Multiple sequence alignment - TraesCS2B01G160900

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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 TraesCS2B01G160900 chr2B 100.000 4195 0 0 1 4195 134255779 134251585 0.000000e+00 7747.0
1 TraesCS2B01G160900 chr2B 79.718 779 156 2 10 787 134569747 134568970 2.830000e-156 562.0
2 TraesCS2B01G160900 chr2B 76.761 809 180 8 147 951 134479510 134478706 2.980000e-121 446.0
3 TraesCS2B01G160900 chr2B 81.859 441 77 3 2747 3186 134477351 134476913 6.630000e-98 368.0
4 TraesCS2B01G160900 chr2B 79.336 542 94 13 2746 3277 134600935 134600402 8.570000e-97 364.0
5 TraesCS2B01G160900 chr2D 95.176 2073 71 4 6 2051 82228182 82226112 0.000000e+00 3247.0
6 TraesCS2B01G160900 chr2D 90.123 891 50 15 2747 3624 82226127 82225262 0.000000e+00 1123.0
7 TraesCS2B01G160900 chr2D 78.296 751 156 6 975 1723 82873461 82872716 1.060000e-130 477.0
8 TraesCS2B01G160900 chr2D 82.556 493 66 18 2778 3261 82645646 82645165 2.330000e-112 416.0
9 TraesCS2B01G160900 chr2D 93.478 276 16 1 3822 4097 82224754 82224481 3.900000e-110 409.0
10 TraesCS2B01G160900 chr2D 81.800 500 80 8 2766 3261 82834913 82834421 3.900000e-110 409.0
11 TraesCS2B01G160900 chr2D 81.034 522 85 9 2746 3261 82872527 82872014 1.820000e-108 403.0
12 TraesCS2B01G160900 chr2D 79.926 538 92 11 2746 3274 82891818 82891288 8.510000e-102 381.0
13 TraesCS2B01G160900 chr2D 84.574 188 12 8 3667 3837 82224997 82224810 2.010000e-38 171.0
14 TraesCS2B01G160900 chr7B 98.512 672 10 0 2053 2724 380073315 380072644 0.000000e+00 1186.0
15 TraesCS2B01G160900 chr7B 98.333 660 11 0 2052 2711 648273504 648274163 0.000000e+00 1158.0
16 TraesCS2B01G160900 chr6B 98.220 674 12 0 2051 2724 61212193 61211520 0.000000e+00 1179.0
17 TraesCS2B01G160900 chr5B 98.068 673 13 0 2052 2724 710235622 710236294 0.000000e+00 1171.0
18 TraesCS2B01G160900 chrUn 98.063 671 13 0 2053 2723 136395341 136394671 0.000000e+00 1168.0
19 TraesCS2B01G160900 chrUn 86.765 68 7 2 3379 3444 28319413 28319480 1.620000e-09 75.0
20 TraesCS2B01G160900 chr3B 97.920 673 14 0 2052 2724 534159666 534158994 0.000000e+00 1166.0
21 TraesCS2B01G160900 chr3B 97.761 670 15 0 2052 2721 463484172 463483503 0.000000e+00 1155.0
22 TraesCS2B01G160900 chr3B 97.470 672 17 0 2053 2724 707026858 707027529 0.000000e+00 1147.0
23 TraesCS2B01G160900 chr3B 97.059 34 1 0 3786 3819 250275874 250275907 1.630000e-04 58.4
24 TraesCS2B01G160900 chr6A 97.853 652 14 0 2051 2702 591940301 591940952 0.000000e+00 1127.0
25 TraesCS2B01G160900 chr6A 88.710 62 7 0 3383 3444 303403665 303403604 4.500000e-10 76.8
26 TraesCS2B01G160900 chr2A 81.238 517 92 5 2746 3261 83585225 83584713 3.020000e-111 412.0
27 TraesCS2B01G160900 chr2A 78.909 550 106 5 2746 3287 83640017 83639470 8.570000e-97 364.0
28 TraesCS2B01G160900 chr2A 82.100 419 72 3 2770 3186 83440011 83439594 5.160000e-94 355.0
29 TraesCS2B01G160900 chr2A 91.935 62 3 2 3383 3443 702944226 702944286 7.470000e-13 86.1
30 TraesCS2B01G160900 chr4A 95.082 61 3 0 3383 3443 70315938 70315998 3.450000e-16 97.1
31 TraesCS2B01G160900 chr4D 94.828 58 2 1 3385 3442 74265662 74265606 5.780000e-14 89.8
32 TraesCS2B01G160900 chr5A 86.420 81 10 1 3383 3462 680984941 680984861 2.080000e-13 87.9
33 TraesCS2B01G160900 chr5A 90.625 64 6 0 3383 3446 469102562 469102499 7.470000e-13 86.1
34 TraesCS2B01G160900 chr1D 88.710 62 7 0 3383 3444 239547773 239547712 4.500000e-10 76.8
35 TraesCS2B01G160900 chr1A 88.710 62 7 0 3383 3444 240301167 240301106 4.500000e-10 76.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G160900 chr2B 134251585 134255779 4194 True 7747.0 7747 100.00000 1 4195 1 chr2B.!!$R1 4194
1 TraesCS2B01G160900 chr2B 134568970 134569747 777 True 562.0 562 79.71800 10 787 1 chr2B.!!$R2 777
2 TraesCS2B01G160900 chr2B 134476913 134479510 2597 True 407.0 446 79.31000 147 3186 2 chr2B.!!$R4 3039
3 TraesCS2B01G160900 chr2B 134600402 134600935 533 True 364.0 364 79.33600 2746 3277 1 chr2B.!!$R3 531
4 TraesCS2B01G160900 chr2D 82224481 82228182 3701 True 1237.5 3247 90.83775 6 4097 4 chr2D.!!$R4 4091
5 TraesCS2B01G160900 chr2D 82872014 82873461 1447 True 440.0 477 79.66500 975 3261 2 chr2D.!!$R5 2286
6 TraesCS2B01G160900 chr2D 82891288 82891818 530 True 381.0 381 79.92600 2746 3274 1 chr2D.!!$R3 528
7 TraesCS2B01G160900 chr7B 380072644 380073315 671 True 1186.0 1186 98.51200 2053 2724 1 chr7B.!!$R1 671
8 TraesCS2B01G160900 chr7B 648273504 648274163 659 False 1158.0 1158 98.33300 2052 2711 1 chr7B.!!$F1 659
9 TraesCS2B01G160900 chr6B 61211520 61212193 673 True 1179.0 1179 98.22000 2051 2724 1 chr6B.!!$R1 673
10 TraesCS2B01G160900 chr5B 710235622 710236294 672 False 1171.0 1171 98.06800 2052 2724 1 chr5B.!!$F1 672
11 TraesCS2B01G160900 chrUn 136394671 136395341 670 True 1168.0 1168 98.06300 2053 2723 1 chrUn.!!$R1 670
12 TraesCS2B01G160900 chr3B 534158994 534159666 672 True 1166.0 1166 97.92000 2052 2724 1 chr3B.!!$R2 672
13 TraesCS2B01G160900 chr3B 463483503 463484172 669 True 1155.0 1155 97.76100 2052 2721 1 chr3B.!!$R1 669
14 TraesCS2B01G160900 chr3B 707026858 707027529 671 False 1147.0 1147 97.47000 2053 2724 1 chr3B.!!$F2 671
15 TraesCS2B01G160900 chr6A 591940301 591940952 651 False 1127.0 1127 97.85300 2051 2702 1 chr6A.!!$F1 651
16 TraesCS2B01G160900 chr2A 83584713 83585225 512 True 412.0 412 81.23800 2746 3261 1 chr2A.!!$R2 515
17 TraesCS2B01G160900 chr2A 83639470 83640017 547 True 364.0 364 78.90900 2746 3287 1 chr2A.!!$R3 541

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
375 376 0.179084 TTCATTCATCCTCCGGCGAC 60.179 55.0 9.30 0.00 0.00 5.19 F
571 572 0.815615 GGGGTTCAGATGATCCACGC 60.816 60.0 11.15 2.81 35.99 5.34 F
858 859 1.106285 GGCCAAACAAGATGCCCTAG 58.894 55.0 0.00 0.00 37.94 3.02 F
2594 2683 0.326927 CTAAAAACGGAGCCCTCCCA 59.673 55.0 8.68 0.00 46.96 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1226 1265 0.320421 TCGCAGAGCTACACCAAACC 60.320 55.0 0.00 0.00 0.00 3.27 R
2343 2432 0.516001 GCTCGTCTACGTCTGTGTGA 59.484 55.0 0.00 0.00 40.80 3.58 R
2620 2709 0.261696 TGGTCCTCGGATCATGGAGA 59.738 55.0 8.70 0.00 29.14 3.71 R
4166 4614 0.035247 TTTACGGGCGGCCTACAAAT 60.035 50.0 27.04 6.71 0.00 2.32 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
94 95 2.622942 TGGTGTCAACTTTTCATGGCTC 59.377 45.455 0.00 0.00 0.00 4.70
114 115 3.964909 TCAGTTCGGTACATGATCATCG 58.035 45.455 4.86 6.71 0.00 3.84
218 219 0.459585 CGCGCCTTATACCACAGTGT 60.460 55.000 0.00 0.00 0.00 3.55
250 251 2.754472 TGATGAACGTGTTGACAGGAG 58.246 47.619 10.45 0.00 35.83 3.69
260 261 1.340248 GTTGACAGGAGAACACTCGGA 59.660 52.381 0.00 0.00 0.00 4.55
309 310 6.885918 TCTCAATATATTGTATGCCATGGTGG 59.114 38.462 21.89 0.00 38.58 4.61
375 376 0.179084 TTCATTCATCCTCCGGCGAC 60.179 55.000 9.30 0.00 0.00 5.19
410 411 2.022428 TGCTGGATTTAGAGGTCCCCTA 60.022 50.000 0.00 0.00 31.76 3.53
493 494 2.499289 TGCTTGCTCCAAAGAAAACCAA 59.501 40.909 0.00 0.00 0.00 3.67
507 508 9.048446 CAAAGAAAACCAATCTCATCACATTTT 57.952 29.630 0.00 0.00 0.00 1.82
517 518 8.743099 CAATCTCATCACATTTTCAATCGATTG 58.257 33.333 28.48 28.48 39.10 2.67
551 552 5.886960 ACTCACCAAAGATGCAATTCTAC 57.113 39.130 0.00 0.00 0.00 2.59
571 572 0.815615 GGGGTTCAGATGATCCACGC 60.816 60.000 11.15 2.81 35.99 5.34
711 712 1.169661 ATCGTTTGCCGCAAAGGTCA 61.170 50.000 28.43 16.66 43.70 4.02
799 800 4.022503 ACTTCTAGACACTACCCACGAAAC 60.023 45.833 0.00 0.00 0.00 2.78
858 859 1.106285 GGCCAAACAAGATGCCCTAG 58.894 55.000 0.00 0.00 37.94 3.02
877 878 2.508526 AGTTGAGCAAGTTAGCAAGGG 58.491 47.619 0.00 0.00 36.85 3.95
892 893 1.122019 AAGGGCAGACAGAACTCCGT 61.122 55.000 0.00 0.00 0.00 4.69
1176 1215 4.065088 GTGAGACAGACCAAACAATGCTA 58.935 43.478 0.00 0.00 0.00 3.49
1226 1265 5.153950 AGACTTACAAGCACTAAAGGGAG 57.846 43.478 0.00 0.00 0.00 4.30
1287 1326 4.520492 CCTTTCCTGTTGAGTAACATTGCT 59.480 41.667 0.00 0.00 45.16 3.91
1364 1403 7.662258 AGAGATCATTAGAAATCTTGCCATGAG 59.338 37.037 0.00 0.00 32.43 2.90
1428 1467 7.452562 TCATTAGCAGATTGATGTATGCCTTA 58.547 34.615 0.00 0.00 39.51 2.69
1665 1704 1.476007 AAGCTCGGCCTGTTCTGAGT 61.476 55.000 0.00 0.00 40.67 3.41
1696 1735 8.087750 CAGACCTGAAGAATATCTCTTACATCC 58.912 40.741 0.00 0.00 44.82 3.51
1835 1881 9.556030 GTGCCTTACATCATTACTAAAGAAAAC 57.444 33.333 0.00 0.00 0.00 2.43
1930 2019 5.304778 TGCAACTGAGTAAGCTATTGTTGA 58.695 37.500 10.59 3.17 34.37 3.18
2019 2108 8.956617 TTTGCAAATTTAACCAAAGTTTTGTC 57.043 26.923 8.05 0.00 37.42 3.18
2256 2345 1.538950 GTAGACAGTCGGGAAGTCGTT 59.461 52.381 0.00 0.00 37.36 3.85
2343 2432 0.329596 GGAAGGATCCAACCTGCAGT 59.670 55.000 15.82 0.00 45.79 4.40
2594 2683 0.326927 CTAAAAACGGAGCCCTCCCA 59.673 55.000 8.68 0.00 46.96 4.37
2616 2705 4.856801 CAAGGGCCGGGATCCACG 62.857 72.222 15.23 14.37 0.00 4.94
2711 2800 4.329545 GAGTTGGGCGTGGGCAGA 62.330 66.667 0.00 0.00 42.47 4.26
2724 2813 2.660064 GGCAGAAGGAGCGAAGGGA 61.660 63.158 0.00 0.00 0.00 4.20
2725 2814 1.296715 GCAGAAGGAGCGAAGGGAA 59.703 57.895 0.00 0.00 0.00 3.97
2726 2815 0.321653 GCAGAAGGAGCGAAGGGAAA 60.322 55.000 0.00 0.00 0.00 3.13
2727 2816 1.680249 GCAGAAGGAGCGAAGGGAAAT 60.680 52.381 0.00 0.00 0.00 2.17
2728 2817 2.420129 GCAGAAGGAGCGAAGGGAAATA 60.420 50.000 0.00 0.00 0.00 1.40
2729 2818 3.745797 GCAGAAGGAGCGAAGGGAAATAT 60.746 47.826 0.00 0.00 0.00 1.28
2730 2819 3.812053 CAGAAGGAGCGAAGGGAAATATG 59.188 47.826 0.00 0.00 0.00 1.78
2731 2820 2.938956 AGGAGCGAAGGGAAATATGG 57.061 50.000 0.00 0.00 0.00 2.74
2732 2821 1.202818 AGGAGCGAAGGGAAATATGGC 60.203 52.381 0.00 0.00 0.00 4.40
2733 2822 1.202818 GGAGCGAAGGGAAATATGGCT 60.203 52.381 0.00 0.00 0.00 4.75
2734 2823 2.147150 GAGCGAAGGGAAATATGGCTC 58.853 52.381 0.00 0.00 37.67 4.70
2735 2824 1.771255 AGCGAAGGGAAATATGGCTCT 59.229 47.619 0.00 0.00 0.00 4.09
2736 2825 2.173569 AGCGAAGGGAAATATGGCTCTT 59.826 45.455 0.00 0.00 0.00 2.85
2737 2826 3.391296 AGCGAAGGGAAATATGGCTCTTA 59.609 43.478 0.00 0.00 0.00 2.10
2742 2831 6.238484 CGAAGGGAAATATGGCTCTTAGTTTG 60.238 42.308 0.00 0.00 0.00 2.93
2743 2832 6.079712 AGGGAAATATGGCTCTTAGTTTGT 57.920 37.500 0.00 0.00 0.00 2.83
2744 2833 5.888161 AGGGAAATATGGCTCTTAGTTTGTG 59.112 40.000 0.00 0.00 0.00 3.33
2756 2845 7.119997 GCTCTTAGTTTGTGTTAATCATAGCG 58.880 38.462 0.00 0.00 0.00 4.26
2850 2942 3.503748 CCTTCTTGGCCTTAGTTCACAAG 59.496 47.826 3.32 0.00 39.76 3.16
2867 2959 6.474819 TCACAAGTATGTAATGTTGTTCCG 57.525 37.500 0.00 0.00 37.82 4.30
2907 2999 8.367660 AGAACTAGATTGTGGTGAGATTAAGA 57.632 34.615 0.00 0.00 0.00 2.10
3084 3206 4.227300 TGGAAGCACTGGTAATGGTAGAAT 59.773 41.667 0.00 0.00 0.00 2.40
3086 3208 3.545703 AGCACTGGTAATGGTAGAATGC 58.454 45.455 0.00 0.00 0.00 3.56
3168 3290 1.613437 GCATACCTCTCTCTGCTCTCC 59.387 57.143 0.00 0.00 0.00 3.71
3318 3450 4.578913 GCTCACTGCAGTAGCGAA 57.421 55.556 21.20 2.04 46.23 4.70
3404 3536 8.510243 AACATGACATAGAATTTAGATGTGCA 57.490 30.769 0.00 0.00 33.99 4.57
3409 3541 9.612066 TGACATAGAATTTAGATGTGCAATACA 57.388 29.630 5.76 0.00 44.87 2.29
3484 3622 5.730550 TGTACATAGGACCAACTTGTGATC 58.269 41.667 0.00 0.00 0.00 2.92
3491 3629 3.274288 GACCAACTTGTGATCCAGATCC 58.726 50.000 5.22 0.00 37.02 3.36
3501 3639 6.173427 TGTGATCCAGATCCGAAATATTCA 57.827 37.500 5.22 0.00 37.02 2.57
3510 3648 7.096023 CCAGATCCGAAATATTCAGTAAGTTCG 60.096 40.741 0.00 0.00 35.39 3.95
3512 3650 7.980099 AGATCCGAAATATTCAGTAAGTTCGTT 59.020 33.333 4.57 0.00 34.55 3.85
3513 3651 9.241317 GATCCGAAATATTCAGTAAGTTCGTTA 57.759 33.333 4.57 0.00 34.55 3.18
3514 3652 8.624701 TCCGAAATATTCAGTAAGTTCGTTAG 57.375 34.615 4.57 0.00 34.55 2.34
3524 3662 8.997621 TCAGTAAGTTCGTTAGATTAATTGCT 57.002 30.769 0.00 0.00 0.00 3.91
3530 3668 8.997621 AGTTCGTTAGATTAATTGCTCAACTA 57.002 30.769 0.00 0.00 0.00 2.24
3547 3685 5.304778 TCAACTAGCTACACTGATTTTGCA 58.695 37.500 0.00 0.00 0.00 4.08
3556 3694 5.046910 ACACTGATTTTGCATAAGAACCG 57.953 39.130 0.00 0.00 0.00 4.44
3560 3698 2.323939 TTTTGCATAAGAACCGTGCG 57.676 45.000 0.00 0.00 41.61 5.34
3582 3720 1.131303 TTGGTCGTCAATGGGGGAGT 61.131 55.000 0.00 0.00 0.00 3.85
3583 3721 1.131303 TGGTCGTCAATGGGGGAGTT 61.131 55.000 0.00 0.00 0.00 3.01
3584 3722 0.037734 GGTCGTCAATGGGGGAGTTT 59.962 55.000 0.00 0.00 0.00 2.66
3585 3723 1.165270 GTCGTCAATGGGGGAGTTTG 58.835 55.000 0.00 0.00 0.00 2.93
3586 3724 0.608035 TCGTCAATGGGGGAGTTTGC 60.608 55.000 0.00 0.00 0.00 3.68
3587 3725 1.883021 GTCAATGGGGGAGTTTGCG 59.117 57.895 0.00 0.00 0.00 4.85
3588 3726 0.608035 GTCAATGGGGGAGTTTGCGA 60.608 55.000 0.00 0.00 0.00 5.10
3589 3727 0.331278 TCAATGGGGGAGTTTGCGAT 59.669 50.000 0.00 0.00 0.00 4.58
3611 3749 7.421613 GCGATTTAAACGATTATAATGCGGTAG 59.578 37.037 1.78 0.00 0.00 3.18
3613 3751 8.611654 ATTTAAACGATTATAATGCGGTAGGT 57.388 30.769 1.78 0.00 0.00 3.08
3624 3762 1.086696 GCGGTAGGTACGACACAGTA 58.913 55.000 0.00 0.00 35.02 2.74
3625 3763 1.202076 GCGGTAGGTACGACACAGTAC 60.202 57.143 0.00 0.00 44.50 2.73
3626 3764 2.350522 CGGTAGGTACGACACAGTACT 58.649 52.381 7.14 0.00 44.59 2.73
3629 3767 4.253685 GGTAGGTACGACACAGTACTACA 58.746 47.826 0.00 0.00 44.59 2.74
3630 3768 4.878397 GGTAGGTACGACACAGTACTACAT 59.122 45.833 0.00 0.00 44.59 2.29
3641 3978 2.789339 CAGTACTACATGCATTCGTCCG 59.211 50.000 0.00 0.00 0.00 4.79
3644 3981 1.498865 CTACATGCATTCGTCCGGCC 61.499 60.000 0.00 0.00 0.00 6.13
3680 4040 2.727544 GGCAGCGGCAAAGAACAA 59.272 55.556 11.88 0.00 43.71 2.83
3681 4041 1.372128 GGCAGCGGCAAAGAACAAG 60.372 57.895 11.88 0.00 43.71 3.16
3695 4055 1.470098 GAACAAGCCATGCGAGAACAT 59.530 47.619 0.00 0.00 0.00 2.71
3758 4133 2.623416 CTGGATATACAGGCAGTGACGA 59.377 50.000 7.10 0.00 34.84 4.20
3788 4163 1.783711 GATATGACAACTCTCGCAGCG 59.216 52.381 9.06 9.06 0.00 5.18
3798 4173 1.137614 CTCGCAGCGACTCTAGCAA 59.862 57.895 15.11 0.00 37.01 3.91
3799 4174 0.456824 CTCGCAGCGACTCTAGCAAA 60.457 55.000 15.11 0.00 37.01 3.68
3802 4177 0.933796 GCAGCGACTCTAGCAAATCC 59.066 55.000 0.00 0.00 37.01 3.01
3811 4186 6.647067 GCGACTCTAGCAAATCCTGTATAAAT 59.353 38.462 0.00 0.00 34.19 1.40
3855 4303 9.553064 TTGTTCATACTGCAATTTAAAAACCAT 57.447 25.926 0.00 0.00 0.00 3.55
3869 4317 5.343307 AAAAACCATATTCACCCTCATGC 57.657 39.130 0.00 0.00 0.00 4.06
3874 4322 2.627515 TATTCACCCTCATGCAGCTC 57.372 50.000 0.00 0.00 0.00 4.09
3875 4323 0.106819 ATTCACCCTCATGCAGCTCC 60.107 55.000 0.00 0.00 0.00 4.70
3950 4398 2.575461 GGCTGCTTGGAATGCCAC 59.425 61.111 0.00 0.00 45.94 5.01
4016 4464 2.126346 GTGAGTTTGCATGGCGGC 60.126 61.111 0.00 0.00 0.00 6.53
4065 4513 1.788258 CACTTCCGATCATGGATCCG 58.212 55.000 7.39 0.00 38.00 4.18
4066 4514 1.069204 CACTTCCGATCATGGATCCGT 59.931 52.381 7.39 3.27 38.00 4.69
4085 4533 2.548480 CGTGAGAAAGGGGAAGAAACAC 59.452 50.000 0.00 0.00 0.00 3.32
4086 4534 3.551846 GTGAGAAAGGGGAAGAAACACA 58.448 45.455 0.00 0.00 0.00 3.72
4088 4536 4.022849 GTGAGAAAGGGGAAGAAACACATG 60.023 45.833 0.00 0.00 0.00 3.21
4089 4537 4.145052 GAGAAAGGGGAAGAAACACATGT 58.855 43.478 0.00 0.00 0.00 3.21
4090 4538 3.891366 AGAAAGGGGAAGAAACACATGTG 59.109 43.478 24.25 24.25 0.00 3.21
4091 4539 2.292828 AGGGGAAGAAACACATGTGG 57.707 50.000 28.64 11.73 34.19 4.17
4092 4540 0.603065 GGGGAAGAAACACATGTGGC 59.397 55.000 28.64 17.28 34.19 5.01
4093 4541 1.620822 GGGAAGAAACACATGTGGCT 58.379 50.000 28.64 19.11 34.19 4.75
4094 4542 2.554344 GGGGAAGAAACACATGTGGCTA 60.554 50.000 28.64 0.00 34.19 3.93
4095 4543 3.153919 GGGAAGAAACACATGTGGCTAA 58.846 45.455 28.64 0.00 34.19 3.09
4096 4544 3.763897 GGGAAGAAACACATGTGGCTAAT 59.236 43.478 28.64 12.48 34.19 1.73
4097 4545 4.380867 GGGAAGAAACACATGTGGCTAATG 60.381 45.833 28.64 3.16 34.19 1.90
4098 4546 4.458989 GGAAGAAACACATGTGGCTAATGA 59.541 41.667 28.64 0.00 34.19 2.57
4099 4547 5.048083 GGAAGAAACACATGTGGCTAATGAA 60.048 40.000 28.64 0.00 34.19 2.57
4100 4548 6.403866 AAGAAACACATGTGGCTAATGAAA 57.596 33.333 28.64 0.00 34.19 2.69
4101 4549 6.017400 AGAAACACATGTGGCTAATGAAAG 57.983 37.500 28.64 0.23 34.19 2.62
4102 4550 4.789012 AACACATGTGGCTAATGAAAGG 57.211 40.909 28.64 0.02 34.19 3.11
4103 4551 4.032960 ACACATGTGGCTAATGAAAGGA 57.967 40.909 28.64 0.00 34.19 3.36
4104 4552 4.012374 ACACATGTGGCTAATGAAAGGAG 58.988 43.478 28.64 0.00 34.19 3.69
4105 4553 4.263462 ACACATGTGGCTAATGAAAGGAGA 60.263 41.667 28.64 0.00 34.19 3.71
4106 4554 4.095483 CACATGTGGCTAATGAAAGGAGAC 59.905 45.833 18.51 0.00 0.00 3.36
4107 4555 2.972625 TGTGGCTAATGAAAGGAGACG 58.027 47.619 0.00 0.00 0.00 4.18
4108 4556 2.280628 GTGGCTAATGAAAGGAGACGG 58.719 52.381 0.00 0.00 0.00 4.79
4109 4557 1.300481 GGCTAATGAAAGGAGACGGC 58.700 55.000 0.00 0.00 0.00 5.68
4110 4558 0.931005 GCTAATGAAAGGAGACGGCG 59.069 55.000 4.80 4.80 0.00 6.46
4111 4559 1.571919 CTAATGAAAGGAGACGGCGG 58.428 55.000 13.24 0.00 0.00 6.13
4112 4560 1.136305 CTAATGAAAGGAGACGGCGGA 59.864 52.381 13.24 0.00 0.00 5.54
4113 4561 0.108138 AATGAAAGGAGACGGCGGAG 60.108 55.000 13.24 0.00 0.00 4.63
4138 4586 3.642901 GAGCTTATCCAGAACGCGA 57.357 52.632 15.93 0.00 0.00 5.87
4139 4587 1.922570 GAGCTTATCCAGAACGCGAA 58.077 50.000 15.93 0.00 0.00 4.70
4140 4588 1.588861 GAGCTTATCCAGAACGCGAAC 59.411 52.381 15.93 6.10 0.00 3.95
4141 4589 0.651031 GCTTATCCAGAACGCGAACC 59.349 55.000 15.93 0.22 0.00 3.62
4142 4590 1.287425 CTTATCCAGAACGCGAACCC 58.713 55.000 15.93 0.00 0.00 4.11
4143 4591 0.899720 TTATCCAGAACGCGAACCCT 59.100 50.000 15.93 0.13 0.00 4.34
4144 4592 1.766494 TATCCAGAACGCGAACCCTA 58.234 50.000 15.93 0.00 0.00 3.53
4145 4593 0.899720 ATCCAGAACGCGAACCCTAA 59.100 50.000 15.93 0.00 0.00 2.69
4146 4594 0.680618 TCCAGAACGCGAACCCTAAA 59.319 50.000 15.93 0.00 0.00 1.85
4147 4595 1.276989 TCCAGAACGCGAACCCTAAAT 59.723 47.619 15.93 0.00 0.00 1.40
4148 4596 2.496871 TCCAGAACGCGAACCCTAAATA 59.503 45.455 15.93 0.00 0.00 1.40
4149 4597 3.133362 TCCAGAACGCGAACCCTAAATAT 59.867 43.478 15.93 0.00 0.00 1.28
4150 4598 4.341806 TCCAGAACGCGAACCCTAAATATA 59.658 41.667 15.93 0.00 0.00 0.86
4151 4599 4.684703 CCAGAACGCGAACCCTAAATATAG 59.315 45.833 15.93 0.00 0.00 1.31
4152 4600 4.150098 CAGAACGCGAACCCTAAATATAGC 59.850 45.833 15.93 0.00 0.00 2.97
4154 4602 1.990563 CGCGAACCCTAAATATAGCGG 59.009 52.381 0.00 0.00 42.24 5.52
4155 4603 1.730612 GCGAACCCTAAATATAGCGGC 59.269 52.381 0.00 0.00 0.00 6.53
4156 4604 1.990563 CGAACCCTAAATATAGCGGCG 59.009 52.381 0.51 0.51 0.00 6.46
4157 4605 2.344025 GAACCCTAAATATAGCGGCGG 58.656 52.381 9.78 0.00 0.00 6.13
4158 4606 1.636148 ACCCTAAATATAGCGGCGGA 58.364 50.000 9.78 0.00 0.00 5.54
4159 4607 1.274447 ACCCTAAATATAGCGGCGGAC 59.726 52.381 9.78 0.00 0.00 4.79
4160 4608 1.405121 CCCTAAATATAGCGGCGGACC 60.405 57.143 9.78 0.00 0.00 4.46
4172 4620 2.184836 CGGACCGGCGGATTTGTA 59.815 61.111 35.78 0.00 0.00 2.41
4173 4621 1.881252 CGGACCGGCGGATTTGTAG 60.881 63.158 35.78 12.09 0.00 2.74
4174 4622 1.523032 GGACCGGCGGATTTGTAGG 60.523 63.158 35.78 2.05 0.00 3.18
4175 4623 2.124860 ACCGGCGGATTTGTAGGC 60.125 61.111 35.78 0.00 0.00 3.93
4176 4624 2.900337 CCGGCGGATTTGTAGGCC 60.900 66.667 24.41 0.00 42.14 5.19
4180 4628 2.900337 CGGATTTGTAGGCCGCCC 60.900 66.667 5.55 0.00 38.46 6.13
4181 4629 2.900337 GGATTTGTAGGCCGCCCG 60.900 66.667 5.55 0.00 35.76 6.13
4182 4630 2.124860 GATTTGTAGGCCGCCCGT 60.125 61.111 5.55 0.00 35.76 5.28
4183 4631 1.144496 GATTTGTAGGCCGCCCGTA 59.856 57.895 5.55 0.00 35.76 4.02
4184 4632 0.462403 GATTTGTAGGCCGCCCGTAA 60.462 55.000 5.55 0.00 35.76 3.18
4185 4633 0.035247 ATTTGTAGGCCGCCCGTAAA 60.035 50.000 5.55 5.44 35.76 2.01
4186 4634 0.250640 TTTGTAGGCCGCCCGTAAAA 60.251 50.000 5.55 0.00 35.76 1.52
4187 4635 0.250640 TTGTAGGCCGCCCGTAAAAA 60.251 50.000 5.55 0.00 35.76 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.256461 CAGTTTGCGGCCAAGAGC 59.744 61.111 2.24 0.00 42.60 4.09
1 2 2.956987 CCAGTTTGCGGCCAAGAG 59.043 61.111 2.24 0.00 31.52 2.85
2 3 3.294493 GCCAGTTTGCGGCCAAGA 61.294 61.111 2.24 0.00 44.22 3.02
94 95 2.472861 GCGATGATCATGTACCGAACTG 59.527 50.000 14.30 0.00 0.00 3.16
218 219 5.972935 ACACGTTCATCATCACCATAGTAA 58.027 37.500 0.00 0.00 0.00 2.24
250 251 5.471257 AGTTTGTCTTATCTCCGAGTGTTC 58.529 41.667 0.00 0.00 0.00 3.18
309 310 4.216411 TGTAGAGTATTCCTTGGCCAAC 57.784 45.455 16.05 4.12 0.00 3.77
375 376 1.164662 CCAGCAAGATGGATGAGCGG 61.165 60.000 0.00 0.00 43.57 5.52
410 411 5.359194 ACAAATCGACATATTCCACTCCT 57.641 39.130 0.00 0.00 0.00 3.69
449 450 2.094675 ACCCCTCTCATGCATTTTTCG 58.905 47.619 0.00 0.00 0.00 3.46
493 494 7.993101 ACAATCGATTGAAAATGTGATGAGAT 58.007 30.769 37.75 12.16 40.14 2.75
507 508 9.816354 TGAGTTTGATTCTATACAATCGATTGA 57.184 29.630 37.75 23.75 40.14 2.57
517 518 8.125448 GCATCTTTGGTGAGTTTGATTCTATAC 58.875 37.037 0.00 0.00 0.00 1.47
551 552 0.530650 CGTGGATCATCTGAACCCCG 60.531 60.000 4.27 1.04 36.29 5.73
571 572 5.367302 TCAATGGCTCCTTTTTCAAAAAGG 58.633 37.500 29.28 29.28 46.28 3.11
651 652 6.239345 CCTCTACTAGTCCAACCCAACATATC 60.239 46.154 0.00 0.00 0.00 1.63
711 712 1.558756 ACTCTTAGCAAGCTCAGCCAT 59.441 47.619 0.00 0.00 0.00 4.40
799 800 6.928492 GTCTAGCAGAGGATCCTTTATTTCTG 59.072 42.308 17.42 17.70 34.84 3.02
858 859 1.068264 GCCCTTGCTAACTTGCTCAAC 60.068 52.381 0.00 0.00 33.53 3.18
877 878 0.389166 CCTCACGGAGTTCTGTCTGC 60.389 60.000 0.00 0.00 41.61 4.26
892 893 3.826157 CTGTTTCCACCATTTAAGCCTCA 59.174 43.478 0.00 0.00 0.00 3.86
1176 1215 4.590222 AGCACCTTCAATGATGAACCTTTT 59.410 37.500 0.00 0.00 40.59 2.27
1226 1265 0.320421 TCGCAGAGCTACACCAAACC 60.320 55.000 0.00 0.00 0.00 3.27
1287 1326 5.697633 GCTCTTGCTTTCATCCAAAATTTCA 59.302 36.000 0.00 0.00 36.03 2.69
1364 1403 2.346803 TCTCTGCGCTTGTATTTCCAC 58.653 47.619 9.73 0.00 0.00 4.02
1428 1467 2.676176 CGATGGTGCATCTTGTCTGAGT 60.676 50.000 0.00 0.00 38.59 3.41
1468 1507 1.224075 CCAGCGATCATTGGTAGCAG 58.776 55.000 4.80 0.00 0.00 4.24
1470 1509 1.510480 GCCCAGCGATCATTGGTAGC 61.510 60.000 10.62 0.00 32.40 3.58
1665 1704 8.830915 AAGAGATATTCTTCAGGTCTGAGTTA 57.169 34.615 0.75 0.00 42.54 2.24
1769 1812 3.119388 TGCAGCATGTAAGGAAAGATTGC 60.119 43.478 0.00 0.00 39.31 3.56
1898 1944 4.934602 GCTTACTCAGTTGCATCTCTCTTT 59.065 41.667 0.00 0.00 0.00 2.52
1900 1946 3.768757 AGCTTACTCAGTTGCATCTCTCT 59.231 43.478 5.46 0.00 0.00 3.10
1901 1947 4.122143 AGCTTACTCAGTTGCATCTCTC 57.878 45.455 5.46 0.00 0.00 3.20
1902 1948 5.867903 ATAGCTTACTCAGTTGCATCTCT 57.132 39.130 0.00 0.00 0.00 3.10
1903 1949 5.814705 ACAATAGCTTACTCAGTTGCATCTC 59.185 40.000 0.00 0.00 0.00 2.75
1904 1950 5.738909 ACAATAGCTTACTCAGTTGCATCT 58.261 37.500 0.00 0.00 0.00 2.90
1905 1951 6.092670 TCAACAATAGCTTACTCAGTTGCATC 59.907 38.462 0.00 0.00 34.56 3.91
1912 1965 8.988934 TGTTTTAGTCAACAATAGCTTACTCAG 58.011 33.333 0.00 0.00 33.60 3.35
1971 2060 9.065871 CAAAGTTGCATCTATTTAGTTAAGTGC 57.934 33.333 0.00 0.00 0.00 4.40
1993 2082 8.962857 ACAAAACTTTGGTTAAATTTGCAAAG 57.037 26.923 18.19 0.00 42.34 2.77
2343 2432 0.516001 GCTCGTCTACGTCTGTGTGA 59.484 55.000 0.00 0.00 40.80 3.58
2490 2579 6.642733 TCTTGAAGATGGAATAAGGTCCTT 57.357 37.500 9.62 9.62 38.62 3.36
2620 2709 0.261696 TGGTCCTCGGATCATGGAGA 59.738 55.000 8.70 0.00 29.14 3.71
2684 2773 1.048724 CGCCCAACTCCCATCTAGGA 61.049 60.000 0.00 0.00 41.22 2.94
2711 2800 2.749800 GCCATATTTCCCTTCGCTCCTT 60.750 50.000 0.00 0.00 0.00 3.36
2725 2814 9.461312 TGATTAACACAAACTAAGAGCCATATT 57.539 29.630 0.00 0.00 0.00 1.28
2726 2815 9.632638 ATGATTAACACAAACTAAGAGCCATAT 57.367 29.630 0.00 0.00 0.00 1.78
2728 2817 7.944729 ATGATTAACACAAACTAAGAGCCAT 57.055 32.000 0.00 0.00 0.00 4.40
2729 2818 7.065803 GCTATGATTAACACAAACTAAGAGCCA 59.934 37.037 0.00 0.00 0.00 4.75
2730 2819 7.410485 GCTATGATTAACACAAACTAAGAGCC 58.590 38.462 0.00 0.00 0.00 4.70
2731 2820 7.119997 CGCTATGATTAACACAAACTAAGAGC 58.880 38.462 0.00 0.00 0.00 4.09
2732 2821 8.186178 ACGCTATGATTAACACAAACTAAGAG 57.814 34.615 0.00 0.00 0.00 2.85
2733 2822 9.079833 GTACGCTATGATTAACACAAACTAAGA 57.920 33.333 0.00 0.00 0.00 2.10
2734 2823 8.865978 TGTACGCTATGATTAACACAAACTAAG 58.134 33.333 0.00 0.00 0.00 2.18
2735 2824 8.760103 TGTACGCTATGATTAACACAAACTAA 57.240 30.769 0.00 0.00 0.00 2.24
2736 2825 8.813282 CATGTACGCTATGATTAACACAAACTA 58.187 33.333 0.00 0.00 0.00 2.24
2737 2826 7.547722 TCATGTACGCTATGATTAACACAAACT 59.452 33.333 0.00 0.00 30.03 2.66
2742 2831 7.148950 GCTAGTCATGTACGCTATGATTAACAC 60.149 40.741 0.00 0.00 36.96 3.32
2743 2832 6.861572 GCTAGTCATGTACGCTATGATTAACA 59.138 38.462 0.00 0.00 36.96 2.41
2744 2833 7.085116 AGCTAGTCATGTACGCTATGATTAAC 58.915 38.462 0.00 0.00 36.96 2.01
2850 2942 5.873164 AGTCTTCCGGAACAACATTACATAC 59.127 40.000 14.35 0.00 0.00 2.39
2867 2959 1.157585 GTTCTCGGGCAAAGTCTTCC 58.842 55.000 0.00 0.00 0.00 3.46
2907 2999 8.561738 TCGACAAGCCTCTTTATAAATCTTTT 57.438 30.769 0.00 0.00 0.00 2.27
3168 3290 0.731417 CATCTTTTCGCTCTGGCCAG 59.269 55.000 27.87 27.87 34.44 4.85
3204 3331 2.196749 CACTGCTGATACCTTGTAGCG 58.803 52.381 0.00 0.00 38.96 4.26
3205 3332 3.190874 GACACTGCTGATACCTTGTAGC 58.809 50.000 0.00 0.00 36.72 3.58
3206 3333 4.177026 GTGACACTGCTGATACCTTGTAG 58.823 47.826 0.00 0.00 0.00 2.74
3207 3334 3.056107 GGTGACACTGCTGATACCTTGTA 60.056 47.826 5.39 0.00 0.00 2.41
3208 3335 2.289694 GGTGACACTGCTGATACCTTGT 60.290 50.000 5.39 0.00 0.00 3.16
3209 3336 2.027745 AGGTGACACTGCTGATACCTTG 60.028 50.000 5.39 0.00 35.24 3.61
3210 3337 2.027745 CAGGTGACACTGCTGATACCTT 60.028 50.000 5.39 0.00 36.06 3.50
3269 3401 5.396436 GCCTGTGTACAAGTCCCAGTATATT 60.396 44.000 0.00 0.00 0.00 1.28
3318 3450 6.638096 TCATGGATCGCAATGAATAACAAT 57.362 33.333 0.00 0.00 29.97 2.71
3389 3521 8.997323 GCTCTATGTATTGCACATCTAAATTCT 58.003 33.333 0.00 0.00 44.99 2.40
3390 3522 8.777413 TGCTCTATGTATTGCACATCTAAATTC 58.223 33.333 0.00 0.00 44.99 2.17
3391 3523 8.681486 TGCTCTATGTATTGCACATCTAAATT 57.319 30.769 0.00 0.00 44.99 1.82
3401 3533 8.534496 ACATATAGATGTGCTCTATGTATTGCA 58.466 33.333 1.31 0.00 45.07 4.08
3428 3560 8.180317 TCTTTGTAAAACAGTTTTGCTAAAGC 57.820 30.769 25.71 0.00 35.74 3.51
3459 3597 6.860790 TCACAAGTTGGTCCTATGTACATA 57.139 37.500 14.75 14.75 0.00 2.29
3461 3599 5.730550 GATCACAAGTTGGTCCTATGTACA 58.269 41.667 7.96 0.00 27.45 2.90
3471 3609 2.355108 CGGATCTGGATCACAAGTTGGT 60.355 50.000 7.96 0.00 39.54 3.67
3472 3610 2.093500 TCGGATCTGGATCACAAGTTGG 60.093 50.000 7.96 0.00 39.54 3.77
3484 3622 7.096023 CGAACTTACTGAATATTTCGGATCTGG 60.096 40.741 0.62 0.00 39.38 3.86
3501 3639 8.997621 TGAGCAATTAATCTAACGAACTTACT 57.002 30.769 0.00 0.00 0.00 2.24
3524 3662 5.304778 TGCAAAATCAGTGTAGCTAGTTGA 58.695 37.500 0.00 0.00 0.00 3.18
3530 3668 6.127897 GGTTCTTATGCAAAATCAGTGTAGCT 60.128 38.462 0.00 0.00 0.00 3.32
3534 3672 4.518970 ACGGTTCTTATGCAAAATCAGTGT 59.481 37.500 0.00 0.00 0.00 3.55
3547 3685 2.676342 GACCAAATCGCACGGTTCTTAT 59.324 45.455 0.00 0.00 31.63 1.73
3560 3698 1.102978 CCCCCATTGACGACCAAATC 58.897 55.000 0.00 0.00 38.43 2.17
3569 3707 0.608035 TCGCAAACTCCCCCATTGAC 60.608 55.000 0.00 0.00 0.00 3.18
3571 3709 1.185315 AATCGCAAACTCCCCCATTG 58.815 50.000 0.00 0.00 0.00 2.82
3572 3710 1.937191 AAATCGCAAACTCCCCCATT 58.063 45.000 0.00 0.00 0.00 3.16
3582 3720 7.112287 CCGCATTATAATCGTTTAAATCGCAAA 59.888 33.333 12.90 0.00 0.00 3.68
3583 3721 6.575572 CCGCATTATAATCGTTTAAATCGCAA 59.424 34.615 12.90 0.00 0.00 4.85
3584 3722 6.074642 CCGCATTATAATCGTTTAAATCGCA 58.925 36.000 12.90 0.00 0.00 5.10
3585 3723 6.075280 ACCGCATTATAATCGTTTAAATCGC 58.925 36.000 12.90 3.14 0.00 4.58
3586 3724 7.896274 CCTACCGCATTATAATCGTTTAAATCG 59.104 37.037 12.90 0.00 0.00 3.34
3587 3725 8.715088 ACCTACCGCATTATAATCGTTTAAATC 58.285 33.333 12.90 0.00 0.00 2.17
3588 3726 8.611654 ACCTACCGCATTATAATCGTTTAAAT 57.388 30.769 12.90 0.00 0.00 1.40
3589 3727 8.977505 GTACCTACCGCATTATAATCGTTTAAA 58.022 33.333 12.90 0.00 0.00 1.52
3611 3749 3.119743 TGCATGTAGTACTGTGTCGTACC 60.120 47.826 5.39 0.00 40.42 3.34
3613 3751 4.976224 ATGCATGTAGTACTGTGTCGTA 57.024 40.909 5.39 0.00 0.00 3.43
3624 3762 0.810031 GCCGGACGAATGCATGTAGT 60.810 55.000 5.05 0.04 0.00 2.73
3625 3763 1.498865 GGCCGGACGAATGCATGTAG 61.499 60.000 5.05 0.00 0.00 2.74
3626 3764 1.522806 GGCCGGACGAATGCATGTA 60.523 57.895 5.05 0.00 0.00 2.29
3629 3767 4.108299 TGGGCCGGACGAATGCAT 62.108 61.111 5.05 0.00 0.00 3.96
3664 4001 2.018324 GCTTGTTCTTTGCCGCTGC 61.018 57.895 0.00 0.00 38.26 5.25
3666 4003 3.042560 GGCTTGTTCTTTGCCGCT 58.957 55.556 0.00 0.00 37.11 5.52
3669 4006 1.010419 CGCATGGCTTGTTCTTTGCC 61.010 55.000 2.12 0.00 46.26 4.52
3680 4040 1.153086 GGGATGTTCTCGCATGGCT 60.153 57.895 0.00 0.00 36.83 4.75
3681 4041 1.442526 CTGGGATGTTCTCGCATGGC 61.443 60.000 0.00 0.00 44.86 4.40
3685 4045 0.955428 GTTGCTGGGATGTTCTCGCA 60.955 55.000 0.00 0.00 43.89 5.10
3758 4133 2.094700 AGTTGTCATATCAGTGCGTCGT 60.095 45.455 0.00 0.00 0.00 4.34
3788 4163 7.329717 CCGATTTATACAGGATTTGCTAGAGTC 59.670 40.741 0.00 0.00 0.00 3.36
3798 4173 6.041637 TCTGCAGTACCGATTTATACAGGATT 59.958 38.462 14.67 0.00 0.00 3.01
3799 4174 5.538813 TCTGCAGTACCGATTTATACAGGAT 59.461 40.000 14.67 0.00 0.00 3.24
3802 4177 6.088217 CGATTCTGCAGTACCGATTTATACAG 59.912 42.308 14.67 0.00 0.00 2.74
3811 4186 2.288579 ACAAACGATTCTGCAGTACCGA 60.289 45.455 14.67 0.00 0.00 4.69
3855 4303 1.141657 GGAGCTGCATGAGGGTGAATA 59.858 52.381 0.00 0.00 0.00 1.75
3869 4317 3.130160 GCCGGCTTCAAGGAGCTG 61.130 66.667 22.15 2.01 46.35 4.24
3874 4322 4.659172 TGTGGGCCGGCTTCAAGG 62.659 66.667 28.56 0.00 0.00 3.61
3875 4323 3.365265 GTGTGGGCCGGCTTCAAG 61.365 66.667 28.56 0.00 0.00 3.02
3972 4420 4.200283 CGAGGAGGCCGACAGCTC 62.200 72.222 0.00 0.00 43.05 4.09
3987 4435 0.317160 AAACTCACTCGGCATGACGA 59.683 50.000 24.69 24.69 41.13 4.20
4054 4502 2.105477 CCCTTTCTCACGGATCCATGAT 59.895 50.000 11.61 0.00 0.00 2.45
4065 4513 3.551846 TGTGTTTCTTCCCCTTTCTCAC 58.448 45.455 0.00 0.00 0.00 3.51
4066 4514 3.943671 TGTGTTTCTTCCCCTTTCTCA 57.056 42.857 0.00 0.00 0.00 3.27
4085 4533 3.310774 CGTCTCCTTTCATTAGCCACATG 59.689 47.826 0.00 0.00 0.00 3.21
4086 4534 3.535561 CGTCTCCTTTCATTAGCCACAT 58.464 45.455 0.00 0.00 0.00 3.21
4088 4536 2.280628 CCGTCTCCTTTCATTAGCCAC 58.719 52.381 0.00 0.00 0.00 5.01
4089 4537 1.406887 GCCGTCTCCTTTCATTAGCCA 60.407 52.381 0.00 0.00 0.00 4.75
4090 4538 1.300481 GCCGTCTCCTTTCATTAGCC 58.700 55.000 0.00 0.00 0.00 3.93
4091 4539 0.931005 CGCCGTCTCCTTTCATTAGC 59.069 55.000 0.00 0.00 0.00 3.09
4092 4540 1.136305 TCCGCCGTCTCCTTTCATTAG 59.864 52.381 0.00 0.00 0.00 1.73
4093 4541 1.136305 CTCCGCCGTCTCCTTTCATTA 59.864 52.381 0.00 0.00 0.00 1.90
4094 4542 0.108138 CTCCGCCGTCTCCTTTCATT 60.108 55.000 0.00 0.00 0.00 2.57
4095 4543 1.517832 CTCCGCCGTCTCCTTTCAT 59.482 57.895 0.00 0.00 0.00 2.57
4096 4544 2.970639 CTCCGCCGTCTCCTTTCA 59.029 61.111 0.00 0.00 0.00 2.69
4097 4545 2.509561 GCTCCGCCGTCTCCTTTC 60.510 66.667 0.00 0.00 0.00 2.62
4098 4546 3.302347 CTGCTCCGCCGTCTCCTTT 62.302 63.158 0.00 0.00 0.00 3.11
4099 4547 3.764466 CTGCTCCGCCGTCTCCTT 61.764 66.667 0.00 0.00 0.00 3.36
4109 4557 3.157217 ATAAGCTCCGCCTGCTCCG 62.157 63.158 0.00 0.00 40.22 4.63
4110 4558 1.301322 GATAAGCTCCGCCTGCTCC 60.301 63.158 0.00 0.00 40.22 4.70
4111 4559 1.301322 GGATAAGCTCCGCCTGCTC 60.301 63.158 0.00 0.00 40.22 4.26
4112 4560 2.825264 GGATAAGCTCCGCCTGCT 59.175 61.111 0.00 0.00 43.32 4.24
4119 4567 0.102481 TCGCGTTCTGGATAAGCTCC 59.898 55.000 5.77 0.00 45.19 4.70
4120 4568 1.588861 GTTCGCGTTCTGGATAAGCTC 59.411 52.381 5.77 0.00 0.00 4.09
4121 4569 1.641577 GTTCGCGTTCTGGATAAGCT 58.358 50.000 5.77 0.00 0.00 3.74
4122 4570 0.651031 GGTTCGCGTTCTGGATAAGC 59.349 55.000 5.77 0.00 0.00 3.09
4123 4571 1.134788 AGGGTTCGCGTTCTGGATAAG 60.135 52.381 5.77 0.00 0.00 1.73
4124 4572 0.899720 AGGGTTCGCGTTCTGGATAA 59.100 50.000 5.77 0.00 0.00 1.75
4125 4573 1.766494 TAGGGTTCGCGTTCTGGATA 58.234 50.000 5.77 0.00 0.00 2.59
4126 4574 0.899720 TTAGGGTTCGCGTTCTGGAT 59.100 50.000 5.77 0.00 0.00 3.41
4127 4575 0.680618 TTTAGGGTTCGCGTTCTGGA 59.319 50.000 5.77 0.00 0.00 3.86
4128 4576 1.734163 ATTTAGGGTTCGCGTTCTGG 58.266 50.000 5.77 0.00 0.00 3.86
4129 4577 4.150098 GCTATATTTAGGGTTCGCGTTCTG 59.850 45.833 5.77 0.00 0.00 3.02
4130 4578 4.304939 GCTATATTTAGGGTTCGCGTTCT 58.695 43.478 5.77 2.24 0.00 3.01
4131 4579 3.120782 CGCTATATTTAGGGTTCGCGTTC 59.879 47.826 5.77 0.00 34.54 3.95
4132 4580 3.054878 CGCTATATTTAGGGTTCGCGTT 58.945 45.455 5.77 0.00 34.54 4.84
4133 4581 2.608752 CCGCTATATTTAGGGTTCGCGT 60.609 50.000 5.77 0.00 36.82 6.01
4134 4582 1.990563 CCGCTATATTTAGGGTTCGCG 59.009 52.381 0.00 0.00 36.82 5.87
4135 4583 1.730612 GCCGCTATATTTAGGGTTCGC 59.269 52.381 6.52 0.54 36.82 4.70
4136 4584 1.990563 CGCCGCTATATTTAGGGTTCG 59.009 52.381 6.52 5.90 36.82 3.95
4137 4585 2.028748 TCCGCCGCTATATTTAGGGTTC 60.029 50.000 6.52 0.00 36.82 3.62
4138 4586 1.972795 TCCGCCGCTATATTTAGGGTT 59.027 47.619 6.52 0.00 36.82 4.11
4139 4587 1.274447 GTCCGCCGCTATATTTAGGGT 59.726 52.381 6.52 0.00 36.82 4.34
4140 4588 1.405121 GGTCCGCCGCTATATTTAGGG 60.405 57.143 0.96 0.96 37.95 3.53
4141 4589 2.005971 GGTCCGCCGCTATATTTAGG 57.994 55.000 0.00 0.00 0.00 2.69
4155 4603 1.881252 CTACAAATCCGCCGGTCCG 60.881 63.158 1.63 3.60 0.00 4.79
4156 4604 1.523032 CCTACAAATCCGCCGGTCC 60.523 63.158 1.63 0.00 0.00 4.46
4157 4605 2.178235 GCCTACAAATCCGCCGGTC 61.178 63.158 1.63 0.00 0.00 4.79
4158 4606 2.124860 GCCTACAAATCCGCCGGT 60.125 61.111 1.63 0.00 0.00 5.28
4159 4607 2.900337 GGCCTACAAATCCGCCGG 60.900 66.667 0.00 0.00 0.00 6.13
4163 4611 2.900337 GGGCGGCCTACAAATCCG 60.900 66.667 22.87 0.00 45.46 4.18
4164 4612 2.314415 TACGGGCGGCCTACAAATCC 62.314 60.000 27.04 0.00 0.00 3.01
4165 4613 0.462403 TTACGGGCGGCCTACAAATC 60.462 55.000 27.04 0.00 0.00 2.17
4166 4614 0.035247 TTTACGGGCGGCCTACAAAT 60.035 50.000 27.04 6.71 0.00 2.32
4167 4615 0.250640 TTTTACGGGCGGCCTACAAA 60.251 50.000 27.04 18.61 0.00 2.83
4168 4616 0.250640 TTTTTACGGGCGGCCTACAA 60.251 50.000 27.04 13.68 0.00 2.41
4169 4617 1.374190 TTTTTACGGGCGGCCTACA 59.626 52.632 27.04 7.75 0.00 2.74
4170 4618 4.299756 TTTTTACGGGCGGCCTAC 57.700 55.556 27.04 1.58 0.00 3.18


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

AutoCloner maintained by Alex Coulton.