Multiple sequence alignment - TraesCS5D01G268100

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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 TraesCS5D01G268100 chr5D 100.000 3182 0 0 1 3182 371635300 371632119 0.000000e+00 5877.0
1 TraesCS5D01G268100 chr5D 85.910 511 68 2 2547 3053 238133249 238133759 2.790000e-150 542.0
2 TraesCS5D01G268100 chr5B 87.869 2572 152 63 9 2501 441528898 441526408 0.000000e+00 2874.0
3 TraesCS5D01G268100 chr2D 85.797 866 71 20 1370 2196 296704652 296705504 0.000000e+00 870.0
4 TraesCS5D01G268100 chr2D 85.737 638 64 5 2565 3177 423273034 423273669 0.000000e+00 649.0
5 TraesCS5D01G268100 chr2D 94.954 218 11 0 1157 1374 296699401 296699618 3.040000e-90 342.0
6 TraesCS5D01G268100 chr2D 93.617 47 1 2 2500 2545 419358098 419358143 5.700000e-08 69.4
7 TraesCS5D01G268100 chr2A 91.479 622 37 8 850 1468 369204509 369203901 0.000000e+00 841.0
8 TraesCS5D01G268100 chr2A 88.475 564 43 10 1460 2008 369202582 369202026 0.000000e+00 662.0
9 TraesCS5D01G268100 chr1B 88.746 622 64 4 2565 3182 641871401 641872020 0.000000e+00 756.0
10 TraesCS5D01G268100 chr7B 86.698 639 79 4 2548 3182 562478815 562479451 0.000000e+00 704.0
11 TraesCS5D01G268100 chr7B 85.795 528 72 2 2656 3182 587638529 587639054 9.970000e-155 556.0
12 TraesCS5D01G268100 chr5A 87.263 581 66 6 2605 3180 575213199 575212622 0.000000e+00 656.0
13 TraesCS5D01G268100 chr7D 85.948 612 75 6 2575 3182 238969103 238968499 0.000000e+00 643.0
14 TraesCS5D01G268100 chr7D 85.312 640 60 6 2547 3182 486221585 486220976 5.790000e-177 630.0
15 TraesCS5D01G268100 chr2B 84.914 643 84 10 2547 3182 641874652 641874016 3.460000e-179 638.0
16 TraesCS5D01G268100 chr3B 84.516 620 83 9 2569 3182 628719622 628719010 4.540000e-168 601.0
17 TraesCS5D01G268100 chr4D 87.500 64 8 0 112 175 140889136 140889199 1.220000e-09 75.0


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 TraesCS5D01G268100 chr5D 371632119 371635300 3181 True 5877.0 5877 100.000 1 3182 1 chr5D.!!$R1 3181
1 TraesCS5D01G268100 chr5D 238133249 238133759 510 False 542.0 542 85.910 2547 3053 1 chr5D.!!$F1 506
2 TraesCS5D01G268100 chr5B 441526408 441528898 2490 True 2874.0 2874 87.869 9 2501 1 chr5B.!!$R1 2492
3 TraesCS5D01G268100 chr2D 296704652 296705504 852 False 870.0 870 85.797 1370 2196 1 chr2D.!!$F2 826
4 TraesCS5D01G268100 chr2D 423273034 423273669 635 False 649.0 649 85.737 2565 3177 1 chr2D.!!$F4 612
5 TraesCS5D01G268100 chr2A 369202026 369204509 2483 True 751.5 841 89.977 850 2008 2 chr2A.!!$R1 1158
6 TraesCS5D01G268100 chr1B 641871401 641872020 619 False 756.0 756 88.746 2565 3182 1 chr1B.!!$F1 617
7 TraesCS5D01G268100 chr7B 562478815 562479451 636 False 704.0 704 86.698 2548 3182 1 chr7B.!!$F1 634
8 TraesCS5D01G268100 chr7B 587638529 587639054 525 False 556.0 556 85.795 2656 3182 1 chr7B.!!$F2 526
9 TraesCS5D01G268100 chr5A 575212622 575213199 577 True 656.0 656 87.263 2605 3180 1 chr5A.!!$R1 575
10 TraesCS5D01G268100 chr7D 238968499 238969103 604 True 643.0 643 85.948 2575 3182 1 chr7D.!!$R1 607
11 TraesCS5D01G268100 chr7D 486220976 486221585 609 True 630.0 630 85.312 2547 3182 1 chr7D.!!$R2 635
12 TraesCS5D01G268100 chr2B 641874016 641874652 636 True 638.0 638 84.914 2547 3182 1 chr2B.!!$R1 635
13 TraesCS5D01G268100 chr3B 628719010 628719622 612 True 601.0 601 84.516 2569 3182 1 chr3B.!!$R1 613

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
992 1068 0.110238 CAATCCGCAACCACGTCTTG 60.11 55.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2504 3955 0.03759 ATTTGCAAGTCCAGGCCGTA 59.962 50.0 0.0 0.0 0.0 4.02 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
101 104 1.081376 CATCGTCGCTCCGTATCCC 60.081 63.158 0.00 0.00 0.00 3.85
112 115 2.116383 CGTATCCCGGAGCAAGAGT 58.884 57.895 0.73 0.00 0.00 3.24
123 126 1.966451 GCAAGAGTTGGTCCGGTGG 60.966 63.158 0.00 0.00 0.00 4.61
131 134 1.122632 TTGGTCCGGTGGTGCTCTTA 61.123 55.000 0.00 0.00 0.00 2.10
144 147 1.522569 CTCTTAGAGCGGGGGTTGG 59.477 63.158 0.00 0.00 0.00 3.77
183 186 3.213402 CCGCGAGTCTCCTCCTCC 61.213 72.222 8.23 0.00 33.93 4.30
186 189 2.684104 CGAGTCTCCTCCTCCCCA 59.316 66.667 0.00 0.00 33.93 4.96
538 589 1.648467 GGCAAGATCAACAGGACGCC 61.648 60.000 0.00 0.00 0.00 5.68
541 592 1.827399 AAGATCAACAGGACGCCGGT 61.827 55.000 1.90 0.00 32.35 5.28
587 638 2.785921 CTAGCGTCGACGAGCAGT 59.214 61.111 39.74 19.82 43.02 4.40
606 657 4.100084 CAGAGTGGCGGCCCATCA 62.100 66.667 17.97 0.00 44.51 3.07
612 663 4.740822 GGCGGCCCATCAGGTGTT 62.741 66.667 8.12 0.00 38.26 3.32
613 664 2.676471 GCGGCCCATCAGGTGTTT 60.676 61.111 0.00 0.00 38.26 2.83
614 665 2.993471 GCGGCCCATCAGGTGTTTG 61.993 63.158 0.00 0.00 38.26 2.93
615 666 1.303236 CGGCCCATCAGGTGTTTGA 60.303 57.895 0.00 0.00 38.26 2.69
625 676 0.591170 AGGTGTTTGACGAAATGCCG 59.409 50.000 0.00 0.00 0.00 5.69
630 681 0.312416 TTTGACGAAATGCCGGGTTG 59.688 50.000 2.18 0.00 0.00 3.77
655 706 1.244019 GCCCAAAATGCGTCTGTCCT 61.244 55.000 0.00 0.00 0.00 3.85
658 709 0.453282 CAAAATGCGTCTGTCCTGCG 60.453 55.000 0.00 0.00 0.00 5.18
663 714 2.738521 CGTCTGTCCTGCGTTGGG 60.739 66.667 0.00 0.00 0.00 4.12
674 725 1.153249 GCGTTGGGCATACTGGCTA 60.153 57.895 0.55 0.00 43.20 3.93
695 747 6.349860 GGCTAACCTAAATGAAAAACGGACAT 60.350 38.462 0.00 0.00 0.00 3.06
697 749 5.385509 ACCTAAATGAAAAACGGACATGG 57.614 39.130 0.00 0.00 0.00 3.66
701 753 5.467035 AAATGAAAAACGGACATGGATGT 57.533 34.783 0.00 0.00 45.16 3.06
710 762 2.516448 ACATGGATGTCCGATCGGT 58.484 52.632 32.15 15.04 35.87 4.69
726 778 1.135774 TCGGTCGATCGAAACAGACAG 60.136 52.381 20.25 7.76 36.12 3.51
731 783 4.376109 GGTCGATCGAAACAGACAGAAAAC 60.376 45.833 21.31 2.16 35.49 2.43
733 785 3.424198 CGATCGAAACAGACAGAAAACGA 59.576 43.478 10.26 0.00 0.00 3.85
746 798 2.032426 AGAAAACGAACAAAATCCGCGT 59.968 40.909 4.92 0.00 36.68 6.01
748 800 1.223187 AACGAACAAAATCCGCGTCT 58.777 45.000 4.92 0.00 33.66 4.18
758 810 1.289109 ATCCGCGTCTGTTTGGTTCG 61.289 55.000 4.92 0.00 0.00 3.95
762 814 1.082756 CGTCTGTTTGGTTCGCTGC 60.083 57.895 0.00 0.00 0.00 5.25
769 821 1.377366 TTTGGTTCGCTGCGTTGGAA 61.377 50.000 22.48 5.83 0.00 3.53
773 825 0.729140 GTTCGCTGCGTTGGAATTGG 60.729 55.000 22.48 0.00 0.00 3.16
779 831 2.414161 GCTGCGTTGGAATTGGTCTAAC 60.414 50.000 0.00 0.00 42.68 2.34
987 1063 2.749865 ATCGCAATCCGCAACCACG 61.750 57.895 0.00 0.00 42.60 4.94
992 1068 0.110238 CAATCCGCAACCACGTCTTG 60.110 55.000 0.00 0.00 0.00 3.02
1003 1079 1.078759 CACGTCTTGGACCTCGATGC 61.079 60.000 0.00 0.00 0.00 3.91
1468 2877 3.060615 CGAAGGTCGACGGGGAGT 61.061 66.667 9.92 0.00 43.74 3.85
1644 3062 2.488820 GACCTGTACGCGAGGGTC 59.511 66.667 15.93 19.24 40.86 4.46
1818 3236 3.884900 GCCATTTGCGAGGTACGT 58.115 55.556 0.00 0.00 44.60 3.57
1819 3237 3.053662 GCCATTTGCGAGGTACGTA 57.946 52.632 0.00 0.00 44.60 3.57
1822 3246 2.473984 GCCATTTGCGAGGTACGTATAC 59.526 50.000 0.00 0.00 44.60 1.47
1833 3257 6.249359 CGAGGTACGTATACTAGCATCATTC 58.751 44.000 0.00 0.00 37.22 2.67
1835 3259 4.792189 GGTACGTATACTAGCATCATTCGC 59.208 45.833 0.00 0.00 0.00 4.70
1838 3262 3.854240 CGTATACTAGCATCATTCGCAGG 59.146 47.826 0.56 0.00 0.00 4.85
1880 3320 5.174761 GTCTTTCTCTGACGCTATTAGCATG 59.825 44.000 15.64 3.07 42.58 4.06
1881 3321 3.018598 TCTCTGACGCTATTAGCATGC 57.981 47.619 10.51 10.51 42.58 4.06
1882 3322 2.362077 TCTCTGACGCTATTAGCATGCA 59.638 45.455 21.98 0.00 42.58 3.96
1883 3323 2.730404 CTCTGACGCTATTAGCATGCAG 59.270 50.000 21.98 16.41 42.58 4.41
1884 3324 2.101415 TCTGACGCTATTAGCATGCAGT 59.899 45.455 21.98 7.60 42.58 4.40
1885 3325 3.317993 TCTGACGCTATTAGCATGCAGTA 59.682 43.478 21.98 8.40 42.58 2.74
1890 3330 2.989840 GCTATTAGCATGCAGTACTCCG 59.010 50.000 21.98 1.29 41.89 4.63
1899 3339 1.145803 GCAGTACTCCGGTTCACAAC 58.854 55.000 0.00 0.00 0.00 3.32
2054 3496 0.986874 CGCAGTTTTCACAAGACGCG 60.987 55.000 3.53 3.53 33.15 6.01
2057 3499 2.629022 CAGTTTTCACAAGACGCGAAG 58.371 47.619 15.93 1.12 0.00 3.79
2083 3531 0.820226 TCCTGAATCTCTCACGCTGG 59.180 55.000 0.00 0.00 0.00 4.85
2146 3594 0.175302 AGAGAGATTCACGGCTGCAG 59.825 55.000 10.11 10.11 0.00 4.41
2147 3595 1.427592 GAGAGATTCACGGCTGCAGC 61.428 60.000 30.88 30.88 41.14 5.25
2200 3651 5.716703 TCATAGCAGCTGTTGATAGGCTATA 59.283 40.000 16.64 0.00 41.24 1.31
2201 3652 6.382282 TCATAGCAGCTGTTGATAGGCTATAT 59.618 38.462 16.64 0.00 41.24 0.86
2202 3653 7.561356 TCATAGCAGCTGTTGATAGGCTATATA 59.439 37.037 16.64 2.70 41.24 0.86
2203 3654 6.805016 AGCAGCTGTTGATAGGCTATATAT 57.195 37.500 16.64 0.00 34.71 0.86
2204 3655 7.904558 AGCAGCTGTTGATAGGCTATATATA 57.095 36.000 16.64 0.00 34.71 0.86
2223 3674 0.396974 AGGTCCTGCAACCAAAAGCA 60.397 50.000 10.18 0.00 42.12 3.91
2252 3703 5.449107 TCAAGCACGTCTTCTAACTTACT 57.551 39.130 0.00 0.00 31.27 2.24
2253 3704 5.220381 TCAAGCACGTCTTCTAACTTACTG 58.780 41.667 0.00 0.00 31.27 2.74
2254 3705 4.850347 AGCACGTCTTCTAACTTACTGT 57.150 40.909 0.00 0.00 0.00 3.55
2267 3718 8.306680 TCTAACTTACTGTACATTTGAAGTGC 57.693 34.615 0.00 0.00 0.00 4.40
2288 3739 3.001127 GCCGCGTAAACAATAATCCGTAA 59.999 43.478 4.92 0.00 0.00 3.18
2289 3740 4.318974 GCCGCGTAAACAATAATCCGTAAT 60.319 41.667 4.92 0.00 0.00 1.89
2290 3741 5.134640 CCGCGTAAACAATAATCCGTAATG 58.865 41.667 4.92 0.00 0.00 1.90
2291 3742 4.605594 CGCGTAAACAATAATCCGTAATGC 59.394 41.667 0.00 0.00 0.00 3.56
2292 3743 5.503498 GCGTAAACAATAATCCGTAATGCA 58.497 37.500 0.00 0.00 0.00 3.96
2293 3744 5.619607 GCGTAAACAATAATCCGTAATGCAG 59.380 40.000 0.00 0.00 0.00 4.41
2294 3745 6.711579 CGTAAACAATAATCCGTAATGCAGT 58.288 36.000 0.00 0.00 0.00 4.40
2299 3750 8.460831 AACAATAATCCGTAATGCAGTTTTTC 57.539 30.769 0.00 0.00 0.00 2.29
2312 3763 8.504812 AATGCAGTTTTTCTTTTAATGTTGGT 57.495 26.923 0.00 0.00 0.00 3.67
2313 3764 9.606631 AATGCAGTTTTTCTTTTAATGTTGGTA 57.393 25.926 0.00 0.00 0.00 3.25
2419 3870 1.202604 TCTTTCGAATATCGGGTGCCC 60.203 52.381 0.00 0.00 40.88 5.36
2469 3920 0.805711 CTCACGCCGTGCACATGATA 60.806 55.000 18.64 0.00 32.98 2.15
2498 3949 3.055094 ACTCCCTGCATGTAGGTTGTAAG 60.055 47.826 25.92 16.80 36.02 2.34
2501 3952 2.617788 CCTGCATGTAGGTTGTAAGGCA 60.618 50.000 20.86 0.00 32.99 4.75
2502 3953 3.282021 CTGCATGTAGGTTGTAAGGCAT 58.718 45.455 2.35 0.00 0.00 4.40
2503 3954 3.278574 TGCATGTAGGTTGTAAGGCATC 58.721 45.455 0.00 0.00 0.00 3.91
2504 3955 3.054434 TGCATGTAGGTTGTAAGGCATCT 60.054 43.478 0.00 0.00 0.00 2.90
2505 3956 4.163268 TGCATGTAGGTTGTAAGGCATCTA 59.837 41.667 0.00 0.00 0.00 1.98
2506 3957 4.511826 GCATGTAGGTTGTAAGGCATCTAC 59.488 45.833 0.00 0.00 36.08 2.59
2507 3958 4.380841 TGTAGGTTGTAAGGCATCTACG 57.619 45.455 0.00 0.00 37.19 3.51
2508 3959 2.981859 AGGTTGTAAGGCATCTACGG 57.018 50.000 0.00 0.00 0.00 4.02
2509 3960 1.134491 AGGTTGTAAGGCATCTACGGC 60.134 52.381 0.00 0.00 0.00 5.68
2516 3967 3.221222 GCATCTACGGCCTGGACT 58.779 61.111 0.00 0.00 0.00 3.85
2517 3968 1.522569 GCATCTACGGCCTGGACTT 59.477 57.895 0.00 0.00 0.00 3.01
2518 3969 0.811616 GCATCTACGGCCTGGACTTG 60.812 60.000 0.00 0.00 0.00 3.16
2519 3970 0.811616 CATCTACGGCCTGGACTTGC 60.812 60.000 0.00 0.00 0.00 4.01
2520 3971 1.264749 ATCTACGGCCTGGACTTGCA 61.265 55.000 0.00 0.00 0.00 4.08
2521 3972 1.003839 CTACGGCCTGGACTTGCAA 60.004 57.895 0.00 0.00 0.00 4.08
2522 3973 0.605319 CTACGGCCTGGACTTGCAAA 60.605 55.000 0.00 0.00 0.00 3.68
2523 3974 0.037590 TACGGCCTGGACTTGCAAAT 59.962 50.000 0.00 0.00 0.00 2.32
2524 3975 1.244019 ACGGCCTGGACTTGCAAATC 61.244 55.000 0.00 0.00 0.00 2.17
2525 3976 0.962356 CGGCCTGGACTTGCAAATCT 60.962 55.000 7.95 0.00 0.00 2.40
2526 3977 0.529378 GGCCTGGACTTGCAAATCTG 59.471 55.000 7.95 1.55 0.00 2.90
2527 3978 0.529378 GCCTGGACTTGCAAATCTGG 59.471 55.000 7.95 11.21 0.00 3.86
2528 3979 0.529378 CCTGGACTTGCAAATCTGGC 59.471 55.000 7.95 0.00 0.00 4.85
2529 3980 0.529378 CTGGACTTGCAAATCTGGCC 59.471 55.000 7.95 4.52 0.00 5.36
2530 3981 0.899717 TGGACTTGCAAATCTGGCCC 60.900 55.000 7.95 0.00 0.00 5.80
2531 3982 0.613012 GGACTTGCAAATCTGGCCCT 60.613 55.000 7.95 0.00 0.00 5.19
2532 3983 1.260544 GACTTGCAAATCTGGCCCTT 58.739 50.000 0.00 0.00 0.00 3.95
2533 3984 1.203287 GACTTGCAAATCTGGCCCTTC 59.797 52.381 0.00 0.00 0.00 3.46
2534 3985 1.259609 CTTGCAAATCTGGCCCTTCA 58.740 50.000 0.00 0.00 0.00 3.02
2535 3986 1.619827 CTTGCAAATCTGGCCCTTCAA 59.380 47.619 0.00 0.00 0.00 2.69
2536 3987 1.714541 TGCAAATCTGGCCCTTCAAA 58.285 45.000 0.00 0.00 0.00 2.69
2537 3988 1.344114 TGCAAATCTGGCCCTTCAAAC 59.656 47.619 0.00 0.00 0.00 2.93
2538 3989 1.669795 GCAAATCTGGCCCTTCAAACG 60.670 52.381 0.00 0.00 0.00 3.60
2539 3990 0.603065 AAATCTGGCCCTTCAAACGC 59.397 50.000 0.00 0.00 0.00 4.84
2540 3991 1.250840 AATCTGGCCCTTCAAACGCC 61.251 55.000 0.00 0.00 43.32 5.68
2541 3992 3.373565 CTGGCCCTTCAAACGCCC 61.374 66.667 0.00 0.00 42.29 6.13
2546 3997 4.084888 CCTTCAAACGCCCGCGAC 62.085 66.667 17.16 0.00 42.83 5.19
2547 3998 3.342627 CTTCAAACGCCCGCGACA 61.343 61.111 17.16 0.00 42.83 4.35
2548 3999 3.573489 CTTCAAACGCCCGCGACAC 62.573 63.158 17.16 0.00 42.83 3.67
2590 4041 7.010738 CCGTACATTCACATACCGTAAATTTCT 59.989 37.037 0.00 0.00 0.00 2.52
2597 4048 8.657074 TCACATACCGTAAATTTCTATCCTTG 57.343 34.615 0.00 0.00 0.00 3.61
2630 4084 1.605232 TGCACGTCGATCATACGGTAT 59.395 47.619 18.54 0.00 44.48 2.73
2653 4107 9.040939 GTATAAACTGTTTGAATGCCAAAGTTT 57.959 29.630 15.69 10.50 44.64 2.66
2713 4170 6.548171 GGACATTGCAAAATGAAATCAATGG 58.452 36.000 1.71 1.63 44.76 3.16
2737 4194 3.771160 GTGACGGATGCCCTCGGT 61.771 66.667 0.00 0.00 39.88 4.69
2813 4291 4.804420 ATCCGGGCAGCCTCCTCA 62.804 66.667 12.43 0.00 0.00 3.86
2819 4297 3.715097 GCAGCCTCCTCAGCCTGT 61.715 66.667 0.00 0.00 0.00 4.00
2907 4385 2.123428 GCCGCCTCGTAGTCCCTAA 61.123 63.158 0.00 0.00 0.00 2.69
2912 4390 1.684248 GCCTCGTAGTCCCTAAGGTCA 60.684 57.143 0.00 0.00 0.00 4.02
2994 4479 1.873486 CGCCAACATGATCCTCGCATA 60.873 52.381 0.00 0.00 0.00 3.14
3009 4494 1.227147 CATATTCCGCGTCCCGTGT 60.227 57.895 4.92 0.00 35.46 4.49
3015 4500 3.103911 CGCGTCCCGTGTGAGTTC 61.104 66.667 0.00 0.00 32.40 3.01
3082 4569 1.207089 TCGAACTCCCATTTGATCGCT 59.793 47.619 0.00 0.00 0.00 4.93
3102 4589 1.677576 TGCTTGTTGCTTCTCCAACTG 59.322 47.619 6.59 1.86 44.12 3.16
3112 4599 3.197549 GCTTCTCCAACTGGATCTTCTCT 59.802 47.826 0.00 0.00 44.46 3.10
3113 4600 4.680440 GCTTCTCCAACTGGATCTTCTCTC 60.680 50.000 0.00 0.00 44.46 3.20
3126 4613 6.183360 TGGATCTTCTCTCTCTCTCAATTTCG 60.183 42.308 0.00 0.00 0.00 3.46
3169 4656 1.341089 GGTTCCACTCCATCCTTTCCC 60.341 57.143 0.00 0.00 0.00 3.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 104 4.285851 GGACCAACTCTTGCTCCG 57.714 61.111 0.00 0.00 0.00 4.63
112 115 1.122632 TAAGAGCACCACCGGACCAA 61.123 55.000 9.46 0.00 0.00 3.67
144 147 4.736896 GACACCACCGACGGCCTC 62.737 72.222 15.39 0.00 0.00 4.70
173 176 4.779733 GGCGTGGGGAGGAGGAGA 62.780 72.222 0.00 0.00 0.00 3.71
515 566 2.099062 CTGTTGATCTTGCCGCGC 59.901 61.111 0.00 0.00 0.00 6.86
523 574 2.283529 ACCGGCGTCCTGTTGATCT 61.284 57.895 6.01 0.00 0.00 2.75
552 603 3.782244 CACCGAGCTCTTGTGCGC 61.782 66.667 17.04 0.00 38.13 6.09
553 604 3.782244 GCACCGAGCTCTTGTGCG 61.782 66.667 30.12 11.88 44.95 5.34
562 613 4.175489 TCGACGCTAGCACCGAGC 62.175 66.667 20.16 0.97 46.19 5.03
563 614 2.277373 GTCGACGCTAGCACCGAG 60.277 66.667 23.26 6.83 0.00 4.63
564 615 4.156622 CGTCGACGCTAGCACCGA 62.157 66.667 26.59 20.16 0.00 4.69
565 616 4.156622 TCGTCGACGCTAGCACCG 62.157 66.667 32.19 16.61 39.60 4.94
568 619 3.382591 CTGCTCGTCGACGCTAGCA 62.383 63.158 36.47 36.47 43.66 3.49
577 628 0.730834 CCACTCTGAACTGCTCGTCG 60.731 60.000 0.00 0.00 0.00 5.12
587 638 3.329542 GATGGGCCGCCACTCTGAA 62.330 63.158 12.58 0.00 0.00 3.02
606 657 0.591170 CGGCATTTCGTCAAACACCT 59.409 50.000 0.00 0.00 0.00 4.00
609 660 0.820074 ACCCGGCATTTCGTCAAACA 60.820 50.000 0.00 0.00 0.00 2.83
610 661 0.312729 AACCCGGCATTTCGTCAAAC 59.687 50.000 0.00 0.00 0.00 2.93
611 662 0.312416 CAACCCGGCATTTCGTCAAA 59.688 50.000 0.00 0.00 0.00 2.69
612 663 1.953017 CAACCCGGCATTTCGTCAA 59.047 52.632 0.00 0.00 0.00 3.18
613 664 2.622011 GCAACCCGGCATTTCGTCA 61.622 57.895 0.00 0.00 0.00 4.35
614 665 2.178273 GCAACCCGGCATTTCGTC 59.822 61.111 0.00 0.00 0.00 4.20
615 666 2.596046 TGCAACCCGGCATTTCGT 60.596 55.556 0.00 0.00 39.25 3.85
625 676 0.036590 ATTTTGGGCATGTGCAACCC 59.963 50.000 7.36 8.13 44.36 4.11
630 681 1.353609 GACGCATTTTGGGCATGTGC 61.354 55.000 0.00 0.00 35.86 4.57
658 709 1.064685 AGGTTAGCCAGTATGCCCAAC 60.065 52.381 0.00 0.00 37.19 3.77
663 714 6.693315 TTTCATTTAGGTTAGCCAGTATGC 57.307 37.500 0.00 0.00 37.19 3.14
666 717 6.149807 CCGTTTTTCATTTAGGTTAGCCAGTA 59.850 38.462 0.00 0.00 37.19 2.74
670 721 5.048573 TGTCCGTTTTTCATTTAGGTTAGCC 60.049 40.000 0.00 0.00 0.00 3.93
674 725 5.536916 TCCATGTCCGTTTTTCATTTAGGTT 59.463 36.000 0.00 0.00 0.00 3.50
695 747 3.116463 CGACCGATCGGACATCCA 58.884 61.111 39.55 0.00 44.99 3.41
705 757 1.471287 TGTCTGTTTCGATCGACCGAT 59.529 47.619 19.26 4.42 38.45 4.18
710 762 3.424198 CGTTTTCTGTCTGTTTCGATCGA 59.576 43.478 15.15 15.15 0.00 3.59
715 767 4.253352 TGTTCGTTTTCTGTCTGTTTCG 57.747 40.909 0.00 0.00 0.00 3.46
716 768 6.921332 TTTTGTTCGTTTTCTGTCTGTTTC 57.079 33.333 0.00 0.00 0.00 2.78
720 772 4.670621 CGGATTTTGTTCGTTTTCTGTCTG 59.329 41.667 0.00 0.00 0.00 3.51
726 778 2.377880 ACGCGGATTTTGTTCGTTTTC 58.622 42.857 12.47 0.00 0.00 2.29
731 783 0.511221 ACAGACGCGGATTTTGTTCG 59.489 50.000 12.47 0.00 0.00 3.95
733 785 2.542824 CCAAACAGACGCGGATTTTGTT 60.543 45.455 12.47 10.35 33.73 2.83
746 798 1.092921 AACGCAGCGAACCAAACAGA 61.093 50.000 24.65 0.00 0.00 3.41
748 800 1.063327 CAACGCAGCGAACCAAACA 59.937 52.632 24.65 0.00 0.00 2.83
758 810 1.448985 TAGACCAATTCCAACGCAGC 58.551 50.000 0.00 0.00 0.00 5.25
762 814 2.690786 TCGGTTAGACCAATTCCAACG 58.309 47.619 0.00 0.00 38.47 4.10
769 821 2.433436 GCCTTGTTCGGTTAGACCAAT 58.567 47.619 0.00 0.00 38.47 3.16
773 825 1.632948 GCGGCCTTGTTCGGTTAGAC 61.633 60.000 0.00 0.00 0.00 2.59
853 905 1.985614 CTCCCATCTGAGCACACCA 59.014 57.895 0.00 0.00 0.00 4.17
987 1063 1.519455 CGGCATCGAGGTCCAAGAC 60.519 63.158 10.34 0.00 39.00 3.01
992 1068 2.105128 CTGACGGCATCGAGGTCC 59.895 66.667 0.00 0.00 40.11 4.46
1077 1153 2.760385 AGCTCCTCCACCCTACGC 60.760 66.667 0.00 0.00 0.00 4.42
1479 2888 3.381983 ATGACACTCTCGCCGCCA 61.382 61.111 0.00 0.00 0.00 5.69
1537 2955 3.369471 CCCATGTCTTTCGTGTACTCCAT 60.369 47.826 0.00 0.00 0.00 3.41
1810 3228 6.249359 CGAATGATGCTAGTATACGTACCTC 58.751 44.000 0.00 0.00 0.00 3.85
1817 3235 3.614616 GCCTGCGAATGATGCTAGTATAC 59.385 47.826 0.00 0.00 0.00 1.47
1818 3236 3.368427 GGCCTGCGAATGATGCTAGTATA 60.368 47.826 0.00 0.00 0.00 1.47
1819 3237 2.613977 GGCCTGCGAATGATGCTAGTAT 60.614 50.000 0.00 0.00 0.00 2.12
1822 3246 0.250209 AGGCCTGCGAATGATGCTAG 60.250 55.000 3.11 0.00 0.00 3.42
1835 3259 2.046507 GTCAGACCTGCAGGCCTG 60.047 66.667 35.96 35.96 45.65 4.85
1838 3262 1.079266 CTGAGTCAGACCTGCAGGC 60.079 63.158 33.06 23.88 39.32 4.85
1880 3320 1.145803 GTTGTGAACCGGAGTACTGC 58.854 55.000 9.46 0.73 0.00 4.40
1881 3321 1.269413 ACGTTGTGAACCGGAGTACTG 60.269 52.381 9.46 1.11 0.00 2.74
1882 3322 1.035139 ACGTTGTGAACCGGAGTACT 58.965 50.000 9.46 0.00 0.00 2.73
1883 3323 1.788886 GAACGTTGTGAACCGGAGTAC 59.211 52.381 9.46 3.90 0.00 2.73
1884 3324 1.600164 CGAACGTTGTGAACCGGAGTA 60.600 52.381 9.46 0.00 0.00 2.59
1885 3325 0.872881 CGAACGTTGTGAACCGGAGT 60.873 55.000 9.46 0.00 0.00 3.85
1890 3330 3.632189 ACTACTACGAACGTTGTGAACC 58.368 45.455 20.10 0.00 35.82 3.62
1899 3339 8.219436 TGAATTTGAAGTTACTACTACGAACG 57.781 34.615 0.00 0.00 33.17 3.95
2054 3496 5.119434 GTGAGAGATTCAGGAAACGTTCTTC 59.881 44.000 0.00 0.00 36.21 2.87
2057 3499 3.365220 CGTGAGAGATTCAGGAAACGTTC 59.635 47.826 0.00 0.00 42.85 3.95
2083 3531 2.127758 CGACGACAAGCCAAACGC 60.128 61.111 0.00 0.00 37.98 4.84
2106 3554 1.137872 AGAAGTAGAAGCATGCCGAGG 59.862 52.381 15.66 0.00 0.00 4.63
2170 3621 2.093816 TCAACAGCTGCTATGAGTCCAG 60.094 50.000 15.27 0.00 0.00 3.86
2200 3651 3.954258 GCTTTTGGTTGCAGGACCTATAT 59.046 43.478 8.97 0.00 40.47 0.86
2201 3652 3.245087 TGCTTTTGGTTGCAGGACCTATA 60.245 43.478 8.97 0.00 40.47 1.31
2202 3653 2.171003 GCTTTTGGTTGCAGGACCTAT 58.829 47.619 8.97 0.00 40.47 2.57
2203 3654 1.133637 TGCTTTTGGTTGCAGGACCTA 60.134 47.619 8.97 0.00 40.47 3.08
2204 3655 0.396974 TGCTTTTGGTTGCAGGACCT 60.397 50.000 8.97 0.00 40.47 3.85
2223 3674 3.668447 AGAAGACGTGCTTGAATCACAT 58.332 40.909 0.00 0.00 36.83 3.21
2252 3703 0.515127 CGCGGCACTTCAAATGTACA 59.485 50.000 0.00 0.00 0.00 2.90
2253 3704 0.515564 ACGCGGCACTTCAAATGTAC 59.484 50.000 12.47 0.00 0.00 2.90
2254 3705 2.081725 TACGCGGCACTTCAAATGTA 57.918 45.000 12.47 0.00 0.00 2.29
2267 3718 4.775440 TTACGGATTATTGTTTACGCGG 57.225 40.909 12.47 0.00 0.00 6.46
2288 3739 9.777297 ATACCAACATTAAAAGAAAAACTGCAT 57.223 25.926 0.00 0.00 0.00 3.96
2299 3750 7.169982 CGAGCTCTCCTATACCAACATTAAAAG 59.830 40.741 12.85 0.00 0.00 2.27
2312 3763 1.815613 GATGCAGCGAGCTCTCCTATA 59.184 52.381 12.85 1.32 45.94 1.31
2313 3764 0.602562 GATGCAGCGAGCTCTCCTAT 59.397 55.000 12.85 0.00 45.94 2.57
2419 3870 0.530650 AACAGAGCGTGTGGTCAGTG 60.531 55.000 0.00 0.00 45.10 3.66
2457 3908 4.085055 GGAGTTCGTTATATCATGTGCACG 60.085 45.833 13.13 0.00 0.00 5.34
2469 3920 3.181465 CCTACATGCAGGGAGTTCGTTAT 60.181 47.826 10.21 0.00 31.47 1.89
2501 3952 1.264749 TGCAAGTCCAGGCCGTAGAT 61.265 55.000 0.00 0.00 0.00 1.98
2502 3953 1.476845 TTGCAAGTCCAGGCCGTAGA 61.477 55.000 0.00 0.00 0.00 2.59
2503 3954 0.605319 TTTGCAAGTCCAGGCCGTAG 60.605 55.000 0.00 0.00 0.00 3.51
2504 3955 0.037590 ATTTGCAAGTCCAGGCCGTA 59.962 50.000 0.00 0.00 0.00 4.02
2505 3956 1.228552 ATTTGCAAGTCCAGGCCGT 60.229 52.632 0.00 0.00 0.00 5.68
2506 3957 0.962356 AGATTTGCAAGTCCAGGCCG 60.962 55.000 17.41 0.00 0.00 6.13
2507 3958 0.529378 CAGATTTGCAAGTCCAGGCC 59.471 55.000 17.41 0.00 0.00 5.19
2508 3959 0.529378 CCAGATTTGCAAGTCCAGGC 59.471 55.000 17.41 0.00 0.00 4.85
2509 3960 0.529378 GCCAGATTTGCAAGTCCAGG 59.471 55.000 20.23 20.23 0.00 4.45
2510 3961 0.529378 GGCCAGATTTGCAAGTCCAG 59.471 55.000 17.41 10.69 0.00 3.86
2511 3962 0.899717 GGGCCAGATTTGCAAGTCCA 60.900 55.000 17.41 0.00 0.00 4.02
2512 3963 0.613012 AGGGCCAGATTTGCAAGTCC 60.613 55.000 17.41 8.19 0.00 3.85
2513 3964 1.203287 GAAGGGCCAGATTTGCAAGTC 59.797 52.381 13.69 13.69 0.00 3.01
2514 3965 1.260544 GAAGGGCCAGATTTGCAAGT 58.739 50.000 6.18 0.00 0.00 3.16
2515 3966 1.259609 TGAAGGGCCAGATTTGCAAG 58.740 50.000 6.18 0.00 0.00 4.01
2516 3967 1.714541 TTGAAGGGCCAGATTTGCAA 58.285 45.000 6.18 0.00 0.00 4.08
2517 3968 1.344114 GTTTGAAGGGCCAGATTTGCA 59.656 47.619 6.18 0.00 0.00 4.08
2518 3969 1.669795 CGTTTGAAGGGCCAGATTTGC 60.670 52.381 6.18 0.00 0.00 3.68
2519 3970 1.669795 GCGTTTGAAGGGCCAGATTTG 60.670 52.381 6.18 0.00 0.00 2.32
2520 3971 0.603065 GCGTTTGAAGGGCCAGATTT 59.397 50.000 6.18 0.00 0.00 2.17
2521 3972 1.250840 GGCGTTTGAAGGGCCAGATT 61.251 55.000 6.18 0.00 46.13 2.40
2522 3973 1.678970 GGCGTTTGAAGGGCCAGAT 60.679 57.895 6.18 0.00 46.13 2.90
2523 3974 2.282180 GGCGTTTGAAGGGCCAGA 60.282 61.111 6.18 0.00 46.13 3.86
2529 3980 4.084888 GTCGCGGGCGTTTGAAGG 62.085 66.667 13.21 0.00 40.74 3.46
2530 3981 3.342627 TGTCGCGGGCGTTTGAAG 61.343 61.111 13.21 0.00 40.74 3.02
2531 3982 3.641986 GTGTCGCGGGCGTTTGAA 61.642 61.111 13.21 0.00 40.74 2.69
2543 3994 5.630680 ACGGTATAATATTTAAGGCGTGTCG 59.369 40.000 0.00 0.00 0.00 4.35
2544 3995 7.594758 TGTACGGTATAATATTTAAGGCGTGTC 59.405 37.037 0.00 0.00 0.00 3.67
2545 3996 7.432869 TGTACGGTATAATATTTAAGGCGTGT 58.567 34.615 0.00 0.00 0.00 4.49
2546 3997 7.872163 TGTACGGTATAATATTTAAGGCGTG 57.128 36.000 0.00 0.00 0.00 5.34
2547 3998 9.143631 GAATGTACGGTATAATATTTAAGGCGT 57.856 33.333 0.00 0.00 0.00 5.68
2548 3999 9.142515 TGAATGTACGGTATAATATTTAAGGCG 57.857 33.333 0.00 0.00 0.00 5.52
2630 4084 9.436957 TTTAAACTTTGGCATTCAAACAGTTTA 57.563 25.926 0.00 9.70 41.16 2.01
2730 4187 1.517832 CCAGCTAGTGAACCGAGGG 59.482 63.158 0.00 0.00 0.00 4.30
2907 4385 5.250313 ACAAGAAGAAGGAGATCAATGACCT 59.750 40.000 0.00 0.00 0.00 3.85
2912 4390 4.764172 CGGACAAGAAGAAGGAGATCAAT 58.236 43.478 0.00 0.00 0.00 2.57
3009 4494 2.900546 GAGAAGGAGAGGTTGGAACTCA 59.099 50.000 0.00 0.00 37.43 3.41
3015 4500 1.627834 AGCTTGAGAAGGAGAGGTTGG 59.372 52.381 0.00 0.00 0.00 3.77
3082 4569 3.588755 CCAGTTGGAGAAGCAACAAGCA 61.589 50.000 0.00 0.00 41.58 3.91
3102 4589 6.039270 TCGAAATTGAGAGAGAGAGAAGATCC 59.961 42.308 0.00 0.00 0.00 3.36
3112 4599 5.184864 AGAAGAAGCTCGAAATTGAGAGAGA 59.815 40.000 12.89 0.00 38.28 3.10
3113 4600 5.410067 AGAAGAAGCTCGAAATTGAGAGAG 58.590 41.667 12.89 5.34 38.28 3.20
3126 4613 1.142965 GAGGGCGGAGAAGAAGCTC 59.857 63.158 0.00 0.00 0.00 4.09


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

AutoCloner maintained by Alex Coulton.