Multiple sequence alignment - TraesCS6D01G217800

Loading Multiple Alignment...

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 TraesCS6D01G217800 chr6D 100.000 3374 0 0 1 3374 307519111 307515738 0.000000e+00 6231.0
1 TraesCS6D01G217800 chr6D 94.286 35 1 1 2744 2778 97559641 97559674 6.000000e-03 52.8
2 TraesCS6D01G217800 chr6B 94.279 3129 106 25 3 3111 474751055 474747980 0.000000e+00 4719.0
3 TraesCS6D01G217800 chr6B 94.286 35 1 1 2744 2778 27633303 27633270 6.000000e-03 52.8
4 TraesCS6D01G217800 chr6A 93.386 2540 108 27 883 3374 444675343 444672816 0.000000e+00 3705.0
5 TraesCS6D01G217800 chr6A 88.388 732 25 22 99 782 444676446 444675727 0.000000e+00 826.0
6 TraesCS6D01G217800 chr2A 86.982 338 38 5 1522 1856 616992668 616993002 3.180000e-100 375.0
7 TraesCS6D01G217800 chr2B 86.944 337 38 5 1522 1855 555384883 555385216 1.140000e-99 374.0
8 TraesCS6D01G217800 chr2D 86.310 336 40 5 1522 1854 474512336 474512668 8.900000e-96 361.0
9 TraesCS6D01G217800 chr2D 82.203 118 17 3 3126 3243 507114891 507114778 7.700000e-17 99.0
10 TraesCS6D01G217800 chr7B 83.854 192 31 0 1628 1819 99089374 99089183 2.070000e-42 183.0
11 TraesCS6D01G217800 chr7B 94.286 35 1 1 2744 2778 145928576 145928543 6.000000e-03 52.8
12 TraesCS6D01G217800 chr7A 83.333 192 32 0 1628 1819 135689646 135689455 9.620000e-41 178.0
13 TraesCS6D01G217800 chr7D 82.812 192 33 0 1628 1819 136204684 136204493 4.480000e-39 172.0
14 TraesCS6D01G217800 chr5D 83.978 181 27 2 1628 1807 304163177 304162998 4.480000e-39 172.0
15 TraesCS6D01G217800 chr5B 94.286 35 1 1 2744 2778 504044652 504044685 6.000000e-03 52.8
16 TraesCS6D01G217800 chr4D 94.286 35 1 1 2744 2778 455258045 455258012 6.000000e-03 52.8
17 TraesCS6D01G217800 chr3B 94.286 35 1 1 2744 2778 85094444 85094411 6.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G217800 chr6D 307515738 307519111 3373 True 6231.0 6231 100.000 1 3374 1 chr6D.!!$R1 3373
1 TraesCS6D01G217800 chr6B 474747980 474751055 3075 True 4719.0 4719 94.279 3 3111 1 chr6B.!!$R2 3108
2 TraesCS6D01G217800 chr6A 444672816 444676446 3630 True 2265.5 3705 90.887 99 3374 2 chr6A.!!$R1 3275

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
903 1281 1.080434 AGCTTCTCTCGTTCGCCAC 60.08 57.895 0.0 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2413 2834 0.60813 TGCATCTCACAGCGTAGGTT 59.392 50.0 0.0 0.0 33.74 3.5 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
53 54 5.249393 AGAATGGACCATAGACAGACAGTTT 59.751 40.000 7.59 0.00 0.00 2.66
54 55 6.440647 AGAATGGACCATAGACAGACAGTTTA 59.559 38.462 7.59 0.00 0.00 2.01
55 56 5.661056 TGGACCATAGACAGACAGTTTAG 57.339 43.478 0.00 0.00 0.00 1.85
86 87 2.114871 ACAAGGTCCTAAACTAGGGGGA 59.885 50.000 0.00 0.00 46.24 4.81
95 96 3.646736 AAACTAGGGGGAAATTCCTCG 57.353 47.619 12.28 0.00 38.13 4.63
112 113 2.072298 CTCGGCCAGTTCTTTTCTGAG 58.928 52.381 2.24 0.00 35.20 3.35
157 160 7.707035 CACTAGTTAAAGTAGCTAATCCACTGG 59.293 40.741 0.00 2.38 0.00 4.00
211 252 9.178427 GCAATTGTTATTAGTAGTACTCCGTAG 57.822 37.037 5.96 0.00 0.00 3.51
320 362 8.352942 ACAGTACTCAATGATTGGAAGAAAAAC 58.647 33.333 5.20 0.00 0.00 2.43
321 363 7.809806 CAGTACTCAATGATTGGAAGAAAAACC 59.190 37.037 5.20 0.00 0.00 3.27
322 364 6.983906 ACTCAATGATTGGAAGAAAAACCT 57.016 33.333 5.20 0.00 0.00 3.50
334 376 6.072175 TGGAAGAAAAACCTGTCGGAATATTG 60.072 38.462 0.00 0.00 0.00 1.90
335 377 5.897377 AGAAAAACCTGTCGGAATATTGG 57.103 39.130 0.00 0.00 0.00 3.16
336 378 5.566469 AGAAAAACCTGTCGGAATATTGGA 58.434 37.500 0.00 0.00 0.00 3.53
337 379 5.648092 AGAAAAACCTGTCGGAATATTGGAG 59.352 40.000 0.00 0.00 0.00 3.86
338 380 4.837093 AAACCTGTCGGAATATTGGAGA 57.163 40.909 0.00 0.00 0.00 3.71
339 381 4.837093 AACCTGTCGGAATATTGGAGAA 57.163 40.909 0.00 0.00 0.00 2.87
340 382 4.408182 ACCTGTCGGAATATTGGAGAAG 57.592 45.455 0.00 0.00 0.00 2.85
341 383 3.134458 CCTGTCGGAATATTGGAGAAGC 58.866 50.000 0.00 0.00 0.00 3.86
342 384 2.797156 CTGTCGGAATATTGGAGAAGCG 59.203 50.000 0.00 0.00 0.00 4.68
380 440 3.387962 TGGAAGTGATAGGCATTCTCCT 58.612 45.455 0.00 0.00 40.21 3.69
394 454 1.210538 TCTCCTACTCGGTCAGCCTA 58.789 55.000 0.00 0.00 0.00 3.93
395 455 1.141254 TCTCCTACTCGGTCAGCCTAG 59.859 57.143 0.00 0.00 34.09 3.02
398 458 1.103803 CTACTCGGTCAGCCTAGCAA 58.896 55.000 0.00 0.00 31.28 3.91
405 465 2.079925 GGTCAGCCTAGCAACAAGAAG 58.920 52.381 0.00 0.00 0.00 2.85
406 466 2.551071 GGTCAGCCTAGCAACAAGAAGT 60.551 50.000 0.00 0.00 0.00 3.01
416 476 3.882888 AGCAACAAGAAGTCGATTTTGGA 59.117 39.130 0.00 0.00 0.00 3.53
417 477 4.023707 AGCAACAAGAAGTCGATTTTGGAG 60.024 41.667 0.00 0.00 0.00 3.86
418 478 4.222114 CAACAAGAAGTCGATTTTGGAGC 58.778 43.478 0.00 0.00 0.00 4.70
419 479 2.814336 ACAAGAAGTCGATTTTGGAGCC 59.186 45.455 0.00 0.00 0.00 4.70
814 888 6.556974 ATCTCTCCAAATCAGATCAGAACA 57.443 37.500 0.00 0.00 0.00 3.18
841 915 1.695597 CATTGGCTCCCCTCCTCCT 60.696 63.158 0.00 0.00 0.00 3.69
842 916 1.385206 ATTGGCTCCCCTCCTCCTC 60.385 63.158 0.00 0.00 0.00 3.71
843 917 2.923852 ATTGGCTCCCCTCCTCCTCC 62.924 65.000 0.00 0.00 0.00 4.30
890 1268 4.430423 CGTTCGCCACGCAGCTTC 62.430 66.667 0.00 0.00 43.37 3.86
891 1269 3.044305 GTTCGCCACGCAGCTTCT 61.044 61.111 0.00 0.00 0.00 2.85
892 1270 2.738521 TTCGCCACGCAGCTTCTC 60.739 61.111 0.00 0.00 0.00 2.87
893 1271 3.226429 TTCGCCACGCAGCTTCTCT 62.226 57.895 0.00 0.00 0.00 3.10
894 1272 3.184683 CGCCACGCAGCTTCTCTC 61.185 66.667 0.00 0.00 0.00 3.20
895 1273 3.184683 GCCACGCAGCTTCTCTCG 61.185 66.667 0.00 0.00 0.00 4.04
896 1274 2.259818 CCACGCAGCTTCTCTCGT 59.740 61.111 0.00 0.00 35.35 4.18
897 1275 1.373497 CCACGCAGCTTCTCTCGTT 60.373 57.895 0.00 0.00 32.38 3.85
898 1276 1.347817 CCACGCAGCTTCTCTCGTTC 61.348 60.000 0.00 0.00 32.38 3.95
899 1277 1.442857 ACGCAGCTTCTCTCGTTCG 60.443 57.895 0.00 0.00 0.00 3.95
900 1278 2.783064 CGCAGCTTCTCTCGTTCGC 61.783 63.158 0.00 0.00 0.00 4.70
901 1279 2.448705 GCAGCTTCTCTCGTTCGCC 61.449 63.158 0.00 0.00 0.00 5.54
902 1280 1.080501 CAGCTTCTCTCGTTCGCCA 60.081 57.895 0.00 0.00 0.00 5.69
903 1281 1.080434 AGCTTCTCTCGTTCGCCAC 60.080 57.895 0.00 0.00 0.00 5.01
918 1296 1.207593 CCACGCAGCTTTGTACAGC 59.792 57.895 0.00 0.00 40.44 4.40
984 1379 3.100191 CGGAGGATTCGCGCGATC 61.100 66.667 35.21 28.61 0.00 3.69
1314 1721 4.619140 GCGTACGATCCGTCCCCG 62.619 72.222 21.65 0.00 41.54 5.73
1360 1767 2.656069 TTGCGGTACTCCTCCAGCC 61.656 63.158 0.00 0.00 0.00 4.85
1422 1835 2.633657 CACACACCTTCGCAGCAC 59.366 61.111 0.00 0.00 0.00 4.40
1973 2386 4.012895 GCAACAGCACACGGACGG 62.013 66.667 0.00 0.00 0.00 4.79
1985 2398 3.723348 GGACGGGCAAGCGAACAC 61.723 66.667 0.00 0.00 0.00 3.32
1991 2404 2.617274 GGCAAGCGAACACTGGACC 61.617 63.158 0.00 0.00 0.00 4.46
2000 2413 0.108019 AACACTGGACCGAAACCTCC 59.892 55.000 0.00 0.00 0.00 4.30
2028 2441 4.704833 GCAGAGCAGGACGGCCAA 62.705 66.667 11.69 0.00 36.29 4.52
2073 2486 0.035317 TCCAGAACGCAGAGCAACAT 59.965 50.000 0.00 0.00 0.00 2.71
2244 2657 4.116328 TCTCGCTTCGCCGGTGAG 62.116 66.667 18.66 13.25 41.17 3.51
2379 2792 6.471233 TTCATGTGGAAGGACTAGATACAG 57.529 41.667 0.00 0.00 0.00 2.74
2381 2794 6.194967 TCATGTGGAAGGACTAGATACAGAA 58.805 40.000 0.00 0.00 0.00 3.02
2382 2795 6.841229 TCATGTGGAAGGACTAGATACAGAAT 59.159 38.462 0.00 0.00 0.00 2.40
2388 2801 6.954684 GGAAGGACTAGATACAGAATCCCATA 59.045 42.308 0.00 0.00 34.90 2.74
2413 2834 3.118445 TGAACATCTCACACACAGAACCA 60.118 43.478 0.00 0.00 0.00 3.67
2478 2899 2.946990 CAGCTTGTGGCATCATCACATA 59.053 45.455 0.00 0.00 43.53 2.29
2494 2915 4.953667 TCACATAGCAGGAACATCTCATC 58.046 43.478 0.00 0.00 0.00 2.92
2544 2965 5.505181 TCTCCTGAAAATAGCAAGGAAGT 57.495 39.130 0.00 0.00 0.00 3.01
2549 2970 2.420058 AAATAGCAAGGAAGTCCCCG 57.580 50.000 0.00 0.00 36.42 5.73
2576 2997 4.202151 GCATTTTATAGGCTGGGACAAAGG 60.202 45.833 0.00 0.00 38.70 3.11
2580 3001 0.474854 TAGGCTGGGACAAAGGTGGA 60.475 55.000 0.00 0.00 38.70 4.02
2963 3385 2.171448 CTCATTTTGGATCGGAGGGAGT 59.829 50.000 0.00 0.00 0.00 3.85
3078 3500 9.772973 ACTAGTACATGAACAGTGATTTTGTTA 57.227 29.630 0.00 0.00 38.78 2.41
3090 3512 8.280497 ACAGTGATTTTGTTATCAACTCGTTAC 58.720 33.333 0.00 0.00 36.37 2.50
3128 3550 5.426689 AGAGATTAAGTTGCTCATGTGGA 57.573 39.130 0.00 0.00 0.00 4.02
3142 3564 1.745232 TGTGGAAGCGTGAGTTTGTT 58.255 45.000 0.00 0.00 33.53 2.83
3143 3565 1.668751 TGTGGAAGCGTGAGTTTGTTC 59.331 47.619 0.00 0.00 33.53 3.18
3144 3566 1.940613 GTGGAAGCGTGAGTTTGTTCT 59.059 47.619 0.00 0.00 33.53 3.01
3145 3567 3.128349 GTGGAAGCGTGAGTTTGTTCTA 58.872 45.455 0.00 0.00 33.53 2.10
3146 3568 3.184581 GTGGAAGCGTGAGTTTGTTCTAG 59.815 47.826 0.00 0.00 33.53 2.43
3147 3569 3.181469 TGGAAGCGTGAGTTTGTTCTAGT 60.181 43.478 0.00 0.00 33.53 2.57
3158 3580 8.035984 GTGAGTTTGTTCTAGTTAAGATAGCCT 58.964 37.037 0.00 0.00 33.05 4.58
3162 3584 6.222038 TGTTCTAGTTAAGATAGCCTGGTG 57.778 41.667 0.00 0.00 33.05 4.17
3181 3603 6.656693 CCTGGTGACAAAATAGAGTTTCTCAT 59.343 38.462 0.00 0.00 42.06 2.90
3200 3622 5.001237 TCATTGTCTTGCCAATTATGCTG 57.999 39.130 1.40 0.00 32.81 4.41
3228 3650 1.577421 GCAATACCGCGTGTTGGTT 59.423 52.632 4.92 0.00 40.96 3.67
3245 3667 1.339727 GGTTACATCGAGGGCCACTTT 60.340 52.381 6.18 0.00 0.00 2.66
3312 3734 7.256190 GCTTTGAAATAAAACTCTTTACCCCCT 60.256 37.037 0.00 0.00 29.82 4.79
3314 3736 6.250711 TGAAATAAAACTCTTTACCCCCTCC 58.749 40.000 0.00 0.00 29.82 4.30
3316 3738 1.379776 AAACTCTTTACCCCCTCCCC 58.620 55.000 0.00 0.00 0.00 4.81
3366 3792 5.292101 GGGTTTCATGATCTTCTCTAACACG 59.708 44.000 0.00 0.00 0.00 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 9.372189 AGTTTAGGACCTTGTCTTTTACTACTA 57.628 33.333 0.00 0.00 32.47 1.82
54 55 8.260099 AGTTTAGGACCTTGTCTTTTACTACT 57.740 34.615 0.00 0.00 32.47 2.57
55 56 9.636879 CTAGTTTAGGACCTTGTCTTTTACTAC 57.363 37.037 0.00 0.00 32.47 2.73
86 87 2.586648 AAGAACTGGCCGAGGAATTT 57.413 45.000 0.00 0.00 0.00 1.82
95 96 1.801178 CGTCTCAGAAAAGAACTGGCC 59.199 52.381 0.00 0.00 36.22 5.36
112 113 2.284417 GTGAACCAATCGGCTTATCGTC 59.716 50.000 0.00 0.00 34.57 4.20
211 252 1.922545 GCGGAAGATCTTTGCATTTGC 59.077 47.619 21.88 10.57 42.50 3.68
320 362 3.134458 GCTTCTCCAATATTCCGACAGG 58.866 50.000 0.00 0.00 39.46 4.00
321 363 2.797156 CGCTTCTCCAATATTCCGACAG 59.203 50.000 0.00 0.00 0.00 3.51
322 364 2.483013 CCGCTTCTCCAATATTCCGACA 60.483 50.000 0.00 0.00 0.00 4.35
334 376 0.822164 TAAGCTGGTACCGCTTCTCC 59.178 55.000 32.67 8.94 43.79 3.71
335 377 2.269172 GTTAAGCTGGTACCGCTTCTC 58.731 52.381 32.67 25.07 43.79 2.87
336 378 1.621814 TGTTAAGCTGGTACCGCTTCT 59.378 47.619 32.67 20.58 43.79 2.85
337 379 2.088950 TGTTAAGCTGGTACCGCTTC 57.911 50.000 32.67 24.08 43.79 3.86
339 381 1.346722 AGTTGTTAAGCTGGTACCGCT 59.653 47.619 20.83 20.83 39.94 5.52
340 382 1.463444 CAGTTGTTAAGCTGGTACCGC 59.537 52.381 17.54 17.54 0.00 5.68
341 383 2.073816 CCAGTTGTTAAGCTGGTACCG 58.926 52.381 7.57 3.32 45.28 4.02
380 440 0.815734 GTTGCTAGGCTGACCGAGTA 59.184 55.000 0.00 0.00 40.61 2.59
394 454 3.882888 TCCAAAATCGACTTCTTGTTGCT 59.117 39.130 0.00 0.00 0.00 3.91
395 455 4.222114 CTCCAAAATCGACTTCTTGTTGC 58.778 43.478 0.00 0.00 0.00 4.17
398 458 2.814336 GGCTCCAAAATCGACTTCTTGT 59.186 45.455 0.00 0.00 0.00 3.16
405 465 1.661112 CTTCTCGGCTCCAAAATCGAC 59.339 52.381 0.00 0.00 0.00 4.20
406 466 1.548719 TCTTCTCGGCTCCAAAATCGA 59.451 47.619 0.00 0.00 0.00 3.59
416 476 4.392940 CCCATTATTCATTCTTCTCGGCT 58.607 43.478 0.00 0.00 0.00 5.52
417 477 3.503748 CCCCATTATTCATTCTTCTCGGC 59.496 47.826 0.00 0.00 0.00 5.54
418 478 3.503748 GCCCCATTATTCATTCTTCTCGG 59.496 47.826 0.00 0.00 0.00 4.63
419 479 3.503748 GGCCCCATTATTCATTCTTCTCG 59.496 47.826 0.00 0.00 0.00 4.04
630 699 2.434185 GCATTGACCCGTCAGCGA 60.434 61.111 0.00 0.00 41.13 4.93
796 870 3.436704 GCGTTGTTCTGATCTGATTTGGA 59.563 43.478 2.84 0.00 0.00 3.53
884 1262 1.080501 TGGCGAACGAGAGAAGCTG 60.081 57.895 0.00 0.00 0.00 4.24
885 1263 1.080434 GTGGCGAACGAGAGAAGCT 60.080 57.895 0.00 0.00 0.00 3.74
886 1264 3.464628 GTGGCGAACGAGAGAAGC 58.535 61.111 0.00 0.00 0.00 3.86
895 1273 1.837538 TACAAAGCTGCGTGGCGAAC 61.838 55.000 10.43 0.00 37.29 3.95
896 1274 1.595655 TACAAAGCTGCGTGGCGAA 60.596 52.632 10.43 0.00 37.29 4.70
897 1275 2.029815 TACAAAGCTGCGTGGCGA 59.970 55.556 10.43 0.00 37.29 5.54
898 1276 2.173382 GTACAAAGCTGCGTGGCG 59.827 61.111 10.43 0.00 37.29 5.69
899 1277 1.207593 CTGTACAAAGCTGCGTGGC 59.792 57.895 10.43 4.51 0.00 5.01
900 1278 1.207593 GCTGTACAAAGCTGCGTGG 59.792 57.895 10.43 0.00 40.20 4.94
901 1279 4.826600 GCTGTACAAAGCTGCGTG 57.173 55.556 0.00 5.04 40.20 5.34
918 1296 1.990563 CCCAAGCAACTAACGTACGAG 59.009 52.381 24.41 12.54 0.00 4.18
982 1377 2.002586 CATTCCAACAACTCGCTCGAT 58.997 47.619 0.00 0.00 0.00 3.59
984 1379 0.443869 CCATTCCAACAACTCGCTCG 59.556 55.000 0.00 0.00 0.00 5.03
1422 1835 2.001812 CGAAGGATATCATCTGCGGG 57.998 55.000 4.83 0.00 0.00 6.13
1463 1876 4.749310 CCGCCTCGAACTGCTGCT 62.749 66.667 0.00 0.00 0.00 4.24
1740 2153 3.036084 CGATCGTACGCCATGGCC 61.036 66.667 30.79 16.00 37.98 5.36
1973 2386 2.617274 GGTCCAGTGTTCGCTTGCC 61.617 63.158 0.00 0.00 0.00 4.52
1985 2398 2.434359 GCGGAGGTTTCGGTCCAG 60.434 66.667 0.00 0.00 32.55 3.86
1991 2404 2.202623 CGGAGAGCGGAGGTTTCG 60.203 66.667 0.00 0.00 40.20 3.46
2027 2440 1.886542 GATTTTGCTCTGGTTCCGGTT 59.113 47.619 0.00 0.00 0.00 4.44
2028 2441 1.534729 GATTTTGCTCTGGTTCCGGT 58.465 50.000 0.00 0.00 0.00 5.28
2244 2657 4.175337 TAGTCCATGCCGGCCTGC 62.175 66.667 26.77 12.95 33.14 4.85
2259 2672 4.814294 GGCGCACTGGGGACGTAG 62.814 72.222 10.83 0.00 0.00 3.51
2321 2734 3.855853 GAGGAGAAGGGGGAGCGC 61.856 72.222 0.00 0.00 0.00 5.92
2375 2788 7.510343 TGAGATGTTCAGATATGGGATTCTGTA 59.490 37.037 0.00 0.00 40.22 2.74
2378 2791 6.328410 TGTGAGATGTTCAGATATGGGATTCT 59.672 38.462 0.00 0.00 36.21 2.40
2379 2792 6.426328 GTGTGAGATGTTCAGATATGGGATTC 59.574 42.308 0.00 0.00 36.21 2.52
2381 2794 5.367644 TGTGTGAGATGTTCAGATATGGGAT 59.632 40.000 0.00 0.00 36.21 3.85
2382 2795 4.716287 TGTGTGAGATGTTCAGATATGGGA 59.284 41.667 0.00 0.00 36.21 4.37
2388 2801 4.879197 TCTGTGTGTGAGATGTTCAGAT 57.121 40.909 0.00 0.00 36.21 2.90
2413 2834 0.608130 TGCATCTCACAGCGTAGGTT 59.392 50.000 0.00 0.00 33.74 3.50
2478 2899 2.194859 AGGTGATGAGATGTTCCTGCT 58.805 47.619 0.00 0.00 0.00 4.24
2494 2915 5.928839 TCGATCAGAGAGAAAAGAAAAGGTG 59.071 40.000 0.00 0.00 0.00 4.00
2534 2955 4.035102 GCCGGGGACTTCCTTGCT 62.035 66.667 2.18 0.00 35.95 3.91
2544 2965 1.202879 CCTATAAAATGCAGCCGGGGA 60.203 52.381 2.18 0.00 0.00 4.81
2549 2970 1.615392 CCCAGCCTATAAAATGCAGCC 59.385 52.381 0.00 0.00 0.00 4.85
2576 2997 7.684529 AGGATGGAGAATCAAATATAGTCCAC 58.315 38.462 0.00 0.00 35.49 4.02
2608 3029 5.363868 TCATCTTAGAATCATCACGGAAGGT 59.636 40.000 0.00 0.00 0.00 3.50
2656 3077 7.986085 AAGATGCAGTAAACAACTAATGAGT 57.014 32.000 0.00 0.00 35.76 3.41
2662 3083 8.556194 CACAACTAAAGATGCAGTAAACAACTA 58.444 33.333 0.00 0.00 35.76 2.24
2671 3092 4.640201 ACACAACACAACTAAAGATGCAGT 59.360 37.500 0.00 0.00 0.00 4.40
2963 3385 9.832445 AGAAGACTTCATTGACTAAAACAAGTA 57.168 29.630 17.34 0.00 0.00 2.24
3078 3500 4.202223 ACAAGTGACCAGTAACGAGTTGAT 60.202 41.667 0.00 0.00 0.00 2.57
3090 3512 7.657761 ACTTAATCTCTTGTAACAAGTGACCAG 59.342 37.037 0.00 0.00 0.00 4.00
3128 3550 6.278363 TCTTAACTAGAACAAACTCACGCTT 58.722 36.000 0.00 0.00 0.00 4.68
3142 3564 5.516044 TGTCACCAGGCTATCTTAACTAGA 58.484 41.667 0.00 0.00 37.28 2.43
3143 3565 5.854010 TGTCACCAGGCTATCTTAACTAG 57.146 43.478 0.00 0.00 0.00 2.57
3144 3566 6.614694 TTTGTCACCAGGCTATCTTAACTA 57.385 37.500 0.00 0.00 0.00 2.24
3145 3567 5.499004 TTTGTCACCAGGCTATCTTAACT 57.501 39.130 0.00 0.00 0.00 2.24
3146 3568 6.759497 ATTTTGTCACCAGGCTATCTTAAC 57.241 37.500 0.00 0.00 0.00 2.01
3147 3569 7.857456 TCTATTTTGTCACCAGGCTATCTTAA 58.143 34.615 0.00 0.00 0.00 1.85
3158 3580 7.502226 ACAATGAGAAACTCTATTTTGTCACCA 59.498 33.333 0.00 0.00 40.43 4.17
3162 3584 9.604626 CAAGACAATGAGAAACTCTATTTTGTC 57.395 33.333 17.91 17.91 37.25 3.18
3181 3603 3.872511 CCAGCATAATTGGCAAGACAA 57.127 42.857 5.96 0.00 34.41 3.18
3200 3622 1.901650 GCGGTATTGCGAGCTATGCC 61.902 60.000 14.25 14.25 32.68 4.40
3210 3632 0.797542 TAACCAACACGCGGTATTGC 59.202 50.000 12.47 0.00 34.99 3.56
3220 3642 1.084289 GCCCTCGATGTAACCAACAC 58.916 55.000 0.00 0.00 42.09 3.32
3228 3650 2.871096 AAAAAGTGGCCCTCGATGTA 57.129 45.000 0.00 0.00 0.00 2.29
3314 3736 3.137360 TCCCATTGTTTTCTTTTTGGGGG 59.863 43.478 5.99 0.00 43.30 5.40
3316 3738 5.436175 AGTTCCCATTGTTTTCTTTTTGGG 58.564 37.500 0.00 0.00 44.26 4.12
3319 3741 7.092623 ACCCTAAGTTCCCATTGTTTTCTTTTT 60.093 33.333 0.00 0.00 0.00 1.94
3322 3744 5.464069 ACCCTAAGTTCCCATTGTTTTCTT 58.536 37.500 0.00 0.00 0.00 2.52
3324 3746 5.801531 AACCCTAAGTTCCCATTGTTTTC 57.198 39.130 0.00 0.00 30.99 2.29


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

AutoCloner maintained by Alex Coulton.