Multiple sequence alignment - TraesCS3D01G113200

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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 TraesCS3D01G113200 chr3D 100.000 2672 0 0 1 2672 67350033 67352704 0.000000e+00 4935.0
1 TraesCS3D01G113200 chr3D 87.963 108 13 0 1451 1558 286190173 286190280 7.760000e-26 128.0
2 TraesCS3D01G113200 chr3B 88.303 2009 108 52 1 1962 111941822 111943750 0.000000e+00 2290.0
3 TraesCS3D01G113200 chr3B 85.397 541 47 14 2133 2669 111943809 111944321 1.410000e-147 532.0
4 TraesCS3D01G113200 chr3A 91.218 1617 73 29 383 1962 78709621 78711205 0.000000e+00 2135.0
5 TraesCS3D01G113200 chr3A 87.973 582 37 16 2083 2657 78711215 78711770 0.000000e+00 656.0
6 TraesCS3D01G113200 chr3A 85.028 354 18 16 1 348 78709298 78709622 7.130000e-86 327.0
7 TraesCS3D01G113200 chr3A 78.723 235 35 11 2442 2666 720844077 720844306 2.770000e-30 143.0
8 TraesCS3D01G113200 chr3A 87.963 108 13 0 1451 1558 374446646 374446753 7.760000e-26 128.0
9 TraesCS3D01G113200 chr1A 86.222 225 31 0 1346 1570 135182902 135182678 7.390000e-61 244.0
10 TraesCS3D01G113200 chr2B 80.519 231 28 13 2201 2426 105853452 105853234 7.650000e-36 161.0
11 TraesCS3D01G113200 chr2B 100.000 30 0 0 2441 2470 774064942 774064971 3.720000e-04 56.5
12 TraesCS3D01G113200 chr6D 81.633 147 21 4 2442 2585 224751671 224751528 1.680000e-22 117.0
13 TraesCS3D01G113200 chr6B 77.852 149 26 5 2486 2629 43063950 43064096 4.740000e-13 86.1
14 TraesCS3D01G113200 chr2D 92.308 39 2 1 2436 2473 376131306 376131344 1.000000e-03 54.7


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 TraesCS3D01G113200 chr3D 67350033 67352704 2671 False 4935.000000 4935 100.000 1 2672 1 chr3D.!!$F1 2671
1 TraesCS3D01G113200 chr3B 111941822 111944321 2499 False 1411.000000 2290 86.850 1 2669 2 chr3B.!!$F1 2668
2 TraesCS3D01G113200 chr3A 78709298 78711770 2472 False 1039.333333 2135 88.073 1 2657 3 chr3A.!!$F3 2656

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
357 404 0.392706 TGTCATCACAGTTGCGACCT 59.607 50.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1688 1773 0.029567 GCTCCGTACTGGTCGATCAG 59.97 60.0 24.08 24.08 39.52 2.9 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
31 32 1.914634 CTAGCTAGGTGTCGCTTGTG 58.085 55.000 13.32 0.00 37.68 3.33
74 75 1.669184 CACCGCACGTACACAAAATG 58.331 50.000 0.00 0.00 0.00 2.32
171 176 1.270550 GTCAGCTGGATTTTGGGTGTG 59.729 52.381 15.13 0.00 0.00 3.82
180 191 1.391157 TTTTGGGTGTGCTCCACTGC 61.391 55.000 6.97 0.00 43.94 4.40
197 208 3.880846 CTGCGGATTTGAGCGCCC 61.881 66.667 2.29 0.00 35.87 6.13
198 244 4.713735 TGCGGATTTGAGCGCCCA 62.714 61.111 2.29 0.00 35.87 5.36
207 253 1.600511 TTGAGCGCCCATGTCTCGTA 61.601 55.000 2.29 0.00 0.00 3.43
210 256 0.750546 AGCGCCCATGTCTCGTAGTA 60.751 55.000 2.29 0.00 0.00 1.82
215 261 4.806330 CGCCCATGTCTCGTAGTAATTAT 58.194 43.478 0.00 0.00 0.00 1.28
217 263 6.384224 CGCCCATGTCTCGTAGTAATTATAA 58.616 40.000 0.00 0.00 0.00 0.98
218 264 7.033791 CGCCCATGTCTCGTAGTAATTATAAT 58.966 38.462 0.00 0.00 0.00 1.28
219 265 7.220300 CGCCCATGTCTCGTAGTAATTATAATC 59.780 40.741 0.00 0.00 0.00 1.75
222 268 9.908152 CCATGTCTCGTAGTAATTATAATCACA 57.092 33.333 1.57 0.00 0.00 3.58
224 270 8.998558 TGTCTCGTAGTAATTATAATCACACG 57.001 34.615 13.27 13.27 0.00 4.49
225 271 8.615211 TGTCTCGTAGTAATTATAATCACACGT 58.385 33.333 16.44 0.00 0.00 4.49
228 274 9.868389 CTCGTAGTAATTATAATCACACGTACA 57.132 33.333 16.44 4.76 0.00 2.90
289 336 3.380954 TGAGCCCGATGTTTATACGTACA 59.619 43.478 0.00 0.00 0.00 2.90
290 337 3.709987 AGCCCGATGTTTATACGTACAC 58.290 45.455 0.00 0.00 0.00 2.90
291 338 3.130869 AGCCCGATGTTTATACGTACACA 59.869 43.478 0.00 1.71 0.00 3.72
292 339 3.488310 GCCCGATGTTTATACGTACACAG 59.512 47.826 0.00 0.00 0.00 3.66
293 340 4.675510 CCCGATGTTTATACGTACACAGT 58.324 43.478 0.00 0.00 0.00 3.55
294 341 5.733091 GCCCGATGTTTATACGTACACAGTA 60.733 44.000 0.00 0.00 0.00 2.74
295 342 5.682862 CCCGATGTTTATACGTACACAGTAC 59.317 44.000 0.00 0.00 0.00 2.73
309 356 9.350357 ACGTACACAGTACAGTATTATTTTCTG 57.650 33.333 7.93 0.00 35.60 3.02
344 391 1.920574 CACCGATGTCTCGTTGTCATC 59.079 52.381 0.00 0.00 43.49 2.92
348 395 2.595977 CGATGTCTCGTTGTCATCACAG 59.404 50.000 14.12 0.00 39.87 3.66
349 396 3.579709 GATGTCTCGTTGTCATCACAGT 58.420 45.455 11.00 0.00 39.73 3.55
350 397 3.452755 TGTCTCGTTGTCATCACAGTT 57.547 42.857 0.00 0.00 32.71 3.16
351 398 3.123050 TGTCTCGTTGTCATCACAGTTG 58.877 45.455 0.00 0.00 32.71 3.16
352 399 2.096713 GTCTCGTTGTCATCACAGTTGC 60.097 50.000 0.00 0.00 32.71 4.17
353 400 0.858583 TCGTTGTCATCACAGTTGCG 59.141 50.000 0.00 0.00 32.71 4.85
354 401 0.858583 CGTTGTCATCACAGTTGCGA 59.141 50.000 0.00 0.00 32.71 5.10
355 402 1.397190 CGTTGTCATCACAGTTGCGAC 60.397 52.381 0.00 0.00 32.71 5.19
356 403 1.069906 GTTGTCATCACAGTTGCGACC 60.070 52.381 0.00 0.00 32.71 4.79
357 404 0.392706 TGTCATCACAGTTGCGACCT 59.607 50.000 0.00 0.00 0.00 3.85
358 405 1.202639 TGTCATCACAGTTGCGACCTT 60.203 47.619 0.00 0.00 0.00 3.50
419 466 1.004745 ACCCAAAATCCAGCTGACGAT 59.995 47.619 17.39 7.53 0.00 3.73
424 471 3.548745 AAATCCAGCTGACGATGATCA 57.451 42.857 17.39 0.00 0.00 2.92
430 477 3.554337 CCAGCTGACGATGATCATGATGA 60.554 47.826 17.39 4.76 0.00 2.92
431 478 4.246458 CAGCTGACGATGATCATGATGAT 58.754 43.478 14.30 10.68 40.34 2.45
432 479 4.092091 CAGCTGACGATGATCATGATGATG 59.908 45.833 14.30 7.84 37.20 3.07
433 480 4.021368 AGCTGACGATGATCATGATGATGA 60.021 41.667 14.30 4.58 42.92 2.92
483 530 7.255173 GCGAGGAACGTACATAGATGGATATAT 60.255 40.741 0.00 0.00 44.60 0.86
484 531 8.622157 CGAGGAACGTACATAGATGGATATATT 58.378 37.037 0.00 0.00 37.22 1.28
578 629 3.420839 GCGTACTGCTGCCAATTAAAT 57.579 42.857 0.00 0.00 41.73 1.40
580 631 3.607439 CGTACTGCTGCCAATTAAATCG 58.393 45.455 0.00 0.00 0.00 3.34
581 632 2.566952 ACTGCTGCCAATTAAATCGC 57.433 45.000 0.00 0.00 0.00 4.58
582 633 1.202177 ACTGCTGCCAATTAAATCGCG 60.202 47.619 0.00 0.00 0.00 5.87
583 634 0.525242 TGCTGCCAATTAAATCGCGC 60.525 50.000 0.00 0.00 0.00 6.86
617 668 4.648626 CCATCCATCGGCGGCCAT 62.649 66.667 20.71 8.91 0.00 4.40
672 723 2.153034 AGTCTCCTCTTGACTAGCCC 57.847 55.000 0.00 0.00 42.28 5.19
691 746 1.745489 GGCCGTTGCTTCTTCGGAT 60.745 57.895 7.01 0.00 46.05 4.18
1040 1113 1.207488 ACCACCAGCCATGAAGCCTA 61.207 55.000 0.00 0.00 0.00 3.93
1045 1118 1.765314 CCAGCCATGAAGCCTACTACT 59.235 52.381 0.00 0.00 0.00 2.57
1077 1150 0.541863 CGGCCTCCTCCTTGTACAAT 59.458 55.000 9.13 0.00 0.00 2.71
1081 1154 2.678336 GCCTCCTCCTTGTACAATTTCG 59.322 50.000 9.13 0.00 0.00 3.46
1149 1222 3.068691 TTCCCGGAGCTCGTGGAG 61.069 66.667 21.69 13.18 38.66 3.86
1284 1357 3.554692 GGCGCGTGGATGTTCGAG 61.555 66.667 8.43 0.00 0.00 4.04
1286 1359 2.180769 CGCGTGGATGTTCGAGGA 59.819 61.111 0.00 0.00 0.00 3.71
1395 1468 2.050350 GGAGGTGATGGACGACGGA 61.050 63.158 0.00 0.00 0.00 4.69
1503 1576 4.436998 AAGAAGCGGGTCGAGCGG 62.437 66.667 16.86 16.86 40.04 5.52
1682 1767 3.358118 AGTCCTACTGAACTGAGCTACC 58.642 50.000 0.00 0.00 0.00 3.18
1683 1768 2.097791 GTCCTACTGAACTGAGCTACCG 59.902 54.545 0.00 0.00 0.00 4.02
1684 1769 2.026542 TCCTACTGAACTGAGCTACCGA 60.027 50.000 0.00 0.00 0.00 4.69
1685 1770 2.753452 CCTACTGAACTGAGCTACCGAA 59.247 50.000 0.00 0.00 0.00 4.30
1686 1771 3.381908 CCTACTGAACTGAGCTACCGAAT 59.618 47.826 0.00 0.00 0.00 3.34
1687 1772 4.579340 CCTACTGAACTGAGCTACCGAATA 59.421 45.833 0.00 0.00 0.00 1.75
1688 1773 4.373348 ACTGAACTGAGCTACCGAATAC 57.627 45.455 0.00 0.00 0.00 1.89
1764 1851 4.025396 CAGAAATCTCACGGATGCATGTAC 60.025 45.833 2.46 0.00 34.45 2.90
1799 1890 2.731691 GATGGTGGTGTGCCGTCACT 62.732 60.000 0.00 0.00 43.49 3.41
1835 1927 1.958715 CCACGTCCATTGTGCACGA 60.959 57.895 9.77 9.77 37.00 4.35
1912 2004 2.747989 TGCACGAACAGGTTAACAAACA 59.252 40.909 8.10 0.00 0.00 2.83
1937 2031 4.447724 ACATACGTACGGCAATCATTCATC 59.552 41.667 21.06 0.00 0.00 2.92
1962 2056 2.834113 AGTTGGTAGGCTCCACATACT 58.166 47.619 5.34 4.66 37.20 2.12
1963 2057 3.182152 AGTTGGTAGGCTCCACATACTT 58.818 45.455 5.34 0.00 37.20 2.24
1964 2058 4.359105 AGTTGGTAGGCTCCACATACTTA 58.641 43.478 5.34 0.00 37.20 2.24
1965 2059 4.161754 AGTTGGTAGGCTCCACATACTTAC 59.838 45.833 5.34 1.00 37.20 2.34
1966 2060 3.990369 TGGTAGGCTCCACATACTTACT 58.010 45.455 0.00 0.00 31.96 2.24
1967 2061 3.958798 TGGTAGGCTCCACATACTTACTC 59.041 47.826 0.00 0.00 31.96 2.59
1968 2062 3.004524 GGTAGGCTCCACATACTTACTCG 59.995 52.174 0.00 0.00 0.00 4.18
1969 2063 2.032620 AGGCTCCACATACTTACTCGG 58.967 52.381 0.00 0.00 0.00 4.63
1970 2064 1.755380 GGCTCCACATACTTACTCGGT 59.245 52.381 0.00 0.00 0.00 4.69
1971 2065 2.167900 GGCTCCACATACTTACTCGGTT 59.832 50.000 0.00 0.00 0.00 4.44
1972 2066 3.382546 GGCTCCACATACTTACTCGGTTA 59.617 47.826 0.00 0.00 0.00 2.85
1973 2067 4.357996 GCTCCACATACTTACTCGGTTAC 58.642 47.826 0.00 0.00 0.00 2.50
1974 2068 4.097589 GCTCCACATACTTACTCGGTTACT 59.902 45.833 0.00 0.00 0.00 2.24
1975 2069 5.297776 GCTCCACATACTTACTCGGTTACTA 59.702 44.000 0.00 0.00 0.00 1.82
1976 2070 6.183360 GCTCCACATACTTACTCGGTTACTAA 60.183 42.308 0.00 0.00 0.00 2.24
1977 2071 7.629222 GCTCCACATACTTACTCGGTTACTAAA 60.629 40.741 0.00 0.00 0.00 1.85
1978 2072 8.297470 TCCACATACTTACTCGGTTACTAAAT 57.703 34.615 0.00 0.00 0.00 1.40
1979 2073 9.407380 TCCACATACTTACTCGGTTACTAAATA 57.593 33.333 0.00 0.00 0.00 1.40
2018 2112 9.103048 GAGTGTACATTTACTCATTTTGTTTCG 57.897 33.333 0.00 0.00 42.18 3.46
2019 2113 8.617809 AGTGTACATTTACTCATTTTGTTTCGT 58.382 29.630 0.00 0.00 0.00 3.85
2020 2114 9.866936 GTGTACATTTACTCATTTTGTTTCGTA 57.133 29.630 0.00 0.00 0.00 3.43
2024 2118 9.825972 ACATTTACTCATTTTGTTTCGTATGAG 57.174 29.630 0.00 0.00 45.92 2.90
2029 2123 5.927030 TCATTTTGTTTCGTATGAGTCTGC 58.073 37.500 0.00 0.00 0.00 4.26
2030 2124 5.468409 TCATTTTGTTTCGTATGAGTCTGCA 59.532 36.000 0.00 0.00 0.00 4.41
2031 2125 5.940192 TTTTGTTTCGTATGAGTCTGCAT 57.060 34.783 0.00 0.00 0.00 3.96
2032 2126 5.940192 TTTGTTTCGTATGAGTCTGCATT 57.060 34.783 0.00 0.00 0.00 3.56
2033 2127 4.926860 TGTTTCGTATGAGTCTGCATTG 57.073 40.909 0.00 0.00 0.00 2.82
2034 2128 3.684305 TGTTTCGTATGAGTCTGCATTGG 59.316 43.478 0.00 0.00 0.00 3.16
2035 2129 3.885724 TTCGTATGAGTCTGCATTGGA 57.114 42.857 0.00 0.00 0.00 3.53
2036 2130 3.885724 TCGTATGAGTCTGCATTGGAA 57.114 42.857 0.00 0.00 0.00 3.53
2037 2131 4.406648 TCGTATGAGTCTGCATTGGAAT 57.593 40.909 0.00 0.00 0.00 3.01
2038 2132 4.371786 TCGTATGAGTCTGCATTGGAATC 58.628 43.478 0.00 0.00 0.00 2.52
2039 2133 4.100035 TCGTATGAGTCTGCATTGGAATCT 59.900 41.667 3.95 0.00 0.00 2.40
2040 2134 5.301805 TCGTATGAGTCTGCATTGGAATCTA 59.698 40.000 3.95 0.00 0.00 1.98
2041 2135 6.015095 TCGTATGAGTCTGCATTGGAATCTAT 60.015 38.462 3.95 0.13 0.00 1.98
2042 2136 7.176690 TCGTATGAGTCTGCATTGGAATCTATA 59.823 37.037 3.95 0.00 0.00 1.31
2043 2137 7.274468 CGTATGAGTCTGCATTGGAATCTATAC 59.726 40.741 3.95 8.10 0.00 1.47
2044 2138 5.532557 TGAGTCTGCATTGGAATCTATACG 58.467 41.667 3.95 0.00 0.00 3.06
2045 2139 5.301805 TGAGTCTGCATTGGAATCTATACGA 59.698 40.000 3.95 0.00 0.00 3.43
2046 2140 5.777802 AGTCTGCATTGGAATCTATACGAG 58.222 41.667 0.00 0.00 0.00 4.18
2047 2141 4.926238 GTCTGCATTGGAATCTATACGAGG 59.074 45.833 0.00 0.00 0.00 4.63
2048 2142 4.832823 TCTGCATTGGAATCTATACGAGGA 59.167 41.667 0.00 0.00 0.00 3.71
2049 2143 5.047731 TCTGCATTGGAATCTATACGAGGAG 60.048 44.000 0.00 0.00 0.00 3.69
2050 2144 4.588951 TGCATTGGAATCTATACGAGGAGT 59.411 41.667 0.00 0.00 0.00 3.85
2051 2145 5.070446 TGCATTGGAATCTATACGAGGAGTT 59.930 40.000 0.00 0.00 0.00 3.01
2052 2146 6.266786 TGCATTGGAATCTATACGAGGAGTTA 59.733 38.462 0.00 0.00 0.00 2.24
2053 2147 7.039011 TGCATTGGAATCTATACGAGGAGTTAT 60.039 37.037 0.00 0.00 0.00 1.89
2054 2148 8.467598 GCATTGGAATCTATACGAGGAGTTATA 58.532 37.037 0.00 0.00 0.00 0.98
2091 2185 3.717707 AGTATCACAATGAATCCGTCCG 58.282 45.455 0.00 0.00 0.00 4.79
2121 2215 7.715265 TCAGATCCTCTTAAAATAATGTCGC 57.285 36.000 0.00 0.00 0.00 5.19
2126 2220 8.682936 ATCCTCTTAAAATAATGTCGCTCAAT 57.317 30.769 0.00 0.00 0.00 2.57
2142 2244 2.807967 CTCAATGAGCTTTCGTGGACAA 59.192 45.455 0.00 0.00 0.00 3.18
2143 2245 2.807967 TCAATGAGCTTTCGTGGACAAG 59.192 45.455 0.00 0.00 0.00 3.16
2152 2254 1.581934 TCGTGGACAAGACTGCAAAG 58.418 50.000 0.00 0.00 0.00 2.77
2172 2274 1.336056 GGAGTTGAGTTCGAGCGAGTT 60.336 52.381 0.00 0.00 0.00 3.01
2173 2275 1.716581 GAGTTGAGTTCGAGCGAGTTG 59.283 52.381 0.00 0.00 0.00 3.16
2174 2276 1.337071 AGTTGAGTTCGAGCGAGTTGA 59.663 47.619 0.00 0.00 0.00 3.18
2175 2277 2.124903 GTTGAGTTCGAGCGAGTTGAA 58.875 47.619 0.00 0.00 0.00 2.69
2176 2278 2.724977 TGAGTTCGAGCGAGTTGAAT 57.275 45.000 0.00 0.00 30.78 2.57
2177 2279 2.328473 TGAGTTCGAGCGAGTTGAATG 58.672 47.619 0.00 0.00 30.78 2.67
2178 2280 2.288213 TGAGTTCGAGCGAGTTGAATGT 60.288 45.455 0.00 0.00 30.78 2.71
2216 2318 2.029365 GGCACTAAAATTCGAGCGACTC 59.971 50.000 0.00 0.00 0.00 3.36
2226 2328 3.587797 TCGAGCGACTCCAAACTAATT 57.412 42.857 0.00 0.00 0.00 1.40
2258 2360 4.944317 AGGTCAAGCTATAAAAAGTGGCTC 59.056 41.667 0.00 0.00 32.46 4.70
2276 2378 2.681848 GCTCATGCTCAGCTTGTAATGT 59.318 45.455 12.05 0.00 35.60 2.71
2304 2406 8.356533 TCAAGTCGATTTTAAACTAGTTTCGT 57.643 30.769 23.76 8.93 34.23 3.85
2375 2478 6.663953 ACTAGATAGGACACACACAACATAGT 59.336 38.462 0.00 0.00 0.00 2.12
2508 2612 3.509967 TCGTGGATGAGCTAACAAGAGAA 59.490 43.478 0.00 0.00 0.00 2.87
2577 2682 6.238648 GGATAGTTAACACATTGGCCATGTAC 60.239 42.308 6.09 4.43 45.06 2.90
2593 2701 4.202503 CCATGTACCATCTTGAGGCCTAAT 60.203 45.833 4.42 0.00 0.00 1.73
2622 2730 7.934457 TCTCCAGCTTAATTAAGATTCAATGC 58.066 34.615 26.00 10.79 35.33 3.56
2638 2746 9.790344 AGATTCAATGCTTGCTAGTAGATAAAT 57.210 29.630 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 2.959707 CCTGACCAGGGTAGTCTATCAC 59.040 54.545 8.17 0.00 44.87 3.06
74 75 4.036498 TCGATCGAATCCCACTAACTCTTC 59.964 45.833 16.99 0.00 0.00 2.87
151 156 1.270550 CACACCCAAAATCCAGCTGAC 59.729 52.381 17.39 0.00 0.00 3.51
198 244 9.608617 CGTGTGATTATAATTACTACGAGACAT 57.391 33.333 24.32 0.00 34.61 3.06
254 300 1.442526 GGGCTCAGATCCGCATTGTG 61.443 60.000 0.00 0.00 0.00 3.33
257 303 1.762522 ATCGGGCTCAGATCCGCATT 61.763 55.000 7.31 0.00 45.31 3.56
258 304 2.212811 ATCGGGCTCAGATCCGCAT 61.213 57.895 7.31 1.43 45.31 4.73
309 356 1.406898 TCGGTGCTCTGATGTCTGATC 59.593 52.381 0.00 0.00 0.00 2.92
311 358 1.135721 CATCGGTGCTCTGATGTCTGA 59.864 52.381 23.53 0.00 46.57 3.27
312 359 1.568606 CATCGGTGCTCTGATGTCTG 58.431 55.000 23.53 5.66 46.57 3.51
317 364 0.383590 CGAGACATCGGTGCTCTGAT 59.616 55.000 15.09 4.23 45.39 2.90
318 365 1.803289 CGAGACATCGGTGCTCTGA 59.197 57.895 15.09 0.00 45.39 3.27
344 391 2.407361 CGTACTTAAGGTCGCAACTGTG 59.593 50.000 7.53 0.00 0.00 3.66
348 395 3.826466 ACTACGTACTTAAGGTCGCAAC 58.174 45.455 17.16 2.32 0.00 4.17
349 396 5.818136 ATACTACGTACTTAAGGTCGCAA 57.182 39.130 17.16 8.41 0.00 4.85
350 397 5.818136 AATACTACGTACTTAAGGTCGCA 57.182 39.130 17.16 7.56 0.00 5.10
351 398 6.258160 TGAAATACTACGTACTTAAGGTCGC 58.742 40.000 17.16 1.10 0.00 5.19
352 399 7.688372 TCTGAAATACTACGTACTTAAGGTCG 58.312 38.462 16.13 16.13 0.00 4.79
353 400 9.662545 GATCTGAAATACTACGTACTTAAGGTC 57.337 37.037 7.53 0.00 0.00 3.85
354 401 8.628280 GGATCTGAAATACTACGTACTTAAGGT 58.372 37.037 7.53 0.00 0.00 3.50
355 402 7.802251 CGGATCTGAAATACTACGTACTTAAGG 59.198 40.741 7.53 0.00 0.00 2.69
356 403 7.323177 GCGGATCTGAAATACTACGTACTTAAG 59.677 40.741 5.48 0.00 0.00 1.85
357 404 7.134815 GCGGATCTGAAATACTACGTACTTAA 58.865 38.462 5.48 0.00 0.00 1.85
358 405 6.260714 TGCGGATCTGAAATACTACGTACTTA 59.739 38.462 5.48 0.00 0.00 2.24
419 466 4.248058 GCGGTACATCATCATCATGATCA 58.752 43.478 4.86 0.00 45.26 2.92
424 471 1.338105 CGGGCGGTACATCATCATCAT 60.338 52.381 0.00 0.00 0.00 2.45
430 477 1.176619 TCGATCGGGCGGTACATCAT 61.177 55.000 16.41 0.00 0.00 2.45
431 478 1.176619 ATCGATCGGGCGGTACATCA 61.177 55.000 16.41 0.00 0.00 3.07
432 479 0.456312 GATCGATCGGGCGGTACATC 60.456 60.000 16.41 4.35 0.00 3.06
433 480 1.585006 GATCGATCGGGCGGTACAT 59.415 57.895 16.41 0.00 0.00 2.29
434 481 2.900167 CGATCGATCGGGCGGTACA 61.900 63.158 34.54 0.00 45.93 2.90
483 530 7.011669 TCGACGATCGCACAGGATATATATAAA 59.988 37.037 16.60 0.00 40.21 1.40
484 531 6.480981 TCGACGATCGCACAGGATATATATAA 59.519 38.462 16.60 0.00 40.21 0.98
489 536 2.419667 TCGACGATCGCACAGGATATA 58.580 47.619 16.60 0.00 40.21 0.86
490 537 1.235724 TCGACGATCGCACAGGATAT 58.764 50.000 16.60 0.00 40.21 1.63
499 546 4.925576 ACGGCCATCGACGATCGC 62.926 66.667 17.73 17.73 40.21 4.58
567 618 1.063327 CGGCGCGATTTAATTGGCA 59.937 52.632 12.10 0.00 0.00 4.92
617 668 3.709141 TGGATCATTCATCTGGACCGTTA 59.291 43.478 0.00 0.00 0.00 3.18
672 723 3.788766 CCGAAGAAGCAACGGCCG 61.789 66.667 26.86 26.86 42.56 6.13
946 1012 0.811281 GCTACGTTACCGGTAGTGGT 59.189 55.000 15.20 15.45 46.26 4.16
947 1013 0.810648 TGCTACGTTACCGGTAGTGG 59.189 55.000 15.20 13.10 38.78 4.00
1077 1150 1.078708 GGGATCACCGGCTTCGAAA 60.079 57.895 0.00 0.00 36.97 3.46
1081 1154 1.521681 CGAAGGGATCACCGGCTTC 60.522 63.158 0.00 4.09 46.96 3.86
1158 1231 3.138798 GGCGAGTAGTCGGAGGCA 61.139 66.667 20.94 0.00 46.91 4.75
1249 1322 1.297451 CGTCGCAGTAGTACGAGGC 60.297 63.158 0.29 0.00 39.30 4.70
1395 1468 0.822164 CGTACTTCCTCCACCGGAAT 59.178 55.000 9.46 0.00 41.92 3.01
1520 1593 1.676916 CGTAGGTGGTGAGGACGTAGA 60.677 57.143 0.00 0.00 0.00 2.59
1686 1771 2.558378 CTCCGTACTGGTCGATCAGTA 58.442 52.381 30.17 30.17 45.18 2.74
1688 1773 0.029567 GCTCCGTACTGGTCGATCAG 59.970 60.000 24.08 24.08 39.52 2.90
1704 1789 5.475564 TCATAAAAACCAAGGTAACCAGCTC 59.524 40.000 0.00 0.00 37.17 4.09
1713 1798 6.037830 CCGTAATCGATCATAAAAACCAAGGT 59.962 38.462 0.00 0.00 39.71 3.50
1764 1851 2.030007 ACCATCAAGGCAACAAATCGTG 60.030 45.455 0.00 0.00 43.14 4.35
1799 1890 2.933906 GTGGAAGCGACCGAATTATTCA 59.066 45.455 5.76 0.00 0.00 2.57
1835 1927 1.876714 CGTCGATCGGCGTTTCCAT 60.877 57.895 32.27 0.00 41.80 3.41
1890 1982 3.378742 TGTTTGTTAACCTGTTCGTGCAT 59.621 39.130 2.48 0.00 33.15 3.96
1912 2004 2.658373 TGATTGCCGTACGTATGTGT 57.342 45.000 15.21 0.00 0.00 3.72
1937 2031 1.745489 GGAGCCTACCAACTTGCCG 60.745 63.158 0.00 0.00 0.00 5.69
1992 2086 9.103048 CGAAACAAAATGAGTAAATGTACACTC 57.897 33.333 0.00 0.46 41.31 3.51
1993 2087 8.617809 ACGAAACAAAATGAGTAAATGTACACT 58.382 29.630 0.00 0.00 32.12 3.55
1994 2088 8.776680 ACGAAACAAAATGAGTAAATGTACAC 57.223 30.769 0.00 0.00 32.12 2.90
1998 2092 9.825972 CTCATACGAAACAAAATGAGTAAATGT 57.174 29.630 0.00 0.00 40.18 2.71
2005 2099 6.017933 GCAGACTCATACGAAACAAAATGAG 58.982 40.000 9.10 9.10 46.94 2.90
2006 2100 5.468409 TGCAGACTCATACGAAACAAAATGA 59.532 36.000 0.00 0.00 0.00 2.57
2007 2101 5.688823 TGCAGACTCATACGAAACAAAATG 58.311 37.500 0.00 0.00 0.00 2.32
2008 2102 5.940192 TGCAGACTCATACGAAACAAAAT 57.060 34.783 0.00 0.00 0.00 1.82
2009 2103 5.940192 ATGCAGACTCATACGAAACAAAA 57.060 34.783 0.00 0.00 0.00 2.44
2010 2104 5.334802 CCAATGCAGACTCATACGAAACAAA 60.335 40.000 0.00 0.00 0.00 2.83
2011 2105 4.154015 CCAATGCAGACTCATACGAAACAA 59.846 41.667 0.00 0.00 0.00 2.83
2012 2106 3.684305 CCAATGCAGACTCATACGAAACA 59.316 43.478 0.00 0.00 0.00 2.83
2013 2107 3.932710 TCCAATGCAGACTCATACGAAAC 59.067 43.478 0.00 0.00 0.00 2.78
2014 2108 4.200838 TCCAATGCAGACTCATACGAAA 57.799 40.909 0.00 0.00 0.00 3.46
2015 2109 3.885724 TCCAATGCAGACTCATACGAA 57.114 42.857 0.00 0.00 0.00 3.85
2016 2110 3.885724 TTCCAATGCAGACTCATACGA 57.114 42.857 0.00 0.00 0.00 3.43
2017 2111 4.375272 AGATTCCAATGCAGACTCATACG 58.625 43.478 0.00 0.00 0.00 3.06
2018 2112 7.274468 CGTATAGATTCCAATGCAGACTCATAC 59.726 40.741 0.00 0.13 0.00 2.39
2019 2113 7.176690 TCGTATAGATTCCAATGCAGACTCATA 59.823 37.037 0.00 0.00 0.00 2.15
2020 2114 6.015095 TCGTATAGATTCCAATGCAGACTCAT 60.015 38.462 0.00 0.00 0.00 2.90
2021 2115 5.301805 TCGTATAGATTCCAATGCAGACTCA 59.698 40.000 0.00 0.00 0.00 3.41
2022 2116 5.773575 TCGTATAGATTCCAATGCAGACTC 58.226 41.667 0.00 0.00 0.00 3.36
2023 2117 5.279206 CCTCGTATAGATTCCAATGCAGACT 60.279 44.000 0.00 0.00 0.00 3.24
2024 2118 4.926238 CCTCGTATAGATTCCAATGCAGAC 59.074 45.833 0.00 0.00 0.00 3.51
2025 2119 4.832823 TCCTCGTATAGATTCCAATGCAGA 59.167 41.667 0.00 0.00 0.00 4.26
2026 2120 5.139435 TCCTCGTATAGATTCCAATGCAG 57.861 43.478 0.00 0.00 0.00 4.41
2027 2121 4.588951 ACTCCTCGTATAGATTCCAATGCA 59.411 41.667 0.00 0.00 0.00 3.96
2028 2122 5.140747 ACTCCTCGTATAGATTCCAATGC 57.859 43.478 0.00 0.00 0.00 3.56
2056 2150 9.527157 TCATTGTGATACTCCCTTCATTTTTAA 57.473 29.630 0.00 0.00 0.00 1.52
2057 2151 9.527157 TTCATTGTGATACTCCCTTCATTTTTA 57.473 29.630 0.00 0.00 0.00 1.52
2058 2152 8.421249 TTCATTGTGATACTCCCTTCATTTTT 57.579 30.769 0.00 0.00 0.00 1.94
2059 2153 8.599624 ATTCATTGTGATACTCCCTTCATTTT 57.400 30.769 0.00 0.00 0.00 1.82
2060 2154 7.286316 GGATTCATTGTGATACTCCCTTCATTT 59.714 37.037 0.00 0.00 0.00 2.32
2061 2155 6.774656 GGATTCATTGTGATACTCCCTTCATT 59.225 38.462 0.00 0.00 0.00 2.57
2062 2156 6.302269 GGATTCATTGTGATACTCCCTTCAT 58.698 40.000 0.00 0.00 0.00 2.57
2063 2157 5.684704 GGATTCATTGTGATACTCCCTTCA 58.315 41.667 0.00 0.00 0.00 3.02
2064 2158 4.752101 CGGATTCATTGTGATACTCCCTTC 59.248 45.833 0.00 0.00 0.00 3.46
2065 2159 4.164221 ACGGATTCATTGTGATACTCCCTT 59.836 41.667 0.00 0.00 0.00 3.95
2066 2160 3.711704 ACGGATTCATTGTGATACTCCCT 59.288 43.478 0.00 0.00 0.00 4.20
2067 2161 4.058817 GACGGATTCATTGTGATACTCCC 58.941 47.826 0.00 0.00 0.00 4.30
2068 2162 4.058817 GGACGGATTCATTGTGATACTCC 58.941 47.826 0.00 0.00 0.00 3.85
2069 2163 3.736252 CGGACGGATTCATTGTGATACTC 59.264 47.826 0.00 0.00 0.00 2.59
2070 2164 3.132289 ACGGACGGATTCATTGTGATACT 59.868 43.478 0.00 0.00 0.00 2.12
2071 2165 3.454375 ACGGACGGATTCATTGTGATAC 58.546 45.455 0.00 0.00 0.00 2.24
2072 2166 3.812156 ACGGACGGATTCATTGTGATA 57.188 42.857 0.00 0.00 0.00 2.15
2073 2167 2.691409 ACGGACGGATTCATTGTGAT 57.309 45.000 0.00 0.00 0.00 3.06
2074 2168 2.028476 AGAACGGACGGATTCATTGTGA 60.028 45.455 0.00 0.00 0.00 3.58
2075 2169 2.346803 AGAACGGACGGATTCATTGTG 58.653 47.619 0.00 0.00 0.00 3.33
2076 2170 2.762535 AGAACGGACGGATTCATTGT 57.237 45.000 0.00 0.00 0.00 2.71
2077 2171 3.435327 TGAAAGAACGGACGGATTCATTG 59.565 43.478 0.00 0.00 0.00 2.82
2078 2172 3.670625 TGAAAGAACGGACGGATTCATT 58.329 40.909 0.00 0.00 0.00 2.57
2079 2173 3.056107 TCTGAAAGAACGGACGGATTCAT 60.056 43.478 0.00 0.00 42.31 2.57
2080 2174 2.297880 TCTGAAAGAACGGACGGATTCA 59.702 45.455 0.00 0.98 42.31 2.57
2121 2215 2.416747 TGTCCACGAAAGCTCATTGAG 58.583 47.619 9.40 9.40 0.00 3.02
2126 2220 1.412710 AGTCTTGTCCACGAAAGCTCA 59.587 47.619 0.00 0.00 0.00 4.26
2142 2244 3.471680 GAACTCAACTCCTTTGCAGTCT 58.528 45.455 0.00 0.00 34.88 3.24
2143 2245 2.221981 CGAACTCAACTCCTTTGCAGTC 59.778 50.000 0.00 0.00 34.88 3.51
2152 2254 0.241481 ACTCGCTCGAACTCAACTCC 59.759 55.000 0.00 0.00 0.00 3.85
2172 2274 4.678044 CGAGCCTAGCTAGTTCAACATTCA 60.678 45.833 19.31 0.00 39.88 2.57
2173 2275 3.799420 CGAGCCTAGCTAGTTCAACATTC 59.201 47.826 19.31 3.88 39.88 2.67
2174 2276 3.430929 CCGAGCCTAGCTAGTTCAACATT 60.431 47.826 19.31 0.00 39.88 2.71
2175 2277 2.101582 CCGAGCCTAGCTAGTTCAACAT 59.898 50.000 19.31 0.00 39.88 2.71
2176 2278 1.476891 CCGAGCCTAGCTAGTTCAACA 59.523 52.381 19.31 0.00 39.88 3.33
2177 2279 1.803252 GCCGAGCCTAGCTAGTTCAAC 60.803 57.143 19.31 7.71 39.88 3.18
2178 2280 0.460311 GCCGAGCCTAGCTAGTTCAA 59.540 55.000 19.31 0.00 39.88 2.69
2226 2328 1.644509 TAGCTTGACCTTGAGCTCCA 58.355 50.000 12.15 0.00 45.68 3.86
2228 2330 6.372937 ACTTTTTATAGCTTGACCTTGAGCTC 59.627 38.462 6.82 6.82 45.68 4.09
2258 2360 4.393990 TGAGAACATTACAAGCTGAGCATG 59.606 41.667 7.39 7.87 33.24 4.06
2348 2450 6.169557 TGTTGTGTGTGTCCTATCTAGTTT 57.830 37.500 0.00 0.00 0.00 2.66
2464 2568 9.517609 CACGATCTTTTGCTATTAAGTAGTACT 57.482 33.333 0.00 0.00 32.72 2.73
2508 2612 3.385755 AGAGCAGATGCACCTTTGTTTTT 59.614 39.130 7.68 0.00 45.16 1.94
2577 2682 5.068329 GGAGAAAAATTAGGCCTCAAGATGG 59.932 44.000 9.68 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.