Multiple sequence alignment - TraesCS2A01G375900

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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 TraesCS2A01G375900 chr2A 100.000 4820 0 0 1 4820 618118565 618113746 0.000000e+00 8901.0
1 TraesCS2A01G375900 chr2D 93.865 3162 169 18 826 3977 476278420 476275274 0.000000e+00 4741.0
2 TraesCS2A01G375900 chr2D 90.313 702 62 4 1 696 476280500 476279799 0.000000e+00 915.0
3 TraesCS2A01G375900 chr2D 85.349 587 64 14 4244 4819 476261693 476261118 5.370000e-164 588.0
4 TraesCS2A01G375900 chr2D 84.722 432 44 14 4195 4622 476275071 476274658 3.470000e-111 412.0
5 TraesCS2A01G375900 chr2D 81.841 391 53 13 4087 4466 7456203 7455820 3.620000e-81 313.0
6 TraesCS2A01G375900 chr2D 88.043 184 22 0 4635 4818 476262092 476261909 8.120000e-53 219.0
7 TraesCS2A01G375900 chr2D 90.909 66 5 1 765 829 476279480 476279415 2.390000e-13 87.9
8 TraesCS2A01G375900 chr2B 94.163 3015 147 20 815 3820 557046962 557043968 0.000000e+00 4566.0
9 TraesCS2A01G375900 chr2B 84.356 505 57 12 185 682 557104601 557104112 4.370000e-130 475.0
10 TraesCS2A01G375900 chr2B 93.333 105 6 1 3821 3925 557043895 557043792 2.320000e-33 154.0
11 TraesCS2A01G375900 chr5A 81.106 434 60 19 4117 4537 316097411 316096987 1.290000e-85 327.0
12 TraesCS2A01G375900 chr7B 82.895 380 47 16 4087 4451 674079357 674078981 4.650000e-85 326.0
13 TraesCS2A01G375900 chr1D 83.288 365 45 14 4087 4441 345710461 345710819 6.020000e-84 322.0
14 TraesCS2A01G375900 chr6D 81.633 392 53 14 4087 4465 13923912 13923527 1.690000e-79 307.0
15 TraesCS2A01G375900 chr6B 82.011 378 45 18 4087 4447 30127919 30128290 2.820000e-77 300.0
16 TraesCS2A01G375900 chr5D 79.814 431 61 17 4117 4534 543615121 543615538 1.700000e-74 291.0
17 TraesCS2A01G375900 chr3D 81.944 360 49 14 4117 4467 460450305 460450657 1.700000e-74 291.0
18 TraesCS2A01G375900 chr7A 84.884 172 21 3 4528 4696 652543769 652543938 8.300000e-38 169.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G375900 chr2A 618113746 618118565 4819 True 8901.000 8901 100.00000 1 4820 1 chr2A.!!$R1 4819
1 TraesCS2A01G375900 chr2D 476274658 476280500 5842 True 1538.975 4741 89.95225 1 4622 4 chr2D.!!$R3 4621
2 TraesCS2A01G375900 chr2D 476261118 476262092 974 True 403.500 588 86.69600 4244 4819 2 chr2D.!!$R2 575
3 TraesCS2A01G375900 chr2B 557043792 557046962 3170 True 2360.000 4566 93.74800 815 3925 2 chr2B.!!$R2 3110

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
510 516 0.037160 TTTTCCCCGTCTTGCTACCC 59.963 55.0 0.0 0.0 0.0 3.69 F
1092 2397 0.179134 CCCTCTACACGGCTTCTTCG 60.179 60.0 0.0 0.0 0.0 3.79 F
1509 2814 0.730840 CCAATTCGTTCCGGTTAGCC 59.269 55.0 0.0 0.0 0.0 3.93 F
1670 2975 1.043673 AGGCCGACTCACTATGACCC 61.044 60.0 0.0 0.0 0.0 4.46 F
3203 4519 0.258774 ACCCAGATGCAATACCACCC 59.741 55.0 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1850 3156 0.178801 AGAAGGGGTGGGGAAAGGAT 60.179 55.0 0.00 0.0 0.00 3.24 R
2520 3831 0.109132 GAAAGGAAACCTGCGCCATG 60.109 55.0 4.18 0.0 32.13 3.66 R
2525 3836 0.517316 CCGAAGAAAGGAAACCTGCG 59.483 55.0 0.00 0.0 32.13 5.18 R
3603 4920 0.031857 TGCCCAAACTTGCATCAACG 59.968 50.0 0.00 0.0 31.31 4.10 R
4597 6013 0.030908 GGTGATCGTCGGAGGACATC 59.969 60.0 2.02 0.0 43.61 3.06 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 1.004745 TCTTCTCTTTGTCCCATGCCC 59.995 52.381 0.00 0.00 0.00 5.36
63 64 4.493547 TCAACTTTTCTTGTGCAAAGTGG 58.506 39.130 0.16 0.00 41.42 4.00
68 69 5.539955 ACTTTTCTTGTGCAAAGTGGGATAT 59.460 36.000 0.00 0.00 40.87 1.63
72 73 5.263599 TCTTGTGCAAAGTGGGATATTCAT 58.736 37.500 0.00 0.00 0.00 2.57
78 79 7.040478 TGTGCAAAGTGGGATATTCATAATAGC 60.040 37.037 0.00 0.00 0.00 2.97
79 80 7.003482 TGCAAAGTGGGATATTCATAATAGCA 58.997 34.615 0.00 0.00 31.54 3.49
80 81 7.670979 TGCAAAGTGGGATATTCATAATAGCAT 59.329 33.333 0.00 0.00 31.54 3.79
81 82 8.526147 GCAAAGTGGGATATTCATAATAGCATT 58.474 33.333 0.00 0.00 31.54 3.56
128 134 3.750371 TGAACCACTTCTACACATTGGG 58.250 45.455 0.00 0.00 0.00 4.12
130 136 2.344592 ACCACTTCTACACATTGGGGA 58.655 47.619 0.00 0.00 0.00 4.81
133 139 1.916181 ACTTCTACACATTGGGGAGGG 59.084 52.381 0.00 0.00 0.00 4.30
211 217 1.021202 TTGTGCGCCCATATGTTAGC 58.979 50.000 4.18 4.45 0.00 3.09
236 242 5.701290 AGTTTCTTTTGTACGAATCCTCCTG 59.299 40.000 0.00 0.00 0.00 3.86
285 291 3.425577 GCCAAATCTGCGATGAATGAA 57.574 42.857 0.00 0.00 0.00 2.57
294 300 5.245531 TCTGCGATGAATGAAAACCTAACT 58.754 37.500 0.00 0.00 0.00 2.24
328 334 2.622470 GAGACCTCTCCGGGTAATACAC 59.378 54.545 0.00 0.00 40.06 2.90
358 364 3.950395 AGAATTCTTGCACTTAGGGATGC 59.050 43.478 0.88 0.00 42.40 3.91
359 365 3.659183 ATTCTTGCACTTAGGGATGCT 57.341 42.857 0.00 0.00 42.55 3.79
361 367 3.543680 TCTTGCACTTAGGGATGCTAC 57.456 47.619 0.00 0.00 42.55 3.58
396 402 1.662044 CAAGTCCTGCCTTGCCAAC 59.338 57.895 0.00 0.00 35.80 3.77
398 404 0.396974 AAGTCCTGCCTTGCCAACAA 60.397 50.000 0.00 0.00 0.00 2.83
407 413 3.894427 TGCCTTGCCAACAAAGAAAGATA 59.106 39.130 0.00 0.00 34.74 1.98
451 457 5.828299 TCCAAGACCGCCTAAATATTTTG 57.172 39.130 5.91 4.28 0.00 2.44
469 475 0.994247 TGGCCAAGTCATCACATCCT 59.006 50.000 0.61 0.00 0.00 3.24
472 478 2.092968 GGCCAAGTCATCACATCCTACA 60.093 50.000 0.00 0.00 0.00 2.74
486 492 2.799017 TCCTACAAGACCTAGCACGAA 58.201 47.619 0.00 0.00 0.00 3.85
491 497 2.567615 ACAAGACCTAGCACGAATTCCT 59.432 45.455 0.00 0.00 0.00 3.36
495 501 4.254492 AGACCTAGCACGAATTCCTTTTC 58.746 43.478 0.00 0.00 0.00 2.29
499 505 0.170339 GCACGAATTCCTTTTCCCCG 59.830 55.000 0.00 0.00 0.00 5.73
508 514 1.002773 TCCTTTTCCCCGTCTTGCTAC 59.997 52.381 0.00 0.00 0.00 3.58
510 516 0.037160 TTTTCCCCGTCTTGCTACCC 59.963 55.000 0.00 0.00 0.00 3.69
565 572 4.270325 GTCACATAAACCTCTCGGCAATAC 59.730 45.833 0.00 0.00 0.00 1.89
576 583 1.643868 CGGCAATACGAAGCAAGCCA 61.644 55.000 0.00 0.00 42.10 4.75
577 584 0.179163 GGCAATACGAAGCAAGCCAC 60.179 55.000 0.00 0.00 41.63 5.01
595 602 3.181485 GCCACTGAGTACACTAGGATGAC 60.181 52.174 0.00 0.00 0.00 3.06
603 610 3.257469 ACACTAGGATGACATGTGCAG 57.743 47.619 1.15 0.00 32.49 4.41
606 613 2.158986 ACTAGGATGACATGTGCAGCTC 60.159 50.000 1.15 0.00 0.00 4.09
631 638 2.305009 GATGAGCATTTCCTTCCCTGG 58.695 52.381 0.00 0.00 0.00 4.45
649 656 4.017126 CCTGGTAAAAGTTTCTCCATCCC 58.983 47.826 10.71 0.00 0.00 3.85
654 661 3.884037 AAAGTTTCTCCATCCCACACT 57.116 42.857 0.00 0.00 0.00 3.55
674 681 4.637534 CACTTTACCATCTCCCACATTCTG 59.362 45.833 0.00 0.00 0.00 3.02
690 697 7.041235 CCCACATTCTGTTGCACAAATATTTTT 60.041 33.333 0.00 0.00 0.00 1.94
699 1006 9.956720 TGTTGCACAAATATTTTTAAAAATGGG 57.043 25.926 28.45 18.86 38.90 4.00
821 1128 6.038050 GCTGATCTATCCCAACTTCTCAAAAG 59.962 42.308 0.00 0.00 0.00 2.27
824 2129 5.560724 TCTATCCCAACTTCTCAAAAGTGG 58.439 41.667 0.00 0.00 0.00 4.00
882 2187 2.746277 GTCCCGCGGCTCAACAAT 60.746 61.111 22.85 0.00 0.00 2.71
889 2194 1.425428 CGGCTCAACAATTCGCTCC 59.575 57.895 0.00 0.00 0.00 4.70
1092 2397 0.179134 CCCTCTACACGGCTTCTTCG 60.179 60.000 0.00 0.00 0.00 3.79
1093 2398 0.809385 CCTCTACACGGCTTCTTCGA 59.191 55.000 0.00 0.00 0.00 3.71
1201 2506 4.704103 TCCCTGCTGCCTCGACCT 62.704 66.667 0.00 0.00 0.00 3.85
1290 2595 3.424962 CCGCTGAACCTCGAGAAATTTTC 60.425 47.826 15.71 8.60 0.00 2.29
1298 2603 1.136363 TCGAGAAATTTTCAGCGTGCG 60.136 47.619 17.83 9.59 33.44 5.34
1329 2634 0.988145 TCCAGATCCGCCCCTGAATT 60.988 55.000 0.00 0.00 32.37 2.17
1333 2638 1.697754 ATCCGCCCCTGAATTCCCT 60.698 57.895 2.27 0.00 0.00 4.20
1344 2649 3.493350 CCTGAATTCCCTACCATCGTCTG 60.493 52.174 2.27 0.00 0.00 3.51
1428 2733 1.181098 AATTCGCCAAGGCTGCACTT 61.181 50.000 9.73 0.00 39.32 3.16
1462 2767 1.676006 CATTTCCTTATGCCACGGTCC 59.324 52.381 0.00 0.00 0.00 4.46
1509 2814 0.730840 CCAATTCGTTCCGGTTAGCC 59.269 55.000 0.00 0.00 0.00 3.93
1517 2822 2.353011 CGTTCCGGTTAGCCAAGAACTA 60.353 50.000 19.65 0.00 41.69 2.24
1518 2823 3.259902 GTTCCGGTTAGCCAAGAACTAG 58.740 50.000 16.65 0.00 41.15 2.57
1519 2824 1.206371 TCCGGTTAGCCAAGAACTAGC 59.794 52.381 0.00 0.00 34.09 3.42
1551 2856 2.490903 CTGATGCTGGCTTGCTTTTACT 59.509 45.455 4.89 0.00 0.00 2.24
1617 2922 1.745653 GCTGATACAGAAAAGTGGGCC 59.254 52.381 0.00 0.00 32.44 5.80
1666 2971 1.399714 TGGTAGGCCGACTCACTATG 58.600 55.000 16.10 0.00 37.67 2.23
1670 2975 1.043673 AGGCCGACTCACTATGACCC 61.044 60.000 0.00 0.00 0.00 4.46
1699 3004 5.469084 CCCTACTTGGTTACTTTGTTCAGAC 59.531 44.000 0.00 0.00 0.00 3.51
1745 3051 7.217200 AGTGAACTTACTGCTTTCTGTGATAA 58.783 34.615 0.00 0.00 0.00 1.75
1772 3078 1.075425 CTGCGTCAGCTGTCAGTAGC 61.075 60.000 14.67 11.42 45.42 3.58
1850 3156 6.042777 CGAGTTGAATCCTTCTGCTGTAATA 58.957 40.000 0.00 0.00 0.00 0.98
1898 3206 5.179368 TGCACGAAATTGAAGTCTTAAGAGG 59.821 40.000 5.12 0.00 0.00 3.69
1904 3212 7.331934 CGAAATTGAAGTCTTAAGAGGTGATGA 59.668 37.037 5.12 0.00 0.00 2.92
1908 3216 7.718334 TGAAGTCTTAAGAGGTGATGACATA 57.282 36.000 5.12 0.00 0.00 2.29
2019 3327 2.031682 CAGGCAAGTTGAGTTTTCTCCG 60.032 50.000 7.16 0.00 45.63 4.63
2067 3375 7.704789 AAGCTTTGCTAATCTTCAAAGTTTG 57.295 32.000 9.44 9.44 45.37 2.93
2138 3446 6.926272 AGAAGCTTCTCAATAACGTATCATCC 59.074 38.462 23.49 0.00 29.94 3.51
2186 3494 6.266103 TCTTTGGCATAATTCCTGATTCATCC 59.734 38.462 0.00 0.00 0.00 3.51
2223 3531 4.202264 GCCCCTCATACCATATATTCTCCG 60.202 50.000 0.00 0.00 0.00 4.63
2306 3616 6.147821 AGTTTGAACACCACTATTCTGAATCG 59.852 38.462 6.10 3.16 0.00 3.34
2314 3624 5.171476 CCACTATTCTGAATCGTTGTGAGT 58.829 41.667 6.10 0.21 0.00 3.41
2319 3629 9.268268 ACTATTCTGAATCGTTGTGAGTTTAAA 57.732 29.630 6.10 0.00 0.00 1.52
2419 3729 1.281899 GCATCCGCTCTGACAACTAC 58.718 55.000 0.00 0.00 34.30 2.73
2437 3747 8.161699 ACAACTACACAATTACCTTCGAAATT 57.838 30.769 0.00 0.00 0.00 1.82
2457 3767 6.765915 AATTGAGGAAGAAAAGTATGAGCC 57.234 37.500 0.00 0.00 0.00 4.70
2460 3770 4.228210 TGAGGAAGAAAAGTATGAGCCCAT 59.772 41.667 0.00 0.00 36.81 4.00
2471 3781 5.150715 AGTATGAGCCCATCTTCTGTATCA 58.849 41.667 0.00 0.00 34.31 2.15
2536 3847 1.973281 CACATGGCGCAGGTTTCCT 60.973 57.895 10.83 0.00 0.00 3.36
2582 3893 4.389382 TCAAATTTGCAAATGAAGCGATGG 59.611 37.500 24.74 5.68 33.85 3.51
2693 4005 2.683867 TGTAAACCAACAACTTGGGTCG 59.316 45.455 4.55 0.00 45.19 4.79
2697 4009 0.673437 CCAACAACTTGGGTCGCAAT 59.327 50.000 2.39 0.00 43.19 3.56
2708 4020 2.124122 GGGTCGCAATGTTTTCACAAC 58.876 47.619 0.00 0.00 36.16 3.32
2815 4127 2.158813 ACAGGTGCCCGTATCTTATTGG 60.159 50.000 0.00 0.00 0.00 3.16
2908 4221 6.862711 ACTTAACTTTTCCTCCTCTTTTCG 57.137 37.500 0.00 0.00 0.00 3.46
3080 4396 6.369065 GCTCGTTCCTATGATATTTTAGGTGG 59.631 42.308 10.22 0.00 37.00 4.61
3098 4414 0.589708 GGTGTACCCTTTTCGTGCAC 59.410 55.000 6.82 6.82 43.56 4.57
3110 4426 0.396435 TCGTGCACTGGGTTCATTCT 59.604 50.000 16.19 0.00 0.00 2.40
3112 4428 2.002586 CGTGCACTGGGTTCATTCTAG 58.997 52.381 16.19 0.00 0.00 2.43
3116 4432 4.811557 GTGCACTGGGTTCATTCTAGTATC 59.188 45.833 10.32 0.00 0.00 2.24
3203 4519 0.258774 ACCCAGATGCAATACCACCC 59.741 55.000 0.00 0.00 0.00 4.61
3288 4604 7.534085 TTGTTTACTGTTTCAGTAGTGAGTG 57.466 36.000 9.11 0.00 45.83 3.51
3367 4683 1.675641 GATTTGAGGCGCCCACAGT 60.676 57.895 26.15 15.68 0.00 3.55
3378 4694 0.326264 GCCCACAGTCAGAGGTGATT 59.674 55.000 4.08 0.00 37.18 2.57
3450 4766 4.917385 TGAGGCTTAATTAGTTTGCCAGA 58.083 39.130 17.16 6.03 45.42 3.86
3457 4773 9.430623 GGCTTAATTAGTTTGCCAGAAAAATTA 57.569 29.630 12.75 0.00 42.79 1.40
3511 4828 1.615116 CCTCAGTTGATGGTGCATGGT 60.615 52.381 0.00 0.00 0.00 3.55
3538 4855 4.083862 GACCTCCCCTGTGTCGCC 62.084 72.222 0.00 0.00 0.00 5.54
3541 4858 4.767255 CTCCCCTGTGTCGCCAGC 62.767 72.222 0.00 0.00 0.00 4.85
3598 4915 4.681978 GAAGCTCACGCGGGTGGT 62.682 66.667 29.45 9.30 44.50 4.16
3599 4916 4.250305 AAGCTCACGCGGGTGGTT 62.250 61.111 29.45 20.85 44.50 3.67
3600 4917 4.988598 AGCTCACGCGGGTGGTTG 62.989 66.667 29.45 20.49 44.50 3.77
3601 4918 4.980805 GCTCACGCGGGTGGTTGA 62.981 66.667 29.45 11.68 44.50 3.18
3602 4919 2.047274 CTCACGCGGGTGGTTGAT 60.047 61.111 29.45 0.00 44.50 2.57
3603 4920 2.047655 TCACGCGGGTGGTTGATC 60.048 61.111 29.45 0.00 44.50 2.92
3699 5016 9.793252 GTCTAATTTCAAGTCATGTTGCATTAT 57.207 29.630 0.00 0.00 0.00 1.28
3788 5107 7.259882 TGTATAGCATGGCTTTTCAGAATTTG 58.740 34.615 0.00 0.00 40.44 2.32
3872 5264 8.589629 GTTTTTAATCAATTGAGTGCAGCATAG 58.410 33.333 18.22 0.00 0.00 2.23
3891 5283 1.061411 CATGGATGCACGCGACAAG 59.939 57.895 15.93 0.00 0.00 3.16
3966 5358 2.689471 TGCCAGCATCATTGATACCAAC 59.311 45.455 0.00 0.00 34.72 3.77
3967 5359 2.035066 GCCAGCATCATTGATACCAACC 59.965 50.000 0.00 0.00 34.72 3.77
3968 5360 3.289836 CCAGCATCATTGATACCAACCA 58.710 45.455 0.00 0.00 34.72 3.67
3969 5361 3.067180 CCAGCATCATTGATACCAACCAC 59.933 47.826 0.00 0.00 34.72 4.16
3970 5362 3.067180 CAGCATCATTGATACCAACCACC 59.933 47.826 0.00 0.00 34.72 4.61
3971 5363 3.053395 AGCATCATTGATACCAACCACCT 60.053 43.478 0.00 0.00 34.72 4.00
3972 5364 4.165950 AGCATCATTGATACCAACCACCTA 59.834 41.667 0.00 0.00 34.72 3.08
3973 5365 5.072741 GCATCATTGATACCAACCACCTAT 58.927 41.667 0.00 0.00 34.72 2.57
3974 5366 5.536161 GCATCATTGATACCAACCACCTATT 59.464 40.000 0.00 0.00 34.72 1.73
3975 5367 6.515531 GCATCATTGATACCAACCACCTATTG 60.516 42.308 0.00 0.00 34.72 1.90
3976 5368 6.073447 TCATTGATACCAACCACCTATTGT 57.927 37.500 0.00 0.00 34.72 2.71
3977 5369 6.119536 TCATTGATACCAACCACCTATTGTC 58.880 40.000 0.00 0.00 34.72 3.18
3978 5370 5.506730 TTGATACCAACCACCTATTGTCA 57.493 39.130 0.00 0.00 0.00 3.58
3979 5371 5.506730 TGATACCAACCACCTATTGTCAA 57.493 39.130 0.00 0.00 0.00 3.18
3980 5372 6.073447 TGATACCAACCACCTATTGTCAAT 57.927 37.500 3.06 3.06 0.00 2.57
3981 5373 6.489603 TGATACCAACCACCTATTGTCAATT 58.510 36.000 2.79 0.00 0.00 2.32
3982 5374 6.601613 TGATACCAACCACCTATTGTCAATTC 59.398 38.462 2.79 0.00 0.00 2.17
3983 5375 4.735369 ACCAACCACCTATTGTCAATTCA 58.265 39.130 2.79 0.00 0.00 2.57
3984 5376 5.144100 ACCAACCACCTATTGTCAATTCAA 58.856 37.500 2.79 0.00 0.00 2.69
3985 5377 5.600484 ACCAACCACCTATTGTCAATTCAAA 59.400 36.000 2.79 0.00 0.00 2.69
3986 5378 6.098982 ACCAACCACCTATTGTCAATTCAAAA 59.901 34.615 2.79 0.00 0.00 2.44
3987 5379 6.989169 CCAACCACCTATTGTCAATTCAAAAA 59.011 34.615 2.79 0.00 0.00 1.94
4035 5427 9.474313 AATCAATCTACCACTAGCCAATTAAAA 57.526 29.630 0.00 0.00 0.00 1.52
4055 5447 1.731433 TAGGGCGACGCTACATGTCC 61.731 60.000 20.77 10.34 32.68 4.02
4056 5448 2.183300 GGCGACGCTACATGTCCA 59.817 61.111 20.77 0.00 32.68 4.02
4077 5469 5.835113 CACCGGTGGATTAATTGAAAGAT 57.165 39.130 27.57 0.00 0.00 2.40
4078 5470 5.581605 CACCGGTGGATTAATTGAAAGATG 58.418 41.667 27.57 0.00 0.00 2.90
4079 5471 5.125417 CACCGGTGGATTAATTGAAAGATGT 59.875 40.000 27.57 0.00 0.00 3.06
4080 5472 5.125417 ACCGGTGGATTAATTGAAAGATGTG 59.875 40.000 6.12 0.00 0.00 3.21
4081 5473 5.125417 CCGGTGGATTAATTGAAAGATGTGT 59.875 40.000 0.00 0.00 0.00 3.72
4082 5474 6.350110 CCGGTGGATTAATTGAAAGATGTGTT 60.350 38.462 0.00 0.00 0.00 3.32
4083 5475 7.148154 CCGGTGGATTAATTGAAAGATGTGTTA 60.148 37.037 0.00 0.00 0.00 2.41
4084 5476 8.405531 CGGTGGATTAATTGAAAGATGTGTTAT 58.594 33.333 0.00 0.00 0.00 1.89
4093 5485 9.491675 AATTGAAAGATGTGTTATCAATTGCAA 57.508 25.926 0.00 0.00 44.58 4.08
4094 5486 7.872163 TGAAAGATGTGTTATCAATTGCAAC 57.128 32.000 0.00 13.04 0.00 4.17
4095 5487 7.432059 TGAAAGATGTGTTATCAATTGCAACA 58.568 30.769 16.76 16.76 0.00 3.33
4096 5488 7.924947 TGAAAGATGTGTTATCAATTGCAACAA 59.075 29.630 20.31 13.83 34.20 2.83
4097 5489 7.878477 AAGATGTGTTATCAATTGCAACAAG 57.122 32.000 20.31 0.00 34.20 3.16
4098 5490 6.392354 AGATGTGTTATCAATTGCAACAAGG 58.608 36.000 20.31 0.00 34.20 3.61
4099 5491 5.528043 TGTGTTATCAATTGCAACAAGGT 57.472 34.783 20.31 0.00 34.20 3.50
4100 5492 6.641169 TGTGTTATCAATTGCAACAAGGTA 57.359 33.333 20.31 9.71 34.20 3.08
4101 5493 6.676950 TGTGTTATCAATTGCAACAAGGTAG 58.323 36.000 20.31 0.00 34.20 3.18
4102 5494 6.488344 TGTGTTATCAATTGCAACAAGGTAGA 59.512 34.615 20.31 0.00 34.20 2.59
4105 5497 7.176515 TGTTATCAATTGCAACAAGGTAGATGT 59.823 33.333 17.81 0.00 0.00 3.06
4106 5498 6.594788 ATCAATTGCAACAAGGTAGATGTT 57.405 33.333 0.00 0.00 41.50 2.71
4110 5502 4.032960 TGCAACAAGGTAGATGTTCCAT 57.967 40.909 0.00 0.00 38.90 3.41
4112 5504 5.185454 TGCAACAAGGTAGATGTTCCATAG 58.815 41.667 0.00 0.00 38.90 2.23
4113 5505 4.035675 GCAACAAGGTAGATGTTCCATAGC 59.964 45.833 0.00 0.00 38.90 2.97
4115 5507 5.283457 ACAAGGTAGATGTTCCATAGCTC 57.717 43.478 0.00 0.00 0.00 4.09
4118 5510 2.297597 GGTAGATGTTCCATAGCTCGCT 59.702 50.000 0.00 0.00 0.00 4.93
4119 5511 2.810439 AGATGTTCCATAGCTCGCTC 57.190 50.000 0.00 0.00 0.00 5.03
4121 5513 2.035704 AGATGTTCCATAGCTCGCTCTG 59.964 50.000 0.00 0.00 0.00 3.35
4122 5514 0.179100 TGTTCCATAGCTCGCTCTGC 60.179 55.000 0.00 0.00 0.00 4.26
4123 5515 0.179100 GTTCCATAGCTCGCTCTGCA 60.179 55.000 0.00 0.00 0.00 4.41
4125 5517 0.179100 TCCATAGCTCGCTCTGCAAC 60.179 55.000 0.00 0.00 0.00 4.17
4126 5518 0.460811 CCATAGCTCGCTCTGCAACA 60.461 55.000 0.00 0.00 0.00 3.33
4127 5519 0.928922 CATAGCTCGCTCTGCAACAG 59.071 55.000 0.00 0.00 0.00 3.16
4128 5520 0.534412 ATAGCTCGCTCTGCAACAGT 59.466 50.000 0.00 0.00 32.61 3.55
4129 5521 0.318441 TAGCTCGCTCTGCAACAGTT 59.682 50.000 0.00 0.00 32.61 3.16
4130 5522 1.206072 GCTCGCTCTGCAACAGTTG 59.794 57.895 9.12 9.12 32.61 3.16
4147 5539 2.975732 TTGCTTTGTTGCAACCATCA 57.024 40.000 26.14 15.31 46.43 3.07
4148 5540 2.975732 TGCTTTGTTGCAACCATCAA 57.024 40.000 26.14 11.39 40.29 2.57
4151 5543 3.865224 CTTTGTTGCAACCATCAAAGC 57.135 42.857 26.14 0.00 44.85 3.51
4152 5544 1.850377 TTGTTGCAACCATCAAAGCG 58.150 45.000 26.14 0.00 30.05 4.68
4153 5545 0.743688 TGTTGCAACCATCAAAGCGT 59.256 45.000 26.14 0.00 0.00 5.07
4154 5546 1.135915 TGTTGCAACCATCAAAGCGTT 59.864 42.857 26.14 0.00 0.00 4.84
4156 5548 3.005261 TGTTGCAACCATCAAAGCGTTAT 59.995 39.130 26.14 0.00 0.00 1.89
4157 5549 3.932545 TGCAACCATCAAAGCGTTATT 57.067 38.095 0.00 0.00 0.00 1.40
4158 5550 4.250116 TGCAACCATCAAAGCGTTATTT 57.750 36.364 0.00 0.00 0.00 1.40
4159 5551 4.626042 TGCAACCATCAAAGCGTTATTTT 58.374 34.783 0.00 0.00 0.00 1.82
4160 5552 4.683781 TGCAACCATCAAAGCGTTATTTTC 59.316 37.500 0.00 0.00 0.00 2.29
4211 5603 5.422666 TTTAAACATAGATGATGCTGCGG 57.577 39.130 0.00 0.00 39.39 5.69
4212 5604 1.888215 AACATAGATGATGCTGCGGG 58.112 50.000 0.00 0.00 39.39 6.13
4215 5607 0.612229 ATAGATGATGCTGCGGGAGG 59.388 55.000 0.00 0.00 0.00 4.30
4216 5608 2.104572 TAGATGATGCTGCGGGAGGC 62.105 60.000 0.00 0.00 43.96 4.70
4220 5612 4.052518 ATGCTGCGGGAGGCCTTT 62.053 61.111 6.77 0.00 42.61 3.11
4222 5614 3.752339 GCTGCGGGAGGCCTTTTG 61.752 66.667 6.77 0.00 42.61 2.44
4223 5615 3.752339 CTGCGGGAGGCCTTTTGC 61.752 66.667 6.77 12.12 42.61 3.68
4224 5616 4.594854 TGCGGGAGGCCTTTTGCA 62.595 61.111 19.15 19.15 43.89 4.08
4225 5617 3.302344 GCGGGAGGCCTTTTGCAA 61.302 61.111 6.77 0.00 43.89 4.08
4226 5618 2.649129 GCGGGAGGCCTTTTGCAAT 61.649 57.895 6.77 0.00 43.89 3.56
4227 5619 1.319614 GCGGGAGGCCTTTTGCAATA 61.320 55.000 6.77 0.00 43.89 1.90
4233 5625 3.317430 GGAGGCCTTTTGCAATAGAGATG 59.683 47.826 17.31 3.01 43.89 2.90
4234 5626 3.294214 AGGCCTTTTGCAATAGAGATGG 58.706 45.455 17.31 7.00 43.89 3.51
4236 5628 3.181483 GGCCTTTTGCAATAGAGATGGTG 60.181 47.826 17.31 1.38 43.89 4.17
4237 5629 3.445096 GCCTTTTGCAATAGAGATGGTGT 59.555 43.478 17.31 0.00 40.77 4.16
4238 5630 4.082026 GCCTTTTGCAATAGAGATGGTGTT 60.082 41.667 17.31 0.00 40.77 3.32
4239 5631 5.404946 CCTTTTGCAATAGAGATGGTGTTG 58.595 41.667 17.31 0.00 0.00 3.33
4240 5632 4.439305 TTTGCAATAGAGATGGTGTTGC 57.561 40.909 0.00 0.00 43.93 4.17
4242 5634 3.011818 TGCAATAGAGATGGTGTTGCAG 58.988 45.455 6.95 0.00 46.98 4.41
4244 5636 3.441572 GCAATAGAGATGGTGTTGCAGTT 59.558 43.478 3.76 0.00 43.33 3.16
4245 5637 4.082571 GCAATAGAGATGGTGTTGCAGTTT 60.083 41.667 3.76 0.00 43.33 2.66
4246 5638 5.565439 GCAATAGAGATGGTGTTGCAGTTTT 60.565 40.000 3.76 0.00 43.33 2.43
4332 5740 8.538409 AATAATGTTGCAGAATTTCTTTCACC 57.462 30.769 0.00 0.00 36.75 4.02
4345 5753 6.633500 TTTCTTTCACCGAAAAGATGATGT 57.367 33.333 7.96 0.00 43.02 3.06
4347 5755 5.304778 TCTTTCACCGAAAAGATGATGTCA 58.695 37.500 4.22 0.00 39.67 3.58
4365 5773 2.668457 GTCATCTGTGGTGTGAATCGAC 59.332 50.000 0.00 0.00 0.00 4.20
4373 5781 4.226761 GTGGTGTGAATCGACAAATTTCC 58.773 43.478 0.00 0.00 0.00 3.13
4431 5839 1.045911 AAGGCCCTTGTTGCGGAAAA 61.046 50.000 0.00 0.00 0.00 2.29
4432 5840 1.006220 GGCCCTTGTTGCGGAAAAG 60.006 57.895 0.00 0.00 0.00 2.27
4433 5841 1.739667 GCCCTTGTTGCGGAAAAGT 59.260 52.632 0.00 0.00 0.00 2.66
4434 5842 0.955905 GCCCTTGTTGCGGAAAAGTA 59.044 50.000 0.00 0.00 0.00 2.24
4435 5843 1.544246 GCCCTTGTTGCGGAAAAGTAT 59.456 47.619 0.00 0.00 0.00 2.12
4467 5875 4.477975 GACTGGAGCGACGACGGG 62.478 72.222 9.67 0.00 40.15 5.28
4471 5879 4.814294 GGAGCGACGACGGGCATT 62.814 66.667 9.67 0.00 40.15 3.56
4484 5899 3.424105 GCATTGGGAGGGGAGGCT 61.424 66.667 0.00 0.00 0.00 4.58
4493 5908 3.650950 GGGGAGGCTGAAGTGGCA 61.651 66.667 0.00 0.00 34.73 4.92
4496 5911 1.001641 GGAGGCTGAAGTGGCACAT 60.002 57.895 21.41 8.00 44.52 3.21
4500 5915 0.321919 GGCTGAAGTGGCACATCTCA 60.322 55.000 21.80 17.56 44.52 3.27
4503 5918 0.320683 TGAAGTGGCACATCTCACCG 60.321 55.000 21.80 0.00 44.52 4.94
4547 5963 1.512996 CGAGCGGGCGTAAGGAGATA 61.513 60.000 0.00 0.00 38.28 1.98
4560 5976 3.338110 AGGAGATAGGGAAAGGAGGAC 57.662 52.381 0.00 0.00 0.00 3.85
4595 6011 0.836400 AGAGGAGAAAGGACGGCCAA 60.836 55.000 11.69 0.00 36.29 4.52
4637 6053 2.357034 GGCGGACTCGTGAAAGCA 60.357 61.111 0.00 0.00 38.89 3.91
4643 6059 0.110464 GACTCGTGAAAGCAGCTTGC 60.110 55.000 8.88 7.44 45.46 4.01
4660 6076 2.772739 GCAGTAGTGTGCAGGATGG 58.227 57.895 0.00 0.00 43.41 3.51
4692 6108 4.312231 CACTTGTGGCGTGTGGCG 62.312 66.667 0.00 0.00 44.92 5.69
4716 6132 3.474570 GAGCACGGCTGGGAGGAT 61.475 66.667 0.00 0.00 39.88 3.24
4721 6137 1.690633 ACGGCTGGGAGGATGACAT 60.691 57.895 0.00 0.00 0.00 3.06
4725 6141 1.144503 GGCTGGGAGGATGACATGAAT 59.855 52.381 0.00 0.00 0.00 2.57
4727 6143 3.558746 GGCTGGGAGGATGACATGAATAG 60.559 52.174 0.00 0.00 0.00 1.73
4734 6150 7.397476 TGGGAGGATGACATGAATAGTAGATAC 59.603 40.741 0.00 0.00 0.00 2.24
4735 6151 7.397476 GGGAGGATGACATGAATAGTAGATACA 59.603 40.741 0.00 0.00 0.00 2.29
4759 6175 7.336176 ACAGATACAGACAAGAACGTAGTATGA 59.664 37.037 10.55 0.00 45.00 2.15
4768 6184 3.380637 AGAACGTAGTATGATGCTCGGTT 59.619 43.478 0.00 3.93 45.00 4.44
4780 6196 1.601903 TGCTCGGTTCATTTCACACAC 59.398 47.619 0.00 0.00 0.00 3.82
4785 6201 2.223144 CGGTTCATTTCACACACGACAT 59.777 45.455 0.00 0.00 0.00 3.06
4806 6222 0.745128 TGTTGAACGTTGGAAGCGGT 60.745 50.000 5.00 0.00 0.00 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 6.698329 TGCACAAGAAAAGTTGATGATTTCTG 59.302 34.615 1.20 0.10 41.28 3.02
68 69 8.476447 TCCTTTTGATGCAAATGCTATTATGAA 58.524 29.630 6.97 0.00 42.66 2.57
78 79 8.314143 AGTGTTTATTCCTTTTGATGCAAATG 57.686 30.769 0.00 0.00 33.19 2.32
79 80 8.907222 AAGTGTTTATTCCTTTTGATGCAAAT 57.093 26.923 0.00 0.00 33.19 2.32
80 81 7.440856 GGAAGTGTTTATTCCTTTTGATGCAAA 59.559 33.333 0.00 0.00 42.52 3.68
81 82 6.928492 GGAAGTGTTTATTCCTTTTGATGCAA 59.072 34.615 0.00 0.00 42.52 4.08
107 108 3.497763 CCCCAATGTGTAGAAGTGGTTCA 60.498 47.826 0.00 0.00 34.82 3.18
140 146 7.042051 ACGCATAGTACATCAATGGTTCAATAC 60.042 37.037 0.00 0.00 0.00 1.89
144 150 4.765273 ACGCATAGTACATCAATGGTTCA 58.235 39.130 0.00 0.00 0.00 3.18
146 152 3.802139 CGACGCATAGTACATCAATGGTT 59.198 43.478 0.00 0.00 0.00 3.67
152 158 0.741915 TGCCGACGCATAGTACATCA 59.258 50.000 0.00 0.00 41.12 3.07
180 186 2.390599 CGCACAACTGGATCCCACG 61.391 63.158 9.90 0.00 0.00 4.94
211 217 5.701290 AGGAGGATTCGTACAAAAGAAACTG 59.299 40.000 0.00 0.00 0.00 3.16
272 278 5.551760 AGTTAGGTTTTCATTCATCGCAG 57.448 39.130 0.00 0.00 0.00 5.18
277 283 4.589908 AGCCGAGTTAGGTTTTCATTCAT 58.410 39.130 0.00 0.00 0.00 2.57
285 291 2.943036 TTGGAAGCCGAGTTAGGTTT 57.057 45.000 0.00 0.00 37.42 3.27
294 300 1.002087 GAGGTCTCTTTTGGAAGCCGA 59.998 52.381 0.00 0.00 32.75 5.54
328 334 4.500603 AGTGCAAGAATTCTCAAAGCAG 57.499 40.909 18.95 3.62 0.00 4.24
424 430 3.426787 TTTAGGCGGTCTTGGATTTCA 57.573 42.857 0.00 0.00 0.00 2.69
430 436 4.736464 GCCAAAATATTTAGGCGGTCTTGG 60.736 45.833 0.01 3.51 37.41 3.61
451 457 2.092968 TGTAGGATGTGATGACTTGGCC 60.093 50.000 0.00 0.00 0.00 5.36
455 461 4.780021 AGGTCTTGTAGGATGTGATGACTT 59.220 41.667 0.00 0.00 0.00 3.01
462 468 3.735208 CGTGCTAGGTCTTGTAGGATGTG 60.735 52.174 0.00 0.00 0.00 3.21
469 475 3.767673 AGGAATTCGTGCTAGGTCTTGTA 59.232 43.478 0.00 0.00 0.00 2.41
472 478 3.983044 AAGGAATTCGTGCTAGGTCTT 57.017 42.857 0.58 0.00 0.00 3.01
486 492 1.075536 AGCAAGACGGGGAAAAGGAAT 59.924 47.619 0.00 0.00 0.00 3.01
491 497 0.037160 GGGTAGCAAGACGGGGAAAA 59.963 55.000 0.00 0.00 0.00 2.29
495 501 3.006728 TGGGGTAGCAAGACGGGG 61.007 66.667 0.00 0.00 0.00 5.73
508 514 3.081061 TCATTCGACAATTCTTGTGGGG 58.919 45.455 0.00 0.00 45.52 4.96
510 516 7.530010 ACTTAATCATTCGACAATTCTTGTGG 58.470 34.615 0.00 0.00 45.52 4.17
519 525 7.654116 TGACAGTGTTACTTAATCATTCGACAA 59.346 33.333 0.00 0.00 0.00 3.18
565 572 1.071605 GTACTCAGTGGCTTGCTTCG 58.928 55.000 0.00 0.00 0.00 3.79
576 583 5.126222 CACATGTCATCCTAGTGTACTCAGT 59.874 44.000 0.00 0.00 0.00 3.41
577 584 5.586339 CACATGTCATCCTAGTGTACTCAG 58.414 45.833 0.00 0.00 0.00 3.35
595 602 0.738975 CATCAAGGGAGCTGCACATG 59.261 55.000 7.79 2.57 0.00 3.21
606 613 2.692041 GGAAGGAAATGCTCATCAAGGG 59.308 50.000 0.00 0.00 0.00 3.95
619 626 5.773091 AGAAACTTTTACCAGGGAAGGAAA 58.227 37.500 0.00 0.00 0.00 3.13
631 638 5.070685 AGTGTGGGATGGAGAAACTTTTAC 58.929 41.667 0.00 0.00 0.00 2.01
649 656 3.417069 TGTGGGAGATGGTAAAGTGTG 57.583 47.619 0.00 0.00 0.00 3.82
674 681 9.958234 ACCCATTTTTAAAAATATTTGTGCAAC 57.042 25.926 22.44 0.00 36.52 4.17
803 1110 4.079253 GCCACTTTTGAGAAGTTGGGATA 58.921 43.478 0.00 0.00 0.00 2.59
824 2129 3.558411 CTTGCTAGCCTCGCGTGC 61.558 66.667 13.29 10.87 33.87 5.34
912 2217 1.130749 CCAACGAGTCACGGACTAGAG 59.869 57.143 16.71 9.93 43.53 2.43
1092 2397 4.580551 CCGGTATGGGACGGCGTC 62.581 72.222 30.72 30.72 43.96 5.19
1201 2506 0.319211 ATCACGAAAACTGCGGACGA 60.319 50.000 0.00 0.00 0.00 4.20
1312 2617 0.536006 GGAATTCAGGGGCGGATCTG 60.536 60.000 7.93 0.00 0.00 2.90
1329 2634 1.379443 ACGCAGACGATGGTAGGGA 60.379 57.895 0.00 0.00 43.93 4.20
1333 2638 3.441163 GATAAACACGCAGACGATGGTA 58.559 45.455 0.00 0.00 43.93 3.25
1462 2767 2.478200 GGAAAGAGAGGAGCGTAGAACG 60.478 54.545 0.00 0.00 45.88 3.95
1509 2814 2.485814 GGTTTCTGCTGGCTAGTTCTTG 59.514 50.000 0.00 0.00 0.00 3.02
1517 2822 0.964358 GCATCAGGTTTCTGCTGGCT 60.964 55.000 0.00 0.00 40.69 4.75
1518 2823 0.964358 AGCATCAGGTTTCTGCTGGC 60.964 55.000 0.00 0.00 44.21 4.85
1519 2824 3.261250 AGCATCAGGTTTCTGCTGG 57.739 52.632 0.00 0.00 44.21 4.85
1551 2856 4.035091 CAGACCTTCAACATTTCACAACGA 59.965 41.667 0.00 0.00 0.00 3.85
1629 2934 2.223971 ACCAATTCCTATGTAGCGACCG 60.224 50.000 0.00 0.00 0.00 4.79
1666 2971 2.732619 CCAAGTAGGGGCTCGGGTC 61.733 68.421 0.00 0.00 0.00 4.46
1670 2975 1.192428 AGTAACCAAGTAGGGGCTCG 58.808 55.000 0.00 0.00 43.89 5.03
1699 3004 8.693120 TCACTATAGGTACAAGATTCAGGTAG 57.307 38.462 4.43 0.00 0.00 3.18
1712 3018 8.468399 AGAAAGCAGTAAGTTCACTATAGGTAC 58.532 37.037 4.43 0.00 0.00 3.34
1714 3020 7.038941 ACAGAAAGCAGTAAGTTCACTATAGGT 60.039 37.037 4.43 0.00 0.00 3.08
1772 3078 2.014554 CCACAGTTCACGGTCGTCG 61.015 63.158 0.00 0.00 45.88 5.12
1850 3156 0.178801 AGAAGGGGTGGGGAAAGGAT 60.179 55.000 0.00 0.00 0.00 3.24
1898 3206 5.858381 ACAGACCACCATATATGTCATCAC 58.142 41.667 11.73 0.00 0.00 3.06
2067 3375 7.559590 AGCATAACTATCTTTCAACATGGAC 57.440 36.000 0.00 0.00 0.00 4.02
2186 3494 2.108075 TGAGGGGCCATACCATATTGTG 59.892 50.000 4.39 0.00 42.05 3.33
2277 3587 8.149973 TCAGAATAGTGGTGTTCAAACTAAAC 57.850 34.615 0.00 0.00 30.61 2.01
2419 3729 6.494893 TCCTCAATTTCGAAGGTAATTGTG 57.505 37.500 16.08 14.11 39.30 3.33
2437 3747 3.587061 TGGGCTCATACTTTTCTTCCTCA 59.413 43.478 0.00 0.00 0.00 3.86
2457 3767 8.196802 TGAACGTAAATTGATACAGAAGATGG 57.803 34.615 0.00 0.00 0.00 3.51
2520 3831 0.109132 GAAAGGAAACCTGCGCCATG 60.109 55.000 4.18 0.00 32.13 3.66
2525 3836 0.517316 CCGAAGAAAGGAAACCTGCG 59.483 55.000 0.00 0.00 32.13 5.18
2582 3893 2.424956 GGACCAGGCAATGATTCTCAAC 59.575 50.000 0.00 0.00 0.00 3.18
2599 3910 0.696501 TAAGGCTGGGAAAGTGGACC 59.303 55.000 0.00 0.00 0.00 4.46
2815 4127 5.527582 ACTTCATGGAAATAACATAGGCGTC 59.472 40.000 0.00 0.00 0.00 5.19
2853 4165 8.909708 TGCAAATAAATGTTACTATGAAGCAC 57.090 30.769 0.00 0.00 0.00 4.40
2891 4203 6.619801 TTCTTTCGAAAAGAGGAGGAAAAG 57.380 37.500 12.41 0.00 0.00 2.27
3080 4396 1.263217 CAGTGCACGAAAAGGGTACAC 59.737 52.381 12.01 0.00 41.63 2.90
3093 4409 3.059352 ACTAGAATGAACCCAGTGCAC 57.941 47.619 9.40 9.40 0.00 4.57
3098 4414 5.630415 TTGGGATACTAGAATGAACCCAG 57.370 43.478 0.00 0.00 45.00 4.45
3110 4426 3.492656 GCACTGAGCGAATTGGGATACTA 60.493 47.826 0.00 0.00 0.00 1.82
3112 4428 1.599542 GCACTGAGCGAATTGGGATAC 59.400 52.381 0.00 0.00 0.00 2.24
3203 4519 1.069513 TCTGGGTCAGGTGTTACAACG 59.930 52.381 0.00 0.00 31.51 4.10
3281 4597 4.228824 TCAGGGGTTAACTAACACTCACT 58.771 43.478 5.42 0.00 39.50 3.41
3288 4604 6.569801 GCTGTTTCAATCAGGGGTTAACTAAC 60.570 42.308 5.42 0.00 33.98 2.34
3367 4683 3.711704 GGGTCTATTGGAATCACCTCTGA 59.288 47.826 0.00 0.00 39.86 3.27
3378 4694 4.410228 CCTTTCTGATCAGGGTCTATTGGA 59.590 45.833 22.42 0.00 0.00 3.53
3457 4773 9.845214 ATTACCCCAAGTCTATATCTACATCTT 57.155 33.333 0.00 0.00 0.00 2.40
3511 4828 0.842030 AGGGGAGGTCACAAGCATGA 60.842 55.000 0.00 0.00 0.00 3.07
3541 4858 5.163744 CCTTTTGACATGAGCTTCAGATCAG 60.164 44.000 0.00 0.00 44.18 2.90
3598 4915 3.305267 CCCAAACTTGCATCAACGATCAA 60.305 43.478 0.00 0.00 0.00 2.57
3599 4916 2.228582 CCCAAACTTGCATCAACGATCA 59.771 45.455 0.00 0.00 0.00 2.92
3600 4917 2.867429 CCCAAACTTGCATCAACGATC 58.133 47.619 0.00 0.00 0.00 3.69
3601 4918 1.067635 GCCCAAACTTGCATCAACGAT 60.068 47.619 0.00 0.00 0.00 3.73
3602 4919 0.313672 GCCCAAACTTGCATCAACGA 59.686 50.000 0.00 0.00 0.00 3.85
3603 4920 0.031857 TGCCCAAACTTGCATCAACG 59.968 50.000 0.00 0.00 31.31 4.10
3699 5016 6.144845 ACCTTGTACTACTAGTTAGGACCA 57.855 41.667 0.00 0.00 40.68 4.02
3748 5067 4.331962 GCTATACAAAGCACGCAACTTAC 58.668 43.478 0.00 0.00 42.30 2.34
3788 5107 2.902705 TTCACAGTCACACTACCACC 57.097 50.000 0.00 0.00 0.00 4.61
3891 5283 4.054671 CAGCTGGTATAACTCTTGCTAGC 58.945 47.826 8.10 8.10 0.00 3.42
4022 5414 4.084013 CGTCGCCCTATTTTAATTGGCTAG 60.084 45.833 11.51 0.00 31.13 3.42
4024 5416 2.616842 CGTCGCCCTATTTTAATTGGCT 59.383 45.455 11.51 0.00 31.13 4.75
4035 5427 0.314302 GACATGTAGCGTCGCCCTAT 59.686 55.000 14.86 2.60 0.00 2.57
4055 5447 5.125417 ACATCTTTCAATTAATCCACCGGTG 59.875 40.000 28.26 28.26 0.00 4.94
4056 5448 5.125417 CACATCTTTCAATTAATCCACCGGT 59.875 40.000 0.00 0.00 0.00 5.28
4075 5467 6.158598 ACCTTGTTGCAATTGATAACACATC 58.841 36.000 21.14 5.73 34.38 3.06
4076 5468 6.100404 ACCTTGTTGCAATTGATAACACAT 57.900 33.333 21.14 11.41 34.38 3.21
4077 5469 5.528043 ACCTTGTTGCAATTGATAACACA 57.472 34.783 21.14 14.23 34.38 3.72
4078 5470 6.908825 TCTACCTTGTTGCAATTGATAACAC 58.091 36.000 21.14 6.96 34.38 3.32
4079 5471 7.176515 ACATCTACCTTGTTGCAATTGATAACA 59.823 33.333 18.84 18.84 32.93 2.41
4080 5472 7.538575 ACATCTACCTTGTTGCAATTGATAAC 58.461 34.615 10.34 13.46 0.00 1.89
4081 5473 7.701539 ACATCTACCTTGTTGCAATTGATAA 57.298 32.000 10.34 0.19 0.00 1.75
4082 5474 7.148086 GGAACATCTACCTTGTTGCAATTGATA 60.148 37.037 10.34 0.00 42.77 2.15
4083 5475 6.350445 GGAACATCTACCTTGTTGCAATTGAT 60.350 38.462 10.34 0.00 42.77 2.57
4084 5476 5.048083 GGAACATCTACCTTGTTGCAATTGA 60.048 40.000 10.34 0.00 42.77 2.57
4086 5478 5.391312 GGAACATCTACCTTGTTGCAATT 57.609 39.130 0.59 0.00 42.77 2.32
4105 5497 0.536724 TTGCAGAGCGAGCTATGGAA 59.463 50.000 19.70 19.70 41.82 3.53
4106 5498 0.179100 GTTGCAGAGCGAGCTATGGA 60.179 55.000 19.44 14.95 35.96 3.41
4110 5502 0.318441 AACTGTTGCAGAGCGAGCTA 59.682 50.000 0.00 0.00 35.18 3.32
4112 5504 1.206072 CAACTGTTGCAGAGCGAGC 59.794 57.895 7.70 0.00 35.18 5.03
4129 5521 2.975732 TTGATGGTTGCAACAAAGCA 57.024 40.000 29.55 22.19 43.99 3.91
4130 5522 3.865224 CTTTGATGGTTGCAACAAAGC 57.135 42.857 29.55 19.98 41.22 3.51
4132 5524 2.200067 CGCTTTGATGGTTGCAACAAA 58.800 42.857 29.55 19.45 0.00 2.83
4133 5525 1.135915 ACGCTTTGATGGTTGCAACAA 59.864 42.857 29.55 20.93 0.00 2.83
4134 5526 0.743688 ACGCTTTGATGGTTGCAACA 59.256 45.000 29.55 16.61 0.00 3.33
4135 5527 1.851658 AACGCTTTGATGGTTGCAAC 58.148 45.000 21.59 21.59 0.00 4.17
4136 5528 3.932545 ATAACGCTTTGATGGTTGCAA 57.067 38.095 0.00 0.00 0.00 4.08
4137 5529 3.932545 AATAACGCTTTGATGGTTGCA 57.067 38.095 0.00 0.00 0.00 4.08
4139 5531 5.420258 CGAAAATAACGCTTTGATGGTTG 57.580 39.130 0.00 0.00 0.00 3.77
4187 5579 6.264832 CCGCAGCATCATCTATGTTTAAAAA 58.735 36.000 0.00 0.00 37.93 1.94
4190 5582 3.814842 CCCGCAGCATCATCTATGTTTAA 59.185 43.478 0.00 0.00 37.93 1.52
4194 5586 1.001746 CTCCCGCAGCATCATCTATGT 59.998 52.381 0.00 0.00 37.93 2.29
4195 5587 1.675116 CCTCCCGCAGCATCATCTATG 60.675 57.143 0.00 0.00 38.74 2.23
4198 5590 2.827423 CCTCCCGCAGCATCATCT 59.173 61.111 0.00 0.00 0.00 2.90
4199 5591 2.976903 GCCTCCCGCAGCATCATC 60.977 66.667 0.00 0.00 37.47 2.92
4202 5594 4.496336 AAGGCCTCCCGCAGCATC 62.496 66.667 5.23 0.00 40.31 3.91
4204 5596 4.284550 AAAAGGCCTCCCGCAGCA 62.285 61.111 5.23 0.00 40.31 4.41
4205 5597 3.752339 CAAAAGGCCTCCCGCAGC 61.752 66.667 5.23 0.00 40.31 5.25
4207 5599 3.957260 TATTGCAAAAGGCCTCCCGCA 62.957 52.381 16.56 16.56 43.89 5.69
4208 5600 1.319614 TATTGCAAAAGGCCTCCCGC 61.320 55.000 5.23 9.75 43.89 6.13
4210 5602 2.027385 CTCTATTGCAAAAGGCCTCCC 58.973 52.381 5.23 0.00 43.89 4.30
4211 5603 3.004752 TCTCTATTGCAAAAGGCCTCC 57.995 47.619 5.23 0.00 43.89 4.30
4212 5604 3.317430 CCATCTCTATTGCAAAAGGCCTC 59.683 47.826 5.23 0.00 43.89 4.70
4215 5607 3.445096 ACACCATCTCTATTGCAAAAGGC 59.555 43.478 1.71 0.00 45.13 4.35
4216 5608 5.404946 CAACACCATCTCTATTGCAAAAGG 58.595 41.667 1.71 0.00 0.00 3.11
4222 5614 3.012518 ACTGCAACACCATCTCTATTGC 58.987 45.455 0.00 0.00 44.66 3.56
4223 5615 5.633830 AAACTGCAACACCATCTCTATTG 57.366 39.130 0.00 0.00 0.00 1.90
4224 5616 6.655078 AAAAACTGCAACACCATCTCTATT 57.345 33.333 0.00 0.00 0.00 1.73
4248 5640 8.939201 TGTTGCAAAAACTATGAAGATGAAAA 57.061 26.923 0.00 0.00 0.00 2.29
4251 5643 9.230122 TCTATGTTGCAAAAACTATGAAGATGA 57.770 29.630 0.00 0.00 0.00 2.92
4254 5646 9.230122 TCATCTATGTTGCAAAAACTATGAAGA 57.770 29.630 0.00 0.00 0.00 2.87
4320 5728 7.661040 ACATCATCTTTTCGGTGAAAGAAATT 58.339 30.769 11.58 0.00 45.68 1.82
4325 5733 5.611796 TGACATCATCTTTTCGGTGAAAG 57.388 39.130 0.00 0.00 37.85 2.62
4345 5753 2.298729 TGTCGATTCACACCACAGATGA 59.701 45.455 0.00 0.00 0.00 2.92
4347 5755 3.401033 TTGTCGATTCACACCACAGAT 57.599 42.857 0.00 0.00 0.00 2.90
4365 5773 4.424061 TCATCTCTGTTGCGGAAATTTG 57.576 40.909 0.00 0.00 0.00 2.32
4467 5875 3.424105 AGCCTCCCCTCCCAATGC 61.424 66.667 0.00 0.00 0.00 3.56
4470 5878 1.925455 CTTCAGCCTCCCCTCCCAA 60.925 63.158 0.00 0.00 0.00 4.12
4471 5879 2.285668 CTTCAGCCTCCCCTCCCA 60.286 66.667 0.00 0.00 0.00 4.37
4484 5899 0.320683 CGGTGAGATGTGCCACTTCA 60.321 55.000 12.61 3.78 33.99 3.02
4500 5915 2.351276 GCTCCAACCACCATCGGT 59.649 61.111 0.00 0.00 42.71 4.69
4503 5918 1.589716 GCTGTGCTCCAACCACCATC 61.590 60.000 0.00 0.00 32.30 3.51
4547 5963 1.152271 TCTCCAAGTCCTCCTTTCCCT 59.848 52.381 0.00 0.00 0.00 4.20
4560 5976 2.024464 TCCTCTCCTCTTCCTCTCCAAG 60.024 54.545 0.00 0.00 0.00 3.61
4595 6011 0.746923 TGATCGTCGGAGGACATCGT 60.747 55.000 2.02 0.00 43.61 3.73
4597 6013 0.030908 GGTGATCGTCGGAGGACATC 59.969 60.000 2.02 0.00 43.61 3.06
4598 6014 1.725557 CGGTGATCGTCGGAGGACAT 61.726 60.000 2.02 0.00 43.61 3.06
4629 6045 1.876156 ACTACTGCAAGCTGCTTTCAC 59.124 47.619 13.10 6.04 45.31 3.18
4630 6046 1.875514 CACTACTGCAAGCTGCTTTCA 59.124 47.619 13.10 13.49 45.31 2.69
4633 6049 1.233019 CACACTACTGCAAGCTGCTT 58.767 50.000 9.53 9.53 45.31 3.91
4637 6053 0.604780 CCTGCACACTACTGCAAGCT 60.605 55.000 0.00 0.00 46.46 3.74
4643 6059 0.251354 AGCCATCCTGCACACTACTG 59.749 55.000 0.00 0.00 0.00 2.74
4696 6112 4.767255 CTCCCAGCCGTGCTCCAC 62.767 72.222 0.00 0.00 36.40 4.02
4710 6126 8.354711 TGTATCTACTATTCATGTCATCCTCC 57.645 38.462 0.00 0.00 0.00 4.30
4725 6141 9.043079 CGTTCTTGTCTGTATCTGTATCTACTA 57.957 37.037 0.00 0.00 0.00 1.82
4727 6143 7.695820 ACGTTCTTGTCTGTATCTGTATCTAC 58.304 38.462 0.00 0.00 0.00 2.59
4734 6150 7.694886 TCATACTACGTTCTTGTCTGTATCTG 58.305 38.462 0.00 0.00 0.00 2.90
4735 6151 7.860918 TCATACTACGTTCTTGTCTGTATCT 57.139 36.000 0.00 0.00 0.00 1.98
4740 6156 5.344066 AGCATCATACTACGTTCTTGTCTG 58.656 41.667 0.00 0.00 0.00 3.51
4741 6157 5.583495 GAGCATCATACTACGTTCTTGTCT 58.417 41.667 0.00 0.00 33.17 3.41
4748 6164 3.129813 TGAACCGAGCATCATACTACGTT 59.870 43.478 0.00 0.00 33.17 3.99
4759 6175 2.226437 GTGTGTGAAATGAACCGAGCAT 59.774 45.455 0.00 0.00 0.00 3.79
4780 6196 1.595328 TCCAACGTTCAACACATGTCG 59.405 47.619 0.00 0.00 35.15 4.35
4785 6201 0.375454 CGCTTCCAACGTTCAACACA 59.625 50.000 0.00 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.