Multiple sequence alignment - TraesCS6D01G349200

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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 TraesCS6D01G349200 chr6D 100.000 2465 0 0 1 2465 446947457 446949921 0.000000e+00 4553.0
1 TraesCS6D01G349200 chr6D 83.804 531 41 20 989 1490 446902017 446902531 1.730000e-126 462.0
2 TraesCS6D01G349200 chr6D 84.400 500 35 13 995 1456 446934808 446935302 3.740000e-123 451.0
3 TraesCS6D01G349200 chr6D 91.304 253 18 1 320 568 447216357 447216105 2.350000e-90 342.0
4 TraesCS6D01G349200 chr6D 78.383 569 49 35 994 1517 446882319 446882858 3.980000e-78 302.0
5 TraesCS6D01G349200 chr6D 78.462 520 62 23 989 1469 447761145 447761653 6.670000e-76 294.0
6 TraesCS6D01G349200 chr6D 89.252 214 21 2 2252 2464 446957220 446957432 1.450000e-67 267.0
7 TraesCS6D01G349200 chr6D 79.101 378 33 22 332 698 447214692 447214350 4.130000e-53 219.0
8 TraesCS6D01G349200 chr6D 84.746 177 14 6 340 511 446929813 446929981 5.450000e-37 165.0
9 TraesCS6D01G349200 chr6D 94.000 50 2 1 570 619 446745466 446745514 9.450000e-10 75.0
10 TraesCS6D01G349200 chr6D 97.674 43 1 0 2190 2232 446957095 446957137 9.450000e-10 75.0
11 TraesCS6D01G349200 chr6B 87.460 1579 101 37 394 1896 676135738 676137295 0.000000e+00 1729.0
12 TraesCS6D01G349200 chr6B 84.493 1825 141 58 1 1712 675569538 675567743 0.000000e+00 1672.0
13 TraesCS6D01G349200 chr6B 83.300 503 46 17 985 1459 675626749 675626257 1.750000e-116 429.0
14 TraesCS6D01G349200 chr6B 80.400 500 41 29 990 1456 676123572 676124047 6.570000e-86 327.0
15 TraesCS6D01G349200 chr6B 86.111 216 25 4 2252 2465 675564230 675564018 6.860000e-56 228.0
16 TraesCS6D01G349200 chr6B 82.014 278 20 9 320 589 676498895 676498640 2.480000e-50 209.0
17 TraesCS6D01G349200 chr6B 82.759 232 29 8 1055 1280 677129367 677129141 1.930000e-46 196.0
18 TraesCS6D01G349200 chr6B 84.500 200 14 10 160 342 676135536 676135735 5.420000e-42 182.0
19 TraesCS6D01G349200 chr6B 87.117 163 11 4 442 598 676035639 676035797 2.520000e-40 176.0
20 TraesCS6D01G349200 chr6B 82.759 203 24 9 1300 1496 678357396 678357593 1.170000e-38 171.0
21 TraesCS6D01G349200 chr6B 79.537 259 31 14 887 1131 675614517 675614267 5.450000e-37 165.0
22 TraesCS6D01G349200 chr6B 97.619 42 0 1 2190 2230 676140188 676140229 1.220000e-08 71.3
23 TraesCS6D01G349200 chr6A 84.687 1613 131 50 368 1901 593791675 593793250 0.000000e+00 1504.0
24 TraesCS6D01G349200 chr6A 83.267 502 41 17 990 1456 593785714 593786207 2.930000e-114 422.0
25 TraesCS6D01G349200 chr6A 82.800 500 48 19 985 1456 593777177 593777666 1.760000e-111 412.0
26 TraesCS6D01G349200 chr6A 87.554 233 23 3 320 548 593930792 593930562 5.230000e-67 265.0
27 TraesCS6D01G349200 chr6A 81.973 294 33 13 1049 1332 593992277 593991994 5.300000e-57 231.0
28 TraesCS6D01G349200 chr6A 80.272 294 35 11 1049 1332 594254130 594253850 1.490000e-47 200.0
29 TraesCS6D01G349200 chr6A 79.853 273 24 14 441 696 593776408 593776666 1.170000e-38 171.0
30 TraesCS6D01G349200 chr6A 89.130 92 10 0 2084 2175 593793555 593793646 5.570000e-22 115.0


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 TraesCS6D01G349200 chr6D 446947457 446949921 2464 False 4553.000000 4553 100.000000 1 2465 1 chr6D.!!$F6 2464
1 TraesCS6D01G349200 chr6D 446902017 446902531 514 False 462.000000 462 83.804000 989 1490 1 chr6D.!!$F3 501
2 TraesCS6D01G349200 chr6D 446882319 446882858 539 False 302.000000 302 78.383000 994 1517 1 chr6D.!!$F2 523
3 TraesCS6D01G349200 chr6D 447761145 447761653 508 False 294.000000 294 78.462000 989 1469 1 chr6D.!!$F7 480
4 TraesCS6D01G349200 chr6D 447214350 447216357 2007 True 280.500000 342 85.202500 320 698 2 chr6D.!!$R1 378
5 TraesCS6D01G349200 chr6B 675564018 675569538 5520 True 950.000000 1672 85.302000 1 2465 2 chr6B.!!$R5 2464
6 TraesCS6D01G349200 chr6B 676135536 676140229 4693 False 660.766667 1729 89.859667 160 2230 3 chr6B.!!$F4 2070
7 TraesCS6D01G349200 chr6A 593791675 593793646 1971 False 809.500000 1504 86.908500 368 2175 2 chr6A.!!$F3 1807
8 TraesCS6D01G349200 chr6A 593776408 593777666 1258 False 291.500000 412 81.326500 441 1456 2 chr6A.!!$F2 1015

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
62 63 0.31702 GTCCTTTGCTGCGTTGTCAC 60.317 55.0 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1828 3948 0.170561 CACCGTCTCAGGAGGTAACG 59.829 60.0 0.0 0.0 36.34 3.18 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
50 51 1.873903 CGACACCAGGACTGTCCTTTG 60.874 57.143 26.37 25.12 46.91 2.77
61 62 0.746204 TGTCCTTTGCTGCGTTGTCA 60.746 50.000 0.00 0.00 0.00 3.58
62 63 0.317020 GTCCTTTGCTGCGTTGTCAC 60.317 55.000 0.00 0.00 0.00 3.67
93 96 5.435686 TTACTGATTATGCCCACAGACTT 57.564 39.130 0.00 0.00 34.88 3.01
96 99 4.225042 ACTGATTATGCCCACAGACTTACA 59.775 41.667 0.00 0.00 34.88 2.41
97 100 5.172687 TGATTATGCCCACAGACTTACAA 57.827 39.130 0.00 0.00 0.00 2.41
104 107 2.487265 CCCACAGACTTACAAAGGCACT 60.487 50.000 0.00 0.00 39.74 4.40
105 108 2.549754 CCACAGACTTACAAAGGCACTG 59.450 50.000 0.00 0.00 40.86 3.66
125 128 2.423874 CACTGGGCACACCGTGTA 59.576 61.111 3.25 0.00 44.64 2.90
134 137 1.263217 GCACACCGTGTAAAACAGAGG 59.737 52.381 3.25 1.31 35.75 3.69
136 139 3.199677 CACACCGTGTAAAACAGAGGAA 58.800 45.455 3.25 0.00 33.12 3.36
137 140 3.813166 CACACCGTGTAAAACAGAGGAAT 59.187 43.478 3.25 0.00 33.12 3.01
138 141 4.992319 CACACCGTGTAAAACAGAGGAATA 59.008 41.667 3.25 0.00 33.12 1.75
139 142 5.642063 CACACCGTGTAAAACAGAGGAATAT 59.358 40.000 3.25 0.00 33.12 1.28
141 144 4.634443 ACCGTGTAAAACAGAGGAATATGC 59.366 41.667 8.07 0.00 33.12 3.14
144 147 5.447279 CGTGTAAAACAGAGGAATATGCACC 60.447 44.000 0.00 0.00 0.00 5.01
145 148 5.648092 GTGTAAAACAGAGGAATATGCACCT 59.352 40.000 0.00 0.00 39.41 4.00
154 157 6.364945 GAGGAATATGCACCTCTGTTTAAC 57.635 41.667 12.66 0.00 46.28 2.01
157 160 5.648092 GGAATATGCACCTCTGTTTAACAGT 59.352 40.000 22.36 3.97 46.03 3.55
166 187 4.036734 CCTCTGTTTAACAGTGTGCATGTT 59.963 41.667 22.36 9.03 46.03 2.71
173 194 1.151221 AGTGTGCATGTTGCCAGGA 59.849 52.632 0.00 0.00 44.23 3.86
211 232 6.316390 AGTGAAACAACGAAGATCAAAAGACT 59.684 34.615 0.00 0.00 41.43 3.24
213 234 6.093495 TGAAACAACGAAGATCAAAAGACTGT 59.907 34.615 0.00 0.00 0.00 3.55
218 239 7.042658 ACAACGAAGATCAAAAGACTGTAAGAC 60.043 37.037 0.00 0.00 37.43 3.01
254 291 1.004440 GGCAGTGAAAGAGACGGCT 60.004 57.895 0.00 0.00 35.20 5.52
380 422 1.492176 GCTCCATGATCCCTTCCTTCA 59.508 52.381 0.00 0.00 0.00 3.02
439 481 2.499289 AGTGAACAGATTCGGAGAGCAT 59.501 45.455 0.00 0.00 38.43 3.79
495 546 1.548973 CCACTGTGTCGAGCGTTCAC 61.549 60.000 7.08 11.45 0.00 3.18
525 2215 1.791103 CGTTTCAAGCAAAGCGGGGA 61.791 55.000 0.00 0.00 0.00 4.81
540 2230 3.546543 GGACGATCCCATGGCCGA 61.547 66.667 20.97 9.37 0.00 5.54
704 2418 0.667487 CTGACAGCAACGTCGGATGT 60.667 55.000 10.35 10.35 43.75 3.06
748 2668 8.899427 TCAAAATATTCAAATCAAGTTGGCAA 57.101 26.923 2.34 0.00 0.00 4.52
764 2707 7.396540 AGTTGGCAAGAGTCCTAAAATATTG 57.603 36.000 0.00 0.00 0.00 1.90
835 2780 3.446873 CACTGCTTTATGCCCATTAACCA 59.553 43.478 0.00 0.00 42.00 3.67
863 2808 9.072375 AGTTAGTTAGTTAACTCGACCTTAACT 57.928 33.333 12.39 19.92 44.77 2.24
869 2814 7.516198 AGTTAACTCGACCTTAACTCAGTTA 57.484 36.000 14.02 0.00 39.27 2.24
871 2816 4.416505 ACTCGACCTTAACTCAGTTACG 57.583 45.455 0.00 0.00 0.00 3.18
903 2848 0.935942 TACCAGAATACCCCTCCCGA 59.064 55.000 0.00 0.00 0.00 5.14
916 2861 4.161102 CCCCTCCCGACTCTATAAATTCT 58.839 47.826 0.00 0.00 0.00 2.40
929 2874 0.331616 AAATTCTGCCTAACCCGCCT 59.668 50.000 0.00 0.00 0.00 5.52
932 2877 3.399181 CTGCCTAACCCGCCTCCA 61.399 66.667 0.00 0.00 0.00 3.86
950 2897 5.659463 CCTCCATCTCAGTTTACTCTCAAG 58.341 45.833 0.00 0.00 0.00 3.02
955 2902 4.480115 TCTCAGTTTACTCTCAAGTCCCA 58.520 43.478 0.00 0.00 36.92 4.37
956 2903 4.899457 TCTCAGTTTACTCTCAAGTCCCAA 59.101 41.667 0.00 0.00 36.92 4.12
958 2905 6.043243 TCTCAGTTTACTCTCAAGTCCCAAAT 59.957 38.462 0.00 0.00 36.92 2.32
959 2906 6.231211 TCAGTTTACTCTCAAGTCCCAAATC 58.769 40.000 0.00 0.00 36.92 2.17
960 2907 6.043243 TCAGTTTACTCTCAAGTCCCAAATCT 59.957 38.462 0.00 0.00 36.92 2.40
963 2910 3.251484 ACTCTCAAGTCCCAAATCTCCA 58.749 45.455 0.00 0.00 0.00 3.86
964 2911 3.652869 ACTCTCAAGTCCCAAATCTCCAA 59.347 43.478 0.00 0.00 0.00 3.53
967 2914 4.827284 TCTCAAGTCCCAAATCTCCAAAAC 59.173 41.667 0.00 0.00 0.00 2.43
970 2917 3.500343 AGTCCCAAATCTCCAAAACCAG 58.500 45.455 0.00 0.00 0.00 4.00
974 2921 3.834231 CCCAAATCTCCAAAACCAGACAT 59.166 43.478 0.00 0.00 0.00 3.06
975 2922 4.284234 CCCAAATCTCCAAAACCAGACATT 59.716 41.667 0.00 0.00 0.00 2.71
979 2926 2.171003 CTCCAAAACCAGACATTCCCC 58.829 52.381 0.00 0.00 0.00 4.81
980 2927 1.786441 TCCAAAACCAGACATTCCCCT 59.214 47.619 0.00 0.00 0.00 4.79
987 2961 4.467084 GACATTCCCCTCGGCGCA 62.467 66.667 10.83 0.00 0.00 6.09
1012 2989 4.498520 CTCTCATGGCGACGGCGT 62.499 66.667 14.65 14.65 41.24 5.68
1129 3127 2.033602 TCAGCGTCTCGTCTCCCA 59.966 61.111 0.00 0.00 0.00 4.37
1643 3729 5.647658 TGGCGTTAATTGAGATTCAAGATGT 59.352 36.000 0.00 0.00 40.05 3.06
1724 3839 1.405661 GGTGATTTCAGAGTCCCGTCC 60.406 57.143 0.00 0.00 0.00 4.79
1729 3844 3.775654 CAGAGTCCCGTCCCTGCC 61.776 72.222 0.00 0.00 0.00 4.85
1759 3878 6.263617 GGTTTATTAATCGGTATTTGGAGGCA 59.736 38.462 0.00 0.00 0.00 4.75
1827 3947 1.534595 CAGTTCAGGTTCAGAAGCAGC 59.465 52.381 14.73 0.00 0.00 5.25
1828 3948 0.877743 GTTCAGGTTCAGAAGCAGCC 59.122 55.000 14.73 0.00 0.00 4.85
1850 6594 2.005370 TACCTCCTGAGACGGTGTTT 57.995 50.000 3.39 0.00 32.36 2.83
1877 6621 2.827921 GAGAAAATGTTGATGCTGGGGT 59.172 45.455 0.00 0.00 0.00 4.95
1880 6624 4.403432 AGAAAATGTTGATGCTGGGGTATG 59.597 41.667 0.00 0.00 0.00 2.39
1882 6626 1.294041 TGTTGATGCTGGGGTATGGA 58.706 50.000 0.00 0.00 0.00 3.41
1887 6631 2.580322 TGATGCTGGGGTATGGAAGAAA 59.420 45.455 0.00 0.00 0.00 2.52
1889 6633 3.085952 TGCTGGGGTATGGAAGAAAAG 57.914 47.619 0.00 0.00 0.00 2.27
1905 9234 7.822822 TGGAAGAAAAGGTAGCTTGTTATAGAC 59.177 37.037 8.16 0.00 0.00 2.59
1906 9235 8.041919 GGAAGAAAAGGTAGCTTGTTATAGACT 58.958 37.037 8.16 0.00 0.00 3.24
1909 9238 9.872721 AGAAAAGGTAGCTTGTTATAGACTAAC 57.127 33.333 8.16 0.00 0.00 2.34
1916 9245 6.574350 AGCTTGTTATAGACTAACGCAGATT 58.426 36.000 0.00 0.00 0.00 2.40
1921 9250 7.201145 TGTTATAGACTAACGCAGATTTCCTC 58.799 38.462 0.00 0.00 0.00 3.71
1948 9343 8.400186 TGAACTAATGATGCAACATTGATACTG 58.600 33.333 27.00 14.20 40.15 2.74
1967 9362 1.010125 GTTGCTGTTTTCGCTGCGA 60.010 52.632 22.24 22.24 36.33 5.10
2004 9399 3.317993 ACAAAACCCATCTGTACAAGTGC 59.682 43.478 0.00 0.00 0.00 4.40
2005 9400 2.949177 AACCCATCTGTACAAGTGCA 57.051 45.000 0.00 0.00 0.00 4.57
2007 9402 4.568072 AACCCATCTGTACAAGTGCATA 57.432 40.909 0.00 0.00 0.00 3.14
2035 9436 0.032912 AGACCATGGCAATGCATCCA 60.033 50.000 13.04 9.40 36.70 3.41
2070 9472 2.092538 TCAAACGGTCCAACTAAACCCA 60.093 45.455 0.00 0.00 31.49 4.51
2080 9482 6.014584 GGTCCAACTAAACCCATCTGAAATTT 60.015 38.462 0.00 0.00 0.00 1.82
2117 9754 2.224843 TGATGAGCCTCATGGTGTTGTT 60.225 45.455 12.92 0.00 37.20 2.83
2152 9789 1.269723 CACAGCTTCTACACTGGTCGA 59.730 52.381 0.00 0.00 38.25 4.20
2159 9796 2.017782 TCTACACTGGTCGATGCTCTC 58.982 52.381 0.00 0.00 0.00 3.20
2171 9808 3.514777 TGCTCTCGCAAAATCGTCT 57.485 47.368 0.00 0.00 44.62 4.18
2172 9809 1.795768 TGCTCTCGCAAAATCGTCTT 58.204 45.000 0.00 0.00 44.62 3.01
2173 9810 2.143122 TGCTCTCGCAAAATCGTCTTT 58.857 42.857 0.00 0.00 44.62 2.52
2174 9811 2.548057 TGCTCTCGCAAAATCGTCTTTT 59.452 40.909 0.00 0.00 44.62 2.27
2175 9812 3.003275 TGCTCTCGCAAAATCGTCTTTTT 59.997 39.130 0.00 0.00 44.62 1.94
2236 9877 8.969260 ATGGAGATGCTTTTCTTTTTCTTTTT 57.031 26.923 0.00 0.00 0.00 1.94
2266 9977 4.864704 TTTGCCTCAAAGATTGTTACCC 57.135 40.909 0.00 0.00 0.00 3.69
2269 9980 2.432444 CCTCAAAGATTGTTACCCGCA 58.568 47.619 0.00 0.00 0.00 5.69
2270 9981 2.161609 CCTCAAAGATTGTTACCCGCAC 59.838 50.000 0.00 0.00 0.00 5.34
2271 9982 1.801771 TCAAAGATTGTTACCCGCACG 59.198 47.619 0.00 0.00 0.00 5.34
2277 9988 4.448210 AGATTGTTACCCGCACGAATTAT 58.552 39.130 0.00 0.00 0.00 1.28
2281 9992 5.373981 TGTTACCCGCACGAATTATTTTT 57.626 34.783 0.00 0.00 0.00 1.94
2300 10011 5.818136 TTTTTCATAGTCACATGGCTAGC 57.182 39.130 6.04 6.04 35.49 3.42
2314 10025 3.154473 TAGCCAGCCGGATCGCTT 61.154 61.111 19.00 1.56 36.82 4.68
2318 10029 1.137404 CCAGCCGGATCGCTTTTTG 59.863 57.895 5.05 0.00 36.82 2.44
2321 10032 0.035820 AGCCGGATCGCTTTTTGGTA 60.036 50.000 5.05 0.00 34.73 3.25
2324 10035 1.333619 CCGGATCGCTTTTTGGTATGG 59.666 52.381 0.00 0.00 0.00 2.74
2327 10038 3.119637 CGGATCGCTTTTTGGTATGGTTT 60.120 43.478 0.00 0.00 0.00 3.27
2328 10039 4.173256 GGATCGCTTTTTGGTATGGTTTG 58.827 43.478 0.00 0.00 0.00 2.93
2329 10040 4.321675 GGATCGCTTTTTGGTATGGTTTGT 60.322 41.667 0.00 0.00 0.00 2.83
2330 10041 5.106078 GGATCGCTTTTTGGTATGGTTTGTA 60.106 40.000 0.00 0.00 0.00 2.41
2336 10047 7.371936 GCTTTTTGGTATGGTTTGTATACACA 58.628 34.615 4.68 0.75 33.66 3.72
2342 10053 5.290158 GGTATGGTTTGTATACACACAGTCG 59.710 44.000 20.67 0.00 33.30 4.18
2351 10062 5.818857 TGTATACACACAGTCGATAGCTACA 59.181 40.000 0.08 0.00 0.00 2.74
2410 10123 0.322187 AAACGGTTCGAGGGGAATGG 60.322 55.000 0.00 0.00 36.92 3.16
2416 10129 0.252513 TTCGAGGGGAATGGGAGACA 60.253 55.000 0.00 0.00 0.00 3.41
2417 10130 0.252513 TCGAGGGGAATGGGAGACAA 60.253 55.000 0.00 0.00 0.00 3.18
2418 10131 0.839946 CGAGGGGAATGGGAGACAAT 59.160 55.000 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 0.319641 GGACAGTCCTGGTGTCGTTC 60.320 60.000 12.94 0.00 44.52 3.95
29 30 3.456317 GGACAGTCCTGGTGTCGT 58.544 61.111 12.94 0.00 44.52 4.34
39 40 0.040958 CAACGCAGCAAAGGACAGTC 60.041 55.000 0.00 0.00 0.00 3.51
50 51 2.974698 AGCCAGTGACAACGCAGC 60.975 61.111 0.00 0.00 0.00 5.25
61 62 4.392940 GCATAATCAGTAATCCAGCCAGT 58.607 43.478 0.00 0.00 0.00 4.00
62 63 3.755378 GGCATAATCAGTAATCCAGCCAG 59.245 47.826 0.00 0.00 39.35 4.85
93 96 0.537143 CAGTGCCCAGTGCCTTTGTA 60.537 55.000 0.00 0.00 40.16 2.41
96 99 2.203538 CCAGTGCCCAGTGCCTTT 60.204 61.111 0.00 0.00 40.16 3.11
97 100 4.290622 CCCAGTGCCCAGTGCCTT 62.291 66.667 0.00 0.00 40.16 4.35
112 115 0.309612 CTGTTTTACACGGTGTGCCC 59.690 55.000 23.36 9.13 36.98 5.36
114 117 1.263217 CCTCTGTTTTACACGGTGTGC 59.737 52.381 23.36 11.08 36.98 4.57
118 121 4.634443 GCATATTCCTCTGTTTTACACGGT 59.366 41.667 0.00 0.00 32.85 4.83
119 122 4.634004 TGCATATTCCTCTGTTTTACACGG 59.366 41.667 0.00 0.00 0.00 4.94
120 123 5.447279 GGTGCATATTCCTCTGTTTTACACG 60.447 44.000 0.00 0.00 0.00 4.49
144 147 6.512828 GCAACATGCACACTGTTAAACAGAG 61.513 44.000 0.00 0.00 45.26 3.35
145 148 4.733230 GCAACATGCACACTGTTAAACAGA 60.733 41.667 0.00 0.00 45.26 3.41
147 150 3.443037 GCAACATGCACACTGTTAAACA 58.557 40.909 3.94 0.00 44.26 2.83
166 187 2.029964 GAACGTCCGTTCCTGGCA 59.970 61.111 19.09 0.00 46.21 4.92
173 194 1.662122 GTTTCACTGTGAACGTCCGTT 59.338 47.619 21.95 4.52 35.89 4.44
211 232 1.738350 CGGCTCTCTCTTCGTCTTACA 59.262 52.381 0.00 0.00 0.00 2.41
213 234 1.065636 TCCGGCTCTCTCTTCGTCTTA 60.066 52.381 0.00 0.00 0.00 2.10
218 239 2.411290 GCTCCGGCTCTCTCTTCG 59.589 66.667 0.00 0.00 35.22 3.79
254 291 1.715585 GACCGGACGATCGAACGTA 59.284 57.895 24.34 0.00 46.52 3.57
288 325 2.928313 CTACTGCTCTGCGTCCGCTC 62.928 65.000 13.31 0.76 42.51 5.03
439 481 1.470805 CGTAATGGCAGTGTCCATCGA 60.471 52.381 16.32 7.81 45.64 3.59
525 2215 4.221422 CGTCGGCCATGGGATCGT 62.221 66.667 15.13 0.00 0.00 3.73
748 2668 6.942976 TCGGTTCACAATATTTTAGGACTCT 58.057 36.000 0.00 0.00 0.00 3.24
835 2780 6.890979 AGGTCGAGTTAACTAACTAACTGT 57.109 37.500 8.42 0.00 45.84 3.55
852 2797 4.320494 GGTTCGTAACTGAGTTAAGGTCGA 60.320 45.833 16.21 13.25 30.69 4.20
863 2808 4.360951 AAATTCAGGGGTTCGTAACTGA 57.639 40.909 0.00 0.00 38.12 3.41
869 2814 2.640826 TCTGGTAAATTCAGGGGTTCGT 59.359 45.455 0.00 0.00 33.36 3.85
871 2816 5.593095 GGTATTCTGGTAAATTCAGGGGTTC 59.407 44.000 0.00 0.00 33.36 3.62
903 2848 5.742255 GCGGGTTAGGCAGAATTTATAGAGT 60.742 44.000 0.00 0.00 0.00 3.24
916 2861 2.690881 ATGGAGGCGGGTTAGGCA 60.691 61.111 0.00 0.00 39.37 4.75
929 2874 5.186021 GGACTTGAGAGTAAACTGAGATGGA 59.814 44.000 0.00 0.00 35.88 3.41
932 2877 5.087323 TGGGACTTGAGAGTAAACTGAGAT 58.913 41.667 0.00 0.00 35.88 2.75
950 2897 3.255888 GTCTGGTTTTGGAGATTTGGGAC 59.744 47.826 0.00 0.00 0.00 4.46
955 2902 4.528206 GGGAATGTCTGGTTTTGGAGATTT 59.472 41.667 0.00 0.00 0.00 2.17
956 2903 4.089361 GGGAATGTCTGGTTTTGGAGATT 58.911 43.478 0.00 0.00 0.00 2.40
958 2905 2.225017 GGGGAATGTCTGGTTTTGGAGA 60.225 50.000 0.00 0.00 0.00 3.71
959 2906 2.171003 GGGGAATGTCTGGTTTTGGAG 58.829 52.381 0.00 0.00 0.00 3.86
960 2907 1.786441 AGGGGAATGTCTGGTTTTGGA 59.214 47.619 0.00 0.00 0.00 3.53
963 2910 1.271926 CCGAGGGGAATGTCTGGTTTT 60.272 52.381 0.00 0.00 34.06 2.43
964 2911 0.328258 CCGAGGGGAATGTCTGGTTT 59.672 55.000 0.00 0.00 34.06 3.27
967 2914 2.190578 GCCGAGGGGAATGTCTGG 59.809 66.667 0.00 0.00 34.06 3.86
970 2917 4.467084 TGCGCCGAGGGGAATGTC 62.467 66.667 4.18 0.00 34.06 3.06
974 2921 3.949885 TAGAGTGCGCCGAGGGGAA 62.950 63.158 4.18 0.00 34.06 3.97
975 2922 3.949885 TTAGAGTGCGCCGAGGGGA 62.950 63.158 4.18 0.00 34.06 4.81
979 2926 0.665835 AGAGATTAGAGTGCGCCGAG 59.334 55.000 4.18 0.00 0.00 4.63
980 2927 0.663688 GAGAGATTAGAGTGCGCCGA 59.336 55.000 4.18 0.00 0.00 5.54
987 2961 2.292016 CGTCGCCATGAGAGATTAGAGT 59.708 50.000 0.00 0.00 0.00 3.24
1530 3601 4.590850 AAACTCCAATTCTTCAGGCAAC 57.409 40.909 0.00 0.00 0.00 4.17
1643 3729 0.893270 CCCAACCAACGATTGCCTGA 60.893 55.000 0.00 0.00 0.00 3.86
1724 3839 4.202111 CCGATTAATAAACCCAAAGGCAGG 60.202 45.833 0.00 0.00 36.11 4.85
1729 3844 8.688151 TCCAAATACCGATTAATAAACCCAAAG 58.312 33.333 0.00 0.00 0.00 2.77
1759 3878 6.576662 TTCTGAATCTTCGTCAGTTCTAGT 57.423 37.500 1.67 0.00 42.63 2.57
1827 3947 1.807886 CCGTCTCAGGAGGTAACGG 59.192 63.158 11.93 11.93 45.79 4.44
1828 3948 0.170561 CACCGTCTCAGGAGGTAACG 59.829 60.000 0.00 0.00 36.34 3.18
1850 6594 3.575256 AGCATCAACATTTTCTCTTGGCA 59.425 39.130 0.00 0.00 0.00 4.92
1877 6621 9.832445 CTATAACAAGCTACCTTTTCTTCCATA 57.168 33.333 0.00 0.00 0.00 2.74
1880 6624 8.041919 AGTCTATAACAAGCTACCTTTTCTTCC 58.958 37.037 0.00 0.00 0.00 3.46
1887 6631 6.127535 TGCGTTAGTCTATAACAAGCTACCTT 60.128 38.462 0.00 0.00 0.00 3.50
1889 6633 5.585390 TGCGTTAGTCTATAACAAGCTACC 58.415 41.667 0.00 0.00 0.00 3.18
1916 9245 5.559770 TGTTGCATCATTAGTTCAGAGGAA 58.440 37.500 0.00 0.00 0.00 3.36
1921 9250 8.618677 AGTATCAATGTTGCATCATTAGTTCAG 58.381 33.333 19.87 9.09 36.44 3.02
1927 9322 7.482474 CAACCAGTATCAATGTTGCATCATTA 58.518 34.615 19.87 10.85 36.44 1.90
1948 9343 2.010817 CGCAGCGAAAACAGCAACC 61.011 57.895 9.98 0.00 37.01 3.77
1967 9362 4.497842 GGGTTTTGTTAACGGACGAACATT 60.498 41.667 0.26 0.00 35.57 2.71
1984 9379 3.561143 TGCACTTGTACAGATGGGTTTT 58.439 40.909 9.69 0.00 0.00 2.43
2004 9399 6.822667 TTGCCATGGTCTATTTAGCATATG 57.177 37.500 14.67 0.00 35.88 1.78
2005 9400 6.127535 GCATTGCCATGGTCTATTTAGCATAT 60.128 38.462 14.67 0.00 35.88 1.78
2007 9402 4.021719 GCATTGCCATGGTCTATTTAGCAT 60.022 41.667 14.67 0.00 38.07 3.79
2035 9436 2.418628 CCGTTTGATTCGGCACTTGTAT 59.581 45.455 0.00 0.00 41.48 2.29
2070 9472 4.529377 AGCCATCCAACACAAATTTCAGAT 59.471 37.500 0.00 0.00 0.00 2.90
2080 9482 2.026075 TCATCATGAGCCATCCAACACA 60.026 45.455 0.09 0.00 0.00 3.72
2111 9748 5.163612 TGTGGACAATTCAAATCGAACAACA 60.164 36.000 0.00 0.00 36.12 3.33
2117 9754 3.411446 AGCTGTGGACAATTCAAATCGA 58.589 40.909 0.00 0.00 0.00 3.59
2175 9812 3.039011 TGATTTTGTTCCCCCGGAAAAA 58.961 40.909 0.73 0.32 43.86 1.94
2176 9813 2.679082 TGATTTTGTTCCCCCGGAAAA 58.321 42.857 0.73 0.03 43.86 2.29
2177 9814 2.383442 TGATTTTGTTCCCCCGGAAA 57.617 45.000 0.73 0.00 43.86 3.13
2178 9815 2.042433 AGATGATTTTGTTCCCCCGGAA 59.958 45.455 0.73 0.00 39.66 4.30
2179 9816 1.638589 AGATGATTTTGTTCCCCCGGA 59.361 47.619 0.73 0.00 0.00 5.14
2180 9817 2.143876 AGATGATTTTGTTCCCCCGG 57.856 50.000 0.00 0.00 0.00 5.73
2181 9818 4.535526 AAAAGATGATTTTGTTCCCCCG 57.464 40.909 0.00 0.00 0.00 5.73
2182 9819 6.649141 GTGTTAAAAGATGATTTTGTTCCCCC 59.351 38.462 0.00 0.00 0.00 5.40
2183 9820 6.364976 CGTGTTAAAAGATGATTTTGTTCCCC 59.635 38.462 0.00 0.00 0.00 4.81
2184 9821 6.364976 CCGTGTTAAAAGATGATTTTGTTCCC 59.635 38.462 0.00 0.00 0.00 3.97
2185 9822 6.364976 CCCGTGTTAAAAGATGATTTTGTTCC 59.635 38.462 0.00 0.00 0.00 3.62
2186 9823 7.142680 TCCCGTGTTAAAAGATGATTTTGTTC 58.857 34.615 0.00 0.00 0.00 3.18
2187 9824 7.045126 TCCCGTGTTAAAAGATGATTTTGTT 57.955 32.000 0.00 0.00 0.00 2.83
2188 9825 6.642707 TCCCGTGTTAAAAGATGATTTTGT 57.357 33.333 0.00 0.00 0.00 2.83
2247 9888 2.432444 CGGGTAACAATCTTTGAGGCA 58.568 47.619 0.00 0.00 39.74 4.75
2248 9889 1.132453 GCGGGTAACAATCTTTGAGGC 59.868 52.381 0.00 0.00 39.74 4.70
2250 9891 2.159707 CGTGCGGGTAACAATCTTTGAG 60.160 50.000 0.00 0.00 39.74 3.02
2281 9992 2.771372 TGGCTAGCCATGTGACTATGAA 59.229 45.455 32.88 4.77 41.89 2.57
2284 9995 1.071385 GCTGGCTAGCCATGTGACTAT 59.929 52.381 35.93 0.00 46.15 2.12
2285 9996 0.465705 GCTGGCTAGCCATGTGACTA 59.534 55.000 35.93 11.50 46.15 2.59
2300 10011 1.137404 CAAAAAGCGATCCGGCTGG 59.863 57.895 4.71 4.71 43.93 4.85
2314 10025 7.502895 ACTGTGTGTATACAAACCATACCAAAA 59.497 33.333 21.07 1.13 38.82 2.44
2318 10029 5.290158 CGACTGTGTGTATACAAACCATACC 59.710 44.000 21.07 7.21 38.82 2.73
2321 10032 5.142061 TCGACTGTGTGTATACAAACCAT 57.858 39.130 21.07 10.66 38.82 3.55
2324 10035 6.034591 AGCTATCGACTGTGTGTATACAAAC 58.965 40.000 17.87 17.87 38.82 2.93
2327 10038 5.818857 TGTAGCTATCGACTGTGTGTATACA 59.181 40.000 0.08 0.08 0.00 2.29
2328 10039 6.134730 GTGTAGCTATCGACTGTGTGTATAC 58.865 44.000 0.00 0.00 0.00 1.47
2329 10040 5.818857 TGTGTAGCTATCGACTGTGTGTATA 59.181 40.000 0.00 0.00 0.00 1.47
2330 10041 4.638865 TGTGTAGCTATCGACTGTGTGTAT 59.361 41.667 0.00 0.00 0.00 2.29
2342 10053 7.435488 CACCGGCTAAATATATGTGTAGCTATC 59.565 40.741 18.12 4.56 39.15 2.08
2374 10086 7.254151 CGAACCGTTTCAAATAACATGGTTTTT 60.254 33.333 0.00 0.00 34.19 1.94
2376 10088 5.688176 CGAACCGTTTCAAATAACATGGTTT 59.312 36.000 0.00 0.00 34.19 3.27
2380 10093 5.086058 CCTCGAACCGTTTCAAATAACATG 58.914 41.667 0.00 0.00 0.00 3.21
2410 10123 8.608844 ACGAAAATATATCTTGGATTGTCTCC 57.391 34.615 0.00 0.00 45.19 3.71
2437 10150 6.634035 CGCACAATCGTGATTATTCAAATGAT 59.366 34.615 0.00 0.00 46.80 2.45
2442 10155 5.538067 TTCGCACAATCGTGATTATTCAA 57.462 34.783 0.00 0.00 46.80 2.69


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

AutoCloner maintained by Alex Coulton.