Multiple sequence alignment - TraesCS6B01G284400

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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 TraesCS6B01G284400 chr6B 100.000 4685 0 0 1 4685 512870738 512875422 0.000000e+00 8652.0
1 TraesCS6B01G284400 chr6B 96.774 31 1 0 3526 3556 205236226 205236256 8.000000e-03 52.8
2 TraesCS6B01G284400 chr6D 94.617 2991 110 22 1099 4062 313283663 313280697 0.000000e+00 4584.0
3 TraesCS6B01G284400 chr6D 93.478 1196 56 6 1 1179 313284857 313283667 0.000000e+00 1757.0
4 TraesCS6B01G284400 chr6D 92.373 354 25 2 4124 4477 313280304 313279953 1.950000e-138 503.0
5 TraesCS6B01G284400 chr6A 93.077 2990 113 38 1099 4062 450466929 450464008 0.000000e+00 4289.0
6 TraesCS6B01G284400 chr6A 92.525 1204 60 10 1 1179 450468131 450466933 0.000000e+00 1698.0
7 TraesCS6B01G284400 chr6A 92.883 562 38 2 4124 4685 450463548 450462989 0.000000e+00 815.0
8 TraesCS6B01G284400 chr6A 81.699 153 17 8 1222 1373 103263898 103264040 2.960000e-22 117.0
9 TraesCS6B01G284400 chr6A 96.774 31 1 0 3526 3556 144249019 144249049 8.000000e-03 52.8
10 TraesCS6B01G284400 chr5A 86.806 288 32 6 2793 3077 708807367 708807083 2.720000e-82 316.0
11 TraesCS6B01G284400 chr4B 86.806 288 32 6 2793 3077 671632090 671631806 2.720000e-82 316.0
12 TraesCS6B01G284400 chrUn 86.458 288 33 6 2793 3077 28396946 28397230 1.270000e-80 311.0
13 TraesCS6B01G284400 chr2D 84.839 310 41 6 2778 3084 492509741 492509435 1.640000e-79 307.0
14 TraesCS6B01G284400 chr2D 88.889 162 18 0 2074 2235 492510808 492510647 2.860000e-47 200.0
15 TraesCS6B01G284400 chr2B 84.839 310 41 6 2778 3084 578137537 578137231 1.640000e-79 307.0
16 TraesCS6B01G284400 chr2B 89.017 173 17 1 2074 2246 578138610 578138440 3.670000e-51 213.0
17 TraesCS6B01G284400 chr2A 86.429 280 36 2 2806 3084 637678930 637678652 5.890000e-79 305.0
18 TraesCS6B01G284400 chr2A 90.123 162 16 0 2074 2235 637680040 637679879 1.320000e-50 211.0
19 TraesCS6B01G284400 chr1D 85.614 285 36 4 2801 3082 231465072 231464790 1.270000e-75 294.0
20 TraesCS6B01G284400 chr1D 83.660 153 23 2 2073 2224 231466171 231466020 4.890000e-30 143.0
21 TraesCS6B01G284400 chr1A 83.333 156 24 2 2070 2224 317812280 317812434 4.890000e-30 143.0
22 TraesCS6B01G284400 chr1B 82.051 156 26 2 2070 2224 365020386 365020540 1.060000e-26 132.0


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 TraesCS6B01G284400 chr6B 512870738 512875422 4684 False 8652.000000 8652 100.000000 1 4685 1 chr6B.!!$F2 4684
1 TraesCS6B01G284400 chr6D 313279953 313284857 4904 True 2281.333333 4584 93.489333 1 4477 3 chr6D.!!$R1 4476
2 TraesCS6B01G284400 chr6A 450462989 450468131 5142 True 2267.333333 4289 92.828333 1 4685 3 chr6A.!!$R1 4684
3 TraesCS6B01G284400 chr2D 492509435 492510808 1373 True 253.500000 307 86.864000 2074 3084 2 chr2D.!!$R1 1010
4 TraesCS6B01G284400 chr2B 578137231 578138610 1379 True 260.000000 307 86.928000 2074 3084 2 chr2B.!!$R1 1010
5 TraesCS6B01G284400 chr2A 637678652 637680040 1388 True 258.000000 305 88.276000 2074 3084 2 chr2A.!!$R1 1010
6 TraesCS6B01G284400 chr1D 231464790 231466171 1381 True 218.500000 294 84.637000 2073 3082 2 chr1D.!!$R1 1009

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
553 571 0.607489 GCTTTCTCTGCCTGCCTTCA 60.607 55.000 0.00 0.0 0.00 3.02 F
1224 1354 0.249155 TCAACTTCCACCACGACGAC 60.249 55.000 0.00 0.0 0.00 4.34 F
1232 1362 0.937699 CACCACGACGACGACAACAT 60.938 55.000 15.32 0.0 42.66 2.71 F
1417 1547 1.001406 CCAGGTGAGAAAGAAGCGAGT 59.999 52.381 0.00 0.0 0.00 4.18 F
3095 3877 1.069296 CAAGAAGCAATTCGCCGTGAA 60.069 47.619 0.00 0.0 44.04 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2181 2321 0.606604 GGTAGTTCTTGCCGTCCTGA 59.393 55.000 0.00 0.0 0.00 3.86 R
3069 3851 1.064060 GCGAATTGCTTCTTGCGGTAT 59.936 47.619 0.00 0.0 46.63 2.73 R
3165 3947 1.152881 CCAGGGGTTATGCTGCTCC 60.153 63.158 0.00 0.0 0.00 4.70 R
3336 4118 2.504585 AGCTCTTGCATGGAGAGATTCA 59.495 45.455 16.44 0.0 42.57 2.57 R
4506 5825 0.539986 GTCAGCGTTATGAGGGGGAA 59.460 55.000 0.00 0.0 0.00 3.97 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
76 77 9.899226 TCGTAGATCTTTTATGTATGAGATGTG 57.101 33.333 0.00 0.00 0.00 3.21
128 129 3.811083 AGATCTGGTCGTATCTTCTCGT 58.189 45.455 0.00 0.00 0.00 4.18
130 131 3.263489 TCTGGTCGTATCTTCTCGTCT 57.737 47.619 0.00 0.00 0.00 4.18
132 133 2.937149 CTGGTCGTATCTTCTCGTCTCA 59.063 50.000 0.00 0.00 0.00 3.27
135 136 4.398358 TGGTCGTATCTTCTCGTCTCAAAT 59.602 41.667 0.00 0.00 0.00 2.32
138 139 5.452944 GTCGTATCTTCTCGTCTCAAATGAC 59.547 44.000 0.00 0.00 0.00 3.06
145 146 4.174009 TCTCGTCTCAAATGACCGATTTC 58.826 43.478 0.00 0.00 31.41 2.17
157 158 6.564709 ATGACCGATTTCCATCATACATTG 57.435 37.500 0.00 0.00 30.01 2.82
180 181 5.810587 TGAAGGACAAATATGCGAGAGTAAC 59.189 40.000 0.00 0.00 0.00 2.50
181 182 5.599999 AGGACAAATATGCGAGAGTAACT 57.400 39.130 0.00 0.00 0.00 2.24
185 186 8.204836 AGGACAAATATGCGAGAGTAACTTAAT 58.795 33.333 0.00 0.00 0.00 1.40
292 295 7.047891 TGGAAGAAACAGCCTACATACTAATG 58.952 38.462 0.00 0.00 39.17 1.90
417 433 4.214986 TCTTTTGACATTAGATGGCCGA 57.785 40.909 0.00 0.00 37.55 5.54
422 438 3.732212 TGACATTAGATGGCCGATCAAG 58.268 45.455 14.93 6.39 37.55 3.02
456 472 4.710324 ACATTTACGAAACCTGAGTCCAA 58.290 39.130 0.00 0.00 0.00 3.53
511 529 8.539770 TTTTTCTGAGATATCAGTGAAGACAC 57.460 34.615 16.60 0.00 46.24 3.67
553 571 0.607489 GCTTTCTCTGCCTGCCTTCA 60.607 55.000 0.00 0.00 0.00 3.02
581 600 4.985538 TCTTTGCCTTTCCAGTTGTCTAT 58.014 39.130 0.00 0.00 0.00 1.98
641 660 4.394712 GCCGCCCACTGTACAGCT 62.395 66.667 22.90 7.43 0.00 4.24
644 663 2.125512 GCCCACTGTACAGCTCCG 60.126 66.667 22.90 8.90 0.00 4.63
758 777 2.270527 GGAGAGGAGCTTGCACCC 59.729 66.667 5.49 1.20 0.00 4.61
838 857 6.034161 AGAGTACTTGTTGGTGGTACATAC 57.966 41.667 0.00 0.00 44.52 2.39
839 858 5.541101 AGAGTACTTGTTGGTGGTACATACA 59.459 40.000 0.00 0.00 44.52 2.29
840 859 6.212791 AGAGTACTTGTTGGTGGTACATACAT 59.787 38.462 0.00 0.00 44.52 2.29
841 860 7.398047 AGAGTACTTGTTGGTGGTACATACATA 59.602 37.037 0.00 0.00 44.52 2.29
912 931 4.344865 TGGAGCTTTCCGCCACCC 62.345 66.667 0.00 0.00 38.59 4.61
989 1008 2.006805 AAGGAAGGTGGTGTGGTGGG 62.007 60.000 0.00 0.00 0.00 4.61
1060 1082 2.499205 CGCCGCTTACAGGGATGA 59.501 61.111 0.00 0.00 0.00 2.92
1074 1096 1.602323 GATGACCCCGTTGTTGCCA 60.602 57.895 0.00 0.00 0.00 4.92
1120 1142 4.148825 GCAGCATCCCGTCTCCGT 62.149 66.667 0.00 0.00 0.00 4.69
1179 1207 3.064324 GACCAATTGCCAGCCGCT 61.064 61.111 0.00 0.00 38.78 5.52
1180 1208 3.346631 GACCAATTGCCAGCCGCTG 62.347 63.158 13.82 13.82 38.78 5.18
1216 1346 3.723348 GCGCGGTCAACTTCCACC 61.723 66.667 8.83 0.00 0.00 4.61
1224 1354 0.249155 TCAACTTCCACCACGACGAC 60.249 55.000 0.00 0.00 0.00 4.34
1225 1355 1.299620 AACTTCCACCACGACGACG 60.300 57.895 5.58 5.58 45.75 5.12
1229 1359 2.002509 TTCCACCACGACGACGACAA 62.003 55.000 15.32 0.00 42.66 3.18
1230 1360 2.297912 CCACCACGACGACGACAAC 61.298 63.158 15.32 0.00 42.66 3.32
1231 1361 1.586826 CACCACGACGACGACAACA 60.587 57.895 15.32 0.00 42.66 3.33
1232 1362 0.937699 CACCACGACGACGACAACAT 60.938 55.000 15.32 0.00 42.66 2.71
1235 1365 1.007734 ACGACGACGACAACATGCT 60.008 52.632 15.32 0.00 42.66 3.79
1349 1479 4.570663 CCGGTCGGAGATGGACGC 62.571 72.222 2.83 0.00 40.67 5.19
1414 1544 1.719600 CTCCAGGTGAGAAAGAAGCG 58.280 55.000 0.00 0.00 44.42 4.68
1417 1547 1.001406 CCAGGTGAGAAAGAAGCGAGT 59.999 52.381 0.00 0.00 0.00 4.18
1418 1548 2.064762 CAGGTGAGAAAGAAGCGAGTG 58.935 52.381 0.00 0.00 0.00 3.51
1433 1563 4.648651 AGCGAGTGGTACTGGTAAAAATT 58.351 39.130 0.00 0.00 0.00 1.82
1439 1569 6.607019 AGTGGTACTGGTAAAAATTTCCTCA 58.393 36.000 0.00 0.00 0.00 3.86
1477 1607 3.062234 GCTAACGGTTTCAGAGAATTCGG 59.938 47.826 0.00 0.00 0.00 4.30
1736 1876 2.719739 CCATTGATGCACTCTGGTCTT 58.280 47.619 0.00 0.00 0.00 3.01
1750 1890 2.893489 CTGGTCTTTGGGAAAAGAAGGG 59.107 50.000 2.63 0.00 40.15 3.95
1751 1891 2.516277 TGGTCTTTGGGAAAAGAAGGGA 59.484 45.455 2.63 0.00 40.15 4.20
1752 1892 3.157881 GGTCTTTGGGAAAAGAAGGGAG 58.842 50.000 2.63 0.00 40.15 4.30
1753 1893 3.436615 GGTCTTTGGGAAAAGAAGGGAGT 60.437 47.826 2.63 0.00 40.15 3.85
1754 1894 4.202535 GGTCTTTGGGAAAAGAAGGGAGTA 60.203 45.833 2.63 0.00 40.15 2.59
1755 1895 5.004448 GTCTTTGGGAAAAGAAGGGAGTAG 58.996 45.833 2.63 0.00 40.15 2.57
1756 1896 4.663592 TCTTTGGGAAAAGAAGGGAGTAGT 59.336 41.667 0.00 0.00 35.99 2.73
1757 1897 5.847817 TCTTTGGGAAAAGAAGGGAGTAGTA 59.152 40.000 0.00 0.00 35.99 1.82
1758 1898 5.757099 TTGGGAAAAGAAGGGAGTAGTAG 57.243 43.478 0.00 0.00 0.00 2.57
1759 1899 5.019657 TGGGAAAAGAAGGGAGTAGTAGA 57.980 43.478 0.00 0.00 0.00 2.59
1760 1900 5.024118 TGGGAAAAGAAGGGAGTAGTAGAG 58.976 45.833 0.00 0.00 0.00 2.43
1761 1901 5.024785 GGGAAAAGAAGGGAGTAGTAGAGT 58.975 45.833 0.00 0.00 0.00 3.24
1762 1902 6.193504 GGGAAAAGAAGGGAGTAGTAGAGTA 58.806 44.000 0.00 0.00 0.00 2.59
1763 1903 6.840181 GGGAAAAGAAGGGAGTAGTAGAGTAT 59.160 42.308 0.00 0.00 0.00 2.12
1820 1960 7.732996 TCTGATGAATTAATCTGCATCTCTCA 58.267 34.615 18.66 5.67 38.31 3.27
2049 2189 1.337071 AGACGTGAAAGCAAGAGACGA 59.663 47.619 0.00 0.00 34.22 4.20
2487 2882 2.048127 ACGGAGAAGCAAGACGCC 60.048 61.111 0.00 0.00 44.04 5.68
3086 3868 4.152402 CGCTATATACCGCAAGAAGCAATT 59.848 41.667 0.00 0.00 46.13 2.32
3087 3869 5.622378 GCTATATACCGCAAGAAGCAATTC 58.378 41.667 0.00 0.00 46.13 2.17
3095 3877 1.069296 CAAGAAGCAATTCGCCGTGAA 60.069 47.619 0.00 0.00 44.04 3.18
3329 4111 4.201589 CGCTACAAACAAGGTAATGACTCG 60.202 45.833 0.00 0.00 0.00 4.18
3330 4112 4.092968 GCTACAAACAAGGTAATGACTCGG 59.907 45.833 0.00 0.00 0.00 4.63
3336 4118 4.969484 ACAAGGTAATGACTCGGACTTTT 58.031 39.130 0.00 0.00 0.00 2.27
3355 4139 5.415077 ACTTTTGAATCTCTCCATGCAAGAG 59.585 40.000 14.21 14.21 41.38 2.85
3356 4140 2.915349 TGAATCTCTCCATGCAAGAGC 58.085 47.619 15.14 5.83 40.11 4.09
3363 4147 3.693807 TCTCCATGCAAGAGCTTTTCAT 58.306 40.909 11.34 0.00 42.74 2.57
3405 4195 4.259734 CGCAACTTAATCGGAATTTTCGTG 59.740 41.667 0.00 0.00 0.00 4.35
3745 4541 0.607489 GGTTCATGAGCACCAGCAGT 60.607 55.000 11.93 0.00 45.49 4.40
4008 4804 3.129462 GGAGCCTCTGTTTTGCCTATTTC 59.871 47.826 0.00 0.00 0.00 2.17
4010 4806 3.507622 AGCCTCTGTTTTGCCTATTTCAC 59.492 43.478 0.00 0.00 0.00 3.18
4096 5365 2.032223 CAGAGTGTGCAGCAGGCT 59.968 61.111 0.00 0.00 45.15 4.58
4133 5452 7.663493 CAGGAGAGAAGAAAGAATACCAAGTTT 59.337 37.037 0.00 0.00 0.00 2.66
4209 5528 5.965922 TGATCTTGCTTAATTCGAGTCTCA 58.034 37.500 0.00 0.00 0.00 3.27
4223 5542 4.583489 TCGAGTCTCAATGGTATACCTTCC 59.417 45.833 22.41 4.24 36.82 3.46
4225 5544 5.508153 CGAGTCTCAATGGTATACCTTCCTG 60.508 48.000 22.41 12.24 36.82 3.86
4228 5547 6.215636 AGTCTCAATGGTATACCTTCCTGTTT 59.784 38.462 22.41 0.00 36.82 2.83
4357 5676 1.135083 GTGGACTAGGGTGTGTCGATG 60.135 57.143 0.00 0.00 34.31 3.84
4362 5681 2.165845 ACTAGGGTGTGTCGATGTAAGC 59.834 50.000 0.00 0.00 0.00 3.09
4399 5718 7.417456 GCTTGGGGGTTAAAGATTTACATAAGG 60.417 40.741 0.00 0.00 0.00 2.69
4428 5747 6.833041 TGTTAGTCTCCTTACAAAATGGTGA 58.167 36.000 0.00 0.00 27.88 4.02
4429 5748 7.284074 TGTTAGTCTCCTTACAAAATGGTGAA 58.716 34.615 0.00 0.00 27.88 3.18
4466 5785 6.208599 TGAGAATGGTCTTTAGCGGAAAATTT 59.791 34.615 0.00 0.00 32.80 1.82
4483 5802 7.391016 GGAAAATTTTGCGTGCTATGTATTTC 58.609 34.615 8.47 0.00 0.00 2.17
4484 5803 6.885735 AAATTTTGCGTGCTATGTATTTCC 57.114 33.333 0.00 0.00 0.00 3.13
4491 5810 1.137282 TGCTATGTATTTCCGTCGCCA 59.863 47.619 0.00 0.00 0.00 5.69
4515 5834 2.686106 GGCTACGGTTCCCCCTCA 60.686 66.667 0.00 0.00 0.00 3.86
4520 5839 1.068127 CTACGGTTCCCCCTCATAACG 59.932 57.143 0.00 0.00 0.00 3.18
4522 5841 1.912971 GGTTCCCCCTCATAACGCT 59.087 57.895 0.00 0.00 0.00 5.07
4533 5852 3.490078 CCTCATAACGCTGACTCTCCTTC 60.490 52.174 0.00 0.00 0.00 3.46
4549 5868 8.554490 ACTCTCCTTCTTGGAAAGCTATTATA 57.446 34.615 0.00 0.00 45.70 0.98
4582 5901 1.940613 GTATACCTTGCCGGCAGAAAG 59.059 52.381 30.75 23.74 35.61 2.62
4593 5912 3.188048 GCCGGCAGAAAGATCATGATTAG 59.812 47.826 24.80 0.00 0.00 1.73
4595 5914 3.120752 CGGCAGAAAGATCATGATTAGCG 60.121 47.826 10.14 0.00 0.00 4.26
4601 5920 3.692257 AGATCATGATTAGCGAAGGGG 57.308 47.619 10.14 0.00 0.00 4.79
4624 5943 2.158957 TCTGGTGAGACTGTGGTTTGAC 60.159 50.000 0.00 0.00 0.00 3.18
4639 5958 0.181587 TTGACTGTTGGGCTTCGGAA 59.818 50.000 0.00 0.00 0.00 4.30
4643 5962 1.856265 CTGTTGGGCTTCGGAAGTGC 61.856 60.000 18.32 6.52 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 9.899226 TCACATCTCATACATAAAAGATCTACG 57.101 33.333 0.00 0.00 0.00 3.51
108 109 3.810941 AGACGAGAAGATACGACCAGATC 59.189 47.826 0.00 0.00 0.00 2.75
128 129 4.842574 TGATGGAAATCGGTCATTTGAGA 58.157 39.130 0.00 0.00 34.60 3.27
130 131 6.118852 TGTATGATGGAAATCGGTCATTTGA 58.881 36.000 5.03 0.00 34.60 2.69
132 133 7.285172 TCAATGTATGATGGAAATCGGTCATTT 59.715 33.333 5.03 0.00 33.23 2.32
135 136 5.679601 TCAATGTATGATGGAAATCGGTCA 58.320 37.500 0.00 0.00 31.50 4.02
157 158 6.043411 AGTTACTCTCGCATATTTGTCCTTC 58.957 40.000 0.00 0.00 0.00 3.46
292 295 6.633668 AGATATTTATCATTACTGTCGCGC 57.366 37.500 0.00 0.00 35.17 6.86
409 425 5.240891 TCAAAGATATCTTGATCGGCCATC 58.759 41.667 18.61 5.87 36.12 3.51
412 428 6.166279 TGTATCAAAGATATCTTGATCGGCC 58.834 40.000 18.61 11.59 36.12 6.13
456 472 2.760092 ACGTGTGTGTTATATACCCGGT 59.240 45.455 0.00 0.00 0.00 5.28
493 511 4.892934 AGAGGGTGTCTTCACTGATATCTC 59.107 45.833 3.98 0.00 43.41 2.75
553 571 2.173569 ACTGGAAAGGCAAAGAGAGTGT 59.826 45.455 0.00 0.00 0.00 3.55
581 600 2.593026 GTGGTGAAAAAGATGGGGTCA 58.407 47.619 0.00 0.00 0.00 4.02
641 660 1.452801 GGGAAGTTGGGAACACGGA 59.547 57.895 0.00 0.00 42.67 4.69
644 663 1.602605 CGGGGGAAGTTGGGAACAC 60.603 63.158 0.00 0.00 42.67 3.32
758 777 1.804372 GCTTGTACGCCCATCTCTCTG 60.804 57.143 0.00 0.00 0.00 3.35
773 792 6.479884 ACTAGATTGGAGAATTCTTGCTTGT 58.520 36.000 9.87 7.19 0.00 3.16
841 860 7.945664 CCCTCTTCTCCTACACTACAAGTATAT 59.054 40.741 0.00 0.00 0.00 0.86
861 880 4.202803 ACCTACCACTAGTTTCTCCCTCTT 60.203 45.833 0.00 0.00 0.00 2.85
912 931 1.153823 CCTTACCGGAGTGAGTGCG 60.154 63.158 9.46 0.00 40.28 5.34
1161 1189 4.133796 GCGGCTGGCAATTGGTCC 62.134 66.667 7.72 1.11 42.87 4.46
1203 1333 1.219522 CGTCGTGGTGGAAGTTGACC 61.220 60.000 0.00 0.00 0.00 4.02
1208 1338 2.188829 TCGTCGTCGTGGTGGAAGT 61.189 57.895 1.33 0.00 38.33 3.01
1216 1346 1.127817 GCATGTTGTCGTCGTCGTG 59.872 57.895 1.33 0.00 38.33 4.35
1225 1355 1.781555 CGTCGACCAGCATGTTGTC 59.218 57.895 10.58 5.25 0.00 3.18
1311 1441 2.434884 CTGATGAGCGCCACCGTT 60.435 61.111 2.29 0.00 36.67 4.44
1408 1538 2.211250 TACCAGTACCACTCGCTTCT 57.789 50.000 0.00 0.00 0.00 2.85
1412 1542 5.366829 AAATTTTTACCAGTACCACTCGC 57.633 39.130 0.00 0.00 0.00 5.03
1414 1544 6.713450 TGAGGAAATTTTTACCAGTACCACTC 59.287 38.462 0.00 0.00 0.00 3.51
1417 1547 5.771165 GGTGAGGAAATTTTTACCAGTACCA 59.229 40.000 0.00 0.00 0.00 3.25
1418 1548 5.184479 GGGTGAGGAAATTTTTACCAGTACC 59.816 44.000 6.26 6.31 0.00 3.34
1433 1563 2.905996 ATTGCGCAGGGGTGAGGAA 61.906 57.895 11.31 0.00 0.00 3.36
1500 1634 1.221414 GCAGGATAACTCGCCATCAC 58.779 55.000 0.00 0.00 0.00 3.06
1511 1645 2.431997 AGATGGGGAATGGCAGGATAA 58.568 47.619 0.00 0.00 0.00 1.75
1736 1876 5.408824 TCTACTACTCCCTTCTTTTCCCAA 58.591 41.667 0.00 0.00 0.00 4.12
1751 1891 8.905850 GCAAAAGACTTCCTATACTCTACTACT 58.094 37.037 0.00 0.00 0.00 2.57
1752 1892 8.905850 AGCAAAAGACTTCCTATACTCTACTAC 58.094 37.037 0.00 0.00 0.00 2.73
1753 1893 9.122779 GAGCAAAAGACTTCCTATACTCTACTA 57.877 37.037 0.00 0.00 0.00 1.82
1754 1894 7.068962 GGAGCAAAAGACTTCCTATACTCTACT 59.931 40.741 0.00 0.00 0.00 2.57
1755 1895 7.204604 GGAGCAAAAGACTTCCTATACTCTAC 58.795 42.308 0.00 0.00 0.00 2.59
1756 1896 6.324254 GGGAGCAAAAGACTTCCTATACTCTA 59.676 42.308 0.00 0.00 29.15 2.43
1757 1897 5.129650 GGGAGCAAAAGACTTCCTATACTCT 59.870 44.000 0.00 0.00 29.15 3.24
1758 1898 5.104900 TGGGAGCAAAAGACTTCCTATACTC 60.105 44.000 0.00 0.00 33.47 2.59
1759 1899 4.783227 TGGGAGCAAAAGACTTCCTATACT 59.217 41.667 0.00 0.00 33.47 2.12
1760 1900 5.099042 TGGGAGCAAAAGACTTCCTATAC 57.901 43.478 0.00 0.00 33.47 1.47
1761 1901 5.163195 GGATGGGAGCAAAAGACTTCCTATA 60.163 44.000 0.00 0.00 33.47 1.31
1762 1902 4.385754 GGATGGGAGCAAAAGACTTCCTAT 60.386 45.833 0.00 0.00 33.47 2.57
1763 1903 3.054361 GGATGGGAGCAAAAGACTTCCTA 60.054 47.826 0.00 0.00 33.47 2.94
1820 1960 3.612247 GATGGCACTGTCAGCGGGT 62.612 63.158 0.00 0.00 0.00 5.28
1919 2059 7.657761 CACAAGTACTAGGATGAGTCAAAACTT 59.342 37.037 0.00 0.00 35.28 2.66
1978 2118 4.547532 GCATGAGTGGTAATCCGTAGTAG 58.452 47.826 0.00 0.00 36.30 2.57
1979 2119 3.319972 GGCATGAGTGGTAATCCGTAGTA 59.680 47.826 0.00 0.00 36.30 1.82
1980 2120 2.102588 GGCATGAGTGGTAATCCGTAGT 59.897 50.000 0.00 0.00 36.30 2.73
1981 2121 2.102420 TGGCATGAGTGGTAATCCGTAG 59.898 50.000 0.00 0.00 36.30 3.51
1984 2124 2.146342 GATGGCATGAGTGGTAATCCG 58.854 52.381 3.81 0.00 36.30 4.18
2049 2189 3.498774 AATCTTGTTGCTGTCAGAGGT 57.501 42.857 3.32 0.00 0.00 3.85
2100 2240 1.079127 GCACTTCTTGGCGCTCCTA 60.079 57.895 7.64 0.00 0.00 2.94
2181 2321 0.606604 GGTAGTTCTTGCCGTCCTGA 59.393 55.000 0.00 0.00 0.00 3.86
2431 2826 1.958205 CGAAGAGCGCCATCATCCC 60.958 63.158 2.29 0.00 0.00 3.85
2811 3593 2.003548 GACCTCCTCCTTGGGCCAT 61.004 63.158 7.26 0.00 36.20 4.40
3069 3851 1.064060 GCGAATTGCTTCTTGCGGTAT 59.936 47.619 0.00 0.00 46.63 2.73
3165 3947 1.152881 CCAGGGGTTATGCTGCTCC 60.153 63.158 0.00 0.00 0.00 4.70
3329 4111 4.012374 TGCATGGAGAGATTCAAAAGTCC 58.988 43.478 0.00 0.00 0.00 3.85
3330 4112 5.413833 TCTTGCATGGAGAGATTCAAAAGTC 59.586 40.000 0.00 0.00 0.00 3.01
3336 4118 2.504585 AGCTCTTGCATGGAGAGATTCA 59.495 45.455 16.44 0.00 42.57 2.57
3405 4195 2.533266 TGTCTTCAGACTTCTGTGCC 57.467 50.000 8.41 0.00 44.99 5.01
3675 4471 3.307906 ACGGGCGCCTACTGAACA 61.308 61.111 28.56 0.00 0.00 3.18
3745 4541 3.119319 TGGTATAGGATGTTGCCAAGGA 58.881 45.455 0.00 0.00 0.00 3.36
3978 4774 0.602905 AACAGAGGCTCCGGTTTTCG 60.603 55.000 11.71 0.00 38.88 3.46
4030 4826 8.482128 GGAATGGAGGGAGTAGAATATAATCTG 58.518 40.741 0.24 0.00 0.00 2.90
4062 4858 5.412594 ACACTCTGTGCATCGTTTTCATTAT 59.587 36.000 0.00 0.00 36.98 1.28
4096 5365 6.945636 TTCTTCTCTCCTGGTTTGGTAATA 57.054 37.500 0.00 0.00 0.00 0.98
4209 5528 8.557450 AGACATAAAACAGGAAGGTATACCATT 58.443 33.333 23.87 14.30 38.89 3.16
4225 5544 9.832445 TGTTAAGGAGGATCATAGACATAAAAC 57.168 33.333 0.00 0.00 36.25 2.43
4228 5547 9.434275 TCTTGTTAAGGAGGATCATAGACATAA 57.566 33.333 0.00 0.00 36.25 1.90
4357 5676 2.354821 CCAAGCCTCCAAATACGCTTAC 59.645 50.000 0.00 0.00 39.48 2.34
4362 5681 0.751643 CCCCCAAGCCTCCAAATACG 60.752 60.000 0.00 0.00 0.00 3.06
4366 5685 0.861155 TTAACCCCCAAGCCTCCAAA 59.139 50.000 0.00 0.00 0.00 3.28
4371 5690 3.560357 AAATCTTTAACCCCCAAGCCT 57.440 42.857 0.00 0.00 0.00 4.58
4399 5718 8.669243 CCATTTTGTAAGGAGACTAACATTCTC 58.331 37.037 0.00 0.00 42.68 2.87
4410 5729 5.576563 TCCTTCACCATTTTGTAAGGAGA 57.423 39.130 0.00 0.00 40.53 3.71
4413 5732 5.009210 TCGTTTCCTTCACCATTTTGTAAGG 59.991 40.000 0.00 0.00 38.44 2.69
4428 5747 3.325135 ACCATTCTCAGTCTCGTTTCCTT 59.675 43.478 0.00 0.00 0.00 3.36
4429 5748 2.900546 ACCATTCTCAGTCTCGTTTCCT 59.099 45.455 0.00 0.00 0.00 3.36
4466 5785 2.605818 GACGGAAATACATAGCACGCAA 59.394 45.455 0.00 0.00 0.00 4.85
4470 5789 1.525619 GGCGACGGAAATACATAGCAC 59.474 52.381 0.00 0.00 0.00 4.40
4473 5792 2.538449 GTGTGGCGACGGAAATACATAG 59.462 50.000 0.00 0.00 0.00 2.23
4491 5810 1.370064 GGAACCGTAGCCACAGTGT 59.630 57.895 0.00 0.00 0.00 3.55
4506 5825 0.539986 GTCAGCGTTATGAGGGGGAA 59.460 55.000 0.00 0.00 0.00 3.97
4515 5834 3.118956 CCAAGAAGGAGAGTCAGCGTTAT 60.119 47.826 0.00 0.00 41.22 1.89
4533 5852 8.624776 CCTTGACCTTTATAATAGCTTTCCAAG 58.375 37.037 0.00 0.00 0.00 3.61
4573 5892 3.120752 CGCTAATCATGATCTTTCTGCCG 60.121 47.826 9.06 0.59 0.00 5.69
4582 5901 3.685139 TCCCCTTCGCTAATCATGATC 57.315 47.619 9.06 0.00 0.00 2.92
4593 5912 1.144936 CTCACCAGATCCCCTTCGC 59.855 63.158 0.00 0.00 0.00 4.70
4595 5914 1.484240 CAGTCTCACCAGATCCCCTTC 59.516 57.143 0.00 0.00 0.00 3.46
4601 5920 3.070018 CAAACCACAGTCTCACCAGATC 58.930 50.000 0.00 0.00 0.00 2.75
4624 5943 1.856265 GCACTTCCGAAGCCCAACAG 61.856 60.000 8.11 0.00 0.00 3.16
4639 5958 2.651382 ACCGAGTTTTAAAGGGCACT 57.349 45.000 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.