Multiple sequence alignment - TraesCS1A01G048000

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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 TraesCS1A01G048000 chr1A 100.000 4010 0 0 1 4010 29795584 29799593 0.000000e+00 7406
1 TraesCS1A01G048000 chr1B 93.512 3961 178 40 58 4010 47175776 47179665 0.000000e+00 5818
2 TraesCS1A01G048000 chr1D 94.692 2600 110 17 457 3045 28569599 28572181 0.000000e+00 4012
3 TraesCS1A01G048000 chr1D 82.895 304 43 6 3560 3862 28572391 28572686 8.550000e-67 265
4 TraesCS1A01G048000 chr1D 82.927 205 19 11 3031 3223 28572193 28572393 1.920000e-38 171


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 TraesCS1A01G048000 chr1A 29795584 29799593 4009 False 7406.000000 7406 100.000 1 4010 1 chr1A.!!$F1 4009
1 TraesCS1A01G048000 chr1B 47175776 47179665 3889 False 5818.000000 5818 93.512 58 4010 1 chr1B.!!$F1 3952
2 TraesCS1A01G048000 chr1D 28569599 28572686 3087 False 1482.666667 4012 86.838 457 3862 3 chr1D.!!$F1 3405

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
291 295 0.035056 GCCACCAGCCACAACTAGAT 60.035 55.0 0.00 0.00 34.35 1.98 F
786 798 0.518636 CCTCAATCCACACGTGCTTG 59.481 55.0 17.22 13.98 0.00 4.01 F
1311 1340 0.782384 CTGTCTCGTACGTGTTTGCC 59.218 55.0 16.05 1.78 0.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1278 1307 0.036022 AGACAGCAAAGGACTGAGGC 59.964 55.000 0.00 0.0 38.55 4.70 R
2679 2708 0.749454 ATGTTGGCTCGATGGGCTTC 60.749 55.000 0.00 0.0 0.00 3.86 R
3160 3236 1.469308 CGCCCGACATATCTAGGTCTC 59.531 57.143 1.16 0.0 35.06 3.36 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
24 25 6.579865 TCGAGTAGAATAACATTTTCTCCCC 58.420 40.000 0.00 0.00 35.19 4.81
25 26 5.758784 CGAGTAGAATAACATTTTCTCCCCC 59.241 44.000 0.00 0.00 35.19 5.40
39 40 3.587840 CCCCCTTCACCCACAGAA 58.412 61.111 0.00 0.00 0.00 3.02
40 41 1.850549 CCCCCTTCACCCACAGAAA 59.149 57.895 0.00 0.00 0.00 2.52
41 42 0.187361 CCCCCTTCACCCACAGAAAA 59.813 55.000 0.00 0.00 0.00 2.29
42 43 1.412361 CCCCCTTCACCCACAGAAAAA 60.412 52.381 0.00 0.00 0.00 1.94
43 44 1.963515 CCCCTTCACCCACAGAAAAAG 59.036 52.381 0.00 0.00 0.00 2.27
44 45 1.963515 CCCTTCACCCACAGAAAAAGG 59.036 52.381 0.00 0.00 34.38 3.11
45 46 2.424234 CCCTTCACCCACAGAAAAAGGA 60.424 50.000 0.00 0.00 36.24 3.36
46 47 2.887152 CCTTCACCCACAGAAAAAGGAG 59.113 50.000 0.00 0.00 36.24 3.69
47 48 3.555966 CTTCACCCACAGAAAAAGGAGT 58.444 45.455 0.00 0.00 0.00 3.85
48 49 2.930950 TCACCCACAGAAAAAGGAGTG 58.069 47.619 0.00 0.00 0.00 3.51
49 50 2.507886 TCACCCACAGAAAAAGGAGTGA 59.492 45.455 0.00 0.00 33.99 3.41
50 51 3.053991 TCACCCACAGAAAAAGGAGTGAA 60.054 43.478 0.00 0.00 33.05 3.18
51 52 3.066760 CACCCACAGAAAAAGGAGTGAAC 59.933 47.826 0.00 0.00 33.99 3.18
52 53 3.053619 ACCCACAGAAAAAGGAGTGAACT 60.054 43.478 0.00 0.00 33.99 3.01
53 54 3.565902 CCCACAGAAAAAGGAGTGAACTC 59.434 47.826 1.63 1.63 42.14 3.01
54 55 4.455606 CCACAGAAAAAGGAGTGAACTCT 58.544 43.478 10.17 0.00 42.48 3.24
55 56 4.884164 CCACAGAAAAAGGAGTGAACTCTT 59.116 41.667 10.17 0.00 42.48 2.85
56 57 5.220931 CCACAGAAAAAGGAGTGAACTCTTG 60.221 44.000 10.17 1.94 42.48 3.02
61 62 4.503714 AAAGGAGTGAACTCTTGGACAA 57.496 40.909 10.17 0.00 42.48 3.18
146 150 8.255905 ACACTAACAATGACTAATACCCTACAC 58.744 37.037 0.00 0.00 0.00 2.90
147 151 8.255206 CACTAACAATGACTAATACCCTACACA 58.745 37.037 0.00 0.00 0.00 3.72
151 155 6.439375 ACAATGACTAATACCCTACACAGACA 59.561 38.462 0.00 0.00 0.00 3.41
153 157 6.921486 TGACTAATACCCTACACAGACAAA 57.079 37.500 0.00 0.00 0.00 2.83
154 158 6.931838 TGACTAATACCCTACACAGACAAAG 58.068 40.000 0.00 0.00 0.00 2.77
172 176 8.877779 CAGACAAAGGAGTTATGACTTATGAAG 58.122 37.037 0.00 0.00 35.88 3.02
244 248 2.030540 CACAACATGAGAACTTGGCCAG 60.031 50.000 5.11 2.72 0.00 4.85
257 261 1.604593 GGCCAGATGCACCACACTT 60.605 57.895 0.00 0.00 43.89 3.16
259 263 1.582968 CCAGATGCACCACACTTGC 59.417 57.895 0.00 0.00 40.63 4.01
272 276 3.311106 CACACTTGCAGCAAGGTAATTG 58.689 45.455 33.54 24.89 44.81 2.32
291 295 0.035056 GCCACCAGCCACAACTAGAT 60.035 55.000 0.00 0.00 34.35 1.98
332 336 7.175467 TGCTCATCAACAAGTCAAAGATTATGT 59.825 33.333 0.00 0.00 0.00 2.29
390 394 6.287525 CAAAGTAATTTCCACCAACCACAAT 58.712 36.000 0.00 0.00 0.00 2.71
475 479 3.129813 CAGGTCCACCATTGTTCATGATG 59.870 47.826 0.00 0.00 38.89 3.07
496 500 4.468713 TGTCCACAACTTCCATGAAATCA 58.531 39.130 0.00 0.00 0.00 2.57
502 506 6.239120 CCACAACTTCCATGAAATCAGAGTTT 60.239 38.462 0.00 0.00 0.00 2.66
512 516 0.610232 ATCAGAGTTTGCCACCAGCC 60.610 55.000 0.00 0.00 42.71 4.85
617 626 4.439305 TGTGCAAGTCAAAGATTATGCC 57.561 40.909 0.00 0.00 33.01 4.40
618 627 3.825585 TGTGCAAGTCAAAGATTATGCCA 59.174 39.130 0.00 0.00 33.01 4.92
679 690 4.100344 GGTAATTTCCACCAACCACAACTT 59.900 41.667 0.00 0.00 36.01 2.66
680 691 5.302313 GGTAATTTCCACCAACCACAACTTA 59.698 40.000 0.00 0.00 36.01 2.24
681 692 5.529581 AATTTCCACCAACCACAACTTAG 57.470 39.130 0.00 0.00 0.00 2.18
682 693 3.935818 TTCCACCAACCACAACTTAGA 57.064 42.857 0.00 0.00 0.00 2.10
683 694 3.485463 TCCACCAACCACAACTTAGAG 57.515 47.619 0.00 0.00 0.00 2.43
685 696 3.456644 TCCACCAACCACAACTTAGAGAA 59.543 43.478 0.00 0.00 0.00 2.87
686 697 4.080243 TCCACCAACCACAACTTAGAGAAA 60.080 41.667 0.00 0.00 0.00 2.52
687 698 4.827284 CCACCAACCACAACTTAGAGAAAT 59.173 41.667 0.00 0.00 0.00 2.17
737 748 4.572985 TTCATTGACCTTGACTTTGCAG 57.427 40.909 0.00 0.00 0.00 4.41
754 766 2.584166 CAGTGTAAGACTGCTTTGCG 57.416 50.000 0.00 0.00 45.72 4.85
760 772 2.345942 GTAAGACTGCTTTGCGTCTAGC 59.654 50.000 13.81 0.00 39.77 3.42
761 773 2.231478 TAAGACTGCTTTGCGTCTAGCT 59.769 45.455 13.81 0.00 39.77 3.32
762 774 3.673594 TAAGACTGCTTTGCGTCTAGCTC 60.674 47.826 13.81 0.00 39.77 4.09
763 775 6.112384 TAAGACTGCTTTGCGTCTAGCTCA 62.112 45.833 13.81 0.00 39.77 4.26
764 776 7.514984 TAAGACTGCTTTGCGTCTAGCTCAA 62.515 44.000 13.81 0.00 39.77 3.02
765 777 8.729157 TAAGACTGCTTTGCGTCTAGCTCAAT 62.729 42.308 13.81 4.09 39.77 2.57
786 798 0.518636 CCTCAATCCACACGTGCTTG 59.481 55.000 17.22 13.98 0.00 4.01
798 810 5.260900 CACACGTGCTTGATATGAATGAAG 58.739 41.667 17.22 0.00 30.26 3.02
868 882 2.009681 TACTGCAGGAGTTGGTCAGA 57.990 50.000 19.93 0.00 35.96 3.27
869 883 1.131638 ACTGCAGGAGTTGGTCAGAA 58.868 50.000 19.93 0.00 0.00 3.02
1032 1046 1.153667 GCGTCTCTCCTTGCTCCAG 60.154 63.158 0.00 0.00 0.00 3.86
1044 1058 3.684693 GCTCCAGCATCTCCTCTTC 57.315 57.895 0.00 0.00 41.59 2.87
1045 1059 1.122227 GCTCCAGCATCTCCTCTTCT 58.878 55.000 0.00 0.00 41.59 2.85
1046 1060 1.485895 GCTCCAGCATCTCCTCTTCTT 59.514 52.381 0.00 0.00 41.59 2.52
1047 1061 2.483538 GCTCCAGCATCTCCTCTTCTTC 60.484 54.545 0.00 0.00 41.59 2.87
1048 1062 3.033184 CTCCAGCATCTCCTCTTCTTCT 58.967 50.000 0.00 0.00 0.00 2.85
1049 1063 3.448934 TCCAGCATCTCCTCTTCTTCTT 58.551 45.455 0.00 0.00 0.00 2.52
1050 1064 3.450457 TCCAGCATCTCCTCTTCTTCTTC 59.550 47.826 0.00 0.00 0.00 2.87
1051 1065 3.432046 CCAGCATCTCCTCTTCTTCTTCC 60.432 52.174 0.00 0.00 0.00 3.46
1052 1066 3.451902 CAGCATCTCCTCTTCTTCTTCCT 59.548 47.826 0.00 0.00 0.00 3.36
1053 1067 3.706086 AGCATCTCCTCTTCTTCTTCCTC 59.294 47.826 0.00 0.00 0.00 3.71
1054 1068 3.706086 GCATCTCCTCTTCTTCTTCCTCT 59.294 47.826 0.00 0.00 0.00 3.69
1057 1071 4.349365 TCTCCTCTTCTTCTTCCTCTTCC 58.651 47.826 0.00 0.00 0.00 3.46
1066 1095 3.835478 TCTTCCTCTTCCTCTTCCTCA 57.165 47.619 0.00 0.00 0.00 3.86
1071 1100 2.965147 CCTCTTCCTCTTCCTCATCCTC 59.035 54.545 0.00 0.00 0.00 3.71
1240 1269 1.279271 CTTTCCACCCGACTCCATTCT 59.721 52.381 0.00 0.00 0.00 2.40
1246 1275 2.496070 CACCCGACTCCATTCTACTTCA 59.504 50.000 0.00 0.00 0.00 3.02
1250 1279 3.443037 CGACTCCATTCTACTTCAGCAG 58.557 50.000 0.00 0.00 0.00 4.24
1311 1340 0.782384 CTGTCTCGTACGTGTTTGCC 59.218 55.000 16.05 1.78 0.00 4.52
1321 1350 1.155889 CGTGTTTGCCATCTACTGCA 58.844 50.000 0.00 0.00 35.27 4.41
1542 1571 2.607038 CGACATCAACAACCTCGTCTCA 60.607 50.000 0.00 0.00 0.00 3.27
1548 1577 3.118920 TCAACAACCTCGTCTCAGTGAAA 60.119 43.478 0.00 0.00 0.00 2.69
1764 1793 2.874457 GCTCCCAGACATGGTTTACGTT 60.874 50.000 0.00 0.00 46.10 3.99
1773 1802 2.922740 TGGTTTACGTTGGCTTCTCT 57.077 45.000 0.00 0.00 0.00 3.10
1909 1938 2.900546 CCGAAGCCTAGATCCAAGGTAT 59.099 50.000 12.17 3.24 36.43 2.73
1939 1968 4.395854 TCGTACTACCAATAGTTTCTGCGA 59.604 41.667 0.00 0.00 41.99 5.10
2016 2045 2.880963 ATGCCGAGCTTAGAGAAGAC 57.119 50.000 0.00 0.00 34.25 3.01
2022 2051 2.357637 CGAGCTTAGAGAAGACTGGGAG 59.642 54.545 0.00 0.00 34.25 4.30
2133 2162 3.955524 TTTGGAAAGGTGTACAAGGGA 57.044 42.857 0.00 0.00 0.00 4.20
2196 2225 0.970937 CCCACGACTCTAAGCAGGGA 60.971 60.000 0.00 0.00 36.96 4.20
2296 2325 1.792941 CGCAAGGCTGAGCTTCTTC 59.207 57.895 3.72 0.00 0.00 2.87
2307 2336 4.180057 CTGAGCTTCTTCTGGTGTATGAC 58.820 47.826 0.00 0.00 0.00 3.06
2361 2390 3.389329 TGTATGATCAGGAGAAGAAGCCC 59.611 47.826 0.09 0.00 0.00 5.19
2418 2447 1.174712 ACATTGCGTCTGCCTTGCTT 61.175 50.000 0.00 0.00 41.78 3.91
2514 2543 4.740822 AATGGGCGGCTGGGTGAC 62.741 66.667 9.56 0.00 0.00 3.67
2523 2552 1.295423 GCTGGGTGACTTCGGCTTA 59.705 57.895 3.76 0.00 32.87 3.09
2637 2666 2.910319 AGCAACCCCACTTAGTGATGTA 59.090 45.455 14.66 0.00 35.23 2.29
2679 2708 2.358737 GAGGTCACTTGTGGGCGG 60.359 66.667 0.64 0.00 0.00 6.13
2695 2724 2.272146 GGAAGCCCATCGAGCCAA 59.728 61.111 0.00 0.00 0.00 4.52
2755 2784 0.409092 TGACCATTGGCACCAAGGAT 59.591 50.000 15.30 0.00 39.72 3.24
2787 2816 0.179073 CAGTGGATACCAAGCTCCGG 60.179 60.000 0.00 0.00 34.18 5.14
2853 2882 0.399833 TGCTGTGCTCACACCCATTA 59.600 50.000 0.00 0.00 46.86 1.90
2860 2889 4.398988 TGTGCTCACACCCATTAATCAATC 59.601 41.667 0.00 0.00 46.86 2.67
2884 2913 3.976704 CCCAACATGAGGCAGGTTA 57.023 52.632 0.00 0.00 36.20 2.85
2922 2951 2.158019 TGATATGCCACCCCCAGATCTA 60.158 50.000 0.00 0.00 33.35 1.98
2967 2996 3.698040 ACATTCCATCCTTGATGCAGAAC 59.302 43.478 0.00 0.00 38.59 3.01
2976 3005 8.746623 CATCCTTGATGCAGAACGAAGTTTCC 62.747 46.154 0.00 0.00 41.51 3.13
3023 3052 7.595819 TGATGGTGTAAATTCCACTTTCTTT 57.404 32.000 7.81 0.00 36.50 2.52
3083 3158 7.010367 CCATTTGTCCAATGTATTTACATGTGC 59.990 37.037 9.11 0.00 45.55 4.57
3160 3236 6.046593 TGGTTTATCATAGCCTGTAAGAACG 58.953 40.000 0.00 0.00 34.07 3.95
3175 3251 7.308109 CCTGTAAGAACGAGACCTAGATATGTC 60.308 44.444 0.00 0.00 34.07 3.06
3258 3334 1.250154 TTGTTGGGCAGTAGCATGGC 61.250 55.000 0.00 2.09 44.61 4.40
3264 3340 1.303309 GGCAGTAGCATGGCAACTAG 58.697 55.000 0.00 0.00 44.71 2.57
3365 3441 0.890683 GAACCCATGCCTTCAAGTGG 59.109 55.000 0.00 0.00 0.00 4.00
3383 3459 2.937519 TGGTGTGCCACTTAATGAACA 58.062 42.857 0.00 0.00 40.46 3.18
3402 3478 2.224744 ACACATACATGCCTCCAACACA 60.225 45.455 0.00 0.00 0.00 3.72
3424 3500 7.041372 ACACAAACTCATATACACACTTGTTCC 60.041 37.037 0.00 0.00 37.15 3.62
3428 3504 8.718102 AACTCATATACACACTTGTTCCATAC 57.282 34.615 0.00 0.00 37.15 2.39
3429 3505 7.847096 ACTCATATACACACTTGTTCCATACA 58.153 34.615 0.00 0.00 37.15 2.29
3461 3537 2.052782 TGAGCGACCAGAGCATAGTA 57.947 50.000 0.00 0.00 37.01 1.82
3545 3621 3.325425 TGGTGATGGTTTAGTCTTCGGAA 59.675 43.478 0.00 0.00 0.00 4.30
3567 3643 1.700186 GGCCCTCCAATACCTTAGGAG 59.300 57.143 4.77 0.00 46.71 3.69
3590 3666 3.380479 ACTCTTTTCGTCGAACCATGA 57.620 42.857 7.29 1.51 0.00 3.07
3608 3684 9.906660 GAACCATGACATTTTAATCTTTGTACA 57.093 29.630 0.00 0.00 0.00 2.90
3623 3700 4.811555 TTGTACAGTGAGTTTGTCATGC 57.188 40.909 0.00 0.00 37.56 4.06
3647 3724 0.323957 GTGGTGAAGTACTCCCCACC 59.676 60.000 24.08 24.08 46.82 4.61
3656 3733 1.774856 GTACTCCCCACCTATGCCAAT 59.225 52.381 0.00 0.00 0.00 3.16
3657 3734 1.308877 ACTCCCCACCTATGCCAATT 58.691 50.000 0.00 0.00 0.00 2.32
3658 3735 1.063717 ACTCCCCACCTATGCCAATTG 60.064 52.381 0.00 0.00 0.00 2.32
3659 3736 0.396974 TCCCCACCTATGCCAATTGC 60.397 55.000 0.00 0.00 41.77 3.56
3660 3737 1.402107 CCCCACCTATGCCAATTGCC 61.402 60.000 0.00 0.00 40.16 4.52
3661 3738 0.687098 CCCACCTATGCCAATTGCCA 60.687 55.000 0.00 0.00 40.16 4.92
3668 3745 1.648116 ATGCCAATTGCCAAGAGGTT 58.352 45.000 0.00 0.00 40.16 3.50
3669 3746 0.968405 TGCCAATTGCCAAGAGGTTC 59.032 50.000 0.00 0.00 40.16 3.62
3672 3749 2.242043 CCAATTGCCAAGAGGTTCTGT 58.758 47.619 0.00 0.00 37.19 3.41
3673 3750 2.029649 CCAATTGCCAAGAGGTTCTGTG 60.030 50.000 0.00 0.00 37.19 3.66
3679 3756 2.135933 CCAAGAGGTTCTGTGTTCGAC 58.864 52.381 0.00 0.00 0.00 4.20
3680 3757 2.483013 CCAAGAGGTTCTGTGTTCGACA 60.483 50.000 0.00 0.00 0.00 4.35
3739 3817 3.791545 TGCCTTGTATAATCCTTTCCCCT 59.208 43.478 0.00 0.00 0.00 4.79
3753 3831 2.204090 CCCTACCCCACCTGGTGT 60.204 66.667 24.32 9.68 39.53 4.16
3817 3896 3.606687 AGTTCGTCTTTGTTTGGACTGT 58.393 40.909 0.00 0.00 0.00 3.55
3829 3908 0.953727 TGGACTGTTGTGCATCTTGC 59.046 50.000 0.00 0.00 45.29 4.01
3862 3941 2.612972 CGGGTGTGAACTCTATGCAGTT 60.613 50.000 0.00 0.00 39.43 3.16
3863 3942 2.744202 GGGTGTGAACTCTATGCAGTTG 59.256 50.000 0.00 0.00 36.71 3.16
3864 3943 2.744202 GGTGTGAACTCTATGCAGTTGG 59.256 50.000 0.00 0.00 36.71 3.77
3867 3946 4.389077 GTGTGAACTCTATGCAGTTGGTAC 59.611 45.833 0.00 0.00 36.71 3.34
3870 3949 2.176889 ACTCTATGCAGTTGGTACCGT 58.823 47.619 7.57 0.00 0.00 4.83
3882 3961 0.108992 GGTACCGTCTCGATGCAACA 60.109 55.000 0.00 0.00 0.00 3.33
3892 3971 2.349590 TCGATGCAACATTGGAGTCAG 58.650 47.619 0.00 0.00 30.13 3.51
3901 3980 4.899352 ACATTGGAGTCAGTAAAGCTCT 57.101 40.909 0.00 0.00 0.00 4.09
3903 3982 4.284490 ACATTGGAGTCAGTAAAGCTCTCA 59.716 41.667 0.00 0.00 0.00 3.27
3904 3983 5.046014 ACATTGGAGTCAGTAAAGCTCTCAT 60.046 40.000 0.00 0.00 0.00 2.90
3905 3984 5.489792 TTGGAGTCAGTAAAGCTCTCATT 57.510 39.130 0.00 0.00 0.00 2.57
3906 3985 6.605471 TTGGAGTCAGTAAAGCTCTCATTA 57.395 37.500 0.00 0.00 0.00 1.90
3907 3986 6.798427 TGGAGTCAGTAAAGCTCTCATTAT 57.202 37.500 0.00 0.00 0.00 1.28
3908 3987 7.187824 TGGAGTCAGTAAAGCTCTCATTATT 57.812 36.000 0.00 0.00 0.00 1.40
3948 4027 4.221924 TCCTACAACGATTCCTGACAATGA 59.778 41.667 0.00 0.00 0.00 2.57
3949 4028 4.935205 CCTACAACGATTCCTGACAATGAA 59.065 41.667 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.407752 GGGGGAGAAAATGTTATTCTACTCGA 60.408 42.308 0.00 0.00 38.85 4.04
1 2 5.758784 GGGGGAGAAAATGTTATTCTACTCG 59.241 44.000 0.00 0.00 38.85 4.18
22 23 0.187361 TTTTCTGTGGGTGAAGGGGG 59.813 55.000 0.00 0.00 0.00 5.40
23 24 1.963515 CTTTTTCTGTGGGTGAAGGGG 59.036 52.381 0.00 0.00 0.00 4.79
24 25 1.963515 CCTTTTTCTGTGGGTGAAGGG 59.036 52.381 0.00 0.00 32.08 3.95
25 26 2.887152 CTCCTTTTTCTGTGGGTGAAGG 59.113 50.000 0.00 0.00 35.98 3.46
26 27 3.316308 CACTCCTTTTTCTGTGGGTGAAG 59.684 47.826 0.00 0.00 0.00 3.02
27 28 3.053991 TCACTCCTTTTTCTGTGGGTGAA 60.054 43.478 0.00 0.00 32.39 3.18
28 29 2.507886 TCACTCCTTTTTCTGTGGGTGA 59.492 45.455 0.00 0.00 32.65 4.02
29 30 2.930950 TCACTCCTTTTTCTGTGGGTG 58.069 47.619 0.00 0.00 0.00 4.61
30 31 3.053619 AGTTCACTCCTTTTTCTGTGGGT 60.054 43.478 0.00 0.00 0.00 4.51
31 32 3.555966 AGTTCACTCCTTTTTCTGTGGG 58.444 45.455 0.00 0.00 0.00 4.61
32 33 4.455606 AGAGTTCACTCCTTTTTCTGTGG 58.544 43.478 3.20 0.00 43.88 4.17
33 34 5.220931 CCAAGAGTTCACTCCTTTTTCTGTG 60.221 44.000 3.20 0.00 43.88 3.66
34 35 4.884164 CCAAGAGTTCACTCCTTTTTCTGT 59.116 41.667 3.20 0.00 43.88 3.41
35 36 5.008118 GTCCAAGAGTTCACTCCTTTTTCTG 59.992 44.000 3.20 0.00 43.88 3.02
36 37 5.126779 GTCCAAGAGTTCACTCCTTTTTCT 58.873 41.667 3.20 0.00 43.88 2.52
37 38 4.881850 TGTCCAAGAGTTCACTCCTTTTTC 59.118 41.667 3.20 0.00 43.88 2.29
38 39 4.855340 TGTCCAAGAGTTCACTCCTTTTT 58.145 39.130 3.20 0.00 43.88 1.94
39 40 4.503714 TGTCCAAGAGTTCACTCCTTTT 57.496 40.909 3.20 0.00 43.88 2.27
40 41 4.503714 TTGTCCAAGAGTTCACTCCTTT 57.496 40.909 3.20 0.00 43.88 3.11
41 42 4.503714 TTTGTCCAAGAGTTCACTCCTT 57.496 40.909 3.20 0.00 43.88 3.36
42 43 4.200092 GTTTTGTCCAAGAGTTCACTCCT 58.800 43.478 3.20 0.00 43.88 3.69
43 44 3.945285 TGTTTTGTCCAAGAGTTCACTCC 59.055 43.478 3.20 0.00 43.88 3.85
44 45 5.332707 GTTGTTTTGTCCAAGAGTTCACTC 58.667 41.667 0.00 0.00 43.17 3.51
45 46 4.157840 GGTTGTTTTGTCCAAGAGTTCACT 59.842 41.667 0.00 0.00 0.00 3.41
46 47 4.082463 TGGTTGTTTTGTCCAAGAGTTCAC 60.082 41.667 0.00 0.00 0.00 3.18
47 48 4.082845 TGGTTGTTTTGTCCAAGAGTTCA 58.917 39.130 0.00 0.00 0.00 3.18
48 49 4.712122 TGGTTGTTTTGTCCAAGAGTTC 57.288 40.909 0.00 0.00 0.00 3.01
49 50 4.282195 TGTTGGTTGTTTTGTCCAAGAGTT 59.718 37.500 0.00 0.00 41.09 3.01
50 51 3.829601 TGTTGGTTGTTTTGTCCAAGAGT 59.170 39.130 0.00 0.00 41.09 3.24
51 52 4.448537 TGTTGGTTGTTTTGTCCAAGAG 57.551 40.909 0.00 0.00 41.09 2.85
52 53 6.723298 ATATGTTGGTTGTTTTGTCCAAGA 57.277 33.333 0.00 0.00 41.09 3.02
87 88 1.825090 TGCCTGAATGCGATTTGTCT 58.175 45.000 0.00 0.00 0.00 3.41
98 99 2.159338 CGCAGCACTAAATTGCCTGAAT 60.159 45.455 0.00 0.00 44.14 2.57
103 104 0.521291 TGTCGCAGCACTAAATTGCC 59.479 50.000 0.00 0.00 44.14 4.52
146 150 8.777865 TTCATAAGTCATAACTCCTTTGTCTG 57.222 34.615 0.00 0.00 33.48 3.51
147 151 7.550906 GCTTCATAAGTCATAACTCCTTTGTCT 59.449 37.037 0.00 0.00 33.48 3.41
151 155 6.721318 TGGCTTCATAAGTCATAACTCCTTT 58.279 36.000 0.00 0.00 38.40 3.11
153 157 5.957771 TGGCTTCATAAGTCATAACTCCT 57.042 39.130 0.00 0.00 38.40 3.69
193 197 1.159713 TGGCTTGCACAAGTCAGTCG 61.160 55.000 13.41 0.00 46.83 4.18
272 276 0.035056 ATCTAGTTGTGGCTGGTGGC 60.035 55.000 0.00 0.00 40.90 5.01
291 295 8.645110 TGTTGATGAGCAGATATATTTCTCTGA 58.355 33.333 11.67 1.20 41.13 3.27
332 336 5.186021 TGGCCAAGTTCTTTTTAAGTTGTGA 59.814 36.000 0.61 0.00 37.86 3.58
390 394 9.920133 GTCAGATGTGCAGATATATTTCTCTAA 57.080 33.333 0.00 0.00 0.00 2.10
413 417 3.683365 TGAAAGCTAGCTGTGATGTCA 57.317 42.857 20.16 11.94 0.00 3.58
475 479 4.761739 TCTGATTTCATGGAAGTTGTGGAC 59.238 41.667 0.00 0.00 0.00 4.02
496 500 1.073897 GAGGCTGGTGGCAAACTCT 59.926 57.895 0.00 0.00 44.01 3.24
502 506 2.149383 ACTCAAGAGGCTGGTGGCA 61.149 57.895 0.00 0.00 44.01 4.92
512 516 5.341872 AGATTGTGGAGATCACTCAAGAG 57.658 43.478 0.00 0.00 46.20 2.85
679 690 6.264518 TGTCGGTGTGCAGATATATTTCTCTA 59.735 38.462 0.00 0.00 0.00 2.43
680 691 5.069119 TGTCGGTGTGCAGATATATTTCTCT 59.931 40.000 0.00 0.00 0.00 3.10
681 692 5.289595 TGTCGGTGTGCAGATATATTTCTC 58.710 41.667 0.00 0.00 0.00 2.87
682 693 5.276461 TGTCGGTGTGCAGATATATTTCT 57.724 39.130 0.00 0.00 0.00 2.52
683 694 5.696270 TGATGTCGGTGTGCAGATATATTTC 59.304 40.000 0.00 0.00 0.00 2.17
685 696 4.991056 GTGATGTCGGTGTGCAGATATATT 59.009 41.667 0.00 0.00 0.00 1.28
686 697 4.039124 TGTGATGTCGGTGTGCAGATATAT 59.961 41.667 0.00 0.00 0.00 0.86
687 698 3.383185 TGTGATGTCGGTGTGCAGATATA 59.617 43.478 0.00 0.00 0.00 0.86
737 748 2.135933 AGACGCAAAGCAGTCTTACAC 58.864 47.619 9.51 0.00 38.47 2.90
754 766 3.137533 GGATTGAGGCATTGAGCTAGAC 58.862 50.000 0.00 0.00 44.79 2.59
760 772 1.399440 CGTGTGGATTGAGGCATTGAG 59.601 52.381 0.00 0.00 0.00 3.02
761 773 1.271325 ACGTGTGGATTGAGGCATTGA 60.271 47.619 0.00 0.00 0.00 2.57
762 774 1.135603 CACGTGTGGATTGAGGCATTG 60.136 52.381 7.58 0.00 0.00 2.82
763 775 1.167851 CACGTGTGGATTGAGGCATT 58.832 50.000 7.58 0.00 0.00 3.56
764 776 1.308069 GCACGTGTGGATTGAGGCAT 61.308 55.000 18.38 0.00 0.00 4.40
765 777 1.965930 GCACGTGTGGATTGAGGCA 60.966 57.895 18.38 0.00 0.00 4.75
766 778 1.237285 AAGCACGTGTGGATTGAGGC 61.237 55.000 18.38 0.00 0.00 4.70
767 779 0.518636 CAAGCACGTGTGGATTGAGG 59.481 55.000 18.38 0.00 0.00 3.86
786 798 4.820716 ACTTCTGCTGGCTTCATTCATATC 59.179 41.667 0.00 0.00 0.00 1.63
798 810 2.627515 TGGATCATACTTCTGCTGGC 57.372 50.000 0.00 0.00 0.00 4.85
802 814 4.637534 TGCTTCTTTGGATCATACTTCTGC 59.362 41.667 0.00 0.00 0.00 4.26
868 882 5.647225 GTCAGATTCTCTGGAAAAGCATCTT 59.353 40.000 4.43 0.00 44.39 2.40
869 883 5.184711 GTCAGATTCTCTGGAAAAGCATCT 58.815 41.667 4.43 0.00 44.39 2.90
1032 1046 3.706086 AGAGGAAGAAGAAGAGGAGATGC 59.294 47.826 0.00 0.00 0.00 3.91
1040 1054 4.775253 GGAAGAGGAAGAGGAAGAAGAAGA 59.225 45.833 0.00 0.00 0.00 2.87
1041 1055 4.777366 AGGAAGAGGAAGAGGAAGAAGAAG 59.223 45.833 0.00 0.00 0.00 2.85
1042 1056 4.757692 AGGAAGAGGAAGAGGAAGAAGAA 58.242 43.478 0.00 0.00 0.00 2.52
1043 1057 4.202727 TGAGGAAGAGGAAGAGGAAGAAGA 60.203 45.833 0.00 0.00 0.00 2.87
1044 1058 4.093011 TGAGGAAGAGGAAGAGGAAGAAG 58.907 47.826 0.00 0.00 0.00 2.85
1045 1059 4.133526 TGAGGAAGAGGAAGAGGAAGAA 57.866 45.455 0.00 0.00 0.00 2.52
1046 1060 3.835478 TGAGGAAGAGGAAGAGGAAGA 57.165 47.619 0.00 0.00 0.00 2.87
1047 1061 3.387699 GGATGAGGAAGAGGAAGAGGAAG 59.612 52.174 0.00 0.00 0.00 3.46
1048 1062 3.013417 AGGATGAGGAAGAGGAAGAGGAA 59.987 47.826 0.00 0.00 0.00 3.36
1049 1063 2.589664 AGGATGAGGAAGAGGAAGAGGA 59.410 50.000 0.00 0.00 0.00 3.71
1050 1064 2.965147 GAGGATGAGGAAGAGGAAGAGG 59.035 54.545 0.00 0.00 0.00 3.69
1051 1065 2.622942 CGAGGATGAGGAAGAGGAAGAG 59.377 54.545 0.00 0.00 0.00 2.85
1052 1066 2.242452 TCGAGGATGAGGAAGAGGAAGA 59.758 50.000 0.00 0.00 0.00 2.87
1053 1067 2.660572 TCGAGGATGAGGAAGAGGAAG 58.339 52.381 0.00 0.00 0.00 3.46
1054 1068 2.828661 TCGAGGATGAGGAAGAGGAA 57.171 50.000 0.00 0.00 0.00 3.36
1057 1071 4.340666 TGAAAGATCGAGGATGAGGAAGAG 59.659 45.833 0.00 0.00 0.00 2.85
1066 1095 3.740764 GCAAGCTCTGAAAGATCGAGGAT 60.741 47.826 0.00 0.00 45.62 3.24
1071 1100 2.863137 GGTAGCAAGCTCTGAAAGATCG 59.137 50.000 0.00 0.00 45.62 3.69
1240 1269 4.096003 GGGCGCCCTGCTGAAGTA 62.096 66.667 38.76 0.00 45.43 2.24
1277 1306 1.294659 GACAGCAAAGGACTGAGGCG 61.295 60.000 0.00 0.00 38.55 5.52
1278 1307 0.036022 AGACAGCAAAGGACTGAGGC 59.964 55.000 0.00 0.00 38.55 4.70
1279 1308 1.671261 CGAGACAGCAAAGGACTGAGG 60.671 57.143 0.00 0.00 38.55 3.86
1311 1340 0.250640 GGGCCTGGATGCAGTAGATG 60.251 60.000 13.65 0.00 0.00 2.90
1542 1571 2.042831 GGCGCTGCTGGATTTCACT 61.043 57.895 7.64 0.00 0.00 3.41
1683 1712 1.072266 TGGGTTTGGCCATGTCTACT 58.928 50.000 6.09 0.00 39.65 2.57
1840 1869 1.134699 GGTGATGTCGATTGCTGGAGA 60.135 52.381 0.00 0.00 0.00 3.71
1887 1916 1.343075 ACCTTGGATCTAGGCTTCGGA 60.343 52.381 12.56 0.00 36.17 4.55
1909 1938 8.316214 AGAAACTATTGGTAGTACGATTTCCAA 58.684 33.333 10.68 10.68 40.24 3.53
1923 1952 4.518970 ACAAATGTCGCAGAAACTATTGGT 59.481 37.500 0.00 0.00 39.69 3.67
1939 1968 1.069049 GCCCACAGCAAGAACAAATGT 59.931 47.619 0.00 0.00 42.97 2.71
1962 1991 3.202097 TCGCACAAGAAGAATGACAACA 58.798 40.909 0.00 0.00 0.00 3.33
1963 1992 3.878086 TCGCACAAGAAGAATGACAAC 57.122 42.857 0.00 0.00 0.00 3.32
2016 2045 1.467920 GCCCAAATTCAGTCTCCCAG 58.532 55.000 0.00 0.00 0.00 4.45
2022 2051 2.310538 CTATGGGGCCCAAATTCAGTC 58.689 52.381 32.57 2.47 36.95 3.51
2133 2162 2.614057 CACTTTCGACTTTGGAAGCACT 59.386 45.455 0.00 0.00 0.00 4.40
2196 2225 3.512724 CCTCTGCCACAAATTCCTTCATT 59.487 43.478 0.00 0.00 0.00 2.57
2277 2306 2.250841 GAAGAAGCTCAGCCTTGCGC 62.251 60.000 0.00 0.00 35.28 6.09
2307 2336 3.487711 CGAGACTTCCATTCGACAGGTAG 60.488 52.174 7.23 7.23 36.49 3.18
2361 2390 2.162681 CTCTGGGCCCAAGTTAAAGTG 58.837 52.381 28.29 11.02 0.00 3.16
2514 2543 5.177696 GTCATATAACCTTGCTAAGCCGAAG 59.822 44.000 0.00 0.00 0.00 3.79
2523 2552 3.704566 TCTCGTGGTCATATAACCTTGCT 59.295 43.478 0.00 0.00 40.20 3.91
2637 2666 5.683681 AGAACAAACATGCCAAAGGAAAAT 58.316 33.333 0.00 0.00 0.00 1.82
2679 2708 0.749454 ATGTTGGCTCGATGGGCTTC 60.749 55.000 0.00 0.00 0.00 3.86
2695 2724 1.956477 GAGTTGGTTGCCTTGTGATGT 59.044 47.619 0.00 0.00 0.00 3.06
2755 2784 3.708403 ATCCACTGCATCTGTGAGAAA 57.292 42.857 6.16 0.00 35.76 2.52
2787 2816 2.684881 CTCATCAACATTGTAGGCACCC 59.315 50.000 0.00 0.00 0.00 4.61
2853 2882 4.870636 TCATGTTGGGCCTTAGATTGATT 58.129 39.130 4.53 0.00 0.00 2.57
2860 2889 2.799176 GCCTCATGTTGGGCCTTAG 58.201 57.895 4.53 0.00 42.30 2.18
2884 2913 5.646793 GCATATCACCATTGAGATACTGCAT 59.353 40.000 16.73 0.00 31.65 3.96
2922 2951 4.392047 TGAAGCTCATGTGTGTCAGATTT 58.608 39.130 0.00 0.00 0.00 2.17
2967 2996 2.608467 AGTCGTCTACGGAAACTTCG 57.392 50.000 2.24 0.00 40.29 3.79
3023 3052 6.873076 GGACAAATGTGCATCTAAATTGGAAA 59.127 34.615 0.00 0.00 36.33 3.13
3160 3236 1.469308 CGCCCGACATATCTAGGTCTC 59.531 57.143 1.16 0.00 35.06 3.36
3175 3251 2.342279 TTCTCCTGAACACGCCCG 59.658 61.111 0.00 0.00 0.00 6.13
3331 3407 2.096248 GGGTTCCACTTGTTGAACACA 58.904 47.619 16.07 0.00 42.97 3.72
3335 3411 1.686052 GCATGGGTTCCACTTGTTGAA 59.314 47.619 0.00 0.00 35.80 2.69
3365 3441 5.049060 TGTATGTGTTCATTAAGTGGCACAC 60.049 40.000 21.41 7.73 46.40 3.82
3383 3459 2.877097 TGTGTTGGAGGCATGTATGT 57.123 45.000 0.00 0.00 0.00 2.29
3424 3500 4.418392 GCTCAAAGCAAAGACCATGTATG 58.582 43.478 0.00 0.00 41.89 2.39
3428 3504 1.536766 TCGCTCAAAGCAAAGACCATG 59.463 47.619 0.00 0.00 42.58 3.66
3429 3505 1.537202 GTCGCTCAAAGCAAAGACCAT 59.463 47.619 0.00 0.00 42.58 3.55
3495 3571 1.831580 AAACATCTCCTTGGCTGCTC 58.168 50.000 0.00 0.00 0.00 4.26
3545 3621 1.129058 CTAAGGTATTGGAGGGCCGT 58.871 55.000 0.00 0.00 36.79 5.68
3547 3623 1.700186 CTCCTAAGGTATTGGAGGGCC 59.300 57.143 0.00 0.00 42.55 5.80
3567 3643 3.017265 TGGTTCGACGAAAAGAGTACC 57.983 47.619 12.67 8.73 0.00 3.34
3608 3684 1.878088 CTGCAGCATGACAAACTCACT 59.122 47.619 0.00 0.00 39.69 3.41
3623 3700 1.338200 GGGAGTACTTCACCACTGCAG 60.338 57.143 13.48 13.48 35.05 4.41
3656 3733 2.297701 GAACACAGAACCTCTTGGCAA 58.702 47.619 0.00 0.00 36.63 4.52
3657 3734 1.810031 CGAACACAGAACCTCTTGGCA 60.810 52.381 0.00 0.00 36.63 4.92
3658 3735 0.868406 CGAACACAGAACCTCTTGGC 59.132 55.000 0.00 0.00 36.63 4.52
3659 3736 2.135933 GTCGAACACAGAACCTCTTGG 58.864 52.381 0.00 0.00 39.83 3.61
3660 3737 2.821546 TGTCGAACACAGAACCTCTTG 58.178 47.619 0.00 0.00 0.00 3.02
3672 3749 1.538204 GCAGAGAGGTTGTGTCGAACA 60.538 52.381 0.00 0.00 36.85 3.18
3673 3750 1.140816 GCAGAGAGGTTGTGTCGAAC 58.859 55.000 0.00 0.00 0.00 3.95
3679 3756 1.068748 GTGCAATGCAGAGAGGTTGTG 60.069 52.381 8.73 0.00 40.08 3.33
3680 3757 1.202855 AGTGCAATGCAGAGAGGTTGT 60.203 47.619 8.73 0.00 40.08 3.32
3683 3760 0.982704 AGAGTGCAATGCAGAGAGGT 59.017 50.000 8.73 0.00 40.08 3.85
3753 3831 2.621070 ACCCAGTTCTAGAAGCTTCCA 58.379 47.619 22.81 8.79 0.00 3.53
3785 3864 0.033090 AGACGAACTCACCCGGAAAC 59.967 55.000 0.73 0.00 0.00 2.78
3789 3868 0.249741 ACAAAGACGAACTCACCCGG 60.250 55.000 0.00 0.00 0.00 5.73
3829 3908 0.243907 CACACCCGGTCTGTACAGAG 59.756 60.000 25.81 16.02 38.27 3.35
3862 3941 0.108992 GTTGCATCGAGACGGTACCA 60.109 55.000 13.54 0.00 0.00 3.25
3863 3942 0.108992 TGTTGCATCGAGACGGTACC 60.109 55.000 0.16 0.16 0.00 3.34
3864 3943 1.922570 ATGTTGCATCGAGACGGTAC 58.077 50.000 0.00 0.00 0.00 3.34
3867 3946 0.374758 CCAATGTTGCATCGAGACGG 59.625 55.000 0.00 0.00 0.00 4.79
3870 3949 2.028203 TGACTCCAATGTTGCATCGAGA 60.028 45.455 10.95 0.00 0.00 4.04
3882 3961 5.690464 ATGAGAGCTTTACTGACTCCAAT 57.310 39.130 0.00 0.00 0.00 3.16
3907 3986 9.457436 GTTGTAGGATAACCCTTTTCTCAATAA 57.543 33.333 0.00 0.00 44.85 1.40
3908 3987 7.767198 CGTTGTAGGATAACCCTTTTCTCAATA 59.233 37.037 0.00 0.00 44.85 1.90
3924 4003 4.819105 TTGTCAGGAATCGTTGTAGGAT 57.181 40.909 0.00 0.00 0.00 3.24
3935 4014 9.865321 CATTCTAAATTGTTCATTGTCAGGAAT 57.135 29.630 0.00 0.00 0.00 3.01
3965 4044 4.434545 AAGGCAGACGTCTAGGAGTATA 57.565 45.455 19.57 0.00 0.00 1.47


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

AutoCloner maintained by Alex Coulton.