Multiple sequence alignment - TraesCS2D01G588000

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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 TraesCS2D01G588000 chr2D 100.000 2579 0 0 1 2579 645662797 645660219 0.000000e+00 4763
1 TraesCS2D01G588000 chr2D 83.981 643 91 4 950 1580 544566459 544565817 7.890000e-170 606
2 TraesCS2D01G588000 chr2D 84.488 606 91 3 975 1580 544326985 544326383 1.710000e-166 595
3 TraesCS2D01G588000 chr2D 83.594 640 93 3 950 1580 544464875 544464239 7.950000e-165 590
4 TraesCS2D01G588000 chr2D 94.186 86 3 2 1 85 5908724 5908640 2.080000e-26 130
5 TraesCS2D01G588000 chr2B 90.348 1896 83 56 504 2352 789964154 789965996 0.000000e+00 2396
6 TraesCS2D01G588000 chr2B 83.906 640 91 3 950 1580 649750233 649749597 3.670000e-168 601
7 TraesCS2D01G588000 chr2B 83.750 640 92 7 950 1580 649756122 649755486 1.710000e-166 595
8 TraesCS2D01G588000 chr2B 83.281 640 95 8 950 1580 649714073 649713437 1.720000e-161 579
9 TraesCS2D01G588000 chr2B 83.281 640 91 10 950 1579 649708242 649707609 2.230000e-160 575
10 TraesCS2D01G588000 chr2B 87.381 420 23 6 76 479 789963752 789964157 3.030000e-124 455
11 TraesCS2D01G588000 chr2B 91.031 223 12 8 2360 2577 789966075 789966294 6.980000e-76 294
12 TraesCS2D01G588000 chr2A 91.093 1628 68 48 528 2105 771339560 771341160 0.000000e+00 2132
13 TraesCS2D01G588000 chr2A 82.330 764 105 17 835 1580 686802027 686801276 1.010000e-178 636
14 TraesCS2D01G588000 chr2A 80.301 863 125 31 731 1580 686812593 686811763 6.100000e-171 610
15 TraesCS2D01G588000 chr2A 83.906 640 91 4 950 1580 686805641 686805005 3.670000e-168 601
16 TraesCS2D01G588000 chr2A 81.555 759 109 18 835 1580 686807756 686807016 4.750000e-167 597
17 TraesCS2D01G588000 chr2A 83.486 327 24 14 2138 2444 771341312 771341628 7.030000e-71 278
18 TraesCS2D01G588000 chr2A 81.728 301 27 14 76 375 771339121 771339394 2.580000e-55 226
19 TraesCS2D01G588000 chr2A 93.396 106 4 3 2475 2577 771341628 771341733 1.240000e-33 154
20 TraesCS2D01G588000 chr3A 97.468 79 2 0 1 79 743838018 743838096 4.480000e-28 135
21 TraesCS2D01G588000 chr7D 97.436 78 2 0 1 78 578386541 578386618 1.610000e-27 134
22 TraesCS2D01G588000 chr7D 97.436 78 2 0 1 78 578394832 578394909 1.610000e-27 134
23 TraesCS2D01G588000 chr5A 96.296 81 3 0 1 81 100642070 100641990 1.610000e-27 134
24 TraesCS2D01G588000 chr5A 94.118 85 4 1 1 85 693135852 693135769 7.490000e-26 128
25 TraesCS2D01G588000 chr4A 96.296 81 3 0 1 81 596540302 596540222 1.610000e-27 134
26 TraesCS2D01G588000 chr1B 97.436 78 2 0 1 78 52004600 52004523 1.610000e-27 134
27 TraesCS2D01G588000 chr1D 95.181 83 4 0 1 83 291850150 291850068 5.790000e-27 132


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 TraesCS2D01G588000 chr2D 645660219 645662797 2578 True 4763.000000 4763 100.000000 1 2579 1 chr2D.!!$R5 2578
1 TraesCS2D01G588000 chr2D 544565817 544566459 642 True 606.000000 606 83.981000 950 1580 1 chr2D.!!$R4 630
2 TraesCS2D01G588000 chr2D 544326383 544326985 602 True 595.000000 595 84.488000 975 1580 1 chr2D.!!$R2 605
3 TraesCS2D01G588000 chr2D 544464239 544464875 636 True 590.000000 590 83.594000 950 1580 1 chr2D.!!$R3 630
4 TraesCS2D01G588000 chr2B 789963752 789966294 2542 False 1048.333333 2396 89.586667 76 2577 3 chr2B.!!$F1 2501
5 TraesCS2D01G588000 chr2B 649749597 649750233 636 True 601.000000 601 83.906000 950 1580 1 chr2B.!!$R3 630
6 TraesCS2D01G588000 chr2B 649755486 649756122 636 True 595.000000 595 83.750000 950 1580 1 chr2B.!!$R4 630
7 TraesCS2D01G588000 chr2B 649713437 649714073 636 True 579.000000 579 83.281000 950 1580 1 chr2B.!!$R2 630
8 TraesCS2D01G588000 chr2B 649707609 649708242 633 True 575.000000 575 83.281000 950 1579 1 chr2B.!!$R1 629
9 TraesCS2D01G588000 chr2A 771339121 771341733 2612 False 697.500000 2132 87.425750 76 2577 4 chr2A.!!$F1 2501
10 TraesCS2D01G588000 chr2A 686801276 686807756 6480 True 611.333333 636 82.597000 835 1580 3 chr2A.!!$R2 745
11 TraesCS2D01G588000 chr2A 686811763 686812593 830 True 610.000000 610 80.301000 731 1580 1 chr2A.!!$R1 849

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
55 56 0.102481 AGGTATACGCGCAGGACTTG 59.898 55.0 5.73 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1629 3748 0.173481 CGAGGAAAGCATGGACGAGA 59.827 55.0 0.0 0.0 0.0 4.04 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
38 39 9.627123 TTAGGATGATAAAATTGACAACCTAGG 57.373 33.333 7.41 7.41 38.39 3.02
39 40 7.643123 AGGATGATAAAATTGACAACCTAGGT 58.357 34.615 9.21 9.21 34.64 3.08
40 41 8.778059 AGGATGATAAAATTGACAACCTAGGTA 58.222 33.333 16.67 0.00 34.64 3.08
41 42 9.574516 GGATGATAAAATTGACAACCTAGGTAT 57.425 33.333 16.67 6.57 0.00 2.73
44 45 9.537192 TGATAAAATTGACAACCTAGGTATACG 57.463 33.333 16.67 6.92 0.00 3.06
45 46 6.673154 AAAATTGACAACCTAGGTATACGC 57.327 37.500 16.67 4.11 0.00 4.42
46 47 3.425577 TTGACAACCTAGGTATACGCG 57.574 47.619 16.67 3.53 0.00 6.01
47 48 1.066002 TGACAACCTAGGTATACGCGC 59.934 52.381 16.67 0.00 0.00 6.86
48 49 1.066002 GACAACCTAGGTATACGCGCA 59.934 52.381 16.67 0.00 0.00 6.09
49 50 1.066605 ACAACCTAGGTATACGCGCAG 59.933 52.381 16.67 2.42 0.00 5.18
50 51 0.672342 AACCTAGGTATACGCGCAGG 59.328 55.000 16.67 6.39 0.00 4.85
51 52 0.179009 ACCTAGGTATACGCGCAGGA 60.179 55.000 14.41 0.00 0.00 3.86
52 53 0.240411 CCTAGGTATACGCGCAGGAC 59.760 60.000 5.73 0.00 0.00 3.85
53 54 1.236628 CTAGGTATACGCGCAGGACT 58.763 55.000 5.73 1.68 0.00 3.85
54 55 1.607628 CTAGGTATACGCGCAGGACTT 59.392 52.381 5.73 0.00 0.00 3.01
55 56 0.102481 AGGTATACGCGCAGGACTTG 59.898 55.000 5.73 0.00 0.00 3.16
56 57 0.179119 GGTATACGCGCAGGACTTGT 60.179 55.000 5.73 0.00 0.00 3.16
57 58 1.066002 GGTATACGCGCAGGACTTGTA 59.934 52.381 5.73 0.00 0.00 2.41
58 59 2.480073 GGTATACGCGCAGGACTTGTAA 60.480 50.000 5.73 0.00 0.00 2.41
59 60 1.922570 ATACGCGCAGGACTTGTAAG 58.077 50.000 5.73 0.00 0.00 2.34
60 61 0.734942 TACGCGCAGGACTTGTAAGC 60.735 55.000 5.73 0.00 0.00 3.09
61 62 1.738099 CGCGCAGGACTTGTAAGCT 60.738 57.895 8.75 0.00 0.00 3.74
62 63 1.790387 GCGCAGGACTTGTAAGCTG 59.210 57.895 0.30 0.00 0.00 4.24
63 64 0.670546 GCGCAGGACTTGTAAGCTGA 60.671 55.000 0.30 0.00 0.00 4.26
64 65 1.795768 CGCAGGACTTGTAAGCTGAA 58.204 50.000 0.00 0.00 0.00 3.02
65 66 2.143122 CGCAGGACTTGTAAGCTGAAA 58.857 47.619 0.00 0.00 0.00 2.69
66 67 2.096218 CGCAGGACTTGTAAGCTGAAAC 60.096 50.000 0.00 0.00 0.00 2.78
67 68 2.096218 GCAGGACTTGTAAGCTGAAACG 60.096 50.000 0.00 0.00 0.00 3.60
68 69 2.480419 CAGGACTTGTAAGCTGAAACGG 59.520 50.000 0.00 0.00 0.00 4.44
69 70 2.367567 AGGACTTGTAAGCTGAAACGGA 59.632 45.455 0.00 0.00 0.00 4.69
70 71 2.737252 GGACTTGTAAGCTGAAACGGAG 59.263 50.000 0.00 0.00 0.00 4.63
71 72 2.737252 GACTTGTAAGCTGAAACGGAGG 59.263 50.000 0.00 0.00 0.00 4.30
72 73 2.104281 ACTTGTAAGCTGAAACGGAGGT 59.896 45.455 0.00 0.00 0.00 3.85
73 74 3.322828 ACTTGTAAGCTGAAACGGAGGTA 59.677 43.478 0.00 0.00 0.00 3.08
74 75 3.587797 TGTAAGCTGAAACGGAGGTAG 57.412 47.619 0.00 0.00 0.00 3.18
87 88 6.591750 AACGGAGGTAGTATATTCATGAGG 57.408 41.667 0.00 0.00 0.00 3.86
157 158 6.153067 GCAGTGAGTAGTGACATATACATCC 58.847 44.000 0.00 0.00 0.00 3.51
177 178 1.874345 GCATGCACTGCCAGAAAGCT 61.874 55.000 14.21 0.00 45.66 3.74
179 180 1.400846 CATGCACTGCCAGAAAGCTAG 59.599 52.381 0.00 0.00 0.00 3.42
182 183 1.367659 CACTGCCAGAAAGCTAGCTC 58.632 55.000 19.65 6.80 29.59 4.09
194 195 1.753368 GCTAGCTCCCAGCCCACTAG 61.753 65.000 7.70 0.00 43.77 2.57
230 231 4.523083 TGTCAAACAGGAAAACAGCTAGT 58.477 39.130 0.00 0.00 0.00 2.57
231 232 4.574828 TGTCAAACAGGAAAACAGCTAGTC 59.425 41.667 0.00 0.00 0.00 2.59
256 257 4.562963 CCCGTAACAGAAACTCTAAAGCCT 60.563 45.833 0.00 0.00 0.00 4.58
259 260 5.869888 CGTAACAGAAACTCTAAAGCCTGAT 59.130 40.000 0.00 0.00 0.00 2.90
269 275 1.813102 AAAGCCTGATCCTCCCCTAG 58.187 55.000 0.00 0.00 0.00 3.02
270 276 0.766288 AAGCCTGATCCTCCCCTAGC 60.766 60.000 0.00 0.00 0.00 3.42
271 277 1.152139 GCCTGATCCTCCCCTAGCT 60.152 63.158 0.00 0.00 0.00 3.32
272 278 1.479368 GCCTGATCCTCCCCTAGCTG 61.479 65.000 0.00 0.00 0.00 4.24
273 279 0.835543 CCTGATCCTCCCCTAGCTGG 60.836 65.000 0.00 0.00 0.00 4.85
274 280 0.189574 CTGATCCTCCCCTAGCTGGA 59.810 60.000 0.00 0.00 38.35 3.86
276 282 1.152139 ATCCTCCCCTAGCTGGAGC 60.152 63.158 17.12 0.00 46.69 4.70
304 310 5.316327 TGCTAGATCTCTTACGCATATGG 57.684 43.478 0.00 0.00 0.00 2.74
311 317 3.818773 TCTCTTACGCATATGGATGACGA 59.181 43.478 4.56 0.00 36.62 4.20
320 326 6.310467 ACGCATATGGATGACGACAATAATAC 59.690 38.462 4.56 0.00 36.62 1.89
328 341 7.030165 GGATGACGACAATAATACTGATCGAT 58.970 38.462 0.00 0.00 33.88 3.59
329 342 8.182227 GGATGACGACAATAATACTGATCGATA 58.818 37.037 0.00 0.00 33.88 2.92
441 487 0.822532 AGACAGGACCAGACGTCGTT 60.823 55.000 10.46 0.00 42.99 3.85
480 536 1.617755 CGTTGCACCACACGAGCTAG 61.618 60.000 2.49 0.00 0.00 3.42
481 537 1.667830 TTGCACCACACGAGCTAGC 60.668 57.895 6.62 6.62 0.00 3.42
482 538 2.099652 TTGCACCACACGAGCTAGCT 62.100 55.000 19.45 19.45 0.00 3.32
483 539 1.248101 TGCACCACACGAGCTAGCTA 61.248 55.000 19.38 0.00 0.00 3.32
484 540 0.526524 GCACCACACGAGCTAGCTAG 60.527 60.000 19.38 20.70 0.00 3.42
500 556 5.003967 GCTAGCTAGCGAAGATAATTAAGCG 59.996 44.000 28.89 0.00 39.82 4.68
502 558 3.181529 GCTAGCGAAGATAATTAAGCGGC 60.182 47.826 0.00 0.00 0.00 6.53
503 559 2.833794 AGCGAAGATAATTAAGCGGCA 58.166 42.857 1.45 0.00 0.00 5.69
505 561 2.663063 GCGAAGATAATTAAGCGGCAGC 60.663 50.000 0.00 0.00 45.58 5.25
519 575 2.901292 GCAGCTGTGTCTGTGTGGC 61.901 63.158 16.64 0.00 36.49 5.01
524 580 1.609061 GCTGTGTCTGTGTGGCTGTAT 60.609 52.381 0.00 0.00 0.00 2.29
663 719 7.281999 GGATGTCAAAAGAGAGGAAAAGATAGG 59.718 40.741 0.00 0.00 0.00 2.57
774 832 3.092301 AGCACTAATGGGAGAAAAAGGC 58.908 45.455 0.00 0.00 0.00 4.35
900 962 3.136791 GCTTGCTACCTGCCTGCC 61.137 66.667 0.00 0.00 42.00 4.85
901 963 2.673523 CTTGCTACCTGCCTGCCT 59.326 61.111 0.00 0.00 42.00 4.75
904 966 4.182433 GCTACCTGCCTGCCTCCC 62.182 72.222 0.00 0.00 35.15 4.30
905 967 3.854669 CTACCTGCCTGCCTCCCG 61.855 72.222 0.00 0.00 0.00 5.14
1628 3747 2.643790 CGTCACCGATCGTCGTCG 60.644 66.667 15.09 9.95 38.40 5.12
1629 3748 2.477845 GTCACCGATCGTCGTCGT 59.522 61.111 15.09 0.80 38.40 4.34
1633 3752 2.054156 CCGATCGTCGTCGTCTCG 60.054 66.667 15.09 17.06 38.40 4.04
1634 3753 2.693874 CGATCGTCGTCGTCTCGT 59.306 61.111 7.03 0.00 37.94 4.18
1635 3754 1.365110 CGATCGTCGTCGTCTCGTC 60.365 63.158 7.03 4.06 37.94 4.20
1659 3779 1.480954 GCTTTCCTCGTGATCCTACCA 59.519 52.381 0.00 0.00 0.00 3.25
1752 4118 2.561885 CCGTGCGTCTCGTCTTCT 59.438 61.111 0.00 0.00 0.00 2.85
1770 4136 6.690957 CGTCTTCTCTAGTTAATTCTCTGCTG 59.309 42.308 0.00 0.00 0.00 4.41
1773 4139 6.537453 TCTCTAGTTAATTCTCTGCTGCTT 57.463 37.500 0.00 0.00 0.00 3.91
1775 4141 8.067751 TCTCTAGTTAATTCTCTGCTGCTTAA 57.932 34.615 0.00 0.00 0.00 1.85
1830 4207 3.116463 CATGCATGCCACGCTGAT 58.884 55.556 14.93 0.00 0.00 2.90
1891 4289 4.240096 ACTGCACCATGTAACGTTACTAC 58.760 43.478 32.10 15.17 34.77 2.73
1893 4291 4.239304 TGCACCATGTAACGTTACTACTG 58.761 43.478 32.10 25.31 34.77 2.74
1896 4294 5.622007 GCACCATGTAACGTTACTACTGGTA 60.622 44.000 34.41 20.40 38.42 3.25
1897 4295 5.801947 CACCATGTAACGTTACTACTGGTAC 59.198 44.000 34.41 17.66 38.42 3.34
1898 4296 5.030295 CCATGTAACGTTACTACTGGTACG 58.970 45.833 32.10 14.19 34.77 3.67
1900 4298 6.183360 CCATGTAACGTTACTACTGGTACGTA 60.183 42.308 32.10 13.12 37.26 3.57
1902 4300 5.929992 TGTAACGTTACTACTGGTACGTACT 59.070 40.000 32.10 8.34 37.26 2.73
1903 4301 7.092079 TGTAACGTTACTACTGGTACGTACTA 58.908 38.462 32.10 18.04 37.26 1.82
1904 4302 6.648725 AACGTTACTACTGGTACGTACTAG 57.351 41.667 30.61 30.61 40.22 2.57
1906 4304 6.860080 ACGTTACTACTGGTACGTACTAGTA 58.140 40.000 35.25 35.25 44.66 1.82
1907 4305 6.750963 ACGTTACTACTGGTACGTACTAGTAC 59.249 42.308 34.72 28.51 44.66 2.73
1908 4306 6.973474 CGTTACTACTGGTACGTACTAGTACT 59.027 42.308 34.72 29.00 44.66 2.73
2013 6118 0.729116 CCATGCAAGTCAAGCCGTAG 59.271 55.000 0.00 0.00 0.00 3.51
2183 6424 3.707316 ACTCTAGCCATGTCTTGAGACT 58.293 45.455 19.60 0.00 44.99 3.24
2184 6425 4.093011 ACTCTAGCCATGTCTTGAGACTT 58.907 43.478 19.60 3.50 44.99 3.01
2189 6430 3.326006 AGCCATGTCTTGAGACTTGAGAA 59.674 43.478 21.74 0.09 46.77 2.87
2190 6431 4.067896 GCCATGTCTTGAGACTTGAGAAA 58.932 43.478 21.74 0.00 46.77 2.52
2195 6436 6.465439 TGTCTTGAGACTTGAGAAACAGTA 57.535 37.500 12.00 0.00 44.99 2.74
2196 6437 7.055667 TGTCTTGAGACTTGAGAAACAGTAT 57.944 36.000 12.00 0.00 44.99 2.12
2245 6488 2.996621 CAAAGAATCACGAGTCCACTCC 59.003 50.000 1.01 0.00 39.79 3.85
2355 6614 2.940994 TTTGCCACACAGCTACCTAA 57.059 45.000 0.00 0.00 0.00 2.69
2443 7609 1.527311 GTCCGAGCTCAACACAAAGAC 59.473 52.381 15.40 3.36 0.00 3.01
2445 7611 1.541233 CCGAGCTCAACACAAAGACCT 60.541 52.381 15.40 0.00 0.00 3.85
2446 7612 2.288825 CCGAGCTCAACACAAAGACCTA 60.289 50.000 15.40 0.00 0.00 3.08
2448 7614 3.728845 GAGCTCAACACAAAGACCTACA 58.271 45.455 9.40 0.00 0.00 2.74
2559 7987 4.445162 CCGCACCCCCTTCAATACTTATTA 60.445 45.833 0.00 0.00 0.00 0.98
2563 7991 7.201875 CGCACCCCCTTCAATACTTATTATTTT 60.202 37.037 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 9.627123 CCTAGGTTGTCAATTTTATCATCCTAA 57.373 33.333 0.00 0.00 34.20 2.69
13 14 8.778059 ACCTAGGTTGTCAATTTTATCATCCTA 58.222 33.333 9.21 0.00 33.70 2.94
14 15 7.643123 ACCTAGGTTGTCAATTTTATCATCCT 58.357 34.615 9.21 0.00 35.23 3.24
15 16 7.881775 ACCTAGGTTGTCAATTTTATCATCC 57.118 36.000 9.21 0.00 0.00 3.51
18 19 9.537192 CGTATACCTAGGTTGTCAATTTTATCA 57.463 33.333 22.11 0.00 0.00 2.15
19 20 8.493547 GCGTATACCTAGGTTGTCAATTTTATC 58.506 37.037 22.11 0.00 0.00 1.75
20 21 7.170320 CGCGTATACCTAGGTTGTCAATTTTAT 59.830 37.037 22.11 5.71 0.00 1.40
21 22 6.476380 CGCGTATACCTAGGTTGTCAATTTTA 59.524 38.462 22.11 0.00 0.00 1.52
22 23 5.292589 CGCGTATACCTAGGTTGTCAATTTT 59.707 40.000 22.11 0.00 0.00 1.82
23 24 4.807304 CGCGTATACCTAGGTTGTCAATTT 59.193 41.667 22.11 0.00 0.00 1.82
24 25 4.365723 CGCGTATACCTAGGTTGTCAATT 58.634 43.478 22.11 0.00 0.00 2.32
25 26 3.797865 GCGCGTATACCTAGGTTGTCAAT 60.798 47.826 22.11 9.64 0.00 2.57
26 27 2.480073 GCGCGTATACCTAGGTTGTCAA 60.480 50.000 22.11 0.75 0.00 3.18
27 28 1.066002 GCGCGTATACCTAGGTTGTCA 59.934 52.381 22.11 1.21 0.00 3.58
28 29 1.066002 TGCGCGTATACCTAGGTTGTC 59.934 52.381 22.11 9.56 0.00 3.18
29 30 1.066605 CTGCGCGTATACCTAGGTTGT 59.933 52.381 22.11 12.13 0.00 3.32
30 31 1.602165 CCTGCGCGTATACCTAGGTTG 60.602 57.143 22.11 9.15 0.00 3.77
31 32 0.672342 CCTGCGCGTATACCTAGGTT 59.328 55.000 22.11 10.62 0.00 3.50
32 33 0.179009 TCCTGCGCGTATACCTAGGT 60.179 55.000 20.57 20.57 0.00 3.08
33 34 0.240411 GTCCTGCGCGTATACCTAGG 59.760 60.000 7.41 7.41 0.00 3.02
34 35 1.236628 AGTCCTGCGCGTATACCTAG 58.763 55.000 8.43 0.00 0.00 3.02
35 36 1.335810 CAAGTCCTGCGCGTATACCTA 59.664 52.381 8.43 0.00 0.00 3.08
36 37 0.102481 CAAGTCCTGCGCGTATACCT 59.898 55.000 8.43 0.00 0.00 3.08
37 38 0.179119 ACAAGTCCTGCGCGTATACC 60.179 55.000 8.43 0.00 0.00 2.73
38 39 2.480224 TACAAGTCCTGCGCGTATAC 57.520 50.000 8.43 4.74 0.00 1.47
39 40 2.797087 GCTTACAAGTCCTGCGCGTATA 60.797 50.000 8.43 0.00 0.00 1.47
40 41 1.922570 CTTACAAGTCCTGCGCGTAT 58.077 50.000 8.43 0.00 0.00 3.06
41 42 0.734942 GCTTACAAGTCCTGCGCGTA 60.735 55.000 8.43 0.71 0.00 4.42
42 43 2.027625 GCTTACAAGTCCTGCGCGT 61.028 57.895 8.43 0.00 0.00 6.01
43 44 1.738099 AGCTTACAAGTCCTGCGCG 60.738 57.895 0.00 0.00 0.00 6.86
44 45 0.670546 TCAGCTTACAAGTCCTGCGC 60.671 55.000 0.00 0.00 0.00 6.09
45 46 1.795768 TTCAGCTTACAAGTCCTGCG 58.204 50.000 0.00 0.00 0.00 5.18
46 47 2.096218 CGTTTCAGCTTACAAGTCCTGC 60.096 50.000 0.00 0.00 0.00 4.85
47 48 2.480419 CCGTTTCAGCTTACAAGTCCTG 59.520 50.000 0.00 0.00 0.00 3.86
48 49 2.367567 TCCGTTTCAGCTTACAAGTCCT 59.632 45.455 0.00 0.00 0.00 3.85
49 50 2.737252 CTCCGTTTCAGCTTACAAGTCC 59.263 50.000 0.00 0.00 0.00 3.85
50 51 2.737252 CCTCCGTTTCAGCTTACAAGTC 59.263 50.000 0.00 0.00 0.00 3.01
51 52 2.104281 ACCTCCGTTTCAGCTTACAAGT 59.896 45.455 0.00 0.00 0.00 3.16
52 53 2.767505 ACCTCCGTTTCAGCTTACAAG 58.232 47.619 0.00 0.00 0.00 3.16
53 54 2.922740 ACCTCCGTTTCAGCTTACAA 57.077 45.000 0.00 0.00 0.00 2.41
54 55 2.895404 ACTACCTCCGTTTCAGCTTACA 59.105 45.455 0.00 0.00 0.00 2.41
55 56 3.589495 ACTACCTCCGTTTCAGCTTAC 57.411 47.619 0.00 0.00 0.00 2.34
56 57 7.286087 TGAATATACTACCTCCGTTTCAGCTTA 59.714 37.037 0.00 0.00 0.00 3.09
57 58 6.097839 TGAATATACTACCTCCGTTTCAGCTT 59.902 38.462 0.00 0.00 0.00 3.74
58 59 5.597182 TGAATATACTACCTCCGTTTCAGCT 59.403 40.000 0.00 0.00 0.00 4.24
59 60 5.839621 TGAATATACTACCTCCGTTTCAGC 58.160 41.667 0.00 0.00 0.00 4.26
60 61 7.658261 TCATGAATATACTACCTCCGTTTCAG 58.342 38.462 0.00 0.00 0.00 3.02
61 62 7.255836 CCTCATGAATATACTACCTCCGTTTCA 60.256 40.741 0.00 0.00 0.00 2.69
62 63 7.039923 TCCTCATGAATATACTACCTCCGTTTC 60.040 40.741 0.00 0.00 0.00 2.78
63 64 6.781014 TCCTCATGAATATACTACCTCCGTTT 59.219 38.462 0.00 0.00 0.00 3.60
64 65 6.312529 TCCTCATGAATATACTACCTCCGTT 58.687 40.000 0.00 0.00 0.00 4.44
65 66 5.888901 TCCTCATGAATATACTACCTCCGT 58.111 41.667 0.00 0.00 0.00 4.69
66 67 6.603599 TGATCCTCATGAATATACTACCTCCG 59.396 42.308 0.00 0.00 0.00 4.63
67 68 7.962995 TGATCCTCATGAATATACTACCTCC 57.037 40.000 0.00 0.00 0.00 4.30
68 69 9.194972 TGATGATCCTCATGAATATACTACCTC 57.805 37.037 0.00 0.00 37.20 3.85
69 70 8.976353 GTGATGATCCTCATGAATATACTACCT 58.024 37.037 3.88 0.00 37.20 3.08
70 71 8.200792 GGTGATGATCCTCATGAATATACTACC 58.799 40.741 3.88 0.00 37.20 3.18
71 72 8.753133 TGGTGATGATCCTCATGAATATACTAC 58.247 37.037 3.88 0.00 37.20 2.73
72 73 8.899887 TGGTGATGATCCTCATGAATATACTA 57.100 34.615 3.88 0.00 37.20 1.82
73 74 7.803487 TGGTGATGATCCTCATGAATATACT 57.197 36.000 3.88 0.00 37.20 2.12
74 75 9.458727 AAATGGTGATGATCCTCATGAATATAC 57.541 33.333 3.88 0.00 37.20 1.47
87 88 6.860080 AGTGTTCATTGAAATGGTGATGATC 58.140 36.000 0.00 0.00 37.03 2.92
170 171 1.631071 GGGCTGGGAGCTAGCTTTCT 61.631 60.000 20.42 0.00 41.99 2.52
177 178 1.075226 CCTAGTGGGCTGGGAGCTA 60.075 63.158 0.00 0.00 45.17 3.32
194 195 2.237393 TTGACAAATTTGTGCTGGCC 57.763 45.000 27.85 12.78 42.43 5.36
230 231 2.019807 AGAGTTTCTGTTACGGGGGA 57.980 50.000 0.00 0.00 0.00 4.81
231 232 3.967332 TTAGAGTTTCTGTTACGGGGG 57.033 47.619 0.00 0.00 0.00 5.40
256 257 0.189574 CTCCAGCTAGGGGAGGATCA 59.810 60.000 10.17 0.00 46.65 2.92
269 275 1.818785 CTAGCAAGCCAGCTCCAGC 60.819 63.158 3.49 0.00 45.26 4.85
270 276 0.469070 ATCTAGCAAGCCAGCTCCAG 59.531 55.000 3.49 0.00 45.26 3.86
271 277 0.467384 GATCTAGCAAGCCAGCTCCA 59.533 55.000 3.49 0.00 45.26 3.86
272 278 0.758123 AGATCTAGCAAGCCAGCTCC 59.242 55.000 3.49 0.00 45.26 4.70
273 279 1.688197 AGAGATCTAGCAAGCCAGCTC 59.312 52.381 3.49 0.00 45.26 4.09
274 280 6.288084 CGTAAGAGATCTAGCAAGCCAGCT 62.288 50.000 0.00 5.76 44.99 4.24
275 281 2.618442 AAGAGATCTAGCAAGCCAGC 57.382 50.000 0.00 0.00 0.00 4.85
276 282 3.637432 CGTAAGAGATCTAGCAAGCCAG 58.363 50.000 0.00 0.00 43.02 4.85
277 283 2.223829 GCGTAAGAGATCTAGCAAGCCA 60.224 50.000 0.00 0.00 43.02 4.75
278 284 2.223829 TGCGTAAGAGATCTAGCAAGCC 60.224 50.000 0.00 0.00 43.02 4.35
279 285 3.085443 TGCGTAAGAGATCTAGCAAGC 57.915 47.619 0.00 0.00 43.02 4.01
280 286 5.804473 CCATATGCGTAAGAGATCTAGCAAG 59.196 44.000 0.00 0.00 43.02 4.01
281 287 5.476945 TCCATATGCGTAAGAGATCTAGCAA 59.523 40.000 0.00 0.00 43.02 3.91
282 288 5.010282 TCCATATGCGTAAGAGATCTAGCA 58.990 41.667 0.00 3.51 43.02 3.49
304 310 9.001049 GTATCGATCAGTATTATTGTCGTCATC 57.999 37.037 0.00 0.00 0.00 2.92
320 326 8.707938 TTTCCTTGCATATATGTATCGATCAG 57.292 34.615 14.14 3.25 0.00 2.90
328 341 8.859090 CCTTTGGATTTTCCTTGCATATATGTA 58.141 33.333 14.14 7.00 37.46 2.29
329 342 7.687592 GCCTTTGGATTTTCCTTGCATATATGT 60.688 37.037 14.14 0.00 37.46 2.29
335 348 2.026915 GGCCTTTGGATTTTCCTTGCAT 60.027 45.455 0.00 0.00 37.46 3.96
441 487 3.006133 TGCATGGGTAGACCGGCA 61.006 61.111 0.00 7.09 46.11 5.69
480 536 3.181529 GCCGCTTAATTATCTTCGCTAGC 60.182 47.826 4.06 4.06 0.00 3.42
481 537 3.987868 TGCCGCTTAATTATCTTCGCTAG 59.012 43.478 0.00 0.00 0.00 3.42
482 538 3.985008 TGCCGCTTAATTATCTTCGCTA 58.015 40.909 0.00 0.00 0.00 4.26
483 539 2.802816 CTGCCGCTTAATTATCTTCGCT 59.197 45.455 0.00 0.00 0.00 4.93
484 540 2.663063 GCTGCCGCTTAATTATCTTCGC 60.663 50.000 0.00 0.00 0.00 4.70
485 541 2.802816 AGCTGCCGCTTAATTATCTTCG 59.197 45.455 0.00 0.00 46.47 3.79
486 542 3.561725 ACAGCTGCCGCTTAATTATCTTC 59.438 43.478 15.27 0.00 46.47 2.87
487 543 3.313526 CACAGCTGCCGCTTAATTATCTT 59.686 43.478 15.27 0.00 46.47 2.40
488 544 2.874701 CACAGCTGCCGCTTAATTATCT 59.125 45.455 15.27 0.00 46.47 1.98
489 545 2.614057 ACACAGCTGCCGCTTAATTATC 59.386 45.455 15.27 0.00 46.47 1.75
500 556 2.256591 CCACACAGACACAGCTGCC 61.257 63.158 15.27 3.20 39.51 4.85
502 558 1.227764 AGCCACACAGACACAGCTG 60.228 57.895 13.48 13.48 41.63 4.24
503 559 1.227764 CAGCCACACAGACACAGCT 60.228 57.895 0.00 0.00 0.00 4.24
505 561 2.071540 CATACAGCCACACAGACACAG 58.928 52.381 0.00 0.00 0.00 3.66
506 562 1.691434 TCATACAGCCACACAGACACA 59.309 47.619 0.00 0.00 0.00 3.72
512 568 4.280677 TCGATCATATCATACAGCCACACA 59.719 41.667 0.00 0.00 0.00 3.72
519 575 8.454106 TGAGTGTACATCGATCATATCATACAG 58.546 37.037 0.00 0.00 0.00 2.74
524 580 5.241506 TGCTGAGTGTACATCGATCATATCA 59.758 40.000 0.00 0.00 0.00 2.15
587 643 1.816835 GATCGACCACACACCTAGACA 59.183 52.381 0.00 0.00 0.00 3.41
663 719 0.178990 GGCCCTCTCTCTCTCTCTCC 60.179 65.000 0.00 0.00 0.00 3.71
774 832 4.559063 CATGCCGCTCTCCCCCTG 62.559 72.222 0.00 0.00 0.00 4.45
900 962 3.941188 AGTGGTGTGTGGCGGGAG 61.941 66.667 0.00 0.00 0.00 4.30
901 963 4.248842 CAGTGGTGTGTGGCGGGA 62.249 66.667 0.00 0.00 0.00 5.14
905 967 3.595758 GTGGCAGTGGTGTGTGGC 61.596 66.667 0.00 0.00 39.62 5.01
906 968 2.906897 GGTGGCAGTGGTGTGTGG 60.907 66.667 0.00 0.00 0.00 4.17
907 969 1.518056 GATGGTGGCAGTGGTGTGTG 61.518 60.000 0.00 0.00 0.00 3.82
908 970 1.228245 GATGGTGGCAGTGGTGTGT 60.228 57.895 0.00 0.00 0.00 3.72
909 971 0.957395 GAGATGGTGGCAGTGGTGTG 60.957 60.000 0.00 0.00 0.00 3.82
910 972 1.376466 GAGATGGTGGCAGTGGTGT 59.624 57.895 0.00 0.00 0.00 4.16
1628 3747 1.646189 GAGGAAAGCATGGACGAGAC 58.354 55.000 0.00 0.00 0.00 3.36
1629 3748 0.173481 CGAGGAAAGCATGGACGAGA 59.827 55.000 0.00 0.00 0.00 4.04
1633 3752 1.936547 GATCACGAGGAAAGCATGGAC 59.063 52.381 0.00 0.00 0.00 4.02
1634 3753 1.134401 GGATCACGAGGAAAGCATGGA 60.134 52.381 0.00 0.00 0.00 3.41
1635 3754 1.134280 AGGATCACGAGGAAAGCATGG 60.134 52.381 0.00 0.00 0.00 3.66
1659 3779 2.239124 CGTTGGCACCACGTACGTT 61.239 57.895 20.23 1.62 0.00 3.99
1701 3821 2.048222 CATGCACGGACGTCAGGT 60.048 61.111 19.84 12.72 0.00 4.00
1744 4110 6.600032 AGCAGAGAATTAACTAGAGAAGACGA 59.400 38.462 0.00 0.00 0.00 4.20
1745 4111 6.690957 CAGCAGAGAATTAACTAGAGAAGACG 59.309 42.308 0.00 0.00 0.00 4.18
1746 4112 6.475402 GCAGCAGAGAATTAACTAGAGAAGAC 59.525 42.308 0.00 0.00 0.00 3.01
1752 4118 9.319143 GAATTAAGCAGCAGAGAATTAACTAGA 57.681 33.333 0.00 0.00 0.00 2.43
1824 4201 1.064505 CTGGCCAATGTTACATCAGCG 59.935 52.381 7.01 0.00 0.00 5.18
1826 4203 2.098607 CAGCTGGCCAATGTTACATCAG 59.901 50.000 7.01 2.98 0.00 2.90
1827 4204 2.093890 CAGCTGGCCAATGTTACATCA 58.906 47.619 7.01 0.00 0.00 3.07
1829 4206 0.819582 GCAGCTGGCCAATGTTACAT 59.180 50.000 17.12 0.00 36.11 2.29
1830 4207 0.539207 TGCAGCTGGCCAATGTTACA 60.539 50.000 17.12 0.00 43.89 2.41
1891 4289 6.459298 CCCAATCAAGTACTAGTACGTACCAG 60.459 46.154 23.87 19.78 40.42 4.00
1893 4291 5.590259 TCCCAATCAAGTACTAGTACGTACC 59.410 44.000 23.87 6.46 40.42 3.34
1896 4294 4.643784 CCTCCCAATCAAGTACTAGTACGT 59.356 45.833 23.87 19.50 40.80 3.57
1897 4295 4.643784 ACCTCCCAATCAAGTACTAGTACG 59.356 45.833 23.87 13.15 40.80 3.67
1898 4296 5.163437 CCACCTCCCAATCAAGTACTAGTAC 60.163 48.000 23.03 23.03 36.35 2.73
1900 4298 3.775316 CCACCTCCCAATCAAGTACTAGT 59.225 47.826 0.00 0.00 0.00 2.57
1902 4300 4.069312 TCCACCTCCCAATCAAGTACTA 57.931 45.455 0.00 0.00 0.00 1.82
1903 4301 2.915869 TCCACCTCCCAATCAAGTACT 58.084 47.619 0.00 0.00 0.00 2.73
1904 4302 3.263425 TCTTCCACCTCCCAATCAAGTAC 59.737 47.826 0.00 0.00 0.00 2.73
1905 4303 3.526899 TCTTCCACCTCCCAATCAAGTA 58.473 45.455 0.00 0.00 0.00 2.24
1906 4304 2.348472 TCTTCCACCTCCCAATCAAGT 58.652 47.619 0.00 0.00 0.00 3.16
1907 4305 3.350833 CTTCTTCCACCTCCCAATCAAG 58.649 50.000 0.00 0.00 0.00 3.02
1908 4306 2.041620 CCTTCTTCCACCTCCCAATCAA 59.958 50.000 0.00 0.00 0.00 2.57
1992 6097 1.675310 CGGCTTGACTTGCATGGGA 60.675 57.895 4.44 0.00 0.00 4.37
2013 6118 4.853924 AGTTGAACAATGAACACATCCC 57.146 40.909 0.00 0.00 0.00 3.85
2018 6131 6.494842 TCAAGCTTAGTTGAACAATGAACAC 58.505 36.000 0.00 0.00 33.41 3.32
2067 6180 5.647658 CCACACTGCTAATATTGTCCTCAAA 59.352 40.000 0.00 0.00 37.11 2.69
2073 6196 3.941483 ACTGCCACACTGCTAATATTGTC 59.059 43.478 0.00 0.00 0.00 3.18
2159 6400 4.629200 GTCTCAAGACATGGCTAGAGTTTG 59.371 45.833 0.00 0.00 44.18 2.93
2183 6424 8.978539 CGCTGCTAATTATATACTGTTTCTCAA 58.021 33.333 0.00 0.00 0.00 3.02
2184 6425 8.141909 ACGCTGCTAATTATATACTGTTTCTCA 58.858 33.333 0.00 0.00 0.00 3.27
2189 6430 7.207383 TGTCACGCTGCTAATTATATACTGTT 58.793 34.615 0.00 0.00 0.00 3.16
2190 6431 6.745116 TGTCACGCTGCTAATTATATACTGT 58.255 36.000 0.00 0.00 0.00 3.55
2195 6436 4.449068 GCACTGTCACGCTGCTAATTATAT 59.551 41.667 0.00 0.00 0.00 0.86
2196 6437 3.802139 GCACTGTCACGCTGCTAATTATA 59.198 43.478 0.00 0.00 0.00 0.98
2443 7609 6.519679 TGGGTACGTAGCAATATATGTAGG 57.480 41.667 24.76 0.00 29.84 3.18
2445 7611 7.395206 AGTGATGGGTACGTAGCAATATATGTA 59.605 37.037 24.76 1.83 0.00 2.29
2446 7612 6.210784 AGTGATGGGTACGTAGCAATATATGT 59.789 38.462 24.76 0.00 0.00 2.29
2448 7614 6.210784 ACAGTGATGGGTACGTAGCAATATAT 59.789 38.462 24.76 11.15 0.00 0.86
2488 7913 2.876581 CCCTCCAAAAGTTGCTACCTT 58.123 47.619 0.00 0.00 0.00 3.50


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

AutoCloner maintained by Alex Coulton.