Multiple sequence alignment - TraesCS3B01G466700

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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 TraesCS3B01G466700 chr3B 100.000 2111 0 0 1 2111 709268639 709270749 0.000000e+00 3899.0
1 TraesCS3B01G466700 chr3B 93.991 699 25 8 642 1335 709075036 709075722 0.000000e+00 1042.0
2 TraesCS3B01G466700 chr3B 94.833 658 20 6 687 1335 708954408 708955060 0.000000e+00 1014.0
3 TraesCS3B01G466700 chr3B 93.207 633 20 7 1 625 709074450 709075067 0.000000e+00 909.0
4 TraesCS3B01G466700 chr3B 94.521 584 23 3 1 575 708953800 708954383 0.000000e+00 893.0
5 TraesCS3B01G466700 chr3B 86.391 338 22 8 258 579 790629958 790630287 4.310000e-92 348.0
6 TraesCS3B01G466700 chr3B 100.000 52 0 0 642 693 709269232 709269283 1.720000e-16 97.1
7 TraesCS3B01G466700 chr3B 100.000 52 0 0 594 645 709269280 709269331 1.720000e-16 97.1
8 TraesCS3B01G466700 chr3D 91.576 641 43 6 720 1352 536880594 536881231 0.000000e+00 874.0
9 TraesCS3B01G466700 chr3D 88.920 704 63 10 643 1335 536590010 536590709 0.000000e+00 854.0
10 TraesCS3B01G466700 chr3D 88.826 707 62 12 642 1335 536668375 536669077 0.000000e+00 852.0
11 TraesCS3B01G466700 chr3D 88.794 705 64 10 642 1335 536511793 536512493 0.000000e+00 850.0
12 TraesCS3B01G466700 chr3D 90.502 558 28 9 11 559 536439157 536439698 0.000000e+00 713.0
13 TraesCS3B01G466700 chr3D 87.776 589 46 9 11 579 536787402 536787984 0.000000e+00 665.0
14 TraesCS3B01G466700 chr3D 87.900 562 38 15 11 559 536879635 536880179 2.950000e-178 634.0
15 TraesCS3B01G466700 chr3D 86.995 569 36 14 11 559 536589122 536589672 6.440000e-170 606.0
16 TraesCS3B01G466700 chr3D 86.772 567 39 14 11 559 536667476 536668024 1.080000e-167 599.0
17 TraesCS3B01G466700 chr3D 86.286 525 36 11 1588 2111 536881646 536882135 2.380000e-149 538.0
18 TraesCS3B01G466700 chr3D 95.575 113 3 1 1474 1586 536881374 536881484 1.660000e-41 180.0
19 TraesCS3B01G466700 chrUn 89.362 705 60 10 642 1335 404927266 404926566 0.000000e+00 872.0
20 TraesCS3B01G466700 chrUn 89.124 708 61 11 639 1335 466163942 466164644 0.000000e+00 867.0
21 TraesCS3B01G466700 chrUn 89.078 705 62 10 642 1335 359852248 359852948 0.000000e+00 861.0
22 TraesCS3B01G466700 chrUn 89.632 299 14 5 274 559 359851617 359851911 4.280000e-97 364.0
23 TraesCS3B01G466700 chrUn 89.632 299 14 5 274 559 404927897 404927603 4.280000e-97 364.0
24 TraesCS3B01G466700 chr3A 89.869 612 43 11 1503 2111 672089458 672090053 0.000000e+00 769.0
25 TraesCS3B01G466700 chr3A 88.468 607 43 21 863 1445 672088853 672089456 0.000000e+00 708.0
26 TraesCS3B01G466700 chr3A 90.558 466 31 5 10 468 672088317 672088776 2.320000e-169 604.0
27 TraesCS3B01G466700 chr3A 84.703 438 39 11 1503 1931 672092575 672092993 1.510000e-111 412.0
28 TraesCS3B01G466700 chr3A 82.589 224 26 9 1228 1445 672092357 672092573 3.580000e-43 185.0
29 TraesCS3B01G466700 chr7B 86.391 338 22 9 258 579 500217390 500217719 4.310000e-92 348.0
30 TraesCS3B01G466700 chr5B 87.037 324 18 8 258 565 233905312 233904997 5.580000e-91 344.0


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 TraesCS3B01G466700 chr3B 709268639 709270749 2110 False 1364.4 3899 100.00000 1 2111 3 chr3B.!!$F4 2110
1 TraesCS3B01G466700 chr3B 709074450 709075722 1272 False 975.5 1042 93.59900 1 1335 2 chr3B.!!$F3 1334
2 TraesCS3B01G466700 chr3B 708953800 708955060 1260 False 953.5 1014 94.67700 1 1335 2 chr3B.!!$F2 1334
3 TraesCS3B01G466700 chr3D 536511793 536512493 700 False 850.0 850 88.79400 642 1335 1 chr3D.!!$F2 693
4 TraesCS3B01G466700 chr3D 536589122 536590709 1587 False 730.0 854 87.95750 11 1335 2 chr3D.!!$F4 1324
5 TraesCS3B01G466700 chr3D 536667476 536669077 1601 False 725.5 852 87.79900 11 1335 2 chr3D.!!$F5 1324
6 TraesCS3B01G466700 chr3D 536439157 536439698 541 False 713.0 713 90.50200 11 559 1 chr3D.!!$F1 548
7 TraesCS3B01G466700 chr3D 536787402 536787984 582 False 665.0 665 87.77600 11 579 1 chr3D.!!$F3 568
8 TraesCS3B01G466700 chr3D 536879635 536882135 2500 False 556.5 874 90.33425 11 2111 4 chr3D.!!$F6 2100
9 TraesCS3B01G466700 chrUn 466163942 466164644 702 False 867.0 867 89.12400 639 1335 1 chrUn.!!$F1 696
10 TraesCS3B01G466700 chrUn 404926566 404927897 1331 True 618.0 872 89.49700 274 1335 2 chrUn.!!$R1 1061
11 TraesCS3B01G466700 chrUn 359851617 359852948 1331 False 612.5 861 89.35500 274 1335 2 chrUn.!!$F2 1061
12 TraesCS3B01G466700 chr3A 672088317 672092993 4676 False 535.6 769 87.23740 10 2111 5 chr3A.!!$F1 2101

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
584 632 0.326264 GCCATGACACAGGAAGGACT 59.674 55.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1468 4996 0.898326 AAAATTCACACGGGCCTCCC 60.898 55.0 0.84 0.0 41.09 4.3 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
114 123 8.668510 ACAGCTAAGGTATCTTTTGATATGTG 57.331 34.615 0.00 0.00 42.66 3.21
173 185 0.807496 GATCAACTGTTGGCCTGCTC 59.193 55.000 19.55 4.98 0.00 4.26
204 216 4.164294 GACTTGTTAGTAGTGGTAGCACG 58.836 47.826 18.73 4.55 33.84 5.34
276 288 4.431416 ACAAACTGACTATGGTGTGGAA 57.569 40.909 0.00 0.00 0.00 3.53
372 406 5.119694 GGTGGAGATTGTGGAGAAGTAATC 58.880 45.833 0.00 0.00 0.00 1.75
475 509 4.729868 AGATTAAAAGTCCCACACTGCTT 58.270 39.130 0.00 0.00 34.56 3.91
575 623 2.977456 GGTGTGCGCCATGACACA 60.977 61.111 24.55 10.94 43.61 3.72
579 627 1.965930 GTGCGCCATGACACAGGAA 60.966 57.895 4.18 0.00 36.77 3.36
580 628 1.672030 TGCGCCATGACACAGGAAG 60.672 57.895 4.18 0.00 0.00 3.46
581 629 2.401766 GCGCCATGACACAGGAAGG 61.402 63.158 0.00 0.00 0.00 3.46
583 631 1.021390 CGCCATGACACAGGAAGGAC 61.021 60.000 0.00 0.00 0.00 3.85
584 632 0.326264 GCCATGACACAGGAAGGACT 59.674 55.000 0.00 0.00 0.00 3.85
585 633 1.271597 GCCATGACACAGGAAGGACTT 60.272 52.381 0.00 0.00 0.00 3.01
586 634 2.815589 GCCATGACACAGGAAGGACTTT 60.816 50.000 0.00 0.00 0.00 2.66
587 635 3.490348 CCATGACACAGGAAGGACTTTT 58.510 45.455 0.00 0.00 0.00 2.27
589 637 3.644966 TGACACAGGAAGGACTTTTGT 57.355 42.857 0.00 0.00 0.00 2.83
590 638 3.278574 TGACACAGGAAGGACTTTTGTG 58.721 45.455 19.86 19.86 40.77 3.33
591 639 3.054728 TGACACAGGAAGGACTTTTGTGA 60.055 43.478 24.55 10.42 39.06 3.58
592 640 4.137543 GACACAGGAAGGACTTTTGTGAT 58.862 43.478 24.55 15.04 39.06 3.06
593 641 4.536765 ACACAGGAAGGACTTTTGTGATT 58.463 39.130 24.55 10.42 39.06 2.57
594 642 5.690865 ACACAGGAAGGACTTTTGTGATTA 58.309 37.500 24.55 0.00 39.06 1.75
595 643 6.306987 ACACAGGAAGGACTTTTGTGATTAT 58.693 36.000 24.55 9.71 39.06 1.28
596 644 7.458397 ACACAGGAAGGACTTTTGTGATTATA 58.542 34.615 24.55 0.00 39.06 0.98
612 744 8.621532 TGTGATTATAAACAGAAGAACAAGCT 57.378 30.769 0.00 0.00 0.00 3.74
613 745 9.719355 TGTGATTATAAACAGAAGAACAAGCTA 57.281 29.630 0.00 0.00 0.00 3.32
615 747 8.883731 TGATTATAAACAGAAGAACAAGCTAGC 58.116 33.333 6.62 6.62 0.00 3.42
616 748 7.611213 TTATAAACAGAAGAACAAGCTAGCC 57.389 36.000 12.13 0.00 0.00 3.93
617 749 3.778954 AACAGAAGAACAAGCTAGCCT 57.221 42.857 12.13 0.00 0.00 4.58
618 750 3.051081 ACAGAAGAACAAGCTAGCCTG 57.949 47.619 12.13 12.00 0.00 4.85
619 751 1.736681 CAGAAGAACAAGCTAGCCTGC 59.263 52.381 13.36 0.41 0.00 4.85
620 752 1.090728 GAAGAACAAGCTAGCCTGCC 58.909 55.000 13.36 5.80 0.00 4.85
622 754 0.401738 AGAACAAGCTAGCCTGCCAA 59.598 50.000 13.36 0.00 0.00 4.52
623 755 1.202927 AGAACAAGCTAGCCTGCCAAA 60.203 47.619 13.36 0.00 0.00 3.28
624 756 1.821136 GAACAAGCTAGCCTGCCAAAT 59.179 47.619 13.36 0.00 0.00 2.32
625 757 1.467920 ACAAGCTAGCCTGCCAAATC 58.532 50.000 13.36 0.00 0.00 2.17
626 758 1.005215 ACAAGCTAGCCTGCCAAATCT 59.995 47.619 13.36 0.00 0.00 2.40
627 759 1.404391 CAAGCTAGCCTGCCAAATCTG 59.596 52.381 12.13 0.00 0.00 2.90
628 760 0.914644 AGCTAGCCTGCCAAATCTGA 59.085 50.000 12.13 0.00 0.00 3.27
629 761 1.283029 AGCTAGCCTGCCAAATCTGAA 59.717 47.619 12.13 0.00 0.00 3.02
630 762 1.403323 GCTAGCCTGCCAAATCTGAAC 59.597 52.381 2.29 0.00 0.00 3.18
631 763 2.019984 CTAGCCTGCCAAATCTGAACC 58.980 52.381 0.00 0.00 0.00 3.62
632 764 0.407139 AGCCTGCCAAATCTGAACCT 59.593 50.000 0.00 0.00 0.00 3.50
633 765 1.203100 AGCCTGCCAAATCTGAACCTT 60.203 47.619 0.00 0.00 0.00 3.50
635 767 3.026694 GCCTGCCAAATCTGAACCTTAT 58.973 45.455 0.00 0.00 0.00 1.73
636 768 4.079787 AGCCTGCCAAATCTGAACCTTATA 60.080 41.667 0.00 0.00 0.00 0.98
637 769 4.829492 GCCTGCCAAATCTGAACCTTATAT 59.171 41.667 0.00 0.00 0.00 0.86
638 770 6.003950 GCCTGCCAAATCTGAACCTTATATA 58.996 40.000 0.00 0.00 0.00 0.86
639 771 6.660949 GCCTGCCAAATCTGAACCTTATATAT 59.339 38.462 0.00 0.00 0.00 0.86
640 772 7.829211 GCCTGCCAAATCTGAACCTTATATATA 59.171 37.037 0.00 0.00 0.00 0.86
685 992 4.829492 GCCTGCCAAATCTGAACCTTATAT 59.171 41.667 0.00 0.00 0.00 0.86
686 993 6.003950 GCCTGCCAAATCTGAACCTTATATA 58.996 40.000 0.00 0.00 0.00 0.86
687 994 6.660949 GCCTGCCAAATCTGAACCTTATATAT 59.339 38.462 0.00 0.00 0.00 0.86
688 995 7.829211 GCCTGCCAAATCTGAACCTTATATATA 59.171 37.037 0.00 0.00 0.00 0.86
818 1146 4.278170 CCTAGAAGCTCTCATGGACTGTAG 59.722 50.000 0.00 0.00 0.00 2.74
860 1193 3.321039 TGCATATCTCCAGAGGGTCAAT 58.679 45.455 0.00 0.00 34.93 2.57
1335 4816 1.006102 CCTGTCGGAGTGCGTTCTT 60.006 57.895 3.30 0.00 0.00 2.52
1364 4845 2.573869 CTGAGGCGACGTGGTGAT 59.426 61.111 0.00 0.00 0.00 3.06
1366 4847 0.385751 CTGAGGCGACGTGGTGATAT 59.614 55.000 0.00 0.00 0.00 1.63
1370 4898 3.822167 TGAGGCGACGTGGTGATATAATA 59.178 43.478 0.00 0.00 0.00 0.98
1385 4913 6.915300 GTGATATAATAGATCAGCAGCGTAGG 59.085 42.308 0.00 0.00 34.02 3.18
1387 4915 0.242286 ATAGATCAGCAGCGTAGGCG 59.758 55.000 1.05 0.00 46.35 5.52
1419 4947 0.593128 GCACTTGTGAAGACGCCAAT 59.407 50.000 4.79 0.00 0.00 3.16
1433 4961 2.677199 CGCCAATCGTAGCATCATAGT 58.323 47.619 0.00 0.00 0.00 2.12
1446 4974 2.706555 TCATAGTAGCATCGAAGCCG 57.293 50.000 9.36 0.00 34.23 5.52
1449 4977 2.402282 TAGTAGCATCGAAGCCGCGG 62.402 60.000 24.05 24.05 35.37 6.46
1484 5012 3.728373 GGGGAGGCCCGTGTGAAT 61.728 66.667 0.00 0.00 46.66 2.57
1485 5013 2.355115 GGGAGGCCCGTGTGAATT 59.645 61.111 0.00 0.00 32.13 2.17
1599 5287 8.339714 AGTAATCTAATCTTTTCGAGAGAGACG 58.660 37.037 6.71 0.00 43.69 4.18
1615 5303 3.823873 AGAGACGCATATAGTGGAAGAGG 59.176 47.826 0.00 0.00 0.00 3.69
1622 5310 5.573282 CGCATATAGTGGAAGAGGTAATTCG 59.427 44.000 0.00 0.00 0.00 3.34
1648 5336 3.766051 CCCAAGCAAATAAAAGAGAGCCT 59.234 43.478 0.00 0.00 0.00 4.58
1659 5347 9.857656 AAATAAAAGAGAGCCTGAATATCATGA 57.142 29.630 0.00 0.00 0.00 3.07
1668 5356 7.728981 AGAGCCTGAATATCATGAATCCAATTT 59.271 33.333 0.00 0.00 0.00 1.82
1718 5406 5.280945 TCAGCTGTGCAAAATTTCTTACAC 58.719 37.500 14.67 0.00 0.00 2.90
1719 5407 4.146961 CAGCTGTGCAAAATTTCTTACACG 59.853 41.667 5.25 0.00 0.00 4.49
1720 5408 4.041723 GCTGTGCAAAATTTCTTACACGT 58.958 39.130 0.00 0.00 0.00 4.49
1721 5409 5.008217 AGCTGTGCAAAATTTCTTACACGTA 59.992 36.000 0.00 0.00 0.00 3.57
1722 5410 5.856455 GCTGTGCAAAATTTCTTACACGTAT 59.144 36.000 0.00 0.00 0.00 3.06
1723 5411 7.018826 GCTGTGCAAAATTTCTTACACGTATA 58.981 34.615 0.00 0.00 0.00 1.47
1724 5412 7.007099 GCTGTGCAAAATTTCTTACACGTATAC 59.993 37.037 0.00 0.00 0.00 1.47
1725 5413 7.862648 TGTGCAAAATTTCTTACACGTATACA 58.137 30.769 3.32 0.00 0.00 2.29
1774 5467 2.582728 TCAACCAAGTTGCAAGCAAG 57.417 45.000 7.88 0.00 42.55 4.01
1786 5479 5.532406 AGTTGCAAGCAAGTCATTCTAAAGA 59.468 36.000 7.88 0.00 34.84 2.52
1788 5481 5.946298 TGCAAGCAAGTCATTCTAAAGATG 58.054 37.500 0.00 0.00 0.00 2.90
1814 5508 7.361127 CCTGACATAGCTCATTTCATTTCATC 58.639 38.462 0.00 0.00 0.00 2.92
1818 5512 8.969260 ACATAGCTCATTTCATTTCATCTGTA 57.031 30.769 0.00 0.00 0.00 2.74
1839 5533 9.273016 TCTGTAAAAGGAGTTTACTGAGAAATG 57.727 33.333 11.98 0.00 46.91 2.32
1877 5580 4.463891 CACAAAATTACAGAGCCCCAATCT 59.536 41.667 0.00 0.00 0.00 2.40
1897 5600 4.133820 TCTTGTCACAGTAAACCACCATG 58.866 43.478 0.00 0.00 0.00 3.66
1933 5636 5.181245 AGCGCAAAGTCTTATCTTTTTAGCA 59.819 36.000 11.47 0.00 35.77 3.49
1935 5638 6.528072 GCGCAAAGTCTTATCTTTTTAGCAAT 59.472 34.615 0.30 0.00 35.77 3.56
1936 5639 7.062255 GCGCAAAGTCTTATCTTTTTAGCAATT 59.938 33.333 0.30 0.00 35.77 2.32
1994 5697 6.705381 TGCCAGAACAAAATAACCAATTTCTG 59.295 34.615 0.00 0.00 36.76 3.02
2021 5724 6.229936 AGTACGAGCCCAAATTAGTTCATA 57.770 37.500 0.00 0.00 0.00 2.15
2048 5751 9.911980 GAAAAGGCGAATATACTAACTTGTTAC 57.088 33.333 0.00 0.00 0.00 2.50
2052 5755 8.693625 AGGCGAATATACTAACTTGTTACTTCT 58.306 33.333 0.00 0.00 0.00 2.85
2061 5764 6.992715 ACTAACTTGTTACTTCTGATGCTTGT 59.007 34.615 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 70 4.202524 ACTTGAAATGGGTGGTTAGCTGTA 60.203 41.667 0.00 0.00 0.00 2.74
94 103 9.851686 AGAATGCACATATCAAAAGATACCTTA 57.148 29.630 0.00 0.00 31.15 2.69
114 123 3.141398 TCTCACAGGAAACACAGAATGC 58.859 45.455 0.00 0.00 42.53 3.56
173 185 7.099764 ACCACTACTAACAAGTCAATGAGATG 58.900 38.462 0.00 0.00 0.00 2.90
204 216 3.418684 TTCACTTCCTGGAAACCTAGC 57.581 47.619 10.86 0.00 0.00 3.42
354 366 4.383118 CCACCGATTACTTCTCCACAATCT 60.383 45.833 0.00 0.00 0.00 2.40
372 406 1.966451 GGAGGAAACACAGCCACCG 60.966 63.158 0.00 0.00 0.00 4.94
468 502 8.707781 GATTCACCAAATCCTCACAAGCAGTG 62.708 46.154 3.16 3.16 42.38 3.66
475 509 3.073678 CACGATTCACCAAATCCTCACA 58.926 45.455 0.00 0.00 40.69 3.58
575 623 8.934023 TGTTTATAATCACAAAAGTCCTTCCT 57.066 30.769 0.00 0.00 0.00 3.36
579 627 9.793259 TCTTCTGTTTATAATCACAAAAGTCCT 57.207 29.630 4.19 0.00 0.00 3.85
585 633 9.677567 GCTTGTTCTTCTGTTTATAATCACAAA 57.322 29.630 0.00 0.00 0.00 2.83
586 634 9.066892 AGCTTGTTCTTCTGTTTATAATCACAA 57.933 29.630 0.00 0.00 0.00 3.33
587 635 8.621532 AGCTTGTTCTTCTGTTTATAATCACA 57.378 30.769 0.00 0.00 0.00 3.58
589 637 8.883731 GCTAGCTTGTTCTTCTGTTTATAATCA 58.116 33.333 7.70 0.00 0.00 2.57
590 638 8.338986 GGCTAGCTTGTTCTTCTGTTTATAATC 58.661 37.037 15.72 0.00 0.00 1.75
591 639 8.049721 AGGCTAGCTTGTTCTTCTGTTTATAAT 58.950 33.333 15.72 0.00 0.00 1.28
592 640 7.334421 CAGGCTAGCTTGTTCTTCTGTTTATAA 59.666 37.037 18.20 0.00 0.00 0.98
593 641 6.818644 CAGGCTAGCTTGTTCTTCTGTTTATA 59.181 38.462 18.20 0.00 0.00 0.98
594 642 5.645497 CAGGCTAGCTTGTTCTTCTGTTTAT 59.355 40.000 18.20 0.00 0.00 1.40
595 643 4.997395 CAGGCTAGCTTGTTCTTCTGTTTA 59.003 41.667 18.20 0.00 0.00 2.01
596 644 3.817647 CAGGCTAGCTTGTTCTTCTGTTT 59.182 43.478 18.20 0.00 0.00 2.83
607 739 1.404391 CAGATTTGGCAGGCTAGCTTG 59.596 52.381 21.74 21.74 34.17 4.01
608 740 1.283029 TCAGATTTGGCAGGCTAGCTT 59.717 47.619 15.72 3.40 34.17 3.74
609 741 0.914644 TCAGATTTGGCAGGCTAGCT 59.085 50.000 15.72 0.00 34.17 3.32
612 744 1.635487 AGGTTCAGATTTGGCAGGCTA 59.365 47.619 0.00 0.00 0.00 3.93
613 745 0.407139 AGGTTCAGATTTGGCAGGCT 59.593 50.000 0.00 0.00 0.00 4.58
614 746 1.260544 AAGGTTCAGATTTGGCAGGC 58.739 50.000 0.00 0.00 0.00 4.85
615 747 9.911788 ATATATATAAGGTTCAGATTTGGCAGG 57.088 33.333 0.00 0.00 0.00 4.85
638 770 9.495572 GGCTAGCTTGTTCTTCTGTTTATATAT 57.504 33.333 15.72 0.00 0.00 0.86
639 771 8.705594 AGGCTAGCTTGTTCTTCTGTTTATATA 58.294 33.333 15.72 0.00 0.00 0.86
640 772 7.497249 CAGGCTAGCTTGTTCTTCTGTTTATAT 59.503 37.037 18.20 0.00 0.00 0.86
711 1018 5.047092 GTGGAGTTGGTTTGATCAAATGGAT 60.047 40.000 23.05 9.39 39.53 3.41
860 1193 9.922477 ACCCCAACCAAATCTTAAAATTAAAAA 57.078 25.926 0.00 0.00 0.00 1.94
1346 4827 1.663379 TATCACCACGTCGCCTCAGG 61.663 60.000 0.00 0.00 0.00 3.86
1352 4833 5.637809 TGATCTATTATATCACCACGTCGC 58.362 41.667 0.00 0.00 0.00 5.19
1353 4834 5.739630 GCTGATCTATTATATCACCACGTCG 59.260 44.000 0.00 0.00 30.38 5.12
1354 4835 6.621613 TGCTGATCTATTATATCACCACGTC 58.378 40.000 0.00 0.00 30.38 4.34
1355 4836 6.590234 TGCTGATCTATTATATCACCACGT 57.410 37.500 0.00 0.00 30.38 4.49
1356 4837 5.518128 GCTGCTGATCTATTATATCACCACG 59.482 44.000 0.00 0.00 30.38 4.94
1357 4838 5.518128 CGCTGCTGATCTATTATATCACCAC 59.482 44.000 0.00 0.00 30.38 4.16
1358 4839 5.185828 ACGCTGCTGATCTATTATATCACCA 59.814 40.000 0.00 0.00 30.38 4.17
1359 4840 5.655488 ACGCTGCTGATCTATTATATCACC 58.345 41.667 0.00 0.00 30.38 4.02
1360 4841 6.915300 CCTACGCTGCTGATCTATTATATCAC 59.085 42.308 0.00 0.00 30.38 3.06
1361 4842 6.460261 GCCTACGCTGCTGATCTATTATATCA 60.460 42.308 0.00 0.00 32.56 2.15
1362 4843 5.918011 GCCTACGCTGCTGATCTATTATATC 59.082 44.000 0.00 0.00 0.00 1.63
1364 4845 4.201920 CGCCTACGCTGCTGATCTATTATA 60.202 45.833 0.00 0.00 0.00 0.98
1366 4847 2.095212 CGCCTACGCTGCTGATCTATTA 60.095 50.000 0.00 0.00 0.00 0.98
1370 4898 2.415010 CGCCTACGCTGCTGATCT 59.585 61.111 0.00 0.00 0.00 2.75
1419 4947 4.000988 TCGATGCTACTATGATGCTACGA 58.999 43.478 0.00 0.00 34.85 3.43
1432 4960 3.330853 CCGCGGCTTCGATGCTAC 61.331 66.667 14.67 13.01 35.61 3.58
1468 4996 0.898326 AAAATTCACACGGGCCTCCC 60.898 55.000 0.84 0.00 41.09 4.30
1469 4997 0.966179 AAAAATTCACACGGGCCTCC 59.034 50.000 0.84 0.00 0.00 4.30
1494 5022 1.135803 CACCGCCTTACCAAATCAACG 60.136 52.381 0.00 0.00 0.00 4.10
1599 5287 5.869888 CCGAATTACCTCTTCCACTATATGC 59.130 44.000 0.00 0.00 0.00 3.14
1668 5356 8.608844 ATGGTTTGTTTGTTTGTTTGTTTAGA 57.391 26.923 0.00 0.00 0.00 2.10
1672 5360 7.707104 TGAAATGGTTTGTTTGTTTGTTTGTT 58.293 26.923 0.00 0.00 0.00 2.83
1673 5361 7.264373 TGAAATGGTTTGTTTGTTTGTTTGT 57.736 28.000 0.00 0.00 0.00 2.83
1674 5362 6.305160 GCTGAAATGGTTTGTTTGTTTGTTTG 59.695 34.615 0.00 0.00 0.00 2.93
1675 5363 6.206438 AGCTGAAATGGTTTGTTTGTTTGTTT 59.794 30.769 0.00 0.00 0.00 2.83
1676 5364 5.704978 AGCTGAAATGGTTTGTTTGTTTGTT 59.295 32.000 0.00 0.00 0.00 2.83
1677 5365 5.122082 CAGCTGAAATGGTTTGTTTGTTTGT 59.878 36.000 8.42 0.00 0.00 2.83
1678 5366 5.122082 ACAGCTGAAATGGTTTGTTTGTTTG 59.878 36.000 23.35 0.00 0.00 2.93
1723 5411 9.844257 TTCCATTCTTGTTTAAATTCCAAATGT 57.156 25.926 0.00 0.00 0.00 2.71
1737 5430 7.595819 TGGTTGATAGTTTTCCATTCTTGTT 57.404 32.000 0.00 0.00 0.00 2.83
1774 5467 6.073331 GCTATGTCAGGCATCTTTAGAATGAC 60.073 42.308 0.00 0.00 38.94 3.06
1786 5479 4.160642 TGAAATGAGCTATGTCAGGCAT 57.839 40.909 0.00 0.00 41.42 4.40
1788 5481 5.066893 TGAAATGAAATGAGCTATGTCAGGC 59.933 40.000 0.00 0.00 36.48 4.85
1851 5554 5.186256 TGGGGCTCTGTAATTTTGTGATA 57.814 39.130 0.00 0.00 0.00 2.15
1877 5580 3.880490 GTCATGGTGGTTTACTGTGACAA 59.120 43.478 0.00 0.00 40.29 3.18
1953 5656 8.177119 TGTTCTGGCAAGTACTAAATGAAAAT 57.823 30.769 0.00 0.00 0.00 1.82
1954 5657 7.575414 TGTTCTGGCAAGTACTAAATGAAAA 57.425 32.000 0.00 0.00 0.00 2.29
1955 5658 7.575414 TTGTTCTGGCAAGTACTAAATGAAA 57.425 32.000 0.00 0.00 0.00 2.69
1956 5659 7.575414 TTTGTTCTGGCAAGTACTAAATGAA 57.425 32.000 0.00 0.00 0.00 2.57
1957 5660 7.575414 TTTTGTTCTGGCAAGTACTAAATGA 57.425 32.000 0.00 0.00 28.77 2.57
1958 5661 9.906660 TTATTTTGTTCTGGCAAGTACTAAATG 57.093 29.630 21.81 0.00 38.53 2.32
1959 5662 9.908152 GTTATTTTGTTCTGGCAAGTACTAAAT 57.092 29.630 18.85 18.85 39.99 1.40
1960 5663 8.354426 GGTTATTTTGTTCTGGCAAGTACTAAA 58.646 33.333 9.25 9.25 34.69 1.85
1961 5664 7.502895 TGGTTATTTTGTTCTGGCAAGTACTAA 59.497 33.333 0.00 0.00 0.00 2.24
1962 5665 6.999272 TGGTTATTTTGTTCTGGCAAGTACTA 59.001 34.615 0.00 0.00 0.00 1.82
1963 5666 5.830991 TGGTTATTTTGTTCTGGCAAGTACT 59.169 36.000 0.00 0.00 0.00 2.73
1964 5667 6.079424 TGGTTATTTTGTTCTGGCAAGTAC 57.921 37.500 0.00 0.00 0.00 2.73
1965 5668 6.716934 TTGGTTATTTTGTTCTGGCAAGTA 57.283 33.333 0.00 0.00 0.00 2.24
1966 5669 5.606348 TTGGTTATTTTGTTCTGGCAAGT 57.394 34.783 0.00 0.00 0.00 3.16
1971 5674 7.656707 CCAGAAATTGGTTATTTTGTTCTGG 57.343 36.000 13.45 13.45 42.41 3.86
1994 5697 4.763073 ACTAATTTGGGCTCGTACTTACC 58.237 43.478 0.00 0.00 0.00 2.85
2001 5704 5.353394 TCTATGAACTAATTTGGGCTCGT 57.647 39.130 0.00 0.00 0.00 4.18
2003 5706 7.484140 CCTTTTCTATGAACTAATTTGGGCTC 58.516 38.462 0.00 0.00 0.00 4.70
2021 5724 8.788325 AACAAGTTAGTATATTCGCCTTTTCT 57.212 30.769 0.00 0.00 0.00 2.52
2048 5751 7.967178 AGTTTTTCAAAAACAAGCATCAGAAG 58.033 30.769 24.33 0.00 32.81 2.85
2052 5755 8.250332 AGAGTAGTTTTTCAAAAACAAGCATCA 58.750 29.630 24.33 1.67 32.81 3.07


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

AutoCloner maintained by Alex Coulton.