Multiple sequence alignment - TraesCS6B01G141000

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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 TraesCS6B01G141000 chr6B 100.000 3302 0 0 1 3302 140452417 140449116 0.000000e+00 6098
1 TraesCS6B01G141000 chr6B 98.977 1857 9 4 1456 3302 140434372 140432516 0.000000e+00 3315
2 TraesCS6B01G141000 chr6B 98.921 1854 12 4 1456 3302 140413214 140411362 0.000000e+00 3306
3 TraesCS6B01G141000 chr6B 98.813 1854 15 3 1456 3302 140423851 140421998 0.000000e+00 3295
4 TraesCS6B01G141000 chr6B 85.511 842 101 11 997 1832 147961480 147962306 0.000000e+00 859
5 TraesCS6B01G141000 chr6B 84.824 850 105 8 983 1832 566537923 566537098 0.000000e+00 833
6 TraesCS6B01G141000 chr6B 80.970 536 95 7 1853 2386 147962399 147962929 5.100000e-113 418
7 TraesCS6B01G141000 chr6D 92.930 2065 112 19 647 2692 65390395 65388346 0.000000e+00 2974
8 TraesCS6B01G141000 chr6D 85.731 841 98 11 997 1832 73587990 73588813 0.000000e+00 869
9 TraesCS6B01G141000 chr6D 84.561 855 104 14 983 1832 379721447 379722278 0.000000e+00 822
10 TraesCS6B01G141000 chr6D 92.844 545 19 10 76 608 65390933 65390397 0.000000e+00 773
11 TraesCS6B01G141000 chr6D 82.753 574 88 10 1844 2411 73588891 73589459 4.920000e-138 501
12 TraesCS6B01G141000 chr6D 88.994 318 25 3 2994 3301 10706912 10706595 5.170000e-103 385
13 TraesCS6B01G141000 chr6A 92.563 2017 123 13 692 2692 83361859 83363864 0.000000e+00 2868
14 TraesCS6B01G141000 chr6A 85.047 856 107 12 983 1832 90032669 90033509 0.000000e+00 852
15 TraesCS6B01G141000 chr6A 84.642 853 107 8 983 1832 520872462 520871631 0.000000e+00 828
16 TraesCS6B01G141000 chrUn 98.690 840 2 3 2472 3302 398950424 398949585 0.000000e+00 1482
17 TraesCS6B01G141000 chrUn 87.789 303 23 10 3010 3302 2671951 2671653 3.160000e-90 342
18 TraesCS6B01G141000 chr5A 95.620 274 6 5 2694 2961 618474385 618474658 5.060000e-118 435
19 TraesCS6B01G141000 chr4A 95.620 274 6 5 2694 2961 716768677 716768404 5.060000e-118 435
20 TraesCS6B01G141000 chr4A 90.031 321 22 3 2992 3302 282085327 282085007 1.100000e-109 407
21 TraesCS6B01G141000 chr4B 94.982 279 8 5 2690 2962 658966493 658966215 1.820000e-117 433
22 TraesCS6B01G141000 chr2A 93.471 291 9 9 2692 2976 5434546 5434260 1.100000e-114 424
23 TraesCS6B01G141000 chr7A 94.286 280 9 6 2692 2965 416498685 416498963 3.940000e-114 422
24 TraesCS6B01G141000 chr7B 89.655 319 23 3 2992 3300 104010998 104010680 6.640000e-107 398
25 TraesCS6B01G141000 chr7D 89.028 319 25 3 2994 3302 4620770 4621088 1.440000e-103 387


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 TraesCS6B01G141000 chr6B 140449116 140452417 3301 True 6098.0 6098 100.0000 1 3302 1 chr6B.!!$R4 3301
1 TraesCS6B01G141000 chr6B 140432516 140434372 1856 True 3315.0 3315 98.9770 1456 3302 1 chr6B.!!$R3 1846
2 TraesCS6B01G141000 chr6B 140411362 140413214 1852 True 3306.0 3306 98.9210 1456 3302 1 chr6B.!!$R1 1846
3 TraesCS6B01G141000 chr6B 140421998 140423851 1853 True 3295.0 3295 98.8130 1456 3302 1 chr6B.!!$R2 1846
4 TraesCS6B01G141000 chr6B 566537098 566537923 825 True 833.0 833 84.8240 983 1832 1 chr6B.!!$R5 849
5 TraesCS6B01G141000 chr6B 147961480 147962929 1449 False 638.5 859 83.2405 997 2386 2 chr6B.!!$F1 1389
6 TraesCS6B01G141000 chr6D 65388346 65390933 2587 True 1873.5 2974 92.8870 76 2692 2 chr6D.!!$R2 2616
7 TraesCS6B01G141000 chr6D 379721447 379722278 831 False 822.0 822 84.5610 983 1832 1 chr6D.!!$F1 849
8 TraesCS6B01G141000 chr6D 73587990 73589459 1469 False 685.0 869 84.2420 997 2411 2 chr6D.!!$F2 1414
9 TraesCS6B01G141000 chr6A 83361859 83363864 2005 False 2868.0 2868 92.5630 692 2692 1 chr6A.!!$F1 2000
10 TraesCS6B01G141000 chr6A 90032669 90033509 840 False 852.0 852 85.0470 983 1832 1 chr6A.!!$F2 849
11 TraesCS6B01G141000 chr6A 520871631 520872462 831 True 828.0 828 84.6420 983 1832 1 chr6A.!!$R1 849
12 TraesCS6B01G141000 chrUn 398949585 398950424 839 True 1482.0 1482 98.6900 2472 3302 1 chrUn.!!$R2 830

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
136 137 0.255890 TGGGCATGAGCTAGGGTTTC 59.744 55.0 0.0 0.0 41.7 2.78 F
800 817 0.687354 TCTGACAAAGTGGAGGGCTC 59.313 55.0 0.0 0.0 0.0 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1183 1200 0.254747 TTATACTGCGCCCCAAGCTT 59.745 50.000 4.18 0.0 40.39 3.74 R
2624 2745 6.204495 GCAAGCATAATTTTGGAAAACAAGGA 59.796 34.615 0.00 0.0 40.82 3.36 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
26 27 2.185608 GCCTCCTGCTCGAGTTCC 59.814 66.667 15.13 0.00 36.87 3.62
27 28 2.896443 CCTCCTGCTCGAGTTCCC 59.104 66.667 15.13 0.00 0.00 3.97
28 29 2.726351 CCTCCTGCTCGAGTTCCCC 61.726 68.421 15.13 0.00 0.00 4.81
29 30 2.683933 TCCTGCTCGAGTTCCCCC 60.684 66.667 15.13 0.00 0.00 5.40
30 31 3.003173 CCTGCTCGAGTTCCCCCA 61.003 66.667 15.13 0.93 0.00 4.96
31 32 2.581354 CTGCTCGAGTTCCCCCAG 59.419 66.667 15.13 7.66 0.00 4.45
32 33 3.672295 CTGCTCGAGTTCCCCCAGC 62.672 68.421 15.13 0.00 0.00 4.85
33 34 4.475135 GCTCGAGTTCCCCCAGCC 62.475 72.222 15.13 0.00 0.00 4.85
34 35 4.148825 CTCGAGTTCCCCCAGCCG 62.149 72.222 3.62 0.00 0.00 5.52
52 53 3.534056 GCGCCGAAGCCCTAGGTA 61.534 66.667 8.29 0.00 34.57 3.08
53 54 3.085119 GCGCCGAAGCCCTAGGTAA 62.085 63.158 8.29 0.00 34.57 2.85
54 55 1.067582 CGCCGAAGCCCTAGGTAAG 59.932 63.158 8.29 0.00 34.57 2.34
55 56 1.673808 CGCCGAAGCCCTAGGTAAGT 61.674 60.000 8.29 0.00 34.57 2.24
56 57 1.406903 GCCGAAGCCCTAGGTAAGTA 58.593 55.000 8.29 0.00 0.00 2.24
57 58 1.758862 GCCGAAGCCCTAGGTAAGTAA 59.241 52.381 8.29 0.00 0.00 2.24
58 59 2.482664 GCCGAAGCCCTAGGTAAGTAAC 60.483 54.545 8.29 0.00 0.00 2.50
73 74 7.517343 GGTAAGTAACCTCGTTCTGTATTTC 57.483 40.000 0.00 0.00 45.75 2.17
74 75 6.533012 GGTAAGTAACCTCGTTCTGTATTTCC 59.467 42.308 0.00 0.00 45.75 3.13
136 137 0.255890 TGGGCATGAGCTAGGGTTTC 59.744 55.000 0.00 0.00 41.70 2.78
156 157 3.819368 TCGTTGGGTGTCCTCGTATATA 58.181 45.455 0.00 0.00 34.64 0.86
161 162 6.183360 CGTTGGGTGTCCTCGTATATATAGAG 60.183 46.154 9.83 9.83 0.00 2.43
162 163 6.631763 TGGGTGTCCTCGTATATATAGAGA 57.368 41.667 15.59 8.39 34.13 3.10
163 164 6.651086 TGGGTGTCCTCGTATATATAGAGAG 58.349 44.000 15.59 14.71 34.13 3.20
194 195 5.963140 TCTTAGTATCGTCGACTACTGTG 57.037 43.478 21.52 15.33 30.98 3.66
200 201 2.216046 TCGTCGACTACTGTGTCTGTT 58.784 47.619 14.70 0.00 35.00 3.16
271 272 2.380084 TTGATCTCCACGGTTGTAGC 57.620 50.000 0.00 0.00 0.00 3.58
311 312 5.116680 GCGTTCGTAGCGTATATTTGATTCT 59.883 40.000 0.00 0.00 0.00 2.40
313 314 6.141844 CGTTCGTAGCGTATATTTGATTCTGT 59.858 38.462 0.00 0.00 0.00 3.41
446 457 3.368948 GGGACCTAGAGCAGAAGTGAAAG 60.369 52.174 0.00 0.00 0.00 2.62
447 458 3.368948 GGACCTAGAGCAGAAGTGAAAGG 60.369 52.174 0.00 0.00 0.00 3.11
504 517 1.062525 GATGAACATGCGGCCGTTC 59.937 57.895 28.70 21.94 41.53 3.95
512 525 4.025401 GCGGCCGTTCTGTGTTGG 62.025 66.667 28.70 0.00 0.00 3.77
525 538 1.001487 TGTGTTGGATTTGCTTCTGCG 60.001 47.619 0.00 0.00 43.34 5.18
557 570 3.799286 TTGCACGGAACCATGCCCA 62.799 57.895 9.34 0.00 41.33 5.36
592 605 9.905713 TTCTAGGCACTATCTGATTTTGTTTAT 57.094 29.630 0.00 0.00 41.70 1.40
604 617 7.717436 TCTGATTTTGTTTATACAGTCCACACA 59.283 33.333 0.00 0.00 35.28 3.72
605 618 8.402798 TGATTTTGTTTATACAGTCCACACAT 57.597 30.769 0.00 0.00 35.28 3.21
606 619 8.296000 TGATTTTGTTTATACAGTCCACACATG 58.704 33.333 0.00 0.00 35.28 3.21
607 620 7.575414 TTTTGTTTATACAGTCCACACATGT 57.425 32.000 0.00 0.00 35.28 3.21
608 621 7.575414 TTTGTTTATACAGTCCACACATGTT 57.425 32.000 0.00 0.00 35.28 2.71
609 622 6.795098 TGTTTATACAGTCCACACATGTTC 57.205 37.500 0.00 0.00 0.00 3.18
610 623 6.530120 TGTTTATACAGTCCACACATGTTCT 58.470 36.000 0.00 0.00 0.00 3.01
611 624 7.672240 TGTTTATACAGTCCACACATGTTCTA 58.328 34.615 0.00 0.00 0.00 2.10
612 625 8.318412 TGTTTATACAGTCCACACATGTTCTAT 58.682 33.333 0.00 0.00 0.00 1.98
613 626 9.162764 GTTTATACAGTCCACACATGTTCTATT 57.837 33.333 0.00 0.00 0.00 1.73
614 627 9.733556 TTTATACAGTCCACACATGTTCTATTT 57.266 29.630 0.00 0.00 0.00 1.40
615 628 5.947228 ACAGTCCACACATGTTCTATTTG 57.053 39.130 0.00 0.00 0.00 2.32
616 629 4.761739 ACAGTCCACACATGTTCTATTTGG 59.238 41.667 0.00 0.00 0.00 3.28
617 630 5.003160 CAGTCCACACATGTTCTATTTGGA 58.997 41.667 0.00 0.00 0.00 3.53
618 631 5.473162 CAGTCCACACATGTTCTATTTGGAA 59.527 40.000 0.00 0.00 33.53 3.53
619 632 6.151648 CAGTCCACACATGTTCTATTTGGAAT 59.848 38.462 0.00 0.00 33.53 3.01
620 633 6.151648 AGTCCACACATGTTCTATTTGGAATG 59.848 38.462 0.00 0.00 33.53 2.67
621 634 6.009589 TCCACACATGTTCTATTTGGAATGT 58.990 36.000 0.00 0.00 0.00 2.71
622 635 6.493115 TCCACACATGTTCTATTTGGAATGTT 59.507 34.615 0.00 0.00 0.00 2.71
623 636 6.587226 CCACACATGTTCTATTTGGAATGTTG 59.413 38.462 0.00 0.00 0.00 3.33
624 637 7.369607 CACACATGTTCTATTTGGAATGTTGA 58.630 34.615 0.00 0.00 0.00 3.18
625 638 8.030692 CACACATGTTCTATTTGGAATGTTGAT 58.969 33.333 0.00 0.00 0.00 2.57
626 639 8.587608 ACACATGTTCTATTTGGAATGTTGATT 58.412 29.630 0.00 0.00 0.00 2.57
627 640 8.865978 CACATGTTCTATTTGGAATGTTGATTG 58.134 33.333 0.00 0.00 0.00 2.67
628 641 7.546667 ACATGTTCTATTTGGAATGTTGATTGC 59.453 33.333 0.00 0.00 0.00 3.56
629 642 6.397272 TGTTCTATTTGGAATGTTGATTGCC 58.603 36.000 0.00 0.00 0.00 4.52
630 643 6.014755 TGTTCTATTTGGAATGTTGATTGCCA 60.015 34.615 0.00 0.00 0.00 4.92
631 644 6.795144 TCTATTTGGAATGTTGATTGCCAT 57.205 33.333 0.00 0.00 0.00 4.40
632 645 7.894753 TCTATTTGGAATGTTGATTGCCATA 57.105 32.000 0.00 0.00 0.00 2.74
633 646 8.481492 TCTATTTGGAATGTTGATTGCCATAT 57.519 30.769 0.00 0.00 0.00 1.78
634 647 8.361889 TCTATTTGGAATGTTGATTGCCATATG 58.638 33.333 0.00 0.00 0.00 1.78
635 648 4.940905 TGGAATGTTGATTGCCATATGG 57.059 40.909 18.07 18.07 38.53 2.74
636 649 4.544683 TGGAATGTTGATTGCCATATGGA 58.455 39.130 26.47 5.69 37.39 3.41
637 650 5.149239 TGGAATGTTGATTGCCATATGGAT 58.851 37.500 26.47 10.89 37.39 3.41
638 651 5.603395 TGGAATGTTGATTGCCATATGGATT 59.397 36.000 26.47 12.80 37.39 3.01
639 652 5.929992 GGAATGTTGATTGCCATATGGATTG 59.070 40.000 26.47 0.00 37.39 2.67
640 653 6.239373 GGAATGTTGATTGCCATATGGATTGA 60.239 38.462 26.47 7.54 37.39 2.57
641 654 6.928348 ATGTTGATTGCCATATGGATTGAT 57.072 33.333 26.47 11.95 37.39 2.57
642 655 8.425237 AATGTTGATTGCCATATGGATTGATA 57.575 30.769 26.47 3.54 37.39 2.15
643 656 8.603898 ATGTTGATTGCCATATGGATTGATAT 57.396 30.769 26.47 7.98 37.39 1.63
644 657 8.425237 TGTTGATTGCCATATGGATTGATATT 57.575 30.769 26.47 0.26 37.39 1.28
645 658 8.308207 TGTTGATTGCCATATGGATTGATATTG 58.692 33.333 26.47 0.00 37.39 1.90
671 684 2.089980 CTCTGTTCCCTTTCTGGCATG 58.910 52.381 0.00 0.00 0.00 4.06
678 691 4.090761 TCCCTTTCTGGCATGATGATAC 57.909 45.455 0.00 0.00 0.00 2.24
685 698 2.371179 CTGGCATGATGATACACCTCCT 59.629 50.000 0.00 0.00 0.00 3.69
691 704 3.311990 TGATGATACACCTCCTGCTGAT 58.688 45.455 0.00 0.00 0.00 2.90
693 706 4.164796 TGATGATACACCTCCTGCTGATTT 59.835 41.667 0.00 0.00 0.00 2.17
717 734 6.647334 TTTTGTCAATCTTGCCTTGTATGA 57.353 33.333 0.00 0.00 0.00 2.15
754 771 6.591062 TGCATGATCTTTGGCTTGTTTAAATC 59.409 34.615 0.00 0.00 0.00 2.17
760 777 5.365314 TCTTTGGCTTGTTTAAATCCAGGTT 59.635 36.000 0.00 0.00 0.00 3.50
768 785 6.418057 TGTTTAAATCCAGGTTGCAGAATT 57.582 33.333 0.00 0.00 0.00 2.17
800 817 0.687354 TCTGACAAAGTGGAGGGCTC 59.313 55.000 0.00 0.00 0.00 4.70
831 848 5.278169 CCAAGTTTCTTTCATGTCTGGACAG 60.278 44.000 9.33 0.00 45.48 3.51
877 894 1.480954 GATTGCCGGGAGAGTGTTCTA 59.519 52.381 2.18 0.00 32.53 2.10
883 900 3.288964 CCGGGAGAGTGTTCTAGTACAT 58.711 50.000 5.42 0.00 32.53 2.29
901 918 7.184067 AGTACATCGAGAAAAAGGGATAAGT 57.816 36.000 0.00 0.00 0.00 2.24
1077 1094 3.196254 AGATGCCCAAAATGCTAACCAAG 59.804 43.478 0.00 0.00 0.00 3.61
1134 1151 2.222796 CGTGAACATGGTTGACATAGCG 60.223 50.000 0.00 0.00 37.84 4.26
1177 1194 7.225931 CAGCTTCCTACACAACAAAGTACTTTA 59.774 37.037 20.15 2.75 0.00 1.85
1182 1199 5.169836 ACACAACAAAGTACTTTAGCTGC 57.830 39.130 20.15 0.00 0.00 5.25
1183 1200 4.638421 ACACAACAAAGTACTTTAGCTGCA 59.362 37.500 20.15 0.00 0.00 4.41
1302 1319 5.611796 TCATCAACAAGTATGTTCAGTGC 57.388 39.130 0.00 0.00 46.78 4.40
1341 1358 3.653344 TGAAACAGAGGTTGTCATCTCG 58.347 45.455 0.00 0.00 39.73 4.04
1342 1359 2.751166 AACAGAGGTTGTCATCTCGG 57.249 50.000 0.00 0.00 39.73 4.63
1356 1373 0.241213 TCTCGGAGAAACAGACGCTG 59.759 55.000 4.96 5.47 34.09 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.185608 GGAACTCGAGCAGGAGGC 59.814 66.667 13.61 0.00 45.30 4.70
10 11 2.726351 GGGGAACTCGAGCAGGAGG 61.726 68.421 13.61 0.00 38.39 4.30
11 12 2.726351 GGGGGAACTCGAGCAGGAG 61.726 68.421 13.61 2.80 39.97 3.69
12 13 2.683933 GGGGGAACTCGAGCAGGA 60.684 66.667 13.61 0.00 0.00 3.86
13 14 3.003173 TGGGGGAACTCGAGCAGG 61.003 66.667 13.61 0.00 0.00 4.85
14 15 2.581354 CTGGGGGAACTCGAGCAG 59.419 66.667 13.61 6.72 0.00 4.24
15 16 3.706373 GCTGGGGGAACTCGAGCA 61.706 66.667 13.61 0.00 35.74 4.26
16 17 4.475135 GGCTGGGGGAACTCGAGC 62.475 72.222 13.61 0.00 35.17 5.03
17 18 4.148825 CGGCTGGGGGAACTCGAG 62.149 72.222 11.84 11.84 0.00 4.04
36 37 1.067582 CTTACCTAGGGCTTCGGCG 59.932 63.158 14.81 0.00 42.91 6.46
37 38 1.406903 TACTTACCTAGGGCTTCGGC 58.593 55.000 14.81 0.00 40.88 5.54
38 39 2.102084 GGTTACTTACCTAGGGCTTCGG 59.898 54.545 14.81 0.00 44.10 4.30
39 40 3.449528 GGTTACTTACCTAGGGCTTCG 57.550 52.381 14.81 0.00 44.10 3.79
50 51 7.318893 AGGAAATACAGAACGAGGTTACTTAC 58.681 38.462 0.00 0.00 0.00 2.34
51 52 7.472334 AGGAAATACAGAACGAGGTTACTTA 57.528 36.000 0.00 0.00 0.00 2.24
52 53 6.356186 AGGAAATACAGAACGAGGTTACTT 57.644 37.500 0.00 0.00 0.00 2.24
53 54 5.997384 AGGAAATACAGAACGAGGTTACT 57.003 39.130 0.00 0.00 0.00 2.24
54 55 7.430992 AAAAGGAAATACAGAACGAGGTTAC 57.569 36.000 0.00 0.00 0.00 2.50
56 57 6.954487 AAAAAGGAAATACAGAACGAGGTT 57.046 33.333 0.00 0.00 0.00 3.50
90 91 5.163764 CCACAGCAACAATCGCTAGATTTAA 60.164 40.000 0.00 0.00 44.11 1.52
91 92 4.332543 CCACAGCAACAATCGCTAGATTTA 59.667 41.667 0.00 0.00 44.11 1.40
92 93 3.127548 CCACAGCAACAATCGCTAGATTT 59.872 43.478 0.00 0.00 44.11 2.17
94 95 2.093500 TCCACAGCAACAATCGCTAGAT 60.093 45.455 0.00 0.00 37.72 1.98
95 96 1.275010 TCCACAGCAACAATCGCTAGA 59.725 47.619 0.00 0.00 37.72 2.43
96 97 1.394917 GTCCACAGCAACAATCGCTAG 59.605 52.381 0.00 0.00 37.72 3.42
136 137 4.778534 ATATATACGAGGACACCCAACG 57.221 45.455 0.00 0.00 39.24 4.10
170 171 6.538021 ACACAGTAGTCGACGATACTAAGATT 59.462 38.462 14.94 0.00 31.48 2.40
194 195 0.681733 TCAGGTCCAGCTCAACAGAC 59.318 55.000 0.00 0.00 0.00 3.51
271 272 2.176273 CGCTGAATCGCTTCCAGGG 61.176 63.158 0.00 0.00 0.00 4.45
311 312 5.527951 CAATAAACCAAAACTAGCAGCACA 58.472 37.500 0.00 0.00 0.00 4.57
313 314 4.280677 AGCAATAAACCAAAACTAGCAGCA 59.719 37.500 0.00 0.00 0.00 4.41
353 354 6.942532 ATGCGTGGACTGAACAATATTTAT 57.057 33.333 0.00 0.00 0.00 1.40
434 445 1.312815 ACTGCACCTTTCACTTCTGC 58.687 50.000 0.00 0.00 0.00 4.26
436 447 3.763897 ACAAAACTGCACCTTTCACTTCT 59.236 39.130 0.00 0.00 0.00 2.85
446 457 1.748493 TGGACTGAACAAAACTGCACC 59.252 47.619 0.00 0.00 0.00 5.01
447 458 3.502191 TTGGACTGAACAAAACTGCAC 57.498 42.857 0.00 0.00 0.00 4.57
504 517 2.669364 GCAGAAGCAAATCCAACACAG 58.331 47.619 0.00 0.00 41.58 3.66
512 525 1.578618 CGCGACGCAGAAGCAAATC 60.579 57.895 21.35 0.00 42.27 2.17
525 538 0.708918 GTGCAAACTAGAGACGCGAC 59.291 55.000 15.93 6.86 0.00 5.19
592 605 5.937540 CCAAATAGAACATGTGTGGACTGTA 59.062 40.000 0.00 0.00 0.00 2.74
604 617 7.043565 GGCAATCAACATTCCAAATAGAACAT 58.956 34.615 0.00 0.00 0.00 2.71
605 618 6.014755 TGGCAATCAACATTCCAAATAGAACA 60.015 34.615 0.00 0.00 0.00 3.18
606 619 6.397272 TGGCAATCAACATTCCAAATAGAAC 58.603 36.000 0.00 0.00 0.00 3.01
607 620 6.602410 TGGCAATCAACATTCCAAATAGAA 57.398 33.333 0.00 0.00 0.00 2.10
608 621 6.795144 ATGGCAATCAACATTCCAAATAGA 57.205 33.333 0.00 0.00 0.00 1.98
609 622 7.601130 CCATATGGCAATCAACATTCCAAATAG 59.399 37.037 9.29 0.00 0.00 1.73
610 623 7.289549 TCCATATGGCAATCAACATTCCAAATA 59.710 33.333 17.58 0.00 34.44 1.40
611 624 6.099990 TCCATATGGCAATCAACATTCCAAAT 59.900 34.615 17.58 0.00 34.44 2.32
612 625 5.424573 TCCATATGGCAATCAACATTCCAAA 59.575 36.000 17.58 0.00 34.44 3.28
613 626 4.961099 TCCATATGGCAATCAACATTCCAA 59.039 37.500 17.58 0.00 34.44 3.53
614 627 4.544683 TCCATATGGCAATCAACATTCCA 58.455 39.130 17.58 0.00 34.44 3.53
615 628 5.733620 ATCCATATGGCAATCAACATTCC 57.266 39.130 17.58 0.00 34.44 3.01
616 629 6.751157 TCAATCCATATGGCAATCAACATTC 58.249 36.000 17.58 0.00 34.44 2.67
617 630 6.734502 TCAATCCATATGGCAATCAACATT 57.265 33.333 17.58 6.08 34.44 2.71
618 631 6.928348 ATCAATCCATATGGCAATCAACAT 57.072 33.333 17.58 0.00 34.44 2.71
619 632 8.308207 CAATATCAATCCATATGGCAATCAACA 58.692 33.333 17.58 0.00 34.44 3.33
620 633 8.308931 ACAATATCAATCCATATGGCAATCAAC 58.691 33.333 17.58 0.00 34.44 3.18
621 634 8.425237 ACAATATCAATCCATATGGCAATCAA 57.575 30.769 17.58 0.00 34.44 2.57
622 635 9.531158 TTACAATATCAATCCATATGGCAATCA 57.469 29.630 17.58 0.00 34.44 2.57
625 638 8.970020 GGATTACAATATCAATCCATATGGCAA 58.030 33.333 17.58 0.61 46.37 4.52
626 639 8.523915 GGATTACAATATCAATCCATATGGCA 57.476 34.615 17.58 6.61 46.37 4.92
635 648 8.160106 AGGGAACAGAGGATTACAATATCAATC 58.840 37.037 0.00 0.00 0.00 2.67
636 649 8.050316 AGGGAACAGAGGATTACAATATCAAT 57.950 34.615 0.00 0.00 0.00 2.57
637 650 7.451731 AGGGAACAGAGGATTACAATATCAA 57.548 36.000 0.00 0.00 0.00 2.57
638 651 7.451731 AAGGGAACAGAGGATTACAATATCA 57.548 36.000 0.00 0.00 0.00 2.15
639 652 8.214364 AGAAAGGGAACAGAGGATTACAATATC 58.786 37.037 0.00 0.00 0.00 1.63
640 653 7.995488 CAGAAAGGGAACAGAGGATTACAATAT 59.005 37.037 0.00 0.00 0.00 1.28
641 654 7.338710 CAGAAAGGGAACAGAGGATTACAATA 58.661 38.462 0.00 0.00 0.00 1.90
642 655 6.183347 CAGAAAGGGAACAGAGGATTACAAT 58.817 40.000 0.00 0.00 0.00 2.71
643 656 5.514834 CCAGAAAGGGAACAGAGGATTACAA 60.515 44.000 0.00 0.00 0.00 2.41
644 657 4.019321 CCAGAAAGGGAACAGAGGATTACA 60.019 45.833 0.00 0.00 0.00 2.41
645 658 4.518249 CCAGAAAGGGAACAGAGGATTAC 58.482 47.826 0.00 0.00 0.00 1.89
671 684 4.348863 AATCAGCAGGAGGTGTATCATC 57.651 45.455 0.00 0.00 43.57 2.92
693 706 7.048629 TCATACAAGGCAAGATTGACAAAAA 57.951 32.000 0.47 0.00 39.18 1.94
698 715 6.500684 TTCTTCATACAAGGCAAGATTGAC 57.499 37.500 0.00 0.00 36.08 3.18
717 734 6.436261 CAAAGATCATGCATTAGCGATTCTT 58.564 36.000 0.00 0.90 46.23 2.52
754 771 3.062042 GCAAAGAAATTCTGCAACCTGG 58.938 45.455 0.00 0.00 36.09 4.45
760 777 6.207221 TCAGATTGTAGCAAAGAAATTCTGCA 59.793 34.615 9.39 0.00 38.58 4.41
768 785 6.238731 CCACTTTGTCAGATTGTAGCAAAGAA 60.239 38.462 18.29 0.00 44.97 2.52
800 817 4.275936 ACATGAAAGAAACTTGGACTTCCG 59.724 41.667 0.00 0.00 39.43 4.30
831 848 0.382515 ATCCGAAGTAGAGCGAGTGC 59.617 55.000 0.00 0.00 43.24 4.40
877 894 7.184067 ACTTATCCCTTTTTCTCGATGTACT 57.816 36.000 0.00 0.00 0.00 2.73
901 918 1.774254 TGGCAAGTGAGGGAAGAGAAA 59.226 47.619 0.00 0.00 0.00 2.52
1134 1151 2.151049 CTGGCCTGGCAAGTGCTTTC 62.151 60.000 22.05 0.00 41.70 2.62
1182 1199 0.463654 TATACTGCGCCCCAAGCTTG 60.464 55.000 19.93 19.93 40.39 4.01
1183 1200 0.254747 TTATACTGCGCCCCAAGCTT 59.745 50.000 4.18 0.00 40.39 3.74
1194 1211 7.912250 CCTGTCTTGTCATCAAATTTATACTGC 59.088 37.037 0.00 0.00 32.87 4.40
1199 1216 8.641498 AACTCCTGTCTTGTCATCAAATTTAT 57.359 30.769 0.00 0.00 32.87 1.40
1302 1319 3.627395 TCAGGGTTGCCACACTTATAG 57.373 47.619 0.00 0.00 32.56 1.31
1341 1358 1.704070 GAGACAGCGTCTGTTTCTCC 58.296 55.000 14.47 5.77 45.44 3.71
1356 1373 1.467734 CAGGCAGCACATTTCAGAGAC 59.532 52.381 0.00 0.00 0.00 3.36
2623 2744 7.255070 GCAAGCATAATTTTGGAAAACAAGGAA 60.255 33.333 0.00 0.00 40.82 3.36
2624 2745 6.204495 GCAAGCATAATTTTGGAAAACAAGGA 59.796 34.615 0.00 0.00 40.82 3.36


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

AutoCloner maintained by Alex Coulton.