Multiple sequence alignment - TraesCS6D01G253100

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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 TraesCS6D01G253100 chr6D 100.000 5137 0 0 1 5137 357349746 357344610 0.000000e+00 9487
1 TraesCS6D01G253100 chr6D 86.738 279 34 3 4594 4870 78794104 78793827 1.800000e-79 307
2 TraesCS6D01G253100 chr6A 96.289 4581 143 15 570 5137 499594451 499589885 0.000000e+00 7492
3 TraesCS6D01G253100 chr6A 89.897 485 29 10 36 513 499594939 499594468 1.580000e-169 606
4 TraesCS6D01G253100 chr6B 95.275 4360 151 17 98 4447 538951614 538947300 0.000000e+00 6859
5 TraesCS6D01G253100 chr6B 96.350 137 5 0 4438 4574 538946871 538946735 5.180000e-55 226
6 TraesCS6D01G253100 chr2D 83.438 477 54 9 4636 5088 633299395 633298920 2.210000e-113 420


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 TraesCS6D01G253100 chr6D 357344610 357349746 5136 True 9487.0 9487 100.0000 1 5137 1 chr6D.!!$R2 5136
1 TraesCS6D01G253100 chr6A 499589885 499594939 5054 True 4049.0 7492 93.0930 36 5137 2 chr6A.!!$R1 5101
2 TraesCS6D01G253100 chr6B 538946735 538951614 4879 True 3542.5 6859 95.8125 98 4574 2 chr6B.!!$R1 4476

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
969 980 0.110486 TGGACAGTTCAAGGCCCTTC 59.890 55.000 0.00 0.0 0.00 3.46 F
989 1000 1.003545 CAGATTAAGATTGGTGCGCCG 60.004 52.381 12.58 0.0 37.67 6.46 F
2748 2765 1.814394 GAGCAATTGCATGGTCACTCA 59.186 47.619 30.89 0.0 44.99 3.41 F
3524 3541 1.140312 TCACTCCTCCTGTTTTGGCT 58.860 50.000 0.00 0.0 0.00 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2448 2465 0.682852 TAGGTGGTGTGGTTTCTCCG 59.317 55.000 0.00 0.0 39.52 4.63 R
2799 2816 5.021033 TGCTGTGGTCAATCACAAAATTT 57.979 34.783 0.00 0.0 45.60 1.82 R
3708 3725 0.034670 AGCACCATGGCTTCTTCCTC 60.035 55.000 13.04 0.0 42.71 3.71 R
4757 5216 0.105039 GCCCGACCTATCTTCACCAG 59.895 60.000 0.00 0.0 0.00 4.00 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
19 20 1.180029 AGGGATGTTGTGCTTGATGC 58.820 50.000 0.00 0.00 43.25 3.91
20 21 0.174162 GGGATGTTGTGCTTGATGCC 59.826 55.000 0.00 0.00 42.00 4.40
21 22 1.180029 GGATGTTGTGCTTGATGCCT 58.820 50.000 0.00 0.00 42.00 4.75
22 23 1.133790 GGATGTTGTGCTTGATGCCTC 59.866 52.381 0.00 0.00 42.00 4.70
23 24 1.814394 GATGTTGTGCTTGATGCCTCA 59.186 47.619 0.00 0.00 42.00 3.86
24 25 1.913778 TGTTGTGCTTGATGCCTCAT 58.086 45.000 0.00 0.00 42.00 2.90
25 26 1.542472 TGTTGTGCTTGATGCCTCATG 59.458 47.619 0.00 0.00 42.00 3.07
28 29 2.719979 GCTTGATGCCTCATGCGG 59.280 61.111 12.78 0.00 45.60 5.69
29 30 2.842256 GCTTGATGCCTCATGCGGG 61.842 63.158 12.78 2.01 45.60 6.13
30 31 1.452651 CTTGATGCCTCATGCGGGT 60.453 57.895 3.43 0.00 45.60 5.28
31 32 1.001020 TTGATGCCTCATGCGGGTT 60.001 52.632 3.43 0.00 45.60 4.11
32 33 0.611618 TTGATGCCTCATGCGGGTTT 60.612 50.000 3.43 0.00 45.60 3.27
33 34 1.314534 TGATGCCTCATGCGGGTTTG 61.315 55.000 3.43 0.00 45.60 2.93
34 35 1.001020 ATGCCTCATGCGGGTTTGA 60.001 52.632 3.43 0.00 45.60 2.69
35 36 0.396139 ATGCCTCATGCGGGTTTGAT 60.396 50.000 3.43 0.00 45.60 2.57
36 37 0.611618 TGCCTCATGCGGGTTTGATT 60.612 50.000 3.43 0.00 45.60 2.57
37 38 0.179129 GCCTCATGCGGGTTTGATTG 60.179 55.000 3.43 0.00 0.00 2.67
38 39 1.462616 CCTCATGCGGGTTTGATTGA 58.537 50.000 0.00 0.00 0.00 2.57
39 40 2.026641 CCTCATGCGGGTTTGATTGAT 58.973 47.619 0.00 0.00 0.00 2.57
40 41 3.213506 CCTCATGCGGGTTTGATTGATA 58.786 45.455 0.00 0.00 0.00 2.15
41 42 3.003689 CCTCATGCGGGTTTGATTGATAC 59.996 47.826 0.00 0.00 0.00 2.24
42 43 3.879295 CTCATGCGGGTTTGATTGATACT 59.121 43.478 0.00 0.00 0.00 2.12
43 44 4.269183 TCATGCGGGTTTGATTGATACTT 58.731 39.130 0.00 0.00 0.00 2.24
44 45 4.096231 TCATGCGGGTTTGATTGATACTTG 59.904 41.667 0.00 0.00 0.00 3.16
45 46 3.680490 TGCGGGTTTGATTGATACTTGA 58.320 40.909 0.00 0.00 0.00 3.02
76 77 6.248433 ACTACACCAACTGATCAATGGATTT 58.752 36.000 26.18 15.11 37.66 2.17
120 121 2.093288 CCTCTGTGCCTATGCTTCTTGA 60.093 50.000 0.00 0.00 38.71 3.02
125 126 4.334552 TGTGCCTATGCTTCTTGAATCAA 58.665 39.130 0.00 0.00 38.71 2.57
186 191 3.924686 CGACTGGTAGTTTGTCATGTACC 59.075 47.826 0.00 0.00 36.27 3.34
209 214 1.270785 CCCATTGGCACCCTTTGAAAC 60.271 52.381 0.00 0.00 0.00 2.78
269 275 5.476599 TCCGTGATTTGATTTCTTCAACCAT 59.523 36.000 0.00 0.00 43.99 3.55
286 292 2.775384 ACCATTTGTATAAGGCGGAGGA 59.225 45.455 0.00 0.00 0.00 3.71
293 299 5.304686 TGTATAAGGCGGAGGAATGAAAT 57.695 39.130 0.00 0.00 0.00 2.17
410 417 5.461032 TTCAATAATGGTGGTGGTTCAAC 57.539 39.130 0.00 0.00 0.00 3.18
478 485 3.015145 TGGGAGTTGGGCTAGGGC 61.015 66.667 0.00 0.00 37.82 5.19
513 521 5.620206 TGTTACTGATGACATGTCTTGGTT 58.380 37.500 25.55 10.54 0.00 3.67
516 524 4.978099 ACTGATGACATGTCTTGGTTTCT 58.022 39.130 25.55 1.67 0.00 2.52
545 553 6.129194 CGATTAATCATTGTTCGTAGATGCGA 60.129 38.462 15.57 0.00 39.28 5.10
546 554 7.410835 CGATTAATCATTGTTCGTAGATGCGAT 60.411 37.037 15.57 0.00 40.76 4.58
547 555 5.582439 AATCATTGTTCGTAGATGCGATC 57.418 39.130 0.00 0.00 40.76 3.69
548 556 4.307443 TCATTGTTCGTAGATGCGATCT 57.693 40.909 0.00 4.45 40.76 2.75
549 557 5.432885 TCATTGTTCGTAGATGCGATCTA 57.567 39.130 0.00 2.81 40.76 1.98
550 558 5.452777 TCATTGTTCGTAGATGCGATCTAG 58.547 41.667 6.23 0.00 42.20 2.43
551 559 4.895224 TTGTTCGTAGATGCGATCTAGT 57.105 40.909 6.23 0.00 42.20 2.57
552 560 4.895224 TGTTCGTAGATGCGATCTAGTT 57.105 40.909 6.23 0.00 42.20 2.24
553 561 5.996669 TGTTCGTAGATGCGATCTAGTTA 57.003 39.130 6.23 0.00 42.20 2.24
554 562 6.555812 TGTTCGTAGATGCGATCTAGTTAT 57.444 37.500 6.23 0.00 42.20 1.89
555 563 6.371389 TGTTCGTAGATGCGATCTAGTTATG 58.629 40.000 6.23 0.00 42.20 1.90
556 564 4.971008 TCGTAGATGCGATCTAGTTATGC 58.029 43.478 6.23 0.00 42.20 3.14
557 565 4.454504 TCGTAGATGCGATCTAGTTATGCA 59.545 41.667 0.00 0.00 42.20 3.96
558 566 4.790651 CGTAGATGCGATCTAGTTATGCAG 59.209 45.833 0.00 0.00 42.20 4.41
559 567 4.862902 AGATGCGATCTAGTTATGCAGT 57.137 40.909 0.00 0.00 39.17 4.40
560 568 5.207110 AGATGCGATCTAGTTATGCAGTT 57.793 39.130 0.00 0.00 39.17 3.16
561 569 4.987285 AGATGCGATCTAGTTATGCAGTTG 59.013 41.667 0.00 0.00 39.17 3.16
562 570 3.457234 TGCGATCTAGTTATGCAGTTGG 58.543 45.455 0.00 0.00 0.00 3.77
563 571 3.118775 TGCGATCTAGTTATGCAGTTGGT 60.119 43.478 0.00 0.00 0.00 3.67
564 572 3.491267 GCGATCTAGTTATGCAGTTGGTC 59.509 47.826 0.00 0.00 0.00 4.02
565 573 4.051922 CGATCTAGTTATGCAGTTGGTCC 58.948 47.826 0.00 0.00 0.00 4.46
566 574 4.202161 CGATCTAGTTATGCAGTTGGTCCT 60.202 45.833 0.00 0.00 0.00 3.85
567 575 4.471904 TCTAGTTATGCAGTTGGTCCTG 57.528 45.455 0.00 0.00 35.49 3.86
568 576 3.838317 TCTAGTTATGCAGTTGGTCCTGT 59.162 43.478 0.00 0.00 34.84 4.00
611 619 5.794687 TTGATAGTTTTGACCATAGCACG 57.205 39.130 0.00 0.00 0.00 5.34
614 622 0.515564 GTTTTGACCATAGCACGCGT 59.484 50.000 5.58 5.58 0.00 6.01
755 766 2.094390 CCTTGATGCAACAATCCACCAG 60.094 50.000 10.06 0.00 0.00 4.00
777 788 8.579006 ACCAGCATACCATATAAATTTGACATG 58.421 33.333 0.00 0.00 0.00 3.21
842 853 3.768468 TGCATACATCACAAGCACATG 57.232 42.857 0.00 0.00 0.00 3.21
898 909 5.430886 TCTTCAGTGTCATGATATGGTTGG 58.569 41.667 0.00 0.00 0.00 3.77
912 923 7.581814 TGATATGGTTGGATTTCCATGACTTA 58.418 34.615 0.00 0.00 46.97 2.24
936 947 6.839124 ATTCACAGCATTTTCCTGACATTA 57.161 33.333 0.00 0.00 34.47 1.90
969 980 0.110486 TGGACAGTTCAAGGCCCTTC 59.890 55.000 0.00 0.00 0.00 3.46
983 994 3.529319 AGGCCCTTCAGATTAAGATTGGT 59.471 43.478 0.00 0.00 0.00 3.67
985 996 3.067320 GCCCTTCAGATTAAGATTGGTGC 59.933 47.826 0.00 0.00 0.00 5.01
986 997 3.313526 CCCTTCAGATTAAGATTGGTGCG 59.686 47.826 0.00 0.00 0.00 5.34
988 999 2.288666 TCAGATTAAGATTGGTGCGCC 58.711 47.619 10.11 10.11 0.00 6.53
989 1000 1.003545 CAGATTAAGATTGGTGCGCCG 60.004 52.381 12.58 0.00 37.67 6.46
1044 1055 3.555586 GGCGTAACTCTTGTCCAAAGGTA 60.556 47.826 0.00 0.00 0.00 3.08
1117 1129 3.244146 GCATGGGCATTTGGTTATATGCA 60.244 43.478 9.02 0.00 46.91 3.96
1571 1587 3.749665 TTGGTGCTTTTGGAAGGATTG 57.250 42.857 0.00 0.00 35.58 2.67
1792 1808 7.922699 AGGATAAATATAGCATAGTCCCTCC 57.077 40.000 0.00 0.00 0.00 4.30
2122 2139 6.348786 GCAATCTGATGCAACTGAAGAACTTA 60.349 38.462 7.61 0.00 45.70 2.24
2430 2447 5.690097 GCCAACATACTTCCAGGGATATGAA 60.690 44.000 13.34 0.00 0.00 2.57
2721 2738 5.938125 TCCAAGCAAAGATTCCTACAGTTAC 59.062 40.000 0.00 0.00 0.00 2.50
2748 2765 1.814394 GAGCAATTGCATGGTCACTCA 59.186 47.619 30.89 0.00 44.99 3.41
2799 2816 2.241941 TCTAATTGCTGGGAATGCCAGA 59.758 45.455 25.31 4.67 37.47 3.86
3129 3146 6.727824 TTCCTCGAATTCTTGAGAAATGAC 57.272 37.500 10.84 0.00 37.61 3.06
3130 3147 4.864806 TCCTCGAATTCTTGAGAAATGACG 59.135 41.667 10.84 2.71 37.61 4.35
3131 3148 4.864806 CCTCGAATTCTTGAGAAATGACGA 59.135 41.667 10.84 6.26 37.61 4.20
3269 3286 2.806945 TTAGATTGGGGTTCAGGCAG 57.193 50.000 0.00 0.00 0.00 4.85
3447 3464 6.923508 GCTAAAAACTGAAGCTTTGTTGGTAT 59.076 34.615 16.07 8.20 33.40 2.73
3524 3541 1.140312 TCACTCCTCCTGTTTTGGCT 58.860 50.000 0.00 0.00 0.00 4.75
3581 3598 6.855065 AGCTTCCCTTGAAGATTATCTGTGAC 60.855 42.308 6.50 0.00 44.54 3.67
3654 3671 3.303938 TCAAAGCTGGTTCCCATTTTGA 58.696 40.909 14.21 14.21 40.87 2.69
3701 3718 3.641437 TTGGAGATTTTGCGGAACTTG 57.359 42.857 0.00 0.00 0.00 3.16
3708 3725 2.368131 TTTGCGGAACTTGTGCGACG 62.368 55.000 0.00 0.00 45.26 5.12
3709 3726 3.033764 GCGGAACTTGTGCGACGA 61.034 61.111 0.00 0.00 45.26 4.20
3719 3736 2.095252 GTGCGACGAGGAAGAAGCC 61.095 63.158 0.00 0.00 0.00 4.35
3749 3766 2.380084 TTACCAGAACAGACCGATGC 57.620 50.000 0.00 0.00 0.00 3.91
3756 3773 0.606401 AACAGACCGATGCCTTGGTG 60.606 55.000 5.51 0.00 39.45 4.17
4044 4061 1.456705 GATCCTCCCACCGAGAGCT 60.457 63.158 0.00 0.00 41.63 4.09
4229 4246 4.406648 TGGATAGATGGTAGCAGTTGTG 57.593 45.455 0.00 0.00 0.00 3.33
4239 4256 0.461135 AGCAGTTGTGTTGCCCAAAG 59.539 50.000 0.00 0.00 42.48 2.77
4284 4301 6.378564 TCTTTATCATCCTCGAGTCTTTCAGT 59.621 38.462 12.31 0.00 0.00 3.41
4285 4302 7.556635 TCTTTATCATCCTCGAGTCTTTCAGTA 59.443 37.037 12.31 0.00 0.00 2.74
4286 4303 7.825331 TTATCATCCTCGAGTCTTTCAGTAT 57.175 36.000 12.31 0.00 0.00 2.12
4287 4304 8.919777 TTATCATCCTCGAGTCTTTCAGTATA 57.080 34.615 12.31 0.00 0.00 1.47
4355 4376 7.867752 TGTGTGTATAAGAAGTAAAAACAGCC 58.132 34.615 0.00 0.00 0.00 4.85
4531 4990 2.443255 TGCAAGAAAAGAGTTCCCTCCT 59.557 45.455 0.00 0.00 38.58 3.69
4588 5047 8.717821 TGGAACTTTATCAATAACTCTGAAACG 58.282 33.333 0.00 0.00 0.00 3.60
4592 5051 9.099454 ACTTTATCAATAACTCTGAAACGATCC 57.901 33.333 0.00 0.00 0.00 3.36
4684 5143 1.528542 CCATCTCCCTCGTCGCCTA 60.529 63.158 0.00 0.00 0.00 3.93
4753 5212 2.820787 CGAGGATCTACCCTATTCGCTT 59.179 50.000 0.00 0.00 40.05 4.68
4757 5216 3.580731 GATCTACCCTATTCGCTTCTGC 58.419 50.000 0.00 0.00 0.00 4.26
4764 5223 2.621338 CTATTCGCTTCTGCTGGTGAA 58.379 47.619 0.00 0.00 36.58 3.18
4775 5234 0.105039 GCTGGTGAAGATAGGTCGGG 59.895 60.000 0.00 0.00 0.00 5.14
4776 5235 0.105039 CTGGTGAAGATAGGTCGGGC 59.895 60.000 0.00 0.00 0.00 6.13
4778 5237 0.389757 GGTGAAGATAGGTCGGGCTC 59.610 60.000 0.00 0.00 0.00 4.70
4807 5266 2.464459 GCTTCAACGATGAGGGCGG 61.464 63.158 6.92 0.00 36.78 6.13
4898 5357 2.997897 AGAGGAGGTGGTCACGGC 60.998 66.667 0.00 0.00 0.00 5.68
4907 5366 3.463585 GGTCACGGCGTGGGGATA 61.464 66.667 36.30 16.95 33.87 2.59
4986 5445 3.407967 GGCTGGTTCGATCCCCCA 61.408 66.667 10.02 2.17 0.00 4.96
5006 5465 1.550976 ACGAGTTCCTCTTCATGGGAC 59.449 52.381 0.00 0.00 33.29 4.46
5009 5468 1.912043 AGTTCCTCTTCATGGGACCTG 59.088 52.381 0.00 0.00 33.58 4.00
5038 5497 2.153401 TGGTGGGAGTTGGACTGGG 61.153 63.158 0.00 0.00 0.00 4.45
5039 5498 1.846124 GGTGGGAGTTGGACTGGGA 60.846 63.158 0.00 0.00 0.00 4.37
5040 5499 1.679898 GTGGGAGTTGGACTGGGAG 59.320 63.158 0.00 0.00 0.00 4.30
5041 5500 2.224159 TGGGAGTTGGACTGGGAGC 61.224 63.158 0.00 0.00 0.00 4.70
5042 5501 1.920835 GGGAGTTGGACTGGGAGCT 60.921 63.158 0.00 0.00 0.00 4.09
5043 5502 1.599576 GGAGTTGGACTGGGAGCTC 59.400 63.158 4.71 4.71 0.00 4.09
5053 5512 0.324738 CTGGGAGCTCTGTACAGGGA 60.325 60.000 27.25 5.75 0.00 4.20
5066 5525 0.930726 ACAGGGAAAACCCTTGGTCA 59.069 50.000 4.95 0.00 45.57 4.02
5067 5526 1.133482 ACAGGGAAAACCCTTGGTCAG 60.133 52.381 4.95 0.00 45.57 3.51
5095 5554 3.118454 CACGACATCGGTGGTGCC 61.118 66.667 0.00 0.00 44.81 5.01
5096 5555 3.621805 ACGACATCGGTGGTGCCA 61.622 61.111 0.00 0.00 44.95 4.92
5118 5577 4.530857 CGCCGGATCCCCAGTGAC 62.531 72.222 5.05 0.00 0.00 3.67
5126 5585 3.402681 CCCCAGTGACGGAGCCAT 61.403 66.667 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.180029 GCATCAAGCACAACATCCCT 58.820 50.000 0.00 0.00 44.79 4.20
1 2 3.727419 GCATCAAGCACAACATCCC 57.273 52.632 0.00 0.00 44.79 3.85
4 5 5.534563 GCATGAGGCATCAAGCACAACAT 62.535 47.826 22.16 0.00 46.80 2.71
5 6 4.285966 GCATGAGGCATCAAGCACAACA 62.286 50.000 22.16 0.00 46.80 3.33
6 7 1.734707 GCATGAGGCATCAAGCACAAC 60.735 52.381 22.16 0.00 46.80 3.32
8 9 2.186155 GCATGAGGCATCAAGCACA 58.814 52.632 22.16 0.00 46.80 4.57
11 12 2.719979 CCGCATGAGGCATCAAGC 59.280 61.111 17.84 17.84 44.71 4.01
12 13 1.033746 AACCCGCATGAGGCATCAAG 61.034 55.000 10.45 1.09 45.17 3.02
13 14 0.611618 AAACCCGCATGAGGCATCAA 60.612 50.000 10.45 0.00 45.17 2.57
14 15 1.001020 AAACCCGCATGAGGCATCA 60.001 52.632 10.45 2.36 45.17 3.07
15 16 1.031571 TCAAACCCGCATGAGGCATC 61.032 55.000 10.45 0.00 45.17 3.91
16 17 0.396139 ATCAAACCCGCATGAGGCAT 60.396 50.000 10.45 0.00 45.17 4.40
17 18 0.611618 AATCAAACCCGCATGAGGCA 60.612 50.000 10.45 0.00 45.17 4.75
18 19 0.179129 CAATCAAACCCGCATGAGGC 60.179 55.000 10.45 0.00 39.90 4.70
19 20 1.462616 TCAATCAAACCCGCATGAGG 58.537 50.000 8.78 8.78 0.00 3.86
20 21 3.879295 AGTATCAATCAAACCCGCATGAG 59.121 43.478 0.00 0.00 0.00 2.90
21 22 3.884895 AGTATCAATCAAACCCGCATGA 58.115 40.909 0.00 0.00 0.00 3.07
22 23 4.096231 TCAAGTATCAATCAAACCCGCATG 59.904 41.667 0.00 0.00 0.00 4.06
23 24 4.269183 TCAAGTATCAATCAAACCCGCAT 58.731 39.130 0.00 0.00 0.00 4.73
24 25 3.680490 TCAAGTATCAATCAAACCCGCA 58.320 40.909 0.00 0.00 0.00 5.69
25 26 4.900635 ATCAAGTATCAATCAAACCCGC 57.099 40.909 0.00 0.00 0.00 6.13
26 27 6.918892 TGTATCAAGTATCAATCAAACCCG 57.081 37.500 0.00 0.00 0.00 5.28
36 37 9.811995 GTTGGTGTAGTATTGTATCAAGTATCA 57.188 33.333 0.00 0.00 0.00 2.15
38 39 9.817809 CAGTTGGTGTAGTATTGTATCAAGTAT 57.182 33.333 0.00 0.00 0.00 2.12
39 40 9.027202 TCAGTTGGTGTAGTATTGTATCAAGTA 57.973 33.333 0.00 0.00 0.00 2.24
40 41 7.903145 TCAGTTGGTGTAGTATTGTATCAAGT 58.097 34.615 0.00 0.00 0.00 3.16
41 42 8.948631 ATCAGTTGGTGTAGTATTGTATCAAG 57.051 34.615 0.00 0.00 0.00 3.02
42 43 8.536175 TGATCAGTTGGTGTAGTATTGTATCAA 58.464 33.333 0.00 0.00 0.00 2.57
43 44 8.073467 TGATCAGTTGGTGTAGTATTGTATCA 57.927 34.615 0.00 0.00 0.00 2.15
44 45 8.942338 TTGATCAGTTGGTGTAGTATTGTATC 57.058 34.615 0.00 0.00 0.00 2.24
45 46 9.330063 CATTGATCAGTTGGTGTAGTATTGTAT 57.670 33.333 0.00 0.00 0.00 2.29
56 57 5.121142 GCAAAAATCCATTGATCAGTTGGTG 59.879 40.000 20.30 14.21 0.00 4.17
76 77 5.453198 GGAAAGGAGAATGGAGTTTTGCAAA 60.453 40.000 8.05 8.05 0.00 3.68
120 121 4.589216 TTTGCAACTGCTAAGCTTGATT 57.411 36.364 9.86 0.00 42.66 2.57
125 126 5.010012 ACATACTTTTTGCAACTGCTAAGCT 59.990 36.000 0.00 0.00 42.66 3.74
209 214 8.918961 AATAAAGAAACGAGACATAGTCTGAG 57.081 34.615 4.12 1.53 43.53 3.35
269 275 4.764050 TCATTCCTCCGCCTTATACAAA 57.236 40.909 0.00 0.00 0.00 2.83
286 292 5.653255 ATAGGCCAGTAGACCATTTCATT 57.347 39.130 5.01 0.00 0.00 2.57
293 299 5.216622 AGTTGATTATAGGCCAGTAGACCA 58.783 41.667 5.01 0.00 0.00 4.02
352 358 1.576421 GCAGCCGGTCTCTTTGTTG 59.424 57.895 1.90 0.00 0.00 3.33
410 417 4.457603 TCAACTGATTGGTCAAAATACGGG 59.542 41.667 0.00 0.00 36.39 5.28
440 447 2.576191 AGTGACCCAGCTTAGCCAATAA 59.424 45.455 0.00 0.00 0.00 1.40
457 464 0.909610 CCTAGCCCAACTCCCAGTGA 60.910 60.000 0.00 0.00 0.00 3.41
478 485 6.266330 TGTCATCAGTAACAGAGAGGATATGG 59.734 42.308 0.00 0.00 0.00 2.74
487 495 5.579904 CCAAGACATGTCATCAGTAACAGAG 59.420 44.000 27.02 0.11 0.00 3.35
513 521 7.359262 ACGAACAATGATTAATCGTCAAGAA 57.641 32.000 10.59 0.00 42.48 2.52
516 524 8.539674 CATCTACGAACAATGATTAATCGTCAA 58.460 33.333 17.03 9.70 44.65 3.18
545 553 4.471386 ACAGGACCAACTGCATAACTAGAT 59.529 41.667 0.00 0.00 42.21 1.98
546 554 3.838317 ACAGGACCAACTGCATAACTAGA 59.162 43.478 0.00 0.00 42.21 2.43
547 555 4.207891 ACAGGACCAACTGCATAACTAG 57.792 45.455 0.00 0.00 42.21 2.57
548 556 5.247564 ACTTACAGGACCAACTGCATAACTA 59.752 40.000 0.00 0.00 42.21 2.24
549 557 4.041691 ACTTACAGGACCAACTGCATAACT 59.958 41.667 0.00 0.00 42.21 2.24
550 558 4.154195 CACTTACAGGACCAACTGCATAAC 59.846 45.833 0.00 0.00 42.21 1.89
551 559 4.202419 ACACTTACAGGACCAACTGCATAA 60.202 41.667 0.00 0.00 42.21 1.90
552 560 3.326588 ACACTTACAGGACCAACTGCATA 59.673 43.478 0.00 0.00 42.21 3.14
553 561 2.106511 ACACTTACAGGACCAACTGCAT 59.893 45.455 0.00 0.00 42.21 3.96
554 562 1.488812 ACACTTACAGGACCAACTGCA 59.511 47.619 0.00 0.00 42.21 4.41
555 563 2.256117 ACACTTACAGGACCAACTGC 57.744 50.000 0.00 0.00 42.21 4.40
556 564 4.315803 CCTTACACTTACAGGACCAACTG 58.684 47.826 0.00 0.00 44.03 3.16
557 565 3.326880 CCCTTACACTTACAGGACCAACT 59.673 47.826 0.00 0.00 0.00 3.16
558 566 3.558533 CCCCTTACACTTACAGGACCAAC 60.559 52.174 0.00 0.00 0.00 3.77
559 567 2.640826 CCCCTTACACTTACAGGACCAA 59.359 50.000 0.00 0.00 0.00 3.67
560 568 2.158127 TCCCCTTACACTTACAGGACCA 60.158 50.000 0.00 0.00 0.00 4.02
561 569 2.500504 CTCCCCTTACACTTACAGGACC 59.499 54.545 0.00 0.00 0.00 4.46
562 570 3.171528 ACTCCCCTTACACTTACAGGAC 58.828 50.000 0.00 0.00 0.00 3.85
563 571 3.555117 ACTCCCCTTACACTTACAGGA 57.445 47.619 0.00 0.00 0.00 3.86
564 572 4.324267 CAAACTCCCCTTACACTTACAGG 58.676 47.826 0.00 0.00 0.00 4.00
565 573 3.751698 GCAAACTCCCCTTACACTTACAG 59.248 47.826 0.00 0.00 0.00 2.74
566 574 3.393278 AGCAAACTCCCCTTACACTTACA 59.607 43.478 0.00 0.00 0.00 2.41
567 575 4.017177 AGCAAACTCCCCTTACACTTAC 57.983 45.455 0.00 0.00 0.00 2.34
568 576 4.717279 AAGCAAACTCCCCTTACACTTA 57.283 40.909 0.00 0.00 0.00 2.24
611 619 1.000060 TCATAACTATGCCGGGTACGC 60.000 52.381 2.18 0.00 33.95 4.42
614 622 5.067273 CCATTTTCATAACTATGCCGGGTA 58.933 41.667 2.18 0.00 33.76 3.69
755 766 7.060979 CGCACATGTCAAATTTATATGGTATGC 59.939 37.037 0.00 10.38 0.00 3.14
777 788 2.413837 ACAATAGTCCAGTCAACGCAC 58.586 47.619 0.00 0.00 0.00 5.34
870 881 6.765036 ACCATATCATGACACTGAAGAATGAC 59.235 38.462 0.00 0.00 30.53 3.06
898 909 6.855836 TGCTGTGAATTAAGTCATGGAAATC 58.144 36.000 9.08 0.00 0.00 2.17
912 923 5.733620 ATGTCAGGAAAATGCTGTGAATT 57.266 34.783 0.00 0.00 37.12 2.17
969 980 1.003545 CGGCGCACCAATCTTAATCTG 60.004 52.381 10.83 0.00 34.57 2.90
983 994 3.932580 ATCGACAAAGAGCGGCGCA 62.933 57.895 35.02 10.27 0.00 6.09
985 996 2.697425 CATCGACAAAGAGCGGCG 59.303 61.111 0.51 0.51 0.00 6.46
986 997 3.093278 CCATCGACAAAGAGCGGC 58.907 61.111 0.00 0.00 0.00 6.53
988 999 1.351430 TTCGCCATCGACAAAGAGCG 61.351 55.000 0.00 0.00 45.43 5.03
989 1000 0.095417 GTTCGCCATCGACAAAGAGC 59.905 55.000 0.00 0.00 45.43 4.09
1044 1055 9.981460 AAAAATGGAGAGGTAATTCAGTATTCT 57.019 29.630 0.00 0.00 0.00 2.40
1117 1129 8.773033 AGAGGGTTTCATCTTGCATAATAAAT 57.227 30.769 0.00 0.00 28.47 1.40
1363 1379 3.007398 CCTGTATTCCTGCTCTACATCCC 59.993 52.174 0.00 0.00 0.00 3.85
1592 1608 4.326826 TCTCCAGTAATTGCCTGAAACAG 58.673 43.478 8.16 0.00 31.38 3.16
1792 1808 3.853831 TTGCATGATAAGCAACACTGG 57.146 42.857 0.00 0.00 46.13 4.00
2122 2139 3.881688 GCCTGCATGAATGTCTGAAGTAT 59.118 43.478 0.00 0.00 0.00 2.12
2430 2447 6.375830 TCTCCGGACATACTACTCTGATAT 57.624 41.667 0.00 0.00 0.00 1.63
2448 2465 0.682852 TAGGTGGTGTGGTTTCTCCG 59.317 55.000 0.00 0.00 39.52 4.63
2598 2615 6.636850 TCATCGCAAAGTTTTCTAGCTTTTTC 59.363 34.615 0.00 0.00 33.19 2.29
2748 2765 5.873712 TGAAACATTGTGCAAACTTGACATT 59.126 32.000 0.00 0.00 0.00 2.71
2799 2816 5.021033 TGCTGTGGTCAATCACAAAATTT 57.979 34.783 0.00 0.00 45.60 1.82
3129 3146 2.851805 TCATACTGTAGCTGCTGTCG 57.148 50.000 17.14 10.45 0.00 4.35
3130 3147 3.308323 GCTTTCATACTGTAGCTGCTGTC 59.692 47.826 17.14 6.08 0.00 3.51
3131 3148 3.055530 AGCTTTCATACTGTAGCTGCTGT 60.056 43.478 17.68 17.68 42.07 4.40
3295 3312 2.094417 GCCTGAGATACGCACAAAACTC 59.906 50.000 0.00 0.00 0.00 3.01
3401 3418 0.317479 CCGAACTGAGGAAGGACGTT 59.683 55.000 0.00 0.00 0.00 3.99
3447 3464 3.007940 AGGTGTCGAATCAGTTCATGGAA 59.992 43.478 0.00 0.00 33.86 3.53
3524 3541 6.127338 CCTCGATATCTTCAGGTGCCAATATA 60.127 42.308 0.34 0.00 0.00 0.86
3581 3598 2.289820 CACATCAGCATCGGATGAAAGG 59.710 50.000 21.69 9.45 43.62 3.11
3654 3671 0.959553 TCGACGAAGCTTCCTTCTGT 59.040 50.000 20.62 11.94 44.24 3.41
3701 3718 2.095252 GGCTTCTTCCTCGTCGCAC 61.095 63.158 0.00 0.00 0.00 5.34
3708 3725 0.034670 AGCACCATGGCTTCTTCCTC 60.035 55.000 13.04 0.00 42.71 3.71
3709 3726 2.081955 AGCACCATGGCTTCTTCCT 58.918 52.632 13.04 0.00 42.71 3.36
3719 3736 5.065218 GTCTGTTCTGGTAATAAGCACCATG 59.935 44.000 0.00 0.00 44.89 3.66
3756 3773 2.216898 GTCCAGATACTCTGCAATGGC 58.783 52.381 0.00 0.00 42.98 4.40
3773 3790 1.628846 TCTTTAGGGCTTCCTGTGTCC 59.371 52.381 0.00 0.00 41.87 4.02
3881 3898 3.311110 GACAGGTCCACGAGGGCA 61.311 66.667 5.68 0.00 43.06 5.36
4010 4027 0.952280 GATCCTCTATCACGTCGGCA 59.048 55.000 0.00 0.00 34.46 5.69
4044 4061 3.664025 CTGGCCGCCTGTGAATCGA 62.664 63.158 11.61 0.00 0.00 3.59
4229 4246 2.145536 CAAGCATTTCCTTTGGGCAAC 58.854 47.619 0.00 0.00 0.00 4.17
4239 4256 3.760684 AGAACATCTCACCAAGCATTTCC 59.239 43.478 0.00 0.00 0.00 3.13
4301 4318 4.077300 TCAGCAAGACTCACAAATCTGT 57.923 40.909 0.00 0.00 35.63 3.41
4311 4328 5.063186 CACACATCTACAATCAGCAAGACTC 59.937 44.000 0.00 0.00 0.00 3.36
4349 4366 3.199071 TGGATGAAACTATACCGGCTGTT 59.801 43.478 0.00 0.00 0.00 3.16
4355 4376 6.018751 CACAAGACATGGATGAAACTATACCG 60.019 42.308 0.00 0.00 0.00 4.02
4531 4990 8.463055 AATTACTAATCCTATCCCAAGGCATA 57.537 34.615 0.00 0.00 36.51 3.14
4575 5034 2.483188 GGCCGGATCGTTTCAGAGTTAT 60.483 50.000 5.05 0.00 0.00 1.89
4577 5036 0.391263 GGCCGGATCGTTTCAGAGTT 60.391 55.000 5.05 0.00 0.00 3.01
4582 5041 3.006728 AGGGGCCGGATCGTTTCA 61.007 61.111 5.05 0.00 0.00 2.69
4583 5042 2.513897 CAGGGGCCGGATCGTTTC 60.514 66.667 5.05 0.00 0.00 2.78
4708 5167 1.517257 CTCTTCACCAGCGGCTACG 60.517 63.158 0.26 0.00 44.63 3.51
4753 5212 1.751351 CGACCTATCTTCACCAGCAGA 59.249 52.381 0.00 0.00 0.00 4.26
4757 5216 0.105039 GCCCGACCTATCTTCACCAG 59.895 60.000 0.00 0.00 0.00 4.00
4785 5244 1.026718 CCCTCATCGTTGAAGCCACC 61.027 60.000 0.00 0.00 0.00 4.61
4787 5246 1.377202 GCCCTCATCGTTGAAGCCA 60.377 57.895 6.83 0.00 0.00 4.75
4794 5253 4.814294 GACGCCGCCCTCATCGTT 62.814 66.667 0.00 0.00 35.12 3.85
4872 5331 2.681778 ACCTCCTCTGTGCCCTCG 60.682 66.667 0.00 0.00 0.00 4.63
4904 5363 1.425448 CCATGGGGAAGAAGGGGTATC 59.575 57.143 2.85 0.00 35.59 2.24
4905 5364 1.534338 CCATGGGGAAGAAGGGGTAT 58.466 55.000 2.85 0.00 35.59 2.73
4906 5365 1.286305 GCCATGGGGAAGAAGGGGTA 61.286 60.000 15.13 0.00 35.59 3.69
4907 5366 2.626467 GCCATGGGGAAGAAGGGGT 61.626 63.158 15.13 0.00 35.59 4.95
4911 5370 0.554792 ATCTGGCCATGGGGAAGAAG 59.445 55.000 15.13 0.00 33.63 2.85
5006 5465 2.173669 CACCACGCTAATCGCCAGG 61.174 63.158 0.00 0.00 43.23 4.45
5009 5468 2.895372 CCCACCACGCTAATCGCC 60.895 66.667 0.00 0.00 43.23 5.54
5038 5497 2.701107 GGTTTTCCCTGTACAGAGCTC 58.299 52.381 24.68 5.27 0.00 4.09
5039 5498 2.861147 GGTTTTCCCTGTACAGAGCT 57.139 50.000 24.68 0.00 0.00 4.09
5053 5512 2.200337 GCCGCTGACCAAGGGTTTT 61.200 57.895 0.00 0.00 35.25 2.43


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

AutoCloner maintained by Alex Coulton.