Multiple sequence alignment - TraesCS6D01G094300

Loading Multiple Alignment...

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 TraesCS6D01G094300 chr6D 100.000 6205 0 0 1 6205 58699355 58693151 0.000000e+00 11459.0
1 TraesCS6D01G094300 chr6A 94.488 4699 178 29 550 5207 73998862 73994204 0.000000e+00 7167.0
2 TraesCS6D01G094300 chr6A 95.613 1003 27 9 5208 6205 73994171 73993181 0.000000e+00 1592.0
3 TraesCS6D01G094300 chr6B 94.682 2877 136 12 2345 5207 132317039 132314166 0.000000e+00 4449.0
4 TraesCS6D01G094300 chr6B 92.254 1717 99 15 646 2346 132318788 132317090 0.000000e+00 2403.0
5 TraesCS6D01G094300 chr6B 93.680 538 26 5 5208 5738 132314133 132313597 0.000000e+00 798.0
6 TraesCS6D01G094300 chr6B 94.224 277 9 3 5934 6205 132313500 132313226 3.460000e-112 416.0
7 TraesCS6D01G094300 chr6B 95.745 47 2 0 5796 5842 132313578 132313532 6.670000e-10 76.8
8 TraesCS6D01G094300 chr3A 85.057 609 76 9 62 657 584028633 584028027 1.910000e-169 606.0
9 TraesCS6D01G094300 chr3D 85.050 602 74 11 66 655 29565246 29565843 3.200000e-167 599.0
10 TraesCS6D01G094300 chr3D 84.884 602 75 11 66 655 29493377 29493974 1.490000e-165 593.0
11 TraesCS6D01G094300 chr3D 84.385 602 78 11 66 655 29528306 29528903 1.500000e-160 577.0
12 TraesCS6D01G094300 chrUn 84.884 602 75 11 66 655 223001724 223002321 1.490000e-165 593.0
13 TraesCS6D01G094300 chr7D 83.677 631 86 9 39 655 80797275 80797902 4.170000e-161 579.0
14 TraesCS6D01G094300 chr7D 81.864 601 90 9 66 654 49384962 49385555 7.230000e-134 488.0
15 TraesCS6D01G094300 chr5B 83.967 605 79 12 67 655 530654042 530653440 1.170000e-156 564.0
16 TraesCS6D01G094300 chr7A 82.363 601 90 10 68 655 555457388 555457985 5.550000e-140 508.0
17 TraesCS6D01G094300 chr2B 86.400 375 45 4 1511 1882 147672577 147672948 7.490000e-109 405.0
18 TraesCS6D01G094300 chr2A 89.850 266 25 2 1623 1886 234451988 234451723 2.140000e-89 340.0


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 TraesCS6D01G094300 chr6D 58693151 58699355 6204 True 11459.00 11459 100.0000 1 6205 1 chr6D.!!$R1 6204
1 TraesCS6D01G094300 chr6A 73993181 73998862 5681 True 4379.50 7167 95.0505 550 6205 2 chr6A.!!$R1 5655
2 TraesCS6D01G094300 chr6B 132313226 132318788 5562 True 1628.56 4449 94.1170 646 6205 5 chr6B.!!$R1 5559
3 TraesCS6D01G094300 chr3A 584028027 584028633 606 True 606.00 606 85.0570 62 657 1 chr3A.!!$R1 595
4 TraesCS6D01G094300 chr3D 29565246 29565843 597 False 599.00 599 85.0500 66 655 1 chr3D.!!$F3 589
5 TraesCS6D01G094300 chr3D 29493377 29493974 597 False 593.00 593 84.8840 66 655 1 chr3D.!!$F1 589
6 TraesCS6D01G094300 chr3D 29528306 29528903 597 False 577.00 577 84.3850 66 655 1 chr3D.!!$F2 589
7 TraesCS6D01G094300 chrUn 223001724 223002321 597 False 593.00 593 84.8840 66 655 1 chrUn.!!$F1 589
8 TraesCS6D01G094300 chr7D 80797275 80797902 627 False 579.00 579 83.6770 39 655 1 chr7D.!!$F2 616
9 TraesCS6D01G094300 chr7D 49384962 49385555 593 False 488.00 488 81.8640 66 654 1 chr7D.!!$F1 588
10 TraesCS6D01G094300 chr5B 530653440 530654042 602 True 564.00 564 83.9670 67 655 1 chr5B.!!$R1 588
11 TraesCS6D01G094300 chr7A 555457388 555457985 597 False 508.00 508 82.3630 68 655 1 chr7A.!!$F1 587

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
64 65 0.318360 CTTGTGTCGCTGGTGTCGTA 60.318 55.0 0.00 0.0 0.00 3.43 F
250 260 0.388520 TTCTGTCGTCGCACATCCAG 60.389 55.0 0.00 0.0 0.00 3.86 F
661 680 0.539518 TTCGCTCCAAATCGGGATCA 59.460 50.0 0.00 0.0 36.09 2.92 F
688 707 0.613572 TGTGGAGCCCGAGTGTGATA 60.614 55.0 0.00 0.0 0.00 2.15 F
2374 2480 0.712380 ATTTTGGCCCCATGGAGACT 59.288 50.0 15.22 0.0 0.00 3.24 F
4030 4158 0.810031 GTACAGCTGGTGTATGGCGG 60.810 60.0 21.04 0.0 43.70 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1579 1631 0.634465 ATTTATCCAAACCCCGCCCT 59.366 50.000 0.00 0.00 0.00 5.19 R
2071 2125 2.477176 GCGTCACCAGCAACCACAA 61.477 57.895 0.00 0.00 34.19 3.33 R
2374 2480 2.297315 CGAGGCATAGAGATAAGGTGCA 59.703 50.000 0.00 0.00 37.53 4.57 R
2376 2482 3.823873 AGACGAGGCATAGAGATAAGGTG 59.176 47.826 0.00 0.00 0.00 4.00 R
4314 4443 0.674581 TGAAGAGATTGGCAGCACCG 60.675 55.000 0.00 0.00 43.94 4.94 R
5630 5797 0.524414 AAATAAAGAACGCCACGGGC 59.476 50.000 4.96 4.96 46.75 6.13 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 1.517242 GCACTTGCAAGCAGAGTAGT 58.483 50.000 26.27 1.47 41.59 2.73
32 33 1.876156 GCACTTGCAAGCAGAGTAGTT 59.124 47.619 26.27 0.04 41.59 2.24
33 34 2.096019 GCACTTGCAAGCAGAGTAGTTC 60.096 50.000 26.27 0.00 41.59 3.01
34 35 2.481952 CACTTGCAAGCAGAGTAGTTCC 59.518 50.000 26.27 0.00 0.00 3.62
35 36 2.104792 ACTTGCAAGCAGAGTAGTTCCA 59.895 45.455 26.27 0.00 0.00 3.53
36 37 2.928801 TGCAAGCAGAGTAGTTCCAA 57.071 45.000 0.00 0.00 0.00 3.53
37 38 2.771089 TGCAAGCAGAGTAGTTCCAAG 58.229 47.619 0.00 0.00 0.00 3.61
38 39 2.368548 TGCAAGCAGAGTAGTTCCAAGA 59.631 45.455 0.00 0.00 0.00 3.02
39 40 2.999355 GCAAGCAGAGTAGTTCCAAGAG 59.001 50.000 0.00 0.00 0.00 2.85
40 41 3.594134 CAAGCAGAGTAGTTCCAAGAGG 58.406 50.000 0.00 0.00 0.00 3.69
41 42 3.176924 AGCAGAGTAGTTCCAAGAGGA 57.823 47.619 0.00 0.00 43.93 3.71
42 43 3.718723 AGCAGAGTAGTTCCAAGAGGAT 58.281 45.455 0.00 0.00 45.26 3.24
43 44 4.100373 AGCAGAGTAGTTCCAAGAGGATT 58.900 43.478 0.00 0.00 45.26 3.01
44 45 4.534103 AGCAGAGTAGTTCCAAGAGGATTT 59.466 41.667 0.00 0.00 45.26 2.17
45 46 4.873259 GCAGAGTAGTTCCAAGAGGATTTC 59.127 45.833 0.00 0.00 45.26 2.17
46 47 5.337975 GCAGAGTAGTTCCAAGAGGATTTCT 60.338 44.000 0.00 0.00 45.26 2.52
57 58 1.734465 GAGGATTTCTTGTGTCGCTGG 59.266 52.381 0.00 0.00 0.00 4.85
58 59 1.072331 AGGATTTCTTGTGTCGCTGGT 59.928 47.619 0.00 0.00 0.00 4.00
64 65 0.318360 CTTGTGTCGCTGGTGTCGTA 60.318 55.000 0.00 0.00 0.00 3.43
89 91 6.216456 AGTCATCTGAGAAATTTAGGTCCCTT 59.784 38.462 0.00 0.00 0.00 3.95
95 97 6.003950 TGAGAAATTTAGGTCCCTTGTCTTG 58.996 40.000 0.00 0.00 0.00 3.02
96 98 6.183361 TGAGAAATTTAGGTCCCTTGTCTTGA 60.183 38.462 0.00 0.00 0.00 3.02
107 109 2.008329 CTTGTCTTGAGCTGCCATCTC 58.992 52.381 0.00 0.00 0.00 2.75
112 114 1.830587 TTGAGCTGCCATCTCGGTGT 61.831 55.000 0.00 0.00 36.97 4.16
148 151 3.055747 ACCTCGGATTTTCAAGACCTCTC 60.056 47.826 0.00 0.00 0.00 3.20
238 248 5.122512 TGAGGTTAGAGAGTTTTCTGTCG 57.877 43.478 0.00 0.00 43.78 4.35
244 254 1.452399 GAGAGTTTTCTGTCGTCGCAC 59.548 52.381 0.00 0.00 32.53 5.34
250 260 0.388520 TTCTGTCGTCGCACATCCAG 60.389 55.000 0.00 0.00 0.00 3.86
267 277 5.532406 ACATCCAGTTATTCGGATTTGATGG 59.468 40.000 0.00 0.00 40.12 3.51
342 354 6.093495 GGTGAAATCTTTTATCGACACCATGA 59.907 38.462 0.00 0.00 43.75 3.07
349 361 6.535150 TCTTTTATCGACACCATGATGAAGAC 59.465 38.462 0.00 0.00 30.24 3.01
371 383 2.125552 TGATTCGACGGCCTGCAG 60.126 61.111 6.78 6.78 0.00 4.41
400 412 4.487714 GGATCATCCCTGACACAAGTAA 57.512 45.455 0.00 0.00 33.22 2.24
466 480 4.494484 AGGCGCTTTCAAAAACCATTATC 58.506 39.130 7.64 0.00 0.00 1.75
468 482 4.162812 GCGCTTTCAAAAACCATTATCGA 58.837 39.130 0.00 0.00 0.00 3.59
506 520 4.034048 GTGAAAGAGTGACAACATCGTTGT 59.966 41.667 12.05 12.05 37.82 3.32
557 573 7.878127 TGAAGTCTTTGGAGTATTTCTTCGAAT 59.122 33.333 0.00 0.00 34.64 3.34
573 592 9.443323 TTTCTTCGAATAAAGATTGATACCACA 57.557 29.630 0.00 0.00 35.30 4.17
596 615 7.009540 CACAAAGGTGTTTTCAAGAGATTTCAC 59.990 37.037 0.00 0.00 40.24 3.18
608 627 7.810658 TCAAGAGATTTCACTGTAATTCTTGC 58.189 34.615 17.19 0.00 39.83 4.01
609 628 7.445096 TCAAGAGATTTCACTGTAATTCTTGCA 59.555 33.333 17.19 0.00 39.83 4.08
610 629 7.375106 AGAGATTTCACTGTAATTCTTGCAG 57.625 36.000 3.81 3.81 46.98 4.41
618 637 4.012374 CTGTAATTCTTGCAGTCATGGGT 58.988 43.478 0.00 0.00 38.39 4.51
661 680 0.539518 TTCGCTCCAAATCGGGATCA 59.460 50.000 0.00 0.00 36.09 2.92
688 707 0.613572 TGTGGAGCCCGAGTGTGATA 60.614 55.000 0.00 0.00 0.00 2.15
696 715 4.526970 AGCCCGAGTGTGATAATTGAATT 58.473 39.130 0.00 0.00 0.00 2.17
741 760 3.364267 CGTGGAAACGGTTAAAGCTTACC 60.364 47.826 8.18 8.18 0.00 2.85
742 761 3.817084 GTGGAAACGGTTAAAGCTTACCT 59.183 43.478 14.95 0.00 32.08 3.08
746 765 5.579904 GGAAACGGTTAAAGCTTACCTCTAG 59.420 44.000 14.95 3.81 32.08 2.43
758 777 5.766174 AGCTTACCTCTAGTAGTAGATGTGC 59.234 44.000 19.98 16.38 35.56 4.57
760 779 4.521536 ACCTCTAGTAGTAGATGTGCCA 57.478 45.455 13.03 0.00 34.03 4.92
769 788 5.835819 AGTAGTAGATGTGCCAGATGTGTAT 59.164 40.000 0.00 0.00 0.00 2.29
770 789 7.004691 AGTAGTAGATGTGCCAGATGTGTATA 58.995 38.462 0.00 0.00 0.00 1.47
771 790 6.924913 AGTAGATGTGCCAGATGTGTATAT 57.075 37.500 0.00 0.00 0.00 0.86
772 791 6.929625 AGTAGATGTGCCAGATGTGTATATC 58.070 40.000 0.00 0.00 0.00 1.63
773 792 4.814147 AGATGTGCCAGATGTGTATATCG 58.186 43.478 0.00 0.00 32.33 2.92
774 793 2.754472 TGTGCCAGATGTGTATATCGC 58.246 47.619 0.00 0.00 32.33 4.58
775 794 2.102252 TGTGCCAGATGTGTATATCGCA 59.898 45.455 0.00 0.00 40.97 5.10
776 795 2.476619 GTGCCAGATGTGTATATCGCAC 59.523 50.000 4.40 4.40 39.47 5.34
1377 1427 2.555547 GCTGGCACCGCTTGAAAGT 61.556 57.895 0.00 0.00 0.00 2.66
1383 1433 2.545742 GGCACCGCTTGAAAGTTGAAAT 60.546 45.455 0.00 0.00 0.00 2.17
1469 1519 3.350909 TACCTGCAGCGCCGTACTG 62.351 63.158 8.66 0.00 38.22 2.74
1470 1520 4.742201 CCTGCAGCGCCGTACTGT 62.742 66.667 8.66 0.00 37.47 3.55
1484 1534 3.427863 CCGTACTGTCGAAACTTTCCTTC 59.572 47.826 0.00 0.00 0.00 3.46
1524 1574 4.379082 GGGTGTTGACATTGTCGATAAACC 60.379 45.833 19.03 19.03 34.95 3.27
1526 1576 3.120477 TGTTGACATTGTCGATAAACCGC 60.120 43.478 9.92 0.00 34.95 5.68
1527 1577 2.967362 TGACATTGTCGATAAACCGCT 58.033 42.857 11.97 0.00 34.95 5.52
1567 1619 3.207778 AGTAGTATCACGCTCAGGACTC 58.792 50.000 0.00 0.00 0.00 3.36
1569 1621 2.447443 AGTATCACGCTCAGGACTCAA 58.553 47.619 0.00 0.00 0.00 3.02
1579 1631 4.442052 CGCTCAGGACTCAATGAGGAATTA 60.442 45.833 15.38 0.00 42.62 1.40
1711 1763 5.330455 TGTTATGTGAAAACAGTTGCCAA 57.670 34.783 0.00 0.00 33.13 4.52
1712 1764 5.105752 TGTTATGTGAAAACAGTTGCCAAC 58.894 37.500 0.00 0.00 33.13 3.77
1719 1771 4.037446 TGAAAACAGTTGCCAACATAGGTC 59.963 41.667 10.69 2.39 0.00 3.85
2071 2125 9.758651 GTTTGGTTAGTAAGTTTTGGATCAAAT 57.241 29.630 0.00 0.00 33.19 2.32
2076 2130 9.191995 GTTAGTAAGTTTTGGATCAAATTGTGG 57.808 33.333 0.00 0.00 33.19 4.17
2083 2137 2.299582 TGGATCAAATTGTGGTTGCTGG 59.700 45.455 0.00 0.00 0.00 4.85
2087 2141 2.100584 TCAAATTGTGGTTGCTGGTGAC 59.899 45.455 0.00 0.00 0.00 3.67
2093 2147 2.607892 GGTTGCTGGTGACGCTCAC 61.608 63.158 8.94 8.94 46.23 3.51
2172 2226 8.729805 TGCATCAACATATGAAAGTGTGTATA 57.270 30.769 10.38 0.00 42.54 1.47
2177 2231 9.171877 TCAACATATGAAAGTGTGTATATGCAA 57.828 29.630 10.38 0.00 37.13 4.08
2188 2242 7.761409 AGTGTGTATATGCAATTTTACACCTG 58.239 34.615 20.01 0.00 40.80 4.00
2288 2342 8.049721 TGGTTATACCATGTACATTCAACATCA 58.950 33.333 5.37 0.00 44.79 3.07
2309 2363 8.464404 ACATCATAATTCTGTGAAATGGTCAAG 58.536 33.333 0.00 0.00 38.23 3.02
2374 2480 0.712380 ATTTTGGCCCCATGGAGACT 59.288 50.000 15.22 0.00 0.00 3.24
2376 2482 2.786512 TTTGGCCCCATGGAGACTGC 62.787 60.000 15.22 7.44 0.00 4.40
2380 2486 2.304056 CCCCATGGAGACTGCACCT 61.304 63.158 15.22 0.00 0.00 4.00
2385 2491 2.437281 CCATGGAGACTGCACCTTATCT 59.563 50.000 5.56 0.00 0.00 1.98
2408 2514 2.724977 TGCCTCGTCTAGTTGAACAG 57.275 50.000 0.00 0.00 0.00 3.16
2451 2557 5.819825 AAACCACTCTTGTTGAAGTCTTC 57.180 39.130 5.58 5.58 0.00 2.87
2498 2604 6.932947 ACTAGCTTACTTTCTTGTCGGTTAT 58.067 36.000 0.00 0.00 0.00 1.89
2567 2674 4.635765 TCTGTTGACTATGGCTTAATGCAC 59.364 41.667 0.00 0.00 45.15 4.57
2568 2675 3.694072 TGTTGACTATGGCTTAATGCACC 59.306 43.478 0.00 0.00 45.15 5.01
2657 2765 2.508526 GGTGTGAGGACAGCTTGAATT 58.491 47.619 0.00 0.00 45.46 2.17
2678 2786 9.056005 TGAATTCCACATGCTAAGAATGTATAC 57.944 33.333 2.27 0.00 36.10 1.47
2748 2858 5.988287 TCAGATTATTGTGCCACTGTATGA 58.012 37.500 0.00 0.00 0.00 2.15
3896 4023 6.983890 GCTTTCTTTGGTTTCAATGGTAAGAA 59.016 34.615 0.00 0.00 32.28 2.52
3898 4025 7.654022 TTCTTTGGTTTCAATGGTAAGAACT 57.346 32.000 0.00 0.00 32.28 3.01
3944 4071 1.527034 TCAATGAAGCCTGACACTGC 58.473 50.000 0.00 0.00 0.00 4.40
4024 4152 2.036733 GTCAACAGGTACAGCTGGTGTA 59.963 50.000 22.03 15.14 40.94 2.90
4030 4158 0.810031 GTACAGCTGGTGTATGGCGG 60.810 60.000 21.04 0.00 43.70 6.13
4157 4285 9.793259 ATGTAGGTGATATAAGGGTATGTTTTG 57.207 33.333 0.00 0.00 0.00 2.44
4158 4286 7.717875 TGTAGGTGATATAAGGGTATGTTTTGC 59.282 37.037 0.00 0.00 0.00 3.68
4159 4287 5.763204 AGGTGATATAAGGGTATGTTTTGCG 59.237 40.000 0.00 0.00 0.00 4.85
4314 4443 0.393537 AGCAGCATAGGTGGACTTGC 60.394 55.000 0.00 0.00 35.10 4.01
4399 4528 1.757682 ACCTCACCGCAAAAGACAAA 58.242 45.000 0.00 0.00 0.00 2.83
4577 4706 5.119694 GTTCCTGAAGTCCATATTCCTGTC 58.880 45.833 0.00 0.00 0.00 3.51
4592 4721 1.584724 CTGTCTGGGGGTTGGTCTAT 58.415 55.000 0.00 0.00 0.00 1.98
4601 4730 3.586174 GGGGGTTGGTCTATATTCCTACC 59.414 52.174 14.09 14.09 44.60 3.18
4611 4740 3.604875 ATATTCCTACCGCCATTACCG 57.395 47.619 0.00 0.00 0.00 4.02
4649 4778 7.068702 TCAGAAATCCTGGGTATGCATTATTT 58.931 34.615 3.54 0.64 43.12 1.40
4818 4947 1.630148 GTTTACTCGAGACTGCGCAT 58.370 50.000 21.68 0.17 0.00 4.73
4869 4998 1.135333 GGAGATCTGGTGAAGGACGAC 59.865 57.143 0.00 0.00 0.00 4.34
5031 5160 2.871633 GTGCTTCAAACCCCAACATTTG 59.128 45.455 0.00 0.00 37.19 2.32
5032 5161 1.872952 GCTTCAAACCCCAACATTTGC 59.127 47.619 0.00 0.00 36.06 3.68
5063 5193 5.552870 GGATTTACATCCCTGAGCTCTTA 57.447 43.478 16.19 0.00 43.29 2.10
5336 5499 4.261801 AGTATTGGATTTGAGGGTTCGTG 58.738 43.478 0.00 0.00 0.00 4.35
5448 5613 9.388506 AGATTCCAAGTTATTGAGACTGTAATG 57.611 33.333 0.00 0.00 38.83 1.90
5597 5764 0.368907 CCGTTCGAACCATTGCTACG 59.631 55.000 22.07 8.06 0.00 3.51
5843 6017 8.867097 AGTTTAGAGGATACACAAGTTAACTGA 58.133 33.333 9.34 0.00 41.41 3.41
5992 6169 0.393537 AGCTAACATCCAGCCAGCAC 60.394 55.000 0.00 0.00 39.99 4.40
6123 6300 8.978874 TGCAAGGAACACATCAAGTAATATAT 57.021 30.769 0.00 0.00 0.00 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.517242 ACTACTCTGCTTGCAAGTGC 58.483 50.000 26.55 15.49 42.50 4.40
13 14 2.481952 GGAACTACTCTGCTTGCAAGTG 59.518 50.000 26.55 19.15 0.00 3.16
14 15 2.104792 TGGAACTACTCTGCTTGCAAGT 59.895 45.455 26.55 10.69 0.00 3.16
15 16 2.771089 TGGAACTACTCTGCTTGCAAG 58.229 47.619 22.44 22.44 0.00 4.01
16 17 2.928801 TGGAACTACTCTGCTTGCAA 57.071 45.000 0.00 0.00 0.00 4.08
17 18 2.368548 TCTTGGAACTACTCTGCTTGCA 59.631 45.455 0.00 0.00 0.00 4.08
18 19 2.999355 CTCTTGGAACTACTCTGCTTGC 59.001 50.000 0.00 0.00 0.00 4.01
19 20 3.259374 TCCTCTTGGAACTACTCTGCTTG 59.741 47.826 0.00 0.00 39.87 4.01
20 21 3.511477 TCCTCTTGGAACTACTCTGCTT 58.489 45.455 0.00 0.00 39.87 3.91
21 22 3.176924 TCCTCTTGGAACTACTCTGCT 57.823 47.619 0.00 0.00 39.87 4.24
22 23 4.479786 AATCCTCTTGGAACTACTCTGC 57.520 45.455 0.00 0.00 46.80 4.26
23 24 6.293004 AGAAATCCTCTTGGAACTACTCTG 57.707 41.667 0.00 0.00 46.80 3.35
24 25 6.943899 AAGAAATCCTCTTGGAACTACTCT 57.056 37.500 0.00 0.00 46.80 3.24
35 36 3.070018 CAGCGACACAAGAAATCCTCTT 58.930 45.455 0.00 0.00 45.80 2.85
36 37 2.613977 CCAGCGACACAAGAAATCCTCT 60.614 50.000 0.00 0.00 35.13 3.69
37 38 1.734465 CCAGCGACACAAGAAATCCTC 59.266 52.381 0.00 0.00 0.00 3.71
38 39 1.072331 ACCAGCGACACAAGAAATCCT 59.928 47.619 0.00 0.00 0.00 3.24
39 40 1.197721 CACCAGCGACACAAGAAATCC 59.802 52.381 0.00 0.00 0.00 3.01
40 41 1.873591 ACACCAGCGACACAAGAAATC 59.126 47.619 0.00 0.00 0.00 2.17
41 42 1.873591 GACACCAGCGACACAAGAAAT 59.126 47.619 0.00 0.00 0.00 2.17
42 43 1.295792 GACACCAGCGACACAAGAAA 58.704 50.000 0.00 0.00 0.00 2.52
43 44 0.874175 CGACACCAGCGACACAAGAA 60.874 55.000 0.00 0.00 0.00 2.52
44 45 1.299850 CGACACCAGCGACACAAGA 60.300 57.895 0.00 0.00 0.00 3.02
45 46 0.318360 TACGACACCAGCGACACAAG 60.318 55.000 0.00 0.00 0.00 3.16
46 47 0.318360 CTACGACACCAGCGACACAA 60.318 55.000 0.00 0.00 0.00 3.33
47 48 1.284715 CTACGACACCAGCGACACA 59.715 57.895 0.00 0.00 0.00 3.72
57 58 6.952935 AAATTTCTCAGATGACTACGACAC 57.047 37.500 0.00 0.00 0.00 3.67
58 59 7.093902 ACCTAAATTTCTCAGATGACTACGACA 60.094 37.037 0.00 0.00 0.00 4.35
64 65 5.728741 AGGGACCTAAATTTCTCAGATGACT 59.271 40.000 0.00 0.00 0.00 3.41
89 91 0.108472 CGAGATGGCAGCTCAAGACA 60.108 55.000 29.78 0.00 32.67 3.41
95 97 1.078848 AACACCGAGATGGCAGCTC 60.079 57.895 22.31 22.31 43.94 4.09
96 98 1.376424 CAACACCGAGATGGCAGCT 60.376 57.895 4.21 4.21 43.94 4.24
107 109 2.347490 CCCCACCTCTCAACACCG 59.653 66.667 0.00 0.00 0.00 4.94
148 151 5.596268 TGATGATCGTTGACAAAGAACAG 57.404 39.130 16.51 0.00 0.00 3.16
238 248 1.593006 CCGAATAACTGGATGTGCGAC 59.407 52.381 0.00 0.00 0.00 5.19
244 254 5.048504 CCCATCAAATCCGAATAACTGGATG 60.049 44.000 0.00 0.00 44.16 3.51
250 260 7.712797 ACATAAACCCATCAAATCCGAATAAC 58.287 34.615 0.00 0.00 0.00 1.89
267 277 4.932146 AGCTTGACACAACAACATAAACC 58.068 39.130 0.00 0.00 0.00 3.27
295 307 3.633986 CCTCATAAAGAATCAGGCCAACC 59.366 47.826 5.01 0.00 0.00 3.77
301 313 7.059156 AGATTTCACCCTCATAAAGAATCAGG 58.941 38.462 0.00 0.00 0.00 3.86
342 354 4.611943 CCGTCGAATCACTATGTCTTCAT 58.388 43.478 0.00 0.00 38.00 2.57
349 361 1.491670 CAGGCCGTCGAATCACTATG 58.508 55.000 0.00 0.00 0.00 2.23
393 405 4.759782 CCTTGATCGATGGACTTACTTGT 58.240 43.478 0.54 0.00 0.00 3.16
400 412 1.139853 GGAAGCCTTGATCGATGGACT 59.860 52.381 0.54 0.00 0.00 3.85
466 480 5.293324 TCTTTCACCCGAATGAACATTATCG 59.707 40.000 0.00 1.64 38.31 2.92
468 482 6.094048 CACTCTTTCACCCGAATGAACATTAT 59.906 38.462 0.00 0.00 38.31 1.28
477 491 3.139077 GTTGTCACTCTTTCACCCGAAT 58.861 45.455 0.00 0.00 0.00 3.34
479 493 1.483004 TGTTGTCACTCTTTCACCCGA 59.517 47.619 0.00 0.00 0.00 5.14
515 529 3.142174 ACTTCAGTAAAGAGGCTGCAAC 58.858 45.455 0.50 0.00 38.44 4.17
573 592 7.093771 ACAGTGAAATCTCTTGAAAACACCTTT 60.094 33.333 0.00 0.00 0.00 3.11
596 615 4.012374 ACCCATGACTGCAAGAATTACAG 58.988 43.478 0.00 0.00 45.01 2.74
607 626 2.884639 ACAAAGTAACACCCATGACTGC 59.115 45.455 0.00 0.00 0.00 4.40
608 627 6.817765 AATACAAAGTAACACCCATGACTG 57.182 37.500 0.00 0.00 0.00 3.51
609 628 7.724061 AGAAAATACAAAGTAACACCCATGACT 59.276 33.333 0.00 0.00 0.00 3.41
610 629 7.882179 AGAAAATACAAAGTAACACCCATGAC 58.118 34.615 0.00 0.00 0.00 3.06
611 630 8.356657 CAAGAAAATACAAAGTAACACCCATGA 58.643 33.333 0.00 0.00 0.00 3.07
614 633 6.834451 TCCAAGAAAATACAAAGTAACACCCA 59.166 34.615 0.00 0.00 0.00 4.51
615 634 7.279750 TCCAAGAAAATACAAAGTAACACCC 57.720 36.000 0.00 0.00 0.00 4.61
644 663 1.151668 GATGATCCCGATTTGGAGCG 58.848 55.000 0.00 0.00 43.85 5.03
661 680 0.909610 TCGGGCTCCACAAGAAGGAT 60.910 55.000 0.00 0.00 33.99 3.24
688 707 9.565213 GAATCAAGTCTTTCGATCAATTCAATT 57.435 29.630 0.00 0.00 0.00 2.32
721 740 4.067192 GAGGTAAGCTTTAACCGTTTCCA 58.933 43.478 3.20 0.00 40.88 3.53
741 760 5.767665 ACATCTGGCACATCTACTACTAGAG 59.232 44.000 0.00 0.00 38.20 2.43
742 761 5.532779 CACATCTGGCACATCTACTACTAGA 59.467 44.000 0.00 0.00 38.20 2.43
746 765 4.392921 ACACATCTGGCACATCTACTAC 57.607 45.455 0.00 0.00 38.20 2.73
758 777 3.182372 CGTTGTGCGATATACACATCTGG 59.818 47.826 10.86 0.34 46.72 3.86
760 779 4.041740 ACGTTGTGCGATATACACATCT 57.958 40.909 10.86 1.13 46.72 2.90
769 788 1.135315 GGTACCTGACGTTGTGCGATA 60.135 52.381 4.06 0.00 44.77 2.92
770 789 0.389426 GGTACCTGACGTTGTGCGAT 60.389 55.000 4.06 0.00 44.77 4.58
771 790 1.007038 GGTACCTGACGTTGTGCGA 60.007 57.895 4.06 0.00 44.77 5.10
773 792 0.598158 TTCGGTACCTGACGTTGTGC 60.598 55.000 10.90 0.00 0.00 4.57
774 793 1.790623 CTTTCGGTACCTGACGTTGTG 59.209 52.381 10.90 0.00 0.00 3.33
775 794 1.870993 GCTTTCGGTACCTGACGTTGT 60.871 52.381 10.90 0.00 0.00 3.32
776 795 0.788391 GCTTTCGGTACCTGACGTTG 59.212 55.000 10.90 0.00 0.00 4.10
1364 1411 3.060339 GCAATTTCAACTTTCAAGCGGTG 60.060 43.478 0.00 0.00 0.00 4.94
1365 1412 3.123050 GCAATTTCAACTTTCAAGCGGT 58.877 40.909 0.00 0.00 0.00 5.68
1431 1481 7.086376 CAGGTACATTTCAACTTTGAATCAGG 58.914 38.462 5.26 0.00 45.65 3.86
1433 1483 6.040278 TGCAGGTACATTTCAACTTTGAATCA 59.960 34.615 5.26 0.00 45.65 2.57
1469 1519 2.132762 TCGCAGAAGGAAAGTTTCGAC 58.867 47.619 9.46 3.84 0.00 4.20
1470 1520 2.519377 TCGCAGAAGGAAAGTTTCGA 57.481 45.000 9.46 0.00 0.00 3.71
1484 1534 1.812571 ACCCAAAGCTACATTTCGCAG 59.187 47.619 0.00 0.00 0.00 5.18
1567 1619 1.609208 CCCGCCCTAATTCCTCATTG 58.391 55.000 0.00 0.00 0.00 2.82
1569 1621 0.697854 ACCCCGCCCTAATTCCTCAT 60.698 55.000 0.00 0.00 0.00 2.90
1579 1631 0.634465 ATTTATCCAAACCCCGCCCT 59.366 50.000 0.00 0.00 0.00 5.19
1711 1763 6.225318 TGTAAACAAAACGCTAGACCTATGT 58.775 36.000 0.00 0.00 0.00 2.29
1712 1764 6.715344 TGTAAACAAAACGCTAGACCTATG 57.285 37.500 0.00 0.00 0.00 2.23
1719 1771 5.220228 CCGAGAGATGTAAACAAAACGCTAG 60.220 44.000 0.00 0.00 0.00 3.42
2050 2104 9.191995 CCACAATTTGATCCAAAACTTACTAAC 57.808 33.333 2.79 0.00 36.90 2.34
2054 2108 7.518211 GCAACCACAATTTGATCCAAAACTTAC 60.518 37.037 2.79 0.00 36.90 2.34
2071 2125 2.477176 GCGTCACCAGCAACCACAA 61.477 57.895 0.00 0.00 34.19 3.33
2072 2126 2.899838 GCGTCACCAGCAACCACA 60.900 61.111 0.00 0.00 34.19 4.17
2076 2130 2.939022 GTGAGCGTCACCAGCAAC 59.061 61.111 6.82 0.00 41.37 4.17
2087 2141 3.348309 CATGAATCATTTCACGTGAGCG 58.652 45.455 19.11 11.11 44.36 5.03
2093 2147 3.127376 TCTGGTGCATGAATCATTTCACG 59.873 43.478 14.87 6.62 44.36 4.35
2172 2226 3.577848 TGGAAGCAGGTGTAAAATTGCAT 59.422 39.130 0.00 0.00 38.97 3.96
2288 2342 7.605449 CAACCTTGACCATTTCACAGAATTAT 58.395 34.615 0.00 0.00 32.26 1.28
2309 2363 6.209391 ACCCATGCTTAGATTAATATGCAACC 59.791 38.462 0.00 0.00 38.73 3.77
2374 2480 2.297315 CGAGGCATAGAGATAAGGTGCA 59.703 50.000 0.00 0.00 37.53 4.57
2376 2482 3.823873 AGACGAGGCATAGAGATAAGGTG 59.176 47.826 0.00 0.00 0.00 4.00
2380 2486 6.296803 TCAACTAGACGAGGCATAGAGATAA 58.703 40.000 0.00 0.00 0.00 1.75
2385 2491 4.014406 TGTTCAACTAGACGAGGCATAGA 58.986 43.478 0.00 0.00 0.00 1.98
2408 2514 8.131100 TGGTTTATAACTAGTACGTATGTCAGC 58.869 37.037 0.00 0.00 0.00 4.26
2525 2632 9.111613 TCAACAGAAATTTCAAGCAATCAAATT 57.888 25.926 19.99 0.00 32.30 1.82
2544 2651 4.635765 GTGCATTAAGCCATAGTCAACAGA 59.364 41.667 0.00 0.00 44.83 3.41
2657 2765 6.040504 ACTCGTATACATTCTTAGCATGTGGA 59.959 38.462 7.71 0.31 35.57 4.02
2678 2786 7.794810 CAGACTATCTTTCACTTCGTATACTCG 59.205 40.741 0.56 0.00 0.00 4.18
2766 2876 2.233922 GCTCCACTAGTTCCTGCACTTA 59.766 50.000 0.00 0.00 0.00 2.24
3386 3509 6.769134 TTCTGTCATAGGATACGACAAAGA 57.231 37.500 0.00 0.00 39.07 2.52
3770 3897 3.187227 AGCATCGTAGTTCACTGCAAAAG 59.813 43.478 0.00 0.00 35.32 2.27
3922 4049 3.144506 CAGTGTCAGGCTTCATTGAAGT 58.855 45.455 23.66 6.06 41.27 3.01
3944 4071 9.748708 TTCAAATGAACCATTTCAAGAAACTAG 57.251 29.630 2.27 0.00 45.01 2.57
4024 4152 4.225042 TCATTAATAGCAGATACCCGCCAT 59.775 41.667 0.00 0.00 0.00 4.40
4030 4158 7.233389 TCCTGACTCATTAATAGCAGATACC 57.767 40.000 0.00 0.00 0.00 2.73
4157 4285 2.423538 ACTATTTGGAATTGCAGACCGC 59.576 45.455 0.00 0.00 42.89 5.68
4158 4286 4.082787 ACAACTATTTGGAATTGCAGACCG 60.083 41.667 0.00 0.00 37.00 4.79
4159 4287 5.391312 ACAACTATTTGGAATTGCAGACC 57.609 39.130 0.00 0.00 37.00 3.85
4211 4340 7.290061 ACTTGTAATGATGTAGGGCACAATAT 58.710 34.615 0.00 0.00 41.55 1.28
4314 4443 0.674581 TGAAGAGATTGGCAGCACCG 60.675 55.000 0.00 0.00 43.94 4.94
4577 4706 3.327439 AGGAATATAGACCAACCCCCAG 58.673 50.000 0.00 0.00 0.00 4.45
4592 4721 2.297033 GACGGTAATGGCGGTAGGAATA 59.703 50.000 0.00 0.00 0.00 1.75
4601 4730 1.334059 GCATTCATGACGGTAATGGCG 60.334 52.381 5.64 0.00 32.44 5.69
4611 4740 4.583489 AGGATTTCTGATGGCATTCATGAC 59.417 41.667 0.00 0.00 35.97 3.06
4649 4778 1.961394 AGCTGTACTCTGGACGAAACA 59.039 47.619 0.00 0.00 0.00 2.83
4712 4841 0.324368 ATGGAGAGACCTGGCGTACA 60.324 55.000 0.00 0.00 39.86 2.90
4818 4947 6.212589 TCTCAGTAACTACCCAATCATTCACA 59.787 38.462 0.00 0.00 0.00 3.58
4869 4998 3.423539 TCAAGGAGTGGGACATCAAAG 57.576 47.619 0.00 0.00 44.52 2.77
5021 5150 2.931246 GCAAAGGGCAAATGTTGGG 58.069 52.632 0.00 0.00 43.97 4.12
5031 5160 2.101415 GGATGTAAATCCTGCAAAGGGC 59.899 50.000 4.48 0.00 45.13 5.19
5032 5161 2.695147 GGGATGTAAATCCTGCAAAGGG 59.305 50.000 11.89 0.00 40.54 3.95
5063 5193 0.677098 TCAAGAGGTAGAGCGCGAGT 60.677 55.000 12.10 0.00 0.00 4.18
5296 5459 9.822727 TCCAATACTCATCTACCATTCTGTATA 57.177 33.333 0.00 0.00 0.00 1.47
5336 5499 6.591935 TCCATCATTGTACAACTAGGATTCC 58.408 40.000 11.22 0.00 0.00 3.01
5426 5591 7.602644 GTGTCATTACAGTCTCAATAACTTGGA 59.397 37.037 0.00 0.00 35.91 3.53
5448 5613 3.940209 TTCATTGCCTTTCATGGTGTC 57.060 42.857 0.00 0.00 0.00 3.67
5493 5658 1.203994 GCTGCTCTACCTCGGTACAAA 59.796 52.381 0.00 0.00 0.00 2.83
5534 5701 3.679980 GCACGAGACAGCAAATAAGAGAA 59.320 43.478 0.00 0.00 0.00 2.87
5535 5702 3.254060 GCACGAGACAGCAAATAAGAGA 58.746 45.455 0.00 0.00 0.00 3.10
5597 5764 1.358759 GCGACTCCTCTCTAGCTGC 59.641 63.158 0.00 0.00 0.00 5.25
5630 5797 0.524414 AAATAAAGAACGCCACGGGC 59.476 50.000 4.96 4.96 46.75 6.13
5843 6017 0.952010 AAAATACAACCGGCTCGCGT 60.952 50.000 5.77 0.00 0.00 6.01
5992 6169 1.091771 ATGCCTCGATTTGTCAGCGG 61.092 55.000 0.00 0.00 0.00 5.52
6123 6300 6.590292 GCCGCTCTTCATAGCTTATTGTATTA 59.410 38.462 0.00 0.00 40.49 0.98
6124 6301 5.409826 GCCGCTCTTCATAGCTTATTGTATT 59.590 40.000 0.00 0.00 40.49 1.89


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

AutoCloner maintained by Alex Coulton.