Multiple sequence alignment - TraesCS6D01G368900

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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 TraesCS6D01G368900 chr6D 100.000 4259 0 0 1 4259 455900781 455896523 0.000000e+00 7866.0
1 TraesCS6D01G368900 chr6D 86.581 1401 115 32 1017 2368 455907769 455906393 0.000000e+00 1478.0
2 TraesCS6D01G368900 chr6D 86.941 1095 87 29 2622 3711 455906387 455905344 0.000000e+00 1179.0
3 TraesCS6D01G368900 chr6D 85.227 704 69 20 1063 1745 455935638 455934949 0.000000e+00 691.0
4 TraesCS6D01G368900 chr6D 89.504 524 39 11 1043 1551 455970027 455969505 0.000000e+00 649.0
5 TraesCS6D01G368900 chr6D 87.461 319 32 5 2985 3302 455934167 455933856 1.130000e-95 361.0
6 TraesCS6D01G368900 chr6D 87.748 302 32 5 3002 3302 455968677 455968380 8.760000e-92 348.0
7 TraesCS6D01G368900 chr6D 81.707 246 23 15 3732 3967 455905357 455905124 7.270000e-43 185.0
8 TraesCS6D01G368900 chr6D 82.589 224 22 12 3979 4200 455933241 455933033 9.410000e-42 182.0
9 TraesCS6D01G368900 chr6B 93.426 1293 47 16 2402 3685 693131832 693130569 0.000000e+00 1882.0
10 TraesCS6D01G368900 chr6B 87.475 1525 113 43 888 2379 693133301 693131822 0.000000e+00 1687.0
11 TraesCS6D01G368900 chr6B 83.734 1039 95 40 2604 3625 693300334 693299353 0.000000e+00 915.0
12 TraesCS6D01G368900 chr6B 87.069 696 66 18 1063 1745 693324353 693323669 0.000000e+00 765.0
13 TraesCS6D01G368900 chr6B 86.390 698 55 17 1018 1699 693302785 693302112 0.000000e+00 726.0
14 TraesCS6D01G368900 chr6B 86.413 552 51 13 1697 2229 693301087 693300541 2.210000e-162 582.0
15 TraesCS6D01G368900 chr6B 93.059 389 26 1 93 480 693136139 693135751 6.180000e-158 568.0
16 TraesCS6D01G368900 chr6B 87.461 319 32 6 2985 3302 693322790 693322479 1.130000e-95 361.0
17 TraesCS6D01G368900 chr6B 92.032 251 15 3 630 880 693133625 693133380 8.760000e-92 348.0
18 TraesCS6D01G368900 chr6B 93.976 166 10 0 3683 3848 693130466 693130301 7.070000e-63 252.0
19 TraesCS6D01G368900 chr6B 91.875 160 6 2 4033 4192 693130224 693130072 2.580000e-52 217.0
20 TraesCS6D01G368900 chr6B 94.444 108 3 2 4091 4195 693321840 693321733 3.410000e-36 163.0
21 TraesCS6D01G368900 chr6B 90.196 102 7 2 4154 4252 693129539 693129438 3.460000e-26 130.0
22 TraesCS6D01G368900 chr6B 97.368 76 1 1 3879 3954 693130303 693130229 1.240000e-25 128.0
23 TraesCS6D01G368900 chr6B 94.937 79 4 0 3633 3711 693296849 693296771 1.610000e-24 124.0
24 TraesCS6D01G368900 chr6B 98.529 68 1 0 1 68 693136398 693136331 2.080000e-23 121.0
25 TraesCS6D01G368900 chr6B 81.761 159 13 8 3824 3973 693322261 693322110 7.480000e-23 119.0
26 TraesCS6D01G368900 chr6B 80.899 89 12 3 666 750 431800341 431800254 9.880000e-07 65.8
27 TraesCS6D01G368900 chr6A 85.900 1078 89 33 2598 3671 602715983 602714965 0.000000e+00 1090.0
28 TraesCS6D01G368900 chr6A 87.793 811 71 18 1801 2588 602717013 602716208 0.000000e+00 924.0
29 TraesCS6D01G368900 chr6A 88.643 678 52 17 1017 1682 602717679 602717015 0.000000e+00 802.0
30 TraesCS6D01G368900 chr6A 84.552 725 72 28 1059 1753 602740573 602739859 0.000000e+00 682.0
31 TraesCS6D01G368900 chr6A 79.183 1028 131 47 1063 2056 602727028 602726050 1.670000e-178 636.0
32 TraesCS6D01G368900 chr6A 87.473 471 36 9 3732 4193 602714962 602714506 4.880000e-144 521.0
33 TraesCS6D01G368900 chr6A 86.207 319 36 6 2985 3302 602725540 602725229 5.280000e-89 339.0
34 TraesCS6D01G368900 chr6A 87.072 263 31 3 3002 3264 602739201 602738942 1.160000e-75 294.0
35 TraesCS6D01G368900 chr6A 79.275 386 58 15 2202 2579 596485287 596485658 2.540000e-62 250.0
36 TraesCS6D01G368900 chr6A 83.732 209 34 0 2610 2818 596485824 596486032 9.340000e-47 198.0
37 TraesCS6D01G368900 chr6A 87.500 176 5 11 4019 4193 602724667 602724508 2.020000e-43 187.0
38 TraesCS6D01G368900 chr6A 86.806 144 10 5 3824 3966 602725028 602724893 7.380000e-33 152.0
39 TraesCS6D01G368900 chr6A 73.874 333 74 10 405 733 520435707 520435384 2.080000e-23 121.0
40 TraesCS6D01G368900 chr6A 86.022 93 7 5 661 753 103952906 103952820 1.260000e-15 95.3
41 TraesCS6D01G368900 chr3D 83.067 313 44 6 2600 2910 457057202 457057507 4.190000e-70 276.0
42 TraesCS6D01G368900 chr3D 91.034 145 13 0 1414 1558 457047667 457047811 3.360000e-46 196.0
43 TraesCS6D01G368900 chr3B 91.057 123 7 3 4080 4202 822111744 822111862 3.410000e-36 163.0
44 TraesCS6D01G368900 chr3B 93.458 107 7 0 4086 4192 821796316 821796422 4.410000e-35 159.0
45 TraesCS6D01G368900 chr3B 92.593 108 7 1 4086 4192 821759276 821759383 2.050000e-33 154.0
46 TraesCS6D01G368900 chr3A 88.800 125 8 4 4079 4201 743875880 743876000 9.540000e-32 148.0
47 TraesCS6D01G368900 chr5A 88.525 122 10 3 4081 4202 44979600 44979717 1.230000e-30 145.0
48 TraesCS6D01G368900 chr5A 90.909 55 4 1 659 713 431654907 431654960 5.910000e-09 73.1


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 TraesCS6D01G368900 chr6D 455896523 455900781 4258 True 7866.000000 7866 100.000000 1 4259 1 chr6D.!!$R1 4258
1 TraesCS6D01G368900 chr6D 455905124 455907769 2645 True 947.333333 1478 85.076333 1017 3967 3 chr6D.!!$R2 2950
2 TraesCS6D01G368900 chr6D 455968380 455970027 1647 True 498.500000 649 88.626000 1043 3302 2 chr6D.!!$R4 2259
3 TraesCS6D01G368900 chr6D 455933033 455935638 2605 True 411.333333 691 85.092333 1063 4200 3 chr6D.!!$R3 3137
4 TraesCS6D01G368900 chr6B 693129438 693136398 6960 True 592.555556 1882 93.104000 1 4252 9 chr6B.!!$R2 4251
5 TraesCS6D01G368900 chr6B 693296771 693302785 6014 True 586.750000 915 87.868500 1018 3711 4 chr6B.!!$R3 2693
6 TraesCS6D01G368900 chr6B 693321733 693324353 2620 True 352.000000 765 87.683750 1063 4195 4 chr6B.!!$R4 3132
7 TraesCS6D01G368900 chr6A 602714506 602717679 3173 True 834.250000 1090 87.452250 1017 4193 4 chr6A.!!$R3 3176
8 TraesCS6D01G368900 chr6A 602738942 602740573 1631 True 488.000000 682 85.812000 1059 3264 2 chr6A.!!$R5 2205
9 TraesCS6D01G368900 chr6A 602724508 602727028 2520 True 328.500000 636 84.924000 1063 4193 4 chr6A.!!$R4 3130
10 TraesCS6D01G368900 chr6A 596485287 596486032 745 False 224.000000 250 81.503500 2202 2818 2 chr6A.!!$F1 616

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
979 3199 0.106419 ACACCCACACCCGAACAAAT 60.106 50.0 0.00 0.00 0.00 2.32 F
1539 3808 0.106419 GGATCCCACTCGAGGACTCT 60.106 60.0 18.41 0.00 35.85 3.24 F
1797 5194 0.179029 ATTTCGGCATAGTTCCCGGG 60.179 55.0 16.85 16.85 44.45 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2913 6826 0.106469 CCTCCTCATCGTCCTCCTCA 60.106 60.0 0.0 0.00 0.0 3.86 R
2925 6838 0.560193 CCTCATCCTCCTCCTCCTCA 59.440 60.0 0.0 0.00 0.0 3.86 R
3728 10280 0.035630 AGAAGAGCAGTGCATGACCC 60.036 55.0 19.2 1.05 0.0 4.46 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
60 61 2.554032 ACTCGGCTCAACTCAATTTTGG 59.446 45.455 0.00 0.00 0.00 3.28
68 69 6.294731 GGCTCAACTCAATTTTGGTGACTAAT 60.295 38.462 0.00 0.00 0.00 1.73
69 70 7.147976 GCTCAACTCAATTTTGGTGACTAATT 58.852 34.615 0.00 0.00 0.00 1.40
70 71 7.653311 GCTCAACTCAATTTTGGTGACTAATTT 59.347 33.333 0.00 0.00 0.00 1.82
71 72 9.533253 CTCAACTCAATTTTGGTGACTAATTTT 57.467 29.630 0.00 0.00 0.00 1.82
75 76 9.758651 ACTCAATTTTGGTGACTAATTTTAACC 57.241 29.630 0.00 0.00 0.00 2.85
76 77 9.757227 CTCAATTTTGGTGACTAATTTTAACCA 57.243 29.630 0.00 0.00 39.11 3.67
82 83 6.289834 TGGTGACTAATTTTAACCAACTCGA 58.710 36.000 0.00 0.00 37.96 4.04
83 84 6.766944 TGGTGACTAATTTTAACCAACTCGAA 59.233 34.615 0.00 0.00 37.96 3.71
84 85 7.282675 TGGTGACTAATTTTAACCAACTCGAAA 59.717 33.333 0.00 0.00 37.96 3.46
85 86 8.130469 GGTGACTAATTTTAACCAACTCGAAAA 58.870 33.333 0.00 0.00 0.00 2.29
86 87 9.673454 GTGACTAATTTTAACCAACTCGAAAAT 57.327 29.630 0.00 0.00 33.92 1.82
87 88 9.887406 TGACTAATTTTAACCAACTCGAAAATC 57.113 29.630 0.00 0.00 31.87 2.17
88 89 9.887406 GACTAATTTTAACCAACTCGAAAATCA 57.113 29.630 0.00 0.00 31.87 2.57
90 91 9.672086 CTAATTTTAACCAACTCGAAAATCACA 57.328 29.630 0.00 0.00 31.87 3.58
92 93 7.979115 TTTTAACCAACTCGAAAATCACAAG 57.021 32.000 0.00 0.00 0.00 3.16
93 94 6.928979 TTAACCAACTCGAAAATCACAAGA 57.071 33.333 0.00 0.00 0.00 3.02
94 95 7.504924 TTAACCAACTCGAAAATCACAAGAT 57.495 32.000 0.00 0.00 35.53 2.40
96 97 5.762045 ACCAACTCGAAAATCACAAGATTG 58.238 37.500 0.00 0.00 43.52 2.67
113 281 6.375455 ACAAGATTGGTGGAGAAATGTATGTC 59.625 38.462 0.00 0.00 0.00 3.06
115 283 6.352516 AGATTGGTGGAGAAATGTATGTCTC 58.647 40.000 3.85 3.85 39.70 3.36
200 368 4.698583 TGAGTTAAACGAGCTACCTCTC 57.301 45.455 0.00 0.00 35.90 3.20
231 399 1.546476 AGTCGAGCCGAATTTGACTCT 59.454 47.619 7.35 0.00 37.72 3.24
242 410 5.164080 CCGAATTTGACTCTGAACTCGTTAC 60.164 44.000 0.00 0.00 0.00 2.50
300 468 2.571757 CTGTAACGAGCCGAGCCA 59.428 61.111 1.50 0.00 0.00 4.75
335 503 1.676014 CCACCCATTCGAAGAGACCAC 60.676 57.143 3.35 0.00 38.43 4.16
370 538 5.783111 AGATGGCTGACAAATTTTACAACC 58.217 37.500 0.00 6.78 0.00 3.77
390 558 2.126031 GGAGAGTTGGACGGCGAC 60.126 66.667 16.62 7.58 0.00 5.19
410 578 1.534175 CGTGGACGCTGGAGAGAATAC 60.534 57.143 0.00 0.00 0.00 1.89
414 582 0.456221 ACGCTGGAGAGAATACCACG 59.544 55.000 0.00 0.00 37.04 4.94
416 584 1.135083 CGCTGGAGAGAATACCACGTT 60.135 52.381 0.00 0.00 32.44 3.99
418 586 2.893637 CTGGAGAGAATACCACGTTGG 58.106 52.381 2.92 2.92 45.02 3.77
422 590 3.259902 GAGAGAATACCACGTTGGAACC 58.740 50.000 10.46 0.00 40.96 3.62
462 631 9.571816 AACCAATGAAAACCACATAAAAATGAT 57.428 25.926 0.00 0.00 0.00 2.45
516 698 8.974060 AATATGGGATGTTAAAAGTATGACGT 57.026 30.769 0.00 0.00 0.00 4.34
517 699 8.974060 ATATGGGATGTTAAAAGTATGACGTT 57.026 30.769 0.00 0.00 0.00 3.99
519 701 5.998981 TGGGATGTTAAAAGTATGACGTTGT 59.001 36.000 0.00 0.00 0.00 3.32
520 702 7.160049 TGGGATGTTAAAAGTATGACGTTGTA 58.840 34.615 0.00 0.00 0.00 2.41
521 703 7.118101 TGGGATGTTAAAAGTATGACGTTGTAC 59.882 37.037 0.00 0.00 0.00 2.90
522 704 7.332678 GGGATGTTAAAAGTATGACGTTGTACT 59.667 37.037 7.70 7.70 32.75 2.73
523 705 9.357652 GGATGTTAAAAGTATGACGTTGTACTA 57.642 33.333 12.39 0.02 31.25 1.82
526 708 7.866898 TGTTAAAAGTATGACGTTGTACTAGCA 59.133 33.333 12.39 5.21 31.25 3.49
527 709 8.866956 GTTAAAAGTATGACGTTGTACTAGCAT 58.133 33.333 12.39 1.65 31.25 3.79
528 710 6.887376 AAAGTATGACGTTGTACTAGCATG 57.113 37.500 12.39 0.00 31.25 4.06
530 712 5.340803 AGTATGACGTTGTACTAGCATGTG 58.659 41.667 10.86 0.00 29.75 3.21
531 713 3.926821 TGACGTTGTACTAGCATGTGA 57.073 42.857 0.00 0.00 0.00 3.58
532 714 4.245845 TGACGTTGTACTAGCATGTGAA 57.754 40.909 0.00 0.00 0.00 3.18
533 715 4.623002 TGACGTTGTACTAGCATGTGAAA 58.377 39.130 0.00 0.00 0.00 2.69
535 717 6.391537 TGACGTTGTACTAGCATGTGAAATA 58.608 36.000 0.00 0.00 0.00 1.40
537 719 6.395629 ACGTTGTACTAGCATGTGAAATACT 58.604 36.000 0.00 0.00 0.00 2.12
539 721 6.530181 CGTTGTACTAGCATGTGAAATACTCA 59.470 38.462 0.00 0.00 0.00 3.41
542 724 5.350504 ACTAGCATGTGAAATACTCAGCT 57.649 39.130 0.00 0.00 33.60 4.24
543 725 5.738909 ACTAGCATGTGAAATACTCAGCTT 58.261 37.500 0.00 0.00 33.60 3.74
545 727 7.331026 ACTAGCATGTGAAATACTCAGCTTTA 58.669 34.615 0.00 0.00 33.60 1.85
546 728 7.824289 ACTAGCATGTGAAATACTCAGCTTTAA 59.176 33.333 0.00 0.00 33.60 1.52
548 730 7.308435 AGCATGTGAAATACTCAGCTTTAAAC 58.692 34.615 0.00 0.00 33.60 2.01
549 731 7.040478 AGCATGTGAAATACTCAGCTTTAAACA 60.040 33.333 0.00 0.00 33.60 2.83
550 732 7.061094 GCATGTGAAATACTCAGCTTTAAACAC 59.939 37.037 0.00 0.00 33.60 3.32
551 733 7.561021 TGTGAAATACTCAGCTTTAAACACA 57.439 32.000 0.00 0.00 33.60 3.72
552 734 8.165239 TGTGAAATACTCAGCTTTAAACACAT 57.835 30.769 0.00 0.00 33.60 3.21
553 735 8.629158 TGTGAAATACTCAGCTTTAAACACATT 58.371 29.630 0.00 0.00 33.60 2.71
565 747 7.910162 AGCTTTAAACACATTATCATTAGTGCG 59.090 33.333 0.00 0.00 35.47 5.34
566 748 7.165812 GCTTTAAACACATTATCATTAGTGCGG 59.834 37.037 0.00 0.00 35.47 5.69
567 749 7.618502 TTAAACACATTATCATTAGTGCGGT 57.381 32.000 0.00 0.00 35.47 5.68
569 751 7.801716 AAACACATTATCATTAGTGCGGTAT 57.198 32.000 0.00 0.00 35.47 2.73
570 752 6.785488 ACACATTATCATTAGTGCGGTATG 57.215 37.500 0.00 0.00 35.47 2.39
571 753 6.521162 ACACATTATCATTAGTGCGGTATGA 58.479 36.000 0.00 0.00 35.47 2.15
572 754 6.989759 ACACATTATCATTAGTGCGGTATGAA 59.010 34.615 0.00 0.00 35.47 2.57
573 755 7.497579 ACACATTATCATTAGTGCGGTATGAAA 59.502 33.333 0.00 0.00 35.47 2.69
574 756 8.341903 CACATTATCATTAGTGCGGTATGAAAA 58.658 33.333 0.00 0.00 32.54 2.29
576 758 8.773645 CATTATCATTAGTGCGGTATGAAAAGA 58.226 33.333 0.00 0.00 32.54 2.52
581 763 3.482436 AGTGCGGTATGAAAAGACCAAA 58.518 40.909 0.00 0.00 35.26 3.28
582 764 3.886505 AGTGCGGTATGAAAAGACCAAAA 59.113 39.130 0.00 0.00 35.26 2.44
583 765 4.522789 AGTGCGGTATGAAAAGACCAAAAT 59.477 37.500 0.00 0.00 35.26 1.82
584 766 4.857037 GTGCGGTATGAAAAGACCAAAATC 59.143 41.667 0.00 0.00 35.26 2.17
585 767 4.520874 TGCGGTATGAAAAGACCAAAATCA 59.479 37.500 0.00 0.00 35.26 2.57
586 768 5.184864 TGCGGTATGAAAAGACCAAAATCAT 59.815 36.000 0.00 0.00 35.26 2.45
587 769 5.743872 GCGGTATGAAAAGACCAAAATCATC 59.256 40.000 0.00 0.00 35.26 2.92
589 771 7.483307 CGGTATGAAAAGACCAAAATCATCAT 58.517 34.615 0.00 0.00 35.26 2.45
590 772 7.975616 CGGTATGAAAAGACCAAAATCATCATT 59.024 33.333 0.00 0.00 35.26 2.57
591 773 9.090692 GGTATGAAAAGACCAAAATCATCATTG 57.909 33.333 0.00 0.00 35.65 2.82
595 777 8.202811 TGAAAAGACCAAAATCATCATTGAACA 58.797 29.630 0.00 0.00 34.96 3.18
597 779 6.906157 AGACCAAAATCATCATTGAACAGT 57.094 33.333 0.00 0.00 34.96 3.55
598 780 6.684686 AGACCAAAATCATCATTGAACAGTG 58.315 36.000 0.00 0.00 34.96 3.66
599 781 6.266103 AGACCAAAATCATCATTGAACAGTGT 59.734 34.615 0.00 0.00 34.96 3.55
600 782 6.449698 ACCAAAATCATCATTGAACAGTGTC 58.550 36.000 0.00 0.00 34.96 3.67
601 783 6.266103 ACCAAAATCATCATTGAACAGTGTCT 59.734 34.615 0.00 0.00 34.96 3.41
603 785 7.364970 CAAAATCATCATTGAACAGTGTCTGA 58.635 34.615 0.00 0.00 34.96 3.27
604 786 7.698506 AAATCATCATTGAACAGTGTCTGAT 57.301 32.000 0.00 0.72 34.96 2.90
605 787 6.679327 ATCATCATTGAACAGTGTCTGATG 57.321 37.500 20.83 20.83 40.68 3.07
606 788 4.939439 TCATCATTGAACAGTGTCTGATGG 59.061 41.667 23.60 13.62 40.07 3.51
607 789 4.356405 TCATTGAACAGTGTCTGATGGT 57.644 40.909 0.00 0.00 35.18 3.55
608 790 5.482163 TCATTGAACAGTGTCTGATGGTA 57.518 39.130 0.00 0.00 35.18 3.25
626 1344 2.315901 GTAAACACCAGCGTTCATTGC 58.684 47.619 0.00 0.00 0.00 3.56
645 2790 8.133754 TCATTGCTGAATTTGTTCTTTCAAAG 57.866 30.769 0.00 0.00 40.00 2.77
648 2793 5.750067 TGCTGAATTTGTTCTTTCAAAGCTC 59.250 36.000 0.00 0.00 40.00 4.09
659 2804 7.174253 TGTTCTTTCAAAGCTCGTAAATGGTAT 59.826 33.333 0.00 0.00 0.00 2.73
673 2818 6.305399 CGTAAATGGTATTGTGCTTGAACTTG 59.695 38.462 0.00 0.00 0.00 3.16
680 2825 7.437862 TGGTATTGTGCTTGAACTTGAAATTTC 59.562 33.333 11.41 11.41 0.00 2.17
686 2831 4.143263 GCTTGAACTTGAAATTTCGCATGG 60.143 41.667 13.34 4.40 0.00 3.66
698 2843 3.696281 TTCGCATGGCAATAGAACATG 57.304 42.857 0.00 0.00 43.58 3.21
714 2859 3.959495 ACATGGCCCTCTTAACATCAT 57.041 42.857 0.00 0.00 0.00 2.45
822 2967 4.272748 TGATATTCTCTGGTCTCGTGTACG 59.727 45.833 0.00 0.00 41.45 3.67
833 2978 1.199859 CGTGTACGTTGCGTTGACC 59.800 57.895 0.00 0.00 41.54 4.02
845 2990 0.242825 CGTTGACCTAGACGAGCCAA 59.757 55.000 0.00 0.00 41.53 4.52
897 3113 7.647715 CGTAGTGCCAAATTAATCCCAAATTAG 59.352 37.037 0.00 0.00 0.00 1.73
923 3139 1.021390 ATCAAACCGCTGCTTCTCCG 61.021 55.000 0.00 0.00 0.00 4.63
924 3140 1.961277 CAAACCGCTGCTTCTCCGT 60.961 57.895 0.00 0.00 0.00 4.69
925 3141 1.668151 AAACCGCTGCTTCTCCGTC 60.668 57.895 0.00 0.00 0.00 4.79
948 3168 2.938539 CTTCGTCGCTAAGCCTCCGG 62.939 65.000 0.00 0.00 0.00 5.14
966 3186 4.308458 CCGCGTTCTCCACACCCA 62.308 66.667 4.92 0.00 0.00 4.51
967 3187 3.041940 CGCGTTCTCCACACCCAC 61.042 66.667 0.00 0.00 0.00 4.61
968 3188 2.110213 GCGTTCTCCACACCCACA 59.890 61.111 0.00 0.00 0.00 4.17
969 3189 2.251642 GCGTTCTCCACACCCACAC 61.252 63.158 0.00 0.00 0.00 3.82
970 3190 1.597027 CGTTCTCCACACCCACACC 60.597 63.158 0.00 0.00 0.00 4.16
971 3191 1.228154 GTTCTCCACACCCACACCC 60.228 63.158 0.00 0.00 0.00 4.61
972 3192 2.813726 TTCTCCACACCCACACCCG 61.814 63.158 0.00 0.00 0.00 5.28
973 3193 3.238497 CTCCACACCCACACCCGA 61.238 66.667 0.00 0.00 0.00 5.14
974 3194 2.768769 TCCACACCCACACCCGAA 60.769 61.111 0.00 0.00 0.00 4.30
975 3195 2.593436 CCACACCCACACCCGAAC 60.593 66.667 0.00 0.00 0.00 3.95
976 3196 2.190843 CACACCCACACCCGAACA 59.809 61.111 0.00 0.00 0.00 3.18
977 3197 1.452289 CACACCCACACCCGAACAA 60.452 57.895 0.00 0.00 0.00 2.83
978 3198 1.032657 CACACCCACACCCGAACAAA 61.033 55.000 0.00 0.00 0.00 2.83
979 3199 0.106419 ACACCCACACCCGAACAAAT 60.106 50.000 0.00 0.00 0.00 2.32
980 3200 0.596082 CACCCACACCCGAACAAATC 59.404 55.000 0.00 0.00 0.00 2.17
981 3201 0.538746 ACCCACACCCGAACAAATCC 60.539 55.000 0.00 0.00 0.00 3.01
982 3202 1.582610 CCCACACCCGAACAAATCCG 61.583 60.000 0.00 0.00 0.00 4.18
983 3203 0.887387 CCACACCCGAACAAATCCGT 60.887 55.000 0.00 0.00 0.00 4.69
984 3204 0.237235 CACACCCGAACAAATCCGTG 59.763 55.000 0.00 0.00 33.23 4.94
985 3205 0.887387 ACACCCGAACAAATCCGTGG 60.887 55.000 0.00 0.00 31.93 4.94
986 3206 1.302993 ACCCGAACAAATCCGTGGG 60.303 57.895 0.00 0.00 42.50 4.61
987 3207 2.043980 CCCGAACAAATCCGTGGGG 61.044 63.158 0.00 0.00 32.85 4.96
1004 3224 1.002624 GGACTGCGATCCCCAAACA 60.003 57.895 0.00 0.00 31.94 2.83
1369 3629 3.023735 GCTGACCCCAATCCCCCT 61.024 66.667 0.00 0.00 0.00 4.79
1373 3634 1.005690 GACCCCAATCCCCCTAGGT 59.994 63.158 8.29 0.00 36.75 3.08
1539 3808 0.106419 GGATCCCACTCGAGGACTCT 60.106 60.000 18.41 0.00 35.85 3.24
1774 5171 2.367241 CCAAAACCCGAAACCCAGAAAT 59.633 45.455 0.00 0.00 0.00 2.17
1797 5194 0.179029 ATTTCGGCATAGTTCCCGGG 60.179 55.000 16.85 16.85 44.45 5.73
1798 5195 1.555477 TTTCGGCATAGTTCCCGGGT 61.555 55.000 22.86 3.24 44.45 5.28
1873 5284 5.728351 TGAAACTGTTTGAAACGGACTAG 57.272 39.130 22.56 7.28 40.26 2.57
1885 5298 2.872732 ACGGACTAGGTTGAAGTCAGA 58.127 47.619 9.77 0.00 44.25 3.27
2058 5478 5.296780 ACACTTTGTGTAAAGGATGTGACTG 59.703 40.000 1.12 0.00 45.56 3.51
2059 5479 5.527214 CACTTTGTGTAAAGGATGTGACTGA 59.473 40.000 4.96 0.00 46.01 3.41
2060 5480 5.527582 ACTTTGTGTAAAGGATGTGACTGAC 59.472 40.000 4.96 0.00 46.01 3.51
2062 5482 4.883083 TGTGTAAAGGATGTGACTGACTC 58.117 43.478 0.00 0.00 0.00 3.36
2063 5483 4.343814 TGTGTAAAGGATGTGACTGACTCA 59.656 41.667 0.00 0.00 0.00 3.41
2100 5532 2.033675 TGCTGTGAATGTTTCTGTGCTG 59.966 45.455 0.00 0.00 0.00 4.41
2220 5657 3.013219 TCGATTGCAATTCATTTCGGGA 58.987 40.909 14.33 0.00 33.87 5.14
2236 5745 3.625853 TCGGGATTAATTGGTGCAATCA 58.374 40.909 0.00 0.00 32.43 2.57
2262 5773 4.471386 AGCAGTGTAAGTTGTAGGATGGAT 59.529 41.667 0.00 0.00 0.00 3.41
2265 5776 5.812642 CAGTGTAAGTTGTAGGATGGATGAC 59.187 44.000 0.00 0.00 0.00 3.06
2283 5794 4.819105 TGACTAAACTACCCTGTGGATG 57.181 45.455 0.00 0.00 34.81 3.51
2398 5911 5.063944 TGAAAGAGATTAAATCGCAGTCAGC 59.936 40.000 0.00 0.00 40.87 4.26
2400 5913 4.367450 AGAGATTAAATCGCAGTCAGCTC 58.633 43.478 0.00 0.00 42.61 4.09
2404 5917 2.007360 AAATCGCAGTCAGCTCTCAG 57.993 50.000 0.00 0.00 42.61 3.35
2421 5934 5.928839 GCTCTCAGTTTGAAATCAGAGTACA 59.071 40.000 0.00 0.00 0.00 2.90
2517 6043 2.287103 GCACGCCCTTTACAACTATAGC 59.713 50.000 0.00 0.00 0.00 2.97
2536 6084 4.445452 AGCCATAAATGACACTTTGCAG 57.555 40.909 0.00 0.00 0.00 4.41
2546 6095 6.882610 ATGACACTTTGCAGAAAGAATACA 57.117 33.333 5.15 1.31 41.12 2.29
2588 6144 8.589335 TGTTCACTGTAGACTTTTGAGTATTC 57.411 34.615 0.00 0.00 0.00 1.75
2781 6637 3.007940 ACATGGTCTTCAAGATGGACGAA 59.992 43.478 0.00 0.00 0.00 3.85
2899 6812 0.569810 CGAGGACGAGTACGAGTACG 59.430 60.000 7.64 0.53 42.66 3.67
2901 6814 4.150404 CGAGGACGAGTACGAGTACGTG 62.150 59.091 0.00 6.97 46.54 4.49
2910 6823 2.395651 CGAGTACGTGGAGGAGGAG 58.604 63.158 0.00 0.00 34.56 3.69
2913 6826 0.927767 AGTACGTGGAGGAGGAGGAT 59.072 55.000 0.00 0.00 0.00 3.24
2916 6829 0.396417 ACGTGGAGGAGGAGGATGAG 60.396 60.000 0.00 0.00 0.00 2.90
2925 6838 0.856982 AGGAGGATGAGGAGGACGAT 59.143 55.000 0.00 0.00 0.00 3.73
2952 6871 2.247358 GAGGAGGATGAGGATGAGGAC 58.753 57.143 0.00 0.00 0.00 3.85
3173 7092 0.749049 CAGGGCATCGAGATCAGACA 59.251 55.000 0.00 0.00 0.00 3.41
3244 7166 6.327154 CCCGGGTCAAAAGTAAATGAATAAC 58.673 40.000 14.18 0.00 0.00 1.89
3265 7187 6.560253 AACGAAAAGCATGTCTTCTGTAAT 57.440 33.333 0.00 0.00 32.88 1.89
3266 7188 5.931532 ACGAAAAGCATGTCTTCTGTAATG 58.068 37.500 0.00 0.00 32.88 1.90
3314 7237 3.771299 GCAAATTCTGCGCGCAAT 58.229 50.000 35.50 23.77 42.37 3.56
3480 7423 2.289565 GGCTACTTGGCATCTGGTTAC 58.710 52.381 0.00 0.00 41.37 2.50
3481 7424 1.933853 GCTACTTGGCATCTGGTTACG 59.066 52.381 0.00 0.00 0.00 3.18
3482 7425 1.933853 CTACTTGGCATCTGGTTACGC 59.066 52.381 0.00 0.00 0.00 4.42
3515 7458 1.757731 TGGCTTGTGGCTGCTTTGT 60.758 52.632 0.00 0.00 41.46 2.83
3516 7459 1.300388 GGCTTGTGGCTGCTTTGTG 60.300 57.895 0.00 0.00 41.46 3.33
3517 7460 1.952635 GCTTGTGGCTGCTTTGTGC 60.953 57.895 0.00 0.00 43.25 4.57
3518 7461 1.737816 CTTGTGGCTGCTTTGTGCT 59.262 52.632 0.00 0.00 43.37 4.40
3519 7462 0.103572 CTTGTGGCTGCTTTGTGCTT 59.896 50.000 0.00 0.00 43.37 3.91
3520 7463 0.536260 TTGTGGCTGCTTTGTGCTTT 59.464 45.000 0.00 0.00 43.37 3.51
3521 7464 0.179105 TGTGGCTGCTTTGTGCTTTG 60.179 50.000 0.00 0.00 43.37 2.77
3605 7555 1.194218 AGGTGCCAAAATGCCATACC 58.806 50.000 0.00 0.00 0.00 2.73
3609 7559 3.261580 GTGCCAAAATGCCATACCTTTC 58.738 45.455 0.00 0.00 0.00 2.62
3630 7580 2.619849 CCACTCACATCTGGATGCCTTT 60.620 50.000 10.13 0.00 42.39 3.11
3631 7581 2.422479 CACTCACATCTGGATGCCTTTG 59.578 50.000 10.13 2.36 42.39 2.77
3720 10272 0.529555 GCACTGCTTTCCCGCAAAAA 60.530 50.000 0.00 0.00 39.80 1.94
3743 10295 2.439156 GGGGGTCATGCACTGCTC 60.439 66.667 1.98 0.00 0.00 4.26
3793 10345 2.991866 GCTTTCATTCTTTGGCAAGAGC 59.008 45.455 0.00 0.00 40.28 4.09
3866 10429 2.223135 GGCTGCGAGCATTTAGTTCTTC 60.223 50.000 9.78 0.00 44.75 2.87
3876 10439 8.119226 CGAGCATTTAGTTCTTCTATTTTCCTG 58.881 37.037 0.00 0.00 0.00 3.86
3973 10597 2.951229 TGTCAAGGAAAGGGGAGTTC 57.049 50.000 0.00 0.00 0.00 3.01
3993 10617 3.181329 TCCTGCAGGAAGATGGTTTCTA 58.819 45.455 33.41 5.30 42.18 2.10
4077 10947 7.543520 AGTGAAGAAAAGAAAAGTTGCAGAAAG 59.456 33.333 0.00 0.00 0.00 2.62
4202 11643 2.359354 CCGCCCCATCGTTGTTCA 60.359 61.111 0.00 0.00 0.00 3.18
4204 11645 2.686816 CGCCCCATCGTTGTTCACC 61.687 63.158 0.00 0.00 0.00 4.02
4205 11646 2.686816 GCCCCATCGTTGTTCACCG 61.687 63.158 0.00 0.00 0.00 4.94
4227 11668 3.748989 GCCCATCTCCAACCTCCTTTATC 60.749 52.174 0.00 0.00 0.00 1.75
4232 11676 3.775316 TCTCCAACCTCCTTTATCTCACC 59.225 47.826 0.00 0.00 0.00 4.02
4237 11681 2.576648 ACCTCCTTTATCTCACCCAACC 59.423 50.000 0.00 0.00 0.00 3.77
4239 11683 3.370953 CCTCCTTTATCTCACCCAACCAG 60.371 52.174 0.00 0.00 0.00 4.00
4252 11696 0.962356 CAACCAGCACTCCACCATCC 60.962 60.000 0.00 0.00 0.00 3.51
4253 11697 1.426251 AACCAGCACTCCACCATCCA 61.426 55.000 0.00 0.00 0.00 3.41
4254 11698 1.210204 ACCAGCACTCCACCATCCAT 61.210 55.000 0.00 0.00 0.00 3.41
4255 11699 0.465097 CCAGCACTCCACCATCCATC 60.465 60.000 0.00 0.00 0.00 3.51
4256 11700 0.545171 CAGCACTCCACCATCCATCT 59.455 55.000 0.00 0.00 0.00 2.90
4257 11701 1.064906 CAGCACTCCACCATCCATCTT 60.065 52.381 0.00 0.00 0.00 2.40
4258 11702 1.211457 AGCACTCCACCATCCATCTTC 59.789 52.381 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 9.673454 ATTTTCGAGTTGGTTAAAATTAGTCAC 57.327 29.630 0.00 0.00 29.55 3.67
68 69 7.763356 TCTTGTGATTTTCGAGTTGGTTAAAA 58.237 30.769 0.00 0.00 0.00 1.52
69 70 7.323049 TCTTGTGATTTTCGAGTTGGTTAAA 57.677 32.000 0.00 0.00 0.00 1.52
70 71 6.928979 TCTTGTGATTTTCGAGTTGGTTAA 57.071 33.333 0.00 0.00 0.00 2.01
71 72 7.359595 CAATCTTGTGATTTTCGAGTTGGTTA 58.640 34.615 0.00 0.00 40.61 2.85
72 73 6.208644 CAATCTTGTGATTTTCGAGTTGGTT 58.791 36.000 0.00 0.00 40.61 3.67
73 74 5.278463 CCAATCTTGTGATTTTCGAGTTGGT 60.278 40.000 0.00 0.00 40.61 3.67
74 75 5.156355 CCAATCTTGTGATTTTCGAGTTGG 58.844 41.667 0.00 0.00 40.61 3.77
75 76 5.626543 CACCAATCTTGTGATTTTCGAGTTG 59.373 40.000 0.00 0.00 40.61 3.16
76 77 5.278463 CCACCAATCTTGTGATTTTCGAGTT 60.278 40.000 0.00 0.00 40.61 3.01
77 78 4.216257 CCACCAATCTTGTGATTTTCGAGT 59.784 41.667 0.00 0.00 40.61 4.18
79 80 4.393834 TCCACCAATCTTGTGATTTTCGA 58.606 39.130 0.00 0.00 40.61 3.71
80 81 4.455533 TCTCCACCAATCTTGTGATTTTCG 59.544 41.667 0.00 0.00 40.61 3.46
82 83 6.729690 TTTCTCCACCAATCTTGTGATTTT 57.270 33.333 0.00 0.00 40.61 1.82
83 84 6.268387 ACATTTCTCCACCAATCTTGTGATTT 59.732 34.615 0.00 0.00 40.61 2.17
84 85 5.776716 ACATTTCTCCACCAATCTTGTGATT 59.223 36.000 0.00 0.00 43.10 2.57
85 86 5.327732 ACATTTCTCCACCAATCTTGTGAT 58.672 37.500 0.00 0.00 33.70 3.06
86 87 4.728772 ACATTTCTCCACCAATCTTGTGA 58.271 39.130 0.00 0.00 0.00 3.58
87 88 6.151648 ACATACATTTCTCCACCAATCTTGTG 59.848 38.462 0.00 0.00 0.00 3.33
88 89 6.248433 ACATACATTTCTCCACCAATCTTGT 58.752 36.000 0.00 0.00 0.00 3.16
90 91 6.725364 AGACATACATTTCTCCACCAATCTT 58.275 36.000 0.00 0.00 0.00 2.40
92 93 6.259608 CAGAGACATACATTTCTCCACCAATC 59.740 42.308 2.48 0.00 39.36 2.67
93 94 6.118170 CAGAGACATACATTTCTCCACCAAT 58.882 40.000 2.48 0.00 39.36 3.16
94 95 5.013079 ACAGAGACATACATTTCTCCACCAA 59.987 40.000 2.48 0.00 39.36 3.67
96 97 5.091261 ACAGAGACATACATTTCTCCACC 57.909 43.478 2.48 0.00 39.36 4.61
179 347 4.698583 GAGAGGTAGCTCGTTTAACTCA 57.301 45.455 15.91 0.00 37.33 3.41
200 368 0.520827 GGCTCGACTCGTGTAACTCG 60.521 60.000 0.00 0.00 33.90 4.18
242 410 1.324736 GCTCGGCTTGACTCGTTAATG 59.675 52.381 0.00 0.00 0.00 1.90
257 425 1.710013 ACAATAACACGTGAGCTCGG 58.290 50.000 25.01 9.28 34.94 4.63
300 468 3.170717 TGGGTGGAATTCTAGTCGAGTT 58.829 45.455 5.23 0.00 0.00 3.01
314 482 0.902531 GGTCTCTTCGAATGGGTGGA 59.097 55.000 0.00 0.00 0.00 4.02
335 503 2.046285 GCCATCTCCAACCAACCGG 61.046 63.158 0.00 0.00 38.77 5.28
349 517 5.296748 GTGGTTGTAAAATTTGTCAGCCAT 58.703 37.500 23.34 0.00 41.54 4.40
370 538 2.432628 GCCGTCCAACTCTCCGTG 60.433 66.667 0.00 0.00 0.00 4.94
390 558 0.738975 TATTCTCTCCAGCGTCCACG 59.261 55.000 0.00 0.00 43.27 4.94
396 564 0.456221 ACGTGGTATTCTCTCCAGCG 59.544 55.000 0.00 0.00 34.16 5.18
401 569 3.259902 GGTTCCAACGTGGTATTCTCTC 58.740 50.000 0.00 0.00 39.03 3.20
410 578 1.268335 CGAAACTTGGTTCCAACGTGG 60.268 52.381 0.00 0.00 39.43 4.94
414 582 1.003223 CCGTCGAAACTTGGTTCCAAC 60.003 52.381 0.00 0.00 0.00 3.77
416 584 0.464870 TCCGTCGAAACTTGGTTCCA 59.535 50.000 0.00 0.00 0.00 3.53
505 687 6.310467 CACATGCTAGTACAACGTCATACTTT 59.690 38.462 14.76 0.00 33.65 2.66
507 689 5.124936 TCACATGCTAGTACAACGTCATACT 59.875 40.000 14.18 14.18 35.76 2.12
508 690 5.337554 TCACATGCTAGTACAACGTCATAC 58.662 41.667 0.00 0.00 0.00 2.39
509 691 5.570234 TCACATGCTAGTACAACGTCATA 57.430 39.130 0.00 0.00 0.00 2.15
511 693 3.926821 TCACATGCTAGTACAACGTCA 57.073 42.857 0.00 0.00 0.00 4.35
512 694 5.779806 ATTTCACATGCTAGTACAACGTC 57.220 39.130 0.00 0.00 0.00 4.34
513 695 6.395629 AGTATTTCACATGCTAGTACAACGT 58.604 36.000 0.00 0.00 0.00 3.99
515 697 7.464710 GCTGAGTATTTCACATGCTAGTACAAC 60.465 40.741 0.00 0.00 0.00 3.32
516 698 6.535150 GCTGAGTATTTCACATGCTAGTACAA 59.465 38.462 0.00 0.00 0.00 2.41
517 699 6.042777 GCTGAGTATTTCACATGCTAGTACA 58.957 40.000 0.00 0.00 0.00 2.90
519 701 6.471233 AGCTGAGTATTTCACATGCTAGTA 57.529 37.500 0.00 0.00 0.00 1.82
520 702 5.350504 AGCTGAGTATTTCACATGCTAGT 57.649 39.130 0.00 0.00 0.00 2.57
521 703 6.674694 AAAGCTGAGTATTTCACATGCTAG 57.325 37.500 0.00 0.00 0.00 3.42
522 704 8.450964 GTTTAAAGCTGAGTATTTCACATGCTA 58.549 33.333 0.00 0.00 0.00 3.49
523 705 7.040478 TGTTTAAAGCTGAGTATTTCACATGCT 60.040 33.333 0.00 0.00 0.00 3.79
524 706 7.061094 GTGTTTAAAGCTGAGTATTTCACATGC 59.939 37.037 0.00 0.00 0.00 4.06
526 708 8.165239 TGTGTTTAAAGCTGAGTATTTCACAT 57.835 30.769 0.00 0.00 0.00 3.21
527 709 7.561021 TGTGTTTAAAGCTGAGTATTTCACA 57.439 32.000 0.00 0.00 0.00 3.58
539 721 7.910162 CGCACTAATGATAATGTGTTTAAAGCT 59.090 33.333 0.00 0.00 33.44 3.74
542 724 8.046294 ACCGCACTAATGATAATGTGTTTAAA 57.954 30.769 0.00 0.00 33.44 1.52
543 725 7.618502 ACCGCACTAATGATAATGTGTTTAA 57.381 32.000 0.00 0.00 33.44 1.52
545 727 7.497579 TCATACCGCACTAATGATAATGTGTTT 59.502 33.333 0.00 0.00 33.44 2.83
546 728 6.989759 TCATACCGCACTAATGATAATGTGTT 59.010 34.615 0.00 0.00 33.44 3.32
548 730 7.420184 TTCATACCGCACTAATGATAATGTG 57.580 36.000 0.00 0.00 30.17 3.21
549 731 8.445275 TTTTCATACCGCACTAATGATAATGT 57.555 30.769 0.00 0.00 30.17 2.71
550 732 8.773645 TCTTTTCATACCGCACTAATGATAATG 58.226 33.333 0.00 0.00 30.17 1.90
551 733 8.774586 GTCTTTTCATACCGCACTAATGATAAT 58.225 33.333 0.00 0.00 30.17 1.28
552 734 7.225931 GGTCTTTTCATACCGCACTAATGATAA 59.774 37.037 0.00 0.00 30.17 1.75
553 735 6.704493 GGTCTTTTCATACCGCACTAATGATA 59.296 38.462 0.00 0.00 30.17 2.15
554 736 5.527582 GGTCTTTTCATACCGCACTAATGAT 59.472 40.000 0.00 0.00 30.17 2.45
555 737 4.873827 GGTCTTTTCATACCGCACTAATGA 59.126 41.667 0.00 0.00 0.00 2.57
556 738 4.634004 TGGTCTTTTCATACCGCACTAATG 59.366 41.667 0.00 0.00 38.70 1.90
557 739 4.839121 TGGTCTTTTCATACCGCACTAAT 58.161 39.130 0.00 0.00 38.70 1.73
558 740 4.274602 TGGTCTTTTCATACCGCACTAA 57.725 40.909 0.00 0.00 38.70 2.24
559 741 3.965379 TGGTCTTTTCATACCGCACTA 57.035 42.857 0.00 0.00 38.70 2.74
560 742 2.851263 TGGTCTTTTCATACCGCACT 57.149 45.000 0.00 0.00 38.70 4.40
562 744 4.520874 TGATTTTGGTCTTTTCATACCGCA 59.479 37.500 0.00 0.00 38.70 5.69
563 745 5.054390 TGATTTTGGTCTTTTCATACCGC 57.946 39.130 0.00 0.00 38.70 5.68
565 747 9.090692 CAATGATGATTTTGGTCTTTTCATACC 57.909 33.333 0.00 0.00 36.24 2.73
566 748 9.859427 TCAATGATGATTTTGGTCTTTTCATAC 57.141 29.630 0.00 0.00 0.00 2.39
569 751 8.202811 TGTTCAATGATGATTTTGGTCTTTTCA 58.797 29.630 0.00 0.00 34.96 2.69
570 752 8.592105 TGTTCAATGATGATTTTGGTCTTTTC 57.408 30.769 0.00 0.00 34.96 2.29
571 753 8.206189 ACTGTTCAATGATGATTTTGGTCTTTT 58.794 29.630 0.00 0.00 34.96 2.27
572 754 7.654520 CACTGTTCAATGATGATTTTGGTCTTT 59.345 33.333 0.00 0.00 34.96 2.52
573 755 7.149973 CACTGTTCAATGATGATTTTGGTCTT 58.850 34.615 0.00 0.00 34.96 3.01
574 756 6.266103 ACACTGTTCAATGATGATTTTGGTCT 59.734 34.615 0.00 0.00 34.96 3.85
576 758 6.266103 AGACACTGTTCAATGATGATTTTGGT 59.734 34.615 0.00 0.00 34.96 3.67
581 763 6.095021 CCATCAGACACTGTTCAATGATGATT 59.905 38.462 19.21 0.00 44.22 2.57
582 764 5.589050 CCATCAGACACTGTTCAATGATGAT 59.411 40.000 19.21 6.88 44.22 2.45
583 765 4.939439 CCATCAGACACTGTTCAATGATGA 59.061 41.667 19.21 5.45 44.22 2.92
584 766 4.698780 ACCATCAGACACTGTTCAATGATG 59.301 41.667 14.59 14.59 42.22 3.07
585 767 4.914983 ACCATCAGACACTGTTCAATGAT 58.085 39.130 0.00 0.00 32.61 2.45
586 768 4.356405 ACCATCAGACACTGTTCAATGA 57.644 40.909 0.00 0.00 32.61 2.57
587 769 6.017192 TGTTTACCATCAGACACTGTTCAATG 60.017 38.462 0.00 0.00 32.61 2.82
589 771 5.295787 GTGTTTACCATCAGACACTGTTCAA 59.704 40.000 0.00 0.00 39.33 2.69
590 772 4.814234 GTGTTTACCATCAGACACTGTTCA 59.186 41.667 0.00 0.00 39.33 3.18
591 773 4.213482 GGTGTTTACCATCAGACACTGTTC 59.787 45.833 5.59 0.00 46.71 3.18
593 775 3.740115 GGTGTTTACCATCAGACACTGT 58.260 45.455 5.59 0.00 46.71 3.55
606 788 2.031157 AGCAATGAACGCTGGTGTTTAC 60.031 45.455 1.04 0.00 38.60 2.01
607 789 2.226330 AGCAATGAACGCTGGTGTTTA 58.774 42.857 1.04 0.00 38.60 2.01
608 790 1.032014 AGCAATGAACGCTGGTGTTT 58.968 45.000 1.04 0.00 38.60 2.83
619 1337 8.489990 TTTGAAAGAACAAATTCAGCAATGAA 57.510 26.923 0.00 0.00 36.93 2.57
620 1338 7.254522 GCTTTGAAAGAACAAATTCAGCAATGA 60.255 33.333 9.48 0.00 38.73 2.57
626 1344 5.973565 ACGAGCTTTGAAAGAACAAATTCAG 59.026 36.000 9.48 0.00 38.73 3.02
628 1346 7.908193 TTACGAGCTTTGAAAGAACAAATTC 57.092 32.000 9.48 0.00 38.73 2.17
645 2790 4.094294 TCAAGCACAATACCATTTACGAGC 59.906 41.667 0.00 0.00 0.00 5.03
648 2793 5.938322 AGTTCAAGCACAATACCATTTACG 58.062 37.500 0.00 0.00 0.00 3.18
659 2804 4.267452 GCGAAATTTCAAGTTCAAGCACAA 59.733 37.500 17.99 0.00 32.93 3.33
673 2818 5.101628 TGTTCTATTGCCATGCGAAATTTC 58.898 37.500 8.20 8.20 0.00 2.17
680 2825 1.601162 GCCATGTTCTATTGCCATGCG 60.601 52.381 0.00 0.00 35.70 4.73
686 2831 2.355010 AGAGGGCCATGTTCTATTGC 57.645 50.000 6.18 0.00 0.00 3.56
698 2843 2.378038 TGCAATGATGTTAAGAGGGCC 58.622 47.619 0.00 0.00 0.00 5.80
735 2880 9.829507 ATACCATGTTTGAATGTTTTGAAGAAA 57.170 25.926 0.00 0.00 0.00 2.52
736 2881 9.829507 AATACCATGTTTGAATGTTTTGAAGAA 57.170 25.926 0.00 0.00 0.00 2.52
737 2882 9.829507 AAATACCATGTTTGAATGTTTTGAAGA 57.170 25.926 0.00 0.00 0.00 2.87
786 2931 8.900781 ACCAGAGAATATCACATGAAAATCAAG 58.099 33.333 0.00 0.00 0.00 3.02
810 2955 0.936297 AACGCAACGTACACGAGACC 60.936 55.000 9.04 0.00 39.99 3.85
822 2967 1.337821 CTCGTCTAGGTCAACGCAAC 58.662 55.000 0.00 0.00 38.72 4.17
833 2978 1.852895 GCATACGTTTGGCTCGTCTAG 59.147 52.381 8.11 0.00 41.72 2.43
845 2990 3.760537 GAAGACTCTCTTCGCATACGTT 58.239 45.455 0.00 0.00 42.78 3.99
881 3026 9.265862 TGATTGTGGACTAATTTGGGATTAATT 57.734 29.630 0.00 0.00 0.00 1.40
882 3027 8.837099 TGATTGTGGACTAATTTGGGATTAAT 57.163 30.769 0.00 0.00 0.00 1.40
883 3028 8.657387 TTGATTGTGGACTAATTTGGGATTAA 57.343 30.769 0.00 0.00 0.00 1.40
884 3029 8.527810 GTTTGATTGTGGACTAATTTGGGATTA 58.472 33.333 0.00 0.00 0.00 1.75
885 3030 7.386059 GTTTGATTGTGGACTAATTTGGGATT 58.614 34.615 0.00 0.00 0.00 3.01
886 3031 6.070824 GGTTTGATTGTGGACTAATTTGGGAT 60.071 38.462 0.00 0.00 0.00 3.85
897 3113 0.387239 GCAGCGGTTTGATTGTGGAC 60.387 55.000 0.00 0.00 0.00 4.02
923 3139 1.981668 CTTAGCGACGAAGCACGAC 59.018 57.895 0.00 3.43 45.77 4.34
924 3140 1.800315 GCTTAGCGACGAAGCACGA 60.800 57.895 14.41 0.00 46.97 4.35
925 3141 2.689766 GCTTAGCGACGAAGCACG 59.310 61.111 14.41 1.99 46.97 5.34
959 3179 1.032657 TTTGTTCGGGTGTGGGTGTG 61.033 55.000 0.00 0.00 0.00 3.82
960 3180 0.106419 ATTTGTTCGGGTGTGGGTGT 60.106 50.000 0.00 0.00 0.00 4.16
961 3181 0.596082 GATTTGTTCGGGTGTGGGTG 59.404 55.000 0.00 0.00 0.00 4.61
962 3182 0.538746 GGATTTGTTCGGGTGTGGGT 60.539 55.000 0.00 0.00 0.00 4.51
963 3183 1.582610 CGGATTTGTTCGGGTGTGGG 61.583 60.000 0.00 0.00 0.00 4.61
964 3184 0.887387 ACGGATTTGTTCGGGTGTGG 60.887 55.000 0.00 0.00 0.00 4.17
965 3185 0.237235 CACGGATTTGTTCGGGTGTG 59.763 55.000 0.00 0.00 0.00 3.82
966 3186 0.887387 CCACGGATTTGTTCGGGTGT 60.887 55.000 0.00 0.00 31.21 4.16
967 3187 1.582610 CCCACGGATTTGTTCGGGTG 61.583 60.000 0.00 0.00 32.31 4.61
968 3188 1.302993 CCCACGGATTTGTTCGGGT 60.303 57.895 0.00 0.00 0.00 5.28
969 3189 2.043980 CCCCACGGATTTGTTCGGG 61.044 63.158 0.00 0.00 0.00 5.14
970 3190 1.003112 TCCCCACGGATTTGTTCGG 60.003 57.895 0.00 0.00 31.13 4.30
971 3191 0.321298 AGTCCCCACGGATTTGTTCG 60.321 55.000 0.00 0.00 41.40 3.95
972 3192 1.165270 CAGTCCCCACGGATTTGTTC 58.835 55.000 0.00 0.00 41.40 3.18
973 3193 0.893727 GCAGTCCCCACGGATTTGTT 60.894 55.000 0.00 0.00 41.40 2.83
974 3194 1.303317 GCAGTCCCCACGGATTTGT 60.303 57.895 0.00 0.00 41.40 2.83
975 3195 2.398554 CGCAGTCCCCACGGATTTG 61.399 63.158 0.00 0.00 41.40 2.32
976 3196 1.910580 ATCGCAGTCCCCACGGATTT 61.911 55.000 0.00 0.00 41.40 2.17
977 3197 2.311688 GATCGCAGTCCCCACGGATT 62.312 60.000 0.00 0.00 41.40 3.01
978 3198 2.764128 ATCGCAGTCCCCACGGAT 60.764 61.111 0.00 0.00 41.40 4.18
979 3199 3.458163 GATCGCAGTCCCCACGGA 61.458 66.667 0.00 0.00 35.01 4.69
980 3200 4.530857 GGATCGCAGTCCCCACGG 62.531 72.222 0.00 0.00 31.82 4.94
986 3206 0.608035 TTGTTTGGGGATCGCAGTCC 60.608 55.000 12.32 0.00 37.56 3.85
987 3207 0.804989 CTTGTTTGGGGATCGCAGTC 59.195 55.000 12.32 0.00 0.00 3.51
988 3208 0.110486 ACTTGTTTGGGGATCGCAGT 59.890 50.000 12.32 2.35 0.00 4.40
989 3209 0.804989 GACTTGTTTGGGGATCGCAG 59.195 55.000 12.32 1.70 0.00 5.18
990 3210 0.953471 CGACTTGTTTGGGGATCGCA 60.953 55.000 12.32 0.00 0.00 5.10
991 3211 1.794222 CGACTTGTTTGGGGATCGC 59.206 57.895 0.06 0.06 0.00 4.58
992 3212 0.953471 TGCGACTTGTTTGGGGATCG 60.953 55.000 0.00 0.00 0.00 3.69
993 3213 1.068541 GTTGCGACTTGTTTGGGGATC 60.069 52.381 0.00 0.00 0.00 3.36
1004 3224 1.289380 GGTCCGAGAGTTGCGACTT 59.711 57.895 8.34 0.00 35.88 3.01
1369 3629 2.191513 CGATCGGCCGAGGAACCTA 61.192 63.158 33.87 7.83 0.00 3.08
1373 3634 1.461091 ATTAGCGATCGGCCGAGGAA 61.461 55.000 33.87 20.81 45.17 3.36
1428 3697 2.664081 GGTCTCCCTGTCCAGCCAG 61.664 68.421 0.00 0.00 0.00 4.85
1539 3808 1.250328 TGGAAGAGCGAACGAACCTA 58.750 50.000 0.00 0.00 0.00 3.08
1774 5171 1.133915 GGGAACTATGCCGAAATCCCA 60.134 52.381 8.62 0.00 44.81 4.37
1797 5194 7.070183 GTGCTTGTTCTAAAACTTGCTACTAC 58.930 38.462 0.00 0.00 36.22 2.73
1798 5195 6.764085 TGTGCTTGTTCTAAAACTTGCTACTA 59.236 34.615 0.00 0.00 36.22 1.82
1873 5284 5.964958 TCCAAATGAATCTGACTTCAACC 57.035 39.130 6.61 0.00 38.55 3.77
1885 5298 6.721208 AGCATTATTCCGGTATCCAAATGAAT 59.279 34.615 15.41 2.09 0.00 2.57
1986 5402 3.541996 ACAAAGTTGAAAAGGCCCTTG 57.458 42.857 0.00 0.00 0.00 3.61
2058 5478 4.143305 GCACAAAATACTCGAGTGTGAGTC 60.143 45.833 27.73 12.78 45.97 3.36
2060 5480 3.990469 AGCACAAAATACTCGAGTGTGAG 59.010 43.478 27.73 19.00 41.67 3.51
2062 5482 3.494626 ACAGCACAAAATACTCGAGTGTG 59.505 43.478 28.12 24.66 41.96 3.82
2063 5483 3.494626 CACAGCACAAAATACTCGAGTGT 59.505 43.478 28.12 19.24 32.99 3.55
2064 5484 3.740832 TCACAGCACAAAATACTCGAGTG 59.259 43.478 28.12 13.18 0.00 3.51
2065 5485 3.990092 TCACAGCACAAAATACTCGAGT 58.010 40.909 23.66 23.66 0.00 4.18
2066 5486 4.990543 TTCACAGCACAAAATACTCGAG 57.009 40.909 11.84 11.84 0.00 4.04
2067 5487 4.754618 ACATTCACAGCACAAAATACTCGA 59.245 37.500 0.00 0.00 0.00 4.04
2068 5488 5.034554 ACATTCACAGCACAAAATACTCG 57.965 39.130 0.00 0.00 0.00 4.18
2159 5596 4.688879 ACAGCAACATCAAATCAAATGCAG 59.311 37.500 0.00 0.00 34.89 4.41
2175 5612 3.240069 GAGATCACAATGCAACAGCAAC 58.760 45.455 0.00 0.00 42.37 4.17
2236 5745 2.632996 TCCTACAACTTACACTGCTGCT 59.367 45.455 0.00 0.00 0.00 4.24
2262 5773 4.422057 TCATCCACAGGGTAGTTTAGTCA 58.578 43.478 0.00 0.00 34.93 3.41
2265 5776 5.414765 GGTTTTCATCCACAGGGTAGTTTAG 59.585 44.000 0.00 0.00 34.93 1.85
2398 5911 6.090628 GCTGTACTCTGATTTCAAACTGAGAG 59.909 42.308 9.68 0.00 36.45 3.20
2400 5913 5.121454 GGCTGTACTCTGATTTCAAACTGAG 59.879 44.000 0.00 0.00 37.83 3.35
2404 5917 3.746492 ACGGCTGTACTCTGATTTCAAAC 59.254 43.478 0.00 0.00 0.00 2.93
2421 5934 3.451178 ACAAGGACTTATCATGTACGGCT 59.549 43.478 0.00 0.00 0.00 5.52
2517 6043 6.680810 TCTTTCTGCAAAGTGTCATTTATGG 58.319 36.000 0.00 0.00 40.16 2.74
2536 6084 6.529477 GGTACACCGTAGAGTTGTATTCTTTC 59.471 42.308 0.00 0.00 0.00 2.62
2546 6095 3.638160 TGAACAAGGTACACCGTAGAGTT 59.362 43.478 0.00 0.00 42.08 3.01
2899 6812 0.263172 TCCTCATCCTCCTCCTCCAC 59.737 60.000 0.00 0.00 0.00 4.02
2900 6813 0.560193 CTCCTCATCCTCCTCCTCCA 59.440 60.000 0.00 0.00 0.00 3.86
2901 6814 0.178935 CCTCCTCATCCTCCTCCTCC 60.179 65.000 0.00 0.00 0.00 4.30
2906 6819 0.856982 ATCGTCCTCCTCATCCTCCT 59.143 55.000 0.00 0.00 0.00 3.69
2907 6820 0.965439 CATCGTCCTCCTCATCCTCC 59.035 60.000 0.00 0.00 0.00 4.30
2910 6823 0.965439 CCTCATCGTCCTCCTCATCC 59.035 60.000 0.00 0.00 0.00 3.51
2913 6826 0.106469 CCTCCTCATCGTCCTCCTCA 60.106 60.000 0.00 0.00 0.00 3.86
2916 6829 0.825840 CCTCCTCCTCATCGTCCTCC 60.826 65.000 0.00 0.00 0.00 4.30
2925 6838 0.560193 CCTCATCCTCCTCCTCCTCA 59.440 60.000 0.00 0.00 0.00 3.86
2952 6871 1.137314 CGATAGTACTCGTCGTCGTCG 60.137 57.143 17.71 5.50 38.33 5.12
3173 7092 3.494048 CCTCGCTCAGCCTGATTTCTTAT 60.494 47.826 0.00 0.00 0.00 1.73
3244 7166 5.791974 CACATTACAGAAGACATGCTTTTCG 59.208 40.000 0.00 0.00 36.83 3.46
3314 7237 3.926527 CGCAGCATAGTCTGTACAAGAAA 59.073 43.478 0.00 0.00 36.40 2.52
3480 7423 1.081892 CCACAAGGATCTCAACAGCG 58.918 55.000 0.00 0.00 36.89 5.18
3481 7424 0.807496 GCCACAAGGATCTCAACAGC 59.193 55.000 0.00 0.00 36.89 4.40
3482 7425 2.486472 AGCCACAAGGATCTCAACAG 57.514 50.000 0.00 0.00 36.89 3.16
3515 7458 3.008835 AGAGGAAGCATATGCAAAGCA 57.991 42.857 28.62 0.00 45.16 3.91
3516 7459 3.129988 ACAAGAGGAAGCATATGCAAAGC 59.870 43.478 28.62 14.15 45.16 3.51
3517 7460 4.495349 CGACAAGAGGAAGCATATGCAAAG 60.495 45.833 28.62 11.74 45.16 2.77
3518 7461 3.374988 CGACAAGAGGAAGCATATGCAAA 59.625 43.478 28.62 0.00 45.16 3.68
3519 7462 2.938451 CGACAAGAGGAAGCATATGCAA 59.062 45.455 28.62 0.00 45.16 4.08
3520 7463 2.554142 CGACAAGAGGAAGCATATGCA 58.446 47.619 28.62 0.00 45.16 3.96
3521 7464 1.869767 CCGACAAGAGGAAGCATATGC 59.130 52.381 20.36 20.36 42.49 3.14
3566 7516 6.566942 GCACCTTATCTATCTCTGTACAGACG 60.567 46.154 21.74 16.68 33.22 4.18
3567 7517 6.294286 GGCACCTTATCTATCTCTGTACAGAC 60.294 46.154 21.74 6.64 33.22 3.51
3605 7555 2.681848 GCATCCAGATGTGAGTGGAAAG 59.318 50.000 9.29 0.00 46.01 2.62
3609 7559 0.545171 AGGCATCCAGATGTGAGTGG 59.455 55.000 9.29 0.00 40.80 4.00
3726 10278 2.439156 GAGCAGTGCATGACCCCC 60.439 66.667 19.20 0.00 0.00 5.40
3727 10279 1.001641 AAGAGCAGTGCATGACCCC 60.002 57.895 19.20 0.00 0.00 4.95
3728 10280 0.035630 AGAAGAGCAGTGCATGACCC 60.036 55.000 19.20 1.05 0.00 4.46
3732 10284 0.035725 TCCCAGAAGAGCAGTGCATG 60.036 55.000 19.20 7.52 0.00 4.06
3743 10295 2.307098 ACCACCTGATCTTTCCCAGAAG 59.693 50.000 0.00 0.00 34.16 2.85
3876 10439 1.792949 CTAATATTCACAGTCGGCCGC 59.207 52.381 23.51 16.31 0.00 6.53
3973 10597 2.503895 AGAAACCATCTTCCTGCAGG 57.496 50.000 27.87 27.87 33.39 4.85
3983 10607 4.035675 CGGCCAGAAGAAATAGAAACCATC 59.964 45.833 2.24 0.00 0.00 3.51
3985 10609 3.008594 TCGGCCAGAAGAAATAGAAACCA 59.991 43.478 2.24 0.00 0.00 3.67
3993 10617 1.072331 ACACTGTCGGCCAGAAGAAAT 59.928 47.619 2.24 0.00 44.49 2.17
4041 10911 9.410556 CTTTTCTTTTCTTCACTTCAGTTGAAA 57.589 29.630 0.00 0.00 33.07 2.69
4042 10912 8.576442 ACTTTTCTTTTCTTCACTTCAGTTGAA 58.424 29.630 0.00 0.00 0.00 2.69
4098 10968 0.106521 GAGCCTCTCTCAGCCCATTC 59.893 60.000 0.00 0.00 41.51 2.67
4105 10975 1.750193 AGAGTTCGAGCCTCTCTCAG 58.250 55.000 10.07 0.00 41.98 3.35
4187 11057 2.686816 CGGTGAACAACGATGGGGC 61.687 63.158 6.38 0.00 45.97 5.80
4202 11643 2.610859 AGGTTGGAGATGGGCGGT 60.611 61.111 0.00 0.00 0.00 5.68
4204 11645 1.915078 AAGGAGGTTGGAGATGGGCG 61.915 60.000 0.00 0.00 0.00 6.13
4205 11646 0.332972 AAAGGAGGTTGGAGATGGGC 59.667 55.000 0.00 0.00 0.00 5.36
4227 11668 1.302832 GGAGTGCTGGTTGGGTGAG 60.303 63.158 0.00 0.00 0.00 3.51
4232 11676 0.962356 GATGGTGGAGTGCTGGTTGG 60.962 60.000 0.00 0.00 0.00 3.77
4237 11681 0.545171 AGATGGATGGTGGAGTGCTG 59.455 55.000 0.00 0.00 0.00 4.41
4239 11683 1.673168 GAAGATGGATGGTGGAGTGC 58.327 55.000 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.