Multiple sequence alignment - TraesCS1A01G208400

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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 TraesCS1A01G208400 chr1A 100.000 5302 0 0 1 5302 370026126 370020825 0.000000e+00 9792.0
1 TraesCS1A01G208400 chr1B 94.597 3572 139 21 1059 4617 400147170 400143640 0.000000e+00 5478.0
2 TraesCS1A01G208400 chr1B 88.873 701 44 13 4607 5302 400141324 400140653 0.000000e+00 832.0
3 TraesCS1A01G208400 chr1B 93.204 412 12 7 819 1220 400147862 400147457 4.570000e-165 592.0
4 TraesCS1A01G208400 chr1D 97.039 2364 63 7 1059 3421 297392460 297390103 0.000000e+00 3971.0
5 TraesCS1A01G208400 chr1D 94.932 888 31 3 3705 4579 297389801 297388915 0.000000e+00 1378.0
6 TraesCS1A01G208400 chr1D 91.144 734 29 14 4584 5302 297387808 297387096 0.000000e+00 963.0
7 TraesCS1A01G208400 chr1D 91.393 244 21 0 3461 3704 297390100 297389857 8.510000e-88 335.0
8 TraesCS1A01G208400 chr1D 94.527 201 10 1 812 1011 297392799 297392599 5.160000e-80 309.0
9 TraesCS1A01G208400 chr6B 91.363 741 48 5 1 727 159695903 159695165 0.000000e+00 1000.0
10 TraesCS1A01G208400 chrUn 91.071 728 64 1 2 728 86405736 86406463 0.000000e+00 983.0
11 TraesCS1A01G208400 chr2B 90.771 726 62 4 3 727 239813295 239812574 0.000000e+00 965.0
12 TraesCS1A01G208400 chr2B 87.802 746 74 9 1 734 211612050 211612790 0.000000e+00 857.0
13 TraesCS1A01G208400 chr6D 90.684 687 58 4 42 726 386297789 386297107 0.000000e+00 909.0
14 TraesCS1A01G208400 chr7D 88.950 733 67 9 4 725 497567780 497568509 0.000000e+00 893.0
15 TraesCS1A01G208400 chr4A 89.019 683 70 2 18 699 542826710 542827388 0.000000e+00 841.0
16 TraesCS1A01G208400 chr5D 91.723 592 46 3 1 591 477875324 477874735 0.000000e+00 819.0
17 TraesCS1A01G208400 chr7A 85.967 734 89 12 2 728 347067050 347066324 0.000000e+00 773.0
18 TraesCS1A01G208400 chr7A 87.059 85 10 1 643 727 521562576 521562493 1.570000e-15 95.3
19 TraesCS1A01G208400 chr4B 83.824 748 98 13 1 726 600913853 600914599 0.000000e+00 689.0
20 TraesCS1A01G208400 chr6A 85.321 218 30 2 510 726 531401374 531401158 1.920000e-54 224.0
21 TraesCS1A01G208400 chr5B 100.000 33 0 0 5270 5302 112263658 112263626 1.590000e-05 62.1


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 TraesCS1A01G208400 chr1A 370020825 370026126 5301 True 9792.000000 9792 100.000000 1 5302 1 chr1A.!!$R1 5301
1 TraesCS1A01G208400 chr1B 400140653 400147862 7209 True 2300.666667 5478 92.224667 819 5302 3 chr1B.!!$R1 4483
2 TraesCS1A01G208400 chr1D 297387096 297392799 5703 True 1391.200000 3971 93.807000 812 5302 5 chr1D.!!$R1 4490
3 TraesCS1A01G208400 chr6B 159695165 159695903 738 True 1000.000000 1000 91.363000 1 727 1 chr6B.!!$R1 726
4 TraesCS1A01G208400 chrUn 86405736 86406463 727 False 983.000000 983 91.071000 2 728 1 chrUn.!!$F1 726
5 TraesCS1A01G208400 chr2B 239812574 239813295 721 True 965.000000 965 90.771000 3 727 1 chr2B.!!$R1 724
6 TraesCS1A01G208400 chr2B 211612050 211612790 740 False 857.000000 857 87.802000 1 734 1 chr2B.!!$F1 733
7 TraesCS1A01G208400 chr6D 386297107 386297789 682 True 909.000000 909 90.684000 42 726 1 chr6D.!!$R1 684
8 TraesCS1A01G208400 chr7D 497567780 497568509 729 False 893.000000 893 88.950000 4 725 1 chr7D.!!$F1 721
9 TraesCS1A01G208400 chr4A 542826710 542827388 678 False 841.000000 841 89.019000 18 699 1 chr4A.!!$F1 681
10 TraesCS1A01G208400 chr5D 477874735 477875324 589 True 819.000000 819 91.723000 1 591 1 chr5D.!!$R1 590
11 TraesCS1A01G208400 chr7A 347066324 347067050 726 True 773.000000 773 85.967000 2 728 1 chr7A.!!$R1 726
12 TraesCS1A01G208400 chr4B 600913853 600914599 746 False 689.000000 689 83.824000 1 726 1 chr4B.!!$F1 725

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
371 372 0.250640 GATCATGGAGGAGCGGCAAT 60.251 55.0 1.45 0.0 0.00 3.56 F
972 1024 0.588252 CACCTTTCCTGTTGTCAGCG 59.412 55.0 0.00 0.0 40.09 5.18 F
2139 2639 0.656259 CTGCTGCATCAGGTGATTCG 59.344 55.0 9.75 0.0 31.21 3.34 F
2860 3360 0.395173 ACACCGCCTCCACAAAGTTT 60.395 50.0 0.00 0.0 0.00 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2262 2762 0.447801 GCCTAACATTGGTCAGCACG 59.552 55.000 0.00 0.0 0.00 5.34 R
2385 2885 0.109735 GTGCGCTCGGATCATCGATA 60.110 55.000 9.73 0.0 38.55 2.92 R
3489 3991 2.039480 ACAAGAGCCAAGATCAGCTTCA 59.961 45.455 6.40 0.0 40.11 3.02 R
4649 8652 0.173255 GCCATGCAAACGCCACTTAT 59.827 50.000 0.00 0.0 0.00 1.73 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
36 37 3.751175 CCATCAACAACCACAACTACGAT 59.249 43.478 0.00 0.00 0.00 3.73
119 120 1.618837 CAACCCTGTCGGAGAGAAGAA 59.381 52.381 3.35 0.00 36.95 2.52
133 134 5.391416 GGAGAGAAGAAGAAAAGATTTGCCG 60.391 44.000 0.00 0.00 0.00 5.69
167 168 1.728672 CTAGGAAGGACGTCGAGCC 59.271 63.158 9.92 10.09 0.00 4.70
247 248 0.318441 CACGAAGAAGCTGTGGGAGA 59.682 55.000 0.00 0.00 0.00 3.71
354 355 2.440409 GGTGAGAATGTTGTGCCTGAT 58.560 47.619 0.00 0.00 0.00 2.90
371 372 0.250640 GATCATGGAGGAGCGGCAAT 60.251 55.000 1.45 0.00 0.00 3.56
384 385 3.836949 AGCGGCAATGTTTGAATAGTTG 58.163 40.909 1.45 0.00 0.00 3.16
450 453 6.207213 GCAATTGCAAAATGATTTGGTTGAA 58.793 32.000 25.36 0.00 44.93 2.69
607 643 7.531534 GCTTGTGAAAATTTGTGCATATTTGTC 59.468 33.333 0.00 0.00 0.00 3.18
750 799 4.389576 GCTGCCGCGTTGGAGTTG 62.390 66.667 4.92 0.00 42.00 3.16
751 800 4.389576 CTGCCGCGTTGGAGTTGC 62.390 66.667 4.92 0.00 42.00 4.17
752 801 4.927782 TGCCGCGTTGGAGTTGCT 62.928 61.111 4.92 0.00 42.00 3.91
753 802 4.090057 GCCGCGTTGGAGTTGCTC 62.090 66.667 4.92 0.00 42.00 4.26
754 803 2.357517 CCGCGTTGGAGTTGCTCT 60.358 61.111 4.92 0.00 42.00 4.09
755 804 2.671177 CCGCGTTGGAGTTGCTCTG 61.671 63.158 4.92 0.00 42.00 3.35
756 805 1.664649 CGCGTTGGAGTTGCTCTGA 60.665 57.895 0.00 0.00 0.00 3.27
757 806 1.621301 CGCGTTGGAGTTGCTCTGAG 61.621 60.000 0.00 0.00 0.00 3.35
758 807 0.601311 GCGTTGGAGTTGCTCTGAGT 60.601 55.000 6.53 0.00 0.00 3.41
759 808 1.336887 GCGTTGGAGTTGCTCTGAGTA 60.337 52.381 6.53 0.00 0.00 2.59
760 809 2.866460 GCGTTGGAGTTGCTCTGAGTAA 60.866 50.000 3.97 3.97 0.00 2.24
761 810 3.589988 CGTTGGAGTTGCTCTGAGTAAT 58.410 45.455 11.33 1.53 0.00 1.89
762 811 3.997021 CGTTGGAGTTGCTCTGAGTAATT 59.003 43.478 11.33 7.32 0.00 1.40
763 812 4.452455 CGTTGGAGTTGCTCTGAGTAATTT 59.548 41.667 11.33 3.69 0.00 1.82
764 813 5.049405 CGTTGGAGTTGCTCTGAGTAATTTT 60.049 40.000 11.33 1.36 0.00 1.82
765 814 6.513393 CGTTGGAGTTGCTCTGAGTAATTTTT 60.513 38.462 11.33 0.00 0.00 1.94
801 850 8.696410 TTTTGTGAGGTAATGTTTTTGAGAAC 57.304 30.769 0.00 0.00 0.00 3.01
802 851 7.639113 TTGTGAGGTAATGTTTTTGAGAACT 57.361 32.000 0.00 0.00 0.00 3.01
803 852 7.639113 TGTGAGGTAATGTTTTTGAGAACTT 57.361 32.000 0.00 0.00 0.00 2.66
804 853 7.479980 TGTGAGGTAATGTTTTTGAGAACTTG 58.520 34.615 0.00 0.00 0.00 3.16
805 854 6.417930 GTGAGGTAATGTTTTTGAGAACTTGC 59.582 38.462 0.00 0.00 0.00 4.01
806 855 6.096141 TGAGGTAATGTTTTTGAGAACTTGCA 59.904 34.615 0.00 0.00 0.00 4.08
807 856 6.872920 AGGTAATGTTTTTGAGAACTTGCAA 58.127 32.000 0.00 0.00 0.00 4.08
808 857 7.500141 AGGTAATGTTTTTGAGAACTTGCAAT 58.500 30.769 0.00 0.00 0.00 3.56
809 858 7.986889 AGGTAATGTTTTTGAGAACTTGCAATT 59.013 29.630 0.00 0.00 0.00 2.32
810 859 8.275632 GGTAATGTTTTTGAGAACTTGCAATTC 58.724 33.333 0.00 6.55 0.00 2.17
811 860 9.034544 GTAATGTTTTTGAGAACTTGCAATTCT 57.965 29.630 18.18 18.18 39.15 2.40
812 861 8.496707 AATGTTTTTGAGAACTTGCAATTCTT 57.503 26.923 18.78 5.13 36.53 2.52
813 862 7.903995 TGTTTTTGAGAACTTGCAATTCTTT 57.096 28.000 18.78 4.60 36.53 2.52
814 863 8.321650 TGTTTTTGAGAACTTGCAATTCTTTT 57.678 26.923 18.78 2.57 36.53 2.27
815 864 8.229137 TGTTTTTGAGAACTTGCAATTCTTTTG 58.771 29.630 18.78 2.66 36.53 2.44
816 865 8.442384 GTTTTTGAGAACTTGCAATTCTTTTGA 58.558 29.630 18.78 8.70 36.53 2.69
817 866 7.760131 TTTGAGAACTTGCAATTCTTTTGAG 57.240 32.000 18.78 1.15 36.53 3.02
818 867 6.455360 TGAGAACTTGCAATTCTTTTGAGT 57.545 33.333 18.78 1.71 36.53 3.41
819 868 7.566760 TGAGAACTTGCAATTCTTTTGAGTA 57.433 32.000 18.78 4.87 36.53 2.59
820 869 7.995289 TGAGAACTTGCAATTCTTTTGAGTAA 58.005 30.769 18.78 3.48 36.53 2.24
821 870 7.915397 TGAGAACTTGCAATTCTTTTGAGTAAC 59.085 33.333 18.78 8.62 36.53 2.50
949 1001 2.277084 CGTCTTCCCCAATCCTAAACG 58.723 52.381 0.00 0.00 0.00 3.60
972 1024 0.588252 CACCTTTCCTGTTGTCAGCG 59.412 55.000 0.00 0.00 40.09 5.18
977 1029 2.636778 TTCCTGTTGTCAGCGACGCA 62.637 55.000 23.70 0.00 40.09 5.24
1049 1107 2.204464 CCCCTTCCCCTTCCCCTT 60.204 66.667 0.00 0.00 0.00 3.95
1051 1109 2.317378 CCCTTCCCCTTCCCCTTCC 61.317 68.421 0.00 0.00 0.00 3.46
1057 1115 2.127297 CCTTCCCCTTCCCCTCCA 59.873 66.667 0.00 0.00 0.00 3.86
1748 2248 3.706373 GCTCTCGGGGGTGCAGAA 61.706 66.667 0.00 0.00 0.00 3.02
2061 2561 2.044946 GCCATGGGTGTCAGGACC 60.045 66.667 15.13 0.00 34.96 4.46
2079 2579 4.637771 GGCATGGTAGGCGTTCTT 57.362 55.556 0.00 0.00 0.00 2.52
2139 2639 0.656259 CTGCTGCATCAGGTGATTCG 59.344 55.000 9.75 0.00 31.21 3.34
2259 2759 8.178964 GTGGACAGTGAGATAGATTACGATATC 58.821 40.741 0.00 0.00 0.00 1.63
2262 2762 6.183360 ACAGTGAGATAGATTACGATATCGCC 60.183 42.308 24.59 11.43 44.43 5.54
2292 2792 4.469227 ACCAATGTTAGGCATGCCAATTTA 59.531 37.500 37.18 18.86 37.96 1.40
2307 2807 4.454678 CCAATTTAGAGGCTAGCATGACA 58.545 43.478 18.24 0.00 0.00 3.58
2523 3023 2.610727 CCTGTTTGAGACGGAGGTTCTC 60.611 54.545 0.00 0.00 36.72 2.87
2553 3053 1.064060 CCGCACGGAATCCTTGAAATC 59.936 52.381 10.18 0.00 37.50 2.17
2697 3197 2.906354 GGTCGGTGTGAGCTAATTGAT 58.094 47.619 0.00 0.00 41.93 2.57
2821 3321 6.663523 TGTCACTGGTATGATACTTTCTCTCA 59.336 38.462 2.24 0.00 0.00 3.27
2822 3322 7.343057 TGTCACTGGTATGATACTTTCTCTCAT 59.657 37.037 2.24 0.00 34.22 2.90
2823 3323 8.851145 GTCACTGGTATGATACTTTCTCTCATA 58.149 37.037 2.24 0.00 32.20 2.15
2824 3324 8.851145 TCACTGGTATGATACTTTCTCTCATAC 58.149 37.037 11.60 11.60 45.62 2.39
2845 3345 9.378551 TCATACAATAGTTCTCATTAACACACC 57.621 33.333 0.00 0.00 0.00 4.16
2860 3360 0.395173 ACACCGCCTCCACAAAGTTT 60.395 50.000 0.00 0.00 0.00 2.66
2861 3361 1.134037 ACACCGCCTCCACAAAGTTTA 60.134 47.619 0.00 0.00 0.00 2.01
2862 3362 2.159382 CACCGCCTCCACAAAGTTTAT 58.841 47.619 0.00 0.00 0.00 1.40
2863 3363 3.244630 ACACCGCCTCCACAAAGTTTATA 60.245 43.478 0.00 0.00 0.00 0.98
2864 3364 3.126343 CACCGCCTCCACAAAGTTTATAC 59.874 47.826 0.00 0.00 0.00 1.47
2892 3392 7.305763 GGTTTCAAACTGTTAATTTGCTGTACG 60.306 37.037 0.00 0.00 37.05 3.67
2909 3409 8.657074 TGCTGTACGTTTTGCTATATATTCTT 57.343 30.769 0.00 0.00 0.00 2.52
3021 3521 2.357009 GCCGATGATGACAAAGATTGCT 59.643 45.455 0.00 0.00 0.00 3.91
3421 3923 8.330993 TGTCCATAGTCACCGTATAATCCTATA 58.669 37.037 0.00 0.00 0.00 1.31
3424 3926 9.350951 CCATAGTCACCGTATAATCCTATATGA 57.649 37.037 0.00 0.00 31.12 2.15
3488 3990 7.226720 CGTAGGATCCTGTGTAAAAATGCTTAT 59.773 37.037 25.28 0.00 0.00 1.73
3489 3991 7.961326 AGGATCCTGTGTAAAAATGCTTATT 57.039 32.000 15.29 0.00 0.00 1.40
3517 4019 4.914983 TGATCTTGGCTCTTGTCAGATTT 58.085 39.130 0.00 0.00 0.00 2.17
3518 4020 5.319453 TGATCTTGGCTCTTGTCAGATTTT 58.681 37.500 0.00 0.00 0.00 1.82
3520 4022 6.942005 TGATCTTGGCTCTTGTCAGATTTTAA 59.058 34.615 0.00 0.00 0.00 1.52
3521 4023 7.613022 TGATCTTGGCTCTTGTCAGATTTTAAT 59.387 33.333 0.00 0.00 0.00 1.40
3590 4092 6.705302 AGAATGTAGAACATGCTCAGAAAGA 58.295 36.000 0.00 0.00 40.45 2.52
3621 4123 8.011844 AGTAGATTGATGTGTTACTATCTGCA 57.988 34.615 0.00 0.00 35.20 4.41
3623 4125 6.882656 AGATTGATGTGTTACTATCTGCAGT 58.117 36.000 14.67 3.75 30.39 4.40
3624 4126 7.334090 AGATTGATGTGTTACTATCTGCAGTT 58.666 34.615 14.67 8.22 30.39 3.16
3736 4293 1.059098 ACTGCTGACCATCTTCCACA 58.941 50.000 0.00 0.00 0.00 4.17
3743 4300 2.108075 TGACCATCTTCCACATGTTGGT 59.892 45.455 15.80 15.80 46.97 3.67
3752 4309 1.820519 CCACATGTTGGTCCATCTTGG 59.179 52.381 16.31 9.70 41.10 3.61
3773 4330 5.332743 TGGTCCTTATTCCTGATTGCTTTT 58.667 37.500 0.00 0.00 0.00 2.27
4040 4597 1.686052 TGCCTTAACACTTTGGCCTTG 59.314 47.619 3.32 0.00 44.32 3.61
4127 4684 7.993183 ACACGATATAAATTCCAGTCCAATTCT 59.007 33.333 0.00 0.00 0.00 2.40
4160 4729 4.971220 CCTTGCATTTTGTGATTTTTGCAC 59.029 37.500 0.00 0.00 39.57 4.57
4204 4774 4.476628 TTGCATCAGAGATTCTGCTGTA 57.523 40.909 10.50 4.67 43.95 2.74
4209 4779 3.701664 TCAGAGATTCTGCTGTACCAGA 58.298 45.455 1.23 0.00 43.95 3.86
4231 4801 3.896648 TTCCTCTTTTGCAATGTCGTC 57.103 42.857 0.00 0.00 0.00 4.20
4247 4817 2.869801 GTCGTCTCACATGAAAACCACA 59.130 45.455 0.00 0.00 0.00 4.17
4273 4843 2.722094 ACTGATCTCGCTTCTCTCTGT 58.278 47.619 0.00 0.00 0.00 3.41
4579 5149 1.176527 CCGGGTTCTTCATGTGCAAT 58.823 50.000 0.00 0.00 0.00 3.56
4580 5150 1.545582 CCGGGTTCTTCATGTGCAATT 59.454 47.619 0.00 0.00 0.00 2.32
4581 5151 2.029110 CCGGGTTCTTCATGTGCAATTT 60.029 45.455 0.00 0.00 0.00 1.82
4582 5152 3.554752 CCGGGTTCTTCATGTGCAATTTT 60.555 43.478 0.00 0.00 0.00 1.82
4611 8610 0.253044 TGTGCTACAATCCAGAGGGC 59.747 55.000 0.00 0.00 0.00 5.19
4629 8628 1.787847 CACACATTTCTCCGACCGC 59.212 57.895 0.00 0.00 0.00 5.68
4649 8652 4.320348 CCGCGTTTGGTACCTTGAAAAATA 60.320 41.667 14.36 0.00 0.00 1.40
4650 8653 5.395642 CGCGTTTGGTACCTTGAAAAATAT 58.604 37.500 14.36 0.00 0.00 1.28
4837 8846 2.659428 GATTTTGACTATGGGCTGCCT 58.341 47.619 19.68 1.54 0.00 4.75
4843 8852 2.042762 TATGGGCTGCCTCTGGGT 59.957 61.111 19.68 1.31 34.45 4.51
4912 8921 8.789767 AAGAGATCTCCATATAAAGAGGTTGA 57.210 34.615 19.30 0.00 0.00 3.18
4965 8974 4.207891 TGCTCTCTATTTGTTGTCTCCC 57.792 45.455 0.00 0.00 0.00 4.30
4984 8993 2.674852 CCCAACATGTCTCGACTTCATG 59.325 50.000 0.00 14.24 42.86 3.07
5067 9076 4.872124 CGAGTTCATCAGACCAATCATCAA 59.128 41.667 0.00 0.00 0.00 2.57
5090 9100 3.898517 GGTGAAAGCTAAACAGTGGTC 57.101 47.619 0.00 0.00 0.00 4.02
5112 9122 1.904287 CCCCCTCGTTGAATTGTTCA 58.096 50.000 0.00 0.00 38.04 3.18
5113 9123 2.235016 CCCCCTCGTTGAATTGTTCAA 58.765 47.619 1.24 1.24 46.68 2.69
5205 9216 3.097614 ACGGTTCAGGCTTAGATACACT 58.902 45.455 0.00 0.00 0.00 3.55
5228 9239 6.610830 ACTGGACATATCATCTCCTATCATCC 59.389 42.308 0.00 0.00 0.00 3.51
5259 9270 5.149977 GCAGATTGCTGTTCTAGTTTTCAC 58.850 41.667 0.00 0.00 44.17 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 5.103940 ACCGTCACCTAGGTAGTATCCTTTA 60.104 44.000 15.80 0.00 39.30 1.85
119 120 3.149196 TGCTCTTCGGCAAATCTTTTCT 58.851 40.909 0.00 0.00 39.43 2.52
167 168 4.685924 AGATTGCAAAACACCAAAGACAG 58.314 39.130 1.71 0.00 0.00 3.51
247 248 3.946606 TGATCACACAAGCAGTCATCAT 58.053 40.909 0.00 0.00 0.00 2.45
327 328 3.304928 GCACAACATTCTCACCCTGAAAG 60.305 47.826 0.00 0.00 0.00 2.62
354 355 1.153107 CATTGCCGCTCCTCCATGA 60.153 57.895 0.00 0.00 0.00 3.07
371 372 7.353414 TGAAATTGGGTCAACTATTCAAACA 57.647 32.000 0.00 0.00 0.00 2.83
384 385 4.365723 GCATGTCATGATGAAATTGGGTC 58.634 43.478 17.24 0.00 0.00 4.46
450 453 5.308976 TGTCAACATGAGCCCACATATAT 57.691 39.130 0.00 0.00 0.00 0.86
607 643 4.419939 GCTGGCCGCCCTTTTTCG 62.420 66.667 7.03 0.00 0.00 3.46
625 661 2.224769 CCCATATTTACCGGCATGGACT 60.225 50.000 16.81 0.00 40.37 3.85
631 667 1.121378 TCGACCCATATTTACCGGCA 58.879 50.000 0.00 0.00 0.00 5.69
733 782 4.389576 CAACTCCAACGCGGCAGC 62.390 66.667 12.47 0.00 40.74 5.25
734 783 4.389576 GCAACTCCAACGCGGCAG 62.390 66.667 12.47 2.39 33.14 4.85
735 784 4.927782 AGCAACTCCAACGCGGCA 62.928 61.111 12.47 0.00 33.14 5.69
736 785 4.090057 GAGCAACTCCAACGCGGC 62.090 66.667 12.47 0.36 33.14 6.53
737 786 2.357517 AGAGCAACTCCAACGCGG 60.358 61.111 12.47 0.00 0.00 6.46
738 787 1.621301 CTCAGAGCAACTCCAACGCG 61.621 60.000 3.53 3.53 0.00 6.01
739 788 0.601311 ACTCAGAGCAACTCCAACGC 60.601 55.000 0.00 0.00 0.00 4.84
740 789 2.724977 TACTCAGAGCAACTCCAACG 57.275 50.000 0.00 0.00 0.00 4.10
741 790 5.948992 AAATTACTCAGAGCAACTCCAAC 57.051 39.130 0.00 0.00 0.00 3.77
742 791 6.959639 AAAAATTACTCAGAGCAACTCCAA 57.040 33.333 0.00 0.00 0.00 3.53
775 824 9.145865 GTTCTCAAAAACATTACCTCACAAAAA 57.854 29.630 0.00 0.00 0.00 1.94
776 825 8.527810 AGTTCTCAAAAACATTACCTCACAAAA 58.472 29.630 0.00 0.00 0.00 2.44
777 826 8.062065 AGTTCTCAAAAACATTACCTCACAAA 57.938 30.769 0.00 0.00 0.00 2.83
778 827 7.639113 AGTTCTCAAAAACATTACCTCACAA 57.361 32.000 0.00 0.00 0.00 3.33
779 828 7.479980 CAAGTTCTCAAAAACATTACCTCACA 58.520 34.615 0.00 0.00 0.00 3.58
780 829 6.417930 GCAAGTTCTCAAAAACATTACCTCAC 59.582 38.462 0.00 0.00 0.00 3.51
781 830 6.096141 TGCAAGTTCTCAAAAACATTACCTCA 59.904 34.615 0.00 0.00 0.00 3.86
782 831 6.503524 TGCAAGTTCTCAAAAACATTACCTC 58.496 36.000 0.00 0.00 0.00 3.85
783 832 6.463995 TGCAAGTTCTCAAAAACATTACCT 57.536 33.333 0.00 0.00 0.00 3.08
784 833 7.713764 ATTGCAAGTTCTCAAAAACATTACC 57.286 32.000 4.94 0.00 0.00 2.85
785 834 9.034544 AGAATTGCAAGTTCTCAAAAACATTAC 57.965 29.630 4.94 0.00 30.34 1.89
786 835 9.598517 AAGAATTGCAAGTTCTCAAAAACATTA 57.401 25.926 18.32 0.00 34.97 1.90
787 836 8.496707 AAGAATTGCAAGTTCTCAAAAACATT 57.503 26.923 18.32 0.00 34.97 2.71
788 837 8.496707 AAAGAATTGCAAGTTCTCAAAAACAT 57.503 26.923 18.32 4.52 34.97 2.71
789 838 7.903995 AAAGAATTGCAAGTTCTCAAAAACA 57.096 28.000 18.32 0.00 34.97 2.83
790 839 8.442384 TCAAAAGAATTGCAAGTTCTCAAAAAC 58.558 29.630 18.32 0.00 34.97 2.43
791 840 8.545229 TCAAAAGAATTGCAAGTTCTCAAAAA 57.455 26.923 18.32 6.90 34.97 1.94
792 841 7.818930 ACTCAAAAGAATTGCAAGTTCTCAAAA 59.181 29.630 18.32 8.96 34.97 2.44
793 842 7.322664 ACTCAAAAGAATTGCAAGTTCTCAAA 58.677 30.769 18.32 8.72 34.97 2.69
794 843 6.866480 ACTCAAAAGAATTGCAAGTTCTCAA 58.134 32.000 18.32 8.50 34.97 3.02
795 844 6.455360 ACTCAAAAGAATTGCAAGTTCTCA 57.545 33.333 18.32 7.73 34.97 3.27
796 845 7.112148 CGTTACTCAAAAGAATTGCAAGTTCTC 59.888 37.037 18.32 8.04 34.97 2.87
797 846 6.912591 CGTTACTCAAAAGAATTGCAAGTTCT 59.087 34.615 4.94 11.18 37.52 3.01
798 847 6.142320 CCGTTACTCAAAAGAATTGCAAGTTC 59.858 38.462 4.94 9.11 0.00 3.01
799 848 5.977129 CCGTTACTCAAAAGAATTGCAAGTT 59.023 36.000 4.94 0.00 0.00 2.66
800 849 5.298276 TCCGTTACTCAAAAGAATTGCAAGT 59.702 36.000 4.94 0.59 0.00 3.16
801 850 5.757886 TCCGTTACTCAAAAGAATTGCAAG 58.242 37.500 4.94 0.00 0.00 4.01
802 851 5.759506 TCCGTTACTCAAAAGAATTGCAA 57.240 34.783 0.00 0.00 0.00 4.08
803 852 5.278266 CCTTCCGTTACTCAAAAGAATTGCA 60.278 40.000 0.00 0.00 0.00 4.08
804 853 5.154222 CCTTCCGTTACTCAAAAGAATTGC 58.846 41.667 0.00 0.00 0.00 3.56
805 854 5.472137 TCCCTTCCGTTACTCAAAAGAATTG 59.528 40.000 0.00 0.00 0.00 2.32
806 855 5.627135 TCCCTTCCGTTACTCAAAAGAATT 58.373 37.500 0.00 0.00 0.00 2.17
807 856 5.221864 ACTCCCTTCCGTTACTCAAAAGAAT 60.222 40.000 0.00 0.00 0.00 2.40
808 857 4.102054 ACTCCCTTCCGTTACTCAAAAGAA 59.898 41.667 0.00 0.00 0.00 2.52
809 858 3.644738 ACTCCCTTCCGTTACTCAAAAGA 59.355 43.478 0.00 0.00 0.00 2.52
810 859 4.004196 ACTCCCTTCCGTTACTCAAAAG 57.996 45.455 0.00 0.00 0.00 2.27
811 860 4.562143 GCTACTCCCTTCCGTTACTCAAAA 60.562 45.833 0.00 0.00 0.00 2.44
812 861 3.056322 GCTACTCCCTTCCGTTACTCAAA 60.056 47.826 0.00 0.00 0.00 2.69
813 862 2.494870 GCTACTCCCTTCCGTTACTCAA 59.505 50.000 0.00 0.00 0.00 3.02
814 863 2.097825 GCTACTCCCTTCCGTTACTCA 58.902 52.381 0.00 0.00 0.00 3.41
815 864 2.377073 AGCTACTCCCTTCCGTTACTC 58.623 52.381 0.00 0.00 0.00 2.59
816 865 2.528673 AGCTACTCCCTTCCGTTACT 57.471 50.000 0.00 0.00 0.00 2.24
817 866 2.479219 CGAAGCTACTCCCTTCCGTTAC 60.479 54.545 0.00 0.00 36.26 2.50
818 867 1.747355 CGAAGCTACTCCCTTCCGTTA 59.253 52.381 0.00 0.00 36.26 3.18
819 868 0.531200 CGAAGCTACTCCCTTCCGTT 59.469 55.000 0.00 0.00 36.26 4.44
820 869 0.611340 ACGAAGCTACTCCCTTCCGT 60.611 55.000 0.00 0.00 36.26 4.69
821 870 0.531200 AACGAAGCTACTCCCTTCCG 59.469 55.000 0.00 0.00 36.26 4.30
949 1001 1.133915 TGACAACAGGAAAGGTGGGAC 60.134 52.381 0.00 0.00 0.00 4.46
972 1024 2.203294 ACTGTGGGGGTTTGCGTC 60.203 61.111 0.00 0.00 0.00 5.19
977 1029 0.763223 AGACGAGACTGTGGGGGTTT 60.763 55.000 0.00 0.00 0.00 3.27
1239 1739 2.669569 TCAGCCTGCTGCCGTTTC 60.670 61.111 14.22 0.00 43.31 2.78
1527 2027 1.296755 CTTCGTCGTCCTCCTCGTCA 61.297 60.000 0.00 0.00 0.00 4.35
1572 2072 2.430244 TCTTCGTCGAGCGGCAAC 60.430 61.111 1.45 0.00 41.72 4.17
1623 2123 1.424302 CGTATCCTGTCCCCCTCTAGA 59.576 57.143 0.00 0.00 0.00 2.43
2061 2561 1.449601 AAGAACGCCTACCATGCCG 60.450 57.895 0.00 0.00 0.00 5.69
2079 2579 3.230284 CCGAAGGCATAGGCTCCA 58.770 61.111 0.00 0.00 46.14 3.86
2139 2639 2.437359 AGCTTCTGCACGGCCATC 60.437 61.111 2.24 0.00 42.74 3.51
2259 2759 1.295357 TAACATTGGTCAGCACGGCG 61.295 55.000 4.80 4.80 0.00 6.46
2262 2762 0.447801 GCCTAACATTGGTCAGCACG 59.552 55.000 0.00 0.00 0.00 5.34
2292 2792 2.556189 CTCGTATGTCATGCTAGCCTCT 59.444 50.000 13.29 0.00 0.00 3.69
2299 2799 1.687123 GTACCCCTCGTATGTCATGCT 59.313 52.381 0.00 0.00 0.00 3.79
2300 2800 1.411246 TGTACCCCTCGTATGTCATGC 59.589 52.381 0.00 0.00 0.00 4.06
2307 2807 1.964223 CTGCTCATGTACCCCTCGTAT 59.036 52.381 0.00 0.00 0.00 3.06
2358 2858 2.992689 TTACGGTGGCGCTCAGGA 60.993 61.111 7.64 0.00 0.00 3.86
2385 2885 0.109735 GTGCGCTCGGATCATCGATA 60.110 55.000 9.73 0.00 38.55 2.92
2523 3023 2.736343 TTCCGTGCGGTGTCTGTACG 62.736 60.000 10.60 11.09 43.62 3.67
2553 3053 0.979665 TTCCAAGCAGTCCAGAGGAG 59.020 55.000 0.00 0.00 29.39 3.69
2679 3179 3.430790 CCTCATCAATTAGCTCACACCGA 60.431 47.826 0.00 0.00 0.00 4.69
2697 3197 1.075482 CCCAAAGGCTTGCTCCTCA 59.925 57.895 0.00 0.00 34.82 3.86
2793 3293 7.984050 AGAGAAAGTATCATACCAGTGACAATG 59.016 37.037 0.00 0.00 0.00 2.82
2821 3321 7.011109 GCGGTGTGTTAATGAGAACTATTGTAT 59.989 37.037 0.00 0.00 0.00 2.29
2822 3322 6.311935 GCGGTGTGTTAATGAGAACTATTGTA 59.688 38.462 0.00 0.00 0.00 2.41
2823 3323 5.121768 GCGGTGTGTTAATGAGAACTATTGT 59.878 40.000 0.00 0.00 0.00 2.71
2824 3324 5.447279 GGCGGTGTGTTAATGAGAACTATTG 60.447 44.000 0.00 0.00 0.00 1.90
2825 3325 4.634443 GGCGGTGTGTTAATGAGAACTATT 59.366 41.667 0.00 0.00 0.00 1.73
2845 3345 3.374058 CCAGTATAAACTTTGTGGAGGCG 59.626 47.826 0.00 0.00 31.97 5.52
2860 3360 9.685828 GCAAATTAACAGTTTGAAACCAGTATA 57.314 29.630 4.14 0.00 38.51 1.47
2861 3361 8.421002 AGCAAATTAACAGTTTGAAACCAGTAT 58.579 29.630 4.14 0.00 38.51 2.12
2862 3362 7.704472 CAGCAAATTAACAGTTTGAAACCAGTA 59.296 33.333 4.14 0.00 38.51 2.74
2863 3363 6.534793 CAGCAAATTAACAGTTTGAAACCAGT 59.465 34.615 4.14 1.17 38.51 4.00
2864 3364 6.534793 ACAGCAAATTAACAGTTTGAAACCAG 59.465 34.615 4.14 0.50 38.51 4.00
2904 3404 9.747898 TGTAATACCACAACCAGAATAAAGAAT 57.252 29.630 0.00 0.00 0.00 2.40
2909 3409 8.788806 CAGTTTGTAATACCACAACCAGAATAA 58.211 33.333 0.00 0.00 38.12 1.40
2915 3415 4.517453 GCTCAGTTTGTAATACCACAACCA 59.483 41.667 0.00 0.00 38.12 3.67
3021 3521 6.262944 ACATAACAACATCACTTTTCTCAGCA 59.737 34.615 0.00 0.00 0.00 4.41
3126 3626 6.989759 TGTGTAAACTTCAGCTCACTCATTTA 59.010 34.615 0.00 0.00 0.00 1.40
3253 3755 3.003230 CCATTTGGTAGGGGCGGA 58.997 61.111 0.00 0.00 0.00 5.54
3421 3923 9.926158 TGTAGCATATTTCAACAATTTGTTCAT 57.074 25.926 11.78 7.39 38.77 2.57
3424 3926 9.762933 AAGTGTAGCATATTTCAACAATTTGTT 57.237 25.926 8.97 8.97 42.08 2.83
3426 3928 9.409312 TCAAGTGTAGCATATTTCAACAATTTG 57.591 29.630 0.00 0.00 0.00 2.32
3488 3990 3.079578 CAAGAGCCAAGATCAGCTTCAA 58.920 45.455 6.40 0.00 40.11 2.69
3489 3991 2.039480 ACAAGAGCCAAGATCAGCTTCA 59.961 45.455 6.40 0.00 40.11 3.02
3565 4067 7.164122 TCTTTCTGAGCATGTTCTACATTCTT 58.836 34.615 11.09 0.00 36.53 2.52
3743 4300 4.370776 TCAGGAATAAGGACCAAGATGGA 58.629 43.478 2.85 0.00 40.96 3.41
3752 4309 6.272822 ACAAAAGCAATCAGGAATAAGGAC 57.727 37.500 0.00 0.00 0.00 3.85
3773 4330 3.136443 AGTGACAACCTGAAGGATGAACA 59.864 43.478 13.06 9.50 40.03 3.18
4054 4611 6.183360 GGAGGCTTGTATTTTCAATAGGACAC 60.183 42.308 0.00 0.00 0.00 3.67
4063 4620 3.517296 TGGTGGAGGCTTGTATTTTCA 57.483 42.857 0.00 0.00 0.00 2.69
4127 4684 5.534278 TCACAAAATGCAAGGTAGATCACAA 59.466 36.000 0.00 0.00 0.00 3.33
4160 4729 1.526575 AATGCGGTCAGGGCAAGTTG 61.527 55.000 0.00 0.00 44.66 3.16
4204 4774 4.590222 ACATTGCAAAAGAGGAAATCTGGT 59.410 37.500 1.71 0.00 38.67 4.00
4209 4779 4.520492 AGACGACATTGCAAAAGAGGAAAT 59.480 37.500 1.71 0.00 0.00 2.17
4231 4801 7.041167 TCAGTAAATCTGTGGTTTTCATGTGAG 60.041 37.037 0.00 0.00 43.97 3.51
4247 4817 5.827797 AGAGAGAAGCGAGATCAGTAAATCT 59.172 40.000 0.00 0.00 38.72 2.40
4261 4831 0.735632 GTGGCAGACAGAGAGAAGCG 60.736 60.000 0.00 0.00 0.00 4.68
4273 4843 1.429930 TTCTGGTAACCTGTGGCAGA 58.570 50.000 0.00 0.00 32.44 4.26
4525 5095 9.515020 TTGTCTATTTTTCATGAAAACTGACAC 57.485 29.630 33.61 25.45 43.88 3.67
4557 5127 1.635663 GCACATGAAGAACCCGGACG 61.636 60.000 0.73 0.00 0.00 4.79
4581 5151 7.446931 TCTGGATTGTAGCACACTTCATAAAAA 59.553 33.333 0.00 0.00 0.00 1.94
4582 5152 6.939730 TCTGGATTGTAGCACACTTCATAAAA 59.060 34.615 0.00 0.00 0.00 1.52
4611 8610 1.787847 GCGGTCGGAGAAATGTGTG 59.212 57.895 0.00 0.00 39.69 3.82
4629 8628 9.337091 CACTTATATTTTTCAAGGTACCAAACG 57.663 33.333 15.94 0.00 0.00 3.60
4649 8652 0.173255 GCCATGCAAACGCCACTTAT 59.827 50.000 0.00 0.00 0.00 1.73
4650 8653 1.175347 TGCCATGCAAACGCCACTTA 61.175 50.000 0.00 0.00 34.76 2.24
4837 8846 4.812476 CGATTGCGCGGACCCAGA 62.812 66.667 8.83 0.00 0.00 3.86
4912 8921 2.288030 GGCGCCGTAGAAGTATGTATGT 60.288 50.000 12.58 0.00 0.00 2.29
5007 9016 1.682323 TGTGCAAGAAGAATGCTGCAA 59.318 42.857 6.36 0.00 45.71 4.08
5067 9076 3.136626 ACCACTGTTTAGCTTTCACCTCT 59.863 43.478 0.00 0.00 0.00 3.69
5144 9155 7.096065 CGATGTCTAGATCGATGCATGTAAAAA 60.096 37.037 2.46 0.00 46.72 1.94
5145 9156 6.363357 CGATGTCTAGATCGATGCATGTAAAA 59.637 38.462 2.46 0.00 46.72 1.52
5146 9157 5.858581 CGATGTCTAGATCGATGCATGTAAA 59.141 40.000 2.46 0.00 46.72 2.01
5147 9158 5.393962 CGATGTCTAGATCGATGCATGTAA 58.606 41.667 2.46 0.00 46.72 2.41
5155 9166 2.143925 TCGTGCGATGTCTAGATCGAT 58.856 47.619 17.74 0.00 46.72 3.59
5205 9216 6.750009 AGGATGATAGGAGATGATATGTCCA 58.250 40.000 7.61 0.00 44.73 4.02
5259 9270 7.832503 ACTTTCAAAACAAGAAACAAGATGG 57.167 32.000 0.00 0.00 32.09 3.51


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

AutoCloner maintained by Alex Coulton.