Multiple sequence alignment - TraesCS6D01G244500

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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 TraesCS6D01G244500 chr6D 100.000 3755 0 0 1 3755 346823682 346827436 0.000000e+00 6935
1 TraesCS6D01G244500 chr6B 96.419 2904 90 3 842 3742 534247085 534244193 0.000000e+00 4774
2 TraesCS6D01G244500 chr6A 95.426 2908 93 14 866 3755 496629652 496626767 0.000000e+00 4597
3 TraesCS6D01G244500 chr6A 91.688 794 58 5 1 790 496630626 496629837 0.000000e+00 1094
4 TraesCS6D01G244500 chr5D 73.691 802 159 36 61 820 216978931 216979722 8.000000e-67 265
5 TraesCS6D01G244500 chr1D 79.048 315 46 11 48 345 439726019 439725708 8.230000e-47 198
6 TraesCS6D01G244500 chr7B 73.985 542 98 25 54 575 479914183 479913665 2.980000e-41 180
7 TraesCS6D01G244500 chr3D 80.083 241 37 5 171 407 515265833 515265600 6.450000e-38 169
8 TraesCS6D01G244500 chr3D 74.619 394 84 12 166 550 574532781 574532395 3.880000e-35 159
9 TraesCS6D01G244500 chr7D 73.019 530 120 12 61 569 554368936 554368409 8.340000e-37 165
10 TraesCS6D01G244500 chr7D 81.928 166 24 6 166 327 205242886 205243049 6.540000e-28 135


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 TraesCS6D01G244500 chr6D 346823682 346827436 3754 False 6935.0 6935 100.000 1 3755 1 chr6D.!!$F1 3754
1 TraesCS6D01G244500 chr6B 534244193 534247085 2892 True 4774.0 4774 96.419 842 3742 1 chr6B.!!$R1 2900
2 TraesCS6D01G244500 chr6A 496626767 496630626 3859 True 2845.5 4597 93.557 1 3755 2 chr6A.!!$R1 3754
3 TraesCS6D01G244500 chr5D 216978931 216979722 791 False 265.0 265 73.691 61 820 1 chr5D.!!$F1 759

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
757 773 0.037326 GGCGGCGATGGAATAGATGA 60.037 55.000 12.98 0.0 0.00 2.92 F
796 812 0.919710 GCAGGTGAGGGGGAGTATTT 59.080 55.000 0.00 0.0 0.00 1.40 F
979 1142 1.000019 CTCGGGCCGATATCCCCTA 60.000 63.158 31.23 3.1 40.75 3.53 F
1962 2285 1.075536 TCAGTGCCAGAGTACCTGAGA 59.924 52.381 11.58 1.8 45.78 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1962 2285 1.425066 TCATCTGCCAACCCAACTCTT 59.575 47.619 0.00 0.0 0.0 2.85 R
2205 2528 3.087031 CTGTGCATTCATCTCCACCTTT 58.913 45.455 0.00 0.0 0.0 3.11 R
2574 2897 4.862574 GGCGCTAATGGTCTTTTAAAAAGG 59.137 41.667 7.64 0.0 0.0 3.11 R
3504 3827 0.329596 GGAGAAGAATGGTGGTGGCT 59.670 55.000 0.00 0.0 0.0 4.75 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
101 102 2.988010 TGCACACTTCTGTCTTGTCT 57.012 45.000 0.00 0.00 0.00 3.41
276 291 1.934849 GCGGCCAATCCAAAGAACAAC 60.935 52.381 2.24 0.00 34.01 3.32
306 322 2.639065 TGGCACTCACTTCGTCTTTTT 58.361 42.857 0.00 0.00 0.00 1.94
329 345 9.802039 TTTTATACTTGTAGAAAACCCATCTGT 57.198 29.630 8.63 0.00 0.00 3.41
360 376 3.127533 GCCCGCTACAAGGTGCAG 61.128 66.667 0.00 0.00 0.00 4.41
366 382 1.386533 GCTACAAGGTGCAGCATCAT 58.613 50.000 19.63 0.00 36.77 2.45
368 384 1.945394 CTACAAGGTGCAGCATCATCC 59.055 52.381 19.63 0.00 0.00 3.51
374 390 2.409055 TGCAGCATCATCCGCCAAC 61.409 57.895 0.00 0.00 0.00 3.77
411 427 4.477975 CGGTGGAGGCTCGTCGAC 62.478 72.222 8.69 5.18 0.00 4.20
427 443 0.249953 CGACGAGCTCCTAGGCTAGA 60.250 60.000 22.99 8.14 43.20 2.43
477 493 4.353437 GTCGGCGGTCGGTCAACT 62.353 66.667 7.21 0.00 39.77 3.16
482 498 2.604174 GCGGTCGGTCAACTGTTGG 61.604 63.158 19.55 4.96 0.00 3.77
487 503 0.762418 TCGGTCAACTGTTGGGATGT 59.238 50.000 19.55 0.00 0.00 3.06
518 534 6.001460 CGAGAGGAGAAGAACATACCTAGAT 58.999 44.000 0.00 0.00 0.00 1.98
524 540 1.344763 AGAACATACCTAGATGCGGCC 59.655 52.381 0.00 0.00 0.00 6.13
581 597 0.736325 CGAATCCCTTCAAGACGCGT 60.736 55.000 13.85 13.85 0.00 6.01
586 602 0.878523 CCCTTCAAGACGCGTCAACA 60.879 55.000 37.85 19.61 0.00 3.33
592 608 2.050714 GACGCGTCAACACCGAGA 60.051 61.111 33.09 0.00 0.00 4.04
602 618 2.023414 AACACCGAGAACCGAGTGCA 62.023 55.000 0.00 0.00 40.58 4.57
619 635 1.071299 CATCGAATCCGGCCATGGA 59.929 57.895 18.40 1.76 43.58 3.41
641 657 2.582687 GTAGATCCGTCGATTTAGGCG 58.417 52.381 0.00 0.00 39.19 5.52
647 663 1.257936 CCGTCGATTTAGGCGTCAATG 59.742 52.381 0.00 0.00 37.56 2.82
702 718 1.077716 GCGGTTGCTATGAGGGGTT 60.078 57.895 0.00 0.00 38.39 4.11
705 721 1.037579 GGTTGCTATGAGGGGTTGGC 61.038 60.000 0.00 0.00 0.00 4.52
728 744 4.758251 CGTGTGATGGCCAGCGGA 62.758 66.667 17.68 1.38 0.00 5.54
729 745 2.821366 GTGTGATGGCCAGCGGAG 60.821 66.667 17.68 0.00 0.00 4.63
734 750 0.107703 TGATGGCCAGCGGAGTAAAG 60.108 55.000 17.68 0.00 0.00 1.85
745 761 3.305177 GAGTAAAGTGGGGCGGCGA 62.305 63.158 12.98 0.00 0.00 5.54
752 768 3.164977 TGGGGCGGCGATGGAATA 61.165 61.111 12.98 0.00 0.00 1.75
757 773 0.037326 GGCGGCGATGGAATAGATGA 60.037 55.000 12.98 0.00 0.00 2.92
761 777 2.029918 CGGCGATGGAATAGATGAGACA 60.030 50.000 0.00 0.00 0.00 3.41
769 785 3.648067 GGAATAGATGAGACATGGGGTGA 59.352 47.826 0.00 0.00 0.00 4.02
771 787 1.504912 AGATGAGACATGGGGTGAGG 58.495 55.000 0.00 0.00 0.00 3.86
773 789 1.139853 GATGAGACATGGGGTGAGGAC 59.860 57.143 0.00 0.00 0.00 3.85
787 803 4.394712 GGACGGTGCAGGTGAGGG 62.395 72.222 0.00 0.00 0.00 4.30
792 808 2.930562 GTGCAGGTGAGGGGGAGT 60.931 66.667 0.00 0.00 0.00 3.85
793 809 1.612442 GTGCAGGTGAGGGGGAGTA 60.612 63.158 0.00 0.00 0.00 2.59
796 812 0.919710 GCAGGTGAGGGGGAGTATTT 59.080 55.000 0.00 0.00 0.00 1.40
797 813 1.285078 GCAGGTGAGGGGGAGTATTTT 59.715 52.381 0.00 0.00 0.00 1.82
799 815 3.053917 GCAGGTGAGGGGGAGTATTTTTA 60.054 47.826 0.00 0.00 0.00 1.52
800 816 4.524053 CAGGTGAGGGGGAGTATTTTTAC 58.476 47.826 0.00 0.00 0.00 2.01
801 817 4.227527 CAGGTGAGGGGGAGTATTTTTACT 59.772 45.833 0.00 0.00 0.00 2.24
802 818 4.473922 AGGTGAGGGGGAGTATTTTTACTC 59.526 45.833 4.87 4.87 44.23 2.59
832 848 9.645128 AGATGGGAGATTGAGTATATATGAGAG 57.355 37.037 0.00 0.00 0.00 3.20
833 849 9.420118 GATGGGAGATTGAGTATATATGAGAGT 57.580 37.037 0.00 0.00 0.00 3.24
834 850 8.815565 TGGGAGATTGAGTATATATGAGAGTC 57.184 38.462 0.00 0.00 0.00 3.36
835 851 7.836685 TGGGAGATTGAGTATATATGAGAGTCC 59.163 40.741 0.00 0.00 0.00 3.85
837 853 7.554835 GGAGATTGAGTATATATGAGAGTCCGT 59.445 40.741 0.00 0.00 0.00 4.69
838 854 8.500753 AGATTGAGTATATATGAGAGTCCGTC 57.499 38.462 0.00 0.00 0.00 4.79
839 855 8.325787 AGATTGAGTATATATGAGAGTCCGTCT 58.674 37.037 0.00 0.00 38.71 4.18
840 856 7.674471 TTGAGTATATATGAGAGTCCGTCTG 57.326 40.000 0.00 0.00 34.71 3.51
851 867 4.730657 AGAGTCCGTCTGTAAACATTACG 58.269 43.478 9.81 9.81 35.92 3.18
853 869 4.730657 AGTCCGTCTGTAAACATTACGAG 58.269 43.478 15.61 8.76 37.33 4.18
863 879 1.851304 ACATTACGAGGGACCGGTTA 58.149 50.000 9.42 0.00 0.00 2.85
879 895 3.254657 CCGGTTAGGTGCAATTTGAAAGA 59.745 43.478 0.00 0.00 34.51 2.52
922 1071 4.811969 TGTAAAGCTTTACAGGGATCGA 57.188 40.909 36.66 19.03 45.70 3.59
935 1084 3.515502 CAGGGATCGATTAGGGATGCTAA 59.484 47.826 0.00 0.00 33.33 3.09
936 1085 3.515901 AGGGATCGATTAGGGATGCTAAC 59.484 47.826 0.00 0.00 33.33 2.34
938 1087 4.080863 GGGATCGATTAGGGATGCTAACAT 60.081 45.833 0.00 0.00 39.98 2.71
940 1089 6.276847 GGATCGATTAGGGATGCTAACATAG 58.723 44.000 0.00 0.00 36.35 2.23
979 1142 1.000019 CTCGGGCCGATATCCCCTA 60.000 63.158 31.23 3.10 40.75 3.53
1059 1222 4.873129 CCACTCATACGCGCCGCT 62.873 66.667 5.73 0.00 0.00 5.52
1383 1546 3.984732 GGCTTGCCCCCTTCCACT 61.985 66.667 0.00 0.00 0.00 4.00
1517 1840 2.606519 CCAAGTCCCTCCCGACCA 60.607 66.667 0.00 0.00 32.91 4.02
1909 2232 2.551270 TCTTACTGAGCAATCCTGGGT 58.449 47.619 0.00 0.00 0.00 4.51
1935 2258 9.781633 TTTTTGGATCTTGATTTTGATGATGTT 57.218 25.926 0.00 0.00 0.00 2.71
1962 2285 1.075536 TCAGTGCCAGAGTACCTGAGA 59.924 52.381 11.58 1.80 45.78 3.27
2205 2528 6.928348 TTCTCAGACAGAATGGTTAAGGTA 57.072 37.500 0.00 0.00 43.62 3.08
2499 2822 3.134458 GGAGTATCTTGATTGCTTCCCG 58.866 50.000 0.00 0.00 33.73 5.14
2574 2897 0.817654 GGTGGCTCCAAAGTTATGGC 59.182 55.000 0.00 0.00 40.46 4.40
2759 3082 8.900781 CCAGCATCCAGATAATGAATAATTAGG 58.099 37.037 0.00 0.00 34.21 2.69
2795 3118 2.355513 GGCATGATTATCAGAGCCGGAT 60.356 50.000 20.33 0.00 40.19 4.18
2801 3124 4.343814 TGATTATCAGAGCCGGATGTACAA 59.656 41.667 5.05 0.00 0.00 2.41
3056 3379 6.255950 GCGGTTATGTATTTCAAGGAAAGAC 58.744 40.000 8.97 8.97 42.04 3.01
3098 3421 7.721402 AGGTGAAAGACTAGCACTGATAATAG 58.279 38.462 7.34 0.00 33.25 1.73
3138 3461 6.354130 TCGATCGTACCATCATCCTCATATA 58.646 40.000 15.94 0.00 0.00 0.86
3259 3582 5.808540 TGACGCAATGGTAAGAACATACTAC 59.191 40.000 0.00 0.00 0.00 2.73
3402 3725 2.824961 GCTCCCTCTGATCTGAGCT 58.175 57.895 20.95 0.00 45.21 4.09
3438 3761 4.153117 CACTGTGTGAGATAAAAGTCCAGC 59.847 45.833 0.00 0.00 35.23 4.85
3467 3790 0.614812 GTAGAAAACCCTACCCGCCA 59.385 55.000 0.00 0.00 34.43 5.69
3504 3827 0.446222 GCGCTCGTTTCCATTGCTTA 59.554 50.000 0.00 0.00 0.00 3.09
3527 3850 1.630369 CACCACCATTCTTCTCCTCCA 59.370 52.381 0.00 0.00 0.00 3.86
3546 3872 1.591280 ATCCTCTCCCCGTGGTAGGT 61.591 60.000 7.67 0.00 37.25 3.08
3618 3944 1.630369 TCTTGAGCAGGGCACAGTTAT 59.370 47.619 0.00 0.00 30.09 1.89
3689 4015 3.559238 AATCACCGCTGAAAACATGTC 57.441 42.857 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 5.067283 AGTGGAGTTTTTAATGAAGTGCGTT 59.933 36.000 0.00 0.00 0.00 4.84
77 78 3.758554 ACAAGACAGAAGTGTGCAAGTTT 59.241 39.130 0.00 0.00 36.88 2.66
101 102 0.843309 TGTCCAAGTTTGAGGAGGCA 59.157 50.000 0.00 0.00 33.85 4.75
130 131 4.528206 TGGTTGCTAGAGATGAGACTGAAA 59.472 41.667 0.00 0.00 0.00 2.69
133 134 4.462508 TTGGTTGCTAGAGATGAGACTG 57.537 45.455 0.00 0.00 0.00 3.51
276 291 2.151202 AGTGAGTGCCATTTTGTACGG 58.849 47.619 0.00 0.00 0.00 4.02
306 322 7.335627 CCACAGATGGGTTTTCTACAAGTATA 58.664 38.462 0.00 0.00 43.04 1.47
352 368 2.117156 GCGGATGATGCTGCACCTT 61.117 57.895 3.57 0.00 39.93 3.50
368 384 1.327460 CAAGTATGATCACCGTTGGCG 59.673 52.381 0.00 0.00 37.95 5.69
383 399 1.191535 CCTCCACCGGTCATCAAGTA 58.808 55.000 2.59 0.00 0.00 2.24
394 410 4.477975 GTCGACGAGCCTCCACCG 62.478 72.222 0.00 0.00 0.00 4.94
409 425 1.519408 CTCTAGCCTAGGAGCTCGTC 58.481 60.000 14.75 0.00 43.67 4.20
427 443 4.148825 CGTTAGCCGGGCTCAGCT 62.149 66.667 27.65 0.00 40.44 4.24
471 487 1.537202 GCTCACATCCCAACAGTTGAC 59.463 52.381 15.36 0.00 0.00 3.18
477 493 2.359850 GGCGCTCACATCCCAACA 60.360 61.111 7.64 0.00 0.00 3.33
482 498 2.279120 CTCTCGGCGCTCACATCC 60.279 66.667 7.64 0.00 0.00 3.51
487 503 2.361230 TTCTCCTCTCGGCGCTCA 60.361 61.111 7.64 0.00 0.00 4.26
514 530 3.916544 CGCTCTGGGCCGCATCTA 61.917 66.667 0.00 0.00 37.74 1.98
524 540 4.135153 CCACCTCGACCGCTCTGG 62.135 72.222 0.00 0.00 46.41 3.86
581 597 0.031585 CACTCGGTTCTCGGTGTTGA 59.968 55.000 0.00 0.00 39.77 3.18
586 602 1.215647 GATGCACTCGGTTCTCGGT 59.784 57.895 0.00 0.00 39.77 4.69
602 618 1.071471 GTCCATGGCCGGATTCGAT 59.929 57.895 5.05 0.00 37.41 3.59
641 657 3.002791 TCGGTTGCTTCTCATCATTGAC 58.997 45.455 0.00 0.00 0.00 3.18
647 663 2.537625 CTCGATTCGGTTGCTTCTCATC 59.462 50.000 6.18 0.00 0.00 2.92
712 728 2.238847 TACTCCGCTGGCCATCACAC 62.239 60.000 5.51 0.00 0.00 3.82
717 733 0.392998 CACTTTACTCCGCTGGCCAT 60.393 55.000 5.51 0.00 0.00 4.40
726 742 2.437895 GCCGCCCCACTTTACTCC 60.438 66.667 0.00 0.00 0.00 3.85
727 743 2.588856 ATCGCCGCCCCACTTTACTC 62.589 60.000 0.00 0.00 0.00 2.59
728 744 2.666098 ATCGCCGCCCCACTTTACT 61.666 57.895 0.00 0.00 0.00 2.24
729 745 2.124860 ATCGCCGCCCCACTTTAC 60.125 61.111 0.00 0.00 0.00 2.01
734 750 3.469863 TATTCCATCGCCGCCCCAC 62.470 63.158 0.00 0.00 0.00 4.61
745 761 4.042560 CACCCCATGTCTCATCTATTCCAT 59.957 45.833 0.00 0.00 0.00 3.41
752 768 1.008815 TCCTCACCCCATGTCTCATCT 59.991 52.381 0.00 0.00 0.00 2.90
757 773 1.990060 CCGTCCTCACCCCATGTCT 60.990 63.158 0.00 0.00 0.00 3.41
761 777 3.717294 GCACCGTCCTCACCCCAT 61.717 66.667 0.00 0.00 0.00 4.00
769 785 3.314331 CCTCACCTGCACCGTCCT 61.314 66.667 0.00 0.00 0.00 3.85
771 787 4.394712 CCCCTCACCTGCACCGTC 62.395 72.222 0.00 0.00 0.00 4.79
779 795 4.445564 AGTAAAAATACTCCCCCTCACCT 58.554 43.478 0.00 0.00 0.00 4.00
806 822 9.645128 CTCTCATATATACTCAATCTCCCATCT 57.355 37.037 0.00 0.00 0.00 2.90
808 824 9.420118 GACTCTCATATATACTCAATCTCCCAT 57.580 37.037 0.00 0.00 0.00 4.00
809 825 7.836685 GGACTCTCATATATACTCAATCTCCCA 59.163 40.741 0.00 0.00 0.00 4.37
813 829 8.325787 AGACGGACTCTCATATATACTCAATCT 58.674 37.037 0.00 0.00 0.00 2.40
815 831 7.885922 ACAGACGGACTCTCATATATACTCAAT 59.114 37.037 0.00 0.00 0.00 2.57
816 832 7.225011 ACAGACGGACTCTCATATATACTCAA 58.775 38.462 0.00 0.00 0.00 3.02
817 833 6.770542 ACAGACGGACTCTCATATATACTCA 58.229 40.000 0.00 0.00 0.00 3.41
819 835 9.001542 GTTTACAGACGGACTCTCATATATACT 57.998 37.037 0.00 0.00 0.00 2.12
821 837 8.913487 TGTTTACAGACGGACTCTCATATATA 57.087 34.615 0.00 0.00 0.00 0.86
822 838 7.818997 TGTTTACAGACGGACTCTCATATAT 57.181 36.000 0.00 0.00 0.00 0.86
823 839 7.818997 ATGTTTACAGACGGACTCTCATATA 57.181 36.000 0.00 0.00 0.00 0.86
824 840 6.716934 ATGTTTACAGACGGACTCTCATAT 57.283 37.500 0.00 0.00 0.00 1.78
826 842 5.407407 AATGTTTACAGACGGACTCTCAT 57.593 39.130 0.00 0.00 0.00 2.90
827 843 4.866508 AATGTTTACAGACGGACTCTCA 57.133 40.909 0.00 0.00 0.00 3.27
829 845 4.456911 TCGTAATGTTTACAGACGGACTCT 59.543 41.667 15.66 0.00 38.73 3.24
831 847 4.380233 CCTCGTAATGTTTACAGACGGACT 60.380 45.833 15.66 0.00 38.73 3.85
832 848 3.855950 CCTCGTAATGTTTACAGACGGAC 59.144 47.826 15.66 0.00 38.73 4.79
833 849 3.119388 CCCTCGTAATGTTTACAGACGGA 60.119 47.826 15.66 6.33 38.73 4.69
834 850 3.119388 TCCCTCGTAATGTTTACAGACGG 60.119 47.826 15.66 9.30 38.73 4.79
835 851 3.855950 GTCCCTCGTAATGTTTACAGACG 59.144 47.826 11.67 11.67 39.22 4.18
837 853 3.119388 CGGTCCCTCGTAATGTTTACAGA 60.119 47.826 0.00 0.00 0.00 3.41
838 854 3.184541 CGGTCCCTCGTAATGTTTACAG 58.815 50.000 0.00 0.00 0.00 2.74
839 855 2.094078 CCGGTCCCTCGTAATGTTTACA 60.094 50.000 0.00 0.00 0.00 2.41
840 856 2.094026 ACCGGTCCCTCGTAATGTTTAC 60.094 50.000 0.00 0.00 0.00 2.01
851 867 1.833787 TTGCACCTAACCGGTCCCTC 61.834 60.000 8.04 0.00 44.93 4.30
853 869 0.323087 AATTGCACCTAACCGGTCCC 60.323 55.000 8.04 0.00 44.93 4.46
863 879 6.536224 CAGTTTTTCTCTTTCAAATTGCACCT 59.464 34.615 0.00 0.00 0.00 4.00
922 1071 7.013220 TCAGACTCTATGTTAGCATCCCTAAT 58.987 38.462 0.00 0.00 38.25 1.73
935 1084 5.046520 GGTTAGGGTTTGTCAGACTCTATGT 60.047 44.000 4.04 0.00 30.60 2.29
936 1085 5.420409 GGTTAGGGTTTGTCAGACTCTATG 58.580 45.833 4.04 0.00 30.60 2.23
938 1087 3.836562 GGGTTAGGGTTTGTCAGACTCTA 59.163 47.826 1.31 0.00 0.00 2.43
940 1089 2.290134 GGGGTTAGGGTTTGTCAGACTC 60.290 54.545 1.31 0.00 0.00 3.36
1059 1222 3.141488 GAGAGGAAGCGGCGGAGA 61.141 66.667 9.78 0.00 0.00 3.71
1164 1327 1.132453 CGCGTTGAGATGAGGTAGTCA 59.868 52.381 0.00 0.00 40.38 3.41
1383 1546 3.706086 TGAGGAACATGAGATCGGAATCA 59.294 43.478 0.00 0.00 34.07 2.57
1517 1840 4.473520 CAAGGCGGGCGGAGATGT 62.474 66.667 0.00 0.00 0.00 3.06
1747 2070 1.620524 CCCAATCTTCACCCCAGCATT 60.621 52.381 0.00 0.00 0.00 3.56
1909 2232 9.781633 AACATCATCAAAATCAAGATCCAAAAA 57.218 25.926 0.00 0.00 0.00 1.94
1962 2285 1.425066 TCATCTGCCAACCCAACTCTT 59.575 47.619 0.00 0.00 0.00 2.85
2205 2528 3.087031 CTGTGCATTCATCTCCACCTTT 58.913 45.455 0.00 0.00 0.00 3.11
2574 2897 4.862574 GGCGCTAATGGTCTTTTAAAAAGG 59.137 41.667 7.64 0.00 0.00 3.11
2795 3118 5.497464 TGGAGATGACAATCCTTTGTACA 57.503 39.130 10.49 0.00 46.01 2.90
2801 3124 5.909621 CACAATTGGAGATGACAATCCTT 57.090 39.130 10.83 0.00 37.55 3.36
2954 3277 8.442632 TTTGCAAAATTGAATTACATGGTTGA 57.557 26.923 10.02 0.00 0.00 3.18
3056 3379 4.948847 TCACCTCGGATCAATACAGAATG 58.051 43.478 0.00 0.00 46.00 2.67
3098 3421 7.899841 GGTACGATCGATAACCAAAAAGTTAAC 59.100 37.037 24.34 0.00 35.90 2.01
3138 3461 6.032956 ACATGAGTTCAACATGATGCAATT 57.967 33.333 13.54 0.00 45.22 2.32
3259 3582 6.849811 CAGAAGCGAGCAATCTATGTTTAATG 59.150 38.462 0.00 0.00 0.00 1.90
3467 3790 3.009714 GAAAGGAGGGGCCCGAGT 61.010 66.667 18.95 1.73 37.37 4.18
3504 3827 0.329596 GGAGAAGAATGGTGGTGGCT 59.670 55.000 0.00 0.00 0.00 4.75
3527 3850 1.233369 CCTACCACGGGGAGAGGAT 59.767 63.158 20.86 0.00 40.93 3.24
3588 3914 0.391395 CTGCTCAAGACAGAGGCTGG 60.391 60.000 0.00 0.00 37.32 4.85
3596 3922 1.071987 CTGTGCCCTGCTCAAGACA 59.928 57.895 0.00 0.00 31.71 3.41
3689 4015 1.950909 GGGTGTCCTGATCTAGAGTCG 59.049 57.143 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.