Multiple sequence alignment - TraesCS3D01G267900

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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 TraesCS3D01G267900 chr3D 100.000 7362 0 0 1 7362 371898034 371890673 0.000000e+00 13596.0
1 TraesCS3D01G267900 chr3D 100.000 34 0 0 4691 4724 371893242 371893209 6.170000e-06 63.9
2 TraesCS3D01G267900 chr3D 100.000 34 0 0 4793 4826 371893344 371893311 6.170000e-06 63.9
3 TraesCS3D01G267900 chr3B 95.205 7278 153 59 53 7237 483000757 482993583 0.000000e+00 11326.0
4 TraesCS3D01G267900 chr3B 96.386 83 1 2 7265 7347 482989853 482989773 1.290000e-27 135.0
5 TraesCS3D01G267900 chr3B 100.000 35 0 0 4793 4827 482996110 482996076 1.710000e-06 65.8
6 TraesCS3D01G267900 chr3B 100.000 34 0 0 4691 4724 482996008 482995975 6.170000e-06 63.9
7 TraesCS3D01G267900 chr3A 91.109 4814 231 65 1 4736 493134618 493129924 0.000000e+00 6336.0
8 TraesCS3D01G267900 chr3A 89.956 2509 162 42 4730 7193 493129688 493127225 0.000000e+00 3155.0
9 TraesCS3D01G267900 chr3A 100.000 34 0 0 4691 4724 493129626 493129593 6.170000e-06 63.9
10 TraesCS3D01G267900 chr3A 97.143 35 1 0 4793 4827 493129969 493129935 7.980000e-05 60.2
11 TraesCS3D01G267900 chr2A 89.021 337 17 9 209 527 740483824 740484158 4.140000e-107 399.0
12 TraesCS3D01G267900 chr5B 97.368 38 1 0 4609 4646 643906056 643906019 1.710000e-06 65.8
13 TraesCS3D01G267900 chr1A 93.023 43 3 0 4609 4651 537057576 537057534 6.170000e-06 63.9


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 TraesCS3D01G267900 chr3D 371890673 371898034 7361 True 13596.000000 13596 100.000000 1 7362 1 chr3D.!!$R1 7361
1 TraesCS3D01G267900 chr3B 482989773 483000757 10984 True 5730.500000 11326 95.795500 53 7347 2 chr3B.!!$R1 7294
2 TraesCS3D01G267900 chr3A 493127225 493134618 7393 True 3184.966667 6336 93.688333 1 7193 3 chr3A.!!$R2 7192

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
365 367 1.354337 CTGACAACCGAGCGATGGTG 61.354 60.000 0.0 0.0 40.35 4.17 F
1102 1159 0.322456 TGATCTCGGGCTTGGGTTTG 60.322 55.000 0.0 0.0 0.00 2.93 F
1103 1160 0.322546 GATCTCGGGCTTGGGTTTGT 60.323 55.000 0.0 0.0 0.00 2.83 F
1106 1163 0.537371 CTCGGGCTTGGGTTTGTCTT 60.537 55.000 0.0 0.0 0.00 3.01 F
1579 1653 0.675083 TTGAGTTTCGCCGTCCTACA 59.325 50.000 0.0 0.0 0.00 2.74 F
3432 3546 0.916358 CTGGATGGGGTTCAGGGACT 60.916 60.000 0.0 0.0 43.88 3.85 F
4724 4845 0.983467 TGGTGTGGCTGAGATGCTTA 59.017 50.000 0.0 0.0 0.00 3.09 F
5341 5705 1.277557 GTCCATGCTTCTCTCTGGTGT 59.722 52.381 0.0 0.0 0.00 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1435 1509 0.390340 GATCTGAAGGAGCACGCACA 60.390 55.000 0.00 0.00 0.00 4.57 R
2191 2287 4.614535 GCATGATATTGCATCCGAAGAACC 60.615 45.833 0.00 0.00 42.31 3.62 R
2431 2528 4.768130 TTCGATCCAGCATAGTAGCTAC 57.232 45.455 16.43 16.43 44.54 3.58 R
2900 3002 5.126222 TGCTTGACCACAATTCTTTGTACAA 59.874 36.000 3.59 3.59 44.24 2.41 R
3442 3556 0.110823 GGTAGTTCGTTTGCTGCACG 60.111 55.000 0.00 3.73 39.08 5.34 R
4779 5141 2.289565 GACCACTAGCATTAACCTGGC 58.710 52.381 0.00 0.00 0.00 4.85 R
6298 6669 0.036483 TGGCTGTATCAAGCTTCGCA 60.036 50.000 0.00 0.00 43.06 5.10 R
7249 7660 0.108851 TCGCGCTCAGCTCATTAACA 60.109 50.000 5.56 0.00 45.59 2.41 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
36 37 2.014128 CCACGCCAGGAAACGATAAAT 58.986 47.619 0.00 0.00 0.00 1.40
56 57 6.882458 AAATTTTCTAGTACCGATCGTGAC 57.118 37.500 15.09 11.21 0.00 3.67
85 87 8.738645 ACCACATATATTCTTCACCTCTTTTC 57.261 34.615 0.00 0.00 0.00 2.29
118 120 1.750193 TATGCCTCGCCCTTCTTTTG 58.250 50.000 0.00 0.00 0.00 2.44
252 254 2.158559 TCGATGTTCATGTTGGTTGGG 58.841 47.619 0.00 0.00 0.00 4.12
365 367 1.354337 CTGACAACCGAGCGATGGTG 61.354 60.000 0.00 0.00 40.35 4.17
386 409 5.423015 GTGGTAGCTTTCATCAGATCAGAA 58.577 41.667 0.00 0.00 0.00 3.02
851 908 2.431942 CTACACCACACGCGACCC 60.432 66.667 15.93 0.00 0.00 4.46
1076 1133 1.197430 ATCCATCCGGAGCTGGATCC 61.197 60.000 27.22 4.20 46.95 3.36
1102 1159 0.322456 TGATCTCGGGCTTGGGTTTG 60.322 55.000 0.00 0.00 0.00 2.93
1103 1160 0.322546 GATCTCGGGCTTGGGTTTGT 60.323 55.000 0.00 0.00 0.00 2.83
1104 1161 0.322546 ATCTCGGGCTTGGGTTTGTC 60.323 55.000 0.00 0.00 0.00 3.18
1105 1162 1.073199 CTCGGGCTTGGGTTTGTCT 59.927 57.895 0.00 0.00 0.00 3.41
1106 1163 0.537371 CTCGGGCTTGGGTTTGTCTT 60.537 55.000 0.00 0.00 0.00 3.01
1107 1164 0.821711 TCGGGCTTGGGTTTGTCTTG 60.822 55.000 0.00 0.00 0.00 3.02
1118 1175 3.058224 GGGTTTGTCTTGTTCTTGGATCG 60.058 47.826 0.00 0.00 0.00 3.69
1119 1176 3.058224 GGTTTGTCTTGTTCTTGGATCGG 60.058 47.826 0.00 0.00 0.00 4.18
1123 1180 1.974957 TCTTGTTCTTGGATCGGTGGA 59.025 47.619 0.00 0.00 0.00 4.02
1124 1181 2.370519 TCTTGTTCTTGGATCGGTGGAA 59.629 45.455 0.00 0.00 0.00 3.53
1127 1184 3.343617 TGTTCTTGGATCGGTGGAATTC 58.656 45.455 0.00 0.00 0.00 2.17
1141 1198 2.618053 GGAATTCGTCCGTGTTCTGAT 58.382 47.619 0.00 0.00 36.40 2.90
1496 1570 3.433343 TGGTGGATCATGTTGCTGAATT 58.567 40.909 0.00 0.00 0.00 2.17
1497 1571 4.598022 TGGTGGATCATGTTGCTGAATTA 58.402 39.130 0.00 0.00 0.00 1.40
1498 1572 5.202765 TGGTGGATCATGTTGCTGAATTAT 58.797 37.500 0.00 0.00 0.00 1.28
1499 1573 5.300034 TGGTGGATCATGTTGCTGAATTATC 59.700 40.000 0.00 0.00 0.00 1.75
1500 1574 5.446709 GTGGATCATGTTGCTGAATTATCG 58.553 41.667 0.00 0.00 0.00 2.92
1501 1575 5.008019 GTGGATCATGTTGCTGAATTATCGT 59.992 40.000 0.00 0.00 0.00 3.73
1502 1576 5.589855 TGGATCATGTTGCTGAATTATCGTT 59.410 36.000 0.00 0.00 0.00 3.85
1503 1577 5.911280 GGATCATGTTGCTGAATTATCGTTG 59.089 40.000 0.00 0.00 0.00 4.10
1504 1578 6.238456 GGATCATGTTGCTGAATTATCGTTGA 60.238 38.462 0.00 0.00 0.00 3.18
1579 1653 0.675083 TTGAGTTTCGCCGTCCTACA 59.325 50.000 0.00 0.00 0.00 2.74
1755 1850 0.940519 GCTGCATGCTGTTTGCGAAA 60.941 50.000 23.42 0.00 46.63 3.46
1788 1884 5.346281 CGTTCAAGTAATGGTCTCTTCACTC 59.654 44.000 0.00 0.00 0.00 3.51
1993 2089 4.458989 CCAGCTATAGAAGAGGCAGTAGAG 59.541 50.000 3.21 0.00 0.00 2.43
2431 2528 3.393609 TCATTTGGAGGATGGGATGAGAG 59.606 47.826 0.00 0.00 0.00 3.20
2900 3002 5.103515 AGGGGATGCTTTTAGTATTCCATGT 60.104 40.000 4.74 0.00 37.68 3.21
3319 3433 5.744300 GCCATATTACTCTGCTGTGATTCCT 60.744 44.000 0.00 0.00 0.00 3.36
3432 3546 0.916358 CTGGATGGGGTTCAGGGACT 60.916 60.000 0.00 0.00 43.88 3.85
3638 3752 7.957002 TGCAAATAAGGTACTGAAAAATTCCA 58.043 30.769 0.00 0.00 40.86 3.53
3884 4001 7.315142 CAGAAGCAAGCTAAATGAATTTGGTA 58.685 34.615 0.00 0.00 31.76 3.25
4392 4510 1.202867 TGTGCCTTGGTAAGACATGCA 60.203 47.619 0.00 0.00 0.00 3.96
4485 4604 7.309438 GGTTCTTGAATTAGGCTCTGTTTCATT 60.309 37.037 0.00 0.00 0.00 2.57
4724 4845 0.983467 TGGTGTGGCTGAGATGCTTA 59.017 50.000 0.00 0.00 0.00 3.09
5026 5388 9.642343 TTGCTTCCACTATCTAACTAGAGAATA 57.358 33.333 0.00 0.00 35.50 1.75
5341 5705 1.277557 GTCCATGCTTCTCTCTGGTGT 59.722 52.381 0.00 0.00 0.00 4.16
5347 5711 1.404047 GCTTCTCTCTGGTGTGCTCTC 60.404 57.143 0.00 0.00 0.00 3.20
5870 6235 6.924111 ACCTGTTGAATGACCATAAATTGAC 58.076 36.000 0.00 0.00 0.00 3.18
5871 6236 6.493115 ACCTGTTGAATGACCATAAATTGACA 59.507 34.615 0.00 0.00 0.00 3.58
6275 6646 5.164620 TGTTGATACATCCAAGAGAAGCA 57.835 39.130 0.00 0.00 0.00 3.91
6404 6781 1.867233 CGGAAGCTACATCCAAATCGG 59.133 52.381 3.87 0.00 36.74 4.18
6501 6883 0.700564 AAATGAGAGCCTTGGAGCCA 59.299 50.000 0.00 0.00 0.00 4.75
6561 6945 2.487265 GGTTTCCGAGGCATATCATGGT 60.487 50.000 0.00 0.00 0.00 3.55
6580 6964 6.615316 TCATGGTTGGTAGAGAATTCTCCATA 59.385 38.462 28.01 14.63 43.88 2.74
6661 7045 7.173863 TCTTGTTATTGTTTCTTCTGTCGTC 57.826 36.000 0.00 0.00 0.00 4.20
6662 7046 5.570262 TGTTATTGTTTCTTCTGTCGTCG 57.430 39.130 0.00 0.00 0.00 5.12
6663 7047 5.045215 TGTTATTGTTTCTTCTGTCGTCGT 58.955 37.500 0.00 0.00 0.00 4.34
6664 7048 5.174398 TGTTATTGTTTCTTCTGTCGTCGTC 59.826 40.000 0.00 0.00 0.00 4.20
6777 7161 4.141018 AGCAAAGGTAGAAAAAGGAAGGGA 60.141 41.667 0.00 0.00 0.00 4.20
6822 7206 4.007659 ACCTGCGTTTTTATTCCACTAGG 58.992 43.478 0.00 0.00 0.00 3.02
6903 7287 2.789409 AAAAAGGGACCGGAGATCTG 57.211 50.000 9.46 0.00 0.00 2.90
6904 7288 1.657804 AAAAGGGACCGGAGATCTGT 58.342 50.000 9.46 0.00 0.00 3.41
6905 7289 1.657804 AAAGGGACCGGAGATCTGTT 58.342 50.000 9.46 0.00 0.00 3.16
6906 7290 1.196012 AAGGGACCGGAGATCTGTTC 58.804 55.000 9.46 0.00 0.00 3.18
6907 7291 0.041238 AGGGACCGGAGATCTGTTCA 59.959 55.000 9.46 0.00 0.00 3.18
6908 7292 1.123928 GGGACCGGAGATCTGTTCAT 58.876 55.000 9.46 0.00 0.00 2.57
6909 7293 1.069358 GGGACCGGAGATCTGTTCATC 59.931 57.143 9.46 0.00 0.00 2.92
6910 7294 1.757118 GGACCGGAGATCTGTTCATCA 59.243 52.381 9.46 0.00 0.00 3.07
6911 7295 2.168521 GGACCGGAGATCTGTTCATCAA 59.831 50.000 9.46 0.00 0.00 2.57
6912 7296 3.190874 GACCGGAGATCTGTTCATCAAC 58.809 50.000 9.46 0.00 0.00 3.18
7113 7516 2.678934 CCACATGGCTGCCTGCTT 60.679 61.111 21.03 0.00 42.39 3.91
7127 7530 1.294659 CTGCTTGTTCTCGGCTCACC 61.295 60.000 0.00 0.00 0.00 4.02
7157 7565 2.683362 TGGCGTGTGTGTACAAAAATCA 59.317 40.909 0.00 0.00 38.82 2.57
7158 7566 3.128764 TGGCGTGTGTGTACAAAAATCAA 59.871 39.130 0.00 0.00 38.82 2.57
7209 7620 4.932200 GTGTGCTTCACTAGATGCTAGTTT 59.068 41.667 4.45 0.00 43.30 2.66
7237 7648 6.726490 TTCCTTTGACACTTGACTAGTACT 57.274 37.500 0.00 0.00 34.56 2.73
7238 7649 7.828508 TTCCTTTGACACTTGACTAGTACTA 57.171 36.000 1.89 1.89 34.56 1.82
7239 7650 8.418597 TTCCTTTGACACTTGACTAGTACTAT 57.581 34.615 2.33 0.00 34.56 2.12
7240 7651 7.827701 TCCTTTGACACTTGACTAGTACTATG 58.172 38.462 2.33 0.20 34.56 2.23
7242 7653 8.737175 CCTTTGACACTTGACTAGTACTATGTA 58.263 37.037 2.33 0.00 34.56 2.29
7244 7655 9.511272 TTTGACACTTGACTAGTACTATGTAGA 57.489 33.333 2.33 0.00 34.56 2.59
7245 7656 8.719560 TGACACTTGACTAGTACTATGTAGAG 57.280 38.462 2.33 7.67 34.56 2.43
7246 7657 8.319881 TGACACTTGACTAGTACTATGTAGAGT 58.680 37.037 2.33 0.00 34.56 3.24
7248 7659 9.517868 ACACTTGACTAGTACTATGTAGAGTTT 57.482 33.333 2.33 3.05 34.56 2.66
7261 7672 9.155975 ACTATGTAGAGTTTTGTTAATGAGCTG 57.844 33.333 0.00 0.00 0.00 4.24
7262 7673 9.371136 CTATGTAGAGTTTTGTTAATGAGCTGA 57.629 33.333 0.00 0.00 0.00 4.26
7263 7674 7.658179 TGTAGAGTTTTGTTAATGAGCTGAG 57.342 36.000 0.00 0.00 0.00 3.35
7265 7676 4.153117 AGAGTTTTGTTAATGAGCTGAGCG 59.847 41.667 0.00 0.00 0.00 5.03
7266 7677 2.900122 TTTGTTAATGAGCTGAGCGC 57.100 45.000 0.00 0.00 39.57 5.92
7267 7678 0.721154 TTGTTAATGAGCTGAGCGCG 59.279 50.000 0.00 0.00 45.59 6.86
7268 7679 0.108851 TGTTAATGAGCTGAGCGCGA 60.109 50.000 12.10 0.00 45.59 5.87
7269 7680 0.299003 GTTAATGAGCTGAGCGCGAC 59.701 55.000 12.10 2.99 45.59 5.19
7273 7684 3.177920 GAGCTGAGCGCGACACTG 61.178 66.667 12.10 5.41 45.59 3.66
7301 11413 1.916000 GATGCTTTGCTGAATTCGTGC 59.084 47.619 14.04 14.04 0.00 5.34
7333 11445 0.034198 CCGTGTGGTGTGGTATGTGA 59.966 55.000 0.00 0.00 0.00 3.58
7347 11459 3.054361 GGTATGTGATCCAGGGTTCACTT 60.054 47.826 23.10 19.98 42.27 3.16
7348 11460 2.859165 TGTGATCCAGGGTTCACTTC 57.141 50.000 23.10 5.27 42.27 3.01
7349 11461 2.054021 TGTGATCCAGGGTTCACTTCA 58.946 47.619 23.10 7.33 42.27 3.02
7350 11462 2.224523 TGTGATCCAGGGTTCACTTCAC 60.225 50.000 23.10 5.94 42.27 3.18
7351 11463 2.039084 GTGATCCAGGGTTCACTTCACT 59.961 50.000 18.07 0.00 40.04 3.41
7352 11464 2.711009 TGATCCAGGGTTCACTTCACTT 59.289 45.455 0.00 0.00 0.00 3.16
7353 11465 2.930826 TCCAGGGTTCACTTCACTTC 57.069 50.000 0.00 0.00 0.00 3.01
7354 11466 1.070134 TCCAGGGTTCACTTCACTTCG 59.930 52.381 0.00 0.00 0.00 3.79
7355 11467 1.070134 CCAGGGTTCACTTCACTTCGA 59.930 52.381 0.00 0.00 0.00 3.71
7356 11468 2.408050 CAGGGTTCACTTCACTTCGAG 58.592 52.381 0.00 0.00 0.00 4.04
7357 11469 2.035961 CAGGGTTCACTTCACTTCGAGA 59.964 50.000 0.00 0.00 0.00 4.04
7358 11470 2.036089 AGGGTTCACTTCACTTCGAGAC 59.964 50.000 0.00 0.00 0.00 3.36
7359 11471 2.405172 GGTTCACTTCACTTCGAGACC 58.595 52.381 0.00 0.00 0.00 3.85
7360 11472 2.405172 GTTCACTTCACTTCGAGACCC 58.595 52.381 0.00 0.00 0.00 4.46
7361 11473 0.966920 TCACTTCACTTCGAGACCCC 59.033 55.000 0.00 0.00 0.00 4.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 4.142534 CCAGTCACGATCGGTACTAGAAAA 60.143 45.833 20.98 0.00 0.00 2.29
56 57 6.042552 AGAGGTGAAGAATATATGTGGTCCAG 59.957 42.308 0.00 0.00 0.00 3.86
85 87 1.043022 GGCATATTTTGGGCCTGGAG 58.957 55.000 4.53 0.00 44.32 3.86
118 120 6.349777 CCAAGATGAGGAATATCGGACTCTAC 60.350 46.154 0.00 0.00 0.00 2.59
171 173 1.752501 GATCAACGGATGCGTGACGG 61.753 60.000 14.66 3.79 32.67 4.79
183 185 7.096844 CACTAGATGTGTTTCGATAGATCAACG 60.097 40.741 0.00 0.00 42.95 4.10
252 254 1.060698 GCAATCGGCGAGAAACTACAC 59.939 52.381 17.22 0.00 0.00 2.90
292 294 1.885850 GTCAAGGTCGCGTGTGGTT 60.886 57.895 5.77 0.00 0.00 3.67
293 295 2.279918 GTCAAGGTCGCGTGTGGT 60.280 61.111 5.77 0.00 0.00 4.16
302 304 1.003580 TGATCCTGGCAAGTCAAGGTC 59.996 52.381 0.00 0.00 0.00 3.85
365 367 7.930865 ACTAATTCTGATCTGATGAAAGCTACC 59.069 37.037 2.84 0.00 0.00 3.18
386 409 2.873472 TGAAAACGTGCCGTCAACTAAT 59.127 40.909 0.00 0.00 39.99 1.73
545 590 9.224267 GAGTTAATCATAGCATTCCACATACAT 57.776 33.333 0.00 0.00 0.00 2.29
546 591 7.661437 GGAGTTAATCATAGCATTCCACATACA 59.339 37.037 0.00 0.00 0.00 2.29
547 592 7.880195 AGGAGTTAATCATAGCATTCCACATAC 59.120 37.037 0.00 0.00 0.00 2.39
548 593 7.977818 AGGAGTTAATCATAGCATTCCACATA 58.022 34.615 0.00 0.00 0.00 2.29
1076 1133 2.332104 CAAGCCCGAGATCATGTATCG 58.668 52.381 0.00 9.11 41.07 2.92
1102 1159 2.076863 CCACCGATCCAAGAACAAGAC 58.923 52.381 0.00 0.00 0.00 3.01
1103 1160 1.974957 TCCACCGATCCAAGAACAAGA 59.025 47.619 0.00 0.00 0.00 3.02
1104 1161 2.472695 TCCACCGATCCAAGAACAAG 57.527 50.000 0.00 0.00 0.00 3.16
1105 1162 2.940994 TTCCACCGATCCAAGAACAA 57.059 45.000 0.00 0.00 0.00 2.83
1106 1163 3.343617 GAATTCCACCGATCCAAGAACA 58.656 45.455 0.00 0.00 0.00 3.18
1107 1164 2.351726 CGAATTCCACCGATCCAAGAAC 59.648 50.000 0.00 0.00 0.00 3.01
1118 1175 0.794473 GAACACGGACGAATTCCACC 59.206 55.000 0.00 2.84 46.29 4.61
1119 1176 1.459592 CAGAACACGGACGAATTCCAC 59.540 52.381 0.00 0.00 46.29 4.02
1123 1180 3.813166 ACAAATCAGAACACGGACGAATT 59.187 39.130 0.00 0.00 0.00 2.17
1124 1181 3.399330 ACAAATCAGAACACGGACGAAT 58.601 40.909 0.00 0.00 0.00 3.34
1127 1184 3.602390 AAACAAATCAGAACACGGACG 57.398 42.857 0.00 0.00 0.00 4.79
1435 1509 0.390340 GATCTGAAGGAGCACGCACA 60.390 55.000 0.00 0.00 0.00 4.57
1488 1562 2.348362 CGCACTCAACGATAATTCAGCA 59.652 45.455 0.00 0.00 0.00 4.41
1496 1570 2.863401 ATGCTACGCACTCAACGATA 57.137 45.000 0.00 0.00 43.04 2.92
1497 1571 2.010145 AATGCTACGCACTCAACGAT 57.990 45.000 0.00 0.00 43.04 3.73
1498 1572 1.790755 AAATGCTACGCACTCAACGA 58.209 45.000 0.00 0.00 43.04 3.85
1499 1573 2.594529 AAAATGCTACGCACTCAACG 57.405 45.000 0.00 0.00 43.04 4.10
1500 1574 3.884169 TGAAAAATGCTACGCACTCAAC 58.116 40.909 0.00 0.00 43.04 3.18
1501 1575 4.475028 CATGAAAAATGCTACGCACTCAA 58.525 39.130 0.00 0.00 43.04 3.02
1502 1576 3.119884 CCATGAAAAATGCTACGCACTCA 60.120 43.478 0.00 0.00 43.04 3.41
1503 1577 3.126858 TCCATGAAAAATGCTACGCACTC 59.873 43.478 0.00 0.00 43.04 3.51
1504 1578 3.081061 TCCATGAAAAATGCTACGCACT 58.919 40.909 0.00 0.00 43.04 4.40
1568 1642 1.497991 CATGGTATTGTAGGACGGCG 58.502 55.000 4.80 4.80 0.00 6.46
1579 1653 2.200081 ACAGAGACCTGCCATGGTATT 58.800 47.619 14.67 0.00 44.16 1.89
1764 1859 5.230942 AGTGAAGAGACCATTACTTGAACG 58.769 41.667 0.00 0.00 0.00 3.95
1993 2089 5.567552 GTGCTAGCATCAATCTTCAAGTTC 58.432 41.667 22.51 0.00 0.00 3.01
2075 2171 5.914033 TCCTTGTACGCTAAGATAAGCAAT 58.086 37.500 0.00 0.00 42.91 3.56
2191 2287 4.614535 GCATGATATTGCATCCGAAGAACC 60.615 45.833 0.00 0.00 42.31 3.62
2431 2528 4.768130 TTCGATCCAGCATAGTAGCTAC 57.232 45.455 16.43 16.43 44.54 3.58
2900 3002 5.126222 TGCTTGACCACAATTCTTTGTACAA 59.874 36.000 3.59 3.59 44.24 2.41
2997 3099 7.639162 AAGTCAACTGTTAAATCGAGTACTG 57.361 36.000 0.00 0.00 0.00 2.74
3067 3174 6.126739 ACCCTAGAATTGATTAGACCAAGGAC 60.127 42.308 0.00 0.00 0.00 3.85
3068 3175 5.970640 ACCCTAGAATTGATTAGACCAAGGA 59.029 40.000 0.00 0.00 0.00 3.36
3069 3176 6.058183 CACCCTAGAATTGATTAGACCAAGG 58.942 44.000 0.00 0.00 0.00 3.61
3070 3177 6.889198 TCACCCTAGAATTGATTAGACCAAG 58.111 40.000 0.00 0.00 0.00 3.61
3071 3178 6.884472 TCACCCTAGAATTGATTAGACCAA 57.116 37.500 0.00 0.00 0.00 3.67
3072 3179 6.443849 AGTTCACCCTAGAATTGATTAGACCA 59.556 38.462 0.00 0.00 0.00 4.02
3073 3180 6.763610 CAGTTCACCCTAGAATTGATTAGACC 59.236 42.308 0.00 0.00 37.40 3.85
3307 3421 2.936928 CTGCACAGGAATCACAGCA 58.063 52.632 0.00 0.00 0.00 4.41
3319 3433 0.685097 GTGTAGAAGGGTCCTGCACA 59.315 55.000 0.00 0.00 43.59 4.57
3432 3546 3.286751 GCTGCACGCCAACAGGAA 61.287 61.111 0.00 0.00 34.38 3.36
3442 3556 0.110823 GGTAGTTCGTTTGCTGCACG 60.111 55.000 0.00 3.73 39.08 5.34
3638 3752 7.656542 GCTTAGAGTAGTTTGTCCTGTTTTACT 59.343 37.037 0.00 0.00 0.00 2.24
3715 3832 2.094752 CCCTTTTGTTATGGAAGCACCG 60.095 50.000 0.00 0.00 42.61 4.94
3884 4001 6.403049 TGTGTTTATCTGATATGTCACGGTT 58.597 36.000 15.52 0.00 0.00 4.44
4363 4481 7.172342 TGTCTTACCAAGGCACACTAAATTAT 58.828 34.615 0.00 0.00 38.40 1.28
4364 4482 6.535540 TGTCTTACCAAGGCACACTAAATTA 58.464 36.000 0.00 0.00 38.40 1.40
4365 4483 5.381757 TGTCTTACCAAGGCACACTAAATT 58.618 37.500 0.00 0.00 38.40 1.82
4431 4549 9.912634 GAGAAACAAAATAATCAAACTGGATGA 57.087 29.630 0.00 0.00 0.00 2.92
4779 5141 2.289565 GACCACTAGCATTAACCTGGC 58.710 52.381 0.00 0.00 0.00 4.85
5026 5388 3.510531 TCTAGCTCTGATCATACCGGT 57.489 47.619 13.98 13.98 0.00 5.28
5341 5705 7.175347 ACATTAACTGATCACTAAGAGAGCA 57.825 36.000 0.00 0.00 0.00 4.26
5693 6057 9.651913 CAGGTAATAAAATTTAGCAAACCATGT 57.348 29.630 10.47 0.00 33.13 3.21
5696 6060 6.809196 CGCAGGTAATAAAATTTAGCAAACCA 59.191 34.615 10.47 0.00 33.13 3.67
5752 6117 2.821378 TCCATGATGCCACAAAGTGAAG 59.179 45.455 0.00 0.00 35.23 3.02
5884 6249 8.708378 TGTGACCTTCTATCACTAATCATGAAT 58.292 33.333 0.00 0.00 45.58 2.57
6158 6529 4.713553 TCACTTGTCTTGGCTGTATCAAA 58.286 39.130 0.00 0.00 0.00 2.69
6275 6646 2.508526 GACCATGTTGCTCTGTTCCTT 58.491 47.619 0.00 0.00 0.00 3.36
6298 6669 0.036483 TGGCTGTATCAAGCTTCGCA 60.036 50.000 0.00 0.00 43.06 5.10
6404 6781 2.414138 ACGTAGCAAGTTTATTGTCGCC 59.586 45.455 0.00 0.00 0.00 5.54
6501 6883 7.938140 TTGAAAATATTTCTCACGGGAAGAT 57.062 32.000 0.10 0.00 0.00 2.40
6542 6926 3.213506 CAACCATGATATGCCTCGGAAA 58.786 45.455 0.00 0.00 0.00 3.13
6546 6930 2.260844 ACCAACCATGATATGCCTCG 57.739 50.000 0.00 0.00 0.00 4.63
6561 6945 7.839705 AGTGTAGTATGGAGAATTCTCTACCAA 59.160 37.037 29.64 15.64 42.48 3.67
6580 6964 6.651225 GCTGAAAAATAGACAAGGAGTGTAGT 59.349 38.462 0.00 0.00 41.96 2.73
6662 7046 1.201855 ACATTAGACGACGACGACGAC 60.202 52.381 25.15 18.88 42.66 4.34
6663 7047 1.059692 GACATTAGACGACGACGACGA 59.940 52.381 25.15 4.05 42.66 4.20
6664 7048 1.440790 GACATTAGACGACGACGACG 58.559 55.000 17.60 17.60 42.66 5.12
6822 7206 6.038997 AGTACAAACTGAGGTCAATCTACC 57.961 41.667 0.00 0.00 35.57 3.18
6902 7286 3.961480 ACGGAGATCTGTTGATGAACA 57.039 42.857 0.00 0.00 39.88 3.18
6903 7287 3.304559 CGAACGGAGATCTGTTGATGAAC 59.695 47.826 11.67 0.00 44.81 3.18
6904 7288 3.056821 ACGAACGGAGATCTGTTGATGAA 60.057 43.478 11.67 0.00 44.81 2.57
6905 7289 2.492088 ACGAACGGAGATCTGTTGATGA 59.508 45.455 11.67 0.00 44.81 2.92
6906 7290 2.881074 ACGAACGGAGATCTGTTGATG 58.119 47.619 11.67 4.56 44.81 3.07
6907 7291 3.594603 AACGAACGGAGATCTGTTGAT 57.405 42.857 11.67 0.00 44.81 2.57
6908 7292 3.366679 GGTAACGAACGGAGATCTGTTGA 60.367 47.826 11.67 0.00 44.81 3.18
6909 7293 2.921754 GGTAACGAACGGAGATCTGTTG 59.078 50.000 11.67 7.00 44.81 3.33
6911 7295 2.935481 GGTAACGAACGGAGATCTGT 57.065 50.000 0.00 0.00 36.96 3.41
7058 7455 1.202582 ACTGGACGTGATTTCTCTCCG 59.797 52.381 0.00 0.00 0.00 4.63
7113 7516 2.203788 AGGGGTGAGCCGAGAACA 60.204 61.111 0.00 0.00 34.97 3.18
7149 7552 8.274939 ACGACAGCAACAATAAATTGATTTTTG 58.725 29.630 9.60 9.30 40.14 2.44
7157 7565 5.851177 CGAAAGACGACAGCAACAATAAATT 59.149 36.000 0.00 0.00 45.77 1.82
7158 7566 5.178623 TCGAAAGACGACAGCAACAATAAAT 59.821 36.000 0.00 0.00 46.45 1.40
7215 7626 7.450634 ACATAGTACTAGTCAAGTGTCAAAGGA 59.549 37.037 8.85 0.00 39.39 3.36
7237 7648 9.371136 CTCAGCTCATTAACAAAACTCTACATA 57.629 33.333 0.00 0.00 0.00 2.29
7238 7649 7.148340 GCTCAGCTCATTAACAAAACTCTACAT 60.148 37.037 0.00 0.00 0.00 2.29
7239 7650 6.147821 GCTCAGCTCATTAACAAAACTCTACA 59.852 38.462 0.00 0.00 0.00 2.74
7240 7651 6.538444 GCTCAGCTCATTAACAAAACTCTAC 58.462 40.000 0.00 0.00 0.00 2.59
7242 7653 4.153117 CGCTCAGCTCATTAACAAAACTCT 59.847 41.667 0.00 0.00 0.00 3.24
7244 7655 3.365364 GCGCTCAGCTCATTAACAAAACT 60.365 43.478 0.00 0.00 44.04 2.66
7245 7656 2.911102 GCGCTCAGCTCATTAACAAAAC 59.089 45.455 0.00 0.00 44.04 2.43
7246 7657 2.412716 CGCGCTCAGCTCATTAACAAAA 60.413 45.455 5.56 0.00 45.59 2.44
7248 7659 0.721154 CGCGCTCAGCTCATTAACAA 59.279 50.000 5.56 0.00 45.59 2.83
7249 7660 0.108851 TCGCGCTCAGCTCATTAACA 60.109 50.000 5.56 0.00 45.59 2.41
7250 7661 0.299003 GTCGCGCTCAGCTCATTAAC 59.701 55.000 5.56 0.00 45.59 2.01
7251 7662 0.108851 TGTCGCGCTCAGCTCATTAA 60.109 50.000 5.56 0.00 45.59 1.40
7254 7665 2.507992 GTGTCGCGCTCAGCTCAT 60.508 61.111 5.56 0.00 45.59 2.90
7255 7666 3.674523 AGTGTCGCGCTCAGCTCA 61.675 61.111 5.56 0.00 45.59 4.26
7256 7667 3.177920 CAGTGTCGCGCTCAGCTC 61.178 66.667 5.56 0.00 45.59 4.09
7257 7668 4.731612 CCAGTGTCGCGCTCAGCT 62.732 66.667 5.56 2.75 45.59 4.24
7261 7672 3.876589 TTTCCCCAGTGTCGCGCTC 62.877 63.158 5.56 0.00 0.00 5.03
7262 7673 3.883744 CTTTCCCCAGTGTCGCGCT 62.884 63.158 5.56 0.00 0.00 5.92
7263 7674 3.423154 CTTTCCCCAGTGTCGCGC 61.423 66.667 0.00 0.00 0.00 6.86
7265 7676 1.026718 CATCCTTTCCCCAGTGTCGC 61.027 60.000 0.00 0.00 0.00 5.19
7266 7677 1.026718 GCATCCTTTCCCCAGTGTCG 61.027 60.000 0.00 0.00 0.00 4.35
7267 7678 0.329596 AGCATCCTTTCCCCAGTGTC 59.670 55.000 0.00 0.00 0.00 3.67
7268 7679 0.779997 AAGCATCCTTTCCCCAGTGT 59.220 50.000 0.00 0.00 0.00 3.55
7269 7680 1.547372 CAAAGCATCCTTTCCCCAGTG 59.453 52.381 0.00 0.00 39.20 3.66
7273 7684 0.533951 CAGCAAAGCATCCTTTCCCC 59.466 55.000 0.00 0.00 39.20 4.81
7333 11445 2.289694 CGAAGTGAAGTGAACCCTGGAT 60.290 50.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.