Multiple sequence alignment - TraesCS2D01G358600

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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 TraesCS2D01G358600 chr2D 100.000 5124 0 0 1 5124 460755797 460760920 0.000000e+00 9463
1 TraesCS2D01G358600 chr2A 92.918 5083 255 46 1 5027 603556912 603561945 0.000000e+00 7295
2 TraesCS2D01G358600 chr2B 94.501 3964 178 20 433 4375 542259405 542263349 0.000000e+00 6076
3 TraesCS2D01G358600 chr2B 92.635 353 22 3 58 407 542258519 542258870 5.920000e-139 505
4 TraesCS2D01G358600 chr2B 91.447 304 15 5 4822 5124 542263744 542264037 1.720000e-109 407


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 TraesCS2D01G358600 chr2D 460755797 460760920 5123 False 9463.000000 9463 100.000 1 5124 1 chr2D.!!$F1 5123
1 TraesCS2D01G358600 chr2A 603556912 603561945 5033 False 7295.000000 7295 92.918 1 5027 1 chr2A.!!$F1 5026
2 TraesCS2D01G358600 chr2B 542258519 542264037 5518 False 2329.333333 6076 92.861 58 5124 3 chr2B.!!$F1 5066


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
960 1505 0.108329 GGCGCAGTTAAGCTCCAGTA 60.108 55.0 10.83 0.0 39.18 2.74 F
993 1538 1.248785 TAGGGAGCGAGCGACAAAGT 61.249 55.0 0.00 0.0 0.00 2.66 F
1878 2423 1.016627 GCAATGCATCCGAGCTACAA 58.983 50.0 0.00 0.0 34.99 2.41 F
2502 3047 0.168128 GTGCGTTATCCCACAACAGC 59.832 55.0 0.00 0.0 32.37 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1815 2360 0.887933 CCAGCATGTTACCACCCAAC 59.112 55.0 0.00 0.0 0.00 3.77 R
1902 2447 0.906282 GGACCCGTCCTCTAAACCCA 60.906 60.0 6.63 0.0 46.16 4.51 R
3703 4248 0.308376 TAAACAACCGCTTCGTTGCC 59.692 50.0 7.78 0.0 45.75 4.52 R
4210 4757 0.033504 AGTTCTACACGGCCACTGTG 59.966 55.0 12.45 10.1 42.99 3.66 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
200 217 1.588597 CGCAGCACTCTTCCTCTCA 59.411 57.895 0.00 0.00 0.00 3.27
300 317 9.956720 GCATTATATGTTAGCTGAAACTGAAAT 57.043 29.630 0.00 0.00 0.00 2.17
368 385 2.749839 GCTACCACCCATGCGCAA 60.750 61.111 17.11 0.00 0.00 4.85
442 968 8.755696 TGATAACGTATACTAAAAACACGGTT 57.244 30.769 0.56 0.00 36.95 4.44
444 970 6.466308 AACGTATACTAAAAACACGGTTCC 57.534 37.500 0.56 0.00 36.95 3.62
484 1012 1.064060 GACGCTGCACTTGTTTCAACT 59.936 47.619 0.00 0.00 0.00 3.16
485 1013 1.472480 ACGCTGCACTTGTTTCAACTT 59.528 42.857 0.00 0.00 0.00 2.66
486 1014 2.094752 ACGCTGCACTTGTTTCAACTTT 60.095 40.909 0.00 0.00 0.00 2.66
487 1015 2.531508 CGCTGCACTTGTTTCAACTTTC 59.468 45.455 0.00 0.00 0.00 2.62
488 1016 3.510719 GCTGCACTTGTTTCAACTTTCA 58.489 40.909 0.00 0.00 0.00 2.69
489 1017 3.925913 GCTGCACTTGTTTCAACTTTCAA 59.074 39.130 0.00 0.00 0.00 2.69
490 1018 4.201618 GCTGCACTTGTTTCAACTTTCAAC 60.202 41.667 0.00 0.00 0.00 3.18
512 1040 6.990908 ACCCTTATTTAGAACTATACGGCT 57.009 37.500 0.00 0.00 0.00 5.52
522 1052 1.000163 ACTATACGGCTTCGCATCAGG 60.000 52.381 0.00 0.00 37.41 3.86
541 1076 2.756760 AGGCTGTACCATTGCTTGAATG 59.243 45.455 0.00 0.00 43.14 2.67
696 1231 0.724549 GTCAAGTGTCAACGTGTGCA 59.275 50.000 0.00 0.00 37.13 4.57
833 1368 3.034635 GGTCCTGTCTCCTGTGATATGT 58.965 50.000 0.00 0.00 0.00 2.29
856 1391 4.734398 ATGCTTCTGAAGACTAGAGGTG 57.266 45.455 21.06 0.00 0.00 4.00
857 1392 2.232452 TGCTTCTGAAGACTAGAGGTGC 59.768 50.000 21.06 3.03 0.00 5.01
858 1393 2.232452 GCTTCTGAAGACTAGAGGTGCA 59.768 50.000 21.06 0.00 0.00 4.57
859 1394 3.843999 CTTCTGAAGACTAGAGGTGCAC 58.156 50.000 12.01 8.80 0.00 4.57
937 1482 8.404000 GCTTCATTCAGATCTTTTACATGTGAT 58.596 33.333 9.11 1.95 0.00 3.06
947 1492 1.655484 TACATGTGATTCAGGCGCAG 58.345 50.000 10.83 0.00 0.00 5.18
952 1497 2.076100 TGTGATTCAGGCGCAGTTAAG 58.924 47.619 10.83 0.00 0.00 1.85
960 1505 0.108329 GGCGCAGTTAAGCTCCAGTA 60.108 55.000 10.83 0.00 39.18 2.74
993 1538 1.248785 TAGGGAGCGAGCGACAAAGT 61.249 55.000 0.00 0.00 0.00 2.66
1140 1685 1.518352 CGCAATCACCGACGATCCA 60.518 57.895 0.00 0.00 0.00 3.41
1211 1756 1.300931 GTGTGAAGTGCAGCCTCGA 60.301 57.895 0.00 0.00 0.00 4.04
1224 1769 2.002127 CCTCGAAGAACATGAGCGC 58.998 57.895 0.00 0.00 34.09 5.92
1245 1790 2.125753 GCAGAGCTGGACCTGTCG 60.126 66.667 0.00 0.00 33.19 4.35
1365 1910 2.769652 ATCTTGGCCGGCTGCAAGAA 62.770 55.000 36.02 25.05 43.89 2.52
1423 1968 2.128035 GGATTATTCCAGTGACGCTCG 58.872 52.381 0.00 0.00 42.12 5.03
1485 2030 4.746466 ACTTATTGGTGGGTGAAATTCCA 58.254 39.130 0.00 0.00 0.00 3.53
1815 2360 2.098770 CCCTAACCTCCGACTTCTTACG 59.901 54.545 0.00 0.00 0.00 3.18
1878 2423 1.016627 GCAATGCATCCGAGCTACAA 58.983 50.000 0.00 0.00 34.99 2.41
1917 2462 3.560636 AATCATGGGTTTAGAGGACGG 57.439 47.619 0.00 0.00 0.00 4.79
1941 2486 3.326880 TCCCACCTTCTCTTGGTAAACTC 59.673 47.826 0.00 0.00 35.80 3.01
1951 2496 0.611714 TGGTAAACTCCCGAAGCTCC 59.388 55.000 0.00 0.00 0.00 4.70
2213 2758 2.180276 GCTAGGACTGGAGGAGAACAA 58.820 52.381 0.00 0.00 0.00 2.83
2214 2759 2.167487 GCTAGGACTGGAGGAGAACAAG 59.833 54.545 0.00 0.00 0.00 3.16
2239 2784 1.417517 CTGGTCCGATTGATGGATGGA 59.582 52.381 0.00 0.00 37.93 3.41
2259 2804 8.641541 GGATGGATTGGAAATCTTGCTAATTTA 58.358 33.333 0.40 0.00 0.00 1.40
2295 2840 5.885352 TCTTCAACAGAACAATTTCACTGGA 59.115 36.000 0.00 0.00 33.72 3.86
2455 3000 8.807948 TCTTCAAGAAAATATACCCAAAGAGG 57.192 34.615 0.00 0.00 37.03 3.69
2502 3047 0.168128 GTGCGTTATCCCACAACAGC 59.832 55.000 0.00 0.00 32.37 4.40
2643 3188 4.519540 CATCAAAATGGACCGGAACTTT 57.480 40.909 9.46 1.64 0.00 2.66
2913 3458 3.694058 ATGCCCCGCTGCTTCTCAG 62.694 63.158 0.00 0.00 45.62 3.35
3037 3582 0.864455 GCTGAGGATGCAGTTATCGC 59.136 55.000 0.00 0.00 38.17 4.58
3159 3704 2.869801 CGGTTCAGTGTACAGAGCAAAA 59.130 45.455 0.00 0.00 0.00 2.44
3167 3712 4.820173 AGTGTACAGAGCAAAACTAAACCC 59.180 41.667 0.00 0.00 0.00 4.11
3178 3723 5.277297 GCAAAACTAAACCCAAAACAGATGC 60.277 40.000 0.00 0.00 0.00 3.91
3249 3794 6.414408 AGTTTCATCTCAGAATGTAAAGCG 57.586 37.500 0.00 0.00 37.40 4.68
3252 3797 4.115516 TCATCTCAGAATGTAAAGCGCTC 58.884 43.478 12.06 0.00 37.40 5.03
3258 3803 4.937620 TCAGAATGTAAAGCGCTCAGAAAT 59.062 37.500 12.06 0.00 37.40 2.17
3267 3812 1.532868 GCGCTCAGAAATATTCGGCAT 59.467 47.619 0.00 0.00 34.02 4.40
3288 3833 5.760253 GCATCGGAATCTTCTTCCAATTCTA 59.240 40.000 4.98 0.00 38.49 2.10
3319 3864 4.035558 GCTCAACAATTGATAATCGAGGCA 59.964 41.667 13.59 0.00 39.30 4.75
3395 3940 1.607801 CTGCACCCGACAGGAGATGA 61.608 60.000 0.00 0.00 41.02 2.92
3401 3946 2.290323 ACCCGACAGGAGATGAAAAAGG 60.290 50.000 0.00 0.00 41.02 3.11
3412 3957 5.308014 GAGATGAAAAAGGCCCAAAACAAT 58.692 37.500 0.00 0.00 0.00 2.71
3442 3987 7.552330 ACCTCTCTCAAAGAATGAAAATAGCTC 59.448 37.037 0.00 0.00 37.67 4.09
3564 4109 0.955919 CAGCTCGTTTGGGGGACTTC 60.956 60.000 0.00 0.00 0.00 3.01
3600 4145 5.164620 TCTACATCAAATCCAAGTCAGCA 57.835 39.130 0.00 0.00 0.00 4.41
3633 4178 5.469479 GGTTTGAGTTCAATGGGTACAATG 58.531 41.667 0.00 0.00 35.55 2.82
3703 4248 4.484236 TCTTGCTGTAAATTTGAATGCGG 58.516 39.130 0.00 0.00 0.00 5.69
3793 4338 0.682292 GCAGCTACCTATCCACCTCC 59.318 60.000 0.00 0.00 0.00 4.30
3897 4442 4.766007 CTTGACATCGTGAACTTTGTCAG 58.234 43.478 12.24 6.58 46.39 3.51
3923 4468 5.051153 GGAACTTTCCGGATCAGATACTTC 58.949 45.833 16.32 9.79 37.65 3.01
3964 4509 0.813821 GGGAAGAATGCCAAGACTGC 59.186 55.000 0.00 0.00 32.29 4.40
3967 4512 1.742268 GAAGAATGCCAAGACTGCTCC 59.258 52.381 0.00 0.00 0.00 4.70
4010 4555 3.168528 AAGTCCACCGGTGCCTGT 61.169 61.111 29.75 11.07 0.00 4.00
4060 4605 0.312416 CGAGCCAGGATCCTAACGAG 59.688 60.000 15.67 0.85 0.00 4.18
4066 4611 2.608261 CCAGGATCCTAACGAGCGAATC 60.608 54.545 15.67 0.00 0.00 2.52
4106 4651 3.114483 GAACTGCACGCGATCGACG 62.114 63.158 21.57 22.84 45.66 5.12
4135 4680 3.664107 TGTGTCTTGAAGTGGATGCTAC 58.336 45.455 0.00 0.00 0.00 3.58
4196 4743 3.761311 AGCGTGTAACTAGAGCTGTAC 57.239 47.619 0.00 0.00 36.73 2.90
4210 4757 6.102897 AGAGCTGTACCATACATTCATACC 57.897 41.667 0.00 0.00 38.15 2.73
4259 4807 7.170393 ACTCTAGAAAATTATTTGTTGGGCC 57.830 36.000 0.00 0.00 0.00 5.80
4261 4809 3.595173 AGAAAATTATTTGTTGGGCCGC 58.405 40.909 0.00 0.00 0.00 6.53
4269 4817 4.700365 GTTGGGCCGCGACTTTGC 62.700 66.667 8.23 0.41 0.00 3.68
4308 4857 2.727798 CTCATCTTTTTGCAAAGCACGG 59.272 45.455 12.41 4.16 38.71 4.94
4384 4933 3.488778 AGATTGCCCTGACATCATCTC 57.511 47.619 0.00 0.00 0.00 2.75
4388 4937 3.438216 TGCCCTGACATCATCTCAAAA 57.562 42.857 0.00 0.00 0.00 2.44
4390 4939 3.507233 TGCCCTGACATCATCTCAAAAAC 59.493 43.478 0.00 0.00 0.00 2.43
4391 4940 3.507233 GCCCTGACATCATCTCAAAAACA 59.493 43.478 0.00 0.00 0.00 2.83
4392 4941 4.022068 GCCCTGACATCATCTCAAAAACAA 60.022 41.667 0.00 0.00 0.00 2.83
4393 4942 5.509501 GCCCTGACATCATCTCAAAAACAAA 60.510 40.000 0.00 0.00 0.00 2.83
4394 4943 6.514947 CCCTGACATCATCTCAAAAACAAAA 58.485 36.000 0.00 0.00 0.00 2.44
4395 4944 6.643770 CCCTGACATCATCTCAAAAACAAAAG 59.356 38.462 0.00 0.00 0.00 2.27
4404 4953 8.819974 TCATCTCAAAAACAAAAGAAAGATTGC 58.180 29.630 0.00 0.00 0.00 3.56
4415 4964 6.916360 AAAGAAAGATTGCCCTGACATTTA 57.084 33.333 0.00 0.00 0.00 1.40
4431 4980 7.408756 TGACATTTAGCTTTTTGCCTGATAT 57.591 32.000 0.00 0.00 44.23 1.63
4432 4981 8.518430 TGACATTTAGCTTTTTGCCTGATATA 57.482 30.769 0.00 0.00 44.23 0.86
4439 4988 5.951747 AGCTTTTTGCCTGATATAAGGTGAA 59.048 36.000 8.02 0.62 44.23 3.18
4450 4999 7.015226 TGATATAAGGTGAATGCAGAAAACG 57.985 36.000 0.00 0.00 0.00 3.60
4458 5007 7.051623 AGGTGAATGCAGAAAACGGTATATTA 58.948 34.615 0.00 0.00 0.00 0.98
4472 5021 6.921914 ACGGTATATTATTGTCAGGCTACTC 58.078 40.000 0.00 0.00 0.00 2.59
4477 5026 1.207791 ATTGTCAGGCTACTCCAGGG 58.792 55.000 0.00 0.00 37.29 4.45
4478 5027 0.178903 TTGTCAGGCTACTCCAGGGT 60.179 55.000 0.00 0.00 37.29 4.34
4516 5075 0.749649 TTTGCACATGTTGGGTCCAC 59.250 50.000 0.00 0.00 0.00 4.02
4519 5078 1.959085 CACATGTTGGGTCCACTGC 59.041 57.895 0.00 0.00 0.00 4.40
4530 5089 2.554344 GGGTCCACTGCCAAGTTGATAA 60.554 50.000 3.87 0.00 32.98 1.75
4532 5091 3.129287 GGTCCACTGCCAAGTTGATAATG 59.871 47.826 3.87 0.00 32.98 1.90
4592 5178 1.494628 GCATATGCGTCGATGCTGG 59.505 57.895 28.53 16.27 44.15 4.85
4658 5247 1.736681 GATGCTGCTCACTGGAAGAAC 59.263 52.381 0.00 0.00 37.43 3.01
4682 5271 9.546428 AACTGAATTGGTATCAAAAGGAAAAAG 57.454 29.630 0.00 0.00 36.36 2.27
4710 5299 0.179020 CTGGGCGCTTCCATTCCATA 60.179 55.000 7.64 0.00 36.05 2.74
4798 5392 5.470437 TGACTAGAGTAGAAGCATCATACGG 59.530 44.000 0.00 0.00 0.00 4.02
4866 5460 2.039974 ATCCGCGCATGTTGCTGAA 61.040 52.632 8.75 0.00 42.25 3.02
4867 5461 1.378882 ATCCGCGCATGTTGCTGAAT 61.379 50.000 8.75 0.00 42.25 2.57
4868 5462 1.870458 CCGCGCATGTTGCTGAATG 60.870 57.895 8.75 0.00 42.25 2.67
4869 5463 2.502123 CGCGCATGTTGCTGAATGC 61.502 57.895 8.75 7.68 42.25 3.56
4870 5464 1.153901 GCGCATGTTGCTGAATGCT 60.154 52.632 0.30 0.00 45.62 3.79
4871 5465 1.410737 GCGCATGTTGCTGAATGCTG 61.411 55.000 0.30 9.48 45.62 4.41
4872 5466 0.169451 CGCATGTTGCTGAATGCTGA 59.831 50.000 13.58 0.00 45.62 4.26
4873 5467 1.202256 CGCATGTTGCTGAATGCTGAT 60.202 47.619 13.58 0.00 45.62 2.90
4874 5468 2.460918 GCATGTTGCTGAATGCTGATC 58.539 47.619 9.80 0.00 44.64 2.92
4875 5469 2.099263 GCATGTTGCTGAATGCTGATCT 59.901 45.455 9.80 0.00 44.64 2.75
4876 5470 3.314357 GCATGTTGCTGAATGCTGATCTA 59.686 43.478 9.80 0.00 44.64 1.98
4881 5475 3.969899 TGCTGAATGCTGATCTACTACG 58.030 45.455 0.00 0.00 43.37 3.51
4903 5497 9.239002 CTACGTCCAGATAAGAAAAGAGTTATG 57.761 37.037 0.00 0.00 0.00 1.90
4946 5540 2.287009 CGTGGAAGGACAGAAAACTTGC 60.287 50.000 0.00 0.00 33.80 4.01
4991 5586 4.396478 GTGGAAAACCTTAGAATCAGCCTC 59.604 45.833 0.00 0.00 0.00 4.70
5003 5598 3.777106 ATCAGCCTCAAACAAGACTGA 57.223 42.857 0.00 0.00 38.42 3.41
5043 5638 3.190118 GCTCAACTGAACAATTCTCCCTG 59.810 47.826 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.049156 TGCTGGTTCTCTCACGCG 60.049 61.111 3.53 3.53 0.00 6.01
55 56 2.046314 TTGCTAGGGTTCGGCTGC 60.046 61.111 0.00 0.00 0.00 5.25
121 133 1.074471 GTGCCATAGGGAGGGAGGA 60.074 63.158 0.00 0.00 35.59 3.71
157 174 2.257371 CGCCGACGGAGAAGACAA 59.743 61.111 20.50 0.00 34.97 3.18
185 202 1.173043 CGACTGAGAGGAAGAGTGCT 58.827 55.000 0.00 0.00 0.00 4.40
283 300 9.730420 TTTAACAAGATTTCAGTTTCAGCTAAC 57.270 29.630 0.00 0.00 0.00 2.34
300 317 6.861065 ACTTTCAGCTCGAATTTAACAAGA 57.139 33.333 0.00 0.00 32.32 3.02
424 441 7.092716 TCTGAGGAACCGTGTTTTTAGTATAC 58.907 38.462 0.00 0.00 0.00 1.47
428 445 4.411256 TCTGAGGAACCGTGTTTTTAGT 57.589 40.909 0.00 0.00 0.00 2.24
442 968 5.358442 GTCAGTACTCTTAAGCATCTGAGGA 59.642 44.000 14.73 0.00 31.93 3.71
444 970 5.270083 CGTCAGTACTCTTAAGCATCTGAG 58.730 45.833 14.73 3.63 31.93 3.35
484 1012 9.603921 CCGTATAGTTCTAAATAAGGGTTGAAA 57.396 33.333 0.00 0.00 0.00 2.69
485 1013 7.712205 GCCGTATAGTTCTAAATAAGGGTTGAA 59.288 37.037 0.00 0.00 30.56 2.69
486 1014 7.070322 AGCCGTATAGTTCTAAATAAGGGTTGA 59.930 37.037 0.00 0.00 35.35 3.18
487 1015 7.215085 AGCCGTATAGTTCTAAATAAGGGTTG 58.785 38.462 0.00 0.00 35.35 3.77
488 1016 7.370905 AGCCGTATAGTTCTAAATAAGGGTT 57.629 36.000 0.00 0.00 35.35 4.11
489 1017 6.990908 AGCCGTATAGTTCTAAATAAGGGT 57.009 37.500 0.00 0.00 34.48 4.34
490 1018 6.585322 CGAAGCCGTATAGTTCTAAATAAGGG 59.415 42.308 0.00 0.00 30.56 3.95
541 1076 4.266739 CGCTTTTACACTTTGTTTGGAACC 59.733 41.667 0.00 0.00 0.00 3.62
771 1306 3.997021 GGTGGAGATGAGTGTTGTAGTTG 59.003 47.826 0.00 0.00 0.00 3.16
833 1368 5.394663 GCACCTCTAGTCTTCAGAAGCATAA 60.395 44.000 5.15 0.00 0.00 1.90
856 1391 2.099921 TCATAGAGAGAAGAAGCGGTGC 59.900 50.000 0.00 0.00 0.00 5.01
857 1392 4.377839 TTCATAGAGAGAAGAAGCGGTG 57.622 45.455 0.00 0.00 0.00 4.94
858 1393 6.909550 ATATTCATAGAGAGAAGAAGCGGT 57.090 37.500 0.00 0.00 0.00 5.68
859 1394 8.494347 CAAAATATTCATAGAGAGAAGAAGCGG 58.506 37.037 0.00 0.00 0.00 5.52
937 1482 0.673644 GGAGCTTAACTGCGCCTGAA 60.674 55.000 4.18 0.00 46.93 3.02
947 1492 4.260375 CGTGATGCAATACTGGAGCTTAAC 60.260 45.833 0.00 0.00 29.43 2.01
952 1497 1.939974 TCGTGATGCAATACTGGAGC 58.060 50.000 0.00 0.00 0.00 4.70
960 1505 2.880890 GCTCCCTATTTCGTGATGCAAT 59.119 45.455 0.00 0.00 0.00 3.56
993 1538 3.618594 GCACGAAGAGCTTCATGACATAA 59.381 43.478 10.15 0.00 41.95 1.90
1036 1581 4.996122 GCTTCCAGATCCATGAGACAATAG 59.004 45.833 0.00 0.00 0.00 1.73
1170 1715 1.024271 GCCAGTTGCAGAAGTGAACA 58.976 50.000 0.00 0.00 40.77 3.18
1171 1716 3.853623 GCCAGTTGCAGAAGTGAAC 57.146 52.632 0.00 0.00 40.77 3.18
1211 1756 1.207593 GCAACGCGCTCATGTTCTT 59.792 52.632 5.73 0.00 37.77 2.52
1224 1769 2.031516 CAGGTCCAGCTCTGCAACG 61.032 63.158 0.00 0.00 0.00 4.10
1245 1790 0.955919 CCCCGACAAAACTCTGCTCC 60.956 60.000 0.00 0.00 0.00 4.70
1281 1826 9.698309 AGATAAGTAAGATATGACATGTTTCCG 57.302 33.333 0.00 0.00 0.00 4.30
1365 1910 3.041946 ACTCAGGTCAAGAAACTCCAGT 58.958 45.455 0.00 0.00 0.00 4.00
1423 1968 1.000938 CCTCAAGTTGGAGCAGTTTGC 60.001 52.381 2.34 0.00 45.46 3.68
1485 2030 4.820775 TGGAGAGTAGGGATATTTCTGCT 58.179 43.478 0.00 0.00 0.00 4.24
1815 2360 0.887933 CCAGCATGTTACCACCCAAC 59.112 55.000 0.00 0.00 0.00 3.77
1902 2447 0.906282 GGACCCGTCCTCTAAACCCA 60.906 60.000 6.63 0.00 46.16 4.51
1917 2462 1.652947 TACCAAGAGAAGGTGGGACC 58.347 55.000 0.00 0.00 40.26 4.46
1951 2496 3.570926 TGTGTCAAGACCTAGCTTACG 57.429 47.619 0.00 0.00 0.00 3.18
2160 2705 7.237263 AGTCTATGGAGATTTCCTATGCTTGAT 59.763 37.037 3.60 0.00 44.36 2.57
2213 2758 2.355108 CCATCAATCGGACCAGTCAACT 60.355 50.000 0.00 0.00 0.00 3.16
2214 2759 2.009774 CCATCAATCGGACCAGTCAAC 58.990 52.381 0.00 0.00 0.00 3.18
2239 2784 8.815912 ACCTTGTAAATTAGCAAGATTTCCAAT 58.184 29.630 18.10 0.00 43.29 3.16
2259 2804 8.918202 TGTTCTGTTGAAGATATAAACCTTGT 57.082 30.769 0.00 0.00 33.93 3.16
2448 2993 5.758924 GTGGCTACACTAAAAACCTCTTTG 58.241 41.667 0.00 0.00 44.29 2.77
2502 3047 3.282885 GTGAGGAATTTGGCCTTCTAGG 58.717 50.000 3.32 0.00 38.80 3.02
2699 3244 5.065731 CCTGAGAGATTGTTATGTGAAAGGC 59.934 44.000 0.00 0.00 0.00 4.35
2913 3458 5.275067 AGTGTTGCCATCTAGATCTTCTC 57.725 43.478 1.03 0.00 0.00 2.87
3098 3643 4.876107 TCAAGTTTGACTCTGTGAAGTTCC 59.124 41.667 0.00 0.00 31.01 3.62
3110 3655 3.652869 TCCTCTCCCAATCAAGTTTGACT 59.347 43.478 0.00 0.00 40.49 3.41
3111 3656 4.021102 TCCTCTCCCAATCAAGTTTGAC 57.979 45.455 0.00 0.00 40.49 3.18
3114 3659 3.075134 AGCTTCCTCTCCCAATCAAGTTT 59.925 43.478 0.00 0.00 0.00 2.66
3159 3704 4.649218 ACAAGCATCTGTTTTGGGTTTAGT 59.351 37.500 0.00 0.00 0.00 2.24
3178 3723 4.327087 GTCAAAAACTTTCACTGCCACAAG 59.673 41.667 0.00 0.00 0.00 3.16
3249 3794 2.158449 CCGATGCCGAATATTTCTGAGC 59.842 50.000 0.00 0.00 38.22 4.26
3252 3797 4.692625 AGATTCCGATGCCGAATATTTCTG 59.307 41.667 0.00 0.00 38.22 3.02
3258 3803 4.307432 GAAGAAGATTCCGATGCCGAATA 58.693 43.478 0.00 0.00 38.22 1.75
3267 3812 6.818644 CAGTTAGAATTGGAAGAAGATTCCGA 59.181 38.462 0.00 0.00 41.43 4.55
3288 3833 4.530710 ATCAATTGTTGAGCATGCAGTT 57.469 36.364 21.98 0.00 43.98 3.16
3319 3864 5.129650 GGTAGACTAGAGCTTTGAAATCCCT 59.870 44.000 0.00 0.00 0.00 4.20
3395 3940 3.951037 GTCCAATTGTTTTGGGCCTTTTT 59.049 39.130 4.53 0.00 38.20 1.94
3401 3946 1.970640 AGAGGTCCAATTGTTTTGGGC 59.029 47.619 4.43 2.55 43.19 5.36
3412 3957 5.567037 TTCATTCTTTGAGAGAGGTCCAA 57.433 39.130 0.00 0.00 35.27 3.53
3442 3987 3.437741 TGCAATGCATCGGCTATATCAAG 59.562 43.478 20.04 0.00 41.91 3.02
3564 4109 0.739462 TGTAGAACCTTGCGATGCCG 60.739 55.000 0.00 0.00 39.16 5.69
3600 4145 2.011617 AACTCAAACCCCCAGCTGCT 62.012 55.000 8.66 0.00 0.00 4.24
3609 4154 3.492337 TGTACCCATTGAACTCAAACCC 58.508 45.455 0.00 0.00 39.55 4.11
3614 4159 5.013079 AGAGTCATTGTACCCATTGAACTCA 59.987 40.000 0.00 0.00 35.07 3.41
3633 4178 1.363744 CAATCGTGCCCTTCAGAGTC 58.636 55.000 0.00 0.00 0.00 3.36
3703 4248 0.308376 TAAACAACCGCTTCGTTGCC 59.692 50.000 7.78 0.00 45.75 4.52
3740 4285 7.417496 ACTCTGAATACCAAGTAAAACGTTC 57.583 36.000 0.00 0.00 0.00 3.95
3751 4296 4.101585 CCTCCTGCATACTCTGAATACCAA 59.898 45.833 0.00 0.00 0.00 3.67
3793 4338 1.790623 CCAAAACTGTACACGTCTCCG 59.209 52.381 0.00 0.00 40.83 4.63
3897 4442 1.831736 TCTGATCCGGAAAGTTCCTCC 59.168 52.381 9.01 0.00 45.33 4.30
3923 4468 3.648009 GGAGAGAAGCGTCAAGGATATG 58.352 50.000 1.61 0.00 0.00 1.78
3984 4529 0.317479 CCGGTGGACTTCGTTCTCTT 59.683 55.000 0.00 0.00 0.00 2.85
3988 4533 2.315386 GCACCGGTGGACTTCGTTC 61.315 63.158 34.58 11.86 0.00 3.95
4010 4555 1.032014 GCCACTTTCAGCAAGGACAA 58.968 50.000 0.00 0.00 36.72 3.18
4060 4605 2.674852 TGCTTCTCTCATGTTGATTCGC 59.325 45.455 0.00 0.00 0.00 4.70
4066 4611 3.617706 CAGTAGCTGCTTCTCTCATGTTG 59.382 47.826 7.79 0.00 0.00 3.33
4106 4651 1.326548 ACTTCAAGACACAAACGACGC 59.673 47.619 0.00 0.00 0.00 5.19
4113 4658 3.213206 AGCATCCACTTCAAGACACAA 57.787 42.857 0.00 0.00 0.00 3.33
4135 4680 8.252964 TGTATGTATGATACAGCTCTAGTACG 57.747 38.462 11.32 0.00 42.77 3.67
4196 4743 3.565482 GCCACTGTGGTATGAATGTATGG 59.435 47.826 26.48 0.00 40.46 2.74
4210 4757 0.033504 AGTTCTACACGGCCACTGTG 59.966 55.000 12.45 10.10 42.99 3.66
4259 4807 2.167861 GGCTAGGAGCAAAGTCGCG 61.168 63.158 0.00 0.00 44.75 5.87
4261 4809 1.734465 CAAAGGCTAGGAGCAAAGTCG 59.266 52.381 0.21 0.00 44.75 4.18
4269 4817 3.614092 TGAGCATTTCAAAGGCTAGGAG 58.386 45.455 9.74 0.00 38.15 3.69
4335 4884 7.719483 AGGAACATGCATACCATCTTTTTATG 58.281 34.615 15.70 0.00 29.71 1.90
4337 4886 7.395772 TGAAGGAACATGCATACCATCTTTTTA 59.604 33.333 16.81 2.20 29.71 1.52
4341 4890 4.858850 TGAAGGAACATGCATACCATCTT 58.141 39.130 16.81 10.46 29.71 2.40
4342 4891 4.508551 TGAAGGAACATGCATACCATCT 57.491 40.909 16.81 4.17 29.71 2.90
4384 4933 6.315891 TCAGGGCAATCTTTCTTTTGTTTTTG 59.684 34.615 0.00 0.00 0.00 2.44
4388 4937 4.405358 TGTCAGGGCAATCTTTCTTTTGTT 59.595 37.500 0.00 0.00 0.00 2.83
4390 4939 4.589216 TGTCAGGGCAATCTTTCTTTTG 57.411 40.909 0.00 0.00 0.00 2.44
4391 4940 5.813513 AATGTCAGGGCAATCTTTCTTTT 57.186 34.783 0.00 0.00 0.00 2.27
4392 4941 5.813513 AAATGTCAGGGCAATCTTTCTTT 57.186 34.783 0.00 0.00 0.00 2.52
4393 4942 5.105595 GCTAAATGTCAGGGCAATCTTTCTT 60.106 40.000 0.00 0.00 0.00 2.52
4394 4943 4.400567 GCTAAATGTCAGGGCAATCTTTCT 59.599 41.667 0.00 0.00 0.00 2.52
4395 4944 4.400567 AGCTAAATGTCAGGGCAATCTTTC 59.599 41.667 0.00 0.00 0.00 2.62
4404 4953 3.259123 AGGCAAAAAGCTAAATGTCAGGG 59.741 43.478 0.00 0.00 44.79 4.45
4415 4964 5.509498 TCACCTTATATCAGGCAAAAAGCT 58.491 37.500 2.65 0.00 44.79 3.74
4431 4980 3.482436 ACCGTTTTCTGCATTCACCTTA 58.518 40.909 0.00 0.00 0.00 2.69
4432 4981 2.306847 ACCGTTTTCTGCATTCACCTT 58.693 42.857 0.00 0.00 0.00 3.50
4439 4988 8.445275 TGACAATAATATACCGTTTTCTGCAT 57.555 30.769 0.00 0.00 0.00 3.96
4450 4999 7.241042 TGGAGTAGCCTGACAATAATATACC 57.759 40.000 0.00 0.00 37.63 2.73
4458 5007 1.207791 CCCTGGAGTAGCCTGACAAT 58.792 55.000 0.00 0.00 37.79 2.71
4477 5026 1.360192 GTTGTGCACTCCAGGCAAC 59.640 57.895 19.41 8.34 43.91 4.17
4478 5027 0.467844 ATGTTGTGCACTCCAGGCAA 60.468 50.000 19.41 0.00 43.91 4.52
4516 5075 6.675026 CATCATACCATTATCAACTTGGCAG 58.325 40.000 0.00 0.00 33.66 4.85
4519 5078 5.047802 GGGCATCATACCATTATCAACTTGG 60.048 44.000 0.00 0.00 36.56 3.61
4530 5089 4.043812 AGAGCATAAAGGGCATCATACCAT 59.956 41.667 0.00 0.00 0.00 3.55
4532 5091 3.755378 CAGAGCATAAAGGGCATCATACC 59.245 47.826 0.00 0.00 0.00 2.73
4617 5204 2.483889 CGATGCTCTCCCCTAAGAAACC 60.484 54.545 0.00 0.00 0.00 3.27
4658 5247 7.603784 CCCTTTTTCCTTTTGATACCAATTCAG 59.396 37.037 0.00 0.00 31.46 3.02
4710 5299 2.283145 AGGCTTTCATTCACACAGCT 57.717 45.000 0.00 0.00 0.00 4.24
4798 5392 8.346300 TGAAGAGAAGATAACGACACTATGATC 58.654 37.037 0.00 0.00 0.00 2.92
4903 5497 4.804139 CGTCTCAGTTACATGTGGGAATAC 59.196 45.833 9.11 0.00 0.00 1.89
4907 5501 2.029380 CACGTCTCAGTTACATGTGGGA 60.029 50.000 9.11 0.00 0.00 4.37
4991 5586 5.505173 AGGTCAAATGTCAGTCTTGTTTG 57.495 39.130 0.00 0.00 0.00 2.93
5043 5638 8.019094 ACTGTACACATTTTAATTTTAGCGACC 58.981 33.333 0.00 0.00 0.00 4.79



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

AutoCloner maintained by Alex Coulton.