Multiple sequence alignment - TraesCS6A01G329400

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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 TraesCS6A01G329400 chr6A 100.000 4271 0 0 1 4271 562689605 562685335 0.000000e+00 7888.0
1 TraesCS6A01G329400 chr6A 82.337 1438 202 30 1058 2480 517559763 517558363 0.000000e+00 1201.0
2 TraesCS6A01G329400 chr6D 94.947 3562 123 24 727 4265 419269017 419265490 0.000000e+00 5528.0
3 TraesCS6A01G329400 chr6D 82.406 1438 201 30 1058 2480 375689405 375688005 0.000000e+00 1206.0
4 TraesCS6A01G329400 chr6D 84.027 745 55 31 21 724 419269795 419269074 0.000000e+00 658.0
5 TraesCS6A01G329400 chr6B 94.460 3574 129 27 727 4271 632182591 632179058 0.000000e+00 5439.0
6 TraesCS6A01G329400 chr6B 81.382 1520 223 32 1058 2552 562489893 562488409 0.000000e+00 1184.0
7 TraesCS6A01G329400 chr6B 85.222 697 50 26 66 729 632183338 632182662 0.000000e+00 667.0
8 TraesCS6A01G329400 chr2B 71.109 1163 267 45 1103 2250 11076238 11077346 5.560000e-54 222.0
9 TraesCS6A01G329400 chr2B 100.000 28 0 0 2682 2709 11077841 11077868 8.000000e-03 52.8
10 TraesCS6A01G329400 chr2D 74.031 516 119 10 1103 1615 273895 274398 3.370000e-46 196.0
11 TraesCS6A01G329400 chr2D 96.667 90 3 0 1516 1605 481595159 481595070 2.660000e-32 150.0
12 TraesCS6A01G329400 chr2D 100.000 28 0 0 2682 2709 275498 275525 8.000000e-03 52.8
13 TraesCS6A01G329400 chr2A 79.152 283 56 2 1106 1388 261926 261647 4.360000e-45 193.0
14 TraesCS6A01G329400 chr2A 100.000 28 0 0 2682 2709 260326 260299 8.000000e-03 52.8


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 TraesCS6A01G329400 chr6A 562685335 562689605 4270 True 7888 7888 100.000 1 4271 1 chr6A.!!$R2 4270
1 TraesCS6A01G329400 chr6A 517558363 517559763 1400 True 1201 1201 82.337 1058 2480 1 chr6A.!!$R1 1422
2 TraesCS6A01G329400 chr6D 419265490 419269795 4305 True 3093 5528 89.487 21 4265 2 chr6D.!!$R2 4244
3 TraesCS6A01G329400 chr6D 375688005 375689405 1400 True 1206 1206 82.406 1058 2480 1 chr6D.!!$R1 1422
4 TraesCS6A01G329400 chr6B 632179058 632183338 4280 True 3053 5439 89.841 66 4271 2 chr6B.!!$R2 4205
5 TraesCS6A01G329400 chr6B 562488409 562489893 1484 True 1184 1184 81.382 1058 2552 1 chr6B.!!$R1 1494

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
439 467 0.033405 TACTCCCTCCTAAGCGTGCT 60.033 55.0 0.00 0.0 0.0 4.40 F
544 576 0.110486 AACCTGGTTGTGGAGCGAAT 59.890 50.0 12.11 0.0 0.0 3.34 F
1852 1986 0.390340 CATACGGATCCCCATGCTCG 60.390 60.0 6.06 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1852 1986 0.109226 CCGTCGAAGTTGGAGACCTC 60.109 60.0 0.00 0.00 0.0 3.85 R
2277 2417 0.589708 TGTCGACGTCGTTCATCAGT 59.410 50.0 34.40 0.00 40.8 3.41 R
3558 3735 0.106708 GGACTCATGCGCTTGGGATA 59.893 55.0 28.02 6.22 0.0 2.59 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
30 31 6.544197 TGCAAAAATACTGTACCAAGTTCAGA 59.456 34.615 8.16 0.00 35.14 3.27
31 32 7.230510 TGCAAAAATACTGTACCAAGTTCAGAT 59.769 33.333 8.16 0.00 35.14 2.90
41 42 3.392616 ACCAAGTTCAGATCAGTTCCACT 59.607 43.478 0.00 0.00 0.00 4.00
44 45 4.000331 AGTTCAGATCAGTTCCACTGTG 58.000 45.455 0.00 0.00 46.03 3.66
59 60 3.244146 CCACTGTGGGCATTGATTTGAAA 60.244 43.478 19.23 0.00 32.67 2.69
60 61 3.742369 CACTGTGGGCATTGATTTGAAAC 59.258 43.478 0.00 0.00 0.00 2.78
61 62 3.244181 ACTGTGGGCATTGATTTGAAACC 60.244 43.478 0.00 0.00 0.00 3.27
63 64 4.155709 TGTGGGCATTGATTTGAAACCTA 58.844 39.130 0.00 0.00 0.00 3.08
68 74 6.172630 GGGCATTGATTTGAAACCTAATTGT 58.827 36.000 0.00 0.00 0.00 2.71
219 227 2.979678 TCAGCTTCTTGGTTTACCCTCT 59.020 45.455 0.00 0.00 34.29 3.69
241 254 8.066595 CCTCTTGAAACGCAGAAGATATTTATG 58.933 37.037 0.00 0.00 0.00 1.90
419 447 6.959361 ACAACACATTCTTTCAGTGACATAC 58.041 36.000 0.00 0.00 37.05 2.39
420 448 6.767902 ACAACACATTCTTTCAGTGACATACT 59.232 34.615 0.00 0.00 41.36 2.12
421 449 7.931407 ACAACACATTCTTTCAGTGACATACTA 59.069 33.333 0.00 0.00 37.60 1.82
422 450 7.891183 ACACATTCTTTCAGTGACATACTAC 57.109 36.000 0.00 0.00 37.60 2.73
423 451 7.671302 ACACATTCTTTCAGTGACATACTACT 58.329 34.615 0.00 0.00 37.60 2.57
424 452 7.815068 ACACATTCTTTCAGTGACATACTACTC 59.185 37.037 0.00 0.00 37.60 2.59
439 467 0.033405 TACTCCCTCCTAAGCGTGCT 60.033 55.000 0.00 0.00 0.00 4.40
452 480 1.488957 CGTGCTGCTCTTTCGTGAC 59.511 57.895 0.00 0.00 0.00 3.67
453 481 1.488957 GTGCTGCTCTTTCGTGACG 59.511 57.895 0.00 0.00 0.00 4.35
455 483 1.215014 TGCTGCTCTTTCGTGACGTG 61.215 55.000 4.40 0.00 0.00 4.49
462 490 3.486584 CTCTTTCGTGACGTGTACCTAC 58.513 50.000 4.40 0.00 0.00 3.18
468 496 2.601979 CGTGACGTGTACCTACGAACAA 60.602 50.000 12.18 0.00 46.46 2.83
494 524 2.768253 TCATCTGCAGAACATTCCGT 57.232 45.000 22.50 0.00 0.00 4.69
497 527 1.511850 TCTGCAGAACATTCCGTGTG 58.488 50.000 15.67 0.00 41.14 3.82
503 533 0.951558 GAACATTCCGTGTGCCTGTT 59.048 50.000 0.00 0.00 41.14 3.16
504 534 2.147958 GAACATTCCGTGTGCCTGTTA 58.852 47.619 0.00 0.00 41.14 2.41
505 535 2.264005 ACATTCCGTGTGCCTGTTAA 57.736 45.000 0.00 0.00 40.28 2.01
506 536 2.577700 ACATTCCGTGTGCCTGTTAAA 58.422 42.857 0.00 0.00 40.28 1.52
508 538 3.243267 ACATTCCGTGTGCCTGTTAAAAC 60.243 43.478 0.00 0.00 40.28 2.43
509 539 2.039818 TCCGTGTGCCTGTTAAAACA 57.960 45.000 0.00 0.00 37.37 2.83
510 540 7.444408 ACATTCCGTGTGCCTGTTAAAACAG 62.444 44.000 14.60 14.60 46.45 3.16
533 565 9.100197 ACAGGAATAAAAATGAATAACCTGGTT 57.900 29.630 17.44 17.44 44.22 3.67
535 567 9.100197 AGGAATAAAAATGAATAACCTGGTTGT 57.900 29.630 22.04 12.89 0.00 3.32
537 569 9.150348 GAATAAAAATGAATAACCTGGTTGTGG 57.850 33.333 22.04 0.00 0.00 4.17
538 570 6.739331 AAAAATGAATAACCTGGTTGTGGA 57.261 33.333 22.04 6.20 0.00 4.02
539 571 5.982890 AAATGAATAACCTGGTTGTGGAG 57.017 39.130 22.04 0.00 0.00 3.86
540 572 2.790433 TGAATAACCTGGTTGTGGAGC 58.210 47.619 22.04 6.99 0.00 4.70
541 573 1.737793 GAATAACCTGGTTGTGGAGCG 59.262 52.381 22.04 0.00 0.00 5.03
542 574 0.981183 ATAACCTGGTTGTGGAGCGA 59.019 50.000 22.04 0.00 0.00 4.93
543 575 0.759959 TAACCTGGTTGTGGAGCGAA 59.240 50.000 22.04 0.00 0.00 4.70
544 576 0.110486 AACCTGGTTGTGGAGCGAAT 59.890 50.000 12.11 0.00 0.00 3.34
545 577 0.981183 ACCTGGTTGTGGAGCGAATA 59.019 50.000 0.00 0.00 0.00 1.75
546 578 1.349688 ACCTGGTTGTGGAGCGAATAA 59.650 47.619 0.00 0.00 0.00 1.40
549 581 3.443681 CCTGGTTGTGGAGCGAATAAAAT 59.556 43.478 0.00 0.00 0.00 1.82
556 588 5.890334 TGTGGAGCGAATAAAATGATTTCC 58.110 37.500 0.00 0.00 0.00 3.13
567 599 8.466086 AATAAAATGATTTCCGAGCAAGTTTC 57.534 30.769 0.00 0.00 0.00 2.78
574 606 3.646520 CGAGCAAGTTTCTCGCAAG 57.353 52.632 11.87 0.00 45.32 4.01
578 610 1.604278 AGCAAGTTTCTCGCAAGGAAC 59.396 47.619 0.00 0.00 38.47 3.62
579 611 1.333619 GCAAGTTTCTCGCAAGGAACA 59.666 47.619 0.00 0.00 38.47 3.18
580 612 2.223479 GCAAGTTTCTCGCAAGGAACAA 60.223 45.455 0.00 0.00 38.47 2.83
581 613 3.621794 CAAGTTTCTCGCAAGGAACAAG 58.378 45.455 0.00 0.00 38.47 3.16
582 614 2.222027 AGTTTCTCGCAAGGAACAAGG 58.778 47.619 0.00 0.00 38.47 3.61
590 622 1.615392 GCAAGGAACAAGGCTGAATGT 59.385 47.619 0.00 0.00 0.00 2.71
600 632 3.904136 AGGCTGAATGTTCTTTTGTCG 57.096 42.857 0.00 0.00 0.00 4.35
605 637 4.906437 GCTGAATGTTCTTTTGTCGAGTTC 59.094 41.667 0.00 0.00 0.00 3.01
606 638 5.277538 GCTGAATGTTCTTTTGTCGAGTTCT 60.278 40.000 0.00 0.00 0.00 3.01
612 652 2.722629 TCTTTTGTCGAGTTCTTACGCG 59.277 45.455 3.53 3.53 46.98 6.01
616 656 1.154093 TCGAGTTCTTACGCGGCTG 60.154 57.895 12.47 0.00 45.86 4.85
633 673 1.656818 CTGCGCCGAAAATGGGTCAT 61.657 55.000 4.18 0.00 0.00 3.06
634 674 1.064134 GCGCCGAAAATGGGTCATC 59.936 57.895 0.00 0.00 0.00 2.92
635 675 1.376609 GCGCCGAAAATGGGTCATCT 61.377 55.000 0.00 0.00 0.00 2.90
640 686 3.499918 GCCGAAAATGGGTCATCTATCTG 59.500 47.826 0.00 0.00 0.00 2.90
646 692 1.062198 TGGGTCATCTATCTGCCTGGA 60.062 52.381 0.00 0.00 0.00 3.86
649 695 3.073650 GGGTCATCTATCTGCCTGGAAAT 59.926 47.826 0.00 0.00 0.00 2.17
650 696 4.322567 GGTCATCTATCTGCCTGGAAATC 58.677 47.826 0.00 0.00 0.00 2.17
651 697 4.322567 GTCATCTATCTGCCTGGAAATCC 58.677 47.826 0.00 0.00 0.00 3.01
659 705 1.095600 GCCTGGAAATCCGGAAAGTC 58.904 55.000 9.01 6.00 45.36 3.01
778 904 4.840005 GGCTAGTCAGGGTGGCGC 62.840 72.222 0.00 0.00 0.00 6.53
804 930 2.048023 ATGGGGCATGTCAGCGTTG 61.048 57.895 0.00 0.00 34.64 4.10
807 933 4.120331 GGCATGTCAGCGTTGGGC 62.120 66.667 0.00 0.00 44.05 5.36
860 986 2.874751 GGAATCAAACCGCCACCG 59.125 61.111 0.00 0.00 0.00 4.94
908 1034 1.368641 TCTCCGACCAAATCATTGCG 58.631 50.000 0.00 0.00 35.10 4.85
940 1069 3.287867 ACTACTGCATGCATTAGCCTT 57.712 42.857 33.13 18.59 41.13 4.35
977 1111 4.135153 CTCGACCAGCCACCGGAG 62.135 72.222 9.46 0.00 0.00 4.63
993 1127 1.511768 GAGGGAAGAACCGACCGAG 59.488 63.158 0.00 0.00 40.11 4.63
994 1128 1.946475 GAGGGAAGAACCGACCGAGG 61.946 65.000 0.00 0.00 40.11 4.63
995 1129 2.125633 GGAAGAACCGACCGAGGC 60.126 66.667 0.00 0.00 33.69 4.70
1852 1986 0.390340 CATACGGATCCCCATGCTCG 60.390 60.000 6.06 0.00 0.00 5.03
1906 2040 1.363744 GGCGAGCTCATATGCCATAC 58.636 55.000 21.35 0.00 46.76 2.39
2439 2591 1.071471 CTTGCCTGAGTGGGTCGTT 59.929 57.895 0.00 0.00 36.00 3.85
2577 2735 2.774799 GGATTGCATCCCGGTGTGC 61.775 63.158 18.44 18.44 43.88 4.57
2607 2765 2.289002 GTCTGCAGGTTGTAGCATATGC 59.711 50.000 20.36 20.36 40.42 3.14
2714 2872 4.307032 AGAAGATTGTGCAGGTTGGTAT 57.693 40.909 0.00 0.00 0.00 2.73
2748 2914 4.151883 ACCAGAAGGAAATTTTGCAGCTA 58.848 39.130 3.39 0.00 38.69 3.32
2759 2925 2.257691 TTGCAGCTACCGGTTGTTAA 57.742 45.000 15.04 2.42 0.00 2.01
2760 2926 2.483014 TGCAGCTACCGGTTGTTAAT 57.517 45.000 15.04 0.00 0.00 1.40
2761 2927 2.785562 TGCAGCTACCGGTTGTTAATT 58.214 42.857 15.04 0.00 0.00 1.40
2762 2928 2.745281 TGCAGCTACCGGTTGTTAATTC 59.255 45.455 15.04 0.00 0.00 2.17
2767 2933 4.080526 AGCTACCGGTTGTTAATTCATCCT 60.081 41.667 15.04 0.00 0.00 3.24
2770 2936 4.658063 ACCGGTTGTTAATTCATCCTTCA 58.342 39.130 0.00 0.00 0.00 3.02
2803 2969 2.545526 CAGATGATGAACGGTACCATGC 59.454 50.000 13.54 0.00 0.00 4.06
2904 3070 1.275291 TCGTCCATCCCTCACTTCAAC 59.725 52.381 0.00 0.00 0.00 3.18
2923 3089 2.068821 GGCCTGAGGATCCTGCTCA 61.069 63.158 22.02 10.68 42.67 4.26
3132 3298 3.909086 GAACAGGCGCTGGCTCCTT 62.909 63.158 7.64 0.00 35.88 3.36
3222 3388 0.332972 GCCTGATCCAGAAACCCCTT 59.667 55.000 0.00 0.00 32.44 3.95
3276 3442 3.099905 AGTCCTTCGGAACTGATGATGA 58.900 45.455 0.00 0.00 31.38 2.92
3325 3493 4.898829 TTGTGTTTCCATCACAAGACAG 57.101 40.909 7.28 0.00 46.35 3.51
3494 3671 1.000731 CAAGAAAATGAAAGGGGCGCA 59.999 47.619 10.83 0.00 0.00 6.09
3526 3703 1.228988 AAAAAGGGAGGGGCAGCAG 60.229 57.895 0.00 0.00 0.00 4.24
3558 3735 3.136077 AGTCACCAAGATAGCAGCATCAT 59.864 43.478 0.00 0.00 0.00 2.45
3624 3801 2.239150 AGCAGATGAACCAGCAGAATCT 59.761 45.455 0.00 0.00 0.00 2.40
3726 3903 1.345176 GCTGCTTGCACGATCGTAC 59.655 57.895 22.26 16.68 42.31 3.67
3759 3936 0.725686 CCTCACTGAAGATGCTTGCG 59.274 55.000 0.00 0.00 0.00 4.85
3812 3990 2.566952 AAACAGCACAGCAACAAGTC 57.433 45.000 0.00 0.00 0.00 3.01
3824 4002 1.002576 CAACAAGTCGCAATCTGCACA 60.003 47.619 0.00 0.00 45.36 4.57
3844 4023 5.105997 GCACAATATTGTTCTCTGCCTCTTT 60.106 40.000 18.50 0.00 39.91 2.52
3845 4024 6.571150 GCACAATATTGTTCTCTGCCTCTTTT 60.571 38.462 18.50 0.00 39.91 2.27
3899 4078 0.897401 TTTGGCATGGACGCATGGAA 60.897 50.000 5.36 0.00 33.41 3.53
3937 4116 9.752961 TGAACATCAATGGCATATGAAAAATAG 57.247 29.630 15.37 5.98 0.00 1.73
3972 4151 1.739371 GCAGATCGTGGAACTGGGTAC 60.739 57.143 5.27 0.00 33.89 3.34
4029 4208 4.141756 ACACCATCAAGCAATGAAAACCAA 60.142 37.500 0.00 0.00 42.54 3.67
4075 4255 0.394216 AATGCAGCCCTAACATCGCA 60.394 50.000 0.00 0.00 0.00 5.10
4193 4374 5.676552 TGAACCTAAAGCAAAGTGACAGTA 58.323 37.500 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.228035 ACTTGGTACAGTATTTTTGCAAACTA 57.772 30.769 12.39 3.33 42.39 2.24
1 2 7.107639 ACTTGGTACAGTATTTTTGCAAACT 57.892 32.000 12.39 3.18 42.39 2.66
2 3 7.489757 TGAACTTGGTACAGTATTTTTGCAAAC 59.510 33.333 12.39 0.37 42.39 2.93
3 4 7.548097 TGAACTTGGTACAGTATTTTTGCAAA 58.452 30.769 8.05 8.05 42.39 3.68
4 5 7.067615 TCTGAACTTGGTACAGTATTTTTGCAA 59.932 33.333 0.00 0.00 42.39 4.08
5 6 6.544197 TCTGAACTTGGTACAGTATTTTTGCA 59.456 34.615 0.00 0.00 42.39 4.08
6 7 6.966021 TCTGAACTTGGTACAGTATTTTTGC 58.034 36.000 0.00 0.00 42.39 3.68
7 8 8.783093 TGATCTGAACTTGGTACAGTATTTTTG 58.217 33.333 0.00 0.00 42.39 2.44
8 9 8.918202 TGATCTGAACTTGGTACAGTATTTTT 57.082 30.769 0.00 0.00 42.39 1.94
9 10 8.157476 ACTGATCTGAACTTGGTACAGTATTTT 58.843 33.333 6.60 0.00 42.39 1.82
10 11 7.680730 ACTGATCTGAACTTGGTACAGTATTT 58.319 34.615 6.60 0.00 42.39 1.40
11 12 7.246171 ACTGATCTGAACTTGGTACAGTATT 57.754 36.000 6.60 0.00 42.39 1.89
12 13 6.859112 ACTGATCTGAACTTGGTACAGTAT 57.141 37.500 6.60 0.00 42.39 2.12
13 14 6.295123 GGAACTGATCTGAACTTGGTACAGTA 60.295 42.308 6.60 0.00 42.39 2.74
14 15 5.511545 GGAACTGATCTGAACTTGGTACAGT 60.512 44.000 6.60 0.00 42.39 3.55
15 16 4.932200 GGAACTGATCTGAACTTGGTACAG 59.068 45.833 6.60 0.00 42.39 2.74
16 17 4.346709 TGGAACTGATCTGAACTTGGTACA 59.653 41.667 6.60 0.00 0.00 2.90
17 18 4.691216 GTGGAACTGATCTGAACTTGGTAC 59.309 45.833 6.60 0.00 0.00 3.34
18 19 4.894784 GTGGAACTGATCTGAACTTGGTA 58.105 43.478 6.60 0.00 0.00 3.25
19 20 3.744660 GTGGAACTGATCTGAACTTGGT 58.255 45.455 6.60 0.00 0.00 3.67
41 42 2.971330 AGGTTTCAAATCAATGCCCACA 59.029 40.909 0.00 0.00 0.00 4.17
44 45 6.092533 CACAATTAGGTTTCAAATCAATGCCC 59.907 38.462 0.00 0.00 0.00 5.36
59 60 4.526970 CTGAATAGGTGCCACAATTAGGT 58.473 43.478 0.00 0.00 0.00 3.08
60 61 3.885297 CCTGAATAGGTGCCACAATTAGG 59.115 47.826 0.00 1.48 39.39 2.69
61 62 3.885297 CCCTGAATAGGTGCCACAATTAG 59.115 47.826 0.00 0.00 42.96 1.73
63 64 2.311542 TCCCTGAATAGGTGCCACAATT 59.688 45.455 0.00 0.00 42.96 2.32
68 74 1.367346 TGTTCCCTGAATAGGTGCCA 58.633 50.000 0.00 0.00 42.96 4.92
219 227 7.082700 TGCATAAATATCTTCTGCGTTTCAA 57.917 32.000 0.00 0.00 35.63 2.69
241 254 7.805071 GCAAACAAGGACATAGACATATATTGC 59.195 37.037 0.00 0.00 0.00 3.56
248 261 3.009723 CGGCAAACAAGGACATAGACAT 58.990 45.455 0.00 0.00 0.00 3.06
256 279 1.299850 GGTTGCGGCAAACAAGGAC 60.300 57.895 24.93 7.99 30.47 3.85
262 285 0.885196 TATTCCTGGTTGCGGCAAAC 59.115 50.000 23.33 23.33 0.00 2.93
377 405 1.000521 TTGGCTTCTCATGGGCCTG 60.001 57.895 4.53 0.24 45.45 4.85
419 447 0.386113 GCACGCTTAGGAGGGAGTAG 59.614 60.000 0.00 0.00 39.04 2.57
420 448 0.033405 AGCACGCTTAGGAGGGAGTA 60.033 55.000 0.00 0.00 39.04 2.59
421 449 1.305381 AGCACGCTTAGGAGGGAGT 60.305 57.895 0.00 0.00 39.04 3.85
422 450 1.142748 CAGCACGCTTAGGAGGGAG 59.857 63.158 0.00 0.00 39.04 4.30
423 451 3.019003 GCAGCACGCTTAGGAGGGA 62.019 63.158 0.00 0.00 39.04 4.20
424 452 2.512515 GCAGCACGCTTAGGAGGG 60.513 66.667 0.00 0.00 41.32 4.30
439 467 1.601162 GGTACACGTCACGAAAGAGCA 60.601 52.381 2.91 0.00 0.00 4.26
447 475 1.069973 TGTTCGTAGGTACACGTCACG 60.070 52.381 0.00 0.00 42.51 4.35
452 480 2.342910 AGCTTGTTCGTAGGTACACG 57.657 50.000 0.00 0.00 43.28 4.49
453 481 3.910648 AGAAGCTTGTTCGTAGGTACAC 58.089 45.455 2.10 0.00 0.00 2.90
455 483 4.553323 TGAAGAAGCTTGTTCGTAGGTAC 58.447 43.478 25.89 6.23 33.55 3.34
462 490 2.481568 TGCAGATGAAGAAGCTTGTTCG 59.518 45.455 25.89 15.46 33.55 3.95
468 496 3.413846 TGTTCTGCAGATGAAGAAGCT 57.586 42.857 19.04 0.00 40.23 3.74
505 535 9.942850 CCAGGTTATTCATTTTTATTCCTGTTT 57.057 29.630 0.00 0.00 38.43 2.83
506 536 9.100197 ACCAGGTTATTCATTTTTATTCCTGTT 57.900 29.630 0.00 0.00 38.43 3.16
508 538 9.369904 CAACCAGGTTATTCATTTTTATTCCTG 57.630 33.333 3.89 0.00 39.40 3.86
509 539 9.100197 ACAACCAGGTTATTCATTTTTATTCCT 57.900 29.630 3.89 0.00 0.00 3.36
510 540 9.150348 CACAACCAGGTTATTCATTTTTATTCC 57.850 33.333 3.89 0.00 0.00 3.01
511 541 9.150348 CCACAACCAGGTTATTCATTTTTATTC 57.850 33.333 3.89 0.00 0.00 1.75
512 542 8.875168 TCCACAACCAGGTTATTCATTTTTATT 58.125 29.630 3.89 0.00 0.00 1.40
516 548 5.279456 GCTCCACAACCAGGTTATTCATTTT 60.279 40.000 3.89 0.00 0.00 1.82
527 559 2.107950 TTATTCGCTCCACAACCAGG 57.892 50.000 0.00 0.00 0.00 4.45
533 565 5.448496 CGGAAATCATTTTATTCGCTCCACA 60.448 40.000 0.00 0.00 0.00 4.17
535 567 4.878971 TCGGAAATCATTTTATTCGCTCCA 59.121 37.500 0.00 0.00 0.00 3.86
537 569 4.906437 GCTCGGAAATCATTTTATTCGCTC 59.094 41.667 0.00 0.00 0.00 5.03
538 570 4.335315 TGCTCGGAAATCATTTTATTCGCT 59.665 37.500 0.00 0.00 0.00 4.93
539 571 4.597079 TGCTCGGAAATCATTTTATTCGC 58.403 39.130 0.00 0.00 0.00 4.70
540 572 6.258160 ACTTGCTCGGAAATCATTTTATTCG 58.742 36.000 0.00 0.00 0.00 3.34
541 573 8.466086 AAACTTGCTCGGAAATCATTTTATTC 57.534 30.769 0.00 0.00 0.00 1.75
542 574 8.306761 AGAAACTTGCTCGGAAATCATTTTATT 58.693 29.630 0.00 0.00 0.00 1.40
543 575 7.830739 AGAAACTTGCTCGGAAATCATTTTAT 58.169 30.769 0.00 0.00 0.00 1.40
544 576 7.214467 AGAAACTTGCTCGGAAATCATTTTA 57.786 32.000 0.00 0.00 0.00 1.52
545 577 6.089249 AGAAACTTGCTCGGAAATCATTTT 57.911 33.333 0.00 0.00 0.00 1.82
546 578 5.703876 GAGAAACTTGCTCGGAAATCATTT 58.296 37.500 0.00 0.00 0.00 2.32
567 599 0.603707 TCAGCCTTGTTCCTTGCGAG 60.604 55.000 0.00 0.00 0.00 5.03
578 610 3.976942 CGACAAAAGAACATTCAGCCTTG 59.023 43.478 0.00 0.00 0.00 3.61
579 611 3.882888 TCGACAAAAGAACATTCAGCCTT 59.117 39.130 0.00 0.00 0.00 4.35
580 612 3.476552 TCGACAAAAGAACATTCAGCCT 58.523 40.909 0.00 0.00 0.00 4.58
581 613 3.251004 ACTCGACAAAAGAACATTCAGCC 59.749 43.478 0.00 0.00 0.00 4.85
582 614 4.474226 ACTCGACAAAAGAACATTCAGC 57.526 40.909 0.00 0.00 0.00 4.26
590 622 3.180980 CGCGTAAGAACTCGACAAAAGAA 59.819 43.478 0.00 0.00 35.89 2.52
600 632 3.081993 GCAGCCGCGTAAGAACTC 58.918 61.111 4.92 0.00 43.02 3.01
616 656 1.064134 GATGACCCATTTTCGGCGC 59.936 57.895 0.00 0.00 0.00 6.53
620 660 3.499918 GGCAGATAGATGACCCATTTTCG 59.500 47.826 0.00 0.00 0.00 3.46
633 673 1.694150 CCGGATTTCCAGGCAGATAGA 59.306 52.381 0.00 0.00 35.14 1.98
634 674 1.694150 TCCGGATTTCCAGGCAGATAG 59.306 52.381 0.00 0.00 35.14 2.08
635 675 1.801242 TCCGGATTTCCAGGCAGATA 58.199 50.000 0.00 0.00 35.14 1.98
640 686 1.095600 GACTTTCCGGATTTCCAGGC 58.904 55.000 4.15 0.00 35.14 4.85
751 870 2.290122 CTGACTAGCCGACAGCCCAG 62.290 65.000 0.00 0.00 45.47 4.45
761 881 4.840005 GCGCCACCCTGACTAGCC 62.840 72.222 0.00 0.00 0.00 3.93
804 930 2.032681 GAGGACAGGTGTGTGCCC 59.967 66.667 0.00 0.00 45.88 5.36
807 933 1.674057 GGGAGAGGACAGGTGTGTG 59.326 63.158 0.00 0.00 36.88 3.82
860 986 3.134792 TGGAGAGAGAGACGCGGC 61.135 66.667 12.47 7.86 0.00 6.53
908 1034 2.068519 TGCAGTAGTATATGCATGCGC 58.931 47.619 14.09 0.00 46.97 6.09
940 1069 1.304134 TAGCTGGTCTGAGCGGTCA 60.304 57.895 17.59 17.59 44.24 4.02
969 1103 2.669240 GGTTCTTCCCTCCGGTGG 59.331 66.667 15.94 15.94 0.00 4.61
971 1105 2.118951 TCGGTTCTTCCCTCCGGT 59.881 61.111 0.00 0.00 43.75 5.28
972 1106 2.577593 GTCGGTTCTTCCCTCCGG 59.422 66.667 0.00 0.00 43.75 5.14
973 1107 2.577593 GGTCGGTTCTTCCCTCCG 59.422 66.667 0.00 0.00 44.76 4.63
974 1108 1.946475 CTCGGTCGGTTCTTCCCTCC 61.946 65.000 0.00 0.00 0.00 4.30
975 1109 1.511768 CTCGGTCGGTTCTTCCCTC 59.488 63.158 0.00 0.00 0.00 4.30
977 1111 2.577593 CCTCGGTCGGTTCTTCCC 59.422 66.667 0.00 0.00 0.00 3.97
978 1112 2.125633 GCCTCGGTCGGTTCTTCC 60.126 66.667 0.00 0.00 0.00 3.46
979 1113 1.446272 CTGCCTCGGTCGGTTCTTC 60.446 63.158 0.00 0.00 0.00 2.87
980 1114 2.657237 CTGCCTCGGTCGGTTCTT 59.343 61.111 0.00 0.00 0.00 2.52
981 1115 4.070552 GCTGCCTCGGTCGGTTCT 62.071 66.667 0.00 0.00 0.00 3.01
1038 1172 4.137872 TAGTACCGCTGCACCGCC 62.138 66.667 0.00 0.00 0.00 6.13
1039 1173 2.884207 GTAGTACCGCTGCACCGC 60.884 66.667 0.00 0.00 0.00 5.68
1040 1174 1.516386 CAGTAGTACCGCTGCACCG 60.516 63.158 0.00 0.00 31.85 4.94
1041 1175 4.496670 CAGTAGTACCGCTGCACC 57.503 61.111 0.00 0.00 31.85 5.01
1718 1852 2.202570 CGATCACGTCCGGGTCAC 60.203 66.667 0.00 0.00 34.56 3.67
1732 1866 0.179121 TCGCTTGCCATTACGTCGAT 60.179 50.000 0.00 0.00 0.00 3.59
1852 1986 0.109226 CCGTCGAAGTTGGAGACCTC 60.109 60.000 0.00 0.00 0.00 3.85
1906 2040 3.257933 GCGAAGAGCCAACACCAG 58.742 61.111 0.00 0.00 40.81 4.00
2277 2417 0.589708 TGTCGACGTCGTTCATCAGT 59.410 50.000 34.40 0.00 40.80 3.41
2465 2617 3.376078 CCGCCATTTGCAGCAGGT 61.376 61.111 0.00 0.00 41.33 4.00
2607 2765 1.021202 TGGCAACCTGAAACTCAACG 58.979 50.000 0.00 0.00 0.00 4.10
2664 2822 3.160047 ATCTGAGAGCTGGCCGGG 61.160 66.667 15.02 1.86 0.00 5.73
2714 2872 6.442541 TTTCCTTCTGGTATACCAAGTGAA 57.557 37.500 24.59 21.28 46.97 3.18
2730 2896 3.501950 CGGTAGCTGCAAAATTTCCTTC 58.498 45.455 3.61 0.00 0.00 3.46
2734 2900 2.986479 CAACCGGTAGCTGCAAAATTTC 59.014 45.455 8.00 0.00 0.00 2.17
2748 2914 4.457949 GTGAAGGATGAATTAACAACCGGT 59.542 41.667 0.00 0.00 37.70 5.28
2759 2925 6.487828 TGAAGAAATGAGGTGAAGGATGAAT 58.512 36.000 0.00 0.00 0.00 2.57
2760 2926 5.879763 TGAAGAAATGAGGTGAAGGATGAA 58.120 37.500 0.00 0.00 0.00 2.57
2761 2927 5.249163 TCTGAAGAAATGAGGTGAAGGATGA 59.751 40.000 0.00 0.00 0.00 2.92
2762 2928 5.494724 TCTGAAGAAATGAGGTGAAGGATG 58.505 41.667 0.00 0.00 0.00 3.51
2767 2933 6.714278 TCATCATCTGAAGAAATGAGGTGAA 58.286 36.000 0.00 0.00 35.69 3.18
2770 2936 5.583854 CGTTCATCATCTGAAGAAATGAGGT 59.416 40.000 0.00 0.00 44.44 3.85
2904 3070 3.160047 AGCAGGATCCTCAGGCCG 61.160 66.667 12.69 0.00 0.00 6.13
2923 3089 2.512286 CATGCCGTCGCCATCTGT 60.512 61.111 0.00 0.00 0.00 3.41
3222 3388 4.063967 CCCAGCGCCGTCAGTGTA 62.064 66.667 2.29 0.00 0.00 2.90
3325 3493 1.452833 GGCTTGTGGATCAGCTCCC 60.453 63.158 3.11 0.00 44.23 4.30
3439 3613 9.932207 ATTGCATGTTTTATTCTTCTGAAATGA 57.068 25.926 0.00 0.00 35.63 2.57
3512 3689 4.664267 TGTCTGCTGCCCCTCCCT 62.664 66.667 0.00 0.00 0.00 4.20
3526 3703 1.412710 TCTTGGTGACTGGTGAGTGTC 59.587 52.381 0.00 0.00 30.16 3.67
3558 3735 0.106708 GGACTCATGCGCTTGGGATA 59.893 55.000 28.02 6.22 0.00 2.59
3759 3936 1.330521 TCGCAAGTTGCAGTGAGTTTC 59.669 47.619 26.56 0.00 45.36 2.78
3802 3980 0.239347 GCAGATTGCGACTTGTTGCT 59.761 50.000 13.37 0.00 31.71 3.91
3824 4002 6.376581 CCAGAAAAGAGGCAGAGAACAATATT 59.623 38.462 0.00 0.00 0.00 1.28
3844 4023 6.522625 TTTTTGTTCTGTTGATGACCAGAA 57.477 33.333 0.00 0.00 0.00 3.02
3845 4024 6.713762 ATTTTTGTTCTGTTGATGACCAGA 57.286 33.333 0.00 0.00 0.00 3.86
3899 4078 5.359009 CCATTGATGTTCAGAAGTTAGGCAT 59.641 40.000 0.00 0.00 0.00 4.40
3937 4116 4.154195 ACGATCTGCCATTAAACAGTTGAC 59.846 41.667 0.00 0.00 35.37 3.18
3972 4151 2.055838 TGCTTAACGTGCGTTACTGAG 58.944 47.619 15.50 11.93 39.90 3.35
4029 4208 6.240894 TCAACTGTAAGAATCCAGCATCTTT 58.759 36.000 0.00 0.00 37.16 2.52
4063 4243 1.204704 TCTGTGTCTGCGATGTTAGGG 59.795 52.381 0.00 0.00 0.00 3.53
4075 4255 4.501071 ACTGTTTTGTAACGTCTGTGTCT 58.499 39.130 0.00 0.00 37.06 3.41
4145 4326 2.373502 AGGTGCTAGTTTTGCTCTTCCT 59.626 45.455 0.00 0.00 0.00 3.36
4161 4342 6.318900 ACTTTGCTTTAGGTTCATATAGGTGC 59.681 38.462 0.00 0.00 0.00 5.01
4193 4374 1.201181 CTCTGTCTGCTGCGTCTAGTT 59.799 52.381 0.00 0.00 0.00 2.24
4241 4422 1.136110 TCAAGTAATGATCAGCGCCGA 59.864 47.619 2.29 0.00 31.50 5.54


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

AutoCloner maintained by Alex Coulton.