Multiple sequence alignment - TraesCS5D01G281100

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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 TraesCS5D01G281100 chr5D 100.000 5091 0 0 1 5091 382419679 382424769 0.000000e+00 9402.0
1 TraesCS5D01G281100 chr5D 96.296 54 2 0 644 697 382420225 382420278 7.020000e-14 89.8
2 TraesCS5D01G281100 chr5D 96.296 54 2 0 547 600 382420322 382420375 7.020000e-14 89.8
3 TraesCS5D01G281100 chr5D 82.524 103 10 7 4360 4454 382423936 382424038 3.270000e-12 84.2
4 TraesCS5D01G281100 chr5D 82.692 104 8 9 4258 4360 382424038 382424132 3.270000e-12 84.2
5 TraesCS5D01G281100 chr5A 96.917 1622 40 7 3399 5012 482788509 482790128 0.000000e+00 2710.0
6 TraesCS5D01G281100 chr5A 94.334 1606 54 13 1805 3402 482786880 482788456 0.000000e+00 2427.0
7 TraesCS5D01G281100 chr5A 94.824 966 38 6 810 1769 482785926 482786885 0.000000e+00 1496.0
8 TraesCS5D01G281100 chr5A 93.407 364 16 7 425 782 482779835 482780196 2.700000e-147 532.0
9 TraesCS5D01G281100 chr5A 97.810 137 3 0 4168 4304 482790327 482790191 2.370000e-58 237.0
10 TraesCS5D01G281100 chr5A 97.183 71 2 0 5021 5091 482790753 482790823 2.490000e-23 121.0
11 TraesCS5D01G281100 chr5A 93.151 73 4 1 4287 4358 482790323 482790395 6.970000e-19 106.0
12 TraesCS5D01G281100 chr5A 92.593 54 4 0 644 697 482779958 482780011 1.520000e-10 78.7
13 TraesCS5D01G281100 chr5B 97.231 1589 41 3 3399 4985 458718026 458719613 0.000000e+00 2687.0
14 TraesCS5D01G281100 chr5B 94.515 1495 54 15 1925 3411 458716510 458717984 0.000000e+00 2281.0
15 TraesCS5D01G281100 chr5B 91.962 1468 68 15 425 1875 458715076 458716510 0.000000e+00 2012.0
16 TraesCS5D01G281100 chr5B 89.209 417 42 3 5 419 458714624 458715039 7.560000e-143 518.0
17 TraesCS5D01G281100 chr5B 95.349 86 4 0 4168 4253 458719945 458719860 2.470000e-28 137.0
18 TraesCS5D01G281100 chr5B 97.183 71 2 0 5021 5091 458720366 458720436 2.490000e-23 121.0
19 TraesCS5D01G281100 chr5B 98.113 53 1 0 4252 4304 458719778 458719726 5.430000e-15 93.5
20 TraesCS5D01G281100 chr5B 96.296 54 2 0 547 600 458715296 458715349 7.020000e-14 89.8
21 TraesCS5D01G281100 chr5B 82.692 104 8 9 4258 4360 458718989 458719083 3.270000e-12 84.2


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 TraesCS5D01G281100 chr5D 382419679 382424769 5090 False 9402.000000 9402 100.000000 1 5091 1 chr5D.!!$F1 5090
1 TraesCS5D01G281100 chr5A 482785926 482790823 4897 False 1372.000000 2710 95.281800 810 5091 5 chr5A.!!$F2 4281
2 TraesCS5D01G281100 chr5B 458714624 458720436 5812 False 1113.285714 2687 92.726857 5 5091 7 chr5B.!!$F1 5086

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
342 344 0.037232 ACCTCTGTACTTTCGCTGCC 60.037 55.0 0.0 0.0 0.0 4.85 F
829 863 0.824109 GTGTGGGAGGATGACGATGA 59.176 55.0 0.0 0.0 0.0 2.92 F
2316 2384 0.169009 GAACAAGCCAAGCCATCGTC 59.831 55.0 0.0 0.0 0.0 4.20 F
2629 2703 0.108138 ATTGTACCTGAGCCAGCGAC 60.108 55.0 0.0 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2262 2310 0.176680 CTGACTGGTCCGATCCTTGG 59.823 60.000 0.00 0.00 0.00 3.61 R
2629 2703 0.108804 AAGACGATACACACGCTGGG 60.109 55.000 0.00 0.00 0.00 4.45 R
3943 4078 0.168788 ATTTCTTCATGCGTGCCACG 59.831 50.000 13.95 13.95 45.88 4.94 R
4189 4324 2.170166 CTGTACACAACCATGGGCAAT 58.830 47.619 18.09 0.00 31.04 3.56 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
44 45 3.385755 GGCCGAGGTAGTCCAACTTAATA 59.614 47.826 0.00 0.00 35.89 0.98
46 47 5.048507 GCCGAGGTAGTCCAACTTAATAAG 58.951 45.833 0.00 0.00 35.89 1.73
66 67 1.348036 GGAAGAGGTTATCCCCATCGG 59.652 57.143 0.00 0.00 0.00 4.18
68 69 0.104934 AGAGGTTATCCCCATCGGCT 60.105 55.000 0.00 0.00 0.00 5.52
76 77 1.454479 CCCCATCGGCTGCTGAAAT 60.454 57.895 16.13 0.00 0.00 2.17
105 106 0.447801 GCCAAGTTCCATGTGTAGCG 59.552 55.000 0.00 0.00 0.00 4.26
107 108 1.155889 CAAGTTCCATGTGTAGCGCA 58.844 50.000 11.47 0.00 0.00 6.09
129 130 0.524414 GTATTGGGGAACGTGGTTGC 59.476 55.000 0.00 0.00 33.16 4.17
133 134 2.357760 GGGAACGTGGTTGCGCTA 60.358 61.111 9.73 0.00 34.73 4.26
143 144 1.001815 TGGTTGCGCTAAAAGTCTTGC 60.002 47.619 9.73 0.00 0.00 4.01
151 152 4.788609 GCGCTAAAAGTCTTGCTTATGTTC 59.211 41.667 0.00 0.00 36.17 3.18
166 167 1.725641 TGTTCAGCTTATCCACTGCG 58.274 50.000 0.00 0.00 33.80 5.18
177 178 1.191489 TCCACTGCGATCCACCTCAA 61.191 55.000 0.00 0.00 0.00 3.02
186 187 3.800604 GCGATCCACCTCAAATCCTAGTC 60.801 52.174 0.00 0.00 0.00 2.59
245 246 8.141268 GGAATACATTGTCAAGTTCTTTTTCCA 58.859 33.333 0.00 0.00 0.00 3.53
250 251 5.186996 TGTCAAGTTCTTTTTCCATGAGC 57.813 39.130 0.00 0.00 0.00 4.26
256 257 6.469782 AGTTCTTTTTCCATGAGCTTCAAA 57.530 33.333 0.00 0.00 0.00 2.69
267 268 6.209986 TCCATGAGCTTCAAATTTCTCAACAT 59.790 34.615 10.35 1.10 38.81 2.71
275 276 9.727627 GCTTCAAATTTCTCAACATATCCTAAG 57.272 33.333 0.00 0.00 0.00 2.18
300 301 4.894784 TCTGATTACGAAAGCTTCACCTT 58.105 39.130 0.00 0.00 0.00 3.50
301 302 4.690748 TCTGATTACGAAAGCTTCACCTTG 59.309 41.667 0.00 0.00 0.00 3.61
311 312 3.487372 AGCTTCACCTTGACCCTTTTAC 58.513 45.455 0.00 0.00 0.00 2.01
328 330 6.884280 CTTTTACAGGAATTGACAACCTCT 57.116 37.500 0.00 0.00 31.06 3.69
336 338 5.998363 AGGAATTGACAACCTCTGTACTTTC 59.002 40.000 0.00 0.00 38.84 2.62
342 344 0.037232 ACCTCTGTACTTTCGCTGCC 60.037 55.000 0.00 0.00 0.00 4.85
344 346 1.608025 CCTCTGTACTTTCGCTGCCAA 60.608 52.381 0.00 0.00 0.00 4.52
345 347 2.350522 CTCTGTACTTTCGCTGCCAAT 58.649 47.619 0.00 0.00 0.00 3.16
347 349 1.061131 CTGTACTTTCGCTGCCAATCG 59.939 52.381 0.00 0.00 0.00 3.34
354 356 4.115199 GCTGCCAATCGGTCCCCT 62.115 66.667 0.00 0.00 33.28 4.79
355 357 2.742116 GCTGCCAATCGGTCCCCTA 61.742 63.158 0.00 0.00 33.28 3.53
365 367 1.618447 GGTCCCCTAAAGCCCCTCA 60.618 63.158 0.00 0.00 0.00 3.86
381 383 2.399916 CTCAAGAAGGAAGCAGGGAG 57.600 55.000 0.00 0.00 0.00 4.30
400 402 2.926242 GGTTGGGGTGGAGTCGGA 60.926 66.667 0.00 0.00 0.00 4.55
401 403 2.298661 GGTTGGGGTGGAGTCGGAT 61.299 63.158 0.00 0.00 0.00 4.18
404 406 1.836999 TTGGGGTGGAGTCGGATGTG 61.837 60.000 0.00 0.00 0.00 3.21
406 408 1.079127 GGGTGGAGTCGGATGTGTG 60.079 63.158 0.00 0.00 0.00 3.82
419 421 3.621214 CGGATGTGTGGAAAATACTCCCA 60.621 47.826 0.00 0.00 34.22 4.37
422 424 3.142951 TGTGTGGAAAATACTCCCAACG 58.857 45.455 0.00 0.00 34.22 4.10
442 475 3.260128 ACGGAAAAACTAGGTACTCCCTG 59.740 47.826 3.10 0.00 45.81 4.45
443 476 3.260128 CGGAAAAACTAGGTACTCCCTGT 59.740 47.826 3.10 0.00 45.81 4.00
444 477 4.576879 GGAAAAACTAGGTACTCCCTGTG 58.423 47.826 0.00 0.00 45.81 3.66
467 500 7.877612 TGTGTCCCATAATATAGTGTGCATTAG 59.122 37.037 0.00 0.00 0.00 1.73
490 523 7.294676 AGTTTTTGCAAAAGTCAATCTTCAC 57.705 32.000 22.78 14.48 35.02 3.18
492 525 7.550196 AGTTTTTGCAAAAGTCAATCTTCACAT 59.450 29.630 22.78 4.20 35.02 3.21
495 528 6.012658 TGCAAAAGTCAATCTTCACATACC 57.987 37.500 0.00 0.00 35.02 2.73
498 531 7.446931 TGCAAAAGTCAATCTTCACATACCTTA 59.553 33.333 0.00 0.00 35.02 2.69
503 536 9.911788 AAGTCAATCTTCACATACCTTAATCAT 57.088 29.630 0.00 0.00 0.00 2.45
611 645 6.312529 TGGTACCCTAGATCTACAATACCAG 58.687 44.000 20.57 4.64 36.71 4.00
787 821 8.292444 TCTGATTATTATTTTTGTGTGGGAGG 57.708 34.615 0.00 0.00 0.00 4.30
789 823 8.837099 TGATTATTATTTTTGTGTGGGAGGAT 57.163 30.769 0.00 0.00 0.00 3.24
790 824 9.265862 TGATTATTATTTTTGTGTGGGAGGATT 57.734 29.630 0.00 0.00 0.00 3.01
829 863 0.824109 GTGTGGGAGGATGACGATGA 59.176 55.000 0.00 0.00 0.00 2.92
932 966 0.834687 ACCATGTCGGCCCCGTATAT 60.835 55.000 6.61 0.00 39.03 0.86
933 967 1.187974 CCATGTCGGCCCCGTATATA 58.812 55.000 6.61 0.00 40.74 0.86
934 968 1.760613 CCATGTCGGCCCCGTATATAT 59.239 52.381 6.61 0.00 40.74 0.86
935 969 2.483013 CCATGTCGGCCCCGTATATATG 60.483 54.545 6.61 2.22 40.74 1.78
936 970 1.187974 TGTCGGCCCCGTATATATGG 58.812 55.000 13.39 13.39 40.74 2.74
964 998 3.793144 CTTCAACCAGCGAGCGCC 61.793 66.667 11.66 0.00 43.17 6.53
1257 1299 8.747538 AATCCATACCCAAATACTAAACTGAC 57.252 34.615 0.00 0.00 0.00 3.51
1259 1301 7.562135 TCCATACCCAAATACTAAACTGACTC 58.438 38.462 0.00 0.00 0.00 3.36
1261 1303 7.365652 CCATACCCAAATACTAAACTGACTCCT 60.366 40.741 0.00 0.00 0.00 3.69
1265 1307 5.582665 CCAAATACTAAACTGACTCCTCTGC 59.417 44.000 0.00 0.00 0.00 4.26
1288 1330 3.797353 TGCTCGCCTGATTCCCCC 61.797 66.667 0.00 0.00 0.00 5.40
1328 1370 1.541310 TTCAGATCGAACTGGGGCGT 61.541 55.000 20.95 0.00 38.31 5.68
1374 1416 2.142292 GACATGTTCAGGCCCCTGGT 62.142 60.000 14.02 3.92 43.75 4.00
1390 1432 1.810030 GGTGCGGAACATCTCGGAC 60.810 63.158 0.00 0.00 44.80 4.79
1429 1471 4.082136 ACTGTCTTTGACCTCGAGGATTAC 60.082 45.833 37.69 22.98 38.94 1.89
1481 1526 3.581024 TGGTAGTAGCACCTAACAACG 57.419 47.619 0.00 0.00 39.50 4.10
1502 1547 1.806496 TCCCCCATATGTGTCTGGAG 58.194 55.000 1.24 0.00 34.24 3.86
1519 1565 5.010012 GTCTGGAGAAAAGCAATGGAAAGAA 59.990 40.000 0.00 0.00 0.00 2.52
1752 1798 3.896122 TCGCTTGAAATTTGGTAAGTGC 58.104 40.909 0.00 0.00 32.33 4.40
1777 1823 7.365741 CACTGCTTTGACATTGTCTTTAGAAT 58.634 34.615 17.26 0.00 33.15 2.40
1782 1828 7.965107 GCTTTGACATTGTCTTTAGAATGTAGG 59.035 37.037 17.26 0.00 46.42 3.18
1847 1893 7.988599 GGTAGCTAGCTAGAGCATTCTATAGTA 59.011 40.741 24.78 0.00 45.43 1.82
1854 1900 6.153680 GCTAGAGCATTCTATAGTACCCACAT 59.846 42.308 0.00 0.00 41.59 3.21
1861 1907 1.511613 ATAGTACCCACATGCCTGCT 58.488 50.000 0.00 0.00 0.00 4.24
1875 1921 1.517257 CTGCTCATCCGTGTCCGAC 60.517 63.158 0.00 0.00 35.63 4.79
1890 1936 1.600957 TCCGACGATTAGCTTCCGTAG 59.399 52.381 0.00 0.00 36.60 3.51
2121 2168 4.758251 CCACGGTGGCAGCGATCA 62.758 66.667 41.06 0.00 42.41 2.92
2139 2187 4.809958 CGATCAATCTGAGCTGATTTGTCT 59.190 41.667 0.00 0.00 34.77 3.41
2190 2238 1.806461 GCCAGCCTACGGATCGATCA 61.806 60.000 25.93 5.76 0.00 2.92
2206 2254 3.445450 TCGATCAGATAATCCAGCCTAGC 59.555 47.826 0.00 0.00 0.00 3.42
2263 2311 2.022764 AAACAAAAGCACAGCCAACC 57.977 45.000 0.00 0.00 0.00 3.77
2264 2312 0.901124 AACAAAAGCACAGCCAACCA 59.099 45.000 0.00 0.00 0.00 3.67
2265 2313 0.901124 ACAAAAGCACAGCCAACCAA 59.099 45.000 0.00 0.00 0.00 3.67
2266 2314 1.134729 ACAAAAGCACAGCCAACCAAG 60.135 47.619 0.00 0.00 0.00 3.61
2267 2315 0.465287 AAAAGCACAGCCAACCAAGG 59.535 50.000 0.00 0.00 0.00 3.61
2268 2316 0.396974 AAAGCACAGCCAACCAAGGA 60.397 50.000 0.00 0.00 0.00 3.36
2269 2317 0.178953 AAGCACAGCCAACCAAGGAT 60.179 50.000 0.00 0.00 0.00 3.24
2270 2318 0.610232 AGCACAGCCAACCAAGGATC 60.610 55.000 0.00 0.00 0.00 3.36
2271 2319 1.926511 GCACAGCCAACCAAGGATCG 61.927 60.000 0.00 0.00 0.00 3.69
2272 2320 1.002134 ACAGCCAACCAAGGATCGG 60.002 57.895 0.00 0.00 0.00 4.18
2273 2321 1.299648 CAGCCAACCAAGGATCGGA 59.700 57.895 0.00 0.00 0.00 4.55
2278 2326 0.324943 CAACCAAGGATCGGACCAGT 59.675 55.000 0.00 0.00 0.00 4.00
2316 2384 0.169009 GAACAAGCCAAGCCATCGTC 59.831 55.000 0.00 0.00 0.00 4.20
2477 2547 5.890419 GTCTTGGTTTAGTACTAGGCTAGGA 59.110 44.000 24.57 14.89 0.00 2.94
2563 2637 2.417933 GTGCAAGCAGAATCGATCAAGT 59.582 45.455 0.00 0.00 0.00 3.16
2580 2654 5.483685 TCAAGTGTAGCCTCTGTATTTGT 57.516 39.130 0.00 0.00 0.00 2.83
2622 2696 0.453390 GCAAGCCATTGTACCTGAGC 59.547 55.000 0.00 0.00 38.76 4.26
2623 2697 1.098050 CAAGCCATTGTACCTGAGCC 58.902 55.000 0.00 0.00 0.00 4.70
2624 2698 0.698238 AAGCCATTGTACCTGAGCCA 59.302 50.000 0.00 0.00 0.00 4.75
2625 2699 0.254178 AGCCATTGTACCTGAGCCAG 59.746 55.000 0.00 0.00 0.00 4.85
2626 2700 1.379642 GCCATTGTACCTGAGCCAGC 61.380 60.000 0.00 0.00 0.00 4.85
2627 2701 1.091771 CCATTGTACCTGAGCCAGCG 61.092 60.000 0.00 0.00 0.00 5.18
2628 2702 0.108186 CATTGTACCTGAGCCAGCGA 60.108 55.000 0.00 0.00 0.00 4.93
2629 2703 0.108138 ATTGTACCTGAGCCAGCGAC 60.108 55.000 0.00 0.00 0.00 5.19
2896 2971 1.227793 TGTCGCCATCAACACTGCA 60.228 52.632 0.00 0.00 0.00 4.41
2906 2981 4.261322 CCATCAACACTGCATATTAGGCAC 60.261 45.833 0.00 0.00 36.11 5.01
2945 3020 1.043673 GTCGGAGGGGTAGCAGTCAT 61.044 60.000 0.00 0.00 0.00 3.06
2980 3055 1.718757 GCCGCTGCCGAGATGAAAAT 61.719 55.000 0.00 0.00 36.29 1.82
3038 3113 1.339929 GCAAAGGGTCATGGAAAACGT 59.660 47.619 0.00 0.00 0.00 3.99
3042 3117 0.596082 GGGTCATGGAAAACGTGTGG 59.404 55.000 0.00 0.00 37.38 4.17
3158 3233 6.318628 CAAGAAGATATAGCTAGGTACTGCG 58.681 44.000 3.24 0.00 41.52 5.18
3211 3286 8.311109 TGATATTATAAAAGCTAGGCGATGACA 58.689 33.333 0.00 0.00 0.00 3.58
3396 3473 3.071602 GCCATGCTTATTGGACTAGGAGA 59.928 47.826 0.00 0.00 36.26 3.71
3578 3712 9.542462 TTACTGTAACTGTGAATTATCTATGGC 57.458 33.333 0.00 0.00 0.00 4.40
3588 3722 9.585099 TGTGAATTATCTATGGCAATTTTGAAC 57.415 29.630 0.00 0.00 0.00 3.18
3613 3747 9.528018 ACTTGACACTACAACCAAAATAAAATG 57.472 29.630 0.00 0.00 0.00 2.32
3879 4014 9.121517 CTGACATTTGATTTAGTTTGTCATCAC 57.878 33.333 4.25 0.00 41.63 3.06
4550 4686 4.083080 TGGGAACAAGGGAGGACTTATA 57.917 45.455 0.00 0.00 37.44 0.98
4710 4846 4.255833 TCCATTGTGCCTTGACAATTTC 57.744 40.909 0.00 0.00 42.69 2.17
4711 4847 3.640498 TCCATTGTGCCTTGACAATTTCA 59.360 39.130 0.00 0.00 42.69 2.69
4727 4863 8.077991 TGACAATTTCAGAATTCAGCAACTAAG 58.922 33.333 8.44 0.00 33.25 2.18
4815 4951 5.735285 TGCATTGGGTTCATTTGATACAA 57.265 34.783 0.00 0.00 0.00 2.41
4820 4956 7.010738 GCATTGGGTTCATTTGATACAATTCTG 59.989 37.037 0.00 0.00 0.00 3.02
4995 5140 6.531240 GTGCTGTTGACAAAATTCTTCTTCAA 59.469 34.615 0.00 0.00 0.00 2.69
5087 5948 6.988580 CCATAGAAAACTCAGATGCATGTCTA 59.011 38.462 2.46 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 1.550130 TTGGACTACCTCGGCCCTTG 61.550 60.000 0.00 0.00 37.04 3.61
30 31 8.445361 AACCTCTTCCTTATTAAGTTGGACTA 57.555 34.615 2.88 0.00 0.00 2.59
44 45 2.706190 CGATGGGGATAACCTCTTCCTT 59.294 50.000 0.00 0.00 37.49 3.36
46 47 1.348036 CCGATGGGGATAACCTCTTCC 59.652 57.143 0.00 0.00 37.49 3.46
66 67 1.398390 CGAGGGTGTTATTTCAGCAGC 59.602 52.381 0.00 0.00 37.53 5.25
68 69 1.448985 GCGAGGGTGTTATTTCAGCA 58.551 50.000 0.00 0.00 37.53 4.41
76 77 0.035739 GGAACTTGGCGAGGGTGTTA 59.964 55.000 6.71 0.00 0.00 2.41
105 106 0.738389 CACGTTCCCCAATACCATGC 59.262 55.000 0.00 0.00 0.00 4.06
107 108 0.996583 ACCACGTTCCCCAATACCAT 59.003 50.000 0.00 0.00 0.00 3.55
129 130 5.927030 TGAACATAAGCAAGACTTTTAGCG 58.073 37.500 0.00 0.00 39.97 4.26
133 134 6.396829 AAGCTGAACATAAGCAAGACTTTT 57.603 33.333 0.00 0.00 43.37 2.27
143 144 4.025396 CGCAGTGGATAAGCTGAACATAAG 60.025 45.833 0.00 0.00 34.87 1.73
151 152 1.202568 TGGATCGCAGTGGATAAGCTG 60.203 52.381 0.00 0.00 35.93 4.24
166 167 4.039852 GGAGACTAGGATTTGAGGTGGATC 59.960 50.000 0.00 0.00 0.00 3.36
186 187 6.876257 GGCAGACATGGATTAACTAATAGGAG 59.124 42.308 0.00 0.00 0.00 3.69
208 209 5.045213 TGACAATGTATTCCTCCTAAAGGCA 60.045 40.000 0.00 0.00 45.78 4.75
223 224 8.231692 TCATGGAAAAAGAACTTGACAATGTA 57.768 30.769 0.00 0.00 0.00 2.29
245 246 8.411683 GGATATGTTGAGAAATTTGAAGCTCAT 58.588 33.333 7.82 3.53 37.25 2.90
267 268 7.451877 AGCTTTCGTAATCAGATCCTTAGGATA 59.548 37.037 14.50 0.00 43.27 2.59
275 276 4.271291 GGTGAAGCTTTCGTAATCAGATCC 59.729 45.833 0.00 0.00 0.00 3.36
279 280 4.690748 TCAAGGTGAAGCTTTCGTAATCAG 59.309 41.667 0.00 0.00 0.00 2.90
311 312 4.899502 AGTACAGAGGTTGTCAATTCCTG 58.100 43.478 0.00 4.91 41.29 3.86
325 327 1.795768 TTGGCAGCGAAAGTACAGAG 58.204 50.000 0.00 0.00 0.00 3.35
328 330 1.075542 CGATTGGCAGCGAAAGTACA 58.924 50.000 6.02 0.00 0.00 2.90
354 356 2.290960 GCTTCCTTCTTGAGGGGCTTTA 60.291 50.000 0.00 0.00 46.31 1.85
355 357 1.548809 GCTTCCTTCTTGAGGGGCTTT 60.549 52.381 0.00 0.00 46.31 3.51
365 367 1.210885 CCCCTCCCTGCTTCCTTCTT 61.211 60.000 0.00 0.00 0.00 2.52
381 383 4.029809 CGACTCCACCCCAACCCC 62.030 72.222 0.00 0.00 0.00 4.95
400 402 3.756434 CGTTGGGAGTATTTTCCACACAT 59.244 43.478 0.00 0.00 39.09 3.21
401 403 3.142951 CGTTGGGAGTATTTTCCACACA 58.857 45.455 0.00 0.00 39.09 3.72
404 406 3.062122 TCCGTTGGGAGTATTTTCCAC 57.938 47.619 0.00 0.00 37.43 4.02
406 408 5.010314 AGTTTTTCCGTTGGGAGTATTTTCC 59.990 40.000 0.00 0.00 44.98 3.13
419 421 4.277515 GGGAGTACCTAGTTTTTCCGTT 57.722 45.455 0.00 0.00 35.85 4.44
444 477 8.848474 AACTAATGCACACTATATTATGGGAC 57.152 34.615 0.00 0.00 0.00 4.46
467 500 7.059448 TGTGAAGATTGACTTTTGCAAAAAC 57.941 32.000 23.92 19.80 39.13 2.43
679 713 9.838339 CTTGTAAACATCTAGGATACCAAATCT 57.162 33.333 0.00 0.00 37.17 2.40
723 757 9.725019 TCTGTCCCAAAATATAGTGCATATTAG 57.275 33.333 0.00 0.00 38.61 1.73
792 826 5.355350 CCCACACAAAAATGTTGGCTAAAAA 59.645 36.000 0.00 0.00 29.39 1.94
793 827 4.878397 CCCACACAAAAATGTTGGCTAAAA 59.122 37.500 0.00 0.00 29.39 1.52
794 828 4.162320 TCCCACACAAAAATGTTGGCTAAA 59.838 37.500 0.00 0.00 35.75 1.85
798 832 2.482864 CTCCCACACAAAAATGTTGGC 58.517 47.619 0.00 0.00 35.75 4.52
799 833 2.697751 TCCTCCCACACAAAAATGTTGG 59.302 45.455 0.00 0.00 36.85 3.77
800 834 4.039004 TCATCCTCCCACACAAAAATGTTG 59.961 41.667 0.00 0.00 0.00 3.33
801 835 4.039124 GTCATCCTCCCACACAAAAATGTT 59.961 41.667 0.00 0.00 0.00 2.71
802 836 3.573967 GTCATCCTCCCACACAAAAATGT 59.426 43.478 0.00 0.00 0.00 2.71
803 837 3.366273 CGTCATCCTCCCACACAAAAATG 60.366 47.826 0.00 0.00 0.00 2.32
829 863 1.275573 GAAGCCTGGTACTCCGAGTTT 59.724 52.381 6.31 0.00 36.30 2.66
920 954 0.462789 GGTCCATATATACGGGGCCG 59.537 60.000 9.52 0.00 46.03 6.13
932 966 3.576550 GGTTGAAGGCTTTTTGGTCCATA 59.423 43.478 0.00 0.00 0.00 2.74
933 967 2.368548 GGTTGAAGGCTTTTTGGTCCAT 59.631 45.455 0.00 0.00 0.00 3.41
934 968 1.760029 GGTTGAAGGCTTTTTGGTCCA 59.240 47.619 0.00 0.00 0.00 4.02
935 969 1.760029 TGGTTGAAGGCTTTTTGGTCC 59.240 47.619 0.00 0.00 0.00 4.46
936 970 2.803133 GCTGGTTGAAGGCTTTTTGGTC 60.803 50.000 0.00 0.00 0.00 4.02
1146 1187 2.360165 CCATGGAGCTTTGGAGTATTGC 59.640 50.000 5.56 0.00 34.81 3.56
1247 1288 2.028567 GCTGCAGAGGAGTCAGTTTAGT 60.029 50.000 20.43 0.00 0.00 2.24
1257 1299 4.079850 AGCACCGCTGCAGAGGAG 62.080 66.667 38.87 32.05 46.97 3.69
1374 1416 0.179111 GATGTCCGAGATGTTCCGCA 60.179 55.000 0.00 0.00 0.00 5.69
1429 1471 0.387622 CAAACAGCATGCCGACTTGG 60.388 55.000 15.66 0.00 42.53 3.61
1481 1526 2.304180 CTCCAGACACATATGGGGGATC 59.696 54.545 10.35 0.00 37.82 3.36
1502 1547 6.536224 CCATATGGTTCTTTCCATTGCTTTTC 59.464 38.462 14.09 0.00 44.75 2.29
1519 1565 4.413189 TGTCAATCAGTGGATCCATATGGT 59.587 41.667 19.62 13.63 36.34 3.55
1752 1798 6.304356 TCTAAAGACAATGTCAAAGCAGTG 57.696 37.500 16.38 0.00 39.92 3.66
1782 1828 9.971922 CCATGAGAATTAAATCAACCTTTATCC 57.028 33.333 0.00 0.00 0.00 2.59
1847 1893 1.077212 GATGAGCAGGCATGTGGGT 60.077 57.895 0.00 0.00 0.00 4.51
1854 1900 2.265739 GACACGGATGAGCAGGCA 59.734 61.111 0.00 0.00 0.00 4.75
1875 1921 2.470821 CAACCCTACGGAAGCTAATCG 58.529 52.381 0.00 0.00 0.00 3.34
1982 2029 1.107114 CGGGATAGGCGATCTATGCT 58.893 55.000 7.54 0.00 43.62 3.79
2121 2168 5.069648 TCCGATAGACAAATCAGCTCAGATT 59.930 40.000 0.00 0.00 37.93 2.40
2139 2187 2.301870 GCCTGGTGATATTGGTCCGATA 59.698 50.000 0.98 0.98 0.00 2.92
2190 2238 2.425312 CGATCGCTAGGCTGGATTATCT 59.575 50.000 0.26 0.00 0.00 1.98
2206 2254 0.598680 GCTGGACTTGGGATCGATCG 60.599 60.000 18.81 9.36 0.00 3.69
2254 2302 1.002134 CCGATCCTTGGTTGGCTGT 60.002 57.895 0.00 0.00 0.00 4.40
2255 2303 1.026718 GTCCGATCCTTGGTTGGCTG 61.027 60.000 0.00 0.00 0.00 4.85
2256 2304 1.299976 GTCCGATCCTTGGTTGGCT 59.700 57.895 0.00 0.00 0.00 4.75
2257 2305 1.749258 GGTCCGATCCTTGGTTGGC 60.749 63.158 0.00 0.00 0.00 4.52
2258 2306 0.392998 CTGGTCCGATCCTTGGTTGG 60.393 60.000 0.00 0.00 0.00 3.77
2259 2307 0.324943 ACTGGTCCGATCCTTGGTTG 59.675 55.000 0.00 0.00 0.00 3.77
2260 2308 0.613777 GACTGGTCCGATCCTTGGTT 59.386 55.000 0.00 0.00 0.00 3.67
2261 2309 0.544357 TGACTGGTCCGATCCTTGGT 60.544 55.000 0.00 0.00 0.00 3.67
2262 2310 0.176680 CTGACTGGTCCGATCCTTGG 59.823 60.000 0.00 0.00 0.00 3.61
2263 2311 0.460987 GCTGACTGGTCCGATCCTTG 60.461 60.000 0.00 0.00 0.00 3.61
2264 2312 1.617947 GGCTGACTGGTCCGATCCTT 61.618 60.000 0.00 0.00 0.00 3.36
2265 2313 2.060980 GGCTGACTGGTCCGATCCT 61.061 63.158 0.00 0.00 0.00 3.24
2266 2314 0.755698 TAGGCTGACTGGTCCGATCC 60.756 60.000 0.00 0.00 0.00 3.36
2267 2315 0.671251 CTAGGCTGACTGGTCCGATC 59.329 60.000 0.00 0.00 0.00 3.69
2268 2316 0.757188 CCTAGGCTGACTGGTCCGAT 60.757 60.000 0.00 0.00 0.00 4.18
2269 2317 1.379977 CCTAGGCTGACTGGTCCGA 60.380 63.158 0.00 0.00 0.00 4.55
2270 2318 0.757188 ATCCTAGGCTGACTGGTCCG 60.757 60.000 2.96 0.00 0.00 4.79
2271 2319 1.044611 GATCCTAGGCTGACTGGTCC 58.955 60.000 2.96 0.00 0.00 4.46
2272 2320 0.671251 CGATCCTAGGCTGACTGGTC 59.329 60.000 2.96 0.00 0.00 4.02
2273 2321 0.259065 TCGATCCTAGGCTGACTGGT 59.741 55.000 2.96 0.00 0.00 4.00
2278 2326 1.531840 GGGCTCGATCCTAGGCTGA 60.532 63.158 2.96 0.36 39.38 4.26
2298 2366 1.244019 GGACGATGGCTTGGCTTGTT 61.244 55.000 0.00 0.00 0.00 2.83
2316 2384 0.179034 GATGGCTAGGCTTGTCAGGG 60.179 60.000 18.18 0.00 0.00 4.45
2361 2431 3.692101 TCAGAAAGCTCGTTTCCAACAAA 59.308 39.130 0.00 0.00 45.16 2.83
2563 2637 3.694043 TGCACAAATACAGAGGCTACA 57.306 42.857 0.00 0.00 0.00 2.74
2580 2654 1.603456 TTGCTTTTCGGTGAGATGCA 58.397 45.000 0.00 0.00 0.00 3.96
2623 2697 2.835701 ATACACACGCTGGGTCGCTG 62.836 60.000 0.00 0.00 34.65 5.18
2624 2698 2.558554 GATACACACGCTGGGTCGCT 62.559 60.000 0.00 0.00 34.65 4.93
2625 2699 2.125673 ATACACACGCTGGGTCGC 60.126 61.111 0.00 0.00 34.65 5.19
2626 2700 1.872234 CGATACACACGCTGGGTCG 60.872 63.158 0.00 0.00 34.65 4.79
2627 2701 0.801067 GACGATACACACGCTGGGTC 60.801 60.000 0.00 0.00 34.65 4.46
2628 2702 1.214589 GACGATACACACGCTGGGT 59.785 57.895 0.00 0.00 37.91 4.51
2629 2703 0.108804 AAGACGATACACACGCTGGG 60.109 55.000 0.00 0.00 0.00 4.45
2896 2971 1.147376 TTGCGCGGGTGCCTAATAT 59.853 52.632 8.83 0.00 38.08 1.28
2906 2981 2.436646 ATCTCTTGGTTGCGCGGG 60.437 61.111 8.83 0.00 0.00 6.13
2969 3044 1.257936 CGCGGTGGTATTTTCATCTCG 59.742 52.381 0.00 0.00 0.00 4.04
2980 3055 4.830765 GCCTGATGCGCGGTGGTA 62.831 66.667 8.83 0.00 0.00 3.25
3038 3113 2.128290 CTCCAGTGACATGGGCCACA 62.128 60.000 9.28 0.00 41.01 4.17
3042 3117 0.038166 TTTCCTCCAGTGACATGGGC 59.962 55.000 0.00 0.00 41.01 5.36
3053 3128 4.811498 TCTATCCCGACTATTTTCCTCCA 58.189 43.478 0.00 0.00 0.00 3.86
3211 3286 3.375699 CCACATGACTCCTTAGGGTACT 58.624 50.000 0.00 0.00 0.00 2.73
3554 3688 7.564793 TGCCATAGATAATTCACAGTTACAGT 58.435 34.615 0.00 0.00 0.00 3.55
3578 3712 7.032580 TGGTTGTAGTGTCAAGTTCAAAATTG 58.967 34.615 0.00 0.00 35.48 2.32
3588 3722 9.743057 TCATTTTATTTTGGTTGTAGTGTCAAG 57.257 29.630 0.00 0.00 0.00 3.02
3879 4014 7.439056 GCATCCTGTATCAACAAATAAAATGGG 59.561 37.037 0.00 0.00 34.49 4.00
3943 4078 0.168788 ATTTCTTCATGCGTGCCACG 59.831 50.000 13.95 13.95 45.88 4.94
4025 4160 9.294030 GCTTGGATAAAACATTATTCTGAACAG 57.706 33.333 0.00 0.00 0.00 3.16
4048 4183 9.833917 CAATCATCATATGGAGATGTATAGCTT 57.166 33.333 2.13 0.00 42.63 3.74
4189 4324 2.170166 CTGTACACAACCATGGGCAAT 58.830 47.619 18.09 0.00 31.04 3.56
4550 4686 5.836024 TTTGGTCTAAGGGTCAACTACAT 57.164 39.130 0.00 0.00 0.00 2.29
4727 4863 9.613957 CTCATGAGAAGAAAATCATATGCAATC 57.386 33.333 18.34 0.00 34.42 2.67
4815 4951 7.650903 GCTCAAACTCTTGAATTTGAACAGAAT 59.349 33.333 8.29 0.00 42.62 2.40
4820 4956 8.801715 TTATGCTCAAACTCTTGAATTTGAAC 57.198 30.769 8.29 5.23 42.62 3.18
5013 5158 9.995003 TGCATTCTATTTAAAAATCCACAAGTT 57.005 25.926 0.00 0.00 0.00 2.66
5014 5159 9.995003 TTGCATTCTATTTAAAAATCCACAAGT 57.005 25.926 0.00 0.00 0.00 3.16
5017 5162 9.941325 ACATTGCATTCTATTTAAAAATCCACA 57.059 25.926 0.00 0.00 0.00 4.17
5019 5164 9.381033 CCACATTGCATTCTATTTAAAAATCCA 57.619 29.630 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.