Multiple sequence alignment - TraesCS7A01G424500

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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 TraesCS7A01G424500 chr7A 100.000 4040 0 0 1 4040 617687789 617691828 0.000000e+00 7461
1 TraesCS7A01G424500 chr7A 84.267 839 120 9 2580 3417 617687152 617686325 0.000000e+00 808
2 TraesCS7A01G424500 chr7D 93.447 3235 143 36 570 3774 535755896 535752701 0.000000e+00 4735
3 TraesCS7A01G424500 chr7D 85.647 843 108 10 2577 3417 535757319 535758150 0.000000e+00 874
4 TraesCS7A01G424500 chr7D 86.175 434 36 13 60 476 535756624 535756198 7.970000e-122 448
5 TraesCS7A01G424500 chr7D 91.935 248 12 3 3794 4040 535752724 535752484 1.390000e-89 340
6 TraesCS7A01G424500 chr7B 92.293 3244 144 49 604 3774 577756453 577753243 0.000000e+00 4508
7 TraesCS7A01G424500 chr7B 84.190 506 69 7 2730 3234 577758083 577758578 7.850000e-132 481
8 TraesCS7A01G424500 chr7B 84.932 365 21 9 81 442 577757394 577757061 5.000000e-89 339
9 TraesCS7A01G424500 chr7B 88.755 249 17 8 3794 4040 577753266 577753027 1.100000e-75 294
10 TraesCS7A01G424500 chr6D 76.508 2039 412 51 1039 3054 75377274 75375280 0.000000e+00 1050
11 TraesCS7A01G424500 chr6B 76.734 1874 388 36 1032 2889 149060037 149058196 0.000000e+00 1002


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 TraesCS7A01G424500 chr7A 617687789 617691828 4039 False 7461.000000 7461 100.000 1 4040 1 chr7A.!!$F1 4039
1 TraesCS7A01G424500 chr7A 617686325 617687152 827 True 808.000000 808 84.267 2580 3417 1 chr7A.!!$R1 837
2 TraesCS7A01G424500 chr7D 535752484 535756624 4140 True 1841.000000 4735 90.519 60 4040 3 chr7D.!!$R1 3980
3 TraesCS7A01G424500 chr7D 535757319 535758150 831 False 874.000000 874 85.647 2577 3417 1 chr7D.!!$F1 840
4 TraesCS7A01G424500 chr7B 577753027 577757394 4367 True 1713.666667 4508 88.660 81 4040 3 chr7B.!!$R1 3959
5 TraesCS7A01G424500 chr6D 75375280 75377274 1994 True 1050.000000 1050 76.508 1039 3054 1 chr6D.!!$R1 2015
6 TraesCS7A01G424500 chr6B 149058196 149060037 1841 True 1002.000000 1002 76.734 1032 2889 1 chr6B.!!$R1 1857

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
389 401 0.106708 CATCCATCCGTCCGTCCAAT 59.893 55.000 0.00 0.00 0.00 3.16 F
889 1452 0.108585 GGCCGGCAGATTGATTCCTA 59.891 55.000 30.85 0.00 0.00 2.94 F
891 1454 1.475034 GCCGGCAGATTGATTCCTACA 60.475 52.381 24.80 0.00 0.00 2.74 F
1933 2504 2.024319 GTTGCTGTCTTCGAGCGCT 61.024 57.895 11.27 11.27 39.47 5.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1488 2059 1.674651 GGGGACGCCCTTGAGTTTC 60.675 63.158 13.58 0.0 44.66 2.78 R
2490 3061 0.944386 GGTGCTTGAAGAAGTGCGAA 59.056 50.000 0.00 0.0 0.00 4.70 R
2590 3161 2.305927 CCCAGCTCTCCCTTAGAAACAA 59.694 50.000 0.00 0.0 32.46 2.83 R
3278 3852 1.073706 GATCTAGGGGAAGGGGGCA 60.074 63.158 0.00 0.0 0.00 5.36 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 3.489391 GCCCGGCCATTAACTAAGT 57.511 52.632 2.24 0.00 0.00 2.24
25 26 1.758936 GCCCGGCCATTAACTAAGTT 58.241 50.000 2.24 0.00 0.00 2.66
26 27 2.097036 GCCCGGCCATTAACTAAGTTT 58.903 47.619 2.24 0.00 0.00 2.66
27 28 3.281158 GCCCGGCCATTAACTAAGTTTA 58.719 45.455 2.24 0.00 0.00 2.01
28 29 3.065786 GCCCGGCCATTAACTAAGTTTAC 59.934 47.826 2.24 0.00 0.00 2.01
29 30 4.520179 CCCGGCCATTAACTAAGTTTACT 58.480 43.478 2.24 0.00 0.00 2.24
30 31 4.573607 CCCGGCCATTAACTAAGTTTACTC 59.426 45.833 2.24 0.00 0.00 2.59
31 32 4.573607 CCGGCCATTAACTAAGTTTACTCC 59.426 45.833 2.24 0.00 0.00 3.85
32 33 5.180271 CGGCCATTAACTAAGTTTACTCCA 58.820 41.667 2.24 0.00 0.00 3.86
33 34 5.064325 CGGCCATTAACTAAGTTTACTCCAC 59.936 44.000 2.24 0.00 0.00 4.02
34 35 5.356190 GGCCATTAACTAAGTTTACTCCACC 59.644 44.000 0.00 0.00 0.00 4.61
35 36 5.064325 GCCATTAACTAAGTTTACTCCACCG 59.936 44.000 0.00 0.00 0.00 4.94
36 37 5.583457 CCATTAACTAAGTTTACTCCACCGG 59.417 44.000 0.00 0.00 0.00 5.28
37 38 2.756840 ACTAAGTTTACTCCACCGGC 57.243 50.000 0.00 0.00 0.00 6.13
38 39 1.277273 ACTAAGTTTACTCCACCGGCC 59.723 52.381 0.00 0.00 0.00 6.13
39 40 0.614812 TAAGTTTACTCCACCGGCCC 59.385 55.000 0.00 0.00 0.00 5.80
40 41 2.045634 GTTTACTCCACCGGCCCC 60.046 66.667 0.00 0.00 0.00 5.80
41 42 2.204029 TTTACTCCACCGGCCCCT 60.204 61.111 0.00 0.00 0.00 4.79
42 43 1.848895 TTTACTCCACCGGCCCCTT 60.849 57.895 0.00 0.00 0.00 3.95
43 44 1.844544 TTTACTCCACCGGCCCCTTC 61.845 60.000 0.00 0.00 0.00 3.46
44 45 3.549433 TACTCCACCGGCCCCTTCA 62.549 63.158 0.00 0.00 0.00 3.02
45 46 3.646715 CTCCACCGGCCCCTTCAA 61.647 66.667 0.00 0.00 0.00 2.69
46 47 3.179339 TCCACCGGCCCCTTCAAA 61.179 61.111 0.00 0.00 0.00 2.69
47 48 2.203567 CCACCGGCCCCTTCAAAA 60.204 61.111 0.00 0.00 0.00 2.44
48 49 1.834822 CCACCGGCCCCTTCAAAAA 60.835 57.895 0.00 0.00 0.00 1.94
112 114 0.108186 ACATTGAAGCGCTCCATCGA 60.108 50.000 12.06 4.93 0.00 3.59
165 170 2.357517 AGAAGCTTCCGGTGCGTG 60.358 61.111 22.81 0.00 35.28 5.34
187 195 1.635663 GATCCACGTTGCTTCCACGG 61.636 60.000 0.00 0.00 0.00 4.94
193 201 1.675641 GTTGCTTCCACGGCATCCT 60.676 57.895 0.00 0.00 39.54 3.24
194 202 1.074775 TTGCTTCCACGGCATCCTT 59.925 52.632 0.00 0.00 39.54 3.36
195 203 0.539438 TTGCTTCCACGGCATCCTTT 60.539 50.000 0.00 0.00 39.54 3.11
196 204 0.960364 TGCTTCCACGGCATCCTTTC 60.960 55.000 0.00 0.00 34.56 2.62
202 210 1.247567 CACGGCATCCTTTCCTTTGT 58.752 50.000 0.00 0.00 0.00 2.83
210 218 4.462483 GCATCCTTTCCTTTGTGGTATCAA 59.538 41.667 0.00 0.00 37.07 2.57
218 226 4.141135 TCCTTTGTGGTATCAAGTTTCCCA 60.141 41.667 0.00 0.00 37.07 4.37
247 255 1.269166 GCATACAGACGTGAACTCCG 58.731 55.000 0.00 0.00 0.00 4.63
347 355 2.539688 GCAACAAAAGTGGCAAAGTAGC 59.460 45.455 0.00 0.00 0.00 3.58
375 387 2.115052 ACAAAGCGGTGGCATCCA 59.885 55.556 0.00 0.00 43.41 3.41
383 395 2.588877 GTGGCATCCATCCGTCCG 60.589 66.667 0.00 0.00 35.28 4.79
384 396 3.080765 TGGCATCCATCCGTCCGT 61.081 61.111 0.00 0.00 0.00 4.69
385 397 2.280186 GGCATCCATCCGTCCGTC 60.280 66.667 0.00 0.00 0.00 4.79
386 398 2.280186 GCATCCATCCGTCCGTCC 60.280 66.667 0.00 0.00 0.00 4.79
387 399 3.088941 GCATCCATCCGTCCGTCCA 62.089 63.158 0.00 0.00 0.00 4.02
388 400 1.520192 CATCCATCCGTCCGTCCAA 59.480 57.895 0.00 0.00 0.00 3.53
389 401 0.106708 CATCCATCCGTCCGTCCAAT 59.893 55.000 0.00 0.00 0.00 3.16
390 402 0.393077 ATCCATCCGTCCGTCCAATC 59.607 55.000 0.00 0.00 0.00 2.67
391 403 1.227556 CCATCCGTCCGTCCAATCC 60.228 63.158 0.00 0.00 0.00 3.01
392 404 1.591594 CATCCGTCCGTCCAATCCG 60.592 63.158 0.00 0.00 0.00 4.18
393 405 1.755395 ATCCGTCCGTCCAATCCGA 60.755 57.895 0.00 0.00 0.00 4.55
394 406 1.735376 ATCCGTCCGTCCAATCCGAG 61.735 60.000 0.00 0.00 0.00 4.63
395 407 2.707849 CCGTCCGTCCAATCCGAGT 61.708 63.158 0.00 0.00 0.00 4.18
396 408 1.516386 CGTCCGTCCAATCCGAGTG 60.516 63.158 0.00 0.00 0.00 3.51
397 409 1.810030 GTCCGTCCAATCCGAGTGC 60.810 63.158 0.00 0.00 0.00 4.40
398 410 2.885644 CCGTCCAATCCGAGTGCG 60.886 66.667 0.00 0.00 37.24 5.34
399 411 3.554692 CGTCCAATCCGAGTGCGC 61.555 66.667 0.00 0.00 35.83 6.09
400 412 3.554692 GTCCAATCCGAGTGCGCG 61.555 66.667 0.00 0.00 35.83 6.86
461 511 1.929836 GATTGAAGTGAGCGTAGGCAG 59.070 52.381 10.48 0.00 43.41 4.85
478 528 3.552604 GCAGTAATTGCGGTGAAAGAA 57.447 42.857 0.00 0.00 44.09 2.52
479 529 3.896122 GCAGTAATTGCGGTGAAAGAAA 58.104 40.909 0.00 0.00 44.09 2.52
486 536 0.110644 GCGGTGAAAGAAACTCGCAG 60.111 55.000 0.00 0.00 42.27 5.18
488 538 0.875059 GGTGAAAGAAACTCGCAGGG 59.125 55.000 0.00 0.00 0.00 4.45
492 542 1.228657 AAAGAAACTCGCAGGGACGC 61.229 55.000 0.00 0.00 0.00 5.19
533 588 1.334054 CGACGTAAACAACCTCGGAG 58.666 55.000 0.00 0.00 34.29 4.63
561 1019 1.669115 CAGCAACCACAGACCGGAG 60.669 63.158 9.46 0.00 0.00 4.63
563 1021 2.738521 CAACCACAGACCGGAGCG 60.739 66.667 9.46 0.00 0.00 5.03
628 1100 1.896465 CCTTCAGTTTCGACTCTCCCT 59.104 52.381 0.00 0.00 0.00 4.20
629 1101 2.094442 CCTTCAGTTTCGACTCTCCCTC 60.094 54.545 0.00 0.00 0.00 4.30
632 1104 0.410270 AGTTTCGACTCTCCCTCCCT 59.590 55.000 0.00 0.00 0.00 4.20
633 1105 0.818938 GTTTCGACTCTCCCTCCCTC 59.181 60.000 0.00 0.00 0.00 4.30
634 1106 0.680280 TTTCGACTCTCCCTCCCTCG 60.680 60.000 0.00 0.00 0.00 4.63
657 1132 0.400594 CCGTGGAAAAACTCTCCCCT 59.599 55.000 0.00 0.00 31.32 4.79
658 1133 1.202891 CCGTGGAAAAACTCTCCCCTT 60.203 52.381 0.00 0.00 31.32 3.95
659 1134 2.583143 CGTGGAAAAACTCTCCCCTTT 58.417 47.619 0.00 0.00 31.32 3.11
660 1135 2.956333 CGTGGAAAAACTCTCCCCTTTT 59.044 45.455 0.00 0.00 31.32 2.27
661 1136 3.004419 CGTGGAAAAACTCTCCCCTTTTC 59.996 47.826 0.00 0.00 38.01 2.29
663 1138 2.557056 GGAAAAACTCTCCCCTTTTCCG 59.443 50.000 9.17 0.00 44.79 4.30
664 1139 1.617322 AAAACTCTCCCCTTTTCCGC 58.383 50.000 0.00 0.00 0.00 5.54
665 1140 0.251209 AAACTCTCCCCTTTTCCGCC 60.251 55.000 0.00 0.00 0.00 6.13
666 1141 1.134438 AACTCTCCCCTTTTCCGCCT 61.134 55.000 0.00 0.00 0.00 5.52
667 1142 1.222113 CTCTCCCCTTTTCCGCCTC 59.778 63.158 0.00 0.00 0.00 4.70
668 1143 2.258748 CTCTCCCCTTTTCCGCCTCC 62.259 65.000 0.00 0.00 0.00 4.30
669 1144 3.335729 TCCCCTTTTCCGCCTCCC 61.336 66.667 0.00 0.00 0.00 4.30
670 1145 4.442454 CCCCTTTTCCGCCTCCCC 62.442 72.222 0.00 0.00 0.00 4.81
671 1146 4.442454 CCCTTTTCCGCCTCCCCC 62.442 72.222 0.00 0.00 0.00 5.40
672 1147 3.339093 CCTTTTCCGCCTCCCCCT 61.339 66.667 0.00 0.00 0.00 4.79
673 1148 2.763902 CTTTTCCGCCTCCCCCTT 59.236 61.111 0.00 0.00 0.00 3.95
674 1149 1.076727 CTTTTCCGCCTCCCCCTTT 59.923 57.895 0.00 0.00 0.00 3.11
757 1286 2.448542 ACCACAGCACCCACCTCT 60.449 61.111 0.00 0.00 0.00 3.69
758 1287 2.348998 CCACAGCACCCACCTCTC 59.651 66.667 0.00 0.00 0.00 3.20
889 1452 0.108585 GGCCGGCAGATTGATTCCTA 59.891 55.000 30.85 0.00 0.00 2.94
891 1454 1.475034 GCCGGCAGATTGATTCCTACA 60.475 52.381 24.80 0.00 0.00 2.74
893 1456 2.213499 CGGCAGATTGATTCCTACACC 58.787 52.381 0.00 0.00 0.00 4.16
1746 2317 4.781959 TACTGCGTGGCGGCGTAC 62.782 66.667 9.37 7.58 38.71 3.67
1933 2504 2.024319 GTTGCTGTCTTCGAGCGCT 61.024 57.895 11.27 11.27 39.47 5.92
2079 2650 5.618056 TTGATGTGTTTGATTCTCTCAGC 57.382 39.130 0.00 0.00 34.68 4.26
2460 3031 4.693283 CAAAGGCGTATGAGGATAAGACA 58.307 43.478 0.00 0.00 0.00 3.41
2490 3061 6.046290 TCTCTCTTCATGATGAACACACAT 57.954 37.500 11.98 0.00 32.21 3.21
2590 3161 2.736347 ACAAGGACTACTACTCGGCAT 58.264 47.619 0.00 0.00 0.00 4.40
2907 3480 2.359230 AGCGCTGAAGGCCTTGAC 60.359 61.111 26.25 10.36 37.74 3.18
3059 3633 4.090761 AGCATCAGTTGAAGAAACTCCA 57.909 40.909 0.00 0.00 46.60 3.86
3278 3852 6.451292 AATCTTTCCTCAGAGCATATGGAT 57.549 37.500 4.56 0.00 0.00 3.41
3295 3869 0.476611 GATGCCCCCTTCCCCTAGAT 60.477 60.000 0.00 0.00 0.00 1.98
3300 3874 2.767048 GCCCCCTTCCCCTAGATCATTA 60.767 54.545 0.00 0.00 0.00 1.90
3302 3876 4.825126 GCCCCCTTCCCCTAGATCATTATA 60.825 50.000 0.00 0.00 0.00 0.98
3514 4094 8.853077 AAATGACTGATCAATTGACTGACTAA 57.147 30.769 11.07 0.00 38.69 2.24
3529 4109 5.376625 ACTGACTAACATGAGGCAAGAAAA 58.623 37.500 0.00 0.00 32.76 2.29
3561 4141 1.871039 CGAAGTTTCGGTTCCACATGT 59.129 47.619 6.38 0.00 46.30 3.21
3593 4174 4.726416 TCTCTTTACGCACTAACTTACCG 58.274 43.478 0.00 0.00 0.00 4.02
3713 4294 6.855914 GTGTTTCATGCGAAAAGAATTAGTGA 59.144 34.615 0.00 0.00 42.66 3.41
3774 4355 6.328934 TCCAGAATTTACTGACCTGGCATATA 59.671 38.462 0.00 0.00 42.97 0.86
3775 4356 7.017551 TCCAGAATTTACTGACCTGGCATATAT 59.982 37.037 0.00 0.00 42.97 0.86
3776 4357 8.321353 CCAGAATTTACTGACCTGGCATATATA 58.679 37.037 0.00 0.00 39.94 0.86
3785 4366 7.607991 ACTGACCTGGCATATATATAACTTTGC 59.392 37.037 7.30 7.30 0.00 3.68
3786 4367 7.457561 TGACCTGGCATATATATAACTTTGCA 58.542 34.615 14.81 0.00 0.00 4.08
3787 4368 7.941790 TGACCTGGCATATATATAACTTTGCAA 59.058 33.333 14.81 0.00 0.00 4.08
3788 4369 8.884124 ACCTGGCATATATATAACTTTGCAAT 57.116 30.769 14.81 0.00 0.00 3.56
3789 4370 8.742777 ACCTGGCATATATATAACTTTGCAATG 58.257 33.333 14.81 10.58 0.00 2.82
3790 4371 8.742777 CCTGGCATATATATAACTTTGCAATGT 58.257 33.333 11.92 11.92 0.00 2.71
3803 4384 8.587952 AACTTTGCAATGTAACCTGAATTTAC 57.412 30.769 17.36 0.00 0.00 2.01
3804 4385 7.951591 ACTTTGCAATGTAACCTGAATTTACT 58.048 30.769 15.73 0.00 31.74 2.24
3805 4386 7.867403 ACTTTGCAATGTAACCTGAATTTACTG 59.133 33.333 15.73 0.00 31.74 2.74
3806 4387 7.517614 TTGCAATGTAACCTGAATTTACTGA 57.482 32.000 0.00 0.00 31.74 3.41
3807 4388 6.908825 TGCAATGTAACCTGAATTTACTGAC 58.091 36.000 0.00 0.00 31.74 3.51
3808 4389 6.072175 TGCAATGTAACCTGAATTTACTGACC 60.072 38.462 0.00 0.00 31.74 4.02
3809 4390 6.151144 GCAATGTAACCTGAATTTACTGACCT 59.849 38.462 0.00 0.00 31.74 3.85
3810 4391 7.530010 CAATGTAACCTGAATTTACTGACCTG 58.470 38.462 0.00 0.00 31.74 4.00
3811 4392 5.556915 TGTAACCTGAATTTACTGACCTGG 58.443 41.667 0.00 0.00 31.74 4.45
3812 4393 4.724279 AACCTGAATTTACTGACCTGGT 57.276 40.909 0.00 0.00 0.00 4.00
3813 4394 5.836024 AACCTGAATTTACTGACCTGGTA 57.164 39.130 0.00 0.00 0.00 3.25
3814 4395 6.388619 AACCTGAATTTACTGACCTGGTAT 57.611 37.500 0.00 0.00 0.00 2.73
3815 4396 7.504926 AACCTGAATTTACTGACCTGGTATA 57.495 36.000 0.00 0.00 0.00 1.47
3816 4397 7.125792 ACCTGAATTTACTGACCTGGTATAG 57.874 40.000 0.00 4.06 0.00 1.31
3817 4398 6.901300 ACCTGAATTTACTGACCTGGTATAGA 59.099 38.462 15.21 0.00 0.00 1.98
3818 4399 7.147707 ACCTGAATTTACTGACCTGGTATAGAC 60.148 40.741 15.21 0.00 0.00 2.59
3850 4431 1.484653 ACTGCTAACTGTGTGTGTCCA 59.515 47.619 0.00 0.00 0.00 4.02
3892 4473 1.523154 TTCGTACCTTGTACGCCGGT 61.523 55.000 19.00 5.93 40.40 5.28
3913 4494 0.673644 ATGGTTCTTCCTCAACGCGG 60.674 55.000 12.47 0.00 37.07 6.46
3921 4502 0.320374 TCCTCAACGCGGTCTTGAAT 59.680 50.000 12.47 0.00 0.00 2.57
3924 4505 2.412847 CCTCAACGCGGTCTTGAATTTC 60.413 50.000 12.47 0.00 0.00 2.17
4016 4597 8.412608 AGATGTTGTCTCAGTATTTGTAATCG 57.587 34.615 0.00 0.00 28.45 3.34
4033 4614 6.664515 TGTAATCGAATTTCACAACCACTTC 58.335 36.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.758936 AACTTAGTTAATGGCCGGGC 58.241 50.000 23.42 23.42 0.00 6.13
7 8 4.520179 AGTAAACTTAGTTAATGGCCGGG 58.480 43.478 2.18 0.00 0.00 5.73
8 9 4.573607 GGAGTAAACTTAGTTAATGGCCGG 59.426 45.833 0.00 0.00 0.00 6.13
9 10 5.064325 GTGGAGTAAACTTAGTTAATGGCCG 59.936 44.000 0.00 0.00 0.00 6.13
10 11 5.356190 GGTGGAGTAAACTTAGTTAATGGCC 59.644 44.000 0.00 0.00 0.00 5.36
11 12 5.064325 CGGTGGAGTAAACTTAGTTAATGGC 59.936 44.000 0.00 0.00 0.00 4.40
12 13 5.583457 CCGGTGGAGTAAACTTAGTTAATGG 59.417 44.000 0.00 0.00 0.00 3.16
13 14 5.064325 GCCGGTGGAGTAAACTTAGTTAATG 59.936 44.000 1.90 0.00 0.00 1.90
14 15 5.181009 GCCGGTGGAGTAAACTTAGTTAAT 58.819 41.667 1.90 0.00 0.00 1.40
15 16 4.563374 GGCCGGTGGAGTAAACTTAGTTAA 60.563 45.833 1.90 0.00 0.00 2.01
16 17 3.055891 GGCCGGTGGAGTAAACTTAGTTA 60.056 47.826 1.90 0.00 0.00 2.24
17 18 2.289882 GGCCGGTGGAGTAAACTTAGTT 60.290 50.000 1.90 0.00 0.00 2.24
18 19 1.277273 GGCCGGTGGAGTAAACTTAGT 59.723 52.381 1.90 0.00 0.00 2.24
19 20 1.406477 GGGCCGGTGGAGTAAACTTAG 60.406 57.143 1.90 0.00 0.00 2.18
20 21 0.614812 GGGCCGGTGGAGTAAACTTA 59.385 55.000 1.90 0.00 0.00 2.24
21 22 1.377612 GGGCCGGTGGAGTAAACTT 59.622 57.895 1.90 0.00 0.00 2.66
22 23 2.599757 GGGGCCGGTGGAGTAAACT 61.600 63.158 1.90 0.00 0.00 2.66
23 24 2.045634 GGGGCCGGTGGAGTAAAC 60.046 66.667 1.90 0.00 0.00 2.01
24 25 1.844544 GAAGGGGCCGGTGGAGTAAA 61.845 60.000 1.90 0.00 0.00 2.01
25 26 2.204029 AAGGGGCCGGTGGAGTAA 60.204 61.111 1.90 0.00 0.00 2.24
26 27 2.686106 GAAGGGGCCGGTGGAGTA 60.686 66.667 1.90 0.00 0.00 2.59
27 28 4.974438 TGAAGGGGCCGGTGGAGT 62.974 66.667 1.90 0.00 0.00 3.85
28 29 2.706952 TTTTGAAGGGGCCGGTGGAG 62.707 60.000 1.90 0.00 0.00 3.86
29 30 2.299727 TTTTTGAAGGGGCCGGTGGA 62.300 55.000 1.90 0.00 0.00 4.02
30 31 1.834822 TTTTTGAAGGGGCCGGTGG 60.835 57.895 1.90 0.00 0.00 4.61
31 32 3.863606 TTTTTGAAGGGGCCGGTG 58.136 55.556 1.90 0.00 0.00 4.94
51 52 1.958579 GGCCGGTGGAGTAAACTTTTT 59.041 47.619 1.90 0.00 0.00 1.94
52 53 1.612676 GGCCGGTGGAGTAAACTTTT 58.387 50.000 1.90 0.00 0.00 2.27
53 54 0.604511 CGGCCGGTGGAGTAAACTTT 60.605 55.000 20.10 0.00 0.00 2.66
54 55 1.004200 CGGCCGGTGGAGTAAACTT 60.004 57.895 20.10 0.00 0.00 2.66
55 56 1.474332 TTCGGCCGGTGGAGTAAACT 61.474 55.000 27.83 0.00 0.00 2.66
56 57 1.004679 TTCGGCCGGTGGAGTAAAC 60.005 57.895 27.83 0.00 0.00 2.01
57 58 1.004679 GTTCGGCCGGTGGAGTAAA 60.005 57.895 27.83 6.40 0.00 2.01
58 59 1.880819 GAGTTCGGCCGGTGGAGTAA 61.881 60.000 27.83 7.28 0.00 2.24
165 170 2.750888 GGAAGCAACGTGGATCGGC 61.751 63.158 0.00 0.00 44.69 5.54
167 175 1.787847 GTGGAAGCAACGTGGATCG 59.212 57.895 0.00 0.00 46.00 3.69
187 195 4.016444 TGATACCACAAAGGAAAGGATGC 58.984 43.478 0.00 0.00 41.22 3.91
193 201 5.303333 GGGAAACTTGATACCACAAAGGAAA 59.697 40.000 0.00 0.00 41.22 3.13
194 202 4.830600 GGGAAACTTGATACCACAAAGGAA 59.169 41.667 0.00 0.00 41.22 3.36
195 203 4.141135 TGGGAAACTTGATACCACAAAGGA 60.141 41.667 0.00 0.00 41.22 3.36
196 204 4.148838 TGGGAAACTTGATACCACAAAGG 58.851 43.478 0.00 0.00 45.67 3.11
202 210 2.622977 GGGCATGGGAAACTTGATACCA 60.623 50.000 0.00 0.00 35.39 3.25
210 218 2.355115 GACGGGGCATGGGAAACT 59.645 61.111 0.00 0.00 0.00 2.66
235 243 3.112709 GCCAGCGGAGTTCACGTC 61.113 66.667 0.00 0.00 0.00 4.34
324 332 2.892374 ACTTTGCCACTTTTGTTGCTC 58.108 42.857 0.00 0.00 41.15 4.26
347 355 3.977244 GCTTTGTGCGTGGGGGTG 61.977 66.667 0.00 0.00 0.00 4.61
375 387 1.735376 CTCGGATTGGACGGACGGAT 61.735 60.000 0.00 0.00 0.00 4.18
383 395 3.554692 CGCGCACTCGGATTGGAC 61.555 66.667 8.75 0.00 35.95 4.02
384 396 3.982372 GACGCGCACTCGGATTGGA 62.982 63.158 5.73 0.00 35.95 3.53
385 397 3.554692 GACGCGCACTCGGATTGG 61.555 66.667 5.73 0.00 35.95 3.16
386 398 3.554692 GGACGCGCACTCGGATTG 61.555 66.667 5.73 0.00 35.95 2.67
387 399 3.989698 CTGGACGCGCACTCGGATT 62.990 63.158 5.73 0.00 35.95 3.01
388 400 4.498520 CTGGACGCGCACTCGGAT 62.499 66.667 5.73 0.00 35.95 4.18
392 404 4.724602 TCTGCTGGACGCGCACTC 62.725 66.667 5.73 0.00 43.27 3.51
393 405 4.731612 CTCTGCTGGACGCGCACT 62.732 66.667 5.73 0.00 43.27 4.40
394 406 4.724602 TCTCTGCTGGACGCGCAC 62.725 66.667 5.73 0.00 43.27 5.34
395 407 4.426112 CTCTCTGCTGGACGCGCA 62.426 66.667 5.73 0.00 43.27 6.09
396 408 4.121669 TCTCTCTGCTGGACGCGC 62.122 66.667 5.73 0.00 43.27 6.86
397 409 2.101965 CTCTCTCTGCTGGACGCG 59.898 66.667 3.53 3.53 43.27 6.01
398 410 2.202730 GCTCTCTCTGCTGGACGC 60.203 66.667 0.00 0.00 39.77 5.19
399 411 2.051518 AGGCTCTCTCTGCTGGACG 61.052 63.158 0.00 0.00 0.00 4.79
400 412 1.516892 CAGGCTCTCTCTGCTGGAC 59.483 63.158 0.00 0.00 0.00 4.02
461 511 4.148891 CGAGTTTCTTTCACCGCAATTAC 58.851 43.478 0.00 0.00 0.00 1.89
476 526 2.357034 TGCGTCCCTGCGAGTTTC 60.357 61.111 0.00 0.00 37.81 2.78
477 527 2.665185 GTGCGTCCCTGCGAGTTT 60.665 61.111 0.00 0.00 37.81 2.66
488 538 1.492319 TTTACCACTGTGCGTGCGTC 61.492 55.000 1.29 0.00 42.42 5.19
492 542 1.870402 TGATGTTTACCACTGTGCGTG 59.130 47.619 1.29 0.00 43.41 5.34
496 546 3.362596 CGTCGTTGATGTTTACCACTGTG 60.363 47.826 0.00 0.00 0.00 3.66
539 594 1.224069 CGGTCTGTGGTTGCTGTCAG 61.224 60.000 0.00 0.00 0.00 3.51
540 595 1.227527 CGGTCTGTGGTTGCTGTCA 60.228 57.895 0.00 0.00 0.00 3.58
541 596 1.961277 CCGGTCTGTGGTTGCTGTC 60.961 63.158 0.00 0.00 0.00 3.51
542 597 2.111043 CCGGTCTGTGGTTGCTGT 59.889 61.111 0.00 0.00 0.00 4.40
543 598 1.669115 CTCCGGTCTGTGGTTGCTG 60.669 63.158 0.00 0.00 0.00 4.41
544 599 2.743718 CTCCGGTCTGTGGTTGCT 59.256 61.111 0.00 0.00 0.00 3.91
545 600 3.050275 GCTCCGGTCTGTGGTTGC 61.050 66.667 0.00 0.00 0.00 4.17
628 1100 4.689549 TTCCACGGGAGCGAGGGA 62.690 66.667 0.00 0.00 31.21 4.20
629 1101 2.741486 TTTTTCCACGGGAGCGAGGG 62.741 60.000 0.00 0.00 31.21 4.30
632 1104 0.601841 GAGTTTTTCCACGGGAGCGA 60.602 55.000 0.00 0.00 31.21 4.93
633 1105 0.602905 AGAGTTTTTCCACGGGAGCG 60.603 55.000 0.00 0.00 31.21 5.03
634 1106 1.157585 GAGAGTTTTTCCACGGGAGC 58.842 55.000 0.00 0.00 31.21 4.70
643 1118 2.030185 GCGGAAAAGGGGAGAGTTTTTC 60.030 50.000 1.42 1.42 39.11 2.29
657 1132 1.076014 GAAAGGGGGAGGCGGAAAA 59.924 57.895 0.00 0.00 0.00 2.29
658 1133 1.432023 AAGAAAGGGGGAGGCGGAAA 61.432 55.000 0.00 0.00 0.00 3.13
659 1134 1.432023 AAAGAAAGGGGGAGGCGGAA 61.432 55.000 0.00 0.00 0.00 4.30
660 1135 1.848886 GAAAGAAAGGGGGAGGCGGA 61.849 60.000 0.00 0.00 0.00 5.54
661 1136 1.378646 GAAAGAAAGGGGGAGGCGG 60.379 63.158 0.00 0.00 0.00 6.13
662 1137 1.378646 GGAAAGAAAGGGGGAGGCG 60.379 63.158 0.00 0.00 0.00 5.52
663 1138 0.114364 TTGGAAAGAAAGGGGGAGGC 59.886 55.000 0.00 0.00 0.00 4.70
741 1248 2.348998 GAGAGGTGGGTGCTGTGG 59.651 66.667 0.00 0.00 0.00 4.17
744 1251 4.087892 CCGGAGAGGTGGGTGCTG 62.088 72.222 0.00 0.00 34.51 4.41
811 1344 0.723790 CGTACTACTTATCCGGCGCG 60.724 60.000 0.00 0.00 0.00 6.86
815 1348 2.349249 CGAGTGCGTACTACTTATCCGG 60.349 54.545 6.01 0.00 37.25 5.14
889 1452 1.675641 GGCTCGCAGGAATTGGTGT 60.676 57.895 0.00 0.00 0.00 4.16
891 1454 1.377725 CTGGCTCGCAGGAATTGGT 60.378 57.895 0.00 0.00 0.00 3.67
893 1456 1.712977 GCTCTGGCTCGCAGGAATTG 61.713 60.000 0.00 0.00 35.22 2.32
987 1558 3.168528 CCCATCCCCCGGTGGTAG 61.169 72.222 1.78 0.00 33.55 3.18
993 1564 4.918360 TCCATCCCCATCCCCCGG 62.918 72.222 0.00 0.00 0.00 5.73
1488 2059 1.674651 GGGGACGCCCTTGAGTTTC 60.675 63.158 13.58 0.00 44.66 2.78
2079 2650 3.190118 GGTTGAAGTCCAATCTGAGCTTG 59.810 47.826 0.00 0.00 37.08 4.01
2226 2797 3.731728 TCAGCTGGGGGTGGCATC 61.732 66.667 15.13 0.00 40.89 3.91
2460 3031 6.070938 TGTTCATCATGAAGAGAGATGACAGT 60.071 38.462 0.00 0.00 45.47 3.55
2490 3061 0.944386 GGTGCTTGAAGAAGTGCGAA 59.056 50.000 0.00 0.00 0.00 4.70
2517 3088 5.736951 CTAAGATCTCCCCCATCTTAGTG 57.263 47.826 16.43 0.14 46.78 2.74
2590 3161 2.305927 CCCAGCTCTCCCTTAGAAACAA 59.694 50.000 0.00 0.00 32.46 2.83
2907 3480 2.706339 AGAGGGTGCTAAGCATCTTG 57.294 50.000 0.00 0.00 41.90 3.02
3059 3633 7.246171 ACACTACTGTACATCCAATCTTTCT 57.754 36.000 0.00 0.00 0.00 2.52
3278 3852 1.073706 GATCTAGGGGAAGGGGGCA 60.074 63.158 0.00 0.00 0.00 5.36
3300 3874 9.311916 GAATGCTAGAGATAAGAATGCGAATAT 57.688 33.333 0.00 0.00 0.00 1.28
3302 3876 7.157347 TGAATGCTAGAGATAAGAATGCGAAT 58.843 34.615 0.00 0.00 0.00 3.34
3339 3913 6.016610 GCTCCACACATAAGTTTCCTAAAACA 60.017 38.462 4.09 0.00 45.94 2.83
3467 4041 4.617253 TTGTCACAGGCAGTAATACACT 57.383 40.909 0.00 0.00 38.32 3.55
3468 4042 5.682943 TTTTGTCACAGGCAGTAATACAC 57.317 39.130 0.00 0.00 0.00 2.90
3469 4043 6.488344 TCATTTTTGTCACAGGCAGTAATACA 59.512 34.615 0.00 0.00 0.00 2.29
3470 4044 6.801862 GTCATTTTTGTCACAGGCAGTAATAC 59.198 38.462 0.00 0.00 0.00 1.89
3514 4094 3.825328 AGACTGTTTTCTTGCCTCATGT 58.175 40.909 0.00 0.00 0.00 3.21
3561 4141 6.920569 AGTGCGTAAAGAGAAAGAAAGAAA 57.079 33.333 0.00 0.00 0.00 2.52
3610 4191 8.952278 AGAGCATACAGAAGTAGCAGTATATAC 58.048 37.037 4.60 4.60 32.86 1.47
3614 4195 5.596361 ACAGAGCATACAGAAGTAGCAGTAT 59.404 40.000 0.00 0.00 32.86 2.12
3615 4196 4.950475 ACAGAGCATACAGAAGTAGCAGTA 59.050 41.667 0.00 0.00 32.86 2.74
3713 4294 3.626930 TCACCAAGCAAGGTAAACTGTT 58.373 40.909 0.00 0.00 40.77 3.16
3778 4359 8.421002 AGTAAATTCAGGTTACATTGCAAAGTT 58.579 29.630 13.15 0.00 34.50 2.66
3779 4360 7.867403 CAGTAAATTCAGGTTACATTGCAAAGT 59.133 33.333 12.50 12.50 34.50 2.66
3780 4361 8.081633 TCAGTAAATTCAGGTTACATTGCAAAG 58.918 33.333 1.71 0.19 34.50 2.77
3781 4362 7.865385 GTCAGTAAATTCAGGTTACATTGCAAA 59.135 33.333 1.71 0.00 34.50 3.68
3782 4363 7.367285 GTCAGTAAATTCAGGTTACATTGCAA 58.633 34.615 0.00 0.00 34.50 4.08
3783 4364 6.072175 GGTCAGTAAATTCAGGTTACATTGCA 60.072 38.462 0.00 0.00 34.50 4.08
3784 4365 6.151144 AGGTCAGTAAATTCAGGTTACATTGC 59.849 38.462 0.00 0.00 34.50 3.56
3785 4366 7.362056 CCAGGTCAGTAAATTCAGGTTACATTG 60.362 40.741 0.00 0.00 34.50 2.82
3786 4367 6.659242 CCAGGTCAGTAAATTCAGGTTACATT 59.341 38.462 0.00 0.00 34.50 2.71
3787 4368 6.180472 CCAGGTCAGTAAATTCAGGTTACAT 58.820 40.000 0.00 0.00 34.50 2.29
3788 4369 5.072600 ACCAGGTCAGTAAATTCAGGTTACA 59.927 40.000 0.00 0.00 34.50 2.41
3789 4370 5.557866 ACCAGGTCAGTAAATTCAGGTTAC 58.442 41.667 0.00 0.00 0.00 2.50
3790 4371 5.836024 ACCAGGTCAGTAAATTCAGGTTA 57.164 39.130 0.00 0.00 0.00 2.85
3791 4372 4.724279 ACCAGGTCAGTAAATTCAGGTT 57.276 40.909 0.00 0.00 0.00 3.50
3792 4373 6.901300 TCTATACCAGGTCAGTAAATTCAGGT 59.099 38.462 0.00 0.00 0.00 4.00
3793 4374 7.070074 AGTCTATACCAGGTCAGTAAATTCAGG 59.930 40.741 0.00 0.00 0.00 3.86
3794 4375 8.012957 AGTCTATACCAGGTCAGTAAATTCAG 57.987 38.462 0.00 0.00 0.00 3.02
3795 4376 7.973048 AGTCTATACCAGGTCAGTAAATTCA 57.027 36.000 0.00 0.00 0.00 2.57
3796 4377 9.099454 CAAAGTCTATACCAGGTCAGTAAATTC 57.901 37.037 0.00 0.00 0.00 2.17
3797 4378 7.553044 GCAAAGTCTATACCAGGTCAGTAAATT 59.447 37.037 0.00 0.00 0.00 1.82
3798 4379 7.048512 GCAAAGTCTATACCAGGTCAGTAAAT 58.951 38.462 0.00 0.00 0.00 1.40
3799 4380 6.014070 TGCAAAGTCTATACCAGGTCAGTAAA 60.014 38.462 0.00 0.00 0.00 2.01
3800 4381 5.482526 TGCAAAGTCTATACCAGGTCAGTAA 59.517 40.000 0.00 0.00 0.00 2.24
3801 4382 5.020795 TGCAAAGTCTATACCAGGTCAGTA 58.979 41.667 0.00 0.00 0.00 2.74
3802 4383 3.838317 TGCAAAGTCTATACCAGGTCAGT 59.162 43.478 0.00 0.00 0.00 3.41
3803 4384 4.471904 TGCAAAGTCTATACCAGGTCAG 57.528 45.455 0.00 0.00 0.00 3.51
3804 4385 4.901197 TTGCAAAGTCTATACCAGGTCA 57.099 40.909 0.00 0.00 0.00 4.02
3805 4386 4.035675 GCATTGCAAAGTCTATACCAGGTC 59.964 45.833 1.71 0.00 0.00 3.85
3806 4387 3.947834 GCATTGCAAAGTCTATACCAGGT 59.052 43.478 1.71 0.00 0.00 4.00
3807 4388 3.947196 TGCATTGCAAAGTCTATACCAGG 59.053 43.478 9.33 0.00 34.76 4.45
3808 4389 5.565592 TTGCATTGCAAAGTCTATACCAG 57.434 39.130 21.24 0.00 45.96 4.00
3850 4431 4.963318 TTCAGTCCATTCTTCTGTGACT 57.037 40.909 0.00 0.00 36.77 3.41
3892 4473 1.808411 GCGTTGAGGAAGAACCATCA 58.192 50.000 0.00 0.00 42.04 3.07
3913 4494 8.475331 AATCATGCTCAATTGAAATTCAAGAC 57.525 30.769 14.10 2.69 40.05 3.01


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

AutoCloner maintained by Alex Coulton.