Multiple sequence alignment - TraesCS7A01G301200

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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 TraesCS7A01G301200 chr7A 100.000 3388 0 0 1 3388 419045411 419042024 0.000000e+00 6257
1 TraesCS7A01G301200 chr7A 98.536 478 6 1 249 726 419054855 419054379 0.000000e+00 843
2 TraesCS7A01G301200 chr6A 97.746 2662 58 1 727 3388 60395722 60398381 0.000000e+00 4582
3 TraesCS7A01G301200 chr2A 96.525 2417 70 5 979 3388 705945433 705947842 0.000000e+00 3986
4 TraesCS7A01G301200 chr2A 98.031 2133 42 0 1256 3388 36893474 36895606 0.000000e+00 3707
5 TraesCS7A01G301200 chr2A 97.378 534 14 0 727 1260 36883795 36884328 0.000000e+00 909
6 TraesCS7A01G301200 chr2A 82.906 702 99 19 35 726 443768814 443768124 2.230000e-171 612
7 TraesCS7A01G301200 chr2A 94.798 346 15 1 381 726 443777629 443777287 1.380000e-148 536
8 TraesCS7A01G301200 chr2A 81.723 476 72 13 27 495 362351698 362351231 1.910000e-102 383
9 TraesCS7A01G301200 chr2A 81.641 463 66 18 8 462 229049321 229048870 1.920000e-97 366
10 TraesCS7A01G301200 chr2A 81.092 476 73 15 27 495 527007613 527008078 6.910000e-97 364
11 TraesCS7A01G301200 chr6B 85.137 841 113 10 1001 1834 664394216 664393381 0.000000e+00 850
12 TraesCS7A01G301200 chr6B 80.785 484 86 7 2088 2568 664393140 664392661 4.130000e-99 372
13 TraesCS7A01G301200 chr3A 85.201 723 101 4 1154 1872 99582175 99582895 0.000000e+00 737
14 TraesCS7A01G301200 chr3A 86.732 407 39 15 9 407 352684937 352684538 4.010000e-119 438
15 TraesCS7A01G301200 chr5A 77.186 938 190 21 874 1798 557068555 557067629 2.990000e-145 525
16 TraesCS7A01G301200 chr5A 79.476 458 87 7 2 454 381954827 381955282 5.460000e-83 318
17 TraesCS7A01G301200 chr5A 89.427 227 23 1 399 625 612786063 612786288 5.530000e-73 285
18 TraesCS7A01G301200 chr1A 86.173 405 47 8 8 407 153357658 153357258 2.420000e-116 429
19 TraesCS7A01G301200 chr4B 83.524 437 58 12 24 453 346816070 346815641 2.450000e-106 396
20 TraesCS7A01G301200 chr4B 78.814 590 94 26 4 574 299796762 299797339 5.340000e-98 368
21 TraesCS7A01G301200 chr4B 80.000 365 60 13 57 415 259122006 259121649 1.210000e-64 257
22 TraesCS7A01G301200 chr4B 80.233 172 25 9 248 415 259129248 259129082 1.650000e-23 121
23 TraesCS7A01G301200 chr5B 78.374 578 98 24 2 565 226730112 226729548 1.930000e-92 350
24 TraesCS7A01G301200 chr2B 81.295 278 39 8 2647 2921 859686 859419 2.650000e-51 213


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 TraesCS7A01G301200 chr7A 419042024 419045411 3387 True 6257 6257 100.000 1 3388 1 chr7A.!!$R1 3387
1 TraesCS7A01G301200 chr6A 60395722 60398381 2659 False 4582 4582 97.746 727 3388 1 chr6A.!!$F1 2661
2 TraesCS7A01G301200 chr2A 705945433 705947842 2409 False 3986 3986 96.525 979 3388 1 chr2A.!!$F4 2409
3 TraesCS7A01G301200 chr2A 36893474 36895606 2132 False 3707 3707 98.031 1256 3388 1 chr2A.!!$F2 2132
4 TraesCS7A01G301200 chr2A 36883795 36884328 533 False 909 909 97.378 727 1260 1 chr2A.!!$F1 533
5 TraesCS7A01G301200 chr2A 443768124 443768814 690 True 612 612 82.906 35 726 1 chr2A.!!$R3 691
6 TraesCS7A01G301200 chr6B 664392661 664394216 1555 True 611 850 82.961 1001 2568 2 chr6B.!!$R1 1567
7 TraesCS7A01G301200 chr3A 99582175 99582895 720 False 737 737 85.201 1154 1872 1 chr3A.!!$F1 718
8 TraesCS7A01G301200 chr5A 557067629 557068555 926 True 525 525 77.186 874 1798 1 chr5A.!!$R1 924
9 TraesCS7A01G301200 chr4B 299796762 299797339 577 False 368 368 78.814 4 574 1 chr4B.!!$F1 570
10 TraesCS7A01G301200 chr5B 226729548 226730112 564 True 350 350 78.374 2 565 1 chr5B.!!$R1 563

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
718 731 0.034186 CTCCCATGCACTTAAGCCCA 60.034 55.0 1.29 0.0 0.0 5.36 F
769 782 0.035152 TCCATTCACAGCGGCAATCT 60.035 50.0 1.45 0.0 0.0 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1637 1661 2.108952 ACCTGCTGGTTTTCAATCTCCT 59.891 45.455 9.88 0.0 46.05 3.69 R
2764 2872 4.136051 CAAATCCACCAACAAAGCCAAAT 58.864 39.130 0.00 0.0 0.00 2.32 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
22 23 4.516195 GCTCCGTCCTTCCCGAGC 62.516 72.222 0.00 0.00 0.00 5.03
23 24 2.756283 CTCCGTCCTTCCCGAGCT 60.756 66.667 0.00 0.00 0.00 4.09
40 41 3.309954 CGAGCTTTCCCCTTATCTTTTCG 59.690 47.826 0.00 0.00 0.00 3.46
41 42 3.621558 AGCTTTCCCCTTATCTTTTCGG 58.378 45.455 0.00 0.00 0.00 4.30
42 43 3.265995 AGCTTTCCCCTTATCTTTTCGGA 59.734 43.478 0.00 0.00 0.00 4.55
49 51 5.248934 TCCCCTTATCTTTTCGGAAAGTACA 59.751 40.000 15.79 0.00 42.32 2.90
54 56 4.759516 TCTTTTCGGAAAGTACAATGGC 57.240 40.909 15.79 0.00 42.32 4.40
59 62 3.950397 TCGGAAAGTACAATGGCAATCT 58.050 40.909 0.00 0.00 0.00 2.40
75 78 2.807967 CAATCTTGCAGAAAGGACGACA 59.192 45.455 0.00 0.00 36.46 4.35
84 87 3.121944 CAGAAAGGACGACAACTTCATCG 59.878 47.826 0.00 0.00 43.97 3.84
90 93 0.716108 CGACAACTTCATCGTGAGGC 59.284 55.000 0.00 0.00 33.63 4.70
91 94 1.795768 GACAACTTCATCGTGAGGCA 58.204 50.000 0.00 0.00 0.00 4.75
92 95 2.350522 GACAACTTCATCGTGAGGCAT 58.649 47.619 0.00 0.00 0.00 4.40
94 97 3.932710 GACAACTTCATCGTGAGGCATTA 59.067 43.478 0.00 0.00 0.00 1.90
96 99 4.393062 ACAACTTCATCGTGAGGCATTAAG 59.607 41.667 0.00 0.00 0.00 1.85
118 121 6.600882 AGGCAAAGAAATGAAGACATCAAT 57.399 33.333 0.00 0.00 42.54 2.57
119 122 6.628185 AGGCAAAGAAATGAAGACATCAATC 58.372 36.000 0.00 0.00 42.54 2.67
164 167 3.506844 AGAGTAACCAAGACCGAGAAGAC 59.493 47.826 0.00 0.00 0.00 3.01
165 168 3.228453 AGTAACCAAGACCGAGAAGACA 58.772 45.455 0.00 0.00 0.00 3.41
217 224 5.425539 CCCTTACTCCACCTCTTAAATCTCA 59.574 44.000 0.00 0.00 0.00 3.27
258 265 2.307686 GGAGGAGATTTGTAACACCCCA 59.692 50.000 0.00 0.00 0.00 4.96
277 284 4.130118 CCCAGGAATCATGCTACAGTAAC 58.870 47.826 0.00 0.00 0.00 2.50
281 288 4.716784 AGGAATCATGCTACAGTAACCTCA 59.283 41.667 0.00 0.00 0.00 3.86
290 297 4.161754 GCTACAGTAACCTCACCCTAATGT 59.838 45.833 0.00 0.00 0.00 2.71
300 309 2.019249 CACCCTAATGTGCCATGTCAG 58.981 52.381 0.00 0.00 0.00 3.51
316 326 6.817270 CATGTCAGCATGTTTTATTAAGCC 57.183 37.500 0.00 0.00 45.48 4.35
322 332 8.170553 GTCAGCATGTTTTATTAAGCCAATTTG 58.829 33.333 0.00 0.00 37.40 2.32
327 337 5.703130 TGTTTTATTAAGCCAATTTGCCACC 59.297 36.000 0.00 0.00 0.00 4.61
342 352 9.824534 CAATTTGCCACCTAATAAAAATCAAAC 57.175 29.630 0.00 0.00 0.00 2.93
343 353 9.566432 AATTTGCCACCTAATAAAAATCAAACA 57.434 25.926 0.00 0.00 0.00 2.83
344 354 8.964476 TTTGCCACCTAATAAAAATCAAACAA 57.036 26.923 0.00 0.00 0.00 2.83
345 355 9.566432 TTTGCCACCTAATAAAAATCAAACAAT 57.434 25.926 0.00 0.00 0.00 2.71
453 463 7.575414 AGTAATTGTCATGTAACAACCAACA 57.425 32.000 2.34 0.00 41.65 3.33
454 464 8.001881 AGTAATTGTCATGTAACAACCAACAA 57.998 30.769 2.34 0.00 41.65 2.83
455 465 8.470805 AGTAATTGTCATGTAACAACCAACAAA 58.529 29.630 2.34 0.00 41.65 2.83
456 466 9.255304 GTAATTGTCATGTAACAACCAACAAAT 57.745 29.630 2.34 0.00 41.65 2.32
460 470 7.968246 TGTCATGTAACAACCAACAAATTTTG 58.032 30.769 7.59 7.59 0.00 2.44
477 487 9.019656 ACAAATTTTGAATTATTAAAAGGCCCC 57.980 29.630 15.81 0.00 0.00 5.80
481 491 9.899661 ATTTTGAATTATTAAAAGGCCCCTAAC 57.100 29.630 0.00 0.00 0.00 2.34
482 492 7.426606 TTGAATTATTAAAAGGCCCCTAACC 57.573 36.000 0.00 0.00 0.00 2.85
496 508 9.863447 AAGGCCCCTAACCTAATTAATATAGTA 57.137 33.333 0.00 0.00 36.14 1.82
497 509 9.276791 AGGCCCCTAACCTAATTAATATAGTAC 57.723 37.037 0.00 0.00 35.10 2.73
518 530 7.172342 AGTACCAGTAGCAAATTAATTGACCA 58.828 34.615 0.39 0.00 41.85 4.02
519 531 6.267496 ACCAGTAGCAAATTAATTGACCAC 57.733 37.500 0.39 0.00 41.85 4.16
582 595 3.790691 TTTTTGTGCACTCCGAGGA 57.209 47.368 19.41 0.00 0.00 3.71
583 596 2.270352 TTTTTGTGCACTCCGAGGAT 57.730 45.000 19.41 0.00 0.00 3.24
584 597 3.410631 TTTTTGTGCACTCCGAGGATA 57.589 42.857 19.41 0.00 0.00 2.59
585 598 3.627395 TTTTGTGCACTCCGAGGATAT 57.373 42.857 19.41 0.00 0.00 1.63
586 599 3.627395 TTTGTGCACTCCGAGGATATT 57.373 42.857 19.41 0.00 0.00 1.28
587 600 4.746535 TTTGTGCACTCCGAGGATATTA 57.253 40.909 19.41 0.00 0.00 0.98
588 601 4.746535 TTGTGCACTCCGAGGATATTAA 57.253 40.909 19.41 0.00 0.00 1.40
589 602 4.054780 TGTGCACTCCGAGGATATTAAC 57.945 45.455 19.41 0.00 0.00 2.01
590 603 3.704566 TGTGCACTCCGAGGATATTAACT 59.295 43.478 19.41 0.00 0.00 2.24
591 604 4.891168 TGTGCACTCCGAGGATATTAACTA 59.109 41.667 19.41 0.00 0.00 2.24
592 605 5.009710 TGTGCACTCCGAGGATATTAACTAG 59.990 44.000 19.41 0.00 0.00 2.57
593 606 5.009811 GTGCACTCCGAGGATATTAACTAGT 59.990 44.000 10.32 0.00 0.00 2.57
594 607 6.206243 GTGCACTCCGAGGATATTAACTAGTA 59.794 42.308 10.32 0.00 0.00 1.82
595 608 6.946583 TGCACTCCGAGGATATTAACTAGTAT 59.053 38.462 0.00 0.00 0.00 2.12
596 609 7.450634 TGCACTCCGAGGATATTAACTAGTATT 59.549 37.037 0.00 0.00 0.00 1.89
597 610 8.305317 GCACTCCGAGGATATTAACTAGTATTT 58.695 37.037 0.00 0.00 0.00 1.40
612 625 8.630054 AACTAGTATTTATGTGCCAAGTTTCA 57.370 30.769 0.00 0.00 0.00 2.69
613 626 8.630054 ACTAGTATTTATGTGCCAAGTTTCAA 57.370 30.769 0.00 0.00 0.00 2.69
614 627 8.512138 ACTAGTATTTATGTGCCAAGTTTCAAC 58.488 33.333 0.00 0.00 0.00 3.18
615 628 7.524717 AGTATTTATGTGCCAAGTTTCAACT 57.475 32.000 0.00 0.00 42.04 3.16
616 629 7.593825 AGTATTTATGTGCCAAGTTTCAACTC 58.406 34.615 0.00 0.00 38.57 3.01
617 630 5.843673 TTTATGTGCCAAGTTTCAACTCA 57.156 34.783 0.00 0.00 38.57 3.41
618 631 5.843673 TTATGTGCCAAGTTTCAACTCAA 57.156 34.783 0.00 0.00 38.57 3.02
619 632 4.734398 ATGTGCCAAGTTTCAACTCAAA 57.266 36.364 0.00 0.00 38.57 2.69
620 633 3.843999 TGTGCCAAGTTTCAACTCAAAC 58.156 40.909 0.00 0.00 38.57 2.93
621 634 3.256879 TGTGCCAAGTTTCAACTCAAACA 59.743 39.130 0.00 0.00 38.57 2.83
622 635 4.241681 GTGCCAAGTTTCAACTCAAACAA 58.758 39.130 0.00 0.00 38.57 2.83
623 636 4.688413 GTGCCAAGTTTCAACTCAAACAAA 59.312 37.500 0.00 0.00 38.57 2.83
624 637 5.178438 GTGCCAAGTTTCAACTCAAACAAAA 59.822 36.000 0.00 0.00 38.57 2.44
625 638 5.760253 TGCCAAGTTTCAACTCAAACAAAAA 59.240 32.000 0.00 0.00 38.57 1.94
665 678 9.734620 TTTCAAATGAATGTAAAACTGAGTCAG 57.265 29.630 18.83 18.83 34.13 3.51
666 679 8.675705 TCAAATGAATGTAAAACTGAGTCAGA 57.324 30.769 26.86 3.11 35.18 3.27
667 680 9.288576 TCAAATGAATGTAAAACTGAGTCAGAT 57.711 29.630 26.86 12.52 35.18 2.90
668 681 9.338291 CAAATGAATGTAAAACTGAGTCAGATG 57.662 33.333 26.86 1.32 35.18 2.90
669 682 8.627208 AATGAATGTAAAACTGAGTCAGATGT 57.373 30.769 26.86 12.74 35.18 3.06
670 683 8.627208 ATGAATGTAAAACTGAGTCAGATGTT 57.373 30.769 26.86 17.34 35.18 2.71
671 684 9.725019 ATGAATGTAAAACTGAGTCAGATGTTA 57.275 29.630 26.86 16.43 35.18 2.41
672 685 9.554395 TGAATGTAAAACTGAGTCAGATGTTAA 57.446 29.630 26.86 8.25 35.18 2.01
675 688 8.725405 TGTAAAACTGAGTCAGATGTTAAACA 57.275 30.769 26.86 18.16 35.18 2.83
676 689 9.337396 TGTAAAACTGAGTCAGATGTTAAACAT 57.663 29.630 26.86 5.11 42.43 2.71
714 727 6.129053 GAGAAAATCTCCCATGCACTTAAG 57.871 41.667 0.00 0.00 37.55 1.85
715 728 4.400567 AGAAAATCTCCCATGCACTTAAGC 59.599 41.667 1.29 0.00 0.00 3.09
716 729 2.355010 ATCTCCCATGCACTTAAGCC 57.645 50.000 1.29 0.00 0.00 4.35
717 730 0.255890 TCTCCCATGCACTTAAGCCC 59.744 55.000 1.29 0.00 0.00 5.19
718 731 0.034186 CTCCCATGCACTTAAGCCCA 60.034 55.000 1.29 0.00 0.00 5.36
719 732 0.630673 TCCCATGCACTTAAGCCCAT 59.369 50.000 1.29 2.54 0.00 4.00
720 733 1.006998 TCCCATGCACTTAAGCCCATT 59.993 47.619 1.29 0.00 0.00 3.16
721 734 2.243478 TCCCATGCACTTAAGCCCATTA 59.757 45.455 1.29 0.00 0.00 1.90
722 735 2.624838 CCCATGCACTTAAGCCCATTAG 59.375 50.000 1.29 0.17 0.00 1.73
723 736 2.624838 CCATGCACTTAAGCCCATTAGG 59.375 50.000 1.29 0.93 39.47 2.69
724 737 3.554934 CATGCACTTAAGCCCATTAGGA 58.445 45.455 1.29 0.00 38.24 2.94
725 738 3.730215 TGCACTTAAGCCCATTAGGAA 57.270 42.857 1.29 0.00 38.24 3.36
731 744 1.286248 AAGCCCATTAGGAAGGACGT 58.714 50.000 0.00 0.00 38.24 4.34
746 759 2.018515 GGACGTGGTTTTTGTCCTTCA 58.981 47.619 0.00 0.00 46.86 3.02
769 782 0.035152 TCCATTCACAGCGGCAATCT 60.035 50.000 1.45 0.00 0.00 2.40
799 812 1.835483 CGCTAGCATGTGGATTCGCC 61.835 60.000 16.45 0.00 37.10 5.54
815 828 3.818787 CCTTGCATGTCGGCCAGC 61.819 66.667 2.24 0.00 0.00 4.85
981 997 0.036952 ACAGAGCATTGACCACGAGG 60.037 55.000 0.00 0.00 42.21 4.63
1016 1032 0.546122 TCAATGGCGCCTAGGAATGT 59.454 50.000 29.70 0.20 0.00 2.71
1070 1086 0.546122 ACGGATCTAAGCCATGGCAA 59.454 50.000 37.18 23.65 44.88 4.52
1231 1248 0.827368 ACCTCCAGAAGAGATTCCGC 59.173 55.000 0.00 0.00 46.50 5.54
1262 1279 6.069331 AGTTCTTCGGCATAGATACTTCCTA 58.931 40.000 0.00 0.00 0.00 2.94
1288 1305 4.082081 CACATAGGTGCCATCACAAAATGT 60.082 41.667 0.00 1.93 44.87 2.71
1318 1335 4.067972 AGAAAAGTGGCTTTCGTCTACA 57.932 40.909 0.00 0.00 39.76 2.74
1533 1557 7.916914 ACTTAGCCGTTCATTAATACAACTT 57.083 32.000 7.51 0.00 0.00 2.66
1592 1616 3.769300 AGGTTGCAGACAAAGAAAAAGGT 59.231 39.130 0.00 0.00 37.58 3.50
1637 1661 3.173151 TGTGGACTGAGAGGAGCAATAA 58.827 45.455 0.00 0.00 0.00 1.40
2011 2035 5.010112 TGTTCGATTTTGTTTCTATTGGCCA 59.990 36.000 0.00 0.00 0.00 5.36
2143 2167 8.445493 GTTCCATAGGCATTTCTTCAATTTTTG 58.555 33.333 0.00 0.00 0.00 2.44
2182 2282 2.549754 AGTTTGTTGCTTCCTGTCATCG 59.450 45.455 0.00 0.00 0.00 3.84
2188 2288 0.824759 GCTTCCTGTCATCGGTACCT 59.175 55.000 10.90 0.00 0.00 3.08
2372 2473 5.366768 AGACCACTGCCAACATATAGTGTAT 59.633 40.000 0.00 0.00 41.14 2.29
2380 2481 6.037720 TGCCAACATATAGTGTATTGTTTCCG 59.962 38.462 0.00 0.00 41.14 4.30
2764 2872 5.416271 AAATCGCTTAGGTTCAGTTCCTA 57.584 39.130 0.00 0.00 36.60 2.94
2850 2958 4.190001 CTCTACACCGACTAGTCAGCTTA 58.810 47.826 22.37 7.27 0.00 3.09
3104 3212 3.195825 GGACAACTAGGCTAGTGTGTCAT 59.804 47.826 36.69 21.60 42.23 3.06
3108 3216 6.185511 ACAACTAGGCTAGTGTGTCATACTA 58.814 40.000 26.87 8.92 39.39 1.82
3227 3335 3.090210 TGAATGATGCCACATTGGTCT 57.910 42.857 9.59 0.00 40.46 3.85
3234 3342 1.271817 TGCCACATTGGTCTGTATGCA 60.272 47.619 0.00 0.00 40.46 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.908483 GGGAAGGACGGAGCTCAAT 59.092 57.895 17.19 1.69 0.00 2.57
23 24 5.637127 ACTTTCCGAAAAGATAAGGGGAAA 58.363 37.500 0.00 3.37 43.90 3.13
54 56 2.807967 TGTCGTCCTTTCTGCAAGATTG 59.192 45.455 0.00 0.00 46.36 2.67
59 62 2.325583 AGTTGTCGTCCTTTCTGCAA 57.674 45.000 0.00 0.00 0.00 4.08
71 74 0.716108 GCCTCACGATGAAGTTGTCG 59.284 55.000 5.88 5.88 43.13 4.35
73 76 2.479566 ATGCCTCACGATGAAGTTGT 57.520 45.000 0.00 0.00 0.00 3.32
75 78 3.941483 CCTTAATGCCTCACGATGAAGTT 59.059 43.478 0.00 0.00 0.00 2.66
84 87 4.519540 TTTCTTTGCCTTAATGCCTCAC 57.480 40.909 0.00 0.00 0.00 3.51
88 91 5.578336 GTCTTCATTTCTTTGCCTTAATGCC 59.422 40.000 0.00 0.00 0.00 4.40
90 93 8.030692 TGATGTCTTCATTTCTTTGCCTTAATG 58.969 33.333 0.00 0.00 34.06 1.90
91 94 8.125978 TGATGTCTTCATTTCTTTGCCTTAAT 57.874 30.769 0.00 0.00 34.06 1.40
92 95 7.523293 TGATGTCTTCATTTCTTTGCCTTAA 57.477 32.000 0.00 0.00 34.06 1.85
94 97 6.409524 TTGATGTCTTCATTTCTTTGCCTT 57.590 33.333 0.00 0.00 33.34 4.35
96 99 6.628185 AGATTGATGTCTTCATTTCTTTGCC 58.372 36.000 0.00 0.00 33.34 4.52
100 103 9.690913 TCCATTAGATTGATGTCTTCATTTCTT 57.309 29.630 6.89 0.00 33.34 2.52
146 149 2.030540 CGTGTCTTCTCGGTCTTGGTTA 60.031 50.000 0.00 0.00 0.00 2.85
190 196 0.496841 AAGAGGTGGAGTAAGGGGGT 59.503 55.000 0.00 0.00 0.00 4.95
217 224 4.087182 TCCACTACAAGAAATCTCGTCCT 58.913 43.478 0.00 0.00 0.00 3.85
258 265 4.716784 TGAGGTTACTGTAGCATGATTCCT 59.283 41.667 0.00 0.00 0.00 3.36
300 309 6.128063 TGGCAAATTGGCTTAATAAAACATGC 60.128 34.615 20.08 0.00 44.10 4.06
305 315 6.120507 AGGTGGCAAATTGGCTTAATAAAA 57.879 33.333 20.08 0.00 44.10 1.52
308 318 8.540507 TTATTAGGTGGCAAATTGGCTTAATA 57.459 30.769 20.08 18.73 44.10 0.98
309 319 5.955961 ATTAGGTGGCAAATTGGCTTAAT 57.044 34.783 20.08 16.30 44.10 1.40
311 321 6.859112 TTTATTAGGTGGCAAATTGGCTTA 57.141 33.333 20.08 7.78 44.10 3.09
312 322 5.753721 TTTATTAGGTGGCAAATTGGCTT 57.246 34.783 20.08 8.69 44.10 4.35
313 323 5.753721 TTTTATTAGGTGGCAAATTGGCT 57.246 34.783 20.08 3.14 44.10 4.75
315 325 8.558973 TTGATTTTTATTAGGTGGCAAATTGG 57.441 30.769 0.00 0.00 0.00 3.16
316 326 9.824534 GTTTGATTTTTATTAGGTGGCAAATTG 57.175 29.630 0.00 0.00 0.00 2.32
426 436 9.953697 GTTGGTTGTTACATGACAATTACTTAA 57.046 29.630 0.00 0.00 41.18 1.85
436 446 8.190888 TCAAAATTTGTTGGTTGTTACATGAC 57.809 30.769 0.00 0.00 0.00 3.06
455 465 9.899661 GTTAGGGGCCTTTTAATAATTCAAAAT 57.100 29.630 0.84 0.00 0.00 1.82
456 466 8.322828 GGTTAGGGGCCTTTTAATAATTCAAAA 58.677 33.333 0.84 0.00 0.00 2.44
460 470 8.771521 TTAGGTTAGGGGCCTTTTAATAATTC 57.228 34.615 0.84 0.00 37.54 2.17
472 482 8.489489 GGTACTATATTAATTAGGTTAGGGGCC 58.511 40.741 0.00 0.00 0.00 5.80
492 504 8.322828 TGGTCAATTAATTTGCTACTGGTACTA 58.677 33.333 0.00 0.00 35.16 1.82
493 505 7.120726 GTGGTCAATTAATTTGCTACTGGTACT 59.879 37.037 0.00 0.00 35.16 2.73
494 506 7.120726 AGTGGTCAATTAATTTGCTACTGGTAC 59.879 37.037 13.40 0.00 34.44 3.34
496 508 6.010219 AGTGGTCAATTAATTTGCTACTGGT 58.990 36.000 13.40 0.00 34.44 4.00
497 509 6.515272 AGTGGTCAATTAATTTGCTACTGG 57.485 37.500 13.40 0.00 34.44 4.00
565 578 3.627395 ATATCCTCGGAGTGCACAAAA 57.373 42.857 21.04 0.07 0.00 2.44
566 579 3.627395 AATATCCTCGGAGTGCACAAA 57.373 42.857 21.04 0.00 0.00 2.83
567 580 4.161565 AGTTAATATCCTCGGAGTGCACAA 59.838 41.667 21.04 0.08 0.00 3.33
568 581 3.704566 AGTTAATATCCTCGGAGTGCACA 59.295 43.478 21.04 0.00 0.00 4.57
569 582 4.323553 AGTTAATATCCTCGGAGTGCAC 57.676 45.455 9.40 9.40 0.00 4.57
570 583 5.138276 ACTAGTTAATATCCTCGGAGTGCA 58.862 41.667 4.02 0.00 0.00 4.57
571 584 5.708877 ACTAGTTAATATCCTCGGAGTGC 57.291 43.478 4.02 0.00 0.00 4.40
586 599 9.727859 TGAAACTTGGCACATAAATACTAGTTA 57.272 29.630 0.00 0.00 39.30 2.24
587 600 8.630054 TGAAACTTGGCACATAAATACTAGTT 57.370 30.769 0.00 0.00 39.30 2.24
588 601 8.512138 GTTGAAACTTGGCACATAAATACTAGT 58.488 33.333 0.00 0.00 39.30 2.57
589 602 8.730680 AGTTGAAACTTGGCACATAAATACTAG 58.269 33.333 0.00 0.00 39.30 2.57
590 603 8.630054 AGTTGAAACTTGGCACATAAATACTA 57.370 30.769 0.00 0.00 39.30 1.82
591 604 7.230510 TGAGTTGAAACTTGGCACATAAATACT 59.769 33.333 0.00 0.00 39.88 2.12
592 605 7.367285 TGAGTTGAAACTTGGCACATAAATAC 58.633 34.615 0.00 0.00 39.88 1.89
593 606 7.517614 TGAGTTGAAACTTGGCACATAAATA 57.482 32.000 0.00 0.00 39.88 1.40
594 607 6.403866 TGAGTTGAAACTTGGCACATAAAT 57.596 33.333 0.00 0.00 39.88 1.40
595 608 5.843673 TGAGTTGAAACTTGGCACATAAA 57.156 34.783 0.00 0.00 39.88 1.40
596 609 5.843673 TTGAGTTGAAACTTGGCACATAA 57.156 34.783 0.00 0.00 39.88 1.90
597 610 5.126222 TGTTTGAGTTGAAACTTGGCACATA 59.874 36.000 0.00 0.00 39.88 2.29
598 611 4.081752 TGTTTGAGTTGAAACTTGGCACAT 60.082 37.500 0.00 0.00 39.88 3.21
599 612 3.256879 TGTTTGAGTTGAAACTTGGCACA 59.743 39.130 0.00 0.00 39.88 4.57
600 613 3.843999 TGTTTGAGTTGAAACTTGGCAC 58.156 40.909 0.00 0.00 39.88 5.01
601 614 4.527509 TTGTTTGAGTTGAAACTTGGCA 57.472 36.364 0.00 0.00 39.88 4.92
602 615 5.854431 TTTTGTTTGAGTTGAAACTTGGC 57.146 34.783 0.00 0.00 39.88 4.52
639 652 9.734620 CTGACTCAGTTTTACATTCATTTGAAA 57.265 29.630 0.00 0.00 37.61 2.69
640 653 9.119418 TCTGACTCAGTTTTACATTCATTTGAA 57.881 29.630 5.94 0.00 34.14 2.69
641 654 8.675705 TCTGACTCAGTTTTACATTCATTTGA 57.324 30.769 5.94 0.00 32.61 2.69
642 655 9.338291 CATCTGACTCAGTTTTACATTCATTTG 57.662 33.333 5.94 0.00 32.61 2.32
643 656 9.071276 ACATCTGACTCAGTTTTACATTCATTT 57.929 29.630 5.94 0.00 32.61 2.32
644 657 8.627208 ACATCTGACTCAGTTTTACATTCATT 57.373 30.769 5.94 0.00 32.61 2.57
645 658 8.627208 AACATCTGACTCAGTTTTACATTCAT 57.373 30.769 5.94 0.00 32.61 2.57
646 659 9.554395 TTAACATCTGACTCAGTTTTACATTCA 57.446 29.630 5.94 0.00 32.61 2.57
649 662 9.337396 TGTTTAACATCTGACTCAGTTTTACAT 57.663 29.630 5.94 0.00 32.61 2.29
650 663 8.725405 TGTTTAACATCTGACTCAGTTTTACA 57.275 30.769 5.94 4.55 32.61 2.41
691 704 5.449725 GCTTAAGTGCATGGGAGATTTTCTC 60.450 44.000 4.02 0.00 42.66 2.87
692 705 4.400567 GCTTAAGTGCATGGGAGATTTTCT 59.599 41.667 4.02 0.00 0.00 2.52
693 706 4.440663 GGCTTAAGTGCATGGGAGATTTTC 60.441 45.833 4.02 0.00 34.04 2.29
694 707 3.448660 GGCTTAAGTGCATGGGAGATTTT 59.551 43.478 4.02 0.00 34.04 1.82
695 708 3.026694 GGCTTAAGTGCATGGGAGATTT 58.973 45.455 4.02 0.00 34.04 2.17
696 709 2.659428 GGCTTAAGTGCATGGGAGATT 58.341 47.619 4.02 0.00 34.04 2.40
697 710 1.133668 GGGCTTAAGTGCATGGGAGAT 60.134 52.381 4.02 0.00 34.04 2.75
698 711 0.255890 GGGCTTAAGTGCATGGGAGA 59.744 55.000 4.02 0.00 34.04 3.71
699 712 0.034186 TGGGCTTAAGTGCATGGGAG 60.034 55.000 4.02 0.00 34.04 4.30
700 713 0.630673 ATGGGCTTAAGTGCATGGGA 59.369 50.000 4.02 0.00 34.04 4.37
701 714 1.488390 AATGGGCTTAAGTGCATGGG 58.512 50.000 4.02 0.00 34.04 4.00
702 715 2.624838 CCTAATGGGCTTAAGTGCATGG 59.375 50.000 4.02 0.00 34.04 3.66
703 716 3.554934 TCCTAATGGGCTTAAGTGCATG 58.445 45.455 4.02 0.00 34.39 4.06
704 717 3.951563 TCCTAATGGGCTTAAGTGCAT 57.048 42.857 4.02 0.00 34.39 3.96
705 718 3.620488 CTTCCTAATGGGCTTAAGTGCA 58.380 45.455 4.02 0.00 34.39 4.57
706 719 2.952310 CCTTCCTAATGGGCTTAAGTGC 59.048 50.000 4.02 0.00 34.39 4.40
707 720 4.200092 GTCCTTCCTAATGGGCTTAAGTG 58.800 47.826 4.02 0.00 34.39 3.16
708 721 3.118371 CGTCCTTCCTAATGGGCTTAAGT 60.118 47.826 4.02 0.00 34.39 2.24
709 722 3.118371 ACGTCCTTCCTAATGGGCTTAAG 60.118 47.826 0.00 0.00 34.39 1.85
710 723 2.841881 ACGTCCTTCCTAATGGGCTTAA 59.158 45.455 0.00 0.00 34.39 1.85
711 724 2.169769 CACGTCCTTCCTAATGGGCTTA 59.830 50.000 0.00 0.00 34.39 3.09
712 725 1.065418 CACGTCCTTCCTAATGGGCTT 60.065 52.381 0.00 0.00 34.39 4.35
713 726 0.541863 CACGTCCTTCCTAATGGGCT 59.458 55.000 0.00 0.00 34.39 5.19
714 727 0.463833 CCACGTCCTTCCTAATGGGC 60.464 60.000 0.00 0.00 34.39 5.36
715 728 0.909623 ACCACGTCCTTCCTAATGGG 59.090 55.000 0.00 0.00 0.00 4.00
716 729 2.781681 AACCACGTCCTTCCTAATGG 57.218 50.000 0.00 0.00 0.00 3.16
717 730 4.277423 ACAAAAACCACGTCCTTCCTAATG 59.723 41.667 0.00 0.00 0.00 1.90
718 731 4.466827 ACAAAAACCACGTCCTTCCTAAT 58.533 39.130 0.00 0.00 0.00 1.73
719 732 3.878699 GACAAAAACCACGTCCTTCCTAA 59.121 43.478 0.00 0.00 0.00 2.69
720 733 3.469739 GACAAAAACCACGTCCTTCCTA 58.530 45.455 0.00 0.00 0.00 2.94
721 734 2.294979 GACAAAAACCACGTCCTTCCT 58.705 47.619 0.00 0.00 0.00 3.36
722 735 1.335810 GGACAAAAACCACGTCCTTCC 59.664 52.381 0.00 0.00 44.82 3.46
723 736 2.768833 GGACAAAAACCACGTCCTTC 57.231 50.000 0.00 0.00 44.82 3.46
731 744 2.424246 GGAACGTGAAGGACAAAAACCA 59.576 45.455 0.00 0.00 0.00 3.67
746 759 2.325082 GCCGCTGTGAATGGAACGT 61.325 57.895 0.00 0.00 0.00 3.99
799 812 3.057548 TGCTGGCCGACATGCAAG 61.058 61.111 0.00 0.00 35.26 4.01
815 828 0.108615 GTCATCGGTCCCACTCTGTG 60.109 60.000 0.00 0.00 0.00 3.66
981 997 3.364366 CCATTGACGCTGAGAAAGAACAC 60.364 47.826 0.00 0.00 0.00 3.32
1016 1032 2.000803 TCCCTCCTTCTCCTGTGTAGA 58.999 52.381 0.00 0.00 0.00 2.59
1070 1086 4.148128 AGAGATTCGCCTGATTCAACAT 57.852 40.909 0.00 0.00 0.00 2.71
1231 1248 2.322355 ATGCCGAAGAACTCTGGATG 57.678 50.000 0.00 0.00 0.00 3.51
1262 1279 1.845791 TGTGATGGCACCTATGTGGAT 59.154 47.619 0.00 0.00 44.51 3.41
1288 1305 1.032014 GCCACTTTTCTTGCTGGACA 58.968 50.000 0.00 0.00 0.00 4.02
1592 1616 6.485830 ACTCTAAGTATGCTTGCTCCATTA 57.514 37.500 6.28 0.00 36.22 1.90
1637 1661 2.108952 ACCTGCTGGTTTTCAATCTCCT 59.891 45.455 9.88 0.00 46.05 3.69
2011 2035 6.686630 TCAATGGAAAATAATTCTTGCACGT 58.313 32.000 0.00 0.00 0.00 4.49
2143 2167 5.291128 ACAAACTGTATACTTATCACAGCGC 59.709 40.000 0.00 0.00 42.76 5.92
2372 2473 6.566942 CGACCAAACTTCATAATCGGAAACAA 60.567 38.462 0.00 0.00 0.00 2.83
2380 2481 8.015658 GGTATAATGCGACCAAACTTCATAATC 58.984 37.037 0.00 0.00 35.65 1.75
2534 2642 5.772672 ACATTGTTAAAGTACTGGGAATGCA 59.227 36.000 0.00 0.00 0.00 3.96
2764 2872 4.136051 CAAATCCACCAACAAAGCCAAAT 58.864 39.130 0.00 0.00 0.00 2.32
2850 2958 3.244422 TGCAAGTCTCCGACCAGTTTATT 60.244 43.478 0.00 0.00 32.18 1.40
3227 3335 8.409371 TGTTCTCAGTTAATTGTTTTGCATACA 58.591 29.630 0.00 0.00 0.00 2.29
3234 3342 6.476706 GCAAGCTGTTCTCAGTTAATTGTTTT 59.523 34.615 0.00 0.00 43.05 2.43


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

AutoCloner maintained by Alex Coulton.