Multiple sequence alignment - TraesCS5A01G261800

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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 TraesCS5A01G261800 chr5A 100.000 2222 0 0 1 2222 475376947 475379168 0.000000e+00 4104.0
1 TraesCS5A01G261800 chr5A 83.736 621 73 18 663 1264 650189280 650188669 1.490000e-156 562.0
2 TraesCS5A01G261800 chr5A 84.135 208 23 6 1853 2057 255588758 255588558 2.250000e-45 193.0
3 TraesCS5A01G261800 chr5A 84.135 208 23 6 1853 2057 257331878 257331678 2.250000e-45 193.0
4 TraesCS5A01G261800 chr5B 99.295 1560 10 1 663 2222 640414836 640416394 0.000000e+00 2819.0
5 TraesCS5A01G261800 chr5B 81.686 617 88 19 670 1266 672101089 672101700 7.130000e-135 490.0
6 TraesCS5A01G261800 chr5B 84.270 267 34 5 324 589 442378380 442378121 1.020000e-63 254.0
7 TraesCS5A01G261800 chr5B 87.368 190 22 2 5 192 442378954 442378765 1.340000e-52 217.0
8 TraesCS5A01G261800 chrUn 98.391 1554 22 1 669 2222 62068750 62070300 0.000000e+00 2728.0
9 TraesCS5A01G261800 chrUn 99.862 723 1 0 1500 2222 428748801 428749523 0.000000e+00 1330.0
10 TraesCS5A01G261800 chr6A 98.074 1558 28 2 667 2222 33404182 33402625 0.000000e+00 2710.0
11 TraesCS5A01G261800 chr2D 86.689 601 68 8 675 1266 83846736 83847333 0.000000e+00 656.0
12 TraesCS5A01G261800 chr1A 84.202 614 70 16 667 1266 157082961 157083561 2.480000e-159 571.0
13 TraesCS5A01G261800 chr4B 82.476 622 87 15 663 1266 570151227 570150610 1.950000e-145 525.0
14 TraesCS5A01G261800 chr5D 89.461 427 25 10 255 671 372044829 372044413 2.530000e-144 521.0
15 TraesCS5A01G261800 chr5D 91.379 58 5 0 196 253 372044954 372044897 1.830000e-11 80.5
16 TraesCS5A01G261800 chr6D 81.517 633 78 23 660 1264 93428538 93429159 3.320000e-133 484.0
17 TraesCS5A01G261800 chr4A 80.331 544 84 17 670 1195 638429949 638430487 7.440000e-105 390.0
18 TraesCS5A01G261800 chr7B 87.013 77 10 0 1190 1266 501559515 501559439 1.090000e-13 87.9


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 TraesCS5A01G261800 chr5A 475376947 475379168 2221 False 4104.00 4104 100.000 1 2222 1 chr5A.!!$F1 2221
1 TraesCS5A01G261800 chr5A 650188669 650189280 611 True 562.00 562 83.736 663 1264 1 chr5A.!!$R3 601
2 TraesCS5A01G261800 chr5B 640414836 640416394 1558 False 2819.00 2819 99.295 663 2222 1 chr5B.!!$F1 1559
3 TraesCS5A01G261800 chr5B 672101089 672101700 611 False 490.00 490 81.686 670 1266 1 chr5B.!!$F2 596
4 TraesCS5A01G261800 chr5B 442378121 442378954 833 True 235.50 254 85.819 5 589 2 chr5B.!!$R1 584
5 TraesCS5A01G261800 chrUn 62068750 62070300 1550 False 2728.00 2728 98.391 669 2222 1 chrUn.!!$F1 1553
6 TraesCS5A01G261800 chrUn 428748801 428749523 722 False 1330.00 1330 99.862 1500 2222 1 chrUn.!!$F2 722
7 TraesCS5A01G261800 chr6A 33402625 33404182 1557 True 2710.00 2710 98.074 667 2222 1 chr6A.!!$R1 1555
8 TraesCS5A01G261800 chr2D 83846736 83847333 597 False 656.00 656 86.689 675 1266 1 chr2D.!!$F1 591
9 TraesCS5A01G261800 chr1A 157082961 157083561 600 False 571.00 571 84.202 667 1266 1 chr1A.!!$F1 599
10 TraesCS5A01G261800 chr4B 570150610 570151227 617 True 525.00 525 82.476 663 1266 1 chr4B.!!$R1 603
11 TraesCS5A01G261800 chr5D 372044413 372044954 541 True 300.75 521 90.420 196 671 2 chr5D.!!$R1 475
12 TraesCS5A01G261800 chr6D 93428538 93429159 621 False 484.00 484 81.517 660 1264 1 chr6D.!!$F1 604
13 TraesCS5A01G261800 chr4A 638429949 638430487 538 False 390.00 390 80.331 670 1195 1 chr4A.!!$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
578 869 0.034896 TTCTGCCGTCCTTTCCAGAC 59.965 55.0 0.0 0.0 34.36 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2184 2554 6.319141 GTTTGTAGAAACTTTGCTCCATCT 57.681 37.5 8.18 0.0 38.78 2.9 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
31 32 7.862372 TGCTCTGTTCTCACATTTTGTAATTTC 59.138 33.333 0.00 0.00 30.39 2.17
34 35 7.862372 TCTGTTCTCACATTTTGTAATTTCAGC 59.138 33.333 0.00 0.00 30.39 4.26
40 41 9.630098 CTCACATTTTGTAATTTCAGCTTATGT 57.370 29.630 0.00 0.00 0.00 2.29
51 52 8.922058 AATTTCAGCTTATGTTGATCATTGAC 57.078 30.769 0.00 0.00 37.91 3.18
72 73 3.945285 ACGTTGGGCTATAGGAACAATTG 59.055 43.478 3.24 3.24 0.00 2.32
86 88 5.104569 AGGAACAATTGGTGAAAATTGGTGT 60.105 36.000 10.83 0.34 45.28 4.16
90 92 8.152309 AACAATTGGTGAAAATTGGTGTATTG 57.848 30.769 10.83 0.00 43.98 1.90
93 95 3.249917 GGTGAAAATTGGTGTATTGCCG 58.750 45.455 0.00 0.00 0.00 5.69
94 96 3.305744 GGTGAAAATTGGTGTATTGCCGT 60.306 43.478 0.00 0.00 0.00 5.68
123 125 4.338400 TCGTCGACCTATGATCAAATGACT 59.662 41.667 10.58 0.00 0.00 3.41
130 132 7.380870 CGACCTATGATCAAATGACTTAGAGTG 59.619 40.741 0.00 0.00 0.00 3.51
132 134 6.933521 CCTATGATCAAATGACTTAGAGTGGG 59.066 42.308 0.00 0.00 0.00 4.61
135 137 5.248248 TGATCAAATGACTTAGAGTGGGTGA 59.752 40.000 0.00 0.00 0.00 4.02
136 138 4.894784 TCAAATGACTTAGAGTGGGTGAC 58.105 43.478 0.00 0.00 0.00 3.67
156 158 5.241728 GTGACCCTATTGATAAAATGCCCTC 59.758 44.000 0.00 0.00 0.00 4.30
173 176 2.746362 CCCTCAGTTGACAAGCATCTTC 59.254 50.000 0.00 0.00 0.00 2.87
177 180 3.817084 TCAGTTGACAAGCATCTTCAAGG 59.183 43.478 0.00 0.00 29.97 3.61
180 183 4.276926 AGTTGACAAGCATCTTCAAGGTTC 59.723 41.667 0.00 0.00 29.97 3.62
194 197 3.381370 GGTTCGGCCTACAGGATTC 57.619 57.895 0.00 0.00 37.39 2.52
220 223 9.525007 CTGTTTACAAAATAACATCACGTAGTC 57.475 33.333 0.00 0.00 33.90 2.59
222 225 8.497554 GTTTACAAAATAACATCACGTAGTCCA 58.502 33.333 0.00 0.00 41.61 4.02
369 660 2.710377 TCAACCCAAATCCATCTCACG 58.290 47.619 0.00 0.00 0.00 4.35
392 683 4.569564 GGAACTAGGGTTTACTACATTGCG 59.430 45.833 0.00 0.00 35.58 4.85
395 686 0.375803 GGGTTTACTACATTGCGCCG 59.624 55.000 4.18 0.00 0.00 6.46
443 734 3.766051 GAGGAAATGAGGTGGCAGAAAAT 59.234 43.478 0.00 0.00 0.00 1.82
453 744 3.013921 GTGGCAGAAAATGGAACCGATA 58.986 45.455 0.00 0.00 0.00 2.92
466 757 3.437867 CGATAGGCTCACCTCGCT 58.562 61.111 0.00 0.00 46.34 4.93
467 758 1.007964 CGATAGGCTCACCTCGCTG 60.008 63.158 0.00 0.00 46.34 5.18
468 759 1.300542 GATAGGCTCACCTCGCTGC 60.301 63.158 0.00 0.00 46.34 5.25
469 760 2.707529 GATAGGCTCACCTCGCTGCC 62.708 65.000 0.00 0.00 46.34 4.85
499 790 4.154347 CAGCCGCTGGGAGGACTC 62.154 72.222 12.93 0.00 34.06 3.36
502 793 3.827898 CCGCTGGGAGGACTCGAC 61.828 72.222 0.00 0.00 34.06 4.20
503 794 4.180946 CGCTGGGAGGACTCGACG 62.181 72.222 0.00 0.00 0.00 5.12
504 795 4.500116 GCTGGGAGGACTCGACGC 62.500 72.222 0.00 0.00 0.00 5.19
505 796 3.827898 CTGGGAGGACTCGACGCC 61.828 72.222 0.00 0.00 0.00 5.68
545 836 3.882013 CGGCCGCACAAACACACA 61.882 61.111 14.67 0.00 0.00 3.72
546 837 2.026014 GGCCGCACAAACACACAG 59.974 61.111 0.00 0.00 0.00 3.66
547 838 2.477176 GGCCGCACAAACACACAGA 61.477 57.895 0.00 0.00 0.00 3.41
548 839 1.009675 GCCGCACAAACACACAGAG 60.010 57.895 0.00 0.00 0.00 3.35
549 840 1.436195 GCCGCACAAACACACAGAGA 61.436 55.000 0.00 0.00 0.00 3.10
550 841 0.583438 CCGCACAAACACACAGAGAG 59.417 55.000 0.00 0.00 0.00 3.20
551 842 1.570813 CGCACAAACACACAGAGAGA 58.429 50.000 0.00 0.00 0.00 3.10
552 843 1.524355 CGCACAAACACACAGAGAGAG 59.476 52.381 0.00 0.00 0.00 3.20
553 844 1.869767 GCACAAACACACAGAGAGAGG 59.130 52.381 0.00 0.00 0.00 3.69
554 845 2.487934 CACAAACACACAGAGAGAGGG 58.512 52.381 0.00 0.00 0.00 4.30
555 846 2.103094 CACAAACACACAGAGAGAGGGA 59.897 50.000 0.00 0.00 0.00 4.20
556 847 2.103263 ACAAACACACAGAGAGAGGGAC 59.897 50.000 0.00 0.00 0.00 4.46
557 848 0.962489 AACACACAGAGAGAGGGACG 59.038 55.000 0.00 0.00 0.00 4.79
558 849 0.178987 ACACACAGAGAGAGGGACGT 60.179 55.000 0.00 0.00 0.00 4.34
559 850 0.962489 CACACAGAGAGAGGGACGTT 59.038 55.000 0.00 0.00 0.00 3.99
560 851 1.341531 CACACAGAGAGAGGGACGTTT 59.658 52.381 0.00 0.00 0.00 3.60
561 852 1.614413 ACACAGAGAGAGGGACGTTTC 59.386 52.381 0.00 0.00 0.00 2.78
562 853 1.889829 CACAGAGAGAGGGACGTTTCT 59.110 52.381 0.00 0.00 0.00 2.52
563 854 1.889829 ACAGAGAGAGGGACGTTTCTG 59.110 52.381 0.00 0.00 0.00 3.02
564 855 0.892063 AGAGAGAGGGACGTTTCTGC 59.108 55.000 0.00 0.00 0.00 4.26
565 856 0.108567 GAGAGAGGGACGTTTCTGCC 60.109 60.000 0.00 0.00 0.00 4.85
566 857 1.446272 GAGAGGGACGTTTCTGCCG 60.446 63.158 0.00 0.00 0.00 5.69
567 858 2.156051 GAGAGGGACGTTTCTGCCGT 62.156 60.000 0.00 0.00 42.06 5.68
571 862 4.355925 GACGTTTCTGCCGTCCTT 57.644 55.556 1.72 0.00 46.73 3.36
572 863 2.613390 GACGTTTCTGCCGTCCTTT 58.387 52.632 1.72 0.00 46.73 3.11
573 864 0.511653 GACGTTTCTGCCGTCCTTTC 59.488 55.000 1.72 0.00 46.73 2.62
574 865 0.883370 ACGTTTCTGCCGTCCTTTCC 60.883 55.000 0.00 0.00 31.97 3.13
575 866 0.882927 CGTTTCTGCCGTCCTTTCCA 60.883 55.000 0.00 0.00 0.00 3.53
576 867 0.875059 GTTTCTGCCGTCCTTTCCAG 59.125 55.000 0.00 0.00 0.00 3.86
577 868 0.762418 TTTCTGCCGTCCTTTCCAGA 59.238 50.000 0.00 0.00 32.90 3.86
578 869 0.034896 TTCTGCCGTCCTTTCCAGAC 59.965 55.000 0.00 0.00 34.36 3.51
583 874 3.119096 GTCCTTTCCAGACGCCGC 61.119 66.667 0.00 0.00 0.00 6.53
584 875 4.388499 TCCTTTCCAGACGCCGCC 62.388 66.667 0.00 0.00 0.00 6.13
585 876 4.697756 CCTTTCCAGACGCCGCCA 62.698 66.667 0.00 0.00 0.00 5.69
586 877 3.423154 CTTTCCAGACGCCGCCAC 61.423 66.667 0.00 0.00 0.00 5.01
600 891 2.902846 CCACCACGCCGTTTCCAA 60.903 61.111 0.00 0.00 0.00 3.53
601 892 2.482333 CCACCACGCCGTTTCCAAA 61.482 57.895 0.00 0.00 0.00 3.28
602 893 1.298788 CACCACGCCGTTTCCAAAC 60.299 57.895 0.00 0.00 35.59 2.93
603 894 1.452470 ACCACGCCGTTTCCAAACT 60.452 52.632 0.00 0.00 36.77 2.66
604 895 1.033202 ACCACGCCGTTTCCAAACTT 61.033 50.000 0.00 0.00 36.77 2.66
605 896 0.317519 CCACGCCGTTTCCAAACTTC 60.318 55.000 0.00 0.00 36.77 3.01
606 897 0.317519 CACGCCGTTTCCAAACTTCC 60.318 55.000 0.00 0.00 36.77 3.46
607 898 0.748729 ACGCCGTTTCCAAACTTCCA 60.749 50.000 0.91 0.00 36.77 3.53
608 899 0.317519 CGCCGTTTCCAAACTTCCAC 60.318 55.000 0.91 0.00 36.77 4.02
609 900 1.029681 GCCGTTTCCAAACTTCCACT 58.970 50.000 0.91 0.00 36.77 4.00
610 901 1.407618 GCCGTTTCCAAACTTCCACTT 59.592 47.619 0.91 0.00 36.77 3.16
611 902 2.543031 GCCGTTTCCAAACTTCCACTTC 60.543 50.000 0.91 0.00 36.77 3.01
612 903 2.034179 CCGTTTCCAAACTTCCACTTCC 59.966 50.000 0.91 0.00 36.77 3.46
613 904 2.034179 CGTTTCCAAACTTCCACTTCCC 59.966 50.000 0.91 0.00 36.77 3.97
614 905 2.364324 GTTTCCAAACTTCCACTTCCCC 59.636 50.000 0.00 0.00 36.03 4.81
615 906 0.481128 TCCAAACTTCCACTTCCCCC 59.519 55.000 0.00 0.00 0.00 5.40
630 921 3.249687 CCCCCAAGTGAGCTAACAC 57.750 57.895 3.43 0.04 40.60 3.32
631 922 0.673644 CCCCCAAGTGAGCTAACACG 60.674 60.000 3.43 0.00 44.35 4.49
632 923 0.320374 CCCCAAGTGAGCTAACACGA 59.680 55.000 3.43 0.00 44.35 4.35
633 924 1.270625 CCCCAAGTGAGCTAACACGAA 60.271 52.381 3.43 0.00 44.35 3.85
634 925 2.489971 CCCAAGTGAGCTAACACGAAA 58.510 47.619 3.43 0.00 44.35 3.46
635 926 3.074412 CCCAAGTGAGCTAACACGAAAT 58.926 45.455 3.43 0.00 44.35 2.17
636 927 3.502211 CCCAAGTGAGCTAACACGAAATT 59.498 43.478 3.43 0.00 44.35 1.82
637 928 4.466828 CCAAGTGAGCTAACACGAAATTG 58.533 43.478 3.43 0.00 44.35 2.32
638 929 4.024048 CCAAGTGAGCTAACACGAAATTGT 60.024 41.667 3.43 0.00 44.35 2.71
639 930 5.178623 CCAAGTGAGCTAACACGAAATTGTA 59.821 40.000 3.43 0.00 44.35 2.41
640 931 6.293190 CCAAGTGAGCTAACACGAAATTGTAA 60.293 38.462 3.43 0.00 44.35 2.41
641 932 6.854496 AGTGAGCTAACACGAAATTGTAAA 57.146 33.333 3.43 0.00 44.35 2.01
642 933 6.656003 AGTGAGCTAACACGAAATTGTAAAC 58.344 36.000 3.43 0.00 44.35 2.01
643 934 5.849604 GTGAGCTAACACGAAATTGTAAACC 59.150 40.000 0.00 0.00 0.00 3.27
644 935 5.761234 TGAGCTAACACGAAATTGTAAACCT 59.239 36.000 0.00 0.00 0.00 3.50
645 936 6.930164 TGAGCTAACACGAAATTGTAAACCTA 59.070 34.615 0.00 0.00 0.00 3.08
646 937 7.441760 TGAGCTAACACGAAATTGTAAACCTAA 59.558 33.333 0.00 0.00 0.00 2.69
647 938 8.156994 AGCTAACACGAAATTGTAAACCTAAA 57.843 30.769 0.00 0.00 0.00 1.85
648 939 8.623030 AGCTAACACGAAATTGTAAACCTAAAA 58.377 29.630 0.00 0.00 0.00 1.52
649 940 9.401873 GCTAACACGAAATTGTAAACCTAAAAT 57.598 29.630 0.00 0.00 0.00 1.82
652 943 9.458374 AACACGAAATTGTAAACCTAAAATCTG 57.542 29.630 0.00 0.00 0.00 2.90
653 944 8.842280 ACACGAAATTGTAAACCTAAAATCTGA 58.158 29.630 0.00 0.00 0.00 3.27
654 945 9.840427 CACGAAATTGTAAACCTAAAATCTGAT 57.160 29.630 0.00 0.00 0.00 2.90
802 1093 5.567037 TCCATATTACATCAAGGGTCTGG 57.433 43.478 0.00 0.00 0.00 3.86
841 1132 4.037858 CAGATTAAATGTTCTGCCAGCC 57.962 45.455 0.00 0.00 33.56 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.348863 AAATGTGAGAACAGAGCACTCT 57.651 40.909 0.00 0.00 41.37 3.24
2 3 4.274459 ACAAAATGTGAGAACAGAGCACTC 59.726 41.667 0.00 0.00 33.83 3.51
31 32 5.475273 ACGTCAATGATCAACATAAGCTG 57.525 39.130 0.00 0.00 38.38 4.24
34 35 5.572211 CCCAACGTCAATGATCAACATAAG 58.428 41.667 0.00 0.00 38.38 1.73
40 41 2.198827 AGCCCAACGTCAATGATCAA 57.801 45.000 0.00 0.00 0.00 2.57
45 46 3.469008 TCCTATAGCCCAACGTCAATG 57.531 47.619 0.00 0.00 0.00 2.82
47 48 2.568062 TGTTCCTATAGCCCAACGTCAA 59.432 45.455 0.00 0.00 0.00 3.18
51 52 3.315191 CCAATTGTTCCTATAGCCCAACG 59.685 47.826 4.43 0.00 0.00 4.10
72 73 3.249917 CGGCAATACACCAATTTTCACC 58.750 45.455 0.00 0.00 0.00 4.02
86 88 1.068402 TCGACGAACTTGACGGCAATA 60.068 47.619 2.94 0.00 38.84 1.90
90 92 2.370393 GGTCGACGAACTTGACGGC 61.370 63.158 9.92 0.00 34.32 5.68
93 95 3.482722 TCATAGGTCGACGAACTTGAC 57.517 47.619 22.34 0.00 29.72 3.18
94 96 3.692593 TGATCATAGGTCGACGAACTTGA 59.307 43.478 22.34 21.87 29.72 3.02
130 132 4.280929 GGCATTTTATCAATAGGGTCACCC 59.719 45.833 3.85 3.85 45.90 4.61
132 134 5.140454 AGGGCATTTTATCAATAGGGTCAC 58.860 41.667 0.00 0.00 0.00 3.67
135 137 5.103515 ACTGAGGGCATTTTATCAATAGGGT 60.104 40.000 0.00 0.00 0.00 4.34
136 138 5.388654 ACTGAGGGCATTTTATCAATAGGG 58.611 41.667 0.00 0.00 0.00 3.53
140 142 5.716228 TGTCAACTGAGGGCATTTTATCAAT 59.284 36.000 0.00 0.00 0.00 2.57
156 158 3.567164 ACCTTGAAGATGCTTGTCAACTG 59.433 43.478 0.00 0.00 0.00 3.16
177 180 1.941325 CAGAATCCTGTAGGCCGAAC 58.059 55.000 0.00 0.00 35.70 3.95
193 196 9.263538 ACTACGTGATGTTATTTTGTAAACAGA 57.736 29.630 0.00 0.00 38.87 3.41
194 197 9.525007 GACTACGTGATGTTATTTTGTAAACAG 57.475 33.333 0.00 0.00 38.87 3.16
201 204 6.147164 AGTGTGGACTACGTGATGTTATTTTG 59.853 38.462 0.00 0.00 0.00 2.44
206 209 3.613193 GCAGTGTGGACTACGTGATGTTA 60.613 47.826 0.00 0.00 0.00 2.41
218 221 2.353011 CCATTTCCATTGCAGTGTGGAC 60.353 50.000 14.79 0.00 43.85 4.02
220 223 1.894466 TCCATTTCCATTGCAGTGTGG 59.106 47.619 8.53 9.09 36.82 4.17
222 225 1.547372 GCTCCATTTCCATTGCAGTGT 59.453 47.619 8.53 0.00 0.00 3.55
286 511 5.514834 CCCGGTATAATTGTCCTGGATCAAT 60.515 44.000 14.67 14.67 36.07 2.57
295 520 3.733443 ACGTACCCGGTATAATTGTCC 57.267 47.619 0.00 0.00 38.78 4.02
306 531 1.728425 GCAGAAAAACTACGTACCCGG 59.272 52.381 0.00 0.00 38.78 5.73
369 660 4.569564 CGCAATGTAGTAAACCCTAGTTCC 59.430 45.833 0.00 0.00 34.19 3.62
392 683 4.450082 ACCCTATGTTTTGATTTTCGGC 57.550 40.909 0.00 0.00 0.00 5.54
395 686 5.861787 CCGTGAACCCTATGTTTTGATTTTC 59.138 40.000 0.00 0.00 37.29 2.29
443 734 0.325296 AGGTGAGCCTATCGGTTCCA 60.325 55.000 0.00 0.00 44.90 3.53
482 773 4.154347 GAGTCCTCCCAGCGGCTG 62.154 72.222 22.84 22.84 0.00 4.85
485 776 3.827898 GTCGAGTCCTCCCAGCGG 61.828 72.222 0.00 0.00 0.00 5.52
486 777 4.180946 CGTCGAGTCCTCCCAGCG 62.181 72.222 0.00 0.00 0.00 5.18
487 778 4.500116 GCGTCGAGTCCTCCCAGC 62.500 72.222 0.00 0.00 0.00 4.85
488 779 3.827898 GGCGTCGAGTCCTCCCAG 61.828 72.222 0.00 0.00 0.00 4.45
528 819 3.805385 CTGTGTGTTTGTGCGGCCG 62.805 63.158 24.05 24.05 0.00 6.13
529 820 2.026014 CTGTGTGTTTGTGCGGCC 59.974 61.111 0.00 0.00 0.00 6.13
530 821 1.009675 CTCTGTGTGTTTGTGCGGC 60.010 57.895 0.00 0.00 0.00 6.53
531 822 0.583438 CTCTCTGTGTGTTTGTGCGG 59.417 55.000 0.00 0.00 0.00 5.69
532 823 1.524355 CTCTCTCTGTGTGTTTGTGCG 59.476 52.381 0.00 0.00 0.00 5.34
533 824 1.869767 CCTCTCTCTGTGTGTTTGTGC 59.130 52.381 0.00 0.00 0.00 4.57
534 825 2.103094 TCCCTCTCTCTGTGTGTTTGTG 59.897 50.000 0.00 0.00 0.00 3.33
535 826 2.103263 GTCCCTCTCTCTGTGTGTTTGT 59.897 50.000 0.00 0.00 0.00 2.83
536 827 2.760374 GTCCCTCTCTCTGTGTGTTTG 58.240 52.381 0.00 0.00 0.00 2.93
537 828 1.341531 CGTCCCTCTCTCTGTGTGTTT 59.658 52.381 0.00 0.00 0.00 2.83
538 829 0.962489 CGTCCCTCTCTCTGTGTGTT 59.038 55.000 0.00 0.00 0.00 3.32
539 830 0.178987 ACGTCCCTCTCTCTGTGTGT 60.179 55.000 0.00 0.00 0.00 3.72
540 831 0.962489 AACGTCCCTCTCTCTGTGTG 59.038 55.000 0.00 0.00 0.00 3.82
541 832 1.614413 GAAACGTCCCTCTCTCTGTGT 59.386 52.381 0.00 0.00 0.00 3.72
542 833 1.889829 AGAAACGTCCCTCTCTCTGTG 59.110 52.381 0.00 0.00 0.00 3.66
543 834 1.889829 CAGAAACGTCCCTCTCTCTGT 59.110 52.381 0.00 0.00 0.00 3.41
544 835 1.403514 GCAGAAACGTCCCTCTCTCTG 60.404 57.143 0.00 0.00 34.69 3.35
545 836 0.892063 GCAGAAACGTCCCTCTCTCT 59.108 55.000 0.00 0.00 0.00 3.10
546 837 0.108567 GGCAGAAACGTCCCTCTCTC 60.109 60.000 0.00 0.00 0.00 3.20
547 838 1.878656 CGGCAGAAACGTCCCTCTCT 61.879 60.000 0.00 0.00 0.00 3.10
548 839 1.446272 CGGCAGAAACGTCCCTCTC 60.446 63.158 0.00 0.00 0.00 3.20
549 840 2.207924 ACGGCAGAAACGTCCCTCT 61.208 57.895 0.00 0.00 41.25 3.69
550 841 2.342648 ACGGCAGAAACGTCCCTC 59.657 61.111 0.00 0.00 41.25 4.30
556 847 0.882927 TGGAAAGGACGGCAGAAACG 60.883 55.000 0.00 0.00 37.36 3.60
557 848 0.875059 CTGGAAAGGACGGCAGAAAC 59.125 55.000 0.00 0.00 0.00 2.78
558 849 0.762418 TCTGGAAAGGACGGCAGAAA 59.238 50.000 0.00 0.00 0.00 2.52
559 850 0.034896 GTCTGGAAAGGACGGCAGAA 59.965 55.000 0.00 0.00 0.00 3.02
560 851 1.671742 GTCTGGAAAGGACGGCAGA 59.328 57.895 0.00 0.00 0.00 4.26
561 852 4.285851 GTCTGGAAAGGACGGCAG 57.714 61.111 0.00 0.00 0.00 4.85
566 857 3.119096 GCGGCGTCTGGAAAGGAC 61.119 66.667 9.37 0.00 0.00 3.85
567 858 4.388499 GGCGGCGTCTGGAAAGGA 62.388 66.667 9.37 0.00 0.00 3.36
568 859 4.697756 TGGCGGCGTCTGGAAAGG 62.698 66.667 14.51 0.00 0.00 3.11
569 860 3.423154 GTGGCGGCGTCTGGAAAG 61.423 66.667 14.51 0.00 0.00 2.62
583 874 2.482333 TTTGGAAACGGCGTGGTGG 61.482 57.895 15.70 0.00 0.00 4.61
584 875 1.298788 GTTTGGAAACGGCGTGGTG 60.299 57.895 15.70 0.00 0.00 4.17
585 876 1.033202 AAGTTTGGAAACGGCGTGGT 61.033 50.000 15.70 4.32 43.51 4.16
586 877 0.317519 GAAGTTTGGAAACGGCGTGG 60.318 55.000 15.70 0.00 43.51 4.94
587 878 0.317519 GGAAGTTTGGAAACGGCGTG 60.318 55.000 15.70 0.00 43.51 5.34
588 879 0.748729 TGGAAGTTTGGAAACGGCGT 60.749 50.000 6.77 6.77 43.51 5.68
589 880 0.317519 GTGGAAGTTTGGAAACGGCG 60.318 55.000 4.80 4.80 43.51 6.46
590 881 1.029681 AGTGGAAGTTTGGAAACGGC 58.970 50.000 0.00 0.00 43.51 5.68
591 882 2.034179 GGAAGTGGAAGTTTGGAAACGG 59.966 50.000 0.00 0.00 43.51 4.44
592 883 2.034179 GGGAAGTGGAAGTTTGGAAACG 59.966 50.000 0.00 0.00 43.51 3.60
593 884 2.364324 GGGGAAGTGGAAGTTTGGAAAC 59.636 50.000 0.00 0.00 39.17 2.78
594 885 2.673258 GGGGAAGTGGAAGTTTGGAAA 58.327 47.619 0.00 0.00 0.00 3.13
595 886 1.133294 GGGGGAAGTGGAAGTTTGGAA 60.133 52.381 0.00 0.00 0.00 3.53
596 887 0.481128 GGGGGAAGTGGAAGTTTGGA 59.519 55.000 0.00 0.00 0.00 3.53
597 888 3.051617 GGGGGAAGTGGAAGTTTGG 57.948 57.895 0.00 0.00 0.00 3.28
612 903 0.673644 CGTGTTAGCTCACTTGGGGG 60.674 60.000 0.00 0.00 36.33 5.40
613 904 0.320374 TCGTGTTAGCTCACTTGGGG 59.680 55.000 0.00 0.00 36.33 4.96
614 905 2.163818 TTCGTGTTAGCTCACTTGGG 57.836 50.000 0.00 0.00 36.33 4.12
615 906 4.024048 ACAATTTCGTGTTAGCTCACTTGG 60.024 41.667 0.00 0.00 36.33 3.61
616 907 5.095691 ACAATTTCGTGTTAGCTCACTTG 57.904 39.130 0.00 0.00 36.33 3.16
617 908 6.854496 TTACAATTTCGTGTTAGCTCACTT 57.146 33.333 0.00 0.00 36.33 3.16
618 909 6.293244 GGTTTACAATTTCGTGTTAGCTCACT 60.293 38.462 0.00 0.00 36.33 3.41
619 910 5.849604 GGTTTACAATTTCGTGTTAGCTCAC 59.150 40.000 0.00 0.00 32.75 3.51
620 911 5.761234 AGGTTTACAATTTCGTGTTAGCTCA 59.239 36.000 0.00 0.00 32.75 4.26
621 912 6.237313 AGGTTTACAATTTCGTGTTAGCTC 57.763 37.500 0.00 0.00 32.75 4.09
622 913 7.733402 TTAGGTTTACAATTTCGTGTTAGCT 57.267 32.000 0.00 0.00 32.75 3.32
623 914 8.785468 TTTTAGGTTTACAATTTCGTGTTAGC 57.215 30.769 0.00 0.00 32.75 3.09
626 917 9.458374 CAGATTTTAGGTTTACAATTTCGTGTT 57.542 29.630 0.00 0.00 32.75 3.32
627 918 8.842280 TCAGATTTTAGGTTTACAATTTCGTGT 58.158 29.630 0.00 0.00 35.43 4.49
628 919 9.840427 ATCAGATTTTAGGTTTACAATTTCGTG 57.160 29.630 0.00 0.00 0.00 4.35
777 1068 6.656693 CCAGACCCTTGATGTAATATGGATTC 59.343 42.308 0.00 0.00 0.00 2.52
802 1093 1.980844 CTGCATCGTTCATTTGTGTGC 59.019 47.619 0.00 0.00 0.00 4.57
841 1132 2.100603 GACGAAGGAGGAGCGTCG 59.899 66.667 0.00 0.00 43.76 5.12
2184 2554 6.319141 GTTTGTAGAAACTTTGCTCCATCT 57.681 37.500 8.18 0.00 38.78 2.90


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

AutoCloner maintained by Alex Coulton.