Multiple sequence alignment - TraesCS7A01G341900

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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 TraesCS7A01G341900 chr7A 100.000 2354 0 0 1 2354 501920436 501922789 0.000000e+00 4348
1 TraesCS7A01G341900 chr7B 91.138 2144 154 22 7 2124 448640877 448638744 0.000000e+00 2874
2 TraesCS7A01G341900 chr7B 81.818 242 31 10 2111 2340 448638729 448638489 8.590000e-45 191
3 TraesCS7A01G341900 chr7D 91.963 1095 67 11 688 1762 431121048 431119955 0.000000e+00 1515
4 TraesCS7A01G341900 chr7D 85.434 714 77 15 1 691 431151503 431150794 0.000000e+00 717
5 TraesCS7A01G341900 chr7D 93.207 368 23 2 1759 2124 431080033 431079666 7.400000e-150 540


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 TraesCS7A01G341900 chr7A 501920436 501922789 2353 False 4348.0 4348 100.000 1 2354 1 chr7A.!!$F1 2353
1 TraesCS7A01G341900 chr7B 448638489 448640877 2388 True 1532.5 2874 86.478 7 2340 2 chr7B.!!$R1 2333
2 TraesCS7A01G341900 chr7D 431119955 431121048 1093 True 1515.0 1515 91.963 688 1762 1 chr7D.!!$R2 1074
3 TraesCS7A01G341900 chr7D 431150794 431151503 709 True 717.0 717 85.434 1 691 1 chr7D.!!$R3 690

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
119 120 0.031314 CGATAGTGATCCTGCGTGCT 59.969 55.0 0.0 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1500 1539 0.180171 CAACATCCATGCTCCCCGTA 59.82 55.0 0.0 0.0 0.0 4.02 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
26 27 1.259142 TGTAATCCTTCGGTGGCGGA 61.259 55.000 0.00 0.00 0.00 5.54
56 57 1.065126 GGCAGACAGGAGGCTACAAAT 60.065 52.381 0.00 0.00 0.00 2.32
64 65 4.161565 ACAGGAGGCTACAAATGACGATTA 59.838 41.667 0.00 0.00 0.00 1.75
97 98 2.352715 GGGAACATTTGTTGCTACCAGC 60.353 50.000 13.52 0.00 44.36 4.85
103 104 4.496670 GTTGCTACCAGCGACGAT 57.503 55.556 0.00 0.00 44.79 3.73
104 105 3.635433 GTTGCTACCAGCGACGATA 57.365 52.632 0.00 0.00 44.79 2.92
119 120 0.031314 CGATAGTGATCCTGCGTGCT 59.969 55.000 0.00 0.00 0.00 4.40
133 134 4.408396 TGCTAGGGGAGGGGCGAA 62.408 66.667 0.00 0.00 0.00 4.70
208 218 0.971386 TCTCTGTGTCATGCTGCTCA 59.029 50.000 0.00 0.00 0.00 4.26
224 234 1.843149 GCTCATAATCTATCTCGCGCG 59.157 52.381 26.76 26.76 0.00 6.86
257 267 4.392940 GAAGATAGGGAATGATGGGTGTG 58.607 47.826 0.00 0.00 0.00 3.82
262 272 1.299541 GGAATGATGGGTGTGCGTAG 58.700 55.000 0.00 0.00 0.00 3.51
267 277 1.067142 TGATGGGTGTGCGTAGAGAAC 60.067 52.381 0.00 0.00 0.00 3.01
271 281 2.094390 TGGGTGTGCGTAGAGAACATAC 60.094 50.000 0.00 0.00 0.00 2.39
272 282 2.094390 GGGTGTGCGTAGAGAACATACA 60.094 50.000 0.00 0.00 0.00 2.29
277 287 5.910166 GTGTGCGTAGAGAACATACAGATAG 59.090 44.000 0.00 0.00 0.00 2.08
298 308 9.191479 AGATAGGATCTAGACGGTTAATAATGG 57.809 37.037 0.00 0.00 38.00 3.16
306 332 8.526147 TCTAGACGGTTAATAATGGGCTAATAC 58.474 37.037 0.00 0.00 0.00 1.89
310 336 7.092716 ACGGTTAATAATGGGCTAATACTACG 58.907 38.462 0.00 0.00 0.00 3.51
325 351 0.673333 CTACGACAAGCATGTGCCCA 60.673 55.000 0.00 0.00 40.74 5.36
339 365 0.409092 TGCCCAACATGAACCCTGAT 59.591 50.000 0.00 0.00 0.00 2.90
368 394 4.260784 GCCCGACATGTAGCTTTTTGATAG 60.261 45.833 0.00 0.00 0.00 2.08
411 439 5.619220 AGTCAGCATTCTTGTTTCTCTCTT 58.381 37.500 0.00 0.00 0.00 2.85
510 538 6.533819 TGTTGTACGAAATTCCTACTGTTG 57.466 37.500 0.00 0.00 0.00 3.33
512 540 6.539464 TGTTGTACGAAATTCCTACTGTTGTT 59.461 34.615 0.00 0.00 0.00 2.83
527 556 9.360093 CCTACTGTTGTTGTCAATAAAAACAAA 57.640 29.630 2.08 0.00 43.32 2.83
577 606 7.445402 GCTATCATGTATGAACTGTGGGTAATT 59.555 37.037 0.00 0.00 40.69 1.40
588 617 9.116067 TGAACTGTGGGTAATTAGCATTTATAC 57.884 33.333 16.07 5.94 0.00 1.47
672 701 5.106830 GGTGTCCTAAAACAGTACGGAAATG 60.107 44.000 0.00 0.00 0.00 2.32
867 896 3.979501 ATGTAATTGATTCCTGCCCCT 57.020 42.857 0.00 0.00 0.00 4.79
869 898 3.364549 TGTAATTGATTCCTGCCCCTTG 58.635 45.455 0.00 0.00 0.00 3.61
872 901 0.998928 TTGATTCCTGCCCCTTGCTA 59.001 50.000 0.00 0.00 42.00 3.49
873 902 0.998928 TGATTCCTGCCCCTTGCTAA 59.001 50.000 0.00 0.00 42.00 3.09
901 933 5.119279 GCTCAAGCCAACATATATAGTGTCG 59.881 44.000 0.00 0.00 34.31 4.35
913 945 3.963428 ATAGTGTCGTCTTCTTTGCCT 57.037 42.857 0.00 0.00 0.00 4.75
955 987 7.373493 CAAGCCTCATCTTAAACTTCACAAAT 58.627 34.615 0.00 0.00 0.00 2.32
962 994 6.494893 TCTTAAACTTCACAAATCCCATCG 57.505 37.500 0.00 0.00 0.00 3.84
1048 1080 1.078497 GCCACCATCGTCCATGTCA 60.078 57.895 0.00 0.00 0.00 3.58
1052 1084 2.358957 CACCATCGTCCATGTCATTGT 58.641 47.619 0.00 0.00 0.00 2.71
1055 1087 4.576053 CACCATCGTCCATGTCATTGTTAT 59.424 41.667 0.00 0.00 0.00 1.89
1104 1136 4.394920 TGGTTTAAGATCAAGAACATCGCC 59.605 41.667 0.00 0.00 0.00 5.54
1147 1179 0.687354 CAAGTGGGCAGTACTGGAGT 59.313 55.000 23.95 0.00 0.00 3.85
1203 1240 1.296715 GAAGGTGGTGAGTGGCGAT 59.703 57.895 0.00 0.00 0.00 4.58
1245 1282 2.493713 ACTATCGGCTCGTCATTGAC 57.506 50.000 6.73 6.73 0.00 3.18
1321 1358 3.056035 GGACTCGAGTAACCCAAAGACAT 60.056 47.826 20.09 0.00 0.00 3.06
1335 1372 5.008019 CCCAAAGACATGGAAGTTCATATCG 59.992 44.000 5.01 0.00 43.54 2.92
1386 1423 6.183360 CGATCCGATGATATTTAGACTAGCCA 60.183 42.308 0.00 0.00 0.00 4.75
1424 1461 8.292444 TGTAATAAGAAATGTCAAGGGATTGG 57.708 34.615 0.00 0.00 0.00 3.16
1429 1466 4.901250 AGAAATGTCAAGGGATTGGTGTTT 59.099 37.500 0.00 0.00 0.00 2.83
1434 1471 4.142049 TGTCAAGGGATTGGTGTTTTGTTC 60.142 41.667 0.00 0.00 0.00 3.18
1435 1472 4.099419 GTCAAGGGATTGGTGTTTTGTTCT 59.901 41.667 0.00 0.00 0.00 3.01
1436 1473 5.300792 GTCAAGGGATTGGTGTTTTGTTCTA 59.699 40.000 0.00 0.00 0.00 2.10
1437 1474 5.300792 TCAAGGGATTGGTGTTTTGTTCTAC 59.699 40.000 0.00 0.00 0.00 2.59
1439 1476 4.141018 AGGGATTGGTGTTTTGTTCTACCT 60.141 41.667 0.00 0.00 34.32 3.08
1440 1477 5.073965 AGGGATTGGTGTTTTGTTCTACCTA 59.926 40.000 0.00 0.00 34.32 3.08
1455 1493 9.444600 TTGTTCTACCTAACAGATTATGGAAAC 57.555 33.333 0.00 0.00 40.29 2.78
1479 1517 2.093890 TCATCATTGGCAACTCGCAAT 58.906 42.857 0.00 0.00 45.17 3.56
1486 1524 3.717400 TGGCAACTCGCAATGTTTTAA 57.283 38.095 0.00 0.00 45.17 1.52
1513 1552 0.600255 GACGATTACGGGGAGCATGG 60.600 60.000 0.00 0.00 44.46 3.66
1587 1637 8.369192 GTTATGAAACACAAGATGGCACAACAA 61.369 37.037 0.00 0.00 37.46 2.83
1624 1674 2.159128 TGGTTGTGAAATGTGCACCTTG 60.159 45.455 15.69 0.00 35.43 3.61
1626 1676 1.774110 TGTGAAATGTGCACCTTGGT 58.226 45.000 15.69 0.00 35.43 3.67
1630 1680 2.296752 TGAAATGTGCACCTTGGTCATG 59.703 45.455 15.69 0.00 0.00 3.07
1652 1702 7.719193 TCATGAAGTTAAGAAACACAAGATGGA 59.281 33.333 0.00 0.00 38.12 3.41
1654 1704 6.826231 TGAAGTTAAGAAACACAAGATGGACA 59.174 34.615 0.00 0.00 38.12 4.02
1656 1706 7.823745 AGTTAAGAAACACAAGATGGACATT 57.176 32.000 0.00 0.00 38.12 2.71
1675 1725 6.823689 GGACATTAAAAAGAGACTAGATGGCA 59.176 38.462 0.00 0.00 0.00 4.92
1707 1757 8.836268 TTTAAGATAACTATTGTGGTCGTTGT 57.164 30.769 0.00 0.00 0.00 3.32
1756 1806 6.211785 TGTCTTGGTGTTGGTATATGTGACTA 59.788 38.462 0.00 0.00 0.00 2.59
1764 1814 7.541091 GTGTTGGTATATGTGACTATGTATCCG 59.459 40.741 0.00 0.00 0.00 4.18
1779 1829 1.305201 ATCCGCGTTGTTTTGTCACT 58.695 45.000 4.92 0.00 0.00 3.41
1780 1830 0.375454 TCCGCGTTGTTTTGTCACTG 59.625 50.000 4.92 0.00 0.00 3.66
1792 1842 0.451383 TGTCACTGTGTTGTTGCAGC 59.549 50.000 7.79 0.00 36.26 5.25
1797 1847 0.734309 CTGTGTTGTTGCAGCAGTCA 59.266 50.000 2.72 4.97 0.00 3.41
1798 1848 1.335810 CTGTGTTGTTGCAGCAGTCAT 59.664 47.619 2.72 0.00 0.00 3.06
1864 1914 6.845758 TTCTCCAAAAGAATTGCATCTCAT 57.154 33.333 0.00 0.00 39.12 2.90
1886 1936 9.537192 CTCATACCATGTTTGCATAAAATCATT 57.463 29.630 0.00 0.00 33.30 2.57
1909 1959 4.746535 AAACCGGTTGTCCTTTGAAATT 57.253 36.364 23.08 0.00 0.00 1.82
1978 2028 8.239314 ACTAGACATGTTGCTCATAAAACATTG 58.761 33.333 0.00 0.00 42.85 2.82
1996 2046 4.713321 ACATTGAGCCCTAATGCATTTTCT 59.287 37.500 18.75 9.41 38.72 2.52
2078 2128 0.683504 GGGAACTAGAGGCTCCACGA 60.684 60.000 11.71 0.00 0.00 4.35
2080 2130 0.456628 GAACTAGAGGCTCCACGACC 59.543 60.000 11.71 0.00 0.00 4.79
2086 2136 4.008933 GGCTCCACGACCACTGCT 62.009 66.667 0.00 0.00 0.00 4.24
2111 2162 2.039613 GCTTAGCTAGGCCAATCTGGAT 59.960 50.000 16.64 0.00 40.96 3.41
2130 2209 8.183830 TCTGGATTGCTATTTTTATTTTTGCG 57.816 30.769 0.00 0.00 0.00 4.85
2197 2278 1.070105 GGGCGCCCATGTACGATAA 59.930 57.895 40.73 0.00 35.81 1.75
2198 2279 1.226030 GGGCGCCCATGTACGATAAC 61.226 60.000 40.73 7.78 35.81 1.89
2248 2329 8.178313 AGAAAGGTTTCGATTGTATTTTTCCT 57.822 30.769 0.00 0.00 41.92 3.36
2252 2333 8.812147 AGGTTTCGATTGTATTTTTCCTTTTC 57.188 30.769 0.00 0.00 0.00 2.29
2255 2336 8.699749 GTTTCGATTGTATTTTTCCTTTTCCAG 58.300 33.333 0.00 0.00 0.00 3.86
2257 2338 7.367285 TCGATTGTATTTTTCCTTTTCCAGTG 58.633 34.615 0.00 0.00 0.00 3.66
2258 2339 7.013846 TCGATTGTATTTTTCCTTTTCCAGTGT 59.986 33.333 0.00 0.00 0.00 3.55
2259 2340 7.651704 CGATTGTATTTTTCCTTTTCCAGTGTT 59.348 33.333 0.00 0.00 0.00 3.32
2260 2341 9.325198 GATTGTATTTTTCCTTTTCCAGTGTTT 57.675 29.630 0.00 0.00 0.00 2.83
2262 2343 8.710835 TGTATTTTTCCTTTTCCAGTGTTTTC 57.289 30.769 0.00 0.00 0.00 2.29
2263 2344 8.314751 TGTATTTTTCCTTTTCCAGTGTTTTCA 58.685 29.630 0.00 0.00 0.00 2.69
2265 2346 7.608308 TTTTTCCTTTTCCAGTGTTTTCATG 57.392 32.000 0.00 0.00 0.00 3.07
2266 2347 5.930837 TTCCTTTTCCAGTGTTTTCATGT 57.069 34.783 0.00 0.00 0.00 3.21
2267 2348 5.261209 TCCTTTTCCAGTGTTTTCATGTG 57.739 39.130 0.00 0.00 0.00 3.21
2269 2350 5.043248 CCTTTTCCAGTGTTTTCATGTGTC 58.957 41.667 0.00 0.00 0.00 3.67
2270 2351 3.961477 TTCCAGTGTTTTCATGTGTCG 57.039 42.857 0.00 0.00 0.00 4.35
2271 2352 2.217750 TCCAGTGTTTTCATGTGTCGG 58.782 47.619 0.00 0.00 0.00 4.79
2276 2364 4.034626 CAGTGTTTTCATGTGTCGGTTGTA 59.965 41.667 0.00 0.00 0.00 2.41
2291 2379 3.606153 CGGTTGTAGCGGTTTTCTTTCAG 60.606 47.826 0.00 0.00 35.16 3.02
2295 2383 3.949113 TGTAGCGGTTTTCTTTCAGGTTT 59.051 39.130 0.00 0.00 0.00 3.27
2298 2386 4.180817 AGCGGTTTTCTTTCAGGTTTTTG 58.819 39.130 0.00 0.00 0.00 2.44
2301 2389 5.106869 GCGGTTTTCTTTCAGGTTTTTGTTT 60.107 36.000 0.00 0.00 0.00 2.83
2333 2421 8.073467 TCAAGTTTTATTTCCTGTGTCCTTTT 57.927 30.769 0.00 0.00 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 3.265791 GTCATTTGTAGCCTCCTGTCTG 58.734 50.000 0.00 0.00 0.00 3.51
41 42 1.899814 TCGTCATTTGTAGCCTCCTGT 59.100 47.619 0.00 0.00 0.00 4.00
43 44 3.914426 AATCGTCATTTGTAGCCTCCT 57.086 42.857 0.00 0.00 0.00 3.69
56 57 3.132289 CCCTTGTAGCTTCCTAATCGTCA 59.868 47.826 0.00 0.00 0.00 4.35
64 65 4.082125 CAAATGTTCCCTTGTAGCTTCCT 58.918 43.478 0.00 0.00 0.00 3.36
97 98 0.308068 ACGCAGGATCACTATCGTCG 59.692 55.000 0.00 0.00 34.01 5.12
102 103 1.615883 CCTAGCACGCAGGATCACTAT 59.384 52.381 0.00 0.00 34.91 2.12
103 104 1.032794 CCTAGCACGCAGGATCACTA 58.967 55.000 0.00 0.00 34.91 2.74
104 105 1.680522 CCCTAGCACGCAGGATCACT 61.681 60.000 8.52 0.00 34.91 3.41
109 110 2.759973 CTCCCCTAGCACGCAGGA 60.760 66.667 8.52 0.91 34.91 3.86
116 117 4.408396 TTCGCCCCTCCCCTAGCA 62.408 66.667 0.00 0.00 0.00 3.49
117 118 3.551407 CTTCGCCCCTCCCCTAGC 61.551 72.222 0.00 0.00 0.00 3.42
141 142 3.254024 ATCACCACTCGCCCCACAC 62.254 63.158 0.00 0.00 0.00 3.82
144 145 2.606213 TCATCACCACTCGCCCCA 60.606 61.111 0.00 0.00 0.00 4.96
187 197 0.389556 AGCAGCATGACACAGAGACG 60.390 55.000 0.00 0.00 39.69 4.18
208 218 1.901538 CAGCGCGCGAGATAGATTAT 58.098 50.000 37.18 0.00 0.00 1.28
224 234 0.316841 CCTATCTTCCTCTCGGCAGC 59.683 60.000 0.00 0.00 0.00 5.25
240 250 0.180171 CGCACACCCATCATTCCCTA 59.820 55.000 0.00 0.00 0.00 3.53
257 267 5.943706 TCCTATCTGTATGTTCTCTACGC 57.056 43.478 0.00 0.00 0.00 4.42
262 272 7.065324 CCGTCTAGATCCTATCTGTATGTTCTC 59.935 44.444 0.00 0.00 40.51 2.87
267 277 8.563123 TTAACCGTCTAGATCCTATCTGTATG 57.437 38.462 0.00 0.00 40.51 2.39
272 282 9.191479 CCATTATTAACCGTCTAGATCCTATCT 57.809 37.037 0.00 0.00 43.33 1.98
277 287 5.046520 AGCCCATTATTAACCGTCTAGATCC 60.047 44.000 0.00 0.00 0.00 3.36
298 308 4.209288 CACATGCTTGTCGTAGTATTAGCC 59.791 45.833 1.56 0.00 32.34 3.93
306 332 0.673333 TGGGCACATGCTTGTCGTAG 60.673 55.000 1.56 0.00 41.70 3.51
310 336 0.604578 ATGTTGGGCACATGCTTGTC 59.395 50.000 1.56 0.00 45.12 3.18
325 351 1.405526 CGACCGATCAGGGTTCATGTT 60.406 52.381 8.20 0.00 46.96 2.71
353 379 7.921786 ATGTAAGCACTATCAAAAAGCTACA 57.078 32.000 0.00 0.00 34.66 2.74
422 450 5.428131 AGAGAAGTTCAGAAGGGAGCAATAT 59.572 40.000 5.50 0.00 0.00 1.28
465 493 9.423427 CAACATACATTTTTGTGTTTTCATGTG 57.577 29.630 0.00 0.00 31.47 3.21
487 515 6.050432 ACAACAGTAGGAATTTCGTACAACA 58.950 36.000 23.77 0.00 39.46 3.33
505 533 9.687717 GTGATTTGTTTTTATTGACAACAACAG 57.312 29.630 0.00 0.00 39.52 3.16
512 540 9.944663 GTGACTAGTGATTTGTTTTTATTGACA 57.055 29.630 0.00 0.00 0.00 3.58
527 556 5.661759 CCTAGTTAAAGGGGTGACTAGTGAT 59.338 44.000 0.00 0.00 39.78 3.06
534 563 4.407945 TGATAGCCTAGTTAAAGGGGTGAC 59.592 45.833 0.00 0.00 37.11 3.67
577 606 7.998383 ACAAGGTGATCAATGGTATAAATGCTA 59.002 33.333 0.00 0.00 0.00 3.49
588 617 8.279970 TGTTAGATTTACAAGGTGATCAATGG 57.720 34.615 0.00 0.00 0.00 3.16
620 649 9.854668 ACTCTCGTAGCCATATAAGATATGTAT 57.145 33.333 5.89 0.00 0.00 2.29
625 654 7.769507 CACCTACTCTCGTAGCCATATAAGATA 59.230 40.741 0.00 0.00 41.44 1.98
640 669 4.217983 ACTGTTTTAGGACACCTACTCTCG 59.782 45.833 0.00 0.00 35.63 4.04
872 901 9.224267 CACTATATATGTTGGCTTGAGCTTATT 57.776 33.333 2.66 0.00 41.70 1.40
873 902 8.378565 ACACTATATATGTTGGCTTGAGCTTAT 58.621 33.333 2.66 0.00 41.70 1.73
888 920 7.148641 AGGCAAAGAAGACGACACTATATATG 58.851 38.462 0.00 0.00 0.00 1.78
896 928 3.585862 TGATAGGCAAAGAAGACGACAC 58.414 45.455 0.00 0.00 0.00 3.67
901 933 3.338249 TGTGCTGATAGGCAAAGAAGAC 58.662 45.455 0.00 0.00 44.18 3.01
913 945 2.094597 GCTTGCAATGGTTGTGCTGATA 60.095 45.455 0.00 0.00 42.69 2.15
955 987 1.202806 GCCTTGGATCAATCGATGGGA 60.203 52.381 0.00 0.00 32.73 4.37
962 994 3.080319 GCTATCTGGCCTTGGATCAATC 58.920 50.000 3.32 0.00 0.00 2.67
1048 1080 2.246469 TGCTGTGGTTGGCATAACAAT 58.754 42.857 5.59 0.00 33.23 2.71
1052 1084 1.824230 GGATTGCTGTGGTTGGCATAA 59.176 47.619 0.00 0.00 38.30 1.90
1055 1087 1.907807 GGGATTGCTGTGGTTGGCA 60.908 57.895 0.00 0.00 36.62 4.92
1104 1136 1.811266 CTCTTGGATGTGCGGGTCG 60.811 63.158 0.00 0.00 0.00 4.79
1119 1151 2.282745 GCCCACTTGCCAAGCTCT 60.283 61.111 3.88 0.00 0.00 4.09
1141 1173 3.935993 CCAGTTGGGTGTACTCCAG 57.064 57.895 15.56 2.37 35.48 3.86
1203 1240 1.421268 ACACCCTTCACAATCTGCTCA 59.579 47.619 0.00 0.00 0.00 4.26
1218 1255 1.135721 ACGAGCCGATAGTTTACACCC 59.864 52.381 1.50 0.00 0.00 4.61
1245 1282 1.880340 GCCATCGAGTCTCAAGGCG 60.880 63.158 10.39 0.00 31.88 5.52
1321 1358 3.370103 GGGGTGAACGATATGAACTTCCA 60.370 47.826 0.00 0.00 0.00 3.53
1335 1372 1.337167 GCTCAATTTGCAGGGGTGAAC 60.337 52.381 0.00 0.00 0.00 3.18
1398 1435 8.748412 CCAATCCCTTGACATTTCTTATTACAA 58.252 33.333 0.00 0.00 34.04 2.41
1419 1456 7.227910 TCTGTTAGGTAGAACAAAACACCAATC 59.772 37.037 0.00 0.00 38.80 2.67
1429 1466 9.444600 GTTTCCATAATCTGTTAGGTAGAACAA 57.555 33.333 0.00 0.00 38.80 2.83
1455 1493 3.313249 TGCGAGTTGCCAATGATGAATAG 59.687 43.478 0.00 0.00 45.60 1.73
1495 1534 1.046472 TCCATGCTCCCCGTAATCGT 61.046 55.000 0.00 0.00 35.01 3.73
1500 1539 0.180171 CAACATCCATGCTCCCCGTA 59.820 55.000 0.00 0.00 0.00 4.02
1513 1552 4.913924 GCAATGAGTTCAAGTGACAACATC 59.086 41.667 0.00 0.00 0.00 3.06
1563 1602 4.582240 TGTTGTGCCATCTTGTGTTTCATA 59.418 37.500 0.00 0.00 0.00 2.15
1564 1603 3.384146 TGTTGTGCCATCTTGTGTTTCAT 59.616 39.130 0.00 0.00 0.00 2.57
1565 1604 2.757314 TGTTGTGCCATCTTGTGTTTCA 59.243 40.909 0.00 0.00 0.00 2.69
1566 1605 3.435105 TGTTGTGCCATCTTGTGTTTC 57.565 42.857 0.00 0.00 0.00 2.78
1567 1606 3.883830 TTGTTGTGCCATCTTGTGTTT 57.116 38.095 0.00 0.00 0.00 2.83
1569 1608 3.225104 AGATTGTTGTGCCATCTTGTGT 58.775 40.909 0.00 0.00 0.00 3.72
1570 1609 3.928727 AGATTGTTGTGCCATCTTGTG 57.071 42.857 0.00 0.00 0.00 3.33
1571 1610 5.948162 AGAATAGATTGTTGTGCCATCTTGT 59.052 36.000 0.00 0.00 0.00 3.16
1572 1611 6.446781 AGAATAGATTGTTGTGCCATCTTG 57.553 37.500 0.00 0.00 0.00 3.02
1624 1674 7.259290 TCTTGTGTTTCTTAACTTCATGACC 57.741 36.000 0.00 0.00 35.24 4.02
1626 1676 7.719193 TCCATCTTGTGTTTCTTAACTTCATGA 59.281 33.333 0.00 0.00 35.24 3.07
1630 1680 7.259290 TGTCCATCTTGTGTTTCTTAACTTC 57.741 36.000 0.00 0.00 35.24 3.01
1652 1702 8.814038 AATGCCATCTAGTCTCTTTTTAATGT 57.186 30.769 0.00 0.00 0.00 2.71
1654 1704 9.466497 TGAAATGCCATCTAGTCTCTTTTTAAT 57.534 29.630 0.00 0.00 0.00 1.40
1656 1706 8.103305 AGTGAAATGCCATCTAGTCTCTTTTTA 58.897 33.333 0.00 0.00 0.00 1.52
1707 1757 9.077885 ACAAAAGGACATAAATAGCAAGAAGAA 57.922 29.630 0.00 0.00 0.00 2.52
1756 1806 2.809119 TGACAAAACAACGCGGATACAT 59.191 40.909 12.47 0.00 0.00 2.29
1764 1814 2.256445 ACACAGTGACAAAACAACGC 57.744 45.000 7.81 0.00 0.00 4.84
1779 1829 1.065851 CATGACTGCTGCAACAACACA 59.934 47.619 3.02 0.00 0.00 3.72
1780 1830 1.762419 CATGACTGCTGCAACAACAC 58.238 50.000 3.02 0.00 0.00 3.32
1886 1936 5.855740 ATTTCAAAGGACAACCGGTTTAA 57.144 34.783 19.55 1.49 41.83 1.52
1909 1959 6.772233 TGACATTTGTCCAATTTCTCTGAGAA 59.228 34.615 15.82 15.82 44.15 2.87
1978 2028 7.981225 TCAAAAATAGAAAATGCATTAGGGCTC 59.019 33.333 13.39 5.01 34.04 4.70
2032 2082 2.810852 TGCAAACATGCACATCTTACGA 59.189 40.909 0.00 0.00 40.23 3.43
2033 2083 3.200294 TGCAAACATGCACATCTTACG 57.800 42.857 0.00 0.00 40.23 3.18
2086 2136 0.918983 ATTGGCCTAGCTAAGCACCA 59.081 50.000 16.01 7.95 31.62 4.17
2111 2162 6.400515 CCTTCGCGCAAAAATAAAAATAGCAA 60.401 34.615 8.75 0.00 0.00 3.91
2142 2221 1.751437 CTACCCCTTGGTTAGCAAGC 58.249 55.000 17.59 0.00 44.75 4.01
2159 2238 1.270412 CCAATATAACGCGTGGGGCTA 60.270 52.381 14.98 0.00 40.44 3.93
2161 2240 1.512156 CCCAATATAACGCGTGGGGC 61.512 60.000 14.98 0.00 46.04 5.80
2207 2288 6.803154 ACCTTTCTAAAACTTCCAGAATCG 57.197 37.500 0.00 0.00 0.00 3.34
2246 2327 5.009854 ACACATGAAAACACTGGAAAAGG 57.990 39.130 0.00 0.00 0.00 3.11
2248 2329 4.439426 CCGACACATGAAAACACTGGAAAA 60.439 41.667 0.00 0.00 0.00 2.29
2252 2333 1.946768 ACCGACACATGAAAACACTGG 59.053 47.619 0.00 0.00 0.00 4.00
2255 2336 3.414549 ACAACCGACACATGAAAACAC 57.585 42.857 0.00 0.00 0.00 3.32
2257 2338 3.551551 GCTACAACCGACACATGAAAAC 58.448 45.455 0.00 0.00 0.00 2.43
2258 2339 2.222213 CGCTACAACCGACACATGAAAA 59.778 45.455 0.00 0.00 0.00 2.29
2259 2340 1.795872 CGCTACAACCGACACATGAAA 59.204 47.619 0.00 0.00 0.00 2.69
2260 2341 1.424403 CGCTACAACCGACACATGAA 58.576 50.000 0.00 0.00 0.00 2.57
2262 2343 0.669318 ACCGCTACAACCGACACATG 60.669 55.000 0.00 0.00 0.00 3.21
2263 2344 0.034337 AACCGCTACAACCGACACAT 59.966 50.000 0.00 0.00 0.00 3.21
2265 2346 0.939419 AAAACCGCTACAACCGACAC 59.061 50.000 0.00 0.00 0.00 3.67
2266 2347 1.202557 AGAAAACCGCTACAACCGACA 60.203 47.619 0.00 0.00 0.00 4.35
2267 2348 1.505425 AGAAAACCGCTACAACCGAC 58.495 50.000 0.00 0.00 0.00 4.79
2269 2350 2.288458 TGAAAGAAAACCGCTACAACCG 59.712 45.455 0.00 0.00 0.00 4.44
2270 2351 3.304458 CCTGAAAGAAAACCGCTACAACC 60.304 47.826 0.00 0.00 34.07 3.77
2271 2352 3.314357 ACCTGAAAGAAAACCGCTACAAC 59.686 43.478 0.00 0.00 34.07 3.32
2276 2364 4.180817 CAAAAACCTGAAAGAAAACCGCT 58.819 39.130 0.00 0.00 34.07 5.52
2308 2396 7.654022 AAAGGACACAGGAAATAAAACTTGA 57.346 32.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.