Multiple sequence alignment - TraesCS5D01G298600

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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 TraesCS5D01G298600 chr5D 100.000 2774 0 0 1 2774 396368998 396371771 0.000000e+00 5123.0
1 TraesCS5D01G298600 chr5B 92.147 2534 86 44 1 2471 476168997 476171480 0.000000e+00 3472.0
2 TraesCS5D01G298600 chr5B 90.000 140 14 0 2477 2616 476173292 476173431 6.100000e-42 182.0
3 TraesCS5D01G298600 chr5B 82.883 111 18 1 2650 2759 649003603 649003493 6.320000e-17 99.0
4 TraesCS5D01G298600 chr5B 97.143 35 1 0 1480 1514 535700294 535700328 2.980000e-05 60.2
5 TraesCS5D01G298600 chr5A 88.889 2259 113 50 470 2643 502071168 502073373 0.000000e+00 2654.0
6 TraesCS5D01G298600 chr5A 90.805 348 8 13 1 336 502070675 502071010 7.050000e-121 444.0
7 TraesCS5D01G298600 chr5A 92.683 41 3 0 1477 1517 680843356 680843316 2.980000e-05 60.2
8 TraesCS5D01G298600 chr6D 93.478 46 2 1 1484 1528 27819924 27819879 1.780000e-07 67.6
9 TraesCS5D01G298600 chr6B 95.349 43 1 1 1484 1525 51580035 51579993 1.780000e-07 67.6
10 TraesCS5D01G298600 chr6A 95.122 41 2 0 1484 1524 30190853 30190813 6.410000e-07 65.8
11 TraesCS5D01G298600 chr2B 91.111 45 4 0 1045 1089 82361338 82361382 8.300000e-06 62.1
12 TraesCS5D01G298600 chr2B 91.111 45 4 0 1045 1089 82713832 82713876 8.300000e-06 62.1
13 TraesCS5D01G298600 chr2B 89.583 48 4 1 1042 1089 82851730 82851776 2.980000e-05 60.2
14 TraesCS5D01G298600 chr2A 91.111 45 4 0 1045 1089 54111938 54111982 8.300000e-06 62.1
15 TraesCS5D01G298600 chr4B 92.683 41 3 0 1477 1517 643311116 643311076 2.980000e-05 60.2
16 TraesCS5D01G298600 chr4D 94.595 37 2 0 1481 1517 500023785 500023749 1.070000e-04 58.4


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 TraesCS5D01G298600 chr5D 396368998 396371771 2773 False 5123 5123 100.0000 1 2774 1 chr5D.!!$F1 2773
1 TraesCS5D01G298600 chr5B 476168997 476173431 4434 False 1827 3472 91.0735 1 2616 2 chr5B.!!$F2 2615
2 TraesCS5D01G298600 chr5A 502070675 502073373 2698 False 1549 2654 89.8470 1 2643 2 chr5A.!!$F1 2642


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
336 357 0.530288 AAAATACACGTGCATGGCCC 59.47 50.0 17.22 0.0 0.0 5.8 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1803 1990 0.034767 CTCTCTTTGGGAGGCATGCA 60.035 55.0 21.36 0.0 42.1 3.96 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
90 92 6.863275 AGTTTAAGGGTTGCTAATGTAATGC 58.137 36.000 0.00 0.00 0.00 3.56
136 138 5.241662 AGCTACAAGTAGAAGCAAAGGAAG 58.758 41.667 11.25 0.00 38.75 3.46
199 215 3.307410 CCCAGTTCACATGTGGTAGCTTA 60.307 47.826 25.16 1.24 0.00 3.09
200 216 3.935203 CCAGTTCACATGTGGTAGCTTAG 59.065 47.826 25.16 5.17 0.00 2.18
201 217 3.372206 CAGTTCACATGTGGTAGCTTAGC 59.628 47.826 25.16 6.59 0.00 3.09
202 218 3.007940 AGTTCACATGTGGTAGCTTAGCA 59.992 43.478 25.16 0.00 0.00 3.49
203 219 3.251479 TCACATGTGGTAGCTTAGCAG 57.749 47.619 25.16 0.00 36.78 4.24
204 220 2.567169 TCACATGTGGTAGCTTAGCAGT 59.433 45.455 25.16 0.00 36.78 4.40
205 221 3.767131 TCACATGTGGTAGCTTAGCAGTA 59.233 43.478 25.16 0.00 36.78 2.74
206 222 4.405680 TCACATGTGGTAGCTTAGCAGTAT 59.594 41.667 25.16 0.00 36.78 2.12
220 241 7.040340 AGCTTAGCAGTATCGTATCACATAGTT 60.040 37.037 7.07 0.00 0.00 2.24
332 353 3.188254 TCCAGTCAAAATACACGTGCATG 59.812 43.478 17.22 3.82 0.00 4.06
333 354 3.491356 CAGTCAAAATACACGTGCATGG 58.509 45.455 17.22 2.27 0.00 3.66
334 355 2.095263 AGTCAAAATACACGTGCATGGC 60.095 45.455 17.22 9.16 0.00 4.40
335 356 1.201181 TCAAAATACACGTGCATGGCC 59.799 47.619 17.22 0.00 0.00 5.36
336 357 0.530288 AAAATACACGTGCATGGCCC 59.470 50.000 17.22 0.00 0.00 5.80
337 358 0.610509 AAATACACGTGCATGGCCCA 60.611 50.000 17.22 0.00 0.00 5.36
338 359 1.312371 AATACACGTGCATGGCCCAC 61.312 55.000 17.22 0.00 0.00 4.61
381 448 2.001812 GCTCGAGCAAACATCTCTCA 57.998 50.000 31.91 0.00 41.59 3.27
382 449 2.341257 GCTCGAGCAAACATCTCTCAA 58.659 47.619 31.91 0.00 41.59 3.02
383 450 2.348059 GCTCGAGCAAACATCTCTCAAG 59.652 50.000 31.91 0.00 41.59 3.02
400 467 5.618236 TCTCAAGCAAGCAAGAGCATATAT 58.382 37.500 8.36 0.00 45.49 0.86
405 472 5.243981 AGCAAGCAAGAGCATATATGGTAG 58.756 41.667 17.08 11.23 45.49 3.18
406 473 4.142730 GCAAGCAAGAGCATATATGGTAGC 60.143 45.833 17.08 19.00 45.49 3.58
407 474 4.897509 AGCAAGAGCATATATGGTAGCA 57.102 40.909 25.40 0.00 45.49 3.49
420 487 3.297391 GTAGCATCAGTAGCTGCCC 57.703 57.895 0.00 0.00 43.33 5.36
453 532 6.036083 GCTCTGTGTGTATAACGATCACAATT 59.964 38.462 0.00 0.00 42.39 2.32
454 533 7.289587 TCTGTGTGTATAACGATCACAATTG 57.710 36.000 3.24 3.24 42.39 2.32
461 540 5.984233 ATAACGATCACAATTGCATACGT 57.016 34.783 5.05 10.05 0.00 3.57
462 541 7.648510 TGTATAACGATCACAATTGCATACGTA 59.351 33.333 16.90 0.00 32.66 3.57
463 542 4.772046 ACGATCACAATTGCATACGTAC 57.228 40.909 15.68 0.00 0.00 3.67
464 543 3.242016 ACGATCACAATTGCATACGTACG 59.758 43.478 15.01 15.01 0.00 3.67
468 547 2.077627 ACAATTGCATACGTACGCCAA 58.922 42.857 16.72 13.61 0.00 4.52
483 562 1.326548 CGCCAAGCCATTACGTACTTC 59.673 52.381 0.00 0.00 0.00 3.01
495 574 9.525409 GCCATTACGTACTTCGGATTTATATAT 57.475 33.333 0.00 0.00 44.69 0.86
527 646 5.109903 AGCAAGCAAGACTAGTTTATACGG 58.890 41.667 0.00 0.00 0.00 4.02
538 657 8.566260 AGACTAGTTTATACGGATACATGACAC 58.434 37.037 0.00 0.00 0.00 3.67
543 662 2.868020 CGGATACATGACACCGTCG 58.132 57.895 16.28 0.00 40.42 5.12
604 742 8.248253 AGTGTCAAATACATATGTACGTGAGAA 58.752 33.333 22.04 14.65 41.10 2.87
719 858 2.243736 ACTGGAAGAGTTGGGGAACAAA 59.756 45.455 0.00 0.00 38.03 2.83
800 939 4.899239 GACGGCGGCAGGATGGAG 62.899 72.222 8.47 0.00 35.86 3.86
888 1027 0.970937 TCCACTCCACTCATCGACCC 60.971 60.000 0.00 0.00 0.00 4.46
954 1103 1.371022 CAGGACTGATCGCCGATCG 60.371 63.158 21.00 17.28 41.51 3.69
962 1111 1.215655 GATCGCCGATCGGTTTCTGG 61.216 60.000 33.33 16.36 39.05 3.86
1326 1505 3.512680 CGAATCGGCTTACTTCTTCAGT 58.487 45.455 0.00 0.00 39.87 3.41
1328 1507 3.528597 ATCGGCTTACTTCTTCAGTCC 57.471 47.619 0.00 0.00 36.88 3.85
1335 1514 0.605589 ACTTCTTCAGTCCGAGGCAG 59.394 55.000 0.00 0.00 0.00 4.85
1641 1820 2.024871 GAGACGACCGGCGATCAG 59.975 66.667 22.10 0.00 44.57 2.90
1713 1892 2.310233 CCACACTTGTCACGCTCCG 61.310 63.158 0.00 0.00 0.00 4.63
1738 1917 1.004080 GAAGAGGTCAGCAGCAGCA 60.004 57.895 3.17 0.00 45.49 4.41
1739 1918 1.297456 GAAGAGGTCAGCAGCAGCAC 61.297 60.000 3.17 0.00 45.49 4.40
1740 1919 2.031616 GAGGTCAGCAGCAGCACA 59.968 61.111 3.17 0.00 45.49 4.57
1777 1959 0.311165 GCATCCGAGACGCTAAGCTA 59.689 55.000 0.00 0.00 0.00 3.32
1778 1960 1.664588 GCATCCGAGACGCTAAGCTAG 60.665 57.143 0.00 0.00 0.00 3.42
1798 1985 3.778097 TTCCAGCTGCTGCAGTGCA 62.778 57.895 28.50 18.58 42.74 4.57
1801 1988 1.154016 CAGCTGCTGCAGTGCAATC 60.154 57.895 28.50 14.06 42.83 2.67
1802 1989 1.602605 AGCTGCTGCAGTGCAATCA 60.603 52.632 28.50 17.75 42.83 2.57
1803 1990 0.965866 AGCTGCTGCAGTGCAATCAT 60.966 50.000 28.50 3.53 42.83 2.45
1804 1991 0.802222 GCTGCTGCAGTGCAATCATG 60.802 55.000 28.50 8.13 42.83 3.07
2086 2290 1.272781 CTCGATCAGCTGTCGTTTCC 58.727 55.000 26.56 7.32 39.91 3.13
2087 2291 0.456142 TCGATCAGCTGTCGTTTCCG 60.456 55.000 26.56 15.77 39.91 4.30
2088 2292 1.710339 GATCAGCTGTCGTTTCCGC 59.290 57.895 14.67 0.00 0.00 5.54
2089 2293 2.014093 GATCAGCTGTCGTTTCCGCG 62.014 60.000 14.67 0.00 0.00 6.46
2122 2326 0.542333 GGTCCCTTTGGCTCTACTCC 59.458 60.000 0.00 0.00 0.00 3.85
2374 2584 3.966543 CCTTGGACGCAGGGGGTT 61.967 66.667 0.00 0.00 0.00 4.11
2434 2644 3.400007 GCGGAAGGCGATCTGTTC 58.600 61.111 0.00 0.00 0.00 3.18
2466 2676 1.241990 ACGGCTCTGAACTCTGCGTA 61.242 55.000 0.00 0.00 0.00 4.42
2473 2683 3.353557 TCTGAACTCTGCGTATAGGTGT 58.646 45.455 0.00 0.00 0.00 4.16
2508 4524 0.661552 GCACTAGCGACGATGGAGTA 59.338 55.000 2.68 0.00 0.00 2.59
2562 4578 4.082571 CCTTTTTCTGCCAGTACAATGAGG 60.083 45.833 0.00 0.00 0.00 3.86
2570 4586 3.127548 GCCAGTACAATGAGGACACAATG 59.872 47.826 0.00 0.00 0.00 2.82
2631 4647 3.328237 AAAAACTACTGACGCGTTTGG 57.672 42.857 15.53 9.40 31.82 3.28
2636 4652 1.500512 TACTGACGCGTTTGGTTGCC 61.501 55.000 15.53 0.00 0.00 4.52
2643 4659 0.173255 GCGTTTGGTTGCCTGCATAT 59.827 50.000 0.00 0.00 0.00 1.78
2644 4660 1.403679 GCGTTTGGTTGCCTGCATATA 59.596 47.619 0.00 0.00 0.00 0.86
2645 4661 2.541588 GCGTTTGGTTGCCTGCATATAG 60.542 50.000 0.00 0.00 0.00 1.31
2646 4662 2.541588 CGTTTGGTTGCCTGCATATAGC 60.542 50.000 0.00 0.00 45.96 2.97
2647 4663 1.691196 TTGGTTGCCTGCATATAGCC 58.309 50.000 0.00 0.00 44.83 3.93
2648 4664 0.178992 TGGTTGCCTGCATATAGCCC 60.179 55.000 0.00 0.00 44.83 5.19
2649 4665 0.178992 GGTTGCCTGCATATAGCCCA 60.179 55.000 0.00 0.00 44.83 5.36
2650 4666 1.691196 GTTGCCTGCATATAGCCCAA 58.309 50.000 0.00 0.00 44.83 4.12
2651 4667 1.338020 GTTGCCTGCATATAGCCCAAC 59.662 52.381 0.00 0.00 44.83 3.77
2652 4668 0.846015 TGCCTGCATATAGCCCAACT 59.154 50.000 0.00 0.00 44.83 3.16
2653 4669 2.054021 TGCCTGCATATAGCCCAACTA 58.946 47.619 0.00 0.00 44.83 2.24
2654 4670 2.038952 TGCCTGCATATAGCCCAACTAG 59.961 50.000 0.00 0.00 44.83 2.57
2655 4671 2.616510 GCCTGCATATAGCCCAACTAGG 60.617 54.545 0.00 0.00 44.83 3.02
2663 4679 4.157120 CCCAACTAGGCCCGGACG 62.157 72.222 0.73 0.00 35.39 4.79
2664 4680 3.072468 CCAACTAGGCCCGGACGA 61.072 66.667 0.73 0.00 0.00 4.20
2665 4681 2.652095 CCAACTAGGCCCGGACGAA 61.652 63.158 0.73 0.00 0.00 3.85
2666 4682 1.294138 CAACTAGGCCCGGACGAAA 59.706 57.895 0.73 0.00 0.00 3.46
2667 4683 0.107848 CAACTAGGCCCGGACGAAAT 60.108 55.000 0.73 0.00 0.00 2.17
2668 4684 0.107848 AACTAGGCCCGGACGAAATG 60.108 55.000 0.73 0.00 0.00 2.32
2669 4685 0.974010 ACTAGGCCCGGACGAAATGA 60.974 55.000 0.73 0.00 0.00 2.57
2670 4686 0.177141 CTAGGCCCGGACGAAATGAA 59.823 55.000 0.73 0.00 0.00 2.57
2671 4687 0.614294 TAGGCCCGGACGAAATGAAA 59.386 50.000 0.73 0.00 0.00 2.69
2672 4688 0.250989 AGGCCCGGACGAAATGAAAA 60.251 50.000 0.73 0.00 0.00 2.29
2673 4689 0.599060 GGCCCGGACGAAATGAAAAA 59.401 50.000 0.73 0.00 0.00 1.94
2693 4709 3.851976 AAACTTGTTTGGTTGCGTACA 57.148 38.095 0.00 0.00 0.00 2.90
2694 4710 3.414549 AACTTGTTTGGTTGCGTACAG 57.585 42.857 0.00 0.00 0.00 2.74
2695 4711 1.673920 ACTTGTTTGGTTGCGTACAGG 59.326 47.619 0.00 0.00 0.00 4.00
2696 4712 1.001815 CTTGTTTGGTTGCGTACAGGG 60.002 52.381 0.00 0.00 0.00 4.45
2697 4713 0.180642 TGTTTGGTTGCGTACAGGGA 59.819 50.000 0.00 0.00 0.00 4.20
2698 4714 0.872388 GTTTGGTTGCGTACAGGGAG 59.128 55.000 0.00 0.00 0.00 4.30
2699 4715 0.759959 TTTGGTTGCGTACAGGGAGA 59.240 50.000 0.00 0.00 0.00 3.71
2700 4716 0.034337 TTGGTTGCGTACAGGGAGAC 59.966 55.000 0.00 0.00 0.00 3.36
2713 4729 2.471255 GGAGACCTGGTTTGCATCG 58.529 57.895 0.00 0.00 0.00 3.84
2714 4730 0.036388 GGAGACCTGGTTTGCATCGA 60.036 55.000 0.00 0.00 0.00 3.59
2715 4731 1.079503 GAGACCTGGTTTGCATCGAC 58.920 55.000 0.00 0.00 0.00 4.20
2716 4732 0.396435 AGACCTGGTTTGCATCGACA 59.604 50.000 0.00 0.00 0.00 4.35
2717 4733 0.517316 GACCTGGTTTGCATCGACAC 59.483 55.000 0.00 0.00 0.00 3.67
2718 4734 0.179032 ACCTGGTTTGCATCGACACA 60.179 50.000 0.00 0.00 0.00 3.72
2719 4735 0.950836 CCTGGTTTGCATCGACACAA 59.049 50.000 0.00 0.00 0.00 3.33
2720 4736 1.336440 CCTGGTTTGCATCGACACAAA 59.664 47.619 9.88 9.88 33.55 2.83
2721 4737 2.223688 CCTGGTTTGCATCGACACAAAA 60.224 45.455 14.32 2.37 37.50 2.44
2722 4738 3.552684 CCTGGTTTGCATCGACACAAAAT 60.553 43.478 14.32 0.00 37.50 1.82
2723 4739 4.050553 CTGGTTTGCATCGACACAAAATT 58.949 39.130 14.32 0.00 37.50 1.82
2724 4740 4.437239 TGGTTTGCATCGACACAAAATTT 58.563 34.783 14.32 0.00 37.50 1.82
2725 4741 5.592054 TGGTTTGCATCGACACAAAATTTA 58.408 33.333 14.32 2.09 37.50 1.40
2726 4742 6.042777 TGGTTTGCATCGACACAAAATTTAA 58.957 32.000 14.32 0.05 37.50 1.52
2727 4743 6.535150 TGGTTTGCATCGACACAAAATTTAAA 59.465 30.769 14.32 0.00 37.50 1.52
2728 4744 7.062848 GGTTTGCATCGACACAAAATTTAAAG 58.937 34.615 14.32 0.00 37.50 1.85
2729 4745 5.820926 TGCATCGACACAAAATTTAAAGC 57.179 34.783 0.00 0.00 0.00 3.51
2730 4746 5.284864 TGCATCGACACAAAATTTAAAGCA 58.715 33.333 0.00 0.00 0.00 3.91
2731 4747 5.174761 TGCATCGACACAAAATTTAAAGCAC 59.825 36.000 0.00 0.00 0.00 4.40
2732 4748 5.388371 GCATCGACACAAAATTTAAAGCACC 60.388 40.000 0.00 0.00 0.00 5.01
2733 4749 4.612943 TCGACACAAAATTTAAAGCACCC 58.387 39.130 0.00 0.00 0.00 4.61
2734 4750 3.738791 CGACACAAAATTTAAAGCACCCC 59.261 43.478 0.00 0.00 0.00 4.95
2735 4751 4.698575 GACACAAAATTTAAAGCACCCCA 58.301 39.130 0.00 0.00 0.00 4.96
2736 4752 4.702831 ACACAAAATTTAAAGCACCCCAG 58.297 39.130 0.00 0.00 0.00 4.45
2737 4753 4.407296 ACACAAAATTTAAAGCACCCCAGA 59.593 37.500 0.00 0.00 0.00 3.86
2738 4754 4.990426 CACAAAATTTAAAGCACCCCAGAG 59.010 41.667 0.00 0.00 0.00 3.35
2739 4755 3.961480 AAATTTAAAGCACCCCAGAGC 57.039 42.857 0.00 0.00 0.00 4.09
2740 4756 1.852633 ATTTAAAGCACCCCAGAGCC 58.147 50.000 0.00 0.00 0.00 4.70
2741 4757 0.777446 TTTAAAGCACCCCAGAGCCT 59.223 50.000 0.00 0.00 0.00 4.58
2742 4758 0.038166 TTAAAGCACCCCAGAGCCTG 59.962 55.000 0.00 0.00 0.00 4.85
2743 4759 0.840288 TAAAGCACCCCAGAGCCTGA 60.840 55.000 4.00 0.00 32.44 3.86
2744 4760 2.417558 AAAGCACCCCAGAGCCTGAC 62.418 60.000 4.00 0.00 32.44 3.51
2745 4761 3.325753 GCACCCCAGAGCCTGACT 61.326 66.667 4.00 0.00 32.44 3.41
2746 4762 2.985456 CACCCCAGAGCCTGACTC 59.015 66.667 4.00 0.00 46.66 3.36
2753 4769 3.941081 GAGCCTGACTCGATGGGA 58.059 61.111 0.00 0.00 35.18 4.37
2754 4770 2.202866 GAGCCTGACTCGATGGGAA 58.797 57.895 0.00 0.00 35.18 3.97
2755 4771 0.179097 GAGCCTGACTCGATGGGAAC 60.179 60.000 0.00 0.00 35.18 3.62
2756 4772 2.838738 GAGCCTGACTCGATGGGAACA 61.839 57.143 0.00 0.00 39.65 3.18
2757 4773 4.921416 GAGCCTGACTCGATGGGAACAC 62.921 59.091 0.00 0.00 38.52 3.32
2767 4783 2.941210 TGGGAACACTTGAATCCGC 58.059 52.632 0.00 0.00 33.90 5.54
2768 4784 0.400213 TGGGAACACTTGAATCCGCT 59.600 50.000 0.00 0.00 33.90 5.52
2769 4785 0.804989 GGGAACACTTGAATCCGCTG 59.195 55.000 0.00 0.00 33.90 5.18
2770 4786 1.523758 GGAACACTTGAATCCGCTGT 58.476 50.000 0.00 0.00 0.00 4.40
2771 4787 1.880027 GGAACACTTGAATCCGCTGTT 59.120 47.619 0.00 0.00 0.00 3.16
2772 4788 2.293399 GGAACACTTGAATCCGCTGTTT 59.707 45.455 0.00 0.00 0.00 2.83
2773 4789 3.555518 GAACACTTGAATCCGCTGTTTC 58.444 45.455 0.00 0.00 0.00 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
199 215 6.392625 ACAACTATGTGATACGATACTGCT 57.607 37.500 0.00 0.00 38.69 4.24
200 216 7.361127 AGTACAACTATGTGATACGATACTGC 58.639 38.462 0.00 0.00 40.84 4.40
202 218 9.775854 ACTAGTACAACTATGTGATACGATACT 57.224 33.333 0.00 0.00 40.84 2.12
220 241 7.491372 GTGCTCTGCATGTTAATTACTAGTACA 59.509 37.037 0.91 0.00 41.91 2.90
335 356 1.750399 CTTTCATGGCCCCTCGTGG 60.750 63.158 0.00 0.00 0.00 4.94
336 357 2.409870 GCTTTCATGGCCCCTCGTG 61.410 63.158 0.00 0.00 0.00 4.35
337 358 2.044946 GCTTTCATGGCCCCTCGT 60.045 61.111 0.00 0.00 0.00 4.18
338 359 2.830370 GGCTTTCATGGCCCCTCG 60.830 66.667 0.00 0.00 43.49 4.63
344 365 1.807886 CAGAGCAGGCTTTCATGGC 59.192 57.895 0.00 0.00 0.00 4.40
345 366 0.680280 AGCAGAGCAGGCTTTCATGG 60.680 55.000 0.00 0.00 38.81 3.66
346 367 0.733729 GAGCAGAGCAGGCTTTCATG 59.266 55.000 0.00 0.00 42.78 3.07
347 368 0.743701 CGAGCAGAGCAGGCTTTCAT 60.744 55.000 0.00 0.00 42.78 2.57
348 369 1.375140 CGAGCAGAGCAGGCTTTCA 60.375 57.895 0.00 0.00 42.78 2.69
349 370 1.079543 TCGAGCAGAGCAGGCTTTC 60.080 57.895 0.00 0.00 42.78 2.62
350 371 1.079266 CTCGAGCAGAGCAGGCTTT 60.079 57.895 0.00 0.00 42.78 3.51
351 372 2.578128 CTCGAGCAGAGCAGGCTT 59.422 61.111 0.00 0.00 42.78 4.35
369 436 3.909776 TGCTTGCTTGAGAGATGTTTG 57.090 42.857 0.00 0.00 0.00 2.93
372 439 3.336468 CTCTTGCTTGCTTGAGAGATGT 58.664 45.455 12.36 0.00 38.27 3.06
373 440 2.096174 GCTCTTGCTTGCTTGAGAGATG 59.904 50.000 18.05 2.35 38.27 2.90
374 441 2.290134 TGCTCTTGCTTGCTTGAGAGAT 60.290 45.455 18.05 0.00 38.27 2.75
375 442 1.071228 TGCTCTTGCTTGCTTGAGAGA 59.929 47.619 18.05 5.04 38.27 3.10
376 443 1.520494 TGCTCTTGCTTGCTTGAGAG 58.480 50.000 15.26 14.08 40.48 3.20
377 444 2.195741 ATGCTCTTGCTTGCTTGAGA 57.804 45.000 15.26 6.66 40.48 3.27
378 445 5.334957 CCATATATGCTCTTGCTTGCTTGAG 60.335 44.000 7.24 9.64 40.48 3.02
379 446 4.517832 CCATATATGCTCTTGCTTGCTTGA 59.482 41.667 7.24 0.00 40.48 3.02
380 447 4.277672 ACCATATATGCTCTTGCTTGCTTG 59.722 41.667 7.24 0.00 40.48 4.01
381 448 4.467769 ACCATATATGCTCTTGCTTGCTT 58.532 39.130 7.24 0.00 40.48 3.91
382 449 4.096190 ACCATATATGCTCTTGCTTGCT 57.904 40.909 7.24 0.00 40.48 3.91
383 450 4.142730 GCTACCATATATGCTCTTGCTTGC 60.143 45.833 7.24 0.00 40.48 4.01
431 510 5.959527 GCAATTGTGATCGTTATACACACAG 59.040 40.000 7.40 0.00 42.80 3.66
432 511 5.409826 TGCAATTGTGATCGTTATACACACA 59.590 36.000 7.40 0.00 42.80 3.72
433 512 5.863898 TGCAATTGTGATCGTTATACACAC 58.136 37.500 7.40 0.00 42.80 3.82
435 514 6.785633 CGTATGCAATTGTGATCGTTATACAC 59.214 38.462 7.40 0.00 35.45 2.90
453 532 1.812093 GGCTTGGCGTACGTATGCA 60.812 57.895 33.99 20.67 39.92 3.96
454 533 1.157870 ATGGCTTGGCGTACGTATGC 61.158 55.000 27.89 27.89 37.49 3.14
461 540 1.477700 AGTACGTAATGGCTTGGCGTA 59.522 47.619 0.00 0.00 37.05 4.42
462 541 0.248289 AGTACGTAATGGCTTGGCGT 59.752 50.000 0.00 7.42 39.23 5.68
463 542 1.326548 GAAGTACGTAATGGCTTGGCG 59.673 52.381 0.00 0.00 0.00 5.69
464 543 1.326548 CGAAGTACGTAATGGCTTGGC 59.673 52.381 0.00 0.00 37.22 4.52
468 547 3.814005 AATCCGAAGTACGTAATGGCT 57.186 42.857 0.00 0.00 40.78 4.75
495 574 3.808728 AGTCTTGCTTGCTACACAAAGA 58.191 40.909 0.00 0.00 37.96 2.52
496 575 4.752101 ACTAGTCTTGCTTGCTACACAAAG 59.248 41.667 0.00 0.00 37.96 2.77
510 589 9.395707 GTCATGTATCCGTATAAACTAGTCTTG 57.604 37.037 0.00 0.00 0.00 3.02
511 590 9.128404 TGTCATGTATCCGTATAAACTAGTCTT 57.872 33.333 0.00 0.00 0.00 3.01
512 591 8.566260 GTGTCATGTATCCGTATAAACTAGTCT 58.434 37.037 0.00 0.00 0.00 3.24
527 646 1.522676 CATGCGACGGTGTCATGTATC 59.477 52.381 0.00 0.00 34.48 2.24
538 657 2.223021 CCTTGTTCAATACATGCGACGG 60.223 50.000 0.00 0.00 36.44 4.79
604 742 2.373169 AGGGATGTGATAATGCCATCGT 59.627 45.455 0.00 0.00 40.37 3.73
719 858 0.898320 CGTCTCCCTCACCACTGAAT 59.102 55.000 0.00 0.00 0.00 2.57
888 1027 1.952621 TTTGGTAGAGAGGTGAGGGG 58.047 55.000 0.00 0.00 0.00 4.79
891 1030 4.608948 ACAGTTTTGGTAGAGAGGTGAG 57.391 45.455 0.00 0.00 0.00 3.51
937 1079 2.556459 CCGATCGGCGATCAGTCCT 61.556 63.158 39.10 13.50 44.57 3.85
938 1080 2.049985 CCGATCGGCGATCAGTCC 60.050 66.667 39.10 20.23 44.57 3.85
954 1103 1.813178 GCAAGTAGAAGGCCAGAAACC 59.187 52.381 5.01 0.00 0.00 3.27
962 1111 3.190744 GGTTTAAGGTGCAAGTAGAAGGC 59.809 47.826 0.00 0.00 0.00 4.35
1305 1484 3.512680 ACTGAAGAAGTAAGCCGATTCG 58.487 45.455 0.00 0.00 37.36 3.34
1366 1545 3.400054 GGCCTTCCAGTACCCGCT 61.400 66.667 0.00 0.00 0.00 5.52
1454 1633 4.680237 CGCGGTGGAAGGTGAGCA 62.680 66.667 0.00 0.00 0.00 4.26
1779 1961 2.979197 GCACTGCAGCAGCTGGAAG 61.979 63.158 24.13 16.66 43.24 3.46
1780 1962 2.981909 GCACTGCAGCAGCTGGAA 60.982 61.111 24.13 0.00 43.24 3.53
1781 1963 3.778097 TTGCACTGCAGCAGCTGGA 62.778 57.895 24.13 20.53 46.54 3.86
1782 1964 2.543687 GATTGCACTGCAGCAGCTGG 62.544 60.000 24.13 13.16 46.54 4.85
1784 1966 0.965866 ATGATTGCACTGCAGCAGCT 60.966 50.000 26.04 11.96 46.54 4.24
1798 1985 1.760613 CTTTGGGAGGCATGCATGATT 59.239 47.619 30.64 16.51 0.00 2.57
1801 1988 0.744874 CTCTTTGGGAGGCATGCATG 59.255 55.000 22.70 22.70 38.35 4.06
1802 1989 0.627451 TCTCTTTGGGAGGCATGCAT 59.373 50.000 21.36 13.78 42.10 3.96
1803 1990 0.034767 CTCTCTTTGGGAGGCATGCA 60.035 55.000 21.36 0.00 42.10 3.96
1804 1991 0.750911 CCTCTCTTTGGGAGGCATGC 60.751 60.000 9.90 9.90 42.95 4.06
1832 2019 3.739209 GCTGGAATTTAAATGCCTGGCTC 60.739 47.826 25.67 11.46 34.93 4.70
1833 2020 2.169144 GCTGGAATTTAAATGCCTGGCT 59.831 45.455 25.67 1.67 34.93 4.75
1834 2021 2.554142 GCTGGAATTTAAATGCCTGGC 58.446 47.619 25.67 22.80 34.93 4.85
1835 2022 3.183793 GGCTGGAATTTAAATGCCTGG 57.816 47.619 25.67 18.68 34.93 4.45
2006 2206 4.642885 CGGGCTTAATTAATCCTGGTTTCA 59.357 41.667 16.20 0.00 0.00 2.69
2122 2326 7.435305 AGGCCATTTTTCCATTTCAAATTTTG 58.565 30.769 5.01 2.59 0.00 2.44
2271 2475 4.200283 CCGGTCGCTCTGCCTCTC 62.200 72.222 0.00 0.00 0.00 3.20
2374 2584 4.916293 GATCCGCATCCGCAGCCA 62.916 66.667 0.00 0.00 38.40 4.75
2466 2676 1.497161 GCCTGTCACCCTACACCTAT 58.503 55.000 0.00 0.00 0.00 2.57
2493 4509 1.878088 GACCATACTCCATCGTCGCTA 59.122 52.381 0.00 0.00 0.00 4.26
2498 4514 2.168521 CCACAAGACCATACTCCATCGT 59.831 50.000 0.00 0.00 0.00 3.73
2619 4635 2.051345 GGCAACCAAACGCGTCAG 60.051 61.111 14.44 8.23 0.00 3.51
2623 4639 2.193865 TATGCAGGCAACCAAACGCG 62.194 55.000 3.53 3.53 37.17 6.01
2631 4647 1.338020 GTTGGGCTATATGCAGGCAAC 59.662 52.381 0.00 0.00 45.15 4.17
2646 4662 4.157120 CGTCCGGGCCTAGTTGGG 62.157 72.222 0.00 0.00 36.00 4.12
2647 4663 2.175035 TTTCGTCCGGGCCTAGTTGG 62.175 60.000 0.00 0.00 39.35 3.77
2648 4664 0.107848 ATTTCGTCCGGGCCTAGTTG 60.108 55.000 0.00 0.00 0.00 3.16
2649 4665 0.107848 CATTTCGTCCGGGCCTAGTT 60.108 55.000 0.00 0.00 0.00 2.24
2650 4666 0.974010 TCATTTCGTCCGGGCCTAGT 60.974 55.000 0.00 0.00 0.00 2.57
2651 4667 0.177141 TTCATTTCGTCCGGGCCTAG 59.823 55.000 0.00 0.00 0.00 3.02
2652 4668 0.614294 TTTCATTTCGTCCGGGCCTA 59.386 50.000 0.00 0.00 0.00 3.93
2653 4669 0.250989 TTTTCATTTCGTCCGGGCCT 60.251 50.000 0.00 0.00 0.00 5.19
2654 4670 0.599060 TTTTTCATTTCGTCCGGGCC 59.401 50.000 0.00 0.00 0.00 5.80
2671 4687 4.557205 TGTACGCAACCAAACAAGTTTTT 58.443 34.783 0.00 0.00 0.00 1.94
2672 4688 4.170256 CTGTACGCAACCAAACAAGTTTT 58.830 39.130 0.00 0.00 0.00 2.43
2673 4689 3.428316 CCTGTACGCAACCAAACAAGTTT 60.428 43.478 0.00 0.00 0.00 2.66
2674 4690 2.098443 CCTGTACGCAACCAAACAAGTT 59.902 45.455 0.00 0.00 0.00 2.66
2675 4691 1.673920 CCTGTACGCAACCAAACAAGT 59.326 47.619 0.00 0.00 0.00 3.16
2676 4692 1.001815 CCCTGTACGCAACCAAACAAG 60.002 52.381 0.00 0.00 0.00 3.16
2677 4693 1.025812 CCCTGTACGCAACCAAACAA 58.974 50.000 0.00 0.00 0.00 2.83
2678 4694 0.180642 TCCCTGTACGCAACCAAACA 59.819 50.000 0.00 0.00 0.00 2.83
2679 4695 0.872388 CTCCCTGTACGCAACCAAAC 59.128 55.000 0.00 0.00 0.00 2.93
2680 4696 0.759959 TCTCCCTGTACGCAACCAAA 59.240 50.000 0.00 0.00 0.00 3.28
2681 4697 0.034337 GTCTCCCTGTACGCAACCAA 59.966 55.000 0.00 0.00 0.00 3.67
2682 4698 1.669440 GTCTCCCTGTACGCAACCA 59.331 57.895 0.00 0.00 0.00 3.67
2683 4699 1.079336 GGTCTCCCTGTACGCAACC 60.079 63.158 0.00 0.00 0.00 3.77
2684 4700 1.972978 AGGTCTCCCTGTACGCAAC 59.027 57.895 0.00 0.00 40.58 4.17
2685 4701 4.533318 AGGTCTCCCTGTACGCAA 57.467 55.556 0.00 0.00 40.58 4.85
2693 4709 0.329596 GATGCAAACCAGGTCTCCCT 59.670 55.000 0.00 0.00 44.02 4.20
2694 4710 1.026718 CGATGCAAACCAGGTCTCCC 61.027 60.000 0.00 0.00 0.00 4.30
2695 4711 0.036388 TCGATGCAAACCAGGTCTCC 60.036 55.000 0.00 0.00 0.00 3.71
2696 4712 1.079503 GTCGATGCAAACCAGGTCTC 58.920 55.000 0.00 0.00 0.00 3.36
2697 4713 0.396435 TGTCGATGCAAACCAGGTCT 59.604 50.000 0.00 0.00 0.00 3.85
2698 4714 0.517316 GTGTCGATGCAAACCAGGTC 59.483 55.000 0.00 0.00 0.00 3.85
2699 4715 0.179032 TGTGTCGATGCAAACCAGGT 60.179 50.000 0.00 0.00 0.00 4.00
2700 4716 0.950836 TTGTGTCGATGCAAACCAGG 59.049 50.000 0.00 0.00 0.00 4.45
2701 4717 2.772568 TTTGTGTCGATGCAAACCAG 57.227 45.000 11.58 0.00 30.68 4.00
2702 4718 3.724508 ATTTTGTGTCGATGCAAACCA 57.275 38.095 14.19 4.82 34.77 3.67
2703 4719 6.517914 TTAAATTTTGTGTCGATGCAAACC 57.482 33.333 14.19 0.00 34.77 3.27
2704 4720 6.569693 GCTTTAAATTTTGTGTCGATGCAAAC 59.430 34.615 14.19 0.00 34.77 2.93
2705 4721 6.256539 TGCTTTAAATTTTGTGTCGATGCAAA 59.743 30.769 11.58 11.58 33.40 3.68
2706 4722 5.750547 TGCTTTAAATTTTGTGTCGATGCAA 59.249 32.000 0.00 0.00 0.00 4.08
2707 4723 5.174761 GTGCTTTAAATTTTGTGTCGATGCA 59.825 36.000 0.00 0.00 0.00 3.96
2708 4724 5.388371 GGTGCTTTAAATTTTGTGTCGATGC 60.388 40.000 0.00 0.00 0.00 3.91
2709 4725 5.118510 GGGTGCTTTAAATTTTGTGTCGATG 59.881 40.000 0.00 0.00 0.00 3.84
2710 4726 5.227152 GGGTGCTTTAAATTTTGTGTCGAT 58.773 37.500 0.00 0.00 0.00 3.59
2711 4727 4.500035 GGGGTGCTTTAAATTTTGTGTCGA 60.500 41.667 0.00 0.00 0.00 4.20
2712 4728 3.738791 GGGGTGCTTTAAATTTTGTGTCG 59.261 43.478 0.00 0.00 0.00 4.35
2713 4729 4.698575 TGGGGTGCTTTAAATTTTGTGTC 58.301 39.130 0.00 0.00 0.00 3.67
2714 4730 4.407296 TCTGGGGTGCTTTAAATTTTGTGT 59.593 37.500 0.00 0.00 0.00 3.72
2715 4731 4.954875 TCTGGGGTGCTTTAAATTTTGTG 58.045 39.130 0.00 0.00 0.00 3.33
2716 4732 4.503123 GCTCTGGGGTGCTTTAAATTTTGT 60.503 41.667 0.00 0.00 0.00 2.83
2717 4733 3.996363 GCTCTGGGGTGCTTTAAATTTTG 59.004 43.478 0.00 0.00 0.00 2.44
2718 4734 3.007940 GGCTCTGGGGTGCTTTAAATTTT 59.992 43.478 0.00 0.00 33.10 1.82
2719 4735 2.567169 GGCTCTGGGGTGCTTTAAATTT 59.433 45.455 0.00 0.00 33.10 1.82
2720 4736 2.179427 GGCTCTGGGGTGCTTTAAATT 58.821 47.619 0.00 0.00 33.10 1.82
2721 4737 1.359130 AGGCTCTGGGGTGCTTTAAAT 59.641 47.619 0.00 0.00 33.10 1.40
2722 4738 0.777446 AGGCTCTGGGGTGCTTTAAA 59.223 50.000 0.00 0.00 33.10 1.52
2723 4739 0.038166 CAGGCTCTGGGGTGCTTTAA 59.962 55.000 0.00 0.00 33.10 1.52
2724 4740 0.840288 TCAGGCTCTGGGGTGCTTTA 60.840 55.000 2.86 0.00 33.10 1.85
2725 4741 2.156098 TCAGGCTCTGGGGTGCTTT 61.156 57.895 2.86 0.00 33.10 3.51
2726 4742 2.530151 TCAGGCTCTGGGGTGCTT 60.530 61.111 2.86 0.00 33.10 3.91
2727 4743 3.325753 GTCAGGCTCTGGGGTGCT 61.326 66.667 2.86 0.00 33.10 4.40
2728 4744 3.322318 GAGTCAGGCTCTGGGGTGC 62.322 68.421 0.00 0.00 40.98 5.01
2729 4745 2.985456 GAGTCAGGCTCTGGGGTG 59.015 66.667 0.00 0.00 40.98 4.61
2730 4746 2.522198 ATCGAGTCAGGCTCTGGGGT 62.522 60.000 0.00 0.00 41.98 4.95
2731 4747 1.760086 ATCGAGTCAGGCTCTGGGG 60.760 63.158 0.00 0.00 41.98 4.96
2732 4748 1.440893 CATCGAGTCAGGCTCTGGG 59.559 63.158 0.00 0.00 41.98 4.45
2733 4749 1.440893 CCATCGAGTCAGGCTCTGG 59.559 63.158 0.00 0.00 41.98 3.86
2734 4750 1.039785 TCCCATCGAGTCAGGCTCTG 61.040 60.000 0.00 0.00 41.98 3.35
2735 4751 0.324738 TTCCCATCGAGTCAGGCTCT 60.325 55.000 0.00 0.00 41.98 4.09
2736 4752 0.179097 GTTCCCATCGAGTCAGGCTC 60.179 60.000 0.00 0.00 40.77 4.70
2737 4753 0.904865 TGTTCCCATCGAGTCAGGCT 60.905 55.000 0.00 0.00 0.00 4.58
2738 4754 0.741221 GTGTTCCCATCGAGTCAGGC 60.741 60.000 0.00 0.00 0.00 4.85
2739 4755 0.898320 AGTGTTCCCATCGAGTCAGG 59.102 55.000 0.00 0.00 0.00 3.86
2740 4756 2.029020 TCAAGTGTTCCCATCGAGTCAG 60.029 50.000 0.00 0.00 0.00 3.51
2741 4757 1.967779 TCAAGTGTTCCCATCGAGTCA 59.032 47.619 0.00 0.00 0.00 3.41
2742 4758 2.743636 TCAAGTGTTCCCATCGAGTC 57.256 50.000 0.00 0.00 0.00 3.36
2743 4759 3.600388 GATTCAAGTGTTCCCATCGAGT 58.400 45.455 0.00 0.00 0.00 4.18
2744 4760 2.939103 GGATTCAAGTGTTCCCATCGAG 59.061 50.000 0.00 0.00 0.00 4.04
2745 4761 2.676750 CGGATTCAAGTGTTCCCATCGA 60.677 50.000 0.00 0.00 0.00 3.59
2746 4762 1.665679 CGGATTCAAGTGTTCCCATCG 59.334 52.381 0.00 0.00 0.00 3.84
2747 4763 1.401905 GCGGATTCAAGTGTTCCCATC 59.598 52.381 0.00 0.00 0.00 3.51
2748 4764 1.004745 AGCGGATTCAAGTGTTCCCAT 59.995 47.619 0.00 0.00 0.00 4.00
2749 4765 0.400213 AGCGGATTCAAGTGTTCCCA 59.600 50.000 0.00 0.00 0.00 4.37
2750 4766 0.804989 CAGCGGATTCAAGTGTTCCC 59.195 55.000 0.00 0.00 0.00 3.97
2751 4767 1.523758 ACAGCGGATTCAAGTGTTCC 58.476 50.000 0.00 0.00 0.00 3.62
2752 4768 3.555518 GAAACAGCGGATTCAAGTGTTC 58.444 45.455 2.08 0.00 31.04 3.18
2753 4769 3.626028 GAAACAGCGGATTCAAGTGTT 57.374 42.857 2.08 0.00 32.75 3.32



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

AutoCloner maintained by Alex Coulton.