Multiple sequence alignment - TraesCS1A01G141200

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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 TraesCS1A01G141200 chr1A 100.000 3485 0 0 1 3485 239099007 239102491 0.000000e+00 6436
1 TraesCS1A01G141200 chr1A 84.961 512 66 10 1 510 331371676 331372178 3.100000e-140 508
2 TraesCS1A01G141200 chr1D 96.711 2615 65 9 877 3485 193357922 193360521 0.000000e+00 4333
3 TraesCS1A01G141200 chr1D 85.450 866 69 18 1 863 193357072 193357883 0.000000e+00 848
4 TraesCS1A01G141200 chr1B 96.614 2599 62 11 894 3485 267965580 267968159 0.000000e+00 4289
5 TraesCS1A01G141200 chr1B 83.789 512 72 10 4 513 115252077 115251575 3.150000e-130 475
6 TraesCS1A01G141200 chr5D 85.149 505 68 6 7 511 114419161 114418664 8.630000e-141 510
7 TraesCS1A01G141200 chr4A 84.496 516 68 10 1 513 743881608 743882114 1.870000e-137 499
8 TraesCS1A01G141200 chr6B 84.436 514 63 12 4 513 70370104 70369604 1.120000e-134 490
9 TraesCS1A01G141200 chr6B 83.953 511 66 13 4 513 610458655 610458160 3.150000e-130 475
10 TraesCS1A01G141200 chr3A 84.086 509 72 8 4 511 676692871 676692371 1.880000e-132 483
11 TraesCS1A01G141200 chr5B 83.398 512 70 8 4 513 669964438 669963940 8.810000e-126 460


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 TraesCS1A01G141200 chr1A 239099007 239102491 3484 False 6436.0 6436 100.0000 1 3485 1 chr1A.!!$F1 3484
1 TraesCS1A01G141200 chr1A 331371676 331372178 502 False 508.0 508 84.9610 1 510 1 chr1A.!!$F2 509
2 TraesCS1A01G141200 chr1D 193357072 193360521 3449 False 2590.5 4333 91.0805 1 3485 2 chr1D.!!$F1 3484
3 TraesCS1A01G141200 chr1B 267965580 267968159 2579 False 4289.0 4289 96.6140 894 3485 1 chr1B.!!$F1 2591
4 TraesCS1A01G141200 chr1B 115251575 115252077 502 True 475.0 475 83.7890 4 513 1 chr1B.!!$R1 509
5 TraesCS1A01G141200 chr4A 743881608 743882114 506 False 499.0 499 84.4960 1 513 1 chr4A.!!$F1 512
6 TraesCS1A01G141200 chr6B 70369604 70370104 500 True 490.0 490 84.4360 4 513 1 chr6B.!!$R1 509
7 TraesCS1A01G141200 chr3A 676692371 676692871 500 True 483.0 483 84.0860 4 511 1 chr3A.!!$R1 507

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
957 1004 0.100325 TGCAAAATAATGCCGGCTCG 59.900 50.0 29.7 7.74 45.83 5.03 F
992 1039 0.836400 TGCTCTCCTCCTTCCGGTTT 60.836 55.0 0.0 0.00 0.00 3.27 F
1838 1885 0.242825 CTTGCAGTGCATGGGTTGAG 59.757 55.0 20.5 7.52 38.76 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1838 1885 0.179000 AATCTCCACCGACTCCATGC 59.821 55.000 0.00 0.0 0.0 4.06 R
2178 2225 3.007473 TCATGATCTGGCTGCAATTGA 57.993 42.857 10.34 0.0 0.0 2.57 R
3194 3245 1.140852 TCCGGATGTTTGGCCTGATAG 59.859 52.381 0.00 0.0 0.0 2.08 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
58 59 8.568794 TGTCGATTATTGAATTACCACACAAAA 58.431 29.630 0.00 0.00 0.00 2.44
78 79 7.951591 ACAAAAATTGATTGTGCTACCTAGTT 58.048 30.769 8.61 0.00 39.43 2.24
100 102 6.040842 AGTTCATGTTTATGGTGCACTCTTTT 59.959 34.615 17.98 0.00 34.97 2.27
105 107 7.144722 TGTTTATGGTGCACTCTTTTATCAG 57.855 36.000 17.98 0.00 0.00 2.90
159 161 7.513781 TCCTTTGATCATATCATCTTGGTCCTA 59.486 37.037 0.00 0.00 39.39 2.94
202 204 6.641314 CGAGCTTAGTAACATATCGATGGTTT 59.359 38.462 18.44 7.32 37.39 3.27
248 250 5.105228 CGAAAGTATTACTAGGTTGTCCCCA 60.105 44.000 0.00 0.00 0.00 4.96
258 260 1.406477 GGTTGTCCCCAGACCGTTATC 60.406 57.143 0.00 0.00 42.81 1.75
326 330 4.261801 CGAGAATTTGTGTTGGATACCCT 58.738 43.478 0.00 0.00 0.00 4.34
350 354 7.067494 CCTTGAGCTAGTTGGTTATGCTTAAAT 59.933 37.037 0.00 0.00 33.83 1.40
365 369 6.254281 TGCTTAAATAACAACTTGGAGAGC 57.746 37.500 0.00 0.00 0.00 4.09
406 411 6.480763 TGCCTAATGTAGTTCATTCAAAGGA 58.519 36.000 11.85 0.00 44.50 3.36
454 459 1.265635 GTGTGTGTGTGTGTGTGTTGT 59.734 47.619 0.00 0.00 0.00 3.32
455 460 1.265365 TGTGTGTGTGTGTGTGTTGTG 59.735 47.619 0.00 0.00 0.00 3.33
459 464 1.809547 TGTGTGTGTGTGTTGTGAAGG 59.190 47.619 0.00 0.00 0.00 3.46
533 538 2.417257 GCGGGGCAAAGATCATGCA 61.417 57.895 20.74 0.00 45.60 3.96
575 581 0.755686 GGTGGTGGCTCTAGATGAGG 59.244 60.000 0.00 0.00 42.87 3.86
581 587 1.182385 GGCTCTAGATGAGGGTCGGG 61.182 65.000 0.00 0.00 42.87 5.14
591 597 0.908180 GAGGGTCGGGAGGGAGAAAA 60.908 60.000 0.00 0.00 0.00 2.29
598 604 3.115390 TCGGGAGGGAGAAAATGAAGAT 58.885 45.455 0.00 0.00 0.00 2.40
608 614 3.830755 AGAAAATGAAGATTGGCTGCTGT 59.169 39.130 0.00 0.00 0.00 4.40
609 615 4.282703 AGAAAATGAAGATTGGCTGCTGTT 59.717 37.500 0.00 0.00 0.00 3.16
610 616 3.587797 AATGAAGATTGGCTGCTGTTG 57.412 42.857 0.00 0.00 0.00 3.33
611 617 2.275134 TGAAGATTGGCTGCTGTTGA 57.725 45.000 0.00 0.00 0.00 3.18
612 618 2.156917 TGAAGATTGGCTGCTGTTGAG 58.843 47.619 0.00 0.00 0.00 3.02
613 619 2.224597 TGAAGATTGGCTGCTGTTGAGA 60.225 45.455 0.00 0.00 0.00 3.27
614 620 2.574006 AGATTGGCTGCTGTTGAGAA 57.426 45.000 0.00 0.00 0.00 2.87
615 621 2.867624 AGATTGGCTGCTGTTGAGAAA 58.132 42.857 0.00 0.00 0.00 2.52
616 622 2.555757 AGATTGGCTGCTGTTGAGAAAC 59.444 45.455 0.00 0.00 0.00 2.78
617 623 1.761449 TTGGCTGCTGTTGAGAAACA 58.239 45.000 0.00 0.00 0.00 2.83
618 624 1.024271 TGGCTGCTGTTGAGAAACAC 58.976 50.000 0.00 0.00 0.00 3.32
619 625 1.024271 GGCTGCTGTTGAGAAACACA 58.976 50.000 0.00 0.00 0.00 3.72
620 626 1.610522 GGCTGCTGTTGAGAAACACAT 59.389 47.619 0.00 0.00 0.00 3.21
621 627 2.606308 GGCTGCTGTTGAGAAACACATG 60.606 50.000 0.00 0.00 0.00 3.21
622 628 2.291465 GCTGCTGTTGAGAAACACATGA 59.709 45.455 0.00 0.00 0.00 3.07
623 629 3.057736 GCTGCTGTTGAGAAACACATGAT 60.058 43.478 0.00 0.00 0.00 2.45
624 630 4.558095 GCTGCTGTTGAGAAACACATGATT 60.558 41.667 0.00 0.00 0.00 2.57
625 631 4.862350 TGCTGTTGAGAAACACATGATTG 58.138 39.130 0.00 0.00 0.00 2.67
626 632 4.579753 TGCTGTTGAGAAACACATGATTGA 59.420 37.500 0.00 0.00 0.00 2.57
627 633 4.913924 GCTGTTGAGAAACACATGATTGAC 59.086 41.667 0.00 0.00 0.00 3.18
628 634 5.278169 GCTGTTGAGAAACACATGATTGACT 60.278 40.000 0.00 0.00 0.00 3.41
629 635 6.063640 TGTTGAGAAACACATGATTGACTG 57.936 37.500 0.00 0.00 0.00 3.51
630 636 4.754372 TGAGAAACACATGATTGACTGC 57.246 40.909 0.00 0.00 0.00 4.40
631 637 4.392047 TGAGAAACACATGATTGACTGCT 58.608 39.130 0.00 0.00 0.00 4.24
632 638 4.214758 TGAGAAACACATGATTGACTGCTG 59.785 41.667 0.00 0.00 0.00 4.41
647 653 1.677576 CTGCTGAGAGAGAAGAGCGAT 59.322 52.381 0.00 0.00 33.97 4.58
660 666 8.402798 AGAGAAGAGCGATGAGATAGATTTTA 57.597 34.615 0.00 0.00 0.00 1.52
679 685 9.892130 AGATTTTATAGAGACAAACACCTAAGG 57.108 33.333 0.00 0.00 0.00 2.69
687 693 6.954684 AGAGACAAACACCTAAGGAGATAAGA 59.045 38.462 0.00 0.00 0.00 2.10
702 708 7.782049 AGGAGATAAGATTCAACAACGATGTA 58.218 34.615 0.00 0.00 39.40 2.29
711 717 5.448926 TCAACAACGATGTATGAATCACG 57.551 39.130 0.00 0.00 39.40 4.35
712 718 4.328712 TCAACAACGATGTATGAATCACGG 59.671 41.667 0.00 0.00 39.40 4.94
750 756 2.282251 AGGCGGTCGACTCACTGA 60.282 61.111 16.46 0.00 0.00 3.41
758 764 3.366070 CGGTCGACTCACTGACTGTAATT 60.366 47.826 16.46 0.00 36.85 1.40
765 771 4.402793 ACTCACTGACTGTAATTAGCCGAT 59.597 41.667 0.00 0.00 0.00 4.18
769 775 5.005779 CACTGACTGTAATTAGCCGATTGAC 59.994 44.000 0.00 0.00 0.00 3.18
794 801 7.056635 CAGGAAAGCTTTTCCTTATCATAGGA 58.943 38.462 20.82 0.00 46.21 2.94
798 805 7.399674 AAGCTTTTCCTTATCATAGGAGGAT 57.600 36.000 0.00 0.00 44.82 3.24
800 807 6.560304 AGCTTTTCCTTATCATAGGAGGATGA 59.440 38.462 0.00 0.00 44.82 2.92
823 830 2.222027 GGACGAATGGATGATGGGAAC 58.778 52.381 0.00 0.00 0.00 3.62
841 848 7.313951 TGGGAACAAAAATGAAACATGAAAC 57.686 32.000 0.00 0.00 37.44 2.78
846 853 7.306205 ACAAAAATGAAACATGAAACTGTGG 57.694 32.000 0.00 0.00 0.00 4.17
850 857 7.581213 AAATGAAACATGAAACTGTGGTAGA 57.419 32.000 0.00 0.00 0.00 2.59
856 863 6.227298 ACATGAAACTGTGGTAGAGATAGG 57.773 41.667 0.00 0.00 0.00 2.57
859 866 5.529289 TGAAACTGTGGTAGAGATAGGGAT 58.471 41.667 0.00 0.00 0.00 3.85
860 867 5.964477 TGAAACTGTGGTAGAGATAGGGATT 59.036 40.000 0.00 0.00 0.00 3.01
861 868 6.443849 TGAAACTGTGGTAGAGATAGGGATTT 59.556 38.462 0.00 0.00 0.00 2.17
862 869 6.893020 AACTGTGGTAGAGATAGGGATTTT 57.107 37.500 0.00 0.00 0.00 1.82
863 870 6.487299 ACTGTGGTAGAGATAGGGATTTTC 57.513 41.667 0.00 0.00 0.00 2.29
864 871 6.206042 ACTGTGGTAGAGATAGGGATTTTCT 58.794 40.000 0.00 0.00 0.00 2.52
865 872 7.363031 ACTGTGGTAGAGATAGGGATTTTCTA 58.637 38.462 0.00 0.00 0.00 2.10
866 873 7.288158 ACTGTGGTAGAGATAGGGATTTTCTAC 59.712 40.741 2.24 2.24 39.48 2.59
867 874 6.264744 TGTGGTAGAGATAGGGATTTTCTACG 59.735 42.308 4.47 0.00 40.54 3.51
868 875 5.773680 TGGTAGAGATAGGGATTTTCTACGG 59.226 44.000 4.47 0.00 40.54 4.02
869 876 6.008960 GGTAGAGATAGGGATTTTCTACGGA 58.991 44.000 4.47 0.00 40.54 4.69
870 877 6.072008 GGTAGAGATAGGGATTTTCTACGGAC 60.072 46.154 4.47 0.00 40.54 4.79
871 878 5.455872 AGAGATAGGGATTTTCTACGGACA 58.544 41.667 0.00 0.00 0.00 4.02
872 879 5.536916 AGAGATAGGGATTTTCTACGGACAG 59.463 44.000 0.00 0.00 0.00 3.51
957 1004 0.100325 TGCAAAATAATGCCGGCTCG 59.900 50.000 29.70 7.74 45.83 5.03
992 1039 0.836400 TGCTCTCCTCCTTCCGGTTT 60.836 55.000 0.00 0.00 0.00 3.27
1539 1586 3.660111 GAGGCGCTGGCGTTGTTT 61.660 61.111 16.21 0.00 41.24 2.83
1766 1813 1.597027 CGCTTGAGGTGTTTCGGGT 60.597 57.895 0.00 0.00 0.00 5.28
1838 1885 0.242825 CTTGCAGTGCATGGGTTGAG 59.757 55.000 20.50 7.52 38.76 3.02
1852 1899 1.021390 GTTGAGCATGGAGTCGGTGG 61.021 60.000 0.00 0.00 0.00 4.61
1967 2014 2.026262 GTGAGGCCTGGAGGTTATTTCA 60.026 50.000 12.00 0.00 37.57 2.69
2001 2048 0.773644 AAGGGCTCAGACCACATGTT 59.226 50.000 0.00 0.00 29.21 2.71
2151 2198 2.171237 TCTGCATGGATGGGTAGAGTTG 59.829 50.000 0.00 0.00 0.00 3.16
2178 2225 2.111999 TAGTCGGCAGGCAGCTTGTT 62.112 55.000 6.36 0.00 44.79 2.83
2532 2583 3.309388 GCATTCTGATCATGCATTCTGC 58.691 45.455 13.62 5.21 45.50 4.26
2630 2681 4.465886 TGCCAAACATAACCTAGTTGTGT 58.534 39.130 4.28 4.28 46.64 3.72
2797 2848 3.779759 CTGGACAGCAATCAGAGAGTAC 58.220 50.000 0.00 0.00 0.00 2.73
2798 2849 2.497675 TGGACAGCAATCAGAGAGTACC 59.502 50.000 0.00 0.00 0.00 3.34
2799 2850 2.497675 GGACAGCAATCAGAGAGTACCA 59.502 50.000 0.00 0.00 0.00 3.25
2846 2897 3.370840 TGGCTTCTGCTTGTATGGATT 57.629 42.857 0.00 0.00 39.59 3.01
2857 2908 8.158789 TCTGCTTGTATGGATTATTGATCATCA 58.841 33.333 0.00 0.00 36.43 3.07
2858 2909 8.331730 TGCTTGTATGGATTATTGATCATCAG 57.668 34.615 0.00 0.00 36.43 2.90
2859 2910 8.158789 TGCTTGTATGGATTATTGATCATCAGA 58.841 33.333 0.00 0.00 36.43 3.27
2860 2911 9.175312 GCTTGTATGGATTATTGATCATCAGAT 57.825 33.333 0.00 0.00 36.43 2.90
2893 2944 2.627699 GGCAAGAACATTCCAAAGACCA 59.372 45.455 0.00 0.00 0.00 4.02
2978 3029 7.243487 ACAAGTATGCTTCACAAATTGATACG 58.757 34.615 0.00 0.00 32.84 3.06
3014 3065 6.791887 TTTCTCAAGAATCTGCAGTTGTAG 57.208 37.500 14.67 9.88 33.54 2.74
3051 3102 1.632409 AGGATCATGTGCCAGAACTGT 59.368 47.619 8.84 0.00 0.00 3.55
3384 3437 3.903714 CCTTTTTCCCCACATTTTCTCCT 59.096 43.478 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 9.114952 TGGTAATTCAATAATCGACATGCTAAA 57.885 29.630 0.00 0.00 0.00 1.85
58 59 6.886459 ACATGAACTAGGTAGCACAATCAATT 59.114 34.615 0.00 0.00 0.00 2.32
78 79 7.392953 TGATAAAAGAGTGCACCATAAACATGA 59.607 33.333 14.63 0.00 0.00 3.07
100 102 6.850752 TGACACAATCCTAACTCACTGATA 57.149 37.500 0.00 0.00 0.00 2.15
105 107 4.636206 GGGATTGACACAATCCTAACTCAC 59.364 45.833 29.81 15.80 44.35 3.51
159 161 6.625873 AGCTCGAGAACAATCTTTCTTTTT 57.374 33.333 18.75 0.00 35.90 1.94
202 204 6.569780 TCGAGAAGATATTCGGAAAATCACA 58.430 36.000 0.00 0.00 37.42 3.58
248 250 3.504906 TCACGAACTCAAGATAACGGTCT 59.495 43.478 0.00 0.00 0.00 3.85
296 300 2.427506 ACACAAATTCTCGGAGAAGGC 58.572 47.619 23.38 0.00 37.69 4.35
326 330 7.938140 ATTTAAGCATAACCAACTAGCTCAA 57.062 32.000 0.00 0.00 33.83 3.02
350 354 3.646162 TCTTCCAGCTCTCCAAGTTGTTA 59.354 43.478 1.45 0.00 34.59 2.41
365 369 6.515272 TTAGGCAAAGCTTTTATCTTCCAG 57.485 37.500 9.53 0.00 0.00 3.86
406 411 5.120053 CACACACACACACACATACGATATT 59.880 40.000 0.00 0.00 0.00 1.28
412 417 2.675844 ACACACACACACACACACATAC 59.324 45.455 0.00 0.00 0.00 2.39
414 419 1.468127 CACACACACACACACACACAT 59.532 47.619 0.00 0.00 0.00 3.21
522 527 2.362736 ACAGATGCGTGCATGATCTTT 58.637 42.857 12.81 5.76 36.70 2.52
523 528 2.034104 ACAGATGCGTGCATGATCTT 57.966 45.000 12.81 4.32 36.70 2.40
553 559 2.036992 CTCATCTAGAGCCACCACCATC 59.963 54.545 0.00 0.00 37.59 3.51
575 581 0.909623 TCATTTTCTCCCTCCCGACC 59.090 55.000 0.00 0.00 0.00 4.79
581 587 4.097589 CAGCCAATCTTCATTTTCTCCCTC 59.902 45.833 0.00 0.00 0.00 4.30
591 597 2.753452 CTCAACAGCAGCCAATCTTCAT 59.247 45.455 0.00 0.00 0.00 2.57
598 604 1.405105 GTGTTTCTCAACAGCAGCCAA 59.595 47.619 0.00 0.00 43.83 4.52
608 614 4.823442 AGCAGTCAATCATGTGTTTCTCAA 59.177 37.500 0.00 0.00 0.00 3.02
609 615 4.214758 CAGCAGTCAATCATGTGTTTCTCA 59.785 41.667 0.00 0.00 0.00 3.27
610 616 4.453478 TCAGCAGTCAATCATGTGTTTCTC 59.547 41.667 0.00 0.00 0.00 2.87
611 617 4.392047 TCAGCAGTCAATCATGTGTTTCT 58.608 39.130 0.00 0.00 0.00 2.52
612 618 4.453478 TCTCAGCAGTCAATCATGTGTTTC 59.547 41.667 0.00 0.00 0.00 2.78
613 619 4.392047 TCTCAGCAGTCAATCATGTGTTT 58.608 39.130 0.00 0.00 0.00 2.83
614 620 4.001652 CTCTCAGCAGTCAATCATGTGTT 58.998 43.478 0.00 0.00 0.00 3.32
615 621 3.260128 TCTCTCAGCAGTCAATCATGTGT 59.740 43.478 0.00 0.00 0.00 3.72
616 622 3.858247 TCTCTCAGCAGTCAATCATGTG 58.142 45.455 0.00 0.00 0.00 3.21
617 623 3.768215 TCTCTCTCAGCAGTCAATCATGT 59.232 43.478 0.00 0.00 0.00 3.21
618 624 4.388378 TCTCTCTCAGCAGTCAATCATG 57.612 45.455 0.00 0.00 0.00 3.07
619 625 4.710865 TCTTCTCTCTCAGCAGTCAATCAT 59.289 41.667 0.00 0.00 0.00 2.45
620 626 4.085009 TCTTCTCTCTCAGCAGTCAATCA 58.915 43.478 0.00 0.00 0.00 2.57
621 627 4.675510 CTCTTCTCTCTCAGCAGTCAATC 58.324 47.826 0.00 0.00 0.00 2.67
622 628 3.119029 GCTCTTCTCTCTCAGCAGTCAAT 60.119 47.826 0.00 0.00 0.00 2.57
623 629 2.230992 GCTCTTCTCTCTCAGCAGTCAA 59.769 50.000 0.00 0.00 0.00 3.18
624 630 1.818060 GCTCTTCTCTCTCAGCAGTCA 59.182 52.381 0.00 0.00 0.00 3.41
625 631 1.202177 CGCTCTTCTCTCTCAGCAGTC 60.202 57.143 0.00 0.00 0.00 3.51
626 632 0.810648 CGCTCTTCTCTCTCAGCAGT 59.189 55.000 0.00 0.00 0.00 4.40
627 633 1.093972 TCGCTCTTCTCTCTCAGCAG 58.906 55.000 0.00 0.00 0.00 4.24
628 634 1.404748 CATCGCTCTTCTCTCTCAGCA 59.595 52.381 0.00 0.00 0.00 4.41
629 635 1.675483 TCATCGCTCTTCTCTCTCAGC 59.325 52.381 0.00 0.00 0.00 4.26
630 636 3.205338 TCTCATCGCTCTTCTCTCTCAG 58.795 50.000 0.00 0.00 0.00 3.35
631 637 3.274095 TCTCATCGCTCTTCTCTCTCA 57.726 47.619 0.00 0.00 0.00 3.27
632 638 5.237815 TCTATCTCATCGCTCTTCTCTCTC 58.762 45.833 0.00 0.00 0.00 3.20
660 666 8.840200 TTATCTCCTTAGGTGTTTGTCTCTAT 57.160 34.615 0.00 0.00 0.00 1.98
673 679 7.265673 TCGTTGTTGAATCTTATCTCCTTAGG 58.734 38.462 0.00 0.00 0.00 2.69
676 682 7.106239 ACATCGTTGTTGAATCTTATCTCCTT 58.894 34.615 0.00 0.00 29.55 3.36
679 685 9.249457 TCATACATCGTTGTTGAATCTTATCTC 57.751 33.333 4.14 0.00 37.28 2.75
687 693 6.456853 CCGTGATTCATACATCGTTGTTGAAT 60.457 38.462 22.64 22.64 41.24 2.57
702 708 1.449601 GCGTGTCCCCGTGATTCAT 60.450 57.895 0.00 0.00 0.00 2.57
734 740 2.126424 GTCAGTGAGTCGACCGCC 60.126 66.667 13.01 2.43 0.00 6.13
744 750 5.105513 TCAATCGGCTAATTACAGTCAGTGA 60.106 40.000 0.00 0.00 0.00 3.41
750 756 4.161565 TCCTGTCAATCGGCTAATTACAGT 59.838 41.667 0.00 0.00 32.84 3.55
758 764 1.555075 AGCTTTCCTGTCAATCGGCTA 59.445 47.619 0.00 0.00 0.00 3.93
794 801 3.392285 TCATCCATTCGTCCAATCATCCT 59.608 43.478 0.00 0.00 0.00 3.24
798 805 3.479489 CCATCATCCATTCGTCCAATCA 58.521 45.455 0.00 0.00 0.00 2.57
800 807 2.442878 TCCCATCATCCATTCGTCCAAT 59.557 45.455 0.00 0.00 0.00 3.16
823 830 7.306205 ACCACAGTTTCATGTTTCATTTTTG 57.694 32.000 0.00 0.00 0.00 2.44
824 831 8.474025 TCTACCACAGTTTCATGTTTCATTTTT 58.526 29.630 0.00 0.00 0.00 1.94
825 832 8.006298 TCTACCACAGTTTCATGTTTCATTTT 57.994 30.769 0.00 0.00 0.00 1.82
841 848 6.739331 AGAAAATCCCTATCTCTACCACAG 57.261 41.667 0.00 0.00 0.00 3.66
846 853 6.489361 TGTCCGTAGAAAATCCCTATCTCTAC 59.511 42.308 0.00 0.00 36.63 2.59
850 857 5.069251 CACTGTCCGTAGAAAATCCCTATCT 59.931 44.000 0.00 0.00 0.00 1.98
856 863 5.684550 AAAACACTGTCCGTAGAAAATCC 57.315 39.130 0.00 0.00 0.00 3.01
859 866 8.891671 AGTATAAAAACACTGTCCGTAGAAAA 57.108 30.769 0.00 0.00 0.00 2.29
860 867 8.891671 AAGTATAAAAACACTGTCCGTAGAAA 57.108 30.769 0.00 0.00 0.00 2.52
861 868 8.143193 TGAAGTATAAAAACACTGTCCGTAGAA 58.857 33.333 0.00 0.00 0.00 2.10
862 869 7.660112 TGAAGTATAAAAACACTGTCCGTAGA 58.340 34.615 0.00 0.00 0.00 2.59
863 870 7.878477 TGAAGTATAAAAACACTGTCCGTAG 57.122 36.000 0.00 0.00 0.00 3.51
864 871 8.836268 AATGAAGTATAAAAACACTGTCCGTA 57.164 30.769 0.00 0.00 0.00 4.02
865 872 7.739498 AATGAAGTATAAAAACACTGTCCGT 57.261 32.000 0.00 0.00 0.00 4.69
912 959 3.445805 ACAACGTTTGGTCACTCCATTTT 59.554 39.130 0.00 0.00 46.60 1.82
957 1004 1.298638 GCAAGCGCGGGAATTGATC 60.299 57.895 18.01 0.00 0.00 2.92
992 1039 2.184322 GAGGCCGCATTCGTCTCA 59.816 61.111 0.00 0.00 35.58 3.27
1380 1427 0.253044 CGAGAAGGGCATTCCAGGAA 59.747 55.000 8.47 3.72 38.84 3.36
1440 1487 3.186047 GGCATCCGGTCGAACACG 61.186 66.667 0.00 0.00 0.00 4.49
1539 1586 1.114627 CCGTGGTCTCCATCATCTCA 58.885 55.000 0.00 0.00 35.28 3.27
1606 1653 1.592669 GATGAGCACACGCGCCTAT 60.593 57.895 5.73 0.00 45.49 2.57
1766 1813 3.545574 TGCTGGTCACTGGCACGA 61.546 61.111 0.00 0.00 0.00 4.35
1838 1885 0.179000 AATCTCCACCGACTCCATGC 59.821 55.000 0.00 0.00 0.00 4.06
1852 1899 4.012374 TGTTGCATCTCCTGGAAAATCTC 58.988 43.478 0.00 0.00 36.90 2.75
1887 1934 4.504514 CCAAGGTATGTGATCTCATCTGGG 60.505 50.000 13.32 9.01 0.00 4.45
2061 2108 3.331150 TGGCATACTCTTAACAACACCG 58.669 45.455 0.00 0.00 0.00 4.94
2151 2198 3.155167 CTGCCGACTACCTCCCCC 61.155 72.222 0.00 0.00 0.00 5.40
2178 2225 3.007473 TCATGATCTGGCTGCAATTGA 57.993 42.857 10.34 0.00 0.00 2.57
2797 2848 6.912591 GTGAAACAGTTACTGAAGATGTTTGG 59.087 38.462 20.07 0.00 42.44 3.28
2798 2849 6.912591 GGTGAAACAGTTACTGAAGATGTTTG 59.087 38.462 20.07 0.00 42.44 2.93
2799 2850 6.828785 AGGTGAAACAGTTACTGAAGATGTTT 59.171 34.615 20.07 8.50 44.39 2.83
2857 2908 8.677870 ATGTTCTTGCCCTTATCTATCTATCT 57.322 34.615 0.00 0.00 0.00 1.98
2858 2909 9.377312 GAATGTTCTTGCCCTTATCTATCTATC 57.623 37.037 0.00 0.00 0.00 2.08
2859 2910 8.325046 GGAATGTTCTTGCCCTTATCTATCTAT 58.675 37.037 0.00 0.00 0.00 1.98
2860 2911 7.292356 TGGAATGTTCTTGCCCTTATCTATCTA 59.708 37.037 0.00 0.00 0.00 1.98
2893 2944 5.371526 CACCATCTGGCATAAATAGTCAGT 58.628 41.667 0.00 0.00 39.32 3.41
2978 3029 3.758554 TCTTGAGAAAAACTATGGCCAGC 59.241 43.478 13.05 0.00 0.00 4.85
3014 3065 6.942532 TGATCCTAGCAATTGGTACATTTC 57.057 37.500 13.22 8.64 39.30 2.17
3194 3245 1.140852 TCCGGATGTTTGGCCTGATAG 59.859 52.381 0.00 0.00 0.00 2.08
3200 3251 1.754234 ATGCTCCGGATGTTTGGCC 60.754 57.895 3.57 0.00 0.00 5.36
3314 3365 4.387256 GCTAACTGCTCTTTGTGTACTCTG 59.613 45.833 0.00 0.00 38.95 3.35


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

AutoCloner maintained by Alex Coulton.