Multiple sequence alignment - TraesCS6D01G193000

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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 TraesCS6D01G193000 chr6D 100.000 3413 0 0 1 3413 267199556 267202968 0.000000e+00 6303.0
1 TraesCS6D01G193000 chr6A 94.965 2820 66 23 535 3302 380109803 380112598 0.000000e+00 4351.0
2 TraesCS6D01G193000 chr6A 92.537 201 12 1 2 202 380109364 380109561 5.570000e-73 285.0
3 TraesCS6D01G193000 chr6A 84.912 285 17 3 231 514 380109559 380109818 7.260000e-67 265.0
4 TraesCS6D01G193000 chr6B 96.899 2096 37 7 651 2744 415729624 415731693 0.000000e+00 3485.0
5 TraesCS6D01G193000 chr6B 93.569 311 15 2 3106 3413 415732431 415732739 3.100000e-125 459.0
6 TraesCS6D01G193000 chr6B 93.578 218 10 2 2925 3138 415732212 415732429 4.250000e-84 322.0
7 TraesCS6D01G193000 chr6B 95.604 91 4 0 2786 2876 415731901 415731991 2.740000e-31 147.0
8 TraesCS6D01G193000 chr6B 100.000 37 0 0 535 571 415729511 415729547 6.110000e-08 69.4
9 TraesCS6D01G193000 chr5D 93.506 77 5 0 1211 1287 552784603 552784527 7.740000e-22 115.0
10 TraesCS6D01G193000 chr5B 93.506 77 5 0 1211 1287 697679891 697679967 7.740000e-22 115.0
11 TraesCS6D01G193000 chr5B 90.909 77 7 0 1211 1287 697778088 697778164 1.680000e-18 104.0
12 TraesCS6D01G193000 chr4A 92.208 77 6 0 1211 1287 615212962 615213038 3.600000e-20 110.0


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 TraesCS6D01G193000 chr6D 267199556 267202968 3412 False 6303.000000 6303 100.000000 1 3413 1 chr6D.!!$F1 3412
1 TraesCS6D01G193000 chr6A 380109364 380112598 3234 False 1633.666667 4351 90.804667 2 3302 3 chr6A.!!$F1 3300
2 TraesCS6D01G193000 chr6B 415729511 415732739 3228 False 896.480000 3485 95.930000 535 3413 5 chr6B.!!$F1 2878


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
933 995 0.796255 CCCTCTCCCTATCCATCCCT 59.204 60.000 0.0 0.0 0.0 4.20 F
934 996 1.153132 CCCTCTCCCTATCCATCCCTT 59.847 57.143 0.0 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2271 2333 1.304381 ACCCGGCATGCACATCTTT 60.304 52.632 21.36 0.0 0.0 2.52 R
2613 2675 4.060205 CAAGAGGAAAACAAAATGGCCAG 58.940 43.478 13.05 0.0 0.0 4.85 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
40 41 3.742369 GTGCCCAAAGAATGTTGTGAATG 59.258 43.478 0.00 0.00 0.00 2.67
43 44 4.813027 CCCAAAGAATGTTGTGAATGGAG 58.187 43.478 0.00 0.00 0.00 3.86
65 66 6.321435 GGAGCATAGCAAATAGGTTAGGTTTT 59.679 38.462 0.00 0.00 0.00 2.43
112 113 8.677300 TGCAGATTCAAGTCCTAAATTTATCAC 58.323 33.333 0.00 0.00 0.00 3.06
135 136 4.498009 CGAATGCTCGCCTTTTATTGGATT 60.498 41.667 0.00 0.00 38.45 3.01
136 137 5.343307 AATGCTCGCCTTTTATTGGATTT 57.657 34.783 0.00 0.00 0.00 2.17
137 138 6.463995 AATGCTCGCCTTTTATTGGATTTA 57.536 33.333 0.00 0.00 0.00 1.40
168 169 1.879380 CCTTTTGGTGATGTTCGCTCA 59.121 47.619 0.00 0.00 34.07 4.26
178 179 3.006217 TGATGTTCGCTCATAGGAGATGG 59.994 47.826 8.95 0.00 44.26 3.51
181 182 1.735920 CGCTCATAGGAGATGGCGC 60.736 63.158 8.95 0.00 44.26 6.53
206 207 6.296365 CATGTTGACTACAAGATGCCTATG 57.704 41.667 7.04 0.00 45.67 2.23
207 208 5.675684 TGTTGACTACAAGATGCCTATGA 57.324 39.130 0.00 0.00 36.64 2.15
208 209 6.239217 TGTTGACTACAAGATGCCTATGAT 57.761 37.500 0.00 0.00 36.64 2.45
209 210 6.051074 TGTTGACTACAAGATGCCTATGATG 58.949 40.000 0.00 0.00 36.64 3.07
210 211 6.127083 TGTTGACTACAAGATGCCTATGATGA 60.127 38.462 0.00 0.00 36.64 2.92
211 212 6.676990 TGACTACAAGATGCCTATGATGAT 57.323 37.500 0.00 0.00 0.00 2.45
212 213 7.071069 TGACTACAAGATGCCTATGATGATT 57.929 36.000 0.00 0.00 0.00 2.57
213 214 7.157347 TGACTACAAGATGCCTATGATGATTC 58.843 38.462 0.00 0.00 0.00 2.52
214 215 7.015974 TGACTACAAGATGCCTATGATGATTCT 59.984 37.037 0.00 0.00 0.00 2.40
215 216 8.427902 ACTACAAGATGCCTATGATGATTCTA 57.572 34.615 0.00 0.00 0.00 2.10
216 217 9.044646 ACTACAAGATGCCTATGATGATTCTAT 57.955 33.333 0.00 0.00 0.00 1.98
217 218 9.531942 CTACAAGATGCCTATGATGATTCTATC 57.468 37.037 0.00 0.00 0.00 2.08
218 219 7.914859 ACAAGATGCCTATGATGATTCTATCA 58.085 34.615 0.00 0.00 44.55 2.15
219 220 8.380867 ACAAGATGCCTATGATGATTCTATCAA 58.619 33.333 0.00 0.00 43.50 2.57
220 221 9.397280 CAAGATGCCTATGATGATTCTATCAAT 57.603 33.333 0.00 0.00 43.50 2.57
221 222 9.616156 AAGATGCCTATGATGATTCTATCAATC 57.384 33.333 0.00 0.00 43.50 2.67
222 223 8.212312 AGATGCCTATGATGATTCTATCAATCC 58.788 37.037 0.00 0.00 43.50 3.01
223 224 6.656902 TGCCTATGATGATTCTATCAATCCC 58.343 40.000 0.00 0.00 43.50 3.85
224 225 6.216046 TGCCTATGATGATTCTATCAATCCCA 59.784 38.462 0.00 0.00 43.50 4.37
225 226 7.092128 TGCCTATGATGATTCTATCAATCCCAT 60.092 37.037 0.00 0.00 43.50 4.00
226 227 7.228906 GCCTATGATGATTCTATCAATCCCATG 59.771 40.741 0.00 0.00 43.50 3.66
227 228 7.720074 CCTATGATGATTCTATCAATCCCATGG 59.280 40.741 4.14 4.14 43.50 3.66
228 229 6.458630 TGATGATTCTATCAATCCCATGGT 57.541 37.500 11.73 0.00 43.50 3.55
229 230 6.855667 TGATGATTCTATCAATCCCATGGTT 58.144 36.000 11.73 0.00 43.50 3.67
230 231 7.299896 TGATGATTCTATCAATCCCATGGTTT 58.700 34.615 11.73 0.74 43.50 3.27
231 232 6.964807 TGATTCTATCAATCCCATGGTTTG 57.035 37.500 11.73 13.92 36.11 2.93
232 233 5.302568 TGATTCTATCAATCCCATGGTTTGC 59.697 40.000 11.73 1.05 36.11 3.68
233 234 4.524802 TCTATCAATCCCATGGTTTGCT 57.475 40.909 11.73 8.41 33.73 3.91
234 235 4.209538 TCTATCAATCCCATGGTTTGCTG 58.790 43.478 11.73 7.70 33.73 4.41
235 236 1.559368 TCAATCCCATGGTTTGCTGG 58.441 50.000 11.73 0.00 33.73 4.85
325 327 4.985538 AAATGTCCGTGTTGGTGTAAAA 57.014 36.364 0.00 0.00 39.52 1.52
387 389 7.201145 GCTAGACTAATCCTACGAATGTCAAA 58.799 38.462 0.00 0.00 0.00 2.69
398 400 3.689649 ACGAATGTCAAAGATACCTTGGC 59.310 43.478 0.00 0.00 31.91 4.52
407 409 6.016276 GTCAAAGATACCTTGGCTTTTTGAGA 60.016 38.462 8.01 0.00 34.78 3.27
415 417 2.985896 TGGCTTTTTGAGAGATACCCG 58.014 47.619 0.00 0.00 0.00 5.28
438 440 5.523552 CGTGAAATACCATGATGAGTAAGCA 59.476 40.000 0.00 0.00 0.00 3.91
460 462 5.487433 CACCTGTGTCTGTACCATAATTCA 58.513 41.667 0.00 0.00 0.00 2.57
492 494 2.508891 CGAAGACACCGCGAGATGC 61.509 63.158 8.23 0.00 41.47 3.91
498 500 3.147595 ACCGCGAGATGCTGCCTA 61.148 61.111 8.23 0.00 43.27 3.93
499 501 2.106938 CCGCGAGATGCTGCCTAA 59.893 61.111 8.23 0.00 43.27 2.69
500 502 1.521457 CCGCGAGATGCTGCCTAAA 60.521 57.895 8.23 0.00 43.27 1.85
501 503 1.638467 CGCGAGATGCTGCCTAAAC 59.362 57.895 0.00 0.00 43.27 2.01
502 504 1.638467 GCGAGATGCTGCCTAAACG 59.362 57.895 0.00 0.00 41.73 3.60
503 505 1.084370 GCGAGATGCTGCCTAAACGT 61.084 55.000 0.00 0.00 41.73 3.99
504 506 1.801395 GCGAGATGCTGCCTAAACGTA 60.801 52.381 0.00 0.00 41.73 3.57
505 507 2.536365 CGAGATGCTGCCTAAACGTAA 58.464 47.619 0.00 0.00 0.00 3.18
506 508 2.927477 CGAGATGCTGCCTAAACGTAAA 59.073 45.455 0.00 0.00 0.00 2.01
507 509 3.241995 CGAGATGCTGCCTAAACGTAAAC 60.242 47.826 0.00 0.00 0.00 2.01
508 510 3.670625 AGATGCTGCCTAAACGTAAACA 58.329 40.909 0.00 0.00 0.00 2.83
509 511 3.684788 AGATGCTGCCTAAACGTAAACAG 59.315 43.478 0.00 0.00 0.00 3.16
510 512 2.841215 TGCTGCCTAAACGTAAACAGT 58.159 42.857 0.00 0.00 0.00 3.55
511 513 2.803956 TGCTGCCTAAACGTAAACAGTC 59.196 45.455 0.00 0.00 0.00 3.51
512 514 2.803956 GCTGCCTAAACGTAAACAGTCA 59.196 45.455 0.00 0.00 0.00 3.41
513 515 3.363673 GCTGCCTAAACGTAAACAGTCAC 60.364 47.826 0.00 0.00 0.00 3.67
514 516 4.056050 CTGCCTAAACGTAAACAGTCACT 58.944 43.478 0.00 0.00 0.00 3.41
515 517 4.444536 TGCCTAAACGTAAACAGTCACTT 58.555 39.130 0.00 0.00 0.00 3.16
516 518 5.599732 TGCCTAAACGTAAACAGTCACTTA 58.400 37.500 0.00 0.00 0.00 2.24
517 519 5.463061 TGCCTAAACGTAAACAGTCACTTAC 59.537 40.000 0.00 0.00 0.00 2.34
518 520 5.693555 GCCTAAACGTAAACAGTCACTTACT 59.306 40.000 0.00 0.00 39.81 2.24
519 521 6.128982 GCCTAAACGTAAACAGTCACTTACTC 60.129 42.308 0.00 0.00 35.76 2.59
520 522 6.919662 CCTAAACGTAAACAGTCACTTACTCA 59.080 38.462 0.00 0.00 35.76 3.41
521 523 6.579491 AAACGTAAACAGTCACTTACTCAC 57.421 37.500 0.00 0.00 35.76 3.51
522 524 5.511234 ACGTAAACAGTCACTTACTCACT 57.489 39.130 0.00 0.00 35.76 3.41
523 525 5.899299 ACGTAAACAGTCACTTACTCACTT 58.101 37.500 0.00 0.00 35.76 3.16
524 526 5.975939 ACGTAAACAGTCACTTACTCACTTC 59.024 40.000 0.00 0.00 35.76 3.01
525 527 5.401674 CGTAAACAGTCACTTACTCACTTCC 59.598 44.000 0.00 0.00 35.76 3.46
526 528 5.615925 AAACAGTCACTTACTCACTTCCT 57.384 39.130 0.00 0.00 35.76 3.36
527 529 5.615925 AACAGTCACTTACTCACTTCCTT 57.384 39.130 0.00 0.00 35.76 3.36
528 530 6.726490 AACAGTCACTTACTCACTTCCTTA 57.274 37.500 0.00 0.00 35.76 2.69
529 531 6.726490 ACAGTCACTTACTCACTTCCTTAA 57.274 37.500 0.00 0.00 35.76 1.85
530 532 7.120923 ACAGTCACTTACTCACTTCCTTAAA 57.879 36.000 0.00 0.00 35.76 1.52
531 533 7.210873 ACAGTCACTTACTCACTTCCTTAAAG 58.789 38.462 0.00 0.00 35.76 1.85
532 534 7.069578 ACAGTCACTTACTCACTTCCTTAAAGA 59.930 37.037 0.00 0.00 35.76 2.52
533 535 7.926555 CAGTCACTTACTCACTTCCTTAAAGAA 59.073 37.037 0.00 0.00 35.76 2.52
577 579 4.202264 ACTCCTCTAGAAAATATGCACCCG 60.202 45.833 0.00 0.00 0.00 5.28
933 995 0.796255 CCCTCTCCCTATCCATCCCT 59.204 60.000 0.00 0.00 0.00 4.20
934 996 1.153132 CCCTCTCCCTATCCATCCCTT 59.847 57.143 0.00 0.00 0.00 3.95
935 997 2.545810 CCTCTCCCTATCCATCCCTTC 58.454 57.143 0.00 0.00 0.00 3.46
936 998 2.545810 CTCTCCCTATCCATCCCTTCC 58.454 57.143 0.00 0.00 0.00 3.46
1950 2012 2.567049 GACCCAGTCGACCTCGTG 59.433 66.667 13.01 3.52 40.80 4.35
1977 2039 3.134127 GAGACCCGCAATGCCACC 61.134 66.667 0.00 0.00 0.00 4.61
2271 2333 0.904865 ACGACAAGGATGAGGAGGCA 60.905 55.000 0.00 0.00 0.00 4.75
2613 2675 2.668457 CTGTCGTTATGTCCTTGACTGC 59.332 50.000 0.00 0.00 33.15 4.40
2668 2730 8.963725 TGCTTGAAGATGATTCATTATTCTTGT 58.036 29.630 18.61 0.00 0.00 3.16
2721 2783 6.824305 TGGAGGTATACGGTTATAGCTTAC 57.176 41.667 0.00 4.58 45.20 2.34
2740 2802 6.148480 AGCTTACTTGTTTACTGCTTCAGATG 59.852 38.462 0.29 0.00 35.18 2.90
2843 3071 1.268625 CTGCAGCAATCATGTGTGTGT 59.731 47.619 0.00 0.00 0.00 3.72
2910 3152 5.631096 CGTGCTCATCATCGTAGTTCATATT 59.369 40.000 0.00 0.00 0.00 1.28
2912 3154 5.928264 TGCTCATCATCGTAGTTCATATTGG 59.072 40.000 0.00 0.00 0.00 3.16
2970 3373 1.078848 GCGTCTGCTCATCTGGGTT 60.079 57.895 0.00 0.00 38.39 4.11
3080 3487 4.383552 GGTCATCTCAACCTATGCACTTCT 60.384 45.833 0.00 0.00 33.78 2.85
3112 3519 0.998226 CTGTTGCGTGCATGTTTCCG 60.998 55.000 7.93 0.00 0.00 4.30
3113 3520 1.729131 GTTGCGTGCATGTTTCCGG 60.729 57.895 7.93 0.00 0.00 5.14
3172 3616 2.290367 TGTGTTCCAAAATGCAGACTCG 59.710 45.455 0.00 0.00 0.00 4.18
3266 3726 4.649267 TGAACTCCATTAACATCACCCA 57.351 40.909 0.00 0.00 0.00 4.51
3336 3796 6.919721 GGTCTAGCATTATAGAGAAGACCAG 58.080 44.000 12.51 0.00 46.94 4.00
3342 3802 5.295950 CATTATAGAGAAGACCAGCCACAG 58.704 45.833 0.00 0.00 0.00 3.66
3362 3822 2.503356 AGGTTCATGAAGCAGGGAGTAG 59.497 50.000 32.68 0.00 40.96 2.57
3374 3834 1.268283 GGGAGTAGCAGCTGGGAACT 61.268 60.000 17.12 6.32 0.00 3.01
3375 3835 1.486211 GGAGTAGCAGCTGGGAACTA 58.514 55.000 17.12 5.24 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.030185 GCACAAGAGGACGAACTCACTA 60.030 50.000 12.26 0.00 39.97 2.74
7 8 0.181587 TTTGGGCACAAGAGGACGAA 59.818 50.000 0.00 0.00 37.97 3.85
9 10 0.250295 TCTTTGGGCACAAGAGGACG 60.250 55.000 0.00 0.00 37.97 4.79
40 41 4.974399 ACCTAACCTATTTGCTATGCTCC 58.026 43.478 0.00 0.00 0.00 4.70
65 66 4.996122 GCATGGATTGGTTTCATCACAAAA 59.004 37.500 0.00 0.00 0.00 2.44
87 88 7.852945 CGTGATAAATTTAGGACTTGAATCTGC 59.147 37.037 3.94 0.00 0.00 4.26
137 138 9.178758 GAACATCACCAAAAGGTCTAGAATAAT 57.821 33.333 0.00 0.00 0.00 1.28
146 147 1.880027 AGCGAACATCACCAAAAGGTC 59.120 47.619 0.00 0.00 0.00 3.85
168 169 1.346062 ACATGAGCGCCATCTCCTAT 58.654 50.000 2.29 0.00 31.94 2.57
178 179 2.337583 TCTTGTAGTCAACATGAGCGC 58.662 47.619 0.00 0.00 37.35 5.92
181 182 4.511527 AGGCATCTTGTAGTCAACATGAG 58.488 43.478 0.00 0.00 43.29 2.90
202 203 8.272889 ACCATGGGATTGATAGAATCATCATAG 58.727 37.037 18.09 0.00 39.39 2.23
203 204 8.166479 ACCATGGGATTGATAGAATCATCATA 57.834 34.615 18.09 0.00 39.39 2.15
205 206 6.458630 ACCATGGGATTGATAGAATCATCA 57.541 37.500 18.09 0.00 39.39 3.07
206 207 7.600065 CAAACCATGGGATTGATAGAATCATC 58.400 38.462 21.74 0.00 37.62 2.92
207 208 6.014840 GCAAACCATGGGATTGATAGAATCAT 60.015 38.462 27.43 0.00 37.62 2.45
208 209 5.302568 GCAAACCATGGGATTGATAGAATCA 59.697 40.000 27.43 0.00 37.62 2.57
209 210 5.537674 AGCAAACCATGGGATTGATAGAATC 59.462 40.000 27.43 13.25 37.62 2.52
210 211 5.303589 CAGCAAACCATGGGATTGATAGAAT 59.696 40.000 27.43 9.44 37.62 2.40
211 212 4.646040 CAGCAAACCATGGGATTGATAGAA 59.354 41.667 27.43 0.00 37.62 2.10
212 213 4.209538 CAGCAAACCATGGGATTGATAGA 58.790 43.478 27.43 0.00 37.62 1.98
213 214 3.319972 CCAGCAAACCATGGGATTGATAG 59.680 47.826 27.43 15.93 37.62 2.08
214 215 3.298619 CCAGCAAACCATGGGATTGATA 58.701 45.455 27.43 0.00 37.62 2.15
215 216 2.112998 CCAGCAAACCATGGGATTGAT 58.887 47.619 27.43 21.70 37.62 2.57
216 217 1.203162 ACCAGCAAACCATGGGATTGA 60.203 47.619 27.43 0.00 37.62 2.57
217 218 1.269012 ACCAGCAAACCATGGGATTG 58.731 50.000 21.87 21.87 41.13 2.67
218 219 2.028561 AACCAGCAAACCATGGGATT 57.971 45.000 18.09 8.02 41.13 3.01
219 220 1.624813 CAAACCAGCAAACCATGGGAT 59.375 47.619 18.09 0.78 41.13 3.85
220 221 1.047002 CAAACCAGCAAACCATGGGA 58.953 50.000 18.09 0.00 41.13 4.37
221 222 0.035176 CCAAACCAGCAAACCATGGG 59.965 55.000 18.09 0.00 41.13 4.00
222 223 0.758123 ACCAAACCAGCAAACCATGG 59.242 50.000 11.19 11.19 42.60 3.66
223 224 1.688197 AGACCAAACCAGCAAACCATG 59.312 47.619 0.00 0.00 0.00 3.66
224 225 2.086610 AGACCAAACCAGCAAACCAT 57.913 45.000 0.00 0.00 0.00 3.55
225 226 1.859302 AAGACCAAACCAGCAAACCA 58.141 45.000 0.00 0.00 0.00 3.67
226 227 2.798145 CGAAAGACCAAACCAGCAAACC 60.798 50.000 0.00 0.00 0.00 3.27
227 228 2.098443 TCGAAAGACCAAACCAGCAAAC 59.902 45.455 0.00 0.00 33.31 2.93
228 229 2.370349 TCGAAAGACCAAACCAGCAAA 58.630 42.857 0.00 0.00 33.31 3.68
229 230 2.045561 TCGAAAGACCAAACCAGCAA 57.954 45.000 0.00 0.00 33.31 3.91
230 231 2.045561 TTCGAAAGACCAAACCAGCA 57.954 45.000 0.00 0.00 41.84 4.41
231 232 3.430333 TTTTCGAAAGACCAAACCAGC 57.570 42.857 10.98 0.00 41.84 4.85
232 233 3.735746 GCATTTTCGAAAGACCAAACCAG 59.264 43.478 10.98 0.00 41.84 4.00
233 234 3.383185 AGCATTTTCGAAAGACCAAACCA 59.617 39.130 10.98 0.00 41.84 3.67
234 235 3.977427 AGCATTTTCGAAAGACCAAACC 58.023 40.909 10.98 0.00 41.84 3.27
235 236 4.803613 ACAAGCATTTTCGAAAGACCAAAC 59.196 37.500 10.98 0.00 41.84 2.93
339 341 8.392372 AGCGAAATACAGTATAGACATAGACA 57.608 34.615 0.00 0.00 0.00 3.41
340 342 9.976255 CTAGCGAAATACAGTATAGACATAGAC 57.024 37.037 0.00 0.00 0.00 2.59
341 343 9.939802 TCTAGCGAAATACAGTATAGACATAGA 57.060 33.333 0.00 0.00 0.00 1.98
342 344 9.976255 GTCTAGCGAAATACAGTATAGACATAG 57.024 37.037 11.65 5.43 38.22 2.23
343 345 9.722184 AGTCTAGCGAAATACAGTATAGACATA 57.278 33.333 16.29 0.57 39.90 2.29
344 346 8.624367 AGTCTAGCGAAATACAGTATAGACAT 57.376 34.615 16.29 4.54 39.90 3.06
345 347 9.551734 TTAGTCTAGCGAAATACAGTATAGACA 57.448 33.333 16.29 5.15 39.90 3.41
348 350 9.991388 GGATTAGTCTAGCGAAATACAGTATAG 57.009 37.037 0.00 0.00 0.00 1.31
349 351 9.736414 AGGATTAGTCTAGCGAAATACAGTATA 57.264 33.333 0.00 0.00 0.00 1.47
350 352 8.638629 AGGATTAGTCTAGCGAAATACAGTAT 57.361 34.615 0.00 0.00 0.00 2.12
351 353 8.997323 GTAGGATTAGTCTAGCGAAATACAGTA 58.003 37.037 0.00 0.00 0.00 2.74
352 354 6.963083 AGGATTAGTCTAGCGAAATACAGT 57.037 37.500 0.00 0.00 0.00 3.55
353 355 7.016466 CGTAGGATTAGTCTAGCGAAATACAG 58.984 42.308 0.00 0.00 0.00 2.74
354 356 6.707608 TCGTAGGATTAGTCTAGCGAAATACA 59.292 38.462 0.00 0.00 0.00 2.29
355 357 7.126726 TCGTAGGATTAGTCTAGCGAAATAC 57.873 40.000 0.00 0.00 0.00 1.89
356 358 7.734924 TTCGTAGGATTAGTCTAGCGAAATA 57.265 36.000 0.00 0.00 32.80 1.40
357 359 6.630444 TTCGTAGGATTAGTCTAGCGAAAT 57.370 37.500 0.00 0.00 32.80 2.17
358 360 6.039047 ACATTCGTAGGATTAGTCTAGCGAAA 59.961 38.462 12.13 2.16 35.80 3.46
359 361 5.530171 ACATTCGTAGGATTAGTCTAGCGAA 59.470 40.000 11.13 11.13 36.17 4.70
360 362 5.061853 ACATTCGTAGGATTAGTCTAGCGA 58.938 41.667 0.00 0.00 0.00 4.93
361 363 5.049612 TGACATTCGTAGGATTAGTCTAGCG 60.050 44.000 11.26 0.00 0.00 4.26
362 364 6.315091 TGACATTCGTAGGATTAGTCTAGC 57.685 41.667 11.26 0.00 0.00 3.42
387 389 5.505181 TCTCTCAAAAAGCCAAGGTATCT 57.495 39.130 0.00 0.00 0.00 1.98
398 400 6.743575 ATTTCACGGGTATCTCTCAAAAAG 57.256 37.500 0.00 0.00 0.00 2.27
407 409 5.306937 TCATCATGGTATTTCACGGGTATCT 59.693 40.000 0.00 0.00 0.00 1.98
415 417 6.238484 GGTGCTTACTCATCATGGTATTTCAC 60.238 42.308 0.00 0.00 0.00 3.18
460 462 5.519722 GGTGTCTTCGACAATTGATTTTGT 58.480 37.500 13.59 0.00 44.49 2.83
492 494 4.056050 AGTGACTGTTTACGTTTAGGCAG 58.944 43.478 0.00 0.00 0.00 4.85
496 498 7.646922 AGTGAGTAAGTGACTGTTTACGTTTAG 59.353 37.037 0.00 0.00 39.06 1.85
498 500 6.335777 AGTGAGTAAGTGACTGTTTACGTTT 58.664 36.000 0.00 0.00 39.06 3.60
499 501 5.899299 AGTGAGTAAGTGACTGTTTACGTT 58.101 37.500 0.00 0.00 39.06 3.99
500 502 5.511234 AGTGAGTAAGTGACTGTTTACGT 57.489 39.130 0.00 0.00 39.06 3.57
501 503 5.401674 GGAAGTGAGTAAGTGACTGTTTACG 59.598 44.000 0.00 0.00 39.06 3.18
502 504 6.514063 AGGAAGTGAGTAAGTGACTGTTTAC 58.486 40.000 0.00 0.00 39.06 2.01
503 505 6.726490 AGGAAGTGAGTAAGTGACTGTTTA 57.274 37.500 0.00 0.00 39.06 2.01
504 506 5.615925 AGGAAGTGAGTAAGTGACTGTTT 57.384 39.130 0.00 0.00 39.06 2.83
505 507 5.615925 AAGGAAGTGAGTAAGTGACTGTT 57.384 39.130 0.00 0.00 39.06 3.16
506 508 6.726490 TTAAGGAAGTGAGTAAGTGACTGT 57.274 37.500 0.00 0.00 39.06 3.55
507 509 7.434492 TCTTTAAGGAAGTGAGTAAGTGACTG 58.566 38.462 0.00 0.00 36.15 3.51
508 510 7.598759 TCTTTAAGGAAGTGAGTAAGTGACT 57.401 36.000 0.00 0.00 37.61 3.41
509 511 8.658499 TTTCTTTAAGGAAGTGAGTAAGTGAC 57.342 34.615 0.00 0.00 36.70 3.67
510 512 9.326413 CTTTTCTTTAAGGAAGTGAGTAAGTGA 57.674 33.333 0.00 0.00 36.70 3.41
511 513 9.110502 ACTTTTCTTTAAGGAAGTGAGTAAGTG 57.889 33.333 10.36 0.00 36.70 3.16
520 522 6.930731 TGTTTGCACTTTTCTTTAAGGAAGT 58.069 32.000 0.00 8.19 36.70 3.01
521 523 7.035612 ACTGTTTGCACTTTTCTTTAAGGAAG 58.964 34.615 0.00 7.21 36.67 3.46
522 524 6.930731 ACTGTTTGCACTTTTCTTTAAGGAA 58.069 32.000 0.00 0.00 0.00 3.36
523 525 6.151985 TGACTGTTTGCACTTTTCTTTAAGGA 59.848 34.615 0.00 0.00 0.00 3.36
524 526 6.253512 GTGACTGTTTGCACTTTTCTTTAAGG 59.746 38.462 0.00 0.00 32.44 2.69
525 527 6.021468 CGTGACTGTTTGCACTTTTCTTTAAG 60.021 38.462 0.00 0.00 32.98 1.85
526 528 5.797934 CGTGACTGTTTGCACTTTTCTTTAA 59.202 36.000 0.00 0.00 32.98 1.52
527 529 5.328691 CGTGACTGTTTGCACTTTTCTTTA 58.671 37.500 0.00 0.00 32.98 1.85
528 530 4.165779 CGTGACTGTTTGCACTTTTCTTT 58.834 39.130 0.00 0.00 32.98 2.52
529 531 3.427503 CCGTGACTGTTTGCACTTTTCTT 60.428 43.478 0.00 0.00 32.98 2.52
530 532 2.097466 CCGTGACTGTTTGCACTTTTCT 59.903 45.455 0.00 0.00 32.98 2.52
531 533 2.159435 ACCGTGACTGTTTGCACTTTTC 60.159 45.455 0.00 0.00 32.98 2.29
532 534 1.816224 ACCGTGACTGTTTGCACTTTT 59.184 42.857 0.00 0.00 32.98 2.27
533 535 1.400494 GACCGTGACTGTTTGCACTTT 59.600 47.619 0.00 0.00 32.98 2.66
577 579 1.784283 CATTTCACGGGAAAACGCAAC 59.216 47.619 18.20 0.00 45.52 4.17
633 681 3.764466 CCGGCTCCACGCTCTCTT 61.764 66.667 0.00 0.00 39.13 2.85
649 697 1.581447 CTTGCCTTTCTGCCGTTCC 59.419 57.895 0.00 0.00 0.00 3.62
933 995 1.382695 GTCGGGGGAGAGGATGGAA 60.383 63.158 0.00 0.00 0.00 3.53
934 996 2.282446 GTCGGGGGAGAGGATGGA 59.718 66.667 0.00 0.00 0.00 3.41
935 997 2.844839 GGTCGGGGGAGAGGATGG 60.845 72.222 0.00 0.00 0.00 3.51
936 998 2.844839 GGGTCGGGGGAGAGGATG 60.845 72.222 0.00 0.00 0.00 3.51
985 1047 2.586245 CATGGAGGCGGCTTCTGA 59.414 61.111 19.35 0.00 0.00 3.27
986 1048 2.515523 CCATGGAGGCGGCTTCTG 60.516 66.667 19.35 13.37 0.00 3.02
1359 1421 1.286501 CGGTGTTGATGGTGATACCG 58.713 55.000 0.00 0.00 42.58 4.02
1950 2012 3.866582 CGGGTCTCCCTGATGCCC 61.867 72.222 3.25 0.00 42.67 5.36
1977 2039 2.154854 ACATCTCAACACCAGTGACG 57.845 50.000 4.48 0.00 0.00 4.35
2271 2333 1.304381 ACCCGGCATGCACATCTTT 60.304 52.632 21.36 0.00 0.00 2.52
2613 2675 4.060205 CAAGAGGAAAACAAAATGGCCAG 58.940 43.478 13.05 0.00 0.00 4.85
2721 2783 6.093219 AGCATACATCTGAAGCAGTAAACAAG 59.907 38.462 0.00 0.00 32.61 3.16
2740 2802 7.256756 AGATAAATCTGTCAAGCAAGCATAC 57.743 36.000 0.00 0.00 35.42 2.39
2780 2854 9.294030 GCTGAAAATCAATATGAACTACCAAAG 57.706 33.333 0.00 0.00 0.00 2.77
2843 3071 8.266392 ACTGTTTTTGCATTGAAAAAGATGAA 57.734 26.923 12.33 0.00 35.89 2.57
2896 3138 6.823689 AGCAGAAAACCAATATGAACTACGAT 59.176 34.615 0.00 0.00 0.00 3.73
2897 3139 6.092122 CAGCAGAAAACCAATATGAACTACGA 59.908 38.462 0.00 0.00 0.00 3.43
2898 3140 6.250819 CAGCAGAAAACCAATATGAACTACG 58.749 40.000 0.00 0.00 0.00 3.51
3080 3487 5.123027 TGCACGCAACAGATTGTTATGATTA 59.877 36.000 0.00 0.00 38.77 1.75
3172 3616 5.049405 CACCACAAGACAGGTACAAAAGATC 60.049 44.000 0.00 0.00 36.07 2.75
3266 3726 7.334421 CAGCATGTTACTCCACTATAAAACACT 59.666 37.037 0.00 0.00 30.40 3.55
3321 3781 3.706594 CCTGTGGCTGGTCTTCTCTATAA 59.293 47.826 0.00 0.00 0.00 0.98
3336 3796 0.524862 CTGCTTCATGAACCTGTGGC 59.475 55.000 3.38 6.11 0.00 5.01
3342 3802 2.911484 CTACTCCCTGCTTCATGAACC 58.089 52.381 3.38 0.00 0.00 3.62
3362 3822 1.079503 CGACTTTAGTTCCCAGCTGC 58.920 55.000 8.66 0.00 0.00 5.25
3374 3834 6.147164 CACCTTACAATTCTTGAGCGACTTTA 59.853 38.462 0.00 0.00 0.00 1.85
3375 3835 5.049405 CACCTTACAATTCTTGAGCGACTTT 60.049 40.000 0.00 0.00 0.00 2.66



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

AutoCloner maintained by Alex Coulton.