Multiple sequence alignment - TraesCS1A01G163200

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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 TraesCS1A01G163200 chr1A 100.000 4632 0 0 1 4632 292882737 292878106 0.000000e+00 8554
1 TraesCS1A01G163200 chr1B 92.351 4040 203 37 1 3979 324777676 324781670 0.000000e+00 5651
2 TraesCS1A01G163200 chr1B 94.295 298 13 2 4336 4629 324790283 324790580 1.960000e-123 453
3 TraesCS1A01G163200 chr1B 93.382 272 17 1 4021 4291 324789701 324789972 7.220000e-108 401
4 TraesCS1A01G163200 chr1B 93.976 83 5 0 3897 3979 324781790 324781872 4.870000e-25 126
5 TraesCS1A01G163200 chr1D 95.576 2170 79 7 831 2995 225059099 225061256 0.000000e+00 3459
6 TraesCS1A01G163200 chr1D 92.909 959 47 9 3037 3991 225061259 225062200 0.000000e+00 1375
7 TraesCS1A01G163200 chr1D 94.703 623 25 3 4015 4632 225062423 225063042 0.000000e+00 961
8 TraesCS1A01G163200 chr1D 92.157 204 15 1 1 204 225002954 225003156 2.110000e-73 287
9 TraesCS1A01G163200 chr1D 81.122 392 34 17 193 546 225003171 225003560 1.270000e-70 278
10 TraesCS1A01G163200 chr1D 87.234 188 20 2 508 695 225038711 225038894 1.310000e-50 211
11 TraesCS1A01G163200 chr4A 91.453 117 7 3 770 885 582505979 582505865 1.730000e-34 158
12 TraesCS1A01G163200 chr4B 93.750 96 5 1 791 885 30842652 30842747 4.830000e-30 143
13 TraesCS1A01G163200 chr4B 92.708 96 6 1 788 882 30841018 30841113 2.250000e-28 137
14 TraesCS1A01G163200 chr4D 96.341 82 3 0 805 886 18735311 18735392 8.080000e-28 135
15 TraesCS1A01G163200 chr4D 91.209 91 4 2 791 881 18734056 18734142 2.260000e-23 121
16 TraesCS1A01G163200 chr5A 92.500 80 6 0 806 885 510463908 510463987 1.050000e-21 115
17 TraesCS1A01G163200 chr6D 92.405 79 5 1 806 884 306137321 306137398 1.360000e-20 111


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 TraesCS1A01G163200 chr1A 292878106 292882737 4631 True 8554.000000 8554 100.0000 1 4632 1 chr1A.!!$R1 4631
1 TraesCS1A01G163200 chr1B 324777676 324781872 4196 False 2888.500000 5651 93.1635 1 3979 2 chr1B.!!$F1 3978
2 TraesCS1A01G163200 chr1B 324789701 324790580 879 False 427.000000 453 93.8385 4021 4629 2 chr1B.!!$F2 608
3 TraesCS1A01G163200 chr1D 225059099 225063042 3943 False 1931.666667 3459 94.3960 831 4632 3 chr1D.!!$F3 3801
4 TraesCS1A01G163200 chr1D 225002954 225003560 606 False 282.500000 287 86.6395 1 546 2 chr1D.!!$F2 545

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
561 626 1.001860 AGGTCAAGCAGCAGAGAAGAC 59.998 52.381 0.00 0.0 0.0 3.01 F
1308 1412 0.811616 CCATCTTCTCGCCCTTTCCG 60.812 60.000 0.00 0.0 0.0 4.30 F
1319 1423 1.228429 CCTTTCCGCTGGGGTTTGA 60.228 57.895 10.81 0.0 37.0 2.69 F
3133 3242 0.543749 CATCCCCCTCCACTGAACTC 59.456 60.000 0.00 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2539 2647 1.217001 TGAGCAGTTGCACTAACACG 58.783 50.000 6.9 0.0 45.16 4.49 R
3113 3222 0.178861 AGTTCAGTGGAGGGGGATGT 60.179 55.000 0.0 0.0 0.00 3.06 R
3264 3373 1.203052 CTTTTTGGTCGCCATCTGCAT 59.797 47.619 0.0 0.0 41.33 3.96 R
4001 4325 0.107643 TGCACATGTTGGTTCTCGGA 59.892 50.000 0.0 0.0 0.00 4.55 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
190 191 4.147653 TCTTCGTTGAATCGTCGAAAGAAC 59.852 41.667 0.00 1.50 45.01 3.01
204 205 6.853872 CGTCGAAAGAACCAAATTGATAAACA 59.146 34.615 0.00 0.00 45.01 2.83
219 246 5.803552 TGATAAACATGAGTGTGTGGATCA 58.196 37.500 0.00 0.00 38.92 2.92
247 274 8.003784 GCAACAAAGTTCATTCGGAAATAAAAG 58.996 33.333 0.00 0.00 37.23 2.27
266 293 1.628846 AGGATGTTCCTTAGTTGGCGT 59.371 47.619 0.00 0.00 46.91 5.68
308 335 6.594788 ATGCAGACCATGAACTTGTAAATT 57.405 33.333 0.00 0.00 31.48 1.82
310 337 5.534278 TGCAGACCATGAACTTGTAAATTGA 59.466 36.000 0.00 0.00 0.00 2.57
316 343 6.092092 CCATGAACTTGTAAATTGATCGCAA 58.908 36.000 0.00 0.00 38.60 4.85
317 344 6.252015 CCATGAACTTGTAAATTGATCGCAAG 59.748 38.462 0.00 0.00 41.40 4.01
368 404 6.302269 AGGGTTTCCATCAGATGATATGAAC 58.698 40.000 12.41 8.39 32.63 3.18
421 486 3.668141 TGTGAGCCCATGGTGAATAAT 57.332 42.857 11.73 0.00 0.00 1.28
470 535 6.443792 AGTAAAAGCAAAAATTACCTGTCGG 58.556 36.000 0.00 0.00 31.43 4.79
506 571 5.452078 TCCATCAAACTTTGCTCGAAAAT 57.548 34.783 0.00 0.00 0.00 1.82
550 615 4.507710 CAATAAGCAGAGTAGGTCAAGCA 58.492 43.478 0.00 0.00 32.44 3.91
554 619 2.006056 GCAGAGTAGGTCAAGCAGCAG 61.006 57.143 0.00 0.00 0.00 4.24
561 626 1.001860 AGGTCAAGCAGCAGAGAAGAC 59.998 52.381 0.00 0.00 0.00 3.01
576 641 4.219288 AGAGAAGACAAATTGTGGGAATGC 59.781 41.667 2.20 0.00 0.00 3.56
579 644 2.299867 AGACAAATTGTGGGAATGCCAC 59.700 45.455 17.42 17.42 38.52 5.01
582 647 2.208132 AATTGTGGGAATGCCACGTA 57.792 45.000 18.86 9.98 40.66 3.57
585 650 2.208132 TGTGGGAATGCCACGTAAAT 57.792 45.000 18.86 0.00 40.66 1.40
591 656 4.638421 TGGGAATGCCACGTAAATAGAAAG 59.362 41.667 0.00 0.00 35.15 2.62
600 665 6.128526 GCCACGTAAATAGAAAGGCTATGATC 60.129 42.308 0.00 0.00 39.73 2.92
612 677 9.064706 AGAAAGGCTATGATCAAAGAACATATG 57.935 33.333 0.00 0.00 29.49 1.78
616 681 8.095792 AGGCTATGATCAAAGAACATATGAGAG 58.904 37.037 10.38 0.00 29.49 3.20
626 691 9.003658 CAAAGAACATATGAGAGGTTGTAAAGT 57.996 33.333 10.38 0.00 30.59 2.66
672 737 7.872483 GAAAATATTCAGATGGAGACTCTCTCC 59.128 40.741 10.89 10.89 46.93 3.71
747 845 7.945033 AAATTACAAATCGTTGCAAGTGAAT 57.055 28.000 0.00 0.00 38.39 2.57
749 847 3.641648 ACAAATCGTTGCAAGTGAATGG 58.358 40.909 0.00 0.00 38.39 3.16
759 857 3.069872 TGCAAGTGAATGGCAAATTGTCT 59.930 39.130 0.00 0.00 34.05 3.41
760 858 4.060205 GCAAGTGAATGGCAAATTGTCTT 58.940 39.130 0.00 0.00 31.45 3.01
761 859 5.221402 TGCAAGTGAATGGCAAATTGTCTTA 60.221 36.000 0.00 0.00 34.05 2.10
762 860 5.346822 GCAAGTGAATGGCAAATTGTCTTAG 59.653 40.000 0.00 0.00 31.45 2.18
763 861 6.449698 CAAGTGAATGGCAAATTGTCTTAGT 58.550 36.000 0.00 0.00 0.00 2.24
765 863 5.183904 AGTGAATGGCAAATTGTCTTAGTCC 59.816 40.000 0.00 0.00 0.00 3.85
768 866 6.267471 TGAATGGCAAATTGTCTTAGTCCTTT 59.733 34.615 0.00 0.00 0.00 3.11
769 867 7.450014 TGAATGGCAAATTGTCTTAGTCCTTTA 59.550 33.333 0.00 0.00 0.00 1.85
770 868 7.775053 ATGGCAAATTGTCTTAGTCCTTTAA 57.225 32.000 0.00 0.00 0.00 1.52
940 1044 5.801350 AACCACGATGTTGATTATGTCTG 57.199 39.130 0.00 0.00 0.00 3.51
944 1048 3.310774 ACGATGTTGATTATGTCTGCTGC 59.689 43.478 0.00 0.00 0.00 5.25
1269 1373 1.001269 GCCTCACCCAACCCTAACC 60.001 63.158 0.00 0.00 0.00 2.85
1271 1375 1.298667 CTCACCCAACCCTAACCCG 59.701 63.158 0.00 0.00 0.00 5.28
1274 1378 1.229593 ACCCAACCCTAACCCGCTA 60.230 57.895 0.00 0.00 0.00 4.26
1308 1412 0.811616 CCATCTTCTCGCCCTTTCCG 60.812 60.000 0.00 0.00 0.00 4.30
1310 1414 1.617947 ATCTTCTCGCCCTTTCCGCT 61.618 55.000 0.00 0.00 0.00 5.52
1319 1423 1.228429 CCTTTCCGCTGGGGTTTGA 60.228 57.895 10.81 0.00 37.00 2.69
1390 1494 2.799371 CTCACGGCGTCCCTCTAC 59.201 66.667 10.85 0.00 0.00 2.59
1393 1497 3.437795 ACGGCGTCCCTCTACGTG 61.438 66.667 6.77 0.00 44.64 4.49
1538 1642 6.154203 ACTTCAGCGAATCTCTCAATATGA 57.846 37.500 0.00 0.00 0.00 2.15
1564 1668 6.539826 TGATACAAACTGGTCATGAGCTTATG 59.460 38.462 24.30 18.59 0.00 1.90
1583 1689 8.795786 GCTTATGAGCTTCTTCGGATATATAG 57.204 38.462 1.49 0.00 45.65 1.31
1646 1752 9.258826 CATTTTGATATTCAGGAAAAACACACA 57.741 29.630 0.00 0.00 0.00 3.72
1651 1757 8.637099 TGATATTCAGGAAAAACACACAATCAA 58.363 29.630 0.00 0.00 0.00 2.57
1687 1793 3.821033 AGTTGCCATGAAAGTTCCACTAC 59.179 43.478 0.00 0.00 0.00 2.73
1767 1873 1.882623 CCTTGTTTGGTGAGGAGAAGC 59.117 52.381 0.00 0.00 32.11 3.86
2182 2290 3.181434 TGGAGGACAAATGTTAGCCTGTT 60.181 43.478 0.00 0.00 0.00 3.16
2360 2468 4.981674 GTGCTTTAAGCTTGTAACATGCAA 59.018 37.500 18.20 0.00 42.97 4.08
2421 2529 4.814234 GTCTTGACTTGTGTTGACATACCA 59.186 41.667 0.00 0.00 30.13 3.25
2761 2870 8.692110 AAGCATGTTACAAATATGACATTGTG 57.308 30.769 0.00 0.00 39.89 3.33
2995 3104 7.159372 ACGAACCTAGTATTTGATTGTCAGTT 58.841 34.615 0.00 0.00 0.00 3.16
3093 3202 6.599244 TCTCTATTTGGAAGGCACAACTTATG 59.401 38.462 0.00 0.00 0.00 1.90
3113 3222 0.958822 TTGAGCTACACTGCGACTCA 59.041 50.000 0.00 0.00 38.13 3.41
3133 3242 0.543749 CATCCCCCTCCACTGAACTC 59.456 60.000 0.00 0.00 0.00 3.01
3264 3373 7.234166 TGGCAGATGATCACTCTATTCTTCATA 59.766 37.037 0.00 0.00 0.00 2.15
3299 3408 5.259632 ACCAAAAAGAAGAGCATAGCAGAT 58.740 37.500 0.00 0.00 0.00 2.90
3367 3476 1.209383 CGAGTTCGTGAGAGCGGAA 59.791 57.895 0.00 0.00 46.75 4.30
3394 3503 0.032540 CCTGTCCCTTGCTTTGTTGC 59.967 55.000 0.00 0.00 0.00 4.17
3395 3504 0.032540 CTGTCCCTTGCTTTGTTGCC 59.967 55.000 0.00 0.00 0.00 4.52
3396 3505 0.396974 TGTCCCTTGCTTTGTTGCCT 60.397 50.000 0.00 0.00 0.00 4.75
3397 3506 0.752658 GTCCCTTGCTTTGTTGCCTT 59.247 50.000 0.00 0.00 0.00 4.35
3398 3507 0.752054 TCCCTTGCTTTGTTGCCTTG 59.248 50.000 0.00 0.00 0.00 3.61
3399 3508 0.465287 CCCTTGCTTTGTTGCCTTGT 59.535 50.000 0.00 0.00 0.00 3.16
3400 3509 1.134431 CCCTTGCTTTGTTGCCTTGTT 60.134 47.619 0.00 0.00 0.00 2.83
3401 3510 1.935199 CCTTGCTTTGTTGCCTTGTTG 59.065 47.619 0.00 0.00 0.00 3.33
3515 3624 2.185004 TTACTGAAACAGCCTGCTCC 57.815 50.000 0.00 0.00 34.37 4.70
3548 3657 6.653989 ACTTCATCCTCGAGTAATTTGGAAT 58.346 36.000 12.31 0.00 0.00 3.01
3566 3675 3.434299 GGAATTCGGTATCAAACGTGTGT 59.566 43.478 5.45 0.00 0.00 3.72
3654 3766 4.875536 GTCTGGATGCTTGGTTTTGTTTTT 59.124 37.500 0.00 0.00 0.00 1.94
3671 3783 2.312722 TTTGCATGCTGTTGTTGCTT 57.687 40.000 20.33 0.00 37.28 3.91
3690 3802 4.707448 TGCTTTTCCTGGTACTTGTTGAAA 59.293 37.500 0.00 0.00 0.00 2.69
3696 3808 3.199677 CTGGTACTTGTTGAAACCGTCA 58.800 45.455 0.00 0.00 34.60 4.35
3697 3809 3.811083 TGGTACTTGTTGAAACCGTCAT 58.189 40.909 0.00 0.00 35.70 3.06
3771 3883 7.778853 TGTACCACTAAGTTGGGAATGTTAAAA 59.221 33.333 0.00 0.00 41.49 1.52
3824 3936 4.836825 ACAGTATGAGGAAGAACCACATG 58.163 43.478 0.00 0.00 46.43 3.21
3835 3947 5.242838 GGAAGAACCACATGGACACAAATTA 59.757 40.000 4.53 0.00 38.94 1.40
3979 4303 5.774690 TGCTCAATGGTTTTGAGGAAGTTAT 59.225 36.000 15.07 0.00 42.53 1.89
3980 4304 6.267471 TGCTCAATGGTTTTGAGGAAGTTATT 59.733 34.615 15.07 0.00 42.53 1.40
3981 4305 7.450014 TGCTCAATGGTTTTGAGGAAGTTATTA 59.550 33.333 15.07 0.00 42.53 0.98
3982 4306 8.303876 GCTCAATGGTTTTGAGGAAGTTATTAA 58.696 33.333 15.07 0.00 44.46 1.40
3988 4312 8.581578 TGGTTTTGAGGAAGTTATTAAATGTCC 58.418 33.333 0.00 0.00 0.00 4.02
3989 4313 8.581578 GGTTTTGAGGAAGTTATTAAATGTCCA 58.418 33.333 0.00 0.00 0.00 4.02
3994 4318 8.044309 TGAGGAAGTTATTAAATGTCCATCGAA 58.956 33.333 0.00 0.00 0.00 3.71
3995 4319 8.209917 AGGAAGTTATTAAATGTCCATCGAAC 57.790 34.615 0.00 0.00 0.00 3.95
3996 4320 7.827236 AGGAAGTTATTAAATGTCCATCGAACA 59.173 33.333 0.00 0.00 0.00 3.18
3997 4321 8.122952 GGAAGTTATTAAATGTCCATCGAACAG 58.877 37.037 0.00 0.00 0.00 3.16
3998 4322 7.016361 AGTTATTAAATGTCCATCGAACAGC 57.984 36.000 0.00 0.00 0.00 4.40
3999 4323 4.900635 ATTAAATGTCCATCGAACAGCC 57.099 40.909 0.00 0.00 0.00 4.85
4000 4324 1.463674 AAATGTCCATCGAACAGCCC 58.536 50.000 0.00 0.00 0.00 5.19
4001 4325 0.620556 AATGTCCATCGAACAGCCCT 59.379 50.000 0.00 0.00 0.00 5.19
4004 4328 2.202932 CCATCGAACAGCCCTCCG 60.203 66.667 0.00 0.00 0.00 4.63
4005 4329 2.721167 CCATCGAACAGCCCTCCGA 61.721 63.158 0.00 0.00 35.43 4.55
4006 4330 1.227089 CATCGAACAGCCCTCCGAG 60.227 63.158 0.00 0.00 34.40 4.63
4008 4332 0.970937 ATCGAACAGCCCTCCGAGAA 60.971 55.000 0.00 0.00 34.40 2.87
4011 4335 1.827399 GAACAGCCCTCCGAGAACCA 61.827 60.000 0.00 0.00 0.00 3.67
4014 4338 1.841556 AGCCCTCCGAGAACCAACA 60.842 57.895 0.00 0.00 0.00 3.33
4015 4339 1.201429 AGCCCTCCGAGAACCAACAT 61.201 55.000 0.00 0.00 0.00 2.71
4016 4340 1.026718 GCCCTCCGAGAACCAACATG 61.027 60.000 0.00 0.00 0.00 3.21
4037 4558 1.994467 CACGCTCGAATCTGCTGAC 59.006 57.895 0.00 0.00 0.00 3.51
4054 4575 3.858877 GCTGACCAATATCGCTACTGAGG 60.859 52.174 0.00 0.00 0.00 3.86
4072 4593 1.740296 GTGCGTACATGGGCGTCTT 60.740 57.895 11.68 0.00 0.00 3.01
4077 4598 1.519408 GTACATGGGCGTCTTGTGTT 58.481 50.000 0.00 0.00 35.66 3.32
4095 4616 2.622942 TGTTCCCAATCAAGAACACAGC 59.377 45.455 1.63 0.00 45.53 4.40
4100 4621 3.087031 CCAATCAAGAACACAGCCATCT 58.913 45.455 0.00 0.00 0.00 2.90
4182 4704 9.541143 CTTCTATATCCTTTTTGTCTTCCTCTC 57.459 37.037 0.00 0.00 0.00 3.20
4219 4741 7.153985 TCAAGCTTGATTGGAAATAAACCTTG 58.846 34.615 25.16 0.00 31.01 3.61
4256 4778 2.409870 GCAGGGAAGGAATGCCACG 61.410 63.158 0.00 0.00 43.29 4.94
4278 4800 8.697067 CCACGTCTTATACCAGTATAAAAATCG 58.303 37.037 10.59 12.88 37.51 3.34
4362 5150 2.682856 TGAAGGTTGACAGCTTGTTCAC 59.317 45.455 0.00 0.00 40.97 3.18
4368 5156 4.275936 GGTTGACAGCTTGTTCACAGTAAT 59.724 41.667 0.00 0.00 0.00 1.89
4395 5183 5.353394 AAGGTTCACAGACTACTCAACAA 57.647 39.130 0.00 0.00 0.00 2.83
4521 5313 2.534298 CGAGATATGATGGCATCGTCC 58.466 52.381 24.68 17.24 35.94 4.79
4522 5314 2.165234 CGAGATATGATGGCATCGTCCT 59.835 50.000 24.68 21.12 35.94 3.85
4523 5315 3.367806 CGAGATATGATGGCATCGTCCTT 60.368 47.826 24.68 11.71 35.94 3.36
4531 5326 2.109126 GCATCGTCCTTCACCTGCC 61.109 63.158 0.00 0.00 0.00 4.85
4545 5340 1.106944 CCTGCCCAAAGGTTTCACGT 61.107 55.000 0.00 0.00 34.57 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 9.601810 TTCTTCTCCTGCTCCTAACATAATATA 57.398 33.333 0.00 0.00 0.00 0.86
154 155 7.413000 CGATTCAACGAAGAAGTCATTACCAAT 60.413 37.037 0.00 0.00 35.09 3.16
190 191 6.587226 CCACACACTCATGTTTATCAATTTGG 59.413 38.462 0.00 0.00 36.72 3.28
204 205 0.986527 TGCCTGATCCACACACTCAT 59.013 50.000 0.00 0.00 0.00 2.90
219 246 2.582052 TCCGAATGAACTTTGTTGCCT 58.418 42.857 0.00 0.00 0.00 4.75
247 274 2.109425 ACGCCAACTAAGGAACATCC 57.891 50.000 0.00 0.00 36.58 3.51
257 284 1.001181 GTGGTACTCCAACGCCAACTA 59.999 52.381 0.00 0.00 46.15 2.24
266 293 1.180456 TTCCTCGCGTGGTACTCCAA 61.180 55.000 25.10 9.60 46.15 3.53
308 335 3.089284 TCTACCTTGAGTCTTGCGATCA 58.911 45.455 0.00 0.00 0.00 2.92
310 337 4.744795 ATTCTACCTTGAGTCTTGCGAT 57.255 40.909 0.00 0.00 0.00 4.58
316 343 8.840200 TTTACCATCTATTCTACCTTGAGTCT 57.160 34.615 0.00 0.00 0.00 3.24
317 344 8.915036 TCTTTACCATCTATTCTACCTTGAGTC 58.085 37.037 0.00 0.00 0.00 3.36
319 346 9.757227 CTTCTTTACCATCTATTCTACCTTGAG 57.243 37.037 0.00 0.00 0.00 3.02
320 347 8.705594 CCTTCTTTACCATCTATTCTACCTTGA 58.294 37.037 0.00 0.00 0.00 3.02
321 348 7.934120 CCCTTCTTTACCATCTATTCTACCTTG 59.066 40.741 0.00 0.00 0.00 3.61
322 349 7.628101 ACCCTTCTTTACCATCTATTCTACCTT 59.372 37.037 0.00 0.00 0.00 3.50
368 404 5.717119 ACTTGCCATTTTAATCTTGCAGAG 58.283 37.500 0.00 0.00 0.00 3.35
498 563 6.424812 TCATAGGCATATGTGACATTTTCGAG 59.575 38.462 17.26 0.00 39.90 4.04
506 571 3.716601 CGTGTCATAGGCATATGTGACA 58.283 45.455 18.09 18.09 45.48 3.58
550 615 3.152341 CCCACAATTTGTCTTCTCTGCT 58.848 45.455 0.00 0.00 0.00 4.24
554 619 4.488879 GCATTCCCACAATTTGTCTTCTC 58.511 43.478 0.00 0.00 0.00 2.87
576 641 6.929049 TGATCATAGCCTTTCTATTTACGTGG 59.071 38.462 0.00 0.00 35.86 4.94
579 644 9.261180 TCTTTGATCATAGCCTTTCTATTTACG 57.739 33.333 8.19 0.00 35.86 3.18
582 647 9.466497 TGTTCTTTGATCATAGCCTTTCTATTT 57.534 29.630 8.19 0.00 35.86 1.40
591 656 7.333921 CCTCTCATATGTTCTTTGATCATAGCC 59.666 40.741 8.19 2.80 30.85 3.93
600 665 9.003658 ACTTTACAACCTCTCATATGTTCTTTG 57.996 33.333 1.90 4.37 0.00 2.77
642 707 9.917887 AGAGTCTCCATCTGAATATTTTCATTT 57.082 29.630 0.00 0.00 40.95 2.32
664 729 1.985116 GGTCCTTGCGGGAGAGAGT 60.985 63.158 0.00 0.00 46.10 3.24
668 733 1.281419 TTAATGGTCCTTGCGGGAGA 58.719 50.000 0.00 0.00 46.10 3.71
726 815 5.218885 CCATTCACTTGCAACGATTTGTAA 58.781 37.500 0.00 0.00 35.23 2.41
734 824 1.850377 TTTGCCATTCACTTGCAACG 58.150 45.000 0.00 0.00 44.02 4.10
747 845 7.589958 TTTAAAGGACTAAGACAATTTGCCA 57.410 32.000 0.00 0.00 0.00 4.92
794 892 2.041612 GGGGGCATGGCATCCTTT 60.042 61.111 22.06 0.00 0.00 3.11
795 893 2.718364 ATGGGGGCATGGCATCCTT 61.718 57.895 22.06 15.82 0.00 3.36
797 895 2.920912 CATGGGGGCATGGCATCC 60.921 66.667 22.06 20.56 0.00 3.51
915 1019 7.180079 CAGACATAATCAACATCGTGGTTTAC 58.820 38.462 0.00 0.00 0.00 2.01
1251 1355 1.001269 GGTTAGGGTTGGGTGAGGC 60.001 63.158 0.00 0.00 0.00 4.70
1252 1356 1.689412 GGGTTAGGGTTGGGTGAGG 59.311 63.158 0.00 0.00 0.00 3.86
1253 1357 1.298667 CGGGTTAGGGTTGGGTGAG 59.701 63.158 0.00 0.00 0.00 3.51
1254 1358 2.897762 GCGGGTTAGGGTTGGGTGA 61.898 63.158 0.00 0.00 0.00 4.02
1255 1359 1.555477 TAGCGGGTTAGGGTTGGGTG 61.555 60.000 0.00 0.00 0.00 4.61
1256 1360 0.622446 ATAGCGGGTTAGGGTTGGGT 60.622 55.000 0.00 0.00 0.00 4.51
1257 1361 0.549469 AATAGCGGGTTAGGGTTGGG 59.451 55.000 0.00 0.00 0.00 4.12
1258 1362 1.489230 AGAATAGCGGGTTAGGGTTGG 59.511 52.381 0.00 0.00 0.00 3.77
1271 1375 1.291132 GGAACGCTGTGGAGAATAGC 58.709 55.000 0.00 0.00 39.53 2.97
1274 1378 1.556911 AGATGGAACGCTGTGGAGAAT 59.443 47.619 0.00 0.00 0.00 2.40
1319 1423 3.421844 AGCCGCAGAAGAAAAGGTTAAT 58.578 40.909 0.00 0.00 0.00 1.40
1507 1611 4.642437 AGAGATTCGCTGAAGTAGTGATGA 59.358 41.667 0.00 0.00 44.85 2.92
1508 1612 4.930963 AGAGATTCGCTGAAGTAGTGATG 58.069 43.478 0.00 0.00 44.85 3.07
1509 1613 4.642437 TGAGAGATTCGCTGAAGTAGTGAT 59.358 41.667 0.00 0.00 44.85 3.06
1538 1642 5.108187 AGCTCATGACCAGTTTGTATCAT 57.892 39.130 0.00 0.00 31.93 2.45
1564 1668 6.777213 TTCCCTATATATCCGAAGAAGCTC 57.223 41.667 0.00 0.00 0.00 4.09
1583 1689 6.530181 CGGCAAATACTATGTTTCTTTTTCCC 59.470 38.462 0.00 0.00 0.00 3.97
1604 1710 2.208132 AATGTCACCAATAACCGGCA 57.792 45.000 0.00 0.00 0.00 5.69
1606 1712 4.775058 TCAAAATGTCACCAATAACCGG 57.225 40.909 0.00 0.00 0.00 5.28
1687 1793 4.898829 TGGATGATTTCGGTGCAATAAG 57.101 40.909 0.00 0.00 0.00 1.73
1983 2089 4.201871 CGACAGGCGGCAGATAAAATAAAA 60.202 41.667 13.08 0.00 36.03 1.52
2342 2450 5.782893 AGGTTTGCATGTTACAAGCTTAA 57.217 34.783 13.64 5.55 0.00 1.85
2360 2468 4.746535 AATTCGACCAAACCAAAAGGTT 57.253 36.364 0.00 0.00 35.36 3.50
2539 2647 1.217001 TGAGCAGTTGCACTAACACG 58.783 50.000 6.90 0.00 45.16 4.49
2683 2792 1.549203 ATTGTGACCAGGTGCATTCC 58.451 50.000 0.00 0.00 0.00 3.01
3093 3202 1.335964 TGAGTCGCAGTGTAGCTCAAC 60.336 52.381 0.00 0.00 33.84 3.18
3103 3212 2.660064 GGGGGATGTGAGTCGCAGT 61.660 63.158 12.66 0.68 33.13 4.40
3113 3222 0.178861 AGTTCAGTGGAGGGGGATGT 60.179 55.000 0.00 0.00 0.00 3.06
3133 3242 2.863740 TCATATTTAGCGCCGAGTGTTG 59.136 45.455 2.29 0.00 0.00 3.33
3180 3289 2.019984 CCTTGCAGTTGAGGAATAGCC 58.980 52.381 0.00 0.00 34.91 3.93
3264 3373 1.203052 CTTTTTGGTCGCCATCTGCAT 59.797 47.619 0.00 0.00 41.33 3.96
3299 3408 1.969208 TGCAGAAACATGCCCATTTCA 59.031 42.857 8.66 0.00 45.91 2.69
3372 3481 2.282462 AAAGCAAGGGACAGGGCG 60.282 61.111 0.00 0.00 0.00 6.13
3423 3532 4.704103 TCCCTGAGGGCTGCGAGT 62.704 66.667 14.20 0.00 43.94 4.18
3449 3558 2.607038 CGGCCAAAACAGCTAAAGAACC 60.607 50.000 2.24 0.00 0.00 3.62
3515 3624 2.356069 TCGAGGATGAAGTCTGACGATG 59.644 50.000 1.52 0.00 0.00 3.84
3548 3657 2.796031 GACACACACGTTTGATACCGAA 59.204 45.455 9.03 0.00 0.00 4.30
3628 3740 3.006110 ACAAAACCAAGCATCCAGACATG 59.994 43.478 0.00 0.00 0.00 3.21
3654 3766 2.203401 GAAAAGCAACAACAGCATGCA 58.797 42.857 21.98 0.00 42.53 3.96
3671 3783 3.628487 CGGTTTCAACAAGTACCAGGAAA 59.372 43.478 0.00 0.00 0.00 3.13
3690 3802 8.480501 AGTACTTTTTACACCATATATGACGGT 58.519 33.333 14.54 10.81 0.00 4.83
3771 3883 7.849322 AAACATAGTAACCAGGGATTTTTGT 57.151 32.000 0.00 0.00 0.00 2.83
3824 3936 6.258507 GCAATCCATGGAAATAATTTGTGTCC 59.741 38.462 20.67 1.22 0.00 4.02
3835 3947 3.513517 CCCATAGGCAATCCATGGAAAT 58.486 45.455 20.67 8.17 40.47 2.17
3979 4303 3.013921 GGGCTGTTCGATGGACATTTAA 58.986 45.455 0.00 0.00 0.00 1.52
3980 4304 2.238646 AGGGCTGTTCGATGGACATTTA 59.761 45.455 0.00 0.00 0.00 1.40
3981 4305 1.004745 AGGGCTGTTCGATGGACATTT 59.995 47.619 0.00 0.00 0.00 2.32
3982 4306 0.620556 AGGGCTGTTCGATGGACATT 59.379 50.000 0.00 0.00 0.00 2.71
3983 4307 0.179000 GAGGGCTGTTCGATGGACAT 59.821 55.000 0.00 0.00 0.00 3.06
3984 4308 1.596934 GAGGGCTGTTCGATGGACA 59.403 57.895 0.00 0.00 0.00 4.02
3985 4309 1.153349 GGAGGGCTGTTCGATGGAC 60.153 63.158 0.00 0.00 0.00 4.02
3986 4310 2.721167 CGGAGGGCTGTTCGATGGA 61.721 63.158 0.00 0.00 0.00 3.41
3987 4311 2.202932 CGGAGGGCTGTTCGATGG 60.203 66.667 0.00 0.00 0.00 3.51
3988 4312 1.227089 CTCGGAGGGCTGTTCGATG 60.227 63.158 0.00 0.00 0.00 3.84
3989 4313 0.970937 TTCTCGGAGGGCTGTTCGAT 60.971 55.000 4.96 0.00 0.00 3.59
3991 4315 1.446272 GTTCTCGGAGGGCTGTTCG 60.446 63.158 4.96 0.00 0.00 3.95
3994 4318 1.841556 TTGGTTCTCGGAGGGCTGT 60.842 57.895 4.96 0.00 0.00 4.40
3995 4319 1.376037 GTTGGTTCTCGGAGGGCTG 60.376 63.158 4.96 0.00 0.00 4.85
3996 4320 1.201429 ATGTTGGTTCTCGGAGGGCT 61.201 55.000 4.96 0.00 0.00 5.19
3997 4321 1.026718 CATGTTGGTTCTCGGAGGGC 61.027 60.000 4.96 0.00 0.00 5.19
3998 4322 0.324943 ACATGTTGGTTCTCGGAGGG 59.675 55.000 4.96 0.00 0.00 4.30
3999 4323 1.442769 CACATGTTGGTTCTCGGAGG 58.557 55.000 4.96 0.00 0.00 4.30
4000 4324 0.798776 GCACATGTTGGTTCTCGGAG 59.201 55.000 0.00 0.00 0.00 4.63
4001 4325 0.107643 TGCACATGTTGGTTCTCGGA 59.892 50.000 0.00 0.00 0.00 4.55
4004 4328 0.385974 GCGTGCACATGTTGGTTCTC 60.386 55.000 18.64 0.00 0.00 2.87
4005 4329 0.819259 AGCGTGCACATGTTGGTTCT 60.819 50.000 18.64 0.00 0.00 3.01
4006 4330 0.385974 GAGCGTGCACATGTTGGTTC 60.386 55.000 18.64 2.94 0.00 3.62
4008 4332 2.606961 CGAGCGTGCACATGTTGGT 61.607 57.895 18.64 5.28 0.00 3.67
4011 4335 0.443869 GATTCGAGCGTGCACATGTT 59.556 50.000 18.64 0.00 0.00 2.71
4014 4338 1.699656 GCAGATTCGAGCGTGCACAT 61.700 55.000 18.64 4.15 35.91 3.21
4015 4339 2.382746 GCAGATTCGAGCGTGCACA 61.383 57.895 18.64 0.00 35.91 4.57
4016 4340 2.097038 AGCAGATTCGAGCGTGCAC 61.097 57.895 6.82 6.82 38.44 4.57
4037 4558 2.408050 GCACCTCAGTAGCGATATTGG 58.592 52.381 3.25 0.00 0.00 3.16
4054 4575 1.740296 AAGACGCCCATGTACGCAC 60.740 57.895 4.67 0.71 0.00 5.34
4077 4598 1.144708 TGGCTGTGTTCTTGATTGGGA 59.855 47.619 0.00 0.00 0.00 4.37
4095 4616 2.297033 CCACCCAGAACAAACAAGATGG 59.703 50.000 0.00 0.00 0.00 3.51
4100 4621 2.516227 TGTCCACCCAGAACAAACAA 57.484 45.000 0.00 0.00 0.00 2.83
4182 4704 4.959446 GCTTGAAGCTTGCTGGTG 57.041 55.556 10.44 0.00 38.45 4.17
4211 4733 6.424883 TGGAAGTGGAAGTTTACAAGGTTTA 58.575 36.000 0.00 0.00 0.00 2.01
4219 4741 1.197036 GCGCTGGAAGTGGAAGTTTAC 59.803 52.381 0.00 0.00 46.73 2.01
4256 4778 8.290663 ACGCGATTTTTATACTGGTATAAGAC 57.709 34.615 15.93 6.09 38.70 3.01
4278 4800 7.669438 TGTAACGTATCATAGAACTTTACGC 57.331 36.000 0.00 0.00 39.27 4.42
4347 5135 8.840833 TTATATTACTGTGAACAAGCTGTCAA 57.159 30.769 0.00 0.00 0.00 3.18
4368 5156 8.644216 TGTTGAGTAGTCTGTGAACCTTTTATA 58.356 33.333 0.00 0.00 0.00 0.98
4395 5183 7.015584 AGCCTTGAACCTTCATGTTTTCTTTAT 59.984 33.333 0.00 0.00 37.00 1.40
4477 5265 0.739462 CGAGCTGTGAATAACCGCCA 60.739 55.000 0.00 0.00 39.67 5.69
4478 5266 1.429148 CCGAGCTGTGAATAACCGCC 61.429 60.000 0.00 0.00 39.67 6.13
4521 5313 4.929807 ACCTTTGGGCAGGTGAAG 57.070 55.556 0.00 0.00 46.22 3.02
4531 5326 3.127895 TGTCTTGAACGTGAAACCTTTGG 59.872 43.478 0.00 0.00 0.00 3.28
4545 5340 5.534278 TGATTGCTTGGTTACATGTCTTGAA 59.466 36.000 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.