Multiple sequence alignment - TraesCS2B01G340600

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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 TraesCS2B01G340600 chr2B 100.000 2783 0 0 1 2783 486116004 486118786 0.000000e+00 5140
1 TraesCS2B01G340600 chr2B 91.721 918 55 11 1870 2783 569522388 569521488 0.000000e+00 1254
2 TraesCS2B01G340600 chr2B 91.992 487 16 3 1 464 526383419 526382933 0.000000e+00 662
3 TraesCS2B01G340600 chr2D 86.578 1870 83 66 74 1855 412831399 412833188 0.000000e+00 1908
4 TraesCS2B01G340600 chrUn 93.844 926 48 8 1863 2783 348808994 348808073 0.000000e+00 1386
5 TraesCS2B01G340600 chrUn 94.505 728 34 6 2058 2783 424290749 424290026 0.000000e+00 1118
6 TraesCS2B01G340600 chrUn 91.176 170 12 2 1863 2029 289181698 289181867 7.750000e-56 228
7 TraesCS2B01G340600 chrUn 91.176 170 12 2 1863 2029 289187615 289187784 7.750000e-56 228
8 TraesCS2B01G340600 chr3B 93.405 925 52 8 1863 2783 804348568 804347649 0.000000e+00 1362
9 TraesCS2B01G340600 chr7B 91.176 918 71 7 1863 2779 497924963 497925871 0.000000e+00 1238
10 TraesCS2B01G340600 chr7D 87.473 926 91 11 1860 2780 545338163 545339068 0.000000e+00 1044
11 TraesCS2B01G340600 chr5D 90.415 772 66 7 2012 2780 158173204 158173970 0.000000e+00 1009
12 TraesCS2B01G340600 chr2A 84.902 1020 58 32 74 1056 579970881 579971841 0.000000e+00 942
13 TraesCS2B01G340600 chr2A 87.135 754 37 23 1057 1779 579971880 579972604 0.000000e+00 800


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 TraesCS2B01G340600 chr2B 486116004 486118786 2782 False 5140 5140 100.0000 1 2783 1 chr2B.!!$F1 2782
1 TraesCS2B01G340600 chr2B 569521488 569522388 900 True 1254 1254 91.7210 1870 2783 1 chr2B.!!$R2 913
2 TraesCS2B01G340600 chr2D 412831399 412833188 1789 False 1908 1908 86.5780 74 1855 1 chr2D.!!$F1 1781
3 TraesCS2B01G340600 chrUn 348808073 348808994 921 True 1386 1386 93.8440 1863 2783 1 chrUn.!!$R1 920
4 TraesCS2B01G340600 chrUn 424290026 424290749 723 True 1118 1118 94.5050 2058 2783 1 chrUn.!!$R2 725
5 TraesCS2B01G340600 chr3B 804347649 804348568 919 True 1362 1362 93.4050 1863 2783 1 chr3B.!!$R1 920
6 TraesCS2B01G340600 chr7B 497924963 497925871 908 False 1238 1238 91.1760 1863 2779 1 chr7B.!!$F1 916
7 TraesCS2B01G340600 chr7D 545338163 545339068 905 False 1044 1044 87.4730 1860 2780 1 chr7D.!!$F1 920
8 TraesCS2B01G340600 chr5D 158173204 158173970 766 False 1009 1009 90.4150 2012 2780 1 chr5D.!!$F1 768
9 TraesCS2B01G340600 chr2A 579970881 579972604 1723 False 871 942 86.0185 74 1779 2 chr2A.!!$F1 1705

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
342 381 0.03582 AACAAGTGTCACCACCGTGT 60.036 50.0 0.0 0.0 42.88 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1852 1999 0.180406 AGCCGCGTCCAAATCCTTAT 59.82 50.0 4.92 0.0 0.0 1.73 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
19 20 1.866015 TCCTCATTCATCTCCACCGT 58.134 50.000 0.00 0.00 0.00 4.83
20 21 2.187958 TCCTCATTCATCTCCACCGTT 58.812 47.619 0.00 0.00 0.00 4.44
21 22 2.093500 TCCTCATTCATCTCCACCGTTG 60.093 50.000 0.00 0.00 0.00 4.10
22 23 2.355108 CCTCATTCATCTCCACCGTTGT 60.355 50.000 0.00 0.00 0.00 3.32
23 24 2.674852 CTCATTCATCTCCACCGTTGTG 59.325 50.000 0.00 0.00 42.39 3.33
33 34 3.030652 CCGTTGTGGTGTTGCTCC 58.969 61.111 0.00 0.00 0.00 4.70
34 35 1.821759 CCGTTGTGGTGTTGCTCCA 60.822 57.895 0.00 0.00 0.00 3.86
35 36 1.648720 CGTTGTGGTGTTGCTCCAG 59.351 57.895 0.00 0.00 35.49 3.86
36 37 1.785041 CGTTGTGGTGTTGCTCCAGG 61.785 60.000 0.00 0.00 35.49 4.45
37 38 0.465460 GTTGTGGTGTTGCTCCAGGA 60.465 55.000 0.00 0.00 35.49 3.86
38 39 0.257328 TTGTGGTGTTGCTCCAGGAA 59.743 50.000 0.00 0.00 35.49 3.36
39 40 0.465460 TGTGGTGTTGCTCCAGGAAC 60.465 55.000 4.11 4.11 45.04 3.62
40 41 0.179018 GTGGTGTTGCTCCAGGAACT 60.179 55.000 11.68 0.00 45.06 3.01
41 42 1.071699 GTGGTGTTGCTCCAGGAACTA 59.928 52.381 11.68 0.00 45.06 2.24
42 43 1.347707 TGGTGTTGCTCCAGGAACTAG 59.652 52.381 11.68 0.00 45.06 2.57
43 44 1.443802 GTGTTGCTCCAGGAACTAGC 58.556 55.000 11.68 0.00 45.06 3.42
44 45 1.002544 GTGTTGCTCCAGGAACTAGCT 59.997 52.381 11.68 0.00 45.06 3.32
45 46 1.276421 TGTTGCTCCAGGAACTAGCTC 59.724 52.381 11.68 0.00 45.06 4.09
46 47 1.276421 GTTGCTCCAGGAACTAGCTCA 59.724 52.381 3.85 0.00 40.45 4.26
47 48 1.644509 TGCTCCAGGAACTAGCTCAA 58.355 50.000 0.00 0.00 40.45 3.02
48 49 1.552337 TGCTCCAGGAACTAGCTCAAG 59.448 52.381 0.00 0.00 40.45 3.02
49 50 1.552792 GCTCCAGGAACTAGCTCAAGT 59.447 52.381 0.00 0.00 37.11 3.16
50 51 2.027653 GCTCCAGGAACTAGCTCAAGTT 60.028 50.000 1.40 1.40 42.36 2.66
51 52 3.558109 GCTCCAGGAACTAGCTCAAGTTT 60.558 47.826 3.44 0.00 39.78 2.66
52 53 4.646572 CTCCAGGAACTAGCTCAAGTTTT 58.353 43.478 3.44 0.00 39.78 2.43
53 54 4.642429 TCCAGGAACTAGCTCAAGTTTTC 58.358 43.478 3.44 0.75 39.78 2.29
54 55 3.753797 CCAGGAACTAGCTCAAGTTTTCC 59.246 47.826 3.44 1.92 39.78 3.13
55 56 3.433615 CAGGAACTAGCTCAAGTTTTCCG 59.566 47.826 3.44 0.00 39.78 4.30
56 57 2.159824 GGAACTAGCTCAAGTTTTCCGC 59.840 50.000 3.44 0.00 39.78 5.54
57 58 2.543777 ACTAGCTCAAGTTTTCCGCA 57.456 45.000 0.00 0.00 0.00 5.69
58 59 2.846193 ACTAGCTCAAGTTTTCCGCAA 58.154 42.857 0.00 0.00 0.00 4.85
59 60 3.211045 ACTAGCTCAAGTTTTCCGCAAA 58.789 40.909 0.00 0.00 0.00 3.68
60 61 3.630312 ACTAGCTCAAGTTTTCCGCAAAA 59.370 39.130 0.00 0.00 0.00 2.44
61 62 3.518634 AGCTCAAGTTTTCCGCAAAAA 57.481 38.095 0.00 0.00 33.17 1.94
89 90 7.977789 TTCAAGTAGTGCAGATTTCAATACA 57.022 32.000 0.00 0.00 37.44 2.29
90 91 7.601073 TCAAGTAGTGCAGATTTCAATACAG 57.399 36.000 0.00 0.00 37.44 2.74
99 100 5.726138 GCAGATTTCAATACAGACTGAAGCG 60.726 44.000 10.08 0.00 33.30 4.68
100 101 4.872691 AGATTTCAATACAGACTGAAGCGG 59.127 41.667 10.08 0.00 33.30 5.52
102 103 1.275010 TCAATACAGACTGAAGCGGCA 59.725 47.619 10.08 0.00 0.00 5.69
103 104 2.076100 CAATACAGACTGAAGCGGCAA 58.924 47.619 10.08 0.00 0.00 4.52
104 105 1.726853 ATACAGACTGAAGCGGCAAC 58.273 50.000 10.08 0.00 0.00 4.17
145 148 0.890996 CCTGCTCAGGTGGTTCCAAC 60.891 60.000 7.75 0.00 43.61 3.77
160 163 2.257207 TCCAACCCAGTAAGTCTCAGG 58.743 52.381 0.00 0.00 0.00 3.86
184 187 0.183731 CAGTTCATAGCCCCCTTCCC 59.816 60.000 0.00 0.00 0.00 3.97
185 188 0.253630 AGTTCATAGCCCCCTTCCCA 60.254 55.000 0.00 0.00 0.00 4.37
187 190 1.149101 TTCATAGCCCCCTTCCCATC 58.851 55.000 0.00 0.00 0.00 3.51
188 191 0.271927 TCATAGCCCCCTTCCCATCT 59.728 55.000 0.00 0.00 0.00 2.90
190 193 2.089638 TCATAGCCCCCTTCCCATCTAA 60.090 50.000 0.00 0.00 0.00 2.10
191 194 2.835696 TAGCCCCCTTCCCATCTAAT 57.164 50.000 0.00 0.00 0.00 1.73
192 195 1.152649 AGCCCCCTTCCCATCTAATG 58.847 55.000 0.00 0.00 0.00 1.90
208 211 7.876936 CATCTAATGGATGGATGGAATTAGG 57.123 40.000 0.00 0.00 45.85 2.69
209 212 7.408543 CATCTAATGGATGGATGGAATTAGGT 58.591 38.462 0.00 0.00 45.85 3.08
210 213 7.406620 TCTAATGGATGGATGGAATTAGGTT 57.593 36.000 0.00 0.00 33.55 3.50
211 214 7.825709 TCTAATGGATGGATGGAATTAGGTTT 58.174 34.615 0.00 0.00 33.55 3.27
212 215 6.983906 AATGGATGGATGGAATTAGGTTTC 57.016 37.500 0.00 0.00 0.00 2.78
214 217 4.080015 TGGATGGATGGAATTAGGTTTCGT 60.080 41.667 0.00 0.00 0.00 3.85
219 222 5.949354 TGGATGGAATTAGGTTTCGTTTGAT 59.051 36.000 0.00 0.00 0.00 2.57
220 223 7.113437 TGGATGGAATTAGGTTTCGTTTGATA 58.887 34.615 0.00 0.00 0.00 2.15
221 224 7.066525 TGGATGGAATTAGGTTTCGTTTGATAC 59.933 37.037 0.00 0.00 0.00 2.24
255 261 4.561105 GTTATCTGGGAAGAGCCTATTCG 58.439 47.826 0.00 0.00 36.66 3.34
270 276 1.950828 ATTCGCTCATCCAGAAGCTG 58.049 50.000 0.00 0.00 0.00 4.24
288 294 2.420129 GCTGGTATCCCACGAACTCAAT 60.420 50.000 0.00 0.00 35.17 2.57
298 304 4.332819 CCCACGAACTCAATCTAATTCCAC 59.667 45.833 0.00 0.00 0.00 4.02
342 381 0.035820 AACAAGTGTCACCACCGTGT 60.036 50.000 0.00 0.00 42.88 4.49
343 382 0.461339 ACAAGTGTCACCACCGTGTC 60.461 55.000 0.00 0.00 42.88 3.67
344 383 0.461163 CAAGTGTCACCACCGTGTCA 60.461 55.000 0.00 0.00 42.88 3.58
345 384 0.179084 AAGTGTCACCACCGTGTCAG 60.179 55.000 0.00 0.00 42.88 3.51
346 385 1.040893 AGTGTCACCACCGTGTCAGA 61.041 55.000 0.00 0.00 42.88 3.27
347 386 0.874607 GTGTCACCACCGTGTCAGAC 60.875 60.000 0.00 0.00 38.46 3.51
355 394 2.279186 CGTGTCAGACGCACACCA 60.279 61.111 14.49 0.00 42.21 4.17
356 395 2.585869 CGTGTCAGACGCACACCAC 61.586 63.158 14.49 0.00 42.21 4.16
357 396 1.520564 GTGTCAGACGCACACCACA 60.521 57.895 9.36 0.00 38.61 4.17
358 397 1.087202 GTGTCAGACGCACACCACAA 61.087 55.000 9.36 0.00 38.61 3.33
359 398 0.391793 TGTCAGACGCACACCACAAA 60.392 50.000 0.00 0.00 0.00 2.83
360 399 0.304705 GTCAGACGCACACCACAAAG 59.695 55.000 0.00 0.00 0.00 2.77
361 400 0.176910 TCAGACGCACACCACAAAGA 59.823 50.000 0.00 0.00 0.00 2.52
362 401 1.013596 CAGACGCACACCACAAAGAA 58.986 50.000 0.00 0.00 0.00 2.52
363 402 1.014352 AGACGCACACCACAAAGAAC 58.986 50.000 0.00 0.00 0.00 3.01
364 403 1.014352 GACGCACACCACAAAGAACT 58.986 50.000 0.00 0.00 0.00 3.01
365 404 1.400494 GACGCACACCACAAAGAACTT 59.600 47.619 0.00 0.00 0.00 2.66
366 405 1.132262 ACGCACACCACAAAGAACTTG 59.868 47.619 0.00 0.00 41.19 3.16
416 465 0.676466 CCGGTCCATGCACAGCTTAA 60.676 55.000 0.00 0.00 0.00 1.85
433 482 3.434637 CTTAAATGCGCGCCATTAAACT 58.565 40.909 30.77 14.42 43.22 2.66
440 489 2.348856 CGCCATTAAACTGCGCAAC 58.651 52.632 13.05 0.00 41.95 4.17
500 549 3.962063 TGACCAGAGTTGTTGTACCAGTA 59.038 43.478 0.00 0.00 0.00 2.74
524 573 3.788766 CCGAACCAAAGAGGCGCG 61.789 66.667 0.00 0.00 43.14 6.86
670 733 4.452251 TCCTTCGGCCGGCCTCTA 62.452 66.667 41.01 24.61 0.00 2.43
683 746 2.443016 CTCTACCCCGGCTGCTCT 60.443 66.667 0.00 0.00 0.00 4.09
752 819 2.736721 CGATGAGGGGCATAAATACGTG 59.263 50.000 0.00 0.00 37.34 4.49
753 820 1.961793 TGAGGGGCATAAATACGTGC 58.038 50.000 0.00 0.00 40.55 5.34
761 828 1.946768 CATAAATACGTGCCAGGTGGG 59.053 52.381 0.00 0.00 40.85 4.61
814 884 2.287668 GCTAGTGGGCACATCTACTACG 60.288 54.545 0.00 0.00 0.00 3.51
955 1030 0.038801 CTCTGACTCTGAAGCGTGCA 60.039 55.000 0.00 0.00 0.00 4.57
969 1044 1.154672 GTGCATGCGTACGTGTGTG 60.155 57.895 17.90 11.32 35.09 3.82
970 1045 1.592939 TGCATGCGTACGTGTGTGT 60.593 52.632 17.90 0.00 35.09 3.72
971 1046 1.154672 GCATGCGTACGTGTGTGTG 60.155 57.895 17.90 7.99 35.09 3.82
1040 1115 0.179166 GTCTCGCTGTCTGCTCTCTG 60.179 60.000 0.00 0.00 40.11 3.35
1050 1125 0.176219 CTGCTCTCTGGCTTCCTCAG 59.824 60.000 0.00 0.00 0.00 3.35
1066 1179 1.228063 CAGTTCCTGCTGTGGTGCT 60.228 57.895 0.00 0.00 0.00 4.40
1073 1186 4.394712 GCTGTGGTGCTAGCCGGT 62.395 66.667 13.29 0.00 33.89 5.28
1733 1880 1.514678 TTGGCGTGATGCTTGTGGAC 61.515 55.000 0.00 0.00 45.43 4.02
1764 1911 6.432607 TCCTCGAGTGTTGTAAGTATGTAG 57.567 41.667 12.31 0.00 0.00 2.74
1765 1912 5.942236 TCCTCGAGTGTTGTAAGTATGTAGT 59.058 40.000 12.31 0.00 0.00 2.73
1766 1913 7.105588 TCCTCGAGTGTTGTAAGTATGTAGTA 58.894 38.462 12.31 0.00 0.00 1.82
1790 1937 5.409643 AAGTTAATGTGCTGCGACATATC 57.590 39.130 14.84 10.00 35.43 1.63
1792 1939 4.271049 AGTTAATGTGCTGCGACATATCAC 59.729 41.667 14.84 12.16 35.43 3.06
1852 1999 1.252215 TGATCACGGGTTAGCGGTCA 61.252 55.000 0.00 0.00 0.00 4.02
1853 2000 0.104304 GATCACGGGTTAGCGGTCAT 59.896 55.000 0.00 0.00 0.00 3.06
1854 2001 1.338973 GATCACGGGTTAGCGGTCATA 59.661 52.381 0.00 0.00 0.00 2.15
1856 2003 1.135527 TCACGGGTTAGCGGTCATAAG 59.864 52.381 0.00 0.00 0.00 1.73
1857 2004 0.462789 ACGGGTTAGCGGTCATAAGG 59.537 55.000 0.00 0.00 0.00 2.69
1858 2005 0.748450 CGGGTTAGCGGTCATAAGGA 59.252 55.000 0.00 0.00 0.00 3.36
1859 2006 1.343465 CGGGTTAGCGGTCATAAGGAT 59.657 52.381 0.00 0.00 0.00 3.24
1860 2007 2.224209 CGGGTTAGCGGTCATAAGGATT 60.224 50.000 0.00 0.00 0.00 3.01
1861 2008 3.743269 CGGGTTAGCGGTCATAAGGATTT 60.743 47.826 0.00 0.00 0.00 2.17
1877 2024 1.906105 ATTTGGACGCGGCTAGGGAA 61.906 55.000 13.91 0.00 36.53 3.97
1907 2054 4.609018 CCCTAGCATCCCGTGGCG 62.609 72.222 0.00 0.00 34.54 5.69
1921 2068 0.885196 GTGGCGGCCTGTCATAAAAA 59.115 50.000 21.46 0.00 32.65 1.94
1962 2112 4.953579 TGACAAAAAGGAAAACTAGCCAGT 59.046 37.500 0.00 0.00 36.19 4.00
1994 2145 1.680651 CGCTCTCCTCACCTGGTCT 60.681 63.158 0.00 0.00 0.00 3.85
2031 2182 0.034089 CTTCCGCTCCCTCCCAAAAT 60.034 55.000 0.00 0.00 0.00 1.82
2055 2206 1.411787 CCCCTTCTCCTGACGATACCT 60.412 57.143 0.00 0.00 0.00 3.08
2087 2239 2.236395 CCCGTGTACCCATCTTCTTCTT 59.764 50.000 0.00 0.00 0.00 2.52
2106 2258 7.518188 TCTTCTTCATCAAGTTAGGGTTTTCT 58.482 34.615 0.00 0.00 0.00 2.52
2133 2286 4.324563 CCCAAGATCCAGAAAGCTTCCTTA 60.325 45.833 0.00 0.00 0.00 2.69
2159 2312 0.537143 CAATGGCGGCATAAGGGCTA 60.537 55.000 26.05 0.00 40.61 3.93
2192 2345 3.486875 CCAAACTGACGGACAAAACTCAC 60.487 47.826 0.00 0.00 0.00 3.51
2200 2355 3.374058 ACGGACAAAACTCACAACAGAAG 59.626 43.478 0.00 0.00 0.00 2.85
2350 2515 2.092753 GCATCTCCCTTTCTCATGTGGA 60.093 50.000 0.00 0.00 0.00 4.02
2525 2691 1.747355 GATCTGGGCAAGACACCAATG 59.253 52.381 0.00 0.00 37.88 2.82
2698 2864 0.322975 CCTGAGTAACTGCAGGTGCT 59.677 55.000 23.30 23.30 45.21 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.283298 CAACGGTGGAGATGAATGAGG 58.717 52.381 0.00 0.00 0.00 3.86
2 3 2.674852 CACAACGGTGGAGATGAATGAG 59.325 50.000 4.97 0.00 41.45 2.90
3 4 2.698803 CACAACGGTGGAGATGAATGA 58.301 47.619 4.97 0.00 41.45 2.57
16 17 1.785041 CTGGAGCAACACCACAACGG 61.785 60.000 0.00 0.00 42.50 4.44
17 18 1.648720 CTGGAGCAACACCACAACG 59.351 57.895 0.00 0.00 33.57 4.10
18 19 0.465460 TCCTGGAGCAACACCACAAC 60.465 55.000 0.00 0.00 33.57 3.32
19 20 0.257328 TTCCTGGAGCAACACCACAA 59.743 50.000 0.00 0.00 33.57 3.33
20 21 0.465460 GTTCCTGGAGCAACACCACA 60.465 55.000 5.59 0.00 33.57 4.17
21 22 0.179018 AGTTCCTGGAGCAACACCAC 60.179 55.000 13.26 0.00 33.57 4.16
22 23 1.347707 CTAGTTCCTGGAGCAACACCA 59.652 52.381 13.26 0.00 35.96 4.17
23 24 1.946283 GCTAGTTCCTGGAGCAACACC 60.946 57.143 13.26 0.00 36.20 4.16
24 25 1.002544 AGCTAGTTCCTGGAGCAACAC 59.997 52.381 13.26 0.18 38.73 3.32
25 26 1.276421 GAGCTAGTTCCTGGAGCAACA 59.724 52.381 13.26 0.00 38.73 3.33
26 27 1.276421 TGAGCTAGTTCCTGGAGCAAC 59.724 52.381 13.26 0.95 38.73 4.17
27 28 1.644509 TGAGCTAGTTCCTGGAGCAA 58.355 50.000 13.26 0.00 38.73 3.91
28 29 1.552337 CTTGAGCTAGTTCCTGGAGCA 59.448 52.381 13.26 0.00 38.73 4.26
29 30 1.552792 ACTTGAGCTAGTTCCTGGAGC 59.447 52.381 1.81 1.81 36.42 4.70
30 31 3.971245 AACTTGAGCTAGTTCCTGGAG 57.029 47.619 3.94 0.40 33.12 3.86
31 32 4.505039 GGAAAACTTGAGCTAGTTCCTGGA 60.505 45.833 3.94 0.00 37.37 3.86
32 33 3.753797 GGAAAACTTGAGCTAGTTCCTGG 59.246 47.826 3.94 0.00 37.37 4.45
33 34 3.433615 CGGAAAACTTGAGCTAGTTCCTG 59.566 47.826 3.94 0.00 37.37 3.86
34 35 3.665190 CGGAAAACTTGAGCTAGTTCCT 58.335 45.455 3.94 0.00 37.37 3.36
35 36 2.159824 GCGGAAAACTTGAGCTAGTTCC 59.840 50.000 3.94 0.60 37.37 3.62
36 37 2.806244 TGCGGAAAACTTGAGCTAGTTC 59.194 45.455 2.38 0.00 37.37 3.01
37 38 2.846193 TGCGGAAAACTTGAGCTAGTT 58.154 42.857 0.00 0.00 39.97 2.24
38 39 2.543777 TGCGGAAAACTTGAGCTAGT 57.456 45.000 0.00 0.00 0.00 2.57
39 40 3.896648 TTTGCGGAAAACTTGAGCTAG 57.103 42.857 0.00 0.00 0.00 3.42
40 41 4.640789 TTTTTGCGGAAAACTTGAGCTA 57.359 36.364 14.81 0.00 32.44 3.32
41 42 3.518634 TTTTTGCGGAAAACTTGAGCT 57.481 38.095 14.81 0.00 32.44 4.09
60 61 9.768662 ATTGAAATCTGCACTACTTGAATTTTT 57.231 25.926 0.00 0.00 0.00 1.94
62 63 9.846248 GTATTGAAATCTGCACTACTTGAATTT 57.154 29.630 0.00 0.00 0.00 1.82
63 64 9.013229 TGTATTGAAATCTGCACTACTTGAATT 57.987 29.630 0.00 0.00 0.00 2.17
64 65 8.565896 TGTATTGAAATCTGCACTACTTGAAT 57.434 30.769 0.00 0.00 0.00 2.57
65 66 7.877612 TCTGTATTGAAATCTGCACTACTTGAA 59.122 33.333 0.00 0.00 0.00 2.69
66 67 7.331934 GTCTGTATTGAAATCTGCACTACTTGA 59.668 37.037 0.00 0.00 0.00 3.02
67 68 7.332926 AGTCTGTATTGAAATCTGCACTACTTG 59.667 37.037 0.00 0.00 0.00 3.16
68 69 7.332926 CAGTCTGTATTGAAATCTGCACTACTT 59.667 37.037 0.00 0.00 0.00 2.24
69 70 6.815641 CAGTCTGTATTGAAATCTGCACTACT 59.184 38.462 0.00 0.00 0.00 2.57
70 71 6.813649 TCAGTCTGTATTGAAATCTGCACTAC 59.186 38.462 0.00 0.00 0.00 2.73
71 72 6.935167 TCAGTCTGTATTGAAATCTGCACTA 58.065 36.000 0.00 0.00 0.00 2.74
72 73 5.798132 TCAGTCTGTATTGAAATCTGCACT 58.202 37.500 0.00 0.00 0.00 4.40
75 76 5.567552 GCTTCAGTCTGTATTGAAATCTGC 58.432 41.667 0.00 0.00 31.72 4.26
89 90 0.179045 ACTTGTTGCCGCTTCAGTCT 60.179 50.000 0.00 0.00 0.00 3.24
90 91 0.663153 AACTTGTTGCCGCTTCAGTC 59.337 50.000 0.00 0.00 0.00 3.51
145 148 2.303022 TGAAAGCCTGAGACTTACTGGG 59.697 50.000 0.00 0.00 0.00 4.45
149 152 4.632153 TGAACTGAAAGCCTGAGACTTAC 58.368 43.478 0.00 0.00 37.60 2.34
150 153 4.955811 TGAACTGAAAGCCTGAGACTTA 57.044 40.909 0.00 0.00 37.60 2.24
160 163 1.064389 AGGGGGCTATGAACTGAAAGC 60.064 52.381 0.00 0.00 37.60 3.51
185 188 7.594849 ACCTAATTCCATCCATCCATTAGAT 57.405 36.000 0.00 0.00 31.61 1.98
187 190 7.094634 CGAAACCTAATTCCATCCATCCATTAG 60.095 40.741 0.00 0.00 0.00 1.73
188 191 6.714810 CGAAACCTAATTCCATCCATCCATTA 59.285 38.462 0.00 0.00 0.00 1.90
190 193 5.072741 CGAAACCTAATTCCATCCATCCAT 58.927 41.667 0.00 0.00 0.00 3.41
191 194 4.080015 ACGAAACCTAATTCCATCCATCCA 60.080 41.667 0.00 0.00 0.00 3.41
192 195 4.461198 ACGAAACCTAATTCCATCCATCC 58.539 43.478 0.00 0.00 0.00 3.51
195 198 5.317808 TCAAACGAAACCTAATTCCATCCA 58.682 37.500 0.00 0.00 0.00 3.41
214 217 8.233868 CAGATAACCACAACAATTCGTATCAAA 58.766 33.333 0.00 0.00 0.00 2.69
219 222 4.938832 CCCAGATAACCACAACAATTCGTA 59.061 41.667 0.00 0.00 0.00 3.43
220 223 3.756434 CCCAGATAACCACAACAATTCGT 59.244 43.478 0.00 0.00 0.00 3.85
221 224 4.006989 TCCCAGATAACCACAACAATTCG 58.993 43.478 0.00 0.00 0.00 3.34
223 226 5.640147 TCTTCCCAGATAACCACAACAATT 58.360 37.500 0.00 0.00 0.00 2.32
225 228 4.651778 CTCTTCCCAGATAACCACAACAA 58.348 43.478 0.00 0.00 0.00 2.83
226 229 3.559171 GCTCTTCCCAGATAACCACAACA 60.559 47.826 0.00 0.00 0.00 3.33
229 232 1.559682 GGCTCTTCCCAGATAACCACA 59.440 52.381 0.00 0.00 0.00 4.17
232 235 4.561734 CGAATAGGCTCTTCCCAGATAACC 60.562 50.000 7.01 0.00 34.51 2.85
237 240 0.753262 GCGAATAGGCTCTTCCCAGA 59.247 55.000 7.01 0.00 34.51 3.86
274 280 4.224147 TGGAATTAGATTGAGTTCGTGGGA 59.776 41.667 0.00 0.00 0.00 4.37
288 294 2.777692 GGGTCTGATGGGTGGAATTAGA 59.222 50.000 0.00 0.00 0.00 2.10
298 304 1.524621 GCATCGTGGGTCTGATGGG 60.525 63.158 4.57 0.00 41.76 4.00
342 381 0.176910 TCTTTGTGGTGTGCGTCTGA 59.823 50.000 0.00 0.00 0.00 3.27
343 382 1.013596 TTCTTTGTGGTGTGCGTCTG 58.986 50.000 0.00 0.00 0.00 3.51
344 383 1.014352 GTTCTTTGTGGTGTGCGTCT 58.986 50.000 0.00 0.00 0.00 4.18
345 384 1.014352 AGTTCTTTGTGGTGTGCGTC 58.986 50.000 0.00 0.00 0.00 5.19
346 385 1.132262 CAAGTTCTTTGTGGTGTGCGT 59.868 47.619 0.00 0.00 31.92 5.24
347 386 1.533756 CCAAGTTCTTTGTGGTGTGCG 60.534 52.381 0.00 0.00 34.87 5.34
348 387 1.802508 GCCAAGTTCTTTGTGGTGTGC 60.803 52.381 0.00 0.00 34.87 4.57
349 388 1.476085 TGCCAAGTTCTTTGTGGTGTG 59.524 47.619 0.00 0.00 34.87 3.82
350 389 1.750778 CTGCCAAGTTCTTTGTGGTGT 59.249 47.619 0.00 0.00 34.87 4.16
351 390 1.536709 GCTGCCAAGTTCTTTGTGGTG 60.537 52.381 0.00 0.00 34.87 4.17
352 391 0.746659 GCTGCCAAGTTCTTTGTGGT 59.253 50.000 0.00 0.00 34.87 4.16
353 392 0.318107 CGCTGCCAAGTTCTTTGTGG 60.318 55.000 0.00 0.00 34.87 4.17
354 393 0.381801 ACGCTGCCAAGTTCTTTGTG 59.618 50.000 0.00 0.00 34.87 3.33
355 394 0.663153 GACGCTGCCAAGTTCTTTGT 59.337 50.000 0.00 0.00 34.87 2.83
356 395 0.662619 TGACGCTGCCAAGTTCTTTG 59.337 50.000 0.00 0.00 36.50 2.77
357 396 0.947244 CTGACGCTGCCAAGTTCTTT 59.053 50.000 0.00 0.00 0.00 2.52
358 397 0.106708 TCTGACGCTGCCAAGTTCTT 59.893 50.000 0.00 0.00 0.00 2.52
359 398 0.601311 GTCTGACGCTGCCAAGTTCT 60.601 55.000 0.00 0.00 0.00 3.01
360 399 0.880278 TGTCTGACGCTGCCAAGTTC 60.880 55.000 2.98 0.00 0.00 3.01
361 400 1.146041 TGTCTGACGCTGCCAAGTT 59.854 52.632 2.98 0.00 0.00 2.66
362 401 1.595382 GTGTCTGACGCTGCCAAGT 60.595 57.895 13.82 0.00 0.00 3.16
363 402 2.661566 CGTGTCTGACGCTGCCAAG 61.662 63.158 18.17 0.00 42.21 3.61
364 403 2.661537 CGTGTCTGACGCTGCCAA 60.662 61.111 18.17 0.00 42.21 4.52
390 429 2.897350 GCATGGACCGGCTGCTAC 60.897 66.667 0.00 0.00 33.15 3.58
416 465 0.801836 GCAGTTTAATGGCGCGCATT 60.802 50.000 34.42 28.41 0.00 3.56
433 482 3.046087 GAGCTGCTCTGTTGCGCA 61.046 61.111 21.93 5.66 35.88 6.09
468 517 3.635268 CTCTGGTCAAGCTGGGCCC 62.635 68.421 17.59 17.59 0.00 5.80
474 523 2.717639 ACAACAACTCTGGTCAAGCT 57.282 45.000 0.00 0.00 0.00 3.74
500 549 2.817844 GCCTCTTTGGTTCGGTTAATGT 59.182 45.455 0.00 0.00 38.35 2.71
524 573 2.512057 GCTCTGCTCTGCTCTGCC 60.512 66.667 0.00 0.00 0.00 4.85
563 612 1.424493 CTGAAATCCTGAGCGCGACC 61.424 60.000 12.10 0.00 0.00 4.79
670 733 3.710722 CAGAAGAGCAGCCGGGGT 61.711 66.667 2.18 0.00 0.00 4.95
752 819 1.595382 CGATCGATTCCCACCTGGC 60.595 63.158 10.26 0.00 0.00 4.85
753 820 0.681733 ATCGATCGATTCCCACCTGG 59.318 55.000 24.60 0.00 0.00 4.45
799 869 0.032267 GAGGCGTAGTAGATGTGCCC 59.968 60.000 0.00 0.00 46.92 5.36
814 884 1.061485 GAACACGAAGAAGACGAGGC 58.939 55.000 0.00 0.00 34.70 4.70
849 919 2.268076 ATGGAACCCTTGTGCGTGC 61.268 57.895 0.00 0.00 0.00 5.34
850 920 1.172180 ACATGGAACCCTTGTGCGTG 61.172 55.000 0.00 0.00 39.83 5.34
851 921 1.150536 ACATGGAACCCTTGTGCGT 59.849 52.632 0.00 0.00 39.83 5.24
852 922 1.580942 CACATGGAACCCTTGTGCG 59.419 57.895 15.81 0.00 46.98 5.34
955 1030 2.357327 ATACACACACACGTACGCAT 57.643 45.000 16.72 0.00 0.00 4.73
1050 1125 1.301677 GCTAGCACCACAGCAGGAAC 61.302 60.000 10.63 0.00 37.73 3.62
1066 1179 1.140252 GCCTCCTCATTAAACCGGCTA 59.860 52.381 0.00 0.00 33.47 3.93
1073 1186 1.064463 CCAGCAGGCCTCCTCATTAAA 60.064 52.381 0.00 0.00 0.00 1.52
1148 1261 3.753539 GTCACGCACGAGCACGAC 61.754 66.667 11.40 6.75 42.27 4.34
1302 1415 2.182842 GGCGCCTGAACCTGCATAG 61.183 63.158 22.15 0.00 0.00 2.23
1435 1551 4.548513 CTCCTCCTCCCCCTCCCG 62.549 77.778 0.00 0.00 0.00 5.14
1733 1880 1.260561 CAACACTCGAGGAACAAACGG 59.739 52.381 18.41 0.00 0.00 4.44
1764 1911 4.778904 TGTCGCAGCACATTAACTTTTAC 58.221 39.130 0.00 0.00 0.00 2.01
1765 1912 5.621197 ATGTCGCAGCACATTAACTTTTA 57.379 34.783 5.04 0.00 32.81 1.52
1766 1913 3.980646 TGTCGCAGCACATTAACTTTT 57.019 38.095 0.00 0.00 0.00 2.27
1780 1927 4.991153 AAGAAGAGAGTGATATGTCGCA 57.009 40.909 5.77 0.00 37.33 5.10
1810 1957 6.984474 TCAGTCATCGTCTACTTGTTCTTTTT 59.016 34.615 0.00 0.00 0.00 1.94
1811 1958 6.513180 TCAGTCATCGTCTACTTGTTCTTTT 58.487 36.000 0.00 0.00 0.00 2.27
1812 1959 6.085555 TCAGTCATCGTCTACTTGTTCTTT 57.914 37.500 0.00 0.00 0.00 2.52
1813 1960 5.707242 TCAGTCATCGTCTACTTGTTCTT 57.293 39.130 0.00 0.00 0.00 2.52
1814 1961 5.416013 TGATCAGTCATCGTCTACTTGTTCT 59.584 40.000 0.00 0.00 33.61 3.01
1815 1962 5.513495 GTGATCAGTCATCGTCTACTTGTTC 59.487 44.000 0.00 0.00 36.60 3.18
1852 1999 0.180406 AGCCGCGTCCAAATCCTTAT 59.820 50.000 4.92 0.00 0.00 1.73
1853 2000 0.825410 TAGCCGCGTCCAAATCCTTA 59.175 50.000 4.92 0.00 0.00 2.69
1854 2001 0.462047 CTAGCCGCGTCCAAATCCTT 60.462 55.000 4.92 0.00 0.00 3.36
1856 2003 1.887707 CCTAGCCGCGTCCAAATCC 60.888 63.158 4.92 0.00 0.00 3.01
1857 2004 1.887707 CCCTAGCCGCGTCCAAATC 60.888 63.158 4.92 0.00 0.00 2.17
1858 2005 1.906105 TTCCCTAGCCGCGTCCAAAT 61.906 55.000 4.92 0.00 0.00 2.32
1859 2006 2.585341 TTCCCTAGCCGCGTCCAAA 61.585 57.895 4.92 0.00 0.00 3.28
1860 2007 2.998480 TTCCCTAGCCGCGTCCAA 60.998 61.111 4.92 0.00 0.00 3.53
1861 2008 3.766691 GTTCCCTAGCCGCGTCCA 61.767 66.667 4.92 0.00 0.00 4.02
1950 2099 0.605589 GGCGTGGACTGGCTAGTTTT 60.606 55.000 3.47 0.00 37.25 2.43
2031 2182 2.683933 GTCAGGAGAAGGGGGCGA 60.684 66.667 0.00 0.00 0.00 5.54
2055 2206 0.909133 GTACACGGGGGAAGGGGTTA 60.909 60.000 0.00 0.00 0.00 2.85
2087 2239 6.238648 GGAAGAGAAAACCCTAACTTGATGA 58.761 40.000 0.00 0.00 0.00 2.92
2106 2258 2.915604 AGCTTTCTGGATCTTGGGAAGA 59.084 45.455 0.00 0.00 42.69 2.87
2133 2286 0.467844 TATGCCGCCATTGCAGGAAT 60.468 50.000 0.00 2.14 42.92 3.01
2217 2372 0.823356 GTTGAGCAAACCTGGCCTCA 60.823 55.000 3.32 0.00 32.13 3.86
2525 2691 7.636359 CGATTTTCTTACAACACTGCTATTAGC 59.364 37.037 8.80 8.80 42.82 3.09
2545 2711 5.819059 TGCGTAAAACTGGTAAACGATTTT 58.181 33.333 4.19 0.00 35.66 1.82
2737 2906 4.827284 ACTACTTGCCTAAAACAAGCATGT 59.173 37.500 3.52 7.70 46.81 3.21


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

AutoCloner maintained by Alex Coulton.