Multiple sequence alignment - TraesCS5D01G211200

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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 TraesCS5D01G211200 chr5D 100.000 4297 0 0 1 4297 319507794 319503498 0.000000e+00 7936
1 TraesCS5D01G211200 chr5B 90.949 4143 170 65 99 4133 369638625 369634580 0.000000e+00 5384
2 TraesCS5D01G211200 chr5A 91.680 2548 116 46 1203 3707 414754612 414757106 0.000000e+00 3443
3 TraesCS5D01G211200 chr5A 81.073 1268 80 59 3 1197 414753367 414754547 0.000000e+00 865
4 TraesCS5D01G211200 chr5A 85.926 540 44 15 3772 4297 414757139 414757660 8.120000e-152 547
5 TraesCS5D01G211200 chr7D 85.785 809 84 19 1602 2394 624903514 624902721 0.000000e+00 828
6 TraesCS5D01G211200 chr6D 81.200 750 92 27 1209 1928 39582182 39582912 3.750000e-155 558
7 TraesCS5D01G211200 chr3B 82.734 556 61 21 1394 1928 806991470 806992011 3.030000e-126 462
8 TraesCS5D01G211200 chr7A 78.723 752 115 29 1205 1928 492097719 492098453 1.090000e-125 460


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 TraesCS5D01G211200 chr5D 319503498 319507794 4296 True 7936.000000 7936 100.000000 1 4297 1 chr5D.!!$R1 4296
1 TraesCS5D01G211200 chr5B 369634580 369638625 4045 True 5384.000000 5384 90.949000 99 4133 1 chr5B.!!$R1 4034
2 TraesCS5D01G211200 chr5A 414753367 414757660 4293 False 1618.333333 3443 86.226333 3 4297 3 chr5A.!!$F1 4294
3 TraesCS5D01G211200 chr7D 624902721 624903514 793 True 828.000000 828 85.785000 1602 2394 1 chr7D.!!$R1 792
4 TraesCS5D01G211200 chr6D 39582182 39582912 730 False 558.000000 558 81.200000 1209 1928 1 chr6D.!!$F1 719
5 TraesCS5D01G211200 chr3B 806991470 806992011 541 False 462.000000 462 82.734000 1394 1928 1 chr3B.!!$F1 534
6 TraesCS5D01G211200 chr7A 492097719 492098453 734 False 460.000000 460 78.723000 1205 1928 1 chr7A.!!$F1 723

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
104 105 0.032815 CCCCGTGGACGCAAATTTTT 59.967 50.0 0.00 0.00 38.18 1.94 F
1180 1297 0.179073 AATCTCGGGATTGACAGCGG 60.179 55.0 10.42 0.00 40.30 5.52 F
1328 1510 0.568192 CCCCTCCCCATCTTCTCCTA 59.432 60.0 0.00 0.00 0.00 2.94 F
2745 3017 0.026544 GACCTCGTCGTCGACTCATC 59.973 60.0 22.18 10.97 41.35 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1447 1630 0.108615 AGATTTGGCGTGTCTCTCCG 60.109 55.0 0.00 0.0 0.00 4.63 R
2253 2503 0.324275 GGGCTTTGGCATGTCCCTTA 60.324 55.0 10.19 0.0 40.87 2.69 R
3194 3466 0.176680 TGCTTGAGAAGGCGATCTCC 59.823 55.0 17.09 0.0 44.27 3.71 R
4236 4558 0.743701 TACCCTCGACGAGTGAGAGC 60.744 60.0 22.61 0.0 35.43 4.09 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
42 43 4.586421 TCATGGCCACAAGACATAAACAAA 59.414 37.500 8.16 0.00 0.00 2.83
50 51 2.496111 AGACATAAACAAAACCGGCGA 58.504 42.857 9.30 0.00 0.00 5.54
85 86 4.631740 CCCCACCCCAACCCCAAC 62.632 72.222 0.00 0.00 0.00 3.77
87 88 4.631740 CCACCCCAACCCCAACCC 62.632 72.222 0.00 0.00 0.00 4.11
88 89 4.631740 CACCCCAACCCCAACCCC 62.632 72.222 0.00 0.00 0.00 4.95
91 92 4.986708 CCCAACCCCAACCCCGTG 62.987 72.222 0.00 0.00 0.00 4.94
92 93 4.986708 CCAACCCCAACCCCGTGG 62.987 72.222 0.00 0.00 38.51 4.94
93 94 3.892162 CAACCCCAACCCCGTGGA 61.892 66.667 0.00 0.00 41.65 4.02
94 95 3.893399 AACCCCAACCCCGTGGAC 61.893 66.667 0.00 0.00 41.65 4.02
98 99 4.939368 CCAACCCCGTGGACGCAA 62.939 66.667 0.00 0.00 41.65 4.85
99 100 2.902846 CAACCCCGTGGACGCAAA 60.903 61.111 0.00 0.00 38.18 3.68
100 101 2.114411 AACCCCGTGGACGCAAAT 59.886 55.556 0.00 0.00 38.18 2.32
101 102 1.529713 AACCCCGTGGACGCAAATT 60.530 52.632 0.00 0.00 38.18 1.82
102 103 1.110518 AACCCCGTGGACGCAAATTT 61.111 50.000 0.00 0.00 38.18 1.82
103 104 1.110518 ACCCCGTGGACGCAAATTTT 61.111 50.000 0.00 0.00 38.18 1.82
104 105 0.032815 CCCCGTGGACGCAAATTTTT 59.967 50.000 0.00 0.00 38.18 1.94
148 149 5.897377 AAAAAGGAACATCACGGGATTAG 57.103 39.130 0.00 0.00 0.00 1.73
600 628 3.056328 GCTCGCCACACCTTTCCC 61.056 66.667 0.00 0.00 0.00 3.97
641 669 9.705290 AATCGGTTTTGCTTGTTTATTTATCTT 57.295 25.926 0.00 0.00 0.00 2.40
642 670 8.514136 TCGGTTTTGCTTGTTTATTTATCTTG 57.486 30.769 0.00 0.00 0.00 3.02
643 671 8.138712 TCGGTTTTGCTTGTTTATTTATCTTGT 58.861 29.630 0.00 0.00 0.00 3.16
644 672 8.760569 CGGTTTTGCTTGTTTATTTATCTTGTT 58.239 29.630 0.00 0.00 0.00 2.83
701 731 0.689745 CCCACCCGATCTAACCTCCA 60.690 60.000 0.00 0.00 0.00 3.86
702 732 0.464452 CCACCCGATCTAACCTCCAC 59.536 60.000 0.00 0.00 0.00 4.02
716 746 1.131693 CCTCCACGGCCGAAAATAAAC 59.868 52.381 35.90 0.00 0.00 2.01
799 836 5.303078 CAGGAGTACTGGAGCAGTATACATT 59.697 44.000 0.00 0.00 46.56 2.71
815 859 1.566703 ACATTCGAGAGAGAGAGGGGA 59.433 52.381 0.00 0.00 43.69 4.81
816 860 2.024846 ACATTCGAGAGAGAGAGGGGAA 60.025 50.000 0.00 0.00 43.69 3.97
818 862 2.428544 TCGAGAGAGAGAGGGGAAAG 57.571 55.000 0.00 0.00 34.84 2.62
819 863 1.064314 TCGAGAGAGAGAGGGGAAAGG 60.064 57.143 0.00 0.00 34.84 3.11
820 864 1.119684 GAGAGAGAGAGGGGAAAGGC 58.880 60.000 0.00 0.00 0.00 4.35
822 866 0.829990 GAGAGAGAGGGGAAAGGCAG 59.170 60.000 0.00 0.00 0.00 4.85
844 891 1.621672 GGTCAAGGCTGGGAGAGAGG 61.622 65.000 0.00 0.00 0.00 3.69
848 895 1.522917 AAGGCTGGGAGAGAGGGAGA 61.523 60.000 0.00 0.00 0.00 3.71
849 896 1.457455 GGCTGGGAGAGAGGGAGAG 60.457 68.421 0.00 0.00 0.00 3.20
877 932 0.860203 TCGTCGTCGTCATCATTCGC 60.860 55.000 1.33 0.00 38.33 4.70
911 983 2.238646 GAGTGAGAGAGTCAGAGGAGGA 59.761 54.545 0.00 0.00 35.13 3.71
919 991 1.435168 AGTCAGAGGAGGAAGGAAGGT 59.565 52.381 0.00 0.00 0.00 3.50
920 992 2.158081 AGTCAGAGGAGGAAGGAAGGTT 60.158 50.000 0.00 0.00 0.00 3.50
921 993 2.235155 GTCAGAGGAGGAAGGAAGGTTC 59.765 54.545 0.00 0.00 0.00 3.62
1038 1130 2.590007 GCCATAGGCCACGAGCAG 60.590 66.667 5.01 0.00 44.06 4.24
1039 1131 2.590007 CCATAGGCCACGAGCAGC 60.590 66.667 5.01 0.00 46.50 5.25
1040 1132 2.503061 CATAGGCCACGAGCAGCT 59.497 61.111 5.01 0.00 46.50 4.24
1041 1133 1.886313 CATAGGCCACGAGCAGCTG 60.886 63.158 10.11 10.11 46.50 4.24
1042 1134 3.746949 ATAGGCCACGAGCAGCTGC 62.747 63.158 31.53 31.53 46.50 5.25
1047 1139 3.789858 CACGAGCAGCTGCAGCAG 61.790 66.667 38.24 31.89 45.16 4.24
1118 1222 2.420687 CCAGAAAGGAGTCAGGTATGCC 60.421 54.545 0.00 0.00 41.22 4.40
1119 1223 1.840635 AGAAAGGAGTCAGGTATGCCC 59.159 52.381 0.00 0.00 34.57 5.36
1122 1229 0.399233 AGGAGTCAGGTATGCCCCTC 60.399 60.000 0.00 0.00 34.57 4.30
1180 1297 0.179073 AATCTCGGGATTGACAGCGG 60.179 55.000 10.42 0.00 40.30 5.52
1207 1381 2.355986 ATGCCCGTAACCGCTCTCA 61.356 57.895 0.00 0.00 0.00 3.27
1305 1484 5.774498 ATTTCTCGCCTTTCTTTCAGTTT 57.226 34.783 0.00 0.00 0.00 2.66
1325 1507 0.766288 CCTCCCCTCCCCATCTTCTC 60.766 65.000 0.00 0.00 0.00 2.87
1328 1510 0.568192 CCCCTCCCCATCTTCTCCTA 59.432 60.000 0.00 0.00 0.00 2.94
1339 1521 4.035675 CCATCTTCTCCTATTGTTTTCGGC 59.964 45.833 0.00 0.00 0.00 5.54
1345 1528 5.067273 TCTCCTATTGTTTTCGGCAAAAGA 58.933 37.500 0.00 0.00 31.92 2.52
1447 1630 1.003718 CGGTTCTGGTTCCAGGGAC 60.004 63.158 17.37 15.25 35.01 4.46
1560 1759 4.148825 ATCCGTGCCTGTCTCGCC 62.149 66.667 0.00 0.00 0.00 5.54
1566 1765 2.894387 GCCTGTCTCGCCTCATGC 60.894 66.667 0.00 0.00 0.00 4.06
1889 2127 5.065602 TGTTGATTGATTGCTCTGTCTATGC 59.934 40.000 0.00 0.00 0.00 3.14
2130 2373 2.223711 ACCACCTTTTGCGATGAACAAC 60.224 45.455 0.00 0.00 0.00 3.32
2196 2439 3.775261 ATTTGCCCTGTTTGATTTGCT 57.225 38.095 0.00 0.00 0.00 3.91
2209 2452 9.294030 CTGTTTGATTTGCTGAAAATACTATCC 57.706 33.333 0.00 0.00 38.64 2.59
2233 2476 8.130469 TCCGTAAAATCCAACTTTAAACTGAAC 58.870 33.333 0.00 0.00 0.00 3.18
2235 2482 9.511144 CGTAAAATCCAACTTTAAACTGAACTT 57.489 29.630 0.00 0.00 0.00 2.66
2253 2503 9.174166 ACTGAACTTTAACTTGTCTTGTATGTT 57.826 29.630 0.00 0.00 0.00 2.71
2272 2522 0.324275 TAAGGGACATGCCAAAGCCC 60.324 55.000 8.20 0.00 38.95 5.19
2332 2582 5.107645 TGTCAATGTATTCAACAACGTCTCG 60.108 40.000 0.00 0.00 42.70 4.04
2355 2615 5.470368 GGCAGAAAAGGTACAATTTCTTCC 58.530 41.667 18.37 18.37 41.62 3.46
2415 2675 4.013050 GGCTAAGCTGAAGAATTGTTCCT 58.987 43.478 12.39 1.12 0.00 3.36
2416 2676 4.460731 GGCTAAGCTGAAGAATTGTTCCTT 59.539 41.667 12.39 11.19 0.00 3.36
2417 2677 5.397326 GCTAAGCTGAAGAATTGTTCCTTG 58.603 41.667 12.39 4.71 0.00 3.61
2519 2779 2.893489 AGATGCAACCTTTTTCACTCCC 59.107 45.455 0.00 0.00 0.00 4.30
2531 2791 1.080093 CACTCCCGCTAAACTCGCA 60.080 57.895 0.00 0.00 0.00 5.10
2727 2987 1.754745 GTGCCTCCCACAAGTCAGA 59.245 57.895 0.00 0.00 44.06 3.27
2738 3010 0.452950 CAAGTCAGACCTCGTCGTCG 60.453 60.000 0.00 0.00 37.67 5.12
2739 3011 0.602106 AAGTCAGACCTCGTCGTCGA 60.602 55.000 4.42 4.42 44.12 4.20
2740 3012 1.132232 GTCAGACCTCGTCGTCGAC 59.868 63.158 15.51 15.51 41.35 4.20
2741 3013 1.005275 TCAGACCTCGTCGTCGACT 60.005 57.895 22.18 4.15 41.35 4.18
2742 3014 1.013005 TCAGACCTCGTCGTCGACTC 61.013 60.000 22.18 13.08 41.35 3.36
2743 3015 1.005275 AGACCTCGTCGTCGACTCA 60.005 57.895 22.18 8.54 41.35 3.41
2744 3016 0.391395 AGACCTCGTCGTCGACTCAT 60.391 55.000 22.18 5.97 41.35 2.90
2745 3017 0.026544 GACCTCGTCGTCGACTCATC 59.973 60.000 22.18 10.97 41.35 2.92
2746 3018 1.352404 CCTCGTCGTCGACTCATCC 59.648 63.158 22.18 0.00 41.35 3.51
2747 3019 1.090625 CCTCGTCGTCGACTCATCCT 61.091 60.000 22.18 0.00 41.35 3.24
2748 3020 0.026933 CTCGTCGTCGACTCATCCTG 59.973 60.000 22.18 5.89 41.35 3.86
2749 3021 0.672711 TCGTCGTCGACTCATCCTGT 60.673 55.000 22.18 0.00 41.35 4.00
2913 3185 2.346766 TTTCAGCTGTTCCTCAAGCA 57.653 45.000 14.67 0.00 0.00 3.91
3020 3292 3.568007 TGCAGAACATTTACCAGTGAACC 59.432 43.478 0.00 0.00 0.00 3.62
3083 3355 7.209475 TGATATTCATCATGTCTTCGTGCTTA 58.791 34.615 0.00 0.00 36.22 3.09
3185 3457 1.261619 GACAACAACAGCAAGTCCTCG 59.738 52.381 0.00 0.00 0.00 4.63
3263 3535 2.619074 GCCCAGGAACATCAGCTTTAGT 60.619 50.000 0.00 0.00 0.00 2.24
3357 3630 3.348119 TGGCTGATGCAAAACCGTAATA 58.652 40.909 0.00 0.00 41.91 0.98
3358 3631 3.759086 TGGCTGATGCAAAACCGTAATAA 59.241 39.130 0.00 0.00 41.91 1.40
3359 3632 4.142491 TGGCTGATGCAAAACCGTAATAAG 60.142 41.667 0.00 0.00 41.91 1.73
3432 3725 5.817988 GCAGGCAGCATGATATATGTTATG 58.182 41.667 12.24 0.47 44.79 1.90
3465 3758 9.495754 GCTCTTATTCTTGTTTATGATGTGTTC 57.504 33.333 0.00 0.00 0.00 3.18
3671 3966 0.449388 CCATCGGTTGCAAAGCTCTC 59.551 55.000 0.00 0.00 43.41 3.20
3707 4006 7.473027 TCTTCTGTTTTTACCAACTTCTACG 57.527 36.000 0.00 0.00 0.00 3.51
3709 4008 5.916318 TCTGTTTTTACCAACTTCTACGGA 58.084 37.500 0.00 0.00 0.00 4.69
3740 4039 1.268625 TGTTGCATGCTTGAGCTCTTG 59.731 47.619 20.33 8.65 42.66 3.02
3757 4057 4.874977 GCGGGCGCTCTGGTCTAC 62.875 72.222 5.36 0.00 38.26 2.59
3758 4058 4.208686 CGGGCGCTCTGGTCTACC 62.209 72.222 5.36 0.00 0.00 3.18
3764 4064 0.248661 CGCTCTGGTCTACCACATCG 60.249 60.000 0.00 0.00 42.01 3.84
3769 4069 1.410517 CTGGTCTACCACATCGCTGAT 59.589 52.381 0.00 0.00 42.01 2.90
3803 4103 2.744202 CAATAGCGCTGTGGGAATATCC 59.256 50.000 22.90 0.00 35.23 2.59
3876 4182 2.859165 CCACTACCGGCATCCATAAT 57.141 50.000 0.00 0.00 0.00 1.28
3880 4187 5.067273 CCACTACCGGCATCCATAATTTAA 58.933 41.667 0.00 0.00 0.00 1.52
4044 4363 0.833287 CCTCCCAGATGAACACCGAT 59.167 55.000 0.00 0.00 0.00 4.18
4134 4456 6.170506 CCCAAATTGCTTGTACTACTAGTGA 58.829 40.000 5.39 0.00 32.65 3.41
4137 4459 8.391106 CCAAATTGCTTGTACTACTAGTGATTC 58.609 37.037 5.39 0.00 32.65 2.52
4152 4474 3.321968 AGTGATTCTTGCTTTGGGTTTCC 59.678 43.478 0.00 0.00 0.00 3.13
4236 4558 4.561735 TTTGGTCGAGCACTTTAAAAGG 57.438 40.909 18.42 0.00 0.00 3.11
4237 4559 1.877443 TGGTCGAGCACTTTAAAAGGC 59.123 47.619 14.39 3.23 0.00 4.35
4250 4572 0.959553 AAAAGGCTCTCACTCGTCGA 59.040 50.000 0.00 0.00 0.00 4.20
4273 4595 6.040616 CGAGGGTAAGTGTGAGAATATAGGTT 59.959 42.308 0.00 0.00 0.00 3.50
4274 4596 7.230108 CGAGGGTAAGTGTGAGAATATAGGTTA 59.770 40.741 0.00 0.00 0.00 2.85
4282 4604 8.855110 AGTGTGAGAATATAGGTTATCTCAGTG 58.145 37.037 4.68 0.00 46.39 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 3.760738 TGTTTATGTCTTGTGGCCATGA 58.239 40.909 9.72 5.20 0.00 3.07
70 71 4.631740 GGGTTGGGGTTGGGGTGG 62.632 72.222 0.00 0.00 0.00 4.61
75 76 4.986708 CCACGGGGTTGGGGTTGG 62.987 72.222 0.00 0.00 32.35 3.77
77 78 3.893399 GTCCACGGGGTTGGGGTT 61.893 66.667 2.12 0.00 37.24 4.11
81 82 4.939368 TTGCGTCCACGGGGTTGG 62.939 66.667 2.12 0.00 40.23 3.77
82 83 1.801309 AATTTGCGTCCACGGGGTTG 61.801 55.000 2.12 0.00 40.23 3.77
84 85 1.110518 AAAATTTGCGTCCACGGGGT 61.111 50.000 2.12 0.00 40.23 4.95
85 86 0.032815 AAAAATTTGCGTCCACGGGG 59.967 50.000 0.00 0.00 40.23 5.73
701 731 1.400500 CGCTTGTTTATTTTCGGCCGT 60.400 47.619 27.15 8.36 0.00 5.68
702 732 1.135916 TCGCTTGTTTATTTTCGGCCG 60.136 47.619 22.12 22.12 0.00 6.13
716 746 2.106074 TGGTGCCGCTAATCGCTTG 61.106 57.895 0.00 0.00 36.73 4.01
758 792 2.191641 GGCCAAGCCTAGCCTCTG 59.808 66.667 0.00 0.00 46.69 3.35
799 836 1.064314 CCTTTCCCCTCTCTCTCTCGA 60.064 57.143 0.00 0.00 0.00 4.04
815 859 1.600916 GCCTTGACCGTCTGCCTTT 60.601 57.895 0.00 0.00 0.00 3.11
816 860 2.032681 GCCTTGACCGTCTGCCTT 59.967 61.111 0.00 0.00 0.00 4.35
818 862 2.743928 CAGCCTTGACCGTCTGCC 60.744 66.667 0.00 0.00 0.00 4.85
819 863 2.743928 CCAGCCTTGACCGTCTGC 60.744 66.667 0.00 0.53 0.00 4.26
820 864 2.046892 CCCAGCCTTGACCGTCTG 60.047 66.667 0.00 0.00 0.00 3.51
822 866 2.232298 CTCTCCCAGCCTTGACCGTC 62.232 65.000 0.00 0.00 0.00 4.79
844 891 1.791103 CGACGATGCTCTCCCTCTCC 61.791 65.000 0.00 0.00 0.00 3.71
848 895 2.473760 CGACGACGATGCTCTCCCT 61.474 63.158 0.00 0.00 42.66 4.20
849 896 2.024871 CGACGACGATGCTCTCCC 59.975 66.667 0.00 0.00 42.66 4.30
877 932 2.155279 TCTCACTCCTCTGTGAACGAG 58.845 52.381 0.00 0.00 44.98 4.18
911 983 1.068121 CACTCCCCTGAACCTTCCTT 58.932 55.000 0.00 0.00 0.00 3.36
919 991 1.712056 TCGTTTCTCACTCCCCTGAA 58.288 50.000 0.00 0.00 0.00 3.02
920 992 1.712056 TTCGTTTCTCACTCCCCTGA 58.288 50.000 0.00 0.00 0.00 3.86
921 993 2.543777 TTTCGTTTCTCACTCCCCTG 57.456 50.000 0.00 0.00 0.00 4.45
1118 1222 1.694525 GAGAAAGGGGAGGGGAGGG 60.695 68.421 0.00 0.00 0.00 4.30
1119 1223 2.066999 CGAGAAAGGGGAGGGGAGG 61.067 68.421 0.00 0.00 0.00 4.30
1122 1229 0.919710 AAATCGAGAAAGGGGAGGGG 59.080 55.000 0.00 0.00 0.00 4.79
1197 1314 1.154016 CGACGATGTGAGAGCGGTT 60.154 57.895 0.00 0.00 37.96 4.44
1198 1315 2.485582 CGACGATGTGAGAGCGGT 59.514 61.111 0.00 0.00 37.96 5.68
1283 1462 5.278512 GGAAACTGAAAGAAAGGCGAGAAAT 60.279 40.000 0.00 0.00 37.43 2.17
1305 1484 1.238896 AGAAGATGGGGAGGGGAGGA 61.239 60.000 0.00 0.00 0.00 3.71
1325 1507 5.371115 TCTCTTTTGCCGAAAACAATAGG 57.629 39.130 0.00 0.00 30.08 2.57
1328 1510 3.642705 GCTCTCTTTTGCCGAAAACAAT 58.357 40.909 0.00 0.00 0.00 2.71
1339 1521 1.429463 ACCTAACGCGCTCTCTTTTG 58.571 50.000 5.73 0.00 0.00 2.44
1345 1528 1.740285 CCCATACCTAACGCGCTCT 59.260 57.895 5.73 0.00 0.00 4.09
1447 1630 0.108615 AGATTTGGCGTGTCTCTCCG 60.109 55.000 0.00 0.00 0.00 4.63
1566 1765 1.975407 ATATAGGGGGACGGACGCG 60.975 63.158 3.53 3.53 0.00 6.01
1577 1781 3.689224 CGACGGCGTACATATAGGG 57.311 57.895 14.74 0.00 0.00 3.53
1800 2033 0.321671 GCAGCTCCAGTTACCTGTGA 59.678 55.000 0.00 0.00 36.95 3.58
1889 2127 1.462283 CACCAAACGATCTCTGCACAG 59.538 52.381 0.00 0.00 0.00 3.66
2130 2373 3.188786 GTAGAAGCAGCCACCGCG 61.189 66.667 0.00 0.00 41.18 6.46
2196 2439 9.675464 AGTTGGATTTTACGGATAGTATTTTCA 57.325 29.630 0.00 0.00 34.88 2.69
2209 2452 9.511144 AAGTTCAGTTTAAAGTTGGATTTTACG 57.489 29.630 0.00 0.00 0.00 3.18
2233 2476 9.280174 TCCCTTAACATACAAGACAAGTTAAAG 57.720 33.333 0.00 0.00 35.14 1.85
2235 2482 8.212312 TGTCCCTTAACATACAAGACAAGTTAA 58.788 33.333 0.00 0.00 34.58 2.01
2247 2494 4.440112 GCTTTGGCATGTCCCTTAACATAC 60.440 45.833 0.00 0.00 37.78 2.39
2249 2496 2.497273 GCTTTGGCATGTCCCTTAACAT 59.503 45.455 0.00 0.00 40.49 2.71
2253 2503 0.324275 GGGCTTTGGCATGTCCCTTA 60.324 55.000 10.19 0.00 40.87 2.69
2272 2522 4.177026 AGATAGTTAACTGCGCTGTCTTG 58.823 43.478 20.71 0.25 28.53 3.02
2332 2582 5.470368 GGAAGAAATTGTACCTTTTCTGCC 58.530 41.667 20.69 20.69 45.79 4.85
2366 2626 6.238703 GCAAACCCAAAATGTCATGAAAATGT 60.239 34.615 0.00 0.00 0.00 2.71
2377 2637 1.130777 AGCCAGCAAACCCAAAATGT 58.869 45.000 0.00 0.00 0.00 2.71
2405 2665 5.183904 AGCCTGTAATGACAAGGAACAATTC 59.816 40.000 3.54 0.00 34.35 2.17
2415 2675 3.616956 CTCCTGAGCCTGTAATGACAA 57.383 47.619 0.00 0.00 34.35 3.18
2519 2779 1.738099 AGGTGCTGCGAGTTTAGCG 60.738 57.895 0.00 0.00 42.74 4.26
2531 2791 1.845205 AGGTGAAGCCTCAGGTGCT 60.845 57.895 0.00 0.00 46.96 4.40
2570 2830 1.196808 GGTGAAACACGCTGTGGTATG 59.803 52.381 12.18 0.00 39.98 2.39
2738 3010 3.958704 CGATAGTGTCACAGGATGAGTC 58.041 50.000 5.62 0.00 39.69 3.36
2893 3165 2.555757 GTGCTTGAGGAACAGCTGAAAT 59.444 45.455 23.35 5.87 0.00 2.17
2977 3249 5.416639 TGCAACACTCGGATAGTAAAGACTA 59.583 40.000 0.00 0.00 42.41 2.59
3020 3292 7.411486 AATACAGGCTATGGTATGTAGCTAG 57.589 40.000 0.00 0.00 43.15 3.42
3083 3355 2.987149 CGTAGTCGTCACTCTGCAAAAT 59.013 45.455 0.00 0.00 33.62 1.82
3185 3457 3.248171 GCGATCTCCGTGCACGAC 61.248 66.667 39.10 21.56 43.02 4.34
3194 3466 0.176680 TGCTTGAGAAGGCGATCTCC 59.823 55.000 17.09 0.00 44.27 3.71
3357 3630 3.167485 TGCCTGGATGCAAAATCTTCTT 58.833 40.909 0.00 0.00 38.56 2.52
3358 3631 2.758979 CTGCCTGGATGCAAAATCTTCT 59.241 45.455 0.00 0.00 41.51 2.85
3359 3632 2.159142 CCTGCCTGGATGCAAAATCTTC 60.159 50.000 0.00 0.00 41.51 2.87
3432 3725 9.060347 TCATAAACAAGAATAAGAGCATCATCC 57.940 33.333 0.00 0.00 37.82 3.51
3465 3758 4.016113 GGTTGCGAGCTAACCAAAATAG 57.984 45.455 11.33 0.00 45.43 1.73
3671 3966 7.488150 GGTAAAAACAGAAGAACAAGAACCAAG 59.512 37.037 0.00 0.00 0.00 3.61
3707 4006 3.444916 CATGCAACATCATGAAGCTTCC 58.555 45.455 23.42 6.48 44.94 3.46
3709 4008 2.496070 AGCATGCAACATCATGAAGCTT 59.504 40.909 21.98 0.00 44.94 3.74
3740 4039 4.874977 GTAGACCAGAGCGCCCGC 62.875 72.222 2.29 4.20 42.33 6.13
3757 4057 2.421073 ACAAATGTGATCAGCGATGTGG 59.579 45.455 0.00 0.00 0.00 4.17
3758 4058 3.752412 ACAAATGTGATCAGCGATGTG 57.248 42.857 0.00 0.00 0.00 3.21
3803 4103 5.982516 GCTGACCTAGACAGATCTACAATTG 59.017 44.000 16.98 3.24 37.54 2.32
3872 4178 9.830975 AGTTTCAAGCAAAACCACTTAAATTAT 57.169 25.926 5.95 0.00 39.46 1.28
3876 4182 6.367422 CACAGTTTCAAGCAAAACCACTTAAA 59.633 34.615 5.95 0.00 39.46 1.52
3880 4187 3.368323 CCACAGTTTCAAGCAAAACCACT 60.368 43.478 5.95 0.00 39.46 4.00
3981 4299 9.699703 CCAACGGAGAATAAAATAAAAAGGAAA 57.300 29.630 0.00 0.00 0.00 3.13
3982 4300 8.862085 ACCAACGGAGAATAAAATAAAAAGGAA 58.138 29.630 0.00 0.00 0.00 3.36
3983 4301 8.411991 ACCAACGGAGAATAAAATAAAAAGGA 57.588 30.769 0.00 0.00 0.00 3.36
3984 4302 8.921670 CAACCAACGGAGAATAAAATAAAAAGG 58.078 33.333 0.00 0.00 0.00 3.11
3985 4303 9.471084 ACAACCAACGGAGAATAAAATAAAAAG 57.529 29.630 0.00 0.00 0.00 2.27
3986 4304 9.819267 AACAACCAACGGAGAATAAAATAAAAA 57.181 25.926 0.00 0.00 0.00 1.94
4044 4363 4.261801 GTCAAAGTAAGCCCATGAAGCTA 58.738 43.478 10.19 0.00 40.49 3.32
4090 4412 3.099141 GGGGCATCTTTCTTGGAATTCA 58.901 45.455 7.93 0.00 0.00 2.57
4134 4456 3.575805 TCAGGAAACCCAAAGCAAGAAT 58.424 40.909 0.00 0.00 0.00 2.40
4137 4459 5.665916 AATATCAGGAAACCCAAAGCAAG 57.334 39.130 0.00 0.00 0.00 4.01
4152 4474 3.814283 GAGCTCAGCTGGGAAAATATCAG 59.186 47.826 20.53 2.21 39.88 2.90
4231 4553 0.959553 TCGACGAGTGAGAGCCTTTT 59.040 50.000 0.00 0.00 0.00 2.27
4236 4558 0.743701 TACCCTCGACGAGTGAGAGC 60.744 60.000 22.61 0.00 35.43 4.09
4237 4559 1.666700 CTTACCCTCGACGAGTGAGAG 59.333 57.143 22.61 11.17 35.43 3.20
4250 4572 9.091220 GATAACCTATATTCTCACACTTACCCT 57.909 37.037 0.00 0.00 0.00 4.34
4273 4595 5.339008 AAATTAGCACCGACACTGAGATA 57.661 39.130 0.00 0.00 0.00 1.98
4274 4596 3.895232 AATTAGCACCGACACTGAGAT 57.105 42.857 0.00 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.