Multiple sequence alignment - TraesCS4A01G250700

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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 TraesCS4A01G250700 chr4A 100.000 2796 0 0 1 2796 562282608 562279813 0.000000e+00 5164.0
1 TraesCS4A01G250700 chr4A 88.679 53 4 2 818 869 47742607 47742556 2.330000e-06 63.9
2 TraesCS4A01G250700 chr2B 98.590 851 11 1 1946 2796 161702030 161702879 0.000000e+00 1504.0
3 TraesCS4A01G250700 chr2B 98.227 846 15 0 1951 2796 409662330 409661485 0.000000e+00 1480.0
4 TraesCS4A01G250700 chr7B 98.582 846 12 0 1951 2796 458854607 458853762 0.000000e+00 1496.0
5 TraesCS4A01G250700 chr7B 98.111 847 12 2 1951 2796 503143137 503143980 0.000000e+00 1472.0
6 TraesCS4A01G250700 chr7B 97.991 846 17 0 1951 2796 23388178 23387333 0.000000e+00 1469.0
7 TraesCS4A01G250700 chr7B 92.857 42 2 1 1853 1893 253696489 253696448 3.010000e-05 60.2
8 TraesCS4A01G250700 chr7B 94.595 37 2 0 818 854 97502686 97502650 1.080000e-04 58.4
9 TraesCS4A01G250700 chr7B 100.000 30 0 0 758 787 495658536 495658565 3.890000e-04 56.5
10 TraesCS4A01G250700 chrUn 98.227 846 15 0 1951 2796 63227193 63228038 0.000000e+00 1480.0
11 TraesCS4A01G250700 chrUn 90.909 44 4 0 818 861 177410755 177410712 3.010000e-05 60.2
12 TraesCS4A01G250700 chrUn 90.909 44 4 0 818 861 415132015 415131972 3.010000e-05 60.2
13 TraesCS4A01G250700 chr6A 98.113 848 14 1 1951 2796 569696533 569697380 0.000000e+00 1476.0
14 TraesCS4A01G250700 chr7A 97.895 855 13 3 1945 2796 162727983 162728835 0.000000e+00 1474.0
15 TraesCS4A01G250700 chr7A 95.349 43 2 0 818 860 33452919 33452877 5.000000e-08 69.4
16 TraesCS4A01G250700 chr7A 92.857 42 2 1 1853 1893 316018765 316018724 3.010000e-05 60.2
17 TraesCS4A01G250700 chr1B 97.993 847 17 0 1950 2796 647615997 647616843 0.000000e+00 1471.0
18 TraesCS4A01G250700 chr4B 92.193 807 34 12 1 785 56985968 56985169 0.000000e+00 1114.0
19 TraesCS4A01G250700 chr4B 91.482 587 33 10 858 1432 56985071 56984490 0.000000e+00 791.0
20 TraesCS4A01G250700 chr4B 90.643 342 20 5 1464 1803 56984491 56984160 7.110000e-121 444.0
21 TraesCS4A01G250700 chr4D 93.918 707 37 4 1 707 39209250 39208550 0.000000e+00 1062.0
22 TraesCS4A01G250700 chr4D 90.388 593 28 13 858 1430 39208282 39207699 0.000000e+00 752.0
23 TraesCS4A01G250700 chr4D 92.286 350 12 6 1464 1804 39207696 39207353 1.510000e-132 483.0
24 TraesCS4A01G250700 chr2D 95.238 42 2 0 815 856 7103212 7103253 1.800000e-07 67.6
25 TraesCS4A01G250700 chr7D 94.872 39 2 0 818 856 180730314 180730352 8.360000e-06 62.1
26 TraesCS4A01G250700 chr7D 92.857 42 2 1 1853 1893 279743618 279743659 3.010000e-05 60.2
27 TraesCS4A01G250700 chr6B 100.000 29 0 0 828 856 476123598 476123570 1.000000e-03 54.7


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G250700 chr4A 562279813 562282608 2795 True 5164.000000 5164 100.000000 1 2796 1 chr4A.!!$R2 2795
1 TraesCS4A01G250700 chr2B 161702030 161702879 849 False 1504.000000 1504 98.590000 1946 2796 1 chr2B.!!$F1 850
2 TraesCS4A01G250700 chr2B 409661485 409662330 845 True 1480.000000 1480 98.227000 1951 2796 1 chr2B.!!$R1 845
3 TraesCS4A01G250700 chr7B 458853762 458854607 845 True 1496.000000 1496 98.582000 1951 2796 1 chr7B.!!$R4 845
4 TraesCS4A01G250700 chr7B 503143137 503143980 843 False 1472.000000 1472 98.111000 1951 2796 1 chr7B.!!$F2 845
5 TraesCS4A01G250700 chr7B 23387333 23388178 845 True 1469.000000 1469 97.991000 1951 2796 1 chr7B.!!$R1 845
6 TraesCS4A01G250700 chrUn 63227193 63228038 845 False 1480.000000 1480 98.227000 1951 2796 1 chrUn.!!$F1 845
7 TraesCS4A01G250700 chr6A 569696533 569697380 847 False 1476.000000 1476 98.113000 1951 2796 1 chr6A.!!$F1 845
8 TraesCS4A01G250700 chr7A 162727983 162728835 852 False 1474.000000 1474 97.895000 1945 2796 1 chr7A.!!$F1 851
9 TraesCS4A01G250700 chr1B 647615997 647616843 846 False 1471.000000 1471 97.993000 1950 2796 1 chr1B.!!$F1 846
10 TraesCS4A01G250700 chr4B 56984160 56985968 1808 True 783.000000 1114 91.439333 1 1803 3 chr4B.!!$R1 1802
11 TraesCS4A01G250700 chr4D 39207353 39209250 1897 True 765.666667 1062 92.197333 1 1804 3 chr4D.!!$R1 1803

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
675 698 0.739813 ACGGGAAAGATAGCGTGTGC 60.74 55.0 0.0 0.0 43.24 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1902 2099 0.033601 ACAGGGACAAAGTTGCCACA 60.034 50.0 6.77 0.0 0.0 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
142 144 8.579682 AATCATTAAACAACAGAGCTTTTCAC 57.420 30.769 0.00 0.00 0.00 3.18
156 158 3.872696 CTTTTCACCTTTGCAAAAGGGT 58.127 40.909 23.11 19.79 41.71 4.34
166 168 1.039856 GCAAAAGGGTGCTTCCTGAA 58.960 50.000 0.00 0.00 41.51 3.02
182 184 3.066064 TCCTGAACAAATGTGAAACCGTG 59.934 43.478 0.00 0.00 34.36 4.94
241 248 2.996621 GTCCTGACTTTGATTCCTCACG 59.003 50.000 0.00 0.00 0.00 4.35
263 270 8.717821 TCACGTCCTTGTTTTTCTATCTATTTG 58.282 33.333 0.00 0.00 0.00 2.32
334 341 3.012959 ACTCCTCTTCTCCATACTGGGAA 59.987 47.826 0.00 0.00 38.32 3.97
356 363 1.134280 GTGATGTACATGCAGGGAGCT 60.134 52.381 14.43 0.00 45.94 4.09
437 444 4.442332 CCAAACAAAGACAAGTTTACCCCC 60.442 45.833 0.00 0.00 36.28 5.40
528 551 2.626266 TCTGTCGAACTTCCAGTTAGCA 59.374 45.455 0.00 0.00 38.80 3.49
546 569 8.514594 CAGTTAGCAACATTTTATCTTTCCTCA 58.485 33.333 0.00 0.00 0.00 3.86
642 665 7.867909 TGTCGACTTGATTATATGTTCTCCATC 59.132 37.037 17.92 0.00 34.86 3.51
643 666 7.867909 GTCGACTTGATTATATGTTCTCCATCA 59.132 37.037 8.70 0.00 34.86 3.07
675 698 0.739813 ACGGGAAAGATAGCGTGTGC 60.740 55.000 0.00 0.00 43.24 4.57
714 737 8.610248 TTGTAAACAACTAAAATCTCATCCGA 57.390 30.769 0.00 0.00 0.00 4.55
741 784 7.667575 ATGAGTTACAGAAGATGGTCACTAT 57.332 36.000 0.00 0.00 0.00 2.12
747 790 9.988815 GTTACAGAAGATGGTCACTATGATATT 57.011 33.333 0.00 0.00 0.00 1.28
787 859 6.326843 ACCACTCCCTCTGTTCCTAAATATAC 59.673 42.308 0.00 0.00 0.00 1.47
788 860 6.326583 CCACTCCCTCTGTTCCTAAATATACA 59.673 42.308 0.00 0.00 0.00 2.29
792 864 8.195165 TCCCTCTGTTCCTAAATATACATCTG 57.805 38.462 0.00 0.00 0.00 2.90
795 959 9.915629 CCTCTGTTCCTAAATATACATCTGTAC 57.084 37.037 0.00 0.00 32.72 2.90
822 986 9.847224 TGAAATCTCTAAAATGTCTTATACCCC 57.153 33.333 0.00 0.00 0.00 4.95
826 990 8.030913 TCTCTAAAATGTCTTATACCCCTTCC 57.969 38.462 0.00 0.00 0.00 3.46
827 991 6.823497 TCTAAAATGTCTTATACCCCTTCCG 58.177 40.000 0.00 0.00 0.00 4.30
828 992 5.446260 AAAATGTCTTATACCCCTTCCGT 57.554 39.130 0.00 0.00 0.00 4.69
829 993 4.684484 AATGTCTTATACCCCTTCCGTC 57.316 45.455 0.00 0.00 0.00 4.79
830 994 2.391678 TGTCTTATACCCCTTCCGTCC 58.608 52.381 0.00 0.00 0.00 4.79
831 995 1.690893 GTCTTATACCCCTTCCGTCCC 59.309 57.143 0.00 0.00 0.00 4.46
832 996 1.291637 TCTTATACCCCTTCCGTCCCA 59.708 52.381 0.00 0.00 0.00 4.37
833 997 2.090380 TCTTATACCCCTTCCGTCCCAT 60.090 50.000 0.00 0.00 0.00 4.00
835 999 2.500269 ATACCCCTTCCGTCCCATAA 57.500 50.000 0.00 0.00 0.00 1.90
837 1001 2.500269 ACCCCTTCCGTCCCATAATA 57.500 50.000 0.00 0.00 0.00 0.98
838 1002 2.999928 ACCCCTTCCGTCCCATAATAT 58.000 47.619 0.00 0.00 0.00 1.28
839 1003 4.150516 ACCCCTTCCGTCCCATAATATA 57.849 45.455 0.00 0.00 0.00 0.86
840 1004 4.505367 ACCCCTTCCGTCCCATAATATAA 58.495 43.478 0.00 0.00 0.00 0.98
841 1005 4.534897 ACCCCTTCCGTCCCATAATATAAG 59.465 45.833 0.00 0.00 0.00 1.73
842 1006 4.781087 CCCCTTCCGTCCCATAATATAAGA 59.219 45.833 0.00 0.00 0.00 2.10
843 1007 5.104900 CCCCTTCCGTCCCATAATATAAGAG 60.105 48.000 0.00 0.00 0.00 2.85
844 1008 5.420409 CCTTCCGTCCCATAATATAAGAGC 58.580 45.833 0.00 0.00 0.00 4.09
845 1009 4.713824 TCCGTCCCATAATATAAGAGCG 57.286 45.455 0.00 0.00 0.00 5.03
846 1010 4.338012 TCCGTCCCATAATATAAGAGCGA 58.662 43.478 0.00 0.00 0.00 4.93
847 1011 4.954202 TCCGTCCCATAATATAAGAGCGAT 59.046 41.667 0.00 0.00 0.00 4.58
848 1012 5.421056 TCCGTCCCATAATATAAGAGCGATT 59.579 40.000 0.00 0.00 0.00 3.34
849 1013 6.070995 TCCGTCCCATAATATAAGAGCGATTT 60.071 38.462 0.00 0.00 0.00 2.17
850 1014 6.594159 CCGTCCCATAATATAAGAGCGATTTT 59.406 38.462 0.00 0.00 0.00 1.82
851 1015 7.413000 CCGTCCCATAATATAAGAGCGATTTTG 60.413 40.741 0.00 0.00 0.00 2.44
852 1016 7.330946 CGTCCCATAATATAAGAGCGATTTTGA 59.669 37.037 0.00 0.00 0.00 2.69
853 1017 8.443937 GTCCCATAATATAAGAGCGATTTTGAC 58.556 37.037 0.00 0.00 0.00 3.18
854 1018 8.154203 TCCCATAATATAAGAGCGATTTTGACA 58.846 33.333 0.00 0.00 0.00 3.58
855 1019 8.230486 CCCATAATATAAGAGCGATTTTGACAC 58.770 37.037 0.00 0.00 0.00 3.67
856 1020 8.230486 CCATAATATAAGAGCGATTTTGACACC 58.770 37.037 0.00 0.00 0.00 4.16
857 1021 8.773645 CATAATATAAGAGCGATTTTGACACCA 58.226 33.333 0.00 0.00 0.00 4.17
858 1022 6.851222 ATATAAGAGCGATTTTGACACCAG 57.149 37.500 0.00 0.00 0.00 4.00
859 1023 2.550830 AGAGCGATTTTGACACCAGT 57.449 45.000 0.00 0.00 0.00 4.00
860 1024 2.146342 AGAGCGATTTTGACACCAGTG 58.854 47.619 0.00 0.00 0.00 3.66
890 1054 4.518970 TCCACTAGGTGAAAATCTTGTTGC 59.481 41.667 0.00 0.00 35.23 4.17
891 1055 4.466828 CACTAGGTGAAAATCTTGTTGCG 58.533 43.478 0.00 0.00 35.23 4.85
909 1078 2.685380 AGGAAGGAGCCGAGGTGG 60.685 66.667 0.00 0.00 42.50 4.61
956 1125 7.147585 ACAGTGATAGATGATGCCTTCTAACTT 60.148 37.037 0.00 0.00 34.18 2.66
957 1126 7.171167 CAGTGATAGATGATGCCTTCTAACTTG 59.829 40.741 0.00 0.00 34.18 3.16
997 1166 9.710900 CATTGTGACTATTATATGCTCAACCTA 57.289 33.333 0.00 0.00 0.00 3.08
1029 1198 0.097674 CGCTGGAGTTTAGCACATGC 59.902 55.000 0.00 0.00 41.18 4.06
1078 1247 1.754803 TGGGATACACAGTGATCGGTC 59.245 52.381 7.81 0.00 39.74 4.79
1135 1304 1.746787 CATATGTCAAGCCTGCTGCAA 59.253 47.619 3.02 0.00 44.83 4.08
1150 1319 2.882876 CAAGCAGGCCAGTGATGC 59.117 61.111 5.01 5.48 40.29 3.91
1280 1462 5.814705 ACAGTAACAGAAGCAGCAGAATATC 59.185 40.000 0.00 0.00 0.00 1.63
1365 1547 2.311463 TCAGCCGGAGATTAGAGAAGG 58.689 52.381 5.05 0.00 0.00 3.46
1366 1548 2.091830 TCAGCCGGAGATTAGAGAAGGA 60.092 50.000 5.05 0.00 0.00 3.36
1441 1629 3.038280 CGGAGGGCATCTCTCTCG 58.962 66.667 0.00 0.00 42.10 4.04
1442 1630 1.826054 CGGAGGGCATCTCTCTCGT 60.826 63.158 0.00 0.00 42.10 4.18
1443 1631 1.791103 CGGAGGGCATCTCTCTCGTC 61.791 65.000 0.00 0.00 42.10 4.20
1444 1632 1.652012 GAGGGCATCTCTCTCGTCG 59.348 63.158 0.00 0.00 39.38 5.12
1445 1633 1.791103 GAGGGCATCTCTCTCGTCGG 61.791 65.000 0.00 0.00 39.38 4.79
1446 1634 2.122167 GGGCATCTCTCTCGTCGGT 61.122 63.158 0.00 0.00 0.00 4.69
1447 1635 1.064946 GGCATCTCTCTCGTCGGTG 59.935 63.158 0.00 0.00 0.00 4.94
1448 1636 1.658686 GGCATCTCTCTCGTCGGTGT 61.659 60.000 0.00 0.00 0.00 4.16
1449 1637 1.015109 GCATCTCTCTCGTCGGTGTA 58.985 55.000 0.00 0.00 0.00 2.90
1450 1638 1.268133 GCATCTCTCTCGTCGGTGTAC 60.268 57.143 0.00 0.00 0.00 2.90
1451 1639 1.004821 CATCTCTCTCGTCGGTGTACG 60.005 57.143 0.00 0.00 44.19 3.67
1452 1640 1.060622 CTCTCTCGTCGGTGTACGC 59.939 63.158 0.00 0.00 42.56 4.42
1453 1641 1.360194 CTCTCTCGTCGGTGTACGCT 61.360 60.000 6.35 0.00 42.56 5.07
1454 1642 1.226046 CTCTCGTCGGTGTACGCTG 60.226 63.158 9.06 9.06 42.56 5.18
1455 1643 1.909141 CTCTCGTCGGTGTACGCTGT 61.909 60.000 14.73 0.00 42.56 4.40
1456 1644 1.796355 CTCGTCGGTGTACGCTGTG 60.796 63.158 14.73 9.09 42.56 3.66
1457 1645 2.803670 CGTCGGTGTACGCTGTGG 60.804 66.667 14.73 4.77 43.86 4.17
1458 1646 2.431942 GTCGGTGTACGCTGTGGG 60.432 66.667 14.73 0.00 43.86 4.61
1459 1647 4.367023 TCGGTGTACGCTGTGGGC 62.367 66.667 14.73 0.00 43.86 5.36
1480 1668 1.651240 CCGCCTGAAAGCCACTGATG 61.651 60.000 0.00 0.00 0.00 3.07
1513 1701 2.261361 CACCCGTGATCGAGCACA 59.739 61.111 30.82 9.89 38.69 4.57
1531 1726 3.370276 CACAGAGCAGACTGATCATACG 58.630 50.000 22.00 10.03 40.63 3.06
1542 1737 1.134175 TGATCATACGCAGCGACTTCA 59.866 47.619 24.65 13.38 0.00 3.02
1720 1917 1.413008 GGAAAATGGCGCATGCGTTC 61.413 55.000 37.54 30.15 44.10 3.95
1732 1929 2.045926 GCGTTCCCATCTGCAGGT 60.046 61.111 15.13 2.68 0.00 4.00
1733 1930 1.675641 GCGTTCCCATCTGCAGGTT 60.676 57.895 15.13 0.00 0.00 3.50
1792 1989 2.148768 CACCGTTTCAACCTCCCTTAC 58.851 52.381 0.00 0.00 0.00 2.34
1804 2001 3.983410 ACCTCCCTTACTGATGGCATATT 59.017 43.478 0.00 0.00 0.00 1.28
1805 2002 4.042187 ACCTCCCTTACTGATGGCATATTC 59.958 45.833 0.00 0.00 0.00 1.75
1806 2003 4.042062 CCTCCCTTACTGATGGCATATTCA 59.958 45.833 0.00 0.00 0.00 2.57
1807 2004 5.456619 CCTCCCTTACTGATGGCATATTCAA 60.457 44.000 0.00 0.00 0.00 2.69
1808 2005 6.204852 TCCCTTACTGATGGCATATTCAAT 57.795 37.500 0.00 0.00 0.00 2.57
1809 2006 7.328404 TCCCTTACTGATGGCATATTCAATA 57.672 36.000 0.00 0.00 0.00 1.90
1810 2007 7.754624 TCCCTTACTGATGGCATATTCAATAA 58.245 34.615 0.00 0.00 0.00 1.40
1811 2008 8.224025 TCCCTTACTGATGGCATATTCAATAAA 58.776 33.333 0.00 0.00 0.00 1.40
1812 2009 8.859090 CCCTTACTGATGGCATATTCAATAAAA 58.141 33.333 0.00 0.00 0.00 1.52
1816 2013 7.899973 ACTGATGGCATATTCAATAAAATCCC 58.100 34.615 0.00 0.00 0.00 3.85
1817 2014 6.923012 TGATGGCATATTCAATAAAATCCCG 58.077 36.000 0.00 0.00 0.00 5.14
1818 2015 6.718912 TGATGGCATATTCAATAAAATCCCGA 59.281 34.615 0.00 0.00 0.00 5.14
1819 2016 6.968263 TGGCATATTCAATAAAATCCCGAA 57.032 33.333 0.00 0.00 0.00 4.30
1820 2017 6.744112 TGGCATATTCAATAAAATCCCGAAC 58.256 36.000 0.00 0.00 0.00 3.95
1821 2018 6.322456 TGGCATATTCAATAAAATCCCGAACA 59.678 34.615 0.00 0.00 0.00 3.18
1822 2019 7.015098 TGGCATATTCAATAAAATCCCGAACAT 59.985 33.333 0.00 0.00 0.00 2.71
1823 2020 7.872483 GGCATATTCAATAAAATCCCGAACATT 59.128 33.333 0.00 0.00 0.00 2.71
1824 2021 8.915654 GCATATTCAATAAAATCCCGAACATTC 58.084 33.333 0.00 0.00 0.00 2.67
1827 2024 7.695480 TTCAATAAAATCCCGAACATTCTGA 57.305 32.000 0.00 0.00 0.00 3.27
1828 2025 7.880160 TCAATAAAATCCCGAACATTCTGAT 57.120 32.000 0.00 0.00 0.00 2.90
1829 2026 8.292444 TCAATAAAATCCCGAACATTCTGATT 57.708 30.769 0.00 2.24 31.76 2.57
1830 2027 8.748412 TCAATAAAATCCCGAACATTCTGATTT 58.252 29.630 10.68 10.68 37.64 2.17
1831 2028 9.369904 CAATAAAATCCCGAACATTCTGATTTT 57.630 29.630 22.00 22.00 42.38 1.82
1834 2031 8.986477 AAAATCCCGAACATTCTGATTTTAAG 57.014 30.769 19.50 0.00 40.47 1.85
1835 2032 5.560966 TCCCGAACATTCTGATTTTAAGC 57.439 39.130 0.00 0.00 0.00 3.09
1836 2033 5.007034 TCCCGAACATTCTGATTTTAAGCA 58.993 37.500 0.00 0.00 0.00 3.91
1837 2034 5.652014 TCCCGAACATTCTGATTTTAAGCAT 59.348 36.000 0.00 0.00 0.00 3.79
1838 2035 5.745294 CCCGAACATTCTGATTTTAAGCATG 59.255 40.000 0.00 0.00 0.00 4.06
1839 2036 5.230726 CCGAACATTCTGATTTTAAGCATGC 59.769 40.000 10.51 10.51 0.00 4.06
1840 2037 5.230726 CGAACATTCTGATTTTAAGCATGCC 59.769 40.000 15.66 0.00 0.00 4.40
1841 2038 5.664294 ACATTCTGATTTTAAGCATGCCA 57.336 34.783 15.66 1.89 0.00 4.92
1842 2039 6.229936 ACATTCTGATTTTAAGCATGCCAT 57.770 33.333 15.66 6.44 0.00 4.40
1843 2040 6.278363 ACATTCTGATTTTAAGCATGCCATC 58.722 36.000 15.66 9.02 0.00 3.51
1844 2041 4.556942 TCTGATTTTAAGCATGCCATCG 57.443 40.909 15.66 5.73 0.00 3.84
1845 2042 3.947196 TCTGATTTTAAGCATGCCATCGT 59.053 39.130 15.66 0.00 0.00 3.73
1846 2043 4.031418 TGATTTTAAGCATGCCATCGTG 57.969 40.909 15.66 0.00 0.00 4.35
1847 2044 3.693578 TGATTTTAAGCATGCCATCGTGA 59.306 39.130 15.66 0.00 0.00 4.35
1848 2045 4.157472 TGATTTTAAGCATGCCATCGTGAA 59.843 37.500 15.66 0.98 0.00 3.18
1849 2046 4.717233 TTTTAAGCATGCCATCGTGAAT 57.283 36.364 15.66 0.00 0.00 2.57
1850 2047 3.696281 TTAAGCATGCCATCGTGAATG 57.304 42.857 15.66 0.00 34.93 2.67
1851 2048 1.466856 AAGCATGCCATCGTGAATGT 58.533 45.000 15.66 0.00 33.13 2.71
1852 2049 1.466856 AGCATGCCATCGTGAATGTT 58.533 45.000 15.66 0.00 33.13 2.71
1853 2050 1.820519 AGCATGCCATCGTGAATGTTT 59.179 42.857 15.66 0.00 33.13 2.83
1854 2051 2.231964 AGCATGCCATCGTGAATGTTTT 59.768 40.909 15.66 0.00 33.13 2.43
1855 2052 2.995258 GCATGCCATCGTGAATGTTTTT 59.005 40.909 6.36 0.00 33.13 1.94
1876 2073 7.626144 TTTTTATGGCAACTTTAGTTAACGC 57.374 32.000 0.00 0.00 36.32 4.84
1877 2074 2.953640 TGGCAACTTTAGTTAACGCG 57.046 45.000 3.53 3.53 36.32 6.01
1878 2075 2.481854 TGGCAACTTTAGTTAACGCGA 58.518 42.857 15.93 0.00 36.32 5.87
1879 2076 2.477375 TGGCAACTTTAGTTAACGCGAG 59.523 45.455 15.93 0.00 36.32 5.03
1880 2077 2.159747 GGCAACTTTAGTTAACGCGAGG 60.160 50.000 15.93 0.00 36.32 4.63
1881 2078 2.477754 GCAACTTTAGTTAACGCGAGGT 59.522 45.455 15.93 0.00 36.32 3.85
1882 2079 3.663493 GCAACTTTAGTTAACGCGAGGTG 60.663 47.826 15.93 7.03 36.32 4.00
1883 2080 2.680577 ACTTTAGTTAACGCGAGGTGG 58.319 47.619 15.93 0.00 0.00 4.61
1884 2081 1.392510 CTTTAGTTAACGCGAGGTGGC 59.607 52.381 15.93 0.00 0.00 5.01
1885 2082 0.317799 TTAGTTAACGCGAGGTGGCA 59.682 50.000 15.93 0.00 0.00 4.92
1886 2083 0.317799 TAGTTAACGCGAGGTGGCAA 59.682 50.000 15.93 0.00 0.00 4.52
1887 2084 1.205820 GTTAACGCGAGGTGGCAAC 59.794 57.895 15.93 0.00 0.00 4.17
1888 2085 1.070105 TTAACGCGAGGTGGCAACT 59.930 52.632 15.93 3.75 37.61 3.16
1889 2086 0.533308 TTAACGCGAGGTGGCAACTT 60.533 50.000 15.93 0.00 37.61 2.66
1890 2087 0.533308 TAACGCGAGGTGGCAACTTT 60.533 50.000 15.93 0.00 37.61 2.66
1891 2088 0.533308 AACGCGAGGTGGCAACTTTA 60.533 50.000 15.93 0.00 37.61 1.85
1892 2089 0.949105 ACGCGAGGTGGCAACTTTAG 60.949 55.000 15.93 3.35 37.61 1.85
1893 2090 0.669318 CGCGAGGTGGCAACTTTAGA 60.669 55.000 6.46 0.00 37.61 2.10
1894 2091 1.739067 GCGAGGTGGCAACTTTAGAT 58.261 50.000 6.46 0.00 37.61 1.98
1895 2092 1.398390 GCGAGGTGGCAACTTTAGATG 59.602 52.381 6.46 0.00 37.61 2.90
1896 2093 2.699954 CGAGGTGGCAACTTTAGATGT 58.300 47.619 6.46 0.00 37.61 3.06
1897 2094 3.074412 CGAGGTGGCAACTTTAGATGTT 58.926 45.455 6.46 0.00 37.61 2.71
1898 2095 4.250464 CGAGGTGGCAACTTTAGATGTTA 58.750 43.478 6.46 0.00 37.61 2.41
1899 2096 4.330074 CGAGGTGGCAACTTTAGATGTTAG 59.670 45.833 6.46 0.00 37.61 2.34
1900 2097 5.488341 GAGGTGGCAACTTTAGATGTTAGA 58.512 41.667 6.46 0.00 37.61 2.10
1901 2098 5.876357 AGGTGGCAACTTTAGATGTTAGAA 58.124 37.500 0.00 0.00 37.61 2.10
1902 2099 6.485171 AGGTGGCAACTTTAGATGTTAGAAT 58.515 36.000 0.00 0.00 37.61 2.40
1903 2100 6.375455 AGGTGGCAACTTTAGATGTTAGAATG 59.625 38.462 0.00 0.00 37.61 2.67
1904 2101 6.151144 GGTGGCAACTTTAGATGTTAGAATGT 59.849 38.462 0.00 0.00 37.61 2.71
1905 2102 7.023575 GTGGCAACTTTAGATGTTAGAATGTG 58.976 38.462 0.00 0.00 37.61 3.21
1906 2103 6.150976 TGGCAACTTTAGATGTTAGAATGTGG 59.849 38.462 0.00 0.00 37.61 4.17
1907 2104 6.030228 GCAACTTTAGATGTTAGAATGTGGC 58.970 40.000 0.00 0.00 0.00 5.01
1908 2105 6.349280 GCAACTTTAGATGTTAGAATGTGGCA 60.349 38.462 0.00 0.00 31.03 4.92
1909 2106 7.592938 CAACTTTAGATGTTAGAATGTGGCAA 58.407 34.615 0.00 0.00 0.00 4.52
1910 2107 7.145932 ACTTTAGATGTTAGAATGTGGCAAC 57.854 36.000 0.00 0.00 0.00 4.17
1911 2108 6.942576 ACTTTAGATGTTAGAATGTGGCAACT 59.057 34.615 0.00 0.00 37.61 3.16
1912 2109 7.448469 ACTTTAGATGTTAGAATGTGGCAACTT 59.552 33.333 0.00 0.00 37.61 2.66
1913 2110 7.759489 TTAGATGTTAGAATGTGGCAACTTT 57.241 32.000 0.00 0.00 37.61 2.66
1914 2111 6.017400 AGATGTTAGAATGTGGCAACTTTG 57.983 37.500 0.00 0.00 37.61 2.77
1915 2112 5.536161 AGATGTTAGAATGTGGCAACTTTGT 59.464 36.000 0.00 0.00 37.61 2.83
1916 2113 5.181690 TGTTAGAATGTGGCAACTTTGTC 57.818 39.130 0.00 0.00 37.61 3.18
1917 2114 4.037446 TGTTAGAATGTGGCAACTTTGTCC 59.963 41.667 0.00 0.00 37.61 4.02
1918 2115 1.963515 AGAATGTGGCAACTTTGTCCC 59.036 47.619 0.00 0.00 37.61 4.46
1919 2116 1.963515 GAATGTGGCAACTTTGTCCCT 59.036 47.619 0.00 0.00 37.61 4.20
1920 2117 1.331214 ATGTGGCAACTTTGTCCCTG 58.669 50.000 0.00 0.00 37.61 4.45
1921 2118 0.033601 TGTGGCAACTTTGTCCCTGT 60.034 50.000 0.00 0.00 37.61 4.00
1922 2119 1.111277 GTGGCAACTTTGTCCCTGTT 58.889 50.000 0.00 0.00 37.61 3.16
1923 2120 2.303175 GTGGCAACTTTGTCCCTGTTA 58.697 47.619 0.00 0.00 37.61 2.41
1924 2121 2.293399 GTGGCAACTTTGTCCCTGTTAG 59.707 50.000 0.00 0.00 37.61 2.34
1925 2122 2.092103 TGGCAACTTTGTCCCTGTTAGT 60.092 45.455 0.00 0.00 37.61 2.24
1926 2123 2.956333 GGCAACTTTGTCCCTGTTAGTT 59.044 45.455 0.00 0.00 0.00 2.24
1927 2124 3.004419 GGCAACTTTGTCCCTGTTAGTTC 59.996 47.826 0.00 0.00 0.00 3.01
1928 2125 3.883489 GCAACTTTGTCCCTGTTAGTTCT 59.117 43.478 0.00 0.00 0.00 3.01
1929 2126 4.338400 GCAACTTTGTCCCTGTTAGTTCTT 59.662 41.667 0.00 0.00 0.00 2.52
1930 2127 5.163550 GCAACTTTGTCCCTGTTAGTTCTTT 60.164 40.000 0.00 0.00 0.00 2.52
1931 2128 6.627287 GCAACTTTGTCCCTGTTAGTTCTTTT 60.627 38.462 0.00 0.00 0.00 2.27
1932 2129 7.415877 GCAACTTTGTCCCTGTTAGTTCTTTTA 60.416 37.037 0.00 0.00 0.00 1.52
1933 2130 8.630037 CAACTTTGTCCCTGTTAGTTCTTTTAT 58.370 33.333 0.00 0.00 0.00 1.40
1934 2131 8.166422 ACTTTGTCCCTGTTAGTTCTTTTATG 57.834 34.615 0.00 0.00 0.00 1.90
1935 2132 7.230712 ACTTTGTCCCTGTTAGTTCTTTTATGG 59.769 37.037 0.00 0.00 0.00 2.74
1936 2133 5.566469 TGTCCCTGTTAGTTCTTTTATGGG 58.434 41.667 0.00 0.00 0.00 4.00
1937 2134 5.311121 TGTCCCTGTTAGTTCTTTTATGGGA 59.689 40.000 0.00 0.00 38.72 4.37
1938 2135 6.183361 TGTCCCTGTTAGTTCTTTTATGGGAA 60.183 38.462 0.00 0.00 42.09 3.97
1939 2136 6.717997 GTCCCTGTTAGTTCTTTTATGGGAAA 59.282 38.462 0.00 0.00 42.09 3.13
1940 2137 7.231925 GTCCCTGTTAGTTCTTTTATGGGAAAA 59.768 37.037 0.00 0.00 42.09 2.29
1941 2138 7.450323 TCCCTGTTAGTTCTTTTATGGGAAAAG 59.550 37.037 0.00 3.84 38.17 2.27
1942 2139 7.232737 CCCTGTTAGTTCTTTTATGGGAAAAGT 59.767 37.037 9.05 0.00 38.17 2.66
1943 2140 8.082242 CCTGTTAGTTCTTTTATGGGAAAAGTG 58.918 37.037 9.05 0.00 38.17 3.16
1944 2141 8.528044 TGTTAGTTCTTTTATGGGAAAAGTGT 57.472 30.769 9.05 0.39 38.17 3.55
2028 2227 8.869986 ATATATATGTGATAGGCCACCCTTAA 57.130 34.615 5.01 0.00 42.87 1.85
2316 2525 3.441290 CGTCGGCTCCCTCTTCGT 61.441 66.667 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
142 144 1.541015 GGAAGCACCCTTTTGCAAAGG 60.541 52.381 14.01 14.01 45.62 3.11
156 158 4.441356 GGTTTCACATTTGTTCAGGAAGCA 60.441 41.667 0.00 0.00 0.00 3.91
166 168 3.013921 ACACTCACGGTTTCACATTTGT 58.986 40.909 0.00 0.00 0.00 2.83
182 184 2.560542 TGAAGAGCAGGAGAGAACACTC 59.439 50.000 0.00 0.00 36.31 3.51
334 341 2.681976 GCTCCCTGCATGTACATCACTT 60.682 50.000 5.07 0.00 42.31 3.16
356 363 3.468071 TCTGTAGAACCCTAGGAAGCA 57.532 47.619 11.48 0.00 0.00 3.91
497 507 3.113260 AGTTCGACAGAAAAGAGGTGG 57.887 47.619 0.00 0.00 38.23 4.61
528 551 8.571336 CAGTCAACTGAGGAAAGATAAAATGTT 58.429 33.333 4.05 0.00 46.59 2.71
568 591 0.392998 CGGCCTTACCTTGTCAGCAT 60.393 55.000 0.00 0.00 35.61 3.79
573 596 1.534163 GACAAACGGCCTTACCTTGTC 59.466 52.381 8.91 8.91 42.83 3.18
616 639 7.107639 TGGAGAACATATAATCAAGTCGACA 57.892 36.000 19.50 0.00 0.00 4.35
617 640 7.867909 TGATGGAGAACATATAATCAAGTCGAC 59.132 37.037 7.70 7.70 40.72 4.20
642 665 4.458989 TCTTTCCCGTCATTTCCAAGAATG 59.541 41.667 0.00 0.00 38.16 2.67
643 666 4.662278 TCTTTCCCGTCATTTCCAAGAAT 58.338 39.130 0.00 0.00 0.00 2.40
675 698 0.881159 TTACAAACTGGCGACCACGG 60.881 55.000 0.00 0.00 40.15 4.94
712 735 6.368791 TGACCATCTTCTGTAACTCATTTTCG 59.631 38.462 0.00 0.00 0.00 3.46
714 737 7.227156 AGTGACCATCTTCTGTAACTCATTTT 58.773 34.615 0.00 0.00 0.00 1.82
747 790 7.036863 AGAGGGAGTGGTTTATAAAATCTTCCA 60.037 37.037 17.64 11.00 0.00 3.53
764 836 7.361457 TGTATATTTAGGAACAGAGGGAGTG 57.639 40.000 0.00 0.00 0.00 3.51
819 983 4.781087 TCTTATATTATGGGACGGAAGGGG 59.219 45.833 0.00 0.00 0.00 4.79
820 984 5.627040 GCTCTTATATTATGGGACGGAAGGG 60.627 48.000 0.00 0.00 0.00 3.95
821 985 5.420409 GCTCTTATATTATGGGACGGAAGG 58.580 45.833 0.00 0.00 0.00 3.46
822 986 5.103000 CGCTCTTATATTATGGGACGGAAG 58.897 45.833 0.00 0.00 0.00 3.46
823 987 4.768448 TCGCTCTTATATTATGGGACGGAA 59.232 41.667 0.00 0.00 0.00 4.30
824 988 4.338012 TCGCTCTTATATTATGGGACGGA 58.662 43.478 0.00 0.00 0.00 4.69
825 989 4.713824 TCGCTCTTATATTATGGGACGG 57.286 45.455 0.00 0.00 0.00 4.79
826 990 7.330946 TCAAAATCGCTCTTATATTATGGGACG 59.669 37.037 0.00 0.00 0.00 4.79
827 991 8.443937 GTCAAAATCGCTCTTATATTATGGGAC 58.556 37.037 0.00 0.00 0.00 4.46
828 992 8.154203 TGTCAAAATCGCTCTTATATTATGGGA 58.846 33.333 0.00 0.00 0.00 4.37
829 993 8.230486 GTGTCAAAATCGCTCTTATATTATGGG 58.770 37.037 0.00 0.00 0.00 4.00
830 994 8.230486 GGTGTCAAAATCGCTCTTATATTATGG 58.770 37.037 0.00 0.00 0.00 2.74
831 995 8.773645 TGGTGTCAAAATCGCTCTTATATTATG 58.226 33.333 0.00 0.00 0.00 1.90
832 996 8.902540 TGGTGTCAAAATCGCTCTTATATTAT 57.097 30.769 0.00 0.00 0.00 1.28
833 997 7.985184 ACTGGTGTCAAAATCGCTCTTATATTA 59.015 33.333 0.00 0.00 0.00 0.98
835 999 6.258727 CACTGGTGTCAAAATCGCTCTTATAT 59.741 38.462 0.00 0.00 0.00 0.86
837 1001 4.393062 CACTGGTGTCAAAATCGCTCTTAT 59.607 41.667 0.00 0.00 0.00 1.73
838 1002 3.745975 CACTGGTGTCAAAATCGCTCTTA 59.254 43.478 0.00 0.00 0.00 2.10
839 1003 2.549754 CACTGGTGTCAAAATCGCTCTT 59.450 45.455 0.00 0.00 0.00 2.85
840 1004 2.146342 CACTGGTGTCAAAATCGCTCT 58.854 47.619 0.00 0.00 0.00 4.09
841 1005 2.143122 TCACTGGTGTCAAAATCGCTC 58.857 47.619 0.53 0.00 0.00 5.03
842 1006 2.146342 CTCACTGGTGTCAAAATCGCT 58.854 47.619 0.53 0.00 0.00 4.93
843 1007 2.143122 TCTCACTGGTGTCAAAATCGC 58.857 47.619 0.53 0.00 0.00 4.58
844 1008 3.425359 GCATCTCACTGGTGTCAAAATCG 60.425 47.826 0.53 0.00 0.00 3.34
845 1009 3.755378 AGCATCTCACTGGTGTCAAAATC 59.245 43.478 0.53 0.00 0.00 2.17
846 1010 3.755378 GAGCATCTCACTGGTGTCAAAAT 59.245 43.478 0.53 0.00 0.00 1.82
847 1011 3.141398 GAGCATCTCACTGGTGTCAAAA 58.859 45.455 0.53 0.00 0.00 2.44
848 1012 2.550855 GGAGCATCTCACTGGTGTCAAA 60.551 50.000 0.53 0.00 33.73 2.69
849 1013 1.002430 GGAGCATCTCACTGGTGTCAA 59.998 52.381 0.53 0.00 33.73 3.18
850 1014 0.610174 GGAGCATCTCACTGGTGTCA 59.390 55.000 0.53 0.00 33.73 3.58
851 1015 0.610174 TGGAGCATCTCACTGGTGTC 59.390 55.000 0.53 0.00 33.73 3.67
852 1016 0.322975 GTGGAGCATCTCACTGGTGT 59.677 55.000 0.53 0.00 34.71 4.16
853 1017 0.612229 AGTGGAGCATCTCACTGGTG 59.388 55.000 0.00 0.00 42.39 4.17
854 1018 2.106566 CTAGTGGAGCATCTCACTGGT 58.893 52.381 6.27 0.00 43.32 4.00
855 1019 1.411977 CCTAGTGGAGCATCTCACTGG 59.588 57.143 6.27 3.47 43.32 4.00
856 1020 2.106566 ACCTAGTGGAGCATCTCACTG 58.893 52.381 6.27 0.00 43.32 3.66
857 1021 2.106566 CACCTAGTGGAGCATCTCACT 58.893 52.381 0.00 0.00 44.77 3.41
858 1022 2.103373 TCACCTAGTGGAGCATCTCAC 58.897 52.381 0.00 0.00 36.81 3.51
859 1023 2.532250 TCACCTAGTGGAGCATCTCA 57.468 50.000 0.00 0.00 37.04 3.27
860 1024 3.895232 TTTCACCTAGTGGAGCATCTC 57.105 47.619 0.00 0.00 37.04 2.75
890 1054 2.756283 ACCTCGGCTCCTTCCTCG 60.756 66.667 0.00 0.00 0.00 4.63
891 1055 2.726351 CCACCTCGGCTCCTTCCTC 61.726 68.421 0.00 0.00 0.00 3.71
956 1125 7.151999 AGTCACAATGTACAACAAAGTTTCA 57.848 32.000 0.00 0.00 0.00 2.69
957 1126 9.730420 AATAGTCACAATGTACAACAAAGTTTC 57.270 29.630 0.00 0.00 0.00 2.78
997 1166 1.002888 CTCCAGCGCCATCCTCATAAT 59.997 52.381 2.29 0.00 0.00 1.28
1029 1198 2.049156 TCTCTGCGACGCAACCAG 60.049 61.111 24.51 18.47 38.41 4.00
1033 1202 2.431430 CTGCTCTCTGCGACGCAA 60.431 61.111 24.51 13.46 46.63 4.85
1078 1247 4.125703 GTCTGATACAAGGAAGCTCCATG 58.874 47.826 5.21 5.66 40.81 3.66
1135 1304 4.790962 CCGCATCACTGGCCTGCT 62.791 66.667 9.95 0.00 33.75 4.24
1141 1310 3.664025 TTCCTCGCCGCATCACTGG 62.664 63.158 0.00 0.00 0.00 4.00
1150 1319 1.362406 GCCTCTTCTTTTCCTCGCCG 61.362 60.000 0.00 0.00 0.00 6.46
1280 1462 1.376609 GCCTGTACCTCGGCCATTTG 61.377 60.000 2.24 0.00 40.43 2.32
1356 1538 1.905512 GGCGGCCTTCCTTCTCTAA 59.094 57.895 12.87 0.00 0.00 2.10
1358 1540 3.775654 CGGCGGCCTTCCTTCTCT 61.776 66.667 18.34 0.00 0.00 3.10
1360 1542 4.083862 GACGGCGGCCTTCCTTCT 62.084 66.667 18.34 0.00 0.00 2.85
1385 1567 4.760047 CTGTTGGACGGGAGCGGG 62.760 72.222 0.00 0.00 0.00 6.13
1386 1568 3.934391 GACTGTTGGACGGGAGCGG 62.934 68.421 0.00 0.00 0.00 5.52
1388 1570 2.432628 CGACTGTTGGACGGGAGC 60.433 66.667 0.00 0.00 0.00 4.70
1394 1581 1.226746 CCTTTGACCGACTGTTGGAC 58.773 55.000 20.92 14.79 0.00 4.02
1395 1582 0.534203 GCCTTTGACCGACTGTTGGA 60.534 55.000 20.92 0.00 0.00 3.53
1429 1617 1.064946 CACCGACGAGAGAGATGCC 59.935 63.158 0.00 0.00 0.00 4.40
1431 1619 1.004821 CGTACACCGACGAGAGAGATG 60.005 57.143 0.00 0.00 45.82 2.90
1432 1620 1.288350 CGTACACCGACGAGAGAGAT 58.712 55.000 0.00 0.00 45.82 2.75
1433 1621 1.357258 GCGTACACCGACGAGAGAGA 61.357 60.000 0.00 0.00 45.82 3.10
1434 1622 1.060622 GCGTACACCGACGAGAGAG 59.939 63.158 0.00 0.00 45.82 3.20
1435 1623 1.375140 AGCGTACACCGACGAGAGA 60.375 57.895 0.00 0.00 45.82 3.10
1436 1624 1.226046 CAGCGTACACCGACGAGAG 60.226 63.158 0.00 0.00 45.82 3.20
1437 1625 1.962822 ACAGCGTACACCGACGAGA 60.963 57.895 0.00 0.00 45.82 4.04
1438 1626 1.796355 CACAGCGTACACCGACGAG 60.796 63.158 0.00 0.00 45.82 4.18
1439 1627 2.253154 CACAGCGTACACCGACGA 59.747 61.111 0.00 0.00 45.82 4.20
1440 1628 2.803670 CCACAGCGTACACCGACG 60.804 66.667 0.00 0.00 45.70 5.12
1441 1629 2.431942 CCCACAGCGTACACCGAC 60.432 66.667 0.00 0.00 39.56 4.79
1442 1630 4.367023 GCCCACAGCGTACACCGA 62.367 66.667 0.00 0.00 39.56 4.69
1460 1648 3.741476 CAGTGGCTTTCAGGCGGC 61.741 66.667 0.00 0.00 44.78 6.53
1461 1649 1.377725 ATCAGTGGCTTTCAGGCGG 60.378 57.895 0.00 0.00 44.78 6.13
1462 1650 1.651240 CCATCAGTGGCTTTCAGGCG 61.651 60.000 0.00 0.00 44.78 5.52
1487 1675 3.589654 ATCACGGGTGTGCCTGACG 62.590 63.158 0.00 0.00 46.01 4.35
1488 1676 1.741770 GATCACGGGTGTGCCTGAC 60.742 63.158 0.00 0.00 46.01 3.51
1513 1701 2.027385 TGCGTATGATCAGTCTGCTCT 58.973 47.619 0.09 0.00 0.00 4.09
1520 1715 0.741326 AGTCGCTGCGTATGATCAGT 59.259 50.000 22.48 0.18 33.09 3.41
1531 1726 4.430423 CGCCGTTGAAGTCGCTGC 62.430 66.667 0.00 0.00 0.00 5.25
1720 1917 2.629617 ACTTGAAAAACCTGCAGATGGG 59.370 45.455 17.39 0.66 0.00 4.00
1732 1929 1.760029 GCCAACCCCAGACTTGAAAAA 59.240 47.619 0.00 0.00 0.00 1.94
1733 1930 1.063266 AGCCAACCCCAGACTTGAAAA 60.063 47.619 0.00 0.00 0.00 2.29
1792 1989 7.031372 CGGGATTTTATTGAATATGCCATCAG 58.969 38.462 0.00 0.00 0.00 2.90
1804 2001 7.880160 ATCAGAATGTTCGGGATTTTATTGA 57.120 32.000 0.00 0.00 37.40 2.57
1805 2002 8.931385 AAATCAGAATGTTCGGGATTTTATTG 57.069 30.769 15.96 0.00 40.12 1.90
1809 2006 7.545615 GCTTAAAATCAGAATGTTCGGGATTTT 59.454 33.333 25.79 25.79 45.95 1.82
1810 2007 7.035612 GCTTAAAATCAGAATGTTCGGGATTT 58.964 34.615 15.96 15.96 42.38 2.17
1811 2008 6.152661 TGCTTAAAATCAGAATGTTCGGGATT 59.847 34.615 8.76 8.76 37.54 3.01
1812 2009 5.652014 TGCTTAAAATCAGAATGTTCGGGAT 59.348 36.000 0.00 0.00 37.40 3.85
1813 2010 5.007034 TGCTTAAAATCAGAATGTTCGGGA 58.993 37.500 0.00 0.00 37.40 5.14
1814 2011 5.309323 TGCTTAAAATCAGAATGTTCGGG 57.691 39.130 0.00 0.00 37.40 5.14
1815 2012 5.230726 GCATGCTTAAAATCAGAATGTTCGG 59.769 40.000 11.37 0.00 37.40 4.30
1816 2013 5.230726 GGCATGCTTAAAATCAGAATGTTCG 59.769 40.000 18.92 0.00 37.40 3.95
1817 2014 6.101332 TGGCATGCTTAAAATCAGAATGTTC 58.899 36.000 18.92 0.00 37.40 3.18
1818 2015 6.040209 TGGCATGCTTAAAATCAGAATGTT 57.960 33.333 18.92 0.00 37.40 2.71
1819 2016 5.664294 TGGCATGCTTAAAATCAGAATGT 57.336 34.783 18.92 0.00 37.40 2.71
1820 2017 5.401376 CGATGGCATGCTTAAAATCAGAATG 59.599 40.000 18.92 0.00 31.02 2.67
1821 2018 5.068198 ACGATGGCATGCTTAAAATCAGAAT 59.932 36.000 18.92 0.00 0.00 2.40
1822 2019 4.398988 ACGATGGCATGCTTAAAATCAGAA 59.601 37.500 18.92 0.00 0.00 3.02
1823 2020 3.947196 ACGATGGCATGCTTAAAATCAGA 59.053 39.130 18.92 0.00 0.00 3.27
1824 2021 4.039703 CACGATGGCATGCTTAAAATCAG 58.960 43.478 18.92 11.10 0.00 2.90
1825 2022 3.693578 TCACGATGGCATGCTTAAAATCA 59.306 39.130 18.92 5.25 0.00 2.57
1826 2023 4.291540 TCACGATGGCATGCTTAAAATC 57.708 40.909 18.92 11.67 0.00 2.17
1827 2024 4.717233 TTCACGATGGCATGCTTAAAAT 57.283 36.364 18.92 3.96 0.00 1.82
1828 2025 4.082300 ACATTCACGATGGCATGCTTAAAA 60.082 37.500 18.92 3.95 40.21 1.52
1829 2026 3.443329 ACATTCACGATGGCATGCTTAAA 59.557 39.130 18.92 1.32 40.21 1.52
1830 2027 3.016031 ACATTCACGATGGCATGCTTAA 58.984 40.909 18.92 4.07 40.21 1.85
1831 2028 2.642427 ACATTCACGATGGCATGCTTA 58.358 42.857 18.92 7.69 40.21 3.09
1832 2029 1.466856 ACATTCACGATGGCATGCTT 58.533 45.000 18.92 5.43 40.21 3.91
1833 2030 1.466856 AACATTCACGATGGCATGCT 58.533 45.000 18.92 0.00 40.21 3.79
1834 2031 2.282701 AAACATTCACGATGGCATGC 57.717 45.000 9.90 9.90 40.21 4.06
1852 2049 6.360148 CGCGTTAACTAAAGTTGCCATAAAAA 59.640 34.615 5.62 0.00 38.90 1.94
1853 2050 5.852229 CGCGTTAACTAAAGTTGCCATAAAA 59.148 36.000 5.62 0.00 38.90 1.52
1854 2051 5.178996 TCGCGTTAACTAAAGTTGCCATAAA 59.821 36.000 5.77 0.00 38.90 1.40
1855 2052 4.689812 TCGCGTTAACTAAAGTTGCCATAA 59.310 37.500 5.77 0.00 38.90 1.90
1856 2053 4.244066 TCGCGTTAACTAAAGTTGCCATA 58.756 39.130 5.77 0.00 38.90 2.74
1857 2054 3.068560 TCGCGTTAACTAAAGTTGCCAT 58.931 40.909 5.77 0.00 38.90 4.40
1858 2055 2.477375 CTCGCGTTAACTAAAGTTGCCA 59.523 45.455 5.77 0.00 38.90 4.92
1859 2056 2.159747 CCTCGCGTTAACTAAAGTTGCC 60.160 50.000 5.77 0.00 38.90 4.52
1860 2057 2.477754 ACCTCGCGTTAACTAAAGTTGC 59.522 45.455 5.77 0.23 38.90 4.17
1861 2058 3.120786 CCACCTCGCGTTAACTAAAGTTG 60.121 47.826 5.77 0.00 38.90 3.16
1862 2059 3.062042 CCACCTCGCGTTAACTAAAGTT 58.938 45.455 5.77 0.39 41.73 2.66
1863 2060 2.680577 CCACCTCGCGTTAACTAAAGT 58.319 47.619 5.77 0.00 0.00 2.66
1864 2061 1.392510 GCCACCTCGCGTTAACTAAAG 59.607 52.381 5.77 0.00 0.00 1.85
1865 2062 1.270199 TGCCACCTCGCGTTAACTAAA 60.270 47.619 5.77 0.00 0.00 1.85
1866 2063 0.317799 TGCCACCTCGCGTTAACTAA 59.682 50.000 5.77 0.00 0.00 2.24
1867 2064 0.317799 TTGCCACCTCGCGTTAACTA 59.682 50.000 5.77 0.00 0.00 2.24
1868 2065 1.070105 TTGCCACCTCGCGTTAACT 59.930 52.632 5.77 0.00 0.00 2.24
1869 2066 1.205820 GTTGCCACCTCGCGTTAAC 59.794 57.895 5.77 0.00 0.00 2.01
1870 2067 0.533308 AAGTTGCCACCTCGCGTTAA 60.533 50.000 5.77 0.00 0.00 2.01
1871 2068 0.533308 AAAGTTGCCACCTCGCGTTA 60.533 50.000 5.77 0.00 0.00 3.18
1872 2069 0.533308 TAAAGTTGCCACCTCGCGTT 60.533 50.000 5.77 0.00 0.00 4.84
1873 2070 0.949105 CTAAAGTTGCCACCTCGCGT 60.949 55.000 5.77 0.00 0.00 6.01
1874 2071 0.669318 TCTAAAGTTGCCACCTCGCG 60.669 55.000 0.00 0.00 0.00 5.87
1875 2072 1.398390 CATCTAAAGTTGCCACCTCGC 59.602 52.381 0.00 0.00 0.00 5.03
1876 2073 2.699954 ACATCTAAAGTTGCCACCTCG 58.300 47.619 0.00 0.00 0.00 4.63
1877 2074 5.488341 TCTAACATCTAAAGTTGCCACCTC 58.512 41.667 0.00 0.00 0.00 3.85
1878 2075 5.499004 TCTAACATCTAAAGTTGCCACCT 57.501 39.130 0.00 0.00 0.00 4.00
1879 2076 6.151144 ACATTCTAACATCTAAAGTTGCCACC 59.849 38.462 0.00 0.00 0.00 4.61
1880 2077 7.023575 CACATTCTAACATCTAAAGTTGCCAC 58.976 38.462 0.00 0.00 0.00 5.01
1881 2078 6.150976 CCACATTCTAACATCTAAAGTTGCCA 59.849 38.462 0.00 0.00 0.00 4.92
1882 2079 6.555315 CCACATTCTAACATCTAAAGTTGCC 58.445 40.000 0.00 0.00 0.00 4.52
1883 2080 6.030228 GCCACATTCTAACATCTAAAGTTGC 58.970 40.000 0.00 0.00 0.00 4.17
1884 2081 7.144722 TGCCACATTCTAACATCTAAAGTTG 57.855 36.000 0.00 0.00 0.00 3.16
1885 2082 7.448469 AGTTGCCACATTCTAACATCTAAAGTT 59.552 33.333 0.00 0.00 0.00 2.66
1886 2083 6.942576 AGTTGCCACATTCTAACATCTAAAGT 59.057 34.615 0.00 0.00 0.00 2.66
1887 2084 7.383102 AGTTGCCACATTCTAACATCTAAAG 57.617 36.000 0.00 0.00 0.00 1.85
1888 2085 7.759489 AAGTTGCCACATTCTAACATCTAAA 57.241 32.000 0.00 0.00 0.00 1.85
1889 2086 7.230510 ACAAAGTTGCCACATTCTAACATCTAA 59.769 33.333 0.00 0.00 0.00 2.10
1890 2087 6.714810 ACAAAGTTGCCACATTCTAACATCTA 59.285 34.615 0.00 0.00 0.00 1.98
1891 2088 5.536161 ACAAAGTTGCCACATTCTAACATCT 59.464 36.000 0.00 0.00 0.00 2.90
1892 2089 5.772521 ACAAAGTTGCCACATTCTAACATC 58.227 37.500 0.00 0.00 0.00 3.06
1893 2090 5.278957 GGACAAAGTTGCCACATTCTAACAT 60.279 40.000 0.00 0.00 0.00 2.71
1894 2091 4.037446 GGACAAAGTTGCCACATTCTAACA 59.963 41.667 0.00 0.00 0.00 2.41
1895 2092 4.546570 GGACAAAGTTGCCACATTCTAAC 58.453 43.478 0.00 0.00 0.00 2.34
1896 2093 3.572255 GGGACAAAGTTGCCACATTCTAA 59.428 43.478 6.77 0.00 0.00 2.10
1897 2094 3.153919 GGGACAAAGTTGCCACATTCTA 58.846 45.455 6.77 0.00 0.00 2.10
1898 2095 1.963515 GGGACAAAGTTGCCACATTCT 59.036 47.619 6.77 0.00 0.00 2.40
1899 2096 1.963515 AGGGACAAAGTTGCCACATTC 59.036 47.619 6.77 0.00 0.00 2.67
1900 2097 1.688197 CAGGGACAAAGTTGCCACATT 59.312 47.619 6.77 0.00 0.00 2.71
1901 2098 1.331214 CAGGGACAAAGTTGCCACAT 58.669 50.000 6.77 0.00 0.00 3.21
1902 2099 0.033601 ACAGGGACAAAGTTGCCACA 60.034 50.000 6.77 0.00 0.00 4.17
1903 2100 1.111277 AACAGGGACAAAGTTGCCAC 58.889 50.000 6.77 0.00 0.00 5.01
1904 2101 2.092103 ACTAACAGGGACAAAGTTGCCA 60.092 45.455 6.77 0.00 0.00 4.92
1905 2102 2.583143 ACTAACAGGGACAAAGTTGCC 58.417 47.619 0.00 0.00 0.00 4.52
1906 2103 3.883489 AGAACTAACAGGGACAAAGTTGC 59.117 43.478 0.00 0.00 30.83 4.17
1907 2104 6.451064 AAAGAACTAACAGGGACAAAGTTG 57.549 37.500 0.00 0.00 30.83 3.16
1908 2105 8.630037 CATAAAAGAACTAACAGGGACAAAGTT 58.370 33.333 0.00 0.00 33.26 2.66
1909 2106 7.230712 CCATAAAAGAACTAACAGGGACAAAGT 59.769 37.037 0.00 0.00 0.00 2.66
1910 2107 7.309194 CCCATAAAAGAACTAACAGGGACAAAG 60.309 40.741 0.00 0.00 35.81 2.77
1911 2108 6.492087 CCCATAAAAGAACTAACAGGGACAAA 59.508 38.462 0.00 0.00 35.81 2.83
1912 2109 6.007703 CCCATAAAAGAACTAACAGGGACAA 58.992 40.000 0.00 0.00 35.81 3.18
1913 2110 5.311121 TCCCATAAAAGAACTAACAGGGACA 59.689 40.000 0.00 0.00 37.85 4.02
1914 2111 5.812286 TCCCATAAAAGAACTAACAGGGAC 58.188 41.667 0.00 0.00 37.85 4.46
1915 2112 6.457159 TTCCCATAAAAGAACTAACAGGGA 57.543 37.500 0.00 0.00 40.83 4.20
1916 2113 7.232737 ACTTTTCCCATAAAAGAACTAACAGGG 59.767 37.037 15.15 0.00 39.04 4.45
1917 2114 8.082242 CACTTTTCCCATAAAAGAACTAACAGG 58.918 37.037 15.15 0.00 39.04 4.00
1918 2115 8.630037 ACACTTTTCCCATAAAAGAACTAACAG 58.370 33.333 15.15 0.86 39.04 3.16
1919 2116 8.528044 ACACTTTTCCCATAAAAGAACTAACA 57.472 30.769 15.15 0.00 39.04 2.41
1920 2117 8.626526 TGACACTTTTCCCATAAAAGAACTAAC 58.373 33.333 15.15 3.80 39.04 2.34
1921 2118 8.754991 TGACACTTTTCCCATAAAAGAACTAA 57.245 30.769 15.15 0.00 39.04 2.24
1922 2119 8.792633 CATGACACTTTTCCCATAAAAGAACTA 58.207 33.333 15.15 2.39 39.04 2.24
1923 2120 7.287696 ACATGACACTTTTCCCATAAAAGAACT 59.712 33.333 15.15 0.00 39.04 3.01
1924 2121 7.433680 ACATGACACTTTTCCCATAAAAGAAC 58.566 34.615 15.15 7.68 39.04 3.01
1925 2122 7.595819 ACATGACACTTTTCCCATAAAAGAA 57.404 32.000 15.15 1.46 39.04 2.52
1926 2123 7.069331 ACAACATGACACTTTTCCCATAAAAGA 59.931 33.333 15.15 0.00 39.04 2.52
1927 2124 7.209475 ACAACATGACACTTTTCCCATAAAAG 58.791 34.615 0.00 8.32 41.63 2.27
1928 2125 7.118496 ACAACATGACACTTTTCCCATAAAA 57.882 32.000 0.00 0.00 0.00 1.52
1929 2126 6.723298 ACAACATGACACTTTTCCCATAAA 57.277 33.333 0.00 0.00 0.00 1.40
1930 2127 6.723298 AACAACATGACACTTTTCCCATAA 57.277 33.333 0.00 0.00 0.00 1.90
1931 2128 7.174253 GTCTAACAACATGACACTTTTCCCATA 59.826 37.037 0.00 0.00 0.00 2.74
1932 2129 6.016276 GTCTAACAACATGACACTTTTCCCAT 60.016 38.462 0.00 0.00 0.00 4.00
1933 2130 5.298276 GTCTAACAACATGACACTTTTCCCA 59.702 40.000 0.00 0.00 0.00 4.37
1934 2131 5.531287 AGTCTAACAACATGACACTTTTCCC 59.469 40.000 0.00 0.00 33.56 3.97
1935 2132 6.038271 ACAGTCTAACAACATGACACTTTTCC 59.962 38.462 0.00 0.00 33.56 3.13
1936 2133 7.016361 ACAGTCTAACAACATGACACTTTTC 57.984 36.000 0.00 0.00 33.56 2.29
1937 2134 8.677148 ATACAGTCTAACAACATGACACTTTT 57.323 30.769 0.00 0.00 33.56 2.27
1938 2135 8.677148 AATACAGTCTAACAACATGACACTTT 57.323 30.769 0.00 0.00 33.56 2.66
1939 2136 8.677148 AAATACAGTCTAACAACATGACACTT 57.323 30.769 0.00 0.00 33.56 3.16
1940 2137 9.204570 GTAAATACAGTCTAACAACATGACACT 57.795 33.333 0.00 0.00 33.56 3.55
1941 2138 8.984764 TGTAAATACAGTCTAACAACATGACAC 58.015 33.333 0.00 0.00 33.56 3.67
1942 2139 9.719355 ATGTAAATACAGTCTAACAACATGACA 57.281 29.630 0.00 0.00 39.92 3.58
1943 2140 9.973246 CATGTAAATACAGTCTAACAACATGAC 57.027 33.333 0.00 0.00 42.55 3.06
1944 2141 9.719355 ACATGTAAATACAGTCTAACAACATGA 57.281 29.630 16.06 0.00 42.55 3.07
2028 2227 4.599036 GGAACCAGCACAACCCTT 57.401 55.556 0.00 0.00 0.00 3.95
2749 2961 2.679716 GCCTGATCCTGCCCTGTT 59.320 61.111 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.