Multiple sequence alignment - TraesCS7B01G152200

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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 TraesCS7B01G152200 chr7B 100.000 2786 0 0 1 2786 202358464 202361249 0.000000e+00 5145
1 TraesCS7B01G152200 chr7D 92.435 1811 78 30 652 2422 230941433 230943224 0.000000e+00 2531
2 TraesCS7B01G152200 chr7D 90.349 487 16 14 1 464 230940825 230941303 6.600000e-171 610
3 TraesCS7B01G152200 chr7D 89.474 361 25 10 2409 2760 230943240 230943596 7.080000e-121 444
4 TraesCS7B01G152200 chr7A 94.301 1158 39 10 652 1792 243694247 243695394 0.000000e+00 1748
5 TraesCS7B01G152200 chr7A 86.502 889 53 37 1875 2730 243695395 243696249 0.000000e+00 915
6 TraesCS7B01G152200 chr7A 89.438 445 30 10 5 434 243667435 243667877 1.890000e-151 545
7 TraesCS7B01G152200 chr5A 75.734 511 116 4 1070 1579 488038542 488039045 1.660000e-62 250
8 TraesCS7B01G152200 chr5D 75.634 513 113 7 1070 1579 386209869 386210372 7.710000e-61 244


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 TraesCS7B01G152200 chr7B 202358464 202361249 2785 False 5145.0 5145 100.000000 1 2786 1 chr7B.!!$F1 2785
1 TraesCS7B01G152200 chr7D 230940825 230943596 2771 False 1195.0 2531 90.752667 1 2760 3 chr7D.!!$F1 2759
2 TraesCS7B01G152200 chr7A 243694247 243696249 2002 False 1331.5 1748 90.401500 652 2730 2 chr7A.!!$F2 2078
3 TraesCS7B01G152200 chr5A 488038542 488039045 503 False 250.0 250 75.734000 1070 1579 1 chr5A.!!$F1 509
4 TraesCS7B01G152200 chr5D 386209869 386210372 503 False 244.0 244 75.634000 1070 1579 1 chr5D.!!$F1 509

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
633 656 0.038744 CTGTGCCCAGAAACCCATCT 59.961 55.0 0.0 0.0 41.5 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2589 2731 0.250467 TGCCTCCTTGCTCAGTGTTC 60.25 55.0 0.0 0.0 0.0 3.18 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
51 52 4.051922 CCATGAGCGTGGAATAGTAGTTC 58.948 47.826 2.49 0.00 42.02 3.01
55 56 5.168569 TGAGCGTGGAATAGTAGTTCTTTG 58.831 41.667 0.00 0.00 0.00 2.77
56 57 5.047590 TGAGCGTGGAATAGTAGTTCTTTGA 60.048 40.000 0.00 0.00 0.00 2.69
57 58 5.978814 AGCGTGGAATAGTAGTTCTTTGAT 58.021 37.500 0.00 0.00 0.00 2.57
58 59 6.043411 AGCGTGGAATAGTAGTTCTTTGATC 58.957 40.000 0.00 0.00 0.00 2.92
59 60 5.234543 GCGTGGAATAGTAGTTCTTTGATCC 59.765 44.000 0.00 0.00 0.00 3.36
60 61 6.338146 CGTGGAATAGTAGTTCTTTGATCCA 58.662 40.000 0.00 0.00 0.00 3.41
61 62 6.986817 CGTGGAATAGTAGTTCTTTGATCCAT 59.013 38.462 0.00 0.00 0.00 3.41
93 112 7.396419 AGATATTTCACACGCATTTAACGTAC 58.604 34.615 0.00 0.00 42.96 3.67
94 113 5.600908 ATTTCACACGCATTTAACGTACT 57.399 34.783 0.00 0.00 42.96 2.73
107 126 2.450609 ACGTACTTGCCGTGAAAGAT 57.549 45.000 0.00 0.00 37.12 2.40
111 130 3.185594 CGTACTTGCCGTGAAAGATGAAA 59.814 43.478 0.00 0.00 0.00 2.69
135 154 0.606130 ATCAGTCCACATGCAACGCA 60.606 50.000 0.00 0.00 44.86 5.24
136 155 0.817229 TCAGTCCACATGCAACGCAA 60.817 50.000 0.00 0.00 43.62 4.85
158 177 2.250031 ACTTGCAATGAAATGAGCCCA 58.750 42.857 0.00 0.00 0.00 5.36
204 223 0.250727 TTCTTGGGAAGTTCGGCCAG 60.251 55.000 2.24 0.00 0.00 4.85
254 276 9.578439 CCATTGATTGGTTATCTTCTTTCTTTC 57.422 33.333 0.00 0.00 40.99 2.62
262 284 9.862149 TGGTTATCTTCTTTCTTTCTTTTAGGT 57.138 29.630 0.00 0.00 0.00 3.08
284 306 1.816863 CTCTGGTGGTGCGGTGTAGT 61.817 60.000 0.00 0.00 0.00 2.73
285 307 1.667830 CTGGTGGTGCGGTGTAGTG 60.668 63.158 0.00 0.00 0.00 2.74
286 308 3.047877 GGTGGTGCGGTGTAGTGC 61.048 66.667 0.00 0.00 0.00 4.40
289 311 3.423154 GGTGCGGTGTAGTGCTGC 61.423 66.667 0.00 0.00 38.62 5.25
307 329 3.379445 GACTGGTCCGGCTCCGAA 61.379 66.667 10.28 0.00 42.83 4.30
308 330 2.920912 ACTGGTCCGGCTCCGAAA 60.921 61.111 10.28 0.00 42.83 3.46
456 479 2.658538 CGAGGCATCGTCTTGTCTG 58.341 57.895 13.51 0.00 44.09 3.51
464 487 2.839486 TCGTCTTGTCTGGCTTCAAT 57.161 45.000 0.00 0.00 0.00 2.57
466 489 1.466167 CGTCTTGTCTGGCTTCAATGG 59.534 52.381 0.00 0.00 0.00 3.16
467 490 1.200948 GTCTTGTCTGGCTTCAATGGC 59.799 52.381 0.00 0.00 0.00 4.40
473 496 3.621225 GGCTTCAATGGCCTTCCC 58.379 61.111 3.32 0.00 45.57 3.97
474 497 2.060383 GGCTTCAATGGCCTTCCCC 61.060 63.158 3.32 0.00 45.57 4.81
475 498 1.000866 GCTTCAATGGCCTTCCCCT 59.999 57.895 3.32 0.00 0.00 4.79
476 499 0.615827 GCTTCAATGGCCTTCCCCTT 60.616 55.000 3.32 0.00 0.00 3.95
477 500 1.942776 CTTCAATGGCCTTCCCCTTT 58.057 50.000 3.32 0.00 0.00 3.11
478 501 1.827344 CTTCAATGGCCTTCCCCTTTC 59.173 52.381 3.32 0.00 0.00 2.62
479 502 0.323360 TCAATGGCCTTCCCCTTTCG 60.323 55.000 3.32 0.00 0.00 3.46
480 503 1.682344 AATGGCCTTCCCCTTTCGC 60.682 57.895 3.32 0.00 0.00 4.70
481 504 3.995506 ATGGCCTTCCCCTTTCGCG 62.996 63.158 3.32 0.00 0.00 5.87
484 507 4.715523 CCTTCCCCTTTCGCGCCA 62.716 66.667 0.00 0.00 0.00 5.69
485 508 2.671619 CTTCCCCTTTCGCGCCAA 60.672 61.111 0.00 0.00 0.00 4.52
486 509 2.034999 TTCCCCTTTCGCGCCAAT 59.965 55.556 0.00 0.00 0.00 3.16
487 510 1.595093 CTTCCCCTTTCGCGCCAATT 61.595 55.000 0.00 0.00 0.00 2.32
488 511 1.591504 TTCCCCTTTCGCGCCAATTC 61.592 55.000 0.00 0.00 0.00 2.17
489 512 2.339556 CCCCTTTCGCGCCAATTCA 61.340 57.895 0.00 0.00 0.00 2.57
490 513 1.137404 CCCTTTCGCGCCAATTCAG 59.863 57.895 0.00 0.00 0.00 3.02
491 514 1.586154 CCCTTTCGCGCCAATTCAGT 61.586 55.000 0.00 0.00 0.00 3.41
516 539 5.959554 CGAGTTATCGGTAGCACAAAATAC 58.040 41.667 0.00 0.00 45.39 1.89
517 540 5.747197 CGAGTTATCGGTAGCACAAAATACT 59.253 40.000 0.00 0.00 45.39 2.12
518 541 6.914215 CGAGTTATCGGTAGCACAAAATACTA 59.086 38.462 0.00 0.00 45.39 1.82
538 561 9.635520 AATACTATACAGACCATGCGTAATAAC 57.364 33.333 0.00 0.00 0.00 1.89
540 563 6.921857 ACTATACAGACCATGCGTAATAACAC 59.078 38.462 0.00 0.00 0.00 3.32
541 564 4.202245 ACAGACCATGCGTAATAACACT 57.798 40.909 0.00 0.00 0.00 3.55
547 570 7.436970 CAGACCATGCGTAATAACACTATTACA 59.563 37.037 12.93 0.00 45.53 2.41
548 571 7.652105 AGACCATGCGTAATAACACTATTACAG 59.348 37.037 12.93 8.24 45.53 2.74
549 572 7.270047 ACCATGCGTAATAACACTATTACAGT 58.730 34.615 12.93 2.86 45.53 3.55
550 573 8.415553 ACCATGCGTAATAACACTATTACAGTA 58.584 33.333 12.93 7.48 45.53 2.74
551 574 8.912658 CCATGCGTAATAACACTATTACAGTAG 58.087 37.037 12.93 1.74 45.53 2.57
552 575 9.459640 CATGCGTAATAACACTATTACAGTAGT 57.540 33.333 12.93 0.00 45.53 2.73
554 577 9.935682 TGCGTAATAACACTATTACAGTAGTAC 57.064 33.333 12.93 0.00 45.53 2.73
555 578 9.935682 GCGTAATAACACTATTACAGTAGTACA 57.064 33.333 2.52 0.00 45.53 2.90
596 619 3.126000 GTCTTCAGAAATTTCGAGCTGGG 59.874 47.826 12.42 3.53 0.00 4.45
607 630 2.281761 AGCTGGGCAAGTTCACCG 60.282 61.111 0.00 0.00 0.00 4.94
608 631 3.365265 GCTGGGCAAGTTCACCGG 61.365 66.667 0.00 0.00 0.00 5.28
609 632 2.672996 CTGGGCAAGTTCACCGGG 60.673 66.667 6.32 0.00 0.00 5.73
610 633 3.491598 CTGGGCAAGTTCACCGGGT 62.492 63.158 6.32 0.00 0.00 5.28
611 634 2.983592 GGGCAAGTTCACCGGGTG 60.984 66.667 21.27 21.27 34.45 4.61
612 635 2.983592 GGCAAGTTCACCGGGTGG 60.984 66.667 26.07 11.30 42.84 4.61
613 636 3.670377 GCAAGTTCACCGGGTGGC 61.670 66.667 26.07 17.14 39.70 5.01
614 637 2.983592 CAAGTTCACCGGGTGGCC 60.984 66.667 26.07 16.47 39.70 5.36
615 638 3.175710 AAGTTCACCGGGTGGCCT 61.176 61.111 26.07 18.33 39.70 5.19
616 639 3.491598 AAGTTCACCGGGTGGCCTG 62.492 63.158 26.07 0.94 39.70 4.85
617 640 4.265056 GTTCACCGGGTGGCCTGT 62.265 66.667 26.07 0.00 39.70 4.00
618 641 4.263572 TTCACCGGGTGGCCTGTG 62.264 66.667 26.07 3.97 39.70 3.66
629 652 2.991540 GCCTGTGCCCAGAAACCC 60.992 66.667 0.00 0.00 41.50 4.11
630 653 2.520458 CCTGTGCCCAGAAACCCA 59.480 61.111 0.00 0.00 41.50 4.51
631 654 1.077265 CCTGTGCCCAGAAACCCAT 59.923 57.895 0.00 0.00 41.50 4.00
632 655 0.967380 CCTGTGCCCAGAAACCCATC 60.967 60.000 0.00 0.00 41.50 3.51
633 656 0.038744 CTGTGCCCAGAAACCCATCT 59.961 55.000 0.00 0.00 41.50 2.90
634 657 0.251297 TGTGCCCAGAAACCCATCTG 60.251 55.000 0.00 0.00 45.19 2.90
635 658 1.304381 TGCCCAGAAACCCATCTGC 60.304 57.895 0.00 0.00 44.43 4.26
636 659 1.304381 GCCCAGAAACCCATCTGCA 60.304 57.895 0.00 0.00 44.43 4.41
637 660 0.685458 GCCCAGAAACCCATCTGCAT 60.685 55.000 0.00 0.00 44.43 3.96
638 661 1.410083 GCCCAGAAACCCATCTGCATA 60.410 52.381 0.00 0.00 44.43 3.14
639 662 2.301346 CCCAGAAACCCATCTGCATAC 58.699 52.381 0.00 0.00 44.43 2.39
676 709 0.109458 GATTCCGTTTGAAACCCCGC 60.109 55.000 2.00 0.00 36.33 6.13
677 710 1.529152 ATTCCGTTTGAAACCCCGCC 61.529 55.000 2.00 0.00 36.33 6.13
678 711 4.032987 CCGTTTGAAACCCCGCCG 62.033 66.667 2.00 0.00 0.00 6.46
744 787 5.694006 CGCAACTCATTTCAACCCATTTTTA 59.306 36.000 0.00 0.00 0.00 1.52
759 806 4.499040 CCATTTTTAATCGCCGACATTCAC 59.501 41.667 0.00 0.00 0.00 3.18
761 808 4.335082 TTTTAATCGCCGACATTCACTG 57.665 40.909 0.00 0.00 0.00 3.66
796 844 8.029642 AGAAAGGTTTCATTAGTCATTACACG 57.970 34.615 5.30 0.00 39.61 4.49
875 924 7.696453 CACCTAAAATCTTCGAAAATTACGCAT 59.304 33.333 0.00 0.00 0.00 4.73
910 961 4.018779 CCCTGTTATAAAACCTCACCCTCA 60.019 45.833 0.00 0.00 34.49 3.86
923 974 3.391382 CCTCACCCGTCCTCACCC 61.391 72.222 0.00 0.00 0.00 4.61
924 975 3.391382 CTCACCCGTCCTCACCCC 61.391 72.222 0.00 0.00 0.00 4.95
925 976 3.907027 CTCACCCGTCCTCACCCCT 62.907 68.421 0.00 0.00 0.00 4.79
979 1030 1.476007 GGCCTCACTCACTCACCAGT 61.476 60.000 0.00 0.00 0.00 4.00
993 1044 0.836400 ACCAGTGACACCCCGAATCT 60.836 55.000 0.84 0.00 0.00 2.40
1188 1244 1.592400 CCTACGACGAGGCCAAGTCA 61.592 60.000 24.16 9.87 37.23 3.41
1767 1823 2.434185 GTGCTCGCGTTGATGGGA 60.434 61.111 5.77 0.00 0.00 4.37
1793 1849 1.726791 CGCGGTAGTATGATGGCATTC 59.273 52.381 0.00 0.00 35.94 2.67
1871 1927 2.305009 CATGGGGAGGAAGCATTTCTC 58.695 52.381 0.00 0.00 33.68 2.87
2192 2291 1.742768 CCCGATCTGGCCTAGTGAC 59.257 63.158 3.32 0.00 35.87 3.67
2210 2309 3.366724 GTGACACACGCTGATTCGATTTA 59.633 43.478 0.00 0.00 0.00 1.40
2271 2370 1.672854 TAGGGTCCCTGTCATTCGCG 61.673 60.000 21.83 0.00 34.61 5.87
2275 2374 0.103208 GTCCCTGTCATTCGCGAGAT 59.897 55.000 9.59 3.28 41.60 2.75
2288 2387 8.276325 GTCATTCGCGAGATTTTGAAATATAGT 58.724 33.333 9.59 0.00 41.60 2.12
2317 2421 6.307155 CAAAATTCACGGATTAGAGTGTCAC 58.693 40.000 0.00 0.00 39.25 3.67
2319 2423 1.471287 TCACGGATTAGAGTGTCACGG 59.529 52.381 0.00 0.00 39.25 4.94
2360 2464 7.989741 TGAATAAAAACACATGATTTGTTGGGT 59.010 29.630 0.00 0.00 37.26 4.51
2422 2555 9.781834 TTTATGGTTTGCAATTTCTACTAATCG 57.218 29.630 0.00 0.00 0.00 3.34
2513 2653 1.372872 CCTTTGCCTTTTTCCCGCG 60.373 57.895 0.00 0.00 0.00 6.46
2531 2673 2.223409 CGCGAAAAATAGGCCTTTACCC 60.223 50.000 12.58 0.00 0.00 3.69
2540 2682 7.568128 AAATAGGCCTTTACCCTTCATTTTT 57.432 32.000 12.58 0.00 33.88 1.94
2576 2718 9.605955 CATCACTTTCATTACACGTTTGATTTA 57.394 29.630 0.00 0.00 0.00 1.40
2609 2751 0.250640 AACACTGAGCAAGGAGGCAG 60.251 55.000 0.00 0.00 35.83 4.85
2643 2785 0.038166 GGCAGGTCATCAACAGGGAA 59.962 55.000 0.00 0.00 0.00 3.97
2645 2787 2.092429 GGCAGGTCATCAACAGGGAATA 60.092 50.000 0.00 0.00 0.00 1.75
2649 2793 2.945668 GGTCATCAACAGGGAATACTGC 59.054 50.000 0.00 0.00 42.21 4.40
2730 2879 3.554337 CGAGACCCCGGGTAGATATTTTG 60.554 52.174 21.85 1.55 35.25 2.44
2747 2896 2.038814 TTGTTGACGCTCTCCTGCCA 62.039 55.000 0.00 0.00 0.00 4.92
2760 2909 1.225376 CCTGCCAACGAGTAAACGCA 61.225 55.000 0.00 0.00 36.70 5.24
2761 2910 0.110823 CTGCCAACGAGTAAACGCAC 60.111 55.000 0.00 0.00 36.70 5.34
2762 2911 0.810426 TGCCAACGAGTAAACGCACA 60.810 50.000 0.00 0.00 36.70 4.57
2763 2912 0.305313 GCCAACGAGTAAACGCACAA 59.695 50.000 0.00 0.00 36.70 3.33
2764 2913 1.918543 GCCAACGAGTAAACGCACAAC 60.919 52.381 0.00 0.00 36.70 3.32
2765 2914 1.595794 CCAACGAGTAAACGCACAACT 59.404 47.619 0.00 0.00 36.70 3.16
2766 2915 2.031191 CCAACGAGTAAACGCACAACTT 59.969 45.455 0.00 0.00 36.70 2.66
2767 2916 3.026349 CAACGAGTAAACGCACAACTTG 58.974 45.455 0.00 0.00 36.70 3.16
2768 2917 1.595794 ACGAGTAAACGCACAACTTGG 59.404 47.619 0.00 0.00 36.70 3.61
2769 2918 1.595794 CGAGTAAACGCACAACTTGGT 59.404 47.619 0.00 0.00 0.00 3.67
2770 2919 2.031191 CGAGTAAACGCACAACTTGGTT 59.969 45.455 0.00 0.00 0.00 3.67
2771 2920 3.486209 CGAGTAAACGCACAACTTGGTTT 60.486 43.478 0.00 0.00 34.71 3.27
2772 2921 4.417506 GAGTAAACGCACAACTTGGTTTT 58.582 39.130 0.00 0.00 33.35 2.43
2773 2922 4.811908 AGTAAACGCACAACTTGGTTTTT 58.188 34.783 0.00 0.00 33.35 1.94
2774 2923 4.860352 AGTAAACGCACAACTTGGTTTTTC 59.140 37.500 0.00 0.00 33.35 2.29
2775 2924 3.586100 AACGCACAACTTGGTTTTTCT 57.414 38.095 0.00 0.00 0.00 2.52
2776 2925 3.586100 ACGCACAACTTGGTTTTTCTT 57.414 38.095 0.00 0.00 0.00 2.52
2777 2926 3.920446 ACGCACAACTTGGTTTTTCTTT 58.080 36.364 0.00 0.00 0.00 2.52
2778 2927 4.311606 ACGCACAACTTGGTTTTTCTTTT 58.688 34.783 0.00 0.00 0.00 2.27
2779 2928 4.752604 ACGCACAACTTGGTTTTTCTTTTT 59.247 33.333 0.00 0.00 0.00 1.94
2780 2929 5.927115 ACGCACAACTTGGTTTTTCTTTTTA 59.073 32.000 0.00 0.00 0.00 1.52
2781 2930 6.128769 ACGCACAACTTGGTTTTTCTTTTTAC 60.129 34.615 0.00 0.00 0.00 2.01
2782 2931 6.539324 GCACAACTTGGTTTTTCTTTTTACC 58.461 36.000 0.00 0.00 0.00 2.85
2783 2932 6.671164 GCACAACTTGGTTTTTCTTTTTACCG 60.671 38.462 0.00 0.00 33.29 4.02
2784 2933 6.586844 CACAACTTGGTTTTTCTTTTTACCGA 59.413 34.615 0.00 0.00 33.29 4.69
2785 2934 6.587226 ACAACTTGGTTTTTCTTTTTACCGAC 59.413 34.615 0.00 0.00 33.29 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 3.003689 GTGTGAAATATCTTCCGGCATGG 59.996 47.826 0.00 0.00 40.09 3.66
59 60 3.303329 CGTGTGAAATATCTTCCGGCATG 60.303 47.826 0.00 0.00 0.00 4.06
60 61 2.872245 CGTGTGAAATATCTTCCGGCAT 59.128 45.455 0.00 0.00 0.00 4.40
61 62 2.276201 CGTGTGAAATATCTTCCGGCA 58.724 47.619 0.00 0.00 0.00 5.69
93 112 5.221880 TCATTTTTCATCTTTCACGGCAAG 58.778 37.500 0.00 0.00 0.00 4.01
94 113 5.193663 TCATTTTTCATCTTTCACGGCAA 57.806 34.783 0.00 0.00 0.00 4.52
107 126 4.523558 TGCATGTGGACTGATCATTTTTCA 59.476 37.500 0.00 0.00 0.00 2.69
111 130 3.119743 CGTTGCATGTGGACTGATCATTT 60.120 43.478 0.00 0.00 0.00 2.32
135 154 4.067192 GGGCTCATTTCATTGCAAGTTTT 58.933 39.130 4.94 0.00 0.00 2.43
136 155 3.071312 TGGGCTCATTTCATTGCAAGTTT 59.929 39.130 4.94 0.00 0.00 2.66
254 276 1.073923 ACCACCAGAGCCACCTAAAAG 59.926 52.381 0.00 0.00 0.00 2.27
255 277 1.145571 ACCACCAGAGCCACCTAAAA 58.854 50.000 0.00 0.00 0.00 1.52
256 278 0.400213 CACCACCAGAGCCACCTAAA 59.600 55.000 0.00 0.00 0.00 1.85
257 279 2.066340 CACCACCAGAGCCACCTAA 58.934 57.895 0.00 0.00 0.00 2.69
286 308 4.803426 GAGCCGGACCAGTCGCAG 62.803 72.222 5.05 0.00 0.00 5.18
307 329 0.819259 AACCATGCACGTGACAGCTT 60.819 50.000 22.23 6.72 0.00 3.74
308 330 1.227943 AACCATGCACGTGACAGCT 60.228 52.632 22.23 0.00 0.00 4.24
352 374 2.433318 GCAGAAGAGGCGCGAGTT 60.433 61.111 12.10 0.00 0.00 3.01
464 487 4.715523 CGCGAAAGGGGAAGGCCA 62.716 66.667 5.01 0.00 40.85 5.36
467 490 4.715523 TGGCGCGAAAGGGGAAGG 62.716 66.667 12.10 0.00 45.27 3.46
468 491 1.595093 AATTGGCGCGAAAGGGGAAG 61.595 55.000 12.10 0.00 45.27 3.46
469 492 1.591504 GAATTGGCGCGAAAGGGGAA 61.592 55.000 12.10 0.00 45.27 3.97
471 494 2.270297 CTGAATTGGCGCGAAAGGGG 62.270 60.000 12.10 0.00 45.27 4.79
473 496 0.454957 CACTGAATTGGCGCGAAAGG 60.455 55.000 12.10 2.49 0.00 3.11
474 497 1.067199 GCACTGAATTGGCGCGAAAG 61.067 55.000 12.10 4.79 0.00 2.62
475 498 1.081509 GCACTGAATTGGCGCGAAA 60.082 52.632 12.10 3.06 0.00 3.46
476 499 2.560861 GCACTGAATTGGCGCGAA 59.439 55.556 12.10 7.47 0.00 4.70
481 504 2.285834 CGATAACTCGCACTGAATTGGC 60.286 50.000 0.00 0.00 38.20 4.52
482 505 2.285220 CCGATAACTCGCACTGAATTGG 59.715 50.000 0.00 0.00 43.66 3.16
483 506 2.930040 ACCGATAACTCGCACTGAATTG 59.070 45.455 0.00 0.00 43.66 2.32
484 507 3.247006 ACCGATAACTCGCACTGAATT 57.753 42.857 0.00 0.00 43.66 2.17
485 508 2.961526 ACCGATAACTCGCACTGAAT 57.038 45.000 0.00 0.00 43.66 2.57
486 509 2.479049 GCTACCGATAACTCGCACTGAA 60.479 50.000 0.00 0.00 43.66 3.02
487 510 1.065102 GCTACCGATAACTCGCACTGA 59.935 52.381 0.00 0.00 43.66 3.41
488 511 1.202256 TGCTACCGATAACTCGCACTG 60.202 52.381 0.00 0.00 43.66 3.66
489 512 1.100510 TGCTACCGATAACTCGCACT 58.899 50.000 0.00 0.00 43.66 4.40
490 513 1.197910 GTGCTACCGATAACTCGCAC 58.802 55.000 0.00 0.00 43.66 5.34
491 514 0.812549 TGTGCTACCGATAACTCGCA 59.187 50.000 0.00 0.00 43.66 5.10
505 528 6.260936 GCATGGTCTGTATAGTATTTTGTGCT 59.739 38.462 0.00 0.00 0.00 4.40
513 536 8.799367 TGTTATTACGCATGGTCTGTATAGTAT 58.201 33.333 0.00 0.00 0.00 2.12
514 537 8.077991 GTGTTATTACGCATGGTCTGTATAGTA 58.922 37.037 0.00 0.00 34.87 1.82
515 538 6.921857 GTGTTATTACGCATGGTCTGTATAGT 59.078 38.462 0.00 0.00 34.87 2.12
516 539 7.145985 AGTGTTATTACGCATGGTCTGTATAG 58.854 38.462 0.00 0.00 37.24 1.31
517 540 7.046292 AGTGTTATTACGCATGGTCTGTATA 57.954 36.000 0.00 0.00 37.24 1.47
518 541 5.914033 AGTGTTATTACGCATGGTCTGTAT 58.086 37.500 0.00 0.00 37.24 2.29
551 574 9.092876 AGACGTAAATACTGAGTACTAGTGTAC 57.907 37.037 5.39 0.00 46.89 2.90
552 575 9.658799 AAGACGTAAATACTGAGTACTAGTGTA 57.341 33.333 5.39 0.00 0.00 2.90
553 576 8.558973 AAGACGTAAATACTGAGTACTAGTGT 57.441 34.615 5.39 0.00 0.00 3.55
554 577 8.663025 TGAAGACGTAAATACTGAGTACTAGTG 58.337 37.037 5.39 0.00 0.00 2.74
555 578 8.783833 TGAAGACGTAAATACTGAGTACTAGT 57.216 34.615 0.00 0.00 0.00 2.57
557 580 9.440773 TTCTGAAGACGTAAATACTGAGTACTA 57.559 33.333 0.00 0.00 0.00 1.82
558 581 7.918536 TCTGAAGACGTAAATACTGAGTACT 57.081 36.000 0.00 0.00 0.00 2.73
559 582 8.961294 TTTCTGAAGACGTAAATACTGAGTAC 57.039 34.615 0.00 0.00 0.00 2.73
561 584 9.490379 AAATTTCTGAAGACGTAAATACTGAGT 57.510 29.630 0.00 0.00 0.00 3.41
562 585 9.959775 GAAATTTCTGAAGACGTAAATACTGAG 57.040 33.333 11.05 0.00 0.00 3.35
563 586 8.644619 CGAAATTTCTGAAGACGTAAATACTGA 58.355 33.333 15.92 0.00 0.00 3.41
564 587 8.644619 TCGAAATTTCTGAAGACGTAAATACTG 58.355 33.333 15.92 0.00 0.00 2.74
565 588 8.752766 TCGAAATTTCTGAAGACGTAAATACT 57.247 30.769 15.92 0.00 0.00 2.12
566 589 7.631368 GCTCGAAATTTCTGAAGACGTAAATAC 59.369 37.037 15.92 0.00 0.00 1.89
567 590 7.544566 AGCTCGAAATTTCTGAAGACGTAAATA 59.455 33.333 15.92 0.00 0.00 1.40
568 591 6.369065 AGCTCGAAATTTCTGAAGACGTAAAT 59.631 34.615 15.92 0.00 0.00 1.40
569 592 5.694910 AGCTCGAAATTTCTGAAGACGTAAA 59.305 36.000 15.92 0.00 0.00 2.01
570 593 5.118664 CAGCTCGAAATTTCTGAAGACGTAA 59.881 40.000 15.92 0.00 0.00 3.18
596 619 3.670377 GCCACCCGGTGAACTTGC 61.670 66.667 19.81 9.47 35.23 4.01
612 635 2.991540 GGGTTTCTGGGCACAGGC 60.992 66.667 17.80 6.84 44.99 4.85
613 636 0.967380 GATGGGTTTCTGGGCACAGG 60.967 60.000 17.80 0.00 44.99 4.00
614 637 0.038744 AGATGGGTTTCTGGGCACAG 59.961 55.000 10.61 10.61 46.30 3.66
615 638 0.251297 CAGATGGGTTTCTGGGCACA 60.251 55.000 0.00 0.00 39.58 4.57
616 639 1.598701 GCAGATGGGTTTCTGGGCAC 61.599 60.000 3.85 0.00 42.78 5.01
617 640 1.304381 GCAGATGGGTTTCTGGGCA 60.304 57.895 3.85 0.00 42.78 5.36
618 641 0.685458 ATGCAGATGGGTTTCTGGGC 60.685 55.000 0.00 0.00 42.78 5.36
619 642 2.301346 GTATGCAGATGGGTTTCTGGG 58.699 52.381 0.00 0.00 42.78 4.45
620 643 2.684881 GTGTATGCAGATGGGTTTCTGG 59.315 50.000 0.00 0.00 42.78 3.86
621 644 3.614092 AGTGTATGCAGATGGGTTTCTG 58.386 45.455 0.00 0.00 44.87 3.02
622 645 3.264193 TGAGTGTATGCAGATGGGTTTCT 59.736 43.478 0.00 0.00 0.00 2.52
623 646 3.375299 GTGAGTGTATGCAGATGGGTTTC 59.625 47.826 0.00 0.00 0.00 2.78
624 647 3.347216 GTGAGTGTATGCAGATGGGTTT 58.653 45.455 0.00 0.00 0.00 3.27
625 648 2.356125 GGTGAGTGTATGCAGATGGGTT 60.356 50.000 0.00 0.00 0.00 4.11
626 649 1.210478 GGTGAGTGTATGCAGATGGGT 59.790 52.381 0.00 0.00 0.00 4.51
627 650 1.210234 TGGTGAGTGTATGCAGATGGG 59.790 52.381 0.00 0.00 0.00 4.00
628 651 2.696989 TGGTGAGTGTATGCAGATGG 57.303 50.000 0.00 0.00 0.00 3.51
629 652 4.069300 AGATGGTGAGTGTATGCAGATG 57.931 45.455 0.00 0.00 0.00 2.90
630 653 4.767578 AAGATGGTGAGTGTATGCAGAT 57.232 40.909 0.00 0.00 0.00 2.90
631 654 4.020307 TCAAAGATGGTGAGTGTATGCAGA 60.020 41.667 0.00 0.00 0.00 4.26
632 655 4.256110 TCAAAGATGGTGAGTGTATGCAG 58.744 43.478 0.00 0.00 0.00 4.41
633 656 4.284829 TCAAAGATGGTGAGTGTATGCA 57.715 40.909 0.00 0.00 0.00 3.96
634 657 4.036027 CCATCAAAGATGGTGAGTGTATGC 59.964 45.833 16.10 0.00 40.28 3.14
635 658 5.430886 TCCATCAAAGATGGTGAGTGTATG 58.569 41.667 21.71 0.00 40.28 2.39
636 659 5.698741 TCCATCAAAGATGGTGAGTGTAT 57.301 39.130 21.71 0.00 40.28 2.29
637 660 5.698741 ATCCATCAAAGATGGTGAGTGTA 57.301 39.130 21.71 5.16 40.28 2.90
638 661 4.581309 ATCCATCAAAGATGGTGAGTGT 57.419 40.909 21.71 4.30 40.28 3.55
639 662 4.337555 GGAATCCATCAAAGATGGTGAGTG 59.662 45.833 21.71 0.31 40.28 3.51
678 711 4.408821 TGCTGGCCACGGATGTCC 62.409 66.667 0.00 0.00 0.00 4.02
697 730 1.009675 CTGTGAGTTTGGTGTGCGC 60.010 57.895 0.00 0.00 0.00 6.09
721 759 7.489574 TTAAAAATGGGTTGAAATGAGTTGC 57.510 32.000 0.00 0.00 0.00 4.17
744 787 0.673333 TGCAGTGAATGTCGGCGATT 60.673 50.000 14.79 3.60 0.00 3.34
779 826 8.604640 TTTGGTTACGTGTAATGACTAATGAA 57.395 30.769 0.00 0.00 0.00 2.57
796 844 4.216411 TGCTAGGTCTGGATTTGGTTAC 57.784 45.455 0.00 0.00 0.00 2.50
875 924 1.828602 TAACAGGGGAGGTGGGGCTA 61.829 60.000 0.00 0.00 0.00 3.93
910 961 4.716977 GGAGGGGTGAGGACGGGT 62.717 72.222 0.00 0.00 0.00 5.28
923 974 1.274728 CTTGGAGTGTCAGTGAGGAGG 59.725 57.143 0.00 0.00 0.00 4.30
924 975 1.337635 GCTTGGAGTGTCAGTGAGGAG 60.338 57.143 0.00 0.00 0.00 3.69
925 976 0.681733 GCTTGGAGTGTCAGTGAGGA 59.318 55.000 0.00 0.00 0.00 3.71
1749 1805 2.741985 CCCATCAACGCGAGCACA 60.742 61.111 15.93 0.00 0.00 4.57
1793 1849 3.385749 ATTCGTGCTACCGCCAGGG 62.386 63.158 0.00 0.00 43.47 4.45
1972 2029 6.842163 ACCTAAAAACAACAGCTCGATAATG 58.158 36.000 0.00 0.00 0.00 1.90
2111 2210 2.076100 CAAACACTTGCGCCTCTGATA 58.924 47.619 4.18 0.00 0.00 2.15
2120 2219 0.660488 TGCACTACCAAACACTTGCG 59.340 50.000 0.00 0.00 32.49 4.85
2125 2224 6.164176 AGATACTACTTGCACTACCAAACAC 58.836 40.000 0.00 0.00 0.00 3.32
2192 2291 7.304849 GCTTTAAATAAATCGAATCAGCGTGTG 60.305 37.037 0.00 0.00 0.00 3.82
2210 2309 2.049767 CGGTGCCCGGGCTTTAAAT 61.050 57.895 43.34 0.00 44.15 1.40
2231 2330 1.221466 TTTGACGCTGGTGCTTCTCG 61.221 55.000 0.00 0.00 38.17 4.04
2249 2348 1.831736 CGAATGACAGGGACCCTAGTT 59.168 52.381 14.38 5.65 29.64 2.24
2288 2387 5.640357 ACTCTAATCCGTGAATTTTGCGTTA 59.360 36.000 0.00 0.00 0.00 3.18
2291 2390 4.142902 ACACTCTAATCCGTGAATTTTGCG 60.143 41.667 0.00 0.00 35.23 4.85
2335 2439 8.376889 ACCCAACAAATCATGTGTTTTTATTC 57.623 30.769 0.00 0.00 42.99 1.75
2360 2464 5.716228 ACTTCATACTGCATTTCCCATCAAA 59.284 36.000 0.00 0.00 0.00 2.69
2471 2606 8.596293 AGGCCTTTTTGATTCAGAATTATTGAA 58.404 29.630 0.00 7.17 38.76 2.69
2473 2608 8.782339 AAGGCCTTTTTGATTCAGAATTATTG 57.218 30.769 13.78 0.00 0.00 1.90
2474 2609 9.223099 CAAAGGCCTTTTTGATTCAGAATTATT 57.777 29.630 28.42 0.00 39.79 1.40
2475 2610 7.335171 GCAAAGGCCTTTTTGATTCAGAATTAT 59.665 33.333 28.42 0.00 39.79 1.28
2479 2614 4.379652 GCAAAGGCCTTTTTGATTCAGAA 58.620 39.130 28.42 0.00 39.79 3.02
2480 2615 3.993920 GCAAAGGCCTTTTTGATTCAGA 58.006 40.909 28.42 0.00 39.79 3.27
2513 2653 6.791867 ATGAAGGGTAAAGGCCTATTTTTC 57.208 37.500 5.16 6.69 0.00 2.29
2540 2682 5.549742 AATGAAAGTGATGCCCTTCAAAA 57.450 34.783 0.00 0.00 0.00 2.44
2541 2683 5.538053 TGTAATGAAAGTGATGCCCTTCAAA 59.462 36.000 0.00 0.00 0.00 2.69
2584 2726 2.740981 CTCCTTGCTCAGTGTTCATGAC 59.259 50.000 0.00 0.00 0.00 3.06
2589 2731 0.250467 TGCCTCCTTGCTCAGTGTTC 60.250 55.000 0.00 0.00 0.00 3.18
2591 2733 1.374190 CTGCCTCCTTGCTCAGTGT 59.626 57.895 0.00 0.00 0.00 3.55
2643 2785 2.502947 TGAGCACATGAAGAGGCAGTAT 59.497 45.455 0.00 0.00 0.00 2.12
2645 2787 0.689055 TGAGCACATGAAGAGGCAGT 59.311 50.000 0.00 0.00 0.00 4.40
2730 2879 1.301716 TTGGCAGGAGAGCGTCAAC 60.302 57.895 0.00 0.00 34.64 3.18
2747 2896 2.031191 CCAAGTTGTGCGTTTACTCGTT 59.969 45.455 1.45 0.00 0.00 3.85
2760 2909 6.587226 GTCGGTAAAAAGAAAAACCAAGTTGT 59.413 34.615 1.45 0.00 32.04 3.32
2761 2910 6.985013 GTCGGTAAAAAGAAAAACCAAGTTG 58.015 36.000 0.00 0.00 32.04 3.16


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

AutoCloner maintained by Alex Coulton.