Multiple sequence alignment - TraesCS3D01G339200

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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 TraesCS3D01G339200 chr3D 100.000 2288 0 0 1 2288 452411467 452409180 0.000000e+00 4226.0
1 TraesCS3D01G339200 chr3D 88.105 765 79 2 416 1179 11552736 11553489 0.000000e+00 898.0
2 TraesCS3D01G339200 chr3D 82.797 901 142 11 418 1314 590956382 590955491 0.000000e+00 793.0
3 TraesCS3D01G339200 chr3A 88.284 1579 140 34 731 2280 594650918 594649356 0.000000e+00 1849.0
4 TraesCS3D01G339200 chr3A 86.916 749 79 6 1 737 594664330 594663589 0.000000e+00 822.0
5 TraesCS3D01G339200 chr5A 87.450 996 104 10 331 1314 534623555 534622569 0.000000e+00 1127.0
6 TraesCS3D01G339200 chr5A 84.365 614 80 6 368 965 107749401 107750014 2.530000e-164 588.0
7 TraesCS3D01G339200 chr5A 88.822 331 31 6 1 328 534623925 534623598 3.540000e-108 401.0
8 TraesCS3D01G339200 chr5A 86.061 330 40 5 1 328 107748999 107749324 1.300000e-92 350.0
9 TraesCS3D01G339200 chr5A 81.818 121 14 7 1583 1701 40064598 40064484 6.730000e-16 95.3
10 TraesCS3D01G339200 chr5A 86.207 87 8 4 1581 1665 211617695 211617611 8.700000e-15 91.6
11 TraesCS3D01G339200 chr2A 82.099 905 161 1 411 1314 728564293 728565197 0.000000e+00 773.0
12 TraesCS3D01G339200 chr7A 80.361 998 179 9 331 1314 654918827 654917833 0.000000e+00 741.0
13 TraesCS3D01G339200 chr7A 79.404 772 143 13 527 1293 440359301 440358541 4.330000e-147 531.0
14 TraesCS3D01G339200 chr3B 83.123 634 99 5 657 1288 758147856 758148483 2.550000e-159 571.0
15 TraesCS3D01G339200 chr6A 76.096 1004 209 23 331 1314 180929054 180928062 1.580000e-136 496.0
16 TraesCS3D01G339200 chr7D 76.717 859 187 11 439 1293 50643514 50644363 1.240000e-127 466.0
17 TraesCS3D01G339200 chr1D 88.291 316 35 2 15 330 55395390 55395077 5.970000e-101 377.0
18 TraesCS3D01G339200 chr1D 73.469 392 60 24 1658 2036 56619476 56619836 8.640000e-20 108.0
19 TraesCS3D01G339200 chr1D 82.540 126 14 6 1578 1702 332961767 332961649 1.120000e-18 104.0
20 TraesCS3D01G339200 chr1D 85.263 95 11 3 1658 1750 56433035 56433128 6.730000e-16 95.3
21 TraesCS3D01G339200 chr1B 86.585 328 41 3 1 328 90872450 90872126 2.160000e-95 359.0
22 TraesCS3D01G339200 chr4A 84.830 323 45 4 8 328 19631333 19631653 2.840000e-84 322.0
23 TraesCS3D01G339200 chr4B 81.269 331 43 6 1 328 560005102 560004788 1.360000e-62 250.0
24 TraesCS3D01G339200 chr1A 84.874 119 15 3 1658 1774 54457174 54457057 1.440000e-22 117.0


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 TraesCS3D01G339200 chr3D 452409180 452411467 2287 True 4226 4226 100.000 1 2288 1 chr3D.!!$R1 2287
1 TraesCS3D01G339200 chr3D 11552736 11553489 753 False 898 898 88.105 416 1179 1 chr3D.!!$F1 763
2 TraesCS3D01G339200 chr3D 590955491 590956382 891 True 793 793 82.797 418 1314 1 chr3D.!!$R2 896
3 TraesCS3D01G339200 chr3A 594649356 594650918 1562 True 1849 1849 88.284 731 2280 1 chr3A.!!$R1 1549
4 TraesCS3D01G339200 chr3A 594663589 594664330 741 True 822 822 86.916 1 737 1 chr3A.!!$R2 736
5 TraesCS3D01G339200 chr5A 534622569 534623925 1356 True 764 1127 88.136 1 1314 2 chr5A.!!$R3 1313
6 TraesCS3D01G339200 chr5A 107748999 107750014 1015 False 469 588 85.213 1 965 2 chr5A.!!$F1 964
7 TraesCS3D01G339200 chr2A 728564293 728565197 904 False 773 773 82.099 411 1314 1 chr2A.!!$F1 903
8 TraesCS3D01G339200 chr7A 654917833 654918827 994 True 741 741 80.361 331 1314 1 chr7A.!!$R2 983
9 TraesCS3D01G339200 chr7A 440358541 440359301 760 True 531 531 79.404 527 1293 1 chr7A.!!$R1 766
10 TraesCS3D01G339200 chr3B 758147856 758148483 627 False 571 571 83.123 657 1288 1 chr3B.!!$F1 631
11 TraesCS3D01G339200 chr6A 180928062 180929054 992 True 496 496 76.096 331 1314 1 chr6A.!!$R1 983
12 TraesCS3D01G339200 chr7D 50643514 50644363 849 False 466 466 76.717 439 1293 1 chr7D.!!$F1 854

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
924 990 0.313672 TCATTGTTGGCGGAAACTGC 59.686 50.0 0.0 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2174 2287 0.243095 GTTACTCGCTCCCGAAGTGT 59.757 55.0 0.0 0.0 43.87 3.55 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
22 23 4.998788 GAGTTGGAAATGGGCAAACTATC 58.001 43.478 0.00 0.00 31.45 2.08
68 70 2.285220 CCACACGATGCGAATAGGAAAG 59.715 50.000 0.00 0.00 0.00 2.62
75 77 6.146184 CACGATGCGAATAGGAAAGTTATCAT 59.854 38.462 0.00 0.00 0.00 2.45
115 117 5.814705 CCTTCTGTCAAAGGTATGTGATCTC 59.185 44.000 0.00 0.00 40.86 2.75
116 118 5.344743 TCTGTCAAAGGTATGTGATCTCC 57.655 43.478 0.00 0.00 0.00 3.71
132 134 4.885413 GATCTCCTTGATCCAGTGATGAG 58.115 47.826 0.00 0.00 44.34 2.90
188 190 3.101437 TGGCCAATTGATGCTCAAAGAT 58.899 40.909 0.61 0.00 40.12 2.40
192 194 5.172934 GCCAATTGATGCTCAAAGATTTCA 58.827 37.500 7.12 0.00 40.12 2.69
197 199 0.516877 TGCTCAAAGATTTCACGCGG 59.483 50.000 12.47 0.00 0.00 6.46
200 202 2.158841 GCTCAAAGATTTCACGCGGTTA 59.841 45.455 12.47 0.00 0.00 2.85
222 225 7.888546 GGTTACCCTTCCTATGCATAATATGTT 59.111 37.037 8.00 0.00 0.00 2.71
275 278 6.429692 ACATGGTTTGTTCATTGTTCGATCTA 59.570 34.615 0.00 0.00 33.74 1.98
302 305 3.320610 TGGAGGAATGGAACCAACAAA 57.679 42.857 0.00 0.00 0.00 2.83
324 327 9.603921 ACAAAATGGAAGGAAATTGCAATATAG 57.396 29.630 13.39 0.00 43.04 1.31
328 331 9.822185 AATGGAAGGAAATTGCAATATAGAAAC 57.178 29.630 13.39 2.70 43.04 2.78
359 402 4.854587 TTGCCCGGCAAAGGTAAT 57.145 50.000 22.85 0.00 45.96 1.89
360 403 3.059287 TTGCCCGGCAAAGGTAATT 57.941 47.368 22.85 0.00 45.96 1.40
361 404 1.343069 TTGCCCGGCAAAGGTAATTT 58.657 45.000 22.85 0.00 45.96 1.82
403 446 2.126031 GAACTCTCCCGTGCCGTC 60.126 66.667 0.00 0.00 0.00 4.79
409 463 1.883084 CTCCCGTGCCGTCTTATGC 60.883 63.158 0.00 0.00 0.00 3.14
412 466 1.523711 CCGTGCCGTCTTATGCCAT 60.524 57.895 0.00 0.00 0.00 4.40
434 488 1.965754 GAAGGTCTCGCCCATCTGCT 61.966 60.000 0.00 0.00 38.26 4.24
435 489 2.202987 GGTCTCGCCCATCTGCTG 60.203 66.667 0.00 0.00 0.00 4.41
467 521 4.617530 CGAGTGGACCAGAAGATACGAAAA 60.618 45.833 0.00 0.00 0.00 2.29
684 741 2.628657 ACGGTGGGATAGACATAAGCTC 59.371 50.000 0.00 0.00 0.00 4.09
707 764 5.008613 TCGTTCATGAAGGAAAGGTTCAAAG 59.991 40.000 24.56 0.00 37.46 2.77
725 782 1.153958 GCGCTTGCCAATCTTCCAC 60.154 57.895 0.00 0.00 0.00 4.02
772 833 0.837272 TATTAGTGCCCACTCCCAGC 59.163 55.000 3.88 0.00 42.54 4.85
776 837 3.259314 TGCCCACTCCCAGCATGT 61.259 61.111 0.00 0.00 0.00 3.21
788 849 7.220030 CACTCCCAGCATGTATCTAGTAAAAT 58.780 38.462 0.00 0.00 0.00 1.82
924 990 0.313672 TCATTGTTGGCGGAAACTGC 59.686 50.000 0.00 0.00 0.00 4.40
927 993 0.749649 TTGTTGGCGGAAACTGCAAT 59.250 45.000 4.98 0.00 0.00 3.56
968 1035 2.418368 TTGACAGCAGAAGTGTTGGT 57.582 45.000 0.00 0.00 39.14 3.67
1000 1067 3.582647 TGGATTACTTCTTGCACAGAGGA 59.417 43.478 12.59 0.00 32.72 3.71
1064 1131 7.308770 GGAAGTCATCAACACAATGAAGAATGA 60.309 37.037 0.00 0.00 35.04 2.57
1068 1135 5.710513 TCAACACAATGAAGAATGAAGGG 57.289 39.130 0.00 0.00 0.00 3.95
1138 1205 7.496529 TTGTCTTGTGATTTTCCTCTTACTG 57.503 36.000 0.00 0.00 0.00 2.74
1196 1263 4.508662 GCTCATGAACTTGCTAGGTTAGT 58.491 43.478 0.00 0.00 0.00 2.24
1206 1273 6.899114 ACTTGCTAGGTTAGTGAAAATTTCG 58.101 36.000 0.97 0.00 0.00 3.46
1238 1305 0.555769 TGTTTTGAGGAGCCCTTGGT 59.444 50.000 0.00 0.00 31.76 3.67
1332 1428 0.104409 AGGAGTGGTCCCCAGAGTTT 60.104 55.000 0.00 0.00 45.26 2.66
1333 1429 0.036875 GGAGTGGTCCCCAGAGTTTG 59.963 60.000 0.00 0.00 36.76 2.93
1334 1430 0.606673 GAGTGGTCCCCAGAGTTTGC 60.607 60.000 0.00 0.00 32.34 3.68
1335 1431 1.150536 GTGGTCCCCAGAGTTTGCA 59.849 57.895 0.00 0.00 32.34 4.08
1336 1432 0.467290 GTGGTCCCCAGAGTTTGCAA 60.467 55.000 0.00 0.00 32.34 4.08
1337 1433 0.467290 TGGTCCCCAGAGTTTGCAAC 60.467 55.000 0.00 0.00 0.00 4.17
1338 1434 0.467290 GGTCCCCAGAGTTTGCAACA 60.467 55.000 0.00 0.00 0.00 3.33
1339 1435 1.620822 GTCCCCAGAGTTTGCAACAT 58.379 50.000 0.00 0.00 0.00 2.71
1340 1436 1.270550 GTCCCCAGAGTTTGCAACATG 59.729 52.381 0.00 0.00 0.00 3.21
1341 1437 0.037975 CCCCAGAGTTTGCAACATGC 60.038 55.000 0.00 0.00 45.29 4.06
1363 1459 1.948834 TCATGTTGCATATGGGCTTCG 59.051 47.619 4.56 0.00 34.04 3.79
1367 1463 0.455410 TTGCATATGGGCTTCGCAAC 59.545 50.000 4.56 0.00 37.64 4.17
1369 1465 0.670162 GCATATGGGCTTCGCAACAT 59.330 50.000 4.56 0.00 33.62 2.71
1371 1467 1.267806 CATATGGGCTTCGCAACATCC 59.732 52.381 0.00 0.00 32.01 3.51
1379 1475 2.146342 CTTCGCAACATCCTCTGTGTT 58.854 47.619 0.00 0.00 40.23 3.32
1402 1498 1.696832 GAAGGGCTCGCAACATCGTC 61.697 60.000 0.00 0.00 0.00 4.20
1403 1499 2.125512 GGGCTCGCAACATCGTCT 60.126 61.111 0.00 0.00 0.00 4.18
1421 1517 2.295349 GTCTGTGTTACCGAAGTCCTCA 59.705 50.000 0.00 0.00 0.00 3.86
1429 1525 2.285977 ACCGAAGTCCTCACAAACAAC 58.714 47.619 0.00 0.00 0.00 3.32
1445 1541 0.647410 CAACGCTAGCCACTCAATCG 59.353 55.000 9.66 0.00 0.00 3.34
1457 1553 0.737367 CTCAATCGCACCGAAGCTCA 60.737 55.000 0.00 0.00 39.99 4.26
1477 1573 1.814169 GACCCGACCGATCTTTGGC 60.814 63.158 0.00 0.00 0.00 4.52
1478 1574 2.267642 CCCGACCGATCTTTGGCA 59.732 61.111 0.00 0.00 0.00 4.92
1511 1607 0.960364 AGCCAACGCATAACCCACAG 60.960 55.000 0.00 0.00 37.52 3.66
1512 1608 1.933115 GCCAACGCATAACCCACAGG 61.933 60.000 0.00 0.00 35.11 4.00
1614 1710 5.104776 TCCAGCAGATGATGTATAATAGGGC 60.105 44.000 0.00 0.00 0.00 5.19
1623 1719 6.132658 TGATGTATAATAGGGCAGCCAAAAA 58.867 36.000 15.19 0.00 0.00 1.94
1654 1750 4.584327 GGCACCAAAGAGTGTGTTTTAT 57.416 40.909 0.00 0.00 40.04 1.40
1674 1770 1.269517 TGGCACCGAAACATTTTCTGC 60.270 47.619 4.94 4.94 0.00 4.26
1703 1799 5.242393 GCAGATGATGTAAAATAGGGCACAT 59.758 40.000 0.00 0.00 34.41 3.21
1704 1800 6.430925 GCAGATGATGTAAAATAGGGCACATA 59.569 38.462 0.00 0.00 31.94 2.29
1748 1845 6.431198 TCAACTACCAACTGTTCAAACTTC 57.569 37.500 0.00 0.00 0.00 3.01
1751 1848 3.782889 ACCAACTGTTCAAACTTCAGC 57.217 42.857 0.00 0.00 33.12 4.26
1753 1850 3.119495 ACCAACTGTTCAAACTTCAGCAC 60.119 43.478 0.00 0.00 33.12 4.40
1870 1979 2.014857 CATCATCATCATCATCCCCGC 58.985 52.381 0.00 0.00 0.00 6.13
1908 2017 5.065731 CCAAAGCTCCATGAATGACTAAGTC 59.934 44.000 0.00 0.00 0.00 3.01
1916 2025 8.996651 TCCATGAATGACTAAGTCTCACTATA 57.003 34.615 0.00 0.00 33.15 1.31
1920 2029 9.634021 ATGAATGACTAAGTCTCACTATACAGA 57.366 33.333 0.00 0.00 33.15 3.41
1925 2034 9.688091 TGACTAAGTCTCACTATACAGATCTTT 57.312 33.333 0.00 0.00 33.15 2.52
1932 2041 9.767684 GTCTCACTATACAGATCTTTATCATCG 57.232 37.037 4.65 0.00 34.28 3.84
1934 2043 9.767684 CTCACTATACAGATCTTTATCATCGTC 57.232 37.037 4.65 0.00 34.28 4.20
1935 2044 9.284968 TCACTATACAGATCTTTATCATCGTCA 57.715 33.333 4.65 0.00 34.28 4.35
1936 2045 9.899226 CACTATACAGATCTTTATCATCGTCAA 57.101 33.333 4.65 0.00 34.28 3.18
1955 2067 0.888619 AAGTCGAGCTTGATCACCGA 59.111 50.000 7.00 0.00 35.80 4.69
1965 2077 4.115199 ATCACCGAGGGGCTTGCC 62.115 66.667 2.49 2.49 36.48 4.52
1985 2098 3.068873 GCCTCGTATCCTTCTTGATCACT 59.931 47.826 0.00 0.00 0.00 3.41
1999 2112 3.655211 CACTGAGGGGCCAGCCTT 61.655 66.667 4.39 0.00 37.68 4.35
2016 2129 2.533266 CCTTGCCATTTTCTTGATCGC 58.467 47.619 0.00 0.00 0.00 4.58
2053 2166 1.201647 TCCCTACTCGCAAAGAACTCG 59.798 52.381 0.00 0.00 0.00 4.18
2060 2173 1.785951 GCAAAGAACTCGTACCGCC 59.214 57.895 0.00 0.00 0.00 6.13
2067 2180 2.167398 AACTCGTACCGCCTGCACAT 62.167 55.000 0.00 0.00 0.00 3.21
2084 2197 1.959985 ACATGGTGCGGATTTTGTGAA 59.040 42.857 0.00 0.00 0.00 3.18
2117 2230 4.669411 CGCATCGCTCTCATGGAT 57.331 55.556 0.00 0.00 0.00 3.41
2122 2235 2.230992 GCATCGCTCTCATGGATAGAGT 59.769 50.000 10.62 0.00 42.11 3.24
2181 2294 2.476619 GTGAGACACAATCCACACTTCG 59.523 50.000 0.00 0.00 34.37 3.79
2186 2299 0.321653 ACAATCCACACTTCGGGAGC 60.322 55.000 0.00 0.00 36.45 4.70
2204 2317 2.738147 CGAGTAACTTCGCCACCTG 58.262 57.895 0.00 0.00 33.39 4.00
2217 2330 2.104859 CACCTGCCAGCTCATGACG 61.105 63.158 0.00 0.00 0.00 4.35
2221 2334 1.079612 TGCCAGCTCATGACGTCTG 60.080 57.895 17.92 12.33 0.00 3.51
2238 2351 4.003648 CGTCTGGAAAGTTTAGCTTGGAT 58.996 43.478 0.00 0.00 37.52 3.41
2241 2354 6.382608 GTCTGGAAAGTTTAGCTTGGATTTC 58.617 40.000 0.00 0.00 37.52 2.17
2249 2362 2.839486 AGCTTGGATTTCTGTCGACA 57.161 45.000 18.88 18.88 0.00 4.35
2261 2374 7.760340 GGATTTCTGTCGACAGTAAATCTAAGT 59.240 37.037 39.32 28.03 42.28 2.24
2271 2384 7.542477 CGACAGTAAATCTAAGTCACAATGTCT 59.458 37.037 0.00 0.00 32.15 3.41
2280 2393 0.442310 TCACAATGTCTTAAGCGCGC 59.558 50.000 26.66 26.66 0.00 6.86
2281 2394 0.165727 CACAATGTCTTAAGCGCGCA 59.834 50.000 35.10 11.24 0.00 6.09
2282 2395 0.165944 ACAATGTCTTAAGCGCGCAC 59.834 50.000 35.10 22.41 0.00 5.34
2283 2396 0.521242 CAATGTCTTAAGCGCGCACC 60.521 55.000 35.10 13.82 0.00 5.01
2284 2397 0.953471 AATGTCTTAAGCGCGCACCA 60.953 50.000 35.10 18.99 0.00 4.17
2285 2398 1.635663 ATGTCTTAAGCGCGCACCAC 61.636 55.000 35.10 20.96 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 4.572909 TCCATGCATCTCTCCAAATATCG 58.427 43.478 0.00 0.00 0.00 2.92
115 117 3.947868 ACAACTCATCACTGGATCAAGG 58.052 45.455 1.23 0.00 0.00 3.61
116 118 4.155462 CCAACAACTCATCACTGGATCAAG 59.845 45.833 0.00 0.00 0.00 3.02
127 129 2.737252 GTCTTCGTCCCAACAACTCATC 59.263 50.000 0.00 0.00 0.00 2.92
132 134 1.602377 CCAAGTCTTCGTCCCAACAAC 59.398 52.381 0.00 0.00 0.00 3.32
197 199 8.863872 AACATATTATGCATAGGAAGGGTAAC 57.136 34.615 6.50 0.00 0.00 2.50
200 202 8.449423 TCTAACATATTATGCATAGGAAGGGT 57.551 34.615 6.50 0.00 0.00 4.34
222 225 7.791029 TGTATAGCTCCACACAATGAAATCTA 58.209 34.615 0.00 0.00 0.00 1.98
275 278 3.655777 TGGTTCCATTCCTCCAAGTAAGT 59.344 43.478 0.00 0.00 0.00 2.24
302 305 9.822185 GTTTCTATATTGCAATTTCCTTCCATT 57.178 29.630 18.75 0.00 0.00 3.16
324 327 5.388994 CGGGCAAAATAATTTCCAACGTTTC 60.389 40.000 0.00 0.00 0.00 2.78
328 331 2.926838 CCGGGCAAAATAATTTCCAACG 59.073 45.455 0.00 0.00 0.00 4.10
374 417 3.738281 CGGGAGAGTTCGATGCAAAGTAT 60.738 47.826 0.00 0.00 0.00 2.12
403 446 3.681897 GCGAGACCTTCATATGGCATAAG 59.318 47.826 11.86 7.39 0.00 1.73
409 463 0.758734 TGGGCGAGACCTTCATATGG 59.241 55.000 2.13 0.00 39.10 2.74
412 466 1.688735 CAGATGGGCGAGACCTTCATA 59.311 52.381 12.61 0.00 37.20 2.15
434 488 1.216444 GTCCACTCGAGCATGAGCA 59.784 57.895 13.61 0.00 45.49 4.26
435 489 1.520342 GGTCCACTCGAGCATGAGC 60.520 63.158 13.61 12.18 39.68 4.26
542 598 1.600957 CTCCCGCACAATCAATAGCAG 59.399 52.381 0.00 0.00 0.00 4.24
684 741 4.829064 TTGAACCTTTCCTTCATGAACG 57.171 40.909 3.38 0.60 0.00 3.95
707 764 1.153958 GTGGAAGATTGGCAAGCGC 60.154 57.895 10.15 0.00 37.44 5.92
725 782 1.979855 TGTTATGGCATGAATCCCCG 58.020 50.000 10.98 0.00 0.00 5.73
758 819 2.196997 TACATGCTGGGAGTGGGCAC 62.197 60.000 0.00 0.00 38.83 5.01
772 833 9.658799 CCATCCACCTATTTTACTAGATACATG 57.341 37.037 0.00 0.00 0.00 3.21
776 837 7.733047 TGCTCCATCCACCTATTTTACTAGATA 59.267 37.037 0.00 0.00 0.00 1.98
788 849 0.339859 AGGTCTGCTCCATCCACCTA 59.660 55.000 0.00 0.00 35.61 3.08
924 990 5.898174 ACATCAGCACACCAATCAATATTG 58.102 37.500 9.29 9.29 41.90 1.90
927 993 5.981088 AAACATCAGCACACCAATCAATA 57.019 34.783 0.00 0.00 0.00 1.90
968 1035 5.944007 GCAAGAAGTAATCCAAACCTTAGGA 59.056 40.000 4.77 0.00 38.50 2.94
1000 1067 2.425143 ACAAGACGATTGCATCCCAT 57.575 45.000 0.00 0.00 0.00 4.00
1064 1131 2.362889 CTCCCGCCAATTGCCCTT 60.363 61.111 0.00 0.00 36.24 3.95
1138 1205 3.057174 TCCCCATTACAATGTTCAAACGC 60.057 43.478 0.00 0.00 34.60 4.84
1196 1263 3.556999 TCCCTTGTCACCGAAATTTTCA 58.443 40.909 9.66 0.00 0.00 2.69
1206 1273 3.005791 CCTCAAAACAATCCCTTGTCACC 59.994 47.826 0.00 0.00 44.83 4.02
1339 1435 1.023502 CCCATATGCAACATGACGCA 58.976 50.000 14.49 14.49 43.45 5.24
1340 1436 0.318107 GCCCATATGCAACATGACGC 60.318 55.000 12.06 1.36 0.00 5.19
1341 1437 1.311859 AGCCCATATGCAACATGACG 58.688 50.000 12.06 4.50 0.00 4.35
1342 1438 2.287188 CGAAGCCCATATGCAACATGAC 60.287 50.000 12.06 5.31 0.00 3.06
1343 1439 1.948834 CGAAGCCCATATGCAACATGA 59.051 47.619 12.06 0.00 0.00 3.07
1344 1440 2.410785 CGAAGCCCATATGCAACATG 57.589 50.000 0.00 0.00 0.00 3.21
1379 1475 2.669569 GTTGCGAGCCCTTCTGCA 60.670 61.111 0.00 0.00 34.91 4.41
1382 1478 1.448540 CGATGTTGCGAGCCCTTCT 60.449 57.895 0.00 0.00 0.00 2.85
1402 1498 2.035449 TGTGAGGACTTCGGTAACACAG 59.965 50.000 0.00 0.00 33.83 3.66
1403 1499 2.033372 TGTGAGGACTTCGGTAACACA 58.967 47.619 0.00 0.00 35.13 3.72
1421 1517 1.226746 GAGTGGCTAGCGTTGTTTGT 58.773 50.000 9.00 0.00 0.00 2.83
1429 1525 1.519234 TGCGATTGAGTGGCTAGCG 60.519 57.895 9.00 0.00 34.37 4.26
1445 1541 2.109126 GGGTCATGAGCTTCGGTGC 61.109 63.158 23.24 2.27 0.00 5.01
1457 1553 0.178068 CCAAAGATCGGTCGGGTCAT 59.822 55.000 0.00 0.00 0.00 3.06
1536 1632 9.500785 CAAAATAAATTTGGTTGGACAATACCT 57.499 29.630 0.00 0.00 43.85 3.08
1591 1687 5.121811 GCCCTATTATACATCATCTGCTGG 58.878 45.833 0.00 0.00 0.00 4.85
1595 1691 5.121811 GGCTGCCCTATTATACATCATCTG 58.878 45.833 7.66 0.00 0.00 2.90
1623 1719 4.039124 CACTCTTTGGTGCCCTAACAAATT 59.961 41.667 0.00 0.00 34.06 1.82
1625 1721 2.955660 CACTCTTTGGTGCCCTAACAAA 59.044 45.455 0.00 0.00 33.53 2.83
1626 1722 2.092103 ACACTCTTTGGTGCCCTAACAA 60.092 45.455 0.00 0.00 40.52 2.83
1628 1724 1.880027 CACACTCTTTGGTGCCCTAAC 59.120 52.381 0.00 0.00 40.52 2.34
1630 1726 1.136828 ACACACTCTTTGGTGCCCTA 58.863 50.000 0.00 0.00 40.52 3.53
1631 1727 0.258774 AACACACTCTTTGGTGCCCT 59.741 50.000 0.00 0.00 40.52 5.19
1632 1728 1.111277 AAACACACTCTTTGGTGCCC 58.889 50.000 0.00 0.00 40.52 5.36
1633 1729 2.959507 AAAACACACTCTTTGGTGCC 57.040 45.000 0.00 0.00 40.52 5.01
1634 1730 4.298332 CCATAAAACACACTCTTTGGTGC 58.702 43.478 0.00 0.00 40.52 5.01
1654 1750 1.269517 GCAGAAAATGTTTCGGTGCCA 60.270 47.619 4.46 0.00 0.00 4.92
1674 1770 6.094603 GCCCTATTTTACATCATCTGCTATGG 59.905 42.308 0.64 0.00 0.00 2.74
1704 1800 9.661563 AGTTGAAATGTTGAAATATGCAATGAT 57.338 25.926 0.00 0.00 0.00 2.45
1785 1882 8.443937 GGTAGTGAGTCTTTATGTTTAAGCTTG 58.556 37.037 9.86 0.00 0.00 4.01
1786 1883 8.154856 TGGTAGTGAGTCTTTATGTTTAAGCTT 58.845 33.333 3.48 3.48 0.00 3.74
1788 1885 7.900782 TGGTAGTGAGTCTTTATGTTTAAGC 57.099 36.000 0.00 0.00 0.00 3.09
1832 1929 5.665916 TGATGATGATGAGTAGTGTGTGT 57.334 39.130 0.00 0.00 0.00 3.72
1908 2017 9.767684 GACGATGATAAAGATCTGTATAGTGAG 57.232 37.037 5.34 0.54 32.79 3.51
1916 2025 6.473778 CGACTTTGACGATGATAAAGATCTGT 59.526 38.462 0.00 0.00 35.82 3.41
1920 2029 5.460419 GCTCGACTTTGACGATGATAAAGAT 59.540 40.000 0.00 0.00 39.02 2.40
1925 2034 4.105486 CAAGCTCGACTTTGACGATGATA 58.895 43.478 0.00 0.00 36.04 2.15
1926 2035 2.926200 CAAGCTCGACTTTGACGATGAT 59.074 45.455 0.00 0.00 36.04 2.45
1932 2041 2.413453 GGTGATCAAGCTCGACTTTGAC 59.587 50.000 0.00 5.08 36.04 3.18
1934 2043 1.391485 CGGTGATCAAGCTCGACTTTG 59.609 52.381 0.00 0.00 36.04 2.77
1935 2044 1.272490 TCGGTGATCAAGCTCGACTTT 59.728 47.619 0.00 0.00 36.04 2.66
1936 2045 0.888619 TCGGTGATCAAGCTCGACTT 59.111 50.000 0.00 0.00 40.05 3.01
1955 2067 2.444256 GGATACGAGGCAAGCCCCT 61.444 63.158 7.62 0.00 38.12 4.79
1965 2077 5.506686 TCAGTGATCAAGAAGGATACGAG 57.493 43.478 0.00 0.00 46.39 4.18
1999 2112 1.838112 AGGCGATCAAGAAAATGGCA 58.162 45.000 0.00 0.00 30.34 4.92
2003 2116 3.119352 GGCAAGAAGGCGATCAAGAAAAT 60.119 43.478 0.00 0.00 33.57 1.82
2053 2166 2.046314 ACCATGTGCAGGCGGTAC 60.046 61.111 0.00 0.00 0.00 3.34
2067 2180 0.671251 GGTTCACAAAATCCGCACCA 59.329 50.000 0.00 0.00 0.00 4.17
2100 2213 1.200948 TCTATCCATGAGAGCGATGCG 59.799 52.381 0.00 0.00 0.00 4.73
2117 2230 5.125578 CACCTAGTCATGTAGCAACACTCTA 59.874 44.000 0.00 0.00 38.78 2.43
2122 2235 2.903784 ACCACCTAGTCATGTAGCAACA 59.096 45.455 0.00 0.00 40.69 3.33
2174 2287 0.243095 GTTACTCGCTCCCGAAGTGT 59.757 55.000 0.00 0.00 43.87 3.55
2186 2299 1.352156 GCAGGTGGCGAAGTTACTCG 61.352 60.000 0.00 0.00 41.84 4.18
2204 2317 1.812922 CCAGACGTCATGAGCTGGC 60.813 63.158 19.50 6.74 41.17 4.85
2217 2330 5.966742 AATCCAAGCTAAACTTTCCAGAC 57.033 39.130 0.00 0.00 36.04 3.51
2221 2334 6.332735 ACAGAAATCCAAGCTAAACTTTCC 57.667 37.500 0.00 0.00 36.04 3.13
2238 2351 7.594015 GTGACTTAGATTTACTGTCGACAGAAA 59.406 37.037 43.55 34.88 46.59 2.52
2261 2374 0.442310 GCGCGCTTAAGACATTGTGA 59.558 50.000 26.67 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.