Multiple sequence alignment - TraesCS2B01G171200

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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 TraesCS2B01G171200 chr2B 100.000 3817 0 0 1 3817 144434982 144431166 0.000000e+00 7049.0
1 TraesCS2B01G171200 chr2B 74.253 435 81 22 213 632 532160294 532159876 1.840000e-33 154.0
2 TraesCS2B01G171200 chr2B 94.737 38 1 1 3781 3817 694132604 694132641 1.480000e-04 58.4
3 TraesCS2B01G171200 chr2D 93.585 2307 92 26 752 3018 92921399 92919109 0.000000e+00 3389.0
4 TraesCS2B01G171200 chr2D 91.547 698 38 13 3082 3766 92918991 92918302 0.000000e+00 942.0
5 TraesCS2B01G171200 chr2D 72.425 602 112 40 4 581 452379835 452379264 3.970000e-30 143.0
6 TraesCS2B01G171200 chr2A 91.524 2277 116 36 656 2887 90597422 90595178 0.000000e+00 3064.0
7 TraesCS2B01G171200 chr2A 91.691 698 35 17 3082 3766 90594004 90593317 0.000000e+00 946.0
8 TraesCS2B01G171200 chr2A 91.034 145 5 3 2882 3018 90594405 90594261 5.030000e-44 189.0
9 TraesCS2B01G171200 chr2A 100.000 28 0 0 3017 3044 333342421 333342394 7.000000e-03 52.8
10 TraesCS2B01G171200 chr2A 100.000 28 0 0 3017 3044 333354417 333354390 7.000000e-03 52.8
11 TraesCS2B01G171200 chr4B 77.430 607 99 23 6 583 656977950 656978547 1.020000e-85 327.0
12 TraesCS2B01G171200 chr3B 79.947 374 57 12 219 581 479492878 479492512 3.780000e-65 259.0
13 TraesCS2B01G171200 chr3B 82.449 245 37 4 298 541 578226035 578226274 3.860000e-50 209.0
14 TraesCS2B01G171200 chr3B 83.088 136 15 7 222 356 50063841 50063969 2.410000e-22 117.0
15 TraesCS2B01G171200 chr3D 75.714 560 101 24 6 548 18484413 18484954 8.190000e-62 248.0
16 TraesCS2B01G171200 chr3D 100.000 28 0 0 3790 3817 518062403 518062376 7.000000e-03 52.8
17 TraesCS2B01G171200 chr6B 78.273 359 66 11 1637 1989 200009040 200008688 1.790000e-53 220.0
18 TraesCS2B01G171200 chr6B 86.264 182 25 0 2327 2508 200006150 200005969 8.360000e-47 198.0
19 TraesCS2B01G171200 chr6B 100.000 28 0 0 3790 3817 277616126 277616153 7.000000e-03 52.8
20 TraesCS2B01G171200 chr6D 86.264 182 25 0 2327 2508 111059581 111059400 8.360000e-47 198.0
21 TraesCS2B01G171200 chr6D 94.737 38 1 1 3781 3817 467012232 467012195 1.480000e-04 58.4
22 TraesCS2B01G171200 chr6A 86.264 182 25 0 2327 2508 135558770 135558589 8.360000e-47 198.0
23 TraesCS2B01G171200 chr4D 75.581 430 84 20 4 423 40825790 40825372 3.890000e-45 193.0
24 TraesCS2B01G171200 chr7D 72.742 631 127 36 1031 1631 593368960 593369575 1.820000e-38 171.0
25 TraesCS2B01G171200 chr1D 94.737 38 1 1 3781 3817 242331214 242331251 1.480000e-04 58.4
26 TraesCS2B01G171200 chr1D 100.000 28 0 0 3790 3817 488960358 488960331 7.000000e-03 52.8
27 TraesCS2B01G171200 chr1A 94.737 38 1 1 3781 3817 168817910 168817873 1.480000e-04 58.4
28 TraesCS2B01G171200 chr1A 100.000 28 0 0 3017 3044 561333799 561333772 7.000000e-03 52.8
29 TraesCS2B01G171200 chr5B 100.000 28 0 0 3017 3044 591582615 591582642 7.000000e-03 52.8
30 TraesCS2B01G171200 chr5B 100.000 28 0 0 3017 3044 594135899 594135872 7.000000e-03 52.8
31 TraesCS2B01G171200 chr1B 100.000 28 0 0 3017 3044 17382330 17382303 7.000000e-03 52.8


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 TraesCS2B01G171200 chr2B 144431166 144434982 3816 True 7049.000000 7049 100.000000 1 3817 1 chr2B.!!$R1 3816
1 TraesCS2B01G171200 chr2D 92918302 92921399 3097 True 2165.500000 3389 92.566000 752 3766 2 chr2D.!!$R2 3014
2 TraesCS2B01G171200 chr2A 90593317 90597422 4105 True 1399.666667 3064 91.416333 656 3766 3 chr2A.!!$R3 3110
3 TraesCS2B01G171200 chr4B 656977950 656978547 597 False 327.000000 327 77.430000 6 583 1 chr4B.!!$F1 577
4 TraesCS2B01G171200 chr3D 18484413 18484954 541 False 248.000000 248 75.714000 6 548 1 chr3D.!!$F1 542
5 TraesCS2B01G171200 chr6B 200005969 200009040 3071 True 209.000000 220 82.268500 1637 2508 2 chr6B.!!$R1 871

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
801 831 0.041386 GGACCTGGTCTAGTCACCCT 59.959 60.0 25.01 0.0 35.26 4.34 F
2513 4777 0.109412 GTCGTCCCGTGAGTACCAAG 60.109 60.0 0.00 0.0 0.00 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2572 4858 0.530870 GGTCAAGATAGCCTGCCGTC 60.531 60.000 0.0 0.0 0.0 4.79 R
3487 6788 2.502947 TGCCTACAAGAGCTGATGATGT 59.497 45.455 0.0 0.0 0.0 3.06 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
28 29 6.663523 TCCCTAATTTTCAAGTTCTCCCATTC 59.336 38.462 0.00 0.00 0.00 2.67
33 34 7.938140 ATTTTCAAGTTCTCCCATTCGATTA 57.062 32.000 0.00 0.00 0.00 1.75
41 42 7.574607 AGTTCTCCCATTCGATTAAGGTATTT 58.425 34.615 0.00 0.00 0.00 1.40
44 45 9.908747 TTCTCCCATTCGATTAAGGTATTTAAA 57.091 29.630 0.00 0.00 35.03 1.52
68 69 8.620116 AATTTGGATTTGGTTCACTATTTTGG 57.380 30.769 0.00 0.00 0.00 3.28
69 70 6.739331 TTGGATTTGGTTCACTATTTTGGT 57.261 33.333 0.00 0.00 0.00 3.67
70 71 6.739331 TGGATTTGGTTCACTATTTTGGTT 57.261 33.333 0.00 0.00 0.00 3.67
71 72 6.520272 TGGATTTGGTTCACTATTTTGGTTG 58.480 36.000 0.00 0.00 0.00 3.77
78 79 5.286438 GTTCACTATTTTGGTTGGGTCAAC 58.714 41.667 2.46 2.46 42.89 3.18
85 86 8.364894 ACTATTTTGGTTGGGTCAACTATTTTC 58.635 33.333 10.10 0.00 43.14 2.29
91 92 6.100424 TGGTTGGGTCAACTATTTTCCAAATT 59.900 34.615 10.10 0.00 43.14 1.82
118 119 2.094234 GCAACAACCGGCCTATGAAAAT 60.094 45.455 0.00 0.00 0.00 1.82
119 120 3.769536 CAACAACCGGCCTATGAAAATC 58.230 45.455 0.00 0.00 0.00 2.17
120 121 2.375146 ACAACCGGCCTATGAAAATCC 58.625 47.619 0.00 0.00 0.00 3.01
121 122 1.681264 CAACCGGCCTATGAAAATCCC 59.319 52.381 0.00 0.00 0.00 3.85
122 123 0.923358 ACCGGCCTATGAAAATCCCA 59.077 50.000 0.00 0.00 0.00 4.37
125 126 1.676006 CGGCCTATGAAAATCCCACAC 59.324 52.381 0.00 0.00 0.00 3.82
126 127 2.733956 GGCCTATGAAAATCCCACACA 58.266 47.619 0.00 0.00 0.00 3.72
135 145 4.104102 TGAAAATCCCACACACCTCTTACT 59.896 41.667 0.00 0.00 0.00 2.24
168 182 7.944729 AAAAGAGCCAACATGTGATAATACT 57.055 32.000 0.00 0.00 0.00 2.12
169 183 9.461312 AAAAAGAGCCAACATGTGATAATACTA 57.539 29.630 0.00 0.00 0.00 1.82
170 184 9.632638 AAAAGAGCCAACATGTGATAATACTAT 57.367 29.630 0.00 0.00 0.00 2.12
174 188 7.679783 AGCCAACATGTGATAATACTATAGCA 58.320 34.615 0.00 0.00 0.00 3.49
175 189 7.604164 AGCCAACATGTGATAATACTATAGCAC 59.396 37.037 0.00 0.00 41.39 4.40
235 253 6.834168 ACACAAAAGTATGGGTTGATTAGG 57.166 37.500 0.00 0.00 31.37 2.69
244 262 8.511748 AGTATGGGTTGATTAGGAGATAACAT 57.488 34.615 0.00 0.00 0.00 2.71
245 263 8.598041 AGTATGGGTTGATTAGGAGATAACATC 58.402 37.037 0.00 0.00 0.00 3.06
246 264 6.823286 TGGGTTGATTAGGAGATAACATCA 57.177 37.500 0.00 0.00 0.00 3.07
258 276 7.275920 AGGAGATAACATCAAATCACACTACC 58.724 38.462 0.00 0.00 0.00 3.18
279 297 0.544697 AAGGCCTACCATAACACCGG 59.455 55.000 5.16 0.00 39.06 5.28
339 358 3.074412 CACTCGCCAAACCAAATACTCT 58.926 45.455 0.00 0.00 0.00 3.24
342 361 4.003648 CTCGCCAAACCAAATACTCTCTT 58.996 43.478 0.00 0.00 0.00 2.85
348 367 7.521585 CGCCAAACCAAATACTCTCTTAGTTTT 60.522 37.037 0.00 0.00 39.80 2.43
414 433 2.614057 AGTTTTGACCAAGTTCAGAGCG 59.386 45.455 0.00 0.00 0.00 5.03
415 434 1.593196 TTTGACCAAGTTCAGAGCGG 58.407 50.000 0.00 0.00 0.00 5.52
420 439 1.947456 ACCAAGTTCAGAGCGGAAAAC 59.053 47.619 0.00 0.00 0.00 2.43
423 442 3.365364 CCAAGTTCAGAGCGGAAAACATC 60.365 47.826 0.00 0.00 0.00 3.06
424 443 3.409026 AGTTCAGAGCGGAAAACATCT 57.591 42.857 0.00 0.00 0.00 2.90
440 459 8.827677 GGAAAACATCTACATCCACAATACTAC 58.172 37.037 0.00 0.00 0.00 2.73
616 646 7.915293 ACATCACGAAATTCTAATAACACCA 57.085 32.000 0.00 0.00 0.00 4.17
617 647 8.330466 ACATCACGAAATTCTAATAACACCAA 57.670 30.769 0.00 0.00 0.00 3.67
618 648 8.234546 ACATCACGAAATTCTAATAACACCAAC 58.765 33.333 0.00 0.00 0.00 3.77
619 649 7.731882 TCACGAAATTCTAATAACACCAACA 57.268 32.000 0.00 0.00 0.00 3.33
620 650 7.802738 TCACGAAATTCTAATAACACCAACAG 58.197 34.615 0.00 0.00 0.00 3.16
621 651 6.523201 CACGAAATTCTAATAACACCAACAGC 59.477 38.462 0.00 0.00 0.00 4.40
622 652 5.732647 CGAAATTCTAATAACACCAACAGCG 59.267 40.000 0.00 0.00 0.00 5.18
623 653 4.616181 ATTCTAATAACACCAACAGCGC 57.384 40.909 0.00 0.00 0.00 5.92
624 654 3.046968 TCTAATAACACCAACAGCGCA 57.953 42.857 11.47 0.00 0.00 6.09
625 655 3.000041 TCTAATAACACCAACAGCGCAG 59.000 45.455 11.47 3.33 0.00 5.18
639 669 4.062183 GCAGCAAAGCGCATGTAC 57.938 55.556 11.47 0.00 46.13 2.90
640 670 1.514873 GCAGCAAAGCGCATGTACC 60.515 57.895 11.47 0.00 46.13 3.34
641 671 1.875262 CAGCAAAGCGCATGTACCA 59.125 52.632 11.47 0.00 46.13 3.25
642 672 0.452987 CAGCAAAGCGCATGTACCAT 59.547 50.000 11.47 0.00 46.13 3.55
643 673 1.670295 CAGCAAAGCGCATGTACCATA 59.330 47.619 11.47 0.00 46.13 2.74
644 674 1.670811 AGCAAAGCGCATGTACCATAC 59.329 47.619 11.47 0.00 46.13 2.39
645 675 1.268539 GCAAAGCGCATGTACCATACC 60.269 52.381 11.47 0.00 41.79 2.73
646 676 1.003972 CAAAGCGCATGTACCATACCG 60.004 52.381 11.47 0.00 0.00 4.02
647 677 1.157870 AAGCGCATGTACCATACCGC 61.158 55.000 11.47 11.22 37.21 5.68
648 678 2.604174 GCGCATGTACCATACCGCC 61.604 63.158 0.30 0.00 33.01 6.13
649 679 1.959226 CGCATGTACCATACCGCCC 60.959 63.158 0.00 0.00 0.00 6.13
650 680 1.959226 GCATGTACCATACCGCCCG 60.959 63.158 0.00 0.00 0.00 6.13
651 681 1.959226 CATGTACCATACCGCCCGC 60.959 63.158 0.00 0.00 0.00 6.13
652 682 3.509137 ATGTACCATACCGCCCGCG 62.509 63.158 0.00 0.00 39.44 6.46
653 683 4.211502 GTACCATACCGCCCGCGT 62.212 66.667 4.92 0.00 37.81 6.01
654 684 4.210093 TACCATACCGCCCGCGTG 62.210 66.667 4.92 0.00 37.81 5.34
670 700 1.827315 CGTGTTCATGTGCCGACGTT 61.827 55.000 0.00 0.00 0.00 3.99
679 709 2.202756 GCCGACGTTGGAGGCTAG 60.203 66.667 26.69 0.00 46.83 3.42
680 710 2.707849 GCCGACGTTGGAGGCTAGA 61.708 63.158 26.69 0.00 46.83 2.43
683 713 0.872021 CGACGTTGGAGGCTAGATGC 60.872 60.000 0.00 0.00 41.94 3.91
686 716 1.889573 GTTGGAGGCTAGATGCGGC 60.890 63.158 0.00 0.00 44.05 6.53
691 721 2.153547 GAGGCTAGATGCGGCTCCTC 62.154 65.000 0.00 4.20 45.30 3.71
713 743 2.404265 CACGTGTGAAATGCATGTGT 57.596 45.000 7.58 0.00 44.41 3.72
715 745 3.114809 CACGTGTGAAATGCATGTGTTT 58.885 40.909 7.58 0.00 44.41 2.83
716 746 4.286101 CACGTGTGAAATGCATGTGTTTA 58.714 39.130 7.58 0.00 44.41 2.01
717 747 4.916831 CACGTGTGAAATGCATGTGTTTAT 59.083 37.500 7.58 0.00 44.41 1.40
718 748 6.082984 CACGTGTGAAATGCATGTGTTTATA 58.917 36.000 7.58 0.00 44.41 0.98
720 750 7.273164 CACGTGTGAAATGCATGTGTTTATATT 59.727 33.333 7.58 0.00 44.41 1.28
721 751 7.273164 ACGTGTGAAATGCATGTGTTTATATTG 59.727 33.333 0.00 0.00 35.08 1.90
722 752 7.484324 CGTGTGAAATGCATGTGTTTATATTGA 59.516 33.333 0.00 0.00 0.00 2.57
723 753 9.304731 GTGTGAAATGCATGTGTTTATATTGAT 57.695 29.630 0.00 0.00 0.00 2.57
724 754 9.518906 TGTGAAATGCATGTGTTTATATTGATC 57.481 29.630 0.00 0.00 0.00 2.92
726 756 7.861872 TGAAATGCATGTGTTTATATTGATCGG 59.138 33.333 0.00 0.00 0.00 4.18
727 757 5.107109 TGCATGTGTTTATATTGATCGGC 57.893 39.130 0.00 0.00 0.00 5.54
728 758 4.821260 TGCATGTGTTTATATTGATCGGCT 59.179 37.500 0.00 0.00 0.00 5.52
730 760 5.277974 GCATGTGTTTATATTGATCGGCTGT 60.278 40.000 0.00 0.00 0.00 4.40
731 761 6.728200 CATGTGTTTATATTGATCGGCTGTT 58.272 36.000 0.00 0.00 0.00 3.16
733 763 7.151999 TGTGTTTATATTGATCGGCTGTTTT 57.848 32.000 0.00 0.00 0.00 2.43
734 764 7.247728 TGTGTTTATATTGATCGGCTGTTTTC 58.752 34.615 0.00 0.00 0.00 2.29
735 765 7.120579 TGTGTTTATATTGATCGGCTGTTTTCT 59.879 33.333 0.00 0.00 0.00 2.52
736 766 7.640240 GTGTTTATATTGATCGGCTGTTTTCTC 59.360 37.037 0.00 0.00 0.00 2.87
737 767 7.552687 TGTTTATATTGATCGGCTGTTTTCTCT 59.447 33.333 0.00 0.00 0.00 3.10
738 768 7.715265 TTATATTGATCGGCTGTTTTCTCTC 57.285 36.000 0.00 0.00 0.00 3.20
739 769 3.401033 TTGATCGGCTGTTTTCTCTCA 57.599 42.857 0.00 0.00 0.00 3.27
740 770 2.964740 TGATCGGCTGTTTTCTCTCAG 58.035 47.619 0.00 0.00 35.12 3.35
741 771 2.562738 TGATCGGCTGTTTTCTCTCAGA 59.437 45.455 0.00 0.00 34.02 3.27
742 772 3.196469 TGATCGGCTGTTTTCTCTCAGAT 59.804 43.478 0.00 0.00 34.02 2.90
743 773 2.964740 TCGGCTGTTTTCTCTCAGATG 58.035 47.619 0.00 0.00 34.02 2.90
744 774 2.300152 TCGGCTGTTTTCTCTCAGATGT 59.700 45.455 0.00 0.00 34.02 3.06
745 775 3.509967 TCGGCTGTTTTCTCTCAGATGTA 59.490 43.478 0.00 0.00 34.02 2.29
746 776 3.862267 CGGCTGTTTTCTCTCAGATGTAG 59.138 47.826 0.00 0.00 34.02 2.74
750 780 6.874134 GGCTGTTTTCTCTCAGATGTAGTTAA 59.126 38.462 0.00 0.00 34.02 2.01
765 795 3.824414 AGTTAAAAATTCGCACCGAGG 57.176 42.857 0.00 0.00 37.14 4.63
773 803 0.391597 TTCGCACCGAGGTTTCTTCT 59.608 50.000 0.00 0.00 37.14 2.85
779 809 3.645884 CACCGAGGTTTCTTCTACGAAA 58.354 45.455 0.00 0.00 0.00 3.46
787 817 4.629092 GTTTCTTCTACGAAACTGGACCT 58.371 43.478 8.66 0.00 45.71 3.85
792 822 1.893801 CTACGAAACTGGACCTGGTCT 59.106 52.381 25.01 6.01 32.47 3.85
799 829 1.187087 CTGGACCTGGTCTAGTCACC 58.813 60.000 26.80 11.14 36.59 4.02
800 830 0.252103 TGGACCTGGTCTAGTCACCC 60.252 60.000 25.01 8.28 35.26 4.61
801 831 0.041386 GGACCTGGTCTAGTCACCCT 59.959 60.000 25.01 0.00 35.26 4.34
802 832 1.476477 GACCTGGTCTAGTCACCCTC 58.524 60.000 19.53 0.00 35.26 4.30
803 833 1.006162 GACCTGGTCTAGTCACCCTCT 59.994 57.143 19.53 0.00 35.26 3.69
847 878 2.197324 GCAGTCCCCCACCAAACA 59.803 61.111 0.00 0.00 0.00 2.83
855 886 1.455587 CCCACCAAACACCACTGCT 60.456 57.895 0.00 0.00 0.00 4.24
860 891 1.463553 CCAAACACCACTGCTTCCCC 61.464 60.000 0.00 0.00 0.00 4.81
885 916 3.881688 GCTCACTATAAGTACCACTCCGA 59.118 47.826 0.00 0.00 0.00 4.55
964 1012 1.145738 AGCTCCACCAACCAATTCAGT 59.854 47.619 0.00 0.00 0.00 3.41
1251 1305 1.376424 CACGGTGATGCTGCTCCTT 60.376 57.895 0.74 0.00 0.00 3.36
1866 1920 2.721167 CGTCGAGATGGCCAAGGGA 61.721 63.158 10.96 1.67 0.00 4.20
2065 2120 6.046593 CGACCATGCCAGTTAAACTTATCTA 58.953 40.000 0.00 0.00 0.00 1.98
2066 2121 6.706270 CGACCATGCCAGTTAAACTTATCTAT 59.294 38.462 0.00 0.00 0.00 1.98
2067 2122 7.870954 CGACCATGCCAGTTAAACTTATCTATA 59.129 37.037 0.00 0.00 0.00 1.31
2217 2272 0.965866 AGCTCAAGATCGTCGACCCA 60.966 55.000 10.58 0.00 0.00 4.51
2226 2281 2.675772 GTCGACCCAGAGACCGGT 60.676 66.667 6.92 6.92 34.13 5.28
2259 2314 2.614013 AACCAGCCCGGGGAGATT 60.614 61.111 25.28 0.00 40.22 2.40
2513 4777 0.109412 GTCGTCCCGTGAGTACCAAG 60.109 60.000 0.00 0.00 0.00 3.61
2514 4778 1.445582 CGTCCCGTGAGTACCAAGC 60.446 63.158 0.00 0.00 0.00 4.01
2515 4779 1.669440 GTCCCGTGAGTACCAAGCA 59.331 57.895 0.00 0.00 0.00 3.91
2516 4780 0.249398 GTCCCGTGAGTACCAAGCAT 59.751 55.000 0.00 0.00 0.00 3.79
2517 4781 0.535335 TCCCGTGAGTACCAAGCATC 59.465 55.000 0.00 0.00 0.00 3.91
2518 4782 0.249120 CCCGTGAGTACCAAGCATCA 59.751 55.000 0.00 0.00 0.00 3.07
2519 4783 1.645034 CCGTGAGTACCAAGCATCAG 58.355 55.000 0.00 0.00 0.00 2.90
2531 4795 2.716814 GCATCAGCTAGCATTGCCT 58.283 52.632 18.83 0.00 37.91 4.75
2532 4796 1.888215 GCATCAGCTAGCATTGCCTA 58.112 50.000 18.83 0.00 37.91 3.93
2533 4797 1.534595 GCATCAGCTAGCATTGCCTAC 59.465 52.381 18.83 0.00 37.91 3.18
2538 4824 2.122768 AGCTAGCATTGCCTACTCCTT 58.877 47.619 18.83 0.00 0.00 3.36
2578 4864 3.591023 TGATGATTTCTTAACGACGGCA 58.409 40.909 0.00 0.00 0.00 5.69
2590 4882 0.872021 CGACGGCAGGCTATCTTGAC 60.872 60.000 0.00 0.00 0.00 3.18
2777 5069 1.103803 CGTCGGGGAAGATTCTGAGA 58.896 55.000 0.00 0.00 0.00 3.27
2825 5117 1.945394 GGATCGTGCTGATGATGCTTT 59.055 47.619 0.00 0.00 37.47 3.51
2839 5132 7.545489 TGATGATGCTTTATTATTTGTGTGCA 58.455 30.769 0.00 0.00 0.00 4.57
2842 5135 8.599055 TGATGCTTTATTATTTGTGTGCAAAA 57.401 26.923 0.00 0.00 46.23 2.44
2843 5136 9.217278 TGATGCTTTATTATTTGTGTGCAAAAT 57.783 25.926 0.00 0.00 46.23 1.82
2861 5155 6.814644 TGCAAAATATATATACCCGGTTCGAG 59.185 38.462 0.00 0.00 0.00 4.04
2921 5994 1.203523 AGAGTGTGAGCAAGGATCGAC 59.796 52.381 0.00 0.00 0.00 4.20
2957 6030 3.346315 CATGGCATACTGTGTTTCTGGA 58.654 45.455 0.00 0.00 0.00 3.86
2993 6066 5.755375 ACTCCAGATAATGTATTCGCACTTG 59.245 40.000 0.00 0.00 0.00 3.16
3018 6098 8.154203 TGTATATCAGTGAACTGGAAGAAACAA 58.846 33.333 10.45 0.00 43.91 2.83
3020 6100 6.566197 ATCAGTGAACTGGAAGAAACAATC 57.434 37.500 10.45 0.00 43.91 2.67
3023 6103 6.706270 TCAGTGAACTGGAAGAAACAATCTAC 59.294 38.462 10.45 0.00 43.91 2.59
3025 6105 6.931840 AGTGAACTGGAAGAAACAATCTACTC 59.068 38.462 0.00 0.00 37.42 2.59
3026 6106 6.147985 GTGAACTGGAAGAAACAATCTACTCC 59.852 42.308 0.00 0.00 37.42 3.85
3027 6107 5.167303 ACTGGAAGAAACAATCTACTCCC 57.833 43.478 0.00 0.00 37.42 4.30
3029 6109 5.046231 ACTGGAAGAAACAATCTACTCCCTC 60.046 44.000 0.00 0.00 37.42 4.30
3030 6110 4.225267 TGGAAGAAACAATCTACTCCCTCC 59.775 45.833 0.00 0.00 37.42 4.30
3031 6111 4.434520 GAAGAAACAATCTACTCCCTCCG 58.565 47.826 0.00 0.00 37.42 4.63
3034 6114 3.889520 AACAATCTACTCCCTCCGTTC 57.110 47.619 0.00 0.00 0.00 3.95
3035 6115 2.108970 ACAATCTACTCCCTCCGTTCC 58.891 52.381 0.00 0.00 0.00 3.62
3036 6116 2.108168 CAATCTACTCCCTCCGTTCCA 58.892 52.381 0.00 0.00 0.00 3.53
3038 6118 2.314071 TCTACTCCCTCCGTTCCAAA 57.686 50.000 0.00 0.00 0.00 3.28
3039 6119 2.612000 TCTACTCCCTCCGTTCCAAAA 58.388 47.619 0.00 0.00 0.00 2.44
3040 6120 3.178865 TCTACTCCCTCCGTTCCAAAAT 58.821 45.455 0.00 0.00 0.00 1.82
3041 6121 4.355549 TCTACTCCCTCCGTTCCAAAATA 58.644 43.478 0.00 0.00 0.00 1.40
3042 6122 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
3045 6125 2.093128 TCCCTCCGTTCCAAAATAGAGC 60.093 50.000 0.00 0.00 0.00 4.09
3072 6152 3.033764 GCGTCGTGGCAAGTTCGA 61.034 61.111 18.86 8.92 0.00 3.71
3075 6155 1.556564 CGTCGTGGCAAGTTCGATAT 58.443 50.000 12.65 0.00 36.08 1.63
3078 6158 3.734231 CGTCGTGGCAAGTTCGATATAAT 59.266 43.478 12.65 0.00 36.08 1.28
3080 6160 5.432157 GTCGTGGCAAGTTCGATATAATTG 58.568 41.667 0.00 0.00 36.08 2.32
3096 6379 8.745837 CGATATAATTGTTTTGTTCCAAGATGC 58.254 33.333 0.00 0.00 0.00 3.91
3100 6383 5.843673 TTGTTTTGTTCCAAGATGCTGTA 57.156 34.783 0.00 0.00 0.00 2.74
3130 6413 1.602323 GGTGGCATCGGGTTCAACA 60.602 57.895 0.00 0.00 0.00 3.33
3133 6416 0.037447 TGGCATCGGGTTCAACATCA 59.963 50.000 0.00 0.00 0.00 3.07
3140 6423 0.671251 GGGTTCAACATCACGGCAAA 59.329 50.000 0.00 0.00 0.00 3.68
3143 6426 3.389221 GGTTCAACATCACGGCAAATTT 58.611 40.909 0.00 0.00 0.00 1.82
3144 6427 3.184178 GGTTCAACATCACGGCAAATTTG 59.816 43.478 14.03 14.03 0.00 2.32
3184 6485 3.896648 AAAACTGTACCATCTGCAACG 57.103 42.857 0.00 0.00 0.00 4.10
3188 6489 1.011968 TGTACCATCTGCAACGTCGC 61.012 55.000 0.00 0.00 0.00 5.19
3189 6490 1.803922 TACCATCTGCAACGTCGCG 60.804 57.895 0.00 0.00 33.35 5.87
3190 6491 3.853330 CCATCTGCAACGTCGCGG 61.853 66.667 6.13 0.00 39.79 6.46
3191 6492 4.505217 CATCTGCAACGTCGCGGC 62.505 66.667 6.13 1.93 38.22 6.53
3194 6495 4.088762 CTGCAACGTCGCGGCAAT 62.089 61.111 12.89 0.00 37.06 3.56
3195 6496 3.593551 CTGCAACGTCGCGGCAATT 62.594 57.895 12.89 0.33 37.06 2.32
3196 6497 2.428403 GCAACGTCGCGGCAATTT 60.428 55.556 12.89 0.00 0.00 1.82
3197 6498 2.706123 GCAACGTCGCGGCAATTTG 61.706 57.895 12.89 11.88 0.00 2.32
3198 6499 1.369930 CAACGTCGCGGCAATTTGT 60.370 52.632 12.89 0.00 0.00 2.83
3199 6500 1.369930 AACGTCGCGGCAATTTGTG 60.370 52.632 12.89 0.00 0.00 3.33
3200 6501 2.054140 AACGTCGCGGCAATTTGTGT 62.054 50.000 12.89 0.00 0.00 3.72
3201 6502 1.222766 ACGTCGCGGCAATTTGTGTA 61.223 50.000 12.89 0.00 0.00 2.90
3202 6503 0.096281 CGTCGCGGCAATTTGTGTAT 59.904 50.000 12.89 0.00 0.00 2.29
3203 6504 1.325037 CGTCGCGGCAATTTGTGTATA 59.675 47.619 12.89 0.00 0.00 1.47
3383 6684 0.370273 GCTGTCTACATGGTTTCGCG 59.630 55.000 0.00 0.00 0.00 5.87
3414 6715 6.881065 TGAGAACCACAAAGGAAATATCAGAG 59.119 38.462 0.00 0.00 41.22 3.35
3603 6904 3.181461 CGCCAGGAAGAAAGATGGTAGAT 60.181 47.826 0.00 0.00 35.17 1.98
3604 6905 4.133078 GCCAGGAAGAAAGATGGTAGATG 58.867 47.826 0.00 0.00 35.17 2.90
3613 6914 8.594881 AAGAAAGATGGTAGATGCGTTATTAG 57.405 34.615 0.00 0.00 0.00 1.73
3614 6915 7.727181 AGAAAGATGGTAGATGCGTTATTAGT 58.273 34.615 0.00 0.00 0.00 2.24
3615 6916 8.857098 AGAAAGATGGTAGATGCGTTATTAGTA 58.143 33.333 0.00 0.00 0.00 1.82
3616 6917 8.813643 AAAGATGGTAGATGCGTTATTAGTAC 57.186 34.615 0.00 0.00 0.00 2.73
3617 6918 7.520451 AGATGGTAGATGCGTTATTAGTACA 57.480 36.000 0.00 0.00 0.00 2.90
3766 7068 7.414436 CAATCAGAGAGTAAGCACTAGAGTAC 58.586 42.308 0.00 0.00 34.21 2.73
3767 7069 6.051179 TCAGAGAGTAAGCACTAGAGTACA 57.949 41.667 0.00 0.00 34.21 2.90
3768 7070 5.875910 TCAGAGAGTAAGCACTAGAGTACAC 59.124 44.000 0.00 0.00 34.21 2.90
3769 7071 5.878116 CAGAGAGTAAGCACTAGAGTACACT 59.122 44.000 0.00 0.00 34.21 3.55
3770 7072 6.036735 CAGAGAGTAAGCACTAGAGTACACTC 59.963 46.154 0.00 0.91 37.99 3.51
3771 7073 5.806818 AGAGTAAGCACTAGAGTACACTCA 58.193 41.667 11.75 0.00 39.24 3.41
3772 7074 6.419791 AGAGTAAGCACTAGAGTACACTCAT 58.580 40.000 11.75 0.39 39.24 2.90
3773 7075 6.887545 AGAGTAAGCACTAGAGTACACTCATT 59.112 38.462 11.75 0.00 39.24 2.57
3774 7076 7.394923 AGAGTAAGCACTAGAGTACACTCATTT 59.605 37.037 11.75 0.00 39.24 2.32
3775 7077 7.897864 AGTAAGCACTAGAGTACACTCATTTT 58.102 34.615 11.75 0.00 45.21 1.82
3776 7078 7.815068 AGTAAGCACTAGAGTACACTCATTTTG 59.185 37.037 11.75 4.54 45.21 2.44
3777 7079 4.932200 AGCACTAGAGTACACTCATTTTGC 59.068 41.667 11.75 12.64 45.21 3.68
3778 7080 4.932200 GCACTAGAGTACACTCATTTTGCT 59.068 41.667 11.75 0.00 45.21 3.91
3779 7081 5.062809 GCACTAGAGTACACTCATTTTGCTC 59.937 44.000 11.75 0.00 45.21 4.26
3780 7082 5.287274 CACTAGAGTACACTCATTTTGCTCG 59.713 44.000 11.75 0.00 45.21 5.03
3781 7083 4.258702 AGAGTACACTCATTTTGCTCGT 57.741 40.909 11.75 0.00 45.21 4.18
3782 7084 5.386958 AGAGTACACTCATTTTGCTCGTA 57.613 39.130 11.75 0.00 45.21 3.43
3783 7085 5.403246 AGAGTACACTCATTTTGCTCGTAG 58.597 41.667 11.75 0.00 45.21 3.51
3784 7086 5.047943 AGAGTACACTCATTTTGCTCGTAGT 60.048 40.000 11.75 0.00 45.21 2.73
3785 7087 5.162075 AGTACACTCATTTTGCTCGTAGTC 58.838 41.667 0.00 0.00 0.00 2.59
3786 7088 3.326747 ACACTCATTTTGCTCGTAGTCC 58.673 45.455 0.00 0.00 0.00 3.85
3787 7089 3.244078 ACACTCATTTTGCTCGTAGTCCA 60.244 43.478 0.00 0.00 0.00 4.02
3788 7090 3.935203 CACTCATTTTGCTCGTAGTCCAT 59.065 43.478 0.00 0.00 0.00 3.41
3789 7091 4.393062 CACTCATTTTGCTCGTAGTCCATT 59.607 41.667 0.00 0.00 0.00 3.16
3790 7092 5.580691 CACTCATTTTGCTCGTAGTCCATTA 59.419 40.000 0.00 0.00 0.00 1.90
3791 7093 5.812642 ACTCATTTTGCTCGTAGTCCATTAG 59.187 40.000 0.00 0.00 0.00 1.73
3792 7094 5.730550 TCATTTTGCTCGTAGTCCATTAGT 58.269 37.500 0.00 0.00 0.00 2.24
3793 7095 5.580691 TCATTTTGCTCGTAGTCCATTAGTG 59.419 40.000 0.00 0.00 0.00 2.74
3809 7111 6.610741 CATTAGTGGAATCTCTACAAAGGC 57.389 41.667 0.00 0.00 29.47 4.35
3810 7112 6.352516 CATTAGTGGAATCTCTACAAAGGCT 58.647 40.000 0.00 0.00 29.47 4.58
3811 7113 4.917906 AGTGGAATCTCTACAAAGGCTT 57.082 40.909 0.00 0.00 29.47 4.35
3812 7114 7.490657 TTAGTGGAATCTCTACAAAGGCTTA 57.509 36.000 0.00 0.00 29.47 3.09
3813 7115 6.567602 AGTGGAATCTCTACAAAGGCTTAT 57.432 37.500 0.00 0.00 29.47 1.73
3814 7116 7.676683 AGTGGAATCTCTACAAAGGCTTATA 57.323 36.000 0.00 0.00 29.47 0.98
3815 7117 8.268878 AGTGGAATCTCTACAAAGGCTTATAT 57.731 34.615 0.00 0.00 29.47 0.86
3816 7118 8.718656 AGTGGAATCTCTACAAAGGCTTATATT 58.281 33.333 0.00 0.00 29.47 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.187682 GGGAGAACTTGAAAATTAGGGATCA 58.812 40.000 0.00 0.00 0.00 2.92
1 2 6.187682 TGGGAGAACTTGAAAATTAGGGATC 58.812 40.000 0.00 0.00 0.00 3.36
2 3 6.152638 TGGGAGAACTTGAAAATTAGGGAT 57.847 37.500 0.00 0.00 0.00 3.85
3 4 5.592587 TGGGAGAACTTGAAAATTAGGGA 57.407 39.130 0.00 0.00 0.00 4.20
4 5 6.404734 CGAATGGGAGAACTTGAAAATTAGGG 60.405 42.308 0.00 0.00 0.00 3.53
14 15 5.186198 ACCTTAATCGAATGGGAGAACTTG 58.814 41.667 0.00 0.00 0.00 3.16
18 19 9.908747 TTTAAATACCTTAATCGAATGGGAGAA 57.091 29.630 0.00 0.00 29.52 2.87
44 45 7.744733 ACCAAAATAGTGAACCAAATCCAAAT 58.255 30.769 0.00 0.00 0.00 2.32
68 69 9.719355 ATTAATTTGGAAAATAGTTGACCCAAC 57.281 29.630 1.86 1.86 43.83 3.77
70 71 9.717942 CAATTAATTTGGAAAATAGTTGACCCA 57.282 29.630 0.00 0.00 28.27 4.51
100 101 2.375146 GGATTTTCATAGGCCGGTTGT 58.625 47.619 1.90 0.00 0.00 3.32
118 119 2.111255 AGGTAGTAAGAGGTGTGTGGGA 59.889 50.000 0.00 0.00 0.00 4.37
119 120 2.537143 AGGTAGTAAGAGGTGTGTGGG 58.463 52.381 0.00 0.00 0.00 4.61
120 121 4.597004 TCTAGGTAGTAAGAGGTGTGTGG 58.403 47.826 0.00 0.00 0.00 4.17
121 122 6.585695 TTTCTAGGTAGTAAGAGGTGTGTG 57.414 41.667 0.00 0.00 0.00 3.82
122 123 7.607615 TTTTTCTAGGTAGTAAGAGGTGTGT 57.392 36.000 0.00 0.00 0.00 3.72
209 227 8.147704 CCTAATCAACCCATACTTTTGTGTTTT 58.852 33.333 0.00 0.00 0.00 2.43
210 228 7.507616 TCCTAATCAACCCATACTTTTGTGTTT 59.492 33.333 0.00 0.00 0.00 2.83
212 230 6.548321 TCCTAATCAACCCATACTTTTGTGT 58.452 36.000 0.00 0.00 0.00 3.72
235 253 6.978659 TCGGTAGTGTGATTTGATGTTATCTC 59.021 38.462 0.00 0.00 0.00 2.75
244 262 2.614481 GGCCTTCGGTAGTGTGATTTGA 60.614 50.000 0.00 0.00 0.00 2.69
245 263 1.737793 GGCCTTCGGTAGTGTGATTTG 59.262 52.381 0.00 0.00 0.00 2.32
246 264 1.628846 AGGCCTTCGGTAGTGTGATTT 59.371 47.619 0.00 0.00 0.00 2.17
258 276 1.805120 CGGTGTTATGGTAGGCCTTCG 60.805 57.143 12.58 0.00 35.27 3.79
266 284 9.458727 TTTTATTTGTAATCCGGTGTTATGGTA 57.541 29.630 0.00 0.00 0.00 3.25
300 318 1.546476 GTGGAGAGACGATGGAGTGTT 59.454 52.381 0.00 0.00 0.00 3.32
311 329 0.670854 GGTTTGGCGAGTGGAGAGAC 60.671 60.000 0.00 0.00 0.00 3.36
316 334 2.156098 GTATTTGGTTTGGCGAGTGGA 58.844 47.619 0.00 0.00 0.00 4.02
414 433 7.865706 AGTATTGTGGATGTAGATGTTTTCC 57.134 36.000 0.00 0.00 0.00 3.13
415 434 9.378551 TGTAGTATTGTGGATGTAGATGTTTTC 57.621 33.333 0.00 0.00 0.00 2.29
590 620 9.438228 TGGTGTTATTAGAATTTCGTGATGTTA 57.562 29.630 0.00 0.00 0.00 2.41
591 621 8.330466 TGGTGTTATTAGAATTTCGTGATGTT 57.670 30.769 0.00 0.00 0.00 2.71
592 622 7.915293 TGGTGTTATTAGAATTTCGTGATGT 57.085 32.000 0.00 0.00 0.00 3.06
593 623 8.233868 TGTTGGTGTTATTAGAATTTCGTGATG 58.766 33.333 0.00 0.00 0.00 3.07
594 624 8.330466 TGTTGGTGTTATTAGAATTTCGTGAT 57.670 30.769 0.00 0.00 0.00 3.06
595 625 7.572353 GCTGTTGGTGTTATTAGAATTTCGTGA 60.572 37.037 0.00 0.00 0.00 4.35
596 626 6.523201 GCTGTTGGTGTTATTAGAATTTCGTG 59.477 38.462 0.00 0.00 0.00 4.35
597 627 6.608610 GCTGTTGGTGTTATTAGAATTTCGT 58.391 36.000 0.00 0.00 0.00 3.85
598 628 5.732647 CGCTGTTGGTGTTATTAGAATTTCG 59.267 40.000 0.00 0.00 0.00 3.46
599 629 5.511729 GCGCTGTTGGTGTTATTAGAATTTC 59.488 40.000 0.00 0.00 0.00 2.17
600 630 5.048364 TGCGCTGTTGGTGTTATTAGAATTT 60.048 36.000 9.73 0.00 0.00 1.82
601 631 4.457603 TGCGCTGTTGGTGTTATTAGAATT 59.542 37.500 9.73 0.00 0.00 2.17
602 632 4.006989 TGCGCTGTTGGTGTTATTAGAAT 58.993 39.130 9.73 0.00 0.00 2.40
603 633 3.403968 TGCGCTGTTGGTGTTATTAGAA 58.596 40.909 9.73 0.00 0.00 2.10
604 634 3.000041 CTGCGCTGTTGGTGTTATTAGA 59.000 45.455 9.73 0.00 0.00 2.10
605 635 2.476185 GCTGCGCTGTTGGTGTTATTAG 60.476 50.000 16.05 0.00 0.00 1.73
606 636 1.466950 GCTGCGCTGTTGGTGTTATTA 59.533 47.619 16.05 0.00 0.00 0.98
607 637 0.240945 GCTGCGCTGTTGGTGTTATT 59.759 50.000 16.05 0.00 0.00 1.40
608 638 0.888736 TGCTGCGCTGTTGGTGTTAT 60.889 50.000 16.05 0.00 0.00 1.89
609 639 1.098129 TTGCTGCGCTGTTGGTGTTA 61.098 50.000 16.05 0.00 0.00 2.41
610 640 1.943116 TTTGCTGCGCTGTTGGTGTT 61.943 50.000 16.05 0.00 0.00 3.32
611 641 2.340453 CTTTGCTGCGCTGTTGGTGT 62.340 55.000 16.05 0.00 0.00 4.16
612 642 1.659335 CTTTGCTGCGCTGTTGGTG 60.659 57.895 16.05 0.00 0.00 4.17
613 643 2.723746 CTTTGCTGCGCTGTTGGT 59.276 55.556 16.05 0.00 0.00 3.67
614 644 2.732094 GCTTTGCTGCGCTGTTGG 60.732 61.111 16.05 5.44 0.00 3.77
622 652 1.514873 GGTACATGCGCTTTGCTGC 60.515 57.895 9.73 0.00 46.63 5.25
623 653 1.875262 TGGTACATGCGCTTTGCTG 59.125 52.632 9.73 0.83 46.63 4.41
624 654 4.395519 TGGTACATGCGCTTTGCT 57.604 50.000 9.73 0.62 46.63 3.91
634 664 3.509137 CGCGGGCGGTATGGTACAT 62.509 63.158 4.92 0.00 38.52 2.29
635 665 4.210093 CGCGGGCGGTATGGTACA 62.210 66.667 4.92 0.00 38.30 2.90
636 666 4.211502 ACGCGGGCGGTATGGTAC 62.212 66.667 18.03 0.00 44.69 3.34
637 667 4.210093 CACGCGGGCGGTATGGTA 62.210 66.667 18.03 0.00 44.69 3.25
640 670 3.560278 GAACACGCGGGCGGTATG 61.560 66.667 9.12 9.14 44.69 2.39
641 671 3.379865 ATGAACACGCGGGCGGTAT 62.380 57.895 9.12 0.00 44.69 2.73
642 672 4.071875 ATGAACACGCGGGCGGTA 62.072 61.111 9.12 0.00 44.69 4.02
645 675 4.444024 CACATGAACACGCGGGCG 62.444 66.667 9.12 12.04 46.03 6.13
646 676 4.759096 GCACATGAACACGCGGGC 62.759 66.667 9.12 0.00 0.00 6.13
647 677 4.101790 GGCACATGAACACGCGGG 62.102 66.667 6.92 6.92 0.00 6.13
648 678 4.444024 CGGCACATGAACACGCGG 62.444 66.667 12.47 1.27 0.00 6.46
649 679 3.410516 TCGGCACATGAACACGCG 61.411 61.111 3.53 3.53 0.00 6.01
650 680 2.173382 GTCGGCACATGAACACGC 59.827 61.111 0.00 0.00 0.00 5.34
651 681 1.827315 AACGTCGGCACATGAACACG 61.827 55.000 0.00 2.87 0.00 4.49
652 682 0.384230 CAACGTCGGCACATGAACAC 60.384 55.000 0.00 0.00 0.00 3.32
653 683 1.502990 CCAACGTCGGCACATGAACA 61.503 55.000 0.00 0.00 0.00 3.18
654 684 1.206578 CCAACGTCGGCACATGAAC 59.793 57.895 0.00 0.00 0.00 3.18
670 700 2.444706 AGCCGCATCTAGCCTCCA 60.445 61.111 0.00 0.00 41.38 3.86
686 716 0.670546 ATTTCACACGTGCGGAGGAG 60.671 55.000 17.22 0.00 0.00 3.69
691 721 1.066656 CATGCATTTCACACGTGCGG 61.067 55.000 17.22 8.61 41.61 5.69
712 742 7.920738 AGAGAAAACAGCCGATCAATATAAAC 58.079 34.615 0.00 0.00 0.00 2.01
713 743 7.768582 TGAGAGAAAACAGCCGATCAATATAAA 59.231 33.333 0.00 0.00 0.00 1.40
715 745 6.816136 TGAGAGAAAACAGCCGATCAATATA 58.184 36.000 0.00 0.00 0.00 0.86
716 746 5.674525 TGAGAGAAAACAGCCGATCAATAT 58.325 37.500 0.00 0.00 0.00 1.28
717 747 5.084818 TGAGAGAAAACAGCCGATCAATA 57.915 39.130 0.00 0.00 0.00 1.90
718 748 3.937706 CTGAGAGAAAACAGCCGATCAAT 59.062 43.478 0.00 0.00 0.00 2.57
720 750 2.562738 TCTGAGAGAAAACAGCCGATCA 59.437 45.455 0.00 0.00 34.57 2.92
721 751 3.238108 TCTGAGAGAAAACAGCCGATC 57.762 47.619 0.00 0.00 34.57 3.69
722 752 3.055530 ACATCTGAGAGAAAACAGCCGAT 60.056 43.478 0.00 0.00 34.57 4.18
723 753 2.300152 ACATCTGAGAGAAAACAGCCGA 59.700 45.455 0.00 0.00 34.57 5.54
724 754 2.693069 ACATCTGAGAGAAAACAGCCG 58.307 47.619 0.00 0.00 34.57 5.52
726 756 7.891183 TTAACTACATCTGAGAGAAAACAGC 57.109 36.000 0.00 0.00 34.57 4.40
733 763 7.817478 TGCGAATTTTTAACTACATCTGAGAGA 59.183 33.333 0.00 0.00 0.00 3.10
734 764 7.900352 GTGCGAATTTTTAACTACATCTGAGAG 59.100 37.037 0.00 0.00 0.00 3.20
735 765 7.148474 GGTGCGAATTTTTAACTACATCTGAGA 60.148 37.037 0.00 0.00 0.00 3.27
736 766 6.961554 GGTGCGAATTTTTAACTACATCTGAG 59.038 38.462 0.00 0.00 0.00 3.35
737 767 6.401688 CGGTGCGAATTTTTAACTACATCTGA 60.402 38.462 0.00 0.00 0.00 3.27
738 768 5.732647 CGGTGCGAATTTTTAACTACATCTG 59.267 40.000 0.00 0.00 0.00 2.90
739 769 5.640357 TCGGTGCGAATTTTTAACTACATCT 59.360 36.000 0.00 0.00 31.06 2.90
740 770 5.860641 TCGGTGCGAATTTTTAACTACATC 58.139 37.500 0.00 0.00 31.06 3.06
741 771 5.163794 CCTCGGTGCGAATTTTTAACTACAT 60.164 40.000 0.00 0.00 34.74 2.29
742 772 4.152759 CCTCGGTGCGAATTTTTAACTACA 59.847 41.667 0.00 0.00 34.74 2.74
743 773 4.152938 ACCTCGGTGCGAATTTTTAACTAC 59.847 41.667 0.00 0.00 34.74 2.73
744 774 4.317488 ACCTCGGTGCGAATTTTTAACTA 58.683 39.130 0.00 0.00 34.74 2.24
745 775 3.143728 ACCTCGGTGCGAATTTTTAACT 58.856 40.909 0.00 0.00 34.74 2.24
746 776 3.547649 ACCTCGGTGCGAATTTTTAAC 57.452 42.857 0.00 0.00 34.74 2.01
750 780 2.227194 AGAAACCTCGGTGCGAATTTT 58.773 42.857 0.00 0.00 34.74 1.82
773 803 2.005370 AGACCAGGTCCAGTTTCGTA 57.995 50.000 16.72 0.00 32.18 3.43
779 809 1.550409 GGTGACTAGACCAGGTCCAGT 60.550 57.143 19.65 19.65 37.24 4.00
787 817 1.717077 AGGAAGAGGGTGACTAGACCA 59.283 52.381 0.00 0.00 37.80 4.02
792 822 1.288335 GGGAGAGGAAGAGGGTGACTA 59.712 57.143 0.00 0.00 0.00 2.59
798 828 1.758906 GTCCGGGAGAGGAAGAGGG 60.759 68.421 0.00 0.00 42.77 4.30
799 829 0.614979 TTGTCCGGGAGAGGAAGAGG 60.615 60.000 0.00 0.00 42.77 3.69
800 830 0.533032 GTTGTCCGGGAGAGGAAGAG 59.467 60.000 0.00 0.00 42.77 2.85
801 831 0.178944 TGTTGTCCGGGAGAGGAAGA 60.179 55.000 0.00 0.00 42.77 2.87
802 832 0.685097 TTGTTGTCCGGGAGAGGAAG 59.315 55.000 0.00 0.00 42.77 3.46
803 833 0.395312 GTTGTTGTCCGGGAGAGGAA 59.605 55.000 0.00 0.00 42.77 3.36
833 863 1.830847 GTGGTGTTTGGTGGGGGAC 60.831 63.158 0.00 0.00 0.00 4.46
834 864 2.009882 AGTGGTGTTTGGTGGGGGA 61.010 57.895 0.00 0.00 0.00 4.81
860 891 2.957006 AGTGGTACTTATAGTGAGCGGG 59.043 50.000 0.00 0.00 0.00 6.13
866 897 4.023878 GCTCTCGGAGTGGTACTTATAGTG 60.024 50.000 4.69 0.00 31.39 2.74
867 898 4.136051 GCTCTCGGAGTGGTACTTATAGT 58.864 47.826 4.69 0.00 31.39 2.12
885 916 0.411452 TGAGGAGTGGAAGGAGCTCT 59.589 55.000 14.64 0.00 0.00 4.09
942 990 0.890683 GAATTGGTTGGTGGAGCTGG 59.109 55.000 0.00 0.00 0.00 4.85
978 1026 4.406173 CGCCGCGTCTGTCTGTCT 62.406 66.667 4.92 0.00 0.00 3.41
1236 1290 1.452833 GGGAAGGAGCAGCATCACC 60.453 63.158 0.00 0.00 0.00 4.02
1680 1734 3.790437 ATGGGGAGCACGCAGAGG 61.790 66.667 0.00 0.00 45.87 3.69
1873 1927 4.436998 GAGGTCGTGGCGGTCCAG 62.437 72.222 0.00 0.00 44.48 3.86
2065 2120 6.324819 CCTGCTCAAACGAAATGACAAATAT 58.675 36.000 0.00 0.00 0.00 1.28
2066 2121 5.335583 CCCTGCTCAAACGAAATGACAAATA 60.336 40.000 0.00 0.00 0.00 1.40
2067 2122 4.549458 CCTGCTCAAACGAAATGACAAAT 58.451 39.130 0.00 0.00 0.00 2.32
2187 2242 1.374758 CTTGAGCTCCGCGTTCCTT 60.375 57.895 12.15 0.00 0.00 3.36
2217 2272 1.979693 GAGGCACAGACCGGTCTCT 60.980 63.158 34.28 26.59 37.98 3.10
2259 2314 2.940467 TGCCTCCCCCTGATGCAA 60.940 61.111 0.00 0.00 40.98 4.08
2513 4777 1.534595 GTAGGCAATGCTAGCTGATGC 59.465 52.381 23.13 23.13 40.05 3.91
2514 4778 3.065655 GAGTAGGCAATGCTAGCTGATG 58.934 50.000 17.23 12.75 0.00 3.07
2515 4779 2.038295 GGAGTAGGCAATGCTAGCTGAT 59.962 50.000 17.23 0.00 0.00 2.90
2516 4780 1.414181 GGAGTAGGCAATGCTAGCTGA 59.586 52.381 17.23 0.00 0.00 4.26
2517 4781 1.415659 AGGAGTAGGCAATGCTAGCTG 59.584 52.381 17.23 8.00 0.00 4.24
2518 4782 1.799933 AGGAGTAGGCAATGCTAGCT 58.200 50.000 17.23 0.21 0.00 3.32
2519 4783 2.629336 AAGGAGTAGGCAATGCTAGC 57.371 50.000 8.10 8.10 0.00 3.42
2522 4786 4.712476 CTCAATAAGGAGTAGGCAATGCT 58.288 43.478 4.82 0.00 0.00 3.79
2523 4787 3.251972 GCTCAATAAGGAGTAGGCAATGC 59.748 47.826 0.00 0.00 37.24 3.56
2524 4788 4.514441 CAGCTCAATAAGGAGTAGGCAATG 59.486 45.833 0.00 0.00 37.24 2.82
2525 4789 4.164988 ACAGCTCAATAAGGAGTAGGCAAT 59.835 41.667 0.00 0.00 37.24 3.56
2526 4790 3.519510 ACAGCTCAATAAGGAGTAGGCAA 59.480 43.478 0.00 0.00 37.24 4.52
2527 4791 3.107601 ACAGCTCAATAAGGAGTAGGCA 58.892 45.455 0.00 0.00 37.24 4.75
2528 4792 3.828875 ACAGCTCAATAAGGAGTAGGC 57.171 47.619 0.00 0.00 37.24 3.93
2529 4793 6.322712 ACTCTTACAGCTCAATAAGGAGTAGG 59.677 42.308 8.40 0.00 37.24 3.18
2530 4794 7.341445 ACTCTTACAGCTCAATAAGGAGTAG 57.659 40.000 8.40 3.09 37.24 2.57
2531 4795 7.719871 AACTCTTACAGCTCAATAAGGAGTA 57.280 36.000 8.40 0.00 37.24 2.59
2532 4796 6.613153 AACTCTTACAGCTCAATAAGGAGT 57.387 37.500 8.40 7.88 37.24 3.85
2533 4797 8.417106 TCATAACTCTTACAGCTCAATAAGGAG 58.583 37.037 8.40 7.45 37.97 3.69
2572 4858 0.530870 GGTCAAGATAGCCTGCCGTC 60.531 60.000 0.00 0.00 0.00 4.79
2578 4864 3.051940 TCATCCTGGTCAAGATAGCCT 57.948 47.619 0.00 0.00 0.00 4.58
2590 4882 1.144298 TGGCATCATCCTTCATCCTGG 59.856 52.381 0.00 0.00 0.00 4.45
2777 5069 1.592223 CTTCGCTCGGAGGTCCTTT 59.408 57.895 7.20 0.00 0.00 3.11
2839 5132 9.783081 AAAACTCGAACCGGGTATATATATTTT 57.217 29.630 6.32 0.00 40.83 1.82
2842 5135 7.899973 ACAAAACTCGAACCGGGTATATATAT 58.100 34.615 6.32 0.00 40.83 0.86
2843 5136 7.288810 ACAAAACTCGAACCGGGTATATATA 57.711 36.000 6.32 0.00 40.83 0.86
2861 5155 8.895932 AATTAGCATTATGACGAGAACAAAAC 57.104 30.769 0.00 0.00 0.00 2.43
2877 5171 9.005777 TCTTTTCGTGGTACTTTAATTAGCATT 57.994 29.630 0.00 0.00 30.09 3.56
2890 5963 2.475487 GCTCACACTCTTTTCGTGGTAC 59.525 50.000 0.00 0.00 36.71 3.34
2900 5973 1.895798 TCGATCCTTGCTCACACTCTT 59.104 47.619 0.00 0.00 0.00 2.85
2921 5994 1.138036 CATGCACATTGGCGACTGG 59.862 57.895 0.00 0.00 36.28 4.00
2993 6066 8.547967 TTGTTTCTTCCAGTTCACTGATATAC 57.452 34.615 8.61 0.55 46.59 1.47
3018 6098 2.544844 TTGGAACGGAGGGAGTAGAT 57.455 50.000 0.00 0.00 0.00 1.98
3020 6100 3.629142 ATTTTGGAACGGAGGGAGTAG 57.371 47.619 0.00 0.00 0.00 2.57
3023 6103 3.798202 CTCTATTTTGGAACGGAGGGAG 58.202 50.000 0.00 0.00 0.00 4.30
3025 6105 2.289565 GCTCTATTTTGGAACGGAGGG 58.710 52.381 0.00 0.00 0.00 4.30
3026 6106 2.678336 GTGCTCTATTTTGGAACGGAGG 59.322 50.000 0.00 0.00 0.00 4.30
3027 6107 2.678336 GGTGCTCTATTTTGGAACGGAG 59.322 50.000 0.00 0.00 0.00 4.63
3029 6109 2.432444 TGGTGCTCTATTTTGGAACGG 58.568 47.619 0.00 0.00 0.00 4.44
3030 6110 4.414852 CAATGGTGCTCTATTTTGGAACG 58.585 43.478 0.00 0.00 0.00 3.95
3045 6125 2.174107 CACGACGCTGCAATGGTG 59.826 61.111 0.00 0.98 0.00 4.17
3056 6136 1.556564 ATATCGAACTTGCCACGACG 58.443 50.000 0.00 0.00 38.79 5.12
3057 6137 5.006358 ACAATTATATCGAACTTGCCACGAC 59.994 40.000 0.00 0.00 38.79 4.34
3058 6138 5.113383 ACAATTATATCGAACTTGCCACGA 58.887 37.500 0.00 0.00 40.18 4.35
3078 6158 6.183360 ATGTACAGCATCTTGGAACAAAACAA 60.183 34.615 0.33 0.00 36.88 2.83
3080 6160 5.772521 ATGTACAGCATCTTGGAACAAAAC 58.227 37.500 0.33 0.00 36.88 2.43
3096 6379 3.006430 TGCCACCATATACGGATGTACAG 59.994 47.826 0.33 0.00 32.26 2.74
3100 6383 2.353704 CGATGCCACCATATACGGATGT 60.354 50.000 0.00 0.00 0.00 3.06
3168 6469 2.905010 GCGACGTTGCAGATGGTACAG 61.905 57.143 23.02 0.00 36.77 2.74
3184 6485 3.602390 ATATACACAAATTGCCGCGAC 57.398 42.857 8.23 0.00 0.00 5.19
3383 6684 4.021102 TCCTTTGTGGTTCTCATCTTCC 57.979 45.455 0.00 0.00 37.07 3.46
3414 6715 7.226128 TGCTGAAGATGTGATGATGTTAAGATC 59.774 37.037 5.66 5.66 0.00 2.75
3487 6788 2.502947 TGCCTACAAGAGCTGATGATGT 59.497 45.455 0.00 0.00 0.00 3.06
3603 6904 6.813152 GGAACCTACTTTGTACTAATAACGCA 59.187 38.462 0.00 0.00 0.00 5.24
3604 6905 6.020360 CGGAACCTACTTTGTACTAATAACGC 60.020 42.308 0.00 0.00 0.00 4.84
3613 6914 3.683365 TTCCCGGAACCTACTTTGTAC 57.317 47.619 0.73 0.00 0.00 2.90
3614 6915 4.347583 TCTTTTCCCGGAACCTACTTTGTA 59.652 41.667 0.73 0.00 0.00 2.41
3615 6916 3.136992 TCTTTTCCCGGAACCTACTTTGT 59.863 43.478 0.73 0.00 0.00 2.83
3616 6917 3.746940 TCTTTTCCCGGAACCTACTTTG 58.253 45.455 0.73 0.00 0.00 2.77
3617 6918 3.649502 TCTCTTTTCCCGGAACCTACTTT 59.350 43.478 0.73 0.00 0.00 2.66
3749 7051 6.687081 ATGAGTGTACTCTAGTGCTTACTC 57.313 41.667 12.75 10.03 43.25 2.59
3766 7068 3.325870 TGGACTACGAGCAAAATGAGTG 58.674 45.455 0.00 0.00 0.00 3.51
3767 7069 3.678056 TGGACTACGAGCAAAATGAGT 57.322 42.857 0.00 0.00 0.00 3.41
3768 7070 5.812642 ACTAATGGACTACGAGCAAAATGAG 59.187 40.000 0.00 0.00 0.00 2.90
3769 7071 5.580691 CACTAATGGACTACGAGCAAAATGA 59.419 40.000 0.00 0.00 0.00 2.57
3770 7072 5.799960 CACTAATGGACTACGAGCAAAATG 58.200 41.667 0.00 0.00 0.00 2.32
3786 7088 6.352516 AGCCTTTGTAGAGATTCCACTAATG 58.647 40.000 0.00 0.00 0.00 1.90
3787 7089 6.567602 AGCCTTTGTAGAGATTCCACTAAT 57.432 37.500 0.00 0.00 0.00 1.73
3788 7090 6.374417 AAGCCTTTGTAGAGATTCCACTAA 57.626 37.500 0.00 0.00 0.00 2.24
3789 7091 7.676683 ATAAGCCTTTGTAGAGATTCCACTA 57.323 36.000 0.00 0.00 0.00 2.74
3790 7092 4.917906 AAGCCTTTGTAGAGATTCCACT 57.082 40.909 0.00 0.00 0.00 4.00
3791 7093 8.910351 AATATAAGCCTTTGTAGAGATTCCAC 57.090 34.615 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.