Multiple sequence alignment - TraesCS4D01G119200

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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 TraesCS4D01G119200 chr4D 100.000 6227 0 0 1 6227 100561119 100567345 0.000000e+00 11500.0
1 TraesCS4D01G119200 chr4B 93.461 1621 69 17 1 1605 142912800 142914399 0.000000e+00 2372.0
2 TraesCS4D01G119200 chr4B 94.818 1370 48 11 4868 6227 142917572 142918928 0.000000e+00 2115.0
3 TraesCS4D01G119200 chr4B 91.316 1497 83 21 2722 4191 142915498 142916974 0.000000e+00 2001.0
4 TraesCS4D01G119200 chr4B 94.135 1023 44 8 1604 2616 142914482 142915498 0.000000e+00 1543.0
5 TraesCS4D01G119200 chr4B 95.786 617 24 2 4203 4819 142916956 142917570 0.000000e+00 994.0
6 TraesCS4D01G119200 chr4B 82.212 208 29 4 503 703 10946843 10947049 8.300000e-39 172.0
7 TraesCS4D01G119200 chr4B 92.105 38 3 0 2614 2651 100947496 100947533 3.000000e-03 54.7
8 TraesCS4D01G119200 chr4A 90.824 1395 84 31 150 1522 475919975 475918603 0.000000e+00 1827.0
9 TraesCS4D01G119200 chr4A 90.418 1388 73 20 4867 6227 475915312 475913958 0.000000e+00 1772.0
10 TraesCS4D01G119200 chr4A 90.494 1357 66 20 2860 4191 475917239 475915921 0.000000e+00 1733.0
11 TraesCS4D01G119200 chr4A 92.705 1083 54 11 1541 2613 475918617 475917550 0.000000e+00 1539.0
12 TraesCS4D01G119200 chr4A 93.164 629 33 4 4203 4821 475915939 475915311 0.000000e+00 915.0
13 TraesCS4D01G119200 chr4A 92.949 156 8 2 2713 2868 475917478 475917326 2.260000e-54 224.0
14 TraesCS4D01G119200 chr4A 89.231 130 14 0 2483 2612 45839235 45839364 4.990000e-36 163.0
15 TraesCS4D01G119200 chr4A 78.855 227 29 13 521 741 557254620 557254407 1.090000e-27 135.0
16 TraesCS4D01G119200 chr5D 83.285 347 34 16 414 743 478288455 478288116 1.310000e-76 298.0
17 TraesCS4D01G119200 chr5D 88.785 107 11 1 2614 2720 509228120 509228225 5.070000e-26 130.0
18 TraesCS4D01G119200 chr5D 80.337 178 27 8 2434 2609 13885919 13886090 1.820000e-25 128.0
19 TraesCS4D01G119200 chr5D 93.750 64 4 0 4804 4867 250069612 250069675 5.140000e-16 97.1
20 TraesCS4D01G119200 chr5D 96.491 57 2 0 4811 4867 519201534 519201478 1.850000e-15 95.3
21 TraesCS4D01G119200 chr7D 81.690 355 34 17 412 738 32374993 32375344 3.700000e-67 267.0
22 TraesCS4D01G119200 chr7D 78.632 351 50 18 416 745 37101595 37101941 6.330000e-50 209.0
23 TraesCS4D01G119200 chr7D 95.868 121 4 1 2000 2119 604292805 604292925 1.770000e-45 195.0
24 TraesCS4D01G119200 chr7D 91.589 107 9 0 2614 2720 65601766 65601660 1.400000e-31 148.0
25 TraesCS4D01G119200 chr7D 93.651 63 1 3 4820 4881 163351885 163351825 2.390000e-14 91.6
26 TraesCS4D01G119200 chr7B 80.712 337 54 9 414 742 561282750 561282417 1.040000e-62 252.0
27 TraesCS4D01G119200 chr7B 88.372 172 20 0 2441 2612 438988902 438989073 2.280000e-49 207.0
28 TraesCS4D01G119200 chr7B 78.198 344 51 13 414 738 479873470 479873132 1.370000e-46 198.0
29 TraesCS4D01G119200 chr7B 78.198 344 51 13 414 738 479896681 479896343 1.370000e-46 198.0
30 TraesCS4D01G119200 chr7B 91.000 100 8 1 2733 2832 505470164 505470262 3.920000e-27 134.0
31 TraesCS4D01G119200 chr7B 100.000 53 0 0 4815 4867 47339753 47339701 1.430000e-16 99.0
32 TraesCS4D01G119200 chr2D 83.406 229 32 2 2390 2612 361393344 361393572 2.280000e-49 207.0
33 TraesCS4D01G119200 chr2D 93.243 74 3 1 2759 2832 530392083 530392154 2.370000e-19 108.0
34 TraesCS4D01G119200 chr2D 98.276 58 1 0 4810 4867 7542707 7542650 1.100000e-17 102.0
35 TraesCS4D01G119200 chr2D 93.651 63 3 1 4816 4878 441874595 441874656 6.650000e-15 93.5
36 TraesCS4D01G119200 chr6D 96.667 120 4 0 2000 2119 267532933 267532814 3.810000e-47 200.0
37 TraesCS4D01G119200 chr6A 96.667 120 4 0 2000 2119 381088826 381088707 3.810000e-47 200.0
38 TraesCS4D01G119200 chr3A 96.610 118 4 0 2002 2119 685358760 685358877 4.920000e-46 196.0
39 TraesCS4D01G119200 chr3A 81.383 188 19 11 414 595 497296188 497296365 8.420000e-29 139.0
40 TraesCS4D01G119200 chr3A 83.333 114 13 4 2723 2832 57018339 57018228 3.970000e-17 100.0
41 TraesCS4D01G119200 chr5A 94.444 126 5 2 2000 2123 410512153 410512028 6.370000e-45 193.0
42 TraesCS4D01G119200 chr5A 85.906 149 14 5 2466 2612 10916105 10916248 1.080000e-32 152.0
43 TraesCS4D01G119200 chr2B 95.000 120 6 0 2000 2119 380573715 380573834 8.240000e-44 189.0
44 TraesCS4D01G119200 chr2B 87.619 105 12 1 2720 2824 39698043 39697940 3.050000e-23 121.0
45 TraesCS4D01G119200 chr1A 95.000 120 6 0 2000 2119 24135818 24135937 8.240000e-44 189.0
46 TraesCS4D01G119200 chr1A 87.097 93 9 3 2734 2823 262834166 262834258 1.100000e-17 102.0
47 TraesCS4D01G119200 chr5B 78.964 309 40 15 414 703 430731745 430731443 2.960000e-43 187.0
48 TraesCS4D01G119200 chr5B 88.000 100 12 0 2724 2823 118626508 118626607 1.100000e-22 119.0
49 TraesCS4D01G119200 chr5B 82.759 87 14 1 2723 2809 256953014 256952929 6.690000e-10 76.8
50 TraesCS4D01G119200 chrUn 81.279 219 22 15 414 621 87945863 87946073 6.460000e-35 159.0
51 TraesCS4D01G119200 chr3B 90.000 120 8 4 590 706 809044569 809044451 1.080000e-32 152.0
52 TraesCS4D01G119200 chr3D 90.351 114 10 1 2499 2612 582171601 582171489 1.400000e-31 148.0
53 TraesCS4D01G119200 chr3D 93.651 63 1 3 4820 4881 574516552 574516612 2.390000e-14 91.6
54 TraesCS4D01G119200 chr1D 88.793 116 8 5 2498 2612 336556804 336556915 3.030000e-28 137.0
55 TraesCS4D01G119200 chr1D 90.000 70 4 2 4811 4878 415405048 415405116 3.090000e-13 87.9
56 TraesCS4D01G119200 chr7A 90.909 99 9 0 2723 2821 532476374 532476472 3.920000e-27 134.0
57 TraesCS4D01G119200 chr2A 95.238 63 3 0 4805 4867 27327049 27327111 3.970000e-17 100.0


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 TraesCS4D01G119200 chr4D 100561119 100567345 6226 False 11500 11500 100.0000 1 6227 1 chr4D.!!$F1 6226
1 TraesCS4D01G119200 chr4B 142912800 142918928 6128 False 1805 2372 93.9032 1 6227 5 chr4B.!!$F3 6226
2 TraesCS4D01G119200 chr4A 475913958 475919975 6017 True 1335 1827 91.7590 150 6227 6 chr4A.!!$R2 6077

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
675 696 0.109132 GCTCTCAAATTTGGCACGGG 60.109 55.000 17.90 5.9 0.0 5.28 F
1369 1401 0.245539 TGCTAGTGAACGTAGTGCCC 59.754 55.000 0.00 0.0 45.0 5.36 F
2630 2756 1.339097 ACTACTCCCGCTGTTCACTT 58.661 50.000 0.00 0.0 0.0 3.16 F
3113 3336 0.112412 AACCGGTTGCCTGGAAATCT 59.888 50.000 21.56 0.0 0.0 2.40 F
3262 3487 1.395954 GTTACCAGAAATTCCGACCGC 59.604 52.381 0.00 0.0 0.0 5.68 F
4058 4311 1.611673 GGATATCTTCATGGGCGGGTG 60.612 57.143 2.05 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2408 2534 0.186386 AACCAATCCCCGGAACAACA 59.814 50.000 0.73 0.0 0.00 3.33 R
2707 2833 0.181350 AAATGGCACTCCCTCCGATC 59.819 55.000 0.00 0.0 0.00 3.69 R
4208 4462 0.254462 TGCACACAAAGGACACCTCA 59.746 50.000 0.00 0.0 30.89 3.86 R
4210 4464 0.546122 TCTGCACACAAAGGACACCT 59.454 50.000 0.00 0.0 33.87 4.00 R
4211 4465 0.663153 GTCTGCACACAAAGGACACC 59.337 55.000 0.00 0.0 0.00 4.16 R
5772 6060 1.260561 GTGATGAAGAACACGCACGTT 59.739 47.619 0.00 0.0 31.21 3.99 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
42 43 0.978146 TTGCTGGTAGGAGAGGAGGC 60.978 60.000 0.00 0.00 0.00 4.70
47 48 2.698788 TAGGAGAGGAGGCGGGGA 60.699 66.667 0.00 0.00 0.00 4.81
99 100 2.355837 CGTGGCGATATGGGACGG 60.356 66.667 0.00 0.00 0.00 4.79
119 120 2.173382 GCGACGCAACATGGTGAC 59.827 61.111 16.85 4.93 0.00 3.67
135 136 1.819632 GACATGGGATGGTGGCGAC 60.820 63.158 0.00 0.00 33.60 5.19
198 199 2.256158 CGCGAGGGTGTACAACGA 59.744 61.111 0.00 0.00 0.00 3.85
217 219 2.762745 GAAAAGTTCAGACGGCTACCA 58.237 47.619 0.00 0.00 0.00 3.25
265 267 1.235724 GCAAGGGGTGATTATACGGC 58.764 55.000 0.00 0.00 0.00 5.68
527 536 4.442706 AGATATTTTAGTGCGTGAGGTGG 58.557 43.478 0.00 0.00 0.00 4.61
570 579 3.634448 TGGACATCTGAGTAGCTCTTAGC 59.366 47.826 0.00 0.00 42.84 3.09
615 633 7.418337 AACAATAAACTTTTTCACAGACCCT 57.582 32.000 0.00 0.00 0.00 4.34
661 682 5.006552 GCTACTCAGACATTCAAATGCTCTC 59.993 44.000 2.66 0.00 40.04 3.20
675 696 0.109132 GCTCTCAAATTTGGCACGGG 60.109 55.000 17.90 5.90 0.00 5.28
688 709 1.004560 CACGGGCATCACACACTCT 60.005 57.895 0.00 0.00 0.00 3.24
706 727 8.105829 ACACACTCTATCATCTTTCTCCAAAAT 58.894 33.333 0.00 0.00 0.00 1.82
762 790 2.715536 AAAAACACTCCCGGCTCAC 58.284 52.632 0.00 0.00 0.00 3.51
818 846 6.757897 AGAGATTTCAAATTTCGTGCCATA 57.242 33.333 0.00 0.00 0.00 2.74
838 866 1.266178 CCAAATGGAGTGTTTCCCCC 58.734 55.000 0.00 0.00 46.19 5.40
1367 1399 3.982058 GGATATGCTAGTGAACGTAGTGC 59.018 47.826 0.00 0.00 45.00 4.40
1369 1401 0.245539 TGCTAGTGAACGTAGTGCCC 59.754 55.000 0.00 0.00 45.00 5.36
1435 1467 4.042187 AGTGAATGTACCTCCTCTTTGCTT 59.958 41.667 0.00 0.00 0.00 3.91
1528 1560 5.995282 TCGACATATTCCTGTGTTTGTCTTT 59.005 36.000 0.00 0.00 33.14 2.52
1532 1564 9.959749 GACATATTCCTGTGTTTGTCTTTAAAA 57.040 29.630 0.00 0.00 32.69 1.52
1617 1733 7.148355 TCTTGTTTTATAGTTTTAAGGGCCG 57.852 36.000 0.00 0.00 0.00 6.13
1655 1771 3.322211 TGACCGCCTTTTCGAGATTTA 57.678 42.857 0.00 0.00 0.00 1.40
1858 1974 2.505819 ACTGAACCCTTGTGAACTGAGT 59.494 45.455 0.00 0.00 0.00 3.41
1925 2041 3.011257 ACAAGGGGCCAGCTAAAGATAAA 59.989 43.478 4.39 0.00 0.00 1.40
1945 2062 9.193806 AGATAAATTCTACACATGGAAAGCAAT 57.806 29.630 0.00 0.00 30.96 3.56
2032 2155 1.770658 AGCTAGCTATCCATGTGCCAA 59.229 47.619 17.69 0.00 0.00 4.52
2071 2194 3.310774 CGACATCTTATGGGTTTCAGCTG 59.689 47.826 7.63 7.63 33.60 4.24
2127 2253 9.685828 GGCTTTGTTGTTGTTGTTCTATATTTA 57.314 29.630 0.00 0.00 0.00 1.40
2148 2274 8.798859 ATTTAGTACAATCAATGTGAGAAGCT 57.201 30.769 0.00 0.00 43.77 3.74
2408 2534 5.670792 TCAAACTAGATGATAACCCGTGT 57.329 39.130 0.00 0.00 0.00 4.49
2413 2539 3.695830 AGATGATAACCCGTGTGTTGT 57.304 42.857 0.00 0.00 0.00 3.32
2540 2666 8.749026 AATTTCTCATGCATGTTAAGAGAGAT 57.251 30.769 25.43 16.99 36.77 2.75
2541 2667 9.842775 AATTTCTCATGCATGTTAAGAGAGATA 57.157 29.630 25.43 14.04 36.77 1.98
2586 2712 2.617788 GCATGTGTGGTGAGTTGGGATA 60.618 50.000 0.00 0.00 0.00 2.59
2613 2739 8.043113 TGTGCATGTTGAGAGAGAATATAAACT 58.957 33.333 0.00 0.00 0.00 2.66
2614 2740 9.534565 GTGCATGTTGAGAGAGAATATAAACTA 57.465 33.333 0.00 0.00 0.00 2.24
2615 2741 9.534565 TGCATGTTGAGAGAGAATATAAACTAC 57.465 33.333 0.00 0.00 0.00 2.73
2616 2742 9.757227 GCATGTTGAGAGAGAATATAAACTACT 57.243 33.333 0.00 0.00 0.00 2.57
2620 2746 7.747155 TGAGAGAGAATATAAACTACTCCCG 57.253 40.000 0.00 0.00 0.00 5.14
2622 2748 6.308566 AGAGAGAATATAAACTACTCCCGCT 58.691 40.000 0.00 0.00 0.00 5.52
2625 2751 6.324254 AGAGAATATAAACTACTCCCGCTGTT 59.676 38.462 0.00 0.00 0.00 3.16
2626 2752 6.514063 AGAATATAAACTACTCCCGCTGTTC 58.486 40.000 0.00 0.00 0.00 3.18
2630 2756 1.339097 ACTACTCCCGCTGTTCACTT 58.661 50.000 0.00 0.00 0.00 3.16
2631 2757 1.692519 ACTACTCCCGCTGTTCACTTT 59.307 47.619 0.00 0.00 0.00 2.66
2639 2765 4.933400 TCCCGCTGTTCACTTTTATAAGAC 59.067 41.667 0.00 0.00 35.30 3.01
2640 2766 4.693566 CCCGCTGTTCACTTTTATAAGACA 59.306 41.667 0.00 0.00 35.30 3.41
2641 2767 5.354234 CCCGCTGTTCACTTTTATAAGACAT 59.646 40.000 0.00 0.00 35.30 3.06
2660 2786 8.485976 AAGACATTTTAGATAGTTCAGACAGC 57.514 34.615 0.00 0.00 0.00 4.40
2661 2787 7.846066 AGACATTTTAGATAGTTCAGACAGCT 58.154 34.615 0.00 0.00 0.00 4.24
2662 2788 7.978975 AGACATTTTAGATAGTTCAGACAGCTC 59.021 37.037 0.00 0.00 0.00 4.09
2663 2789 7.044798 ACATTTTAGATAGTTCAGACAGCTCC 58.955 38.462 0.00 0.00 0.00 4.70
2665 2791 3.107402 AGATAGTTCAGACAGCTCCCA 57.893 47.619 0.00 0.00 0.00 4.37
2670 2796 2.092429 AGTTCAGACAGCTCCCAAAACA 60.092 45.455 0.00 0.00 0.00 2.83
2671 2797 2.260844 TCAGACAGCTCCCAAAACAG 57.739 50.000 0.00 0.00 0.00 3.16
2673 2799 2.092429 TCAGACAGCTCCCAAAACAGTT 60.092 45.455 0.00 0.00 0.00 3.16
2674 2800 2.033801 CAGACAGCTCCCAAAACAGTTG 59.966 50.000 0.00 0.00 0.00 3.16
2675 2801 2.092429 AGACAGCTCCCAAAACAGTTGA 60.092 45.455 0.00 0.00 0.00 3.18
2677 2803 3.096092 ACAGCTCCCAAAACAGTTGAAA 58.904 40.909 0.00 0.00 0.00 2.69
2680 2806 4.746611 CAGCTCCCAAAACAGTTGAAAATC 59.253 41.667 0.00 0.00 0.00 2.17
2683 2809 4.692228 TCCCAAAACAGTTGAAAATCAGC 58.308 39.130 0.00 0.00 0.00 4.26
2690 2816 4.825546 CAGTTGAAAATCAGCTGTCTGT 57.174 40.909 14.67 0.00 46.36 3.41
2691 2817 5.929697 CAGTTGAAAATCAGCTGTCTGTA 57.070 39.130 14.67 0.00 46.36 2.74
2692 2818 6.304356 CAGTTGAAAATCAGCTGTCTGTAA 57.696 37.500 14.67 1.03 46.36 2.41
2693 2819 6.138761 CAGTTGAAAATCAGCTGTCTGTAAC 58.861 40.000 14.67 12.70 46.36 2.50
2694 2820 5.822519 AGTTGAAAATCAGCTGTCTGTAACA 59.177 36.000 14.67 4.38 36.56 2.41
2695 2821 6.488006 AGTTGAAAATCAGCTGTCTGTAACAT 59.512 34.615 14.67 0.00 36.56 2.71
2696 2822 6.486253 TGAAAATCAGCTGTCTGTAACATC 57.514 37.500 14.67 2.37 41.10 3.06
2697 2823 6.233434 TGAAAATCAGCTGTCTGTAACATCT 58.767 36.000 14.67 0.00 41.10 2.90
2698 2824 6.712095 TGAAAATCAGCTGTCTGTAACATCTT 59.288 34.615 14.67 0.00 41.10 2.40
2699 2825 7.877612 TGAAAATCAGCTGTCTGTAACATCTTA 59.122 33.333 14.67 0.00 41.10 2.10
2700 2826 8.798859 AAAATCAGCTGTCTGTAACATCTTAT 57.201 30.769 14.67 0.00 41.10 1.73
2701 2827 9.890629 AAAATCAGCTGTCTGTAACATCTTATA 57.109 29.630 14.67 0.00 41.10 0.98
2702 2828 9.890629 AAATCAGCTGTCTGTAACATCTTATAA 57.109 29.630 14.67 0.00 41.10 0.98
2703 2829 9.890629 AATCAGCTGTCTGTAACATCTTATAAA 57.109 29.630 14.67 0.00 41.10 1.40
2704 2830 9.890629 ATCAGCTGTCTGTAACATCTTATAAAA 57.109 29.630 14.67 0.00 41.10 1.52
2705 2831 9.719355 TCAGCTGTCTGTAACATCTTATAAAAA 57.281 29.630 14.67 0.00 41.10 1.94
2706 2832 9.979270 CAGCTGTCTGTAACATCTTATAAAAAG 57.021 33.333 5.25 0.00 37.23 2.27
2707 2833 9.167311 AGCTGTCTGTAACATCTTATAAAAAGG 57.833 33.333 0.00 0.00 37.23 3.11
2708 2834 9.162764 GCTGTCTGTAACATCTTATAAAAAGGA 57.837 33.333 0.00 0.00 37.23 3.36
2720 2846 2.789409 AAAAAGGATCGGAGGGAGTG 57.211 50.000 0.00 0.00 0.00 3.51
2747 2873 6.647334 TTTACCATGCATGTTCAGAGAAAA 57.353 33.333 24.58 4.84 0.00 2.29
2796 2922 4.453478 GTGTGCATGTTGAGAGAATTGAGA 59.547 41.667 0.00 0.00 0.00 3.27
2819 2945 4.439253 AGTGGGGATCAACTATTTAGGC 57.561 45.455 0.00 0.00 0.00 3.93
2823 2949 6.275618 AGTGGGGATCAACTATTTAGGCATAT 59.724 38.462 0.00 0.00 0.00 1.78
2824 2950 6.375455 GTGGGGATCAACTATTTAGGCATATG 59.625 42.308 0.00 0.00 0.00 1.78
2859 2985 7.763071 TGACTTATCTCATCACTTCATCAGTTG 59.237 37.037 0.00 0.00 30.92 3.16
2860 2986 7.845037 ACTTATCTCATCACTTCATCAGTTGA 58.155 34.615 0.00 0.00 30.92 3.18
2921 3142 9.662947 ATTGTAGTTATACACTTACCACTTTCC 57.337 33.333 0.00 0.00 41.62 3.13
3046 3267 9.330063 TCTATTTGACTCAAATATGTCATGACC 57.670 33.333 22.85 5.91 42.79 4.02
3048 3269 7.757941 TTTGACTCAAATATGTCATGACCAA 57.242 32.000 22.85 11.26 41.93 3.67
3049 3270 7.943079 TTGACTCAAATATGTCATGACCAAT 57.057 32.000 22.85 13.00 41.93 3.16
3050 3271 7.324354 TGACTCAAATATGTCATGACCAATG 57.676 36.000 22.85 13.93 38.15 2.82
3054 3275 8.246180 ACTCAAATATGTCATGACCAATGTTTC 58.754 33.333 22.85 0.00 37.56 2.78
3102 3325 1.035385 GGGGCTGGAATAACCGGTTG 61.035 60.000 30.08 12.84 46.24 3.77
3110 3333 2.164338 GAATAACCGGTTGCCTGGAAA 58.836 47.619 30.08 7.41 0.00 3.13
3113 3336 0.112412 AACCGGTTGCCTGGAAATCT 59.888 50.000 21.56 0.00 0.00 2.40
3114 3337 0.112412 ACCGGTTGCCTGGAAATCTT 59.888 50.000 0.00 0.00 0.00 2.40
3186 3411 9.927668 AATGAATTCGAACAAATTTTATCCAGT 57.072 25.926 0.00 0.00 0.00 4.00
3191 3416 7.972832 TCGAACAAATTTTATCCAGTACTGT 57.027 32.000 21.18 6.67 0.00 3.55
3229 3454 1.971695 CTGGGTGGCCGAAAGAACC 60.972 63.158 0.00 0.00 0.00 3.62
3262 3487 1.395954 GTTACCAGAAATTCCGACCGC 59.604 52.381 0.00 0.00 0.00 5.68
3267 3492 2.518949 CAGAAATTCCGACCGCAATTG 58.481 47.619 0.00 0.00 0.00 2.32
3281 3506 2.489329 CGCAATTGAGAACCTTGGTCAT 59.511 45.455 10.34 0.00 0.00 3.06
3291 3516 4.279169 AGAACCTTGGTCATGACACAATTG 59.721 41.667 26.47 20.07 0.00 2.32
3318 3543 6.306199 TGCCACCTGCTTATATGTTTCATAT 58.694 36.000 7.30 7.30 42.00 1.78
3354 3579 3.063588 CACATGCTGTAAGTGATGAGCTG 59.936 47.826 0.00 0.00 35.33 4.24
3389 3614 4.252570 AGGAAGCTAGAGTAAGCCAGTA 57.747 45.455 0.00 0.00 43.86 2.74
3407 3632 6.013639 AGCCAGTAACTACAGGAGTTTATGTT 60.014 38.462 2.45 0.00 46.79 2.71
3483 3708 8.360390 TGTAGACATGTGGCACTATTATTAGAG 58.640 37.037 19.83 0.50 0.00 2.43
3527 3752 7.978099 AAGGAATTATGAGCCAAATTAAGGT 57.022 32.000 0.00 0.00 0.00 3.50
3569 3794 9.850628 ATCATATTTTGATGAAATTATGAGCCG 57.149 29.630 19.72 0.71 43.60 5.52
3578 3803 5.901552 TGAAATTATGAGCCGGAATTTTCC 58.098 37.500 5.05 0.00 44.05 3.13
3640 3865 3.066380 GGCAGTTTTAAGCATGGGTTTG 58.934 45.455 0.00 0.00 0.00 2.93
3652 3877 3.674997 CATGGGTTTGGATATCCGGTAG 58.325 50.000 17.04 0.00 39.43 3.18
3707 3959 8.884124 AATCATGGAGGTTATGGGTATAATTG 57.116 34.615 0.00 0.00 31.81 2.32
3908 4160 7.076842 TGAGCTTATTTGCTATGTTTGAGTC 57.923 36.000 0.00 0.00 44.17 3.36
3981 4233 1.909228 TCGGGTATGGGCACGATTT 59.091 52.632 0.00 0.00 39.58 2.17
4030 4282 4.954970 CAAGCACCACCGTGGGCT 62.955 66.667 21.77 21.54 43.37 5.19
4040 4293 3.727258 CGTGGGCTTGGGGATGGA 61.727 66.667 0.00 0.00 0.00 3.41
4053 4306 2.357569 GGGGATGGATATCTTCATGGGC 60.358 54.545 2.05 0.00 33.68 5.36
4058 4311 1.611673 GGATATCTTCATGGGCGGGTG 60.612 57.143 2.05 0.00 0.00 4.61
4081 4334 3.985127 TCCATTGCCATCATTCTCCTTT 58.015 40.909 0.00 0.00 0.00 3.11
4085 4338 6.612456 TCCATTGCCATCATTCTCCTTTAAAT 59.388 34.615 0.00 0.00 0.00 1.40
4124 4378 1.673767 TGAAGGGAGCCTGAAATCCT 58.326 50.000 0.00 0.00 35.80 3.24
4190 4444 4.342092 CCAGTTTGAAATGAGGTGTCCTTT 59.658 41.667 0.00 0.00 31.76 3.11
4191 4445 5.163416 CCAGTTTGAAATGAGGTGTCCTTTT 60.163 40.000 0.00 0.00 31.76 2.27
4192 4446 6.340522 CAGTTTGAAATGAGGTGTCCTTTTT 58.659 36.000 0.00 0.00 31.76 1.94
4212 4466 4.314740 TTTTTGACGGGTTGAAATGAGG 57.685 40.909 0.00 0.00 0.00 3.86
4213 4467 2.649531 TTGACGGGTTGAAATGAGGT 57.350 45.000 0.00 0.00 0.00 3.85
4214 4468 1.890876 TGACGGGTTGAAATGAGGTG 58.109 50.000 0.00 0.00 0.00 4.00
4215 4469 1.142060 TGACGGGTTGAAATGAGGTGT 59.858 47.619 0.00 0.00 0.00 4.16
4216 4470 1.804748 GACGGGTTGAAATGAGGTGTC 59.195 52.381 0.00 0.00 0.00 3.67
4217 4471 1.165270 CGGGTTGAAATGAGGTGTCC 58.835 55.000 0.00 0.00 0.00 4.02
4218 4472 1.271379 CGGGTTGAAATGAGGTGTCCT 60.271 52.381 0.00 0.00 36.03 3.85
4219 4473 2.814097 CGGGTTGAAATGAGGTGTCCTT 60.814 50.000 0.00 0.00 31.76 3.36
4280 4534 8.048514 TCTGTTATTCTCAACCAATCATCATCA 58.951 33.333 0.00 0.00 0.00 3.07
4317 4571 5.121611 CGGTATTGTGCATTCTTCAAGTGTA 59.878 40.000 0.00 0.00 0.00 2.90
4369 4623 2.814336 GACATCCTTTGAAGAAAGCCGT 59.186 45.455 0.00 0.00 37.80 5.68
4472 4726 7.328737 ACGGGTATTTCCTATTATGTGCTATC 58.671 38.462 0.00 0.00 36.25 2.08
4484 4738 9.499479 CTATTATGTGCTATCACCTTCTCATTT 57.501 33.333 0.00 0.00 42.46 2.32
4535 4790 5.163447 ACTGTATATCCGTGCACACTACATT 60.163 40.000 18.64 7.73 0.00 2.71
4659 4917 3.255888 CAGTGCACAAGGTACAGAGAGTA 59.744 47.826 21.04 0.00 34.11 2.59
4675 4933 8.526667 ACAGAGAGTACTTTATCTTGCAGATA 57.473 34.615 0.00 0.00 36.20 1.98
4706 4964 5.412904 GCTGCACCTGTTCTAAGAGTTTATT 59.587 40.000 0.00 0.00 0.00 1.40
4714 4972 8.660373 CCTGTTCTAAGAGTTTATTTAGCAGTG 58.340 37.037 0.00 0.00 0.00 3.66
4803 5067 0.389948 AGAGGCCGCTTGTCTAAACG 60.390 55.000 1.77 0.00 0.00 3.60
4824 5088 5.003061 CGTTGACGTTTCTTTTCTACTCC 57.997 43.478 0.00 0.00 34.11 3.85
4825 5089 4.084693 CGTTGACGTTTCTTTTCTACTCCC 60.085 45.833 0.00 0.00 34.11 4.30
4826 5090 4.950205 TGACGTTTCTTTTCTACTCCCT 57.050 40.909 0.00 0.00 0.00 4.20
4827 5091 4.879598 TGACGTTTCTTTTCTACTCCCTC 58.120 43.478 0.00 0.00 0.00 4.30
4828 5092 4.244066 GACGTTTCTTTTCTACTCCCTCC 58.756 47.826 0.00 0.00 0.00 4.30
4829 5093 3.251571 CGTTTCTTTTCTACTCCCTCCG 58.748 50.000 0.00 0.00 0.00 4.63
4830 5094 3.305881 CGTTTCTTTTCTACTCCCTCCGT 60.306 47.826 0.00 0.00 0.00 4.69
4831 5095 4.244066 GTTTCTTTTCTACTCCCTCCGTC 58.756 47.826 0.00 0.00 0.00 4.79
4832 5096 2.454538 TCTTTTCTACTCCCTCCGTCC 58.545 52.381 0.00 0.00 0.00 4.79
4833 5097 1.481363 CTTTTCTACTCCCTCCGTCCC 59.519 57.143 0.00 0.00 0.00 4.46
4834 5098 0.410663 TTTCTACTCCCTCCGTCCCA 59.589 55.000 0.00 0.00 0.00 4.37
4835 5099 0.635009 TTCTACTCCCTCCGTCCCAT 59.365 55.000 0.00 0.00 0.00 4.00
4836 5100 1.526315 TCTACTCCCTCCGTCCCATA 58.474 55.000 0.00 0.00 0.00 2.74
4837 5101 1.854939 TCTACTCCCTCCGTCCCATAA 59.145 52.381 0.00 0.00 0.00 1.90
4838 5102 2.449730 TCTACTCCCTCCGTCCCATAAT 59.550 50.000 0.00 0.00 0.00 1.28
4839 5103 3.659195 TCTACTCCCTCCGTCCCATAATA 59.341 47.826 0.00 0.00 0.00 0.98
4840 5104 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
4841 5105 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
4842 5106 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
4843 5107 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
4844 5108 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
4845 5109 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
4846 5110 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
4847 5111 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
4848 5112 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
4849 5113 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
4850 5114 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
4851 5115 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
4852 5116 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
4853 5117 7.069569 CGTCCCATAATATAAGAGCGTTTTTG 58.930 38.462 0.00 0.00 0.00 2.44
4854 5118 7.042321 CGTCCCATAATATAAGAGCGTTTTTGA 60.042 37.037 0.00 0.00 0.00 2.69
4855 5119 8.068380 GTCCCATAATATAAGAGCGTTTTTGAC 58.932 37.037 0.00 0.00 0.00 3.18
4856 5120 7.771361 TCCCATAATATAAGAGCGTTTTTGACA 59.229 33.333 0.00 0.00 0.00 3.58
4857 5121 7.855904 CCCATAATATAAGAGCGTTTTTGACAC 59.144 37.037 0.00 0.00 0.00 3.67
4858 5122 8.612619 CCATAATATAAGAGCGTTTTTGACACT 58.387 33.333 0.00 0.00 0.00 3.55
4861 5125 8.542497 AATATAAGAGCGTTTTTGACACTACA 57.458 30.769 0.00 0.00 0.00 2.74
4862 5126 4.531659 AAGAGCGTTTTTGACACTACAC 57.468 40.909 0.00 0.00 0.00 2.90
4863 5127 3.793559 AGAGCGTTTTTGACACTACACT 58.206 40.909 0.00 0.00 0.00 3.55
4864 5128 4.940463 AGAGCGTTTTTGACACTACACTA 58.060 39.130 0.00 0.00 0.00 2.74
4865 5129 4.982916 AGAGCGTTTTTGACACTACACTAG 59.017 41.667 0.00 0.00 0.00 2.57
4888 5152 2.968574 AGTGAAGAAGTCTCAAGAGCCA 59.031 45.455 0.00 0.00 0.00 4.75
4902 5166 6.660521 TCTCAAGAGCCATTTATGTTCATGTT 59.339 34.615 0.00 0.00 0.00 2.71
4903 5167 7.828717 TCTCAAGAGCCATTTATGTTCATGTTA 59.171 33.333 0.00 0.00 0.00 2.41
4904 5168 7.761409 TCAAGAGCCATTTATGTTCATGTTAC 58.239 34.615 0.00 0.00 0.00 2.50
5046 5323 3.134262 TCTCAGATTCTGGCTTGATCAGG 59.866 47.826 13.59 0.00 33.36 3.86
5073 5351 0.822164 TCCCTAGAGCTGGTTAACGC 59.178 55.000 0.00 0.00 0.00 4.84
5091 5369 3.813443 ACGCCATCTGAATTATCTGCTT 58.187 40.909 0.00 0.00 0.00 3.91
5092 5370 4.960938 ACGCCATCTGAATTATCTGCTTA 58.039 39.130 0.00 0.00 0.00 3.09
5323 5602 4.349663 TCCGTTGAAAAGTTCACAACAG 57.650 40.909 18.42 11.36 42.37 3.16
5330 5609 4.394920 TGAAAAGTTCACAACAGTGTCTCC 59.605 41.667 0.00 0.00 35.07 3.71
5459 5744 3.752412 CATGGAATGTACAGTGCAGTG 57.248 47.619 21.67 20.11 40.20 3.66
5460 5745 1.522668 TGGAATGTACAGTGCAGTGC 58.477 50.000 21.57 8.58 0.00 4.40
5461 5746 1.202746 TGGAATGTACAGTGCAGTGCA 60.203 47.619 21.57 15.37 38.46 4.57
5495 5780 3.810373 CAGCTAACAAACGGTGAATGTC 58.190 45.455 0.00 0.00 0.00 3.06
5513 5798 6.255237 TGAATGTCGAAACAAAGTACACGTTA 59.745 34.615 0.00 0.00 39.30 3.18
5533 5820 7.439955 CACGTTAGAAAATGTATATGTGGCCTA 59.560 37.037 3.32 0.00 32.96 3.93
5540 5827 3.045634 TGTATATGTGGCCTAAGCTGGT 58.954 45.455 3.32 0.00 39.73 4.00
5541 5828 4.228010 TGTATATGTGGCCTAAGCTGGTA 58.772 43.478 3.32 0.00 39.73 3.25
5543 5830 1.285280 ATGTGGCCTAAGCTGGTACA 58.715 50.000 3.32 0.00 39.73 2.90
5554 5842 2.422165 TGGTACAGTTGCGCGGAA 59.578 55.556 9.68 9.68 0.00 4.30
5772 6060 0.167908 CATGCTCGGCAAAAGCGTAA 59.832 50.000 2.68 0.00 43.62 3.18
5903 6194 4.277515 ACAGAAACAGATTCAGCAGCTA 57.722 40.909 0.00 0.00 40.72 3.32
5975 6268 3.151022 GAGTGAGGCCCTCCGAGG 61.151 72.222 8.62 7.56 37.47 4.63
6175 6468 1.112916 TCCACCTGCGACACAAGAGA 61.113 55.000 0.00 0.00 0.00 3.10
6210 6507 7.393515 GGTTCACCATTGGAGAACTTATTTACT 59.606 37.037 31.67 0.00 46.98 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 1.440060 GTCCCATATCGCCACGTCA 59.560 57.895 0.00 0.00 0.00 4.35
116 117 2.271821 CGCCACCATCCCATGTCA 59.728 61.111 0.00 0.00 0.00 3.58
119 120 2.896854 CGTCGCCACCATCCCATG 60.897 66.667 0.00 0.00 0.00 3.66
120 121 4.856801 GCGTCGCCACCATCCCAT 62.857 66.667 5.75 0.00 0.00 4.00
123 124 3.799755 GTTGCGTCGCCACCATCC 61.800 66.667 15.88 0.00 0.00 3.51
135 136 4.953868 TCCCGACACCACGTTGCG 62.954 66.667 0.00 0.00 0.00 4.85
198 199 2.767505 CTGGTAGCCGTCTGAACTTTT 58.232 47.619 0.00 0.00 0.00 2.27
217 219 4.142359 ACGTTTACGAGAAGATGATGAGCT 60.142 41.667 9.53 0.00 43.02 4.09
288 293 2.511145 CCCTGCAAGAGCTCTCGC 60.511 66.667 20.02 20.02 42.74 5.03
290 295 0.758123 ATAGCCCTGCAAGAGCTCTC 59.242 55.000 18.55 6.04 42.74 3.20
412 418 5.393068 TCTGGGCTCAGAATTGGATATTT 57.607 39.130 15.68 0.00 46.08 1.40
527 536 4.538917 CAAATGCTTTGAAATTTGGCACC 58.461 39.130 0.00 0.00 43.26 5.01
578 587 6.994421 AGTTTATTGTTTGGACCCTGATTT 57.006 33.333 0.00 0.00 0.00 2.17
579 588 6.994421 AAGTTTATTGTTTGGACCCTGATT 57.006 33.333 0.00 0.00 0.00 2.57
581 590 6.800072 AAAAGTTTATTGTTTGGACCCTGA 57.200 33.333 0.00 0.00 0.00 3.86
582 591 7.011016 GTGAAAAAGTTTATTGTTTGGACCCTG 59.989 37.037 0.00 0.00 0.00 4.45
583 592 7.045416 GTGAAAAAGTTTATTGTTTGGACCCT 58.955 34.615 0.00 0.00 0.00 4.34
584 593 6.819146 TGTGAAAAAGTTTATTGTTTGGACCC 59.181 34.615 0.00 0.00 0.00 4.46
585 594 7.762159 TCTGTGAAAAAGTTTATTGTTTGGACC 59.238 33.333 0.00 0.00 0.00 4.46
586 595 8.592155 GTCTGTGAAAAAGTTTATTGTTTGGAC 58.408 33.333 0.00 0.00 0.00 4.02
615 633 6.476378 AGCTCTCAGCAAAAGGACTAATTTA 58.524 36.000 0.00 0.00 45.56 1.40
661 682 0.037512 TGATGCCCGTGCCAAATTTG 60.038 50.000 11.40 11.40 36.33 2.32
675 696 6.047870 AGAAAGATGATAGAGTGTGTGATGC 58.952 40.000 0.00 0.00 0.00 3.91
762 790 1.228124 TTTGGCTCCCTGGTTCACG 60.228 57.895 0.00 0.00 0.00 4.35
1435 1467 4.909001 ACAAATAACTAACCGTTGGGCTA 58.091 39.130 0.00 0.00 37.05 3.93
1533 1565 9.691362 GTGATAACACAGGAATATGTTTTGTTT 57.309 29.630 0.00 0.00 45.32 2.83
1617 1733 2.378634 ATACCCCTGGCCTCTGCAC 61.379 63.158 3.32 0.00 40.13 4.57
1628 1744 0.255033 GAAAAGGCGGTCATACCCCT 59.745 55.000 1.55 1.55 39.59 4.79
1708 1824 9.618890 ACATGTAGCAGTGAATTATTTACAGAT 57.381 29.630 0.00 0.00 0.00 2.90
1925 2041 4.142093 GCCATTGCTTTCCATGTGTAGAAT 60.142 41.667 0.00 0.00 33.53 2.40
1945 2062 3.477582 TGGACGACCATTCAGCCA 58.522 55.556 1.37 0.00 41.77 4.75
1998 2121 1.305465 TAGCTTCCACGCACCCCTA 60.305 57.895 0.00 0.00 0.00 3.53
2049 2172 3.310774 CAGCTGAAACCCATAAGATGTCG 59.689 47.826 8.42 0.00 0.00 4.35
2052 2175 4.274459 GCTACAGCTGAAACCCATAAGATG 59.726 45.833 23.35 0.00 38.21 2.90
2071 2194 2.817844 CAAACAAGTTGGGGTAGGCTAC 59.182 50.000 16.40 16.40 33.18 3.58
2127 2253 6.471146 AGAAGCTTCTCACATTGATTGTACT 58.529 36.000 23.49 0.00 36.00 2.73
2148 2274 5.734140 TGGAGGGGGAAAAGTTCATATAGAA 59.266 40.000 0.00 0.00 0.00 2.10
2408 2534 0.186386 AACCAATCCCCGGAACAACA 59.814 50.000 0.73 0.00 0.00 3.33
2413 2539 2.614134 ATTTCAACCAATCCCCGGAA 57.386 45.000 0.73 0.00 0.00 4.30
2515 2641 8.749026 ATCTCTCTTAACATGCATGAGAAATT 57.251 30.769 32.75 17.88 34.03 1.82
2540 2666 9.502091 GCCACCTCATCAATTACACTAATTATA 57.498 33.333 0.00 0.00 36.29 0.98
2541 2667 7.998383 TGCCACCTCATCAATTACACTAATTAT 59.002 33.333 0.00 0.00 36.29 1.28
2586 2712 8.834465 GTTTATATTCTCTCTCAACATGCACAT 58.166 33.333 0.00 0.00 0.00 3.21
2613 2739 2.922740 AAAAGTGAACAGCGGGAGTA 57.077 45.000 0.00 0.00 0.00 2.59
2614 2740 2.922740 TAAAAGTGAACAGCGGGAGT 57.077 45.000 0.00 0.00 0.00 3.85
2615 2741 5.063564 GTCTTATAAAAGTGAACAGCGGGAG 59.936 44.000 0.00 0.00 34.13 4.30
2616 2742 4.933400 GTCTTATAAAAGTGAACAGCGGGA 59.067 41.667 0.00 0.00 34.13 5.14
2617 2743 4.693566 TGTCTTATAAAAGTGAACAGCGGG 59.306 41.667 0.00 0.00 34.13 6.13
2639 2765 6.481644 GGGAGCTGTCTGAACTATCTAAAATG 59.518 42.308 0.00 0.00 0.00 2.32
2640 2766 6.156949 TGGGAGCTGTCTGAACTATCTAAAAT 59.843 38.462 0.00 0.00 0.00 1.82
2641 2767 5.483937 TGGGAGCTGTCTGAACTATCTAAAA 59.516 40.000 0.00 0.00 0.00 1.52
2648 2774 3.135712 TGTTTTGGGAGCTGTCTGAACTA 59.864 43.478 0.00 0.00 0.00 2.24
2649 2775 2.092429 TGTTTTGGGAGCTGTCTGAACT 60.092 45.455 0.00 0.00 0.00 3.01
2650 2776 2.291741 CTGTTTTGGGAGCTGTCTGAAC 59.708 50.000 0.00 0.00 0.00 3.18
2651 2777 2.092429 ACTGTTTTGGGAGCTGTCTGAA 60.092 45.455 0.00 0.00 0.00 3.02
2653 2779 1.972872 ACTGTTTTGGGAGCTGTCTG 58.027 50.000 0.00 0.00 0.00 3.51
2655 2781 2.297701 TCAACTGTTTTGGGAGCTGTC 58.702 47.619 0.00 0.00 0.00 3.51
2657 2783 3.799281 TTTCAACTGTTTTGGGAGCTG 57.201 42.857 0.00 0.00 0.00 4.24
2660 2786 4.746611 GCTGATTTTCAACTGTTTTGGGAG 59.253 41.667 0.00 0.00 0.00 4.30
2661 2787 4.405358 AGCTGATTTTCAACTGTTTTGGGA 59.595 37.500 0.00 0.00 0.00 4.37
2662 2788 4.508861 CAGCTGATTTTCAACTGTTTTGGG 59.491 41.667 8.42 0.00 36.22 4.12
2663 2789 5.646467 CAGCTGATTTTCAACTGTTTTGG 57.354 39.130 8.42 0.00 36.22 3.28
2670 2796 5.822519 TGTTACAGACAGCTGATTTTCAACT 59.177 36.000 23.35 0.00 45.17 3.16
2671 2797 6.060028 TGTTACAGACAGCTGATTTTCAAC 57.940 37.500 23.35 15.92 45.17 3.18
2673 2799 6.486253 GATGTTACAGACAGCTGATTTTCA 57.514 37.500 23.35 10.50 45.17 2.69
2686 2812 9.542462 CCGATCCTTTTTATAAGATGTTACAGA 57.458 33.333 0.00 0.00 0.00 3.41
2688 2814 9.542462 CTCCGATCCTTTTTATAAGATGTTACA 57.458 33.333 0.00 0.00 0.00 2.41
2689 2815 8.989980 CCTCCGATCCTTTTTATAAGATGTTAC 58.010 37.037 0.00 0.00 0.00 2.50
2690 2816 8.154856 CCCTCCGATCCTTTTTATAAGATGTTA 58.845 37.037 0.00 0.00 0.00 2.41
2691 2817 6.998673 CCCTCCGATCCTTTTTATAAGATGTT 59.001 38.462 0.00 0.00 0.00 2.71
2692 2818 6.329197 TCCCTCCGATCCTTTTTATAAGATGT 59.671 38.462 0.00 0.00 0.00 3.06
2693 2819 6.769512 TCCCTCCGATCCTTTTTATAAGATG 58.230 40.000 0.00 0.00 0.00 2.90
2694 2820 6.559157 ACTCCCTCCGATCCTTTTTATAAGAT 59.441 38.462 0.00 0.00 0.00 2.40
2695 2821 5.903589 ACTCCCTCCGATCCTTTTTATAAGA 59.096 40.000 0.00 0.00 0.00 2.10
2696 2822 5.992217 CACTCCCTCCGATCCTTTTTATAAG 59.008 44.000 0.00 0.00 0.00 1.73
2697 2823 5.686650 GCACTCCCTCCGATCCTTTTTATAA 60.687 44.000 0.00 0.00 0.00 0.98
2698 2824 4.202326 GCACTCCCTCCGATCCTTTTTATA 60.202 45.833 0.00 0.00 0.00 0.98
2699 2825 3.433740 GCACTCCCTCCGATCCTTTTTAT 60.434 47.826 0.00 0.00 0.00 1.40
2700 2826 2.093128 GCACTCCCTCCGATCCTTTTTA 60.093 50.000 0.00 0.00 0.00 1.52
2701 2827 1.340114 GCACTCCCTCCGATCCTTTTT 60.340 52.381 0.00 0.00 0.00 1.94
2702 2828 0.253327 GCACTCCCTCCGATCCTTTT 59.747 55.000 0.00 0.00 0.00 2.27
2703 2829 1.627297 GGCACTCCCTCCGATCCTTT 61.627 60.000 0.00 0.00 0.00 3.11
2704 2830 2.066999 GGCACTCCCTCCGATCCTT 61.067 63.158 0.00 0.00 0.00 3.36
2705 2831 2.444895 GGCACTCCCTCCGATCCT 60.445 66.667 0.00 0.00 0.00 3.24
2706 2832 1.700042 AATGGCACTCCCTCCGATCC 61.700 60.000 0.00 0.00 0.00 3.36
2707 2833 0.181350 AAATGGCACTCCCTCCGATC 59.819 55.000 0.00 0.00 0.00 3.69
2708 2834 1.141053 GTAAATGGCACTCCCTCCGAT 59.859 52.381 0.00 0.00 0.00 4.18
2709 2835 0.539986 GTAAATGGCACTCCCTCCGA 59.460 55.000 0.00 0.00 0.00 4.55
2710 2836 0.463833 GGTAAATGGCACTCCCTCCG 60.464 60.000 0.00 0.00 0.00 4.63
2711 2837 0.623723 TGGTAAATGGCACTCCCTCC 59.376 55.000 0.00 0.00 0.00 4.30
2720 2846 3.130869 TCTGAACATGCATGGTAAATGGC 59.869 43.478 29.41 11.50 0.00 4.40
2747 2873 3.009723 CACCTCATCACGCCACTAATTT 58.990 45.455 0.00 0.00 0.00 1.82
2751 2877 1.897423 CCACCTCATCACGCCACTA 59.103 57.895 0.00 0.00 0.00 2.74
2796 2922 5.610982 TGCCTAAATAGTTGATCCCCACTAT 59.389 40.000 4.29 4.29 0.00 2.12
2823 2949 8.221251 AGTGATGAGATAAGTCAGTATCCTACA 58.779 37.037 0.00 0.00 31.83 2.74
2824 2950 8.630054 AGTGATGAGATAAGTCAGTATCCTAC 57.370 38.462 0.00 0.00 31.83 3.18
2876 3097 5.993891 ACAATGCGCTGTGATATAAATGAG 58.006 37.500 9.73 0.00 0.00 2.90
2921 3142 4.081198 AGCTTCCTGGATCTGAAAGTGTAG 60.081 45.833 0.00 0.00 33.76 2.74
3046 3267 7.645340 ACAAACAGAATCGAGAAAGAAACATTG 59.355 33.333 0.00 0.00 0.00 2.82
3048 3269 7.264373 ACAAACAGAATCGAGAAAGAAACAT 57.736 32.000 0.00 0.00 0.00 2.71
3049 3270 6.677781 ACAAACAGAATCGAGAAAGAAACA 57.322 33.333 0.00 0.00 0.00 2.83
3050 3271 7.971004 AAACAAACAGAATCGAGAAAGAAAC 57.029 32.000 0.00 0.00 0.00 2.78
3054 3275 6.139169 CGTGAAAACAAACAGAATCGAGAAAG 59.861 38.462 0.00 0.00 0.00 2.62
3102 3325 6.368791 GTGAAAAATAACCAAGATTTCCAGGC 59.631 38.462 0.00 0.00 30.80 4.85
3110 3333 8.435982 TGATTTTGGGTGAAAAATAACCAAGAT 58.564 29.630 0.00 0.00 41.69 2.40
3113 3336 8.986929 ATTGATTTTGGGTGAAAAATAACCAA 57.013 26.923 0.00 0.00 39.31 3.67
3114 3337 8.213679 TGATTGATTTTGGGTGAAAAATAACCA 58.786 29.630 0.00 0.00 39.31 3.67
3160 3383 9.927668 ACTGGATAAAATTTGTTCGAATTCATT 57.072 25.926 0.00 0.00 0.00 2.57
3212 3437 2.114411 GGTTCTTTCGGCCACCCA 59.886 61.111 2.24 0.00 0.00 4.51
3257 3482 1.200020 CCAAGGTTCTCAATTGCGGTC 59.800 52.381 0.00 0.00 0.00 4.79
3262 3487 4.520111 TGTCATGACCAAGGTTCTCAATTG 59.480 41.667 22.85 0.00 0.00 2.32
3267 3492 3.126001 TGTGTCATGACCAAGGTTCTC 57.874 47.619 22.85 0.00 0.00 2.87
3281 3506 1.462731 GGTGGCAGGCAATTGTGTCA 61.463 55.000 7.40 3.16 0.00 3.58
3318 3543 2.026915 AGCATGTGCAATGAGGTAGACA 60.027 45.455 7.83 0.00 45.16 3.41
3354 3579 6.407202 TCTAGCTTCCTAACTGTCCAAAATC 58.593 40.000 0.00 0.00 0.00 2.17
3407 3632 7.870509 AACTCAGTACATAGTTATCCACGTA 57.129 36.000 10.23 0.00 34.23 3.57
3483 3708 5.766670 TCCTTATCATGCAACTTCATCATCC 59.233 40.000 0.00 0.00 0.00 3.51
3569 3794 5.450550 GGATCGAAACATCTGGGAAAATTCC 60.451 44.000 3.49 3.49 46.82 3.01
3578 3803 5.008911 TGCATTATTGGATCGAAACATCTGG 59.991 40.000 0.00 0.00 0.00 3.86
3640 3865 1.469308 CGTCTCAGCTACCGGATATCC 59.531 57.143 9.46 12.14 0.00 2.59
3681 3933 9.973661 CAATTATACCCATAACCTCCATGATTA 57.026 33.333 0.00 0.00 29.44 1.75
3682 3934 7.397192 GCAATTATACCCATAACCTCCATGATT 59.603 37.037 0.00 0.00 29.44 2.57
3683 3935 6.891908 GCAATTATACCCATAACCTCCATGAT 59.108 38.462 0.00 0.00 29.44 2.45
3684 3936 6.045459 AGCAATTATACCCATAACCTCCATGA 59.955 38.462 0.00 0.00 29.44 3.07
3707 3959 4.086547 GGCAACCCATGGGCAAGC 62.087 66.667 31.73 28.57 39.32 4.01
3842 4094 5.924356 ACCACAACATATTATGATGACGGA 58.076 37.500 21.91 0.00 36.65 4.69
3908 4160 6.647212 TCTTCTCAGCATGTACAAATAACG 57.353 37.500 0.00 0.00 37.40 3.18
3976 4228 9.793252 ATGAAGATTTCCATTGTTAGAAAATCG 57.207 29.630 0.00 0.00 35.72 3.34
3981 4233 6.127366 GCCCATGAAGATTTCCATTGTTAGAA 60.127 38.462 0.00 0.00 0.00 2.10
4020 4272 4.047125 ATCCCCAAGCCCACGGTG 62.047 66.667 0.00 0.00 0.00 4.94
4030 4282 3.334581 CCCATGAAGATATCCATCCCCAA 59.665 47.826 0.00 0.00 0.00 4.12
4040 4293 1.434188 TCACCCGCCCATGAAGATAT 58.566 50.000 0.00 0.00 0.00 1.63
4053 4306 0.466007 TGATGGCAATGGATCACCCG 60.466 55.000 0.00 0.00 37.93 5.28
4058 4311 3.764218 AGGAGAATGATGGCAATGGATC 58.236 45.455 0.00 0.00 0.00 3.36
4191 4445 3.702045 ACCTCATTTCAACCCGTCAAAAA 59.298 39.130 0.00 0.00 0.00 1.94
4192 4446 3.067461 CACCTCATTTCAACCCGTCAAAA 59.933 43.478 0.00 0.00 0.00 2.44
4193 4447 2.621055 CACCTCATTTCAACCCGTCAAA 59.379 45.455 0.00 0.00 0.00 2.69
4194 4448 2.226330 CACCTCATTTCAACCCGTCAA 58.774 47.619 0.00 0.00 0.00 3.18
4195 4449 1.142060 ACACCTCATTTCAACCCGTCA 59.858 47.619 0.00 0.00 0.00 4.35
4196 4450 1.804748 GACACCTCATTTCAACCCGTC 59.195 52.381 0.00 0.00 0.00 4.79
4197 4451 1.544759 GGACACCTCATTTCAACCCGT 60.545 52.381 0.00 0.00 0.00 5.28
4198 4452 1.165270 GGACACCTCATTTCAACCCG 58.835 55.000 0.00 0.00 0.00 5.28
4199 4453 2.586648 AGGACACCTCATTTCAACCC 57.413 50.000 0.00 0.00 0.00 4.11
4200 4454 3.636764 ACAAAGGACACCTCATTTCAACC 59.363 43.478 0.00 0.00 27.74 3.77
4201 4455 4.097892 ACACAAAGGACACCTCATTTCAAC 59.902 41.667 0.00 0.00 27.74 3.18
4202 4456 4.097741 CACACAAAGGACACCTCATTTCAA 59.902 41.667 0.00 0.00 27.74 2.69
4203 4457 3.631686 CACACAAAGGACACCTCATTTCA 59.368 43.478 0.00 0.00 27.74 2.69
4204 4458 3.550842 GCACACAAAGGACACCTCATTTC 60.551 47.826 0.00 0.00 27.74 2.17
4205 4459 2.362077 GCACACAAAGGACACCTCATTT 59.638 45.455 0.00 0.00 30.42 2.32
4206 4460 1.956477 GCACACAAAGGACACCTCATT 59.044 47.619 0.00 0.00 30.89 2.57
4207 4461 1.133823 TGCACACAAAGGACACCTCAT 60.134 47.619 0.00 0.00 30.89 2.90
4208 4462 0.254462 TGCACACAAAGGACACCTCA 59.746 50.000 0.00 0.00 30.89 3.86
4209 4463 0.947244 CTGCACACAAAGGACACCTC 59.053 55.000 0.00 0.00 30.89 3.85
4210 4464 0.546122 TCTGCACACAAAGGACACCT 59.454 50.000 0.00 0.00 33.87 4.00
4211 4465 0.663153 GTCTGCACACAAAGGACACC 59.337 55.000 0.00 0.00 0.00 4.16
4212 4466 1.378531 TGTCTGCACACAAAGGACAC 58.621 50.000 0.00 0.00 32.91 3.67
4213 4467 1.742831 GTTGTCTGCACACAAAGGACA 59.257 47.619 9.24 3.87 38.01 4.02
4214 4468 1.065551 GGTTGTCTGCACACAAAGGAC 59.934 52.381 9.24 1.05 38.01 3.85
4215 4469 1.064758 AGGTTGTCTGCACACAAAGGA 60.065 47.619 9.24 0.00 38.01 3.36
4216 4470 1.334869 GAGGTTGTCTGCACACAAAGG 59.665 52.381 9.24 0.00 38.01 3.11
4217 4471 2.016318 TGAGGTTGTCTGCACACAAAG 58.984 47.619 9.24 0.00 38.01 2.77
4218 4472 2.121291 TGAGGTTGTCTGCACACAAA 57.879 45.000 9.24 0.00 38.01 2.83
4219 4473 2.121291 TTGAGGTTGTCTGCACACAA 57.879 45.000 3.14 3.14 33.75 3.33
4263 4517 8.288208 GCTAATAAGTGATGATGATTGGTTGAG 58.712 37.037 0.00 0.00 0.00 3.02
4280 4534 4.684703 GCACAATACCGATCGCTAATAAGT 59.315 41.667 10.32 2.71 0.00 2.24
4317 4571 9.520515 AAGGTAAATTATGATGAGAACAGTTGT 57.479 29.630 0.00 0.00 0.00 3.32
4369 4623 3.185594 CGCCAACATCTGACTCGTTTAAA 59.814 43.478 0.00 0.00 0.00 1.52
4484 4738 6.276832 ACTAACTAGCACAGTATCGGAAAA 57.723 37.500 0.00 0.00 36.04 2.29
4488 4742 7.220300 CAGTAAAACTAACTAGCACAGTATCGG 59.780 40.741 0.00 0.00 36.04 4.18
4535 4790 1.405872 ACCGTCAGTGTCCAACAGTA 58.594 50.000 0.00 0.00 29.11 2.74
4675 4933 1.352352 AGAACAGGTGCAGCAGGTTAT 59.648 47.619 19.63 15.60 0.00 1.89
4726 4990 5.688807 CCTCAGACATAATGGGATCACTTT 58.311 41.667 0.00 0.00 0.00 2.66
4731 4995 3.777106 TGCCTCAGACATAATGGGATC 57.223 47.619 0.00 0.00 0.00 3.36
4803 5067 5.055144 AGGGAGTAGAAAAGAAACGTCAAC 58.945 41.667 0.00 0.00 0.00 3.18
4819 5083 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
4820 5084 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
4821 5085 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
4822 5086 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
4823 5087 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
4824 5088 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
4825 5089 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
4826 5090 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
4827 5091 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
4828 5092 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
4829 5093 8.068380 GTCAAAAACGCTCTTATATTATGGGAC 58.932 37.037 0.00 0.00 0.00 4.46
4830 5094 7.771361 TGTCAAAAACGCTCTTATATTATGGGA 59.229 33.333 0.00 0.00 0.00 4.37
4831 5095 7.855904 GTGTCAAAAACGCTCTTATATTATGGG 59.144 37.037 0.00 0.00 35.42 4.00
4832 5096 8.612619 AGTGTCAAAAACGCTCTTATATTATGG 58.387 33.333 0.00 0.00 45.69 2.74
4835 5099 9.642327 TGTAGTGTCAAAAACGCTCTTATATTA 57.358 29.630 0.00 0.00 45.69 0.98
4836 5100 8.440833 GTGTAGTGTCAAAAACGCTCTTATATT 58.559 33.333 0.00 0.00 45.69 1.28
4837 5101 7.817962 AGTGTAGTGTCAAAAACGCTCTTATAT 59.182 33.333 0.00 0.00 45.69 0.86
4838 5102 7.149973 AGTGTAGTGTCAAAAACGCTCTTATA 58.850 34.615 0.00 0.00 45.69 0.98
4839 5103 5.989777 AGTGTAGTGTCAAAAACGCTCTTAT 59.010 36.000 0.00 0.00 45.69 1.73
4840 5104 5.353938 AGTGTAGTGTCAAAAACGCTCTTA 58.646 37.500 0.00 0.00 45.69 2.10
4841 5105 4.189231 AGTGTAGTGTCAAAAACGCTCTT 58.811 39.130 0.00 0.00 45.69 2.85
4842 5106 3.793559 AGTGTAGTGTCAAAAACGCTCT 58.206 40.909 0.00 0.00 45.69 4.09
4843 5107 4.743644 ACTAGTGTAGTGTCAAAAACGCTC 59.256 41.667 0.00 0.00 45.69 5.03
4845 5109 6.137227 CTACTAGTGTAGTGTCAAAAACGC 57.863 41.667 5.39 0.00 40.81 4.84
4857 5121 7.908827 TGAGACTTCTTCACTACTAGTGTAG 57.091 40.000 14.63 14.27 46.03 2.74
4858 5122 8.155510 TCTTGAGACTTCTTCACTACTAGTGTA 58.844 37.037 14.63 5.85 46.03 2.90
4859 5123 6.999272 TCTTGAGACTTCTTCACTACTAGTGT 59.001 38.462 14.63 0.00 46.03 3.55
4861 5125 6.150474 GCTCTTGAGACTTCTTCACTACTAGT 59.850 42.308 0.00 0.00 0.00 2.57
4862 5126 6.404293 GGCTCTTGAGACTTCTTCACTACTAG 60.404 46.154 1.30 0.00 0.00 2.57
4863 5127 5.416326 GGCTCTTGAGACTTCTTCACTACTA 59.584 44.000 1.30 0.00 0.00 1.82
4864 5128 4.219725 GGCTCTTGAGACTTCTTCACTACT 59.780 45.833 1.30 0.00 0.00 2.57
4865 5129 4.021894 TGGCTCTTGAGACTTCTTCACTAC 60.022 45.833 5.01 0.00 0.00 2.73
4876 5140 6.094603 ACATGAACATAAATGGCTCTTGAGAC 59.905 38.462 0.00 0.00 0.00 3.36
4883 5147 9.669353 CAATAGTAACATGAACATAAATGGCTC 57.331 33.333 0.00 0.00 0.00 4.70
4902 5166 5.597182 AGATCTTGGCGACTAACCAATAGTA 59.403 40.000 0.00 0.00 45.84 1.82
4903 5167 4.406003 AGATCTTGGCGACTAACCAATAGT 59.594 41.667 0.00 0.00 45.84 2.12
4904 5168 4.950050 AGATCTTGGCGACTAACCAATAG 58.050 43.478 0.00 0.00 45.84 1.73
4942 5209 8.973182 AGTTGAAAAACCAGGAAACAATACTAA 58.027 29.630 0.00 0.00 0.00 2.24
4949 5216 7.469537 TCTAAAGTTGAAAAACCAGGAAACA 57.530 32.000 0.00 0.00 0.00 2.83
5046 5323 2.703007 ACCAGCTCTAGGGATCATCAAC 59.297 50.000 0.00 0.00 0.00 3.18
5073 5351 8.944029 CAAGGTATAAGCAGATAATTCAGATGG 58.056 37.037 0.00 0.00 0.00 3.51
5091 5369 3.101437 TCCTCCTGCGAAACAAGGTATA 58.899 45.455 0.00 0.00 29.57 1.47
5092 5370 1.906574 TCCTCCTGCGAAACAAGGTAT 59.093 47.619 0.00 0.00 29.57 2.73
5340 5619 7.016296 TGTAGATGGTCCCAGTATGATAATGA 58.984 38.462 0.88 0.00 39.69 2.57
5341 5620 7.099764 GTGTAGATGGTCCCAGTATGATAATG 58.900 42.308 0.00 0.00 39.69 1.90
5342 5621 6.213600 GGTGTAGATGGTCCCAGTATGATAAT 59.786 42.308 0.00 0.00 39.69 1.28
5457 5742 1.943340 GCTGCTAAGGTATTCCTGCAC 59.057 52.381 0.00 0.00 44.35 4.57
5458 5743 1.839994 AGCTGCTAAGGTATTCCTGCA 59.160 47.619 0.00 3.79 44.35 4.41
5459 5744 2.629336 AGCTGCTAAGGTATTCCTGC 57.371 50.000 0.00 0.00 44.35 4.85
5460 5745 5.023533 TGTTAGCTGCTAAGGTATTCCTG 57.976 43.478 21.62 0.00 44.35 3.86
5495 5780 7.637132 ACATTTTCTAACGTGTACTTTGTTTCG 59.363 33.333 0.00 0.00 0.00 3.46
5513 5798 6.488006 CAGCTTAGGCCACATATACATTTTCT 59.512 38.462 5.01 0.00 39.73 2.52
5533 5820 2.317609 CGCGCAACTGTACCAGCTT 61.318 57.895 8.75 0.00 34.37 3.74
5540 5827 1.373748 GACCTTCCGCGCAACTGTA 60.374 57.895 8.75 0.00 0.00 2.74
5541 5828 2.665185 GACCTTCCGCGCAACTGT 60.665 61.111 8.75 0.00 0.00 3.55
5673 5961 2.561956 CGGCCAGGGATCGTCGTAT 61.562 63.158 2.24 0.00 0.00 3.06
5772 6060 1.260561 GTGATGAAGAACACGCACGTT 59.739 47.619 0.00 0.00 31.21 3.99


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

AutoCloner maintained by Alex Coulton.