Multiple sequence alignment - TraesCS4D01G206100

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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 TraesCS4D01G206100 chr4D 100.000 5149 0 0 1 5149 353762138 353756990 0.000000e+00 9509.0
1 TraesCS4D01G206100 chr4B 95.323 2694 80 19 2357 5040 437214143 437211486 0.000000e+00 4235.0
2 TraesCS4D01G206100 chr4B 94.388 1568 71 9 743 2297 437215705 437214142 0.000000e+00 2392.0
3 TraesCS4D01G206100 chr4B 92.374 695 34 14 1 690 437216663 437215983 0.000000e+00 972.0
4 TraesCS4D01G206100 chr4A 92.065 2659 101 48 2357 4939 111089468 111092092 0.000000e+00 3640.0
5 TraesCS4D01G206100 chr4A 89.969 1306 53 25 461 1733 111087604 111088864 0.000000e+00 1615.0
6 TraesCS4D01G206100 chr4A 94.561 570 19 7 1736 2297 111088904 111089469 0.000000e+00 870.0
7 TraesCS4D01G206100 chr4A 85.282 496 35 18 1 469 111087097 111087581 1.300000e-130 477.0
8 TraesCS4D01G206100 chr2B 81.952 881 93 29 3212 4076 595292856 595293686 0.000000e+00 686.0
9 TraesCS4D01G206100 chr3D 92.689 383 14 4 240 609 14156629 14157010 1.630000e-149 540.0
10 TraesCS4D01G206100 chr3D 95.312 64 2 1 2296 2358 551999731 551999668 3.280000e-17 100.0
11 TraesCS4D01G206100 chr7A 91.000 100 9 0 4840 4939 686006120 686006219 8.990000e-28 135.0
12 TraesCS4D01G206100 chr7A 90.541 74 6 1 2287 2359 663579236 663579163 4.240000e-16 97.1
13 TraesCS4D01G206100 chr7B 96.923 65 2 0 2295 2359 620597828 620597892 5.450000e-20 110.0
14 TraesCS4D01G206100 chr7B 95.385 65 3 0 2294 2358 196390825 196390889 2.540000e-18 104.0
15 TraesCS4D01G206100 chr1D 94.118 68 2 2 2295 2362 48193815 48193880 9.120000e-18 102.0
16 TraesCS4D01G206100 chr1D 91.892 74 2 3 2295 2364 246070233 246070306 3.280000e-17 100.0
17 TraesCS4D01G206100 chr1D 90.541 74 2 1 2295 2363 464799726 464799799 5.490000e-15 93.5
18 TraesCS4D01G206100 chr7D 90.541 74 6 1 2287 2359 574274921 574274848 4.240000e-16 97.1
19 TraesCS4D01G206100 chr6B 91.176 68 4 1 2296 2361 594860785 594860718 1.970000e-14 91.6


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 TraesCS4D01G206100 chr4D 353756990 353762138 5148 True 9509.0 9509 100.000000 1 5149 1 chr4D.!!$R1 5148
1 TraesCS4D01G206100 chr4B 437211486 437216663 5177 True 2533.0 4235 94.028333 1 5040 3 chr4B.!!$R1 5039
2 TraesCS4D01G206100 chr4A 111087097 111092092 4995 False 1650.5 3640 90.469250 1 4939 4 chr4A.!!$F1 4938
3 TraesCS4D01G206100 chr2B 595292856 595293686 830 False 686.0 686 81.952000 3212 4076 1 chr2B.!!$F1 864

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
815 1125 0.254747 CGAACTAAGCCCCAATCCCA 59.745 55.0 0.0 0.0 0.0 4.37 F
2309 2690 0.324091 TGTTCTACTCCCTCCGTCCC 60.324 60.0 0.0 0.0 0.0 4.46 F
2310 2691 0.324091 GTTCTACTCCCTCCGTCCCA 60.324 60.0 0.0 0.0 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2339 2720 0.105349 CTACCCCCTCCGTCCCATAA 60.105 60.000 0.00 0.0 0.00 1.90 R
3689 4082 1.299089 GCGCGTTGCCAAAGAACTT 60.299 52.632 8.43 0.0 37.76 2.66 R
4160 4574 2.227626 TGGTGATGTTGTACGCCAAATG 59.772 45.455 0.00 0.0 42.51 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
32 33 3.564053 TCCCGGATTATTAAAACGCCT 57.436 42.857 0.73 0.00 0.00 5.52
86 87 0.759959 TGGTGCCCACGTTCTTCTAA 59.240 50.000 0.00 0.00 0.00 2.10
101 102 3.780850 TCTTCTAATCCTCCCACTTTCCC 59.219 47.826 0.00 0.00 0.00 3.97
102 103 3.214694 TCTAATCCTCCCACTTTCCCA 57.785 47.619 0.00 0.00 0.00 4.37
182 183 1.423584 TGTCTCAAGCAACCAGGAGA 58.576 50.000 0.00 0.00 34.23 3.71
184 185 0.322975 TCTCAAGCAACCAGGAGAGC 59.677 55.000 0.00 0.00 32.89 4.09
209 213 1.602605 TCTCGAACCCGACAGAGCA 60.603 57.895 0.00 0.00 40.30 4.26
313 332 4.516698 CAGCTAAAGTGTGAAGTCAATGGT 59.483 41.667 0.00 0.00 0.00 3.55
347 366 3.775654 CGAGCACTCCCCCTCCAC 61.776 72.222 0.00 0.00 0.00 4.02
348 367 3.403558 GAGCACTCCCCCTCCACC 61.404 72.222 0.00 0.00 0.00 4.61
609 689 4.579384 CAAGCCGGGTGGTGTGGT 62.579 66.667 7.07 0.00 37.67 4.16
619 699 3.216292 GGTGTGGTGTGGTGTGGC 61.216 66.667 0.00 0.00 0.00 5.01
815 1125 0.254747 CGAACTAAGCCCCAATCCCA 59.745 55.000 0.00 0.00 0.00 4.37
816 1126 1.763968 GAACTAAGCCCCAATCCCAC 58.236 55.000 0.00 0.00 0.00 4.61
854 1164 0.442699 GCGTCCGTTCATTCTCAACC 59.557 55.000 0.00 0.00 0.00 3.77
1135 1455 1.431440 GATCTCGCAGCTCGTGACT 59.569 57.895 10.85 3.82 42.46 3.41
1140 1460 2.872001 GCAGCTCGTGACTCGACG 60.872 66.667 0.00 0.00 44.01 5.12
1197 1517 1.378882 CCAACATGCGGATCCTGGTG 61.379 60.000 10.75 10.31 0.00 4.17
1266 1586 2.746362 GGAGAACGAGAAGAACGAGGTA 59.254 50.000 0.00 0.00 34.70 3.08
1269 1589 4.070716 AGAACGAGAAGAACGAGGTAAGA 58.929 43.478 0.00 0.00 34.70 2.10
1329 1649 2.179018 CGAAATTGGCCTGTGCGG 59.821 61.111 3.32 0.00 38.85 5.69
1350 1670 2.741211 GGTCAACTCCGTTCCGCC 60.741 66.667 0.00 0.00 0.00 6.13
1377 1697 1.662608 AGTGGCACAGTCAGACTCG 59.337 57.895 21.41 0.00 37.51 4.18
1463 1783 1.085091 CAGATCTCAGTGTGCAAGCC 58.915 55.000 0.00 0.00 0.00 4.35
1497 1817 1.678635 GCATGCTGTGGGGCACTAA 60.679 57.895 11.37 0.00 45.36 2.24
1537 1861 0.607620 AGCTCTGCTCCACTCTCAAC 59.392 55.000 0.00 0.00 30.62 3.18
1567 1891 3.834489 ATTACAGAGATCCAGTGGCAG 57.166 47.619 3.51 0.00 0.00 4.85
1587 1911 3.483922 CAGTGCTTTAGAGAACTATCGCG 59.516 47.826 0.00 0.00 39.95 5.87
1590 1914 3.044286 GCTTTAGAGAACTATCGCGGTC 58.956 50.000 6.13 0.00 0.00 4.79
1592 1916 1.224075 TAGAGAACTATCGCGGTCCG 58.776 55.000 6.99 6.99 38.61 4.79
1605 1929 1.221021 GGTCCGAGCTTAACCTGGG 59.779 63.158 0.00 0.00 32.55 4.45
1649 1973 2.354123 CTGAGATCCAGTGGCAATGCC 61.354 57.143 18.95 18.95 40.73 4.40
1659 1983 3.018479 GGCAATGCCTCTGAGATCC 57.982 57.895 18.47 0.00 46.69 3.36
1802 2182 7.930513 TTCAGTATTGTTACTATGCAGATCG 57.069 36.000 0.00 0.00 36.50 3.69
1840 2220 5.748402 AGCAAATGTAGACCAATCTGATCA 58.252 37.500 0.00 0.00 36.29 2.92
1848 2228 5.954153 AGACCAATCTGATCATGTCTTCT 57.046 39.130 0.00 0.00 32.29 2.85
2029 2409 7.566760 TGTGGCCATACTATTTTGTAATGAG 57.433 36.000 9.72 0.00 0.00 2.90
2046 2426 2.946564 TGAGCACAGATAGTTGACACG 58.053 47.619 0.00 0.00 0.00 4.49
2173 2553 6.358178 TGTACAAAAACCATGTCCTGAGTTA 58.642 36.000 0.00 0.00 32.27 2.24
2271 2651 4.155063 TGTCTATGGCATGCTTATGTGT 57.845 40.909 18.92 0.00 0.00 3.72
2282 2662 6.151691 GCATGCTTATGTGTCTTTCTTTTGA 58.848 36.000 11.37 0.00 0.00 2.69
2295 2676 9.396022 TGTCTTTCTTTTGATAACTTCTGTTCT 57.604 29.630 0.00 0.00 37.59 3.01
2300 2681 9.490379 TTCTTTTGATAACTTCTGTTCTACTCC 57.510 33.333 0.00 0.00 37.59 3.85
2301 2682 8.095169 TCTTTTGATAACTTCTGTTCTACTCCC 58.905 37.037 0.00 0.00 37.59 4.30
2302 2683 7.554959 TTTGATAACTTCTGTTCTACTCCCT 57.445 36.000 0.00 0.00 37.59 4.20
2303 2684 6.777213 TGATAACTTCTGTTCTACTCCCTC 57.223 41.667 0.00 0.00 37.59 4.30
2304 2685 5.657302 TGATAACTTCTGTTCTACTCCCTCC 59.343 44.000 0.00 0.00 37.59 4.30
2305 2686 2.448453 ACTTCTGTTCTACTCCCTCCG 58.552 52.381 0.00 0.00 0.00 4.63
2306 2687 2.225066 ACTTCTGTTCTACTCCCTCCGT 60.225 50.000 0.00 0.00 0.00 4.69
2307 2688 2.125773 TCTGTTCTACTCCCTCCGTC 57.874 55.000 0.00 0.00 0.00 4.79
2308 2689 1.104630 CTGTTCTACTCCCTCCGTCC 58.895 60.000 0.00 0.00 0.00 4.79
2309 2690 0.324091 TGTTCTACTCCCTCCGTCCC 60.324 60.000 0.00 0.00 0.00 4.46
2310 2691 0.324091 GTTCTACTCCCTCCGTCCCA 60.324 60.000 0.00 0.00 0.00 4.37
2311 2692 0.635009 TTCTACTCCCTCCGTCCCAT 59.365 55.000 0.00 0.00 0.00 4.00
2312 2693 1.526315 TCTACTCCCTCCGTCCCATA 58.474 55.000 0.00 0.00 0.00 2.74
2313 2694 1.854939 TCTACTCCCTCCGTCCCATAA 59.145 52.381 0.00 0.00 0.00 1.90
2314 2695 2.449730 TCTACTCCCTCCGTCCCATAAT 59.550 50.000 0.00 0.00 0.00 1.28
2315 2696 3.659195 TCTACTCCCTCCGTCCCATAATA 59.341 47.826 0.00 0.00 0.00 0.98
2316 2697 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2317 2698 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2318 2699 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
2319 2700 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
2320 2701 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
2321 2702 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
2322 2703 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
2323 2704 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
2324 2705 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
2325 2706 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
2326 2707 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
2327 2708 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
2328 2709 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
2329 2710 7.069569 CGTCCCATAATATAAGAGCGTTTTTG 58.930 38.462 0.00 0.00 0.00 2.44
2330 2711 7.042321 CGTCCCATAATATAAGAGCGTTTTTGA 60.042 37.037 0.00 0.00 0.00 2.69
2331 2712 8.068380 GTCCCATAATATAAGAGCGTTTTTGAC 58.932 37.037 0.00 0.00 0.00 3.18
2332 2713 7.990886 TCCCATAATATAAGAGCGTTTTTGACT 59.009 33.333 0.00 0.00 0.00 3.41
2333 2714 8.283291 CCCATAATATAAGAGCGTTTTTGACTC 58.717 37.037 0.00 0.00 0.00 3.36
2334 2715 9.046296 CCATAATATAAGAGCGTTTTTGACTCT 57.954 33.333 0.00 0.00 42.51 3.24
2344 2725 9.046296 AGAGCGTTTTTGACTCTTATATTATGG 57.954 33.333 0.00 0.00 37.50 2.74
2345 2726 8.154649 AGCGTTTTTGACTCTTATATTATGGG 57.845 34.615 0.00 0.00 0.00 4.00
2346 2727 7.990886 AGCGTTTTTGACTCTTATATTATGGGA 59.009 33.333 0.00 0.00 0.00 4.37
2347 2728 8.068380 GCGTTTTTGACTCTTATATTATGGGAC 58.932 37.037 0.00 0.00 0.00 4.46
2348 2729 8.273557 CGTTTTTGACTCTTATATTATGGGACG 58.726 37.037 0.00 0.00 0.00 4.79
2349 2730 8.557029 GTTTTTGACTCTTATATTATGGGACGG 58.443 37.037 0.00 0.00 0.00 4.79
2350 2731 7.606135 TTTGACTCTTATATTATGGGACGGA 57.394 36.000 0.00 0.00 0.00 4.69
2351 2732 6.835819 TGACTCTTATATTATGGGACGGAG 57.164 41.667 0.00 0.00 0.00 4.63
2352 2733 5.715279 TGACTCTTATATTATGGGACGGAGG 59.285 44.000 0.00 0.00 0.00 4.30
2353 2734 5.024118 ACTCTTATATTATGGGACGGAGGG 58.976 45.833 0.00 0.00 0.00 4.30
2354 2735 4.359105 TCTTATATTATGGGACGGAGGGG 58.641 47.826 0.00 0.00 0.00 4.79
2355 2736 1.966845 ATATTATGGGACGGAGGGGG 58.033 55.000 0.00 0.00 0.00 5.40
2503 2888 9.630098 CAAATCAGTTTGCTCAAGTGTTATATT 57.370 29.630 4.55 0.00 38.39 1.28
2558 2943 6.785164 CACGTTAATTTTACATTTTGCTGCAC 59.215 34.615 0.00 0.00 0.00 4.57
2679 3064 4.573201 GTGTGTGTAGGCTCTGTTTTTGTA 59.427 41.667 0.00 0.00 0.00 2.41
3017 3402 5.638657 TGTTCATCTGGCAAAAATGTTATGC 59.361 36.000 0.00 0.00 39.33 3.14
3175 3560 8.474831 GGCATTGGTAATACTTTGACCTTAAAT 58.525 33.333 0.00 0.00 34.13 1.40
3680 4073 4.647853 GGAACCCAGGTAAACTTCTTTTGT 59.352 41.667 0.00 0.00 0.00 2.83
3771 4176 2.269023 TCCTGTGGTGATGAACTGGAT 58.731 47.619 0.00 0.00 38.89 3.41
3821 4234 2.935238 GCTGGAACTTGCCGAGAATGTA 60.935 50.000 0.00 0.00 0.00 2.29
4151 4565 1.362224 AGAAGACCAAGGCCTAAGCA 58.638 50.000 5.16 0.00 42.56 3.91
4156 4570 1.384191 CCAAGGCCTAAGCACCCTT 59.616 57.895 5.16 0.00 42.56 3.95
4160 4574 2.275748 GCCTAAGCACCCTTCCCC 59.724 66.667 0.00 0.00 39.53 4.81
4161 4575 2.612493 GCCTAAGCACCCTTCCCCA 61.612 63.158 0.00 0.00 39.53 4.96
4390 4805 6.543831 CCTTATGTTTTAGCCTATGCACTTCT 59.456 38.462 0.00 0.00 41.13 2.85
4469 4888 7.024340 TGCAAAGATATTTCTCTGATGCTTC 57.976 36.000 11.16 0.00 38.63 3.86
4476 4896 1.256812 TCTCTGATGCTTCCACGTCA 58.743 50.000 0.00 0.00 34.47 4.35
4534 4961 4.134563 GACAAGAGACTTAAAAGGCACCA 58.865 43.478 0.00 0.00 36.14 4.17
4559 4986 9.655769 CATGTATTCAGTATCAAGCACATTTAC 57.344 33.333 0.00 0.00 0.00 2.01
4581 5008 3.944015 CCATTCAGGATTTGACACTCCTC 59.056 47.826 3.24 0.00 39.95 3.71
4613 5069 4.141937 ACGCTGATCACCTGTATGTGTTAT 60.142 41.667 0.00 0.00 37.51 1.89
4620 5076 6.043854 TCACCTGTATGTGTTATGCTACAA 57.956 37.500 0.00 0.00 37.51 2.41
4624 5080 7.494298 CACCTGTATGTGTTATGCTACAACATA 59.506 37.037 2.48 0.00 38.13 2.29
4636 5095 9.620259 TTATGCTACAACATACCATATGTTTGA 57.380 29.630 10.75 2.92 39.94 2.69
4660 5119 6.231211 ACCACTACCTTGTCTGATTTACTTG 58.769 40.000 0.00 0.00 0.00 3.16
4770 5247 4.891992 ACTTGCTTAGCTGGAGAAAGTA 57.108 40.909 18.72 2.31 40.44 2.24
4795 5272 3.485431 CTCGACGCTGCAGCCTTG 61.485 66.667 32.07 23.61 37.91 3.61
4880 5357 0.704076 AGCAACCTGAAGGGCCATAA 59.296 50.000 6.18 0.00 40.27 1.90
4894 5371 2.945668 GGCCATAACCTCTGCTTGTAAG 59.054 50.000 0.00 0.00 0.00 2.34
4904 5381 2.647299 TCTGCTTGTAAGGGGGAAATGA 59.353 45.455 0.00 0.00 0.00 2.57
4915 5392 1.404047 GGGGAAATGACATGTTTGCCG 60.404 52.381 11.72 0.00 44.94 5.69
4928 5405 2.074230 TTTGCCGCCTGCTGAAACAG 62.074 55.000 0.00 0.00 42.00 3.16
4973 5450 4.151157 GCAATTCTGCTGATTGTTTTCACC 59.849 41.667 13.25 0.00 45.74 4.02
4976 5453 7.318141 CAATTCTGCTGATTGTTTTCACCTAT 58.682 34.615 0.00 0.00 0.00 2.57
4979 5456 5.412594 TCTGCTGATTGTTTTCACCTATCAC 59.587 40.000 0.00 0.00 0.00 3.06
4983 5460 4.454161 TGATTGTTTTCACCTATCACACGG 59.546 41.667 0.00 0.00 0.00 4.94
4984 5461 2.147958 TGTTTTCACCTATCACACGGC 58.852 47.619 0.00 0.00 0.00 5.68
4988 5465 3.387091 ACCTATCACACGGCGCCA 61.387 61.111 28.98 6.55 0.00 5.69
5007 5484 3.087031 CCATTCAGTTCACTCATTGCCT 58.913 45.455 0.00 0.00 0.00 4.75
5021 5498 3.011517 GCCTGAGGCCTGAGGGAA 61.012 66.667 35.80 2.72 44.06 3.97
5022 5499 3.041469 GCCTGAGGCCTGAGGGAAG 62.041 68.421 35.80 14.10 44.06 3.46
5023 5500 2.588989 CTGAGGCCTGAGGGAAGC 59.411 66.667 12.00 0.00 33.58 3.86
5024 5501 2.203983 TGAGGCCTGAGGGAAGCA 60.204 61.111 12.00 0.00 33.58 3.91
5040 5517 2.985957 AGCAAAACAAAGTGGCACAT 57.014 40.000 21.41 4.57 44.52 3.21
5041 5518 4.367450 GAAGCAAAACAAAGTGGCACATA 58.633 39.130 21.41 0.00 44.52 2.29
5042 5519 4.399004 AGCAAAACAAAGTGGCACATAA 57.601 36.364 21.41 0.00 44.52 1.90
5043 5520 4.370917 AGCAAAACAAAGTGGCACATAAG 58.629 39.130 21.41 9.00 44.52 1.73
5044 5521 3.494251 GCAAAACAAAGTGGCACATAAGG 59.506 43.478 21.41 6.81 44.52 2.69
5045 5522 4.739137 GCAAAACAAAGTGGCACATAAGGA 60.739 41.667 21.41 0.00 44.52 3.36
5046 5523 5.355596 CAAAACAAAGTGGCACATAAGGAA 58.644 37.500 21.41 0.00 44.52 3.36
5047 5524 5.606348 AAACAAAGTGGCACATAAGGAAA 57.394 34.783 21.41 0.00 44.52 3.13
5048 5525 5.606348 AACAAAGTGGCACATAAGGAAAA 57.394 34.783 21.41 0.00 44.52 2.29
5049 5526 5.806654 ACAAAGTGGCACATAAGGAAAAT 57.193 34.783 21.41 0.00 44.52 1.82
5050 5527 6.173427 ACAAAGTGGCACATAAGGAAAATT 57.827 33.333 21.41 0.00 44.52 1.82
5051 5528 6.591001 ACAAAGTGGCACATAAGGAAAATTT 58.409 32.000 21.41 4.41 44.52 1.82
5052 5529 7.053498 ACAAAGTGGCACATAAGGAAAATTTT 58.947 30.769 21.41 2.28 44.52 1.82
5053 5530 7.012232 ACAAAGTGGCACATAAGGAAAATTTTG 59.988 33.333 21.41 17.36 44.52 2.44
5054 5531 6.173427 AGTGGCACATAAGGAAAATTTTGT 57.827 33.333 21.41 0.00 44.52 2.83
5055 5532 7.296628 AGTGGCACATAAGGAAAATTTTGTA 57.703 32.000 21.41 0.00 44.52 2.41
5056 5533 7.731054 AGTGGCACATAAGGAAAATTTTGTAA 58.269 30.769 21.41 0.00 44.52 2.41
5057 5534 8.374743 AGTGGCACATAAGGAAAATTTTGTAAT 58.625 29.630 21.41 0.00 44.52 1.89
5058 5535 8.998377 GTGGCACATAAGGAAAATTTTGTAATT 58.002 29.630 13.86 0.56 44.52 1.40
5059 5536 8.997323 TGGCACATAAGGAAAATTTTGTAATTG 58.003 29.630 8.47 3.55 34.27 2.32
5060 5537 8.998377 GGCACATAAGGAAAATTTTGTAATTGT 58.002 29.630 8.47 4.15 34.27 2.71
5067 5544 8.445275 AGGAAAATTTTGTAATTGTTTGGGAC 57.555 30.769 8.47 0.00 34.27 4.46
5068 5545 7.225734 AGGAAAATTTTGTAATTGTTTGGGACG 59.774 33.333 8.47 0.00 34.27 4.79
5069 5546 6.852858 AAATTTTGTAATTGTTTGGGACGG 57.147 33.333 0.00 0.00 34.27 4.79
5070 5547 5.538849 ATTTTGTAATTGTTTGGGACGGT 57.461 34.783 0.00 0.00 0.00 4.83
5071 5548 3.992260 TTGTAATTGTTTGGGACGGTG 57.008 42.857 0.00 0.00 0.00 4.94
5072 5549 3.210232 TGTAATTGTTTGGGACGGTGA 57.790 42.857 0.00 0.00 0.00 4.02
5073 5550 3.757270 TGTAATTGTTTGGGACGGTGAT 58.243 40.909 0.00 0.00 0.00 3.06
5074 5551 3.754323 TGTAATTGTTTGGGACGGTGATC 59.246 43.478 0.00 0.00 0.00 2.92
5075 5552 1.834188 ATTGTTTGGGACGGTGATCC 58.166 50.000 0.00 0.00 38.13 3.36
5090 5567 3.813724 GGTGATCCGCCTAATTTTCTACC 59.186 47.826 0.00 0.00 0.00 3.18
5091 5568 4.444449 GGTGATCCGCCTAATTTTCTACCT 60.444 45.833 0.00 0.00 0.00 3.08
5092 5569 4.750598 GTGATCCGCCTAATTTTCTACCTC 59.249 45.833 0.00 0.00 0.00 3.85
5093 5570 4.654262 TGATCCGCCTAATTTTCTACCTCT 59.346 41.667 0.00 0.00 0.00 3.69
5094 5571 4.402056 TCCGCCTAATTTTCTACCTCTG 57.598 45.455 0.00 0.00 0.00 3.35
5095 5572 3.773119 TCCGCCTAATTTTCTACCTCTGT 59.227 43.478 0.00 0.00 0.00 3.41
5096 5573 4.957954 TCCGCCTAATTTTCTACCTCTGTA 59.042 41.667 0.00 0.00 0.00 2.74
5097 5574 5.422970 TCCGCCTAATTTTCTACCTCTGTAA 59.577 40.000 0.00 0.00 0.00 2.41
5098 5575 6.099269 TCCGCCTAATTTTCTACCTCTGTAAT 59.901 38.462 0.00 0.00 0.00 1.89
5099 5576 6.766467 CCGCCTAATTTTCTACCTCTGTAATT 59.234 38.462 0.00 0.00 0.00 1.40
5100 5577 7.254795 CCGCCTAATTTTCTACCTCTGTAATTG 60.255 40.741 0.00 0.00 0.00 2.32
5101 5578 7.280205 CGCCTAATTTTCTACCTCTGTAATTGT 59.720 37.037 0.00 0.00 0.00 2.71
5102 5579 8.957466 GCCTAATTTTCTACCTCTGTAATTGTT 58.043 33.333 0.00 0.00 0.00 2.83
5106 5583 7.519032 TTTTCTACCTCTGTAATTGTTTGGG 57.481 36.000 0.00 0.00 0.00 4.12
5107 5584 6.442541 TTCTACCTCTGTAATTGTTTGGGA 57.557 37.500 0.00 0.00 0.00 4.37
5108 5585 6.636454 TCTACCTCTGTAATTGTTTGGGAT 57.364 37.500 0.00 0.00 0.00 3.85
5109 5586 6.414732 TCTACCTCTGTAATTGTTTGGGATG 58.585 40.000 0.00 0.00 0.00 3.51
5110 5587 4.344104 ACCTCTGTAATTGTTTGGGATGG 58.656 43.478 0.00 0.00 0.00 3.51
5111 5588 4.202673 ACCTCTGTAATTGTTTGGGATGGT 60.203 41.667 0.00 0.00 0.00 3.55
5112 5589 4.158394 CCTCTGTAATTGTTTGGGATGGTG 59.842 45.833 0.00 0.00 0.00 4.17
5113 5590 4.991776 TCTGTAATTGTTTGGGATGGTGA 58.008 39.130 0.00 0.00 0.00 4.02
5114 5591 5.579047 TCTGTAATTGTTTGGGATGGTGAT 58.421 37.500 0.00 0.00 0.00 3.06
5115 5592 5.652014 TCTGTAATTGTTTGGGATGGTGATC 59.348 40.000 0.00 0.00 0.00 2.92
5116 5593 4.709397 TGTAATTGTTTGGGATGGTGATCC 59.291 41.667 0.00 0.00 46.99 3.36
5124 5601 2.568623 GGATGGTGATCCGCCTAATT 57.431 50.000 5.23 0.00 39.04 1.40
5125 5602 2.863809 GGATGGTGATCCGCCTAATTT 58.136 47.619 5.23 0.00 39.04 1.82
5126 5603 3.222603 GGATGGTGATCCGCCTAATTTT 58.777 45.455 5.23 0.00 39.04 1.82
5127 5604 3.253432 GGATGGTGATCCGCCTAATTTTC 59.747 47.826 5.23 0.00 39.04 2.29
5128 5605 3.644966 TGGTGATCCGCCTAATTTTCT 57.355 42.857 5.23 0.00 34.70 2.52
5129 5606 3.963129 TGGTGATCCGCCTAATTTTCTT 58.037 40.909 5.23 0.00 34.70 2.52
5130 5607 3.945285 TGGTGATCCGCCTAATTTTCTTC 59.055 43.478 5.23 0.00 34.70 2.87
5131 5608 4.200092 GGTGATCCGCCTAATTTTCTTCT 58.800 43.478 0.00 0.00 0.00 2.85
5132 5609 5.104693 TGGTGATCCGCCTAATTTTCTTCTA 60.105 40.000 5.23 0.00 34.70 2.10
5133 5610 5.236695 GGTGATCCGCCTAATTTTCTTCTAC 59.763 44.000 0.00 0.00 0.00 2.59
5134 5611 5.236695 GTGATCCGCCTAATTTTCTTCTACC 59.763 44.000 0.00 0.00 0.00 3.18
5135 5612 4.829872 TCCGCCTAATTTTCTTCTACCA 57.170 40.909 0.00 0.00 0.00 3.25
5136 5613 4.510571 TCCGCCTAATTTTCTTCTACCAC 58.489 43.478 0.00 0.00 0.00 4.16
5137 5614 3.626217 CCGCCTAATTTTCTTCTACCACC 59.374 47.826 0.00 0.00 0.00 4.61
5138 5615 4.514401 CGCCTAATTTTCTTCTACCACCT 58.486 43.478 0.00 0.00 0.00 4.00
5139 5616 4.571176 CGCCTAATTTTCTTCTACCACCTC 59.429 45.833 0.00 0.00 0.00 3.85
5140 5617 5.627040 CGCCTAATTTTCTTCTACCACCTCT 60.627 44.000 0.00 0.00 0.00 3.69
5141 5618 5.586643 GCCTAATTTTCTTCTACCACCTCTG 59.413 44.000 0.00 0.00 0.00 3.35
5142 5619 6.712276 CCTAATTTTCTTCTACCACCTCTGT 58.288 40.000 0.00 0.00 0.00 3.41
5143 5620 6.819146 CCTAATTTTCTTCTACCACCTCTGTC 59.181 42.308 0.00 0.00 0.00 3.51
5144 5621 5.825593 ATTTTCTTCTACCACCTCTGTCA 57.174 39.130 0.00 0.00 0.00 3.58
5145 5622 5.825593 TTTTCTTCTACCACCTCTGTCAT 57.174 39.130 0.00 0.00 0.00 3.06
5146 5623 4.808414 TTCTTCTACCACCTCTGTCATG 57.192 45.455 0.00 0.00 0.00 3.07
5147 5624 3.099905 TCTTCTACCACCTCTGTCATGG 58.900 50.000 0.00 0.00 39.57 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 3.747529 CACGGCTGCATTATCATATCACA 59.252 43.478 0.50 0.00 0.00 3.58
76 77 4.473477 AAGTGGGAGGATTAGAAGAACG 57.527 45.455 0.00 0.00 0.00 3.95
86 87 3.444029 CAAAATGGGAAAGTGGGAGGAT 58.556 45.455 0.00 0.00 0.00 3.24
101 102 1.202371 AGCAGCATCATCGGCAAAATG 60.202 47.619 0.00 0.00 0.00 2.32
102 103 1.066605 GAGCAGCATCATCGGCAAAAT 59.933 47.619 0.00 0.00 0.00 1.82
140 141 0.249741 ACTACTCGGGTGTGTTGTGC 60.250 55.000 0.00 0.00 0.00 4.57
144 145 2.895404 ACATACACTACTCGGGTGTGTT 59.105 45.455 22.63 11.84 45.83 3.32
250 269 1.751927 GCAGGAGGGTGATGGCTTG 60.752 63.158 0.00 0.00 0.00 4.01
330 349 3.775654 GTGGAGGGGGAGTGCTCG 61.776 72.222 0.00 0.00 0.00 5.03
331 350 3.403558 GGTGGAGGGGGAGTGCTC 61.404 72.222 0.00 0.00 0.00 4.26
619 699 3.550431 AGATCCCATCCCACCGCG 61.550 66.667 0.00 0.00 0.00 6.46
621 701 1.750930 CTCAGATCCCATCCCACCG 59.249 63.158 0.00 0.00 0.00 4.94
690 775 1.446016 ATTTATAAGCGCCTCCCCCT 58.554 50.000 2.29 0.00 0.00 4.79
695 780 1.730612 GGCCGTATTTATAAGCGCCTC 59.269 52.381 2.29 0.00 31.12 4.70
696 781 1.609841 GGGCCGTATTTATAAGCGCCT 60.610 52.381 2.29 0.00 32.82 5.52
838 1148 2.257207 AGGAGGTTGAGAATGAACGGA 58.743 47.619 0.00 0.00 30.92 4.69
1135 1455 1.363145 CCAAAATTAGCGCCCGTCGA 61.363 55.000 2.29 0.00 41.67 4.20
1140 1460 0.738975 GAGTCCCAAAATTAGCGCCC 59.261 55.000 2.29 0.00 0.00 6.13
1290 1610 5.047731 TCGCTAACAGCTAGAATGATGCTAT 60.048 40.000 0.00 0.00 39.60 2.97
1350 1670 0.612229 ACTGTGCCACTCAGATCCAG 59.388 55.000 0.00 0.00 36.81 3.86
1377 1697 2.233305 TCTAGACCCACTCAGTTCCC 57.767 55.000 0.00 0.00 0.00 3.97
1537 1861 7.224362 CACTGGATCTCTGTAATTCTAAAGCAG 59.776 40.741 0.00 0.00 0.00 4.24
1567 1891 2.789893 CCGCGATAGTTCTCTAAAGCAC 59.210 50.000 8.23 0.00 34.61 4.40
1587 1911 1.221021 CCCAGGTTAAGCTCGGACC 59.779 63.158 12.46 5.25 0.00 4.46
1590 1914 0.108138 CAGACCCAGGTTAAGCTCGG 60.108 60.000 15.73 15.73 0.00 4.63
1592 1916 2.861147 AACAGACCCAGGTTAAGCTC 57.139 50.000 3.68 0.00 0.00 4.09
1605 1929 6.426328 AGTTGATCTCACATTCTGAAACAGAC 59.574 38.462 0.74 0.00 40.46 3.51
1649 1973 2.101783 AGTCACAGCAGGATCTCAGAG 58.898 52.381 0.00 0.00 0.00 3.35
1659 1983 5.126222 TCCTAGAATGAAGTAGTCACAGCAG 59.874 44.000 0.00 0.00 39.72 4.24
1784 2164 6.040504 TCTGTACCGATCTGCATAGTAACAAT 59.959 38.462 0.00 0.00 0.00 2.71
1802 2182 6.313744 ACATTTGCTAAGTTTGTCTGTACC 57.686 37.500 0.00 0.00 0.00 3.34
2029 2409 4.421058 TCATACGTGTCAACTATCTGTGC 58.579 43.478 0.00 0.00 0.00 4.57
2046 2426 6.619801 ACAGTGGAAAGAAACAACTCATAC 57.380 37.500 0.00 0.00 0.00 2.39
2173 2553 3.554934 TGCAGGTTCAATTCAACAGACT 58.445 40.909 0.00 0.00 0.00 3.24
2282 2662 4.645588 CGGAGGGAGTAGAACAGAAGTTAT 59.354 45.833 0.00 0.00 38.30 1.89
2295 2676 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
2296 2677 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
2297 2678 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
2298 2679 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
2299 2680 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
2300 2681 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
2301 2682 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
2302 2683 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
2303 2684 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
2304 2685 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
2305 2686 8.068380 GTCAAAAACGCTCTTATATTATGGGAC 58.932 37.037 0.00 0.00 0.00 4.46
2306 2687 7.990886 AGTCAAAAACGCTCTTATATTATGGGA 59.009 33.333 0.00 0.00 0.00 4.37
2307 2688 8.154649 AGTCAAAAACGCTCTTATATTATGGG 57.845 34.615 0.00 0.00 0.00 4.00
2308 2689 9.046296 AGAGTCAAAAACGCTCTTATATTATGG 57.954 33.333 0.00 0.00 36.30 2.74
2318 2699 9.046296 CCATAATATAAGAGTCAAAAACGCTCT 57.954 33.333 0.00 0.00 36.98 4.09
2319 2700 8.283291 CCCATAATATAAGAGTCAAAAACGCTC 58.717 37.037 0.00 0.00 36.98 5.03
2320 2701 7.990886 TCCCATAATATAAGAGTCAAAAACGCT 59.009 33.333 0.00 0.00 40.04 5.07
2321 2702 8.068380 GTCCCATAATATAAGAGTCAAAAACGC 58.932 37.037 0.00 0.00 0.00 4.84
2322 2703 8.273557 CGTCCCATAATATAAGAGTCAAAAACG 58.726 37.037 0.00 0.00 0.00 3.60
2323 2704 8.557029 CCGTCCCATAATATAAGAGTCAAAAAC 58.443 37.037 0.00 0.00 0.00 2.43
2324 2705 8.487848 TCCGTCCCATAATATAAGAGTCAAAAA 58.512 33.333 0.00 0.00 0.00 1.94
2325 2706 8.025270 TCCGTCCCATAATATAAGAGTCAAAA 57.975 34.615 0.00 0.00 0.00 2.44
2326 2707 7.256190 CCTCCGTCCCATAATATAAGAGTCAAA 60.256 40.741 0.00 0.00 0.00 2.69
2327 2708 6.210784 CCTCCGTCCCATAATATAAGAGTCAA 59.789 42.308 0.00 0.00 0.00 3.18
2328 2709 5.715279 CCTCCGTCCCATAATATAAGAGTCA 59.285 44.000 0.00 0.00 0.00 3.41
2329 2710 5.127356 CCCTCCGTCCCATAATATAAGAGTC 59.873 48.000 0.00 0.00 0.00 3.36
2330 2711 5.024118 CCCTCCGTCCCATAATATAAGAGT 58.976 45.833 0.00 0.00 0.00 3.24
2331 2712 4.406003 CCCCTCCGTCCCATAATATAAGAG 59.594 50.000 0.00 0.00 0.00 2.85
2332 2713 4.359105 CCCCTCCGTCCCATAATATAAGA 58.641 47.826 0.00 0.00 0.00 2.10
2333 2714 3.454812 CCCCCTCCGTCCCATAATATAAG 59.545 52.174 0.00 0.00 0.00 1.73
2334 2715 3.181392 ACCCCCTCCGTCCCATAATATAA 60.181 47.826 0.00 0.00 0.00 0.98
2335 2716 2.387861 ACCCCCTCCGTCCCATAATATA 59.612 50.000 0.00 0.00 0.00 0.86
2336 2717 1.153565 ACCCCCTCCGTCCCATAATAT 59.846 52.381 0.00 0.00 0.00 1.28
2337 2718 0.569204 ACCCCCTCCGTCCCATAATA 59.431 55.000 0.00 0.00 0.00 0.98
2338 2719 0.569204 TACCCCCTCCGTCCCATAAT 59.431 55.000 0.00 0.00 0.00 1.28
2339 2720 0.105349 CTACCCCCTCCGTCCCATAA 60.105 60.000 0.00 0.00 0.00 1.90
2340 2721 1.000590 TCTACCCCCTCCGTCCCATA 61.001 60.000 0.00 0.00 0.00 2.74
2341 2722 1.675936 ATCTACCCCCTCCGTCCCAT 61.676 60.000 0.00 0.00 0.00 4.00
2342 2723 1.000590 TATCTACCCCCTCCGTCCCA 61.001 60.000 0.00 0.00 0.00 4.37
2343 2724 0.251698 CTATCTACCCCCTCCGTCCC 60.252 65.000 0.00 0.00 0.00 4.46
2344 2725 0.776176 TCTATCTACCCCCTCCGTCC 59.224 60.000 0.00 0.00 0.00 4.79
2345 2726 2.671896 TTCTATCTACCCCCTCCGTC 57.328 55.000 0.00 0.00 0.00 4.79
2346 2727 2.425975 CCTTTCTATCTACCCCCTCCGT 60.426 54.545 0.00 0.00 0.00 4.69
2347 2728 2.158355 TCCTTTCTATCTACCCCCTCCG 60.158 54.545 0.00 0.00 0.00 4.63
2348 2729 3.241156 GTCCTTTCTATCTACCCCCTCC 58.759 54.545 0.00 0.00 0.00 4.30
2349 2730 2.892215 CGTCCTTTCTATCTACCCCCTC 59.108 54.545 0.00 0.00 0.00 4.30
2350 2731 2.246849 ACGTCCTTTCTATCTACCCCCT 59.753 50.000 0.00 0.00 0.00 4.79
2351 2732 2.627221 GACGTCCTTTCTATCTACCCCC 59.373 54.545 3.51 0.00 0.00 5.40
2352 2733 2.627221 GGACGTCCTTTCTATCTACCCC 59.373 54.545 27.64 0.00 0.00 4.95
2353 2734 3.294214 TGGACGTCCTTTCTATCTACCC 58.706 50.000 33.39 4.64 36.82 3.69
2354 2735 4.796618 GCATGGACGTCCTTTCTATCTACC 60.797 50.000 33.39 5.11 36.82 3.18
2355 2736 4.202121 TGCATGGACGTCCTTTCTATCTAC 60.202 45.833 33.39 11.45 36.82 2.59
2503 2888 4.212425 ACGCACAAGAATGTAATGACGAAA 59.788 37.500 0.00 0.00 37.82 3.46
2536 2921 8.547069 TGAAGTGCAGCAAAATGTAAAATTAAC 58.453 29.630 0.00 0.00 0.00 2.01
2558 2943 2.069273 GTGGTTCGGTGACATCTGAAG 58.931 52.381 1.11 0.00 34.02 3.02
2679 3064 9.717942 GATAGGAGCAGTTATGACAGAATAAAT 57.282 33.333 0.00 0.00 0.00 1.40
3017 3402 6.307155 CGTGGCACAAGTTTAGAAAAGATAG 58.693 40.000 19.09 0.00 44.16 2.08
3555 3946 1.613437 GGTGACCATCCACAGTTTTGG 59.387 52.381 0.00 0.00 38.74 3.28
3689 4082 1.299089 GCGCGTTGCCAAAGAACTT 60.299 52.632 8.43 0.00 37.76 2.66
3821 4234 9.102453 GTATAGAATATCCCACTTACCTCCTTT 57.898 37.037 0.00 0.00 0.00 3.11
4160 4574 2.227626 TGGTGATGTTGTACGCCAAATG 59.772 45.455 0.00 0.00 42.51 2.32
4161 4575 2.509569 TGGTGATGTTGTACGCCAAAT 58.490 42.857 0.00 0.00 42.51 2.32
4390 4805 9.311916 GCACCAACATTGCTATAATTGATTTAA 57.688 29.630 6.06 0.00 37.00 1.52
4520 4946 6.010219 ACTGAATACATGGTGCCTTTTAAGT 58.990 36.000 0.00 0.00 0.00 2.24
4523 4949 7.342581 TGATACTGAATACATGGTGCCTTTTA 58.657 34.615 0.00 0.00 0.00 1.52
4534 4961 8.840321 GGTAAATGTGCTTGATACTGAATACAT 58.160 33.333 0.00 0.00 0.00 2.29
4559 4986 3.944015 GAGGAGTGTCAAATCCTGAATGG 59.056 47.826 11.70 0.00 46.12 3.16
4581 5008 3.246936 CAGGTGATCAGCGTCATATGTTG 59.753 47.826 18.64 5.08 0.00 3.33
4613 5069 6.317642 GGTCAAACATATGGTATGTTGTAGCA 59.682 38.462 14.13 0.00 40.94 3.49
4620 5076 6.157994 AGGTAGTGGTCAAACATATGGTATGT 59.842 38.462 7.80 0.00 0.00 2.29
4624 5080 5.222048 ACAAGGTAGTGGTCAAACATATGGT 60.222 40.000 7.80 0.00 0.00 3.55
4636 5095 6.231211 CAAGTAAATCAGACAAGGTAGTGGT 58.769 40.000 0.00 0.00 0.00 4.16
4719 5183 7.977904 TGCTACAACATCAAACATGAAGATAG 58.022 34.615 0.00 0.00 0.00 2.08
4750 5218 6.749923 ATTTACTTTCTCCAGCTAAGCAAG 57.250 37.500 6.26 6.26 0.00 4.01
4770 5247 2.030946 GCTGCAGCGTCGAGAAATATTT 59.969 45.455 25.23 0.00 0.00 1.40
4795 5272 2.104963 GGTGGATAATCTGACCCTGGTC 59.895 54.545 9.44 9.44 44.77 4.02
4853 5330 1.268899 CCTTCAGGTTGCTGCAGAAAG 59.731 52.381 20.43 1.19 0.00 2.62
4880 5357 0.178873 TCCCCCTTACAAGCAGAGGT 60.179 55.000 0.00 0.00 0.00 3.85
4894 5371 1.066215 GGCAAACATGTCATTTCCCCC 60.066 52.381 0.00 0.00 0.00 5.40
4915 5392 1.818642 ACATCTCTGTTTCAGCAGGC 58.181 50.000 0.00 0.00 37.12 4.85
4928 5405 2.644676 GAGTAAGGGGGCAAACATCTC 58.355 52.381 0.00 0.00 0.00 2.75
4973 5450 0.809636 TGAATGGCGCCGTGTGATAG 60.810 55.000 24.67 0.00 0.00 2.08
4976 5453 2.741985 CTGAATGGCGCCGTGTGA 60.742 61.111 24.67 3.16 0.00 3.58
4979 5456 2.324330 TGAACTGAATGGCGCCGTG 61.324 57.895 24.67 12.79 0.00 4.94
4983 5460 1.089920 ATGAGTGAACTGAATGGCGC 58.910 50.000 0.00 0.00 0.00 6.53
4984 5461 2.730090 GCAATGAGTGAACTGAATGGCG 60.730 50.000 0.00 0.00 0.00 5.69
4988 5465 4.025040 TCAGGCAATGAGTGAACTGAAT 57.975 40.909 5.49 0.00 38.83 2.57
5007 5484 1.426251 TTTGCTTCCCTCAGGCCTCA 61.426 55.000 0.00 0.00 0.00 3.86
5012 5489 2.695147 ACTTTGTTTTGCTTCCCTCAGG 59.305 45.455 0.00 0.00 0.00 3.86
5013 5490 3.491447 CCACTTTGTTTTGCTTCCCTCAG 60.491 47.826 0.00 0.00 0.00 3.35
5014 5491 2.430332 CCACTTTGTTTTGCTTCCCTCA 59.570 45.455 0.00 0.00 0.00 3.86
5016 5493 1.138859 GCCACTTTGTTTTGCTTCCCT 59.861 47.619 0.00 0.00 0.00 4.20
5017 5494 1.134551 TGCCACTTTGTTTTGCTTCCC 60.135 47.619 0.00 0.00 0.00 3.97
5018 5495 1.933181 GTGCCACTTTGTTTTGCTTCC 59.067 47.619 0.00 0.00 0.00 3.46
5019 5496 2.615869 TGTGCCACTTTGTTTTGCTTC 58.384 42.857 0.00 0.00 0.00 3.86
5020 5497 2.758736 TGTGCCACTTTGTTTTGCTT 57.241 40.000 0.00 0.00 0.00 3.91
5021 5498 2.985957 ATGTGCCACTTTGTTTTGCT 57.014 40.000 0.00 0.00 0.00 3.91
5022 5499 3.494251 CCTTATGTGCCACTTTGTTTTGC 59.506 43.478 0.00 0.00 0.00 3.68
5023 5500 4.942852 TCCTTATGTGCCACTTTGTTTTG 58.057 39.130 0.00 0.00 0.00 2.44
5024 5501 5.606348 TTCCTTATGTGCCACTTTGTTTT 57.394 34.783 0.00 0.00 0.00 2.43
5041 5518 8.898761 GTCCCAAACAATTACAAAATTTTCCTT 58.101 29.630 0.00 0.00 32.87 3.36
5042 5519 7.225734 CGTCCCAAACAATTACAAAATTTTCCT 59.774 33.333 0.00 0.00 32.87 3.36
5043 5520 7.348956 CGTCCCAAACAATTACAAAATTTTCC 58.651 34.615 0.00 0.00 32.87 3.13
5044 5521 7.011576 ACCGTCCCAAACAATTACAAAATTTTC 59.988 33.333 0.00 0.00 32.87 2.29
5045 5522 6.824196 ACCGTCCCAAACAATTACAAAATTTT 59.176 30.769 0.00 0.00 32.87 1.82
5046 5523 6.258947 CACCGTCCCAAACAATTACAAAATTT 59.741 34.615 0.00 0.00 32.87 1.82
5047 5524 5.755861 CACCGTCCCAAACAATTACAAAATT 59.244 36.000 0.00 0.00 35.65 1.82
5048 5525 5.069251 TCACCGTCCCAAACAATTACAAAAT 59.931 36.000 0.00 0.00 0.00 1.82
5049 5526 4.401519 TCACCGTCCCAAACAATTACAAAA 59.598 37.500 0.00 0.00 0.00 2.44
5050 5527 3.952323 TCACCGTCCCAAACAATTACAAA 59.048 39.130 0.00 0.00 0.00 2.83
5051 5528 3.552875 TCACCGTCCCAAACAATTACAA 58.447 40.909 0.00 0.00 0.00 2.41
5052 5529 3.210232 TCACCGTCCCAAACAATTACA 57.790 42.857 0.00 0.00 0.00 2.41
5053 5530 3.128068 GGATCACCGTCCCAAACAATTAC 59.872 47.826 0.00 0.00 31.82 1.89
5054 5531 3.349022 GGATCACCGTCCCAAACAATTA 58.651 45.455 0.00 0.00 31.82 1.40
5055 5532 2.167662 GGATCACCGTCCCAAACAATT 58.832 47.619 0.00 0.00 31.82 2.32
5056 5533 1.834188 GGATCACCGTCCCAAACAAT 58.166 50.000 0.00 0.00 31.82 2.71
5057 5534 3.332706 GGATCACCGTCCCAAACAA 57.667 52.632 0.00 0.00 31.82 2.83
5068 5545 3.813724 GGTAGAAAATTAGGCGGATCACC 59.186 47.826 0.00 0.00 0.00 4.02
5069 5546 4.704965 AGGTAGAAAATTAGGCGGATCAC 58.295 43.478 0.00 0.00 0.00 3.06
5070 5547 4.654262 AGAGGTAGAAAATTAGGCGGATCA 59.346 41.667 0.00 0.00 0.00 2.92
5071 5548 4.991687 CAGAGGTAGAAAATTAGGCGGATC 59.008 45.833 0.00 0.00 0.00 3.36
5072 5549 4.409247 ACAGAGGTAGAAAATTAGGCGGAT 59.591 41.667 0.00 0.00 0.00 4.18
5073 5550 3.773119 ACAGAGGTAGAAAATTAGGCGGA 59.227 43.478 0.00 0.00 0.00 5.54
5074 5551 4.138487 ACAGAGGTAGAAAATTAGGCGG 57.862 45.455 0.00 0.00 0.00 6.13
5075 5552 7.280205 ACAATTACAGAGGTAGAAAATTAGGCG 59.720 37.037 0.00 0.00 0.00 5.52
5076 5553 8.507524 ACAATTACAGAGGTAGAAAATTAGGC 57.492 34.615 0.00 0.00 0.00 3.93
5080 5557 8.585018 CCCAAACAATTACAGAGGTAGAAAATT 58.415 33.333 0.00 0.00 0.00 1.82
5081 5558 7.947890 TCCCAAACAATTACAGAGGTAGAAAAT 59.052 33.333 0.00 0.00 0.00 1.82
5082 5559 7.291566 TCCCAAACAATTACAGAGGTAGAAAA 58.708 34.615 0.00 0.00 0.00 2.29
5083 5560 6.843752 TCCCAAACAATTACAGAGGTAGAAA 58.156 36.000 0.00 0.00 0.00 2.52
5084 5561 6.442541 TCCCAAACAATTACAGAGGTAGAA 57.557 37.500 0.00 0.00 0.00 2.10
5085 5562 6.414732 CATCCCAAACAATTACAGAGGTAGA 58.585 40.000 0.00 0.00 0.00 2.59
5086 5563 5.590259 CCATCCCAAACAATTACAGAGGTAG 59.410 44.000 0.00 0.00 0.00 3.18
5087 5564 5.014755 ACCATCCCAAACAATTACAGAGGTA 59.985 40.000 0.00 0.00 0.00 3.08
5088 5565 4.202673 ACCATCCCAAACAATTACAGAGGT 60.203 41.667 0.00 0.00 0.00 3.85
5089 5566 4.158394 CACCATCCCAAACAATTACAGAGG 59.842 45.833 0.00 0.00 0.00 3.69
5090 5567 5.009631 TCACCATCCCAAACAATTACAGAG 58.990 41.667 0.00 0.00 0.00 3.35
5091 5568 4.991776 TCACCATCCCAAACAATTACAGA 58.008 39.130 0.00 0.00 0.00 3.41
5092 5569 5.163519 GGATCACCATCCCAAACAATTACAG 60.164 44.000 0.00 0.00 42.91 2.74
5093 5570 4.709397 GGATCACCATCCCAAACAATTACA 59.291 41.667 0.00 0.00 42.91 2.41
5094 5571 4.202010 CGGATCACCATCCCAAACAATTAC 60.202 45.833 0.00 0.00 45.67 1.89
5095 5572 3.951037 CGGATCACCATCCCAAACAATTA 59.049 43.478 0.00 0.00 45.67 1.40
5096 5573 2.760092 CGGATCACCATCCCAAACAATT 59.240 45.455 0.00 0.00 45.67 2.32
5097 5574 2.378038 CGGATCACCATCCCAAACAAT 58.622 47.619 0.00 0.00 45.67 2.71
5098 5575 1.832883 CGGATCACCATCCCAAACAA 58.167 50.000 0.00 0.00 45.67 2.83
5099 5576 0.679640 GCGGATCACCATCCCAAACA 60.680 55.000 0.00 0.00 45.67 2.83
5100 5577 1.384222 GGCGGATCACCATCCCAAAC 61.384 60.000 0.00 0.00 45.67 2.93
5101 5578 1.077068 GGCGGATCACCATCCCAAA 60.077 57.895 0.00 0.00 45.67 3.28
5102 5579 0.692756 TAGGCGGATCACCATCCCAA 60.693 55.000 6.77 0.00 45.67 4.12
5103 5580 0.692756 TTAGGCGGATCACCATCCCA 60.693 55.000 6.77 0.00 45.67 4.37
5104 5581 0.693049 ATTAGGCGGATCACCATCCC 59.307 55.000 6.77 0.00 45.67 3.85
5105 5582 2.568623 AATTAGGCGGATCACCATCC 57.431 50.000 6.77 0.00 45.04 3.51
5106 5583 4.137543 AGAAAATTAGGCGGATCACCATC 58.862 43.478 6.77 0.00 35.59 3.51
5107 5584 4.170468 AGAAAATTAGGCGGATCACCAT 57.830 40.909 6.77 0.00 35.59 3.55
5108 5585 3.644966 AGAAAATTAGGCGGATCACCA 57.355 42.857 6.77 0.00 35.59 4.17
5109 5586 4.200092 AGAAGAAAATTAGGCGGATCACC 58.800 43.478 0.00 0.00 0.00 4.02
5110 5587 5.236695 GGTAGAAGAAAATTAGGCGGATCAC 59.763 44.000 0.00 0.00 0.00 3.06
5111 5588 5.104693 TGGTAGAAGAAAATTAGGCGGATCA 60.105 40.000 0.00 0.00 0.00 2.92
5112 5589 5.236695 GTGGTAGAAGAAAATTAGGCGGATC 59.763 44.000 0.00 0.00 0.00 3.36
5113 5590 5.123936 GTGGTAGAAGAAAATTAGGCGGAT 58.876 41.667 0.00 0.00 0.00 4.18
5114 5591 4.510571 GTGGTAGAAGAAAATTAGGCGGA 58.489 43.478 0.00 0.00 0.00 5.54
5115 5592 3.626217 GGTGGTAGAAGAAAATTAGGCGG 59.374 47.826 0.00 0.00 0.00 6.13
5116 5593 4.514401 AGGTGGTAGAAGAAAATTAGGCG 58.486 43.478 0.00 0.00 0.00 5.52
5117 5594 5.586643 CAGAGGTGGTAGAAGAAAATTAGGC 59.413 44.000 0.00 0.00 0.00 3.93
5118 5595 6.712276 ACAGAGGTGGTAGAAGAAAATTAGG 58.288 40.000 0.00 0.00 0.00 2.69
5119 5596 7.386851 TGACAGAGGTGGTAGAAGAAAATTAG 58.613 38.462 0.00 0.00 0.00 1.73
5120 5597 7.311092 TGACAGAGGTGGTAGAAGAAAATTA 57.689 36.000 0.00 0.00 0.00 1.40
5121 5598 6.187727 TGACAGAGGTGGTAGAAGAAAATT 57.812 37.500 0.00 0.00 0.00 1.82
5122 5599 5.825593 TGACAGAGGTGGTAGAAGAAAAT 57.174 39.130 0.00 0.00 0.00 1.82
5123 5600 5.513094 CCATGACAGAGGTGGTAGAAGAAAA 60.513 44.000 0.00 0.00 0.00 2.29
5124 5601 4.020218 CCATGACAGAGGTGGTAGAAGAAA 60.020 45.833 0.00 0.00 0.00 2.52
5125 5602 3.515502 CCATGACAGAGGTGGTAGAAGAA 59.484 47.826 0.00 0.00 0.00 2.52
5126 5603 3.099905 CCATGACAGAGGTGGTAGAAGA 58.900 50.000 0.00 0.00 0.00 2.87
5127 5604 2.834549 ACCATGACAGAGGTGGTAGAAG 59.165 50.000 0.00 0.00 44.08 2.85
5128 5605 2.902608 ACCATGACAGAGGTGGTAGAA 58.097 47.619 0.00 0.00 44.08 2.10
5129 5606 2.623418 ACCATGACAGAGGTGGTAGA 57.377 50.000 0.00 0.00 44.08 2.59


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

AutoCloner maintained by Alex Coulton.