Multiple sequence alignment - TraesCS2B01G543200

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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 TraesCS2B01G543200 chr2B 100.000 2792 0 0 1 2792 741008384 741005593 0.000000e+00 5156.0
1 TraesCS2B01G543200 chr2D 90.956 1946 88 29 236 2105 607682044 607680111 0.000000e+00 2538.0
2 TraesCS2B01G543200 chr2D 84.291 522 28 19 2130 2621 607680132 607679635 7.050000e-126 460.0
3 TraesCS2B01G543200 chr2A 88.598 1605 67 41 267 1792 739379899 739378332 0.000000e+00 1844.0
4 TraesCS2B01G543200 chr2A 82.558 516 44 15 2300 2792 739375102 739374610 2.000000e-111 412.0
5 TraesCS2B01G543200 chr2A 83.077 260 27 8 17 275 739380314 739380071 1.300000e-53 220.0
6 TraesCS2B01G543200 chr2A 84.348 230 23 9 1863 2084 739378332 739378108 2.180000e-51 213.0
7 TraesCS2B01G543200 chr2A 87.640 178 12 3 2349 2521 739377605 739377433 6.100000e-47 198.0
8 TraesCS2B01G543200 chr2A 87.861 173 12 6 2132 2298 739378108 739377939 7.890000e-46 195.0
9 TraesCS2B01G543200 chr4B 90.196 51 5 0 94 144 369550877 369550927 1.790000e-07 67.6


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 TraesCS2B01G543200 chr2B 741005593 741008384 2791 True 5156.000000 5156 100.000000 1 2792 1 chr2B.!!$R1 2791
1 TraesCS2B01G543200 chr2D 607679635 607682044 2409 True 1499.000000 2538 87.623500 236 2621 2 chr2D.!!$R1 2385
2 TraesCS2B01G543200 chr2A 739374610 739380314 5704 True 513.666667 1844 85.680333 17 2792 6 chr2A.!!$R1 2775

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
878 1137 0.250467 TTGCCACCAGAGCTTGACTC 60.25 55.0 0.0 0.0 46.66 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2626 5771 0.638292 AGACCAATGGCCAATGGGAT 59.362 50.0 37.28 24.96 41.17 3.85 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
17 18 4.674306 TTGGTGTGTGCATGTGGT 57.326 50.000 0.00 0.00 0.00 4.16
18 19 3.808984 TTGGTGTGTGCATGTGGTA 57.191 47.368 0.00 0.00 0.00 3.25
19 20 2.284754 TTGGTGTGTGCATGTGGTAT 57.715 45.000 0.00 0.00 0.00 2.73
20 21 1.819928 TGGTGTGTGCATGTGGTATC 58.180 50.000 0.00 0.00 0.00 2.24
21 22 1.094785 GGTGTGTGCATGTGGTATCC 58.905 55.000 0.00 0.00 0.00 2.59
22 23 1.094785 GTGTGTGCATGTGGTATCCC 58.905 55.000 0.00 0.00 0.00 3.85
68 69 7.244192 GCAGTTTTGAATTAAGCTAGTTCGAT 58.756 34.615 0.00 0.00 0.00 3.59
71 72 9.220767 AGTTTTGAATTAAGCTAGTTCGATCTT 57.779 29.630 0.48 0.00 0.00 2.40
82 83 7.331791 AGCTAGTTCGATCTTATTCCAAAACT 58.668 34.615 0.48 0.00 0.00 2.66
88 89 5.880332 TCGATCTTATTCCAAAACTGGGAAG 59.120 40.000 0.00 0.00 46.85 3.46
92 93 6.548321 TCTTATTCCAAAACTGGGAAGCTTA 58.452 36.000 0.00 0.00 46.85 3.09
96 97 5.722021 TCCAAAACTGGGAAGCTTATTTC 57.278 39.130 0.00 0.00 0.00 2.17
98 99 5.243730 TCCAAAACTGGGAAGCTTATTTCTG 59.756 40.000 0.00 0.00 0.00 3.02
101 102 6.976934 AAACTGGGAAGCTTATTTCTGAAA 57.023 33.333 5.15 5.15 0.00 2.69
170 171 9.819267 AAAAATACCCACTTAATTGACGAAAAA 57.181 25.926 0.00 0.00 0.00 1.94
171 172 8.806177 AAATACCCACTTAATTGACGAAAAAC 57.194 30.769 0.00 0.00 0.00 2.43
172 173 5.190992 ACCCACTTAATTGACGAAAAACC 57.809 39.130 0.00 0.00 0.00 3.27
173 174 4.223659 CCCACTTAATTGACGAAAAACCG 58.776 43.478 0.00 0.00 0.00 4.44
174 175 4.261280 CCCACTTAATTGACGAAAAACCGT 60.261 41.667 0.00 0.00 46.43 4.83
175 176 4.673311 CCACTTAATTGACGAAAAACCGTG 59.327 41.667 0.00 0.00 43.49 4.94
189 190 1.289109 ACCGTGCGAAAACCGATCTG 61.289 55.000 0.00 0.00 41.76 2.90
191 192 1.225745 GTGCGAAAACCGATCTGCG 60.226 57.895 0.00 0.00 41.76 5.18
193 194 0.946700 TGCGAAAACCGATCTGCGAA 60.947 50.000 0.00 0.00 44.57 4.70
209 210 4.932799 TCTGCGAAACTTATTTGGATCGAA 59.067 37.500 0.00 0.00 32.38 3.71
213 214 4.035208 CGAAACTTATTTGGATCGAAGGGG 59.965 45.833 0.00 0.00 32.38 4.79
224 225 2.272471 GAAGGGGGTAGCAGTGCC 59.728 66.667 12.58 0.00 0.00 5.01
228 229 1.993391 GGGGGTAGCAGTGCCAGTA 60.993 63.158 12.58 0.00 0.00 2.74
234 235 2.083774 GTAGCAGTGCCAGTATTTGCA 58.916 47.619 12.58 0.00 37.24 4.08
238 239 2.669434 GCAGTGCCAGTATTTGCATTTG 59.331 45.455 2.85 0.00 40.07 2.32
303 485 3.673484 CTGGCCCGCCACAAAGTG 61.673 66.667 3.74 0.00 41.89 3.16
330 513 4.703899 CAAAGCTGCATGTTTGAAGAAC 57.296 40.909 13.24 0.00 35.99 3.01
361 544 1.888512 ACGACCAAGGCTACGACTTTA 59.111 47.619 9.48 0.00 0.00 1.85
425 616 0.469917 CACGGCCCCTCTAATGATGT 59.530 55.000 0.00 0.00 0.00 3.06
426 617 0.469917 ACGGCCCCTCTAATGATGTG 59.530 55.000 0.00 0.00 0.00 3.21
459 653 4.056125 CCTCGTGCGGTCAGAGCA 62.056 66.667 0.00 0.00 42.99 4.26
460 654 2.505777 CTCGTGCGGTCAGAGCAG 60.506 66.667 0.00 0.00 46.10 4.24
466 671 1.301716 GCGGTCAGAGCAGAAACCA 60.302 57.895 0.00 0.00 34.19 3.67
550 760 1.331399 CCCGTCTCCTCCCTCCTTTC 61.331 65.000 0.00 0.00 0.00 2.62
564 781 2.049802 TTTCCTCGACACGACCGC 60.050 61.111 0.00 0.00 0.00 5.68
620 847 1.146263 CCTCCGCCCTATGACAACC 59.854 63.158 0.00 0.00 0.00 3.77
630 857 2.970640 CCTATGACAACCCTACCCTACC 59.029 54.545 0.00 0.00 0.00 3.18
750 997 1.467920 CCTAGCTTTTGGAAGGGCTG 58.532 55.000 0.00 0.00 36.40 4.85
751 998 1.467920 CTAGCTTTTGGAAGGGCTGG 58.532 55.000 0.00 0.00 36.40 4.85
814 1061 4.196193 CAAACGGTGGATTAGATTAGGCA 58.804 43.478 0.00 0.00 0.00 4.75
878 1137 0.250467 TTGCCACCAGAGCTTGACTC 60.250 55.000 0.00 0.00 46.66 3.36
962 1233 3.618780 CTGACCACTGAGGCTGGGC 62.619 68.421 0.00 0.00 43.14 5.36
963 1234 3.325753 GACCACTGAGGCTGGGCT 61.326 66.667 0.00 0.00 43.14 5.19
964 1235 2.856000 ACCACTGAGGCTGGGCTT 60.856 61.111 0.00 0.00 43.14 4.35
1178 1451 2.504681 GCACAAATGGCCGAAGCG 60.505 61.111 0.00 0.00 41.24 4.68
1503 1794 2.505407 CCTCATGTACATCTCCAACCCA 59.495 50.000 5.07 0.00 0.00 4.51
1598 1889 3.029570 GGTACGGGATTACAGAGGAAGT 58.970 50.000 0.00 0.00 0.00 3.01
1788 2079 2.793322 CGCGCGCTTCTTCTCTTCC 61.793 63.158 30.48 0.00 0.00 3.46
1797 2088 1.380524 TCTTCTCTTCCTAGTCGCCG 58.619 55.000 0.00 0.00 0.00 6.46
1800 2091 0.464013 TCTCTTCCTAGTCGCCGGAG 60.464 60.000 5.05 0.00 0.00 4.63
1814 2105 0.457851 CCGGAGTAGCAGACCTCTTG 59.542 60.000 0.00 0.00 0.00 3.02
1821 2112 0.390866 AGCAGACCTCTTGTGATGCG 60.391 55.000 0.00 0.00 39.90 4.73
1824 2115 1.204704 CAGACCTCTTGTGATGCGGTA 59.795 52.381 0.00 0.00 0.00 4.02
1839 2130 0.109086 CGGTAGAGTGTGGCTGAGTG 60.109 60.000 0.00 0.00 0.00 3.51
1845 2136 2.495270 AGAGTGTGGCTGAGTGATGTAG 59.505 50.000 0.00 0.00 0.00 2.74
1848 2139 0.807667 GTGGCTGAGTGATGTAGGCG 60.808 60.000 0.00 0.00 39.59 5.52
1853 2144 1.000827 CTGAGTGATGTAGGCGCTAGG 60.001 57.143 7.64 0.00 0.00 3.02
1856 2147 2.226912 GAGTGATGTAGGCGCTAGGTAG 59.773 54.545 7.64 0.00 0.00 3.18
1857 2148 2.158652 AGTGATGTAGGCGCTAGGTAGA 60.159 50.000 7.64 0.00 0.00 2.59
1858 2149 2.820787 GTGATGTAGGCGCTAGGTAGAT 59.179 50.000 7.64 0.00 0.00 1.98
1859 2150 3.082548 TGATGTAGGCGCTAGGTAGATC 58.917 50.000 7.64 8.34 0.00 2.75
1860 2151 2.953284 TGTAGGCGCTAGGTAGATCT 57.047 50.000 7.64 0.00 0.00 2.75
1861 2152 3.225177 TGTAGGCGCTAGGTAGATCTT 57.775 47.619 7.64 0.00 0.00 2.40
1890 2182 3.469899 TTCCATTCATCGTTTTGCTCG 57.530 42.857 0.00 0.00 0.00 5.03
1949 2248 0.177604 TGCACTTGTTTTTGCCAGGG 59.822 50.000 0.00 0.00 38.00 4.45
1994 2293 3.121738 TGGCTAGATGATGCATCAGTG 57.878 47.619 31.36 21.18 42.72 3.66
2012 2313 3.798337 CAGTGTCTGGTTGCAAAATCAAC 59.202 43.478 0.00 0.00 44.07 3.18
2032 2333 2.017049 CCTCGGTTCCATGTTTGATCC 58.983 52.381 0.00 0.00 0.00 3.36
2051 2352 4.602340 TCCACACAAAACTCTCTACTCC 57.398 45.455 0.00 0.00 0.00 3.85
2059 2360 6.153680 CACAAAACTCTCTACTCCCACTCTAT 59.846 42.308 0.00 0.00 0.00 1.98
2071 2372 3.201930 TCCCACTCTATGCCAAAATGCTA 59.798 43.478 0.00 0.00 0.00 3.49
2105 2406 1.221414 GCGCTCTCTCTCTCTCTCTC 58.779 60.000 0.00 0.00 0.00 3.20
2107 2408 2.748605 CGCTCTCTCTCTCTCTCTCTC 58.251 57.143 0.00 0.00 0.00 3.20
2108 2409 2.363680 CGCTCTCTCTCTCTCTCTCTCT 59.636 54.545 0.00 0.00 0.00 3.10
2109 2410 3.551863 CGCTCTCTCTCTCTCTCTCTCTC 60.552 56.522 0.00 0.00 0.00 3.20
2110 2411 3.640967 GCTCTCTCTCTCTCTCTCTCTCT 59.359 52.174 0.00 0.00 0.00 3.10
2111 2412 4.261994 GCTCTCTCTCTCTCTCTCTCTCTC 60.262 54.167 0.00 0.00 0.00 3.20
2112 2413 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
2113 2414 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2114 2415 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2115 2416 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2116 2417 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2117 2418 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2118 2419 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2119 2420 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2120 2421 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2121 2422 4.892345 TCTCTCTCTCTCTCTCTCTCTCTG 59.108 50.000 0.00 0.00 0.00 3.35
2122 2423 4.614475 TCTCTCTCTCTCTCTCTCTCTGT 58.386 47.826 0.00 0.00 0.00 3.41
2123 2424 4.646945 TCTCTCTCTCTCTCTCTCTCTGTC 59.353 50.000 0.00 0.00 0.00 3.51
2124 2425 4.614475 TCTCTCTCTCTCTCTCTCTGTCT 58.386 47.826 0.00 0.00 0.00 3.41
2125 2426 4.646945 TCTCTCTCTCTCTCTCTCTGTCTC 59.353 50.000 0.00 0.00 0.00 3.36
2126 2427 4.614475 TCTCTCTCTCTCTCTCTGTCTCT 58.386 47.826 0.00 0.00 0.00 3.10
2127 2428 4.646945 TCTCTCTCTCTCTCTCTGTCTCTC 59.353 50.000 0.00 0.00 0.00 3.20
2128 2429 4.614475 TCTCTCTCTCTCTCTGTCTCTCT 58.386 47.826 0.00 0.00 0.00 3.10
2129 2430 4.646945 TCTCTCTCTCTCTCTGTCTCTCTC 59.353 50.000 0.00 0.00 0.00 3.20
2130 2431 4.614475 TCTCTCTCTCTCTGTCTCTCTCT 58.386 47.826 0.00 0.00 0.00 3.10
2131 2432 4.646945 TCTCTCTCTCTCTGTCTCTCTCTC 59.353 50.000 0.00 0.00 0.00 3.20
2132 2433 4.614475 TCTCTCTCTCTGTCTCTCTCTCT 58.386 47.826 0.00 0.00 0.00 3.10
2133 2434 4.646945 TCTCTCTCTCTGTCTCTCTCTCTC 59.353 50.000 0.00 0.00 0.00 3.20
2134 2435 4.614475 TCTCTCTCTGTCTCTCTCTCTCT 58.386 47.826 0.00 0.00 0.00 3.10
2135 2436 5.766590 TCTCTCTCTGTCTCTCTCTCTCTA 58.233 45.833 0.00 0.00 0.00 2.43
2136 2437 6.377080 TCTCTCTCTGTCTCTCTCTCTCTAT 58.623 44.000 0.00 0.00 0.00 1.98
2137 2438 6.491745 TCTCTCTCTGTCTCTCTCTCTCTATC 59.508 46.154 0.00 0.00 0.00 2.08
2138 2439 6.377080 TCTCTCTGTCTCTCTCTCTCTATCT 58.623 44.000 0.00 0.00 0.00 1.98
2139 2440 6.491745 TCTCTCTGTCTCTCTCTCTCTATCTC 59.508 46.154 0.00 0.00 0.00 2.75
2140 2441 6.377080 TCTCTGTCTCTCTCTCTCTATCTCT 58.623 44.000 0.00 0.00 0.00 3.10
2141 2442 6.491745 TCTCTGTCTCTCTCTCTCTATCTCTC 59.508 46.154 0.00 0.00 0.00 3.20
2142 2443 6.377080 TCTGTCTCTCTCTCTCTATCTCTCT 58.623 44.000 0.00 0.00 0.00 3.10
2143 2444 6.491745 TCTGTCTCTCTCTCTCTATCTCTCTC 59.508 46.154 0.00 0.00 0.00 3.20
2144 2445 6.377080 TGTCTCTCTCTCTCTATCTCTCTCT 58.623 44.000 0.00 0.00 0.00 3.10
2145 2446 6.491745 TGTCTCTCTCTCTCTATCTCTCTCTC 59.508 46.154 0.00 0.00 0.00 3.20
2146 2447 6.719370 GTCTCTCTCTCTCTATCTCTCTCTCT 59.281 46.154 0.00 0.00 0.00 3.10
2147 2448 6.718912 TCTCTCTCTCTCTATCTCTCTCTCTG 59.281 46.154 0.00 0.00 0.00 3.35
2225 2526 7.137426 GCTTTGATGATTCCAATGATCAGTAC 58.863 38.462 0.09 0.00 39.56 2.73
2226 2527 7.013083 GCTTTGATGATTCCAATGATCAGTACT 59.987 37.037 0.09 0.00 39.56 2.73
2227 2528 9.551734 CTTTGATGATTCCAATGATCAGTACTA 57.448 33.333 0.09 0.00 39.56 1.82
2232 2533 7.492524 TGATTCCAATGATCAGTACTACTCAC 58.507 38.462 0.09 0.00 0.00 3.51
2279 2582 8.787852 ACAAAGAAAGATAACAACTCTCCAATC 58.212 33.333 0.00 0.00 0.00 2.67
2280 2583 8.786898 CAAAGAAAGATAACAACTCTCCAATCA 58.213 33.333 0.00 0.00 0.00 2.57
2281 2584 8.558973 AAGAAAGATAACAACTCTCCAATCAG 57.441 34.615 0.00 0.00 0.00 2.90
2282 2585 7.108847 AGAAAGATAACAACTCTCCAATCAGG 58.891 38.462 0.00 0.00 39.47 3.86
2320 2648 3.081329 AGTATTTAGCGAGCGTTCTCC 57.919 47.619 0.00 0.00 35.94 3.71
2322 2650 0.527817 ATTTAGCGAGCGTTCTCCGG 60.528 55.000 0.00 0.00 35.94 5.14
2374 2964 2.708216 TTTGTTCTGAGCTGGTGTCA 57.292 45.000 0.00 0.00 0.00 3.58
2375 2965 2.245159 TTGTTCTGAGCTGGTGTCAG 57.755 50.000 0.00 0.00 42.51 3.51
2376 2966 1.413118 TGTTCTGAGCTGGTGTCAGA 58.587 50.000 0.00 0.00 46.97 3.27
2426 3021 1.375523 GTAGGAGCCGTTGTGGTGG 60.376 63.158 0.00 0.00 41.21 4.61
2429 3024 2.110213 GAGCCGTTGTGGTGGTCA 59.890 61.111 0.00 0.00 41.21 4.02
2437 3032 0.396435 TTGTGGTGGTCAAGCTCGAT 59.604 50.000 0.00 0.00 0.00 3.59
2545 5680 3.300388 ACTCTGTGAAACACTCCTCTGA 58.700 45.455 0.00 0.00 45.67 3.27
2546 5681 3.706594 ACTCTGTGAAACACTCCTCTGAA 59.293 43.478 0.00 0.00 45.67 3.02
2547 5682 4.346418 ACTCTGTGAAACACTCCTCTGAAT 59.654 41.667 0.00 0.00 45.67 2.57
2559 5694 8.162878 ACACTCCTCTGAATAATAATGCATTG 57.837 34.615 22.27 2.48 0.00 2.82
2566 5701 9.459640 CTCTGAATAATAATGCATTGGTGAAAG 57.540 33.333 22.27 10.89 0.00 2.62
2626 5771 6.798476 CGTCGATCAAACAACTACTACACTTA 59.202 38.462 0.00 0.00 0.00 2.24
2631 5776 7.305813 TCAAACAACTACTACACTTATCCCA 57.694 36.000 0.00 0.00 0.00 4.37
2633 5778 8.380099 TCAAACAACTACTACACTTATCCCATT 58.620 33.333 0.00 0.00 0.00 3.16
2634 5779 8.450964 CAAACAACTACTACACTTATCCCATTG 58.549 37.037 0.00 0.00 0.00 2.82
2643 5788 2.023113 ACTTATCCCATTGGCCATTGGT 60.023 45.455 34.01 23.72 31.65 3.67
2655 5800 0.254178 CCATTGGTCTCCCTGGAGTG 59.746 60.000 12.77 3.77 42.49 3.51
2713 5858 1.664965 GCACGGCATATCTCGGGTC 60.665 63.158 0.00 0.00 31.65 4.46
2715 5860 1.152525 ACGGCATATCTCGGGTCCT 60.153 57.895 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.158559 GATACCACATGCACACACCAA 58.841 47.619 0.00 0.00 0.00 3.67
2 3 1.094785 GGATACCACATGCACACACC 58.905 55.000 0.00 0.00 0.00 4.16
16 17 5.262804 ACTAACTATGGATCGGAGGGATAC 58.737 45.833 0.00 0.00 36.43 2.24
17 18 5.531753 ACTAACTATGGATCGGAGGGATA 57.468 43.478 0.00 0.00 34.82 2.59
18 19 4.405756 ACTAACTATGGATCGGAGGGAT 57.594 45.455 0.00 0.00 38.35 3.85
19 20 3.897657 ACTAACTATGGATCGGAGGGA 57.102 47.619 0.00 0.00 0.00 4.20
20 21 4.558898 CGAAACTAACTATGGATCGGAGGG 60.559 50.000 0.00 0.00 0.00 4.30
21 22 4.547532 CGAAACTAACTATGGATCGGAGG 58.452 47.826 0.00 0.00 0.00 4.30
22 23 3.982058 GCGAAACTAACTATGGATCGGAG 59.018 47.826 0.00 0.00 0.00 4.63
82 83 3.756434 CCGTTTCAGAAATAAGCTTCCCA 59.244 43.478 0.00 0.00 0.00 4.37
88 89 3.924686 TCGTCTCCGTTTCAGAAATAAGC 59.075 43.478 0.00 0.00 35.01 3.09
92 93 4.628074 TCTTTCGTCTCCGTTTCAGAAAT 58.372 39.130 0.00 0.00 35.01 2.17
96 97 4.702392 CAAATCTTTCGTCTCCGTTTCAG 58.298 43.478 0.00 0.00 35.01 3.02
98 99 3.479949 GCAAATCTTTCGTCTCCGTTTC 58.520 45.455 0.00 0.00 35.01 2.78
101 102 1.002087 AGGCAAATCTTTCGTCTCCGT 59.998 47.619 0.00 0.00 35.01 4.69
145 146 9.251792 GTTTTTCGTCAATTAAGTGGGTATTTT 57.748 29.630 2.65 0.00 0.00 1.82
146 147 7.868922 GGTTTTTCGTCAATTAAGTGGGTATTT 59.131 33.333 2.65 0.00 0.00 1.40
147 148 7.372714 GGTTTTTCGTCAATTAAGTGGGTATT 58.627 34.615 2.65 0.00 0.00 1.89
148 149 6.348704 CGGTTTTTCGTCAATTAAGTGGGTAT 60.349 38.462 2.65 0.00 0.00 2.73
149 150 5.049543 CGGTTTTTCGTCAATTAAGTGGGTA 60.050 40.000 2.65 0.00 0.00 3.69
150 151 4.261280 CGGTTTTTCGTCAATTAAGTGGGT 60.261 41.667 2.65 0.00 0.00 4.51
151 152 4.223659 CGGTTTTTCGTCAATTAAGTGGG 58.776 43.478 2.65 0.00 0.00 4.61
152 153 4.673311 CACGGTTTTTCGTCAATTAAGTGG 59.327 41.667 2.65 0.00 41.86 4.00
153 154 4.145756 GCACGGTTTTTCGTCAATTAAGTG 59.854 41.667 0.00 0.00 41.86 3.16
154 155 4.284485 GCACGGTTTTTCGTCAATTAAGT 58.716 39.130 0.00 0.00 41.86 2.24
155 156 3.356658 CGCACGGTTTTTCGTCAATTAAG 59.643 43.478 0.00 0.00 41.86 1.85
156 157 3.002042 TCGCACGGTTTTTCGTCAATTAA 59.998 39.130 0.00 0.00 41.86 1.40
158 159 1.331138 TCGCACGGTTTTTCGTCAATT 59.669 42.857 0.00 0.00 41.86 2.32
160 161 0.725686 TTCGCACGGTTTTTCGTCAA 59.274 45.000 0.00 0.00 41.86 3.18
161 162 0.725686 TTTCGCACGGTTTTTCGTCA 59.274 45.000 0.00 0.00 41.86 4.35
162 163 1.509934 GTTTTCGCACGGTTTTTCGTC 59.490 47.619 0.00 0.00 41.86 4.20
163 164 1.537212 GTTTTCGCACGGTTTTTCGT 58.463 45.000 0.00 0.00 44.91 3.85
164 165 0.841356 GGTTTTCGCACGGTTTTTCG 59.159 50.000 0.00 0.00 0.00 3.46
165 166 0.841356 CGGTTTTCGCACGGTTTTTC 59.159 50.000 0.00 0.00 0.00 2.29
166 167 0.450983 TCGGTTTTCGCACGGTTTTT 59.549 45.000 0.00 0.00 39.05 1.94
167 168 0.664224 ATCGGTTTTCGCACGGTTTT 59.336 45.000 0.00 0.00 39.05 2.43
168 169 0.236449 GATCGGTTTTCGCACGGTTT 59.764 50.000 0.00 0.00 39.05 3.27
169 170 0.601841 AGATCGGTTTTCGCACGGTT 60.602 50.000 0.00 0.00 39.05 4.44
170 171 1.005394 AGATCGGTTTTCGCACGGT 60.005 52.632 0.00 0.00 39.05 4.83
171 172 1.419922 CAGATCGGTTTTCGCACGG 59.580 57.895 0.00 0.00 39.05 4.94
172 173 1.225745 GCAGATCGGTTTTCGCACG 60.226 57.895 0.00 0.00 39.05 5.34
173 174 1.225745 CGCAGATCGGTTTTCGCAC 60.226 57.895 0.00 0.00 39.05 5.34
174 175 0.946700 TTCGCAGATCGGTTTTCGCA 60.947 50.000 0.00 0.00 39.05 5.10
175 176 0.165079 TTTCGCAGATCGGTTTTCGC 59.835 50.000 0.00 0.00 39.05 4.70
189 190 4.495844 CCCTTCGATCCAAATAAGTTTCGC 60.496 45.833 0.00 0.00 0.00 4.70
191 192 4.338400 CCCCCTTCGATCCAAATAAGTTTC 59.662 45.833 0.00 0.00 0.00 2.78
193 194 3.268595 ACCCCCTTCGATCCAAATAAGTT 59.731 43.478 0.00 0.00 0.00 2.66
209 210 2.471084 TACTGGCACTGCTACCCCCT 62.471 60.000 0.00 0.00 0.00 4.79
213 214 1.401905 GCAAATACTGGCACTGCTACC 59.598 52.381 0.00 0.00 0.00 3.18
224 225 4.090354 CGTTTCAGGCAAATGCAAATACTG 59.910 41.667 7.80 5.15 44.36 2.74
228 229 3.383620 TCGTTTCAGGCAAATGCAAAT 57.616 38.095 7.80 0.00 44.36 2.32
234 235 4.554723 CGAGAGTTTTCGTTTCAGGCAAAT 60.555 41.667 0.00 0.00 35.91 2.32
238 239 2.579013 CGAGAGTTTTCGTTTCAGGC 57.421 50.000 0.00 0.00 35.91 4.85
303 485 2.144482 AACATGCAGCTTTGCTTCAC 57.856 45.000 0.00 0.00 34.36 3.18
361 544 1.597797 CCGCATGACTGGCATTTGGT 61.598 55.000 0.00 0.00 34.15 3.67
449 643 0.249868 TGTGGTTTCTGCTCTGACCG 60.250 55.000 0.00 0.00 34.90 4.79
458 652 5.105997 GGATCCAAAGATTCTGTGGTTTCTG 60.106 44.000 20.23 0.00 39.74 3.02
459 653 5.012893 GGATCCAAAGATTCTGTGGTTTCT 58.987 41.667 20.23 6.32 39.74 2.52
460 654 4.142600 CGGATCCAAAGATTCTGTGGTTTC 60.143 45.833 20.23 17.21 39.74 2.78
466 671 2.359900 GTGCGGATCCAAAGATTCTGT 58.640 47.619 13.41 0.00 30.90 3.41
550 760 4.477975 GAGGCGGTCGTGTCGAGG 62.478 72.222 0.00 0.00 36.23 4.63
564 781 0.322008 AGCGCAAAGGAGAAAGGAGG 60.322 55.000 11.47 0.00 0.00 4.30
620 847 3.222121 GCGACGGGGTAGGGTAGG 61.222 72.222 0.00 0.00 0.00 3.18
797 1044 5.885912 TCAAAGTTGCCTAATCTAATCCACC 59.114 40.000 0.00 0.00 0.00 4.61
814 1061 3.939592 GGTTAGAGCGGCTAATCAAAGTT 59.060 43.478 0.60 0.00 40.94 2.66
878 1137 1.335964 CGAGTGTAGTGGTCACTGGTG 60.336 57.143 13.32 0.00 44.68 4.17
879 1138 0.959553 CGAGTGTAGTGGTCACTGGT 59.040 55.000 13.32 0.00 44.68 4.00
962 1233 2.884685 CTCAGCTCGCTCGCCAAG 60.885 66.667 0.00 0.00 0.00 3.61
963 1234 4.441695 CCTCAGCTCGCTCGCCAA 62.442 66.667 0.00 0.00 0.00 4.52
1587 1878 1.987855 CCCCCGCACTTCCTCTGTA 60.988 63.158 0.00 0.00 0.00 2.74
1788 2079 0.814410 TCTGCTACTCCGGCGACTAG 60.814 60.000 9.30 5.31 0.00 2.57
1797 2088 2.171840 TCACAAGAGGTCTGCTACTCC 58.828 52.381 0.00 0.00 34.27 3.85
1800 2091 2.275318 GCATCACAAGAGGTCTGCTAC 58.725 52.381 0.00 0.00 34.10 3.58
1814 2105 1.084370 GCCACACTCTACCGCATCAC 61.084 60.000 0.00 0.00 0.00 3.06
1821 2112 1.257743 TCACTCAGCCACACTCTACC 58.742 55.000 0.00 0.00 0.00 3.18
1824 2115 1.346062 ACATCACTCAGCCACACTCT 58.654 50.000 0.00 0.00 0.00 3.24
1839 2130 3.349022 AGATCTACCTAGCGCCTACATC 58.651 50.000 2.29 0.00 0.00 3.06
1845 2136 2.823154 AGATCAAGATCTACCTAGCGCC 59.177 50.000 10.72 0.00 45.69 6.53
1848 2139 7.096551 GGAATCAAGATCAAGATCTACCTAGC 58.903 42.308 12.62 2.65 46.75 3.42
1853 2144 8.899427 TGAATGGAATCAAGATCAAGATCTAC 57.101 34.615 12.62 3.71 46.75 2.59
1856 2147 7.172875 ACGATGAATGGAATCAAGATCAAGATC 59.827 37.037 1.81 1.81 38.09 2.75
1857 2148 6.996879 ACGATGAATGGAATCAAGATCAAGAT 59.003 34.615 0.00 0.00 32.06 2.40
1858 2149 6.351711 ACGATGAATGGAATCAAGATCAAGA 58.648 36.000 0.00 0.00 32.06 3.02
1859 2150 6.615264 ACGATGAATGGAATCAAGATCAAG 57.385 37.500 0.00 0.00 32.06 3.02
1860 2151 7.395190 AAACGATGAATGGAATCAAGATCAA 57.605 32.000 0.00 0.00 32.06 2.57
1861 2152 7.252708 CAAAACGATGAATGGAATCAAGATCA 58.747 34.615 0.00 0.00 32.06 2.92
1890 2182 1.376037 CAACAGAACCGAGGAGCCC 60.376 63.158 0.00 0.00 0.00 5.19
2012 2313 2.017049 GGATCAAACATGGAACCGAGG 58.983 52.381 0.00 0.00 0.00 4.63
2016 2317 2.890311 TGTGTGGATCAAACATGGAACC 59.110 45.455 0.00 0.00 0.00 3.62
2032 2333 4.058817 GTGGGAGTAGAGAGTTTTGTGTG 58.941 47.826 0.00 0.00 0.00 3.82
2051 2352 5.581126 TTTAGCATTTTGGCATAGAGTGG 57.419 39.130 0.00 0.00 35.83 4.00
2084 2385 2.105960 GAGAGAGAGAGAGAGCGCGC 62.106 65.000 26.66 26.66 0.00 6.86
2086 2387 1.202580 AGAGAGAGAGAGAGAGAGCGC 60.203 57.143 0.00 0.00 0.00 5.92
2087 2388 2.363680 AGAGAGAGAGAGAGAGAGAGCG 59.636 54.545 0.00 0.00 0.00 5.03
2105 2406 4.648762 AGAGAGACAGAGAGAGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
2107 2408 4.648762 AGAGAGAGACAGAGAGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
2108 2409 4.614475 AGAGAGAGACAGAGAGAGAGAGA 58.386 47.826 0.00 0.00 0.00 3.10
2109 2410 4.648762 AGAGAGAGAGACAGAGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
2110 2411 4.614475 AGAGAGAGAGACAGAGAGAGAGA 58.386 47.826 0.00 0.00 0.00 3.10
2111 2412 4.648762 AGAGAGAGAGAGACAGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
2112 2413 4.614475 AGAGAGAGAGAGACAGAGAGAGA 58.386 47.826 0.00 0.00 0.00 3.10
2113 2414 6.493115 AGATAGAGAGAGAGAGACAGAGAGAG 59.507 46.154 0.00 0.00 0.00 3.20
2114 2415 6.377080 AGATAGAGAGAGAGAGACAGAGAGA 58.623 44.000 0.00 0.00 0.00 3.10
2115 2416 6.493115 AGAGATAGAGAGAGAGAGACAGAGAG 59.507 46.154 0.00 0.00 0.00 3.20
2116 2417 6.377080 AGAGATAGAGAGAGAGAGACAGAGA 58.623 44.000 0.00 0.00 0.00 3.10
2117 2418 6.493115 AGAGAGATAGAGAGAGAGAGACAGAG 59.507 46.154 0.00 0.00 0.00 3.35
2118 2419 6.377080 AGAGAGATAGAGAGAGAGAGACAGA 58.623 44.000 0.00 0.00 0.00 3.41
2119 2420 6.493115 AGAGAGAGATAGAGAGAGAGAGACAG 59.507 46.154 0.00 0.00 0.00 3.51
2120 2421 6.377080 AGAGAGAGATAGAGAGAGAGAGACA 58.623 44.000 0.00 0.00 0.00 3.41
2121 2422 6.719370 AGAGAGAGAGATAGAGAGAGAGAGAC 59.281 46.154 0.00 0.00 0.00 3.36
2122 2423 6.718912 CAGAGAGAGAGATAGAGAGAGAGAGA 59.281 46.154 0.00 0.00 0.00 3.10
2123 2424 6.493115 ACAGAGAGAGAGATAGAGAGAGAGAG 59.507 46.154 0.00 0.00 0.00 3.20
2124 2425 6.377080 ACAGAGAGAGAGATAGAGAGAGAGA 58.623 44.000 0.00 0.00 0.00 3.10
2125 2426 6.493115 AGACAGAGAGAGAGATAGAGAGAGAG 59.507 46.154 0.00 0.00 0.00 3.20
2126 2427 6.377080 AGACAGAGAGAGAGATAGAGAGAGA 58.623 44.000 0.00 0.00 0.00 3.10
2127 2428 6.662865 AGACAGAGAGAGAGATAGAGAGAG 57.337 45.833 0.00 0.00 0.00 3.20
2128 2429 6.183361 CCAAGACAGAGAGAGAGATAGAGAGA 60.183 46.154 0.00 0.00 0.00 3.10
2129 2430 5.994054 CCAAGACAGAGAGAGAGATAGAGAG 59.006 48.000 0.00 0.00 0.00 3.20
2130 2431 5.687441 GCCAAGACAGAGAGAGAGATAGAGA 60.687 48.000 0.00 0.00 0.00 3.10
2131 2432 4.516698 GCCAAGACAGAGAGAGAGATAGAG 59.483 50.000 0.00 0.00 0.00 2.43
2132 2433 4.080072 TGCCAAGACAGAGAGAGAGATAGA 60.080 45.833 0.00 0.00 0.00 1.98
2133 2434 4.206375 TGCCAAGACAGAGAGAGAGATAG 58.794 47.826 0.00 0.00 0.00 2.08
2134 2435 4.242336 TGCCAAGACAGAGAGAGAGATA 57.758 45.455 0.00 0.00 0.00 1.98
2135 2436 3.098774 TGCCAAGACAGAGAGAGAGAT 57.901 47.619 0.00 0.00 0.00 2.75
2136 2437 2.593925 TGCCAAGACAGAGAGAGAGA 57.406 50.000 0.00 0.00 0.00 3.10
2137 2438 3.587923 CTTTGCCAAGACAGAGAGAGAG 58.412 50.000 0.00 0.00 30.57 3.20
2138 2439 2.301296 CCTTTGCCAAGACAGAGAGAGA 59.699 50.000 0.00 0.00 30.57 3.10
2139 2440 2.301296 TCCTTTGCCAAGACAGAGAGAG 59.699 50.000 0.00 0.00 30.57 3.20
2140 2441 2.329267 TCCTTTGCCAAGACAGAGAGA 58.671 47.619 0.00 0.00 30.57 3.10
2141 2442 2.847327 TCCTTTGCCAAGACAGAGAG 57.153 50.000 0.00 0.00 30.57 3.20
2142 2443 3.214328 GTTTCCTTTGCCAAGACAGAGA 58.786 45.455 0.00 0.00 30.57 3.10
2143 2444 2.294512 GGTTTCCTTTGCCAAGACAGAG 59.705 50.000 0.00 0.00 30.57 3.35
2144 2445 2.306847 GGTTTCCTTTGCCAAGACAGA 58.693 47.619 0.00 0.00 30.57 3.41
2145 2446 2.031120 TGGTTTCCTTTGCCAAGACAG 58.969 47.619 0.00 0.00 30.57 3.51
2146 2447 2.151502 TGGTTTCCTTTGCCAAGACA 57.848 45.000 0.00 0.00 30.57 3.41
2254 2555 8.786898 TGATTGGAGAGTTGTTATCTTTCTTTG 58.213 33.333 0.00 0.00 0.00 2.77
2320 2648 1.002468 CCTGAAGAACAGTGCAAACCG 60.002 52.381 0.00 0.00 44.40 4.44
2322 2650 1.269257 GCCCTGAAGAACAGTGCAAAC 60.269 52.381 0.00 0.00 46.41 2.93
2340 2668 5.643777 TCAGAACAAAAGCTACTATTGAGCC 59.356 40.000 8.05 0.00 41.06 4.70
2342 2670 6.593382 AGCTCAGAACAAAAGCTACTATTGAG 59.407 38.462 8.05 7.14 44.28 3.02
2374 2964 2.695666 CGGACTCTCTCTCTCTCTCTCT 59.304 54.545 0.00 0.00 0.00 3.10
2375 2965 2.693591 TCGGACTCTCTCTCTCTCTCTC 59.306 54.545 0.00 0.00 0.00 3.20
2376 2966 2.695666 CTCGGACTCTCTCTCTCTCTCT 59.304 54.545 0.00 0.00 0.00 3.10
2426 3021 1.658095 GCAACTCTGATCGAGCTTGAC 59.342 52.381 5.59 1.25 43.85 3.18
2429 3024 1.274728 ACAGCAACTCTGATCGAGCTT 59.725 47.619 0.90 5.88 45.72 3.74
2437 3032 2.355756 GACAAAGCAACAGCAACTCTGA 59.644 45.455 0.00 0.00 45.72 3.27
2545 5680 8.636213 CCTCTCTTTCACCAATGCATTATTATT 58.364 33.333 12.53 0.00 0.00 1.40
2546 5681 8.000709 TCCTCTCTTTCACCAATGCATTATTAT 58.999 33.333 12.53 0.00 0.00 1.28
2547 5682 7.283127 GTCCTCTCTTTCACCAATGCATTATTA 59.717 37.037 12.53 0.00 0.00 0.98
2559 5694 2.849294 AGCAAGTCCTCTCTTTCACC 57.151 50.000 0.00 0.00 0.00 4.02
2566 5701 7.120432 ACATTTTGAGAATTAGCAAGTCCTCTC 59.880 37.037 0.00 0.00 0.00 3.20
2626 5771 0.638292 AGACCAATGGCCAATGGGAT 59.362 50.000 37.28 24.96 41.17 3.85
2655 5800 2.181521 TGCGTGGTTTCCGTGGAAC 61.182 57.895 0.00 0.00 33.41 3.62
2698 5843 1.587054 GAGGACCCGAGATATGCCG 59.413 63.158 0.00 0.00 0.00 5.69
2704 5849 2.506065 CTTTCCGAGGACCCGAGAT 58.494 57.895 4.18 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.