Multiple sequence alignment - TraesCS5D01G153300

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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 TraesCS5D01G153300 chr5D 100.000 2288 0 0 1 2288 241952697 241950410 0.000000e+00 4226.0
1 TraesCS5D01G153300 chr5D 97.727 44 1 0 319 362 241952342 241952299 2.440000e-10 76.8
2 TraesCS5D01G153300 chr5D 97.727 44 1 0 356 399 241952379 241952336 2.440000e-10 76.8
3 TraesCS5D01G153300 chr5A 94.485 1632 69 9 356 1978 311944438 311942819 0.000000e+00 2495.0
4 TraesCS5D01G153300 chr5A 89.239 381 22 4 1 362 311944775 311944395 2.070000e-125 459.0
5 TraesCS5D01G153300 chr5A 89.865 148 4 4 2150 2286 311941352 311941205 1.810000e-41 180.0
6 TraesCS5D01G153300 chr5A 75.145 346 73 13 953 1290 81480876 81481216 1.420000e-32 150.0
7 TraesCS5D01G153300 chr5A 74.928 347 78 7 953 1293 142845117 142845460 1.420000e-32 150.0
8 TraesCS5D01G153300 chr5A 94.521 73 3 1 2032 2103 311941405 311941333 6.680000e-21 111.0
9 TraesCS5D01G153300 chr5B 88.920 713 65 12 1395 2103 256904967 256904265 0.000000e+00 867.0
10 TraesCS5D01G153300 chr5B 88.129 497 47 4 905 1398 256914389 256913902 4.240000e-162 580.0
11 TraesCS5D01G153300 chr5B 85.740 547 54 7 374 909 256914874 256914341 7.140000e-155 556.0
12 TraesCS5D01G153300 chr5B 92.405 79 6 0 2150 2228 256904284 256904206 1.860000e-21 113.0
13 TraesCS5D01G153300 chr7A 87.603 363 35 7 955 1314 110476768 110477123 1.640000e-111 412.0
14 TraesCS5D01G153300 chr7B 90.228 307 27 2 953 1256 64122252 64122558 4.580000e-107 398.0
15 TraesCS5D01G153300 chr6D 81.818 363 62 4 960 1319 37907263 37907624 3.690000e-78 302.0
16 TraesCS5D01G153300 chr1D 81.717 361 57 8 964 1315 241261043 241260683 2.220000e-75 292.0
17 TraesCS5D01G153300 chr4B 80.812 271 39 5 1055 1315 570102938 570102671 1.390000e-47 200.0


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 TraesCS5D01G153300 chr5D 241950410 241952697 2287 True 1459.866667 4226 98.484667 1 2288 3 chr5D.!!$R1 2287
1 TraesCS5D01G153300 chr5A 311941205 311944775 3570 True 811.250000 2495 92.027500 1 2286 4 chr5A.!!$R1 2285
2 TraesCS5D01G153300 chr5B 256913902 256914874 972 True 568.000000 580 86.934500 374 1398 2 chr5B.!!$R2 1024
3 TraesCS5D01G153300 chr5B 256904206 256904967 761 True 490.000000 867 90.662500 1395 2228 2 chr5B.!!$R1 833

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
78 80 0.597377 CAAGCAAAGCCGGTGGTTTC 60.597 55.0 1.9 0.0 40.06 2.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1917 1960 0.31812 CCAAAAGCGCTGGGTTTCAT 59.682 50.0 12.58 0.0 42.66 2.57 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
33 34 7.255486 GCTCAAAGTAGGTTTACCAGACAAAAT 60.255 37.037 1.13 0.00 38.89 1.82
52 54 8.877864 ACAAAATGATAAGTCTAACATTCCCA 57.122 30.769 0.00 0.00 31.34 4.37
76 78 2.498056 CCAAGCAAAGCCGGTGGTT 61.498 57.895 1.90 2.20 37.18 3.67
78 80 0.597377 CAAGCAAAGCCGGTGGTTTC 60.597 55.000 1.90 0.00 40.06 2.78
110 112 5.056480 GGCCAGCTAAAACAAAAGTTTCAT 58.944 37.500 0.00 0.00 0.00 2.57
118 120 9.849607 GCTAAAACAAAAGTTTCATTAAAGAGC 57.150 29.630 0.00 0.00 0.00 4.09
200 220 9.859692 CGAATACCCTCGTTTAAAAGAATAATC 57.140 33.333 5.35 1.69 34.08 1.75
203 223 6.175471 ACCCTCGTTTAAAAGAATAATCCGT 58.825 36.000 5.35 0.00 0.00 4.69
209 229 8.557864 TCGTTTAAAAGAATAATCCGTTGAACA 58.442 29.630 1.03 0.00 0.00 3.18
218 238 9.463443 AGAATAATCCGTTGAACAAAGAAAAAG 57.537 29.630 0.00 0.00 0.00 2.27
228 248 7.467557 TGAACAAAGAAAAAGCACATTCATC 57.532 32.000 0.00 0.00 0.00 2.92
302 322 8.733092 TCTGAGGATCCTTTATAGATGTTGAT 57.267 34.615 17.42 0.00 0.00 2.57
322 342 6.867519 TGATCTTTATCCAACTACCAGTCA 57.132 37.500 0.00 0.00 0.00 3.41
323 343 7.252612 TGATCTTTATCCAACTACCAGTCAA 57.747 36.000 0.00 0.00 0.00 3.18
324 344 7.861629 TGATCTTTATCCAACTACCAGTCAAT 58.138 34.615 0.00 0.00 0.00 2.57
325 345 8.328758 TGATCTTTATCCAACTACCAGTCAATT 58.671 33.333 0.00 0.00 0.00 2.32
326 346 8.738645 ATCTTTATCCAACTACCAGTCAATTC 57.261 34.615 0.00 0.00 0.00 2.17
327 347 7.685481 TCTTTATCCAACTACCAGTCAATTCA 58.315 34.615 0.00 0.00 0.00 2.57
328 348 7.606456 TCTTTATCCAACTACCAGTCAATTCAC 59.394 37.037 0.00 0.00 0.00 3.18
329 349 4.015872 TCCAACTACCAGTCAATTCACC 57.984 45.455 0.00 0.00 0.00 4.02
330 350 3.650942 TCCAACTACCAGTCAATTCACCT 59.349 43.478 0.00 0.00 0.00 4.00
331 351 4.841813 TCCAACTACCAGTCAATTCACCTA 59.158 41.667 0.00 0.00 0.00 3.08
332 352 5.046591 TCCAACTACCAGTCAATTCACCTAG 60.047 44.000 0.00 0.00 0.00 3.02
333 353 5.046591 CCAACTACCAGTCAATTCACCTAGA 60.047 44.000 0.00 0.00 0.00 2.43
334 354 6.464222 CAACTACCAGTCAATTCACCTAGAA 58.536 40.000 0.00 0.00 41.28 2.10
336 356 6.879400 ACTACCAGTCAATTCACCTAGAATC 58.121 40.000 0.00 0.00 46.09 2.52
337 357 5.104259 ACCAGTCAATTCACCTAGAATCC 57.896 43.478 0.00 0.00 46.09 3.01
338 358 4.785376 ACCAGTCAATTCACCTAGAATCCT 59.215 41.667 0.00 0.00 46.09 3.24
339 359 5.964477 ACCAGTCAATTCACCTAGAATCCTA 59.036 40.000 0.00 0.00 46.09 2.94
340 360 6.098982 ACCAGTCAATTCACCTAGAATCCTAG 59.901 42.308 0.00 0.00 46.09 3.02
341 361 6.325028 CCAGTCAATTCACCTAGAATCCTAGA 59.675 42.308 0.00 0.00 46.09 2.43
342 362 7.016072 CCAGTCAATTCACCTAGAATCCTAGAT 59.984 40.741 0.00 0.00 46.09 1.98
343 363 9.083422 CAGTCAATTCACCTAGAATCCTAGATA 57.917 37.037 0.00 0.00 46.09 1.98
344 364 9.661954 AGTCAATTCACCTAGAATCCTAGATAA 57.338 33.333 0.00 0.00 46.09 1.75
527 547 4.334203 GTGAGTGATGTGTGTGTTTGGTTA 59.666 41.667 0.00 0.00 0.00 2.85
559 580 1.303282 GAAAGTCCCGGCCCAATCT 59.697 57.895 0.00 0.00 0.00 2.40
617 638 1.270358 ACTCCTCTGAAGCCGTTGAAC 60.270 52.381 0.00 0.00 0.00 3.18
646 667 4.144297 CACTTCAAAGTTCAGGGGATTGA 58.856 43.478 0.00 0.00 37.08 2.57
710 731 4.164843 AGTTTCACTAGGCTTTGTTCCA 57.835 40.909 0.00 0.00 0.00 3.53
864 895 4.760204 AGCCCATTGAACAAACAGTACTAC 59.240 41.667 0.00 0.00 0.00 2.73
895 926 7.684670 TGCTTTGTCATATAAAGAACATCGTC 58.315 34.615 0.00 0.00 37.33 4.20
896 927 7.333174 TGCTTTGTCATATAAAGAACATCGTCA 59.667 33.333 0.00 0.00 37.33 4.35
914 945 9.431887 ACATCGTCATAAAACTTACTATTGTGT 57.568 29.630 0.00 0.00 0.00 3.72
938 969 5.109210 TGCTCTATTGTACAAGGAACATCG 58.891 41.667 14.65 4.37 0.00 3.84
969 1000 0.953960 CTACGGCGGAAACTTTGGCT 60.954 55.000 13.24 0.00 0.00 4.75
1381 1415 4.821260 TGTATTGCTGCAGAACTGAAAAGA 59.179 37.500 20.43 0.00 0.00 2.52
1489 1525 0.108992 AAGCATTGTTCGCATGCCAG 60.109 50.000 13.15 0.00 41.88 4.85
1490 1526 2.162754 GCATTGTTCGCATGCCAGC 61.163 57.895 13.15 1.26 35.44 4.85
1728 1771 0.452184 CATGCACTAGTCGACGAGGT 59.548 55.000 26.31 15.86 0.00 3.85
1806 1849 2.203280 CCACCTTCGTTGTGGCCA 60.203 61.111 0.00 0.00 46.13 5.36
1856 1899 1.836802 GGGAGAGAGGAGCAACTCATT 59.163 52.381 9.87 0.00 39.97 2.57
1926 1969 3.266477 TTGATTCCCCAATGAAACCCA 57.734 42.857 0.00 0.00 0.00 4.51
1927 1970 2.818921 TGATTCCCCAATGAAACCCAG 58.181 47.619 0.00 0.00 0.00 4.45
1928 1971 1.482182 GATTCCCCAATGAAACCCAGC 59.518 52.381 0.00 0.00 0.00 4.85
1929 1972 0.897863 TTCCCCAATGAAACCCAGCG 60.898 55.000 0.00 0.00 0.00 5.18
1930 1973 2.573340 CCCAATGAAACCCAGCGC 59.427 61.111 0.00 0.00 0.00 5.92
1931 1974 1.978617 CCCAATGAAACCCAGCGCT 60.979 57.895 2.64 2.64 0.00 5.92
1932 1975 1.535204 CCCAATGAAACCCAGCGCTT 61.535 55.000 7.50 0.00 0.00 4.68
1933 1976 0.318120 CCAATGAAACCCAGCGCTTT 59.682 50.000 7.50 0.00 0.00 3.51
1934 1977 1.270252 CCAATGAAACCCAGCGCTTTT 60.270 47.619 7.50 6.14 0.00 2.27
1935 1978 1.794116 CAATGAAACCCAGCGCTTTTG 59.206 47.619 7.50 0.66 0.00 2.44
1936 1979 0.318120 ATGAAACCCAGCGCTTTTGG 59.682 50.000 7.50 11.90 35.41 3.28
1937 1980 0.753479 TGAAACCCAGCGCTTTTGGA 60.753 50.000 20.93 1.76 37.96 3.53
1938 1981 0.387565 GAAACCCAGCGCTTTTGGAA 59.612 50.000 20.93 0.00 37.96 3.53
1939 1982 0.389025 AAACCCAGCGCTTTTGGAAG 59.611 50.000 20.93 6.63 37.96 3.46
1940 1983 1.463553 AACCCAGCGCTTTTGGAAGG 61.464 55.000 20.93 11.86 37.96 3.46
1941 1984 2.639327 CCCAGCGCTTTTGGAAGGG 61.639 63.158 7.50 10.25 45.70 3.95
1942 1985 1.603455 CCAGCGCTTTTGGAAGGGA 60.603 57.895 7.50 0.00 45.78 4.20
1943 1986 1.581447 CAGCGCTTTTGGAAGGGAC 59.419 57.895 7.50 0.12 45.78 4.46
1944 1987 1.603739 AGCGCTTTTGGAAGGGACC 60.604 57.895 2.64 0.00 45.78 4.46
1945 1988 2.978018 GCGCTTTTGGAAGGGACCG 61.978 63.158 0.00 0.00 45.78 4.79
1946 1989 2.332654 CGCTTTTGGAAGGGACCGG 61.333 63.158 0.00 0.00 45.78 5.28
1947 1990 2.636412 GCTTTTGGAAGGGACCGGC 61.636 63.158 0.00 0.00 33.34 6.13
1948 1991 1.977009 CTTTTGGAAGGGACCGGCC 60.977 63.158 0.00 3.33 0.00 6.13
1949 1992 3.853698 TTTTGGAAGGGACCGGCCG 62.854 63.158 21.04 21.04 37.63 6.13
1957 2000 3.384532 GGACCGGCCGAGGTGTAA 61.385 66.667 30.73 0.00 46.09 2.41
1958 2001 2.125793 GACCGGCCGAGGTGTAAC 60.126 66.667 30.73 0.48 46.09 2.50
1987 2030 2.555325 GGGTTTAACCAAAGAGAACCCG 59.445 50.000 16.58 0.00 46.95 5.28
1988 2031 2.555325 GGTTTAACCAAAGAGAACCCGG 59.445 50.000 9.56 0.00 38.42 5.73
2005 2106 0.746563 CGGCGCTTTTGGAAGGGATA 60.747 55.000 7.64 0.00 45.78 2.59
2064 3587 1.484240 AGAGATACCAAGCTCACCTGC 59.516 52.381 0.00 0.00 40.75 4.85
2078 3601 1.607178 CCTGCATTTCACCCCAGCA 60.607 57.895 0.00 0.00 0.00 4.41
2079 3602 1.888018 CTGCATTTCACCCCAGCAG 59.112 57.895 0.00 0.00 45.44 4.24
2090 3613 4.362476 CCAGCAGGGCAAAACCGC 62.362 66.667 0.00 0.00 40.62 5.68
2091 3614 3.297620 CAGCAGGGCAAAACCGCT 61.298 61.111 0.00 0.00 40.62 5.52
2092 3615 3.297620 AGCAGGGCAAAACCGCTG 61.298 61.111 2.34 2.34 40.62 5.18
2093 3616 4.362476 GCAGGGCAAAACCGCTGG 62.362 66.667 8.06 0.00 40.62 4.85
2094 3617 3.683937 CAGGGCAAAACCGCTGGG 61.684 66.667 0.00 0.00 40.62 4.45
2104 3627 2.511600 CCGCTGGGTTCGATCACC 60.512 66.667 0.00 0.00 35.88 4.02
2105 3628 2.264480 CGCTGGGTTCGATCACCA 59.736 61.111 8.50 5.93 38.79 4.17
2106 3629 2.100631 CGCTGGGTTCGATCACCAC 61.101 63.158 8.50 0.00 38.79 4.16
2107 3630 1.003839 GCTGGGTTCGATCACCACA 60.004 57.895 8.50 3.58 38.79 4.17
2108 3631 0.392998 GCTGGGTTCGATCACCACAT 60.393 55.000 8.50 0.00 38.79 3.21
2109 3632 1.372582 CTGGGTTCGATCACCACATG 58.627 55.000 8.50 0.00 38.79 3.21
2110 3633 0.980423 TGGGTTCGATCACCACATGA 59.020 50.000 8.50 0.00 43.13 3.07
2111 3634 1.338674 TGGGTTCGATCACCACATGAC 60.339 52.381 8.50 0.00 41.24 3.06
2112 3635 1.338674 GGGTTCGATCACCACATGACA 60.339 52.381 8.50 0.00 41.24 3.58
2113 3636 1.732259 GGTTCGATCACCACATGACAC 59.268 52.381 0.00 0.00 41.24 3.67
2114 3637 2.412870 GTTCGATCACCACATGACACA 58.587 47.619 0.00 0.00 41.24 3.72
2115 3638 3.002791 GTTCGATCACCACATGACACAT 58.997 45.455 0.00 0.00 41.24 3.21
2116 3639 2.620242 TCGATCACCACATGACACATG 58.380 47.619 0.00 9.72 41.24 3.21
2117 3640 2.028203 TCGATCACCACATGACACATGT 60.028 45.455 10.94 10.94 41.24 3.21
2118 3641 2.094734 CGATCACCACATGACACATGTG 59.905 50.000 27.39 27.39 46.49 3.21
2129 3652 7.268199 ACATGACACATGTGATAATCAATCC 57.732 36.000 31.94 7.88 33.22 3.01
2130 3653 6.829811 ACATGACACATGTGATAATCAATCCA 59.170 34.615 31.94 12.45 33.22 3.41
2131 3654 7.339976 ACATGACACATGTGATAATCAATCCAA 59.660 33.333 31.94 2.80 33.22 3.53
2132 3655 7.700022 TGACACATGTGATAATCAATCCAAA 57.300 32.000 31.94 0.00 33.22 3.28
2133 3656 7.537715 TGACACATGTGATAATCAATCCAAAC 58.462 34.615 31.94 1.41 33.22 2.93
2134 3657 7.176340 TGACACATGTGATAATCAATCCAAACA 59.824 33.333 31.94 3.76 33.22 2.83
2135 3658 7.894708 ACACATGTGATAATCAATCCAAACAA 58.105 30.769 31.94 0.00 33.22 2.83
2136 3659 8.533657 ACACATGTGATAATCAATCCAAACAAT 58.466 29.630 31.94 0.00 33.22 2.71
2137 3660 9.373603 CACATGTGATAATCAATCCAAACAATT 57.626 29.630 21.64 0.00 33.22 2.32
2138 3661 9.590451 ACATGTGATAATCAATCCAAACAATTC 57.410 29.630 0.00 0.00 33.22 2.17
2139 3662 9.589111 CATGTGATAATCAATCCAAACAATTCA 57.411 29.630 0.00 0.00 33.22 2.57
2141 3664 9.993454 TGTGATAATCAATCCAAACAATTCAAA 57.007 25.926 0.00 0.00 33.22 2.69
2147 3670 9.835389 AATCAATCCAAACAATTCAAAAGAAGA 57.165 25.926 0.00 0.00 0.00 2.87
2148 3671 9.835389 ATCAATCCAAACAATTCAAAAGAAGAA 57.165 25.926 0.00 0.00 0.00 2.52
2234 3757 1.182667 CCTCGGGGATTTTGGTTTCC 58.817 55.000 0.00 0.00 33.58 3.13
2280 3812 9.333724 CTAACCGGTGACCACTTTATTATATTT 57.666 33.333 8.52 0.00 0.00 1.40
2282 3814 9.683870 AACCGGTGACCACTTTATTATATTTAA 57.316 29.630 8.52 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 8.706322 ATCATTTTGTCTGGTAAACCTACTTT 57.294 30.769 0.02 0.00 36.82 2.66
33 34 5.957771 AGCTGGGAATGTTAGACTTATCA 57.042 39.130 0.00 0.00 0.00 2.15
70 72 1.154197 GCCGTGACTAAGAAACCACC 58.846 55.000 0.00 0.00 0.00 4.61
76 78 1.552578 TAGCTGGCCGTGACTAAGAA 58.447 50.000 0.00 0.00 0.00 2.52
78 80 2.380084 TTTAGCTGGCCGTGACTAAG 57.620 50.000 0.00 0.00 0.00 2.18
110 112 4.553330 ATTCCTTGAGGACGCTCTTTAA 57.447 40.909 0.00 0.00 45.39 1.52
146 166 3.556004 GGATGGTAGCTCTGGAATAGCAC 60.556 52.174 0.00 0.00 42.62 4.40
151 171 2.224719 GCATGGATGGTAGCTCTGGAAT 60.225 50.000 0.00 0.00 0.00 3.01
155 175 1.590932 GTGCATGGATGGTAGCTCTG 58.409 55.000 0.00 0.00 0.00 3.35
200 220 3.923461 TGTGCTTTTTCTTTGTTCAACGG 59.077 39.130 0.00 0.00 0.00 4.44
203 223 7.765360 AGATGAATGTGCTTTTTCTTTGTTCAA 59.235 29.630 0.00 0.00 0.00 2.69
228 248 0.527385 CAACCGTTTTGCACCCACAG 60.527 55.000 0.00 0.00 0.00 3.66
277 297 8.733092 ATCAACATCTATAAAGGATCCTCAGA 57.267 34.615 16.52 15.11 0.00 3.27
302 322 7.606456 GTGAATTGACTGGTAGTTGGATAAAGA 59.394 37.037 0.00 0.00 0.00 2.52
307 327 4.289672 AGGTGAATTGACTGGTAGTTGGAT 59.710 41.667 0.00 0.00 0.00 3.41
310 330 6.037786 TCTAGGTGAATTGACTGGTAGTTG 57.962 41.667 0.00 0.00 0.00 3.16
352 372 9.661954 TCTAGGATTCTAGGTGAATTGACTATT 57.338 33.333 8.25 0.00 44.70 1.73
353 373 9.836179 ATCTAGGATTCTAGGTGAATTGACTAT 57.164 33.333 8.25 0.00 44.70 2.12
355 375 9.661954 TTATCTAGGATTCTAGGTGAATTGACT 57.338 33.333 8.25 0.00 44.70 3.41
399 419 1.341531 GATGTAGGTGGGTCCATCTCG 59.658 57.143 5.98 0.00 38.50 4.04
437 457 6.332735 AGACCTCAACTTTAAAAGGAATGC 57.667 37.500 10.08 0.00 32.99 3.56
544 565 2.070650 GGTAGATTGGGCCGGGACT 61.071 63.158 2.18 0.00 0.00 3.85
617 638 3.243068 CCTGAACTTTGAAGTGGGTTTCG 60.243 47.826 0.00 0.00 39.66 3.46
646 667 9.911788 AATTAGGTTGATCTCATACTTGTGAAT 57.088 29.630 0.00 0.00 0.00 2.57
864 895 6.426980 TCTTTATATGACAAAGCAGCACAG 57.573 37.500 0.00 0.00 33.82 3.66
914 945 5.580691 CGATGTTCCTTGTACAATAGAGCAA 59.419 40.000 21.11 10.74 0.00 3.91
921 952 7.660208 AGTTTTCTACGATGTTCCTTGTACAAT 59.340 33.333 9.13 0.00 0.00 2.71
938 969 4.096732 TCCGCCGTAGTAAGTTTTCTAC 57.903 45.455 7.45 7.45 34.84 2.59
955 986 0.519077 CTGAGAGCCAAAGTTTCCGC 59.481 55.000 0.00 0.00 0.00 5.54
969 1000 0.537188 GGGCAAGACCGAATCTGAGA 59.463 55.000 0.00 0.00 37.88 3.27
1089 1120 5.119588 GGAATGATAACAGTCGTCGAAAACA 59.880 40.000 0.00 0.00 41.27 2.83
1331 1365 5.248640 ACACAGCAGTACTTGAAAGCATAT 58.751 37.500 1.53 0.00 0.00 1.78
1332 1366 4.641396 ACACAGCAGTACTTGAAAGCATA 58.359 39.130 1.53 0.00 0.00 3.14
1349 1383 3.003585 TCTGCAGCAATACAACAACACAG 59.996 43.478 9.47 0.00 0.00 3.66
1489 1525 6.139048 TGGAACCTGTAAGTTTTTAAGTGC 57.861 37.500 0.00 0.00 0.00 4.40
1490 1526 7.540299 TGTTGGAACCTGTAAGTTTTTAAGTG 58.460 34.615 0.00 0.00 0.00 3.16
1584 1627 5.717119 ATTCTGAACTACCCTATGGCTTT 57.283 39.130 0.00 0.00 33.59 3.51
1728 1771 1.545614 GACTTTCGCGAGCGTGTCAA 61.546 55.000 23.20 0.00 40.74 3.18
1806 1849 3.003113 GCGAACCCTAGGCGACAGT 62.003 63.158 11.00 0.00 0.00 3.55
1917 1960 0.318120 CCAAAAGCGCTGGGTTTCAT 59.682 50.000 12.58 0.00 42.66 2.57
1926 1969 1.603739 GGTCCCTTCCAAAAGCGCT 60.604 57.895 2.64 2.64 0.00 5.92
1927 1970 2.962569 GGTCCCTTCCAAAAGCGC 59.037 61.111 0.00 0.00 0.00 5.92
1928 1971 2.332654 CCGGTCCCTTCCAAAAGCG 61.333 63.158 0.00 0.00 0.00 4.68
1929 1972 2.636412 GCCGGTCCCTTCCAAAAGC 61.636 63.158 1.90 0.00 0.00 3.51
1930 1973 1.977009 GGCCGGTCCCTTCCAAAAG 60.977 63.158 1.90 0.00 0.00 2.27
1931 1974 2.116556 GGCCGGTCCCTTCCAAAA 59.883 61.111 1.90 0.00 0.00 2.44
1932 1975 4.338710 CGGCCGGTCCCTTCCAAA 62.339 66.667 20.10 0.00 0.00 3.28
1940 1983 3.384532 TTACACCTCGGCCGGTCC 61.385 66.667 27.83 2.02 34.29 4.46
1941 1984 2.125793 GTTACACCTCGGCCGGTC 60.126 66.667 27.83 0.00 34.29 4.79
1942 1985 3.698820 GGTTACACCTCGGCCGGT 61.699 66.667 27.83 17.80 37.93 5.28
1943 1986 4.462280 GGGTTACACCTCGGCCGG 62.462 72.222 27.83 16.14 38.64 6.13
1944 1987 3.697747 TGGGTTACACCTCGGCCG 61.698 66.667 22.12 22.12 38.64 6.13
1945 1988 2.046604 GTGGGTTACACCTCGGCC 60.047 66.667 0.00 0.00 44.49 6.13
1959 2002 2.688958 TCTTTGGTTAAACCCAACGTGG 59.311 45.455 0.00 0.00 44.03 4.94
1960 2003 3.628487 TCTCTTTGGTTAAACCCAACGTG 59.372 43.478 0.00 0.00 44.03 4.49
1961 2004 3.888583 TCTCTTTGGTTAAACCCAACGT 58.111 40.909 0.00 0.00 44.03 3.99
1962 2005 4.498513 GGTTCTCTTTGGTTAAACCCAACG 60.499 45.833 0.00 0.00 44.03 4.10
1963 2006 4.940463 GGTTCTCTTTGGTTAAACCCAAC 58.060 43.478 0.00 0.00 44.03 3.77
1967 2010 2.555325 CCGGGTTCTCTTTGGTTAAACC 59.445 50.000 0.00 0.00 38.90 3.27
1968 2011 2.030540 GCCGGGTTCTCTTTGGTTAAAC 60.031 50.000 2.18 0.00 0.00 2.01
1969 2012 2.232399 GCCGGGTTCTCTTTGGTTAAA 58.768 47.619 2.18 0.00 0.00 1.52
1970 2013 1.878948 CGCCGGGTTCTCTTTGGTTAA 60.879 52.381 2.18 0.00 0.00 2.01
1971 2014 0.320946 CGCCGGGTTCTCTTTGGTTA 60.321 55.000 2.18 0.00 0.00 2.85
1972 2015 1.599797 CGCCGGGTTCTCTTTGGTT 60.600 57.895 2.18 0.00 0.00 3.67
1973 2016 2.032071 CGCCGGGTTCTCTTTGGT 59.968 61.111 2.18 0.00 0.00 3.67
1974 2017 3.431725 GCGCCGGGTTCTCTTTGG 61.432 66.667 2.18 0.00 0.00 3.28
1975 2018 1.515521 AAAGCGCCGGGTTCTCTTTG 61.516 55.000 2.29 0.00 32.40 2.77
1976 2019 0.822121 AAAAGCGCCGGGTTCTCTTT 60.822 50.000 2.29 0.00 32.40 2.52
1977 2020 1.228154 AAAAGCGCCGGGTTCTCTT 60.228 52.632 2.29 0.00 32.40 2.85
1978 2021 1.966451 CAAAAGCGCCGGGTTCTCT 60.966 57.895 2.29 0.00 32.40 3.10
1979 2022 2.561373 CAAAAGCGCCGGGTTCTC 59.439 61.111 2.29 0.00 32.40 2.87
1980 2023 2.969300 TTCCAAAAGCGCCGGGTTCT 62.969 55.000 2.29 0.00 32.40 3.01
1981 2024 2.472232 CTTCCAAAAGCGCCGGGTTC 62.472 60.000 2.29 0.00 32.40 3.62
1982 2025 2.519780 TTCCAAAAGCGCCGGGTT 60.520 55.556 2.29 0.00 34.82 4.11
1983 2026 2.983592 CTTCCAAAAGCGCCGGGT 60.984 61.111 2.29 0.00 0.00 5.28
1984 2027 3.747976 CCTTCCAAAAGCGCCGGG 61.748 66.667 2.29 0.00 0.00 5.73
1985 2028 3.747976 CCCTTCCAAAAGCGCCGG 61.748 66.667 2.29 0.00 0.00 6.13
1986 2029 0.746563 TATCCCTTCCAAAAGCGCCG 60.747 55.000 2.29 0.00 0.00 6.46
1987 2030 1.025041 CTATCCCTTCCAAAAGCGCC 58.975 55.000 2.29 0.00 0.00 6.53
1988 2031 1.025041 CCTATCCCTTCCAAAAGCGC 58.975 55.000 0.00 0.00 0.00 5.92
2024 2125 4.714632 TCTCTCTTTGGTTAAACCCACAG 58.285 43.478 0.00 0.00 37.50 3.66
2078 3601 4.218686 ACCCAGCGGTTTTGCCCT 62.219 61.111 0.00 0.00 40.58 5.19
2087 3610 2.511600 GGTGATCGAACCCAGCGG 60.512 66.667 0.00 0.00 33.79 5.52
2088 3611 2.100631 GTGGTGATCGAACCCAGCG 61.101 63.158 3.84 0.00 39.70 5.18
2089 3612 0.392998 ATGTGGTGATCGAACCCAGC 60.393 55.000 3.84 6.04 39.70 4.85
2090 3613 1.066215 TCATGTGGTGATCGAACCCAG 60.066 52.381 3.84 0.00 39.70 4.45
2091 3614 0.980423 TCATGTGGTGATCGAACCCA 59.020 50.000 3.84 1.72 39.70 4.51
2092 3615 1.338674 TGTCATGTGGTGATCGAACCC 60.339 52.381 3.84 0.00 39.70 4.11
2093 3616 1.732259 GTGTCATGTGGTGATCGAACC 59.268 52.381 0.00 0.00 39.48 3.62
2094 3617 2.412870 TGTGTCATGTGGTGATCGAAC 58.587 47.619 0.00 0.00 39.48 3.95
2095 3618 2.829741 TGTGTCATGTGGTGATCGAA 57.170 45.000 0.00 0.00 39.48 3.71
2096 3619 2.028203 ACATGTGTCATGTGGTGATCGA 60.028 45.455 13.47 0.00 39.48 3.59
2097 3620 2.094734 CACATGTGTCATGTGGTGATCG 59.905 50.000 25.74 7.15 44.04 3.69
2098 3621 3.337358 TCACATGTGTCATGTGGTGATC 58.663 45.455 29.73 0.00 46.78 2.92
2099 3622 3.421919 TCACATGTGTCATGTGGTGAT 57.578 42.857 29.73 3.58 46.78 3.06
2100 3623 2.926778 TCACATGTGTCATGTGGTGA 57.073 45.000 29.73 16.30 46.78 4.02
2101 3624 5.354792 TGATTATCACATGTGTCATGTGGTG 59.645 40.000 29.73 14.32 46.78 4.17
2102 3625 5.499313 TGATTATCACATGTGTCATGTGGT 58.501 37.500 29.73 27.41 46.78 4.16
2103 3626 6.439675 TTGATTATCACATGTGTCATGTGG 57.560 37.500 29.73 17.92 46.78 4.17
2105 3628 6.829811 TGGATTGATTATCACATGTGTCATGT 59.170 34.615 24.63 12.45 34.77 3.21
2106 3629 7.266922 TGGATTGATTATCACATGTGTCATG 57.733 36.000 24.63 7.99 34.77 3.07
2107 3630 7.885009 TTGGATTGATTATCACATGTGTCAT 57.115 32.000 24.63 14.56 34.77 3.06
2108 3631 7.176340 TGTTTGGATTGATTATCACATGTGTCA 59.824 33.333 24.63 17.67 34.77 3.58
2109 3632 7.537715 TGTTTGGATTGATTATCACATGTGTC 58.462 34.615 24.63 15.33 34.77 3.67
2110 3633 7.465353 TGTTTGGATTGATTATCACATGTGT 57.535 32.000 24.63 14.61 34.77 3.72
2111 3634 8.936070 ATTGTTTGGATTGATTATCACATGTG 57.064 30.769 20.18 20.18 34.77 3.21
2112 3635 9.590451 GAATTGTTTGGATTGATTATCACATGT 57.410 29.630 0.00 0.00 34.77 3.21
2113 3636 9.589111 TGAATTGTTTGGATTGATTATCACATG 57.411 29.630 0.00 0.00 34.77 3.21
2115 3638 9.993454 TTTGAATTGTTTGGATTGATTATCACA 57.007 25.926 0.00 0.00 34.77 3.58
2121 3644 9.835389 TCTTCTTTTGAATTGTTTGGATTGATT 57.165 25.926 0.00 0.00 37.85 2.57
2122 3645 9.835389 TTCTTCTTTTGAATTGTTTGGATTGAT 57.165 25.926 0.00 0.00 37.85 2.57
2123 3646 9.664332 TTTCTTCTTTTGAATTGTTTGGATTGA 57.336 25.926 0.00 0.00 37.85 2.57


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

AutoCloner maintained by Alex Coulton.