Multiple sequence alignment - TraesCS5B01G068400

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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 TraesCS5B01G068400 chr5B 100.000 4566 0 0 1 4566 77849843 77845278 0.000000e+00 8432
1 TraesCS5B01G068400 chr5D 93.369 3137 132 30 504 3583 74424516 74427633 0.000000e+00 4571
2 TraesCS5B01G068400 chr5D 87.323 986 104 8 3582 4555 340063713 340064689 0.000000e+00 1109
3 TraesCS5B01G068400 chr5D 93.976 249 12 2 12 259 74423968 74424214 1.550000e-99 374
4 TraesCS5B01G068400 chr5D 94.444 216 10 2 258 471 74424296 74424511 9.470000e-87 331
5 TraesCS5B01G068400 chr5A 91.350 2786 150 39 823 3536 69795363 69798129 0.000000e+00 3725
6 TraesCS5B01G068400 chr1D 88.528 985 96 5 3586 4555 379462194 379461212 0.000000e+00 1177
7 TraesCS5B01G068400 chr6D 87.867 989 101 5 3585 4555 418228676 418227689 0.000000e+00 1144
8 TraesCS5B01G068400 chr2D 87.805 984 104 7 3585 4553 619859835 619860817 0.000000e+00 1138
9 TraesCS5B01G068400 chr2D 87.310 985 104 9 3585 4552 12768477 12769457 0.000000e+00 1107
10 TraesCS5B01G068400 chr2D 86.051 975 122 9 3585 4555 603407942 603408906 0.000000e+00 1035
11 TraesCS5B01G068400 chr7D 87.437 995 108 5 3577 4555 615884251 615885244 0.000000e+00 1129
12 TraesCS5B01G068400 chr7D 87.159 989 106 7 3580 4555 531052108 531053088 0.000000e+00 1103
13 TraesCS5B01G068400 chr3B 86.420 972 121 5 3585 4555 55005005 55005966 0.000000e+00 1053
14 TraesCS5B01G068400 chr3B 80.102 392 53 18 3585 3958 227427482 227427098 7.530000e-68 268
15 TraesCS5B01G068400 chr3D 80.751 213 29 2 3585 3786 348172082 348171871 6.120000e-34 156
16 TraesCS5B01G068400 chr7A 76.744 215 39 6 3585 3788 564622450 564622236 4.830000e-20 110


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 TraesCS5B01G068400 chr5B 77845278 77849843 4565 True 8432.000000 8432 100.000000 1 4566 1 chr5B.!!$R1 4565
1 TraesCS5B01G068400 chr5D 74423968 74427633 3665 False 1758.666667 4571 93.929667 12 3583 3 chr5D.!!$F2 3571
2 TraesCS5B01G068400 chr5D 340063713 340064689 976 False 1109.000000 1109 87.323000 3582 4555 1 chr5D.!!$F1 973
3 TraesCS5B01G068400 chr5A 69795363 69798129 2766 False 3725.000000 3725 91.350000 823 3536 1 chr5A.!!$F1 2713
4 TraesCS5B01G068400 chr1D 379461212 379462194 982 True 1177.000000 1177 88.528000 3586 4555 1 chr1D.!!$R1 969
5 TraesCS5B01G068400 chr6D 418227689 418228676 987 True 1144.000000 1144 87.867000 3585 4555 1 chr6D.!!$R1 970
6 TraesCS5B01G068400 chr2D 619859835 619860817 982 False 1138.000000 1138 87.805000 3585 4553 1 chr2D.!!$F3 968
7 TraesCS5B01G068400 chr2D 12768477 12769457 980 False 1107.000000 1107 87.310000 3585 4552 1 chr2D.!!$F1 967
8 TraesCS5B01G068400 chr2D 603407942 603408906 964 False 1035.000000 1035 86.051000 3585 4555 1 chr2D.!!$F2 970
9 TraesCS5B01G068400 chr7D 615884251 615885244 993 False 1129.000000 1129 87.437000 3577 4555 1 chr7D.!!$F2 978
10 TraesCS5B01G068400 chr7D 531052108 531053088 980 False 1103.000000 1103 87.159000 3580 4555 1 chr7D.!!$F1 975
11 TraesCS5B01G068400 chr3B 55005005 55005966 961 False 1053.000000 1053 86.420000 3585 4555 1 chr3B.!!$F1 970

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
928 1026 0.616395 TCTCTGATACGTGGGCCCAA 60.616 55.0 30.64 12.75 0.00 4.12 F
2078 2205 0.387929 ACTCTGTTCGAACCGAGCAA 59.612 50.0 35.36 14.71 45.22 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2085 2212 0.954452 GCTGCCTGCTACAAAACTGT 59.046 50.0 0.0 0.0 38.95 3.55 R
3959 4159 0.320421 GCTAGGGTTTGCTGTCGTCA 60.320 55.0 0.0 0.0 0.00 4.35 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
21 22 1.841556 ACTGTTCGGGGCTCCTTCA 60.842 57.895 0.00 0.00 0.00 3.02
36 37 7.665559 GGGGCTCCTTCAATTTAAAAGATTTTT 59.334 33.333 0.00 0.00 0.00 1.94
83 84 6.403333 TCCTTCGAATGTTTTCTATGTTCG 57.597 37.500 0.00 0.00 42.00 3.95
101 102 9.318041 CTATGTTCGTTGTTTGATTTGTAAGAG 57.682 33.333 0.00 0.00 0.00 2.85
109 110 7.621832 TGTTTGATTTGTAAGAGCAAATTCG 57.378 32.000 5.66 0.00 45.68 3.34
206 207 6.267471 AGAATCCTTTGTTTTCCTGTAATGCA 59.733 34.615 0.00 0.00 0.00 3.96
207 208 5.860941 TCCTTTGTTTTCCTGTAATGCAA 57.139 34.783 0.00 0.00 0.00 4.08
269 354 5.304101 TGACATGGCAATTATATGTTTCCCC 59.696 40.000 0.00 0.00 35.35 4.81
274 359 6.648192 TGGCAATTATATGTTTCCCCTTTTG 58.352 36.000 0.00 0.00 0.00 2.44
275 360 5.527214 GGCAATTATATGTTTCCCCTTTTGC 59.473 40.000 0.00 0.00 36.05 3.68
330 416 9.571804 CGTTTTTGAAATTCTGCTAATCAAAAG 57.428 29.630 10.64 0.28 45.35 2.27
346 432 7.523703 AATCAAAAGGCCCCCTAAAAATTAT 57.476 32.000 0.00 0.00 31.13 1.28
408 495 0.811281 GAAAATTGCCTCCGGGTGAG 59.189 55.000 0.00 0.00 41.07 3.51
429 516 6.980397 GTGAGTGTTTGGATTCTTGTGAAATT 59.020 34.615 0.00 0.00 35.63 1.82
471 558 8.462016 ACTTTCCTGCATTTTACTATTCATCAC 58.538 33.333 0.00 0.00 0.00 3.06
472 559 6.603237 TCCTGCATTTTACTATTCATCACG 57.397 37.500 0.00 0.00 0.00 4.35
475 562 6.183360 CCTGCATTTTACTATTCATCACGGTT 60.183 38.462 0.00 0.00 0.00 4.44
476 563 6.781138 TGCATTTTACTATTCATCACGGTTC 58.219 36.000 0.00 0.00 0.00 3.62
478 565 7.120579 TGCATTTTACTATTCATCACGGTTCTT 59.879 33.333 0.00 0.00 0.00 2.52
479 566 7.640240 GCATTTTACTATTCATCACGGTTCTTC 59.360 37.037 0.00 0.00 0.00 2.87
480 567 7.605410 TTTTACTATTCATCACGGTTCTTCC 57.395 36.000 0.00 0.00 0.00 3.46
481 568 6.540438 TTACTATTCATCACGGTTCTTCCT 57.460 37.500 0.00 0.00 0.00 3.36
482 569 5.422214 ACTATTCATCACGGTTCTTCCTT 57.578 39.130 0.00 0.00 0.00 3.36
483 570 5.420409 ACTATTCATCACGGTTCTTCCTTC 58.580 41.667 0.00 0.00 0.00 3.46
484 571 2.363788 TCATCACGGTTCTTCCTTCG 57.636 50.000 0.00 0.00 0.00 3.79
485 572 1.616865 TCATCACGGTTCTTCCTTCGT 59.383 47.619 0.00 0.00 36.19 3.85
487 574 3.284197 CACGGTTCTTCCTTCGTGT 57.716 52.632 6.55 0.00 45.15 4.49
488 575 1.578583 CACGGTTCTTCCTTCGTGTT 58.421 50.000 6.55 0.00 45.15 3.32
489 576 1.260561 CACGGTTCTTCCTTCGTGTTG 59.739 52.381 6.55 0.00 45.15 3.33
490 577 1.137479 ACGGTTCTTCCTTCGTGTTGA 59.863 47.619 0.00 0.00 34.40 3.18
491 578 2.206750 CGGTTCTTCCTTCGTGTTGAA 58.793 47.619 0.00 0.00 34.74 2.69
492 579 2.033151 CGGTTCTTCCTTCGTGTTGAAC 60.033 50.000 0.00 0.00 34.74 3.18
504 591 3.926003 TTGAACGCAACAAGGGCA 58.074 50.000 0.00 0.00 0.00 5.36
505 592 1.435515 TTGAACGCAACAAGGGCAC 59.564 52.632 0.00 0.00 0.00 5.01
512 599 1.470632 CGCAACAAGGGCACTGAAAAA 60.471 47.619 0.00 0.00 0.00 1.94
519 606 1.880027 AGGGCACTGAAAAATGTCGAC 59.120 47.619 9.11 9.11 0.00 4.20
520 607 1.606668 GGGCACTGAAAAATGTCGACA 59.393 47.619 22.48 22.48 0.00 4.35
542 629 4.825546 AATGGCTCGCTAAATGAATCAG 57.174 40.909 0.00 0.00 0.00 2.90
546 633 2.598439 GCTCGCTAAATGAATCAGTGCG 60.598 50.000 8.72 8.72 42.70 5.34
550 637 3.699067 GCTAAATGAATCAGTGCGCAAT 58.301 40.909 14.00 8.77 0.00 3.56
555 642 4.914312 ATGAATCAGTGCGCAATTTTTG 57.086 36.364 14.00 6.21 0.00 2.44
557 644 4.864633 TGAATCAGTGCGCAATTTTTGTA 58.135 34.783 14.00 0.00 0.00 2.41
568 655 7.113684 GTGCGCAATTTTTGTACTAATAACACA 59.886 33.333 14.00 0.00 0.00 3.72
600 687 6.361481 TGCGATATAGCACGTTAATAGTGAAC 59.639 38.462 6.39 2.31 42.92 3.18
623 721 5.240183 ACTTTAAGTCCGATATAGCGTGCTA 59.760 40.000 9.83 3.73 0.00 3.49
687 785 7.006509 TCTCTCATTCCAAGTTTCCTTTGATT 58.993 34.615 0.00 0.00 0.00 2.57
724 822 6.718522 TTTTAGGGGACTTTGATCGTTTTT 57.281 33.333 0.00 0.00 43.67 1.94
725 823 7.820578 TTTTAGGGGACTTTGATCGTTTTTA 57.179 32.000 0.00 0.00 43.67 1.52
729 827 9.517868 TTAGGGGACTTTGATCGTTTTTATTTA 57.482 29.630 0.00 0.00 43.67 1.40
784 882 6.093404 GGATCCGAAGTTTCCTTTCAAATTC 58.907 40.000 0.00 0.00 0.00 2.17
785 883 6.294508 GGATCCGAAGTTTCCTTTCAAATTCA 60.295 38.462 0.00 0.00 0.00 2.57
796 894 5.048782 TCCTTTCAAATTCATGTGAACCGAG 60.049 40.000 0.00 0.00 36.80 4.63
821 919 0.774908 CCTAAACTTGACCCACCCCA 59.225 55.000 0.00 0.00 0.00 4.96
882 980 2.357517 CTGGCCGCTTGTCGAACT 60.358 61.111 0.00 0.00 41.67 3.01
900 998 3.856508 CCGCAACGGCTATATCGG 58.143 61.111 0.00 0.00 41.17 4.18
928 1026 0.616395 TCTCTGATACGTGGGCCCAA 60.616 55.000 30.64 12.75 0.00 4.12
988 1088 2.223852 GCCCTTGACTTTTAAACGCCAA 60.224 45.455 0.00 0.00 0.00 4.52
996 1096 5.124138 TGACTTTTAAACGCCAAAAGACTCA 59.876 36.000 18.24 11.87 42.86 3.41
1241 1352 2.814341 CACGAGCTGCTCCTGCTG 60.814 66.667 22.97 11.49 38.70 4.41
1452 1563 2.513666 CCATTAGGAAGGCGCGCA 60.514 61.111 34.42 11.01 36.89 6.09
1556 1667 1.187087 GGAAGGAGGACGACATGAGT 58.813 55.000 0.00 0.00 0.00 3.41
1674 1788 5.883673 TCCTAGTAACTGCTGTTGTTGTTTT 59.116 36.000 18.22 0.00 37.59 2.43
1745 1859 1.313812 AAGGGTCGTCGAGCTAGTGG 61.314 60.000 22.48 0.00 0.00 4.00
1809 1923 6.973642 TGGGATCCATGTTCTTCTTATCTTT 58.026 36.000 15.23 0.00 0.00 2.52
1870 1984 7.766278 TGATCTGCTACTCTTTTACCTCAAATC 59.234 37.037 0.00 0.00 0.00 2.17
1969 2083 1.448985 TTTGTCAGCTGGGCGTTATC 58.551 50.000 15.13 0.00 0.00 1.75
2049 2176 3.921119 TGATCATTTGTGCCACAGAAC 57.079 42.857 0.00 0.00 0.00 3.01
2067 2194 6.360148 CACAGAACTAGTTCGTTACTCTGTTC 59.640 42.308 25.92 18.90 43.39 3.18
2078 2205 0.387929 ACTCTGTTCGAACCGAGCAA 59.612 50.000 35.36 14.71 45.22 3.91
2079 2206 1.000955 ACTCTGTTCGAACCGAGCAAT 59.999 47.619 35.36 21.47 45.22 3.56
2085 2212 5.870433 TCTGTTCGAACCGAGCAATTAATTA 59.130 36.000 24.78 0.61 45.22 1.40
2117 2249 3.056328 GCAGCCGGTGAGGGAAAC 61.056 66.667 1.90 0.00 41.48 2.78
2146 2278 5.436175 TCCAGTTGACTGAAAAAGATGTGA 58.564 37.500 12.54 0.00 46.59 3.58
2288 2420 2.346803 TCGTTCTGGCTGAAGCATAAC 58.653 47.619 7.09 4.46 44.36 1.89
2289 2421 2.028112 TCGTTCTGGCTGAAGCATAACT 60.028 45.455 7.09 0.00 44.36 2.24
2298 2432 4.705023 GGCTGAAGCATAACTTTTTCCCTA 59.295 41.667 4.43 0.00 44.36 3.53
2364 2498 0.884704 TGCCTGTTCTTCTGTTCGGC 60.885 55.000 0.00 0.00 36.64 5.54
2373 2507 2.158841 TCTTCTGTTCGGCGCAAAATAC 59.841 45.455 10.83 0.00 0.00 1.89
2383 2517 2.264813 GCGCAAAATACGGTAGTCTGA 58.735 47.619 0.30 0.00 0.00 3.27
2433 2570 9.924650 ACAGGTACAAAAGACATAAAGTACTAG 57.075 33.333 0.00 0.00 34.02 2.57
2643 2792 7.201644 CCCAAACTCATAGCATAACACTAACAG 60.202 40.741 0.00 0.00 0.00 3.16
2750 2899 0.033504 CGGGTACAGCAGTGACAGTT 59.966 55.000 0.00 0.00 0.00 3.16
2804 2953 0.847373 TGGCAGGTACAGTTGGGAAA 59.153 50.000 0.00 0.00 0.00 3.13
2925 3079 3.071312 AGCCTTGATTTGCACATGGAAAA 59.929 39.130 10.78 0.00 38.79 2.29
2926 3080 3.814283 GCCTTGATTTGCACATGGAAAAA 59.186 39.130 10.78 0.00 38.79 1.94
2996 3150 5.444176 AGAATCTAGAAAGAAATGGCCTGG 58.556 41.667 3.32 0.00 34.73 4.45
3086 3258 1.461127 GAGCTTTAGACACTTGGTGCG 59.539 52.381 0.00 0.00 36.98 5.34
3261 3446 2.124983 CAGGGCTGGTGTGATCCG 60.125 66.667 0.00 0.00 0.00 4.18
3330 3515 4.287552 TGGAGGTAGAACCATAGAAGACC 58.712 47.826 0.00 0.00 41.95 3.85
3368 3553 4.615682 CGCAGGAATGCTTTTGATGTGTAA 60.616 41.667 0.00 0.00 0.00 2.41
3374 3559 8.370182 AGGAATGCTTTTGATGTGTAAAAAGAT 58.630 29.630 11.08 1.40 0.00 2.40
3463 3649 2.055838 TGTAACAACGAACTAGCAGCG 58.944 47.619 0.00 0.00 0.00 5.18
3495 3681 2.854963 GCATATTGCAGGATCAGGACA 58.145 47.619 0.00 0.00 44.26 4.02
3538 3724 9.866655 TCTCCACTCCTGCAATTTTATAATATT 57.133 29.630 0.00 0.00 0.00 1.28
3564 3750 3.652274 AGCCATTTCATTGAACGTTTGG 58.348 40.909 0.46 4.51 0.00 3.28
3572 3758 2.663826 TTGAACGTTTGGCAAAAGCT 57.336 40.000 22.85 13.10 0.00 3.74
3583 3769 6.129088 CGTTTGGCAAAAGCTAATTCTTCTTC 60.129 38.462 15.29 0.00 0.00 2.87
3604 3790 1.976474 GCAACTCCAATGGGGCGAA 60.976 57.895 0.00 0.00 36.21 4.70
3606 3792 0.893270 CAACTCCAATGGGGCGAACA 60.893 55.000 0.00 0.00 36.21 3.18
3726 3923 2.676463 GCCCAAAATTGCGCCTGAAATA 60.676 45.455 4.18 0.00 0.00 1.40
3734 3931 1.807981 CGCCTGAAATACGTCGGCA 60.808 57.895 0.00 0.00 37.17 5.69
3736 3933 1.702491 GCCTGAAATACGTCGGCACC 61.702 60.000 0.00 0.00 37.25 5.01
3794 3991 2.047655 CGCGTGCCCACCTTTAGA 60.048 61.111 0.00 0.00 0.00 2.10
3933 4133 3.402681 CCCGTCCACATCTGGCCT 61.403 66.667 3.32 0.00 37.49 5.19
3959 4159 1.298014 CTCCCTTTGCTTCCTCGCT 59.702 57.895 0.00 0.00 0.00 4.93
3961 4161 1.003355 CCCTTTGCTTCCTCGCTGA 60.003 57.895 0.00 0.00 0.00 4.26
4009 4210 1.822990 CCTCTTTGGCAGCATCAATGT 59.177 47.619 0.00 0.00 0.00 2.71
4060 4261 3.775654 GTCCTCCCGTGCTCCCTG 61.776 72.222 0.00 0.00 0.00 4.45
4109 4316 4.514577 CCTGATCGTCGGCGCCTT 62.515 66.667 26.68 3.40 38.14 4.35
4118 4325 4.776322 CGGCGCCTTCACATCCCA 62.776 66.667 26.68 0.00 0.00 4.37
4167 4374 4.436998 GGCAGCCGCTGTCGTACT 62.437 66.667 21.29 0.00 38.60 2.73
4202 4409 2.639327 GCACCATTGGCACCTGGAC 61.639 63.158 19.34 9.03 34.68 4.02
4312 4519 3.730761 GCGTTGGCTGCCTGAGTG 61.731 66.667 21.03 6.43 35.83 3.51
4383 4590 2.974148 AACGGCGTTCGGGTTTCC 60.974 61.111 21.19 0.00 44.45 3.13
4475 4682 2.266055 CAAGCCACCCTCGAGGAC 59.734 66.667 33.39 18.00 39.89 3.85
4543 4750 2.679716 GGATGGGCTGGAGCAAGT 59.320 61.111 0.20 0.00 44.36 3.16
4557 4764 3.658398 CAAGTCCTTGCCCTGTGAT 57.342 52.632 0.00 0.00 33.45 3.06
4558 4765 1.171308 CAAGTCCTTGCCCTGTGATG 58.829 55.000 0.00 0.00 33.45 3.07
4559 4766 0.038744 AAGTCCTTGCCCTGTGATGG 59.961 55.000 0.00 0.00 0.00 3.51
4560 4767 0.842030 AGTCCTTGCCCTGTGATGGA 60.842 55.000 0.00 0.00 0.00 3.41
4561 4768 0.678048 GTCCTTGCCCTGTGATGGAC 60.678 60.000 0.00 0.00 37.42 4.02
4562 4769 1.133181 TCCTTGCCCTGTGATGGACA 61.133 55.000 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.553095 AAGGAGCCCCGAACAGTGC 62.553 63.158 0.00 0.00 37.58 4.40
2 3 1.376037 GAAGGAGCCCCGAACAGTG 60.376 63.158 0.00 0.00 37.58 3.66
3 4 1.415672 TTGAAGGAGCCCCGAACAGT 61.416 55.000 0.00 0.00 37.58 3.55
5 6 0.404040 AATTGAAGGAGCCCCGAACA 59.596 50.000 0.00 0.00 37.58 3.18
6 7 1.545841 AAATTGAAGGAGCCCCGAAC 58.454 50.000 0.00 0.00 37.58 3.95
7 8 3.443145 TTAAATTGAAGGAGCCCCGAA 57.557 42.857 0.00 0.00 37.58 4.30
8 9 3.443145 TTTAAATTGAAGGAGCCCCGA 57.557 42.857 0.00 0.00 37.58 5.14
9 10 3.761752 TCTTTTAAATTGAAGGAGCCCCG 59.238 43.478 0.00 0.00 37.58 5.73
10 11 5.939764 ATCTTTTAAATTGAAGGAGCCCC 57.060 39.130 0.00 0.00 0.00 5.80
36 37 8.525290 GATTCCAATCCTTCAAAATTCCTAGA 57.475 34.615 0.00 0.00 0.00 2.43
63 64 6.950545 ACAACGAACATAGAAAACATTCGAA 58.049 32.000 11.24 0.00 43.66 3.71
83 84 7.998212 CGAATTTGCTCTTACAAATCAAACAAC 59.002 33.333 3.21 0.00 46.80 3.32
101 102 7.862873 CCTTAGGAAAAATCCTATCGAATTTGC 59.137 37.037 5.48 0.00 41.55 3.68
165 166 4.530946 AGGATTCTTTCGAGGGTTTCAGTA 59.469 41.667 0.00 0.00 0.00 2.74
269 354 5.649782 AACATAGGATTGACCAGCAAAAG 57.350 39.130 0.00 0.00 40.48 2.27
274 359 5.841957 ATGAAAACATAGGATTGACCAGC 57.158 39.130 0.00 0.00 42.04 4.85
275 360 9.347240 AGAATATGAAAACATAGGATTGACCAG 57.653 33.333 0.00 0.00 42.04 4.00
316 402 1.341976 GGGGGCCTTTTGATTAGCAGA 60.342 52.381 0.84 0.00 0.00 4.26
330 416 7.336176 CGTAGATAGAATAATTTTTAGGGGGCC 59.664 40.741 0.00 0.00 0.00 5.80
346 432 2.617308 CCGGAAGAGCACGTAGATAGAA 59.383 50.000 0.00 0.00 0.00 2.10
381 468 0.820226 GAGGCAATTTTCCCTGAGGC 59.180 55.000 0.00 0.00 0.00 4.70
408 495 7.538303 ACAAATTTCACAAGAATCCAAACAC 57.462 32.000 0.00 0.00 32.89 3.32
455 542 8.047310 AGGAAGAACCGTGATGAATAGTAAAAT 58.953 33.333 0.00 0.00 44.74 1.82
471 558 1.860676 TCAACACGAAGGAAGAACCG 58.139 50.000 0.00 0.00 44.74 4.44
472 559 3.604065 GTTCAACACGAAGGAAGAACC 57.396 47.619 0.00 0.00 33.09 3.62
487 574 1.034838 AGTGCCCTTGTTGCGTTCAA 61.035 50.000 0.00 0.00 0.00 2.69
488 575 1.453015 AGTGCCCTTGTTGCGTTCA 60.453 52.632 0.00 0.00 0.00 3.18
489 576 1.008538 CAGTGCCCTTGTTGCGTTC 60.009 57.895 0.00 0.00 0.00 3.95
490 577 1.034838 TTCAGTGCCCTTGTTGCGTT 61.035 50.000 0.00 0.00 0.00 4.84
491 578 1.034838 TTTCAGTGCCCTTGTTGCGT 61.035 50.000 0.00 0.00 0.00 5.24
492 579 0.102120 TTTTCAGTGCCCTTGTTGCG 59.898 50.000 0.00 0.00 0.00 4.85
493 580 2.307934 TTTTTCAGTGCCCTTGTTGC 57.692 45.000 0.00 0.00 0.00 4.17
494 581 3.795877 ACATTTTTCAGTGCCCTTGTTG 58.204 40.909 0.00 0.00 0.00 3.33
495 582 3.490761 CGACATTTTTCAGTGCCCTTGTT 60.491 43.478 0.00 0.00 0.00 2.83
496 583 2.034558 CGACATTTTTCAGTGCCCTTGT 59.965 45.455 0.00 0.00 0.00 3.16
497 584 2.293122 TCGACATTTTTCAGTGCCCTTG 59.707 45.455 0.00 0.00 0.00 3.61
498 585 2.293399 GTCGACATTTTTCAGTGCCCTT 59.707 45.455 11.55 0.00 0.00 3.95
499 586 1.880027 GTCGACATTTTTCAGTGCCCT 59.120 47.619 11.55 0.00 0.00 5.19
500 587 1.606668 TGTCGACATTTTTCAGTGCCC 59.393 47.619 15.76 0.00 0.00 5.36
501 588 3.347958 TTGTCGACATTTTTCAGTGCC 57.652 42.857 20.80 0.00 0.00 5.01
502 589 4.148696 CCATTTGTCGACATTTTTCAGTGC 59.851 41.667 20.80 0.00 0.00 4.40
503 590 4.148696 GCCATTTGTCGACATTTTTCAGTG 59.851 41.667 20.80 9.94 0.00 3.66
504 591 4.037923 AGCCATTTGTCGACATTTTTCAGT 59.962 37.500 20.80 0.00 0.00 3.41
505 592 4.549458 AGCCATTTGTCGACATTTTTCAG 58.451 39.130 20.80 6.10 0.00 3.02
512 599 0.391661 AGCGAGCCATTTGTCGACAT 60.392 50.000 20.80 2.29 38.50 3.06
519 606 4.923893 TGATTCATTTAGCGAGCCATTTG 58.076 39.130 0.00 0.00 0.00 2.32
520 607 4.641989 ACTGATTCATTTAGCGAGCCATTT 59.358 37.500 0.00 0.00 0.00 2.32
542 629 7.113684 TGTGTTATTAGTACAAAAATTGCGCAC 59.886 33.333 11.12 0.00 0.00 5.34
600 687 4.547532 AGCACGCTATATCGGACTTAAAG 58.452 43.478 0.57 0.00 0.00 1.85
733 831 9.413048 ACTAAAAACGATTTTGACTCAAACAAA 57.587 25.926 13.06 0.00 39.09 2.83
734 832 8.855279 CACTAAAAACGATTTTGACTCAAACAA 58.145 29.630 13.06 0.00 39.09 2.83
735 833 7.486551 CCACTAAAAACGATTTTGACTCAAACA 59.513 33.333 13.06 0.00 39.09 2.83
737 835 7.763356 TCCACTAAAAACGATTTTGACTCAAA 58.237 30.769 13.06 0.00 39.09 2.69
738 836 7.323049 TCCACTAAAAACGATTTTGACTCAA 57.677 32.000 13.06 0.00 39.09 3.02
739 837 6.928979 TCCACTAAAAACGATTTTGACTCA 57.071 33.333 13.06 0.00 39.09 3.41
740 838 7.021790 GGATCCACTAAAAACGATTTTGACTC 58.978 38.462 13.06 2.67 39.09 3.36
741 839 6.348213 CGGATCCACTAAAAACGATTTTGACT 60.348 38.462 13.41 0.00 39.09 3.41
742 840 5.793457 CGGATCCACTAAAAACGATTTTGAC 59.207 40.000 13.41 0.00 39.09 3.18
743 841 5.701750 TCGGATCCACTAAAAACGATTTTGA 59.298 36.000 13.41 2.90 39.09 2.69
744 842 5.933790 TCGGATCCACTAAAAACGATTTTG 58.066 37.500 13.41 6.30 39.09 2.44
745 843 6.206048 ACTTCGGATCCACTAAAAACGATTTT 59.794 34.615 13.41 8.51 41.50 1.82
746 844 5.704053 ACTTCGGATCCACTAAAAACGATTT 59.296 36.000 13.41 0.00 0.00 2.17
747 845 5.243207 ACTTCGGATCCACTAAAAACGATT 58.757 37.500 13.41 0.00 0.00 3.34
784 882 2.401766 GGCCTGCTCGGTTCACATG 61.402 63.158 0.00 0.00 34.25 3.21
785 883 2.045926 GGCCTGCTCGGTTCACAT 60.046 61.111 0.00 0.00 34.25 3.21
796 894 0.965866 GGGTCAAGTTTAGGGCCTGC 60.966 60.000 18.53 6.38 0.00 4.85
821 919 4.690719 TCGCGAATGGCCCGTTGT 62.691 61.111 6.20 0.00 38.94 3.32
900 998 0.671251 CGTATCAGAGAGGAGGTGCC 59.329 60.000 0.00 0.00 0.00 5.01
918 1016 0.179056 ATAGATTCGTTGGGCCCACG 60.179 55.000 28.70 29.36 0.00 4.94
928 1026 5.502153 AAAGCGAGACTACATAGATTCGT 57.498 39.130 13.89 0.00 36.17 3.85
988 1088 1.749286 CGGGTTTGGGTGTGAGTCTTT 60.749 52.381 0.00 0.00 0.00 2.52
996 1096 2.518349 CTGTGCGGGTTTGGGTGT 60.518 61.111 0.00 0.00 0.00 4.16
1130 1241 3.092511 GCCATGGGCTCCTCCTCA 61.093 66.667 15.13 0.00 46.69 3.86
1301 1412 4.514577 AGGCTCGAATCCACGCCG 62.515 66.667 5.56 0.00 46.85 6.46
1437 1548 2.203070 CCTGCGCGCCTTCCTAAT 60.203 61.111 30.77 0.00 0.00 1.73
1439 1550 3.838271 CTCCTGCGCGCCTTCCTA 61.838 66.667 30.77 7.64 0.00 2.94
1556 1667 0.827507 GAGCAGGAACCAAGGCCAAA 60.828 55.000 5.01 0.00 0.00 3.28
1674 1788 2.885266 AGAGCGTCAGTTTCTGTGACTA 59.115 45.455 2.06 0.00 41.91 2.59
1708 1822 2.310052 CCTTTCCCAGAGACTTTCCCAT 59.690 50.000 0.00 0.00 0.00 4.00
1745 1859 2.981977 TTCGCCACGTCCTTCCACAC 62.982 60.000 0.00 0.00 0.00 3.82
1809 1923 6.678568 AAGTGATCTCTCTTGAAAAGGAGA 57.321 37.500 0.00 9.25 46.61 3.71
1870 1984 8.062065 AGGAAGAAACATAGAACAGAGTAGAG 57.938 38.462 0.00 0.00 0.00 2.43
1969 2083 6.127619 CCTTAAAGAAGGCTAGACCCAAAATG 60.128 42.308 0.00 0.00 45.91 2.32
2014 2128 7.430211 CACAAATGATCATTGGTTCATACTTCG 59.570 37.037 23.38 7.55 32.83 3.79
2035 2152 2.869801 CGAACTAGTTCTGTGGCACAAA 59.130 45.455 28.30 15.14 37.52 2.83
2067 2194 5.464965 ACTGTAATTAATTGCTCGGTTCG 57.535 39.130 15.93 0.00 0.00 3.95
2078 2205 7.461182 TGCCTGCTACAAAACTGTAATTAAT 57.539 32.000 0.00 0.00 0.00 1.40
2079 2206 6.569610 GCTGCCTGCTACAAAACTGTAATTAA 60.570 38.462 0.00 0.00 38.95 1.40
2085 2212 0.954452 GCTGCCTGCTACAAAACTGT 59.046 50.000 0.00 0.00 38.95 3.55
2259 2391 2.166459 TCAGCCAGAACGATCCAGTTAG 59.834 50.000 0.00 0.00 34.00 2.34
2261 2393 0.976641 TCAGCCAGAACGATCCAGTT 59.023 50.000 0.00 0.00 36.99 3.16
2323 2457 8.715191 GGCAATACCTAAGATTCAGATATCAG 57.285 38.462 5.32 0.00 34.51 2.90
2364 2498 5.331309 CGTAATCAGACTACCGTATTTTGCG 60.331 44.000 0.00 0.00 0.00 4.85
2373 2507 3.817084 TCCATACCGTAATCAGACTACCG 59.183 47.826 0.00 0.00 0.00 4.02
2383 2517 3.258622 GCTAGAAGCCTCCATACCGTAAT 59.741 47.826 0.00 0.00 34.48 1.89
2433 2570 4.906423 CAGTCATGCTAAGATTGTTCTGC 58.094 43.478 0.00 0.00 30.72 4.26
2485 2631 3.513515 ACTGGTGAAGAAACCTGCAAAAA 59.486 39.130 0.00 0.00 41.54 1.94
2643 2792 2.941064 GGGTAAAAAGGGTAGACATCGC 59.059 50.000 0.00 0.00 0.00 4.58
2706 2855 2.171209 AATTTCTTGCGGGGGCAAGC 62.171 55.000 20.72 0.00 44.67 4.01
2750 2899 7.918562 GTCTTAACACTAAACAAATTCCAGCAA 59.081 33.333 0.00 0.00 0.00 3.91
2885 3038 6.599244 TCAAGGCTCATATGGTAAACTTCTTG 59.401 38.462 2.13 6.52 0.00 3.02
2886 3039 6.721318 TCAAGGCTCATATGGTAAACTTCTT 58.279 36.000 2.13 0.00 0.00 2.52
2887 3040 6.313519 TCAAGGCTCATATGGTAAACTTCT 57.686 37.500 2.13 0.00 0.00 2.85
2925 3079 5.885912 ACAGGTGTCAGAATTTACACAACTT 59.114 36.000 16.61 2.43 46.22 2.66
2926 3080 5.437060 ACAGGTGTCAGAATTTACACAACT 58.563 37.500 16.61 8.48 46.22 3.16
3195 3380 1.542492 ACTGAAATGAAGGCTGCCAG 58.458 50.000 22.65 9.14 0.00 4.85
3330 3515 0.454957 CTGCGGCAAATTCAACTCCG 60.455 55.000 3.44 0.00 42.68 4.63
3463 3649 3.743521 TGCAATATGCCTCATGTCTACC 58.256 45.455 0.00 0.00 44.23 3.18
3495 3681 3.071892 TGGAGAACAATACGGTGGAACTT 59.928 43.478 0.00 0.00 36.74 2.66
3538 3724 7.543868 CCAAACGTTCAATGAAATGGCTTATTA 59.456 33.333 0.00 0.00 0.00 0.98
3564 3750 4.790651 GCTCGAAGAAGAATTAGCTTTTGC 59.209 41.667 0.00 0.00 41.16 3.68
3572 3758 5.147330 TGGAGTTGCTCGAAGAAGAATTA 57.853 39.130 0.00 0.00 34.09 1.40
3583 3769 2.409870 GCCCCATTGGAGTTGCTCG 61.410 63.158 3.62 0.00 35.39 5.03
3604 3790 2.677003 CGCAGGCCGACGAAATTGT 61.677 57.895 14.43 0.00 40.02 2.71
3606 3792 2.358247 ACGCAGGCCGACGAAATT 60.358 55.556 24.47 1.78 41.02 1.82
3615 3801 3.451894 CCCAAATGGACGCAGGCC 61.452 66.667 0.00 0.00 37.39 5.19
3658 3844 2.096406 CGTTTGAGTCGGCGCATG 59.904 61.111 10.83 0.00 0.00 4.06
3776 3973 2.047655 CTAAAGGTGGGCACGCGA 60.048 61.111 15.93 0.00 0.00 5.87
3782 3979 1.001269 GGGTGGTCTAAAGGTGGGC 60.001 63.158 0.00 0.00 0.00 5.36
3790 3987 2.148052 TGGCGGTTGGGTGGTCTAA 61.148 57.895 0.00 0.00 0.00 2.10
3845 4043 4.606071 CACTGGCTGACTAGTGGC 57.394 61.111 0.00 4.35 40.38 5.01
3933 4133 1.360393 AAGCAAAGGGAGTGGTGGGA 61.360 55.000 0.00 0.00 0.00 4.37
3959 4159 0.320421 GCTAGGGTTTGCTGTCGTCA 60.320 55.000 0.00 0.00 0.00 4.35
3961 4161 1.374252 CGCTAGGGTTTGCTGTCGT 60.374 57.895 0.00 0.00 0.00 4.34
4009 4210 2.118076 CCTTGCCCTTGCCCTTGA 59.882 61.111 0.00 0.00 36.33 3.02
4109 4316 0.250858 CTTGGTGCACTGGGATGTGA 60.251 55.000 17.98 0.00 40.12 3.58
4167 4374 4.794439 CGGCAGCGTGACATCGGA 62.794 66.667 0.00 0.00 0.00 4.55
4350 4557 0.937699 CGTTGCTCCTCGTGTTCGAA 60.938 55.000 0.00 0.00 45.61 3.71
4425 4632 1.525923 CCTCCATGTCCTCCAGCTG 59.474 63.158 6.78 6.78 0.00 4.24
4508 4715 1.367471 CCAGTGTGCGTCCTTCTCA 59.633 57.895 0.00 0.00 0.00 3.27
4512 4719 1.003355 CATCCCAGTGTGCGTCCTT 60.003 57.895 0.00 0.00 0.00 3.36
4543 4750 1.133181 TGTCCATCACAGGGCAAGGA 61.133 55.000 0.00 0.00 41.07 3.36


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

AutoCloner maintained by Alex Coulton.