Multiple sequence alignment - TraesCS5B01G139100

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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 TraesCS5B01G139100 chr5B 100.000 4106 0 0 1 4106 262821274 262825379 0.000000e+00 7583
1 TraesCS5B01G139100 chr5A 94.493 1725 64 13 1 1705 312918336 312920049 0.000000e+00 2630
2 TraesCS5B01G139100 chr5A 96.805 1064 26 2 2076 3131 312920513 312921576 0.000000e+00 1770
3 TraesCS5B01G139100 chr5A 96.667 780 21 2 3329 4106 312921572 312922348 0.000000e+00 1291
4 TraesCS5B01G139100 chr5A 95.664 369 15 1 1711 2078 312920112 312920480 3.530000e-165 592
5 TraesCS5B01G139100 chr5D 93.975 1726 77 13 1 1705 240851469 240849750 0.000000e+00 2586
6 TraesCS5B01G139100 chr5D 97.547 1060 22 2 2076 3131 240849286 240848227 0.000000e+00 1810
7 TraesCS5B01G139100 chr5D 97.436 780 15 3 3329 4106 240848231 240847455 0.000000e+00 1325
8 TraesCS5B01G139100 chr5D 94.580 369 19 1 1711 2078 240849687 240849319 1.660000e-158 569
9 TraesCS5B01G139100 chr5D 91.866 209 12 3 3125 3332 530795039 530794835 1.870000e-73 287
10 TraesCS5B01G139100 chr3B 99.512 205 1 0 3128 3332 518618200 518618404 1.390000e-99 374
11 TraesCS5B01G139100 chr2B 95.431 197 8 1 3132 3327 569130983 569130787 3.080000e-81 313
12 TraesCS5B01G139100 chr2B 93.023 215 11 4 3125 3337 438929387 438929175 1.110000e-80 311
13 TraesCS5B01G139100 chr4D 94.388 196 10 1 3132 3326 470124421 470124616 2.400000e-77 300
14 TraesCS5B01G139100 chr4D 82.128 235 39 3 1717 1949 417623140 417622907 9.000000e-47 198
15 TraesCS5B01G139100 chr2D 93.532 201 12 1 3131 3330 82890012 82889812 8.630000e-77 298
16 TraesCS5B01G139100 chr1D 92.754 207 14 1 3126 3331 459178276 459178482 8.630000e-77 298
17 TraesCS5B01G139100 chr1D 81.780 236 30 10 1723 1951 282290847 282290618 7.010000e-43 185
18 TraesCS5B01G139100 chr7B 93.500 200 12 1 3132 3330 554524156 554524355 3.100000e-76 296
19 TraesCS5B01G139100 chr7B 80.417 240 41 5 1718 1953 702171848 702171611 1.170000e-40 178
20 TraesCS5B01G139100 chr6A 92.308 208 14 2 3132 3337 1763104 1763311 1.120000e-75 294
21 TraesCS5B01G139100 chr4B 85.135 222 29 4 1723 1942 82417414 82417633 1.490000e-54 224
22 TraesCS5B01G139100 chr4B 79.237 236 39 10 1718 1948 395663362 395663592 5.500000e-34 156
23 TraesCS5B01G139100 chr1B 84.000 225 29 7 1733 1951 383801419 383801196 4.160000e-50 209
24 TraesCS5B01G139100 chr7D 84.940 166 21 4 1789 1951 400447858 400447694 9.130000e-37 165


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 TraesCS5B01G139100 chr5B 262821274 262825379 4105 False 7583.00 7583 100.00000 1 4106 1 chr5B.!!$F1 4105
1 TraesCS5B01G139100 chr5A 312918336 312922348 4012 False 1570.75 2630 95.90725 1 4106 4 chr5A.!!$F1 4105
2 TraesCS5B01G139100 chr5D 240847455 240851469 4014 True 1572.50 2586 95.88450 1 4106 4 chr5D.!!$R2 4105

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
563 566 1.371635 CAAACGGCCGGAGCAAAAG 60.372 57.895 31.76 6.14 42.56 2.27 F
1455 1475 0.036010 CCTCATCTGCCAGGTTCGTT 60.036 55.000 0.00 0.00 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1708 1728 0.107703 CCGAGGTGGTACATGCATGT 60.108 55.0 33.20 33.20 44.52 3.21 R
3301 3423 0.102120 TGGTTCGCTGCCAAAGTTTG 59.898 50.0 8.73 8.73 32.29 2.93 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 3.565482 GTGTGATCAGTCCACAAATGTGT 59.435 43.478 12.21 0.00 44.91 3.72
30 31 2.849942 TCAGTCCACAAATGTGTCAGG 58.150 47.619 12.21 0.00 44.21 3.86
137 138 6.801539 TCGAGCATAACTGAAACAAGATTT 57.198 33.333 0.00 0.00 0.00 2.17
142 143 7.715657 AGCATAACTGAAACAAGATTTGACAA 58.284 30.769 0.00 0.00 0.00 3.18
192 193 2.254546 TGCCTAGGAAATGTATGCGG 57.745 50.000 14.75 0.00 0.00 5.69
199 200 1.476488 GGAAATGTATGCGGGTTTGCT 59.524 47.619 0.00 0.00 35.36 3.91
266 267 2.214387 AAAGCAAAACAGAGCACAGC 57.786 45.000 0.00 0.00 0.00 4.40
297 298 9.753674 TCTAGAAAATGGGACTACATTGATTTT 57.246 29.630 0.00 0.00 40.71 1.82
301 302 8.831715 AAAATGGGACTACATTGATTTTCAAC 57.168 30.769 0.00 0.00 39.45 3.18
310 311 6.790285 ACATTGATTTTCAACAATTCTGCC 57.210 33.333 0.00 0.00 39.45 4.85
563 566 1.371635 CAAACGGCCGGAGCAAAAG 60.372 57.895 31.76 6.14 42.56 2.27
599 603 3.784573 CGGAGCTAGGGATCAGGG 58.215 66.667 0.00 0.00 0.00 4.45
607 611 2.426561 GCTAGGGATCAGGGGAGTACTT 60.427 54.545 0.00 0.00 0.00 2.24
684 688 2.126850 CGCGTCTTCGTCAGCAGA 60.127 61.111 0.00 0.00 39.49 4.26
717 721 1.517257 CGACATCTCGCCTCCACAC 60.517 63.158 0.00 0.00 31.91 3.82
851 858 2.566111 TAAATGGGCCGGGCTGAAGG 62.566 60.000 28.80 0.00 0.00 3.46
919 928 5.249780 TGAGCCCAGGTTTAGTTTATTCA 57.750 39.130 0.00 0.00 0.00 2.57
932 943 8.515414 GTTTAGTTTATTCATTCACTGCCTCTT 58.485 33.333 0.00 0.00 0.00 2.85
1069 1080 4.020617 CTCCGAGGCCCACTGCAA 62.021 66.667 0.00 0.00 43.89 4.08
1088 1099 4.168291 GGGCCGCTTCCTCTCCAG 62.168 72.222 0.00 0.00 0.00 3.86
1097 1108 2.757508 CCTCTCCAGCTCCGCTCA 60.758 66.667 0.00 0.00 36.40 4.26
1290 1310 3.264450 GGACCTCTTCTTCATTCCTTGGA 59.736 47.826 0.00 0.00 0.00 3.53
1455 1475 0.036010 CCTCATCTGCCAGGTTCGTT 60.036 55.000 0.00 0.00 0.00 3.85
1522 1542 1.090052 GCAGCATGGGTTCGGTAGTC 61.090 60.000 0.00 0.00 35.86 2.59
1525 1545 0.804933 GCATGGGTTCGGTAGTCGTC 60.805 60.000 0.00 0.00 40.32 4.20
1546 1566 1.173913 GTTGGTTAATTGCCGAGCCT 58.826 50.000 0.00 0.00 0.00 4.58
1552 1572 1.173043 TAATTGCCGAGCCTTGGTTG 58.827 50.000 0.00 0.00 0.00 3.77
1559 1579 1.678728 CCGAGCCTTGGTTGCAAGATA 60.679 52.381 0.00 0.00 34.26 1.98
1586 1606 4.823989 CCTCTTGTTCAGTTCTGTTTGGAT 59.176 41.667 0.00 0.00 0.00 3.41
1596 1616 6.706270 TCAGTTCTGTTTGGATCTTCTTGTAC 59.294 38.462 0.00 0.00 0.00 2.90
1668 1688 9.409312 CAGTCAATGTAATATTGCACAAGAAAA 57.591 29.630 8.50 0.00 0.00 2.29
1739 1817 1.134491 CCACCTCGGTCCAGGTTTATC 60.134 57.143 9.57 0.00 45.24 1.75
1951 2030 1.864669 ATAAACCCGGACGGAGGTAA 58.135 50.000 13.13 0.00 34.45 2.85
1978 2057 3.627395 TGTAGTCTGGTAATGGCAAGG 57.373 47.619 0.00 0.00 0.00 3.61
1979 2058 2.238646 TGTAGTCTGGTAATGGCAAGGG 59.761 50.000 0.00 0.00 0.00 3.95
2119 2233 6.262496 AGTTTAGCACTAAAGAGAAAACCCAC 59.738 38.462 3.12 0.00 35.90 4.61
2168 2282 3.193479 TGTAAGTCTGATCATGCACGAGT 59.807 43.478 0.00 0.00 0.00 4.18
2226 2343 3.421826 CGAGCAGACGTGTAATTGACAAC 60.422 47.826 0.00 0.00 40.66 3.32
3075 3197 4.793216 GCATGGAACGTGATTTTGTCATAC 59.207 41.667 0.00 0.00 39.48 2.39
3105 3227 5.300034 TCATAAGAAGGTTATCGCGGAGTAA 59.700 40.000 6.13 0.49 0.00 2.24
3135 3257 9.732130 AATAGGTAATCTTCAAATCTATGAGCC 57.268 33.333 0.00 0.00 0.00 4.70
3136 3258 7.385894 AGGTAATCTTCAAATCTATGAGCCT 57.614 36.000 0.00 0.00 0.00 4.58
3137 3259 8.497910 AGGTAATCTTCAAATCTATGAGCCTA 57.502 34.615 0.00 0.00 0.00 3.93
3138 3260 8.938883 AGGTAATCTTCAAATCTATGAGCCTAA 58.061 33.333 0.00 0.00 0.00 2.69
3139 3261 9.732130 GGTAATCTTCAAATCTATGAGCCTAAT 57.268 33.333 0.00 0.00 0.00 1.73
3142 3264 8.632906 ATCTTCAAATCTATGAGCCTAATTGG 57.367 34.615 0.00 0.00 39.35 3.16
3143 3265 7.577303 TCTTCAAATCTATGAGCCTAATTGGT 58.423 34.615 0.00 0.00 38.35 3.67
3144 3266 8.055181 TCTTCAAATCTATGAGCCTAATTGGTT 58.945 33.333 0.00 0.00 38.35 3.67
3145 3267 8.593945 TTCAAATCTATGAGCCTAATTGGTTT 57.406 30.769 0.00 0.00 38.35 3.27
3146 3268 7.999679 TCAAATCTATGAGCCTAATTGGTTTG 58.000 34.615 3.57 3.57 34.33 2.93
3147 3269 6.966534 AATCTATGAGCCTAATTGGTTTGG 57.033 37.500 0.00 0.00 38.35 3.28
3148 3270 5.450818 TCTATGAGCCTAATTGGTTTGGT 57.549 39.130 0.00 0.00 38.35 3.67
3149 3271 5.192927 TCTATGAGCCTAATTGGTTTGGTG 58.807 41.667 0.00 0.00 38.35 4.17
3150 3272 1.892474 TGAGCCTAATTGGTTTGGTGC 59.108 47.619 0.00 0.00 38.35 5.01
3151 3273 1.204704 GAGCCTAATTGGTTTGGTGCC 59.795 52.381 0.00 0.00 38.35 5.01
3152 3274 0.972883 GCCTAATTGGTTTGGTGCCA 59.027 50.000 0.00 0.00 38.35 4.92
3190 3312 8.730970 CCAATTGTTGGCAAATCTAAAATTTG 57.269 30.769 0.00 6.21 45.17 2.32
3191 3313 7.808856 CCAATTGTTGGCAAATCTAAAATTTGG 59.191 33.333 0.00 3.48 45.17 3.28
3196 3318 4.926860 GCAAATCTAAAATTTGGCGCTT 57.073 36.364 7.64 0.00 38.91 4.68
3198 3320 6.401955 GCAAATCTAAAATTTGGCGCTTAA 57.598 33.333 7.64 1.72 38.91 1.85
3199 3321 7.003939 GCAAATCTAAAATTTGGCGCTTAAT 57.996 32.000 7.64 4.41 38.91 1.40
3200 3322 7.463544 GCAAATCTAAAATTTGGCGCTTAATT 58.536 30.769 7.64 10.74 38.91 1.40
3201 3323 7.426169 GCAAATCTAAAATTTGGCGCTTAATTG 59.574 33.333 16.89 9.26 38.91 2.32
3202 3324 7.538303 AATCTAAAATTTGGCGCTTAATTGG 57.462 32.000 16.89 11.90 0.00 3.16
3203 3325 6.031751 TCTAAAATTTGGCGCTTAATTGGT 57.968 33.333 16.89 12.15 0.00 3.67
3204 3326 6.459923 TCTAAAATTTGGCGCTTAATTGGTT 58.540 32.000 16.89 12.36 0.00 3.67
3205 3327 6.931840 TCTAAAATTTGGCGCTTAATTGGTTT 59.068 30.769 16.89 11.86 0.00 3.27
3206 3328 5.355467 AAATTTGGCGCTTAATTGGTTTG 57.645 34.783 16.89 0.00 0.00 2.93
3207 3329 1.789506 TTGGCGCTTAATTGGTTTGC 58.210 45.000 7.64 0.00 0.00 3.68
3208 3330 0.965439 TGGCGCTTAATTGGTTTGCT 59.035 45.000 7.64 0.00 0.00 3.91
3209 3331 2.163509 TGGCGCTTAATTGGTTTGCTA 58.836 42.857 7.64 0.00 0.00 3.49
3210 3332 2.094957 TGGCGCTTAATTGGTTTGCTAC 60.095 45.455 7.64 0.00 0.00 3.58
3228 3350 3.912899 CCAATTGGTTCTTGCCCAC 57.087 52.632 16.90 0.00 0.00 4.61
3229 3351 0.321346 CCAATTGGTTCTTGCCCACC 59.679 55.000 16.90 0.00 0.00 4.61
3230 3352 1.341080 CAATTGGTTCTTGCCCACCT 58.659 50.000 0.00 0.00 33.76 4.00
3231 3353 2.524306 CAATTGGTTCTTGCCCACCTA 58.476 47.619 0.00 0.00 33.76 3.08
3232 3354 3.099141 CAATTGGTTCTTGCCCACCTAT 58.901 45.455 0.00 0.00 33.76 2.57
3233 3355 2.507407 TTGGTTCTTGCCCACCTATC 57.493 50.000 0.00 0.00 33.76 2.08
3234 3356 1.367346 TGGTTCTTGCCCACCTATCA 58.633 50.000 0.00 0.00 33.76 2.15
3235 3357 1.707989 TGGTTCTTGCCCACCTATCAA 59.292 47.619 0.00 0.00 33.76 2.57
3236 3358 2.109128 TGGTTCTTGCCCACCTATCAAA 59.891 45.455 0.00 0.00 33.76 2.69
3237 3359 3.161866 GGTTCTTGCCCACCTATCAAAA 58.838 45.455 0.00 0.00 0.00 2.44
3238 3360 3.576550 GGTTCTTGCCCACCTATCAAAAA 59.423 43.478 0.00 0.00 0.00 1.94
3239 3361 4.222810 GGTTCTTGCCCACCTATCAAAAAT 59.777 41.667 0.00 0.00 0.00 1.82
3240 3362 5.279960 GGTTCTTGCCCACCTATCAAAAATT 60.280 40.000 0.00 0.00 0.00 1.82
3241 3363 6.230472 GTTCTTGCCCACCTATCAAAAATTT 58.770 36.000 0.00 0.00 0.00 1.82
3242 3364 5.792741 TCTTGCCCACCTATCAAAAATTTG 58.207 37.500 0.00 0.00 39.48 2.32
3243 3365 3.936564 TGCCCACCTATCAAAAATTTGC 58.063 40.909 0.98 0.00 38.05 3.68
3244 3366 3.270027 GCCCACCTATCAAAAATTTGCC 58.730 45.455 0.98 0.00 38.05 4.52
3245 3367 3.307339 GCCCACCTATCAAAAATTTGCCA 60.307 43.478 0.98 0.00 38.05 4.92
3246 3368 4.805609 GCCCACCTATCAAAAATTTGCCAA 60.806 41.667 0.98 0.00 38.05 4.52
3247 3369 5.499313 CCCACCTATCAAAAATTTGCCAAT 58.501 37.500 0.98 0.00 38.05 3.16
3248 3370 5.945191 CCCACCTATCAAAAATTTGCCAATT 59.055 36.000 0.98 0.00 38.05 2.32
3249 3371 6.433716 CCCACCTATCAAAAATTTGCCAATTT 59.566 34.615 2.76 2.76 43.29 1.82
3268 3390 7.896894 CCAATTTTTGGCAACTTTTGATTTTG 58.103 30.769 0.00 0.00 45.17 2.44
3269 3391 7.392556 CAATTTTTGGCAACTTTTGATTTTGC 58.607 30.769 0.00 0.00 44.05 3.68
3276 3398 5.580661 GCAACTTTTGATTTTGCCAAATGT 58.419 33.333 0.00 0.00 40.94 2.71
3277 3399 6.035217 GCAACTTTTGATTTTGCCAAATGTT 58.965 32.000 0.00 5.81 44.92 2.71
3287 3409 3.702147 CCAAATGTTGGCTTGCCAA 57.298 47.368 21.59 21.59 45.17 4.52
3288 3410 1.964552 CCAAATGTTGGCTTGCCAAA 58.035 45.000 26.12 17.09 45.17 3.28
3289 3411 2.506444 CCAAATGTTGGCTTGCCAAAT 58.494 42.857 26.12 18.32 45.17 2.32
3290 3412 3.672808 CCAAATGTTGGCTTGCCAAATA 58.327 40.909 26.12 18.73 45.17 1.40
3291 3413 4.263435 CCAAATGTTGGCTTGCCAAATAT 58.737 39.130 26.12 19.92 45.17 1.28
3292 3414 4.701171 CCAAATGTTGGCTTGCCAAATATT 59.299 37.500 26.12 23.52 45.17 1.28
3293 3415 5.392165 CCAAATGTTGGCTTGCCAAATATTG 60.392 40.000 26.12 25.13 45.17 1.90
3318 3440 2.885502 CCAAACTTTGGCAGCGAAC 58.114 52.632 7.63 0.00 45.17 3.95
3319 3441 0.597377 CCAAACTTTGGCAGCGAACC 60.597 55.000 7.63 0.00 45.17 3.62
3320 3442 0.102120 CAAACTTTGGCAGCGAACCA 59.898 50.000 0.00 0.00 34.65 3.67
3321 3443 0.820871 AAACTTTGGCAGCGAACCAA 59.179 45.000 4.28 4.28 45.37 3.67
3322 3444 1.039856 AACTTTGGCAGCGAACCAAT 58.960 45.000 8.64 0.00 46.25 3.16
3323 3445 1.039856 ACTTTGGCAGCGAACCAATT 58.960 45.000 8.64 0.00 46.25 2.32
3324 3446 2.235016 ACTTTGGCAGCGAACCAATTA 58.765 42.857 8.64 0.00 46.25 1.40
3325 3447 2.228822 ACTTTGGCAGCGAACCAATTAG 59.771 45.455 8.64 7.12 46.25 1.73
3326 3448 0.525761 TTGGCAGCGAACCAATTAGC 59.474 50.000 4.28 0.00 42.23 3.09
3327 3449 1.312371 TGGCAGCGAACCAATTAGCC 61.312 55.000 0.00 0.00 37.16 3.93
3328 3450 1.032114 GGCAGCGAACCAATTAGCCT 61.032 55.000 0.00 0.00 37.16 4.58
3329 3451 0.378610 GCAGCGAACCAATTAGCCTC 59.621 55.000 0.00 0.00 37.16 4.70
3330 3452 2.014068 GCAGCGAACCAATTAGCCTCT 61.014 52.381 0.00 0.00 37.16 3.69
3331 3453 2.741878 GCAGCGAACCAATTAGCCTCTA 60.742 50.000 0.00 0.00 37.16 2.43
3332 3454 3.733337 CAGCGAACCAATTAGCCTCTAT 58.267 45.455 0.00 0.00 37.16 1.98
3374 3496 4.202202 CCTGCCTATAGTTCTTCAGTCCTG 60.202 50.000 0.00 0.00 0.00 3.86
3477 3600 4.737855 TGTCTGCCTACTATTTCCAGTC 57.262 45.455 0.00 0.00 0.00 3.51
3726 3849 4.044426 CCAAGACTTTACTGCTTTGTTGC 58.956 43.478 0.00 0.00 0.00 4.17
4023 4146 4.635223 TGATCTTCACAAAGTCAGACCTG 58.365 43.478 0.00 0.00 33.95 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 1.351017 CTGCCCTACCTTTTCACCTGA 59.649 52.381 0.00 0.00 0.00 3.86
30 31 2.861147 ACTCTGCCCTACCTTTTCAC 57.139 50.000 0.00 0.00 0.00 3.18
108 109 5.185454 TGTTTCAGTTATGCTCGATCCAAT 58.815 37.500 0.00 0.00 0.00 3.16
160 161 4.634012 TCCTAGGCAAGCTTCAAACTAA 57.366 40.909 2.96 0.00 0.00 2.24
161 162 4.634012 TTCCTAGGCAAGCTTCAAACTA 57.366 40.909 2.96 0.00 0.00 2.24
266 267 3.810310 AGTCCCATTTTCTAGAGCGAG 57.190 47.619 0.00 0.00 0.00 5.03
297 298 5.771666 AGATGAAAGAAGGCAGAATTGTTGA 59.228 36.000 0.00 0.00 0.00 3.18
342 343 8.671384 ATGATTGCATTTCCTTTATCATTTGG 57.329 30.769 1.30 0.00 30.76 3.28
412 413 6.306643 TGGTATTGTCCACAACATCATCTA 57.693 37.500 0.00 0.00 38.86 1.98
563 566 0.032815 GCCTCTCCACTTCCGCTATC 59.967 60.000 0.00 0.00 0.00 2.08
596 600 2.162264 GGAGCAGTAAGTACTCCCCT 57.838 55.000 0.00 0.00 43.54 4.79
607 611 0.543277 CTCAAGGCCATGGAGCAGTA 59.457 55.000 18.40 0.00 0.00 2.74
684 688 1.299165 GTCGTACATGCGAGGCGAT 60.299 57.895 0.00 0.00 41.85 4.58
932 943 5.010282 GGTTCTAGAAAATTCCAGAGCCAA 58.990 41.667 15.76 0.00 42.66 4.52
1455 1475 2.354510 GCAACTAATAGCGTTGGCATCA 59.645 45.455 5.23 0.00 41.45 3.07
1522 1542 1.801771 TCGGCAATTAACCAACTGACG 59.198 47.619 0.00 0.00 41.73 4.35
1525 1545 1.135402 GGCTCGGCAATTAACCAACTG 60.135 52.381 0.00 0.00 0.00 3.16
1546 1566 2.301870 AGAGGTCGTATCTTGCAACCAA 59.698 45.455 0.00 0.00 32.25 3.67
1559 1579 2.431057 ACAGAACTGAACAAGAGGTCGT 59.569 45.455 8.87 0.00 0.00 4.34
1586 1606 8.475639 GGGTAATCATTCACTAGTACAAGAAGA 58.524 37.037 0.00 0.00 0.00 2.87
1596 1616 4.771114 TGGTGGGGTAATCATTCACTAG 57.229 45.455 0.00 0.00 0.00 2.57
1668 1688 6.370994 CAGCATGTCTAACATTCAGACTCTTT 59.629 38.462 4.32 0.00 42.43 2.52
1702 1722 3.263170 AGGTGGTACATGCATGTGACTAA 59.737 43.478 36.72 17.91 44.52 2.24
1704 1724 1.630369 AGGTGGTACATGCATGTGACT 59.370 47.619 36.72 23.96 44.52 3.41
1705 1725 2.009774 GAGGTGGTACATGCATGTGAC 58.990 52.381 36.72 28.46 44.52 3.67
1707 1727 1.009078 CGAGGTGGTACATGCATGTG 58.991 55.000 36.72 17.26 44.52 3.21
1708 1728 0.107703 CCGAGGTGGTACATGCATGT 60.108 55.000 33.20 33.20 44.52 3.21
1709 1729 2.694065 CCGAGGTGGTACATGCATG 58.306 57.895 25.09 25.09 44.52 4.06
1731 1809 1.400530 CGAGGAGGCCCGATAAACCT 61.401 60.000 0.00 0.00 37.58 3.50
1739 1817 0.177141 TCAAAATACGAGGAGGCCCG 59.823 55.000 0.00 0.00 37.58 6.13
1951 2030 5.069914 TGCCATTACCAGACTACATTACGAT 59.930 40.000 0.00 0.00 0.00 3.73
1978 2057 8.579863 CCATTCTTGAATGAATAATAGTTCCCC 58.420 37.037 20.95 0.00 35.18 4.81
1979 2058 9.354673 TCCATTCTTGAATGAATAATAGTTCCC 57.645 33.333 20.95 0.00 35.18 3.97
2103 2217 6.265577 CACAAAGTGTGGGTTTTCTCTTTAG 58.734 40.000 0.25 0.00 44.27 1.85
2119 2233 1.000233 GCATCACGCAGCACAAAGTG 61.000 55.000 0.00 0.00 41.79 3.16
2168 2282 6.884295 CACATCAAAACTAAGAAGGGATGGTA 59.116 38.462 0.00 0.00 36.02 3.25
2404 2521 9.374838 GAGGCAAATTATCAATCAAACAAGAAT 57.625 29.630 0.00 0.00 0.00 2.40
2405 2522 7.818930 GGAGGCAAATTATCAATCAAACAAGAA 59.181 33.333 0.00 0.00 0.00 2.52
3075 3197 5.557136 CGCGATAACCTTCTTATGAGCTTTG 60.557 44.000 0.00 0.00 0.00 2.77
3131 3253 1.204704 GGCACCAAACCAATTAGGCTC 59.795 52.381 0.00 0.00 43.14 4.70
3132 3254 1.266178 GGCACCAAACCAATTAGGCT 58.734 50.000 0.00 0.00 43.14 4.58
3133 3255 0.972883 TGGCACCAAACCAATTAGGC 59.027 50.000 0.00 0.00 43.14 3.93
3140 3262 3.692257 CCAATTATTGGCACCAAACCA 57.308 42.857 11.33 0.00 45.17 3.67
3166 3288 7.326547 GCCAAATTTTAGATTTGCCAACAATTG 59.673 33.333 3.24 3.24 37.60 2.32
3167 3289 7.369607 GCCAAATTTTAGATTTGCCAACAATT 58.630 30.769 3.07 0.00 37.60 2.32
3168 3290 6.348376 CGCCAAATTTTAGATTTGCCAACAAT 60.348 34.615 3.07 0.00 37.60 2.71
3169 3291 5.049818 CGCCAAATTTTAGATTTGCCAACAA 60.050 36.000 3.07 0.00 37.60 2.83
3170 3292 4.450419 CGCCAAATTTTAGATTTGCCAACA 59.550 37.500 3.07 0.00 37.60 3.33
3171 3293 4.668941 GCGCCAAATTTTAGATTTGCCAAC 60.669 41.667 0.00 0.00 37.60 3.77
3172 3294 3.434984 GCGCCAAATTTTAGATTTGCCAA 59.565 39.130 0.00 0.00 37.60 4.52
3173 3295 2.999355 GCGCCAAATTTTAGATTTGCCA 59.001 40.909 0.00 0.00 37.60 4.92
3174 3296 3.261580 AGCGCCAAATTTTAGATTTGCC 58.738 40.909 2.29 0.00 37.60 4.52
3175 3297 4.926860 AAGCGCCAAATTTTAGATTTGC 57.073 36.364 2.29 0.00 37.60 3.68
3176 3298 7.904461 CCAATTAAGCGCCAAATTTTAGATTTG 59.096 33.333 13.27 1.75 38.39 2.32
3177 3299 7.606073 ACCAATTAAGCGCCAAATTTTAGATTT 59.394 29.630 13.27 0.00 0.00 2.17
3178 3300 7.102993 ACCAATTAAGCGCCAAATTTTAGATT 58.897 30.769 13.27 0.00 0.00 2.40
3179 3301 6.639563 ACCAATTAAGCGCCAAATTTTAGAT 58.360 32.000 13.27 0.00 0.00 1.98
3180 3302 6.031751 ACCAATTAAGCGCCAAATTTTAGA 57.968 33.333 13.27 0.00 0.00 2.10
3181 3303 6.720012 AACCAATTAAGCGCCAAATTTTAG 57.280 33.333 13.27 8.91 0.00 1.85
3182 3304 6.566753 GCAAACCAATTAAGCGCCAAATTTTA 60.567 34.615 13.27 0.00 0.00 1.52
3183 3305 5.756849 CAAACCAATTAAGCGCCAAATTTT 58.243 33.333 13.27 5.76 0.00 1.82
3184 3306 4.320129 GCAAACCAATTAAGCGCCAAATTT 60.320 37.500 13.27 0.00 0.00 1.82
3185 3307 3.188254 GCAAACCAATTAAGCGCCAAATT 59.812 39.130 2.29 7.83 0.00 1.82
3186 3308 2.741517 GCAAACCAATTAAGCGCCAAAT 59.258 40.909 2.29 0.41 0.00 2.32
3187 3309 2.139118 GCAAACCAATTAAGCGCCAAA 58.861 42.857 2.29 0.00 0.00 3.28
3188 3310 1.342819 AGCAAACCAATTAAGCGCCAA 59.657 42.857 2.29 0.00 0.00 4.52
3189 3311 0.965439 AGCAAACCAATTAAGCGCCA 59.035 45.000 2.29 0.00 0.00 5.69
3190 3312 2.526077 GTAGCAAACCAATTAAGCGCC 58.474 47.619 2.29 0.00 0.00 6.53
3210 3332 0.321346 GGTGGGCAAGAACCAATTGG 59.679 55.000 23.31 23.31 40.24 3.16
3211 3333 1.341080 AGGTGGGCAAGAACCAATTG 58.659 50.000 0.00 0.00 40.24 2.32
3212 3334 2.990740 TAGGTGGGCAAGAACCAATT 57.009 45.000 0.00 0.00 40.24 2.32
3213 3335 2.311542 TGATAGGTGGGCAAGAACCAAT 59.688 45.455 0.00 0.00 40.24 3.16
3214 3336 1.707989 TGATAGGTGGGCAAGAACCAA 59.292 47.619 0.00 0.00 40.24 3.67
3215 3337 1.367346 TGATAGGTGGGCAAGAACCA 58.633 50.000 0.00 0.00 39.05 3.67
3216 3338 2.507407 TTGATAGGTGGGCAAGAACC 57.493 50.000 0.00 0.00 36.66 3.62
3217 3339 4.864704 TTTTTGATAGGTGGGCAAGAAC 57.135 40.909 0.00 0.00 0.00 3.01
3218 3340 6.229733 CAAATTTTTGATAGGTGGGCAAGAA 58.770 36.000 0.00 0.00 40.55 2.52
3219 3341 5.792741 CAAATTTTTGATAGGTGGGCAAGA 58.207 37.500 0.00 0.00 40.55 3.02
3220 3342 4.392754 GCAAATTTTTGATAGGTGGGCAAG 59.607 41.667 7.21 0.00 40.55 4.01
3221 3343 4.322567 GCAAATTTTTGATAGGTGGGCAA 58.677 39.130 7.21 0.00 40.55 4.52
3222 3344 3.307339 GGCAAATTTTTGATAGGTGGGCA 60.307 43.478 7.21 0.00 40.55 5.36
3223 3345 3.270027 GGCAAATTTTTGATAGGTGGGC 58.730 45.455 7.21 0.00 40.55 5.36
3224 3346 4.550076 TGGCAAATTTTTGATAGGTGGG 57.450 40.909 7.21 0.00 40.55 4.61
3225 3347 7.451501 AAATTGGCAAATTTTTGATAGGTGG 57.548 32.000 5.94 0.00 42.14 4.61
3244 3366 7.392556 GCAAAATCAAAAGTTGCCAAAAATTG 58.607 30.769 0.00 0.00 41.41 2.32
3245 3367 7.522901 GCAAAATCAAAAGTTGCCAAAAATT 57.477 28.000 0.00 0.00 41.41 1.82
3253 3375 5.580661 ACATTTGGCAAAATCAAAAGTTGC 58.419 33.333 17.70 0.00 45.48 4.17
3254 3376 7.439204 CAACATTTGGCAAAATCAAAAGTTG 57.561 32.000 17.70 17.09 46.81 3.16
3255 3377 6.562518 CCAACATTTGGCAAAATCAAAAGTT 58.437 32.000 17.70 9.90 45.17 2.66
3256 3378 6.134040 CCAACATTTGGCAAAATCAAAAGT 57.866 33.333 17.70 4.62 45.17 2.66
3301 3423 0.102120 TGGTTCGCTGCCAAAGTTTG 59.898 50.000 8.73 8.73 32.29 2.93
3302 3424 0.820871 TTGGTTCGCTGCCAAAGTTT 59.179 45.000 0.00 0.00 42.39 2.66
3303 3425 2.499214 TTGGTTCGCTGCCAAAGTT 58.501 47.368 0.00 0.00 42.39 2.66
3304 3426 4.251246 TTGGTTCGCTGCCAAAGT 57.749 50.000 0.00 0.00 42.39 2.66
3308 3430 1.312371 GGCTAATTGGTTCGCTGCCA 61.312 55.000 0.00 0.00 38.79 4.92
3309 3431 1.032114 AGGCTAATTGGTTCGCTGCC 61.032 55.000 0.00 0.00 39.19 4.85
3310 3432 0.378610 GAGGCTAATTGGTTCGCTGC 59.621 55.000 0.00 0.00 0.00 5.25
3311 3433 2.029838 AGAGGCTAATTGGTTCGCTG 57.970 50.000 0.00 0.00 0.00 5.18
3312 3434 5.482175 AGATATAGAGGCTAATTGGTTCGCT 59.518 40.000 0.00 0.00 0.00 4.93
3313 3435 5.578727 CAGATATAGAGGCTAATTGGTTCGC 59.421 44.000 0.00 0.00 0.00 4.70
3314 3436 6.692486 ACAGATATAGAGGCTAATTGGTTCG 58.308 40.000 0.00 0.00 0.00 3.95
3315 3437 8.585881 TGTACAGATATAGAGGCTAATTGGTTC 58.414 37.037 0.00 0.00 0.00 3.62
3316 3438 8.492415 TGTACAGATATAGAGGCTAATTGGTT 57.508 34.615 0.00 0.00 0.00 3.67
3317 3439 8.535335 CATGTACAGATATAGAGGCTAATTGGT 58.465 37.037 0.33 0.00 0.00 3.67
3318 3440 8.535335 ACATGTACAGATATAGAGGCTAATTGG 58.465 37.037 0.00 0.00 0.00 3.16
3322 3444 9.582648 TGTTACATGTACAGATATAGAGGCTAA 57.417 33.333 4.68 0.00 0.00 3.09
3323 3445 9.232473 CTGTTACATGTACAGATATAGAGGCTA 57.768 37.037 21.31 0.00 44.52 3.93
3324 3446 7.726291 ACTGTTACATGTACAGATATAGAGGCT 59.274 37.037 27.57 0.00 44.52 4.58
3325 3447 7.887381 ACTGTTACATGTACAGATATAGAGGC 58.113 38.462 27.57 0.00 44.52 4.70
3326 3448 8.516234 GGACTGTTACATGTACAGATATAGAGG 58.484 40.741 27.57 10.67 44.52 3.69
3327 3449 9.290988 AGGACTGTTACATGTACAGATATAGAG 57.709 37.037 27.57 14.57 44.52 2.43
3328 3450 9.067986 CAGGACTGTTACATGTACAGATATAGA 57.932 37.037 27.57 5.62 44.52 1.98
3329 3451 7.810282 GCAGGACTGTTACATGTACAGATATAG 59.190 40.741 27.57 15.40 44.52 1.31
3330 3452 7.255836 GGCAGGACTGTTACATGTACAGATATA 60.256 40.741 27.57 5.13 44.52 0.86
3331 3453 6.463049 GGCAGGACTGTTACATGTACAGATAT 60.463 42.308 27.57 14.66 44.52 1.63
3332 3454 5.163447 GGCAGGACTGTTACATGTACAGATA 60.163 44.000 27.57 6.34 44.52 1.98
3420 3543 9.999660 TTTGTTACTATGTGGTGAAACTGTATA 57.000 29.630 0.00 0.00 36.74 1.47
3421 3544 8.911918 TTTGTTACTATGTGGTGAAACTGTAT 57.088 30.769 0.00 0.00 36.74 2.29
3422 3545 8.734218 TTTTGTTACTATGTGGTGAAACTGTA 57.266 30.769 0.00 0.00 36.74 2.74
3423 3546 7.338449 ACTTTTGTTACTATGTGGTGAAACTGT 59.662 33.333 0.00 0.00 36.74 3.55
3424 3547 7.643764 CACTTTTGTTACTATGTGGTGAAACTG 59.356 37.037 0.00 0.00 36.74 3.16
3426 3549 6.416750 GCACTTTTGTTACTATGTGGTGAAAC 59.583 38.462 0.00 0.00 0.00 2.78
3432 3555 5.689383 AGTGCACTTTTGTTACTATGTGG 57.311 39.130 15.25 0.00 0.00 4.17
3477 3600 4.906065 TTGATAAAAGGCTGCTATGCTG 57.094 40.909 0.00 0.00 0.00 4.41
3726 3849 3.120854 GCAATAAATTCTCGGCTAGCTCG 60.121 47.826 15.72 16.19 0.00 5.03
3855 3978 5.181690 TCAAGTAATGCAAGACCACAAAC 57.818 39.130 0.00 0.00 0.00 2.93
4023 4146 8.748380 ATAGCAAAAGTTTTATTGAAGCTGAC 57.252 30.769 15.22 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.