Multiple sequence alignment - TraesCS2D01G263500

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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 TraesCS2D01G263500 chr2D 100.000 5057 0 0 1 5057 322126243 322121187 0.000000e+00 9339.0
1 TraesCS2D01G263500 chr2B 96.174 4025 83 17 570 4567 390366126 390362146 0.000000e+00 6514.0
2 TraesCS2D01G263500 chr2B 90.706 581 40 10 1 570 734717742 734717165 0.000000e+00 761.0
3 TraesCS2D01G263500 chr2B 86.538 520 49 12 4537 5055 390362136 390361637 2.060000e-153 553.0
4 TraesCS2D01G263500 chr2A 96.117 3940 109 20 636 4568 409435939 409439841 0.000000e+00 6388.0
5 TraesCS2D01G263500 chr2A 95.176 539 26 0 1 539 692949874 692950412 0.000000e+00 852.0
6 TraesCS2D01G263500 chr2A 82.222 495 40 14 4565 5057 409440676 409441124 2.860000e-102 383.0
7 TraesCS2D01G263500 chr3D 94.502 582 22 1 1 572 475028635 475029216 0.000000e+00 889.0
8 TraesCS2D01G263500 chr7D 94.107 577 23 9 1 567 254586836 254587411 0.000000e+00 867.0
9 TraesCS2D01G263500 chr5D 93.934 577 25 1 1 567 14028051 14028627 0.000000e+00 863.0
10 TraesCS2D01G263500 chr5D 95.362 539 24 1 1 539 212483906 212484443 0.000000e+00 856.0
11 TraesCS2D01G263500 chr5D 94.805 539 26 2 1 538 476615746 476616283 0.000000e+00 839.0
12 TraesCS2D01G263500 chr5D 81.659 458 79 4 2134 2587 561803837 561803381 4.780000e-100 375.0
13 TraesCS2D01G263500 chr5D 81.922 437 71 6 2134 2564 562414392 562413958 3.720000e-96 363.0
14 TraesCS2D01G263500 chr5D 83.784 333 51 2 2133 2462 450204633 450204301 3.800000e-81 313.0
15 TraesCS2D01G263500 chr5D 82.635 334 53 4 2133 2462 562533426 562533094 1.780000e-74 291.0
16 TraesCS2D01G263500 chr5D 81.026 195 37 0 2360 2554 543830918 543831112 6.780000e-34 156.0
17 TraesCS2D01G263500 chr5D 95.349 43 1 1 531 572 37203828 37203786 3.270000e-07 67.6
18 TraesCS2D01G263500 chr1D 95.556 540 22 2 1 539 375968780 375969318 0.000000e+00 863.0
19 TraesCS2D01G263500 chr6A 93.471 582 26 9 1 572 88127200 88127779 0.000000e+00 854.0
20 TraesCS2D01G263500 chr6D 94.776 536 28 0 1 536 407229185 407229720 0.000000e+00 835.0
21 TraesCS2D01G263500 chr6D 83.871 155 13 7 428 572 357780372 357780524 2.460000e-28 137.0
22 TraesCS2D01G263500 chr3A 90.223 583 43 10 1 572 620773266 620772687 0.000000e+00 749.0
23 TraesCS2D01G263500 chr7B 81.250 448 79 4 2135 2578 1020872 1021318 1.730000e-94 357.0
24 TraesCS2D01G263500 chr7B 81.604 424 74 3 2134 2554 229403 229825 1.040000e-91 348.0
25 TraesCS2D01G263500 chr7B 82.278 158 18 5 428 575 721732389 721732232 1.480000e-25 128.0
26 TraesCS2D01G263500 chr5B 83.784 333 51 2 2133 2462 550216873 550216541 3.800000e-81 313.0
27 TraesCS2D01G263500 chr5B 83.125 160 16 7 428 577 65089980 65090138 8.830000e-28 135.0
28 TraesCS2D01G263500 chr3B 84.177 158 15 5 428 575 21596595 21596438 1.470000e-30 145.0
29 TraesCS2D01G263500 chr3B 81.761 159 15 9 428 575 551512191 551512346 2.470000e-23 121.0
30 TraesCS2D01G263500 chr4A 88.462 52 3 3 531 581 537960003 537960052 5.470000e-05 60.2


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 TraesCS2D01G263500 chr2D 322121187 322126243 5056 True 9339.0 9339 100.0000 1 5057 1 chr2D.!!$R1 5056
1 TraesCS2D01G263500 chr2B 390361637 390366126 4489 True 3533.5 6514 91.3560 570 5055 2 chr2B.!!$R2 4485
2 TraesCS2D01G263500 chr2B 734717165 734717742 577 True 761.0 761 90.7060 1 570 1 chr2B.!!$R1 569
3 TraesCS2D01G263500 chr2A 409435939 409441124 5185 False 3385.5 6388 89.1695 636 5057 2 chr2A.!!$F2 4421
4 TraesCS2D01G263500 chr2A 692949874 692950412 538 False 852.0 852 95.1760 1 539 1 chr2A.!!$F1 538
5 TraesCS2D01G263500 chr3D 475028635 475029216 581 False 889.0 889 94.5020 1 572 1 chr3D.!!$F1 571
6 TraesCS2D01G263500 chr7D 254586836 254587411 575 False 867.0 867 94.1070 1 567 1 chr7D.!!$F1 566
7 TraesCS2D01G263500 chr5D 14028051 14028627 576 False 863.0 863 93.9340 1 567 1 chr5D.!!$F1 566
8 TraesCS2D01G263500 chr5D 212483906 212484443 537 False 856.0 856 95.3620 1 539 1 chr5D.!!$F2 538
9 TraesCS2D01G263500 chr5D 476615746 476616283 537 False 839.0 839 94.8050 1 538 1 chr5D.!!$F3 537
10 TraesCS2D01G263500 chr1D 375968780 375969318 538 False 863.0 863 95.5560 1 539 1 chr1D.!!$F1 538
11 TraesCS2D01G263500 chr6A 88127200 88127779 579 False 854.0 854 93.4710 1 572 1 chr6A.!!$F1 571
12 TraesCS2D01G263500 chr6D 407229185 407229720 535 False 835.0 835 94.7760 1 536 1 chr6D.!!$F2 535
13 TraesCS2D01G263500 chr3A 620772687 620773266 579 True 749.0 749 90.2230 1 572 1 chr3A.!!$R1 571

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
717 735 0.038310 TCACGCCCAGAGAAGAGAGA 59.962 55.0 0.00 0.0 0.00 3.10 F
919 966 0.243095 ACAACTCGAGCGTTACTCCC 59.757 55.0 13.61 0.0 43.01 4.30 F
920 967 0.458025 CAACTCGAGCGTTACTCCCC 60.458 60.0 13.61 0.0 43.01 4.81 F
2397 2444 0.620410 TCCCCTCGTGGATTGGTGAT 60.620 55.0 4.76 0.0 35.39 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2253 2300 0.550914 ACACCTCCAGGCTGTTGAAA 59.449 50.000 14.43 0.0 39.32 2.69 R
2855 2902 1.070134 TGAAGGTGAAGAACTGTCCCG 59.930 52.381 0.00 0.0 0.00 5.14 R
2929 2976 5.576563 TTAGTTTCCCCAGACTGATTCAA 57.423 39.130 3.32 0.0 0.00 2.69 R
4389 4445 1.134699 CGAAGGCAGAGATAGCACCAA 60.135 52.381 0.00 0.0 0.00 3.67 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
137 139 3.011708 AGGTGAAAATATTGAGCCCCTGT 59.988 43.478 0.00 0.00 0.00 4.00
170 172 3.181476 GGCCACATTTGAACAGTTTGTCT 60.181 43.478 0.00 0.00 0.00 3.41
196 198 0.246360 ACCGTGAGATGCGTGATTGA 59.754 50.000 0.00 0.00 0.00 2.57
404 407 8.410141 TGGGTTGTAAAACTAGTTTTGATGAAG 58.590 33.333 33.75 0.00 42.18 3.02
420 423 4.462132 TGATGAAGATTCGGGCATTTTTGA 59.538 37.500 0.00 0.00 0.00 2.69
524 529 0.252012 CCCATTGCCCTACCCAAACA 60.252 55.000 0.00 0.00 0.00 2.83
525 530 1.638529 CCATTGCCCTACCCAAACAA 58.361 50.000 0.00 0.00 0.00 2.83
534 549 3.069016 CCCTACCCAAACAAACAGAAACC 59.931 47.826 0.00 0.00 0.00 3.27
536 551 1.478916 ACCCAAACAAACAGAAACCGG 59.521 47.619 0.00 0.00 0.00 5.28
537 552 1.751924 CCCAAACAAACAGAAACCGGA 59.248 47.619 9.46 0.00 0.00 5.14
538 553 2.480587 CCCAAACAAACAGAAACCGGAC 60.481 50.000 9.46 0.00 0.00 4.79
596 611 2.261361 GCCAATTTCACACCGGCC 59.739 61.111 0.00 0.00 36.73 6.13
657 672 1.469308 TGCGGTAGTTTTTAATGGGCG 59.531 47.619 0.00 0.00 0.00 6.13
716 734 0.455410 CTCACGCCCAGAGAAGAGAG 59.545 60.000 0.00 0.00 35.09 3.20
717 735 0.038310 TCACGCCCAGAGAAGAGAGA 59.962 55.000 0.00 0.00 0.00 3.10
840 882 4.253257 CCTACTCCGCCGCGTCTC 62.253 72.222 12.58 0.00 0.00 3.36
902 949 0.532640 TGCTGCTTCTGCTTCGAACA 60.533 50.000 0.00 0.00 40.48 3.18
919 966 0.243095 ACAACTCGAGCGTTACTCCC 59.757 55.000 13.61 0.00 43.01 4.30
920 967 0.458025 CAACTCGAGCGTTACTCCCC 60.458 60.000 13.61 0.00 43.01 4.81
921 968 1.602327 AACTCGAGCGTTACTCCCCC 61.602 60.000 13.61 0.00 43.01 5.40
936 983 2.689034 CCCCTCCACTCCACTCCC 60.689 72.222 0.00 0.00 0.00 4.30
1782 1829 1.179152 TATCCGTCAACCGCTTCTCA 58.821 50.000 0.00 0.00 34.38 3.27
2253 2300 1.152440 TGAAAACGGCAATGGGGGT 60.152 52.632 0.00 0.00 0.00 4.95
2297 2344 3.201290 CTCTTGGCGATTGTGCTCTAAT 58.799 45.455 0.00 0.00 34.52 1.73
2397 2444 0.620410 TCCCCTCGTGGATTGGTGAT 60.620 55.000 4.76 0.00 35.39 3.06
2649 2696 1.981256 TCTGGCCTGAGTTTGGAAAC 58.019 50.000 8.48 0.00 39.17 2.78
2751 2798 3.257393 CTTGGAGGTTCTTGATCTGTCG 58.743 50.000 0.00 0.00 0.00 4.35
3195 3242 1.276421 TCTGCCAAGGAGCTAACTGTC 59.724 52.381 0.00 0.00 0.00 3.51
3354 3401 2.283529 GGAGAGGGAGTTCCGTGCA 61.284 63.158 0.00 0.00 41.52 4.57
3816 3863 0.322975 TCTTGCTGGAGCTTCTCACC 59.677 55.000 0.00 0.00 42.66 4.02
3955 4002 0.903236 AGAGCATGAGAAGCAGCTGA 59.097 50.000 20.43 0.00 37.48 4.26
4041 4088 1.531149 CAAGTCGTTGTTTGGCTCGAT 59.469 47.619 0.00 0.00 34.93 3.59
4087 4134 8.923270 TCATGTTATTTTCCCAGTTCTCTTTTT 58.077 29.630 0.00 0.00 0.00 1.94
4133 4180 3.307480 GGTGGGTGATAAACAGTAGCAGT 60.307 47.826 0.00 0.00 0.00 4.40
4197 4244 3.337694 TCTGGTGTAAATAACCGTGGG 57.662 47.619 0.00 0.00 40.86 4.61
4221 4268 6.183360 GGTTTCTTTCTTATAGACGCTGAACC 60.183 42.308 0.00 0.00 0.00 3.62
4242 4289 3.182967 CGGCAGAGAATGACTACAAGTC 58.817 50.000 0.01 0.01 45.26 3.01
4256 4303 1.615392 ACAAGTCCTGCCATTTCTTGC 59.385 47.619 0.00 0.00 38.99 4.01
4257 4304 1.891150 CAAGTCCTGCCATTTCTTGCT 59.109 47.619 0.00 0.00 31.19 3.91
4258 4305 1.542492 AGTCCTGCCATTTCTTGCTG 58.458 50.000 0.00 0.00 0.00 4.41
4259 4306 1.074405 AGTCCTGCCATTTCTTGCTGA 59.926 47.619 0.00 0.00 0.00 4.26
4260 4307 2.097825 GTCCTGCCATTTCTTGCTGAT 58.902 47.619 0.00 0.00 0.00 2.90
4261 4308 2.097036 TCCTGCCATTTCTTGCTGATG 58.903 47.619 0.00 0.00 0.00 3.07
4262 4309 1.470979 CCTGCCATTTCTTGCTGATGC 60.471 52.381 0.00 0.00 40.20 3.91
4263 4310 1.476891 CTGCCATTTCTTGCTGATGCT 59.523 47.619 0.00 0.00 40.48 3.79
4275 4330 1.069022 GCTGATGCTCTGCGTTTCAAA 60.069 47.619 0.00 0.00 31.90 2.69
4332 4387 0.397941 TGCTGCAGCCTGAACTTACT 59.602 50.000 34.64 0.00 41.18 2.24
4334 4389 2.237143 TGCTGCAGCCTGAACTTACTAT 59.763 45.455 34.64 0.00 41.18 2.12
4338 4394 4.261801 TGCAGCCTGAACTTACTATTTCC 58.738 43.478 0.00 0.00 0.00 3.13
4358 4414 5.683876 TCCCTCCTCTAGAAACTGATTTG 57.316 43.478 0.00 0.00 0.00 2.32
4373 4429 4.263462 ACTGATTTGAGGACAGCCATGTTA 60.263 41.667 0.00 0.00 40.68 2.41
4378 4434 6.418057 TTTGAGGACAGCCATGTTATTTTT 57.582 33.333 0.00 0.00 40.68 1.94
4437 4493 7.988737 TGTTACCAATCTCATTTATCTTGCAG 58.011 34.615 0.00 0.00 0.00 4.41
4532 4588 8.690203 TTTGATTTTTACCAATCTCTGTCAGA 57.310 30.769 1.78 1.78 34.66 3.27
4533 4589 8.690203 TTGATTTTTACCAATCTCTGTCAGAA 57.310 30.769 3.67 0.00 34.66 3.02
4547 4603 6.880529 TCTCTGTCAGAATGCATAATTGTTGA 59.119 34.615 0.00 0.00 34.76 3.18
4569 4625 8.989980 GTTGATACAAGCTGTTTAGAGTAACTT 58.010 33.333 0.00 0.00 0.00 2.66
4671 5567 1.271379 GGCGTCATATGGGTGTCGATA 59.729 52.381 2.13 0.00 33.53 2.92
4674 5570 2.817844 CGTCATATGGGTGTCGATAGGA 59.182 50.000 2.13 0.00 33.53 2.94
4723 5619 4.945246 TCAATAAATGGTCTCGTAGCCTC 58.055 43.478 0.00 0.00 0.00 4.70
4731 5627 3.709653 TGGTCTCGTAGCCTCCATATTTT 59.290 43.478 0.00 0.00 0.00 1.82
4783 5679 3.230990 AAAGCCCAACCGCCAACC 61.231 61.111 0.00 0.00 0.00 3.77
4815 5711 1.242076 TTCAGCTTCTTCCTGCTTGC 58.758 50.000 0.00 0.00 37.44 4.01
4819 5715 1.968017 CTTCTTCCTGCTTGCGCCA 60.968 57.895 4.18 0.00 34.43 5.69
4820 5716 2.192608 CTTCTTCCTGCTTGCGCCAC 62.193 60.000 4.18 0.00 34.43 5.01
4821 5717 2.956799 TTCTTCCTGCTTGCGCCACA 62.957 55.000 4.18 0.00 34.43 4.17
4822 5718 2.974489 CTTCCTGCTTGCGCCACAG 61.974 63.158 4.18 9.79 34.43 3.66
4823 5719 3.772853 TTCCTGCTTGCGCCACAGT 62.773 57.895 16.96 0.00 34.43 3.55
4824 5720 3.730761 CCTGCTTGCGCCACAGTC 61.731 66.667 16.96 4.11 34.43 3.51
4825 5721 2.974148 CTGCTTGCGCCACAGTCA 60.974 61.111 4.18 0.57 34.43 3.41
4826 5722 2.515757 TGCTTGCGCCACAGTCAA 60.516 55.556 4.18 0.00 34.43 3.18
4827 5723 2.253452 GCTTGCGCCACAGTCAAG 59.747 61.111 4.18 0.14 39.95 3.02
4828 5724 2.546494 GCTTGCGCCACAGTCAAGT 61.546 57.895 4.18 0.00 39.36 3.16
4829 5725 2.024918 CTTGCGCCACAGTCAAGTT 58.975 52.632 4.18 0.00 34.20 2.66
4830 5726 0.381801 CTTGCGCCACAGTCAAGTTT 59.618 50.000 4.18 0.00 34.20 2.66
4831 5727 0.380378 TTGCGCCACAGTCAAGTTTC 59.620 50.000 4.18 0.00 0.00 2.78
4832 5728 0.746204 TGCGCCACAGTCAAGTTTCA 60.746 50.000 4.18 0.00 0.00 2.69
4833 5729 0.380378 GCGCCACAGTCAAGTTTCAA 59.620 50.000 0.00 0.00 0.00 2.69
4834 5730 1.202245 GCGCCACAGTCAAGTTTCAAA 60.202 47.619 0.00 0.00 0.00 2.69
4835 5731 2.733858 GCGCCACAGTCAAGTTTCAAAA 60.734 45.455 0.00 0.00 0.00 2.44
4836 5732 3.705604 CGCCACAGTCAAGTTTCAAAAT 58.294 40.909 0.00 0.00 0.00 1.82
4837 5733 4.111916 CGCCACAGTCAAGTTTCAAAATT 58.888 39.130 0.00 0.00 0.00 1.82
4838 5734 4.026640 CGCCACAGTCAAGTTTCAAAATTG 60.027 41.667 3.86 3.86 0.00 2.32
4839 5735 4.869861 GCCACAGTCAAGTTTCAAAATTGT 59.130 37.500 9.98 0.00 0.00 2.71
4840 5736 5.220453 GCCACAGTCAAGTTTCAAAATTGTG 60.220 40.000 9.98 5.03 34.68 3.33
4841 5737 5.220453 CCACAGTCAAGTTTCAAAATTGTGC 60.220 40.000 9.98 5.18 33.84 4.57
4842 5738 5.348179 CACAGTCAAGTTTCAAAATTGTGCA 59.652 36.000 9.98 0.00 0.00 4.57
4843 5739 5.577945 ACAGTCAAGTTTCAAAATTGTGCAG 59.422 36.000 9.98 4.85 0.00 4.41
4844 5740 4.567959 AGTCAAGTTTCAAAATTGTGCAGC 59.432 37.500 9.98 0.00 0.00 5.25
4845 5741 3.870419 TCAAGTTTCAAAATTGTGCAGCC 59.130 39.130 9.98 0.00 0.00 4.85
4846 5742 3.825143 AGTTTCAAAATTGTGCAGCCT 57.175 38.095 0.00 0.00 0.00 4.58
4847 5743 3.721035 AGTTTCAAAATTGTGCAGCCTC 58.279 40.909 0.00 0.00 0.00 4.70
4848 5744 2.420628 TTCAAAATTGTGCAGCCTCG 57.579 45.000 0.00 0.00 0.00 4.63
4849 5745 0.597568 TCAAAATTGTGCAGCCTCGG 59.402 50.000 0.00 0.00 0.00 4.63
4879 5775 3.132646 AGTTTTGAAATTGTGCAGCCTCA 59.867 39.130 0.00 0.00 0.00 3.86
4893 5803 4.742201 CTCAGACGCACCACCCGG 62.742 72.222 0.00 0.00 38.77 5.73
4907 5817 0.746563 ACCCGGCCATTAATGTCACG 60.747 55.000 14.25 13.80 0.00 4.35
4914 5824 0.732571 CATTAATGTCACGCCCGCTT 59.267 50.000 7.32 0.00 0.00 4.68
4931 5841 2.069273 GCTTCATCGGATATTCGTGGG 58.931 52.381 2.72 0.00 0.00 4.61
4967 5877 0.811616 GCCACGTGACATCATCTCCC 60.812 60.000 19.30 0.00 0.00 4.30
4974 5884 2.093973 GTGACATCATCTCCCGTCTTGT 60.094 50.000 0.00 0.00 0.00 3.16
4983 5893 2.310233 CCCGTCTTGTGTGTGAGCG 61.310 63.158 0.00 0.00 0.00 5.03
4987 5897 0.814010 GTCTTGTGTGTGAGCGGGTT 60.814 55.000 0.00 0.00 0.00 4.11
4990 5900 2.110213 GTGTGTGAGCGGGTTGGA 59.890 61.111 0.00 0.00 0.00 3.53
5007 5917 1.277273 TGGAAGGTGATGTCTGAGCAG 59.723 52.381 0.00 0.00 0.00 4.24
5022 5932 2.983930 GCAGTCGAGAGGCGTGAGT 61.984 63.158 0.00 0.00 43.49 3.41
5049 5959 1.806542 GCTTTTCTCACCATGAAGCGA 59.193 47.619 0.00 0.00 34.18 4.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 97 7.638444 TCACCTTGATAATCAAATCCTTGGTA 58.362 34.615 0.00 0.00 35.73 3.25
137 139 1.493854 AATGTGGCCGGGTCTTGGTA 61.494 55.000 2.18 0.00 0.00 3.25
170 172 1.206132 ACGCATCTCACGGTGGAATTA 59.794 47.619 8.50 0.00 34.00 1.40
404 407 1.824852 AGGGTCAAAAATGCCCGAATC 59.175 47.619 0.00 0.00 46.69 2.52
408 411 0.243636 GTCAGGGTCAAAAATGCCCG 59.756 55.000 0.00 0.00 46.69 6.13
438 442 2.439156 GGCCGCATCTCTTTGCCT 60.439 61.111 0.00 0.00 39.52 4.75
524 529 3.300711 CGGAGTCCGGTTTCTGTTT 57.699 52.632 24.39 0.00 44.15 2.83
536 551 2.165301 CGCGATCCCAAACGGAGTC 61.165 63.158 0.00 0.00 46.60 3.36
537 552 2.125673 CGCGATCCCAAACGGAGT 60.126 61.111 0.00 0.00 46.60 3.85
538 553 3.564027 GCGCGATCCCAAACGGAG 61.564 66.667 12.10 0.00 46.60 4.63
614 629 1.359117 GGCATCGCGTCTAGCTACA 59.641 57.895 5.77 0.00 45.59 2.74
716 734 1.154197 CCCCGTTCCGTTTCTTTCTC 58.846 55.000 0.00 0.00 0.00 2.87
717 735 0.760572 TCCCCGTTCCGTTTCTTTCT 59.239 50.000 0.00 0.00 0.00 2.52
840 882 0.102120 GTGATGTGCGGAGAGGAGAG 59.898 60.000 0.00 0.00 0.00 3.20
902 949 1.602327 GGGGGAGTAACGCTCGAGTT 61.602 60.000 15.13 4.71 45.03 3.01
919 966 2.689034 GGGAGTGGAGTGGAGGGG 60.689 72.222 0.00 0.00 0.00 4.79
920 967 2.689034 GGGGAGTGGAGTGGAGGG 60.689 72.222 0.00 0.00 0.00 4.30
921 968 1.687493 GAGGGGAGTGGAGTGGAGG 60.687 68.421 0.00 0.00 0.00 4.30
922 969 1.687493 GGAGGGGAGTGGAGTGGAG 60.687 68.421 0.00 0.00 0.00 3.86
923 970 2.450243 GGAGGGGAGTGGAGTGGA 59.550 66.667 0.00 0.00 0.00 4.02
924 971 2.689034 GGGAGGGGAGTGGAGTGG 60.689 72.222 0.00 0.00 0.00 4.00
925 972 2.689034 GGGGAGGGGAGTGGAGTG 60.689 72.222 0.00 0.00 0.00 3.51
926 973 4.400251 CGGGGAGGGGAGTGGAGT 62.400 72.222 0.00 0.00 0.00 3.85
927 974 4.400251 ACGGGGAGGGGAGTGGAG 62.400 72.222 0.00 0.00 0.00 3.86
928 975 4.393778 GACGGGGAGGGGAGTGGA 62.394 72.222 0.00 0.00 0.00 4.02
2241 2288 1.291906 GTTGAAACCCCCATTGCCG 59.708 57.895 0.00 0.00 0.00 5.69
2253 2300 0.550914 ACACCTCCAGGCTGTTGAAA 59.449 50.000 14.43 0.00 39.32 2.69
2297 2344 2.126372 ATTCCGGAACCCTCCCCA 59.874 61.111 21.56 0.00 38.71 4.96
2382 2429 2.932614 GTCAAGATCACCAATCCACGAG 59.067 50.000 0.00 0.00 34.67 4.18
2397 2444 3.244215 CCAAGTAGCTCAAGTGGTCAAGA 60.244 47.826 0.00 0.00 0.00 3.02
2649 2696 3.875727 CCATCACATGTAGCTCCTTCAAG 59.124 47.826 0.00 0.00 0.00 3.02
2730 2777 3.257393 CGACAGATCAAGAACCTCCAAG 58.743 50.000 0.00 0.00 0.00 3.61
2751 2798 5.201713 TCGATCCAGTGAGATTATTGGAC 57.798 43.478 0.00 0.00 42.12 4.02
2781 2828 4.360889 AGAAAGTGAGATCTGTCAGGGAT 58.639 43.478 0.00 0.00 0.00 3.85
2855 2902 1.070134 TGAAGGTGAAGAACTGTCCCG 59.930 52.381 0.00 0.00 0.00 5.14
2929 2976 5.576563 TTAGTTTCCCCAGACTGATTCAA 57.423 39.130 3.32 0.00 0.00 2.69
3354 3401 2.659610 GACAGCGCTTCCACCTCT 59.340 61.111 7.50 0.00 0.00 3.69
3537 3584 4.052518 CCCCTGGCTGAACCCTGG 62.053 72.222 0.00 0.00 42.05 4.45
3955 4002 1.270094 TGCCGTTTCGAGAACAGACAT 60.270 47.619 9.90 0.00 0.00 3.06
4041 4088 3.377798 TGATGTATTACGGTGACACGCTA 59.622 43.478 0.00 0.00 37.37 4.26
4163 4210 7.432148 TTTACACCAGATAAGCTCCATCTTA 57.568 36.000 7.83 0.00 30.18 2.10
4197 4244 6.453922 CGGTTCAGCGTCTATAAGAAAGAAAC 60.454 42.308 0.00 0.00 0.00 2.78
4221 4268 3.182967 GACTTGTAGTCATTCTCTGCCG 58.817 50.000 2.08 0.00 44.45 5.69
4242 4289 1.470979 GCATCAGCAAGAAATGGCAGG 60.471 52.381 0.00 0.00 41.58 4.85
4256 4303 2.481568 TCTTTGAAACGCAGAGCATCAG 59.518 45.455 0.00 0.00 37.82 2.90
4257 4304 2.493035 TCTTTGAAACGCAGAGCATCA 58.507 42.857 0.00 0.00 37.82 3.07
4258 4305 3.542712 TTCTTTGAAACGCAGAGCATC 57.457 42.857 0.00 0.00 0.00 3.91
4259 4306 3.988379 TTTCTTTGAAACGCAGAGCAT 57.012 38.095 0.00 0.00 0.00 3.79
4260 4307 3.988379 ATTTCTTTGAAACGCAGAGCA 57.012 38.095 0.00 0.00 0.00 4.26
4261 4308 4.739716 TGAAATTTCTTTGAAACGCAGAGC 59.260 37.500 18.64 0.00 0.00 4.09
4262 4309 5.173854 GGTGAAATTTCTTTGAAACGCAGAG 59.826 40.000 18.64 0.00 0.00 3.35
4263 4310 5.040635 GGTGAAATTTCTTTGAAACGCAGA 58.959 37.500 18.64 0.00 0.00 4.26
4332 4387 7.996758 AATCAGTTTCTAGAGGAGGGAAATA 57.003 36.000 0.00 0.00 32.71 1.40
4334 4389 6.272324 TCAAATCAGTTTCTAGAGGAGGGAAA 59.728 38.462 0.00 0.00 0.00 3.13
4338 4394 5.423610 TCCTCAAATCAGTTTCTAGAGGAGG 59.576 44.000 0.00 0.00 38.30 4.30
4358 4414 7.391148 TTCTAAAAATAACATGGCTGTCCTC 57.609 36.000 0.00 0.00 33.36 3.71
4378 4434 8.840321 GCAGAGATAGCACCAATTTTATTTCTA 58.160 33.333 0.00 0.00 0.00 2.10
4389 4445 1.134699 CGAAGGCAGAGATAGCACCAA 60.135 52.381 0.00 0.00 0.00 3.67
4392 4448 2.799412 CAATCGAAGGCAGAGATAGCAC 59.201 50.000 0.00 0.00 0.00 4.40
4425 4481 8.121305 TGTACCAACAATTCTGCAAGATAAAT 57.879 30.769 0.00 0.00 36.01 1.40
4430 4486 4.261572 GCTTGTACCAACAATTCTGCAAGA 60.262 41.667 0.00 0.00 44.43 3.02
4437 4493 6.966021 TCTAAACAGCTTGTACCAACAATTC 58.034 36.000 0.00 0.00 44.43 2.17
4532 4588 7.549839 ACAGCTTGTATCAACAATTATGCATT 58.450 30.769 3.54 0.00 44.43 3.56
4533 4589 7.104043 ACAGCTTGTATCAACAATTATGCAT 57.896 32.000 3.79 3.79 44.43 3.96
4671 5567 8.718656 AGTTTCATAGCTCCATAAACTATTCCT 58.281 33.333 12.22 0.00 38.31 3.36
4674 5570 9.331282 GTGAGTTTCATAGCTCCATAAACTATT 57.669 33.333 13.30 0.00 39.72 1.73
4746 5642 1.365633 GAGCGAGCTCCATACTGGG 59.634 63.158 13.73 0.00 38.32 4.45
4783 5679 0.695347 AGCTGAAACTTCCCTCCCAG 59.305 55.000 0.00 0.00 0.00 4.45
4815 5711 2.842208 TTTGAAACTTGACTGTGGCG 57.158 45.000 0.00 0.00 0.00 5.69
4819 5715 5.477510 TGCACAATTTTGAAACTTGACTGT 58.522 33.333 13.83 0.00 0.00 3.55
4820 5716 5.501252 GCTGCACAATTTTGAAACTTGACTG 60.501 40.000 13.83 10.10 0.00 3.51
4821 5717 4.567959 GCTGCACAATTTTGAAACTTGACT 59.432 37.500 13.83 0.00 0.00 3.41
4822 5718 4.260334 GGCTGCACAATTTTGAAACTTGAC 60.260 41.667 13.83 6.85 0.00 3.18
4823 5719 3.870419 GGCTGCACAATTTTGAAACTTGA 59.130 39.130 13.83 0.00 0.00 3.02
4824 5720 3.872771 AGGCTGCACAATTTTGAAACTTG 59.127 39.130 6.48 6.48 0.00 3.16
4825 5721 4.122046 GAGGCTGCACAATTTTGAAACTT 58.878 39.130 0.50 0.00 0.00 2.66
4826 5722 3.721035 GAGGCTGCACAATTTTGAAACT 58.279 40.909 0.50 0.00 0.00 2.66
4827 5723 2.472488 CGAGGCTGCACAATTTTGAAAC 59.528 45.455 0.50 0.00 0.00 2.78
4828 5724 2.545532 CCGAGGCTGCACAATTTTGAAA 60.546 45.455 0.50 0.00 0.00 2.69
4829 5725 1.000385 CCGAGGCTGCACAATTTTGAA 60.000 47.619 0.50 0.00 0.00 2.69
4830 5726 0.597568 CCGAGGCTGCACAATTTTGA 59.402 50.000 0.50 0.00 0.00 2.69
4831 5727 0.597568 TCCGAGGCTGCACAATTTTG 59.402 50.000 0.50 0.00 0.00 2.44
4832 5728 0.598065 GTCCGAGGCTGCACAATTTT 59.402 50.000 0.50 0.00 0.00 1.82
4833 5729 0.537143 TGTCCGAGGCTGCACAATTT 60.537 50.000 0.50 0.00 0.00 1.82
4834 5730 0.957395 CTGTCCGAGGCTGCACAATT 60.957 55.000 0.50 0.00 0.00 2.32
4835 5731 1.376424 CTGTCCGAGGCTGCACAAT 60.376 57.895 0.50 0.00 0.00 2.71
4836 5732 2.031012 CTGTCCGAGGCTGCACAA 59.969 61.111 0.50 0.00 0.00 3.33
4837 5733 3.226429 GACTGTCCGAGGCTGCACA 62.226 63.158 0.50 0.00 0.00 4.57
4838 5734 2.433318 GACTGTCCGAGGCTGCAC 60.433 66.667 0.50 0.00 0.00 4.57
4839 5735 2.440385 CTTGACTGTCCGAGGCTGCA 62.440 60.000 5.17 0.00 0.00 4.41
4840 5736 1.739562 CTTGACTGTCCGAGGCTGC 60.740 63.158 5.17 0.00 0.00 5.25
4841 5737 0.034059 AACTTGACTGTCCGAGGCTG 59.966 55.000 5.17 0.00 0.00 4.85
4842 5738 0.759346 AAACTTGACTGTCCGAGGCT 59.241 50.000 5.17 0.00 0.00 4.58
4843 5739 1.264288 CAAAACTTGACTGTCCGAGGC 59.736 52.381 5.17 0.00 0.00 4.70
4844 5740 2.833794 TCAAAACTTGACTGTCCGAGG 58.166 47.619 5.17 0.00 34.08 4.63
4845 5741 4.875544 TTTCAAAACTTGACTGTCCGAG 57.124 40.909 5.17 6.08 39.87 4.63
4846 5742 5.124776 ACAATTTCAAAACTTGACTGTCCGA 59.875 36.000 5.17 0.00 39.87 4.55
4847 5743 5.229887 CACAATTTCAAAACTTGACTGTCCG 59.770 40.000 5.17 0.00 39.87 4.79
4848 5744 5.005682 GCACAATTTCAAAACTTGACTGTCC 59.994 40.000 5.17 0.00 39.87 4.02
4849 5745 5.576384 TGCACAATTTCAAAACTTGACTGTC 59.424 36.000 0.00 0.00 39.87 3.51
4893 5803 1.355210 CGGGCGTGACATTAATGGC 59.645 57.895 19.37 17.24 35.98 4.40
4914 5824 1.270094 GCACCCACGAATATCCGATGA 60.270 52.381 0.00 0.00 0.00 2.92
4941 5851 1.003839 ATGTCACGTGGCGTCCATT 60.004 52.632 16.50 0.00 38.32 3.16
4967 5877 2.310233 CCCGCTCACACACAAGACG 61.310 63.158 0.00 0.00 0.00 4.18
4974 5884 1.227823 CTTCCAACCCGCTCACACA 60.228 57.895 0.00 0.00 0.00 3.72
4983 5893 1.351017 TCAGACATCACCTTCCAACCC 59.649 52.381 0.00 0.00 0.00 4.11
4987 5897 1.277273 CTGCTCAGACATCACCTTCCA 59.723 52.381 0.00 0.00 0.00 3.53
4990 5900 1.067283 CGACTGCTCAGACATCACCTT 60.067 52.381 3.60 0.00 0.00 3.50
5007 5917 1.442857 CACACTCACGCCTCTCGAC 60.443 63.158 0.00 0.00 41.67 4.20
5022 5932 1.896660 GGTGAGAAAAGCGGCCACA 60.897 57.895 2.24 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.