Multiple sequence alignment - TraesCS4B01G093900

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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 TraesCS4B01G093900 chr4B 100.000 3064 0 0 1 3064 96629413 96632476 0.000000e+00 5659.0
1 TraesCS4B01G093900 chr4B 98.113 689 13 0 1 689 636043587 636042899 0.000000e+00 1201.0
2 TraesCS4B01G093900 chr4B 100.000 30 0 0 3779 3808 96633191 96633220 5.310000e-04 56.5
3 TraesCS4B01G093900 chr4A 89.815 1355 88 16 691 2004 529635483 529634138 0.000000e+00 1692.0
4 TraesCS4B01G093900 chr4A 95.186 727 33 2 2027 2751 529634142 529633416 0.000000e+00 1147.0
5 TraesCS4B01G093900 chr4A 76.642 685 125 22 1114 1782 531105224 531104559 2.820000e-91 346.0
6 TraesCS4B01G093900 chr4D 93.124 1018 37 9 943 1934 65860326 65861336 0.000000e+00 1461.0
7 TraesCS4B01G093900 chr4D 94.185 791 43 3 1963 2751 65861326 65862115 0.000000e+00 1203.0
8 TraesCS4B01G093900 chr4D 92.823 209 12 3 691 898 65859592 65859798 2.220000e-77 300.0
9 TraesCS4B01G093900 chr4D 86.154 65 9 0 2311 2375 65078979 65078915 1.900000e-08 71.3
10 TraesCS4B01G093900 chr3B 98.694 689 8 1 1 689 267228791 267228104 0.000000e+00 1221.0
11 TraesCS4B01G093900 chr3B 76.555 209 31 11 2320 2519 70980707 70980508 8.710000e-17 99.0
12 TraesCS4B01G093900 chr3B 93.878 49 3 0 2308 2356 799449236 799449284 1.470000e-09 75.0
13 TraesCS4B01G093900 chr5B 97.674 688 16 0 1 688 429187150 429187837 0.000000e+00 1182.0
14 TraesCS4B01G093900 chr5B 77.487 382 71 10 1176 1554 508351808 508351439 8.290000e-52 215.0
15 TraesCS4B01G093900 chr1D 94.835 697 29 6 1 693 249621330 249620637 0.000000e+00 1081.0
16 TraesCS4B01G093900 chr7B 94.935 691 32 2 1 691 478838694 478838007 0.000000e+00 1079.0
17 TraesCS4B01G093900 chr7B 100.000 28 0 0 3779 3806 616751478 616751451 7.000000e-03 52.8
18 TraesCS4B01G093900 chr6B 94.453 685 38 0 1 685 135940176 135940860 0.000000e+00 1055.0
19 TraesCS4B01G093900 chr6A 93.169 688 45 2 1 687 589638694 589639380 0.000000e+00 1009.0
20 TraesCS4B01G093900 chr6A 93.159 687 45 2 1 686 589510051 589510736 0.000000e+00 1007.0
21 TraesCS4B01G093900 chr6A 91.849 687 51 3 1 686 589465708 589466390 0.000000e+00 953.0
22 TraesCS4B01G093900 chr2D 89.327 684 65 7 1107 1786 55315407 55316086 0.000000e+00 852.0
23 TraesCS4B01G093900 chr2D 88.756 667 70 5 1122 1786 39832029 39831366 0.000000e+00 811.0
24 TraesCS4B01G093900 chr2D 83.534 498 74 8 2027 2520 55357182 55356689 3.470000e-125 459.0
25 TraesCS4B01G093900 chr2D 82.558 516 79 7 2006 2520 55316246 55316751 9.710000e-121 444.0
26 TraesCS4B01G093900 chr2D 81.903 536 82 14 2006 2532 39831207 39830678 4.520000e-119 438.0
27 TraesCS4B01G093900 chr2D 78.363 684 120 24 1111 1782 476912929 476913596 5.880000e-113 418.0
28 TraesCS4B01G093900 chr2A 89.181 684 66 7 1107 1786 56916689 56917368 0.000000e+00 846.0
29 TraesCS4B01G093900 chr2A 83.431 513 71 12 2017 2520 56917539 56918046 7.450000e-127 464.0
30 TraesCS4B01G093900 chr2A 78.394 685 122 21 1111 1782 619238299 619238970 4.550000e-114 422.0
31 TraesCS4B01G093900 chr2B 88.559 673 71 5 1122 1791 87841303 87841972 0.000000e+00 811.0
32 TraesCS4B01G093900 chr2B 81.481 513 84 11 2027 2533 87842166 87842673 9.850000e-111 411.0
33 TraesCS4B01G093900 chr5D 78.060 629 112 17 1172 1789 506210230 506210843 1.290000e-99 374.0
34 TraesCS4B01G093900 chr5A 74.861 541 114 17 1176 1712 535487604 535487082 3.830000e-55 226.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G093900 chr4B 96629413 96633220 3807 False 2857.75 5659 100.000000 1 3808 2 chr4B.!!$F1 3807
1 TraesCS4B01G093900 chr4B 636042899 636043587 688 True 1201.00 1201 98.113000 1 689 1 chr4B.!!$R1 688
2 TraesCS4B01G093900 chr4A 529633416 529635483 2067 True 1419.50 1692 92.500500 691 2751 2 chr4A.!!$R2 2060
3 TraesCS4B01G093900 chr4A 531104559 531105224 665 True 346.00 346 76.642000 1114 1782 1 chr4A.!!$R1 668
4 TraesCS4B01G093900 chr4D 65859592 65862115 2523 False 988.00 1461 93.377333 691 2751 3 chr4D.!!$F1 2060
5 TraesCS4B01G093900 chr3B 267228104 267228791 687 True 1221.00 1221 98.694000 1 689 1 chr3B.!!$R2 688
6 TraesCS4B01G093900 chr5B 429187150 429187837 687 False 1182.00 1182 97.674000 1 688 1 chr5B.!!$F1 687
7 TraesCS4B01G093900 chr1D 249620637 249621330 693 True 1081.00 1081 94.835000 1 693 1 chr1D.!!$R1 692
8 TraesCS4B01G093900 chr7B 478838007 478838694 687 True 1079.00 1079 94.935000 1 691 1 chr7B.!!$R1 690
9 TraesCS4B01G093900 chr6B 135940176 135940860 684 False 1055.00 1055 94.453000 1 685 1 chr6B.!!$F1 684
10 TraesCS4B01G093900 chr6A 589638694 589639380 686 False 1009.00 1009 93.169000 1 687 1 chr6A.!!$F3 686
11 TraesCS4B01G093900 chr6A 589510051 589510736 685 False 1007.00 1007 93.159000 1 686 1 chr6A.!!$F2 685
12 TraesCS4B01G093900 chr6A 589465708 589466390 682 False 953.00 953 91.849000 1 686 1 chr6A.!!$F1 685
13 TraesCS4B01G093900 chr2D 55315407 55316751 1344 False 648.00 852 85.942500 1107 2520 2 chr2D.!!$F2 1413
14 TraesCS4B01G093900 chr2D 39830678 39832029 1351 True 624.50 811 85.329500 1122 2532 2 chr2D.!!$R2 1410
15 TraesCS4B01G093900 chr2D 476912929 476913596 667 False 418.00 418 78.363000 1111 1782 1 chr2D.!!$F1 671
16 TraesCS4B01G093900 chr2A 56916689 56918046 1357 False 655.00 846 86.306000 1107 2520 2 chr2A.!!$F2 1413
17 TraesCS4B01G093900 chr2A 619238299 619238970 671 False 422.00 422 78.394000 1111 1782 1 chr2A.!!$F1 671
18 TraesCS4B01G093900 chr2B 87841303 87842673 1370 False 611.00 811 85.020000 1122 2533 2 chr2B.!!$F1 1411
19 TraesCS4B01G093900 chr5D 506210230 506210843 613 False 374.00 374 78.060000 1172 1789 1 chr5D.!!$F1 617
20 TraesCS4B01G093900 chr5A 535487082 535487604 522 True 226.00 226 74.861000 1176 1712 1 chr5A.!!$R1 536

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
422 426 1.078528 TGTCCCTCGACATCACCCT 59.921 57.895 0.00 0.0 44.20 4.34 F
712 717 1.135915 AGAGCTCAATGTCGAATCGCT 59.864 47.619 17.77 0.0 0.00 4.93 F
1737 2278 1.296715 GGGATGAGCAGTTCGTGGT 59.703 57.895 0.00 0.0 40.54 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1974 2581 0.364515 GGTCGACGACGTGTTATTGC 59.635 55.0 20.92 0.84 40.69 3.56 R
2025 2632 0.394565 GAAGTGTGTGGAGCTGGAGT 59.605 55.0 0.00 0.00 0.00 3.85 R
2914 3529 0.033228 CCCGAAACAATTTGGCAGCA 59.967 50.0 0.78 0.00 38.60 4.41 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
274 278 2.295253 ACTTGCTAATCGTCCCGAAG 57.705 50.000 0.00 0.00 39.99 3.79
422 426 1.078528 TGTCCCTCGACATCACCCT 59.921 57.895 0.00 0.00 44.20 4.34
712 717 1.135915 AGAGCTCAATGTCGAATCGCT 59.864 47.619 17.77 0.00 0.00 4.93
717 722 2.270923 TCAATGTCGAATCGCTTGAGG 58.729 47.619 0.00 0.00 0.00 3.86
735 740 2.046023 TCATCCACTTGGCGCTGG 60.046 61.111 7.64 7.31 34.44 4.85
780 786 2.942376 AGAGCACACGACAAAATTGACA 59.058 40.909 0.00 0.00 0.00 3.58
781 787 3.376859 AGAGCACACGACAAAATTGACAA 59.623 39.130 0.00 0.00 0.00 3.18
828 848 3.302365 TTTCTTGCTTAAGTGCATGCC 57.698 42.857 16.68 6.65 42.96 4.40
924 950 7.760340 AGACATTAGGAGTACAAATTCGAGAAC 59.240 37.037 0.00 0.00 0.00 3.01
963 1469 8.554835 TCACGGATTGATTCAACTTGTAATAA 57.445 30.769 0.15 0.00 0.00 1.40
964 1470 9.173021 TCACGGATTGATTCAACTTGTAATAAT 57.827 29.630 0.15 0.00 0.00 1.28
1027 1533 4.644685 ACCCAAGCAACATAATCACATACC 59.355 41.667 0.00 0.00 0.00 2.73
1033 1539 6.595682 AGCAACATAATCACATACCTTAGCT 58.404 36.000 0.00 0.00 0.00 3.32
1045 1551 3.085443 ACCTTAGCTGTCATCGAATCG 57.915 47.619 0.00 0.00 0.00 3.34
1073 1579 1.468565 CGTGATCTCTAAACCGGCGAA 60.469 52.381 9.30 0.00 0.00 4.70
1078 1584 1.822990 TCTCTAAACCGGCGAACATCT 59.177 47.619 9.30 0.00 0.00 2.90
1079 1585 1.927174 CTCTAAACCGGCGAACATCTG 59.073 52.381 9.30 0.00 0.00 2.90
1080 1586 1.546923 TCTAAACCGGCGAACATCTGA 59.453 47.619 9.30 0.00 0.00 3.27
1105 1637 2.285368 AGGAGGGATCCGCCACAA 60.285 61.111 20.69 0.00 46.18 3.33
1570 2108 2.279408 GTCCTCGGCCCTAGGTCT 59.721 66.667 16.54 0.00 35.48 3.85
1737 2278 1.296715 GGGATGAGCAGTTCGTGGT 59.703 57.895 0.00 0.00 40.54 4.16
1831 2438 2.358619 CCCGCCCCATTCTTTCCA 59.641 61.111 0.00 0.00 0.00 3.53
1929 2536 1.958579 CGGTCCGTATCCATACTCCAA 59.041 52.381 2.08 0.00 0.00 3.53
1987 2594 2.398036 GGCGGCAATAACACGTCG 59.602 61.111 3.07 0.00 0.00 5.12
2014 2621 1.663695 CGTCCTCCAACAACAACAGT 58.336 50.000 0.00 0.00 0.00 3.55
2025 2632 7.883217 TCCAACAACAACAGTAACAACTTTAA 58.117 30.769 0.00 0.00 0.00 1.52
2041 2648 2.543777 TTAACTCCAGCTCCACACAC 57.456 50.000 0.00 0.00 0.00 3.82
2446 3057 2.159517 GGTGGATTTCGTTGCTGATCAC 60.160 50.000 0.00 0.00 0.00 3.06
2470 3081 3.252215 CGTTTGCCTACTTCATTGTGGAA 59.748 43.478 0.00 0.00 0.00 3.53
2478 3089 4.550076 ACTTCATTGTGGAAGAGGAGAG 57.450 45.455 9.67 0.00 45.66 3.20
2533 3145 2.159170 CCCCTCGAGAGAAAGTTAGCAG 60.159 54.545 15.71 0.00 41.32 4.24
2562 3174 4.088648 CCGAATTTCAAATACAGTGCGTC 58.911 43.478 0.00 0.00 0.00 5.19
2571 3183 3.706802 ATACAGTGCGTCTGAGATGAG 57.293 47.619 5.73 0.00 46.27 2.90
2578 3190 0.467384 CGTCTGAGATGAGGGCCAAT 59.533 55.000 6.18 0.00 0.00 3.16
2658 3271 9.793259 AACAGTTAGGATTCAGTTCTTCAATTA 57.207 29.630 0.00 0.00 0.00 1.40
2706 3319 2.919666 TAGCATTTCAAAAGCGCCTC 57.080 45.000 2.29 0.00 0.00 4.70
2751 3366 3.701040 CCCTTTGAACCCTTGTCCATATG 59.299 47.826 0.00 0.00 0.00 1.78
2752 3367 4.569653 CCCTTTGAACCCTTGTCCATATGA 60.570 45.833 3.65 0.00 0.00 2.15
2753 3368 4.641989 CCTTTGAACCCTTGTCCATATGAG 59.358 45.833 3.65 0.00 0.00 2.90
2754 3369 5.500234 CTTTGAACCCTTGTCCATATGAGA 58.500 41.667 3.65 0.00 0.00 3.27
2755 3370 4.760530 TGAACCCTTGTCCATATGAGAG 57.239 45.455 3.65 0.00 0.00 3.20
2756 3371 4.104086 TGAACCCTTGTCCATATGAGAGT 58.896 43.478 3.65 0.00 0.00 3.24
2757 3372 4.080919 TGAACCCTTGTCCATATGAGAGTG 60.081 45.833 3.65 0.00 0.00 3.51
2758 3373 2.774234 ACCCTTGTCCATATGAGAGTGG 59.226 50.000 3.65 0.99 36.82 4.00
2759 3374 3.041211 CCCTTGTCCATATGAGAGTGGA 58.959 50.000 3.65 0.00 42.03 4.02
2760 3375 3.649981 CCCTTGTCCATATGAGAGTGGAT 59.350 47.826 3.65 0.00 45.57 3.41
2761 3376 4.103785 CCCTTGTCCATATGAGAGTGGATT 59.896 45.833 3.65 0.00 45.57 3.01
2762 3377 5.398353 CCCTTGTCCATATGAGAGTGGATTT 60.398 44.000 3.65 0.00 45.57 2.17
2763 3378 6.125029 CCTTGTCCATATGAGAGTGGATTTT 58.875 40.000 3.65 0.00 45.57 1.82
2764 3379 6.261826 CCTTGTCCATATGAGAGTGGATTTTC 59.738 42.308 3.65 0.00 45.57 2.29
2765 3380 6.312141 TGTCCATATGAGAGTGGATTTTCA 57.688 37.500 3.65 0.00 45.57 2.69
2766 3381 6.351711 TGTCCATATGAGAGTGGATTTTCAG 58.648 40.000 3.65 0.00 45.57 3.02
2767 3382 5.238214 GTCCATATGAGAGTGGATTTTCAGC 59.762 44.000 3.65 0.00 45.57 4.26
2768 3383 5.131642 TCCATATGAGAGTGGATTTTCAGCT 59.868 40.000 3.65 0.00 39.51 4.24
2769 3384 5.469421 CCATATGAGAGTGGATTTTCAGCTC 59.531 44.000 3.65 0.00 37.72 4.09
2770 3385 3.340814 TGAGAGTGGATTTTCAGCTCC 57.659 47.619 0.00 0.00 0.00 4.70
2771 3386 2.909006 TGAGAGTGGATTTTCAGCTCCT 59.091 45.455 0.00 0.00 32.47 3.69
2772 3387 3.269178 GAGAGTGGATTTTCAGCTCCTG 58.731 50.000 0.00 0.00 32.47 3.86
2773 3388 2.026449 AGAGTGGATTTTCAGCTCCTGG 60.026 50.000 0.00 0.00 32.47 4.45
2774 3389 1.988107 AGTGGATTTTCAGCTCCTGGA 59.012 47.619 0.00 0.00 32.47 3.86
2775 3390 2.579860 AGTGGATTTTCAGCTCCTGGAT 59.420 45.455 0.00 0.00 32.47 3.41
2776 3391 2.686915 GTGGATTTTCAGCTCCTGGATG 59.313 50.000 0.00 0.00 32.47 3.51
2777 3392 1.680207 GGATTTTCAGCTCCTGGATGC 59.320 52.381 0.00 3.36 31.51 3.91
2778 3393 2.372264 GATTTTCAGCTCCTGGATGCA 58.628 47.619 16.74 0.00 31.51 3.96
2779 3394 2.519771 TTTTCAGCTCCTGGATGCAT 57.480 45.000 16.74 0.00 31.51 3.96
2780 3395 3.650281 TTTTCAGCTCCTGGATGCATA 57.350 42.857 16.74 5.19 31.51 3.14
2781 3396 2.924757 TTCAGCTCCTGGATGCATAG 57.075 50.000 16.74 0.00 31.51 2.23
2782 3397 1.054231 TCAGCTCCTGGATGCATAGG 58.946 55.000 8.99 8.99 35.34 2.57
2783 3398 0.605860 CAGCTCCTGGATGCATAGGC 60.606 60.000 10.27 7.19 41.68 3.93
2796 3411 2.772287 GCATAGGCACCCTCTATGAAC 58.228 52.381 13.35 0.00 43.98 3.18
2797 3412 2.104792 GCATAGGCACCCTCTATGAACA 59.895 50.000 13.35 0.00 43.98 3.18
2798 3413 3.805108 GCATAGGCACCCTCTATGAACAG 60.805 52.174 13.35 0.00 43.98 3.16
2799 3414 1.958288 AGGCACCCTCTATGAACAGT 58.042 50.000 0.00 0.00 0.00 3.55
2800 3415 3.116096 AGGCACCCTCTATGAACAGTA 57.884 47.619 0.00 0.00 0.00 2.74
2801 3416 3.450904 AGGCACCCTCTATGAACAGTAA 58.549 45.455 0.00 0.00 0.00 2.24
2802 3417 3.844211 AGGCACCCTCTATGAACAGTAAA 59.156 43.478 0.00 0.00 0.00 2.01
2803 3418 4.288626 AGGCACCCTCTATGAACAGTAAAA 59.711 41.667 0.00 0.00 0.00 1.52
2804 3419 5.044846 AGGCACCCTCTATGAACAGTAAAAT 60.045 40.000 0.00 0.00 0.00 1.82
2805 3420 6.157994 AGGCACCCTCTATGAACAGTAAAATA 59.842 38.462 0.00 0.00 0.00 1.40
2806 3421 6.826741 GGCACCCTCTATGAACAGTAAAATAA 59.173 38.462 0.00 0.00 0.00 1.40
2807 3422 7.338449 GGCACCCTCTATGAACAGTAAAATAAA 59.662 37.037 0.00 0.00 0.00 1.40
2808 3423 8.736244 GCACCCTCTATGAACAGTAAAATAAAA 58.264 33.333 0.00 0.00 0.00 1.52
2845 3460 3.629548 GCAATTTGCAACCATGGGT 57.370 47.368 18.09 6.57 44.26 4.51
2846 3461 2.758736 GCAATTTGCAACCATGGGTA 57.241 45.000 18.09 0.00 44.26 3.69
2847 3462 3.264998 GCAATTTGCAACCATGGGTAT 57.735 42.857 18.09 0.00 44.26 2.73
2848 3463 2.937799 GCAATTTGCAACCATGGGTATG 59.062 45.455 18.09 13.01 44.26 2.39
2849 3464 3.619487 GCAATTTGCAACCATGGGTATGT 60.619 43.478 18.09 0.00 44.26 2.29
2850 3465 4.577875 CAATTTGCAACCATGGGTATGTT 58.422 39.130 18.09 0.00 33.12 2.71
2851 3466 4.906747 ATTTGCAACCATGGGTATGTTT 57.093 36.364 18.09 0.00 33.12 2.83
2852 3467 4.696479 TTTGCAACCATGGGTATGTTTT 57.304 36.364 18.09 0.00 33.12 2.43
2853 3468 5.808366 TTTGCAACCATGGGTATGTTTTA 57.192 34.783 18.09 0.00 33.12 1.52
2854 3469 4.792521 TGCAACCATGGGTATGTTTTAC 57.207 40.909 18.09 0.00 33.12 2.01
2855 3470 4.411927 TGCAACCATGGGTATGTTTTACT 58.588 39.130 18.09 0.00 33.12 2.24
2856 3471 4.219507 TGCAACCATGGGTATGTTTTACTG 59.780 41.667 18.09 0.00 33.12 2.74
2857 3472 4.219725 GCAACCATGGGTATGTTTTACTGT 59.780 41.667 18.09 0.00 33.12 3.55
2858 3473 5.416326 GCAACCATGGGTATGTTTTACTGTA 59.584 40.000 18.09 0.00 33.12 2.74
2859 3474 6.624204 GCAACCATGGGTATGTTTTACTGTAC 60.624 42.308 18.09 0.00 33.12 2.90
2860 3475 6.129414 ACCATGGGTATGTTTTACTGTACA 57.871 37.500 18.09 0.00 32.11 2.90
2861 3476 6.177610 ACCATGGGTATGTTTTACTGTACAG 58.822 40.000 21.44 21.44 32.11 2.74
2862 3477 6.013206 ACCATGGGTATGTTTTACTGTACAGA 60.013 38.462 29.30 10.19 32.11 3.41
2863 3478 7.054124 CCATGGGTATGTTTTACTGTACAGAT 58.946 38.462 29.30 15.29 32.21 2.90
2864 3479 7.012327 CCATGGGTATGTTTTACTGTACAGATG 59.988 40.741 29.30 15.69 32.21 2.90
2865 3480 6.411376 TGGGTATGTTTTACTGTACAGATGG 58.589 40.000 29.30 3.91 0.00 3.51
2866 3481 6.213802 TGGGTATGTTTTACTGTACAGATGGA 59.786 38.462 29.30 9.45 0.00 3.41
2867 3482 7.092623 TGGGTATGTTTTACTGTACAGATGGAT 60.093 37.037 29.30 14.02 0.00 3.41
2868 3483 7.226720 GGGTATGTTTTACTGTACAGATGGATG 59.773 40.741 29.30 1.90 0.00 3.51
2869 3484 7.226720 GGTATGTTTTACTGTACAGATGGATGG 59.773 40.741 29.30 1.10 0.00 3.51
2870 3485 4.941263 TGTTTTACTGTACAGATGGATGGC 59.059 41.667 29.30 11.07 0.00 4.40
2871 3486 4.835284 TTTACTGTACAGATGGATGGCA 57.165 40.909 29.30 0.00 0.00 4.92
2872 3487 5.372343 TTTACTGTACAGATGGATGGCAT 57.628 39.130 29.30 0.00 0.00 4.40
2873 3488 3.204306 ACTGTACAGATGGATGGCATG 57.796 47.619 29.30 0.00 0.00 4.06
2874 3489 2.507058 ACTGTACAGATGGATGGCATGT 59.493 45.455 29.30 0.00 0.00 3.21
2875 3490 3.054139 ACTGTACAGATGGATGGCATGTT 60.054 43.478 29.30 0.00 0.00 2.71
2876 3491 3.281158 TGTACAGATGGATGGCATGTTG 58.719 45.455 3.81 0.00 0.00 3.33
2877 3492 1.108776 ACAGATGGATGGCATGTTGC 58.891 50.000 3.81 0.00 44.08 4.17
2887 3502 3.411808 GCATGTTGCAGTGACCATG 57.588 52.632 10.88 10.88 44.26 3.66
2888 3503 0.108992 GCATGTTGCAGTGACCATGG 60.109 55.000 11.19 11.19 44.26 3.66
2889 3504 0.528924 CATGTTGCAGTGACCATGGG 59.471 55.000 18.09 0.00 32.87 4.00
2890 3505 1.252904 ATGTTGCAGTGACCATGGGC 61.253 55.000 18.09 15.32 0.00 5.36
2891 3506 1.902918 GTTGCAGTGACCATGGGCA 60.903 57.895 19.12 19.12 0.00 5.36
2892 3507 1.077086 TTGCAGTGACCATGGGCAT 59.923 52.632 26.67 10.32 34.03 4.40
2893 3508 0.966875 TTGCAGTGACCATGGGCATC 60.967 55.000 26.67 17.49 34.03 3.91
2894 3509 1.077212 GCAGTGACCATGGGCATCT 60.077 57.895 26.67 19.57 0.00 2.90
2895 3510 0.682209 GCAGTGACCATGGGCATCTT 60.682 55.000 26.67 10.18 0.00 2.40
2896 3511 1.843368 CAGTGACCATGGGCATCTTT 58.157 50.000 26.67 7.34 0.00 2.52
2897 3512 2.173519 CAGTGACCATGGGCATCTTTT 58.826 47.619 26.67 4.54 0.00 2.27
2898 3513 2.094390 CAGTGACCATGGGCATCTTTTG 60.094 50.000 26.67 13.47 0.00 2.44
2899 3514 1.895131 GTGACCATGGGCATCTTTTGT 59.105 47.619 26.67 0.00 0.00 2.83
2900 3515 3.088532 GTGACCATGGGCATCTTTTGTA 58.911 45.455 26.67 0.00 0.00 2.41
2901 3516 3.509575 GTGACCATGGGCATCTTTTGTAA 59.490 43.478 26.67 0.00 0.00 2.41
2902 3517 4.160252 GTGACCATGGGCATCTTTTGTAAT 59.840 41.667 26.67 0.00 0.00 1.89
2903 3518 4.776837 TGACCATGGGCATCTTTTGTAATT 59.223 37.500 19.12 0.00 0.00 1.40
2904 3519 5.088680 ACCATGGGCATCTTTTGTAATTG 57.911 39.130 18.09 0.00 0.00 2.32
2905 3520 4.080975 ACCATGGGCATCTTTTGTAATTGG 60.081 41.667 18.09 0.00 0.00 3.16
2906 3521 3.608316 TGGGCATCTTTTGTAATTGGC 57.392 42.857 0.00 0.00 0.00 4.52
2907 3522 2.902486 TGGGCATCTTTTGTAATTGGCA 59.098 40.909 0.00 0.00 34.82 4.92
2908 3523 3.518705 TGGGCATCTTTTGTAATTGGCAT 59.481 39.130 0.00 0.00 34.82 4.40
2909 3524 3.872771 GGGCATCTTTTGTAATTGGCATG 59.127 43.478 0.00 0.00 34.82 4.06
2910 3525 4.506758 GGCATCTTTTGTAATTGGCATGT 58.493 39.130 0.00 0.00 33.49 3.21
2911 3526 4.937015 GGCATCTTTTGTAATTGGCATGTT 59.063 37.500 0.00 0.00 33.49 2.71
2912 3527 5.063817 GGCATCTTTTGTAATTGGCATGTTC 59.936 40.000 0.00 0.00 33.49 3.18
2913 3528 5.220265 GCATCTTTTGTAATTGGCATGTTCG 60.220 40.000 0.00 0.00 0.00 3.95
2914 3529 5.446143 TCTTTTGTAATTGGCATGTTCGT 57.554 34.783 0.00 0.00 0.00 3.85
2915 3530 5.218885 TCTTTTGTAATTGGCATGTTCGTG 58.781 37.500 0.00 0.00 0.00 4.35
2916 3531 2.627863 TGTAATTGGCATGTTCGTGC 57.372 45.000 8.31 8.31 44.31 5.34
2917 3532 2.158559 TGTAATTGGCATGTTCGTGCT 58.841 42.857 15.14 0.43 44.45 4.40
2918 3533 2.095314 TGTAATTGGCATGTTCGTGCTG 60.095 45.455 15.14 0.00 44.45 4.41
2919 3534 0.388907 AATTGGCATGTTCGTGCTGC 60.389 50.000 15.14 0.00 44.45 5.25
2922 3537 2.644418 GCATGTTCGTGCTGCCAA 59.356 55.556 9.41 0.00 41.82 4.52
2923 3538 1.007502 GCATGTTCGTGCTGCCAAA 60.008 52.632 9.41 0.00 41.82 3.28
2924 3539 0.388907 GCATGTTCGTGCTGCCAAAT 60.389 50.000 9.41 0.00 41.82 2.32
2925 3540 1.936203 GCATGTTCGTGCTGCCAAATT 60.936 47.619 9.41 0.00 41.82 1.82
2926 3541 1.722464 CATGTTCGTGCTGCCAAATTG 59.278 47.619 0.00 0.00 0.00 2.32
2927 3542 0.743688 TGTTCGTGCTGCCAAATTGT 59.256 45.000 0.00 0.00 0.00 2.71
2928 3543 1.135915 TGTTCGTGCTGCCAAATTGTT 59.864 42.857 0.00 0.00 0.00 2.83
2929 3544 2.200899 GTTCGTGCTGCCAAATTGTTT 58.799 42.857 0.00 0.00 0.00 2.83
2930 3545 2.132740 TCGTGCTGCCAAATTGTTTC 57.867 45.000 0.00 0.00 0.00 2.78
2931 3546 0.777631 CGTGCTGCCAAATTGTTTCG 59.222 50.000 0.00 0.00 0.00 3.46
2932 3547 1.139163 GTGCTGCCAAATTGTTTCGG 58.861 50.000 0.00 0.00 0.00 4.30
2933 3548 0.033228 TGCTGCCAAATTGTTTCGGG 59.967 50.000 0.00 0.00 0.00 5.14
2934 3549 0.033366 GCTGCCAAATTGTTTCGGGT 59.967 50.000 0.00 0.00 0.00 5.28
2935 3550 1.540146 GCTGCCAAATTGTTTCGGGTT 60.540 47.619 0.00 0.00 0.00 4.11
2936 3551 2.134346 CTGCCAAATTGTTTCGGGTTG 58.866 47.619 0.00 0.00 0.00 3.77
2937 3552 1.482593 TGCCAAATTGTTTCGGGTTGT 59.517 42.857 0.00 0.00 0.00 3.32
2938 3553 2.093447 TGCCAAATTGTTTCGGGTTGTT 60.093 40.909 0.00 0.00 0.00 2.83
2939 3554 2.286563 GCCAAATTGTTTCGGGTTGTTG 59.713 45.455 0.00 0.00 0.00 3.33
2940 3555 2.286563 CCAAATTGTTTCGGGTTGTTGC 59.713 45.455 0.00 0.00 0.00 4.17
2941 3556 2.932614 CAAATTGTTTCGGGTTGTTGCA 59.067 40.909 0.00 0.00 0.00 4.08
2942 3557 3.467374 AATTGTTTCGGGTTGTTGCAT 57.533 38.095 0.00 0.00 0.00 3.96
2943 3558 2.215907 TTGTTTCGGGTTGTTGCATG 57.784 45.000 0.00 0.00 0.00 4.06
2944 3559 0.249238 TGTTTCGGGTTGTTGCATGC 60.249 50.000 11.82 11.82 0.00 4.06
2945 3560 1.007964 TTTCGGGTTGTTGCATGCG 60.008 52.632 14.09 0.00 0.00 4.73
2946 3561 1.729470 TTTCGGGTTGTTGCATGCGT 61.729 50.000 14.09 0.00 0.00 5.24
2947 3562 1.729470 TTCGGGTTGTTGCATGCGTT 61.729 50.000 14.09 0.00 0.00 4.84
2948 3563 2.015627 CGGGTTGTTGCATGCGTTG 61.016 57.895 14.09 0.00 0.00 4.10
2949 3564 1.664333 GGGTTGTTGCATGCGTTGG 60.664 57.895 14.09 0.00 0.00 3.77
2950 3565 1.361993 GGTTGTTGCATGCGTTGGA 59.638 52.632 14.09 0.00 0.00 3.53
2951 3566 0.038343 GGTTGTTGCATGCGTTGGAT 60.038 50.000 14.09 0.00 0.00 3.41
2952 3567 1.605202 GGTTGTTGCATGCGTTGGATT 60.605 47.619 14.09 0.00 0.00 3.01
2953 3568 2.352225 GGTTGTTGCATGCGTTGGATTA 60.352 45.455 14.09 0.00 0.00 1.75
2954 3569 2.627863 TGTTGCATGCGTTGGATTAC 57.372 45.000 14.09 1.68 0.00 1.89
2955 3570 1.135831 TGTTGCATGCGTTGGATTACG 60.136 47.619 14.09 0.00 44.09 3.18
2956 3571 0.449786 TTGCATGCGTTGGATTACGG 59.550 50.000 14.09 0.00 41.65 4.02
2957 3572 0.391793 TGCATGCGTTGGATTACGGA 60.392 50.000 14.09 0.00 45.70 4.69
2962 3577 2.428491 TGCGTTGGATTACGGATTTGT 58.572 42.857 0.00 0.00 41.65 2.83
2963 3578 2.814919 TGCGTTGGATTACGGATTTGTT 59.185 40.909 0.00 0.00 41.65 2.83
2964 3579 3.168193 GCGTTGGATTACGGATTTGTTG 58.832 45.455 0.00 0.00 41.65 3.33
2965 3580 3.168193 CGTTGGATTACGGATTTGTTGC 58.832 45.455 0.00 0.00 37.86 4.17
2966 3581 3.365465 CGTTGGATTACGGATTTGTTGCA 60.365 43.478 0.00 0.00 37.86 4.08
2967 3582 4.551388 GTTGGATTACGGATTTGTTGCAA 58.449 39.130 0.00 0.00 0.00 4.08
2968 3583 4.167554 TGGATTACGGATTTGTTGCAAC 57.832 40.909 22.83 22.83 0.00 4.17
2969 3584 3.057174 TGGATTACGGATTTGTTGCAACC 60.057 43.478 26.14 9.98 0.00 3.77
2970 3585 3.057174 GGATTACGGATTTGTTGCAACCA 60.057 43.478 26.14 13.54 0.00 3.67
2971 3586 4.551388 GATTACGGATTTGTTGCAACCAA 58.449 39.130 26.14 21.65 0.00 3.67
2972 3587 4.592485 TTACGGATTTGTTGCAACCAAT 57.408 36.364 24.40 24.40 32.75 3.16
2973 3588 2.753296 ACGGATTTGTTGCAACCAATG 58.247 42.857 27.94 18.59 32.75 2.82
2974 3589 2.363680 ACGGATTTGTTGCAACCAATGA 59.636 40.909 27.94 7.96 32.75 2.57
2975 3590 3.181471 ACGGATTTGTTGCAACCAATGAA 60.181 39.130 27.94 13.36 32.75 2.57
2976 3591 3.995705 CGGATTTGTTGCAACCAATGAAT 59.004 39.130 27.94 18.27 32.75 2.57
2977 3592 4.451774 CGGATTTGTTGCAACCAATGAATT 59.548 37.500 27.94 12.22 32.75 2.17
2978 3593 5.615106 CGGATTTGTTGCAACCAATGAATTG 60.615 40.000 27.94 12.29 37.52 2.32
2989 3604 7.655236 CAACCAATGAATTGCACAGATAAAA 57.345 32.000 0.00 0.00 36.48 1.52
2990 3605 8.085720 CAACCAATGAATTGCACAGATAAAAA 57.914 30.769 0.00 0.00 36.48 1.94
3011 3626 7.982761 AAAAATATTTCATGGTGTGTTGCAT 57.017 28.000 0.10 0.00 0.00 3.96
3012 3627 6.971527 AAATATTTCATGGTGTGTTGCATG 57.028 33.333 0.00 0.00 0.00 4.06
3013 3628 5.664294 ATATTTCATGGTGTGTTGCATGT 57.336 34.783 0.00 0.00 0.00 3.21
3014 3629 3.367992 TTTCATGGTGTGTTGCATGTC 57.632 42.857 0.00 0.00 0.00 3.06
3015 3630 2.275134 TCATGGTGTGTTGCATGTCT 57.725 45.000 0.00 0.00 0.00 3.41
3016 3631 2.585330 TCATGGTGTGTTGCATGTCTT 58.415 42.857 0.00 0.00 0.00 3.01
3017 3632 2.957680 TCATGGTGTGTTGCATGTCTTT 59.042 40.909 0.00 0.00 0.00 2.52
3018 3633 4.140536 TCATGGTGTGTTGCATGTCTTTA 58.859 39.130 0.00 0.00 0.00 1.85
3019 3634 4.582240 TCATGGTGTGTTGCATGTCTTTAA 59.418 37.500 0.00 0.00 0.00 1.52
3020 3635 4.991153 TGGTGTGTTGCATGTCTTTAAA 57.009 36.364 0.00 0.00 0.00 1.52
3021 3636 5.330455 TGGTGTGTTGCATGTCTTTAAAA 57.670 34.783 0.00 0.00 0.00 1.52
3022 3637 5.911752 TGGTGTGTTGCATGTCTTTAAAAT 58.088 33.333 0.00 0.00 0.00 1.82
3023 3638 7.043961 TGGTGTGTTGCATGTCTTTAAAATA 57.956 32.000 0.00 0.00 0.00 1.40
3024 3639 7.665690 TGGTGTGTTGCATGTCTTTAAAATAT 58.334 30.769 0.00 0.00 0.00 1.28
3025 3640 7.598118 TGGTGTGTTGCATGTCTTTAAAATATG 59.402 33.333 0.00 0.00 0.00 1.78
3026 3641 7.812191 GGTGTGTTGCATGTCTTTAAAATATGA 59.188 33.333 9.10 0.00 0.00 2.15
3027 3642 8.853345 GTGTGTTGCATGTCTTTAAAATATGAG 58.147 33.333 9.10 0.00 0.00 2.90
3028 3643 8.028354 TGTGTTGCATGTCTTTAAAATATGAGG 58.972 33.333 9.10 0.00 0.00 3.86
3029 3644 8.243426 GTGTTGCATGTCTTTAAAATATGAGGA 58.757 33.333 9.10 0.00 0.00 3.71
3030 3645 8.801299 TGTTGCATGTCTTTAAAATATGAGGAA 58.199 29.630 9.10 0.00 0.00 3.36
3031 3646 9.638239 GTTGCATGTCTTTAAAATATGAGGAAA 57.362 29.630 9.10 0.00 0.00 3.13
3058 3673 7.810766 ATGTTGCGATATTGTTTACTTTTGG 57.189 32.000 0.00 0.00 0.00 3.28
3059 3674 6.971602 TGTTGCGATATTGTTTACTTTTGGA 58.028 32.000 0.00 0.00 0.00 3.53
3060 3675 7.426410 TGTTGCGATATTGTTTACTTTTGGAA 58.574 30.769 0.00 0.00 0.00 3.53
3061 3676 7.921214 TGTTGCGATATTGTTTACTTTTGGAAA 59.079 29.630 0.00 0.00 0.00 3.13
3062 3677 7.861176 TGCGATATTGTTTACTTTTGGAAAC 57.139 32.000 0.00 0.00 36.33 2.78
3063 3678 7.426410 TGCGATATTGTTTACTTTTGGAAACA 58.574 30.769 2.79 2.79 42.31 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
274 278 0.388134 TACGAGCTTCGCCAGTGAAC 60.388 55.000 5.63 0.00 45.12 3.18
365 369 2.667199 AACCTAACGCACCGCACC 60.667 61.111 0.00 0.00 0.00 5.01
422 426 7.988599 ACACCATAAAAGACACAAGTAGTTGTA 59.011 33.333 15.48 0.00 45.57 2.41
702 707 1.855360 GATGACCTCAAGCGATTCGAC 59.145 52.381 10.88 1.21 0.00 4.20
712 717 0.321564 CGCCAAGTGGATGACCTCAA 60.322 55.000 0.18 0.00 37.39 3.02
717 722 2.401766 CCAGCGCCAAGTGGATGAC 61.402 63.158 7.62 0.00 35.67 3.06
781 787 8.297470 TCTTGGCAGCTATATTTCTGATTTTT 57.703 30.769 7.77 0.00 32.26 1.94
828 848 2.028125 TAATCCCCTCTTCGCGCAGG 62.028 60.000 8.75 6.34 0.00 4.85
898 918 7.406031 TCTCGAATTTGTACTCCTAATGTCT 57.594 36.000 0.00 0.00 0.00 3.41
899 919 7.253684 CGTTCTCGAATTTGTACTCCTAATGTC 60.254 40.741 0.00 0.00 39.71 3.06
924 950 6.081693 TCAATCCGTGATCGTTACATATACG 58.918 40.000 0.00 0.00 40.23 3.06
963 1469 6.630188 GCCAAGGGTTTGAAGCATATTTGTAT 60.630 38.462 0.00 0.00 36.36 2.29
964 1470 5.337169 GCCAAGGGTTTGAAGCATATTTGTA 60.337 40.000 0.00 0.00 36.36 2.41
965 1471 4.563374 GCCAAGGGTTTGAAGCATATTTGT 60.563 41.667 0.00 0.00 36.36 2.83
966 1472 3.934579 GCCAAGGGTTTGAAGCATATTTG 59.065 43.478 0.00 0.00 36.36 2.32
968 1474 3.172339 TGCCAAGGGTTTGAAGCATATT 58.828 40.909 0.00 0.00 36.36 1.28
970 1476 2.298729 GTTGCCAAGGGTTTGAAGCATA 59.701 45.455 0.00 0.00 36.36 3.14
973 1479 0.597377 CGTTGCCAAGGGTTTGAAGC 60.597 55.000 0.00 0.00 36.36 3.86
995 1501 0.890683 GTTGCTTGGGTTGCTGCTAT 59.109 50.000 0.00 0.00 0.00 2.97
1027 1533 2.463876 TGCGATTCGATGACAGCTAAG 58.536 47.619 10.88 0.00 0.00 2.18
1033 1539 1.878069 CCGCTGCGATTCGATGACA 60.878 57.895 25.45 0.00 0.00 3.58
1045 1551 0.100682 TTAGAGATCACGACCGCTGC 59.899 55.000 0.00 0.00 0.00 5.25
1073 1579 2.305928 CCTCCTCATCGTCTCAGATGT 58.694 52.381 6.82 0.00 45.96 3.06
1078 1584 1.479573 GGATCCCTCCTCATCGTCTCA 60.480 57.143 0.00 0.00 38.65 3.27
1079 1585 1.253100 GGATCCCTCCTCATCGTCTC 58.747 60.000 0.00 0.00 38.65 3.36
1080 1586 0.538516 CGGATCCCTCCTCATCGTCT 60.539 60.000 6.06 0.00 39.65 4.18
1570 2108 3.299977 CGGGTGGACTCGGTCACA 61.300 66.667 6.41 0.54 33.68 3.58
1929 2536 2.361104 ATGCGTTTGGATGGCCGT 60.361 55.556 0.00 0.00 36.79 5.68
1974 2581 0.364515 GGTCGACGACGTGTTATTGC 59.635 55.000 20.92 0.84 40.69 3.56
1987 2594 4.047059 TTGGAGGACGCGGTCGAC 62.047 66.667 12.47 7.13 39.41 4.20
2000 2607 5.968528 AAGTTGTTACTGTTGTTGTTGGA 57.031 34.783 0.00 0.00 34.01 3.53
2014 2621 5.061179 GTGGAGCTGGAGTTAAAGTTGTTA 58.939 41.667 0.00 0.00 0.00 2.41
2025 2632 0.394565 GAAGTGTGTGGAGCTGGAGT 59.605 55.000 0.00 0.00 0.00 3.85
2041 2648 3.269178 GAGGAAGATGCACAAGGAGAAG 58.731 50.000 0.00 0.00 0.00 2.85
2424 3032 2.290260 TGATCAGCAACGAAATCCACCT 60.290 45.455 0.00 0.00 0.00 4.00
2437 3048 1.971167 GGCAAACGGGTGATCAGCA 60.971 57.895 25.18 0.00 0.00 4.41
2446 3057 2.095263 CACAATGAAGTAGGCAAACGGG 60.095 50.000 0.00 0.00 0.00 5.28
2533 3145 5.123344 ACTGTATTTGAAATTCGGCCTACAC 59.877 40.000 0.00 0.00 0.00 2.90
2562 3174 3.677976 GCAAAAATTGGCCCTCATCTCAG 60.678 47.826 0.00 0.00 0.00 3.35
2571 3183 6.751425 GCTAAAATAATTGCAAAAATTGGCCC 59.249 34.615 1.71 0.00 0.00 5.80
2680 3293 5.576774 GGCGCTTTTGAAATGCTAAAATAGT 59.423 36.000 7.64 0.00 0.00 2.12
2681 3294 5.807011 AGGCGCTTTTGAAATGCTAAAATAG 59.193 36.000 7.64 0.00 0.00 1.73
2706 3319 8.034804 AGGGTGCAAAGCTTATTTACAAATTAG 58.965 33.333 0.00 0.00 0.00 1.73
2751 3366 3.269178 CAGGAGCTGAAAATCCACTCTC 58.731 50.000 0.00 0.00 38.12 3.20
2752 3367 2.026449 CCAGGAGCTGAAAATCCACTCT 60.026 50.000 0.00 0.00 38.12 3.24
2753 3368 2.026822 TCCAGGAGCTGAAAATCCACTC 60.027 50.000 0.00 0.00 38.12 3.51
2754 3369 1.988107 TCCAGGAGCTGAAAATCCACT 59.012 47.619 0.00 0.00 38.12 4.00
2755 3370 2.496899 TCCAGGAGCTGAAAATCCAC 57.503 50.000 0.00 0.00 38.12 4.02
2756 3371 2.947243 GCATCCAGGAGCTGAAAATCCA 60.947 50.000 0.00 0.00 38.12 3.41
2757 3372 1.680207 GCATCCAGGAGCTGAAAATCC 59.320 52.381 0.00 0.00 32.44 3.01
2758 3373 2.372264 TGCATCCAGGAGCTGAAAATC 58.628 47.619 0.00 0.00 32.44 2.17
2759 3374 2.519771 TGCATCCAGGAGCTGAAAAT 57.480 45.000 0.00 0.00 32.44 1.82
2760 3375 2.519771 ATGCATCCAGGAGCTGAAAA 57.480 45.000 0.00 0.00 32.44 2.29
2761 3376 2.158711 CCTATGCATCCAGGAGCTGAAA 60.159 50.000 9.61 0.00 33.42 2.69
2762 3377 1.419012 CCTATGCATCCAGGAGCTGAA 59.581 52.381 9.61 0.00 33.42 3.02
2763 3378 1.054231 CCTATGCATCCAGGAGCTGA 58.946 55.000 9.61 0.00 33.42 4.26
2764 3379 0.605860 GCCTATGCATCCAGGAGCTG 60.606 60.000 18.11 0.00 37.47 4.24
2765 3380 1.058428 TGCCTATGCATCCAGGAGCT 61.058 55.000 18.11 0.00 44.23 4.09
2766 3381 1.453235 TGCCTATGCATCCAGGAGC 59.547 57.895 18.11 7.46 44.23 4.70
2776 3391 2.104792 TGTTCATAGAGGGTGCCTATGC 59.895 50.000 0.00 0.00 41.82 3.14
2777 3392 3.389329 ACTGTTCATAGAGGGTGCCTATG 59.611 47.826 0.00 0.00 42.84 2.23
2778 3393 3.658725 ACTGTTCATAGAGGGTGCCTAT 58.341 45.455 0.00 0.00 31.76 2.57
2779 3394 3.116096 ACTGTTCATAGAGGGTGCCTA 57.884 47.619 0.00 0.00 31.76 3.93
2780 3395 1.958288 ACTGTTCATAGAGGGTGCCT 58.042 50.000 0.00 0.00 36.03 4.75
2781 3396 3.906720 TTACTGTTCATAGAGGGTGCC 57.093 47.619 0.00 0.00 0.00 5.01
2782 3397 7.859325 TTATTTTACTGTTCATAGAGGGTGC 57.141 36.000 0.00 0.00 0.00 5.01
2818 3433 4.205587 TGGTTGCAAATTGCCATCTTTTT 58.794 34.783 15.98 0.00 44.23 1.94
2819 3434 3.818180 TGGTTGCAAATTGCCATCTTTT 58.182 36.364 15.98 0.00 44.23 2.27
2820 3435 3.488778 TGGTTGCAAATTGCCATCTTT 57.511 38.095 15.98 0.00 44.23 2.52
2821 3436 3.340034 CATGGTTGCAAATTGCCATCTT 58.660 40.909 15.98 0.00 44.23 2.40
2822 3437 2.355310 CCATGGTTGCAAATTGCCATCT 60.355 45.455 15.98 0.00 44.23 2.90
2823 3438 2.011222 CCATGGTTGCAAATTGCCATC 58.989 47.619 15.98 5.34 44.23 3.51
2824 3439 1.340211 CCCATGGTTGCAAATTGCCAT 60.340 47.619 15.98 12.33 44.23 4.40
2825 3440 0.036448 CCCATGGTTGCAAATTGCCA 59.964 50.000 15.98 8.78 44.23 4.92
2826 3441 0.036590 ACCCATGGTTGCAAATTGCC 59.963 50.000 15.98 0.00 44.23 4.52
2827 3442 2.758736 TACCCATGGTTGCAAATTGC 57.241 45.000 11.58 11.58 39.58 3.56
2828 3443 4.205065 ACATACCCATGGTTGCAAATTG 57.795 40.909 11.73 0.00 37.09 2.32
2829 3444 4.906747 AACATACCCATGGTTGCAAATT 57.093 36.364 11.73 0.00 37.09 1.82
2830 3445 4.906747 AAACATACCCATGGTTGCAAAT 57.093 36.364 11.73 0.00 40.65 2.32
2831 3446 4.696479 AAAACATACCCATGGTTGCAAA 57.304 36.364 11.73 0.00 41.34 3.68
2832 3447 4.835615 AGTAAAACATACCCATGGTTGCAA 59.164 37.500 11.73 0.00 41.34 4.08
2833 3448 4.219507 CAGTAAAACATACCCATGGTTGCA 59.780 41.667 11.73 0.00 41.34 4.08
2834 3449 4.219725 ACAGTAAAACATACCCATGGTTGC 59.780 41.667 11.73 0.00 41.34 4.17
2835 3450 5.975693 ACAGTAAAACATACCCATGGTTG 57.024 39.130 11.73 7.96 41.34 3.77
2836 3451 6.544650 TGTACAGTAAAACATACCCATGGTT 58.455 36.000 11.73 0.00 44.15 3.67
2837 3452 6.013206 TCTGTACAGTAAAACATACCCATGGT 60.013 38.462 21.99 1.30 40.16 3.55
2838 3453 6.411376 TCTGTACAGTAAAACATACCCATGG 58.589 40.000 21.99 4.14 36.39 3.66
2839 3454 7.012327 CCATCTGTACAGTAAAACATACCCATG 59.988 40.741 21.99 12.69 38.21 3.66
2840 3455 7.054124 CCATCTGTACAGTAAAACATACCCAT 58.946 38.462 21.99 1.14 0.00 4.00
2841 3456 6.213802 TCCATCTGTACAGTAAAACATACCCA 59.786 38.462 21.99 0.00 0.00 4.51
2842 3457 6.646267 TCCATCTGTACAGTAAAACATACCC 58.354 40.000 21.99 0.00 0.00 3.69
2843 3458 7.226720 CCATCCATCTGTACAGTAAAACATACC 59.773 40.741 21.99 0.00 0.00 2.73
2844 3459 7.254795 GCCATCCATCTGTACAGTAAAACATAC 60.255 40.741 21.99 3.76 0.00 2.39
2845 3460 6.765989 GCCATCCATCTGTACAGTAAAACATA 59.234 38.462 21.99 0.81 0.00 2.29
2846 3461 5.590259 GCCATCCATCTGTACAGTAAAACAT 59.410 40.000 21.99 4.77 0.00 2.71
2847 3462 4.941263 GCCATCCATCTGTACAGTAAAACA 59.059 41.667 21.99 2.35 0.00 2.83
2848 3463 4.941263 TGCCATCCATCTGTACAGTAAAAC 59.059 41.667 21.99 6.80 0.00 2.43
2849 3464 5.172687 TGCCATCCATCTGTACAGTAAAA 57.827 39.130 21.99 3.51 0.00 1.52
2850 3465 4.835284 TGCCATCCATCTGTACAGTAAA 57.165 40.909 21.99 3.90 0.00 2.01
2851 3466 4.164030 ACATGCCATCCATCTGTACAGTAA 59.836 41.667 21.99 4.68 29.71 2.24
2852 3467 3.711190 ACATGCCATCCATCTGTACAGTA 59.289 43.478 21.99 9.79 29.71 2.74
2853 3468 2.507058 ACATGCCATCCATCTGTACAGT 59.493 45.455 21.99 7.40 29.71 3.55
2854 3469 3.204306 ACATGCCATCCATCTGTACAG 57.796 47.619 17.17 17.17 29.71 2.74
2855 3470 3.281158 CAACATGCCATCCATCTGTACA 58.719 45.455 0.00 0.00 29.71 2.90
2856 3471 2.033801 GCAACATGCCATCCATCTGTAC 59.966 50.000 0.00 0.00 37.42 2.90
2857 3472 2.300433 GCAACATGCCATCCATCTGTA 58.700 47.619 0.00 0.00 37.42 2.74
2858 3473 1.108776 GCAACATGCCATCCATCTGT 58.891 50.000 0.00 0.00 37.42 3.41
2859 3474 1.067060 CTGCAACATGCCATCCATCTG 59.933 52.381 0.00 0.00 44.23 2.90
2860 3475 1.341679 ACTGCAACATGCCATCCATCT 60.342 47.619 0.00 0.00 44.23 2.90
2861 3476 1.108776 ACTGCAACATGCCATCCATC 58.891 50.000 0.00 0.00 44.23 3.51
2862 3477 0.821517 CACTGCAACATGCCATCCAT 59.178 50.000 0.00 0.00 44.23 3.41
2863 3478 0.251253 TCACTGCAACATGCCATCCA 60.251 50.000 0.00 0.00 44.23 3.41
2864 3479 0.171903 GTCACTGCAACATGCCATCC 59.828 55.000 0.00 0.00 44.23 3.51
2865 3480 0.171903 GGTCACTGCAACATGCCATC 59.828 55.000 0.00 0.00 44.23 3.51
2866 3481 0.540133 TGGTCACTGCAACATGCCAT 60.540 50.000 0.00 0.00 44.23 4.40
2867 3482 0.540133 ATGGTCACTGCAACATGCCA 60.540 50.000 0.00 9.34 44.23 4.92
2868 3483 0.108992 CATGGTCACTGCAACATGCC 60.109 55.000 0.00 0.00 44.23 4.40
2869 3484 0.108992 CCATGGTCACTGCAACATGC 60.109 55.000 2.57 0.00 45.29 4.06
2870 3485 0.528924 CCCATGGTCACTGCAACATG 59.471 55.000 11.73 0.00 40.17 3.21
2871 3486 1.252904 GCCCATGGTCACTGCAACAT 61.253 55.000 11.73 0.00 0.00 2.71
2872 3487 1.902918 GCCCATGGTCACTGCAACA 60.903 57.895 11.73 0.00 0.00 3.33
2873 3488 1.252904 ATGCCCATGGTCACTGCAAC 61.253 55.000 15.31 0.00 35.30 4.17
2874 3489 0.966875 GATGCCCATGGTCACTGCAA 60.967 55.000 15.31 1.66 35.30 4.08
2875 3490 1.378911 GATGCCCATGGTCACTGCA 60.379 57.895 13.97 13.97 36.23 4.41
2876 3491 0.682209 AAGATGCCCATGGTCACTGC 60.682 55.000 11.73 7.00 0.00 4.40
2877 3492 1.843368 AAAGATGCCCATGGTCACTG 58.157 50.000 11.73 0.00 0.00 3.66
2878 3493 2.173519 CAAAAGATGCCCATGGTCACT 58.826 47.619 11.73 1.44 0.00 3.41
2879 3494 1.895131 ACAAAAGATGCCCATGGTCAC 59.105 47.619 11.73 0.00 0.00 3.67
2880 3495 2.307496 ACAAAAGATGCCCATGGTCA 57.693 45.000 11.73 3.83 0.00 4.02
2881 3496 5.111293 CAATTACAAAAGATGCCCATGGTC 58.889 41.667 11.73 0.00 0.00 4.02
2882 3497 4.080975 CCAATTACAAAAGATGCCCATGGT 60.081 41.667 11.73 0.00 0.00 3.55
2883 3498 4.444536 CCAATTACAAAAGATGCCCATGG 58.555 43.478 4.14 4.14 0.00 3.66
2884 3499 3.872771 GCCAATTACAAAAGATGCCCATG 59.127 43.478 0.00 0.00 0.00 3.66
2885 3500 3.518705 TGCCAATTACAAAAGATGCCCAT 59.481 39.130 0.00 0.00 0.00 4.00
2886 3501 2.902486 TGCCAATTACAAAAGATGCCCA 59.098 40.909 0.00 0.00 0.00 5.36
2887 3502 3.608316 TGCCAATTACAAAAGATGCCC 57.392 42.857 0.00 0.00 0.00 5.36
2888 3503 4.506758 ACATGCCAATTACAAAAGATGCC 58.493 39.130 0.00 0.00 0.00 4.40
2889 3504 5.220265 CGAACATGCCAATTACAAAAGATGC 60.220 40.000 0.00 0.00 0.00 3.91
2890 3505 5.863397 ACGAACATGCCAATTACAAAAGATG 59.137 36.000 0.00 0.00 0.00 2.90
2891 3506 5.863397 CACGAACATGCCAATTACAAAAGAT 59.137 36.000 0.00 0.00 0.00 2.40
2892 3507 5.218885 CACGAACATGCCAATTACAAAAGA 58.781 37.500 0.00 0.00 0.00 2.52
2893 3508 4.143347 GCACGAACATGCCAATTACAAAAG 60.143 41.667 0.00 0.00 39.86 2.27
2894 3509 3.738282 GCACGAACATGCCAATTACAAAA 59.262 39.130 0.00 0.00 39.86 2.44
2895 3510 3.312828 GCACGAACATGCCAATTACAAA 58.687 40.909 0.00 0.00 39.86 2.83
2896 3511 2.940147 GCACGAACATGCCAATTACAA 58.060 42.857 0.00 0.00 39.86 2.41
2897 3512 2.627863 GCACGAACATGCCAATTACA 57.372 45.000 0.00 0.00 39.86 2.41
2905 3520 0.388907 ATTTGGCAGCACGAACATGC 60.389 50.000 0.00 0.00 46.50 4.06
2906 3521 1.722464 CAATTTGGCAGCACGAACATG 59.278 47.619 0.00 0.00 0.00 3.21
2907 3522 1.340889 ACAATTTGGCAGCACGAACAT 59.659 42.857 0.78 0.00 0.00 2.71
2908 3523 0.743688 ACAATTTGGCAGCACGAACA 59.256 45.000 0.78 0.00 0.00 3.18
2909 3524 1.851658 AACAATTTGGCAGCACGAAC 58.148 45.000 0.78 0.00 0.00 3.95
2910 3525 2.468831 GAAACAATTTGGCAGCACGAA 58.531 42.857 0.78 0.00 0.00 3.85
2911 3526 1.599171 CGAAACAATTTGGCAGCACGA 60.599 47.619 0.78 0.00 0.00 4.35
2912 3527 0.777631 CGAAACAATTTGGCAGCACG 59.222 50.000 0.78 0.00 0.00 5.34
2913 3528 1.139163 CCGAAACAATTTGGCAGCAC 58.861 50.000 0.78 0.00 33.29 4.40
2914 3529 0.033228 CCCGAAACAATTTGGCAGCA 59.967 50.000 0.78 0.00 38.60 4.41
2915 3530 0.033366 ACCCGAAACAATTTGGCAGC 59.967 50.000 0.78 0.00 38.60 5.25
2916 3531 2.134346 CAACCCGAAACAATTTGGCAG 58.866 47.619 0.78 0.00 38.60 4.85
2917 3532 1.482593 ACAACCCGAAACAATTTGGCA 59.517 42.857 0.78 0.00 38.60 4.92
2918 3533 2.232756 ACAACCCGAAACAATTTGGC 57.767 45.000 0.78 0.00 38.60 4.52
2919 3534 2.286563 GCAACAACCCGAAACAATTTGG 59.713 45.455 0.78 0.00 39.52 3.28
2920 3535 2.932614 TGCAACAACCCGAAACAATTTG 59.067 40.909 0.00 0.00 0.00 2.32
2921 3536 3.252974 TGCAACAACCCGAAACAATTT 57.747 38.095 0.00 0.00 0.00 1.82
2922 3537 2.969628 TGCAACAACCCGAAACAATT 57.030 40.000 0.00 0.00 0.00 2.32
2923 3538 2.753296 CATGCAACAACCCGAAACAAT 58.247 42.857 0.00 0.00 0.00 2.71
2924 3539 1.804372 GCATGCAACAACCCGAAACAA 60.804 47.619 14.21 0.00 0.00 2.83
2925 3540 0.249238 GCATGCAACAACCCGAAACA 60.249 50.000 14.21 0.00 0.00 2.83
2926 3541 1.274798 CGCATGCAACAACCCGAAAC 61.275 55.000 19.57 0.00 0.00 2.78
2927 3542 1.007964 CGCATGCAACAACCCGAAA 60.008 52.632 19.57 0.00 0.00 3.46
2928 3543 1.729470 AACGCATGCAACAACCCGAA 61.729 50.000 19.57 0.00 0.00 4.30
2929 3544 2.190170 AACGCATGCAACAACCCGA 61.190 52.632 19.57 0.00 0.00 5.14
2930 3545 2.015627 CAACGCATGCAACAACCCG 61.016 57.895 19.57 0.50 0.00 5.28
2931 3546 1.664333 CCAACGCATGCAACAACCC 60.664 57.895 19.57 0.00 0.00 4.11
2932 3547 0.038343 ATCCAACGCATGCAACAACC 60.038 50.000 19.57 0.00 0.00 3.77
2933 3548 1.782044 AATCCAACGCATGCAACAAC 58.218 45.000 19.57 0.00 0.00 3.32
2934 3549 2.666895 CGTAATCCAACGCATGCAACAA 60.667 45.455 19.57 0.00 35.87 2.83
2935 3550 1.135831 CGTAATCCAACGCATGCAACA 60.136 47.619 19.57 0.00 35.87 3.33
2936 3551 1.534028 CGTAATCCAACGCATGCAAC 58.466 50.000 19.57 1.42 35.87 4.17
2937 3552 0.449786 CCGTAATCCAACGCATGCAA 59.550 50.000 19.57 0.00 41.51 4.08
2938 3553 0.391793 TCCGTAATCCAACGCATGCA 60.392 50.000 19.57 0.00 41.51 3.96
2939 3554 0.944386 ATCCGTAATCCAACGCATGC 59.056 50.000 7.91 7.91 41.51 4.06
2940 3555 3.181501 ACAAATCCGTAATCCAACGCATG 60.182 43.478 0.00 0.00 41.51 4.06
2941 3556 3.013921 ACAAATCCGTAATCCAACGCAT 58.986 40.909 0.00 0.00 41.51 4.73
2942 3557 2.428491 ACAAATCCGTAATCCAACGCA 58.572 42.857 0.00 0.00 41.51 5.24
2943 3558 3.168193 CAACAAATCCGTAATCCAACGC 58.832 45.455 0.00 0.00 41.51 4.84
2944 3559 3.168193 GCAACAAATCCGTAATCCAACG 58.832 45.455 0.00 0.00 42.49 4.10
2945 3560 4.167554 TGCAACAAATCCGTAATCCAAC 57.832 40.909 0.00 0.00 0.00 3.77
2946 3561 4.551388 GTTGCAACAAATCCGTAATCCAA 58.449 39.130 24.52 0.00 0.00 3.53
2947 3562 3.057174 GGTTGCAACAAATCCGTAATCCA 60.057 43.478 29.55 0.00 0.00 3.41
2948 3563 3.057174 TGGTTGCAACAAATCCGTAATCC 60.057 43.478 29.55 9.24 0.00 3.01
2949 3564 4.167554 TGGTTGCAACAAATCCGTAATC 57.832 40.909 29.55 9.23 0.00 1.75
2950 3565 4.592485 TTGGTTGCAACAAATCCGTAAT 57.408 36.364 29.55 0.00 0.00 1.89
2951 3566 4.038042 TCATTGGTTGCAACAAATCCGTAA 59.962 37.500 26.14 9.43 30.18 3.18
2952 3567 3.570125 TCATTGGTTGCAACAAATCCGTA 59.430 39.130 26.14 11.58 30.18 4.02
2953 3568 2.363680 TCATTGGTTGCAACAAATCCGT 59.636 40.909 26.14 6.95 30.18 4.69
2954 3569 3.023946 TCATTGGTTGCAACAAATCCG 57.976 42.857 26.14 17.36 30.18 4.18
2955 3570 5.691815 CAATTCATTGGTTGCAACAAATCC 58.308 37.500 26.14 12.20 30.18 3.01
2965 3580 7.655236 TTTTATCTGTGCAATTCATTGGTTG 57.345 32.000 1.77 0.22 38.21 3.77
2987 3602 7.444792 ACATGCAACACACCATGAAATATTTTT 59.555 29.630 1.43 0.00 40.92 1.94
2988 3603 6.935771 ACATGCAACACACCATGAAATATTTT 59.064 30.769 1.43 0.00 40.92 1.82
2989 3604 6.465948 ACATGCAACACACCATGAAATATTT 58.534 32.000 0.00 0.00 40.92 1.40
2990 3605 6.040209 ACATGCAACACACCATGAAATATT 57.960 33.333 7.53 0.00 40.92 1.28
2991 3606 5.419788 AGACATGCAACACACCATGAAATAT 59.580 36.000 7.53 0.00 40.92 1.28
2992 3607 4.766373 AGACATGCAACACACCATGAAATA 59.234 37.500 7.53 0.00 40.92 1.40
2993 3608 3.575256 AGACATGCAACACACCATGAAAT 59.425 39.130 7.53 0.00 40.92 2.17
2994 3609 2.957680 AGACATGCAACACACCATGAAA 59.042 40.909 7.53 0.00 40.92 2.69
2995 3610 2.585330 AGACATGCAACACACCATGAA 58.415 42.857 7.53 0.00 40.92 2.57
2996 3611 2.275134 AGACATGCAACACACCATGA 57.725 45.000 7.53 0.00 40.92 3.07
2997 3612 3.374220 AAAGACATGCAACACACCATG 57.626 42.857 0.00 0.00 43.34 3.66
2998 3613 5.528043 TTTAAAGACATGCAACACACCAT 57.472 34.783 0.00 0.00 0.00 3.55
2999 3614 4.991153 TTTAAAGACATGCAACACACCA 57.009 36.364 0.00 0.00 0.00 4.17
3000 3615 7.812191 TCATATTTTAAAGACATGCAACACACC 59.188 33.333 0.00 0.00 0.00 4.16
3001 3616 8.741101 TCATATTTTAAAGACATGCAACACAC 57.259 30.769 0.00 0.00 0.00 3.82
3002 3617 8.028354 CCTCATATTTTAAAGACATGCAACACA 58.972 33.333 0.00 0.00 0.00 3.72
3003 3618 8.243426 TCCTCATATTTTAAAGACATGCAACAC 58.757 33.333 0.00 0.00 0.00 3.32
3004 3619 8.347004 TCCTCATATTTTAAAGACATGCAACA 57.653 30.769 0.00 0.00 0.00 3.33
3005 3620 9.638239 TTTCCTCATATTTTAAAGACATGCAAC 57.362 29.630 0.00 0.00 0.00 4.17
3032 3647 8.707839 CCAAAAGTAAACAATATCGCAACATTT 58.292 29.630 0.00 0.00 0.00 2.32
3033 3648 8.085296 TCCAAAAGTAAACAATATCGCAACATT 58.915 29.630 0.00 0.00 0.00 2.71
3034 3649 7.598278 TCCAAAAGTAAACAATATCGCAACAT 58.402 30.769 0.00 0.00 0.00 2.71
3035 3650 6.971602 TCCAAAAGTAAACAATATCGCAACA 58.028 32.000 0.00 0.00 0.00 3.33
3036 3651 7.861176 TTCCAAAAGTAAACAATATCGCAAC 57.139 32.000 0.00 0.00 0.00 4.17
3037 3652 7.921214 TGTTTCCAAAAGTAAACAATATCGCAA 59.079 29.630 0.00 0.00 41.34 4.85
3038 3653 7.426410 TGTTTCCAAAAGTAAACAATATCGCA 58.574 30.769 0.00 0.00 41.34 5.10
3039 3654 7.861176 TGTTTCCAAAAGTAAACAATATCGC 57.139 32.000 0.00 0.00 41.34 4.58


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

AutoCloner maintained by Alex Coulton.