Multiple sequence alignment - TraesCS6B01G296300

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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 TraesCS6B01G296300 chr6B 100.000 4351 0 0 1 4351 532140712 532145062 0.000000e+00 8035
1 TraesCS6B01G296300 chr6D 89.992 2538 106 37 7 2477 348038342 348035886 0.000000e+00 3144
2 TraesCS6B01G296300 chr6D 88.466 1838 132 41 2545 4349 348035848 348034058 0.000000e+00 2146
3 TraesCS6B01G296300 chr6A 87.983 2588 162 50 1840 4349 495458847 495461363 0.000000e+00 2918
4 TraesCS6B01G296300 chr6A 91.420 676 12 16 110 762 495457336 495457988 0.000000e+00 885
5 TraesCS6B01G296300 chr6A 89.500 600 32 11 792 1363 495457980 495458576 0.000000e+00 730
6 TraesCS6B01G296300 chr6A 87.204 211 11 7 1532 1726 495458640 495458850 4.380000e-55 226
7 TraesCS6B01G296300 chr1D 89.591 269 19 1 2976 3244 455204960 455204701 2.510000e-87 333


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 TraesCS6B01G296300 chr6B 532140712 532145062 4350 False 8035.00 8035 100.00000 1 4351 1 chr6B.!!$F1 4350
1 TraesCS6B01G296300 chr6D 348034058 348038342 4284 True 2645.00 3144 89.22900 7 4349 2 chr6D.!!$R1 4342
2 TraesCS6B01G296300 chr6A 495457336 495461363 4027 False 1189.75 2918 89.02675 110 4349 4 chr6A.!!$F1 4239

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
415 450 0.179161 CGGTCGGTTGTCTAGCTCTG 60.179 60.0 0.00 0.0 0.0 3.35 F
1559 1657 0.394216 TCGATCTGTGGCCCCATTTG 60.394 55.0 0.00 0.0 0.0 2.32 F
2631 2945 0.601558 GTCGCCGGCCTGAGATTATA 59.398 55.0 23.46 0.0 0.0 0.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2401 2698 0.316204 GACATGCATGCATAAGGCCC 59.684 55.0 31.73 13.6 43.89 5.80 R
3028 3376 0.803117 TGTCTCTAGGTTCGCGTCTG 59.197 55.0 5.77 0.0 0.00 3.51 R
3822 4180 0.106268 AGACATGCAAACCACCACCA 60.106 50.0 0.00 0.0 0.00 4.17 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
42 43 5.870706 TGGTATATGCGGTATTTTGATCCA 58.129 37.500 0.00 0.00 0.00 3.41
50 51 5.063880 GCGGTATTTTGATCCATCTACCTT 58.936 41.667 8.92 0.00 0.00 3.50
59 60 3.491766 TCCATCTACCTTCCTTGGTCT 57.508 47.619 0.00 0.00 41.22 3.85
63 64 1.076677 TCTACCTTCCTTGGTCTCGGT 59.923 52.381 0.00 0.00 41.22 4.69
67 68 1.263356 CTTCCTTGGTCTCGGTGGTA 58.737 55.000 0.00 0.00 0.00 3.25
69 70 1.719529 TCCTTGGTCTCGGTGGTAAA 58.280 50.000 0.00 0.00 0.00 2.01
88 89 1.287191 CCGATGGAGCGATCGATGT 59.713 57.895 21.57 1.32 46.72 3.06
196 222 3.243877 GTCATGATCGATCGGAACAACAG 59.756 47.826 20.03 7.87 30.65 3.16
197 223 3.130340 TCATGATCGATCGGAACAACAGA 59.870 43.478 20.03 9.73 30.65 3.41
198 224 2.876091 TGATCGATCGGAACAACAGAC 58.124 47.619 20.03 0.00 0.00 3.51
415 450 0.179161 CGGTCGGTTGTCTAGCTCTG 60.179 60.000 0.00 0.00 0.00 3.35
417 452 1.135344 GGTCGGTTGTCTAGCTCTGTC 60.135 57.143 0.00 0.00 0.00 3.51
418 453 1.135344 GTCGGTTGTCTAGCTCTGTCC 60.135 57.143 0.00 0.00 0.00 4.02
866 919 1.887198 CCTTGCTACGTCGGGAGATAT 59.113 52.381 0.00 0.00 43.27 1.63
868 921 3.119919 CCTTGCTACGTCGGGAGATATAC 60.120 52.174 0.00 0.00 43.27 1.47
884 937 0.908910 ATACCACCAGTTGATCGGCA 59.091 50.000 0.00 0.00 0.00 5.69
934 992 2.139323 TGCTAACTAGGAGGCGAAGA 57.861 50.000 0.00 0.00 0.00 2.87
935 993 2.453521 TGCTAACTAGGAGGCGAAGAA 58.546 47.619 0.00 0.00 0.00 2.52
936 994 2.427453 TGCTAACTAGGAGGCGAAGAAG 59.573 50.000 0.00 0.00 0.00 2.85
937 995 2.688958 GCTAACTAGGAGGCGAAGAAGA 59.311 50.000 0.00 0.00 0.00 2.87
938 996 3.130693 GCTAACTAGGAGGCGAAGAAGAA 59.869 47.826 0.00 0.00 0.00 2.52
965 1026 2.646143 GGAGGCGCTATCGAGGTC 59.354 66.667 7.64 0.00 38.10 3.85
983 1044 3.437795 GACGGACGGAGGCGAGAA 61.438 66.667 0.00 0.00 0.00 2.87
1151 1212 2.125673 CCCCGACAGTAAGCACCG 60.126 66.667 0.00 0.00 0.00 4.94
1383 1473 0.442310 GTGTGCGCACATGTATTCGT 59.558 50.000 42.22 0.00 43.97 3.85
1389 1479 2.667171 GCGCACATGTATTCGTGGTTTT 60.667 45.455 0.30 0.00 35.12 2.43
1390 1480 3.560503 CGCACATGTATTCGTGGTTTTT 58.439 40.909 0.00 0.00 35.12 1.94
1396 1486 7.168469 GCACATGTATTCGTGGTTTTTACTTTT 59.832 33.333 0.00 0.00 35.12 2.27
1405 1495 9.934190 TTCGTGGTTTTTACTTTTATGAAGTAC 57.066 29.630 3.75 0.00 32.94 2.73
1406 1496 9.107177 TCGTGGTTTTTACTTTTATGAAGTACA 57.893 29.630 0.00 0.00 32.94 2.90
1407 1497 9.377383 CGTGGTTTTTACTTTTATGAAGTACAG 57.623 33.333 0.00 0.00 32.94 2.74
1408 1498 9.177304 GTGGTTTTTACTTTTATGAAGTACAGC 57.823 33.333 0.00 0.00 32.94 4.40
1409 1499 8.904834 TGGTTTTTACTTTTATGAAGTACAGCA 58.095 29.630 0.00 0.00 32.94 4.41
1410 1500 9.908152 GGTTTTTACTTTTATGAAGTACAGCAT 57.092 29.630 0.00 0.47 32.94 3.79
1425 1515 4.935352 ACAGCATAGAGAGTGAAGGATC 57.065 45.455 0.00 0.00 0.00 3.36
1559 1657 0.394216 TCGATCTGTGGCCCCATTTG 60.394 55.000 0.00 0.00 0.00 2.32
1590 1689 2.775960 TCTGTTCTGATCCATCCATGCT 59.224 45.455 0.00 0.00 0.00 3.79
1603 1702 4.330894 CCATCCATGCTTGTAGTATATGCG 59.669 45.833 0.00 0.00 0.00 4.73
1710 1824 1.272807 GGCTCACCTTGTACCACCTA 58.727 55.000 0.00 0.00 0.00 3.08
1723 1963 3.636153 ACCACCTAAAGAGCCATCTTC 57.364 47.619 0.00 0.00 45.25 2.87
1724 1964 2.912956 ACCACCTAAAGAGCCATCTTCA 59.087 45.455 0.00 0.00 45.25 3.02
1725 1965 3.054802 ACCACCTAAAGAGCCATCTTCAG 60.055 47.826 0.00 0.00 45.25 3.02
1727 1967 3.922171 CCTAAAGAGCCATCTTCAGGT 57.078 47.619 0.00 0.00 43.65 4.00
1728 1968 4.227864 CCTAAAGAGCCATCTTCAGGTT 57.772 45.455 0.00 0.00 43.65 3.50
1729 1969 4.593956 CCTAAAGAGCCATCTTCAGGTTT 58.406 43.478 0.00 0.00 43.65 3.27
1730 1970 4.637977 CCTAAAGAGCCATCTTCAGGTTTC 59.362 45.833 0.00 0.00 43.65 2.78
1731 1971 2.797177 AGAGCCATCTTCAGGTTTCC 57.203 50.000 0.00 0.00 28.57 3.13
1732 1972 1.988107 AGAGCCATCTTCAGGTTTCCA 59.012 47.619 0.00 0.00 28.57 3.53
1733 1973 2.087646 GAGCCATCTTCAGGTTTCCAC 58.912 52.381 0.00 0.00 0.00 4.02
1734 1974 1.707427 AGCCATCTTCAGGTTTCCACT 59.293 47.619 0.00 0.00 0.00 4.00
1735 1975 2.087646 GCCATCTTCAGGTTTCCACTC 58.912 52.381 0.00 0.00 0.00 3.51
1736 1976 2.553028 GCCATCTTCAGGTTTCCACTCA 60.553 50.000 0.00 0.00 0.00 3.41
1737 1977 3.754965 CCATCTTCAGGTTTCCACTCAA 58.245 45.455 0.00 0.00 0.00 3.02
1738 1978 3.503748 CCATCTTCAGGTTTCCACTCAAC 59.496 47.826 0.00 0.00 0.00 3.18
1739 1979 3.924114 TCTTCAGGTTTCCACTCAACA 57.076 42.857 0.00 0.00 0.00 3.33
1740 1980 4.437682 TCTTCAGGTTTCCACTCAACAT 57.562 40.909 0.00 0.00 0.00 2.71
1741 1981 4.389374 TCTTCAGGTTTCCACTCAACATC 58.611 43.478 0.00 0.00 0.00 3.06
1742 1982 3.855255 TCAGGTTTCCACTCAACATCA 57.145 42.857 0.00 0.00 0.00 3.07
1743 1983 3.476552 TCAGGTTTCCACTCAACATCAC 58.523 45.455 0.00 0.00 0.00 3.06
1744 1984 3.136443 TCAGGTTTCCACTCAACATCACT 59.864 43.478 0.00 0.00 0.00 3.41
1745 1985 3.251729 CAGGTTTCCACTCAACATCACTG 59.748 47.826 0.00 0.00 0.00 3.66
1746 1986 2.030805 GGTTTCCACTCAACATCACTGC 60.031 50.000 0.00 0.00 0.00 4.40
1747 1987 2.618241 GTTTCCACTCAACATCACTGCA 59.382 45.455 0.00 0.00 0.00 4.41
1748 1988 2.636647 TCCACTCAACATCACTGCAA 57.363 45.000 0.00 0.00 0.00 4.08
1749 1989 2.929641 TCCACTCAACATCACTGCAAA 58.070 42.857 0.00 0.00 0.00 3.68
1750 1990 2.618241 TCCACTCAACATCACTGCAAAC 59.382 45.455 0.00 0.00 0.00 2.93
1751 1991 2.620115 CCACTCAACATCACTGCAAACT 59.380 45.455 0.00 0.00 0.00 2.66
1752 1992 3.814842 CCACTCAACATCACTGCAAACTA 59.185 43.478 0.00 0.00 0.00 2.24
1753 1993 4.083643 CCACTCAACATCACTGCAAACTAG 60.084 45.833 0.00 0.00 0.00 2.57
1754 1994 4.512944 CACTCAACATCACTGCAAACTAGT 59.487 41.667 0.00 0.00 0.00 2.57
1755 1995 5.008019 CACTCAACATCACTGCAAACTAGTT 59.992 40.000 1.12 1.12 0.00 2.24
1756 1996 6.202762 CACTCAACATCACTGCAAACTAGTTA 59.797 38.462 8.92 0.00 0.00 2.24
1757 1997 6.936900 ACTCAACATCACTGCAAACTAGTTAT 59.063 34.615 8.92 0.00 0.00 1.89
1758 1998 7.445402 ACTCAACATCACTGCAAACTAGTTATT 59.555 33.333 8.92 0.00 0.00 1.40
1759 1999 7.806690 TCAACATCACTGCAAACTAGTTATTC 58.193 34.615 8.92 1.85 0.00 1.75
1760 2000 6.743575 ACATCACTGCAAACTAGTTATTCC 57.256 37.500 8.92 0.00 0.00 3.01
1761 2001 5.648092 ACATCACTGCAAACTAGTTATTCCC 59.352 40.000 8.92 0.00 0.00 3.97
1762 2002 5.499004 TCACTGCAAACTAGTTATTCCCT 57.501 39.130 8.92 0.00 0.00 4.20
1763 2003 6.614694 TCACTGCAAACTAGTTATTCCCTA 57.385 37.500 8.92 0.00 0.00 3.53
1764 2004 6.403878 TCACTGCAAACTAGTTATTCCCTAC 58.596 40.000 8.92 0.00 0.00 3.18
1765 2005 6.014070 TCACTGCAAACTAGTTATTCCCTACA 60.014 38.462 8.92 0.00 0.00 2.74
1766 2006 6.653320 CACTGCAAACTAGTTATTCCCTACAA 59.347 38.462 8.92 0.00 0.00 2.41
1767 2007 7.174253 CACTGCAAACTAGTTATTCCCTACAAA 59.826 37.037 8.92 0.00 0.00 2.83
1768 2008 7.722285 ACTGCAAACTAGTTATTCCCTACAAAA 59.278 33.333 8.92 0.00 0.00 2.44
1769 2009 8.106247 TGCAAACTAGTTATTCCCTACAAAAG 57.894 34.615 8.92 0.00 0.00 2.27
1770 2010 7.940137 TGCAAACTAGTTATTCCCTACAAAAGA 59.060 33.333 8.92 0.00 0.00 2.52
1771 2011 8.789762 GCAAACTAGTTATTCCCTACAAAAGAA 58.210 33.333 8.92 0.00 0.00 2.52
1773 2013 9.856162 AAACTAGTTATTCCCTACAAAAGAACA 57.144 29.630 8.92 0.00 30.88 3.18
1774 2014 9.503399 AACTAGTTATTCCCTACAAAAGAACAG 57.497 33.333 6.26 0.00 30.88 3.16
1775 2015 6.819397 AGTTATTCCCTACAAAAGAACAGC 57.181 37.500 0.00 0.00 30.88 4.40
1776 2016 6.543735 AGTTATTCCCTACAAAAGAACAGCT 58.456 36.000 0.00 0.00 30.88 4.24
1777 2017 6.431234 AGTTATTCCCTACAAAAGAACAGCTG 59.569 38.462 13.48 13.48 30.88 4.24
1778 2018 3.857157 TCCCTACAAAAGAACAGCTGT 57.143 42.857 15.25 15.25 0.00 4.40
1779 2019 4.967084 TCCCTACAAAAGAACAGCTGTA 57.033 40.909 22.01 0.00 0.00 2.74
1780 2020 4.638304 TCCCTACAAAAGAACAGCTGTAC 58.362 43.478 22.01 0.00 0.00 2.90
1781 2021 4.101898 TCCCTACAAAAGAACAGCTGTACA 59.898 41.667 22.01 0.00 0.00 2.90
1782 2022 5.003804 CCCTACAAAAGAACAGCTGTACAT 58.996 41.667 22.01 4.06 0.00 2.29
1783 2023 6.014070 TCCCTACAAAAGAACAGCTGTACATA 60.014 38.462 22.01 5.38 0.00 2.29
1784 2024 6.823689 CCCTACAAAAGAACAGCTGTACATAT 59.176 38.462 22.01 3.13 0.00 1.78
1785 2025 7.985184 CCCTACAAAAGAACAGCTGTACATATA 59.015 37.037 22.01 6.41 0.00 0.86
1786 2026 9.547753 CCTACAAAAGAACAGCTGTACATATAT 57.452 33.333 22.01 1.33 0.00 0.86
1788 2028 8.131455 ACAAAAGAACAGCTGTACATATATCG 57.869 34.615 22.01 6.15 0.00 2.92
1789 2029 7.764443 ACAAAAGAACAGCTGTACATATATCGT 59.236 33.333 22.01 7.44 0.00 3.73
1790 2030 8.604035 CAAAAGAACAGCTGTACATATATCGTT 58.396 33.333 22.01 13.23 0.00 3.85
1791 2031 7.700322 AAGAACAGCTGTACATATATCGTTG 57.300 36.000 22.01 0.00 0.00 4.10
1792 2032 5.692204 AGAACAGCTGTACATATATCGTTGC 59.308 40.000 22.01 0.00 0.00 4.17
1793 2033 5.201713 ACAGCTGTACATATATCGTTGCT 57.798 39.130 20.16 0.00 0.00 3.91
1794 2034 5.506644 CAGCTGTACATATATCGTTGCTG 57.493 43.478 5.25 11.89 39.16 4.41
1795 2035 4.984785 CAGCTGTACATATATCGTTGCTGT 59.015 41.667 15.84 4.81 40.03 4.40
1796 2036 5.463392 CAGCTGTACATATATCGTTGCTGTT 59.537 40.000 15.84 0.00 40.03 3.16
1797 2037 6.018751 CAGCTGTACATATATCGTTGCTGTTT 60.019 38.462 15.84 0.00 40.03 2.83
1798 2038 6.538742 AGCTGTACATATATCGTTGCTGTTTT 59.461 34.615 0.00 0.00 0.00 2.43
1799 2039 7.065803 AGCTGTACATATATCGTTGCTGTTTTT 59.934 33.333 0.00 0.00 0.00 1.94
1800 2040 8.332464 GCTGTACATATATCGTTGCTGTTTTTA 58.668 33.333 0.00 0.00 0.00 1.52
1805 2045 9.935682 ACATATATCGTTGCTGTTTTTATTGAG 57.064 29.630 0.00 0.00 0.00 3.02
1806 2046 9.935682 CATATATCGTTGCTGTTTTTATTGAGT 57.064 29.630 0.00 0.00 0.00 3.41
1807 2047 9.935682 ATATATCGTTGCTGTTTTTATTGAGTG 57.064 29.630 0.00 0.00 0.00 3.51
1808 2048 4.286910 TCGTTGCTGTTTTTATTGAGTGC 58.713 39.130 0.00 0.00 0.00 4.40
1809 2049 4.036262 TCGTTGCTGTTTTTATTGAGTGCT 59.964 37.500 0.00 0.00 0.00 4.40
1810 2050 5.237561 TCGTTGCTGTTTTTATTGAGTGCTA 59.762 36.000 0.00 0.00 0.00 3.49
1811 2051 5.912396 CGTTGCTGTTTTTATTGAGTGCTAA 59.088 36.000 0.00 0.00 0.00 3.09
1812 2052 6.582295 CGTTGCTGTTTTTATTGAGTGCTAAT 59.418 34.615 0.00 0.00 0.00 1.73
1813 2053 7.114811 CGTTGCTGTTTTTATTGAGTGCTAATT 59.885 33.333 0.00 0.00 0.00 1.40
1814 2054 8.427774 GTTGCTGTTTTTATTGAGTGCTAATTC 58.572 33.333 0.00 0.00 0.00 2.17
1815 2055 7.090173 TGCTGTTTTTATTGAGTGCTAATTCC 58.910 34.615 0.00 0.00 0.00 3.01
1816 2056 7.039784 TGCTGTTTTTATTGAGTGCTAATTCCT 60.040 33.333 0.00 0.00 0.00 3.36
1817 2057 8.458843 GCTGTTTTTATTGAGTGCTAATTCCTA 58.541 33.333 0.00 0.00 0.00 2.94
1822 2062 9.959721 TTTTATTGAGTGCTAATTCCTAACTCT 57.040 29.630 10.19 0.00 38.44 3.24
1823 2063 9.601217 TTTATTGAGTGCTAATTCCTAACTCTC 57.399 33.333 10.19 0.00 38.44 3.20
1824 2064 5.250235 TGAGTGCTAATTCCTAACTCTCG 57.750 43.478 10.19 0.00 38.44 4.04
1825 2065 4.948004 TGAGTGCTAATTCCTAACTCTCGA 59.052 41.667 10.19 0.00 38.44 4.04
1826 2066 5.594725 TGAGTGCTAATTCCTAACTCTCGAT 59.405 40.000 10.19 0.00 38.44 3.59
1827 2067 6.079424 AGTGCTAATTCCTAACTCTCGATC 57.921 41.667 0.00 0.00 0.00 3.69
1828 2068 5.594725 AGTGCTAATTCCTAACTCTCGATCA 59.405 40.000 0.00 0.00 0.00 2.92
1829 2069 5.688176 GTGCTAATTCCTAACTCTCGATCAC 59.312 44.000 0.00 0.00 0.00 3.06
1830 2070 4.912766 GCTAATTCCTAACTCTCGATCACG 59.087 45.833 0.00 0.00 41.26 4.35
1831 2071 4.985538 AATTCCTAACTCTCGATCACGT 57.014 40.909 0.00 0.00 40.69 4.49
1832 2072 4.555348 ATTCCTAACTCTCGATCACGTC 57.445 45.455 0.00 0.00 40.69 4.34
1833 2073 2.981898 TCCTAACTCTCGATCACGTCA 58.018 47.619 0.00 0.00 40.69 4.35
1834 2074 3.340928 TCCTAACTCTCGATCACGTCAA 58.659 45.455 0.00 0.00 40.69 3.18
1835 2075 3.754850 TCCTAACTCTCGATCACGTCAAA 59.245 43.478 0.00 0.00 40.69 2.69
1836 2076 4.216902 TCCTAACTCTCGATCACGTCAAAA 59.783 41.667 0.00 0.00 40.69 2.44
1837 2077 4.323868 CCTAACTCTCGATCACGTCAAAAC 59.676 45.833 0.00 0.00 40.69 2.43
1838 2078 2.673833 ACTCTCGATCACGTCAAAACC 58.326 47.619 0.00 0.00 40.69 3.27
1875 2115 3.087781 GGGAAAGCAGAGCAAGAAAGAT 58.912 45.455 0.00 0.00 0.00 2.40
1914 2154 1.773052 AGAGGAGGTATGCATGCATGT 59.227 47.619 37.43 23.87 37.82 3.21
1917 2157 2.439135 AGGAGGTATGCATGCATGTACA 59.561 45.455 37.43 19.07 37.82 2.90
1996 2260 6.833342 AAGAAACAACATGACAAAGCATTC 57.167 33.333 0.00 0.00 0.00 2.67
2014 2278 3.887339 TTCGACGTTGATGCATTTTGA 57.113 38.095 6.27 0.00 0.00 2.69
2027 2291 4.061596 TGCATTTTGATTTTCGTTTCCCC 58.938 39.130 0.00 0.00 0.00 4.81
2056 2322 2.170166 GTTCCAAATCTCACATGCCCA 58.830 47.619 0.00 0.00 0.00 5.36
2062 2328 1.830279 ATCTCACATGCCCACAACTG 58.170 50.000 0.00 0.00 0.00 3.16
2117 2383 3.385384 CTCCTCTGCGGTGCCTCA 61.385 66.667 0.00 0.00 0.00 3.86
2118 2384 3.368190 CTCCTCTGCGGTGCCTCAG 62.368 68.421 2.00 2.00 0.00 3.35
2166 2432 3.282021 CATGGGGTGAGTCAACCTTATG 58.718 50.000 26.30 23.79 41.74 1.90
2385 2673 3.947868 AGGGACATCAATCTGTTGACTG 58.052 45.455 0.00 0.00 46.43 3.51
2387 2675 3.438087 GGGACATCAATCTGTTGACTGTG 59.562 47.826 9.37 1.77 46.43 3.66
2401 2698 7.922811 TCTGTTGACTGTGTAAGCATATAGATG 59.077 37.037 0.00 0.00 36.02 2.90
2490 2790 5.995897 ACCAACATCACCTAAAGTACTTCAC 59.004 40.000 8.95 0.00 0.00 3.18
2492 2792 6.147821 CCAACATCACCTAAAGTACTTCACAG 59.852 42.308 8.95 6.71 0.00 3.66
2501 2801 7.827729 ACCTAAAGTACTTCACAGAAACAACTT 59.172 33.333 8.95 0.00 0.00 2.66
2537 2837 1.541147 ACACAAAATGCCGGATCAGTG 59.459 47.619 5.05 8.16 0.00 3.66
2538 2838 1.541147 CACAAAATGCCGGATCAGTGT 59.459 47.619 5.05 0.00 0.00 3.55
2539 2839 2.030007 CACAAAATGCCGGATCAGTGTT 60.030 45.455 5.05 0.00 0.00 3.32
2540 2840 2.228822 ACAAAATGCCGGATCAGTGTTC 59.771 45.455 5.05 0.00 0.00 3.18
2541 2841 2.198827 AAATGCCGGATCAGTGTTCA 57.801 45.000 5.05 0.00 0.00 3.18
2542 2842 2.425143 AATGCCGGATCAGTGTTCAT 57.575 45.000 5.05 0.00 0.00 2.57
2543 2843 1.671979 ATGCCGGATCAGTGTTCATG 58.328 50.000 5.05 0.00 0.00 3.07
2556 2870 6.335777 TCAGTGTTCATGATCAGTCTATGTG 58.664 40.000 10.57 0.00 0.00 3.21
2625 2939 2.436646 AAATGTCGCCGGCCTGAG 60.437 61.111 23.46 6.82 0.00 3.35
2626 2940 2.852495 GAAATGTCGCCGGCCTGAGA 62.852 60.000 23.46 12.65 0.00 3.27
2627 2941 2.257409 AAATGTCGCCGGCCTGAGAT 62.257 55.000 23.46 14.58 0.00 2.75
2629 2943 1.399744 ATGTCGCCGGCCTGAGATTA 61.400 55.000 23.46 6.17 0.00 1.75
2630 2944 1.367840 GTCGCCGGCCTGAGATTAT 59.632 57.895 23.46 0.00 0.00 1.28
2631 2945 0.601558 GTCGCCGGCCTGAGATTATA 59.398 55.000 23.46 0.00 0.00 0.98
2692 3022 1.450312 CTGAAGCGGTGCCCCTAAG 60.450 63.158 0.00 0.00 0.00 2.18
2697 3027 0.981277 AGCGGTGCCCCTAAGTACAT 60.981 55.000 0.00 0.00 0.00 2.29
2699 3029 1.139455 GCGGTGCCCCTAAGTACATTA 59.861 52.381 0.00 0.00 0.00 1.90
2703 3033 5.613329 CGGTGCCCCTAAGTACATTATTTA 58.387 41.667 0.00 0.00 0.00 1.40
2706 3036 7.879160 CGGTGCCCCTAAGTACATTATTTATTA 59.121 37.037 0.00 0.00 0.00 0.98
2707 3037 9.577222 GGTGCCCCTAAGTACATTATTTATTAA 57.423 33.333 0.00 0.00 0.00 1.40
2844 3185 2.062971 ACCATCATCAACATGAGCCC 57.937 50.000 0.00 0.00 42.53 5.19
2875 3223 1.566298 ATCCCTGCCTCCAGAACCAC 61.566 60.000 0.00 0.00 41.77 4.16
2877 3225 1.455849 CCTGCCTCCAGAACCACAA 59.544 57.895 0.00 0.00 41.77 3.33
2878 3226 0.607489 CCTGCCTCCAGAACCACAAG 60.607 60.000 0.00 0.00 41.77 3.16
2879 3227 0.607489 CTGCCTCCAGAACCACAAGG 60.607 60.000 0.00 0.00 41.77 3.61
2894 3242 3.068024 CCACAAGGTAGTTGCACAATGTT 59.932 43.478 0.00 0.00 40.15 2.71
2902 3250 6.041523 AGGTAGTTGCACAATGTTTTAACCAT 59.958 34.615 0.00 0.00 0.00 3.55
2920 3268 5.894298 ACCATTCAGTATTCTCCTATGCA 57.106 39.130 0.00 0.00 0.00 3.96
3020 3368 3.243336 CCAGAAAAACCTCTCGTACGAG 58.757 50.000 34.21 34.21 43.21 4.18
3077 3425 0.034059 AGCTCACCGACTTCAACCTG 59.966 55.000 0.00 0.00 0.00 4.00
3200 3548 1.605058 GCTTCCAGCTCTACCACGGA 61.605 60.000 0.00 0.00 38.45 4.69
3201 3549 0.457851 CTTCCAGCTCTACCACGGAG 59.542 60.000 0.00 0.00 0.00 4.63
3203 3551 0.680280 TCCAGCTCTACCACGGAGTC 60.680 60.000 0.00 0.00 41.61 3.36
3204 3552 1.668101 CCAGCTCTACCACGGAGTCC 61.668 65.000 0.00 0.00 41.61 3.85
3205 3553 0.965866 CAGCTCTACCACGGAGTCCA 60.966 60.000 10.49 0.00 41.61 4.02
3206 3554 0.966370 AGCTCTACCACGGAGTCCAC 60.966 60.000 10.49 0.00 41.61 4.02
3207 3555 1.801332 CTCTACCACGGAGTCCACG 59.199 63.158 10.49 0.00 41.61 4.94
3208 3556 0.675837 CTCTACCACGGAGTCCACGA 60.676 60.000 10.49 0.00 41.61 4.35
3284 3632 3.199946 ACATCAAAGGTGGGTACGATCAT 59.800 43.478 0.00 0.00 0.00 2.45
3294 3642 0.669077 GTACGATCATCGGCTGTCCT 59.331 55.000 12.67 0.00 45.59 3.85
3453 3808 2.301870 AGGATGCTTGTTTACGGTCTGA 59.698 45.455 0.00 0.00 0.00 3.27
3471 3826 6.634436 CGGTCTGATTACACTTTATACGTACC 59.366 42.308 0.00 0.00 0.00 3.34
3482 3837 7.088272 CACTTTATACGTACCTATGCATGCTA 58.912 38.462 20.33 5.73 0.00 3.49
3492 3847 8.289618 CGTACCTATGCATGCTAATGTAAAATT 58.710 33.333 20.33 0.00 36.08 1.82
3515 3870 2.948315 GTGGAAATTGAGATCCAGGCTC 59.052 50.000 0.00 0.00 46.01 4.70
3547 3902 3.574284 AGCTAGATGATGATCGAGTGC 57.426 47.619 4.39 0.19 34.63 4.40
3559 3914 2.311124 TCGAGTGCGAGATCTGACTA 57.689 50.000 0.00 0.00 42.51 2.59
3566 3921 3.374367 GTGCGAGATCTGACTACACTGTA 59.626 47.826 0.00 0.00 0.00 2.74
3592 3947 4.982916 CGTACCTCCTAAAATTCTGATCGG 59.017 45.833 0.00 0.00 0.00 4.18
3596 3951 5.221541 ACCTCCTAAAATTCTGATCGGCTAG 60.222 44.000 0.00 0.00 0.00 3.42
3603 3961 7.721286 AAAATTCTGATCGGCTAGAACATAG 57.279 36.000 0.00 0.00 35.91 2.23
3604 3962 6.412362 AATTCTGATCGGCTAGAACATAGT 57.588 37.500 0.00 0.00 35.91 2.12
3605 3963 7.526142 AATTCTGATCGGCTAGAACATAGTA 57.474 36.000 0.00 0.00 35.91 1.82
3628 3986 1.745232 TCGTGGAGTGTTTTTGCTGT 58.255 45.000 0.00 0.00 0.00 4.40
3640 3998 4.646945 TGTTTTTGCTGTTGTTGAGGGATA 59.353 37.500 0.00 0.00 0.00 2.59
3650 4008 6.604171 TGTTGTTGAGGGATAGCATTATGAT 58.396 36.000 0.00 0.00 0.00 2.45
3651 4009 6.487668 TGTTGTTGAGGGATAGCATTATGATG 59.512 38.462 0.00 0.00 36.32 3.07
3652 4010 5.563592 TGTTGAGGGATAGCATTATGATGG 58.436 41.667 0.00 0.00 33.72 3.51
3822 4180 1.075536 GGGAGGTGGAAGTCAATGGTT 59.924 52.381 0.00 0.00 0.00 3.67
3922 4280 7.498900 TGAAAGTGCACTTCTTAATTCTGAAGA 59.501 33.333 31.20 6.13 41.38 2.87
3924 4282 7.807977 AGTGCACTTCTTAATTCTGAAGAAA 57.192 32.000 15.25 8.02 41.24 2.52
3947 4305 3.462483 TGTCAACACACGTATCCTTGT 57.538 42.857 0.00 0.00 0.00 3.16
3949 4307 4.193090 TGTCAACACACGTATCCTTGTTT 58.807 39.130 0.00 0.00 29.65 2.83
3950 4308 4.636648 TGTCAACACACGTATCCTTGTTTT 59.363 37.500 0.00 0.00 29.65 2.43
4001 4359 4.749245 ATCCAAACGAGTAGTGCAAAAG 57.251 40.909 0.00 0.00 0.00 2.27
4002 4360 2.875933 TCCAAACGAGTAGTGCAAAAGG 59.124 45.455 0.00 0.00 0.00 3.11
4006 4364 1.202770 ACGAGTAGTGCAAAAGGCCTT 60.203 47.619 13.78 13.78 43.89 4.35
4013 4371 4.155063 AGTGCAAAAGGCCTTGAAAAAT 57.845 36.364 21.33 0.00 43.89 1.82
4015 4373 5.679601 AGTGCAAAAGGCCTTGAAAAATAA 58.320 33.333 21.33 0.00 43.89 1.40
4016 4374 6.118852 AGTGCAAAAGGCCTTGAAAAATAAA 58.881 32.000 21.33 0.00 43.89 1.40
4017 4375 6.601217 AGTGCAAAAGGCCTTGAAAAATAAAA 59.399 30.769 21.33 0.00 43.89 1.52
4018 4376 7.121907 AGTGCAAAAGGCCTTGAAAAATAAAAA 59.878 29.630 21.33 0.00 43.89 1.94
4019 4377 7.431960 GTGCAAAAGGCCTTGAAAAATAAAAAG 59.568 33.333 21.33 0.00 43.89 2.27
4037 4395 2.781681 AGTTACATTGAAGTCCCCGG 57.218 50.000 0.00 0.00 0.00 5.73
4059 4417 1.556911 GGCTGACCATCTTCTTCCTCA 59.443 52.381 0.00 0.00 35.26 3.86
4062 4420 3.594134 CTGACCATCTTCTTCCTCACAC 58.406 50.000 0.00 0.00 0.00 3.82
4064 4422 3.390967 TGACCATCTTCTTCCTCACACAA 59.609 43.478 0.00 0.00 0.00 3.33
4076 4436 1.081906 CACACAACTGATGGCGCAC 60.082 57.895 10.83 0.00 0.00 5.34
4113 4473 0.900647 ACGCTGGAGTGAGCTTACCT 60.901 55.000 4.79 0.00 36.77 3.08
4121 4481 3.498777 GGAGTGAGCTTACCTTTGTTGAC 59.501 47.826 4.79 0.00 0.00 3.18
4126 4486 2.158871 AGCTTACCTTTGTTGACCACGA 60.159 45.455 0.00 0.00 0.00 4.35
4151 4511 4.102524 TGGTAAGTCATCAAGGTCACAGTT 59.897 41.667 0.00 0.00 0.00 3.16
4155 4515 6.365970 AAGTCATCAAGGTCACAGTTCTAT 57.634 37.500 0.00 0.00 0.00 1.98
4171 4531 1.216930 TCTATCGGACCATCACCCTGA 59.783 52.381 0.00 0.00 0.00 3.86
4180 4540 4.145052 GACCATCACCCTGAAAAAGAAGT 58.855 43.478 0.00 0.00 0.00 3.01
4182 4542 4.342092 ACCATCACCCTGAAAAAGAAGTTG 59.658 41.667 0.00 0.00 0.00 3.16
4185 4545 3.625764 TCACCCTGAAAAAGAAGTTGTCG 59.374 43.478 0.00 0.00 0.00 4.35
4259 4620 2.203640 ACGAGACACCAGGGAGCA 60.204 61.111 0.00 0.00 0.00 4.26
4282 4643 3.447229 TGCTAATGTGACGAAGATGAGGA 59.553 43.478 0.00 0.00 0.00 3.71
4288 4649 2.233922 GTGACGAAGATGAGGAGGGAAA 59.766 50.000 0.00 0.00 0.00 3.13
4297 4658 1.132332 TGAGGAGGGAAAACCCACCTA 60.132 52.381 20.75 9.48 43.57 3.08
4298 4659 1.560146 GAGGAGGGAAAACCCACCTAG 59.440 57.143 20.75 0.00 43.57 3.02
4299 4660 0.624254 GGAGGGAAAACCCACCTAGG 59.376 60.000 7.41 7.41 41.63 3.02
4329 4690 1.649815 CCGCCGCTGTGTTACAAAA 59.350 52.632 0.00 0.00 0.00 2.44
4349 4710 2.330216 ACCTATGACCCTAGCATCACC 58.670 52.381 0.00 0.00 0.00 4.02
4350 4711 1.273606 CCTATGACCCTAGCATCACCG 59.726 57.143 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.173913 ATACCAAAACGAGGCCAAGC 58.826 50.000 5.01 0.00 0.00 4.01
9 10 1.263217 CGCATATACCAAAACGAGGCC 59.737 52.381 0.00 0.00 0.00 5.19
14 15 6.487960 TCAAAATACCGCATATACCAAAACG 58.512 36.000 0.00 0.00 0.00 3.60
42 43 2.292323 ACCGAGACCAAGGAAGGTAGAT 60.292 50.000 0.00 0.00 43.38 1.98
50 51 1.345415 GTTTACCACCGAGACCAAGGA 59.655 52.381 0.00 0.00 0.00 3.36
63 64 0.828022 ATCGCTCCATCGGTTTACCA 59.172 50.000 0.00 0.00 35.14 3.25
67 68 0.389391 ATCGATCGCTCCATCGGTTT 59.611 50.000 11.09 0.00 44.85 3.27
69 70 1.287191 CATCGATCGCTCCATCGGT 59.713 57.895 11.09 0.64 44.85 4.69
88 89 2.805671 GGTCAATGATCACGACAACACA 59.194 45.455 22.21 0.00 0.00 3.72
196 222 2.507324 GAGGAAGGCGCTGTCGTC 60.507 66.667 7.64 12.20 41.36 4.20
197 223 4.421479 CGAGGAAGGCGCTGTCGT 62.421 66.667 7.64 6.57 38.14 4.34
415 450 2.288213 GCTAGGGTGCAAAACAAAGGAC 60.288 50.000 0.00 0.00 0.00 3.85
417 452 1.335872 CGCTAGGGTGCAAAACAAAGG 60.336 52.381 0.00 0.00 0.00 3.11
418 453 1.930371 GCGCTAGGGTGCAAAACAAAG 60.930 52.381 8.77 0.00 46.98 2.77
469 504 4.580044 GATCATGCGTGCGGTGCG 62.580 66.667 0.00 0.00 34.24 5.34
515 550 2.858158 CATCGCATCGCATCGCAT 59.142 55.556 0.00 0.00 0.00 4.73
516 551 4.004241 GCATCGCATCGCATCGCA 62.004 61.111 0.00 0.00 0.00 5.10
517 552 4.731503 GGCATCGCATCGCATCGC 62.732 66.667 0.00 0.00 0.00 4.58
518 553 4.081030 GGGCATCGCATCGCATCG 62.081 66.667 0.00 0.00 0.00 3.84
519 554 4.081030 CGGGCATCGCATCGCATC 62.081 66.667 0.00 0.00 0.00 3.91
866 919 0.687920 TTGCCGATCAACTGGTGGTA 59.312 50.000 0.00 0.00 0.00 3.25
868 921 4.395519 TTGCCGATCAACTGGTGG 57.604 55.556 0.00 0.00 0.00 4.61
983 1044 2.037901 ACATGATGATCTCCAGCGAGT 58.962 47.619 0.00 0.00 37.40 4.18
989 1050 2.366590 CCCTCGAACATGATGATCTCCA 59.633 50.000 0.00 0.00 0.00 3.86
1134 1195 2.125673 CGGTGCTTACTGTCGGGG 60.126 66.667 0.00 0.00 0.00 5.73
1151 1212 4.173924 GGCAGGAGCAGAGGAGGC 62.174 72.222 0.00 0.00 44.61 4.70
1241 1314 4.864334 GTGAGCTGGGCGATGGGG 62.864 72.222 0.00 0.00 0.00 4.96
1265 1346 2.401766 GGCTGCCGGACATGAACAG 61.402 63.158 5.05 1.33 0.00 3.16
1383 1473 8.904834 TGCTGTACTTCATAAAAGTAAAAACCA 58.095 29.630 0.00 0.00 34.84 3.67
1396 1486 7.013750 CCTTCACTCTCTATGCTGTACTTCATA 59.986 40.741 0.00 1.34 0.00 2.15
1398 1488 5.126222 CCTTCACTCTCTATGCTGTACTTCA 59.874 44.000 0.00 0.00 0.00 3.02
1401 1491 4.861196 TCCTTCACTCTCTATGCTGTACT 58.139 43.478 0.00 0.00 0.00 2.73
1402 1492 5.300539 TGATCCTTCACTCTCTATGCTGTAC 59.699 44.000 0.00 0.00 0.00 2.90
1403 1493 5.449553 TGATCCTTCACTCTCTATGCTGTA 58.550 41.667 0.00 0.00 0.00 2.74
1405 1495 4.933505 TGATCCTTCACTCTCTATGCTG 57.066 45.455 0.00 0.00 0.00 4.41
1425 1515 0.531200 GAGAGTGGTAACCTCCGGTG 59.469 60.000 0.00 0.00 35.34 4.94
1461 1551 6.019479 GTGATCATAACACACGGATCTTTCTC 60.019 42.308 0.00 0.00 37.60 2.87
1504 1602 5.389935 CGTCTCAAAGAAAAAGGAAGATCGG 60.390 44.000 0.00 0.00 0.00 4.18
1535 1633 1.690219 GGGGCCACAGATCGAGTGAT 61.690 60.000 18.99 0.00 39.30 3.06
1536 1634 2.359169 GGGGCCACAGATCGAGTGA 61.359 63.158 18.99 0.00 39.30 3.41
1537 1635 1.976132 ATGGGGCCACAGATCGAGTG 61.976 60.000 15.99 12.65 36.76 3.51
1559 1657 6.317789 TGGATCAGAACAGAAAACAATCAC 57.682 37.500 0.00 0.00 0.00 3.06
1590 1689 8.626526 TCAAATCAGTACTCGCATATACTACAA 58.373 33.333 0.00 0.00 30.36 2.41
1603 1702 6.242508 GGAAACCAAGTCAAATCAGTACTC 57.757 41.667 0.00 0.00 0.00 2.59
1710 1824 3.181429 TGGAAACCTGAAGATGGCTCTTT 60.181 43.478 1.66 0.00 41.87 2.52
1722 1962 3.136443 AGTGATGTTGAGTGGAAACCTGA 59.864 43.478 0.00 0.00 0.00 3.86
1723 1963 3.251729 CAGTGATGTTGAGTGGAAACCTG 59.748 47.826 0.00 0.00 0.00 4.00
1724 1964 3.480470 CAGTGATGTTGAGTGGAAACCT 58.520 45.455 0.00 0.00 0.00 3.50
1725 1965 2.030805 GCAGTGATGTTGAGTGGAAACC 60.031 50.000 0.00 0.00 0.00 3.27
1726 1966 2.618241 TGCAGTGATGTTGAGTGGAAAC 59.382 45.455 0.00 0.00 0.00 2.78
1727 1967 2.929641 TGCAGTGATGTTGAGTGGAAA 58.070 42.857 0.00 0.00 0.00 3.13
1728 1968 2.636647 TGCAGTGATGTTGAGTGGAA 57.363 45.000 0.00 0.00 0.00 3.53
1729 1969 2.618241 GTTTGCAGTGATGTTGAGTGGA 59.382 45.455 0.00 0.00 0.00 4.02
1730 1970 2.620115 AGTTTGCAGTGATGTTGAGTGG 59.380 45.455 0.00 0.00 0.00 4.00
1731 1971 3.976793 AGTTTGCAGTGATGTTGAGTG 57.023 42.857 0.00 0.00 0.00 3.51
1732 1972 4.708177 ACTAGTTTGCAGTGATGTTGAGT 58.292 39.130 0.00 0.00 0.00 3.41
1733 1973 5.679734 AACTAGTTTGCAGTGATGTTGAG 57.320 39.130 1.12 0.00 0.00 3.02
1734 1974 7.094805 GGAATAACTAGTTTGCAGTGATGTTGA 60.095 37.037 14.49 0.00 0.00 3.18
1735 1975 7.023575 GGAATAACTAGTTTGCAGTGATGTTG 58.976 38.462 14.49 0.00 0.00 3.33
1736 1976 6.151144 GGGAATAACTAGTTTGCAGTGATGTT 59.849 38.462 14.49 0.00 0.00 2.71
1737 1977 5.648092 GGGAATAACTAGTTTGCAGTGATGT 59.352 40.000 14.49 0.00 0.00 3.06
1738 1978 5.882557 AGGGAATAACTAGTTTGCAGTGATG 59.117 40.000 14.49 0.00 0.00 3.07
1739 1979 6.067217 AGGGAATAACTAGTTTGCAGTGAT 57.933 37.500 14.49 0.00 0.00 3.06
1740 1980 5.499004 AGGGAATAACTAGTTTGCAGTGA 57.501 39.130 14.49 0.00 0.00 3.41
1741 1981 6.170506 TGTAGGGAATAACTAGTTTGCAGTG 58.829 40.000 14.49 0.00 0.00 3.66
1742 1982 6.368779 TGTAGGGAATAACTAGTTTGCAGT 57.631 37.500 14.49 0.00 0.00 4.40
1743 1983 7.681939 TTTGTAGGGAATAACTAGTTTGCAG 57.318 36.000 14.49 0.00 0.00 4.41
1744 1984 7.940137 TCTTTTGTAGGGAATAACTAGTTTGCA 59.060 33.333 14.49 1.31 0.00 4.08
1745 1985 8.331730 TCTTTTGTAGGGAATAACTAGTTTGC 57.668 34.615 14.49 1.54 0.00 3.68
1747 1987 9.856162 TGTTCTTTTGTAGGGAATAACTAGTTT 57.144 29.630 14.49 0.00 0.00 2.66
1748 1988 9.503399 CTGTTCTTTTGTAGGGAATAACTAGTT 57.497 33.333 13.68 13.68 0.00 2.24
1749 1989 7.606839 GCTGTTCTTTTGTAGGGAATAACTAGT 59.393 37.037 0.00 0.00 0.00 2.57
1750 1990 7.824779 AGCTGTTCTTTTGTAGGGAATAACTAG 59.175 37.037 0.00 0.00 0.00 2.57
1751 1991 7.606456 CAGCTGTTCTTTTGTAGGGAATAACTA 59.394 37.037 5.25 0.00 0.00 2.24
1752 1992 6.431234 CAGCTGTTCTTTTGTAGGGAATAACT 59.569 38.462 5.25 0.00 0.00 2.24
1753 1993 6.206829 ACAGCTGTTCTTTTGTAGGGAATAAC 59.793 38.462 15.25 0.00 0.00 1.89
1754 1994 6.303839 ACAGCTGTTCTTTTGTAGGGAATAA 58.696 36.000 15.25 0.00 0.00 1.40
1755 1995 5.876357 ACAGCTGTTCTTTTGTAGGGAATA 58.124 37.500 15.25 0.00 0.00 1.75
1756 1996 4.729868 ACAGCTGTTCTTTTGTAGGGAAT 58.270 39.130 15.25 0.00 0.00 3.01
1757 1997 4.164843 ACAGCTGTTCTTTTGTAGGGAA 57.835 40.909 15.25 0.00 0.00 3.97
1758 1998 3.857157 ACAGCTGTTCTTTTGTAGGGA 57.143 42.857 15.25 0.00 0.00 4.20
1759 1999 4.385825 TGTACAGCTGTTCTTTTGTAGGG 58.614 43.478 27.06 0.00 0.00 3.53
1760 2000 7.849804 ATATGTACAGCTGTTCTTTTGTAGG 57.150 36.000 27.06 0.00 0.00 3.18
1762 2002 9.244799 CGATATATGTACAGCTGTTCTTTTGTA 57.755 33.333 27.06 11.55 0.00 2.41
1763 2003 7.764443 ACGATATATGTACAGCTGTTCTTTTGT 59.236 33.333 27.06 11.22 0.00 2.83
1764 2004 8.131455 ACGATATATGTACAGCTGTTCTTTTG 57.869 34.615 27.06 9.48 0.00 2.44
1765 2005 8.604035 CAACGATATATGTACAGCTGTTCTTTT 58.396 33.333 27.06 14.93 0.00 2.27
1766 2006 7.254455 GCAACGATATATGTACAGCTGTTCTTT 60.254 37.037 27.06 11.25 0.00 2.52
1767 2007 6.201044 GCAACGATATATGTACAGCTGTTCTT 59.799 38.462 27.06 19.74 0.00 2.52
1768 2008 5.692204 GCAACGATATATGTACAGCTGTTCT 59.308 40.000 27.06 12.40 0.00 3.01
1769 2009 5.692204 AGCAACGATATATGTACAGCTGTTC 59.308 40.000 27.06 20.96 0.00 3.18
1770 2010 5.463392 CAGCAACGATATATGTACAGCTGTT 59.537 40.000 27.06 10.01 41.31 3.16
1771 2011 4.984785 CAGCAACGATATATGTACAGCTGT 59.015 41.667 25.12 25.12 41.31 4.40
1772 2012 5.506644 CAGCAACGATATATGTACAGCTG 57.493 43.478 13.48 13.48 40.57 4.24
1773 2013 5.201713 ACAGCAACGATATATGTACAGCT 57.798 39.130 0.33 0.00 0.00 4.24
1774 2014 5.907197 AACAGCAACGATATATGTACAGC 57.093 39.130 0.33 0.00 0.00 4.40
1779 2019 9.935682 CTCAATAAAAACAGCAACGATATATGT 57.064 29.630 0.00 0.00 0.00 2.29
1780 2020 9.935682 ACTCAATAAAAACAGCAACGATATATG 57.064 29.630 0.00 0.00 0.00 1.78
1781 2021 9.935682 CACTCAATAAAAACAGCAACGATATAT 57.064 29.630 0.00 0.00 0.00 0.86
1782 2022 7.908082 GCACTCAATAAAAACAGCAACGATATA 59.092 33.333 0.00 0.00 0.00 0.86
1783 2023 6.747280 GCACTCAATAAAAACAGCAACGATAT 59.253 34.615 0.00 0.00 0.00 1.63
1784 2024 6.072728 AGCACTCAATAAAAACAGCAACGATA 60.073 34.615 0.00 0.00 0.00 2.92
1785 2025 4.917415 GCACTCAATAAAAACAGCAACGAT 59.083 37.500 0.00 0.00 0.00 3.73
1786 2026 4.036262 AGCACTCAATAAAAACAGCAACGA 59.964 37.500 0.00 0.00 0.00 3.85
1787 2027 4.290155 AGCACTCAATAAAAACAGCAACG 58.710 39.130 0.00 0.00 0.00 4.10
1788 2028 7.873739 ATTAGCACTCAATAAAAACAGCAAC 57.126 32.000 0.00 0.00 0.00 4.17
1789 2029 7.598493 GGAATTAGCACTCAATAAAAACAGCAA 59.402 33.333 0.00 0.00 0.00 3.91
1790 2030 7.039784 AGGAATTAGCACTCAATAAAAACAGCA 60.040 33.333 0.00 0.00 0.00 4.41
1791 2031 7.315890 AGGAATTAGCACTCAATAAAAACAGC 58.684 34.615 0.00 0.00 0.00 4.40
1796 2036 9.959721 AGAGTTAGGAATTAGCACTCAATAAAA 57.040 29.630 8.48 0.00 37.02 1.52
1797 2037 9.601217 GAGAGTTAGGAATTAGCACTCAATAAA 57.399 33.333 8.48 0.00 37.02 1.40
1798 2038 7.921214 CGAGAGTTAGGAATTAGCACTCAATAA 59.079 37.037 8.48 0.00 37.02 1.40
1799 2039 7.284716 TCGAGAGTTAGGAATTAGCACTCAATA 59.715 37.037 8.48 0.00 37.02 1.90
1800 2040 6.096987 TCGAGAGTTAGGAATTAGCACTCAAT 59.903 38.462 8.48 0.00 37.02 2.57
1801 2041 5.417894 TCGAGAGTTAGGAATTAGCACTCAA 59.582 40.000 8.48 0.00 37.02 3.02
1802 2042 4.948004 TCGAGAGTTAGGAATTAGCACTCA 59.052 41.667 8.48 0.00 37.02 3.41
1803 2043 5.502153 TCGAGAGTTAGGAATTAGCACTC 57.498 43.478 0.00 0.00 35.13 3.51
1804 2044 5.594725 TGATCGAGAGTTAGGAATTAGCACT 59.405 40.000 0.00 0.00 0.00 4.40
1805 2045 5.688176 GTGATCGAGAGTTAGGAATTAGCAC 59.312 44.000 0.00 0.00 0.00 4.40
1806 2046 5.505819 CGTGATCGAGAGTTAGGAATTAGCA 60.506 44.000 0.00 0.00 39.71 3.49
1807 2047 4.912766 CGTGATCGAGAGTTAGGAATTAGC 59.087 45.833 0.00 0.00 39.71 3.09
1808 2048 6.062434 ACGTGATCGAGAGTTAGGAATTAG 57.938 41.667 0.00 0.00 40.62 1.73
1809 2049 5.587443 TGACGTGATCGAGAGTTAGGAATTA 59.413 40.000 0.00 0.00 40.62 1.40
1810 2050 4.398358 TGACGTGATCGAGAGTTAGGAATT 59.602 41.667 0.00 0.00 40.62 2.17
1811 2051 3.945921 TGACGTGATCGAGAGTTAGGAAT 59.054 43.478 0.00 0.00 40.62 3.01
1812 2052 3.340928 TGACGTGATCGAGAGTTAGGAA 58.659 45.455 0.00 0.00 40.62 3.36
1813 2053 2.981898 TGACGTGATCGAGAGTTAGGA 58.018 47.619 0.00 0.00 40.62 2.94
1814 2054 3.759527 TTGACGTGATCGAGAGTTAGG 57.240 47.619 0.00 0.00 40.62 2.69
1815 2055 4.323868 GGTTTTGACGTGATCGAGAGTTAG 59.676 45.833 0.00 0.00 40.62 2.34
1816 2056 4.022589 AGGTTTTGACGTGATCGAGAGTTA 60.023 41.667 0.00 0.00 40.62 2.24
1817 2057 3.057734 GGTTTTGACGTGATCGAGAGTT 58.942 45.455 0.00 0.00 40.62 3.01
1818 2058 2.296471 AGGTTTTGACGTGATCGAGAGT 59.704 45.455 0.00 0.00 40.62 3.24
1819 2059 2.917971 GAGGTTTTGACGTGATCGAGAG 59.082 50.000 0.00 0.00 40.62 3.20
1820 2060 2.295070 TGAGGTTTTGACGTGATCGAGA 59.705 45.455 0.00 0.00 40.62 4.04
1821 2061 2.663602 CTGAGGTTTTGACGTGATCGAG 59.336 50.000 0.00 0.00 40.62 4.04
1822 2062 2.295070 TCTGAGGTTTTGACGTGATCGA 59.705 45.455 0.00 0.00 40.62 3.59
1823 2063 2.672714 TCTGAGGTTTTGACGTGATCG 58.327 47.619 0.00 0.00 43.34 3.69
1824 2064 5.613358 ATTTCTGAGGTTTTGACGTGATC 57.387 39.130 0.00 0.00 0.00 2.92
1825 2065 5.995282 TGTATTTCTGAGGTTTTGACGTGAT 59.005 36.000 0.00 0.00 0.00 3.06
1826 2066 5.361427 TGTATTTCTGAGGTTTTGACGTGA 58.639 37.500 0.00 0.00 0.00 4.35
1827 2067 5.334105 CCTGTATTTCTGAGGTTTTGACGTG 60.334 44.000 0.00 0.00 0.00 4.49
1828 2068 4.755123 CCTGTATTTCTGAGGTTTTGACGT 59.245 41.667 0.00 0.00 0.00 4.34
1829 2069 4.994852 TCCTGTATTTCTGAGGTTTTGACG 59.005 41.667 0.00 0.00 0.00 4.35
1830 2070 6.127897 CCATCCTGTATTTCTGAGGTTTTGAC 60.128 42.308 0.00 0.00 0.00 3.18
1831 2071 5.945784 CCATCCTGTATTTCTGAGGTTTTGA 59.054 40.000 0.00 0.00 0.00 2.69
1832 2072 5.126061 CCCATCCTGTATTTCTGAGGTTTTG 59.874 44.000 0.00 0.00 0.00 2.44
1833 2073 5.015178 TCCCATCCTGTATTTCTGAGGTTTT 59.985 40.000 0.00 0.00 0.00 2.43
1834 2074 4.540099 TCCCATCCTGTATTTCTGAGGTTT 59.460 41.667 0.00 0.00 0.00 3.27
1835 2075 4.111577 TCCCATCCTGTATTTCTGAGGTT 58.888 43.478 0.00 0.00 0.00 3.50
1836 2076 3.736094 TCCCATCCTGTATTTCTGAGGT 58.264 45.455 0.00 0.00 0.00 3.85
1837 2077 4.778213 TTCCCATCCTGTATTTCTGAGG 57.222 45.455 0.00 0.00 0.00 3.86
1838 2078 4.578105 GCTTTCCCATCCTGTATTTCTGAG 59.422 45.833 0.00 0.00 0.00 3.35
1875 2115 2.103432 TCTGTTGGTTTCGAAGCCTGTA 59.897 45.455 28.20 14.73 0.00 2.74
1996 2260 5.499268 AAAATCAAAATGCATCAACGTCG 57.501 34.783 0.00 0.00 0.00 5.12
2014 2278 3.323691 CAGGGAAAAGGGGAAACGAAAAT 59.676 43.478 0.00 0.00 0.00 1.82
2027 2291 4.584325 TGTGAGATTTGGAACAGGGAAAAG 59.416 41.667 0.00 0.00 42.39 2.27
2062 2328 1.208614 CGAAGGCTGTGCAAAGAGC 59.791 57.895 8.49 6.58 45.96 4.09
2166 2432 2.594592 AACCACCACGCTCTTGGC 60.595 61.111 0.00 0.00 40.77 4.52
2176 2442 7.016153 ACTAGAAATTAGACATGAACCACCA 57.984 36.000 0.00 0.00 0.00 4.17
2385 2673 4.559862 AGGCCCATCTATATGCTTACAC 57.440 45.455 0.00 0.00 0.00 2.90
2387 2675 5.529060 GCATAAGGCCCATCTATATGCTTAC 59.471 44.000 17.15 0.00 43.32 2.34
2401 2698 0.316204 GACATGCATGCATAAGGCCC 59.684 55.000 31.73 13.60 43.89 5.80
2469 2769 7.062749 TCTGTGAAGTACTTTAGGTGATGTT 57.937 36.000 10.02 0.00 0.00 2.71
2501 2801 9.601971 GCATTTTGTGTTACTCGTCTATTTTAA 57.398 29.630 0.00 0.00 0.00 1.52
2511 2811 1.801771 TCCGGCATTTTGTGTTACTCG 59.198 47.619 0.00 0.00 0.00 4.18
2537 2837 5.687730 CGGTACACATAGACTGATCATGAAC 59.312 44.000 0.00 0.00 0.00 3.18
2538 2838 5.592688 TCGGTACACATAGACTGATCATGAA 59.407 40.000 0.00 0.00 0.00 2.57
2539 2839 5.130350 TCGGTACACATAGACTGATCATGA 58.870 41.667 0.00 0.00 0.00 3.07
2540 2840 5.438761 TCGGTACACATAGACTGATCATG 57.561 43.478 0.00 0.00 0.00 3.07
2541 2841 6.265422 TGATTCGGTACACATAGACTGATCAT 59.735 38.462 0.00 0.00 31.15 2.45
2542 2842 5.592688 TGATTCGGTACACATAGACTGATCA 59.407 40.000 0.00 0.00 31.15 2.92
2543 2843 6.073327 TGATTCGGTACACATAGACTGATC 57.927 41.667 0.00 0.00 31.15 2.92
2844 3185 1.406903 GCAGGGATTTGGAGGAATGG 58.593 55.000 0.00 0.00 0.00 3.16
2875 3223 6.200097 GGTTAAAACATTGTGCAACTACCTTG 59.800 38.462 0.00 0.00 38.04 3.61
2877 3225 5.361285 TGGTTAAAACATTGTGCAACTACCT 59.639 36.000 0.00 0.00 38.04 3.08
2878 3226 5.593010 TGGTTAAAACATTGTGCAACTACC 58.407 37.500 0.00 0.00 38.04 3.18
2879 3227 7.436673 TGAATGGTTAAAACATTGTGCAACTAC 59.563 33.333 10.40 0.00 38.57 2.73
2881 3229 6.344500 TGAATGGTTAAAACATTGTGCAACT 58.656 32.000 10.40 0.00 38.57 3.16
2885 3233 8.532977 AATACTGAATGGTTAAAACATTGTGC 57.467 30.769 10.40 0.07 38.57 4.57
2894 3242 8.271458 TGCATAGGAGAATACTGAATGGTTAAA 58.729 33.333 0.00 0.00 0.00 1.52
2902 3250 6.048732 TGTGTTGCATAGGAGAATACTGAA 57.951 37.500 0.00 0.00 0.00 3.02
2920 3268 3.213206 TCTTCTGAACCTGCATGTGTT 57.787 42.857 0.00 0.00 0.00 3.32
3028 3376 0.803117 TGTCTCTAGGTTCGCGTCTG 59.197 55.000 5.77 0.00 0.00 3.51
3035 3383 2.094649 CGACCTGGTTGTCTCTAGGTTC 60.095 54.545 0.00 0.00 43.28 3.62
3037 3385 1.546961 CGACCTGGTTGTCTCTAGGT 58.453 55.000 0.00 1.59 45.77 3.08
3077 3425 1.144936 CATGAACCCCGAGAGAGCC 59.855 63.158 0.00 0.00 0.00 4.70
3131 3479 3.263259 AAGGCCTTGGCCAGCTCT 61.263 61.111 29.79 8.44 0.00 4.09
3206 3554 3.884581 TTTCACGTCCTCGCCGTCG 62.885 63.158 0.00 0.00 41.18 5.12
3207 3555 1.445582 ATTTCACGTCCTCGCCGTC 60.446 57.895 0.00 0.00 41.18 4.79
3208 3556 1.736645 CATTTCACGTCCTCGCCGT 60.737 57.895 0.00 0.00 41.18 5.68
3453 3808 9.419297 CATGCATAGGTACGTATAAAGTGTAAT 57.581 33.333 7.72 0.00 0.00 1.89
3471 3826 8.757789 CCACAAATTTTACATTAGCATGCATAG 58.242 33.333 21.98 9.13 33.05 2.23
3474 3829 6.695429 TCCACAAATTTTACATTAGCATGCA 58.305 32.000 21.98 0.00 33.05 3.96
3475 3830 7.593875 TTCCACAAATTTTACATTAGCATGC 57.406 32.000 10.51 10.51 33.05 4.06
3492 3847 3.091545 GCCTGGATCTCAATTTCCACAA 58.908 45.455 0.00 0.00 37.10 3.33
3515 3870 6.914259 TCATCATCTAGCTACACTTATTCGG 58.086 40.000 0.00 0.00 0.00 4.30
3547 3902 5.462729 ACGTATACAGTGTAGTCAGATCTCG 59.537 44.000 9.25 3.93 0.00 4.04
3557 3912 7.792374 TTTAGGAGGTACGTATACAGTGTAG 57.208 40.000 9.25 0.00 32.40 2.74
3559 3914 7.651027 ATTTTAGGAGGTACGTATACAGTGT 57.349 36.000 0.00 0.00 32.40 3.55
3566 3921 7.368833 CGATCAGAATTTTAGGAGGTACGTAT 58.631 38.462 0.00 0.00 0.00 3.06
3592 3947 4.023107 TCCACGATGCTACTATGTTCTAGC 60.023 45.833 0.00 0.00 36.65 3.42
3596 3951 4.045104 CACTCCACGATGCTACTATGTTC 58.955 47.826 0.00 0.00 0.00 3.18
3603 3961 3.810373 CAAAAACACTCCACGATGCTAC 58.190 45.455 0.00 0.00 0.00 3.58
3604 3962 2.225491 GCAAAAACACTCCACGATGCTA 59.775 45.455 0.00 0.00 0.00 3.49
3605 3963 1.001378 GCAAAAACACTCCACGATGCT 60.001 47.619 0.00 0.00 0.00 3.79
3628 3986 6.005823 CCATCATAATGCTATCCCTCAACAA 58.994 40.000 0.00 0.00 0.00 2.83
3640 3998 3.623703 TGCAACACTCCATCATAATGCT 58.376 40.909 0.00 0.00 33.87 3.79
3752 4110 6.365247 GCTTACTCGACAAGACATTAGAAACA 59.635 38.462 6.26 0.00 0.00 2.83
3822 4180 0.106268 AGACATGCAAACCACCACCA 60.106 50.000 0.00 0.00 0.00 4.17
3911 4269 9.515020 GTGTGTTGACATTTTTCTTCAGAATTA 57.485 29.630 0.00 0.00 33.63 1.40
3922 4280 6.205784 CAAGGATACGTGTGTTGACATTTTT 58.794 36.000 0.00 0.00 41.54 1.94
3924 4282 5.356882 CAAGGATACGTGTGTTGACATTT 57.643 39.130 0.00 0.00 41.54 2.32
3957 4315 9.922305 GGATAATAGATTTGAGTGTTTTTCGAG 57.078 33.333 0.00 0.00 0.00 4.04
3958 4316 9.443323 TGGATAATAGATTTGAGTGTTTTTCGA 57.557 29.630 0.00 0.00 0.00 3.71
3965 4323 8.041323 ACTCGTTTGGATAATAGATTTGAGTGT 58.959 33.333 0.00 0.00 31.23 3.55
3972 4330 7.497595 TGCACTACTCGTTTGGATAATAGATT 58.502 34.615 0.00 0.00 0.00 2.40
3977 4335 6.128007 CCTTTTGCACTACTCGTTTGGATAAT 60.128 38.462 0.00 0.00 0.00 1.28
3980 4338 3.502211 CCTTTTGCACTACTCGTTTGGAT 59.498 43.478 0.00 0.00 0.00 3.41
4001 4359 9.877137 CAATGTAACTTTTTATTTTTCAAGGCC 57.123 29.630 0.00 0.00 0.00 5.19
4013 4371 5.474189 CCGGGGACTTCAATGTAACTTTTTA 59.526 40.000 0.00 0.00 0.00 1.52
4015 4373 3.824443 CCGGGGACTTCAATGTAACTTTT 59.176 43.478 0.00 0.00 0.00 2.27
4016 4374 3.418047 CCGGGGACTTCAATGTAACTTT 58.582 45.455 0.00 0.00 0.00 2.66
4017 4375 2.290705 CCCGGGGACTTCAATGTAACTT 60.291 50.000 14.71 0.00 0.00 2.66
4018 4376 1.280998 CCCGGGGACTTCAATGTAACT 59.719 52.381 14.71 0.00 0.00 2.24
4019 4377 1.680860 CCCCGGGGACTTCAATGTAAC 60.681 57.143 38.41 0.00 37.50 2.50
4037 4395 0.106967 GGAAGAAGATGGTCAGCCCC 60.107 60.000 0.00 0.00 0.00 5.80
4047 4405 4.963318 TCAGTTGTGTGAGGAAGAAGAT 57.037 40.909 0.00 0.00 0.00 2.40
4059 4417 2.260869 GGTGCGCCATCAGTTGTGT 61.261 57.895 12.58 0.00 34.09 3.72
4076 4436 1.152567 TTGGAGCTGTTTGGGGTGG 60.153 57.895 0.00 0.00 0.00 4.61
4104 4464 2.223377 CGTGGTCAACAAAGGTAAGCTC 59.777 50.000 0.00 0.00 0.00 4.09
4113 4473 4.200874 ACTTACCATTCGTGGTCAACAAA 58.799 39.130 2.92 0.00 42.99 2.83
4121 4481 3.623060 CCTTGATGACTTACCATTCGTGG 59.377 47.826 0.00 0.00 0.00 4.94
4126 4486 5.221925 ACTGTGACCTTGATGACTTACCATT 60.222 40.000 0.00 0.00 0.00 3.16
4151 4511 1.216930 TCAGGGTGATGGTCCGATAGA 59.783 52.381 0.00 0.00 39.76 1.98
4155 4515 1.060729 TTTTCAGGGTGATGGTCCGA 58.939 50.000 0.00 0.00 0.00 4.55
4171 4531 2.420722 TCGGTTGCGACAACTTCTTTTT 59.579 40.909 17.89 0.00 0.00 1.94
4180 4540 1.503818 GGCTCTTTCGGTTGCGACAA 61.504 55.000 6.39 0.00 0.00 3.18
4182 4542 1.228657 AAGGCTCTTTCGGTTGCGAC 61.229 55.000 0.00 0.00 0.00 5.19
4185 4545 2.094762 TCTAAGGCTCTTTCGGTTGC 57.905 50.000 0.00 0.00 0.00 4.17
4259 4620 4.100035 TCCTCATCTTCGTCACATTAGCAT 59.900 41.667 0.00 0.00 0.00 3.79
4282 4643 3.372395 CCTTCCTAGGTGGGTTTTCCCT 61.372 54.545 9.08 0.00 45.88 4.20
4288 4649 1.082194 TCATCCCTTCCTAGGTGGGTT 59.918 52.381 28.98 22.55 40.19 4.11
4297 4658 4.162690 GCGGCGTCATCCCTTCCT 62.163 66.667 9.37 0.00 0.00 3.36
4320 4681 5.013287 TGCTAGGGTCATAGGTTTTGTAACA 59.987 40.000 0.00 0.00 35.92 2.41
4321 4682 5.493809 TGCTAGGGTCATAGGTTTTGTAAC 58.506 41.667 0.00 0.00 0.00 2.50
4329 4690 2.330216 GGTGATGCTAGGGTCATAGGT 58.670 52.381 0.00 0.00 0.00 3.08


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

AutoCloner maintained by Alex Coulton.