Multiple sequence alignment - TraesCS1B01G118200

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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 TraesCS1B01G118200 chr1B 100.000 7698 0 0 1 7698 138035771 138043468 0.000000e+00 14216.0
1 TraesCS1B01G118200 chr1D 94.112 5978 222 45 1 5908 85642839 85648756 0.000000e+00 8970.0
2 TraesCS1B01G118200 chr1D 95.598 886 34 4 5920 6801 85648712 85649596 0.000000e+00 1415.0
3 TraesCS1B01G118200 chr1A 95.785 5124 126 31 830 5908 80189946 80195024 0.000000e+00 8183.0
4 TraesCS1B01G118200 chr1A 93.789 950 47 9 5920 6864 80194980 80195922 0.000000e+00 1417.0
5 TraesCS1B01G118200 chr1A 88.761 952 82 15 1 934 80188417 80189361 0.000000e+00 1142.0
6 TraesCS1B01G118200 chr7B 88.406 828 94 2 6872 7698 13321368 13320542 0.000000e+00 996.0
7 TraesCS1B01G118200 chr7B 87.560 828 99 3 6872 7698 332919625 332920449 0.000000e+00 955.0
8 TraesCS1B01G118200 chr2D 88.164 828 95 3 6872 7698 370049428 370048603 0.000000e+00 983.0
9 TraesCS1B01G118200 chr2D 100.000 45 0 0 1630 1674 130726046 130726002 4.950000e-12 84.2
10 TraesCS1B01G118200 chr3A 88.164 828 93 5 6872 7698 59463669 59462846 0.000000e+00 981.0
11 TraesCS1B01G118200 chr3A 87.334 829 101 4 6872 7698 82464209 82463383 0.000000e+00 946.0
12 TraesCS1B01G118200 chr5A 87.470 830 103 1 6869 7698 417294754 417295582 0.000000e+00 955.0
13 TraesCS1B01G118200 chr5A 100.000 43 0 0 1630 1672 382114857 382114899 6.400000e-11 80.5
14 TraesCS1B01G118200 chr6B 87.380 832 100 5 6869 7698 290708726 290709554 0.000000e+00 950.0
15 TraesCS1B01G118200 chr6A 87.229 830 106 0 6869 7698 52699786 52700615 0.000000e+00 946.0
16 TraesCS1B01G118200 chr2A 87.304 827 105 0 6872 7698 554048278 554047452 0.000000e+00 946.0
17 TraesCS1B01G118200 chr2A 77.540 187 34 7 111 294 82987407 82987588 1.060000e-18 106.0
18 TraesCS1B01G118200 chr5B 92.188 64 3 1 1631 1692 706166244 706166181 1.060000e-13 89.8
19 TraesCS1B01G118200 chr6D 91.935 62 5 0 4212 4273 313014239 313014300 3.830000e-13 87.9
20 TraesCS1B01G118200 chr4B 100.000 44 0 0 1629 1672 131352008 131352051 1.780000e-11 82.4
21 TraesCS1B01G118200 chr4B 94.118 51 1 2 1631 1680 83310533 83310582 8.280000e-10 76.8
22 TraesCS1B01G118200 chr4A 97.826 46 1 0 1630 1675 662286503 662286458 6.400000e-11 80.5
23 TraesCS1B01G118200 chr4A 100.000 30 0 0 5371 5400 537547418 537547447 1.000000e-03 56.5
24 TraesCS1B01G118200 chr7A 91.071 56 4 1 1619 1674 124792612 124792666 2.980000e-09 75.0
25 TraesCS1B01G118200 chr7D 100.000 29 0 0 5371 5399 403773186 403773214 4.000000e-03 54.7
26 TraesCS1B01G118200 chr3B 100.000 29 0 0 5371 5399 710390441 710390413 4.000000e-03 54.7


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 TraesCS1B01G118200 chr1B 138035771 138043468 7697 False 14216.000000 14216 100.000000 1 7698 1 chr1B.!!$F1 7697
1 TraesCS1B01G118200 chr1D 85642839 85649596 6757 False 5192.500000 8970 94.855000 1 6801 2 chr1D.!!$F1 6800
2 TraesCS1B01G118200 chr1A 80188417 80195922 7505 False 3580.666667 8183 92.778333 1 6864 3 chr1A.!!$F1 6863
3 TraesCS1B01G118200 chr7B 13320542 13321368 826 True 996.000000 996 88.406000 6872 7698 1 chr7B.!!$R1 826
4 TraesCS1B01G118200 chr7B 332919625 332920449 824 False 955.000000 955 87.560000 6872 7698 1 chr7B.!!$F1 826
5 TraesCS1B01G118200 chr2D 370048603 370049428 825 True 983.000000 983 88.164000 6872 7698 1 chr2D.!!$R2 826
6 TraesCS1B01G118200 chr3A 59462846 59463669 823 True 981.000000 981 88.164000 6872 7698 1 chr3A.!!$R1 826
7 TraesCS1B01G118200 chr3A 82463383 82464209 826 True 946.000000 946 87.334000 6872 7698 1 chr3A.!!$R2 826
8 TraesCS1B01G118200 chr5A 417294754 417295582 828 False 955.000000 955 87.470000 6869 7698 1 chr5A.!!$F2 829
9 TraesCS1B01G118200 chr6B 290708726 290709554 828 False 950.000000 950 87.380000 6869 7698 1 chr6B.!!$F1 829
10 TraesCS1B01G118200 chr6A 52699786 52700615 829 False 946.000000 946 87.229000 6869 7698 1 chr6A.!!$F1 829
11 TraesCS1B01G118200 chr2A 554047452 554048278 826 True 946.000000 946 87.304000 6872 7698 1 chr2A.!!$R1 826

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
381 383 0.181824 GCGGAATAGGCTAACCCCAA 59.818 55.000 13.08 0.0 36.11 4.12 F
1029 1744 0.250727 CAGACCACCAACCCGACAAT 60.251 55.000 0.00 0.0 0.00 2.71 F
1484 2199 0.678048 GTGCCTCAGGTTGTGGGATC 60.678 60.000 0.00 0.0 34.05 3.36 F
2470 3188 2.170187 TGGTGCCCGTATTTTATACCGT 59.830 45.455 0.00 0.0 0.00 4.83 F
3131 3857 2.523245 TGTAGTTCATTGCCATGCCAA 58.477 42.857 0.00 0.0 0.00 4.52 F
4069 4817 3.142174 GGTATGTTAGCTGCCCTCATTC 58.858 50.000 0.00 0.0 0.00 2.67 F
5539 6292 1.549170 CCCGTGGTACTCTAAAGCAGT 59.451 52.381 0.00 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1301 2016 0.034198 GCCTAGCCTAGCCTAGCAAC 59.966 60.000 2.10 0.00 34.74 4.17 R
1915 2630 1.448985 TTCGCTGCCGCTCTTTAAAT 58.551 45.000 0.00 0.00 0.00 1.40 R
3074 3800 2.813754 TGTTGAGTGCCACTTTCATAGC 59.186 45.455 0.00 0.00 0.00 2.97 R
4119 4867 2.095364 CGAGTATATACTGCACGGGGAC 60.095 54.545 20.13 1.67 36.50 4.46 R
4121 4869 2.156917 TCGAGTATATACTGCACGGGG 58.843 52.381 20.13 1.35 36.50 5.73 R
5872 6636 0.833287 TATTCTGAGAGGGCCACAGC 59.167 55.000 6.18 0.00 38.76 4.40 R
6826 7591 0.111266 GCGCGCAAGTAATCCGTATG 60.111 55.000 29.10 0.00 41.68 2.39 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
89 90 4.209080 TGCGTATGTTGAGAGAAATATGCG 59.791 41.667 0.00 0.00 39.37 4.73
101 102 6.283694 AGAGAAATATGCGAGTGAATGCTAA 58.716 36.000 0.00 0.00 0.00 3.09
109 110 6.494893 TGCGAGTGAATGCTAACTTTTTAT 57.505 33.333 0.00 0.00 0.00 1.40
113 114 7.518161 CGAGTGAATGCTAACTTTTTATGACA 58.482 34.615 0.00 0.00 0.00 3.58
163 164 3.806422 TCTTCGTCGCATCGCCGA 61.806 61.111 0.00 0.00 34.40 5.54
169 170 2.571757 TCGCATCGCCGACTCTTT 59.428 55.556 0.00 0.00 31.36 2.52
175 176 1.328680 CATCGCCGACTCTTTCAATGG 59.671 52.381 0.00 0.00 0.00 3.16
197 198 1.847506 TGTGGGGCTCATGAGGTGT 60.848 57.895 23.89 0.00 0.00 4.16
211 212 5.306937 TCATGAGGTGTTTTCTAGGAAGTGA 59.693 40.000 0.00 0.00 0.00 3.41
221 222 6.544928 TTTCTAGGAAGTGATGCATGTCTA 57.455 37.500 2.46 0.00 0.00 2.59
224 225 6.365520 TCTAGGAAGTGATGCATGTCTACTA 58.634 40.000 2.46 7.66 0.00 1.82
259 260 2.588877 GGTGGCGCGTGCTATGAT 60.589 61.111 21.89 0.00 42.25 2.45
307 309 0.464452 GGGGCACATACGCTAGACTT 59.536 55.000 0.00 0.00 0.00 3.01
310 312 0.931005 GCACATACGCTAGACTTGGC 59.069 55.000 0.00 0.00 0.00 4.52
325 327 0.817013 TTGGCGATGGCTTTGGATTC 59.183 50.000 0.00 0.00 39.81 2.52
331 333 1.669999 ATGGCTTTGGATTCTGGCGC 61.670 55.000 0.00 0.00 0.00 6.53
356 358 0.969894 CTTCCGACCCAGTGACTTCT 59.030 55.000 0.00 0.00 0.00 2.85
357 359 1.344763 CTTCCGACCCAGTGACTTCTT 59.655 52.381 0.00 0.00 0.00 2.52
361 363 1.341531 CGACCCAGTGACTTCTTGTCT 59.658 52.381 0.00 0.00 45.54 3.41
375 377 2.764010 TCTTGTCTGCGGAATAGGCTAA 59.236 45.455 0.00 0.00 0.00 3.09
381 383 0.181824 GCGGAATAGGCTAACCCCAA 59.818 55.000 13.08 0.00 36.11 4.12
391 393 2.903784 GGCTAACCCCAAATTCAAGGTT 59.096 45.455 9.96 9.96 44.61 3.50
406 408 2.817396 GTTGAGGAGGAGCAGCGC 60.817 66.667 0.00 0.00 0.00 5.92
409 411 4.828925 GAGGAGGAGCAGCGCCAC 62.829 72.222 18.51 11.24 0.00 5.01
435 448 1.377202 TCTTGGAAGCCATGGTCGC 60.377 57.895 14.67 0.00 31.53 5.19
515 528 7.658261 AGGCCGAGCTTTTAATAAAAATATCC 58.342 34.615 0.00 0.00 34.18 2.59
516 529 6.581166 GGCCGAGCTTTTAATAAAAATATCCG 59.419 38.462 0.00 0.72 34.18 4.18
517 530 6.581166 GCCGAGCTTTTAATAAAAATATCCGG 59.419 38.462 0.00 0.00 36.87 5.14
528 541 1.972872 AATATCCGGCTCCTGCAAAG 58.027 50.000 0.00 0.00 41.91 2.77
625 642 9.871238 AAGTCATCTATTCACACGTTATTACTT 57.129 29.630 0.00 0.00 0.00 2.24
626 643 9.517609 AGTCATCTATTCACACGTTATTACTTC 57.482 33.333 0.00 0.00 0.00 3.01
634 651 8.836268 TTCACACGTTATTACTTCCAAAGTAT 57.164 30.769 0.71 0.00 43.09 2.12
745 762 9.660180 ACTTTAGTGATCTATGAAAGGTCTTTC 57.340 33.333 14.55 14.55 46.71 2.62
785 802 9.561069 AGAGAGAGAGTATTTTTGTAAAGCAAA 57.439 29.630 0.00 0.00 44.52 3.68
792 809 5.726729 ATTTTTGTAAAGCAAACAACCGG 57.273 34.783 0.00 0.00 45.70 5.28
804 821 5.475564 AGCAAACAACCGGTTCTACATATTT 59.524 36.000 19.24 6.71 39.29 1.40
811 828 3.066203 CCGGTTCTACATATTTTGGGCAC 59.934 47.826 0.00 0.00 0.00 5.01
813 830 4.035208 CGGTTCTACATATTTTGGGCACTC 59.965 45.833 0.00 0.00 0.00 3.51
866 883 9.696917 ATAGTTGAAGGAACAAAATCATCAAAC 57.303 29.630 0.00 0.00 36.98 2.93
868 885 7.707893 AGTTGAAGGAACAAAATCATCAAACTG 59.292 33.333 0.00 0.00 36.98 3.16
954 1667 2.572191 TCATCACGGCTAGGTAAACG 57.428 50.000 0.00 0.00 0.00 3.60
970 1683 0.318955 AACGCACTGCTTTGCCATTC 60.319 50.000 0.00 0.00 39.53 2.67
976 1689 3.460103 CACTGCTTTGCCATTCTGTTTT 58.540 40.909 0.00 0.00 0.00 2.43
977 1690 3.492011 CACTGCTTTGCCATTCTGTTTTC 59.508 43.478 0.00 0.00 0.00 2.29
1029 1744 0.250727 CAGACCACCAACCCGACAAT 60.251 55.000 0.00 0.00 0.00 2.71
1301 2016 2.260869 CCACCCTTGCGGAGTTGTG 61.261 63.158 0.00 0.00 34.64 3.33
1302 2017 1.525995 CACCCTTGCGGAGTTGTGT 60.526 57.895 0.00 0.00 34.64 3.72
1338 2053 1.413008 GCATGGTTGGAATTTCGCGC 61.413 55.000 0.00 0.00 0.00 6.86
1355 2070 0.736325 CGCTTCGTCTTCGGGAATGT 60.736 55.000 0.00 0.00 37.69 2.71
1383 2098 3.136077 GGATTAGGGTTTACTGGGTCTCC 59.864 52.174 0.00 0.00 0.00 3.71
1397 2112 2.552031 GGTCTCCTTCGAAATGGCTAC 58.448 52.381 0.00 0.00 0.00 3.58
1402 2117 2.494471 TCCTTCGAAATGGCTACGAGAA 59.506 45.455 0.00 0.00 37.36 2.87
1415 2130 3.737355 GCTACGAGAATGGGTGAGGTTAC 60.737 52.174 0.00 0.00 0.00 2.50
1426 2141 3.243816 AGGTTACGGTGCCGGGTT 61.244 61.111 15.44 0.00 44.69 4.11
1431 2146 0.954938 TTACGGTGCCGGGTTTTAGC 60.955 55.000 15.44 0.00 44.69 3.09
1449 2164 4.090057 GGCTGGCGTTCGCTTGAC 62.090 66.667 16.40 8.33 0.00 3.18
1450 2165 4.430423 GCTGGCGTTCGCTTGACG 62.430 66.667 16.40 0.00 45.62 4.35
1484 2199 0.678048 GTGCCTCAGGTTGTGGGATC 60.678 60.000 0.00 0.00 34.05 3.36
1538 2253 3.443045 CCATGACCTGCAACCGGC 61.443 66.667 0.00 0.00 45.13 6.13
1578 2293 3.023939 AGGCATTCCCTCAGAAAATCC 57.976 47.619 0.00 0.00 41.21 3.01
1723 2438 5.991606 GGTTTAAGAAGGTAACACCGTAACT 59.008 40.000 0.00 0.00 44.90 2.24
1790 2505 6.978338 AGTTGATTCGACTCTGTTGTTACTA 58.022 36.000 4.29 0.00 0.00 1.82
1798 2513 5.078411 ACTCTGTTGTTACTAGGCATCAG 57.922 43.478 12.28 12.28 35.12 2.90
1820 2535 2.356125 GGGCAGCTCCTGATTAGTTTGA 60.356 50.000 0.00 0.00 32.44 2.69
1839 2554 3.950397 TGACCACTTCTGTTGTTCAACT 58.050 40.909 15.18 0.00 0.00 3.16
1915 2630 8.506168 AAACGAAAAGGATATTGCTTGAGATA 57.494 30.769 0.00 0.00 0.00 1.98
2035 2750 7.753630 AGCTCTGGTTCTTATATTCCATGATT 58.246 34.615 0.00 0.00 0.00 2.57
2313 3028 6.530601 ACCACCTTATGATTTAGGCCTTAT 57.469 37.500 12.58 4.91 34.79 1.73
2454 3172 2.491675 AAGGTAAGGTAGCTTGGTGC 57.508 50.000 17.34 4.91 44.11 5.01
2470 3188 2.170187 TGGTGCCCGTATTTTATACCGT 59.830 45.455 0.00 0.00 0.00 4.83
2611 3329 5.728351 TTTCTCGTTTTGTGTCTAACAGG 57.272 39.130 0.00 0.00 40.74 4.00
2714 3432 8.849168 TCTGTGTTCATTCTAATGTTCATGTTT 58.151 29.630 2.80 0.00 37.65 2.83
2998 3724 6.389091 TGTGCTTCATTTTTAGCTGTAATGG 58.611 36.000 13.77 4.43 38.22 3.16
3062 3788 6.918022 CCATTCTTACCCGATTAAGATTTTGC 59.082 38.462 6.55 0.00 37.80 3.68
3074 3800 9.110617 CGATTAAGATTTTGCTGCATAATGTAG 57.889 33.333 20.40 5.80 33.01 2.74
3131 3857 2.523245 TGTAGTTCATTGCCATGCCAA 58.477 42.857 0.00 0.00 0.00 4.52
3134 3860 3.255969 AGTTCATTGCCATGCCAATTC 57.744 42.857 0.00 0.00 33.35 2.17
3191 3917 8.647796 TCCTTGTCTTTATAGAGAAACAACTGA 58.352 33.333 0.00 0.00 33.72 3.41
3319 4057 4.010667 AGACTGGACCGCTAGATAGTAG 57.989 50.000 0.00 0.00 0.00 2.57
3766 4505 6.128282 TGTTCTTTATGCGAGGAATTGTCTTC 60.128 38.462 0.00 0.00 0.00 2.87
3874 4613 9.936329 TCAGGTAATAGCTATATGGATCACATA 57.064 33.333 6.68 0.72 45.60 2.29
3905 4647 6.700960 TGCAAATTTGGTCATCTTGTACTTTG 59.299 34.615 19.47 0.00 0.00 2.77
3915 4657 7.017645 GTCATCTTGTACTTTGCAGTGTAATG 58.982 38.462 5.47 5.47 34.06 1.90
4069 4817 3.142174 GGTATGTTAGCTGCCCTCATTC 58.858 50.000 0.00 0.00 0.00 2.67
4119 4867 4.800993 TGCACCAAGTTACATTGTTTTTCG 59.199 37.500 0.00 0.00 0.00 3.46
4121 4869 5.051973 GCACCAAGTTACATTGTTTTTCGTC 60.052 40.000 0.00 0.00 0.00 4.20
4140 4888 2.095364 GTCCCCGTGCAGTATATACTCG 60.095 54.545 12.62 12.85 33.46 4.18
4285 5033 8.248945 AGATCTTCGTCGAAAGAGGTTAAAATA 58.751 33.333 9.30 0.00 45.61 1.40
4298 5046 5.372373 AGGTTAAAATATGCTCTCTGCTCC 58.628 41.667 0.00 0.00 43.37 4.70
4454 5202 7.816640 ACGAATACAGAATAACAATGCAGTTT 58.183 30.769 0.00 0.00 33.07 2.66
4550 5298 6.046593 TGAGAGCTTTCTCGACTTTGTTTTA 58.953 36.000 5.77 0.00 44.02 1.52
4619 5367 1.623311 TGCCTTGATCTCAACGGAAGA 59.377 47.619 10.64 0.00 0.00 2.87
4625 5373 4.826274 TGATCTCAACGGAAGAGGATTT 57.174 40.909 0.00 0.00 33.92 2.17
4711 5463 5.105635 TGTGTAGTATTGTGGTGGTAGCTAC 60.106 44.000 15.88 15.88 0.00 3.58
4724 5476 7.820872 GTGGTGGTAGCTACTTTTTCTACAATA 59.179 37.037 22.74 0.97 35.58 1.90
4928 5680 4.191544 GCACAAGACATAGCACCATTCTA 58.808 43.478 0.00 0.00 0.00 2.10
4937 5689 7.497249 AGACATAGCACCATTCTATTCAAAGTC 59.503 37.037 0.00 0.00 0.00 3.01
4957 5709 7.745620 AAGTCGAGAACAACCTTGATAAATT 57.254 32.000 0.00 0.00 0.00 1.82
4966 5718 7.360113 ACAACCTTGATAAATTTTGACCAGT 57.640 32.000 0.00 0.00 0.00 4.00
5002 5754 9.606631 ATCTCTTCCTCAATAACTTTATGTCAC 57.393 33.333 0.00 0.00 0.00 3.67
5140 5892 4.045636 CTGTTTTCTGAACAGGGGTTTG 57.954 45.455 10.29 0.00 42.83 2.93
5154 5906 4.022329 CAGGGGTTTGAACAATTCTGTACC 60.022 45.833 0.00 0.00 33.45 3.34
5421 6173 8.660295 TTTTACACTCTCAAGTTCCCTATCTA 57.340 34.615 0.00 0.00 31.71 1.98
5491 6244 1.933853 GTCACTCGCAATGGTATCCAC 59.066 52.381 0.00 0.00 35.80 4.02
5539 6292 1.549170 CCCGTGGTACTCTAAAGCAGT 59.451 52.381 0.00 0.00 0.00 4.40
5874 6638 9.737844 ATTAATGTGACCAAAATTTTAATGGCT 57.262 25.926 2.44 0.00 37.77 4.75
5875 6639 7.437793 AATGTGACCAAAATTTTAATGGCTG 57.562 32.000 2.44 0.00 37.77 4.85
5876 6640 5.923204 TGTGACCAAAATTTTAATGGCTGT 58.077 33.333 2.44 0.00 37.77 4.40
5877 6641 5.757320 TGTGACCAAAATTTTAATGGCTGTG 59.243 36.000 2.44 0.00 37.77 3.66
5878 6642 5.179182 GTGACCAAAATTTTAATGGCTGTGG 59.821 40.000 2.44 0.69 37.77 4.17
5879 6643 4.071423 ACCAAAATTTTAATGGCTGTGGC 58.929 39.130 2.44 0.00 37.77 5.01
5889 6653 3.072476 GCTGTGGCCCTCTCAGAA 58.928 61.111 15.26 0.00 38.80 3.02
5890 6654 1.606531 GCTGTGGCCCTCTCAGAAT 59.393 57.895 15.26 0.00 38.80 2.40
5891 6655 0.833287 GCTGTGGCCCTCTCAGAATA 59.167 55.000 15.26 0.00 38.80 1.75
5892 6656 1.474143 GCTGTGGCCCTCTCAGAATAC 60.474 57.143 15.26 0.00 38.80 1.89
5893 6657 1.139853 CTGTGGCCCTCTCAGAATACC 59.860 57.143 0.00 0.00 38.80 2.73
5894 6658 1.273838 TGTGGCCCTCTCAGAATACCT 60.274 52.381 0.00 0.00 0.00 3.08
5895 6659 2.023404 TGTGGCCCTCTCAGAATACCTA 60.023 50.000 0.00 0.00 0.00 3.08
5896 6660 2.365941 GTGGCCCTCTCAGAATACCTAC 59.634 54.545 0.00 0.00 0.00 3.18
5897 6661 2.023404 TGGCCCTCTCAGAATACCTACA 60.023 50.000 0.00 0.00 0.00 2.74
5898 6662 2.630580 GGCCCTCTCAGAATACCTACAG 59.369 54.545 0.00 0.00 0.00 2.74
5899 6663 2.630580 GCCCTCTCAGAATACCTACAGG 59.369 54.545 0.00 0.00 42.17 4.00
5900 6664 2.630580 CCCTCTCAGAATACCTACAGGC 59.369 54.545 0.00 0.00 39.32 4.85
5901 6665 2.630580 CCTCTCAGAATACCTACAGGCC 59.369 54.545 0.00 0.00 39.32 5.19
5902 6666 3.300388 CTCTCAGAATACCTACAGGCCA 58.700 50.000 5.01 0.00 39.32 5.36
5903 6667 3.706594 CTCTCAGAATACCTACAGGCCAA 59.293 47.826 5.01 0.00 39.32 4.52
5904 6668 4.101114 TCTCAGAATACCTACAGGCCAAA 58.899 43.478 5.01 0.00 39.32 3.28
5905 6669 4.534500 TCTCAGAATACCTACAGGCCAAAA 59.466 41.667 5.01 0.00 39.32 2.44
5906 6670 5.191722 TCTCAGAATACCTACAGGCCAAAAT 59.808 40.000 5.01 0.00 39.32 1.82
5907 6671 6.385759 TCTCAGAATACCTACAGGCCAAAATA 59.614 38.462 5.01 0.00 39.32 1.40
5908 6672 6.964464 TCAGAATACCTACAGGCCAAAATAA 58.036 36.000 5.01 0.00 39.32 1.40
5909 6673 7.582719 TCAGAATACCTACAGGCCAAAATAAT 58.417 34.615 5.01 0.00 39.32 1.28
5910 6674 7.719633 TCAGAATACCTACAGGCCAAAATAATC 59.280 37.037 5.01 0.00 39.32 1.75
5911 6675 7.004691 AGAATACCTACAGGCCAAAATAATCC 58.995 38.462 5.01 0.00 39.32 3.01
5912 6676 4.601406 ACCTACAGGCCAAAATAATCCA 57.399 40.909 5.01 0.00 39.32 3.41
5913 6677 4.941713 ACCTACAGGCCAAAATAATCCAA 58.058 39.130 5.01 0.00 39.32 3.53
5914 6678 4.956075 ACCTACAGGCCAAAATAATCCAAG 59.044 41.667 5.01 0.00 39.32 3.61
5915 6679 4.342092 CCTACAGGCCAAAATAATCCAAGG 59.658 45.833 5.01 0.00 0.00 3.61
5916 6680 2.501316 ACAGGCCAAAATAATCCAAGGC 59.499 45.455 5.01 0.00 41.29 4.35
5917 6681 2.500910 CAGGCCAAAATAATCCAAGGCA 59.499 45.455 5.01 0.00 43.72 4.75
5918 6682 3.135167 CAGGCCAAAATAATCCAAGGCAT 59.865 43.478 5.01 0.00 43.72 4.40
5919 6683 4.344679 CAGGCCAAAATAATCCAAGGCATA 59.655 41.667 5.01 0.00 43.72 3.14
5920 6684 5.012354 CAGGCCAAAATAATCCAAGGCATAT 59.988 40.000 5.01 0.00 43.72 1.78
5921 6685 5.608015 AGGCCAAAATAATCCAAGGCATATT 59.392 36.000 5.01 0.00 43.72 1.28
5922 6686 6.101588 AGGCCAAAATAATCCAAGGCATATTT 59.898 34.615 5.01 4.25 43.72 1.40
5923 6687 6.427853 GGCCAAAATAATCCAAGGCATATTTC 59.572 38.462 0.00 0.73 43.72 2.17
6005 6769 9.462174 TTGTGAAATCAGAATGTGTTGAATAAC 57.538 29.630 0.00 0.00 37.40 1.89
6068 6832 9.941664 AGTAATCTTTGATTGCATTTCTAATCG 57.058 29.630 10.11 0.00 36.36 3.34
6073 6837 9.859427 TCTTTGATTGCATTTCTAATCGAAAAT 57.141 25.926 0.00 0.00 44.25 1.82
6114 6878 4.632327 TGTATTGACCTCATGACAACCA 57.368 40.909 0.00 0.00 0.00 3.67
6294 7058 0.185901 TCCTTTCCTGCAAGCAAGGT 59.814 50.000 12.65 0.00 41.36 3.50
6303 7067 1.340017 TGCAAGCAAGGTGGGACTATC 60.340 52.381 0.00 0.00 0.00 2.08
6427 7191 1.009829 CAAACTATGGTGCTCCGCTC 58.990 55.000 0.00 0.00 36.30 5.03
6432 7196 1.448119 TATGGTGCTCCGCTCTCTCG 61.448 60.000 0.00 0.00 36.30 4.04
6436 7200 2.402572 TGCTCCGCTCTCTCGACAG 61.403 63.158 0.00 0.00 0.00 3.51
6438 7202 1.090625 GCTCCGCTCTCTCGACAGTA 61.091 60.000 0.00 0.00 0.00 2.74
6442 7206 1.360820 CGCTCTCTCGACAGTAGTGA 58.639 55.000 4.09 0.00 0.00 3.41
6547 7311 3.866703 TGTGTGAGTGGGTTAAATCCA 57.133 42.857 0.00 0.00 0.00 3.41
6566 7330 6.963049 ATCCAAGTGATTACGAGTTTGTAC 57.037 37.500 0.00 0.00 0.00 2.90
6609 7373 4.141846 GCTAACTGTGGATCATTCTCAGGA 60.142 45.833 0.05 0.00 32.38 3.86
6707 7472 3.502123 TCTGTTTCTCCCACCGATTTT 57.498 42.857 0.00 0.00 0.00 1.82
6717 7482 2.556622 CCCACCGATTTTTAACTGCAGT 59.443 45.455 15.25 15.25 0.00 4.40
6740 7505 1.344438 CTATGCGCTCCCTTGTGGATA 59.656 52.381 9.73 0.00 44.07 2.59
6760 7525 9.376075 GTGGATATGATCTATTTGTACCTGATG 57.624 37.037 0.00 0.00 0.00 3.07
6769 7534 7.118723 TCTATTTGTACCTGATGGAATTTGCT 58.881 34.615 0.00 0.00 37.04 3.91
6802 7567 7.784633 TTTTTGGAAATAGAGGCAAAGTTTG 57.215 32.000 11.41 11.41 0.00 2.93
6805 7570 7.589958 TTGGAAATAGAGGCAAAGTTTGTTA 57.410 32.000 16.70 5.79 0.00 2.41
6806 7571 6.977213 TGGAAATAGAGGCAAAGTTTGTTAC 58.023 36.000 16.70 7.98 0.00 2.50
6807 7572 6.547880 TGGAAATAGAGGCAAAGTTTGTTACA 59.452 34.615 16.70 5.70 0.00 2.41
6808 7573 7.068839 TGGAAATAGAGGCAAAGTTTGTTACAA 59.931 33.333 16.70 0.00 0.00 2.41
6809 7574 7.595130 GGAAATAGAGGCAAAGTTTGTTACAAG 59.405 37.037 16.70 0.00 0.00 3.16
6810 7575 7.817418 AATAGAGGCAAAGTTTGTTACAAGA 57.183 32.000 16.70 0.00 0.00 3.02
6811 7576 5.500645 AGAGGCAAAGTTTGTTACAAGAC 57.499 39.130 16.70 0.69 0.00 3.01
6812 7577 4.947388 AGAGGCAAAGTTTGTTACAAGACA 59.053 37.500 16.70 0.00 0.00 3.41
6813 7578 5.594317 AGAGGCAAAGTTTGTTACAAGACAT 59.406 36.000 16.70 0.00 0.00 3.06
6814 7579 6.770785 AGAGGCAAAGTTTGTTACAAGACATA 59.229 34.615 16.70 0.00 0.00 2.29
6815 7580 6.970484 AGGCAAAGTTTGTTACAAGACATAG 58.030 36.000 16.70 0.00 0.00 2.23
6816 7581 6.770785 AGGCAAAGTTTGTTACAAGACATAGA 59.229 34.615 16.70 0.00 0.00 1.98
6817 7582 7.284489 AGGCAAAGTTTGTTACAAGACATAGAA 59.716 33.333 16.70 0.00 0.00 2.10
6819 7584 9.463443 GCAAAGTTTGTTACAAGACATAGAAAT 57.537 29.630 16.70 0.00 0.00 2.17
6826 7591 8.456904 TGTTACAAGACATAGAAATACACGAC 57.543 34.615 0.00 0.00 0.00 4.34
6828 7593 9.084164 GTTACAAGACATAGAAATACACGACAT 57.916 33.333 0.00 0.00 0.00 3.06
6830 7595 8.630278 ACAAGACATAGAAATACACGACATAC 57.370 34.615 0.00 0.00 0.00 2.39
6843 7610 1.189446 CGACATACGGATTACTTGCGC 59.811 52.381 0.00 0.00 43.91 6.09
6864 7631 4.330620 CGCGCAATAAAAGACCCTAGTTTA 59.669 41.667 8.75 0.00 0.00 2.01
6865 7632 5.566623 GCGCAATAAAAGACCCTAGTTTAC 58.433 41.667 0.30 0.00 0.00 2.01
6866 7633 5.122711 GCGCAATAAAAGACCCTAGTTTACA 59.877 40.000 0.30 0.00 0.00 2.41
6867 7634 6.348704 GCGCAATAAAAGACCCTAGTTTACAA 60.349 38.462 0.30 0.00 0.00 2.41
6868 7635 7.586747 CGCAATAAAAGACCCTAGTTTACAAA 58.413 34.615 0.00 0.00 0.00 2.83
6869 7636 7.749126 CGCAATAAAAGACCCTAGTTTACAAAG 59.251 37.037 0.00 0.00 0.00 2.77
6870 7637 8.027189 GCAATAAAAGACCCTAGTTTACAAAGG 58.973 37.037 0.00 0.00 0.00 3.11
6890 7657 3.008049 AGGTGGACGAAAGCAAGATTAGT 59.992 43.478 0.00 0.00 0.00 2.24
6900 7667 1.686115 GCAAGATTAGTGGTGGGGCAT 60.686 52.381 0.00 0.00 0.00 4.40
6927 7694 9.528489 TCTTATGCTTAAAAACCCTTATGTTCT 57.472 29.630 0.00 0.00 0.00 3.01
6985 7752 0.678048 GAGGCCTTGGCTTGTCGATT 60.678 55.000 6.77 0.00 38.98 3.34
6992 7759 2.574212 GCTTGTCGATTTGGCGCG 60.574 61.111 0.00 0.00 0.00 6.86
6993 7760 2.860293 CTTGTCGATTTGGCGCGT 59.140 55.556 8.43 0.00 0.00 6.01
6994 7761 1.206578 CTTGTCGATTTGGCGCGTT 59.793 52.632 8.43 0.00 0.00 4.84
6995 7762 1.059657 CTTGTCGATTTGGCGCGTTG 61.060 55.000 8.43 0.00 0.00 4.10
6999 7766 2.202298 GATTTGGCGCGTTGTCGG 60.202 61.111 8.43 0.00 37.56 4.79
7019 7786 2.730094 CAAGTGCTTGCCCACCAC 59.270 61.111 0.00 0.00 36.38 4.16
7033 7800 1.069513 CCACCACTCTTCAACCGTGTA 59.930 52.381 0.00 0.00 0.00 2.90
7034 7801 2.404215 CACCACTCTTCAACCGTGTAG 58.596 52.381 0.00 0.00 0.00 2.74
7045 7812 1.740296 CCGTGTAGAACAAGGGCCG 60.740 63.158 0.00 0.00 42.82 6.13
7046 7813 2.388232 CGTGTAGAACAAGGGCCGC 61.388 63.158 0.00 0.00 0.00 6.53
7049 7816 1.302192 GTAGAACAAGGGCCGCACA 60.302 57.895 0.00 0.00 0.00 4.57
7092 7859 5.598754 TGGGGAATTTCCTAATGACCAAAT 58.401 37.500 14.95 0.00 36.57 2.32
7136 7903 2.472029 CACTGGTAGAAGAGATGGGGT 58.528 52.381 0.00 0.00 0.00 4.95
7187 7954 2.223845 GCAAACATCACAATTTGGCCAC 59.776 45.455 3.88 0.00 36.51 5.01
7192 7959 0.187117 TCACAATTTGGCCACCCTCA 59.813 50.000 3.88 0.00 0.00 3.86
7205 7972 1.542915 CACCCTCACTTTGCCAATCTG 59.457 52.381 0.00 0.00 0.00 2.90
7232 7999 4.626042 CCGTCCAGATTCTATCTTGAAGG 58.374 47.826 7.83 7.83 41.60 3.46
7235 8002 3.392616 TCCAGATTCTATCTTGAAGGGCC 59.607 47.826 0.00 0.00 37.58 5.80
7237 8004 4.385643 CCAGATTCTATCTTGAAGGGCCAA 60.386 45.833 6.18 0.00 37.58 4.52
7245 8012 0.471591 TTGAAGGGCCAACCAAGCAT 60.472 50.000 6.18 0.00 43.89 3.79
7304 8074 3.901222 TCATCCTATACATGGGCGAAAGA 59.099 43.478 0.00 0.00 0.00 2.52
7315 8085 1.664873 GGCGAAAGAACCATCCCTAC 58.335 55.000 0.00 0.00 0.00 3.18
7356 8126 2.746277 CCGCCAAGTACTGCCCAC 60.746 66.667 0.00 0.00 0.00 4.61
7388 8158 5.266788 TGCTTCCAAATGATTTCATCCTCT 58.733 37.500 0.00 0.00 35.10 3.69
7408 8178 0.247736 GTGAGCTCGTCAAGGTGGAT 59.752 55.000 9.64 0.00 36.74 3.41
7415 8185 3.866651 CTCGTCAAGGTGGATCTCATTT 58.133 45.455 0.00 0.00 0.00 2.32
7418 8188 4.466370 TCGTCAAGGTGGATCTCATTTAGT 59.534 41.667 0.00 0.00 0.00 2.24
7421 8191 6.284459 GTCAAGGTGGATCTCATTTAGTAGG 58.716 44.000 0.00 0.00 0.00 3.18
7432 8202 6.821388 TCTCATTTAGTAGGATCCAAAGAGC 58.179 40.000 15.82 0.00 0.00 4.09
7455 8225 1.466167 AGAATTGTGTGATGTGCTCGC 59.534 47.619 0.00 0.00 34.82 5.03
7462 8232 2.202932 GATGTGCTCGCCGGTGAT 60.203 61.111 19.93 2.25 0.00 3.06
7519 8289 1.210204 TGCTTGAGGGCCTCCTTGAT 61.210 55.000 30.03 0.00 45.05 2.57
7527 8297 1.005924 GGGCCTCCTTGATCTTCCAAA 59.994 52.381 0.84 0.00 0.00 3.28
7528 8298 2.557452 GGGCCTCCTTGATCTTCCAAAA 60.557 50.000 0.84 0.00 0.00 2.44
7551 8321 9.702494 AAAATTTTCTCTTGGAAGCTTCATAAG 57.298 29.630 27.02 25.97 35.16 1.73
7556 8326 4.256920 TCTTGGAAGCTTCATAAGTGAGC 58.743 43.478 27.69 12.33 35.39 4.26
7598 8368 0.251341 GCCCAAGAAGCCAAGGAGAA 60.251 55.000 0.00 0.00 0.00 2.87
7676 8446 1.519455 GTTGAGGTCCTCCGCATCG 60.519 63.158 16.60 0.00 42.66 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 2.229784 GCATGGGAAAAACTCACCTCAG 59.770 50.000 0.00 0.00 0.00 3.35
89 90 9.118236 GTTGTCATAAAAAGTTAGCATTCACTC 57.882 33.333 0.00 0.00 0.00 3.51
101 102 2.614983 ACCACGCGTTGTCATAAAAAGT 59.385 40.909 10.22 0.00 0.00 2.66
109 110 2.094757 ATCCTCACCACGCGTTGTCA 62.095 55.000 13.70 0.00 0.00 3.58
113 114 1.066430 ACAATATCCTCACCACGCGTT 60.066 47.619 10.22 0.00 0.00 4.84
163 164 1.238439 CACACCGCCATTGAAAGAGT 58.762 50.000 0.00 0.00 0.00 3.24
175 176 4.408821 TCATGAGCCCCACACCGC 62.409 66.667 0.00 0.00 0.00 5.68
189 190 5.825593 TCACTTCCTAGAAAACACCTCAT 57.174 39.130 0.00 0.00 0.00 2.90
197 198 5.809001 AGACATGCATCACTTCCTAGAAAA 58.191 37.500 0.00 0.00 0.00 2.29
211 212 3.070734 CCCAAGAGCTAGTAGACATGCAT 59.929 47.826 0.00 0.00 0.00 3.96
221 222 0.117340 ACTCCACCCCAAGAGCTAGT 59.883 55.000 0.00 0.00 33.18 2.57
224 225 1.763770 CAACTCCACCCCAAGAGCT 59.236 57.895 0.00 0.00 33.18 4.09
307 309 0.034186 AGAATCCAAAGCCATCGCCA 60.034 50.000 0.00 0.00 34.57 5.69
310 312 0.383231 GCCAGAATCCAAAGCCATCG 59.617 55.000 0.00 0.00 0.00 3.84
325 327 3.121030 CGGAAGAACCAGCGCCAG 61.121 66.667 2.29 0.00 38.90 4.85
356 358 2.419574 GGTTAGCCTATTCCGCAGACAA 60.420 50.000 0.00 0.00 0.00 3.18
357 359 1.138266 GGTTAGCCTATTCCGCAGACA 59.862 52.381 0.00 0.00 0.00 3.41
361 363 0.983905 TGGGGTTAGCCTATTCCGCA 60.984 55.000 0.00 8.42 39.83 5.69
375 377 2.178984 TCCTCAACCTTGAATTTGGGGT 59.821 45.455 5.71 0.00 43.09 4.95
381 383 2.376518 TGCTCCTCCTCAACCTTGAATT 59.623 45.455 0.00 0.00 36.64 2.17
406 408 1.242076 CTTCCAAGACAAGCCAGTGG 58.758 55.000 4.20 4.20 0.00 4.00
435 448 0.105658 TAAGTCCCTCTGGATCCCGG 60.106 60.000 9.90 7.07 44.28 5.73
467 480 7.703058 CTTACAAGGAGACCCATAAAACAAT 57.297 36.000 0.00 0.00 33.88 2.71
515 528 1.238439 TTCTTTCTTTGCAGGAGCCG 58.762 50.000 0.00 0.00 41.13 5.52
516 529 2.673326 GCATTCTTTCTTTGCAGGAGCC 60.673 50.000 0.00 0.00 41.13 4.70
517 530 2.230750 AGCATTCTTTCTTTGCAGGAGC 59.769 45.455 0.00 0.00 38.84 4.70
604 621 9.661563 TTTGGAAGTAATAACGTGTGAATAGAT 57.338 29.630 0.00 0.00 0.00 1.98
637 654 8.234546 GCTCCGAAAGTTCATATTTGTCTTTAA 58.765 33.333 8.16 0.00 32.72 1.52
643 660 4.000988 ACGCTCCGAAAGTTCATATTTGT 58.999 39.130 0.00 0.00 0.00 2.83
775 792 3.018149 AGAACCGGTTGTTTGCTTTACA 58.982 40.909 27.87 0.00 37.29 2.41
785 802 4.703093 CCCAAAATATGTAGAACCGGTTGT 59.297 41.667 27.87 24.56 0.00 3.32
792 809 4.634443 ACGAGTGCCCAAAATATGTAGAAC 59.366 41.667 0.00 0.00 0.00 3.01
804 821 0.604578 GTACTACCACGAGTGCCCAA 59.395 55.000 0.00 0.00 0.00 4.12
841 858 8.912988 AGTTTGATGATTTTGTTCCTTCAACTA 58.087 29.630 0.00 0.00 35.79 2.24
850 867 6.562086 GCCGTTTCAGTTTGATGATTTTGTTC 60.562 38.462 0.00 0.00 0.00 3.18
861 878 2.613026 TCTCAGCCGTTTCAGTTTGA 57.387 45.000 0.00 0.00 0.00 2.69
862 879 3.621794 CTTTCTCAGCCGTTTCAGTTTG 58.378 45.455 0.00 0.00 0.00 2.93
863 880 2.033424 GCTTTCTCAGCCGTTTCAGTTT 59.967 45.455 0.00 0.00 43.65 2.66
864 881 1.604278 GCTTTCTCAGCCGTTTCAGTT 59.396 47.619 0.00 0.00 43.65 3.16
865 882 1.230324 GCTTTCTCAGCCGTTTCAGT 58.770 50.000 0.00 0.00 43.65 3.41
897 1599 3.359654 ACGAAATTGAAGCGTGTTTCAC 58.640 40.909 0.00 0.00 36.84 3.18
913 1615 9.325150 GATGATTACTTTTTGAATTCGACGAAA 57.675 29.630 15.22 0.00 0.00 3.46
954 1667 0.316204 ACAGAATGGCAAAGCAGTGC 59.684 50.000 7.13 7.13 43.62 4.40
970 1683 1.002502 GGGGGAGACGGGAAAACAG 60.003 63.158 0.00 0.00 0.00 3.16
1029 1744 2.970639 GCGTGGGACTGTAGCTGA 59.029 61.111 0.00 0.00 0.00 4.26
1273 1988 3.966543 AAGGGTGGTGGGCGGAAG 61.967 66.667 0.00 0.00 0.00 3.46
1274 1989 4.278513 CAAGGGTGGTGGGCGGAA 62.279 66.667 0.00 0.00 0.00 4.30
1301 2016 0.034198 GCCTAGCCTAGCCTAGCAAC 59.966 60.000 2.10 0.00 34.74 4.17
1302 2017 0.398522 TGCCTAGCCTAGCCTAGCAA 60.399 55.000 2.10 0.00 34.74 3.91
1338 2053 1.269166 CGACATTCCCGAAGACGAAG 58.731 55.000 0.00 0.00 42.66 3.79
1355 2070 3.962718 CCAGTAAACCCTAATCCTACCGA 59.037 47.826 0.00 0.00 0.00 4.69
1383 2098 3.246226 CCATTCTCGTAGCCATTTCGAAG 59.754 47.826 0.00 0.00 33.32 3.79
1397 2112 1.470979 CCGTAACCTCACCCATTCTCG 60.471 57.143 0.00 0.00 0.00 4.04
1402 2117 1.298667 GCACCGTAACCTCACCCAT 59.701 57.895 0.00 0.00 0.00 4.00
1415 2130 3.795342 CGCTAAAACCCGGCACCG 61.795 66.667 1.02 1.02 39.44 4.94
1426 2141 3.115892 CGAACGCCAGCCGCTAAA 61.116 61.111 0.00 0.00 41.76 1.85
1445 2160 3.021695 ACGGTAATCTCATCCTCGTCAA 58.978 45.455 0.00 0.00 0.00 3.18
1449 2164 1.603172 GGCACGGTAATCTCATCCTCG 60.603 57.143 0.00 0.00 0.00 4.63
1450 2165 1.689273 AGGCACGGTAATCTCATCCTC 59.311 52.381 0.00 0.00 0.00 3.71
1451 2166 1.689273 GAGGCACGGTAATCTCATCCT 59.311 52.381 0.00 0.00 0.00 3.24
1452 2167 1.412710 TGAGGCACGGTAATCTCATCC 59.587 52.381 4.01 0.00 32.10 3.51
1484 2199 2.325761 GTATGACGGCCGCATTACTAG 58.674 52.381 30.48 3.85 0.00 2.57
1538 2253 0.618458 TCCCCTCTCAACCCAAATCG 59.382 55.000 0.00 0.00 0.00 3.34
1593 2308 3.885901 GGGTCTCTTATGGAAAATGGAGC 59.114 47.826 0.00 0.00 0.00 4.70
1596 2311 4.641989 CAGTGGGTCTCTTATGGAAAATGG 59.358 45.833 0.00 0.00 0.00 3.16
1723 2438 2.863740 CAAGTGCACACGACTAAAGTCA 59.136 45.455 21.04 0.00 44.99 3.41
1790 2505 3.806667 GAGCTGCCCCTGATGCCT 61.807 66.667 0.00 0.00 0.00 4.75
1798 2513 0.548510 AACTAATCAGGAGCTGCCCC 59.451 55.000 0.00 0.00 37.37 5.80
1820 2535 5.469479 CAAAAGTTGAACAACAGAAGTGGT 58.531 37.500 17.85 0.00 43.47 4.16
1839 2554 3.204306 TGCCACATGGAAAATGCAAAA 57.796 38.095 0.87 0.00 37.39 2.44
1915 2630 1.448985 TTCGCTGCCGCTCTTTAAAT 58.551 45.000 0.00 0.00 0.00 1.40
1921 2636 2.125753 CTCTTTCGCTGCCGCTCT 60.126 61.111 0.00 0.00 0.00 4.09
2454 3172 5.472148 TCTGCATACGGTATAAAATACGGG 58.528 41.667 0.00 0.00 0.00 5.28
2470 3188 7.819644 AGCGCAAAATTGAATATATCTGCATA 58.180 30.769 11.47 0.00 0.00 3.14
2998 3724 6.316390 AGTGTAGGCTTTTGTTGCATATAGTC 59.684 38.462 0.00 0.00 0.00 2.59
3062 3788 6.567321 GCCACTTTCATAGCTACATTATGCAG 60.567 42.308 0.00 0.00 0.00 4.41
3074 3800 2.813754 TGTTGAGTGCCACTTTCATAGC 59.186 45.455 0.00 0.00 0.00 2.97
3078 3804 3.737663 GCAATTGTTGAGTGCCACTTTCA 60.738 43.478 7.40 0.00 43.27 2.69
3080 3806 2.825205 GCAATTGTTGAGTGCCACTTT 58.175 42.857 7.40 0.00 43.27 2.66
3134 3860 8.507249 CCTCCTAATTCTTAACAAACTCAACAG 58.493 37.037 0.00 0.00 0.00 3.16
3191 3917 9.216117 GTGTTCTGAAAATACCAGTACTATTGT 57.784 33.333 0.00 0.00 34.41 2.71
3538 4277 8.459521 TGCAAATAAAATTAAGGAATGTGACG 57.540 30.769 0.00 0.00 0.00 4.35
3874 4613 5.280654 AGATGACCAAATTTGCACAAAGT 57.719 34.783 12.92 4.02 33.32 2.66
3905 4647 5.794687 TGTATAGTGCAACATTACACTGC 57.205 39.130 7.61 0.00 46.31 4.40
3915 4657 9.712305 AGTCCAGAATATATTGTATAGTGCAAC 57.288 33.333 1.78 0.00 0.00 4.17
4069 4817 4.796038 ATGACCTCAATGGCAAAAGAAG 57.204 40.909 0.00 0.00 40.22 2.85
4119 4867 2.095364 CGAGTATATACTGCACGGGGAC 60.095 54.545 20.13 1.67 36.50 4.46
4121 4869 2.156917 TCGAGTATATACTGCACGGGG 58.843 52.381 20.13 1.35 36.50 5.73
4298 5046 5.914635 TGCTTTAGAAGAAACAATGAAAGCG 59.085 36.000 10.74 0.00 46.43 4.68
4430 5178 8.673626 AAAACTGCATTGTTATTCTGTATTCG 57.326 30.769 0.00 0.00 0.00 3.34
4454 5202 9.868277 ACATGTTCATCAAAAACTGAAAAGTAA 57.132 25.926 0.00 0.00 37.67 2.24
4550 5298 2.303311 GGTGTCTTTGTTCTCTAGGGCT 59.697 50.000 0.00 0.00 0.00 5.19
4619 5367 3.777106 TCAGCAGTTGTCAGAAATCCT 57.223 42.857 0.00 0.00 0.00 3.24
4625 5373 7.069208 AGAGTATGAATATCAGCAGTTGTCAGA 59.931 37.037 0.00 0.00 0.00 3.27
4697 5449 4.699925 AGAAAAAGTAGCTACCACCACA 57.300 40.909 20.31 0.00 0.00 4.17
4928 5680 5.123227 TCAAGGTTGTTCTCGACTTTGAAT 58.877 37.500 9.58 0.00 44.99 2.57
4937 5689 7.326063 GGTCAAAATTTATCAAGGTTGTTCTCG 59.674 37.037 0.00 0.00 0.00 4.04
4957 5709 8.519799 AAGAGATTAACAAAAGACTGGTCAAA 57.480 30.769 3.51 0.00 0.00 2.69
5140 5892 7.360575 ACGAATAACAGGTACAGAATTGTTC 57.639 36.000 0.00 0.00 38.76 3.18
5154 5906 5.633182 CCCAATTTGGTGAAACGAATAACAG 59.367 40.000 14.26 0.00 38.12 3.16
5481 6234 3.263425 AGTTCAAGGTTCGTGGATACCAT 59.737 43.478 0.00 0.00 35.28 3.55
5483 6236 3.329929 AGTTCAAGGTTCGTGGATACC 57.670 47.619 0.00 0.00 34.54 2.73
5491 6244 3.252458 CCCCAAGTTTAGTTCAAGGTTCG 59.748 47.826 0.00 0.00 0.00 3.95
5872 6636 0.833287 TATTCTGAGAGGGCCACAGC 59.167 55.000 6.18 0.00 38.76 4.40
5873 6637 1.139853 GGTATTCTGAGAGGGCCACAG 59.860 57.143 6.18 12.46 0.00 3.66
5874 6638 1.204146 GGTATTCTGAGAGGGCCACA 58.796 55.000 6.18 1.75 0.00 4.17
5875 6639 1.501582 AGGTATTCTGAGAGGGCCAC 58.498 55.000 6.18 0.00 0.00 5.01
5876 6640 2.023404 TGTAGGTATTCTGAGAGGGCCA 60.023 50.000 6.18 0.00 0.00 5.36
5877 6641 2.630580 CTGTAGGTATTCTGAGAGGGCC 59.369 54.545 0.00 0.00 0.00 5.80
5878 6642 2.630580 CCTGTAGGTATTCTGAGAGGGC 59.369 54.545 0.00 0.00 0.00 5.19
5879 6643 2.630580 GCCTGTAGGTATTCTGAGAGGG 59.369 54.545 0.00 0.00 37.57 4.30
5880 6644 2.630580 GGCCTGTAGGTATTCTGAGAGG 59.369 54.545 0.00 0.00 37.57 3.69
5881 6645 3.300388 TGGCCTGTAGGTATTCTGAGAG 58.700 50.000 3.32 0.00 37.57 3.20
5882 6646 3.398318 TGGCCTGTAGGTATTCTGAGA 57.602 47.619 3.32 0.00 37.57 3.27
5883 6647 4.487714 TTTGGCCTGTAGGTATTCTGAG 57.512 45.455 3.32 0.00 37.57 3.35
5884 6648 4.919774 TTTTGGCCTGTAGGTATTCTGA 57.080 40.909 3.32 0.00 37.57 3.27
5885 6649 7.040409 GGATTATTTTGGCCTGTAGGTATTCTG 60.040 40.741 3.32 0.00 37.57 3.02
5886 6650 7.004691 GGATTATTTTGGCCTGTAGGTATTCT 58.995 38.462 3.32 0.00 37.57 2.40
5887 6651 6.775629 TGGATTATTTTGGCCTGTAGGTATTC 59.224 38.462 3.32 0.00 37.57 1.75
5888 6652 6.678547 TGGATTATTTTGGCCTGTAGGTATT 58.321 36.000 3.32 0.00 37.57 1.89
5889 6653 6.274322 TGGATTATTTTGGCCTGTAGGTAT 57.726 37.500 3.32 0.00 37.57 2.73
5890 6654 5.718801 TGGATTATTTTGGCCTGTAGGTA 57.281 39.130 3.32 0.00 37.57 3.08
5891 6655 4.601406 TGGATTATTTTGGCCTGTAGGT 57.399 40.909 3.32 0.00 37.57 3.08
5892 6656 4.342092 CCTTGGATTATTTTGGCCTGTAGG 59.658 45.833 3.32 0.00 38.53 3.18
5893 6657 4.202151 GCCTTGGATTATTTTGGCCTGTAG 60.202 45.833 3.32 0.00 34.81 2.74
5894 6658 3.704061 GCCTTGGATTATTTTGGCCTGTA 59.296 43.478 3.32 0.00 34.81 2.74
5895 6659 2.501316 GCCTTGGATTATTTTGGCCTGT 59.499 45.455 3.32 0.00 34.81 4.00
5896 6660 2.500910 TGCCTTGGATTATTTTGGCCTG 59.499 45.455 3.32 0.00 39.60 4.85
5897 6661 2.831565 TGCCTTGGATTATTTTGGCCT 58.168 42.857 3.32 0.00 39.60 5.19
5898 6662 3.843893 ATGCCTTGGATTATTTTGGCC 57.156 42.857 0.00 0.00 39.60 5.36
5899 6663 6.991531 TGAAATATGCCTTGGATTATTTTGGC 59.008 34.615 0.00 0.00 40.62 4.52
5900 6664 8.961294 TTGAAATATGCCTTGGATTATTTTGG 57.039 30.769 0.00 0.00 0.00 3.28
5902 6666 9.563748 CCATTGAAATATGCCTTGGATTATTTT 57.436 29.630 0.00 0.00 0.00 1.82
5903 6667 7.662669 GCCATTGAAATATGCCTTGGATTATTT 59.337 33.333 0.00 6.85 0.00 1.40
5904 6668 7.016858 AGCCATTGAAATATGCCTTGGATTATT 59.983 33.333 0.00 0.00 0.00 1.40
5905 6669 6.499350 AGCCATTGAAATATGCCTTGGATTAT 59.501 34.615 0.00 0.00 0.00 1.28
5906 6670 5.840149 AGCCATTGAAATATGCCTTGGATTA 59.160 36.000 0.00 0.00 0.00 1.75
5907 6671 4.657039 AGCCATTGAAATATGCCTTGGATT 59.343 37.500 0.00 0.00 0.00 3.01
5908 6672 4.039973 CAGCCATTGAAATATGCCTTGGAT 59.960 41.667 0.00 0.00 0.00 3.41
5909 6673 3.385433 CAGCCATTGAAATATGCCTTGGA 59.615 43.478 0.00 0.00 0.00 3.53
5910 6674 3.133362 ACAGCCATTGAAATATGCCTTGG 59.867 43.478 0.00 0.00 0.00 3.61
5911 6675 4.116961 CACAGCCATTGAAATATGCCTTG 58.883 43.478 0.00 0.00 0.00 3.61
5912 6676 3.133362 CCACAGCCATTGAAATATGCCTT 59.867 43.478 0.00 0.00 0.00 4.35
5913 6677 2.696707 CCACAGCCATTGAAATATGCCT 59.303 45.455 0.00 0.00 0.00 4.75
5914 6678 2.804212 GCCACAGCCATTGAAATATGCC 60.804 50.000 0.00 0.00 0.00 4.40
5915 6679 2.476821 GCCACAGCCATTGAAATATGC 58.523 47.619 0.00 0.00 0.00 3.14
6005 6769 9.793259 ACAACTATGATACCAAATATAAGGTGG 57.207 33.333 8.80 2.10 38.87 4.61
6114 6878 2.353406 GCATGAGACAAAATGGCTGCTT 60.353 45.455 0.00 0.00 34.53 3.91
6294 7058 1.447217 CATGCTGGCGATAGTCCCA 59.553 57.895 0.00 0.00 42.82 4.37
6303 7067 0.786581 CGTCTATAAGCATGCTGGCG 59.213 55.000 23.48 18.15 39.27 5.69
6427 7191 1.813178 TGGCTTCACTACTGTCGAGAG 59.187 52.381 8.24 8.24 0.00 3.20
6432 7196 2.005451 CATGCTGGCTTCACTACTGTC 58.995 52.381 0.00 0.00 0.00 3.51
6436 7200 0.449388 GCACATGCTGGCTTCACTAC 59.551 55.000 0.00 0.00 38.21 2.73
6438 7202 3.677527 GCACATGCTGGCTTCACT 58.322 55.556 0.00 0.00 38.21 3.41
6547 7311 5.174398 CACACGTACAAACTCGTAATCACTT 59.826 40.000 0.00 0.00 38.52 3.16
6596 7360 6.606768 GTTCAAACAAGTCCTGAGAATGATC 58.393 40.000 0.00 0.00 0.00 2.92
6609 7373 2.159296 GGCTTTCACCGTTCAAACAAGT 60.159 45.455 0.00 0.00 0.00 3.16
6707 7472 2.167693 AGCGCATAGGTACTGCAGTTAA 59.832 45.455 27.06 4.60 41.52 2.01
6717 7482 0.464036 CACAAGGGAGCGCATAGGTA 59.536 55.000 11.47 0.00 0.00 3.08
6740 7505 9.872684 AAATTCCATCAGGTACAAATAGATCAT 57.127 29.630 0.00 0.00 35.89 2.45
6784 7549 8.349983 TCTTGTAACAAACTTTGCCTCTATTTC 58.650 33.333 1.14 0.00 0.00 2.17
6785 7550 8.135529 GTCTTGTAACAAACTTTGCCTCTATTT 58.864 33.333 1.14 0.00 0.00 1.40
6786 7551 7.284489 TGTCTTGTAACAAACTTTGCCTCTATT 59.716 33.333 1.14 0.00 0.00 1.73
6788 7553 6.116806 TGTCTTGTAACAAACTTTGCCTCTA 58.883 36.000 1.14 0.00 0.00 2.43
6790 7555 5.243426 TGTCTTGTAACAAACTTTGCCTC 57.757 39.130 1.14 0.00 0.00 4.70
6791 7556 5.852282 ATGTCTTGTAACAAACTTTGCCT 57.148 34.783 1.14 0.00 31.81 4.75
6793 7558 8.850454 TTTCTATGTCTTGTAACAAACTTTGC 57.150 30.769 1.14 0.00 31.81 3.68
6798 7563 9.525007 CGTGTATTTCTATGTCTTGTAACAAAC 57.475 33.333 0.00 0.00 31.81 2.93
6799 7564 9.478768 TCGTGTATTTCTATGTCTTGTAACAAA 57.521 29.630 0.00 0.00 31.81 2.83
6800 7565 8.918658 GTCGTGTATTTCTATGTCTTGTAACAA 58.081 33.333 0.00 0.00 31.81 2.83
6801 7566 8.083462 TGTCGTGTATTTCTATGTCTTGTAACA 58.917 33.333 0.00 0.00 0.00 2.41
6802 7567 8.456904 TGTCGTGTATTTCTATGTCTTGTAAC 57.543 34.615 0.00 0.00 0.00 2.50
6805 7570 7.431376 CGTATGTCGTGTATTTCTATGTCTTGT 59.569 37.037 0.00 0.00 34.52 3.16
6806 7571 7.096599 CCGTATGTCGTGTATTTCTATGTCTTG 60.097 40.741 0.00 0.00 37.94 3.02
6807 7572 6.916387 CCGTATGTCGTGTATTTCTATGTCTT 59.084 38.462 0.00 0.00 37.94 3.01
6808 7573 6.261603 TCCGTATGTCGTGTATTTCTATGTCT 59.738 38.462 0.00 0.00 37.94 3.41
6809 7574 6.432936 TCCGTATGTCGTGTATTTCTATGTC 58.567 40.000 0.00 0.00 37.94 3.06
6810 7575 6.381481 TCCGTATGTCGTGTATTTCTATGT 57.619 37.500 0.00 0.00 37.94 2.29
6811 7576 7.869016 AATCCGTATGTCGTGTATTTCTATG 57.131 36.000 0.00 0.00 37.94 2.23
6812 7577 8.790718 AGTAATCCGTATGTCGTGTATTTCTAT 58.209 33.333 0.00 0.00 37.94 1.98
6813 7578 8.158169 AGTAATCCGTATGTCGTGTATTTCTA 57.842 34.615 0.00 0.00 37.94 2.10
6814 7579 7.035840 AGTAATCCGTATGTCGTGTATTTCT 57.964 36.000 0.00 0.00 37.94 2.52
6815 7580 7.553034 CAAGTAATCCGTATGTCGTGTATTTC 58.447 38.462 0.00 0.00 37.94 2.17
6816 7581 6.019318 GCAAGTAATCCGTATGTCGTGTATTT 60.019 38.462 0.00 0.00 37.94 1.40
6817 7582 5.461078 GCAAGTAATCCGTATGTCGTGTATT 59.539 40.000 0.00 0.00 37.94 1.89
6819 7584 4.353737 GCAAGTAATCCGTATGTCGTGTA 58.646 43.478 0.00 0.00 37.94 2.90
6821 7586 2.215587 CGCAAGTAATCCGTATGTCGTG 59.784 50.000 0.00 0.00 37.94 4.35
6823 7588 1.189446 GCGCAAGTAATCCGTATGTCG 59.811 52.381 0.30 0.00 41.68 4.35
6826 7591 0.111266 GCGCGCAAGTAATCCGTATG 60.111 55.000 29.10 0.00 41.68 2.39
6828 7593 0.736672 TTGCGCGCAAGTAATCCGTA 60.737 50.000 40.23 16.85 41.68 4.02
6830 7595 0.579630 TATTGCGCGCAAGTAATCCG 59.420 50.000 43.73 0.00 39.47 4.18
6831 7596 2.748461 TTATTGCGCGCAAGTAATCC 57.252 45.000 43.73 10.16 39.47 3.01
6832 7597 4.202358 GTCTTTTATTGCGCGCAAGTAATC 59.798 41.667 43.73 27.61 39.47 1.75
6833 7598 4.095610 GTCTTTTATTGCGCGCAAGTAAT 58.904 39.130 43.73 32.04 39.47 1.89
6839 7606 0.958382 AGGGTCTTTTATTGCGCGCA 60.958 50.000 33.09 33.09 0.00 6.09
6843 7610 6.730960 TGTAAACTAGGGTCTTTTATTGCG 57.269 37.500 0.00 0.00 0.00 4.85
6864 7631 1.676006 CTTGCTTTCGTCCACCTTTGT 59.324 47.619 0.00 0.00 0.00 2.83
6865 7632 1.946768 TCTTGCTTTCGTCCACCTTTG 59.053 47.619 0.00 0.00 0.00 2.77
6866 7633 2.341846 TCTTGCTTTCGTCCACCTTT 57.658 45.000 0.00 0.00 0.00 3.11
6867 7634 2.568623 ATCTTGCTTTCGTCCACCTT 57.431 45.000 0.00 0.00 0.00 3.50
6868 7635 2.568623 AATCTTGCTTTCGTCCACCT 57.431 45.000 0.00 0.00 0.00 4.00
6869 7636 3.125316 CACTAATCTTGCTTTCGTCCACC 59.875 47.826 0.00 0.00 0.00 4.61
6870 7637 3.125316 CCACTAATCTTGCTTTCGTCCAC 59.875 47.826 0.00 0.00 0.00 4.02
6927 7694 8.343546 GTCTCTTGGACAATTTGGAACAAGCA 62.344 42.308 17.69 9.34 44.02 3.91
7019 7786 3.741344 CCTTGTTCTACACGGTTGAAGAG 59.259 47.826 2.33 4.17 33.30 2.85
7033 7800 2.281761 CTGTGCGGCCCTTGTTCT 60.282 61.111 0.00 0.00 0.00 3.01
7034 7801 1.856265 CTTCTGTGCGGCCCTTGTTC 61.856 60.000 0.00 0.00 0.00 3.18
7046 7813 2.142357 TCGGGCTCGACACTTCTGTG 62.142 60.000 3.45 0.00 40.88 3.66
7049 7816 2.995872 GCTCGGGCTCGACACTTCT 61.996 63.158 3.45 0.00 40.88 2.85
7092 7859 4.708386 CACCCGGCGCCTTTGGTA 62.708 66.667 26.68 0.00 0.00 3.25
7120 7887 1.041437 CGGACCCCATCTCTTCTACC 58.959 60.000 0.00 0.00 0.00 3.18
7160 7927 4.503643 CCAAATTGTGATGTTTGCCCTCTT 60.504 41.667 0.00 0.00 34.75 2.85
7187 7954 1.815003 GACAGATTGGCAAAGTGAGGG 59.185 52.381 16.52 1.21 0.00 4.30
7192 7959 1.244019 GGCGGACAGATTGGCAAAGT 61.244 55.000 3.01 3.29 0.00 2.66
7205 7972 0.674534 ATAGAATCTGGACGGCGGAC 59.325 55.000 13.24 3.63 0.00 4.79
7253 8023 3.117663 AGGTTTGAGCACCTCCAAAAGTA 60.118 43.478 0.00 0.00 44.63 2.24
7268 8038 7.638444 TGTATAGGATGATTTGGAAGGTTTGA 58.362 34.615 0.00 0.00 0.00 2.69
7282 8052 3.901222 TCTTTCGCCCATGTATAGGATGA 59.099 43.478 0.00 0.00 0.00 2.92
7304 8074 1.663695 CGCAATTCGTAGGGATGGTT 58.336 50.000 0.00 0.00 0.00 3.67
7315 8085 2.858729 GCATACAAGGCGCAATTCG 58.141 52.632 10.83 1.44 42.12 3.34
7356 8126 2.938451 TCATTTGGAAGCATACGAGCAG 59.062 45.455 0.00 0.00 36.85 4.24
7388 8158 1.112916 TCCACCTTGACGAGCTCACA 61.113 55.000 15.40 10.43 0.00 3.58
7408 8178 6.461648 CGCTCTTTGGATCCTACTAAATGAGA 60.462 42.308 20.29 9.07 0.00 3.27
7415 8185 4.533815 TCTTCGCTCTTTGGATCCTACTA 58.466 43.478 14.23 0.00 0.00 1.82
7418 8188 5.118990 CAATTCTTCGCTCTTTGGATCCTA 58.881 41.667 14.23 1.56 0.00 2.94
7421 8191 4.154918 ACACAATTCTTCGCTCTTTGGATC 59.845 41.667 0.00 0.00 0.00 3.36
7432 8202 3.722957 CGAGCACATCACACAATTCTTCG 60.723 47.826 0.00 0.00 0.00 3.79
7455 8225 1.453745 CCCCCATCAACATCACCGG 60.454 63.158 0.00 0.00 0.00 5.28
7462 8232 3.541242 AGATCAAAACCCCCATCAACA 57.459 42.857 0.00 0.00 0.00 3.33
7527 8297 8.302438 CACTTATGAAGCTTCCAAGAGAAAATT 58.698 33.333 30.12 13.39 32.88 1.82
7528 8298 7.667219 TCACTTATGAAGCTTCCAAGAGAAAAT 59.333 33.333 30.12 16.17 32.88 1.82
7551 8321 1.244019 AAAGACATTGCCCCGCTCAC 61.244 55.000 0.00 0.00 0.00 3.51
7556 8326 1.079888 GCCAAAAGACATTGCCCCG 60.080 57.895 0.00 0.00 0.00 5.73
7575 8345 0.394352 CCTTGGCTTCTTGGGCGTAT 60.394 55.000 0.00 0.00 34.31 3.06
7610 8380 2.202531 GGTAACGACGCGAGGACC 60.203 66.667 15.93 14.10 0.00 4.46


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

AutoCloner maintained by Alex Coulton.