Multiple sequence alignment - TraesCS5D01G434600

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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 TraesCS5D01G434600 chr5D 100.000 5086 0 0 1 5086 490007874 490002789 0.000000e+00 9393.0
1 TraesCS5D01G434600 chr5A 91.298 4884 220 94 1 4784 611633924 611629146 0.000000e+00 6475.0
2 TraesCS5D01G434600 chr5A 95.868 242 10 0 1999 2240 645413292 645413051 4.770000e-105 392.0
3 TraesCS5D01G434600 chr5A 95.789 95 4 0 2286 2380 645413048 645412954 2.450000e-33 154.0
4 TraesCS5D01G434600 chr5A 84.146 82 3 4 4838 4909 611607954 611607873 2.540000e-08 71.3
5 TraesCS5D01G434600 chr5B 90.831 4995 198 107 1 4875 604145182 604140328 0.000000e+00 6447.0
6 TraesCS5D01G434600 chr2D 85.094 1221 159 17 1176 2383 298942652 298941442 0.000000e+00 1225.0
7 TraesCS5D01G434600 chr2A 85.094 1221 159 16 1176 2383 372737280 372736070 0.000000e+00 1225.0
8 TraesCS5D01G434600 chr2B 84.967 1224 158 17 1176 2383 356316207 356317420 0.000000e+00 1218.0
9 TraesCS5D01G434600 chr2B 94.000 50 3 0 1284 1333 165799932 165799883 5.460000e-10 76.8
10 TraesCS5D01G434600 chr3A 86.557 424 48 6 1170 1593 12562516 12562930 4.640000e-125 459.0
11 TraesCS5D01G434600 chr3B 89.610 308 28 1 1191 1498 10172041 10171738 6.180000e-104 388.0
12 TraesCS5D01G434600 chr3B 98.485 66 1 0 2315 2380 826146449 826146514 3.220000e-22 117.0
13 TraesCS5D01G434600 chr3D 87.842 329 29 6 1170 1498 7969837 7969520 4.810000e-100 375.0
14 TraesCS5D01G434600 chr1D 77.221 619 99 16 995 1613 108361668 108362244 1.770000e-84 324.0
15 TraesCS5D01G434600 chr7A 93.277 119 6 1 1988 2104 83536073 83536191 1.880000e-39 174.0
16 TraesCS5D01G434600 chr7A 97.895 95 1 1 2283 2376 83536219 83536313 4.070000e-36 163.0
17 TraesCS5D01G434600 chr4A 98.851 87 1 0 2286 2372 21864730 21864816 6.820000e-34 156.0
18 TraesCS5D01G434600 chr4A 92.453 106 8 0 1999 2104 21864592 21864697 8.820000e-33 152.0
19 TraesCS5D01G434600 chr4B 98.462 65 1 0 2316 2380 27405159 27405095 1.160000e-21 115.0


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 TraesCS5D01G434600 chr5D 490002789 490007874 5085 True 9393 9393 100.000 1 5086 1 chr5D.!!$R1 5085
1 TraesCS5D01G434600 chr5A 611629146 611633924 4778 True 6475 6475 91.298 1 4784 1 chr5A.!!$R2 4783
2 TraesCS5D01G434600 chr5B 604140328 604145182 4854 True 6447 6447 90.831 1 4875 1 chr5B.!!$R1 4874
3 TraesCS5D01G434600 chr2D 298941442 298942652 1210 True 1225 1225 85.094 1176 2383 1 chr2D.!!$R1 1207
4 TraesCS5D01G434600 chr2A 372736070 372737280 1210 True 1225 1225 85.094 1176 2383 1 chr2A.!!$R1 1207
5 TraesCS5D01G434600 chr2B 356316207 356317420 1213 False 1218 1218 84.967 1176 2383 1 chr2B.!!$F1 1207
6 TraesCS5D01G434600 chr1D 108361668 108362244 576 False 324 324 77.221 995 1613 1 chr1D.!!$F1 618

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
45 46 0.239879 GAAATCCGCAGAAACCGCAA 59.760 50.000 0.00 0.0 0.00 4.85 F
780 837 0.746563 CGTCTCTCGCTCTCCCTCTT 60.747 60.000 0.00 0.0 0.00 2.85 F
2406 2500 0.176680 CAGATCTGAACCCCACTCCG 59.823 60.000 18.34 0.0 0.00 4.63 F
2836 2948 1.066215 GGCCAGCCGATTGGAATTTTT 60.066 47.619 1.98 0.0 40.87 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2406 2500 5.047306 GCTAATTTAATAATGGGGGAGGTGC 60.047 44.0 0.00 0.0 0.00 5.01 R
3001 3124 1.050204 GGCCAGAGATCTGAGCTGAT 58.950 55.0 11.44 0.0 46.59 2.90 R
3516 3655 0.391263 GAGTGGCTACAAGGAACGGG 60.391 60.0 2.02 0.0 0.00 5.28 R
5042 5231 0.036388 AAACACACGGCCAGATCGAT 60.036 50.0 2.24 0.0 0.00 3.59 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 0.447801 CCTGAAATCCGCAGAAACCG 59.552 55.000 0.00 0.00 35.39 4.44
45 46 0.239879 GAAATCCGCAGAAACCGCAA 59.760 50.000 0.00 0.00 0.00 4.85
53 54 2.414559 CGCAGAAACCGCAAAATCAGAT 60.415 45.455 0.00 0.00 0.00 2.90
90 91 3.413846 AGACATCATCGCCATTGCTAT 57.586 42.857 0.00 0.00 34.43 2.97
133 134 7.148306 TGCATTATTACGAGGAAGGAAAGAAAC 60.148 37.037 0.00 0.00 0.00 2.78
134 135 7.148306 GCATTATTACGAGGAAGGAAAGAAACA 60.148 37.037 0.00 0.00 0.00 2.83
135 136 8.893727 CATTATTACGAGGAAGGAAAGAAACAT 58.106 33.333 0.00 0.00 0.00 2.71
136 137 6.986904 ATTACGAGGAAGGAAAGAAACATC 57.013 37.500 0.00 0.00 0.00 3.06
137 138 3.326747 ACGAGGAAGGAAAGAAACATCG 58.673 45.455 0.00 0.00 39.86 3.84
138 139 2.673368 CGAGGAAGGAAAGAAACATCGG 59.327 50.000 0.00 0.00 32.60 4.18
140 141 4.324267 GAGGAAGGAAAGAAACATCGGAA 58.676 43.478 0.00 0.00 0.00 4.30
141 142 4.327680 AGGAAGGAAAGAAACATCGGAAG 58.672 43.478 0.00 0.00 0.00 3.46
161 172 2.571202 AGAAAGAAGCAGGAGGAAGGAG 59.429 50.000 0.00 0.00 0.00 3.69
499 533 1.235281 GGAGACCTCACGGCCAAAAC 61.235 60.000 2.24 0.00 0.00 2.43
701 740 2.874648 TACGCCGCGTCTTCCTCCTA 62.875 60.000 23.94 0.00 41.54 2.94
702 741 2.846652 CGCCGCGTCTTCCTCCTAT 61.847 63.158 4.92 0.00 0.00 2.57
703 742 1.300233 GCCGCGTCTTCCTCCTATG 60.300 63.158 4.92 0.00 0.00 2.23
776 833 3.894947 GCCGTCTCTCGCTCTCCC 61.895 72.222 0.00 0.00 38.35 4.30
780 837 0.746563 CGTCTCTCGCTCTCCCTCTT 60.747 60.000 0.00 0.00 0.00 2.85
794 851 4.165372 TCTCCCTCTTTCTCTCTCTAGACC 59.835 50.000 0.00 0.00 0.00 3.85
2022 2113 2.262915 CTGACCACGGACCAGCTC 59.737 66.667 0.00 0.00 0.00 4.09
2406 2500 0.176680 CAGATCTGAACCCCACTCCG 59.823 60.000 18.34 0.00 0.00 4.63
2492 2592 2.817844 GCCACCGAAAATTTACAGTCCT 59.182 45.455 0.00 0.00 0.00 3.85
2507 2607 7.642082 TTACAGTCCTCAACCTAGATTCTAC 57.358 40.000 0.00 0.00 0.00 2.59
2508 2608 5.833340 ACAGTCCTCAACCTAGATTCTACT 58.167 41.667 0.00 0.00 0.00 2.57
2509 2609 5.889289 ACAGTCCTCAACCTAGATTCTACTC 59.111 44.000 0.00 0.00 0.00 2.59
2528 2628 7.215789 TCTACTCCGGTTAGTAGTAGATGAAG 58.784 42.308 22.92 5.11 46.07 3.02
2536 2636 1.762957 GTAGTAGATGAAGCTGCCCCA 59.237 52.381 0.00 0.00 0.00 4.96
2661 2765 2.017113 GCAATTAGGGTTCCGTCCTGG 61.017 57.143 0.00 0.00 35.92 4.45
2772 2883 2.591923 TGGAGTTTTATGCAGCCACAA 58.408 42.857 0.00 0.00 0.00 3.33
2836 2948 1.066215 GGCCAGCCGATTGGAATTTTT 60.066 47.619 1.98 0.00 40.87 1.94
2837 2949 2.001872 GCCAGCCGATTGGAATTTTTG 58.998 47.619 1.98 0.00 40.87 2.44
2858 2970 3.129113 TGTTGAGAAATCCATTGGCATCG 59.871 43.478 0.00 0.00 0.00 3.84
2956 3079 1.134220 TGTTGGTGGGTCACTGTCTTC 60.134 52.381 0.00 0.00 34.40 2.87
2986 3109 4.569966 GTCTCCTGATTGATGCTGTTACTG 59.430 45.833 0.00 0.00 0.00 2.74
2988 3111 2.947652 CCTGATTGATGCTGTTACTGGG 59.052 50.000 0.00 0.00 0.00 4.45
2989 3112 2.947652 CTGATTGATGCTGTTACTGGGG 59.052 50.000 0.00 0.00 0.00 4.96
3040 3163 1.272490 CTGTGTCTTCTTCACGCCCTA 59.728 52.381 0.00 0.00 38.48 3.53
3113 3236 1.612726 GCTCAAGCCTTGGTCACTCAT 60.613 52.381 4.30 0.00 34.31 2.90
3128 3251 4.569966 GTCACTCATATCCTTGCTGTCTTG 59.430 45.833 0.00 0.00 0.00 3.02
3153 3276 5.801380 CACTAGTTTGGTGTAATGGTAGGT 58.199 41.667 0.00 0.00 0.00 3.08
3205 3328 2.739287 CGAACCCGTGCGCCTTTA 60.739 61.111 4.18 0.00 0.00 1.85
3256 3380 6.753279 CCTGCACATGTAACCAATAATTCTTG 59.247 38.462 0.00 0.00 0.00 3.02
3314 3440 7.914427 ATAGATAACTCCTGTGTGGTATTGA 57.086 36.000 0.00 0.00 37.07 2.57
3317 3443 4.640771 AACTCCTGTGTGGTATTGATGT 57.359 40.909 0.00 0.00 37.07 3.06
3363 3494 2.227194 GGGCCATTATTTGTAGACCCG 58.773 52.381 4.39 0.00 0.00 5.28
3364 3495 2.158726 GGGCCATTATTTGTAGACCCGA 60.159 50.000 4.39 0.00 0.00 5.14
3385 3516 6.258230 CGACCTCGGTTTATGTATATGGTA 57.742 41.667 0.00 0.00 35.37 3.25
3436 3567 5.758296 GTGAAATCAGATGACCGGCTATTTA 59.242 40.000 0.00 0.00 0.00 1.40
3480 3612 4.082463 TGGACAAAACTTGGTGTTGAGTTC 60.082 41.667 7.48 0.00 39.13 3.01
3510 3649 4.574892 TGTGTGATGATAAAGCGAGGAAA 58.425 39.130 0.00 0.00 0.00 3.13
3511 3650 4.631377 TGTGTGATGATAAAGCGAGGAAAG 59.369 41.667 0.00 0.00 0.00 2.62
3516 3655 7.224753 TGTGATGATAAAGCGAGGAAAGTTATC 59.775 37.037 0.00 0.00 33.63 1.75
3604 3745 2.575735 TCCCAATAGCCTGTGAATCACA 59.424 45.455 15.88 15.88 42.45 3.58
3612 3757 2.704572 CCTGTGAATCACAACCTCCTC 58.295 52.381 17.41 0.00 44.08 3.71
3635 3781 3.063861 TGATTTCCTGCGATTTCGACATG 59.936 43.478 3.77 0.00 43.02 3.21
3636 3782 2.378445 TTCCTGCGATTTCGACATGA 57.622 45.000 0.00 1.98 43.02 3.07
3648 3794 1.410517 TCGACATGAGAGAGGCCATTC 59.589 52.381 5.01 1.10 0.00 2.67
3678 3824 7.945033 TGCACACAAAATTATTCCTCTTTTC 57.055 32.000 0.00 0.00 0.00 2.29
3680 3826 8.855110 TGCACACAAAATTATTCCTCTTTTCTA 58.145 29.630 0.00 0.00 0.00 2.10
3755 3906 6.564854 GACAAGATGTCAAAATATGCAAGC 57.435 37.500 5.65 0.00 46.22 4.01
3826 3977 4.209080 TGATTTGATAGCGCGTCTGTTATG 59.791 41.667 8.43 0.00 0.00 1.90
4191 4346 4.383861 GGGCTGGGCTTTGCTTGC 62.384 66.667 0.00 0.00 0.00 4.01
4192 4347 3.308705 GGCTGGGCTTTGCTTGCT 61.309 61.111 0.00 0.00 0.00 3.91
4193 4348 2.739132 GCTGGGCTTTGCTTGCTT 59.261 55.556 0.00 0.00 0.00 3.91
4194 4349 1.666872 GCTGGGCTTTGCTTGCTTG 60.667 57.895 0.00 0.00 0.00 4.01
4195 4350 1.666872 CTGGGCTTTGCTTGCTTGC 60.667 57.895 0.00 0.00 0.00 4.01
4196 4351 2.095978 CTGGGCTTTGCTTGCTTGCT 62.096 55.000 3.47 0.00 0.00 3.91
4197 4352 1.070275 GGGCTTTGCTTGCTTGCTT 59.930 52.632 3.47 0.00 0.00 3.91
4198 4353 1.226030 GGGCTTTGCTTGCTTGCTTG 61.226 55.000 3.47 0.00 0.00 4.01
4199 4354 1.226030 GGCTTTGCTTGCTTGCTTGG 61.226 55.000 3.47 0.00 0.00 3.61
4200 4355 0.249573 GCTTTGCTTGCTTGCTTGGA 60.250 50.000 3.47 0.00 0.00 3.53
4201 4356 1.779569 CTTTGCTTGCTTGCTTGGAG 58.220 50.000 3.47 0.00 0.00 3.86
4202 4357 0.249573 TTTGCTTGCTTGCTTGGAGC 60.250 50.000 3.47 0.00 42.82 4.70
4203 4358 2.091102 TTGCTTGCTTGCTTGGAGCC 62.091 55.000 0.00 0.00 41.51 4.70
4204 4359 2.273912 GCTTGCTTGCTTGGAGCCT 61.274 57.895 0.00 0.00 41.51 4.58
4317 4472 1.911702 TTGTTGGTGTGTCCGGTCCA 61.912 55.000 0.00 0.00 39.52 4.02
4365 4521 7.952671 TGTTTATACTCGAAGGCTATGATCTT 58.047 34.615 0.00 0.00 0.00 2.40
4366 4522 8.082852 TGTTTATACTCGAAGGCTATGATCTTC 58.917 37.037 0.00 0.00 36.84 2.87
4367 4523 8.301002 GTTTATACTCGAAGGCTATGATCTTCT 58.699 37.037 0.00 0.00 37.73 2.85
4368 4524 4.582701 ACTCGAAGGCTATGATCTTCTG 57.417 45.455 0.00 0.00 37.73 3.02
4453 4614 0.108281 GTCTAACGGGGTTCTGGAGC 60.108 60.000 0.00 0.00 0.00 4.70
4468 4629 1.168714 GGAGCGAAGAAGGTTGCATT 58.831 50.000 0.00 0.00 0.00 3.56
4469 4630 1.541588 GGAGCGAAGAAGGTTGCATTT 59.458 47.619 0.00 0.00 0.00 2.32
4470 4631 2.589014 GAGCGAAGAAGGTTGCATTTG 58.411 47.619 0.00 0.00 0.00 2.32
4471 4632 1.270550 AGCGAAGAAGGTTGCATTTGG 59.729 47.619 0.00 0.00 0.00 3.28
4472 4633 1.269448 GCGAAGAAGGTTGCATTTGGA 59.731 47.619 0.00 0.00 0.00 3.53
4473 4634 2.094545 GCGAAGAAGGTTGCATTTGGAT 60.095 45.455 0.00 0.00 0.00 3.41
4474 4635 3.762779 CGAAGAAGGTTGCATTTGGATC 58.237 45.455 0.00 0.00 0.00 3.36
4475 4636 3.191162 CGAAGAAGGTTGCATTTGGATCA 59.809 43.478 0.00 0.00 0.00 2.92
4546 4707 9.651913 TGGTACAACTATACATATACATGCATG 57.348 33.333 25.09 25.09 32.28 4.06
4567 4728 5.319140 TGGCTTGATGATTCATGTTCTTG 57.681 39.130 3.32 0.00 31.38 3.02
4576 4737 7.827729 TGATGATTCATGTTCTTGTCAAGATCT 59.172 33.333 15.95 1.69 37.38 2.75
4577 4738 7.991084 TGATTCATGTTCTTGTCAAGATCTT 57.009 32.000 15.95 10.44 37.38 2.40
4594 4755 7.391554 TCAAGATCTTTGGTACATTCTTCCTTG 59.608 37.037 4.86 0.00 39.30 3.61
4595 4756 6.784031 AGATCTTTGGTACATTCTTCCTTGT 58.216 36.000 0.00 0.00 39.30 3.16
4596 4757 6.656693 AGATCTTTGGTACATTCTTCCTTGTG 59.343 38.462 0.00 0.00 39.30 3.33
4597 4758 4.518970 TCTTTGGTACATTCTTCCTTGTGC 59.481 41.667 0.00 0.00 39.30 4.57
4598 4759 3.788227 TGGTACATTCTTCCTTGTGCT 57.212 42.857 0.00 0.00 0.00 4.40
4611 4781 7.996385 TCTTCCTTGTGCTTAAAATATAAGGC 58.004 34.615 0.00 0.00 34.62 4.35
4657 4827 1.376037 CCGTCTTTCTCCTGGTGCC 60.376 63.158 0.00 0.00 0.00 5.01
4689 4860 2.677836 TCGCATTGTTCATGTAGGAAGC 59.322 45.455 0.00 0.00 34.98 3.86
4709 4880 0.445436 CAGCTGTGCGAATCAACTCC 59.555 55.000 5.25 0.00 0.00 3.85
4711 4882 1.648467 GCTGTGCGAATCAACTCCCC 61.648 60.000 0.00 0.00 0.00 4.81
4748 4928 6.651975 AAGGCAGGTGTATATGTAGAGTAC 57.348 41.667 0.00 0.00 0.00 2.73
4749 4929 5.954757 AGGCAGGTGTATATGTAGAGTACT 58.045 41.667 0.00 0.00 0.00 2.73
4752 4932 7.447853 AGGCAGGTGTATATGTAGAGTACTAAC 59.552 40.741 0.00 0.00 0.00 2.34
4753 4933 7.447853 GGCAGGTGTATATGTAGAGTACTAACT 59.552 40.741 0.00 0.00 39.21 2.24
4754 4934 9.499479 GCAGGTGTATATGTAGAGTACTAACTA 57.501 37.037 0.00 0.00 35.56 2.24
4786 4966 4.764172 AGATGCTTGCTCCAACTAAGTAG 58.236 43.478 0.00 0.00 0.00 2.57
4787 4967 4.467795 AGATGCTTGCTCCAACTAAGTAGA 59.532 41.667 0.00 0.00 0.00 2.59
4788 4968 4.193826 TGCTTGCTCCAACTAAGTAGAG 57.806 45.455 0.00 0.00 0.00 2.43
4807 4987 5.033589 AGAGCAGTAGCAATTAAGCAGAT 57.966 39.130 0.00 0.00 45.49 2.90
4808 4988 5.055812 AGAGCAGTAGCAATTAAGCAGATC 58.944 41.667 0.00 0.00 45.49 2.75
4810 4990 3.557595 GCAGTAGCAATTAAGCAGATCGT 59.442 43.478 0.00 0.00 41.58 3.73
4812 4992 4.568359 CAGTAGCAATTAAGCAGATCGTGT 59.432 41.667 0.00 0.00 36.85 4.49
4814 4994 5.643777 AGTAGCAATTAAGCAGATCGTGTTT 59.356 36.000 0.00 0.00 36.85 2.83
4815 4995 6.816640 AGTAGCAATTAAGCAGATCGTGTTTA 59.183 34.615 0.00 0.00 36.85 2.01
4816 4996 6.111768 AGCAATTAAGCAGATCGTGTTTAG 57.888 37.500 0.00 0.00 33.80 1.85
4817 4997 5.643777 AGCAATTAAGCAGATCGTGTTTAGT 59.356 36.000 0.00 0.00 33.80 2.24
4818 4998 6.816640 AGCAATTAAGCAGATCGTGTTTAGTA 59.183 34.615 0.00 0.00 33.80 1.82
4826 5006 8.897457 AGCAGATCGTGTTTAGTATATTATCG 57.103 34.615 0.00 0.00 0.00 2.92
4828 5008 8.786955 GCAGATCGTGTTTAGTATATTATCGAC 58.213 37.037 0.00 0.00 0.00 4.20
4829 5009 9.275231 CAGATCGTGTTTAGTATATTATCGACC 57.725 37.037 0.00 0.00 0.00 4.79
4833 5022 8.579006 TCGTGTTTAGTATATTATCGACCCAAT 58.421 33.333 0.00 0.00 0.00 3.16
4870 5059 1.958579 TGACTTTGCTTGATGCTGCTT 59.041 42.857 0.00 0.00 43.37 3.91
4872 5061 3.569277 TGACTTTGCTTGATGCTGCTTTA 59.431 39.130 0.00 0.00 43.37 1.85
4873 5062 4.219070 TGACTTTGCTTGATGCTGCTTTAT 59.781 37.500 0.00 0.00 43.37 1.40
4874 5063 4.741342 ACTTTGCTTGATGCTGCTTTATC 58.259 39.130 0.00 0.00 43.37 1.75
4875 5064 3.409851 TTGCTTGATGCTGCTTTATCG 57.590 42.857 0.00 0.00 43.37 2.92
4876 5065 2.358957 TGCTTGATGCTGCTTTATCGT 58.641 42.857 0.00 0.00 43.37 3.73
4877 5066 2.352651 TGCTTGATGCTGCTTTATCGTC 59.647 45.455 0.00 0.00 43.37 4.20
4878 5067 2.352651 GCTTGATGCTGCTTTATCGTCA 59.647 45.455 0.00 0.00 38.95 4.35
4879 5068 3.181507 GCTTGATGCTGCTTTATCGTCAA 60.182 43.478 0.00 0.00 38.95 3.18
4880 5069 4.497006 GCTTGATGCTGCTTTATCGTCAAT 60.497 41.667 0.00 0.00 35.82 2.57
4881 5070 4.801147 TGATGCTGCTTTATCGTCAATC 57.199 40.909 0.00 0.00 0.00 2.67
4882 5071 4.445453 TGATGCTGCTTTATCGTCAATCT 58.555 39.130 0.00 0.00 0.00 2.40
4883 5072 4.509230 TGATGCTGCTTTATCGTCAATCTC 59.491 41.667 0.00 0.00 0.00 2.75
4884 5073 4.128925 TGCTGCTTTATCGTCAATCTCT 57.871 40.909 0.00 0.00 0.00 3.10
4885 5074 4.115516 TGCTGCTTTATCGTCAATCTCTC 58.884 43.478 0.00 0.00 0.00 3.20
4886 5075 3.181377 GCTGCTTTATCGTCAATCTCTCG 59.819 47.826 0.00 0.00 0.00 4.04
4887 5076 3.706698 TGCTTTATCGTCAATCTCTCGG 58.293 45.455 0.00 0.00 0.00 4.63
4888 5077 3.130516 TGCTTTATCGTCAATCTCTCGGT 59.869 43.478 0.00 0.00 0.00 4.69
4889 5078 3.487574 GCTTTATCGTCAATCTCTCGGTG 59.512 47.826 0.00 0.00 0.00 4.94
4890 5079 3.710326 TTATCGTCAATCTCTCGGTGG 57.290 47.619 0.00 0.00 0.00 4.61
4891 5080 0.103208 ATCGTCAATCTCTCGGTGGC 59.897 55.000 0.00 0.00 0.00 5.01
4892 5081 1.874019 CGTCAATCTCTCGGTGGCG 60.874 63.158 0.00 0.00 33.66 5.69
4893 5082 1.519455 GTCAATCTCTCGGTGGCGG 60.519 63.158 0.00 0.00 0.00 6.13
4894 5083 1.680989 TCAATCTCTCGGTGGCGGA 60.681 57.895 0.00 0.00 0.00 5.54
4895 5084 1.519455 CAATCTCTCGGTGGCGGAC 60.519 63.158 0.00 0.00 0.00 4.79
4896 5085 1.982395 AATCTCTCGGTGGCGGACA 60.982 57.895 0.00 0.00 0.00 4.02
4904 5093 2.982130 GTGGCGGACACCTCAGAT 59.018 61.111 1.44 0.00 44.49 2.90
4905 5094 1.448540 GTGGCGGACACCTCAGATG 60.449 63.158 1.44 0.00 44.49 2.90
4906 5095 1.609210 TGGCGGACACCTCAGATGA 60.609 57.895 0.00 0.00 0.00 2.92
4907 5096 1.142748 GGCGGACACCTCAGATGAG 59.857 63.158 2.72 2.72 41.71 2.90
4917 5106 1.719529 CTCAGATGAGGGATCCAGCT 58.280 55.000 15.23 1.45 38.48 4.24
4918 5107 1.345089 CTCAGATGAGGGATCCAGCTG 59.655 57.143 15.23 11.68 46.12 4.24
4919 5108 0.250381 CAGATGAGGGATCCAGCTGC 60.250 60.000 15.23 0.00 40.47 5.25
4920 5109 0.400237 AGATGAGGGATCCAGCTGCT 60.400 55.000 15.23 0.00 0.00 4.24
4921 5110 0.250381 GATGAGGGATCCAGCTGCTG 60.250 60.000 22.44 22.44 0.00 4.41
4922 5111 0.987081 ATGAGGGATCCAGCTGCTGT 60.987 55.000 26.41 10.66 0.00 4.40
4923 5112 1.203441 TGAGGGATCCAGCTGCTGTT 61.203 55.000 26.41 14.63 0.00 3.16
4924 5113 0.463474 GAGGGATCCAGCTGCTGTTC 60.463 60.000 26.41 21.15 0.00 3.18
4925 5114 1.203441 AGGGATCCAGCTGCTGTTCA 61.203 55.000 26.41 11.67 0.00 3.18
4926 5115 0.747283 GGGATCCAGCTGCTGTTCAG 60.747 60.000 26.41 12.46 45.62 3.02
4927 5116 0.035630 GGATCCAGCTGCTGTTCAGT 60.036 55.000 26.41 8.74 44.66 3.41
4928 5117 1.612726 GGATCCAGCTGCTGTTCAGTT 60.613 52.381 26.41 7.76 44.66 3.16
4929 5118 1.736681 GATCCAGCTGCTGTTCAGTTC 59.263 52.381 26.41 12.49 44.66 3.01
4930 5119 0.469494 TCCAGCTGCTGTTCAGTTCA 59.531 50.000 26.41 0.00 44.66 3.18
4931 5120 0.873054 CCAGCTGCTGTTCAGTTCAG 59.127 55.000 26.41 5.70 44.66 3.02
4932 5121 1.590932 CAGCTGCTGTTCAGTTCAGT 58.409 50.000 21.21 0.00 44.66 3.41
4933 5122 1.263484 CAGCTGCTGTTCAGTTCAGTG 59.737 52.381 21.21 0.00 44.66 3.66
4934 5123 0.590195 GCTGCTGTTCAGTTCAGTGG 59.410 55.000 0.00 0.00 44.66 4.00
4935 5124 1.959042 CTGCTGTTCAGTTCAGTGGT 58.041 50.000 1.78 0.00 38.02 4.16
4936 5125 2.292267 CTGCTGTTCAGTTCAGTGGTT 58.708 47.619 1.78 0.00 38.02 3.67
4937 5126 2.016318 TGCTGTTCAGTTCAGTGGTTG 58.984 47.619 1.78 0.00 35.60 3.77
4938 5127 1.334869 GCTGTTCAGTTCAGTGGTTGG 59.665 52.381 1.78 0.00 35.60 3.77
4939 5128 2.643551 CTGTTCAGTTCAGTGGTTGGT 58.356 47.619 0.00 0.00 0.00 3.67
4940 5129 3.804036 CTGTTCAGTTCAGTGGTTGGTA 58.196 45.455 0.00 0.00 0.00 3.25
4941 5130 4.196193 CTGTTCAGTTCAGTGGTTGGTAA 58.804 43.478 0.00 0.00 0.00 2.85
4942 5131 4.590918 TGTTCAGTTCAGTGGTTGGTAAA 58.409 39.130 0.00 0.00 0.00 2.01
4943 5132 5.010933 TGTTCAGTTCAGTGGTTGGTAAAA 58.989 37.500 0.00 0.00 0.00 1.52
4944 5133 5.106078 TGTTCAGTTCAGTGGTTGGTAAAAC 60.106 40.000 0.00 0.00 0.00 2.43
4945 5134 4.590918 TCAGTTCAGTGGTTGGTAAAACA 58.409 39.130 0.00 0.00 0.00 2.83
4946 5135 4.638421 TCAGTTCAGTGGTTGGTAAAACAG 59.362 41.667 0.00 0.00 32.29 3.16
4947 5136 3.380320 AGTTCAGTGGTTGGTAAAACAGC 59.620 43.478 0.00 0.00 32.29 4.40
4948 5137 3.006112 TCAGTGGTTGGTAAAACAGCA 57.994 42.857 0.00 0.00 32.29 4.41
4949 5138 3.357203 TCAGTGGTTGGTAAAACAGCAA 58.643 40.909 0.00 0.00 42.23 3.91
4950 5139 3.764434 TCAGTGGTTGGTAAAACAGCAAA 59.236 39.130 0.00 0.00 45.74 3.68
4951 5140 4.111916 CAGTGGTTGGTAAAACAGCAAAG 58.888 43.478 0.00 0.00 45.74 2.77
4952 5141 2.863740 GTGGTTGGTAAAACAGCAAAGC 59.136 45.455 0.00 0.00 45.74 3.51
4953 5142 2.497675 TGGTTGGTAAAACAGCAAAGCA 59.502 40.909 0.00 0.00 45.74 3.91
4954 5143 3.133721 TGGTTGGTAAAACAGCAAAGCAT 59.866 39.130 0.00 0.00 45.74 3.79
4955 5144 4.342378 TGGTTGGTAAAACAGCAAAGCATA 59.658 37.500 0.00 0.00 45.74 3.14
4956 5145 4.923281 GGTTGGTAAAACAGCAAAGCATAG 59.077 41.667 0.00 0.00 45.74 2.23
4957 5146 4.173036 TGGTAAAACAGCAAAGCATAGC 57.827 40.909 0.00 0.00 0.00 2.97
4958 5147 3.826157 TGGTAAAACAGCAAAGCATAGCT 59.174 39.130 0.00 0.00 42.56 3.32
4989 5178 2.827604 ACGCGAGTTTCATCCTGTG 58.172 52.632 15.93 0.00 46.40 3.66
4990 5179 0.670546 ACGCGAGTTTCATCCTGTGG 60.671 55.000 15.93 0.00 46.40 4.17
4991 5180 0.670546 CGCGAGTTTCATCCTGTGGT 60.671 55.000 0.00 0.00 0.00 4.16
4992 5181 1.403647 CGCGAGTTTCATCCTGTGGTA 60.404 52.381 0.00 0.00 0.00 3.25
4993 5182 2.695359 GCGAGTTTCATCCTGTGGTAA 58.305 47.619 0.00 0.00 0.00 2.85
4994 5183 2.673368 GCGAGTTTCATCCTGTGGTAAG 59.327 50.000 0.00 0.00 0.00 2.34
4995 5184 2.673368 CGAGTTTCATCCTGTGGTAAGC 59.327 50.000 0.00 0.00 0.00 3.09
4996 5185 3.674997 GAGTTTCATCCTGTGGTAAGCA 58.325 45.455 0.00 0.00 0.00 3.91
4997 5186 4.072131 GAGTTTCATCCTGTGGTAAGCAA 58.928 43.478 0.00 0.00 0.00 3.91
4998 5187 4.469657 AGTTTCATCCTGTGGTAAGCAAA 58.530 39.130 0.00 0.00 0.00 3.68
4999 5188 5.079643 AGTTTCATCCTGTGGTAAGCAAAT 58.920 37.500 0.00 0.00 0.00 2.32
5000 5189 5.047802 AGTTTCATCCTGTGGTAAGCAAATG 60.048 40.000 0.00 0.00 0.00 2.32
5001 5190 2.754552 TCATCCTGTGGTAAGCAAATGC 59.245 45.455 0.00 0.00 42.49 3.56
5012 5201 2.022520 GCAAATGCGGTAGTAGGCC 58.977 57.895 0.00 0.00 0.00 5.19
5013 5202 1.444917 GCAAATGCGGTAGTAGGCCC 61.445 60.000 0.00 0.00 0.00 5.80
5014 5203 0.818040 CAAATGCGGTAGTAGGCCCC 60.818 60.000 0.00 0.00 0.00 5.80
5015 5204 1.276140 AAATGCGGTAGTAGGCCCCA 61.276 55.000 0.00 0.00 0.00 4.96
5016 5205 1.276140 AATGCGGTAGTAGGCCCCAA 61.276 55.000 0.00 0.00 0.00 4.12
5017 5206 1.276140 ATGCGGTAGTAGGCCCCAAA 61.276 55.000 0.00 0.00 0.00 3.28
5018 5207 1.450848 GCGGTAGTAGGCCCCAAAC 60.451 63.158 0.00 0.00 0.00 2.93
5019 5208 1.153509 CGGTAGTAGGCCCCAAACG 60.154 63.158 0.00 0.00 0.00 3.60
5020 5209 1.222661 GGTAGTAGGCCCCAAACGG 59.777 63.158 0.00 0.00 0.00 4.44
5040 5229 3.403277 GCGGTAGCACAGCATGAG 58.597 61.111 0.00 0.00 44.35 2.90
5049 5238 1.867166 CACAGCATGAGCATCGATCT 58.133 50.000 0.00 0.00 45.49 2.75
5050 5239 1.527311 CACAGCATGAGCATCGATCTG 59.473 52.381 0.00 0.27 45.49 2.90
5051 5240 1.149148 CAGCATGAGCATCGATCTGG 58.851 55.000 0.00 0.00 45.49 3.86
5052 5241 0.603172 AGCATGAGCATCGATCTGGC 60.603 55.000 0.00 0.00 45.49 4.85
5053 5242 1.575576 GCATGAGCATCGATCTGGCC 61.576 60.000 0.00 0.00 41.58 5.36
5054 5243 1.005275 ATGAGCATCGATCTGGCCG 60.005 57.895 0.00 0.00 38.61 6.13
5055 5244 1.752358 ATGAGCATCGATCTGGCCGT 61.752 55.000 0.00 0.00 38.61 5.68
5056 5245 1.953138 GAGCATCGATCTGGCCGTG 60.953 63.158 0.00 0.00 0.00 4.94
5057 5246 2.202932 GCATCGATCTGGCCGTGT 60.203 61.111 0.00 0.00 0.00 4.49
5058 5247 2.528743 GCATCGATCTGGCCGTGTG 61.529 63.158 0.00 0.00 0.00 3.82
5059 5248 1.153568 CATCGATCTGGCCGTGTGT 60.154 57.895 0.00 0.00 0.00 3.72
5060 5249 0.740868 CATCGATCTGGCCGTGTGTT 60.741 55.000 0.00 0.00 0.00 3.32
5061 5250 0.036388 ATCGATCTGGCCGTGTGTTT 60.036 50.000 0.00 0.00 0.00 2.83
5062 5251 0.250124 TCGATCTGGCCGTGTGTTTT 60.250 50.000 0.00 0.00 0.00 2.43
5063 5252 0.591170 CGATCTGGCCGTGTGTTTTT 59.409 50.000 0.00 0.00 0.00 1.94
5064 5253 1.662876 CGATCTGGCCGTGTGTTTTTG 60.663 52.381 0.00 0.00 0.00 2.44
5065 5254 0.673437 ATCTGGCCGTGTGTTTTTGG 59.327 50.000 0.00 0.00 0.00 3.28
5066 5255 1.591327 CTGGCCGTGTGTTTTTGGC 60.591 57.895 0.00 0.00 46.82 4.52
5068 5257 3.699671 GCCGTGTGTTTTTGGCAC 58.300 55.556 0.00 0.00 46.76 5.01
5069 5258 1.153745 GCCGTGTGTTTTTGGCACA 60.154 52.632 0.00 0.00 46.76 4.57
5084 5273 4.607293 TGGCACAAGCATCTACCTATAG 57.393 45.455 0.00 0.00 44.61 1.31
5085 5274 3.967326 TGGCACAAGCATCTACCTATAGT 59.033 43.478 0.00 0.00 44.61 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.063654 TTTCAGGGAGGGGTTTCGGT 61.064 55.000 0.00 0.00 0.00 4.69
42 43 1.227060 GGCGGGCATCTGATTTTGC 60.227 57.895 0.00 0.00 38.14 3.68
45 46 3.211963 GCGGCGGGCATCTGATTT 61.212 61.111 9.78 0.00 42.87 2.17
90 91 1.594194 GCATTGTGGATGTTCGGCCA 61.594 55.000 2.24 0.00 38.07 5.36
133 134 2.935201 CTCCTGCTTCTTTCTTCCGATG 59.065 50.000 0.00 0.00 0.00 3.84
134 135 2.093235 CCTCCTGCTTCTTTCTTCCGAT 60.093 50.000 0.00 0.00 0.00 4.18
135 136 1.276421 CCTCCTGCTTCTTTCTTCCGA 59.724 52.381 0.00 0.00 0.00 4.55
136 137 1.276421 TCCTCCTGCTTCTTTCTTCCG 59.724 52.381 0.00 0.00 0.00 4.30
137 138 3.342719 CTTCCTCCTGCTTCTTTCTTCC 58.657 50.000 0.00 0.00 0.00 3.46
138 139 3.008485 TCCTTCCTCCTGCTTCTTTCTTC 59.992 47.826 0.00 0.00 0.00 2.87
140 141 2.571202 CTCCTTCCTCCTGCTTCTTTCT 59.429 50.000 0.00 0.00 0.00 2.52
141 142 2.939198 GCTCCTTCCTCCTGCTTCTTTC 60.939 54.545 0.00 0.00 0.00 2.62
142 143 1.004161 GCTCCTTCCTCCTGCTTCTTT 59.996 52.381 0.00 0.00 0.00 2.52
149 159 0.684805 ACCGTAGCTCCTTCCTCCTG 60.685 60.000 0.00 0.00 0.00 3.86
150 160 0.924823 TACCGTAGCTCCTTCCTCCT 59.075 55.000 0.00 0.00 0.00 3.69
283 294 3.630204 GCATCGATGCGATTCGGT 58.370 55.556 32.60 0.00 44.59 4.69
352 363 4.660938 AAACTCCAGCCACCCGCC 62.661 66.667 0.00 0.00 38.78 6.13
471 486 2.184579 GAGGTCTCCCGCCTTTCG 59.815 66.667 0.00 0.00 36.29 3.46
546 580 3.712881 GGTTGGCAGCACGTCGTC 61.713 66.667 3.14 0.00 0.00 4.20
553 587 2.192861 CAAGGTTCGGTTGGCAGCA 61.193 57.895 3.14 0.00 0.00 4.41
554 588 1.856265 CTCAAGGTTCGGTTGGCAGC 61.856 60.000 0.00 0.00 0.00 5.25
555 589 0.535102 ACTCAAGGTTCGGTTGGCAG 60.535 55.000 0.00 0.00 0.00 4.85
671 710 2.740826 CGGCGTAGTTGGTGGTGG 60.741 66.667 0.00 0.00 0.00 4.61
672 711 3.419759 GCGGCGTAGTTGGTGGTG 61.420 66.667 9.37 0.00 0.00 4.17
701 740 2.435372 ACCGAAGAGAGAGAGAGCAT 57.565 50.000 0.00 0.00 0.00 3.79
702 741 2.208132 AACCGAAGAGAGAGAGAGCA 57.792 50.000 0.00 0.00 0.00 4.26
703 742 5.562113 GCTTATAACCGAAGAGAGAGAGAGC 60.562 48.000 0.00 0.00 0.00 4.09
776 833 7.392113 TGTTTAGTGGTCTAGAGAGAGAAAGAG 59.608 40.741 0.00 0.00 30.20 2.85
780 837 7.834881 TTTGTTTAGTGGTCTAGAGAGAGAA 57.165 36.000 0.00 0.00 30.20 2.87
794 851 4.725490 TCTTCCCCCTCTTTTGTTTAGTG 58.275 43.478 0.00 0.00 0.00 2.74
953 1035 4.232878 CCGCTCTAGCTGCCCCTG 62.233 72.222 0.00 0.00 39.32 4.45
2406 2500 5.047306 GCTAATTTAATAATGGGGGAGGTGC 60.047 44.000 0.00 0.00 0.00 5.01
2492 2592 4.246712 ACCGGAGTAGAATCTAGGTTGA 57.753 45.455 9.46 0.00 30.01 3.18
2507 2607 4.822896 AGCTTCATCTACTACTAACCGGAG 59.177 45.833 9.46 0.00 0.00 4.63
2508 2608 4.579340 CAGCTTCATCTACTACTAACCGGA 59.421 45.833 9.46 0.00 0.00 5.14
2509 2609 4.793353 GCAGCTTCATCTACTACTAACCGG 60.793 50.000 0.00 0.00 0.00 5.28
2528 2628 2.101415 GAGGTTAATCAATTGGGGCAGC 59.899 50.000 5.42 0.00 0.00 5.25
2536 2636 6.400568 CAACCAGCATTGAGGTTAATCAATT 58.599 36.000 11.97 0.00 45.44 2.32
2661 2765 2.894387 GCCATGAGCAGAGGACGC 60.894 66.667 0.00 0.00 42.97 5.19
2772 2883 8.287503 GTGATAAAATCGCCGGAGTATTTAATT 58.712 33.333 5.05 0.00 33.78 1.40
2809 2921 2.059786 AATCGGCTGGCCAATTGGG 61.060 57.895 25.73 10.56 40.85 4.12
2824 2936 8.606040 TGGATTTCTCAACAAAAATTCCAATC 57.394 30.769 0.00 0.00 0.00 2.67
2836 2948 3.129113 CGATGCCAATGGATTTCTCAACA 59.871 43.478 2.05 0.00 0.00 3.33
2837 2949 3.378112 TCGATGCCAATGGATTTCTCAAC 59.622 43.478 2.05 0.00 0.00 3.18
2858 2970 7.657023 TCTAATACTACCCTCCAAGTTTCTC 57.343 40.000 0.00 0.00 0.00 2.87
2956 3079 3.193263 CATCAATCAGGAGACGGTGAAG 58.807 50.000 0.00 0.00 0.00 3.02
2986 3109 1.664321 CTGATCTTGCTTGCAGCCCC 61.664 60.000 5.82 0.00 41.51 5.80
2988 3111 1.139095 GCTGATCTTGCTTGCAGCC 59.861 57.895 0.00 0.00 45.92 4.85
2989 3112 4.787999 GCTGATCTTGCTTGCAGC 57.212 55.556 0.00 0.00 45.64 5.25
3001 3124 1.050204 GGCCAGAGATCTGAGCTGAT 58.950 55.000 11.44 0.00 46.59 2.90
3040 3163 4.401519 AGCTATGAATTGTTGCTCATGCTT 59.598 37.500 0.00 0.00 35.12 3.91
3113 3236 1.630369 AGTGCCAAGACAGCAAGGATA 59.370 47.619 0.00 0.00 43.02 2.59
3128 3251 3.418047 ACCATTACACCAAACTAGTGCC 58.582 45.455 0.00 0.00 38.87 5.01
3153 3276 5.652014 GTCACTCATTCCATAACCATTTGGA 59.348 40.000 3.01 0.00 40.24 3.53
3293 3419 6.258727 CACATCAATACCACACAGGAGTTATC 59.741 42.308 0.00 0.00 41.22 1.75
3314 3440 1.282157 GGCACCTAAGGGTCTTCACAT 59.718 52.381 0.00 0.00 45.41 3.21
3317 3443 1.440618 TTGGCACCTAAGGGTCTTCA 58.559 50.000 0.00 0.00 45.41 3.02
3363 3494 6.088824 CGTACCATATACATAAACCGAGGTC 58.911 44.000 0.00 0.00 0.00 3.85
3364 3495 5.536161 ACGTACCATATACATAAACCGAGGT 59.464 40.000 0.00 0.00 0.00 3.85
3382 3513 5.051816 TGCTATTTGTAGGCAATACGTACC 58.948 41.667 0.00 0.00 38.58 3.34
3383 3514 6.128634 GGATGCTATTTGTAGGCAATACGTAC 60.129 42.308 0.00 0.00 39.46 3.67
3385 3516 4.755123 GGATGCTATTTGTAGGCAATACGT 59.245 41.667 0.00 0.00 39.46 3.57
3436 3567 1.145738 AGCCAATGTGTCCAAAGGTCT 59.854 47.619 0.00 0.00 0.00 3.85
3480 3612 5.685068 CGCTTTATCATCACACAGAGACTAG 59.315 44.000 0.00 0.00 0.00 2.57
3510 3649 2.169978 GGCTACAAGGAACGGGATAACT 59.830 50.000 0.00 0.00 0.00 2.24
3511 3650 2.093341 TGGCTACAAGGAACGGGATAAC 60.093 50.000 0.00 0.00 0.00 1.89
3516 3655 0.391263 GAGTGGCTACAAGGAACGGG 60.391 60.000 2.02 0.00 0.00 5.28
3604 3745 1.065854 CGCAGGAAATCAGAGGAGGTT 60.066 52.381 0.00 0.00 0.00 3.50
3612 3757 2.672874 TGTCGAAATCGCAGGAAATCAG 59.327 45.455 0.00 0.00 39.60 2.90
3635 3781 0.915364 AAGGTGGAATGGCCTCTCTC 59.085 55.000 3.32 0.00 37.63 3.20
3636 3782 0.622665 CAAGGTGGAATGGCCTCTCT 59.377 55.000 3.32 0.00 37.63 3.10
3648 3794 4.690280 GGAATAATTTTGTGTGCAAGGTGG 59.310 41.667 0.00 0.00 35.82 4.61
3773 3924 0.833287 CCTGCTGCCTACTATGTGGT 59.167 55.000 0.00 0.00 0.00 4.16
4106 4261 7.804843 ACCAATCATGAGATCAATCTTCTTC 57.195 36.000 0.09 0.00 37.25 2.87
4107 4262 7.832685 TCAACCAATCATGAGATCAATCTTCTT 59.167 33.333 0.09 0.00 37.25 2.52
4108 4263 7.282675 GTCAACCAATCATGAGATCAATCTTCT 59.717 37.037 0.09 0.00 37.25 2.85
4179 4334 1.070275 AAGCAAGCAAGCAAAGCCC 59.930 52.632 3.19 0.00 36.85 5.19
4180 4335 1.226030 CCAAGCAAGCAAGCAAAGCC 61.226 55.000 3.19 0.00 36.85 4.35
4191 4346 2.282674 TGGCAGGCTCCAAGCAAG 60.283 61.111 0.86 0.00 44.75 4.01
4192 4347 2.282674 CTGGCAGGCTCCAAGCAA 60.283 61.111 6.61 0.00 44.75 3.91
4203 4358 2.369257 ATATCGTGGACGGCTGGCAG 62.369 60.000 10.94 10.94 40.29 4.85
4204 4359 1.966901 AATATCGTGGACGGCTGGCA 61.967 55.000 0.00 0.00 40.29 4.92
4365 4521 5.884232 ACGTTCCTATACATACACAGACAGA 59.116 40.000 0.00 0.00 0.00 3.41
4366 4522 6.132791 ACGTTCCTATACATACACAGACAG 57.867 41.667 0.00 0.00 0.00 3.51
4367 4523 6.519679 AACGTTCCTATACATACACAGACA 57.480 37.500 0.00 0.00 0.00 3.41
4368 4524 7.823149 AAAACGTTCCTATACATACACAGAC 57.177 36.000 0.00 0.00 0.00 3.51
4453 4614 3.191162 TGATCCAAATGCAACCTTCTTCG 59.809 43.478 0.00 0.00 0.00 3.79
4468 4629 6.022315 ACTTTTAACCCATCCAATGATCCAA 58.978 36.000 0.00 0.00 0.00 3.53
4469 4630 5.588845 ACTTTTAACCCATCCAATGATCCA 58.411 37.500 0.00 0.00 0.00 3.41
4470 4631 6.544928 AACTTTTAACCCATCCAATGATCC 57.455 37.500 0.00 0.00 0.00 3.36
4471 4632 9.936759 TTTTAACTTTTAACCCATCCAATGATC 57.063 29.630 0.00 0.00 0.00 2.92
4472 4633 9.942850 CTTTTAACTTTTAACCCATCCAATGAT 57.057 29.630 0.00 0.00 0.00 2.45
4473 4634 8.929487 ACTTTTAACTTTTAACCCATCCAATGA 58.071 29.630 0.00 0.00 0.00 2.57
4474 4635 8.987890 CACTTTTAACTTTTAACCCATCCAATG 58.012 33.333 0.00 0.00 0.00 2.82
4475 4636 8.710239 ACACTTTTAACTTTTAACCCATCCAAT 58.290 29.630 0.00 0.00 0.00 3.16
4546 4707 5.106038 TGACAAGAACATGAATCATCAAGCC 60.106 40.000 0.00 0.00 39.49 4.35
4567 4728 6.881602 AGGAAGAATGTACCAAAGATCTTGAC 59.118 38.462 9.17 5.99 0.00 3.18
4576 4737 4.469657 AGCACAAGGAAGAATGTACCAAA 58.530 39.130 0.00 0.00 0.00 3.28
4577 4738 4.098914 AGCACAAGGAAGAATGTACCAA 57.901 40.909 0.00 0.00 0.00 3.67
4594 4755 5.418310 TCGCAGCCTTATATTTTAAGCAC 57.582 39.130 0.00 0.00 0.00 4.40
4595 4756 5.588648 AGTTCGCAGCCTTATATTTTAAGCA 59.411 36.000 0.00 0.00 0.00 3.91
4596 4757 5.909610 CAGTTCGCAGCCTTATATTTTAAGC 59.090 40.000 0.00 0.00 0.00 3.09
4597 4758 6.907212 CACAGTTCGCAGCCTTATATTTTAAG 59.093 38.462 0.00 0.00 0.00 1.85
4598 4759 6.596106 TCACAGTTCGCAGCCTTATATTTTAA 59.404 34.615 0.00 0.00 0.00 1.52
4611 4781 3.062763 AGAGACAAATCACAGTTCGCAG 58.937 45.455 0.00 0.00 0.00 5.18
4669 4839 2.223340 GGCTTCCTACATGAACAATGCG 60.223 50.000 0.00 0.00 40.22 4.73
4672 4842 3.019564 GCTGGCTTCCTACATGAACAAT 58.980 45.455 0.00 0.00 0.00 2.71
4689 4860 0.445436 GAGTTGATTCGCACAGCTGG 59.555 55.000 19.93 8.27 0.00 4.85
4709 4880 0.958822 CCTTTTGTCCGTTCTTGGGG 59.041 55.000 0.00 0.00 0.00 4.96
4711 4882 1.001378 CTGCCTTTTGTCCGTTCTTGG 60.001 52.381 0.00 0.00 0.00 3.61
4752 4932 8.060931 TGGAGCAAGCATCTATCTATAGTTAG 57.939 38.462 10.48 10.48 0.00 2.34
4753 4933 8.307483 GTTGGAGCAAGCATCTATCTATAGTTA 58.693 37.037 0.00 0.00 0.00 2.24
4754 4934 6.924913 TGGAGCAAGCATCTATCTATAGTT 57.075 37.500 0.00 0.00 0.00 2.24
4755 4935 6.496565 AGTTGGAGCAAGCATCTATCTATAGT 59.503 38.462 0.00 0.00 0.00 2.12
4756 4936 6.934056 AGTTGGAGCAAGCATCTATCTATAG 58.066 40.000 0.00 0.00 0.00 1.31
4757 4937 6.924913 AGTTGGAGCAAGCATCTATCTATA 57.075 37.500 0.00 0.00 0.00 1.31
4758 4938 5.822132 AGTTGGAGCAAGCATCTATCTAT 57.178 39.130 0.00 0.00 0.00 1.98
4759 4939 6.325028 ACTTAGTTGGAGCAAGCATCTATCTA 59.675 38.462 0.00 0.00 0.00 1.98
4760 4940 5.130145 ACTTAGTTGGAGCAAGCATCTATCT 59.870 40.000 0.00 0.00 0.00 1.98
4761 4941 5.363939 ACTTAGTTGGAGCAAGCATCTATC 58.636 41.667 0.00 0.00 0.00 2.08
4786 4966 4.084641 CGATCTGCTTAATTGCTACTGCTC 60.085 45.833 0.00 0.00 40.48 4.26
4787 4967 3.806521 CGATCTGCTTAATTGCTACTGCT 59.193 43.478 0.00 0.00 40.48 4.24
4788 4968 3.557595 ACGATCTGCTTAATTGCTACTGC 59.442 43.478 0.00 0.00 40.20 4.40
4789 4969 4.568359 ACACGATCTGCTTAATTGCTACTG 59.432 41.667 0.00 0.00 0.00 2.74
4790 4970 4.759782 ACACGATCTGCTTAATTGCTACT 58.240 39.130 0.00 0.00 0.00 2.57
4807 4987 7.509141 TGGGTCGATAATATACTAAACACGA 57.491 36.000 0.00 0.00 0.00 4.35
4808 4988 8.644619 CATTGGGTCGATAATATACTAAACACG 58.355 37.037 0.00 0.00 0.00 4.49
4810 4990 8.098286 CCCATTGGGTCGATAATATACTAAACA 58.902 37.037 14.10 0.00 38.25 2.83
4829 5009 4.021280 TCAAATCACATTCACACCCATTGG 60.021 41.667 0.00 0.00 37.80 3.16
4833 5022 3.831323 AGTCAAATCACATTCACACCCA 58.169 40.909 0.00 0.00 0.00 4.51
4837 5026 5.518848 AGCAAAGTCAAATCACATTCACA 57.481 34.783 0.00 0.00 0.00 3.58
4870 5059 2.223735 GCCACCGAGAGATTGACGATAA 60.224 50.000 0.00 0.00 0.00 1.75
4872 5061 0.103208 GCCACCGAGAGATTGACGAT 59.897 55.000 0.00 0.00 0.00 3.73
4873 5062 1.511305 GCCACCGAGAGATTGACGA 59.489 57.895 0.00 0.00 0.00 4.20
4874 5063 1.874019 CGCCACCGAGAGATTGACG 60.874 63.158 0.00 0.00 36.29 4.35
4875 5064 1.519455 CCGCCACCGAGAGATTGAC 60.519 63.158 0.00 0.00 36.29 3.18
4876 5065 1.680989 TCCGCCACCGAGAGATTGA 60.681 57.895 0.00 0.00 36.29 2.57
4877 5066 1.519455 GTCCGCCACCGAGAGATTG 60.519 63.158 0.00 0.00 36.29 2.67
4878 5067 1.982395 TGTCCGCCACCGAGAGATT 60.982 57.895 0.00 0.00 36.29 2.40
4879 5068 2.362503 TGTCCGCCACCGAGAGAT 60.363 61.111 0.00 0.00 36.29 2.75
4880 5069 3.371063 GTGTCCGCCACCGAGAGA 61.371 66.667 0.00 0.00 38.18 3.10
4887 5076 1.448540 CATCTGAGGTGTCCGCCAC 60.449 63.158 0.00 0.00 43.74 5.01
4888 5077 1.607801 CTCATCTGAGGTGTCCGCCA 61.608 60.000 0.00 0.00 38.48 5.69
4889 5078 1.142748 CTCATCTGAGGTGTCCGCC 59.857 63.158 0.00 0.00 38.48 6.13
4890 5079 4.823276 CTCATCTGAGGTGTCCGC 57.177 61.111 0.00 0.00 38.48 5.54
4898 5087 1.345089 CAGCTGGATCCCTCATCTGAG 59.655 57.143 9.90 0.00 41.71 3.35
4899 5088 1.421480 CAGCTGGATCCCTCATCTGA 58.579 55.000 9.90 0.00 0.00 3.27
4900 5089 0.250381 GCAGCTGGATCCCTCATCTG 60.250 60.000 17.12 9.90 0.00 2.90
4901 5090 0.400237 AGCAGCTGGATCCCTCATCT 60.400 55.000 17.12 0.00 0.00 2.90
4902 5091 0.250381 CAGCAGCTGGATCCCTCATC 60.250 60.000 17.12 0.00 0.00 2.92
4903 5092 0.987081 ACAGCAGCTGGATCCCTCAT 60.987 55.000 26.38 0.00 35.51 2.90
4904 5093 1.203441 AACAGCAGCTGGATCCCTCA 61.203 55.000 26.38 0.00 35.51 3.86
4905 5094 0.463474 GAACAGCAGCTGGATCCCTC 60.463 60.000 26.38 8.84 35.51 4.30
4906 5095 1.203441 TGAACAGCAGCTGGATCCCT 61.203 55.000 26.38 0.79 35.51 4.20
4907 5096 0.747283 CTGAACAGCAGCTGGATCCC 60.747 60.000 26.38 10.43 37.90 3.85
4908 5097 2.777969 CTGAACAGCAGCTGGATCC 58.222 57.895 26.38 4.20 37.90 3.36
4917 5106 2.016318 CAACCACTGAACTGAACAGCA 58.984 47.619 1.46 0.00 38.74 4.41
4918 5107 1.334869 CCAACCACTGAACTGAACAGC 59.665 52.381 1.46 0.00 38.74 4.40
4919 5108 2.643551 ACCAACCACTGAACTGAACAG 58.356 47.619 0.00 0.00 40.68 3.16
4920 5109 2.799126 ACCAACCACTGAACTGAACA 57.201 45.000 0.00 0.00 0.00 3.18
4921 5110 5.106078 TGTTTTACCAACCACTGAACTGAAC 60.106 40.000 0.00 0.00 0.00 3.18
4922 5111 5.010933 TGTTTTACCAACCACTGAACTGAA 58.989 37.500 0.00 0.00 0.00 3.02
4923 5112 4.590918 TGTTTTACCAACCACTGAACTGA 58.409 39.130 0.00 0.00 0.00 3.41
4924 5113 4.733523 GCTGTTTTACCAACCACTGAACTG 60.734 45.833 0.00 0.00 0.00 3.16
4925 5114 3.380320 GCTGTTTTACCAACCACTGAACT 59.620 43.478 0.00 0.00 0.00 3.01
4926 5115 3.129638 TGCTGTTTTACCAACCACTGAAC 59.870 43.478 0.00 0.00 0.00 3.18
4927 5116 3.357203 TGCTGTTTTACCAACCACTGAA 58.643 40.909 0.00 0.00 0.00 3.02
4928 5117 3.006112 TGCTGTTTTACCAACCACTGA 57.994 42.857 0.00 0.00 0.00 3.41
4929 5118 3.791973 TTGCTGTTTTACCAACCACTG 57.208 42.857 0.00 0.00 0.00 3.66
4930 5119 3.430236 GCTTTGCTGTTTTACCAACCACT 60.430 43.478 0.00 0.00 0.00 4.00
4931 5120 2.863740 GCTTTGCTGTTTTACCAACCAC 59.136 45.455 0.00 0.00 0.00 4.16
4932 5121 2.497675 TGCTTTGCTGTTTTACCAACCA 59.502 40.909 0.00 0.00 0.00 3.67
4933 5122 3.172229 TGCTTTGCTGTTTTACCAACC 57.828 42.857 0.00 0.00 0.00 3.77
4934 5123 4.385748 GCTATGCTTTGCTGTTTTACCAAC 59.614 41.667 0.00 0.00 0.00 3.77
4935 5124 4.280677 AGCTATGCTTTGCTGTTTTACCAA 59.719 37.500 7.71 0.00 33.89 3.67
4936 5125 3.826157 AGCTATGCTTTGCTGTTTTACCA 59.174 39.130 7.71 0.00 33.89 3.25
4937 5126 4.440839 AGCTATGCTTTGCTGTTTTACC 57.559 40.909 7.71 0.00 33.89 2.85
4963 5152 4.955774 AAACTCGCGTTCGCCCGT 62.956 61.111 5.77 5.98 35.26 5.28
4964 5153 4.130281 GAAACTCGCGTTCGCCCG 62.130 66.667 5.77 5.38 35.26 6.13
4965 5154 2.292802 GATGAAACTCGCGTTCGCCC 62.293 60.000 5.77 0.00 35.26 6.13
4966 5155 1.058903 GATGAAACTCGCGTTCGCC 59.941 57.895 5.77 0.00 35.26 5.54
4967 5156 1.058903 GGATGAAACTCGCGTTCGC 59.941 57.895 5.77 7.14 35.26 4.70
4968 5157 0.366871 CAGGATGAAACTCGCGTTCG 59.633 55.000 5.77 0.00 39.69 3.95
4969 5158 1.126846 CACAGGATGAAACTCGCGTTC 59.873 52.381 5.77 3.11 39.69 3.95
4970 5159 1.148310 CACAGGATGAAACTCGCGTT 58.852 50.000 5.77 0.00 39.69 4.84
4971 5160 0.670546 CCACAGGATGAAACTCGCGT 60.671 55.000 5.77 0.00 39.69 6.01
4972 5161 0.670546 ACCACAGGATGAAACTCGCG 60.671 55.000 0.00 0.00 39.69 5.87
4973 5162 2.380084 TACCACAGGATGAAACTCGC 57.620 50.000 0.00 0.00 39.69 5.03
4974 5163 2.673368 GCTTACCACAGGATGAAACTCG 59.327 50.000 0.00 0.00 39.69 4.18
4975 5164 3.674997 TGCTTACCACAGGATGAAACTC 58.325 45.455 0.00 0.00 39.69 3.01
4976 5165 3.788227 TGCTTACCACAGGATGAAACT 57.212 42.857 0.00 0.00 39.69 2.66
4977 5166 4.846779 TTTGCTTACCACAGGATGAAAC 57.153 40.909 0.00 0.00 39.69 2.78
4978 5167 4.321899 GCATTTGCTTACCACAGGATGAAA 60.322 41.667 0.00 0.00 37.59 2.69
4979 5168 3.193267 GCATTTGCTTACCACAGGATGAA 59.807 43.478 0.00 0.00 37.59 2.57
4980 5169 2.754552 GCATTTGCTTACCACAGGATGA 59.245 45.455 0.00 0.00 37.59 2.92
4981 5170 2.478370 CGCATTTGCTTACCACAGGATG 60.478 50.000 0.51 0.00 40.13 3.51
4982 5171 1.745087 CGCATTTGCTTACCACAGGAT 59.255 47.619 0.51 0.00 39.32 3.24
4983 5172 1.164411 CGCATTTGCTTACCACAGGA 58.836 50.000 0.51 0.00 39.32 3.86
4984 5173 0.171007 CCGCATTTGCTTACCACAGG 59.829 55.000 0.51 0.00 39.32 4.00
4985 5174 0.881118 ACCGCATTTGCTTACCACAG 59.119 50.000 0.51 0.00 39.32 3.66
4986 5175 2.080693 CTACCGCATTTGCTTACCACA 58.919 47.619 0.51 0.00 39.32 4.17
4987 5176 2.081462 ACTACCGCATTTGCTTACCAC 58.919 47.619 0.51 0.00 39.32 4.16
4988 5177 2.483014 ACTACCGCATTTGCTTACCA 57.517 45.000 0.51 0.00 39.32 3.25
4989 5178 2.870411 CCTACTACCGCATTTGCTTACC 59.130 50.000 0.51 0.00 39.32 2.85
4990 5179 2.287103 GCCTACTACCGCATTTGCTTAC 59.713 50.000 0.51 0.00 39.32 2.34
4991 5180 2.557317 GCCTACTACCGCATTTGCTTA 58.443 47.619 0.51 0.00 39.32 3.09
4992 5181 1.379527 GCCTACTACCGCATTTGCTT 58.620 50.000 0.51 0.00 39.32 3.91
4993 5182 0.463833 GGCCTACTACCGCATTTGCT 60.464 55.000 0.00 0.00 39.32 3.91
4994 5183 1.444917 GGGCCTACTACCGCATTTGC 61.445 60.000 0.84 0.00 37.78 3.68
4995 5184 0.818040 GGGGCCTACTACCGCATTTG 60.818 60.000 0.84 0.00 39.80 2.32
4996 5185 1.276140 TGGGGCCTACTACCGCATTT 61.276 55.000 0.84 0.00 44.39 2.32
4997 5186 1.691337 TGGGGCCTACTACCGCATT 60.691 57.895 0.84 0.00 44.39 3.56
4998 5187 2.041301 TGGGGCCTACTACCGCAT 60.041 61.111 0.84 0.00 44.39 4.73
5000 5189 1.450848 GTTTGGGGCCTACTACCGC 60.451 63.158 0.84 0.00 40.42 5.68
5001 5190 1.153509 CGTTTGGGGCCTACTACCG 60.154 63.158 0.84 0.00 0.00 4.02
5002 5191 1.222661 CCGTTTGGGGCCTACTACC 59.777 63.158 0.84 0.00 0.00 3.18
5003 5192 4.948257 CCGTTTGGGGCCTACTAC 57.052 61.111 0.84 0.00 0.00 2.73
5021 5210 3.566853 CATGCTGTGCTACCGCCG 61.567 66.667 0.00 0.00 34.43 6.46
5022 5211 2.125147 TCATGCTGTGCTACCGCC 60.125 61.111 0.00 0.00 34.43 6.13
5023 5212 2.817423 GCTCATGCTGTGCTACCGC 61.817 63.158 0.00 0.00 34.37 5.68
5024 5213 0.812811 ATGCTCATGCTGTGCTACCG 60.813 55.000 10.19 0.00 37.71 4.02
5025 5214 0.942962 GATGCTCATGCTGTGCTACC 59.057 55.000 10.19 0.00 37.71 3.18
5026 5215 0.580578 CGATGCTCATGCTGTGCTAC 59.419 55.000 10.19 5.25 37.71 3.58
5027 5216 0.461135 TCGATGCTCATGCTGTGCTA 59.539 50.000 10.19 0.97 37.71 3.49
5028 5217 0.179054 ATCGATGCTCATGCTGTGCT 60.179 50.000 0.00 0.00 37.71 4.40
5029 5218 0.235144 GATCGATGCTCATGCTGTGC 59.765 55.000 0.54 4.06 40.48 4.57
5030 5219 1.527311 CAGATCGATGCTCATGCTGTG 59.473 52.381 0.54 0.00 40.48 3.66
5031 5220 1.540580 CCAGATCGATGCTCATGCTGT 60.541 52.381 0.54 0.00 40.48 4.40
5032 5221 1.149148 CCAGATCGATGCTCATGCTG 58.851 55.000 0.54 1.48 40.48 4.41
5033 5222 0.603172 GCCAGATCGATGCTCATGCT 60.603 55.000 0.54 0.00 40.48 3.79
5034 5223 1.575576 GGCCAGATCGATGCTCATGC 61.576 60.000 0.54 2.90 40.20 4.06
5035 5224 1.289800 CGGCCAGATCGATGCTCATG 61.290 60.000 0.54 0.00 0.00 3.07
5036 5225 1.005275 CGGCCAGATCGATGCTCAT 60.005 57.895 0.54 0.00 0.00 2.90
5037 5226 2.418777 CGGCCAGATCGATGCTCA 59.581 61.111 0.54 0.00 0.00 4.26
5038 5227 1.953138 CACGGCCAGATCGATGCTC 60.953 63.158 0.54 0.00 0.00 4.26
5039 5228 2.107750 CACGGCCAGATCGATGCT 59.892 61.111 0.54 0.00 0.00 3.79
5040 5229 2.202932 ACACGGCCAGATCGATGC 60.203 61.111 0.54 0.00 0.00 3.91
5041 5230 0.740868 AACACACGGCCAGATCGATG 60.741 55.000 0.54 0.00 0.00 3.84
5042 5231 0.036388 AAACACACGGCCAGATCGAT 60.036 50.000 2.24 0.00 0.00 3.59
5043 5232 0.250124 AAAACACACGGCCAGATCGA 60.250 50.000 2.24 0.00 0.00 3.59
5044 5233 0.591170 AAAAACACACGGCCAGATCG 59.409 50.000 2.24 0.00 0.00 3.69
5045 5234 1.335872 CCAAAAACACACGGCCAGATC 60.336 52.381 2.24 0.00 0.00 2.75
5046 5235 0.673437 CCAAAAACACACGGCCAGAT 59.327 50.000 2.24 0.00 0.00 2.90
5047 5236 2.010582 GCCAAAAACACACGGCCAGA 62.011 55.000 2.24 0.00 38.67 3.86
5048 5237 1.591327 GCCAAAAACACACGGCCAG 60.591 57.895 2.24 0.00 38.67 4.85
5049 5238 2.351244 TGCCAAAAACACACGGCCA 61.351 52.632 2.24 0.00 44.22 5.36
5050 5239 1.880796 GTGCCAAAAACACACGGCC 60.881 57.895 0.00 0.00 44.22 6.13
5051 5240 1.153745 TGTGCCAAAAACACACGGC 60.154 52.632 0.00 0.00 42.88 5.68
5055 5244 2.168106 AGATGCTTGTGCCAAAAACACA 59.832 40.909 0.00 0.00 45.90 3.72
5056 5245 2.825205 AGATGCTTGTGCCAAAAACAC 58.175 42.857 0.00 0.00 38.71 3.32
5057 5246 3.243704 GGTAGATGCTTGTGCCAAAAACA 60.244 43.478 0.00 0.00 38.71 2.83
5058 5247 3.005791 AGGTAGATGCTTGTGCCAAAAAC 59.994 43.478 6.64 0.00 38.71 2.43
5059 5248 3.230134 AGGTAGATGCTTGTGCCAAAAA 58.770 40.909 6.64 0.00 38.71 1.94
5060 5249 2.875296 AGGTAGATGCTTGTGCCAAAA 58.125 42.857 6.64 0.00 38.71 2.44
5061 5250 2.584835 AGGTAGATGCTTGTGCCAAA 57.415 45.000 6.64 0.00 38.71 3.28
5062 5251 3.931907 ATAGGTAGATGCTTGTGCCAA 57.068 42.857 6.64 0.00 38.71 4.52
5063 5252 3.967326 ACTATAGGTAGATGCTTGTGCCA 59.033 43.478 4.43 0.00 38.71 4.92
5064 5253 4.608948 ACTATAGGTAGATGCTTGTGCC 57.391 45.455 4.43 0.00 38.71 5.01


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

AutoCloner maintained by Alex Coulton.