Multiple sequence alignment - TraesCS2A01G199000

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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 TraesCS2A01G199000 chr2A 100.000 2537 0 0 1 2537 171608317 171610853 0.000000e+00 4686
1 TraesCS2A01G199000 chr2A 76.316 342 49 22 1140 1456 511076399 511076733 1.220000e-33 154
2 TraesCS2A01G199000 chr2D 90.106 1415 77 25 476 1844 160212135 160210738 0.000000e+00 1779
3 TraesCS2A01G199000 chr2D 92.000 275 21 1 2242 2516 160210165 160209892 3.960000e-103 385
4 TraesCS2A01G199000 chr2D 80.753 478 86 6 3 476 527497154 527496679 3.990000e-98 368
5 TraesCS2A01G199000 chr2D 78.916 332 40 12 1874 2175 160210592 160210261 5.540000e-47 198
6 TraesCS2A01G199000 chr2D 76.106 339 55 16 1140 1456 377122188 377122522 1.220000e-33 154
7 TraesCS2A01G199000 chr2B 90.992 1210 64 24 669 1844 216965841 216964643 0.000000e+00 1589
8 TraesCS2A01G199000 chr2B 83.144 706 62 14 1874 2537 216964496 216963806 2.170000e-165 592
9 TraesCS2A01G199000 chr2B 82.667 450 60 11 37 477 528199415 528199855 1.420000e-102 383
10 TraesCS2A01G199000 chr2B 76.190 336 54 16 1140 1453 448695069 448695400 1.220000e-33 154
11 TraesCS2A01G199000 chr4D 82.274 519 75 11 1 507 81965514 81966027 1.390000e-117 433
12 TraesCS2A01G199000 chr4D 85.859 99 12 2 1747 1844 50391061 50390964 1.240000e-18 104
13 TraesCS2A01G199000 chr7A 82.822 489 68 9 1 476 584358359 584357874 8.390000e-115 424
14 TraesCS2A01G199000 chr7A 78.879 232 38 8 2 222 700066479 700066248 2.030000e-31 147
15 TraesCS2A01G199000 chr5B 82.077 491 75 7 1 483 133900309 133899824 8.450000e-110 407
16 TraesCS2A01G199000 chr5B 80.364 494 73 16 1 476 382379104 382379591 1.120000e-93 353
17 TraesCS2A01G199000 chr6A 79.960 504 84 12 1 491 593282789 593283288 3.100000e-94 355
18 TraesCS2A01G199000 chr6A 80.761 447 63 14 38 477 64653514 64653084 6.770000e-86 327
19 TraesCS2A01G199000 chr1B 79.916 478 83 12 1 470 296323314 296323786 3.130000e-89 339
20 TraesCS2A01G199000 chr7B 76.965 369 55 17 1 359 748715242 748715590 1.550000e-42 183
21 TraesCS2A01G199000 chr5A 89.474 95 7 2 1875 1967 535158689 535158596 1.590000e-22 117
22 TraesCS2A01G199000 chr4A 87.255 102 11 2 1870 1971 574924435 574924534 5.740000e-22 115


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 TraesCS2A01G199000 chr2A 171608317 171610853 2536 False 4686.000000 4686 100.000000 1 2537 1 chr2A.!!$F1 2536
1 TraesCS2A01G199000 chr2D 160209892 160212135 2243 True 787.333333 1779 87.007333 476 2516 3 chr2D.!!$R2 2040
2 TraesCS2A01G199000 chr2B 216963806 216965841 2035 True 1090.500000 1589 87.068000 669 2537 2 chr2B.!!$R1 1868
3 TraesCS2A01G199000 chr4D 81965514 81966027 513 False 433.000000 433 82.274000 1 507 1 chr4D.!!$F1 506

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
105 106 0.179032 ACATCACGAAAGGTGCACCA 60.179 50.0 36.39 15.55 46.56 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2032 2244 0.319555 TAATATCTGCAGACGCGCCC 60.32 55.0 20.97 0.0 42.97 6.13 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 6.653320 ACCAATATGTTATATGCAACTACCGG 59.347 38.462 0.00 0.00 0.00 5.28
34 35 6.653320 CCAATATGTTATATGCAACTACCGGT 59.347 38.462 13.98 13.98 0.00 5.28
35 36 7.148474 CCAATATGTTATATGCAACTACCGGTC 60.148 40.741 12.40 0.00 0.00 4.79
38 39 4.081031 TGTTATATGCAACTACCGGTCCAA 60.081 41.667 12.40 0.00 0.00 3.53
45 46 3.985279 GCAACTACCGGTCCAAAAATTTC 59.015 43.478 12.40 0.00 0.00 2.17
46 47 4.261867 GCAACTACCGGTCCAAAAATTTCT 60.262 41.667 12.40 0.00 0.00 2.52
47 48 5.737922 GCAACTACCGGTCCAAAAATTTCTT 60.738 40.000 12.40 0.00 0.00 2.52
79 80 3.926058 AGGTTGGTTAGCGGATAACAT 57.074 42.857 16.93 0.00 44.81 2.71
92 93 5.928839 AGCGGATAACATAGAATCACATCAC 59.071 40.000 0.00 0.00 0.00 3.06
99 100 5.734720 ACATAGAATCACATCACGAAAGGT 58.265 37.500 0.00 0.00 0.00 3.50
102 103 2.183478 ATCACATCACGAAAGGTGCA 57.817 45.000 0.00 0.00 46.56 4.57
105 106 0.179032 ACATCACGAAAGGTGCACCA 60.179 50.000 36.39 15.55 46.56 4.17
112 113 2.627699 ACGAAAGGTGCACCAAATCAAT 59.372 40.909 36.39 18.07 38.89 2.57
124 125 8.199176 TGCACCAAATCAATGCATTATAAAAG 57.801 30.769 12.53 3.02 44.17 2.27
147 155 6.113411 AGAAACATGTTCTATTACTTCCCCG 58.887 40.000 12.39 0.00 0.00 5.73
151 159 1.487558 GTTCTATTACTTCCCCGCCCA 59.512 52.381 0.00 0.00 0.00 5.36
157 165 2.414658 TACTTCCCCGCCCACCAAAC 62.415 60.000 0.00 0.00 0.00 2.93
158 166 3.503839 TTCCCCGCCCACCAAACT 61.504 61.111 0.00 0.00 0.00 2.66
165 173 3.028130 CCCGCCCACCAAACTAAATATT 58.972 45.455 0.00 0.00 0.00 1.28
166 174 3.067601 CCCGCCCACCAAACTAAATATTC 59.932 47.826 0.00 0.00 0.00 1.75
167 175 3.697045 CCGCCCACCAAACTAAATATTCA 59.303 43.478 0.00 0.00 0.00 2.57
169 177 5.099575 CGCCCACCAAACTAAATATTCAAC 58.900 41.667 0.00 0.00 0.00 3.18
172 180 6.519213 GCCCACCAAACTAAATATTCAACCAA 60.519 38.462 0.00 0.00 0.00 3.67
245 253 4.370364 TTGGTCAAGTTCAGAGCAAAAC 57.630 40.909 5.46 0.00 46.67 2.43
249 257 5.470098 TGGTCAAGTTCAGAGCAAAACTATC 59.530 40.000 0.00 0.00 40.19 2.08
250 258 5.470098 GGTCAAGTTCAGAGCAAAACTATCA 59.530 40.000 0.00 0.00 34.71 2.15
258 266 6.182627 TCAGAGCAAAACTATCAACATCCAT 58.817 36.000 0.00 0.00 0.00 3.41
444 457 2.793278 AGAAATCCAACAACGCCAAC 57.207 45.000 0.00 0.00 0.00 3.77
471 484 3.418744 AAAACGCGCGCAACCCTTT 62.419 52.632 32.58 18.82 0.00 3.11
486 499 6.764560 CGCAACCCTTTTAGTAGTAATACCAT 59.235 38.462 0.00 0.00 0.00 3.55
501 514 7.852263 AGTAATACCATGTCTGAAAAGTAGCT 58.148 34.615 0.00 0.00 0.00 3.32
614 632 6.449635 TGGAACTATTGAAATACATGGCAC 57.550 37.500 0.00 0.00 0.00 5.01
631 649 3.050619 GGCACCAGTTCGATAATACTCG 58.949 50.000 0.00 0.00 39.99 4.18
632 650 3.490419 GGCACCAGTTCGATAATACTCGT 60.490 47.826 0.00 0.00 39.62 4.18
642 660 7.914346 AGTTCGATAATACTCGTAGTCCTTTTG 59.086 37.037 0.00 0.00 39.62 2.44
645 663 8.246180 TCGATAATACTCGTAGTCCTTTTGTTT 58.754 33.333 0.00 0.00 39.62 2.83
646 664 8.866956 CGATAATACTCGTAGTCCTTTTGTTTT 58.133 33.333 0.00 0.00 34.00 2.43
724 745 2.475371 ATCGGAGCAGCAGCCTTGTT 62.475 55.000 0.00 0.00 43.56 2.83
751 772 2.358615 CAGCTACACCGGCAGCAA 60.359 61.111 21.34 0.00 40.36 3.91
753 774 3.431725 GCTACACCGGCAGCAACC 61.432 66.667 16.17 0.00 37.73 3.77
754 775 2.031919 CTACACCGGCAGCAACCA 59.968 61.111 0.00 0.00 0.00 3.67
755 776 2.031919 TACACCGGCAGCAACCAG 59.968 61.111 0.00 0.00 0.00 4.00
756 777 3.545124 TACACCGGCAGCAACCAGG 62.545 63.158 0.00 0.00 0.00 4.45
814 839 5.070580 GGTATCTAATGCCCCTATCGCTATT 59.929 44.000 0.00 0.00 0.00 1.73
819 844 4.946478 ATGCCCCTATCGCTATTATCTC 57.054 45.455 0.00 0.00 0.00 2.75
893 918 8.348507 GCCTTTATTATGTCTTTCCATTCTCTG 58.651 37.037 0.00 0.00 0.00 3.35
942 967 0.759346 AGTCACTGGGCGAGTTCTTT 59.241 50.000 0.00 0.00 29.75 2.52
947 972 4.215613 GTCACTGGGCGAGTTCTTTTTAAT 59.784 41.667 0.00 0.00 29.75 1.40
960 985 8.063200 AGTTCTTTTTAATTATACTGCCCACC 57.937 34.615 0.00 0.00 0.00 4.61
1000 1026 1.140052 TCTGCTCAACTCACCGGAAAA 59.860 47.619 9.46 0.00 0.00 2.29
1001 1027 2.154462 CTGCTCAACTCACCGGAAAAT 58.846 47.619 9.46 0.00 0.00 1.82
1002 1028 1.879380 TGCTCAACTCACCGGAAAATG 59.121 47.619 9.46 0.00 0.00 2.32
1003 1029 1.200020 GCTCAACTCACCGGAAAATGG 59.800 52.381 9.46 0.00 0.00 3.16
1004 1030 1.200020 CTCAACTCACCGGAAAATGGC 59.800 52.381 9.46 0.00 0.00 4.40
1005 1031 0.243636 CAACTCACCGGAAAATGGCC 59.756 55.000 9.46 0.00 0.00 5.36
1009 1035 1.153588 CACCGGAAAATGGCCATGC 60.154 57.895 21.63 11.94 0.00 4.06
1237 1281 2.299521 GTATGTACGTCCTCTGCCTCT 58.700 52.381 0.00 0.00 0.00 3.69
1245 1289 1.107114 TCCTCTGCCTCTTCATCGTC 58.893 55.000 0.00 0.00 0.00 4.20
1507 1551 1.734477 CCACAGAACGGTGCTCTCG 60.734 63.158 0.00 0.00 37.46 4.04
1596 1641 3.519510 ACCCGGATGGATACTGAATATGG 59.480 47.826 0.73 0.00 37.49 2.74
1597 1642 3.118261 CCCGGATGGATACTGAATATGGG 60.118 52.174 0.73 0.00 37.49 4.00
1601 1646 5.046304 CGGATGGATACTGAATATGGGAAGT 60.046 44.000 0.00 0.00 37.61 3.01
1669 1721 3.581332 TCCTCCTTGGTTCGACATAACTT 59.419 43.478 0.00 0.00 37.07 2.66
1670 1722 4.041198 TCCTCCTTGGTTCGACATAACTTT 59.959 41.667 0.00 0.00 37.07 2.66
1671 1723 5.246656 TCCTCCTTGGTTCGACATAACTTTA 59.753 40.000 0.00 0.00 37.07 1.85
1672 1724 6.070424 TCCTCCTTGGTTCGACATAACTTTAT 60.070 38.462 0.00 0.00 37.07 1.40
1675 1727 9.158233 CTCCTTGGTTCGACATAACTTTATAAA 57.842 33.333 0.00 0.00 0.00 1.40
1707 1772 7.703058 ACCTGACGGAATTCTCAAATTTAAT 57.297 32.000 5.23 0.00 35.21 1.40
1731 1796 3.773418 TCAAACGAATTAGACCCCACA 57.227 42.857 0.00 0.00 0.00 4.17
1732 1797 4.295141 TCAAACGAATTAGACCCCACAT 57.705 40.909 0.00 0.00 0.00 3.21
1734 1799 2.710096 ACGAATTAGACCCCACATGG 57.290 50.000 0.00 0.00 0.00 3.66
1755 1822 3.411454 AGGTCTCTCCCTCATGATTGA 57.589 47.619 0.00 0.00 36.75 2.57
1757 1824 2.768527 GGTCTCTCCCTCATGATTGACA 59.231 50.000 0.00 0.00 0.00 3.58
1778 1845 1.691219 GATGAGGGTGAAGGGGCAA 59.309 57.895 0.00 0.00 0.00 4.52
1798 1865 1.870402 ACGCACACACATGATTTCGAA 59.130 42.857 0.00 0.00 0.00 3.71
1801 1868 3.358700 CGCACACACATGATTTCGAAAAG 59.641 43.478 15.66 7.93 0.00 2.27
1802 1869 4.290155 GCACACACATGATTTCGAAAAGT 58.710 39.130 15.66 8.56 0.00 2.66
1812 1879 2.607631 TTCGAAAAGTCCGGTGTTCT 57.392 45.000 0.00 0.00 0.00 3.01
1814 1881 1.409790 TCGAAAAGTCCGGTGTTCTGA 59.590 47.619 0.00 1.44 0.00 3.27
1822 1889 1.519455 CGGTGTTCTGATCCGCCTC 60.519 63.158 0.00 0.00 37.90 4.70
1857 1934 1.481772 AGAGAGCTTCTGGAGATGCAC 59.518 52.381 14.85 9.68 44.66 4.57
1865 1942 1.003839 TGGAGATGCACCGACAACC 60.004 57.895 0.00 0.00 0.00 3.77
1879 2063 3.561503 CGACAACCGCGAGATCAATATA 58.438 45.455 8.23 0.00 0.00 0.86
1971 2155 0.170116 TTGGCCAAAATGATCGACGC 59.830 50.000 17.98 0.00 0.00 5.19
1972 2156 0.957888 TGGCCAAAATGATCGACGCA 60.958 50.000 0.61 0.00 0.00 5.24
1973 2157 0.170116 GGCCAAAATGATCGACGCAA 59.830 50.000 0.00 0.00 0.00 4.85
1978 2162 3.543494 CCAAAATGATCGACGCAAATGTC 59.457 43.478 0.00 0.00 35.49 3.06
1988 2192 5.617609 TCGACGCAAATGTCTTGAAAATAG 58.382 37.500 0.00 0.00 36.71 1.73
1989 2193 4.788100 CGACGCAAATGTCTTGAAAATAGG 59.212 41.667 0.00 0.00 36.71 2.57
1997 2201 4.326826 TGTCTTGAAAATAGGAGCTGTGG 58.673 43.478 0.00 0.00 0.00 4.17
2006 2210 2.584835 AGGAGCTGTGGTTGCAAATA 57.415 45.000 0.00 0.00 0.00 1.40
2019 2223 7.171167 TGTGGTTGCAAATAACAAGATTTGATG 59.829 33.333 0.00 0.00 45.70 3.07
2048 2263 4.569023 CGGGCGCGTCTGCAGATA 62.569 66.667 21.47 0.00 42.97 1.98
2050 2265 1.595382 GGGCGCGTCTGCAGATATT 60.595 57.895 21.47 0.00 42.97 1.28
2051 2266 0.319555 GGGCGCGTCTGCAGATATTA 60.320 55.000 21.47 0.00 42.97 0.98
2052 2267 1.673033 GGGCGCGTCTGCAGATATTAT 60.673 52.381 21.47 0.00 42.97 1.28
2054 2269 2.061773 GCGCGTCTGCAGATATTATGT 58.938 47.619 21.47 0.00 42.97 2.29
2067 2284 7.339466 TGCAGATATTATGTCTCGGATTAGCTA 59.661 37.037 0.00 0.00 0.00 3.32
2068 2285 7.646130 GCAGATATTATGTCTCGGATTAGCTAC 59.354 40.741 0.00 0.00 0.00 3.58
2070 2287 8.056400 AGATATTATGTCTCGGATTAGCTACCT 58.944 37.037 0.00 0.00 0.00 3.08
2071 2288 9.339850 GATATTATGTCTCGGATTAGCTACCTA 57.660 37.037 0.00 0.00 0.00 3.08
2086 2303 4.656112 AGCTACCTATGGTTGTAGATGCTT 59.344 41.667 0.00 0.00 37.26 3.91
2089 2306 6.017852 GCTACCTATGGTTGTAGATGCTTTTC 60.018 42.308 0.00 0.00 37.26 2.29
2097 2314 6.995686 TGGTTGTAGATGCTTTTCTGTTTCTA 59.004 34.615 0.00 0.00 0.00 2.10
2098 2315 7.500892 TGGTTGTAGATGCTTTTCTGTTTCTAA 59.499 33.333 0.00 0.00 0.00 2.10
2145 2362 1.369692 CAGGCACCAGGTCGTACAA 59.630 57.895 0.00 0.00 0.00 2.41
2165 2382 8.011673 CGTACAATATGTTGAATATTGCTCCAG 58.988 37.037 9.40 3.22 42.63 3.86
2181 2398 3.243569 GCTCCAGTGCGAGTTACATCTAT 60.244 47.826 9.48 0.00 32.11 1.98
2182 2399 4.023107 GCTCCAGTGCGAGTTACATCTATA 60.023 45.833 9.48 0.00 32.11 1.31
2183 2400 5.690997 TCCAGTGCGAGTTACATCTATAG 57.309 43.478 0.00 0.00 0.00 1.31
2185 2402 5.593095 TCCAGTGCGAGTTACATCTATAGTT 59.407 40.000 0.00 0.00 0.00 2.24
2186 2403 5.687730 CCAGTGCGAGTTACATCTATAGTTG 59.312 44.000 8.92 8.92 0.00 3.16
2212 2472 6.650807 CACACTGTATCATAGTTTTGTGGAGT 59.349 38.462 0.00 0.00 0.00 3.85
2225 2485 3.616956 TGTGGAGTTCCTATGCTTCTG 57.383 47.619 0.00 0.00 36.82 3.02
2227 2487 4.093743 TGTGGAGTTCCTATGCTTCTGTA 58.906 43.478 0.00 0.00 36.82 2.74
2228 2488 4.160439 TGTGGAGTTCCTATGCTTCTGTAG 59.840 45.833 0.00 0.00 36.82 2.74
2229 2489 4.402793 GTGGAGTTCCTATGCTTCTGTAGA 59.597 45.833 0.00 0.00 36.82 2.59
2230 2490 5.069781 GTGGAGTTCCTATGCTTCTGTAGAT 59.930 44.000 0.00 0.00 36.82 1.98
2231 2491 5.069648 TGGAGTTCCTATGCTTCTGTAGATG 59.930 44.000 0.00 0.00 36.82 2.90
2232 2492 5.510520 GGAGTTCCTATGCTTCTGTAGATGG 60.511 48.000 0.00 0.00 0.00 3.51
2233 2493 5.211973 AGTTCCTATGCTTCTGTAGATGGA 58.788 41.667 0.00 0.00 0.00 3.41
2234 2494 5.843421 AGTTCCTATGCTTCTGTAGATGGAT 59.157 40.000 6.92 6.92 35.22 3.41
2235 2495 6.328672 AGTTCCTATGCTTCTGTAGATGGATT 59.671 38.462 7.00 0.00 33.57 3.01
2236 2496 6.753913 TCCTATGCTTCTGTAGATGGATTT 57.246 37.500 7.00 0.00 33.57 2.17
2237 2497 7.141758 TCCTATGCTTCTGTAGATGGATTTT 57.858 36.000 7.00 0.00 33.57 1.82
2238 2498 6.994496 TCCTATGCTTCTGTAGATGGATTTTG 59.006 38.462 7.00 0.92 33.57 2.44
2239 2499 6.769822 CCTATGCTTCTGTAGATGGATTTTGT 59.230 38.462 7.00 0.00 33.57 2.83
2240 2500 6.690194 ATGCTTCTGTAGATGGATTTTGTC 57.310 37.500 0.00 0.00 28.52 3.18
2254 2514 3.773860 TTTTGTCGCTGCTTTTCAGAA 57.226 38.095 0.00 0.00 45.72 3.02
2261 2521 3.752747 TCGCTGCTTTTCAGAATTCATCA 59.247 39.130 8.44 0.00 45.72 3.07
2323 2587 4.759516 AATTCGCTGATTTAACACGGTT 57.240 36.364 0.00 0.00 0.00 4.44
2330 2594 3.472652 TGATTTAACACGGTTGACAGCT 58.527 40.909 0.00 0.00 0.00 4.24
2378 2643 5.486735 TTTACCGGAGTTGGAGAACAATA 57.513 39.130 9.46 0.00 41.95 1.90
2471 2736 7.226720 TCAGTTTAACCAGACTGACTCAAATTC 59.773 37.037 3.32 0.00 45.26 2.17
2473 2738 6.861065 TTAACCAGACTGACTCAAATTCAC 57.139 37.500 3.32 0.00 0.00 3.18
2477 2742 4.556233 CAGACTGACTCAAATTCACGGTA 58.444 43.478 0.00 0.00 0.00 4.02
2504 2769 7.707624 ATCATCAGAAGGCAAAAATAAGTGA 57.292 32.000 0.00 0.00 0.00 3.41
2516 2781 7.542130 GGCAAAAATAAGTGACATCCTGTTTAG 59.458 37.037 0.00 0.00 0.00 1.85
2534 2799 0.039617 AGATATCGCACGAGCTGCTC 60.040 55.000 19.53 19.53 44.64 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 6.653320 ACCGGTAGTTGCATATAACATATTGG 59.347 38.462 4.49 0.00 33.02 3.16
16 17 4.062677 TGGACCGGTAGTTGCATATAAC 57.937 45.455 7.34 0.00 0.00 1.89
45 46 8.495949 CGCTAACCAACCTATATTTATGTGAAG 58.504 37.037 0.00 0.00 0.00 3.02
46 47 7.442969 CCGCTAACCAACCTATATTTATGTGAA 59.557 37.037 0.00 0.00 0.00 3.18
47 48 6.932400 CCGCTAACCAACCTATATTTATGTGA 59.068 38.462 0.00 0.00 0.00 3.58
79 80 3.932710 GCACCTTTCGTGATGTGATTCTA 59.067 43.478 0.00 0.00 46.20 2.10
92 93 2.791383 TTGATTTGGTGCACCTTTCG 57.209 45.000 34.75 0.00 36.82 3.46
100 101 8.422973 TCTTTTATAATGCATTGATTTGGTGC 57.577 30.769 22.27 0.00 39.26 5.01
123 124 6.113411 CGGGGAAGTAATAGAACATGTTTCT 58.887 40.000 13.36 13.09 0.00 2.52
124 125 5.220796 GCGGGGAAGTAATAGAACATGTTTC 60.221 44.000 13.36 6.25 0.00 2.78
128 129 3.139077 GGCGGGGAAGTAATAGAACATG 58.861 50.000 0.00 0.00 0.00 3.21
129 130 2.105993 GGGCGGGGAAGTAATAGAACAT 59.894 50.000 0.00 0.00 0.00 2.71
130 131 1.487558 GGGCGGGGAAGTAATAGAACA 59.512 52.381 0.00 0.00 0.00 3.18
131 132 1.487558 TGGGCGGGGAAGTAATAGAAC 59.512 52.381 0.00 0.00 0.00 3.01
132 133 1.487558 GTGGGCGGGGAAGTAATAGAA 59.512 52.381 0.00 0.00 0.00 2.10
133 134 1.125633 GTGGGCGGGGAAGTAATAGA 58.874 55.000 0.00 0.00 0.00 1.98
135 136 0.620990 TGGTGGGCGGGGAAGTAATA 60.621 55.000 0.00 0.00 0.00 0.98
136 137 1.502527 TTGGTGGGCGGGGAAGTAAT 61.503 55.000 0.00 0.00 0.00 1.89
137 138 1.717038 TTTGGTGGGCGGGGAAGTAA 61.717 55.000 0.00 0.00 0.00 2.24
138 139 2.154747 TTTGGTGGGCGGGGAAGTA 61.155 57.895 0.00 0.00 0.00 2.24
139 140 3.503839 TTTGGTGGGCGGGGAAGT 61.504 61.111 0.00 0.00 0.00 3.01
142 150 1.717038 TTTAGTTTGGTGGGCGGGGA 61.717 55.000 0.00 0.00 0.00 4.81
147 155 5.046950 TGGTTGAATATTTAGTTTGGTGGGC 60.047 40.000 0.00 0.00 0.00 5.36
151 159 8.875168 TGGAATTGGTTGAATATTTAGTTTGGT 58.125 29.630 0.00 0.00 0.00 3.67
165 173 6.962902 ACCCCTTATATTTTGGAATTGGTTGA 59.037 34.615 0.00 0.00 0.00 3.18
166 174 7.194112 ACCCCTTATATTTTGGAATTGGTTG 57.806 36.000 0.00 0.00 0.00 3.77
167 175 9.514093 AATACCCCTTATATTTTGGAATTGGTT 57.486 29.630 0.00 0.00 0.00 3.67
227 235 6.545504 TGATAGTTTTGCTCTGAACTTGAC 57.454 37.500 0.00 0.00 37.32 3.18
430 443 3.587933 GCCGTTGGCGTTGTTGGA 61.588 61.111 0.00 0.00 39.62 3.53
456 469 2.961669 CTAAAAGGGTTGCGCGCGT 61.962 57.895 32.35 10.56 34.93 6.01
458 471 0.096454 CTACTAAAAGGGTTGCGCGC 59.904 55.000 27.26 27.26 0.00 6.86
462 475 7.555195 ACATGGTATTACTACTAAAAGGGTTGC 59.445 37.037 0.00 0.00 0.00 4.17
465 478 8.483758 CAGACATGGTATTACTACTAAAAGGGT 58.516 37.037 0.00 0.00 0.00 4.34
486 499 5.238650 GGCACTAAAAGCTACTTTTCAGACA 59.761 40.000 8.49 0.00 41.88 3.41
493 506 6.648879 TCAATTGGCACTAAAAGCTACTTT 57.351 33.333 5.42 0.00 34.94 2.66
501 514 6.321717 CGCTAGATTTCAATTGGCACTAAAA 58.678 36.000 5.42 0.00 0.00 1.52
598 611 4.142403 CGAACTGGTGCCATGTATTTCAAT 60.142 41.667 0.00 0.00 0.00 2.57
614 632 5.469421 AGGACTACGAGTATTATCGAACTGG 59.531 44.000 2.78 0.00 45.56 4.00
645 663 5.538118 TGTGAGTCTTATCTTCTCGCAAAA 58.462 37.500 5.40 0.00 42.86 2.44
646 664 5.134202 TGTGAGTCTTATCTTCTCGCAAA 57.866 39.130 5.40 0.00 42.86 3.68
647 665 4.218635 ACTGTGAGTCTTATCTTCTCGCAA 59.781 41.667 8.56 0.00 44.33 4.85
648 666 3.759086 ACTGTGAGTCTTATCTTCTCGCA 59.241 43.478 7.29 7.29 43.35 5.10
649 667 4.347813 GACTGTGAGTCTTATCTTCTCGC 58.652 47.826 0.00 0.00 41.88 5.03
650 668 4.495019 CGGACTGTGAGTCTTATCTTCTCG 60.495 50.000 3.85 0.00 44.46 4.04
651 669 4.396790 ACGGACTGTGAGTCTTATCTTCTC 59.603 45.833 3.85 0.00 44.46 2.87
652 670 4.337145 ACGGACTGTGAGTCTTATCTTCT 58.663 43.478 3.85 0.00 44.46 2.85
653 671 4.705337 ACGGACTGTGAGTCTTATCTTC 57.295 45.455 3.85 0.00 44.46 2.87
654 672 4.641094 CCTACGGACTGTGAGTCTTATCTT 59.359 45.833 0.00 0.00 44.46 2.40
661 682 1.531423 TGACCTACGGACTGTGAGTC 58.469 55.000 10.30 10.30 44.32 3.36
724 745 1.272490 CGGTGTAGCTGTCTCTTCCAA 59.728 52.381 0.00 0.00 0.00 3.53
755 776 5.127031 GGATAGCAGATAGAGGATGTCTTCC 59.873 48.000 0.00 0.00 45.85 3.46
756 777 5.127031 GGGATAGCAGATAGAGGATGTCTTC 59.873 48.000 0.00 0.00 36.64 2.87
814 839 6.688073 AGGAACAAGAACAAGGAAGAGATA 57.312 37.500 0.00 0.00 0.00 1.98
819 844 8.171164 AGAAAATAGGAACAAGAACAAGGAAG 57.829 34.615 0.00 0.00 0.00 3.46
861 886 8.995027 TGGAAAGACATAATAAAGGCATACAT 57.005 30.769 0.00 0.00 0.00 2.29
862 887 8.995027 ATGGAAAGACATAATAAAGGCATACA 57.005 30.769 0.00 0.00 0.00 2.29
863 888 9.899226 GAATGGAAAGACATAATAAAGGCATAC 57.101 33.333 0.00 0.00 0.00 2.39
893 918 3.261981 TGGAAAGCGAGGAATTCTACC 57.738 47.619 5.23 0.00 0.00 3.18
942 967 5.587043 CGAGTTGGTGGGCAGTATAATTAAA 59.413 40.000 0.00 0.00 0.00 1.52
947 972 1.903860 ACGAGTTGGTGGGCAGTATAA 59.096 47.619 0.00 0.00 0.00 0.98
1117 1161 2.111878 CATCGTCCCCATCCCAGC 59.888 66.667 0.00 0.00 0.00 4.85
1237 1281 1.136774 CGAGCGTGAGGACGATGAA 59.863 57.895 0.00 0.00 46.15 2.57
1362 1406 0.463295 CAGCCAGCATCACCAGGTAG 60.463 60.000 0.00 0.00 0.00 3.18
1507 1551 2.896443 CTCAGCCTCCGAGGGAAC 59.104 66.667 16.51 0.00 35.37 3.62
1629 1674 7.657352 AGGAGGAGGAGTACTAGAATAATCT 57.343 40.000 0.00 0.00 39.82 2.40
1630 1675 7.177744 CCAAGGAGGAGGAGTACTAGAATAATC 59.822 44.444 0.00 0.00 41.22 1.75
1640 1692 1.477295 CGAACCAAGGAGGAGGAGTAC 59.523 57.143 0.00 0.00 41.22 2.73
1675 1727 3.951680 AGAATTCCGTCAGGTTGTGTTTT 59.048 39.130 0.65 0.00 39.05 2.43
1677 1729 3.139077 GAGAATTCCGTCAGGTTGTGTT 58.861 45.455 0.65 0.00 39.05 3.32
1678 1730 2.104111 TGAGAATTCCGTCAGGTTGTGT 59.896 45.455 0.65 0.00 39.05 3.72
1679 1731 2.766313 TGAGAATTCCGTCAGGTTGTG 58.234 47.619 0.65 0.00 39.05 3.33
1681 1733 5.376854 AATTTGAGAATTCCGTCAGGTTG 57.623 39.130 0.65 0.00 39.05 3.77
1684 1736 8.986477 AAATTAAATTTGAGAATTCCGTCAGG 57.014 30.769 0.65 0.00 34.44 3.86
1707 1772 5.360144 TGTGGGGTCTAATTCGTTTGAAAAA 59.640 36.000 0.00 0.00 37.71 1.94
1716 1781 2.485479 CCTCCATGTGGGGTCTAATTCG 60.485 54.545 0.00 0.00 37.22 3.34
1755 1822 0.995024 CCCTTCACCCTCATCCTTGT 59.005 55.000 0.00 0.00 0.00 3.16
1757 1824 1.575447 GCCCCTTCACCCTCATCCTT 61.575 60.000 0.00 0.00 0.00 3.36
1778 1845 1.507562 TCGAAATCATGTGTGTGCGT 58.492 45.000 0.00 0.00 0.00 5.24
1781 1848 4.911610 GGACTTTTCGAAATCATGTGTGTG 59.088 41.667 12.12 0.00 0.00 3.82
1782 1849 4.319477 CGGACTTTTCGAAATCATGTGTGT 60.319 41.667 12.12 1.48 0.00 3.72
1786 1853 3.188460 CACCGGACTTTTCGAAATCATGT 59.812 43.478 9.46 8.51 0.00 3.21
1798 1865 1.337823 CGGATCAGAACACCGGACTTT 60.338 52.381 9.46 0.00 42.48 2.66
1801 1868 1.810030 GCGGATCAGAACACCGGAC 60.810 63.158 9.46 0.00 45.66 4.79
1802 1869 2.577059 GCGGATCAGAACACCGGA 59.423 61.111 9.46 0.00 45.66 5.14
1822 1889 1.078848 CTCTGCCTCTTGTTCCGGG 60.079 63.158 0.00 0.00 0.00 5.73
1849 1926 2.740714 GCGGTTGTCGGTGCATCTC 61.741 63.158 0.00 0.00 39.69 2.75
1851 1928 4.147322 CGCGGTTGTCGGTGCATC 62.147 66.667 0.00 0.00 39.69 3.91
1857 1934 0.806102 ATTGATCTCGCGGTTGTCGG 60.806 55.000 6.13 0.00 39.69 4.79
1865 1942 8.864024 AGTTCAAACATATATATTGATCTCGCG 58.136 33.333 0.00 0.00 31.00 5.87
1917 2101 4.208047 TGCACACGAATACAAATTGTTTGC 59.792 37.500 3.17 0.00 44.39 3.68
1971 2155 6.805271 CACAGCTCCTATTTTCAAGACATTTG 59.195 38.462 0.00 0.00 0.00 2.32
1972 2156 6.071728 CCACAGCTCCTATTTTCAAGACATTT 60.072 38.462 0.00 0.00 0.00 2.32
1973 2157 5.416952 CCACAGCTCCTATTTTCAAGACATT 59.583 40.000 0.00 0.00 0.00 2.71
1978 2162 4.616835 GCAACCACAGCTCCTATTTTCAAG 60.617 45.833 0.00 0.00 0.00 3.02
1988 2192 2.295909 TGTTATTTGCAACCACAGCTCC 59.704 45.455 0.00 0.00 0.00 4.70
1989 2193 3.641437 TGTTATTTGCAACCACAGCTC 57.359 42.857 0.00 0.00 0.00 4.09
1997 2201 6.402442 GGGCATCAAATCTTGTTATTTGCAAC 60.402 38.462 0.00 0.00 43.49 4.17
2006 2210 2.627699 ACAACGGGCATCAAATCTTGTT 59.372 40.909 0.00 0.00 0.00 2.83
2032 2244 0.319555 TAATATCTGCAGACGCGCCC 60.320 55.000 20.97 0.00 42.97 6.13
2038 2250 5.378292 TCCGAGACATAATATCTGCAGAC 57.622 43.478 20.97 3.29 0.00 3.51
2041 2253 6.153510 AGCTAATCCGAGACATAATATCTGCA 59.846 38.462 0.00 0.00 0.00 4.41
2044 2259 8.056400 AGGTAGCTAATCCGAGACATAATATCT 58.944 37.037 0.00 0.00 0.00 1.98
2047 2262 9.121658 CATAGGTAGCTAATCCGAGACATAATA 57.878 37.037 5.62 0.00 0.00 0.98
2048 2263 7.068839 CCATAGGTAGCTAATCCGAGACATAAT 59.931 40.741 5.62 0.00 0.00 1.28
2050 2265 5.886474 CCATAGGTAGCTAATCCGAGACATA 59.114 44.000 5.62 0.00 0.00 2.29
2051 2266 4.707448 CCATAGGTAGCTAATCCGAGACAT 59.293 45.833 5.62 0.00 0.00 3.06
2052 2267 4.079970 CCATAGGTAGCTAATCCGAGACA 58.920 47.826 5.62 0.00 0.00 3.41
2054 2269 4.383931 ACCATAGGTAGCTAATCCGAGA 57.616 45.455 5.62 0.00 32.11 4.04
2067 2284 5.882557 CAGAAAAGCATCTACAACCATAGGT 59.117 40.000 0.00 0.00 37.65 3.08
2068 2285 5.882557 ACAGAAAAGCATCTACAACCATAGG 59.117 40.000 0.00 0.00 0.00 2.57
2070 2287 7.665559 AGAAACAGAAAAGCATCTACAACCATA 59.334 33.333 0.00 0.00 0.00 2.74
2071 2288 6.491403 AGAAACAGAAAAGCATCTACAACCAT 59.509 34.615 0.00 0.00 0.00 3.55
2086 2303 4.219115 TGGTGCCCAATTAGAAACAGAAA 58.781 39.130 0.00 0.00 0.00 2.52
2089 2306 3.420893 TCTGGTGCCCAATTAGAAACAG 58.579 45.455 0.00 0.00 30.80 3.16
2097 2314 5.134725 AGAATAGAATCTGGTGCCCAATT 57.865 39.130 0.00 0.19 30.80 2.32
2098 2315 4.803329 AGAATAGAATCTGGTGCCCAAT 57.197 40.909 0.00 0.00 30.80 3.16
2108 2325 6.709846 GTGCCTGCTTATCAAGAATAGAATCT 59.290 38.462 0.00 0.00 0.00 2.40
2122 2339 1.221840 CGACCTGGTGCCTGCTTAT 59.778 57.895 2.82 0.00 0.00 1.73
2145 2362 5.049198 CGCACTGGAGCAATATTCAACATAT 60.049 40.000 0.00 0.00 0.00 1.78
2165 2382 5.041287 TGCAACTATAGATGTAACTCGCAC 58.959 41.667 6.78 0.00 0.00 5.34
2181 2398 7.659799 ACAAAACTATGATACAGTGTGCAACTA 59.340 33.333 5.88 0.00 36.83 2.24
2182 2399 6.486657 ACAAAACTATGATACAGTGTGCAACT 59.513 34.615 5.88 0.00 40.93 3.16
2183 2400 6.578545 CACAAAACTATGATACAGTGTGCAAC 59.421 38.462 5.88 0.00 37.35 4.17
2185 2402 5.181056 CCACAAAACTATGATACAGTGTGCA 59.819 40.000 5.88 4.51 0.00 4.57
2186 2403 5.411361 TCCACAAAACTATGATACAGTGTGC 59.589 40.000 5.88 0.00 0.00 4.57
2212 2472 6.753913 AATCCATCTACAGAAGCATAGGAA 57.246 37.500 0.00 0.00 0.00 3.36
2225 2485 2.939103 AGCAGCGACAAAATCCATCTAC 59.061 45.455 0.00 0.00 0.00 2.59
2227 2487 2.119801 AGCAGCGACAAAATCCATCT 57.880 45.000 0.00 0.00 0.00 2.90
2228 2488 2.927553 AAGCAGCGACAAAATCCATC 57.072 45.000 0.00 0.00 0.00 3.51
2229 2489 3.005684 TGAAAAGCAGCGACAAAATCCAT 59.994 39.130 0.00 0.00 0.00 3.41
2230 2490 2.360483 TGAAAAGCAGCGACAAAATCCA 59.640 40.909 0.00 0.00 0.00 3.41
2231 2491 2.982470 CTGAAAAGCAGCGACAAAATCC 59.018 45.455 0.00 0.00 37.90 3.01
2232 2492 3.888934 TCTGAAAAGCAGCGACAAAATC 58.111 40.909 0.00 0.00 44.52 2.17
2233 2493 3.988379 TCTGAAAAGCAGCGACAAAAT 57.012 38.095 0.00 0.00 44.52 1.82
2234 2494 3.773860 TTCTGAAAAGCAGCGACAAAA 57.226 38.095 0.00 0.00 44.52 2.44
2235 2495 3.988379 ATTCTGAAAAGCAGCGACAAA 57.012 38.095 0.00 0.00 44.52 2.83
2236 2496 3.314913 TGAATTCTGAAAAGCAGCGACAA 59.685 39.130 7.05 0.00 44.52 3.18
2237 2497 2.877786 TGAATTCTGAAAAGCAGCGACA 59.122 40.909 7.05 0.00 44.52 4.35
2238 2498 3.542712 TGAATTCTGAAAAGCAGCGAC 57.457 42.857 7.05 0.00 44.52 5.19
2239 2499 3.752747 TGATGAATTCTGAAAAGCAGCGA 59.247 39.130 7.05 0.00 44.52 4.93
2240 2500 4.087510 TGATGAATTCTGAAAAGCAGCG 57.912 40.909 7.05 0.00 44.52 5.18
2254 2514 6.690530 ACGTCATGTGGAAAATTTGATGAAT 58.309 32.000 0.00 0.00 0.00 2.57
2323 2587 0.036952 GCCTTGTGCTCTAGCTGTCA 60.037 55.000 0.00 0.00 42.66 3.58
2330 2594 2.949177 TCTTTTGGCCTTGTGCTCTA 57.051 45.000 3.32 0.00 40.92 2.43
2361 2625 5.880054 ACATTTATTGTTCTCCAACTCCG 57.120 39.130 0.00 0.00 33.74 4.63
2369 2634 6.555315 CCTTGTGCCTACATTTATTGTTCTC 58.445 40.000 0.00 0.00 39.87 2.87
2471 2736 4.631131 TGCCTTCTGATGATTATACCGTG 58.369 43.478 0.00 0.00 0.00 4.94
2473 2738 6.618287 TTTTGCCTTCTGATGATTATACCG 57.382 37.500 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.