5.27 0.00 44.90 4.02
1609 1743 0.597568 TGTGTACGAGGTTGTACCGG 59.402 55.000 0.00 0.00 44.90 5.28
1610 1744 0.881118 GTGTACGAGGTTGTACCGGA 59.119 55.000 9.46 0.00 44.90 5.14
1611 1745 1.135575 GTGTACGAGGTTGTACCGGAG 60.136 57.143 9.46 0.00 44.90 4.63
1612 1746 1.271325 TGTACGAGGTTGTACCGGAGA 60.271 52.381 9.46 0.00 44.90 3.71
1613 1747 1.399791 GTACGAGGTTGTACCGGAGAG 59.600 57.143 9.46 0.00 44.90 3.20
1614 1748 0.964358 ACGAGGTTGTACCGGAGAGG 60.964 60.000 9.46 0.00 44.90 3.69
1626 1760 3.906720 CCGGAGAGGTGATTTTTAGGA 57.093 47.619 0.00 0.00 34.51 2.94
1627 1761 3.532542 CCGGAGAGGTGATTTTTAGGAC 58.467 50.000 0.00 0.00 34.51 3.85
1628 1762 3.532542 CGGAGAGGTGATTTTTAGGACC 58.467 50.000 0.00 0.00 0.00 4.46
1629 1763 3.055385 CGGAGAGGTGATTTTTAGGACCA 60.055 47.826 0.00 0.00 0.00 4.02
1630 1764 4.384208 CGGAGAGGTGATTTTTAGGACCAT 60.384 45.833 0.00 0.00 0.00 3.55
1631 1765 4.884164 GGAGAGGTGATTTTTAGGACCATG 59.116 45.833 0.00 0.00 0.00 3.66
1632 1766 4.860022 AGAGGTGATTTTTAGGACCATGG 58.140 43.478 11.19 11.19 0.00 3.66
1633 1767 4.292306 AGAGGTGATTTTTAGGACCATGGT 59.708 41.667 19.89 19.89 0.00 3.55
1634 1768 5.010708 AGGTGATTTTTAGGACCATGGTT 57.989 39.130 20.85 6.57 0.00 3.67
1635 1769 5.016831 AGGTGATTTTTAGGACCATGGTTC 58.983 41.667 20.85 18.49 0.00 3.62
1636 1770 4.770010 GGTGATTTTTAGGACCATGGTTCA 59.230 41.667 25.54 15.88 0.00 3.18
1637 1771 5.245075 GGTGATTTTTAGGACCATGGTTCAA 59.755 40.000 25.54 13.98 0.00 2.69
1638 1772 6.156519 GTGATTTTTAGGACCATGGTTCAAC 58.843 40.000 25.54 13.00 0.00 3.18
1639 1773 5.245075 TGATTTTTAGGACCATGGTTCAACC 59.755 40.000 25.54 18.22 39.22 3.77
1640 1774 2.483014 TTAGGACCATGGTTCAACCG 57.517 50.000 25.54 0.00 42.58 4.44
1641 1775 1.646912 TAGGACCATGGTTCAACCGA 58.353 50.000 25.54 12.17 42.58 4.69
1642 1776 0.768622 AGGACCATGGTTCAACCGAA 59.231 50.000 25.54 0.00 42.58 4.30
1643 1777 1.354368 AGGACCATGGTTCAACCGAAT 59.646 47.619 25.54 0.00 42.58 3.34
1644 1778 1.743394 GGACCATGGTTCAACCGAATC 59.257 52.381 20.85 1.18 42.58 2.52
1645 1779 2.618045 GGACCATGGTTCAACCGAATCT 60.618 50.000 20.85 0.00 42.58 2.40
1646 1780 3.370103 GGACCATGGTTCAACCGAATCTA 60.370 47.826 20.85 0.00 42.58 1.98
1647 1781 4.451900 GACCATGGTTCAACCGAATCTAT 58.548 43.478 20.85 0.00 42.58 1.98
1648 1782 4.199310 ACCATGGTTCAACCGAATCTATG 58.801 43.478 13.00 0.00 42.58 2.23
1649 1783 3.565482 CCATGGTTCAACCGAATCTATGG 59.435 47.826 2.57 6.90 42.58 2.74
1650 1784 4.450976 CATGGTTCAACCGAATCTATGGA 58.549 43.478 1.02 0.00 42.58 3.41
1651 1785 3.869065 TGGTTCAACCGAATCTATGGAC 58.131 45.455 1.02 0.00 42.58 4.02
1652 1786 3.203716 GGTTCAACCGAATCTATGGACC 58.796 50.000 0.00 0.00 34.44 4.46
1653 1787 3.370103 GGTTCAACCGAATCTATGGACCA 60.370 47.826 0.00 0.00 40.54 4.02
1654 1788 4.451900 GTTCAACCGAATCTATGGACCAT 58.548 43.478 12.67 12.67 32.61 3.55
1655 1789 4.071961 TCAACCGAATCTATGGACCATG 57.928 45.455 17.73 7.34 0.00 3.66
1656 1790 3.141398 CAACCGAATCTATGGACCATGG 58.859 50.000 17.73 14.57 0.00 3.66
1657 1791 2.408565 ACCGAATCTATGGACCATGGT 58.591 47.619 19.89 19.89 0.00 3.55
1658 1792 2.368875 ACCGAATCTATGGACCATGGTC 59.631 50.000 33.14 33.14 43.87 4.02
1668 1802 2.799126 GACCATGGTCCCATACAACA 57.201 50.000 31.37 0.00 39.08 3.33
1669 1803 3.297134 GACCATGGTCCCATACAACAT 57.703 47.619 31.37 0.00 39.08 2.71
1670 1804 3.631250 GACCATGGTCCCATACAACATT 58.369 45.455 31.37 0.00 39.08 2.71
1671 1805 3.631250 ACCATGGTCCCATACAACATTC 58.369 45.455 13.00 0.00 34.91 2.67
1672 1806 3.269381 ACCATGGTCCCATACAACATTCT 59.731 43.478 13.00 0.00 34.91 2.40
1673 1807 4.264352 ACCATGGTCCCATACAACATTCTT 60.264 41.667 13.00 0.00 34.91 2.52
1674 1808 4.098349 CCATGGTCCCATACAACATTCTTG 59.902 45.833 2.57 0.00 34.91 3.02
1700 1834 0.524862 ACCATCGTCAGTCGTGTACC 59.475 55.000 0.00 0.00 40.80 3.34
1703 1837 2.356695 CCATCGTCAGTCGTGTACCATA 59.643 50.000 0.00 0.00 40.80 2.74
1704 1838 3.004419 CCATCGTCAGTCGTGTACCATAT 59.996 47.826 0.00 0.00 40.80 1.78
1705 1839 4.214758 CCATCGTCAGTCGTGTACCATATA 59.785 45.833 0.00 0.00 40.80 0.86
1706 1840 5.106277 CCATCGTCAGTCGTGTACCATATAT 60.106 44.000 0.00 0.00 40.80 0.86
1707 1841 5.602458 TCGTCAGTCGTGTACCATATATC 57.398 43.478 0.00 0.00 40.80 1.63
1708 1842 5.303165 TCGTCAGTCGTGTACCATATATCT 58.697 41.667 0.00 0.00 40.80 1.98
1717 1851 7.170828 GTCGTGTACCATATATCTGATTTGCAA 59.829 37.037 0.00 0.00 0.00 4.08
1834 2009 0.817654 TGGCGAGTCTAGACATGTGG 59.182 55.000 24.44 6.93 0.00 4.17
1928 2103 2.323968 TGCGCTTATATGCCAGTGAA 57.676 45.000 9.73 0.00 0.00 3.18
1941 2116 1.534595 CCAGTGAACTGCAGCAACAAC 60.535 52.381 15.27 5.58 42.47 3.32
1952 2128 1.608590 CAGCAACAACCAACGGAAGAT 59.391 47.619 0.00 0.00 0.00 2.40
2069 2252 9.541143 TTGAGAGAAAAGTTCTTTTGTTGTTTT 57.459 25.926 14.07 0.00 40.87 2.43
2079 2262 5.448438 TCTTTTGTTGTTTTCCGATGATCG 58.552 37.500 8.05 8.05 40.07 3.69
2085 2268 6.280643 TGTTGTTTTCCGATGATCGAGATAT 58.719 36.000 17.52 0.00 43.74 1.63
2092 2275 3.996363 CCGATGATCGAGATATGGCAAAA 59.004 43.478 17.52 0.00 43.74 2.44
2097 2280 3.194005 TCGAGATATGGCAAAACCCTC 57.806 47.619 0.00 0.00 37.83 4.30
2099 2282 2.222027 GAGATATGGCAAAACCCTCCG 58.778 52.381 0.00 0.00 37.83 4.63
2129 2312 6.698008 TCTAGGAAAACATGCAACATATGG 57.302 37.500 7.80 0.00 0.00 2.74
2146 2331 6.129179 ACATATGGTGCCTTTTGTAAGCTAT 58.871 36.000 7.80 0.00 0.00 2.97
2147 2332 7.287061 ACATATGGTGCCTTTTGTAAGCTATA 58.713 34.615 7.80 0.00 0.00 1.31
2148 2333 7.777910 ACATATGGTGCCTTTTGTAAGCTATAA 59.222 33.333 7.80 0.00 0.00 0.98
2149 2334 6.699575 ATGGTGCCTTTTGTAAGCTATAAG 57.300 37.500 0.00 0.00 0.00 1.73
2150 2335 4.398044 TGGTGCCTTTTGTAAGCTATAAGC 59.602 41.667 0.00 0.00 42.84 3.09
2174 2359 6.704493 GCTGGGACGATATTGAAGTAATTGTA 59.296 38.462 0.00 0.00 0.00 2.41
2236 2421 4.142609 TCTAGTTGTGATGGATCCAAGC 57.857 45.455 20.67 14.55 0.00 4.01
2243 2428 2.068277 GATGGATCCAAGCCAAGCGC 62.068 60.000 20.67 0.00 39.21 5.92
2283 2468 1.330521 TCGTTGCTGCAGTTTCACTTC 59.669 47.619 16.64 0.00 0.00 3.01
2294 2479 1.069227 GTTTCACTTCGGTGGTCATGC 60.069 52.381 0.00 0.00 45.34 4.06
2339 2524 2.663826 CAGCTGGACTGGTCTAAGAC 57.336 55.000 5.57 0.00 43.19 3.01
2340 2525 2.175202 CAGCTGGACTGGTCTAAGACT 58.825 52.381 5.57 0.18 43.19 3.24
2341 2526 2.094286 CAGCTGGACTGGTCTAAGACTG 60.094 54.545 5.57 7.11 43.19 3.51
2342 2527 1.896465 GCTGGACTGGTCTAAGACTGT 59.104 52.381 0.67 0.00 32.47 3.55
2343 2528 3.090037 GCTGGACTGGTCTAAGACTGTA 58.910 50.000 0.67 0.00 32.47 2.74
2344 2529 3.129638 GCTGGACTGGTCTAAGACTGTAG 59.870 52.174 0.67 0.00 32.47 2.74
2345 2530 4.590918 CTGGACTGGTCTAAGACTGTAGA 58.409 47.826 0.67 0.00 32.47 2.59
2346 2531 4.333690 TGGACTGGTCTAAGACTGTAGAC 58.666 47.826 12.64 12.64 46.27 2.59
2364 2549 8.597662 CTGTAGACAGTAGGAGTAATCTCTAC 57.402 42.308 1.28 9.46 38.58 2.59
2365 2550 8.321621 TGTAGACAGTAGGAGTAATCTCTACT 57.678 38.462 12.62 12.62 40.29 2.57
2366 2551 8.423349 TGTAGACAGTAGGAGTAATCTCTACTC 58.577 40.741 14.49 3.75 42.28 2.59
2377 2562 8.911918 GAGTAATCTCTACTCCTAATGTCTGA 57.088 38.462 1.21 0.00 38.33 3.27
2378 2563 8.918202 AGTAATCTCTACTCCTAATGTCTGAG 57.082 38.462 0.00 0.00 0.00 3.35
2379 2564 8.499406 AGTAATCTCTACTCCTAATGTCTGAGT 58.501 37.037 0.00 0.00 41.88 3.41
2380 2565 9.127277 GTAATCTCTACTCCTAATGTCTGAGTT 57.873 37.037 0.00 0.00 39.84 3.01
2381 2566 7.581213 ATCTCTACTCCTAATGTCTGAGTTG 57.419 40.000 0.00 0.00 39.84 3.16
2382 2567 5.888724 TCTCTACTCCTAATGTCTGAGTTGG 59.111 44.000 0.00 0.00 39.84 3.77
2383 2568 5.580998 TCTACTCCTAATGTCTGAGTTGGT 58.419 41.667 0.00 0.00 39.84 3.67
2384 2569 6.017192 TCTACTCCTAATGTCTGAGTTGGTT 58.983 40.000 0.00 0.00 39.84 3.67
2385 2570 4.899502 ACTCCTAATGTCTGAGTTGGTTG 58.100 43.478 0.00 0.00 35.93 3.77
2386 2571 4.593206 ACTCCTAATGTCTGAGTTGGTTGA 59.407 41.667 0.00 0.00 35.93 3.18
2387 2572 5.071788 ACTCCTAATGTCTGAGTTGGTTGAA 59.928 40.000 0.00 0.00 35.93 2.69
2388 2573 6.126863 TCCTAATGTCTGAGTTGGTTGAAT 57.873 37.500 0.00 0.00 0.00 2.57
2389 2574 7.038302 ACTCCTAATGTCTGAGTTGGTTGAATA 60.038 37.037 0.00 0.00 35.93 1.75
2390 2575 7.331026 TCCTAATGTCTGAGTTGGTTGAATAG 58.669 38.462 0.00 0.00 0.00 1.73
2391 2576 7.038302 TCCTAATGTCTGAGTTGGTTGAATAGT 60.038 37.037 0.00 0.00 0.00 2.12
2392 2577 8.258007 CCTAATGTCTGAGTTGGTTGAATAGTA 58.742 37.037 0.00 0.00 0.00 1.82
2393 2578 9.653287 CTAATGTCTGAGTTGGTTGAATAGTAA 57.347 33.333 0.00 0.00 0.00 2.24
2394 2579 8.553459 AATGTCTGAGTTGGTTGAATAGTAAG 57.447 34.615 0.00 0.00 0.00 2.34
2395 2580 6.464222 TGTCTGAGTTGGTTGAATAGTAAGG 58.536 40.000 0.00 0.00 0.00 2.69
2396 2581 6.042781 TGTCTGAGTTGGTTGAATAGTAAGGT 59.957 38.462 0.00 0.00 0.00 3.50
2397 2582 6.935208 GTCTGAGTTGGTTGAATAGTAAGGTT 59.065 38.462 0.00 0.00 0.00 3.50
2398 2583 8.092687 GTCTGAGTTGGTTGAATAGTAAGGTTA 58.907 37.037 0.00 0.00 0.00 2.85
2399 2584 8.653191 TCTGAGTTGGTTGAATAGTAAGGTTAA 58.347 33.333 0.00 0.00 0.00 2.01
2400 2585 9.449719 CTGAGTTGGTTGAATAGTAAGGTTAAT 57.550 33.333 0.00 0.00 0.00 1.40
2401 2586 9.802039 TGAGTTGGTTGAATAGTAAGGTTAATT 57.198 29.630 0.00 0.00 0.00 1.40
2406 2591 9.287373 TGGTTGAATAGTAAGGTTAATTTTCGT 57.713 29.630 0.00 0.00 0.00 3.85
2407 2592 9.764870 GGTTGAATAGTAAGGTTAATTTTCGTC 57.235 33.333 0.00 0.00 0.00 4.20
2408 2593 9.764870 GTTGAATAGTAAGGTTAATTTTCGTCC 57.235 33.333 0.00 0.00 0.00 4.79
2409 2594 8.496707 TGAATAGTAAGGTTAATTTTCGTCCC 57.503 34.615 0.00 0.00 0.00 4.46
2410 2595 8.102047 TGAATAGTAAGGTTAATTTTCGTCCCA 58.898 33.333 0.00 0.00 0.00 4.37
2411 2596 9.117183 GAATAGTAAGGTTAATTTTCGTCCCAT 57.883 33.333 0.00 0.00 0.00 4.00
2412 2597 6.997239 AGTAAGGTTAATTTTCGTCCCATC 57.003 37.500 0.00 0.00 0.00 3.51
2413 2598 6.478129 AGTAAGGTTAATTTTCGTCCCATCA 58.522 36.000 0.00 0.00 0.00 3.07
2414 2599 7.116736 AGTAAGGTTAATTTTCGTCCCATCAT 58.883 34.615 0.00 0.00 0.00 2.45
2415 2600 6.850752 AAGGTTAATTTTCGTCCCATCATT 57.149 33.333 0.00 0.00 0.00 2.57
2416 2601 6.850752 AGGTTAATTTTCGTCCCATCATTT 57.149 33.333 0.00 0.00 0.00 2.32
2417 2602 7.239763 AGGTTAATTTTCGTCCCATCATTTT 57.760 32.000 0.00 0.00 0.00 1.82
2418 2603 7.320399 AGGTTAATTTTCGTCCCATCATTTTC 58.680 34.615 0.00 0.00 0.00 2.29
2419 2604 7.039363 AGGTTAATTTTCGTCCCATCATTTTCA 60.039 33.333 0.00 0.00 0.00 2.69
2420 2605 7.600752 GGTTAATTTTCGTCCCATCATTTTCAA 59.399 33.333 0.00 0.00 0.00 2.69
2421 2606 8.432359 GTTAATTTTCGTCCCATCATTTTCAAC 58.568 33.333 0.00 0.00 0.00 3.18
2422 2607 4.513198 TTTCGTCCCATCATTTTCAACC 57.487 40.909 0.00 0.00 0.00 3.77
2423 2608 2.080693 TCGTCCCATCATTTTCAACCG 58.919 47.619 0.00 0.00 0.00 4.44
2424 2609 1.810151 CGTCCCATCATTTTCAACCGT 59.190 47.619 0.00 0.00 0.00 4.83
2425 2610 2.227865 CGTCCCATCATTTTCAACCGTT 59.772 45.455 0.00 0.00 0.00 4.44
2426 2611 3.305064 CGTCCCATCATTTTCAACCGTTT 60.305 43.478 0.00 0.00 0.00 3.60
2427 2612 4.627058 GTCCCATCATTTTCAACCGTTTT 58.373 39.130 0.00 0.00 0.00 2.43
2428 2613 5.563085 CGTCCCATCATTTTCAACCGTTTTA 60.563 40.000 0.00 0.00 0.00 1.52
2429 2614 6.394809 GTCCCATCATTTTCAACCGTTTTAT 58.605 36.000 0.00 0.00 0.00 1.40
2430 2615 6.871492 GTCCCATCATTTTCAACCGTTTTATT 59.129 34.615 0.00 0.00 0.00 1.40
2431 2616 7.386573 GTCCCATCATTTTCAACCGTTTTATTT 59.613 33.333 0.00 0.00 0.00 1.40
2432 2617 7.600752 TCCCATCATTTTCAACCGTTTTATTTC 59.399 33.333 0.00 0.00 0.00 2.17
2433 2618 7.411372 CCCATCATTTTCAACCGTTTTATTTCG 60.411 37.037 0.00 0.00 0.00 3.46
2434 2619 7.115663 CCATCATTTTCAACCGTTTTATTTCGT 59.884 33.333 0.00 0.00 0.00 3.85
2435 2620 7.988904 TCATTTTCAACCGTTTTATTTCGTT 57.011 28.000 0.00 0.00 0.00 3.85
2436 2621 7.832550 TCATTTTCAACCGTTTTATTTCGTTG 58.167 30.769 0.00 0.00 0.00 4.10
2437 2622 6.570690 TTTTCAACCGTTTTATTTCGTTGG 57.429 33.333 0.00 0.00 0.00 3.77
2438 2623 4.897025 TCAACCGTTTTATTTCGTTGGT 57.103 36.364 0.00 0.00 0.00 3.67
2439 2624 5.246145 TCAACCGTTTTATTTCGTTGGTT 57.754 34.783 0.00 0.00 38.69 3.67
2440 2625 5.648572 TCAACCGTTTTATTTCGTTGGTTT 58.351 33.333 0.00 0.00 36.15 3.27
2441 2626 6.098017 TCAACCGTTTTATTTCGTTGGTTTT 58.902 32.000 0.00 0.00 36.15 2.43
2442 2627 6.589139 TCAACCGTTTTATTTCGTTGGTTTTT 59.411 30.769 0.00 0.00 36.15 1.94
2443 2628 6.572153 ACCGTTTTATTTCGTTGGTTTTTC 57.428 33.333 0.00 0.00 0.00 2.29
2444 2629 6.331845 ACCGTTTTATTTCGTTGGTTTTTCT 58.668 32.000 0.00 0.00 0.00 2.52
2445 2630 6.473131 ACCGTTTTATTTCGTTGGTTTTTCTC 59.527 34.615 0.00 0.00 0.00 2.87
2446 2631 6.344390 CCGTTTTATTTCGTTGGTTTTTCTCG 60.344 38.462 0.00 0.00 0.00 4.04
2447 2632 6.195060 CGTTTTATTTCGTTGGTTTTTCTCGT 59.805 34.615 0.00 0.00 0.00 4.18
2448 2633 7.541243 GTTTTATTTCGTTGGTTTTTCTCGTC 58.459 34.615 0.00 0.00 0.00 4.20
2449 2634 6.607735 TTATTTCGTTGGTTTTTCTCGTCT 57.392 33.333 0.00 0.00 0.00 4.18
2450 2635 3.936902 TTCGTTGGTTTTTCTCGTCTG 57.063 42.857 0.00 0.00 0.00 3.51
2451 2636 2.206750 TCGTTGGTTTTTCTCGTCTGG 58.793 47.619 0.00 0.00 0.00 3.86
2452 2637 1.937899 CGTTGGTTTTTCTCGTCTGGT 59.062 47.619 0.00 0.00 0.00 4.00
2453 2638 2.353579 CGTTGGTTTTTCTCGTCTGGTT 59.646 45.455 0.00 0.00 0.00 3.67
2454 2639 3.181504 CGTTGGTTTTTCTCGTCTGGTTT 60.182 43.478 0.00 0.00 0.00 3.27
2455 2640 4.034279 CGTTGGTTTTTCTCGTCTGGTTTA 59.966 41.667 0.00 0.00 0.00 2.01
2456 2641 5.277634 CGTTGGTTTTTCTCGTCTGGTTTAT 60.278 40.000 0.00 0.00 0.00 1.40
2457 2642 6.500910 GTTGGTTTTTCTCGTCTGGTTTATT 58.499 36.000 0.00 0.00 0.00 1.40
2458 2643 6.702716 TGGTTTTTCTCGTCTGGTTTATTT 57.297 33.333 0.00 0.00 0.00 1.40
2459 2644 7.102847 TGGTTTTTCTCGTCTGGTTTATTTT 57.897 32.000 0.00 0.00 0.00 1.82
2460 2645 7.197703 TGGTTTTTCTCGTCTGGTTTATTTTC 58.802 34.615 0.00 0.00 0.00 2.29
2461 2646 6.358822 GGTTTTTCTCGTCTGGTTTATTTTCG 59.641 38.462 0.00 0.00 0.00 3.46
2462 2647 6.607735 TTTTCTCGTCTGGTTTATTTTCGT 57.392 33.333 0.00 0.00 0.00 3.85
2463 2648 5.834239 TTCTCGTCTGGTTTATTTTCGTC 57.166 39.130 0.00 0.00 0.00 4.20
2464 2649 4.240096 TCTCGTCTGGTTTATTTTCGTCC 58.760 43.478 0.00 0.00 0.00 4.79
2465 2650 3.328505 TCGTCTGGTTTATTTTCGTCCC 58.671 45.455 0.00 0.00 0.00 4.46
2466 2651 3.068560 CGTCTGGTTTATTTTCGTCCCA 58.931 45.455 0.00 0.00 0.00 4.37
2467 2652 3.687698 CGTCTGGTTTATTTTCGTCCCAT 59.312 43.478 0.00 0.00 0.00 4.00
2468 2653 4.201783 CGTCTGGTTTATTTTCGTCCCATC 60.202 45.833 0.00 0.00 0.00 3.51
2469 2654 4.941873 GTCTGGTTTATTTTCGTCCCATCT 59.058 41.667 0.00 0.00 0.00 2.90
2470 2655 5.064834 GTCTGGTTTATTTTCGTCCCATCTC 59.935 44.000 0.00 0.00 0.00 2.75
2471 2656 4.266714 TGGTTTATTTTCGTCCCATCTCC 58.733 43.478 0.00 0.00 0.00 3.71
2472 2657 3.630769 GGTTTATTTTCGTCCCATCTCCC 59.369 47.826 0.00 0.00 0.00 4.30
2473 2658 4.266714 GTTTATTTTCGTCCCATCTCCCA 58.733 43.478 0.00 0.00 0.00 4.37
2474 2659 2.420058 ATTTTCGTCCCATCTCCCAC 57.580 50.000 0.00 0.00 0.00 4.61
2475 2660 0.326927 TTTTCGTCCCATCTCCCACC 59.673 55.000 0.00 0.00 0.00 4.61
2476 2661 1.895020 TTTCGTCCCATCTCCCACCG 61.895 60.000 0.00 0.00 0.00 4.94
2477 2662 3.075005 CGTCCCATCTCCCACCGT 61.075 66.667 0.00 0.00 0.00 4.83
2478 2663 2.901042 GTCCCATCTCCCACCGTC 59.099 66.667 0.00 0.00 0.00 4.79
2479 2664 1.987855 GTCCCATCTCCCACCGTCA 60.988 63.158 0.00 0.00 0.00 4.35
2480 2665 1.002921 TCCCATCTCCCACCGTCAT 59.997 57.895 0.00 0.00 0.00 3.06
2481 2666 1.146930 CCCATCTCCCACCGTCATG 59.853 63.158 0.00 0.00 0.00 3.07
2482 2667 1.626356 CCCATCTCCCACCGTCATGT 61.626 60.000 0.00 0.00 0.00 3.21
2483 2668 0.179073 CCATCTCCCACCGTCATGTC 60.179 60.000 0.00 0.00 0.00 3.06
2484 2669 0.179073 CATCTCCCACCGTCATGTCC 60.179 60.000 0.00 0.00 0.00 4.02
2485 2670 0.325671 ATCTCCCACCGTCATGTCCT 60.326 55.000 0.00 0.00 0.00 3.85
2486 2671 0.970937 TCTCCCACCGTCATGTCCTC 60.971 60.000 0.00 0.00 0.00 3.71
2487 2672 1.229051 TCCCACCGTCATGTCCTCA 60.229 57.895 0.00 0.00 0.00 3.86
2488 2673 0.617535 TCCCACCGTCATGTCCTCAT 60.618 55.000 0.00 0.00 34.21 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 75 9.293404 TCTATCTATGTATGCCGTAGTAGTTTT 57.707 33.333 0.00 0.00 34.73 2.43
352 366 2.194212 GGAGGACGAGCGAGCCATA 61.194 63.158 0.00 0.00 0.00 2.74
504 518 1.078426 GCGTGGCACTTGGATAGGT 60.078 57.895 16.72 0.00 0.00 3.08
713 727 3.916392 CTCGTCGCTTCGCCACCTT 62.916 63.158 0.00 0.00 0.00 3.50
727 741 3.382832 CTCCCCTCGCAACCTCGT 61.383 66.667 0.00 0.00 0.00 4.18
750 772 3.663176 GCGCACACACACAGCCAT 61.663 61.111 0.30 0.00 0.00 4.40
833 875 2.665185 GCACGCGTGGGAGAAAGT 60.665 61.111 37.47 0.00 0.00 2.66
930 974 4.693915 TCAGGGTTGGGGGAGGGG 62.694 72.222 0.00 0.00 0.00 4.79
931 975 3.017581 CTCAGGGTTGGGGGAGGG 61.018 72.222 0.00 0.00 0.00 4.30
932 976 3.017581 CCTCAGGGTTGGGGGAGG 61.018 72.222 0.00 0.00 41.66 4.30
933 977 3.732849 GCCTCAGGGTTGGGGGAG 61.733 72.222 0.00 0.00 45.84 4.30
934 978 4.608514 TGCCTCAGGGTTGGGGGA 62.609 66.667 0.00 0.00 45.84 4.81
935 979 4.052518 CTGCCTCAGGGTTGGGGG 62.053 72.222 0.00 0.00 45.84 5.40
937 981 0.895559 GTTTCTGCCTCAGGGTTGGG 60.896 60.000 0.00 0.00 34.45 4.12
938 982 0.895559 GGTTTCTGCCTCAGGGTTGG 60.896 60.000 0.00 0.00 34.45 3.77
939 983 0.111253 AGGTTTCTGCCTCAGGGTTG 59.889 55.000 0.00 0.00 32.39 3.77
940 984 2.556849 AGGTTTCTGCCTCAGGGTT 58.443 52.632 0.00 0.00 32.39 4.11
941 985 4.339335 AGGTTTCTGCCTCAGGGT 57.661 55.556 0.00 0.00 32.39 4.34
949 993 0.315251 GTTTGGGCTGAGGTTTCTGC 59.685 55.000 0.00 0.00 44.75 4.26
950 994 0.961753 GGTTTGGGCTGAGGTTTCTG 59.038 55.000 0.00 0.00 0.00 3.02
951 995 0.555769 TGGTTTGGGCTGAGGTTTCT 59.444 50.000 0.00 0.00 0.00 2.52
952 996 0.961753 CTGGTTTGGGCTGAGGTTTC 59.038 55.000 0.00 0.00 0.00 2.78
982 1026 2.175499 CCATGGCTTTGAGGATTAGGGA 59.825 50.000 0.00 0.00 0.00 4.20
1538 1649 5.734720 AGCTGCAACATTAAAGAGTAGCTA 58.265 37.500 14.55 0.00 37.23 3.32
1539 1650 4.583871 AGCTGCAACATTAAAGAGTAGCT 58.416 39.130 1.02 11.93 34.45 3.32
1574 1703 7.224753 CCTCGTACACACAATAGATATTTGCTT 59.775 37.037 0.00 0.00 0.00 3.91
1577 1706 8.328146 CAACCTCGTACACACAATAGATATTTG 58.672 37.037 0.00 0.00 0.00 2.32
1579 1708 7.553334 ACAACCTCGTACACACAATAGATATT 58.447 34.615 0.00 0.00 0.00 1.28
1580 1709 7.108841 ACAACCTCGTACACACAATAGATAT 57.891 36.000 0.00 0.00 0.00 1.63
1595 1729 0.964358 CCTCTCCGGTACAACCTCGT 60.964 60.000 0.00 0.00 35.66 4.18
1598 1732 0.113776 TCACCTCTCCGGTACAACCT 59.886 55.000 0.00 0.00 46.94 3.50
1599 1733 1.192428 ATCACCTCTCCGGTACAACC 58.808 55.000 0.00 0.00 46.94 3.77
1600 1734 3.329929 AAATCACCTCTCCGGTACAAC 57.670 47.619 0.00 0.00 46.94 3.32
1601 1735 4.360951 AAAAATCACCTCTCCGGTACAA 57.639 40.909 0.00 0.00 46.94 2.41
1602 1736 4.081309 CCTAAAAATCACCTCTCCGGTACA 60.081 45.833 0.00 0.00 46.94 2.90
1603 1737 4.161001 TCCTAAAAATCACCTCTCCGGTAC 59.839 45.833 0.00 0.00 46.94 3.34
1604 1738 4.161001 GTCCTAAAAATCACCTCTCCGGTA 59.839 45.833 0.00 0.00 46.94 4.02
1606 1740 3.532542 GTCCTAAAAATCACCTCTCCGG 58.467 50.000 0.00 0.00 39.35 5.14
1607 1741 3.055385 TGGTCCTAAAAATCACCTCTCCG 60.055 47.826 0.00 0.00 0.00 4.63
1608 1742 4.569719 TGGTCCTAAAAATCACCTCTCC 57.430 45.455 0.00 0.00 0.00 3.71
1609 1743 4.884164 CCATGGTCCTAAAAATCACCTCTC 59.116 45.833 2.57 0.00 0.00 3.20
1610 1744 4.292306 ACCATGGTCCTAAAAATCACCTCT 59.708 41.667 13.00 0.00 0.00 3.69
1611 1745 4.600062 ACCATGGTCCTAAAAATCACCTC 58.400 43.478 13.00 0.00 0.00 3.85
1612 1746 4.675063 ACCATGGTCCTAAAAATCACCT 57.325 40.909 13.00 0.00 0.00 4.00
1613 1747 4.770010 TGAACCATGGTCCTAAAAATCACC 59.230 41.667 20.07 0.00 0.00 4.02
1614 1748 5.975693 TGAACCATGGTCCTAAAAATCAC 57.024 39.130 20.07 0.00 0.00 3.06
1615 1749 5.245075 GGTTGAACCATGGTCCTAAAAATCA 59.755 40.000 20.07 12.70 38.42 2.57
1616 1750 5.621329 CGGTTGAACCATGGTCCTAAAAATC 60.621 44.000 20.07 9.96 38.47 2.17
1617 1751 4.219725 CGGTTGAACCATGGTCCTAAAAAT 59.780 41.667 20.07 0.00 38.47 1.82
1618 1752 3.570550 CGGTTGAACCATGGTCCTAAAAA 59.429 43.478 20.07 3.91 38.47 1.94
1619 1753 3.150767 CGGTTGAACCATGGTCCTAAAA 58.849 45.455 20.07 5.74 38.47 1.52
1620 1754 2.372504 TCGGTTGAACCATGGTCCTAAA 59.627 45.455 20.07 7.60 38.47 1.85
1621 1755 1.979308 TCGGTTGAACCATGGTCCTAA 59.021 47.619 20.07 10.92 38.47 2.69
1622 1756 1.646912 TCGGTTGAACCATGGTCCTA 58.353 50.000 20.07 0.00 38.47 2.94
1623 1757 0.768622 TTCGGTTGAACCATGGTCCT 59.231 50.000 20.07 2.47 38.47 3.85
1624 1758 1.743394 GATTCGGTTGAACCATGGTCC 59.257 52.381 20.07 14.14 38.47 4.46
1625 1759 2.711542 AGATTCGGTTGAACCATGGTC 58.288 47.619 20.07 12.36 38.47 4.02
1626 1760 2.879103 AGATTCGGTTGAACCATGGT 57.121 45.000 13.00 13.00 38.47 3.55
1627 1761 3.565482 CCATAGATTCGGTTGAACCATGG 59.435 47.826 15.58 11.19 38.47 3.66
1628 1762 4.273480 GTCCATAGATTCGGTTGAACCATG 59.727 45.833 15.58 8.92 38.47 3.66
1629 1763 4.451900 GTCCATAGATTCGGTTGAACCAT 58.548 43.478 15.58 0.50 38.47 3.55
1630 1764 3.370103 GGTCCATAGATTCGGTTGAACCA 60.370 47.826 15.58 0.00 38.47 3.67
1631 1765 3.203716 GGTCCATAGATTCGGTTGAACC 58.796 50.000 3.76 3.76 36.81 3.62
1632 1766 3.869065 TGGTCCATAGATTCGGTTGAAC 58.131 45.455 0.00 0.00 36.81 3.18
1633 1767 4.450976 CATGGTCCATAGATTCGGTTGAA 58.549 43.478 3.38 0.00 38.76 2.69
1634 1768 3.181455 CCATGGTCCATAGATTCGGTTGA 60.181 47.826 3.38 0.00 0.00 3.18
1635 1769 3.141398 CCATGGTCCATAGATTCGGTTG 58.859 50.000 3.38 0.00 0.00 3.77
1636 1770 2.777692 ACCATGGTCCATAGATTCGGTT 59.222 45.455 13.00 0.00 0.00 4.44
1637 1771 2.368875 GACCATGGTCCATAGATTCGGT 59.631 50.000 31.37 6.52 39.08 4.69
1638 1772 3.045601 GACCATGGTCCATAGATTCGG 57.954 52.381 31.37 3.00 39.08 4.30
1649 1783 2.799126 TGTTGTATGGGACCATGGTC 57.201 50.000 33.14 33.14 43.87 4.02
1650 1784 3.269381 AGAATGTTGTATGGGACCATGGT 59.731 43.478 19.89 19.89 37.82 3.55
1651 1785 3.902218 AGAATGTTGTATGGGACCATGG 58.098 45.455 11.19 11.19 37.82 3.66
1652 1786 4.098349 CCAAGAATGTTGTATGGGACCATG 59.902 45.833 13.97 0.00 37.82 3.66
1653 1787 4.280819 CCAAGAATGTTGTATGGGACCAT 58.719 43.478 9.11 9.11 40.19 3.55
1654 1788 3.696045 CCAAGAATGTTGTATGGGACCA 58.304 45.455 0.00 0.00 0.00 4.02
1674 1808 4.287186 ACGACTGACGATGGTACAACCC 62.287 54.545 6.52 0.00 44.39 4.11
1706 1840 9.502091 ACAGTAGTAGTTAAATTGCAAATCAGA 57.498 29.630 1.71 0.00 0.00 3.27
1834 2009 3.312828 CGATCGATGAAGGAATCTCACC 58.687 50.000 10.26 0.00 0.00 4.02
1928 2103 1.433064 CGTTGGTTGTTGCTGCAGT 59.567 52.632 16.64 0.00 0.00 4.40
1941 2116 4.137116 TCCATCAAGTATCTTCCGTTGG 57.863 45.455 0.00 0.00 0.00 3.77
1952 2128 8.267183 ACATCACATGAATAGTTCCATCAAGTA 58.733 33.333 0.00 0.00 0.00 2.24
2027 2209 5.533482 TCTCTCAAACTTTAGCAGTCACTC 58.467 41.667 0.00 0.00 32.94 3.51
2069 2252 2.446435 TGCCATATCTCGATCATCGGA 58.554 47.619 7.33 3.91 40.88 4.55
2079 2262 2.222027 CGGAGGGTTTTGCCATATCTC 58.778 52.381 0.00 0.00 39.65 2.75
2085 2268 2.203422 CCACGGAGGGTTTTGCCA 60.203 61.111 0.00 0.00 39.65 4.92
2097 2280 3.343941 TGTTTTCCTAGAATCCCACGG 57.656 47.619 0.00 0.00 0.00 4.94
2099 2282 4.016444 TGCATGTTTTCCTAGAATCCCAC 58.984 43.478 0.00 0.00 0.00 4.61
2146 2331 6.474140 TTACTTCAATATCGTCCCAGCTTA 57.526 37.500 0.00 0.00 0.00 3.09
2147 2332 3.914426 ACTTCAATATCGTCCCAGCTT 57.086 42.857 0.00 0.00 0.00 3.74
2148 2333 5.552870 ATTACTTCAATATCGTCCCAGCT 57.447 39.130 0.00 0.00 0.00 4.24
2149 2334 5.527582 ACAATTACTTCAATATCGTCCCAGC 59.472 40.000 0.00 0.00 0.00 4.85
2150 2335 7.926555 AGTACAATTACTTCAATATCGTCCCAG 59.073 37.037 0.00 0.00 34.66 4.45
2151 2336 7.788026 AGTACAATTACTTCAATATCGTCCCA 58.212 34.615 0.00 0.00 34.66 4.37
2152 2337 8.658499 AAGTACAATTACTTCAATATCGTCCC 57.342 34.615 0.00 0.00 43.91 4.46
2206 2391 7.768120 GGATCCATCACAACTAGATCAATATCC 59.232 40.741 6.95 0.00 36.00 2.59
2283 2468 2.362397 AGTATCAGTAGCATGACCACCG 59.638 50.000 0.00 0.00 30.46 4.94
2339 2524 8.426489 AGTAGAGATTACTCCTACTGTCTACAG 58.574 40.741 8.56 8.56 44.99 2.74
2340 2525 8.321621 AGTAGAGATTACTCCTACTGTCTACA 57.678 38.462 8.45 0.00 43.53 2.74
2341 2526 8.822652 GAGTAGAGATTACTCCTACTGTCTAC 57.177 42.308 12.70 6.47 43.53 2.59
2352 2537 8.911918 TCAGACATTAGGAGTAGAGATTACTC 57.088 38.462 5.91 5.91 42.28 2.59
2353 2538 8.499406 ACTCAGACATTAGGAGTAGAGATTACT 58.501 37.037 0.00 0.00 39.95 2.24
2354 2539 8.685838 ACTCAGACATTAGGAGTAGAGATTAC 57.314 38.462 0.00 0.00 39.95 1.89
2355 2540 9.126151 CAACTCAGACATTAGGAGTAGAGATTA 57.874 37.037 0.00 0.00 40.80 1.75
2356 2541 7.069331 CCAACTCAGACATTAGGAGTAGAGATT 59.931 40.741 0.00 0.00 40.80 2.40
2357 2542 6.549364 CCAACTCAGACATTAGGAGTAGAGAT 59.451 42.308 0.00 0.00 40.80 2.75
2358 2543 5.888724 CCAACTCAGACATTAGGAGTAGAGA 59.111 44.000 0.00 0.00 40.80 3.10
2359 2544 5.654650 ACCAACTCAGACATTAGGAGTAGAG 59.345 44.000 0.00 0.00 40.80 2.43
2360 2545 5.580998 ACCAACTCAGACATTAGGAGTAGA 58.419 41.667 0.00 0.00 40.80 2.59
2361 2546 5.923733 ACCAACTCAGACATTAGGAGTAG 57.076 43.478 0.00 0.00 40.80 2.57
2362 2547 5.778241 TCAACCAACTCAGACATTAGGAGTA 59.222 40.000 0.00 0.00 40.80 2.59
2363 2548 4.593206 TCAACCAACTCAGACATTAGGAGT 59.407 41.667 0.00 0.00 43.35 3.85
2364 2549 5.152623 TCAACCAACTCAGACATTAGGAG 57.847 43.478 0.00 0.00 34.85 3.69
2365 2550 5.560722 TTCAACCAACTCAGACATTAGGA 57.439 39.130 0.00 0.00 0.00 2.94
2366 2551 7.106239 ACTATTCAACCAACTCAGACATTAGG 58.894 38.462 0.00 0.00 0.00 2.69
2367 2552 9.653287 TTACTATTCAACCAACTCAGACATTAG 57.347 33.333 0.00 0.00 0.00 1.73
2368 2553 9.653287 CTTACTATTCAACCAACTCAGACATTA 57.347 33.333 0.00 0.00 0.00 1.90
2369 2554 7.607991 CCTTACTATTCAACCAACTCAGACATT 59.392 37.037 0.00 0.00 0.00 2.71
2370 2555 7.106239 CCTTACTATTCAACCAACTCAGACAT 58.894 38.462 0.00 0.00 0.00 3.06
2371 2556 6.042781 ACCTTACTATTCAACCAACTCAGACA 59.957 38.462 0.00 0.00 0.00 3.41
2372 2557 6.465084 ACCTTACTATTCAACCAACTCAGAC 58.535 40.000 0.00 0.00 0.00 3.51
2373 2558 6.681729 ACCTTACTATTCAACCAACTCAGA 57.318 37.500 0.00 0.00 0.00 3.27
2374 2559 8.842358 TTAACCTTACTATTCAACCAACTCAG 57.158 34.615 0.00 0.00 0.00 3.35
2375 2560 9.802039 AATTAACCTTACTATTCAACCAACTCA 57.198 29.630 0.00 0.00 0.00 3.41
2380 2565 9.287373 ACGAAAATTAACCTTACTATTCAACCA 57.713 29.630 0.00 0.00 0.00 3.67
2381 2566 9.764870 GACGAAAATTAACCTTACTATTCAACC 57.235 33.333 0.00 0.00 0.00 3.77
2382 2567 9.764870 GGACGAAAATTAACCTTACTATTCAAC 57.235 33.333 0.00 0.00 0.00 3.18
2383 2568 8.949177 GGGACGAAAATTAACCTTACTATTCAA 58.051 33.333 0.00 0.00 0.00 2.69
2384 2569 8.102047 TGGGACGAAAATTAACCTTACTATTCA 58.898 33.333 0.00 0.00 0.00 2.57
2385 2570 8.496707 TGGGACGAAAATTAACCTTACTATTC 57.503 34.615 0.00 0.00 0.00 1.75
2386 2571 9.117183 GATGGGACGAAAATTAACCTTACTATT 57.883 33.333 0.00 0.00 0.00 1.73
2387 2572 8.269317 TGATGGGACGAAAATTAACCTTACTAT 58.731 33.333 0.00 0.00 0.00 2.12
2388 2573 7.622713 TGATGGGACGAAAATTAACCTTACTA 58.377 34.615 0.00 0.00 0.00 1.82
2389 2574 6.478129 TGATGGGACGAAAATTAACCTTACT 58.522 36.000 0.00 0.00 0.00 2.24
2390 2575 6.746745 TGATGGGACGAAAATTAACCTTAC 57.253 37.500 0.00 0.00 0.00 2.34
2391 2576 7.948034 AATGATGGGACGAAAATTAACCTTA 57.052 32.000 0.00 0.00 0.00 2.69
2392 2577 6.850752 AATGATGGGACGAAAATTAACCTT 57.149 33.333 0.00 0.00 0.00 3.50
2393 2578 6.850752 AAATGATGGGACGAAAATTAACCT 57.149 33.333 0.00 0.00 0.00 3.50
2394 2579 7.093992 TGAAAATGATGGGACGAAAATTAACC 58.906 34.615 0.00 0.00 0.00 2.85
2395 2580 8.432359 GTTGAAAATGATGGGACGAAAATTAAC 58.568 33.333 0.00 0.00 0.00 2.01
2396 2581 7.600752 GGTTGAAAATGATGGGACGAAAATTAA 59.399 33.333 0.00 0.00 0.00 1.40
2397 2582 7.093992 GGTTGAAAATGATGGGACGAAAATTA 58.906 34.615 0.00 0.00 0.00 1.40
2398 2583 5.931724 GGTTGAAAATGATGGGACGAAAATT 59.068 36.000 0.00 0.00 0.00 1.82
2399 2584 5.478407 GGTTGAAAATGATGGGACGAAAAT 58.522 37.500 0.00 0.00 0.00 1.82
2400 2585 4.557695 CGGTTGAAAATGATGGGACGAAAA 60.558 41.667 0.00 0.00 0.00 2.29
2401 2586 3.057876 CGGTTGAAAATGATGGGACGAAA 60.058 43.478 0.00 0.00 0.00 3.46
2402 2587 2.486203 CGGTTGAAAATGATGGGACGAA 59.514 45.455 0.00 0.00 0.00 3.85
2403 2588 2.080693 CGGTTGAAAATGATGGGACGA 58.919 47.619 0.00 0.00 0.00 4.20
2404 2589 1.810151 ACGGTTGAAAATGATGGGACG 59.190 47.619 0.00 0.00 0.00 4.79
2405 2590 3.934457 AACGGTTGAAAATGATGGGAC 57.066 42.857 0.00 0.00 0.00 4.46
2406 2591 4.946478 AAAACGGTTGAAAATGATGGGA 57.054 36.364 0.00 0.00 0.00 4.37
2407 2592 7.411372 CGAAATAAAACGGTTGAAAATGATGGG 60.411 37.037 0.00 0.00 0.00 4.00
2408 2593 7.115663 ACGAAATAAAACGGTTGAAAATGATGG 59.884 33.333 0.00 0.00 0.00 3.51
2409 2594 8.002433 ACGAAATAAAACGGTTGAAAATGATG 57.998 30.769 0.00 0.00 0.00 3.07
2410 2595 8.484008 CAACGAAATAAAACGGTTGAAAATGAT 58.516 29.630 0.00 0.00 0.00 2.45
2411 2596 7.043325 CCAACGAAATAAAACGGTTGAAAATGA 60.043 33.333 0.00 0.00 0.00 2.57
2412 2597 7.060422 CCAACGAAATAAAACGGTTGAAAATG 58.940 34.615 0.00 0.00 0.00 2.32
2413 2598 6.757478 ACCAACGAAATAAAACGGTTGAAAAT 59.243 30.769 0.00 0.00 0.00 1.82
2414 2599 6.098017 ACCAACGAAATAAAACGGTTGAAAA 58.902 32.000 0.00 0.00 0.00 2.29
2415 2600 5.648572 ACCAACGAAATAAAACGGTTGAAA 58.351 33.333 0.00 0.00 0.00 2.69
2416 2601 5.246145 ACCAACGAAATAAAACGGTTGAA 57.754 34.783 0.00 0.00 0.00 2.69
2417 2602 4.897025 ACCAACGAAATAAAACGGTTGA 57.103 36.364 0.00 0.00 0.00 3.18
2418 2603 5.952698 AAACCAACGAAATAAAACGGTTG 57.047 34.783 0.00 0.00 0.00 3.77
2419 2604 6.812656 AGAAAAACCAACGAAATAAAACGGTT 59.187 30.769 0.00 0.00 0.00 4.44
2420 2605 6.331845 AGAAAAACCAACGAAATAAAACGGT 58.668 32.000 0.00 0.00 0.00 4.83
2421 2606 6.344390 CGAGAAAAACCAACGAAATAAAACGG 60.344 38.462 0.00 0.00 0.00 4.44
2422 2607 6.195060 ACGAGAAAAACCAACGAAATAAAACG 59.805 34.615 0.00 0.00 0.00 3.60
2423 2608 7.430211 AGACGAGAAAAACCAACGAAATAAAAC 59.570 33.333 0.00 0.00 0.00 2.43
2424 2609 7.429920 CAGACGAGAAAAACCAACGAAATAAAA 59.570 33.333 0.00 0.00 0.00 1.52
2425 2610 6.908284 CAGACGAGAAAAACCAACGAAATAAA 59.092 34.615 0.00 0.00 0.00 1.40
2426 2611 6.423862 CAGACGAGAAAAACCAACGAAATAA 58.576 36.000 0.00 0.00 0.00 1.40
2427 2612 5.049954 CCAGACGAGAAAAACCAACGAAATA 60.050 40.000 0.00 0.00 0.00 1.40
2428 2613 4.261031 CCAGACGAGAAAAACCAACGAAAT 60.261 41.667 0.00 0.00 0.00 2.17
2429 2614 3.064271 CCAGACGAGAAAAACCAACGAAA 59.936 43.478 0.00 0.00 0.00 3.46
2430 2615 2.610374 CCAGACGAGAAAAACCAACGAA 59.390 45.455 0.00 0.00 0.00 3.85
2431 2616 2.206750 CCAGACGAGAAAAACCAACGA 58.793 47.619 0.00 0.00 0.00 3.85
2432 2617 1.937899 ACCAGACGAGAAAAACCAACG 59.062 47.619 0.00 0.00 0.00 4.10
2433 2618 4.365899 AAACCAGACGAGAAAAACCAAC 57.634 40.909 0.00 0.00 0.00 3.77
2434 2619 6.702716 AATAAACCAGACGAGAAAAACCAA 57.297 33.333 0.00 0.00 0.00 3.67
2435 2620 6.702716 AAATAAACCAGACGAGAAAAACCA 57.297 33.333 0.00 0.00 0.00 3.67
2436 2621 6.358822 CGAAAATAAACCAGACGAGAAAAACC 59.641 38.462 0.00 0.00 0.00 3.27
2437 2622 6.908820 ACGAAAATAAACCAGACGAGAAAAAC 59.091 34.615 0.00 0.00 0.00 2.43
2438 2623 7.018635 ACGAAAATAAACCAGACGAGAAAAA 57.981 32.000 0.00 0.00 0.00 1.94
2439 2624 6.293027 GGACGAAAATAAACCAGACGAGAAAA 60.293 38.462 0.00 0.00 0.00 2.29
2440 2625 5.178067 GGACGAAAATAAACCAGACGAGAAA 59.822 40.000 0.00 0.00 0.00 2.52
2441 2626 4.687483 GGACGAAAATAAACCAGACGAGAA 59.313 41.667 0.00 0.00 0.00 2.87
2442 2627 4.240096 GGACGAAAATAAACCAGACGAGA 58.760 43.478 0.00 0.00 0.00 4.04
2443 2628 3.370061 GGGACGAAAATAAACCAGACGAG 59.630 47.826 0.00 0.00 0.00 4.18
2444 2629 3.244146 TGGGACGAAAATAAACCAGACGA 60.244 43.478 0.00 0.00 0.00 4.20
2445 2630 3.068560 TGGGACGAAAATAAACCAGACG 58.931 45.455 0.00 0.00 0.00 4.18
2446 2631 4.941873 AGATGGGACGAAAATAAACCAGAC 59.058 41.667 0.00 0.00 0.00 3.51
2447 2632 5.174037 AGATGGGACGAAAATAAACCAGA 57.826 39.130 0.00 0.00 0.00 3.86
2448 2633 4.335594 GGAGATGGGACGAAAATAAACCAG 59.664 45.833 0.00 0.00 0.00 4.00
2449 2634 4.266714 GGAGATGGGACGAAAATAAACCA 58.733 43.478 0.00 0.00 0.00 3.67
2450 2635 3.630769 GGGAGATGGGACGAAAATAAACC 59.369 47.826 0.00 0.00 0.00 3.27
2451 2636 4.095932 GTGGGAGATGGGACGAAAATAAAC 59.904 45.833 0.00 0.00 0.00 2.01
2452 2637 4.266714 GTGGGAGATGGGACGAAAATAAA 58.733 43.478 0.00 0.00 0.00 1.40
2453 2638 3.371166 GGTGGGAGATGGGACGAAAATAA 60.371 47.826 0.00 0.00 0.00 1.40
2454 2639 2.171870 GGTGGGAGATGGGACGAAAATA 59.828 50.000 0.00 0.00 0.00 1.40
2455 2640 1.064685 GGTGGGAGATGGGACGAAAAT 60.065 52.381 0.00 0.00 0.00 1.82
2456 2641 0.326927 GGTGGGAGATGGGACGAAAA 59.673 55.000 0.00 0.00 0.00 2.29
2457 2642 1.895020 CGGTGGGAGATGGGACGAAA 61.895 60.000 0.00 0.00 0.00 3.46
2458 2643 2.355986 CGGTGGGAGATGGGACGAA 61.356 63.158 0.00 0.00 0.00 3.85
2459 2644 2.758327 CGGTGGGAGATGGGACGA 60.758 66.667 0.00 0.00 0.00 4.20
2460 2645 3.075005 ACGGTGGGAGATGGGACG 61.075 66.667 0.00 0.00 0.00 4.79
2461 2646 1.338136 ATGACGGTGGGAGATGGGAC 61.338 60.000 0.00 0.00 0.00 4.46
2462 2647 1.002921 ATGACGGTGGGAGATGGGA 59.997 57.895 0.00 0.00 0.00 4.37
2463 2648 1.146930 CATGACGGTGGGAGATGGG 59.853 63.158 0.00 0.00 0.00 4.00
2464 2649 0.179073 GACATGACGGTGGGAGATGG 60.179 60.000 0.00 0.00 0.00 3.51
2465 2650 0.179073 GGACATGACGGTGGGAGATG 60.179 60.000 0.00 0.00 0.00 2.90
2466 2651 0.325671 AGGACATGACGGTGGGAGAT 60.326 55.000 0.00 0.00 0.00 2.75
2467 2652 0.970937 GAGGACATGACGGTGGGAGA 60.971 60.000 0.00 0.00 0.00 3.71
2468 2653 1.257750 TGAGGACATGACGGTGGGAG 61.258 60.000 0.00 0.00 0.00 4.30
2469 2654 0.617535 ATGAGGACATGACGGTGGGA 60.618 55.000 0.00 0.00 35.21 4.37
2470 2655 1.907739 ATGAGGACATGACGGTGGG 59.092 57.895 0.00 0.00 35.21 4.61


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

AutoCloner maintained by Alex Coulton.