Multiple sequence alignment - TraesCS5B01G058200

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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 TraesCS5B01G058200 chr5B 100.000 2480 0 0 1 2480 63851945 63849466 0.000000e+00 4580.0
1 TraesCS5B01G058200 chr5B 91.324 1095 45 16 628 1679 72259132 72258045 0.000000e+00 1450.0
2 TraesCS5B01G058200 chr5B 92.754 138 6 1 2312 2445 72257885 72257748 1.950000e-46 196.0
3 TraesCS5B01G058200 chr5B 93.939 132 4 1 2312 2439 72821778 72821909 1.950000e-46 196.0
4 TraesCS5B01G058200 chr5B 89.394 132 14 0 1548 1679 72821487 72821618 1.530000e-37 167.0
5 TraesCS5B01G058200 chr5B 95.876 97 4 0 2215 2311 72258024 72257928 9.180000e-35 158.0
6 TraesCS5B01G058200 chr5B 95.876 97 4 0 2215 2311 72821639 72821735 9.180000e-35 158.0
7 TraesCS5B01G058200 chr5B 78.000 250 31 12 437 663 72259954 72259706 4.300000e-28 135.0
8 TraesCS5B01G058200 chr5B 100.000 32 0 0 2000 2031 12320519 12320550 2.660000e-05 60.2
9 TraesCS5B01G058200 chr5B 100.000 31 0 0 2000 2030 548667214 548667244 9.580000e-05 58.4
10 TraesCS5B01G058200 chr5D 90.430 1139 59 18 438 1552 58686786 58685674 0.000000e+00 1454.0
11 TraesCS5B01G058200 chr5D 88.476 538 39 8 1710 2235 58685256 58684730 1.620000e-176 628.0
12 TraesCS5B01G058200 chr5D 84.348 345 47 7 98 437 58687165 58686823 5.110000e-87 331.0
13 TraesCS5B01G058200 chr5D 91.908 173 10 1 2312 2480 58684502 58684330 3.190000e-59 239.0
14 TraesCS5B01G058200 chr5D 82.117 274 36 12 1734 2003 287865554 287865290 3.210000e-54 222.0
15 TraesCS5B01G058200 chr5D 95.522 67 3 0 1546 1612 58685646 58685580 9.380000e-20 108.0
16 TraesCS5B01G058200 chr5A 85.781 1294 74 53 436 1674 47128869 47127631 0.000000e+00 1269.0
17 TraesCS5B01G058200 chr5A 84.753 728 57 41 769 1483 582107887 582107201 0.000000e+00 680.0
18 TraesCS5B01G058200 chr5A 90.141 497 34 9 1744 2236 47127632 47127147 1.250000e-177 632.0
19 TraesCS5B01G058200 chr1B 88.048 661 51 11 832 1489 344375803 344375168 0.000000e+00 758.0
20 TraesCS5B01G058200 chr1B 93.148 467 29 3 1034 1500 620551691 620552154 0.000000e+00 682.0
21 TraesCS5B01G058200 chr1B 95.704 419 18 0 1063 1481 621059389 621059807 0.000000e+00 675.0
22 TraesCS5B01G058200 chr1B 92.634 448 30 3 1034 1481 620786171 620786615 2.080000e-180 641.0
23 TraesCS5B01G058200 chr1B 80.095 211 30 11 1797 2003 513974427 513974629 1.990000e-31 147.0
24 TraesCS5B01G058200 chr6B 86.807 667 40 30 833 1483 61800038 61799404 0.000000e+00 701.0
25 TraesCS5B01G058200 chr6B 100.000 31 0 0 2000 2030 31522800 31522770 9.580000e-05 58.4
26 TraesCS5B01G058200 chr1A 93.750 448 25 3 1034 1481 542168012 542168456 0.000000e+00 669.0
27 TraesCS5B01G058200 chr1A 95.465 419 19 0 1063 1481 546216520 546216938 0.000000e+00 669.0
28 TraesCS5B01G058200 chr1A 85.207 169 23 2 2063 2230 344188779 344188612 3.280000e-39 172.0
29 TraesCS5B01G058200 chr1A 78.673 211 33 11 1797 2003 46479355 46479153 2.000000e-26 130.0
30 TraesCS5B01G058200 chr1A 81.481 162 26 3 2060 2220 400956973 400957131 2.000000e-26 130.0
31 TraesCS5B01G058200 chr1A 85.455 55 7 1 2371 2425 400957816 400957869 3.450000e-04 56.5
32 TraesCS5B01G058200 chr4D 82.482 274 36 11 1734 2003 457301489 457301224 1.920000e-56 230.0
33 TraesCS5B01G058200 chr3A 81.387 274 38 8 1734 2003 401135154 401135418 6.950000e-51 211.0
34 TraesCS5B01G058200 chr1D 87.791 172 14 4 2316 2480 321332043 321332214 7.000000e-46 195.0
35 TraesCS5B01G058200 chr1D 86.420 162 20 2 2063 2223 271836555 271836395 2.530000e-40 176.0
36 TraesCS5B01G058200 chr1D 81.991 211 26 11 1797 2003 66761021 66761223 4.240000e-38 169.0
37 TraesCS5B01G058200 chr1D 83.019 159 24 2 2063 2220 321709513 321709357 9.250000e-30 141.0
38 TraesCS5B01G058200 chr7A 81.517 211 27 11 1797 2003 559986304 559986506 1.970000e-36 163.0
39 TraesCS5B01G058200 chr7A 81.517 211 27 11 1797 2003 727860595 727860797 1.970000e-36 163.0
40 TraesCS5B01G058200 chr3D 80.569 211 29 12 1797 2003 21937510 21937712 4.270000e-33 152.0
41 TraesCS5B01G058200 chr2A 80.569 211 29 9 1797 2003 675201528 675201326 4.270000e-33 152.0
42 TraesCS5B01G058200 chrUn 79.621 211 31 11 1797 2003 62124317 62124115 9.250000e-30 141.0
43 TraesCS5B01G058200 chr4B 79.147 211 32 11 1797 2003 509513345 509513547 4.300000e-28 135.0
44 TraesCS5B01G058200 chr6A 95.522 67 3 0 1802 1868 483051050 483050984 9.380000e-20 108.0
45 TraesCS5B01G058200 chr7D 85.897 78 11 0 2146 2223 58207067 58206990 1.580000e-12 84.2
46 TraesCS5B01G058200 chr3B 100.000 31 0 0 2000 2030 354641204 354641174 9.580000e-05 58.4


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 TraesCS5B01G058200 chr5B 63849466 63851945 2479 True 4580.00 4580 100.0000 1 2480 1 chr5B.!!$R1 2479
1 TraesCS5B01G058200 chr5B 72257748 72259954 2206 True 484.75 1450 89.4885 437 2445 4 chr5B.!!$R2 2008
2 TraesCS5B01G058200 chr5D 58684330 58687165 2835 True 552.00 1454 90.1368 98 2480 5 chr5D.!!$R2 2382
3 TraesCS5B01G058200 chr5A 47127147 47128869 1722 True 950.50 1269 87.9610 436 2236 2 chr5A.!!$R2 1800
4 TraesCS5B01G058200 chr5A 582107201 582107887 686 True 680.00 680 84.7530 769 1483 1 chr5A.!!$R1 714
5 TraesCS5B01G058200 chr1B 344375168 344375803 635 True 758.00 758 88.0480 832 1489 1 chr1B.!!$R1 657
6 TraesCS5B01G058200 chr6B 61799404 61800038 634 True 701.00 701 86.8070 833 1483 1 chr6B.!!$R2 650

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
679 1365 0.313672 TCCAAAACCATTGTCGCAGC 59.686 50.0 0.0 0.0 0.0 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2163 3199 0.178932 AGCCTCCATATGCCTACGGA 60.179 55.0 0.0 0.0 0.0 4.69 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 3.803082 CAGTGTCGGGCGCCATTG 61.803 66.667 30.85 17.68 0.00 2.82
55 56 3.799755 GCCATTGGTCGCCGTGTC 61.800 66.667 4.26 0.00 0.00 3.67
56 57 3.487202 CCATTGGTCGCCGTGTCG 61.487 66.667 0.00 0.00 0.00 4.35
57 58 4.147322 CATTGGTCGCCGTGTCGC 62.147 66.667 0.00 0.00 0.00 5.19
67 68 4.201679 CGTGTCGCCTGCCCGATA 62.202 66.667 0.00 0.00 39.67 2.92
68 69 2.185867 GTGTCGCCTGCCCGATAA 59.814 61.111 0.00 0.00 39.67 1.75
69 70 1.883084 GTGTCGCCTGCCCGATAAG 60.883 63.158 0.00 0.00 39.67 1.73
70 71 2.280186 GTCGCCTGCCCGATAAGG 60.280 66.667 0.00 0.00 39.67 2.69
78 79 4.800554 CCCGATAAGGCATGGACC 57.199 61.111 0.00 0.00 39.21 4.46
79 80 1.301716 CCCGATAAGGCATGGACCG 60.302 63.158 0.00 0.00 39.21 4.79
80 81 1.961277 CCGATAAGGCATGGACCGC 60.961 63.158 0.00 0.00 33.69 5.68
81 82 2.310233 CGATAAGGCATGGACCGCG 61.310 63.158 0.00 0.00 33.69 6.46
82 83 1.227556 GATAAGGCATGGACCGCGT 60.228 57.895 4.92 0.00 33.69 6.01
83 84 1.222115 GATAAGGCATGGACCGCGTC 61.222 60.000 4.92 2.44 33.69 5.19
84 85 2.971428 ATAAGGCATGGACCGCGTCG 62.971 60.000 4.92 0.00 32.65 5.12
124 125 3.857309 GAGCTGCAAGTGCCCACCT 62.857 63.158 1.02 0.00 41.18 4.00
170 171 4.222847 GCTCCCGCCCCGAACTAG 62.223 72.222 0.00 0.00 0.00 2.57
192 193 2.879462 GAGCGGCGGAGTACAACG 60.879 66.667 9.78 0.00 0.00 4.10
197 198 2.767697 GCGGAGTACAACGCGAAC 59.232 61.111 15.93 5.25 46.58 3.95
198 199 2.723719 GCGGAGTACAACGCGAACC 61.724 63.158 15.93 4.06 46.58 3.62
211 212 4.681978 GAACCGCCAGCTCCACGT 62.682 66.667 0.00 0.00 0.00 4.49
227 229 2.430942 CGTTTTCGCCGTCGACGAT 61.431 57.895 37.65 0.00 45.43 3.73
239 241 0.463116 TCGACGATCTCGATGGTCCA 60.463 55.000 13.92 0.00 46.75 4.02
241 243 0.317103 GACGATCTCGATGGTCCACG 60.317 60.000 6.60 0.14 39.62 4.94
242 244 1.008424 CGATCTCGATGGTCCACGG 60.008 63.158 12.09 0.24 43.02 4.94
258 260 1.214062 CGGCGAGCTTCTCTCAGTT 59.786 57.895 0.00 0.00 41.98 3.16
263 265 2.538437 CGAGCTTCTCTCAGTTGATGG 58.462 52.381 0.00 0.00 41.98 3.51
265 267 3.734597 CGAGCTTCTCTCAGTTGATGGAG 60.735 52.174 0.00 0.00 41.98 3.86
286 288 1.072930 AGGGATAGGGCGGGGAAAT 60.073 57.895 0.00 0.00 0.00 2.17
329 331 0.519077 GCGGAAAGGCTGAGAAAGTG 59.481 55.000 0.00 0.00 0.00 3.16
338 340 0.868406 CTGAGAAAGTGCGGTTGACC 59.132 55.000 0.00 0.00 0.00 4.02
359 361 0.467290 GGGTTTGGTGTCAGGCTTCA 60.467 55.000 0.00 0.00 0.00 3.02
368 370 2.427095 GTGTCAGGCTTCAGGTTTTTGT 59.573 45.455 0.00 0.00 0.00 2.83
372 374 1.063266 AGGCTTCAGGTTTTTGTGGGA 60.063 47.619 0.00 0.00 0.00 4.37
374 376 2.368548 GGCTTCAGGTTTTTGTGGGAAT 59.631 45.455 0.00 0.00 0.00 3.01
375 377 3.392882 GCTTCAGGTTTTTGTGGGAATG 58.607 45.455 0.00 0.00 0.00 2.67
376 378 3.803368 GCTTCAGGTTTTTGTGGGAATGG 60.803 47.826 0.00 0.00 0.00 3.16
379 381 1.221781 AGGTTTTTGTGGGAATGGGGA 59.778 47.619 0.00 0.00 0.00 4.81
388 390 1.054406 GGGAATGGGGATGAGGACGA 61.054 60.000 0.00 0.00 0.00 4.20
393 395 2.348888 GGGGATGAGGACGACACGT 61.349 63.158 0.00 0.00 45.10 4.49
394 396 1.033746 GGGGATGAGGACGACACGTA 61.034 60.000 0.00 0.00 41.37 3.57
397 399 0.806868 GATGAGGACGACACGTACCA 59.193 55.000 2.83 2.19 42.35 3.25
402 404 3.198068 GAGGACGACACGTACCATAGTA 58.802 50.000 2.83 0.00 42.35 1.82
404 406 2.289002 GGACGACACGTACCATAGTAGG 59.711 54.545 0.00 0.00 41.37 3.18
405 407 3.198068 GACGACACGTACCATAGTAGGA 58.802 50.000 0.00 0.00 41.37 2.94
422 424 1.141881 GATGGCCTGACGTGACGAT 59.858 57.895 13.70 0.00 0.00 3.73
426 428 1.805945 GCCTGACGTGACGATGGTC 60.806 63.158 13.70 0.12 43.71 4.02
430 432 0.521735 TGACGTGACGATGGTCTCTG 59.478 55.000 13.70 5.16 43.79 3.35
469 509 3.927555 GGACAACCCAGATGTTCGA 57.072 52.632 0.00 0.00 34.14 3.71
520 569 0.542333 TTTGTCGGACAGTGACCCAA 59.458 50.000 11.14 2.99 35.46 4.12
523 572 0.600255 GTCGGACAGTGACCCAACAG 60.600 60.000 6.04 0.00 0.00 3.16
580 653 3.270877 GTGGTTGTAGGTGCTCTAATGG 58.729 50.000 0.00 0.00 0.00 3.16
630 709 2.067932 TTAGGTGCTTGCTGGTGGCT 62.068 55.000 0.00 0.00 42.39 4.75
672 1358 2.995258 CCTGCGAAATCCAAAACCATTG 59.005 45.455 0.00 0.00 0.00 2.82
677 1363 3.648009 GAAATCCAAAACCATTGTCGCA 58.352 40.909 0.00 0.00 0.00 5.10
679 1365 0.313672 TCCAAAACCATTGTCGCAGC 59.686 50.000 0.00 0.00 0.00 5.25
704 1396 0.462789 GCTCCCCTTCCGTAATCGAA 59.537 55.000 0.00 0.00 39.71 3.71
705 1397 1.134610 GCTCCCCTTCCGTAATCGAAA 60.135 52.381 0.00 0.00 39.71 3.46
707 1399 3.391049 CTCCCCTTCCGTAATCGAAATC 58.609 50.000 0.00 0.00 39.71 2.17
709 1401 2.158871 CCCCTTCCGTAATCGAAATCCA 60.159 50.000 0.00 0.00 39.71 3.41
710 1402 3.537580 CCCTTCCGTAATCGAAATCCAA 58.462 45.455 0.00 0.00 39.71 3.53
711 1403 3.942748 CCCTTCCGTAATCGAAATCCAAA 59.057 43.478 0.00 0.00 39.71 3.28
712 1404 4.396790 CCCTTCCGTAATCGAAATCCAAAA 59.603 41.667 0.00 0.00 39.71 2.44
713 1405 5.329493 CCTTCCGTAATCGAAATCCAAAAC 58.671 41.667 0.00 0.00 39.71 2.43
714 1406 4.950434 TCCGTAATCGAAATCCAAAACC 57.050 40.909 0.00 0.00 39.71 3.27
995 1709 2.471084 ATCCCCCACTCTCCCGAACA 62.471 60.000 0.00 0.00 0.00 3.18
1521 2263 8.984891 TTGTATCTATCTAGTAGTAGCGACTC 57.015 38.462 1.52 0.00 37.10 3.36
1545 2287 4.714632 AGCTGGTTCTGTTGCTTTAGTTA 58.285 39.130 0.00 0.00 30.96 2.24
1596 2372 2.029623 GATGGATGACTGCCAATGCTT 58.970 47.619 0.00 0.00 39.21 3.91
1611 2387 0.752054 TGCTTTGTTGCCTCTTTGGG 59.248 50.000 0.00 0.00 36.00 4.12
1662 2438 8.810652 TTGGCAAACTGATATTTCAAAAGTAC 57.189 30.769 0.00 0.00 0.00 2.73
1669 2445 7.906160 ACTGATATTTCAAAAGTACGGATTCG 58.094 34.615 0.00 0.00 43.02 3.34
1703 2479 4.408182 GTGGTTACTATCTCTGCCACAT 57.592 45.455 6.64 0.00 44.00 3.21
1713 2744 2.014857 CTCTGCCACATGATTGTCCTG 58.985 52.381 0.00 0.00 32.34 3.86
1716 2747 3.455543 TCTGCCACATGATTGTCCTGATA 59.544 43.478 0.00 0.00 32.34 2.15
1719 2750 4.823442 TGCCACATGATTGTCCTGATATTC 59.177 41.667 0.00 0.00 32.34 1.75
1725 2756 6.430308 ACATGATTGTCCTGATATTCTGCATC 59.570 38.462 0.00 0.00 0.00 3.91
1734 2765 4.700700 TGATATTCTGCATCAGGTGAGTG 58.299 43.478 0.00 0.00 31.51 3.51
1735 2766 4.162888 TGATATTCTGCATCAGGTGAGTGT 59.837 41.667 0.00 0.00 31.51 3.55
1746 2777 1.156736 GGTGAGTGTTGTCCAATCGG 58.843 55.000 0.00 0.00 41.02 4.18
1763 2794 0.107214 CGGCTGGGCTTATTTCCTGA 60.107 55.000 0.00 0.00 0.00 3.86
1767 2798 2.620585 GCTGGGCTTATTTCCTGATGTC 59.379 50.000 0.00 0.00 0.00 3.06
1773 2804 7.068702 TGGGCTTATTTCCTGATGTCATTATT 58.931 34.615 0.00 0.00 0.00 1.40
1902 2934 3.135530 AGCTTGGTCCTGATCCTATTGAC 59.864 47.826 0.00 0.00 0.00 3.18
1903 2935 3.118261 GCTTGGTCCTGATCCTATTGACA 60.118 47.826 0.00 0.00 0.00 3.58
1921 2953 7.807977 ATTGACAGTGTTACTCTGAAAATGT 57.192 32.000 19.40 0.00 36.81 2.71
1923 2955 7.015226 TGACAGTGTTACTCTGAAAATGTTG 57.985 36.000 19.40 0.00 36.81 3.33
1968 3001 3.073798 TGTCCAATTCTTGCTGGAAGGTA 59.926 43.478 9.11 0.00 43.32 3.08
1969 3002 3.691609 GTCCAATTCTTGCTGGAAGGTAG 59.308 47.826 9.11 0.00 43.32 3.18
1970 3003 3.019564 CCAATTCTTGCTGGAAGGTAGG 58.980 50.000 9.11 3.20 34.35 3.18
1971 3004 3.562176 CCAATTCTTGCTGGAAGGTAGGT 60.562 47.826 9.11 0.00 34.35 3.08
2058 3094 4.161189 TCTTCAGGCTGTATCTTCTTCAGG 59.839 45.833 15.27 0.00 0.00 3.86
2072 3108 5.477984 TCTTCTTCAGGTATTGCAGCAATTT 59.522 36.000 25.54 6.19 35.54 1.82
2097 3133 6.603095 AGAGATCGTTTAACTTCACAATTGC 58.397 36.000 5.05 0.00 0.00 3.56
2102 3138 3.658757 TTAACTTCACAATTGCCTGGC 57.341 42.857 12.87 12.87 0.00 4.85
2113 3149 2.437359 GCCTGGCGAGTGCTTCAT 60.437 61.111 1.35 0.00 42.25 2.57
2114 3150 2.042831 GCCTGGCGAGTGCTTCATT 61.043 57.895 1.35 0.00 42.25 2.57
2209 3252 3.253188 TGAAACCATCAAGAAGAAAGCCG 59.747 43.478 0.00 0.00 34.30 5.52
2250 3403 1.679153 TGCCGAACCTTCCAAAAAGAC 59.321 47.619 0.00 0.00 0.00 3.01
2255 3408 3.702330 GAACCTTCCAAAAAGACAACCG 58.298 45.455 0.00 0.00 0.00 4.44
2279 3432 7.334421 CCGAAAGAAAAACATGGATCTTCTAGA 59.666 37.037 0.00 0.00 31.20 2.43
2295 3448 7.019621 ATCTTCTAGATAGGCAAATCTGCAGC 61.020 42.308 9.47 0.00 40.95 5.25
2329 3524 2.223805 CCTTGCCTTTTCTTCACCACAC 60.224 50.000 0.00 0.00 0.00 3.82
2330 3525 2.136298 TGCCTTTTCTTCACCACACA 57.864 45.000 0.00 0.00 0.00 3.72
2439 3638 3.376859 TGAAAAGAACACACACGCTGATT 59.623 39.130 0.00 0.00 0.00 2.57
2450 3649 7.194278 ACACACACGCTGATTAACTATAGTAG 58.806 38.462 5.65 0.34 0.00 2.57
2452 3651 6.150318 CACACGCTGATTAACTATAGTAGGG 58.850 44.000 5.65 10.06 0.00 3.53
2456 3655 7.595502 CACGCTGATTAACTATAGTAGGGAAAG 59.404 40.741 18.45 9.26 0.00 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 3.803082 CAATGGCGCCCGACACTG 61.803 66.667 26.77 0.01 35.10 3.66
38 39 3.799755 GACACGGCGACCAATGGC 61.800 66.667 16.62 0.00 0.00 4.40
39 40 3.487202 CGACACGGCGACCAATGG 61.487 66.667 16.62 0.00 0.00 3.16
40 41 4.147322 GCGACACGGCGACCAATG 62.147 66.667 16.62 2.74 0.00 2.82
50 51 3.709880 TTATCGGGCAGGCGACACG 62.710 63.158 0.00 0.00 0.00 4.49
51 52 1.883084 CTTATCGGGCAGGCGACAC 60.883 63.158 0.00 0.00 0.00 3.67
52 53 2.499205 CTTATCGGGCAGGCGACA 59.501 61.111 0.00 0.00 0.00 4.35
53 54 2.280186 CCTTATCGGGCAGGCGAC 60.280 66.667 0.00 0.00 0.00 5.19
61 62 1.301716 CGGTCCATGCCTTATCGGG 60.302 63.158 0.00 0.00 0.00 5.14
62 63 1.961277 GCGGTCCATGCCTTATCGG 60.961 63.158 0.00 0.00 0.00 4.18
63 64 2.310233 CGCGGTCCATGCCTTATCG 61.310 63.158 0.00 0.00 0.00 2.92
64 65 1.222115 GACGCGGTCCATGCCTTATC 61.222 60.000 12.47 0.00 0.00 1.75
65 66 1.227556 GACGCGGTCCATGCCTTAT 60.228 57.895 12.47 0.00 0.00 1.73
66 67 2.185867 GACGCGGTCCATGCCTTA 59.814 61.111 12.47 0.00 0.00 2.69
98 99 3.782244 CTTGCAGCTCCGCGACAC 61.782 66.667 8.23 0.00 33.35 3.67
99 100 4.299547 ACTTGCAGCTCCGCGACA 62.300 61.111 8.23 0.00 33.35 4.35
100 101 3.782244 CACTTGCAGCTCCGCGAC 61.782 66.667 8.23 0.00 33.35 5.19
105 106 3.368571 GTGGGCACTTGCAGCTCC 61.369 66.667 3.15 0.00 44.36 4.70
106 107 3.368571 GGTGGGCACTTGCAGCTC 61.369 66.667 3.15 0.00 44.36 4.09
107 108 3.894638 AGGTGGGCACTTGCAGCT 61.895 61.111 3.15 0.00 44.36 4.24
108 109 3.677648 CAGGTGGGCACTTGCAGC 61.678 66.667 3.15 0.00 44.36 5.25
109 110 2.987547 CCAGGTGGGCACTTGCAG 60.988 66.667 3.15 0.00 44.36 4.41
180 181 2.723719 GGTTCGCGTTGTACTCCGC 61.724 63.158 16.43 16.43 46.10 5.54
195 196 3.767630 AAACGTGGAGCTGGCGGTT 62.768 57.895 0.00 0.00 0.00 4.44
197 198 2.966309 GAAAACGTGGAGCTGGCGG 61.966 63.158 0.00 0.00 0.00 6.13
198 199 2.556287 GAAAACGTGGAGCTGGCG 59.444 61.111 0.00 0.00 0.00 5.69
201 202 2.556287 GGCGAAAACGTGGAGCTG 59.444 61.111 0.00 0.00 0.00 4.24
224 226 1.008424 CCGTGGACCATCGAGATCG 60.008 63.158 15.29 5.01 41.45 3.69
227 229 3.822192 CGCCGTGGACCATCGAGA 61.822 66.667 15.29 0.00 0.00 4.04
236 238 2.676822 AGAGAAGCTCGCCGTGGA 60.677 61.111 0.00 0.00 35.36 4.02
258 260 0.542938 CCCTATCCCTCGCTCCATCA 60.543 60.000 0.00 0.00 0.00 3.07
263 265 3.686045 CCGCCCTATCCCTCGCTC 61.686 72.222 0.00 0.00 0.00 5.03
281 283 4.494091 TCATCTCCTCACCTTCATTTCC 57.506 45.455 0.00 0.00 0.00 3.13
286 288 3.008375 CCACTTTCATCTCCTCACCTTCA 59.992 47.826 0.00 0.00 0.00 3.02
329 331 2.561037 CCAAACCCTGGTCAACCGC 61.561 63.158 0.00 0.00 40.78 5.68
338 340 0.468029 AAGCCTGACACCAAACCCTG 60.468 55.000 0.00 0.00 0.00 4.45
352 354 1.063266 TCCCACAAAAACCTGAAGCCT 60.063 47.619 0.00 0.00 0.00 4.58
359 361 1.221781 TCCCCATTCCCACAAAAACCT 59.778 47.619 0.00 0.00 0.00 3.50
368 370 1.344953 CGTCCTCATCCCCATTCCCA 61.345 60.000 0.00 0.00 0.00 4.37
372 374 0.541863 GTGTCGTCCTCATCCCCATT 59.458 55.000 0.00 0.00 0.00 3.16
374 376 2.348104 CGTGTCGTCCTCATCCCCA 61.348 63.158 0.00 0.00 0.00 4.96
375 377 1.033746 TACGTGTCGTCCTCATCCCC 61.034 60.000 0.00 0.00 41.54 4.81
376 378 0.100146 GTACGTGTCGTCCTCATCCC 59.900 60.000 0.00 0.00 41.54 3.85
379 381 1.471119 ATGGTACGTGTCGTCCTCAT 58.529 50.000 0.00 0.00 41.54 2.90
388 390 2.626743 GCCATCCTACTATGGTACGTGT 59.373 50.000 0.00 0.00 46.93 4.49
393 395 3.507411 GTCAGGCCATCCTACTATGGTA 58.493 50.000 5.01 0.00 46.93 3.25
394 396 2.330216 GTCAGGCCATCCTACTATGGT 58.670 52.381 5.01 0.00 46.93 3.55
397 399 1.964223 CACGTCAGGCCATCCTACTAT 59.036 52.381 5.01 0.00 41.93 2.12
402 404 2.982130 GTCACGTCAGGCCATCCT 59.018 61.111 5.01 0.00 45.66 3.24
404 406 1.141881 ATCGTCACGTCAGGCCATC 59.858 57.895 5.01 0.00 0.00 3.51
405 407 1.153568 CATCGTCACGTCAGGCCAT 60.154 57.895 5.01 0.00 0.00 4.40
409 411 0.179161 GAGACCATCGTCACGTCAGG 60.179 60.000 0.00 0.00 41.87 3.86
426 428 4.609018 CCATACCCGCGCCCAGAG 62.609 72.222 0.00 0.00 0.00 3.35
459 499 4.212004 TCTCAAACAAAGCTCGAACATCTG 59.788 41.667 0.00 0.00 0.00 2.90
469 509 0.954452 CGGCCTTCTCAAACAAAGCT 59.046 50.000 0.00 0.00 0.00 3.74
520 569 2.034879 CAAACGCTCGATGGCCTGT 61.035 57.895 3.32 0.00 0.00 4.00
523 572 0.531974 TATCCAAACGCTCGATGGCC 60.532 55.000 0.00 0.00 34.13 5.36
558 624 3.270877 CATTAGAGCACCTACAACCACC 58.729 50.000 0.00 0.00 0.00 4.61
559 625 3.270877 CCATTAGAGCACCTACAACCAC 58.729 50.000 0.00 0.00 0.00 4.16
560 626 2.910319 ACCATTAGAGCACCTACAACCA 59.090 45.455 0.00 0.00 0.00 3.67
630 709 5.649395 CAGGCTCAGATTTTGAATCCTACAA 59.351 40.000 0.00 0.00 36.97 2.41
729 1421 3.679639 GCAAAAATGATCTTGGCGGGAAT 60.680 43.478 0.00 0.00 0.00 3.01
804 1500 1.012234 GATGCGTTCGCCGATGTTC 60.012 57.895 14.44 0.00 39.56 3.18
995 1709 4.447342 CCTTGGGGGCCATCGCTT 62.447 66.667 4.39 0.00 31.53 4.68
1176 1903 2.270986 CGCCTTGCTGCCCTTCTTT 61.271 57.895 0.00 0.00 0.00 2.52
1521 2263 4.319177 ACTAAAGCAACAGAACCAGCTAG 58.681 43.478 0.00 0.00 36.07 3.42
1545 2287 2.762327 CCCATCCAGCAATAAAAGCACT 59.238 45.455 0.00 0.00 0.00 4.40
1596 2372 2.691011 GTTACACCCAAAGAGGCAACAA 59.309 45.455 0.00 0.00 41.41 2.83
1611 2387 6.265577 AGAAGCACAAATTCAGTTGTTACAC 58.734 36.000 0.00 0.00 39.73 2.90
1662 2438 1.328680 CAGGCTGATGAAACGAATCCG 59.671 52.381 9.42 0.00 42.50 4.18
1669 2445 3.412386 AGTAACCACAGGCTGATGAAAC 58.588 45.455 23.66 12.99 0.00 2.78
1680 2456 3.786635 GTGGCAGAGATAGTAACCACAG 58.213 50.000 5.15 0.00 45.45 3.66
1703 2479 5.932455 TGATGCAGAATATCAGGACAATCA 58.068 37.500 0.00 0.00 31.35 2.57
1713 2744 4.701765 ACACTCACCTGATGCAGAATATC 58.298 43.478 0.00 0.00 32.44 1.63
1716 2747 3.079578 CAACACTCACCTGATGCAGAAT 58.920 45.455 0.00 0.00 32.44 2.40
1719 2750 1.802960 GACAACACTCACCTGATGCAG 59.197 52.381 0.00 0.00 0.00 4.41
1725 2756 1.800586 CGATTGGACAACACTCACCTG 59.199 52.381 0.00 0.00 0.00 4.00
1729 2760 0.396435 AGCCGATTGGACAACACTCA 59.604 50.000 1.98 0.00 37.49 3.41
1734 2765 2.700773 GCCCAGCCGATTGGACAAC 61.701 63.158 1.98 0.00 40.87 3.32
1735 2766 2.361104 GCCCAGCCGATTGGACAA 60.361 61.111 1.98 0.00 40.87 3.18
1746 2777 2.620585 GACATCAGGAAATAAGCCCAGC 59.379 50.000 0.00 0.00 0.00 4.85
1773 2804 7.716799 AACCATTGGAATGCTCTTATTAACA 57.283 32.000 10.37 0.00 35.08 2.41
1817 2849 6.237728 GCAAAGCAAACTACTACCAAAACAAC 60.238 38.462 0.00 0.00 0.00 3.32
1902 2934 6.138761 GCTCAACATTTTCAGAGTAACACTG 58.861 40.000 0.00 0.00 36.80 3.66
1903 2935 5.050091 CGCTCAACATTTTCAGAGTAACACT 60.050 40.000 0.00 0.00 0.00 3.55
1921 2953 5.577164 GCTAGTCTAATTTTCTCACGCTCAA 59.423 40.000 0.00 0.00 0.00 3.02
1923 2955 5.231147 CAGCTAGTCTAATTTTCTCACGCTC 59.769 44.000 0.00 0.00 0.00 5.03
1971 3004 6.530120 TCTAGCACATCTTGTTTAAGGAACA 58.470 36.000 0.00 0.00 46.19 3.18
2058 3094 6.292389 ACGATCTCTAAATTGCTGCAATAC 57.708 37.500 26.48 10.54 32.43 1.89
2072 3108 7.148474 GGCAATTGTGAAGTTAAACGATCTCTA 60.148 37.037 7.40 0.00 0.00 2.43
2094 3130 2.669569 GAAGCACTCGCCAGGCAA 60.670 61.111 13.30 0.00 39.83 4.52
2097 3133 0.883833 AAAATGAAGCACTCGCCAGG 59.116 50.000 0.00 0.00 39.83 4.45
2126 3162 9.143155 AGACCACCAAAATCAGTAAATTACTTT 57.857 29.630 2.41 0.00 36.76 2.66
2132 3168 9.479549 AATATCAGACCACCAAAATCAGTAAAT 57.520 29.630 0.00 0.00 0.00 1.40
2163 3199 0.178932 AGCCTCCATATGCCTACGGA 60.179 55.000 0.00 0.00 0.00 4.69
2209 3252 1.216710 CGACAGAGAACAGGAGCCC 59.783 63.158 0.00 0.00 0.00 5.19
2250 3403 5.772521 AGATCCATGTTTTTCTTTCGGTTG 58.227 37.500 0.00 0.00 0.00 3.77
2295 3448 3.599584 CAAGGATGCTGTGGCTGG 58.400 61.111 0.00 0.00 39.59 4.85
2450 3649 4.816925 GGCACTTGATATCTGTACTTTCCC 59.183 45.833 3.98 0.00 0.00 3.97
2452 3651 6.478344 CAGAGGCACTTGATATCTGTACTTTC 59.522 42.308 3.98 2.03 41.55 2.62
2456 3655 4.054671 GCAGAGGCACTTGATATCTGTAC 58.945 47.826 3.98 0.00 41.55 2.90


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

AutoCloner maintained by Alex Coulton.