Multiple sequence alignment - TraesCS1A01G158200

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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 TraesCS1A01G158200 chr1A 100.000 2468 0 0 1 2468 281649088 281651555 0.000000e+00 4558.0
1 TraesCS1A01G158200 chr1B 92.130 1385 43 27 476 1827 312919217 312920568 0.000000e+00 1893.0
2 TraesCS1A01G158200 chr1B 93.080 448 22 4 1 443 312918777 312919220 0.000000e+00 647.0
3 TraesCS1A01G158200 chr1B 87.555 458 45 6 1822 2275 312920634 312921083 1.010000e-143 520.0
4 TraesCS1A01G158200 chr1B 88.325 197 14 2 2247 2434 312923730 312923926 6.870000e-56 228.0
5 TraesCS1A01G158200 chr1B 87.817 197 15 2 2247 2434 312924686 312924882 3.190000e-54 222.0
6 TraesCS1A01G158200 chr1B 88.068 176 12 2 2266 2432 312922791 312922966 1.500000e-47 200.0
7 TraesCS1A01G158200 chr1D 93.158 1257 27 15 474 1689 218895351 218896589 0.000000e+00 1790.0
8 TraesCS1A01G158200 chr1D 95.642 436 14 2 1 435 218894676 218895107 0.000000e+00 695.0
9 TraesCS1A01G158200 chr1D 100.000 36 0 0 2433 2468 293463617 293463652 1.580000e-07 67.6
10 TraesCS1A01G158200 chrUn 100.000 35 0 0 2434 2468 102470866 102470832 5.700000e-07 65.8
11 TraesCS1A01G158200 chr7D 100.000 35 0 0 2434 2468 328423224 328423258 5.700000e-07 65.8
12 TraesCS1A01G158200 chr5B 100.000 35 0 0 2434 2468 52882939 52882973 5.700000e-07 65.8
13 TraesCS1A01G158200 chr5A 95.122 41 2 0 2428 2468 241275579 241275619 5.700000e-07 65.8
14 TraesCS1A01G158200 chr4D 100.000 35 0 0 2431 2465 172750399 172750433 5.700000e-07 65.8
15 TraesCS1A01G158200 chr4B 100.000 35 0 0 2434 2468 278460737 278460771 5.700000e-07 65.8
16 TraesCS1A01G158200 chr4B 100.000 35 0 0 2434 2468 278788425 278788459 5.700000e-07 65.8
17 TraesCS1A01G158200 chr3D 100.000 35 0 0 2434 2468 256893058 256893024 5.700000e-07 65.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G158200 chr1A 281649088 281651555 2467 False 4558.000000 4558 100.000000 1 2468 1 chr1A.!!$F1 2467
1 TraesCS1A01G158200 chr1B 312918777 312924882 6105 False 618.333333 1893 89.495833 1 2434 6 chr1B.!!$F1 2433
2 TraesCS1A01G158200 chr1D 218894676 218896589 1913 False 1242.500000 1790 94.400000 1 1689 2 chr1D.!!$F2 1688

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
898 1119 0.037232 GCTTGCGTACCTCTTCCAGT 60.037 55.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1952 2296 0.03831 AAGTTTGCAGGAGTAGGGGC 59.962 55.0 0.0 0.0 0.0 5.8 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
75 76 2.981560 GCACCATTCACCTGCGTGG 61.982 63.158 0.00 0.00 40.65 4.94
313 315 3.191371 GCCTTTCAGGAAATCGATTGTGT 59.809 43.478 12.25 0.00 37.67 3.72
322 324 6.963242 CAGGAAATCGATTGTGTATGTTTCTG 59.037 38.462 12.25 3.83 0.00 3.02
362 368 4.018506 TGAGGATGAAGCTGGGTGATTTAA 60.019 41.667 0.00 0.00 0.00 1.52
363 369 5.134725 AGGATGAAGCTGGGTGATTTAAT 57.865 39.130 0.00 0.00 0.00 1.40
364 370 5.522641 AGGATGAAGCTGGGTGATTTAATT 58.477 37.500 0.00 0.00 0.00 1.40
365 371 6.672593 AGGATGAAGCTGGGTGATTTAATTA 58.327 36.000 0.00 0.00 0.00 1.40
410 416 5.225899 TCTCATGCAGTTTTGATCGAATG 57.774 39.130 0.00 0.00 0.00 2.67
465 471 4.585955 GAGTATATCTCTCACCCGCAAA 57.414 45.455 3.81 0.00 39.86 3.68
467 473 5.353394 AGTATATCTCTCACCCGCAAAAA 57.647 39.130 0.00 0.00 0.00 1.94
897 1118 1.078759 CGCTTGCGTACCTCTTCCAG 61.079 60.000 6.86 0.00 0.00 3.86
898 1119 0.037232 GCTTGCGTACCTCTTCCAGT 60.037 55.000 0.00 0.00 0.00 4.00
899 1120 1.608283 GCTTGCGTACCTCTTCCAGTT 60.608 52.381 0.00 0.00 0.00 3.16
900 1121 2.338500 CTTGCGTACCTCTTCCAGTTC 58.662 52.381 0.00 0.00 0.00 3.01
901 1122 0.606604 TGCGTACCTCTTCCAGTTCC 59.393 55.000 0.00 0.00 0.00 3.62
902 1123 0.606604 GCGTACCTCTTCCAGTTCCA 59.393 55.000 0.00 0.00 0.00 3.53
903 1124 1.672145 GCGTACCTCTTCCAGTTCCAC 60.672 57.143 0.00 0.00 0.00 4.02
904 1125 1.067071 CGTACCTCTTCCAGTTCCACC 60.067 57.143 0.00 0.00 0.00 4.61
905 1126 2.258109 GTACCTCTTCCAGTTCCACCT 58.742 52.381 0.00 0.00 0.00 4.00
906 1127 2.715763 ACCTCTTCCAGTTCCACCTA 57.284 50.000 0.00 0.00 0.00 3.08
907 1128 2.541466 ACCTCTTCCAGTTCCACCTAG 58.459 52.381 0.00 0.00 0.00 3.02
1039 1264 0.613292 GGTGGTGCTCTCTCTCCTGA 60.613 60.000 0.00 0.00 0.00 3.86
1439 1664 2.031163 GCAAGGTGACGCTGAGGT 59.969 61.111 0.00 0.00 0.00 3.85
1545 1793 4.510340 GGGCTGGTAGTGTGTAAATTATCG 59.490 45.833 0.00 0.00 0.00 2.92
1578 1826 1.729284 GAGCGACGGGAAAATGGTTA 58.271 50.000 0.00 0.00 0.00 2.85
1596 1849 1.913778 TACAGGCGACTTCCACTGTA 58.086 50.000 0.00 0.00 43.34 2.74
1640 1911 1.726248 TCGTGCTGTGAACAATCATCG 59.274 47.619 0.00 0.00 38.01 3.84
1673 1944 1.230324 ACCTCAGAGAACGCTTTTGC 58.770 50.000 0.00 0.00 43.23 3.68
1679 1950 0.179238 GAGAACGCTTTTGCTCGAGC 60.179 55.000 30.42 30.42 44.80 5.03
1683 1954 4.733643 GCTTTTGCTCGAGCGAAG 57.266 55.556 32.73 32.56 44.44 3.79
1702 1973 3.454371 AGTGCACCTATAGCCGTTAAG 57.546 47.619 14.63 0.00 0.00 1.85
1711 1982 7.011669 GCACCTATAGCCGTTAAGTTATTTCAA 59.988 37.037 0.00 0.00 0.00 2.69
1745 2016 2.770164 ATCCCTCAACTCAGAAACCG 57.230 50.000 0.00 0.00 0.00 4.44
1747 2018 0.250295 CCCTCAACTCAGAAACCGCA 60.250 55.000 0.00 0.00 0.00 5.69
1748 2019 0.868406 CCTCAACTCAGAAACCGCAC 59.132 55.000 0.00 0.00 0.00 5.34
1749 2020 1.541233 CCTCAACTCAGAAACCGCACT 60.541 52.381 0.00 0.00 0.00 4.40
1750 2021 2.213499 CTCAACTCAGAAACCGCACTT 58.787 47.619 0.00 0.00 0.00 3.16
1751 2022 3.390135 CTCAACTCAGAAACCGCACTTA 58.610 45.455 0.00 0.00 0.00 2.24
1752 2023 3.128349 TCAACTCAGAAACCGCACTTAC 58.872 45.455 0.00 0.00 0.00 2.34
1753 2024 2.869801 CAACTCAGAAACCGCACTTACA 59.130 45.455 0.00 0.00 0.00 2.41
1754 2025 2.755650 ACTCAGAAACCGCACTTACAG 58.244 47.619 0.00 0.00 0.00 2.74
1755 2026 2.102588 ACTCAGAAACCGCACTTACAGT 59.897 45.455 0.00 0.00 0.00 3.55
1756 2027 3.319972 ACTCAGAAACCGCACTTACAGTA 59.680 43.478 0.00 0.00 0.00 2.74
1757 2028 3.645884 TCAGAAACCGCACTTACAGTAC 58.354 45.455 0.00 0.00 0.00 2.73
1758 2029 3.068448 TCAGAAACCGCACTTACAGTACA 59.932 43.478 0.00 0.00 0.00 2.90
1759 2030 3.428870 CAGAAACCGCACTTACAGTACAG 59.571 47.826 0.00 0.00 0.00 2.74
1760 2031 3.069158 AGAAACCGCACTTACAGTACAGT 59.931 43.478 0.00 0.00 0.00 3.55
1761 2032 4.279169 AGAAACCGCACTTACAGTACAGTA 59.721 41.667 0.00 0.00 0.00 2.74
1762 2033 4.589216 AACCGCACTTACAGTACAGTAA 57.411 40.909 10.10 10.10 33.28 2.24
1771 2042 8.274248 GCACTTACAGTACAGTAAACTTCTTTC 58.726 37.037 11.45 0.00 33.89 2.62
1818 2089 5.634896 GTGCAATGAATAGTGAGACCTTTG 58.365 41.667 0.00 0.00 0.00 2.77
1822 2093 7.025963 GCAATGAATAGTGAGACCTTTGAAAG 58.974 38.462 0.00 0.00 0.00 2.62
1827 2098 9.793259 TGAATAGTGAGACCTTTGAAAGTATTT 57.207 29.630 4.02 0.00 43.98 1.40
1858 2198 3.133721 TCTCTTAGAATGCTCAAGGGCTC 59.866 47.826 0.00 0.00 0.00 4.70
1863 2203 2.262774 AATGCTCAAGGGCTCGGGAG 62.263 60.000 3.44 3.44 0.00 4.30
1901 2245 2.682856 GTGTGAGTTGTGACCATGTTGT 59.317 45.455 0.00 0.00 0.00 3.32
1912 2256 0.168788 CCATGTTGTGTTAGCTGCCG 59.831 55.000 0.00 0.00 0.00 5.69
1913 2257 1.155889 CATGTTGTGTTAGCTGCCGA 58.844 50.000 0.00 0.00 0.00 5.54
1919 2263 2.076100 TGTGTTAGCTGCCGATCTTTG 58.924 47.619 0.00 0.00 0.00 2.77
1930 2274 1.611673 CCGATCTTTGGGTCACTTGCT 60.612 52.381 0.00 0.00 0.00 3.91
1934 2278 1.140052 TCTTTGGGTCACTTGCTTCGA 59.860 47.619 0.00 0.00 0.00 3.71
1940 2284 2.067013 GGTCACTTGCTTCGAGGTAAC 58.933 52.381 0.00 0.00 0.00 2.50
1952 2296 1.467035 CGAGGTAACGAAACTCTCCCG 60.467 57.143 6.13 0.00 46.39 5.14
1955 2299 0.738762 GTAACGAAACTCTCCCGCCC 60.739 60.000 0.00 0.00 0.00 6.13
1962 2306 2.522193 CTCTCCCGCCCCTACTCC 60.522 72.222 0.00 0.00 0.00 3.85
1986 2330 3.982475 CAAACTTTGCTCTTTCCTTCCC 58.018 45.455 0.00 0.00 0.00 3.97
1996 2340 4.324176 GCTCTTTCCTTCCCTCTCATCTTT 60.324 45.833 0.00 0.00 0.00 2.52
1998 2342 4.226168 TCTTTCCTTCCCTCTCATCTTTCC 59.774 45.833 0.00 0.00 0.00 3.13
2004 2348 2.642807 TCCCTCTCATCTTTCCGGTTTT 59.357 45.455 0.00 0.00 0.00 2.43
2011 2355 0.748729 TCTTTCCGGTTTTGCCACGT 60.749 50.000 0.00 0.00 36.97 4.49
2034 2378 1.028330 ATGTGGATGGCAGCAAGACG 61.028 55.000 4.64 0.00 0.00 4.18
2035 2379 2.046023 TGGATGGCAGCAAGACGG 60.046 61.111 4.64 0.00 0.00 4.79
2044 2388 1.813092 GCAGCAAGACGGGATCATCAT 60.813 52.381 0.00 0.00 0.00 2.45
2046 2390 1.487976 AGCAAGACGGGATCATCATGT 59.512 47.619 0.00 0.00 0.00 3.21
2048 2392 2.130395 CAAGACGGGATCATCATGTCG 58.870 52.381 0.00 0.00 34.82 4.35
2059 2403 6.111382 GGATCATCATGTCGTGGATCATAAT 58.889 40.000 11.27 0.00 36.86 1.28
2087 2431 0.249073 CCTCATCTCGGTTAGCCACG 60.249 60.000 0.00 0.00 34.09 4.94
2091 2435 1.673808 ATCTCGGTTAGCCACGGGAC 61.674 60.000 0.00 0.00 43.05 4.46
2094 2438 2.046604 GGTTAGCCACGGGACCAC 60.047 66.667 0.00 0.00 34.09 4.16
2097 2441 2.886134 TTAGCCACGGGACCACCAC 61.886 63.158 0.00 0.00 40.22 4.16
2117 2461 0.810031 CGACCTCGGCCTAACCATTG 60.810 60.000 0.00 0.00 39.03 2.82
2134 2478 2.969821 TTGCCAATGTGTACTTCCCT 57.030 45.000 0.00 0.00 0.00 4.20
2136 2480 1.702401 TGCCAATGTGTACTTCCCTGA 59.298 47.619 0.00 0.00 0.00 3.86
2138 2482 2.749621 GCCAATGTGTACTTCCCTGAAG 59.250 50.000 2.40 2.40 44.37 3.02
2152 2496 7.461749 ACTTCCCTGAAGATCATTTCTTACAA 58.538 34.615 10.62 0.00 44.88 2.41
2159 2503 7.742151 TGAAGATCATTTCTTACAATGTGACG 58.258 34.615 0.00 0.00 44.88 4.35
2160 2504 7.387673 TGAAGATCATTTCTTACAATGTGACGT 59.612 33.333 0.00 0.00 44.88 4.34
2196 2540 9.326413 CGTAATGGATAGTGAGACCTTTAAAAT 57.674 33.333 0.00 0.00 0.00 1.82
2227 2571 2.268762 TGTCCTACAATGTGCAAGCA 57.731 45.000 0.00 0.00 0.00 3.91
2250 5269 4.633126 ACCGAGAGATGATGAAATGTGTTG 59.367 41.667 0.00 0.00 0.00 3.33
2254 5273 5.240891 AGAGATGATGAAATGTGTTGTCGT 58.759 37.500 0.00 0.00 0.00 4.34
2333 5352 2.140717 CCAACCACGACTCCTACAAAC 58.859 52.381 0.00 0.00 0.00 2.93
2336 5355 3.107642 ACCACGACTCCTACAAACTTG 57.892 47.619 0.00 0.00 0.00 3.16
2358 5377 3.645687 GGCTCTTCCATTACCTCTCATCT 59.354 47.826 0.00 0.00 34.01 2.90
2372 6348 0.911769 TCATCTCTCCGGTTTGCCAT 59.088 50.000 0.00 0.00 34.09 4.40
2375 6351 2.745884 TCTCCGGTTTGCCATGCG 60.746 61.111 0.00 0.00 34.09 4.73
2398 6374 2.240500 GCAGACGATAGCAAGGCGG 61.241 63.158 0.00 0.00 42.67 6.13
2420 6404 6.092807 GCGGGATCTGATATCCTAAAATGTTC 59.907 42.308 0.00 0.00 38.26 3.18
2427 6411 9.426534 TCTGATATCCTAAAATGTTCTCTCTCA 57.573 33.333 0.00 0.00 0.00 3.27
2434 6418 3.584406 AATGTTCTCTCTCACCTCGTG 57.416 47.619 0.00 0.00 34.45 4.35
2435 6419 1.982660 TGTTCTCTCTCACCTCGTGT 58.017 50.000 0.00 0.00 34.79 4.49
2436 6420 2.307768 TGTTCTCTCTCACCTCGTGTT 58.692 47.619 0.00 0.00 34.79 3.32
2437 6421 2.034685 TGTTCTCTCTCACCTCGTGTTG 59.965 50.000 0.00 0.00 34.79 3.33
2438 6422 1.982660 TCTCTCTCACCTCGTGTTGT 58.017 50.000 0.00 0.00 34.79 3.32
2439 6423 3.136009 TCTCTCTCACCTCGTGTTGTA 57.864 47.619 0.00 0.00 34.79 2.41
2440 6424 3.075148 TCTCTCTCACCTCGTGTTGTAG 58.925 50.000 0.00 0.00 34.79 2.74
2441 6425 2.160205 TCTCTCACCTCGTGTTGTAGG 58.840 52.381 0.00 0.00 38.93 3.18
2442 6426 1.202582 CTCTCACCTCGTGTTGTAGGG 59.797 57.143 0.00 0.00 37.18 3.53
2443 6427 0.966920 CTCACCTCGTGTTGTAGGGT 59.033 55.000 0.00 0.00 37.18 4.34
2444 6428 0.677288 TCACCTCGTGTTGTAGGGTG 59.323 55.000 0.00 0.00 46.03 4.61
2445 6429 0.320421 CACCTCGTGTTGTAGGGTGG 60.320 60.000 0.00 0.00 42.39 4.61
2446 6430 0.470456 ACCTCGTGTTGTAGGGTGGA 60.470 55.000 0.00 0.00 37.18 4.02
2447 6431 0.682852 CCTCGTGTTGTAGGGTGGAA 59.317 55.000 0.00 0.00 0.00 3.53
2448 6432 1.607251 CCTCGTGTTGTAGGGTGGAAC 60.607 57.143 0.00 0.00 0.00 3.62
2464 6448 5.117406 GTGGAACCCTAAGATGGATCTTT 57.883 43.478 7.19 0.00 44.28 2.52
2465 6449 5.510430 GTGGAACCCTAAGATGGATCTTTT 58.490 41.667 7.19 0.00 44.28 2.27
2466 6450 5.590663 GTGGAACCCTAAGATGGATCTTTTC 59.409 44.000 7.19 5.39 44.28 2.29
2467 6451 5.252863 TGGAACCCTAAGATGGATCTTTTCA 59.747 40.000 7.19 0.00 44.28 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 7.857885 CGCCTTTACTCATCCATCTTTAATTTC 59.142 37.037 0.00 0.00 0.00 2.17
175 177 3.937079 TCGATACGTACTCAAGAGCAAGA 59.063 43.478 0.00 0.00 0.00 3.02
322 324 3.263425 TCCTCATACCACCCTGAAAAGTC 59.737 47.826 0.00 0.00 0.00 3.01
379 385 9.745880 GATCAAAACTGCATGAGATATGAATTT 57.254 29.630 0.00 0.00 0.00 1.82
384 390 6.535274 TCGATCAAAACTGCATGAGATATG 57.465 37.500 0.00 0.00 0.00 1.78
393 399 4.827304 TTCACATTCGATCAAAACTGCA 57.173 36.364 0.00 0.00 0.00 4.41
444 450 4.585955 TTTGCGGGTGAGAGATATACTC 57.414 45.455 0.00 0.00 45.22 2.59
445 451 5.353394 TTTTTGCGGGTGAGAGATATACT 57.647 39.130 0.00 0.00 0.00 2.12
796 1017 1.542987 GGAGCAGAATGATGAGGAGGC 60.543 57.143 0.00 0.00 39.69 4.70
897 1118 2.287909 CGATGAGCTAGCTAGGTGGAAC 60.288 54.545 29.22 15.22 33.58 3.62
898 1119 1.957177 CGATGAGCTAGCTAGGTGGAA 59.043 52.381 29.22 14.88 33.58 3.53
899 1120 1.133761 ACGATGAGCTAGCTAGGTGGA 60.134 52.381 29.22 15.79 33.58 4.02
900 1121 1.268352 GACGATGAGCTAGCTAGGTGG 59.732 57.143 29.22 16.79 33.58 4.61
901 1122 2.226330 AGACGATGAGCTAGCTAGGTG 58.774 52.381 29.22 16.89 33.58 4.00
902 1123 2.649531 AGACGATGAGCTAGCTAGGT 57.350 50.000 24.94 24.94 36.62 3.08
903 1124 8.339714 GTTTATATAGACGATGAGCTAGCTAGG 58.660 40.741 19.38 9.61 0.00 3.02
904 1125 8.884726 TGTTTATATAGACGATGAGCTAGCTAG 58.115 37.037 19.38 16.84 0.00 3.42
905 1126 8.666573 GTGTTTATATAGACGATGAGCTAGCTA 58.333 37.037 19.38 6.79 0.00 3.32
906 1127 7.175119 TGTGTTTATATAGACGATGAGCTAGCT 59.825 37.037 19.45 19.45 0.00 3.32
907 1128 7.306213 TGTGTTTATATAGACGATGAGCTAGC 58.694 38.462 6.62 6.62 0.00 3.42
1308 1533 4.314440 GCACGGACAGCTCCACCA 62.314 66.667 0.00 0.00 36.12 4.17
1448 1673 1.365699 TTAAGCATTCGACTTCGGCC 58.634 50.000 0.00 0.00 40.29 6.13
1545 1793 1.324736 GTCGCTCGATGATGAAACACC 59.675 52.381 0.00 0.00 0.00 4.16
1578 1826 1.066858 CATACAGTGGAAGTCGCCTGT 60.067 52.381 0.00 0.00 0.00 4.00
1640 1911 7.323177 CGTTCTCTGAGGTTTATATTAGTACGC 59.677 40.741 4.59 0.00 0.00 4.42
1673 1944 0.101399 ATAGGTGCACTTCGCTCGAG 59.899 55.000 17.98 8.45 43.06 4.04
1679 1950 0.102481 ACGGCTATAGGTGCACTTCG 59.898 55.000 17.98 11.00 0.00 3.79
1683 1954 3.175109 ACTTAACGGCTATAGGTGCAC 57.825 47.619 8.80 8.80 0.00 4.57
1695 1966 5.084055 GGACGCTTTGAAATAACTTAACGG 58.916 41.667 0.00 0.00 0.00 4.44
1702 1973 9.952341 GATAAAAATTGGACGCTTTGAAATAAC 57.048 29.630 0.00 0.00 0.00 1.89
1711 1982 4.340617 TGAGGGATAAAAATTGGACGCTT 58.659 39.130 0.00 0.00 0.00 4.68
1747 2018 8.408601 TCGAAAGAAGTTTACTGTACTGTAAGT 58.591 33.333 20.35 12.28 45.55 2.24
1748 2019 8.792831 TCGAAAGAAGTTTACTGTACTGTAAG 57.207 34.615 20.35 9.65 37.23 2.34
1749 2020 8.408601 ACTCGAAAGAAGTTTACTGTACTGTAA 58.591 33.333 18.27 18.27 41.32 2.41
1750 2021 7.934457 ACTCGAAAGAAGTTTACTGTACTGTA 58.066 34.615 8.40 8.40 41.32 2.74
1751 2022 6.803642 ACTCGAAAGAAGTTTACTGTACTGT 58.196 36.000 10.46 10.46 41.32 3.55
1752 2023 7.434307 TGAACTCGAAAGAAGTTTACTGTACTG 59.566 37.037 0.00 0.00 41.32 2.74
1753 2024 7.486647 TGAACTCGAAAGAAGTTTACTGTACT 58.513 34.615 0.00 0.00 41.32 2.73
1754 2025 7.096147 CCTGAACTCGAAAGAAGTTTACTGTAC 60.096 40.741 0.00 0.00 41.32 2.90
1755 2026 6.921857 CCTGAACTCGAAAGAAGTTTACTGTA 59.078 38.462 0.00 0.00 41.32 2.74
1756 2027 5.753921 CCTGAACTCGAAAGAAGTTTACTGT 59.246 40.000 0.00 0.00 41.32 3.55
1757 2028 5.753921 ACCTGAACTCGAAAGAAGTTTACTG 59.246 40.000 0.00 0.00 41.32 2.74
1758 2029 5.915175 ACCTGAACTCGAAAGAAGTTTACT 58.085 37.500 0.00 0.00 41.32 2.24
1759 2030 5.984323 AGACCTGAACTCGAAAGAAGTTTAC 59.016 40.000 0.00 0.00 41.32 2.01
1760 2031 5.983720 CAGACCTGAACTCGAAAGAAGTTTA 59.016 40.000 0.00 0.00 41.32 2.01
1761 2032 4.811557 CAGACCTGAACTCGAAAGAAGTTT 59.188 41.667 0.00 0.00 41.32 2.66
1762 2033 4.372656 CAGACCTGAACTCGAAAGAAGTT 58.627 43.478 0.00 0.00 41.32 2.66
1771 2042 0.389166 GAGCACCAGACCTGAACTCG 60.389 60.000 0.00 0.00 0.00 4.18
1827 2098 9.755804 CTTGAGCATTCTAAGAGAACACATATA 57.244 33.333 0.00 0.00 37.00 0.86
1828 2099 7.714377 CCTTGAGCATTCTAAGAGAACACATAT 59.286 37.037 0.00 0.00 37.00 1.78
1840 2180 1.134401 CCGAGCCCTTGAGCATTCTAA 60.134 52.381 0.00 0.00 34.23 2.10
1858 2198 1.202582 AGAACTTGTCATCGTCTCCCG 59.797 52.381 0.00 0.00 38.13 5.14
1863 2203 2.405357 CACACGAGAACTTGTCATCGTC 59.595 50.000 9.28 0.00 45.85 4.20
1869 2209 3.000322 CACAACTCACACGAGAACTTGTC 60.000 47.826 0.00 0.00 42.34 3.18
1901 2245 1.678728 CCCAAAGATCGGCAGCTAACA 60.679 52.381 0.00 0.00 0.00 2.41
1912 2256 2.160417 CGAAGCAAGTGACCCAAAGATC 59.840 50.000 0.00 0.00 0.00 2.75
1913 2257 2.154462 CGAAGCAAGTGACCCAAAGAT 58.846 47.619 0.00 0.00 0.00 2.40
1919 2263 0.606604 TACCTCGAAGCAAGTGACCC 59.393 55.000 0.00 0.00 0.00 4.46
1930 2274 2.229784 GGGAGAGTTTCGTTACCTCGAA 59.770 50.000 0.00 0.00 45.87 3.71
1934 2278 0.245813 GCGGGAGAGTTTCGTTACCT 59.754 55.000 0.00 0.00 0.00 3.08
1940 2284 2.056223 TAGGGGCGGGAGAGTTTCG 61.056 63.158 0.00 0.00 0.00 3.46
1952 2296 0.038310 AAGTTTGCAGGAGTAGGGGC 59.962 55.000 0.00 0.00 0.00 5.80
1986 2330 2.162408 GGCAAAACCGGAAAGATGAGAG 59.838 50.000 9.46 0.00 0.00 3.20
1996 2340 2.124653 ACACGTGGCAAAACCGGA 60.125 55.556 21.57 0.00 43.94 5.14
1998 2342 0.660005 CATCACACGTGGCAAAACCG 60.660 55.000 21.57 0.00 43.94 4.44
2011 2355 0.251253 TTGCTGCCATCCACATCACA 60.251 50.000 0.00 0.00 0.00 3.58
2034 2378 2.037641 TGATCCACGACATGATGATCCC 59.962 50.000 0.00 0.00 32.70 3.85
2035 2379 3.391506 TGATCCACGACATGATGATCC 57.608 47.619 0.00 0.00 32.70 3.36
2059 2403 0.752009 CCGAGATGAGGGAGAACGGA 60.752 60.000 0.00 0.00 41.09 4.69
2062 2406 2.223852 GCTAACCGAGATGAGGGAGAAC 60.224 54.545 0.00 0.00 0.00 3.01
2067 2411 0.105039 GTGGCTAACCGAGATGAGGG 59.895 60.000 0.00 0.00 39.70 4.30
2087 2431 3.703127 GAGGTCGGTGGTGGTCCC 61.703 72.222 0.00 0.00 0.00 4.46
2111 2455 2.825532 GGAAGTACACATTGGCAATGGT 59.174 45.455 35.77 30.49 43.21 3.55
2117 2461 2.489938 TCAGGGAAGTACACATTGGC 57.510 50.000 0.00 0.00 0.00 4.52
2134 2478 7.387673 ACGTCACATTGTAAGAAATGATCTTCA 59.612 33.333 4.04 0.00 45.42 3.02
2138 2482 7.269084 CACAACGTCACATTGTAAGAAATGATC 59.731 37.037 0.00 0.00 38.22 2.92
2196 2540 6.884295 CACATTGTAGGACAAGAGGGAAATAA 59.116 38.462 0.00 0.00 41.94 1.40
2197 2541 6.414732 CACATTGTAGGACAAGAGGGAAATA 58.585 40.000 0.00 0.00 41.94 1.40
2201 2545 2.027192 GCACATTGTAGGACAAGAGGGA 60.027 50.000 0.00 0.00 41.94 4.20
2202 2546 2.290260 TGCACATTGTAGGACAAGAGGG 60.290 50.000 0.00 0.00 41.94 4.30
2203 2547 3.057969 TGCACATTGTAGGACAAGAGG 57.942 47.619 0.00 0.00 41.94 3.69
2227 2571 4.478206 ACACATTTCATCATCTCTCGGT 57.522 40.909 0.00 0.00 0.00 4.69
2250 5269 5.151632 ACTAAAACAACATCACACACGAC 57.848 39.130 0.00 0.00 0.00 4.34
2254 5273 5.351740 TCGACAACTAAAACAACATCACACA 59.648 36.000 0.00 0.00 0.00 3.72
2309 5328 2.100989 GTAGGAGTCGTGGTTGGAGAT 58.899 52.381 0.00 0.00 0.00 2.75
2336 5355 3.645687 AGATGAGAGGTAATGGAAGAGCC 59.354 47.826 0.00 0.00 37.10 4.70
2358 5377 2.745884 CGCATGGCAAACCGGAGA 60.746 61.111 9.46 0.00 39.70 3.71
2375 6351 1.506493 CTTGCTATCGTCTGCATCCC 58.494 55.000 0.00 0.00 39.07 3.85
2382 6358 1.115930 ATCCCGCCTTGCTATCGTCT 61.116 55.000 0.00 0.00 0.00 4.18
2398 6374 9.651913 GAGAGAACATTTTAGGATATCAGATCC 57.348 37.037 4.83 0.00 38.47 3.36
2420 6404 2.162608 CCTACAACACGAGGTGAGAGAG 59.837 54.545 4.45 0.00 36.96 3.20
2427 6411 0.470456 TCCACCCTACAACACGAGGT 60.470 55.000 0.00 0.00 0.00 3.85
2440 6424 4.212204 AGATCCATCTTAGGGTTCCACCC 61.212 52.174 3.47 3.47 46.70 4.61
2441 6425 3.049344 AGATCCATCTTAGGGTTCCACC 58.951 50.000 0.00 0.00 33.09 4.61
2442 6426 4.779993 AAGATCCATCTTAGGGTTCCAC 57.220 45.455 0.00 0.00 44.80 4.02
2443 6427 5.252863 TGAAAAGATCCATCTTAGGGTTCCA 59.747 40.000 2.17 0.00 45.83 3.53
2444 6428 5.755849 TGAAAAGATCCATCTTAGGGTTCC 58.244 41.667 2.17 0.00 45.83 3.62


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

AutoCloner maintained by Alex Coulton.