Multiple sequence alignment - TraesCS4D01G074900

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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 TraesCS4D01G074900 chr4D 100.000 3611 0 0 1 3611 49501851 49498241 0.000000e+00 6669
1 TraesCS4D01G074900 chr4A 90.594 3062 150 59 653 3611 547928329 547931355 0.000000e+00 3932
2 TraesCS4D01G074900 chr4A 88.551 428 26 11 1 416 547927804 547928220 6.960000e-137 497
3 TraesCS4D01G074900 chr4B 94.787 1995 70 12 657 2623 73101605 73103593 0.000000e+00 3077
4 TraesCS4D01G074900 chr4B 84.511 1033 78 28 2649 3611 73103645 73104665 0.000000e+00 946
5 TraesCS4D01G074900 chr4B 85.891 567 43 18 1 554 73100906 73101448 1.450000e-158 569


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 TraesCS4D01G074900 chr4D 49498241 49501851 3610 True 6669.000000 6669 100.000000 1 3611 1 chr4D.!!$R1 3610
1 TraesCS4D01G074900 chr4A 547927804 547931355 3551 False 2214.500000 3932 89.572500 1 3611 2 chr4A.!!$F1 3610
2 TraesCS4D01G074900 chr4B 73100906 73104665 3759 False 1530.666667 3077 88.396333 1 3611 3 chr4B.!!$F1 3610

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
572 591 0.179097 GTTGTCATCGGCTCTCCCTC 60.179 60.0 0.00 0.0 0.00 4.30 F
581 600 0.609406 GGCTCTCCCTCACCAAAACC 60.609 60.0 0.00 0.0 0.00 3.27 F
746 869 0.742635 TGAAAGTGTGCAGCGTCACA 60.743 50.0 18.51 9.5 43.93 3.58 F
1928 2069 0.179097 GCCGGCTTCTCCTACTTCAG 60.179 60.0 22.15 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1516 1657 0.108567 GCCGACAGGAGGAAGAAGAC 60.109 60.000 0.00 0.0 41.02 3.01 R
1857 1998 0.742281 CGGTTGTGCCTCTGATCCAG 60.742 60.000 0.00 0.0 34.25 3.86 R
2245 2386 1.205893 GAAGAAGGCAGAGACGGTGAT 59.794 52.381 0.00 0.0 0.00 3.06 R
3517 3824 0.387622 CCAGGCGCATGAACAGTTTG 60.388 55.000 25.72 0.0 0.00 2.93 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
55 61 4.771590 TCATTCAAACAGATTGCTGGAC 57.228 40.909 0.00 0.00 46.60 4.02
76 83 6.040955 TGGACTGCTTCACCTACTCTATAATG 59.959 42.308 0.00 0.00 0.00 1.90
79 86 5.601662 TGCTTCACCTACTCTATAATGTGC 58.398 41.667 0.00 0.00 0.00 4.57
81 88 5.736492 GCTTCACCTACTCTATAATGTGCGT 60.736 44.000 0.00 0.00 0.00 5.24
83 90 6.947644 TCACCTACTCTATAATGTGCGTTA 57.052 37.500 0.00 0.00 0.00 3.18
84 91 7.337480 TCACCTACTCTATAATGTGCGTTAA 57.663 36.000 0.00 0.00 0.00 2.01
85 92 7.198390 TCACCTACTCTATAATGTGCGTTAAC 58.802 38.462 0.00 0.00 0.00 2.01
86 93 6.976349 CACCTACTCTATAATGTGCGTTAACA 59.024 38.462 6.39 0.00 0.00 2.41
87 94 7.490079 CACCTACTCTATAATGTGCGTTAACAA 59.510 37.037 6.39 0.00 32.81 2.83
88 95 8.036575 ACCTACTCTATAATGTGCGTTAACAAA 58.963 33.333 6.39 0.00 32.81 2.83
89 96 8.325997 CCTACTCTATAATGTGCGTTAACAAAC 58.674 37.037 6.39 3.67 32.81 2.93
91 98 7.515643 ACTCTATAATGTGCGTTAACAAACAC 58.484 34.615 11.40 12.59 32.81 3.32
96 103 3.439293 TGTGCGTTAACAAACACATTGG 58.561 40.909 17.43 0.00 43.66 3.16
97 104 3.128764 TGTGCGTTAACAAACACATTGGA 59.871 39.130 17.43 1.05 43.66 3.53
98 105 4.106197 GTGCGTTAACAAACACATTGGAA 58.894 39.130 14.99 0.00 43.66 3.53
99 106 4.742659 GTGCGTTAACAAACACATTGGAAT 59.257 37.500 14.99 0.00 43.66 3.01
100 107 5.915758 GTGCGTTAACAAACACATTGGAATA 59.084 36.000 14.99 0.00 43.66 1.75
101 108 6.584563 GTGCGTTAACAAACACATTGGAATAT 59.415 34.615 14.99 0.00 43.66 1.28
102 109 7.751348 GTGCGTTAACAAACACATTGGAATATA 59.249 33.333 14.99 0.00 43.66 0.86
103 110 7.751348 TGCGTTAACAAACACATTGGAATATAC 59.249 33.333 6.39 0.00 43.66 1.47
146 158 1.043022 CCTGCTTGGCCAAACTTCTT 58.957 50.000 20.91 0.00 0.00 2.52
317 333 2.738314 GGAAATGCACCAAAACTGATGC 59.262 45.455 0.00 0.00 38.59 3.91
326 342 4.860352 CACCAAAACTGATGCATACATGTG 59.140 41.667 9.11 0.00 36.35 3.21
356 372 4.890088 TGCTATCTACCACAACGAACTTT 58.110 39.130 0.00 0.00 0.00 2.66
435 451 4.727235 AAGAAGGTAGTTTTCTTTCGCG 57.273 40.909 0.00 0.00 40.92 5.87
438 454 0.800631 GGTAGTTTTCTTTCGCGGGG 59.199 55.000 6.13 0.00 0.00 5.73
450 466 1.611519 TCGCGGGGAAAACTTTTGAT 58.388 45.000 6.13 0.00 0.00 2.57
457 473 5.061684 GCGGGGAAAACTTTTGATTTATTCG 59.938 40.000 0.00 0.00 0.00 3.34
460 476 7.971722 CGGGGAAAACTTTTGATTTATTCGTAT 59.028 33.333 0.00 0.00 0.00 3.06
472 489 8.614469 TGATTTATTCGTATAACATCATGCCA 57.386 30.769 11.70 0.00 29.22 4.92
487 505 5.733226 TCATGCCAGTACAAATAACATCG 57.267 39.130 0.00 0.00 0.00 3.84
508 526 7.822334 ACATCGAAGTAACAGAAATTACATCCA 59.178 33.333 0.00 0.00 37.49 3.41
512 530 9.093970 CGAAGTAACAGAAATTACATCCATGTA 57.906 33.333 0.00 0.00 41.97 2.29
515 533 9.601217 AGTAACAGAAATTACATCCATGTAGAC 57.399 33.333 0.00 0.00 43.44 2.59
516 534 9.601217 GTAACAGAAATTACATCCATGTAGACT 57.399 33.333 0.00 0.00 43.44 3.24
518 536 9.823647 AACAGAAATTACATCCATGTAGACTAG 57.176 33.333 0.00 0.00 43.44 2.57
526 545 7.455641 ACATCCATGTAGACTAGTACATAGC 57.544 40.000 10.29 0.00 40.90 2.97
550 569 1.914634 ATTACAAGCACTCGAGCGAG 58.085 50.000 13.61 17.46 46.91 5.03
556 575 3.175240 CACTCGAGCGAGCCGTTG 61.175 66.667 18.80 6.80 45.54 4.10
557 576 3.671411 ACTCGAGCGAGCCGTTGT 61.671 61.111 18.80 0.00 45.54 3.32
559 578 3.610791 CTCGAGCGAGCCGTTGTCA 62.611 63.158 6.99 0.00 35.31 3.58
561 580 2.508891 CGAGCGAGCCGTTGTCATC 61.509 63.158 0.00 0.00 0.00 2.92
562 581 2.507102 AGCGAGCCGTTGTCATCG 60.507 61.111 0.00 0.00 38.19 3.84
568 587 4.094684 CCGTTGTCATCGGCTCTC 57.905 61.111 9.33 0.00 41.48 3.20
569 588 1.519455 CCGTTGTCATCGGCTCTCC 60.519 63.158 9.33 0.00 41.48 3.71
570 589 1.519455 CGTTGTCATCGGCTCTCCC 60.519 63.158 0.00 0.00 0.00 4.30
571 590 1.901085 GTTGTCATCGGCTCTCCCT 59.099 57.895 0.00 0.00 0.00 4.20
572 591 0.179097 GTTGTCATCGGCTCTCCCTC 60.179 60.000 0.00 0.00 0.00 4.30
573 592 0.614697 TTGTCATCGGCTCTCCCTCA 60.615 55.000 0.00 0.00 0.00 3.86
574 593 1.323271 TGTCATCGGCTCTCCCTCAC 61.323 60.000 0.00 0.00 0.00 3.51
575 594 1.758514 TCATCGGCTCTCCCTCACC 60.759 63.158 0.00 0.00 0.00 4.02
576 595 2.060383 CATCGGCTCTCCCTCACCA 61.060 63.158 0.00 0.00 0.00 4.17
579 598 1.125093 TCGGCTCTCCCTCACCAAAA 61.125 55.000 0.00 0.00 0.00 2.44
581 600 0.609406 GGCTCTCCCTCACCAAAACC 60.609 60.000 0.00 0.00 0.00 3.27
584 603 1.303317 CTCCCTCACCAAAACCGGG 60.303 63.158 6.32 0.00 36.21 5.73
585 604 2.064242 CTCCCTCACCAAAACCGGGT 62.064 60.000 6.32 0.00 39.88 5.28
609 628 7.066284 GGTAACCTTATTGTAGTAGACAGTCGA 59.934 40.741 0.00 0.00 39.88 4.20
610 629 7.458409 AACCTTATTGTAGTAGACAGTCGAA 57.542 36.000 0.00 0.00 39.88 3.71
619 638 9.917129 TTGTAGTAGACAGTCGAAATGATAAAA 57.083 29.630 5.93 0.00 39.88 1.52
620 639 9.569167 TGTAGTAGACAGTCGAAATGATAAAAG 57.431 33.333 5.93 0.00 32.86 2.27
621 640 9.784680 GTAGTAGACAGTCGAAATGATAAAAGA 57.215 33.333 5.93 0.00 0.00 2.52
623 642 9.706691 AGTAGACAGTCGAAATGATAAAAGAAA 57.293 29.630 5.93 0.00 0.00 2.52
638 657 9.705290 TGATAAAAGAAAAATTAAGCCCAACTC 57.295 29.630 0.00 0.00 0.00 3.01
639 658 8.757164 ATAAAAGAAAAATTAAGCCCAACTCG 57.243 30.769 0.00 0.00 0.00 4.18
651 670 4.636249 AGCCCAACTCGAGATGATATTTC 58.364 43.478 22.88 6.11 0.00 2.17
746 869 0.742635 TGAAAGTGTGCAGCGTCACA 60.743 50.000 18.51 9.50 43.93 3.58
778 903 4.202326 ACCAGTACGATGAGTTTCCTTTGT 60.202 41.667 0.00 0.00 0.00 2.83
779 904 4.152402 CCAGTACGATGAGTTTCCTTTGTG 59.848 45.833 0.00 0.00 0.00 3.33
780 905 4.750098 CAGTACGATGAGTTTCCTTTGTGT 59.250 41.667 0.00 0.00 0.00 3.72
781 906 5.924254 CAGTACGATGAGTTTCCTTTGTGTA 59.076 40.000 0.00 0.00 0.00 2.90
782 907 5.924825 AGTACGATGAGTTTCCTTTGTGTAC 59.075 40.000 0.00 0.00 0.00 2.90
787 912 6.970043 CGATGAGTTTCCTTTGTGTACAAAAA 59.030 34.615 10.76 10.76 44.24 1.94
788 913 7.044314 CGATGAGTTTCCTTTGTGTACAAAAAC 60.044 37.037 7.14 11.72 44.24 2.43
789 914 6.982852 TGAGTTTCCTTTGTGTACAAAAACA 58.017 32.000 18.29 0.00 44.24 2.83
790 915 7.434492 TGAGTTTCCTTTGTGTACAAAAACAA 58.566 30.769 18.29 0.00 44.24 2.83
791 916 7.926555 TGAGTTTCCTTTGTGTACAAAAACAAA 59.073 29.630 18.29 7.96 44.24 2.83
792 917 8.840833 AGTTTCCTTTGTGTACAAAAACAAAT 57.159 26.923 18.29 0.00 44.24 2.32
793 918 9.930693 AGTTTCCTTTGTGTACAAAAACAAATA 57.069 25.926 18.29 0.00 44.24 1.40
1030 1171 2.360350 CACCATGGCGCAGGTTCT 60.360 61.111 13.04 0.00 35.52 3.01
1098 1239 2.548057 CGGCAAGTACTTCAAGCTTGAA 59.452 45.455 33.65 33.65 44.31 2.69
1281 1422 2.673523 GAGTGCATGCTGGGGACT 59.326 61.111 20.33 13.39 39.80 3.85
1293 1434 4.043100 GGGACTTCCAACCCGGGG 62.043 72.222 27.92 12.73 36.56 5.73
1369 1510 3.313874 CCATGGTCGGCTCCTTCT 58.686 61.111 2.57 0.00 0.00 2.85
1370 1511 1.604378 CCATGGTCGGCTCCTTCTT 59.396 57.895 2.57 0.00 0.00 2.52
1569 1710 3.295273 AGGCTCGCGCGGATGATA 61.295 61.111 31.69 8.41 36.88 2.15
1770 1911 4.681978 ACGTTCTGGCTGGGCGTC 62.682 66.667 7.89 0.00 0.00 5.19
1857 1998 4.651008 TTCGTCACGGCCGTGTCC 62.651 66.667 46.56 36.90 45.55 4.02
1872 2013 0.545071 TGTCCTGGATCAGAGGCACA 60.545 55.000 0.00 7.73 32.44 4.57
1874 2015 0.615331 TCCTGGATCAGAGGCACAAC 59.385 55.000 5.32 0.00 32.44 3.32
1928 2069 0.179097 GCCGGCTTCTCCTACTTCAG 60.179 60.000 22.15 0.00 0.00 3.02
1958 2099 2.029020 TGGACTTCCACACGATCAAGAG 60.029 50.000 0.00 0.00 42.01 2.85
2081 2222 1.731433 TACTCCATGGCCGAGTACGC 61.731 60.000 6.96 0.00 40.93 4.42
2202 2343 1.134560 GTGACCACCTACATCGAGTCC 59.865 57.143 0.00 0.00 0.00 3.85
2256 2397 2.750637 ACCGCGATCACCGTCTCT 60.751 61.111 8.23 0.00 41.15 3.10
2361 2502 2.250485 GCCATGATGATGCGCGTC 59.750 61.111 22.77 22.77 0.00 5.19
2506 2647 2.203728 ACTGGTACGACTGGGCCA 60.204 61.111 5.85 5.85 0.00 5.36
2623 2773 1.947642 GTGTGACCGTGTCCGTGTC 60.948 63.158 2.23 0.00 35.88 3.67
2624 2774 2.355481 GTGACCGTGTCCGTGTCC 60.355 66.667 2.23 0.00 35.04 4.02
2625 2775 3.608662 TGACCGTGTCCGTGTCCC 61.609 66.667 2.23 0.00 35.04 4.46
2626 2776 3.300765 GACCGTGTCCGTGTCCCT 61.301 66.667 0.00 0.00 31.94 4.20
2627 2777 3.569049 GACCGTGTCCGTGTCCCTG 62.569 68.421 0.00 0.00 31.94 4.45
2628 2778 3.612681 CCGTGTCCGTGTCCCTGT 61.613 66.667 0.00 0.00 0.00 4.00
2631 2781 1.006102 GTGTCCGTGTCCCTGTGAG 60.006 63.158 0.00 0.00 0.00 3.51
2632 2782 2.207229 TGTCCGTGTCCCTGTGAGG 61.207 63.158 0.00 0.00 34.30 3.86
2634 2784 1.078528 TCCGTGTCCCTGTGAGGAT 59.921 57.895 0.00 0.00 37.67 3.24
2635 2785 0.333652 TCCGTGTCCCTGTGAGGATA 59.666 55.000 0.00 0.00 37.67 2.59
2636 2786 0.747255 CCGTGTCCCTGTGAGGATAG 59.253 60.000 0.00 0.00 37.67 2.08
2638 2788 1.405821 CGTGTCCCTGTGAGGATAGAC 59.594 57.143 0.00 0.00 37.67 2.59
2639 2789 2.741145 GTGTCCCTGTGAGGATAGACT 58.259 52.381 0.00 0.00 37.67 3.24
2641 2791 3.131400 GTGTCCCTGTGAGGATAGACTTC 59.869 52.174 0.00 0.00 37.67 3.01
2642 2792 2.696187 GTCCCTGTGAGGATAGACTTCC 59.304 54.545 0.00 0.00 37.67 3.46
2662 2838 4.461198 TCCTCGTAGCTAGTTGATGATGA 58.539 43.478 0.00 0.00 0.00 2.92
2686 2862 3.079578 AGTTTGGACACAGAGCATCATG 58.920 45.455 0.00 0.00 37.82 3.07
2788 3008 2.363306 TTGATGTGCAAGGAGGTGTT 57.637 45.000 0.00 0.00 31.55 3.32
2865 3105 7.008628 CACGTTTATTTTCTCATGGATTTGAGC 59.991 37.037 0.00 0.00 42.37 4.26
2898 3155 3.565902 GGCAGGTCAAAGCTATCATTACC 59.434 47.826 0.00 0.00 0.00 2.85
2914 3171 3.728076 TTACCTGCAGGACGTATGATC 57.272 47.619 39.19 0.00 38.94 2.92
2990 3266 4.504461 CAGTAGTATCGGATGCAACTTGTC 59.496 45.833 8.78 0.00 0.00 3.18
3000 3276 1.369689 CAACTTGTCAGCAGCACGC 60.370 57.895 0.00 0.00 42.91 5.34
3005 3281 3.807538 GTCAGCAGCACGCCATGG 61.808 66.667 7.63 7.63 44.04 3.66
3029 3310 6.149640 GGTCTCTTGTGAGGTTATTTTCTTCC 59.850 42.308 0.00 0.00 40.58 3.46
3067 3361 8.134895 TGAAAGTATAAAAGGTTTTCAGTGCTG 58.865 33.333 0.00 0.00 34.04 4.41
3111 3405 1.823169 GCCGTGTACCCAACTCCTGA 61.823 60.000 0.00 0.00 0.00 3.86
3133 3427 2.433491 TGCGTCATGGGCACGTAC 60.433 61.111 8.07 0.00 39.54 3.67
3134 3428 3.550992 GCGTCATGGGCACGTACG 61.551 66.667 15.01 15.01 39.54 3.67
3135 3429 3.550992 CGTCATGGGCACGTACGC 61.551 66.667 16.72 0.00 32.41 4.42
3136 3430 2.125673 GTCATGGGCACGTACGCT 60.126 61.111 16.72 0.00 0.00 5.07
3137 3431 2.125713 TCATGGGCACGTACGCTG 60.126 61.111 16.72 13.72 0.00 5.18
3206 3500 2.979649 GGAGTGGGAACGGAGGAC 59.020 66.667 0.00 0.00 0.00 3.85
3291 3596 1.743772 CGTGTGGATTGGGGATGTCTC 60.744 57.143 0.00 0.00 0.00 3.36
3320 3625 0.673644 GACGGCTGCTGCTTTCCTTA 60.674 55.000 15.64 0.00 39.59 2.69
3440 3745 3.625897 TGGTCTGGTGTCCCGCAG 61.626 66.667 0.00 0.00 0.00 5.18
3468 3773 5.707242 TGATTCGGAGAATATAGCTTCGT 57.293 39.130 0.00 0.00 45.90 3.85
3497 3804 3.353557 TCTCGTATTATCGGATCCCCAG 58.646 50.000 6.06 0.00 0.00 4.45
3498 3805 2.427453 CTCGTATTATCGGATCCCCAGG 59.573 54.545 6.06 0.00 0.00 4.45
3499 3806 1.480954 CGTATTATCGGATCCCCAGGG 59.519 57.143 6.06 0.00 0.00 4.45
3500 3807 2.547990 GTATTATCGGATCCCCAGGGT 58.452 52.381 6.06 0.00 36.47 4.34
3501 3808 2.133858 ATTATCGGATCCCCAGGGTT 57.866 50.000 6.06 0.00 36.47 4.11
3543 3850 1.625417 TTCATGCGCCTGGATCCTCA 61.625 55.000 14.23 3.69 0.00 3.86
3544 3851 1.890979 CATGCGCCTGGATCCTCAC 60.891 63.158 14.23 0.68 0.00 3.51
3546 3853 2.037620 ATGCGCCTGGATCCTCACTC 62.038 60.000 14.23 0.21 0.00 3.51
3558 3865 4.938226 GGATCCTCACTCAAGTTAAGTTGG 59.062 45.833 20.32 14.10 0.00 3.77
3561 3868 4.407621 TCCTCACTCAAGTTAAGTTGGTCA 59.592 41.667 20.32 5.82 0.00 4.02
3573 3880 8.926715 AGTTAAGTTGGTCAAGAAATTTCAAC 57.073 30.769 19.99 13.90 35.93 3.18
3576 3886 5.339990 AGTTGGTCAAGAAATTTCAACGTG 58.660 37.500 19.99 11.69 39.30 4.49
3578 3888 4.667262 TGGTCAAGAAATTTCAACGTGTG 58.333 39.130 19.99 7.97 0.00 3.82
3583 3893 6.195798 GTCAAGAAATTTCAACGTGTGGTTAC 59.804 38.462 19.99 3.53 36.49 2.50
3592 3902 2.420628 CGTGTGGTTACGTGGAGTTA 57.579 50.000 0.00 0.00 39.13 2.24
3595 3905 3.555139 CGTGTGGTTACGTGGAGTTAAAA 59.445 43.478 0.00 0.00 39.13 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 61 5.694006 GCACATTATAGAGTAGGTGAAGCAG 59.306 44.000 0.00 0.00 0.00 4.24
84 91 9.609346 GGTAGTAGTATATTCCAATGTGTTTGT 57.391 33.333 0.00 0.00 33.15 2.83
85 92 8.761497 CGGTAGTAGTATATTCCAATGTGTTTG 58.239 37.037 0.00 0.00 34.93 2.93
86 93 8.480501 ACGGTAGTAGTATATTCCAATGTGTTT 58.519 33.333 0.00 0.00 0.00 2.83
87 94 8.015185 ACGGTAGTAGTATATTCCAATGTGTT 57.985 34.615 0.00 0.00 0.00 3.32
88 95 7.592885 ACGGTAGTAGTATATTCCAATGTGT 57.407 36.000 0.00 0.00 0.00 3.72
89 96 9.970395 TTTACGGTAGTAGTATATTCCAATGTG 57.030 33.333 0.00 0.00 33.87 3.21
99 106 9.411801 CACGAGATACTTTACGGTAGTAGTATA 57.588 37.037 17.65 2.97 34.19 1.47
100 107 7.386299 CCACGAGATACTTTACGGTAGTAGTAT 59.614 40.741 17.65 17.65 35.79 2.12
101 108 6.701841 CCACGAGATACTTTACGGTAGTAGTA 59.298 42.308 11.95 11.95 33.87 1.82
102 109 5.525378 CCACGAGATACTTTACGGTAGTAGT 59.475 44.000 9.15 9.15 33.87 2.73
103 110 5.559799 GCCACGAGATACTTTACGGTAGTAG 60.560 48.000 0.00 0.00 33.87 2.57
146 158 0.250381 TGGCTTCCCGCGAAAAAGTA 60.250 50.000 8.23 0.00 40.44 2.24
253 266 3.435566 AGTTGTACGATGCGTGTAGATG 58.564 45.455 2.33 0.00 41.39 2.90
256 269 3.059044 GTGAAGTTGTACGATGCGTGTAG 59.941 47.826 2.33 0.00 41.39 2.74
385 401 8.636843 CGAGTTTACAACAACTAGTATCTCAAC 58.363 37.037 0.00 0.00 37.11 3.18
416 432 2.159037 CCCGCGAAAGAAAACTACCTTC 59.841 50.000 8.23 0.00 0.00 3.46
419 435 0.800631 CCCCGCGAAAGAAAACTACC 59.199 55.000 8.23 0.00 0.00 3.18
420 436 1.799544 TCCCCGCGAAAGAAAACTAC 58.200 50.000 8.23 0.00 0.00 2.73
432 448 2.432206 AATCAAAAGTTTTCCCCGCG 57.568 45.000 0.00 0.00 0.00 6.46
450 466 8.984764 GTACTGGCATGATGTTATACGAATAAA 58.015 33.333 0.00 0.00 29.41 1.40
457 473 9.878599 GTTATTTGTACTGGCATGATGTTATAC 57.121 33.333 0.00 0.00 0.00 1.47
460 476 7.929941 TGTTATTTGTACTGGCATGATGTTA 57.070 32.000 0.00 0.00 0.00 2.41
465 481 5.423886 TCGATGTTATTTGTACTGGCATGA 58.576 37.500 0.00 0.00 0.00 3.07
472 489 9.701098 TTCTGTTACTTCGATGTTATTTGTACT 57.299 29.630 9.44 0.00 0.00 2.73
512 530 9.587772 CTTGTAATTGTTGCTATGTACTAGTCT 57.412 33.333 0.00 0.00 0.00 3.24
513 531 8.328864 GCTTGTAATTGTTGCTATGTACTAGTC 58.671 37.037 0.00 0.00 0.00 2.59
515 533 8.116753 GTGCTTGTAATTGTTGCTATGTACTAG 58.883 37.037 0.00 0.00 0.00 2.57
516 534 7.822334 AGTGCTTGTAATTGTTGCTATGTACTA 59.178 33.333 0.00 0.00 0.00 1.82
517 535 6.655003 AGTGCTTGTAATTGTTGCTATGTACT 59.345 34.615 0.00 0.00 0.00 2.73
518 536 6.842163 AGTGCTTGTAATTGTTGCTATGTAC 58.158 36.000 0.00 0.00 0.00 2.90
522 541 4.935205 TCGAGTGCTTGTAATTGTTGCTAT 59.065 37.500 0.00 0.00 0.00 2.97
525 544 3.482786 CTCGAGTGCTTGTAATTGTTGC 58.517 45.455 3.62 0.00 0.00 4.17
526 545 3.482786 GCTCGAGTGCTTGTAATTGTTG 58.517 45.455 15.13 0.00 0.00 3.33
554 573 0.614697 TGAGGGAGAGCCGATGACAA 60.615 55.000 0.00 0.00 33.83 3.18
555 574 1.000359 TGAGGGAGAGCCGATGACA 60.000 57.895 0.00 0.00 33.83 3.58
556 575 1.439644 GTGAGGGAGAGCCGATGAC 59.560 63.158 0.00 0.00 33.83 3.06
557 576 1.758514 GGTGAGGGAGAGCCGATGA 60.759 63.158 0.00 0.00 33.83 2.92
559 578 0.909610 TTTGGTGAGGGAGAGCCGAT 60.910 55.000 0.00 0.00 33.83 4.18
561 580 0.955919 GTTTTGGTGAGGGAGAGCCG 60.956 60.000 0.00 0.00 33.83 5.52
562 581 0.609406 GGTTTTGGTGAGGGAGAGCC 60.609 60.000 0.00 0.00 0.00 4.70
563 582 0.955919 CGGTTTTGGTGAGGGAGAGC 60.956 60.000 0.00 0.00 0.00 4.09
564 583 0.321653 CCGGTTTTGGTGAGGGAGAG 60.322 60.000 0.00 0.00 0.00 3.20
565 584 1.758592 CCGGTTTTGGTGAGGGAGA 59.241 57.895 0.00 0.00 0.00 3.71
567 586 0.767446 TACCCGGTTTTGGTGAGGGA 60.767 55.000 0.00 0.00 44.70 4.20
569 588 1.241165 GTTACCCGGTTTTGGTGAGG 58.759 55.000 0.00 0.00 36.57 3.86
570 589 1.202842 AGGTTACCCGGTTTTGGTGAG 60.203 52.381 0.00 0.00 36.57 3.51
571 590 0.845337 AGGTTACCCGGTTTTGGTGA 59.155 50.000 0.00 0.00 36.57 4.02
572 591 1.694844 AAGGTTACCCGGTTTTGGTG 58.305 50.000 0.00 0.00 36.57 4.17
573 592 3.812611 ATAAGGTTACCCGGTTTTGGT 57.187 42.857 0.00 0.00 39.97 3.67
574 593 3.827876 ACAATAAGGTTACCCGGTTTTGG 59.172 43.478 0.00 0.00 35.12 3.28
575 594 5.706833 ACTACAATAAGGTTACCCGGTTTTG 59.293 40.000 0.00 0.00 35.12 2.44
576 595 5.879763 ACTACAATAAGGTTACCCGGTTTT 58.120 37.500 0.00 0.00 35.12 2.43
579 598 5.360999 GTCTACTACAATAAGGTTACCCGGT 59.639 44.000 0.00 0.00 35.12 5.28
581 600 6.096001 ACTGTCTACTACAATAAGGTTACCCG 59.904 42.308 0.00 0.00 37.74 5.28
584 603 7.978982 TCGACTGTCTACTACAATAAGGTTAC 58.021 38.462 6.21 0.00 37.74 2.50
585 604 8.565896 TTCGACTGTCTACTACAATAAGGTTA 57.434 34.615 6.21 0.00 37.74 2.85
616 635 6.811954 TCGAGTTGGGCTTAATTTTTCTTTT 58.188 32.000 0.00 0.00 0.00 2.27
617 636 6.264518 TCTCGAGTTGGGCTTAATTTTTCTTT 59.735 34.615 13.13 0.00 0.00 2.52
618 637 5.768164 TCTCGAGTTGGGCTTAATTTTTCTT 59.232 36.000 13.13 0.00 0.00 2.52
619 638 5.313712 TCTCGAGTTGGGCTTAATTTTTCT 58.686 37.500 13.13 0.00 0.00 2.52
620 639 5.622770 TCTCGAGTTGGGCTTAATTTTTC 57.377 39.130 13.13 0.00 0.00 2.29
621 640 5.710099 TCATCTCGAGTTGGGCTTAATTTTT 59.290 36.000 20.51 0.00 0.00 1.94
622 641 5.253330 TCATCTCGAGTTGGGCTTAATTTT 58.747 37.500 20.51 0.00 0.00 1.82
623 642 4.843728 TCATCTCGAGTTGGGCTTAATTT 58.156 39.130 20.51 0.00 0.00 1.82
624 643 4.487714 TCATCTCGAGTTGGGCTTAATT 57.512 40.909 20.51 0.00 0.00 1.40
625 644 4.696479 ATCATCTCGAGTTGGGCTTAAT 57.304 40.909 20.51 5.67 0.00 1.40
628 647 4.696479 AATATCATCTCGAGTTGGGCTT 57.304 40.909 20.51 10.28 0.00 4.35
671 785 8.985805 AGGTTACTTCTAACGTATTGTTTCTTG 58.014 33.333 0.00 0.00 42.09 3.02
746 869 6.830873 ACTCATCGTACTGGTACTACTTTT 57.169 37.500 8.89 0.00 34.04 2.27
790 915 8.914011 GGCCCACTTTTCAGTTATCTATTTATT 58.086 33.333 0.00 0.00 0.00 1.40
791 916 7.505923 GGGCCCACTTTTCAGTTATCTATTTAT 59.494 37.037 19.95 0.00 0.00 1.40
792 917 6.831868 GGGCCCACTTTTCAGTTATCTATTTA 59.168 38.462 19.95 0.00 0.00 1.40
793 918 5.656859 GGGCCCACTTTTCAGTTATCTATTT 59.343 40.000 19.95 0.00 0.00 1.40
798 923 2.492088 GTGGGCCCACTTTTCAGTTATC 59.508 50.000 42.23 15.80 43.12 1.75
1073 1214 1.068474 CTTGAAGTACTTGCCGACGG 58.932 55.000 14.14 10.29 0.00 4.79
1098 1239 4.385405 AAGGAGCTCTTGCGCGCT 62.385 61.111 33.29 10.95 45.42 5.92
1271 1412 2.840753 GGGTTGGAAGTCCCCAGCA 61.841 63.158 0.00 0.00 38.92 4.41
1278 1419 1.297689 GTACCCCGGGTTGGAAGTC 59.702 63.158 21.85 0.00 42.00 3.01
1281 1422 2.203758 TCGTACCCCGGGTTGGAA 60.204 61.111 21.85 0.00 42.00 3.53
1504 1645 0.539051 AAGAAGACGATGCCCTCCAG 59.461 55.000 0.00 0.00 0.00 3.86
1516 1657 0.108567 GCCGACAGGAGGAAGAAGAC 60.109 60.000 0.00 0.00 41.02 3.01
1609 1750 1.672356 CGGTGAAGGCCAGGAACAG 60.672 63.158 5.01 0.00 0.00 3.16
1770 1911 2.892425 GTGATGAGGAAGCCGGCG 60.892 66.667 23.20 0.00 0.00 6.46
1857 1998 0.742281 CGGTTGTGCCTCTGATCCAG 60.742 60.000 0.00 0.00 34.25 3.86
1949 2090 3.257561 CGGCCGTGCTCTTGATCG 61.258 66.667 19.50 0.00 0.00 3.69
2245 2386 1.205893 GAAGAAGGCAGAGACGGTGAT 59.794 52.381 0.00 0.00 0.00 3.06
2361 2502 1.227089 CCACTCGATCTCCTTGGCG 60.227 63.158 0.00 0.00 0.00 5.69
2406 2547 2.434884 AGCGCCATGGTGACGAAG 60.435 61.111 29.49 5.51 0.00 3.79
2514 2655 4.659172 TTCCCCACCTTGCCGCAG 62.659 66.667 0.00 0.00 0.00 5.18
2631 2781 4.644498 ACTAGCTACGAGGAAGTCTATCC 58.356 47.826 0.00 0.00 39.96 2.59
2632 2782 5.759273 TCAACTAGCTACGAGGAAGTCTATC 59.241 44.000 0.00 0.00 0.00 2.08
2634 2784 5.095145 TCAACTAGCTACGAGGAAGTCTA 57.905 43.478 0.00 0.00 0.00 2.59
2635 2785 3.952931 TCAACTAGCTACGAGGAAGTCT 58.047 45.455 0.00 0.00 0.00 3.24
2636 2786 4.335874 TCATCAACTAGCTACGAGGAAGTC 59.664 45.833 0.00 0.00 0.00 3.01
2638 2788 4.902443 TCATCAACTAGCTACGAGGAAG 57.098 45.455 0.00 0.00 0.00 3.46
2639 2789 4.887655 TCATCATCAACTAGCTACGAGGAA 59.112 41.667 0.00 0.00 0.00 3.36
2641 2791 4.837896 TCATCATCAACTAGCTACGAGG 57.162 45.455 0.00 0.00 0.00 4.63
2642 2792 7.589395 ACTAATCATCATCAACTAGCTACGAG 58.411 38.462 0.00 0.00 0.00 4.18
2643 2793 7.511959 ACTAATCATCATCAACTAGCTACGA 57.488 36.000 0.00 0.00 0.00 3.43
2644 2794 8.483218 CAAACTAATCATCATCAACTAGCTACG 58.517 37.037 0.00 0.00 0.00 3.51
2645 2795 8.768955 CCAAACTAATCATCATCAACTAGCTAC 58.231 37.037 0.00 0.00 0.00 3.58
2646 2796 8.704668 TCCAAACTAATCATCATCAACTAGCTA 58.295 33.333 0.00 0.00 0.00 3.32
2647 2797 7.497249 GTCCAAACTAATCATCATCAACTAGCT 59.503 37.037 0.00 0.00 0.00 3.32
2662 2838 4.910195 TGATGCTCTGTGTCCAAACTAAT 58.090 39.130 0.00 0.00 0.00 1.73
2686 2862 3.967987 AGTAGTCCTAATCCCATGTCACC 59.032 47.826 0.00 0.00 0.00 4.02
2783 3003 1.002142 GGCCGTCAAAGTACAAACACC 60.002 52.381 0.00 0.00 0.00 4.16
2784 3004 1.671845 TGGCCGTCAAAGTACAAACAC 59.328 47.619 0.00 0.00 0.00 3.32
2785 3005 2.039818 TGGCCGTCAAAGTACAAACA 57.960 45.000 0.00 0.00 0.00 2.83
2788 3008 2.552599 TCATGGCCGTCAAAGTACAA 57.447 45.000 0.00 0.00 0.00 2.41
2817 3050 3.059325 GCTAGCTAGCGAAATCAATGTGG 60.059 47.826 28.89 0.00 39.82 4.17
2853 3086 5.808540 CCAGTACAATTTGCTCAAATCCATG 59.191 40.000 8.14 6.23 39.88 3.66
2865 3105 4.549458 CTTTGACCTGCCAGTACAATTTG 58.451 43.478 0.00 0.00 0.00 2.32
2898 3155 0.941463 GGCGATCATACGTCCTGCAG 60.941 60.000 6.78 6.78 35.59 4.41
2914 3171 2.878406 TCTCAAAGTTCTTTTGGAGGCG 59.122 45.455 10.55 0.00 45.05 5.52
2954 3213 5.199000 CGATACTACTGTTGACTGTCGATC 58.801 45.833 0.21 0.00 0.00 3.69
2959 3218 4.440250 GCATCCGATACTACTGTTGACTGT 60.440 45.833 0.00 0.00 0.00 3.55
2990 3266 3.807538 GACCATGGCGTGCTGCTG 61.808 66.667 13.04 0.00 45.43 4.41
3000 3276 2.867109 AACCTCACAAGAGACCATGG 57.133 50.000 11.19 11.19 44.98 3.66
3005 3281 6.149640 GGGAAGAAAATAACCTCACAAGAGAC 59.850 42.308 0.00 0.00 44.98 3.36
3029 3310 5.856126 TTATACTTTCACGCTTGACTTGG 57.144 39.130 0.00 0.00 0.00 3.61
3111 3405 4.334118 TGCCCATGACGCAGCAGT 62.334 61.111 0.00 0.00 0.00 4.40
3135 3429 5.758924 TGACAGTAACTATATACAGCGCAG 58.241 41.667 11.47 3.33 0.00 5.18
3136 3430 5.758924 CTGACAGTAACTATATACAGCGCA 58.241 41.667 11.47 0.00 0.00 6.09
3137 3431 4.617645 GCTGACAGTAACTATATACAGCGC 59.382 45.833 0.00 0.00 39.59 5.92
3291 3596 3.114616 CAGCCGTCGTCAGCCTTG 61.115 66.667 0.00 0.00 0.00 3.61
3440 3745 6.402222 AGCTATATTCTCCGAATCATTGACC 58.598 40.000 0.00 0.00 0.00 4.02
3452 3757 5.010213 AGGACAAGACGAAGCTATATTCTCC 59.990 44.000 0.00 0.00 0.00 3.71
3468 3773 4.711399 TCCGATAATACGAGAGGACAAGA 58.289 43.478 0.00 0.00 35.09 3.02
3510 3817 3.362831 GCGCATGAACAGTTTGAGATTTG 59.637 43.478 0.30 0.00 0.00 2.32
3517 3824 0.387622 CCAGGCGCATGAACAGTTTG 60.388 55.000 25.72 0.00 0.00 2.93
3543 3850 7.881775 ATTTCTTGACCAACTTAACTTGAGT 57.118 32.000 0.00 0.00 0.00 3.41
3544 3851 9.237846 GAAATTTCTTGACCAACTTAACTTGAG 57.762 33.333 11.05 0.00 0.00 3.02
3546 3853 8.925161 TGAAATTTCTTGACCAACTTAACTTG 57.075 30.769 18.64 0.00 0.00 3.16
3558 3865 4.668289 ACCACACGTTGAAATTTCTTGAC 58.332 39.130 18.64 12.95 0.00 3.18
3561 3868 5.267776 CGTAACCACACGTTGAAATTTCTT 58.732 37.500 18.64 4.56 37.16 2.52
3576 3886 5.697633 TCAGATTTTAACTCCACGTAACCAC 59.302 40.000 0.00 0.00 0.00 4.16
3578 3888 6.790285 TTCAGATTTTAACTCCACGTAACC 57.210 37.500 0.00 0.00 0.00 2.85
3583 3893 6.912591 GCCATAATTCAGATTTTAACTCCACG 59.087 38.462 0.00 0.00 0.00 4.94
3585 3895 7.953005 TGCCATAATTCAGATTTTAACTCCA 57.047 32.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.