Multiple sequence alignment - TraesCS5B01G391800

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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 TraesCS5B01G391800 chr5B 100.000 3325 0 0 1 3325 570931662 570928338 0.000000e+00 6141.0
1 TraesCS5B01G391800 chr5B 87.037 54 7 0 3055 3108 543285120 543285173 9.960000e-06 62.1
2 TraesCS5B01G391800 chr5D 93.237 2484 90 27 871 3325 464073094 464070660 0.000000e+00 3585.0
3 TraesCS5B01G391800 chr5D 91.481 810 42 19 1 799 464074254 464073461 0.000000e+00 1088.0
4 TraesCS5B01G391800 chr5A 92.451 2477 125 27 870 3325 584456134 584453699 0.000000e+00 3482.0
5 TraesCS5B01G391800 chr5A 90.851 776 40 15 1 756 584457401 584456637 0.000000e+00 1011.0
6 TraesCS5B01G391800 chr2B 87.863 585 67 4 1 583 752834377 752834959 0.000000e+00 684.0
7 TraesCS5B01G391800 chr2A 86.986 584 70 5 1 582 746981775 746982354 0.000000e+00 652.0
8 TraesCS5B01G391800 chr2A 86.047 559 66 5 27 583 747153440 747153988 1.030000e-164 590.0
9 TraesCS5B01G391800 chr2D 86.806 576 70 6 1 573 617077369 617077941 3.620000e-179 638.0
10 TraesCS5B01G391800 chr2D 90.698 43 4 0 3055 3097 14814285 14814243 1.290000e-04 58.4
11 TraesCS5B01G391800 chrUn 84.369 499 76 2 1 498 35329700 35329203 3.860000e-134 488.0
12 TraesCS5B01G391800 chrUn 83.936 498 78 2 1 497 35311389 35310893 3.000000e-130 475.0
13 TraesCS5B01G391800 chr1B 83.396 530 81 7 1 526 10085325 10085851 4.990000e-133 484.0
14 TraesCS5B01G391800 chr3D 88.372 86 8 1 3052 3135 370115713 370115798 5.870000e-18 102.0
15 TraesCS5B01G391800 chr6A 87.952 83 10 0 3055 3137 66388082 66388164 7.590000e-17 99.0
16 TraesCS5B01G391800 chr7D 87.654 81 10 0 3055 3135 623531385 623531465 9.820000e-16 95.3
17 TraesCS5B01G391800 chr7A 100.000 38 0 0 3055 3092 127774872 127774909 1.650000e-08 71.3
18 TraesCS5B01G391800 chr3A 97.436 39 1 0 3098 3136 516801720 516801682 2.140000e-07 67.6
19 TraesCS5B01G391800 chr1A 82.051 78 7 5 3055 3128 300771474 300771548 3.580000e-05 60.2


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 TraesCS5B01G391800 chr5B 570928338 570931662 3324 True 6141.0 6141 100.000 1 3325 1 chr5B.!!$R1 3324
1 TraesCS5B01G391800 chr5D 464070660 464074254 3594 True 2336.5 3585 92.359 1 3325 2 chr5D.!!$R1 3324
2 TraesCS5B01G391800 chr5A 584453699 584457401 3702 True 2246.5 3482 91.651 1 3325 2 chr5A.!!$R1 3324
3 TraesCS5B01G391800 chr2B 752834377 752834959 582 False 684.0 684 87.863 1 583 1 chr2B.!!$F1 582
4 TraesCS5B01G391800 chr2A 746981775 746982354 579 False 652.0 652 86.986 1 582 1 chr2A.!!$F1 581
5 TraesCS5B01G391800 chr2A 747153440 747153988 548 False 590.0 590 86.047 27 583 1 chr2A.!!$F2 556
6 TraesCS5B01G391800 chr2D 617077369 617077941 572 False 638.0 638 86.806 1 573 1 chr2D.!!$F1 572
7 TraesCS5B01G391800 chr1B 10085325 10085851 526 False 484.0 484 83.396 1 526 1 chr1B.!!$F1 525

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
605 610 0.248743 TATCGCTCTTTACCGTGGCG 60.249 55.0 0.0 0.0 45.93 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2536 3007 0.452987 TTTGCTCGCATGATTCTGCC 59.547 50.0 0.0 0.0 39.0 4.85 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
135 136 1.560923 GCACTATGGGCTATATCGCG 58.439 55.000 0.00 0.00 0.00 5.87
339 340 2.404215 CTTACTGTGGAAGTGACACCG 58.596 52.381 0.84 0.00 40.26 4.94
498 499 3.903090 AGCCATTTGTCCCATCTGAAAAA 59.097 39.130 0.00 0.00 0.00 1.94
589 594 9.710900 TGGATATAGTTGATTCATGTGTGTATC 57.289 33.333 0.00 0.00 33.99 2.24
602 607 2.597305 GTGTGTATCGCTCTTTACCGTG 59.403 50.000 0.00 0.00 0.00 4.94
605 610 0.248743 TATCGCTCTTTACCGTGGCG 60.249 55.000 0.00 0.00 45.93 5.69
618 623 2.031314 TGGCGCGGTTTCTAGCAA 59.969 55.556 8.83 0.00 0.00 3.91
619 624 1.376683 TGGCGCGGTTTCTAGCAAT 60.377 52.632 8.83 0.00 0.00 3.56
620 625 1.062525 GGCGCGGTTTCTAGCAATG 59.937 57.895 8.83 0.00 0.00 2.82
621 626 1.644786 GGCGCGGTTTCTAGCAATGT 61.645 55.000 8.83 0.00 0.00 2.71
622 627 1.003851 GCGCGGTTTCTAGCAATGTA 58.996 50.000 8.83 0.00 0.00 2.29
630 635 7.564988 GCGGTTTCTAGCAATGTAGTATAAAG 58.435 38.462 0.00 0.00 0.00 1.85
631 636 7.224167 GCGGTTTCTAGCAATGTAGTATAAAGT 59.776 37.037 0.00 0.00 0.00 2.66
632 637 9.095065 CGGTTTCTAGCAATGTAGTATAAAGTT 57.905 33.333 0.00 0.00 0.00 2.66
655 670 6.403866 TTCTATTGCCAAGTCAATTGTGTT 57.596 33.333 5.13 0.00 37.75 3.32
656 671 7.517614 TTCTATTGCCAAGTCAATTGTGTTA 57.482 32.000 5.13 0.00 37.75 2.41
659 674 5.590530 TTGCCAAGTCAATTGTGTTAGTT 57.409 34.783 5.13 0.00 37.17 2.24
660 675 6.701145 TTGCCAAGTCAATTGTGTTAGTTA 57.299 33.333 5.13 0.00 37.17 2.24
661 676 6.067263 TGCCAAGTCAATTGTGTTAGTTAC 57.933 37.500 5.13 0.00 37.17 2.50
662 677 5.009210 TGCCAAGTCAATTGTGTTAGTTACC 59.991 40.000 5.13 0.00 37.17 2.85
663 678 5.009210 GCCAAGTCAATTGTGTTAGTTACCA 59.991 40.000 5.13 0.00 37.17 3.25
664 679 6.294508 GCCAAGTCAATTGTGTTAGTTACCAT 60.295 38.462 5.13 0.00 37.17 3.55
665 680 7.305474 CCAAGTCAATTGTGTTAGTTACCATC 58.695 38.462 5.13 0.00 37.17 3.51
667 682 8.514594 CAAGTCAATTGTGTTAGTTACCATCAT 58.485 33.333 5.13 0.00 33.95 2.45
668 683 8.044060 AGTCAATTGTGTTAGTTACCATCATG 57.956 34.615 5.13 0.00 0.00 3.07
669 684 6.747280 GTCAATTGTGTTAGTTACCATCATGC 59.253 38.462 5.13 0.00 0.00 4.06
670 685 5.835113 ATTGTGTTAGTTACCATCATGCC 57.165 39.130 0.00 0.00 0.00 4.40
678 701 3.461085 AGTTACCATCATGCCTCCTGATT 59.539 43.478 0.00 0.00 31.00 2.57
683 706 4.070716 CCATCATGCCTCCTGATTTAGTC 58.929 47.826 0.00 0.00 31.00 2.59
722 747 7.459795 TTGTAATACTGGATTTGATGTGCAA 57.540 32.000 0.00 0.00 33.88 4.08
727 752 5.471556 ACTGGATTTGATGTGCAATGAAA 57.528 34.783 0.00 0.00 36.15 2.69
747 772 5.642919 TGAAATAGTTGAAAATGCCATTGCC 59.357 36.000 0.00 0.00 36.33 4.52
756 781 2.766345 ATGCCATTGCCGTGATTTTT 57.234 40.000 0.00 0.00 36.33 1.94
799 824 7.672983 AATTTCAGTTGTGTAGTATCCACTG 57.327 36.000 0.00 0.00 36.14 3.66
801 826 4.157246 TCAGTTGTGTAGTATCCACTGGT 58.843 43.478 0.00 0.00 36.14 4.00
802 827 4.591498 TCAGTTGTGTAGTATCCACTGGTT 59.409 41.667 0.00 0.00 36.14 3.67
803 828 4.929808 CAGTTGTGTAGTATCCACTGGTTC 59.070 45.833 0.00 0.00 36.14 3.62
807 884 2.045326 TGTAGTATCCACTGGTTCCCCT 59.955 50.000 0.00 0.00 36.14 4.79
808 885 3.272818 TGTAGTATCCACTGGTTCCCCTA 59.727 47.826 0.00 0.00 36.14 3.53
811 888 4.180723 AGTATCCACTGGTTCCCCTAAAA 58.819 43.478 0.00 0.00 32.25 1.52
824 901 6.243148 GTTCCCCTAAAACACAAGAGGATTA 58.757 40.000 0.00 0.00 0.00 1.75
826 903 7.039722 TCCCCTAAAACACAAGAGGATTATT 57.960 36.000 0.00 0.00 0.00 1.40
828 905 8.272173 TCCCCTAAAACACAAGAGGATTATTAG 58.728 37.037 0.00 0.00 0.00 1.73
830 907 9.110502 CCCTAAAACACAAGAGGATTATTAGTC 57.889 37.037 0.00 0.00 0.00 2.59
831 908 9.110502 CCTAAAACACAAGAGGATTATTAGTCC 57.889 37.037 0.00 0.00 35.94 3.85
834 911 5.675538 ACACAAGAGGATTATTAGTCCAGC 58.324 41.667 7.85 0.23 38.25 4.85
835 912 5.189736 ACACAAGAGGATTATTAGTCCAGCA 59.810 40.000 7.85 0.00 38.25 4.41
836 913 6.115446 CACAAGAGGATTATTAGTCCAGCAA 58.885 40.000 7.85 0.00 38.25 3.91
864 1065 8.422577 AAAGATACTTGCCTCCTATTTTGTTT 57.577 30.769 0.00 0.00 0.00 2.83
865 1066 7.396540 AGATACTTGCCTCCTATTTTGTTTG 57.603 36.000 0.00 0.00 0.00 2.93
866 1067 7.175104 AGATACTTGCCTCCTATTTTGTTTGA 58.825 34.615 0.00 0.00 0.00 2.69
868 1069 6.029346 ACTTGCCTCCTATTTTGTTTGATG 57.971 37.500 0.00 0.00 0.00 3.07
876 1323 9.362539 CCTCCTATTTTGTTTGATGAAAATGAG 57.637 33.333 0.00 0.00 34.42 2.90
887 1334 6.012658 TGATGAAAATGAGAGGAAAAACGG 57.987 37.500 0.00 0.00 0.00 4.44
888 1335 5.767665 TGATGAAAATGAGAGGAAAAACGGA 59.232 36.000 0.00 0.00 0.00 4.69
910 1357 2.618709 CCAAAATATCGAAGAGGCCACC 59.381 50.000 5.01 0.00 43.63 4.61
913 1360 0.759346 ATATCGAAGAGGCCACCCAC 59.241 55.000 5.01 0.00 43.63 4.61
915 1362 2.185310 ATCGAAGAGGCCACCCACAC 62.185 60.000 5.01 0.00 43.63 3.82
916 1363 2.836154 GAAGAGGCCACCCACACA 59.164 61.111 5.01 0.00 0.00 3.72
917 1364 1.600916 GAAGAGGCCACCCACACAC 60.601 63.158 5.01 0.00 0.00 3.82
919 1366 2.594592 GAGGCCACCCACACACAC 60.595 66.667 5.01 0.00 0.00 3.82
1084 1531 1.645034 CTCATGGAAGCACAGTACCG 58.355 55.000 0.00 0.00 0.00 4.02
1114 1561 0.039617 CAGCTCCTCGAGGCTAATCG 60.040 60.000 27.39 8.68 44.07 3.34
1458 1905 3.706373 ATGGACTTCCGGTGCGCT 61.706 61.111 9.73 0.00 39.22 5.92
2022 2469 4.329545 GCGCCCAGGGAGTTCACA 62.330 66.667 10.89 0.00 0.00 3.58
2072 2530 6.218746 GCAAAACTGAAGAAGGATCACAAAT 58.781 36.000 0.00 0.00 0.00 2.32
2073 2531 6.703165 GCAAAACTGAAGAAGGATCACAAATT 59.297 34.615 0.00 0.00 0.00 1.82
2074 2532 7.095899 GCAAAACTGAAGAAGGATCACAAATTC 60.096 37.037 0.00 0.00 0.00 2.17
2075 2533 7.587037 AAACTGAAGAAGGATCACAAATTCA 57.413 32.000 0.00 0.00 0.00 2.57
2076 2534 6.566197 ACTGAAGAAGGATCACAAATTCAC 57.434 37.500 0.00 0.00 0.00 3.18
2077 2535 6.064060 ACTGAAGAAGGATCACAAATTCACA 58.936 36.000 0.00 0.00 0.00 3.58
2078 2536 6.206243 ACTGAAGAAGGATCACAAATTCACAG 59.794 38.462 0.00 0.00 35.97 3.66
2079 2537 5.048504 TGAAGAAGGATCACAAATTCACAGC 60.049 40.000 0.00 0.00 0.00 4.40
2080 2538 4.660168 AGAAGGATCACAAATTCACAGCT 58.340 39.130 0.00 0.00 0.00 4.24
2081 2539 4.458295 AGAAGGATCACAAATTCACAGCTG 59.542 41.667 13.48 13.48 0.00 4.24
2082 2540 4.025040 AGGATCACAAATTCACAGCTGA 57.975 40.909 23.35 0.00 0.00 4.26
2098 2556 2.297315 AGCTGAACTGACGAACTGATGA 59.703 45.455 0.00 0.00 0.00 2.92
2186 2644 0.798771 GCTTCGAGGAGCTGTACGTG 60.799 60.000 0.00 0.00 39.57 4.49
2195 2653 4.278956 CTGTACGTGTTCAGCCCC 57.721 61.111 0.00 0.00 0.00 5.80
2332 2790 1.064758 CCCAAACCTGTAGGCATAGCA 60.065 52.381 0.00 0.00 39.32 3.49
2346 2804 3.244353 GGCATAGCATGTCTGGATGTACT 60.244 47.826 0.00 0.00 30.66 2.73
2347 2805 4.021104 GGCATAGCATGTCTGGATGTACTA 60.021 45.833 0.00 0.00 30.66 1.82
2348 2806 5.337894 GGCATAGCATGTCTGGATGTACTAT 60.338 44.000 0.00 0.00 30.66 2.12
2351 2809 5.876651 AGCATGTCTGGATGTACTATCAA 57.123 39.130 0.00 0.00 0.00 2.57
2380 2839 7.864108 TTTGTAGATATACAGCAGCAACAAT 57.136 32.000 0.00 0.00 0.00 2.71
2381 2840 8.956533 TTTGTAGATATACAGCAGCAACAATA 57.043 30.769 0.00 0.00 0.00 1.90
2508 2976 1.673665 CTGCACCTCCAGCTCAACC 60.674 63.158 0.00 0.00 0.00 3.77
2509 2980 2.401699 CTGCACCTCCAGCTCAACCA 62.402 60.000 0.00 0.00 0.00 3.67
2517 2988 0.524862 CCAGCTCAACCAAGATGCAC 59.475 55.000 0.00 0.00 31.30 4.57
2522 2993 2.719739 CTCAACCAAGATGCACCAGAT 58.280 47.619 0.00 0.00 0.00 2.90
2536 3007 2.267174 CCAGATAATGGTGCTCAGGG 57.733 55.000 0.00 0.00 44.91 4.45
2586 3057 4.348656 TGACGCTTAATAGACATCACGAC 58.651 43.478 0.00 0.00 0.00 4.34
2598 3069 9.661563 AATAGACATCACGACCAAAGTAAAATA 57.338 29.630 0.00 0.00 0.00 1.40
2675 3146 0.748005 ACAACAGAACACGCCAAGCT 60.748 50.000 0.00 0.00 0.00 3.74
2750 3221 5.240844 ACCAAAATAAGACCACACTGTAAGC 59.759 40.000 0.00 0.00 37.60 3.09
2864 3335 2.046217 GGAAAGTCTGGGCCGACC 60.046 66.667 19.96 8.91 40.81 4.79
2959 3430 2.502538 ACGACCCAAGAATTATCCCGAA 59.497 45.455 0.00 0.00 0.00 4.30
2960 3431 3.054948 ACGACCCAAGAATTATCCCGAAA 60.055 43.478 0.00 0.00 0.00 3.46
2966 3437 5.394115 CCCAAGAATTATCCCGAAAACAAGG 60.394 44.000 0.00 0.00 0.00 3.61
3053 3524 1.674817 CGGCGATTGACTACCAAGGTT 60.675 52.381 0.00 0.00 38.31 3.50
3076 3547 9.847224 GGTTCTCCCTCTGTATCAAAATATAAA 57.153 33.333 0.00 0.00 0.00 1.40
3149 3622 3.775316 AGGGAGTATTGAATTCCAGTCGT 59.225 43.478 2.27 0.00 32.50 4.34
3173 3646 7.275920 GTGGGCTATTAGATTTTGAAGAGAGA 58.724 38.462 0.00 0.00 0.00 3.10
3210 3683 4.984161 GTCATGTGGGTGTTTTTCTCAATG 59.016 41.667 0.00 0.00 0.00 2.82
3215 3688 3.181467 TGGGTGTTTTTCTCAATGGCTTG 60.181 43.478 0.00 0.00 0.00 4.01
3220 3693 4.869297 TGTTTTTCTCAATGGCTTGTGTTG 59.131 37.500 0.00 0.00 33.87 3.33
3262 3735 3.591196 TTATGTGAAATTGCAGTGGGC 57.409 42.857 0.00 0.00 45.13 5.36
3287 3775 8.062448 GCGTTACTAGTTAACAATCATGATTCC 58.938 37.037 18.16 4.56 40.30 3.01
3298 3786 7.756395 ACAATCATGATTCCTTCATATGTCC 57.244 36.000 18.16 0.00 43.40 4.02
3316 3804 5.048846 TGTCCCTGGATAAGCTTAATTCC 57.951 43.478 16.27 16.27 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
339 340 1.813178 CTCGCCTTTTCTTTCCCTTCC 59.187 52.381 0.00 0.00 0.00 3.46
378 379 3.506067 GGTTCCACTGAATACACCAAAGG 59.494 47.826 0.00 0.00 31.98 3.11
498 499 0.469494 TGTCTATGGCATGCGGTGAT 59.531 50.000 12.44 3.59 0.00 3.06
563 568 9.710900 GATACACACATGAATCAACTATATCCA 57.289 33.333 0.00 0.00 0.00 3.41
602 607 1.062525 CATTGCTAGAAACCGCGCC 59.937 57.895 0.00 0.00 0.00 6.53
605 610 7.224167 ACTTTATACTACATTGCTAGAAACCGC 59.776 37.037 0.00 0.00 0.00 5.68
619 624 9.953565 ACTTGGCAATAGAAACTTTATACTACA 57.046 29.630 0.00 0.00 0.00 2.74
622 627 9.515226 TTGACTTGGCAATAGAAACTTTATACT 57.485 29.630 0.00 0.00 0.00 2.12
630 635 6.215845 ACACAATTGACTTGGCAATAGAAAC 58.784 36.000 13.59 0.00 37.50 2.78
631 636 6.403866 ACACAATTGACTTGGCAATAGAAA 57.596 33.333 13.59 0.00 37.50 2.52
632 637 6.403866 AACACAATTGACTTGGCAATAGAA 57.596 33.333 13.59 0.00 37.50 2.10
633 638 6.714810 ACTAACACAATTGACTTGGCAATAGA 59.285 34.615 13.59 0.00 37.50 1.98
634 639 6.913170 ACTAACACAATTGACTTGGCAATAG 58.087 36.000 13.59 0.00 37.50 1.73
649 654 4.917385 AGGCATGATGGTAACTAACACAA 58.083 39.130 0.00 0.00 37.61 3.33
655 670 3.653164 TCAGGAGGCATGATGGTAACTA 58.347 45.455 0.00 0.00 37.61 2.24
656 671 2.481441 TCAGGAGGCATGATGGTAACT 58.519 47.619 0.00 0.00 37.61 2.24
659 674 4.660303 ACTAAATCAGGAGGCATGATGGTA 59.340 41.667 0.00 0.00 37.46 3.25
660 675 3.461085 ACTAAATCAGGAGGCATGATGGT 59.539 43.478 0.00 0.00 37.46 3.55
661 676 4.070716 GACTAAATCAGGAGGCATGATGG 58.929 47.826 0.00 0.00 37.46 3.51
662 677 4.070716 GGACTAAATCAGGAGGCATGATG 58.929 47.826 0.00 0.00 37.46 3.07
663 678 3.718434 TGGACTAAATCAGGAGGCATGAT 59.282 43.478 0.00 0.00 39.06 2.45
664 679 3.114606 TGGACTAAATCAGGAGGCATGA 58.885 45.455 0.00 0.00 0.00 3.07
665 680 3.565764 TGGACTAAATCAGGAGGCATG 57.434 47.619 0.00 0.00 0.00 4.06
667 682 3.114606 TCATGGACTAAATCAGGAGGCA 58.885 45.455 0.00 0.00 0.00 4.75
668 683 3.737850 CTCATGGACTAAATCAGGAGGC 58.262 50.000 0.00 0.00 37.92 4.70
669 684 3.495806 GGCTCATGGACTAAATCAGGAGG 60.496 52.174 7.03 0.00 40.73 4.30
670 685 3.135348 TGGCTCATGGACTAAATCAGGAG 59.865 47.826 0.00 0.00 42.53 3.69
683 706 8.896744 CCAGTATTACAATATAATGGCTCATGG 58.103 37.037 0.00 0.00 38.81 3.66
722 747 6.316890 GGCAATGGCATTTTCAACTATTTCAT 59.683 34.615 10.65 0.00 43.71 2.57
727 752 3.195396 ACGGCAATGGCATTTTCAACTAT 59.805 39.130 10.65 0.00 43.71 2.12
756 781 9.462174 CTGAAATTAATAACTGCACAAGTCAAA 57.538 29.630 0.00 0.00 38.56 2.69
757 782 8.629158 ACTGAAATTAATAACTGCACAAGTCAA 58.371 29.630 0.00 0.00 38.56 3.18
761 786 8.693504 CACAACTGAAATTAATAACTGCACAAG 58.306 33.333 0.00 0.00 0.00 3.16
762 787 8.194104 ACACAACTGAAATTAATAACTGCACAA 58.806 29.630 0.00 0.00 0.00 3.33
764 789 9.329913 CTACACAACTGAAATTAATAACTGCAC 57.670 33.333 0.00 0.00 0.00 4.57
772 797 9.959721 AGTGGATACTACACAACTGAAATTAAT 57.040 29.630 0.00 0.00 41.21 1.40
773 798 9.214957 CAGTGGATACTACACAACTGAAATTAA 57.785 33.333 0.00 0.00 41.21 1.40
774 799 7.822334 CCAGTGGATACTACACAACTGAAATTA 59.178 37.037 1.68 0.00 41.21 1.40
775 800 6.655003 CCAGTGGATACTACACAACTGAAATT 59.345 38.462 1.68 0.00 41.21 1.82
776 801 6.173339 CCAGTGGATACTACACAACTGAAAT 58.827 40.000 1.68 0.00 41.21 2.17
801 826 5.333566 AATCCTCTTGTGTTTTAGGGGAA 57.666 39.130 0.00 0.00 44.01 3.97
802 827 6.652205 ATAATCCTCTTGTGTTTTAGGGGA 57.348 37.500 0.00 0.00 44.87 4.81
803 828 8.053355 ACTAATAATCCTCTTGTGTTTTAGGGG 58.947 37.037 0.00 0.00 33.01 4.79
807 884 9.667107 CTGGACTAATAATCCTCTTGTGTTTTA 57.333 33.333 0.00 0.00 37.13 1.52
808 885 7.121315 GCTGGACTAATAATCCTCTTGTGTTTT 59.879 37.037 0.00 0.00 37.13 2.43
811 888 5.189736 TGCTGGACTAATAATCCTCTTGTGT 59.810 40.000 0.00 0.00 37.13 3.72
856 1057 9.835389 TTTCCTCTCATTTTCATCAAACAAAAT 57.165 25.926 0.00 0.00 33.37 1.82
857 1058 9.664332 TTTTCCTCTCATTTTCATCAAACAAAA 57.336 25.926 0.00 0.00 0.00 2.44
859 1060 9.097257 GTTTTTCCTCTCATTTTCATCAAACAA 57.903 29.630 0.00 0.00 0.00 2.83
861 1062 7.096065 CCGTTTTTCCTCTCATTTTCATCAAAC 60.096 37.037 0.00 0.00 0.00 2.93
864 1065 5.767665 TCCGTTTTTCCTCTCATTTTCATCA 59.232 36.000 0.00 0.00 0.00 3.07
865 1066 6.086871 GTCCGTTTTTCCTCTCATTTTCATC 58.913 40.000 0.00 0.00 0.00 2.92
866 1067 5.048013 GGTCCGTTTTTCCTCTCATTTTCAT 60.048 40.000 0.00 0.00 0.00 2.57
868 1069 4.277423 TGGTCCGTTTTTCCTCTCATTTTC 59.723 41.667 0.00 0.00 0.00 2.29
876 1323 5.122711 TCGATATTTTGGTCCGTTTTTCCTC 59.877 40.000 0.00 0.00 0.00 3.71
887 1334 3.312697 GTGGCCTCTTCGATATTTTGGTC 59.687 47.826 3.32 0.00 0.00 4.02
888 1335 3.279434 GTGGCCTCTTCGATATTTTGGT 58.721 45.455 3.32 0.00 0.00 3.67
950 1397 2.237143 AGCCTTATCTGCACTGCAACTA 59.763 45.455 4.99 0.00 38.41 2.24
1059 1506 2.124983 TGCTTCCATGAGCTCGGC 60.125 61.111 9.64 6.91 43.11 5.54
1084 1531 0.534873 GAGGAGCTGAGGAAGGTGAC 59.465 60.000 0.00 0.00 36.52 3.67
1242 1689 2.915659 ACGGCCTCGAAGGTGACA 60.916 61.111 0.00 0.00 37.80 3.58
2022 2469 0.809385 CACGTACCCTGTCGATGACT 59.191 55.000 0.00 0.00 33.15 3.41
2047 2494 3.250762 TGTGATCCTTCTTCAGTTTTGCG 59.749 43.478 0.00 0.00 0.00 4.85
2072 2530 2.159099 AGTTCGTCAGTTCAGCTGTGAA 60.159 45.455 14.67 0.00 45.23 3.18
2073 2531 1.409064 AGTTCGTCAGTTCAGCTGTGA 59.591 47.619 14.67 7.56 45.23 3.58
2074 2532 1.524355 CAGTTCGTCAGTTCAGCTGTG 59.476 52.381 14.67 4.92 45.23 3.66
2075 2533 1.409064 TCAGTTCGTCAGTTCAGCTGT 59.591 47.619 14.67 0.00 45.23 4.40
2076 2534 2.140065 TCAGTTCGTCAGTTCAGCTG 57.860 50.000 7.63 7.63 46.34 4.24
2077 2535 2.297315 TCATCAGTTCGTCAGTTCAGCT 59.703 45.455 0.00 0.00 0.00 4.24
2078 2536 2.677199 TCATCAGTTCGTCAGTTCAGC 58.323 47.619 0.00 0.00 0.00 4.26
2079 2537 5.852738 ATTTCATCAGTTCGTCAGTTCAG 57.147 39.130 0.00 0.00 0.00 3.02
2080 2538 5.991606 AGAATTTCATCAGTTCGTCAGTTCA 59.008 36.000 0.00 0.00 0.00 3.18
2081 2539 6.473397 AGAATTTCATCAGTTCGTCAGTTC 57.527 37.500 0.00 0.00 0.00 3.01
2082 2540 6.260936 ACAAGAATTTCATCAGTTCGTCAGTT 59.739 34.615 0.00 0.00 0.00 3.16
2088 2546 5.611796 TCCACAAGAATTTCATCAGTTCG 57.388 39.130 0.00 0.00 0.00 3.95
2168 2626 0.522180 ACACGTACAGCTCCTCGAAG 59.478 55.000 7.73 0.00 0.00 3.79
2186 2644 1.452108 CTTGGATCCGGGGCTGAAC 60.452 63.158 7.39 0.00 0.00 3.18
2195 2653 0.815734 ACCACTCGTACTTGGATCCG 59.184 55.000 7.39 0.00 36.28 4.18
2332 2790 9.857656 AAATGATTTGATAGTACATCCAGACAT 57.142 29.630 0.00 0.00 0.00 3.06
2348 2806 8.777413 GCTGCTGTATATCTACAAATGATTTGA 58.223 33.333 23.37 7.27 43.26 2.69
2351 2809 8.562892 GTTGCTGCTGTATATCTACAAATGATT 58.437 33.333 0.00 0.00 37.41 2.57
2402 2867 4.271696 TCTCCCTGTTTCACATGTGTAG 57.728 45.455 24.63 17.19 0.00 2.74
2498 2966 0.524862 GTGCATCTTGGTTGAGCTGG 59.475 55.000 0.00 0.00 0.00 4.85
2522 2993 0.913934 TCTGCCCCTGAGCACCATTA 60.914 55.000 0.00 0.00 38.00 1.90
2536 3007 0.452987 TTTGCTCGCATGATTCTGCC 59.547 50.000 0.00 0.00 39.00 4.85
2586 3057 8.733458 GGTAACCTGGTAACTATTTTACTTTGG 58.267 37.037 0.00 0.00 37.61 3.28
2598 3069 3.050835 AGGTGTTGGTAACCTGGTAACT 58.949 45.455 0.00 0.00 46.51 2.24
2621 3092 5.504010 CGCCGCAAACAATCTATCATAGTTT 60.504 40.000 0.00 0.00 33.09 2.66
2699 3170 0.881796 TATATGCTGGAGAGGACGCG 59.118 55.000 3.53 3.53 0.00 6.01
2750 3221 4.497473 TCAATTTGTAAGGAGGCGTTTG 57.503 40.909 0.00 0.00 0.00 2.93
2880 3351 0.317020 GTTTGCTCGCCAGTGTTGAC 60.317 55.000 0.00 0.00 0.00 3.18
2959 3430 2.310538 CTTGAAGTCAGCCCCTTGTTT 58.689 47.619 0.00 0.00 0.00 2.83
2960 3431 1.479389 CCTTGAAGTCAGCCCCTTGTT 60.479 52.381 0.00 0.00 0.00 2.83
2966 3437 1.376037 CGTCCCTTGAAGTCAGCCC 60.376 63.158 0.00 0.00 0.00 5.19
2996 3467 2.571202 TCCTCACATGTACCTGCAATCA 59.429 45.455 0.00 0.00 0.00 2.57
2999 3470 3.500448 TTTCCTCACATGTACCTGCAA 57.500 42.857 0.00 0.00 0.00 4.08
3053 3524 9.542462 CGTTTTATATTTTGATACAGAGGGAGA 57.458 33.333 0.00 0.00 0.00 3.71
3149 3622 7.419518 CCTCTCTCTTCAAAATCTAATAGCCCA 60.420 40.741 0.00 0.00 0.00 5.36
3173 3646 4.324563 CCCACATGACATCCTTCTTTACCT 60.325 45.833 0.00 0.00 0.00 3.08
3210 3683 8.357402 CCTATAATTAATTACCCAACACAAGCC 58.643 37.037 10.07 0.00 0.00 4.35
3215 3688 7.008332 AGGCCCTATAATTAATTACCCAACAC 58.992 38.462 10.07 0.03 0.00 3.32
3262 3735 9.314321 AGGAATCATGATTGTTAACTAGTAACG 57.686 33.333 25.37 0.00 44.46 3.18
3287 3775 5.495926 AGCTTATCCAGGGACATATGAAG 57.504 43.478 10.38 0.26 0.00 3.02
3290 3778 7.337942 GGAATTAAGCTTATCCAGGGACATATG 59.662 40.741 17.67 0.00 32.08 1.78


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

AutoCloner maintained by Alex Coulton.