Multiple sequence alignment - TraesCS6B01G242600

Loading Multiple Alignment...

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 TraesCS6B01G242600 chr6B 100.000 2537 0 0 1 2537 430872865 430870329 0.000000e+00 4686
1 TraesCS6B01G242600 chr6B 85.030 501 62 8 1 495 133055001 133055494 4.870000e-137 497
2 TraesCS6B01G242600 chr6B 76.910 576 129 4 1852 2425 118687722 118687149 8.750000e-85 324
3 TraesCS6B01G242600 chr6B 75.622 603 135 11 1855 2451 719313243 719312647 3.190000e-74 289
4 TraesCS6B01G242600 chr2A 95.985 1918 75 2 622 2537 611112596 611114513 0.000000e+00 3114
5 TraesCS6B01G242600 chr1B 94.746 552 14 1 1 552 677950651 677951187 0.000000e+00 845
6 TraesCS6B01G242600 chr1B 84.461 547 61 10 1 537 547591911 547591379 3.740000e-143 518
7 TraesCS6B01G242600 chr5D 85.267 543 60 8 1 537 41775947 41776475 2.220000e-150 542
8 TraesCS6B01G242600 chr4B 84.461 547 61 10 1 537 523438283 523438815 3.740000e-143 518
9 TraesCS6B01G242600 chr3A 84.461 547 61 10 1 537 495022250 495021718 3.740000e-143 518
10 TraesCS6B01G242600 chr3A 79.630 486 86 9 1938 2416 555726676 555727155 1.120000e-88 337
11 TraesCS6B01G242600 chr3A 81.280 422 66 10 1938 2353 555759150 555759564 1.880000e-86 329
12 TraesCS6B01G242600 chr1A 84.095 547 63 10 1 537 504265169 504264637 8.100000e-140 507
13 TraesCS6B01G242600 chr6D 76.845 691 150 8 1851 2536 433506322 433505637 5.120000e-102 381
14 TraesCS6B01G242600 chr6D 79.302 401 79 3 1851 2248 188892655 188892256 6.910000e-71 278
15 TraesCS6B01G242600 chr2D 76.778 689 152 8 1851 2535 101348084 101347400 1.840000e-101 379
16 TraesCS6B01G242600 chr6A 75.789 570 129 7 1851 2416 291494242 291493678 1.920000e-71 279


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 TraesCS6B01G242600 chr6B 430870329 430872865 2536 True 4686 4686 100.000 1 2537 1 chr6B.!!$R2 2536
1 TraesCS6B01G242600 chr6B 118687149 118687722 573 True 324 324 76.910 1852 2425 1 chr6B.!!$R1 573
2 TraesCS6B01G242600 chr6B 719312647 719313243 596 True 289 289 75.622 1855 2451 1 chr6B.!!$R3 596
3 TraesCS6B01G242600 chr2A 611112596 611114513 1917 False 3114 3114 95.985 622 2537 1 chr2A.!!$F1 1915
4 TraesCS6B01G242600 chr1B 677950651 677951187 536 False 845 845 94.746 1 552 1 chr1B.!!$F1 551
5 TraesCS6B01G242600 chr1B 547591379 547591911 532 True 518 518 84.461 1 537 1 chr1B.!!$R1 536
6 TraesCS6B01G242600 chr5D 41775947 41776475 528 False 542 542 85.267 1 537 1 chr5D.!!$F1 536
7 TraesCS6B01G242600 chr4B 523438283 523438815 532 False 518 518 84.461 1 537 1 chr4B.!!$F1 536
8 TraesCS6B01G242600 chr3A 495021718 495022250 532 True 518 518 84.461 1 537 1 chr3A.!!$R1 536
9 TraesCS6B01G242600 chr1A 504264637 504265169 532 True 507 507 84.095 1 537 1 chr1A.!!$R1 536
10 TraesCS6B01G242600 chr6D 433505637 433506322 685 True 381 381 76.845 1851 2536 1 chr6D.!!$R2 685
11 TraesCS6B01G242600 chr2D 101347400 101348084 684 True 379 379 76.778 1851 2535 1 chr2D.!!$R1 684
12 TraesCS6B01G242600 chr6A 291493678 291494242 564 True 279 279 75.789 1851 2416 1 chr6A.!!$R1 565

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
580 591 0.039074 CCGATATGTCAGGAGCGTCC 60.039 60.0 0.0 0.0 36.58 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1792 1805 0.320374 CGTTGTTGCACCTCCCTCTA 59.68 55.0 0.0 0.0 0.0 2.43 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
33 34 9.342308 TGAATCATACAGGAAGATACAAAATCC 57.658 33.333 0.00 0.00 0.00 3.01
34 35 9.342308 GAATCATACAGGAAGATACAAAATCCA 57.658 33.333 0.00 0.00 34.30 3.41
35 36 9.699410 AATCATACAGGAAGATACAAAATCCAA 57.301 29.630 0.00 0.00 34.30 3.53
38 39 6.824305 ACAGGAAGATACAAAATCCAAGTG 57.176 37.500 0.00 0.00 34.30 3.16
91 96 8.520351 GCTGGTTCCTTACACACTAAATAAAAT 58.480 33.333 0.00 0.00 0.00 1.82
196 201 3.057174 CGGTGAGATCTATGCTCTTACCC 60.057 52.174 0.00 0.00 43.16 3.69
472 483 6.764308 ATGATCGGTGAAAGACAATGAAAT 57.236 33.333 0.00 0.00 0.00 2.17
495 506 1.891150 AGGCAAACAATCTTCAGGCTG 59.109 47.619 8.58 8.58 0.00 4.85
506 517 4.948341 TCTTCAGGCTGTGTAACTACAA 57.052 40.909 15.27 0.00 38.04 2.41
553 564 6.328641 GGCTACACCTAATCGATAGAAAGA 57.671 41.667 0.00 0.00 42.59 2.52
554 565 6.151004 GGCTACACCTAATCGATAGAAAGAC 58.849 44.000 0.00 0.00 42.59 3.01
555 566 6.238953 GGCTACACCTAATCGATAGAAAGACA 60.239 42.308 0.00 0.00 42.59 3.41
556 567 7.524038 GGCTACACCTAATCGATAGAAAGACAT 60.524 40.741 0.00 0.00 42.59 3.06
562 573 2.826428 TCGATAGAAAGACATGCAGCC 58.174 47.619 0.00 0.00 46.15 4.85
563 574 1.524355 CGATAGAAAGACATGCAGCCG 59.476 52.381 0.00 0.00 39.76 5.52
564 575 2.799562 CGATAGAAAGACATGCAGCCGA 60.800 50.000 0.00 0.00 39.76 5.54
565 576 2.988010 TAGAAAGACATGCAGCCGAT 57.012 45.000 0.00 0.00 0.00 4.18
566 577 2.988010 AGAAAGACATGCAGCCGATA 57.012 45.000 0.00 0.00 0.00 2.92
567 578 3.482156 AGAAAGACATGCAGCCGATAT 57.518 42.857 0.00 0.00 0.00 1.63
568 579 3.136763 AGAAAGACATGCAGCCGATATG 58.863 45.455 0.00 0.00 0.00 1.78
569 580 2.627515 AAGACATGCAGCCGATATGT 57.372 45.000 0.00 0.00 37.72 2.29
570 581 2.160822 AGACATGCAGCCGATATGTC 57.839 50.000 13.36 13.36 46.83 3.06
571 582 1.869774 GACATGCAGCCGATATGTCA 58.130 50.000 15.45 0.00 46.12 3.58
572 583 1.797046 GACATGCAGCCGATATGTCAG 59.203 52.381 15.45 0.00 46.12 3.51
573 584 1.154197 CATGCAGCCGATATGTCAGG 58.846 55.000 0.00 0.00 0.00 3.86
574 585 1.051008 ATGCAGCCGATATGTCAGGA 58.949 50.000 0.00 0.00 0.00 3.86
575 586 0.390492 TGCAGCCGATATGTCAGGAG 59.610 55.000 4.90 0.00 0.00 3.69
576 587 0.948141 GCAGCCGATATGTCAGGAGC 60.948 60.000 4.90 4.37 0.00 4.70
577 588 0.665670 CAGCCGATATGTCAGGAGCG 60.666 60.000 4.90 0.00 0.00 5.03
578 589 1.109920 AGCCGATATGTCAGGAGCGT 61.110 55.000 4.90 0.00 0.00 5.07
579 590 0.664767 GCCGATATGTCAGGAGCGTC 60.665 60.000 4.90 0.00 0.00 5.19
580 591 0.039074 CCGATATGTCAGGAGCGTCC 60.039 60.000 0.00 0.00 36.58 4.79
581 592 0.039074 CGATATGTCAGGAGCGTCCC 60.039 60.000 1.06 0.00 37.19 4.46
582 593 1.333177 GATATGTCAGGAGCGTCCCT 58.667 55.000 1.06 0.00 37.19 4.20
583 594 2.515854 GATATGTCAGGAGCGTCCCTA 58.484 52.381 0.00 0.00 37.19 3.53
584 595 2.447408 TATGTCAGGAGCGTCCCTAA 57.553 50.000 0.00 0.00 37.19 2.69
585 596 0.824759 ATGTCAGGAGCGTCCCTAAC 59.175 55.000 0.00 0.00 37.19 2.34
586 597 0.251653 TGTCAGGAGCGTCCCTAACT 60.252 55.000 0.00 0.00 37.19 2.24
587 598 0.456628 GTCAGGAGCGTCCCTAACTC 59.543 60.000 0.00 0.00 37.19 3.01
588 599 0.331954 TCAGGAGCGTCCCTAACTCT 59.668 55.000 0.00 0.00 37.19 3.24
589 600 1.187087 CAGGAGCGTCCCTAACTCTT 58.813 55.000 0.00 0.00 37.19 2.85
590 601 1.135333 CAGGAGCGTCCCTAACTCTTC 59.865 57.143 0.00 0.00 37.19 2.87
591 602 1.006162 AGGAGCGTCCCTAACTCTTCT 59.994 52.381 0.00 0.00 37.19 2.85
592 603 2.241685 AGGAGCGTCCCTAACTCTTCTA 59.758 50.000 0.00 0.00 37.19 2.10
593 604 2.619646 GGAGCGTCCCTAACTCTTCTAG 59.380 54.545 0.00 0.00 0.00 2.43
594 605 2.025898 AGCGTCCCTAACTCTTCTAGC 58.974 52.381 0.00 0.00 0.00 3.42
595 606 2.025898 GCGTCCCTAACTCTTCTAGCT 58.974 52.381 0.00 0.00 0.00 3.32
596 607 3.117963 AGCGTCCCTAACTCTTCTAGCTA 60.118 47.826 0.00 0.00 0.00 3.32
597 608 3.003585 GCGTCCCTAACTCTTCTAGCTAC 59.996 52.174 0.00 0.00 0.00 3.58
598 609 3.248125 CGTCCCTAACTCTTCTAGCTACG 59.752 52.174 0.00 0.00 0.00 3.51
599 610 4.450053 GTCCCTAACTCTTCTAGCTACGA 58.550 47.826 0.00 0.00 0.00 3.43
600 611 4.512571 GTCCCTAACTCTTCTAGCTACGAG 59.487 50.000 0.00 7.90 0.00 4.18
601 612 3.816523 CCCTAACTCTTCTAGCTACGAGG 59.183 52.174 12.19 5.77 0.00 4.63
602 613 4.444591 CCCTAACTCTTCTAGCTACGAGGA 60.445 50.000 12.19 8.83 0.00 3.71
603 614 5.310451 CCTAACTCTTCTAGCTACGAGGAT 58.690 45.833 12.19 5.78 0.00 3.24
604 615 5.766174 CCTAACTCTTCTAGCTACGAGGATT 59.234 44.000 12.19 3.50 0.00 3.01
605 616 6.263617 CCTAACTCTTCTAGCTACGAGGATTT 59.736 42.308 12.19 11.18 0.00 2.17
606 617 5.761165 ACTCTTCTAGCTACGAGGATTTC 57.239 43.478 12.19 0.00 0.00 2.17
607 618 5.194432 ACTCTTCTAGCTACGAGGATTTCA 58.806 41.667 12.19 0.00 0.00 2.69
608 619 5.066764 ACTCTTCTAGCTACGAGGATTTCAC 59.933 44.000 12.19 0.00 0.00 3.18
609 620 4.338682 TCTTCTAGCTACGAGGATTTCACC 59.661 45.833 0.00 0.00 0.00 4.02
610 621 3.628008 TCTAGCTACGAGGATTTCACCA 58.372 45.455 0.00 0.00 0.00 4.17
611 622 4.215908 TCTAGCTACGAGGATTTCACCAT 58.784 43.478 0.00 0.00 0.00 3.55
612 623 5.382616 TCTAGCTACGAGGATTTCACCATA 58.617 41.667 0.00 0.00 0.00 2.74
613 624 5.831525 TCTAGCTACGAGGATTTCACCATAA 59.168 40.000 0.00 0.00 0.00 1.90
614 625 4.694339 AGCTACGAGGATTTCACCATAAC 58.306 43.478 0.00 0.00 0.00 1.89
615 626 3.808174 GCTACGAGGATTTCACCATAACC 59.192 47.826 0.00 0.00 0.00 2.85
616 627 2.901249 ACGAGGATTTCACCATAACCG 58.099 47.619 0.00 0.00 0.00 4.44
617 628 2.498481 ACGAGGATTTCACCATAACCGA 59.502 45.455 0.00 0.00 0.00 4.69
618 629 3.123804 CGAGGATTTCACCATAACCGAG 58.876 50.000 0.00 0.00 0.00 4.63
619 630 3.430374 CGAGGATTTCACCATAACCGAGT 60.430 47.826 0.00 0.00 0.00 4.18
620 631 4.514401 GAGGATTTCACCATAACCGAGTT 58.486 43.478 0.00 0.00 0.00 3.01
679 690 3.370633 GCCTCGGAAAGAAACTTCCCTAT 60.371 47.826 0.00 0.00 41.73 2.57
751 762 2.354805 GGGTTTGCTATATCCCCTAGCG 60.355 54.545 0.00 0.00 43.65 4.26
833 844 2.383527 CGACGAGGCTTGTTCCTGC 61.384 63.158 9.18 0.00 36.38 4.85
843 854 4.096003 GTTCCTGCGGGGCTAGCA 62.096 66.667 18.24 7.16 42.99 3.49
867 878 3.462678 GGGTCTCAGTCCTCGGCC 61.463 72.222 0.00 0.00 0.00 6.13
872 883 1.079543 CTCAGTCCTCGGCCAACAG 60.080 63.158 2.24 0.00 0.00 3.16
948 959 1.764054 CCAGGAGCGGGAGGAAGAT 60.764 63.158 0.00 0.00 0.00 2.40
954 965 1.144936 GCGGGAGGAAGATGACCTG 59.855 63.158 0.00 0.00 37.93 4.00
1030 1041 1.204704 CGAGGGTGCACACTGATAGAA 59.795 52.381 29.98 0.00 0.00 2.10
1086 1097 2.882876 GCATGGAGCTTGGCACAG 59.117 61.111 0.00 0.00 42.39 3.66
1103 1114 1.071699 ACAGGGTGCGACATTTACTGT 59.928 47.619 0.00 0.00 42.15 3.55
1104 1115 2.151202 CAGGGTGCGACATTTACTGTT 58.849 47.619 0.00 0.00 38.54 3.16
1110 1121 2.287308 TGCGACATTTACTGTTGTTGGC 60.287 45.455 0.00 2.33 40.84 4.52
1145 1156 2.113860 ATCACGGTGAATTGTCTGGG 57.886 50.000 15.72 0.00 0.00 4.45
1194 1205 1.363744 CTTGGCTCTTCCGTGATCAC 58.636 55.000 16.21 16.21 37.80 3.06
1265 1276 4.261405 CGTCCTTAATAGGCTCTCAGTCTG 60.261 50.000 0.00 0.00 41.69 3.51
1269 1280 5.279406 CCTTAATAGGCTCTCAGTCTGGATG 60.279 48.000 0.00 0.00 33.99 3.51
1290 1301 3.134458 GCAAATAGTTGATCTCCCTCCG 58.866 50.000 7.18 0.00 36.83 4.63
1308 1319 0.108186 CGCTGTACAGGAAGGATGCA 60.108 55.000 23.95 0.00 0.00 3.96
1430 1441 2.554142 TGTTGATCAGCCTCTTATGCG 58.446 47.619 7.13 0.00 0.00 4.73
1452 1463 5.555552 CGTTTTGTTTCCATCACCAAAAAC 58.444 37.500 0.00 0.00 38.20 2.43
1491 1502 8.705048 ACTACTCGGTTCTTTATGAGAAAATC 57.295 34.615 0.00 0.00 45.59 2.17
1493 1504 5.880887 ACTCGGTTCTTTATGAGAAAATCCC 59.119 40.000 0.00 0.00 45.59 3.85
1527 1539 0.332293 ATGTGGATGCATGGGTCACA 59.668 50.000 2.46 13.40 41.64 3.58
1529 1541 1.377072 TGGATGCATGGGTCACACG 60.377 57.895 2.46 0.00 0.00 4.49
1595 1607 2.352422 GGTGAGTGGATGCTGGCA 59.648 61.111 0.00 0.00 0.00 4.92
1635 1647 1.815003 CAACGCGATCATGGGAGCA 60.815 57.895 15.93 0.00 0.00 4.26
1697 1710 5.665916 AAAACATGAAGGATGGATTGGTC 57.334 39.130 0.00 0.00 36.23 4.02
1701 1714 1.486310 TGAAGGATGGATTGGTCGAGG 59.514 52.381 0.00 0.00 0.00 4.63
1773 1786 0.387565 GTCAAACCAATTGGGCACGT 59.612 50.000 27.89 3.92 42.05 4.49
1789 1802 0.249868 ACGTTGCAAGCTGCTACAGA 60.250 50.000 0.90 0.00 46.67 3.41
1792 1805 2.868583 CGTTGCAAGCTGCTACAGATAT 59.131 45.455 0.90 0.00 46.67 1.63
1811 1824 0.320374 TAGAGGGAGGTGCAACAACG 59.680 55.000 3.64 0.00 39.98 4.10
1904 1917 3.199946 AGAGGTCAAAGAAGGACAACACA 59.800 43.478 0.00 0.00 37.00 3.72
1994 2007 1.610363 TTTATGTTGGAACTGCCGCA 58.390 45.000 0.00 0.00 40.66 5.69
2050 2063 1.144936 GATCCAAGGGCGAGTCAGG 59.855 63.158 0.00 0.00 0.00 3.86
2114 2127 2.868899 AGGCAGAAAAGTTGAGAAGGG 58.131 47.619 0.00 0.00 0.00 3.95
2395 2408 7.274250 GCTGGTGATTTCAATGAGATTTTACAC 59.726 37.037 0.00 0.00 0.00 2.90
2454 2467 4.215965 CGCTGTATGCAAGTTTTTAACGT 58.784 39.130 0.00 0.00 43.06 3.99
2456 2469 5.209240 GCTGTATGCAAGTTTTTAACGTCA 58.791 37.500 0.00 0.00 42.31 4.35
2485 2498 3.314635 GTGATTGTGGCTTGGATGATCTC 59.685 47.826 0.00 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 0.030504 TGCATTGCACGAACCACTTG 59.969 50.000 7.38 0.00 31.71 3.16
34 35 0.961019 ATGCATTGCACGAACCACTT 59.039 45.000 14.66 0.00 43.04 3.16
35 36 1.819928 TATGCATTGCACGAACCACT 58.180 45.000 14.66 0.00 43.04 4.00
38 39 2.529151 CCTTTATGCATTGCACGAACC 58.471 47.619 14.66 0.00 43.04 3.62
134 139 5.426504 CATCAGGTAAGCAGAAGACTGAAT 58.573 41.667 0.00 0.00 46.03 2.57
472 483 4.022068 CAGCCTGAAGATTGTTTGCCTTTA 60.022 41.667 0.00 0.00 0.00 1.85
506 517 7.442656 CCTACGGAGAATAGGAACAATAACAT 58.557 38.462 0.00 0.00 41.70 2.71
552 563 1.797046 CTGACATATCGGCTGCATGTC 59.203 52.381 23.15 23.15 45.66 3.06
553 564 1.541889 CCTGACATATCGGCTGCATGT 60.542 52.381 11.17 11.17 35.65 3.21
554 565 1.154197 CCTGACATATCGGCTGCATG 58.846 55.000 0.50 0.00 0.00 4.06
555 566 1.001746 CTCCTGACATATCGGCTGCAT 59.998 52.381 0.50 0.00 0.00 3.96
556 567 0.390492 CTCCTGACATATCGGCTGCA 59.610 55.000 0.50 0.00 0.00 4.41
557 568 0.948141 GCTCCTGACATATCGGCTGC 60.948 60.000 0.00 0.00 0.00 5.25
558 569 0.665670 CGCTCCTGACATATCGGCTG 60.666 60.000 0.00 0.00 0.00 4.85
559 570 1.109920 ACGCTCCTGACATATCGGCT 61.110 55.000 0.00 0.00 0.00 5.52
560 571 0.664767 GACGCTCCTGACATATCGGC 60.665 60.000 0.00 0.00 0.00 5.54
561 572 0.039074 GGACGCTCCTGACATATCGG 60.039 60.000 0.00 0.00 32.53 4.18
562 573 0.039074 GGGACGCTCCTGACATATCG 60.039 60.000 4.41 0.00 36.57 2.92
563 574 1.333177 AGGGACGCTCCTGACATATC 58.667 55.000 0.00 0.00 36.57 1.63
564 575 2.628657 GTTAGGGACGCTCCTGACATAT 59.371 50.000 12.58 0.00 41.43 1.78
565 576 2.029623 GTTAGGGACGCTCCTGACATA 58.970 52.381 12.58 0.00 41.43 2.29
566 577 0.824759 GTTAGGGACGCTCCTGACAT 59.175 55.000 12.58 0.00 41.43 3.06
567 578 0.251653 AGTTAGGGACGCTCCTGACA 60.252 55.000 17.55 0.00 43.43 3.58
568 579 0.456628 GAGTTAGGGACGCTCCTGAC 59.543 60.000 10.34 10.34 41.92 3.51
569 580 0.331954 AGAGTTAGGGACGCTCCTGA 59.668 55.000 7.34 0.00 37.75 3.86
570 581 1.135333 GAAGAGTTAGGGACGCTCCTG 59.865 57.143 7.34 0.00 37.42 3.86
571 582 1.006162 AGAAGAGTTAGGGACGCTCCT 59.994 52.381 0.00 2.63 37.42 3.69
572 583 1.476477 AGAAGAGTTAGGGACGCTCC 58.524 55.000 0.00 0.00 37.42 4.70
573 584 2.033675 GCTAGAAGAGTTAGGGACGCTC 59.966 54.545 0.00 0.00 37.42 5.03
574 585 2.025898 GCTAGAAGAGTTAGGGACGCT 58.974 52.381 0.00 0.00 40.37 5.07
575 586 2.025898 AGCTAGAAGAGTTAGGGACGC 58.974 52.381 0.00 0.00 0.00 5.19
576 587 3.248125 CGTAGCTAGAAGAGTTAGGGACG 59.752 52.174 0.00 0.00 0.00 4.79
577 588 4.450053 TCGTAGCTAGAAGAGTTAGGGAC 58.550 47.826 0.00 0.00 30.22 4.46
578 589 4.444591 CCTCGTAGCTAGAAGAGTTAGGGA 60.445 50.000 15.47 0.00 30.22 4.20
579 590 3.816523 CCTCGTAGCTAGAAGAGTTAGGG 59.183 52.174 15.47 2.56 30.22 3.53
580 591 4.706035 TCCTCGTAGCTAGAAGAGTTAGG 58.294 47.826 15.47 5.96 0.00 2.69
581 592 6.870971 AATCCTCGTAGCTAGAAGAGTTAG 57.129 41.667 15.47 5.30 0.00 2.34
582 593 6.827251 TGAAATCCTCGTAGCTAGAAGAGTTA 59.173 38.462 15.47 7.40 0.00 2.24
583 594 5.652891 TGAAATCCTCGTAGCTAGAAGAGTT 59.347 40.000 15.47 10.27 0.00 3.01
584 595 5.066764 GTGAAATCCTCGTAGCTAGAAGAGT 59.933 44.000 15.47 4.04 0.00 3.24
585 596 5.506649 GGTGAAATCCTCGTAGCTAGAAGAG 60.507 48.000 11.74 11.74 0.00 2.85
586 597 4.338682 GGTGAAATCCTCGTAGCTAGAAGA 59.661 45.833 0.00 0.00 0.00 2.87
587 598 4.098044 TGGTGAAATCCTCGTAGCTAGAAG 59.902 45.833 0.00 0.00 0.00 2.85
588 599 4.021229 TGGTGAAATCCTCGTAGCTAGAA 58.979 43.478 0.00 0.00 0.00 2.10
589 600 3.628008 TGGTGAAATCCTCGTAGCTAGA 58.372 45.455 0.00 0.00 0.00 2.43
590 601 4.592485 ATGGTGAAATCCTCGTAGCTAG 57.408 45.455 0.00 0.00 0.00 3.42
591 602 5.221382 GGTTATGGTGAAATCCTCGTAGCTA 60.221 44.000 0.00 0.00 0.00 3.32
592 603 4.443034 GGTTATGGTGAAATCCTCGTAGCT 60.443 45.833 0.00 0.00 0.00 3.32
593 604 3.808174 GGTTATGGTGAAATCCTCGTAGC 59.192 47.826 0.00 0.00 0.00 3.58
594 605 4.049186 CGGTTATGGTGAAATCCTCGTAG 58.951 47.826 0.00 0.00 0.00 3.51
595 606 3.700539 TCGGTTATGGTGAAATCCTCGTA 59.299 43.478 0.00 0.00 0.00 3.43
596 607 2.498481 TCGGTTATGGTGAAATCCTCGT 59.502 45.455 0.00 0.00 0.00 4.18
597 608 3.123804 CTCGGTTATGGTGAAATCCTCG 58.876 50.000 0.00 0.00 0.00 4.63
598 609 4.138487 ACTCGGTTATGGTGAAATCCTC 57.862 45.455 0.00 0.00 0.00 3.71
599 610 4.019681 TCAACTCGGTTATGGTGAAATCCT 60.020 41.667 0.00 0.00 0.00 3.24
600 611 4.258543 TCAACTCGGTTATGGTGAAATCC 58.741 43.478 0.00 0.00 0.00 3.01
601 612 5.175859 TCTCAACTCGGTTATGGTGAAATC 58.824 41.667 0.00 0.00 0.00 2.17
602 613 5.160607 TCTCAACTCGGTTATGGTGAAAT 57.839 39.130 0.00 0.00 0.00 2.17
603 614 4.610605 TCTCAACTCGGTTATGGTGAAA 57.389 40.909 0.00 0.00 0.00 2.69
604 615 4.503910 CATCTCAACTCGGTTATGGTGAA 58.496 43.478 0.00 0.00 0.00 3.18
605 616 3.118775 CCATCTCAACTCGGTTATGGTGA 60.119 47.826 0.00 0.00 29.50 4.02
606 617 3.198068 CCATCTCAACTCGGTTATGGTG 58.802 50.000 0.00 0.00 29.50 4.17
607 618 2.838202 ACCATCTCAACTCGGTTATGGT 59.162 45.455 12.91 12.91 37.48 3.55
608 619 3.543680 ACCATCTCAACTCGGTTATGG 57.456 47.619 12.04 12.04 36.08 2.74
609 620 6.106673 ACTAAACCATCTCAACTCGGTTATG 58.893 40.000 0.00 0.00 40.84 1.90
610 621 6.295719 ACTAAACCATCTCAACTCGGTTAT 57.704 37.500 0.00 0.00 40.84 1.89
611 622 5.733620 ACTAAACCATCTCAACTCGGTTA 57.266 39.130 0.00 0.00 40.84 2.85
612 623 4.618920 ACTAAACCATCTCAACTCGGTT 57.381 40.909 0.00 0.00 43.55 4.44
613 624 4.618920 AACTAAACCATCTCAACTCGGT 57.381 40.909 0.00 0.00 0.00 4.69
614 625 4.091509 CGAAACTAAACCATCTCAACTCGG 59.908 45.833 0.00 0.00 0.00 4.63
615 626 4.434330 GCGAAACTAAACCATCTCAACTCG 60.434 45.833 0.00 0.00 0.00 4.18
616 627 4.142881 GGCGAAACTAAACCATCTCAACTC 60.143 45.833 0.00 0.00 0.00 3.01
617 628 3.751698 GGCGAAACTAAACCATCTCAACT 59.248 43.478 0.00 0.00 0.00 3.16
618 629 3.424433 CGGCGAAACTAAACCATCTCAAC 60.424 47.826 0.00 0.00 0.00 3.18
619 630 2.739913 CGGCGAAACTAAACCATCTCAA 59.260 45.455 0.00 0.00 0.00 3.02
620 631 2.289195 ACGGCGAAACTAAACCATCTCA 60.289 45.455 16.62 0.00 0.00 3.27
679 690 2.175069 AGGCTGACCCTAGTTATCTCGA 59.825 50.000 0.00 0.00 44.08 4.04
735 746 1.557099 CACCGCTAGGGGATATAGCA 58.443 55.000 31.00 0.00 46.39 3.49
751 762 3.116079 TCTGAACCCTAAAACGTCACC 57.884 47.619 0.00 0.00 0.00 4.02
794 805 5.117592 GTCGCAATGAACAAATCTTCAAAGG 59.882 40.000 0.00 0.00 33.85 3.11
833 844 2.903855 CTGCCATTGCTAGCCCCG 60.904 66.667 13.29 0.00 38.71 5.73
843 854 0.548682 AGGACTGAGACCCTGCCATT 60.549 55.000 0.00 0.00 0.00 3.16
849 860 2.363147 GCCGAGGACTGAGACCCT 60.363 66.667 0.00 0.00 35.02 4.34
867 878 4.389576 GCCACCTTCGCGCTGTTG 62.390 66.667 5.56 0.00 0.00 3.33
895 906 4.335416 CCTAACAATTCATCCACACCTGT 58.665 43.478 0.00 0.00 0.00 4.00
897 908 3.245229 TGCCTAACAATTCATCCACACCT 60.245 43.478 0.00 0.00 0.00 4.00
948 959 1.203013 TCCTCCTCGAAGTTCAGGTCA 60.203 52.381 16.26 3.38 0.00 4.02
954 965 2.738964 CGGGAATTCCTCCTCGAAGTTC 60.739 54.545 23.63 1.91 44.68 3.01
987 998 3.686227 ATTACCATGAATTCTGCCCCA 57.314 42.857 7.05 0.00 0.00 4.96
988 999 3.493176 GCAATTACCATGAATTCTGCCCC 60.493 47.826 7.05 0.00 0.00 5.80
993 1004 3.885297 CCCTCGCAATTACCATGAATTCT 59.115 43.478 7.05 0.00 0.00 2.40
1030 1041 2.624674 AAAGCACCACGGCTGAAGGT 62.625 55.000 0.00 3.77 45.07 3.50
1086 1097 1.877443 ACAACAGTAAATGTCGCACCC 59.123 47.619 0.00 0.00 43.00 4.61
1095 1106 5.003804 AGATTCTCGCCAACAACAGTAAAT 58.996 37.500 0.00 0.00 0.00 1.40
1103 1114 4.832248 AGTGAATAGATTCTCGCCAACAA 58.168 39.130 4.02 0.00 37.67 2.83
1104 1115 4.471904 AGTGAATAGATTCTCGCCAACA 57.528 40.909 4.02 0.00 37.67 3.33
1110 1121 5.853810 CACCGTGATAGTGAATAGATTCTCG 59.146 44.000 4.02 0.00 37.42 4.04
1145 1156 2.298163 TCTGTAACTCGTTTCCAGTCCC 59.702 50.000 8.20 0.00 0.00 4.46
1194 1205 6.662414 TCATAGCTTTCAATTAGAACACCG 57.338 37.500 0.00 0.00 35.56 4.94
1265 1276 4.723309 AGGGAGATCAACTATTTGCATCC 58.277 43.478 0.00 0.00 32.17 3.51
1269 1280 3.134458 CGGAGGGAGATCAACTATTTGC 58.866 50.000 0.00 0.00 32.17 3.68
1290 1301 2.113860 TTGCATCCTTCCTGTACAGC 57.886 50.000 17.86 4.94 0.00 4.40
1308 1319 5.393068 TCTTTGCCAGGGATCTAATGATT 57.607 39.130 0.00 0.00 32.19 2.57
1404 1415 3.726557 AGAGGCTGATCAACATCCAAA 57.273 42.857 7.13 0.00 37.26 3.28
1452 1463 4.220163 ACCGAGTAGTAAACCTTCTTCTGG 59.780 45.833 0.00 0.00 0.00 3.86
1491 1502 5.007034 TCCACATACATACAAAACACTGGG 58.993 41.667 0.00 0.00 0.00 4.45
1493 1504 6.029607 GCATCCACATACATACAAAACACTG 58.970 40.000 0.00 0.00 0.00 3.66
1527 1539 2.432628 GCCGTGCTCTAAGTGCGT 60.433 61.111 0.00 0.00 0.00 5.24
1529 1541 1.497722 GTTGCCGTGCTCTAAGTGC 59.502 57.895 0.00 0.00 0.00 4.40
1635 1647 8.571336 CATATCAACTTCTTTCAGTCCTTTGTT 58.429 33.333 0.00 0.00 0.00 2.83
1670 1682 6.071221 CCAATCCATCCTTCATGTTTTTCAGA 60.071 38.462 0.00 0.00 0.00 3.27
1697 1710 1.142748 CCTGCTAGAAGGCACCTCG 59.857 63.158 2.98 0.00 37.29 4.63
1701 1714 3.059352 TCTTTTCCTGCTAGAAGGCAC 57.941 47.619 12.63 0.00 37.29 5.01
1745 1758 4.175516 CCAATTGGTTTGACATTGGATCG 58.824 43.478 16.90 0.00 43.16 3.69
1789 1802 3.181465 CGTTGTTGCACCTCCCTCTATAT 60.181 47.826 0.00 0.00 0.00 0.86
1792 1805 0.320374 CGTTGTTGCACCTCCCTCTA 59.680 55.000 0.00 0.00 0.00 2.43
1811 1824 5.977725 CAGTGCATGATTCTGAATTTCCATC 59.022 40.000 4.11 0.00 0.00 3.51
1904 1917 4.979657 CTGGCATCCATCACAGCT 57.020 55.556 0.00 0.00 30.82 4.24
1994 2007 3.854669 CGCGGGCTTCCTCATCCT 61.855 66.667 0.00 0.00 0.00 3.24
2066 2079 7.040201 AGCTTTATTCAAATGAGCTTCAGACAA 60.040 33.333 8.68 0.00 36.48 3.18
2114 2127 3.513515 TCCATTACATCAAAACCAAGCCC 59.486 43.478 0.00 0.00 0.00 5.19
2395 2408 0.994995 CACCGTCTTTCTCATCAGCG 59.005 55.000 0.00 0.00 0.00 5.18
2456 2469 3.157087 CCAAGCCACAATCACTTAAGGT 58.843 45.455 7.53 0.00 0.00 3.50
2470 2483 0.982852 ACCCGAGATCATCCAAGCCA 60.983 55.000 0.00 0.00 0.00 4.75
2485 2498 3.862394 TTTGTCGCCCGTGTACCCG 62.862 63.158 0.00 0.00 0.00 5.28


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

AutoCloner maintained by Alex Coulton.