Multiple sequence alignment - TraesCS6B01G360100

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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 TraesCS6B01G360100 chr6B 100.000 2930 0 0 1 2930 632175797 632178726 0.000000e+00 5411.0
1 TraesCS6B01G360100 chr6D 92.964 2274 94 22 634 2886 419262880 419265108 0.000000e+00 3253.0
2 TraesCS6B01G360100 chr6D 85.833 480 52 10 65 534 419262391 419262864 2.030000e-136 496.0
3 TraesCS6B01G360100 chr6A 94.081 1588 53 14 575 2150 562682744 562684302 0.000000e+00 2374.0
4 TraesCS6B01G360100 chr6A 89.875 721 51 9 2176 2886 562684283 562684991 0.000000e+00 907.0
5 TraesCS6B01G360100 chr6A 94.444 36 2 0 575 610 562673241 562673276 4.080000e-04 56.5
6 TraesCS6B01G360100 chr7A 79.035 539 89 16 9 531 526618948 526618418 6.010000e-92 348.0
7 TraesCS6B01G360100 chr7A 89.474 114 10 1 418 529 16692142 16692255 3.040000e-30 143.0
8 TraesCS6B01G360100 chr3D 80.140 428 58 17 105 507 297888822 297888397 7.940000e-76 294.0
9 TraesCS6B01G360100 chr7D 87.805 246 29 1 2248 2493 223980351 223980107 1.330000e-73 287.0
10 TraesCS6B01G360100 chr7D 100.000 31 0 0 1630 1660 256228718 256228688 1.130000e-04 58.4
11 TraesCS6B01G360100 chr4D 77.207 487 80 19 66 529 464147322 464147800 3.750000e-64 255.0
12 TraesCS6B01G360100 chr4B 74.255 470 90 22 65 517 527012532 527012077 5.020000e-38 169.0
13 TraesCS6B01G360100 chr3A 74.750 400 75 20 119 517 387784580 387784206 3.910000e-34 156.0
14 TraesCS6B01G360100 chr1D 87.736 106 12 1 231 336 477187616 477187512 3.970000e-24 122.0
15 TraesCS6B01G360100 chr4A 88.372 86 10 0 247 332 571675769 571675854 1.440000e-18 104.0
16 TraesCS6B01G360100 chr1B 75.203 246 41 11 253 488 43978365 43978130 6.680000e-17 99.0
17 TraesCS6B01G360100 chr3B 87.302 63 7 1 31 93 659993549 659993610 1.460000e-08 71.3


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 TraesCS6B01G360100 chr6B 632175797 632178726 2929 False 5411.0 5411 100.0000 1 2930 1 chr6B.!!$F1 2929
1 TraesCS6B01G360100 chr6D 419262391 419265108 2717 False 1874.5 3253 89.3985 65 2886 2 chr6D.!!$F1 2821
2 TraesCS6B01G360100 chr6A 562682744 562684991 2247 False 1640.5 2374 91.9780 575 2886 2 chr6A.!!$F2 2311
3 TraesCS6B01G360100 chr7A 526618418 526618948 530 True 348.0 348 79.0350 9 531 1 chr7A.!!$R1 522

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
60 61 0.038744 CCACCTCCTGCAGACCATTT 59.961 55.0 17.39 0.0 0.0 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1951 2013 0.815734 AAGAGCAGATGCAACATGGC 59.184 50.0 7.68 0.0 45.16 4.4 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
25 26 1.134530 GAGCATCTTGTCGACGTCCG 61.135 60.000 10.58 5.50 40.25 4.79
28 29 3.678717 ATCTTGTCGACGTCCGCGG 62.679 63.158 22.12 22.12 43.45 6.46
59 60 0.842030 TCCACCTCCTGCAGACCATT 60.842 55.000 17.39 0.00 0.00 3.16
60 61 0.038744 CCACCTCCTGCAGACCATTT 59.961 55.000 17.39 0.00 0.00 2.32
61 62 1.548582 CCACCTCCTGCAGACCATTTT 60.549 52.381 17.39 0.00 0.00 1.82
62 63 1.542915 CACCTCCTGCAGACCATTTTG 59.457 52.381 17.39 0.00 0.00 2.44
63 64 1.145738 ACCTCCTGCAGACCATTTTGT 59.854 47.619 17.39 0.00 0.00 2.83
121 122 2.044946 GCCTCCACCGCCAATTCT 60.045 61.111 0.00 0.00 0.00 2.40
202 203 1.324005 CCACGTCCTTCTCCTCCTCC 61.324 65.000 0.00 0.00 0.00 4.30
205 206 0.753848 CGTCCTTCTCCTCCTCCTCC 60.754 65.000 0.00 0.00 0.00 4.30
206 207 0.397957 GTCCTTCTCCTCCTCCTCCC 60.398 65.000 0.00 0.00 0.00 4.30
208 209 1.456705 CTTCTCCTCCTCCTCCCCG 60.457 68.421 0.00 0.00 0.00 5.73
228 232 2.279073 CTCGTGCTCCTCCCCCTA 59.721 66.667 0.00 0.00 0.00 3.53
244 248 2.832733 CCCCTATTCCTCCGGATCTAAC 59.167 54.545 3.57 0.00 0.00 2.34
245 249 3.507411 CCCTATTCCTCCGGATCTAACA 58.493 50.000 3.57 0.00 0.00 2.41
251 255 2.039418 CCTCCGGATCTAACACATCCA 58.961 52.381 3.57 0.00 40.09 3.41
263 267 1.762460 ACATCCAGAGGTAGCCCCG 60.762 63.158 0.00 0.00 38.74 5.73
282 286 3.930012 GGCTATCCGGGCTTCGCT 61.930 66.667 0.00 0.00 37.59 4.93
317 322 4.711949 CAAGGAGCTGCAGCCGGT 62.712 66.667 34.39 17.46 43.38 5.28
383 409 2.144833 TAGCGAAAAGTGGCGGACGA 62.145 55.000 0.00 0.00 32.92 4.20
384 410 2.388232 GCGAAAAGTGGCGGACGAT 61.388 57.895 0.00 0.00 0.00 3.73
455 492 3.708544 TAGGGTTTCGGTGCCGGG 61.709 66.667 10.94 0.00 40.25 5.73
470 507 3.784642 CGGGGGTCGGCTTAAATAA 57.215 52.632 0.00 0.00 34.75 1.40
473 510 1.064537 GGGGGTCGGCTTAAATAACCA 60.065 52.381 0.00 0.00 0.00 3.67
488 525 0.546747 AACCAGGCTAGGGCACTACA 60.547 55.000 0.00 0.00 40.87 2.74
489 526 0.326618 ACCAGGCTAGGGCACTACAT 60.327 55.000 0.00 0.00 40.87 2.29
496 533 0.324923 TAGGGCACTACATGGTCCGT 60.325 55.000 0.00 0.00 0.00 4.69
502 539 0.323178 ACTACATGGTCCGTCGGAGT 60.323 55.000 15.95 11.65 29.39 3.85
539 576 4.790861 GGAGACGTCCGTTCGCCC 62.791 72.222 13.01 0.00 31.37 6.13
549 586 3.059386 GTTCGCCCGGGCATTTGA 61.059 61.111 42.78 29.42 42.06 2.69
550 587 2.044451 TTCGCCCGGGCATTTGAT 60.044 55.556 42.78 0.00 42.06 2.57
551 588 2.413963 TTCGCCCGGGCATTTGATG 61.414 57.895 42.78 25.66 42.06 3.07
552 589 3.140141 CGCCCGGGCATTTGATGT 61.140 61.111 42.78 0.00 42.06 3.06
553 590 2.709883 CGCCCGGGCATTTGATGTT 61.710 57.895 42.78 0.00 42.06 2.71
554 591 1.153588 GCCCGGGCATTTGATGTTG 60.154 57.895 40.73 0.00 41.49 3.33
555 592 1.516892 CCCGGGCATTTGATGTTGG 59.483 57.895 8.08 0.00 0.00 3.77
556 593 1.257055 CCCGGGCATTTGATGTTGGT 61.257 55.000 8.08 0.00 0.00 3.67
557 594 0.607620 CCGGGCATTTGATGTTGGTT 59.392 50.000 0.00 0.00 0.00 3.67
558 595 1.001860 CCGGGCATTTGATGTTGGTTT 59.998 47.619 0.00 0.00 0.00 3.27
559 596 2.067766 CGGGCATTTGATGTTGGTTTG 58.932 47.619 0.00 0.00 0.00 2.93
560 597 2.425539 GGGCATTTGATGTTGGTTTGG 58.574 47.619 0.00 0.00 0.00 3.28
561 598 2.425539 GGCATTTGATGTTGGTTTGGG 58.574 47.619 0.00 0.00 0.00 4.12
562 599 2.038295 GGCATTTGATGTTGGTTTGGGA 59.962 45.455 0.00 0.00 0.00 4.37
563 600 3.066380 GCATTTGATGTTGGTTTGGGAC 58.934 45.455 0.00 0.00 0.00 4.46
564 601 3.316283 CATTTGATGTTGGTTTGGGACG 58.684 45.455 0.00 0.00 0.00 4.79
565 602 0.671251 TTGATGTTGGTTTGGGACGC 59.329 50.000 0.00 0.00 0.00 5.19
566 603 1.175983 TGATGTTGGTTTGGGACGCC 61.176 55.000 0.00 0.00 0.00 5.68
567 604 1.873270 GATGTTGGTTTGGGACGCCC 61.873 60.000 7.87 7.87 45.71 6.13
580 617 3.610669 CGCCCGGCTCTAGATGCT 61.611 66.667 8.05 0.00 0.00 3.79
610 649 2.225041 CCAGGAGGTGACCGATCCTATA 60.225 54.545 11.66 0.00 41.60 1.31
624 663 1.754803 TCCTATACTTGCACCAGTCGG 59.245 52.381 0.00 0.00 38.77 4.79
627 666 2.536997 ATACTTGCACCAGTCGGCCC 62.537 60.000 0.00 0.00 34.57 5.80
629 668 3.925630 CTTGCACCAGTCGGCCCAT 62.926 63.158 0.00 0.00 34.57 4.00
641 680 2.746277 GCCCATCGACGCCAAACT 60.746 61.111 0.00 0.00 0.00 2.66
647 686 0.872388 ATCGACGCCAAACTTTGACC 59.128 50.000 2.87 0.00 0.00 4.02
716 755 5.437060 AGAAAGGTCTGAGCAAGTTTACAA 58.563 37.500 9.78 0.00 30.83 2.41
719 758 6.715347 AAGGTCTGAGCAAGTTTACAAAAT 57.285 33.333 9.78 0.00 0.00 1.82
749 796 4.034510 GCGGCATATATGAGAGCAAATACC 59.965 45.833 17.10 3.12 0.00 2.73
763 810 0.519961 AATACCAACGTTTCTGCGGC 59.480 50.000 0.00 0.00 35.98 6.53
838 885 2.125753 CGCTCTGCCTCTGGTCAC 60.126 66.667 0.00 0.00 0.00 3.67
1659 1721 1.215679 AGGAGGACGAGGAGGAGGAA 61.216 60.000 0.00 0.00 0.00 3.36
1664 1726 3.441290 CGAGGAGGAGGAACGCGT 61.441 66.667 5.58 5.58 0.00 6.01
1746 1808 2.609299 TGGAAGACGGATGGCCCA 60.609 61.111 0.00 0.00 34.14 5.36
1947 2009 3.067461 CCTAGCTCTGGTATGACTGTCAC 59.933 52.174 13.50 0.95 0.00 3.67
1951 2013 0.175760 CTGGTATGACTGTCACCCCG 59.824 60.000 13.50 8.74 0.00 5.73
1952 2014 1.153429 GGTATGACTGTCACCCCGC 60.153 63.158 13.50 1.95 0.00 6.13
1966 2030 2.103538 CCGCCATGTTGCATCTGC 59.896 61.111 0.00 0.00 42.50 4.26
1988 2052 5.989777 TGCTCTTCAGGAAACAACTTAGTAC 59.010 40.000 0.00 0.00 0.00 2.73
1996 2060 8.306038 TCAGGAAACAACTTAGTACGCTATTTA 58.694 33.333 0.00 0.00 0.00 1.40
2068 2132 7.061094 GCTGTGCATTCTGTTATTTAGTGTTTC 59.939 37.037 0.00 0.00 0.00 2.78
2176 2240 5.762045 AGCACATTAACTTTACAGTTGCTG 58.238 37.500 4.49 4.60 43.54 4.41
2236 2303 9.936329 ATATTTTGTCATAAATGGTAACCCTCT 57.064 29.630 0.00 0.00 0.00 3.69
2312 2379 4.498345 CCCGTCAGCTAGAAGATACTGTTC 60.498 50.000 0.00 0.00 0.00 3.18
2327 2394 8.430801 AGATACTGTTCAATTCTGCAGTTATC 57.569 34.615 14.67 0.25 41.67 1.75
2358 2425 2.987149 AGTGCGAACGAAGTAACATCTG 59.013 45.455 0.00 0.00 45.00 2.90
2392 2460 2.157668 GCGAAAAATCTGAACTCGAGCA 59.842 45.455 13.61 2.06 0.00 4.26
2425 2493 4.098807 AGCTTGGTTTCGGTTTGTTTACAT 59.901 37.500 0.00 0.00 0.00 2.29
2465 2533 6.932356 TTGCATAACTTGGATCTCAGATTC 57.068 37.500 0.00 0.00 0.00 2.52
2525 2593 4.568072 TCTAAATTGCCAGCAACTCCTA 57.432 40.909 7.31 0.00 38.88 2.94
2533 2601 3.326588 TGCCAGCAACTCCTAAGTTCTTA 59.673 43.478 0.00 0.00 43.99 2.10
2540 2608 7.442666 CAGCAACTCCTAAGTTCTTAGTTTTCT 59.557 37.037 15.51 5.87 43.99 2.52
2564 2632 8.316214 TCTTGTACTGTAACCCTTAATTCGATT 58.684 33.333 0.00 0.00 0.00 3.34
2632 2700 6.972901 TCAGCTATCTATTCAACACGTTACTG 59.027 38.462 0.00 0.00 0.00 2.74
2636 2707 7.378995 GCTATCTATTCAACACGTTACTGGTAG 59.621 40.741 0.00 0.00 0.00 3.18
2652 2723 0.036010 GTAGCTGAGAAGCCAGGCAA 60.036 55.000 15.80 0.00 34.82 4.52
2656 2727 1.611673 GCTGAGAAGCCAGGCAAAGTA 60.612 52.381 15.80 0.00 34.82 2.24
2657 2728 2.354259 CTGAGAAGCCAGGCAAAGTAG 58.646 52.381 15.80 2.27 0.00 2.57
2662 2739 3.044059 GCCAGGCAAAGTAGCTGCG 62.044 63.158 6.55 0.00 40.88 5.18
2669 2746 0.166814 CAAAGTAGCTGCGAAGGCAC 59.833 55.000 0.00 0.00 46.21 5.01
2707 2784 9.955208 TTATAATTGTGCTTCTTCTATGCAATG 57.045 29.630 0.00 0.00 39.71 2.82
2708 2785 5.909621 ATTGTGCTTCTTCTATGCAATGT 57.090 34.783 0.00 0.00 39.71 2.71
2735 2812 7.309177 ACAGTACGATCTATGCAATCTATGTC 58.691 38.462 0.00 0.00 0.00 3.06
2736 2813 6.749578 CAGTACGATCTATGCAATCTATGTCC 59.250 42.308 0.00 0.00 0.00 4.02
2737 2814 5.078411 ACGATCTATGCAATCTATGTCCC 57.922 43.478 0.00 0.00 0.00 4.46
2738 2815 4.774726 ACGATCTATGCAATCTATGTCCCT 59.225 41.667 0.00 0.00 0.00 4.20
2739 2816 5.952347 ACGATCTATGCAATCTATGTCCCTA 59.048 40.000 0.00 0.00 0.00 3.53
2740 2817 6.127591 ACGATCTATGCAATCTATGTCCCTAC 60.128 42.308 0.00 0.00 0.00 3.18
2741 2818 5.644977 TCTATGCAATCTATGTCCCTACG 57.355 43.478 0.00 0.00 0.00 3.51
2742 2819 5.321927 TCTATGCAATCTATGTCCCTACGA 58.678 41.667 0.00 0.00 0.00 3.43
2762 2839 2.307686 GACCCTACCCCACTTGAAATCA 59.692 50.000 0.00 0.00 0.00 2.57
2763 2840 2.719705 ACCCTACCCCACTTGAAATCAA 59.280 45.455 0.00 0.00 0.00 2.57
2764 2841 3.089284 CCCTACCCCACTTGAAATCAAC 58.911 50.000 0.00 0.00 0.00 3.18
2766 2843 3.245264 CCTACCCCACTTGAAATCAACCT 60.245 47.826 0.00 0.00 0.00 3.50
2815 2892 2.902486 AGATGCTGTCTGGACTTCTTGA 59.098 45.455 2.38 0.00 35.31 3.02
2886 2963 4.072131 GGTTTCACATTCCTTAGAGCACA 58.928 43.478 0.00 0.00 0.00 4.57
2887 2964 4.702131 GGTTTCACATTCCTTAGAGCACAT 59.298 41.667 0.00 0.00 0.00 3.21
2888 2965 5.183904 GGTTTCACATTCCTTAGAGCACATT 59.816 40.000 0.00 0.00 0.00 2.71
2889 2966 6.317857 GTTTCACATTCCTTAGAGCACATTC 58.682 40.000 0.00 0.00 0.00 2.67
2890 2967 4.517285 TCACATTCCTTAGAGCACATTCC 58.483 43.478 0.00 0.00 0.00 3.01
2891 2968 4.225942 TCACATTCCTTAGAGCACATTCCT 59.774 41.667 0.00 0.00 0.00 3.36
2892 2969 4.946157 CACATTCCTTAGAGCACATTCCTT 59.054 41.667 0.00 0.00 0.00 3.36
2893 2970 6.070251 TCACATTCCTTAGAGCACATTCCTTA 60.070 38.462 0.00 0.00 0.00 2.69
2894 2971 6.599244 CACATTCCTTAGAGCACATTCCTTAA 59.401 38.462 0.00 0.00 0.00 1.85
2895 2972 6.825721 ACATTCCTTAGAGCACATTCCTTAAG 59.174 38.462 0.00 0.00 0.00 1.85
2896 2973 6.620877 TTCCTTAGAGCACATTCCTTAAGA 57.379 37.500 3.36 0.00 0.00 2.10
2897 2974 6.227298 TCCTTAGAGCACATTCCTTAAGAG 57.773 41.667 3.36 0.00 0.00 2.85
2898 2975 4.813697 CCTTAGAGCACATTCCTTAAGAGC 59.186 45.833 3.36 0.00 0.00 4.09
2899 2976 3.988976 AGAGCACATTCCTTAAGAGCA 57.011 42.857 3.36 0.00 0.00 4.26
2900 2977 3.604582 AGAGCACATTCCTTAAGAGCAC 58.395 45.455 3.36 0.00 0.00 4.40
2901 2978 2.680339 GAGCACATTCCTTAAGAGCACC 59.320 50.000 3.36 0.00 0.00 5.01
2902 2979 2.307098 AGCACATTCCTTAAGAGCACCT 59.693 45.455 3.36 0.00 0.00 4.00
2903 2980 2.421424 GCACATTCCTTAAGAGCACCTG 59.579 50.000 3.36 0.00 0.00 4.00
2904 2981 3.869912 GCACATTCCTTAAGAGCACCTGA 60.870 47.826 3.36 0.00 0.00 3.86
2905 2982 4.326826 CACATTCCTTAAGAGCACCTGAA 58.673 43.478 3.36 0.00 0.00 3.02
2906 2983 4.946157 CACATTCCTTAAGAGCACCTGAAT 59.054 41.667 3.36 0.00 0.00 2.57
2907 2984 5.065731 CACATTCCTTAAGAGCACCTGAATC 59.934 44.000 3.36 0.00 0.00 2.52
2908 2985 5.045286 ACATTCCTTAAGAGCACCTGAATCT 60.045 40.000 3.36 0.00 0.00 2.40
2909 2986 5.505181 TTCCTTAAGAGCACCTGAATCTT 57.495 39.130 3.36 0.00 37.13 2.40
2910 2987 5.091261 TCCTTAAGAGCACCTGAATCTTC 57.909 43.478 3.36 0.00 35.09 2.87
2911 2988 4.780021 TCCTTAAGAGCACCTGAATCTTCT 59.220 41.667 3.36 0.00 35.09 2.85
2912 2989 5.958380 TCCTTAAGAGCACCTGAATCTTCTA 59.042 40.000 3.36 0.00 35.09 2.10
2913 2990 6.097554 TCCTTAAGAGCACCTGAATCTTCTAG 59.902 42.308 3.36 0.00 35.09 2.43
2914 2991 3.817709 AGAGCACCTGAATCTTCTAGC 57.182 47.619 0.00 0.00 0.00 3.42
2915 2992 2.433970 AGAGCACCTGAATCTTCTAGCC 59.566 50.000 0.00 0.00 0.00 3.93
2916 2993 1.137872 AGCACCTGAATCTTCTAGCCG 59.862 52.381 0.00 0.00 0.00 5.52
2917 2994 1.576356 CACCTGAATCTTCTAGCCGC 58.424 55.000 0.00 0.00 0.00 6.53
2918 2995 0.466124 ACCTGAATCTTCTAGCCGCC 59.534 55.000 0.00 0.00 0.00 6.13
2919 2996 0.465705 CCTGAATCTTCTAGCCGCCA 59.534 55.000 0.00 0.00 0.00 5.69
2920 2997 1.071385 CCTGAATCTTCTAGCCGCCAT 59.929 52.381 0.00 0.00 0.00 4.40
2921 2998 2.300152 CCTGAATCTTCTAGCCGCCATA 59.700 50.000 0.00 0.00 0.00 2.74
2922 2999 3.583806 CTGAATCTTCTAGCCGCCATAG 58.416 50.000 0.00 0.00 0.00 2.23
2923 3000 2.965831 TGAATCTTCTAGCCGCCATAGT 59.034 45.455 0.00 0.00 0.00 2.12
2924 3001 4.149598 TGAATCTTCTAGCCGCCATAGTA 58.850 43.478 0.00 0.00 0.00 1.82
2925 3002 4.218635 TGAATCTTCTAGCCGCCATAGTAG 59.781 45.833 0.00 0.00 0.00 2.57
2926 3003 3.503800 TCTTCTAGCCGCCATAGTAGA 57.496 47.619 0.00 0.00 0.00 2.59
2927 3004 3.147629 TCTTCTAGCCGCCATAGTAGAC 58.852 50.000 0.00 0.00 0.00 2.59
2928 3005 2.651382 TCTAGCCGCCATAGTAGACA 57.349 50.000 0.00 0.00 0.00 3.41
2929 3006 3.156288 TCTAGCCGCCATAGTAGACAT 57.844 47.619 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.515088 CGACAAGATGCTCGCGACT 60.515 57.895 3.71 0.00 0.00 4.18
1 2 1.514228 TCGACAAGATGCTCGCGAC 60.514 57.895 3.71 2.83 0.00 5.19
2 3 1.514228 GTCGACAAGATGCTCGCGA 60.514 57.895 11.55 9.26 0.00 5.87
3 4 2.839438 CGTCGACAAGATGCTCGCG 61.839 63.158 17.16 0.00 0.00 5.87
4 5 1.734359 GACGTCGACAAGATGCTCGC 61.734 60.000 17.16 0.00 39.47 5.03
5 6 1.134530 GGACGTCGACAAGATGCTCG 61.135 60.000 17.16 0.08 39.47 5.03
6 7 1.134530 CGGACGTCGACAAGATGCTC 61.135 60.000 17.16 0.00 42.43 4.26
7 8 1.154016 CGGACGTCGACAAGATGCT 60.154 57.895 17.16 0.00 42.43 3.79
30 31 2.579738 GAGGTGGAGGCGGAGAAC 59.420 66.667 0.00 0.00 0.00 3.01
32 33 3.673597 AGGAGGTGGAGGCGGAGA 61.674 66.667 0.00 0.00 0.00 3.71
37 38 3.005539 TCTGCAGGAGGTGGAGGC 61.006 66.667 15.13 0.00 44.63 4.70
43 44 1.145738 ACAAAATGGTCTGCAGGAGGT 59.854 47.619 15.13 0.00 0.00 3.85
110 111 2.046314 CCGGTCAGAATTGGCGGT 60.046 61.111 0.00 0.00 0.00 5.68
131 132 2.892425 GCAGGCGATCCTCGGTTG 60.892 66.667 0.00 0.00 41.93 3.77
183 184 1.324005 GGAGGAGGAGAAGGACGTGG 61.324 65.000 0.00 0.00 0.00 4.94
192 193 4.144727 GCGGGGAGGAGGAGGAGA 62.145 72.222 0.00 0.00 0.00 3.71
244 248 1.832912 GGGGCTACCTCTGGATGTG 59.167 63.158 0.00 0.00 36.80 3.21
245 249 1.762460 CGGGGCTACCTCTGGATGT 60.762 63.158 0.00 0.00 36.97 3.06
317 322 3.766151 CAACTTATCTAACGTCGGAGCA 58.234 45.455 0.00 0.00 0.00 4.26
324 329 2.733227 CGTCGGGCAACTTATCTAACGT 60.733 50.000 0.00 0.00 0.00 3.99
326 331 2.199236 CCGTCGGGCAACTTATCTAAC 58.801 52.381 2.34 0.00 0.00 2.34
348 353 2.025226 TCGCTAGTAGCTATGCCCCTAT 60.025 50.000 19.66 0.00 39.60 2.57
350 355 0.112606 TCGCTAGTAGCTATGCCCCT 59.887 55.000 19.66 0.00 39.60 4.79
383 409 2.436646 CCGCCACTTTCCGCTCAT 60.437 61.111 0.00 0.00 0.00 2.90
404 430 2.045926 CTCCCCTCCTGTTTGCCG 60.046 66.667 0.00 0.00 0.00 5.69
408 434 2.204306 CCCCCTCCCCTCCTGTTT 60.204 66.667 0.00 0.00 0.00 2.83
427 464 1.677820 CGAAACCCTACCCATCCACAC 60.678 57.143 0.00 0.00 0.00 3.82
455 492 2.294979 CCTGGTTATTTAAGCCGACCC 58.705 52.381 0.00 0.00 33.00 4.46
470 507 0.326618 ATGTAGTGCCCTAGCCTGGT 60.327 55.000 0.00 0.00 38.69 4.00
473 510 0.326618 ACCATGTAGTGCCCTAGCCT 60.327 55.000 0.00 0.00 38.69 4.58
488 525 3.771160 GCCACTCCGACGGACCAT 61.771 66.667 13.88 0.00 0.00 3.55
511 548 1.367599 GACGTCTCCTCCATCGTCGT 61.368 60.000 8.70 0.00 41.89 4.34
514 551 2.113433 CGGACGTCTCCTCCATCGT 61.113 63.158 16.46 0.00 39.21 3.73
534 571 2.828095 CATCAAATGCCCGGGCGA 60.828 61.111 39.00 29.69 45.51 5.54
535 572 2.709883 AACATCAAATGCCCGGGCG 61.710 57.895 39.00 25.40 45.51 6.13
537 574 1.257055 ACCAACATCAAATGCCCGGG 61.257 55.000 19.09 19.09 0.00 5.73
538 575 0.607620 AACCAACATCAAATGCCCGG 59.392 50.000 0.00 0.00 0.00 5.73
539 576 2.067766 CAAACCAACATCAAATGCCCG 58.932 47.619 0.00 0.00 0.00 6.13
540 577 2.425539 CCAAACCAACATCAAATGCCC 58.574 47.619 0.00 0.00 0.00 5.36
541 578 2.038295 TCCCAAACCAACATCAAATGCC 59.962 45.455 0.00 0.00 0.00 4.40
542 579 3.066380 GTCCCAAACCAACATCAAATGC 58.934 45.455 0.00 0.00 0.00 3.56
543 580 3.316283 CGTCCCAAACCAACATCAAATG 58.684 45.455 0.00 0.00 0.00 2.32
544 581 2.288763 GCGTCCCAAACCAACATCAAAT 60.289 45.455 0.00 0.00 0.00 2.32
545 582 1.067821 GCGTCCCAAACCAACATCAAA 59.932 47.619 0.00 0.00 0.00 2.69
546 583 0.671251 GCGTCCCAAACCAACATCAA 59.329 50.000 0.00 0.00 0.00 2.57
547 584 1.175983 GGCGTCCCAAACCAACATCA 61.176 55.000 0.00 0.00 0.00 3.07
549 586 1.906333 GGGCGTCCCAAACCAACAT 60.906 57.895 9.72 0.00 44.65 2.71
550 587 2.519780 GGGCGTCCCAAACCAACA 60.520 61.111 9.72 0.00 44.65 3.33
551 588 3.666253 CGGGCGTCCCAAACCAAC 61.666 66.667 14.17 0.00 45.83 3.77
552 589 4.958897 CCGGGCGTCCCAAACCAA 62.959 66.667 14.17 0.00 45.83 3.67
560 597 2.913060 ATCTAGAGCCGGGCGTCC 60.913 66.667 14.39 0.00 0.00 4.79
561 598 2.336809 CATCTAGAGCCGGGCGTC 59.663 66.667 14.39 11.53 0.00 5.19
562 599 3.917760 GCATCTAGAGCCGGGCGT 61.918 66.667 14.39 7.81 0.00 5.68
563 600 3.565910 GAGCATCTAGAGCCGGGCG 62.566 68.421 14.39 0.00 0.00 6.13
564 601 2.341911 GAGCATCTAGAGCCGGGC 59.658 66.667 12.11 12.11 0.00 6.13
573 610 7.857868 ACCTCCTGGTTCGTAAGAGCATCTA 62.858 48.000 0.00 0.00 46.17 1.98
580 617 1.891150 GTCACCTCCTGGTTCGTAAGA 59.109 52.381 0.00 0.00 46.05 2.10
610 649 4.643387 GGGCCGACTGGTGCAAGT 62.643 66.667 0.00 0.00 37.67 3.16
624 663 1.862602 AAAGTTTGGCGTCGATGGGC 61.863 55.000 6.79 6.41 0.00 5.36
627 666 1.399727 GGTCAAAGTTTGGCGTCGATG 60.400 52.381 15.47 0.00 35.72 3.84
629 668 0.462225 TGGTCAAAGTTTGGCGTCGA 60.462 50.000 15.47 0.00 35.72 4.20
716 755 4.765273 TCATATATGCCGCGGATACATTT 58.235 39.130 33.48 19.42 0.00 2.32
719 758 3.020984 TCTCATATATGCCGCGGATACA 58.979 45.455 33.48 18.89 0.00 2.29
749 796 2.425124 CACGCCGCAGAAACGTTG 60.425 61.111 0.00 0.00 38.09 4.10
763 810 2.554032 AGAAAATTTCCTGCCTGACACG 59.446 45.455 1.57 0.00 0.00 4.49
906 953 2.809601 GGTGCTGGTGCGAGTACG 60.810 66.667 0.00 0.00 43.34 3.67
907 954 2.434359 GGGTGCTGGTGCGAGTAC 60.434 66.667 0.00 0.00 43.34 2.73
908 955 4.063967 CGGGTGCTGGTGCGAGTA 62.064 66.667 0.00 0.00 43.34 2.59
1644 1706 3.066233 GCGTTCCTCCTCCTCGTCC 62.066 68.421 0.00 0.00 0.00 4.79
1765 1827 1.005215 CTTTGACAGCCCCTTCTCCAT 59.995 52.381 0.00 0.00 0.00 3.41
1947 2009 2.440796 AGATGCAACATGGCGGGG 60.441 61.111 0.00 0.00 36.28 5.73
1951 2013 0.815734 AAGAGCAGATGCAACATGGC 59.184 50.000 7.68 0.00 45.16 4.40
1952 2014 2.089201 TGAAGAGCAGATGCAACATGG 58.911 47.619 7.68 0.00 45.16 3.66
1966 2030 5.118817 GCGTACTAAGTTGTTTCCTGAAGAG 59.881 44.000 0.00 0.00 0.00 2.85
1988 2052 7.124347 TGTTAAACTGGTGAAGTAAATAGCG 57.876 36.000 0.00 0.00 38.56 4.26
1996 2060 6.625081 GCAAGAAGTTGTTAAACTGGTGAAGT 60.625 38.462 0.00 0.00 46.15 3.01
2068 2132 7.770897 AGCAAATCTACTGTAATTGACCCTAAG 59.229 37.037 10.20 0.00 0.00 2.18
2176 2240 6.402550 CCAGACACTACATAACAAGAATGCAC 60.403 42.308 0.00 0.00 0.00 4.57
2236 2303 5.204409 ACGAAGTCATACTACCACACAAA 57.796 39.130 0.00 0.00 29.74 2.83
2312 2379 3.117738 AGGGGAGGATAACTGCAGAATTG 60.118 47.826 23.35 0.00 39.67 2.32
2327 2394 1.376037 GTTCGCACTGAAGGGGAGG 60.376 63.158 0.00 0.00 37.23 4.30
2358 2425 2.478547 TTTTCGCAGTTTTTCCGACC 57.521 45.000 0.00 0.00 0.00 4.79
2377 2445 2.687700 AGCATGCTCGAGTTCAGATT 57.312 45.000 16.30 0.00 0.00 2.40
2413 2481 4.521256 TGGGCTTAGTCATGTAAACAAACC 59.479 41.667 0.00 0.00 0.00 3.27
2425 2493 4.502105 TGCAATTATCTGGGCTTAGTCA 57.498 40.909 0.00 0.00 0.00 3.41
2497 2565 4.707030 TGCTGGCAATTTAGAACTGATG 57.293 40.909 0.00 0.00 0.00 3.07
2498 2566 4.768968 AGTTGCTGGCAATTTAGAACTGAT 59.231 37.500 11.22 0.00 38.28 2.90
2533 2601 9.636789 AATTAAGGGTTACAGTACAAGAAAACT 57.363 29.630 0.00 0.00 0.00 2.66
2540 2608 8.851541 AAATCGAATTAAGGGTTACAGTACAA 57.148 30.769 0.00 0.00 0.00 2.41
2564 2632 4.202346 TGAGAATCGGATGTGCATGGATAA 60.202 41.667 0.00 0.00 38.61 1.75
2612 2680 7.067859 AGCTACCAGTAACGTGTTGAATAGATA 59.932 37.037 0.00 0.00 0.00 1.98
2632 2700 1.153269 GCCTGGCTTCTCAGCTACC 60.153 63.158 12.43 0.00 46.44 3.18
2636 2707 0.892814 ACTTTGCCTGGCTTCTCAGC 60.893 55.000 21.03 0.00 46.52 4.26
2687 2764 5.710513 AACATTGCATAGAAGAAGCACAA 57.289 34.783 0.00 0.00 38.11 3.33
2707 2784 9.066939 CATAGATTGCATAGATCGTACTGTAAC 57.933 37.037 0.00 0.00 0.00 2.50
2708 2785 8.793592 ACATAGATTGCATAGATCGTACTGTAA 58.206 33.333 0.00 0.00 0.00 2.41
2735 2812 1.759692 GTGGGGTAGGGTCGTAGGG 60.760 68.421 0.00 0.00 0.00 3.53
2736 2813 0.325016 AAGTGGGGTAGGGTCGTAGG 60.325 60.000 0.00 0.00 0.00 3.18
2737 2814 0.822164 CAAGTGGGGTAGGGTCGTAG 59.178 60.000 0.00 0.00 0.00 3.51
2738 2815 0.409092 TCAAGTGGGGTAGGGTCGTA 59.591 55.000 0.00 0.00 0.00 3.43
2739 2816 0.472352 TTCAAGTGGGGTAGGGTCGT 60.472 55.000 0.00 0.00 0.00 4.34
2740 2817 0.688487 TTTCAAGTGGGGTAGGGTCG 59.312 55.000 0.00 0.00 0.00 4.79
2741 2818 2.307686 TGATTTCAAGTGGGGTAGGGTC 59.692 50.000 0.00 0.00 0.00 4.46
2742 2819 2.354328 TGATTTCAAGTGGGGTAGGGT 58.646 47.619 0.00 0.00 0.00 4.34
2762 2839 5.102953 TGCATAGAAGAAGCACATAGGTT 57.897 39.130 0.00 0.00 41.46 3.50
2763 2840 4.760530 TGCATAGAAGAAGCACATAGGT 57.239 40.909 0.00 0.00 32.55 3.08
2764 2841 5.761726 TCATTGCATAGAAGAAGCACATAGG 59.238 40.000 0.00 0.00 38.11 2.57
2766 2843 8.152898 AGTATCATTGCATAGAAGAAGCACATA 58.847 33.333 0.00 0.00 38.11 2.29
2871 2948 7.050377 TCTTAAGGAATGTGCTCTAAGGAATG 58.950 38.462 1.85 0.00 0.00 2.67
2886 2963 5.707066 AGATTCAGGTGCTCTTAAGGAAT 57.293 39.130 1.85 1.87 0.00 3.01
2887 2964 5.249393 AGAAGATTCAGGTGCTCTTAAGGAA 59.751 40.000 1.85 0.00 29.64 3.36
2888 2965 4.780021 AGAAGATTCAGGTGCTCTTAAGGA 59.220 41.667 1.85 0.00 29.64 3.36
2889 2966 5.096443 AGAAGATTCAGGTGCTCTTAAGG 57.904 43.478 1.85 0.00 29.64 2.69
2890 2967 5.752955 GCTAGAAGATTCAGGTGCTCTTAAG 59.247 44.000 0.00 0.00 29.64 1.85
2891 2968 5.395768 GGCTAGAAGATTCAGGTGCTCTTAA 60.396 44.000 0.00 0.00 29.64 1.85
2892 2969 4.100189 GGCTAGAAGATTCAGGTGCTCTTA 59.900 45.833 0.00 0.00 29.64 2.10
2893 2970 3.118445 GGCTAGAAGATTCAGGTGCTCTT 60.118 47.826 0.00 0.00 32.09 2.85
2894 2971 2.433970 GGCTAGAAGATTCAGGTGCTCT 59.566 50.000 0.00 0.00 0.00 4.09
2895 2972 2.801342 CGGCTAGAAGATTCAGGTGCTC 60.801 54.545 0.00 0.00 0.00 4.26
2896 2973 1.137872 CGGCTAGAAGATTCAGGTGCT 59.862 52.381 0.00 0.00 0.00 4.40
2897 2974 1.576356 CGGCTAGAAGATTCAGGTGC 58.424 55.000 0.00 0.00 0.00 5.01
2898 2975 1.576356 GCGGCTAGAAGATTCAGGTG 58.424 55.000 0.00 0.00 0.00 4.00
2899 2976 0.466124 GGCGGCTAGAAGATTCAGGT 59.534 55.000 0.00 0.00 0.00 4.00
2900 2977 0.465705 TGGCGGCTAGAAGATTCAGG 59.534 55.000 11.43 0.00 0.00 3.86
2901 2978 2.540265 ATGGCGGCTAGAAGATTCAG 57.460 50.000 11.43 0.00 0.00 3.02
2902 2979 2.965831 ACTATGGCGGCTAGAAGATTCA 59.034 45.455 11.43 0.00 0.00 2.57
2903 2980 3.669251 ACTATGGCGGCTAGAAGATTC 57.331 47.619 11.43 0.00 0.00 2.52
2904 2981 4.218852 GTCTACTATGGCGGCTAGAAGATT 59.781 45.833 11.43 0.00 0.00 2.40
2905 2982 3.759618 GTCTACTATGGCGGCTAGAAGAT 59.240 47.826 11.43 0.00 0.00 2.40
2906 2983 3.147629 GTCTACTATGGCGGCTAGAAGA 58.852 50.000 11.43 4.08 0.00 2.87
2907 2984 2.885266 TGTCTACTATGGCGGCTAGAAG 59.115 50.000 11.43 4.76 0.00 2.85
2908 2985 2.940158 TGTCTACTATGGCGGCTAGAA 58.060 47.619 11.43 0.00 0.00 2.10
2909 2986 2.651382 TGTCTACTATGGCGGCTAGA 57.349 50.000 11.43 6.03 0.00 2.43


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

AutoCloner maintained by Alex Coulton.