Multiple sequence alignment - TraesCS6D01G213500

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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 TraesCS6D01G213500 chr6D 100.000 5682 0 0 1 5682 303467388 303461707 0.000000e+00 10493
1 TraesCS6D01G213500 chr6B 93.985 5270 166 58 1 5183 469078268 469073063 0.000000e+00 7836
2 TraesCS6D01G213500 chr6B 80.828 459 49 11 5182 5606 469073025 469072572 1.970000e-84 324
3 TraesCS6D01G213500 chr6A 92.223 3819 131 60 1 3724 411941553 411937806 0.000000e+00 5254
4 TraesCS6D01G213500 chr6A 97.132 1604 23 11 3743 5324 411937821 411936219 0.000000e+00 2686
5 TraesCS6D01G213500 chr6A 94.118 272 10 2 5364 5629 411936218 411935947 5.300000e-110 409
6 TraesCS6D01G213500 chr1D 89.531 1003 72 10 744 1714 23445104 23446105 0.000000e+00 1240
7 TraesCS6D01G213500 chr5A 94.000 200 10 2 1516 1714 565720982 565720784 9.250000e-78 302
8 TraesCS6D01G213500 chr1A 94.000 200 10 2 1516 1714 354536827 354536629 9.250000e-78 302


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 TraesCS6D01G213500 chr6D 303461707 303467388 5681 True 10493 10493 100.0000 1 5682 1 chr6D.!!$R1 5681
1 TraesCS6D01G213500 chr6B 469072572 469078268 5696 True 4080 7836 87.4065 1 5606 2 chr6B.!!$R1 5605
2 TraesCS6D01G213500 chr6A 411935947 411941553 5606 True 2783 5254 94.4910 1 5629 3 chr6A.!!$R1 5628
3 TraesCS6D01G213500 chr1D 23445104 23446105 1001 False 1240 1240 89.5310 744 1714 1 chr1D.!!$F1 970

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
20 21 0.098200 TCTTGATCTGGTACGTCGCG 59.902 55.000 0.00 0.00 0.00 5.87 F
941 997 1.371337 GAGCTCACCATTGATGCGCA 61.371 55.000 14.96 14.96 33.55 6.09 F
1964 2057 1.677820 CCACCTAATGTCGGTTGACCC 60.678 57.143 0.00 0.00 44.86 4.46 F
3719 3829 0.109153 TTTTGCTCTGCAGCCTCTGA 59.891 50.000 9.47 0.00 46.26 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1189 1245 1.816863 GAAGTGTCCAGGCAGACCGA 61.817 60.000 5.38 0.00 42.76 4.69 R
2261 2354 1.008538 GCGGGACAACAGCACAAAG 60.009 57.895 0.00 0.00 0.00 2.77 R
3728 3838 0.599728 GCTGCATTCCCGCAAAAACA 60.600 50.000 0.00 0.00 42.45 2.83 R
5635 5849 0.105039 GTAGCTTAGCACGGGCATCT 59.895 55.000 14.57 5.23 44.61 2.90 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
19 20 2.273370 TTCTTGATCTGGTACGTCGC 57.727 50.000 0.00 0.00 0.00 5.19
20 21 0.098200 TCTTGATCTGGTACGTCGCG 59.902 55.000 0.00 0.00 0.00 5.87
21 22 1.472276 CTTGATCTGGTACGTCGCGC 61.472 60.000 0.00 0.00 0.00 6.86
53 54 4.464244 CAGTAGGAGGATTCTGACTTGTGA 59.536 45.833 0.00 0.00 0.00 3.58
60 68 1.444933 TTCTGACTTGTGATGGGGGT 58.555 50.000 0.00 0.00 0.00 4.95
115 123 2.284151 GGTTGGGTTGGGTTGGGT 59.716 61.111 0.00 0.00 0.00 4.51
178 186 2.749076 CCTTTCCTGCAATCATCGTTGA 59.251 45.455 0.00 0.00 36.00 3.18
258 285 2.175202 TCTCTTCTCTTCTCCACTGCC 58.825 52.381 0.00 0.00 0.00 4.85
357 392 1.674441 TCGACCCTGTTATCGCTGTAG 59.326 52.381 0.00 0.00 38.24 2.74
365 400 4.051922 CTGTTATCGCTGTAGGGATTCAC 58.948 47.826 15.31 12.86 43.95 3.18
374 409 5.760253 CGCTGTAGGGATTCACTTTGATTAT 59.240 40.000 0.00 0.00 0.00 1.28
478 522 4.834357 AAAATTTGAACTTTGGCCATGC 57.166 36.364 6.09 0.00 0.00 4.06
479 523 3.488778 AATTTGAACTTTGGCCATGCA 57.511 38.095 6.09 0.00 0.00 3.96
480 524 3.706600 ATTTGAACTTTGGCCATGCAT 57.293 38.095 6.09 0.00 0.00 3.96
481 525 3.488778 TTTGAACTTTGGCCATGCATT 57.511 38.095 6.09 0.00 0.00 3.56
482 526 2.747396 TGAACTTTGGCCATGCATTC 57.253 45.000 6.09 9.38 0.00 2.67
483 527 2.250031 TGAACTTTGGCCATGCATTCT 58.750 42.857 6.09 0.00 0.00 2.40
484 528 2.633967 TGAACTTTGGCCATGCATTCTT 59.366 40.909 6.09 0.00 0.00 2.52
485 529 3.071312 TGAACTTTGGCCATGCATTCTTT 59.929 39.130 6.09 0.00 0.00 2.52
586 632 9.798994 GCTTCAATTCAAAATAGATGACTGATT 57.201 29.630 0.00 0.00 0.00 2.57
687 736 1.812571 CTACCATTCCAAGCGCAAAGT 59.187 47.619 11.47 0.00 0.00 2.66
731 781 7.700656 AGTTTAACTTTCATGTAGTTTGTGTGC 59.299 33.333 16.97 6.65 37.12 4.57
941 997 1.371337 GAGCTCACCATTGATGCGCA 61.371 55.000 14.96 14.96 33.55 6.09
990 1046 1.909700 TTTGTCCCCTCATTGCAGAC 58.090 50.000 0.00 0.00 0.00 3.51
1393 1449 4.884164 GCCTCCATAAGTATGTTTTCTGCT 59.116 41.667 0.00 0.00 31.82 4.24
1451 1512 7.369803 TGAGAAAGAGAGCATTTTATCACAC 57.630 36.000 0.00 0.00 31.71 3.82
1529 1618 4.123497 TGACACCTGGATCAGAATAACG 57.877 45.455 0.00 0.00 32.44 3.18
1666 1759 9.670719 CTTTCTTTTATCTTTCAGACAAAGGAC 57.329 33.333 7.14 0.00 28.46 3.85
1669 1762 9.408648 TCTTTTATCTTTCAGACAAAGGACTTT 57.591 29.630 7.14 0.00 32.58 2.66
1915 2008 8.651389 ACCCGATTCATCTAATCTATTCTGAAA 58.349 33.333 0.00 0.00 41.68 2.69
1936 2029 8.908786 TGAAACATCTAGATCACACTTTTTCT 57.091 30.769 1.03 0.00 0.00 2.52
1937 2030 8.777413 TGAAACATCTAGATCACACTTTTTCTG 58.223 33.333 1.03 0.00 0.00 3.02
1959 2052 3.104512 TCAGATCCACCTAATGTCGGTT 58.895 45.455 0.00 0.00 30.82 4.44
1964 2057 1.677820 CCACCTAATGTCGGTTGACCC 60.678 57.143 0.00 0.00 44.86 4.46
2261 2354 1.132500 CTGGTCCTCCCAAGTATCCC 58.868 60.000 0.00 0.00 44.65 3.85
2380 2473 5.616270 TGTTAGCAATGGTTGTGTCTCTAA 58.384 37.500 0.00 0.00 0.00 2.10
2393 2486 8.753175 GGTTGTGTCTCTAATAATATCGTCAAC 58.247 37.037 0.00 0.00 0.00 3.18
2412 2505 6.268566 GTCAACAGGATATCCAATGAAAAGC 58.731 40.000 23.81 8.69 38.89 3.51
2444 2537 3.121261 CGTGTTTCATGACAAAAGCATGC 60.121 43.478 10.51 10.51 42.13 4.06
2672 2765 5.680619 TGAAAAGAGGTAACAGAAGCAGAA 58.319 37.500 0.00 0.00 41.41 3.02
2673 2766 6.299141 TGAAAAGAGGTAACAGAAGCAGAAT 58.701 36.000 0.00 0.00 41.41 2.40
2946 3054 8.060813 ATAGTCTTTCTAGGAAGCAACTTCTGC 61.061 40.741 9.74 0.00 40.07 4.26
2983 3091 7.118680 CAGAAGCATGCACTAAATTTGGAATTT 59.881 33.333 21.98 0.00 0.00 1.82
3046 3154 5.350504 TCCCTTGCAAAAATGAAGTTGAA 57.649 34.783 0.00 0.00 0.00 2.69
3050 3158 6.093909 CCCTTGCAAAAATGAAGTTGAAAAGT 59.906 34.615 0.00 0.00 0.00 2.66
3051 3159 6.962678 CCTTGCAAAAATGAAGTTGAAAAGTG 59.037 34.615 0.00 0.00 0.00 3.16
3052 3160 7.361116 CCTTGCAAAAATGAAGTTGAAAAGTGT 60.361 33.333 0.00 0.00 0.00 3.55
3115 3224 2.040278 TCTCAGGACAAAATGGTGGAGG 59.960 50.000 0.00 0.00 0.00 4.30
3127 3236 1.003839 GTGGAGGCGTCATTGTGGA 60.004 57.895 8.91 0.00 0.00 4.02
3302 3411 3.483808 TCATGTTTCACTGCCTGTGTA 57.516 42.857 1.49 0.00 46.27 2.90
3318 3427 7.777095 TGCCTGTGTAATAAAAAGTTTGAAGT 58.223 30.769 0.00 0.00 0.00 3.01
3429 3538 6.978659 TCGTATTCCTATGCTTTGTGAGTTAG 59.021 38.462 0.00 0.00 0.00 2.34
3445 3554 4.254492 GAGTTAGGGTGTTTCCTAGCTTG 58.746 47.826 8.32 0.00 46.41 4.01
3450 3559 4.589908 AGGGTGTTTCCTAGCTTGTAATG 58.410 43.478 0.00 0.00 34.92 1.90
3501 3611 3.631227 GCTCTGATGCAATTCCTAGCTTT 59.369 43.478 0.00 0.00 0.00 3.51
3515 3625 3.637229 CCTAGCTTTGGACTCCTTCGATA 59.363 47.826 0.00 0.00 0.00 2.92
3525 3635 5.105473 TGGACTCCTTCGATAGTTACTTTGG 60.105 44.000 0.00 0.00 37.40 3.28
3607 3717 9.005777 GTTTTCCCTGTGTATATGAAAACTGTA 57.994 33.333 15.22 0.00 45.53 2.74
3610 3720 7.101054 TCCCTGTGTATATGAAAACTGTACAC 58.899 38.462 0.00 6.94 43.20 2.90
3638 3748 8.780249 TGTTTAAATGAACTAGAACTTACCAGC 58.220 33.333 0.00 0.00 0.00 4.85
3664 3774 7.951591 TCTCAGTACAAGCATATGCAGTTATA 58.048 34.615 28.62 7.00 45.16 0.98
3666 3776 6.929049 TCAGTACAAGCATATGCAGTTATACC 59.071 38.462 28.62 9.04 45.16 2.73
3690 3800 6.058183 CCAGGTCCTATTTTCTAATGACCAG 58.942 44.000 8.98 1.13 38.43 4.00
3714 3824 2.086869 TCTACATTTTGCTCTGCAGCC 58.913 47.619 9.47 2.80 46.26 4.85
3718 3828 1.135373 CATTTTGCTCTGCAGCCTCTG 60.135 52.381 9.47 0.00 46.26 3.35
3719 3829 0.109153 TTTTGCTCTGCAGCCTCTGA 59.891 50.000 9.47 0.00 46.26 3.27
3720 3830 0.604780 TTTGCTCTGCAGCCTCTGAC 60.605 55.000 9.47 0.00 46.26 3.51
3721 3831 1.761500 TTGCTCTGCAGCCTCTGACA 61.761 55.000 9.47 0.00 46.26 3.58
3722 3832 1.221293 GCTCTGCAGCCTCTGACAT 59.779 57.895 9.47 0.00 40.14 3.06
3723 3833 0.810823 GCTCTGCAGCCTCTGACATC 60.811 60.000 9.47 0.00 40.14 3.06
3724 3834 0.825410 CTCTGCAGCCTCTGACATCT 59.175 55.000 9.47 0.00 32.44 2.90
3725 3835 1.207570 CTCTGCAGCCTCTGACATCTT 59.792 52.381 9.47 0.00 32.44 2.40
3726 3836 1.627329 TCTGCAGCCTCTGACATCTTT 59.373 47.619 9.47 0.00 32.44 2.52
3727 3837 2.008329 CTGCAGCCTCTGACATCTTTC 58.992 52.381 0.00 0.00 32.44 2.62
3728 3838 1.627329 TGCAGCCTCTGACATCTTTCT 59.373 47.619 0.00 0.00 32.44 2.52
3729 3839 2.008329 GCAGCCTCTGACATCTTTCTG 58.992 52.381 0.00 0.00 32.44 3.02
3730 3840 2.614987 GCAGCCTCTGACATCTTTCTGT 60.615 50.000 0.00 0.00 32.44 3.41
3731 3841 3.672808 CAGCCTCTGACATCTTTCTGTT 58.327 45.455 0.00 0.00 32.44 3.16
3732 3842 4.070716 CAGCCTCTGACATCTTTCTGTTT 58.929 43.478 0.00 0.00 32.44 2.83
3733 3843 4.518211 CAGCCTCTGACATCTTTCTGTTTT 59.482 41.667 0.00 0.00 32.44 2.43
3734 3844 5.009410 CAGCCTCTGACATCTTTCTGTTTTT 59.991 40.000 0.00 0.00 32.44 1.94
3735 3845 5.009410 AGCCTCTGACATCTTTCTGTTTTTG 59.991 40.000 0.00 0.00 0.00 2.44
3736 3846 5.218139 CCTCTGACATCTTTCTGTTTTTGC 58.782 41.667 0.00 0.00 0.00 3.68
3841 3951 3.665745 ATTTTGACATCACAGGTTGGC 57.334 42.857 0.00 0.00 0.00 4.52
3881 3991 8.442374 GGTAGGAGTAATATTGTTATTTCCCCA 58.558 37.037 0.00 0.00 29.96 4.96
3934 4044 9.995003 TTGTGCAGGAGTTAAATTCATTTTAAT 57.005 25.926 0.00 0.00 40.82 1.40
4265 4375 5.626955 GCTGTTCAGATTGTTAAGTTTGAGC 59.373 40.000 3.84 0.00 0.00 4.26
4797 4923 6.546395 CAAGAAACATCCATCTTTTCCTACG 58.454 40.000 0.00 0.00 33.73 3.51
4805 4931 8.095169 ACATCCATCTTTTCCTACGTAATATCC 58.905 37.037 0.00 0.00 0.00 2.59
5158 5288 6.448207 TCAACACAACACAAATCTCATCAA 57.552 33.333 0.00 0.00 0.00 2.57
5333 5535 3.111853 ACATGACATGTATACAGCCGG 57.888 47.619 19.53 0.00 42.78 6.13
5361 5563 2.365293 GTGGTGCAGATCTTGGGTTTTT 59.635 45.455 0.00 0.00 0.00 1.94
5513 5716 8.858003 TCATATCGTTCATAGTGAGACTTTTC 57.142 34.615 0.00 0.00 0.00 2.29
5515 5718 8.750416 CATATCGTTCATAGTGAGACTTTTCTG 58.250 37.037 0.00 0.00 29.47 3.02
5516 5719 4.923871 TCGTTCATAGTGAGACTTTTCTGC 59.076 41.667 0.00 0.00 29.47 4.26
5614 5828 6.611381 ACAATATGACACAAAAATCTGGTCG 58.389 36.000 0.00 0.00 0.00 4.79
5629 5843 4.374399 TCTGGTCGACTTCTTTTGGTTAC 58.626 43.478 16.46 0.00 0.00 2.50
5630 5844 4.100498 TCTGGTCGACTTCTTTTGGTTACT 59.900 41.667 16.46 0.00 0.00 2.24
5631 5845 5.302568 TCTGGTCGACTTCTTTTGGTTACTA 59.697 40.000 16.46 0.00 0.00 1.82
5632 5846 5.535333 TGGTCGACTTCTTTTGGTTACTAG 58.465 41.667 16.46 0.00 0.00 2.57
5633 5847 5.069516 TGGTCGACTTCTTTTGGTTACTAGT 59.930 40.000 16.46 0.00 0.00 2.57
5634 5848 6.265196 TGGTCGACTTCTTTTGGTTACTAGTA 59.735 38.462 16.46 0.00 0.00 1.82
5635 5849 7.147976 GGTCGACTTCTTTTGGTTACTAGTAA 58.852 38.462 16.46 11.38 0.00 2.24
5636 5850 7.328005 GGTCGACTTCTTTTGGTTACTAGTAAG 59.672 40.741 15.68 5.10 0.00 2.34
5637 5851 8.078596 GTCGACTTCTTTTGGTTACTAGTAAGA 58.921 37.037 15.68 7.45 0.00 2.10
5638 5852 8.800332 TCGACTTCTTTTGGTTACTAGTAAGAT 58.200 33.333 15.68 0.00 0.00 2.40
5639 5853 8.861101 CGACTTCTTTTGGTTACTAGTAAGATG 58.139 37.037 15.68 13.43 0.00 2.90
5640 5854 8.549338 ACTTCTTTTGGTTACTAGTAAGATGC 57.451 34.615 15.68 4.18 0.00 3.91
5641 5855 7.606839 ACTTCTTTTGGTTACTAGTAAGATGCC 59.393 37.037 15.68 13.19 0.00 4.40
5642 5856 6.412214 TCTTTTGGTTACTAGTAAGATGCCC 58.588 40.000 15.68 12.85 0.00 5.36
5643 5857 4.395959 TTGGTTACTAGTAAGATGCCCG 57.604 45.455 15.68 0.00 0.00 6.13
5644 5858 3.368248 TGGTTACTAGTAAGATGCCCGT 58.632 45.455 15.68 0.00 0.00 5.28
5645 5859 3.131577 TGGTTACTAGTAAGATGCCCGTG 59.868 47.826 15.68 0.00 0.00 4.94
5646 5860 3.121544 GTTACTAGTAAGATGCCCGTGC 58.878 50.000 15.68 0.00 38.26 5.34
5647 5861 1.486211 ACTAGTAAGATGCCCGTGCT 58.514 50.000 0.00 0.00 38.71 4.40
5648 5862 2.662866 ACTAGTAAGATGCCCGTGCTA 58.337 47.619 0.00 0.00 38.71 3.49
5649 5863 3.028850 ACTAGTAAGATGCCCGTGCTAA 58.971 45.455 0.00 0.00 38.71 3.09
5650 5864 2.604046 AGTAAGATGCCCGTGCTAAG 57.396 50.000 0.00 0.00 38.71 2.18
5651 5865 0.938008 GTAAGATGCCCGTGCTAAGC 59.062 55.000 0.00 0.00 38.71 3.09
5652 5866 0.830648 TAAGATGCCCGTGCTAAGCT 59.169 50.000 0.00 0.00 38.71 3.74
5653 5867 0.830648 AAGATGCCCGTGCTAAGCTA 59.169 50.000 0.00 0.00 38.71 3.32
5654 5868 0.105039 AGATGCCCGTGCTAAGCTAC 59.895 55.000 0.00 0.00 38.71 3.58
5655 5869 1.215655 GATGCCCGTGCTAAGCTACG 61.216 60.000 0.00 0.00 39.83 3.51
5659 5873 2.890371 CGTGCTAAGCTACGGGGT 59.110 61.111 0.00 0.00 36.71 4.95
5660 5874 2.109431 CGTGCTAAGCTACGGGGTA 58.891 57.895 0.00 0.00 36.71 3.69
5661 5875 0.457035 CGTGCTAAGCTACGGGGTAA 59.543 55.000 0.00 0.00 36.71 2.85
5662 5876 1.535437 CGTGCTAAGCTACGGGGTAAG 60.535 57.143 0.00 0.00 36.71 2.34
5663 5877 1.753073 GTGCTAAGCTACGGGGTAAGA 59.247 52.381 0.00 0.00 0.00 2.10
5664 5878 2.167075 GTGCTAAGCTACGGGGTAAGAA 59.833 50.000 0.00 0.00 0.00 2.52
5665 5879 2.833338 TGCTAAGCTACGGGGTAAGAAA 59.167 45.455 0.00 0.00 0.00 2.52
5666 5880 3.453353 TGCTAAGCTACGGGGTAAGAAAT 59.547 43.478 0.00 0.00 0.00 2.17
5667 5881 3.808174 GCTAAGCTACGGGGTAAGAAATG 59.192 47.826 0.00 0.00 0.00 2.32
5668 5882 4.442472 GCTAAGCTACGGGGTAAGAAATGA 60.442 45.833 0.00 0.00 0.00 2.57
5669 5883 4.772886 AAGCTACGGGGTAAGAAATGAT 57.227 40.909 0.00 0.00 0.00 2.45
5670 5884 4.772886 AGCTACGGGGTAAGAAATGATT 57.227 40.909 0.00 0.00 0.00 2.57
5671 5885 5.881923 AGCTACGGGGTAAGAAATGATTA 57.118 39.130 0.00 0.00 0.00 1.75
5672 5886 5.855045 AGCTACGGGGTAAGAAATGATTAG 58.145 41.667 0.00 0.00 0.00 1.73
5673 5887 5.365895 AGCTACGGGGTAAGAAATGATTAGT 59.634 40.000 0.00 0.00 0.00 2.24
5674 5888 6.552350 AGCTACGGGGTAAGAAATGATTAGTA 59.448 38.462 0.00 0.00 0.00 1.82
5675 5889 6.867293 GCTACGGGGTAAGAAATGATTAGTAG 59.133 42.308 0.00 0.00 0.00 2.57
5676 5890 7.255730 GCTACGGGGTAAGAAATGATTAGTAGA 60.256 40.741 0.00 0.00 31.27 2.59
5677 5891 7.427989 ACGGGGTAAGAAATGATTAGTAGAA 57.572 36.000 0.00 0.00 0.00 2.10
5678 5892 8.030913 ACGGGGTAAGAAATGATTAGTAGAAT 57.969 34.615 0.00 0.00 0.00 2.40
5679 5893 9.151177 ACGGGGTAAGAAATGATTAGTAGAATA 57.849 33.333 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 4.880537 CTCCTACTGGCGCTGGCG 62.881 72.222 7.64 10.80 41.24 5.69
22 23 4.537433 CCTCCTACTGGCGCTGGC 62.537 72.222 7.64 0.00 38.90 4.85
23 24 1.690219 AATCCTCCTACTGGCGCTGG 61.690 60.000 7.64 2.58 0.00 4.85
24 25 0.249657 GAATCCTCCTACTGGCGCTG 60.250 60.000 7.64 2.99 0.00 5.18
25 26 0.397816 AGAATCCTCCTACTGGCGCT 60.398 55.000 7.64 0.00 0.00 5.92
178 186 8.615211 GTTTGAAAAGGAAGAAAGCAAATCAAT 58.385 29.630 0.00 0.00 0.00 2.57
258 285 0.574454 GCGAACGCTAATCTGCTCTG 59.426 55.000 11.97 0.00 38.26 3.35
338 373 1.269102 CCTACAGCGATAACAGGGTCG 60.269 57.143 0.00 0.00 40.62 4.79
357 392 8.078596 GCAGACATAATAATCAAAGTGAATCCC 58.921 37.037 0.00 0.00 0.00 3.85
365 400 7.223582 ACTCAGACGCAGACATAATAATCAAAG 59.776 37.037 0.00 0.00 0.00 2.77
374 409 6.505044 TTACTAACTCAGACGCAGACATAA 57.495 37.500 0.00 0.00 0.00 1.90
478 522 7.269937 GTGACGATGACAAAGAATGAAAGAATG 59.730 37.037 0.00 0.00 0.00 2.67
479 523 7.041167 TGTGACGATGACAAAGAATGAAAGAAT 60.041 33.333 0.00 0.00 0.00 2.40
480 524 6.259829 TGTGACGATGACAAAGAATGAAAGAA 59.740 34.615 0.00 0.00 0.00 2.52
481 525 5.757808 TGTGACGATGACAAAGAATGAAAGA 59.242 36.000 0.00 0.00 0.00 2.52
482 526 5.848036 GTGTGACGATGACAAAGAATGAAAG 59.152 40.000 0.00 0.00 0.00 2.62
483 527 5.277779 GGTGTGACGATGACAAAGAATGAAA 60.278 40.000 0.00 0.00 0.00 2.69
484 528 4.213270 GGTGTGACGATGACAAAGAATGAA 59.787 41.667 0.00 0.00 0.00 2.57
485 529 3.745975 GGTGTGACGATGACAAAGAATGA 59.254 43.478 0.00 0.00 0.00 2.57
586 632 0.976641 CTGGGGAGTAGCACTGAACA 59.023 55.000 0.00 0.00 0.00 3.18
941 997 3.815401 GCACAAGTTACATCTCCACAGTT 59.185 43.478 0.00 0.00 0.00 3.16
990 1046 4.497473 TGATTTTGCTACCCAACTTTCG 57.503 40.909 0.00 0.00 31.97 3.46
1189 1245 1.816863 GAAGTGTCCAGGCAGACCGA 61.817 60.000 5.38 0.00 42.76 4.69
1426 1487 7.201591 CGTGTGATAAAATGCTCTCTTTCTCAT 60.202 37.037 0.00 0.00 0.00 2.90
1451 1512 9.731819 ACTATATGAATTAACTCGGCATATACG 57.268 33.333 0.00 0.00 34.84 3.06
1529 1618 7.285783 TGACGCACTAACATAATAAACACTC 57.714 36.000 0.00 0.00 0.00 3.51
1681 1774 5.266733 ACACAACTCATTGCAACAAGATT 57.733 34.783 14.97 0.68 39.66 2.40
1915 2008 7.445121 TGACAGAAAAAGTGTGATCTAGATGT 58.555 34.615 10.74 0.00 0.00 3.06
1936 2029 2.430694 CCGACATTAGGTGGATCTGACA 59.569 50.000 0.00 0.00 0.00 3.58
1937 2030 2.431057 ACCGACATTAGGTGGATCTGAC 59.569 50.000 0.00 0.00 41.10 3.51
1959 2052 9.267084 GCATTTCAAAGTTTTAAATAAGGGTCA 57.733 29.630 7.30 0.00 0.00 4.02
1992 2085 5.839621 AGAATGGATAAACATCTTGCATGC 58.160 37.500 11.82 11.82 0.00 4.06
1993 2086 7.273320 AGAGAATGGATAAACATCTTGCATG 57.727 36.000 0.00 0.00 0.00 4.06
2261 2354 1.008538 GCGGGACAACAGCACAAAG 60.009 57.895 0.00 0.00 0.00 2.77
2380 2473 9.605275 CATTGGATATCCTGTTGACGATATTAT 57.395 33.333 22.35 0.00 32.94 1.28
2393 2486 6.489022 TGATCAGCTTTTCATTGGATATCCTG 59.511 38.462 22.35 13.33 36.82 3.86
2412 2505 4.866486 TGTCATGAAACACGAGATGATCAG 59.134 41.667 0.09 0.00 33.36 2.90
2574 2667 1.131315 GGAAAAGACAAGCCAGCGATC 59.869 52.381 0.00 0.00 0.00 3.69
2577 2670 1.808411 TAGGAAAAGACAAGCCAGCG 58.192 50.000 0.00 0.00 0.00 5.18
2610 2703 5.689383 TTTCTTGAGCGCTCTACAATTTT 57.311 34.783 35.27 0.00 0.00 1.82
2623 2716 6.074005 CACTACTTGAAACGATTTCTTGAGC 58.926 40.000 10.41 0.00 40.32 4.26
2672 2765 4.322057 AGACAAAGCTCAACCCCAATAT 57.678 40.909 0.00 0.00 0.00 1.28
2673 2766 3.806949 AGACAAAGCTCAACCCCAATA 57.193 42.857 0.00 0.00 0.00 1.90
2983 3091 5.247337 AGAACCAACTTCCCTTTTCACAAAA 59.753 36.000 0.00 0.00 0.00 2.44
2994 3102 3.020984 TGACAAACAGAACCAACTTCCC 58.979 45.455 0.00 0.00 0.00 3.97
2995 3103 4.712122 TTGACAAACAGAACCAACTTCC 57.288 40.909 0.00 0.00 0.00 3.46
3000 3108 9.921637 GGAAATATATTTGACAAACAGAACCAA 57.078 29.630 15.39 0.00 0.00 3.67
3025 3133 6.093909 ACTTTTCAACTTCATTTTTGCAAGGG 59.906 34.615 0.00 0.00 0.00 3.95
3115 3224 3.483574 CGATTGTTAGTCCACAATGACGC 60.484 47.826 3.82 0.00 45.55 5.19
3127 3236 5.120399 TGTTGGAACAGAACGATTGTTAGT 58.880 37.500 0.00 0.00 42.39 2.24
3201 3310 4.899457 TGACCTACCAACCTCCATATACAG 59.101 45.833 0.00 0.00 0.00 2.74
3207 3316 2.305927 CAAGTGACCTACCAACCTCCAT 59.694 50.000 0.00 0.00 0.00 3.41
3318 3427 7.184936 TCCCAAATCCCTAAGTTACTTGGAATA 59.815 37.037 10.06 0.00 34.97 1.75
3398 3507 5.648092 ACAAAGCATAGGAATACGAAAAGCT 59.352 36.000 0.00 0.00 0.00 3.74
3400 3509 7.072177 TCACAAAGCATAGGAATACGAAAAG 57.928 36.000 0.00 0.00 0.00 2.27
3429 3538 4.585879 TCATTACAAGCTAGGAAACACCC 58.414 43.478 0.00 0.00 40.05 4.61
3466 3575 4.195416 GCATCAGAGCTTAGTAAAAGGCT 58.805 43.478 0.00 0.00 37.77 4.58
3468 3577 6.690194 ATTGCATCAGAGCTTAGTAAAAGG 57.310 37.500 0.00 0.00 34.99 3.11
3501 3611 5.105473 CCAAAGTAACTATCGAAGGAGTCCA 60.105 44.000 12.86 0.00 0.00 4.02
3515 3625 6.040247 GCAAAAGTTTAGCACCAAAGTAACT 58.960 36.000 0.00 0.00 0.00 2.24
3525 3635 4.307443 AGTTCCAGCAAAAGTTTAGCAC 57.693 40.909 0.00 0.00 0.00 4.40
3626 3736 4.408276 TGTACTGAGAGCTGGTAAGTTCT 58.592 43.478 0.00 0.00 45.72 3.01
3627 3737 4.785511 TGTACTGAGAGCTGGTAAGTTC 57.214 45.455 0.00 0.00 34.04 3.01
3638 3748 4.691175 ACTGCATATGCTTGTACTGAGAG 58.309 43.478 27.13 14.61 42.66 3.20
3664 3774 5.104067 GGTCATTAGAAAATAGGACCTGGGT 60.104 44.000 3.53 0.00 36.18 4.51
3666 3776 6.001449 TGGTCATTAGAAAATAGGACCTGG 57.999 41.667 3.53 0.00 38.29 4.45
3690 3800 4.479619 CTGCAGAGCAAAATGTAGAAACC 58.520 43.478 8.42 0.00 38.41 3.27
3714 3824 4.908156 CGCAAAAACAGAAAGATGTCAGAG 59.092 41.667 0.00 0.00 31.50 3.35
3718 3828 3.004315 TCCCGCAAAAACAGAAAGATGTC 59.996 43.478 0.00 0.00 31.50 3.06
3719 3829 2.955660 TCCCGCAAAAACAGAAAGATGT 59.044 40.909 0.00 0.00 33.96 3.06
3720 3830 3.641437 TCCCGCAAAAACAGAAAGATG 57.359 42.857 0.00 0.00 0.00 2.90
3721 3831 4.559153 CATTCCCGCAAAAACAGAAAGAT 58.441 39.130 0.00 0.00 0.00 2.40
3722 3832 3.798548 GCATTCCCGCAAAAACAGAAAGA 60.799 43.478 0.00 0.00 0.00 2.52
3723 3833 2.476241 GCATTCCCGCAAAAACAGAAAG 59.524 45.455 0.00 0.00 0.00 2.62
3724 3834 2.159043 TGCATTCCCGCAAAAACAGAAA 60.159 40.909 0.00 0.00 39.45 2.52
3725 3835 1.410517 TGCATTCCCGCAAAAACAGAA 59.589 42.857 0.00 0.00 39.45 3.02
3726 3836 1.000385 CTGCATTCCCGCAAAAACAGA 60.000 47.619 0.00 0.00 42.45 3.41
3727 3837 1.421382 CTGCATTCCCGCAAAAACAG 58.579 50.000 0.00 0.00 42.45 3.16
3728 3838 0.599728 GCTGCATTCCCGCAAAAACA 60.600 50.000 0.00 0.00 42.45 2.83
3729 3839 1.291184 GGCTGCATTCCCGCAAAAAC 61.291 55.000 0.50 0.00 42.45 2.43
3730 3840 1.005156 GGCTGCATTCCCGCAAAAA 60.005 52.632 0.50 0.00 42.45 1.94
3731 3841 1.876497 GAGGCTGCATTCCCGCAAAA 61.876 55.000 0.50 0.00 42.45 2.44
3732 3842 2.283101 AGGCTGCATTCCCGCAAA 60.283 55.556 0.50 0.00 42.45 3.68
3733 3843 2.751436 GAGGCTGCATTCCCGCAA 60.751 61.111 0.50 0.00 42.45 4.85
3734 3844 3.720601 AGAGGCTGCATTCCCGCA 61.721 61.111 0.50 0.00 40.32 5.69
3735 3845 3.207669 CAGAGGCTGCATTCCCGC 61.208 66.667 0.50 0.00 0.00 6.13
3736 3846 1.817099 GTCAGAGGCTGCATTCCCG 60.817 63.158 0.50 0.00 0.00 5.14
3881 3991 2.086869 CTCCCGTGCACAAGAAATCAT 58.913 47.619 18.64 0.00 0.00 2.45
4225 4335 1.546029 ACAGCGCTAGAACACTGATCA 59.454 47.619 10.99 0.00 34.25 2.92
4265 4375 9.149225 GTACATCAGAGGCTAAGATATTGATTG 57.851 37.037 1.35 0.00 0.00 2.67
4413 4533 4.891756 AGTATCAGCAGCCAAGCAAATTAT 59.108 37.500 0.00 0.00 36.85 1.28
4797 4923 2.628657 AGTGTGGCTCTCCGGATATTAC 59.371 50.000 3.57 1.64 34.14 1.89
5158 5288 6.879458 AGCTTTATCTACCAACGTTCTTGATT 59.121 34.615 0.00 0.00 0.00 2.57
5341 5543 2.380064 AAAACCCAAGATCTGCACCA 57.620 45.000 0.00 0.00 0.00 4.17
5382 5584 7.280876 TGAATCAGCTTAGCCAAACAGTATAAG 59.719 37.037 0.00 0.00 0.00 1.73
5390 5592 4.216257 TGACTTGAATCAGCTTAGCCAAAC 59.784 41.667 0.00 0.00 0.00 2.93
5513 5716 3.674528 TCCAGTCTTTTCTCTCTGCAG 57.325 47.619 7.63 7.63 0.00 4.41
5515 5718 4.320129 GCTTTTCCAGTCTTTTCTCTCTGC 60.320 45.833 0.00 0.00 0.00 4.26
5516 5719 4.818546 TGCTTTTCCAGTCTTTTCTCTCTG 59.181 41.667 0.00 0.00 0.00 3.35
5530 5737 4.687901 TCGGATATGAGATGCTTTTCCA 57.312 40.909 0.00 0.00 0.00 3.53
5614 5828 8.657729 GCATCTTACTAGTAACCAAAAGAAGTC 58.342 37.037 11.38 0.00 0.00 3.01
5629 5843 3.643763 CTTAGCACGGGCATCTTACTAG 58.356 50.000 14.57 0.00 44.61 2.57
5630 5844 2.223971 GCTTAGCACGGGCATCTTACTA 60.224 50.000 14.57 0.00 44.61 1.82
5631 5845 1.473434 GCTTAGCACGGGCATCTTACT 60.473 52.381 14.57 0.00 44.61 2.24
5632 5846 0.938008 GCTTAGCACGGGCATCTTAC 59.062 55.000 14.57 0.00 44.61 2.34
5633 5847 0.830648 AGCTTAGCACGGGCATCTTA 59.169 50.000 14.57 0.00 44.61 2.10
5634 5848 0.830648 TAGCTTAGCACGGGCATCTT 59.169 50.000 14.57 0.00 44.61 2.40
5635 5849 0.105039 GTAGCTTAGCACGGGCATCT 59.895 55.000 14.57 5.23 44.61 2.90
5636 5850 1.215655 CGTAGCTTAGCACGGGCATC 61.216 60.000 14.57 0.00 44.61 3.91
5637 5851 1.227263 CGTAGCTTAGCACGGGCAT 60.227 57.895 14.57 0.00 44.61 4.40
5638 5852 2.183300 CGTAGCTTAGCACGGGCA 59.817 61.111 14.57 0.00 44.61 5.36
5639 5853 2.585247 CCGTAGCTTAGCACGGGC 60.585 66.667 27.73 0.00 43.66 6.13
5641 5855 1.386525 TACCCCGTAGCTTAGCACGG 61.387 60.000 28.14 28.14 45.37 4.94
5642 5856 0.457035 TTACCCCGTAGCTTAGCACG 59.543 55.000 17.49 17.49 34.67 5.34
5643 5857 1.753073 TCTTACCCCGTAGCTTAGCAC 59.247 52.381 7.07 1.87 0.00 4.40
5644 5858 2.148446 TCTTACCCCGTAGCTTAGCA 57.852 50.000 7.07 0.00 0.00 3.49
5645 5859 3.531934 TTTCTTACCCCGTAGCTTAGC 57.468 47.619 0.00 0.00 0.00 3.09
5646 5860 5.272283 TCATTTCTTACCCCGTAGCTTAG 57.728 43.478 0.00 0.00 0.00 2.18
5647 5861 5.881923 ATCATTTCTTACCCCGTAGCTTA 57.118 39.130 0.00 0.00 0.00 3.09
5648 5862 4.772886 ATCATTTCTTACCCCGTAGCTT 57.227 40.909 0.00 0.00 0.00 3.74
5649 5863 4.772886 AATCATTTCTTACCCCGTAGCT 57.227 40.909 0.00 0.00 0.00 3.32
5650 5864 5.608449 ACTAATCATTTCTTACCCCGTAGC 58.392 41.667 0.00 0.00 0.00 3.58
5651 5865 8.174733 TCTACTAATCATTTCTTACCCCGTAG 57.825 38.462 0.00 0.00 0.00 3.51
5652 5866 8.537728 TTCTACTAATCATTTCTTACCCCGTA 57.462 34.615 0.00 0.00 0.00 4.02
5653 5867 7.427989 TTCTACTAATCATTTCTTACCCCGT 57.572 36.000 0.00 0.00 0.00 5.28


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

AutoCloner maintained by Alex Coulton.