Multiple sequence alignment - TraesCS5A01G396000

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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 TraesCS5A01G396000 chr5A 100.000 2759 0 0 1 2759 591080866 591083624 0.000000e+00 5096.0
1 TraesCS5A01G396000 chr5A 95.853 627 26 0 1 627 21962754 21962128 0.000000e+00 1014.0
2 TraesCS5A01G396000 chr5A 95.853 627 26 0 1 627 345512703 345512077 0.000000e+00 1014.0
3 TraesCS5A01G396000 chr5A 94.852 641 31 2 1 640 408551606 408550967 0.000000e+00 1000.0
4 TraesCS5A01G396000 chr5D 91.959 2052 81 38 685 2713 470376772 470378762 0.000000e+00 2798.0
5 TraesCS5A01G396000 chr5B 91.908 1520 49 25 820 2313 577659583 577661054 0.000000e+00 2058.0
6 TraesCS5A01G396000 chr4A 96.019 628 24 1 1 627 448068271 448068898 0.000000e+00 1020.0
7 TraesCS5A01G396000 chr7A 95.866 629 24 1 1 627 494179646 494180274 0.000000e+00 1016.0
8 TraesCS5A01G396000 chr7A 95.694 627 27 0 1 627 431416857 431416231 0.000000e+00 1009.0
9 TraesCS5A01G396000 chr2A 95.440 636 28 1 1 635 411695741 411696376 0.000000e+00 1013.0
10 TraesCS5A01G396000 chr2A 95.694 627 27 0 1 627 701144976 701144350 0.000000e+00 1009.0
11 TraesCS5A01G396000 chr2A 80.791 354 50 13 1206 1545 120098959 120099308 7.580000e-66 261.0
12 TraesCS5A01G396000 chr1A 95.701 628 27 0 1 628 469282499 469281872 0.000000e+00 1011.0
13 TraesCS5A01G396000 chr2D 80.833 360 48 16 1206 1548 118245601 118245956 2.110000e-66 263.0
14 TraesCS5A01G396000 chr2B 81.050 343 48 10 1206 1535 169864592 169864930 9.800000e-65 257.0
15 TraesCS5A01G396000 chr2B 74.352 386 79 13 991 1375 5489963 5490329 2.210000e-31 147.0
16 TraesCS5A01G396000 chr2B 81.875 160 24 5 1379 1535 5490800 5490957 2.230000e-26 130.0
17 TraesCS5A01G396000 chr1D 86.792 53 7 0 1356 1408 407696438 407696490 2.970000e-05 60.2


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 TraesCS5A01G396000 chr5A 591080866 591083624 2758 False 5096 5096 100.000 1 2759 1 chr5A.!!$F1 2758
1 TraesCS5A01G396000 chr5A 21962128 21962754 626 True 1014 1014 95.853 1 627 1 chr5A.!!$R1 626
2 TraesCS5A01G396000 chr5A 345512077 345512703 626 True 1014 1014 95.853 1 627 1 chr5A.!!$R2 626
3 TraesCS5A01G396000 chr5A 408550967 408551606 639 True 1000 1000 94.852 1 640 1 chr5A.!!$R3 639
4 TraesCS5A01G396000 chr5D 470376772 470378762 1990 False 2798 2798 91.959 685 2713 1 chr5D.!!$F1 2028
5 TraesCS5A01G396000 chr5B 577659583 577661054 1471 False 2058 2058 91.908 820 2313 1 chr5B.!!$F1 1493
6 TraesCS5A01G396000 chr4A 448068271 448068898 627 False 1020 1020 96.019 1 627 1 chr4A.!!$F1 626
7 TraesCS5A01G396000 chr7A 494179646 494180274 628 False 1016 1016 95.866 1 627 1 chr7A.!!$F1 626
8 TraesCS5A01G396000 chr7A 431416231 431416857 626 True 1009 1009 95.694 1 627 1 chr7A.!!$R1 626
9 TraesCS5A01G396000 chr2A 411695741 411696376 635 False 1013 1013 95.440 1 635 1 chr2A.!!$F2 634
10 TraesCS5A01G396000 chr2A 701144350 701144976 626 True 1009 1009 95.694 1 627 1 chr2A.!!$R1 626
11 TraesCS5A01G396000 chr1A 469281872 469282499 627 True 1011 1011 95.701 1 628 1 chr1A.!!$R1 627

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
860 869 0.322456 CGGCCCAAATCCACTTCTCA 60.322 55.0 0.0 0.0 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1930 1972 0.031585 CTCATGGATTTGGCGGCATG 59.968 55.0 14.32 7.13 0.0 4.06 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 1.453015 TGCAAAGCCACCGAACACT 60.453 52.632 0.00 0.00 0.00 3.55
216 218 1.452953 CTGTGCGTCTAGGCCGGATA 61.453 60.000 5.05 0.00 0.00 2.59
370 372 2.434702 GGCTAAACCCTAGAAGCTAGCA 59.565 50.000 18.83 0.00 34.72 3.49
389 393 7.984050 AGCTAGCATATGGTATGATTGTATGTC 59.016 37.037 18.83 0.00 0.00 3.06
628 633 2.324541 CTAATCCAGGACTCCCTCAGG 58.675 57.143 0.00 0.00 42.02 3.86
644 649 0.890683 CAGGCACCCTGCTAAAAAGG 59.109 55.000 0.00 0.00 45.13 3.11
645 650 0.482887 AGGCACCCTGCTAAAAAGGT 59.517 50.000 0.00 0.00 44.28 3.50
646 651 1.133167 AGGCACCCTGCTAAAAAGGTT 60.133 47.619 0.00 0.00 44.28 3.50
647 652 2.109304 AGGCACCCTGCTAAAAAGGTTA 59.891 45.455 0.00 0.00 44.28 2.85
648 653 3.096852 GGCACCCTGCTAAAAAGGTTAT 58.903 45.455 0.00 0.00 44.28 1.89
649 654 4.017867 AGGCACCCTGCTAAAAAGGTTATA 60.018 41.667 0.00 0.00 44.28 0.98
650 655 4.338400 GGCACCCTGCTAAAAAGGTTATAG 59.662 45.833 0.00 0.00 44.28 1.31
651 656 4.202020 GCACCCTGCTAAAAAGGTTATAGC 60.202 45.833 0.00 0.00 40.96 2.97
656 661 4.855340 TGCTAAAAAGGTTATAGCAGGCT 58.145 39.130 2.79 0.00 45.10 4.58
657 662 5.996644 TGCTAAAAAGGTTATAGCAGGCTA 58.003 37.500 3.11 3.11 45.10 3.93
658 663 6.601332 TGCTAAAAAGGTTATAGCAGGCTAT 58.399 36.000 17.12 17.12 45.10 2.97
659 664 7.741785 TGCTAAAAAGGTTATAGCAGGCTATA 58.258 34.615 15.21 15.21 45.10 1.31
660 665 7.878127 TGCTAAAAAGGTTATAGCAGGCTATAG 59.122 37.037 17.64 8.64 45.10 1.31
661 666 7.148390 GCTAAAAAGGTTATAGCAGGCTATAGC 60.148 40.741 20.39 20.39 41.02 2.97
662 667 4.457834 AAGGTTATAGCAGGCTATAGCG 57.542 45.455 21.20 6.94 40.95 4.26
663 668 2.761208 AGGTTATAGCAGGCTATAGCGG 59.239 50.000 21.20 13.73 40.95 5.52
664 669 2.758979 GGTTATAGCAGGCTATAGCGGA 59.241 50.000 21.20 7.41 40.95 5.54
665 670 3.181485 GGTTATAGCAGGCTATAGCGGAG 60.181 52.174 21.20 11.30 40.95 4.63
666 671 2.516227 ATAGCAGGCTATAGCGGAGA 57.484 50.000 18.30 3.29 43.26 3.71
667 672 2.516227 TAGCAGGCTATAGCGGAGAT 57.484 50.000 18.30 11.40 43.26 2.75
668 673 2.516227 AGCAGGCTATAGCGGAGATA 57.484 50.000 18.30 0.00 43.26 1.98
669 674 3.025322 AGCAGGCTATAGCGGAGATAT 57.975 47.619 18.30 0.00 43.63 1.63
670 675 4.171878 AGCAGGCTATAGCGGAGATATA 57.828 45.455 18.30 0.00 40.68 0.86
681 686 3.802948 CGGAGATATAGCCGGCTATTT 57.197 47.619 44.65 38.07 43.67 1.40
682 687 4.913335 CGGAGATATAGCCGGCTATTTA 57.087 45.455 44.65 32.02 43.67 1.40
683 688 5.258456 CGGAGATATAGCCGGCTATTTAA 57.742 43.478 44.65 31.35 43.67 1.52
684 689 5.657474 CGGAGATATAGCCGGCTATTTAAA 58.343 41.667 44.65 31.02 43.67 1.52
685 690 6.103997 CGGAGATATAGCCGGCTATTTAAAA 58.896 40.000 44.65 30.67 43.67 1.52
686 691 6.035758 CGGAGATATAGCCGGCTATTTAAAAC 59.964 42.308 44.65 30.15 43.67 2.43
687 692 7.104290 GGAGATATAGCCGGCTATTTAAAACT 58.896 38.462 44.65 31.87 39.65 2.66
688 693 7.064728 GGAGATATAGCCGGCTATTTAAAACTG 59.935 40.741 44.65 0.00 39.65 3.16
689 694 7.450903 AGATATAGCCGGCTATTTAAAACTGT 58.549 34.615 44.65 25.26 39.65 3.55
690 695 5.751243 ATAGCCGGCTATTTAAAACTGTG 57.249 39.130 37.79 0.00 35.92 3.66
813 818 3.323136 GAGCGCGGCGACTATGTG 61.323 66.667 28.54 0.00 0.00 3.21
816 821 2.025584 CGCGGCGACTATGTGCTA 59.974 61.111 19.16 0.00 0.00 3.49
818 823 1.065928 GCGGCGACTATGTGCTAGT 59.934 57.895 12.98 0.00 43.57 2.57
830 839 7.521871 ACTATGTGCTAGTAGTATAACACCC 57.478 40.000 0.00 0.00 38.96 4.61
860 869 0.322456 CGGCCCAAATCCACTTCTCA 60.322 55.000 0.00 0.00 0.00 3.27
861 870 1.467920 GGCCCAAATCCACTTCTCAG 58.532 55.000 0.00 0.00 0.00 3.35
862 871 1.004745 GGCCCAAATCCACTTCTCAGA 59.995 52.381 0.00 0.00 0.00 3.27
863 872 2.087646 GCCCAAATCCACTTCTCAGAC 58.912 52.381 0.00 0.00 0.00 3.51
864 873 2.553028 GCCCAAATCCACTTCTCAGACA 60.553 50.000 0.00 0.00 0.00 3.41
865 874 3.077359 CCCAAATCCACTTCTCAGACAC 58.923 50.000 0.00 0.00 0.00 3.67
866 875 3.496692 CCCAAATCCACTTCTCAGACACA 60.497 47.826 0.00 0.00 0.00 3.72
867 876 3.499918 CCAAATCCACTTCTCAGACACAC 59.500 47.826 0.00 0.00 0.00 3.82
931 942 2.463589 AATTCCCAGCCGAGAACGCA 62.464 55.000 0.00 0.00 38.29 5.24
970 981 1.595993 CGTCGGGAGGAGCAGAAGAA 61.596 60.000 0.00 0.00 0.00 2.52
1602 1631 4.803426 GTCGAGGCGGCCAGAGTG 62.803 72.222 23.09 5.73 0.00 3.51
1905 1947 6.566079 ATCCTGTGAACAAGATCTATGGAA 57.434 37.500 0.00 0.00 0.00 3.53
1911 1953 6.769341 TGTGAACAAGATCTATGGAATGGATG 59.231 38.462 0.00 0.00 45.22 3.51
1912 1954 6.206243 GTGAACAAGATCTATGGAATGGATGG 59.794 42.308 0.00 0.00 45.22 3.51
1913 1955 6.101588 TGAACAAGATCTATGGAATGGATGGA 59.898 38.462 0.00 0.00 45.22 3.41
1914 1956 5.874093 ACAAGATCTATGGAATGGATGGAC 58.126 41.667 0.00 0.00 45.22 4.02
1930 1972 0.931005 GGACACATCTCGGCGATTTC 59.069 55.000 11.27 0.00 0.00 2.17
1931 1973 1.640428 GACACATCTCGGCGATTTCA 58.360 50.000 11.27 0.00 0.00 2.69
1955 1997 2.486013 CCGCCAAATCCATGAGATCTGA 60.486 50.000 0.00 0.00 32.47 3.27
1956 1998 2.806818 CGCCAAATCCATGAGATCTGAG 59.193 50.000 0.00 0.00 32.47 3.35
2040 2082 8.882415 TTTTACCATGCAGTAATACTACTAGC 57.118 34.615 0.00 0.00 36.14 3.42
2088 2130 1.800655 GCTGTCCATGTCGAGCAGTAG 60.801 57.143 0.00 0.00 0.00 2.57
2089 2131 0.173481 TGTCCATGTCGAGCAGTAGC 59.827 55.000 0.00 0.00 42.56 3.58
2155 2197 3.864583 GCAGATGTTGACTAGAGAAGCAG 59.135 47.826 0.00 0.00 0.00 4.24
2171 2213 1.485838 GCAGCTGGATCATGACGACG 61.486 60.000 17.12 0.00 0.00 5.12
2175 2217 0.377203 CTGGATCATGACGACGACGA 59.623 55.000 15.32 0.00 42.66 4.20
2199 2241 5.351465 ACAACAGCAACAAATATCCGAGTAG 59.649 40.000 0.00 0.00 0.00 2.57
2210 2252 3.892918 ATCCGAGTAGACCGTATTTCG 57.107 47.619 0.00 0.00 39.52 3.46
2211 2253 2.632377 TCCGAGTAGACCGTATTTCGT 58.368 47.619 0.00 0.00 37.94 3.85
2212 2254 3.792401 TCCGAGTAGACCGTATTTCGTA 58.208 45.455 0.00 0.00 37.94 3.43
2213 2255 3.555956 TCCGAGTAGACCGTATTTCGTAC 59.444 47.826 0.00 0.00 37.94 3.67
2320 2365 6.039270 ACCGACTCATTTGAAAATTGAACTGA 59.961 34.615 0.00 0.00 35.98 3.41
2358 2403 7.254522 CGCCCCAATCAAATCATAAAAAGAATG 60.255 37.037 0.00 0.00 0.00 2.67
2371 2416 7.395772 TCATAAAAAGAATGAGGCCACATACAA 59.604 33.333 16.56 0.00 0.00 2.41
2377 2422 1.885887 TGAGGCCACATACAAAACAGC 59.114 47.619 5.01 0.00 0.00 4.40
2382 2427 1.401409 CCACATACAAAACAGCTGCCG 60.401 52.381 15.27 1.88 0.00 5.69
2390 2435 0.671796 AAACAGCTGCCGGGTTTTAC 59.328 50.000 15.27 0.00 31.09 2.01
2404 2449 4.509616 GGGTTTTACTTTTTGCAACCAGT 58.490 39.130 13.05 13.05 38.99 4.00
2447 2492 3.245371 TGCCTCCTTGATTGTCCTCAAAT 60.245 43.478 0.00 0.00 37.11 2.32
2457 2502 7.366847 TGATTGTCCTCAAATTTAACCCAAA 57.633 32.000 0.00 0.00 37.11 3.28
2485 2530 0.472471 TTCCTGCTTCAAGTCCCGTT 59.528 50.000 0.00 0.00 0.00 4.44
2486 2531 0.034896 TCCTGCTTCAAGTCCCGTTC 59.965 55.000 0.00 0.00 0.00 3.95
2487 2532 1.291877 CCTGCTTCAAGTCCCGTTCG 61.292 60.000 0.00 0.00 0.00 3.95
2488 2533 1.901650 CTGCTTCAAGTCCCGTTCGC 61.902 60.000 0.00 0.00 0.00 4.70
2489 2534 1.959226 GCTTCAAGTCCCGTTCGCA 60.959 57.895 0.00 0.00 0.00 5.10
2490 2535 1.503818 GCTTCAAGTCCCGTTCGCAA 61.504 55.000 0.00 0.00 0.00 4.85
2510 2555 5.427082 GCAATTCAGAGTGTATTTCGATCG 58.573 41.667 9.36 9.36 0.00 3.69
2523 2568 2.795175 TCGATCGTAGAGGAAATGGC 57.205 50.000 15.94 0.00 43.63 4.40
2524 2569 1.001706 TCGATCGTAGAGGAAATGGCG 60.002 52.381 15.94 0.00 43.63 5.69
2549 2595 5.462729 CAGACTCTGCTCATTTACATAGCTG 59.537 44.000 0.00 0.00 37.16 4.24
2556 2602 4.039730 GCTCATTTACATAGCTGGAGGAGA 59.960 45.833 0.00 0.00 33.40 3.71
2560 2606 6.556495 TCATTTACATAGCTGGAGGAGATTCT 59.444 38.462 0.00 0.00 0.00 2.40
2588 2634 0.108963 CTCTCTATCGGGTCCGTCCT 59.891 60.000 9.36 0.00 40.74 3.85
2589 2635 0.179026 TCTCTATCGGGTCCGTCCTG 60.179 60.000 9.36 0.00 43.70 3.86
2620 2666 0.960364 TTTGACCGCCTTGCATCCTC 60.960 55.000 0.00 0.00 0.00 3.71
2627 2673 2.402388 CTTGCATCCTCGCTTGCG 59.598 61.111 8.87 8.87 41.80 4.85
2648 2694 0.550147 ACACCCCAGGTCCATAGCTT 60.550 55.000 0.00 0.00 31.02 3.74
2652 2698 1.630878 CCCCAGGTCCATAGCTTATCC 59.369 57.143 0.00 0.00 0.00 2.59
2654 2700 2.915604 CCCAGGTCCATAGCTTATCCAT 59.084 50.000 0.00 0.00 0.00 3.41
2655 2701 3.054802 CCCAGGTCCATAGCTTATCCATC 60.055 52.174 0.00 0.00 0.00 3.51
2656 2702 3.368843 CCAGGTCCATAGCTTATCCATCG 60.369 52.174 0.00 0.00 0.00 3.84
2657 2703 3.259374 CAGGTCCATAGCTTATCCATCGT 59.741 47.826 0.00 0.00 0.00 3.73
2659 2705 5.047306 CAGGTCCATAGCTTATCCATCGTTA 60.047 44.000 0.00 0.00 0.00 3.18
2660 2706 5.047235 AGGTCCATAGCTTATCCATCGTTAC 60.047 44.000 0.00 0.00 0.00 2.50
2662 2708 5.864474 GTCCATAGCTTATCCATCGTTACTG 59.136 44.000 0.00 0.00 0.00 2.74
2663 2709 5.047306 TCCATAGCTTATCCATCGTTACTGG 60.047 44.000 0.00 0.00 34.93 4.00
2664 2710 5.279506 CCATAGCTTATCCATCGTTACTGGT 60.280 44.000 0.00 0.00 35.19 4.00
2665 2711 4.060038 AGCTTATCCATCGTTACTGGTG 57.940 45.455 0.00 0.00 35.19 4.17
2666 2712 3.704566 AGCTTATCCATCGTTACTGGTGA 59.295 43.478 0.00 0.00 35.19 4.02
2667 2713 4.345257 AGCTTATCCATCGTTACTGGTGAT 59.655 41.667 0.00 0.00 35.19 3.06
2668 2714 4.686554 GCTTATCCATCGTTACTGGTGATC 59.313 45.833 0.00 0.00 35.19 2.92
2669 2715 3.753294 ATCCATCGTTACTGGTGATCC 57.247 47.619 0.00 0.00 35.19 3.36
2670 2716 2.747177 TCCATCGTTACTGGTGATCCT 58.253 47.619 0.00 0.00 35.19 3.24
2671 2717 2.693591 TCCATCGTTACTGGTGATCCTC 59.306 50.000 0.00 0.00 35.19 3.71
2676 2722 2.430694 CGTTACTGGTGATCCTCATCCA 59.569 50.000 0.00 0.00 34.23 3.41
2686 2732 5.960811 GGTGATCCTCATCCATCCTATCTAA 59.039 44.000 0.00 0.00 0.00 2.10
2727 2773 9.765795 ATTACAGAATTAGAATTTACTCTCCCG 57.234 33.333 0.00 0.00 0.00 5.14
2728 2774 7.184067 ACAGAATTAGAATTTACTCTCCCGT 57.816 36.000 0.00 0.00 0.00 5.28
2729 2775 7.621796 ACAGAATTAGAATTTACTCTCCCGTT 58.378 34.615 0.00 0.00 0.00 4.44
2730 2776 7.764901 ACAGAATTAGAATTTACTCTCCCGTTC 59.235 37.037 0.00 0.00 0.00 3.95
2731 2777 7.982354 CAGAATTAGAATTTACTCTCCCGTTCT 59.018 37.037 0.00 0.00 0.00 3.01
2732 2778 9.198475 AGAATTAGAATTTACTCTCCCGTTCTA 57.802 33.333 0.00 0.00 0.00 2.10
2733 2779 9.813446 GAATTAGAATTTACTCTCCCGTTCTAA 57.187 33.333 7.55 7.55 40.39 2.10
2738 2784 9.597170 AGAATTTACTCTCCCGTTCTAAATTAC 57.403 33.333 0.00 0.00 30.65 1.89
2739 2785 9.597170 GAATTTACTCTCCCGTTCTAAATTACT 57.403 33.333 0.00 0.00 30.65 2.24
2740 2786 9.955102 AATTTACTCTCCCGTTCTAAATTACTT 57.045 29.630 0.00 0.00 29.36 2.24
2744 2790 8.302515 ACTCTCCCGTTCTAAATTACTTATCA 57.697 34.615 0.00 0.00 0.00 2.15
2745 2791 8.925338 ACTCTCCCGTTCTAAATTACTTATCAT 58.075 33.333 0.00 0.00 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 2.840640 TTCTCCCCGGACAGATCTTA 57.159 50.000 0.73 0.00 0.00 2.10
92 93 3.778954 GGCTTGATGGCTCCTACTATT 57.221 47.619 0.00 0.00 38.32 1.73
138 139 2.598589 CGACATTGGTGCTTTCATTGG 58.401 47.619 0.00 0.00 0.00 3.16
216 218 0.910088 GTCCCCTGCCTCCTGTTACT 60.910 60.000 0.00 0.00 0.00 2.24
370 372 7.482169 AGGACGACATACAATCATACCATAT 57.518 36.000 0.00 0.00 0.00 1.78
481 486 2.643551 GAAGGCAAGCTAGGCAATACA 58.356 47.619 11.85 0.00 36.37 2.29
546 551 6.644347 ACTGTTGGACTATGAAGATACAAGG 58.356 40.000 0.00 0.00 0.00 3.61
607 612 2.359781 CCTGAGGGAGTCCTGGATTAGT 60.360 54.545 9.58 0.00 45.05 2.24
628 633 4.202020 GCTATAACCTTTTTAGCAGGGTGC 60.202 45.833 4.18 0.00 45.46 5.01
637 642 6.872020 CGCTATAGCCTGCTATAACCTTTTTA 59.128 38.462 19.00 0.00 39.94 1.52
638 643 5.701290 CGCTATAGCCTGCTATAACCTTTTT 59.299 40.000 19.00 0.00 39.94 1.94
641 646 3.195825 CCGCTATAGCCTGCTATAACCTT 59.804 47.826 19.00 0.00 39.94 3.50
642 647 2.761208 CCGCTATAGCCTGCTATAACCT 59.239 50.000 19.00 0.00 39.94 3.50
643 648 2.758979 TCCGCTATAGCCTGCTATAACC 59.241 50.000 19.00 11.32 39.94 2.85
644 649 3.695060 TCTCCGCTATAGCCTGCTATAAC 59.305 47.826 19.00 12.88 39.94 1.89
645 650 3.964411 TCTCCGCTATAGCCTGCTATAA 58.036 45.455 19.00 4.76 39.94 0.98
646 651 3.646736 TCTCCGCTATAGCCTGCTATA 57.353 47.619 19.00 15.94 39.65 1.31
647 652 2.516227 TCTCCGCTATAGCCTGCTAT 57.484 50.000 19.00 15.41 41.58 2.97
648 653 2.516227 ATCTCCGCTATAGCCTGCTA 57.484 50.000 19.00 0.64 37.91 3.49
649 654 2.516227 TATCTCCGCTATAGCCTGCT 57.484 50.000 19.00 0.00 37.91 4.24
650 655 3.305064 GCTATATCTCCGCTATAGCCTGC 60.305 52.174 19.00 6.48 44.19 4.85
651 656 4.497473 GCTATATCTCCGCTATAGCCTG 57.503 50.000 19.00 10.54 44.19 4.85
655 660 2.226912 GCCGGCTATATCTCCGCTATAG 59.773 54.545 22.15 0.00 44.01 1.31
656 661 2.158652 AGCCGGCTATATCTCCGCTATA 60.159 50.000 31.86 0.00 44.01 1.31
657 662 1.033574 GCCGGCTATATCTCCGCTAT 58.966 55.000 22.15 0.00 44.01 2.97
658 663 0.034380 AGCCGGCTATATCTCCGCTA 60.034 55.000 31.86 0.00 44.01 4.26
659 664 0.034380 TAGCCGGCTATATCTCCGCT 60.034 55.000 32.24 6.88 44.01 5.52
660 665 1.033574 ATAGCCGGCTATATCTCCGC 58.966 55.000 41.03 5.41 44.01 5.54
661 666 3.802948 AAATAGCCGGCTATATCTCCG 57.197 47.619 41.53 8.21 44.89 4.63
662 667 7.064728 CAGTTTTAAATAGCCGGCTATATCTCC 59.935 40.741 41.53 27.96 38.20 3.71
663 668 7.603024 ACAGTTTTAAATAGCCGGCTATATCTC 59.397 37.037 41.53 28.58 38.20 2.75
664 669 7.387948 CACAGTTTTAAATAGCCGGCTATATCT 59.612 37.037 41.53 30.77 38.20 1.98
665 670 7.386848 TCACAGTTTTAAATAGCCGGCTATATC 59.613 37.037 41.53 26.38 38.20 1.63
666 671 7.221450 TCACAGTTTTAAATAGCCGGCTATAT 58.779 34.615 41.53 29.39 38.20 0.86
667 672 6.584488 TCACAGTTTTAAATAGCCGGCTATA 58.416 36.000 41.53 28.18 38.20 1.31
668 673 5.433526 TCACAGTTTTAAATAGCCGGCTAT 58.566 37.500 37.79 37.79 40.63 2.97
669 674 4.834534 TCACAGTTTTAAATAGCCGGCTA 58.165 39.130 36.88 36.88 0.00 3.93
670 675 3.681593 TCACAGTTTTAAATAGCCGGCT 58.318 40.909 34.85 34.85 0.00 5.52
671 676 4.632538 ATCACAGTTTTAAATAGCCGGC 57.367 40.909 21.89 21.89 0.00 6.13
813 818 3.057666 GCGAGGGGTGTTATACTACTAGC 60.058 52.174 0.00 0.00 31.37 3.42
814 819 3.505293 GGCGAGGGGTGTTATACTACTAG 59.495 52.174 0.00 0.00 0.00 2.57
815 820 3.139025 AGGCGAGGGGTGTTATACTACTA 59.861 47.826 0.00 0.00 0.00 1.82
816 821 2.091444 AGGCGAGGGGTGTTATACTACT 60.091 50.000 0.00 0.00 0.00 2.57
818 823 2.313317 CAGGCGAGGGGTGTTATACTA 58.687 52.381 0.00 0.00 0.00 1.82
860 869 1.270571 TGTGTGTGTGTGTGTGTGTCT 60.271 47.619 0.00 0.00 0.00 3.41
861 870 1.136085 GTGTGTGTGTGTGTGTGTGTC 60.136 52.381 0.00 0.00 0.00 3.67
862 871 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
863 872 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
864 873 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
865 874 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
866 875 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
867 876 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
909 920 1.032114 GTTCTCGGCTGGGAATTGGG 61.032 60.000 11.92 0.00 0.00 4.12
910 921 1.369091 CGTTCTCGGCTGGGAATTGG 61.369 60.000 11.92 0.14 0.00 3.16
931 942 2.685380 CCTCTCTTCCCCAGCCGT 60.685 66.667 0.00 0.00 0.00 5.68
1455 1475 2.367202 GGGGAAGATGGGCGACTCA 61.367 63.158 0.00 0.00 0.00 3.41
1815 1850 5.814705 TGTACAATTTGCTTCCTTTTTGGTG 59.185 36.000 0.00 0.00 37.07 4.17
1911 1953 0.931005 GAAATCGCCGAGATGTGTCC 59.069 55.000 0.00 0.00 40.02 4.02
1912 1954 1.640428 TGAAATCGCCGAGATGTGTC 58.360 50.000 0.00 0.00 40.02 3.67
1913 1955 1.935873 CATGAAATCGCCGAGATGTGT 59.064 47.619 0.00 0.00 40.02 3.72
1914 1956 1.333524 GCATGAAATCGCCGAGATGTG 60.334 52.381 0.00 0.00 40.02 3.21
1930 1972 0.031585 CTCATGGATTTGGCGGCATG 59.968 55.000 14.32 7.13 0.00 4.06
1931 1973 0.106569 TCTCATGGATTTGGCGGCAT 60.107 50.000 14.32 0.00 0.00 4.40
2023 2065 3.550233 GCGCTGCTAGTAGTATTACTGCA 60.550 47.826 13.43 16.02 40.33 4.41
2036 2078 2.935201 AGAATTCAGAAAGCGCTGCTAG 59.065 45.455 12.58 1.62 38.25 3.42
2037 2079 2.674852 CAGAATTCAGAAAGCGCTGCTA 59.325 45.455 12.58 0.00 38.25 3.49
2040 2082 3.373130 TCATCAGAATTCAGAAAGCGCTG 59.627 43.478 12.58 0.00 37.24 5.18
2088 2130 1.215647 CCTCCACAGTACACTCGGC 59.784 63.158 0.00 0.00 0.00 5.54
2089 2131 1.215647 GCCTCCACAGTACACTCGG 59.784 63.158 0.00 0.00 0.00 4.63
2128 2170 4.600062 TCTCTAGTCAACATCTGCCTACA 58.400 43.478 0.00 0.00 0.00 2.74
2155 2197 1.202973 CGTCGTCGTCATGATCCAGC 61.203 60.000 0.00 0.00 0.00 4.85
2171 2213 4.403453 GGATATTTGTTGCTGTTGTCGTC 58.597 43.478 0.00 0.00 0.00 4.20
2175 2217 4.072131 ACTCGGATATTTGTTGCTGTTGT 58.928 39.130 0.00 0.00 0.00 3.32
2210 2252 6.141685 CCAGCTCAACAAAACAAAATACGTAC 59.858 38.462 0.00 0.00 0.00 3.67
2211 2253 6.038382 TCCAGCTCAACAAAACAAAATACGTA 59.962 34.615 0.00 0.00 0.00 3.57
2212 2254 5.040635 CCAGCTCAACAAAACAAAATACGT 58.959 37.500 0.00 0.00 0.00 3.57
2213 2255 5.277825 TCCAGCTCAACAAAACAAAATACG 58.722 37.500 0.00 0.00 0.00 3.06
2339 2384 7.983484 GTGGCCTCATTCTTTTTATGATTTGAT 59.017 33.333 3.32 0.00 32.00 2.57
2358 2403 2.095059 CAGCTGTTTTGTATGTGGCCTC 60.095 50.000 5.25 0.00 0.00 4.70
2371 2416 0.671796 GTAAAACCCGGCAGCTGTTT 59.328 50.000 16.64 9.15 33.86 2.83
2377 2422 2.131972 GCAAAAAGTAAAACCCGGCAG 58.868 47.619 0.00 0.00 0.00 4.85
2382 2427 4.509616 ACTGGTTGCAAAAAGTAAAACCC 58.490 39.130 12.38 1.54 39.65 4.11
2425 2470 1.361204 TGAGGACAATCAAGGAGGCA 58.639 50.000 0.00 0.00 0.00 4.75
2447 2492 3.006003 GGAAAGCACGGATTTGGGTTAAA 59.994 43.478 0.00 0.00 0.00 1.52
2457 2502 0.036732 TGAAGCAGGAAAGCACGGAT 59.963 50.000 0.00 0.00 36.85 4.18
2485 2530 4.490743 TCGAAATACACTCTGAATTGCGA 58.509 39.130 0.00 0.00 38.12 5.10
2486 2531 4.840401 TCGAAATACACTCTGAATTGCG 57.160 40.909 0.00 0.00 33.76 4.85
2487 2532 5.005779 ACGATCGAAATACACTCTGAATTGC 59.994 40.000 24.34 0.00 0.00 3.56
2488 2533 6.575083 ACGATCGAAATACACTCTGAATTG 57.425 37.500 24.34 0.00 0.00 2.32
2489 2534 7.704271 TCTACGATCGAAATACACTCTGAATT 58.296 34.615 24.34 0.00 0.00 2.17
2490 2535 7.260558 TCTACGATCGAAATACACTCTGAAT 57.739 36.000 24.34 0.00 0.00 2.57
2510 2555 1.134670 AGTCTGCGCCATTTCCTCTAC 60.135 52.381 4.18 0.00 0.00 2.59
2536 2582 6.767456 AGAATCTCCTCCAGCTATGTAAATG 58.233 40.000 0.00 0.00 0.00 2.32
2537 2583 7.222872 CAAGAATCTCCTCCAGCTATGTAAAT 58.777 38.462 0.00 0.00 0.00 1.40
2542 2588 3.401182 GCAAGAATCTCCTCCAGCTATG 58.599 50.000 0.00 0.00 0.00 2.23
2543 2589 2.036992 CGCAAGAATCTCCTCCAGCTAT 59.963 50.000 0.00 0.00 43.02 2.97
2549 2595 2.545731 GAGAACGCAAGAATCTCCTCC 58.454 52.381 0.00 0.00 43.22 4.30
2556 2602 4.261405 CCGATAGAGAGAGAACGCAAGAAT 60.261 45.833 0.00 0.00 39.24 2.40
2560 2606 1.676529 CCCGATAGAGAGAGAACGCAA 59.323 52.381 0.00 0.00 39.76 4.85
2588 2634 2.235016 CGGTCAAATTCCCCTTGTTCA 58.765 47.619 0.00 0.00 0.00 3.18
2589 2635 1.067846 GCGGTCAAATTCCCCTTGTTC 60.068 52.381 0.00 0.00 0.00 3.18
2604 2650 2.892425 CGAGGATGCAAGGCGGTC 60.892 66.667 0.00 0.00 0.00 4.79
2627 2673 1.224592 CTATGGACCTGGGGTGTGC 59.775 63.158 0.00 0.00 35.25 4.57
2636 2682 3.511477 ACGATGGATAAGCTATGGACCT 58.489 45.455 0.00 0.00 0.00 3.85
2648 2694 4.480115 AGGATCACCAGTAACGATGGATA 58.520 43.478 0.00 0.00 40.51 2.59
2652 2698 3.801114 TGAGGATCACCAGTAACGATG 57.199 47.619 0.00 0.00 42.56 3.84
2663 2709 7.364585 CCTTTAGATAGGATGGATGAGGATCAC 60.365 44.444 0.00 0.00 42.96 3.06
2664 2710 6.671340 CCTTTAGATAGGATGGATGAGGATCA 59.329 42.308 0.00 0.00 43.88 2.92
2665 2711 6.900186 TCCTTTAGATAGGATGGATGAGGATC 59.100 42.308 0.00 0.00 39.40 3.36
2666 2712 6.820205 TCCTTTAGATAGGATGGATGAGGAT 58.180 40.000 0.00 0.00 39.40 3.24
2667 2713 6.233045 TCCTTTAGATAGGATGGATGAGGA 57.767 41.667 0.00 0.00 39.40 3.71
2706 2752 8.080363 AGAACGGGAGAGTAAATTCTAATTCT 57.920 34.615 0.00 0.00 0.00 2.40
2713 2759 9.597170 AGTAATTTAGAACGGGAGAGTAAATTC 57.403 33.333 0.00 0.00 35.82 2.17
2714 2760 9.955102 AAGTAATTTAGAACGGGAGAGTAAATT 57.045 29.630 0.00 0.00 36.91 1.82
2718 2764 9.412460 TGATAAGTAATTTAGAACGGGAGAGTA 57.588 33.333 0.00 0.00 0.00 2.59
2719 2765 8.302515 TGATAAGTAATTTAGAACGGGAGAGT 57.697 34.615 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.