Multiple sequence alignment - TraesCS2D01G476700

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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 TraesCS2D01G476700 chr2D 100.000 3593 0 0 1 3593 578962036 578965628 0.000000e+00 6636.0
1 TraesCS2D01G476700 chr2B 89.850 2729 184 35 899 3537 695888989 695891714 0.000000e+00 3419.0
2 TraesCS2D01G476700 chr2B 82.030 601 76 14 131 729 695886773 695887343 1.940000e-132 483.0
3 TraesCS2D01G476700 chr2B 85.632 174 18 4 741 911 695887388 695887557 3.690000e-40 176.0
4 TraesCS2D01G476700 chr2A 91.176 2482 155 22 849 3268 716499313 716501792 0.000000e+00 3312.0
5 TraesCS2D01G476700 chr2A 87.376 404 39 9 52 452 716498860 716499254 1.520000e-123 453.0
6 TraesCS2D01G476700 chr2A 92.333 300 18 2 3298 3593 716501793 716502091 4.290000e-114 422.0
7 TraesCS2D01G476700 chr3A 80.813 1918 329 21 1064 2952 589792452 589794359 0.000000e+00 1467.0
8 TraesCS2D01G476700 chr3A 74.302 681 169 5 1064 1744 589606326 589607000 2.110000e-72 283.0
9 TraesCS2D01G476700 chr3B 80.519 1889 317 29 1099 2952 588471030 588472902 0.000000e+00 1402.0
10 TraesCS2D01G476700 chr3B 80.165 1331 230 21 1633 2934 588420705 588422030 0.000000e+00 965.0
11 TraesCS2D01G476700 chr3B 89.744 78 6 2 1 78 459274665 459274590 8.210000e-17 99.0
12 TraesCS2D01G476700 chr3D 80.202 1884 332 27 1099 2952 448427986 448429858 0.000000e+00 1375.0
13 TraesCS2D01G476700 chr3D 89.873 79 6 2 1 77 75993146 75993068 2.280000e-17 100.0
14 TraesCS2D01G476700 chr7A 94.286 70 2 2 1 70 462450820 462450753 4.910000e-19 106.0
15 TraesCS2D01G476700 chr7A 88.235 85 8 2 1 85 250694648 250694566 2.280000e-17 100.0
16 TraesCS2D01G476700 chr6B 90.667 75 7 0 1 75 492526665 492526591 2.280000e-17 100.0
17 TraesCS2D01G476700 chr4D 92.857 70 3 2 1 70 312306899 312306966 2.280000e-17 100.0
18 TraesCS2D01G476700 chr1B 90.789 76 6 1 1 75 279930349 279930274 2.280000e-17 100.0
19 TraesCS2D01G476700 chr1A 87.356 87 9 2 14 100 454325077 454325161 8.210000e-17 99.0
20 TraesCS2D01G476700 chr7D 85.714 91 7 5 1 91 154260627 154260711 1.370000e-14 91.6


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 TraesCS2D01G476700 chr2D 578962036 578965628 3592 False 6636.000000 6636 100.000000 1 3593 1 chr2D.!!$F1 3592
1 TraesCS2D01G476700 chr2B 695886773 695891714 4941 False 1359.333333 3419 85.837333 131 3537 3 chr2B.!!$F1 3406
2 TraesCS2D01G476700 chr2A 716498860 716502091 3231 False 1395.666667 3312 90.295000 52 3593 3 chr2A.!!$F1 3541
3 TraesCS2D01G476700 chr3A 589792452 589794359 1907 False 1467.000000 1467 80.813000 1064 2952 1 chr3A.!!$F2 1888
4 TraesCS2D01G476700 chr3A 589606326 589607000 674 False 283.000000 283 74.302000 1064 1744 1 chr3A.!!$F1 680
5 TraesCS2D01G476700 chr3B 588471030 588472902 1872 False 1402.000000 1402 80.519000 1099 2952 1 chr3B.!!$F2 1853
6 TraesCS2D01G476700 chr3B 588420705 588422030 1325 False 965.000000 965 80.165000 1633 2934 1 chr3B.!!$F1 1301
7 TraesCS2D01G476700 chr3D 448427986 448429858 1872 False 1375.000000 1375 80.202000 1099 2952 1 chr3D.!!$F1 1853

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
982 2474 0.036164 TTCGTGTAGCCCATGCAAGT 59.964 50.0 0.0 0.0 41.13 3.16 F
1341 2845 0.109086 TCTCCGCTCTGCTTTCTTCG 60.109 55.0 0.0 0.0 0.00 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2169 3682 0.396435 CATACTTCCCGGCATGGCTA 59.604 55.0 18.09 1.76 35.87 3.93 R
2727 4253 0.813610 CTGTGAGTGCCAACCAACGA 60.814 55.0 0.00 0.00 0.00 3.85 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
41 42 7.881775 AACAACTTTATTATTGCCTCTAGGG 57.118 36.000 0.00 0.00 35.18 3.53
54 55 4.982241 CCTCTAGGGCATATTTCCTTCA 57.018 45.455 0.00 0.00 34.75 3.02
55 56 4.904241 CCTCTAGGGCATATTTCCTTCAG 58.096 47.826 0.00 0.00 34.75 3.02
56 57 4.263243 CCTCTAGGGCATATTTCCTTCAGG 60.263 50.000 0.00 2.64 34.75 3.86
57 58 4.566837 TCTAGGGCATATTTCCTTCAGGA 58.433 43.478 0.00 0.00 43.73 3.86
70 71 5.346782 TCCTTCAGGAAGCCTCTATATCT 57.653 43.478 3.48 0.00 42.18 1.98
80 81 8.064389 AGGAAGCCTCTATATCTATATGAAGCA 58.936 37.037 0.00 0.00 0.00 3.91
106 107 6.037830 CGCTCCATATGCATTATGATCATCAA 59.962 38.462 12.53 5.83 40.22 2.57
108 109 7.067129 GCTCCATATGCATTATGATCATCAACT 59.933 37.037 12.53 0.00 40.22 3.16
116 117 9.947433 TGCATTATGATCATCAACTATATGACA 57.053 29.630 12.53 6.01 36.24 3.58
138 139 8.342634 TGACAAATCTGTTAAAGTTGCTCTAAC 58.657 33.333 0.00 0.00 35.30 2.34
145 146 5.178623 TGTTAAAGTTGCTCTAACATGGTCG 59.821 40.000 0.00 0.00 41.88 4.79
185 186 5.500234 TGATCCCTACAAAACTCATCTTGG 58.500 41.667 0.00 0.00 0.00 3.61
217 218 7.918076 TGATATCTAGAAACAACTTGGGAGTT 58.082 34.615 3.98 0.00 46.85 3.01
224 225 7.712204 AGAAACAACTTGGGAGTTAAAAGAA 57.288 32.000 0.00 0.00 44.14 2.52
273 274 4.101942 GTGTTTGTCAAAACTCGCATTGA 58.898 39.130 0.00 0.00 45.01 2.57
280 281 5.468409 TGTCAAAACTCGCATTGATTGAGTA 59.532 36.000 6.96 0.00 41.88 2.59
286 288 6.500684 ACTCGCATTGATTGAGTATGTTTT 57.499 33.333 5.24 0.00 40.98 2.43
289 291 6.314018 TCGCATTGATTGAGTATGTTTTGAC 58.686 36.000 0.00 0.00 0.00 3.18
357 361 7.311364 TGTTGTAAGGTTTGACTAAGTTCAC 57.689 36.000 0.00 0.00 0.00 3.18
407 411 4.743057 AAATTAAGGGCATCTCCAAAGC 57.257 40.909 0.00 0.00 36.21 3.51
416 420 2.544685 CATCTCCAAAGCTGTACCTCG 58.455 52.381 0.00 0.00 0.00 4.63
432 436 0.673644 CTCGAACCTCCCGCAAACAT 60.674 55.000 0.00 0.00 0.00 2.71
443 447 3.129113 TCCCGCAAACATTTCAGATCATG 59.871 43.478 0.00 0.00 0.00 3.07
474 478 5.149973 ACACATTTTGCCATCTAATGCAA 57.850 34.783 0.00 0.00 45.12 4.08
485 489 5.951747 GCCATCTAATGCAATCCCCTAAATA 59.048 40.000 0.00 0.00 0.00 1.40
487 491 7.124750 GCCATCTAATGCAATCCCCTAAATATT 59.875 37.037 0.00 0.00 0.00 1.28
490 494 5.391312 AATGCAATCCCCTAAATATTCGC 57.609 39.130 0.00 0.00 0.00 4.70
491 495 3.826524 TGCAATCCCCTAAATATTCGCA 58.173 40.909 0.00 0.00 0.00 5.10
493 497 4.072131 GCAATCCCCTAAATATTCGCAGA 58.928 43.478 0.00 0.00 0.00 4.26
507 511 1.790387 GCAGACCACTTCGCATGTC 59.210 57.895 0.00 0.00 0.00 3.06
537 541 3.591023 CCCAAACCAAAAACAAACTCGT 58.409 40.909 0.00 0.00 0.00 4.18
542 548 3.888583 ACCAAAAACAAACTCGTAGGGA 58.111 40.909 0.00 0.00 0.00 4.20
545 551 4.261447 CCAAAAACAAACTCGTAGGGAAGG 60.261 45.833 0.00 0.00 0.00 3.46
548 554 1.272807 CAAACTCGTAGGGAAGGGGA 58.727 55.000 0.00 0.00 0.00 4.81
570 576 1.077716 GGCTTTGCGGGGAGTACAT 60.078 57.895 0.00 0.00 0.00 2.29
578 584 1.965643 GCGGGGAGTACATACACCATA 59.034 52.381 7.66 0.00 38.49 2.74
581 587 2.298163 GGGGAGTACATACACCATACGG 59.702 54.545 7.66 0.00 38.49 4.02
598 604 2.034221 GAGGTCCACTTGGCCCAC 59.966 66.667 0.00 0.00 35.16 4.61
599 605 3.569200 GAGGTCCACTTGGCCCACC 62.569 68.421 0.00 0.00 35.16 4.61
600 606 4.678743 GGTCCACTTGGCCCACCC 62.679 72.222 0.00 0.00 32.34 4.61
602 608 2.780924 TCCACTTGGCCCACCCTT 60.781 61.111 0.00 0.00 33.59 3.95
608 614 0.404040 CTTGGCCCACCCTTAGTTGA 59.596 55.000 0.00 0.00 33.59 3.18
616 622 3.081804 CCACCCTTAGTTGAACCACATC 58.918 50.000 0.00 0.00 0.00 3.06
617 623 3.244911 CCACCCTTAGTTGAACCACATCT 60.245 47.826 0.00 0.00 33.72 2.90
622 628 5.103000 CCTTAGTTGAACCACATCTACTCG 58.897 45.833 0.00 0.00 36.86 4.18
623 629 2.960819 AGTTGAACCACATCTACTCGC 58.039 47.619 0.00 0.00 31.16 5.03
624 630 2.299013 AGTTGAACCACATCTACTCGCA 59.701 45.455 0.00 0.00 31.16 5.10
626 632 3.165058 TGAACCACATCTACTCGCATC 57.835 47.619 0.00 0.00 0.00 3.91
643 649 2.762327 GCATCCCATGTGATTTGTCCTT 59.238 45.455 0.00 0.00 0.00 3.36
644 650 3.953612 GCATCCCATGTGATTTGTCCTTA 59.046 43.478 0.00 0.00 0.00 2.69
649 655 4.772100 CCCATGTGATTTGTCCTTAAGGTT 59.228 41.667 21.04 2.77 36.34 3.50
653 659 3.751698 GTGATTTGTCCTTAAGGTTCGCT 59.248 43.478 21.04 5.02 36.34 4.93
655 661 4.215399 TGATTTGTCCTTAAGGTTCGCTTG 59.785 41.667 21.04 0.00 36.34 4.01
657 663 0.803117 GTCCTTAAGGTTCGCTTGGC 59.197 55.000 21.04 0.00 36.34 4.52
669 675 2.971598 GCTTGGCCCACCTCTGCTA 61.972 63.158 0.00 0.00 36.63 3.49
670 676 1.918253 CTTGGCCCACCTCTGCTAT 59.082 57.895 0.00 0.00 36.63 2.97
672 678 1.971505 TTGGCCCACCTCTGCTATCG 61.972 60.000 0.00 0.00 36.63 2.92
673 679 2.423446 GCCCACCTCTGCTATCGG 59.577 66.667 0.00 0.00 0.00 4.18
690 696 5.392380 GCTATCGGGATTTGATGCCTATTTG 60.392 44.000 0.00 0.00 38.84 2.32
703 709 2.223340 GCCTATTTGAGCGACATGGTTG 60.223 50.000 0.00 0.00 0.00 3.77
706 712 0.109532 TTTGAGCGACATGGTTGGGA 59.890 50.000 0.00 0.00 0.00 4.37
709 715 0.460987 GAGCGACATGGTTGGGAGAG 60.461 60.000 0.00 0.00 0.00 3.20
711 717 1.811266 CGACATGGTTGGGAGAGCG 60.811 63.158 0.00 0.00 0.00 5.03
716 722 1.201429 ATGGTTGGGAGAGCGGTTCT 61.201 55.000 0.00 0.00 39.43 3.01
725 731 2.957006 GGAGAGCGGTTCTTGTATCCTA 59.043 50.000 0.00 0.00 35.87 2.94
729 735 2.633481 AGCGGTTCTTGTATCCTATCCC 59.367 50.000 0.00 0.00 0.00 3.85
730 736 2.289506 GCGGTTCTTGTATCCTATCCCC 60.290 54.545 0.00 0.00 0.00 4.81
731 737 2.969950 CGGTTCTTGTATCCTATCCCCA 59.030 50.000 0.00 0.00 0.00 4.96
732 738 3.244112 CGGTTCTTGTATCCTATCCCCAC 60.244 52.174 0.00 0.00 0.00 4.61
734 740 4.351111 GGTTCTTGTATCCTATCCCCACAT 59.649 45.833 0.00 0.00 0.00 3.21
735 741 5.163088 GGTTCTTGTATCCTATCCCCACATT 60.163 44.000 0.00 0.00 0.00 2.71
738 744 5.669904 TCTTGTATCCTATCCCCACATTTGA 59.330 40.000 0.00 0.00 0.00 2.69
739 745 5.567037 TGTATCCTATCCCCACATTTGAG 57.433 43.478 0.00 0.00 0.00 3.02
751 790 5.515106 CCCACATTTGAGTTTAGGGGATAA 58.485 41.667 0.00 0.00 36.40 1.75
760 799 3.054875 AGTTTAGGGGATAACGTTGGGAC 60.055 47.826 11.99 0.00 0.00 4.46
761 800 2.250921 TAGGGGATAACGTTGGGACA 57.749 50.000 11.99 0.00 0.00 4.02
833 874 9.448294 CTCTATTCGGTGTTATAGTAGTTGTTC 57.552 37.037 0.00 0.00 0.00 3.18
880 921 4.946784 AAGTATGCATCGTTTGACTTCC 57.053 40.909 0.19 0.00 0.00 3.46
907 2393 7.315890 AGAAAATCAATAGGCTTTCTTTTCGG 58.684 34.615 0.00 0.00 35.15 4.30
938 2424 7.040823 ACACCATTTTTCTGAAACTTTTTGCAA 60.041 29.630 1.58 0.00 0.00 4.08
979 2471 1.375853 GCATTCGTGTAGCCCATGCA 61.376 55.000 0.00 0.00 40.06 3.96
980 2472 1.093972 CATTCGTGTAGCCCATGCAA 58.906 50.000 0.00 0.00 41.13 4.08
982 2474 0.036164 TTCGTGTAGCCCATGCAAGT 59.964 50.000 0.00 0.00 41.13 3.16
1034 2538 1.079127 AACATCTTCCACCTCCGCG 60.079 57.895 0.00 0.00 0.00 6.46
1035 2539 2.202932 CATCTTCCACCTCCGCGG 60.203 66.667 22.12 22.12 39.35 6.46
1172 2676 3.712907 GGCCCTTGCGGTCCTACA 61.713 66.667 0.00 0.00 38.85 2.74
1173 2677 2.349755 GCCCTTGCGGTCCTACAA 59.650 61.111 0.00 0.00 0.00 2.41
1236 2740 3.873883 GCTGTCATCTGCTGCGCC 61.874 66.667 4.18 0.00 35.98 6.53
1329 2833 2.829458 GCGTACCTCCTCTCCGCT 60.829 66.667 0.00 0.00 41.06 5.52
1335 2839 2.057408 CCTCCTCTCCGCTCTGCTT 61.057 63.158 0.00 0.00 0.00 3.91
1341 2845 0.109086 TCTCCGCTCTGCTTTCTTCG 60.109 55.000 0.00 0.00 0.00 3.79
1346 2850 1.651138 CGCTCTGCTTTCTTCGTACTG 59.349 52.381 0.00 0.00 0.00 2.74
1458 2962 2.106938 GTCATCTCCGGATGCGCA 59.893 61.111 14.96 14.96 46.41 6.09
1656 3160 2.216898 GCCAACTGCCTCATATCTGTC 58.783 52.381 0.00 0.00 0.00 3.51
1788 3292 4.373116 GCTGTGGACGCCCTCGAA 62.373 66.667 0.00 0.00 39.41 3.71
1922 3435 1.730612 CTACGTGCGTGAGAGACTACA 59.269 52.381 7.55 0.00 0.00 2.74
1979 3492 2.401583 ATCAACTTCCATGCACGCTA 57.598 45.000 0.00 0.00 0.00 4.26
2109 3622 4.735369 TGGCCATTAAACTCTTCCAAAGA 58.265 39.130 0.00 0.00 35.87 2.52
2125 3638 1.813513 AAGAATGGTGTCAGAAGGCG 58.186 50.000 0.00 0.00 0.00 5.52
2129 3642 0.973632 ATGGTGTCAGAAGGCGTACA 59.026 50.000 0.00 0.00 0.00 2.90
2169 3682 4.681978 GCCCTCTTGTCGGCGTGT 62.682 66.667 6.85 0.00 34.94 4.49
2223 3736 5.489792 AGTACTTCTTTGCAATGGAGAGA 57.510 39.130 23.70 10.28 0.00 3.10
2284 3797 1.477685 GGTGGACCTTCTTGGACGGA 61.478 60.000 0.00 0.00 39.71 4.69
2340 3853 4.214266 ATGCCCATGCCAGCCGAT 62.214 61.111 0.00 0.00 36.33 4.18
2395 3908 6.974622 GTGCAAGATACATAAAAATGTGGAGG 59.025 38.462 1.34 0.00 36.08 4.30
2438 3951 5.651172 CATGTTATTATGCTCGAACCGAA 57.349 39.130 0.00 0.00 34.74 4.30
2577 4091 0.974383 CTACCTCGAACACAAGGGGT 59.026 55.000 0.00 0.00 36.95 4.95
2643 4157 2.711542 AGGGAATTTACGAGCTTGTGG 58.288 47.619 17.36 0.00 0.00 4.17
2727 4253 4.020218 TGCTTGACAAGAAGGTAGCTGTAT 60.020 41.667 19.51 0.00 0.00 2.29
2830 4368 2.923035 CCTGAGGTGTGGGGACGT 60.923 66.667 0.00 0.00 0.00 4.34
2880 4418 2.265904 GCCAACCGGGTGTTTCTCC 61.266 63.158 20.34 0.00 39.65 3.71
2881 4419 1.964373 CCAACCGGGTGTTTCTCCG 60.964 63.158 20.34 0.00 45.29 4.63
2904 4442 2.019984 GGGATTCGAGCTGCTTTCATT 58.980 47.619 2.53 0.00 0.00 2.57
2977 4515 1.416401 TGGTCCTCACTGTGAAGGAAC 59.584 52.381 24.96 24.96 34.27 3.62
3002 4549 3.814601 TGGTTGCACCGGATACCT 58.185 55.556 9.46 0.00 42.58 3.08
3004 4551 0.828022 TGGTTGCACCGGATACCTAG 59.172 55.000 9.46 0.00 42.58 3.02
3005 4552 0.828677 GGTTGCACCGGATACCTAGT 59.171 55.000 9.46 0.00 0.00 2.57
3107 4704 1.679139 CAGGCTGGACAAACAACAGA 58.321 50.000 6.61 0.00 34.21 3.41
3157 4754 5.463392 TGATGCTCAACTATGTAAAGATCGC 59.537 40.000 0.00 0.00 0.00 4.58
3162 4759 5.769367 TCAACTATGTAAAGATCGCGCTAT 58.231 37.500 5.56 0.00 0.00 2.97
3164 4761 5.122512 ACTATGTAAAGATCGCGCTATGT 57.877 39.130 5.56 0.00 0.00 2.29
3165 4762 6.250344 ACTATGTAAAGATCGCGCTATGTA 57.750 37.500 5.56 0.00 0.00 2.29
3256 4855 1.168714 CAAGTTTCCCTACAGGCTGC 58.831 55.000 15.89 0.00 34.51 5.25
3268 4867 0.107945 CAGGCTGCTCTTGTACTCCC 60.108 60.000 0.00 0.00 0.00 4.30
3273 4872 0.888619 TGCTCTTGTACTCCCGAGTG 59.111 55.000 7.63 0.00 42.52 3.51
3286 4885 1.442526 CCGAGTGGGATGCTGAATGC 61.443 60.000 0.00 0.00 39.43 3.56
3287 4886 1.442526 CGAGTGGGATGCTGAATGCC 61.443 60.000 0.00 0.00 46.82 4.40
3292 4891 0.761702 GGGATGCTGAATGCCCCATT 60.762 55.000 0.00 0.00 40.88 3.16
3323 4922 6.974622 GGTTCAATGGCTGATAACTAATTGTG 59.025 38.462 0.00 0.00 32.78 3.33
3347 4946 5.596845 GAGTATCCTGATTTCAGAGGTGTC 58.403 45.833 9.15 0.00 46.59 3.67
3437 5044 1.539496 GCACCGTTCAGTTCAGTGGTA 60.539 52.381 0.00 0.00 0.00 3.25
3530 5141 7.090808 GGAAAGTTTCACTGAAATATGGAACC 58.909 38.462 17.16 3.00 35.25 3.62
3549 5160 5.446143 AACCAAATGTTTTCATACTCGCA 57.554 34.783 0.00 0.00 39.94 5.10
3561 5172 4.007644 CTCGCAGGTGTGGGCTGA 62.008 66.667 0.00 0.00 36.56 4.26
3568 5179 0.839946 AGGTGTGGGCTGATGATACC 59.160 55.000 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 9.574516 CCCTAGAGGCAATAATAAAGTTGTTAT 57.425 33.333 0.00 0.00 0.00 1.89
16 17 8.974060 CCCTAGAGGCAATAATAAAGTTGTTA 57.026 34.615 0.00 0.00 0.00 2.41
17 18 7.881775 CCCTAGAGGCAATAATAAAGTTGTT 57.118 36.000 0.00 0.00 0.00 2.83
33 34 4.263243 CCTGAAGGAAATATGCCCTAGAGG 60.263 50.000 0.00 0.00 37.39 3.69
34 35 4.594920 TCCTGAAGGAAATATGCCCTAGAG 59.405 45.833 0.00 0.00 42.18 2.43
35 36 4.566837 TCCTGAAGGAAATATGCCCTAGA 58.433 43.478 0.00 0.00 42.18 2.43
36 37 4.982241 TCCTGAAGGAAATATGCCCTAG 57.018 45.455 0.00 0.00 42.18 3.02
48 49 5.346782 AGATATAGAGGCTTCCTGAAGGA 57.653 43.478 8.85 0.00 43.73 3.36
49 50 8.859090 CATATAGATATAGAGGCTTCCTGAAGG 58.141 40.741 8.85 0.00 38.80 3.46
50 51 9.639563 TCATATAGATATAGAGGCTTCCTGAAG 57.360 37.037 2.48 2.48 41.24 3.02
51 52 9.997172 TTCATATAGATATAGAGGCTTCCTGAA 57.003 33.333 0.00 0.00 31.76 3.02
52 53 9.639563 CTTCATATAGATATAGAGGCTTCCTGA 57.360 37.037 0.00 0.00 31.76 3.86
53 54 8.359642 GCTTCATATAGATATAGAGGCTTCCTG 58.640 40.741 0.00 0.00 31.76 3.86
54 55 8.064389 TGCTTCATATAGATATAGAGGCTTCCT 58.936 37.037 0.00 0.00 36.03 3.36
55 56 8.141268 GTGCTTCATATAGATATAGAGGCTTCC 58.859 40.741 0.00 0.00 0.00 3.46
56 57 7.860373 CGTGCTTCATATAGATATAGAGGCTTC 59.140 40.741 0.00 0.00 0.00 3.86
57 58 7.683222 GCGTGCTTCATATAGATATAGAGGCTT 60.683 40.741 0.00 0.00 0.00 4.35
58 59 6.238897 GCGTGCTTCATATAGATATAGAGGCT 60.239 42.308 0.00 0.00 0.00 4.58
59 60 5.918011 GCGTGCTTCATATAGATATAGAGGC 59.082 44.000 0.00 0.00 0.00 4.70
60 61 7.270757 AGCGTGCTTCATATAGATATAGAGG 57.729 40.000 0.00 0.00 0.00 3.69
61 62 7.012799 TGGAGCGTGCTTCATATAGATATAGAG 59.987 40.741 0.00 0.00 0.00 2.43
62 63 6.828785 TGGAGCGTGCTTCATATAGATATAGA 59.171 38.462 0.00 0.00 0.00 1.98
63 64 7.032377 TGGAGCGTGCTTCATATAGATATAG 57.968 40.000 0.00 0.00 0.00 1.31
64 65 7.588497 ATGGAGCGTGCTTCATATAGATATA 57.412 36.000 13.93 0.00 40.28 0.86
65 66 5.921962 TGGAGCGTGCTTCATATAGATAT 57.078 39.130 0.00 0.00 0.00 1.63
80 81 4.835678 TGATCATAATGCATATGGAGCGT 58.164 39.130 0.00 0.00 41.53 5.07
113 114 8.342634 TGTTAGAGCAACTTTAACAGATTTGTC 58.657 33.333 6.62 0.00 36.56 3.18
116 117 8.299570 CCATGTTAGAGCAACTTTAACAGATTT 58.700 33.333 13.85 0.00 41.80 2.17
118 119 6.942576 ACCATGTTAGAGCAACTTTAACAGAT 59.057 34.615 13.85 2.87 41.80 2.90
121 122 5.178623 CGACCATGTTAGAGCAACTTTAACA 59.821 40.000 11.64 11.64 42.38 2.41
125 126 3.997021 CTCGACCATGTTAGAGCAACTTT 59.003 43.478 0.00 0.00 38.05 2.66
224 225 7.835822 TGTGCAAGGCATGTAAATTATAGTTT 58.164 30.769 0.00 0.00 41.91 2.66
237 238 1.795872 CAAACACATGTGCAAGGCATG 59.204 47.619 25.68 12.80 46.51 4.06
321 323 6.391227 AACCTTACAACATTTGAGTTCTGG 57.609 37.500 0.00 0.00 0.00 3.86
384 388 5.957774 AGCTTTGGAGATGCCCTTAATTTTA 59.042 36.000 0.00 0.00 34.97 1.52
385 389 4.779489 AGCTTTGGAGATGCCCTTAATTTT 59.221 37.500 0.00 0.00 34.97 1.82
407 411 1.807886 CGGGAGGTTCGAGGTACAG 59.192 63.158 0.00 0.00 0.00 2.74
416 420 1.611491 TGAAATGTTTGCGGGAGGTTC 59.389 47.619 0.00 0.00 0.00 3.62
432 436 3.327464 TGTCAGGACCACATGATCTGAAA 59.673 43.478 0.00 0.00 39.00 2.69
443 447 1.000274 GGCAAAATGTGTCAGGACCAC 60.000 52.381 0.00 0.00 0.00 4.16
474 478 3.650942 TGGTCTGCGAATATTTAGGGGAT 59.349 43.478 0.00 0.00 0.00 3.85
485 489 0.391661 ATGCGAAGTGGTCTGCGAAT 60.392 50.000 0.00 0.00 44.90 3.34
487 491 1.737735 CATGCGAAGTGGTCTGCGA 60.738 57.895 0.00 0.00 44.90 5.10
490 494 1.354337 CGGACATGCGAAGTGGTCTG 61.354 60.000 0.00 0.00 0.00 3.51
491 495 1.079819 CGGACATGCGAAGTGGTCT 60.080 57.895 0.00 0.00 0.00 3.85
493 497 0.534203 AAACGGACATGCGAAGTGGT 60.534 50.000 0.00 0.00 0.00 4.16
522 526 4.261447 CCTTCCCTACGAGTTTGTTTTTGG 60.261 45.833 0.00 0.00 0.00 3.28
525 529 3.483421 CCCTTCCCTACGAGTTTGTTTT 58.517 45.455 0.00 0.00 0.00 2.43
528 532 0.981943 CCCCTTCCCTACGAGTTTGT 59.018 55.000 0.00 0.00 0.00 2.83
537 541 4.810184 GCCCCGTCCCCTTCCCTA 62.810 72.222 0.00 0.00 0.00 3.53
542 548 4.678743 GCAAAGCCCCGTCCCCTT 62.679 66.667 0.00 0.00 0.00 3.95
560 566 2.298163 CCGTATGGTGTATGTACTCCCC 59.702 54.545 8.37 0.00 38.69 4.81
570 576 1.006281 AGTGGACCTCCGTATGGTGTA 59.994 52.381 0.00 0.00 38.03 2.90
578 584 3.637273 GGCCAAGTGGACCTCCGT 61.637 66.667 0.00 0.00 37.19 4.69
598 604 5.420409 GAGTAGATGTGGTTCAACTAAGGG 58.580 45.833 0.00 0.00 34.17 3.95
599 605 5.103000 CGAGTAGATGTGGTTCAACTAAGG 58.897 45.833 0.00 0.00 34.17 2.69
600 606 4.563184 GCGAGTAGATGTGGTTCAACTAAG 59.437 45.833 0.00 0.00 34.17 2.18
602 608 3.508402 TGCGAGTAGATGTGGTTCAACTA 59.492 43.478 0.00 0.00 31.70 2.24
608 614 1.139058 GGGATGCGAGTAGATGTGGTT 59.861 52.381 0.00 0.00 0.00 3.67
616 622 2.827800 ATCACATGGGATGCGAGTAG 57.172 50.000 10.38 0.00 0.00 2.57
617 623 3.205338 CAAATCACATGGGATGCGAGTA 58.795 45.455 12.19 0.00 0.00 2.59
622 628 2.381911 AGGACAAATCACATGGGATGC 58.618 47.619 12.19 1.61 0.00 3.91
623 629 5.068198 CCTTAAGGACAAATCACATGGGATG 59.932 44.000 17.21 3.83 37.39 3.51
624 630 5.203528 CCTTAAGGACAAATCACATGGGAT 58.796 41.667 17.21 4.06 37.39 3.85
626 632 4.344104 ACCTTAAGGACAAATCACATGGG 58.656 43.478 28.52 0.00 38.94 4.00
643 649 1.302993 GTGGGCCAAGCGAACCTTA 60.303 57.895 8.40 0.00 31.00 2.69
644 650 2.597510 GTGGGCCAAGCGAACCTT 60.598 61.111 8.40 0.00 0.00 3.50
649 655 4.020617 CAGAGGTGGGCCAAGCGA 62.021 66.667 8.40 0.00 37.19 4.93
653 659 1.915228 GATAGCAGAGGTGGGCCAA 59.085 57.895 8.40 0.00 37.19 4.52
655 661 2.423446 CGATAGCAGAGGTGGGCC 59.577 66.667 0.00 0.00 0.00 5.80
657 663 0.833834 ATCCCGATAGCAGAGGTGGG 60.834 60.000 0.00 0.00 38.02 4.61
667 673 5.939883 TCAAATAGGCATCAAATCCCGATAG 59.060 40.000 0.00 0.00 0.00 2.08
669 675 4.728772 TCAAATAGGCATCAAATCCCGAT 58.271 39.130 0.00 0.00 0.00 4.18
670 676 4.136796 CTCAAATAGGCATCAAATCCCGA 58.863 43.478 0.00 0.00 0.00 5.14
672 678 3.304928 CGCTCAAATAGGCATCAAATCCC 60.305 47.826 0.00 0.00 0.00 3.85
673 679 3.565482 TCGCTCAAATAGGCATCAAATCC 59.435 43.478 0.00 0.00 0.00 3.01
690 696 0.460987 CTCTCCCAACCATGTCGCTC 60.461 60.000 0.00 0.00 0.00 5.03
703 709 1.202545 GGATACAAGAACCGCTCTCCC 60.203 57.143 0.00 0.00 31.02 4.30
706 712 3.574826 GGATAGGATACAAGAACCGCTCT 59.425 47.826 0.00 0.00 41.41 4.09
709 715 2.289506 GGGGATAGGATACAAGAACCGC 60.290 54.545 0.00 0.00 41.41 5.68
711 717 3.714798 TGTGGGGATAGGATACAAGAACC 59.285 47.826 0.00 0.00 41.41 3.62
716 722 5.431731 ACTCAAATGTGGGGATAGGATACAA 59.568 40.000 0.00 0.00 41.41 2.41
725 731 3.981212 CCCTAAACTCAAATGTGGGGAT 58.019 45.455 0.00 0.00 34.94 3.85
729 735 5.065988 CGTTATCCCCTAAACTCAAATGTGG 59.934 44.000 0.00 0.00 0.00 4.17
730 736 5.646360 ACGTTATCCCCTAAACTCAAATGTG 59.354 40.000 0.00 0.00 0.00 3.21
731 737 5.812286 ACGTTATCCCCTAAACTCAAATGT 58.188 37.500 0.00 0.00 0.00 2.71
732 738 6.404293 CCAACGTTATCCCCTAAACTCAAATG 60.404 42.308 0.00 0.00 0.00 2.32
734 740 5.005094 CCAACGTTATCCCCTAAACTCAAA 58.995 41.667 0.00 0.00 0.00 2.69
735 741 4.566070 CCCAACGTTATCCCCTAAACTCAA 60.566 45.833 0.00 0.00 0.00 3.02
738 744 3.054875 GTCCCAACGTTATCCCCTAAACT 60.055 47.826 0.00 0.00 0.00 2.66
739 745 3.273434 GTCCCAACGTTATCCCCTAAAC 58.727 50.000 0.00 0.00 0.00 2.01
751 790 4.764050 TGATATTATGGTGTCCCAACGT 57.236 40.909 0.00 0.00 46.04 3.99
826 867 7.996644 TGTTTGTAGGGAAAATCTAGAACAACT 59.003 33.333 0.00 0.00 0.00 3.16
833 874 7.611213 AATCGTGTTTGTAGGGAAAATCTAG 57.389 36.000 0.00 0.00 0.00 2.43
835 876 7.989416 TTAATCGTGTTTGTAGGGAAAATCT 57.011 32.000 0.00 0.00 0.00 2.40
880 921 7.217070 CGAAAAGAAAGCCTATTGATTTTCTCG 59.783 37.037 0.00 0.00 38.54 4.04
938 2424 2.798847 GTTCTTTCGGCTAGTGTTCGTT 59.201 45.455 0.00 0.00 0.00 3.85
979 2471 2.852075 TGGAACTGGGGCCGACTT 60.852 61.111 0.00 0.00 0.00 3.01
980 2472 3.322466 CTGGAACTGGGGCCGACT 61.322 66.667 0.00 0.00 0.00 4.18
1329 2833 1.668919 CGGCAGTACGAAGAAAGCAGA 60.669 52.381 0.00 0.00 35.47 4.26
1335 2839 1.214589 GAGGCGGCAGTACGAAGAA 59.785 57.895 13.08 0.00 35.47 2.52
1758 3262 0.247460 CCACAGCGAGACCATTCTGA 59.753 55.000 0.00 0.00 29.47 3.27
1874 3387 1.534476 TCCAGGCCAACACTACGGA 60.534 57.895 5.01 0.00 0.00 4.69
1911 3424 2.168496 CGAAACCCCTGTAGTCTCTCA 58.832 52.381 0.00 0.00 0.00 3.27
1922 3435 1.152830 ACATTGGCACGAAACCCCT 59.847 52.632 0.00 0.00 0.00 4.79
2109 3622 1.346395 TGTACGCCTTCTGACACCATT 59.654 47.619 0.00 0.00 0.00 3.16
2125 3638 2.821546 TGCGACATTATCTGGCTGTAC 58.178 47.619 0.00 0.00 0.00 2.90
2129 3642 2.224606 CCATTGCGACATTATCTGGCT 58.775 47.619 0.00 0.00 0.00 4.75
2169 3682 0.396435 CATACTTCCCGGCATGGCTA 59.604 55.000 18.09 1.76 35.87 3.93
2223 3736 1.550130 TAGGCCGCAGCTTGTAGGTT 61.550 55.000 0.00 0.00 39.73 3.50
2340 3853 2.194597 GCACCCCACACAGAACCA 59.805 61.111 0.00 0.00 0.00 3.67
2395 3908 2.142292 TTGAAAGCCTCCTCCCCTGC 62.142 60.000 0.00 0.00 0.00 4.85
2438 3951 1.674817 GCACGTAGTAGCCCACATTGT 60.675 52.381 0.00 0.00 41.61 2.71
2577 4091 5.168569 GTCGTCCATTAACAGATGAACTCA 58.831 41.667 1.11 0.00 30.11 3.41
2625 4139 3.500680 TCAACCACAAGCTCGTAAATTCC 59.499 43.478 0.00 0.00 0.00 3.01
2643 4157 4.818534 TGACAATCTGCTCAAGTTCAAC 57.181 40.909 0.00 0.00 0.00 3.18
2727 4253 0.813610 CTGTGAGTGCCAACCAACGA 60.814 55.000 0.00 0.00 0.00 3.85
2830 4368 1.550524 CCATCTTCAGGAACGAGTGGA 59.449 52.381 0.00 0.00 0.00 4.02
2880 4418 3.267860 GCAGCTCGAATCCCTGCG 61.268 66.667 10.08 0.00 41.99 5.18
2904 4442 2.922503 TGCTCCACCCTCGAAGCA 60.923 61.111 3.15 3.15 42.16 3.91
2935 4473 9.956720 GACCAAATCCAATTATTCATCAGTAAG 57.043 33.333 0.00 0.00 0.00 2.34
3002 4549 6.054860 AGATTTGGAGCAAAAGCTAGACTA 57.945 37.500 0.00 0.00 36.90 2.59
3004 4551 5.414144 AGAAGATTTGGAGCAAAAGCTAGAC 59.586 40.000 0.00 0.00 34.82 2.59
3005 4552 5.413833 CAGAAGATTTGGAGCAAAAGCTAGA 59.586 40.000 0.00 0.00 34.82 2.43
3077 4646 1.757118 GTCCAGCCTGCAGTACTATGA 59.243 52.381 13.81 7.06 0.00 2.15
3079 4648 1.866015 TGTCCAGCCTGCAGTACTAT 58.134 50.000 13.81 0.00 0.00 2.12
3107 4704 1.203187 TGAGGGTACTGGCTGTCTCTT 60.203 52.381 0.00 0.00 0.00 2.85
3157 4754 5.687730 CAGGTTCTACTCAACATACATAGCG 59.312 44.000 0.00 0.00 0.00 4.26
3162 4759 5.084519 ACCTCAGGTTCTACTCAACATACA 58.915 41.667 0.00 0.00 27.29 2.29
3268 4867 2.020131 GCATTCAGCATCCCACTCG 58.980 57.895 0.00 0.00 44.79 4.18
3273 4872 2.707384 GAATGGGGCATTCAGCATCCC 61.707 57.143 0.00 0.00 46.50 3.85
3286 4885 3.876341 CCATTGAACCAAATGAATGGGG 58.124 45.455 0.00 0.00 45.18 4.96
3287 4886 3.054948 AGCCATTGAACCAAATGAATGGG 60.055 43.478 0.00 0.00 45.18 4.00
3292 4891 5.716228 AGTTATCAGCCATTGAACCAAATGA 59.284 36.000 0.00 0.00 39.46 2.57
3296 4895 7.178274 ACAATTAGTTATCAGCCATTGAACCAA 59.822 33.333 0.00 0.00 39.77 3.67
3347 4946 5.437289 TCTGGTTAAAATCTGCACTTGTG 57.563 39.130 0.00 0.00 0.00 3.33
3376 4983 1.260561 GTGTTTCTGGTGTACACTGCG 59.739 52.381 24.55 13.33 39.18 5.18
3377 4984 1.602377 GGTGTTTCTGGTGTACACTGC 59.398 52.381 24.55 10.37 41.37 4.40
3381 4988 1.069513 CTCGGGTGTTTCTGGTGTACA 59.930 52.381 0.00 0.00 0.00 2.90
3420 5027 5.163550 TGAGATATACCACTGAACTGAACGG 60.164 44.000 0.00 0.00 0.00 4.44
3530 5141 4.853196 CACCTGCGAGTATGAAAACATTTG 59.147 41.667 0.00 0.00 0.00 2.32
3549 5160 0.839946 GGTATCATCAGCCCACACCT 59.160 55.000 0.00 0.00 0.00 4.00
3561 5172 4.767578 ATTCACTGTCAGCTGGTATCAT 57.232 40.909 15.13 0.00 0.00 2.45
3568 5179 5.174579 CACGACATATATTCACTGTCAGCTG 59.825 44.000 7.63 7.63 39.36 4.24


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

AutoCloner maintained by Alex Coulton.