Multiple sequence alignment - TraesCS2D01G313000

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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 TraesCS2D01G313000 chr2D 100.000 4963 0 0 1 4963 402709078 402714040 0.000000e+00 9166.0
1 TraesCS2D01G313000 chr2B 95.871 2955 95 15 1 2944 476556543 476559481 0.000000e+00 4756.0
2 TraesCS2D01G313000 chr2B 93.333 1560 66 21 2930 4474 476559635 476561171 0.000000e+00 2270.0
3 TraesCS2D01G313000 chr2B 86.111 180 18 7 4754 4930 476561309 476561484 2.360000e-43 187.0
4 TraesCS2D01G313000 chr2B 93.578 109 5 2 4465 4573 458623247 458623141 1.430000e-35 161.0
5 TraesCS2D01G313000 chr2A 94.160 2774 115 23 1 2743 539963977 539966734 0.000000e+00 4181.0
6 TraesCS2D01G313000 chr2A 95.771 1608 51 7 2789 4387 539966735 539968334 0.000000e+00 2577.0
7 TraesCS2D01G313000 chr2A 93.023 86 6 0 4568 4653 539968391 539968476 5.220000e-25 126.0
8 TraesCS2D01G313000 chr2A 84.173 139 6 1 4774 4912 539970408 539970530 2.430000e-23 121.0
9 TraesCS2D01G313000 chr2A 100.000 29 0 0 4935 4963 539970536 539970564 2.000000e-03 54.7
10 TraesCS2D01G313000 chr7D 80.286 350 43 14 1617 1965 624657878 624658202 1.790000e-59 241.0
11 TraesCS2D01G313000 chr7D 80.347 346 43 13 1617 1962 624087726 624088046 6.420000e-59 239.0
12 TraesCS2D01G313000 chr7D 80.347 346 43 13 1617 1962 624415531 624415851 6.420000e-59 239.0
13 TraesCS2D01G313000 chr7D 80.347 346 43 15 1617 1962 624486835 624487155 6.420000e-59 239.0
14 TraesCS2D01G313000 chr7D 80.290 345 43 13 1617 1961 624387068 624387387 2.310000e-58 237.0
15 TraesCS2D01G313000 chr7D 80.058 346 44 13 1617 1962 624313839 624314159 2.990000e-57 233.0
16 TraesCS2D01G313000 chr7D 82.824 262 40 5 1617 1876 624184576 624184834 3.860000e-56 230.0
17 TraesCS2D01G313000 chr7D 96.939 98 2 1 4474 4571 80971195 80971099 3.980000e-36 163.0
18 TraesCS2D01G313000 chrUn 82.482 274 43 5 1620 1891 449424837 449424567 8.310000e-58 235.0
19 TraesCS2D01G313000 chr7B 93.103 116 6 2 4466 4581 747370736 747370623 8.540000e-38 169.0
20 TraesCS2D01G313000 chr3B 95.146 103 3 2 4474 4575 674424194 674424295 1.430000e-35 161.0
21 TraesCS2D01G313000 chr5D 94.231 104 5 1 4468 4571 299412218 299412320 1.850000e-34 158.0
22 TraesCS2D01G313000 chr7A 95.000 100 4 1 4472 4571 628008476 628008574 6.650000e-34 156.0
23 TraesCS2D01G313000 chr1B 90.000 120 9 3 4464 4582 328139793 328139676 8.600000e-33 152.0
24 TraesCS2D01G313000 chr4B 90.435 115 7 4 4469 4582 538218850 538218739 1.110000e-31 148.0
25 TraesCS2D01G313000 chr6B 85.315 143 13 8 4463 4602 179356669 179356806 1.860000e-29 141.0


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 TraesCS2D01G313000 chr2D 402709078 402714040 4962 False 9166.000000 9166 100.000000 1 4963 1 chr2D.!!$F1 4962
1 TraesCS2D01G313000 chr2B 476556543 476561484 4941 False 2404.333333 4756 91.771667 1 4930 3 chr2B.!!$F1 4929
2 TraesCS2D01G313000 chr2A 539963977 539970564 6587 False 1411.940000 4181 93.425400 1 4963 5 chr2A.!!$F1 4962

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
35 36 1.271597 GGCCCTCTGTCACAATCAGTT 60.272 52.381 0.00 0.0 34.86 3.16 F
386 387 1.321743 CAATGCTTGTAGTCGTCGCTC 59.678 52.381 0.00 0.0 0.00 5.03 F
1316 1352 1.807981 TTGGATAACGCAGGCGACG 60.808 57.895 21.62 0.6 42.83 5.12 F
2821 2865 1.372683 GCTTCCTCAGCTGACACCA 59.627 57.895 13.74 0.0 46.27 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1661 1697 0.247974 GTCACCGATGTCCTCGTACG 60.248 60.000 9.53 9.53 46.18 3.67 R
1973 2009 1.358152 TCATGGAAAGTCGGGACCTT 58.642 50.000 0.00 0.00 0.00 3.50 R
2992 3204 3.640967 AGGCTCCTCATCATTGTCTCTAC 59.359 47.826 0.00 0.00 0.00 2.59 R
3973 4185 0.035176 TCGTCCCTTTTGGTAACCCG 59.965 55.000 0.00 0.00 38.10 5.28 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
35 36 1.271597 GGCCCTCTGTCACAATCAGTT 60.272 52.381 0.00 0.00 34.86 3.16
349 350 2.627515 AGCCTATCATGCACGACAAT 57.372 45.000 0.00 0.00 0.00 2.71
386 387 1.321743 CAATGCTTGTAGTCGTCGCTC 59.678 52.381 0.00 0.00 0.00 5.03
412 413 4.028131 TGTCTACGGACCTGGATGTAATT 58.972 43.478 0.00 0.00 41.47 1.40
694 698 1.864082 GCACCGTGGAAAACCAAAATG 59.136 47.619 0.00 0.00 0.00 2.32
782 800 2.579873 CCATCCTGCAATACTCAAGGG 58.420 52.381 0.00 0.00 0.00 3.95
1197 1228 2.511600 CACCCAGGTCCGCGATTC 60.512 66.667 8.23 0.00 0.00 2.52
1273 1309 2.038689 TGGTTGCCATCCTGTTACGTTA 59.961 45.455 0.00 0.00 0.00 3.18
1303 1339 4.261572 CGTGTCTGATTTTGTTGGTTGGAT 60.262 41.667 0.00 0.00 0.00 3.41
1316 1352 1.807981 TTGGATAACGCAGGCGACG 60.808 57.895 21.62 0.60 42.83 5.12
1587 1623 8.512138 TGATGATGCAATTGATGATAGTTGATC 58.488 33.333 10.34 0.00 34.84 2.92
1661 1697 7.377766 TCCTTAAGTATTTTGTCAGTGATGC 57.622 36.000 0.00 0.00 0.00 3.91
1840 1876 6.455647 CCATGCCGTTCTATTACTGATTCTA 58.544 40.000 0.00 0.00 0.00 2.10
1857 1893 1.906574 TCTAACGAGCCTGGGATGTTT 59.093 47.619 0.00 0.00 0.00 2.83
1973 2009 5.104982 GGTAATGCTTCCAATTCCATTTCCA 60.105 40.000 0.00 0.00 36.06 3.53
2040 2076 6.932356 AATGTGCATAGGAGAACTATTGTG 57.068 37.500 0.00 0.00 40.42 3.33
2097 2139 5.118286 TGTCTGCATGTGTATATCAGGTTG 58.882 41.667 0.00 0.00 0.00 3.77
2098 2140 5.104982 TGTCTGCATGTGTATATCAGGTTGA 60.105 40.000 0.00 0.00 0.00 3.18
2099 2141 5.817296 GTCTGCATGTGTATATCAGGTTGAA 59.183 40.000 0.00 0.00 0.00 2.69
2100 2142 6.018425 GTCTGCATGTGTATATCAGGTTGAAG 60.018 42.308 0.00 0.00 0.00 3.02
2101 2143 5.744171 TGCATGTGTATATCAGGTTGAAGT 58.256 37.500 0.00 0.00 0.00 3.01
2102 2144 6.179756 TGCATGTGTATATCAGGTTGAAGTT 58.820 36.000 0.00 0.00 0.00 2.66
2107 2149 7.564793 TGTGTATATCAGGTTGAAGTTAGCAT 58.435 34.615 0.00 0.00 0.00 3.79
2108 2150 7.495606 TGTGTATATCAGGTTGAAGTTAGCATG 59.504 37.037 0.00 0.00 0.00 4.06
2123 2165 9.331282 GAAGTTAGCATGGATTAGTATTTCACT 57.669 33.333 0.00 0.00 41.62 3.41
2241 2285 7.523052 GCATTGTTAACTGTCCTTATTTGTCCA 60.523 37.037 7.22 0.00 0.00 4.02
2517 2561 6.270156 AGAAGAGTTCTAAAGGTAGTTCCG 57.730 41.667 0.00 0.00 38.49 4.30
2652 2696 5.279406 CCCCTTGCTGATTTGTTTAATCACA 60.279 40.000 0.00 0.00 45.91 3.58
2670 2714 5.764487 TCACAATGAAGCAACATGTGTTA 57.236 34.783 0.00 0.00 36.32 2.41
2821 2865 1.372683 GCTTCCTCAGCTGACACCA 59.627 57.895 13.74 0.00 46.27 4.17
2992 3204 8.630278 GATGGAATCATCTCATTTCTTTGTTG 57.370 34.615 0.00 0.00 44.70 3.33
3305 3517 5.011023 TCTCAGTACTTTCAATGCTCAGTGA 59.989 40.000 0.00 0.00 33.21 3.41
3556 3768 3.146618 AGCGTACTCGTATCCTTGTTG 57.853 47.619 0.00 0.00 39.49 3.33
3722 3934 7.173218 CCTGATACATGCGGTTAGTTCATAATT 59.827 37.037 0.00 0.00 0.00 1.40
3741 3953 9.060347 TCATAATTTCTTATGATCCTGTCTTGC 57.940 33.333 4.38 0.00 45.23 4.01
3825 4037 5.128991 GGGGTAGGACATATATACTGCTTCC 59.871 48.000 0.00 0.00 0.00 3.46
3875 4087 6.241207 TGTTTCGATTCTGATTTGTTCTCC 57.759 37.500 0.00 0.00 0.00 3.71
3930 4142 0.963962 ACCGCCGAACTCAACTCTTA 59.036 50.000 0.00 0.00 0.00 2.10
3973 4185 1.067776 CGTACAGTGAAGAGGTGACCC 60.068 57.143 0.00 0.00 0.00 4.46
3974 4186 1.067776 GTACAGTGAAGAGGTGACCCG 60.068 57.143 0.00 0.00 35.12 5.28
4031 4245 3.088532 TGTGCAAGTTCAAGAAACACCT 58.911 40.909 0.00 0.00 40.56 4.00
4040 4254 5.952347 AGTTCAAGAAACACCTTTTTCCTCT 59.048 36.000 0.00 0.00 40.56 3.69
4050 4264 1.394917 CTTTTTCCTCTGTCATCGCCG 59.605 52.381 0.00 0.00 0.00 6.46
4094 4312 7.533426 TCCTACAGTCGTCTTTATGTACTTTC 58.467 38.462 0.00 0.00 0.00 2.62
4111 4329 7.261325 TGTACTTTCTTCATCAGCTCTACATC 58.739 38.462 0.00 0.00 0.00 3.06
4139 4358 3.602104 CCATCTGGGCTTTGTGGAT 57.398 52.632 0.00 0.00 31.59 3.41
4143 4364 3.346631 CTGGGCTTTGTGGATGCGC 62.347 63.158 0.00 0.00 40.44 6.09
4220 4441 6.513230 CGTTTTGACATTCTTCTGGAATCACA 60.513 38.462 0.00 0.00 42.20 3.58
4223 4444 4.999311 TGACATTCTTCTGGAATCACACTG 59.001 41.667 0.00 0.00 42.20 3.66
4299 4528 3.157087 AGTTGCTCCATTTTCCGTTCAT 58.843 40.909 0.00 0.00 0.00 2.57
4364 4593 3.966665 TCTGATTTTCCACCTTTTGGCTT 59.033 39.130 0.00 0.00 46.47 4.35
4380 4609 0.796927 GCTTAAGTCGACTGTTGCCC 59.203 55.000 20.85 2.19 0.00 5.36
4401 4630 2.355716 CCAAATCTAAGGACGCTTCCCA 60.356 50.000 5.45 0.00 44.10 4.37
4403 4632 0.466124 ATCTAAGGACGCTTCCCAGC 59.534 55.000 5.45 0.00 44.10 4.85
4439 4668 5.512232 GCAGGAGAAAATATCCGGAGAGAAT 60.512 44.000 11.34 0.00 42.02 2.40
4451 4680 3.628942 CCGGAGAGAATCATGCAATTTCA 59.371 43.478 0.00 0.00 37.82 2.69
4452 4681 4.277672 CCGGAGAGAATCATGCAATTTCAT 59.722 41.667 0.00 0.00 37.82 2.57
4486 4715 9.896263 CTAAATAATTTAGTACTCTCTCCGTCC 57.104 37.037 0.00 0.00 38.21 4.79
4487 4716 6.897706 ATAATTTAGTACTCTCTCCGTCCC 57.102 41.667 0.00 0.00 0.00 4.46
4490 4719 2.599408 AGTACTCTCTCCGTCCCAAA 57.401 50.000 0.00 0.00 0.00 3.28
4491 4720 2.885616 AGTACTCTCTCCGTCCCAAAA 58.114 47.619 0.00 0.00 0.00 2.44
4492 4721 3.442076 AGTACTCTCTCCGTCCCAAAAT 58.558 45.455 0.00 0.00 0.00 1.82
4494 4723 5.021458 AGTACTCTCTCCGTCCCAAAATAA 58.979 41.667 0.00 0.00 0.00 1.40
4495 4724 4.903045 ACTCTCTCCGTCCCAAAATAAA 57.097 40.909 0.00 0.00 0.00 1.40
4496 4725 5.437191 ACTCTCTCCGTCCCAAAATAAAT 57.563 39.130 0.00 0.00 0.00 1.40
4498 4727 5.174037 TCTCTCCGTCCCAAAATAAATGT 57.826 39.130 0.00 0.00 0.00 2.71
4499 4728 5.183228 TCTCTCCGTCCCAAAATAAATGTC 58.817 41.667 0.00 0.00 0.00 3.06
4501 4730 5.183228 TCTCCGTCCCAAAATAAATGTCTC 58.817 41.667 0.00 0.00 0.00 3.36
4504 4733 5.414454 TCCGTCCCAAAATAAATGTCTCAAG 59.586 40.000 0.00 0.00 0.00 3.02
4505 4734 5.095490 CGTCCCAAAATAAATGTCTCAAGC 58.905 41.667 0.00 0.00 0.00 4.01
4506 4735 5.106157 CGTCCCAAAATAAATGTCTCAAGCT 60.106 40.000 0.00 0.00 0.00 3.74
4507 4736 6.570378 CGTCCCAAAATAAATGTCTCAAGCTT 60.570 38.462 0.00 0.00 0.00 3.74
4508 4737 7.361713 CGTCCCAAAATAAATGTCTCAAGCTTA 60.362 37.037 0.00 0.00 0.00 3.09
4509 4738 7.970614 GTCCCAAAATAAATGTCTCAAGCTTAG 59.029 37.037 0.00 0.00 0.00 2.18
4510 4739 7.669722 TCCCAAAATAAATGTCTCAAGCTTAGT 59.330 33.333 0.00 0.00 0.00 2.24
4511 4740 8.956426 CCCAAAATAAATGTCTCAAGCTTAGTA 58.044 33.333 0.00 0.00 0.00 1.82
4512 4741 9.774742 CCAAAATAAATGTCTCAAGCTTAGTAC 57.225 33.333 0.00 0.00 0.00 2.73
4516 4745 9.726438 AATAAATGTCTCAAGCTTAGTACAACT 57.274 29.630 0.00 0.00 0.00 3.16
4517 4746 9.726438 ATAAATGTCTCAAGCTTAGTACAACTT 57.274 29.630 0.00 4.81 0.00 2.66
4518 4747 8.451908 AAATGTCTCAAGCTTAGTACAACTTT 57.548 30.769 0.00 0.08 0.00 2.66
4519 4748 6.844696 TGTCTCAAGCTTAGTACAACTTTG 57.155 37.500 0.00 0.00 0.00 2.77
4520 4749 6.346096 TGTCTCAAGCTTAGTACAACTTTGT 58.654 36.000 0.00 0.00 44.86 2.83
4521 4750 7.494211 TGTCTCAAGCTTAGTACAACTTTGTA 58.506 34.615 0.00 0.00 42.35 2.41
4536 4765 8.174733 ACAACTTTGTACTAGAGCTAAGTACA 57.825 34.615 26.36 26.36 44.25 2.90
4543 4772 8.400184 TGTACTAGAGCTAAGTACAAAGTTGA 57.600 34.615 27.28 11.49 43.37 3.18
4544 4773 8.512956 TGTACTAGAGCTAAGTACAAAGTTGAG 58.487 37.037 27.28 0.00 43.37 3.02
4545 4774 7.762588 ACTAGAGCTAAGTACAAAGTTGAGA 57.237 36.000 0.00 0.00 0.00 3.27
4546 4775 7.595604 ACTAGAGCTAAGTACAAAGTTGAGAC 58.404 38.462 0.00 0.00 0.00 3.36
4547 4776 6.406692 AGAGCTAAGTACAAAGTTGAGACA 57.593 37.500 0.00 0.00 0.00 3.41
4548 4777 6.217294 AGAGCTAAGTACAAAGTTGAGACAC 58.783 40.000 0.00 0.00 0.00 3.67
4549 4778 6.041069 AGAGCTAAGTACAAAGTTGAGACACT 59.959 38.462 0.00 0.00 0.00 3.55
4550 4779 6.583562 AGCTAAGTACAAAGTTGAGACACTT 58.416 36.000 0.00 4.72 38.74 3.16
4551 4780 7.723324 AGCTAAGTACAAAGTTGAGACACTTA 58.277 34.615 0.00 5.48 35.87 2.24
4552 4781 8.368668 AGCTAAGTACAAAGTTGAGACACTTAT 58.631 33.333 0.00 0.00 35.87 1.73
4553 4782 8.989980 GCTAAGTACAAAGTTGAGACACTTATT 58.010 33.333 0.00 0.00 35.87 1.40
4557 4786 8.621286 AGTACAAAGTTGAGACACTTATTTTGG 58.379 33.333 0.00 0.00 35.87 3.28
4558 4787 6.805713 ACAAAGTTGAGACACTTATTTTGGG 58.194 36.000 0.00 0.00 35.87 4.12
4559 4788 6.605594 ACAAAGTTGAGACACTTATTTTGGGA 59.394 34.615 0.00 0.00 35.87 4.37
4560 4789 7.287696 ACAAAGTTGAGACACTTATTTTGGGAT 59.712 33.333 0.00 0.00 35.87 3.85
4561 4790 6.824305 AGTTGAGACACTTATTTTGGGATG 57.176 37.500 0.00 0.00 0.00 3.51
4562 4791 5.711976 AGTTGAGACACTTATTTTGGGATGG 59.288 40.000 0.00 0.00 0.00 3.51
4563 4792 5.512942 TGAGACACTTATTTTGGGATGGA 57.487 39.130 0.00 0.00 0.00 3.41
4564 4793 5.500234 TGAGACACTTATTTTGGGATGGAG 58.500 41.667 0.00 0.00 0.00 3.86
4565 4794 4.860022 AGACACTTATTTTGGGATGGAGG 58.140 43.478 0.00 0.00 0.00 4.30
4566 4795 3.954258 GACACTTATTTTGGGATGGAGGG 59.046 47.826 0.00 0.00 0.00 4.30
4567 4796 3.596046 ACACTTATTTTGGGATGGAGGGA 59.404 43.478 0.00 0.00 0.00 4.20
4568 4797 4.210331 CACTTATTTTGGGATGGAGGGAG 58.790 47.826 0.00 0.00 0.00 4.30
4569 4798 3.858638 ACTTATTTTGGGATGGAGGGAGT 59.141 43.478 0.00 0.00 0.00 3.85
4574 4803 4.569676 TTTGGGATGGAGGGAGTAGATA 57.430 45.455 0.00 0.00 0.00 1.98
4639 4868 5.997732 AGCGAAAATGAAAACAATCATCG 57.002 34.783 0.00 0.00 39.08 3.84
4660 4889 8.458052 TCATCGTTATACATTGCTGAATTTGTT 58.542 29.630 0.00 0.00 0.00 2.83
4661 4890 9.075519 CATCGTTATACATTGCTGAATTTGTTT 57.924 29.630 0.00 0.00 0.00 2.83
4662 4891 9.638239 ATCGTTATACATTGCTGAATTTGTTTT 57.362 25.926 0.00 0.00 0.00 2.43
4663 4892 9.123709 TCGTTATACATTGCTGAATTTGTTTTC 57.876 29.630 0.00 0.00 0.00 2.29
4664 4893 9.128107 CGTTATACATTGCTGAATTTGTTTTCT 57.872 29.630 0.00 0.00 0.00 2.52
4666 4895 5.662211 ACATTGCTGAATTTGTTTTCTGC 57.338 34.783 8.54 8.54 45.46 4.26
4684 4913 6.599356 TTCTGCATACCTTGAACTAGTACA 57.401 37.500 0.00 0.00 0.00 2.90
4790 6867 3.672808 AGAAGAGAACATCACCTGCTTG 58.327 45.455 0.00 0.00 0.00 4.01
4791 6868 1.818642 AGAGAACATCACCTGCTTGC 58.181 50.000 0.00 0.00 0.00 4.01
4856 6934 4.780815 TGAGTTTTCACTGTGATCTGGTT 58.219 39.130 11.86 0.00 31.22 3.67
4859 6937 6.152661 TGAGTTTTCACTGTGATCTGGTTTTT 59.847 34.615 11.86 0.00 31.22 1.94
4863 6941 4.973168 TCACTGTGATCTGGTTTTTAGCT 58.027 39.130 6.36 0.00 0.00 3.32
4925 7003 3.563808 TGCGTACTTGCAGAAATTTCAGT 59.436 39.130 19.99 15.56 40.62 3.41
4926 7004 4.752604 TGCGTACTTGCAGAAATTTCAGTA 59.247 37.500 19.99 14.64 40.62 2.74
4928 7006 6.072728 TGCGTACTTGCAGAAATTTCAGTAAT 60.073 34.615 19.99 10.04 40.62 1.89
4931 7009 8.629986 CGTACTTGCAGAAATTTCAGTAATTTG 58.370 33.333 19.99 8.67 44.46 2.32
4932 7010 9.463443 GTACTTGCAGAAATTTCAGTAATTTGT 57.537 29.630 19.99 13.30 44.46 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 8.773033 AGAGACCTAATAAACCCTTATCGTTA 57.227 34.615 0.00 0.00 0.00 3.18
386 387 3.198068 CATCCAGGTCCGTAGACAATTG 58.802 50.000 3.24 3.24 45.48 2.32
589 592 8.675040 TTTTTGCGTTTATTTTTCCTTTTTGG 57.325 26.923 0.00 0.00 37.10 3.28
782 800 2.676076 ACTTGTGCGATTTGATTTGGC 58.324 42.857 0.00 0.00 0.00 4.52
1041 1066 1.632046 GAGAAATTGACGGCGGCGAA 61.632 55.000 38.93 23.06 0.00 4.70
1042 1067 2.047655 AGAAATTGACGGCGGCGA 60.048 55.556 38.93 16.95 0.00 5.54
1129 1160 1.448013 GTGCGTGTAGGGCTTCTCC 60.448 63.158 0.00 0.00 0.00 3.71
1197 1228 1.038280 ATCGTAGGTTAAGGGCGAGG 58.962 55.000 0.00 0.00 35.03 4.63
1273 1309 3.476552 ACAAAATCAGACACGGTCACAT 58.523 40.909 6.78 0.00 34.60 3.21
1373 1409 3.503748 GCTCCTTGTTCTTAACAGTGCAT 59.496 43.478 0.00 0.00 43.27 3.96
1587 1623 4.572389 CGACCAGAGAAAATAATCCCAGTG 59.428 45.833 0.00 0.00 0.00 3.66
1661 1697 0.247974 GTCACCGATGTCCTCGTACG 60.248 60.000 9.53 9.53 46.18 3.67
1826 1862 6.153067 CCAGGCTCGTTAGAATCAGTAATAG 58.847 44.000 0.00 0.00 0.00 1.73
1840 1876 1.906574 TCTAAACATCCCAGGCTCGTT 59.093 47.619 0.00 0.00 0.00 3.85
1857 1893 4.642437 AGTCTGAATCATCTTCGCTGTCTA 59.358 41.667 0.00 0.00 0.00 2.59
1973 2009 1.358152 TCATGGAAAGTCGGGACCTT 58.642 50.000 0.00 0.00 0.00 3.50
2040 2076 3.566523 GCCTACATACGACTGACTATGC 58.433 50.000 0.00 0.00 0.00 3.14
2097 2139 9.331282 AGTGAAATACTAATCCATGCTAACTTC 57.669 33.333 0.00 0.00 38.04 3.01
2098 2140 9.113838 CAGTGAAATACTAATCCATGCTAACTT 57.886 33.333 0.00 0.00 37.60 2.66
2099 2141 7.716998 CCAGTGAAATACTAATCCATGCTAACT 59.283 37.037 0.00 0.00 37.60 2.24
2100 2142 7.499232 ACCAGTGAAATACTAATCCATGCTAAC 59.501 37.037 0.00 0.00 37.60 2.34
2101 2143 7.498900 CACCAGTGAAATACTAATCCATGCTAA 59.501 37.037 0.00 0.00 37.60 3.09
2102 2144 6.992123 CACCAGTGAAATACTAATCCATGCTA 59.008 38.462 0.00 0.00 37.60 3.49
2123 2165 5.708736 ATACCATCTAATCCAACACACCA 57.291 39.130 0.00 0.00 0.00 4.17
2652 2696 7.856894 GCAAAATTTAACACATGTTGCTTCATT 59.143 29.630 7.53 0.00 38.90 2.57
2670 2714 3.967332 CTGGGATGACAGGCAAAATTT 57.033 42.857 0.00 0.00 34.84 1.82
2821 2865 4.405116 TTTTCTTCTGTTTGGCTGCAAT 57.595 36.364 0.50 0.00 0.00 3.56
2992 3204 3.640967 AGGCTCCTCATCATTGTCTCTAC 59.359 47.826 0.00 0.00 0.00 2.59
3305 3517 5.954335 GCAAAGGCAAGTACATACTGATTT 58.046 37.500 0.00 0.00 40.72 2.17
3556 3768 9.139174 CATGAAAGTGACATTAAAACCAATACC 57.861 33.333 0.00 0.00 0.00 2.73
3670 3882 7.734924 ATGGAGTAGTACAACATATGCAATG 57.265 36.000 1.58 2.47 0.00 2.82
3722 3934 4.637534 GCAAGCAAGACAGGATCATAAGAA 59.362 41.667 0.00 0.00 0.00 2.52
3741 3953 3.559655 TGCGCATACCTATAACAAGCAAG 59.440 43.478 5.66 0.00 0.00 4.01
3825 4037 3.242543 GCTCCTGATGTAAAAGCGATGTG 60.243 47.826 0.00 0.00 0.00 3.21
3875 4087 4.843728 TCTGGTTTCCATAGCTACAAAGG 58.156 43.478 0.00 0.00 30.82 3.11
3930 4142 5.163723 CGTTCATTAGCTCCACATCAAACAT 60.164 40.000 0.00 0.00 0.00 2.71
3973 4185 0.035176 TCGTCCCTTTTGGTAACCCG 59.965 55.000 0.00 0.00 38.10 5.28
3974 4186 1.612462 CCTCGTCCCTTTTGGTAACCC 60.612 57.143 0.00 0.00 38.10 4.11
4031 4245 1.270625 ACGGCGATGACAGAGGAAAAA 60.271 47.619 16.62 0.00 0.00 1.94
4040 4254 0.179137 CTGAAGCTACGGCGATGACA 60.179 55.000 16.62 5.04 44.37 3.58
4050 4264 4.319177 AGGATGTTGTTGACTGAAGCTAC 58.681 43.478 0.00 0.00 0.00 3.58
4094 4312 5.904941 AGTTGAGATGTAGAGCTGATGAAG 58.095 41.667 0.00 0.00 0.00 3.02
4134 4353 1.806758 GCCAATGTTGCGCATCCAC 60.807 57.895 12.75 7.47 36.67 4.02
4137 4356 1.517694 CAGGCCAATGTTGCGCATC 60.518 57.895 12.75 12.06 36.67 3.91
4138 4357 2.574929 CAGGCCAATGTTGCGCAT 59.425 55.556 12.75 0.00 40.03 4.73
4139 4358 3.682885 CCAGGCCAATGTTGCGCA 61.683 61.111 5.66 5.66 0.00 6.09
4143 4364 2.975536 CAGCCCAGGCCAATGTTG 59.024 61.111 5.01 0.00 43.17 3.33
4220 4441 6.013379 TCCATTCCTTCATAACAAGTCTCAGT 60.013 38.462 0.00 0.00 0.00 3.41
4223 4444 5.819901 CCTCCATTCCTTCATAACAAGTCTC 59.180 44.000 0.00 0.00 0.00 3.36
4299 4528 4.299586 TCCAACCAAGATACAGAATGCA 57.700 40.909 0.00 0.00 42.53 3.96
4364 4593 0.759959 TTGGGGCAACAGTCGACTTA 59.240 50.000 17.26 0.00 39.74 2.24
4380 4609 2.289565 GGGAAGCGTCCTTAGATTTGG 58.710 52.381 18.54 0.00 44.28 3.28
4401 4630 0.250234 TCCTGCGCTTTCATACAGCT 59.750 50.000 9.73 0.00 34.88 4.24
4403 4632 2.299993 TCTCCTGCGCTTTCATACAG 57.700 50.000 9.73 0.00 0.00 2.74
4474 4703 4.903045 TTTATTTTGGGACGGAGAGAGT 57.097 40.909 0.00 0.00 0.00 3.24
4475 4704 5.186198 ACATTTATTTTGGGACGGAGAGAG 58.814 41.667 0.00 0.00 0.00 3.20
4476 4705 5.045869 AGACATTTATTTTGGGACGGAGAGA 60.046 40.000 0.00 0.00 0.00 3.10
4477 4706 5.186198 AGACATTTATTTTGGGACGGAGAG 58.814 41.667 0.00 0.00 0.00 3.20
4478 4707 5.174037 AGACATTTATTTTGGGACGGAGA 57.826 39.130 0.00 0.00 0.00 3.71
4479 4708 4.941263 TGAGACATTTATTTTGGGACGGAG 59.059 41.667 0.00 0.00 0.00 4.63
4480 4709 4.912586 TGAGACATTTATTTTGGGACGGA 58.087 39.130 0.00 0.00 0.00 4.69
4481 4710 5.637006 TTGAGACATTTATTTTGGGACGG 57.363 39.130 0.00 0.00 0.00 4.79
4483 4712 6.272822 AGCTTGAGACATTTATTTTGGGAC 57.727 37.500 0.00 0.00 0.00 4.46
4485 4714 7.830739 ACTAAGCTTGAGACATTTATTTTGGG 58.169 34.615 9.86 0.00 0.00 4.12
4486 4715 9.774742 GTACTAAGCTTGAGACATTTATTTTGG 57.225 33.333 9.86 0.00 0.00 3.28
4490 4719 9.726438 AGTTGTACTAAGCTTGAGACATTTATT 57.274 29.630 9.86 0.00 0.00 1.40
4491 4720 9.726438 AAGTTGTACTAAGCTTGAGACATTTAT 57.274 29.630 9.86 0.00 0.00 1.40
4492 4721 9.555727 AAAGTTGTACTAAGCTTGAGACATTTA 57.444 29.630 9.86 0.00 0.00 1.40
4494 4723 7.499232 ACAAAGTTGTACTAAGCTTGAGACATT 59.501 33.333 9.86 0.05 40.16 2.71
4495 4724 6.992715 ACAAAGTTGTACTAAGCTTGAGACAT 59.007 34.615 9.86 0.00 40.16 3.06
4496 4725 6.346096 ACAAAGTTGTACTAAGCTTGAGACA 58.654 36.000 9.86 7.12 40.16 3.41
4510 4739 9.288576 TGTACTTAGCTCTAGTACAAAGTTGTA 57.711 33.333 26.95 11.00 43.37 2.41
4511 4740 8.174733 TGTACTTAGCTCTAGTACAAAGTTGT 57.825 34.615 26.95 1.75 43.37 3.32
4518 4747 8.400184 TCAACTTTGTACTTAGCTCTAGTACA 57.600 34.615 26.05 26.05 44.25 2.90
4519 4748 8.728833 TCTCAACTTTGTACTTAGCTCTAGTAC 58.271 37.037 22.81 22.81 38.93 2.73
4520 4749 8.728833 GTCTCAACTTTGTACTTAGCTCTAGTA 58.271 37.037 0.00 0.00 0.00 1.82
4521 4750 7.230913 TGTCTCAACTTTGTACTTAGCTCTAGT 59.769 37.037 6.64 6.64 0.00 2.57
4522 4751 7.539366 GTGTCTCAACTTTGTACTTAGCTCTAG 59.461 40.741 0.00 0.00 0.00 2.43
4523 4752 7.230913 AGTGTCTCAACTTTGTACTTAGCTCTA 59.769 37.037 0.00 0.00 0.00 2.43
4524 4753 6.041069 AGTGTCTCAACTTTGTACTTAGCTCT 59.959 38.462 0.00 0.00 0.00 4.09
4525 4754 6.217294 AGTGTCTCAACTTTGTACTTAGCTC 58.783 40.000 0.00 0.00 0.00 4.09
4526 4755 6.163135 AGTGTCTCAACTTTGTACTTAGCT 57.837 37.500 0.00 0.00 0.00 3.32
4527 4756 6.846325 AAGTGTCTCAACTTTGTACTTAGC 57.154 37.500 0.00 0.00 37.05 3.09
4531 4760 8.621286 CCAAAATAAGTGTCTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
4532 4761 7.860872 CCCAAAATAAGTGTCTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
4533 4762 7.776030 TCCCAAAATAAGTGTCTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
4534 4763 6.605594 TCCCAAAATAAGTGTCTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
4535 4764 7.038154 TCCCAAAATAAGTGTCTCAACTTTG 57.962 36.000 0.00 0.00 40.77 2.77
4536 4765 7.255942 CCATCCCAAAATAAGTGTCTCAACTTT 60.256 37.037 0.00 0.00 40.77 2.66
4537 4766 6.209391 CCATCCCAAAATAAGTGTCTCAACTT 59.791 38.462 0.00 0.00 42.89 2.66
4538 4767 5.711976 CCATCCCAAAATAAGTGTCTCAACT 59.288 40.000 0.00 0.00 0.00 3.16
4539 4768 5.710099 TCCATCCCAAAATAAGTGTCTCAAC 59.290 40.000 0.00 0.00 0.00 3.18
4540 4769 5.886609 TCCATCCCAAAATAAGTGTCTCAA 58.113 37.500 0.00 0.00 0.00 3.02
4541 4770 5.500234 CTCCATCCCAAAATAAGTGTCTCA 58.500 41.667 0.00 0.00 0.00 3.27
4542 4771 4.884164 CCTCCATCCCAAAATAAGTGTCTC 59.116 45.833 0.00 0.00 0.00 3.36
4543 4772 4.325344 CCCTCCATCCCAAAATAAGTGTCT 60.325 45.833 0.00 0.00 0.00 3.41
4544 4773 3.954258 CCCTCCATCCCAAAATAAGTGTC 59.046 47.826 0.00 0.00 0.00 3.67
4545 4774 3.596046 TCCCTCCATCCCAAAATAAGTGT 59.404 43.478 0.00 0.00 0.00 3.55
4546 4775 4.210331 CTCCCTCCATCCCAAAATAAGTG 58.790 47.826 0.00 0.00 0.00 3.16
4547 4776 3.858638 ACTCCCTCCATCCCAAAATAAGT 59.141 43.478 0.00 0.00 0.00 2.24
4548 4777 4.526438 ACTCCCTCCATCCCAAAATAAG 57.474 45.455 0.00 0.00 0.00 1.73
4549 4778 5.293643 TCTACTCCCTCCATCCCAAAATAA 58.706 41.667 0.00 0.00 0.00 1.40
4550 4779 4.903149 TCTACTCCCTCCATCCCAAAATA 58.097 43.478 0.00 0.00 0.00 1.40
4551 4780 3.747852 TCTACTCCCTCCATCCCAAAAT 58.252 45.455 0.00 0.00 0.00 1.82
4552 4781 3.214694 TCTACTCCCTCCATCCCAAAA 57.785 47.619 0.00 0.00 0.00 2.44
4553 4782 2.961536 TCTACTCCCTCCATCCCAAA 57.038 50.000 0.00 0.00 0.00 3.28
4554 4783 3.471306 ACTATCTACTCCCTCCATCCCAA 59.529 47.826 0.00 0.00 0.00 4.12
4555 4784 3.072086 ACTATCTACTCCCTCCATCCCA 58.928 50.000 0.00 0.00 0.00 4.37
4556 4785 3.837399 ACTATCTACTCCCTCCATCCC 57.163 52.381 0.00 0.00 0.00 3.85
4631 4860 9.454585 AAATTCAGCAATGTATAACGATGATTG 57.545 29.630 0.00 0.00 0.00 2.67
4660 4889 6.999950 TGTACTAGTTCAAGGTATGCAGAAA 58.000 36.000 0.00 0.00 0.00 2.52
4661 4890 6.599356 TGTACTAGTTCAAGGTATGCAGAA 57.401 37.500 0.00 0.00 0.00 3.02
4662 4891 6.599356 TTGTACTAGTTCAAGGTATGCAGA 57.401 37.500 10.55 0.00 0.00 4.26
4663 4892 7.849804 AATTGTACTAGTTCAAGGTATGCAG 57.150 36.000 18.21 0.00 0.00 4.41
4664 4893 9.378551 CTAAATTGTACTAGTTCAAGGTATGCA 57.621 33.333 18.21 0.00 0.00 3.96
4665 4894 9.595823 TCTAAATTGTACTAGTTCAAGGTATGC 57.404 33.333 18.21 0.00 0.00 3.14
4755 6832 6.616947 TGTTCTCTTCTCGCAAAAAGAAAAA 58.383 32.000 0.00 0.00 32.60 1.94
4756 6833 6.189677 TGTTCTCTTCTCGCAAAAAGAAAA 57.810 33.333 0.00 0.00 32.60 2.29
4757 6834 5.811399 TGTTCTCTTCTCGCAAAAAGAAA 57.189 34.783 0.00 0.00 32.60 2.52
4758 6835 5.527214 TGATGTTCTCTTCTCGCAAAAAGAA 59.473 36.000 0.00 0.00 31.45 2.52
4759 6836 5.050091 GTGATGTTCTCTTCTCGCAAAAAGA 60.050 40.000 0.00 0.00 0.00 2.52
4760 6837 5.142962 GTGATGTTCTCTTCTCGCAAAAAG 58.857 41.667 0.00 0.00 0.00 2.27
4761 6838 4.024048 GGTGATGTTCTCTTCTCGCAAAAA 60.024 41.667 0.00 0.00 0.00 1.94
4762 6839 3.498397 GGTGATGTTCTCTTCTCGCAAAA 59.502 43.478 0.00 0.00 0.00 2.44
4763 6840 3.067106 GGTGATGTTCTCTTCTCGCAAA 58.933 45.455 0.00 0.00 0.00 3.68
4764 6841 2.300152 AGGTGATGTTCTCTTCTCGCAA 59.700 45.455 0.00 0.00 0.00 4.85
4765 6842 1.895798 AGGTGATGTTCTCTTCTCGCA 59.104 47.619 0.00 0.00 0.00 5.10
4766 6843 2.266554 CAGGTGATGTTCTCTTCTCGC 58.733 52.381 0.00 0.00 0.00 5.03
4767 6844 2.094286 AGCAGGTGATGTTCTCTTCTCG 60.094 50.000 0.00 0.00 0.00 4.04
4768 6845 3.608316 AGCAGGTGATGTTCTCTTCTC 57.392 47.619 0.00 0.00 0.00 2.87
4769 6846 3.672808 CAAGCAGGTGATGTTCTCTTCT 58.327 45.455 0.00 0.00 0.00 2.85
4770 6847 2.161211 GCAAGCAGGTGATGTTCTCTTC 59.839 50.000 0.00 0.00 0.00 2.87
4771 6848 2.157738 GCAAGCAGGTGATGTTCTCTT 58.842 47.619 0.00 0.00 0.00 2.85
4772 6849 1.612726 GGCAAGCAGGTGATGTTCTCT 60.613 52.381 0.00 0.00 0.00 3.10
4859 6937 8.771920 TCTATTTTTCGAGAAAATGTCAGCTA 57.228 30.769 19.57 2.84 39.69 3.32
4925 7003 9.469807 ACAATTGCACTTCGAAAATACAAATTA 57.530 25.926 5.05 0.00 0.00 1.40
4926 7004 8.364129 ACAATTGCACTTCGAAAATACAAATT 57.636 26.923 5.05 0.00 0.00 1.82
4928 7006 7.763172 AACAATTGCACTTCGAAAATACAAA 57.237 28.000 5.05 0.00 0.00 2.83
4931 7009 7.617557 ACAAAACAATTGCACTTCGAAAATAC 58.382 30.769 5.05 0.00 0.00 1.89
4932 7010 7.763172 ACAAAACAATTGCACTTCGAAAATA 57.237 28.000 5.05 0.00 0.00 1.40
4933 7011 6.660887 ACAAAACAATTGCACTTCGAAAAT 57.339 29.167 5.05 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.