Multiple sequence alignment - TraesCS1A01G118200

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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 TraesCS1A01G118200 chr1A 100.000 3757 0 0 1 3757 126855907 126852151 0.000000e+00 6938.0
1 TraesCS1A01G118200 chr1B 93.543 3113 112 26 1 3099 176999468 176996431 0.000000e+00 4553.0
2 TraesCS1A01G118200 chr1B 89.329 328 20 7 3434 3757 176994700 176994384 7.560000e-107 398.0
3 TraesCS1A01G118200 chr1D 96.306 2301 74 5 1 2299 115575421 115573130 0.000000e+00 3768.0
4 TraesCS1A01G118200 chr1D 96.400 500 16 1 2603 3100 115571316 115570817 0.000000e+00 822.0
5 TraesCS1A01G118200 chr1D 97.070 273 6 1 2286 2558 115573115 115572845 3.420000e-125 459.0
6 TraesCS1A01G118200 chr1D 90.385 208 18 2 3550 3757 115566480 115566275 4.780000e-69 272.0
7 TraesCS1A01G118200 chr1D 86.290 124 6 2 3435 3558 115570702 115570590 1.420000e-24 124.0
8 TraesCS1A01G118200 chr1D 95.238 63 2 1 2543 2604 115571463 115571401 8.590000e-17 99.0
9 TraesCS1A01G118200 chr1D 97.917 48 1 0 1324 1371 379456743 379456790 2.400000e-12 84.2
10 TraesCS1A01G118200 chr5D 85.926 135 13 3 3247 3376 271934724 271934591 5.060000e-29 139.0
11 TraesCS1A01G118200 chr5D 96.000 50 2 0 1322 1371 490514799 490514848 8.650000e-12 82.4
12 TraesCS1A01G118200 chr7D 84.559 136 13 6 3242 3371 312221145 312221012 1.100000e-25 128.0
13 TraesCS1A01G118200 chr7D 84.524 84 6 6 2673 2751 52526546 52526627 4.020000e-10 76.8
14 TraesCS1A01G118200 chr7D 83.333 84 7 6 2673 2751 52664317 52664398 1.870000e-08 71.3
15 TraesCS1A01G118200 chr6B 81.429 140 11 4 3242 3376 133166050 133165921 2.390000e-17 100.0
16 TraesCS1A01G118200 chrUn 100.000 50 0 0 1322 1371 42338336 42338385 4.000000e-15 93.5
17 TraesCS1A01G118200 chrUn 100.000 50 0 0 1322 1371 42530613 42530564 4.000000e-15 93.5
18 TraesCS1A01G118200 chrUn 100.000 50 0 0 1322 1371 474064266 474064217 4.000000e-15 93.5
19 TraesCS1A01G118200 chr7A 84.444 90 7 6 2673 2757 54961810 54961723 8.650000e-12 82.4
20 TraesCS1A01G118200 chr7A 84.524 84 6 6 2673 2751 54997025 54997106 4.020000e-10 76.8
21 TraesCS1A01G118200 chr3A 96.000 50 1 1 1322 1370 150715883 150715932 3.110000e-11 80.5
22 TraesCS1A01G118200 chr2B 91.228 57 4 1 1315 1370 622913998 622914054 4.020000e-10 76.8
23 TraesCS1A01G118200 chr4A 82.222 90 9 6 2673 2757 667174470 667174383 1.870000e-08 71.3
24 TraesCS1A01G118200 chr4A 88.136 59 4 3 2695 2750 667063313 667063371 2.420000e-07 67.6


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 TraesCS1A01G118200 chr1A 126852151 126855907 3756 True 6938.0 6938 100.0000 1 3757 1 chr1A.!!$R1 3756
1 TraesCS1A01G118200 chr1B 176994384 176999468 5084 True 2475.5 4553 91.4360 1 3757 2 chr1B.!!$R1 3756
2 TraesCS1A01G118200 chr1D 115570590 115575421 4831 True 1054.4 3768 94.2608 1 3558 5 chr1D.!!$R2 3557

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
860 861 2.183478 TCGACCTGACACATTGCAAT 57.817 45.0 5.99 5.99 0.00 3.56 F
2256 2268 0.031994 TTGCCGGCAAAGCTTTCTTC 59.968 50.0 38.61 0.00 32.44 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2277 2289 0.034477 AACTGGGGCCTTATTGACGG 60.034 55.0 0.84 0.0 0.00 4.79 R
3291 6432 0.105039 CTTGGAGTAGCCGATGGGTC 59.895 60.0 0.00 0.0 40.66 4.46 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
65 66 4.397103 ACATGTTCTGGTATTGCACATCTG 59.603 41.667 0.00 0.00 0.00 2.90
144 145 8.843262 CATGATAAATATCAAAGTCTTGGCTCA 58.157 33.333 7.17 0.00 44.96 4.26
155 156 5.192327 AGTCTTGGCTCAACATTGAAAAG 57.808 39.130 0.00 1.49 36.64 2.27
254 255 5.065218 CCTTCATTGTCAGCAGTGGTATTAC 59.935 44.000 0.00 0.00 33.75 1.89
417 418 8.447200 TCAATGGTAATCAATTCCATCCATCTA 58.553 33.333 0.00 0.00 40.52 1.98
505 506 5.621193 ACGGATTTAGTCCCATCCAATTAG 58.379 41.667 0.00 0.00 44.77 1.73
677 678 8.192774 TGAAGAATTTCCTATGCTGCTATTTTG 58.807 33.333 0.00 0.00 32.09 2.44
685 686 7.505258 TCCTATGCTGCTATTTTGTGTACATA 58.495 34.615 0.00 0.00 0.00 2.29
792 793 2.632028 TGCCACAGTTACGTTTACCCTA 59.368 45.455 0.00 0.00 0.00 3.53
800 801 6.183360 ACAGTTACGTTTACCCTAGTCAAGTT 60.183 38.462 0.00 0.00 0.00 2.66
839 840 4.065088 GTGCTTGATAGTTGGACACTTGA 58.935 43.478 0.00 0.00 36.88 3.02
840 841 4.515191 GTGCTTGATAGTTGGACACTTGAA 59.485 41.667 0.00 0.00 36.88 2.69
854 855 3.244215 ACACTTGAATCGACCTGACACAT 60.244 43.478 0.00 0.00 0.00 3.21
860 861 2.183478 TCGACCTGACACATTGCAAT 57.817 45.000 5.99 5.99 0.00 3.56
1012 1021 3.814504 ACATCAAGATGGACAACCCTT 57.185 42.857 14.04 0.00 42.91 3.95
1019 1028 3.170717 AGATGGACAACCCTTCGAGTAA 58.829 45.455 0.00 0.00 42.30 2.24
1308 1318 0.869880 TGATATTGCTCGTGGCGTCG 60.870 55.000 0.00 0.00 45.43 5.12
1371 1381 2.409975 TGACGCTGCTTTAGTACAACC 58.590 47.619 0.00 0.00 0.00 3.77
1397 1407 9.265901 CAGGGAGTATTATGTATTTCTGACTTG 57.734 37.037 0.00 0.00 0.00 3.16
1416 1426 5.772521 ACTTGTCAATAACCTGTTTGATGC 58.227 37.500 0.00 0.00 34.60 3.91
1550 1560 6.534079 CGTCGTTTACCTTTCTCATATTTCCT 59.466 38.462 0.00 0.00 0.00 3.36
1694 1704 7.054124 AGGATTATGCTTCTTCGGAAATGTTA 58.946 34.615 0.00 0.00 33.12 2.41
1702 1712 7.121168 TGCTTCTTCGGAAATGTTATTGAGAAT 59.879 33.333 0.00 0.00 33.12 2.40
1743 1754 3.468770 ACTGCTTTGCATGCAATTTCAA 58.531 36.364 32.27 16.92 40.13 2.69
1818 1829 5.476599 TGAAAACTATGGCAAACACTATGCT 59.523 36.000 0.00 0.00 43.34 3.79
2061 2072 6.653526 TTCAGAACATGGTGAAAATGATGT 57.346 33.333 0.00 0.00 29.66 3.06
2063 2074 5.769162 TCAGAACATGGTGAAAATGATGTGA 59.231 36.000 0.00 0.00 30.84 3.58
2256 2268 0.031994 TTGCCGGCAAAGCTTTCTTC 59.968 50.000 38.61 0.00 32.44 2.87
2277 2289 3.572255 TCCAAAACATTTCCAGCACCTAC 59.428 43.478 0.00 0.00 0.00 3.18
2283 2295 0.759959 TTTCCAGCACCTACCGTCAA 59.240 50.000 0.00 0.00 0.00 3.18
2464 2504 1.329906 GTCATCTTCATGCAGCTTCGG 59.670 52.381 0.00 0.00 0.00 4.30
2532 2572 4.815308 CCATCAAATCAGTCTGAGATCACC 59.185 45.833 8.82 0.00 0.00 4.02
2798 4322 2.767960 TGTTGCATGGAGATCTAGCAGA 59.232 45.455 0.00 0.00 36.47 4.26
2894 4419 8.363755 CGAATAAAAACTGTAGTTACGTCTCTG 58.636 37.037 0.00 0.00 37.25 3.35
3054 4582 5.993748 ACTTTTAAACACCCCACCATATG 57.006 39.130 0.00 0.00 0.00 1.78
3069 4597 7.016072 CCCCACCATATGCCAATATAAAAAGAA 59.984 37.037 0.00 0.00 0.00 2.52
3090 4618 2.002586 CGAGTTGCGAAGATCCAACAT 58.997 47.619 13.00 1.65 42.77 2.71
3149 6040 3.925913 GCACCATGCGTGTTTTCATTAAT 59.074 39.130 4.96 0.00 44.97 1.40
3181 6322 5.699839 CACCTTGCTCTGGTTAAAACATAC 58.300 41.667 0.00 0.00 35.28 2.39
3219 6360 9.226345 GCTAATCAAGTAATTAATGTGTTCAGC 57.774 33.333 0.00 0.00 0.00 4.26
3238 6379 3.013276 GCACCTTGCTCTGGTTAAAAC 57.987 47.619 0.00 0.00 40.96 2.43
3239 6380 2.360801 GCACCTTGCTCTGGTTAAAACA 59.639 45.455 0.00 0.00 40.96 2.83
3240 6381 3.005791 GCACCTTGCTCTGGTTAAAACAT 59.994 43.478 0.00 0.00 40.96 2.71
3241 6382 4.217550 GCACCTTGCTCTGGTTAAAACATA 59.782 41.667 0.00 0.00 40.96 2.29
3242 6383 5.105756 GCACCTTGCTCTGGTTAAAACATAT 60.106 40.000 0.00 0.00 40.96 1.78
3243 6384 6.094881 GCACCTTGCTCTGGTTAAAACATATA 59.905 38.462 0.00 0.00 40.96 0.86
3244 6385 7.472543 CACCTTGCTCTGGTTAAAACATATAC 58.527 38.462 0.00 0.00 35.28 1.47
3245 6386 6.602009 ACCTTGCTCTGGTTAAAACATATACC 59.398 38.462 0.00 0.00 33.34 2.73
3246 6387 6.828785 CCTTGCTCTGGTTAAAACATATACCT 59.171 38.462 0.00 0.00 0.00 3.08
3247 6388 7.990886 CCTTGCTCTGGTTAAAACATATACCTA 59.009 37.037 0.00 0.00 0.00 3.08
3248 6389 8.958119 TTGCTCTGGTTAAAACATATACCTAG 57.042 34.615 0.00 0.00 0.00 3.02
3249 6390 6.990349 TGCTCTGGTTAAAACATATACCTAGC 59.010 38.462 0.00 0.00 39.10 3.42
3250 6391 6.145696 GCTCTGGTTAAAACATATACCTAGCG 59.854 42.308 0.00 0.00 33.75 4.26
3251 6392 5.987347 TCTGGTTAAAACATATACCTAGCGC 59.013 40.000 0.00 0.00 0.00 5.92
3252 6393 5.058490 TGGTTAAAACATATACCTAGCGCC 58.942 41.667 2.29 0.00 0.00 6.53
3253 6394 5.163280 TGGTTAAAACATATACCTAGCGCCT 60.163 40.000 2.29 0.00 0.00 5.52
3254 6395 5.178809 GGTTAAAACATATACCTAGCGCCTG 59.821 44.000 2.29 0.00 0.00 4.85
3255 6396 4.417426 AAAACATATACCTAGCGCCTGT 57.583 40.909 2.29 0.68 0.00 4.00
3256 6397 4.417426 AAACATATACCTAGCGCCTGTT 57.583 40.909 2.29 0.00 0.00 3.16
3257 6398 4.417426 AACATATACCTAGCGCCTGTTT 57.583 40.909 2.29 0.00 0.00 2.83
3258 6399 3.728845 ACATATACCTAGCGCCTGTTTG 58.271 45.455 2.29 1.07 0.00 2.93
3259 6400 2.902705 TATACCTAGCGCCTGTTTGG 57.097 50.000 2.29 0.00 39.35 3.28
3269 6410 3.344703 CCTGTTTGGCAGTCATCCA 57.655 52.632 0.00 0.00 43.55 3.41
3270 6411 1.171308 CCTGTTTGGCAGTCATCCAG 58.829 55.000 0.00 0.00 43.55 3.86
3271 6412 0.524862 CTGTTTGGCAGTCATCCAGC 59.475 55.000 0.00 0.00 40.27 4.85
3272 6413 0.111061 TGTTTGGCAGTCATCCAGCT 59.889 50.000 0.00 0.00 34.66 4.24
3273 6414 0.807496 GTTTGGCAGTCATCCAGCTC 59.193 55.000 0.00 0.00 34.66 4.09
3274 6415 0.322816 TTTGGCAGTCATCCAGCTCC 60.323 55.000 0.00 0.00 34.66 4.70
3275 6416 1.491274 TTGGCAGTCATCCAGCTCCA 61.491 55.000 0.00 0.00 34.66 3.86
3276 6417 1.451028 GGCAGTCATCCAGCTCCAC 60.451 63.158 0.00 0.00 0.00 4.02
3277 6418 1.812922 GCAGTCATCCAGCTCCACG 60.813 63.158 0.00 0.00 0.00 4.94
3278 6419 1.153489 CAGTCATCCAGCTCCACGG 60.153 63.158 0.00 0.00 0.00 4.94
3279 6420 1.305297 AGTCATCCAGCTCCACGGA 60.305 57.895 0.00 0.00 35.27 4.69
3280 6421 1.142748 GTCATCCAGCTCCACGGAG 59.857 63.158 8.84 8.84 44.56 4.63
3293 6434 4.477975 CGGAGTGGACGGAGCGAC 62.478 72.222 0.00 0.00 0.00 5.19
3294 6435 4.131088 GGAGTGGACGGAGCGACC 62.131 72.222 0.00 0.00 41.53 4.79
3295 6436 4.131088 GAGTGGACGGAGCGACCC 62.131 72.222 0.00 0.00 40.57 4.46
3296 6437 4.988716 AGTGGACGGAGCGACCCA 62.989 66.667 0.00 0.00 40.57 4.51
3297 6438 3.771160 GTGGACGGAGCGACCCAT 61.771 66.667 0.00 0.00 40.57 4.00
3298 6439 3.458163 TGGACGGAGCGACCCATC 61.458 66.667 0.00 0.00 40.57 3.51
3307 6448 2.728817 CGACCCATCGGCTACTCC 59.271 66.667 0.00 0.00 44.99 3.85
3308 6449 2.125326 CGACCCATCGGCTACTCCA 61.125 63.158 0.00 0.00 44.99 3.86
3309 6450 1.672854 CGACCCATCGGCTACTCCAA 61.673 60.000 0.00 0.00 44.99 3.53
3310 6451 0.105039 GACCCATCGGCTACTCCAAG 59.895 60.000 0.00 0.00 34.01 3.61
3311 6452 0.325296 ACCCATCGGCTACTCCAAGA 60.325 55.000 0.00 0.00 34.01 3.02
3312 6453 0.830648 CCCATCGGCTACTCCAAGAA 59.169 55.000 0.00 0.00 34.01 2.52
3313 6454 1.209504 CCCATCGGCTACTCCAAGAAA 59.790 52.381 0.00 0.00 34.01 2.52
3314 6455 2.355716 CCCATCGGCTACTCCAAGAAAA 60.356 50.000 0.00 0.00 34.01 2.29
3315 6456 3.545703 CCATCGGCTACTCCAAGAAAAT 58.454 45.455 0.00 0.00 34.01 1.82
3316 6457 4.444306 CCCATCGGCTACTCCAAGAAAATA 60.444 45.833 0.00 0.00 34.01 1.40
3317 6458 4.752101 CCATCGGCTACTCCAAGAAAATAG 59.248 45.833 0.00 0.00 34.01 1.73
3318 6459 4.402056 TCGGCTACTCCAAGAAAATAGG 57.598 45.455 0.00 0.00 34.01 2.57
3319 6460 3.773119 TCGGCTACTCCAAGAAAATAGGT 59.227 43.478 0.00 0.00 34.01 3.08
3320 6461 4.120589 CGGCTACTCCAAGAAAATAGGTC 58.879 47.826 0.00 0.00 34.01 3.85
3321 6462 4.120589 GGCTACTCCAAGAAAATAGGTCG 58.879 47.826 0.00 0.00 34.01 4.79
3322 6463 3.556365 GCTACTCCAAGAAAATAGGTCGC 59.444 47.826 0.00 0.00 0.00 5.19
3323 6464 2.618053 ACTCCAAGAAAATAGGTCGCG 58.382 47.619 0.00 0.00 0.00 5.87
3324 6465 1.933853 CTCCAAGAAAATAGGTCGCGG 59.066 52.381 6.13 0.00 0.00 6.46
3325 6466 0.377203 CCAAGAAAATAGGTCGCGGC 59.623 55.000 6.13 3.04 0.00 6.53
3326 6467 0.377203 CAAGAAAATAGGTCGCGGCC 59.623 55.000 25.39 25.39 0.00 6.13
3327 6468 0.746923 AAGAAAATAGGTCGCGGCCC 60.747 55.000 29.22 17.17 0.00 5.80
3328 6469 2.512974 AAAATAGGTCGCGGCCCG 60.513 61.111 29.22 0.00 38.61 6.13
3375 6516 2.662596 CTGCCGAACAGGGTGCTA 59.337 61.111 0.00 0.00 43.19 3.49
3376 6517 1.003839 CTGCCGAACAGGGTGCTAA 60.004 57.895 0.00 0.00 43.19 3.09
3377 6518 0.392998 CTGCCGAACAGGGTGCTAAT 60.393 55.000 0.00 0.00 43.19 1.73
3378 6519 0.906066 TGCCGAACAGGGTGCTAATA 59.094 50.000 0.00 0.00 41.48 0.98
3379 6520 1.488812 TGCCGAACAGGGTGCTAATAT 59.511 47.619 0.00 0.00 41.48 1.28
3380 6521 2.143925 GCCGAACAGGGTGCTAATATC 58.856 52.381 0.00 0.00 41.48 1.63
3381 6522 2.484770 GCCGAACAGGGTGCTAATATCA 60.485 50.000 0.00 0.00 41.48 2.15
3382 6523 3.393800 CCGAACAGGGTGCTAATATCAG 58.606 50.000 0.00 0.00 35.97 2.90
3383 6524 3.181465 CCGAACAGGGTGCTAATATCAGT 60.181 47.826 0.00 0.00 35.97 3.41
3384 6525 3.804325 CGAACAGGGTGCTAATATCAGTG 59.196 47.826 0.00 0.00 0.00 3.66
3385 6526 3.199880 ACAGGGTGCTAATATCAGTGC 57.800 47.619 0.00 0.00 0.00 4.40
3386 6527 2.774234 ACAGGGTGCTAATATCAGTGCT 59.226 45.455 0.00 0.00 0.00 4.40
3387 6528 3.967326 ACAGGGTGCTAATATCAGTGCTA 59.033 43.478 0.00 0.00 0.00 3.49
3388 6529 4.408921 ACAGGGTGCTAATATCAGTGCTAA 59.591 41.667 0.00 0.00 0.00 3.09
3389 6530 5.072329 ACAGGGTGCTAATATCAGTGCTAAT 59.928 40.000 0.00 0.00 0.00 1.73
3390 6531 5.641209 CAGGGTGCTAATATCAGTGCTAATC 59.359 44.000 0.00 0.00 0.00 1.75
3391 6532 5.307976 AGGGTGCTAATATCAGTGCTAATCA 59.692 40.000 0.00 0.00 0.00 2.57
3392 6533 5.997746 GGGTGCTAATATCAGTGCTAATCAA 59.002 40.000 0.00 0.00 0.00 2.57
3393 6534 6.148480 GGGTGCTAATATCAGTGCTAATCAAG 59.852 42.308 0.00 0.00 0.00 3.02
3394 6535 6.708054 GGTGCTAATATCAGTGCTAATCAAGT 59.292 38.462 0.00 0.00 0.00 3.16
3395 6536 7.872993 GGTGCTAATATCAGTGCTAATCAAGTA 59.127 37.037 0.00 0.00 0.00 2.24
3396 6537 9.261180 GTGCTAATATCAGTGCTAATCAAGTAA 57.739 33.333 0.00 0.00 0.00 2.24
3405 6546 9.890629 TCAGTGCTAATCAAGTAATTACATTCT 57.109 29.630 17.65 1.21 0.00 2.40
3432 6573 9.950680 ACTAACAAGAAATGCAATTAATATCCG 57.049 29.630 0.00 0.00 33.67 4.18
3544 6685 8.437360 TGTGCATTGATTACTAGTGGAAATAG 57.563 34.615 5.39 0.00 41.00 1.73
3566 6707 2.674357 GCACGGAAATACTCGGCTTTTA 59.326 45.455 0.00 0.00 0.00 1.52
3640 6781 4.537135 TTGTGTGTAGAACCTGATCCTC 57.463 45.455 0.00 0.00 0.00 3.71
3641 6782 3.506398 TGTGTGTAGAACCTGATCCTCA 58.494 45.455 0.00 0.00 0.00 3.86
3653 6794 3.552875 CTGATCCTCAGCCATGTTCATT 58.447 45.455 0.00 0.00 37.72 2.57
3696 6841 3.405823 TTCGTTTGGGTCCTTCGTTAT 57.594 42.857 0.00 0.00 0.00 1.89
3697 6842 2.690786 TCGTTTGGGTCCTTCGTTATG 58.309 47.619 0.00 0.00 0.00 1.90
3707 6852 1.659098 CCTTCGTTATGGTCAACTCGC 59.341 52.381 0.00 0.00 0.00 5.03
3711 6856 2.066262 CGTTATGGTCAACTCGCTGTT 58.934 47.619 0.00 0.00 39.92 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 6.019318 CCTTAATTATGCAGCAATGTTCTTGC 60.019 38.462 0.00 1.78 45.22 4.01
155 156 8.483307 TCCAGACGTTAAAAATATAAGGACAC 57.517 34.615 0.00 0.00 0.00 3.67
254 255 8.315391 ACATCATCCATGATAACAGTTAATCG 57.685 34.615 1.64 0.00 45.23 3.34
417 418 2.551459 GAGAAATGTGCACTGAGCTTGT 59.449 45.455 19.41 2.62 45.94 3.16
505 506 6.100714 TGGGGATAACTAGACAGGTTAAATCC 59.899 42.308 0.00 0.00 33.99 3.01
612 613 8.473358 TGTATTTCTAGATCCTTGAATCGGTA 57.527 34.615 0.00 0.00 0.00 4.02
645 646 8.193438 AGCAGCATAGGAAATTCTTCATTTTAC 58.807 33.333 0.00 0.00 35.02 2.01
677 678 8.780249 ACAGTTTGTTCAATAAGGTATGTACAC 58.220 33.333 0.00 0.00 0.00 2.90
792 793 6.318900 CCAGTAGGAACAAAAAGAACTTGACT 59.681 38.462 0.00 0.00 36.89 3.41
800 801 4.164843 AGCACCAGTAGGAACAAAAAGA 57.835 40.909 0.00 0.00 38.69 2.52
839 840 2.183478 TGCAATGTGTCAGGTCGATT 57.817 45.000 0.00 0.00 0.00 3.34
840 841 2.183478 TTGCAATGTGTCAGGTCGAT 57.817 45.000 0.00 0.00 0.00 3.59
854 855 7.994425 TTTATAGACCAACTCAAGATTGCAA 57.006 32.000 0.00 0.00 0.00 4.08
860 861 7.234782 TGAGACCTTTTATAGACCAACTCAAGA 59.765 37.037 0.00 0.00 0.00 3.02
1012 1021 1.476891 GGACATGTCCTGCTTACTCGA 59.523 52.381 33.47 0.00 46.16 4.04
1139 1148 7.968405 AGAACTCGACCAAAATGCATATTTAAC 59.032 33.333 0.00 0.00 35.50 2.01
1140 1149 8.050778 AGAACTCGACCAAAATGCATATTTAA 57.949 30.769 0.00 0.00 35.50 1.52
1141 1150 7.624360 AGAACTCGACCAAAATGCATATTTA 57.376 32.000 0.00 0.00 35.50 1.40
1142 1151 6.515272 AGAACTCGACCAAAATGCATATTT 57.485 33.333 0.00 0.16 38.11 1.40
1143 1152 6.071952 ACAAGAACTCGACCAAAATGCATATT 60.072 34.615 0.00 0.00 0.00 1.28
1144 1153 5.415701 ACAAGAACTCGACCAAAATGCATAT 59.584 36.000 0.00 0.00 0.00 1.78
1145 1154 4.759693 ACAAGAACTCGACCAAAATGCATA 59.240 37.500 0.00 0.00 0.00 3.14
1296 1306 2.717809 GAACTTCGACGCCACGAGC 61.718 63.158 0.00 0.00 43.04 5.03
1371 1381 9.265901 CAAGTCAGAAATACATAATACTCCCTG 57.734 37.037 0.00 0.00 0.00 4.45
1397 1407 5.527951 TGTTGCATCAAACAGGTTATTGAC 58.472 37.500 0.00 0.00 38.29 3.18
1446 1456 3.910170 GCGTATGTTAGAATGATCGCGTA 59.090 43.478 5.77 0.00 33.79 4.42
1550 1560 7.043565 GGTTTAATAACAAGATACGGGACTCA 58.956 38.462 0.00 0.00 35.92 3.41
1887 1898 4.811908 TGCCATGTTGAATTCACATGAAG 58.188 39.130 31.18 22.97 42.60 3.02
2032 2043 7.835682 TCATTTTCACCATGTTCTGAATCCTAT 59.164 33.333 0.00 0.00 0.00 2.57
2035 2046 6.271488 TCATTTTCACCATGTTCTGAATCC 57.729 37.500 0.00 0.00 0.00 3.01
2096 2108 1.388547 TGCATTTCCGGGCTATTGTC 58.611 50.000 0.00 0.00 0.00 3.18
2216 2228 1.213678 GGAAGTAATGTACCCCACCCC 59.786 57.143 0.00 0.00 0.00 4.95
2256 2268 3.306019 GGTAGGTGCTGGAAATGTTTTGG 60.306 47.826 0.00 0.00 0.00 3.28
2277 2289 0.034477 AACTGGGGCCTTATTGACGG 60.034 55.000 0.84 0.00 0.00 4.79
2283 2295 1.005924 CTCACCAAACTGGGGCCTTAT 59.994 52.381 0.84 0.00 41.90 1.73
2464 2504 1.129437 GTGCGAAAGACAAGATCCAGC 59.871 52.381 0.00 0.00 0.00 4.85
2522 2562 1.211212 TGCATCTTGGGGTGATCTCAG 59.789 52.381 0.00 0.00 0.00 3.35
2532 2572 6.271488 TCTGAAAATTACTTGCATCTTGGG 57.729 37.500 0.00 0.00 0.00 4.12
2624 4148 3.207778 CAGTTGTTAACCAGAAACCGGA 58.792 45.455 9.46 0.00 0.00 5.14
2793 4317 0.833834 ACAGTACAGCCCAGTCTGCT 60.834 55.000 0.00 0.00 40.41 4.24
2798 4322 1.136828 TTTCCACAGTACAGCCCAGT 58.863 50.000 0.00 0.00 0.00 4.00
2894 4419 4.463209 CGACCAACAACATACATGACAAC 58.537 43.478 0.00 0.00 0.00 3.32
3049 4577 9.950680 AACTCGTTCTTTTTATATTGGCATATG 57.049 29.630 0.00 0.00 0.00 1.78
3054 4582 5.227184 CGCAACTCGTTCTTTTTATATTGGC 59.773 40.000 0.00 0.00 0.00 4.52
3069 4597 1.270094 TGTTGGATCTTCGCAACTCGT 60.270 47.619 12.04 0.00 39.67 4.18
3169 6060 9.338622 AGCACTGATATTAGGTATGTTTTAACC 57.661 33.333 0.00 0.00 35.91 2.85
3193 6334 9.226345 GCTGAACACATTAATTACTTGATTAGC 57.774 33.333 2.41 0.00 0.00 3.09
3218 6359 2.360801 TGTTTTAACCAGAGCAAGGTGC 59.639 45.455 0.00 0.00 45.46 5.01
3219 6360 4.853924 ATGTTTTAACCAGAGCAAGGTG 57.146 40.909 0.00 0.00 39.86 4.00
3220 6361 6.602009 GGTATATGTTTTAACCAGAGCAAGGT 59.398 38.462 0.00 0.00 42.34 3.50
3221 6362 6.828785 AGGTATATGTTTTAACCAGAGCAAGG 59.171 38.462 0.00 0.00 34.29 3.61
3222 6363 7.865706 AGGTATATGTTTTAACCAGAGCAAG 57.134 36.000 0.00 0.00 34.29 4.01
3223 6364 7.497909 GCTAGGTATATGTTTTAACCAGAGCAA 59.502 37.037 10.60 0.00 40.36 3.91
3224 6365 6.990349 GCTAGGTATATGTTTTAACCAGAGCA 59.010 38.462 10.60 0.00 40.36 4.26
3225 6366 6.145696 CGCTAGGTATATGTTTTAACCAGAGC 59.854 42.308 0.00 0.00 38.70 4.09
3226 6367 6.145696 GCGCTAGGTATATGTTTTAACCAGAG 59.854 42.308 0.00 0.00 34.29 3.35
3227 6368 5.987347 GCGCTAGGTATATGTTTTAACCAGA 59.013 40.000 0.00 0.00 34.29 3.86
3228 6369 5.178809 GGCGCTAGGTATATGTTTTAACCAG 59.821 44.000 7.64 0.00 34.29 4.00
3229 6370 5.058490 GGCGCTAGGTATATGTTTTAACCA 58.942 41.667 7.64 0.00 34.29 3.67
3230 6371 5.178809 CAGGCGCTAGGTATATGTTTTAACC 59.821 44.000 7.64 0.00 0.00 2.85
3231 6372 5.756833 ACAGGCGCTAGGTATATGTTTTAAC 59.243 40.000 7.64 0.00 0.00 2.01
3232 6373 5.920903 ACAGGCGCTAGGTATATGTTTTAA 58.079 37.500 7.64 0.00 0.00 1.52
3233 6374 5.540400 ACAGGCGCTAGGTATATGTTTTA 57.460 39.130 7.64 0.00 0.00 1.52
3234 6375 4.417426 ACAGGCGCTAGGTATATGTTTT 57.583 40.909 7.64 0.00 0.00 2.43
3235 6376 4.417426 AACAGGCGCTAGGTATATGTTT 57.583 40.909 7.64 0.00 0.00 2.83
3236 6377 4.127171 CAAACAGGCGCTAGGTATATGTT 58.873 43.478 7.64 3.43 0.00 2.71
3237 6378 3.494398 CCAAACAGGCGCTAGGTATATGT 60.494 47.826 7.64 0.00 0.00 2.29
3238 6379 3.067106 CCAAACAGGCGCTAGGTATATG 58.933 50.000 7.64 4.11 0.00 1.78
3239 6380 3.402628 CCAAACAGGCGCTAGGTATAT 57.597 47.619 7.64 0.00 0.00 0.86
3240 6381 2.902705 CCAAACAGGCGCTAGGTATA 57.097 50.000 7.64 0.00 0.00 1.47
3241 6382 3.780624 CCAAACAGGCGCTAGGTAT 57.219 52.632 7.64 0.00 0.00 2.73
3253 6394 0.111061 AGCTGGATGACTGCCAAACA 59.889 50.000 0.00 0.00 44.29 2.83
3254 6395 0.807496 GAGCTGGATGACTGCCAAAC 59.193 55.000 0.00 0.00 44.29 2.93
3255 6396 0.322816 GGAGCTGGATGACTGCCAAA 60.323 55.000 0.00 0.00 44.29 3.28
3256 6397 1.300963 GGAGCTGGATGACTGCCAA 59.699 57.895 0.00 0.00 44.29 4.52
3257 6398 1.919816 TGGAGCTGGATGACTGCCA 60.920 57.895 0.00 0.00 44.29 4.92
3258 6399 1.451028 GTGGAGCTGGATGACTGCC 60.451 63.158 0.00 0.00 44.29 4.85
3259 6400 1.812922 CGTGGAGCTGGATGACTGC 60.813 63.158 0.00 0.00 43.63 4.40
3260 6401 1.153489 CCGTGGAGCTGGATGACTG 60.153 63.158 0.00 0.00 0.00 3.51
3261 6402 1.305297 TCCGTGGAGCTGGATGACT 60.305 57.895 0.00 0.00 0.00 3.41
3262 6403 1.142748 CTCCGTGGAGCTGGATGAC 59.857 63.158 2.38 0.00 35.31 3.06
3263 6404 1.305297 ACTCCGTGGAGCTGGATGA 60.305 57.895 15.80 0.00 45.54 2.92
3264 6405 1.153489 CACTCCGTGGAGCTGGATG 60.153 63.158 15.80 2.64 45.54 3.51
3265 6406 3.303189 CACTCCGTGGAGCTGGAT 58.697 61.111 15.80 0.00 45.54 3.41
3274 6415 4.778415 CGCTCCGTCCACTCCGTG 62.778 72.222 0.00 0.00 0.00 4.94
3276 6417 4.477975 GTCGCTCCGTCCACTCCG 62.478 72.222 0.00 0.00 0.00 4.63
3277 6418 4.131088 GGTCGCTCCGTCCACTCC 62.131 72.222 0.00 0.00 35.36 3.85
3278 6419 4.131088 GGGTCGCTCCGTCCACTC 62.131 72.222 3.60 0.00 36.84 3.51
3279 6420 4.988716 TGGGTCGCTCCGTCCACT 62.989 66.667 3.60 0.00 36.84 4.00
3280 6421 3.718210 GATGGGTCGCTCCGTCCAC 62.718 68.421 3.60 0.00 36.84 4.02
3281 6422 3.458163 GATGGGTCGCTCCGTCCA 61.458 66.667 3.60 4.57 36.84 4.02
3282 6423 4.570663 CGATGGGTCGCTCCGTCC 62.571 72.222 9.48 0.00 41.49 4.79
3283 6424 4.570663 CCGATGGGTCGCTCCGTC 62.571 72.222 6.15 6.15 46.32 4.79
3286 6427 3.224324 TAGCCGATGGGTCGCTCC 61.224 66.667 0.00 0.00 46.32 4.70
3287 6428 2.027751 GTAGCCGATGGGTCGCTC 59.972 66.667 0.00 0.00 46.32 5.03
3288 6429 2.442272 AGTAGCCGATGGGTCGCT 60.442 61.111 0.00 0.00 46.32 4.93
3289 6430 2.027751 GAGTAGCCGATGGGTCGC 59.972 66.667 0.00 0.00 46.32 5.19
3291 6432 0.105039 CTTGGAGTAGCCGATGGGTC 59.895 60.000 0.00 0.00 40.66 4.46
3292 6433 0.325296 TCTTGGAGTAGCCGATGGGT 60.325 55.000 0.00 0.00 40.66 4.51
3293 6434 0.830648 TTCTTGGAGTAGCCGATGGG 59.169 55.000 0.00 0.00 40.66 4.00
3294 6435 2.691409 TTTCTTGGAGTAGCCGATGG 57.309 50.000 0.00 0.00 40.66 3.51
3295 6436 4.752101 CCTATTTTCTTGGAGTAGCCGATG 59.248 45.833 0.00 0.00 40.66 3.84
3296 6437 4.409247 ACCTATTTTCTTGGAGTAGCCGAT 59.591 41.667 0.00 0.00 40.66 4.18
3297 6438 3.773119 ACCTATTTTCTTGGAGTAGCCGA 59.227 43.478 0.00 0.00 40.66 5.54
3298 6439 4.120589 GACCTATTTTCTTGGAGTAGCCG 58.879 47.826 0.00 0.00 40.66 5.52
3299 6440 4.120589 CGACCTATTTTCTTGGAGTAGCC 58.879 47.826 0.00 0.00 37.10 3.93
3300 6441 3.556365 GCGACCTATTTTCTTGGAGTAGC 59.444 47.826 0.00 0.00 0.00 3.58
3301 6442 3.797256 CGCGACCTATTTTCTTGGAGTAG 59.203 47.826 0.00 0.00 0.00 2.57
3302 6443 3.429822 CCGCGACCTATTTTCTTGGAGTA 60.430 47.826 8.23 0.00 0.00 2.59
3303 6444 2.618053 CGCGACCTATTTTCTTGGAGT 58.382 47.619 0.00 0.00 0.00 3.85
3304 6445 1.933853 CCGCGACCTATTTTCTTGGAG 59.066 52.381 8.23 0.00 0.00 3.86
3305 6446 2.010043 GCCGCGACCTATTTTCTTGGA 61.010 52.381 8.23 0.00 0.00 3.53
3306 6447 0.377203 GCCGCGACCTATTTTCTTGG 59.623 55.000 8.23 0.00 0.00 3.61
3307 6448 0.377203 GGCCGCGACCTATTTTCTTG 59.623 55.000 8.23 0.00 0.00 3.02
3308 6449 0.746923 GGGCCGCGACCTATTTTCTT 60.747 55.000 12.39 0.00 0.00 2.52
3309 6450 1.153229 GGGCCGCGACCTATTTTCT 60.153 57.895 12.39 0.00 0.00 2.52
3310 6451 2.531376 CGGGCCGCGACCTATTTTC 61.531 63.158 15.42 0.00 0.00 2.29
3311 6452 2.512974 CGGGCCGCGACCTATTTT 60.513 61.111 15.42 0.00 0.00 1.82
3350 6491 4.742201 TGTTCGGCAGCTCTCCGC 62.742 66.667 16.83 2.19 46.05 5.54
3352 6493 2.125350 CCTGTTCGGCAGCTCTCC 60.125 66.667 0.00 0.00 43.71 3.71
3353 6494 2.125350 CCCTGTTCGGCAGCTCTC 60.125 66.667 0.00 0.00 43.71 3.20
3354 6495 2.925170 ACCCTGTTCGGCAGCTCT 60.925 61.111 0.00 0.00 43.71 4.09
3355 6496 2.743928 CACCCTGTTCGGCAGCTC 60.744 66.667 0.00 0.00 43.71 4.09
3357 6498 3.605749 TAGCACCCTGTTCGGCAGC 62.606 63.158 2.96 0.00 43.71 5.25
3358 6499 0.392998 ATTAGCACCCTGTTCGGCAG 60.393 55.000 1.70 1.70 44.63 4.85
3359 6500 0.906066 TATTAGCACCCTGTTCGGCA 59.094 50.000 0.00 0.00 0.00 5.69
3360 6501 2.143925 GATATTAGCACCCTGTTCGGC 58.856 52.381 0.00 0.00 0.00 5.54
3361 6502 3.181465 ACTGATATTAGCACCCTGTTCGG 60.181 47.826 0.00 0.00 0.00 4.30
3362 6503 3.804325 CACTGATATTAGCACCCTGTTCG 59.196 47.826 0.00 0.00 0.00 3.95
3363 6504 3.561725 GCACTGATATTAGCACCCTGTTC 59.438 47.826 0.00 0.00 0.00 3.18
3364 6505 3.200825 AGCACTGATATTAGCACCCTGTT 59.799 43.478 0.00 0.00 0.00 3.16
3365 6506 2.774234 AGCACTGATATTAGCACCCTGT 59.226 45.455 0.00 0.00 0.00 4.00
3366 6507 3.482156 AGCACTGATATTAGCACCCTG 57.518 47.619 0.00 0.00 0.00 4.45
3367 6508 5.307976 TGATTAGCACTGATATTAGCACCCT 59.692 40.000 0.00 0.00 0.00 4.34
3368 6509 5.551233 TGATTAGCACTGATATTAGCACCC 58.449 41.667 0.00 0.00 0.00 4.61
3369 6510 6.708054 ACTTGATTAGCACTGATATTAGCACC 59.292 38.462 0.00 0.00 0.00 5.01
3370 6511 7.721286 ACTTGATTAGCACTGATATTAGCAC 57.279 36.000 0.00 0.00 0.00 4.40
3379 6520 9.890629 AGAATGTAATTACTTGATTAGCACTGA 57.109 29.630 16.33 0.00 36.07 3.41
3406 6547 9.950680 CGGATATTAATTGCATTTCTTGTTAGT 57.049 29.630 0.00 0.00 0.00 2.24
3407 6548 8.905702 GCGGATATTAATTGCATTTCTTGTTAG 58.094 33.333 0.00 0.00 0.00 2.34
3408 6549 7.865385 GGCGGATATTAATTGCATTTCTTGTTA 59.135 33.333 0.00 0.00 0.00 2.41
3409 6550 6.701400 GGCGGATATTAATTGCATTTCTTGTT 59.299 34.615 0.00 0.00 0.00 2.83
3410 6551 6.040842 AGGCGGATATTAATTGCATTTCTTGT 59.959 34.615 0.00 0.00 0.00 3.16
3411 6552 6.449698 AGGCGGATATTAATTGCATTTCTTG 58.550 36.000 0.00 0.00 0.00 3.02
3412 6553 6.655078 AGGCGGATATTAATTGCATTTCTT 57.345 33.333 0.00 0.00 0.00 2.52
3413 6554 7.759489 TTAGGCGGATATTAATTGCATTTCT 57.241 32.000 0.00 0.00 0.00 2.52
3416 6557 9.407380 TGATATTAGGCGGATATTAATTGCATT 57.593 29.630 0.00 0.00 0.00 3.56
3417 6558 8.978874 TGATATTAGGCGGATATTAATTGCAT 57.021 30.769 0.00 0.00 0.00 3.96
3418 6559 8.800370 TTGATATTAGGCGGATATTAATTGCA 57.200 30.769 0.00 0.00 0.00 4.08
3419 6560 9.722056 CTTTGATATTAGGCGGATATTAATTGC 57.278 33.333 0.00 0.00 0.00 3.56
3423 6564 9.109393 GCATCTTTGATATTAGGCGGATATTAA 57.891 33.333 0.00 0.00 0.00 1.40
3424 6565 8.264347 TGCATCTTTGATATTAGGCGGATATTA 58.736 33.333 0.00 0.00 0.00 0.98
3425 6566 7.112122 TGCATCTTTGATATTAGGCGGATATT 58.888 34.615 0.00 0.00 0.00 1.28
3426 6567 6.653020 TGCATCTTTGATATTAGGCGGATAT 58.347 36.000 0.00 0.00 0.00 1.63
3427 6568 6.048732 TGCATCTTTGATATTAGGCGGATA 57.951 37.500 0.00 0.00 0.00 2.59
3428 6569 4.910195 TGCATCTTTGATATTAGGCGGAT 58.090 39.130 0.00 0.00 0.00 4.18
3429 6570 4.202357 ACTGCATCTTTGATATTAGGCGGA 60.202 41.667 0.00 0.00 0.00 5.54
3430 6571 4.067896 ACTGCATCTTTGATATTAGGCGG 58.932 43.478 0.00 0.00 0.00 6.13
3431 6572 5.679734 AACTGCATCTTTGATATTAGGCG 57.320 39.130 0.00 0.00 0.00 5.52
3475 6616 9.979578 ACAAGACATTAATTGCATTTCTTGTTA 57.020 25.926 18.98 0.00 41.50 2.41
3476 6617 8.891671 ACAAGACATTAATTGCATTTCTTGTT 57.108 26.923 18.98 10.10 41.50 2.83
3512 6653 9.006839 CCACTAGTAATCAATGCACATGATATT 57.993 33.333 15.15 6.39 36.53 1.28
3513 6654 8.377799 TCCACTAGTAATCAATGCACATGATAT 58.622 33.333 15.15 8.68 36.53 1.63
3514 6655 7.734942 TCCACTAGTAATCAATGCACATGATA 58.265 34.615 15.15 2.00 36.53 2.15
3515 6656 6.594744 TCCACTAGTAATCAATGCACATGAT 58.405 36.000 10.29 10.29 39.15 2.45
3516 6657 5.988287 TCCACTAGTAATCAATGCACATGA 58.012 37.500 0.00 6.50 0.00 3.07
3517 6658 6.682423 TTCCACTAGTAATCAATGCACATG 57.318 37.500 0.00 0.00 0.00 3.21
3518 6659 7.886629 ATTTCCACTAGTAATCAATGCACAT 57.113 32.000 0.00 0.00 0.00 3.21
3544 6685 0.743345 AAGCCGAGTATTTCCGTGCC 60.743 55.000 0.00 0.00 0.00 5.01
3566 6707 8.106247 ACAAAATTGTATGTAACCTTCGACAT 57.894 30.769 0.00 0.00 40.16 3.06
3587 6728 6.348950 CGATTTAGGTGCTGGTTGATAACAAA 60.349 38.462 0.00 0.00 37.77 2.83
3640 6781 2.426024 CCTCTTCCAATGAACATGGCTG 59.574 50.000 0.00 0.00 37.88 4.85
3641 6782 2.042162 ACCTCTTCCAATGAACATGGCT 59.958 45.455 0.00 0.00 37.88 4.75
3653 6794 5.576563 TTGGTAGAAATGAACCTCTTCCA 57.423 39.130 0.00 0.00 37.35 3.53
3707 6852 2.365617 AGTAGAGGTCACCACACAACAG 59.634 50.000 0.00 0.00 0.00 3.16
3711 6856 3.162666 CCTAAGTAGAGGTCACCACACA 58.837 50.000 0.00 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.