Multiple sequence alignment - TraesCS6A01G343200

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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 TraesCS6A01G343200 chr6A 100.000 4175 0 0 1 4175 577077955 577073781 0.000000e+00 7710
1 TraesCS6A01G343200 chr6D 83.106 2498 253 81 1661 4083 430532430 430530027 0.000000e+00 2119
2 TraesCS6A01G343200 chr6D 92.282 907 51 10 1 898 430534006 430533110 0.000000e+00 1269
3 TraesCS6A01G343200 chr6D 90.219 777 60 5 896 1670 430533080 430532318 0.000000e+00 1000
4 TraesCS6A01G343200 chr6D 82.538 922 125 19 2257 3163 430415975 430415075 0.000000e+00 778
5 TraesCS6A01G343200 chr6D 93.713 509 25 7 3670 4175 430414063 430413559 0.000000e+00 756
6 TraesCS6A01G343200 chr6D 77.619 210 23 12 3322 3515 430415034 430414833 5.710000e-19 106
7 TraesCS6A01G343200 chr6B 90.394 989 71 13 1630 2602 648859172 648858192 0.000000e+00 1279
8 TraesCS6A01G343200 chr6B 90.394 989 71 13 1630 2602 648894976 648893996 0.000000e+00 1279
9 TraesCS6A01G343200 chr6B 91.713 905 52 16 1 896 648860718 648859828 0.000000e+00 1234
10 TraesCS6A01G343200 chr6B 91.713 905 52 16 1 896 648896522 648895632 0.000000e+00 1234
11 TraesCS6A01G343200 chr6B 92.949 780 30 5 896 1670 648859788 648859029 0.000000e+00 1112
12 TraesCS6A01G343200 chr6B 92.949 780 30 5 896 1670 648895592 648894833 0.000000e+00 1112
13 TraesCS6A01G343200 chr6B 90.874 515 33 8 2660 3164 648858191 648857681 0.000000e+00 678
14 TraesCS6A01G343200 chr6B 90.874 515 33 8 2660 3164 648893995 648893485 0.000000e+00 678
15 TraesCS6A01G343200 chr6B 93.269 208 9 3 3973 4175 648784578 648784371 6.780000e-78 302
16 TraesCS6A01G343200 chr6B 81.481 162 21 5 3360 3515 648857587 648857429 1.580000e-24 124
17 TraesCS6A01G343200 chr6B 81.481 162 21 5 3360 3515 648893391 648893233 1.580000e-24 124
18 TraesCS6A01G343200 chr1B 84.970 825 107 13 1 819 635881109 635881922 0.000000e+00 821
19 TraesCS6A01G343200 chr1B 84.091 836 117 14 1 831 635160480 635161304 0.000000e+00 793
20 TraesCS6A01G343200 chr1B 83.871 837 117 16 1 831 634991314 634992138 0.000000e+00 782
21 TraesCS6A01G343200 chr4A 83.314 845 106 22 1 836 548346081 548345263 0.000000e+00 747
22 TraesCS6A01G343200 chr3B 82.472 793 123 13 46 833 729725845 729726626 0.000000e+00 680
23 TraesCS6A01G343200 chr2D 81.375 800 127 20 46 840 209119082 209118300 2.120000e-177 632
24 TraesCS6A01G343200 chrUn 93.269 208 9 3 3973 4175 362855093 362854886 6.780000e-78 302


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 TraesCS6A01G343200 chr6A 577073781 577077955 4174 True 7710.000000 7710 100.000000 1 4175 1 chr6A.!!$R1 4174
1 TraesCS6A01G343200 chr6D 430530027 430534006 3979 True 1462.666667 2119 88.535667 1 4083 3 chr6D.!!$R2 4082
2 TraesCS6A01G343200 chr6D 430413559 430415975 2416 True 546.666667 778 84.623333 2257 4175 3 chr6D.!!$R1 1918
3 TraesCS6A01G343200 chr6B 648857429 648860718 3289 True 885.400000 1279 89.482200 1 3515 5 chr6B.!!$R2 3514
4 TraesCS6A01G343200 chr6B 648893233 648896522 3289 True 885.400000 1279 89.482200 1 3515 5 chr6B.!!$R3 3514
5 TraesCS6A01G343200 chr1B 635881109 635881922 813 False 821.000000 821 84.970000 1 819 1 chr1B.!!$F3 818
6 TraesCS6A01G343200 chr1B 635160480 635161304 824 False 793.000000 793 84.091000 1 831 1 chr1B.!!$F2 830
7 TraesCS6A01G343200 chr1B 634991314 634992138 824 False 782.000000 782 83.871000 1 831 1 chr1B.!!$F1 830
8 TraesCS6A01G343200 chr4A 548345263 548346081 818 True 747.000000 747 83.314000 1 836 1 chr4A.!!$R1 835
9 TraesCS6A01G343200 chr3B 729725845 729726626 781 False 680.000000 680 82.472000 46 833 1 chr3B.!!$F1 787
10 TraesCS6A01G343200 chr2D 209118300 209119082 782 True 632.000000 632 81.375000 46 840 1 chr2D.!!$R1 794

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
995 1062 1.012086 CTGCCATCCACTGAATGACG 58.988 55.0 0.0 0.0 0.0 4.35 F
1710 1782 0.031585 TGCACGTAGACAAGCTCGTT 59.968 50.0 0.0 0.0 34.3 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2203 2281 0.250901 GAAAGAACTGCTGGGGCTGA 60.251 55.0 0.0 0.0 40.03 4.26 R
3538 4110 0.031857 TTTTGGACATGCCGCAACAG 59.968 50.0 0.0 0.0 40.66 3.16 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
62 63 8.650490 ACCCAAATATGAAACTGAAAAGTCAAT 58.350 29.630 0.00 0.00 31.88 2.57
283 288 9.887406 GTAATGGTTTATTTCGAAAGAGTGAAA 57.113 29.630 16.80 8.29 43.69 2.69
346 353 1.620822 GTGAAACAAGCCAGTGGGAT 58.379 50.000 12.15 0.00 36.32 3.85
707 725 9.760660 GTCTTTGTGACATGAGTTCAAATATAC 57.239 33.333 0.00 2.20 44.73 1.47
809 829 4.039124 GCATTTGTTTGGGAGAGAGGAAAA 59.961 41.667 0.00 0.00 0.00 2.29
979 1046 2.094597 TGCAGTGCAACCAAATATCTGC 60.095 45.455 17.26 11.88 44.39 4.26
995 1062 1.012086 CTGCCATCCACTGAATGACG 58.988 55.000 0.00 0.00 0.00 4.35
1000 1067 2.485302 CCATCCACTGAATGACGGCATA 60.485 50.000 2.90 0.00 33.44 3.14
1001 1068 3.405831 CATCCACTGAATGACGGCATAT 58.594 45.455 2.90 0.00 33.44 1.78
1025 1095 4.475345 CCCTACCTAGTAATCAGTCTGCT 58.525 47.826 0.00 0.00 0.00 4.24
1033 1103 4.499183 AGTAATCAGTCTGCTCGGAAAAG 58.501 43.478 0.00 0.00 0.00 2.27
1035 1105 3.685139 ATCAGTCTGCTCGGAAAAGAA 57.315 42.857 0.00 0.00 0.00 2.52
1039 1109 3.312421 CAGTCTGCTCGGAAAAGAAAACA 59.688 43.478 0.00 0.00 0.00 2.83
1040 1110 3.312697 AGTCTGCTCGGAAAAGAAAACAC 59.687 43.478 0.00 0.00 0.00 3.32
1041 1111 3.064820 GTCTGCTCGGAAAAGAAAACACA 59.935 43.478 0.00 0.00 0.00 3.72
1042 1112 3.692101 TCTGCTCGGAAAAGAAAACACAA 59.308 39.130 0.00 0.00 0.00 3.33
1043 1113 3.765026 TGCTCGGAAAAGAAAACACAAC 58.235 40.909 0.00 0.00 0.00 3.32
1044 1114 3.113322 GCTCGGAAAAGAAAACACAACC 58.887 45.455 0.00 0.00 0.00 3.77
1085 1155 2.697425 CGACCGAATGAAGCGCAG 59.303 61.111 11.47 0.00 0.00 5.18
1104 1174 3.449042 CGTGAGGCGTTCGACTTC 58.551 61.111 1.15 0.00 35.54 3.01
1105 1175 1.371267 CGTGAGGCGTTCGACTTCA 60.371 57.895 1.15 0.00 35.54 3.02
1106 1176 0.937699 CGTGAGGCGTTCGACTTCAA 60.938 55.000 1.15 0.00 35.54 2.69
1107 1177 0.507358 GTGAGGCGTTCGACTTCAAC 59.493 55.000 1.15 0.00 0.00 3.18
1153 1223 0.516877 CAAGATGTGCGGCGAAGAAA 59.483 50.000 12.98 0.00 0.00 2.52
1283 1355 1.966451 CGGCGCCTTCTTCCTTGTT 60.966 57.895 26.68 0.00 0.00 2.83
1384 1456 2.282958 ACGACGGCAAGAGGAGGA 60.283 61.111 0.00 0.00 0.00 3.71
1487 1559 2.890847 CTAGCGGCAGAACTGTCCGG 62.891 65.000 25.61 0.00 44.45 5.14
1555 1627 1.544691 AGATCGAGGTAAACGTGTGCT 59.455 47.619 0.00 0.00 0.00 4.40
1660 1732 1.300971 TGGCAGCAAGATCGTTGAGC 61.301 55.000 8.52 9.94 0.00 4.26
1662 1734 0.731417 GCAGCAAGATCGTTGAGCAT 59.269 50.000 8.52 0.00 0.00 3.79
1667 1739 2.674852 GCAAGATCGTTGAGCATGAAGA 59.325 45.455 0.00 0.00 0.00 2.87
1669 1741 2.534298 AGATCGTTGAGCATGAAGACG 58.466 47.619 0.00 0.72 35.24 4.18
1670 1742 1.002366 ATCGTTGAGCATGAAGACGC 58.998 50.000 0.00 0.00 34.04 5.19
1671 1743 0.319469 TCGTTGAGCATGAAGACGCA 60.319 50.000 0.00 0.00 34.04 5.24
1672 1744 0.094216 CGTTGAGCATGAAGACGCAG 59.906 55.000 0.00 0.00 0.00 5.18
1673 1745 0.179205 GTTGAGCATGAAGACGCAGC 60.179 55.000 0.00 0.00 0.00 5.25
1674 1746 1.300971 TTGAGCATGAAGACGCAGCC 61.301 55.000 0.00 0.00 0.00 4.85
1675 1747 2.437359 AGCATGAAGACGCAGCCC 60.437 61.111 0.00 0.00 0.00 5.19
1676 1748 2.437359 GCATGAAGACGCAGCCCT 60.437 61.111 0.00 0.00 0.00 5.19
1677 1749 2.758089 GCATGAAGACGCAGCCCTG 61.758 63.158 0.00 0.00 0.00 4.45
1678 1750 1.376424 CATGAAGACGCAGCCCTGT 60.376 57.895 0.00 0.00 0.00 4.00
1679 1751 0.957395 CATGAAGACGCAGCCCTGTT 60.957 55.000 0.00 0.00 0.00 3.16
1680 1752 0.674895 ATGAAGACGCAGCCCTGTTC 60.675 55.000 0.00 0.00 0.00 3.18
1681 1753 2.357517 AAGACGCAGCCCTGTTCG 60.358 61.111 0.00 0.00 0.00 3.95
1682 1754 2.765250 GAAGACGCAGCCCTGTTCGA 62.765 60.000 3.03 0.00 0.00 3.71
1683 1755 2.771763 AAGACGCAGCCCTGTTCGAG 62.772 60.000 3.03 0.00 0.00 4.04
1685 1757 4.749310 CGCAGCCCTGTTCGAGCT 62.749 66.667 0.00 0.00 37.32 4.09
1686 1758 2.579201 GCAGCCCTGTTCGAGCTA 59.421 61.111 0.00 0.00 34.38 3.32
1687 1759 1.079127 GCAGCCCTGTTCGAGCTAA 60.079 57.895 0.00 0.00 34.38 3.09
1688 1760 0.673644 GCAGCCCTGTTCGAGCTAAA 60.674 55.000 0.00 0.00 34.38 1.85
1689 1761 1.363744 CAGCCCTGTTCGAGCTAAAG 58.636 55.000 0.00 0.00 34.38 1.85
1690 1762 0.250513 AGCCCTGTTCGAGCTAAAGG 59.749 55.000 0.00 0.00 34.38 3.11
1691 1763 0.036294 GCCCTGTTCGAGCTAAAGGT 60.036 55.000 0.00 0.00 0.00 3.50
1692 1764 1.726853 CCCTGTTCGAGCTAAAGGTG 58.273 55.000 0.00 0.00 0.00 4.00
1693 1765 1.079503 CCTGTTCGAGCTAAAGGTGC 58.920 55.000 0.00 0.00 0.00 5.01
1694 1766 1.608025 CCTGTTCGAGCTAAAGGTGCA 60.608 52.381 0.00 0.00 0.00 4.57
1695 1767 1.461127 CTGTTCGAGCTAAAGGTGCAC 59.539 52.381 8.80 8.80 0.00 4.57
1696 1768 0.438830 GTTCGAGCTAAAGGTGCACG 59.561 55.000 11.45 0.00 43.65 5.34
1697 1769 0.032952 TTCGAGCTAAAGGTGCACGT 59.967 50.000 11.45 8.83 43.03 4.49
1698 1770 0.883153 TCGAGCTAAAGGTGCACGTA 59.117 50.000 13.22 2.99 43.03 3.57
1699 1771 1.135489 TCGAGCTAAAGGTGCACGTAG 60.135 52.381 13.22 13.48 43.03 3.51
1700 1772 1.135489 CGAGCTAAAGGTGCACGTAGA 60.135 52.381 13.22 2.86 39.08 2.59
1701 1773 2.260481 GAGCTAAAGGTGCACGTAGAC 58.740 52.381 13.22 9.10 0.00 2.59
1702 1774 1.616865 AGCTAAAGGTGCACGTAGACA 59.383 47.619 13.22 0.00 0.00 3.41
1703 1775 2.036733 AGCTAAAGGTGCACGTAGACAA 59.963 45.455 13.22 0.00 0.00 3.18
1704 1776 2.412089 GCTAAAGGTGCACGTAGACAAG 59.588 50.000 13.22 7.21 0.00 3.16
1705 1777 1.226746 AAAGGTGCACGTAGACAAGC 58.773 50.000 13.22 0.00 0.00 4.01
1706 1778 0.393077 AAGGTGCACGTAGACAAGCT 59.607 50.000 13.22 0.00 0.00 3.74
1707 1779 0.038159 AGGTGCACGTAGACAAGCTC 60.038 55.000 10.95 0.00 0.00 4.09
1708 1780 1.344942 GGTGCACGTAGACAAGCTCG 61.345 60.000 11.45 0.00 0.00 5.03
1709 1781 0.663568 GTGCACGTAGACAAGCTCGT 60.664 55.000 0.00 0.00 36.99 4.18
1710 1782 0.031585 TGCACGTAGACAAGCTCGTT 59.968 50.000 0.00 0.00 34.30 3.85
1711 1783 1.267533 TGCACGTAGACAAGCTCGTTA 59.732 47.619 0.00 0.00 34.30 3.18
1712 1784 2.287728 TGCACGTAGACAAGCTCGTTAA 60.288 45.455 0.00 0.00 34.30 2.01
1713 1785 2.727798 GCACGTAGACAAGCTCGTTAAA 59.272 45.455 0.00 0.00 34.30 1.52
1714 1786 3.182972 GCACGTAGACAAGCTCGTTAAAA 59.817 43.478 0.00 0.00 34.30 1.52
1715 1787 4.685020 CACGTAGACAAGCTCGTTAAAAC 58.315 43.478 0.00 0.00 34.30 2.43
1732 1804 2.638154 CGAGGGATCCGTCGCTAC 59.362 66.667 35.73 11.33 46.45 3.58
1733 1805 2.905807 CGAGGGATCCGTCGCTACC 61.906 68.421 35.73 10.65 46.45 3.18
1734 1806 2.521224 AGGGATCCGTCGCTACCC 60.521 66.667 5.45 9.72 44.86 3.69
1735 1807 3.613689 GGGATCCGTCGCTACCCC 61.614 72.222 5.45 0.00 35.00 4.95
1736 1808 3.613689 GGATCCGTCGCTACCCCC 61.614 72.222 0.00 0.00 0.00 5.40
1737 1809 2.521224 GATCCGTCGCTACCCCCT 60.521 66.667 0.00 0.00 0.00 4.79
1738 1810 2.521224 ATCCGTCGCTACCCCCTC 60.521 66.667 0.00 0.00 0.00 4.30
1739 1811 3.369410 ATCCGTCGCTACCCCCTCA 62.369 63.158 0.00 0.00 0.00 3.86
1740 1812 2.866523 ATCCGTCGCTACCCCCTCAA 62.867 60.000 0.00 0.00 0.00 3.02
1741 1813 2.494918 CGTCGCTACCCCCTCAAG 59.505 66.667 0.00 0.00 0.00 3.02
1742 1814 2.050350 CGTCGCTACCCCCTCAAGA 61.050 63.158 0.00 0.00 0.00 3.02
1743 1815 1.392710 CGTCGCTACCCCCTCAAGAT 61.393 60.000 0.00 0.00 0.00 2.40
1744 1816 0.105039 GTCGCTACCCCCTCAAGATG 59.895 60.000 0.00 0.00 0.00 2.90
1745 1817 0.032515 TCGCTACCCCCTCAAGATGA 60.033 55.000 0.00 0.00 0.00 2.92
1746 1818 0.105039 CGCTACCCCCTCAAGATGAC 59.895 60.000 0.00 0.00 0.00 3.06
1747 1819 0.105039 GCTACCCCCTCAAGATGACG 59.895 60.000 0.00 0.00 0.00 4.35
1748 1820 0.753262 CTACCCCCTCAAGATGACGG 59.247 60.000 0.00 0.00 0.00 4.79
1749 1821 1.335132 TACCCCCTCAAGATGACGGC 61.335 60.000 0.00 0.00 0.00 5.68
1750 1822 2.669133 CCCCCTCAAGATGACGGCA 61.669 63.158 0.00 0.00 0.00 5.69
1751 1823 1.299648 CCCCTCAAGATGACGGCAA 59.700 57.895 0.00 0.00 0.00 4.52
1752 1824 0.745845 CCCCTCAAGATGACGGCAAG 60.746 60.000 0.00 0.00 0.00 4.01
1753 1825 0.250234 CCCTCAAGATGACGGCAAGA 59.750 55.000 0.00 0.00 0.00 3.02
1754 1826 1.134280 CCCTCAAGATGACGGCAAGAT 60.134 52.381 0.00 0.00 0.00 2.40
1755 1827 1.938577 CCTCAAGATGACGGCAAGATG 59.061 52.381 0.00 0.00 0.00 2.90
1756 1828 1.938577 CTCAAGATGACGGCAAGATGG 59.061 52.381 0.00 0.00 0.00 3.51
1757 1829 1.278985 TCAAGATGACGGCAAGATGGT 59.721 47.619 0.00 0.00 0.00 3.55
1758 1830 2.086869 CAAGATGACGGCAAGATGGTT 58.913 47.619 0.00 0.00 0.00 3.67
1759 1831 1.742761 AGATGACGGCAAGATGGTTG 58.257 50.000 0.00 0.00 0.00 3.77
1760 1832 1.278985 AGATGACGGCAAGATGGTTGA 59.721 47.619 0.00 0.00 0.00 3.18
1761 1833 1.667724 GATGACGGCAAGATGGTTGAG 59.332 52.381 0.00 0.00 0.00 3.02
1762 1834 0.321564 TGACGGCAAGATGGTTGAGG 60.322 55.000 0.00 0.00 0.00 3.86
1822 1894 2.123208 TGTCTCCCGTGGTGACCA 60.123 61.111 0.00 0.00 43.18 4.02
1954 2026 1.734655 AAAGAGGGAGAAGGAGTGCA 58.265 50.000 0.00 0.00 0.00 4.57
1962 2034 1.880340 GAAGGAGTGCATCGCCGAG 60.880 63.158 0.00 0.00 40.97 4.63
1986 2058 2.959707 GGAGGATGATGAGGAGTACGTT 59.040 50.000 0.00 0.00 0.00 3.99
2028 2100 1.676014 CCGGTGGTGTTCCAGAATCTC 60.676 57.143 0.00 0.00 45.24 2.75
2029 2101 1.001974 CGGTGGTGTTCCAGAATCTCA 59.998 52.381 0.00 0.00 45.24 3.27
2030 2102 2.355108 CGGTGGTGTTCCAGAATCTCAT 60.355 50.000 0.00 0.00 45.24 2.90
2092 2164 4.085158 GCGATTCTGATTCTGATTCAGACG 60.085 45.833 24.30 23.97 46.92 4.18
2163 2241 1.153289 CCACTGCGATGAGAAGGGG 60.153 63.158 0.00 0.00 44.33 4.79
2203 2281 3.841255 AGTTCTTCCTAAGGTTAGCAGCT 59.159 43.478 0.00 0.00 0.00 4.24
2208 2289 1.474143 CCTAAGGTTAGCAGCTCAGCC 60.474 57.143 0.00 0.00 34.23 4.85
2233 2314 5.241506 CCAGCAGTTCTTTCCAAAGTGATTA 59.758 40.000 0.00 0.00 37.31 1.75
2303 2384 4.130118 GGAGAACTGAAGAAGCTTGACAA 58.870 43.478 2.10 0.00 0.00 3.18
2337 2418 1.923356 TTCTTCCCAAGGTGAATGGC 58.077 50.000 0.00 0.00 36.58 4.40
2395 2476 1.818642 ACAGAATGCAGAACCAGAGC 58.181 50.000 0.00 0.00 42.53 4.09
2460 2551 0.040058 ATTCTGCTGCCCAACCATCA 59.960 50.000 0.00 0.00 0.00 3.07
2496 2587 2.027469 GGTGGTACCTTTACAGAGTGGG 60.027 54.545 14.36 0.00 34.73 4.61
2517 2608 0.038744 AACCAGCAGGCAAGCATAGT 59.961 50.000 0.00 0.00 39.06 2.12
2531 2622 1.115930 CATAGTAGCCCAGCTCCGGT 61.116 60.000 0.00 0.00 40.44 5.28
2604 2695 3.840666 AGAATGCTGAACCAGAGAAGGTA 59.159 43.478 0.00 0.00 42.25 3.08
2610 2701 2.289694 TGAACCAGAGAAGGTAAGCAGC 60.290 50.000 0.00 0.00 42.25 5.25
2619 2710 2.202756 GTAAGCAGCCCGTCTCCG 60.203 66.667 0.00 0.00 0.00 4.63
2652 2746 2.624838 CAAAGTGGTTGATGGTTCTGCT 59.375 45.455 0.00 0.00 39.87 4.24
2711 2805 4.704540 TGGTTTTGAAACAGAGAAGCTTGA 59.295 37.500 2.10 0.00 40.63 3.02
2737 2831 3.392947 TCCAACTCCAACACCATCAGTTA 59.607 43.478 0.00 0.00 0.00 2.24
2785 2879 0.394192 CCTGCCATCATCGAAGCCTA 59.606 55.000 0.00 0.00 0.00 3.93
2788 2882 1.417517 TGCCATCATCGAAGCCTACAT 59.582 47.619 0.00 0.00 0.00 2.29
2794 2888 1.609072 CATCGAAGCCTACATCGGAGA 59.391 52.381 0.00 0.00 45.75 3.71
2928 3040 1.627297 GGGAGAAAGCCCGTCAGGAT 61.627 60.000 0.00 0.00 41.02 3.24
3001 3113 4.802051 TGGAGCGGCTTGGCATCC 62.802 66.667 2.97 0.00 34.64 3.51
3100 3212 0.820871 GAGGGCTGATGAAGACGACT 59.179 55.000 0.00 0.00 32.90 4.18
3119 3231 4.405671 TGGAGAGCAGCAGCAGCC 62.406 66.667 6.10 1.83 45.49 4.85
3165 3295 2.090494 CCTGGAGGAAGGGGAGATTCTA 60.090 54.545 0.00 0.00 37.39 2.10
3166 3296 2.969262 CTGGAGGAAGGGGAGATTCTAC 59.031 54.545 0.00 0.00 0.00 2.59
3167 3297 2.331166 GGAGGAAGGGGAGATTCTACC 58.669 57.143 6.36 6.36 32.58 3.18
3169 3299 1.291335 AGGAAGGGGAGATTCTACCGT 59.709 52.381 8.90 6.58 34.66 4.83
3170 3300 1.687660 GGAAGGGGAGATTCTACCGTC 59.312 57.143 10.55 11.28 34.66 4.79
3171 3301 1.337387 GAAGGGGAGATTCTACCGTCG 59.663 57.143 10.55 0.00 34.66 5.12
3189 3319 1.234615 CGTAGGGTTGTGGGCTTGTG 61.235 60.000 0.00 0.00 0.00 3.33
3191 3321 2.075355 TAGGGTTGTGGGCTTGTGGG 62.075 60.000 0.00 0.00 0.00 4.61
3192 3322 2.123468 GGTTGTGGGCTTGTGGGT 60.123 61.111 0.00 0.00 0.00 4.51
3193 3323 1.760480 GGTTGTGGGCTTGTGGGTT 60.760 57.895 0.00 0.00 0.00 4.11
3195 3325 0.755327 GTTGTGGGCTTGTGGGTTCT 60.755 55.000 0.00 0.00 0.00 3.01
3196 3326 0.754957 TTGTGGGCTTGTGGGTTCTG 60.755 55.000 0.00 0.00 0.00 3.02
3228 3358 2.756760 AGACATGCCGCATGAAGATTTT 59.243 40.909 34.59 14.31 43.81 1.82
3229 3359 3.947196 AGACATGCCGCATGAAGATTTTA 59.053 39.130 34.59 0.00 43.81 1.52
3236 3366 4.270808 GCCGCATGAAGATTTTATTTTGGG 59.729 41.667 0.00 0.00 0.00 4.12
3237 3367 4.810491 CCGCATGAAGATTTTATTTTGGGG 59.190 41.667 0.00 0.00 0.00 4.96
3238 3368 4.270808 CGCATGAAGATTTTATTTTGGGGC 59.729 41.667 0.00 0.00 0.00 5.80
3243 3373 8.829612 CATGAAGATTTTATTTTGGGGCAATAC 58.170 33.333 0.00 0.00 0.00 1.89
3244 3374 8.144862 TGAAGATTTTATTTTGGGGCAATACT 57.855 30.769 0.00 0.00 0.00 2.12
3245 3375 9.261035 TGAAGATTTTATTTTGGGGCAATACTA 57.739 29.630 0.00 0.00 0.00 1.82
3252 3386 9.660180 TTTATTTTGGGGCAATACTATCAAAAC 57.340 29.630 0.00 0.00 37.07 2.43
3258 3392 6.438741 TGGGGCAATACTATCAAAACAATTGA 59.561 34.615 13.59 0.00 0.00 2.57
3261 3395 7.363793 GGGCAATACTATCAAAACAATTGAGGT 60.364 37.037 13.59 0.00 0.00 3.85
3269 3403 9.533253 CTATCAAAACAATTGAGGTCTGTTTTT 57.467 29.630 13.59 3.01 46.05 1.94
3297 3431 7.504924 TTTTGACAAATTAATCGAGGTCTGT 57.495 32.000 0.50 0.00 0.00 3.41
3298 3432 7.504924 TTTGACAAATTAATCGAGGTCTGTT 57.495 32.000 0.00 0.00 0.00 3.16
3299 3433 7.504924 TTGACAAATTAATCGAGGTCTGTTT 57.495 32.000 0.00 0.00 0.00 2.83
3300 3434 7.504924 TGACAAATTAATCGAGGTCTGTTTT 57.495 32.000 0.00 0.00 0.00 2.43
3301 3435 8.610248 TGACAAATTAATCGAGGTCTGTTTTA 57.390 30.769 0.00 0.00 0.00 1.52
3302 3436 9.058174 TGACAAATTAATCGAGGTCTGTTTTAA 57.942 29.630 0.00 0.00 0.00 1.52
3303 3437 9.326339 GACAAATTAATCGAGGTCTGTTTTAAC 57.674 33.333 0.00 0.00 0.00 2.01
3304 3438 9.063615 ACAAATTAATCGAGGTCTGTTTTAACT 57.936 29.630 0.00 0.00 0.00 2.24
3308 3442 9.715121 ATTAATCGAGGTCTGTTTTAACTAACA 57.285 29.630 0.00 0.00 36.63 2.41
3309 3443 7.417496 AATCGAGGTCTGTTTTAACTAACAC 57.583 36.000 0.00 0.00 34.50 3.32
3319 3453 5.746245 TGTTTTAACTAACACATGCAACAGC 59.254 36.000 0.00 0.00 33.31 4.40
3320 3454 4.497473 TTAACTAACACATGCAACAGCC 57.503 40.909 0.00 0.00 0.00 4.85
3343 3483 2.093890 TGGCTAGCAAACCATGACATG 58.906 47.619 18.24 8.56 0.00 3.21
3354 3518 1.107945 CATGACATGGAGCATTGCCA 58.892 50.000 7.60 0.00 40.24 4.92
3356 3520 1.179152 TGACATGGAGCATTGCCAAG 58.821 50.000 4.70 0.00 39.21 3.61
3410 3585 9.279904 CAGTGACAAACGTTCTTTACAAAAATA 57.720 29.630 0.00 0.00 0.00 1.40
3436 3617 6.100004 TCCAGCTTCTCGTTTTCAAGTATAG 58.900 40.000 0.00 0.00 0.00 1.31
3445 3628 9.932207 TCTCGTTTTCAAGTATAGTTGGATTTA 57.068 29.630 18.17 0.00 0.00 1.40
3468 3651 4.100963 ACTTTCACATACGGCTGGATGATA 59.899 41.667 25.06 8.64 0.00 2.15
3500 3683 4.286297 TGAATTAGCACAACTAGGCTGT 57.714 40.909 0.00 0.00 41.25 4.40
3530 4102 5.643379 ACATGATTTAAAATCGCAGGTGT 57.357 34.783 0.00 0.00 0.00 4.16
3531 4103 5.401550 ACATGATTTAAAATCGCAGGTGTG 58.598 37.500 0.00 0.00 0.00 3.82
3532 4104 5.182950 ACATGATTTAAAATCGCAGGTGTGA 59.817 36.000 0.00 0.00 39.08 3.58
3533 4105 5.895636 TGATTTAAAATCGCAGGTGTGAT 57.104 34.783 0.00 0.00 46.20 3.06
3534 4106 5.639757 TGATTTAAAATCGCAGGTGTGATG 58.360 37.500 6.79 0.00 43.75 3.07
3535 4107 4.433186 TTTAAAATCGCAGGTGTGATGG 57.567 40.909 6.79 0.00 43.75 3.51
3536 4108 2.198827 AAAATCGCAGGTGTGATGGA 57.801 45.000 6.79 0.00 43.75 3.41
3537 4109 1.453155 AAATCGCAGGTGTGATGGAC 58.547 50.000 6.79 0.00 43.75 4.02
3538 4110 0.392998 AATCGCAGGTGTGATGGACC 60.393 55.000 6.79 0.00 43.75 4.46
3546 4118 1.302431 TGTGATGGACCTGTTGCGG 60.302 57.895 0.00 0.00 0.00 5.69
3553 4125 2.672996 ACCTGTTGCGGCATGTCC 60.673 61.111 2.28 0.00 0.00 4.02
3562 4134 0.243365 GCGGCATGTCCAAAATCACA 59.757 50.000 0.00 0.00 34.01 3.58
3567 4139 3.376859 GGCATGTCCAAAATCACACGATA 59.623 43.478 0.00 0.00 34.01 2.92
3570 4142 3.669536 TGTCCAAAATCACACGATAGCA 58.330 40.909 0.00 0.00 42.67 3.49
3575 4147 1.482621 AATCACACGATAGCAGCGCG 61.483 55.000 0.00 0.00 42.67 6.86
3583 4155 0.880278 GATAGCAGCGCGAAATCCCA 60.880 55.000 12.10 0.00 0.00 4.37
3584 4156 1.160329 ATAGCAGCGCGAAATCCCAC 61.160 55.000 12.10 0.00 0.00 4.61
3587 4159 1.578926 CAGCGCGAAATCCCACAAA 59.421 52.632 12.10 0.00 0.00 2.83
3588 4160 0.039617 CAGCGCGAAATCCCACAAAA 60.040 50.000 12.10 0.00 0.00 2.44
3590 4162 1.272212 AGCGCGAAATCCCACAAAATT 59.728 42.857 12.10 0.00 0.00 1.82
3591 4163 2.490115 AGCGCGAAATCCCACAAAATTA 59.510 40.909 12.10 0.00 0.00 1.40
3593 4165 3.672241 GCGCGAAATCCCACAAAATTAGT 60.672 43.478 12.10 0.00 0.00 2.24
3594 4166 3.851403 CGCGAAATCCCACAAAATTAGTG 59.149 43.478 0.00 4.43 36.76 2.74
3595 4167 3.612423 GCGAAATCCCACAAAATTAGTGC 59.388 43.478 5.63 0.00 35.69 4.40
3601 4173 8.601845 AAATCCCACAAAATTAGTGCTAAAAC 57.398 30.769 5.63 0.00 35.69 2.43
3602 4174 6.969993 TCCCACAAAATTAGTGCTAAAACT 57.030 33.333 5.63 0.00 35.69 2.66
3605 4177 7.232534 TCCCACAAAATTAGTGCTAAAACTCAT 59.767 33.333 5.63 0.00 35.69 2.90
3606 4178 7.329226 CCCACAAAATTAGTGCTAAAACTCATG 59.671 37.037 5.63 0.00 35.69 3.07
3607 4179 8.081633 CCACAAAATTAGTGCTAAAACTCATGA 58.918 33.333 0.00 0.00 35.69 3.07
3620 4192 9.736023 GCTAAAACTCATGATTTATGTTAAGGG 57.264 33.333 0.00 0.00 38.01 3.95
3625 4197 6.667414 ACTCATGATTTATGTTAAGGGCCAAA 59.333 34.615 6.18 0.00 38.01 3.28
3626 4198 7.345392 ACTCATGATTTATGTTAAGGGCCAAAT 59.655 33.333 6.18 0.13 38.01 2.32
3628 4200 7.986320 TCATGATTTATGTTAAGGGCCAAATTG 59.014 33.333 6.18 0.00 38.01 2.32
3760 4560 3.263425 ACAAAGAGATAGGGCGAAGGAAA 59.737 43.478 0.00 0.00 0.00 3.13
3785 4585 1.213926 GGGATCAAGAAGCCACTGGAT 59.786 52.381 0.00 0.00 33.74 3.41
3801 4601 2.905085 CTGGATATGGAGAGACTGGCAT 59.095 50.000 0.00 0.00 0.00 4.40
3858 4658 2.800544 CGACACTCATTTCTGAACCGTT 59.199 45.455 0.00 0.00 0.00 4.44
3893 4693 5.505173 ACCACAAGTGAAATCTGAAACTG 57.495 39.130 0.94 0.00 0.00 3.16
3917 4717 5.295787 GTGTCTAATGTCAGGTTGTTTGTCA 59.704 40.000 0.00 0.00 0.00 3.58
3928 4728 5.977129 CAGGTTGTTTGTCAAGTGTATTTCC 59.023 40.000 0.00 0.00 36.66 3.13
3962 4762 6.439636 AGGCTAATATGACCATTGCTAAGA 57.560 37.500 0.00 0.00 0.00 2.10
4047 4847 3.863681 GCACTCGGCAAACAATTCA 57.136 47.368 0.00 0.00 43.97 2.57
4138 4944 8.806146 TCTTCTCCTTTCCATTTTTATTTCCTG 58.194 33.333 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 9.658799 TGTTTCCAAATAAATCAGTTTCACAAA 57.341 25.926 0.00 0.00 0.00 2.83
166 168 7.120726 GGTACATTACACTTTTCACTGGCTTAT 59.879 37.037 0.00 0.00 0.00 1.73
167 169 6.428771 GGTACATTACACTTTTCACTGGCTTA 59.571 38.462 0.00 0.00 0.00 3.09
346 353 6.353323 TCACTTTCAGAACCTACATTTCACA 58.647 36.000 0.00 0.00 0.00 3.58
497 507 4.370364 TTTCACTTTTCACTGGCTTGTC 57.630 40.909 0.00 0.00 0.00 3.18
600 614 6.091169 CACATTTCACATATTTTGCCCACTTC 59.909 38.462 0.00 0.00 0.00 3.01
809 829 1.303309 GTATGCGCTGCCATTCTCTT 58.697 50.000 9.73 0.00 0.00 2.85
835 856 7.658261 TGCATCTCTACGCAGTTAGTATTAAT 58.342 34.615 0.00 0.00 37.78 1.40
836 857 7.034685 TGCATCTCTACGCAGTTAGTATTAA 57.965 36.000 0.00 0.00 37.78 1.40
837 858 6.628919 TGCATCTCTACGCAGTTAGTATTA 57.371 37.500 0.00 0.00 37.78 0.98
842 865 3.711086 ACATGCATCTCTACGCAGTTAG 58.289 45.455 0.00 0.00 37.78 2.34
898 929 7.094463 GGAGATCAATGGATATGAATCACCAAC 60.094 40.741 0.00 0.00 36.00 3.77
900 931 6.044637 TGGAGATCAATGGATATGAATCACCA 59.955 38.462 0.00 0.00 32.67 4.17
901 932 6.479006 TGGAGATCAATGGATATGAATCACC 58.521 40.000 0.00 0.00 32.67 4.02
979 1046 0.392863 TGCCGTCATTCAGTGGATGG 60.393 55.000 11.64 6.66 42.04 3.51
1000 1067 4.835615 CAGACTGATTACTAGGTAGGGCAT 59.164 45.833 0.00 0.00 0.00 4.40
1001 1068 4.215908 CAGACTGATTACTAGGTAGGGCA 58.784 47.826 0.00 0.00 0.00 5.36
1025 1095 2.427812 GGGGTTGTGTTTTCTTTTCCGA 59.572 45.455 0.00 0.00 0.00 4.55
1033 1103 1.037493 GGAGTGGGGGTTGTGTTTTC 58.963 55.000 0.00 0.00 0.00 2.29
1035 1105 1.231928 GGGAGTGGGGGTTGTGTTT 59.768 57.895 0.00 0.00 0.00 2.83
1039 1109 2.531942 GGAGGGAGTGGGGGTTGT 60.532 66.667 0.00 0.00 0.00 3.32
1040 1110 3.339093 GGGAGGGAGTGGGGGTTG 61.339 72.222 0.00 0.00 0.00 3.77
1041 1111 4.695791 GGGGAGGGAGTGGGGGTT 62.696 72.222 0.00 0.00 0.00 4.11
1044 1114 4.825679 GAGGGGGAGGGAGTGGGG 62.826 77.778 0.00 0.00 0.00 4.96
1102 1172 1.343465 GACCTCCTTCCTCACGTTGAA 59.657 52.381 0.00 0.00 0.00 2.69
1103 1173 0.966920 GACCTCCTTCCTCACGTTGA 59.033 55.000 0.00 0.00 0.00 3.18
1104 1174 0.969894 AGACCTCCTTCCTCACGTTG 59.030 55.000 0.00 0.00 0.00 4.10
1105 1175 1.619332 GAAGACCTCCTTCCTCACGTT 59.381 52.381 0.00 0.00 44.27 3.99
1106 1176 1.258676 GAAGACCTCCTTCCTCACGT 58.741 55.000 0.00 0.00 44.27 4.49
1107 1177 0.171455 CGAAGACCTCCTTCCTCACG 59.829 60.000 0.00 0.00 46.65 4.35
1384 1456 0.904865 TCCGCCAGAGGAGTTGTCAT 60.905 55.000 0.00 0.00 34.92 3.06
1555 1627 4.467084 GGCCGCGTCTTCCATGGA 62.467 66.667 11.44 11.44 0.00 3.41
1643 1715 0.731417 ATGCTCAACGATCTTGCTGC 59.269 50.000 0.00 0.00 0.00 5.25
1660 1732 0.957395 AACAGGGCTGCGTCTTCATG 60.957 55.000 0.00 0.00 0.00 3.07
1662 1734 1.301716 GAACAGGGCTGCGTCTTCA 60.302 57.895 0.00 0.00 0.00 3.02
1673 1745 1.726853 CACCTTTAGCTCGAACAGGG 58.273 55.000 0.00 0.00 0.00 4.45
1674 1746 1.079503 GCACCTTTAGCTCGAACAGG 58.920 55.000 0.00 0.00 0.00 4.00
1675 1747 1.461127 GTGCACCTTTAGCTCGAACAG 59.539 52.381 5.22 0.00 0.00 3.16
1676 1748 1.508632 GTGCACCTTTAGCTCGAACA 58.491 50.000 5.22 0.00 0.00 3.18
1681 1753 2.260481 GTCTACGTGCACCTTTAGCTC 58.740 52.381 12.15 3.40 0.00 4.09
1682 1754 1.616865 TGTCTACGTGCACCTTTAGCT 59.383 47.619 12.15 0.00 0.00 3.32
1683 1755 2.074547 TGTCTACGTGCACCTTTAGC 57.925 50.000 12.15 6.74 0.00 3.09
1684 1756 2.412089 GCTTGTCTACGTGCACCTTTAG 59.588 50.000 12.15 9.62 0.00 1.85
1685 1757 2.036733 AGCTTGTCTACGTGCACCTTTA 59.963 45.455 12.15 0.00 0.00 1.85
1686 1758 1.202651 AGCTTGTCTACGTGCACCTTT 60.203 47.619 12.15 0.00 0.00 3.11
1687 1759 0.393077 AGCTTGTCTACGTGCACCTT 59.607 50.000 12.15 0.40 0.00 3.50
1688 1760 0.038159 GAGCTTGTCTACGTGCACCT 60.038 55.000 12.15 1.77 0.00 4.00
1689 1761 1.344942 CGAGCTTGTCTACGTGCACC 61.345 60.000 12.15 0.00 0.00 5.01
1690 1762 0.663568 ACGAGCTTGTCTACGTGCAC 60.664 55.000 6.82 6.82 37.58 4.57
1691 1763 0.031585 AACGAGCTTGTCTACGTGCA 59.968 50.000 7.17 0.00 38.92 4.57
1692 1764 1.973138 TAACGAGCTTGTCTACGTGC 58.027 50.000 7.17 0.00 38.92 5.34
1693 1765 4.685020 GTTTTAACGAGCTTGTCTACGTG 58.315 43.478 7.17 0.00 38.92 4.49
1694 1766 4.961433 GTTTTAACGAGCTTGTCTACGT 57.039 40.909 7.17 0.00 40.64 3.57
1708 1780 1.922545 CGACGGATCCCTCGTTTTAAC 59.077 52.381 20.97 0.00 41.22 2.01
1709 1781 1.736696 GCGACGGATCCCTCGTTTTAA 60.737 52.381 26.92 0.00 41.22 1.52
1710 1782 0.179129 GCGACGGATCCCTCGTTTTA 60.179 55.000 26.92 0.00 41.22 1.52
1711 1783 1.447314 GCGACGGATCCCTCGTTTT 60.447 57.895 26.92 0.00 41.22 2.43
1712 1784 1.033746 TAGCGACGGATCCCTCGTTT 61.034 55.000 26.92 19.77 41.22 3.60
1713 1785 1.452651 TAGCGACGGATCCCTCGTT 60.453 57.895 26.92 24.43 41.22 3.85
1714 1786 2.185494 GTAGCGACGGATCCCTCGT 61.185 63.158 26.92 18.43 44.03 4.18
1715 1787 2.638154 GTAGCGACGGATCCCTCG 59.362 66.667 23.84 23.84 0.00 4.63
1716 1788 2.562876 GGGTAGCGACGGATCCCTC 61.563 68.421 6.06 3.13 35.63 4.30
1717 1789 2.521224 GGGTAGCGACGGATCCCT 60.521 66.667 6.06 0.00 35.63 4.20
1718 1790 3.613689 GGGGTAGCGACGGATCCC 61.614 72.222 6.06 0.00 37.59 3.85
1719 1791 3.613689 GGGGGTAGCGACGGATCC 61.614 72.222 0.00 0.00 0.00 3.36
1720 1792 2.521224 AGGGGGTAGCGACGGATC 60.521 66.667 0.00 0.00 0.00 3.36
1721 1793 2.521224 GAGGGGGTAGCGACGGAT 60.521 66.667 0.00 0.00 0.00 4.18
1722 1794 3.588817 TTGAGGGGGTAGCGACGGA 62.589 63.158 0.00 0.00 0.00 4.69
1723 1795 3.072468 TTGAGGGGGTAGCGACGG 61.072 66.667 0.00 0.00 0.00 4.79
1724 1796 1.392710 ATCTTGAGGGGGTAGCGACG 61.393 60.000 0.00 0.00 0.00 5.12
1725 1797 0.105039 CATCTTGAGGGGGTAGCGAC 59.895 60.000 0.00 0.00 0.00 5.19
1726 1798 0.032515 TCATCTTGAGGGGGTAGCGA 60.033 55.000 0.00 0.00 0.00 4.93
1727 1799 0.105039 GTCATCTTGAGGGGGTAGCG 59.895 60.000 0.00 0.00 0.00 4.26
1728 1800 0.105039 CGTCATCTTGAGGGGGTAGC 59.895 60.000 0.00 0.00 0.00 3.58
1729 1801 0.753262 CCGTCATCTTGAGGGGGTAG 59.247 60.000 8.09 0.00 45.83 3.18
1730 1802 2.910579 CCGTCATCTTGAGGGGGTA 58.089 57.895 8.09 0.00 45.83 3.69
1731 1803 3.727387 CCGTCATCTTGAGGGGGT 58.273 61.111 8.09 0.00 45.83 4.95
1735 1807 1.938577 CATCTTGCCGTCATCTTGAGG 59.061 52.381 0.00 0.00 32.49 3.86
1736 1808 1.938577 CCATCTTGCCGTCATCTTGAG 59.061 52.381 0.00 0.00 0.00 3.02
1737 1809 1.278985 ACCATCTTGCCGTCATCTTGA 59.721 47.619 0.00 0.00 0.00 3.02
1738 1810 1.742761 ACCATCTTGCCGTCATCTTG 58.257 50.000 0.00 0.00 0.00 3.02
1739 1811 2.086869 CAACCATCTTGCCGTCATCTT 58.913 47.619 0.00 0.00 0.00 2.40
1740 1812 1.278985 TCAACCATCTTGCCGTCATCT 59.721 47.619 0.00 0.00 0.00 2.90
1741 1813 1.667724 CTCAACCATCTTGCCGTCATC 59.332 52.381 0.00 0.00 0.00 2.92
1742 1814 1.679944 CCTCAACCATCTTGCCGTCAT 60.680 52.381 0.00 0.00 0.00 3.06
1743 1815 0.321564 CCTCAACCATCTTGCCGTCA 60.322 55.000 0.00 0.00 0.00 4.35
1744 1816 0.036388 TCCTCAACCATCTTGCCGTC 60.036 55.000 0.00 0.00 0.00 4.79
1745 1817 0.620556 ATCCTCAACCATCTTGCCGT 59.379 50.000 0.00 0.00 0.00 5.68
1746 1818 1.019673 CATCCTCAACCATCTTGCCG 58.980 55.000 0.00 0.00 0.00 5.69
1747 1819 2.425143 TCATCCTCAACCATCTTGCC 57.575 50.000 0.00 0.00 0.00 4.52
1748 1820 3.376546 GTCTTCATCCTCAACCATCTTGC 59.623 47.826 0.00 0.00 0.00 4.01
1749 1821 3.620374 CGTCTTCATCCTCAACCATCTTG 59.380 47.826 0.00 0.00 0.00 3.02
1750 1822 3.515502 TCGTCTTCATCCTCAACCATCTT 59.484 43.478 0.00 0.00 0.00 2.40
1751 1823 3.099905 TCGTCTTCATCCTCAACCATCT 58.900 45.455 0.00 0.00 0.00 2.90
1752 1824 3.526931 TCGTCTTCATCCTCAACCATC 57.473 47.619 0.00 0.00 0.00 3.51
1753 1825 3.981071 TTCGTCTTCATCCTCAACCAT 57.019 42.857 0.00 0.00 0.00 3.55
1754 1826 3.762407 TTTCGTCTTCATCCTCAACCA 57.238 42.857 0.00 0.00 0.00 3.67
1755 1827 4.142600 CCATTTTCGTCTTCATCCTCAACC 60.143 45.833 0.00 0.00 0.00 3.77
1756 1828 4.672801 GCCATTTTCGTCTTCATCCTCAAC 60.673 45.833 0.00 0.00 0.00 3.18
1757 1829 3.440173 GCCATTTTCGTCTTCATCCTCAA 59.560 43.478 0.00 0.00 0.00 3.02
1758 1830 3.009723 GCCATTTTCGTCTTCATCCTCA 58.990 45.455 0.00 0.00 0.00 3.86
1759 1831 3.009723 TGCCATTTTCGTCTTCATCCTC 58.990 45.455 0.00 0.00 0.00 3.71
1760 1832 3.012518 CTGCCATTTTCGTCTTCATCCT 58.987 45.455 0.00 0.00 0.00 3.24
1761 1833 2.098117 CCTGCCATTTTCGTCTTCATCC 59.902 50.000 0.00 0.00 0.00 3.51
1762 1834 2.478539 GCCTGCCATTTTCGTCTTCATC 60.479 50.000 0.00 0.00 0.00 2.92
1954 2026 0.468214 TCATCCTCCTTCTCGGCGAT 60.468 55.000 11.27 0.00 0.00 4.58
1962 2034 3.254657 CGTACTCCTCATCATCCTCCTTC 59.745 52.174 0.00 0.00 0.00 3.46
2028 2100 0.604073 TGTGGCTGATTGCACCAATG 59.396 50.000 0.00 0.00 45.15 2.82
2029 2101 1.001181 GTTGTGGCTGATTGCACCAAT 59.999 47.619 0.00 0.00 45.15 3.16
2030 2102 0.388659 GTTGTGGCTGATTGCACCAA 59.611 50.000 0.00 0.00 45.15 3.67
2203 2281 0.250901 GAAAGAACTGCTGGGGCTGA 60.251 55.000 0.00 0.00 40.03 4.26
2208 2289 2.035066 CACTTTGGAAAGAACTGCTGGG 59.965 50.000 6.13 0.00 39.31 4.45
2233 2314 1.453155 GATGGTGGTGCAGAATCGTT 58.547 50.000 0.00 0.00 0.00 3.85
2303 2384 2.652590 GAAGAATTGCTGGAGCTGGAT 58.347 47.619 0.00 0.00 42.66 3.41
2395 2476 3.165058 TGGAGCTAGAATGCTAACGTG 57.835 47.619 0.00 0.00 44.17 4.49
2492 2583 3.808218 TTGCCTGCTGGTTCCCCAC 62.808 63.158 11.69 0.00 35.17 4.61
2496 2587 0.680921 TATGCTTGCCTGCTGGTTCC 60.681 55.000 11.69 0.00 35.27 3.62
2517 2608 1.001248 AAGTACCGGAGCTGGGCTA 59.999 57.895 9.46 0.00 39.88 3.93
2531 2622 2.038033 CCGTTCACCTTGGGAAGAAGTA 59.962 50.000 0.00 0.00 0.00 2.24
2578 2669 4.462508 TCTCTGGTTCAGCATTCTGTAG 57.537 45.455 0.00 0.00 41.10 2.74
2619 2710 2.583143 ACCACTTTGTAAAGGACTGCC 58.417 47.619 9.00 0.00 40.31 4.85
2652 2746 2.997315 CCAGCCTCCAGTGACGGA 60.997 66.667 0.00 0.00 0.00 4.69
2711 2805 0.916086 TGGTGTTGGAGTTGGACTGT 59.084 50.000 0.00 0.00 0.00 3.55
2737 2831 9.471702 AGAACCATCATTGACATTAGAAAGATT 57.528 29.630 0.00 0.00 0.00 2.40
2785 2879 0.904649 TTCTGCACCATCTCCGATGT 59.095 50.000 3.47 0.00 0.00 3.06
2788 2882 0.462581 GCATTCTGCACCATCTCCGA 60.463 55.000 0.00 0.00 44.26 4.55
2867 2979 2.429069 GCCGCTTTTCCAACGCTG 60.429 61.111 0.00 0.00 0.00 5.18
2928 3040 1.000771 CCTCTCCGTCTCCACCAGA 60.001 63.158 0.00 0.00 0.00 3.86
3001 3113 1.395954 CACCATGTGCTCGATGTCAAG 59.604 52.381 0.00 0.00 0.00 3.02
3078 3190 0.820226 CGTCTTCATCAGCCCTCAGA 59.180 55.000 0.00 0.00 0.00 3.27
3100 3212 2.346365 CTGCTGCTGCTCTCCACA 59.654 61.111 17.00 0.00 40.48 4.17
3139 3269 0.547712 TCCCCTTCCTCCAGGTCTTG 60.548 60.000 0.00 0.00 36.34 3.02
3165 3295 2.576832 CCCACAACCCTACGACGGT 61.577 63.158 0.00 0.00 34.07 4.83
3166 3296 2.263540 CCCACAACCCTACGACGG 59.736 66.667 0.00 0.00 0.00 4.79
3167 3297 2.433664 GCCCACAACCCTACGACG 60.434 66.667 0.00 0.00 0.00 5.12
3169 3299 1.373435 CAAGCCCACAACCCTACGA 59.627 57.895 0.00 0.00 0.00 3.43
3170 3300 1.072505 ACAAGCCCACAACCCTACG 59.927 57.895 0.00 0.00 0.00 3.51
3171 3301 0.893727 CCACAAGCCCACAACCCTAC 60.894 60.000 0.00 0.00 0.00 3.18
3191 3321 2.512515 CTAGCAGCGGGCCAGAAC 60.513 66.667 7.23 0.00 46.50 3.01
3192 3322 2.683572 TCTAGCAGCGGGCCAGAA 60.684 61.111 7.23 0.00 46.50 3.02
3193 3323 3.461773 GTCTAGCAGCGGGCCAGA 61.462 66.667 7.23 0.00 46.50 3.86
3195 3325 3.083349 ATGTCTAGCAGCGGGCCA 61.083 61.111 4.39 0.00 46.50 5.36
3196 3326 2.590007 CATGTCTAGCAGCGGGCC 60.590 66.667 0.00 0.00 46.50 5.80
3203 3333 0.107752 TTCATGCGGCATGTCTAGCA 60.108 50.000 34.49 17.24 41.98 3.49
3204 3334 0.585357 CTTCATGCGGCATGTCTAGC 59.415 55.000 34.49 0.00 41.98 3.42
3228 3358 8.367660 TGTTTTGATAGTATTGCCCCAAAATA 57.632 30.769 8.90 5.27 36.38 1.40
3229 3359 7.251321 TGTTTTGATAGTATTGCCCCAAAAT 57.749 32.000 8.90 0.00 36.38 1.82
3236 3366 7.547227 ACCTCAATTGTTTTGATAGTATTGCC 58.453 34.615 5.13 0.00 0.00 4.52
3237 3367 8.462016 AGACCTCAATTGTTTTGATAGTATTGC 58.538 33.333 5.13 0.00 0.00 3.56
3238 3368 9.778993 CAGACCTCAATTGTTTTGATAGTATTG 57.221 33.333 5.13 0.00 0.00 1.90
3273 3407 7.504924 ACAGACCTCGATTAATTTGTCAAAA 57.495 32.000 1.31 0.00 0.00 2.44
3274 3408 7.504924 AACAGACCTCGATTAATTTGTCAAA 57.495 32.000 0.00 0.00 0.00 2.69
3275 3409 7.504924 AAACAGACCTCGATTAATTTGTCAA 57.495 32.000 0.00 0.00 0.00 3.18
3276 3410 7.504924 AAAACAGACCTCGATTAATTTGTCA 57.495 32.000 0.00 0.00 0.00 3.58
3277 3411 9.326339 GTTAAAACAGACCTCGATTAATTTGTC 57.674 33.333 0.00 0.00 0.00 3.18
3278 3412 9.063615 AGTTAAAACAGACCTCGATTAATTTGT 57.936 29.630 0.00 0.00 0.00 2.83
3282 3416 9.715121 TGTTAGTTAAAACAGACCTCGATTAAT 57.285 29.630 0.00 0.00 34.50 1.40
3283 3417 8.981647 GTGTTAGTTAAAACAGACCTCGATTAA 58.018 33.333 0.00 0.00 39.92 1.40
3284 3418 8.143193 TGTGTTAGTTAAAACAGACCTCGATTA 58.857 33.333 0.00 0.00 39.92 1.75
3285 3419 6.987992 TGTGTTAGTTAAAACAGACCTCGATT 59.012 34.615 0.00 0.00 39.92 3.34
3286 3420 6.518493 TGTGTTAGTTAAAACAGACCTCGAT 58.482 36.000 0.00 0.00 39.92 3.59
3287 3421 5.904941 TGTGTTAGTTAAAACAGACCTCGA 58.095 37.500 0.00 0.00 39.92 4.04
3288 3422 6.590357 CATGTGTTAGTTAAAACAGACCTCG 58.410 40.000 1.79 0.00 39.92 4.63
3289 3423 6.017440 TGCATGTGTTAGTTAAAACAGACCTC 60.017 38.462 0.00 0.00 39.92 3.85
3290 3424 5.825679 TGCATGTGTTAGTTAAAACAGACCT 59.174 36.000 0.00 0.00 39.92 3.85
3291 3425 6.067263 TGCATGTGTTAGTTAAAACAGACC 57.933 37.500 0.00 0.00 39.92 3.85
3292 3426 6.970043 TGTTGCATGTGTTAGTTAAAACAGAC 59.030 34.615 0.00 0.00 39.92 3.51
3293 3427 7.089770 TGTTGCATGTGTTAGTTAAAACAGA 57.910 32.000 0.00 0.00 39.92 3.41
3294 3428 6.074888 GCTGTTGCATGTGTTAGTTAAAACAG 60.075 38.462 7.22 7.22 42.93 3.16
3295 3429 5.746245 GCTGTTGCATGTGTTAGTTAAAACA 59.254 36.000 0.00 0.00 37.77 2.83
3296 3430 5.174943 GGCTGTTGCATGTGTTAGTTAAAAC 59.825 40.000 0.00 0.00 41.91 2.43
3297 3431 5.285651 GGCTGTTGCATGTGTTAGTTAAAA 58.714 37.500 0.00 0.00 41.91 1.52
3298 3432 4.555708 CGGCTGTTGCATGTGTTAGTTAAA 60.556 41.667 0.00 0.00 41.91 1.52
3299 3433 3.058570 CGGCTGTTGCATGTGTTAGTTAA 60.059 43.478 0.00 0.00 41.91 2.01
3300 3434 2.482336 CGGCTGTTGCATGTGTTAGTTA 59.518 45.455 0.00 0.00 41.91 2.24
3301 3435 1.266718 CGGCTGTTGCATGTGTTAGTT 59.733 47.619 0.00 0.00 41.91 2.24
3302 3436 0.874390 CGGCTGTTGCATGTGTTAGT 59.126 50.000 0.00 0.00 41.91 2.24
3303 3437 0.874390 ACGGCTGTTGCATGTGTTAG 59.126 50.000 0.00 0.00 41.91 2.34
3304 3438 1.313772 AACGGCTGTTGCATGTGTTA 58.686 45.000 10.90 0.00 41.91 2.41
3305 3439 2.114638 AACGGCTGTTGCATGTGTT 58.885 47.368 10.90 0.00 41.91 3.32
3306 3440 3.840437 AACGGCTGTTGCATGTGT 58.160 50.000 10.90 0.00 41.91 3.72
3319 3453 0.171007 CATGGTTTGCTAGCCAACGG 59.829 55.000 21.51 12.12 38.38 4.44
3320 3454 1.135689 GTCATGGTTTGCTAGCCAACG 60.136 52.381 21.51 10.96 38.38 4.10
3343 3483 1.340889 TGTTCAACTTGGCAATGCTCC 59.659 47.619 4.82 0.00 0.00 4.70
3354 3518 7.209471 TGCTTATAAAACGGATGTTCAACTT 57.791 32.000 0.00 0.00 37.31 2.66
3356 3520 8.460831 AATTGCTTATAAAACGGATGTTCAAC 57.539 30.769 0.00 0.00 37.31 3.18
3410 3585 4.137543 ACTTGAAAACGAGAAGCTGGAAT 58.862 39.130 0.00 0.00 0.00 3.01
3436 3617 5.123344 AGCCGTATGTGAAAGTAAATCCAAC 59.877 40.000 0.00 0.00 0.00 3.77
3445 3628 2.236146 TCATCCAGCCGTATGTGAAAGT 59.764 45.455 0.00 0.00 0.00 2.66
3451 3634 5.127845 CCTTAGATATCATCCAGCCGTATGT 59.872 44.000 5.32 0.00 0.00 2.29
3452 3635 5.127845 ACCTTAGATATCATCCAGCCGTATG 59.872 44.000 5.32 0.00 0.00 2.39
3453 3636 5.273208 ACCTTAGATATCATCCAGCCGTAT 58.727 41.667 5.32 0.00 0.00 3.06
3454 3637 4.673968 ACCTTAGATATCATCCAGCCGTA 58.326 43.478 5.32 0.00 0.00 4.02
3508 3691 5.182950 TCACACCTGCGATTTTAAATCATGT 59.817 36.000 16.57 9.54 0.00 3.21
3513 4085 4.704540 TCCATCACACCTGCGATTTTAAAT 59.295 37.500 0.00 0.00 0.00 1.40
3522 4094 2.665000 AGGTCCATCACACCTGCG 59.335 61.111 0.00 0.00 43.10 5.18
3530 4102 2.359850 GCCGCAACAGGTCCATCA 60.360 61.111 0.00 0.00 0.00 3.07
3531 4103 1.750399 ATGCCGCAACAGGTCCATC 60.750 57.895 0.00 0.00 0.00 3.51
3532 4104 2.048023 CATGCCGCAACAGGTCCAT 61.048 57.895 0.00 0.00 0.00 3.41
3533 4105 2.672651 CATGCCGCAACAGGTCCA 60.673 61.111 0.00 0.00 0.00 4.02
3534 4106 2.672996 ACATGCCGCAACAGGTCC 60.673 61.111 0.00 0.00 25.53 4.46
3535 4107 2.870372 GACATGCCGCAACAGGTC 59.130 61.111 0.00 5.19 43.19 3.85
3536 4108 2.672996 GGACATGCCGCAACAGGT 60.673 61.111 0.00 0.00 37.25 4.00
3537 4109 1.804396 TTTGGACATGCCGCAACAGG 61.804 55.000 0.00 0.00 40.66 4.00
3538 4110 0.031857 TTTTGGACATGCCGCAACAG 59.968 50.000 0.00 0.00 40.66 3.16
3540 4112 1.336702 TGATTTTGGACATGCCGCAAC 60.337 47.619 0.00 0.00 40.66 4.17
3542 4114 0.243365 GTGATTTTGGACATGCCGCA 59.757 50.000 0.00 0.00 40.66 5.69
3546 4118 2.987413 TCGTGTGATTTTGGACATGC 57.013 45.000 0.00 0.00 0.00 4.06
3553 4125 2.697363 CGCTGCTATCGTGTGATTTTG 58.303 47.619 0.00 0.00 35.99 2.44
3562 4134 1.215655 GGATTTCGCGCTGCTATCGT 61.216 55.000 5.56 0.00 0.00 3.73
3567 4139 3.127533 GTGGGATTTCGCGCTGCT 61.128 61.111 5.56 0.00 36.53 4.24
3570 4142 0.887933 ATTTTGTGGGATTTCGCGCT 59.112 45.000 5.56 0.00 39.63 5.92
3575 4147 8.708742 GTTTTAGCACTAATTTTGTGGGATTTC 58.291 33.333 11.92 0.00 36.08 2.17
3594 4166 9.736023 CCCTTAACATAAATCATGAGTTTTAGC 57.264 33.333 14.34 0.00 38.10 3.09
3595 4167 9.736023 GCCCTTAACATAAATCATGAGTTTTAG 57.264 33.333 14.34 7.00 38.10 1.85
3601 4173 6.713762 TTGGCCCTTAACATAAATCATGAG 57.286 37.500 0.00 0.00 38.10 2.90
3602 4174 7.673641 ATTTGGCCCTTAACATAAATCATGA 57.326 32.000 0.00 0.00 38.10 3.07
3605 4177 6.112058 GCAATTTGGCCCTTAACATAAATCA 58.888 36.000 0.00 0.00 0.00 2.57
3606 4178 6.112058 TGCAATTTGGCCCTTAACATAAATC 58.888 36.000 0.00 0.00 0.00 2.17
3607 4179 6.059787 TGCAATTTGGCCCTTAACATAAAT 57.940 33.333 0.00 0.00 0.00 1.40
3609 4181 4.081198 CCTGCAATTTGGCCCTTAACATAA 60.081 41.667 0.00 0.00 0.00 1.90
3610 4182 3.450457 CCTGCAATTTGGCCCTTAACATA 59.550 43.478 0.00 0.00 0.00 2.29
3611 4183 2.236893 CCTGCAATTTGGCCCTTAACAT 59.763 45.455 0.00 0.00 0.00 2.71
3615 4187 1.603236 CGCCTGCAATTTGGCCCTTA 61.603 55.000 8.96 0.00 45.90 2.69
3616 4188 2.946346 CGCCTGCAATTTGGCCCTT 61.946 57.895 8.96 0.00 45.90 3.95
3620 4192 2.292103 TAAATCGCCTGCAATTTGGC 57.708 45.000 4.64 4.64 45.25 4.52
3625 4197 3.874392 AAGCTTTAAATCGCCTGCAAT 57.126 38.095 0.00 0.00 0.00 3.56
3626 4198 3.243704 ACAAAGCTTTAAATCGCCTGCAA 60.244 39.130 12.25 0.00 0.00 4.08
3628 4200 2.663119 CACAAAGCTTTAAATCGCCTGC 59.337 45.455 12.25 0.00 0.00 4.85
3760 4560 1.067295 TGGCTTCTTGATCCCACTGT 58.933 50.000 0.00 0.00 0.00 3.55
3858 4658 3.380004 CACTTGTGGTTCCAAGCTAACAA 59.620 43.478 0.56 0.00 44.55 2.83
3893 4693 5.295787 TGACAAACAACCTGACATTAGACAC 59.704 40.000 0.00 0.00 0.00 3.67
3917 4717 4.628963 AGTACCCAACGGAAATACACTT 57.371 40.909 0.00 0.00 0.00 3.16
3928 4728 5.467705 GTCATATTAGCCTAGTACCCAACG 58.532 45.833 0.00 0.00 0.00 4.10


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

AutoCloner maintained by Alex Coulton.