Multiple sequence alignment - TraesCS1B01G215800

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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 TraesCS1B01G215800 chr1B 100.000 5465 0 0 1 5465 391571406 391576870 0.000000e+00 10093.0
1 TraesCS1B01G215800 chr1A 94.952 5210 157 36 42 5184 362861413 362866583 0.000000e+00 8067.0
2 TraesCS1B01G215800 chr1A 87.045 247 19 5 5230 5463 362866673 362866919 3.250000e-67 267.0
3 TraesCS1B01G215800 chr1A 81.435 237 38 5 4913 5146 541149356 541149589 7.230000e-44 189.0
4 TraesCS1B01G215800 chr1D 95.658 3547 96 22 39 3555 290442527 290446045 0.000000e+00 5644.0
5 TraesCS1B01G215800 chr1D 97.436 1560 39 1 3666 5225 290446589 290448147 0.000000e+00 2658.0
6 TraesCS1B01G215800 chr1D 87.833 263 18 6 5214 5463 290448171 290448432 4.140000e-76 296.0
7 TraesCS1B01G215800 chr1D 98.319 119 2 0 3552 3670 290446350 290446468 5.550000e-50 209.0
8 TraesCS1B01G215800 chr6D 71.730 994 226 36 2137 3101 178005646 178004679 1.530000e-55 228.0
9 TraesCS1B01G215800 chr6D 84.663 163 13 3 5209 5360 430471687 430471848 9.480000e-33 152.0
10 TraesCS1B01G215800 chr3B 82.129 263 38 9 4889 5146 543888322 543888580 3.310000e-52 217.0
11 TraesCS1B01G215800 chr6A 72.513 764 174 24 2359 3101 230707825 230707077 1.190000e-51 215.0
12 TraesCS1B01G215800 chr6A 80.392 102 18 2 2137 2237 230708044 230707944 5.870000e-10 76.8
13 TraesCS1B01G215800 chr2D 81.377 247 40 4 4903 5146 170509446 170509689 4.320000e-46 196.0
14 TraesCS1B01G215800 chr6B 71.127 994 232 35 2137 3101 295767044 295768011 1.550000e-45 195.0
15 TraesCS1B01G215800 chr2A 80.876 251 43 3 4899 5146 756365350 756365598 5.590000e-45 193.0
16 TraesCS1B01G215800 chrUn 80.400 250 37 10 4903 5146 285473811 285474054 4.350000e-41 180.0
17 TraesCS1B01G215800 chrUn 80.400 250 37 10 4903 5146 347527661 347527418 4.350000e-41 180.0
18 TraesCS1B01G215800 chrUn 84.663 163 13 3 5209 5360 246700457 246700618 9.480000e-33 152.0
19 TraesCS1B01G215800 chrUn 84.337 166 14 3 5209 5363 275332914 275332750 9.480000e-33 152.0
20 TraesCS1B01G215800 chrUn 84.337 166 14 3 5209 5363 413342505 413342341 9.480000e-33 152.0
21 TraesCS1B01G215800 chr7A 79.032 248 44 6 4903 5146 352278040 352277797 4.380000e-36 163.0
22 TraesCS1B01G215800 chr5B 84.663 163 13 3 5209 5360 127822462 127822623 9.480000e-33 152.0
23 TraesCS1B01G215800 chr4D 84.337 166 14 3 5209 5363 135046039 135045875 9.480000e-33 152.0
24 TraesCS1B01G215800 chr3D 84.663 163 13 3 5209 5360 202627684 202627845 9.480000e-33 152.0
25 TraesCS1B01G215800 chr4B 97.727 44 1 0 5365 5408 89698144 89698101 5.870000e-10 76.8


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 TraesCS1B01G215800 chr1B 391571406 391576870 5464 False 10093.00 10093 100.0000 1 5465 1 chr1B.!!$F1 5464
1 TraesCS1B01G215800 chr1A 362861413 362866919 5506 False 4167.00 8067 90.9985 42 5463 2 chr1A.!!$F2 5421
2 TraesCS1B01G215800 chr1D 290442527 290448432 5905 False 2201.75 5644 94.8115 39 5463 4 chr1D.!!$F1 5424
3 TraesCS1B01G215800 chr6D 178004679 178005646 967 True 228.00 228 71.7300 2137 3101 1 chr6D.!!$R1 964

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
903 945 0.333312 TGTTCTTGGGGTGTTGGTGT 59.667 50.000 0.0 0.0 0.00 4.16 F
1493 1552 0.179078 CTGCTGTGATCTCTCCAGGC 60.179 60.000 0.0 0.0 0.00 4.85 F
3026 3100 1.410882 GCAGTTGCCAAGGGTACAAAA 59.589 47.619 0.0 0.0 34.31 2.44 F
4215 4727 0.107165 CGGAGATTTTCCCCACCTCC 60.107 60.000 0.0 0.0 43.63 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1826 1885 0.119155 TCCCTCCTGACCCACTGAAT 59.881 55.000 0.00 0.0 0.00 2.57 R
3294 3371 3.938963 CTCGCAATAAGGCTGAAGGTAAA 59.061 43.478 0.00 0.0 0.00 2.01 R
4338 4850 0.036164 AGGCCAGTATGCAAACGACA 59.964 50.000 5.01 0.0 31.97 4.35 R
5269 5863 0.035739 TAAACAAGAGGGGGTCACGC 59.964 55.000 0.00 0.0 0.00 5.34 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
24 25 6.777782 AGATCTTTGTTCATGAACCTCTTCT 58.222 36.000 30.66 22.41 40.46 2.85
25 26 6.878389 AGATCTTTGTTCATGAACCTCTTCTC 59.122 38.462 30.66 20.39 40.46 2.87
26 27 5.928976 TCTTTGTTCATGAACCTCTTCTCA 58.071 37.500 30.66 10.98 40.46 3.27
27 28 5.994054 TCTTTGTTCATGAACCTCTTCTCAG 59.006 40.000 30.66 16.19 40.46 3.35
28 29 4.277515 TGTTCATGAACCTCTTCTCAGG 57.722 45.455 30.66 0.00 40.46 3.86
29 30 3.006247 GTTCATGAACCTCTTCTCAGGC 58.994 50.000 25.26 0.00 36.98 4.85
30 31 2.544721 TCATGAACCTCTTCTCAGGCT 58.455 47.619 0.00 0.00 36.98 4.58
31 32 2.909006 TCATGAACCTCTTCTCAGGCTT 59.091 45.455 0.00 0.00 36.98 4.35
32 33 2.847327 TGAACCTCTTCTCAGGCTTG 57.153 50.000 0.00 0.00 36.98 4.01
33 34 1.349026 TGAACCTCTTCTCAGGCTTGG 59.651 52.381 0.00 0.00 36.98 3.61
34 35 1.625818 GAACCTCTTCTCAGGCTTGGA 59.374 52.381 0.00 0.00 36.98 3.53
35 36 1.734655 ACCTCTTCTCAGGCTTGGAA 58.265 50.000 0.00 0.00 36.98 3.53
36 37 1.349357 ACCTCTTCTCAGGCTTGGAAC 59.651 52.381 0.00 0.00 36.98 3.62
37 38 1.339535 CCTCTTCTCAGGCTTGGAACC 60.340 57.143 0.00 0.00 0.00 3.62
38 39 0.693049 TCTTCTCAGGCTTGGAACCC 59.307 55.000 0.00 0.00 0.00 4.11
39 40 0.401738 CTTCTCAGGCTTGGAACCCA 59.598 55.000 0.00 0.00 0.00 4.51
40 41 1.005215 CTTCTCAGGCTTGGAACCCAT 59.995 52.381 0.00 0.00 31.53 4.00
48 49 3.578282 AGGCTTGGAACCCATGTAAAAAG 59.422 43.478 0.00 0.00 31.53 2.27
52 53 3.161866 TGGAACCCATGTAAAAAGCTCC 58.838 45.455 0.00 0.00 0.00 4.70
53 54 2.496070 GGAACCCATGTAAAAAGCTCCC 59.504 50.000 0.00 0.00 0.00 4.30
59 60 2.891191 TGTAAAAAGCTCCCGGGAAT 57.109 45.000 26.68 13.84 0.00 3.01
66 67 1.147153 GCTCCCGGGAATCTCCTTG 59.853 63.158 26.68 11.41 36.57 3.61
76 77 3.244911 GGGAATCTCCTTGTTCACCTTGA 60.245 47.826 0.00 0.00 36.57 3.02
80 81 3.551846 TCTCCTTGTTCACCTTGAAACC 58.448 45.455 0.00 0.00 38.22 3.27
81 82 3.202151 TCTCCTTGTTCACCTTGAAACCT 59.798 43.478 0.00 0.00 38.22 3.50
82 83 4.410883 TCTCCTTGTTCACCTTGAAACCTA 59.589 41.667 0.00 0.00 38.22 3.08
83 84 4.457466 TCCTTGTTCACCTTGAAACCTAC 58.543 43.478 0.00 0.00 38.22 3.18
84 85 4.165372 TCCTTGTTCACCTTGAAACCTACT 59.835 41.667 0.00 0.00 38.22 2.57
85 86 5.367352 TCCTTGTTCACCTTGAAACCTACTA 59.633 40.000 0.00 0.00 38.22 1.82
95 96 6.183360 ACCTTGAAACCTACTACTACAACGTT 60.183 38.462 0.00 0.00 0.00 3.99
99 100 6.919662 TGAAACCTACTACTACAACGTTCTTG 59.080 38.462 0.00 0.00 0.00 3.02
114 115 7.803189 ACAACGTTCTTGCTACAAAAGATATTG 59.197 33.333 0.00 0.00 33.79 1.90
196 198 6.264744 TGGGAGTCTGAAATTCCGTATAGTAG 59.735 42.308 0.00 0.00 31.59 2.57
348 361 0.877071 GGTTGTCCTACACGAGACGA 59.123 55.000 0.00 0.00 35.71 4.20
349 362 1.135746 GGTTGTCCTACACGAGACGAG 60.136 57.143 0.00 0.00 35.71 4.18
350 363 0.520404 TTGTCCTACACGAGACGAGC 59.480 55.000 0.00 0.00 35.71 5.03
351 364 1.060622 GTCCTACACGAGACGAGCG 59.939 63.158 0.00 0.00 0.00 5.03
352 365 1.079612 TCCTACACGAGACGAGCGA 60.080 57.895 0.00 0.00 0.00 4.93
521 545 4.379243 CCCACGAGGCAGCGTCTT 62.379 66.667 13.11 0.61 43.59 3.01
672 702 2.094659 CGAAATCGACGCCACAGCT 61.095 57.895 0.00 0.00 43.02 4.24
694 724 2.646175 GGGAAAAAGCTTCCGGGGC 61.646 63.158 0.00 6.95 39.46 5.80
757 787 2.435586 CCTCACAGCTTCCCTGCG 60.436 66.667 0.00 0.00 45.78 5.18
758 788 2.659016 CTCACAGCTTCCCTGCGA 59.341 61.111 0.00 0.00 45.78 5.10
759 789 1.447489 CTCACAGCTTCCCTGCGAG 60.447 63.158 0.00 0.00 45.78 5.03
760 790 2.435586 CACAGCTTCCCTGCGAGG 60.436 66.667 0.00 0.00 45.78 4.63
761 791 2.925170 ACAGCTTCCCTGCGAGGT 60.925 61.111 0.00 0.00 45.78 3.85
762 792 2.125350 CAGCTTCCCTGCGAGGTC 60.125 66.667 0.00 0.00 38.13 3.85
763 793 3.394836 AGCTTCCCTGCGAGGTCC 61.395 66.667 0.00 0.00 38.13 4.46
764 794 4.475135 GCTTCCCTGCGAGGTCCC 62.475 72.222 0.00 0.00 31.93 4.46
765 795 4.148825 CTTCCCTGCGAGGTCCCG 62.149 72.222 0.00 0.00 31.93 5.14
784 814 3.984749 GCCCGAGCGGAGATCCTC 61.985 72.222 11.05 0.00 41.58 3.71
844 880 0.450184 GTTTTGTGTGTGCGTGGAGT 59.550 50.000 0.00 0.00 0.00 3.85
852 888 2.360726 TGCGTGGAGTAGAGGCGA 60.361 61.111 0.00 0.00 0.00 5.54
894 936 4.009675 TCGAATCTGATTTGTTCTTGGGG 58.990 43.478 15.46 0.00 0.00 4.96
895 937 3.758554 CGAATCTGATTTGTTCTTGGGGT 59.241 43.478 4.11 0.00 0.00 4.95
896 938 4.379813 CGAATCTGATTTGTTCTTGGGGTG 60.380 45.833 4.11 0.00 0.00 4.61
897 939 3.593442 TCTGATTTGTTCTTGGGGTGT 57.407 42.857 0.00 0.00 0.00 4.16
898 940 3.909732 TCTGATTTGTTCTTGGGGTGTT 58.090 40.909 0.00 0.00 0.00 3.32
899 941 3.636300 TCTGATTTGTTCTTGGGGTGTTG 59.364 43.478 0.00 0.00 0.00 3.33
900 942 2.697751 TGATTTGTTCTTGGGGTGTTGG 59.302 45.455 0.00 0.00 0.00 3.77
901 943 2.239681 TTTGTTCTTGGGGTGTTGGT 57.760 45.000 0.00 0.00 0.00 3.67
902 944 1.479709 TTGTTCTTGGGGTGTTGGTG 58.520 50.000 0.00 0.00 0.00 4.17
903 945 0.333312 TGTTCTTGGGGTGTTGGTGT 59.667 50.000 0.00 0.00 0.00 4.16
904 946 1.029681 GTTCTTGGGGTGTTGGTGTC 58.970 55.000 0.00 0.00 0.00 3.67
905 947 0.464735 TTCTTGGGGTGTTGGTGTCG 60.465 55.000 0.00 0.00 0.00 4.35
906 948 1.153046 CTTGGGGTGTTGGTGTCGT 60.153 57.895 0.00 0.00 0.00 4.34
907 949 1.153127 TTGGGGTGTTGGTGTCGTC 60.153 57.895 0.00 0.00 0.00 4.20
920 974 2.424341 GTGTCGTCGTTGTTGTTTGTC 58.576 47.619 0.00 0.00 0.00 3.18
1112 1169 0.941542 CGTGCTTCCGGAAAAACAGA 59.058 50.000 19.39 0.00 0.00 3.41
1155 1212 0.443869 ACTCTTTATGCTGTTGCGCG 59.556 50.000 0.00 0.00 43.34 6.86
1176 1233 2.520741 CAGGGGCCCGTGTTGTTT 60.521 61.111 32.29 0.00 0.00 2.83
1248 1305 1.207089 TGGTGGAGCTGCATGTAGTAC 59.793 52.381 12.38 6.73 0.00 2.73
1315 1374 6.156519 ACAATCTTTAAAAACCGATCAAGCC 58.843 36.000 0.00 0.00 0.00 4.35
1331 1390 0.605319 AGCCGCTGAAACGAAATCCA 60.605 50.000 0.00 0.00 34.06 3.41
1346 1405 4.708726 AAATCCAAGCAAGATTTCCGAG 57.291 40.909 3.55 0.00 39.20 4.63
1373 1432 2.413351 CGGATCCGTCTCATGCGT 59.587 61.111 26.35 0.00 31.07 5.24
1396 1455 0.376152 CTGCGCATCTGAACCATGAC 59.624 55.000 12.24 0.00 0.00 3.06
1421 1480 2.360801 TCAGTCTGTGTCGACATGTTCA 59.639 45.455 23.12 13.72 36.38 3.18
1425 1484 3.182572 GTCTGTGTCGACATGTTCAGAAC 59.817 47.826 28.06 20.58 34.49 3.01
1488 1547 2.270047 GACTTGCTGCTGTGATCTCTC 58.730 52.381 0.00 0.00 0.00 3.20
1493 1552 0.179078 CTGCTGTGATCTCTCCAGGC 60.179 60.000 0.00 0.00 0.00 4.85
1826 1885 3.648982 CTGAACACGCTGCCGCAA 61.649 61.111 0.00 0.00 38.22 4.85
1928 1987 2.570415 TGCTTGGGGTTTTGTCGATA 57.430 45.000 0.00 0.00 0.00 2.92
2030 2089 2.253452 GCCAAGCGAGTGTTGCAG 59.747 61.111 0.00 0.00 33.85 4.41
2067 2126 4.223032 GGGAAGATGTCTCAGGTTTGTCTA 59.777 45.833 0.00 0.00 0.00 2.59
3026 3100 1.410882 GCAGTTGCCAAGGGTACAAAA 59.589 47.619 0.00 0.00 34.31 2.44
3374 3451 4.051922 CCGATATCAGGTTGCTGTAGTTC 58.948 47.826 3.12 0.00 0.00 3.01
3519 3597 9.535878 GATCTTGTGGTAGAAAGTATAAGAAGG 57.464 37.037 0.00 0.00 0.00 3.46
3814 4326 5.016831 GGGGTTCTTCTATCAAACATTGGT 58.983 41.667 0.00 0.00 0.00 3.67
3941 4453 9.436957 GAAGGTTAGACTTCAGATTTTGTATGA 57.563 33.333 0.00 0.00 44.82 2.15
3971 4483 9.290988 TGTTTACTTGTGATACAATGTGGTATT 57.709 29.630 0.00 0.00 37.48 1.89
4215 4727 0.107165 CGGAGATTTTCCCCACCTCC 60.107 60.000 0.00 0.00 43.63 4.30
4329 4841 1.002502 TCTCGCTGGAGTCTTCGGA 60.003 57.895 0.00 0.00 41.26 4.55
4338 4850 4.322349 GCTGGAGTCTTCGGAATATATGCT 60.322 45.833 0.00 0.00 0.00 3.79
4339 4851 5.139435 TGGAGTCTTCGGAATATATGCTG 57.861 43.478 0.00 0.00 0.00 4.41
4476 4988 2.425312 CACGGACTAGTTGCTCTGATCT 59.575 50.000 0.00 0.00 0.00 2.75
4621 5133 1.588824 AATCGTGTCGTCGTAGGCCA 61.589 55.000 5.01 0.00 0.00 5.36
4765 5277 1.595794 GTTTTTGTCTTGCTCGGTCGA 59.404 47.619 0.00 0.00 0.00 4.20
4997 5542 9.353999 GTTTGTTGGGAAGAACATTTATATGTC 57.646 33.333 0.00 0.00 44.14 3.06
5196 5752 7.744733 TCATTAATATTGATACTCCCTGCACA 58.255 34.615 0.00 0.00 0.00 4.57
5205 5761 2.769209 ACTCCCTGCACATCCTTCTAT 58.231 47.619 0.00 0.00 0.00 1.98
5225 5781 8.934023 TTCTATCACTTGTTTAATCCAACCTT 57.066 30.769 0.00 0.00 0.00 3.50
5251 5845 5.016173 TGTAGAAAATCCCAATTCACCCTG 58.984 41.667 0.00 0.00 0.00 4.45
5262 5856 5.069781 CCCAATTCACCCTGTTTCAAAGTTA 59.930 40.000 0.00 0.00 0.00 2.24
5263 5857 6.407525 CCCAATTCACCCTGTTTCAAAGTTAA 60.408 38.462 0.00 0.00 0.00 2.01
5265 5859 7.011016 CCAATTCACCCTGTTTCAAAGTTAAAC 59.989 37.037 0.00 0.00 37.35 2.01
5266 5860 6.844097 TTCACCCTGTTTCAAAGTTAAACT 57.156 33.333 3.57 0.00 37.64 2.66
5268 5862 7.941431 TCACCCTGTTTCAAAGTTAAACTTA 57.059 32.000 0.00 0.00 37.47 2.24
5269 5863 7.992008 TCACCCTGTTTCAAAGTTAAACTTAG 58.008 34.615 0.00 0.00 37.47 2.18
5270 5864 6.695713 CACCCTGTTTCAAAGTTAAACTTAGC 59.304 38.462 0.00 0.00 37.47 3.09
5368 5964 4.073169 CGTTTTTCATAAACGCTGGCTA 57.927 40.909 9.45 0.00 44.87 3.93
5369 5965 3.844099 CGTTTTTCATAAACGCTGGCTAC 59.156 43.478 9.45 0.00 44.87 3.58
5370 5966 4.163552 GTTTTTCATAAACGCTGGCTACC 58.836 43.478 0.00 0.00 0.00 3.18
5371 5967 1.647346 TTCATAAACGCTGGCTACCG 58.353 50.000 0.00 0.00 0.00 4.02
5372 5968 0.818938 TCATAAACGCTGGCTACCGA 59.181 50.000 0.00 0.00 0.00 4.69
5431 6038 1.135972 AGCGCATACGTTTTCTTGCTG 60.136 47.619 11.47 0.00 42.83 4.41
5434 6041 2.093625 CGCATACGTTTTCTTGCTGCTA 59.906 45.455 0.00 0.00 32.97 3.49
5456 6063 4.748892 AGGTACTTGTCTGATCAATCACG 58.251 43.478 0.00 0.00 27.25 4.35
5457 6064 4.220821 AGGTACTTGTCTGATCAATCACGT 59.779 41.667 0.00 5.64 27.25 4.49
5463 6070 3.428534 TGTCTGATCAATCACGTTGTTCG 59.571 43.478 0.00 0.00 46.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.777782 AGAAGAGGTTCATGAACAAAGATCT 58.222 36.000 33.42 25.32 42.85 2.75
1 2 6.652481 TGAGAAGAGGTTCATGAACAAAGATC 59.348 38.462 33.42 23.92 42.85 2.75
2 3 6.537355 TGAGAAGAGGTTCATGAACAAAGAT 58.463 36.000 33.42 18.46 42.85 2.40
3 4 5.928976 TGAGAAGAGGTTCATGAACAAAGA 58.071 37.500 33.42 10.91 42.85 2.52
4 5 5.180868 CCTGAGAAGAGGTTCATGAACAAAG 59.819 44.000 33.42 19.14 42.85 2.77
5 6 5.065914 CCTGAGAAGAGGTTCATGAACAAA 58.934 41.667 33.42 12.64 42.85 2.83
6 7 4.645535 CCTGAGAAGAGGTTCATGAACAA 58.354 43.478 33.42 11.78 42.85 2.83
7 8 3.557898 GCCTGAGAAGAGGTTCATGAACA 60.558 47.826 33.42 14.27 42.85 3.18
8 9 3.006247 GCCTGAGAAGAGGTTCATGAAC 58.994 50.000 27.16 27.16 40.45 3.18
9 10 2.909006 AGCCTGAGAAGAGGTTCATGAA 59.091 45.455 3.38 3.38 35.29 2.57
10 11 2.544721 AGCCTGAGAAGAGGTTCATGA 58.455 47.619 0.00 0.00 35.29 3.07
11 12 3.008330 CAAGCCTGAGAAGAGGTTCATG 58.992 50.000 0.00 0.00 35.29 3.07
12 13 2.026449 CCAAGCCTGAGAAGAGGTTCAT 60.026 50.000 0.00 0.00 35.29 2.57
13 14 1.349026 CCAAGCCTGAGAAGAGGTTCA 59.651 52.381 0.00 0.00 35.29 3.18
14 15 1.625818 TCCAAGCCTGAGAAGAGGTTC 59.374 52.381 0.00 0.00 35.29 3.62
15 16 1.734655 TCCAAGCCTGAGAAGAGGTT 58.265 50.000 0.00 0.00 35.29 3.50
16 17 1.349357 GTTCCAAGCCTGAGAAGAGGT 59.651 52.381 0.00 0.00 35.29 3.85
17 18 1.339535 GGTTCCAAGCCTGAGAAGAGG 60.340 57.143 0.00 0.00 36.03 3.69
18 19 1.339535 GGGTTCCAAGCCTGAGAAGAG 60.340 57.143 0.00 0.00 43.15 2.85
19 20 0.693049 GGGTTCCAAGCCTGAGAAGA 59.307 55.000 0.00 0.00 43.15 2.87
20 21 0.401738 TGGGTTCCAAGCCTGAGAAG 59.598 55.000 8.93 0.00 46.54 2.85
21 22 1.075601 ATGGGTTCCAAGCCTGAGAA 58.924 50.000 8.93 0.00 46.54 2.87
22 23 0.329261 CATGGGTTCCAAGCCTGAGA 59.671 55.000 8.93 0.00 46.54 3.27
23 24 0.038744 ACATGGGTTCCAAGCCTGAG 59.961 55.000 8.93 1.94 46.54 3.35
24 25 1.367346 TACATGGGTTCCAAGCCTGA 58.633 50.000 8.93 0.00 46.54 3.86
25 26 2.214376 TTACATGGGTTCCAAGCCTG 57.786 50.000 8.93 7.13 46.54 4.85
26 27 2.990740 TTTACATGGGTTCCAAGCCT 57.009 45.000 8.93 0.00 46.54 4.58
27 28 3.864540 GCTTTTTACATGGGTTCCAAGCC 60.865 47.826 0.00 0.24 46.58 4.35
28 29 3.006859 AGCTTTTTACATGGGTTCCAAGC 59.993 43.478 0.00 3.26 36.95 4.01
29 30 4.321974 GGAGCTTTTTACATGGGTTCCAAG 60.322 45.833 0.00 0.00 36.95 3.61
30 31 3.576550 GGAGCTTTTTACATGGGTTCCAA 59.423 43.478 0.00 0.00 36.95 3.53
31 32 3.161866 GGAGCTTTTTACATGGGTTCCA 58.838 45.455 0.00 0.00 38.19 3.53
32 33 2.496070 GGGAGCTTTTTACATGGGTTCC 59.504 50.000 0.00 0.00 0.00 3.62
33 34 2.163613 CGGGAGCTTTTTACATGGGTTC 59.836 50.000 0.00 0.00 0.00 3.62
34 35 2.167662 CGGGAGCTTTTTACATGGGTT 58.832 47.619 0.00 0.00 0.00 4.11
35 36 1.615919 CCGGGAGCTTTTTACATGGGT 60.616 52.381 0.00 0.00 0.00 4.51
36 37 1.102978 CCGGGAGCTTTTTACATGGG 58.897 55.000 0.00 0.00 0.00 4.00
37 38 1.102978 CCCGGGAGCTTTTTACATGG 58.897 55.000 18.48 0.00 0.00 3.66
38 39 2.122783 TCCCGGGAGCTTTTTACATG 57.877 50.000 22.63 0.00 0.00 3.21
39 40 2.891191 TTCCCGGGAGCTTTTTACAT 57.109 45.000 25.26 0.00 0.00 2.29
40 41 2.307686 AGATTCCCGGGAGCTTTTTACA 59.692 45.455 25.26 5.61 0.00 2.41
48 49 1.147153 CAAGGAGATTCCCGGGAGC 59.853 63.158 25.26 19.74 37.19 4.70
52 53 1.679032 GGTGAACAAGGAGATTCCCGG 60.679 57.143 0.00 0.00 37.19 5.73
53 54 1.279271 AGGTGAACAAGGAGATTCCCG 59.721 52.381 0.00 0.00 37.19 5.14
59 60 3.202151 AGGTTTCAAGGTGAACAAGGAGA 59.798 43.478 0.00 0.00 35.89 3.71
66 67 6.752168 TGTAGTAGTAGGTTTCAAGGTGAAC 58.248 40.000 0.00 0.00 35.89 3.18
76 77 5.693555 GCAAGAACGTTGTAGTAGTAGGTTT 59.306 40.000 5.00 0.00 0.00 3.27
80 81 6.605849 TGTAGCAAGAACGTTGTAGTAGTAG 58.394 40.000 5.00 0.00 0.00 2.57
81 82 6.558771 TGTAGCAAGAACGTTGTAGTAGTA 57.441 37.500 5.00 0.00 0.00 1.82
82 83 5.443185 TGTAGCAAGAACGTTGTAGTAGT 57.557 39.130 5.00 0.00 0.00 2.73
83 84 6.758593 TTTGTAGCAAGAACGTTGTAGTAG 57.241 37.500 5.00 0.00 0.00 2.57
84 85 6.979817 TCTTTTGTAGCAAGAACGTTGTAGTA 59.020 34.615 5.00 0.00 0.00 1.82
85 86 5.813672 TCTTTTGTAGCAAGAACGTTGTAGT 59.186 36.000 5.00 0.00 0.00 2.73
95 96 8.726988 GGTTGTACAATATCTTTTGTAGCAAGA 58.273 33.333 12.26 0.00 41.44 3.02
99 100 7.962918 CAGTGGTTGTACAATATCTTTTGTAGC 59.037 37.037 12.26 0.00 41.44 3.58
114 115 0.251033 GGGGGTTCCAGTGGTTGTAC 60.251 60.000 9.54 3.72 35.00 2.90
196 198 1.172180 TGTACCAGCTTGCAACAGGC 61.172 55.000 0.00 0.00 45.13 4.85
348 361 1.181786 CCAACCTTCTCTCTCTCGCT 58.818 55.000 0.00 0.00 0.00 4.93
349 362 1.178276 TCCAACCTTCTCTCTCTCGC 58.822 55.000 0.00 0.00 0.00 5.03
350 363 2.360801 GGATCCAACCTTCTCTCTCTCG 59.639 54.545 6.95 0.00 0.00 4.04
351 364 2.360801 CGGATCCAACCTTCTCTCTCTC 59.639 54.545 13.41 0.00 0.00 3.20
352 365 2.383855 CGGATCCAACCTTCTCTCTCT 58.616 52.381 13.41 0.00 0.00 3.10
545 569 5.121925 CGATTTCTCTACGATATTCCTCCGA 59.878 44.000 0.00 0.00 0.00 4.55
581 608 1.885049 ACTATCATCTGGTGGCCTGT 58.115 50.000 3.32 0.00 0.00 4.00
672 702 0.251165 CCGGAAGCTTTTTCCCTCCA 60.251 55.000 0.00 0.00 35.17 3.86
764 794 4.933064 GATCTCCGCTCGGGCACG 62.933 72.222 8.62 0.00 42.74 5.34
765 795 4.593864 GGATCTCCGCTCGGGCAC 62.594 72.222 8.62 0.00 38.60 5.01
766 796 4.841617 AGGATCTCCGCTCGGGCA 62.842 66.667 8.62 0.00 42.08 5.36
767 797 3.984749 GAGGATCTCCGCTCGGGC 61.985 72.222 8.59 0.00 42.08 6.13
864 906 4.318332 ACAAATCAGATTCGACAGAAGCA 58.682 39.130 0.00 0.00 44.59 3.91
894 936 0.722848 AACAACGACGACACCAACAC 59.277 50.000 0.00 0.00 0.00 3.32
895 937 0.722282 CAACAACGACGACACCAACA 59.278 50.000 0.00 0.00 0.00 3.33
896 938 0.722848 ACAACAACGACGACACCAAC 59.277 50.000 0.00 0.00 0.00 3.77
897 939 1.440708 AACAACAACGACGACACCAA 58.559 45.000 0.00 0.00 0.00 3.67
898 940 1.128878 CAAACAACAACGACGACACCA 59.871 47.619 0.00 0.00 0.00 4.17
899 941 1.129064 ACAAACAACAACGACGACACC 59.871 47.619 0.00 0.00 0.00 4.16
900 942 2.159814 TGACAAACAACAACGACGACAC 60.160 45.455 0.00 0.00 0.00 3.67
901 943 2.067013 TGACAAACAACAACGACGACA 58.933 42.857 0.00 0.00 0.00 4.35
902 944 2.791417 TGACAAACAACAACGACGAC 57.209 45.000 0.00 0.00 0.00 4.34
903 945 4.986034 AGATATGACAAACAACAACGACGA 59.014 37.500 0.00 0.00 0.00 4.20
904 946 5.107645 TGAGATATGACAAACAACAACGACG 60.108 40.000 0.00 0.00 0.00 5.12
905 947 6.071463 GTGAGATATGACAAACAACAACGAC 58.929 40.000 0.00 0.00 0.00 4.34
906 948 5.107645 CGTGAGATATGACAAACAACAACGA 60.108 40.000 0.00 0.00 0.00 3.85
907 949 5.072823 CGTGAGATATGACAAACAACAACG 58.927 41.667 0.00 0.00 0.00 4.10
920 974 1.524355 CGGCAAAGCTCGTGAGATATG 59.476 52.381 0.00 0.00 40.84 1.78
949 1003 0.034574 TCACCACCAACAACAGCACT 60.035 50.000 0.00 0.00 0.00 4.40
1112 1169 1.374252 AACGGCGTCGAAAGAGCAT 60.374 52.632 20.03 0.00 43.49 3.79
1176 1233 3.554934 CCAATAATTGCTGCCTCTACCA 58.445 45.455 0.00 0.00 0.00 3.25
1315 1374 1.069296 TGCTTGGATTTCGTTTCAGCG 60.069 47.619 0.00 0.00 0.00 5.18
1331 1390 3.999663 CAGAGAACTCGGAAATCTTGCTT 59.000 43.478 0.00 0.00 34.09 3.91
1373 1432 0.249955 TGGTTCAGATGCGCAGATCA 59.750 50.000 18.32 6.89 0.00 2.92
1396 1455 3.742882 ACATGTCGACACAGACTGAATTG 59.257 43.478 22.71 13.36 41.47 2.32
1421 1480 1.895798 TCTGCATCGGTTCAGAGTTCT 59.104 47.619 0.00 0.00 34.69 3.01
1425 1484 0.935898 GCATCTGCATCGGTTCAGAG 59.064 55.000 3.99 0.00 41.95 3.35
1493 1552 2.572191 TCTTTATGTACAGGACGGCG 57.428 50.000 4.80 4.80 0.00 6.46
1640 1699 1.064946 GAGGACAGACGAGGCGATG 59.935 63.158 0.00 0.00 0.00 3.84
1826 1885 0.119155 TCCCTCCTGACCCACTGAAT 59.881 55.000 0.00 0.00 0.00 2.57
1928 1987 1.997606 GCAAAGTACATAAGCGACGGT 59.002 47.619 0.00 0.00 0.00 4.83
3026 3100 4.019174 CAGGTTCAAATAGTTCTGCCCAT 58.981 43.478 0.00 0.00 0.00 4.00
3294 3371 3.938963 CTCGCAATAAGGCTGAAGGTAAA 59.061 43.478 0.00 0.00 0.00 2.01
3515 3593 0.391263 CTACCGCACCACCTTCCTTC 60.391 60.000 0.00 0.00 0.00 3.46
3519 3597 1.154197 GTTTCTACCGCACCACCTTC 58.846 55.000 0.00 0.00 0.00 3.46
3644 4031 6.259550 ACTAAACATGAAGCATGGAAGAAC 57.740 37.500 11.61 0.00 45.16 3.01
3814 4326 3.641046 AGATGCAGAGGAAGAGCTTAGA 58.359 45.455 0.00 0.00 0.00 2.10
3971 4483 6.072508 GGTTACTCTTTCATTCACATTCAGCA 60.073 38.462 0.00 0.00 0.00 4.41
4215 4727 1.217585 CTATGCAGATGCCACGGACG 61.218 60.000 1.72 0.00 41.18 4.79
4278 4790 0.103208 GCATCACGGGGAGAGTGTAG 59.897 60.000 0.00 0.00 40.28 2.74
4338 4850 0.036164 AGGCCAGTATGCAAACGACA 59.964 50.000 5.01 0.00 31.97 4.35
4339 4851 1.165270 AAGGCCAGTATGCAAACGAC 58.835 50.000 5.01 0.00 31.97 4.34
4353 4865 4.439057 TCATGTAGACGAATACAAAGGCC 58.561 43.478 0.00 0.00 39.04 5.19
4476 4988 4.794439 CAGCGACGCGGATCACCA 62.794 66.667 15.14 0.00 35.59 4.17
4621 5133 7.439108 AGTACATATCCTACTTCCAAAAGCT 57.561 36.000 0.00 0.00 35.81 3.74
4752 5264 0.888619 ACTGAATCGACCGAGCAAGA 59.111 50.000 0.00 0.00 0.00 3.02
4765 5277 6.272822 GGCAACAAAGAGGATAAACTGAAT 57.727 37.500 0.00 0.00 0.00 2.57
4943 5488 7.658261 AGCCAAAGTTTATAAGGTTTGACTTC 58.342 34.615 17.19 8.06 32.65 3.01
4979 5524 7.920738 AGCTTTCGACATATAAATGTTCTTCC 58.079 34.615 0.00 0.00 46.49 3.46
5189 5745 3.834489 AGTGATAGAAGGATGTGCAGG 57.166 47.619 0.00 0.00 0.00 4.85
5196 5752 9.178758 GTTGGATTAAACAAGTGATAGAAGGAT 57.821 33.333 0.00 0.00 0.00 3.24
5205 5761 7.616313 ACAAAAAGGTTGGATTAAACAAGTGA 58.384 30.769 0.00 0.00 0.00 3.41
5225 5781 6.556874 AGGGTGAATTGGGATTTTCTACAAAA 59.443 34.615 0.00 0.00 35.92 2.44
5251 5845 6.412943 GGTCACGCTAAGTTTAACTTTGAAAC 59.587 38.462 19.96 11.84 39.51 2.78
5262 5856 0.323957 GAGGGGGTCACGCTAAGTTT 59.676 55.000 0.00 0.00 43.22 2.66
5263 5857 0.544595 AGAGGGGGTCACGCTAAGTT 60.545 55.000 0.00 0.00 43.22 2.66
5265 5859 0.108138 CAAGAGGGGGTCACGCTAAG 60.108 60.000 0.00 0.00 43.22 2.18
5266 5860 0.834687 ACAAGAGGGGGTCACGCTAA 60.835 55.000 0.00 0.00 43.22 3.09
5268 5862 1.705997 AAACAAGAGGGGGTCACGCT 61.706 55.000 0.00 0.00 46.25 5.07
5269 5863 0.035739 TAAACAAGAGGGGGTCACGC 59.964 55.000 0.00 0.00 0.00 5.34
5270 5864 1.346722 ACTAAACAAGAGGGGGTCACG 59.653 52.381 0.00 0.00 0.00 4.35
5360 5956 0.669318 TGTTCTTTCGGTAGCCAGCG 60.669 55.000 0.00 0.00 46.87 5.18
5363 5959 1.202710 TGCTTGTTCTTTCGGTAGCCA 60.203 47.619 0.00 0.00 0.00 4.75
5365 5961 2.661979 CGTTGCTTGTTCTTTCGGTAGC 60.662 50.000 0.00 0.00 0.00 3.58
5366 5962 2.798283 TCGTTGCTTGTTCTTTCGGTAG 59.202 45.455 0.00 0.00 0.00 3.18
5368 5964 1.658994 TCGTTGCTTGTTCTTTCGGT 58.341 45.000 0.00 0.00 0.00 4.69
5369 5965 2.748461 TTCGTTGCTTGTTCTTTCGG 57.252 45.000 0.00 0.00 0.00 4.30
5370 5966 4.732923 TGAAATTCGTTGCTTGTTCTTTCG 59.267 37.500 0.00 0.00 0.00 3.46
5371 5967 5.330792 CGTGAAATTCGTTGCTTGTTCTTTC 60.331 40.000 0.00 0.00 0.00 2.62
5372 5968 4.499040 CGTGAAATTCGTTGCTTGTTCTTT 59.501 37.500 0.00 0.00 0.00 2.52
5431 6038 5.751028 GTGATTGATCAGACAAGTACCTAGC 59.249 44.000 0.00 0.00 37.51 3.42
5434 6041 4.220821 ACGTGATTGATCAGACAAGTACCT 59.779 41.667 16.17 0.00 37.51 3.08


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

AutoCloner maintained by Alex Coulton.