Multiple sequence alignment - TraesCS5B01G229900

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 TraesCS5B01G229900 chr5B 100.000 2393 0 0 1 2393 406883071 406885463 0.000000e+00 4420.0
1 TraesCS5B01G229900 chr5B 86.131 274 36 2 1825 2097 593437649 593437921 6.470000e-76 294.0
2 TraesCS5B01G229900 chr5B 87.440 207 26 0 2117 2323 651210073 651210279 3.070000e-59 239.0
3 TraesCS5B01G229900 chr5B 87.879 198 24 0 2126 2323 650977299 650977496 1.430000e-57 233.0
4 TraesCS5B01G229900 chr5D 90.409 2252 138 35 170 2393 344875232 344873031 0.000000e+00 2891.0
5 TraesCS5B01G229900 chr5D 79.301 372 63 10 1739 2100 553868424 553868057 5.110000e-62 248.0
6 TraesCS5B01G229900 chr5D 92.547 161 10 1 1 159 344877029 344876869 1.850000e-56 230.0
7 TraesCS5B01G229900 chr5A 89.803 1471 88 24 1 1443 447308444 447309880 0.000000e+00 1829.0
8 TraesCS5B01G229900 chr3A 88.797 241 25 2 1809 2049 14841772 14842010 6.470000e-76 294.0
9 TraesCS5B01G229900 chr3A 83.045 289 39 5 2108 2386 261344819 261344531 1.100000e-63 254.0
10 TraesCS5B01G229900 chr7D 82.911 316 42 7 2082 2387 523439486 523439173 8.430000e-70 274.0
11 TraesCS5B01G229900 chr7D 81.949 277 40 6 2127 2393 465565126 465564850 2.390000e-55 226.0
12 TraesCS5B01G229900 chr7D 80.455 220 43 0 1825 2044 385401204 385400985 4.090000e-38 169.0
13 TraesCS5B01G229900 chr4D 82.935 293 40 6 2105 2387 69749179 69749471 3.050000e-64 255.0
14 TraesCS5B01G229900 chr4D 85.000 200 30 0 2108 2307 477861194 477860995 1.120000e-48 204.0
15 TraesCS5B01G229900 chr4D 92.793 111 8 0 1934 2044 405023635 405023745 6.850000e-36 161.0
16 TraesCS5B01G229900 chr4D 83.761 117 18 1 2108 2224 473143868 473143983 2.510000e-20 110.0
17 TraesCS5B01G229900 chr7B 82.550 298 42 6 2106 2393 1153079 1153376 1.100000e-63 254.0
18 TraesCS5B01G229900 chr7B 78.644 295 51 9 2108 2391 502686779 502687072 4.060000e-43 185.0
19 TraesCS5B01G229900 chr7B 80.513 195 26 6 2201 2384 436207265 436207458 3.210000e-29 139.0
20 TraesCS5B01G229900 chr1B 81.944 216 36 1 1825 2040 120402107 120402319 1.890000e-41 180.0
21 TraesCS5B01G229900 chr1B 80.465 215 41 1 1827 2041 374315508 374315721 1.900000e-36 163.0
22 TraesCS5B01G229900 chr1B 80.841 214 31 5 2190 2393 17535243 17535456 2.460000e-35 159.0
23 TraesCS5B01G229900 chr3D 80.189 212 42 0 1825 2036 518543549 518543760 2.460000e-35 159.0
24 TraesCS5B01G229900 chr1D 81.429 140 22 4 2093 2231 385044692 385044828 6.990000e-21 111.0
25 TraesCS5B01G229900 chr2D 81.600 125 21 2 2108 2231 194803644 194803521 4.210000e-18 102.0
26 TraesCS5B01G229900 chr3B 76.705 176 29 6 2230 2393 32467729 32467554 1.180000e-13 87.9
27 TraesCS5B01G229900 chr3B 76.471 170 28 6 2230 2387 32545103 32544934 5.480000e-12 82.4
28 TraesCS5B01G229900 chr4B 87.302 63 8 0 2331 2393 502953807 502953869 3.300000e-09 73.1


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 TraesCS5B01G229900 chr5B 406883071 406885463 2392 False 4420.0 4420 100.000 1 2393 1 chr5B.!!$F1 2392
1 TraesCS5B01G229900 chr5D 344873031 344877029 3998 True 1560.5 2891 91.478 1 2393 2 chr5D.!!$R2 2392
2 TraesCS5B01G229900 chr5A 447308444 447309880 1436 False 1829.0 1829 89.803 1 1443 1 chr5A.!!$F1 1442

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
922 2572 0.036952 CAAAGCTTCCGCCTCTCTCA 60.037 55.0 0.0 0.0 36.6 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2338 4008 0.036388 GTGTGTCGGACCATGGTGAT 60.036 55.0 25.52 0.0 0.0 3.06 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
37 38 2.486472 ATGAGTCTTGGCCTGTTCTG 57.514 50.000 3.32 0.00 0.00 3.02
55 56 0.320421 TGTCTGCGTGGGCTTAGTTC 60.320 55.000 0.00 0.00 40.82 3.01
77 78 1.521681 CCGAGAAGATGGCCCGTTC 60.522 63.158 0.00 0.00 0.00 3.95
94 95 1.258445 TTCTCCTGCCGGTTCCTCTC 61.258 60.000 1.90 0.00 0.00 3.20
107 108 4.203226 GGTTCCTCTCATTTTCATCTCCC 58.797 47.826 0.00 0.00 0.00 4.30
123 124 2.116238 CTCCCTGAAACGAATCCCCTA 58.884 52.381 0.00 0.00 0.00 3.53
151 154 6.451064 AAAAACTCCTTGAAACGAATCAGT 57.549 33.333 0.00 0.00 0.00 3.41
204 1833 3.306134 GAGCAGCACTCGCAAGCAC 62.306 63.158 0.00 0.00 42.06 4.40
233 1862 3.004210 AGTCGATCAGATCATGTCCGAAG 59.996 47.826 11.12 0.00 36.30 3.79
296 1929 1.448540 GTGACCATCACGCAGGGAG 60.449 63.158 0.00 0.00 37.67 4.30
342 1975 4.127566 ACGTGTTGCCCGTAGTAATAAT 57.872 40.909 0.00 0.00 36.65 1.28
455 2092 3.071602 AGAAGACATACCTGCTGTGTTGT 59.928 43.478 0.00 0.00 31.04 3.32
494 2132 3.367992 TTCTTAACCACTAACGACGCA 57.632 42.857 0.00 0.00 0.00 5.24
497 2135 2.624316 TAACCACTAACGACGCAGAG 57.376 50.000 0.00 0.00 0.00 3.35
511 2149 1.523258 CAGAGGCCGCAGATCTTGG 60.523 63.158 9.88 6.42 0.00 3.61
519 2157 1.152989 CGCAGATCTTGGCAGAGCTC 61.153 60.000 5.27 5.27 42.42 4.09
878 2528 3.432588 CGCTCGGTCGTCCACTCT 61.433 66.667 0.00 0.00 0.00 3.24
896 2546 2.357637 CTCTCCAACTCTCTCCATCGTC 59.642 54.545 0.00 0.00 0.00 4.20
898 2548 1.095600 CCAACTCTCTCCATCGTCGA 58.904 55.000 0.00 0.00 0.00 4.20
899 2549 1.472878 CCAACTCTCTCCATCGTCGAA 59.527 52.381 0.00 0.00 0.00 3.71
900 2550 2.099921 CCAACTCTCTCCATCGTCGAAT 59.900 50.000 0.00 0.00 0.00 3.34
901 2551 3.367607 CAACTCTCTCCATCGTCGAATC 58.632 50.000 0.00 0.00 0.00 2.52
905 2555 1.409064 CTCTCCATCGTCGAATCCCAA 59.591 52.381 0.00 0.00 0.00 4.12
906 2556 1.828595 TCTCCATCGTCGAATCCCAAA 59.171 47.619 0.00 0.00 0.00 3.28
908 2558 0.657840 CCATCGTCGAATCCCAAAGC 59.342 55.000 0.00 0.00 0.00 3.51
909 2559 1.656652 CATCGTCGAATCCCAAAGCT 58.343 50.000 0.00 0.00 0.00 3.74
912 2562 0.727398 CGTCGAATCCCAAAGCTTCC 59.273 55.000 0.00 0.00 0.00 3.46
913 2563 0.727398 GTCGAATCCCAAAGCTTCCG 59.273 55.000 0.00 0.00 0.00 4.30
914 2564 1.024579 TCGAATCCCAAAGCTTCCGC 61.025 55.000 0.00 0.00 0.00 5.54
915 2565 1.809869 GAATCCCAAAGCTTCCGCC 59.190 57.895 0.00 0.00 36.60 6.13
916 2566 0.681243 GAATCCCAAAGCTTCCGCCT 60.681 55.000 0.00 0.00 36.60 5.52
917 2567 0.681243 AATCCCAAAGCTTCCGCCTC 60.681 55.000 0.00 0.00 36.60 4.70
918 2568 1.566298 ATCCCAAAGCTTCCGCCTCT 61.566 55.000 0.00 0.00 36.60 3.69
919 2569 1.746991 CCCAAAGCTTCCGCCTCTC 60.747 63.158 0.00 0.00 36.60 3.20
920 2570 1.298014 CCAAAGCTTCCGCCTCTCT 59.702 57.895 0.00 0.00 36.60 3.10
921 2571 0.742635 CCAAAGCTTCCGCCTCTCTC 60.743 60.000 0.00 0.00 36.60 3.20
922 2572 0.036952 CAAAGCTTCCGCCTCTCTCA 60.037 55.000 0.00 0.00 36.60 3.27
923 2573 0.687354 AAAGCTTCCGCCTCTCTCAA 59.313 50.000 0.00 0.00 36.60 3.02
924 2574 0.687354 AAGCTTCCGCCTCTCTCAAA 59.313 50.000 0.00 0.00 36.60 2.69
925 2575 0.687354 AGCTTCCGCCTCTCTCAAAA 59.313 50.000 0.00 0.00 36.60 2.44
929 2579 0.608640 TCCGCCTCTCTCAAAACCTC 59.391 55.000 0.00 0.00 0.00 3.85
942 2593 2.935849 CAAAACCTCAAAAACCACCTGC 59.064 45.455 0.00 0.00 0.00 4.85
944 2595 1.402787 ACCTCAAAAACCACCTGCAG 58.597 50.000 6.78 6.78 0.00 4.41
951 2602 2.134789 AAACCACCTGCAGATCATCC 57.865 50.000 17.39 0.00 0.00 3.51
956 2607 0.326904 ACCTGCAGATCATCCCCTCA 60.327 55.000 17.39 0.00 0.00 3.86
961 2612 1.767681 GCAGATCATCCCCTCAGTTCT 59.232 52.381 0.00 0.00 0.00 3.01
1083 2734 1.552337 CTGCACCTCTGCTTCTTCCTA 59.448 52.381 0.00 0.00 44.57 2.94
1134 2785 2.683362 CTGGTACATGAGCTACGAGTCA 59.317 50.000 0.00 0.00 38.20 3.41
1408 3059 3.054582 ACTCTAGTGTCATAGTCACCGGA 60.055 47.826 9.46 0.00 36.58 5.14
1480 3136 3.110447 TGTACCTGTGTAACCCGAAAC 57.890 47.619 0.00 0.00 34.36 2.78
1485 3141 2.225491 CCTGTGTAACCCGAAACATGTG 59.775 50.000 0.00 0.00 34.36 3.21
1518 3174 2.030862 GCACCCGTGTAACCCGAA 59.969 61.111 0.00 0.00 0.00 4.30
1548 3204 6.461509 GGCCATTTCTAACACATCCCAATAAG 60.462 42.308 0.00 0.00 0.00 1.73
1551 3207 7.363705 CCATTTCTAACACATCCCAATAAGCAA 60.364 37.037 0.00 0.00 0.00 3.91
1573 3229 4.957684 AGGAGGATACGGTGGAATAAAG 57.042 45.455 0.00 0.00 46.39 1.85
1592 3254 1.340889 AGAACGCATTTGGTTGCATGT 59.659 42.857 0.00 0.00 42.91 3.21
1596 3258 4.027572 ACGCATTTGGTTGCATGTATAC 57.972 40.909 0.00 0.00 42.91 1.47
1597 3259 3.181491 ACGCATTTGGTTGCATGTATACC 60.181 43.478 0.00 0.00 42.91 2.73
1598 3260 3.181492 CGCATTTGGTTGCATGTATACCA 60.181 43.478 3.00 3.00 42.91 3.25
1599 3261 4.362279 GCATTTGGTTGCATGTATACCAG 58.638 43.478 7.25 0.00 42.48 4.00
1600 3262 4.737352 GCATTTGGTTGCATGTATACCAGG 60.737 45.833 7.25 3.67 42.48 4.45
1635 3305 0.531200 CCTAGGTTCACGGTCAGGTC 59.469 60.000 0.00 0.00 0.00 3.85
1639 3309 1.069090 GTTCACGGTCAGGTCAGCA 59.931 57.895 0.00 0.00 0.00 4.41
1641 3311 0.320683 TTCACGGTCAGGTCAGCATG 60.321 55.000 0.00 0.00 37.54 4.06
1650 3320 3.909662 GTCAGCATGGCACGGAAT 58.090 55.556 0.00 0.00 43.01 3.01
1657 3327 2.825532 AGCATGGCACGGAATTTAAAGT 59.174 40.909 0.00 0.00 0.00 2.66
1678 3348 1.227883 CTCTGGGCATGGCTAGCTG 60.228 63.158 25.43 16.89 0.00 4.24
1679 3349 2.203308 CTGGGCATGGCTAGCTGG 60.203 66.667 19.57 5.58 0.00 4.85
1683 3353 3.214845 GCATGGCTAGCTGGGCAC 61.215 66.667 28.48 13.31 44.25 5.01
1685 3355 4.864334 ATGGCTAGCTGGGCACGC 62.864 66.667 28.48 5.03 44.25 5.34
1690 3360 1.375908 CTAGCTGGGCACGCAAAGA 60.376 57.895 0.00 0.00 0.00 2.52
1697 3367 2.764314 GGCACGCAAAGATCGGCAT 61.764 57.895 7.62 0.00 0.00 4.40
1706 3376 4.361451 CAAAGATCGGCATTTGCTTACT 57.639 40.909 2.12 0.00 41.70 2.24
1707 3377 5.484173 CAAAGATCGGCATTTGCTTACTA 57.516 39.130 2.12 0.00 41.70 1.82
1708 3378 5.505286 CAAAGATCGGCATTTGCTTACTAG 58.495 41.667 2.12 0.00 41.70 2.57
1717 3387 4.865865 GCTTACTAGCCAGGCTGG 57.134 61.111 29.44 29.44 42.85 4.85
1718 3388 1.147153 GCTTACTAGCCAGGCTGGG 59.853 63.158 33.43 19.95 41.48 4.45
1786 3456 4.345547 CCTCCACTAACCTCCTTCCTAATC 59.654 50.000 0.00 0.00 0.00 1.75
1793 3463 6.736179 ACTAACCTCCTTCCTAATCTCCTTTT 59.264 38.462 0.00 0.00 0.00 2.27
1795 3465 6.068461 ACCTCCTTCCTAATCTCCTTTTTC 57.932 41.667 0.00 0.00 0.00 2.29
1802 3472 6.720217 TCCTAATCTCCTTTTTCCCTTCTT 57.280 37.500 0.00 0.00 0.00 2.52
1812 3482 7.175797 TCCTTTTTCCCTTCTTCCTTCTAATC 58.824 38.462 0.00 0.00 0.00 1.75
1822 3492 7.868415 CCTTCTTCCTTCTAATCTATACAACGG 59.132 40.741 0.00 0.00 0.00 4.44
1841 3511 4.689071 ACGGTAAAAGATGCACATCGATA 58.311 39.130 0.00 0.00 42.48 2.92
1844 3514 6.073369 CGGTAAAAGATGCACATCGATATTG 58.927 40.000 0.00 0.00 42.48 1.90
1879 3549 2.245096 CGATCGGTTCGTAGTTTCGTT 58.755 47.619 7.38 0.00 43.01 3.85
1880 3550 3.416277 CGATCGGTTCGTAGTTTCGTTA 58.584 45.455 7.38 0.00 43.01 3.18
1890 3560 6.374707 TCGTAGTTTCGTTAACCGTAAATG 57.625 37.500 0.00 0.00 37.46 2.32
1924 3594 6.017523 TGTGTTCATGTTCGAAGCTATTTTGA 60.018 34.615 0.00 0.00 0.00 2.69
1948 3618 5.559694 CGAATTTTGTCAAATTTGTCGCT 57.440 34.783 17.47 0.00 41.79 4.93
2005 3675 4.082408 CAGCTTCATCACACAATTCCACAT 60.082 41.667 0.00 0.00 0.00 3.21
2012 3682 5.787953 TCACACAATTCCACATGACATTT 57.212 34.783 0.00 0.00 0.00 2.32
2013 3683 5.530712 TCACACAATTCCACATGACATTTG 58.469 37.500 0.00 0.00 0.00 2.32
2024 3694 5.914635 CCACATGACATTTGTGTTGTAAGTC 59.085 40.000 0.00 0.00 42.30 3.01
2045 3715 3.128242 TCTTCTGTTTCGACGATCCTACC 59.872 47.826 0.00 0.00 0.00 3.18
2046 3716 1.399440 TCTGTTTCGACGATCCTACCG 59.601 52.381 0.00 0.00 0.00 4.02
2047 3717 0.179156 TGTTTCGACGATCCTACCGC 60.179 55.000 0.00 0.00 0.00 5.68
2048 3718 0.179156 GTTTCGACGATCCTACCGCA 60.179 55.000 0.00 0.00 0.00 5.69
2049 3719 0.179156 TTTCGACGATCCTACCGCAC 60.179 55.000 0.00 0.00 0.00 5.34
2050 3720 1.028330 TTCGACGATCCTACCGCACT 61.028 55.000 0.00 0.00 0.00 4.40
2051 3721 1.028330 TCGACGATCCTACCGCACTT 61.028 55.000 0.00 0.00 0.00 3.16
2052 3722 0.659427 CGACGATCCTACCGCACTTA 59.341 55.000 0.00 0.00 0.00 2.24
2053 3723 1.596464 CGACGATCCTACCGCACTTAC 60.596 57.143 0.00 0.00 0.00 2.34
2054 3724 0.379669 ACGATCCTACCGCACTTACG 59.620 55.000 0.00 0.00 0.00 3.18
2056 3726 0.596859 GATCCTACCGCACTTACGCC 60.597 60.000 0.00 0.00 0.00 5.68
2057 3727 2.345880 ATCCTACCGCACTTACGCCG 62.346 60.000 0.00 0.00 0.00 6.46
2063 3733 1.138047 CCGCACTTACGCCGAAGTAG 61.138 60.000 0.00 0.00 37.57 2.57
2065 3735 0.108945 GCACTTACGCCGAAGTAGGT 60.109 55.000 0.00 0.00 37.57 3.08
2073 3743 0.245539 GCCGAAGTAGGTGTGCACTA 59.754 55.000 19.41 1.23 0.00 2.74
2079 3749 5.815740 CCGAAGTAGGTGTGCACTATATTTT 59.184 40.000 19.41 6.16 0.00 1.82
2101 3771 6.607004 TTTTTCTCCTTTATCCTCTCTCGT 57.393 37.500 0.00 0.00 0.00 4.18
2117 3787 3.818210 CTCTCGTCTGCATCCTACTACAT 59.182 47.826 0.00 0.00 0.00 2.29
2122 3792 5.358725 TCGTCTGCATCCTACTACATTGTAA 59.641 40.000 0.00 0.00 0.00 2.41
2124 3794 6.701841 CGTCTGCATCCTACTACATTGTAATT 59.298 38.462 0.00 0.00 0.00 1.40
2134 3804 5.387279 ACTACATTGTAATTGTTTTCGGCG 58.613 37.500 0.00 0.00 0.00 6.46
2162 3832 0.316841 CTTGGCCTCCTCTATCTCGC 59.683 60.000 3.32 0.00 0.00 5.03
2163 3833 1.115930 TTGGCCTCCTCTATCTCGCC 61.116 60.000 3.32 0.00 36.91 5.54
2175 3845 1.595993 ATCTCGCCGTACTGCACTGT 61.596 55.000 10.03 0.00 0.00 3.55
2181 3851 1.081442 CGTACTGCACTGTCGCTGA 60.081 57.895 13.03 0.00 35.10 4.26
2186 3856 1.632948 CTGCACTGTCGCTGACATGG 61.633 60.000 10.93 8.04 41.94 3.66
2225 3895 1.272425 CCTCCTCTGTCCACTGTCTCT 60.272 57.143 0.00 0.00 0.00 3.10
2239 3909 1.412710 TGTCTCTGTGCGGACTTTCTT 59.587 47.619 8.99 0.00 34.01 2.52
2247 3917 0.949105 GCGGACTTTCTTTGCGAGGA 60.949 55.000 0.00 0.00 0.00 3.71
2268 3938 1.562017 GAGGCTAGCAACTAGTTCGC 58.438 55.000 18.24 17.19 36.53 4.70
2271 3941 0.647925 GCTAGCAACTAGTTCGCTGC 59.352 55.000 28.06 24.81 36.53 5.25
2318 3988 2.430075 CCGTGCATGTCGTGTCGA 60.430 61.111 4.96 0.00 32.28 4.20
2339 4009 2.985282 CGGCACCACCACAGCAAT 60.985 61.111 0.00 0.00 39.03 3.56
2356 4034 0.690192 AATCACCATGGTCCGACACA 59.310 50.000 16.53 0.00 0.00 3.72
2383 4061 0.725133 TTTCTCCTCCCCCATCCTCT 59.275 55.000 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 0.037232 AGAACTAAGCCCACGCAGAC 60.037 55.000 0.00 0.00 37.52 3.51
77 78 1.333636 ATGAGAGGAACCGGCAGGAG 61.334 60.000 10.86 0.00 41.02 3.69
132 135 5.230942 CACTACTGATTCGTTTCAAGGAGT 58.769 41.667 0.00 0.00 0.00 3.85
151 154 0.909133 TGAGGGATGGTGCTGCACTA 60.909 55.000 29.54 25.57 34.40 2.74
186 1815 3.046087 TGCTTGCGAGTGCTGCTC 61.046 61.111 2.14 0.00 43.34 4.26
204 1833 2.034878 TGATCTGATCGACTGAAGGGG 58.965 52.381 12.65 0.00 0.00 4.79
296 1929 1.153549 GGATCGACCACTGTCCTGC 60.154 63.158 0.00 0.00 38.32 4.85
342 1975 9.929180 CCACTGCAGAGCTATAGTATTTATTTA 57.071 33.333 23.35 0.00 0.00 1.40
455 2092 5.975988 AGAAAGCCCATCTTAAGTGGATA 57.024 39.130 19.62 0.00 39.12 2.59
494 2132 2.906458 CCAAGATCTGCGGCCTCT 59.094 61.111 0.00 0.00 0.00 3.69
497 2135 3.207669 CTGCCAAGATCTGCGGCC 61.208 66.667 26.00 13.47 45.63 6.13
511 2149 1.376553 GTGTCCCCTTGAGCTCTGC 60.377 63.158 16.19 0.00 0.00 4.26
518 2156 3.319198 GAGCCGGTGTCCCCTTGA 61.319 66.667 1.90 0.00 0.00 3.02
519 2157 3.612247 CTGAGCCGGTGTCCCCTTG 62.612 68.421 1.90 0.00 0.00 3.61
867 2517 1.200484 GAGAGTTGGAGAGTGGACGAC 59.800 57.143 0.00 0.00 0.00 4.34
878 2528 1.095600 CGACGATGGAGAGAGTTGGA 58.904 55.000 0.00 0.00 0.00 3.53
908 2558 1.002544 AGGTTTTGAGAGAGGCGGAAG 59.997 52.381 0.00 0.00 0.00 3.46
909 2559 1.002087 GAGGTTTTGAGAGAGGCGGAA 59.998 52.381 0.00 0.00 0.00 4.30
912 2562 2.169832 TTGAGGTTTTGAGAGAGGCG 57.830 50.000 0.00 0.00 0.00 5.52
913 2563 4.499865 GGTTTTTGAGGTTTTGAGAGAGGC 60.500 45.833 0.00 0.00 0.00 4.70
914 2564 4.644685 TGGTTTTTGAGGTTTTGAGAGAGG 59.355 41.667 0.00 0.00 0.00 3.69
915 2565 5.450550 GGTGGTTTTTGAGGTTTTGAGAGAG 60.451 44.000 0.00 0.00 0.00 3.20
916 2566 4.401202 GGTGGTTTTTGAGGTTTTGAGAGA 59.599 41.667 0.00 0.00 0.00 3.10
917 2567 4.402474 AGGTGGTTTTTGAGGTTTTGAGAG 59.598 41.667 0.00 0.00 0.00 3.20
918 2568 4.159506 CAGGTGGTTTTTGAGGTTTTGAGA 59.840 41.667 0.00 0.00 0.00 3.27
919 2569 4.432712 CAGGTGGTTTTTGAGGTTTTGAG 58.567 43.478 0.00 0.00 0.00 3.02
920 2570 3.368948 GCAGGTGGTTTTTGAGGTTTTGA 60.369 43.478 0.00 0.00 0.00 2.69
921 2571 2.935849 GCAGGTGGTTTTTGAGGTTTTG 59.064 45.455 0.00 0.00 0.00 2.44
922 2572 2.569404 TGCAGGTGGTTTTTGAGGTTTT 59.431 40.909 0.00 0.00 0.00 2.43
923 2573 2.168313 CTGCAGGTGGTTTTTGAGGTTT 59.832 45.455 5.57 0.00 0.00 3.27
924 2574 1.756538 CTGCAGGTGGTTTTTGAGGTT 59.243 47.619 5.57 0.00 0.00 3.50
925 2575 1.064017 TCTGCAGGTGGTTTTTGAGGT 60.064 47.619 15.13 0.00 0.00 3.85
929 2579 3.367703 GGATGATCTGCAGGTGGTTTTTG 60.368 47.826 15.13 0.00 0.00 2.44
942 2593 4.082300 CGATAGAACTGAGGGGATGATCTG 60.082 50.000 0.00 0.00 39.76 2.90
944 2595 4.082845 TCGATAGAACTGAGGGGATGATC 58.917 47.826 0.00 0.00 46.15 2.92
961 2612 4.454847 CCTACTACGGCTTCTTGATCGATA 59.545 45.833 0.00 0.00 0.00 2.92
1083 2734 0.318784 GGAAGACGAACAGCACGAGT 60.319 55.000 0.00 0.00 34.70 4.18
1134 2785 4.070552 GCGAAGGTCTCCGCCACT 62.071 66.667 0.00 0.00 45.06 4.00
1408 3059 4.694760 TCCGATGGAAATCAGTCATCAT 57.305 40.909 0.00 0.00 37.67 2.45
1443 3096 4.097437 AGGTACATGCTCATTTGCTCAATG 59.903 41.667 0.00 3.48 43.51 2.82
1461 3114 3.110447 TGTTTCGGGTTACACAGGTAC 57.890 47.619 0.00 0.00 0.00 3.34
1518 3174 5.193679 GGATGTGTTAGAAATGGCCTTAGT 58.806 41.667 3.32 0.00 0.00 2.24
1548 3204 0.539986 TCCACCGTATCCTCCTTTGC 59.460 55.000 0.00 0.00 0.00 3.68
1551 3207 4.966805 TCTTTATTCCACCGTATCCTCCTT 59.033 41.667 0.00 0.00 0.00 3.36
1592 3254 3.542676 CCACGCGGGCCTGGTATA 61.543 66.667 15.02 0.00 0.00 1.47
1597 3259 3.291383 TTTTTCCACGCGGGCCTG 61.291 61.111 12.47 7.41 36.21 4.85
1616 3286 0.531200 GACCTGACCGTGAACCTAGG 59.469 60.000 7.41 7.41 0.00 3.02
1620 3290 1.668151 GCTGACCTGACCGTGAACC 60.668 63.158 0.00 0.00 0.00 3.62
1626 3296 2.821366 GCCATGCTGACCTGACCG 60.821 66.667 0.00 0.00 0.00 4.79
1627 3297 2.042831 GTGCCATGCTGACCTGACC 61.043 63.158 0.00 0.00 0.00 4.02
1635 3305 2.937469 TTAAATTCCGTGCCATGCTG 57.063 45.000 0.00 0.00 0.00 4.41
1639 3309 3.230743 GCACTTTAAATTCCGTGCCAT 57.769 42.857 15.73 0.00 45.08 4.40
1671 3341 3.044059 CTTTGCGTGCCCAGCTAGC 62.044 63.158 6.62 6.62 35.28 3.42
1674 3344 2.034687 ATCTTTGCGTGCCCAGCT 59.965 55.556 0.00 0.00 35.28 4.24
1678 3348 4.179579 GCCGATCTTTGCGTGCCC 62.180 66.667 0.00 0.00 0.00 5.36
1679 3349 2.270297 AATGCCGATCTTTGCGTGCC 62.270 55.000 0.00 0.00 0.00 5.01
1683 3353 2.281359 GCAAATGCCGATCTTTGCG 58.719 52.632 12.62 0.00 45.25 4.85
1685 3355 4.361451 AGTAAGCAAATGCCGATCTTTG 57.639 40.909 0.94 1.76 43.38 2.77
1686 3356 5.741388 CTAGTAAGCAAATGCCGATCTTT 57.259 39.130 0.94 0.00 43.38 2.52
1739 3409 4.123506 GGAAGAAGAAGCAGGTACATAGC 58.876 47.826 0.00 0.00 0.00 2.97
1742 3412 3.307762 GGTGGAAGAAGAAGCAGGTACAT 60.308 47.826 0.00 0.00 0.00 2.29
1786 3456 4.991776 AGAAGGAAGAAGGGAAAAAGGAG 58.008 43.478 0.00 0.00 0.00 3.69
1793 3463 9.502035 TTGTATAGATTAGAAGGAAGAAGGGAA 57.498 33.333 0.00 0.00 0.00 3.97
1795 3465 7.868415 CGTTGTATAGATTAGAAGGAAGAAGGG 59.132 40.741 0.00 0.00 0.00 3.95
1812 3482 6.656314 TGTGCATCTTTTACCGTTGTATAG 57.344 37.500 0.00 0.00 0.00 1.31
1822 3492 5.561499 CGCAATATCGATGTGCATCTTTTAC 59.439 40.000 26.08 4.09 38.19 2.01
1841 3511 2.748605 TCGCAAAAATGAAACCGCAAT 58.251 38.095 0.00 0.00 0.00 3.56
1844 3514 1.317319 CGATCGCAAAAATGAAACCGC 59.683 47.619 0.26 0.00 0.00 5.68
1875 3545 6.142480 CAAAATTGTGCATTTACGGTTAACGA 59.858 34.615 0.00 0.00 38.37 3.85
1924 3594 5.518487 AGCGACAAATTTGACAAAATTCGTT 59.482 32.000 24.64 15.18 43.63 3.85
1928 3598 6.074569 CCGTAAGCGACAAATTTGACAAAATT 60.075 34.615 24.64 12.54 42.76 1.82
1972 3642 0.449388 GATGAAGCTGCCGGTCAAAG 59.551 55.000 1.90 0.00 0.00 2.77
2005 3675 6.597672 ACAGAAGACTTACAACACAAATGTCA 59.402 34.615 0.00 0.00 38.45 3.58
2012 3682 5.290158 GTCGAAACAGAAGACTTACAACACA 59.710 40.000 0.00 0.00 32.58 3.72
2013 3683 5.553952 CGTCGAAACAGAAGACTTACAACAC 60.554 44.000 0.00 0.00 33.10 3.32
2024 3694 3.436496 GGTAGGATCGTCGAAACAGAAG 58.564 50.000 0.00 0.00 0.00 2.85
2045 3715 1.138047 CCTACTTCGGCGTAAGTGCG 61.138 60.000 24.72 17.90 39.95 5.34
2046 3716 0.108945 ACCTACTTCGGCGTAAGTGC 60.109 55.000 24.72 0.00 39.95 4.40
2047 3717 1.068055 ACACCTACTTCGGCGTAAGTG 60.068 52.381 24.72 18.24 39.95 3.16
2048 3718 1.068055 CACACCTACTTCGGCGTAAGT 60.068 52.381 21.81 21.81 42.31 2.24
2049 3719 1.625616 CACACCTACTTCGGCGTAAG 58.374 55.000 6.85 11.83 43.44 2.34
2050 3720 0.388907 GCACACCTACTTCGGCGTAA 60.389 55.000 6.85 0.00 0.00 3.18
2051 3721 1.213537 GCACACCTACTTCGGCGTA 59.786 57.895 6.85 0.00 0.00 4.42
2052 3722 2.048503 GCACACCTACTTCGGCGT 60.049 61.111 6.85 0.00 0.00 5.68
2053 3723 2.048597 TGCACACCTACTTCGGCG 60.049 61.111 0.00 0.00 0.00 6.46
2054 3724 0.245539 TAGTGCACACCTACTTCGGC 59.754 55.000 21.04 0.00 0.00 5.54
2056 3726 6.903883 AAAATATAGTGCACACCTACTTCG 57.096 37.500 21.04 0.00 0.00 3.79
2079 3749 5.952947 AGACGAGAGAGGATAAAGGAGAAAA 59.047 40.000 0.00 0.00 0.00 2.29
2081 3751 4.884744 CAGACGAGAGAGGATAAAGGAGAA 59.115 45.833 0.00 0.00 0.00 2.87
2088 3758 2.887783 GGATGCAGACGAGAGAGGATAA 59.112 50.000 0.00 0.00 0.00 1.75
2097 3767 4.202060 ACAATGTAGTAGGATGCAGACGAG 60.202 45.833 0.00 0.00 0.00 4.18
2101 3771 7.564793 ACAATTACAATGTAGTAGGATGCAGA 58.435 34.615 0.00 0.00 0.00 4.26
2117 3787 2.349627 CCGACGCCGAAAACAATTACAA 60.350 45.455 0.00 0.00 38.22 2.41
2122 3792 0.881159 TGACCGACGCCGAAAACAAT 60.881 50.000 0.00 0.00 38.22 2.71
2124 3794 1.286354 GATGACCGACGCCGAAAACA 61.286 55.000 0.00 0.00 38.22 2.83
2134 3804 1.153349 GGAGGCCAAGATGACCGAC 60.153 63.158 5.01 0.00 0.00 4.79
2162 3832 2.088763 CAGCGACAGTGCAGTACGG 61.089 63.158 17.60 0.00 37.31 4.02
2163 3833 1.081442 TCAGCGACAGTGCAGTACG 60.081 57.895 13.55 13.55 37.31 3.67
2186 3856 2.575262 GAAATGCAGTGCTCGCGC 60.575 61.111 17.60 0.00 0.00 6.86
2225 3895 0.812014 TCGCAAAGAAAGTCCGCACA 60.812 50.000 0.00 0.00 0.00 4.57
2239 3909 3.064987 GCTAGCCTCGTCCTCGCAA 62.065 63.158 2.29 0.00 36.96 4.85
2247 3917 1.132643 CGAACTAGTTGCTAGCCTCGT 59.867 52.381 14.14 2.23 37.65 4.18
2326 3996 0.112995 ATGGTGATTGCTGTGGTGGT 59.887 50.000 0.00 0.00 0.00 4.16
2328 3998 0.528924 CCATGGTGATTGCTGTGGTG 59.471 55.000 2.57 0.00 0.00 4.17
2330 4000 0.813184 GACCATGGTGATTGCTGTGG 59.187 55.000 25.52 0.00 0.00 4.17
2331 4001 0.813184 GGACCATGGTGATTGCTGTG 59.187 55.000 25.52 0.00 0.00 3.66
2332 4002 0.677731 CGGACCATGGTGATTGCTGT 60.678 55.000 25.52 0.00 0.00 4.40
2335 4005 0.676466 TGTCGGACCATGGTGATTGC 60.676 55.000 25.52 7.10 0.00 3.56
2337 4007 0.690192 TGTGTCGGACCATGGTGATT 59.310 50.000 25.52 0.00 0.00 2.57
2338 4008 0.036388 GTGTGTCGGACCATGGTGAT 60.036 55.000 25.52 0.00 0.00 3.06
2339 4009 1.369692 GTGTGTCGGACCATGGTGA 59.630 57.895 25.52 11.96 0.00 4.02
2356 4034 0.329596 GGGGAGGAGAAATGCAGTGT 59.670 55.000 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.