Multiple sequence alignment - TraesCS4A01G091900

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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 TraesCS4A01G091900 chr4A 100.000 6100 0 0 1 6100 98606396 98600297 0.000000e+00 11265.0
1 TraesCS4A01G091900 chr4A 91.005 1045 79 7 4136 5176 56483150 56482117 0.000000e+00 1395.0
2 TraesCS4A01G091900 chr4A 87.121 132 11 4 3588 3713 628209524 628209393 1.770000e-30 145.0
3 TraesCS4A01G091900 chr4B 94.786 3606 113 38 839 4417 450908943 450912500 0.000000e+00 5548.0
4 TraesCS4A01G091900 chr4B 94.648 1009 32 8 4407 5413 450912891 450913879 0.000000e+00 1544.0
5 TraesCS4A01G091900 chr4B 95.770 662 22 4 5442 6100 450914006 450914664 0.000000e+00 1062.0
6 TraesCS4A01G091900 chr4D 96.060 1878 50 13 1743 3602 366318190 366320061 0.000000e+00 3037.0
7 TraesCS4A01G091900 chr4D 95.706 1700 53 8 4407 6100 366321233 366322918 0.000000e+00 2717.0
8 TraesCS4A01G091900 chr4D 95.838 889 27 3 839 1726 366317324 366318203 0.000000e+00 1428.0
9 TraesCS4A01G091900 chr4D 95.541 785 29 4 3639 4417 366320063 366320847 0.000000e+00 1251.0
10 TraesCS4A01G091900 chr4D 92.683 123 9 0 4343 4465 509048867 509048989 1.750000e-40 178.0
11 TraesCS4A01G091900 chr4D 94.737 38 2 0 4314 4351 509048843 509048806 6.600000e-05 60.2
12 TraesCS4A01G091900 chr3D 91.778 1046 71 7 4136 5176 443674070 443673035 0.000000e+00 1441.0
13 TraesCS4A01G091900 chr3D 89.379 838 66 10 1 832 613714823 613715643 0.000000e+00 1033.0
14 TraesCS4A01G091900 chr3D 89.844 128 10 1 3589 3716 477906264 477906140 1.760000e-35 161.0
15 TraesCS4A01G091900 chr3D 90.244 123 10 2 3590 3712 127342839 127342719 6.330000e-35 159.0
16 TraesCS4A01G091900 chr2A 89.367 837 84 3 1 832 47362998 47362162 0.000000e+00 1048.0
17 TraesCS4A01G091900 chr2A 84.726 838 118 7 1 832 673147136 673146303 0.000000e+00 830.0
18 TraesCS4A01G091900 chr2A 89.557 632 66 0 4565 5196 578017975 578017344 0.000000e+00 802.0
19 TraesCS4A01G091900 chr2A 90.147 477 31 11 4108 4580 578033424 578032960 1.880000e-169 606.0
20 TraesCS4A01G091900 chr6D 86.516 838 97 10 1 832 13144533 13143706 0.000000e+00 907.0
21 TraesCS4A01G091900 chrUn 86.260 837 108 5 1 832 362956903 362957737 0.000000e+00 902.0
22 TraesCS4A01G091900 chrUn 86.141 837 109 5 1 832 236902001 236901167 0.000000e+00 896.0
23 TraesCS4A01G091900 chrUn 85.902 837 111 5 1 832 257249085 257248251 0.000000e+00 885.0
24 TraesCS4A01G091900 chrUn 85.783 837 112 5 1 832 291628062 291627228 0.000000e+00 880.0
25 TraesCS4A01G091900 chr5D 85.198 858 97 10 1 832 350796976 350797829 0.000000e+00 854.0
26 TraesCS4A01G091900 chr7D 82.526 475 69 9 361 832 136523528 136523065 7.360000e-109 405.0
27 TraesCS4A01G091900 chr7D 80.430 465 59 18 379 831 426882095 426881651 5.900000e-85 326.0
28 TraesCS4A01G091900 chr6B 92.718 206 14 1 4972 5176 101435317 101435522 4.620000e-76 296.0
29 TraesCS4A01G091900 chr3A 90.840 131 9 1 3589 3716 621323865 621323735 8.130000e-39 172.0
30 TraesCS4A01G091900 chr3A 88.550 131 11 2 3589 3715 420739371 420739501 8.190000e-34 156.0
31 TraesCS4A01G091900 chr2D 90.000 130 10 3 3589 3715 170620064 170619935 1.360000e-36 165.0
32 TraesCS4A01G091900 chr1A 89.147 129 9 2 3589 3712 325046120 325046248 8.190000e-34 156.0
33 TraesCS4A01G091900 chr5A 87.500 136 12 3 3584 3716 367133296 367133163 1.060000e-32 152.0


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 TraesCS4A01G091900 chr4A 98600297 98606396 6099 True 11265.00 11265 100.00000 1 6100 1 chr4A.!!$R2 6099
1 TraesCS4A01G091900 chr4A 56482117 56483150 1033 True 1395.00 1395 91.00500 4136 5176 1 chr4A.!!$R1 1040
2 TraesCS4A01G091900 chr4B 450908943 450914664 5721 False 2718.00 5548 95.06800 839 6100 3 chr4B.!!$F1 5261
3 TraesCS4A01G091900 chr4D 366317324 366322918 5594 False 2108.25 3037 95.78625 839 6100 4 chr4D.!!$F2 5261
4 TraesCS4A01G091900 chr3D 443673035 443674070 1035 True 1441.00 1441 91.77800 4136 5176 1 chr3D.!!$R2 1040
5 TraesCS4A01G091900 chr3D 613714823 613715643 820 False 1033.00 1033 89.37900 1 832 1 chr3D.!!$F1 831
6 TraesCS4A01G091900 chr2A 47362162 47362998 836 True 1048.00 1048 89.36700 1 832 1 chr2A.!!$R1 831
7 TraesCS4A01G091900 chr2A 673146303 673147136 833 True 830.00 830 84.72600 1 832 1 chr2A.!!$R4 831
8 TraesCS4A01G091900 chr2A 578017344 578017975 631 True 802.00 802 89.55700 4565 5196 1 chr2A.!!$R2 631
9 TraesCS4A01G091900 chr6D 13143706 13144533 827 True 907.00 907 86.51600 1 832 1 chr6D.!!$R1 831
10 TraesCS4A01G091900 chrUn 362956903 362957737 834 False 902.00 902 86.26000 1 832 1 chrUn.!!$F1 831
11 TraesCS4A01G091900 chrUn 236901167 236902001 834 True 896.00 896 86.14100 1 832 1 chrUn.!!$R1 831
12 TraesCS4A01G091900 chrUn 257248251 257249085 834 True 885.00 885 85.90200 1 832 1 chrUn.!!$R2 831
13 TraesCS4A01G091900 chrUn 291627228 291628062 834 True 880.00 880 85.78300 1 832 1 chrUn.!!$R3 831
14 TraesCS4A01G091900 chr5D 350796976 350797829 853 False 854.00 854 85.19800 1 832 1 chr5D.!!$F1 831

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
834 866 0.107508 CCGTCAGGCATCAATGGTCT 60.108 55.000 0.00 0.00 0.00 3.85 F
837 869 0.994247 TCAGGCATCAATGGTCTGGT 59.006 50.000 0.00 0.00 0.00 4.00 F
2611 2660 1.145571 TTGGACCAACCTGCTACCTT 58.854 50.000 1.69 0.00 39.86 3.50 F
3778 3837 0.251474 TCCCTGCTTGCTCATGCTTT 60.251 50.000 8.80 0.00 40.48 3.51 F
4341 4408 1.342174 AGCTGGAACAAGCCACAATTG 59.658 47.619 3.24 3.24 38.70 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2428 2472 0.181350 GGCACCGATTGGAAGGATCT 59.819 55.0 5.81 0.00 39.21 2.75 R
2724 2780 5.302823 AGCAATTTCTCTGTTTTGGCTTAGT 59.697 36.0 0.00 0.00 0.00 2.24 R
4087 4148 0.906282 TGGCATGAGCTCCTGACAGA 60.906 55.0 22.17 2.09 41.70 3.41 R
4743 5211 0.899717 ACACCATCACACCCCAATGC 60.900 55.0 0.00 0.00 0.00 3.56 R
5780 6349 0.663269 GGGCGAAAGTTTGGAAAGCG 60.663 55.0 1.30 0.00 29.71 4.68 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
125 126 3.467226 GACCCCGCCTTCATCCGA 61.467 66.667 0.00 0.00 0.00 4.55
163 167 1.667154 CCACGGCGAGAGAAGGATGA 61.667 60.000 16.62 0.00 0.00 2.92
294 298 3.912907 GATCGCGGGGGATGACGT 61.913 66.667 6.13 0.00 0.00 4.34
295 299 3.441011 GATCGCGGGGGATGACGTT 62.441 63.158 6.13 0.00 0.00 3.99
308 312 1.525077 GACGTTGTTGGTGGAGGCA 60.525 57.895 0.00 0.00 0.00 4.75
524 528 4.853142 TCTGGGGGCGCCGAGTAT 62.853 66.667 27.21 0.00 0.00 2.12
573 577 4.003788 CTTGGAGGTGGCGACGGT 62.004 66.667 0.00 0.00 0.00 4.83
614 618 1.671742 GTCGCCTGGAAACCTCTCA 59.328 57.895 0.00 0.00 0.00 3.27
671 699 3.467803 GGAGAGTGTAGCTTTTGTGTGT 58.532 45.455 0.00 0.00 0.00 3.72
674 702 3.120792 GAGTGTAGCTTTTGTGTGTCGA 58.879 45.455 0.00 0.00 0.00 4.20
678 707 4.505191 GTGTAGCTTTTGTGTGTCGAAGTA 59.495 41.667 0.00 0.00 0.00 2.24
736 767 0.596600 CGCCTTTTATAGCCGAGCGA 60.597 55.000 0.00 0.00 44.51 4.93
819 851 2.480555 CTTCATTGTGCCGCCGTC 59.519 61.111 0.00 0.00 0.00 4.79
832 864 4.643795 CCGTCAGGCATCAATGGT 57.356 55.556 0.00 0.00 0.00 3.55
833 865 2.397751 CCGTCAGGCATCAATGGTC 58.602 57.895 0.00 0.00 0.00 4.02
834 866 0.107508 CCGTCAGGCATCAATGGTCT 60.108 55.000 0.00 0.00 0.00 3.85
835 867 1.012086 CGTCAGGCATCAATGGTCTG 58.988 55.000 0.00 0.00 0.00 3.51
836 868 1.386533 GTCAGGCATCAATGGTCTGG 58.613 55.000 0.00 0.00 0.00 3.86
837 869 0.994247 TCAGGCATCAATGGTCTGGT 59.006 50.000 0.00 0.00 0.00 4.00
873 905 6.177610 ACCCCTCAAAAGAAAAAGGAAAAAC 58.822 36.000 0.00 0.00 0.00 2.43
1477 1512 8.026607 CCGATTATTCCTTCTCTCATTCTCTAC 58.973 40.741 0.00 0.00 0.00 2.59
1498 1533 4.147321 ACTGTTGATCTGTTCCTGCATTT 58.853 39.130 0.00 0.00 0.00 2.32
1566 1601 8.607441 TTATATGAGGATGTTGTTATGCTGTC 57.393 34.615 0.00 0.00 0.00 3.51
1578 1613 5.479306 TGTTATGCTGTCTCTAGGTGTTTC 58.521 41.667 0.00 0.00 0.00 2.78
1604 1639 5.123820 CCTAACCACATACTCCAATTGTGTG 59.876 44.000 15.61 15.61 39.23 3.82
1628 1663 2.013400 TGCTACACGGTGGCAATATTG 58.987 47.619 13.48 11.27 46.28 1.90
1990 2025 5.947663 TCTGGGTCTTAGGTGAAAATTGAA 58.052 37.500 0.00 0.00 0.00 2.69
1995 2032 6.434340 GGGTCTTAGGTGAAAATTGAATCTGT 59.566 38.462 0.00 0.00 0.00 3.41
1996 2033 7.308435 GGTCTTAGGTGAAAATTGAATCTGTG 58.692 38.462 0.00 0.00 0.00 3.66
2299 2340 6.071984 TCTATAAACCCCAAAACTTTGCAGA 58.928 36.000 0.00 0.00 36.86 4.26
2511 2555 1.776662 TCATCTGAAGGTACCCTCCG 58.223 55.000 8.74 1.37 30.89 4.63
2611 2660 1.145571 TTGGACCAACCTGCTACCTT 58.854 50.000 1.69 0.00 39.86 3.50
2704 2760 7.550551 TCTCTTTTATGTCTTCTTATGGCACTG 59.449 37.037 0.00 0.00 0.00 3.66
2705 2761 7.394016 TCTTTTATGTCTTCTTATGGCACTGA 58.606 34.615 0.00 0.00 0.00 3.41
2724 2780 5.245531 ACTGATTTTTCTCGGTGATTGCTA 58.754 37.500 0.00 0.00 33.47 3.49
2789 2845 7.956943 CCAGCTGTTTGAAAGTTTTGTTTTTAG 59.043 33.333 13.81 0.00 0.00 1.85
2792 2848 9.313323 GCTGTTTGAAAGTTTTGTTTTTAGAAC 57.687 29.630 0.00 0.00 0.00 3.01
3044 3102 5.338056 TGAATGTTCAGTATAACCGAAGGCT 60.338 40.000 0.00 0.00 41.86 4.58
3130 3188 2.886523 TGCTGCTGCTACTGATTTTTGT 59.113 40.909 17.00 0.00 40.48 2.83
3238 3296 6.525629 ACATCTTGGGCATCTACATAACTAC 58.474 40.000 0.00 0.00 0.00 2.73
3267 3325 6.935741 ATAGAAAATGCAAGTAATGGCGTA 57.064 33.333 0.00 0.00 0.00 4.42
3301 3359 4.617253 AGTTCCATAGTGTTGCTGTGTA 57.383 40.909 0.00 0.00 34.93 2.90
3318 3376 6.544197 TGCTGTGTAAGAAGGATGTGTTTTTA 59.456 34.615 0.00 0.00 0.00 1.52
3319 3377 7.078228 GCTGTGTAAGAAGGATGTGTTTTTAG 58.922 38.462 0.00 0.00 0.00 1.85
3320 3378 7.255139 GCTGTGTAAGAAGGATGTGTTTTTAGT 60.255 37.037 0.00 0.00 0.00 2.24
3363 3422 4.884458 TCTTTGTGTTGCATCGTTGTTA 57.116 36.364 0.00 0.00 0.00 2.41
3380 3439 5.286082 CGTTGTTATTTTTACAGCTGCCATC 59.714 40.000 15.27 0.00 0.00 3.51
3436 3495 5.221048 GGGCCAGTTAAAGCATACTATTGTG 60.221 44.000 4.39 0.00 0.00 3.33
3447 3506 7.578310 AGCATACTATTGTGATCAGCATTTT 57.422 32.000 0.00 0.00 0.00 1.82
3602 3661 0.927767 AGATGTACTCCCTCCGTCCT 59.072 55.000 0.00 0.00 0.00 3.85
3635 3694 7.876936 TGTCTTAGATTTGTCTAGATACCGT 57.123 36.000 0.00 0.00 0.00 4.83
3636 3695 8.969260 TGTCTTAGATTTGTCTAGATACCGTA 57.031 34.615 0.00 0.00 0.00 4.02
3637 3696 9.570468 TGTCTTAGATTTGTCTAGATACCGTAT 57.430 33.333 0.00 0.00 0.00 3.06
3653 3712 8.298140 AGATACCGTATCTAGACATGTTTTAGC 58.702 37.037 17.84 0.00 43.44 3.09
3702 3761 4.069304 TCCAAGACAAGTAATTTGGGACG 58.931 43.478 2.61 0.00 41.25 4.79
3704 3763 3.067684 AGACAAGTAATTTGGGACGGG 57.932 47.619 0.00 0.00 41.25 5.28
3718 3777 3.583966 TGGGACGGGGGTAATATATTGTC 59.416 47.826 8.28 5.67 0.00 3.18
3726 3785 6.183360 CGGGGGTAATATATTGTCGGCTATTA 60.183 42.308 8.28 0.00 0.00 0.98
3727 3786 7.567458 GGGGGTAATATATTGTCGGCTATTAA 58.433 38.462 8.28 0.00 0.00 1.40
3728 3787 7.496920 GGGGGTAATATATTGTCGGCTATTAAC 59.503 40.741 8.28 0.00 0.00 2.01
3776 3835 0.680280 CTTCCCTGCTTGCTCATGCT 60.680 55.000 8.80 0.00 40.48 3.79
3778 3837 0.251474 TCCCTGCTTGCTCATGCTTT 60.251 50.000 8.80 0.00 40.48 3.51
3792 3851 5.021033 TCATGCTTTTCTTTGCAGGAAAA 57.979 34.783 20.55 20.55 45.01 2.29
3923 3982 7.206789 TGTGGATTTACATATTCTGGGAGAA 57.793 36.000 0.00 0.00 38.78 2.87
4004 4063 2.087646 GTCTCCATTGAACAGCCCTTC 58.912 52.381 0.00 0.00 0.00 3.46
4275 4336 1.602920 GCTTTGTGCAAGTTACTGGGC 60.603 52.381 0.00 2.83 42.31 5.36
4341 4408 1.342174 AGCTGGAACAAGCCACAATTG 59.658 47.619 3.24 3.24 38.70 2.32
4409 4476 5.055812 GGTTCTTTGTTTGATTGAATGCCA 58.944 37.500 0.00 0.00 0.00 4.92
4468 4936 7.712205 GCATGATTTGAGTTTAAGGGCATTTAT 59.288 33.333 0.00 0.00 0.00 1.40
4469 4937 9.603921 CATGATTTGAGTTTAAGGGCATTTATT 57.396 29.630 0.00 0.00 0.00 1.40
4544 5012 6.886459 AGTTGAACTGATTGTAGGCACATAAT 59.114 34.615 0.00 0.00 33.76 1.28
4637 5105 1.905215 ACTGTCCAGGGATTCTCTGTG 59.095 52.381 12.50 4.51 0.00 3.66
4995 5463 7.869429 CAGCTTCTTAATTTGTCTTGAATGGTT 59.131 33.333 0.00 0.00 0.00 3.67
5052 5520 8.299990 TCTAAGAATAGAGGAAGAACTTGGAG 57.700 38.462 0.00 0.00 33.17 3.86
5062 5530 2.821679 GAACTTGGAGGCGAAGGGGG 62.822 65.000 0.00 0.00 0.00 5.40
5094 5562 1.734163 AAATTGGAGAACTACCGCGG 58.266 50.000 26.86 26.86 0.00 6.46
5240 5710 3.857010 GCACACATTGGTTTCTTAGGTGC 60.857 47.826 0.00 0.00 41.66 5.01
5246 5716 0.881796 GGTTTCTTAGGTGCAGTGGC 59.118 55.000 0.00 0.00 41.68 5.01
5272 5742 4.729868 ACTGCTGGGACTTTACTTTTGAT 58.270 39.130 0.00 0.00 0.00 2.57
5384 5854 9.237846 GTTTGAAGGAGTAGAGTTTTTCATTTG 57.762 33.333 0.00 0.00 0.00 2.32
5407 5877 7.315247 TGTACAATATACACAGTTCCAATGC 57.685 36.000 0.00 0.00 0.00 3.56
5414 5884 1.955778 CACAGTTCCAATGCACTCCAA 59.044 47.619 0.00 0.00 0.00 3.53
5420 5890 3.731652 TCCAATGCACTCCAAGTTTTG 57.268 42.857 0.00 0.00 0.00 2.44
5422 5892 1.788308 CAATGCACTCCAAGTTTTGCG 59.212 47.619 0.00 0.00 37.82 4.85
5426 5896 2.423892 TGCACTCCAAGTTTTGCGTTTA 59.576 40.909 0.00 0.00 37.82 2.01
5431 5901 6.259638 CACTCCAAGTTTTGCGTTTAAAGTA 58.740 36.000 0.00 0.00 0.00 2.24
5432 5902 6.413818 CACTCCAAGTTTTGCGTTTAAAGTAG 59.586 38.462 0.00 0.00 0.00 2.57
5569 6137 4.321156 GCAAAATGGTGTGCTGAAGTATCA 60.321 41.667 0.00 0.00 37.78 2.15
5605 6173 7.414540 GGCACACAAAGAACTCCTTATATCAAG 60.415 40.741 0.00 0.00 34.00 3.02
5812 6383 1.485294 TTCGCCCTCAAAGCCCACTA 61.485 55.000 0.00 0.00 0.00 2.74
5814 6385 1.097547 CGCCCTCAAAGCCCACTATG 61.098 60.000 0.00 0.00 0.00 2.23
5821 6392 3.881688 CTCAAAGCCCACTATGAAGATGG 59.118 47.826 0.00 0.00 0.00 3.51
5854 6425 4.838152 GATTCAGCAGCCGCCGGA 62.838 66.667 7.68 0.00 39.83 5.14
6090 6661 4.713553 TCAACTGTCACCTGCAAGATTTA 58.286 39.130 0.00 0.00 34.07 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
275 279 3.912907 GTCATCCCCCGCGATCGT 61.913 66.667 17.81 0.00 0.00 3.73
278 282 3.467226 AACGTCATCCCCCGCGAT 61.467 61.111 8.23 0.00 0.00 4.58
279 283 4.444838 CAACGTCATCCCCCGCGA 62.445 66.667 8.23 0.00 0.00 5.87
294 298 1.619654 CAGATTGCCTCCACCAACAA 58.380 50.000 0.00 0.00 0.00 2.83
295 299 0.895100 GCAGATTGCCTCCACCAACA 60.895 55.000 0.00 0.00 37.42 3.33
447 451 2.597217 CCCGGTGCCACATGTGTT 60.597 61.111 23.79 0.00 0.00 3.32
448 452 3.565214 TCCCGGTGCCACATGTGT 61.565 61.111 23.79 0.00 0.00 3.72
474 478 4.803426 GACGTGGAGGCTGAGCGG 62.803 72.222 0.00 0.00 0.00 5.52
614 618 2.125512 GCCGACGAACAGATGGCT 60.126 61.111 0.00 0.00 39.41 4.75
646 651 2.644798 ACAAAAGCTACACTCTCCCCAT 59.355 45.455 0.00 0.00 0.00 4.00
671 699 2.824341 GTTCTCAGTTCCCCTACTTCGA 59.176 50.000 0.00 0.00 0.00 3.71
674 702 2.303311 GCAGTTCTCAGTTCCCCTACTT 59.697 50.000 0.00 0.00 0.00 2.24
678 707 1.674057 CGCAGTTCTCAGTTCCCCT 59.326 57.895 0.00 0.00 0.00 4.79
763 794 4.657824 CCTCACCCGTCACGCGTT 62.658 66.667 10.22 0.00 39.32 4.84
819 851 1.064906 AGACCAGACCATTGATGCCTG 60.065 52.381 0.00 0.00 0.00 4.85
837 869 0.041535 TGAGGGGTAAGGGCGTAAGA 59.958 55.000 0.00 0.00 43.02 2.10
873 905 3.046087 CAGACCAGCACGCTGTGG 61.046 66.667 17.31 7.00 42.15 4.17
1442 1477 0.949397 GGAATAATCGGGGTTTCGGC 59.051 55.000 0.00 0.00 0.00 5.54
1477 1512 4.380233 GGAAATGCAGGAACAGATCAACAG 60.380 45.833 0.00 0.00 0.00 3.16
1498 1533 8.250143 TCATATCTACACAAATAGAGCTTGGA 57.750 34.615 0.00 0.00 34.68 3.53
1535 1570 9.869757 CATAACAACATCCTCATATAATACGGA 57.130 33.333 0.00 0.00 0.00 4.69
1536 1571 8.604035 GCATAACAACATCCTCATATAATACGG 58.396 37.037 0.00 0.00 0.00 4.02
1537 1572 9.371136 AGCATAACAACATCCTCATATAATACG 57.629 33.333 0.00 0.00 0.00 3.06
1554 1589 5.483685 AACACCTAGAGACAGCATAACAA 57.516 39.130 0.00 0.00 0.00 2.83
1566 1601 3.178865 TGGTTAGGGGAAACACCTAGAG 58.821 50.000 0.00 0.00 41.35 2.43
1578 1613 4.207165 CAATTGGAGTATGTGGTTAGGGG 58.793 47.826 0.00 0.00 0.00 4.79
1604 1639 2.815647 GCCACCGTGTAGCAGAGC 60.816 66.667 0.00 0.00 0.00 4.09
1628 1663 2.893682 AATGAAGCTAGCCGGTGCCC 62.894 60.000 12.13 1.71 38.69 5.36
1634 1669 2.565841 AGCCTAAAATGAAGCTAGCCG 58.434 47.619 12.13 0.00 32.73 5.52
1639 1674 3.359950 CAGGGAAGCCTAAAATGAAGCT 58.640 45.455 0.00 0.00 37.10 3.74
1741 1776 9.737427 CACAATCGTACTAAATTGAGATACTCT 57.263 33.333 15.29 0.00 36.57 3.24
1857 1892 3.627123 CAGTCTGAACATGGTTGTCACAA 59.373 43.478 0.00 0.00 34.06 3.33
1990 2025 7.672983 AAGAATTTGTGTTATCGTCACAGAT 57.327 32.000 0.00 0.00 44.71 2.90
2273 2314 7.070074 TCTGCAAAGTTTTGGGGTTTATAGAAA 59.930 33.333 6.72 0.00 38.57 2.52
2299 2340 8.747538 AAACAAGGTAGTAACAATCTCAAACT 57.252 30.769 0.00 0.00 0.00 2.66
2339 2380 8.962884 ATTGATATGTCAAACTACATGTAGCA 57.037 30.769 28.88 19.45 46.67 3.49
2428 2472 0.181350 GGCACCGATTGGAAGGATCT 59.819 55.000 5.81 0.00 39.21 2.75
2611 2660 5.512942 TGTTCCTAGAATGTTTGATGGGA 57.487 39.130 0.00 0.00 0.00 4.37
2704 2760 5.803020 AGTAGCAATCACCGAGAAAAATC 57.197 39.130 0.00 0.00 0.00 2.17
2705 2761 6.183360 GCTTAGTAGCAATCACCGAGAAAAAT 60.183 38.462 0.00 0.00 46.95 1.82
2724 2780 5.302823 AGCAATTTCTCTGTTTTGGCTTAGT 59.697 36.000 0.00 0.00 0.00 2.24
2730 2786 7.769272 TGTTTAAGCAATTTCTCTGTTTTGG 57.231 32.000 0.00 0.00 0.00 3.28
2811 2867 9.715121 ACAAATCATTAGTGAAAATCAGCAAAT 57.285 25.926 0.00 0.00 38.01 2.32
2954 3010 6.998802 TCAAAAGGGAAACTGAGAAACAAAA 58.001 32.000 0.00 0.00 0.00 2.44
2958 3014 4.097892 TGCTCAAAAGGGAAACTGAGAAAC 59.902 41.667 2.21 0.00 38.02 2.78
3044 3102 0.810648 GCCGCAATGACAAGATCCAA 59.189 50.000 0.00 0.00 0.00 3.53
3130 3188 9.832445 GATTTCACTGATTTATCCTTACCTACA 57.168 33.333 0.00 0.00 0.00 2.74
3238 3296 6.757947 CCATTACTTGCATTTTCTATTGGGTG 59.242 38.462 0.00 0.00 0.00 4.61
3251 3309 4.397730 TGAAATGTACGCCATTACTTGCAT 59.602 37.500 1.76 0.00 43.04 3.96
3267 3325 7.624549 ACACTATGGAACTATCTGTGAAATGT 58.375 34.615 0.00 0.00 0.00 2.71
3274 3332 5.046304 ACAGCAACACTATGGAACTATCTGT 60.046 40.000 0.00 0.00 0.00 3.41
3301 3359 8.211629 ACAGTAGACTAAAAACACATCCTTCTT 58.788 33.333 0.00 0.00 0.00 2.52
3318 3376 4.101741 AGAAGCTGGAAAACACAGTAGACT 59.898 41.667 0.00 0.00 38.22 3.24
3319 3377 4.381411 AGAAGCTGGAAAACACAGTAGAC 58.619 43.478 0.00 0.00 38.22 2.59
3320 3378 4.689612 AGAAGCTGGAAAACACAGTAGA 57.310 40.909 0.00 0.00 38.22 2.59
3363 3422 2.094675 AGCGATGGCAGCTGTAAAAAT 58.905 42.857 16.64 2.09 44.22 1.82
3380 3439 1.459592 GTTACACTGTTACAGGCAGCG 59.540 52.381 17.21 2.37 37.47 5.18
3436 3495 4.110482 GTGCCTGATTGAAAATGCTGATC 58.890 43.478 0.00 0.00 0.00 2.92
3447 3506 2.170166 GGTCAAATGGTGCCTGATTGA 58.830 47.619 0.00 0.00 0.00 2.57
3493 3552 7.340999 AGGCCGTACATTTCCAAAAAGTATAAT 59.659 33.333 0.00 0.00 0.00 1.28
3509 3568 2.091541 CCATGTTTCAAGGCCGTACAT 58.908 47.619 0.00 0.00 0.00 2.29
3516 3575 5.055812 TCATTGTTTTCCATGTTTCAAGGC 58.944 37.500 0.00 0.00 0.00 4.35
3633 3692 6.807708 AACGCTAAAACATGTCTAGATACG 57.192 37.500 15.70 12.40 0.00 3.06
3636 3695 9.680315 GTATCTAACGCTAAAACATGTCTAGAT 57.320 33.333 15.70 11.27 0.00 1.98
3637 3696 7.854422 CGTATCTAACGCTAAAACATGTCTAGA 59.146 37.037 15.70 0.00 46.10 2.43
3663 3722 5.978322 GTCTTGGATTTGACTAGATACGGAC 59.022 44.000 0.00 0.00 0.00 4.79
3675 3734 6.780031 TCCCAAATTACTTGTCTTGGATTTGA 59.220 34.615 7.87 0.00 40.72 2.69
3702 3761 3.994931 AGCCGACAATATATTACCCCC 57.005 47.619 0.00 0.00 0.00 5.40
3704 3763 9.439500 TTGTTAATAGCCGACAATATATTACCC 57.561 33.333 0.00 0.00 0.00 3.69
3726 3785 8.470040 TCGCGAAAATAGTAAGACTAATTGTT 57.530 30.769 6.20 0.00 33.89 2.83
3727 3786 7.758528 ACTCGCGAAAATAGTAAGACTAATTGT 59.241 33.333 11.33 0.00 33.89 2.71
3728 3787 8.116624 ACTCGCGAAAATAGTAAGACTAATTG 57.883 34.615 11.33 0.00 33.89 2.32
4004 4063 1.338105 TGCTCCCAGTCATCTTTGTCG 60.338 52.381 0.00 0.00 0.00 4.35
4087 4148 0.906282 TGGCATGAGCTCCTGACAGA 60.906 55.000 22.17 2.09 41.70 3.41
4275 4336 1.476291 GGTATTGTTAGCCTTCGGGGG 60.476 57.143 0.00 0.00 35.16 5.40
4341 4408 6.259550 AGATTGCTGTGGTTAGTCAAAATC 57.740 37.500 0.00 0.00 0.00 2.17
4409 4476 2.683211 AGGCACAAAATGGAAGGAGT 57.317 45.000 0.00 0.00 0.00 3.85
4468 4936 7.119116 CAGGTACTACATTGCATTGTCTGTAAA 59.881 37.037 17.01 0.00 36.02 2.01
4469 4937 6.593770 CAGGTACTACATTGCATTGTCTGTAA 59.406 38.462 17.01 0.00 36.02 2.41
4470 4938 6.071051 TCAGGTACTACATTGCATTGTCTGTA 60.071 38.462 17.01 16.75 36.02 2.74
4471 4939 4.937620 CAGGTACTACATTGCATTGTCTGT 59.062 41.667 17.01 17.59 36.02 3.41
4482 4950 6.931838 TCTTCGTGAATTCAGGTACTACATT 58.068 36.000 23.46 0.00 36.02 2.71
4637 5105 8.732746 AGGAAACACATAATAAGGTACATGAC 57.267 34.615 0.00 0.00 0.00 3.06
4743 5211 0.899717 ACACCATCACACCCCAATGC 60.900 55.000 0.00 0.00 0.00 3.56
4969 5437 7.373493 ACCATTCAAGACAAATTAAGAAGCTG 58.627 34.615 0.00 0.00 0.00 4.24
4995 5463 4.142204 ACACAATGCACACAGTCATCAAAA 60.142 37.500 0.00 0.00 0.00 2.44
5062 5530 1.198178 TCCAATTTTCGCCAGCGTAAC 59.802 47.619 12.32 0.00 40.74 2.50
5094 5562 2.433318 GTGAGCCACGAGTCAGCC 60.433 66.667 0.00 0.00 0.00 4.85
5240 5710 1.970114 CCCAGCAGTTCAGCCACTG 60.970 63.158 4.30 4.30 46.15 3.66
5246 5716 3.409026 AGTAAAGTCCCAGCAGTTCAG 57.591 47.619 0.00 0.00 0.00 3.02
5384 5854 7.065803 AGTGCATTGGAACTGTGTATATTGTAC 59.934 37.037 0.00 0.00 29.09 2.90
5407 5877 5.099575 ACTTTAAACGCAAAACTTGGAGTG 58.900 37.500 0.00 0.00 0.00 3.51
5414 5884 7.311364 TCTGAACTACTTTAAACGCAAAACT 57.689 32.000 0.00 0.00 0.00 2.66
5431 5901 9.036980 ACACTTTGGACTAACTATATCTGAACT 57.963 33.333 0.00 0.00 0.00 3.01
5432 5902 9.654663 AACACTTTGGACTAACTATATCTGAAC 57.345 33.333 0.00 0.00 0.00 3.18
5498 6066 9.391006 GACTGTTCCACAATTTCTACCATATTA 57.609 33.333 0.00 0.00 0.00 0.98
5499 6067 7.065803 CGACTGTTCCACAATTTCTACCATATT 59.934 37.037 0.00 0.00 0.00 1.28
5569 6137 1.406539 CTTTGTGTGCCTCAGTGCTTT 59.593 47.619 0.00 0.00 0.00 3.51
5779 6348 1.275471 GGCGAAAGTTTGGAAAGCGC 61.275 55.000 0.00 0.00 41.95 5.92
5780 6349 0.663269 GGGCGAAAGTTTGGAAAGCG 60.663 55.000 1.30 0.00 29.71 4.68
5812 6383 4.079970 CCTGATTATGCTGCCATCTTCAT 58.920 43.478 0.00 0.00 32.85 2.57
5814 6385 3.748083 TCCTGATTATGCTGCCATCTTC 58.252 45.455 0.00 0.00 32.85 2.87
5821 6392 3.748083 TGAATCCTCCTGATTATGCTGC 58.252 45.455 0.00 0.00 43.81 5.25


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

AutoCloner maintained by Alex Coulton.