Multiple sequence alignment - TraesCS5A01G241100

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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 TraesCS5A01G241100 chr5A 100.000 7764 0 0 1 7764 457075068 457082831 0.000000e+00 14338.0
1 TraesCS5A01G241100 chr5D 94.820 3668 120 31 1 3628 354933612 354937249 0.000000e+00 5657.0
2 TraesCS5A01G241100 chr5D 98.024 1518 25 4 3814 5328 354937242 354938757 0.000000e+00 2632.0
3 TraesCS5A01G241100 chr5D 96.154 1612 44 14 5328 6930 354938828 354940430 0.000000e+00 2617.0
4 TraesCS5A01G241100 chr5D 96.774 186 6 0 3628 3813 232466881 232466696 2.100000e-80 311.0
5 TraesCS5A01G241100 chr5D 96.774 186 6 0 3628 3813 236022597 236022782 2.100000e-80 311.0
6 TraesCS5A01G241100 chr5D 87.500 88 9 2 2968 3055 206683763 206683848 4.960000e-17 100.0
7 TraesCS5A01G241100 chr5B 94.090 3672 156 32 1 3628 419719068 419722722 0.000000e+00 5522.0
8 TraesCS5A01G241100 chr5B 96.034 1513 48 6 3816 5326 419722717 419724219 0.000000e+00 2451.0
9 TraesCS5A01G241100 chr5B 94.458 1263 44 10 5328 6574 419724287 419725539 0.000000e+00 1921.0
10 TraesCS5A01G241100 chr5B 93.091 825 26 5 6947 7764 565782076 565781276 0.000000e+00 1179.0
11 TraesCS5A01G241100 chr5B 89.835 364 23 9 6583 6942 419725593 419725946 9.180000e-124 455.0
12 TraesCS5A01G241100 chr5B 94.898 196 9 1 3629 3823 567157831 567157636 9.790000e-79 305.0
13 TraesCS5A01G241100 chr5B 87.640 89 8 3 2968 3055 219992502 219992588 4.960000e-17 100.0
14 TraesCS5A01G241100 chr5B 87.952 83 7 3 2973 3055 297030390 297030469 2.310000e-15 95.3
15 TraesCS5A01G241100 chr6A 93.229 827 25 4 6945 7764 558156931 558157733 0.000000e+00 1188.0
16 TraesCS5A01G241100 chr6A 96.774 186 6 0 3628 3813 313827018 313826833 2.100000e-80 311.0
17 TraesCS5A01G241100 chr6A 86.207 87 10 2 2969 3055 297630712 297630628 8.290000e-15 93.5
18 TraesCS5A01G241100 chr7A 92.978 826 26 5 6946 7764 545046594 545047394 0.000000e+00 1175.0
19 TraesCS5A01G241100 chr4B 93.074 823 26 2 6949 7764 171668802 171668004 0.000000e+00 1175.0
20 TraesCS5A01G241100 chr4B 85.859 693 63 12 6947 7630 80670505 80669839 0.000000e+00 704.0
21 TraesCS5A01G241100 chr4B 76.043 839 179 18 1000 1833 86072679 86071858 4.330000e-112 416.0
22 TraesCS5A01G241100 chr4B 85.792 183 26 0 1933 2115 86071698 86071516 2.210000e-45 195.0
23 TraesCS5A01G241100 chr4B 86.905 84 11 0 5461 5544 86068329 86068246 2.310000e-15 95.3
24 TraesCS5A01G241100 chr2B 92.970 825 27 4 6947 7764 73993168 73992368 0.000000e+00 1173.0
25 TraesCS5A01G241100 chr2B 86.513 823 77 9 6950 7764 194690568 194689772 0.000000e+00 874.0
26 TraesCS5A01G241100 chr3B 92.831 823 27 9 6949 7764 762334758 762333961 0.000000e+00 1164.0
27 TraesCS5A01G241100 chr3B 86.050 638 47 7 6946 7576 659087869 659088471 0.000000e+00 647.0
28 TraesCS5A01G241100 chr3B 94.686 207 9 2 3616 3822 226085879 226085675 3.500000e-83 320.0
29 TraesCS5A01G241100 chr4A 92.831 823 26 6 6949 7764 558550829 558550033 0.000000e+00 1162.0
30 TraesCS5A01G241100 chr4A 87.500 600 44 4 6949 7541 542505129 542505704 0.000000e+00 664.0
31 TraesCS5A01G241100 chr4A 86.885 183 24 0 1933 2115 539289833 539290015 1.020000e-48 206.0
32 TraesCS5A01G241100 chr4A 86.905 84 11 0 5461 5544 539293277 539293360 2.310000e-15 95.3
33 TraesCS5A01G241100 chr2A 90.287 453 13 5 6948 7393 429788298 429787870 1.460000e-156 564.0
34 TraesCS5A01G241100 chr7B 96.774 186 6 0 3628 3813 168758381 168758196 2.100000e-80 311.0
35 TraesCS5A01G241100 chr1D 96.774 186 6 0 3628 3813 296863944 296864129 2.100000e-80 311.0
36 TraesCS5A01G241100 chr1D 89.873 79 7 1 2977 3055 267794562 267794485 4.960000e-17 100.0
37 TraesCS5A01G241100 chr3A 93.333 210 10 4 3628 3834 68617267 68617475 2.720000e-79 307.0
38 TraesCS5A01G241100 chr3D 94.472 199 9 2 3616 3813 513113035 513113232 9.790000e-79 305.0
39 TraesCS5A01G241100 chr4D 86.339 183 25 0 1933 2115 57487742 57487560 4.750000e-47 200.0
40 TraesCS5A01G241100 chr4D 86.905 84 11 0 5461 5544 57484138 57484055 2.310000e-15 95.3
41 TraesCS5A01G241100 chr1B 89.024 82 8 1 2974 3055 345320529 345320609 4.960000e-17 100.0
42 TraesCS5A01G241100 chr1A 89.024 82 8 1 2974 3055 335028624 335028704 4.960000e-17 100.0
43 TraesCS5A01G241100 chr6B 86.905 84 11 0 5461 5544 551799609 551799526 2.310000e-15 95.3


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 TraesCS5A01G241100 chr5A 457075068 457082831 7763 False 14338.000000 14338 100.000000 1 7764 1 chr5A.!!$F1 7763
1 TraesCS5A01G241100 chr5D 354933612 354940430 6818 False 3635.333333 5657 96.332667 1 6930 3 chr5D.!!$F3 6929
2 TraesCS5A01G241100 chr5B 419719068 419725946 6878 False 2587.250000 5522 93.604250 1 6942 4 chr5B.!!$F3 6941
3 TraesCS5A01G241100 chr5B 565781276 565782076 800 True 1179.000000 1179 93.091000 6947 7764 1 chr5B.!!$R1 817
4 TraesCS5A01G241100 chr6A 558156931 558157733 802 False 1188.000000 1188 93.229000 6945 7764 1 chr6A.!!$F1 819
5 TraesCS5A01G241100 chr7A 545046594 545047394 800 False 1175.000000 1175 92.978000 6946 7764 1 chr7A.!!$F1 818
6 TraesCS5A01G241100 chr4B 171668004 171668802 798 True 1175.000000 1175 93.074000 6949 7764 1 chr4B.!!$R2 815
7 TraesCS5A01G241100 chr4B 80669839 80670505 666 True 704.000000 704 85.859000 6947 7630 1 chr4B.!!$R1 683
8 TraesCS5A01G241100 chr4B 86068246 86072679 4433 True 235.433333 416 82.913333 1000 5544 3 chr4B.!!$R3 4544
9 TraesCS5A01G241100 chr2B 73992368 73993168 800 True 1173.000000 1173 92.970000 6947 7764 1 chr2B.!!$R1 817
10 TraesCS5A01G241100 chr2B 194689772 194690568 796 True 874.000000 874 86.513000 6950 7764 1 chr2B.!!$R2 814
11 TraesCS5A01G241100 chr3B 762333961 762334758 797 True 1164.000000 1164 92.831000 6949 7764 1 chr3B.!!$R2 815
12 TraesCS5A01G241100 chr3B 659087869 659088471 602 False 647.000000 647 86.050000 6946 7576 1 chr3B.!!$F1 630
13 TraesCS5A01G241100 chr4A 558550033 558550829 796 True 1162.000000 1162 92.831000 6949 7764 1 chr4A.!!$R1 815
14 TraesCS5A01G241100 chr4A 542505129 542505704 575 False 664.000000 664 87.500000 6949 7541 1 chr4A.!!$F1 592

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
629 657 0.459585 TCGTGCGGCTATTTGGAGTC 60.460 55.000 0.00 0.00 0.00 3.36 F
2021 2146 0.453390 GAGCTGCATTAAGTGTGGCC 59.547 55.000 1.02 0.00 0.00 5.36 F
3663 4260 0.725117 GCTAGGCGTTAATTGTGCGT 59.275 50.000 0.00 0.00 0.00 5.24 F
3761 4358 0.035176 AATGCGTTTTGCCAATGCCT 59.965 45.000 7.31 0.00 45.60 4.75 F
3771 4368 0.036022 GCCAATGCCTAGAGCCTAGG 59.964 60.000 18.85 18.85 42.71 3.02 F
3781 4378 0.461961 AGAGCCTAGGTGCGCTTAAG 59.538 55.000 11.31 0.00 38.26 1.85 F
4667 5854 1.067516 ACAAGACTGCATTTGTGTGCC 59.932 47.619 9.69 0.00 44.43 5.01 F
5210 6406 1.468520 CAAATGGTGGCCAACGACTAG 59.531 52.381 17.89 0.45 36.95 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2570 2909 1.812235 TTGCAGAACGCTCATCACAT 58.188 45.000 0.00 0.00 43.06 3.21 R
3742 4339 0.035176 AGGCATTGGCAAAACGCATT 59.965 45.000 13.20 6.19 45.17 3.56 R
5194 6390 1.669440 GTCTAGTCGTTGGCCACCA 59.331 57.895 3.88 0.00 0.00 4.17 R
5453 6720 4.378774 CCATCTATCAGCTCCTGAAACAG 58.621 47.826 0.00 0.00 44.04 3.16 R
6016 7283 7.759489 AAGGTAAGCAATTCAGTATGTCAAA 57.241 32.000 0.00 0.00 37.40 2.69 R
6019 7286 7.857885 GCATTAAGGTAAGCAATTCAGTATGTC 59.142 37.037 0.00 0.00 37.40 3.06 R
6091 7360 1.812571 CCACATTTTCCCTCTCCAACG 59.187 52.381 0.00 0.00 0.00 4.10 R
7276 8617 1.141019 GGTTAGCGAGCGACATGGA 59.859 57.895 0.00 0.00 0.00 3.41 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
69 70 2.519780 GAACACCGGCCCCACAAA 60.520 61.111 0.00 0.00 0.00 2.83
114 115 2.363018 TCTCCTCCTGTCGCCTGG 60.363 66.667 0.00 0.00 0.00 4.45
356 381 3.068691 CGAGGCCGTCCTTGGAGA 61.069 66.667 0.00 0.00 44.46 3.71
357 382 2.896443 GAGGCCGTCCTTGGAGAG 59.104 66.667 0.00 0.00 44.46 3.20
365 390 1.747552 CGTCCTTGGAGAGATCTCGGA 60.748 57.143 16.97 13.74 43.76 4.55
384 409 3.957591 GAACTAGGGTTCTCCGTCTTT 57.042 47.619 0.00 0.00 45.90 2.52
394 419 0.526524 CTCCGTCTTTAGCTGCGAGG 60.527 60.000 0.00 0.00 0.00 4.63
481 509 8.283291 GTGGTTTTGTCATAGAAGTAGAACAAG 58.717 37.037 0.00 0.00 0.00 3.16
506 534 3.365265 CAACCCTGGCCACTTCGC 61.365 66.667 0.00 0.00 0.00 4.70
517 545 2.076863 GCCACTTCGCTAGTTTGTGAT 58.923 47.619 8.22 0.00 33.85 3.06
522 550 6.622896 GCCACTTCGCTAGTTTGTGATAATTT 60.623 38.462 8.22 0.00 33.85 1.82
529 557 6.398095 GCTAGTTTGTGATAATTTTGGGCTT 58.602 36.000 0.00 0.00 0.00 4.35
544 572 0.686789 GGCTTCCTGGGTGCAATTTT 59.313 50.000 12.36 0.00 0.00 1.82
553 581 1.559149 GGTGCAATTTTGTGCTGCGG 61.559 55.000 0.00 0.00 45.17 5.69
580 608 6.015856 TCACCACATTCGGTTATTTGTTTGAT 60.016 34.615 0.00 0.00 37.07 2.57
599 627 4.717991 TGATACGAATGCAAAAAGGTTCG 58.282 39.130 14.48 14.48 46.29 3.95
629 657 0.459585 TCGTGCGGCTATTTGGAGTC 60.460 55.000 0.00 0.00 0.00 3.36
630 658 0.739462 CGTGCGGCTATTTGGAGTCA 60.739 55.000 0.00 0.00 0.00 3.41
637 665 4.155280 GCGGCTATTTGGAGTCAAGTTTTA 59.845 41.667 0.00 0.00 33.98 1.52
668 702 7.598759 ATGTATAAACCGGAGAGTTATCAGT 57.401 36.000 9.46 0.00 0.00 3.41
684 718 2.027385 TCAGTAGTGATCGATGCTGCT 58.973 47.619 0.54 7.00 0.00 4.24
685 719 2.428530 TCAGTAGTGATCGATGCTGCTT 59.571 45.455 0.54 0.00 0.00 3.91
696 737 1.538687 ATGCTGCTTGAAGGGTTGGC 61.539 55.000 0.00 0.00 0.00 4.52
702 743 1.135402 GCTTGAAGGGTTGGCGTATTG 60.135 52.381 0.00 0.00 0.00 1.90
705 746 3.916359 TGAAGGGTTGGCGTATTGATA 57.084 42.857 0.00 0.00 0.00 2.15
718 759 6.199531 TGGCGTATTGATATTCGAAGTTGTAC 59.800 38.462 3.35 1.69 0.00 2.90
719 760 6.199531 GGCGTATTGATATTCGAAGTTGTACA 59.800 38.462 3.35 0.00 0.00 2.90
726 767 7.327975 TGATATTCGAAGTTGTACAATCAGGT 58.672 34.615 12.26 0.00 0.00 4.00
731 772 5.235616 TCGAAGTTGTACAATCAGGTTGAAC 59.764 40.000 12.26 0.00 40.37 3.18
735 776 5.473504 AGTTGTACAATCAGGTTGAACCATC 59.526 40.000 17.83 0.00 41.95 3.51
744 785 2.370849 AGGTTGAACCATCGGTTACACT 59.629 45.455 17.83 0.00 46.95 3.55
750 796 3.587797 ACCATCGGTTACACTACTGTG 57.412 47.619 0.00 0.00 40.79 3.66
766 812 1.532868 CTGTGTACTGCCAGCAACTTC 59.467 52.381 0.00 0.00 0.00 3.01
818 865 8.969121 TGTGCAACATTAGAATTTTGATGTAG 57.031 30.769 6.79 0.00 45.67 2.74
861 913 8.985315 ATAGTATTTGAGCAGATTGGATTGAA 57.015 30.769 0.00 0.00 0.00 2.69
877 929 5.009911 TGGATTGAATTGTCTTTCTGTGGTG 59.990 40.000 0.00 0.00 0.00 4.17
897 960 2.095263 TGGTTTTCGCTTGCTTATGCTC 60.095 45.455 1.96 0.00 40.48 4.26
901 964 2.099141 TCGCTTGCTTATGCTCAACT 57.901 45.000 1.96 0.00 40.48 3.16
907 970 4.320788 GCTTGCTTATGCTCAACTGACTTT 60.321 41.667 1.96 0.00 40.48 2.66
964 1027 1.074775 ATTTCACTTGCGGAGGCCA 59.925 52.632 5.01 0.00 38.85 5.36
978 1041 1.279271 GAGGCCACCTGACACAGTTAT 59.721 52.381 5.01 0.00 31.76 1.89
980 1043 1.279271 GGCCACCTGACACAGTTATCT 59.721 52.381 0.00 0.00 0.00 1.98
992 1057 4.932200 ACACAGTTATCTTAAGACTGCTGC 59.068 41.667 21.82 0.00 43.44 5.25
1011 1076 6.457355 TGCTGCATACAAAATGTCTGAATTT 58.543 32.000 0.00 0.00 0.00 1.82
1053 1118 2.519013 GGGATAAGGATGCCATGGAAC 58.481 52.381 18.40 5.27 43.03 3.62
1281 1346 4.020218 CAGTTCCCTCAACACTATTCCTCA 60.020 45.833 0.00 0.00 37.48 3.86
1299 1364 8.647256 ATTCCTCAATCTCAGAAAACAATCTT 57.353 30.769 0.00 0.00 0.00 2.40
1314 1379 5.159273 ACAATCTTCCTCCAGAACTCTTC 57.841 43.478 0.00 0.00 0.00 2.87
1732 1797 1.474855 GCAAACAAAAGCCCACCACAT 60.475 47.619 0.00 0.00 0.00 3.21
2021 2146 0.453390 GAGCTGCATTAAGTGTGGCC 59.547 55.000 1.02 0.00 0.00 5.36
2190 2315 9.288576 CATACTATCACAATTATGGGTTCACAT 57.711 33.333 0.00 0.00 34.90 3.21
2299 2637 7.119605 TGAACATTAAGTCATTTTTGCATGC 57.880 32.000 11.82 11.82 0.00 4.06
2476 2815 5.297527 TGCCAAATTGCTCTGAGTACATATG 59.702 40.000 6.53 0.00 0.00 1.78
2622 3154 9.177608 CAGATTGTATCCAAATCCTTAACAGAA 57.822 33.333 0.00 0.00 33.44 3.02
2703 3235 7.226325 GCTGTTAAGTTCTATGATCAGATTGCT 59.774 37.037 0.09 0.00 0.00 3.91
2975 3507 8.068977 GTGTACTGGAGACAACGTCTATATTAG 58.931 40.741 0.00 0.00 43.53 1.73
3021 3553 8.429641 AGTAGAACCAAAAGTCTGAACTAATGA 58.570 33.333 0.00 0.00 33.48 2.57
3047 3579 8.297470 AGAAAGTTTGCACAATCCACATATAT 57.703 30.769 0.00 0.00 0.00 0.86
3143 3680 6.888105 TGTATGGATAGAAATCAGCTTGTCA 58.112 36.000 0.00 0.00 33.41 3.58
3199 3736 8.158169 TCCTTGATTTTGCAGCTATTACTATG 57.842 34.615 0.00 0.00 0.00 2.23
3367 3904 5.013079 ACATGAACTAGATTCCTGACCAACA 59.987 40.000 0.00 0.00 36.66 3.33
3628 4225 2.066262 CACGGTCATTGTGTGGTACTC 58.934 52.381 0.00 0.00 32.68 2.59
3629 4226 1.689813 ACGGTCATTGTGTGGTACTCA 59.310 47.619 0.00 0.00 0.00 3.41
3630 4227 2.301870 ACGGTCATTGTGTGGTACTCAT 59.698 45.455 0.00 0.00 33.25 2.90
3631 4228 3.512329 ACGGTCATTGTGTGGTACTCATA 59.488 43.478 0.00 0.00 33.25 2.15
3632 4229 4.112634 CGGTCATTGTGTGGTACTCATAG 58.887 47.826 0.00 0.00 33.25 2.23
3633 4230 4.381612 CGGTCATTGTGTGGTACTCATAGT 60.382 45.833 0.00 0.00 33.25 2.12
3634 4231 5.488341 GGTCATTGTGTGGTACTCATAGTT 58.512 41.667 0.00 0.00 33.25 2.24
3635 4232 5.581085 GGTCATTGTGTGGTACTCATAGTTC 59.419 44.000 0.00 0.00 33.25 3.01
3636 4233 6.163476 GTCATTGTGTGGTACTCATAGTTCA 58.837 40.000 0.00 0.00 33.25 3.18
3637 4234 6.649141 GTCATTGTGTGGTACTCATAGTTCAA 59.351 38.462 0.00 0.00 33.25 2.69
3638 4235 7.172532 GTCATTGTGTGGTACTCATAGTTCAAA 59.827 37.037 0.00 0.00 33.25 2.69
3639 4236 7.717436 TCATTGTGTGGTACTCATAGTTCAAAA 59.283 33.333 0.00 0.00 33.25 2.44
3640 4237 7.867305 TTGTGTGGTACTCATAGTTCAAAAA 57.133 32.000 0.00 0.00 33.25 1.94
3662 4259 3.509266 GCTAGGCGTTAATTGTGCG 57.491 52.632 0.00 0.00 0.00 5.34
3663 4260 0.725117 GCTAGGCGTTAATTGTGCGT 59.275 50.000 0.00 0.00 0.00 5.24
3664 4261 1.129811 GCTAGGCGTTAATTGTGCGTT 59.870 47.619 0.00 0.00 0.00 4.84
3665 4262 2.413634 GCTAGGCGTTAATTGTGCGTTT 60.414 45.455 0.00 0.00 0.00 3.60
3666 4263 2.785713 AGGCGTTAATTGTGCGTTTT 57.214 40.000 0.00 0.00 0.00 2.43
3667 4264 2.389998 AGGCGTTAATTGTGCGTTTTG 58.610 42.857 0.00 0.00 0.00 2.44
3668 4265 1.136748 GGCGTTAATTGTGCGTTTTGC 60.137 47.619 0.00 0.00 46.70 3.68
3669 4266 1.136748 GCGTTAATTGTGCGTTTTGCC 60.137 47.619 0.00 0.00 45.60 4.52
3670 4267 2.120232 CGTTAATTGTGCGTTTTGCCA 58.880 42.857 0.00 0.00 45.60 4.92
3671 4268 2.097637 CGTTAATTGTGCGTTTTGCCAC 60.098 45.455 0.00 0.00 45.60 5.01
3672 4269 2.141535 TAATTGTGCGTTTTGCCACC 57.858 45.000 0.00 0.00 45.60 4.61
3673 4270 0.873743 AATTGTGCGTTTTGCCACCG 60.874 50.000 0.00 0.00 45.60 4.94
3674 4271 4.560856 TGTGCGTTTTGCCACCGC 62.561 61.111 0.00 0.00 45.60 5.68
3677 4274 4.279043 GCGTTTTGCCACCGCCTT 62.279 61.111 0.00 0.00 41.50 4.35
3678 4275 2.354539 CGTTTTGCCACCGCCTTG 60.355 61.111 0.00 0.00 0.00 3.61
3679 4276 2.661537 GTTTTGCCACCGCCTTGC 60.662 61.111 0.00 0.00 0.00 4.01
3691 4288 3.767287 GCCTTGCGTTTTACTGACC 57.233 52.632 0.00 0.00 0.00 4.02
3692 4289 0.948678 GCCTTGCGTTTTACTGACCA 59.051 50.000 0.00 0.00 0.00 4.02
3693 4290 1.335496 GCCTTGCGTTTTACTGACCAA 59.665 47.619 0.00 0.00 0.00 3.67
3694 4291 2.223618 GCCTTGCGTTTTACTGACCAAA 60.224 45.455 0.00 0.00 0.00 3.28
3695 4292 3.735514 GCCTTGCGTTTTACTGACCAAAA 60.736 43.478 0.00 0.00 0.00 2.44
3696 4293 3.794564 CCTTGCGTTTTACTGACCAAAAC 59.205 43.478 0.00 0.00 40.74 2.43
3701 4298 4.947077 GTTTTACTGACCAAAACGCATG 57.053 40.909 0.00 0.00 36.47 4.06
3702 4299 2.697431 TTACTGACCAAAACGCATGC 57.303 45.000 7.91 7.91 0.00 4.06
3703 4300 1.890876 TACTGACCAAAACGCATGCT 58.109 45.000 17.13 0.00 0.00 3.79
3704 4301 1.032014 ACTGACCAAAACGCATGCTT 58.968 45.000 17.13 2.67 0.00 3.91
3705 4302 2.226330 ACTGACCAAAACGCATGCTTA 58.774 42.857 17.13 0.00 0.00 3.09
3706 4303 2.819608 ACTGACCAAAACGCATGCTTAT 59.180 40.909 17.13 0.00 0.00 1.73
3707 4304 3.173599 CTGACCAAAACGCATGCTTATG 58.826 45.455 17.13 9.30 0.00 1.90
3708 4305 1.919918 GACCAAAACGCATGCTTATGC 59.080 47.619 17.13 2.29 43.72 3.14
3716 4313 2.693797 GCATGCTTATGCGCAGTTAT 57.306 45.000 18.32 0.10 44.10 1.89
3717 4314 2.313234 GCATGCTTATGCGCAGTTATG 58.687 47.619 18.32 15.92 44.10 1.90
3730 4327 3.914555 CAGTTATGCACAGACTAAGCG 57.085 47.619 0.00 0.00 0.00 4.68
3731 4328 3.254060 CAGTTATGCACAGACTAAGCGT 58.746 45.455 0.00 0.00 0.00 5.07
3732 4329 4.421058 CAGTTATGCACAGACTAAGCGTA 58.579 43.478 0.00 0.00 0.00 4.42
3733 4330 4.500837 CAGTTATGCACAGACTAAGCGTAG 59.499 45.833 5.03 5.03 32.03 3.51
3734 4331 4.158025 AGTTATGCACAGACTAAGCGTAGT 59.842 41.667 12.37 12.37 43.56 2.73
3735 4332 3.594603 ATGCACAGACTAAGCGTAGTT 57.405 42.857 13.70 1.80 40.82 2.24
3736 4333 4.713824 ATGCACAGACTAAGCGTAGTTA 57.286 40.909 13.70 0.00 40.82 2.24
3737 4334 4.713824 TGCACAGACTAAGCGTAGTTAT 57.286 40.909 13.70 3.48 40.82 1.89
3738 4335 4.421058 TGCACAGACTAAGCGTAGTTATG 58.579 43.478 13.70 16.32 40.82 1.90
3739 4336 3.243177 GCACAGACTAAGCGTAGTTATGC 59.757 47.826 19.78 19.78 40.82 3.14
3740 4337 3.482472 CACAGACTAAGCGTAGTTATGCG 59.518 47.826 13.70 6.67 40.82 4.73
3758 4355 3.661229 GCAATGCGTTTTGCCAATG 57.339 47.368 11.84 0.00 44.94 2.82
3759 4356 0.453116 GCAATGCGTTTTGCCAATGC 60.453 50.000 11.84 3.48 44.94 3.56
3760 4357 0.166379 CAATGCGTTTTGCCAATGCC 59.834 50.000 7.31 0.00 45.60 4.40
3761 4358 0.035176 AATGCGTTTTGCCAATGCCT 59.965 45.000 7.31 0.00 45.60 4.75
3762 4359 0.894141 ATGCGTTTTGCCAATGCCTA 59.106 45.000 7.31 0.00 45.60 3.93
3763 4360 0.243365 TGCGTTTTGCCAATGCCTAG 59.757 50.000 7.31 0.00 45.60 3.02
3764 4361 0.525761 GCGTTTTGCCAATGCCTAGA 59.474 50.000 0.00 0.00 37.76 2.43
3765 4362 1.468054 GCGTTTTGCCAATGCCTAGAG 60.468 52.381 0.00 0.00 37.76 2.43
3766 4363 1.468054 CGTTTTGCCAATGCCTAGAGC 60.468 52.381 0.00 0.00 44.14 4.09
3767 4364 1.134995 GTTTTGCCAATGCCTAGAGCC 60.135 52.381 0.00 0.00 42.71 4.70
3768 4365 0.332632 TTTGCCAATGCCTAGAGCCT 59.667 50.000 0.00 0.00 42.71 4.58
3769 4366 1.212375 TTGCCAATGCCTAGAGCCTA 58.788 50.000 0.00 0.00 42.71 3.93
3770 4367 0.761187 TGCCAATGCCTAGAGCCTAG 59.239 55.000 0.00 3.06 42.71 3.02
3771 4368 0.036022 GCCAATGCCTAGAGCCTAGG 59.964 60.000 18.85 18.85 42.71 3.02
3772 4369 1.428869 CCAATGCCTAGAGCCTAGGT 58.571 55.000 22.04 7.50 42.71 3.08
3773 4370 1.071385 CCAATGCCTAGAGCCTAGGTG 59.929 57.143 22.04 15.26 42.71 4.00
3774 4371 0.761802 AATGCCTAGAGCCTAGGTGC 59.238 55.000 22.04 13.29 42.71 5.01
3775 4372 1.467678 ATGCCTAGAGCCTAGGTGCG 61.468 60.000 22.04 5.13 42.71 5.34
3776 4373 2.731374 CCTAGAGCCTAGGTGCGC 59.269 66.667 11.31 0.00 36.02 6.09
3777 4374 1.830408 CCTAGAGCCTAGGTGCGCT 60.830 63.158 11.31 6.56 43.95 5.92
3778 4375 1.395826 CCTAGAGCCTAGGTGCGCTT 61.396 60.000 11.31 0.00 41.75 4.68
3779 4376 1.319541 CTAGAGCCTAGGTGCGCTTA 58.680 55.000 11.31 0.00 41.75 3.09
3780 4377 1.681793 CTAGAGCCTAGGTGCGCTTAA 59.318 52.381 11.31 0.00 41.75 1.85
3781 4378 0.461961 AGAGCCTAGGTGCGCTTAAG 59.538 55.000 11.31 0.00 38.26 1.85
3782 4379 1.153349 AGCCTAGGTGCGCTTAAGC 60.153 57.895 17.83 17.83 36.02 3.09
3825 4422 4.893829 TTAACTATGGTGGTACTGCACA 57.106 40.909 4.89 0.00 0.00 4.57
4010 4755 2.095853 GTGTCCACTATTTGATGCGTGG 59.904 50.000 0.00 0.00 46.35 4.94
4297 5043 2.233922 ACCATAGTGTGAAGGTTCCTCG 59.766 50.000 0.00 0.00 0.00 4.63
4658 5845 4.271049 GCGTATACAATGACAAGACTGCAT 59.729 41.667 3.32 0.00 0.00 3.96
4667 5854 1.067516 ACAAGACTGCATTTGTGTGCC 59.932 47.619 9.69 0.00 44.43 5.01
5194 6390 3.119849 GCGCAGAAGTACAATCCACAAAT 60.120 43.478 0.30 0.00 0.00 2.32
5210 6406 1.468520 CAAATGGTGGCCAACGACTAG 59.531 52.381 17.89 0.45 36.95 2.57
5248 6444 9.965748 CCATAAAAAGTACAAAAACACAACAAG 57.034 29.630 0.00 0.00 0.00 3.16
5558 6825 4.979335 TGAGGTACATCCATGTGTTTCAA 58.021 39.130 4.87 0.00 41.89 2.69
6091 7360 6.371809 TGAAACCGCATATTTTAGGATGAC 57.628 37.500 0.00 0.00 0.00 3.06
6158 7427 7.842887 ACCTTCACTTATATCCTACTCCTTC 57.157 40.000 0.00 0.00 0.00 3.46
6420 7702 1.160137 GTGTGCCTTCCAGTGCTTAG 58.840 55.000 0.00 0.00 0.00 2.18
6567 7850 6.605471 TCTCAGGTAATTCTTCTGCACTTA 57.395 37.500 0.00 0.00 0.00 2.24
6628 7956 1.908299 TCTGAACCTGCAGGCTCGA 60.908 57.895 33.06 25.04 39.32 4.04
6770 8098 1.349067 AGCGGTCCAATAGGGGATAC 58.651 55.000 0.00 0.00 39.62 2.24
6773 8101 2.835764 GCGGTCCAATAGGGGATACATA 59.164 50.000 0.00 0.00 39.62 2.29
6774 8102 3.454812 GCGGTCCAATAGGGGATACATAT 59.545 47.826 0.00 0.00 39.62 1.78
6775 8103 4.652421 GCGGTCCAATAGGGGATACATATA 59.348 45.833 0.00 0.00 39.62 0.86
6777 8105 6.741521 GCGGTCCAATAGGGGATACATATATG 60.742 46.154 11.29 11.29 39.62 1.78
6778 8106 6.553476 CGGTCCAATAGGGGATACATATATGA 59.447 42.308 19.63 3.73 39.62 2.15
6779 8107 7.471539 CGGTCCAATAGGGGATACATATATGAC 60.472 44.444 19.63 9.60 39.62 3.06
6780 8108 7.569111 GGTCCAATAGGGGATACATATATGACT 59.431 40.741 19.63 5.68 39.62 3.41
6781 8109 8.643324 GTCCAATAGGGGATACATATATGACTC 58.357 40.741 19.63 13.59 39.62 3.36
6785 8113 6.423358 AGGGGATACATATATGACTCCTGA 57.577 41.667 24.56 5.25 34.56 3.86
6805 8133 1.891150 AGGAGAGCAATTTTGTGCCAG 59.109 47.619 0.00 0.00 46.14 4.85
6814 8142 2.105006 TTTTGTGCCAGCAAAGCAAA 57.895 40.000 0.00 0.00 43.02 3.68
6851 8179 4.392138 GTGGTGTACAGTAAAGAGGCATTC 59.608 45.833 0.00 0.00 0.00 2.67
6858 8186 4.452455 ACAGTAAAGAGGCATTCTTCGTTG 59.548 41.667 3.52 5.26 45.41 4.10
6868 8196 4.088648 GCATTCTTCGTTGGTGTTTATCG 58.911 43.478 0.00 0.00 0.00 2.92
6891 8220 7.623770 TCGTTCTTGTTACTTTGTATTGTGTC 58.376 34.615 0.00 0.00 0.00 3.67
6892 8221 6.568601 CGTTCTTGTTACTTTGTATTGTGTCG 59.431 38.462 0.00 0.00 0.00 4.35
6893 8222 7.515528 CGTTCTTGTTACTTTGTATTGTGTCGA 60.516 37.037 0.00 0.00 0.00 4.20
6894 8223 7.169035 TCTTGTTACTTTGTATTGTGTCGAC 57.831 36.000 9.11 9.11 0.00 4.20
6898 8227 1.127951 CTTTGTATTGTGTCGACCGGC 59.872 52.381 14.12 4.00 0.00 6.13
6902 8231 1.127951 GTATTGTGTCGACCGGCTTTG 59.872 52.381 14.12 0.00 0.00 2.77
6916 8249 1.069227 GGCTTTGTGCTTCGGTTACAG 60.069 52.381 0.00 0.00 42.39 2.74
6942 8275 5.355350 AGTGTAAAAAGGTGCATGCTATCTC 59.645 40.000 20.33 3.89 0.00 2.75
6943 8276 5.355350 GTGTAAAAAGGTGCATGCTATCTCT 59.645 40.000 20.33 6.16 0.00 3.10
6972 8305 5.376854 TTTTTGCAATTCAGGAGCTCTAC 57.623 39.130 14.64 0.00 0.00 2.59
6983 8316 5.510430 TCAGGAGCTCTACAGATTACTCAA 58.490 41.667 14.64 0.00 0.00 3.02
7006 8346 3.752222 TCGTAAAACATTTGCGGGTACAT 59.248 39.130 12.14 0.00 0.00 2.29
7178 8518 4.756084 GCATAGGACATGCAATAACCTC 57.244 45.455 4.41 0.00 44.00 3.85
7179 8519 3.503748 GCATAGGACATGCAATAACCTCC 59.496 47.826 4.41 0.00 44.00 4.30
7180 8520 4.747931 GCATAGGACATGCAATAACCTCCT 60.748 45.833 4.41 0.00 44.00 3.69
7181 8521 3.287867 AGGACATGCAATAACCTCCTG 57.712 47.619 0.00 0.00 0.00 3.86
7182 8522 1.678101 GGACATGCAATAACCTCCTGC 59.322 52.381 0.00 0.00 36.60 4.85
7187 8527 3.213206 TGCAATAACCTCCTGCATAGG 57.787 47.619 12.56 12.56 46.06 2.57
7276 8617 1.066002 CGATTTTGATCCGCTGCCATT 59.934 47.619 0.00 0.00 0.00 3.16
7599 8943 4.593864 GATCGTCGCTGCTCCCCC 62.594 72.222 0.00 0.00 0.00 5.40
7606 8950 2.759795 GCTGCTCCCCCTGTCTTT 59.240 61.111 0.00 0.00 0.00 2.52
7660 9004 2.663602 CCGCATAAGATCGTACATGCTC 59.336 50.000 12.55 0.00 41.25 4.26
7669 9013 4.627467 AGATCGTACATGCTCAAAAGTGAC 59.373 41.667 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 97 2.716017 CCAGGCGACAGGAGGAGAC 61.716 68.421 0.00 0.00 39.95 3.36
312 337 0.523519 GAAAAGGAAAGGCAGGAGCG 59.476 55.000 0.00 0.00 43.41 5.03
348 373 2.383855 AGTTCCGAGATCTCTCCAAGG 58.616 52.381 20.26 13.32 39.79 3.61
365 390 3.195182 GCTAAAGACGGAGAACCCTAGTT 59.805 47.826 0.00 0.00 39.54 2.24
381 406 2.030946 CCGAAAATCCTCGCAGCTAAAG 59.969 50.000 0.00 0.00 37.51 1.85
384 409 0.535335 ACCGAAAATCCTCGCAGCTA 59.465 50.000 0.00 0.00 37.51 3.32
394 419 3.000727 CCACCAGACACTACCGAAAATC 58.999 50.000 0.00 0.00 0.00 2.17
422 447 1.097547 AGATCGCAATTGCTTCCCGG 61.098 55.000 26.86 11.26 39.32 5.73
481 509 0.608035 TGGCCAGGGTTGATTTCGAC 60.608 55.000 0.00 0.00 0.00 4.20
506 534 7.035612 GGAAGCCCAAAATTATCACAAACTAG 58.964 38.462 0.00 0.00 0.00 2.57
517 545 2.534990 CACCCAGGAAGCCCAAAATTA 58.465 47.619 0.00 0.00 33.88 1.40
522 550 2.384933 ATTGCACCCAGGAAGCCCAA 62.385 55.000 0.00 0.00 33.88 4.12
529 557 0.392336 GCACAAAATTGCACCCAGGA 59.608 50.000 0.00 0.00 42.49 3.86
553 581 3.504520 ACAAATAACCGAATGTGGTGACC 59.495 43.478 0.00 0.00 42.89 4.02
599 627 1.129809 CCGCACGAAACGATCACAC 59.870 57.895 0.00 0.00 0.00 3.82
654 688 4.750598 TCGATCACTACTGATAACTCTCCG 59.249 45.833 0.00 0.00 37.24 4.63
668 702 3.451526 CTTCAAGCAGCATCGATCACTA 58.548 45.455 0.00 0.00 0.00 2.74
684 718 2.570415 TCAATACGCCAACCCTTCAA 57.430 45.000 0.00 0.00 0.00 2.69
685 719 2.799126 ATCAATACGCCAACCCTTCA 57.201 45.000 0.00 0.00 0.00 3.02
696 737 9.779237 GATTGTACAACTTCGAATATCAATACG 57.221 33.333 11.22 0.00 0.00 3.06
702 743 7.772332 ACCTGATTGTACAACTTCGAATATC 57.228 36.000 11.22 1.78 0.00 1.63
705 746 5.995282 TCAACCTGATTGTACAACTTCGAAT 59.005 36.000 11.22 0.00 39.54 3.34
718 759 2.436417 ACCGATGGTTCAACCTGATTG 58.564 47.619 8.40 0.00 39.58 2.67
719 760 2.879103 ACCGATGGTTCAACCTGATT 57.121 45.000 8.40 0.00 39.58 2.57
726 767 4.039488 ACAGTAGTGTAACCGATGGTTCAA 59.961 41.667 4.16 0.00 43.05 2.69
744 785 1.691976 AGTTGCTGGCAGTACACAGTA 59.308 47.619 17.16 6.54 37.07 2.74
750 796 2.914379 ACGAAGTTGCTGGCAGTAC 58.086 52.632 17.16 14.26 37.78 2.73
766 812 6.821665 TCCTAGAATCCTATTTCACCAAAACG 59.178 38.462 0.00 0.00 0.00 3.60
832 879 7.365497 TCCAATCTGCTCAAATACTATCTGA 57.635 36.000 0.00 0.00 0.00 3.27
833 880 8.504815 CAATCCAATCTGCTCAAATACTATCTG 58.495 37.037 0.00 0.00 0.00 2.90
835 882 8.613060 TCAATCCAATCTGCTCAAATACTATC 57.387 34.615 0.00 0.00 0.00 2.08
861 913 4.202010 CGAAAACCACCACAGAAAGACAAT 60.202 41.667 0.00 0.00 0.00 2.71
877 929 2.095263 TGAGCATAAGCAAGCGAAAACC 60.095 45.455 0.00 0.00 45.49 3.27
901 964 6.936335 TCAGATCAATAGCAAGTGAAAAGTCA 59.064 34.615 0.00 0.00 32.66 3.41
907 970 7.543172 GCAAATTTCAGATCAATAGCAAGTGAA 59.457 33.333 0.00 0.00 32.66 3.18
964 1027 6.692486 CAGTCTTAAGATAACTGTGTCAGGT 58.308 40.000 8.75 0.00 36.50 4.00
978 1041 6.430925 ACATTTTGTATGCAGCAGTCTTAAGA 59.569 34.615 0.00 0.00 0.00 2.10
980 1043 6.430925 AGACATTTTGTATGCAGCAGTCTTAA 59.569 34.615 0.00 0.00 30.32 1.85
992 1057 8.857216 GCTCAAGAAATTCAGACATTTTGTATG 58.143 33.333 0.00 0.00 40.66 2.39
1053 1118 2.420022 CTCCTTTGTGCCTGGAATAACG 59.580 50.000 0.00 0.00 0.00 3.18
1281 1346 6.546484 TGGAGGAAGATTGTTTTCTGAGATT 58.454 36.000 0.00 0.00 0.00 2.40
1299 1364 1.433199 TGAGGGAAGAGTTCTGGAGGA 59.567 52.381 0.00 0.00 0.00 3.71
1314 1379 6.776116 TGTACTCAATAGTGGTATACTGAGGG 59.224 42.308 17.17 1.01 40.65 4.30
1732 1797 3.051650 TCCCTAGTTCCAGCTATAACCCA 60.052 47.826 6.71 0.00 0.00 4.51
2021 2146 2.411765 AAACCCCCAAGAGACTGGCG 62.412 60.000 0.00 0.00 34.88 5.69
2190 2315 6.605594 ACCTTTCCAGTTTCACATCTAAACAA 59.394 34.615 0.00 0.00 38.92 2.83
2308 2647 2.136298 TGTCACAAAGCAAAGGTGGA 57.864 45.000 0.00 0.00 33.45 4.02
2309 2648 2.957491 TTGTCACAAAGCAAAGGTGG 57.043 45.000 0.00 0.00 33.45 4.61
2570 2909 1.812235 TTGCAGAACGCTCATCACAT 58.188 45.000 0.00 0.00 43.06 3.21
2579 2918 5.050837 ACAATCTGAAAATTTTGCAGAACGC 60.051 36.000 21.01 6.24 41.48 4.84
2622 3154 2.290641 GTCTTTGTGTGAGCGAATTGGT 59.709 45.455 0.00 0.00 0.00 3.67
2825 3357 8.755028 TGTATATGCTAGGAAACAGTTTACAGA 58.245 33.333 11.04 0.00 0.00 3.41
2931 3463 7.174946 CCAGTACACAACTTTGATCATACCTTT 59.825 37.037 0.00 0.00 35.76 3.11
2975 3507 3.317993 ACTGGTTGGTGCATGAAACTTAC 59.682 43.478 0.00 0.00 0.00 2.34
3021 3553 4.734398 TGTGGATTGTGCAAACTTTCTT 57.266 36.364 0.00 0.00 0.00 2.52
3047 3579 8.668353 GCTTGTCATTATAGACATCTGTTGAAA 58.332 33.333 0.00 0.00 46.90 2.69
3199 3736 2.097791 CGGTTCTAGCTACACACCTCTC 59.902 54.545 8.82 0.00 0.00 3.20
3301 3838 5.461526 GCTGATATCTGACGCACTAACATA 58.538 41.667 13.33 0.00 0.00 2.29
3367 3904 6.720112 AATTTGCATTATGGTGATACTGCT 57.280 33.333 0.00 0.00 40.01 4.24
3441 3978 7.545965 ACTCACACAAATACACAGTAATAGCTC 59.454 37.037 0.00 0.00 0.00 4.09
3550 4147 3.449737 GTGGTCCTATTACACAGCCACTA 59.550 47.826 0.00 0.00 40.99 2.74
3644 4241 0.725117 ACGCACAATTAACGCCTAGC 59.275 50.000 0.00 0.00 0.00 3.42
3645 4242 3.465122 AAACGCACAATTAACGCCTAG 57.535 42.857 0.00 0.00 0.00 3.02
3646 4243 3.556513 CAAAACGCACAATTAACGCCTA 58.443 40.909 0.00 0.00 0.00 3.93
3647 4244 2.389998 CAAAACGCACAATTAACGCCT 58.610 42.857 0.00 0.00 0.00 5.52
3648 4245 1.136748 GCAAAACGCACAATTAACGCC 60.137 47.619 0.00 0.00 41.79 5.68
3649 4246 1.136748 GGCAAAACGCACAATTAACGC 60.137 47.619 0.00 0.00 45.17 4.84
3650 4247 2.097637 GTGGCAAAACGCACAATTAACG 60.098 45.455 0.00 0.00 45.17 3.18
3651 4248 2.219903 GGTGGCAAAACGCACAATTAAC 59.780 45.455 0.00 0.00 45.17 2.01
3652 4249 2.474816 GGTGGCAAAACGCACAATTAA 58.525 42.857 0.00 0.00 45.17 1.40
3653 4250 1.600663 CGGTGGCAAAACGCACAATTA 60.601 47.619 0.00 0.00 45.17 1.40
3654 4251 0.873743 CGGTGGCAAAACGCACAATT 60.874 50.000 0.00 0.00 45.17 2.32
3655 4252 1.299773 CGGTGGCAAAACGCACAAT 60.300 52.632 0.00 0.00 45.17 2.71
3656 4253 2.103143 CGGTGGCAAAACGCACAA 59.897 55.556 0.00 0.00 45.17 3.33
3661 4258 2.354539 CAAGGCGGTGGCAAAACG 60.355 61.111 0.00 0.00 42.47 3.60
3662 4259 2.661537 GCAAGGCGGTGGCAAAAC 60.662 61.111 0.00 0.00 42.47 2.43
3673 4270 0.948678 TGGTCAGTAAAACGCAAGGC 59.051 50.000 0.00 0.00 46.39 4.35
3674 4271 3.701532 TTTGGTCAGTAAAACGCAAGG 57.298 42.857 0.00 0.00 46.39 3.61
3680 4277 3.181575 GCATGCGTTTTGGTCAGTAAAAC 59.818 43.478 0.00 0.00 41.97 2.43
3681 4278 3.067461 AGCATGCGTTTTGGTCAGTAAAA 59.933 39.130 13.01 0.00 0.00 1.52
3682 4279 2.621055 AGCATGCGTTTTGGTCAGTAAA 59.379 40.909 13.01 0.00 0.00 2.01
3683 4280 2.226330 AGCATGCGTTTTGGTCAGTAA 58.774 42.857 13.01 0.00 0.00 2.24
3684 4281 1.890876 AGCATGCGTTTTGGTCAGTA 58.109 45.000 13.01 0.00 0.00 2.74
3685 4282 1.032014 AAGCATGCGTTTTGGTCAGT 58.968 45.000 13.01 0.00 0.00 3.41
3686 4283 2.987413 TAAGCATGCGTTTTGGTCAG 57.013 45.000 12.39 0.00 0.00 3.51
3687 4284 3.214697 CATAAGCATGCGTTTTGGTCA 57.785 42.857 12.39 0.00 0.00 4.02
3698 4295 2.313234 GCATAACTGCGCATAAGCATG 58.687 47.619 12.24 11.51 46.97 4.06
3699 4296 2.693797 GCATAACTGCGCATAAGCAT 57.306 45.000 12.24 0.00 46.97 3.79
3710 4307 3.254060 ACGCTTAGTCTGTGCATAACTG 58.746 45.455 8.38 0.00 0.00 3.16
3711 4308 3.594603 ACGCTTAGTCTGTGCATAACT 57.405 42.857 0.00 0.00 0.00 2.24
3712 4309 4.421948 ACTACGCTTAGTCTGTGCATAAC 58.578 43.478 0.00 0.00 32.67 1.89
3713 4310 4.713824 ACTACGCTTAGTCTGTGCATAA 57.286 40.909 0.00 0.00 32.67 1.90
3714 4311 4.713824 AACTACGCTTAGTCTGTGCATA 57.286 40.909 3.00 0.00 37.59 3.14
3715 4312 3.594603 AACTACGCTTAGTCTGTGCAT 57.405 42.857 3.00 0.00 37.59 3.96
3716 4313 4.421058 CATAACTACGCTTAGTCTGTGCA 58.579 43.478 3.00 0.00 37.59 4.57
3717 4314 3.243177 GCATAACTACGCTTAGTCTGTGC 59.757 47.826 14.36 14.36 37.59 4.57
3718 4315 3.482472 CGCATAACTACGCTTAGTCTGTG 59.518 47.826 3.00 7.51 37.59 3.66
3719 4316 3.692576 CGCATAACTACGCTTAGTCTGT 58.307 45.455 3.00 0.00 37.59 3.41
3741 4338 0.166379 GGCATTGGCAAAACGCATTG 59.834 50.000 17.69 6.25 45.17 2.82
3742 4339 0.035176 AGGCATTGGCAAAACGCATT 59.965 45.000 13.20 6.19 45.17 3.56
3743 4340 0.894141 TAGGCATTGGCAAAACGCAT 59.106 45.000 13.20 14.33 45.17 4.73
3744 4341 0.243365 CTAGGCATTGGCAAAACGCA 59.757 50.000 13.20 2.13 45.17 5.24
3745 4342 0.525761 TCTAGGCATTGGCAAAACGC 59.474 50.000 13.20 7.57 43.71 4.84
3746 4343 1.468054 GCTCTAGGCATTGGCAAAACG 60.468 52.381 13.20 0.00 43.71 3.60
3747 4344 1.134995 GGCTCTAGGCATTGGCAAAAC 60.135 52.381 13.20 0.00 43.71 2.43
3748 4345 1.185315 GGCTCTAGGCATTGGCAAAA 58.815 50.000 13.20 0.00 43.71 2.44
3749 4346 0.332632 AGGCTCTAGGCATTGGCAAA 59.667 50.000 13.20 0.00 43.71 3.68
3750 4347 1.141657 CTAGGCTCTAGGCATTGGCAA 59.858 52.381 13.20 0.68 43.71 4.52
3751 4348 0.761187 CTAGGCTCTAGGCATTGGCA 59.239 55.000 13.20 0.00 43.71 4.92
3752 4349 0.036022 CCTAGGCTCTAGGCATTGGC 59.964 60.000 13.35 1.17 40.17 4.52
3754 4351 1.542108 GCACCTAGGCTCTAGGCATTG 60.542 57.143 21.59 15.68 44.01 2.82
3755 4352 0.761802 GCACCTAGGCTCTAGGCATT 59.238 55.000 21.59 6.24 44.01 3.56
3756 4353 1.467678 CGCACCTAGGCTCTAGGCAT 61.468 60.000 21.59 6.80 44.01 4.40
3757 4354 2.127869 CGCACCTAGGCTCTAGGCA 61.128 63.158 21.59 0.00 44.01 4.75
3758 4355 2.731374 CGCACCTAGGCTCTAGGC 59.269 66.667 21.59 0.69 38.25 3.93
3759 4356 1.395826 AAGCGCACCTAGGCTCTAGG 61.396 60.000 20.58 20.58 38.88 3.02
3760 4357 1.319541 TAAGCGCACCTAGGCTCTAG 58.680 55.000 11.47 0.00 38.88 2.43
3761 4358 1.681793 CTTAAGCGCACCTAGGCTCTA 59.318 52.381 11.47 0.00 38.88 2.43
3762 4359 0.461961 CTTAAGCGCACCTAGGCTCT 59.538 55.000 11.47 0.00 38.88 4.09
3763 4360 1.154814 GCTTAAGCGCACCTAGGCTC 61.155 60.000 12.53 0.00 38.88 4.70
3764 4361 1.153349 GCTTAAGCGCACCTAGGCT 60.153 57.895 12.53 0.00 42.33 4.58
3765 4362 3.410958 GCTTAAGCGCACCTAGGC 58.589 61.111 12.53 6.35 0.00 3.93
3801 4398 6.062749 TGTGCAGTACCACCATAGTTAAAAA 58.937 36.000 0.00 0.00 34.85 1.94
3802 4399 5.622180 TGTGCAGTACCACCATAGTTAAAA 58.378 37.500 0.00 0.00 34.85 1.52
3803 4400 5.230323 TGTGCAGTACCACCATAGTTAAA 57.770 39.130 0.00 0.00 34.85 1.52
3804 4401 4.893829 TGTGCAGTACCACCATAGTTAA 57.106 40.909 0.00 0.00 34.85 2.01
3805 4402 4.383661 CCATGTGCAGTACCACCATAGTTA 60.384 45.833 0.00 0.00 34.85 2.24
3806 4403 3.609853 CATGTGCAGTACCACCATAGTT 58.390 45.455 0.00 0.00 34.85 2.24
3807 4404 2.092968 CCATGTGCAGTACCACCATAGT 60.093 50.000 0.00 0.00 34.85 2.12
3808 4405 2.564771 CCATGTGCAGTACCACCATAG 58.435 52.381 0.00 0.00 34.85 2.23
3809 4406 1.408127 GCCATGTGCAGTACCACCATA 60.408 52.381 0.00 0.00 40.77 2.74
3810 4407 0.680921 GCCATGTGCAGTACCACCAT 60.681 55.000 0.00 0.00 40.77 3.55
3811 4408 1.303236 GCCATGTGCAGTACCACCA 60.303 57.895 0.00 0.00 40.77 4.17
3812 4409 3.590824 GCCATGTGCAGTACCACC 58.409 61.111 0.00 0.00 40.77 4.61
4010 4755 6.694411 CAGACAAAATAACCATGCATCTAAGC 59.306 38.462 0.00 0.00 0.00 3.09
4049 4794 5.634859 CACCAACCTGAAAATCAAGCATAAC 59.365 40.000 0.00 0.00 0.00 1.89
4288 5034 6.911250 ATGGAAATTTTAAACGAGGAACCT 57.089 33.333 0.00 0.00 0.00 3.50
4658 5845 3.793801 GCAACATTAGAACGGCACACAAA 60.794 43.478 0.00 0.00 0.00 2.83
4667 5854 5.450376 ACGATAACTGCAACATTAGAACG 57.550 39.130 0.00 0.00 0.00 3.95
4894 6089 8.922676 CAGAATCAGATTGTTTGGAAAATTGAG 58.077 33.333 0.00 0.00 0.00 3.02
5194 6390 1.669440 GTCTAGTCGTTGGCCACCA 59.331 57.895 3.88 0.00 0.00 4.17
5248 6444 9.399403 CTAAGTTAAGCTTTCCATTCAGTTTTC 57.601 33.333 3.20 0.00 38.57 2.29
5453 6720 4.378774 CCATCTATCAGCTCCTGAAACAG 58.621 47.826 0.00 0.00 44.04 3.16
6016 7283 7.759489 AAGGTAAGCAATTCAGTATGTCAAA 57.241 32.000 0.00 0.00 37.40 2.69
6019 7286 7.857885 GCATTAAGGTAAGCAATTCAGTATGTC 59.142 37.037 0.00 0.00 37.40 3.06
6091 7360 1.812571 CCACATTTTCCCTCTCCAACG 59.187 52.381 0.00 0.00 0.00 4.10
6202 7471 4.022849 CCAACAAAAGGATCTTGTCAGGAC 60.023 45.833 10.06 0.00 35.98 3.85
6628 7956 7.003402 TGGATTTAGCTTTGCCAGTAAAAAT 57.997 32.000 0.00 0.00 0.00 1.82
6779 8107 6.159693 GCACAAAATTGCTCTCCTCAGGAG 62.160 50.000 15.56 15.56 40.89 3.69
6780 8108 3.415212 CACAAAATTGCTCTCCTCAGGA 58.585 45.455 0.00 0.00 0.00 3.86
6781 8109 2.094854 GCACAAAATTGCTCTCCTCAGG 60.095 50.000 0.00 0.00 39.59 3.86
6785 8113 1.891150 CTGGCACAAAATTGCTCTCCT 59.109 47.619 0.00 0.00 42.56 3.69
6805 8133 3.846360 AGAGATGATTGCTTTGCTTTGC 58.154 40.909 0.00 0.00 0.00 3.68
6814 8142 3.430042 ACACCACAAGAGATGATTGCT 57.570 42.857 0.00 0.00 0.00 3.91
6851 8179 4.985044 AGAACGATAAACACCAACGAAG 57.015 40.909 0.00 0.00 0.00 3.79
6858 8186 7.412063 ACAAAGTAACAAGAACGATAAACACC 58.588 34.615 0.00 0.00 0.00 4.16
6868 8196 7.581600 GTCGACACAATACAAAGTAACAAGAAC 59.418 37.037 11.55 0.00 0.00 3.01
6898 8227 3.560068 ACTTCTGTAACCGAAGCACAAAG 59.440 43.478 5.92 0.00 41.13 2.77
6902 8231 2.480845 ACACTTCTGTAACCGAAGCAC 58.519 47.619 5.92 0.00 41.13 4.40
6916 8249 4.243007 AGCATGCACCTTTTTACACTTC 57.757 40.909 21.98 0.00 0.00 3.01
6972 8305 8.788813 GCAAATGTTTTACGATTGAGTAATCTG 58.211 33.333 0.00 0.00 40.43 2.90
6983 8316 3.752222 TGTACCCGCAAATGTTTTACGAT 59.248 39.130 0.00 0.00 0.00 3.73
7006 8346 6.940739 TCAACTTTGTTCCAAATTTTCTCCA 58.059 32.000 0.00 0.00 0.00 3.86
7032 8372 2.352421 GGTTCGTCGGAGATGTCTTTGA 60.352 50.000 0.00 0.00 45.22 2.69
7167 8507 2.777114 TCCTATGCAGGAGGTTATTGCA 59.223 45.455 15.30 0.53 46.58 4.08
7168 8508 3.492102 TCCTATGCAGGAGGTTATTGC 57.508 47.619 15.30 0.00 46.58 3.56
7181 8521 4.096984 GGGCTAATATTGCATGTCCTATGC 59.903 45.833 5.00 5.00 44.76 3.14
7182 8522 5.503927 AGGGCTAATATTGCATGTCCTATG 58.496 41.667 0.00 0.00 0.00 2.23
7183 8523 5.786121 AGGGCTAATATTGCATGTCCTAT 57.214 39.130 0.00 0.00 0.00 2.57
7184 8524 5.582950 AAGGGCTAATATTGCATGTCCTA 57.417 39.130 0.00 0.00 0.00 2.94
7185 8525 4.459852 AAGGGCTAATATTGCATGTCCT 57.540 40.909 0.00 0.00 0.00 3.85
7186 8526 4.584325 TGAAAGGGCTAATATTGCATGTCC 59.416 41.667 0.00 0.00 0.00 4.02
7187 8527 5.772825 TGAAAGGGCTAATATTGCATGTC 57.227 39.130 0.00 0.00 0.00 3.06
7188 8528 6.543430 TTTGAAAGGGCTAATATTGCATGT 57.457 33.333 0.00 0.00 0.00 3.21
7189 8529 6.073440 GCATTTGAAAGGGCTAATATTGCATG 60.073 38.462 0.00 0.00 0.00 4.06
7230 8570 4.202182 ACTGATGCTTTGCAAGTTGTCAAT 60.202 37.500 4.48 0.00 43.62 2.57
7276 8617 1.141019 GGTTAGCGAGCGACATGGA 59.859 57.895 0.00 0.00 0.00 3.41
7599 8943 2.437850 GCGCAATGCCAAAAGACAG 58.562 52.632 0.30 0.00 37.76 3.51
7660 9004 3.146847 GAGGTAAGGTGGGTCACTTTTG 58.853 50.000 1.01 0.00 35.40 2.44
7669 9013 2.047830 GATACAGGGAGGTAAGGTGGG 58.952 57.143 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.