Multiple sequence alignment - TraesCS3D01G105400

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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 TraesCS3D01G105400 chr3D 100.000 2255 0 0 1 2255 57607374 57609628 0.000000e+00 4165
1 TraesCS3D01G105400 chr3D 96.104 77 3 0 2179 2255 181877285 181877361 2.350000e-25 126
2 TraesCS3D01G105400 chr3D 96.104 77 3 0 2179 2255 323607218 323607142 2.350000e-25 126
3 TraesCS3D01G105400 chr4A 95.470 1170 35 6 1013 2179 129031656 129032810 0.000000e+00 1851
4 TraesCS3D01G105400 chr4A 93.039 1020 58 8 2 1014 433609808 433608795 0.000000e+00 1478
5 TraesCS3D01G105400 chr4A 87.121 132 7 8 2056 2178 714634853 714634983 8.400000e-30 141
6 TraesCS3D01G105400 chr3A 94.613 1188 36 8 1013 2178 615135595 615134414 0.000000e+00 1814
7 TraesCS3D01G105400 chr3A 91.167 1200 63 13 1013 2178 702241846 702243036 0.000000e+00 1589
8 TraesCS3D01G105400 chr3A 91.895 1024 67 8 1 1014 615143381 615142364 0.000000e+00 1417
9 TraesCS3D01G105400 chr6D 93.766 1187 43 16 1013 2179 446363239 446362064 0.000000e+00 1753
10 TraesCS3D01G105400 chr6D 92.207 1219 38 24 1013 2181 297170332 297169121 0.000000e+00 1672
11 TraesCS3D01G105400 chr6D 92.752 1021 43 5 1 1014 452662441 452663437 0.000000e+00 1447
12 TraesCS3D01G105400 chr6D 83.810 420 28 19 1016 1431 46519533 46519150 1.650000e-96 363
13 TraesCS3D01G105400 chr6D 96.053 76 3 0 2180 2255 116095240 116095315 8.460000e-25 124
14 TraesCS3D01G105400 chr6D 94.805 77 4 0 2179 2255 90953940 90953864 1.090000e-23 121
15 TraesCS3D01G105400 chr7D 93.505 1201 39 7 1013 2178 17926526 17925330 0.000000e+00 1749
16 TraesCS3D01G105400 chr7D 94.690 1017 51 1 1 1014 103532689 103533705 0.000000e+00 1576
17 TraesCS3D01G105400 chr7D 90.286 1225 52 22 1013 2178 51237709 51236493 0.000000e+00 1541
18 TraesCS3D01G105400 chr7D 96.104 77 3 0 2179 2255 253405948 253406024 2.350000e-25 126
19 TraesCS3D01G105400 chr7D 96.104 77 3 0 2179 2255 256949255 256949331 2.350000e-25 126
20 TraesCS3D01G105400 chr1D 93.411 1199 43 7 1013 2178 463792511 463791316 0.000000e+00 1744
21 TraesCS3D01G105400 chr1D 92.326 821 54 5 1 817 463800963 463800148 0.000000e+00 1158
22 TraesCS3D01G105400 chr1D 85.894 397 20 11 1013 1407 417114154 417114516 7.550000e-105 390
23 TraesCS3D01G105400 chr1D 96.104 77 3 0 2179 2255 98420661 98420737 2.350000e-25 126
24 TraesCS3D01G105400 chr2D 92.993 1213 36 7 1013 2178 645235539 645234329 0.000000e+00 1724
25 TraesCS3D01G105400 chr2D 93.137 1020 57 7 2 1014 645241195 645240182 0.000000e+00 1483
26 TraesCS3D01G105400 chr2D 92.717 1016 65 4 2 1014 397123899 397124908 0.000000e+00 1458
27 TraesCS3D01G105400 chr2D 96.104 77 3 0 2179 2255 130191511 130191435 2.350000e-25 126
28 TraesCS3D01G105400 chr5D 95.182 1017 45 2 1 1014 29809417 29808402 0.000000e+00 1604
29 TraesCS3D01G105400 chr5D 90.433 1223 52 21 1013 2178 384510952 384509738 0.000000e+00 1550
30 TraesCS3D01G105400 chr5D 92.421 475 21 9 1013 1475 29766511 29766040 0.000000e+00 664
31 TraesCS3D01G105400 chr5D 91.789 475 24 9 1013 1475 401783732 401784203 0.000000e+00 647
32 TraesCS3D01G105400 chr7A 90.864 1204 60 25 1013 2178 56075031 56076222 0.000000e+00 1568
33 TraesCS3D01G105400 chr7A 92.043 1018 52 14 1 1014 734436792 734437784 0.000000e+00 1404
34 TraesCS3D01G105400 chr5A 93.314 1017 62 2 1 1014 178868085 178867072 0.000000e+00 1496
35 TraesCS3D01G105400 chr5A 92.457 822 38 15 1377 2178 235676600 235677417 0.000000e+00 1153
36 TraesCS3D01G105400 chr3B 92.724 1017 71 1 1 1014 320731682 320730666 0.000000e+00 1465
37 TraesCS3D01G105400 chr5B 91.577 1021 79 3 1 1014 117419075 117420095 0.000000e+00 1402
38 TraesCS3D01G105400 chr4D 93.162 819 31 8 1377 2178 236671127 236670317 0.000000e+00 1179
39 TraesCS3D01G105400 chr4D 84.404 1199 100 39 1013 2178 239784458 239783314 0.000000e+00 1098
40 TraesCS3D01G105400 chr4D 84.559 408 21 18 1013 1418 261222552 261222185 1.270000e-97 366
41 TraesCS3D01G105400 chr4D 85.780 218 16 9 1270 1475 125903980 125903766 1.360000e-52 217
42 TraesCS3D01G105400 chr4D 96.104 77 3 0 2179 2255 242587368 242587444 2.350000e-25 126
43 TraesCS3D01G105400 chr2A 94.125 766 42 2 1 763 538635058 538634293 0.000000e+00 1162
44 TraesCS3D01G105400 chr1B 76.364 440 69 20 1770 2191 475145708 475145286 1.060000e-48 204


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 TraesCS3D01G105400 chr3D 57607374 57609628 2254 False 4165 4165 100.000 1 2255 1 chr3D.!!$F1 2254
1 TraesCS3D01G105400 chr4A 129031656 129032810 1154 False 1851 1851 95.470 1013 2179 1 chr4A.!!$F1 1166
2 TraesCS3D01G105400 chr4A 433608795 433609808 1013 True 1478 1478 93.039 2 1014 1 chr4A.!!$R1 1012
3 TraesCS3D01G105400 chr3A 615134414 615135595 1181 True 1814 1814 94.613 1013 2178 1 chr3A.!!$R1 1165
4 TraesCS3D01G105400 chr3A 702241846 702243036 1190 False 1589 1589 91.167 1013 2178 1 chr3A.!!$F1 1165
5 TraesCS3D01G105400 chr3A 615142364 615143381 1017 True 1417 1417 91.895 1 1014 1 chr3A.!!$R2 1013
6 TraesCS3D01G105400 chr6D 446362064 446363239 1175 True 1753 1753 93.766 1013 2179 1 chr6D.!!$R4 1166
7 TraesCS3D01G105400 chr6D 297169121 297170332 1211 True 1672 1672 92.207 1013 2181 1 chr6D.!!$R3 1168
8 TraesCS3D01G105400 chr6D 452662441 452663437 996 False 1447 1447 92.752 1 1014 1 chr6D.!!$F2 1013
9 TraesCS3D01G105400 chr7D 17925330 17926526 1196 True 1749 1749 93.505 1013 2178 1 chr7D.!!$R1 1165
10 TraesCS3D01G105400 chr7D 103532689 103533705 1016 False 1576 1576 94.690 1 1014 1 chr7D.!!$F1 1013
11 TraesCS3D01G105400 chr7D 51236493 51237709 1216 True 1541 1541 90.286 1013 2178 1 chr7D.!!$R2 1165
12 TraesCS3D01G105400 chr1D 463791316 463792511 1195 True 1744 1744 93.411 1013 2178 1 chr1D.!!$R1 1165
13 TraesCS3D01G105400 chr1D 463800148 463800963 815 True 1158 1158 92.326 1 817 1 chr1D.!!$R2 816
14 TraesCS3D01G105400 chr2D 645234329 645235539 1210 True 1724 1724 92.993 1013 2178 1 chr2D.!!$R2 1165
15 TraesCS3D01G105400 chr2D 645240182 645241195 1013 True 1483 1483 93.137 2 1014 1 chr2D.!!$R3 1012
16 TraesCS3D01G105400 chr2D 397123899 397124908 1009 False 1458 1458 92.717 2 1014 1 chr2D.!!$F1 1012
17 TraesCS3D01G105400 chr5D 29808402 29809417 1015 True 1604 1604 95.182 1 1014 1 chr5D.!!$R2 1013
18 TraesCS3D01G105400 chr5D 384509738 384510952 1214 True 1550 1550 90.433 1013 2178 1 chr5D.!!$R3 1165
19 TraesCS3D01G105400 chr7A 56075031 56076222 1191 False 1568 1568 90.864 1013 2178 1 chr7A.!!$F1 1165
20 TraesCS3D01G105400 chr7A 734436792 734437784 992 False 1404 1404 92.043 1 1014 1 chr7A.!!$F2 1013
21 TraesCS3D01G105400 chr5A 178867072 178868085 1013 True 1496 1496 93.314 1 1014 1 chr5A.!!$R1 1013
22 TraesCS3D01G105400 chr5A 235676600 235677417 817 False 1153 1153 92.457 1377 2178 1 chr5A.!!$F1 801
23 TraesCS3D01G105400 chr3B 320730666 320731682 1016 True 1465 1465 92.724 1 1014 1 chr3B.!!$R1 1013
24 TraesCS3D01G105400 chr5B 117419075 117420095 1020 False 1402 1402 91.577 1 1014 1 chr5B.!!$F1 1013
25 TraesCS3D01G105400 chr4D 236670317 236671127 810 True 1179 1179 93.162 1377 2178 1 chr4D.!!$R2 801
26 TraesCS3D01G105400 chr4D 239783314 239784458 1144 True 1098 1098 84.404 1013 2178 1 chr4D.!!$R3 1165
27 TraesCS3D01G105400 chr2A 538634293 538635058 765 True 1162 1162 94.125 1 763 1 chr2A.!!$R1 762

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
640 739 0.1023 TATGATGGTGGCTGACGACG 59.898 55.0 0.0 0.0 0.0 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1803 2165 1.067425 TGTTTTGCTCATCTGCATGGC 60.067 47.619 0.0 0.0 42.96 4.4 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
54 55 6.688637 TCCAGTTCTTCGAGATCGTAATTA 57.311 37.500 1.70 0.00 40.80 1.40
160 169 0.895530 CCACTTCTTGACCCTCGCTA 59.104 55.000 0.00 0.00 0.00 4.26
259 268 1.153628 GCTTCGTACGCTGTGGGAT 60.154 57.895 11.24 0.00 0.00 3.85
320 329 2.045045 CCGGCTGGGAGCATTTCA 60.045 61.111 2.57 0.00 44.75 2.69
368 377 3.983044 ATTTCCTTGTCTTCCGCTACT 57.017 42.857 0.00 0.00 0.00 2.57
391 400 2.726691 CGACGCCATGTTCACCGTC 61.727 63.158 0.00 0.00 44.61 4.79
445 454 3.890705 CAGCACGACGACGATGCG 61.891 66.667 15.32 11.66 44.43 4.73
576 627 1.040339 GGGATGACGAGGAGCAGAGT 61.040 60.000 0.00 0.00 0.00 3.24
589 640 1.323271 GCAGAGTGGGGATGACGAGA 61.323 60.000 0.00 0.00 0.00 4.04
617 716 1.183549 ATTCTGGCTAACGACGACCT 58.816 50.000 0.00 0.00 0.00 3.85
618 717 0.963962 TTCTGGCTAACGACGACCTT 59.036 50.000 0.00 0.00 0.00 3.50
619 718 0.242825 TCTGGCTAACGACGACCTTG 59.757 55.000 0.00 0.00 0.00 3.61
620 719 1.352156 CTGGCTAACGACGACCTTGC 61.352 60.000 0.00 0.00 0.00 4.01
621 720 1.080025 GGCTAACGACGACCTTGCT 60.080 57.895 0.00 0.00 0.00 3.91
622 721 0.171903 GGCTAACGACGACCTTGCTA 59.828 55.000 0.00 0.00 0.00 3.49
623 722 1.202382 GGCTAACGACGACCTTGCTAT 60.202 52.381 0.00 0.00 0.00 2.97
624 723 1.852895 GCTAACGACGACCTTGCTATG 59.147 52.381 0.00 0.00 0.00 2.23
625 724 2.479049 GCTAACGACGACCTTGCTATGA 60.479 50.000 0.00 0.00 0.00 2.15
626 725 2.961526 AACGACGACCTTGCTATGAT 57.038 45.000 0.00 0.00 0.00 2.45
627 726 2.209838 ACGACGACCTTGCTATGATG 57.790 50.000 0.00 0.00 0.00 3.07
628 727 1.202417 ACGACGACCTTGCTATGATGG 60.202 52.381 0.00 0.00 0.00 3.51
629 728 1.202417 CGACGACCTTGCTATGATGGT 60.202 52.381 0.00 0.00 35.23 3.55
630 729 2.205074 GACGACCTTGCTATGATGGTG 58.795 52.381 0.00 0.00 32.30 4.17
631 730 1.134401 ACGACCTTGCTATGATGGTGG 60.134 52.381 0.00 0.00 35.03 4.61
632 731 1.312815 GACCTTGCTATGATGGTGGC 58.687 55.000 0.00 0.00 32.30 5.01
633 732 0.921896 ACCTTGCTATGATGGTGGCT 59.078 50.000 0.00 0.00 0.00 4.75
634 733 1.315690 CCTTGCTATGATGGTGGCTG 58.684 55.000 0.00 0.00 0.00 4.85
635 734 1.134007 CCTTGCTATGATGGTGGCTGA 60.134 52.381 0.00 0.00 0.00 4.26
636 735 1.945394 CTTGCTATGATGGTGGCTGAC 59.055 52.381 0.00 0.00 0.00 3.51
637 736 0.179076 TGCTATGATGGTGGCTGACG 60.179 55.000 0.00 0.00 0.00 4.35
638 737 0.104855 GCTATGATGGTGGCTGACGA 59.895 55.000 0.00 0.00 0.00 4.20
639 738 1.858091 CTATGATGGTGGCTGACGAC 58.142 55.000 0.00 0.00 0.00 4.34
640 739 0.102300 TATGATGGTGGCTGACGACG 59.898 55.000 0.00 0.00 0.00 5.12
641 740 1.604147 ATGATGGTGGCTGACGACGA 61.604 55.000 0.00 0.00 0.00 4.20
642 741 1.805945 GATGGTGGCTGACGACGAC 60.806 63.158 0.00 0.00 0.00 4.34
643 742 3.296709 ATGGTGGCTGACGACGACC 62.297 63.158 0.00 0.00 0.00 4.79
644 743 3.681835 GGTGGCTGACGACGACCT 61.682 66.667 0.00 0.00 0.00 3.85
719 899 3.733344 CTATGGTGGTGGCGGACGG 62.733 68.421 0.00 0.00 0.00 4.79
842 1028 2.361610 AATCCCACAGCTTGGCGG 60.362 61.111 8.85 0.00 45.37 6.13
925 1111 3.988976 TCAGGTTGATGAAGGAGAAGG 57.011 47.619 0.00 0.00 0.00 3.46
971 1161 4.605640 AGTGGCAATGTTAAGCATGTTT 57.394 36.364 0.00 0.00 37.96 2.83
1109 1299 2.915738 CTTCAAGCTGAAGTGATGCC 57.084 50.000 14.26 0.00 46.50 4.40
1200 1390 2.344950 CTGCGCAAGAAGTCTCAAGAT 58.655 47.619 13.05 0.00 38.61 2.40
1240 1430 3.415212 CACTTGATGGCTCTCTTTGGAA 58.585 45.455 0.00 0.00 0.00 3.53
1398 1642 2.711009 TGAACCTGGGATCTTGTGAACT 59.289 45.455 0.00 0.00 0.00 3.01
1446 1727 4.021719 ACTTGTGATGGCTCATTTTGGAAG 60.022 41.667 0.00 0.00 32.98 3.46
1576 1928 7.288810 TCTAAATTGAGTTGGACTGCAAAAT 57.711 32.000 0.00 0.00 0.00 1.82
1830 2192 4.338964 TGCAGATGAGCAAAACAAAGAGAA 59.661 37.500 0.00 0.00 42.46 2.87
1905 2273 2.222027 GGACCGGGCTGATTCTATTTG 58.778 52.381 7.57 0.00 0.00 2.32
1906 2274 2.222027 GACCGGGCTGATTCTATTTGG 58.778 52.381 6.32 0.00 0.00 3.28
1979 2347 2.266372 CGTGGTGTGGGCGGATTA 59.734 61.111 0.00 0.00 0.00 1.75
1980 2348 1.153249 CGTGGTGTGGGCGGATTAT 60.153 57.895 0.00 0.00 0.00 1.28
2181 2563 9.561069 AAGTTGACATATTTCTTGTAGTGAACT 57.439 29.630 0.00 0.00 0.00 3.01
2182 2564 8.993121 AGTTGACATATTTCTTGTAGTGAACTG 58.007 33.333 0.00 0.00 0.00 3.16
2183 2565 7.364522 TGACATATTTCTTGTAGTGAACTGC 57.635 36.000 0.00 0.00 0.00 4.40
2184 2566 6.090763 TGACATATTTCTTGTAGTGAACTGCG 59.909 38.462 0.00 0.00 0.00 5.18
2185 2567 6.163476 ACATATTTCTTGTAGTGAACTGCGA 58.837 36.000 0.00 0.00 0.00 5.10
2186 2568 4.992381 ATTTCTTGTAGTGAACTGCGAC 57.008 40.909 0.00 0.00 0.00 5.19
2187 2569 3.728076 TTCTTGTAGTGAACTGCGACT 57.272 42.857 0.00 0.00 0.00 4.18
2188 2570 3.284323 TCTTGTAGTGAACTGCGACTC 57.716 47.619 0.00 0.00 0.00 3.36
2189 2571 2.030185 TCTTGTAGTGAACTGCGACTCC 60.030 50.000 0.00 0.00 0.00 3.85
2190 2572 0.240145 TGTAGTGAACTGCGACTCCG 59.760 55.000 0.00 0.00 39.16 4.63
2191 2573 0.520404 GTAGTGAACTGCGACTCCGA 59.480 55.000 0.00 0.00 38.22 4.55
2192 2574 0.520404 TAGTGAACTGCGACTCCGAC 59.480 55.000 0.00 0.00 38.22 4.79
2193 2575 2.081212 GTGAACTGCGACTCCGACG 61.081 63.158 0.00 0.00 38.22 5.12
2194 2576 2.504244 GAACTGCGACTCCGACGG 60.504 66.667 7.84 7.84 38.22 4.79
2195 2577 2.974489 GAACTGCGACTCCGACGGA 61.974 63.158 17.28 17.28 38.22 4.69
2196 2578 2.467946 GAACTGCGACTCCGACGGAA 62.468 60.000 18.93 1.06 38.22 4.30
2197 2579 2.079020 AACTGCGACTCCGACGGAAA 62.079 55.000 18.93 0.00 38.22 3.13
2198 2580 1.153823 CTGCGACTCCGACGGAAAT 60.154 57.895 18.93 9.14 38.22 2.17
2199 2581 1.140407 CTGCGACTCCGACGGAAATC 61.140 60.000 18.93 16.61 38.22 2.17
2200 2582 1.877165 GCGACTCCGACGGAAATCC 60.877 63.158 18.93 8.81 38.22 3.01
2216 2598 6.793505 GGAAATCCGGGTAGTCATCTATAT 57.206 41.667 0.00 0.00 0.00 0.86
2217 2599 7.893124 GGAAATCCGGGTAGTCATCTATATA 57.107 40.000 0.00 0.00 0.00 0.86
2218 2600 7.714703 GGAAATCCGGGTAGTCATCTATATAC 58.285 42.308 0.00 0.00 0.00 1.47
2219 2601 7.201893 GGAAATCCGGGTAGTCATCTATATACC 60.202 44.444 0.00 0.00 37.53 2.73
2228 2610 7.549488 GGTAGTCATCTATATACCCATTTGTGC 59.451 40.741 0.00 0.00 33.06 4.57
2229 2611 6.166279 AGTCATCTATATACCCATTTGTGCG 58.834 40.000 0.00 0.00 0.00 5.34
2230 2612 5.351465 GTCATCTATATACCCATTTGTGCGG 59.649 44.000 0.00 0.00 0.00 5.69
2231 2613 3.670625 TCTATATACCCATTTGTGCGGC 58.329 45.455 0.00 0.00 0.00 6.53
2232 2614 2.356665 ATATACCCATTTGTGCGGCA 57.643 45.000 0.00 0.00 0.00 5.69
2233 2615 2.130272 TATACCCATTTGTGCGGCAA 57.870 45.000 3.23 0.00 34.87 4.52
2244 2626 3.932545 TGTGCGGCAAAAATATCAAGT 57.067 38.095 3.23 0.00 0.00 3.16
2245 2627 3.573598 TGTGCGGCAAAAATATCAAGTG 58.426 40.909 3.23 0.00 0.00 3.16
2246 2628 3.005261 TGTGCGGCAAAAATATCAAGTGT 59.995 39.130 3.23 0.00 0.00 3.55
2247 2629 3.987220 GTGCGGCAAAAATATCAAGTGTT 59.013 39.130 3.23 0.00 0.00 3.32
2248 2630 4.447389 GTGCGGCAAAAATATCAAGTGTTT 59.553 37.500 3.23 0.00 0.00 2.83
2249 2631 5.050431 GTGCGGCAAAAATATCAAGTGTTTT 60.050 36.000 3.23 0.00 33.21 2.43
2250 2632 5.176590 TGCGGCAAAAATATCAAGTGTTTTC 59.823 36.000 0.00 0.00 30.95 2.29
2251 2633 5.405269 GCGGCAAAAATATCAAGTGTTTTCT 59.595 36.000 0.00 0.00 30.95 2.52
2252 2634 6.399986 GCGGCAAAAATATCAAGTGTTTTCTC 60.400 38.462 0.00 0.00 30.95 2.87
2253 2635 6.863126 CGGCAAAAATATCAAGTGTTTTCTCT 59.137 34.615 0.00 0.00 30.95 3.10
2254 2636 7.148918 CGGCAAAAATATCAAGTGTTTTCTCTG 60.149 37.037 0.00 0.00 30.95 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 8.616377 TTCTTAATTACGATCTCGAAGAACTG 57.384 34.615 6.60 0.00 43.02 3.16
146 155 1.464734 CTCTGTAGCGAGGGTCAAGA 58.535 55.000 0.00 0.00 0.00 3.02
160 169 1.374190 CTTGTCAGGCAGCCTCTGT 59.626 57.895 12.53 0.00 33.43 3.41
249 258 1.600636 ACCAACACATCCCACAGCG 60.601 57.895 0.00 0.00 0.00 5.18
259 268 1.304254 CATCGAACACCACCAACACA 58.696 50.000 0.00 0.00 0.00 3.72
391 400 3.250762 ACATGGTGTTGTCGAACATCTTG 59.749 43.478 12.44 12.44 46.51 3.02
445 454 4.827284 AGAAGATAGGCAGAGAGCTTACTC 59.173 45.833 0.00 0.00 44.79 2.59
576 627 1.900351 CTGCTTCTCGTCATCCCCA 59.100 57.895 0.00 0.00 0.00 4.96
617 716 1.743431 CGTCAGCCACCATCATAGCAA 60.743 52.381 0.00 0.00 0.00 3.91
618 717 0.179076 CGTCAGCCACCATCATAGCA 60.179 55.000 0.00 0.00 0.00 3.49
619 718 0.104855 TCGTCAGCCACCATCATAGC 59.895 55.000 0.00 0.00 0.00 2.97
620 719 1.858091 GTCGTCAGCCACCATCATAG 58.142 55.000 0.00 0.00 0.00 2.23
621 720 0.102300 CGTCGTCAGCCACCATCATA 59.898 55.000 0.00 0.00 0.00 2.15
622 721 1.153568 CGTCGTCAGCCACCATCAT 60.154 57.895 0.00 0.00 0.00 2.45
623 722 2.261361 CGTCGTCAGCCACCATCA 59.739 61.111 0.00 0.00 0.00 3.07
624 723 1.805945 GTCGTCGTCAGCCACCATC 60.806 63.158 0.00 0.00 0.00 3.51
625 724 2.261671 GTCGTCGTCAGCCACCAT 59.738 61.111 0.00 0.00 0.00 3.55
626 725 3.986006 GGTCGTCGTCAGCCACCA 61.986 66.667 0.00 0.00 0.00 4.17
627 726 3.222354 AAGGTCGTCGTCAGCCACC 62.222 63.158 0.00 0.00 0.00 4.61
628 727 2.022129 CAAGGTCGTCGTCAGCCAC 61.022 63.158 0.00 0.00 0.00 5.01
629 728 2.338620 CAAGGTCGTCGTCAGCCA 59.661 61.111 0.00 0.00 0.00 4.75
630 729 2.209064 TAGCAAGGTCGTCGTCAGCC 62.209 60.000 0.00 0.00 0.00 4.85
631 730 0.179134 ATAGCAAGGTCGTCGTCAGC 60.179 55.000 0.00 0.00 0.00 4.26
632 731 1.550065 CATAGCAAGGTCGTCGTCAG 58.450 55.000 0.00 0.00 0.00 3.51
633 732 0.172578 CCATAGCAAGGTCGTCGTCA 59.827 55.000 0.00 0.00 0.00 4.35
634 733 0.172803 ACCATAGCAAGGTCGTCGTC 59.827 55.000 0.00 0.00 32.90 4.20
635 734 0.108804 CACCATAGCAAGGTCGTCGT 60.109 55.000 0.00 0.00 37.23 4.34
636 735 0.806102 CCACCATAGCAAGGTCGTCG 60.806 60.000 0.00 0.00 37.23 5.12
637 736 0.249398 ACCACCATAGCAAGGTCGTC 59.751 55.000 0.00 0.00 37.23 4.20
638 737 0.036388 CACCACCATAGCAAGGTCGT 60.036 55.000 0.00 0.00 37.23 4.34
639 738 0.744414 CCACCACCATAGCAAGGTCG 60.744 60.000 0.00 0.00 37.23 4.79
640 739 1.032114 GCCACCACCATAGCAAGGTC 61.032 60.000 0.00 0.00 37.23 3.85
641 740 1.000896 GCCACCACCATAGCAAGGT 60.001 57.895 0.00 0.00 40.85 3.50
642 741 2.114670 CGCCACCACCATAGCAAGG 61.115 63.158 0.00 0.00 0.00 3.61
643 742 2.114670 CCGCCACCACCATAGCAAG 61.115 63.158 0.00 0.00 0.00 4.01
644 743 1.920734 ATCCGCCACCACCATAGCAA 61.921 55.000 0.00 0.00 0.00 3.91
719 899 2.472909 GCCACCATAGCAAGGTCGC 61.473 63.158 0.00 0.00 37.23 5.19
842 1028 0.108520 CACAATTGGCATGGTCCTGC 60.109 55.000 10.83 5.10 41.53 4.85
925 1111 8.553459 TTCATTTCTTAACATCTTCACTCCTC 57.447 34.615 0.00 0.00 0.00 3.71
971 1161 7.934665 TCAGATTACACTAACAAGCTTAAACCA 59.065 33.333 0.00 0.00 0.00 3.67
1109 1299 1.473677 TGATTGCCGCCAATTCTTCTG 59.526 47.619 0.00 0.00 41.60 3.02
1200 1390 3.904339 AGTGGGCTAACTTCTCTTCTTGA 59.096 43.478 0.00 0.00 0.00 3.02
1240 1430 5.104527 TGCATAGCCATCAAACTACCTTAGT 60.105 40.000 0.00 0.00 41.73 2.24
1398 1642 1.341482 TGGTTCAACAAGTGCTCCCAA 60.341 47.619 0.00 0.00 0.00 4.12
1446 1727 1.198637 GAGCCATCACAAGTTCACTGC 59.801 52.381 0.00 0.00 0.00 4.40
1761 2122 5.422012 GCCTTTTATTTTCTGGGAATGGAGA 59.578 40.000 0.00 0.00 0.00 3.71
1803 2165 1.067425 TGTTTTGCTCATCTGCATGGC 60.067 47.619 0.00 0.00 42.96 4.40
1905 2273 2.347697 GACCAAATGAAAAGGTCGCC 57.652 50.000 0.00 0.00 42.02 5.54
2181 2563 1.153901 GATTTCCGTCGGAGTCGCA 60.154 57.895 14.79 0.00 37.81 5.10
2182 2564 1.877165 GGATTTCCGTCGGAGTCGC 60.877 63.158 14.79 5.60 37.81 5.19
2183 2565 4.396854 GGATTTCCGTCGGAGTCG 57.603 61.111 14.79 0.00 39.05 4.18
2193 2575 6.793505 ATATAGATGACTACCCGGATTTCC 57.206 41.667 0.73 0.00 0.00 3.13
2194 2576 7.201893 GGGTATATAGATGACTACCCGGATTTC 60.202 44.444 0.73 0.00 42.81 2.17
2195 2577 6.610425 GGGTATATAGATGACTACCCGGATTT 59.390 42.308 0.73 0.00 42.81 2.17
2196 2578 6.134754 GGGTATATAGATGACTACCCGGATT 58.865 44.000 0.73 0.00 42.81 3.01
2197 2579 5.703310 GGGTATATAGATGACTACCCGGAT 58.297 45.833 0.73 0.00 42.81 4.18
2198 2580 5.121380 GGGTATATAGATGACTACCCGGA 57.879 47.826 0.73 0.00 42.81 5.14
2202 2584 7.549488 GCACAAATGGGTATATAGATGACTACC 59.451 40.741 0.00 0.00 34.19 3.18
2203 2585 7.275779 CGCACAAATGGGTATATAGATGACTAC 59.724 40.741 0.00 0.00 34.13 2.73
2204 2586 7.320399 CGCACAAATGGGTATATAGATGACTA 58.680 38.462 0.00 0.00 34.13 2.59
2205 2587 6.166279 CGCACAAATGGGTATATAGATGACT 58.834 40.000 0.00 0.00 34.13 3.41
2206 2588 5.351465 CCGCACAAATGGGTATATAGATGAC 59.649 44.000 0.00 0.00 37.06 3.06
2207 2589 5.487433 CCGCACAAATGGGTATATAGATGA 58.513 41.667 0.00 0.00 37.06 2.92
2208 2590 4.094887 GCCGCACAAATGGGTATATAGATG 59.905 45.833 0.00 0.00 37.06 2.90
2209 2591 4.261801 GCCGCACAAATGGGTATATAGAT 58.738 43.478 0.00 0.00 37.06 1.98
2210 2592 3.071747 TGCCGCACAAATGGGTATATAGA 59.928 43.478 0.00 0.00 37.06 1.98
2211 2593 3.407698 TGCCGCACAAATGGGTATATAG 58.592 45.455 0.00 0.00 37.06 1.31
2212 2594 3.493767 TGCCGCACAAATGGGTATATA 57.506 42.857 0.00 0.00 37.06 0.86
2213 2595 2.356665 TGCCGCACAAATGGGTATAT 57.643 45.000 0.00 0.00 37.06 0.86
2214 2596 2.130272 TTGCCGCACAAATGGGTATA 57.870 45.000 0.00 0.00 37.06 1.47
2215 2597 1.261480 TTTGCCGCACAAATGGGTAT 58.739 45.000 0.00 0.00 43.35 2.73
2216 2598 2.733590 TTTGCCGCACAAATGGGTA 58.266 47.368 0.00 0.00 43.35 3.69
2217 2599 3.543537 TTTGCCGCACAAATGGGT 58.456 50.000 0.00 0.00 43.35 4.51
2222 2604 4.447054 CACTTGATATTTTTGCCGCACAAA 59.553 37.500 7.13 7.13 46.51 2.83
2223 2605 3.986572 CACTTGATATTTTTGCCGCACAA 59.013 39.130 0.00 0.00 36.13 3.33
2224 2606 3.005261 ACACTTGATATTTTTGCCGCACA 59.995 39.130 0.00 0.00 0.00 4.57
2225 2607 3.574614 ACACTTGATATTTTTGCCGCAC 58.425 40.909 0.00 0.00 0.00 5.34
2226 2608 3.932545 ACACTTGATATTTTTGCCGCA 57.067 38.095 0.00 0.00 0.00 5.69
2227 2609 5.405269 AGAAAACACTTGATATTTTTGCCGC 59.595 36.000 0.00 0.00 0.00 6.53
2228 2610 6.863126 AGAGAAAACACTTGATATTTTTGCCG 59.137 34.615 0.00 0.00 0.00 5.69
2229 2611 8.011067 CAGAGAAAACACTTGATATTTTTGCC 57.989 34.615 0.00 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.