Multiple sequence alignment - TraesCS1D01G273900

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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 TraesCS1D01G273900 chr1D 100.000 3892 0 0 1 3892 368317147 368321038 0.000000e+00 7188.0
1 TraesCS1D01G273900 chr1D 93.236 547 35 2 3172 3716 369899385 369899931 0.000000e+00 804.0
2 TraesCS1D01G273900 chr1D 94.253 174 9 1 3714 3887 369902255 369902427 8.290000e-67 265.0
3 TraesCS1D01G273900 chr1A 90.152 2427 121 23 529 2901 467255458 467257820 0.000000e+00 3049.0
4 TraesCS1D01G273900 chr1A 90.816 392 19 3 3115 3506 467257842 467258216 3.470000e-140 508.0
5 TraesCS1D01G273900 chr1A 91.243 354 17 7 1 353 467226670 467227010 1.640000e-128 470.0
6 TraesCS1D01G273900 chr1A 85.397 315 18 13 3578 3892 467258212 467258498 6.320000e-78 302.0
7 TraesCS1D01G273900 chr1A 89.362 188 19 1 347 534 467235707 467235893 6.500000e-58 235.0
8 TraesCS1D01G273900 chr1B 87.293 1810 106 59 1 1734 492332585 492334346 0.000000e+00 1954.0
9 TraesCS1D01G273900 chr1B 94.410 1127 60 1 1766 2889 492334716 492335842 0.000000e+00 1729.0
10 TraesCS1D01G273900 chr1B 92.082 783 33 6 3110 3887 492355778 492356536 0.000000e+00 1075.0
11 TraesCS1D01G273900 chr1B 92.254 142 7 1 2885 3022 492355558 492355699 8.530000e-47 198.0
12 TraesCS1D01G273900 chr4B 80.638 847 139 17 1799 2634 642457835 642457003 1.970000e-177 632.0
13 TraesCS1D01G273900 chr4B 77.846 650 115 18 1012 1636 642458745 642458100 3.670000e-100 375.0
14 TraesCS1D01G273900 chr4B 100.000 29 0 0 3115 3143 664760552 664760580 2.000000e-03 54.7
15 TraesCS1D01G273900 chr4D 80.283 847 142 14 1799 2634 499503747 499502915 1.990000e-172 616.0
16 TraesCS1D01G273900 chr4D 85.062 241 26 8 1045 1277 499511668 499511430 1.810000e-58 237.0
17 TraesCS1D01G273900 chr5A 79.152 849 149 19 1799 2634 680503836 680503003 2.630000e-156 562.0
18 TraesCS1D01G273900 chr5A 78.707 634 108 15 1012 1630 680504729 680504108 7.840000e-107 398.0
19 TraesCS1D01G273900 chr5A 85.062 241 26 8 1045 1277 680512096 680511858 1.810000e-58 237.0
20 TraesCS1D01G273900 chr5A 74.812 532 91 28 1574 2086 680726066 680726573 2.370000e-47 200.0
21 TraesCS1D01G273900 chr5A 81.781 247 35 6 1039 1277 627014975 627015219 8.530000e-47 198.0
22 TraesCS1D01G273900 chr5A 79.004 281 42 13 1031 1298 680692382 680692106 4.000000e-40 176.0
23 TraesCS1D01G273900 chr5A 78.229 271 55 4 1968 2236 680669322 680669054 1.860000e-38 171.0
24 TraesCS1D01G273900 chr5A 100.000 28 0 0 3086 3113 422040353 422040380 7.000000e-03 52.8
25 TraesCS1D01G273900 chr5D 82.731 249 29 8 1039 1277 500646691 500646935 3.940000e-50 209.0
26 TraesCS1D01G273900 chr4A 100.000 28 0 0 3086 3113 629483207 629483234 7.000000e-03 52.8
27 TraesCS1D01G273900 chr2D 100.000 28 0 0 3117 3144 467965453 467965480 7.000000e-03 52.8
28 TraesCS1D01G273900 chr2B 100.000 28 0 0 3086 3113 790751447 790751474 7.000000e-03 52.8
29 TraesCS1D01G273900 chr2A 100.000 28 0 0 3110 3137 696242050 696242077 7.000000e-03 52.8


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 TraesCS1D01G273900 chr1D 368317147 368321038 3891 False 7188.000000 7188 100.000000 1 3892 1 chr1D.!!$F1 3891
1 TraesCS1D01G273900 chr1D 369899385 369902427 3042 False 534.500000 804 93.744500 3172 3887 2 chr1D.!!$F2 715
2 TraesCS1D01G273900 chr1A 467255458 467258498 3040 False 1286.333333 3049 88.788333 529 3892 3 chr1A.!!$F3 3363
3 TraesCS1D01G273900 chr1B 492332585 492335842 3257 False 1841.500000 1954 90.851500 1 2889 2 chr1B.!!$F1 2888
4 TraesCS1D01G273900 chr1B 492355558 492356536 978 False 636.500000 1075 92.168000 2885 3887 2 chr1B.!!$F2 1002
5 TraesCS1D01G273900 chr4B 642457003 642458745 1742 True 503.500000 632 79.242000 1012 2634 2 chr4B.!!$R1 1622
6 TraesCS1D01G273900 chr4D 499502915 499503747 832 True 616.000000 616 80.283000 1799 2634 1 chr4D.!!$R1 835
7 TraesCS1D01G273900 chr5A 680503003 680504729 1726 True 480.000000 562 78.929500 1012 2634 2 chr5A.!!$R4 1622

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
404 405 0.179234 TAATCCGAGCCGAATTGCCA 59.821 50.000 0.0 0.0 0.00 4.92 F
765 793 0.251916 TCTTAGCCAACATCACCCCG 59.748 55.000 0.0 0.0 0.00 5.73 F
1473 1594 1.154016 ACGATGCGTCCGTCAAGAG 60.154 57.895 0.0 0.0 33.69 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1567 1688 0.319211 TGCACCTCACGAACTTACCG 60.319 55.0 0.00 0.0 0.00 4.02 R
1812 2408 0.322975 GACAGAGAGGCCTTCAGCAA 59.677 55.0 6.77 0.0 46.50 3.91 R
3056 3669 0.105862 TACGTCATACCAGGGAGGGG 60.106 60.0 0.00 0.0 43.89 4.79 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
54 55 3.067461 CCCTTACTGGAAGAGAGATGTCG 59.933 52.174 0.00 0.00 37.33 4.35
76 77 5.862323 TCGTGTGTTTAACTCTATCTTGAGC 59.138 40.000 0.00 0.00 37.58 4.26
79 80 7.148573 CGTGTGTTTAACTCTATCTTGAGCATT 60.149 37.037 0.00 0.00 37.58 3.56
130 131 6.715344 TGTAAACTTGTTTGCTCGGTATAG 57.285 37.500 13.61 0.00 0.00 1.31
131 132 5.640357 TGTAAACTTGTTTGCTCGGTATAGG 59.360 40.000 13.61 0.00 0.00 2.57
140 141 6.092944 TGTTTGCTCGGTATAGGTGTTTATTG 59.907 38.462 0.00 0.00 0.00 1.90
203 204 0.675837 GCCCGGTAACCAGAACCTTC 60.676 60.000 0.00 0.00 34.66 3.46
223 224 5.511373 CCTTCGGCCATCTATGAAGAATGTA 60.511 44.000 15.10 0.00 40.12 2.29
293 294 1.142688 AGGGCCAAGAGGGAACACAT 61.143 55.000 6.18 0.00 40.01 3.21
294 295 0.967380 GGGCCAAGAGGGAACACATG 60.967 60.000 4.39 0.00 40.01 3.21
295 296 0.251341 GGCCAAGAGGGAACACATGT 60.251 55.000 0.00 0.00 40.01 3.21
298 299 2.288395 GCCAAGAGGGAACACATGTTTG 60.288 50.000 0.00 0.00 40.01 2.93
299 300 2.958355 CCAAGAGGGAACACATGTTTGT 59.042 45.455 0.00 0.00 38.56 2.83
301 302 4.362279 CAAGAGGGAACACATGTTTGTTG 58.638 43.478 6.44 0.00 39.88 3.33
302 303 2.958355 AGAGGGAACACATGTTTGTTGG 59.042 45.455 6.44 0.00 39.88 3.77
304 305 3.103742 AGGGAACACATGTTTGTTGGTT 58.896 40.909 6.44 1.82 39.88 3.67
305 306 3.517500 AGGGAACACATGTTTGTTGGTTT 59.482 39.130 6.44 0.00 39.88 3.27
306 307 4.019771 AGGGAACACATGTTTGTTGGTTTT 60.020 37.500 6.44 0.00 39.88 2.43
307 308 4.697828 GGGAACACATGTTTGTTGGTTTTT 59.302 37.500 6.44 0.00 39.88 1.94
350 351 4.018960 ACATAGCTCAAGGTGGAGAAACAT 60.019 41.667 0.00 0.00 37.05 2.71
368 369 4.134379 ACATCTTCCATACAGAGTGCAG 57.866 45.455 0.00 0.00 0.00 4.41
369 370 3.118482 ACATCTTCCATACAGAGTGCAGG 60.118 47.826 0.00 0.00 0.00 4.85
380 381 3.007940 ACAGAGTGCAGGTACATTAGCAA 59.992 43.478 0.00 0.00 38.91 3.91
386 387 2.158813 GCAGGTACATTAGCAAGGCCTA 60.159 50.000 5.16 0.00 0.00 3.93
387 388 3.684413 GCAGGTACATTAGCAAGGCCTAA 60.684 47.826 5.16 0.00 0.00 2.69
389 390 4.757149 CAGGTACATTAGCAAGGCCTAATC 59.243 45.833 5.16 0.00 36.21 1.75
391 392 2.851195 ACATTAGCAAGGCCTAATCCG 58.149 47.619 5.16 0.00 36.21 4.18
404 405 0.179234 TAATCCGAGCCGAATTGCCA 59.821 50.000 0.00 0.00 0.00 4.92
423 424 3.677424 GCCATTCTTGCTTCTACTCGACT 60.677 47.826 0.00 0.00 0.00 4.18
447 448 6.102663 TGAAAGAAGCTAAGCTATGACTGAC 58.897 40.000 0.00 0.00 38.25 3.51
450 451 3.701532 AGCTAAGCTATGACTGACGAC 57.298 47.619 0.00 0.00 36.99 4.34
477 478 6.480285 GTTTTAGCTAAACACTTTGACGACA 58.520 36.000 18.45 0.00 44.49 4.35
515 516 5.080969 TCTAGTTTTAATCCGTCCTGTGG 57.919 43.478 0.00 0.00 0.00 4.17
610 638 7.218228 ACATTGTGAGAATTGTGCAAATAGA 57.782 32.000 0.00 0.00 0.00 1.98
612 640 8.143193 ACATTGTGAGAATTGTGCAAATAGAAA 58.857 29.630 0.00 0.00 0.00 2.52
613 641 8.980610 CATTGTGAGAATTGTGCAAATAGAAAA 58.019 29.630 0.00 0.00 0.00 2.29
614 642 8.578308 TTGTGAGAATTGTGCAAATAGAAAAG 57.422 30.769 0.00 0.00 0.00 2.27
615 643 7.939782 TGTGAGAATTGTGCAAATAGAAAAGA 58.060 30.769 0.00 0.00 0.00 2.52
616 644 8.412456 TGTGAGAATTGTGCAAATAGAAAAGAA 58.588 29.630 0.00 0.00 0.00 2.52
617 645 8.909671 GTGAGAATTGTGCAAATAGAAAAGAAG 58.090 33.333 0.00 0.00 0.00 2.85
618 646 8.849168 TGAGAATTGTGCAAATAGAAAAGAAGA 58.151 29.630 0.00 0.00 0.00 2.87
619 647 9.852091 GAGAATTGTGCAAATAGAAAAGAAGAT 57.148 29.630 0.00 0.00 0.00 2.40
668 696 5.750352 ATTGGATGGCTGTCATTTTTCTT 57.250 34.783 0.00 0.00 35.97 2.52
669 697 5.549742 TTGGATGGCTGTCATTTTTCTTT 57.450 34.783 0.00 0.00 35.97 2.52
671 699 5.299148 TGGATGGCTGTCATTTTTCTTTTG 58.701 37.500 0.00 0.00 35.97 2.44
719 747 0.872021 GCCTCTACATCAAGCGACGG 60.872 60.000 0.00 0.00 0.00 4.79
735 763 2.870372 GGCGGTTGTCATCTGTGC 59.130 61.111 0.00 0.00 0.00 4.57
741 769 3.002791 CGGTTGTCATCTGTGCAACTAT 58.997 45.455 14.67 0.00 39.79 2.12
752 780 6.727824 TCTGTGCAACTATCTTTTCTTAGC 57.272 37.500 0.00 0.00 38.04 3.09
754 782 5.312895 TGTGCAACTATCTTTTCTTAGCCA 58.687 37.500 0.00 0.00 38.04 4.75
764 792 2.507407 TTCTTAGCCAACATCACCCC 57.493 50.000 0.00 0.00 0.00 4.95
765 793 0.251916 TCTTAGCCAACATCACCCCG 59.748 55.000 0.00 0.00 0.00 5.73
982 1056 6.255887 CGCTTTACTCCTCAAATTTCGACTAT 59.744 38.462 0.00 0.00 0.00 2.12
1009 1083 1.971149 TCCATCCATCCCACAGTTCT 58.029 50.000 0.00 0.00 0.00 3.01
1359 1462 7.754851 TTAATGCATGCATGATGATCTAGTT 57.245 32.000 32.79 15.88 36.68 2.24
1451 1572 3.181516 GCTCAGGTACAATCTTTGCTTCG 60.182 47.826 0.00 0.00 0.00 3.79
1473 1594 1.154016 ACGATGCGTCCGTCAAGAG 60.154 57.895 0.00 0.00 33.69 2.85
1742 2011 6.472686 AGGTAGCACAATTTACTCCTAGAG 57.527 41.667 0.00 0.00 35.52 2.43
1899 2495 0.970427 TCAGGATGCTCGTGCCACTA 60.970 55.000 7.05 0.00 38.71 2.74
1927 2523 2.789092 CGAGCATCAACCAGAAAATCGC 60.789 50.000 0.00 0.00 33.17 4.58
1928 2524 1.131126 AGCATCAACCAGAAAATCGCG 59.869 47.619 0.00 0.00 0.00 5.87
1936 2532 2.028385 ACCAGAAAATCGCGGTAACTCT 60.028 45.455 6.13 0.00 0.00 3.24
1938 2534 3.512680 CAGAAAATCGCGGTAACTCTCT 58.487 45.455 6.13 0.00 0.00 3.10
1953 2555 2.024273 ACTCTCTATGAAGACCCGGGAA 60.024 50.000 32.02 7.31 0.00 3.97
2253 2859 2.202987 GGCATCCTGACTGCTCCG 60.203 66.667 0.00 0.00 39.60 4.63
2432 3038 2.031012 CGTGGCAGAGACAAGGCA 59.969 61.111 0.00 0.00 38.03 4.75
2488 3094 7.944729 AACAAGAGGTACGTAATAAGGTAGA 57.055 36.000 0.00 0.00 0.00 2.59
2530 3139 1.271054 ACCAGTTGCTGTGTCCAGATC 60.271 52.381 0.00 0.00 41.50 2.75
2678 3287 0.745845 ATGAGCCTGGTCGTGCATTC 60.746 55.000 0.00 0.00 0.00 2.67
2707 3316 4.228824 TCAGTAAGTCCTGGTGGTAGTTT 58.771 43.478 0.00 0.00 33.14 2.66
2782 3391 0.951558 CGTTTTGTCCAGTCCCCTTG 59.048 55.000 0.00 0.00 0.00 3.61
2784 3393 0.821711 TTTTGTCCAGTCCCCTTGCG 60.822 55.000 0.00 0.00 0.00 4.85
2791 3400 1.676014 CCAGTCCCCTTGCGAACTTAG 60.676 57.143 0.00 0.00 0.00 2.18
2933 3546 3.765381 TGTTGGAATTGATCTTGGCTGA 58.235 40.909 0.00 0.00 0.00 4.26
2950 3563 3.015327 GCTGACAGCCATGAGAGAAAAT 58.985 45.455 17.01 0.00 34.48 1.82
2971 3584 3.327404 GGGGGTGTGGTCCGTGAT 61.327 66.667 0.00 0.00 0.00 3.06
2972 3585 2.267961 GGGGTGTGGTCCGTGATC 59.732 66.667 0.00 0.00 0.00 2.92
2973 3586 2.125673 GGGTGTGGTCCGTGATCG 60.126 66.667 0.00 0.00 0.00 3.69
2985 3598 1.950472 CGTGATCGGAAGTGCAAAAC 58.050 50.000 0.00 0.00 0.00 2.43
2986 3599 1.262950 CGTGATCGGAAGTGCAAAACA 59.737 47.619 0.00 0.00 0.00 2.83
2987 3600 2.286713 CGTGATCGGAAGTGCAAAACAA 60.287 45.455 0.00 0.00 0.00 2.83
2988 3601 3.701241 GTGATCGGAAGTGCAAAACAAA 58.299 40.909 0.00 0.00 0.00 2.83
2989 3602 4.298332 GTGATCGGAAGTGCAAAACAAAT 58.702 39.130 0.00 0.00 0.00 2.32
2990 3603 4.744631 GTGATCGGAAGTGCAAAACAAATT 59.255 37.500 0.00 0.00 0.00 1.82
2991 3604 5.234116 GTGATCGGAAGTGCAAAACAAATTT 59.766 36.000 0.00 0.00 0.00 1.82
2992 3605 5.814705 TGATCGGAAGTGCAAAACAAATTTT 59.185 32.000 0.00 0.00 38.61 1.82
3007 3620 8.962857 AAACAAATTTTGGTCAAAACACAATC 57.037 26.923 13.42 0.00 42.32 2.67
3008 3621 6.770076 ACAAATTTTGGTCAAAACACAATCG 58.230 32.000 13.42 0.52 42.32 3.34
3009 3622 6.370166 ACAAATTTTGGTCAAAACACAATCGT 59.630 30.769 13.42 1.02 42.32 3.73
3010 3623 6.976636 AATTTTGGTCAAAACACAATCGTT 57.023 29.167 10.56 0.00 42.32 3.85
3011 3624 6.582437 ATTTTGGTCAAAACACAATCGTTC 57.418 33.333 10.56 0.00 42.32 3.95
3012 3625 4.703645 TTGGTCAAAACACAATCGTTCA 57.296 36.364 0.00 0.00 0.00 3.18
3013 3626 4.022464 TGGTCAAAACACAATCGTTCAC 57.978 40.909 0.00 0.00 0.00 3.18
3014 3627 3.692101 TGGTCAAAACACAATCGTTCACT 59.308 39.130 0.00 0.00 0.00 3.41
3015 3628 4.201871 TGGTCAAAACACAATCGTTCACTC 60.202 41.667 0.00 0.00 0.00 3.51
3016 3629 3.960002 GTCAAAACACAATCGTTCACTCG 59.040 43.478 0.00 0.00 0.00 4.18
3017 3630 3.619483 TCAAAACACAATCGTTCACTCGT 59.381 39.130 0.00 0.00 0.00 4.18
3018 3631 4.093703 TCAAAACACAATCGTTCACTCGTT 59.906 37.500 0.00 0.00 0.00 3.85
3019 3632 5.291371 TCAAAACACAATCGTTCACTCGTTA 59.709 36.000 0.00 0.00 0.00 3.18
3020 3633 4.966850 AACACAATCGTTCACTCGTTAG 57.033 40.909 0.00 0.00 0.00 2.34
3021 3634 4.233123 ACACAATCGTTCACTCGTTAGA 57.767 40.909 0.00 0.00 0.00 2.10
3022 3635 3.979495 ACACAATCGTTCACTCGTTAGAC 59.021 43.478 0.00 0.00 0.00 2.59
3023 3636 3.978855 CACAATCGTTCACTCGTTAGACA 59.021 43.478 0.00 0.00 0.00 3.41
3024 3637 3.979495 ACAATCGTTCACTCGTTAGACAC 59.021 43.478 0.00 0.00 0.00 3.67
3025 3638 2.693797 TCGTTCACTCGTTAGACACC 57.306 50.000 0.00 0.00 0.00 4.16
3026 3639 1.948834 TCGTTCACTCGTTAGACACCA 59.051 47.619 0.00 0.00 0.00 4.17
3027 3640 2.049228 CGTTCACTCGTTAGACACCAC 58.951 52.381 0.00 0.00 0.00 4.16
3028 3641 2.401351 GTTCACTCGTTAGACACCACC 58.599 52.381 0.00 0.00 0.00 4.61
3029 3642 1.991121 TCACTCGTTAGACACCACCT 58.009 50.000 0.00 0.00 0.00 4.00
3030 3643 3.144657 TCACTCGTTAGACACCACCTA 57.855 47.619 0.00 0.00 0.00 3.08
3031 3644 3.489355 TCACTCGTTAGACACCACCTAA 58.511 45.455 0.00 0.00 0.00 2.69
3032 3645 3.504906 TCACTCGTTAGACACCACCTAAG 59.495 47.826 0.00 0.00 0.00 2.18
3033 3646 2.824341 ACTCGTTAGACACCACCTAAGG 59.176 50.000 0.00 0.00 34.87 2.69
3034 3647 2.165845 CTCGTTAGACACCACCTAAGGG 59.834 54.545 0.00 0.00 34.54 3.95
3035 3648 2.173519 CGTTAGACACCACCTAAGGGA 58.826 52.381 0.00 0.00 36.25 4.20
3036 3649 2.564062 CGTTAGACACCACCTAAGGGAA 59.436 50.000 0.00 0.00 36.25 3.97
3037 3650 3.368116 CGTTAGACACCACCTAAGGGAAG 60.368 52.174 0.00 0.00 36.25 3.46
3038 3651 1.657804 AGACACCACCTAAGGGAAGG 58.342 55.000 0.00 0.00 42.82 3.46
3039 3652 1.151413 AGACACCACCTAAGGGAAGGA 59.849 52.381 0.00 0.00 39.15 3.36
3040 3653 2.197465 GACACCACCTAAGGGAAGGAT 58.803 52.381 0.00 0.00 39.15 3.24
3041 3654 2.576648 GACACCACCTAAGGGAAGGATT 59.423 50.000 0.00 0.00 39.15 3.01
3042 3655 2.308866 ACACCACCTAAGGGAAGGATTG 59.691 50.000 0.00 0.00 39.15 2.67
3043 3656 2.308866 CACCACCTAAGGGAAGGATTGT 59.691 50.000 0.00 0.00 39.15 2.71
3044 3657 2.993863 ACCACCTAAGGGAAGGATTGTT 59.006 45.455 0.00 0.00 39.15 2.83
3045 3658 3.010250 ACCACCTAAGGGAAGGATTGTTC 59.990 47.826 0.00 0.00 39.15 3.18
3046 3659 3.621558 CACCTAAGGGAAGGATTGTTCC 58.378 50.000 0.00 0.00 44.81 3.62
3052 3665 1.852633 GGAAGGATTGTTCCCTTGGG 58.147 55.000 0.00 0.00 43.59 4.12
3053 3666 1.619704 GGAAGGATTGTTCCCTTGGGG 60.620 57.143 5.78 0.00 43.59 4.96
3069 3682 4.854042 GGAACCCCTCCCTGGTAT 57.146 61.111 0.00 0.00 38.44 2.73
3070 3683 2.231642 GGAACCCCTCCCTGGTATG 58.768 63.158 0.00 0.00 38.44 2.39
3071 3684 0.327191 GGAACCCCTCCCTGGTATGA 60.327 60.000 0.00 0.00 38.44 2.15
3072 3685 0.837940 GAACCCCTCCCTGGTATGAC 59.162 60.000 0.00 0.00 34.15 3.06
3073 3686 0.981277 AACCCCTCCCTGGTATGACG 60.981 60.000 0.00 0.00 34.15 4.35
3074 3687 1.382695 CCCCTCCCTGGTATGACGT 60.383 63.158 0.00 0.00 0.00 4.34
3075 3688 0.105862 CCCCTCCCTGGTATGACGTA 60.106 60.000 0.00 0.00 0.00 3.57
3076 3689 1.038280 CCCTCCCTGGTATGACGTAC 58.962 60.000 0.00 0.00 0.00 3.67
3083 3696 3.841642 GGTATGACGTACCGCTCTC 57.158 57.895 8.12 0.00 43.30 3.20
3084 3697 1.307097 GGTATGACGTACCGCTCTCT 58.693 55.000 8.12 0.00 43.30 3.10
3085 3698 1.674962 GGTATGACGTACCGCTCTCTT 59.325 52.381 8.12 0.00 43.30 2.85
3086 3699 2.541178 GGTATGACGTACCGCTCTCTTG 60.541 54.545 8.12 0.00 43.30 3.02
3087 3700 0.456221 ATGACGTACCGCTCTCTTGG 59.544 55.000 0.00 0.00 0.00 3.61
3088 3701 0.607217 TGACGTACCGCTCTCTTGGA 60.607 55.000 0.00 0.00 0.00 3.53
3089 3702 0.099082 GACGTACCGCTCTCTTGGAG 59.901 60.000 0.00 0.00 44.49 3.86
3090 3703 0.608582 ACGTACCGCTCTCTTGGAGT 60.609 55.000 0.00 0.00 43.62 3.85
3091 3704 1.339438 ACGTACCGCTCTCTTGGAGTA 60.339 52.381 0.00 0.00 43.62 2.59
3092 3705 1.063764 CGTACCGCTCTCTTGGAGTAC 59.936 57.143 0.00 0.00 43.62 2.73
3093 3706 2.367486 GTACCGCTCTCTTGGAGTACT 58.633 52.381 0.00 0.00 43.62 2.73
3094 3707 1.465794 ACCGCTCTCTTGGAGTACTC 58.534 55.000 14.87 14.87 43.62 2.59
3108 3721 5.997384 GGAGTACTCCCTCTGTAAAGAAA 57.003 43.478 28.87 0.00 43.94 2.52
3109 3722 6.547930 GGAGTACTCCCTCTGTAAAGAAAT 57.452 41.667 28.87 0.00 43.94 2.17
3110 3723 7.657023 GGAGTACTCCCTCTGTAAAGAAATA 57.343 40.000 28.87 0.00 43.94 1.40
3111 3724 8.252624 GGAGTACTCCCTCTGTAAAGAAATAT 57.747 38.462 28.87 0.00 43.94 1.28
3112 3725 9.364653 GGAGTACTCCCTCTGTAAAGAAATATA 57.635 37.037 28.87 0.00 43.94 0.86
3114 3727 8.848182 AGTACTCCCTCTGTAAAGAAATATACG 58.152 37.037 0.00 0.00 0.00 3.06
3115 3728 7.893124 ACTCCCTCTGTAAAGAAATATACGA 57.107 36.000 0.00 0.00 0.00 3.43
3266 4039 1.018148 TTTGTCACAACGCGGAACAT 58.982 45.000 12.47 0.00 0.00 2.71
3267 4040 1.867166 TTGTCACAACGCGGAACATA 58.133 45.000 12.47 0.00 0.00 2.29
3268 4041 1.867166 TGTCACAACGCGGAACATAA 58.133 45.000 12.47 0.00 0.00 1.90
3269 4042 1.527736 TGTCACAACGCGGAACATAAC 59.472 47.619 12.47 0.00 0.00 1.89
3270 4043 1.136169 GTCACAACGCGGAACATAACC 60.136 52.381 12.47 0.00 0.00 2.85
3271 4044 1.153353 CACAACGCGGAACATAACCT 58.847 50.000 12.47 0.00 0.00 3.50
3272 4045 1.533731 CACAACGCGGAACATAACCTT 59.466 47.619 12.47 0.00 0.00 3.50
3273 4046 2.031508 CACAACGCGGAACATAACCTTT 60.032 45.455 12.47 0.00 0.00 3.11
3274 4047 2.619646 ACAACGCGGAACATAACCTTTT 59.380 40.909 12.47 0.00 0.00 2.27
3275 4048 3.231160 CAACGCGGAACATAACCTTTTC 58.769 45.455 12.47 0.00 0.00 2.29
3276 4049 2.774687 ACGCGGAACATAACCTTTTCT 58.225 42.857 12.47 0.00 0.00 2.52
3277 4050 3.143728 ACGCGGAACATAACCTTTTCTT 58.856 40.909 12.47 0.00 0.00 2.52
3278 4051 3.566742 ACGCGGAACATAACCTTTTCTTT 59.433 39.130 12.47 0.00 0.00 2.52
3279 4052 4.037089 ACGCGGAACATAACCTTTTCTTTT 59.963 37.500 12.47 0.00 0.00 2.27
3280 4053 5.239087 ACGCGGAACATAACCTTTTCTTTTA 59.761 36.000 12.47 0.00 0.00 1.52
3281 4054 5.793457 CGCGGAACATAACCTTTTCTTTTAG 59.207 40.000 0.00 0.00 0.00 1.85
3282 4055 5.571741 GCGGAACATAACCTTTTCTTTTAGC 59.428 40.000 0.00 0.00 0.00 3.09
3283 4056 6.569801 GCGGAACATAACCTTTTCTTTTAGCT 60.570 38.462 0.00 0.00 0.00 3.32
3284 4057 7.361457 GCGGAACATAACCTTTTCTTTTAGCTA 60.361 37.037 0.00 0.00 0.00 3.32
3285 4058 7.961283 CGGAACATAACCTTTTCTTTTAGCTAC 59.039 37.037 0.00 0.00 0.00 3.58
3286 4059 8.242053 GGAACATAACCTTTTCTTTTAGCTACC 58.758 37.037 0.00 0.00 0.00 3.18
3293 4066 2.218953 TCTTTTAGCTACCCGATGCG 57.781 50.000 0.00 0.00 0.00 4.73
3496 4270 1.796617 GCACGCCAAAGATCAGCAATC 60.797 52.381 0.00 0.00 34.30 2.67
3512 4286 7.080353 TCAGCAATCACATGAAGTTAAGATG 57.920 36.000 0.00 0.00 0.00 2.90
3513 4287 6.880529 TCAGCAATCACATGAAGTTAAGATGA 59.119 34.615 0.00 0.00 0.00 2.92
3520 4294 9.684448 ATCACATGAAGTTAAGATGATACTACG 57.316 33.333 0.00 0.00 0.00 3.51
3591 4365 2.758736 AGTAGAAAGTGCTGCTCTGG 57.241 50.000 4.83 0.00 0.00 3.86
3628 4402 0.988832 AATTCAGTGGCCTTACCCGA 59.011 50.000 3.32 0.00 37.83 5.14
3716 4490 6.861065 ACAGAACACTGAAAATACGACATT 57.139 33.333 0.00 0.00 35.80 2.71
3739 6839 0.395311 CCAGCCTCAGGAATGCACAT 60.395 55.000 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 3.077695 TCTCTCTTCCAGTAAGGGGTTCT 59.922 47.826 0.00 0.00 36.22 3.01
28 29 3.442076 TCTCTCTTCCAGTAAGGGGTTC 58.558 50.000 0.00 0.00 36.22 3.62
29 30 3.562108 TCTCTCTTCCAGTAAGGGGTT 57.438 47.619 0.00 0.00 36.22 4.11
31 32 3.379452 ACATCTCTCTTCCAGTAAGGGG 58.621 50.000 0.00 0.00 36.22 4.79
54 55 7.602517 ATGCTCAAGATAGAGTTAAACACAC 57.397 36.000 0.00 0.00 37.94 3.82
99 100 9.400638 CCGAGCAAACAAGTTTACATTATTAAA 57.599 29.630 0.00 0.00 0.00 1.52
100 101 8.569641 ACCGAGCAAACAAGTTTACATTATTAA 58.430 29.630 0.00 0.00 0.00 1.40
104 105 7.675962 ATACCGAGCAAACAAGTTTACATTA 57.324 32.000 0.00 0.00 0.00 1.90
105 106 4.911514 ACCGAGCAAACAAGTTTACATT 57.088 36.364 0.00 0.00 0.00 2.71
106 107 6.315393 CCTATACCGAGCAAACAAGTTTACAT 59.685 38.462 0.00 0.00 0.00 2.29
108 109 5.640783 ACCTATACCGAGCAAACAAGTTTAC 59.359 40.000 0.00 0.00 0.00 2.01
109 110 5.640357 CACCTATACCGAGCAAACAAGTTTA 59.360 40.000 0.00 0.00 0.00 2.01
110 111 4.454504 CACCTATACCGAGCAAACAAGTTT 59.545 41.667 0.00 0.00 0.00 2.66
111 112 4.000988 CACCTATACCGAGCAAACAAGTT 58.999 43.478 0.00 0.00 0.00 2.66
112 113 3.007614 ACACCTATACCGAGCAAACAAGT 59.992 43.478 0.00 0.00 0.00 3.16
113 114 3.596214 ACACCTATACCGAGCAAACAAG 58.404 45.455 0.00 0.00 0.00 3.16
121 122 5.054477 CCCACAATAAACACCTATACCGAG 58.946 45.833 0.00 0.00 0.00 4.63
122 123 4.141665 CCCCACAATAAACACCTATACCGA 60.142 45.833 0.00 0.00 0.00 4.69
149 150 1.607251 CGCCTGGTAACCGAGTTTCTT 60.607 52.381 0.00 0.00 0.00 2.52
203 204 3.997021 GGTACATTCTTCATAGATGGCCG 59.003 47.826 0.00 0.00 0.00 6.13
223 224 6.238374 CGTGTGAAGTTATGACAAAGAAAGGT 60.238 38.462 0.00 0.00 0.00 3.50
262 263 3.944015 CTCTTGGCCCTTCTAGAACAATG 59.056 47.826 0.00 0.00 0.00 2.82
305 306 5.837438 TGTAATCCCTTTTAACCCCGAAAAA 59.163 36.000 0.00 0.00 0.00 1.94
306 307 5.392125 TGTAATCCCTTTTAACCCCGAAAA 58.608 37.500 0.00 0.00 0.00 2.29
307 308 4.995536 TGTAATCCCTTTTAACCCCGAAA 58.004 39.130 0.00 0.00 0.00 3.46
308 309 4.654389 TGTAATCCCTTTTAACCCCGAA 57.346 40.909 0.00 0.00 0.00 4.30
309 310 4.866327 ATGTAATCCCTTTTAACCCCGA 57.134 40.909 0.00 0.00 0.00 5.14
314 315 7.556635 ACCTTGAGCTATGTAATCCCTTTTAAC 59.443 37.037 0.00 0.00 0.00 2.01
327 328 3.327757 TGTTTCTCCACCTTGAGCTATGT 59.672 43.478 0.00 0.00 32.22 2.29
350 351 2.540383 ACCTGCACTCTGTATGGAAGA 58.460 47.619 0.00 0.00 0.00 2.87
368 369 4.072839 GGATTAGGCCTTGCTAATGTACC 58.927 47.826 12.58 0.00 0.00 3.34
369 370 3.746492 CGGATTAGGCCTTGCTAATGTAC 59.254 47.826 12.58 0.00 0.00 2.90
380 381 1.122019 ATTCGGCTCGGATTAGGCCT 61.122 55.000 11.78 11.78 43.29 5.19
386 387 0.466189 ATGGCAATTCGGCTCGGATT 60.466 50.000 0.00 0.00 41.89 3.01
387 388 0.466189 AATGGCAATTCGGCTCGGAT 60.466 50.000 0.00 0.00 41.89 4.18
389 390 1.097547 AGAATGGCAATTCGGCTCGG 61.098 55.000 8.20 0.00 45.84 4.63
391 392 1.800286 GCAAGAATGGCAATTCGGCTC 60.800 52.381 20.02 5.00 45.84 4.70
396 397 5.573337 AGTAGAAGCAAGAATGGCAATTC 57.427 39.130 5.61 5.61 37.68 2.17
404 405 5.392767 TTCAGTCGAGTAGAAGCAAGAAT 57.607 39.130 0.00 0.00 0.00 2.40
423 424 6.102663 GTCAGTCATAGCTTAGCTTCTTTCA 58.897 40.000 13.44 0.00 40.44 2.69
494 495 4.828829 ACCACAGGACGGATTAAAACTAG 58.171 43.478 0.00 0.00 0.00 2.57
502 503 2.264794 GCGACCACAGGACGGATT 59.735 61.111 9.66 0.00 40.76 3.01
506 507 2.430921 GTCAGCGACCACAGGACG 60.431 66.667 3.64 3.64 43.00 4.79
509 510 0.603707 ACATTGTCAGCGACCACAGG 60.604 55.000 6.30 0.00 0.00 4.00
510 511 2.078849 TACATTGTCAGCGACCACAG 57.921 50.000 0.00 0.00 0.00 3.66
586 614 7.218228 TCTATTTGCACAATTCTCACAATGT 57.782 32.000 0.00 0.00 0.00 2.71
587 615 8.523523 TTTCTATTTGCACAATTCTCACAATG 57.476 30.769 0.00 0.00 0.00 2.82
588 616 9.199982 CTTTTCTATTTGCACAATTCTCACAAT 57.800 29.630 0.00 0.00 0.00 2.71
589 617 8.412456 TCTTTTCTATTTGCACAATTCTCACAA 58.588 29.630 0.00 0.00 0.00 3.33
590 618 7.939782 TCTTTTCTATTTGCACAATTCTCACA 58.060 30.769 0.00 0.00 0.00 3.58
591 619 8.801715 TTCTTTTCTATTTGCACAATTCTCAC 57.198 30.769 0.00 0.00 0.00 3.51
634 662 8.156165 TGACAGCCATCCAATTAAAATCTTTTT 58.844 29.630 0.00 0.00 0.00 1.94
636 664 7.243604 TGACAGCCATCCAATTAAAATCTTT 57.756 32.000 0.00 0.00 0.00 2.52
649 677 5.299949 ACAAAAGAAAAATGACAGCCATCC 58.700 37.500 0.00 0.00 33.53 3.51
668 696 5.373222 TCAATCTCCTCTCCGAAAAACAAA 58.627 37.500 0.00 0.00 0.00 2.83
669 697 4.968259 TCAATCTCCTCTCCGAAAAACAA 58.032 39.130 0.00 0.00 0.00 2.83
671 699 5.334957 GGTTTCAATCTCCTCTCCGAAAAAC 60.335 44.000 0.00 0.00 0.00 2.43
719 747 0.385974 GTTGCACAGATGACAACCGC 60.386 55.000 10.40 0.00 37.11 5.68
726 754 7.065085 GCTAAGAAAAGATAGTTGCACAGATGA 59.935 37.037 0.00 0.00 0.00 2.92
735 763 7.965107 GTGATGTTGGCTAAGAAAAGATAGTTG 59.035 37.037 0.00 0.00 0.00 3.16
741 769 4.079253 GGGTGATGTTGGCTAAGAAAAGA 58.921 43.478 0.00 0.00 0.00 2.52
752 780 2.411628 TATTCACGGGGTGATGTTGG 57.588 50.000 0.00 0.00 42.40 3.77
754 782 3.713826 ACTTATTCACGGGGTGATGTT 57.286 42.857 0.00 0.00 42.40 2.71
866 895 9.095065 TCGTTCCTCTATATGCTTTACTTTTTC 57.905 33.333 0.00 0.00 0.00 2.29
921 969 1.682344 GTTCCCCCATTCCAGTGCC 60.682 63.158 0.00 0.00 0.00 5.01
982 1056 2.306805 GTGGGATGGATGGATATGCAGA 59.693 50.000 2.55 0.00 38.08 4.26
1009 1083 4.398358 CAGACTATTCGTACTGGTTCAGGA 59.602 45.833 0.00 0.00 35.51 3.86
1017 1091 2.165641 TGGGTGCAGACTATTCGTACTG 59.834 50.000 0.00 0.00 0.00 2.74
1187 1269 1.376553 GCAGAGGTTGGAGAGGCAC 60.377 63.158 0.00 0.00 0.00 5.01
1241 1323 0.676466 CATGGCAGGCGTCAACCTTA 60.676 55.000 0.00 0.00 38.26 2.69
1359 1462 3.713826 AGGTCAAGAAATCGGGCTAAA 57.286 42.857 0.00 0.00 0.00 1.85
1416 1532 2.609747 ACCTGAGCCTGAGAACACTAA 58.390 47.619 0.00 0.00 0.00 2.24
1421 1537 3.196685 AGATTGTACCTGAGCCTGAGAAC 59.803 47.826 0.00 0.00 0.00 3.01
1464 1585 3.589654 TTCGGCTGGCTCTTGACGG 62.590 63.158 0.00 0.00 0.00 4.79
1473 1594 2.747855 CCTTCAGGTTCGGCTGGC 60.748 66.667 0.00 0.00 0.00 4.85
1567 1688 0.319211 TGCACCTCACGAACTTACCG 60.319 55.000 0.00 0.00 0.00 4.02
1742 2011 7.100409 ACTAGAGTAGAGAAAATGCTTCAACC 58.900 38.462 0.00 0.00 0.00 3.77
1812 2408 0.322975 GACAGAGAGGCCTTCAGCAA 59.677 55.000 6.77 0.00 46.50 3.91
1823 2419 1.664873 TGGTATCCGACGACAGAGAG 58.335 55.000 0.00 0.00 0.00 3.20
1899 2495 2.086869 CTGGTTGATGCTCGGTTTCAT 58.913 47.619 0.00 0.00 0.00 2.57
1927 2523 3.003482 CGGGTCTTCATAGAGAGTTACCG 59.997 52.174 0.00 0.00 0.00 4.02
1928 2524 3.318557 CCGGGTCTTCATAGAGAGTTACC 59.681 52.174 0.00 0.00 0.00 2.85
1936 2532 2.544844 AGTTCCCGGGTCTTCATAGA 57.455 50.000 22.86 0.00 0.00 1.98
1938 2534 2.542550 TGAAGTTCCCGGGTCTTCATA 58.457 47.619 35.91 25.02 41.33 2.15
1953 2555 6.302269 ACTTGGTCTTGAATTCTGATGAAGT 58.698 36.000 7.05 12.43 35.44 3.01
1982 2584 1.250328 TCTTCTCCTTGGCGTCGTAA 58.750 50.000 0.00 0.00 0.00 3.18
2432 3038 0.762418 TGTCCATCTCCACCACGTTT 59.238 50.000 0.00 0.00 0.00 3.60
2488 3094 8.985315 TGGTCTGCATAAATCTGAAATTCTAT 57.015 30.769 0.00 0.00 0.00 1.98
2530 3139 2.849502 GCAAGACAACGAAACCTCAACG 60.850 50.000 0.00 0.00 0.00 4.10
2678 3287 2.093973 ACCAGGACTTACTGATCAAGCG 60.094 50.000 0.00 0.00 40.97 4.68
2707 3316 8.364142 CCTGGTCATATTAAACAGAACCAAAAA 58.636 33.333 2.11 0.00 0.00 1.94
2782 3391 2.750948 TCAGACACCAACTAAGTTCGC 58.249 47.619 0.00 0.00 0.00 4.70
2784 3393 4.515191 TGCATTCAGACACCAACTAAGTTC 59.485 41.667 0.00 0.00 0.00 3.01
2791 3400 2.163010 CCTCATGCATTCAGACACCAAC 59.837 50.000 0.00 0.00 0.00 3.77
2933 3546 4.952335 CCCTTAATTTTCTCTCATGGCTGT 59.048 41.667 0.00 0.00 0.00 4.40
2950 3563 1.461849 ACGGACCACACCCCCTTAA 60.462 57.895 0.00 0.00 0.00 1.85
2971 3584 4.331168 CCAAAATTTGTTTTGCACTTCCGA 59.669 37.500 4.92 0.00 39.80 4.55
2972 3585 4.094146 ACCAAAATTTGTTTTGCACTTCCG 59.906 37.500 4.92 0.00 39.80 4.30
2973 3586 5.123027 TGACCAAAATTTGTTTTGCACTTCC 59.877 36.000 4.92 0.00 39.80 3.46
2974 3587 6.175712 TGACCAAAATTTGTTTTGCACTTC 57.824 33.333 4.92 3.38 39.80 3.01
2975 3588 6.566197 TTGACCAAAATTTGTTTTGCACTT 57.434 29.167 4.92 0.00 39.80 3.16
2976 3589 6.566197 TTTGACCAAAATTTGTTTTGCACT 57.434 29.167 4.92 0.00 39.80 4.40
2977 3590 6.638468 TGTTTTGACCAAAATTTGTTTTGCAC 59.362 30.769 10.61 5.27 41.64 4.57
2978 3591 6.638468 GTGTTTTGACCAAAATTTGTTTTGCA 59.362 30.769 10.61 0.00 41.64 4.08
2979 3592 6.638468 TGTGTTTTGACCAAAATTTGTTTTGC 59.362 30.769 10.61 0.00 41.64 3.68
2980 3593 8.566008 TTGTGTTTTGACCAAAATTTGTTTTG 57.434 26.923 10.61 6.65 41.64 2.44
2981 3594 9.404348 GATTGTGTTTTGACCAAAATTTGTTTT 57.596 25.926 10.61 0.00 41.64 2.43
2982 3595 7.748241 CGATTGTGTTTTGACCAAAATTTGTTT 59.252 29.630 10.61 0.00 41.64 2.83
2983 3596 7.095017 ACGATTGTGTTTTGACCAAAATTTGTT 60.095 29.630 10.61 0.00 41.64 2.83
2984 3597 6.370166 ACGATTGTGTTTTGACCAAAATTTGT 59.630 30.769 10.61 0.00 41.64 2.83
2985 3598 6.770076 ACGATTGTGTTTTGACCAAAATTTG 58.230 32.000 10.61 0.00 41.64 2.32
2986 3599 6.976636 ACGATTGTGTTTTGACCAAAATTT 57.023 29.167 10.61 0.00 41.64 1.82
2987 3600 6.591834 TGAACGATTGTGTTTTGACCAAAATT 59.408 30.769 10.61 0.04 41.64 1.82
2988 3601 6.035542 GTGAACGATTGTGTTTTGACCAAAAT 59.964 34.615 10.61 0.00 41.64 1.82
2989 3602 5.346281 GTGAACGATTGTGTTTTGACCAAAA 59.654 36.000 4.00 4.00 37.90 2.44
2990 3603 4.859798 GTGAACGATTGTGTTTTGACCAAA 59.140 37.500 0.00 0.00 30.75 3.28
2991 3604 4.156922 AGTGAACGATTGTGTTTTGACCAA 59.843 37.500 0.00 0.00 30.75 3.67
2992 3605 3.692101 AGTGAACGATTGTGTTTTGACCA 59.308 39.130 0.00 0.00 30.75 4.02
2993 3606 4.279659 GAGTGAACGATTGTGTTTTGACC 58.720 43.478 0.00 0.00 30.75 4.02
2994 3607 3.960002 CGAGTGAACGATTGTGTTTTGAC 59.040 43.478 0.00 0.00 35.09 3.18
2995 3608 3.619483 ACGAGTGAACGATTGTGTTTTGA 59.381 39.130 0.00 0.00 37.03 2.69
2996 3609 3.935450 ACGAGTGAACGATTGTGTTTTG 58.065 40.909 0.00 0.00 37.03 2.44
2997 3610 4.609691 AACGAGTGAACGATTGTGTTTT 57.390 36.364 0.00 0.00 37.03 2.43
2998 3611 5.045215 TCTAACGAGTGAACGATTGTGTTT 58.955 37.500 0.00 0.00 37.03 2.83
2999 3612 4.443394 GTCTAACGAGTGAACGATTGTGTT 59.557 41.667 0.00 0.00 37.03 3.32
3000 3613 3.979495 GTCTAACGAGTGAACGATTGTGT 59.021 43.478 0.00 0.00 37.03 3.72
3001 3614 3.978855 TGTCTAACGAGTGAACGATTGTG 59.021 43.478 0.00 0.00 37.03 3.33
3002 3615 3.979495 GTGTCTAACGAGTGAACGATTGT 59.021 43.478 0.00 0.00 37.03 2.71
3003 3616 3.364023 GGTGTCTAACGAGTGAACGATTG 59.636 47.826 0.00 0.00 37.03 2.67
3004 3617 3.005050 TGGTGTCTAACGAGTGAACGATT 59.995 43.478 0.00 0.00 37.03 3.34
3005 3618 2.555325 TGGTGTCTAACGAGTGAACGAT 59.445 45.455 0.00 0.00 37.03 3.73
3006 3619 1.948834 TGGTGTCTAACGAGTGAACGA 59.051 47.619 0.00 0.00 37.03 3.85
3007 3620 2.049228 GTGGTGTCTAACGAGTGAACG 58.951 52.381 0.00 0.00 39.31 3.95
3008 3621 2.035576 AGGTGGTGTCTAACGAGTGAAC 59.964 50.000 0.00 0.00 0.00 3.18
3009 3622 2.313317 AGGTGGTGTCTAACGAGTGAA 58.687 47.619 0.00 0.00 0.00 3.18
3010 3623 1.991121 AGGTGGTGTCTAACGAGTGA 58.009 50.000 0.00 0.00 0.00 3.41
3011 3624 3.367087 CCTTAGGTGGTGTCTAACGAGTG 60.367 52.174 0.00 0.00 0.00 3.51
3012 3625 2.824341 CCTTAGGTGGTGTCTAACGAGT 59.176 50.000 0.00 0.00 0.00 4.18
3013 3626 2.165845 CCCTTAGGTGGTGTCTAACGAG 59.834 54.545 0.00 0.00 0.00 4.18
3014 3627 2.173519 CCCTTAGGTGGTGTCTAACGA 58.826 52.381 0.00 0.00 0.00 3.85
3015 3628 2.173519 TCCCTTAGGTGGTGTCTAACG 58.826 52.381 0.00 0.00 0.00 3.18
3016 3629 3.055312 CCTTCCCTTAGGTGGTGTCTAAC 60.055 52.174 0.00 0.00 0.00 2.34
3017 3630 3.178865 CCTTCCCTTAGGTGGTGTCTAA 58.821 50.000 0.00 0.00 0.00 2.10
3018 3631 2.384375 TCCTTCCCTTAGGTGGTGTCTA 59.616 50.000 0.00 0.00 36.63 2.59
3019 3632 1.151413 TCCTTCCCTTAGGTGGTGTCT 59.849 52.381 0.00 0.00 36.63 3.41
3020 3633 1.652947 TCCTTCCCTTAGGTGGTGTC 58.347 55.000 0.00 0.00 36.63 3.67
3021 3634 2.308866 CAATCCTTCCCTTAGGTGGTGT 59.691 50.000 0.00 0.00 36.63 4.16
3022 3635 2.308866 ACAATCCTTCCCTTAGGTGGTG 59.691 50.000 0.00 0.00 36.63 4.17
3023 3636 2.644151 ACAATCCTTCCCTTAGGTGGT 58.356 47.619 0.00 0.00 36.63 4.16
3024 3637 3.621558 GAACAATCCTTCCCTTAGGTGG 58.378 50.000 0.00 0.00 36.63 4.61
3025 3638 3.621558 GGAACAATCCTTCCCTTAGGTG 58.378 50.000 0.00 0.00 42.93 4.00
3033 3646 1.852633 CCCAAGGGAACAATCCTTCC 58.147 55.000 0.00 0.00 45.77 3.46
3052 3665 0.327191 TCATACCAGGGAGGGGTTCC 60.327 60.000 0.00 0.00 46.00 3.62
3053 3666 0.837940 GTCATACCAGGGAGGGGTTC 59.162 60.000 0.00 0.00 43.89 3.62
3054 3667 0.981277 CGTCATACCAGGGAGGGGTT 60.981 60.000 0.00 0.00 43.89 4.11
3055 3668 1.382695 CGTCATACCAGGGAGGGGT 60.383 63.158 0.00 0.00 43.89 4.95
3056 3669 0.105862 TACGTCATACCAGGGAGGGG 60.106 60.000 0.00 0.00 43.89 4.79
3057 3670 1.038280 GTACGTCATACCAGGGAGGG 58.962 60.000 0.00 0.00 43.89 4.30
3088 3701 8.848182 CGTATATTTCTTTACAGAGGGAGTACT 58.152 37.037 0.00 0.00 0.00 2.73
3089 3702 8.844244 TCGTATATTTCTTTACAGAGGGAGTAC 58.156 37.037 0.00 0.00 0.00 2.73
3090 3703 8.985315 TCGTATATTTCTTTACAGAGGGAGTA 57.015 34.615 0.00 0.00 0.00 2.59
3091 3704 7.893124 TCGTATATTTCTTTACAGAGGGAGT 57.107 36.000 0.00 0.00 0.00 3.85
3092 3705 8.798402 AGATCGTATATTTCTTTACAGAGGGAG 58.202 37.037 0.00 0.00 0.00 4.30
3093 3706 8.707796 AGATCGTATATTTCTTTACAGAGGGA 57.292 34.615 0.00 0.00 0.00 4.20
3266 4039 6.112927 TCGGGTAGCTAAAAGAAAAGGTTA 57.887 37.500 0.00 0.00 0.00 2.85
3267 4040 4.976864 TCGGGTAGCTAAAAGAAAAGGTT 58.023 39.130 0.00 0.00 0.00 3.50
3268 4041 4.628963 TCGGGTAGCTAAAAGAAAAGGT 57.371 40.909 0.00 0.00 0.00 3.50
3269 4042 4.201920 GCATCGGGTAGCTAAAAGAAAAGG 60.202 45.833 0.00 0.00 0.00 3.11
3270 4043 4.494199 CGCATCGGGTAGCTAAAAGAAAAG 60.494 45.833 0.00 0.00 0.00 2.27
3271 4044 3.372822 CGCATCGGGTAGCTAAAAGAAAA 59.627 43.478 0.00 0.00 0.00 2.29
3272 4045 2.933906 CGCATCGGGTAGCTAAAAGAAA 59.066 45.455 0.00 0.00 0.00 2.52
3273 4046 2.546778 CGCATCGGGTAGCTAAAAGAA 58.453 47.619 0.00 0.00 0.00 2.52
3274 4047 1.202486 CCGCATCGGGTAGCTAAAAGA 60.202 52.381 0.00 0.00 44.15 2.52
3275 4048 1.217882 CCGCATCGGGTAGCTAAAAG 58.782 55.000 0.00 0.00 44.15 2.27
3276 4049 3.372795 CCGCATCGGGTAGCTAAAA 57.627 52.632 0.00 0.00 44.15 1.52
3286 4059 3.314045 ACATACACATGTTCCGCATCGG 61.314 50.000 0.00 0.00 42.98 4.18
3293 4066 4.393062 CCTGAAGACACATACACATGTTCC 59.607 45.833 0.00 0.00 42.98 3.62
3345 4119 5.352284 AGGAGATTAAATCACTGTACGCTG 58.648 41.667 0.00 0.00 0.00 5.18
3496 4270 9.684448 ATCGTAGTATCATCTTAACTTCATGTG 57.316 33.333 0.00 0.00 0.00 3.21
3512 4286 9.459640 TGTGCTATTTTACAGAATCGTAGTATC 57.540 33.333 0.00 0.00 0.00 2.24
3513 4287 9.982651 ATGTGCTATTTTACAGAATCGTAGTAT 57.017 29.630 0.00 0.00 0.00 2.12
3628 4402 1.608590 CAGTCTTTCACCGGCAAACAT 59.391 47.619 0.00 0.00 0.00 2.71
3716 4490 0.322816 GCATTCCTGAGGCTGGTGAA 60.323 55.000 0.00 0.00 0.00 3.18
3739 6839 3.466836 CCAGCTGATTACGCTTATCCAA 58.533 45.455 17.39 0.00 35.07 3.53


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

AutoCloner maintained by Alex Coulton.