Multiple sequence alignment - TraesCS6A01G107900

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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 TraesCS6A01G107900 chr6A 100.000 5608 0 0 1 5608 76629948 76635555 0.000000e+00 10357.0
1 TraesCS6A01G107900 chr6A 100.000 28 0 0 2925 2952 76632844 76632871 1.000000e-02 52.8
2 TraesCS6A01G107900 chr6A 100.000 28 0 0 2897 2924 76632872 76632899 1.000000e-02 52.8
3 TraesCS6A01G107900 chr6B 88.030 2005 123 48 937 2874 133992283 133994237 0.000000e+00 2265.0
4 TraesCS6A01G107900 chr6B 89.832 895 46 19 1 869 133846516 133847391 0.000000e+00 1107.0
5 TraesCS6A01G107900 chr6B 84.884 1032 128 15 2926 3951 133994263 133995272 0.000000e+00 1016.0
6 TraesCS6A01G107900 chr6B 89.630 810 46 12 3946 4755 133995506 133996277 0.000000e+00 996.0
7 TraesCS6A01G107900 chr6B 84.595 383 26 12 4794 5148 133996367 133996744 3.220000e-92 350.0
8 TraesCS6A01G107900 chr6B 79.701 468 40 30 5164 5608 133996724 133997159 2.560000e-73 287.0
9 TraesCS6A01G107900 chr6D 93.234 1271 55 9 1681 2924 60139219 60140485 0.000000e+00 1842.0
10 TraesCS6A01G107900 chr6D 95.539 1076 43 4 2925 3998 60140460 60141532 0.000000e+00 1716.0
11 TraesCS6A01G107900 chr6D 92.118 1053 40 17 937 1955 60138141 60139184 0.000000e+00 1445.0
12 TraesCS6A01G107900 chr6D 93.577 794 42 7 1 788 60136463 60137253 0.000000e+00 1175.0
13 TraesCS6A01G107900 chr6D 89.668 784 40 20 4000 4743 60141577 60142359 0.000000e+00 961.0
14 TraesCS6A01G107900 chr6D 80.952 294 32 10 5239 5528 60164776 60165049 1.580000e-50 211.0
15 TraesCS6A01G107900 chr6D 87.288 118 11 3 821 938 60137992 60138105 1.270000e-26 132.0
16 TraesCS6A01G107900 chr6D 100.000 29 0 0 1767 1795 60139187 60139215 3.000000e-03 54.7
17 TraesCS6A01G107900 chr7D 92.593 162 12 0 4433 4594 525771036 525771197 3.380000e-57 233.0
18 TraesCS6A01G107900 chr7D 90.000 140 14 0 3258 3397 525769360 525769499 1.240000e-41 182.0
19 TraesCS6A01G107900 chr7A 91.716 169 12 2 4426 4594 606327501 606327667 3.380000e-57 233.0
20 TraesCS6A01G107900 chr7A 90.714 140 13 0 3258 3397 606324767 606324906 2.670000e-43 187.0
21 TraesCS6A01G107900 chr7A 75.303 413 73 23 1924 2327 606323449 606323841 2.690000e-38 171.0
22 TraesCS6A01G107900 chr7B 91.176 170 13 2 4425 4594 562405559 562405726 4.370000e-56 230.0
23 TraesCS6A01G107900 chr7B 87.857 140 17 0 3258 3397 562403886 562404025 1.250000e-36 165.0


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 TraesCS6A01G107900 chr6A 76629948 76635555 5607 False 3487.533333 10357 100.000000 1 5608 3 chr6A.!!$F1 5607
1 TraesCS6A01G107900 chr6B 133846516 133847391 875 False 1107.000000 1107 89.832000 1 869 1 chr6B.!!$F1 868
2 TraesCS6A01G107900 chr6B 133992283 133997159 4876 False 982.800000 2265 85.368000 937 5608 5 chr6B.!!$F2 4671
3 TraesCS6A01G107900 chr6D 60136463 60142359 5896 False 1046.528571 1842 93.060571 1 4743 7 chr6D.!!$F2 4742
4 TraesCS6A01G107900 chr7D 525769360 525771197 1837 False 207.500000 233 91.296500 3258 4594 2 chr7D.!!$F1 1336

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
632 642 0.041684 TCATCTCCCTCAGGTGCTGA 59.958 55.000 0.00 0.0 38.25 4.26 F
927 1659 0.107945 CAGCTTGCAGGAGGGTCTAC 60.108 60.000 0.00 0.0 0.00 2.59 F
932 1664 0.116342 TGCAGGAGGGTCTACTTGGA 59.884 55.000 0.00 0.0 0.00 3.53 F
2133 3277 0.320858 TTAGTGCCGCGAACAATCCA 60.321 50.000 8.23 0.0 0.00 3.41 F
2242 3386 1.831106 ACATGTCCGCTTCTCACCATA 59.169 47.619 0.00 0.0 0.00 2.74 F
3749 4967 2.093553 AGATGAAGCAGAAGGAGCAGAC 60.094 50.000 0.00 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2062 3206 1.079503 GCGTCTGATGGACAAAGGAC 58.920 55.000 0.00 0.00 44.70 3.85 R
2919 4100 0.626916 TATGTAAACAGGGGGTGCCC 59.373 55.000 0.00 0.00 44.51 5.36 R
2920 4101 2.092103 TCATATGTAAACAGGGGGTGCC 60.092 50.000 1.90 0.00 0.00 5.01 R
4118 5649 3.609175 CGCCAGTCCTTTTGTTACACATG 60.609 47.826 0.00 0.00 0.00 3.21 R
4133 5886 0.749454 AGATCATTTGGCCGCCAGTC 60.749 55.000 12.95 7.35 33.81 3.51 R
5432 7464 0.246635 GCCCATAGCGACGACCATAT 59.753 55.000 0.00 0.00 0.00 1.78 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
132 135 5.867174 TCAAGTATATCGCATATGTTTCCCG 59.133 40.000 4.29 0.00 0.00 5.14
172 176 7.009540 CAGTTTGTGATTGTTTTTCCTCTTGAC 59.990 37.037 0.00 0.00 0.00 3.18
258 262 5.824624 CACCACATCTTATTCTTGCCAGTAT 59.175 40.000 0.00 0.00 0.00 2.12
262 266 6.988580 CACATCTTATTCTTGCCAGTATCTCA 59.011 38.462 0.00 0.00 0.00 3.27
292 296 1.253100 TCTGACCGTATGAGCACACA 58.747 50.000 0.00 0.00 0.00 3.72
294 298 0.676736 TGACCGTATGAGCACACACA 59.323 50.000 0.00 0.00 0.00 3.72
295 299 1.068474 GACCGTATGAGCACACACAC 58.932 55.000 0.00 0.00 0.00 3.82
296 300 0.391228 ACCGTATGAGCACACACACA 59.609 50.000 0.00 0.00 0.00 3.72
470 475 1.733912 GCTGTGTGCAGATTGAATCGA 59.266 47.619 0.00 0.00 45.28 3.59
475 480 0.617935 TGCAGATTGAATCGACCCCA 59.382 50.000 0.00 0.00 0.00 4.96
493 498 1.070134 CCAATCCGTATGGTCCATCGT 59.930 52.381 7.92 0.00 36.30 3.73
498 507 1.157870 CGTATGGTCCATCGTTGGCC 61.158 60.000 7.92 12.22 43.29 5.36
525 535 5.221244 GCAACAGAATACAACCCAGTTTTCT 60.221 40.000 0.00 0.00 39.37 2.52
533 543 5.774498 ACAACCCAGTTTTCTTGAGAATC 57.226 39.130 0.00 0.00 33.54 2.52
593 603 4.125703 CCTCATTAGTCCTGATTGCTGTC 58.874 47.826 0.00 0.00 0.00 3.51
617 627 8.831550 GTCCAGAAAATAGTCCTGTAATTCATC 58.168 37.037 0.00 0.00 0.00 2.92
618 628 8.772250 TCCAGAAAATAGTCCTGTAATTCATCT 58.228 33.333 0.00 0.00 0.00 2.90
619 629 9.050601 CCAGAAAATAGTCCTGTAATTCATCTC 57.949 37.037 0.00 0.00 0.00 2.75
620 630 9.050601 CAGAAAATAGTCCTGTAATTCATCTCC 57.949 37.037 0.00 0.00 0.00 3.71
621 631 8.214364 AGAAAATAGTCCTGTAATTCATCTCCC 58.786 37.037 0.00 0.00 0.00 4.30
622 632 7.698163 AAATAGTCCTGTAATTCATCTCCCT 57.302 36.000 0.00 0.00 0.00 4.20
623 633 6.926630 ATAGTCCTGTAATTCATCTCCCTC 57.073 41.667 0.00 0.00 0.00 4.30
624 634 4.624913 AGTCCTGTAATTCATCTCCCTCA 58.375 43.478 0.00 0.00 0.00 3.86
625 635 4.653341 AGTCCTGTAATTCATCTCCCTCAG 59.347 45.833 0.00 0.00 0.00 3.35
626 636 3.969976 TCCTGTAATTCATCTCCCTCAGG 59.030 47.826 0.00 0.00 41.47 3.86
627 637 3.713764 CCTGTAATTCATCTCCCTCAGGT 59.286 47.826 0.00 0.00 37.16 4.00
628 638 4.444022 CCTGTAATTCATCTCCCTCAGGTG 60.444 50.000 0.00 0.00 37.16 4.00
629 639 2.725221 AATTCATCTCCCTCAGGTGC 57.275 50.000 0.00 0.00 32.48 5.01
630 640 1.890552 ATTCATCTCCCTCAGGTGCT 58.109 50.000 0.00 0.00 32.48 4.40
631 641 0.907486 TTCATCTCCCTCAGGTGCTG 59.093 55.000 0.00 0.00 32.48 4.41
632 642 0.041684 TCATCTCCCTCAGGTGCTGA 59.958 55.000 0.00 0.00 38.25 4.26
651 677 4.679197 GCTGACTAGCTATGTTCGATTCTG 59.321 45.833 0.00 0.00 46.57 3.02
741 767 7.366513 TCATGTGCATCTAATTTTGTCGAAAA 58.633 30.769 0.00 0.00 35.52 2.29
746 772 6.171006 GCATCTAATTTTGTCGAAAATTGCG 58.829 36.000 15.05 8.29 46.58 4.85
764 790 2.258726 GGAAGCACCGCCTTTCGTT 61.259 57.895 0.00 0.00 36.19 3.85
776 802 2.223044 GCCTTTCGTTCGATTTGGCTAG 60.223 50.000 18.42 0.00 36.32 3.42
779 805 4.394795 CTTTCGTTCGATTTGGCTAGTTG 58.605 43.478 0.00 0.00 0.00 3.16
789 815 6.428465 TCGATTTGGCTAGTTGTGTTTATTCA 59.572 34.615 0.00 0.00 0.00 2.57
795 1390 6.149308 TGGCTAGTTGTGTTTATTCAGTGATG 59.851 38.462 0.00 0.00 0.00 3.07
799 1394 9.764870 CTAGTTGTGTTTATTCAGTGATGAATG 57.235 33.333 12.54 0.00 38.76 2.67
815 1410 8.215736 AGTGATGAATGATATCTCCAAACATGA 58.784 33.333 0.00 0.00 0.00 3.07
844 1576 5.373812 AAAATATTGGGTCCACGATCTCT 57.626 39.130 0.00 0.00 0.00 3.10
880 1612 1.206371 ACCGCATGTAAGAGTACACCC 59.794 52.381 0.00 0.00 42.99 4.61
883 1615 2.416296 CGCATGTAAGAGTACACCCGAA 60.416 50.000 0.00 0.00 42.99 4.30
885 1617 3.187700 CATGTAAGAGTACACCCGAAGC 58.812 50.000 0.00 0.00 42.99 3.86
886 1618 2.241160 TGTAAGAGTACACCCGAAGCA 58.759 47.619 0.00 0.00 35.23 3.91
887 1619 2.829720 TGTAAGAGTACACCCGAAGCAT 59.170 45.455 0.00 0.00 35.23 3.79
893 1625 0.738975 TACACCCGAAGCATCTCTCG 59.261 55.000 0.00 0.00 0.00 4.04
900 1632 1.535649 CGAAGCATCTCTCGCTGTCAT 60.536 52.381 0.00 0.00 40.35 3.06
921 1653 2.045536 GGACCAGCTTGCAGGAGG 60.046 66.667 10.99 2.82 0.00 4.30
923 1655 2.856000 ACCAGCTTGCAGGAGGGT 60.856 61.111 10.99 2.70 0.00 4.34
924 1656 2.045536 CCAGCTTGCAGGAGGGTC 60.046 66.667 0.00 0.00 0.00 4.46
925 1657 2.600729 CCAGCTTGCAGGAGGGTCT 61.601 63.158 0.00 0.00 0.00 3.85
926 1658 1.267574 CCAGCTTGCAGGAGGGTCTA 61.268 60.000 0.00 0.00 0.00 2.59
927 1659 0.107945 CAGCTTGCAGGAGGGTCTAC 60.108 60.000 0.00 0.00 0.00 2.59
928 1660 0.252467 AGCTTGCAGGAGGGTCTACT 60.252 55.000 0.00 0.00 0.00 2.57
929 1661 0.615850 GCTTGCAGGAGGGTCTACTT 59.384 55.000 0.00 0.00 0.00 2.24
930 1662 1.677217 GCTTGCAGGAGGGTCTACTTG 60.677 57.143 0.00 0.00 0.00 3.16
931 1663 0.984230 TTGCAGGAGGGTCTACTTGG 59.016 55.000 0.00 0.00 0.00 3.61
932 1664 0.116342 TGCAGGAGGGTCTACTTGGA 59.884 55.000 0.00 0.00 0.00 3.53
933 1665 1.273838 TGCAGGAGGGTCTACTTGGAT 60.274 52.381 0.00 0.00 0.00 3.41
934 1666 1.414550 GCAGGAGGGTCTACTTGGATC 59.585 57.143 0.00 0.00 0.00 3.36
935 1667 2.752030 CAGGAGGGTCTACTTGGATCA 58.248 52.381 0.00 0.00 0.00 2.92
993 1760 1.667830 CGCTTCTCGCCAACCTCAA 60.668 57.895 0.00 0.00 34.21 3.02
1279 2054 2.073037 GATCAGGCCCCTCGTACGTC 62.073 65.000 16.05 0.00 0.00 4.34
1296 2074 0.390860 GTCACATCCCCTCTCATCCG 59.609 60.000 0.00 0.00 0.00 4.18
1555 2351 4.457949 GGGTACAGTTTGGTTGATTGGTAG 59.542 45.833 0.00 0.00 0.00 3.18
1847 2974 6.528072 GCTGGAAAATTAGCAACTATTGTCAC 59.472 38.462 0.00 0.00 39.67 3.67
1849 2976 7.367285 TGGAAAATTAGCAACTATTGTCACAC 58.633 34.615 0.00 0.00 0.00 3.82
2133 3277 0.320858 TTAGTGCCGCGAACAATCCA 60.321 50.000 8.23 0.00 0.00 3.41
2228 3372 9.903682 ATCATTTATGCTAAATGCTAACATGTC 57.096 29.630 17.07 0.00 43.37 3.06
2242 3386 1.831106 ACATGTCCGCTTCTCACCATA 59.169 47.619 0.00 0.00 0.00 2.74
2342 3486 8.633561 GGGAAGATGGTTAGAATTTATTCCTTG 58.366 37.037 0.00 0.00 37.51 3.61
2427 3571 9.965902 AGTGTGATATCCTGAGAATTTTACTTT 57.034 29.630 0.00 0.00 0.00 2.66
2501 3645 5.769367 TGCTACTGTTGTAGACTTGTAGTG 58.231 41.667 7.32 0.00 46.76 2.74
2549 3697 6.443934 TTTCTTCTATCGAGACCAAGAGAG 57.556 41.667 0.00 0.00 0.00 3.20
2655 3803 5.715279 AGTTGCACTGTTAGAGTATACCTGA 59.285 40.000 0.00 0.00 31.73 3.86
2714 3889 8.348285 AGGCTGCAGTTATTACTTTTTAATCA 57.652 30.769 16.64 0.00 30.26 2.57
2865 4045 6.114187 ACATCAATCTGTTACTTCTGACCA 57.886 37.500 0.00 0.00 0.00 4.02
2916 4097 3.864789 CCCCCTGTTTACATATGAGCT 57.135 47.619 10.38 0.00 0.00 4.09
2917 4098 3.480470 CCCCCTGTTTACATATGAGCTG 58.520 50.000 10.38 1.00 0.00 4.24
2918 4099 3.136443 CCCCCTGTTTACATATGAGCTGA 59.864 47.826 10.38 0.00 0.00 4.26
2919 4100 4.384056 CCCCTGTTTACATATGAGCTGAG 58.616 47.826 10.38 0.00 0.00 3.35
2920 4101 4.384056 CCCTGTTTACATATGAGCTGAGG 58.616 47.826 10.38 8.52 0.00 3.86
2921 4102 4.384056 CCTGTTTACATATGAGCTGAGGG 58.616 47.826 10.38 0.00 0.00 4.30
2922 4103 3.808728 TGTTTACATATGAGCTGAGGGC 58.191 45.455 10.38 0.00 42.19 5.19
2923 4104 3.199727 TGTTTACATATGAGCTGAGGGCA 59.800 43.478 10.38 0.00 44.79 5.36
2924 4105 3.475566 TTACATATGAGCTGAGGGCAC 57.524 47.619 10.38 0.00 44.79 5.01
3014 4195 5.185454 TGGATGTGCATTCCAGTTTAGTAG 58.815 41.667 15.29 0.00 0.00 2.57
3202 4399 2.213499 GAATCGGCCTTGTAGTCATGG 58.787 52.381 0.00 0.00 40.49 3.66
3460 4666 5.843019 ATTTTCTTCTCCCCTTGACTACA 57.157 39.130 0.00 0.00 0.00 2.74
3666 4884 3.069158 AGTGACCTAGTACACGCTTTGTT 59.931 43.478 0.00 0.00 39.91 2.83
3673 4891 4.992381 AGTACACGCTTTGTTGATTCTC 57.008 40.909 0.00 0.00 39.91 2.87
3749 4967 2.093553 AGATGAAGCAGAAGGAGCAGAC 60.094 50.000 0.00 0.00 0.00 3.51
3811 5060 6.618287 TCGATCATCAAAGTCTTTGTTTGT 57.382 33.333 21.81 12.47 41.36 2.83
3815 5064 7.096477 CGATCATCAAAGTCTTTGTTTGTTTCC 60.096 37.037 21.81 11.62 41.36 3.13
3826 5075 5.392767 TTGTTTGTTTCCTTGCTTGTGTA 57.607 34.783 0.00 0.00 0.00 2.90
3984 5472 5.572211 CAACCACATCTTCCATATTTCACG 58.428 41.667 0.00 0.00 0.00 4.35
3998 5486 3.414549 TTTCACGTGAAAGCAGAAACC 57.585 42.857 33.86 0.00 38.94 3.27
4118 5649 4.846168 ACCCAGAAGGAGATTTAGGTTC 57.154 45.455 0.00 0.00 39.89 3.62
4182 5935 4.510038 AAGCAAAGCAGACATTTTCGAT 57.490 36.364 0.00 0.00 0.00 3.59
4267 6145 5.429762 ACCCTGAAACTGATCTCCAATATGA 59.570 40.000 0.00 0.00 0.00 2.15
4332 6253 2.109181 GTATCGCCTGCCTGACCC 59.891 66.667 0.00 0.00 0.00 4.46
4423 6344 3.567576 TTGTTTGTAACCGCATGATGG 57.432 42.857 0.00 0.00 0.00 3.51
4594 6515 3.114616 CAACGTCCTCTGCGGCAG 61.115 66.667 23.72 23.72 0.00 4.85
4610 6531 4.821589 AGCAAGCGGCCGTAGCTC 62.822 66.667 28.70 9.61 45.31 4.09
4641 6562 6.692249 GGAAGTCGATTTCTTGTAGTAGTAGC 59.308 42.308 18.64 0.00 0.00 3.58
4682 6620 1.097232 TGCATTGCAGAGTATGTGGC 58.903 50.000 7.38 0.00 33.32 5.01
4749 6690 5.594724 TTCGGTTTGGTGTAATTAACGAG 57.405 39.130 0.00 0.00 0.00 4.18
4775 6729 9.378551 GGCTTTATTTTTAACTGATTTTAGGGG 57.621 33.333 0.00 0.00 0.00 4.79
4776 6730 9.938280 GCTTTATTTTTAACTGATTTTAGGGGT 57.062 29.630 0.00 0.00 0.00 4.95
4780 6734 7.678207 TTTTTAACTGATTTTAGGGGTGGTT 57.322 32.000 0.00 0.00 0.00 3.67
4781 6735 7.678207 TTTTAACTGATTTTAGGGGTGGTTT 57.322 32.000 0.00 0.00 0.00 3.27
4783 6737 7.678207 TTAACTGATTTTAGGGGTGGTTTTT 57.322 32.000 0.00 0.00 0.00 1.94
4807 6799 2.376808 ACTGATGAGAGGTTTGCGAG 57.623 50.000 0.00 0.00 0.00 5.03
4824 6816 4.059136 GAAGGAGACGCTCGTTCG 57.941 61.111 19.08 0.00 42.58 3.95
4828 6820 1.512310 GGAGACGCTCGTTCGTGAG 60.512 63.158 9.16 0.00 43.42 3.51
4973 6968 3.007920 CCCTGCTCTGCTCCCACT 61.008 66.667 0.00 0.00 0.00 4.00
4975 6970 2.591072 CCTGCTCTGCTCCCACTGT 61.591 63.158 0.00 0.00 0.00 3.55
4982 6977 2.109517 CTGCTCCCACTGTGTGCTCT 62.110 60.000 7.08 0.00 31.34 4.09
4989 6984 1.301244 ACTGTGTGCTCTGCTTCCG 60.301 57.895 0.00 0.00 0.00 4.30
4991 6986 0.038251 CTGTGTGCTCTGCTTCCGTA 60.038 55.000 0.00 0.00 0.00 4.02
5005 7000 0.107557 TCCGTAAATTTCTCCGGGGC 60.108 55.000 18.28 0.00 40.78 5.80
5012 7019 2.521958 ATTTCTCCGGGGCTCACACG 62.522 60.000 0.00 0.00 0.00 4.49
5023 7030 2.202810 TCACACGCACGCAGAACA 60.203 55.556 0.00 0.00 0.00 3.18
5027 7034 2.967076 ACGCACGCAGAACACCTG 60.967 61.111 0.00 0.00 45.67 4.00
5035 7042 2.779282 CAGAACACCTGCACACACA 58.221 52.632 0.00 0.00 35.89 3.72
5036 7043 1.093972 CAGAACACCTGCACACACAA 58.906 50.000 0.00 0.00 35.89 3.33
5041 7061 2.328989 CCTGCACACACAACAGCG 59.671 61.111 0.00 0.00 0.00 5.18
5063 7083 2.819595 CACATTCAGGGCCGGACG 60.820 66.667 5.05 3.14 0.00 4.79
5104 7124 2.348998 CACCACCACTGCTCCTCC 59.651 66.667 0.00 0.00 0.00 4.30
5105 7125 2.205462 ACCACCACTGCTCCTCCT 59.795 61.111 0.00 0.00 0.00 3.69
5106 7126 1.915769 ACCACCACTGCTCCTCCTC 60.916 63.158 0.00 0.00 0.00 3.71
5109 7129 1.690845 CCACCACTGCTCCTCCTCTAT 60.691 57.143 0.00 0.00 0.00 1.98
5110 7130 2.114616 CACCACTGCTCCTCCTCTATT 58.885 52.381 0.00 0.00 0.00 1.73
5111 7131 3.300388 CACCACTGCTCCTCCTCTATTA 58.700 50.000 0.00 0.00 0.00 0.98
5112 7132 3.900601 CACCACTGCTCCTCCTCTATTAT 59.099 47.826 0.00 0.00 0.00 1.28
5117 7137 4.410228 ACTGCTCCTCCTCTATTATTTGCA 59.590 41.667 0.00 0.00 0.00 4.08
5140 7160 3.006859 TCATGACATTTCACACCGTCTCT 59.993 43.478 0.00 0.00 33.38 3.10
5144 7164 4.272504 TGACATTTCACACCGTCTCTTTTC 59.727 41.667 0.00 0.00 0.00 2.29
5145 7165 4.451900 ACATTTCACACCGTCTCTTTTCT 58.548 39.130 0.00 0.00 0.00 2.52
5146 7166 5.607477 ACATTTCACACCGTCTCTTTTCTA 58.393 37.500 0.00 0.00 0.00 2.10
5147 7167 5.696724 ACATTTCACACCGTCTCTTTTCTAG 59.303 40.000 0.00 0.00 0.00 2.43
5148 7168 4.931661 TTCACACCGTCTCTTTTCTAGT 57.068 40.909 0.00 0.00 0.00 2.57
5149 7169 6.395426 TTTCACACCGTCTCTTTTCTAGTA 57.605 37.500 0.00 0.00 0.00 1.82
5150 7170 6.585695 TTCACACCGTCTCTTTTCTAGTAT 57.414 37.500 0.00 0.00 0.00 2.12
5151 7171 7.692460 TTCACACCGTCTCTTTTCTAGTATA 57.308 36.000 0.00 0.00 0.00 1.47
5152 7172 7.692460 TCACACCGTCTCTTTTCTAGTATAA 57.308 36.000 0.00 0.00 0.00 0.98
5153 7173 7.533426 TCACACCGTCTCTTTTCTAGTATAAC 58.467 38.462 0.00 0.00 0.00 1.89
5154 7174 6.750963 CACACCGTCTCTTTTCTAGTATAACC 59.249 42.308 0.00 0.00 0.00 2.85
5155 7175 5.970023 CACCGTCTCTTTTCTAGTATAACCG 59.030 44.000 0.00 0.00 0.00 4.44
5156 7176 4.974888 CCGTCTCTTTTCTAGTATAACCGC 59.025 45.833 0.00 0.00 0.00 5.68
5157 7177 4.669728 CGTCTCTTTTCTAGTATAACCGCG 59.330 45.833 0.00 0.00 0.00 6.46
5158 7178 5.503031 CGTCTCTTTTCTAGTATAACCGCGA 60.503 44.000 8.23 0.00 0.00 5.87
5159 7179 6.261118 GTCTCTTTTCTAGTATAACCGCGAA 58.739 40.000 8.23 0.00 0.00 4.70
5160 7180 6.196168 GTCTCTTTTCTAGTATAACCGCGAAC 59.804 42.308 8.23 0.00 0.00 3.95
5161 7181 5.030295 TCTTTTCTAGTATAACCGCGAACG 58.970 41.667 8.23 0.00 39.67 3.95
5162 7182 2.389713 TCTAGTATAACCGCGAACGC 57.610 50.000 8.23 9.20 38.22 4.84
5163 7183 1.942657 TCTAGTATAACCGCGAACGCT 59.057 47.619 8.23 0.01 39.32 5.07
5164 7184 2.355756 TCTAGTATAACCGCGAACGCTT 59.644 45.455 8.23 8.06 39.32 4.68
5165 7185 1.553308 AGTATAACCGCGAACGCTTC 58.447 50.000 8.23 0.00 39.32 3.86
5173 7193 4.117372 CGAACGCTTCGCACCGTC 62.117 66.667 7.09 0.00 46.97 4.79
5174 7194 2.733593 GAACGCTTCGCACCGTCT 60.734 61.111 0.00 0.00 36.56 4.18
5175 7195 2.717809 GAACGCTTCGCACCGTCTC 61.718 63.158 0.00 0.00 36.56 3.36
5176 7196 3.208884 AACGCTTCGCACCGTCTCT 62.209 57.895 0.00 0.00 36.56 3.10
5177 7197 2.876645 CGCTTCGCACCGTCTCTC 60.877 66.667 0.00 0.00 0.00 3.20
5178 7198 2.569134 GCTTCGCACCGTCTCTCT 59.431 61.111 0.00 0.00 0.00 3.10
5179 7199 1.080434 GCTTCGCACCGTCTCTCTT 60.080 57.895 0.00 0.00 0.00 2.85
5204 7224 2.071778 ACCATTTCACACTGCCTGTT 57.928 45.000 0.00 0.00 0.00 3.16
5205 7225 3.222173 ACCATTTCACACTGCCTGTTA 57.778 42.857 0.00 0.00 0.00 2.41
5206 7226 3.561143 ACCATTTCACACTGCCTGTTAA 58.439 40.909 0.00 0.00 0.00 2.01
5207 7227 3.317993 ACCATTTCACACTGCCTGTTAAC 59.682 43.478 0.00 0.00 0.00 2.01
5230 7250 6.907206 CAGGAGTACTACTGTCTACTGTAC 57.093 45.833 24.85 0.00 36.78 2.90
5231 7251 6.642430 CAGGAGTACTACTGTCTACTGTACT 58.358 44.000 24.85 0.00 44.13 2.73
5232 7252 7.104939 CAGGAGTACTACTGTCTACTGTACTT 58.895 42.308 24.85 0.00 42.32 2.24
5233 7253 8.256605 CAGGAGTACTACTGTCTACTGTACTTA 58.743 40.741 24.85 0.00 42.32 2.24
5234 7254 8.257306 AGGAGTACTACTGTCTACTGTACTTAC 58.743 40.741 6.88 0.00 42.32 2.34
5235 7255 8.257306 GGAGTACTACTGTCTACTGTACTTACT 58.743 40.741 0.00 12.13 42.32 2.24
5250 7270 8.738106 ACTGTACTTACTATATATTTCCCTCGC 58.262 37.037 0.00 0.00 0.00 5.03
5251 7271 8.640063 TGTACTTACTATATATTTCCCTCGCA 57.360 34.615 0.00 0.00 0.00 5.10
5252 7272 8.737175 TGTACTTACTATATATTTCCCTCGCAG 58.263 37.037 0.00 0.00 0.00 5.18
5253 7273 8.954350 GTACTTACTATATATTTCCCTCGCAGA 58.046 37.037 0.00 0.00 0.00 4.26
5254 7274 8.418597 ACTTACTATATATTTCCCTCGCAGAA 57.581 34.615 0.00 0.00 34.09 3.02
5255 7275 8.867097 ACTTACTATATATTTCCCTCGCAGAAA 58.133 33.333 0.00 0.00 37.61 2.52
5264 7284 3.139077 TCCCTCGCAGAAAAGAAAAGAC 58.861 45.455 0.00 0.00 34.09 3.01
5267 7287 4.022849 CCCTCGCAGAAAAGAAAAGACAAT 60.023 41.667 0.00 0.00 34.09 2.71
5268 7288 4.913924 CCTCGCAGAAAAGAAAAGACAATG 59.086 41.667 0.00 0.00 34.09 2.82
5269 7289 4.858935 TCGCAGAAAAGAAAAGACAATGG 58.141 39.130 0.00 0.00 0.00 3.16
5276 7296 9.189723 CAGAAAAGAAAAGACAATGGAAATCTC 57.810 33.333 0.00 0.00 0.00 2.75
5282 7302 4.227864 AGACAATGGAAATCTCAGGTCC 57.772 45.455 0.00 0.00 0.00 4.46
5287 7307 0.840617 GGAAATCTCAGGTCCCCTCC 59.159 60.000 0.00 0.00 0.00 4.30
5291 7311 2.937959 ATCTCAGGTCCCCTCCTCGC 62.938 65.000 0.00 0.00 35.37 5.03
5297 7317 1.219393 GTCCCCTCCTCGCTTCTTG 59.781 63.158 0.00 0.00 0.00 3.02
5298 7318 1.229209 TCCCCTCCTCGCTTCTTGT 60.229 57.895 0.00 0.00 0.00 3.16
5301 7321 1.160137 CCCTCCTCGCTTCTTGTTTG 58.840 55.000 0.00 0.00 0.00 2.93
5302 7322 1.270839 CCCTCCTCGCTTCTTGTTTGA 60.271 52.381 0.00 0.00 0.00 2.69
5303 7323 1.801178 CCTCCTCGCTTCTTGTTTGAC 59.199 52.381 0.00 0.00 0.00 3.18
5305 7325 3.306088 CCTCCTCGCTTCTTGTTTGACTA 60.306 47.826 0.00 0.00 0.00 2.59
5309 7329 5.763204 TCCTCGCTTCTTGTTTGACTATTTT 59.237 36.000 0.00 0.00 0.00 1.82
5310 7330 6.073222 TCCTCGCTTCTTGTTTGACTATTTTC 60.073 38.462 0.00 0.00 0.00 2.29
5334 7366 1.669779 CCACGTGTTTGGTTTACCGAA 59.330 47.619 15.65 0.00 39.43 4.30
5343 7375 1.604755 TGGTTTACCGAACACACATGC 59.395 47.619 0.00 0.00 40.13 4.06
5367 7399 1.278637 CCGCACGCTCGTTTTCTTT 59.721 52.632 0.00 0.00 0.00 2.52
5377 7409 4.368315 GCTCGTTTTCTTTCCACCATTTT 58.632 39.130 0.00 0.00 0.00 1.82
5378 7410 4.808895 GCTCGTTTTCTTTCCACCATTTTT 59.191 37.500 0.00 0.00 0.00 1.94
5427 7459 1.504359 CCGCTACACTTGTTCGGAAA 58.496 50.000 14.12 0.00 41.90 3.13
5428 7460 1.193874 CCGCTACACTTGTTCGGAAAC 59.806 52.381 14.12 0.00 41.90 2.78
5430 7462 2.542595 CGCTACACTTGTTCGGAAACTT 59.457 45.455 0.00 0.00 36.30 2.66
5431 7463 3.362693 CGCTACACTTGTTCGGAAACTTC 60.363 47.826 0.00 0.00 36.30 3.01
5432 7464 3.558418 GCTACACTTGTTCGGAAACTTCA 59.442 43.478 0.00 0.00 36.30 3.02
5434 7466 5.407387 GCTACACTTGTTCGGAAACTTCATA 59.593 40.000 0.00 0.00 36.30 2.15
5435 7467 6.092259 GCTACACTTGTTCGGAAACTTCATAT 59.908 38.462 0.00 0.00 36.30 1.78
5436 7468 6.241207 ACACTTGTTCGGAAACTTCATATG 57.759 37.500 0.00 0.00 36.30 1.78
5437 7469 5.181245 ACACTTGTTCGGAAACTTCATATGG 59.819 40.000 2.13 0.00 36.30 2.74
5438 7470 5.181245 CACTTGTTCGGAAACTTCATATGGT 59.819 40.000 2.13 0.00 36.30 3.55
5439 7471 5.411669 ACTTGTTCGGAAACTTCATATGGTC 59.588 40.000 2.13 0.00 36.30 4.02
5440 7472 3.930229 TGTTCGGAAACTTCATATGGTCG 59.070 43.478 2.13 0.00 36.30 4.79
5441 7473 3.880047 TCGGAAACTTCATATGGTCGT 57.120 42.857 2.13 0.00 0.00 4.34
5442 7474 3.777478 TCGGAAACTTCATATGGTCGTC 58.223 45.455 2.13 0.00 0.00 4.20
5443 7475 2.534349 CGGAAACTTCATATGGTCGTCG 59.466 50.000 2.13 0.00 0.00 5.12
5444 7476 2.284417 GGAAACTTCATATGGTCGTCGC 59.716 50.000 2.13 0.00 0.00 5.19
5445 7477 2.961526 AACTTCATATGGTCGTCGCT 57.038 45.000 2.13 0.00 0.00 4.93
5446 7478 4.357142 GAAACTTCATATGGTCGTCGCTA 58.643 43.478 2.13 0.00 0.00 4.26
5447 7479 4.585955 AACTTCATATGGTCGTCGCTAT 57.414 40.909 2.13 0.00 0.00 2.97
5448 7480 3.902150 ACTTCATATGGTCGTCGCTATG 58.098 45.455 2.13 0.00 0.00 2.23
5449 7481 3.245797 CTTCATATGGTCGTCGCTATGG 58.754 50.000 2.13 0.00 0.00 2.74
5450 7482 1.544246 TCATATGGTCGTCGCTATGGG 59.456 52.381 2.13 0.00 0.00 4.00
5451 7483 0.246635 ATATGGTCGTCGCTATGGGC 59.753 55.000 0.00 0.00 37.64 5.36
5452 7484 1.812686 TATGGTCGTCGCTATGGGCC 61.813 60.000 0.00 0.00 37.74 5.80
5479 7511 4.544683 TCACCAGATCAGATCATGAGAGT 58.455 43.478 13.14 0.00 42.53 3.24
5481 7513 5.769162 TCACCAGATCAGATCATGAGAGTAG 59.231 44.000 13.14 0.00 42.53 2.57
5482 7514 5.535783 CACCAGATCAGATCATGAGAGTAGT 59.464 44.000 13.14 0.00 42.53 2.73
5485 7517 5.769162 CAGATCAGATCATGAGAGTAGTGGA 59.231 44.000 13.14 0.00 42.53 4.02
5494 7526 2.557056 TGAGAGTAGTGGAAGGTCAACG 59.443 50.000 0.00 0.00 0.00 4.10
5497 7529 1.343465 AGTAGTGGAAGGTCAACGGTG 59.657 52.381 0.00 0.00 0.00 4.94
5499 7531 1.599797 GTGGAAGGTCAACGGTGGG 60.600 63.158 0.00 0.00 0.00 4.61
5502 7534 2.203294 AAGGTCAACGGTGGGTGC 60.203 61.111 0.00 0.00 0.00 5.01
5555 7599 1.645034 CAATACTGGCTCACTGGTCG 58.355 55.000 0.00 0.00 0.00 4.79
5564 7608 4.694233 CACTGGTCGCTGCCTGCT 62.694 66.667 0.00 0.00 40.11 4.24
5565 7609 3.946201 ACTGGTCGCTGCCTGCTT 61.946 61.111 0.00 0.00 40.11 3.91
5566 7610 2.670934 CTGGTCGCTGCCTGCTTT 60.671 61.111 0.00 0.00 40.11 3.51
5567 7611 2.669569 TGGTCGCTGCCTGCTTTC 60.670 61.111 0.00 0.00 40.11 2.62
5568 7612 2.359230 GGTCGCTGCCTGCTTTCT 60.359 61.111 0.00 0.00 40.11 2.52
5569 7613 1.968540 GGTCGCTGCCTGCTTTCTT 60.969 57.895 0.00 0.00 40.11 2.52
5574 7618 0.525311 GCTGCCTGCTTTCTTCTTCC 59.475 55.000 0.00 0.00 38.95 3.46
5593 7637 6.561614 TCTTCCTTACTACGAGTAGCATTTG 58.438 40.000 9.94 0.00 36.66 2.32
5602 7648 2.480073 CGAGTAGCATTTGGCAAATGGG 60.480 50.000 39.15 24.23 46.47 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
172 176 2.026822 ACTTGTGATCACCCTGGCTTAG 60.027 50.000 22.85 9.33 0.00 2.18
258 262 3.375699 GGTCAGATTTCCTAGGGTGAGA 58.624 50.000 9.46 0.00 0.00 3.27
262 266 2.249309 ACGGTCAGATTTCCTAGGGT 57.751 50.000 9.46 0.00 0.00 4.34
295 299 1.332552 GCGACCGTGTTACACTTTGTG 60.333 52.381 13.86 0.00 39.75 3.33
296 300 0.932399 GCGACCGTGTTACACTTTGT 59.068 50.000 13.86 7.78 31.34 2.83
310 314 0.597118 TGTGCTGCAAAAATGCGACC 60.597 50.000 2.77 0.00 37.69 4.79
470 475 0.622154 TGGACCATACGGATTGGGGT 60.622 55.000 0.00 0.00 38.64 4.95
475 480 2.833794 CAACGATGGACCATACGGATT 58.166 47.619 22.09 11.24 35.59 3.01
493 498 1.202989 TGTATTCTGTTGCCAGGCCAA 60.203 47.619 9.64 0.03 39.31 4.52
498 507 2.489329 CTGGGTTGTATTCTGTTGCCAG 59.511 50.000 0.00 0.00 40.25 4.85
525 535 6.537301 GGGATTACATACACAACGATTCTCAA 59.463 38.462 0.00 0.00 0.00 3.02
533 543 6.971527 TTGTTAGGGATTACATACACAACG 57.028 37.500 0.00 0.00 0.00 4.10
593 603 8.970859 AGATGAATTACAGGACTATTTTCTGG 57.029 34.615 0.00 0.00 33.19 3.86
617 627 1.110442 CTAGTCAGCACCTGAGGGAG 58.890 60.000 2.38 0.00 41.46 4.30
618 628 3.289797 CTAGTCAGCACCTGAGGGA 57.710 57.895 2.38 0.00 41.46 4.20
629 639 5.218885 CCAGAATCGAACATAGCTAGTCAG 58.781 45.833 0.00 0.00 0.00 3.51
630 640 4.645136 ACCAGAATCGAACATAGCTAGTCA 59.355 41.667 0.00 0.00 0.00 3.41
631 641 4.979197 CACCAGAATCGAACATAGCTAGTC 59.021 45.833 0.00 0.00 0.00 2.59
632 642 4.202161 CCACCAGAATCGAACATAGCTAGT 60.202 45.833 0.00 0.00 0.00 2.57
651 677 1.273327 CCATTTTGCTCCAAGACCACC 59.727 52.381 0.00 0.00 0.00 4.61
746 772 2.183858 GAACGAAAGGCGGTGCTTCC 62.184 60.000 0.00 0.00 42.25 3.46
757 783 4.084013 ACAACTAGCCAAATCGAACGAAAG 60.084 41.667 0.12 0.00 0.00 2.62
764 790 6.428465 TGAATAAACACAACTAGCCAAATCGA 59.572 34.615 0.00 0.00 0.00 3.59
789 815 8.215736 TCATGTTTGGAGATATCATTCATCACT 58.784 33.333 5.32 0.00 0.00 3.41
795 1390 8.627403 ACACAATCATGTTTGGAGATATCATTC 58.373 33.333 18.35 0.00 37.82 2.67
807 1402 9.434420 ACCCAATATTTTACACAATCATGTTTG 57.566 29.630 13.75 13.75 37.82 2.93
815 1410 5.946972 TCGTGGACCCAATATTTTACACAAT 59.053 36.000 0.00 0.00 0.00 2.71
830 1562 0.457851 CAGTGAGAGATCGTGGACCC 59.542 60.000 0.00 0.00 0.00 4.46
886 1618 0.463204 CCCACATGACAGCGAGAGAT 59.537 55.000 0.00 0.00 0.00 2.75
887 1619 0.611896 TCCCACATGACAGCGAGAGA 60.612 55.000 0.00 0.00 0.00 3.10
893 1625 2.042831 GCTGGTCCCACATGACAGC 61.043 63.158 0.00 5.69 36.97 4.40
900 1632 2.113774 CTGCAAGCTGGTCCCACA 59.886 61.111 0.00 0.00 0.00 4.17
921 1653 2.748605 CGCTCATGATCCAAGTAGACC 58.251 52.381 0.00 0.00 0.00 3.85
923 1655 1.069204 GGCGCTCATGATCCAAGTAGA 59.931 52.381 7.64 0.00 0.00 2.59
924 1656 1.202568 TGGCGCTCATGATCCAAGTAG 60.203 52.381 7.64 0.00 0.00 2.57
925 1657 0.829990 TGGCGCTCATGATCCAAGTA 59.170 50.000 7.64 0.00 0.00 2.24
926 1658 0.182061 ATGGCGCTCATGATCCAAGT 59.818 50.000 7.64 0.00 34.22 3.16
927 1659 0.873054 GATGGCGCTCATGATCCAAG 59.127 55.000 14.84 0.00 35.97 3.61
928 1660 0.180878 TGATGGCGCTCATGATCCAA 59.819 50.000 14.84 0.00 35.97 3.53
929 1661 0.399075 ATGATGGCGCTCATGATCCA 59.601 50.000 14.84 12.15 35.97 3.41
930 1662 1.085091 GATGATGGCGCTCATGATCC 58.915 55.000 16.02 0.00 39.54 3.36
931 1663 1.085091 GGATGATGGCGCTCATGATC 58.915 55.000 21.29 21.29 43.03 2.92
932 1664 0.399075 TGGATGATGGCGCTCATGAT 59.601 50.000 16.02 12.68 36.01 2.45
933 1665 0.399075 ATGGATGATGGCGCTCATGA 59.601 50.000 16.02 8.48 36.01 3.07
934 1666 0.803117 GATGGATGATGGCGCTCATG 59.197 55.000 16.02 0.00 36.01 3.07
935 1667 0.322277 GGATGGATGATGGCGCTCAT 60.322 55.000 11.55 11.55 38.57 2.90
1279 2054 1.750930 CCGGATGAGAGGGGATGTG 59.249 63.158 0.00 0.00 0.00 3.21
1555 2351 2.226437 CACCTGCACATCAGTACCAAAC 59.774 50.000 0.00 0.00 41.25 2.93
1847 2974 4.962155 ACTAAGACTTGAACAAGAGGGTG 58.038 43.478 19.35 9.63 40.79 4.61
1849 2976 5.639931 GCTAACTAAGACTTGAACAAGAGGG 59.360 44.000 19.35 8.23 40.79 4.30
2020 3164 8.837788 ATGATCTATGCAATTCAATTAGACGA 57.162 30.769 0.00 0.00 0.00 4.20
2039 3183 8.470805 GGACGTCTATGTTATTCCATATGATCT 58.529 37.037 16.46 0.00 0.00 2.75
2062 3206 1.079503 GCGTCTGATGGACAAAGGAC 58.920 55.000 0.00 0.00 44.70 3.85
2133 3277 4.346418 CAGGGTACTTATCCTTGAGCAGAT 59.654 45.833 0.00 0.00 33.57 2.90
2228 3372 2.032620 AGGTAGTATGGTGAGAAGCGG 58.967 52.381 0.00 0.00 0.00 5.52
2242 3386 7.892241 TCAGTGTAGATAACCTAAACAGGTAGT 59.108 37.037 0.00 0.00 42.20 2.73
2386 3530 3.807553 TCACACTGAACTGAAGCAATGA 58.192 40.909 0.00 0.00 0.00 2.57
2457 3601 9.046296 GTAGCAGTATTAAGCAATGAGTGTTAT 57.954 33.333 0.00 0.00 0.00 1.89
2468 3612 7.033791 GTCTACAACAGTAGCAGTATTAAGCA 58.966 38.462 0.00 0.00 36.12 3.91
2534 3682 2.625790 GGTATGCTCTCTTGGTCTCGAT 59.374 50.000 0.00 0.00 0.00 3.59
2549 3697 5.841957 ACATTCTTCCAAATCAGGTATGC 57.158 39.130 0.00 0.00 0.00 3.14
2613 3761 3.185246 ACTCAAGCATGATCTAACGGG 57.815 47.619 0.00 0.00 34.37 5.28
2686 3861 2.604046 AGTAATAACTGCAGCCTCCG 57.396 50.000 15.27 0.00 33.57 4.63
2748 3923 1.734465 CCTCCAAAGCTGCTTACTTCG 59.266 52.381 16.31 3.77 0.00 3.79
2753 3928 3.508845 AAACTCCTCCAAAGCTGCTTA 57.491 42.857 16.31 0.00 0.00 3.09
2909 4090 2.072487 GGGGTGCCCTCAGCTCATA 61.072 63.158 7.26 0.00 40.77 2.15
2910 4091 3.415087 GGGGTGCCCTCAGCTCAT 61.415 66.667 7.26 0.00 40.77 2.90
2915 4096 1.497309 TAAACAGGGGGTGCCCTCAG 61.497 60.000 10.18 3.73 44.66 3.35
2916 4097 1.464395 TAAACAGGGGGTGCCCTCA 60.464 57.895 10.18 0.00 44.66 3.86
2917 4098 1.001269 GTAAACAGGGGGTGCCCTC 60.001 63.158 7.26 2.55 44.66 4.30
2918 4099 1.146544 ATGTAAACAGGGGGTGCCCT 61.147 55.000 7.26 0.00 44.66 5.19
2919 4100 0.626916 TATGTAAACAGGGGGTGCCC 59.373 55.000 0.00 0.00 44.51 5.36
2920 4101 2.092103 TCATATGTAAACAGGGGGTGCC 60.092 50.000 1.90 0.00 0.00 5.01
2921 4102 3.214328 CTCATATGTAAACAGGGGGTGC 58.786 50.000 1.90 0.00 0.00 5.01
2922 4103 3.117888 AGCTCATATGTAAACAGGGGGTG 60.118 47.826 1.90 0.00 0.00 4.61
2923 4104 3.117888 CAGCTCATATGTAAACAGGGGGT 60.118 47.826 1.90 0.00 0.00 4.95
2924 4105 3.136443 TCAGCTCATATGTAAACAGGGGG 59.864 47.826 1.90 0.00 0.00 5.40
2934 4115 4.712051 TTAATGCCCTCAGCTCATATGT 57.288 40.909 1.90 0.00 44.23 2.29
2935 4116 6.349944 GGAATTTAATGCCCTCAGCTCATATG 60.350 42.308 0.00 0.00 44.23 1.78
2936 4117 5.713861 GGAATTTAATGCCCTCAGCTCATAT 59.286 40.000 0.00 0.00 44.23 1.78
3460 4666 7.557358 TCATACACATGATCCTACTTGCAATTT 59.443 33.333 0.00 0.00 36.22 1.82
3673 4891 3.629398 GGCTGGGTTCATCTGATAACTTG 59.371 47.826 0.00 0.00 0.00 3.16
3749 4967 9.831737 CAAAGTAACAGAATTACCAGAAGAATG 57.168 33.333 0.00 0.00 0.00 2.67
3826 5075 8.888579 AATGATAACATAGCTTTTAGTACGCT 57.111 30.769 0.00 0.00 35.50 5.07
3966 5454 6.403636 GCTTTCACGTGAAATATGGAAGATGT 60.404 38.462 36.31 0.00 42.44 3.06
3998 5486 5.856126 TTGTACCTGACGCTAAGAAAATG 57.144 39.130 0.00 0.00 0.00 2.32
4118 5649 3.609175 CGCCAGTCCTTTTGTTACACATG 60.609 47.826 0.00 0.00 0.00 3.21
4133 5886 0.749454 AGATCATTTGGCCGCCAGTC 60.749 55.000 12.95 7.35 33.81 3.51
4212 5965 1.852626 AGGGACAGGGTTCAAGGGG 60.853 63.158 0.00 0.00 0.00 4.79
4267 6145 0.695803 AGGGGATTCTCCGGAGCATT 60.696 55.000 27.39 13.28 37.43 3.56
4332 6253 6.074623 GCATCTCAAATGATCACGTGTAGTAG 60.075 42.308 16.51 4.14 0.00 2.57
4423 6344 0.304705 CGACACCTGAACACAGCAAC 59.695 55.000 0.00 0.00 0.00 4.17
4610 6531 3.679980 ACAAGAAATCGACTTCCGTGATG 59.320 43.478 13.06 4.36 39.75 3.07
4723 6664 1.161843 ATTACACCAAACCGAAGCCG 58.838 50.000 0.00 0.00 0.00 5.52
4749 6690 9.378551 CCCCTAAAATCAGTTAAAAATAAAGCC 57.621 33.333 0.00 0.00 0.00 4.35
4780 6734 6.293407 CGCAAACCTCTCATCAGTTCTAAAAA 60.293 38.462 0.00 0.00 0.00 1.94
4781 6735 5.179368 CGCAAACCTCTCATCAGTTCTAAAA 59.821 40.000 0.00 0.00 0.00 1.52
4783 6737 4.021456 TCGCAAACCTCTCATCAGTTCTAA 60.021 41.667 0.00 0.00 0.00 2.10
4784 6738 3.509967 TCGCAAACCTCTCATCAGTTCTA 59.490 43.478 0.00 0.00 0.00 2.10
4786 6740 2.670414 CTCGCAAACCTCTCATCAGTTC 59.330 50.000 0.00 0.00 0.00 3.01
4787 6741 2.300152 TCTCGCAAACCTCTCATCAGTT 59.700 45.455 0.00 0.00 0.00 3.16
4789 6743 2.662006 TCTCGCAAACCTCTCATCAG 57.338 50.000 0.00 0.00 0.00 2.90
4791 6745 2.093973 TCCTTCTCGCAAACCTCTCATC 60.094 50.000 0.00 0.00 0.00 2.92
4807 6799 1.066114 CACGAACGAGCGTCTCCTTC 61.066 60.000 0.14 5.36 43.59 3.46
4824 6816 1.302033 CCCACCTGTCAGTGCTCAC 60.302 63.158 0.00 0.00 36.38 3.51
4884 6876 2.280797 GTCAAGCTGACCCGTGCA 60.281 61.111 0.00 0.00 41.37 4.57
4957 6952 2.268280 CAGTGGGAGCAGAGCAGG 59.732 66.667 0.00 0.00 0.00 4.85
4973 6968 0.391228 TTACGGAAGCAGAGCACACA 59.609 50.000 0.00 0.00 0.00 3.72
4975 6970 2.472695 ATTTACGGAAGCAGAGCACA 57.527 45.000 0.00 0.00 0.00 4.57
4989 6984 2.014857 GTGAGCCCCGGAGAAATTTAC 58.985 52.381 0.73 0.00 0.00 2.01
4991 6986 0.404040 TGTGAGCCCCGGAGAAATTT 59.596 50.000 0.73 0.00 0.00 1.82
5005 7000 2.237066 TGTTCTGCGTGCGTGTGAG 61.237 57.895 0.00 0.00 0.00 3.51
5023 7030 2.472059 CGCTGTTGTGTGTGCAGGT 61.472 57.895 0.00 0.00 0.00 4.00
5027 7034 3.812166 CTGGCGCTGTTGTGTGTGC 62.812 63.158 7.64 0.00 38.78 4.57
5031 7038 3.585990 GTGCTGGCGCTGTTGTGT 61.586 61.111 7.64 0.00 36.97 3.72
5032 7039 2.410638 AATGTGCTGGCGCTGTTGTG 62.411 55.000 7.64 0.00 36.97 3.33
5033 7040 2.133742 GAATGTGCTGGCGCTGTTGT 62.134 55.000 7.64 0.00 36.97 3.32
5035 7042 1.859427 CTGAATGTGCTGGCGCTGTT 61.859 55.000 7.64 2.98 36.97 3.16
5036 7043 2.281692 TGAATGTGCTGGCGCTGT 60.282 55.556 7.64 0.00 36.97 4.40
5041 7061 3.455469 GGCCCTGAATGTGCTGGC 61.455 66.667 0.00 0.00 41.42 4.85
5047 7067 4.096003 CCGTCCGGCCCTGAATGT 62.096 66.667 0.00 0.00 0.00 2.71
5063 7083 2.740055 CAGGAGTGTGCAGACGCC 60.740 66.667 26.34 26.34 37.32 5.68
5092 7112 5.303971 CAAATAATAGAGGAGGAGCAGTGG 58.696 45.833 0.00 0.00 0.00 4.00
5096 7116 5.072193 TGATGCAAATAATAGAGGAGGAGCA 59.928 40.000 0.00 0.00 0.00 4.26
5105 7125 9.955208 GTGAAATGTCATGATGCAAATAATAGA 57.045 29.630 0.00 0.00 35.80 1.98
5106 7126 9.738832 TGTGAAATGTCATGATGCAAATAATAG 57.261 29.630 0.00 0.00 35.80 1.73
5109 7129 6.812656 GGTGTGAAATGTCATGATGCAAATAA 59.187 34.615 0.00 0.00 35.80 1.40
5110 7130 6.331845 GGTGTGAAATGTCATGATGCAAATA 58.668 36.000 0.00 0.00 35.80 1.40
5111 7131 5.172934 GGTGTGAAATGTCATGATGCAAAT 58.827 37.500 0.00 0.00 35.80 2.32
5112 7132 4.558178 GGTGTGAAATGTCATGATGCAAA 58.442 39.130 0.00 0.00 35.80 3.68
5117 7137 3.935203 GAGACGGTGTGAAATGTCATGAT 59.065 43.478 0.00 0.00 35.80 2.45
5140 7160 3.547468 GCGTTCGCGGTTATACTAGAAAA 59.453 43.478 6.13 0.00 41.67 2.29
5162 7182 1.784525 AAAAGAGAGACGGTGCGAAG 58.215 50.000 0.00 0.00 0.00 3.79
5163 7183 2.555325 TCTAAAAGAGAGACGGTGCGAA 59.445 45.455 0.00 0.00 0.00 4.70
5164 7184 2.156917 TCTAAAAGAGAGACGGTGCGA 58.843 47.619 0.00 0.00 0.00 5.10
5165 7185 2.631418 TCTAAAAGAGAGACGGTGCG 57.369 50.000 0.00 0.00 0.00 5.34
5166 7186 2.994578 GGTTCTAAAAGAGAGACGGTGC 59.005 50.000 0.00 0.00 34.93 5.01
5167 7187 4.252971 TGGTTCTAAAAGAGAGACGGTG 57.747 45.455 0.00 0.00 34.93 4.94
5168 7188 5.485209 AATGGTTCTAAAAGAGAGACGGT 57.515 39.130 0.00 0.00 34.93 4.83
5169 7189 5.932303 TGAAATGGTTCTAAAAGAGAGACGG 59.068 40.000 0.00 0.00 34.93 4.79
5170 7190 6.423905 TGTGAAATGGTTCTAAAAGAGAGACG 59.576 38.462 0.00 0.00 34.93 4.18
5171 7191 7.442666 AGTGTGAAATGGTTCTAAAAGAGAGAC 59.557 37.037 0.00 0.00 34.93 3.36
5172 7192 7.442364 CAGTGTGAAATGGTTCTAAAAGAGAGA 59.558 37.037 0.00 0.00 34.93 3.10
5173 7193 7.579726 CAGTGTGAAATGGTTCTAAAAGAGAG 58.420 38.462 0.00 0.00 34.93 3.20
5174 7194 6.017109 GCAGTGTGAAATGGTTCTAAAAGAGA 60.017 38.462 0.00 0.00 34.60 3.10
5175 7195 6.145535 GCAGTGTGAAATGGTTCTAAAAGAG 58.854 40.000 0.00 0.00 34.60 2.85
5176 7196 5.009610 GGCAGTGTGAAATGGTTCTAAAAGA 59.990 40.000 0.00 0.00 34.60 2.52
5177 7197 5.010012 AGGCAGTGTGAAATGGTTCTAAAAG 59.990 40.000 0.00 0.00 34.60 2.27
5178 7198 4.892934 AGGCAGTGTGAAATGGTTCTAAAA 59.107 37.500 0.00 0.00 34.60 1.52
5179 7199 4.278170 CAGGCAGTGTGAAATGGTTCTAAA 59.722 41.667 0.00 0.00 34.60 1.85
5204 7224 7.013823 ACAGTAGACAGTAGTACTCCTGTTA 57.986 40.000 20.64 12.49 41.80 2.41
5205 7225 5.878627 ACAGTAGACAGTAGTACTCCTGTT 58.121 41.667 20.64 13.32 41.80 3.16
5206 7226 5.502089 ACAGTAGACAGTAGTACTCCTGT 57.498 43.478 19.92 19.92 44.31 4.00
5207 7227 6.642430 AGTACAGTAGACAGTAGTACTCCTG 58.358 44.000 13.49 13.49 40.84 3.86
5224 7244 8.738106 GCGAGGGAAATATATAGTAAGTACAGT 58.262 37.037 0.00 0.00 0.00 3.55
5225 7245 8.737175 TGCGAGGGAAATATATAGTAAGTACAG 58.263 37.037 0.00 0.00 0.00 2.74
5226 7246 8.640063 TGCGAGGGAAATATATAGTAAGTACA 57.360 34.615 0.00 0.00 0.00 2.90
5227 7247 8.954350 TCTGCGAGGGAAATATATAGTAAGTAC 58.046 37.037 0.00 0.00 0.00 2.73
5228 7248 9.524496 TTCTGCGAGGGAAATATATAGTAAGTA 57.476 33.333 0.00 0.00 0.00 2.24
5229 7249 8.418597 TTCTGCGAGGGAAATATATAGTAAGT 57.581 34.615 0.00 0.00 0.00 2.24
5230 7250 9.706691 TTTTCTGCGAGGGAAATATATAGTAAG 57.293 33.333 0.00 0.00 33.51 2.34
5231 7251 9.706691 CTTTTCTGCGAGGGAAATATATAGTAA 57.293 33.333 0.00 0.00 33.51 2.24
5232 7252 9.085645 TCTTTTCTGCGAGGGAAATATATAGTA 57.914 33.333 0.00 0.00 33.51 1.82
5233 7253 7.963532 TCTTTTCTGCGAGGGAAATATATAGT 58.036 34.615 0.00 0.00 33.51 2.12
5234 7254 8.833231 TTCTTTTCTGCGAGGGAAATATATAG 57.167 34.615 0.00 0.00 33.51 1.31
5235 7255 9.621629 TTTTCTTTTCTGCGAGGGAAATATATA 57.378 29.630 0.00 0.00 33.51 0.86
5236 7256 8.519799 TTTTCTTTTCTGCGAGGGAAATATAT 57.480 30.769 0.00 0.00 33.51 0.86
5249 7269 7.654923 AGATTTCCATTGTCTTTTCTTTTCTGC 59.345 33.333 0.00 0.00 0.00 4.26
5250 7270 9.189723 GAGATTTCCATTGTCTTTTCTTTTCTG 57.810 33.333 0.00 0.00 0.00 3.02
5251 7271 8.917088 TGAGATTTCCATTGTCTTTTCTTTTCT 58.083 29.630 0.00 0.00 0.00 2.52
5252 7272 9.189723 CTGAGATTTCCATTGTCTTTTCTTTTC 57.810 33.333 0.00 0.00 0.00 2.29
5253 7273 8.146412 CCTGAGATTTCCATTGTCTTTTCTTTT 58.854 33.333 0.00 0.00 0.00 2.27
5254 7274 7.288621 ACCTGAGATTTCCATTGTCTTTTCTTT 59.711 33.333 0.00 0.00 0.00 2.52
5255 7275 6.779539 ACCTGAGATTTCCATTGTCTTTTCTT 59.220 34.615 0.00 0.00 0.00 2.52
5282 7302 1.160137 CAAACAAGAAGCGAGGAGGG 58.840 55.000 0.00 0.00 0.00 4.30
5287 7307 6.073003 AGGAAAATAGTCAAACAAGAAGCGAG 60.073 38.462 0.00 0.00 0.00 5.03
5291 7311 8.290325 GTGGTAGGAAAATAGTCAAACAAGAAG 58.710 37.037 0.00 0.00 0.00 2.85
5297 7317 5.467735 ACACGTGGTAGGAAAATAGTCAAAC 59.532 40.000 21.57 0.00 0.00 2.93
5298 7318 5.613329 ACACGTGGTAGGAAAATAGTCAAA 58.387 37.500 21.57 0.00 0.00 2.69
5301 7321 5.106830 CCAAACACGTGGTAGGAAAATAGTC 60.107 44.000 21.57 0.00 33.63 2.59
5302 7322 4.758165 CCAAACACGTGGTAGGAAAATAGT 59.242 41.667 21.57 0.00 33.63 2.12
5303 7323 5.291293 CCAAACACGTGGTAGGAAAATAG 57.709 43.478 21.57 0.00 33.63 1.73
5334 7366 3.126879 CGGCATCGGCATGTGTGT 61.127 61.111 0.00 0.00 43.71 3.72
5355 7387 3.643159 AATGGTGGAAAGAAAACGAGC 57.357 42.857 0.00 0.00 0.00 5.03
5377 7409 5.350633 CACACTGATCCTTTGAAGCAAAAA 58.649 37.500 0.00 0.00 32.75 1.94
5378 7410 4.737352 GCACACTGATCCTTTGAAGCAAAA 60.737 41.667 0.00 0.00 32.75 2.44
5379 7411 3.243501 GCACACTGATCCTTTGAAGCAAA 60.244 43.478 0.00 0.00 0.00 3.68
5380 7412 2.294233 GCACACTGATCCTTTGAAGCAA 59.706 45.455 0.00 0.00 0.00 3.91
5381 7413 1.881973 GCACACTGATCCTTTGAAGCA 59.118 47.619 0.00 0.00 0.00 3.91
5390 7422 3.127533 GCACCCGCACACTGATCC 61.128 66.667 0.00 0.00 38.36 3.36
5410 7442 3.558418 TGAAGTTTCCGAACAAGTGTAGC 59.442 43.478 0.00 0.00 38.26 3.58
5411 7443 5.924475 ATGAAGTTTCCGAACAAGTGTAG 57.076 39.130 0.00 0.00 38.26 2.74
5427 7459 3.305403 CCATAGCGACGACCATATGAAGT 60.305 47.826 3.65 0.71 0.00 3.01
5428 7460 3.245797 CCATAGCGACGACCATATGAAG 58.754 50.000 3.65 0.00 0.00 3.02
5430 7462 1.544246 CCCATAGCGACGACCATATGA 59.456 52.381 3.65 0.00 0.00 2.15
5431 7463 1.996292 CCCATAGCGACGACCATATG 58.004 55.000 0.00 0.00 0.00 1.78
5432 7464 0.246635 GCCCATAGCGACGACCATAT 59.753 55.000 0.00 0.00 0.00 1.78
5434 7466 2.421739 GCCCATAGCGACGACCAT 59.578 61.111 0.00 0.00 0.00 3.55
5435 7467 3.845259 GGCCCATAGCGACGACCA 61.845 66.667 0.00 0.00 45.17 4.02
5436 7468 4.944372 CGGCCCATAGCGACGACC 62.944 72.222 0.00 0.00 45.17 4.79
5437 7469 4.944372 CCGGCCCATAGCGACGAC 62.944 72.222 0.00 0.00 45.17 4.34
5440 7472 3.591254 GATCCCGGCCCATAGCGAC 62.591 68.421 0.00 0.00 45.17 5.19
5441 7473 3.311110 GATCCCGGCCCATAGCGA 61.311 66.667 0.00 0.00 45.17 4.93
5442 7474 3.625897 TGATCCCGGCCCATAGCG 61.626 66.667 0.00 0.00 45.17 4.26
5443 7475 2.032681 GTGATCCCGGCCCATAGC 59.967 66.667 0.00 0.00 42.60 2.97
5444 7476 2.116983 CTGGTGATCCCGGCCCATAG 62.117 65.000 0.00 0.00 35.15 2.23
5445 7477 2.040359 TGGTGATCCCGGCCCATA 60.040 61.111 0.00 0.00 35.15 2.74
5446 7478 3.492353 CTGGTGATCCCGGCCCAT 61.492 66.667 0.00 0.00 35.15 4.00
5447 7479 4.731853 TCTGGTGATCCCGGCCCA 62.732 66.667 0.00 0.00 39.73 5.36
5448 7480 3.171388 ATCTGGTGATCCCGGCCC 61.171 66.667 0.00 0.00 39.73 5.80
5449 7481 2.388890 CTGATCTGGTGATCCCGGCC 62.389 65.000 0.00 0.00 46.34 6.13
5450 7482 1.070445 CTGATCTGGTGATCCCGGC 59.930 63.158 0.00 0.00 46.34 6.13
5451 7483 1.274728 GATCTGATCTGGTGATCCCGG 59.725 57.143 10.37 0.00 46.34 5.73
5452 7484 1.966354 TGATCTGATCTGGTGATCCCG 59.034 52.381 17.82 0.00 46.34 5.14
5479 7511 0.682852 CCACCGTTGACCTTCCACTA 59.317 55.000 0.00 0.00 0.00 2.74
5481 7513 1.599797 CCCACCGTTGACCTTCCAC 60.600 63.158 0.00 0.00 0.00 4.02
5482 7514 2.073716 ACCCACCGTTGACCTTCCA 61.074 57.895 0.00 0.00 0.00 3.53
5485 7517 2.203294 GCACCCACCGTTGACCTT 60.203 61.111 0.00 0.00 0.00 3.50
5494 7526 3.640407 TCTGCCTCAGCACCCACC 61.640 66.667 0.00 0.00 46.52 4.61
5497 7529 4.416738 GGGTCTGCCTCAGCACCC 62.417 72.222 14.26 14.26 46.52 4.61
5499 7531 2.046507 CTGGGTCTGCCTCAGCAC 60.047 66.667 0.00 0.00 46.52 4.40
5502 7534 0.321122 GTCAACTGGGTCTGCCTCAG 60.321 60.000 0.00 0.00 38.33 3.35
5515 7547 1.955458 TTTGGGGCCTTGGGTCAACT 61.955 55.000 0.84 0.00 0.00 3.16
5555 7599 0.525311 GGAAGAAGAAAGCAGGCAGC 59.475 55.000 0.00 0.00 46.19 5.25
5564 7608 6.432162 TGCTACTCGTAGTAAGGAAGAAGAAA 59.568 38.462 6.02 0.00 35.65 2.52
5565 7609 5.942236 TGCTACTCGTAGTAAGGAAGAAGAA 59.058 40.000 6.02 0.00 35.65 2.52
5566 7610 5.494724 TGCTACTCGTAGTAAGGAAGAAGA 58.505 41.667 6.02 0.00 35.65 2.87
5567 7611 5.814764 TGCTACTCGTAGTAAGGAAGAAG 57.185 43.478 6.02 0.00 35.65 2.85
5568 7612 6.770746 AATGCTACTCGTAGTAAGGAAGAA 57.229 37.500 6.02 0.00 35.65 2.52
5569 7613 6.405508 CCAAATGCTACTCGTAGTAAGGAAGA 60.406 42.308 6.02 0.00 35.65 2.87
5574 7618 4.430007 TGCCAAATGCTACTCGTAGTAAG 58.570 43.478 6.02 0.00 42.00 2.34


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

AutoCloner maintained by Alex Coulton.