Multiple sequence alignment - TraesCS1B01G331700

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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 TraesCS1B01G331700 chr1B 100.000 3026 0 0 1 3026 557920271 557917246 0.000000e+00 5589.0
1 TraesCS1B01G331700 chr1B 90.000 140 14 0 1913 2052 557544025 557543886 6.660000e-42 182.0
2 TraesCS1B01G331700 chr1D 94.979 1434 56 10 858 2285 413413035 413411612 0.000000e+00 2235.0
3 TraesCS1B01G331700 chr1D 89.756 820 73 7 2110 2923 413314331 413313517 0.000000e+00 1038.0
4 TraesCS1B01G331700 chr1D 88.105 723 69 8 2214 2923 413312578 413311860 0.000000e+00 843.0
5 TraesCS1B01G331700 chr1D 88.427 674 52 16 2367 3026 413409429 413408768 0.000000e+00 789.0
6 TraesCS1B01G331700 chr1D 94.352 301 17 0 1656 1956 413410475 413410175 2.130000e-126 462.0
7 TraesCS1B01G331700 chr1D 82.490 514 63 15 10 505 413414158 413413654 2.790000e-115 425.0
8 TraesCS1B01G331700 chr1D 86.286 350 32 9 507 856 413413457 413413124 1.710000e-97 366.0
9 TraesCS1B01G331700 chr1D 84.393 346 46 5 1945 2284 413335263 413334920 1.740000e-87 333.0
10 TraesCS1B01G331700 chr1D 90.476 147 12 2 1906 2052 413406419 413406275 3.080000e-45 193.0
11 TraesCS1B01G331700 chr1D 79.126 206 27 4 2721 2923 413357275 413357083 8.810000e-26 128.0
12 TraesCS1B01G331700 chr1D 88.571 105 12 0 2160 2264 413357408 413357304 8.810000e-26 128.0
13 TraesCS1B01G331700 chr1D 97.872 47 1 0 1957 2003 413297316 413297270 6.950000e-12 82.4
14 TraesCS1B01G331700 chr1A 92.766 1410 65 16 870 2270 510367551 510366170 0.000000e+00 2004.0
15 TraesCS1B01G331700 chr1A 86.938 689 62 14 8 676 510372152 510371472 0.000000e+00 749.0
16 TraesCS1B01G331700 chr1A 88.435 147 16 1 1906 2052 512453403 512453258 3.100000e-40 176.0
17 TraesCS1B01G331700 chr1A 100.000 31 0 0 697 727 510371465 510371435 1.170000e-04 58.4
18 TraesCS1B01G331700 chr1A 88.889 45 3 1 689 733 510371170 510371128 2.000000e-03 54.7
19 TraesCS1B01G331700 chr7B 83.860 285 32 6 404 678 231203669 231203949 2.990000e-65 259.0
20 TraesCS1B01G331700 chr3B 82.909 275 32 8 404 667 769135903 769136173 1.810000e-57 233.0
21 TraesCS1B01G331700 chr5D 87.831 189 22 1 1292 1480 561621245 561621058 1.410000e-53 220.0
22 TraesCS1B01G331700 chr5D 82.500 160 21 6 2283 2435 56807123 56807282 1.890000e-27 134.0
23 TraesCS1B01G331700 chr5D 84.821 112 9 7 542 651 399624463 399624358 4.130000e-19 106.0
24 TraesCS1B01G331700 chr4D 84.848 165 17 7 2283 2439 460656640 460656804 3.120000e-35 159.0
25 TraesCS1B01G331700 chr4D 84.848 165 17 7 2283 2439 460660740 460660904 3.120000e-35 159.0
26 TraesCS1B01G331700 chr4D 84.848 165 17 7 2283 2439 460663110 460663274 3.120000e-35 159.0
27 TraesCS1B01G331700 chr4D 84.848 165 17 7 2283 2439 460665392 460665556 3.120000e-35 159.0
28 TraesCS1B01G331700 chr4D 84.848 165 17 7 2283 2439 460666657 460666821 3.120000e-35 159.0
29 TraesCS1B01G331700 chr7D 85.185 135 15 5 544 677 197927143 197927013 1.890000e-27 134.0
30 TraesCS1B01G331700 chr7D 83.871 124 14 4 543 666 41281364 41281481 2.470000e-21 113.0
31 TraesCS1B01G331700 chr7D 97.222 36 0 1 1347 1381 579054097 579054132 3.260000e-05 60.2
32 TraesCS1B01G331700 chr2B 83.108 148 21 3 2287 2433 513250104 513250248 6.810000e-27 132.0
33 TraesCS1B01G331700 chr2D 84.821 112 12 5 544 654 13150165 13150058 1.150000e-19 108.0
34 TraesCS1B01G331700 chr2A 82.787 122 15 5 544 664 15186805 15186689 1.480000e-18 104.0
35 TraesCS1B01G331700 chr2A 100.000 30 0 0 1347 1376 553282775 553282746 4.210000e-04 56.5
36 TraesCS1B01G331700 chr4B 78.322 143 28 2 513 655 562441271 562441132 4.160000e-14 89.8


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 TraesCS1B01G331700 chr1B 557917246 557920271 3025 True 5589.000 5589 100.000000 1 3026 1 chr1B.!!$R2 3025
1 TraesCS1B01G331700 chr1D 413311860 413314331 2471 True 940.500 1038 88.930500 2110 2923 2 chr1D.!!$R3 813
2 TraesCS1B01G331700 chr1D 413406275 413414158 7883 True 745.000 2235 89.501667 10 3026 6 chr1D.!!$R5 3016
3 TraesCS1B01G331700 chr1A 510366170 510372152 5982 True 716.525 2004 92.148250 8 2270 4 chr1A.!!$R2 2262

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
812 1318 0.316522 TCTGCTCAGTGCTCACTCAC 59.683 55.0 0.0 0.0 40.2 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2577 8727 0.106868 CTGCATCATGCCTCCCTTCA 60.107 55.0 7.3 0.0 44.23 3.02 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
49 53 8.774890 TGTATACATGTAGCGGTTTTAAAAGA 57.225 30.769 11.91 0.00 0.00 2.52
80 84 7.426456 GCATTTGTATGTATCAGACAACTTTCG 59.574 37.037 9.01 0.20 43.66 3.46
123 127 2.590821 AGCCTGACATGTTCTTTTGCT 58.409 42.857 0.00 0.10 0.00 3.91
124 128 2.295349 AGCCTGACATGTTCTTTTGCTG 59.705 45.455 0.00 0.00 0.00 4.41
133 137 7.175467 TGACATGTTCTTTTGCTGAATCTACAT 59.825 33.333 0.00 0.00 0.00 2.29
134 138 7.889469 ACATGTTCTTTTGCTGAATCTACATT 58.111 30.769 0.00 0.00 0.00 2.71
135 139 8.025445 ACATGTTCTTTTGCTGAATCTACATTC 58.975 33.333 0.00 0.00 39.24 2.67
140 144 9.683069 TTCTTTTGCTGAATCTACATTCTTTTC 57.317 29.630 0.00 0.00 39.49 2.29
173 181 1.270550 CTGGTGAAAACCCATCAGCAC 59.729 52.381 4.47 0.00 46.84 4.40
175 183 1.234821 GTGAAAACCCATCAGCACGA 58.765 50.000 0.00 0.00 0.00 4.35
196 204 9.891828 GCACGATCCAAATATTACAAATTCATA 57.108 29.630 0.00 0.00 0.00 2.15
263 271 4.718961 ACAAGTGTTGGAGAATAGCTGTT 58.281 39.130 0.00 0.00 34.12 3.16
276 284 1.170919 AGCTGTTGCCTGAAGCTGTG 61.171 55.000 0.00 0.00 45.36 3.66
281 289 1.949525 GTTGCCTGAAGCTGTGAGAAA 59.050 47.619 0.00 0.00 44.23 2.52
283 291 0.514691 GCCTGAAGCTGTGAGAAACG 59.485 55.000 0.00 0.00 38.99 3.60
335 343 6.808008 ATGTATTTATGATCTGAAAGCGGG 57.192 37.500 0.00 0.00 0.00 6.13
339 347 1.507140 ATGATCTGAAAGCGGGGGTA 58.493 50.000 0.00 0.00 0.00 3.69
345 353 0.963355 TGAAAGCGGGGGTACATTGC 60.963 55.000 0.00 0.00 0.00 3.56
346 354 1.663379 GAAAGCGGGGGTACATTGCC 61.663 60.000 0.00 0.00 0.00 4.52
347 355 2.433646 AAAGCGGGGGTACATTGCCA 62.434 55.000 0.00 0.00 0.00 4.92
348 356 3.138128 GCGGGGGTACATTGCCAC 61.138 66.667 0.00 0.00 0.00 5.01
354 369 1.544246 GGGGTACATTGCCACTCAAAC 59.456 52.381 0.00 0.00 38.34 2.93
381 396 5.129634 TGGTGTATTGAATCAGTGTGTTGT 58.870 37.500 0.00 0.00 0.00 3.32
426 441 9.661563 TGTTTGTTTGTCGAGATAATATAACCT 57.338 29.630 0.00 0.00 0.00 3.50
450 465 7.277981 CCTGGTTATACTCACTTGTTGATGTAC 59.722 40.741 0.00 0.00 32.17 2.90
515 735 5.183522 TCATTTGCAAACTATCAGATGTGCA 59.816 36.000 15.41 8.17 40.04 4.57
518 738 6.756299 TTGCAAACTATCAGATGTGCATTA 57.244 33.333 0.00 0.00 41.26 1.90
535 755 4.120589 GCATTACTTTAGTTCCTCCCTCG 58.879 47.826 0.00 0.00 0.00 4.63
541 761 4.594491 ACTTTAGTTCCTCCCTCGGTTTTA 59.406 41.667 0.00 0.00 0.00 1.52
557 778 9.946165 CCTCGGTTTTAAATTATAAGATGTTCC 57.054 33.333 0.00 0.00 0.00 3.62
576 797 2.691011 TCCAACTTTTTCTTGAACCGGG 59.309 45.455 6.32 0.00 0.00 5.73
587 808 5.779529 TCTTGAACCGGGTGTATATAGAC 57.220 43.478 6.32 1.36 0.00 2.59
588 809 5.202765 TCTTGAACCGGGTGTATATAGACA 58.797 41.667 6.32 0.00 0.00 3.41
624 845 6.150976 TGTGTTTTGTTCACTCATTTCAGTCT 59.849 34.615 0.00 0.00 36.83 3.24
656 877 7.527457 AGTCTACTTTGAAATATCCAAAACGC 58.473 34.615 5.21 0.00 33.68 4.84
667 888 9.113876 GAAATATCCAAAACGCCTTATAATTCG 57.886 33.333 5.34 5.34 0.00 3.34
668 889 7.972832 ATATCCAAAACGCCTTATAATTCGA 57.027 32.000 11.79 0.00 0.00 3.71
677 898 3.059120 GCCTTATAATTCGAAACGGAGGC 60.059 47.826 19.88 19.88 40.15 4.70
678 899 4.124238 CCTTATAATTCGAAACGGAGGCA 58.876 43.478 0.00 0.00 0.00 4.75
679 900 4.573201 CCTTATAATTCGAAACGGAGGCAA 59.427 41.667 0.00 0.00 0.00 4.52
685 906 3.048337 TCGAAACGGAGGCAATAGTTT 57.952 42.857 0.00 0.37 39.21 2.66
686 907 3.404899 TCGAAACGGAGGCAATAGTTTT 58.595 40.909 0.00 0.00 37.00 2.43
687 908 3.187637 TCGAAACGGAGGCAATAGTTTTG 59.812 43.478 7.56 7.56 37.00 2.44
688 909 3.669557 CGAAACGGAGGCAATAGTTTTGG 60.670 47.826 0.00 0.00 37.00 3.28
689 910 2.579410 ACGGAGGCAATAGTTTTGGT 57.421 45.000 0.00 0.00 0.00 3.67
690 911 2.871453 ACGGAGGCAATAGTTTTGGTT 58.129 42.857 0.00 0.00 0.00 3.67
731 952 2.173519 CTGGTTGCATCCCAGTGATTT 58.826 47.619 19.86 0.00 43.73 2.17
812 1318 0.316522 TCTGCTCAGTGCTCACTCAC 59.683 55.000 0.00 0.00 40.20 3.51
830 1336 9.381033 CTCACTCACTCATTTTCTCTGATAAAT 57.619 33.333 0.00 0.00 0.00 1.40
841 1347 7.765695 TTTCTCTGATAAATTCCAGCAACTT 57.234 32.000 0.00 0.00 0.00 2.66
856 1362 5.474876 CCAGCAACTTATCAGAAAGTCCTTT 59.525 40.000 0.00 0.00 38.76 3.11
919 4891 1.669115 CTGTCAGTGTCCAAGCCCG 60.669 63.158 0.00 0.00 0.00 6.13
939 4916 3.327404 TCCCCCAACTCGCTTCCC 61.327 66.667 0.00 0.00 0.00 3.97
940 4917 4.778143 CCCCCAACTCGCTTCCCG 62.778 72.222 0.00 0.00 38.61 5.14
942 4919 4.697756 CCCAACTCGCTTCCCGCA 62.698 66.667 0.00 0.00 39.08 5.69
1059 5036 0.966179 TCGCACTCAAAGCTCCAGTA 59.034 50.000 0.00 0.00 0.00 2.74
1116 5093 4.399395 CGCCTGCCTGCTCTCCAA 62.399 66.667 0.00 0.00 0.00 3.53
1659 5639 2.904866 GCGGTGCTGTTCAACCCA 60.905 61.111 0.00 0.00 0.00 4.51
1785 5765 1.271656 CTGCTGAGCAAGAAAAAGGGG 59.728 52.381 9.07 0.00 38.41 4.79
1850 5830 1.150081 GGGTGCTCATGATGGAGGG 59.850 63.158 0.00 0.00 35.41 4.30
2034 6014 1.541588 GGGAAGCAGTGACATTGGTTC 59.458 52.381 26.03 26.03 46.76 3.62
2068 6048 0.389948 GTTCACGGCGTCTCCTGAAT 60.390 55.000 10.85 0.00 35.75 2.57
2071 6051 0.721718 CACGGCGTCTCCTGAATTTC 59.278 55.000 10.85 0.00 0.00 2.17
2072 6052 0.608640 ACGGCGTCTCCTGAATTTCT 59.391 50.000 6.77 0.00 0.00 2.52
2076 6056 3.339141 GGCGTCTCCTGAATTTCTTTCT 58.661 45.455 0.00 0.00 35.23 2.52
2077 6057 3.126000 GGCGTCTCCTGAATTTCTTTCTG 59.874 47.826 0.00 0.00 35.23 3.02
2078 6058 3.425492 GCGTCTCCTGAATTTCTTTCTGC 60.425 47.826 0.00 0.00 35.23 4.26
2087 6070 0.944386 TTTCTTTCTGCTGTCGTGCC 59.056 50.000 0.00 0.00 0.00 5.01
2114 6097 4.037923 TGCCTGAAAACTCTGAAATGGTTC 59.962 41.667 0.00 0.00 0.00 3.62
2163 6146 0.390209 AATTCAGGCGGCATTTGCAC 60.390 50.000 13.08 0.00 44.36 4.57
2164 6147 1.534336 ATTCAGGCGGCATTTGCACA 61.534 50.000 13.08 0.00 44.36 4.57
2180 6163 4.075963 TGCACAGCATCTGCAGATTATA 57.924 40.909 26.70 0.00 45.16 0.98
2267 8379 4.903638 TCGAAAGCTTGAGATTAACACG 57.096 40.909 0.00 0.00 0.00 4.49
2339 8479 2.029288 CGCTTTCAGCTCGCTCCAA 61.029 57.895 0.00 0.00 39.60 3.53
2340 8480 1.364626 CGCTTTCAGCTCGCTCCAAT 61.365 55.000 0.00 0.00 39.60 3.16
2342 8482 0.098376 CTTTCAGCTCGCTCCAATGC 59.902 55.000 0.00 0.00 0.00 3.56
2343 8483 0.321919 TTTCAGCTCGCTCCAATGCT 60.322 50.000 0.00 0.00 36.04 3.79
2344 8484 0.321919 TTCAGCTCGCTCCAATGCTT 60.322 50.000 0.00 0.00 33.03 3.91
2345 8485 1.022982 TCAGCTCGCTCCAATGCTTG 61.023 55.000 0.00 0.00 33.03 4.01
2346 8486 1.002868 AGCTCGCTCCAATGCTTGT 60.003 52.632 0.00 0.00 30.96 3.16
2347 8487 0.250234 AGCTCGCTCCAATGCTTGTA 59.750 50.000 0.00 0.00 30.96 2.41
2348 8488 0.654683 GCTCGCTCCAATGCTTGTAG 59.345 55.000 0.00 0.00 0.00 2.74
2350 8490 1.929836 CTCGCTCCAATGCTTGTAGTC 59.070 52.381 0.00 0.00 0.00 2.59
2351 8491 0.647410 CGCTCCAATGCTTGTAGTCG 59.353 55.000 0.00 0.00 0.00 4.18
2352 8492 1.726853 GCTCCAATGCTTGTAGTCGT 58.273 50.000 0.00 0.00 0.00 4.34
2353 8493 1.661112 GCTCCAATGCTTGTAGTCGTC 59.339 52.381 0.00 0.00 0.00 4.20
2354 8494 1.920574 CTCCAATGCTTGTAGTCGTCG 59.079 52.381 0.00 0.00 0.00 5.12
2355 8495 1.271379 TCCAATGCTTGTAGTCGTCGT 59.729 47.619 0.00 0.00 0.00 4.34
2356 8496 2.066262 CCAATGCTTGTAGTCGTCGTT 58.934 47.619 0.00 0.00 0.00 3.85
2357 8497 3.057386 TCCAATGCTTGTAGTCGTCGTTA 60.057 43.478 0.00 0.00 0.00 3.18
2358 8498 3.303495 CCAATGCTTGTAGTCGTCGTTAG 59.697 47.826 0.00 0.00 0.00 2.34
2359 8499 2.624316 TGCTTGTAGTCGTCGTTAGG 57.376 50.000 0.00 0.00 0.00 2.69
2360 8500 1.881973 TGCTTGTAGTCGTCGTTAGGT 59.118 47.619 0.00 0.00 0.00 3.08
2361 8501 2.248487 GCTTGTAGTCGTCGTTAGGTG 58.752 52.381 0.00 0.00 0.00 4.00
2362 8502 2.351157 GCTTGTAGTCGTCGTTAGGTGT 60.351 50.000 0.00 0.00 0.00 4.16
2363 8503 3.854784 GCTTGTAGTCGTCGTTAGGTGTT 60.855 47.826 0.00 0.00 0.00 3.32
2364 8504 3.988379 TGTAGTCGTCGTTAGGTGTTT 57.012 42.857 0.00 0.00 0.00 2.83
2365 8505 4.305989 TGTAGTCGTCGTTAGGTGTTTT 57.694 40.909 0.00 0.00 0.00 2.43
2366 8506 5.431420 TGTAGTCGTCGTTAGGTGTTTTA 57.569 39.130 0.00 0.00 0.00 1.52
2367 8507 6.012658 TGTAGTCGTCGTTAGGTGTTTTAT 57.987 37.500 0.00 0.00 0.00 1.40
2368 8508 5.858049 TGTAGTCGTCGTTAGGTGTTTTATG 59.142 40.000 0.00 0.00 0.00 1.90
2369 8509 4.240096 AGTCGTCGTTAGGTGTTTTATGG 58.760 43.478 0.00 0.00 0.00 2.74
2370 8510 4.022068 AGTCGTCGTTAGGTGTTTTATGGA 60.022 41.667 0.00 0.00 0.00 3.41
2371 8511 4.090498 GTCGTCGTTAGGTGTTTTATGGAC 59.910 45.833 0.00 0.00 0.00 4.02
2372 8512 3.989167 CGTCGTTAGGTGTTTTATGGACA 59.011 43.478 0.00 0.00 0.00 4.02
2373 8513 4.628333 CGTCGTTAGGTGTTTTATGGACAT 59.372 41.667 0.00 0.00 0.00 3.06
2374 8514 5.806502 CGTCGTTAGGTGTTTTATGGACATA 59.193 40.000 0.00 0.00 0.00 2.29
2375 8515 6.020121 CGTCGTTAGGTGTTTTATGGACATAG 60.020 42.308 0.00 0.00 0.00 2.23
2376 8516 7.037438 GTCGTTAGGTGTTTTATGGACATAGA 58.963 38.462 0.00 0.00 0.00 1.98
2377 8517 7.709613 GTCGTTAGGTGTTTTATGGACATAGAT 59.290 37.037 0.00 0.00 0.00 1.98
2378 8518 8.916062 TCGTTAGGTGTTTTATGGACATAGATA 58.084 33.333 0.00 0.00 0.00 1.98
2379 8519 9.706691 CGTTAGGTGTTTTATGGACATAGATAT 57.293 33.333 0.00 0.00 0.00 1.63
2558 8708 2.486951 GCTGCTTTCATTGCGATCAT 57.513 45.000 0.00 0.00 0.00 2.45
2567 8717 2.037641 TCATTGCGATCATAGGACCAGG 59.962 50.000 0.00 0.00 0.00 4.45
2577 8727 0.621571 TAGGACCAGGCCAGCTTGAT 60.622 55.000 5.01 0.00 0.00 2.57
2676 8826 1.134461 CCAGGTCAGAGCATCCTTCTG 60.134 57.143 1.66 0.00 42.68 3.02
2690 8840 0.597637 CTTCTGTCACGGTCGCAACT 60.598 55.000 0.00 0.00 0.00 3.16
2843 8993 7.246171 ACTGCTTGAAGAGATCTAGGTAAAA 57.754 36.000 0.00 0.00 32.32 1.52
2874 9025 0.982852 TCTACAGGTGCATCCAGGGG 60.983 60.000 0.00 0.00 39.02 4.79
2875 9026 1.987807 CTACAGGTGCATCCAGGGGG 61.988 65.000 0.00 0.00 39.02 5.40
2919 9070 4.677673 AATTTTCCATTAGGAGCATGGC 57.322 40.909 0.00 0.00 46.74 4.40
2954 9107 2.422276 AAACGAGGCAAAAGACATGC 57.578 45.000 0.00 0.00 43.08 4.06
2971 9124 9.603921 AAAGACATGCCATTTCATTAATTAAGG 57.396 29.630 3.46 3.46 0.00 2.69
2975 9128 8.980596 ACATGCCATTTCATTAATTAAGGAAGA 58.019 29.630 20.75 14.21 37.30 2.87
2978 9131 9.034800 TGCCATTTCATTAATTAAGGAAGAAGT 57.965 29.630 20.75 9.51 37.30 3.01
2992 9146 5.671493 AGGAAGAAGTATAACAATGTCCGG 58.329 41.667 0.00 0.00 0.00 5.14
2994 9148 6.070424 AGGAAGAAGTATAACAATGTCCGGAA 60.070 38.462 5.23 0.00 0.00 4.30
3010 9164 2.607771 CCGGAAACAACAGCCAAATCTG 60.608 50.000 0.00 0.00 39.86 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 5.548406 ACAGGTTACAGATTGGTAGTCAAC 58.452 41.667 0.00 0.00 38.31 3.18
4 5 5.818678 ACAGGTTACAGATTGGTAGTCAA 57.181 39.130 0.00 0.00 40.01 3.18
5 6 7.616542 TGTATACAGGTTACAGATTGGTAGTCA 59.383 37.037 0.08 0.00 0.00 3.41
6 7 8.004087 TGTATACAGGTTACAGATTGGTAGTC 57.996 38.462 0.08 0.00 0.00 2.59
49 53 6.643388 TGTCTGATACATACAAATGCACTCT 58.357 36.000 0.00 0.00 36.50 3.24
133 137 8.310382 TCACCAGTTCAAATGAAAAGAAAAGAA 58.690 29.630 0.00 0.00 35.58 2.52
134 138 7.835822 TCACCAGTTCAAATGAAAAGAAAAGA 58.164 30.769 0.00 0.00 35.58 2.52
135 139 8.477984 TTCACCAGTTCAAATGAAAAGAAAAG 57.522 30.769 0.00 0.00 35.58 2.27
140 144 6.037062 GGGTTTTCACCAGTTCAAATGAAAAG 59.963 38.462 10.39 0.00 46.30 2.27
235 243 5.390567 GCTATTCTCCAACACTTGTTAACGG 60.391 44.000 0.26 0.00 36.32 4.44
237 245 6.204882 ACAGCTATTCTCCAACACTTGTTAAC 59.795 38.462 0.00 0.00 36.32 2.01
263 271 1.597742 GTTTCTCACAGCTTCAGGCA 58.402 50.000 0.00 0.00 44.79 4.75
335 343 2.228822 CAGTTTGAGTGGCAATGTACCC 59.771 50.000 0.00 0.00 36.15 3.69
339 347 2.559668 CCATCAGTTTGAGTGGCAATGT 59.440 45.455 0.00 0.00 36.15 2.71
345 353 5.003160 TCAATACACCATCAGTTTGAGTGG 58.997 41.667 0.00 0.00 33.89 4.00
346 354 6.558771 TTCAATACACCATCAGTTTGAGTG 57.441 37.500 0.00 0.00 0.00 3.51
347 355 6.942005 TGATTCAATACACCATCAGTTTGAGT 59.058 34.615 0.00 0.00 0.00 3.41
348 356 7.381766 TGATTCAATACACCATCAGTTTGAG 57.618 36.000 0.00 0.00 0.00 3.02
354 369 5.645067 ACACACTGATTCAATACACCATCAG 59.355 40.000 6.49 6.49 45.56 2.90
395 410 9.823647 ATATTATCTCGACAAACAAACAGAGAT 57.176 29.630 10.10 10.10 44.55 2.75
426 441 7.903145 AGTACATCAACAAGTGAGTATAACCA 58.097 34.615 0.00 0.00 40.43 3.67
438 453 7.707104 AGAACAAAAGGAAGTACATCAACAAG 58.293 34.615 0.00 0.00 0.00 3.16
450 465 7.394359 TCCAGGAATATCAAGAACAAAAGGAAG 59.606 37.037 0.00 0.00 0.00 3.46
515 735 4.359996 ACCGAGGGAGGAACTAAAGTAAT 58.640 43.478 0.00 0.00 41.55 1.89
518 738 2.322339 ACCGAGGGAGGAACTAAAGT 57.678 50.000 0.00 0.00 41.55 2.66
557 778 3.119280 ACACCCGGTTCAAGAAAAAGTTG 60.119 43.478 0.00 0.00 0.00 3.16
566 787 5.287226 GTGTCTATATACACCCGGTTCAAG 58.713 45.833 9.65 0.00 43.23 3.02
567 788 4.202040 CGTGTCTATATACACCCGGTTCAA 60.202 45.833 13.93 0.00 45.66 2.69
576 797 6.805271 ACACTGAAACACGTGTCTATATACAC 59.195 38.462 23.61 10.55 45.10 2.90
587 808 3.560503 ACAAAACACACTGAAACACGTG 58.439 40.909 15.48 15.48 37.18 4.49
588 809 3.907894 ACAAAACACACTGAAACACGT 57.092 38.095 0.00 0.00 0.00 4.49
596 817 6.092092 TGAAATGAGTGAACAAAACACACTG 58.908 36.000 0.00 0.00 43.49 3.66
597 818 6.071952 ACTGAAATGAGTGAACAAAACACACT 60.072 34.615 0.00 0.00 45.62 3.55
603 824 6.757897 ACAGACTGAAATGAGTGAACAAAA 57.242 33.333 10.08 0.00 0.00 2.44
656 877 4.124238 TGCCTCCGTTTCGAATTATAAGG 58.876 43.478 0.00 4.33 0.00 2.69
667 888 3.254903 ACCAAAACTATTGCCTCCGTTTC 59.745 43.478 0.00 0.00 0.00 2.78
668 889 3.227614 ACCAAAACTATTGCCTCCGTTT 58.772 40.909 0.00 0.00 0.00 3.60
677 898 7.936584 TCAGACCTACAAAACCAAAACTATTG 58.063 34.615 0.00 0.00 0.00 1.90
678 899 8.706322 ATCAGACCTACAAAACCAAAACTATT 57.294 30.769 0.00 0.00 0.00 1.73
679 900 9.975218 ATATCAGACCTACAAAACCAAAACTAT 57.025 29.630 0.00 0.00 0.00 2.12
685 906 6.884295 CCTTCATATCAGACCTACAAAACCAA 59.116 38.462 0.00 0.00 0.00 3.67
686 907 6.414732 CCTTCATATCAGACCTACAAAACCA 58.585 40.000 0.00 0.00 0.00 3.67
687 908 5.297029 GCCTTCATATCAGACCTACAAAACC 59.703 44.000 0.00 0.00 0.00 3.27
688 909 6.037610 CAGCCTTCATATCAGACCTACAAAAC 59.962 42.308 0.00 0.00 0.00 2.43
689 910 6.115446 CAGCCTTCATATCAGACCTACAAAA 58.885 40.000 0.00 0.00 0.00 2.44
690 911 5.396772 CCAGCCTTCATATCAGACCTACAAA 60.397 44.000 0.00 0.00 0.00 2.83
731 952 0.183492 AGCAAAACAGAGTGGCCTCA 59.817 50.000 3.32 0.00 40.40 3.86
812 1318 7.993101 TGCTGGAATTTATCAGAGAAAATGAG 58.007 34.615 0.00 0.00 33.11 2.90
830 1336 5.003804 GGACTTTCTGATAAGTTGCTGGAA 58.996 41.667 6.66 0.00 38.43 3.53
841 1347 4.655963 AGCTGCAAAAGGACTTTCTGATA 58.344 39.130 1.02 0.00 31.45 2.15
856 1362 1.667212 CGTGCAATATCTGAGCTGCAA 59.333 47.619 11.26 0.00 45.71 4.08
919 4891 3.978571 GAAGCGAGTTGGGGGAGCC 62.979 68.421 0.00 0.00 0.00 4.70
939 4916 4.758251 TCCTCCATGGTGCGTGCG 62.758 66.667 12.58 0.00 37.07 5.34
940 4917 2.821366 CTCCTCCATGGTGCGTGC 60.821 66.667 12.58 0.00 37.07 5.34
941 4918 2.821366 GCTCCTCCATGGTGCGTG 60.821 66.667 12.58 5.92 44.08 5.34
954 4931 2.359230 GGTGTGGTGCTCTGCTCC 60.359 66.667 3.96 3.96 41.88 4.70
1009 4986 1.682684 GAGGAGGGTTCGAGAGGCA 60.683 63.158 0.00 0.00 0.00 4.75
1587 5567 3.649277 CTTCTCCACCTGCGACCGG 62.649 68.421 0.00 0.00 0.00 5.28
1591 5571 2.659016 CAGCTTCTCCACCTGCGA 59.341 61.111 0.00 0.00 0.00 5.10
1659 5639 1.682684 CACCTCGTAGCTCCACCCT 60.683 63.158 0.00 0.00 0.00 4.34
1779 5759 4.351054 CGGAGCAGCACCCCCTTT 62.351 66.667 2.88 0.00 0.00 3.11
1850 5830 4.214327 CCGGCTCCTTCTCCTCGC 62.214 72.222 0.00 0.00 0.00 5.03
2034 6014 1.676006 GTGAACACACAAGTCCAAGGG 59.324 52.381 0.00 0.00 34.98 3.95
2068 6048 0.944386 GGCACGACAGCAGAAAGAAA 59.056 50.000 0.00 0.00 35.83 2.52
2071 6051 0.877071 ATTGGCACGACAGCAGAAAG 59.123 50.000 0.00 0.00 35.83 2.62
2072 6052 1.001487 CAATTGGCACGACAGCAGAAA 60.001 47.619 0.00 0.00 35.83 2.52
2076 6056 2.644418 GCAATTGGCACGACAGCA 59.356 55.556 7.72 0.00 43.97 4.41
2087 6070 5.407387 CCATTTCAGAGTTTTCAGGCAATTG 59.593 40.000 0.00 0.00 0.00 2.32
2114 6097 1.527034 ACATGTTGCTGCACCACTAG 58.473 50.000 0.77 0.00 0.00 2.57
2163 6146 5.878669 TGCCTATTATAATCTGCAGATGCTG 59.121 40.000 29.34 14.45 42.66 4.41
2164 6147 6.058553 TGCCTATTATAATCTGCAGATGCT 57.941 37.500 29.34 20.57 42.66 3.79
2180 6163 4.337145 TCCGTTGGTTAACATTGCCTATT 58.663 39.130 8.10 0.00 36.58 1.73
2267 8379 3.189287 CCGGGCAAGATATCTATTGTTGC 59.811 47.826 15.16 15.16 42.25 4.17
2324 8436 0.321919 AGCATTGGAGCGAGCTGAAA 60.322 50.000 0.84 0.00 40.15 2.69
2328 8440 3.900855 CAAGCATTGGAGCGAGCT 58.099 55.556 0.00 0.00 43.94 4.09
2339 8479 2.490903 ACCTAACGACGACTACAAGCAT 59.509 45.455 0.00 0.00 0.00 3.79
2340 8480 1.881973 ACCTAACGACGACTACAAGCA 59.118 47.619 0.00 0.00 0.00 3.91
2342 8482 3.549299 ACACCTAACGACGACTACAAG 57.451 47.619 0.00 0.00 0.00 3.16
2343 8483 3.988379 AACACCTAACGACGACTACAA 57.012 42.857 0.00 0.00 0.00 2.41
2344 8484 3.988379 AAACACCTAACGACGACTACA 57.012 42.857 0.00 0.00 0.00 2.74
2345 8485 5.287035 CCATAAAACACCTAACGACGACTAC 59.713 44.000 0.00 0.00 0.00 2.73
2346 8486 5.182950 TCCATAAAACACCTAACGACGACTA 59.817 40.000 0.00 0.00 0.00 2.59
2347 8487 4.022068 TCCATAAAACACCTAACGACGACT 60.022 41.667 0.00 0.00 0.00 4.18
2348 8488 4.090498 GTCCATAAAACACCTAACGACGAC 59.910 45.833 0.00 0.00 0.00 4.34
2350 8490 3.989167 TGTCCATAAAACACCTAACGACG 59.011 43.478 0.00 0.00 0.00 5.12
2351 8491 7.037438 TCTATGTCCATAAAACACCTAACGAC 58.963 38.462 0.00 0.00 0.00 4.34
2352 8492 7.172868 TCTATGTCCATAAAACACCTAACGA 57.827 36.000 0.00 0.00 0.00 3.85
2353 8493 9.706691 ATATCTATGTCCATAAAACACCTAACG 57.293 33.333 0.00 0.00 0.00 3.18
2438 8588 2.772568 TGTTGATGTGTTTTCCTGCG 57.227 45.000 0.00 0.00 0.00 5.18
2439 8589 6.012658 TCTATTGTTGATGTGTTTTCCTGC 57.987 37.500 0.00 0.00 0.00 4.85
2440 8590 9.941664 GATATCTATTGTTGATGTGTTTTCCTG 57.058 33.333 0.00 0.00 0.00 3.86
2518 8668 2.029470 CGGTGCCAGCCTTTCATAAAAA 60.029 45.455 0.00 0.00 0.00 1.94
2519 8669 1.543802 CGGTGCCAGCCTTTCATAAAA 59.456 47.619 0.00 0.00 0.00 1.52
2558 8708 0.621571 ATCAAGCTGGCCTGGTCCTA 60.622 55.000 15.21 4.16 0.00 2.94
2567 8717 0.750911 CCTCCCTTCATCAAGCTGGC 60.751 60.000 0.00 0.00 0.00 4.85
2577 8727 0.106868 CTGCATCATGCCTCCCTTCA 60.107 55.000 7.30 0.00 44.23 3.02
2653 8803 2.894387 GATGCTCTGACCTGGCGC 60.894 66.667 0.00 0.00 0.00 6.53
2659 8809 1.552337 TGACAGAAGGATGCTCTGACC 59.448 52.381 16.51 10.17 42.51 4.02
2676 8826 2.964925 TGCAGTTGCGACCGTGAC 60.965 61.111 0.00 0.00 45.83 3.67
2690 8840 1.133823 AGTGTGACTCCAATTGGTGCA 60.134 47.619 23.76 18.70 36.34 4.57
2764 8914 3.699413 TGGAGAATGACAAATGGATGCA 58.301 40.909 0.00 0.00 0.00 3.96
2818 8968 7.956328 TTTACCTAGATCTCTTCAAGCAGTA 57.044 36.000 0.00 0.00 0.00 2.74
2843 8993 2.564947 CACCTGTAGAGCTCCAAAGAGT 59.435 50.000 10.93 0.00 42.59 3.24
2874 9025 3.057526 CCTTTCAAAATTCAGGACGGACC 60.058 47.826 0.00 0.00 39.35 4.46
2875 9026 3.818773 TCCTTTCAAAATTCAGGACGGAC 59.181 43.478 0.00 0.00 29.97 4.79
2934 9087 3.552604 GCATGTCTTTTGCCTCGTTTA 57.447 42.857 0.00 0.00 33.95 2.01
2971 9124 7.118680 TGTTTCCGGACATTGTTATACTTCTTC 59.881 37.037 1.83 0.00 0.00 2.87
2975 9128 6.487331 TGTTGTTTCCGGACATTGTTATACTT 59.513 34.615 1.83 0.00 0.00 2.24
2977 9130 6.243811 TGTTGTTTCCGGACATTGTTATAC 57.756 37.500 1.83 0.00 0.00 1.47
2978 9131 5.106475 GCTGTTGTTTCCGGACATTGTTATA 60.106 40.000 1.83 0.00 0.00 0.98
2979 9132 4.320935 GCTGTTGTTTCCGGACATTGTTAT 60.321 41.667 1.83 0.00 0.00 1.89
2980 9133 3.003897 GCTGTTGTTTCCGGACATTGTTA 59.996 43.478 1.83 0.00 0.00 2.41
2981 9134 2.223711 GCTGTTGTTTCCGGACATTGTT 60.224 45.455 1.83 0.00 0.00 2.83
2984 9137 0.958822 GGCTGTTGTTTCCGGACATT 59.041 50.000 1.83 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.