Multiple sequence alignment - TraesCS6B01G303500

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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 TraesCS6B01G303500 chr6B 100.000 3325 0 0 1 3325 543824502 543827826 0.000000e+00 6141.0
1 TraesCS6B01G303500 chr6B 80.697 1922 215 93 292 2159 544091352 544093171 0.000000e+00 1351.0
2 TraesCS6B01G303500 chr6B 86.731 520 43 14 1409 1909 543940450 543940962 3.750000e-154 555.0
3 TraesCS6B01G303500 chr6B 84.135 561 63 16 2140 2686 543960617 543961165 1.370000e-143 520.0
4 TraesCS6B01G303500 chr6B 88.140 430 28 10 500 908 543909627 543910054 1.070000e-134 490.0
5 TraesCS6B01G303500 chr6B 84.713 314 46 1 1039 1350 543940115 543940428 2.490000e-81 313.0
6 TraesCS6B01G303500 chr6B 89.583 240 13 5 1909 2144 543959893 543960124 9.020000e-76 294.0
7 TraesCS6B01G303500 chr6D 93.009 2875 147 22 486 3325 362858922 362861777 0.000000e+00 4146.0
8 TraesCS6B01G303500 chr6D 91.079 1816 92 39 167 1941 362633485 362635271 0.000000e+00 2392.0
9 TraesCS6B01G303500 chr6D 83.333 1530 165 55 679 2159 362953470 362954958 0.000000e+00 1330.0
10 TraesCS6B01G303500 chr6D 88.717 1099 74 17 1045 2134 362887992 362889049 0.000000e+00 1297.0
11 TraesCS6B01G303500 chr6D 92.351 706 41 7 1936 2633 362635372 362636072 0.000000e+00 992.0
12 TraesCS6B01G303500 chr6D 88.128 657 45 18 2395 3028 362236599 362237245 0.000000e+00 750.0
13 TraesCS6B01G303500 chr6D 85.888 411 39 11 2635 3035 362902267 362902668 1.430000e-113 420.0
14 TraesCS6B01G303500 chr6D 86.464 362 30 14 2675 3028 362636302 362636652 2.420000e-101 379.0
15 TraesCS6B01G303500 chr6D 92.593 216 13 1 2184 2399 362232349 362232561 1.160000e-79 307.0
16 TraesCS6B01G303500 chr6D 87.166 187 14 8 295 476 362942793 362942974 1.560000e-48 204.0
17 TraesCS6B01G303500 chr6D 88.333 60 5 2 2228 2287 362954965 362955022 1.650000e-08 71.3
18 TraesCS6B01G303500 chr6A 89.726 2044 122 31 612 2626 502928594 502930578 0.000000e+00 2531.0
19 TraesCS6B01G303500 chr6A 88.287 1033 72 14 1039 2049 503229975 503230980 0.000000e+00 1192.0
20 TraesCS6B01G303500 chr6A 87.100 1000 81 29 1057 2049 503248753 503249711 0.000000e+00 1088.0
21 TraesCS6B01G303500 chr6A 92.899 338 21 3 124 461 502927509 502927843 3.860000e-134 488.0
22 TraesCS6B01G303500 chr6A 87.952 249 24 3 1079 1327 516341753 516341995 4.200000e-74 289.0
23 TraesCS6B01G303500 chr6A 92.806 139 7 2 476 612 502928177 502928314 7.280000e-47 198.0
24 TraesCS6B01G303500 chr6A 91.089 101 7 2 2047 2145 503231006 503231106 5.790000e-28 135.0
25 TraesCS6B01G303500 chr2B 88.027 593 57 10 976 1561 774846095 774846680 0.000000e+00 689.0


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 TraesCS6B01G303500 chr6B 543824502 543827826 3324 False 6141.000000 6141 100.000000 1 3325 1 chr6B.!!$F1 3324
1 TraesCS6B01G303500 chr6B 544091352 544093171 1819 False 1351.000000 1351 80.697000 292 2159 1 chr6B.!!$F3 1867
2 TraesCS6B01G303500 chr6B 543940115 543940962 847 False 434.000000 555 85.722000 1039 1909 2 chr6B.!!$F4 870
3 TraesCS6B01G303500 chr6B 543959893 543961165 1272 False 407.000000 520 86.859000 1909 2686 2 chr6B.!!$F5 777
4 TraesCS6B01G303500 chr6D 362858922 362861777 2855 False 4146.000000 4146 93.009000 486 3325 1 chr6D.!!$F3 2839
5 TraesCS6B01G303500 chr6D 362887992 362889049 1057 False 1297.000000 1297 88.717000 1045 2134 1 chr6D.!!$F4 1089
6 TraesCS6B01G303500 chr6D 362633485 362636652 3167 False 1254.333333 2392 89.964667 167 3028 3 chr6D.!!$F7 2861
7 TraesCS6B01G303500 chr6D 362236599 362237245 646 False 750.000000 750 88.128000 2395 3028 1 chr6D.!!$F2 633
8 TraesCS6B01G303500 chr6D 362953470 362955022 1552 False 700.650000 1330 85.833000 679 2287 2 chr6D.!!$F8 1608
9 TraesCS6B01G303500 chr6A 503248753 503249711 958 False 1088.000000 1088 87.100000 1057 2049 1 chr6A.!!$F1 992
10 TraesCS6B01G303500 chr6A 502927509 502930578 3069 False 1072.333333 2531 91.810333 124 2626 3 chr6A.!!$F3 2502
11 TraesCS6B01G303500 chr6A 503229975 503231106 1131 False 663.500000 1192 89.688000 1039 2145 2 chr6A.!!$F4 1106
12 TraesCS6B01G303500 chr2B 774846095 774846680 585 False 689.000000 689 88.027000 976 1561 1 chr2B.!!$F1 585

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
769 1412 0.176680 CACAGCTACGGCAAGGATCT 59.823 55.000 0.00 0.0 41.70 2.75 F
2007 2877 1.623834 GATCTCCCAGGTGAAGGAGGT 60.624 57.143 6.23 0.0 46.61 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2026 2896 0.111253 CAGTTCAGTTGCCCCCTCTT 59.889 55.0 0.0 0.0 0.0 2.85 R
3267 4896 1.196766 AGGCTGCTCTCCACACATCA 61.197 55.0 0.0 0.0 0.0 3.07 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
27 28 3.801114 GCCAAAAATTAGGCCGAGAAT 57.199 42.857 0.00 0.00 45.18 2.40
28 29 3.706698 GCCAAAAATTAGGCCGAGAATC 58.293 45.455 0.00 0.00 45.18 2.52
29 30 3.130340 GCCAAAAATTAGGCCGAGAATCA 59.870 43.478 0.00 0.00 45.18 2.57
30 31 4.734695 GCCAAAAATTAGGCCGAGAATCAG 60.735 45.833 0.00 0.00 45.18 2.90
31 32 4.399303 CCAAAAATTAGGCCGAGAATCAGT 59.601 41.667 0.00 0.00 33.17 3.41
32 33 5.335127 CAAAAATTAGGCCGAGAATCAGTG 58.665 41.667 0.00 0.00 33.17 3.66
33 34 3.914426 AATTAGGCCGAGAATCAGTGT 57.086 42.857 0.00 0.00 33.17 3.55
34 35 3.914426 ATTAGGCCGAGAATCAGTGTT 57.086 42.857 0.00 0.00 33.17 3.32
35 36 3.695830 TTAGGCCGAGAATCAGTGTTT 57.304 42.857 0.00 0.00 33.17 2.83
36 37 2.568623 AGGCCGAGAATCAGTGTTTT 57.431 45.000 0.00 0.00 33.17 2.43
37 38 2.863809 AGGCCGAGAATCAGTGTTTTT 58.136 42.857 0.00 0.00 33.17 1.94
59 60 8.770438 TTTTTGCAACAATTTTGTAGAAGTCT 57.230 26.923 0.00 0.00 41.31 3.24
60 61 8.770438 TTTTGCAACAATTTTGTAGAAGTCTT 57.230 26.923 0.00 0.00 41.31 3.01
61 62 8.770438 TTTGCAACAATTTTGTAGAAGTCTTT 57.230 26.923 0.00 0.00 41.31 2.52
62 63 8.770438 TTGCAACAATTTTGTAGAAGTCTTTT 57.230 26.923 0.00 0.00 41.31 2.27
63 64 8.406172 TGCAACAATTTTGTAGAAGTCTTTTC 57.594 30.769 0.00 0.00 41.31 2.29
64 65 8.250332 TGCAACAATTTTGTAGAAGTCTTTTCT 58.750 29.630 0.00 0.00 41.31 2.52
65 66 8.534778 GCAACAATTTTGTAGAAGTCTTTTCTG 58.465 33.333 0.00 0.00 41.31 3.02
66 67 9.573133 CAACAATTTTGTAGAAGTCTTTTCTGT 57.427 29.630 0.00 0.00 41.31 3.41
72 73 9.457436 TTTTGTAGAAGTCTTTTCTGTAAACCT 57.543 29.630 0.00 0.00 0.00 3.50
75 76 9.760077 TGTAGAAGTCTTTTCTGTAAACCTAAG 57.240 33.333 0.00 0.00 0.00 2.18
76 77 7.731882 AGAAGTCTTTTCTGTAAACCTAAGC 57.268 36.000 0.00 0.00 0.00 3.09
77 78 7.510407 AGAAGTCTTTTCTGTAAACCTAAGCT 58.490 34.615 0.00 0.00 0.00 3.74
78 79 7.442666 AGAAGTCTTTTCTGTAAACCTAAGCTG 59.557 37.037 0.00 0.00 0.00 4.24
79 80 6.592870 AGTCTTTTCTGTAAACCTAAGCTGT 58.407 36.000 0.00 0.00 0.00 4.40
80 81 7.732996 AGTCTTTTCTGTAAACCTAAGCTGTA 58.267 34.615 0.00 0.00 0.00 2.74
81 82 8.208903 AGTCTTTTCTGTAAACCTAAGCTGTAA 58.791 33.333 0.00 0.00 0.00 2.41
82 83 9.000486 GTCTTTTCTGTAAACCTAAGCTGTAAT 58.000 33.333 0.00 0.00 0.00 1.89
83 84 8.999431 TCTTTTCTGTAAACCTAAGCTGTAATG 58.001 33.333 0.00 0.00 0.00 1.90
84 85 8.685838 TTTTCTGTAAACCTAAGCTGTAATGT 57.314 30.769 0.00 0.00 0.00 2.71
85 86 9.781633 TTTTCTGTAAACCTAAGCTGTAATGTA 57.218 29.630 0.00 0.00 0.00 2.29
86 87 8.997621 TTCTGTAAACCTAAGCTGTAATGTAG 57.002 34.615 0.00 0.00 0.00 2.74
87 88 8.130671 TCTGTAAACCTAAGCTGTAATGTAGT 57.869 34.615 0.00 0.00 0.00 2.73
88 89 8.033038 TCTGTAAACCTAAGCTGTAATGTAGTG 58.967 37.037 0.00 0.00 0.00 2.74
89 90 7.101054 TGTAAACCTAAGCTGTAATGTAGTGG 58.899 38.462 0.00 0.00 0.00 4.00
90 91 5.757099 AACCTAAGCTGTAATGTAGTGGT 57.243 39.130 0.00 0.00 0.00 4.16
91 92 5.757099 ACCTAAGCTGTAATGTAGTGGTT 57.243 39.130 0.00 0.00 0.00 3.67
92 93 6.123045 ACCTAAGCTGTAATGTAGTGGTTT 57.877 37.500 0.00 0.00 0.00 3.27
93 94 6.540083 ACCTAAGCTGTAATGTAGTGGTTTT 58.460 36.000 0.00 0.00 0.00 2.43
94 95 6.653740 ACCTAAGCTGTAATGTAGTGGTTTTC 59.346 38.462 0.00 0.00 0.00 2.29
95 96 6.879458 CCTAAGCTGTAATGTAGTGGTTTTCT 59.121 38.462 0.00 0.00 0.00 2.52
96 97 6.560253 AAGCTGTAATGTAGTGGTTTTCTG 57.440 37.500 0.00 0.00 0.00 3.02
97 98 4.455877 AGCTGTAATGTAGTGGTTTTCTGC 59.544 41.667 0.00 0.00 0.00 4.26
98 99 4.215399 GCTGTAATGTAGTGGTTTTCTGCA 59.785 41.667 0.00 0.00 32.76 4.41
99 100 5.278266 GCTGTAATGTAGTGGTTTTCTGCAA 60.278 40.000 0.00 0.00 32.08 4.08
100 101 6.570378 GCTGTAATGTAGTGGTTTTCTGCAAT 60.570 38.462 0.00 0.00 32.08 3.56
101 102 7.283625 TGTAATGTAGTGGTTTTCTGCAATT 57.716 32.000 0.00 0.00 32.08 2.32
102 103 7.367285 TGTAATGTAGTGGTTTTCTGCAATTC 58.633 34.615 0.00 0.00 32.08 2.17
103 104 6.403866 AATGTAGTGGTTTTCTGCAATTCA 57.596 33.333 0.00 0.00 32.08 2.57
104 105 5.181690 TGTAGTGGTTTTCTGCAATTCAC 57.818 39.130 0.00 0.00 0.00 3.18
105 106 4.887071 TGTAGTGGTTTTCTGCAATTCACT 59.113 37.500 0.00 0.00 37.66 3.41
106 107 6.058833 TGTAGTGGTTTTCTGCAATTCACTA 58.941 36.000 0.00 0.00 35.84 2.74
107 108 5.695851 AGTGGTTTTCTGCAATTCACTAG 57.304 39.130 0.00 0.00 33.00 2.57
108 109 4.022849 AGTGGTTTTCTGCAATTCACTAGC 60.023 41.667 0.00 0.00 33.00 3.42
109 110 4.022849 GTGGTTTTCTGCAATTCACTAGCT 60.023 41.667 0.00 0.00 0.00 3.32
110 111 5.181245 GTGGTTTTCTGCAATTCACTAGCTA 59.819 40.000 0.00 0.00 0.00 3.32
111 112 5.767665 TGGTTTTCTGCAATTCACTAGCTAA 59.232 36.000 0.00 0.00 0.00 3.09
112 113 6.072508 TGGTTTTCTGCAATTCACTAGCTAAG 60.073 38.462 0.00 0.00 0.00 2.18
113 114 6.317857 GTTTTCTGCAATTCACTAGCTAAGG 58.682 40.000 0.00 0.00 0.00 2.69
114 115 4.826274 TCTGCAATTCACTAGCTAAGGT 57.174 40.909 0.00 0.00 0.00 3.50
115 116 4.507710 TCTGCAATTCACTAGCTAAGGTG 58.492 43.478 6.76 6.76 35.06 4.00
116 117 4.222810 TCTGCAATTCACTAGCTAAGGTGA 59.777 41.667 10.85 10.85 40.17 4.02
117 118 4.507710 TGCAATTCACTAGCTAAGGTGAG 58.492 43.478 13.65 6.32 42.31 3.51
118 119 3.311048 GCAATTCACTAGCTAAGGTGAGC 59.689 47.826 13.65 11.12 42.31 4.26
119 120 4.507710 CAATTCACTAGCTAAGGTGAGCA 58.492 43.478 13.65 3.75 45.43 4.26
120 121 5.121811 CAATTCACTAGCTAAGGTGAGCAT 58.878 41.667 13.65 5.56 45.43 3.79
121 122 4.392921 TTCACTAGCTAAGGTGAGCATC 57.607 45.455 13.65 0.00 45.43 3.91
149 150 6.726490 AGTCATACCGGTGTAAGAACATAT 57.274 37.500 19.93 0.00 38.08 1.78
159 160 8.342634 CCGGTGTAAGAACATATCAATAAAAGG 58.657 37.037 0.00 0.00 38.08 3.11
161 162 8.135529 GGTGTAAGAACATATCAATAAAAGGCC 58.864 37.037 0.00 0.00 38.08 5.19
162 163 8.682710 GTGTAAGAACATATCAATAAAAGGCCA 58.317 33.333 5.01 0.00 38.08 5.36
163 164 9.420118 TGTAAGAACATATCAATAAAAGGCCAT 57.580 29.630 5.01 0.00 0.00 4.40
228 229 3.801698 TGCACTGCCTCTTGATATCTTC 58.198 45.455 3.98 0.00 0.00 2.87
230 231 3.181456 GCACTGCCTCTTGATATCTTCCT 60.181 47.826 3.98 0.00 0.00 3.36
231 232 4.685575 GCACTGCCTCTTGATATCTTCCTT 60.686 45.833 3.98 0.00 0.00 3.36
288 289 1.537202 CTGCTTCTACCACCAACTTGC 59.463 52.381 0.00 0.00 0.00 4.01
347 352 6.199393 GCTCTACGTGTTGTTGAAAGAAAAT 58.801 36.000 0.00 0.00 31.92 1.82
381 389 4.627467 GCAGGATATCAAGGCATTAGTACG 59.373 45.833 4.83 0.00 0.00 3.67
410 432 5.306678 AGGAAATGTAGAAAACCCATTTGCA 59.693 36.000 15.04 0.00 44.43 4.08
411 433 5.994668 GGAAATGTAGAAAACCCATTTGCAA 59.005 36.000 0.00 0.00 42.72 4.08
428 457 1.282817 CAATTGCATGGCCGTGAATG 58.717 50.000 29.54 10.79 0.00 2.67
431 460 0.964700 TTGCATGGCCGTGAATGAAA 59.035 45.000 29.54 9.72 0.00 2.69
529 877 2.125512 GTCGGGAATCTGCAGCGT 60.126 61.111 9.47 0.00 0.00 5.07
531 879 3.869272 CGGGAATCTGCAGCGTGC 61.869 66.667 9.47 4.01 45.29 5.34
572 922 1.849823 ACCTTCTGCTCCCTGCCTT 60.850 57.895 0.00 0.00 42.00 4.35
608 958 1.565067 GTCCCCGTTCCTCTTCCTTA 58.435 55.000 0.00 0.00 0.00 2.69
646 1275 1.197721 CGCACACAATCCTTCCTTCAC 59.802 52.381 0.00 0.00 0.00 3.18
726 1365 3.119096 GGCGGGCGAGTTCTTCAC 61.119 66.667 0.00 0.00 0.00 3.18
769 1412 0.176680 CACAGCTACGGCAAGGATCT 59.823 55.000 0.00 0.00 41.70 2.75
958 1649 3.300934 AAGCCGCTGATCGCACAGA 62.301 57.895 11.66 0.00 39.94 3.41
1015 1718 8.127150 AGATTACATCACATATAGCTGCTACA 57.873 34.615 12.26 0.00 0.00 2.74
1024 1727 2.370281 TAGCTGCTACAACTCACTGC 57.630 50.000 5.02 0.00 0.00 4.40
1825 2589 2.427245 CCGGCGGGAGAAGATCAGT 61.427 63.158 20.56 0.00 34.06 3.41
2007 2877 1.623834 GATCTCCCAGGTGAAGGAGGT 60.624 57.143 6.23 0.00 46.61 3.85
2025 2895 0.940126 GTGCTGGACGCCATCTTATG 59.060 55.000 0.00 0.00 38.05 1.90
2026 2896 0.829990 TGCTGGACGCCATCTTATGA 59.170 50.000 0.00 0.00 38.05 2.15
2049 2960 0.467290 GGGGGCAACTGAACTGAACA 60.467 55.000 0.00 0.00 0.00 3.18
2392 3810 3.304257 CAATTGCGAACGTTTTCCATGA 58.696 40.909 0.46 0.00 0.00 3.07
2542 3965 7.765819 GCATGCCTTTATAAAAGGATGTTTTCT 59.234 33.333 22.04 0.00 39.81 2.52
2626 4063 8.897752 AGCCTAAGCAAATACTATTTCTCTTTG 58.102 33.333 9.28 8.12 43.56 2.77
2745 4370 1.053424 TGGCAACTCTAACCGAACCT 58.947 50.000 0.00 0.00 37.61 3.50
2784 4409 7.219535 CCTTCAAATTGCTCGTCAAATCTTATG 59.780 37.037 0.00 0.00 38.34 1.90
2829 4458 2.490903 TGTAGAGCTAACCGAACACTCC 59.509 50.000 0.00 0.00 0.00 3.85
3095 4724 0.028902 GTGGAAGGACAACACGTTGC 59.971 55.000 9.79 3.30 44.03 4.17
3100 4729 1.160329 AGGACAACACGTTGCTGCTC 61.160 55.000 9.79 0.39 44.03 4.26
3109 4738 1.975407 GTTGCTGCTCCCATGCACT 60.975 57.895 0.00 0.00 38.12 4.40
3141 4770 2.456443 GGGCTCCTCATCCTTCCCC 61.456 68.421 0.00 0.00 0.00 4.81
3164 4793 0.324943 CCCCTTCCACTGACGACAAT 59.675 55.000 0.00 0.00 0.00 2.71
3172 4801 2.414559 CCACTGACGACAATGATTTGGC 60.415 50.000 0.00 0.00 37.52 4.52
3207 4836 2.443016 CCTCCTCCACCTCCTCCG 60.443 72.222 0.00 0.00 0.00 4.63
3211 4840 1.305381 CCTCCACCTCCTCCGTCTT 60.305 63.158 0.00 0.00 0.00 3.01
3218 4847 1.004918 CTCCTCCGTCTTGCCGTTT 60.005 57.895 0.00 0.00 0.00 3.60
3220 4849 0.037975 TCCTCCGTCTTGCCGTTTAC 60.038 55.000 0.00 0.00 0.00 2.01
3239 4868 2.543687 CTTCTGGCACGACGACCGAT 62.544 60.000 0.00 0.00 41.76 4.18
3260 4889 7.281774 ACCGATCGAAGATGTTAGTAGAAGTAA 59.718 37.037 18.66 0.00 45.12 2.24
3267 4896 9.425577 GAAGATGTTAGTAGAAGTAAGCAAAGT 57.574 33.333 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.130340 TGATTCTCGGCCTAATTTTTGGC 59.870 43.478 0.00 7.16 46.29 4.52
8 9 4.399303 ACTGATTCTCGGCCTAATTTTTGG 59.601 41.667 0.00 0.00 0.00 3.28
9 10 5.106157 ACACTGATTCTCGGCCTAATTTTTG 60.106 40.000 0.00 0.00 0.00 2.44
10 11 5.010282 ACACTGATTCTCGGCCTAATTTTT 58.990 37.500 0.00 0.00 0.00 1.94
11 12 4.589908 ACACTGATTCTCGGCCTAATTTT 58.410 39.130 0.00 0.00 0.00 1.82
12 13 4.222124 ACACTGATTCTCGGCCTAATTT 57.778 40.909 0.00 0.00 0.00 1.82
13 14 3.914426 ACACTGATTCTCGGCCTAATT 57.086 42.857 0.00 0.00 0.00 1.40
14 15 3.914426 AACACTGATTCTCGGCCTAAT 57.086 42.857 0.00 0.00 0.00 1.73
15 16 3.695830 AAACACTGATTCTCGGCCTAA 57.304 42.857 0.00 0.00 0.00 2.69
16 17 3.695830 AAAACACTGATTCTCGGCCTA 57.304 42.857 0.00 0.00 0.00 3.93
17 18 2.568623 AAAACACTGATTCTCGGCCT 57.431 45.000 0.00 0.00 0.00 5.19
34 35 8.770438 AGACTTCTACAAAATTGTTGCAAAAA 57.230 26.923 4.10 4.10 42.35 1.94
35 36 8.770438 AAGACTTCTACAAAATTGTTGCAAAA 57.230 26.923 0.00 0.00 42.35 2.44
36 37 8.770438 AAAGACTTCTACAAAATTGTTGCAAA 57.230 26.923 0.00 0.00 42.35 3.68
37 38 8.770438 AAAAGACTTCTACAAAATTGTTGCAA 57.230 26.923 3.85 0.00 42.35 4.08
38 39 8.250332 AGAAAAGACTTCTACAAAATTGTTGCA 58.750 29.630 3.85 0.00 42.35 4.08
39 40 8.534778 CAGAAAAGACTTCTACAAAATTGTTGC 58.465 33.333 3.85 0.00 42.35 4.17
40 41 9.573133 ACAGAAAAGACTTCTACAAAATTGTTG 57.427 29.630 3.85 2.81 42.35 3.33
46 47 9.457436 AGGTTTACAGAAAAGACTTCTACAAAA 57.543 29.630 0.00 0.00 0.00 2.44
49 50 9.760077 CTTAGGTTTACAGAAAAGACTTCTACA 57.240 33.333 0.00 0.00 0.00 2.74
50 51 8.710551 GCTTAGGTTTACAGAAAAGACTTCTAC 58.289 37.037 0.00 0.00 0.00 2.59
51 52 8.648693 AGCTTAGGTTTACAGAAAAGACTTCTA 58.351 33.333 0.00 0.00 0.00 2.10
52 53 7.442666 CAGCTTAGGTTTACAGAAAAGACTTCT 59.557 37.037 0.00 0.00 0.00 2.85
53 54 7.226918 ACAGCTTAGGTTTACAGAAAAGACTTC 59.773 37.037 0.00 0.00 0.00 3.01
54 55 7.054751 ACAGCTTAGGTTTACAGAAAAGACTT 58.945 34.615 0.00 0.00 0.00 3.01
55 56 6.592870 ACAGCTTAGGTTTACAGAAAAGACT 58.407 36.000 0.00 0.00 0.00 3.24
56 57 6.862711 ACAGCTTAGGTTTACAGAAAAGAC 57.137 37.500 0.00 0.00 0.00 3.01
57 58 8.999431 CATTACAGCTTAGGTTTACAGAAAAGA 58.001 33.333 0.00 0.00 0.00 2.52
58 59 8.784043 ACATTACAGCTTAGGTTTACAGAAAAG 58.216 33.333 0.00 0.00 0.00 2.27
59 60 8.685838 ACATTACAGCTTAGGTTTACAGAAAA 57.314 30.769 0.00 0.00 0.00 2.29
60 61 9.431887 CTACATTACAGCTTAGGTTTACAGAAA 57.568 33.333 0.00 0.00 0.00 2.52
61 62 8.591072 ACTACATTACAGCTTAGGTTTACAGAA 58.409 33.333 0.00 0.00 0.00 3.02
62 63 8.033038 CACTACATTACAGCTTAGGTTTACAGA 58.967 37.037 0.00 0.00 0.00 3.41
63 64 7.277981 CCACTACATTACAGCTTAGGTTTACAG 59.722 40.741 0.00 0.00 0.00 2.74
64 65 7.101054 CCACTACATTACAGCTTAGGTTTACA 58.899 38.462 0.00 0.00 0.00 2.41
65 66 7.101700 ACCACTACATTACAGCTTAGGTTTAC 58.898 38.462 0.00 0.00 0.00 2.01
66 67 7.248743 ACCACTACATTACAGCTTAGGTTTA 57.751 36.000 0.00 0.00 0.00 2.01
67 68 6.123045 ACCACTACATTACAGCTTAGGTTT 57.877 37.500 0.00 0.00 0.00 3.27
68 69 5.757099 ACCACTACATTACAGCTTAGGTT 57.243 39.130 0.00 0.00 0.00 3.50
69 70 5.757099 AACCACTACATTACAGCTTAGGT 57.243 39.130 0.00 0.00 0.00 3.08
70 71 6.879458 AGAAAACCACTACATTACAGCTTAGG 59.121 38.462 0.00 0.00 0.00 2.69
71 72 7.624344 GCAGAAAACCACTACATTACAGCTTAG 60.624 40.741 0.00 0.00 0.00 2.18
72 73 6.148811 GCAGAAAACCACTACATTACAGCTTA 59.851 38.462 0.00 0.00 0.00 3.09
73 74 5.048713 GCAGAAAACCACTACATTACAGCTT 60.049 40.000 0.00 0.00 0.00 3.74
74 75 4.455877 GCAGAAAACCACTACATTACAGCT 59.544 41.667 0.00 0.00 0.00 4.24
75 76 4.215399 TGCAGAAAACCACTACATTACAGC 59.785 41.667 0.00 0.00 0.00 4.40
76 77 5.940192 TGCAGAAAACCACTACATTACAG 57.060 39.130 0.00 0.00 0.00 2.74
77 78 6.892658 ATTGCAGAAAACCACTACATTACA 57.107 33.333 0.00 0.00 0.00 2.41
78 79 7.326063 GTGAATTGCAGAAAACCACTACATTAC 59.674 37.037 0.00 0.00 0.00 1.89
79 80 7.230510 AGTGAATTGCAGAAAACCACTACATTA 59.769 33.333 0.00 0.00 34.61 1.90
80 81 6.040842 AGTGAATTGCAGAAAACCACTACATT 59.959 34.615 0.00 0.00 34.61 2.71
81 82 5.536161 AGTGAATTGCAGAAAACCACTACAT 59.464 36.000 0.00 0.00 34.61 2.29
82 83 4.887071 AGTGAATTGCAGAAAACCACTACA 59.113 37.500 0.00 0.00 34.61 2.74
83 84 5.438761 AGTGAATTGCAGAAAACCACTAC 57.561 39.130 0.00 0.00 34.61 2.73
84 85 5.181245 GCTAGTGAATTGCAGAAAACCACTA 59.819 40.000 0.00 0.00 36.50 2.74
85 86 4.022849 GCTAGTGAATTGCAGAAAACCACT 60.023 41.667 0.00 0.00 37.84 4.00
86 87 4.022849 AGCTAGTGAATTGCAGAAAACCAC 60.023 41.667 0.00 0.00 31.38 4.16
87 88 4.144297 AGCTAGTGAATTGCAGAAAACCA 58.856 39.130 0.00 0.00 31.38 3.67
88 89 4.773323 AGCTAGTGAATTGCAGAAAACC 57.227 40.909 0.00 0.00 31.38 3.27
89 90 6.072452 ACCTTAGCTAGTGAATTGCAGAAAAC 60.072 38.462 0.00 0.00 31.38 2.43
90 91 6.003950 ACCTTAGCTAGTGAATTGCAGAAAA 58.996 36.000 0.00 0.00 31.38 2.29
91 92 5.412594 CACCTTAGCTAGTGAATTGCAGAAA 59.587 40.000 7.22 0.00 36.01 2.52
92 93 4.937620 CACCTTAGCTAGTGAATTGCAGAA 59.062 41.667 7.22 0.00 36.01 3.02
93 94 4.222810 TCACCTTAGCTAGTGAATTGCAGA 59.777 41.667 12.15 0.00 39.96 4.26
94 95 4.507710 TCACCTTAGCTAGTGAATTGCAG 58.492 43.478 12.15 0.00 39.96 4.41
95 96 4.507710 CTCACCTTAGCTAGTGAATTGCA 58.492 43.478 14.65 0.00 42.19 4.08
96 97 3.311048 GCTCACCTTAGCTAGTGAATTGC 59.689 47.826 14.65 11.59 42.19 3.56
97 98 4.507710 TGCTCACCTTAGCTAGTGAATTG 58.492 43.478 14.65 6.81 42.19 2.32
98 99 4.826274 TGCTCACCTTAGCTAGTGAATT 57.174 40.909 14.65 0.00 42.19 2.17
99 100 4.406972 TGATGCTCACCTTAGCTAGTGAAT 59.593 41.667 14.65 8.12 42.19 2.57
100 101 3.769300 TGATGCTCACCTTAGCTAGTGAA 59.231 43.478 14.65 4.29 42.19 3.18
101 102 3.365472 TGATGCTCACCTTAGCTAGTGA 58.635 45.455 13.47 13.47 43.19 3.41
102 103 3.808466 TGATGCTCACCTTAGCTAGTG 57.192 47.619 6.76 6.76 43.19 2.74
103 104 3.772025 AGTTGATGCTCACCTTAGCTAGT 59.228 43.478 0.00 0.00 43.19 2.57
104 105 4.399004 AGTTGATGCTCACCTTAGCTAG 57.601 45.455 0.00 0.00 43.19 3.42
105 106 4.956700 ACTAGTTGATGCTCACCTTAGCTA 59.043 41.667 0.00 0.00 43.19 3.32
106 107 3.772025 ACTAGTTGATGCTCACCTTAGCT 59.228 43.478 0.00 0.00 43.19 3.32
107 108 4.116238 GACTAGTTGATGCTCACCTTAGC 58.884 47.826 0.00 0.00 43.08 3.09
108 109 5.330455 TGACTAGTTGATGCTCACCTTAG 57.670 43.478 0.00 0.00 0.00 2.18
109 110 5.939764 ATGACTAGTTGATGCTCACCTTA 57.060 39.130 0.00 0.00 0.00 2.69
110 111 4.833478 ATGACTAGTTGATGCTCACCTT 57.167 40.909 0.00 0.00 0.00 3.50
111 112 4.100189 GGTATGACTAGTTGATGCTCACCT 59.900 45.833 0.00 0.00 0.00 4.00
112 113 4.372656 GGTATGACTAGTTGATGCTCACC 58.627 47.826 0.00 0.00 0.00 4.02
113 114 4.045104 CGGTATGACTAGTTGATGCTCAC 58.955 47.826 0.00 0.00 0.00 3.51
114 115 3.068165 CCGGTATGACTAGTTGATGCTCA 59.932 47.826 0.00 0.00 0.00 4.26
115 116 3.068307 ACCGGTATGACTAGTTGATGCTC 59.932 47.826 4.49 0.00 0.00 4.26
116 117 3.031736 ACCGGTATGACTAGTTGATGCT 58.968 45.455 4.49 0.00 0.00 3.79
117 118 3.123804 CACCGGTATGACTAGTTGATGC 58.876 50.000 6.87 0.00 0.00 3.91
118 119 4.386867 ACACCGGTATGACTAGTTGATG 57.613 45.455 6.87 0.00 0.00 3.07
119 120 5.889853 TCTTACACCGGTATGACTAGTTGAT 59.110 40.000 6.87 0.00 31.04 2.57
120 121 5.255687 TCTTACACCGGTATGACTAGTTGA 58.744 41.667 6.87 0.00 31.04 3.18
121 122 5.571784 TCTTACACCGGTATGACTAGTTG 57.428 43.478 6.87 0.00 31.04 3.16
122 123 5.477984 TGTTCTTACACCGGTATGACTAGTT 59.522 40.000 6.87 0.00 34.49 2.24
288 289 6.019318 TCGTTCCTTAAAGTGAGAAACGAAAG 60.019 38.462 5.11 0.00 0.00 2.62
347 352 6.488006 GCCTTGATATCCTGCTTCTTTCATTA 59.512 38.462 0.00 0.00 0.00 1.90
381 389 6.887626 TGGGTTTTCTACATTTCCTACAAC 57.112 37.500 0.00 0.00 0.00 3.32
410 432 1.184431 TCATTCACGGCCATGCAATT 58.816 45.000 2.24 0.00 0.00 2.32
411 433 1.184431 TTCATTCACGGCCATGCAAT 58.816 45.000 2.24 0.00 0.00 3.56
424 446 3.665745 TGCCTTGCCTTCTTTTCATTC 57.334 42.857 0.00 0.00 0.00 2.67
428 457 2.605580 CGAGTTGCCTTGCCTTCTTTTC 60.606 50.000 0.00 0.00 0.00 2.29
431 460 0.890996 CCGAGTTGCCTTGCCTTCTT 60.891 55.000 0.00 0.00 0.00 2.52
592 942 1.900486 ACTGTAAGGAAGAGGAACGGG 59.100 52.381 0.00 0.00 39.30 5.28
608 958 1.672356 GCAGTGCGGATCCAACTGT 60.672 57.895 30.87 8.02 0.00 3.55
689 1318 2.105128 CTCCATCGCGGGTCTCAC 59.895 66.667 6.13 0.00 34.36 3.51
690 1319 3.838271 GCTCCATCGCGGGTCTCA 61.838 66.667 6.13 0.00 34.36 3.27
958 1649 0.100325 CACTTCGATCGAGCTCTGCT 59.900 55.000 18.54 0.00 43.88 4.24
974 1665 7.123418 GATGTAATCTAGCAGAGTGTTGCACT 61.123 42.308 0.97 0.97 43.47 4.40
1015 1718 4.337145 AGTACTACTAGCTGCAGTGAGTT 58.663 43.478 22.46 11.82 0.00 3.01
1024 1727 9.630098 CTAGCTACTAGTTAGTACTACTAGCTG 57.370 40.741 24.46 20.30 46.97 4.24
1026 1729 8.585018 ACCTAGCTACTAGTTAGTACTACTAGC 58.415 40.741 24.46 18.73 45.76 3.42
1098 1805 4.101790 GAACCCGCCGTCGTACGA 62.102 66.667 15.28 15.28 46.05 3.43
1216 1923 4.351938 CGGCTGGTTCGTCGTGGA 62.352 66.667 0.00 0.00 0.00 4.02
1825 2589 2.915659 AGTGTCCGGAGCCGTTCA 60.916 61.111 3.06 0.00 37.81 3.18
1891 2655 1.827969 ACGTAGCTGAATGCCTTCTCT 59.172 47.619 0.00 3.48 44.23 3.10
2007 2877 5.005693 TCTTCATAAGATGGCGTCCAGCA 62.006 47.826 14.86 0.00 43.12 4.41
2025 2895 0.402121 AGTTCAGTTGCCCCCTCTTC 59.598 55.000 0.00 0.00 0.00 2.87
2026 2896 0.111253 CAGTTCAGTTGCCCCCTCTT 59.889 55.000 0.00 0.00 0.00 2.85
2392 3810 4.512571 GCCATGTGCTTTTGAAGAATTTGT 59.487 37.500 0.00 0.00 36.87 2.83
2421 3839 0.234884 CAGTTTCGACGTTGGGCTTC 59.765 55.000 2.20 0.00 0.00 3.86
2542 3965 4.202182 GCGTACTCATGGTATTCCCTAACA 60.202 45.833 0.00 0.00 32.56 2.41
2702 4327 6.994421 TTATCTTACCTCATGGCTCATACA 57.006 37.500 0.00 0.00 36.63 2.29
2745 4370 6.603201 AGCAATTTGAAGGGATATCTTTCGAA 59.397 34.615 17.72 17.72 0.00 3.71
2856 4485 6.580788 TGAATTTTGAATGACATGGTTGTGT 58.419 32.000 0.00 0.00 35.79 3.72
2961 4590 9.161629 AGCTTTAGTTTTGTGCTTAATGTTTTT 57.838 25.926 0.00 0.00 0.00 1.94
3016 4645 1.741401 CTCCGCCTGCGATTTGTGA 60.741 57.895 13.94 0.00 42.83 3.58
3056 4685 1.342474 CCAGTAGAAGGAGGAGGAGCA 60.342 57.143 0.00 0.00 0.00 4.26
3095 4724 3.138798 GGCAGTGCATGGGAGCAG 61.139 66.667 18.61 0.00 46.69 4.24
3100 4729 2.995077 TTAGGGGGCAGTGCATGGG 61.995 63.158 18.61 0.00 0.00 4.00
3141 4770 2.660064 CGTCAGTGGAAGGGGAGGG 61.660 68.421 0.00 0.00 0.00 4.30
3147 4776 2.455674 TCATTGTCGTCAGTGGAAGG 57.544 50.000 5.43 0.00 33.12 3.46
3153 4782 1.464608 CGCCAAATCATTGTCGTCAGT 59.535 47.619 0.00 0.00 33.52 3.41
3164 4793 2.712944 CCATGCTGCCGCCAAATCA 61.713 57.895 0.00 0.00 34.43 2.57
3172 4801 2.361610 AGAAACCCCATGCTGCCG 60.362 61.111 0.00 0.00 0.00 5.69
3207 4836 1.197036 GCCAGAAGTAAACGGCAAGAC 59.803 52.381 0.00 0.00 44.25 3.01
3218 4847 1.582968 GGTCGTCGTGCCAGAAGTA 59.417 57.895 0.00 0.00 0.00 2.24
3220 4849 2.543687 ATCGGTCGTCGTGCCAGAAG 62.544 60.000 8.73 0.00 40.32 2.85
3239 4868 7.387119 TGCTTACTTCTACTAACATCTTCGA 57.613 36.000 0.00 0.00 0.00 3.71
3241 4870 9.425577 ACTTTGCTTACTTCTACTAACATCTTC 57.574 33.333 0.00 0.00 0.00 2.87
3252 4881 5.700832 CCACACATCACTTTGCTTACTTCTA 59.299 40.000 0.00 0.00 0.00 2.10
3260 4889 2.775890 CTCTCCACACATCACTTTGCT 58.224 47.619 0.00 0.00 0.00 3.91
3267 4896 1.196766 AGGCTGCTCTCCACACATCA 61.197 55.000 0.00 0.00 0.00 3.07
3291 4920 1.377987 TTGCCGCCCTATTCCACAC 60.378 57.895 0.00 0.00 0.00 3.82


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

AutoCloner maintained by Alex Coulton.