Multiple sequence alignment - TraesCS1B01G252600

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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 TraesCS1B01G252600 chr1B 100.000 3962 0 0 1 3962 445430172 445426211 0.000000e+00 7317.0
1 TraesCS1B01G252600 chr1B 81.684 475 71 13 3234 3698 585238745 585238277 8.030000e-102 381.0
2 TraesCS1B01G252600 chr1D 93.606 3378 148 25 1 3356 330545931 330542600 0.000000e+00 4979.0
3 TraesCS1B01G252600 chr1D 88.761 436 31 11 3529 3962 330542104 330541685 5.870000e-143 518.0
4 TraesCS1B01G252600 chr1A 91.319 3686 209 32 309 3962 427814279 427810673 0.000000e+00 4931.0
5 TraesCS1B01G252600 chr1A 86.728 648 69 6 3318 3962 427540861 427540228 0.000000e+00 704.0
6 TraesCS1B01G252600 chr1A 80.244 491 83 10 3234 3718 531656243 531655761 1.350000e-94 357.0
7 TraesCS1B01G252600 chr1A 90.187 214 13 6 1 211 427814543 427814335 5.040000e-69 272.0
8 TraesCS1B01G252600 chr5B 78.347 605 87 17 3234 3830 705098421 705098989 6.300000e-93 351.0
9 TraesCS1B01G252600 chr5B 80.851 235 37 7 3239 3468 688964262 688964031 1.130000e-40 178.0
10 TraesCS1B01G252600 chr5B 81.043 211 34 5 3623 3830 705568378 705568171 3.170000e-36 163.0
11 TraesCS1B01G252600 chr5B 100.000 28 0 0 2962 2989 212629951 212629978 7.000000e-03 52.8
12 TraesCS1B01G252600 chr4B 85.167 209 25 4 3623 3830 54322221 54322424 4.010000e-50 209.0
13 TraesCS1B01G252600 chr2D 84.946 186 28 0 3648 3833 612442338 612442153 5.230000e-44 189.0
14 TraesCS1B01G252600 chrUn 80.851 235 37 7 3239 3468 355885783 355885552 1.130000e-40 178.0
15 TraesCS1B01G252600 chr2B 80.753 239 35 5 3234 3468 713677448 713677679 4.070000e-40 176.0
16 TraesCS1B01G252600 chr2B 82.407 108 16 3 3688 3794 628927527 628927422 1.520000e-14 91.6
17 TraesCS1B01G252600 chr5D 77.740 292 40 15 3544 3830 563352377 563352106 5.300000e-34 156.0
18 TraesCS1B01G252600 chr3B 78.161 261 43 9 3234 3490 144176865 144177115 1.910000e-33 154.0
19 TraesCS1B01G252600 chr3B 85.915 71 2 3 3762 3828 112515929 112515863 7.100000e-08 69.4
20 TraesCS1B01G252600 chr3B 97.143 35 1 0 1280 1314 457200824 457200858 4.280000e-05 60.2
21 TraesCS1B01G252600 chr3D 76.981 265 43 12 3234 3490 94050173 94049919 6.910000e-28 135.0
22 TraesCS1B01G252600 chr7D 80.833 120 13 7 1631 1745 485541580 485541694 7.050000e-13 86.1
23 TraesCS1B01G252600 chr7B 80.833 120 13 7 1631 1745 513304912 513305026 7.050000e-13 86.1


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 TraesCS1B01G252600 chr1B 445426211 445430172 3961 True 7317.0 7317 100.0000 1 3962 1 chr1B.!!$R1 3961
1 TraesCS1B01G252600 chr1D 330541685 330545931 4246 True 2748.5 4979 91.1835 1 3962 2 chr1D.!!$R1 3961
2 TraesCS1B01G252600 chr1A 427810673 427814543 3870 True 2601.5 4931 90.7530 1 3962 2 chr1A.!!$R3 3961
3 TraesCS1B01G252600 chr1A 427540228 427540861 633 True 704.0 704 86.7280 3318 3962 1 chr1A.!!$R1 644
4 TraesCS1B01G252600 chr5B 705098421 705098989 568 False 351.0 351 78.3470 3234 3830 1 chr5B.!!$F2 596

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
369 392 0.388006 TACCGACGATGGCATATGCG 60.388 55.0 21.04 9.96 43.26 4.73 F
396 423 0.389817 TTCGATTCTGCGGAGTGTGG 60.390 55.0 3.10 0.00 0.00 4.17 F
440 467 0.678048 GTAGCCAGGAGCCCAAGTTG 60.678 60.0 0.00 0.00 45.47 3.16 F
2012 2072 0.739813 GACCACGCCAAGTTCGCTAT 60.740 55.0 0.00 0.00 0.00 2.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2289 2349 0.032615 TGGAGGAGAGGAGGAAGCTC 60.033 60.000 0.00 0.0 0.0 4.09 R
2319 2379 2.367377 TGGAGGAGGATGGGCAGG 60.367 66.667 0.00 0.0 0.0 4.85 R
2443 2503 3.541713 GGGCGCCGAGAAGAGGAT 61.542 66.667 22.54 0.0 0.0 3.24 R
2975 3035 0.251787 CAAAAACAGGGGAGGGAGGG 60.252 60.000 0.00 0.0 0.0 4.30 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
83 84 0.961019 TTTCATTGTGCTGAGTGCCC 59.039 50.000 0.00 0.00 42.00 5.36
121 123 2.112718 CTATCCTGCCTGCCTGCC 59.887 66.667 0.00 0.00 0.00 4.85
122 124 2.367377 TATCCTGCCTGCCTGCCT 60.367 61.111 0.00 0.00 0.00 4.75
123 125 1.992519 CTATCCTGCCTGCCTGCCTT 61.993 60.000 0.00 0.00 0.00 4.35
124 126 1.987807 TATCCTGCCTGCCTGCCTTC 61.988 60.000 0.00 0.00 0.00 3.46
125 127 4.355720 CCTGCCTGCCTGCCTTCA 62.356 66.667 0.00 0.00 0.00 3.02
169 171 5.749596 TGTAAACTGCACATATGTATGGC 57.250 39.130 8.32 8.83 38.00 4.40
170 172 5.189180 TGTAAACTGCACATATGTATGGCA 58.811 37.500 16.01 16.01 37.46 4.92
172 174 6.995091 TGTAAACTGCACATATGTATGGCATA 59.005 34.615 16.92 2.32 43.47 3.14
192 194 6.116126 GCATACTTTCCAGTTATCCAAGTCT 58.884 40.000 0.00 0.00 34.06 3.24
220 223 2.436087 AAACTCAGGTCGCGTGGAGG 62.436 60.000 5.77 0.00 0.00 4.30
221 224 3.374402 CTCAGGTCGCGTGGAGGT 61.374 66.667 5.77 0.00 0.00 3.85
227 230 3.381983 TCGCGTGGAGGTGATGCT 61.382 61.111 5.77 0.00 0.00 3.79
234 237 1.209019 GTGGAGGTGATGCTGATCAGT 59.791 52.381 23.38 4.98 39.36 3.41
235 238 1.208776 TGGAGGTGATGCTGATCAGTG 59.791 52.381 23.38 0.72 39.36 3.66
238 241 3.452474 GAGGTGATGCTGATCAGTGTAC 58.548 50.000 23.38 16.10 39.36 2.90
239 242 2.833943 AGGTGATGCTGATCAGTGTACA 59.166 45.455 23.38 13.21 39.36 2.90
240 243 3.453717 AGGTGATGCTGATCAGTGTACAT 59.546 43.478 23.38 17.14 39.36 2.29
265 268 5.728898 GCATTCTCTTCTCGCTACCATTTTG 60.729 44.000 0.00 0.00 0.00 2.44
267 270 5.654603 TCTCTTCTCGCTACCATTTTGTA 57.345 39.130 0.00 0.00 0.00 2.41
286 289 0.980423 ACAGTGGAGAGGAAAGGAGC 59.020 55.000 0.00 0.00 0.00 4.70
317 339 0.817634 TCCACCTCAGCGGTTTGTTG 60.818 55.000 0.00 0.00 46.37 3.33
338 360 0.462047 GCGGTGATCGATGTTTCCCT 60.462 55.000 0.54 0.00 42.43 4.20
363 386 0.730265 GCATTTTACCGACGATGGCA 59.270 50.000 0.00 0.00 0.00 4.92
364 387 1.333619 GCATTTTACCGACGATGGCAT 59.666 47.619 0.00 0.00 0.00 4.40
365 388 2.546368 GCATTTTACCGACGATGGCATA 59.454 45.455 0.00 0.00 0.00 3.14
366 389 3.188460 GCATTTTACCGACGATGGCATAT 59.812 43.478 0.00 0.00 0.00 1.78
367 390 4.711721 CATTTTACCGACGATGGCATATG 58.288 43.478 0.00 0.00 0.00 1.78
368 391 1.790755 TTACCGACGATGGCATATGC 58.209 50.000 19.79 19.79 41.14 3.14
369 392 0.388006 TACCGACGATGGCATATGCG 60.388 55.000 21.04 9.96 43.26 4.73
370 393 1.664649 CCGACGATGGCATATGCGT 60.665 57.895 21.04 13.17 43.26 5.24
371 394 1.221466 CCGACGATGGCATATGCGTT 61.221 55.000 21.04 10.96 43.26 4.84
378 405 1.462616 TGGCATATGCGTTTGCTCTT 58.537 45.000 21.04 0.00 43.34 2.85
384 411 2.813779 ATGCGTTTGCTCTTCGATTC 57.186 45.000 0.00 0.00 43.34 2.52
395 422 0.994995 CTTCGATTCTGCGGAGTGTG 59.005 55.000 3.10 0.00 32.25 3.82
396 423 0.389817 TTCGATTCTGCGGAGTGTGG 60.390 55.000 3.10 0.00 0.00 4.17
432 459 1.341156 ATCTGGGTGTAGCCAGGAGC 61.341 60.000 25.08 0.00 44.25 4.70
439 466 1.133809 TGTAGCCAGGAGCCCAAGTT 61.134 55.000 0.00 0.00 45.47 2.66
440 467 0.678048 GTAGCCAGGAGCCCAAGTTG 60.678 60.000 0.00 0.00 45.47 3.16
459 490 7.378966 CAAGTTGGAAGAGAAGTCAGTATGTA 58.621 38.462 0.00 0.00 37.40 2.29
468 503 1.287146 AGTCAGTATGTACCCCGACCT 59.713 52.381 0.00 0.00 37.40 3.85
503 538 4.396166 ACAAGAGCCGATTTAGATTTGGTG 59.604 41.667 0.00 0.00 0.00 4.17
504 539 4.222124 AGAGCCGATTTAGATTTGGTGT 57.778 40.909 0.00 0.00 0.00 4.16
505 540 4.589908 AGAGCCGATTTAGATTTGGTGTT 58.410 39.130 0.00 0.00 0.00 3.32
506 541 5.741011 AGAGCCGATTTAGATTTGGTGTTA 58.259 37.500 0.00 0.00 0.00 2.41
539 574 0.889186 GTCCAACCGCCAAGACACAT 60.889 55.000 0.00 0.00 0.00 3.21
761 796 4.010667 TGTAACCGGTGTGAAAATAGCT 57.989 40.909 8.52 0.00 0.00 3.32
823 862 4.553330 ACGAACAATCTCAACCTATGGT 57.447 40.909 0.00 0.00 37.65 3.55
848 887 2.736995 GGCGTGCGTGCAAGAGTA 60.737 61.111 11.94 0.00 36.28 2.59
949 999 1.195115 TCCCGCTCATCTACTGCTTT 58.805 50.000 0.00 0.00 0.00 3.51
1047 1104 4.044484 CCGGCGCTCCTCCTATCG 62.044 72.222 7.64 0.00 0.00 2.92
1107 1164 1.112950 CGTCCTTCTCCTTCTACCCC 58.887 60.000 0.00 0.00 0.00 4.95
1155 1212 2.936032 ACCAACCTCTCCTGCCCC 60.936 66.667 0.00 0.00 0.00 5.80
1200 1257 2.672414 CCTCCCGAGGTTCTTGTCT 58.328 57.895 2.31 0.00 43.61 3.41
1207 1267 1.618837 CGAGGTTCTTGTCTTCCTCCA 59.381 52.381 0.00 0.00 42.21 3.86
1210 1270 1.149148 GTTCTTGTCTTCCTCCACGC 58.851 55.000 0.00 0.00 0.00 5.34
1356 1416 3.224324 GGCACCGGCTCCGAGATA 61.224 66.667 10.28 0.00 42.83 1.98
1976 2036 2.068821 AGCTCGCCATGGAGGTCAT 61.069 57.895 18.40 0.00 40.55 3.06
2010 2070 2.665185 GACCACGCCAAGTTCGCT 60.665 61.111 0.00 0.00 0.00 4.93
2011 2071 1.373748 GACCACGCCAAGTTCGCTA 60.374 57.895 0.00 0.00 0.00 4.26
2012 2072 0.739813 GACCACGCCAAGTTCGCTAT 60.740 55.000 0.00 0.00 0.00 2.97
2289 2349 1.449246 CCTCTTCGCCTTCAGCCTG 60.449 63.158 0.00 0.00 38.78 4.85
2400 2460 1.946475 GCCTGTCCTCCTACGTGGTC 61.946 65.000 0.00 0.00 37.07 4.02
2776 2836 3.858868 GAGAAGTGCGTGGCGTGGA 62.859 63.158 0.00 0.00 0.00 4.02
2777 2837 3.712881 GAAGTGCGTGGCGTGGAC 61.713 66.667 0.00 0.00 0.00 4.02
2901 2961 0.034767 TCATGCTGGGCTTCTTCCTG 60.035 55.000 0.00 0.00 0.00 3.86
2973 3033 2.433970 CACTCTCTGATCCTTCCTTCCC 59.566 54.545 0.00 0.00 0.00 3.97
2974 3034 2.317594 ACTCTCTGATCCTTCCTTCCCT 59.682 50.000 0.00 0.00 0.00 4.20
2975 3035 2.965147 CTCTCTGATCCTTCCTTCCCTC 59.035 54.545 0.00 0.00 0.00 4.30
2976 3036 2.046292 CTCTGATCCTTCCTTCCCTCC 58.954 57.143 0.00 0.00 0.00 4.30
2977 3037 1.135960 CTGATCCTTCCTTCCCTCCC 58.864 60.000 0.00 0.00 0.00 4.30
2978 3038 0.725133 TGATCCTTCCTTCCCTCCCT 59.275 55.000 0.00 0.00 0.00 4.20
2979 3039 1.344496 TGATCCTTCCTTCCCTCCCTC 60.344 57.143 0.00 0.00 0.00 4.30
2980 3040 0.029577 ATCCTTCCTTCCCTCCCTCC 60.030 60.000 0.00 0.00 0.00 4.30
2981 3041 1.694525 CCTTCCTTCCCTCCCTCCC 60.695 68.421 0.00 0.00 0.00 4.30
2999 3059 1.202639 CCCTCCCCTGTTTTTGTTTGC 60.203 52.381 0.00 0.00 0.00 3.68
3008 3068 2.999355 TGTTTTTGTTTGCCAGCTTCAC 59.001 40.909 0.00 0.00 0.00 3.18
3020 3080 1.466167 CAGCTTCACTGGTTTGGATCG 59.534 52.381 0.00 0.00 43.19 3.69
3021 3081 0.804989 GCTTCACTGGTTTGGATCGG 59.195 55.000 0.00 0.00 0.00 4.18
3022 3082 1.610624 GCTTCACTGGTTTGGATCGGA 60.611 52.381 0.00 0.00 0.00 4.55
3023 3083 2.941415 GCTTCACTGGTTTGGATCGGAT 60.941 50.000 0.00 0.00 0.00 4.18
3024 3084 2.691409 TCACTGGTTTGGATCGGATC 57.309 50.000 9.54 9.54 0.00 3.36
3050 3111 9.261318 CATATATACAATCGGCGTTATTTGTTG 57.739 33.333 18.98 11.47 34.39 3.33
3051 3112 3.907894 ACAATCGGCGTTATTTGTTGT 57.092 38.095 6.85 5.50 0.00 3.32
3052 3113 4.231718 ACAATCGGCGTTATTTGTTGTT 57.768 36.364 6.85 0.00 0.00 2.83
3068 3129 4.420168 TGTTGTTTGCTTTTCTGCTGTAC 58.580 39.130 0.00 0.00 0.00 2.90
3101 3162 7.421530 TTGTTTAGATGTGCTGAGTAAGAAC 57.578 36.000 0.00 0.00 34.56 3.01
3183 3244 2.367567 TGTCAACCTGTCTACCTGAACC 59.632 50.000 0.00 0.00 0.00 3.62
3205 3266 0.800631 GGGCGTCCTTTTACGGAAAG 59.199 55.000 0.00 0.00 43.06 2.62
3270 3331 2.125310 CGGTGCGGGTAATGCTCA 60.125 61.111 0.00 0.00 0.00 4.26
3272 3333 1.078426 GGTGCGGGTAATGCTCACT 60.078 57.895 0.00 0.00 0.00 3.41
3295 3356 1.043022 ACCCGTATCCGTCCCAATAC 58.957 55.000 0.00 0.00 0.00 1.89
3309 3370 6.602009 CCGTCCCAATACTTTTCTCCTAAATT 59.398 38.462 0.00 0.00 0.00 1.82
3311 3372 7.553044 CGTCCCAATACTTTTCTCCTAAATTCT 59.447 37.037 0.00 0.00 0.00 2.40
3330 3391 1.134560 CTTACTCGTACCTGCACCTCC 59.865 57.143 0.00 0.00 0.00 4.30
3346 3407 4.638865 GCACCTCCGGTTTTATATTGTTCT 59.361 41.667 0.00 0.00 31.02 3.01
3376 3441 2.241880 CCAGCCGCGGGTAATAACG 61.242 63.158 31.92 16.48 0.00 3.18
3382 3447 2.182181 GCGGGTAATAACGGTGGGC 61.182 63.158 0.00 0.00 0.00 5.36
3460 3525 7.359595 TCAGCATTTCAGTATGTAAAACACAC 58.640 34.615 0.00 0.00 40.86 3.82
3470 3535 5.789643 ATGTAAAACACACCATTTCAGCT 57.210 34.783 0.00 0.00 40.86 4.24
3601 4033 3.137728 TGGCTATTAGGCTAGGGTTTTCC 59.862 47.826 17.14 0.00 41.96 3.13
3602 4034 3.137728 GGCTATTAGGCTAGGGTTTTCCA 59.862 47.826 9.87 0.00 38.66 3.53
3603 4035 4.202577 GGCTATTAGGCTAGGGTTTTCCAT 60.203 45.833 9.87 0.00 38.66 3.41
3604 4036 5.386060 GCTATTAGGCTAGGGTTTTCCATT 58.614 41.667 0.00 0.00 42.91 3.16
3605 4037 5.833667 GCTATTAGGCTAGGGTTTTCCATTT 59.166 40.000 0.00 0.00 42.91 2.32
3679 4111 0.682209 AGGCGGGTACACGAGTATGT 60.682 55.000 24.33 0.00 36.56 2.29
3691 4123 5.950965 CACGAGTATGTGTATTGTCTTCC 57.049 43.478 0.00 0.00 35.12 3.46
3692 4124 5.651530 CACGAGTATGTGTATTGTCTTCCT 58.348 41.667 0.00 0.00 35.12 3.36
3693 4125 5.516696 CACGAGTATGTGTATTGTCTTCCTG 59.483 44.000 0.00 0.00 35.12 3.86
3694 4126 5.185249 ACGAGTATGTGTATTGTCTTCCTGT 59.815 40.000 0.00 0.00 0.00 4.00
3695 4127 6.376299 ACGAGTATGTGTATTGTCTTCCTGTA 59.624 38.462 0.00 0.00 0.00 2.74
3696 4128 6.691818 CGAGTATGTGTATTGTCTTCCTGTAC 59.308 42.308 0.00 0.00 0.00 2.90
3697 4129 6.875076 AGTATGTGTATTGTCTTCCTGTACC 58.125 40.000 0.00 0.00 0.00 3.34
3698 4130 6.668283 AGTATGTGTATTGTCTTCCTGTACCT 59.332 38.462 0.00 0.00 0.00 3.08
3699 4131 5.147330 TGTGTATTGTCTTCCTGTACCTG 57.853 43.478 0.00 0.00 0.00 4.00
3711 4154 2.037144 CTGTACCTGTACCCGGCTTAT 58.963 52.381 0.00 0.00 35.26 1.73
3811 4254 0.672401 CCGTCAACATTGCGGGTAGT 60.672 55.000 15.37 0.00 41.12 2.73
3853 4296 1.220529 CTGACATGTCTGCGTGTGTT 58.779 50.000 25.55 0.00 44.20 3.32
3905 4351 1.339151 GGACGGCTCAGAAGGAACAAT 60.339 52.381 0.00 0.00 0.00 2.71
3906 4352 2.093658 GGACGGCTCAGAAGGAACAATA 60.094 50.000 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 104 1.227793 GCAGGCAGGCAGGATAGTC 60.228 63.158 0.00 0.00 0.00 2.59
121 123 8.200364 ACAAAACTGGATGAAACAAAATGAAG 57.800 30.769 0.00 0.00 0.00 3.02
122 124 8.449397 CAACAAAACTGGATGAAACAAAATGAA 58.551 29.630 0.00 0.00 0.00 2.57
123 125 7.605691 ACAACAAAACTGGATGAAACAAAATGA 59.394 29.630 0.00 0.00 0.00 2.57
124 126 7.750769 ACAACAAAACTGGATGAAACAAAATG 58.249 30.769 0.00 0.00 0.00 2.32
125 127 7.920160 ACAACAAAACTGGATGAAACAAAAT 57.080 28.000 0.00 0.00 0.00 1.82
169 171 7.010552 CGAAGACTTGGATAACTGGAAAGTATG 59.989 40.741 0.00 0.00 31.45 2.39
170 172 7.042335 CGAAGACTTGGATAACTGGAAAGTAT 58.958 38.462 0.00 0.00 31.45 2.12
172 174 5.238583 CGAAGACTTGGATAACTGGAAAGT 58.761 41.667 0.00 0.00 33.91 2.66
204 207 3.374402 ACCTCCACGCGACCTGAG 61.374 66.667 15.93 12.25 0.00 3.35
207 210 2.680352 ATCACCTCCACGCGACCT 60.680 61.111 15.93 0.00 0.00 3.85
211 214 2.913054 ATCAGCATCACCTCCACGCG 62.913 60.000 3.53 3.53 0.00 6.01
213 216 0.176449 TGATCAGCATCACCTCCACG 59.824 55.000 0.00 0.00 33.80 4.94
220 223 3.002042 GCATGTACACTGATCAGCATCAC 59.998 47.826 22.83 14.89 33.80 3.06
221 224 3.200483 GCATGTACACTGATCAGCATCA 58.800 45.455 22.83 15.88 36.62 3.07
227 230 5.349061 AGAGAATGCATGTACACTGATCA 57.651 39.130 0.00 0.00 0.00 2.92
234 237 3.118992 AGCGAGAAGAGAATGCATGTACA 60.119 43.478 0.00 0.00 0.00 2.90
235 238 3.452474 AGCGAGAAGAGAATGCATGTAC 58.548 45.455 0.00 0.00 0.00 2.90
238 241 2.799412 GGTAGCGAGAAGAGAATGCATG 59.201 50.000 0.00 0.00 0.00 4.06
239 242 2.432146 TGGTAGCGAGAAGAGAATGCAT 59.568 45.455 0.00 0.00 0.00 3.96
240 243 1.824852 TGGTAGCGAGAAGAGAATGCA 59.175 47.619 0.00 0.00 0.00 3.96
265 268 2.093921 GCTCCTTTCCTCTCCACTGTAC 60.094 54.545 0.00 0.00 0.00 2.90
267 270 0.980423 GCTCCTTTCCTCTCCACTGT 59.020 55.000 0.00 0.00 0.00 3.55
286 289 0.165944 GAGGTGGACGAACAAATGCG 59.834 55.000 0.00 0.00 0.00 4.73
317 339 1.436983 GGAAACATCGATCACCGCCC 61.437 60.000 0.00 0.00 38.37 6.13
338 360 2.768698 TCGTCGGTAAAATGCAAGGAA 58.231 42.857 0.00 0.00 0.00 3.36
363 386 4.025396 CAGAATCGAAGAGCAAACGCATAT 60.025 41.667 0.00 0.00 43.63 1.78
364 387 3.306973 CAGAATCGAAGAGCAAACGCATA 59.693 43.478 0.00 0.00 43.63 3.14
365 388 2.094894 CAGAATCGAAGAGCAAACGCAT 59.905 45.455 0.00 0.00 43.63 4.73
366 389 1.460743 CAGAATCGAAGAGCAAACGCA 59.539 47.619 0.00 0.00 43.63 5.24
367 390 1.788344 GCAGAATCGAAGAGCAAACGC 60.788 52.381 0.00 0.00 43.63 4.84
368 391 1.525784 CGCAGAATCGAAGAGCAAACG 60.526 52.381 0.00 0.00 43.63 3.60
369 392 1.201965 CCGCAGAATCGAAGAGCAAAC 60.202 52.381 0.00 0.00 43.63 2.93
370 393 1.078709 CCGCAGAATCGAAGAGCAAA 58.921 50.000 0.00 0.00 43.63 3.68
371 394 0.246360 TCCGCAGAATCGAAGAGCAA 59.754 50.000 0.00 0.00 43.63 3.91
378 405 1.215382 CCACACTCCGCAGAATCGA 59.785 57.895 0.00 0.00 0.00 3.59
384 411 2.734723 CGACACCACACTCCGCAG 60.735 66.667 0.00 0.00 0.00 5.18
395 422 3.303495 CAGATTATGTTGTCGACGACACC 59.697 47.826 35.05 23.26 42.60 4.16
396 423 3.303495 CCAGATTATGTTGTCGACGACAC 59.697 47.826 35.05 23.76 42.60 3.67
432 459 3.181450 ACTGACTTCTCTTCCAACTTGGG 60.181 47.826 8.01 0.00 38.32 4.12
439 466 4.710375 GGGTACATACTGACTTCTCTTCCA 59.290 45.833 0.00 0.00 0.00 3.53
440 467 4.099727 GGGGTACATACTGACTTCTCTTCC 59.900 50.000 0.00 0.00 0.00 3.46
468 503 2.210116 GGCTCTTGTTTCTTGACGTGA 58.790 47.619 0.00 0.00 0.00 4.35
503 538 2.017458 GACCTAACCGCGCGCTTAAC 62.017 60.000 30.48 11.71 0.00 2.01
504 539 1.806758 GACCTAACCGCGCGCTTAA 60.807 57.895 30.48 10.77 0.00 1.85
505 540 2.202650 GACCTAACCGCGCGCTTA 60.203 61.111 30.48 20.88 0.00 3.09
539 574 3.084786 TGGTGTCATTTGTGTTGTGTGA 58.915 40.909 0.00 0.00 0.00 3.58
823 862 3.353029 CACGCACGCCACCATTCA 61.353 61.111 0.00 0.00 0.00 2.57
848 887 5.640357 TGAAGTTTTCTTGAACGTGTAGTGT 59.360 36.000 0.00 0.00 40.61 3.55
949 999 1.338674 GGGTCGATGTGTGGATTGTGA 60.339 52.381 0.00 0.00 0.00 3.58
1653 1713 2.185867 GCGATGGACACCCGCTTA 59.814 61.111 11.84 0.00 44.83 3.09
1737 1797 3.785859 AGCACGTCCATGGCCGAT 61.786 61.111 23.95 4.24 0.00 4.18
1758 1818 4.687215 GCCACCTCGTGCAGCAGA 62.687 66.667 0.00 0.00 31.34 4.26
1997 2057 1.079127 AGCATAGCGAACTTGGCGT 60.079 52.632 0.00 0.00 35.00 5.68
2010 2070 0.535335 GGTCGTTGTCCCTGAGCATA 59.465 55.000 0.00 0.00 0.00 3.14
2011 2071 1.296715 GGTCGTTGTCCCTGAGCAT 59.703 57.895 0.00 0.00 0.00 3.79
2012 2072 2.099652 CTGGTCGTTGTCCCTGAGCA 62.100 60.000 0.00 0.00 37.75 4.26
2148 2208 2.802667 CTGCTGCGTGCGGTACATC 61.803 63.158 2.18 0.00 46.63 3.06
2289 2349 0.032615 TGGAGGAGAGGAGGAAGCTC 60.033 60.000 0.00 0.00 0.00 4.09
2319 2379 2.367377 TGGAGGAGGATGGGCAGG 60.367 66.667 0.00 0.00 0.00 4.85
2443 2503 3.541713 GGGCGCCGAGAAGAGGAT 61.542 66.667 22.54 0.00 0.00 3.24
2499 2559 1.615107 CGAGCACGAAGAACCCGAAC 61.615 60.000 0.00 0.00 42.66 3.95
2752 2812 2.356313 CACGCACTTCTCGCTGGT 60.356 61.111 0.00 0.00 0.00 4.00
2757 2817 3.767230 CACGCCACGCACTTCTCG 61.767 66.667 0.00 0.00 0.00 4.04
2760 2820 3.712881 GTCCACGCCACGCACTTC 61.713 66.667 0.00 0.00 0.00 3.01
2841 2901 3.077556 CCCTCGTCCACCCCTCTG 61.078 72.222 0.00 0.00 0.00 3.35
2901 2961 2.283298 CAGCACATGATCCTGTACACC 58.717 52.381 0.00 0.00 0.00 4.16
2973 3033 0.846870 AAAACAGGGGAGGGAGGGAG 60.847 60.000 0.00 0.00 0.00 4.30
2974 3034 0.404346 AAAAACAGGGGAGGGAGGGA 60.404 55.000 0.00 0.00 0.00 4.20
2975 3035 0.251787 CAAAAACAGGGGAGGGAGGG 60.252 60.000 0.00 0.00 0.00 4.30
2976 3036 0.482887 ACAAAAACAGGGGAGGGAGG 59.517 55.000 0.00 0.00 0.00 4.30
2977 3037 2.365293 CAAACAAAAACAGGGGAGGGAG 59.635 50.000 0.00 0.00 0.00 4.30
2978 3038 2.393646 CAAACAAAAACAGGGGAGGGA 58.606 47.619 0.00 0.00 0.00 4.20
2979 3039 1.202639 GCAAACAAAAACAGGGGAGGG 60.203 52.381 0.00 0.00 0.00 4.30
2980 3040 1.202639 GGCAAACAAAAACAGGGGAGG 60.203 52.381 0.00 0.00 0.00 4.30
2981 3041 1.484240 TGGCAAACAAAAACAGGGGAG 59.516 47.619 0.00 0.00 0.00 4.30
3008 3068 7.555965 TGTATATATGATCCGATCCAAACCAG 58.444 38.462 5.91 0.00 0.00 4.00
3020 3080 8.589335 AATAACGCCGATTGTATATATGATCC 57.411 34.615 0.00 0.00 0.00 3.36
3021 3081 9.849607 CAAATAACGCCGATTGTATATATGATC 57.150 33.333 0.00 0.00 0.00 2.92
3022 3082 9.378551 ACAAATAACGCCGATTGTATATATGAT 57.621 29.630 0.00 0.00 34.45 2.45
3023 3083 8.766000 ACAAATAACGCCGATTGTATATATGA 57.234 30.769 0.00 0.00 34.45 2.15
3024 3084 9.261318 CAACAAATAACGCCGATTGTATATATG 57.739 33.333 0.00 0.00 35.09 1.78
3050 3111 4.026558 GCAAAGTACAGCAGAAAAGCAAAC 60.027 41.667 0.00 0.00 36.85 2.93
3051 3112 4.111916 GCAAAGTACAGCAGAAAAGCAAA 58.888 39.130 0.00 0.00 36.85 3.68
3052 3113 3.381272 AGCAAAGTACAGCAGAAAAGCAA 59.619 39.130 0.00 0.00 36.85 3.91
3068 3129 5.628193 CAGCACATCTAAACAAAGAGCAAAG 59.372 40.000 0.00 0.00 0.00 2.77
3129 3190 5.701750 TCATGAACCCAAATCAAGCATTTTG 59.298 36.000 0.00 0.00 31.79 2.44
3183 3244 0.391927 TCCGTAAAAGGACGCCCATG 60.392 55.000 0.00 0.00 41.56 3.66
3231 3292 2.665089 CCCTACGGGTGCCATGTCA 61.665 63.158 0.00 0.00 38.25 3.58
3253 3314 2.125310 TGAGCATTACCCGCACCG 60.125 61.111 0.00 0.00 0.00 4.94
3295 3356 9.085250 GGTACGAGTAAGAATTTAGGAGAAAAG 57.915 37.037 0.00 0.00 0.00 2.27
3309 3370 2.089980 GAGGTGCAGGTACGAGTAAGA 58.910 52.381 0.00 0.00 0.00 2.10
3311 3372 1.180029 GGAGGTGCAGGTACGAGTAA 58.820 55.000 0.00 0.00 0.00 2.24
3330 3391 7.795482 TGGGTATGAGAACAATATAAAACCG 57.205 36.000 0.00 0.00 0.00 4.44
3346 3407 1.764571 GCGGCTGGGTATGGGTATGA 61.765 60.000 0.00 0.00 0.00 2.15
3382 3447 3.317993 GGTGATCGGGATGGGTATTTTTG 59.682 47.826 0.00 0.00 0.00 2.44
3396 3461 4.970662 ATGTGAATTGAAAGGTGATCGG 57.029 40.909 0.00 0.00 0.00 4.18
3460 3525 5.593968 TGCTAAATATGCAAGCTGAAATGG 58.406 37.500 8.68 0.00 37.51 3.16
3470 3535 4.337836 TCGGCTGAAATGCTAAATATGCAA 59.662 37.500 0.00 0.00 44.01 4.08
3505 3571 5.222130 ACTCATAGAACACAAACCCCATCTT 60.222 40.000 0.00 0.00 0.00 2.40
3604 4036 9.403583 GTCCCCTATATCATTCACTAACAAAAA 57.596 33.333 0.00 0.00 0.00 1.94
3605 4037 7.996644 GGTCCCCTATATCATTCACTAACAAAA 59.003 37.037 0.00 0.00 0.00 2.44
3609 4041 6.936968 AGGTCCCCTATATCATTCACTAAC 57.063 41.667 0.00 0.00 28.47 2.34
3621 4053 6.724441 CACATCTAACATGTAGGTCCCCTATA 59.276 42.308 0.00 0.00 38.48 1.31
3679 4111 5.186409 GGTACAGGTACAGGAAGACAATACA 59.814 44.000 11.35 0.00 37.78 2.29
3686 4118 1.617804 CCGGGTACAGGTACAGGAAGA 60.618 57.143 14.34 0.00 39.39 2.87
3689 4121 4.770540 CCGGGTACAGGTACAGGA 57.229 61.111 14.34 0.00 39.39 3.86
3745 4188 8.395605 AGGGTTTGGGAAAGTTAAATACTCATA 58.604 33.333 0.00 0.00 35.54 2.15
3749 4192 7.452501 GGTAAGGGTTTGGGAAAGTTAAATACT 59.547 37.037 0.00 0.00 39.32 2.12
3841 4284 2.607892 GGAGGCAACACACGCAGAC 61.608 63.158 0.00 0.00 41.41 3.51
3853 4296 0.977627 ATCTGATGGTCACGGAGGCA 60.978 55.000 0.00 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.