Multiple sequence alignment - TraesCS5B01G352000

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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 TraesCS5B01G352000 chr5B 100.000 2822 0 0 1 2822 531737961 531735140 0.000000e+00 5212
1 TraesCS5B01G352000 chr5D 93.659 2271 40 22 623 2822 437832208 437829971 0.000000e+00 3301
2 TraesCS5B01G352000 chr5D 94.223 502 10 8 1 485 437832704 437832205 0.000000e+00 749
3 TraesCS5B01G352000 chr5A 96.999 833 19 4 1995 2822 552776458 552775627 0.000000e+00 1395
4 TraesCS5B01G352000 chr5A 91.677 805 30 12 1223 1997 552777415 552776618 0.000000e+00 1081
5 TraesCS5B01G352000 chr5A 95.928 614 13 5 623 1232 552783305 552782700 0.000000e+00 985
6 TraesCS5B01G352000 chr5A 95.519 491 15 3 1 485 552783791 552783302 0.000000e+00 778
7 TraesCS5B01G352000 chr1B 99.286 140 1 0 485 624 634163049 634162910 1.300000e-63 254
8 TraesCS5B01G352000 chr1A 89.116 147 16 0 485 631 389771601 389771747 1.730000e-42 183
9 TraesCS5B01G352000 chr7A 91.045 134 12 0 491 624 75200222 75200089 6.210000e-42 182
10 TraesCS5B01G352000 chr7A 87.162 148 19 0 482 629 492846075 492846222 4.830000e-38 169
11 TraesCS5B01G352000 chr7A 86.395 147 18 2 481 626 556166519 556166374 2.910000e-35 159


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 TraesCS5B01G352000 chr5B 531735140 531737961 2821 True 5212.0 5212 100.0000 1 2822 1 chr5B.!!$R1 2821
1 TraesCS5B01G352000 chr5D 437829971 437832704 2733 True 2025.0 3301 93.9410 1 2822 2 chr5D.!!$R1 2821
2 TraesCS5B01G352000 chr5A 552775627 552777415 1788 True 1238.0 1395 94.3380 1223 2822 2 chr5A.!!$R1 1599
3 TraesCS5B01G352000 chr5A 552782700 552783791 1091 True 881.5 985 95.7235 1 1232 2 chr5A.!!$R2 1231

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
514 536 0.105039 GGATTACCTCCGCTCCACAG 59.895 60.0 0.0 0.0 33.29 3.66 F
547 569 0.106149 GCGGGTGGAGTTATAGTGGG 59.894 60.0 0.0 0.0 0.00 4.61 F
583 605 0.250901 TTTTCCTGGCTCCACAGCTC 60.251 55.0 0.0 0.0 46.03 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1599 1686 0.320374 AGGGAAACAATGACGCTCGA 59.680 50.000 0.00 0.0 0.00 4.04 R
1611 1698 2.064014 GTGTACAGTACGCAGGGAAAC 58.936 52.381 17.81 0.0 38.96 2.78 R
2184 2444 2.304180 AGAGCAGATGTAGCCACTTTGT 59.696 45.455 0.00 0.0 0.00 2.83 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
165 166 3.554342 CCATGCGCCCTAGCCTCT 61.554 66.667 4.18 0.00 36.02 3.69
350 354 3.234730 CCGCCCGCTCCTTCCTAT 61.235 66.667 0.00 0.00 0.00 2.57
397 409 7.841956 TGAAATATAGGCATAGGAGAAGTAGC 58.158 38.462 0.00 0.00 0.00 3.58
445 463 7.177184 AGCATATATAGCATGGATGTTTGGAA 58.823 34.615 0.00 0.00 0.00 3.53
481 503 6.481644 CCTCTGGATTTACTGTATTGCTTCTC 59.518 42.308 0.00 0.00 0.00 2.87
482 504 7.187824 TCTGGATTTACTGTATTGCTTCTCT 57.812 36.000 0.00 0.00 0.00 3.10
483 505 7.624549 TCTGGATTTACTGTATTGCTTCTCTT 58.375 34.615 0.00 0.00 0.00 2.85
484 506 8.758829 TCTGGATTTACTGTATTGCTTCTCTTA 58.241 33.333 0.00 0.00 0.00 2.10
485 507 8.718102 TGGATTTACTGTATTGCTTCTCTTAC 57.282 34.615 0.00 0.00 0.00 2.34
486 508 7.491372 TGGATTTACTGTATTGCTTCTCTTACG 59.509 37.037 0.00 0.00 0.00 3.18
487 509 6.642683 TTTACTGTATTGCTTCTCTTACGC 57.357 37.500 0.00 0.00 0.00 4.42
488 510 3.522553 ACTGTATTGCTTCTCTTACGCC 58.477 45.455 0.00 0.00 0.00 5.68
489 511 3.195825 ACTGTATTGCTTCTCTTACGCCT 59.804 43.478 0.00 0.00 0.00 5.52
490 512 4.184629 CTGTATTGCTTCTCTTACGCCTT 58.815 43.478 0.00 0.00 0.00 4.35
491 513 3.932710 TGTATTGCTTCTCTTACGCCTTG 59.067 43.478 0.00 0.00 0.00 3.61
492 514 2.543777 TTGCTTCTCTTACGCCTTGT 57.456 45.000 0.00 0.00 0.00 3.16
493 515 2.543777 TGCTTCTCTTACGCCTTGTT 57.456 45.000 0.00 0.00 0.00 2.83
494 516 2.413837 TGCTTCTCTTACGCCTTGTTC 58.586 47.619 0.00 0.00 0.00 3.18
495 517 1.390463 GCTTCTCTTACGCCTTGTTCG 59.610 52.381 0.00 0.00 0.00 3.95
496 518 1.993370 CTTCTCTTACGCCTTGTTCGG 59.007 52.381 0.00 0.00 0.00 4.30
497 519 1.250328 TCTCTTACGCCTTGTTCGGA 58.750 50.000 0.00 0.00 0.00 4.55
498 520 1.822990 TCTCTTACGCCTTGTTCGGAT 59.177 47.619 0.00 0.00 0.00 4.18
499 521 2.232941 TCTCTTACGCCTTGTTCGGATT 59.767 45.455 0.00 0.00 0.00 3.01
500 522 3.444742 TCTCTTACGCCTTGTTCGGATTA 59.555 43.478 0.00 0.00 0.00 1.75
501 523 3.514645 TCTTACGCCTTGTTCGGATTAC 58.485 45.455 0.00 0.00 0.00 1.89
502 524 2.298411 TACGCCTTGTTCGGATTACC 57.702 50.000 0.00 0.00 0.00 2.85
503 525 0.611714 ACGCCTTGTTCGGATTACCT 59.388 50.000 0.00 0.00 0.00 3.08
504 526 1.287425 CGCCTTGTTCGGATTACCTC 58.713 55.000 0.00 0.00 0.00 3.85
505 527 1.664873 GCCTTGTTCGGATTACCTCC 58.335 55.000 0.00 0.00 41.07 4.30
513 535 2.208527 GGATTACCTCCGCTCCACA 58.791 57.895 0.00 0.00 33.29 4.17
514 536 0.105039 GGATTACCTCCGCTCCACAG 59.895 60.000 0.00 0.00 33.29 3.66
515 537 0.530870 GATTACCTCCGCTCCACAGC 60.531 60.000 0.00 0.00 42.96 4.40
516 538 0.978146 ATTACCTCCGCTCCACAGCT 60.978 55.000 0.00 0.00 44.40 4.24
517 539 1.605058 TTACCTCCGCTCCACAGCTC 61.605 60.000 0.00 0.00 44.40 4.09
518 540 4.154347 CCTCCGCTCCACAGCTCC 62.154 72.222 0.00 0.00 44.40 4.70
519 541 3.385384 CTCCGCTCCACAGCTCCA 61.385 66.667 0.00 0.00 44.40 3.86
520 542 3.655810 CTCCGCTCCACAGCTCCAC 62.656 68.421 0.00 0.00 44.40 4.02
521 543 3.699894 CCGCTCCACAGCTCCACT 61.700 66.667 0.00 0.00 44.40 4.00
522 544 2.125753 CGCTCCACAGCTCCACTC 60.126 66.667 0.00 0.00 44.40 3.51
523 545 2.267324 GCTCCACAGCTCCACTCC 59.733 66.667 0.00 0.00 43.09 3.85
524 546 2.575993 CTCCACAGCTCCACTCCG 59.424 66.667 0.00 0.00 0.00 4.63
525 547 2.997315 TCCACAGCTCCACTCCGG 60.997 66.667 0.00 0.00 0.00 5.14
526 548 4.087892 CCACAGCTCCACTCCGGG 62.088 72.222 0.00 0.00 34.36 5.73
527 549 2.997315 CACAGCTCCACTCCGGGA 60.997 66.667 0.00 0.00 34.36 5.14
540 562 3.072468 CGGGAGCGGGTGGAGTTA 61.072 66.667 0.00 0.00 0.00 2.24
541 563 2.432300 CGGGAGCGGGTGGAGTTAT 61.432 63.158 0.00 0.00 0.00 1.89
542 564 1.111116 CGGGAGCGGGTGGAGTTATA 61.111 60.000 0.00 0.00 0.00 0.98
543 565 0.680061 GGGAGCGGGTGGAGTTATAG 59.320 60.000 0.00 0.00 0.00 1.31
544 566 1.411041 GGAGCGGGTGGAGTTATAGT 58.589 55.000 0.00 0.00 0.00 2.12
545 567 1.068741 GGAGCGGGTGGAGTTATAGTG 59.931 57.143 0.00 0.00 0.00 2.74
546 568 1.068741 GAGCGGGTGGAGTTATAGTGG 59.931 57.143 0.00 0.00 0.00 4.00
547 569 0.106149 GCGGGTGGAGTTATAGTGGG 59.894 60.000 0.00 0.00 0.00 4.61
548 570 1.784358 CGGGTGGAGTTATAGTGGGA 58.216 55.000 0.00 0.00 0.00 4.37
549 571 2.112998 CGGGTGGAGTTATAGTGGGAA 58.887 52.381 0.00 0.00 0.00 3.97
550 572 2.502538 CGGGTGGAGTTATAGTGGGAAA 59.497 50.000 0.00 0.00 0.00 3.13
551 573 3.054948 CGGGTGGAGTTATAGTGGGAAAA 60.055 47.826 0.00 0.00 0.00 2.29
552 574 4.267536 GGGTGGAGTTATAGTGGGAAAAC 58.732 47.826 0.00 0.00 0.00 2.43
553 575 3.937079 GGTGGAGTTATAGTGGGAAAACG 59.063 47.826 0.00 0.00 0.00 3.60
554 576 3.373130 GTGGAGTTATAGTGGGAAAACGC 59.627 47.826 0.00 0.00 0.00 4.84
555 577 2.606272 GGAGTTATAGTGGGAAAACGCG 59.394 50.000 3.53 3.53 0.00 6.01
556 578 2.606272 GAGTTATAGTGGGAAAACGCGG 59.394 50.000 12.47 0.00 0.00 6.46
557 579 2.234414 AGTTATAGTGGGAAAACGCGGA 59.766 45.455 12.47 0.00 0.00 5.54
558 580 2.589798 TATAGTGGGAAAACGCGGAG 57.410 50.000 12.47 0.00 0.00 4.63
572 594 3.431725 GGAGCGCCGTTTTCCTGG 61.432 66.667 2.29 0.00 0.00 4.45
578 600 3.668386 CCGTTTTCCTGGCTCCAC 58.332 61.111 0.00 0.00 0.00 4.02
579 601 1.228124 CCGTTTTCCTGGCTCCACA 60.228 57.895 0.00 0.00 0.00 4.17
580 602 1.237285 CCGTTTTCCTGGCTCCACAG 61.237 60.000 0.00 0.00 38.21 3.66
581 603 1.856265 CGTTTTCCTGGCTCCACAGC 61.856 60.000 0.00 0.00 46.06 4.40
582 604 0.538287 GTTTTCCTGGCTCCACAGCT 60.538 55.000 0.00 0.00 46.03 4.24
583 605 0.250901 TTTTCCTGGCTCCACAGCTC 60.251 55.000 0.00 0.00 46.03 4.09
584 606 2.129555 TTTCCTGGCTCCACAGCTCC 62.130 60.000 0.00 0.00 46.03 4.70
585 607 3.007920 CCTGGCTCCACAGCTCCT 61.008 66.667 0.00 0.00 46.03 3.69
586 608 2.583520 CTGGCTCCACAGCTCCTC 59.416 66.667 0.00 0.00 46.03 3.71
587 609 3.368190 CTGGCTCCACAGCTCCTCG 62.368 68.421 0.00 0.00 46.03 4.63
588 610 3.386237 GGCTCCACAGCTCCTCGT 61.386 66.667 0.00 0.00 46.03 4.18
589 611 2.052690 GGCTCCACAGCTCCTCGTA 61.053 63.158 0.00 0.00 46.03 3.43
590 612 1.395826 GGCTCCACAGCTCCTCGTAT 61.396 60.000 0.00 0.00 46.03 3.06
591 613 0.461961 GCTCCACAGCTCCTCGTATT 59.538 55.000 0.00 0.00 43.09 1.89
592 614 1.134670 GCTCCACAGCTCCTCGTATTT 60.135 52.381 0.00 0.00 43.09 1.40
593 615 2.678190 GCTCCACAGCTCCTCGTATTTT 60.678 50.000 0.00 0.00 43.09 1.82
594 616 2.932614 CTCCACAGCTCCTCGTATTTTG 59.067 50.000 0.00 0.00 0.00 2.44
595 617 1.398390 CCACAGCTCCTCGTATTTTGC 59.602 52.381 0.00 0.00 0.00 3.68
596 618 1.061131 CACAGCTCCTCGTATTTTGCG 59.939 52.381 0.00 0.00 0.00 4.85
597 619 0.652592 CAGCTCCTCGTATTTTGCGG 59.347 55.000 0.00 0.00 0.00 5.69
598 620 0.535335 AGCTCCTCGTATTTTGCGGA 59.465 50.000 0.00 0.00 0.00 5.54
599 621 0.931005 GCTCCTCGTATTTTGCGGAG 59.069 55.000 0.00 0.00 43.18 4.63
743 784 4.023279 CACGAAATCTGATTTGTGGACCAA 60.023 41.667 19.59 0.00 32.60 3.67
766 807 5.857268 AGAACCTTGCATGTGCTTAATTTT 58.143 33.333 6.55 0.00 42.66 1.82
783 824 0.387202 TTTCACAACCAATGGCCGTG 59.613 50.000 13.66 13.66 31.83 4.94
915 956 7.148820 CCATCTGCACGTTAATTAACCTTTTTG 60.149 37.037 20.08 11.57 32.69 2.44
916 957 6.797454 TCTGCACGTTAATTAACCTTTTTGT 58.203 32.000 20.08 9.86 32.69 2.83
917 958 6.913673 TCTGCACGTTAATTAACCTTTTTGTC 59.086 34.615 20.08 7.91 32.69 3.18
940 981 0.761187 TCTCAACCTCTTGCAGCAGT 59.239 50.000 0.00 0.00 0.00 4.40
997 1042 5.310409 ACATCAACCCAAGAAGAAGAAGA 57.690 39.130 0.00 0.00 0.00 2.87
998 1043 5.694995 ACATCAACCCAAGAAGAAGAAGAA 58.305 37.500 0.00 0.00 0.00 2.52
999 1044 6.129179 ACATCAACCCAAGAAGAAGAAGAAA 58.871 36.000 0.00 0.00 0.00 2.52
1128 1181 2.885135 ATGAGCATGTTGTCCAAGGA 57.115 45.000 0.00 0.00 0.00 3.36
1273 1331 1.856597 GTATGGTGTTCGCGGATGTAC 59.143 52.381 6.13 0.00 0.00 2.90
1422 1480 3.067106 ACTTGCATTGGACGACTTACAG 58.933 45.455 0.00 0.00 0.00 2.74
1423 1481 1.438651 TGCATTGGACGACTTACAGC 58.561 50.000 0.00 0.00 0.00 4.40
1425 1483 1.128692 GCATTGGACGACTTACAGCAC 59.871 52.381 0.00 0.00 0.00 4.40
1454 1541 5.951747 TCATTTAATTTACTGAAGCTGGGCT 59.048 36.000 0.00 0.00 42.56 5.19
1490 1577 1.787056 CGGCGCGTTCTTTCGAAAC 60.787 57.895 8.43 0.00 0.00 2.78
1512 1599 4.595781 ACAATGTTCACTACCTACAAGGGA 59.404 41.667 0.00 0.00 40.58 4.20
1553 1640 1.080298 GTCCGGTGGACCAGTTACG 60.080 63.158 0.00 0.00 46.19 3.18
1581 1668 3.674528 ACAGAGTCATTGGAGTCAGTG 57.325 47.619 0.00 0.00 44.45 3.66
1588 1675 4.687215 TGGAGTCAGTGCCGCAGC 62.687 66.667 0.00 0.00 40.48 5.25
1611 1698 1.143838 TGGGGATCGAGCGTCATTG 59.856 57.895 0.00 0.00 0.00 2.82
1621 1708 1.154225 GCGTCATTGTTTCCCTGCG 60.154 57.895 0.00 0.00 0.00 5.18
1684 1771 6.332735 TGTAAGAATTCCAGATCGATCGAT 57.667 37.500 29.76 29.76 37.59 3.59
1706 1793 5.989551 TTTCATTTTTCCTTTGAAGCAGC 57.010 34.783 0.00 0.00 31.54 5.25
2363 2624 3.358111 TGTTGGACAACTCAGGTTTGA 57.642 42.857 15.37 0.00 41.67 2.69
2418 2679 2.769095 AGAGAACACAATCCTAGGCTCC 59.231 50.000 2.96 0.00 0.00 4.70
2440 2701 7.627298 TCCGAGCATATAGATAAAGGTAGAC 57.373 40.000 0.00 0.00 0.00 2.59
2469 2730 9.823647 TTCCATTCTCATTCAGACTAAAGATAC 57.176 33.333 0.00 0.00 0.00 2.24
2538 2799 7.013655 ACCTTCCTTTTTCAATCCGATGATATG 59.986 37.037 0.00 0.00 0.00 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
299 303 2.681848 CACTTCCAGTACTATCGGACGT 59.318 50.000 0.00 0.00 31.95 4.34
377 385 4.700692 CGTGCTACTTCTCCTATGCCTATA 59.299 45.833 0.00 0.00 0.00 1.31
397 409 3.924686 AGCGACCAGAAAATTACTACGTG 59.075 43.478 0.00 0.00 0.00 4.49
445 463 0.257039 ATCCAGAGGCGGCAAAATCT 59.743 50.000 13.08 1.46 0.00 2.40
481 503 2.606272 GGTAATCCGAACAAGGCGTAAG 59.394 50.000 0.00 0.00 43.44 2.34
482 504 2.234414 AGGTAATCCGAACAAGGCGTAA 59.766 45.455 0.00 0.00 39.05 3.18
483 505 1.826720 AGGTAATCCGAACAAGGCGTA 59.173 47.619 0.00 0.00 39.05 4.42
484 506 0.611714 AGGTAATCCGAACAAGGCGT 59.388 50.000 0.00 0.00 39.05 5.68
485 507 1.287425 GAGGTAATCCGAACAAGGCG 58.713 55.000 0.00 0.00 39.05 5.52
486 508 1.664873 GGAGGTAATCCGAACAAGGC 58.335 55.000 0.00 0.00 38.67 4.35
495 517 0.105039 CTGTGGAGCGGAGGTAATCC 59.895 60.000 0.00 0.00 45.64 3.01
496 518 0.530870 GCTGTGGAGCGGAGGTAATC 60.531 60.000 0.00 0.00 39.88 1.75
497 519 1.522569 GCTGTGGAGCGGAGGTAAT 59.477 57.895 0.00 0.00 39.88 1.89
498 520 2.978824 GCTGTGGAGCGGAGGTAA 59.021 61.111 0.00 0.00 39.88 2.85
506 528 2.267324 GGAGTGGAGCTGTGGAGC 59.733 66.667 0.00 0.00 46.64 4.70
507 529 2.575993 CGGAGTGGAGCTGTGGAG 59.424 66.667 0.00 0.00 0.00 3.86
508 530 2.997315 CCGGAGTGGAGCTGTGGA 60.997 66.667 0.00 0.00 42.00 4.02
509 531 4.087892 CCCGGAGTGGAGCTGTGG 62.088 72.222 0.73 0.00 42.00 4.17
510 532 2.997315 TCCCGGAGTGGAGCTGTG 60.997 66.667 0.73 0.00 42.00 3.66
511 533 2.681778 CTCCCGGAGTGGAGCTGT 60.682 66.667 0.73 0.00 45.13 4.40
523 545 1.111116 TATAACTCCACCCGCTCCCG 61.111 60.000 0.00 0.00 0.00 5.14
524 546 0.680061 CTATAACTCCACCCGCTCCC 59.320 60.000 0.00 0.00 0.00 4.30
525 547 1.068741 CACTATAACTCCACCCGCTCC 59.931 57.143 0.00 0.00 0.00 4.70
526 548 1.068741 CCACTATAACTCCACCCGCTC 59.931 57.143 0.00 0.00 0.00 5.03
527 549 1.120530 CCACTATAACTCCACCCGCT 58.879 55.000 0.00 0.00 0.00 5.52
528 550 0.106149 CCCACTATAACTCCACCCGC 59.894 60.000 0.00 0.00 0.00 6.13
529 551 1.784358 TCCCACTATAACTCCACCCG 58.216 55.000 0.00 0.00 0.00 5.28
530 552 4.267536 GTTTTCCCACTATAACTCCACCC 58.732 47.826 0.00 0.00 0.00 4.61
531 553 3.937079 CGTTTTCCCACTATAACTCCACC 59.063 47.826 0.00 0.00 0.00 4.61
532 554 3.373130 GCGTTTTCCCACTATAACTCCAC 59.627 47.826 0.00 0.00 0.00 4.02
533 555 3.602483 GCGTTTTCCCACTATAACTCCA 58.398 45.455 0.00 0.00 0.00 3.86
534 556 2.606272 CGCGTTTTCCCACTATAACTCC 59.394 50.000 0.00 0.00 0.00 3.85
535 557 2.606272 CCGCGTTTTCCCACTATAACTC 59.394 50.000 4.92 0.00 0.00 3.01
536 558 2.234414 TCCGCGTTTTCCCACTATAACT 59.766 45.455 4.92 0.00 0.00 2.24
537 559 2.606272 CTCCGCGTTTTCCCACTATAAC 59.394 50.000 4.92 0.00 0.00 1.89
538 560 2.896168 CTCCGCGTTTTCCCACTATAA 58.104 47.619 4.92 0.00 0.00 0.98
539 561 1.472026 GCTCCGCGTTTTCCCACTATA 60.472 52.381 4.92 0.00 0.00 1.31
540 562 0.743345 GCTCCGCGTTTTCCCACTAT 60.743 55.000 4.92 0.00 0.00 2.12
541 563 1.375013 GCTCCGCGTTTTCCCACTA 60.375 57.895 4.92 0.00 0.00 2.74
542 564 2.668550 GCTCCGCGTTTTCCCACT 60.669 61.111 4.92 0.00 0.00 4.00
555 577 3.431725 CCAGGAAAACGGCGCTCC 61.432 66.667 6.90 11.18 0.00 4.70
556 578 4.103103 GCCAGGAAAACGGCGCTC 62.103 66.667 6.90 0.47 38.82 5.03
561 583 1.228124 TGTGGAGCCAGGAAAACGG 60.228 57.895 0.00 0.00 0.00 4.44
562 584 1.856265 GCTGTGGAGCCAGGAAAACG 61.856 60.000 0.00 0.00 39.57 3.60
563 585 1.959848 GCTGTGGAGCCAGGAAAAC 59.040 57.895 0.00 0.00 39.57 2.43
564 586 4.500265 GCTGTGGAGCCAGGAAAA 57.500 55.556 0.00 0.00 39.57 2.29
572 594 0.461961 AATACGAGGAGCTGTGGAGC 59.538 55.000 0.00 0.00 46.64 4.70
573 595 2.932614 CAAAATACGAGGAGCTGTGGAG 59.067 50.000 0.00 0.00 0.00 3.86
574 596 2.935238 GCAAAATACGAGGAGCTGTGGA 60.935 50.000 0.00 0.00 0.00 4.02
575 597 1.398390 GCAAAATACGAGGAGCTGTGG 59.602 52.381 0.00 0.00 0.00 4.17
576 598 1.061131 CGCAAAATACGAGGAGCTGTG 59.939 52.381 0.00 0.00 0.00 3.66
577 599 1.359848 CGCAAAATACGAGGAGCTGT 58.640 50.000 0.00 0.00 0.00 4.40
578 600 0.652592 CCGCAAAATACGAGGAGCTG 59.347 55.000 0.00 0.00 0.00 4.24
579 601 0.535335 TCCGCAAAATACGAGGAGCT 59.465 50.000 0.00 0.00 0.00 4.09
580 602 0.931005 CTCCGCAAAATACGAGGAGC 59.069 55.000 0.00 0.00 42.42 4.70
582 604 0.804544 CGCTCCGCAAAATACGAGGA 60.805 55.000 0.00 0.00 0.00 3.71
583 605 1.636340 CGCTCCGCAAAATACGAGG 59.364 57.895 0.00 0.00 0.00 4.63
584 606 1.636340 CCGCTCCGCAAAATACGAG 59.364 57.895 0.00 0.00 0.00 4.18
585 607 1.812093 CCCGCTCCGCAAAATACGA 60.812 57.895 0.00 0.00 0.00 3.43
586 608 2.104253 ACCCGCTCCGCAAAATACG 61.104 57.895 0.00 0.00 0.00 3.06
587 609 1.427819 CACCCGCTCCGCAAAATAC 59.572 57.895 0.00 0.00 0.00 1.89
588 610 1.747367 CCACCCGCTCCGCAAAATA 60.747 57.895 0.00 0.00 0.00 1.40
589 611 3.061848 CCACCCGCTCCGCAAAAT 61.062 61.111 0.00 0.00 0.00 1.82
594 616 4.603946 GTATCCCACCCGCTCCGC 62.604 72.222 0.00 0.00 0.00 5.54
595 617 3.925090 GGTATCCCACCCGCTCCG 61.925 72.222 0.00 0.00 42.07 4.63
596 618 3.925090 CGGTATCCCACCCGCTCC 61.925 72.222 0.00 0.00 45.52 4.70
597 619 2.428925 TTCGGTATCCCACCCGCTC 61.429 63.158 0.00 0.00 45.52 5.03
598 620 2.364579 TTCGGTATCCCACCCGCT 60.365 61.111 0.00 0.00 45.52 5.52
599 621 2.202974 GTTCGGTATCCCACCCGC 60.203 66.667 0.00 0.00 45.52 6.13
600 622 1.143183 CTGTTCGGTATCCCACCCG 59.857 63.158 0.00 0.00 45.52 5.28
601 623 1.525442 CCTGTTCGGTATCCCACCC 59.475 63.158 0.00 0.00 45.52 4.61
602 624 1.525442 CCCTGTTCGGTATCCCACC 59.475 63.158 0.00 0.00 44.75 4.61
603 625 1.153229 GCCCTGTTCGGTATCCCAC 60.153 63.158 0.00 0.00 0.00 4.61
604 626 2.372074 GGCCCTGTTCGGTATCCCA 61.372 63.158 0.00 0.00 0.00 4.37
605 627 1.632965 AAGGCCCTGTTCGGTATCCC 61.633 60.000 0.00 0.00 0.00 3.85
606 628 1.125633 TAAGGCCCTGTTCGGTATCC 58.874 55.000 0.00 0.00 0.00 2.59
607 629 2.994186 TTAAGGCCCTGTTCGGTATC 57.006 50.000 0.00 0.00 0.00 2.24
608 630 3.945640 AATTAAGGCCCTGTTCGGTAT 57.054 42.857 0.00 0.00 0.00 2.73
609 631 3.432608 GCTAATTAAGGCCCTGTTCGGTA 60.433 47.826 0.00 0.00 0.00 4.02
610 632 2.682858 GCTAATTAAGGCCCTGTTCGGT 60.683 50.000 0.00 0.00 0.00 4.69
611 633 1.947456 GCTAATTAAGGCCCTGTTCGG 59.053 52.381 0.00 0.00 0.00 4.30
612 634 2.354821 GTGCTAATTAAGGCCCTGTTCG 59.645 50.000 0.00 0.00 0.00 3.95
613 635 2.354821 CGTGCTAATTAAGGCCCTGTTC 59.645 50.000 0.00 0.00 0.00 3.18
614 636 2.365582 CGTGCTAATTAAGGCCCTGTT 58.634 47.619 0.00 0.00 0.00 3.16
615 637 2.017113 GCGTGCTAATTAAGGCCCTGT 61.017 52.381 0.00 0.00 0.00 4.00
616 638 0.663153 GCGTGCTAATTAAGGCCCTG 59.337 55.000 0.00 0.00 0.00 4.45
617 639 0.814010 CGCGTGCTAATTAAGGCCCT 60.814 55.000 0.00 0.00 0.00 5.19
618 640 1.647084 CGCGTGCTAATTAAGGCCC 59.353 57.895 0.00 0.00 0.00 5.80
619 641 1.647084 CCGCGTGCTAATTAAGGCC 59.353 57.895 4.92 0.00 0.00 5.19
620 642 1.647084 CCCGCGTGCTAATTAAGGC 59.353 57.895 4.92 0.00 0.00 4.35
621 643 0.814010 AGCCCGCGTGCTAATTAAGG 60.814 55.000 16.30 0.00 40.56 2.69
743 784 5.473066 AAATTAAGCACATGCAAGGTTCT 57.527 34.783 6.64 0.00 45.16 3.01
766 807 1.900981 CCACGGCCATTGGTTGTGA 60.901 57.895 22.95 0.00 33.85 3.58
783 824 4.084537 CGCGTATGGATGAATGAAACTACC 60.085 45.833 0.00 0.00 0.00 3.18
915 956 3.304324 GCTGCAAGAGGTTGAGAAAAGAC 60.304 47.826 0.00 0.00 35.46 3.01
916 957 2.880890 GCTGCAAGAGGTTGAGAAAAGA 59.119 45.455 0.00 0.00 35.46 2.52
917 958 2.620115 TGCTGCAAGAGGTTGAGAAAAG 59.380 45.455 0.00 0.00 35.46 2.27
940 981 9.667107 AGATAAACTCAAGATATGAAACGGAAA 57.333 29.630 0.00 0.00 37.67 3.13
997 1042 5.163893 CGTCTAACATAAGCACCGACATTTT 60.164 40.000 0.00 0.00 0.00 1.82
998 1043 4.328983 CGTCTAACATAAGCACCGACATTT 59.671 41.667 0.00 0.00 0.00 2.32
999 1044 3.863424 CGTCTAACATAAGCACCGACATT 59.137 43.478 0.00 0.00 0.00 2.71
1128 1181 4.227527 AGCCTAACCCTAACAAACATAGCT 59.772 41.667 0.00 0.00 0.00 3.32
1253 1311 1.856597 GTACATCCGCGAACACCATAC 59.143 52.381 8.23 0.00 0.00 2.39
1273 1331 5.470098 CCGTCCATGGAAAGTTATCAATAGG 59.530 44.000 18.20 0.67 0.00 2.57
1454 1541 3.120338 CGCCGCTGAGAGAAACATAAAAA 60.120 43.478 0.00 0.00 0.00 1.94
1490 1577 5.160607 TCCCTTGTAGGTAGTGAACATTG 57.839 43.478 0.00 0.00 31.93 2.82
1512 1599 2.161855 TCCATGCTGAAGTGCGAAATT 58.838 42.857 0.00 0.00 35.36 1.82
1553 1640 3.944015 CTCCAATGACTCTGTTTCCCATC 59.056 47.826 0.00 0.00 0.00 3.51
1599 1686 0.320374 AGGGAAACAATGACGCTCGA 59.680 50.000 0.00 0.00 0.00 4.04
1611 1698 2.064014 GTGTACAGTACGCAGGGAAAC 58.936 52.381 17.81 0.00 38.96 2.78
1621 1708 7.884816 AACATAAGTGTCATGTGTACAGTAC 57.115 36.000 3.49 3.49 37.67 2.73
1684 1771 5.426504 TGCTGCTTCAAAGGAAAAATGAAA 58.573 33.333 0.00 0.00 33.08 2.69
1721 1809 6.881570 ACAGCCTATAAAGTATAAACGGTGT 58.118 36.000 0.00 0.00 0.00 4.16
1722 1810 7.781548 AACAGCCTATAAAGTATAAACGGTG 57.218 36.000 0.00 0.00 0.00 4.94
1730 1818 9.172060 AGGGATTAGAAACAGCCTATAAAGTAT 57.828 33.333 0.00 0.00 0.00 2.12
1731 1819 8.429641 CAGGGATTAGAAACAGCCTATAAAGTA 58.570 37.037 0.00 0.00 0.00 2.24
1732 1820 7.092399 ACAGGGATTAGAAACAGCCTATAAAGT 60.092 37.037 0.00 0.00 0.00 2.66
1733 1821 7.283329 ACAGGGATTAGAAACAGCCTATAAAG 58.717 38.462 0.00 0.00 0.00 1.85
1902 1991 5.621193 TGCTTTACTTCCTTTCAGCTAGTT 58.379 37.500 0.00 0.00 0.00 2.24
1975 2064 9.203421 CGTACTACATTGCATTAGGAAATATCA 57.797 33.333 0.00 0.00 0.00 2.15
2184 2444 2.304180 AGAGCAGATGTAGCCACTTTGT 59.696 45.455 0.00 0.00 0.00 2.83
2241 2501 7.921786 TGAAATAGTTTTCCACTGTATGAGG 57.078 36.000 0.00 0.00 40.49 3.86
2363 2624 6.042143 CGAGCCAAAATTAGTGCCATTTTAT 58.958 36.000 0.00 0.00 33.05 1.40
2418 2679 9.862371 AAATGTCTACCTTTATCTATATGCTCG 57.138 33.333 0.00 0.00 0.00 5.03
2440 2701 9.170734 TCTTTAGTCTGAATGAGAATGGAAATG 57.829 33.333 0.00 0.00 29.85 2.32
2538 2799 2.710377 TGATCATATGGGCGCATAACC 58.290 47.619 25.14 14.97 0.00 2.85


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

AutoCloner maintained by Alex Coulton.