Multiple sequence alignment - TraesCS5D01G240300

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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 TraesCS5D01G240300 chr5D 100.000 4248 0 0 1 4248 348491678 348495925 0.000000e+00 7845.0
1 TraesCS5D01G240300 chr5B 92.180 3376 126 50 399 3694 408972095 408975412 0.000000e+00 4645.0
2 TraesCS5D01G240300 chr5B 90.341 528 15 15 3697 4216 408975674 408976173 0.000000e+00 660.0
3 TraesCS5D01G240300 chr5B 90.678 354 23 6 1 352 408971734 408972079 2.990000e-126 462.0
4 TraesCS5D01G240300 chr5A 89.465 3626 155 94 150 3626 448627542 448631089 0.000000e+00 4370.0
5 TraesCS5D01G240300 chr5A 84.467 676 48 24 3620 4248 448631271 448631936 7.810000e-172 614.0
6 TraesCS5D01G240300 chr5A 90.598 117 3 1 51 159 448627276 448627392 9.520000e-32 148.0
7 TraesCS5D01G240300 chr2A 100.000 28 0 0 3386 3413 517673976 517673949 8.000000e-03 52.8


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 TraesCS5D01G240300 chr5D 348491678 348495925 4247 False 7845.000000 7845 100.000000 1 4248 1 chr5D.!!$F1 4247
1 TraesCS5D01G240300 chr5B 408971734 408976173 4439 False 1922.333333 4645 91.066333 1 4216 3 chr5B.!!$F1 4215
2 TraesCS5D01G240300 chr5A 448627276 448631936 4660 False 1710.666667 4370 88.176667 51 4248 3 chr5A.!!$F1 4197

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
991 1204 0.031314 CTCACACACACACTCGCTCT 59.969 55.0 0.00 0.00 0.00 4.09 F
1048 1282 0.037790 GCTCATCATACCGAGGGAGC 60.038 60.0 0.00 0.00 43.54 4.70 F
2296 2606 0.391528 ATTTTCAAGGCGCATTGGGC 60.392 50.0 31.66 16.71 40.84 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2564 2880 0.601558 TTTCAACGACGAGGAGGAGG 59.398 55.000 0.00 0.0 0.00 4.30 R
2703 3019 1.673337 GATGCTGCTGCCAGACACA 60.673 57.895 13.47 0.0 41.77 3.72 R
3775 4607 0.037160 TTTACCTTGCTCCCGTTCCC 59.963 55.000 0.00 0.0 0.00 3.97 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
41 42 1.502190 GCTCCAGTAGCCAAAACGC 59.498 57.895 0.00 0.00 46.25 4.84
42 43 0.955919 GCTCCAGTAGCCAAAACGCT 60.956 55.000 0.00 0.00 46.25 5.07
101 102 0.035725 TGTGCATCTCCAAGCAGAGG 60.036 55.000 0.00 0.00 42.14 3.69
167 335 1.407258 GAGATCACCGAACTAGCAGCT 59.593 52.381 0.00 0.00 0.00 4.24
176 344 4.207281 CTAGCAGCTACCCGCGCA 62.207 66.667 8.75 0.00 45.59 6.09
202 371 0.973632 ACCTCCATGTAACAGACGCA 59.026 50.000 0.00 0.00 0.00 5.24
246 420 9.398170 CTTACCATTCACAATAACAAACTCAAG 57.602 33.333 0.00 0.00 0.00 3.02
247 421 7.581213 ACCATTCACAATAACAAACTCAAGA 57.419 32.000 0.00 0.00 0.00 3.02
248 422 7.425606 ACCATTCACAATAACAAACTCAAGAC 58.574 34.615 0.00 0.00 0.00 3.01
249 423 7.068103 ACCATTCACAATAACAAACTCAAGACA 59.932 33.333 0.00 0.00 0.00 3.41
250 424 8.084073 CCATTCACAATAACAAACTCAAGACAT 58.916 33.333 0.00 0.00 0.00 3.06
317 496 1.135199 GCGACACGTGATAAGGGAAGA 60.135 52.381 25.01 0.00 0.00 2.87
326 505 3.933332 GTGATAAGGGAAGACGTCAAAGG 59.067 47.826 19.50 0.00 0.00 3.11
352 531 2.426752 CGACGGCCAAACAAAGCG 60.427 61.111 2.24 0.00 0.00 4.68
353 532 2.887889 CGACGGCCAAACAAAGCGA 61.888 57.895 2.24 0.00 0.00 4.93
354 533 1.082104 GACGGCCAAACAAAGCGAG 60.082 57.895 2.24 0.00 0.00 5.03
355 534 2.429069 CGGCCAAACAAAGCGAGC 60.429 61.111 2.24 0.00 0.00 5.03
356 535 2.727544 GGCCAAACAAAGCGAGCA 59.272 55.556 0.00 0.00 0.00 4.26
357 536 1.372128 GGCCAAACAAAGCGAGCAG 60.372 57.895 0.00 0.00 0.00 4.24
380 559 2.355481 ACAAAGCCGTCCGTCGTC 60.355 61.111 0.00 0.00 37.94 4.20
381 560 3.110178 CAAAGCCGTCCGTCGTCC 61.110 66.667 0.00 0.00 37.94 4.79
382 561 4.712425 AAAGCCGTCCGTCGTCCG 62.712 66.667 0.00 0.00 37.94 4.79
388 567 2.397252 GTCCGTCGTCCGTCGTAG 59.603 66.667 5.71 0.00 40.80 3.51
389 568 3.490759 TCCGTCGTCCGTCGTAGC 61.491 66.667 5.71 0.00 40.80 3.58
390 569 3.792047 CCGTCGTCCGTCGTAGCA 61.792 66.667 5.71 0.00 40.80 3.49
391 570 2.276493 CGTCGTCCGTCGTAGCAG 60.276 66.667 0.00 0.00 40.80 4.24
392 571 2.576317 GTCGTCCGTCGTAGCAGC 60.576 66.667 0.00 0.00 40.80 5.25
393 572 3.051479 TCGTCCGTCGTAGCAGCA 61.051 61.111 0.00 0.00 40.80 4.41
394 573 2.874780 CGTCCGTCGTAGCAGCAC 60.875 66.667 0.00 0.00 34.52 4.40
395 574 2.567049 GTCCGTCGTAGCAGCACT 59.433 61.111 0.00 0.00 0.00 4.40
396 575 1.801913 GTCCGTCGTAGCAGCACTG 60.802 63.158 0.00 0.00 0.00 3.66
397 576 2.507102 CCGTCGTAGCAGCACTGG 60.507 66.667 0.00 0.00 0.00 4.00
502 681 2.159057 AGGCAAAACAAAAGCAGGTGAG 60.159 45.455 0.00 0.00 0.00 3.51
572 752 1.112113 CGGATCGAGGAAGAAGGGAA 58.888 55.000 0.00 0.00 0.00 3.97
574 754 2.112190 GGATCGAGGAAGAAGGGAAGT 58.888 52.381 0.00 0.00 0.00 3.01
583 763 3.429135 GGAAGAAGGGAAGTGTAGCGTAG 60.429 52.174 0.00 0.00 0.00 3.51
673 857 1.346068 GCAAGCCGGGAGATAGAGATT 59.654 52.381 2.18 0.00 0.00 2.40
677 861 2.109128 AGCCGGGAGATAGAGATTGAGA 59.891 50.000 2.18 0.00 0.00 3.27
681 865 4.263287 CCGGGAGATAGAGATTGAGAGAGA 60.263 50.000 0.00 0.00 0.00 3.10
839 1047 2.032071 AGCGGCCAACTGGTGTAC 59.968 61.111 2.24 0.00 37.57 2.90
840 1048 3.053896 GCGGCCAACTGGTGTACC 61.054 66.667 2.24 0.00 37.57 3.34
842 1050 1.375523 CGGCCAACTGGTGTACCTC 60.376 63.158 2.24 0.00 37.57 3.85
843 1051 1.827399 CGGCCAACTGGTGTACCTCT 61.827 60.000 2.24 0.00 37.57 3.69
845 1053 1.207329 GGCCAACTGGTGTACCTCTAG 59.793 57.143 0.00 0.00 37.57 2.43
856 1064 2.496817 CCTCTAGAGGTGGTGCGC 59.503 66.667 28.12 0.00 43.61 6.09
974 1187 4.803426 CACTCTGACCGCCCGCTC 62.803 72.222 0.00 0.00 0.00 5.03
991 1204 0.031314 CTCACACACACACTCGCTCT 59.969 55.000 0.00 0.00 0.00 4.09
1026 1260 1.887242 GCCACACAAGCGAGTGACA 60.887 57.895 16.74 0.00 42.05 3.58
1027 1261 1.436195 GCCACACAAGCGAGTGACAA 61.436 55.000 16.74 0.00 42.05 3.18
1048 1282 0.037790 GCTCATCATACCGAGGGAGC 60.038 60.000 0.00 0.00 43.54 4.70
1096 1330 2.105466 CGCAGGAAAGAGAGCTGCC 61.105 63.158 0.00 0.00 37.73 4.85
1343 1615 1.227999 TGTTTTCCTCTTCGGCAGCG 61.228 55.000 0.00 0.00 0.00 5.18
1508 1780 2.490217 CGACCTCCTGCTGGTACG 59.510 66.667 9.73 7.61 38.03 3.67
1754 2048 3.073062 TCTTTCCTCTGTAAGCAAAGCCT 59.927 43.478 0.00 0.00 29.92 4.58
1763 2057 1.136329 AAGCAAAGCCTCTCCCTCCA 61.136 55.000 0.00 0.00 0.00 3.86
1789 2091 2.034878 CCCTCAGACTCCATTGATCGA 58.965 52.381 0.00 0.00 0.00 3.59
1793 2095 4.111198 CTCAGACTCCATTGATCGACTTG 58.889 47.826 0.00 0.00 0.00 3.16
1990 2293 2.419198 CCGAGGATTAGCAGCGCT 59.581 61.111 2.64 2.64 43.41 5.92
2048 2351 5.455849 CGCATGGTCGCTCAGTAATATATAC 59.544 44.000 0.00 0.00 0.00 1.47
2049 2352 6.330278 GCATGGTCGCTCAGTAATATATACA 58.670 40.000 0.00 0.00 0.00 2.29
2093 2396 0.538118 GGTACGGTAGGATTGCACCA 59.462 55.000 0.00 0.00 34.25 4.17
2094 2397 1.140252 GGTACGGTAGGATTGCACCAT 59.860 52.381 0.00 0.00 34.25 3.55
2095 2398 2.366266 GGTACGGTAGGATTGCACCATA 59.634 50.000 0.00 0.00 34.25 2.74
2296 2606 0.391528 ATTTTCAAGGCGCATTGGGC 60.392 50.000 31.66 16.71 40.84 5.36
2320 2630 8.362639 GGCATGTGAATTGGATGATTATTAACT 58.637 33.333 0.00 0.00 0.00 2.24
2613 2929 1.309499 CGGAAGGTGCTCTCTCGACT 61.309 60.000 0.00 0.00 0.00 4.18
2703 3019 4.067192 AGTAATTAACTTTGACCGGCGTT 58.933 39.130 6.01 0.00 33.35 4.84
2725 3042 3.200593 CTGGCAGCAGCATCGGAC 61.201 66.667 0.00 0.00 44.61 4.79
3052 3385 0.040058 TCCATCATTGCAAGCCCTGT 59.960 50.000 4.94 0.00 0.00 4.00
3054 3387 0.458669 CATCATTGCAAGCCCTGTCC 59.541 55.000 4.94 0.00 0.00 4.02
3155 3499 2.725008 GCTCGATCGCTAGCCAGT 59.275 61.111 15.86 0.00 32.40 4.00
3156 3500 1.659954 GCTCGATCGCTAGCCAGTG 60.660 63.158 15.86 0.00 32.40 3.66
3179 3529 1.139947 GTAGCAGTGCCTCCGAGTC 59.860 63.158 12.58 0.00 0.00 3.36
3220 3577 5.791336 ATGCTCGATTACATAAGGAGTGA 57.209 39.130 0.00 0.00 0.00 3.41
3239 3596 7.939039 AGGAGTGAGTGAGTGAATGAATAAAAA 59.061 33.333 0.00 0.00 0.00 1.94
3260 3617 4.787135 ATCCTTCCATTTCTCTTCTCCC 57.213 45.455 0.00 0.00 0.00 4.30
3357 3726 3.373565 GGAACAAAGCCCGGCTGG 61.374 66.667 14.19 11.27 39.62 4.85
3656 4230 4.444720 GTCCGGCAAAGAGAATATACGAAG 59.555 45.833 0.00 0.00 0.00 3.79
3695 4269 0.108851 GCAGGGCATGGTAAAAACCG 60.109 55.000 0.00 0.00 0.00 4.44
3699 4273 0.318762 GGCATGGTAAAAACCGCCAA 59.681 50.000 8.16 0.00 36.62 4.52
3700 4274 1.270358 GGCATGGTAAAAACCGCCAAA 60.270 47.619 8.16 0.00 36.62 3.28
3701 4275 2.065512 GCATGGTAAAAACCGCCAAAG 58.934 47.619 0.00 0.00 0.00 2.77
3703 4277 3.305471 GCATGGTAAAAACCGCCAAAGTA 60.305 43.478 0.00 0.00 0.00 2.24
3770 4602 1.157585 GAGGAAACGAAAGCAGGGAC 58.842 55.000 0.00 0.00 0.00 4.46
3771 4603 0.602905 AGGAAACGAAAGCAGGGACG 60.603 55.000 0.00 0.00 0.00 4.79
3772 4604 1.574702 GGAAACGAAAGCAGGGACGG 61.575 60.000 0.00 0.00 0.00 4.79
3773 4605 0.601841 GAAACGAAAGCAGGGACGGA 60.602 55.000 0.00 0.00 0.00 4.69
3774 4606 0.883370 AAACGAAAGCAGGGACGGAC 60.883 55.000 0.00 0.00 0.00 4.79
3775 4607 2.809601 CGAAAGCAGGGACGGACG 60.810 66.667 0.00 0.00 0.00 4.79
3846 4681 0.595567 CGCAAAAGCAGAGCAAAGCA 60.596 50.000 0.00 0.00 0.00 3.91
3851 4686 0.898789 AAGCAGAGCAAAGCATGGCT 60.899 50.000 0.00 0.00 44.48 4.75
3991 4836 1.290203 GCCGCGATTCAAATGAGAGA 58.710 50.000 8.23 0.00 0.00 3.10
3996 4841 3.178618 CGCGATTCAAATGAGAGAGTACG 59.821 47.826 0.00 0.00 0.00 3.67
3997 4842 4.106197 GCGATTCAAATGAGAGAGTACGT 58.894 43.478 0.00 0.00 0.00 3.57
3998 4843 5.271625 GCGATTCAAATGAGAGAGTACGTA 58.728 41.667 0.00 0.00 0.00 3.57
4000 4845 6.716438 CGATTCAAATGAGAGAGTACGTAGA 58.284 40.000 0.00 0.00 0.00 2.59
4001 4846 7.356540 CGATTCAAATGAGAGAGTACGTAGAT 58.643 38.462 0.00 0.00 0.00 1.98
4002 4847 7.322461 CGATTCAAATGAGAGAGTACGTAGATG 59.678 40.741 0.00 0.00 0.00 2.90
4029 4874 1.899437 GATCGAGTGGCTGGTGGGAA 61.899 60.000 0.00 0.00 0.00 3.97
4030 4875 1.488705 ATCGAGTGGCTGGTGGGAAA 61.489 55.000 0.00 0.00 0.00 3.13
4032 4877 1.237285 CGAGTGGCTGGTGGGAAAAG 61.237 60.000 0.00 0.00 0.00 2.27
4033 4878 0.178990 GAGTGGCTGGTGGGAAAAGT 60.179 55.000 0.00 0.00 0.00 2.66
4034 4879 0.178990 AGTGGCTGGTGGGAAAAGTC 60.179 55.000 0.00 0.00 0.00 3.01
4036 4881 1.971695 GGCTGGTGGGAAAAGTCGG 60.972 63.158 0.00 0.00 0.00 4.79
4037 4882 1.971695 GCTGGTGGGAAAAGTCGGG 60.972 63.158 0.00 0.00 0.00 5.14
4038 4883 1.303317 CTGGTGGGAAAAGTCGGGG 60.303 63.158 0.00 0.00 0.00 5.73
4039 4884 2.035155 GGTGGGAAAAGTCGGGGG 59.965 66.667 0.00 0.00 0.00 5.40
4040 4885 2.675423 GTGGGAAAAGTCGGGGGC 60.675 66.667 0.00 0.00 0.00 5.80
4041 4886 4.338710 TGGGAAAAGTCGGGGGCG 62.339 66.667 0.00 0.00 0.00 6.13
4044 4889 3.431725 GAAAAGTCGGGGGCGCAG 61.432 66.667 10.83 0.00 0.00 5.18
4045 4890 4.265056 AAAAGTCGGGGGCGCAGT 62.265 61.111 10.83 0.00 0.00 4.40
4119 4976 1.479205 GGGAGATAATGTGGGCATGCA 60.479 52.381 21.36 0.00 35.15 3.96
4221 5081 3.963687 CTGGCTCTGTGGCGCATGA 62.964 63.158 10.83 0.54 45.14 3.07
4235 5095 1.590932 GCATGAATGATCGAGGCTGT 58.409 50.000 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 0.445436 CATCCAAAGACGAGTGCAGC 59.555 55.000 0.00 0.00 0.00 5.25
41 42 0.445436 GCATCCAAAGACGAGTGCAG 59.555 55.000 0.00 0.00 33.09 4.41
42 43 0.250252 TGCATCCAAAGACGAGTGCA 60.250 50.000 0.00 0.00 39.94 4.57
101 102 0.955919 GTTGTAGCACCTGTCCTGGC 60.956 60.000 0.00 0.00 0.00 4.85
167 335 2.740826 GTCAAAGCTGCGCGGGTA 60.741 61.111 23.08 2.76 0.00 3.69
176 344 3.327757 TCTGTTACATGGAGGTCAAAGCT 59.672 43.478 0.00 0.00 0.00 3.74
189 358 0.038618 TCTGCGTGCGTCTGTTACAT 60.039 50.000 0.00 0.00 0.00 2.29
214 383 7.087409 TGTTATTGTGAATGGTAAGCAGATG 57.913 36.000 0.00 0.00 0.00 2.90
246 420 3.245990 GCCTCAAAGTGTGCAAAAATGTC 59.754 43.478 0.00 0.00 0.00 3.06
247 421 3.197265 GCCTCAAAGTGTGCAAAAATGT 58.803 40.909 0.00 0.00 0.00 2.71
248 422 3.196463 TGCCTCAAAGTGTGCAAAAATG 58.804 40.909 0.00 0.00 0.00 2.32
249 423 3.540314 TGCCTCAAAGTGTGCAAAAAT 57.460 38.095 0.00 0.00 0.00 1.82
250 424 2.999355 GTTGCCTCAAAGTGTGCAAAAA 59.001 40.909 0.00 0.00 44.44 1.94
278 457 5.697178 TGTCGCTGCTATTTTACTTGTGTTA 59.303 36.000 0.00 0.00 0.00 2.41
279 458 4.513692 TGTCGCTGCTATTTTACTTGTGTT 59.486 37.500 0.00 0.00 0.00 3.32
352 531 2.175322 GCTTTGTGCTCGCTGCTC 59.825 61.111 0.00 0.00 43.37 4.26
353 532 3.360340 GGCTTTGTGCTCGCTGCT 61.360 61.111 0.00 0.00 43.37 4.24
354 533 4.748679 CGGCTTTGTGCTCGCTGC 62.749 66.667 0.00 0.00 42.39 5.25
355 534 3.300667 GACGGCTTTGTGCTCGCTG 62.301 63.158 0.00 0.00 42.39 5.18
356 535 3.044305 GACGGCTTTGTGCTCGCT 61.044 61.111 0.00 0.00 42.39 4.93
357 536 4.090057 GGACGGCTTTGTGCTCGC 62.090 66.667 0.00 0.00 42.39 5.03
358 537 3.777925 CGGACGGCTTTGTGCTCG 61.778 66.667 0.00 0.00 42.39 5.03
359 538 2.665185 ACGGACGGCTTTGTGCTC 60.665 61.111 0.00 0.00 42.39 4.26
360 539 2.665185 GACGGACGGCTTTGTGCT 60.665 61.111 0.00 0.00 42.39 4.40
361 540 4.072088 CGACGGACGGCTTTGTGC 62.072 66.667 0.00 0.00 41.94 4.57
380 559 2.507102 CCAGTGCTGCTACGACGG 60.507 66.667 0.00 0.00 0.00 4.79
381 560 1.344942 GAACCAGTGCTGCTACGACG 61.345 60.000 0.00 0.00 0.00 5.12
382 561 0.319555 TGAACCAGTGCTGCTACGAC 60.320 55.000 0.00 0.00 0.00 4.34
383 562 0.038251 CTGAACCAGTGCTGCTACGA 60.038 55.000 0.00 0.00 0.00 3.43
385 564 1.719600 CTCTGAACCAGTGCTGCTAC 58.280 55.000 0.00 0.00 32.61 3.58
386 565 0.036952 GCTCTGAACCAGTGCTGCTA 60.037 55.000 12.16 0.00 44.40 3.49
388 567 2.331132 GGCTCTGAACCAGTGCTGC 61.331 63.158 17.00 0.00 46.20 5.25
389 568 1.673665 GGGCTCTGAACCAGTGCTG 60.674 63.158 17.00 0.00 46.20 4.41
390 569 1.835927 GAGGGCTCTGAACCAGTGCT 61.836 60.000 17.00 2.74 46.20 4.40
391 570 1.376553 GAGGGCTCTGAACCAGTGC 60.377 63.158 11.28 11.28 46.23 4.40
392 571 1.079543 CGAGGGCTCTGAACCAGTG 60.080 63.158 0.00 0.00 32.61 3.66
393 572 2.948720 GCGAGGGCTCTGAACCAGT 61.949 63.158 0.00 0.00 35.83 4.00
394 573 2.125350 GCGAGGGCTCTGAACCAG 60.125 66.667 0.00 0.00 35.83 4.00
395 574 3.706373 GGCGAGGGCTCTGAACCA 61.706 66.667 0.00 0.00 39.81 3.67
396 575 4.821589 CGGCGAGGGCTCTGAACC 62.822 72.222 0.00 0.00 39.81 3.62
397 576 3.760035 TCGGCGAGGGCTCTGAAC 61.760 66.667 4.99 0.00 39.81 3.18
502 681 3.000727 TCTTTCGCTTTCTTTCGATCCC 58.999 45.455 0.00 0.00 34.48 3.85
572 752 1.004185 CGATGTACGCTACGCTACACT 60.004 52.381 5.15 0.00 30.98 3.55
574 754 0.305617 CCGATGTACGCTACGCTACA 59.694 55.000 0.00 5.40 41.07 2.74
583 763 4.830765 TGGCTGGCCGATGTACGC 62.831 66.667 7.14 0.00 41.07 4.42
673 857 1.548357 GGTTGGGCTGCTCTCTCTCA 61.548 60.000 0.00 0.00 0.00 3.27
677 861 2.753029 GTGGTTGGGCTGCTCTCT 59.247 61.111 0.00 0.00 0.00 3.10
840 1048 0.382515 GTAGCGCACCACCTCTAGAG 59.617 60.000 11.47 13.18 0.00 2.43
842 1050 1.064296 CGTAGCGCACCACCTCTAG 59.936 63.158 11.47 0.00 0.00 2.43
843 1051 2.412323 CCGTAGCGCACCACCTCTA 61.412 63.158 11.47 0.00 0.00 2.43
845 1053 4.814294 CCCGTAGCGCACCACCTC 62.814 72.222 11.47 0.00 0.00 3.85
865 1073 4.457496 CATGCCGAGTCCACCGCT 62.457 66.667 0.00 0.00 0.00 5.52
971 1184 1.552348 GAGCGAGTGTGTGTGTGAGC 61.552 60.000 0.00 0.00 0.00 4.26
972 1185 0.031314 AGAGCGAGTGTGTGTGTGAG 59.969 55.000 0.00 0.00 0.00 3.51
973 1186 0.030773 GAGAGCGAGTGTGTGTGTGA 59.969 55.000 0.00 0.00 0.00 3.58
974 1187 0.031314 AGAGAGCGAGTGTGTGTGTG 59.969 55.000 0.00 0.00 0.00 3.82
975 1188 0.312416 GAGAGAGCGAGTGTGTGTGT 59.688 55.000 0.00 0.00 0.00 3.72
991 1204 2.109739 GCACCGAGAGCGAGAGAGA 61.110 63.158 0.00 0.00 40.82 3.10
1026 1260 1.051812 CCCTCGGTATGATGAGCCTT 58.948 55.000 0.00 0.00 0.00 4.35
1027 1261 0.188587 TCCCTCGGTATGATGAGCCT 59.811 55.000 0.00 0.00 0.00 4.58
1065 1299 3.200593 CTGCGCTGTCTCCATGGC 61.201 66.667 9.73 0.00 0.00 4.40
1205 1457 2.592993 CCACCCGAGCAGGAAGGAA 61.593 63.158 0.00 0.00 45.00 3.36
1343 1615 1.706287 GAGTTCAATTCTCCGCCGGC 61.706 60.000 19.07 19.07 0.00 6.13
1440 1712 3.474570 GGGACCTGCTGCTCCGAT 61.475 66.667 0.00 0.00 0.00 4.18
1508 1780 4.718961 AGATAAGGATGGGCATTGTGTAC 58.281 43.478 0.00 0.00 0.00 2.90
1722 2016 0.321996 AGAGGAAAGAGTTCGTGGCC 59.678 55.000 0.00 0.00 34.28 5.36
1754 2048 1.630333 AGGGAGGGATGGAGGGAGA 60.630 63.158 0.00 0.00 0.00 3.71
1763 2057 0.948050 ATGGAGTCTGAGGGAGGGAT 59.052 55.000 0.00 0.00 0.00 3.85
1975 2278 3.561725 ACAATTAAGCGCTGCTAATCCTC 59.438 43.478 12.58 0.00 38.25 3.71
1977 2280 3.312421 TGACAATTAAGCGCTGCTAATCC 59.688 43.478 12.58 6.33 38.25 3.01
2048 2351 3.365064 CCGCGATGTAGTACTGGAGTATG 60.365 52.174 8.23 0.00 32.54 2.39
2049 2352 2.812591 CCGCGATGTAGTACTGGAGTAT 59.187 50.000 8.23 0.00 32.54 2.12
2063 2366 1.771073 TACCGTACCGTACCGCGATG 61.771 60.000 8.23 0.00 44.77 3.84
2078 2381 7.103641 ACTATTATTATGGTGCAATCCTACCG 58.896 38.462 0.00 0.00 39.87 4.02
2082 2385 8.960591 GCAATACTATTATTATGGTGCAATCCT 58.039 33.333 0.00 0.00 0.00 3.24
2131 2439 3.819337 TCTACGTGCTCACTAACAAGTCT 59.181 43.478 0.00 0.00 31.02 3.24
2296 2606 9.687210 CCAGTTAATAATCATCCAATTCACATG 57.313 33.333 0.00 0.00 0.00 3.21
2320 2630 1.815003 CGGCAGCGATCATCAACCA 60.815 57.895 0.00 0.00 0.00 3.67
2389 2699 1.057851 ACGGGTGGTTCTTCTCCCAA 61.058 55.000 0.00 0.00 39.87 4.12
2393 2703 0.670854 GAGCACGGGTGGTTCTTCTC 60.671 60.000 4.87 0.00 41.93 2.87
2449 2759 3.160748 GCTGGAGGAGGAGGAGGC 61.161 72.222 0.00 0.00 0.00 4.70
2516 2826 4.947147 TTGGCTCGGTGGTGGTGC 62.947 66.667 0.00 0.00 0.00 5.01
2553 2869 2.520741 GAGGAGGAGCGAGGGAGG 60.521 72.222 0.00 0.00 0.00 4.30
2564 2880 0.601558 TTTCAACGACGAGGAGGAGG 59.398 55.000 0.00 0.00 0.00 4.30
2697 3013 3.716006 CTGCCAGACACAACGCCG 61.716 66.667 0.00 0.00 0.00 6.46
2703 3019 1.673337 GATGCTGCTGCCAGACACA 60.673 57.895 13.47 0.00 41.77 3.72
3156 3500 1.227002 GGAGGCACTGCTACGTAGC 60.227 63.158 35.20 35.20 45.87 3.58
3169 3513 4.593864 GCATCGGGACTCGGAGGC 62.594 72.222 10.23 6.05 41.33 4.70
3171 3515 4.271816 CGGCATCGGGACTCGGAG 62.272 72.222 2.83 2.83 39.77 4.63
3179 3529 3.063452 GCATATAATTACACGGCATCGGG 59.937 47.826 0.00 0.00 46.87 5.14
3220 3577 8.743714 GGAAGGATTTTTATTCATTCACTCACT 58.256 33.333 0.00 0.00 36.02 3.41
3239 3596 3.135530 CGGGAGAAGAGAAATGGAAGGAT 59.864 47.826 0.00 0.00 0.00 3.24
3260 3617 6.505576 CGAGAAGAAGATCAAAAACGAGATCG 60.506 42.308 0.00 0.00 44.10 3.69
3357 3726 2.282462 CACAAGGACAGGGGCCAC 60.282 66.667 4.39 0.00 0.00 5.01
3472 3848 3.430374 GCAGCTCGAATTAAGGTGGAGTA 60.430 47.826 16.80 0.00 41.43 2.59
3473 3849 2.678190 GCAGCTCGAATTAAGGTGGAGT 60.678 50.000 16.80 0.00 41.43 3.85
3476 3852 1.017387 GGCAGCTCGAATTAAGGTGG 58.983 55.000 16.80 4.26 41.43 4.61
3477 3853 1.936547 GAGGCAGCTCGAATTAAGGTG 59.063 52.381 12.79 12.79 43.43 4.00
3478 3854 1.134371 GGAGGCAGCTCGAATTAAGGT 60.134 52.381 0.00 0.00 0.00 3.50
3656 4230 2.223994 GCTCTACCACCGTCTTTATCCC 60.224 54.545 0.00 0.00 0.00 3.85
3771 4603 3.952628 CTTGCTCCCGTTCCCGTCC 62.953 68.421 0.00 0.00 0.00 4.79
3772 4604 2.434359 CTTGCTCCCGTTCCCGTC 60.434 66.667 0.00 0.00 0.00 4.79
3773 4605 4.016706 CCTTGCTCCCGTTCCCGT 62.017 66.667 0.00 0.00 0.00 5.28
3774 4606 2.175035 TTACCTTGCTCCCGTTCCCG 62.175 60.000 0.00 0.00 0.00 5.14
3775 4607 0.037160 TTTACCTTGCTCCCGTTCCC 59.963 55.000 0.00 0.00 0.00 3.97
3778 4610 1.244816 GCTTTTACCTTGCTCCCGTT 58.755 50.000 0.00 0.00 0.00 4.44
3846 4681 4.415150 CAGTGTCCCGGCAGCCAT 62.415 66.667 13.30 0.00 0.00 4.40
3851 4686 4.063967 CGCTACAGTGTCCCGGCA 62.064 66.667 0.00 0.00 0.00 5.69
3974 4810 3.178618 CGTACTCTCTCATTTGAATCGCG 59.821 47.826 0.00 0.00 0.00 5.87
3991 4836 4.863689 CGATCGATCTACCATCTACGTACT 59.136 45.833 22.43 0.00 0.00 2.73
3996 4841 4.093703 CCACTCGATCGATCTACCATCTAC 59.906 50.000 19.78 0.00 0.00 2.59
3997 4842 4.254492 CCACTCGATCGATCTACCATCTA 58.746 47.826 19.78 0.00 0.00 1.98
3998 4843 3.078097 CCACTCGATCGATCTACCATCT 58.922 50.000 19.78 0.00 0.00 2.90
4000 4845 1.542030 GCCACTCGATCGATCTACCAT 59.458 52.381 19.78 1.68 0.00 3.55
4001 4846 0.952280 GCCACTCGATCGATCTACCA 59.048 55.000 19.78 3.79 0.00 3.25
4002 4847 1.068885 CAGCCACTCGATCGATCTACC 60.069 57.143 19.78 6.55 0.00 3.18
4029 4874 4.699522 GACTGCGCCCCCGACTTT 62.700 66.667 4.18 0.00 36.29 2.66
4041 4886 1.845809 CTGGAACCTTGTGCGACTGC 61.846 60.000 0.00 0.00 43.20 4.40
4042 4887 1.230635 CCTGGAACCTTGTGCGACTG 61.231 60.000 0.00 0.00 0.00 3.51
4043 4888 1.071471 CCTGGAACCTTGTGCGACT 59.929 57.895 0.00 0.00 0.00 4.18
4044 4889 1.070786 TCCTGGAACCTTGTGCGAC 59.929 57.895 0.00 0.00 0.00 5.19
4045 4890 1.070786 GTCCTGGAACCTTGTGCGA 59.929 57.895 0.00 0.00 0.00 5.10
4119 4976 3.193267 CGAAATCCCCATGAACAACACAT 59.807 43.478 0.00 0.00 0.00 3.21
4216 5076 1.263484 CACAGCCTCGATCATTCATGC 59.737 52.381 0.00 0.00 0.00 4.06
4218 5078 1.487976 ACCACAGCCTCGATCATTCAT 59.512 47.619 0.00 0.00 0.00 2.57
4221 5081 0.904649 TGACCACAGCCTCGATCATT 59.095 50.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.