Multiple sequence alignment - TraesCS3D01G428200

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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 TraesCS3D01G428200 chr3D 100.000 4935 0 0 1 4935 542386334 542381400 0.000000e+00 9114
1 TraesCS3D01G428200 chr3A 95.155 4417 111 27 480 4871 678504161 678499823 0.000000e+00 6876
2 TraesCS3D01G428200 chr3A 80.965 373 54 10 62 431 678504549 678504191 3.760000e-71 279
3 TraesCS3D01G428200 chr3B 89.925 4784 252 92 62 4768 718293728 718289098 0.000000e+00 5952
4 TraesCS3D01G428200 chr3B 91.803 122 10 0 4814 4935 718289098 718288977 2.360000e-38 171


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 TraesCS3D01G428200 chr3D 542381400 542386334 4934 True 9114.0 9114 100.000 1 4935 1 chr3D.!!$R1 4934
1 TraesCS3D01G428200 chr3A 678499823 678504549 4726 True 3577.5 6876 88.060 62 4871 2 chr3A.!!$R1 4809
2 TraesCS3D01G428200 chr3B 718288977 718293728 4751 True 3061.5 5952 90.864 62 4935 2 chr3B.!!$R1 4873

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
371 373 0.107508 ATGATGACGGGCTGAAGGTG 60.108 55.000 0.00 0.00 0.00 4.00 F
1589 1683 0.535335 AGTTCACGCGTATCCACCAT 59.465 50.000 13.44 0.00 0.00 3.55 F
1656 1750 1.009078 GCATGTAACGATGCTGCTCA 58.991 50.000 0.00 0.00 44.57 4.26 F
1861 1956 1.288752 CGCCAAGGTGCCGAAATTT 59.711 52.632 0.00 0.00 0.00 1.82 F
2241 2346 1.873270 TAGACTGCGCACATGGTCGT 61.873 55.000 18.32 8.67 34.34 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1701 1795 1.219522 ACACGGAGCAGTACAAACGC 61.220 55.000 0.0 0.0 0.00 4.84 R
3309 3414 7.390718 ACATCACTTTGTAACCCTCATTAGAAC 59.609 37.037 0.0 0.0 0.00 3.01 R
3721 3826 3.119245 TCCTCATGTGCTTACCGTAGAAC 60.119 47.826 0.0 0.0 0.00 3.01 R
3832 3937 0.689623 CAGGAACCTTCTGCCACTCT 59.310 55.000 0.0 0.0 0.00 3.24 R
4367 4472 6.370994 AGTGATGCTGATATAATGCTACAAGC 59.629 38.462 0.0 0.0 42.82 4.01 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
26 27 7.948357 ACATATGAACCGTAGCTTAGTTATGA 58.052 34.615 10.38 0.00 0.00 2.15
27 28 8.585881 ACATATGAACCGTAGCTTAGTTATGAT 58.414 33.333 10.38 0.00 0.00 2.45
28 29 8.864024 CATATGAACCGTAGCTTAGTTATGATG 58.136 37.037 0.00 0.00 0.00 3.07
29 30 5.047847 TGAACCGTAGCTTAGTTATGATGC 58.952 41.667 0.00 0.00 0.00 3.91
30 31 4.665833 ACCGTAGCTTAGTTATGATGCA 57.334 40.909 0.00 0.00 0.00 3.96
31 32 5.018539 ACCGTAGCTTAGTTATGATGCAA 57.981 39.130 0.00 0.00 0.00 4.08
32 33 5.424757 ACCGTAGCTTAGTTATGATGCAAA 58.575 37.500 0.00 0.00 0.00 3.68
33 34 5.878116 ACCGTAGCTTAGTTATGATGCAAAA 59.122 36.000 0.00 0.00 0.00 2.44
34 35 6.373216 ACCGTAGCTTAGTTATGATGCAAAAA 59.627 34.615 0.00 0.00 0.00 1.94
35 36 7.067008 ACCGTAGCTTAGTTATGATGCAAAAAT 59.933 33.333 0.00 0.00 0.00 1.82
36 37 8.556194 CCGTAGCTTAGTTATGATGCAAAAATA 58.444 33.333 0.00 0.00 0.00 1.40
37 38 9.929722 CGTAGCTTAGTTATGATGCAAAAATAA 57.070 29.630 0.00 0.00 0.00 1.40
59 60 9.927668 AATAATAATAATCCAAAAATGCCGAGG 57.072 29.630 0.00 0.00 0.00 4.63
60 61 4.670896 AATAATCCAAAAATGCCGAGGG 57.329 40.909 0.00 0.00 0.00 4.30
87 88 3.162666 ACAATGACCTCGGTAGACAAGA 58.837 45.455 0.00 0.00 0.00 3.02
101 102 2.422832 AGACAAGATCTTACCGTCGGAC 59.577 50.000 20.51 0.00 31.62 4.79
103 104 1.475280 CAAGATCTTACCGTCGGACCA 59.525 52.381 20.51 0.00 0.00 4.02
113 114 0.744414 CGTCGGACCAATGCCTCATT 60.744 55.000 1.91 0.00 34.04 2.57
116 117 1.837439 TCGGACCAATGCCTCATTAGT 59.163 47.619 0.00 0.00 32.35 2.24
117 118 1.942657 CGGACCAATGCCTCATTAGTG 59.057 52.381 0.00 0.00 32.35 2.74
120 121 4.718961 GGACCAATGCCTCATTAGTGTAT 58.281 43.478 0.00 0.00 32.35 2.29
145 146 4.891627 CATTTGATGCATGTACCGGTTA 57.108 40.909 15.04 2.23 0.00 2.85
149 150 1.535462 GATGCATGTACCGGTTATGGC 59.465 52.381 24.39 18.89 0.00 4.40
155 156 1.752310 TACCGGTTATGGCGTCGGA 60.752 57.895 15.04 0.00 44.69 4.55
164 165 0.872388 ATGGCGTCGGAAGAACAAAC 59.128 50.000 0.00 0.00 45.01 2.93
170 171 3.057019 CGTCGGAAGAACAAACAGATGA 58.943 45.455 0.00 0.00 45.01 2.92
175 176 5.997746 TCGGAAGAACAAACAGATGAAGAAT 59.002 36.000 0.00 0.00 37.03 2.40
186 187 6.713762 ACAGATGAAGAATAGAGGAGACTG 57.286 41.667 0.00 0.00 44.43 3.51
191 192 4.400884 TGAAGAATAGAGGAGACTGAGTGC 59.599 45.833 0.00 0.00 44.43 4.40
192 193 3.295973 AGAATAGAGGAGACTGAGTGCC 58.704 50.000 0.00 0.00 44.43 5.01
257 258 2.029244 CGTCGTGGATCTTGAAAATCGG 59.971 50.000 0.00 0.00 0.00 4.18
266 267 5.517770 GGATCTTGAAAATCGGCAAAATCAG 59.482 40.000 0.00 0.00 0.00 2.90
269 270 5.185635 TCTTGAAAATCGGCAAAATCAGGAT 59.814 36.000 0.00 0.00 0.00 3.24
293 294 5.186215 TGGACACCTCAGTATCGATGTAAAA 59.814 40.000 8.54 0.00 0.00 1.52
294 295 5.519206 GGACACCTCAGTATCGATGTAAAAC 59.481 44.000 8.54 0.00 0.00 2.43
295 296 6.032956 ACACCTCAGTATCGATGTAAAACA 57.967 37.500 8.54 0.00 0.00 2.83
296 297 6.640518 ACACCTCAGTATCGATGTAAAACAT 58.359 36.000 8.54 0.00 42.43 2.71
297 298 6.535150 ACACCTCAGTATCGATGTAAAACATG 59.465 38.462 8.54 0.00 39.27 3.21
321 323 4.403432 GCCTTCCATTGAAAGAATGATCCA 59.597 41.667 0.00 0.00 0.00 3.41
323 325 5.419788 CCTTCCATTGAAAGAATGATCCACA 59.580 40.000 0.00 0.00 0.00 4.17
326 328 6.189133 TCCATTGAAAGAATGATCCACATCA 58.811 36.000 0.00 0.00 43.45 3.07
333 335 4.927049 AGAATGATCCACATCAACAAGGT 58.073 39.130 0.00 0.00 42.53 3.50
339 341 5.190726 TGATCCACATCAACAAGGTACCATA 59.809 40.000 15.94 0.00 35.99 2.74
342 344 4.580167 CCACATCAACAAGGTACCATATGG 59.420 45.833 20.68 20.68 42.17 2.74
352 354 6.101150 ACAAGGTACCATATGGCTTTGATCTA 59.899 38.462 22.18 0.92 39.32 1.98
371 373 0.107508 ATGATGACGGGCTGAAGGTG 60.108 55.000 0.00 0.00 0.00 4.00
381 383 4.284550 TGAAGGTGCCACTGCCCC 62.285 66.667 0.00 0.00 34.84 5.80
383 385 3.511610 AAGGTGCCACTGCCCCTT 61.512 61.111 0.00 0.00 45.49 3.95
416 418 5.327091 CAAGCATTGGTTGATTAGTTCTCG 58.673 41.667 21.09 0.00 43.94 4.04
431 433 2.281140 TCTCGTCGTGAAAACACACA 57.719 45.000 0.00 0.00 40.34 3.72
432 434 2.608268 TCTCGTCGTGAAAACACACAA 58.392 42.857 0.00 0.00 40.34 3.33
433 435 2.994578 TCTCGTCGTGAAAACACACAAA 59.005 40.909 0.00 0.00 40.34 2.83
434 436 3.088552 CTCGTCGTGAAAACACACAAAC 58.911 45.455 0.00 0.00 40.34 2.93
435 437 2.479275 TCGTCGTGAAAACACACAAACA 59.521 40.909 0.00 0.00 40.34 2.83
436 438 2.586378 CGTCGTGAAAACACACAAACAC 59.414 45.455 0.00 0.00 40.34 3.32
437 439 3.556513 GTCGTGAAAACACACAAACACA 58.443 40.909 0.00 0.00 40.34 3.72
441 443 3.917985 GTGAAAACACACAAACACACTCC 59.082 43.478 0.00 0.00 40.11 3.85
442 444 3.823873 TGAAAACACACAAACACACTCCT 59.176 39.130 0.00 0.00 0.00 3.69
443 445 4.279671 TGAAAACACACAAACACACTCCTT 59.720 37.500 0.00 0.00 0.00 3.36
444 446 4.864704 AAACACACAAACACACTCCTTT 57.135 36.364 0.00 0.00 0.00 3.11
445 447 4.434713 AACACACAAACACACTCCTTTC 57.565 40.909 0.00 0.00 0.00 2.62
447 449 3.823873 ACACACAAACACACTCCTTTCAA 59.176 39.130 0.00 0.00 0.00 2.69
448 450 4.462483 ACACACAAACACACTCCTTTCAAT 59.538 37.500 0.00 0.00 0.00 2.57
450 452 6.151985 ACACACAAACACACTCCTTTCAATAA 59.848 34.615 0.00 0.00 0.00 1.40
451 453 7.147915 ACACACAAACACACTCCTTTCAATAAT 60.148 33.333 0.00 0.00 0.00 1.28
452 454 8.349245 CACACAAACACACTCCTTTCAATAATA 58.651 33.333 0.00 0.00 0.00 0.98
453 455 9.077885 ACACAAACACACTCCTTTCAATAATAT 57.922 29.630 0.00 0.00 0.00 1.28
454 456 9.912634 CACAAACACACTCCTTTCAATAATATT 57.087 29.630 0.00 0.00 0.00 1.28
475 477 2.368311 TTTTTGCGGGGTACTCCTTT 57.632 45.000 10.83 0.00 35.33 3.11
477 479 0.766131 TTTGCGGGGTACTCCTTTCA 59.234 50.000 10.83 2.05 35.33 2.69
478 480 0.766131 TTGCGGGGTACTCCTTTCAA 59.234 50.000 10.83 8.42 35.33 2.69
545 560 2.326550 CAACCGGAACACGCACAC 59.673 61.111 9.46 0.00 42.52 3.82
546 561 2.125065 AACCGGAACACGCACACA 60.125 55.556 9.46 0.00 42.52 3.72
547 562 2.466140 AACCGGAACACGCACACAC 61.466 57.895 9.46 0.00 42.52 3.82
548 563 2.587753 CCGGAACACGCACACACT 60.588 61.111 0.00 0.00 42.52 3.55
549 564 2.594962 CCGGAACACGCACACACTC 61.595 63.158 0.00 0.00 42.52 3.51
700 730 2.594303 CAAAGCGGCCACAGTGGA 60.594 61.111 24.96 0.00 40.96 4.02
701 731 2.281761 AAAGCGGCCACAGTGGAG 60.282 61.111 24.96 16.63 40.96 3.86
1145 1200 2.066999 CCCCTTCCTTCCTCTCCCG 61.067 68.421 0.00 0.00 0.00 5.14
1161 1216 2.052104 CCGCAATCCCCTTTCACCC 61.052 63.158 0.00 0.00 0.00 4.61
1255 1310 2.682876 TTTCGCCGTTTGATCCGCC 61.683 57.895 0.00 0.00 0.00 6.13
1261 1316 4.223964 GTTTGATCCGCCGCGCTC 62.224 66.667 7.42 6.93 0.00 5.03
1295 1372 1.347221 CGGAAATTAGGTCGCGTGC 59.653 57.895 5.77 0.00 0.00 5.34
1321 1410 2.816958 CTGGCGCGCTCAGATTGT 60.817 61.111 32.57 0.00 34.36 2.71
1380 1469 2.882132 CCCCCATCGTTTTTCGCC 59.118 61.111 0.00 0.00 39.67 5.54
1589 1683 0.535335 AGTTCACGCGTATCCACCAT 59.465 50.000 13.44 0.00 0.00 3.55
1634 1728 2.213575 GCGCGACGTAGAGACTATTTTG 59.786 50.000 12.10 0.00 0.00 2.44
1656 1750 1.009078 GCATGTAACGATGCTGCTCA 58.991 50.000 0.00 0.00 44.57 4.26
1741 1835 1.896660 GCAAAGGAACCAGGCGACA 60.897 57.895 0.00 0.00 0.00 4.35
1824 1918 5.992729 TGAACGGAATAGAAAAAGGAAACG 58.007 37.500 0.00 0.00 0.00 3.60
1861 1956 1.288752 CGCCAAGGTGCCGAAATTT 59.711 52.632 0.00 0.00 0.00 1.82
1870 1968 3.439129 AGGTGCCGAAATTTAAGTAGTGC 59.561 43.478 0.00 0.00 0.00 4.40
1882 1980 7.807977 ATTTAAGTAGTGCATATGAACTGGG 57.192 36.000 24.48 0.00 34.09 4.45
2004 2109 5.235850 TGAATAGTGCTTACAGTTTGGGA 57.764 39.130 0.00 0.00 0.00 4.37
2085 2190 3.883489 GGTTTCCTGCGGATAAAGCTATT 59.117 43.478 12.53 0.00 35.28 1.73
2094 2199 8.116753 CCTGCGGATAAAGCTATTATAAAATCG 58.883 37.037 0.00 0.00 35.28 3.34
2123 2228 5.983540 TCCATTGGTTAAAAAGCTGTGTTT 58.016 33.333 1.86 0.00 0.00 2.83
2181 2286 8.649973 AACGATAAACAATCTAGACTCCATTC 57.350 34.615 0.00 0.00 31.87 2.67
2241 2346 1.873270 TAGACTGCGCACATGGTCGT 61.873 55.000 18.32 8.67 34.34 4.34
3309 3414 2.686915 GGATGGTGCTGAATGGAAGAAG 59.313 50.000 0.00 0.00 0.00 2.85
3721 3826 4.454678 TGCCAAATATCTGGTGCTTAGAG 58.545 43.478 0.00 0.00 38.86 2.43
3832 3937 4.036262 GTGATGTACAACCTTGTGAGCAAA 59.964 41.667 0.00 0.00 42.31 3.68
3985 4090 6.419413 TCGCTTTCATTTTGTTACACATTTCC 59.581 34.615 0.00 0.00 0.00 3.13
4276 4381 7.941795 AATATTTGTACTAAATCTCGGGTCG 57.058 36.000 6.56 0.00 0.00 4.79
4354 4459 2.883574 CTCCCGCGTATGTTCTGTTAA 58.116 47.619 4.92 0.00 0.00 2.01
4355 4460 3.454375 CTCCCGCGTATGTTCTGTTAAT 58.546 45.455 4.92 0.00 0.00 1.40
4356 4461 3.450578 TCCCGCGTATGTTCTGTTAATC 58.549 45.455 4.92 0.00 0.00 1.75
4357 4462 3.119065 TCCCGCGTATGTTCTGTTAATCA 60.119 43.478 4.92 0.00 0.00 2.57
4358 4463 3.245284 CCCGCGTATGTTCTGTTAATCAG 59.755 47.826 4.92 0.00 44.85 2.90
4359 4464 3.302480 CCGCGTATGTTCTGTTAATCAGC 60.302 47.826 4.92 0.00 43.32 4.26
4360 4465 3.305897 CGCGTATGTTCTGTTAATCAGCA 59.694 43.478 0.00 0.00 43.32 4.41
4361 4466 4.025730 CGCGTATGTTCTGTTAATCAGCAT 60.026 41.667 0.00 0.00 43.32 3.79
4362 4467 5.435557 GCGTATGTTCTGTTAATCAGCATC 58.564 41.667 0.00 0.00 43.32 3.91
4363 4468 5.006649 GCGTATGTTCTGTTAATCAGCATCA 59.993 40.000 0.00 2.02 43.32 3.07
4364 4469 6.414079 CGTATGTTCTGTTAATCAGCATCAC 58.586 40.000 0.00 0.00 43.32 3.06
4365 4470 6.256539 CGTATGTTCTGTTAATCAGCATCACT 59.743 38.462 0.00 0.00 43.32 3.41
4366 4471 7.201556 CGTATGTTCTGTTAATCAGCATCACTT 60.202 37.037 0.00 0.00 43.32 3.16
4367 4472 6.245115 TGTTCTGTTAATCAGCATCACTTG 57.755 37.500 0.00 0.00 43.32 3.16
4459 4564 2.025037 TCATGGTGAAGGGGGATTTGAG 60.025 50.000 0.00 0.00 0.00 3.02
4513 4618 4.377897 CAAGATGAGATGCTGACATGCTA 58.622 43.478 0.00 0.00 36.35 3.49
4546 4651 0.593128 AAGTTTCCGTGTGCTCATGC 59.407 50.000 2.36 0.00 40.20 4.06
4579 4684 0.887387 TAGCAACAACGCAGGTTCCC 60.887 55.000 0.00 0.00 32.98 3.97
4667 4774 3.335484 AGCCCTCCCCAAGTGTAAAATAA 59.665 43.478 0.00 0.00 0.00 1.40
4717 4824 1.134431 GGCATATTTTTGGGTGGCCAG 60.134 52.381 5.11 0.00 39.66 4.85
4730 4837 2.505819 GGTGGCCAGAAAGATAAGGAGA 59.494 50.000 5.11 0.00 0.00 3.71
4732 4839 4.384940 GTGGCCAGAAAGATAAGGAGATC 58.615 47.826 5.11 0.00 0.00 2.75
4738 4846 7.275920 GCCAGAAAGATAAGGAGATCAGTAAA 58.724 38.462 0.00 0.00 0.00 2.01
4757 4865 6.647895 CAGTAAACAAGATAAAGGTACCGTGT 59.352 38.462 6.18 0.00 0.00 4.49
4770 4878 7.651027 AAGGTACCGTGTTATTCATACTAGT 57.349 36.000 6.18 0.00 0.00 2.57
4775 4883 9.962759 GTACCGTGTTATTCATACTAGTTTTTG 57.037 33.333 0.00 0.00 0.00 2.44
4778 4886 8.714179 CCGTGTTATTCATACTAGTTTTTGTCA 58.286 33.333 0.00 0.00 0.00 3.58
4828 4937 6.020678 GTCAATAAAATTTGCACGCCTCATAC 60.021 38.462 0.00 0.00 0.00 2.39
4831 4940 4.882671 AAATTTGCACGCCTCATACTAG 57.117 40.909 0.00 0.00 0.00 2.57
4853 4962 9.398921 ACTAGGAAAGTTATATCATGGAGGAAT 57.601 33.333 0.00 0.00 33.35 3.01
4887 4996 1.444933 AGAAGGAACATCCACACCCA 58.555 50.000 0.00 0.00 39.61 4.51
4888 4997 1.352352 AGAAGGAACATCCACACCCAG 59.648 52.381 0.00 0.00 39.61 4.45
4893 5002 2.593026 GAACATCCACACCCAGGAAAA 58.407 47.619 0.00 0.00 38.93 2.29
4905 5014 5.245977 ACACCCAGGAAAATATTTCACCTTG 59.754 40.000 18.33 16.71 0.00 3.61
4921 5030 0.884704 CTTGGACACGACACCCTTGG 60.885 60.000 0.00 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.070179 TCATAACTAAGCTACGGTTCATATGTA 57.930 33.333 1.90 0.00 0.00 2.29
1 2 7.948357 TCATAACTAAGCTACGGTTCATATGT 58.052 34.615 1.90 0.00 0.00 2.29
2 3 8.864024 CATCATAACTAAGCTACGGTTCATATG 58.136 37.037 0.00 0.00 0.00 1.78
3 4 7.545965 GCATCATAACTAAGCTACGGTTCATAT 59.454 37.037 0.00 0.00 0.00 1.78
4 5 6.866770 GCATCATAACTAAGCTACGGTTCATA 59.133 38.462 0.00 0.00 0.00 2.15
6 7 5.047847 GCATCATAACTAAGCTACGGTTCA 58.952 41.667 0.00 0.00 0.00 3.18
7 8 5.047847 TGCATCATAACTAAGCTACGGTTC 58.952 41.667 0.00 0.00 0.00 3.62
8 9 5.018539 TGCATCATAACTAAGCTACGGTT 57.981 39.130 0.00 0.00 0.00 4.44
9 10 4.665833 TGCATCATAACTAAGCTACGGT 57.334 40.909 0.00 0.00 0.00 4.83
10 11 5.984233 TTTGCATCATAACTAAGCTACGG 57.016 39.130 0.00 0.00 0.00 4.02
11 12 9.929722 TTATTTTTGCATCATAACTAAGCTACG 57.070 29.630 0.00 0.00 0.00 3.51
33 34 9.927668 CCTCGGCATTTTTGGATTATTATTATT 57.072 29.630 0.00 0.00 0.00 1.40
34 35 8.531146 CCCTCGGCATTTTTGGATTATTATTAT 58.469 33.333 0.00 0.00 0.00 1.28
35 36 7.726291 TCCCTCGGCATTTTTGGATTATTATTA 59.274 33.333 0.00 0.00 0.00 0.98
36 37 6.553100 TCCCTCGGCATTTTTGGATTATTATT 59.447 34.615 0.00 0.00 0.00 1.40
37 38 6.015434 GTCCCTCGGCATTTTTGGATTATTAT 60.015 38.462 0.00 0.00 0.00 1.28
38 39 5.300792 GTCCCTCGGCATTTTTGGATTATTA 59.699 40.000 0.00 0.00 0.00 0.98
39 40 4.099419 GTCCCTCGGCATTTTTGGATTATT 59.901 41.667 0.00 0.00 0.00 1.40
40 41 3.636764 GTCCCTCGGCATTTTTGGATTAT 59.363 43.478 0.00 0.00 0.00 1.28
41 42 3.020984 GTCCCTCGGCATTTTTGGATTA 58.979 45.455 0.00 0.00 0.00 1.75
42 43 1.824852 GTCCCTCGGCATTTTTGGATT 59.175 47.619 0.00 0.00 0.00 3.01
43 44 1.272425 TGTCCCTCGGCATTTTTGGAT 60.272 47.619 0.00 0.00 0.00 3.41
44 45 0.111446 TGTCCCTCGGCATTTTTGGA 59.889 50.000 0.00 0.00 0.00 3.53
45 46 0.243636 GTGTCCCTCGGCATTTTTGG 59.756 55.000 0.00 0.00 0.00 3.28
46 47 0.109781 CGTGTCCCTCGGCATTTTTG 60.110 55.000 0.00 0.00 0.00 2.44
47 48 0.250553 TCGTGTCCCTCGGCATTTTT 60.251 50.000 0.00 0.00 0.00 1.94
48 49 0.953960 GTCGTGTCCCTCGGCATTTT 60.954 55.000 0.00 0.00 32.96 1.82
49 50 1.375523 GTCGTGTCCCTCGGCATTT 60.376 57.895 0.00 0.00 32.96 2.32
50 51 2.107041 TTGTCGTGTCCCTCGGCATT 62.107 55.000 0.00 0.00 42.27 3.56
51 52 1.899437 ATTGTCGTGTCCCTCGGCAT 61.899 55.000 0.00 0.00 42.27 4.40
52 53 2.579657 ATTGTCGTGTCCCTCGGCA 61.580 57.895 0.00 0.00 41.07 5.69
53 54 2.100631 CATTGTCGTGTCCCTCGGC 61.101 63.158 0.00 0.00 0.00 5.54
54 55 0.736325 GTCATTGTCGTGTCCCTCGG 60.736 60.000 0.00 0.00 0.00 4.63
55 56 0.736325 GGTCATTGTCGTGTCCCTCG 60.736 60.000 0.00 0.00 0.00 4.63
56 57 0.608640 AGGTCATTGTCGTGTCCCTC 59.391 55.000 0.00 0.00 0.00 4.30
57 58 0.608640 GAGGTCATTGTCGTGTCCCT 59.391 55.000 0.00 0.00 0.00 4.20
58 59 0.736325 CGAGGTCATTGTCGTGTCCC 60.736 60.000 0.00 0.00 0.00 4.46
59 60 0.736325 CCGAGGTCATTGTCGTGTCC 60.736 60.000 0.00 0.00 34.27 4.02
60 61 0.038526 ACCGAGGTCATTGTCGTGTC 60.039 55.000 0.00 0.00 34.27 3.67
87 88 1.472728 GCATTGGTCCGACGGTAAGAT 60.473 52.381 14.79 1.93 0.00 2.40
101 102 3.748048 CCGATACACTAATGAGGCATTGG 59.252 47.826 3.07 2.79 38.11 3.16
103 104 3.181455 TGCCGATACACTAATGAGGCATT 60.181 43.478 1.80 0.00 46.73 3.56
145 146 0.872388 GTTTGTTCTTCCGACGCCAT 59.128 50.000 0.00 0.00 0.00 4.40
149 150 3.057019 TCATCTGTTTGTTCTTCCGACG 58.943 45.455 0.00 0.00 0.00 5.12
155 156 8.378565 TCCTCTATTCTTCATCTGTTTGTTCTT 58.621 33.333 0.00 0.00 0.00 2.52
164 165 6.547141 ACTCAGTCTCCTCTATTCTTCATCTG 59.453 42.308 0.00 0.00 0.00 2.90
170 171 3.704061 GGCACTCAGTCTCCTCTATTCTT 59.296 47.826 0.00 0.00 0.00 2.52
175 176 1.636003 TCTGGCACTCAGTCTCCTCTA 59.364 52.381 0.00 0.00 43.76 2.43
185 186 2.284921 CCCCTCCTCTGGCACTCA 60.285 66.667 0.00 0.00 0.00 3.41
186 187 3.086600 CCCCCTCCTCTGGCACTC 61.087 72.222 0.00 0.00 0.00 3.51
205 206 3.070748 GTCTTTCTCTTTCCACCTCTGC 58.929 50.000 0.00 0.00 0.00 4.26
208 209 5.049129 CACATTGTCTTTCTCTTTCCACCTC 60.049 44.000 0.00 0.00 0.00 3.85
209 210 4.823989 CACATTGTCTTTCTCTTTCCACCT 59.176 41.667 0.00 0.00 0.00 4.00
213 214 3.569701 TGCCACATTGTCTTTCTCTTTCC 59.430 43.478 0.00 0.00 0.00 3.13
214 215 4.540824 GTGCCACATTGTCTTTCTCTTTC 58.459 43.478 0.00 0.00 0.00 2.62
215 216 3.003689 CGTGCCACATTGTCTTTCTCTTT 59.996 43.478 0.00 0.00 0.00 2.52
257 258 2.424956 GAGGTGTCCATCCTGATTTTGC 59.575 50.000 0.00 0.00 35.20 3.68
266 267 2.307768 TCGATACTGAGGTGTCCATCC 58.692 52.381 0.00 0.00 31.18 3.51
269 270 2.735151 ACATCGATACTGAGGTGTCCA 58.265 47.619 0.00 0.00 30.63 4.02
297 298 4.202192 GGATCATTCTTTCAATGGAAGGCC 60.202 45.833 0.81 0.00 33.82 5.19
316 318 3.950397 TGGTACCTTGTTGATGTGGATC 58.050 45.455 14.36 0.00 0.00 3.36
321 323 4.079787 AGCCATATGGTACCTTGTTGATGT 60.080 41.667 22.79 0.00 37.57 3.06
323 325 4.796110 AGCCATATGGTACCTTGTTGAT 57.204 40.909 22.79 0.00 37.57 2.57
326 328 4.929479 TCAAAGCCATATGGTACCTTGTT 58.071 39.130 22.79 1.88 37.57 2.83
333 335 8.043113 GTCATCATAGATCAAAGCCATATGGTA 58.957 37.037 22.79 5.34 37.57 3.25
339 341 4.321718 CCGTCATCATAGATCAAAGCCAT 58.678 43.478 0.00 0.00 0.00 4.40
342 344 2.481952 GCCCGTCATCATAGATCAAAGC 59.518 50.000 0.00 0.00 0.00 3.51
352 354 0.107508 CACCTTCAGCCCGTCATCAT 60.108 55.000 0.00 0.00 0.00 2.45
371 373 1.378646 GGTTAGAAGGGGCAGTGGC 60.379 63.158 8.47 8.47 40.13 5.01
406 408 5.571778 GTGTTTTCACGACGAGAACTAAT 57.428 39.130 7.24 0.00 39.05 1.73
457 459 1.143277 TGAAAGGAGTACCCCGCAAAA 59.857 47.619 0.00 0.00 36.73 2.44
458 460 0.766131 TGAAAGGAGTACCCCGCAAA 59.234 50.000 0.00 0.00 36.73 3.68
459 461 0.766131 TTGAAAGGAGTACCCCGCAA 59.234 50.000 0.00 0.00 36.73 4.85
460 462 0.323629 CTTGAAAGGAGTACCCCGCA 59.676 55.000 0.00 0.00 36.73 5.69
462 464 3.629142 ATTCTTGAAAGGAGTACCCCG 57.371 47.619 0.00 0.00 36.73 5.73
463 465 4.882427 GCTAATTCTTGAAAGGAGTACCCC 59.118 45.833 0.00 0.00 36.73 4.95
465 467 5.746284 AGGCTAATTCTTGAAAGGAGTACC 58.254 41.667 0.00 0.00 0.00 3.34
466 468 6.476053 CGTAGGCTAATTCTTGAAAGGAGTAC 59.524 42.308 0.00 0.00 0.00 2.73
467 469 6.154021 ACGTAGGCTAATTCTTGAAAGGAGTA 59.846 38.462 0.00 0.00 0.00 2.59
469 471 5.292101 CACGTAGGCTAATTCTTGAAAGGAG 59.708 44.000 0.00 0.00 0.00 3.69
472 474 4.391830 TGCACGTAGGCTAATTCTTGAAAG 59.608 41.667 0.00 0.00 34.04 2.62
473 475 4.320023 TGCACGTAGGCTAATTCTTGAAA 58.680 39.130 0.00 0.00 34.04 2.69
474 476 3.932822 TGCACGTAGGCTAATTCTTGAA 58.067 40.909 0.00 0.00 34.04 2.69
475 477 3.603158 TGCACGTAGGCTAATTCTTGA 57.397 42.857 0.00 0.00 34.04 3.02
477 479 4.049186 CGTATGCACGTAGGCTAATTCTT 58.951 43.478 0.00 0.00 43.31 2.52
478 480 3.639538 CGTATGCACGTAGGCTAATTCT 58.360 45.455 0.00 0.00 43.31 2.40
502 509 3.745975 TGAATGAAACGTAGCAAGGACAG 59.254 43.478 0.00 0.00 0.00 3.51
545 560 6.238374 CGGGTTAAGTTAGCATAATTGGAGTG 60.238 42.308 0.00 0.00 0.00 3.51
546 561 5.820947 CGGGTTAAGTTAGCATAATTGGAGT 59.179 40.000 0.00 0.00 0.00 3.85
547 562 5.277828 GCGGGTTAAGTTAGCATAATTGGAG 60.278 44.000 0.00 0.00 0.00 3.86
548 563 4.577283 GCGGGTTAAGTTAGCATAATTGGA 59.423 41.667 0.00 0.00 0.00 3.53
549 564 4.336993 TGCGGGTTAAGTTAGCATAATTGG 59.663 41.667 0.00 0.00 32.43 3.16
873 919 2.563427 GGCACGCTGCTTTTCTCC 59.437 61.111 9.31 0.00 44.28 3.71
1111 1166 0.907704 GGGGGTTTGGGGATTGGTTC 60.908 60.000 0.00 0.00 0.00 3.62
1145 1200 1.685765 GGGGGTGAAAGGGGATTGC 60.686 63.158 0.00 0.00 0.00 3.56
1161 1216 2.764547 GACGGGGAGAGAAGGGGG 60.765 72.222 0.00 0.00 0.00 5.40
1469 1559 1.488393 GAGGAGGGAACAAGCTAGCAT 59.512 52.381 18.83 0.65 0.00 3.79
1616 1710 4.036352 GCTCCAAAATAGTCTCTACGTCG 58.964 47.826 0.00 0.00 0.00 5.12
1617 1711 4.995124 TGCTCCAAAATAGTCTCTACGTC 58.005 43.478 0.00 0.00 0.00 4.34
1699 1793 2.388232 CGGAGCAGTACAAACGCCC 61.388 63.158 0.00 0.00 0.00 6.13
1700 1794 1.666872 ACGGAGCAGTACAAACGCC 60.667 57.895 0.00 0.00 0.00 5.68
1701 1795 1.219522 ACACGGAGCAGTACAAACGC 61.220 55.000 0.00 0.00 0.00 4.84
1702 1796 1.983605 CTACACGGAGCAGTACAAACG 59.016 52.381 0.00 0.00 0.00 3.60
1703 1797 2.334838 CCTACACGGAGCAGTACAAAC 58.665 52.381 0.00 0.00 33.16 2.93
1741 1835 5.949354 TCAGAATAATCACCATTTCCCGTTT 59.051 36.000 0.00 0.00 0.00 3.60
1824 1918 2.026155 GCGTTAGCGTTCGAGTAAACTC 59.974 50.000 0.00 0.00 40.81 3.01
1836 1931 3.047877 GCACCTTGGCGTTAGCGT 61.048 61.111 0.00 0.00 46.35 5.07
1861 1956 4.966168 TCCCCAGTTCATATGCACTACTTA 59.034 41.667 7.72 0.00 0.00 2.24
1870 1968 5.299279 GGTATGTTGTTCCCCAGTTCATATG 59.701 44.000 0.00 0.00 0.00 1.78
1910 2010 5.122711 TGCATCATCATGTTGTTCACTAGTG 59.877 40.000 17.17 17.17 31.86 2.74
1914 2014 4.676986 GCATGCATCATCATGTTGTTCACT 60.677 41.667 14.21 0.00 44.20 3.41
2004 2109 9.771534 CTTAACTAAGCTAGGCAAGAGATAATT 57.228 33.333 0.00 0.00 0.00 1.40
2051 2156 3.179048 GCAGGAAACCAAACGCATATTC 58.821 45.455 0.00 0.00 0.00 1.75
2085 2190 5.909477 ACCAATGGAGTCGTCGATTTTATA 58.091 37.500 6.16 0.00 29.25 0.98
2094 2199 4.215613 AGCTTTTTAACCAATGGAGTCGTC 59.784 41.667 6.16 0.00 0.00 4.20
2099 2204 5.200368 ACACAGCTTTTTAACCAATGGAG 57.800 39.130 6.16 0.00 0.00 3.86
2123 2228 2.582728 CTTGGTGAGCACAAGCAAAA 57.417 45.000 2.75 0.00 45.49 2.44
2181 2286 4.788925 TCCAAACCCATAGGATTACCAG 57.211 45.455 0.00 0.00 38.94 4.00
2241 2346 4.473520 GCTCTAGGGCAAGCCGCA 62.474 66.667 10.54 0.00 45.17 5.69
3309 3414 7.390718 ACATCACTTTGTAACCCTCATTAGAAC 59.609 37.037 0.00 0.00 0.00 3.01
3721 3826 3.119245 TCCTCATGTGCTTACCGTAGAAC 60.119 47.826 0.00 0.00 0.00 3.01
3832 3937 0.689623 CAGGAACCTTCTGCCACTCT 59.310 55.000 0.00 0.00 0.00 3.24
4367 4472 6.370994 AGTGATGCTGATATAATGCTACAAGC 59.629 38.462 0.00 0.00 42.82 4.01
4368 4473 7.902387 AGTGATGCTGATATAATGCTACAAG 57.098 36.000 0.00 0.00 0.00 3.16
4369 4474 8.091385 CAAGTGATGCTGATATAATGCTACAA 57.909 34.615 0.00 0.00 0.00 2.41
4370 4475 7.662604 CAAGTGATGCTGATATAATGCTACA 57.337 36.000 0.00 0.00 0.00 2.74
4459 4564 5.349543 GGTCATGGCAAATCTCATCAAAAAC 59.650 40.000 0.00 0.00 0.00 2.43
4513 4618 6.317893 ACACGGAAACTTTTCAAGTATTCAGT 59.682 34.615 4.18 10.06 41.91 3.41
4553 4658 2.159653 CCTGCGTTGTTGCTAGCTTTAG 60.160 50.000 17.23 3.87 35.36 1.85
4599 4704 0.250295 CCGGCAGTTTTCCTGTCTCA 60.250 55.000 0.00 0.00 43.93 3.27
4644 4751 0.696501 TTTACACTTGGGGAGGGCTC 59.303 55.000 0.00 0.00 29.07 4.70
4667 4774 7.797121 ATTTCAAATGGAGGGAGTGTATTTT 57.203 32.000 0.00 0.00 0.00 1.82
4717 4824 9.877178 TCTTGTTTACTGATCTCCTTATCTTTC 57.123 33.333 0.00 0.00 0.00 2.62
4730 4837 7.548075 CACGGTACCTTTATCTTGTTTACTGAT 59.452 37.037 10.90 0.00 0.00 2.90
4732 4839 6.647895 ACACGGTACCTTTATCTTGTTTACTG 59.352 38.462 10.90 0.00 0.00 2.74
4738 4846 7.388437 TGAATAACACGGTACCTTTATCTTGT 58.612 34.615 10.90 0.00 0.00 3.16
4768 4876 7.986085 ATAGCACTATCTTGTGACAAAAACT 57.014 32.000 0.00 0.00 40.12 2.66
4803 4911 4.233789 TGAGGCGTGCAAATTTTATTGAC 58.766 39.130 0.00 0.00 31.84 3.18
4813 4921 1.828595 TCCTAGTATGAGGCGTGCAAA 59.171 47.619 0.00 0.00 36.45 3.68
4831 4940 9.454859 CCTAATTCCTCCATGATATAACTTTCC 57.545 37.037 0.00 0.00 0.00 3.13
4887 4996 5.183140 CGTGTCCAAGGTGAAATATTTTCCT 59.817 40.000 15.57 15.57 0.00 3.36
4888 4997 5.182380 TCGTGTCCAAGGTGAAATATTTTCC 59.818 40.000 1.43 8.41 0.00 3.13
4893 5002 4.000988 GTGTCGTGTCCAAGGTGAAATAT 58.999 43.478 0.00 0.00 0.00 1.28
4905 5014 0.393820 TTACCAAGGGTGTCGTGTCC 59.606 55.000 0.00 0.00 36.19 4.02


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

AutoCloner maintained by Alex Coulton.