Multiple sequence alignment - TraesCS6D01G123700

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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 TraesCS6D01G123700 chr6D 100.000 2267 0 0 1 2267 88830981 88833247 0.000000e+00 4187.0
1 TraesCS6D01G123700 chr6B 86.407 1258 72 41 747 1928 169171959 169173193 0.000000e+00 1284.0
2 TraesCS6D01G123700 chr6B 92.500 520 32 7 1 516 204339125 204339641 0.000000e+00 737.0
3 TraesCS6D01G123700 chr6A 88.443 848 49 27 516 1336 106877916 106878741 0.000000e+00 977.0
4 TraesCS6D01G123700 chr6A 83.022 642 49 17 1339 1927 106878772 106879406 5.550000e-146 527.0
5 TraesCS6D01G123700 chr5D 94.434 521 20 5 1 515 385901307 385901824 0.000000e+00 793.0
6 TraesCS6D01G123700 chr5D 81.818 242 31 11 1993 2225 230029446 230029683 8.260000e-45 191.0
7 TraesCS6D01G123700 chr4D 94.286 525 19 7 1 515 437523044 437523567 0.000000e+00 793.0
8 TraesCS6D01G123700 chr4D 94.389 499 16 9 27 516 509076996 509076501 0.000000e+00 756.0
9 TraesCS6D01G123700 chr3D 93.939 528 15 12 1 520 435132193 435132711 0.000000e+00 782.0
10 TraesCS6D01G123700 chr3D 82.449 245 30 11 1989 2225 447631938 447631699 3.820000e-48 202.0
11 TraesCS6D01G123700 chr7D 95.030 503 14 7 22 517 538342912 538342414 0.000000e+00 780.0
12 TraesCS6D01G123700 chr7D 94.177 498 18 11 22 515 558170343 558169853 0.000000e+00 749.0
13 TraesCS6D01G123700 chr7D 86.667 135 16 2 1000 1133 557348245 557348112 5.050000e-32 148.0
14 TraesCS6D01G123700 chr2D 94.622 502 15 10 22 515 157393221 157392724 0.000000e+00 767.0
15 TraesCS6D01G123700 chr2D 80.546 293 34 12 1993 2266 572036404 572036116 1.060000e-48 204.0
16 TraesCS6D01G123700 chr2D 82.573 241 31 9 1993 2225 179186007 179185770 3.820000e-48 202.0
17 TraesCS6D01G123700 chr2D 79.181 293 40 10 1993 2267 202604407 202604696 1.380000e-42 183.0
18 TraesCS6D01G123700 chr2D 88.095 84 8 2 1029 1111 587111797 587111715 5.150000e-17 99.0
19 TraesCS6D01G123700 chr2D 81.720 93 10 7 1009 1099 617957702 617957789 1.120000e-08 71.3
20 TraesCS6D01G123700 chrUn 94.355 496 17 6 27 515 132054414 132054905 0.000000e+00 750.0
21 TraesCS6D01G123700 chrUn 93.421 76 5 0 1058 1133 86733754 86733679 1.840000e-21 113.0
22 TraesCS6D01G123700 chr4A 80.205 293 37 15 1993 2267 474757496 474757785 1.370000e-47 200.0
23 TraesCS6D01G123700 chr3B 79.933 299 38 13 1987 2267 560875383 560875677 1.370000e-47 200.0
24 TraesCS6D01G123700 chr7B 81.481 243 32 11 1986 2220 408514286 408514523 1.070000e-43 187.0
25 TraesCS6D01G123700 chr7B 84.444 135 19 2 1000 1133 605112232 605112099 5.080000e-27 132.0
26 TraesCS6D01G123700 chr7B 84.375 128 20 0 1000 1127 605872268 605872395 2.360000e-25 126.0
27 TraesCS6D01G123700 chr1A 80.913 241 35 8 1993 2225 166213027 166212790 1.790000e-41 180.0
28 TraesCS6D01G123700 chr7A 86.667 135 16 2 1000 1133 643298290 643298423 5.050000e-32 148.0
29 TraesCS6D01G123700 chr2B 88.462 78 8 1 1035 1111 708863243 708863166 2.400000e-15 93.5


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 TraesCS6D01G123700 chr6D 88830981 88833247 2266 False 4187 4187 100.0000 1 2267 1 chr6D.!!$F1 2266
1 TraesCS6D01G123700 chr6B 169171959 169173193 1234 False 1284 1284 86.4070 747 1928 1 chr6B.!!$F1 1181
2 TraesCS6D01G123700 chr6B 204339125 204339641 516 False 737 737 92.5000 1 516 1 chr6B.!!$F2 515
3 TraesCS6D01G123700 chr6A 106877916 106879406 1490 False 752 977 85.7325 516 1927 2 chr6A.!!$F1 1411
4 TraesCS6D01G123700 chr5D 385901307 385901824 517 False 793 793 94.4340 1 515 1 chr5D.!!$F2 514
5 TraesCS6D01G123700 chr4D 437523044 437523567 523 False 793 793 94.2860 1 515 1 chr4D.!!$F1 514
6 TraesCS6D01G123700 chr3D 435132193 435132711 518 False 782 782 93.9390 1 520 1 chr3D.!!$F1 519

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
736 755 0.328592 TAGCGGAGAGAGAGTGTGGT 59.671 55.0 0.0 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1962 2129 0.168128 GGCTTTGCGTTGCTCGTATT 59.832 50.0 4.16 0.0 42.13 1.89 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
393 403 1.903877 CTGGAGTCCAATCGGCCTGT 61.904 60.000 14.17 0.00 30.80 4.00
539 556 0.388649 CTCGCGACTTACAGCCAACT 60.389 55.000 3.71 0.00 0.00 3.16
562 579 3.356290 ACATAATTTGGACTGACAGCCC 58.644 45.455 0.00 0.00 0.00 5.19
563 580 2.507407 TAATTTGGACTGACAGCCCC 57.493 50.000 5.23 6.45 0.00 5.80
627 644 8.900511 TCTTTTGCGAATGAGAGAATAAATTG 57.099 30.769 0.00 0.00 0.00 2.32
628 645 7.485913 TCTTTTGCGAATGAGAGAATAAATTGC 59.514 33.333 0.00 0.00 0.00 3.56
631 648 5.357878 TGCGAATGAGAGAATAAATTGCCTT 59.642 36.000 0.00 0.00 0.00 4.35
647 664 8.879427 AAATTGCCTTTAACCACTAATCTACT 57.121 30.769 0.00 0.00 0.00 2.57
678 697 9.974750 TTTCACGTTCCAAAAACAATTTATTTC 57.025 25.926 0.00 0.00 0.00 2.17
728 747 0.743688 AGCATGTGTAGCGGAGAGAG 59.256 55.000 0.00 0.00 37.01 3.20
729 748 0.741326 GCATGTGTAGCGGAGAGAGA 59.259 55.000 0.00 0.00 0.00 3.10
730 749 1.268999 GCATGTGTAGCGGAGAGAGAG 60.269 57.143 0.00 0.00 0.00 3.20
731 750 2.020720 CATGTGTAGCGGAGAGAGAGT 58.979 52.381 0.00 0.00 0.00 3.24
732 751 1.454201 TGTGTAGCGGAGAGAGAGTG 58.546 55.000 0.00 0.00 0.00 3.51
733 752 1.271434 TGTGTAGCGGAGAGAGAGTGT 60.271 52.381 0.00 0.00 0.00 3.55
734 753 1.131504 GTGTAGCGGAGAGAGAGTGTG 59.868 57.143 0.00 0.00 0.00 3.82
735 754 0.736053 GTAGCGGAGAGAGAGTGTGG 59.264 60.000 0.00 0.00 0.00 4.17
736 755 0.328592 TAGCGGAGAGAGAGTGTGGT 59.671 55.000 0.00 0.00 0.00 4.16
737 756 1.214062 GCGGAGAGAGAGTGTGGTG 59.786 63.158 0.00 0.00 0.00 4.17
738 757 1.214062 CGGAGAGAGAGTGTGGTGC 59.786 63.158 0.00 0.00 0.00 5.01
739 758 1.214062 GGAGAGAGAGTGTGGTGCG 59.786 63.158 0.00 0.00 0.00 5.34
740 759 1.244697 GGAGAGAGAGTGTGGTGCGA 61.245 60.000 0.00 0.00 0.00 5.10
741 760 0.814457 GAGAGAGAGTGTGGTGCGAT 59.186 55.000 0.00 0.00 0.00 4.58
742 761 0.814457 AGAGAGAGTGTGGTGCGATC 59.186 55.000 0.00 0.00 0.00 3.69
743 762 0.524392 GAGAGAGTGTGGTGCGATCG 60.524 60.000 11.69 11.69 0.00 3.69
744 763 2.125912 AGAGTGTGGTGCGATCGC 60.126 61.111 32.48 32.48 42.35 4.58
745 764 3.545481 GAGTGTGGTGCGATCGCG 61.545 66.667 32.64 0.00 45.51 5.87
757 776 1.783416 GCGATCGCGAACTTTCTTGTG 60.783 52.381 26.12 0.00 40.82 3.33
777 798 4.980805 GCCACGTCTTGTCCGCCA 62.981 66.667 0.00 0.00 0.00 5.69
871 893 3.119096 GCCTGTTTCGCGTCTCCC 61.119 66.667 5.77 0.00 0.00 4.30
918 940 1.087501 CAGAGATCACCGACGAGACA 58.912 55.000 0.00 0.00 0.00 3.41
928 950 1.004277 CGACGAGACAACAGCCACTC 61.004 60.000 0.00 0.00 0.00 3.51
942 965 1.429463 CCACTCGAGCAGTAAACCAC 58.571 55.000 13.61 0.00 32.21 4.16
1176 1219 4.877619 TCCGCCTCGCTCTCCGAT 62.878 66.667 0.00 0.00 46.31 4.18
1360 1451 0.969149 TTCGCCAGAGAAAGCAGAGA 59.031 50.000 0.00 0.00 0.00 3.10
1369 1460 2.072298 AGAAAGCAGAGACGTCATTGC 58.928 47.619 27.04 27.04 36.83 3.56
1461 1560 3.085533 TCTCTTCCTCCTCTTCGTCTTG 58.914 50.000 0.00 0.00 0.00 3.02
1466 1565 0.390472 CTCCTCTTCGTCTTGCCCAC 60.390 60.000 0.00 0.00 0.00 4.61
1495 1594 1.153369 TCGTTGCATCTGGCTAGCC 60.153 57.895 27.71 27.71 45.15 3.93
1548 1665 3.146847 GGAGATCACCCGTCTTGTTTTT 58.853 45.455 0.00 0.00 0.00 1.94
1549 1666 3.058224 GGAGATCACCCGTCTTGTTTTTG 60.058 47.826 0.00 0.00 0.00 2.44
1550 1667 3.551846 AGATCACCCGTCTTGTTTTTGT 58.448 40.909 0.00 0.00 0.00 2.83
1551 1668 4.710324 AGATCACCCGTCTTGTTTTTGTA 58.290 39.130 0.00 0.00 0.00 2.41
1552 1669 4.514066 AGATCACCCGTCTTGTTTTTGTAC 59.486 41.667 0.00 0.00 0.00 2.90
1607 1730 0.389948 GGTTGTACTGCGGTGGAGAG 60.390 60.000 8.92 0.00 0.00 3.20
1608 1731 0.389948 GTTGTACTGCGGTGGAGAGG 60.390 60.000 8.92 0.00 0.00 3.69
1658 1781 2.800544 ACTATGCTTGTGTTGTGTCGAC 59.199 45.455 9.11 9.11 0.00 4.20
1660 1783 2.588027 TGCTTGTGTTGTGTCGACTA 57.412 45.000 17.92 2.84 0.00 2.59
1661 1784 2.198406 TGCTTGTGTTGTGTCGACTAC 58.802 47.619 17.92 13.36 0.00 2.73
1662 1785 2.159156 TGCTTGTGTTGTGTCGACTACT 60.159 45.455 17.92 0.00 0.00 2.57
1679 1805 2.046280 ACTTACTGCCCTCCTCCTTT 57.954 50.000 0.00 0.00 0.00 3.11
1750 1893 4.114997 GCGATGGCGTTTGGGGTG 62.115 66.667 0.00 0.00 40.36 4.61
1764 1924 2.097036 TGGGGTGACAGTAGTACATCG 58.903 52.381 2.52 0.00 0.00 3.84
1807 1967 5.872617 CAGTAGTACCGAAATCAAATGGACA 59.127 40.000 0.00 0.00 0.00 4.02
1818 1978 7.359598 CGAAATCAAATGGACATAGCTAGTAGC 60.360 40.741 14.62 14.62 42.84 3.58
1861 2027 6.807230 CGAACTGTACTACTGCTAATGAACTT 59.193 38.462 0.00 0.00 0.00 2.66
1862 2028 7.328737 CGAACTGTACTACTGCTAATGAACTTT 59.671 37.037 0.00 0.00 0.00 2.66
1870 2036 9.216117 ACTACTGCTAATGAACTTTAAATCGTT 57.784 29.630 2.68 2.68 0.00 3.85
1872 2038 6.801862 ACTGCTAATGAACTTTAAATCGTTGC 59.198 34.615 6.54 8.05 0.00 4.17
1885 2051 2.004583 TCGTTGCCATGCTGTAGTAC 57.995 50.000 0.00 0.00 0.00 2.73
1900 2067 3.580895 TGTAGTACCAAGTCAGATGGCAA 59.419 43.478 0.00 0.00 41.89 4.52
1902 2069 3.614092 AGTACCAAGTCAGATGGCAATG 58.386 45.455 0.00 0.00 41.89 2.82
1937 2104 3.306917 TGCAAGATGGCAATGTTTCAG 57.693 42.857 0.00 0.00 41.65 3.02
1938 2105 2.892215 TGCAAGATGGCAATGTTTCAGA 59.108 40.909 0.00 0.00 41.65 3.27
1939 2106 3.321396 TGCAAGATGGCAATGTTTCAGAA 59.679 39.130 0.00 0.00 41.65 3.02
1940 2107 3.676646 GCAAGATGGCAATGTTTCAGAAC 59.323 43.478 0.00 0.00 36.29 3.01
1941 2108 4.560108 GCAAGATGGCAATGTTTCAGAACT 60.560 41.667 0.00 0.00 36.70 3.01
1942 2109 5.535333 CAAGATGGCAATGTTTCAGAACTT 58.465 37.500 0.00 0.00 36.70 2.66
1943 2110 5.382618 AGATGGCAATGTTTCAGAACTTC 57.617 39.130 0.00 0.00 36.70 3.01
1944 2111 4.828939 AGATGGCAATGTTTCAGAACTTCA 59.171 37.500 0.00 0.00 36.70 3.02
1945 2112 4.998671 TGGCAATGTTTCAGAACTTCAA 57.001 36.364 0.00 0.00 36.70 2.69
1946 2113 5.336150 TGGCAATGTTTCAGAACTTCAAA 57.664 34.783 0.00 0.00 36.70 2.69
1947 2114 5.916318 TGGCAATGTTTCAGAACTTCAAAT 58.084 33.333 0.00 0.00 36.70 2.32
1948 2115 6.347696 TGGCAATGTTTCAGAACTTCAAATT 58.652 32.000 0.00 0.00 36.70 1.82
1949 2116 6.822676 TGGCAATGTTTCAGAACTTCAAATTT 59.177 30.769 0.00 0.00 36.70 1.82
1950 2117 7.336427 TGGCAATGTTTCAGAACTTCAAATTTT 59.664 29.630 0.00 0.00 36.70 1.82
1951 2118 8.825745 GGCAATGTTTCAGAACTTCAAATTTTA 58.174 29.630 0.00 0.00 36.70 1.52
1952 2119 9.636965 GCAATGTTTCAGAACTTCAAATTTTAC 57.363 29.630 0.00 0.00 36.70 2.01
1973 2140 9.549509 TTTTACATGATTTACAATACGAGCAAC 57.450 29.630 0.00 0.00 0.00 4.17
1975 2142 4.253352 TGATTTACAATACGAGCAACGC 57.747 40.909 0.00 0.00 46.94 4.84
1976 2143 3.680458 TGATTTACAATACGAGCAACGCA 59.320 39.130 0.00 0.00 46.94 5.24
1977 2144 4.152580 TGATTTACAATACGAGCAACGCAA 59.847 37.500 0.00 0.00 46.94 4.85
1978 2145 4.469625 TTTACAATACGAGCAACGCAAA 57.530 36.364 0.00 0.00 46.94 3.68
1979 2146 2.594529 ACAATACGAGCAACGCAAAG 57.405 45.000 0.00 0.00 46.94 2.77
1980 2147 1.250476 CAATACGAGCAACGCAAAGC 58.750 50.000 0.00 0.00 46.94 3.51
1981 2148 0.168128 AATACGAGCAACGCAAAGCC 59.832 50.000 0.00 0.00 46.94 4.35
1982 2149 0.953471 ATACGAGCAACGCAAAGCCA 60.953 50.000 0.00 0.00 46.94 4.75
1983 2150 1.160946 TACGAGCAACGCAAAGCCAA 61.161 50.000 0.00 0.00 46.94 4.52
1984 2151 1.727022 CGAGCAACGCAAAGCCAAG 60.727 57.895 0.00 0.00 34.51 3.61
1985 2152 1.654220 GAGCAACGCAAAGCCAAGA 59.346 52.632 0.00 0.00 0.00 3.02
1986 2153 0.661483 GAGCAACGCAAAGCCAAGAC 60.661 55.000 0.00 0.00 0.00 3.01
1987 2154 1.065600 GCAACGCAAAGCCAAGACA 59.934 52.632 0.00 0.00 0.00 3.41
1988 2155 0.318955 GCAACGCAAAGCCAAGACAT 60.319 50.000 0.00 0.00 0.00 3.06
1989 2156 1.869342 GCAACGCAAAGCCAAGACATT 60.869 47.619 0.00 0.00 0.00 2.71
1990 2157 2.472816 CAACGCAAAGCCAAGACATTT 58.527 42.857 0.00 0.00 0.00 2.32
1991 2158 2.422276 ACGCAAAGCCAAGACATTTC 57.578 45.000 0.00 0.00 0.00 2.17
1992 2159 1.680735 ACGCAAAGCCAAGACATTTCA 59.319 42.857 0.00 0.00 0.00 2.69
1993 2160 2.287788 ACGCAAAGCCAAGACATTTCAG 60.288 45.455 0.00 0.00 0.00 3.02
1994 2161 2.680577 GCAAAGCCAAGACATTTCAGG 58.319 47.619 0.00 0.00 0.00 3.86
1995 2162 2.611224 GCAAAGCCAAGACATTTCAGGG 60.611 50.000 0.00 0.00 0.00 4.45
1996 2163 1.260544 AAGCCAAGACATTTCAGGGC 58.739 50.000 5.85 5.85 41.33 5.19
1997 2164 0.613012 AGCCAAGACATTTCAGGGCC 60.613 55.000 9.43 0.00 41.74 5.80
1998 2165 0.613012 GCCAAGACATTTCAGGGCCT 60.613 55.000 0.00 0.00 37.28 5.19
1999 2166 1.467920 CCAAGACATTTCAGGGCCTC 58.532 55.000 0.95 0.00 0.00 4.70
2000 2167 1.005215 CCAAGACATTTCAGGGCCTCT 59.995 52.381 0.95 0.00 0.00 3.69
2001 2168 2.556114 CCAAGACATTTCAGGGCCTCTT 60.556 50.000 0.95 0.00 0.00 2.85
2002 2169 3.160269 CAAGACATTTCAGGGCCTCTTT 58.840 45.455 0.95 0.00 0.00 2.52
2003 2170 2.800250 AGACATTTCAGGGCCTCTTTG 58.200 47.619 0.95 1.52 0.00 2.77
2004 2171 2.376518 AGACATTTCAGGGCCTCTTTGA 59.623 45.455 0.95 0.00 0.00 2.69
2005 2172 3.011032 AGACATTTCAGGGCCTCTTTGAT 59.989 43.478 0.95 0.00 0.00 2.57
2006 2173 3.359950 ACATTTCAGGGCCTCTTTGATC 58.640 45.455 0.95 0.00 0.00 2.92
2007 2174 2.514458 TTTCAGGGCCTCTTTGATCC 57.486 50.000 0.95 0.00 0.00 3.36
2008 2175 0.253044 TTCAGGGCCTCTTTGATCCG 59.747 55.000 0.95 0.00 0.00 4.18
2009 2176 1.821332 CAGGGCCTCTTTGATCCGC 60.821 63.158 0.95 0.00 0.00 5.54
2010 2177 2.272146 GGGCCTCTTTGATCCGCA 59.728 61.111 0.84 0.00 0.00 5.69
2011 2178 1.821332 GGGCCTCTTTGATCCGCAG 60.821 63.158 0.84 0.00 0.00 5.18
2031 2198 7.675270 CGCAGGATTTTGAAAATCATAGAAG 57.325 36.000 26.36 12.59 0.00 2.85
2032 2199 7.475015 CGCAGGATTTTGAAAATCATAGAAGA 58.525 34.615 26.36 0.00 0.00 2.87
2033 2200 7.642978 CGCAGGATTTTGAAAATCATAGAAGAG 59.357 37.037 26.36 11.70 0.00 2.85
2034 2201 8.680903 GCAGGATTTTGAAAATCATAGAAGAGA 58.319 33.333 26.36 0.00 0.00 3.10
2049 2216 9.303116 TCATAGAAGAGAAGTATAGGATTGGAC 57.697 37.037 0.00 0.00 0.00 4.02
2050 2217 9.308000 CATAGAAGAGAAGTATAGGATTGGACT 57.692 37.037 0.00 0.00 0.00 3.85
2051 2218 7.595819 AGAAGAGAAGTATAGGATTGGACTG 57.404 40.000 0.00 0.00 0.00 3.51
2052 2219 6.553100 AGAAGAGAAGTATAGGATTGGACTGG 59.447 42.308 0.00 0.00 0.00 4.00
2053 2220 4.591072 AGAGAAGTATAGGATTGGACTGGC 59.409 45.833 0.00 0.00 0.00 4.85
2054 2221 4.298626 AGAAGTATAGGATTGGACTGGCA 58.701 43.478 0.00 0.00 0.00 4.92
2055 2222 4.910304 AGAAGTATAGGATTGGACTGGCAT 59.090 41.667 0.00 0.00 0.00 4.40
2056 2223 5.370880 AGAAGTATAGGATTGGACTGGCATT 59.629 40.000 0.00 0.00 0.00 3.56
2057 2224 4.978099 AGTATAGGATTGGACTGGCATTG 58.022 43.478 0.00 0.00 0.00 2.82
2058 2225 2.057137 TAGGATTGGACTGGCATTGC 57.943 50.000 0.00 0.00 0.00 3.56
2069 2236 3.049227 GGCATTGCCCGTTTGAATC 57.951 52.632 17.28 0.00 44.06 2.52
2070 2237 0.460109 GGCATTGCCCGTTTGAATCC 60.460 55.000 17.28 0.00 44.06 3.01
2071 2238 0.532115 GCATTGCCCGTTTGAATCCT 59.468 50.000 0.00 0.00 0.00 3.24
2072 2239 1.748493 GCATTGCCCGTTTGAATCCTA 59.252 47.619 0.00 0.00 0.00 2.94
2073 2240 2.362077 GCATTGCCCGTTTGAATCCTAT 59.638 45.455 0.00 0.00 0.00 2.57
2074 2241 3.568007 GCATTGCCCGTTTGAATCCTATA 59.432 43.478 0.00 0.00 0.00 1.31
2075 2242 4.320494 GCATTGCCCGTTTGAATCCTATAG 60.320 45.833 0.00 0.00 0.00 1.31
2076 2243 4.764050 TTGCCCGTTTGAATCCTATAGA 57.236 40.909 0.00 0.00 0.00 1.98
2077 2244 4.764050 TGCCCGTTTGAATCCTATAGAA 57.236 40.909 0.00 0.00 0.00 2.10
2078 2245 5.304686 TGCCCGTTTGAATCCTATAGAAT 57.695 39.130 0.00 0.00 0.00 2.40
2079 2246 5.690865 TGCCCGTTTGAATCCTATAGAATT 58.309 37.500 0.00 0.00 0.00 2.17
2080 2247 6.833041 TGCCCGTTTGAATCCTATAGAATTA 58.167 36.000 0.00 0.00 0.00 1.40
2081 2248 6.934645 TGCCCGTTTGAATCCTATAGAATTAG 59.065 38.462 0.00 0.00 0.00 1.73
2082 2249 6.128254 GCCCGTTTGAATCCTATAGAATTAGC 60.128 42.308 0.00 0.00 0.00 3.09
2083 2250 6.934645 CCCGTTTGAATCCTATAGAATTAGCA 59.065 38.462 0.00 0.00 0.00 3.49
2084 2251 7.444183 CCCGTTTGAATCCTATAGAATTAGCAA 59.556 37.037 0.00 0.00 0.00 3.91
2085 2252 9.003658 CCGTTTGAATCCTATAGAATTAGCAAT 57.996 33.333 0.00 0.00 0.00 3.56
2086 2253 9.817365 CGTTTGAATCCTATAGAATTAGCAATG 57.183 33.333 0.00 0.00 0.00 2.82
2090 2257 9.716531 TGAATCCTATAGAATTAGCAATGAGTG 57.283 33.333 0.00 0.00 0.00 3.51
2091 2258 9.717942 GAATCCTATAGAATTAGCAATGAGTGT 57.282 33.333 0.00 0.00 0.00 3.55
2092 2259 9.717942 AATCCTATAGAATTAGCAATGAGTGTC 57.282 33.333 0.00 0.00 0.00 3.67
2093 2260 8.484214 TCCTATAGAATTAGCAATGAGTGTCT 57.516 34.615 0.00 0.00 0.00 3.41
2094 2261 8.363390 TCCTATAGAATTAGCAATGAGTGTCTG 58.637 37.037 0.00 0.00 0.00 3.51
2095 2262 8.363390 CCTATAGAATTAGCAATGAGTGTCTGA 58.637 37.037 0.00 0.00 0.00 3.27
2096 2263 9.926158 CTATAGAATTAGCAATGAGTGTCTGAT 57.074 33.333 0.00 0.00 0.00 2.90
2098 2265 7.551035 AGAATTAGCAATGAGTGTCTGATTC 57.449 36.000 11.02 11.02 37.04 2.52
2099 2266 6.541641 AGAATTAGCAATGAGTGTCTGATTCC 59.458 38.462 13.53 3.13 37.23 3.01
2100 2267 2.996631 AGCAATGAGTGTCTGATTCCC 58.003 47.619 0.00 0.00 0.00 3.97
2101 2268 1.667724 GCAATGAGTGTCTGATTCCCG 59.332 52.381 0.00 0.00 0.00 5.14
2102 2269 2.677902 GCAATGAGTGTCTGATTCCCGA 60.678 50.000 0.00 0.00 0.00 5.14
2103 2270 3.599343 CAATGAGTGTCTGATTCCCGAA 58.401 45.455 0.00 0.00 0.00 4.30
2104 2271 3.533606 ATGAGTGTCTGATTCCCGAAG 57.466 47.619 0.00 0.00 0.00 3.79
2105 2272 2.525368 TGAGTGTCTGATTCCCGAAGA 58.475 47.619 0.00 0.00 0.00 2.87
2106 2273 2.897326 TGAGTGTCTGATTCCCGAAGAA 59.103 45.455 0.00 0.00 39.32 2.52
2107 2274 3.323691 TGAGTGTCTGATTCCCGAAGAAA 59.676 43.478 0.00 0.00 38.21 2.52
2108 2275 4.202315 TGAGTGTCTGATTCCCGAAGAAAA 60.202 41.667 0.00 0.00 38.21 2.29
2109 2276 4.065789 AGTGTCTGATTCCCGAAGAAAAC 58.934 43.478 0.00 0.00 38.21 2.43
2110 2277 3.813166 GTGTCTGATTCCCGAAGAAAACA 59.187 43.478 0.00 0.00 38.21 2.83
2111 2278 4.274950 GTGTCTGATTCCCGAAGAAAACAA 59.725 41.667 0.00 0.00 38.21 2.83
2112 2279 5.048713 GTGTCTGATTCCCGAAGAAAACAAT 60.049 40.000 0.00 0.00 38.21 2.71
2113 2280 5.048782 TGTCTGATTCCCGAAGAAAACAATG 60.049 40.000 0.00 0.00 38.21 2.82
2114 2281 4.458989 TCTGATTCCCGAAGAAAACAATGG 59.541 41.667 0.00 0.00 38.21 3.16
2115 2282 4.402829 TGATTCCCGAAGAAAACAATGGA 58.597 39.130 0.00 0.00 38.21 3.41
2116 2283 4.830046 TGATTCCCGAAGAAAACAATGGAA 59.170 37.500 0.00 0.00 38.21 3.53
2117 2284 5.480073 TGATTCCCGAAGAAAACAATGGAAT 59.520 36.000 0.00 0.00 42.25 3.01
2118 2285 5.799827 TTCCCGAAGAAAACAATGGAATT 57.200 34.783 0.00 0.00 36.63 2.17
2134 2301 5.799827 TGGAATTGTAAAAGAAGGTTGGG 57.200 39.130 0.00 0.00 0.00 4.12
2135 2302 4.591072 TGGAATTGTAAAAGAAGGTTGGGG 59.409 41.667 0.00 0.00 0.00 4.96
2136 2303 4.591498 GGAATTGTAAAAGAAGGTTGGGGT 59.409 41.667 0.00 0.00 0.00 4.95
2137 2304 5.510690 GGAATTGTAAAAGAAGGTTGGGGTG 60.511 44.000 0.00 0.00 0.00 4.61
2138 2305 3.955524 TGTAAAAGAAGGTTGGGGTGA 57.044 42.857 0.00 0.00 0.00 4.02
2139 2306 4.252570 TGTAAAAGAAGGTTGGGGTGAA 57.747 40.909 0.00 0.00 0.00 3.18
2140 2307 4.810345 TGTAAAAGAAGGTTGGGGTGAAT 58.190 39.130 0.00 0.00 0.00 2.57
2141 2308 4.586841 TGTAAAAGAAGGTTGGGGTGAATG 59.413 41.667 0.00 0.00 0.00 2.67
2142 2309 3.328535 AAAGAAGGTTGGGGTGAATGT 57.671 42.857 0.00 0.00 0.00 2.71
2143 2310 3.328535 AAGAAGGTTGGGGTGAATGTT 57.671 42.857 0.00 0.00 0.00 2.71
2144 2311 3.328535 AGAAGGTTGGGGTGAATGTTT 57.671 42.857 0.00 0.00 0.00 2.83
2145 2312 2.965147 AGAAGGTTGGGGTGAATGTTTG 59.035 45.455 0.00 0.00 0.00 2.93
2146 2313 2.765689 AGGTTGGGGTGAATGTTTGA 57.234 45.000 0.00 0.00 0.00 2.69
2147 2314 3.258722 AGGTTGGGGTGAATGTTTGAT 57.741 42.857 0.00 0.00 0.00 2.57
2148 2315 3.586429 AGGTTGGGGTGAATGTTTGATT 58.414 40.909 0.00 0.00 0.00 2.57
2149 2316 3.973305 AGGTTGGGGTGAATGTTTGATTT 59.027 39.130 0.00 0.00 0.00 2.17
2150 2317 4.411869 AGGTTGGGGTGAATGTTTGATTTT 59.588 37.500 0.00 0.00 0.00 1.82
2151 2318 4.754618 GGTTGGGGTGAATGTTTGATTTTC 59.245 41.667 0.00 0.00 0.00 2.29
2152 2319 5.454613 GGTTGGGGTGAATGTTTGATTTTCT 60.455 40.000 0.00 0.00 0.00 2.52
2153 2320 6.239458 GGTTGGGGTGAATGTTTGATTTTCTA 60.239 38.462 0.00 0.00 0.00 2.10
2154 2321 7.386059 GTTGGGGTGAATGTTTGATTTTCTAT 58.614 34.615 0.00 0.00 0.00 1.98
2155 2322 6.934056 TGGGGTGAATGTTTGATTTTCTATG 58.066 36.000 0.00 0.00 0.00 2.23
2156 2323 6.723515 TGGGGTGAATGTTTGATTTTCTATGA 59.276 34.615 0.00 0.00 0.00 2.15
2157 2324 7.234371 TGGGGTGAATGTTTGATTTTCTATGAA 59.766 33.333 0.00 0.00 0.00 2.57
2158 2325 8.093927 GGGGTGAATGTTTGATTTTCTATGAAA 58.906 33.333 0.00 0.00 0.00 2.69
2159 2326 8.925700 GGGTGAATGTTTGATTTTCTATGAAAC 58.074 33.333 0.00 0.00 0.00 2.78
2160 2327 8.638565 GGTGAATGTTTGATTTTCTATGAAACG 58.361 33.333 0.00 0.00 30.65 3.60
2161 2328 9.180678 GTGAATGTTTGATTTTCTATGAAACGT 57.819 29.630 0.00 0.00 30.65 3.99
2162 2329 9.393249 TGAATGTTTGATTTTCTATGAAACGTC 57.607 29.630 0.00 0.00 30.65 4.34
2163 2330 8.434870 AATGTTTGATTTTCTATGAAACGTCG 57.565 30.769 0.00 0.00 30.65 5.12
2164 2331 6.950545 TGTTTGATTTTCTATGAAACGTCGT 58.049 32.000 0.00 0.00 30.65 4.34
2165 2332 8.074474 TGTTTGATTTTCTATGAAACGTCGTA 57.926 30.769 0.00 0.00 30.65 3.43
2166 2333 8.005466 TGTTTGATTTTCTATGAAACGTCGTAC 58.995 33.333 0.00 0.00 30.65 3.67
2167 2334 7.640616 TTGATTTTCTATGAAACGTCGTACA 57.359 32.000 0.00 2.81 0.00 2.90
2168 2335 7.640616 TGATTTTCTATGAAACGTCGTACAA 57.359 32.000 0.00 0.00 0.00 2.41
2169 2336 8.074474 TGATTTTCTATGAAACGTCGTACAAA 57.926 30.769 0.00 0.00 0.00 2.83
2170 2337 8.549548 TGATTTTCTATGAAACGTCGTACAAAA 58.450 29.630 0.00 1.16 31.67 2.44
2171 2338 8.928844 ATTTTCTATGAAACGTCGTACAAAAG 57.071 30.769 0.00 5.35 31.06 2.27
2172 2339 7.697352 TTTCTATGAAACGTCGTACAAAAGA 57.303 32.000 0.00 7.39 0.00 2.52
2173 2340 7.878477 TTCTATGAAACGTCGTACAAAAGAT 57.122 32.000 0.00 0.00 0.00 2.40
2174 2341 7.878477 TCTATGAAACGTCGTACAAAAGATT 57.122 32.000 0.00 0.00 0.00 2.40
2175 2342 8.969121 TCTATGAAACGTCGTACAAAAGATTA 57.031 30.769 0.00 0.00 0.00 1.75
2176 2343 8.853345 TCTATGAAACGTCGTACAAAAGATTAC 58.147 33.333 0.00 0.00 0.00 1.89
2177 2344 6.825284 TGAAACGTCGTACAAAAGATTACA 57.175 33.333 0.00 0.00 0.00 2.41
2178 2345 7.410800 TGAAACGTCGTACAAAAGATTACAT 57.589 32.000 0.00 0.00 0.00 2.29
2179 2346 8.518151 TGAAACGTCGTACAAAAGATTACATA 57.482 30.769 0.00 0.00 0.00 2.29
2180 2347 8.976471 TGAAACGTCGTACAAAAGATTACATAA 58.024 29.630 0.00 0.00 0.00 1.90
2181 2348 9.796062 GAAACGTCGTACAAAAGATTACATAAA 57.204 29.630 0.00 0.00 0.00 1.40
2215 2382 6.734104 GGATCCAAATCCTATGAATCGAAG 57.266 41.667 6.95 0.00 46.97 3.79
2216 2383 5.645497 GGATCCAAATCCTATGAATCGAAGG 59.355 44.000 6.95 0.00 46.97 3.46
2217 2384 5.887214 TCCAAATCCTATGAATCGAAGGA 57.113 39.130 5.29 5.29 43.38 3.36
2218 2385 5.611374 TCCAAATCCTATGAATCGAAGGAC 58.389 41.667 4.93 0.00 42.08 3.85
2219 2386 4.757149 CCAAATCCTATGAATCGAAGGACC 59.243 45.833 4.93 0.00 42.08 4.46
2220 2387 3.944055 ATCCTATGAATCGAAGGACCG 57.056 47.619 4.93 0.00 42.08 4.79
2221 2388 2.940158 TCCTATGAATCGAAGGACCGA 58.060 47.619 0.00 0.00 43.16 4.69
2222 2389 2.621998 TCCTATGAATCGAAGGACCGAC 59.378 50.000 0.00 0.00 41.70 4.79
2223 2390 2.361119 CCTATGAATCGAAGGACCGACA 59.639 50.000 0.00 0.00 41.70 4.35
2224 2391 3.005897 CCTATGAATCGAAGGACCGACAT 59.994 47.826 0.00 0.00 41.70 3.06
2225 2392 2.579207 TGAATCGAAGGACCGACATC 57.421 50.000 0.00 0.00 41.70 3.06
2226 2393 1.136305 TGAATCGAAGGACCGACATCC 59.864 52.381 0.00 0.00 41.70 3.51
2236 2403 4.722361 GGACCGACATCCTAAGGATATC 57.278 50.000 0.00 0.00 40.98 1.63
2237 2404 4.087182 GGACCGACATCCTAAGGATATCA 58.913 47.826 4.83 0.00 40.98 2.15
2238 2405 4.527038 GGACCGACATCCTAAGGATATCAA 59.473 45.833 4.83 0.00 40.98 2.57
2239 2406 5.187967 GGACCGACATCCTAAGGATATCAAT 59.812 44.000 4.83 0.00 40.98 2.57
2240 2407 6.287589 ACCGACATCCTAAGGATATCAATC 57.712 41.667 4.83 0.00 40.98 2.67
2241 2408 9.460748 GGACCGACATCCTAAGGATATCAATCC 62.461 48.148 4.83 0.00 40.98 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
305 309 1.202533 GCTAATTAGCTCGCTGTGGGA 60.203 52.381 26.79 0.00 45.62 4.37
539 556 4.009675 GGCTGTCAGTCCAAATTATGTCA 58.990 43.478 0.93 0.00 0.00 3.58
547 564 2.843545 GGGGGCTGTCAGTCCAAA 59.156 61.111 24.71 0.00 43.30 3.28
551 568 3.192103 AAACCGGGGGCTGTCAGTC 62.192 63.158 6.32 0.00 0.00 3.51
691 710 8.243426 ACACATGCTGAACGTGAAATAAATATT 58.757 29.630 0.00 0.00 38.75 1.28
693 712 7.139896 ACACATGCTGAACGTGAAATAAATA 57.860 32.000 0.00 0.00 38.75 1.40
698 717 3.120199 GCTACACATGCTGAACGTGAAAT 60.120 43.478 0.00 0.00 38.75 2.17
728 747 3.545481 CGCGATCGCACCACACTC 61.545 66.667 36.45 7.19 42.06 3.51
729 748 3.567478 TTCGCGATCGCACCACACT 62.567 57.895 36.45 0.00 42.06 3.55
730 749 3.109547 TTCGCGATCGCACCACAC 61.110 61.111 36.45 8.68 42.06 3.82
731 750 3.109547 GTTCGCGATCGCACCACA 61.110 61.111 36.45 14.40 42.06 4.17
732 751 1.897398 AAAGTTCGCGATCGCACCAC 61.897 55.000 36.45 27.58 42.06 4.16
733 752 1.623081 GAAAGTTCGCGATCGCACCA 61.623 55.000 36.45 18.98 42.06 4.17
734 753 1.058903 GAAAGTTCGCGATCGCACC 59.941 57.895 36.45 23.49 42.06 5.01
735 754 0.438830 AAGAAAGTTCGCGATCGCAC 59.561 50.000 36.45 27.81 42.06 5.34
736 755 0.438445 CAAGAAAGTTCGCGATCGCA 59.562 50.000 36.45 22.14 42.06 5.10
737 756 0.438830 ACAAGAAAGTTCGCGATCGC 59.561 50.000 29.80 29.80 35.26 4.58
738 757 1.783416 GCACAAGAAAGTTCGCGATCG 60.783 52.381 10.88 11.69 0.00 3.69
739 758 1.464189 GGCACAAGAAAGTTCGCGATC 60.464 52.381 10.88 9.88 0.00 3.69
740 759 0.517316 GGCACAAGAAAGTTCGCGAT 59.483 50.000 10.88 0.00 0.00 4.58
741 760 1.827315 CGGCACAAGAAAGTTCGCGA 61.827 55.000 3.71 3.71 0.00 5.87
742 761 1.438710 CGGCACAAGAAAGTTCGCG 60.439 57.895 0.00 0.00 0.00 5.87
743 762 1.725973 GCGGCACAAGAAAGTTCGC 60.726 57.895 0.00 0.00 35.53 4.70
744 763 1.082104 GGCGGCACAAGAAAGTTCG 60.082 57.895 3.07 0.00 0.00 3.95
745 764 0.317854 GTGGCGGCACAAGAAAGTTC 60.318 55.000 34.40 5.14 0.00 3.01
868 890 2.550606 GCCATTTTTATACGCGATGGGA 59.449 45.455 15.93 0.00 38.13 4.37
871 893 5.034554 AGATGCCATTTTTATACGCGATG 57.965 39.130 15.93 3.53 0.00 3.84
918 940 0.679505 TTACTGCTCGAGTGGCTGTT 59.320 50.000 15.13 0.00 41.00 3.16
928 950 1.491563 GCACGTGGTTTACTGCTCG 59.508 57.895 18.88 0.00 33.48 5.03
1401 1492 0.252057 TGATGAACCGTCCTCCTCCA 60.252 55.000 0.00 0.00 0.00 3.86
1431 1530 1.021920 GGAGGAAGAGACGCAAAGGC 61.022 60.000 0.00 0.00 0.00 4.35
1461 1560 3.550436 GCAACGAGATACTACTAGTGGGC 60.550 52.174 11.30 0.00 0.00 5.36
1466 1565 5.694816 CCAGATGCAACGAGATACTACTAG 58.305 45.833 0.00 0.00 0.00 2.57
1548 1665 6.262496 GCACACCTCATCATACTACTAGTACA 59.738 42.308 0.00 0.00 32.84 2.90
1549 1666 6.566187 CGCACACCTCATCATACTACTAGTAC 60.566 46.154 0.00 0.00 32.84 2.73
1550 1667 5.469084 CGCACACCTCATCATACTACTAGTA 59.531 44.000 1.89 1.89 34.82 1.82
1551 1668 4.276183 CGCACACCTCATCATACTACTAGT 59.724 45.833 0.00 0.00 0.00 2.57
1552 1669 4.515567 TCGCACACCTCATCATACTACTAG 59.484 45.833 0.00 0.00 0.00 2.57
1607 1730 0.584876 GTACAACAACGCTGGTCACC 59.415 55.000 0.00 0.00 0.00 4.02
1608 1731 1.578583 AGTACAACAACGCTGGTCAC 58.421 50.000 0.00 0.00 0.00 3.67
1658 1781 2.463047 AGGAGGAGGGCAGTAAGTAG 57.537 55.000 0.00 0.00 0.00 2.57
1660 1783 2.046280 AAAGGAGGAGGGCAGTAAGT 57.954 50.000 0.00 0.00 0.00 2.24
1661 1784 4.779993 AATAAAGGAGGAGGGCAGTAAG 57.220 45.455 0.00 0.00 0.00 2.34
1662 1785 4.291249 ACAAATAAAGGAGGAGGGCAGTAA 59.709 41.667 0.00 0.00 0.00 2.24
1679 1805 6.707608 CCGATTTGAGATCCAGATGACAAATA 59.292 38.462 15.35 0.00 35.45 1.40
1749 1892 2.492088 AGCAAGCGATGTACTACTGTCA 59.508 45.455 0.00 0.00 0.00 3.58
1750 1893 3.152261 AGCAAGCGATGTACTACTGTC 57.848 47.619 0.00 0.00 0.00 3.51
1764 1924 1.608590 TGGCAGTTGAGTTTAGCAAGC 59.391 47.619 0.00 0.00 0.00 4.01
1818 1978 8.417780 ACAGTTCGTACTACTACTATGTACTG 57.582 38.462 0.00 0.00 35.67 2.74
1861 2027 4.006989 ACTACAGCATGGCAACGATTTAA 58.993 39.130 0.00 0.00 43.62 1.52
1862 2028 3.605634 ACTACAGCATGGCAACGATTTA 58.394 40.909 0.00 0.00 43.62 1.40
1870 2036 1.628340 ACTTGGTACTACAGCATGGCA 59.372 47.619 0.00 0.00 43.62 4.92
1872 2038 3.195610 TCTGACTTGGTACTACAGCATGG 59.804 47.826 0.00 0.00 43.62 3.66
1885 2051 3.367703 GGAAACATTGCCATCTGACTTGG 60.368 47.826 0.00 0.00 37.31 3.61
1900 2067 1.539388 TGCATTTTCGCGAGGAAACAT 59.461 42.857 9.59 0.00 42.35 2.71
1902 2069 1.978782 CTTGCATTTTCGCGAGGAAAC 59.021 47.619 9.59 6.36 42.35 2.78
1947 2114 9.549509 GTTGCTCGTATTGTAAATCATGTAAAA 57.450 29.630 0.00 0.00 0.00 1.52
1948 2115 7.900864 CGTTGCTCGTATTGTAAATCATGTAAA 59.099 33.333 0.00 0.00 34.52 2.01
1949 2116 7.395645 CGTTGCTCGTATTGTAAATCATGTAA 58.604 34.615 0.00 0.00 34.52 2.41
1950 2117 6.508880 GCGTTGCTCGTATTGTAAATCATGTA 60.509 38.462 0.00 0.00 42.13 2.29
1951 2118 5.726688 GCGTTGCTCGTATTGTAAATCATGT 60.727 40.000 0.00 0.00 42.13 3.21
1952 2119 4.666176 GCGTTGCTCGTATTGTAAATCATG 59.334 41.667 4.16 0.00 42.13 3.07
1953 2120 4.331443 TGCGTTGCTCGTATTGTAAATCAT 59.669 37.500 4.16 0.00 42.13 2.45
1954 2121 3.680458 TGCGTTGCTCGTATTGTAAATCA 59.320 39.130 4.16 0.00 42.13 2.57
1955 2122 4.253352 TGCGTTGCTCGTATTGTAAATC 57.747 40.909 4.16 0.00 42.13 2.17
1956 2123 4.671880 TTGCGTTGCTCGTATTGTAAAT 57.328 36.364 4.16 0.00 42.13 1.40
1957 2124 4.459606 CTTTGCGTTGCTCGTATTGTAAA 58.540 39.130 4.16 0.00 42.13 2.01
1958 2125 3.665848 GCTTTGCGTTGCTCGTATTGTAA 60.666 43.478 4.16 0.00 42.13 2.41
1959 2126 2.159761 GCTTTGCGTTGCTCGTATTGTA 60.160 45.455 4.16 0.00 42.13 2.41
1960 2127 1.399727 GCTTTGCGTTGCTCGTATTGT 60.400 47.619 4.16 0.00 42.13 2.71
1961 2128 1.250476 GCTTTGCGTTGCTCGTATTG 58.750 50.000 4.16 0.00 42.13 1.90
1962 2129 0.168128 GGCTTTGCGTTGCTCGTATT 59.832 50.000 4.16 0.00 42.13 1.89
1963 2130 0.953471 TGGCTTTGCGTTGCTCGTAT 60.953 50.000 4.16 0.00 42.13 3.06
1964 2131 1.160946 TTGGCTTTGCGTTGCTCGTA 61.161 50.000 4.16 0.00 42.13 3.43
1965 2132 2.392613 CTTGGCTTTGCGTTGCTCGT 62.393 55.000 4.16 0.00 42.13 4.18
1966 2133 1.727022 CTTGGCTTTGCGTTGCTCG 60.727 57.895 0.00 0.00 43.12 5.03
1967 2134 0.661483 GTCTTGGCTTTGCGTTGCTC 60.661 55.000 0.00 0.00 0.00 4.26
1968 2135 1.360192 GTCTTGGCTTTGCGTTGCT 59.640 52.632 0.00 0.00 0.00 3.91
1969 2136 0.318955 ATGTCTTGGCTTTGCGTTGC 60.319 50.000 0.00 0.00 0.00 4.17
1970 2137 2.138596 AATGTCTTGGCTTTGCGTTG 57.861 45.000 0.00 0.00 0.00 4.10
1971 2138 2.100584 TGAAATGTCTTGGCTTTGCGTT 59.899 40.909 0.00 0.00 0.00 4.84
1972 2139 1.680735 TGAAATGTCTTGGCTTTGCGT 59.319 42.857 0.00 0.00 0.00 5.24
1973 2140 2.322161 CTGAAATGTCTTGGCTTTGCG 58.678 47.619 0.00 0.00 0.00 4.85
1974 2141 2.611224 CCCTGAAATGTCTTGGCTTTGC 60.611 50.000 0.00 0.00 0.00 3.68
1975 2142 2.611224 GCCCTGAAATGTCTTGGCTTTG 60.611 50.000 8.52 0.00 37.83 2.77
1976 2143 1.620323 GCCCTGAAATGTCTTGGCTTT 59.380 47.619 8.52 0.00 37.83 3.51
1977 2144 1.260544 GCCCTGAAATGTCTTGGCTT 58.739 50.000 8.52 0.00 37.83 4.35
1978 2145 0.613012 GGCCCTGAAATGTCTTGGCT 60.613 55.000 13.75 0.00 39.61 4.75
1979 2146 0.613012 AGGCCCTGAAATGTCTTGGC 60.613 55.000 0.00 7.51 39.21 4.52
1980 2147 1.005215 AGAGGCCCTGAAATGTCTTGG 59.995 52.381 0.00 0.00 0.00 3.61
1981 2148 2.503895 AGAGGCCCTGAAATGTCTTG 57.496 50.000 0.00 0.00 0.00 3.02
1982 2149 3.160269 CAAAGAGGCCCTGAAATGTCTT 58.840 45.455 0.00 0.00 0.00 3.01
1983 2150 2.376518 TCAAAGAGGCCCTGAAATGTCT 59.623 45.455 0.00 0.00 0.00 3.41
1984 2151 2.795329 TCAAAGAGGCCCTGAAATGTC 58.205 47.619 0.00 0.00 0.00 3.06
1985 2152 2.978156 TCAAAGAGGCCCTGAAATGT 57.022 45.000 0.00 0.00 0.00 2.71
1986 2153 2.692041 GGATCAAAGAGGCCCTGAAATG 59.308 50.000 0.00 0.00 0.00 2.32
1987 2154 2.684927 CGGATCAAAGAGGCCCTGAAAT 60.685 50.000 0.00 0.00 0.00 2.17
1988 2155 1.340017 CGGATCAAAGAGGCCCTGAAA 60.340 52.381 0.00 0.00 0.00 2.69
1989 2156 0.253044 CGGATCAAAGAGGCCCTGAA 59.747 55.000 0.00 0.00 0.00 3.02
1990 2157 1.907739 CGGATCAAAGAGGCCCTGA 59.092 57.895 0.00 0.00 0.00 3.86
1991 2158 1.821332 GCGGATCAAAGAGGCCCTG 60.821 63.158 0.00 0.00 0.00 4.45
1992 2159 2.262774 CTGCGGATCAAAGAGGCCCT 62.263 60.000 0.00 0.00 0.00 5.19
1993 2160 1.821332 CTGCGGATCAAAGAGGCCC 60.821 63.158 0.00 0.00 0.00 5.80
1994 2161 1.821332 CCTGCGGATCAAAGAGGCC 60.821 63.158 0.00 0.00 0.00 5.19
1995 2162 0.179034 ATCCTGCGGATCAAAGAGGC 60.179 55.000 0.00 0.00 38.09 4.70
1996 2163 2.338577 AATCCTGCGGATCAAAGAGG 57.661 50.000 9.96 0.00 42.27 3.69
1997 2164 3.691118 TCAAAATCCTGCGGATCAAAGAG 59.309 43.478 9.96 0.59 42.27 2.85
1998 2165 3.684908 TCAAAATCCTGCGGATCAAAGA 58.315 40.909 9.96 4.88 42.27 2.52
1999 2166 4.439305 TTCAAAATCCTGCGGATCAAAG 57.561 40.909 9.96 3.05 42.27 2.77
2000 2167 4.862902 TTTCAAAATCCTGCGGATCAAA 57.137 36.364 9.96 5.64 42.27 2.69
2001 2168 4.862902 TTTTCAAAATCCTGCGGATCAA 57.137 36.364 9.96 0.84 42.27 2.57
2002 2169 4.462132 TGATTTTCAAAATCCTGCGGATCA 59.538 37.500 18.35 0.00 42.27 2.92
2003 2170 4.997565 TGATTTTCAAAATCCTGCGGATC 58.002 39.130 18.35 0.00 42.27 3.36
2004 2171 5.603170 ATGATTTTCAAAATCCTGCGGAT 57.397 34.783 18.35 3.38 45.46 4.18
2005 2172 5.885352 TCTATGATTTTCAAAATCCTGCGGA 59.115 36.000 18.35 8.17 35.55 5.54
2006 2173 6.135290 TCTATGATTTTCAAAATCCTGCGG 57.865 37.500 18.35 6.33 0.00 5.69
2007 2174 7.475015 TCTTCTATGATTTTCAAAATCCTGCG 58.525 34.615 18.35 6.65 0.00 5.18
2008 2175 8.680903 TCTCTTCTATGATTTTCAAAATCCTGC 58.319 33.333 18.35 0.00 0.00 4.85
2023 2190 9.303116 GTCCAATCCTATACTTCTCTTCTATGA 57.697 37.037 0.00 0.00 0.00 2.15
2024 2191 9.308000 AGTCCAATCCTATACTTCTCTTCTATG 57.692 37.037 0.00 0.00 0.00 2.23
2025 2192 9.308000 CAGTCCAATCCTATACTTCTCTTCTAT 57.692 37.037 0.00 0.00 0.00 1.98
2026 2193 7.726291 CCAGTCCAATCCTATACTTCTCTTCTA 59.274 40.741 0.00 0.00 0.00 2.10
2027 2194 6.553100 CCAGTCCAATCCTATACTTCTCTTCT 59.447 42.308 0.00 0.00 0.00 2.85
2028 2195 6.740122 GCCAGTCCAATCCTATACTTCTCTTC 60.740 46.154 0.00 0.00 0.00 2.87
2029 2196 5.071115 GCCAGTCCAATCCTATACTTCTCTT 59.929 44.000 0.00 0.00 0.00 2.85
2030 2197 4.591072 GCCAGTCCAATCCTATACTTCTCT 59.409 45.833 0.00 0.00 0.00 3.10
2031 2198 4.345257 TGCCAGTCCAATCCTATACTTCTC 59.655 45.833 0.00 0.00 0.00 2.87
2032 2199 4.298626 TGCCAGTCCAATCCTATACTTCT 58.701 43.478 0.00 0.00 0.00 2.85
2033 2200 4.689612 TGCCAGTCCAATCCTATACTTC 57.310 45.455 0.00 0.00 0.00 3.01
2034 2201 5.380043 CAATGCCAGTCCAATCCTATACTT 58.620 41.667 0.00 0.00 0.00 2.24
2035 2202 4.747931 GCAATGCCAGTCCAATCCTATACT 60.748 45.833 0.00 0.00 0.00 2.12
2036 2203 3.503748 GCAATGCCAGTCCAATCCTATAC 59.496 47.826 0.00 0.00 0.00 1.47
2037 2204 3.754965 GCAATGCCAGTCCAATCCTATA 58.245 45.455 0.00 0.00 0.00 1.31
2038 2205 2.590821 GCAATGCCAGTCCAATCCTAT 58.409 47.619 0.00 0.00 0.00 2.57
2039 2206 2.057137 GCAATGCCAGTCCAATCCTA 57.943 50.000 0.00 0.00 0.00 2.94
2040 2207 2.892025 GCAATGCCAGTCCAATCCT 58.108 52.632 0.00 0.00 0.00 3.24
2052 2219 0.532115 AGGATTCAAACGGGCAATGC 59.468 50.000 0.00 0.00 0.00 3.56
2053 2220 5.063204 TCTATAGGATTCAAACGGGCAATG 58.937 41.667 0.00 0.00 0.00 2.82
2054 2221 5.304686 TCTATAGGATTCAAACGGGCAAT 57.695 39.130 0.00 0.00 0.00 3.56
2055 2222 4.764050 TCTATAGGATTCAAACGGGCAA 57.236 40.909 0.00 0.00 0.00 4.52
2056 2223 4.764050 TTCTATAGGATTCAAACGGGCA 57.236 40.909 0.00 0.00 0.00 5.36
2057 2224 6.128254 GCTAATTCTATAGGATTCAAACGGGC 60.128 42.308 9.67 2.08 0.00 6.13
2058 2225 6.934645 TGCTAATTCTATAGGATTCAAACGGG 59.065 38.462 9.67 0.00 0.00 5.28
2059 2226 7.962964 TGCTAATTCTATAGGATTCAAACGG 57.037 36.000 9.67 0.00 0.00 4.44
2060 2227 9.817365 CATTGCTAATTCTATAGGATTCAAACG 57.183 33.333 9.67 2.67 0.00 3.60
2064 2231 9.716531 CACTCATTGCTAATTCTATAGGATTCA 57.283 33.333 9.67 0.57 0.00 2.57
2065 2232 9.717942 ACACTCATTGCTAATTCTATAGGATTC 57.282 33.333 9.67 0.00 0.00 2.52
2066 2233 9.717942 GACACTCATTGCTAATTCTATAGGATT 57.282 33.333 11.13 11.13 0.00 3.01
2067 2234 9.099071 AGACACTCATTGCTAATTCTATAGGAT 57.901 33.333 0.00 0.00 0.00 3.24
2068 2235 8.363390 CAGACACTCATTGCTAATTCTATAGGA 58.637 37.037 0.00 0.00 0.00 2.94
2069 2236 8.363390 TCAGACACTCATTGCTAATTCTATAGG 58.637 37.037 0.00 0.00 0.00 2.57
2070 2237 9.926158 ATCAGACACTCATTGCTAATTCTATAG 57.074 33.333 0.00 0.00 0.00 1.31
2072 2239 9.270640 GAATCAGACACTCATTGCTAATTCTAT 57.729 33.333 0.00 0.00 0.00 1.98
2073 2240 7.712639 GGAATCAGACACTCATTGCTAATTCTA 59.287 37.037 0.00 0.00 0.00 2.10
2074 2241 6.541641 GGAATCAGACACTCATTGCTAATTCT 59.458 38.462 0.00 0.00 0.00 2.40
2075 2242 6.238593 GGGAATCAGACACTCATTGCTAATTC 60.239 42.308 0.00 0.00 0.00 2.17
2076 2243 5.591877 GGGAATCAGACACTCATTGCTAATT 59.408 40.000 0.00 0.00 0.00 1.40
2077 2244 5.128919 GGGAATCAGACACTCATTGCTAAT 58.871 41.667 0.00 0.00 0.00 1.73
2078 2245 4.517285 GGGAATCAGACACTCATTGCTAA 58.483 43.478 0.00 0.00 0.00 3.09
2079 2246 3.430790 CGGGAATCAGACACTCATTGCTA 60.431 47.826 0.00 0.00 0.00 3.49
2080 2247 2.679059 CGGGAATCAGACACTCATTGCT 60.679 50.000 0.00 0.00 0.00 3.91
2081 2248 1.667724 CGGGAATCAGACACTCATTGC 59.332 52.381 0.00 0.00 0.00 3.56
2082 2249 3.251479 TCGGGAATCAGACACTCATTG 57.749 47.619 0.00 0.00 0.00 2.82
2083 2250 3.515502 TCTTCGGGAATCAGACACTCATT 59.484 43.478 0.00 0.00 0.00 2.57
2084 2251 3.099905 TCTTCGGGAATCAGACACTCAT 58.900 45.455 0.00 0.00 0.00 2.90
2085 2252 2.525368 TCTTCGGGAATCAGACACTCA 58.475 47.619 0.00 0.00 0.00 3.41
2086 2253 3.594603 TTCTTCGGGAATCAGACACTC 57.405 47.619 0.00 0.00 0.00 3.51
2087 2254 4.065789 GTTTTCTTCGGGAATCAGACACT 58.934 43.478 0.00 0.00 33.53 3.55
2088 2255 3.813166 TGTTTTCTTCGGGAATCAGACAC 59.187 43.478 0.00 0.00 33.53 3.67
2089 2256 4.079980 TGTTTTCTTCGGGAATCAGACA 57.920 40.909 0.00 0.00 33.53 3.41
2090 2257 5.393962 CATTGTTTTCTTCGGGAATCAGAC 58.606 41.667 0.00 0.00 33.53 3.51
2091 2258 4.458989 CCATTGTTTTCTTCGGGAATCAGA 59.541 41.667 0.00 0.00 33.53 3.27
2092 2259 4.458989 TCCATTGTTTTCTTCGGGAATCAG 59.541 41.667 0.00 0.00 33.53 2.90
2093 2260 4.402829 TCCATTGTTTTCTTCGGGAATCA 58.597 39.130 0.00 0.00 33.53 2.57
2094 2261 5.385509 TTCCATTGTTTTCTTCGGGAATC 57.614 39.130 0.00 0.00 33.53 2.52
2095 2262 6.165577 CAATTCCATTGTTTTCTTCGGGAAT 58.834 36.000 0.00 0.00 43.46 3.01
2096 2263 5.537188 CAATTCCATTGTTTTCTTCGGGAA 58.463 37.500 0.00 0.00 37.35 3.97
2097 2264 5.132897 CAATTCCATTGTTTTCTTCGGGA 57.867 39.130 0.00 0.00 35.57 5.14
2109 2276 6.650390 CCCAACCTTCTTTTACAATTCCATTG 59.350 38.462 0.00 0.00 45.59 2.82
2110 2277 6.239858 CCCCAACCTTCTTTTACAATTCCATT 60.240 38.462 0.00 0.00 0.00 3.16
2111 2278 5.248248 CCCCAACCTTCTTTTACAATTCCAT 59.752 40.000 0.00 0.00 0.00 3.41
2112 2279 4.591072 CCCCAACCTTCTTTTACAATTCCA 59.409 41.667 0.00 0.00 0.00 3.53
2113 2280 4.591498 ACCCCAACCTTCTTTTACAATTCC 59.409 41.667 0.00 0.00 0.00 3.01
2114 2281 5.303333 TCACCCCAACCTTCTTTTACAATTC 59.697 40.000 0.00 0.00 0.00 2.17
2115 2282 5.212745 TCACCCCAACCTTCTTTTACAATT 58.787 37.500 0.00 0.00 0.00 2.32
2116 2283 4.810345 TCACCCCAACCTTCTTTTACAAT 58.190 39.130 0.00 0.00 0.00 2.71
2117 2284 4.252570 TCACCCCAACCTTCTTTTACAA 57.747 40.909 0.00 0.00 0.00 2.41
2118 2285 3.955524 TCACCCCAACCTTCTTTTACA 57.044 42.857 0.00 0.00 0.00 2.41
2119 2286 4.587262 ACATTCACCCCAACCTTCTTTTAC 59.413 41.667 0.00 0.00 0.00 2.01
2120 2287 4.810345 ACATTCACCCCAACCTTCTTTTA 58.190 39.130 0.00 0.00 0.00 1.52
2121 2288 3.653164 ACATTCACCCCAACCTTCTTTT 58.347 40.909 0.00 0.00 0.00 2.27
2122 2289 3.328535 ACATTCACCCCAACCTTCTTT 57.671 42.857 0.00 0.00 0.00 2.52
2123 2290 3.328535 AACATTCACCCCAACCTTCTT 57.671 42.857 0.00 0.00 0.00 2.52
2124 2291 2.965147 CAAACATTCACCCCAACCTTCT 59.035 45.455 0.00 0.00 0.00 2.85
2125 2292 2.962421 TCAAACATTCACCCCAACCTTC 59.038 45.455 0.00 0.00 0.00 3.46
2126 2293 3.039252 TCAAACATTCACCCCAACCTT 57.961 42.857 0.00 0.00 0.00 3.50
2127 2294 2.765689 TCAAACATTCACCCCAACCT 57.234 45.000 0.00 0.00 0.00 3.50
2128 2295 4.350368 AAATCAAACATTCACCCCAACC 57.650 40.909 0.00 0.00 0.00 3.77
2129 2296 5.610398 AGAAAATCAAACATTCACCCCAAC 58.390 37.500 0.00 0.00 0.00 3.77
2130 2297 5.885449 AGAAAATCAAACATTCACCCCAA 57.115 34.783 0.00 0.00 0.00 4.12
2131 2298 6.723515 TCATAGAAAATCAAACATTCACCCCA 59.276 34.615 0.00 0.00 0.00 4.96
2132 2299 7.169158 TCATAGAAAATCAAACATTCACCCC 57.831 36.000 0.00 0.00 0.00 4.95
2133 2300 8.925700 GTTTCATAGAAAATCAAACATTCACCC 58.074 33.333 0.00 0.00 0.00 4.61
2134 2301 8.638565 CGTTTCATAGAAAATCAAACATTCACC 58.361 33.333 0.00 0.00 0.00 4.02
2135 2302 9.180678 ACGTTTCATAGAAAATCAAACATTCAC 57.819 29.630 0.00 0.00 0.00 3.18
2136 2303 9.393249 GACGTTTCATAGAAAATCAAACATTCA 57.607 29.630 0.00 0.00 0.00 2.57
2137 2304 8.567221 CGACGTTTCATAGAAAATCAAACATTC 58.433 33.333 0.00 0.00 0.00 2.67
2138 2305 8.073768 ACGACGTTTCATAGAAAATCAAACATT 58.926 29.630 0.00 0.00 0.00 2.71
2139 2306 7.581476 ACGACGTTTCATAGAAAATCAAACAT 58.419 30.769 0.00 0.00 0.00 2.71
2140 2307 6.950545 ACGACGTTTCATAGAAAATCAAACA 58.049 32.000 0.00 0.00 0.00 2.83
2141 2308 8.005466 TGTACGACGTTTCATAGAAAATCAAAC 58.995 33.333 5.50 0.00 0.00 2.93
2142 2309 8.074474 TGTACGACGTTTCATAGAAAATCAAA 57.926 30.769 5.50 0.00 0.00 2.69
2143 2310 7.640616 TGTACGACGTTTCATAGAAAATCAA 57.359 32.000 5.50 0.00 0.00 2.57
2144 2311 7.640616 TTGTACGACGTTTCATAGAAAATCA 57.359 32.000 5.50 0.00 0.00 2.57
2145 2312 8.922738 TTTTGTACGACGTTTCATAGAAAATC 57.077 30.769 5.50 0.00 0.00 2.17
2146 2313 8.767085 TCTTTTGTACGACGTTTCATAGAAAAT 58.233 29.630 5.50 0.00 0.00 1.82
2147 2314 8.129161 TCTTTTGTACGACGTTTCATAGAAAA 57.871 30.769 5.50 4.29 0.00 2.29
2148 2315 7.697352 TCTTTTGTACGACGTTTCATAGAAA 57.303 32.000 5.50 0.00 0.00 2.52
2149 2316 7.878477 ATCTTTTGTACGACGTTTCATAGAA 57.122 32.000 5.50 0.00 0.00 2.10
2150 2317 7.878477 AATCTTTTGTACGACGTTTCATAGA 57.122 32.000 5.50 11.75 0.00 1.98
2151 2318 8.641155 TGTAATCTTTTGTACGACGTTTCATAG 58.359 33.333 5.50 7.32 0.00 2.23
2152 2319 8.518151 TGTAATCTTTTGTACGACGTTTCATA 57.482 30.769 5.50 0.00 0.00 2.15
2153 2320 7.410800 TGTAATCTTTTGTACGACGTTTCAT 57.589 32.000 5.50 0.00 0.00 2.57
2154 2321 6.825284 TGTAATCTTTTGTACGACGTTTCA 57.175 33.333 5.50 3.49 0.00 2.69
2155 2322 9.796062 TTTATGTAATCTTTTGTACGACGTTTC 57.204 29.630 5.50 0.52 0.00 2.78
2193 2360 6.370166 GTCCTTCGATTCATAGGATTTGGATC 59.630 42.308 6.09 0.00 40.05 3.36
2194 2361 6.234177 GTCCTTCGATTCATAGGATTTGGAT 58.766 40.000 6.09 0.00 40.05 3.41
2195 2362 5.454755 GGTCCTTCGATTCATAGGATTTGGA 60.455 44.000 6.09 0.00 40.05 3.53
2196 2363 4.757149 GGTCCTTCGATTCATAGGATTTGG 59.243 45.833 6.09 0.00 40.05 3.28
2197 2364 4.449068 CGGTCCTTCGATTCATAGGATTTG 59.551 45.833 6.09 0.00 40.05 2.32
2198 2365 4.344102 TCGGTCCTTCGATTCATAGGATTT 59.656 41.667 6.09 0.00 40.05 2.17
2199 2366 3.895656 TCGGTCCTTCGATTCATAGGATT 59.104 43.478 6.09 0.00 40.05 3.01
2200 2367 3.256136 GTCGGTCCTTCGATTCATAGGAT 59.744 47.826 6.09 0.00 40.05 3.24
2201 2368 2.621998 GTCGGTCCTTCGATTCATAGGA 59.378 50.000 0.00 0.00 41.40 2.94
2202 2369 2.361119 TGTCGGTCCTTCGATTCATAGG 59.639 50.000 0.00 0.00 41.40 2.57
2203 2370 3.710326 TGTCGGTCCTTCGATTCATAG 57.290 47.619 0.00 0.00 41.40 2.23
2204 2371 3.005472 GGATGTCGGTCCTTCGATTCATA 59.995 47.826 0.00 0.00 41.40 2.15
2205 2372 2.224066 GGATGTCGGTCCTTCGATTCAT 60.224 50.000 0.00 0.00 41.40 2.57
2206 2373 1.136305 GGATGTCGGTCCTTCGATTCA 59.864 52.381 0.00 0.00 41.40 2.57
2207 2374 1.409427 AGGATGTCGGTCCTTCGATTC 59.591 52.381 0.00 0.00 46.45 2.52
2208 2375 1.486211 AGGATGTCGGTCCTTCGATT 58.514 50.000 0.00 0.00 46.45 3.34
2209 2376 2.359981 TAGGATGTCGGTCCTTCGAT 57.640 50.000 9.63 0.00 46.45 3.59
2210 2377 2.022195 CTTAGGATGTCGGTCCTTCGA 58.978 52.381 9.63 0.00 46.45 3.71
2211 2378 1.067212 CCTTAGGATGTCGGTCCTTCG 59.933 57.143 9.63 3.24 46.45 3.79
2212 2379 2.385803 TCCTTAGGATGTCGGTCCTTC 58.614 52.381 0.00 0.00 46.45 3.46
2213 2380 2.544844 TCCTTAGGATGTCGGTCCTT 57.455 50.000 0.00 0.00 46.45 3.36
2215 2382 4.722361 GATATCCTTAGGATGTCGGTCC 57.278 50.000 22.97 1.26 43.06 4.46


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

AutoCloner maintained by Alex Coulton.