Multiple sequence alignment - TraesCS5D01G237600

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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 TraesCS5D01G237600 chr5D 100.000 3231 0 0 1 3231 345956688 345959918 0.000000e+00 5967
1 TraesCS5D01G237600 chr5B 93.433 2863 120 31 403 3231 405596798 405593970 0.000000e+00 4183
2 TraesCS5D01G237600 chr5A 91.250 3017 145 41 263 3231 445245808 445242863 0.000000e+00 3999
3 TraesCS5D01G237600 chr5A 89.498 219 17 5 4 219 445246487 445246272 4.110000e-69 272
4 TraesCS5D01G237600 chr4A 84.848 231 25 5 49 275 613328180 613327956 1.170000e-54 224
5 TraesCS5D01G237600 chr1A 84.018 219 31 3 59 274 16095783 16096000 1.170000e-49 207
6 TraesCS5D01G237600 chr1A 78.601 243 45 6 44 282 73111269 73111030 1.550000e-33 154
7 TraesCS5D01G237600 chr2B 83.168 202 32 2 49 248 401266826 401266625 1.980000e-42 183
8 TraesCS5D01G237600 chr3D 80.952 231 39 5 46 274 546405306 546405533 9.210000e-41 178
9 TraesCS5D01G237600 chr6B 80.455 220 40 3 50 267 43731053 43730835 7.170000e-37 165
10 TraesCS5D01G237600 chr6D 79.149 235 43 6 44 274 95269855 95269623 1.200000e-34 158
11 TraesCS5D01G237600 chr1D 79.039 229 43 4 42 267 185069590 185069816 5.580000e-33 152


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 TraesCS5D01G237600 chr5D 345956688 345959918 3230 False 5967.0 5967 100.000 1 3231 1 chr5D.!!$F1 3230
1 TraesCS5D01G237600 chr5B 405593970 405596798 2828 True 4183.0 4183 93.433 403 3231 1 chr5B.!!$R1 2828
2 TraesCS5D01G237600 chr5A 445242863 445246487 3624 True 2135.5 3999 90.374 4 3231 2 chr5A.!!$R1 3227

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
54 55 0.104882 TGGTGGTTGTACTCCCTCCA 60.105 55.0 16.40 16.4 40.99 3.86 F
664 1095 0.179150 ATGACTTGCGTCTCTCGAGC 60.179 55.0 7.81 0.0 42.86 5.03 F
1483 1930 0.907486 CACCTCTCTGCCCTTCATCA 59.093 55.0 0.00 0.0 0.00 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1162 1598 0.512952 AGTCTTTGATGTCGTTGCGC 59.487 50.000 0.0 0.0 0.00 6.09 R
1670 2125 1.735973 GGCCCATCGCAGGATTTTC 59.264 57.895 0.0 0.0 40.31 2.29 R
2435 2913 2.227388 GCAGAACTACATGCACAAGCTT 59.773 45.455 0.0 0.0 42.11 3.74 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.049156 TTCCTGAGTCTGCACGCG 60.049 61.111 3.53 3.53 0.00 6.01
34 35 4.333649 AGTCTGCACGCGTACTAATAAGTA 59.666 41.667 13.44 0.00 37.15 2.24
39 40 4.147653 GCACGCGTACTAATAAGTATGGTG 59.852 45.833 13.44 15.01 42.97 4.17
45 46 7.202526 GCGTACTAATAAGTATGGTGGTTGTA 58.797 38.462 6.84 0.00 42.97 2.41
54 55 0.104882 TGGTGGTTGTACTCCCTCCA 60.105 55.000 16.40 16.40 40.99 3.86
55 56 0.323957 GGTGGTTGTACTCCCTCCAC 59.676 60.000 14.05 13.53 45.17 4.02
57 58 1.189524 TGGTTGTACTCCCTCCACCG 61.190 60.000 0.00 0.00 0.00 4.94
69 73 4.284178 TCCCTCCACCGTATATATAAGGC 58.716 47.826 20.75 0.00 35.64 4.35
70 74 4.016851 TCCCTCCACCGTATATATAAGGCT 60.017 45.833 20.75 8.64 35.64 4.58
71 75 4.715297 CCCTCCACCGTATATATAAGGCTT 59.285 45.833 20.75 4.58 35.64 4.35
72 76 5.895534 CCCTCCACCGTATATATAAGGCTTA 59.104 44.000 20.75 9.79 35.64 3.09
91 95 5.278610 GGCTTAATACGGTTTTTGAGGTTGT 60.279 40.000 0.00 0.00 0.00 3.32
98 102 6.399639 ACGGTTTTTGAGGTTGTATTTGAT 57.600 33.333 0.00 0.00 0.00 2.57
219 223 5.866092 CACGCATGTCATATATTACTGCTCT 59.134 40.000 14.20 3.50 0.00 4.09
220 224 7.029563 CACGCATGTCATATATTACTGCTCTA 58.970 38.462 14.20 0.00 0.00 2.43
237 260 6.599638 ACTGCTCTAATTTATGGTCAAAGGAC 59.400 38.462 0.00 0.00 43.55 3.85
291 715 6.656902 AGATGGAGAAAGTAGATGCATTTCA 58.343 36.000 0.00 0.00 35.79 2.69
292 716 6.541641 AGATGGAGAAAGTAGATGCATTTCAC 59.458 38.462 0.00 0.00 35.79 3.18
293 717 5.809001 TGGAGAAAGTAGATGCATTTCACT 58.191 37.500 0.00 1.61 35.79 3.41
294 718 5.877012 TGGAGAAAGTAGATGCATTTCACTC 59.123 40.000 0.00 4.42 35.79 3.51
295 719 5.877012 GGAGAAAGTAGATGCATTTCACTCA 59.123 40.000 0.00 0.00 35.79 3.41
296 720 6.372659 GGAGAAAGTAGATGCATTTCACTCAA 59.627 38.462 0.00 0.00 35.79 3.02
297 721 7.066766 GGAGAAAGTAGATGCATTTCACTCAAT 59.933 37.037 0.00 0.00 35.79 2.57
298 722 7.759465 AGAAAGTAGATGCATTTCACTCAATG 58.241 34.615 0.00 0.00 35.79 2.82
317 741 2.846193 TGCAATAATTACCGAGCCTCC 58.154 47.619 0.00 0.00 0.00 4.30
448 875 5.570234 ACTTTGTTTGCGTCCTTTTTCTA 57.430 34.783 0.00 0.00 0.00 2.10
449 876 5.337554 ACTTTGTTTGCGTCCTTTTTCTAC 58.662 37.500 0.00 0.00 0.00 2.59
450 877 5.124936 ACTTTGTTTGCGTCCTTTTTCTACT 59.875 36.000 0.00 0.00 0.00 2.57
453 880 5.336744 TGTTTGCGTCCTTTTTCTACTTTG 58.663 37.500 0.00 0.00 0.00 2.77
454 881 5.106078 TGTTTGCGTCCTTTTTCTACTTTGT 60.106 36.000 0.00 0.00 0.00 2.83
480 907 0.248012 TCTTAATCGCTCGGTTGGCA 59.752 50.000 0.00 0.00 0.00 4.92
494 921 1.133025 GTTGGCACCATTCAGAATCCG 59.867 52.381 0.00 0.00 0.00 4.18
498 925 1.934589 CACCATTCAGAATCCGCGTA 58.065 50.000 4.92 0.00 0.00 4.42
577 1004 0.522180 CGAGAGGATATTCGGACCGG 59.478 60.000 15.25 0.00 33.39 5.28
579 1006 0.481567 AGAGGATATTCGGACCGGGA 59.518 55.000 15.25 3.47 0.00 5.14
580 1007 0.602060 GAGGATATTCGGACCGGGAC 59.398 60.000 15.25 0.00 0.00 4.46
643 1073 3.731547 CATCCTCTGCTCCCCACA 58.268 61.111 0.00 0.00 0.00 4.17
662 1093 0.881796 ACATGACTTGCGTCTCTCGA 59.118 50.000 0.00 0.00 42.86 4.04
664 1095 0.179150 ATGACTTGCGTCTCTCGAGC 60.179 55.000 7.81 0.00 42.86 5.03
682 1113 2.764314 CCGCGCCAGGATTTCCAAG 61.764 63.158 0.00 0.00 38.89 3.61
689 1120 2.493675 GCCAGGATTTCCAAGAACTTCC 59.506 50.000 0.00 0.00 38.89 3.46
891 1327 5.426689 TTGTTAGAGCTCACCAGATGAAT 57.573 39.130 17.77 0.00 36.69 2.57
905 1341 4.498241 CAGATGAATCGAAGAACTGACCA 58.502 43.478 0.00 0.00 43.58 4.02
934 1370 5.698741 TGTTCATCCATGTCTAACTCCAT 57.301 39.130 0.00 0.00 0.00 3.41
935 1371 5.674525 TGTTCATCCATGTCTAACTCCATC 58.325 41.667 0.00 0.00 0.00 3.51
936 1372 4.963318 TCATCCATGTCTAACTCCATCC 57.037 45.455 0.00 0.00 0.00 3.51
937 1373 4.560739 TCATCCATGTCTAACTCCATCCT 58.439 43.478 0.00 0.00 0.00 3.24
938 1374 4.346127 TCATCCATGTCTAACTCCATCCTG 59.654 45.833 0.00 0.00 0.00 3.86
939 1375 2.435805 TCCATGTCTAACTCCATCCTGC 59.564 50.000 0.00 0.00 0.00 4.85
970 1406 3.306156 GCCTCAGGAGTATAAATCGACCC 60.306 52.174 0.00 0.00 0.00 4.46
972 1408 4.218852 CCTCAGGAGTATAAATCGACCCTC 59.781 50.000 0.00 0.00 0.00 4.30
981 1417 1.115930 AATCGACCCTCCGCTGCTAT 61.116 55.000 0.00 0.00 0.00 2.97
1087 1523 4.664677 GACCGCCGCAGACACAGT 62.665 66.667 0.00 0.00 0.00 3.55
1095 1531 1.595382 GCAGACACAGTGCGAAGGT 60.595 57.895 0.00 0.00 0.00 3.50
1112 1548 3.998672 TGAAGCCGTCCGGACCAC 61.999 66.667 28.52 20.04 37.50 4.16
1146 1582 2.670905 GCCAACTTGTGAACACCAAAAC 59.329 45.455 2.46 0.00 0.00 2.43
1156 1592 2.593436 ACCAAAACGGCGGTGGAG 60.593 61.111 26.49 9.74 39.03 3.86
1184 1620 1.264020 GCAACGACATCAAAGACTGCA 59.736 47.619 0.00 0.00 0.00 4.41
1199 1635 1.276421 ACTGCAGATACGGTGAGCTTT 59.724 47.619 23.35 0.00 0.00 3.51
1227 1663 1.610038 CAGGAGCAATGCACTCAACAA 59.390 47.619 8.35 0.00 35.79 2.83
1228 1664 2.034939 CAGGAGCAATGCACTCAACAAA 59.965 45.455 8.35 0.00 35.79 2.83
1229 1665 2.035066 AGGAGCAATGCACTCAACAAAC 59.965 45.455 8.35 0.00 35.79 2.93
1230 1666 2.223782 GGAGCAATGCACTCAACAAACA 60.224 45.455 8.35 0.00 35.79 2.83
1231 1667 2.791004 GAGCAATGCACTCAACAAACAC 59.209 45.455 8.35 0.00 34.18 3.32
1232 1668 1.860326 GCAATGCACTCAACAAACACC 59.140 47.619 0.00 0.00 0.00 4.16
1233 1669 2.738000 GCAATGCACTCAACAAACACCA 60.738 45.455 0.00 0.00 0.00 4.17
1234 1670 3.117794 CAATGCACTCAACAAACACCAG 58.882 45.455 0.00 0.00 0.00 4.00
1235 1671 2.121291 TGCACTCAACAAACACCAGA 57.879 45.000 0.00 0.00 0.00 3.86
1236 1672 1.742831 TGCACTCAACAAACACCAGAC 59.257 47.619 0.00 0.00 0.00 3.51
1237 1673 1.065551 GCACTCAACAAACACCAGACC 59.934 52.381 0.00 0.00 0.00 3.85
1245 1681 2.092646 ACAAACACCAGACCACTAAGCA 60.093 45.455 0.00 0.00 0.00 3.91
1319 1759 1.379576 GCCCTCATGCTTGAAGCCT 60.380 57.895 15.43 1.09 41.51 4.58
1342 1782 6.868864 CCTATCCACTGTAGCATTACATGTAC 59.131 42.308 4.68 0.00 39.00 2.90
1355 1795 0.940126 CATGTACGGCAGCTTCCATC 59.060 55.000 2.54 0.00 0.00 3.51
1395 1842 6.441274 CGCAATATCTTATTTGCCAAGTGAT 58.559 36.000 2.39 0.00 44.14 3.06
1410 1857 1.973515 AGTGATGCCTCTTGTCTGACA 59.026 47.619 6.36 6.36 0.00 3.58
1423 1870 7.361713 CCTCTTGTCTGACAGTTTTGTGTTTAA 60.362 37.037 10.77 0.00 37.76 1.52
1458 1905 2.999355 TGCTGGTGAAACTTTTGCAAAC 59.001 40.909 12.39 0.08 36.74 2.93
1483 1930 0.907486 CACCTCTCTGCCCTTCATCA 59.093 55.000 0.00 0.00 0.00 3.07
1497 1944 3.552875 CTTCATCATCCTTGGACTGCAT 58.447 45.455 0.00 0.00 0.00 3.96
1516 1963 3.346315 CATACACCAAGGCAAGACATCA 58.654 45.455 0.00 0.00 0.00 3.07
1526 1973 3.118702 AGGCAAGACATCATCTGAGACAG 60.119 47.826 0.00 0.00 37.88 3.51
1607 2062 1.519455 GAACGCTGCCATCTACGCT 60.519 57.895 0.00 0.00 0.00 5.07
1656 2111 1.770658 CAGGCCTGTATCATTCCTCCA 59.229 52.381 25.53 0.00 0.00 3.86
1703 2158 4.261238 CGATGGGCCGACTATACTATGATC 60.261 50.000 0.00 0.00 0.00 2.92
1716 2171 1.337071 CTATGATCGCCACCACTACGT 59.663 52.381 0.00 0.00 0.00 3.57
1733 2188 6.183360 CCACTACGTTGGTGAGTCATATTTTC 60.183 42.308 18.61 0.00 36.89 2.29
1734 2189 6.590292 CACTACGTTGGTGAGTCATATTTTCT 59.410 38.462 13.72 0.00 36.89 2.52
1745 2200 6.929049 TGAGTCATATTTTCTCACTGAAACGT 59.071 34.615 0.00 0.00 43.55 3.99
1759 2215 5.570262 CTGAAACGTTGTTCAGTTATCGA 57.430 39.130 17.97 0.00 46.28 3.59
1774 2230 6.968335 TCAGTTATCGAAATTTGCACATCATG 59.032 34.615 0.00 0.00 0.00 3.07
1904 2361 2.674563 TTTCAGCTGTCCACACCGGG 62.675 60.000 14.67 0.00 34.36 5.73
1925 2382 3.073650 GGATGATGGAGGCAAGTAATCCT 59.926 47.826 0.00 0.00 34.04 3.24
1983 2446 5.334319 CATTTCAATGATCAGCGCTTGTTA 58.666 37.500 7.50 0.00 38.70 2.41
2254 2722 0.960861 GGAACCAACCCTGCTGCTAC 60.961 60.000 0.00 0.00 0.00 3.58
2414 2892 8.251026 TCGTATCTCTCAGAAAGATTTAGCAAA 58.749 33.333 0.00 0.00 35.20 3.68
2435 2913 6.367969 GCAAAGAAAATGAGACGAACTAGGTA 59.632 38.462 0.00 0.00 0.00 3.08
2598 3079 8.597662 TCATTACAACTATAATTTACGGAGCC 57.402 34.615 0.00 0.00 0.00 4.70
2734 3215 7.255035 CGAAGATGGAAACTGATGCATAATTCT 60.255 37.037 0.00 0.00 30.89 2.40
2789 3270 6.094464 TGTGGCAGACTGATCATTTTATCTTG 59.906 38.462 6.65 0.00 0.00 3.02
2875 3358 2.743928 CGTTGCAGTGCTCCCTCC 60.744 66.667 17.60 0.00 0.00 4.30
2880 3363 1.673665 GCAGTGCTCCCTCCAGTTG 60.674 63.158 8.18 0.00 0.00 3.16
3001 3484 4.323417 ACATGCTGGTCTCGTTTTGATTA 58.677 39.130 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.354040 GTGCAGACTCAGGAACATCG 58.646 55.000 0.00 0.00 0.00 3.84
2 3 0.671781 GCGTGCAGACTCAGGAACAT 60.672 55.000 0.00 0.00 0.00 2.71
3 4 1.300931 GCGTGCAGACTCAGGAACA 60.301 57.895 0.00 0.00 0.00 3.18
4 5 2.375766 CGCGTGCAGACTCAGGAAC 61.376 63.158 0.00 0.00 0.00 3.62
5 6 1.520600 TACGCGTGCAGACTCAGGAA 61.521 55.000 24.59 0.00 0.00 3.36
6 7 1.969589 TACGCGTGCAGACTCAGGA 60.970 57.895 24.59 0.00 0.00 3.86
22 23 9.741647 GAGTACAACCACCATACTTATTAGTAC 57.258 37.037 0.00 0.00 39.59 2.73
34 35 1.286248 GGAGGGAGTACAACCACCAT 58.714 55.000 14.52 0.14 0.00 3.55
39 40 1.190178 ACGGTGGAGGGAGTACAACC 61.190 60.000 0.00 0.00 0.00 3.77
45 46 5.516984 CCTTATATATACGGTGGAGGGAGT 58.483 45.833 7.04 0.00 0.00 3.85
69 73 9.902196 AAATACAACCTCAAAAACCGTATTAAG 57.098 29.630 0.00 0.00 30.20 1.85
70 74 9.680315 CAAATACAACCTCAAAAACCGTATTAA 57.320 29.630 0.00 0.00 30.20 1.40
71 75 9.064706 TCAAATACAACCTCAAAAACCGTATTA 57.935 29.630 0.00 0.00 30.20 0.98
72 76 7.942990 TCAAATACAACCTCAAAAACCGTATT 58.057 30.769 0.00 0.00 31.29 1.89
84 88 8.044060 TCTTGTCAATGATCAAATACAACCTC 57.956 34.615 13.18 0.00 0.00 3.85
174 178 6.651308 CGTGTTACACAAAGCATACTGTTAA 58.349 36.000 16.09 0.00 33.40 2.01
179 183 3.135225 TGCGTGTTACACAAAGCATACT 58.865 40.909 16.09 0.00 38.48 2.12
267 691 6.541641 GTGAAATGCATCTACTTTCTCCATCT 59.458 38.462 0.00 0.00 31.66 2.90
291 715 4.275936 GGCTCGGTAATTATTGCATTGAGT 59.724 41.667 0.00 0.00 0.00 3.41
292 716 4.516698 AGGCTCGGTAATTATTGCATTGAG 59.483 41.667 0.00 1.14 0.00 3.02
293 717 4.460263 AGGCTCGGTAATTATTGCATTGA 58.540 39.130 0.00 0.00 0.00 2.57
294 718 4.320494 GGAGGCTCGGTAATTATTGCATTG 60.320 45.833 8.69 0.00 0.00 2.82
295 719 3.821033 GGAGGCTCGGTAATTATTGCATT 59.179 43.478 8.69 0.00 0.00 3.56
296 720 3.073062 AGGAGGCTCGGTAATTATTGCAT 59.927 43.478 8.69 0.00 0.00 3.96
297 721 2.438021 AGGAGGCTCGGTAATTATTGCA 59.562 45.455 8.69 0.00 0.00 4.08
298 722 3.127425 AGGAGGCTCGGTAATTATTGC 57.873 47.619 8.69 0.00 0.00 3.56
317 741 0.250513 AACTTTGGCGAGCCTCCTAG 59.749 55.000 15.75 9.19 36.94 3.02
324 748 1.835121 AAAACGAAACTTTGGCGAGC 58.165 45.000 0.00 0.00 0.00 5.03
369 796 4.093952 CCGCGCCAGTTTCTGCTG 62.094 66.667 0.00 0.00 36.31 4.41
382 809 4.117372 GAACGTCTTGCGACCGCG 62.117 66.667 9.91 0.00 45.51 6.46
480 907 2.093658 ACTTACGCGGATTCTGAATGGT 60.094 45.455 12.47 3.39 0.00 3.55
494 921 2.911819 TGCAGGCAAAATACTTACGC 57.088 45.000 0.00 0.00 0.00 4.42
498 925 5.180271 CAATTCCATGCAGGCAAAATACTT 58.820 37.500 0.00 0.00 37.29 2.24
528 955 2.351726 GCGGCATCGTCAAAACTTAGAT 59.648 45.455 0.00 0.00 38.89 1.98
530 957 1.526986 CGCGGCATCGTCAAAACTTAG 60.527 52.381 0.00 0.00 38.89 2.18
601 1028 0.909623 TCCAAACGGATCTTCCCTCC 59.090 55.000 0.00 0.00 31.13 4.30
664 1095 2.749839 TTGGAAATCCTGGCGCGG 60.750 61.111 8.83 0.00 36.82 6.46
682 1113 0.252197 AGCGTATGGGTGGGAAGTTC 59.748 55.000 0.00 0.00 0.00 3.01
689 1120 4.007659 GGGAATAAATAGCGTATGGGTGG 58.992 47.826 0.00 0.00 0.00 4.61
891 1327 1.006571 GCCGTGGTCAGTTCTTCGA 60.007 57.895 0.00 0.00 0.00 3.71
905 1341 2.435805 AGACATGGATGAACATAGCCGT 59.564 45.455 0.00 0.00 0.00 5.68
970 1406 1.254284 CCCCTCCTATAGCAGCGGAG 61.254 65.000 7.02 7.02 43.11 4.63
972 1408 2.948720 GCCCCTCCTATAGCAGCGG 61.949 68.421 0.00 0.00 0.00 5.52
981 1417 2.390225 TTTTTGCTTTGCCCCTCCTA 57.610 45.000 0.00 0.00 0.00 2.94
1081 1517 1.160329 GCTTCACCTTCGCACTGTGT 61.160 55.000 9.86 0.00 0.00 3.72
1087 1523 2.357034 GACGGCTTCACCTTCGCA 60.357 61.111 0.00 0.00 35.61 5.10
1095 1531 3.998672 GTGGTCCGGACGGCTTCA 61.999 66.667 27.68 16.77 34.68 3.02
1112 1548 0.673644 AGTTGGCGAATCGGTGAAGG 60.674 55.000 4.35 0.00 0.00 3.46
1162 1598 0.512952 AGTCTTTGATGTCGTTGCGC 59.487 50.000 0.00 0.00 0.00 6.09
1164 1600 1.264020 TGCAGTCTTTGATGTCGTTGC 59.736 47.619 0.00 0.00 0.00 4.17
1169 1605 3.553511 CCGTATCTGCAGTCTTTGATGTC 59.446 47.826 14.67 0.00 0.00 3.06
1184 1620 6.582636 TGATTAATGAAAGCTCACCGTATCT 58.417 36.000 0.00 0.00 33.30 1.98
1199 1635 4.529897 AGTGCATTGCTCCTGATTAATGA 58.470 39.130 10.49 0.00 33.50 2.57
1227 1663 2.047061 TCTGCTTAGTGGTCTGGTGTT 58.953 47.619 0.00 0.00 0.00 3.32
1228 1664 1.717032 TCTGCTTAGTGGTCTGGTGT 58.283 50.000 0.00 0.00 0.00 4.16
1229 1665 2.625737 CATCTGCTTAGTGGTCTGGTG 58.374 52.381 0.00 0.00 0.00 4.17
1230 1666 1.065854 GCATCTGCTTAGTGGTCTGGT 60.066 52.381 0.00 0.00 38.21 4.00
1231 1667 1.661341 GCATCTGCTTAGTGGTCTGG 58.339 55.000 0.00 0.00 38.21 3.86
1232 1668 1.065926 TGGCATCTGCTTAGTGGTCTG 60.066 52.381 1.70 0.00 41.70 3.51
1233 1669 1.279496 TGGCATCTGCTTAGTGGTCT 58.721 50.000 1.70 0.00 41.70 3.85
1234 1670 2.158842 AGATGGCATCTGCTTAGTGGTC 60.159 50.000 28.33 0.00 38.44 4.02
1235 1671 1.842562 AGATGGCATCTGCTTAGTGGT 59.157 47.619 28.33 0.76 38.44 4.16
1236 1672 2.634815 AGATGGCATCTGCTTAGTGG 57.365 50.000 28.33 0.00 38.44 4.00
1245 1681 0.545171 CAGGGTGTCAGATGGCATCT 59.455 55.000 24.01 24.01 41.15 2.90
1395 1842 2.945008 CAAAACTGTCAGACAAGAGGCA 59.055 45.455 6.91 0.00 0.00 4.75
1410 1857 5.968528 TGTCACCTGTTAAACACAAAACT 57.031 34.783 0.00 0.00 33.87 2.66
1423 1870 0.892358 CCAGCATGCTTGTCACCTGT 60.892 55.000 19.98 0.00 31.97 4.00
1458 1905 1.374758 GGGCAGAGAGGTGACAACG 60.375 63.158 0.00 0.00 0.00 4.10
1483 1930 1.915489 TGGTGTATGCAGTCCAAGGAT 59.085 47.619 0.00 0.00 0.00 3.24
1497 1944 3.264193 AGATGATGTCTTGCCTTGGTGTA 59.736 43.478 0.00 0.00 31.47 2.90
1516 1963 6.156602 AGACAAAGAATCATCCTGTCTCAGAT 59.843 38.462 0.00 0.00 41.77 2.90
1526 1973 7.040823 ACAAACTCAGAAGACAAAGAATCATCC 60.041 37.037 0.00 0.00 0.00 3.51
1607 2062 1.822990 CCTACTCCAACCAGCGAGTTA 59.177 52.381 0.00 0.00 39.92 2.24
1670 2125 1.735973 GGCCCATCGCAGGATTTTC 59.264 57.895 0.00 0.00 40.31 2.29
1680 2135 3.014623 TCATAGTATAGTCGGCCCATCG 58.985 50.000 0.00 0.00 0.00 3.84
1703 2158 2.029964 ACCAACGTAGTGGTGGCG 59.970 61.111 11.13 0.00 45.00 5.69
1743 2198 5.623264 TGCAAATTTCGATAACTGAACAACG 59.377 36.000 0.00 0.00 0.00 4.10
1745 2200 6.499172 TGTGCAAATTTCGATAACTGAACAA 58.501 32.000 0.00 0.00 0.00 2.83
1752 2208 5.051508 GCCATGATGTGCAAATTTCGATAAC 60.052 40.000 0.00 0.00 0.00 1.89
1774 2230 6.680810 TGCATAGAAAGCATATATGTTTGCC 58.319 36.000 14.64 10.16 39.72 4.52
1904 2361 4.363991 AGGATTACTTGCCTCCATCATC 57.636 45.455 0.00 0.00 0.00 2.92
1925 2382 4.264253 CAGAACAATCTGCCAGGTCATTA 58.736 43.478 0.00 0.00 46.11 1.90
1949 2406 8.938906 GCTGATCATTGAAATGGTTTGTTTTAT 58.061 29.630 0.00 0.00 37.03 1.40
1983 2446 7.116805 CAGTTTTCTTTCAACAAAGACTTGCTT 59.883 33.333 0.00 0.00 46.38 3.91
2414 2892 6.071278 AGCTTACCTAGTTCGTCTCATTTTCT 60.071 38.462 0.00 0.00 0.00 2.52
2435 2913 2.227388 GCAGAACTACATGCACAAGCTT 59.773 45.455 0.00 0.00 42.11 3.74
2644 3125 6.463995 AATGGTTCTAAACTTCTGTTTGCA 57.536 33.333 4.64 0.00 45.01 4.08
2734 3215 3.552132 TTGACTTCTGGTGCAACTGTA 57.448 42.857 2.04 0.00 36.74 2.74
3001 3484 3.334054 GCTGGAGGGAGCTGGGTT 61.334 66.667 0.00 0.00 35.95 4.11


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

AutoCloner maintained by Alex Coulton.