Multiple sequence alignment - TraesCS1A01G240200

Loading Multiple Alignment...

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 TraesCS1A01G240200 chr1A 100.000 2745 0 0 1 2745 427050228 427047484 0.000000e+00 5070.0
1 TraesCS1A01G240200 chr1A 100.000 37 0 0 2030 2066 514668616 514668652 4.910000e-08 69.4
2 TraesCS1A01G240200 chr1D 90.126 2056 99 29 1 2015 330093351 330091359 0.000000e+00 2577.0
3 TraesCS1A01G240200 chr1D 90.409 563 42 4 2195 2745 330090140 330089578 0.000000e+00 730.0
4 TraesCS1A01G240200 chr1D 91.429 105 8 1 2093 2197 330091347 330091244 2.850000e-30 143.0
5 TraesCS1A01G240200 chr1B 88.699 1460 79 39 551 1970 444937759 444936346 0.000000e+00 1703.0
6 TraesCS1A01G240200 chr1B 90.992 655 40 8 2093 2745 444936275 444935638 0.000000e+00 865.0
7 TraesCS1A01G240200 chr1B 85.558 547 54 11 1 544 444942416 444941892 1.440000e-152 549.0
8 TraesCS1A01G240200 chr1B 89.412 85 8 1 2662 2745 444931781 444931697 3.740000e-19 106.0
9 TraesCS1A01G240200 chr1B 83.019 106 18 0 255 360 585693647 585693542 2.250000e-16 97.1
10 TraesCS1A01G240200 chr6A 81.290 155 27 2 209 362 356663646 356663799 1.030000e-24 124.0
11 TraesCS1A01G240200 chr7D 79.221 154 32 0 209 362 188924848 188925001 1.040000e-19 108.0
12 TraesCS1A01G240200 chr3A 84.404 109 15 2 255 362 360473234 360473127 3.740000e-19 106.0
13 TraesCS1A01G240200 chr3A 100.000 34 0 0 2033 2066 96245189 96245156 2.280000e-06 63.9
14 TraesCS1A01G240200 chr2A 81.395 129 22 2 235 362 653637822 653637695 1.340000e-18 104.0
15 TraesCS1A01G240200 chr7B 83.962 106 17 0 255 360 329891864 329891759 4.840000e-18 102.0
16 TraesCS1A01G240200 chr6B 93.617 47 3 0 2018 2064 428629223 428629177 1.360000e-08 71.3
17 TraesCS1A01G240200 chr5A 100.000 38 0 0 2029 2066 285286071 285286108 1.360000e-08 71.3
18 TraesCS1A01G240200 chr5A 97.368 38 1 0 2029 2066 413835979 413835942 6.350000e-07 65.8
19 TraesCS1A01G240200 chr7A 88.136 59 6 1 2013 2070 102331978 102331920 4.910000e-08 69.4
20 TraesCS1A01G240200 chr5B 100.000 36 0 0 2029 2064 447470848 447470883 1.760000e-07 67.6
21 TraesCS1A01G240200 chr4D 97.368 38 1 0 2029 2066 72581994 72582031 6.350000e-07 65.8
22 TraesCS1A01G240200 chr6D 94.444 36 2 0 2029 2064 412626278 412626313 3.820000e-04 56.5
23 TraesCS1A01G240200 chr3D 96.875 32 1 0 2065 2096 94041040 94041071 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 TraesCS1A01G240200 chr1A 427047484 427050228 2744 True 5070.000000 5070 100.000000 1 2745 1 chr1A.!!$R1 2744
1 TraesCS1A01G240200 chr1D 330089578 330093351 3773 True 1150.000000 2577 90.654667 1 2745 3 chr1D.!!$R1 2744
2 TraesCS1A01G240200 chr1B 444931697 444937759 6062 True 891.333333 1703 89.701000 551 2745 3 chr1B.!!$R3 2194
3 TraesCS1A01G240200 chr1B 444941892 444942416 524 True 549.000000 549 85.558000 1 544 1 chr1B.!!$R1 543

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
401 406 0.032813 CCCCCTCAATTGTCTGCCAT 60.033 55.0 5.13 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2325 3532 0.036022 GCCAACAGAGAACCTGCTCT 59.964 55.0 0.0 0.0 46.81 4.09 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
36 37 1.353022 TCCTTTGTATTCACCCGGCTT 59.647 47.619 0.00 0.00 0.00 4.35
50 51 2.338500 CCGGCTTACACAAGAGAGAAC 58.662 52.381 0.00 0.00 33.20 3.01
100 102 1.674651 GAACAGGGGGCTCGAAACC 60.675 63.158 0.00 0.00 0.00 3.27
170 172 3.125316 GTGTCTTGCCTCTACAAAATCCG 59.875 47.826 0.00 0.00 0.00 4.18
198 200 5.022282 TCATGAGTATTGCCTCGAAATCA 57.978 39.130 0.00 0.00 34.04 2.57
252 254 8.928448 TCTATGCTTATAGTTCAACCTCTCAAT 58.072 33.333 0.00 0.00 0.00 2.57
253 255 9.202273 CTATGCTTATAGTTCAACCTCTCAATC 57.798 37.037 0.00 0.00 0.00 2.67
255 257 5.463724 GCTTATAGTTCAACCTCTCAATCGG 59.536 44.000 0.00 0.00 0.00 4.18
266 268 3.445096 CCTCTCAATCGGAATTTGCCTTT 59.555 43.478 0.00 0.00 0.00 3.11
267 269 4.439289 CCTCTCAATCGGAATTTGCCTTTC 60.439 45.833 0.00 0.00 0.00 2.62
278 280 9.179909 TCGGAATTTGCCTTTCAAAGTTATATA 57.820 29.630 0.00 0.00 46.68 0.86
279 281 9.965824 CGGAATTTGCCTTTCAAAGTTATATAT 57.034 29.630 0.00 0.00 46.68 0.86
306 308 7.182817 TGCTAGTGATTATGTTGTAGGAGTT 57.817 36.000 0.00 0.00 0.00 3.01
313 315 8.230486 GTGATTATGTTGTAGGAGTTGTTCTTG 58.770 37.037 0.00 0.00 0.00 3.02
316 318 4.448210 TGTTGTAGGAGTTGTTCTTGGTC 58.552 43.478 0.00 0.00 0.00 4.02
330 333 5.894393 TGTTCTTGGTCAAAGGGTTGATAAA 59.106 36.000 0.00 0.00 45.38 1.40
364 367 4.766404 ACACACTATGCAAGTAAAAGCC 57.234 40.909 0.00 0.00 35.76 4.35
368 371 2.671396 ACTATGCAAGTAAAAGCCGACG 59.329 45.455 0.00 0.00 36.36 5.12
370 373 0.533308 TGCAAGTAAAAGCCGACGGT 60.533 50.000 16.73 0.00 0.00 4.83
382 386 0.437295 CCGACGGTCACGAAATCAAC 59.563 55.000 5.48 0.00 44.60 3.18
388 392 1.450025 GTCACGAAATCAACCCCCTC 58.550 55.000 0.00 0.00 0.00 4.30
390 394 1.422024 TCACGAAATCAACCCCCTCAA 59.578 47.619 0.00 0.00 0.00 3.02
391 395 2.041081 TCACGAAATCAACCCCCTCAAT 59.959 45.455 0.00 0.00 0.00 2.57
393 397 2.825532 ACGAAATCAACCCCCTCAATTG 59.174 45.455 0.00 0.00 0.00 2.32
394 398 2.825532 CGAAATCAACCCCCTCAATTGT 59.174 45.455 5.13 0.00 0.00 2.71
395 399 3.119495 CGAAATCAACCCCCTCAATTGTC 60.119 47.826 5.13 0.00 0.00 3.18
396 400 3.833559 AATCAACCCCCTCAATTGTCT 57.166 42.857 5.13 0.00 0.00 3.41
397 401 2.584835 TCAACCCCCTCAATTGTCTG 57.415 50.000 5.13 0.00 0.00 3.51
398 402 0.890683 CAACCCCCTCAATTGTCTGC 59.109 55.000 5.13 0.00 0.00 4.26
401 406 0.032813 CCCCCTCAATTGTCTGCCAT 60.033 55.000 5.13 0.00 0.00 4.40
404 409 0.458669 CCTCAATTGTCTGCCATGGC 59.541 55.000 30.54 30.54 42.35 4.40
406 411 1.404391 CTCAATTGTCTGCCATGGCTC 59.596 52.381 35.53 24.66 42.51 4.70
418 423 1.776667 CCATGGCTCAAATCCTAGGGA 59.223 52.381 9.46 0.00 35.55 4.20
437 442 3.381590 GGGAGCATGGTGATTTTAAGGAC 59.618 47.826 0.00 0.00 0.00 3.85
441 446 6.016777 GGAGCATGGTGATTTTAAGGACTATG 60.017 42.308 0.00 0.00 32.20 2.23
449 454 3.536956 TTTAAGGACTATGGGCACGAG 57.463 47.619 0.00 0.00 0.00 4.18
454 459 0.818296 GACTATGGGCACGAGACAGT 59.182 55.000 0.00 0.00 0.00 3.55
460 466 2.574955 GGCACGAGACAGTGTCCCT 61.575 63.158 19.71 1.77 43.61 4.20
478 484 2.093658 CCCTGTAAGACCAGCGTGTTAT 60.094 50.000 0.00 0.00 34.07 1.89
495 501 5.851177 CGTGTTATGAAATTGAACTGGTCAC 59.149 40.000 0.00 0.00 35.39 3.67
544 550 5.878116 TGGACCGGTCATATTAGAAAAAGTG 59.122 40.000 34.40 0.00 0.00 3.16
547 553 5.579511 ACCGGTCATATTAGAAAAAGTGACG 59.420 40.000 0.00 0.00 35.51 4.35
722 729 8.210946 TCCAAATCATTCGTTTCATACTCCTAT 58.789 33.333 0.00 0.00 0.00 2.57
723 730 8.840321 CCAAATCATTCGTTTCATACTCCTATT 58.160 33.333 0.00 0.00 0.00 1.73
830 837 2.509651 CCAAGCCAGCCAAAGCCAA 61.510 57.895 0.00 0.00 41.25 4.52
908 915 0.951558 GGCCGCAATAATACCACCAG 59.048 55.000 0.00 0.00 0.00 4.00
909 916 1.675552 GCCGCAATAATACCACCAGT 58.324 50.000 0.00 0.00 0.00 4.00
910 917 1.602377 GCCGCAATAATACCACCAGTC 59.398 52.381 0.00 0.00 0.00 3.51
1000 1015 4.829518 GCCGAAAATCGCACCGCC 62.830 66.667 0.00 0.00 38.82 6.13
1001 1016 4.174129 CCGAAAATCGCACCGCCC 62.174 66.667 0.00 0.00 38.82 6.13
1252 1296 2.041405 GGGTGGAGGAGAGGGAGG 60.041 72.222 0.00 0.00 0.00 4.30
1659 1733 1.444836 TTTTGATTAGGTGCCCGTCG 58.555 50.000 0.00 0.00 0.00 5.12
1678 1752 3.550992 CCGATCCGCCGTTCGTTG 61.551 66.667 6.06 0.00 36.19 4.10
1714 1788 6.961576 TGTACAAAAAGTTTTACATCCGGAG 58.038 36.000 11.34 4.72 27.43 4.63
1737 1811 7.317722 AGAAAGAAGAAGGTATACACAGGTT 57.682 36.000 5.01 0.00 0.00 3.50
1738 1812 7.746703 AGAAAGAAGAAGGTATACACAGGTTT 58.253 34.615 5.01 0.00 0.00 3.27
1739 1813 7.878644 AGAAAGAAGAAGGTATACACAGGTTTC 59.121 37.037 5.01 5.08 0.00 2.78
1807 1882 3.419759 CCTTTTCCACCGTCGGCG 61.420 66.667 12.28 0.29 37.95 6.46
1819 1894 1.713830 GTCGGCGTGTAAAGCATCC 59.286 57.895 6.85 0.00 45.63 3.51
1820 1895 1.017177 GTCGGCGTGTAAAGCATCCA 61.017 55.000 6.85 0.00 45.63 3.41
1821 1896 0.107897 TCGGCGTGTAAAGCATCCAT 60.108 50.000 6.85 0.00 45.63 3.41
1822 1897 0.304705 CGGCGTGTAAAGCATCCATC 59.695 55.000 0.00 0.00 45.63 3.51
1858 1933 4.025401 GGACGCGTTGGTGCCAAG 62.025 66.667 15.53 0.67 36.52 3.61
1870 1945 0.878961 GTGCCAAGAGGAAACGACGT 60.879 55.000 0.00 0.00 36.89 4.34
1884 1959 0.999406 CGACGTGCGATGGATTTTCT 59.001 50.000 0.00 0.00 44.57 2.52
1944 2028 3.612860 CAGTGCGTTGGATTGACTACTAC 59.387 47.826 0.00 0.00 0.00 2.73
1945 2029 3.510360 AGTGCGTTGGATTGACTACTACT 59.490 43.478 0.00 0.00 0.00 2.57
1946 2030 3.612860 GTGCGTTGGATTGACTACTACTG 59.387 47.826 0.00 0.00 0.00 2.74
2015 2113 0.035317 ACATTGCCTTCTCGCTGTGA 59.965 50.000 0.00 0.00 0.00 3.58
2016 2114 0.445436 CATTGCCTTCTCGCTGTGAC 59.555 55.000 0.00 0.00 0.00 3.67
2019 2117 1.211969 GCCTTCTCGCTGTGACGTA 59.788 57.895 0.00 0.00 0.00 3.57
2020 2118 1.071567 GCCTTCTCGCTGTGACGTAC 61.072 60.000 0.00 0.00 0.00 3.67
2021 2119 0.522180 CCTTCTCGCTGTGACGTACT 59.478 55.000 0.00 0.00 0.00 2.73
2022 2120 1.068472 CCTTCTCGCTGTGACGTACTT 60.068 52.381 0.00 0.00 0.00 2.24
2024 2122 2.327081 TCTCGCTGTGACGTACTTTC 57.673 50.000 0.00 0.00 0.00 2.62
2025 2123 1.878088 TCTCGCTGTGACGTACTTTCT 59.122 47.619 0.00 0.00 0.00 2.52
2026 2124 2.292569 TCTCGCTGTGACGTACTTTCTT 59.707 45.455 0.00 0.00 0.00 2.52
2027 2125 3.050619 CTCGCTGTGACGTACTTTCTTT 58.949 45.455 0.00 0.00 0.00 2.52
2028 2126 2.792674 TCGCTGTGACGTACTTTCTTTG 59.207 45.455 0.00 0.00 0.00 2.77
2029 2127 2.538449 CGCTGTGACGTACTTTCTTTGT 59.462 45.455 0.00 0.00 0.00 2.83
2030 2128 3.000925 CGCTGTGACGTACTTTCTTTGTT 59.999 43.478 0.00 0.00 0.00 2.83
2031 2129 4.515432 GCTGTGACGTACTTTCTTTGTTC 58.485 43.478 0.00 0.00 0.00 3.18
2032 2130 4.748023 CTGTGACGTACTTTCTTTGTTCG 58.252 43.478 0.00 0.00 35.05 3.95
2033 2131 3.552699 TGTGACGTACTTTCTTTGTTCGG 59.447 43.478 0.00 0.00 33.61 4.30
2034 2132 3.798337 GTGACGTACTTTCTTTGTTCGGA 59.202 43.478 0.00 0.00 33.61 4.55
2035 2133 4.268405 GTGACGTACTTTCTTTGTTCGGAA 59.732 41.667 0.00 0.00 33.61 4.30
2036 2134 5.050567 GTGACGTACTTTCTTTGTTCGGAAT 60.051 40.000 0.00 0.00 33.61 3.01
2037 2135 5.524646 TGACGTACTTTCTTTGTTCGGAATT 59.475 36.000 0.00 0.00 33.61 2.17
2038 2136 6.700960 TGACGTACTTTCTTTGTTCGGAATTA 59.299 34.615 0.00 0.00 33.61 1.40
2039 2137 6.881017 ACGTACTTTCTTTGTTCGGAATTAC 58.119 36.000 0.00 0.00 33.61 1.89
2040 2138 6.703165 ACGTACTTTCTTTGTTCGGAATTACT 59.297 34.615 0.00 0.00 33.61 2.24
2041 2139 7.225341 ACGTACTTTCTTTGTTCGGAATTACTT 59.775 33.333 0.00 0.00 33.61 2.24
2042 2140 7.529519 CGTACTTTCTTTGTTCGGAATTACTTG 59.470 37.037 0.00 0.00 0.00 3.16
2043 2141 7.329588 ACTTTCTTTGTTCGGAATTACTTGT 57.670 32.000 0.00 0.00 0.00 3.16
2044 2142 7.415229 ACTTTCTTTGTTCGGAATTACTTGTC 58.585 34.615 0.00 0.00 0.00 3.18
2045 2143 6.928979 TTCTTTGTTCGGAATTACTTGTCA 57.071 33.333 0.00 0.00 0.00 3.58
2046 2144 6.295039 TCTTTGTTCGGAATTACTTGTCAC 57.705 37.500 0.00 0.00 0.00 3.67
2047 2145 5.818336 TCTTTGTTCGGAATTACTTGTCACA 59.182 36.000 0.00 0.00 0.00 3.58
2048 2146 5.666969 TTGTTCGGAATTACTTGTCACAG 57.333 39.130 0.00 0.00 0.00 3.66
2049 2147 4.951254 TGTTCGGAATTACTTGTCACAGA 58.049 39.130 0.00 0.00 0.00 3.41
2050 2148 5.361427 TGTTCGGAATTACTTGTCACAGAA 58.639 37.500 0.00 0.00 0.00 3.02
2051 2149 5.818336 TGTTCGGAATTACTTGTCACAGAAA 59.182 36.000 0.00 0.00 0.00 2.52
2052 2150 6.485313 TGTTCGGAATTACTTGTCACAGAAAT 59.515 34.615 0.00 0.00 0.00 2.17
2053 2151 7.658167 TGTTCGGAATTACTTGTCACAGAAATA 59.342 33.333 0.00 0.00 0.00 1.40
2054 2152 7.827819 TCGGAATTACTTGTCACAGAAATAG 57.172 36.000 0.00 0.00 0.00 1.73
2055 2153 7.608153 TCGGAATTACTTGTCACAGAAATAGA 58.392 34.615 0.00 0.00 0.00 1.98
2056 2154 8.258007 TCGGAATTACTTGTCACAGAAATAGAT 58.742 33.333 0.00 0.00 0.00 1.98
2057 2155 8.331022 CGGAATTACTTGTCACAGAAATAGATG 58.669 37.037 0.00 0.00 0.00 2.90
2058 2156 9.167311 GGAATTACTTGTCACAGAAATAGATGT 57.833 33.333 0.00 0.00 0.00 3.06
2087 2185 9.640963 CTAGATATAAGTAATTCCAAACGGAGG 57.359 37.037 0.00 0.00 32.88 4.30
2088 2186 7.450903 AGATATAAGTAATTCCAAACGGAGGG 58.549 38.462 0.00 0.00 32.88 4.30
2089 2187 5.703730 ATAAGTAATTCCAAACGGAGGGA 57.296 39.130 0.00 0.00 32.88 4.20
2090 2188 3.629142 AGTAATTCCAAACGGAGGGAG 57.371 47.619 0.00 0.00 34.02 4.30
2091 2189 2.910977 AGTAATTCCAAACGGAGGGAGT 59.089 45.455 0.00 0.00 34.02 3.85
2164 2262 1.138266 GGGTGACGTGTAGGTATGCAT 59.862 52.381 3.79 3.79 0.00 3.96
2170 2268 4.201980 TGACGTGTAGGTATGCATGTACTC 60.202 45.833 10.16 8.26 40.81 2.59
2171 2269 3.067742 ACGTGTAGGTATGCATGTACTCC 59.932 47.826 10.16 4.20 39.21 3.85
2188 2286 2.706190 ACTCCTACTTGTTGTGCTTCCT 59.294 45.455 0.00 0.00 0.00 3.36
2191 2289 3.644265 TCCTACTTGTTGTGCTTCCTACA 59.356 43.478 0.00 0.00 0.00 2.74
2219 3423 8.819015 CAAGAAATGATCTGATGAAGAGTACAG 58.181 37.037 0.00 0.00 38.67 2.74
2248 3452 2.024117 TTGCATGATCGGGCAATCG 58.976 52.632 16.97 0.00 44.41 3.34
2325 3532 0.605319 ATTTTCTTCTCGCGTGGGCA 60.605 50.000 5.77 0.00 39.92 5.36
2447 3661 0.963962 ATGGTCCACAGCAGCAAAAG 59.036 50.000 0.00 0.00 32.21 2.27
2479 3693 1.866237 CCCAACGACCATGACAACG 59.134 57.895 0.00 0.00 0.00 4.10
2507 3721 1.076549 GAAACCAGCCCCCACATCA 59.923 57.895 0.00 0.00 0.00 3.07
2512 3726 0.552848 CCAGCCCCCACATCACTATT 59.447 55.000 0.00 0.00 0.00 1.73
2514 3728 2.376518 CCAGCCCCCACATCACTATTAT 59.623 50.000 0.00 0.00 0.00 1.28
2641 3856 2.351455 GACTGTTTCAGCCTAAGGAGC 58.649 52.381 0.00 0.00 34.37 4.70
2645 3860 1.470494 GTTTCAGCCTAAGGAGCAAGC 59.530 52.381 0.00 0.00 0.00 4.01
2664 3879 1.680651 CTGCTCCGGTCTCTCAGGT 60.681 63.158 0.00 0.00 33.18 4.00
2712 3928 0.877071 CTTGGGGCGCTTGCATATAG 59.123 55.000 7.64 0.00 41.71 1.31
2716 3932 1.160137 GGGCGCTTGCATATAGAAGG 58.840 55.000 7.64 0.00 41.71 3.46
2739 3955 2.203294 AACCACAAGCCACCGTCC 60.203 61.111 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 2.288825 TGTTCTCTCTTGTGTAAGCCGG 60.289 50.000 0.00 0.00 33.82 6.13
36 37 5.541845 CTTGGATGTGTTCTCTCTTGTGTA 58.458 41.667 0.00 0.00 0.00 2.90
50 51 1.134280 CCCTACTCCTGCTTGGATGTG 60.134 57.143 0.00 0.00 45.16 3.21
170 172 3.186001 CGAGGCAATACTCATGATTCTGC 59.814 47.826 0.00 3.77 37.34 4.26
198 200 0.953960 CTTTCTTAAGGTGCCGCGGT 60.954 55.000 28.70 9.01 0.00 5.68
252 254 4.664150 AACTTTGAAAGGCAAATTCCGA 57.336 36.364 10.02 0.00 44.90 4.55
253 255 9.965824 ATATATAACTTTGAAAGGCAAATTCCG 57.034 29.630 10.02 0.00 44.90 4.30
278 280 7.966812 TCCTACAACATAATCACTAGCATCAT 58.033 34.615 0.00 0.00 0.00 2.45
279 281 7.069950 ACTCCTACAACATAATCACTAGCATCA 59.930 37.037 0.00 0.00 0.00 3.07
287 289 7.907214 AGAACAACTCCTACAACATAATCAC 57.093 36.000 0.00 0.00 0.00 3.06
306 308 3.374042 TCAACCCTTTGACCAAGAACA 57.626 42.857 0.00 0.00 36.79 3.18
340 343 6.084277 GGCTTTTACTTGCATAGTGTGTAAC 58.916 40.000 10.59 0.00 37.73 2.50
344 347 3.435327 TCGGCTTTTACTTGCATAGTGTG 59.565 43.478 10.59 0.00 37.73 3.82
349 352 2.004017 CCGTCGGCTTTTACTTGCATA 58.996 47.619 0.00 0.00 0.00 3.14
364 367 0.437295 GGTTGATTTCGTGACCGTCG 59.563 55.000 0.00 0.00 35.01 5.12
368 371 0.037734 AGGGGGTTGATTTCGTGACC 59.962 55.000 0.00 0.00 0.00 4.02
370 373 1.060729 TGAGGGGGTTGATTTCGTGA 58.939 50.000 0.00 0.00 0.00 4.35
382 386 0.032813 ATGGCAGACAATTGAGGGGG 60.033 55.000 13.59 0.00 0.00 5.40
388 392 1.179152 TGAGCCATGGCAGACAATTG 58.821 50.000 37.18 3.24 44.88 2.32
390 394 1.927487 TTTGAGCCATGGCAGACAAT 58.073 45.000 37.18 16.94 44.88 2.71
391 395 1.820519 GATTTGAGCCATGGCAGACAA 59.179 47.619 37.18 31.48 44.88 3.18
393 397 0.743097 GGATTTGAGCCATGGCAGAC 59.257 55.000 37.18 26.20 44.88 3.51
394 398 0.627451 AGGATTTGAGCCATGGCAGA 59.373 50.000 37.18 20.93 44.88 4.26
395 399 2.228059 CTAGGATTTGAGCCATGGCAG 58.772 52.381 37.18 18.97 44.88 4.85
396 400 1.133699 CCTAGGATTTGAGCCATGGCA 60.134 52.381 37.18 18.41 44.88 4.92
397 401 1.613836 CCTAGGATTTGAGCCATGGC 58.386 55.000 30.12 30.12 42.33 4.40
398 402 1.776667 TCCCTAGGATTTGAGCCATGG 59.223 52.381 11.48 7.63 0.00 3.66
401 406 0.839946 GCTCCCTAGGATTTGAGCCA 59.160 55.000 21.08 0.00 43.40 4.75
404 409 2.441001 ACCATGCTCCCTAGGATTTGAG 59.559 50.000 11.48 9.40 30.14 3.02
406 411 2.173356 TCACCATGCTCCCTAGGATTTG 59.827 50.000 11.48 0.35 30.14 2.32
418 423 5.829924 CCATAGTCCTTAAAATCACCATGCT 59.170 40.000 0.00 0.00 0.00 3.79
437 442 0.532573 ACACTGTCTCGTGCCCATAG 59.467 55.000 0.00 0.00 38.45 2.23
441 446 2.048127 GGACACTGTCTCGTGCCC 60.048 66.667 9.08 0.00 38.45 5.36
460 466 3.945981 TCATAACACGCTGGTCTTACA 57.054 42.857 0.00 0.00 0.00 2.41
522 528 6.237755 CGTCACTTTTTCTAATATGACCGGTC 60.238 42.308 28.17 28.17 34.32 4.79
544 550 5.547465 TGGATGGAATATAATGTGGTCGTC 58.453 41.667 0.00 0.00 0.00 4.20
547 553 8.408043 TCAAATGGATGGAATATAATGTGGTC 57.592 34.615 0.00 0.00 0.00 4.02
685 691 4.461081 CGAATGATTTGGAGGGTGGTTAAA 59.539 41.667 0.00 0.00 0.00 1.52
686 692 4.013728 CGAATGATTTGGAGGGTGGTTAA 58.986 43.478 0.00 0.00 0.00 2.01
688 694 2.225017 ACGAATGATTTGGAGGGTGGTT 60.225 45.455 0.00 0.00 0.00 3.67
830 837 2.212110 CCTTGGCTTGGCTTGGCTT 61.212 57.895 5.64 0.00 0.00 4.35
908 915 2.647680 TTCGGTTCCGTGTGGTGGAC 62.648 60.000 11.04 0.00 34.56 4.02
909 916 1.969200 TTTCGGTTCCGTGTGGTGGA 61.969 55.000 11.04 0.00 36.30 4.02
910 917 0.887387 ATTTCGGTTCCGTGTGGTGG 60.887 55.000 11.04 0.00 36.30 4.61
963 974 1.304052 CTGGTTTGGGGATTGCGGA 60.304 57.895 0.00 0.00 0.00 5.54
964 975 3.005540 GCTGGTTTGGGGATTGCGG 62.006 63.158 0.00 0.00 0.00 5.69
965 976 2.573340 GCTGGTTTGGGGATTGCG 59.427 61.111 0.00 0.00 0.00 4.85
966 977 2.573340 CGCTGGTTTGGGGATTGC 59.427 61.111 0.00 0.00 0.00 3.56
967 978 2.573340 GCGCTGGTTTGGGGATTG 59.427 61.111 0.00 0.00 0.00 2.67
1132 1152 3.578272 CGCCTCTCTCTCCGTCGG 61.578 72.222 4.39 4.39 0.00 4.79
1252 1296 2.753446 GCCTCCCCTGCTTCTTGC 60.753 66.667 0.00 0.00 43.25 4.01
1661 1735 3.550992 CAACGAACGGCGGATCGG 61.551 66.667 30.67 16.68 46.49 4.18
1714 1788 7.878644 AGAAACCTGTGTATACCTTCTTCTTTC 59.121 37.037 0.00 0.15 0.00 2.62
1737 1811 3.817238 GCAACGCGAGGAAAAATAAGAA 58.183 40.909 15.93 0.00 0.00 2.52
1738 1812 3.465122 GCAACGCGAGGAAAAATAAGA 57.535 42.857 15.93 0.00 0.00 2.10
1807 1882 2.544267 GCGGTAGATGGATGCTTTACAC 59.456 50.000 0.00 0.00 0.00 2.90
1819 1894 1.299468 GGCTCTCACGCGGTAGATG 60.299 63.158 12.47 0.00 0.00 2.90
1820 1895 1.109920 ATGGCTCTCACGCGGTAGAT 61.110 55.000 12.47 0.00 0.00 1.98
1821 1896 1.753078 ATGGCTCTCACGCGGTAGA 60.753 57.895 12.47 11.88 0.00 2.59
1822 1897 1.589993 CATGGCTCTCACGCGGTAG 60.590 63.158 12.47 7.42 0.00 3.18
1858 1933 1.683790 CCATCGCACGTCGTTTCCTC 61.684 60.000 0.00 0.00 39.67 3.71
1870 1945 1.745087 GGCAAGAGAAAATCCATCGCA 59.255 47.619 0.00 0.00 0.00 5.10
1944 2028 1.299468 GGCGATCACGGAGTAGCAG 60.299 63.158 0.00 0.00 41.61 4.24
1945 2029 1.320344 AAGGCGATCACGGAGTAGCA 61.320 55.000 0.00 0.00 41.61 3.49
1946 2030 0.179108 AAAGGCGATCACGGAGTAGC 60.179 55.000 0.00 0.00 41.61 3.58
1984 2080 6.225981 AGAAGGCAATGTGAAAAAGTTCTT 57.774 33.333 0.00 0.00 34.60 2.52
2015 2113 5.996669 AATTCCGAACAAAGAAAGTACGT 57.003 34.783 0.00 0.00 0.00 3.57
2016 2114 7.113704 AGTAATTCCGAACAAAGAAAGTACG 57.886 36.000 0.00 0.00 0.00 3.67
2019 2117 7.066525 TGACAAGTAATTCCGAACAAAGAAAGT 59.933 33.333 0.00 0.00 0.00 2.66
2020 2118 7.376072 GTGACAAGTAATTCCGAACAAAGAAAG 59.624 37.037 0.00 0.00 0.00 2.62
2021 2119 7.148222 TGTGACAAGTAATTCCGAACAAAGAAA 60.148 33.333 0.00 0.00 0.00 2.52
2022 2120 6.316640 TGTGACAAGTAATTCCGAACAAAGAA 59.683 34.615 0.00 0.00 0.00 2.52
2024 2122 6.018262 TCTGTGACAAGTAATTCCGAACAAAG 60.018 38.462 0.00 0.00 0.00 2.77
2025 2123 5.818336 TCTGTGACAAGTAATTCCGAACAAA 59.182 36.000 0.00 0.00 0.00 2.83
2026 2124 5.361427 TCTGTGACAAGTAATTCCGAACAA 58.639 37.500 0.00 0.00 0.00 2.83
2027 2125 4.951254 TCTGTGACAAGTAATTCCGAACA 58.049 39.130 0.00 0.00 0.00 3.18
2028 2126 5.917541 TTCTGTGACAAGTAATTCCGAAC 57.082 39.130 0.00 0.00 0.00 3.95
2029 2127 8.092068 TCTATTTCTGTGACAAGTAATTCCGAA 58.908 33.333 0.00 0.00 0.00 4.30
2030 2128 7.608153 TCTATTTCTGTGACAAGTAATTCCGA 58.392 34.615 0.00 0.00 0.00 4.55
2031 2129 7.827819 TCTATTTCTGTGACAAGTAATTCCG 57.172 36.000 0.00 0.00 0.00 4.30
2032 2130 9.167311 ACATCTATTTCTGTGACAAGTAATTCC 57.833 33.333 0.00 0.00 0.00 3.01
2061 2159 9.640963 CCTCCGTTTGGAATTACTTATATCTAG 57.359 37.037 0.00 0.00 45.87 2.43
2062 2160 8.591072 CCCTCCGTTTGGAATTACTTATATCTA 58.409 37.037 0.00 0.00 45.87 1.98
2063 2161 7.291651 TCCCTCCGTTTGGAATTACTTATATCT 59.708 37.037 0.00 0.00 45.87 1.98
2064 2162 7.447594 TCCCTCCGTTTGGAATTACTTATATC 58.552 38.462 0.00 0.00 45.87 1.63
2065 2163 7.072076 ACTCCCTCCGTTTGGAATTACTTATAT 59.928 37.037 0.00 0.00 45.87 0.86
2066 2164 6.384886 ACTCCCTCCGTTTGGAATTACTTATA 59.615 38.462 0.00 0.00 45.87 0.98
2067 2165 5.191124 ACTCCCTCCGTTTGGAATTACTTAT 59.809 40.000 0.00 0.00 45.87 1.73
2068 2166 4.533311 ACTCCCTCCGTTTGGAATTACTTA 59.467 41.667 0.00 0.00 45.87 2.24
2069 2167 3.329814 ACTCCCTCCGTTTGGAATTACTT 59.670 43.478 0.00 0.00 45.87 2.24
2070 2168 2.910977 ACTCCCTCCGTTTGGAATTACT 59.089 45.455 0.00 0.00 45.87 2.24
2071 2169 3.345508 ACTCCCTCCGTTTGGAATTAC 57.654 47.619 0.00 0.00 45.87 1.89
2072 2170 3.118519 GCTACTCCCTCCGTTTGGAATTA 60.119 47.826 0.00 0.00 45.87 1.40
2073 2171 2.355818 GCTACTCCCTCCGTTTGGAATT 60.356 50.000 0.00 0.00 45.87 2.17
2074 2172 1.209747 GCTACTCCCTCCGTTTGGAAT 59.790 52.381 0.00 0.00 45.87 3.01
2075 2173 0.611714 GCTACTCCCTCCGTTTGGAA 59.388 55.000 0.00 0.00 45.87 3.53
2076 2174 0.252103 AGCTACTCCCTCCGTTTGGA 60.252 55.000 0.00 0.00 43.88 3.53
2077 2175 0.108138 CAGCTACTCCCTCCGTTTGG 60.108 60.000 0.00 0.00 0.00 3.28
2078 2176 0.741221 GCAGCTACTCCCTCCGTTTG 60.741 60.000 0.00 0.00 0.00 2.93
2079 2177 1.597461 GCAGCTACTCCCTCCGTTT 59.403 57.895 0.00 0.00 0.00 3.60
2080 2178 2.711922 CGCAGCTACTCCCTCCGTT 61.712 63.158 0.00 0.00 0.00 4.44
2081 2179 3.141488 CGCAGCTACTCCCTCCGT 61.141 66.667 0.00 0.00 0.00 4.69
2164 2262 4.502604 GGAAGCACAACAAGTAGGAGTACA 60.503 45.833 0.00 0.00 0.00 2.90
2170 2268 4.002906 TGTAGGAAGCACAACAAGTAGG 57.997 45.455 0.00 0.00 0.00 3.18
2188 2286 9.159364 CTCTTCATCAGATCATTTCTTGTTGTA 57.841 33.333 0.00 0.00 29.93 2.41
2191 2289 9.160496 GTACTCTTCATCAGATCATTTCTTGTT 57.840 33.333 0.00 0.00 29.93 2.83
2193 3397 8.713737 TGTACTCTTCATCAGATCATTTCTTG 57.286 34.615 0.00 0.00 29.93 3.02
2219 3423 2.778659 GATCATGCAAACGTTCAGAGC 58.221 47.619 0.00 4.64 0.00 4.09
2227 3431 1.505807 TTGCCCGATCATGCAAACG 59.494 52.632 14.54 0.00 43.94 3.60
2248 3452 2.388890 ATAGATGACCTGGGCGCTGC 62.389 60.000 7.64 0.00 0.00 5.25
2278 3482 5.086058 CGACTTTTACGGATGGACAAAATG 58.914 41.667 0.00 0.00 0.00 2.32
2325 3532 0.036022 GCCAACAGAGAACCTGCTCT 59.964 55.000 0.00 0.00 46.81 4.09
2330 3537 1.073897 GCCAGCCAACAGAGAACCT 59.926 57.895 0.00 0.00 0.00 3.50
2391 3598 4.292784 GGAGCTCTCAACAGCACC 57.707 61.111 14.64 0.00 42.08 5.01
2447 3661 1.157585 GTTGGGCTCCTCGTTTCTTC 58.842 55.000 0.00 0.00 0.00 2.87
2479 3693 0.241213 GGCTGGTTTCTTCTTTCGCC 59.759 55.000 0.00 0.00 0.00 5.54
2507 3721 4.609783 GCAATTTTCGCGCCGTATAATAGT 60.610 41.667 0.00 0.00 0.00 2.12
2512 3726 0.305313 GGCAATTTTCGCGCCGTATA 59.695 50.000 0.00 0.00 35.79 1.47
2514 3728 2.481464 GGCAATTTTCGCGCCGTA 59.519 55.556 0.00 0.00 35.79 4.02
2641 3856 2.125350 GAGACCGGAGCAGGCTTG 60.125 66.667 9.46 0.00 33.69 4.01
2645 3860 2.422231 CCTGAGAGACCGGAGCAGG 61.422 68.421 9.46 13.08 40.03 4.85
2651 3866 1.618837 TGAAGAAACCTGAGAGACCGG 59.381 52.381 0.00 0.00 0.00 5.28
2664 3879 9.126151 TGTTGTGGTAAATGTAATCTGAAGAAA 57.874 29.630 0.00 0.00 0.00 2.52
2699 3915 0.519077 GGCCTTCTATATGCAAGCGC 59.481 55.000 0.00 0.00 39.24 5.92


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

AutoCloner maintained by Alex Coulton.