Multiple sequence alignment - TraesCS3A01G223200

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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 TraesCS3A01G223200 chr3A 100.000 9286 0 0 1 9286 417391353 417400638 0 17149
1 TraesCS3A01G223200 chr3A 95.920 5025 147 26 1 4992 662012678 662007679 0 8091
2 TraesCS3A01G223200 chr3A 96.362 2804 88 11 4990 7792 662007646 662004856 0 4601
3 TraesCS3A01G223200 chr3A 96.796 1498 43 4 7791 9286 554833143 554834637 0 2495
4 TraesCS3A01G223200 chr5A 96.299 5836 184 19 3 5835 528069047 528074853 0 9551
5 TraesCS3A01G223200 chr5A 95.974 3701 134 14 1297 4992 142252646 142248956 0 5995
6 TraesCS3A01G223200 chr5A 96.689 3443 101 11 5849 9286 528075314 528078748 0 5714
7 TraesCS3A01G223200 chr5A 96.658 2813 82 11 4982 7792 465656863 465659665 0 4663
8 TraesCS3A01G223200 chr5A 96.294 2806 90 13 4990 7792 34940609 34937815 0 4593
9 TraesCS3A01G223200 chr5A 96.672 2554 78 7 2443 4992 141902276 141904826 0 4239
10 TraesCS3A01G223200 chr5A 96.357 2553 83 8 2443 4992 465654295 465656840 0 4191
11 TraesCS3A01G223200 chr5A 96.893 2446 72 4 1 2445 541974611 541977053 0 4093
12 TraesCS3A01G223200 chr5A 96.865 1499 40 6 7791 9286 465659821 465661315 0 2501
13 TraesCS3A01G223200 chr6A 96.236 5367 169 26 2443 7792 158983266 158977916 0 8761
14 TraesCS3A01G223200 chr6A 96.361 2446 83 6 1 2445 158985734 158983294 0 4019
15 TraesCS3A01G223200 chr2A 96.861 2803 78 9 4990 7792 685101560 685098768 0 4680
16 TraesCS3A01G223200 chr2A 96.481 2813 84 14 4982 7792 284802662 284805461 0 4632
17 TraesCS3A01G223200 chr2A 96.303 2813 92 11 4982 7792 716651425 716648623 0 4608
18 TraesCS3A01G223200 chr2A 96.224 2807 89 13 4990 7792 572967163 572964370 0 4580
19 TraesCS3A01G223200 chr2A 95.663 2813 90 15 4982 7792 80122377 80125159 0 4490
20 TraesCS3A01G223200 chr2A 96.710 2553 77 7 2443 4992 384174711 384172163 0 4242
21 TraesCS3A01G223200 chr2A 96.282 2555 85 8 2443 4992 685104142 685101593 0 4183
22 TraesCS3A01G223200 chr2A 96.201 2553 91 6 2443 4992 284800090 284802639 0 4172
23 TraesCS3A01G223200 chr2A 95.930 2555 88 9 2443 4992 80119811 80122354 0 4128
24 TraesCS3A01G223200 chr2A 96.729 2446 73 6 1 2445 80117344 80119783 0 4067
25 TraesCS3A01G223200 chr2A 96.322 2447 80 6 1 2445 284797624 284800062 0 4012
26 TraesCS3A01G223200 chr2A 96.281 2447 86 5 1 2445 572972210 572969767 0 4010
27 TraesCS3A01G223200 chr2A 95.953 2446 85 6 1 2445 716656441 716654009 0 3956
28 TraesCS3A01G223200 chr2A 97.263 1498 36 5 7791 9286 685098613 685097119 0 2534
29 TraesCS3A01G223200 chr2A 96.798 1499 42 5 7791 9286 284805617 284807112 0 2497
30 TraesCS3A01G223200 chr2A 96.796 1498 43 4 7791 9286 716648468 716646974 0 2495
31 TraesCS3A01G223200 chr2A 96.796 1498 38 6 7791 9286 572964215 572962726 0 2492
32 TraesCS3A01G223200 chr2A 95.552 1304 51 6 6489 7792 384157115 384155819 0 2080
33 TraesCS3A01G223200 chr1A 96.646 2803 80 12 4990 7792 70943007 70940219 0 4643
34 TraesCS3A01G223200 chr1A 96.731 1499 42 5 7791 9286 70940064 70938570 0 2490
35 TraesCS3A01G223200 chr7B 95.626 2446 101 6 1 2445 192835695 192833255 0 3919
36 TraesCS3A01G223200 chr4B 95.421 2446 106 6 1 2445 91923550 91925990 0 3892
37 TraesCS3A01G223200 chr7A 96.996 1498 36 9 7791 9286 245430349 245428859 0 2508


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 TraesCS3A01G223200 chr3A 417391353 417400638 9285 False 17149.000000 17149 100.000000 1 9286 1 chr3A.!!$F1 9285
1 TraesCS3A01G223200 chr3A 662004856 662012678 7822 True 6346.000000 8091 96.141000 1 7792 2 chr3A.!!$R1 7791
2 TraesCS3A01G223200 chr3A 554833143 554834637 1494 False 2495.000000 2495 96.796000 7791 9286 1 chr3A.!!$F2 1495
3 TraesCS3A01G223200 chr5A 528069047 528078748 9701 False 7632.500000 9551 96.494000 3 9286 2 chr5A.!!$F4 9283
4 TraesCS3A01G223200 chr5A 142248956 142252646 3690 True 5995.000000 5995 95.974000 1297 4992 1 chr5A.!!$R2 3695
5 TraesCS3A01G223200 chr5A 34937815 34940609 2794 True 4593.000000 4593 96.294000 4990 7792 1 chr5A.!!$R1 2802
6 TraesCS3A01G223200 chr5A 141902276 141904826 2550 False 4239.000000 4239 96.672000 2443 4992 1 chr5A.!!$F1 2549
7 TraesCS3A01G223200 chr5A 541974611 541977053 2442 False 4093.000000 4093 96.893000 1 2445 1 chr5A.!!$F2 2444
8 TraesCS3A01G223200 chr5A 465654295 465661315 7020 False 3785.000000 4663 96.626667 2443 9286 3 chr5A.!!$F3 6843
9 TraesCS3A01G223200 chr6A 158977916 158985734 7818 True 6390.000000 8761 96.298500 1 7792 2 chr6A.!!$R1 7791
10 TraesCS3A01G223200 chr2A 384172163 384174711 2548 True 4242.000000 4242 96.710000 2443 4992 1 chr2A.!!$R2 2549
11 TraesCS3A01G223200 chr2A 80117344 80125159 7815 False 4228.333333 4490 96.107333 1 7792 3 chr2A.!!$F1 7791
12 TraesCS3A01G223200 chr2A 284797624 284807112 9488 False 3828.250000 4632 96.450500 1 9286 4 chr2A.!!$F2 9285
13 TraesCS3A01G223200 chr2A 685097119 685104142 7023 True 3799.000000 4680 96.802000 2443 9286 3 chr2A.!!$R4 6843
14 TraesCS3A01G223200 chr2A 572962726 572972210 9484 True 3694.000000 4580 96.433667 1 9286 3 chr2A.!!$R3 9285
15 TraesCS3A01G223200 chr2A 716646974 716656441 9467 True 3686.333333 4608 96.350667 1 9286 3 chr2A.!!$R5 9285
16 TraesCS3A01G223200 chr2A 384155819 384157115 1296 True 2080.000000 2080 95.552000 6489 7792 1 chr2A.!!$R1 1303
17 TraesCS3A01G223200 chr1A 70938570 70943007 4437 True 3566.500000 4643 96.688500 4990 9286 2 chr1A.!!$R1 4296
18 TraesCS3A01G223200 chr7B 192833255 192835695 2440 True 3919.000000 3919 95.626000 1 2445 1 chr7B.!!$R1 2444
19 TraesCS3A01G223200 chr4B 91923550 91925990 2440 False 3892.000000 3892 95.421000 1 2445 1 chr4B.!!$F1 2444
20 TraesCS3A01G223200 chr7A 245428859 245430349 1490 True 2508.000000 2508 96.996000 7791 9286 1 chr7A.!!$R1 1495

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
593 595 1.002868 GTCTGTGTGGGCTCAGCAT 60.003 57.895 0.00 0.00 36.48 3.79 F
1061 1064 1.079197 TCGACGCCATGCATTCTGT 60.079 52.632 0.00 0.00 0.00 3.41 F
1819 1824 0.035317 TGACGATGAAGCTGCCAAGT 59.965 50.000 0.00 0.00 0.00 3.16 F
2473 2512 0.882474 ACTCTCAGTCGGCAGTACAC 59.118 55.000 0.00 0.00 0.00 2.90 F
3185 3236 0.464735 CCTCGTTCCCACAAACCACA 60.465 55.000 0.00 0.00 0.00 4.17 F
3422 3473 0.900182 TGGAGATCGTCTGCACCAGT 60.900 55.000 5.39 0.00 39.98 4.00 F
4001 4053 1.765904 TGGTGAAGCACTGGTTCTGTA 59.234 47.619 19.17 5.39 40.24 2.74 F
5374 5507 1.996898 CTAGTAATCCGCACAACGCAA 59.003 47.619 0.00 0.00 42.60 4.85 F
5626 5765 0.101579 GTCAACAAAACACCCCACCG 59.898 55.000 0.00 0.00 0.00 4.94 F
6864 7459 0.179073 CTCCTTCCCACATAGCACCG 60.179 60.000 0.00 0.00 0.00 4.94 F
7040 7635 0.246360 TTGACATCATGCCGAGACGT 59.754 50.000 0.00 0.00 0.00 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1819 1824 0.320771 GCGCTCTTTCCAGGTTGAGA 60.321 55.000 0.00 1.20 0.00 3.27 R
2882 2930 1.336755 GGCATTTTACTATGGCACCGG 59.663 52.381 0.00 0.00 46.89 5.28 R
3185 3236 1.066929 GTGGAAATGGAAGCGGCAATT 60.067 47.619 1.45 0.00 0.00 2.32 R
3361 3412 1.067354 CAACCCCTTTGAGCATTCTGC 60.067 52.381 0.00 0.00 45.46 4.26 R
4585 4644 0.437295 CCATAACTTATACGCGGCGC 59.563 55.000 24.21 24.21 0.00 6.53 R
4717 4776 3.117776 ACAAGGGGAAGTAAAACGAAGGT 60.118 43.478 0.00 0.00 0.00 3.50 R
5419 5558 5.720202 CACTTACCTGAGTGCTTATACACA 58.280 41.667 0.00 0.00 43.23 3.72 R
7021 7616 0.246360 ACGTCTCGGCATGATGTCAA 59.754 50.000 0.00 0.00 0.00 3.18 R
7041 7636 0.250295 CCTTTGAGCGTTCTGGTCCA 60.250 55.000 0.00 0.00 44.62 4.02 R
8017 9084 3.621715 GGCCAAGGAGTCGTAGTATTTTG 59.378 47.826 0.00 0.00 0.00 2.44 R
8624 9695 5.290158 CGTCGAAGGCTACTATTTGCTTTTA 59.710 40.000 0.00 0.00 0.00 1.52 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
363 365 7.506328 ACTTTATTAGAAGTTTTTCCTGCGT 57.494 32.000 0.00 0.00 36.49 5.24
533 535 1.810532 GGCGACAGAGACGGAAGAT 59.189 57.895 0.00 0.00 0.00 2.40
593 595 1.002868 GTCTGTGTGGGCTCAGCAT 60.003 57.895 0.00 0.00 36.48 3.79
821 824 4.144297 TGCAGACAATTAAGGCTGAAAGT 58.856 39.130 2.85 0.00 35.30 2.66
838 841 6.017109 GCTGAAAGTGTTCCAGAGAAATACAA 60.017 38.462 0.00 0.00 35.30 2.41
845 848 6.706270 GTGTTCCAGAGAAATACAAACTCAGA 59.294 38.462 0.00 0.00 32.58 3.27
917 920 3.128349 GAGGACAGTAGCGTCAAACAAA 58.872 45.455 0.00 0.00 37.66 2.83
1029 1032 2.100631 GCGGGTCGTCATGGACAAG 61.101 63.158 4.76 0.00 38.70 3.16
1037 1040 1.136252 CGTCATGGACAAGCTTGAACG 60.136 52.381 32.50 23.01 32.09 3.95
1061 1064 1.079197 TCGACGCCATGCATTCTGT 60.079 52.632 0.00 0.00 0.00 3.41
1253 1256 3.740452 CGAGATCATGAGCTTGATGGTGT 60.740 47.826 21.50 0.00 36.48 4.16
1369 1372 1.860326 GCAAAACACAAGCAGCGAAAT 59.140 42.857 0.00 0.00 0.00 2.17
1471 1474 1.507630 GCATGCGGATTCTGCAACA 59.492 52.632 23.20 1.22 46.87 3.33
1593 1598 2.386661 ACACACATAGCAGCTACACC 57.613 50.000 3.59 0.00 0.00 4.16
1627 1632 1.859080 GCGGAACTGACGGACATAATC 59.141 52.381 0.00 0.00 0.00 1.75
1769 1774 4.093998 CCAATCAGACGAAGACAATGAAGG 59.906 45.833 0.00 0.00 0.00 3.46
1819 1824 0.035317 TGACGATGAAGCTGCCAAGT 59.965 50.000 0.00 0.00 0.00 3.16
1965 1971 3.708403 ATCAGCACACAATGAGGAAGA 57.292 42.857 0.00 0.00 0.00 2.87
1973 1979 5.507817 GCACACAATGAGGAAGAATTTCACA 60.508 40.000 0.00 0.00 34.90 3.58
1980 1986 9.048446 CAATGAGGAAGAATTTCACAAAAACAT 57.952 29.630 0.00 0.00 34.90 2.71
2320 2327 2.669569 GCCCGCTGAAGCAGTGAA 60.670 61.111 9.38 0.00 43.78 3.18
2473 2512 0.882474 ACTCTCAGTCGGCAGTACAC 59.118 55.000 0.00 0.00 0.00 2.90
2502 2541 7.241376 GCATAGTAATAACAAACACACCAGTC 58.759 38.462 0.00 0.00 0.00 3.51
2882 2930 9.582431 TGATAAGTACAGCTTGACTATACAAAC 57.418 33.333 0.00 0.00 38.05 2.93
2891 2939 2.237643 TGACTATACAAACCGGTGCCAT 59.762 45.455 8.52 1.80 0.00 4.40
2936 2985 4.643387 AGGCGTGCAAGTGGGGTC 62.643 66.667 0.59 0.00 0.00 4.46
3126 3175 3.238497 CCTCCCACACACCACCGA 61.238 66.667 0.00 0.00 0.00 4.69
3185 3236 0.464735 CCTCGTTCCCACAAACCACA 60.465 55.000 0.00 0.00 0.00 4.17
3361 3412 3.969631 CGAGAAGCGCGACTACAG 58.030 61.111 12.10 0.00 0.00 2.74
3422 3473 0.900182 TGGAGATCGTCTGCACCAGT 60.900 55.000 5.39 0.00 39.98 4.00
3585 3636 3.664107 GATGAACTCTGCTTGGTGTACA 58.336 45.455 0.00 0.00 0.00 2.90
3639 3690 3.755378 CCTACTCATTTGCCCTGCATATC 59.245 47.826 0.00 0.00 38.76 1.63
3706 3757 5.995282 CACTTGTTTCCCAACTAGATGTACA 59.005 40.000 0.00 0.00 37.81 2.90
3805 3857 9.613428 CTGATACACTGGATTACTATTTGGAAA 57.387 33.333 0.00 0.00 0.00 3.13
3814 3866 8.811017 TGGATTACTATTTGGAAAAATCTTGCA 58.189 29.630 0.00 0.00 0.00 4.08
4001 4053 1.765904 TGGTGAAGCACTGGTTCTGTA 59.234 47.619 19.17 5.39 40.24 2.74
4198 4253 7.667219 ACAACTACTTCATGGATTCATCACTTT 59.333 33.333 0.00 0.00 0.00 2.66
4268 4324 2.517959 TCAAAATGTCTCTGCCCTTGG 58.482 47.619 0.00 0.00 0.00 3.61
4507 4566 5.987347 ACAAAGGCATGAAAAACAAGATCAG 59.013 36.000 0.00 0.00 0.00 2.90
4510 4569 4.222145 AGGCATGAAAAACAAGATCAGCAT 59.778 37.500 0.00 0.00 0.00 3.79
4600 4659 2.510594 CGTGCGCCGCGTATAAGTT 61.511 57.895 15.34 0.00 32.40 2.66
4624 4683 5.535753 TGGTTCATGATCGACTACATCAT 57.464 39.130 0.00 0.00 40.92 2.45
4717 4776 4.774726 GGGATGAAGATACATCAGAGCCTA 59.225 45.833 0.00 0.00 45.68 3.93
4734 4793 3.005554 GCCTACCTTCGTTTTACTTCCC 58.994 50.000 0.00 0.00 0.00 3.97
4943 5006 9.520204 TCAAAATTGAAAAAGTAGCTTCTGAAG 57.480 29.630 13.02 13.02 33.55 3.02
4970 5033 3.120782 CGTTGTCGTTGCTCTAAAGTACC 59.879 47.826 0.00 0.00 0.00 3.34
4996 5129 6.649141 AGTTACGATGCAACTAATCACTTGAA 59.351 34.615 0.00 0.00 34.50 2.69
5374 5507 1.996898 CTAGTAATCCGCACAACGCAA 59.003 47.619 0.00 0.00 42.60 4.85
5626 5765 0.101579 GTCAACAAAACACCCCACCG 59.898 55.000 0.00 0.00 0.00 4.94
6592 7185 2.346244 GCAAAATGCCATCATCACAACG 59.654 45.455 0.00 0.00 37.42 4.10
6633 7226 6.041637 TGGGATTTAGCAGATCGTAAGTACAT 59.958 38.462 0.00 0.00 39.48 2.29
6768 7361 2.260434 CCCCACGACCACTACACG 59.740 66.667 0.00 0.00 0.00 4.49
6839 7434 1.607225 AGCCCCCATTGTCTTCCATA 58.393 50.000 0.00 0.00 0.00 2.74
6848 7443 4.263243 CCATTGTCTTCCATATCTCCCTCC 60.263 50.000 0.00 0.00 0.00 4.30
6864 7459 0.179073 CTCCTTCCCACATAGCACCG 60.179 60.000 0.00 0.00 0.00 4.94
6885 7480 0.326595 TGCCGCTTCCATTTCCACTA 59.673 50.000 0.00 0.00 0.00 2.74
6903 7498 0.753867 TACACACAAACCTCCAGCGA 59.246 50.000 0.00 0.00 0.00 4.93
6926 7521 1.004044 CTCTCCAAAGCCCACAGTCAT 59.996 52.381 0.00 0.00 0.00 3.06
6964 7559 2.112297 GGAACCGTCCACCAAGCA 59.888 61.111 0.00 0.00 44.26 3.91
6994 7589 1.000607 CGAGACGTTGGACAAGAGGAA 60.001 52.381 0.00 0.00 0.00 3.36
7032 7627 0.647410 CGTCCTCGTTGACATCATGC 59.353 55.000 7.61 0.00 34.88 4.06
7033 7628 1.009829 GTCCTCGTTGACATCATGCC 58.990 55.000 0.00 0.00 35.29 4.40
7035 7630 0.460109 CCTCGTTGACATCATGCCGA 60.460 55.000 0.00 0.00 0.00 5.54
7036 7631 0.926155 CTCGTTGACATCATGCCGAG 59.074 55.000 10.01 10.01 34.84 4.63
7037 7632 0.530288 TCGTTGACATCATGCCGAGA 59.470 50.000 0.00 0.00 0.00 4.04
7038 7633 0.647410 CGTTGACATCATGCCGAGAC 59.353 55.000 0.00 0.00 0.00 3.36
7039 7634 0.647410 GTTGACATCATGCCGAGACG 59.353 55.000 0.00 0.00 0.00 4.18
7040 7635 0.246360 TTGACATCATGCCGAGACGT 59.754 50.000 0.00 0.00 0.00 4.34
7041 7636 0.246360 TGACATCATGCCGAGACGTT 59.754 50.000 0.00 0.00 0.00 3.99
7042 7637 0.647410 GACATCATGCCGAGACGTTG 59.353 55.000 0.00 0.00 0.00 4.10
7043 7638 0.740868 ACATCATGCCGAGACGTTGG 60.741 55.000 0.00 0.00 0.00 3.77
7421 8017 9.384764 TGGATACACGATTACATGTTTATCAAA 57.615 29.630 2.30 0.00 46.17 2.69
8187 9254 4.335082 GCATACGCAATGTACAAGTCAA 57.665 40.909 0.00 0.00 37.93 3.18
8188 9255 4.908736 GCATACGCAATGTACAAGTCAAT 58.091 39.130 0.00 0.00 37.93 2.57
8267 9334 2.039879 CCCCTACTACCACTGCAACTTT 59.960 50.000 0.00 0.00 0.00 2.66
8486 9553 6.259550 ACAAGTTTGCTAGCTTCCTATTTG 57.740 37.500 17.23 12.76 0.00 2.32
8558 9625 0.390340 CCACGCAGCACTAGTCATGT 60.390 55.000 0.00 0.00 0.00 3.21
8595 9666 7.706281 ACACATGAATATTTTCGCAAAAACA 57.294 28.000 0.00 0.00 37.20 2.83
8606 9677 8.788409 ATTTTCGCAAAAACAAAAACAAAAGA 57.212 23.077 0.00 0.00 37.20 2.52
8624 9695 6.013293 ACAAAAGAGGCAGACTAACTAAGGAT 60.013 38.462 0.00 0.00 0.00 3.24
8673 9744 4.457949 TCAGTACAGCTTAGACATGAACGA 59.542 41.667 0.00 0.00 0.00 3.85
8742 9815 6.262496 ACACTAAAAAGACTAAGTTTCAGCCC 59.738 38.462 0.00 0.00 0.00 5.19
8954 10027 5.183904 AGCTTCAGTTCGCATTCCTTAAAAT 59.816 36.000 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
363 365 9.474920 GAATGATGACCAAATTGTTAGTTTTCA 57.525 29.630 0.00 0.00 0.00 2.69
593 595 2.904866 GCAACCACCTGGAACGCA 60.905 61.111 0.00 0.00 38.94 5.24
754 757 7.646130 CGCAGAAAAGACCTGTATTTGTTTTTA 59.354 33.333 0.00 0.00 34.29 1.52
821 824 6.826668 TCTGAGTTTGTATTTCTCTGGAACA 58.173 36.000 0.00 0.00 0.00 3.18
838 841 3.746492 GCGTTTGGTGTATCTTCTGAGTT 59.254 43.478 0.00 0.00 0.00 3.01
845 848 0.322322 TCGGGCGTTTGGTGTATCTT 59.678 50.000 0.00 0.00 0.00 2.40
917 920 3.301794 TCAATGCAGTATTGGGATGCT 57.698 42.857 10.96 0.00 45.05 3.79
979 982 2.645838 TGCTCTTGGCTTCTCAAGTT 57.354 45.000 4.79 0.00 43.25 2.66
980 983 2.645838 TTGCTCTTGGCTTCTCAAGT 57.354 45.000 4.79 0.00 43.25 3.16
1029 1032 0.703466 CGTCGAGTTCTCGTTCAAGC 59.297 55.000 19.26 6.08 0.00 4.01
1037 1040 0.807667 ATGCATGGCGTCGAGTTCTC 60.808 55.000 0.00 0.00 0.00 2.87
1061 1064 0.871722 CGCGACACCTCCATTTTCAA 59.128 50.000 0.00 0.00 0.00 2.69
1171 1174 3.429141 CTCCGGTTGCTGCTGCTG 61.429 66.667 17.00 0.77 40.48 4.41
1253 1256 1.000052 TGTCATGTCGTTCGCCTACAA 60.000 47.619 0.00 0.00 0.00 2.41
1471 1474 3.737047 CGGTAGTTATGGTTGCTCACGAT 60.737 47.826 0.00 0.00 0.00 3.73
1580 1585 1.443407 CGGCAGGTGTAGCTGCTAT 59.557 57.895 28.37 0.00 45.11 2.97
1769 1774 2.106332 CGCCCCCGACACTATCAC 59.894 66.667 0.00 0.00 36.29 3.06
1819 1824 0.320771 GCGCTCTTTCCAGGTTGAGA 60.321 55.000 0.00 1.20 0.00 3.27
1852 1857 2.829023 TCTCCTAACTGTCCCCGAATT 58.171 47.619 0.00 0.00 0.00 2.17
1965 1971 8.384365 GGTAAACGACAATGTTTTTGTGAAATT 58.616 29.630 0.00 0.00 41.92 1.82
1973 1979 7.892778 AGTTTTGGTAAACGACAATGTTTTT 57.107 28.000 0.00 0.00 46.54 1.94
1980 1986 8.623030 AGCTAAATAAGTTTTGGTAAACGACAA 58.377 29.630 0.00 0.00 46.54 3.18
2473 2512 7.027161 GGTGTGTTTGTTATTACTATGCCTTG 58.973 38.462 0.00 0.00 0.00 3.61
2879 2927 3.119280 GCATTTTACTATGGCACCGGTTT 60.119 43.478 2.97 0.00 0.00 3.27
2882 2930 1.336755 GGCATTTTACTATGGCACCGG 59.663 52.381 0.00 0.00 46.89 5.28
2891 2939 5.065859 CGGTTGTGATGATGGCATTTTACTA 59.934 40.000 0.00 0.00 34.11 1.82
2921 2969 2.594592 AAGACCCCACTTGCACGC 60.595 61.111 0.00 0.00 0.00 5.34
2936 2985 3.866651 AGCTGTACTTATGACCTGCAAG 58.133 45.455 0.00 0.00 0.00 4.01
3082 3131 2.428622 GGGGGCGTGTGTGTAGTT 59.571 61.111 0.00 0.00 0.00 2.24
3185 3236 1.066929 GTGGAAATGGAAGCGGCAATT 60.067 47.619 1.45 0.00 0.00 2.32
3361 3412 1.067354 CAACCCCTTTGAGCATTCTGC 60.067 52.381 0.00 0.00 45.46 4.26
3422 3473 1.070786 GTCGGCCTTGTCTGGTTCA 59.929 57.895 0.00 0.00 0.00 3.18
3706 3757 3.829601 TCCACTTTTCACAAACCACACTT 59.170 39.130 0.00 0.00 0.00 3.16
3814 3866 9.658799 TCGATCAACTTCAGAATTTAATCTTCT 57.341 29.630 0.00 0.00 33.25 2.85
3977 4029 2.438021 AGAACCAGTGCTTCACCAAGTA 59.562 45.455 1.16 0.00 34.49 2.24
4268 4324 3.435186 GTCAAGCGCTTGGGCCTC 61.435 66.667 41.00 24.84 40.78 4.70
4281 4337 2.327343 GCTGCAGCATGTCGGTCAA 61.327 57.895 33.36 0.00 41.59 3.18
4342 4398 3.304324 GGACAACTTCAGCTTCTCTTTGC 60.304 47.826 0.00 0.00 0.00 3.68
4428 4484 4.828387 AGTCAAGGAGTCGTACTCTTTTCT 59.172 41.667 12.62 9.78 41.00 2.52
4507 4566 3.077359 AGTTTGTAGTCTTCCTGCATGC 58.923 45.455 11.82 11.82 35.58 4.06
4510 4569 3.466836 CACAGTTTGTAGTCTTCCTGCA 58.533 45.455 0.00 0.00 33.58 4.41
4585 4644 0.437295 CCATAACTTATACGCGGCGC 59.563 55.000 24.21 24.21 0.00 6.53
4600 4659 6.648879 TGATGTAGTCGATCATGAACCATA 57.351 37.500 0.00 0.00 0.00 2.74
4624 4683 3.254470 TCGCAAATTCCGAACCATCTA 57.746 42.857 0.00 0.00 0.00 1.98
4717 4776 3.117776 ACAAGGGGAAGTAAAACGAAGGT 60.118 43.478 0.00 0.00 0.00 3.50
4734 4793 4.240096 CAAGATAAAAGGCAAGCACAAGG 58.760 43.478 0.00 0.00 0.00 3.61
4970 5033 6.090763 TCAAGTGATTAGTTGCATCGTAACTG 59.909 38.462 7.60 0.00 38.70 3.16
4996 5129 5.857471 TGTAGTAAGTATGTAATGCCCGT 57.143 39.130 0.00 0.00 0.00 5.28
5179 5312 7.696453 AGTTTTGTGTGAGTGTAATCTTTTTCG 59.304 33.333 0.00 0.00 0.00 3.46
5419 5558 5.720202 CACTTACCTGAGTGCTTATACACA 58.280 41.667 0.00 0.00 43.23 3.72
5626 5765 7.442656 TCTAGTTTGTATAGCTGGGCTTATTC 58.557 38.462 0.00 0.00 40.44 1.75
6592 7185 1.002430 TCCCACTTGCACATCTCTGTC 59.998 52.381 0.00 0.00 31.62 3.51
6633 7226 4.991056 GTGCACTGATTAGTCTTGTCAAGA 59.009 41.667 11.36 11.36 34.07 3.02
6727 7320 1.484227 CCGTTTGCACTTCGTCGTGA 61.484 55.000 10.25 0.00 37.06 4.35
6821 7415 2.108952 AGATATGGAAGACAATGGGGGC 59.891 50.000 0.00 0.00 0.00 5.80
6822 7417 3.245052 GGAGATATGGAAGACAATGGGGG 60.245 52.174 0.00 0.00 0.00 5.40
6839 7434 2.983296 CTATGTGGGAAGGAGGGAGAT 58.017 52.381 0.00 0.00 0.00 2.75
6848 7443 1.086696 CAACGGTGCTATGTGGGAAG 58.913 55.000 0.00 0.00 0.00 3.46
6864 7459 0.388520 GTGGAAATGGAAGCGGCAAC 60.389 55.000 1.45 0.00 0.00 4.17
6885 7480 0.814010 GTCGCTGGAGGTTTGTGTGT 60.814 55.000 0.00 0.00 0.00 3.72
6903 7498 0.689623 CTGTGGGCTTTGGAGAGAGT 59.310 55.000 0.00 0.00 0.00 3.24
6926 7521 3.797353 GCCATGGCCTTCCTCCGA 61.797 66.667 27.24 0.00 34.56 4.55
6964 7559 1.575244 CAACGTCTCGGCATGATGAT 58.425 50.000 0.00 0.00 0.00 2.45
7018 7613 0.530288 TCTCGGCATGATGTCAACGA 59.470 50.000 0.00 1.13 32.60 3.85
7021 7616 0.246360 ACGTCTCGGCATGATGTCAA 59.754 50.000 0.00 0.00 0.00 3.18
7025 7620 0.460109 TCCAACGTCTCGGCATGATG 60.460 55.000 0.00 0.00 0.00 3.07
7027 7622 1.080093 GTCCAACGTCTCGGCATGA 60.080 57.895 0.00 0.00 0.00 3.07
7028 7623 2.100631 GGTCCAACGTCTCGGCATG 61.101 63.158 0.00 0.00 0.00 4.06
7029 7624 2.264794 GGTCCAACGTCTCGGCAT 59.735 61.111 0.00 0.00 0.00 4.40
7030 7625 3.220999 CTGGTCCAACGTCTCGGCA 62.221 63.158 0.00 0.00 0.00 5.69
7031 7626 2.430382 TTCTGGTCCAACGTCTCGGC 62.430 60.000 0.00 0.00 0.00 5.54
7032 7627 0.666577 GTTCTGGTCCAACGTCTCGG 60.667 60.000 0.00 0.00 0.00 4.63
7033 7628 1.002250 CGTTCTGGTCCAACGTCTCG 61.002 60.000 7.78 0.00 41.39 4.04
7035 7630 1.300697 GCGTTCTGGTCCAACGTCT 60.301 57.895 15.67 0.00 46.70 4.18
7036 7631 1.282930 GAGCGTTCTGGTCCAACGTC 61.283 60.000 15.67 9.28 46.70 4.34
7037 7632 1.300697 GAGCGTTCTGGTCCAACGT 60.301 57.895 15.67 4.89 46.70 3.99
7039 7634 1.264288 CTTTGAGCGTTCTGGTCCAAC 59.736 52.381 0.00 0.00 44.62 3.77
7040 7635 1.593196 CTTTGAGCGTTCTGGTCCAA 58.407 50.000 0.00 0.00 44.62 3.53
7041 7636 0.250295 CCTTTGAGCGTTCTGGTCCA 60.250 55.000 0.00 0.00 44.62 4.02
7042 7637 0.955919 CCCTTTGAGCGTTCTGGTCC 60.956 60.000 0.00 0.00 44.62 4.46
7043 7638 0.955919 CCCCTTTGAGCGTTCTGGTC 60.956 60.000 0.00 0.00 45.46 4.02
7421 8017 9.199982 CTTCACAGTTTCAGAAATGCATTTAAT 57.800 29.630 24.15 13.39 34.34 1.40
8017 9084 3.621715 GGCCAAGGAGTCGTAGTATTTTG 59.378 47.826 0.00 0.00 0.00 2.44
8486 9553 6.095377 GTCAACTTCAAATGATGGATGAACC 58.905 40.000 7.91 0.00 39.54 3.62
8595 9666 6.775594 AGTTAGTCTGCCTCTTTTGTTTTT 57.224 33.333 0.00 0.00 0.00 1.94
8606 9677 6.070194 TGCTTTTATCCTTAGTTAGTCTGCCT 60.070 38.462 0.00 0.00 0.00 4.75
8624 9695 5.290158 CGTCGAAGGCTACTATTTGCTTTTA 59.710 40.000 0.00 0.00 0.00 1.52
8742 9815 7.078228 GCTTTTTAGTACTGAATGTTGTCCTG 58.922 38.462 5.39 0.00 0.00 3.86
8954 10027 8.737175 CCACTGTTAACTCTTAGTATGTCACTA 58.263 37.037 7.22 0.00 38.80 2.74
8970 10043 5.682943 TCAGTTGTATTGCCACTGTTAAC 57.317 39.130 0.00 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.