Multiple sequence alignment - TraesCS3D01G327400

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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 TraesCS3D01G327400 chr3D 100.000 5354 0 0 1 5354 439672357 439667004 0.000000e+00 9888
1 TraesCS3D01G327400 chr3A 97.329 4381 97 6 38 4400 579371873 579367495 0.000000e+00 7424
2 TraesCS3D01G327400 chr3A 80.769 598 45 34 4768 5354 579352138 579351600 2.320000e-108 403
3 TraesCS3D01G327400 chr3A 98.400 125 1 1 4399 4523 579367402 579367279 9.030000e-53 219
4 TraesCS3D01G327400 chr3A 92.742 124 4 3 4522 4643 579367155 579367035 1.980000e-39 174
5 TraesCS3D01G327400 chr3B 96.156 3746 132 5 785 4523 576443655 576439915 0.000000e+00 6109
6 TraesCS3D01G327400 chr3B 90.736 734 37 16 38 756 576444555 576443838 0.000000e+00 950
7 TraesCS3D01G327400 chr3B 90.682 719 38 10 4645 5354 576439627 576438929 0.000000e+00 929
8 TraesCS3D01G327400 chr3B 95.161 124 6 0 4522 4645 576439791 576439668 4.230000e-46 196
9 TraesCS3D01G327400 chrUn 100.000 405 0 0 3581 3985 478229310 478228906 0.000000e+00 749


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 TraesCS3D01G327400 chr3D 439667004 439672357 5353 True 9888.000000 9888 100.00000 1 5354 1 chr3D.!!$R1 5353
1 TraesCS3D01G327400 chr3A 579367035 579371873 4838 True 2605.666667 7424 96.15700 38 4643 3 chr3A.!!$R2 4605
2 TraesCS3D01G327400 chr3A 579351600 579352138 538 True 403.000000 403 80.76900 4768 5354 1 chr3A.!!$R1 586
3 TraesCS3D01G327400 chr3B 576438929 576444555 5626 True 2046.000000 6109 93.18375 38 5354 4 chr3B.!!$R1 5316

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
574 590 1.451927 CCATCCACCATCCACCACG 60.452 63.158 0.00 0.00 0.0 4.94 F
1722 1903 1.946768 TGCTTTGACGGGAGAAAACTG 59.053 47.619 0.00 0.00 0.0 3.16 F
2247 2428 0.033228 CAGCTCTGCGGCTAAGCTAT 59.967 55.000 22.87 6.32 44.3 2.97 F
3022 3203 0.394488 TGTTGTCTTGAAACGCCCCA 60.394 50.000 0.00 0.00 0.0 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1932 2113 0.109179 TGCCAACATTCTCATTGCGC 60.109 50.000 0.00 0.00 0.00 6.09 R
3572 3753 0.600057 CTTCTTCAGCTTGGGGCAAC 59.400 55.000 0.00 0.00 44.79 4.17 R
4138 4319 4.698575 AGTGTTTCAAGTGAGGAGACTTC 58.301 43.478 0.00 0.00 44.43 3.01 R
4695 5137 0.670546 ATAGTGTATCGCGCATGGGC 60.671 55.000 23.87 23.87 0.00 5.36 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 5.814764 CATTGATTTCCCTCAACAGAGAG 57.185 43.478 0.00 0.00 37.93 3.20
23 24 5.494724 CATTGATTTCCCTCAACAGAGAGA 58.505 41.667 0.00 0.00 37.93 3.10
24 25 4.815533 TGATTTCCCTCAACAGAGAGAG 57.184 45.455 0.00 0.00 37.87 3.20
25 26 4.420206 TGATTTCCCTCAACAGAGAGAGA 58.580 43.478 0.00 0.00 37.87 3.10
26 27 4.465660 TGATTTCCCTCAACAGAGAGAGAG 59.534 45.833 0.00 0.00 37.87 3.20
27 28 3.816398 TTCCCTCAACAGAGAGAGAGA 57.184 47.619 0.00 0.00 37.87 3.10
28 29 3.364460 TCCCTCAACAGAGAGAGAGAG 57.636 52.381 0.00 0.00 37.87 3.20
29 30 2.916269 TCCCTCAACAGAGAGAGAGAGA 59.084 50.000 0.00 0.00 37.87 3.10
30 31 3.054434 TCCCTCAACAGAGAGAGAGAGAG 60.054 52.174 0.00 0.00 37.87 3.20
31 32 3.054434 CCCTCAACAGAGAGAGAGAGAGA 60.054 52.174 0.00 0.00 37.87 3.10
32 33 4.194640 CCTCAACAGAGAGAGAGAGAGAG 58.805 52.174 0.00 0.00 37.87 3.20
33 34 4.080919 CCTCAACAGAGAGAGAGAGAGAGA 60.081 50.000 0.00 0.00 37.87 3.10
34 35 5.089970 TCAACAGAGAGAGAGAGAGAGAG 57.910 47.826 0.00 0.00 0.00 3.20
35 36 4.777366 TCAACAGAGAGAGAGAGAGAGAGA 59.223 45.833 0.00 0.00 0.00 3.10
36 37 5.105187 TCAACAGAGAGAGAGAGAGAGAGAG 60.105 48.000 0.00 0.00 0.00 3.20
40 41 6.157645 ACAGAGAGAGAGAGAGAGAGAGAAAT 59.842 42.308 0.00 0.00 0.00 2.17
68 69 8.451687 TGATCAGCAGAATGTTTAATTTTTCG 57.548 30.769 0.00 0.00 39.31 3.46
155 156 5.004726 GCAGTCATTCCATTAAACAAATCGC 59.995 40.000 0.00 0.00 0.00 4.58
160 161 6.974048 TCATTCCATTAAACAAATCGCATCTG 59.026 34.615 0.00 0.00 0.00 2.90
186 187 8.462016 GCAACTAAGATATTGAAGGAACACATT 58.538 33.333 0.00 0.00 0.00 2.71
252 262 2.352503 AATTGAGAAATGTGGCACGC 57.647 45.000 13.77 2.35 40.62 5.34
275 286 7.552687 ACGCACCTAATCATTTAGAAAAGATCA 59.447 33.333 0.00 0.00 37.59 2.92
291 302 2.158769 AGATCATGCGTTTCCTATGGCA 60.159 45.455 0.00 0.00 40.06 4.92
419 430 6.727824 TTTTTGAAATCTCGCAAACCAAAA 57.272 29.167 0.00 0.00 34.09 2.44
436 451 6.092346 ACCAAAAGAGGCCCTTAGAATTAT 57.908 37.500 0.00 0.00 34.00 1.28
437 452 7.220890 ACCAAAAGAGGCCCTTAGAATTATA 57.779 36.000 0.00 0.00 34.00 0.98
438 453 7.290813 ACCAAAAGAGGCCCTTAGAATTATAG 58.709 38.462 0.00 0.00 34.00 1.31
439 454 7.128883 ACCAAAAGAGGCCCTTAGAATTATAGA 59.871 37.037 0.00 0.00 34.00 1.98
445 460 5.004448 GGCCCTTAGAATTATAGAACTGCC 58.996 45.833 0.00 0.00 0.00 4.85
451 466 8.429641 CCTTAGAATTATAGAACTGCCCACTTA 58.570 37.037 0.00 0.00 0.00 2.24
478 493 7.810766 TTTCATTTTTGTTCAGTGTCACTTC 57.189 32.000 1.67 0.00 0.00 3.01
489 504 2.169769 AGTGTCACTTCGAAAGGAACCA 59.830 45.455 0.00 0.00 0.00 3.67
512 527 4.532126 ACAATGATTAGGTCCTGTCACTCA 59.468 41.667 0.00 0.00 0.00 3.41
513 528 5.114780 CAATGATTAGGTCCTGTCACTCAG 58.885 45.833 0.00 0.00 43.27 3.35
514 529 2.497675 TGATTAGGTCCTGTCACTCAGC 59.502 50.000 0.00 0.00 42.38 4.26
532 547 3.006430 TCAGCGATAGTGAGGTGTGAAAA 59.994 43.478 0.00 0.00 37.19 2.29
536 551 3.679980 CGATAGTGAGGTGTGAAAACCAG 59.320 47.826 0.00 0.00 43.20 4.00
549 564 5.818857 TGTGAAAACCAGAAGTTAGGTACAC 59.181 40.000 16.09 16.09 37.88 2.90
551 566 3.672767 AACCAGAAGTTAGGTACACCG 57.327 47.619 0.00 0.00 42.08 4.94
554 569 4.347607 ACCAGAAGTTAGGTACACCGTAT 58.652 43.478 0.00 0.00 42.08 3.06
574 590 1.451927 CCATCCACCATCCACCACG 60.452 63.158 0.00 0.00 0.00 4.94
641 657 3.054361 GGGATGGTTCTTCTCCTGCTTAA 60.054 47.826 0.00 0.00 0.00 1.85
642 658 4.567747 GGGATGGTTCTTCTCCTGCTTAAA 60.568 45.833 0.00 0.00 0.00 1.52
810 984 5.241506 TGGTTTCACATGGAAGAGAATTCAC 59.758 40.000 8.44 0.74 36.72 3.18
1479 1660 4.135153 CCGGAGAGGCCACAGTCG 62.135 72.222 5.01 4.13 35.94 4.18
1561 1742 6.127225 GGTGAGGCTCATGCTATCTGATAATA 60.127 42.308 21.84 0.00 39.59 0.98
1629 1810 2.615747 GGGGCTTGGTAAGACAACTCTC 60.616 54.545 0.00 0.00 38.70 3.20
1653 1834 4.587891 TGCAGATGGTGTACAATGATGAA 58.412 39.130 0.00 0.00 0.00 2.57
1656 1837 5.449588 GCAGATGGTGTACAATGATGAAAGG 60.450 44.000 0.00 0.00 0.00 3.11
1704 1885 4.953667 TCTGGATCTATGTGTCTGAATGC 58.046 43.478 0.00 0.00 0.00 3.56
1719 1900 3.218453 TGAATGCTTTGACGGGAGAAAA 58.782 40.909 0.00 0.00 0.00 2.29
1722 1903 1.946768 TGCTTTGACGGGAGAAAACTG 59.053 47.619 0.00 0.00 0.00 3.16
1737 1918 6.238239 GGAGAAAACTGACACAAGAAACTCTC 60.238 42.308 0.00 0.00 0.00 3.20
1782 1963 3.191371 CCTTTCCTAGCACCAACATGAAC 59.809 47.826 0.00 0.00 0.00 3.18
1932 2113 4.092968 GGAAGCAAGATAGTGGTTACAACG 59.907 45.833 0.00 0.00 39.25 4.10
2001 2182 4.683832 AGTTACAGCAACTATCGGATGAC 58.316 43.478 0.00 0.00 45.93 3.06
2013 2194 1.893786 GGATGACGACAGCTGGTCT 59.106 57.895 19.93 6.71 44.68 3.85
2247 2428 0.033228 CAGCTCTGCGGCTAAGCTAT 59.967 55.000 22.87 6.32 44.30 2.97
2676 2857 8.674607 GGATACAATTCTAAAATGTCTCGGTTT 58.325 33.333 0.00 0.00 0.00 3.27
2854 3035 7.974675 TGTCAAGCTCTATAACTTGCAAATAC 58.025 34.615 0.00 0.00 42.41 1.89
3022 3203 0.394488 TGTTGTCTTGAAACGCCCCA 60.394 50.000 0.00 0.00 0.00 4.96
3275 3456 4.479156 TGATTAAAGGTTTTCCAGGGGT 57.521 40.909 0.00 0.00 43.73 4.95
3384 3565 3.895704 TTAGGCCAACTTCCTTTCCTT 57.104 42.857 5.01 0.00 35.21 3.36
3471 3652 5.003160 GGGCAAATAAAATGTTTTCCAGCT 58.997 37.500 0.00 0.00 0.00 4.24
3572 3753 7.388776 TCAATTAACTGAACTTGGTCTCATCAG 59.611 37.037 0.00 0.00 42.43 2.90
3992 4173 3.116096 TGGCCTACAATACTGTCCTCT 57.884 47.619 3.32 0.00 36.96 3.69
4138 4319 0.609957 TTTGCCTCCTGGTCTGCATG 60.610 55.000 8.00 0.00 33.08 4.06
4212 4393 1.376466 GCCAGAAGAAGGTCTGCCA 59.624 57.895 0.00 0.00 43.18 4.92
4523 4797 7.039270 TGAGCAAGCAGTTCGAGTTTATATAA 58.961 34.615 0.00 0.00 0.00 0.98
4525 4799 7.042335 AGCAAGCAGTTCGAGTTTATATAACT 58.958 34.615 0.00 0.00 0.00 2.24
4526 4800 8.195436 AGCAAGCAGTTCGAGTTTATATAACTA 58.805 33.333 0.00 0.00 0.00 2.24
4527 4801 8.267367 GCAAGCAGTTCGAGTTTATATAACTAC 58.733 37.037 0.00 0.00 0.00 2.73
4550 4951 5.829924 ACTAGAAAGTGATTAATGGCCATGG 59.170 40.000 21.63 7.63 33.57 3.66
4573 4974 7.833786 TGGGTGTAATAGTGTACTAGAAAGTG 58.166 38.462 0.00 0.00 36.36 3.16
4678 5120 3.104519 TGGATCATTGCTTGGGTCAAT 57.895 42.857 0.00 0.00 34.74 2.57
4695 5137 2.821378 TCAATTGAGGTTGCATGTGAGG 59.179 45.455 3.38 0.00 0.00 3.86
4711 5153 3.649986 GGCCCATGCGCGATACAC 61.650 66.667 12.10 0.00 38.85 2.90
4713 5155 1.300620 GCCCATGCGCGATACACTA 60.301 57.895 12.10 0.00 0.00 2.74
4714 5156 0.670546 GCCCATGCGCGATACACTAT 60.671 55.000 12.10 0.00 0.00 2.12
4715 5157 1.403647 GCCCATGCGCGATACACTATA 60.404 52.381 12.10 0.00 0.00 1.31
4736 5178 2.299297 AGTAGAAGGTTTCCAGACCACG 59.701 50.000 0.00 0.00 42.35 4.94
4739 5181 1.001633 GAAGGTTTCCAGACCACGCTA 59.998 52.381 0.00 0.00 42.35 4.26
4745 5187 0.541063 TCCAGACCACGCTACCAGAA 60.541 55.000 0.00 0.00 0.00 3.02
4757 5199 3.434453 CGCTACCAGAATTTATCCCCCAA 60.434 47.826 0.00 0.00 0.00 4.12
4870 5321 6.707608 TGCAATCTAGCATTCTTAATGTCGAT 59.292 34.615 0.00 0.09 40.11 3.59
4919 5370 1.872313 CAATTTTGGTTGGCACGCAAT 59.128 42.857 0.00 0.00 0.00 3.56
4931 5390 2.833121 CGCAATGGGGGTTAGGCC 60.833 66.667 0.00 0.00 0.00 5.19
5034 5493 2.877691 GGCTGCGGTTGCCTTTAG 59.122 61.111 0.00 0.00 46.38 1.85
5140 5600 0.765510 GGGGACAGACCTCAACAACT 59.234 55.000 0.00 0.00 39.39 3.16
5148 5608 0.828022 ACCTCAACAACTGTCGTGGA 59.172 50.000 0.00 0.00 0.00 4.02
5156 5616 2.223711 ACAACTGTCGTGGAAAATTGCC 60.224 45.455 0.00 0.00 0.00 4.52
5173 5633 2.325082 CCGAAAACACCCTGCTCGG 61.325 63.158 0.00 0.00 42.68 4.63
5188 5648 4.817063 CGGCGCTCGCAACCATTG 62.817 66.667 16.36 0.00 44.11 2.82
5189 5649 3.430862 GGCGCTCGCAACCATTGA 61.431 61.111 16.36 0.00 44.11 2.57
5190 5650 2.560861 GCGCTCGCAACCATTGAA 59.439 55.556 9.59 0.00 41.49 2.69
5191 5651 1.797537 GCGCTCGCAACCATTGAAC 60.798 57.895 9.59 0.00 41.49 3.18
5192 5652 1.154225 CGCTCGCAACCATTGAACC 60.154 57.895 0.00 0.00 0.00 3.62
5215 5675 3.902112 CACACCCTTGGCCCACCT 61.902 66.667 0.00 0.00 36.63 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.494724 TCTCTCTGTTGAGGGAAATCAATG 58.505 41.667 0.00 0.00 46.01 2.82
8 9 2.916269 TCTCTCTCTCTCTGTTGAGGGA 59.084 50.000 0.00 0.00 46.75 4.20
9 10 3.054434 TCTCTCTCTCTCTCTGTTGAGGG 60.054 52.174 0.00 0.00 42.08 4.30
10 11 4.080919 TCTCTCTCTCTCTCTCTGTTGAGG 60.081 50.000 0.00 0.00 40.58 3.86
11 12 5.089970 TCTCTCTCTCTCTCTCTGTTGAG 57.910 47.826 0.00 0.00 41.51 3.02
12 13 4.777366 TCTCTCTCTCTCTCTCTCTGTTGA 59.223 45.833 0.00 0.00 0.00 3.18
13 14 5.089970 TCTCTCTCTCTCTCTCTCTGTTG 57.910 47.826 0.00 0.00 0.00 3.33
14 15 5.026121 TCTCTCTCTCTCTCTCTCTCTGTT 58.974 45.833 0.00 0.00 0.00 3.16
15 16 4.614475 TCTCTCTCTCTCTCTCTCTCTGT 58.386 47.826 0.00 0.00 0.00 3.41
16 17 5.604758 TTCTCTCTCTCTCTCTCTCTCTG 57.395 47.826 0.00 0.00 0.00 3.35
17 18 6.821616 ATTTCTCTCTCTCTCTCTCTCTCT 57.178 41.667 0.00 0.00 0.00 3.10
18 19 8.997323 CAATATTTCTCTCTCTCTCTCTCTCTC 58.003 40.741 0.00 0.00 0.00 3.20
19 20 8.717717 TCAATATTTCTCTCTCTCTCTCTCTCT 58.282 37.037 0.00 0.00 0.00 3.10
20 21 8.908786 TCAATATTTCTCTCTCTCTCTCTCTC 57.091 38.462 0.00 0.00 0.00 3.20
21 22 9.512588 GATCAATATTTCTCTCTCTCTCTCTCT 57.487 37.037 0.00 0.00 0.00 3.10
22 23 9.288576 TGATCAATATTTCTCTCTCTCTCTCTC 57.711 37.037 0.00 0.00 0.00 3.20
23 24 9.293404 CTGATCAATATTTCTCTCTCTCTCTCT 57.707 37.037 0.00 0.00 0.00 3.10
24 25 8.025445 GCTGATCAATATTTCTCTCTCTCTCTC 58.975 40.741 0.00 0.00 0.00 3.20
25 26 7.506599 TGCTGATCAATATTTCTCTCTCTCTCT 59.493 37.037 0.00 0.00 0.00 3.10
26 27 7.660112 TGCTGATCAATATTTCTCTCTCTCTC 58.340 38.462 0.00 0.00 0.00 3.20
27 28 7.506599 TCTGCTGATCAATATTTCTCTCTCTCT 59.493 37.037 0.00 0.00 0.00 3.10
28 29 7.660112 TCTGCTGATCAATATTTCTCTCTCTC 58.340 38.462 0.00 0.00 0.00 3.20
29 30 7.600231 TCTGCTGATCAATATTTCTCTCTCT 57.400 36.000 0.00 0.00 0.00 3.10
30 31 8.714179 CATTCTGCTGATCAATATTTCTCTCTC 58.286 37.037 0.00 0.00 0.00 3.20
31 32 8.212312 ACATTCTGCTGATCAATATTTCTCTCT 58.788 33.333 0.00 0.00 0.00 3.10
32 33 8.380743 ACATTCTGCTGATCAATATTTCTCTC 57.619 34.615 0.00 0.00 0.00 3.20
33 34 8.749026 AACATTCTGCTGATCAATATTTCTCT 57.251 30.769 0.00 0.00 0.00 3.10
61 62 3.791245 TTTGGCACTTTCTGCGAAAAAT 58.209 36.364 0.65 0.00 46.87 1.82
68 69 4.867608 TGTTTTACTTTTGGCACTTTCTGC 59.132 37.500 0.00 0.00 46.31 4.26
155 156 8.341173 GTTCCTTCAATATCTTAGTTGCAGATG 58.659 37.037 0.00 0.00 32.94 2.90
160 161 7.377766 TGTGTTCCTTCAATATCTTAGTTGC 57.622 36.000 0.00 0.00 0.00 4.17
229 239 4.266029 GCGTGCCACATTTCTCAATTTATG 59.734 41.667 0.00 0.00 0.00 1.90
239 249 0.878416 TTAGGTGCGTGCCACATTTC 59.122 50.000 0.00 0.00 46.50 2.17
242 252 0.035534 TGATTAGGTGCGTGCCACAT 60.036 50.000 0.00 0.00 46.50 3.21
252 262 9.674824 GCATGATCTTTTCTAAATGATTAGGTG 57.325 33.333 0.00 1.27 39.24 4.00
275 286 1.382522 CTGTGCCATAGGAAACGCAT 58.617 50.000 0.00 0.00 33.08 4.73
419 430 6.239743 GCAGTTCTATAATTCTAAGGGCCTCT 60.240 42.308 6.46 0.00 0.00 3.69
436 451 7.775053 AATGAAAAATAAGTGGGCAGTTCTA 57.225 32.000 0.00 0.00 0.00 2.10
437 452 6.670695 AATGAAAAATAAGTGGGCAGTTCT 57.329 33.333 0.00 0.00 0.00 3.01
438 453 7.728847 AAAATGAAAAATAAGTGGGCAGTTC 57.271 32.000 0.00 0.00 0.00 3.01
439 454 7.555914 ACAAAAATGAAAAATAAGTGGGCAGTT 59.444 29.630 0.00 0.00 0.00 3.16
445 460 9.919348 CACTGAACAAAAATGAAAAATAAGTGG 57.081 29.630 0.00 0.00 0.00 4.00
451 466 8.776376 AGTGACACTGAACAAAAATGAAAAAT 57.224 26.923 7.47 0.00 0.00 1.82
478 493 4.700213 ACCTAATCATTGTGGTTCCTTTCG 59.300 41.667 0.00 0.00 0.00 3.46
489 504 4.532126 TGAGTGACAGGACCTAATCATTGT 59.468 41.667 10.14 0.00 31.44 2.71
512 527 3.326747 GTTTTCACACCTCACTATCGCT 58.673 45.455 0.00 0.00 0.00 4.93
513 528 2.415512 GGTTTTCACACCTCACTATCGC 59.584 50.000 0.00 0.00 33.50 4.58
514 529 3.659786 TGGTTTTCACACCTCACTATCG 58.340 45.455 0.00 0.00 37.75 2.92
532 547 2.601905 ACGGTGTACCTAACTTCTGGT 58.398 47.619 0.00 0.00 40.12 4.00
536 551 5.835113 TGGTATACGGTGTACCTAACTTC 57.165 43.478 27.41 6.87 41.73 3.01
549 564 1.974957 TGGATGGTGGATGGTATACGG 59.025 52.381 0.00 0.00 0.00 4.02
551 566 2.708861 TGGTGGATGGTGGATGGTATAC 59.291 50.000 0.00 0.00 0.00 1.47
554 569 0.916086 GTGGTGGATGGTGGATGGTA 59.084 55.000 0.00 0.00 0.00 3.25
574 590 2.039084 TCCTTTGGACAGAGAGCCTTTC 59.961 50.000 0.00 0.00 0.00 2.62
641 657 8.099364 ACTCATCTTCAACACAAACGATTATT 57.901 30.769 0.00 0.00 0.00 1.40
642 658 7.604164 AGACTCATCTTCAACACAAACGATTAT 59.396 33.333 0.00 0.00 0.00 1.28
1479 1660 4.681744 CTGAACTATCCACAAGAGAGCTC 58.318 47.826 5.27 5.27 37.33 4.09
1629 1810 4.577283 TCATCATTGTACACCATCTGCATG 59.423 41.667 0.00 0.00 0.00 4.06
1653 1834 6.154363 TCAATTCAAAGTGTTCTTTCACCCTT 59.846 34.615 0.00 0.00 41.31 3.95
1656 1837 5.979517 CCTCAATTCAAAGTGTTCTTTCACC 59.020 40.000 0.00 0.00 41.31 4.02
1674 1855 6.014413 CAGACACATAGATCCAGATCCTCAAT 60.014 42.308 4.01 0.00 38.58 2.57
1704 1885 3.002348 GTGTCAGTTTTCTCCCGTCAAAG 59.998 47.826 0.00 0.00 0.00 2.77
1719 1900 3.243569 CCTCGAGAGTTTCTTGTGTCAGT 60.244 47.826 15.71 0.00 0.00 3.41
1722 1903 2.062519 GCCTCGAGAGTTTCTTGTGTC 58.937 52.381 15.71 0.00 0.00 3.67
1782 1963 1.467734 GAGAGTGTTTCCTGCAGCATG 59.532 52.381 8.66 0.00 40.87 4.06
1932 2113 0.109179 TGCCAACATTCTCATTGCGC 60.109 50.000 0.00 0.00 0.00 6.09
2013 2194 4.271661 TGAATGCATGGCTCTTGAATACA 58.728 39.130 0.00 0.00 0.00 2.29
2162 2343 2.789323 TAGTATCCCCTTCCACTCCC 57.211 55.000 0.00 0.00 0.00 4.30
2247 2428 5.506730 TCAGATGTGGTGGTAAATGGTTA 57.493 39.130 0.00 0.00 0.00 2.85
2329 2510 4.265073 AGTGCTAGCCAAATCTTAACCAG 58.735 43.478 13.29 0.00 0.00 4.00
2514 2695 2.571653 TCTTGTCCCATCCTCAAATCGT 59.428 45.455 0.00 0.00 0.00 3.73
2664 2845 2.305927 ACCATCAGGAAACCGAGACATT 59.694 45.455 0.00 0.00 38.69 2.71
2676 2857 6.126863 AGTTTCATAAAGACACCATCAGGA 57.873 37.500 0.00 0.00 38.69 3.86
2854 3035 2.682952 CTGCAGTTGTTCAGCTTCAG 57.317 50.000 5.25 2.79 0.00 3.02
3022 3203 6.161855 TCTTAACTCTGTGATGTTGTGTCT 57.838 37.500 0.00 0.00 0.00 3.41
3298 3479 7.094205 GGTTTGCAGATTAGGAAGAAATGAAGA 60.094 37.037 0.00 0.00 0.00 2.87
3384 3565 8.840321 GTTGCTCCTGCTATATTGAGATTTTTA 58.160 33.333 0.00 0.00 40.48 1.52
3572 3753 0.600057 CTTCTTCAGCTTGGGGCAAC 59.400 55.000 0.00 0.00 44.79 4.17
3992 4173 8.199449 AGTCAGAAATTTGAAAATGCTTGAGAA 58.801 29.630 0.00 0.00 0.00 2.87
4138 4319 4.698575 AGTGTTTCAAGTGAGGAGACTTC 58.301 43.478 0.00 0.00 44.43 3.01
4523 4797 7.195374 TGGCCATTAATCACTTTCTAGTAGT 57.805 36.000 0.00 0.00 31.96 2.73
4525 4799 6.998074 CCATGGCCATTAATCACTTTCTAGTA 59.002 38.462 17.92 0.00 31.96 1.82
4526 4800 5.829924 CCATGGCCATTAATCACTTTCTAGT 59.170 40.000 17.92 0.00 34.00 2.57
4527 4801 5.242393 CCCATGGCCATTAATCACTTTCTAG 59.758 44.000 17.92 0.00 0.00 2.43
4550 4951 7.318141 TGCACTTTCTAGTACACTATTACACC 58.682 38.462 0.00 0.00 31.96 4.16
4573 4974 5.831997 ACACTACTTCTTTTCATGGTTTGC 58.168 37.500 0.00 0.00 0.00 3.68
4641 5042 8.573885 CAATGATCCAAGCTGATAAACACATAT 58.426 33.333 0.00 0.00 0.00 1.78
4648 5090 5.163488 CCAAGCAATGATCCAAGCTGATAAA 60.163 40.000 3.99 0.00 37.41 1.40
4656 5098 2.449464 TGACCCAAGCAATGATCCAAG 58.551 47.619 0.00 0.00 0.00 3.61
4659 5101 3.448301 TCAATTGACCCAAGCAATGATCC 59.552 43.478 3.38 0.00 36.20 3.36
4678 5120 0.895100 GGCCTCACATGCAACCTCAA 60.895 55.000 0.00 0.00 0.00 3.02
4695 5137 0.670546 ATAGTGTATCGCGCATGGGC 60.671 55.000 23.87 23.87 0.00 5.36
4711 5153 6.459848 CGTGGTCTGGAAACCTTCTACTATAG 60.460 46.154 0.00 0.00 40.20 1.31
4713 5155 4.159879 CGTGGTCTGGAAACCTTCTACTAT 59.840 45.833 0.00 0.00 40.20 2.12
4714 5156 3.508793 CGTGGTCTGGAAACCTTCTACTA 59.491 47.826 0.00 0.00 40.20 1.82
4715 5157 2.299297 CGTGGTCTGGAAACCTTCTACT 59.701 50.000 0.00 0.00 40.20 2.57
4736 5178 3.876309 TGGGGGATAAATTCTGGTAGC 57.124 47.619 0.00 0.00 0.00 3.58
4739 5181 3.711190 GCAATTGGGGGATAAATTCTGGT 59.289 43.478 7.72 0.00 0.00 4.00
4745 5187 1.585096 AGGGGCAATTGGGGGATAAAT 59.415 47.619 7.72 0.00 0.00 1.40
4757 5199 8.486210 GGATAAATTCTTCTTTTTAGGGGCAAT 58.514 33.333 0.00 0.00 0.00 3.56
4870 5321 1.780025 TTCGTGCGCATGCTGTCAAA 61.780 50.000 24.82 9.81 43.34 2.69
4919 5370 2.895141 TACCCTGGCCTAACCCCCA 61.895 63.158 3.32 0.00 37.83 4.96
4931 5390 2.224523 ACACCAACATGTGAGTACCCTG 60.225 50.000 0.00 0.00 39.57 4.45
5034 5493 3.213402 CTCGTCGGAGGAGAGGCC 61.213 72.222 20.11 0.00 36.61 5.19
5140 5600 1.309950 TTCGGCAATTTTCCACGACA 58.690 45.000 0.00 0.00 32.85 4.35
5148 5608 2.832563 CAGGGTGTTTTCGGCAATTTT 58.167 42.857 0.00 0.00 0.00 1.82
5156 5616 2.966309 GCCGAGCAGGGTGTTTTCG 61.966 63.158 0.34 0.00 41.48 3.46
5173 5633 1.797537 GTTCAATGGTTGCGAGCGC 60.798 57.895 8.08 8.08 42.35 5.92
5184 5644 3.420893 AGGGTGTGTGTATGGTTCAATG 58.579 45.455 0.00 0.00 0.00 2.82
5185 5645 3.806949 AGGGTGTGTGTATGGTTCAAT 57.193 42.857 0.00 0.00 0.00 2.57
5186 5646 3.218453 CAAGGGTGTGTGTATGGTTCAA 58.782 45.455 0.00 0.00 0.00 2.69
5187 5647 2.488167 CCAAGGGTGTGTGTATGGTTCA 60.488 50.000 0.00 0.00 0.00 3.18
5188 5648 2.159382 CCAAGGGTGTGTGTATGGTTC 58.841 52.381 0.00 0.00 0.00 3.62
5189 5649 1.821666 GCCAAGGGTGTGTGTATGGTT 60.822 52.381 0.00 0.00 0.00 3.67
5190 5650 0.251165 GCCAAGGGTGTGTGTATGGT 60.251 55.000 0.00 0.00 0.00 3.55
5191 5651 0.965363 GGCCAAGGGTGTGTGTATGG 60.965 60.000 0.00 0.00 0.00 2.74
5192 5652 0.965363 GGGCCAAGGGTGTGTGTATG 60.965 60.000 4.39 0.00 0.00 2.39
5215 5675 3.891586 GACGACGACTCGCTGCCAA 62.892 63.158 0.00 0.00 44.33 4.52
5232 5693 1.756024 TTTCGCTCGGGGGAAAAGA 59.244 52.632 23.66 2.83 46.42 2.52


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

AutoCloner maintained by Alex Coulton.