Multiple sequence alignment - TraesCS2B01G499900

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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 TraesCS2B01G499900 chr2B 100.000 5354 0 0 1 5354 695589207 695594560 0.000000e+00 9888
1 TraesCS2B01G499900 chr2A 95.462 4584 173 20 1 4573 716229271 716233830 0.000000e+00 7280
2 TraesCS2B01G499900 chr2A 85.425 741 46 26 4631 5354 716233828 716234523 0.000000e+00 713
3 TraesCS2B01G499900 chr2D 92.680 2896 148 36 2504 5354 578700800 578703676 0.000000e+00 4115
4 TraesCS2B01G499900 chr2D 93.680 1788 93 11 1 1783 578698311 578700083 0.000000e+00 2658
5 TraesCS2B01G499900 chr2D 88.922 334 27 6 2166 2498 578700432 578700756 2.320000e-108 403
6 TraesCS2B01G499900 chr2D 90.435 230 17 3 1935 2164 578700123 578700347 1.130000e-76 298


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 TraesCS2B01G499900 chr2B 695589207 695594560 5353 False 9888.0 9888 100.00000 1 5354 1 chr2B.!!$F1 5353
1 TraesCS2B01G499900 chr2A 716229271 716234523 5252 False 3996.5 7280 90.44350 1 5354 2 chr2A.!!$F1 5353
2 TraesCS2B01G499900 chr2D 578698311 578703676 5365 False 1868.5 4115 91.42925 1 5354 4 chr2D.!!$F1 5353

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
916 918 1.492599 TGTCCACAATGAACCTGACCA 59.507 47.619 0.00 0.0 0.0 4.02 F
1235 1238 0.465460 TTGGTTGGACAGTCACAGGC 60.465 55.000 2.17 0.0 0.0 4.85 F
2640 2784 1.089920 ATGCAGAGGTCATTGTTCGC 58.910 50.000 0.00 0.0 0.0 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2250 2356 0.682292 TGTGGTTAGCGTGGATGTGA 59.318 50.0 0.00 0.0 0.0 3.58 R
3075 3220 0.403271 AGTGCTGGCCTGAATTGTCT 59.597 50.0 14.77 0.0 0.0 3.41 R
4540 4703 0.460987 CGAGGTTGGCAGAGGACATC 60.461 60.0 0.00 0.0 0.0 3.06 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
269 270 2.700773 GCCCTGCCGAAATGTGGTC 61.701 63.158 0.00 0.00 0.00 4.02
453 454 5.439721 TGGAGTATTTCACTTCCATGATGG 58.560 41.667 4.74 4.74 37.72 3.51
575 576 2.304761 TGTGGATACTGAACCCAACTCC 59.695 50.000 0.00 0.00 37.61 3.85
656 657 6.418101 AGAAACTGCAGCCAAGAATCTTATA 58.582 36.000 15.27 0.00 0.00 0.98
690 691 5.357314 GCTGAGAGTTCTGTACACTATACCA 59.643 44.000 0.00 0.00 0.00 3.25
707 708 3.302365 ACCATGCTTGCAAACATGTAC 57.698 42.857 30.79 5.56 41.69 2.90
741 742 2.431954 ATGGGAGGATGCTCAAAGTG 57.568 50.000 16.72 0.00 0.00 3.16
916 918 1.492599 TGTCCACAATGAACCTGACCA 59.507 47.619 0.00 0.00 0.00 4.02
923 925 4.221262 CACAATGAACCTGACCAATCCAAT 59.779 41.667 0.00 0.00 0.00 3.16
1177 1180 3.317608 GCGGATGCATGTTTGTCTG 57.682 52.632 2.46 0.00 42.15 3.51
1211 1214 6.873997 TGTCAGTATTCTCAATTATGTCCGT 58.126 36.000 0.00 0.00 0.00 4.69
1219 1222 6.918892 TCTCAATTATGTCCGTTGTATTGG 57.081 37.500 0.00 0.00 0.00 3.16
1235 1238 0.465460 TTGGTTGGACAGTCACAGGC 60.465 55.000 2.17 0.00 0.00 4.85
1347 1353 6.878923 CAGTTTGTGATTCCCTTCTGTACATA 59.121 38.462 0.00 0.00 0.00 2.29
1354 1360 9.915629 GTGATTCCCTTCTGTACATAACTATAG 57.084 37.037 0.00 0.00 0.00 1.31
1355 1361 9.656323 TGATTCCCTTCTGTACATAACTATAGT 57.344 33.333 0.00 0.00 0.00 2.12
1382 1388 2.436911 ACCCTGTTTTTCCACTCTACGT 59.563 45.455 0.00 0.00 0.00 3.57
1405 1411 7.390440 ACGTTATCCATTTCTCTTTTGATGTGA 59.610 33.333 0.00 0.00 0.00 3.58
1655 1661 6.042143 CCATGTGCTGTTGACTTAAGTTTTT 58.958 36.000 10.02 0.00 0.00 1.94
1815 1823 5.064558 AGTATAGTCCTGACTGATACACCG 58.935 45.833 10.02 0.00 42.52 4.94
1817 1825 3.019799 AGTCCTGACTGATACACCGAT 57.980 47.619 0.00 0.00 40.75 4.18
1822 1830 3.491619 CCTGACTGATACACCGATCTTGG 60.492 52.174 0.00 0.00 0.00 3.61
1824 1832 3.513912 TGACTGATACACCGATCTTGGTT 59.486 43.478 0.00 0.00 41.38 3.67
1950 1973 7.336931 GGTTAGTCTTCTTTCAAATGGCATCTA 59.663 37.037 0.00 0.00 0.00 1.98
1966 1989 9.700831 AATGGCATCTAAGGATAATTATTACCC 57.299 33.333 0.00 0.00 0.00 3.69
2065 2088 3.658757 GCACTTTTTAGGAACATGCCA 57.341 42.857 0.00 0.00 0.00 4.92
2067 2090 4.568956 GCACTTTTTAGGAACATGCCATT 58.431 39.130 0.00 0.00 0.00 3.16
2128 2151 3.433274 CCACGATGGATGGTTATCATTCG 59.567 47.826 0.00 0.00 40.96 3.34
2250 2356 8.696374 TCATCCGAGACTATTCTACAATTCTTT 58.304 33.333 0.00 0.00 29.47 2.52
2317 2423 4.953667 TCATATGCTGAAGTCTTAGCCAG 58.046 43.478 0.00 4.27 39.15 4.85
2347 2453 7.227512 ACTGGCTGTGTGATATAAGAAAATAGC 59.772 37.037 0.00 0.00 0.00 2.97
2462 2568 6.051717 ACTGAACTATATAAAGCAGGCTGTG 58.948 40.000 17.16 0.00 0.00 3.66
2463 2569 6.127054 ACTGAACTATATAAAGCAGGCTGTGA 60.127 38.462 17.16 0.00 0.00 3.58
2464 2570 6.283694 TGAACTATATAAAGCAGGCTGTGAG 58.716 40.000 17.16 4.75 0.00 3.51
2465 2571 5.220710 ACTATATAAAGCAGGCTGTGAGG 57.779 43.478 17.16 0.00 0.00 3.86
2466 2572 4.656112 ACTATATAAAGCAGGCTGTGAGGT 59.344 41.667 17.16 2.88 0.00 3.85
2556 2700 5.730296 TTCTCCTTCCTCTTGTCTTACAG 57.270 43.478 0.00 0.00 0.00 2.74
2640 2784 1.089920 ATGCAGAGGTCATTGTTCGC 58.910 50.000 0.00 0.00 0.00 4.70
2848 2992 6.025539 TGATAGCATACCAGGATTACCATCT 58.974 40.000 0.00 0.00 38.94 2.90
3057 3202 7.704271 TCAAGTAAGATAGGTGACATAGTTCG 58.296 38.462 0.00 0.00 0.00 3.95
3064 3209 7.565680 AGATAGGTGACATAGTTCGGAAAAAT 58.434 34.615 0.00 0.00 0.00 1.82
3075 3220 1.064611 TCGGAAAAATGGCGGGGATAA 60.065 47.619 0.00 0.00 0.00 1.75
3079 3224 2.818751 AAAATGGCGGGGATAAGACA 57.181 45.000 0.00 0.00 0.00 3.41
3090 3235 3.217626 GGGATAAGACAATTCAGGCCAG 58.782 50.000 5.01 0.00 0.00 4.85
3121 3266 2.931512 AAACCCACACAGTTTTGACG 57.068 45.000 0.00 0.00 33.73 4.35
3297 3445 2.711547 AGCTTTGAACAACCTACCTCCT 59.288 45.455 0.00 0.00 0.00 3.69
3336 3484 5.696724 CACTCGTAATCTGAACCAGTTCTTT 59.303 40.000 11.56 5.86 40.14 2.52
3393 3541 9.021807 GTGGTTCTGCTAGGTATATACTATTCA 57.978 37.037 12.54 5.77 0.00 2.57
3558 3708 1.213537 GGTGCTCGTTTGCATGCAT 59.786 52.632 23.37 0.00 45.23 3.96
3559 3709 1.074319 GGTGCTCGTTTGCATGCATG 61.074 55.000 23.37 22.70 45.23 4.06
3649 3800 7.201723 GGGAAAACTAAACTTTGTCGGTTCTTA 60.202 37.037 0.00 0.00 0.00 2.10
3723 3878 9.836076 AAAAACAAAGTATAACTCCTTATTCGC 57.164 29.630 0.00 0.00 0.00 4.70
3748 3903 8.445493 GCAAACCAGTACGTACTACATTATTTT 58.555 33.333 26.95 14.53 34.13 1.82
3888 4043 1.273327 GCAGGAAACCATGGAAACTGG 59.727 52.381 21.47 4.77 39.80 4.00
4345 4500 4.166011 GCGCCGTGAACCAGATGC 62.166 66.667 0.00 0.00 0.00 3.91
4395 4550 3.048337 TCATCGGCCCGTAAATTATCC 57.952 47.619 1.63 0.00 0.00 2.59
4471 4634 5.063060 GCATCATTGTCTTTCTTCATTTGCC 59.937 40.000 0.00 0.00 0.00 4.52
4490 4653 3.110358 GCCTTGTTTGTTCGTTTGTACC 58.890 45.455 0.00 0.00 0.00 3.34
4540 4703 7.170151 TGTTTGCTTGATTGATTCAGTGAAATG 59.830 33.333 10.14 0.00 35.27 2.32
4544 4707 7.033791 GCTTGATTGATTCAGTGAAATGATGT 58.966 34.615 10.14 0.00 35.27 3.06
4628 4792 1.512734 CGGCTCGTACACGGTACAC 60.513 63.158 12.62 3.86 40.29 2.90
4769 4941 0.250640 GCTAGCTCCACATGGATGGG 60.251 60.000 7.70 0.00 44.46 4.00
4800 4972 2.001812 CCATCCACTCGTCAACTCTG 57.998 55.000 0.00 0.00 0.00 3.35
4836 5008 4.409247 ACACTCCTTGTACACTTCCTTTCT 59.591 41.667 0.00 0.00 36.32 2.52
4994 5181 9.846248 AGACAACTAATAATCAGCAACATTTTC 57.154 29.630 0.00 0.00 0.00 2.29
4995 5182 9.846248 GACAACTAATAATCAGCAACATTTTCT 57.154 29.630 0.00 0.00 0.00 2.52
5031 5242 7.462571 AAATCCTTTTGTATACACCACCTTC 57.537 36.000 4.68 0.00 0.00 3.46
5032 5243 5.836024 TCCTTTTGTATACACCACCTTCT 57.164 39.130 4.68 0.00 0.00 2.85
5036 5247 7.562088 TCCTTTTGTATACACCACCTTCTTTTT 59.438 33.333 4.68 0.00 0.00 1.94
5037 5248 7.651704 CCTTTTGTATACACCACCTTCTTTTTG 59.348 37.037 4.68 0.00 0.00 2.44
5038 5249 5.699097 TGTATACACCACCTTCTTTTTGC 57.301 39.130 0.08 0.00 0.00 3.68
5039 5250 5.381757 TGTATACACCACCTTCTTTTTGCT 58.618 37.500 0.08 0.00 0.00 3.91
5040 5251 5.472137 TGTATACACCACCTTCTTTTTGCTC 59.528 40.000 0.08 0.00 0.00 4.26
5041 5252 1.676006 ACACCACCTTCTTTTTGCTCG 59.324 47.619 0.00 0.00 0.00 5.03
5042 5253 1.676006 CACCACCTTCTTTTTGCTCGT 59.324 47.619 0.00 0.00 0.00 4.18
5043 5254 1.947456 ACCACCTTCTTTTTGCTCGTC 59.053 47.619 0.00 0.00 0.00 4.20
5044 5255 1.266989 CCACCTTCTTTTTGCTCGTCC 59.733 52.381 0.00 0.00 0.00 4.79
5045 5256 1.946768 CACCTTCTTTTTGCTCGTCCA 59.053 47.619 0.00 0.00 0.00 4.02
5046 5257 2.357637 CACCTTCTTTTTGCTCGTCCAA 59.642 45.455 0.00 0.00 0.00 3.53
5047 5258 3.004734 CACCTTCTTTTTGCTCGTCCAAT 59.995 43.478 0.00 0.00 0.00 3.16
5048 5259 3.004734 ACCTTCTTTTTGCTCGTCCAATG 59.995 43.478 0.00 0.00 0.00 2.82
5049 5260 3.253188 CCTTCTTTTTGCTCGTCCAATGA 59.747 43.478 0.00 0.00 0.00 2.57
5050 5261 4.082571 CCTTCTTTTTGCTCGTCCAATGAT 60.083 41.667 0.00 0.00 0.00 2.45
5051 5262 5.452078 TTCTTTTTGCTCGTCCAATGATT 57.548 34.783 0.00 0.00 0.00 2.57
5052 5263 6.349280 CCTTCTTTTTGCTCGTCCAATGATTA 60.349 38.462 0.00 0.00 0.00 1.75
5053 5264 6.757897 TCTTTTTGCTCGTCCAATGATTAT 57.242 33.333 0.00 0.00 0.00 1.28
5054 5265 6.785191 TCTTTTTGCTCGTCCAATGATTATC 58.215 36.000 0.00 0.00 0.00 1.75
5055 5266 6.374053 TCTTTTTGCTCGTCCAATGATTATCA 59.626 34.615 0.00 0.00 0.00 2.15
5056 5267 6.698008 TTTTGCTCGTCCAATGATTATCAT 57.302 33.333 1.25 1.25 39.09 2.45
5057 5268 5.929697 TTGCTCGTCCAATGATTATCATC 57.070 39.130 8.26 0.00 35.76 2.92
5067 5292 5.048504 CCAATGATTATCATCCCAAGTTCCG 60.049 44.000 8.26 0.00 35.76 4.30
5085 5310 1.403780 CCGAACCGAAAGACGAGGAAT 60.404 52.381 0.00 0.00 45.77 3.01
5088 5313 2.959275 CCGAAAGACGAGGAATCGG 58.041 57.895 2.46 0.00 45.88 4.18
5090 5315 2.273370 CGAAAGACGAGGAATCGGAA 57.727 50.000 2.46 0.00 45.77 4.30
5091 5316 2.810650 CGAAAGACGAGGAATCGGAAT 58.189 47.619 2.46 0.00 45.77 3.01
5214 5444 1.147600 GGGCCAGTATAACACCCGG 59.852 63.158 4.39 0.00 0.00 5.73
5222 5452 2.299867 AGTATAACACCCGGAACAACGT 59.700 45.455 0.73 0.00 0.00 3.99
5238 5468 3.246699 ACAACGTCGTAATCAAACCTGTG 59.753 43.478 0.00 0.00 0.00 3.66
5303 5545 4.740822 CCGAACAAGGGGGCAGGG 62.741 72.222 0.00 0.00 0.00 4.45
5304 5546 4.740822 CGAACAAGGGGGCAGGGG 62.741 72.222 0.00 0.00 0.00 4.79
5305 5547 3.590574 GAACAAGGGGGCAGGGGT 61.591 66.667 0.00 0.00 0.00 4.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 94 5.706833 TGAGACATGACACATTAGCACAAAT 59.293 36.000 0.00 0.00 0.00 2.32
269 270 4.569966 GCAGTAATGAGTGAAGTCCATGAG 59.430 45.833 0.00 0.00 0.00 2.90
453 454 2.132762 CGGATCAATACCGTACTTGCC 58.867 52.381 0.00 0.00 44.57 4.52
575 576 2.430465 AGCATAGCGCCCAATATTGAG 58.570 47.619 17.23 4.64 44.04 3.02
656 657 4.101741 ACAGAACTCTCAGCACCTTTACTT 59.898 41.667 0.00 0.00 0.00 2.24
690 691 1.269174 TGCGTACATGTTTGCAAGCAT 59.731 42.857 21.53 21.53 33.80 3.79
707 708 5.551233 TCCTCCCATAAATTAGATTCTGCG 58.449 41.667 0.00 0.00 0.00 5.18
741 742 5.237048 TGTTTCAGCCATTAATTTCCTTGC 58.763 37.500 0.00 0.00 0.00 4.01
817 818 9.894783 CATTATCTGAATATCTTGGAAAGCAAG 57.105 33.333 0.00 0.00 45.70 4.01
849 850 1.142936 TGGTGCATCTATCAGGGCAT 58.857 50.000 0.00 0.00 38.68 4.40
916 918 5.158141 TCTGGAGGCTCTACATATTGGATT 58.842 41.667 15.23 0.00 0.00 3.01
923 925 5.211973 ACAAAGATCTGGAGGCTCTACATA 58.788 41.667 15.23 0.00 0.00 2.29
1174 1177 9.025041 TGAGAATACTGACAAGACTTTATCAGA 57.975 33.333 23.93 13.11 40.92 3.27
1211 1214 4.133820 CTGTGACTGTCCAACCAATACAA 58.866 43.478 5.17 0.00 0.00 2.41
1219 1222 2.543777 TAAGCCTGTGACTGTCCAAC 57.456 50.000 5.17 0.00 0.00 3.77
1259 1262 6.274157 TCAGATAGAGACAACTTGGAAGTC 57.726 41.667 0.00 0.00 38.57 3.01
1310 1316 6.657541 GGAATCACAAACTGGTTTATCCACTA 59.342 38.462 0.00 0.00 41.93 2.74
1330 1336 9.915629 CACTATAGTTATGTACAGAAGGGAATC 57.084 37.037 2.50 0.00 0.00 2.52
1347 1353 5.609533 AAACAGGGTATCGCACTATAGTT 57.390 39.130 1.56 0.00 0.00 2.24
1354 1360 2.095415 GTGGAAAAACAGGGTATCGCAC 60.095 50.000 0.00 0.00 0.00 5.34
1355 1361 2.156098 GTGGAAAAACAGGGTATCGCA 58.844 47.619 0.00 0.00 0.00 5.10
1382 1388 8.868522 ACTCACATCAAAAGAGAAATGGATAA 57.131 30.769 0.00 0.00 33.69 1.75
1620 1626 3.620488 ACAGCACATGGGTTCGAATAAT 58.380 40.909 0.00 0.00 0.00 1.28
1624 1630 0.950836 CAACAGCACATGGGTTCGAA 59.049 50.000 0.00 0.00 0.00 3.71
1815 1823 2.370281 TCGAGCTGACAACCAAGATC 57.630 50.000 0.00 0.00 0.00 2.75
1817 1825 1.618343 TGATCGAGCTGACAACCAAGA 59.382 47.619 0.90 0.00 0.00 3.02
1822 1830 1.585668 CGTCATGATCGAGCTGACAAC 59.414 52.381 23.32 7.69 39.36 3.32
1824 1832 1.094785 TCGTCATGATCGAGCTGACA 58.905 50.000 23.32 13.33 39.36 3.58
1966 1989 9.712305 ATATTATTTAGGGAACGACTGATTCTG 57.288 33.333 0.00 0.00 0.00 3.02
2065 2088 5.171476 CCGACACTCTTAAGATGTGACAAT 58.829 41.667 27.40 14.20 35.83 2.71
2067 2090 3.572682 ACCGACACTCTTAAGATGTGACA 59.427 43.478 27.40 0.00 35.83 3.58
2164 2187 7.786030 TCCAGAAGTTAAGGATCTGTAATCTG 58.214 38.462 9.84 3.38 39.10 2.90
2250 2356 0.682292 TGTGGTTAGCGTGGATGTGA 59.318 50.000 0.00 0.00 0.00 3.58
2317 2423 6.392625 TCTTATATCACACAGCCAGTAGAC 57.607 41.667 0.00 0.00 0.00 2.59
2347 2453 2.679837 CCTACATGCCTTTACAGCTGTG 59.320 50.000 29.57 13.53 0.00 3.66
2498 2604 4.917415 GTCTGTAAACCATGTTGTGAATGC 59.083 41.667 0.00 0.00 0.00 3.56
2556 2700 2.710096 TGCATAACACTAAGGAGGGC 57.290 50.000 0.00 0.00 0.00 5.19
2640 2784 2.538512 TGATCCTGGCAATCTCATCG 57.461 50.000 1.24 0.00 0.00 3.84
2848 2992 2.809696 GTTCGGTTCCGATTCCTTTTCA 59.190 45.455 14.70 0.00 38.30 2.69
3044 3188 4.674362 GCCATTTTTCCGAACTATGTCACC 60.674 45.833 0.00 0.00 0.00 4.02
3057 3202 2.361119 GTCTTATCCCCGCCATTTTTCC 59.639 50.000 0.00 0.00 0.00 3.13
3064 3209 1.562008 TGAATTGTCTTATCCCCGCCA 59.438 47.619 0.00 0.00 0.00 5.69
3075 3220 0.403271 AGTGCTGGCCTGAATTGTCT 59.597 50.000 14.77 0.00 0.00 3.41
3079 3224 4.428845 CCAGTGCTGGCCTGAATT 57.571 55.556 14.77 0.00 44.73 2.17
3090 3235 2.421314 GGGTTTTGCCACCAGTGC 59.579 61.111 0.00 0.00 38.79 4.40
3393 3541 6.182627 TCATGCATTGAGTTTAGTTCCTGAT 58.817 36.000 0.00 0.00 0.00 2.90
3558 3708 5.125417 GCTTGATTAACCCATTGCTTAGTCA 59.875 40.000 0.00 0.00 0.00 3.41
3559 3709 5.125417 TGCTTGATTAACCCATTGCTTAGTC 59.875 40.000 0.00 0.00 0.00 2.59
3603 3753 2.352715 CCGTCTCTGTTGACTATGCACA 60.353 50.000 0.00 0.00 35.00 4.57
3608 3758 4.283722 AGTTTTCCCGTCTCTGTTGACTAT 59.716 41.667 0.00 0.00 35.00 2.12
3609 3759 3.640029 AGTTTTCCCGTCTCTGTTGACTA 59.360 43.478 0.00 0.00 35.00 2.59
3748 3903 0.574454 GCGCGTGCAAAATGAACAAA 59.426 45.000 17.66 0.00 42.15 2.83
3749 3904 2.211675 GCGCGTGCAAAATGAACAA 58.788 47.368 17.66 0.00 42.15 2.83
3888 4043 4.797471 TGCATGAACAAGTTAGAATGTGC 58.203 39.130 0.00 0.00 0.00 4.57
4248 4403 1.079819 CATGGACGCCACGAAGTCT 60.080 57.895 0.50 0.00 41.61 3.24
4340 4495 2.280389 CGGCCTACATGCGCATCT 60.280 61.111 22.51 12.42 0.00 2.90
4395 4550 9.173021 TCAATTATACAATACCCACAGACTTTG 57.827 33.333 0.00 0.00 0.00 2.77
4509 4672 8.339714 CACTGAATCAATCAAGCAAACATTTTT 58.660 29.630 0.00 0.00 37.67 1.94
4540 4703 0.460987 CGAGGTTGGCAGAGGACATC 60.461 60.000 0.00 0.00 0.00 3.06
4544 4707 0.614697 TCATCGAGGTTGGCAGAGGA 60.615 55.000 0.00 0.00 0.00 3.71
4608 4771 1.061570 GTACCGTGTACGAGCCGAG 59.938 63.158 5.91 0.00 43.02 4.63
4628 4792 2.069273 CAGCCTCAAGTTTCCTGTACG 58.931 52.381 0.00 0.00 0.00 3.67
4800 4972 0.871057 GGAGTGTGAGACAAGCTTGC 59.129 55.000 26.27 18.03 0.00 4.01
5012 5199 7.169140 GCAAAAAGAAGGTGGTGTATACAAAAG 59.831 37.037 7.25 0.00 0.00 2.27
5031 5242 6.554419 TGATAATCATTGGACGAGCAAAAAG 58.446 36.000 0.00 0.00 0.00 2.27
5032 5243 6.507958 TGATAATCATTGGACGAGCAAAAA 57.492 33.333 0.00 0.00 0.00 1.94
5036 5247 4.318332 GGATGATAATCATTGGACGAGCA 58.682 43.478 0.00 0.00 37.20 4.26
5037 5248 3.686726 GGGATGATAATCATTGGACGAGC 59.313 47.826 0.00 0.00 37.20 5.03
5038 5249 4.898320 TGGGATGATAATCATTGGACGAG 58.102 43.478 0.00 0.00 37.20 4.18
5039 5250 4.972751 TGGGATGATAATCATTGGACGA 57.027 40.909 0.00 0.00 37.20 4.20
5040 5251 5.065914 ACTTGGGATGATAATCATTGGACG 58.934 41.667 0.00 0.00 37.20 4.79
5041 5252 6.015940 GGAACTTGGGATGATAATCATTGGAC 60.016 42.308 0.00 0.00 37.20 4.02
5042 5253 6.070656 GGAACTTGGGATGATAATCATTGGA 58.929 40.000 0.00 0.00 37.20 3.53
5043 5254 5.048504 CGGAACTTGGGATGATAATCATTGG 60.049 44.000 0.00 0.00 37.20 3.16
5044 5255 5.764686 TCGGAACTTGGGATGATAATCATTG 59.235 40.000 0.00 0.00 37.20 2.82
5045 5256 5.940617 TCGGAACTTGGGATGATAATCATT 58.059 37.500 0.00 0.00 37.20 2.57
5046 5257 5.567037 TCGGAACTTGGGATGATAATCAT 57.433 39.130 0.00 0.00 40.34 2.45
5047 5258 5.123227 GTTCGGAACTTGGGATGATAATCA 58.877 41.667 13.49 0.00 0.00 2.57
5048 5259 4.515567 GGTTCGGAACTTGGGATGATAATC 59.484 45.833 19.40 0.00 0.00 1.75
5049 5260 4.461198 GGTTCGGAACTTGGGATGATAAT 58.539 43.478 19.40 0.00 0.00 1.28
5050 5261 3.680475 CGGTTCGGAACTTGGGATGATAA 60.680 47.826 19.40 0.00 0.00 1.75
5051 5262 2.159014 CGGTTCGGAACTTGGGATGATA 60.159 50.000 19.40 0.00 0.00 2.15
5052 5263 1.406887 CGGTTCGGAACTTGGGATGAT 60.407 52.381 19.40 0.00 0.00 2.45
5053 5264 0.036765 CGGTTCGGAACTTGGGATGA 60.037 55.000 19.40 0.00 0.00 2.92
5054 5265 0.036765 TCGGTTCGGAACTTGGGATG 60.037 55.000 19.40 3.13 0.00 3.51
5055 5266 0.688487 TTCGGTTCGGAACTTGGGAT 59.312 50.000 19.40 0.00 0.00 3.85
5056 5267 0.469070 TTTCGGTTCGGAACTTGGGA 59.531 50.000 19.40 9.78 0.00 4.37
5057 5268 0.872388 CTTTCGGTTCGGAACTTGGG 59.128 55.000 19.40 7.84 0.00 4.12
5067 5292 1.918609 CGATTCCTCGTCTTTCGGTTC 59.081 52.381 0.00 0.00 40.07 3.62
5088 5313 6.307318 CGAGCTTTGGTGTACGGTATATATTC 59.693 42.308 0.00 0.00 0.00 1.75
5089 5314 6.016024 TCGAGCTTTGGTGTACGGTATATATT 60.016 38.462 0.00 0.00 0.00 1.28
5090 5315 5.474532 TCGAGCTTTGGTGTACGGTATATAT 59.525 40.000 0.00 0.00 0.00 0.86
5091 5316 4.821260 TCGAGCTTTGGTGTACGGTATATA 59.179 41.667 0.00 0.00 0.00 0.86
5214 5444 4.025480 ACAGGTTTGATTACGACGTTGTTC 60.025 41.667 14.93 7.22 0.00 3.18
5222 5452 2.161410 GCATGCACAGGTTTGATTACGA 59.839 45.455 14.21 0.00 0.00 3.43
5258 5500 2.877582 CCCTACGTGCGTGCGTAC 60.878 66.667 7.55 2.83 45.06 3.67
5259 5501 4.781959 GCCCTACGTGCGTGCGTA 62.782 66.667 7.55 11.70 45.06 4.42
5266 5508 3.701604 CTCTGGTCGCCCTACGTGC 62.702 68.421 0.00 0.00 44.19 5.34


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

AutoCloner maintained by Alex Coulton.