Multiple sequence alignment - TraesCS2D01G396800

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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 TraesCS2D01G396800 chr2D 100.000 2507 0 0 1 2507 508048856 508046350 0.000000e+00 4630.0
1 TraesCS2D01G396800 chr2A 88.562 1224 69 26 719 1912 652520610 652519428 0.000000e+00 1419.0
2 TraesCS2D01G396800 chr2A 91.798 317 13 4 286 591 652524092 652523778 1.780000e-116 429.0
3 TraesCS2D01G396800 chr2A 92.742 248 15 3 2062 2306 652519059 652518812 3.070000e-94 355.0
4 TraesCS2D01G396800 chr2A 87.912 273 11 8 40 290 652524394 652524122 4.050000e-78 302.0
5 TraesCS2D01G396800 chr2A 93.333 60 4 0 1946 2005 652519127 652519068 3.430000e-14 89.8
6 TraesCS2D01G396800 chr2A 85.870 92 4 6 593 675 652523711 652523620 3.430000e-14 89.8
7 TraesCS2D01G396800 chr2B 91.480 939 49 15 813 1736 596898758 596897836 0.000000e+00 1262.0
8 TraesCS2D01G396800 chr2B 92.880 309 13 7 284 591 596899333 596899033 8.230000e-120 440.0
9 TraesCS2D01G396800 chr2B 91.760 267 20 2 2052 2316 596896085 596895819 1.100000e-98 370.0
10 TraesCS2D01G396800 chr2B 90.681 279 9 3 27 290 596899637 596899361 3.070000e-94 355.0
11 TraesCS2D01G396800 chr2B 95.833 72 3 0 1723 1794 596896305 596896234 1.580000e-22 117.0
12 TraesCS2D01G396800 chr2B 95.522 67 3 0 1938 2004 596896157 596896091 9.480000e-20 108.0
13 TraesCS2D01G396800 chr2B 84.348 115 9 4 2393 2507 596894056 596893951 1.230000e-18 104.0
14 TraesCS2D01G396800 chr5B 87.375 602 30 26 27 591 44983241 44982649 0.000000e+00 649.0
15 TraesCS2D01G396800 chr5B 97.674 43 1 0 2001 2043 644346937 644346895 9.620000e-10 75.0
16 TraesCS2D01G396800 chrUn 92.880 309 13 7 284 591 477936315 477936615 8.230000e-120 440.0
17 TraesCS2D01G396800 chr3B 95.833 48 2 0 2001 2048 741467676 741467629 7.430000e-11 78.7
18 TraesCS2D01G396800 chr3B 97.619 42 1 0 2002 2043 31404286 31404327 3.460000e-09 73.1
19 TraesCS2D01G396800 chr7B 97.674 43 1 0 2001 2043 605906288 605906246 9.620000e-10 75.0
20 TraesCS2D01G396800 chr4D 97.674 43 1 0 2001 2043 456056425 456056467 9.620000e-10 75.0
21 TraesCS2D01G396800 chr4A 97.674 43 1 0 2001 2043 639990926 639990884 9.620000e-10 75.0
22 TraesCS2D01G396800 chr1D 93.750 48 3 0 2001 2048 467938806 467938759 3.460000e-09 73.1
23 TraesCS2D01G396800 chr7A 93.750 48 2 1 1997 2043 669410789 669410742 1.240000e-08 71.3
24 TraesCS2D01G396800 chr5D 90.741 54 3 1 1997 2048 451485841 451485894 1.240000e-08 71.3


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 TraesCS2D01G396800 chr2D 508046350 508048856 2506 True 4630.000000 4630 100.000000 1 2507 1 chr2D.!!$R1 2506
1 TraesCS2D01G396800 chr2A 652518812 652524394 5582 True 447.433333 1419 90.036167 40 2306 6 chr2A.!!$R1 2266
2 TraesCS2D01G396800 chr2B 596893951 596899637 5686 True 393.714286 1262 91.786286 27 2507 7 chr2B.!!$R1 2480
3 TraesCS2D01G396800 chr5B 44982649 44983241 592 True 649.000000 649 87.375000 27 591 1 chr5B.!!$R1 564

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
936 4168 1.035139 CCATTAATCAGCACTGCCCC 58.965 55.0 0.0 0.0 0.0 5.8 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2458 9238 0.25143 TCCTGTTAAAAAGGGCCCCG 60.251 55.0 21.43 0.0 35.35 5.73 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
29 30 2.741985 CGCCATCTGTGCGTGGAA 60.742 61.111 0.00 0.00 46.59 3.53
231 251 2.892425 CCAGCCGGCACTCGATTC 60.892 66.667 31.54 0.00 42.43 2.52
250 286 2.324330 CCGTTGCTGAATGGACGCA 61.324 57.895 0.00 0.00 40.35 5.24
251 287 1.647545 CCGTTGCTGAATGGACGCAT 61.648 55.000 0.00 0.00 40.35 4.73
394 468 1.447314 CGGGAGGAACGTACCAAGC 60.447 63.158 0.00 0.00 0.00 4.01
479 560 3.479370 GACACATGTGGCTCGCTC 58.521 61.111 28.64 12.86 35.21 5.03
538 619 2.645838 ATGGCTCCGCTAATCATTGT 57.354 45.000 0.00 0.00 0.00 2.71
546 627 3.130633 CCGCTAATCATTGTCATTCCGA 58.869 45.455 0.00 0.00 0.00 4.55
689 911 4.289672 TGCCTAAAGGAAGAAGAGAATGGT 59.710 41.667 0.00 0.00 37.39 3.55
690 912 5.222130 TGCCTAAAGGAAGAAGAGAATGGTT 60.222 40.000 0.00 0.00 37.39 3.67
692 914 6.716284 CCTAAAGGAAGAAGAGAATGGTTCT 58.284 40.000 0.00 0.00 39.30 3.01
693 915 7.171653 CCTAAAGGAAGAAGAGAATGGTTCTT 58.828 38.462 0.00 0.00 44.03 2.52
694 916 6.890979 AAAGGAAGAAGAGAATGGTTCTTG 57.109 37.500 2.17 0.00 41.94 3.02
695 917 5.832539 AGGAAGAAGAGAATGGTTCTTGA 57.167 39.130 2.17 0.00 41.94 3.02
696 918 6.192970 AGGAAGAAGAGAATGGTTCTTGAA 57.807 37.500 2.17 0.00 41.94 2.69
697 919 6.788218 AGGAAGAAGAGAATGGTTCTTGAAT 58.212 36.000 2.17 0.00 41.94 2.57
698 920 7.922382 AGGAAGAAGAGAATGGTTCTTGAATA 58.078 34.615 2.17 0.00 41.94 1.75
700 922 8.835439 GGAAGAAGAGAATGGTTCTTGAATATC 58.165 37.037 2.17 0.00 41.94 1.63
702 924 7.286313 AGAAGAGAATGGTTCTTGAATATCCC 58.714 38.462 0.00 0.00 40.87 3.85
703 925 5.946486 AGAGAATGGTTCTTGAATATCCCC 58.054 41.667 0.00 0.00 40.87 4.81
704 926 4.718961 AGAATGGTTCTTGAATATCCCCG 58.281 43.478 0.00 0.00 36.36 5.73
706 928 1.562008 TGGTTCTTGAATATCCCCGCA 59.438 47.619 0.00 0.00 0.00 5.69
707 929 2.025793 TGGTTCTTGAATATCCCCGCAA 60.026 45.455 0.00 0.00 0.00 4.85
778 3969 2.945447 ACGCAGCATTTTACATGCAT 57.055 40.000 6.11 0.00 46.77 3.96
822 4053 8.842358 ACTAGTACTAAAATTTAGCAGCAACA 57.158 30.769 12.28 0.00 0.00 3.33
870 4101 4.630069 ACAATTGGCATGTCGTACTACTTC 59.370 41.667 10.83 0.00 0.00 3.01
871 4102 4.737855 ATTGGCATGTCGTACTACTTCT 57.262 40.909 0.00 0.00 0.00 2.85
872 4103 5.847111 ATTGGCATGTCGTACTACTTCTA 57.153 39.130 0.00 0.00 0.00 2.10
873 4104 4.627611 TGGCATGTCGTACTACTTCTAC 57.372 45.455 0.00 0.00 0.00 2.59
874 4105 4.267536 TGGCATGTCGTACTACTTCTACT 58.732 43.478 0.00 0.00 0.00 2.57
875 4106 4.334759 TGGCATGTCGTACTACTTCTACTC 59.665 45.833 0.00 0.00 0.00 2.59
900 4131 7.168972 TCAGAAGCAAACAACCAAATTATTTCG 59.831 33.333 0.00 0.00 0.00 3.46
936 4168 1.035139 CCATTAATCAGCACTGCCCC 58.965 55.000 0.00 0.00 0.00 5.80
1047 4279 1.398041 GTTCCACGTTATAAACCGCCC 59.602 52.381 0.00 0.00 0.00 6.13
1284 4536 2.772691 GGAGACCGCGGACGAAGAT 61.773 63.158 35.90 9.47 43.93 2.40
1410 4662 2.434884 ATCAGCGACAAGTGCGGG 60.435 61.111 0.00 0.00 37.44 6.13
1506 4758 0.035739 GGCCGACCAAGAACACCTAA 59.964 55.000 0.00 0.00 35.26 2.69
1509 4761 1.002087 CCGACCAAGAACACCTAAGCT 59.998 52.381 0.00 0.00 0.00 3.74
1511 4763 2.737252 CGACCAAGAACACCTAAGCTTC 59.263 50.000 0.00 0.00 0.00 3.86
1512 4764 3.740115 GACCAAGAACACCTAAGCTTCA 58.260 45.455 0.00 0.00 0.00 3.02
1523 4775 2.143122 CTAAGCTTCAGCCGTTTGACA 58.857 47.619 0.00 0.00 43.38 3.58
1524 4776 1.609208 AAGCTTCAGCCGTTTGACAT 58.391 45.000 0.00 0.00 43.38 3.06
1525 4777 0.877071 AGCTTCAGCCGTTTGACATG 59.123 50.000 0.00 0.00 43.38 3.21
1526 4778 0.109597 GCTTCAGCCGTTTGACATGG 60.110 55.000 0.00 0.00 34.31 3.66
1535 4787 2.009051 CGTTTGACATGGATGCTGCTA 58.991 47.619 0.00 0.00 0.00 3.49
1601 4858 2.895680 CTCCCTGCGCTGCTTCTA 59.104 61.111 9.73 0.00 0.00 2.10
1605 4862 1.493950 CCCTGCGCTGCTTCTATTCG 61.494 60.000 9.73 0.00 0.00 3.34
1606 4863 0.807667 CCTGCGCTGCTTCTATTCGT 60.808 55.000 9.73 0.00 0.00 3.85
1607 4864 1.002366 CTGCGCTGCTTCTATTCGTT 58.998 50.000 9.73 0.00 0.00 3.85
1608 4865 0.721154 TGCGCTGCTTCTATTCGTTG 59.279 50.000 9.73 0.00 0.00 4.10
1613 4870 2.729156 GCTGCTTCTATTCGTTGGTTGC 60.729 50.000 0.00 0.00 0.00 4.17
1636 4893 3.831323 TGCTTTGATCCTTTCCTTGTCA 58.169 40.909 0.00 0.00 0.00 3.58
1721 4980 8.971032 ATATTAAGAGGATGATGAGAGGTCTT 57.029 34.615 0.00 0.00 0.00 3.01
1760 6563 0.107165 GAATGGCCCGGCTCTAGTTT 60.107 55.000 9.86 0.00 0.00 2.66
1882 6685 4.099419 ACGTGGCTTTTCTTTTCATTTCCT 59.901 37.500 0.00 0.00 0.00 3.36
1921 6730 9.840427 GTGCATATTAAGTTGTAACAAAGATGT 57.160 29.630 13.79 0.00 43.14 3.06
1922 6731 9.838975 TGCATATTAAGTTGTAACAAAGATGTG 57.161 29.630 13.79 4.23 40.46 3.21
1928 6737 7.566760 AAGTTGTAACAAAGATGTGATGTCA 57.433 32.000 0.00 0.00 40.46 3.58
1929 6738 7.566760 AGTTGTAACAAAGATGTGATGTCAA 57.433 32.000 0.00 0.00 40.46 3.18
1932 6741 9.081997 GTTGTAACAAAGATGTGATGTCAAAAA 57.918 29.630 0.00 0.00 40.46 1.94
1983 7053 8.066247 ACAGGAGACCTACCTACATAGTTTATT 58.934 37.037 0.00 0.00 35.84 1.40
2012 7082 7.434492 AGAAAACTGTATGTATACTCCATCCG 58.566 38.462 4.17 0.00 34.41 4.18
2013 7083 6.726490 AAACTGTATGTATACTCCATCCGT 57.274 37.500 4.17 0.00 34.41 4.69
2014 7084 6.726490 AACTGTATGTATACTCCATCCGTT 57.274 37.500 4.17 0.00 34.41 4.44
2015 7085 6.726490 ACTGTATGTATACTCCATCCGTTT 57.274 37.500 4.17 0.00 34.41 3.60
2016 7086 7.120923 ACTGTATGTATACTCCATCCGTTTT 57.879 36.000 4.17 0.00 34.41 2.43
2017 7087 8.241497 ACTGTATGTATACTCCATCCGTTTTA 57.759 34.615 4.17 0.00 34.41 1.52
2018 7088 8.698210 ACTGTATGTATACTCCATCCGTTTTAA 58.302 33.333 4.17 0.00 34.41 1.52
2019 7089 9.537192 CTGTATGTATACTCCATCCGTTTTAAA 57.463 33.333 4.17 0.00 34.41 1.52
2020 7090 9.887629 TGTATGTATACTCCATCCGTTTTAAAA 57.112 29.630 4.17 0.00 34.41 1.52
2028 7098 8.209917 ACTCCATCCGTTTTAAAATAGATGAC 57.790 34.615 27.83 8.57 34.68 3.06
2029 7099 8.047310 ACTCCATCCGTTTTAAAATAGATGACT 58.953 33.333 27.83 15.65 34.68 3.41
2030 7100 8.433421 TCCATCCGTTTTAAAATAGATGACTC 57.567 34.615 27.83 6.91 34.68 3.36
2031 7101 8.044309 TCCATCCGTTTTAAAATAGATGACTCA 58.956 33.333 27.83 15.21 34.68 3.41
2032 7102 8.673711 CCATCCGTTTTAAAATAGATGACTCAA 58.326 33.333 27.83 2.49 34.68 3.02
2033 7103 9.490663 CATCCGTTTTAAAATAGATGACTCAAC 57.509 33.333 24.78 3.54 34.68 3.18
2034 7104 8.842358 TCCGTTTTAAAATAGATGACTCAACT 57.158 30.769 3.52 0.00 0.00 3.16
2035 7105 9.280174 TCCGTTTTAAAATAGATGACTCAACTT 57.720 29.630 3.52 0.00 0.00 2.66
2036 7106 9.893305 CCGTTTTAAAATAGATGACTCAACTTT 57.107 29.630 3.52 0.00 0.00 2.66
2050 7120 9.751542 ATGACTCAACTTTATACTAGTACATGC 57.248 33.333 4.31 0.00 0.00 4.06
2140 7210 6.540189 CAGTTAAATGAAATCGATGAGGGAGT 59.460 38.462 0.00 0.00 0.00 3.85
2150 7220 5.521906 TCGATGAGGGAGTTCTCTTTATG 57.478 43.478 0.00 0.00 34.98 1.90
2196 7268 2.350522 CCTTCGATTCAGGTTGGAGTG 58.649 52.381 0.00 0.00 0.00 3.51
2215 7287 3.153364 CACACAAGTGCTTTCTGCG 57.847 52.632 0.00 0.00 46.63 5.18
2266 7339 0.744281 ACGGCAAGAAACCCAAACTG 59.256 50.000 0.00 0.00 0.00 3.16
2267 7340 1.028905 CGGCAAGAAACCCAAACTGA 58.971 50.000 0.00 0.00 0.00 3.41
2271 7344 3.321968 GGCAAGAAACCCAAACTGAAGAT 59.678 43.478 0.00 0.00 0.00 2.40
2308 7381 4.661993 CTGCAAGTGAAACGTAATAGCA 57.338 40.909 0.00 0.00 45.86 3.49
2311 7384 6.918892 TGCAAGTGAAACGTAATAGCATAT 57.081 33.333 0.00 0.00 45.86 1.78
2316 7389 7.941795 AGTGAAACGTAATAGCATATGTACC 57.058 36.000 4.29 0.00 45.86 3.34
2318 7391 7.982919 AGTGAAACGTAATAGCATATGTACCAA 59.017 33.333 4.29 0.00 45.86 3.67
2319 7392 8.060090 GTGAAACGTAATAGCATATGTACCAAC 58.940 37.037 4.29 0.00 0.00 3.77
2320 7393 7.982919 TGAAACGTAATAGCATATGTACCAACT 59.017 33.333 4.29 0.00 0.00 3.16
2321 7394 9.467258 GAAACGTAATAGCATATGTACCAACTA 57.533 33.333 4.29 0.00 0.00 2.24
2322 7395 9.820725 AAACGTAATAGCATATGTACCAACTAA 57.179 29.630 4.29 0.00 0.00 2.24
2324 7397 9.419297 ACGTAATAGCATATGTACCAACTAATG 57.581 33.333 4.29 0.00 0.00 1.90
2325 7398 8.380644 CGTAATAGCATATGTACCAACTAATGC 58.619 37.037 4.29 0.00 41.16 3.56
2326 7399 7.687941 AATAGCATATGTACCAACTAATGCC 57.312 36.000 4.29 0.00 41.48 4.40
2327 7400 4.065088 AGCATATGTACCAACTAATGCCG 58.935 43.478 4.29 0.00 41.48 5.69
2329 7402 4.152402 GCATATGTACCAACTAATGCCGAG 59.848 45.833 4.29 0.00 37.94 4.63
2330 7403 3.906720 ATGTACCAACTAATGCCGAGT 57.093 42.857 0.00 0.00 0.00 4.18
2331 7404 6.452242 CATATGTACCAACTAATGCCGAGTA 58.548 40.000 0.00 0.00 0.00 2.59
2332 7405 4.114058 TGTACCAACTAATGCCGAGTAC 57.886 45.455 0.00 0.00 0.00 2.73
2334 7407 3.975168 ACCAACTAATGCCGAGTACTT 57.025 42.857 0.00 0.00 0.00 2.24
2336 7409 3.259876 ACCAACTAATGCCGAGTACTTGA 59.740 43.478 12.02 0.00 0.00 3.02
2337 7410 3.865745 CCAACTAATGCCGAGTACTTGAG 59.134 47.826 12.02 3.14 0.00 3.02
2338 7411 3.166489 ACTAATGCCGAGTACTTGAGC 57.834 47.619 12.02 13.03 0.00 4.26
2340 7413 2.015736 AATGCCGAGTACTTGAGCAG 57.984 50.000 22.64 6.20 36.80 4.24
2342 7415 0.966179 TGCCGAGTACTTGAGCAGAA 59.034 50.000 17.46 1.78 0.00 3.02
2343 7416 1.336887 TGCCGAGTACTTGAGCAGAAC 60.337 52.381 17.46 0.00 0.00 3.01
2344 7417 1.336887 GCCGAGTACTTGAGCAGAACA 60.337 52.381 12.02 0.00 0.00 3.18
2345 7418 2.866460 GCCGAGTACTTGAGCAGAACAA 60.866 50.000 12.02 0.00 0.00 2.83
2355 9135 3.489180 GAGCAGAACAAGTAGCTCGTA 57.511 47.619 0.00 0.00 43.27 3.43
2363 9143 7.063074 GCAGAACAAGTAGCTCGTATCTTTTTA 59.937 37.037 0.00 0.00 0.00 1.52
2364 9144 8.587950 CAGAACAAGTAGCTCGTATCTTTTTAG 58.412 37.037 0.00 0.00 0.00 1.85
2367 9147 8.240883 ACAAGTAGCTCGTATCTTTTTAGTTG 57.759 34.615 0.00 0.00 0.00 3.16
2370 9150 7.600065 AGTAGCTCGTATCTTTTTAGTTGTCA 58.400 34.615 0.00 0.00 0.00 3.58
2371 9151 8.086522 AGTAGCTCGTATCTTTTTAGTTGTCAA 58.913 33.333 0.00 0.00 0.00 3.18
2372 9152 7.724305 AGCTCGTATCTTTTTAGTTGTCAAA 57.276 32.000 0.00 0.00 0.00 2.69
2373 9153 8.149973 AGCTCGTATCTTTTTAGTTGTCAAAA 57.850 30.769 0.00 0.00 0.00 2.44
2374 9154 8.617809 AGCTCGTATCTTTTTAGTTGTCAAAAA 58.382 29.630 0.00 0.00 34.58 1.94
2444 9224 4.021925 GCGAGTCCCCTTGCCACT 62.022 66.667 0.00 0.00 41.56 4.00
2446 9226 2.266055 GAGTCCCCTTGCCACTCG 59.734 66.667 0.00 0.00 0.00 4.18
2447 9227 3.959991 GAGTCCCCTTGCCACTCGC 62.960 68.421 0.00 0.00 38.31 5.03
2451 9231 4.641645 CCCTTGCCACTCGCCACA 62.642 66.667 0.00 0.00 36.24 4.17
2452 9232 3.357079 CCTTGCCACTCGCCACAC 61.357 66.667 0.00 0.00 36.24 3.82
2453 9233 2.591429 CTTGCCACTCGCCACACA 60.591 61.111 0.00 0.00 36.24 3.72
2454 9234 2.896801 CTTGCCACTCGCCACACAC 61.897 63.158 0.00 0.00 36.24 3.82
2455 9235 4.927782 TGCCACTCGCCACACACC 62.928 66.667 0.00 0.00 36.24 4.16
2474 9254 1.909287 GCCGGGGCCCTTTTTAACA 60.909 57.895 24.38 0.00 34.56 2.41
2475 9255 1.884075 GCCGGGGCCCTTTTTAACAG 61.884 60.000 24.38 0.49 34.56 3.16
2481 9261 1.272490 GGCCCTTTTTAACAGGAGCAC 59.728 52.381 0.00 0.00 32.41 4.40
2492 9272 3.459710 ACAGGAGCACTAACTAGAGGT 57.540 47.619 0.00 0.00 0.00 3.85
2504 9284 2.627933 ACTAGAGGTTACCCCTTGCAA 58.372 47.619 0.00 0.00 46.51 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.870372 GTTCCACGCACAGATGGC 59.130 61.111 0.00 0.00 35.81 4.40
14 15 3.168271 CGTTCCACGCACAGATGG 58.832 61.111 0.00 0.00 33.65 3.51
24 25 1.065109 GCAAACCCACACGTTCCAC 59.935 57.895 0.00 0.00 0.00 4.02
25 26 0.965866 TTGCAAACCCACACGTTCCA 60.966 50.000 0.00 0.00 0.00 3.53
29 30 0.107116 TACCTTGCAAACCCACACGT 60.107 50.000 0.00 0.00 0.00 4.49
35 36 3.005791 GCATATCCATACCTTGCAAACCC 59.994 47.826 0.00 0.00 33.58 4.11
38 39 4.823442 CAGAGCATATCCATACCTTGCAAA 59.177 41.667 0.00 0.00 35.79 3.68
231 251 3.039202 GCGTCCATTCAGCAACGGG 62.039 63.158 0.00 0.00 35.74 5.28
275 311 1.837538 CGCCGTCCGTTGTGTTCATT 61.838 55.000 0.00 0.00 0.00 2.57
308 378 2.126071 TCGCCGCTACAGCAACTC 60.126 61.111 1.61 0.00 42.21 3.01
336 406 1.101049 ACACCAAAAGCGTCACCTGG 61.101 55.000 0.00 0.00 0.00 4.45
394 468 2.660552 GTGTGTCCGTGTCCACCG 60.661 66.667 0.00 0.00 0.00 4.94
538 619 4.698201 TTAGGTATTGGCATCGGAATGA 57.302 40.909 0.00 0.00 34.61 2.57
546 627 3.380320 GCTCCGTTTTTAGGTATTGGCAT 59.620 43.478 0.00 0.00 0.00 4.40
675 897 8.835439 GGATATTCAAGAACCATTCTCTTCTTC 58.165 37.037 0.00 0.00 39.61 2.87
676 898 7.777440 GGGATATTCAAGAACCATTCTCTTCTT 59.223 37.037 0.00 0.00 39.61 2.52
677 899 7.286313 GGGATATTCAAGAACCATTCTCTTCT 58.714 38.462 0.00 0.00 39.61 2.85
678 900 6.488344 GGGGATATTCAAGAACCATTCTCTTC 59.512 42.308 0.00 0.00 39.61 2.87
680 902 5.455326 CGGGGATATTCAAGAACCATTCTCT 60.455 44.000 0.00 0.00 39.61 3.10
681 903 4.757149 CGGGGATATTCAAGAACCATTCTC 59.243 45.833 0.00 0.00 39.61 2.87
682 904 4.718961 CGGGGATATTCAAGAACCATTCT 58.281 43.478 0.00 0.00 43.15 2.40
683 905 3.253432 GCGGGGATATTCAAGAACCATTC 59.747 47.826 0.00 0.00 0.00 2.67
686 908 1.562008 TGCGGGGATATTCAAGAACCA 59.438 47.619 0.00 0.00 0.00 3.67
739 3927 7.945178 GCTGCGTTATATTCGTTTAGTCATTAG 59.055 37.037 0.00 0.00 0.00 1.73
741 3929 6.256975 TGCTGCGTTATATTCGTTTAGTCATT 59.743 34.615 0.00 0.00 0.00 2.57
754 3942 6.070897 TGCATGTAAAATGCTGCGTTATAT 57.929 33.333 7.64 1.38 44.79 0.86
818 4049 4.713824 ATTCAATGCTCCAGTGATGTTG 57.286 40.909 0.00 0.00 38.25 3.33
822 4053 3.446161 CACCAATTCAATGCTCCAGTGAT 59.554 43.478 0.00 0.00 38.25 3.06
870 4101 5.499139 TTTGGTTGTTTGCTTCTGAGTAG 57.501 39.130 0.00 0.00 0.00 2.57
871 4102 6.463995 AATTTGGTTGTTTGCTTCTGAGTA 57.536 33.333 0.00 0.00 0.00 2.59
872 4103 5.343307 AATTTGGTTGTTTGCTTCTGAGT 57.657 34.783 0.00 0.00 0.00 3.41
873 4104 7.951530 AATAATTTGGTTGTTTGCTTCTGAG 57.048 32.000 0.00 0.00 0.00 3.35
874 4105 7.168972 CGAAATAATTTGGTTGTTTGCTTCTGA 59.831 33.333 0.00 0.00 32.16 3.27
875 4106 7.282916 CGAAATAATTTGGTTGTTTGCTTCTG 58.717 34.615 0.00 0.00 32.16 3.02
900 4131 3.953542 ATGGTGGTTATCTTCTTCCCC 57.046 47.619 0.00 0.00 0.00 4.81
963 4195 1.477377 GGTTTGGTAAACGTGGGGAGT 60.477 52.381 0.00 0.00 42.29 3.85
1066 4304 4.351054 CCTTGCCTGGCTTCGGGT 62.351 66.667 21.03 0.00 39.16 5.28
1355 4607 4.073200 CCCCGACCACGTACACCC 62.073 72.222 0.00 0.00 37.88 4.61
1410 4662 1.153628 CTCCACGATGAACGGGTCC 60.154 63.158 0.00 0.00 44.77 4.46
1506 4758 0.877071 CATGTCAAACGGCTGAAGCT 59.123 50.000 0.00 0.00 41.70 3.74
1509 4761 1.811965 CATCCATGTCAAACGGCTGAA 59.188 47.619 0.00 0.00 0.00 3.02
1511 4763 0.179156 GCATCCATGTCAAACGGCTG 60.179 55.000 0.00 0.00 0.00 4.85
1512 4764 0.322816 AGCATCCATGTCAAACGGCT 60.323 50.000 0.00 0.00 0.00 5.52
1523 4775 0.105593 CACGGAGTAGCAGCATCCAT 59.894 55.000 10.86 0.00 41.61 3.41
1524 4776 1.257750 ACACGGAGTAGCAGCATCCA 61.258 55.000 10.86 0.00 41.61 3.41
1525 4777 0.807667 CACACGGAGTAGCAGCATCC 60.808 60.000 0.00 0.00 41.61 3.51
1526 4778 1.424493 GCACACGGAGTAGCAGCATC 61.424 60.000 0.00 0.00 41.61 3.91
1550 4802 3.093566 CGAGTTATCGCTCATCCCG 57.906 57.895 0.00 0.00 42.97 5.14
1564 4816 1.604185 GCACAGCAGAACTCTTCGAGT 60.604 52.381 0.00 0.00 45.64 4.18
1601 4858 2.100584 TCAAAGCAAGCAACCAACGAAT 59.899 40.909 0.00 0.00 0.00 3.34
1605 4862 2.036346 AGGATCAAAGCAAGCAACCAAC 59.964 45.455 0.00 0.00 0.00 3.77
1606 4863 2.318908 AGGATCAAAGCAAGCAACCAA 58.681 42.857 0.00 0.00 0.00 3.67
1607 4864 1.999648 AGGATCAAAGCAAGCAACCA 58.000 45.000 0.00 0.00 0.00 3.67
1608 4865 3.320626 GAAAGGATCAAAGCAAGCAACC 58.679 45.455 0.00 0.00 0.00 3.77
1613 4870 4.279169 TGACAAGGAAAGGATCAAAGCAAG 59.721 41.667 0.00 0.00 0.00 4.01
1636 4893 4.038271 TCAAGATGAAGATGGGCAGTTT 57.962 40.909 0.00 0.00 0.00 2.66
1747 6550 3.404899 TGTAAAACAAACTAGAGCCGGG 58.595 45.455 2.18 0.00 0.00 5.73
1838 6641 4.025647 CGTCTTTCCAAGAAGTCAGAACAC 60.026 45.833 0.00 0.00 39.67 3.32
1840 6643 4.025647 CACGTCTTTCCAAGAAGTCAGAAC 60.026 45.833 2.54 0.00 45.07 3.01
1882 6685 6.495872 ACTTAATATGCACGGGAAGTATCCTA 59.504 38.462 0.00 0.00 45.77 2.94
1932 6741 6.872920 TGAGCCATCTTTGTTACAACTTTTT 58.127 32.000 0.00 0.00 0.00 1.94
1933 6742 6.463995 TGAGCCATCTTTGTTACAACTTTT 57.536 33.333 0.00 0.00 0.00 2.27
1936 6745 4.887071 TGTTGAGCCATCTTTGTTACAACT 59.113 37.500 0.00 0.00 37.71 3.16
1987 7057 7.069578 ACGGATGGAGTATACATACAGTTTTCT 59.930 37.037 5.50 0.00 35.74 2.52
1989 7059 7.120923 ACGGATGGAGTATACATACAGTTTT 57.879 36.000 5.50 0.00 35.74 2.43
2005 7075 8.044309 TGAGTCATCTATTTTAAAACGGATGGA 58.956 33.333 26.84 18.23 34.20 3.41
2007 7077 9.490663 GTTGAGTCATCTATTTTAAAACGGATG 57.509 33.333 24.31 24.31 34.46 3.51
2008 7078 9.449719 AGTTGAGTCATCTATTTTAAAACGGAT 57.550 29.630 1.97 7.14 0.00 4.18
2009 7079 8.842358 AGTTGAGTCATCTATTTTAAAACGGA 57.158 30.769 1.97 5.09 0.00 4.69
2010 7080 9.893305 AAAGTTGAGTCATCTATTTTAAAACGG 57.107 29.630 1.97 0.00 0.00 4.44
2024 7094 9.751542 GCATGTACTAGTATAAAGTTGAGTCAT 57.248 33.333 5.75 0.00 0.00 3.06
2025 7095 8.967918 AGCATGTACTAGTATAAAGTTGAGTCA 58.032 33.333 5.75 0.00 0.00 3.41
2040 7110 6.945938 ACCTGTCTAACTAGCATGTACTAG 57.054 41.667 5.98 5.98 44.38 2.57
2041 7111 7.341030 TGTACCTGTCTAACTAGCATGTACTA 58.659 38.462 17.09 0.00 35.40 1.82
2042 7112 6.185511 TGTACCTGTCTAACTAGCATGTACT 58.814 40.000 17.09 0.00 35.40 2.73
2043 7113 6.446781 TGTACCTGTCTAACTAGCATGTAC 57.553 41.667 0.00 13.40 35.21 2.90
2044 7114 6.831868 TGATGTACCTGTCTAACTAGCATGTA 59.168 38.462 0.00 0.00 0.00 2.29
2045 7115 5.656859 TGATGTACCTGTCTAACTAGCATGT 59.343 40.000 0.00 0.00 0.00 3.21
2046 7116 6.149129 TGATGTACCTGTCTAACTAGCATG 57.851 41.667 0.00 0.00 0.00 4.06
2047 7117 6.791867 TTGATGTACCTGTCTAACTAGCAT 57.208 37.500 0.00 0.00 0.00 3.79
2048 7118 6.599356 TTTGATGTACCTGTCTAACTAGCA 57.401 37.500 0.00 0.00 0.00 3.49
2049 7119 9.250624 CTAATTTGATGTACCTGTCTAACTAGC 57.749 37.037 0.00 0.00 0.00 3.42
2131 7201 7.979786 TTCTACATAAAGAGAACTCCCTCAT 57.020 36.000 0.00 0.00 35.68 2.90
2159 7230 4.657039 TCGAAGGGCCTGGTTATACTATTT 59.343 41.667 6.92 0.00 0.00 1.40
2173 7245 1.032114 CCAACCTGAATCGAAGGGCC 61.032 60.000 6.59 0.00 39.30 5.80
2215 7287 4.514066 ACCTAACAAGACGTTTTGGATCAC 59.486 41.667 21.34 0.00 39.14 3.06
2266 7339 1.300971 TGCAGCGCCACTTGATCTTC 61.301 55.000 2.29 0.00 0.00 2.87
2267 7340 0.890542 TTGCAGCGCCACTTGATCTT 60.891 50.000 2.29 0.00 0.00 2.40
2271 7344 2.203195 AGTTGCAGCGCCACTTGA 60.203 55.556 2.29 0.00 30.18 3.02
2306 7379 4.062293 TCGGCATTAGTTGGTACATATGC 58.938 43.478 1.58 0.00 40.07 3.14
2308 7381 5.546621 ACTCGGCATTAGTTGGTACATAT 57.453 39.130 0.00 0.00 39.30 1.78
2311 7384 3.765511 AGTACTCGGCATTAGTTGGTACA 59.234 43.478 0.00 0.00 33.00 2.90
2316 7389 3.307242 GCTCAAGTACTCGGCATTAGTTG 59.693 47.826 0.00 0.00 32.15 3.16
2318 7391 2.496070 TGCTCAAGTACTCGGCATTAGT 59.504 45.455 11.57 0.00 0.00 2.24
2319 7392 3.119291 CTGCTCAAGTACTCGGCATTAG 58.881 50.000 14.65 4.00 32.39 1.73
2320 7393 2.758423 TCTGCTCAAGTACTCGGCATTA 59.242 45.455 14.65 6.74 32.39 1.90
2321 7394 1.550524 TCTGCTCAAGTACTCGGCATT 59.449 47.619 14.65 0.00 32.39 3.56
2322 7395 1.186200 TCTGCTCAAGTACTCGGCAT 58.814 50.000 14.65 0.00 32.39 4.40
2324 7397 1.336887 TGTTCTGCTCAAGTACTCGGC 60.337 52.381 0.00 1.71 0.00 5.54
2325 7398 2.724977 TGTTCTGCTCAAGTACTCGG 57.275 50.000 0.00 0.00 0.00 4.63
2336 7409 3.697045 AGATACGAGCTACTTGTTCTGCT 59.303 43.478 0.00 0.00 38.59 4.24
2337 7410 4.035278 AGATACGAGCTACTTGTTCTGC 57.965 45.455 0.00 0.00 29.93 4.26
2338 7411 6.952935 AAAAGATACGAGCTACTTGTTCTG 57.047 37.500 0.00 0.00 29.93 3.02
2340 7413 8.463456 ACTAAAAAGATACGAGCTACTTGTTC 57.537 34.615 0.00 0.00 29.93 3.18
2342 7415 7.871463 ACAACTAAAAAGATACGAGCTACTTGT 59.129 33.333 0.00 0.00 32.27 3.16
2343 7416 8.240883 ACAACTAAAAAGATACGAGCTACTTG 57.759 34.615 0.00 0.00 0.00 3.16
2344 7417 8.086522 TGACAACTAAAAAGATACGAGCTACTT 58.913 33.333 0.00 0.00 0.00 2.24
2345 7418 7.600065 TGACAACTAAAAAGATACGAGCTACT 58.400 34.615 0.00 0.00 0.00 2.57
2347 7420 8.821147 TTTGACAACTAAAAAGATACGAGCTA 57.179 30.769 0.00 0.00 0.00 3.32
2348 7421 7.724305 TTTGACAACTAAAAAGATACGAGCT 57.276 32.000 0.00 0.00 0.00 4.09
2349 7422 8.776680 TTTTTGACAACTAAAAAGATACGAGC 57.223 30.769 0.00 0.00 33.47 5.03
2394 9174 8.752005 AGATATGAGCTACTGGCATTTAAAAA 57.248 30.769 0.00 0.00 44.79 1.94
2395 9175 9.273016 GTAGATATGAGCTACTGGCATTTAAAA 57.727 33.333 0.00 0.00 44.79 1.52
2396 9176 7.878127 GGTAGATATGAGCTACTGGCATTTAAA 59.122 37.037 0.00 0.00 44.79 1.52
2397 9177 7.386851 GGTAGATATGAGCTACTGGCATTTAA 58.613 38.462 0.00 0.00 44.79 1.52
2398 9178 6.350194 CGGTAGATATGAGCTACTGGCATTTA 60.350 42.308 3.31 0.00 44.79 1.40
2454 9234 4.744478 TAAAAAGGGCCCCGGCGG 62.744 66.667 21.43 21.46 43.06 6.13
2455 9235 2.677172 TTAAAAAGGGCCCCGGCG 60.677 61.111 21.43 0.00 43.06 6.46
2456 9236 1.884075 CTGTTAAAAAGGGCCCCGGC 61.884 60.000 21.43 2.41 41.06 6.13
2457 9237 1.254975 CCTGTTAAAAAGGGCCCCGG 61.255 60.000 21.43 5.91 0.00 5.73
2458 9238 0.251430 TCCTGTTAAAAAGGGCCCCG 60.251 55.000 21.43 0.00 35.35 5.73
2459 9239 1.557099 CTCCTGTTAAAAAGGGCCCC 58.443 55.000 21.43 0.46 35.35 5.80
2474 9254 4.279982 GGTAACCTCTAGTTAGTGCTCCT 58.720 47.826 0.00 0.00 41.63 3.69
2475 9255 4.652421 GGTAACCTCTAGTTAGTGCTCC 57.348 50.000 0.00 0.00 41.63 4.70


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

AutoCloner maintained by Alex Coulton.