Multiple sequence alignment - TraesCS3A01G397100

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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 TraesCS3A01G397100 chr3A 100.000 3912 0 0 1 3912 644683098 644679187 0.000000e+00 7225.0
1 TraesCS3A01G397100 chr3A 93.500 600 33 5 1 596 90872996 90873593 0.000000e+00 887.0
2 TraesCS3A01G397100 chr3D 95.272 1523 56 4 2394 3912 506009802 506008292 0.000000e+00 2399.0
3 TraesCS3A01G397100 chr3D 94.433 1509 67 6 771 2270 506011302 506009802 0.000000e+00 2305.0
4 TraesCS3A01G397100 chr3B 92.249 787 45 6 706 1483 667719549 667718770 0.000000e+00 1101.0
5 TraesCS3A01G397100 chr3B 86.718 783 74 17 3138 3912 667717460 667716700 0.000000e+00 843.0
6 TraesCS3A01G397100 chr3B 86.598 485 33 14 50 505 808963660 808963179 1.250000e-139 507.0
7 TraesCS3A01G397100 chr3B 85.376 465 48 10 2681 3139 667717973 667717523 7.660000e-127 464.0
8 TraesCS3A01G397100 chr3B 90.400 250 22 2 1541 1790 667718771 667718524 1.050000e-85 327.0
9 TraesCS3A01G397100 chr3B 78.864 440 63 16 1861 2275 667718491 667718057 1.790000e-68 270.0
10 TraesCS3A01G397100 chr3B 83.146 178 13 14 321 492 791767454 791767288 3.150000e-31 147.0
11 TraesCS3A01G397100 chr3B 90.000 90 8 1 50 138 810325220 810325309 8.880000e-22 115.0
12 TraesCS3A01G397100 chr1A 87.771 507 51 8 1 504 112367286 112366788 2.030000e-162 582.0
13 TraesCS3A01G397100 chr5B 86.542 483 37 9 50 505 536220606 536220125 1.250000e-139 507.0
14 TraesCS3A01G397100 chr7B 86.141 469 50 10 49 505 705694517 705694982 3.510000e-135 492.0
15 TraesCS3A01G397100 chr7B 85.774 478 35 14 50 505 678643767 678644233 3.540000e-130 475.0
16 TraesCS3A01G397100 chr7B 81.165 515 53 25 9 497 91799632 91800128 1.330000e-99 374.0
17 TraesCS3A01G397100 chr7B 78.435 524 66 32 1 498 189709581 189710083 8.220000e-77 298.0
18 TraesCS3A01G397100 chr7B 85.057 87 10 3 2439 2523 181409928 181410013 6.960000e-13 86.1
19 TraesCS3A01G397100 chr4B 84.130 523 46 26 1 505 554014728 554015231 4.580000e-129 472.0
20 TraesCS3A01G397100 chr4B 81.102 508 64 24 5 496 622127427 622127918 1.030000e-100 377.0
21 TraesCS3A01G397100 chr4A 82.249 507 48 19 13 505 173699356 173698878 2.190000e-107 399.0
22 TraesCS3A01G397100 chr4A 78.588 425 67 17 94 501 524293735 524294152 3.880000e-65 259.0
23 TraesCS3A01G397100 chr1B 77.393 606 88 28 1 594 675928766 675928198 8.160000e-82 315.0
24 TraesCS3A01G397100 chr1B 80.843 261 25 14 241 498 498077954 498077716 8.630000e-42 182.0
25 TraesCS3A01G397100 chr1B 93.333 60 4 0 535 594 614189389 614189330 5.380000e-14 89.8
26 TraesCS3A01G397100 chr5D 87.455 279 21 9 237 505 537329312 537329586 3.800000e-80 309.0
27 TraesCS3A01G397100 chr7A 80.392 408 46 22 120 505 728070952 728070557 2.980000e-71 279.0
28 TraesCS3A01G397100 chr7A 93.443 61 2 2 535 594 728070552 728070493 5.380000e-14 89.8
29 TraesCS3A01G397100 chr6A 76.054 522 63 34 1 505 119193608 119193132 8.510000e-52 215.0
30 TraesCS3A01G397100 chr2B 77.716 359 53 17 5 356 84975469 84975131 1.110000e-45 195.0
31 TraesCS3A01G397100 chrUn 75.750 400 58 24 1 383 15632101 15632478 8.700000e-37 165.0
32 TraesCS3A01G397100 chrUn 75.439 399 58 25 1 383 15848931 15849305 1.460000e-34 158.0
33 TraesCS3A01G397100 chr2A 83.439 157 15 9 342 496 763143523 763143670 6.820000e-28 135.0
34 TraesCS3A01G397100 chr5A 94.286 35 0 2 2429 2462 260333464 260333497 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 TraesCS3A01G397100 chr3A 644679187 644683098 3911 True 7225 7225 100.0000 1 3912 1 chr3A.!!$R1 3911
1 TraesCS3A01G397100 chr3A 90872996 90873593 597 False 887 887 93.5000 1 596 1 chr3A.!!$F1 595
2 TraesCS3A01G397100 chr3D 506008292 506011302 3010 True 2352 2399 94.8525 771 3912 2 chr3D.!!$R1 3141
3 TraesCS3A01G397100 chr3B 667716700 667719549 2849 True 601 1101 86.7214 706 3912 5 chr3B.!!$R3 3206
4 TraesCS3A01G397100 chr7B 189709581 189710083 502 False 298 298 78.4350 1 498 1 chr7B.!!$F3 497
5 TraesCS3A01G397100 chr4B 554014728 554015231 503 False 472 472 84.1300 1 505 1 chr4B.!!$F1 504
6 TraesCS3A01G397100 chr1B 675928198 675928766 568 True 315 315 77.3930 1 594 1 chr1B.!!$R3 593

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
658 740 0.030908 GCCTCGATCTGTTACTCGGG 59.969 60.0 0.00 0.0 35.64 5.14 F
659 741 0.030908 CCTCGATCTGTTACTCGGGC 59.969 60.0 0.00 0.0 34.03 6.13 F
660 742 0.030908 CTCGATCTGTTACTCGGGCC 59.969 60.0 0.00 0.0 35.64 5.80 F
1113 1209 0.687354 ACGGCCAACTCTCTCATTGT 59.313 50.0 2.24 0.0 0.00 2.71 F
2277 2400 0.907704 TTCGCCTTCCCTCTTGCCTA 60.908 55.0 0.00 0.0 0.00 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2532 2672 1.146774 TCAGATTCAAAACAGCCCCCA 59.853 47.619 0.00 0.0 0.00 4.96 R
2649 2789 5.499139 TTGATCAGTCAAAAACAGGTCAC 57.501 39.130 0.00 0.0 41.22 3.67 R
2676 2816 8.684386 TTTGTGGTATGTTTCTGAAGACAATA 57.316 30.769 8.65 0.0 0.00 1.90 R
2832 2972 4.440880 CTTCAGGTCAAAATTGCAACCAA 58.559 39.130 0.00 0.0 35.01 3.67 R
3359 3570 0.966179 AAAATGACGAAAGGTGGGGC 59.034 50.000 0.00 0.0 0.00 5.80 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
87 92 7.992754 TTTGGGATTTGTGGATAATTTTTGG 57.007 32.000 0.00 0.00 0.00 3.28
167 198 8.472683 TTTTGTAAGACAAGAACAATTGTTGG 57.527 30.769 27.85 18.05 43.32 3.77
187 218 6.313905 TGTTGGAACGTGCAAAACAATATTTT 59.686 30.769 10.70 0.00 26.96 1.82
190 221 8.420374 TGGAACGTGCAAAACAATATTTTAAA 57.580 26.923 0.00 0.00 0.00 1.52
340 411 7.767250 ACATAAGAAAGGAAAGGAAAGAAGG 57.233 36.000 0.00 0.00 0.00 3.46
543 625 2.279120 CTCGCACTGGGAGATCGC 60.279 66.667 16.34 0.00 43.87 4.58
596 678 1.533731 GCGTCAAACAGGATTTTCGGA 59.466 47.619 0.00 0.00 0.00 4.55
597 679 2.412847 GCGTCAAACAGGATTTTCGGAG 60.413 50.000 0.00 0.00 0.00 4.63
598 680 3.064207 CGTCAAACAGGATTTTCGGAGA 58.936 45.455 0.00 0.00 0.00 3.71
599 681 3.684788 CGTCAAACAGGATTTTCGGAGAT 59.315 43.478 0.00 0.00 35.04 2.75
600 682 4.868171 CGTCAAACAGGATTTTCGGAGATA 59.132 41.667 0.00 0.00 35.04 1.98
601 683 5.220416 CGTCAAACAGGATTTTCGGAGATAC 60.220 44.000 0.00 0.00 35.04 2.24
602 684 4.868171 TCAAACAGGATTTTCGGAGATACG 59.132 41.667 0.00 0.00 35.04 3.06
603 685 4.467198 AACAGGATTTTCGGAGATACGT 57.533 40.909 0.00 0.00 35.04 3.57
604 686 3.782046 ACAGGATTTTCGGAGATACGTG 58.218 45.455 0.00 0.00 35.04 4.49
605 687 3.123804 CAGGATTTTCGGAGATACGTGG 58.876 50.000 0.00 0.00 35.04 4.94
606 688 1.865340 GGATTTTCGGAGATACGTGGC 59.135 52.381 0.00 0.00 35.04 5.01
607 689 2.483188 GGATTTTCGGAGATACGTGGCT 60.483 50.000 0.00 0.00 35.04 4.75
608 690 2.754946 TTTTCGGAGATACGTGGCTT 57.245 45.000 0.00 0.00 35.04 4.35
609 691 2.004583 TTTCGGAGATACGTGGCTTG 57.995 50.000 0.00 0.00 35.04 4.01
610 692 1.179152 TTCGGAGATACGTGGCTTGA 58.821 50.000 0.00 0.00 35.04 3.02
611 693 1.399714 TCGGAGATACGTGGCTTGAT 58.600 50.000 0.00 0.00 34.94 2.57
612 694 2.578786 TCGGAGATACGTGGCTTGATA 58.421 47.619 0.00 0.00 34.94 2.15
613 695 3.154710 TCGGAGATACGTGGCTTGATAT 58.845 45.455 0.00 0.00 34.94 1.63
614 696 3.057526 TCGGAGATACGTGGCTTGATATG 60.058 47.826 0.00 0.00 34.94 1.78
615 697 3.305403 CGGAGATACGTGGCTTGATATGT 60.305 47.826 0.00 0.00 0.00 2.29
616 698 4.632153 GGAGATACGTGGCTTGATATGTT 58.368 43.478 0.00 0.00 0.00 2.71
617 699 5.057149 GGAGATACGTGGCTTGATATGTTT 58.943 41.667 0.00 0.00 0.00 2.83
618 700 5.527582 GGAGATACGTGGCTTGATATGTTTT 59.472 40.000 0.00 0.00 0.00 2.43
619 701 6.038271 GGAGATACGTGGCTTGATATGTTTTT 59.962 38.462 0.00 0.00 0.00 1.94
650 732 4.853924 AAAAATTTGTGCCTCGATCTGT 57.146 36.364 0.00 0.00 0.00 3.41
651 733 4.853924 AAAATTTGTGCCTCGATCTGTT 57.146 36.364 0.00 0.00 0.00 3.16
652 734 5.957842 AAAATTTGTGCCTCGATCTGTTA 57.042 34.783 0.00 0.00 0.00 2.41
653 735 4.946784 AATTTGTGCCTCGATCTGTTAC 57.053 40.909 0.00 0.00 0.00 2.50
654 736 3.678056 TTTGTGCCTCGATCTGTTACT 57.322 42.857 0.00 0.00 0.00 2.24
655 737 2.941453 TGTGCCTCGATCTGTTACTC 57.059 50.000 0.00 0.00 0.00 2.59
656 738 1.132453 TGTGCCTCGATCTGTTACTCG 59.868 52.381 0.00 0.00 36.25 4.18
657 739 0.738975 TGCCTCGATCTGTTACTCGG 59.261 55.000 0.00 0.00 35.64 4.63
658 740 0.030908 GCCTCGATCTGTTACTCGGG 59.969 60.000 0.00 0.00 35.64 5.14
659 741 0.030908 CCTCGATCTGTTACTCGGGC 59.969 60.000 0.00 0.00 34.03 6.13
660 742 0.030908 CTCGATCTGTTACTCGGGCC 59.969 60.000 0.00 0.00 35.64 5.80
661 743 1.299165 CGATCTGTTACTCGGGCCG 60.299 63.158 22.51 22.51 0.00 6.13
662 744 1.591863 GATCTGTTACTCGGGCCGC 60.592 63.158 23.83 7.39 0.00 6.53
663 745 2.017559 GATCTGTTACTCGGGCCGCT 62.018 60.000 23.83 11.37 0.00 5.52
664 746 2.298158 ATCTGTTACTCGGGCCGCTG 62.298 60.000 23.83 18.73 0.00 5.18
665 747 3.296709 CTGTTACTCGGGCCGCTGT 62.297 63.158 23.83 23.43 0.00 4.40
666 748 2.813908 GTTACTCGGGCCGCTGTG 60.814 66.667 23.83 13.43 0.00 3.66
667 749 4.752879 TTACTCGGGCCGCTGTGC 62.753 66.667 23.83 0.00 0.00 4.57
675 757 2.590007 GCCGCTGTGCCAGATAGG 60.590 66.667 6.40 6.83 41.84 2.57
676 758 2.109799 CCGCTGTGCCAGATAGGG 59.890 66.667 6.40 0.00 38.09 3.53
684 766 2.590007 CCAGATAGGGCAGCACGC 60.590 66.667 0.00 0.00 41.28 5.34
685 767 2.963854 CAGATAGGGCAGCACGCG 60.964 66.667 3.53 3.53 43.84 6.01
686 768 3.461773 AGATAGGGCAGCACGCGT 61.462 61.111 5.58 5.58 43.84 6.01
687 769 3.264897 GATAGGGCAGCACGCGTG 61.265 66.667 34.01 34.01 43.84 5.34
702 784 4.692475 GTGCCGGCCCGTGTACTT 62.692 66.667 26.77 0.00 0.00 2.24
703 785 2.996153 TGCCGGCCCGTGTACTTA 60.996 61.111 26.77 0.00 0.00 2.24
704 786 2.202837 GCCGGCCCGTGTACTTAG 60.203 66.667 18.11 0.00 0.00 2.18
737 819 2.209315 CCAGTTGGCCAGGTTTGGG 61.209 63.158 5.11 0.00 45.16 4.12
738 820 1.457455 CAGTTGGCCAGGTTTGGGT 60.457 57.895 5.11 0.00 45.16 4.51
739 821 1.048160 CAGTTGGCCAGGTTTGGGTT 61.048 55.000 5.11 0.00 45.16 4.11
740 822 1.048160 AGTTGGCCAGGTTTGGGTTG 61.048 55.000 5.11 0.00 45.16 3.77
743 825 3.989787 GCCAGGTTTGGGTTGGCG 61.990 66.667 0.00 0.00 46.82 5.69
744 826 2.520741 CCAGGTTTGGGTTGGCGT 60.521 61.111 0.00 0.00 41.05 5.68
745 827 2.561037 CCAGGTTTGGGTTGGCGTC 61.561 63.158 0.00 0.00 41.05 5.19
757 839 2.737376 GGCGTCACCTGTTCCGTC 60.737 66.667 0.00 0.00 34.51 4.79
769 851 1.682684 TTCCGTCCTCAGCCTCCTC 60.683 63.158 0.00 0.00 0.00 3.71
819 909 0.761323 TTCCACTCCACTTCCACGGA 60.761 55.000 0.00 0.00 0.00 4.69
863 953 1.221021 CAAGGTCGGGCTAGGGTTC 59.779 63.158 0.00 0.00 0.00 3.62
1109 1205 0.904865 ATCCACGGCCAACTCTCTCA 60.905 55.000 2.24 0.00 0.00 3.27
1110 1206 0.904865 TCCACGGCCAACTCTCTCAT 60.905 55.000 2.24 0.00 0.00 2.90
1113 1209 0.687354 ACGGCCAACTCTCTCATTGT 59.313 50.000 2.24 0.00 0.00 2.71
1167 1263 1.533625 CAGGCGTTGATGGGAAGAAA 58.466 50.000 0.00 0.00 0.00 2.52
1351 1447 2.038813 TGAGCGATGGGGACTGGA 59.961 61.111 0.00 0.00 0.00 3.86
1432 1528 1.893062 CAGAGACTGATGGCCGACA 59.107 57.895 0.00 0.00 32.44 4.35
1450 1546 1.734465 ACAAGCAAGAAGAGCGTATGC 59.266 47.619 0.00 0.00 43.24 3.14
1484 1580 7.674471 AACTGAACTTCTTTAGCCACTATTC 57.326 36.000 0.00 0.00 0.00 1.75
1503 1599 8.028354 CACTATTCTCTTATGATAGCTCTGTGG 58.972 40.741 0.00 0.00 0.00 4.17
1523 1619 2.356125 GGATTGCTCTGCCCTGTTCTTA 60.356 50.000 0.00 0.00 0.00 2.10
1532 1628 6.151144 GCTCTGCCCTGTTCTTAAAGAAAATA 59.849 38.462 0.00 0.00 35.75 1.40
1627 1726 3.190874 GCATACGAAAGAAGGTGGAGAG 58.809 50.000 0.00 0.00 0.00 3.20
1638 1737 2.614969 TGGAGAGGGCAATGGGCT 60.615 61.111 0.00 0.00 44.01 5.19
1639 1738 2.240918 TGGAGAGGGCAATGGGCTT 61.241 57.895 0.00 0.00 44.01 4.35
1817 1916 2.302157 ACCTGTAGTTGGAGTAAGTGGC 59.698 50.000 0.00 0.00 0.00 5.01
1824 1923 5.864418 AGTTGGAGTAAGTGGCGATAATA 57.136 39.130 0.00 0.00 0.00 0.98
1987 2086 7.902087 AGAATAAGAGCCAGAGGTTATATCAC 58.098 38.462 0.00 0.00 0.00 3.06
2011 2114 5.404946 TGTGCTAATTACTTCACCTACGAC 58.595 41.667 0.00 0.00 0.00 4.34
2035 2138 4.760530 TGTGACTGCTATAAGATGGCTT 57.239 40.909 0.00 0.00 37.67 4.35
2037 2140 5.601662 TGTGACTGCTATAAGATGGCTTAC 58.398 41.667 0.00 0.00 39.29 2.34
2045 2148 7.434492 TGCTATAAGATGGCTTACTTAGTGAC 58.566 38.462 0.00 0.00 39.29 3.67
2113 2221 2.860735 GTTCATGTCATGAGTAGGCGTC 59.139 50.000 14.98 0.00 40.94 5.19
2139 2247 6.482835 CGTTTATGCAATTGATTACCTCGAA 58.517 36.000 10.34 0.00 0.00 3.71
2275 2398 1.746991 CTTCGCCTTCCCTCTTGCC 60.747 63.158 0.00 0.00 0.00 4.52
2276 2399 2.190488 CTTCGCCTTCCCTCTTGCCT 62.190 60.000 0.00 0.00 0.00 4.75
2277 2400 0.907704 TTCGCCTTCCCTCTTGCCTA 60.908 55.000 0.00 0.00 0.00 3.93
2300 2440 9.120538 CCTACTGTGGCAGTAAATTACATTAAT 57.879 33.333 5.89 0.00 44.80 1.40
2307 2447 9.757227 TGGCAGTAAATTACATTAATTAATGGC 57.243 29.630 31.69 23.30 45.54 4.40
2308 2448 9.981114 GGCAGTAAATTACATTAATTAATGGCT 57.019 29.630 31.69 19.58 45.54 4.75
2326 2466 3.516700 TGGCTTACTGTTAACCTAGTCCC 59.483 47.826 2.48 3.90 0.00 4.46
2327 2467 3.773667 GGCTTACTGTTAACCTAGTCCCT 59.226 47.826 2.48 0.00 0.00 4.20
2331 2471 6.295745 GCTTACTGTTAACCTAGTCCCTCTTT 60.296 42.308 2.48 0.00 0.00 2.52
2338 2478 2.907042 ACCTAGTCCCTCTTTCCACAAG 59.093 50.000 0.00 0.00 0.00 3.16
2340 2480 3.777522 CCTAGTCCCTCTTTCCACAAGAT 59.222 47.826 0.00 0.00 0.00 2.40
2342 2482 5.069781 CCTAGTCCCTCTTTCCACAAGATAG 59.930 48.000 0.00 0.00 0.00 2.08
2343 2483 4.689062 AGTCCCTCTTTCCACAAGATAGA 58.311 43.478 0.00 0.00 32.40 1.98
2344 2484 5.284582 AGTCCCTCTTTCCACAAGATAGAT 58.715 41.667 0.00 0.00 32.86 1.98
2345 2485 5.130145 AGTCCCTCTTTCCACAAGATAGATG 59.870 44.000 0.00 0.00 32.86 2.90
2346 2486 4.133078 CCCTCTTTCCACAAGATAGATGC 58.867 47.826 0.00 0.00 32.86 3.91
2347 2487 4.133078 CCTCTTTCCACAAGATAGATGCC 58.867 47.826 0.00 0.00 32.86 4.40
2348 2488 4.133078 CTCTTTCCACAAGATAGATGCCC 58.867 47.826 0.00 0.00 32.86 5.36
2349 2489 3.782523 TCTTTCCACAAGATAGATGCCCT 59.217 43.478 0.00 0.00 28.73 5.19
2350 2490 4.968719 TCTTTCCACAAGATAGATGCCCTA 59.031 41.667 0.00 0.00 28.73 3.53
2351 2491 5.428457 TCTTTCCACAAGATAGATGCCCTAA 59.572 40.000 0.00 0.00 28.73 2.69
2352 2492 4.963318 TCCACAAGATAGATGCCCTAAG 57.037 45.455 0.00 0.00 0.00 2.18
2353 2493 4.298626 TCCACAAGATAGATGCCCTAAGT 58.701 43.478 0.00 0.00 0.00 2.24
2354 2494 4.721776 TCCACAAGATAGATGCCCTAAGTT 59.278 41.667 0.00 0.00 0.00 2.66
2355 2495 5.191722 TCCACAAGATAGATGCCCTAAGTTT 59.808 40.000 0.00 0.00 0.00 2.66
2356 2496 5.888161 CCACAAGATAGATGCCCTAAGTTTT 59.112 40.000 0.00 0.00 0.00 2.43
2357 2497 6.183360 CCACAAGATAGATGCCCTAAGTTTTG 60.183 42.308 0.00 0.00 0.00 2.44
2358 2498 6.375455 CACAAGATAGATGCCCTAAGTTTTGT 59.625 38.462 0.00 0.00 0.00 2.83
2359 2499 6.599638 ACAAGATAGATGCCCTAAGTTTTGTC 59.400 38.462 0.00 0.00 0.00 3.18
2360 2500 6.567602 AGATAGATGCCCTAAGTTTTGTCT 57.432 37.500 0.00 0.00 0.00 3.41
2361 2501 6.963322 AGATAGATGCCCTAAGTTTTGTCTT 58.037 36.000 0.00 0.00 0.00 3.01
2362 2502 7.406104 AGATAGATGCCCTAAGTTTTGTCTTT 58.594 34.615 0.00 0.00 0.00 2.52
2363 2503 8.548877 AGATAGATGCCCTAAGTTTTGTCTTTA 58.451 33.333 0.00 0.00 0.00 1.85
2364 2504 8.738645 ATAGATGCCCTAAGTTTTGTCTTTAG 57.261 34.615 0.00 0.00 0.00 1.85
2365 2505 6.543735 AGATGCCCTAAGTTTTGTCTTTAGT 58.456 36.000 0.00 0.00 0.00 2.24
2366 2506 6.655425 AGATGCCCTAAGTTTTGTCTTTAGTC 59.345 38.462 0.00 0.00 0.00 2.59
2367 2507 5.686753 TGCCCTAAGTTTTGTCTTTAGTCA 58.313 37.500 0.00 0.00 0.00 3.41
2368 2508 5.529800 TGCCCTAAGTTTTGTCTTTAGTCAC 59.470 40.000 0.00 0.00 0.00 3.67
2369 2509 5.529800 GCCCTAAGTTTTGTCTTTAGTCACA 59.470 40.000 0.00 0.00 0.00 3.58
2370 2510 6.512903 GCCCTAAGTTTTGTCTTTAGTCACAC 60.513 42.308 0.00 0.00 0.00 3.82
2371 2511 6.766467 CCCTAAGTTTTGTCTTTAGTCACACT 59.234 38.462 0.00 0.00 0.00 3.55
2372 2512 7.282450 CCCTAAGTTTTGTCTTTAGTCACACTT 59.718 37.037 0.00 0.00 0.00 3.16
2373 2513 8.674607 CCTAAGTTTTGTCTTTAGTCACACTTT 58.325 33.333 6.26 0.00 0.00 2.66
2375 2515 8.965986 AAGTTTTGTCTTTAGTCACACTTTTC 57.034 30.769 0.00 0.00 0.00 2.29
2376 2516 8.336801 AGTTTTGTCTTTAGTCACACTTTTCT 57.663 30.769 0.00 0.00 0.00 2.52
2377 2517 8.237267 AGTTTTGTCTTTAGTCACACTTTTCTG 58.763 33.333 0.00 0.00 0.00 3.02
2378 2518 7.915293 TTTGTCTTTAGTCACACTTTTCTGA 57.085 32.000 0.00 0.00 0.00 3.27
2379 2519 7.915293 TTGTCTTTAGTCACACTTTTCTGAA 57.085 32.000 0.00 0.00 0.00 3.02
2380 2520 7.539712 TGTCTTTAGTCACACTTTTCTGAAG 57.460 36.000 0.00 0.00 0.00 3.02
2381 2521 7.103641 TGTCTTTAGTCACACTTTTCTGAAGT 58.896 34.615 0.00 0.00 0.00 3.01
2382 2522 7.277981 TGTCTTTAGTCACACTTTTCTGAAGTC 59.722 37.037 0.00 0.00 0.00 3.01
2383 2523 7.492994 GTCTTTAGTCACACTTTTCTGAAGTCT 59.507 37.037 0.00 0.00 0.00 3.24
2384 2524 7.492669 TCTTTAGTCACACTTTTCTGAAGTCTG 59.507 37.037 0.00 0.00 0.00 3.51
2385 2525 5.344743 AGTCACACTTTTCTGAAGTCTGA 57.655 39.130 0.00 0.00 0.00 3.27
2386 2526 5.112686 AGTCACACTTTTCTGAAGTCTGAC 58.887 41.667 15.13 15.13 42.59 3.51
2387 2527 4.271291 GTCACACTTTTCTGAAGTCTGACC 59.729 45.833 13.09 0.00 39.03 4.02
2388 2528 4.081142 TCACACTTTTCTGAAGTCTGACCA 60.081 41.667 3.76 0.00 0.00 4.02
2389 2529 4.635765 CACACTTTTCTGAAGTCTGACCAA 59.364 41.667 3.76 0.00 0.00 3.67
2390 2530 4.878397 ACACTTTTCTGAAGTCTGACCAAG 59.122 41.667 3.76 0.09 0.00 3.61
2391 2531 4.878397 CACTTTTCTGAAGTCTGACCAAGT 59.122 41.667 3.76 6.31 32.52 3.16
2392 2532 5.355350 CACTTTTCTGAAGTCTGACCAAGTT 59.645 40.000 3.76 0.00 31.21 2.66
2412 2552 7.201548 CCAAGTTTATGCACAAAAATATCAGCC 60.202 37.037 0.00 0.00 0.00 4.85
2547 2687 3.252554 ACTTATGGGGGCTGTTTTGAA 57.747 42.857 0.00 0.00 0.00 2.69
2823 2963 4.751060 TCTGATTTGGAATTTGAGCATGC 58.249 39.130 10.51 10.51 0.00 4.06
3036 3176 5.036117 TCTTATGTTGTCCAGATTAGGCC 57.964 43.478 0.00 0.00 0.00 5.19
3110 3256 8.631797 TGGTTGTAGTATGATGTAACGCTAATA 58.368 33.333 0.00 0.00 0.00 0.98
3111 3257 9.467258 GGTTGTAGTATGATGTAACGCTAATAA 57.533 33.333 0.00 0.00 0.00 1.40
3258 3469 8.039603 TGAAAGTTGAAATCGTGCTGTATAAT 57.960 30.769 0.00 0.00 0.00 1.28
3271 3482 5.049818 GTGCTGTATAATTCCTGATCACTGC 60.050 44.000 0.00 0.00 0.00 4.40
3348 3559 1.241929 AGGACTCCCCTGGTTGGAA 59.758 57.895 0.00 0.00 45.61 3.53
3359 3570 3.763897 CCCTGGTTGGAATAGAACTTTGG 59.236 47.826 0.00 0.00 38.35 3.28
3508 3721 7.879160 ACTCATGGTGCATTAAACATTTCAATT 59.121 29.630 0.00 0.00 0.00 2.32
3524 3737 5.982465 TTCAATTTTCCTTTTGCTTTCCG 57.018 34.783 0.00 0.00 0.00 4.30
3629 3845 5.179929 CAGAATGTGTGAGTAGCATTGTCAA 59.820 40.000 0.00 0.00 33.56 3.18
3674 3892 2.879002 TTTTGGCAAATTCGTGCTGA 57.121 40.000 14.29 0.00 44.31 4.26
3723 3941 9.715121 AAAATGCAAGAACATATTTCAAGATGT 57.285 25.926 0.00 0.00 42.17 3.06
3724 3942 8.922058 AATGCAAGAACATATTTCAAGATGTC 57.078 30.769 0.42 0.00 39.71 3.06
3725 3943 7.692460 TGCAAGAACATATTTCAAGATGTCT 57.308 32.000 0.42 0.00 39.71 3.41
3726 3944 7.532571 TGCAAGAACATATTTCAAGATGTCTG 58.467 34.615 0.42 1.44 39.71 3.51
3727 3945 7.391275 TGCAAGAACATATTTCAAGATGTCTGA 59.609 33.333 0.42 0.00 39.71 3.27
3728 3946 7.909121 GCAAGAACATATTTCAAGATGTCTGAG 59.091 37.037 0.42 0.00 39.71 3.35
3729 3947 7.551035 AGAACATATTTCAAGATGTCTGAGC 57.449 36.000 0.42 0.00 39.71 4.26
3730 3948 7.337167 AGAACATATTTCAAGATGTCTGAGCT 58.663 34.615 0.42 0.00 39.71 4.09
3731 3949 8.481314 AGAACATATTTCAAGATGTCTGAGCTA 58.519 33.333 0.42 0.00 39.71 3.32
3732 3950 8.659925 AACATATTTCAAGATGTCTGAGCTAG 57.340 34.615 0.42 0.00 39.71 3.42
3733 3951 7.790027 ACATATTTCAAGATGTCTGAGCTAGT 58.210 34.615 0.00 0.00 36.16 2.57
3766 3984 4.605718 CCATCTTGGATGAGCTAGCAAGC 61.606 52.174 18.83 7.34 44.58 4.01
3817 4035 4.155099 TGTGCAAATATTCCTTGTGGTACG 59.845 41.667 0.00 0.00 34.23 3.67
3886 4104 8.087750 CCTGATCTAGAAATAGCTTACCTCTTG 58.912 40.741 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 6.369629 TCCAGGAGTTTCAAAAATGTTCCTA 58.630 36.000 0.00 0.00 32.57 2.94
62 63 8.389366 TCCAAAAATTATCCACAAATCCCAAAT 58.611 29.630 0.00 0.00 0.00 2.32
163 194 5.898630 AATATTGTTTTGCACGTTCCAAC 57.101 34.783 0.00 0.00 0.00 3.77
194 225 9.701355 AAAATCACAATTTCGAAAAATGTTCAC 57.299 25.926 22.65 0.00 35.27 3.18
385 465 7.116819 CAGTTTTATGGTTTTCTTTCGTTTGC 58.883 34.615 0.00 0.00 0.00 3.68
532 614 2.887568 GCACACGCGATCTCCCAG 60.888 66.667 15.93 0.00 0.00 4.45
543 625 1.686566 ATGTCGAGCATTCGCACACG 61.687 55.000 0.00 0.00 46.28 4.49
584 666 3.123804 CCACGTATCTCCGAAAATCCTG 58.876 50.000 0.00 0.00 0.00 3.86
629 711 4.853924 ACAGATCGAGGCACAAATTTTT 57.146 36.364 0.00 0.00 0.00 1.94
630 712 4.853924 AACAGATCGAGGCACAAATTTT 57.146 36.364 0.00 0.00 0.00 1.82
631 713 5.003804 AGTAACAGATCGAGGCACAAATTT 58.996 37.500 0.00 0.00 0.00 1.82
632 714 4.579869 AGTAACAGATCGAGGCACAAATT 58.420 39.130 0.00 0.00 0.00 1.82
633 715 4.184629 GAGTAACAGATCGAGGCACAAAT 58.815 43.478 0.00 0.00 0.00 2.32
634 716 3.585862 GAGTAACAGATCGAGGCACAAA 58.414 45.455 0.00 0.00 0.00 2.83
635 717 2.415491 CGAGTAACAGATCGAGGCACAA 60.415 50.000 0.00 0.00 41.40 3.33
636 718 1.132453 CGAGTAACAGATCGAGGCACA 59.868 52.381 0.00 0.00 41.40 4.57
637 719 1.534175 CCGAGTAACAGATCGAGGCAC 60.534 57.143 0.00 0.00 41.40 5.01
638 720 0.738975 CCGAGTAACAGATCGAGGCA 59.261 55.000 0.00 0.00 41.40 4.75
639 721 0.030908 CCCGAGTAACAGATCGAGGC 59.969 60.000 0.00 0.00 41.40 4.70
640 722 0.030908 GCCCGAGTAACAGATCGAGG 59.969 60.000 0.00 0.00 41.40 4.63
641 723 0.030908 GGCCCGAGTAACAGATCGAG 59.969 60.000 0.00 0.00 41.40 4.04
642 724 1.721664 CGGCCCGAGTAACAGATCGA 61.722 60.000 0.00 0.00 41.40 3.59
643 725 1.299165 CGGCCCGAGTAACAGATCG 60.299 63.158 0.00 0.00 38.65 3.69
644 726 1.591863 GCGGCCCGAGTAACAGATC 60.592 63.158 7.68 0.00 0.00 2.75
645 727 2.058595 AGCGGCCCGAGTAACAGAT 61.059 57.895 7.68 0.00 0.00 2.90
646 728 2.678934 AGCGGCCCGAGTAACAGA 60.679 61.111 7.68 0.00 0.00 3.41
647 729 2.509336 CAGCGGCCCGAGTAACAG 60.509 66.667 7.68 0.00 0.00 3.16
648 730 3.307906 ACAGCGGCCCGAGTAACA 61.308 61.111 7.68 0.00 0.00 2.41
649 731 2.813908 CACAGCGGCCCGAGTAAC 60.814 66.667 7.68 0.00 0.00 2.50
650 732 4.752879 GCACAGCGGCCCGAGTAA 62.753 66.667 7.68 0.00 0.00 2.24
667 749 2.590007 GCGTGCTGCCCTATCTGG 60.590 66.667 0.00 0.00 37.76 3.86
668 750 2.963854 CGCGTGCTGCCCTATCTG 60.964 66.667 0.00 0.00 42.08 2.90
669 751 3.461773 ACGCGTGCTGCCCTATCT 61.462 61.111 12.93 0.00 42.08 1.98
670 752 3.264897 CACGCGTGCTGCCCTATC 61.265 66.667 28.16 0.00 42.08 2.08
685 767 3.299524 TAAGTACACGGGCCGGCAC 62.300 63.158 31.78 26.77 0.00 5.01
686 768 2.996153 TAAGTACACGGGCCGGCA 60.996 61.111 31.78 11.85 0.00 5.69
687 769 2.202837 CTAAGTACACGGGCCGGC 60.203 66.667 31.78 21.18 0.00 6.13
688 770 2.202837 GCTAAGTACACGGGCCGG 60.203 66.667 31.78 21.03 0.00 6.13
689 771 2.581409 CGCTAAGTACACGGGCCG 60.581 66.667 27.06 27.06 0.00 6.13
690 772 1.808390 CACGCTAAGTACACGGGCC 60.808 63.158 0.00 0.00 0.00 5.80
691 773 3.776656 CACGCTAAGTACACGGGC 58.223 61.111 0.00 0.00 0.00 6.13
692 774 1.808390 GGCACGCTAAGTACACGGG 60.808 63.158 0.00 0.00 0.00 5.28
693 775 3.776656 GGCACGCTAAGTACACGG 58.223 61.111 0.00 0.00 0.00 4.94
722 804 1.445518 CAACCCAAACCTGGCCAAC 59.554 57.895 7.01 0.00 41.99 3.77
736 818 2.258726 GGAACAGGTGACGCCAACC 61.259 63.158 7.99 1.25 40.61 3.77
737 819 2.604174 CGGAACAGGTGACGCCAAC 61.604 63.158 7.99 0.00 40.61 3.77
738 820 2.280524 CGGAACAGGTGACGCCAA 60.281 61.111 7.99 0.00 40.61 4.52
739 821 3.509137 GACGGAACAGGTGACGCCA 62.509 63.158 7.99 0.00 40.61 5.69
740 822 2.737376 GACGGAACAGGTGACGCC 60.737 66.667 0.00 0.00 37.58 5.68
742 824 1.080705 GAGGACGGAACAGGTGACG 60.081 63.158 0.00 0.00 0.00 4.35
743 825 0.038159 CTGAGGACGGAACAGGTGAC 60.038 60.000 0.00 0.00 0.00 3.67
744 826 1.816863 GCTGAGGACGGAACAGGTGA 61.817 60.000 0.00 0.00 33.00 4.02
745 827 1.374758 GCTGAGGACGGAACAGGTG 60.375 63.158 0.00 0.00 33.00 4.00
798 888 0.105964 CGTGGAAGTGGAGTGGAACA 59.894 55.000 0.00 0.00 41.43 3.18
993 1089 1.821332 CGGAGCCTGCATTTCCTCC 60.821 63.158 10.42 10.42 40.33 4.30
1089 1185 0.179097 GAGAGAGTTGGCCGTGGATC 60.179 60.000 0.00 0.00 0.00 3.36
1094 1190 0.687354 ACAATGAGAGAGTTGGCCGT 59.313 50.000 0.00 0.00 0.00 5.68
1099 1195 2.740981 GGTCAGCACAATGAGAGAGTTG 59.259 50.000 0.00 0.00 0.00 3.16
1109 1205 3.058160 GCAGCGGGTCAGCACAAT 61.058 61.111 0.00 0.00 40.15 2.71
1207 1303 3.151022 GAGGTCTCCCAGGGCTCG 61.151 72.222 0.00 0.00 0.00 5.03
1341 1437 1.002069 AGCATTTCATCCAGTCCCCA 58.998 50.000 0.00 0.00 0.00 4.96
1351 1447 1.660560 GCCCACTCGCAGCATTTCAT 61.661 55.000 0.00 0.00 0.00 2.57
1450 1546 9.439537 GCTAAAGAAGTTCAGTTAAACAGAAAG 57.560 33.333 5.50 0.00 0.00 2.62
1484 1580 5.638657 GCAATCCACAGAGCTATCATAAGAG 59.361 44.000 0.00 0.00 0.00 2.85
1503 1599 1.831580 AAGAACAGGGCAGAGCAATC 58.168 50.000 0.00 0.00 0.00 2.67
1627 1726 3.985877 GCAAAAAGCCCATTGCCC 58.014 55.556 6.67 0.00 44.72 5.36
1638 1737 3.295093 TGTCCATGGAGACTTGCAAAAA 58.705 40.909 16.81 0.00 37.66 1.94
1639 1738 2.886523 CTGTCCATGGAGACTTGCAAAA 59.113 45.455 16.81 0.00 37.66 2.44
1985 2084 5.288712 CGTAGGTGAAGTAATTAGCACAGTG 59.711 44.000 12.44 0.00 33.09 3.66
1987 2086 5.515626 GTCGTAGGTGAAGTAATTAGCACAG 59.484 44.000 12.44 4.40 33.09 3.66
2011 2114 3.812053 GCCATCTTATAGCAGTCACAAGG 59.188 47.826 0.00 0.00 0.00 3.61
2035 2138 6.713903 AGTAACACTGTGCTAGTCACTAAGTA 59.286 38.462 7.90 3.26 45.81 2.24
2037 2140 5.859114 CAGTAACACTGTGCTAGTCACTAAG 59.141 44.000 7.90 9.58 45.81 2.18
2045 2148 5.065704 AGTCATCAGTAACACTGTGCTAG 57.934 43.478 7.90 0.00 46.03 3.42
2113 2221 4.597079 AGGTAATCAATTGCATAAACGCG 58.403 39.130 3.53 3.53 33.35 6.01
2139 2247 9.566331 TCCAGGGATATCTAAGATACATTCAAT 57.434 33.333 2.05 0.00 0.00 2.57
2298 2438 9.392259 GACTAGGTTAACAGTAAGCCATTAATT 57.608 33.333 8.10 0.00 38.28 1.40
2300 2440 7.333323 GGACTAGGTTAACAGTAAGCCATTAA 58.667 38.462 8.10 0.00 38.28 1.40
2305 2445 3.773667 AGGGACTAGGTTAACAGTAAGCC 59.226 47.826 8.10 1.50 38.28 4.35
2306 2446 4.710865 AGAGGGACTAGGTTAACAGTAAGC 59.289 45.833 8.10 0.00 41.55 3.09
2307 2447 6.854091 AAGAGGGACTAGGTTAACAGTAAG 57.146 41.667 8.10 1.47 41.55 2.34
2308 2448 6.212187 GGAAAGAGGGACTAGGTTAACAGTAA 59.788 42.308 8.10 0.00 41.55 2.24
2315 2455 4.136341 TGTGGAAAGAGGGACTAGGTTA 57.864 45.455 0.00 0.00 41.55 2.85
2316 2456 2.986050 TGTGGAAAGAGGGACTAGGTT 58.014 47.619 0.00 0.00 41.55 3.50
2317 2457 2.715763 TGTGGAAAGAGGGACTAGGT 57.284 50.000 0.00 0.00 41.55 3.08
2318 2458 3.173965 TCTTGTGGAAAGAGGGACTAGG 58.826 50.000 0.00 0.00 41.55 3.02
2320 2460 5.838955 TCTATCTTGTGGAAAGAGGGACTA 58.161 41.667 0.00 0.00 41.55 2.59
2323 2463 4.141620 GCATCTATCTTGTGGAAAGAGGGA 60.142 45.833 0.00 0.00 0.00 4.20
2326 2466 4.133078 GGGCATCTATCTTGTGGAAAGAG 58.867 47.826 0.00 0.00 0.00 2.85
2327 2467 3.782523 AGGGCATCTATCTTGTGGAAAGA 59.217 43.478 0.00 0.00 0.00 2.52
2331 2471 4.298626 ACTTAGGGCATCTATCTTGTGGA 58.701 43.478 0.00 0.00 0.00 4.02
2338 2478 7.631717 AAAGACAAAACTTAGGGCATCTATC 57.368 36.000 0.00 0.00 0.00 2.08
2340 2480 7.686434 ACTAAAGACAAAACTTAGGGCATCTA 58.314 34.615 0.00 0.00 0.00 1.98
2342 2482 6.430000 TGACTAAAGACAAAACTTAGGGCATC 59.570 38.462 0.00 0.00 0.00 3.91
2343 2483 6.206829 GTGACTAAAGACAAAACTTAGGGCAT 59.793 38.462 0.00 0.00 0.00 4.40
2344 2484 5.529800 GTGACTAAAGACAAAACTTAGGGCA 59.470 40.000 0.00 0.00 0.00 5.36
2345 2485 5.529800 TGTGACTAAAGACAAAACTTAGGGC 59.470 40.000 0.00 0.00 0.00 5.19
2346 2486 6.766467 AGTGTGACTAAAGACAAAACTTAGGG 59.234 38.462 0.00 0.00 0.00 3.53
2347 2487 7.787725 AGTGTGACTAAAGACAAAACTTAGG 57.212 36.000 0.00 0.00 0.00 2.69
2350 2490 8.793592 AGAAAAGTGTGACTAAAGACAAAACTT 58.206 29.630 6.19 6.19 33.71 2.66
2351 2491 8.237267 CAGAAAAGTGTGACTAAAGACAAAACT 58.763 33.333 0.00 0.00 0.00 2.66
2352 2492 8.234546 TCAGAAAAGTGTGACTAAAGACAAAAC 58.765 33.333 0.00 0.00 0.00 2.43
2353 2493 8.330466 TCAGAAAAGTGTGACTAAAGACAAAA 57.670 30.769 0.00 0.00 0.00 2.44
2354 2494 7.915293 TCAGAAAAGTGTGACTAAAGACAAA 57.085 32.000 0.00 0.00 0.00 2.83
2355 2495 7.606456 ACTTCAGAAAAGTGTGACTAAAGACAA 59.394 33.333 0.00 0.00 0.00 3.18
2356 2496 7.103641 ACTTCAGAAAAGTGTGACTAAAGACA 58.896 34.615 0.00 0.00 0.00 3.41
2357 2497 7.492994 AGACTTCAGAAAAGTGTGACTAAAGAC 59.507 37.037 0.00 0.00 0.00 3.01
2358 2498 7.492669 CAGACTTCAGAAAAGTGTGACTAAAGA 59.507 37.037 8.85 0.00 42.18 2.52
2359 2499 7.492669 TCAGACTTCAGAAAAGTGTGACTAAAG 59.507 37.037 12.18 0.00 42.99 1.85
2360 2500 7.327975 TCAGACTTCAGAAAAGTGTGACTAAA 58.672 34.615 12.18 0.00 42.99 1.85
2361 2501 6.873997 TCAGACTTCAGAAAAGTGTGACTAA 58.126 36.000 12.18 0.00 42.99 2.24
2362 2502 6.465439 TCAGACTTCAGAAAAGTGTGACTA 57.535 37.500 12.18 0.00 42.99 2.59
2363 2503 5.344743 TCAGACTTCAGAAAAGTGTGACT 57.655 39.130 12.18 0.00 42.99 3.41
2365 2505 4.081142 TGGTCAGACTTCAGAAAAGTGTGA 60.081 41.667 12.18 12.18 44.79 3.58
2366 2506 4.191544 TGGTCAGACTTCAGAAAAGTGTG 58.808 43.478 8.34 8.34 41.31 3.82
2367 2507 4.487714 TGGTCAGACTTCAGAAAAGTGT 57.512 40.909 0.00 0.00 0.00 3.55
2368 2508 4.878397 ACTTGGTCAGACTTCAGAAAAGTG 59.122 41.667 0.00 0.00 0.00 3.16
2369 2509 5.104259 ACTTGGTCAGACTTCAGAAAAGT 57.896 39.130 0.00 0.00 0.00 2.66
2370 2510 6.442513 AAACTTGGTCAGACTTCAGAAAAG 57.557 37.500 0.00 0.00 0.00 2.27
2371 2511 7.468631 GCATAAACTTGGTCAGACTTCAGAAAA 60.469 37.037 0.00 0.00 0.00 2.29
2372 2512 6.017109 GCATAAACTTGGTCAGACTTCAGAAA 60.017 38.462 0.00 0.00 0.00 2.52
2373 2513 5.470098 GCATAAACTTGGTCAGACTTCAGAA 59.530 40.000 0.00 0.00 0.00 3.02
2374 2514 4.997395 GCATAAACTTGGTCAGACTTCAGA 59.003 41.667 0.00 0.00 0.00 3.27
2375 2515 4.756642 TGCATAAACTTGGTCAGACTTCAG 59.243 41.667 0.00 0.00 0.00 3.02
2376 2516 4.515191 GTGCATAAACTTGGTCAGACTTCA 59.485 41.667 0.00 0.00 0.00 3.02
2377 2517 4.515191 TGTGCATAAACTTGGTCAGACTTC 59.485 41.667 0.00 0.00 0.00 3.01
2378 2518 4.460263 TGTGCATAAACTTGGTCAGACTT 58.540 39.130 0.00 0.00 0.00 3.01
2379 2519 4.085357 TGTGCATAAACTTGGTCAGACT 57.915 40.909 0.00 0.00 0.00 3.24
2380 2520 4.829064 TTGTGCATAAACTTGGTCAGAC 57.171 40.909 0.00 0.00 0.00 3.51
2381 2521 5.843673 TTTTGTGCATAAACTTGGTCAGA 57.156 34.783 8.26 0.00 0.00 3.27
2382 2522 8.761575 ATATTTTTGTGCATAAACTTGGTCAG 57.238 30.769 8.26 0.00 0.00 3.51
2383 2523 8.363390 TGATATTTTTGTGCATAAACTTGGTCA 58.637 29.630 8.26 7.02 0.00 4.02
2384 2524 8.755696 TGATATTTTTGTGCATAAACTTGGTC 57.244 30.769 8.26 4.74 0.00 4.02
2385 2525 7.331687 GCTGATATTTTTGTGCATAAACTTGGT 59.668 33.333 8.26 0.00 0.00 3.67
2386 2526 7.201548 GGCTGATATTTTTGTGCATAAACTTGG 60.202 37.037 8.26 0.00 0.00 3.61
2387 2527 7.546667 AGGCTGATATTTTTGTGCATAAACTTG 59.453 33.333 8.26 0.00 0.00 3.16
2388 2528 7.614494 AGGCTGATATTTTTGTGCATAAACTT 58.386 30.769 8.26 1.95 0.00 2.66
2389 2529 7.174107 AGGCTGATATTTTTGTGCATAAACT 57.826 32.000 8.26 2.12 0.00 2.66
2390 2530 7.761249 AGAAGGCTGATATTTTTGTGCATAAAC 59.239 33.333 8.26 0.00 0.00 2.01
2391 2531 7.839907 AGAAGGCTGATATTTTTGTGCATAAA 58.160 30.769 4.30 4.30 0.00 1.40
2392 2532 7.408756 AGAAGGCTGATATTTTTGTGCATAA 57.591 32.000 0.00 0.00 0.00 1.90
2487 2627 9.846248 AGCAAGTTCATAGAACAAAATATCAAC 57.154 29.630 11.92 0.00 0.00 3.18
2532 2672 1.146774 TCAGATTCAAAACAGCCCCCA 59.853 47.619 0.00 0.00 0.00 4.96
2547 2687 7.308589 CCGGTTTCACAGAAACTAAATTCAGAT 60.309 37.037 18.65 0.00 0.00 2.90
2608 2748 9.678260 AGCATACAGATAAAGTTTGAAGAAGAT 57.322 29.630 0.00 0.00 0.00 2.40
2646 2786 7.078666 TTGATCAGTCAAAAACAGGTCACTGA 61.079 38.462 1.21 2.26 43.00 3.41
2649 2789 5.499139 TTGATCAGTCAAAAACAGGTCAC 57.501 39.130 0.00 0.00 41.22 3.67
2676 2816 8.684386 TTTGTGGTATGTTTCTGAAGACAATA 57.316 30.769 8.65 0.00 0.00 1.90
2832 2972 4.440880 CTTCAGGTCAAAATTGCAACCAA 58.559 39.130 0.00 0.00 35.01 3.67
2896 3036 4.824289 TGAAACCTCAACGGAGTAATACC 58.176 43.478 0.00 0.00 45.00 2.73
3258 3469 5.608449 CTCAATATGAGCAGTGATCAGGAA 58.392 41.667 17.22 5.35 37.72 3.36
3348 3559 1.382914 AGGTGGGGCCAAAGTTCTAT 58.617 50.000 4.39 0.00 40.61 1.98
3359 3570 0.966179 AAAATGACGAAAGGTGGGGC 59.034 50.000 0.00 0.00 0.00 5.80
3402 3615 5.147162 GCCTACAACTGAATGAAAAGAACG 58.853 41.667 0.00 0.00 0.00 3.95
3508 3721 6.150396 TCAATTACGGAAAGCAAAAGGAAA 57.850 33.333 0.00 0.00 0.00 3.13
3655 3873 2.741612 CTCAGCACGAATTTGCCAAAA 58.258 42.857 0.00 0.00 44.14 2.44
3658 3876 1.171549 TGCTCAGCACGAATTTGCCA 61.172 50.000 0.00 0.00 44.14 4.92
3674 3892 2.417924 CCAGTAAGATGCGAGAAGTGCT 60.418 50.000 0.00 0.00 0.00 4.40
3721 3939 6.041182 TGGTTAGTGTTTTACTAGCTCAGACA 59.959 38.462 0.00 0.00 42.57 3.41
3722 3940 6.453092 TGGTTAGTGTTTTACTAGCTCAGAC 58.547 40.000 0.00 0.00 42.57 3.51
3723 3941 6.659745 TGGTTAGTGTTTTACTAGCTCAGA 57.340 37.500 0.00 0.00 42.57 3.27
3724 3942 7.324178 AGATGGTTAGTGTTTTACTAGCTCAG 58.676 38.462 0.00 0.00 42.57 3.35
3725 3943 7.241042 AGATGGTTAGTGTTTTACTAGCTCA 57.759 36.000 0.00 0.00 42.57 4.26
3726 3944 7.064728 CCAAGATGGTTAGTGTTTTACTAGCTC 59.935 40.741 0.00 0.00 42.57 4.09
3727 3945 6.879458 CCAAGATGGTTAGTGTTTTACTAGCT 59.121 38.462 0.00 0.00 42.57 3.32
3728 3946 6.877322 TCCAAGATGGTTAGTGTTTTACTAGC 59.123 38.462 0.00 0.00 38.53 3.42
3729 3947 8.883731 CATCCAAGATGGTTAGTGTTTTACTAG 58.116 37.037 0.00 0.00 38.53 2.57
3730 3948 8.598916 TCATCCAAGATGGTTAGTGTTTTACTA 58.401 33.333 4.83 0.00 38.62 1.82
3731 3949 7.458397 TCATCCAAGATGGTTAGTGTTTTACT 58.542 34.615 4.83 0.00 40.02 2.24
3732 3950 7.626452 GCTCATCCAAGATGGTTAGTGTTTTAC 60.626 40.741 4.83 0.00 39.03 2.01
3733 3951 6.374333 GCTCATCCAAGATGGTTAGTGTTTTA 59.626 38.462 4.83 0.00 39.03 1.52
3766 3984 4.634883 AGCATTCAGACATCTGCTAAACTG 59.365 41.667 3.88 0.00 42.85 3.16
3817 4035 7.814587 AGGCTGAGAAAACAAAATATTAACTGC 59.185 33.333 0.00 0.00 0.00 4.40
3886 4104 5.008613 TGTTTCTTGAACTGCCATTACTGAC 59.991 40.000 0.00 0.00 39.08 3.51


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

AutoCloner maintained by Alex Coulton.