Multiple sequence alignment - TraesCS1A01G105400

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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 TraesCS1A01G105400 chr1A 100.000 2468 0 0 1 2468 101336645 101334178 0.000000e+00 4558
1 TraesCS1A01G105400 chr1A 87.896 1041 78 31 916 1936 563184186 563183174 0.000000e+00 1181
2 TraesCS1A01G105400 chr1A 96.691 544 17 1 946 1488 563180442 563179899 0.000000e+00 904
3 TraesCS1A01G105400 chr1A 98.450 129 2 0 2340 2468 535105926 535106054 6.870000e-56 228
4 TraesCS1A01G105400 chr1A 77.404 208 47 0 20 227 256936241 256936448 9.270000e-25 124
5 TraesCS1A01G105400 chr1D 92.404 1672 77 22 557 2190 103472493 103474152 0.000000e+00 2338
6 TraesCS1A01G105400 chr1D 87.448 1211 100 33 922 2111 469890655 469889476 0.000000e+00 1347
7 TraesCS1A01G105400 chr1D 84.040 1203 110 50 928 2111 469887327 469886188 0.000000e+00 1083
8 TraesCS1A01G105400 chr1D 90.519 559 49 1 3 561 103422132 103422686 0.000000e+00 736
9 TraesCS1A01G105400 chr1D 92.715 151 11 0 2193 2343 103474262 103474412 4.130000e-53 219
10 TraesCS1A01G105400 chr1B 92.080 1452 67 26 753 2186 162806479 162805058 0.000000e+00 2001
11 TraesCS1A01G105400 chr1B 86.519 1261 96 41 899 2117 651561400 651560172 0.000000e+00 1319
12 TraesCS1A01G105400 chr1B 85.229 1178 82 39 946 2110 651558196 651557098 0.000000e+00 1127
13 TraesCS1A01G105400 chr1B 87.251 753 72 10 4 756 162808137 162807409 0.000000e+00 837
14 TraesCS1A01G105400 chrUn 100.000 399 0 0 988 1386 478858132 478857734 0.000000e+00 737
15 TraesCS1A01G105400 chr4B 98.462 130 2 0 2339 2468 616303254 616303383 1.910000e-56 230
16 TraesCS1A01G105400 chr6B 98.450 129 2 0 2340 2468 201448826 201448954 6.870000e-56 228
17 TraesCS1A01G105400 chr6B 97.710 131 3 0 2338 2468 12041228 12041098 2.470000e-55 226
18 TraesCS1A01G105400 chr3B 84.746 236 22 6 1740 1963 758008721 758008488 8.880000e-55 224
19 TraesCS1A01G105400 chr2B 75.342 511 94 20 3 509 179048264 179048746 1.490000e-52 217
20 TraesCS1A01G105400 chr2B 96.899 129 4 0 2340 2468 718394040 718393912 1.490000e-52 217
21 TraesCS1A01G105400 chr4A 96.154 130 5 0 2339 2468 666272259 666272388 1.920000e-51 213
22 TraesCS1A01G105400 chr4A 96.124 129 5 0 2340 2468 143706139 143706011 6.910000e-51 211
23 TraesCS1A01G105400 chr6D 82.558 86 14 1 65 149 413069131 413069046 9.470000e-10 75


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 TraesCS1A01G105400 chr1A 101334178 101336645 2467 True 4558.0 4558 100.0000 1 2468 1 chr1A.!!$R1 2467
1 TraesCS1A01G105400 chr1A 563179899 563184186 4287 True 1042.5 1181 92.2935 916 1936 2 chr1A.!!$R2 1020
2 TraesCS1A01G105400 chr1D 103472493 103474412 1919 False 1278.5 2338 92.5595 557 2343 2 chr1D.!!$F2 1786
3 TraesCS1A01G105400 chr1D 469886188 469890655 4467 True 1215.0 1347 85.7440 922 2111 2 chr1D.!!$R1 1189
4 TraesCS1A01G105400 chr1D 103422132 103422686 554 False 736.0 736 90.5190 3 561 1 chr1D.!!$F1 558
5 TraesCS1A01G105400 chr1B 162805058 162808137 3079 True 1419.0 2001 89.6655 4 2186 2 chr1B.!!$R1 2182
6 TraesCS1A01G105400 chr1B 651557098 651561400 4302 True 1223.0 1319 85.8740 899 2117 2 chr1B.!!$R2 1218

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
416 417 0.386476 TGTGACCCGACACACACTAC 59.614 55.0 0.0 0.0 44.29 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1997 3107 0.099436 GCAATCATCGAACTGCCACC 59.901 55.0 0.0 0.0 0.0 4.61 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
42 43 0.884514 GAAGAAGGCCAAACTCCAGC 59.115 55.000 5.01 0.00 0.00 4.85
58 59 2.091852 CAGCAGAAGAAGGTGGAGAC 57.908 55.000 0.00 0.00 0.00 3.36
119 120 6.823182 TCAAGGTGACATAATTGAATGACGAT 59.177 34.615 0.00 0.00 0.00 3.73
131 132 5.823209 TGAATGACGATGCAAGAATGATT 57.177 34.783 0.00 0.00 0.00 2.57
162 163 1.439365 CGCTTCAAGACGTTGCAGC 60.439 57.895 2.27 2.27 46.09 5.25
186 187 4.285517 GGCAGAAGAATGATATGGAGAGGA 59.714 45.833 0.00 0.00 0.00 3.71
311 312 1.255882 TCCGGCAAGACAAAATGCAT 58.744 45.000 0.00 0.00 44.32 3.96
312 313 1.067706 TCCGGCAAGACAAAATGCATG 60.068 47.619 0.00 0.00 44.32 4.06
363 364 5.587289 TCGGGCATGTAAAAATTAAGCATC 58.413 37.500 0.00 0.00 0.00 3.91
367 368 7.496747 GGGCATGTAAAAATTAAGCATCCTTA 58.503 34.615 0.00 0.00 32.47 2.69
368 369 7.653311 GGGCATGTAAAAATTAAGCATCCTTAG 59.347 37.037 0.00 0.00 35.13 2.18
402 403 2.120232 GTGATCGTCCGATGATGTGAC 58.880 52.381 7.87 0.00 34.60 3.67
408 409 0.968393 TCCGATGATGTGACCCGACA 60.968 55.000 0.00 0.00 0.00 4.35
416 417 0.386476 TGTGACCCGACACACACTAC 59.614 55.000 0.00 0.00 44.29 2.73
423 424 1.068125 CCGACACACACTACGGATCAA 60.068 52.381 0.00 0.00 46.94 2.57
485 486 1.842562 AGTGGCTAGCATTGGATGACT 59.157 47.619 18.24 1.99 0.00 3.41
493 494 0.466922 CATTGGATGACTGGCTCCCC 60.467 60.000 0.00 0.00 0.00 4.81
510 511 2.294839 CCCACCCATGTCCACGGTA 61.295 63.158 0.00 0.00 0.00 4.02
533 534 1.224315 CCCATGCATTCCTCGGACA 59.776 57.895 0.00 0.00 0.00 4.02
546 547 1.872952 CTCGGACAAATGCAGTGTTCA 59.127 47.619 11.19 0.10 0.00 3.18
594 595 2.688507 TGCGAGAAATCAACTCCTGTC 58.311 47.619 0.00 0.00 0.00 3.51
605 606 3.515502 TCAACTCCTGTCCGAGAAATGAT 59.484 43.478 0.00 0.00 33.83 2.45
608 609 3.385111 ACTCCTGTCCGAGAAATGATACC 59.615 47.826 0.00 0.00 33.83 2.73
609 610 3.639094 CTCCTGTCCGAGAAATGATACCT 59.361 47.826 0.00 0.00 30.97 3.08
646 647 9.847224 TTAGGAAATACAGTAGAAATGAATCCC 57.153 33.333 0.00 0.00 0.00 3.85
651 652 5.536497 ACAGTAGAAATGAATCCCCCTTT 57.464 39.130 0.00 0.00 0.00 3.11
671 672 1.871080 AGTGAACTTCTTGGCGTCTG 58.129 50.000 0.00 0.00 0.00 3.51
690 691 7.151103 CGTCTGTACGGAGATATTTTTCTTC 57.849 40.000 4.12 0.00 45.50 2.87
692 693 7.488471 CGTCTGTACGGAGATATTTTTCTTCTT 59.512 37.037 4.12 0.00 45.50 2.52
693 694 9.152595 GTCTGTACGGAGATATTTTTCTTCTTT 57.847 33.333 4.12 0.00 0.00 2.52
694 695 9.367444 TCTGTACGGAGATATTTTTCTTCTTTC 57.633 33.333 0.00 0.00 0.00 2.62
695 696 9.372369 CTGTACGGAGATATTTTTCTTCTTTCT 57.628 33.333 0.00 0.00 0.00 2.52
696 697 9.720769 TGTACGGAGATATTTTTCTTCTTTCTT 57.279 29.630 0.00 0.00 0.00 2.52
697 698 9.974750 GTACGGAGATATTTTTCTTCTTTCTTG 57.025 33.333 0.00 0.00 0.00 3.02
794 1739 1.186917 TTGGAGCCAAAGCCCACATG 61.187 55.000 0.00 0.00 38.55 3.21
884 1830 2.814336 CGCCCATTCTCCTTATAAAGCC 59.186 50.000 0.00 0.00 0.00 4.35
925 1882 2.759973 CCTAGCCTCCACTCCGCA 60.760 66.667 0.00 0.00 0.00 5.69
1472 2430 2.711547 ACAACCAGAAGGCTTAGAGGTT 59.288 45.455 19.05 19.05 39.76 3.50
1480 2438 0.673644 GGCTTAGAGGTTGCTTGCGA 60.674 55.000 0.00 0.00 0.00 5.10
1498 2456 2.675348 GCGATTGCTCTGCTCTTTTACT 59.325 45.455 0.00 0.00 38.39 2.24
1564 2528 6.183360 TGTCGTTTAAACTGAAACCTTGAGTC 60.183 38.462 16.01 0.00 36.18 3.36
1602 2566 2.579207 TCATCGCCTACTGCTGTAAC 57.421 50.000 4.91 0.00 38.05 2.50
1718 2688 0.108615 GGTGGTGTGATCACGGAGAG 60.109 60.000 20.54 0.00 44.68 3.20
1757 2727 9.098355 GATACATGTGTTCTTGAGCTTATAACA 57.902 33.333 9.11 3.64 0.00 2.41
1759 2729 7.755591 ACATGTGTTCTTGAGCTTATAACATG 58.244 34.615 16.49 16.49 44.87 3.21
1810 2781 4.494091 AGCTATGCAGGTCTTACATGTT 57.506 40.909 2.30 0.00 31.66 2.71
1832 2807 8.861033 TGTTGATGAATATTTTGCTATTGCTC 57.139 30.769 0.00 0.00 40.48 4.26
1903 2999 4.889832 ATTCAGTTCATTCCAAGCGATC 57.110 40.909 0.00 0.00 0.00 3.69
1915 3011 0.319083 AAGCGATCGTGTGGTTGGTA 59.681 50.000 17.81 0.00 0.00 3.25
1924 3020 3.827876 TCGTGTGGTTGGTATGTTCTAGA 59.172 43.478 0.00 0.00 0.00 2.43
1966 3075 6.162079 ACATAGATGTGTCTGAAACTGTGAG 58.838 40.000 0.00 0.00 40.03 3.51
1969 3078 5.533482 AGATGTGTCTGAAACTGTGAGTAC 58.467 41.667 0.00 0.00 32.13 2.73
1997 3107 2.230508 TCAGTTACCTTGGCTGTAGACG 59.769 50.000 0.00 0.00 0.00 4.18
2006 3116 1.004918 GCTGTAGACGGTGGCAGTT 60.005 57.895 0.00 0.00 0.00 3.16
2020 3130 1.262683 GGCAGTTCGATGATTGCTAGC 59.737 52.381 8.10 8.10 36.79 3.42
2068 3178 6.326375 GTTTAACCATCAGTTTTGTGTGTGA 58.674 36.000 0.00 0.00 40.05 3.58
2072 3189 4.276678 ACCATCAGTTTTGTGTGTGATCAG 59.723 41.667 0.00 0.00 0.00 2.90
2117 3239 5.128205 GGTGGTAATATTGGTTGGGTCTAC 58.872 45.833 0.00 0.00 0.00 2.59
2134 3546 4.021368 GGTCTACCGTGCCATATGTCTATT 60.021 45.833 1.24 0.00 0.00 1.73
2143 3555 6.037720 CGTGCCATATGTCTATTGGTTTACAA 59.962 38.462 1.24 0.00 44.54 2.41
2144 3556 7.414651 CGTGCCATATGTCTATTGGTTTACAAA 60.415 37.037 1.24 0.00 43.46 2.83
2171 3591 4.718961 AGATGTAGGTGAGTTTTGCTGTT 58.281 39.130 0.00 0.00 0.00 3.16
2189 4376 4.701765 CTGTTCTCTTGGGATGTGATAGG 58.298 47.826 0.00 0.00 0.00 2.57
2194 4381 6.672266 TCTCTTGGGATGTGATAGGATTAC 57.328 41.667 0.00 0.00 0.00 1.89
2202 4389 8.210946 TGGGATGTGATAGGATTACTTTACAAG 58.789 37.037 0.00 0.00 0.00 3.16
2221 4445 1.082117 GTGCCGACGTAATCAGTGGG 61.082 60.000 0.00 0.00 39.95 4.61
2236 4460 2.766263 CAGTGGGCTGGTTCAGTATCTA 59.234 50.000 0.00 0.00 39.01 1.98
2283 4508 0.887933 ATTGGCCCAACGCTGTTTAG 59.112 50.000 0.00 0.00 37.74 1.85
2302 4527 2.025418 GCAACAGTGGCATTGCTGC 61.025 57.895 20.09 20.09 46.21 5.25
2343 4604 4.039366 CCCTGTAGCTGGGATTTAGTACTC 59.961 50.000 0.00 0.00 44.09 2.59
2344 4605 4.039366 CCTGTAGCTGGGATTTAGTACTCC 59.961 50.000 0.00 0.00 0.00 3.85
2350 4611 2.675583 GGGATTTAGTACTCCCTCCGT 58.324 52.381 10.08 0.00 46.55 4.69
2351 4612 3.036819 GGGATTTAGTACTCCCTCCGTT 58.963 50.000 10.08 0.00 46.55 4.44
2353 4614 3.069300 GGATTTAGTACTCCCTCCGTTCC 59.931 52.174 0.00 0.00 0.00 3.62
2354 4615 2.905415 TTAGTACTCCCTCCGTTCCA 57.095 50.000 0.00 0.00 0.00 3.53
2355 4616 2.431954 TAGTACTCCCTCCGTTCCAG 57.568 55.000 0.00 0.00 0.00 3.86
2356 4617 0.702902 AGTACTCCCTCCGTTCCAGA 59.297 55.000 0.00 0.00 0.00 3.86
2359 4620 1.196012 ACTCCCTCCGTTCCAGATTC 58.804 55.000 0.00 0.00 0.00 2.52
2361 4622 2.024273 ACTCCCTCCGTTCCAGATTCTA 60.024 50.000 0.00 0.00 0.00 2.10
2362 4623 2.625790 CTCCCTCCGTTCCAGATTCTAG 59.374 54.545 0.00 0.00 0.00 2.43
2364 4625 2.101582 CCCTCCGTTCCAGATTCTAGTG 59.898 54.545 0.00 0.00 0.00 2.74
2365 4626 2.482142 CCTCCGTTCCAGATTCTAGTGC 60.482 54.545 0.00 0.00 0.00 4.40
2366 4627 1.134367 TCCGTTCCAGATTCTAGTGCG 59.866 52.381 0.00 0.00 0.00 5.34
2367 4628 1.135083 CCGTTCCAGATTCTAGTGCGT 60.135 52.381 0.00 0.00 0.00 5.24
2368 4629 2.098607 CCGTTCCAGATTCTAGTGCGTA 59.901 50.000 0.00 0.00 0.00 4.42
2370 4631 4.023450 CCGTTCCAGATTCTAGTGCGTATA 60.023 45.833 0.00 0.00 0.00 1.47
2371 4632 5.147865 CGTTCCAGATTCTAGTGCGTATAG 58.852 45.833 0.00 0.00 0.00 1.31
2374 4635 6.710597 TCCAGATTCTAGTGCGTATAGTTT 57.289 37.500 0.00 0.00 0.00 2.66
2375 4636 7.108841 TCCAGATTCTAGTGCGTATAGTTTT 57.891 36.000 0.00 0.00 0.00 2.43
2395 4656 4.811555 TTTTGGCTTCGATTCCGATATG 57.188 40.909 0.00 0.00 45.10 1.78
2396 4657 3.469008 TTGGCTTCGATTCCGATATGT 57.531 42.857 0.00 0.00 45.10 2.29
2397 4658 4.594123 TTGGCTTCGATTCCGATATGTA 57.406 40.909 0.00 0.00 45.10 2.29
2398 4659 4.174411 TGGCTTCGATTCCGATATGTAG 57.826 45.455 0.00 0.00 45.10 2.74
2400 4661 3.921021 GGCTTCGATTCCGATATGTAGTG 59.079 47.826 0.00 0.00 45.10 2.74
2401 4662 3.365220 GCTTCGATTCCGATATGTAGTGC 59.635 47.826 0.00 0.00 45.10 4.40
2402 4663 3.197434 TCGATTCCGATATGTAGTGCG 57.803 47.619 0.00 0.00 40.30 5.34
2403 4664 1.649171 CGATTCCGATATGTAGTGCGC 59.351 52.381 0.00 0.00 38.22 6.09
2406 4667 3.926821 TTCCGATATGTAGTGCGCATA 57.073 42.857 15.91 0.55 33.91 3.14
2407 4668 3.926821 TCCGATATGTAGTGCGCATAA 57.073 42.857 15.91 0.84 33.23 1.90
2410 4671 2.923655 CGATATGTAGTGCGCATAAGGG 59.076 50.000 15.91 0.00 33.23 3.95
2421 5306 0.737219 GCATAAGGGCTGTGAAGCTG 59.263 55.000 0.00 0.00 34.73 4.24
2426 5311 1.035139 AGGGCTGTGAAGCTGTTTTG 58.965 50.000 0.00 0.00 34.73 2.44
2429 5314 1.269257 GGCTGTGAAGCTGTTTTGGAC 60.269 52.381 0.00 0.00 34.73 4.02
2430 5315 1.597937 GCTGTGAAGCTGTTTTGGACG 60.598 52.381 0.00 0.00 0.00 4.79
2433 5318 2.750166 TGTGAAGCTGTTTTGGACGAAA 59.250 40.909 0.00 0.00 0.00 3.46
2434 5319 3.380004 TGTGAAGCTGTTTTGGACGAAAT 59.620 39.130 0.00 0.00 0.00 2.17
2437 5322 5.398416 GTGAAGCTGTTTTGGACGAAATAAC 59.602 40.000 0.00 0.00 0.00 1.89
2438 5323 4.499037 AGCTGTTTTGGACGAAATAACC 57.501 40.909 0.00 0.00 0.00 2.85
2439 5324 3.254903 AGCTGTTTTGGACGAAATAACCC 59.745 43.478 0.00 0.00 0.00 4.11
2440 5325 3.254903 GCTGTTTTGGACGAAATAACCCT 59.745 43.478 0.00 0.00 0.00 4.34
2441 5326 4.615223 GCTGTTTTGGACGAAATAACCCTC 60.615 45.833 0.00 0.00 0.00 4.30
2442 5327 4.462133 TGTTTTGGACGAAATAACCCTCA 58.538 39.130 0.00 0.00 0.00 3.86
2443 5328 4.888239 TGTTTTGGACGAAATAACCCTCAA 59.112 37.500 0.00 0.00 0.00 3.02
2444 5329 5.217393 GTTTTGGACGAAATAACCCTCAAC 58.783 41.667 0.00 0.00 0.00 3.18
2447 5332 3.007635 GGACGAAATAACCCTCAACTGG 58.992 50.000 0.00 0.00 0.00 4.00
2453 5938 2.536761 TAACCCTCAACTGGTTCACG 57.463 50.000 0.00 0.00 44.79 4.35
2454 5939 0.179029 AACCCTCAACTGGTTCACGG 60.179 55.000 0.00 0.00 42.38 4.94
2458 5943 0.532862 CTCAACTGGTTCACGGCAGT 60.533 55.000 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.104855 TCAATCATCGCCCTCTTCCG 59.895 55.000 0.00 0.00 0.00 4.30
1 2 2.332063 TTCAATCATCGCCCTCTTCC 57.668 50.000 0.00 0.00 0.00 3.46
11 12 6.949352 TTGGCCTTCTTCTATTCAATCATC 57.051 37.500 3.32 0.00 0.00 2.92
17 18 4.042809 TGGAGTTTGGCCTTCTTCTATTCA 59.957 41.667 3.32 0.00 0.00 2.57
42 43 0.390472 GCGGTCTCCACCTTCTTCTG 60.390 60.000 0.00 0.00 41.17 3.02
62 63 3.056328 GTGTCCTCCAAAGCGGCC 61.056 66.667 0.00 0.00 33.14 6.13
119 120 2.610976 GGCTTGCACAATCATTCTTGCA 60.611 45.455 0.00 0.00 43.11 4.08
162 163 4.244066 CTCTCCATATCATTCTTCTGCCG 58.756 47.826 0.00 0.00 0.00 5.69
186 187 1.826054 CGATCTCCTCCTGCTCCGT 60.826 63.158 0.00 0.00 0.00 4.69
257 258 3.185797 GCCTCTACGTTCAATTTGTCGTT 59.814 43.478 19.97 10.05 37.66 3.85
264 265 1.822990 TCCGAGCCTCTACGTTCAATT 59.177 47.619 0.00 0.00 0.00 2.32
296 297 2.991190 CAGTCCATGCATTTTGTCTTGC 59.009 45.455 0.00 0.00 39.33 4.01
312 313 6.929606 ACGAAAGAATAATAGTATGGCAGTCC 59.070 38.462 0.00 0.00 0.00 3.85
325 326 3.804036 TGCCCGATCACGAAAGAATAAT 58.196 40.909 0.00 0.00 42.66 1.28
326 327 3.254470 TGCCCGATCACGAAAGAATAA 57.746 42.857 0.00 0.00 42.66 1.40
402 403 0.179145 GATCCGTAGTGTGTGTCGGG 60.179 60.000 0.00 0.00 42.71 5.14
408 409 6.876789 TCAAATATGTTTGATCCGTAGTGTGT 59.123 34.615 13.03 0.00 46.49 3.72
452 453 3.071023 GCTAGCCACTATATGTCCACCAA 59.929 47.826 2.29 0.00 0.00 3.67
493 494 1.220749 CTACCGTGGACATGGGTGG 59.779 63.158 14.61 5.24 41.81 4.61
517 518 3.074504 CATTTGTCCGAGGAATGCATG 57.925 47.619 0.00 0.00 0.00 4.06
520 521 3.629858 GCATTTGTCCGAGGAATGC 57.370 52.632 10.41 10.41 45.82 3.56
533 534 3.004315 CCCGTAAACTGAACACTGCATTT 59.996 43.478 0.00 0.00 0.00 2.32
546 547 0.601841 CCAACGCTGACCCGTAAACT 60.602 55.000 0.00 0.00 41.16 2.66
630 631 6.543831 CACTAAAGGGGGATTCATTTCTACTG 59.456 42.308 0.00 0.00 0.00 2.74
646 647 2.484264 CGCCAAGAAGTTCACTAAAGGG 59.516 50.000 5.50 0.00 0.00 3.95
651 652 2.364324 ACAGACGCCAAGAAGTTCACTA 59.636 45.455 5.50 0.00 0.00 2.74
671 672 9.974750 CAAGAAAGAAGAAAAATATCTCCGTAC 57.025 33.333 0.00 0.00 0.00 3.67
687 688 7.934457 TCTCCATTCTCAAAACAAGAAAGAAG 58.066 34.615 0.00 0.00 36.41 2.85
884 1830 2.583520 GAGGCCTGGAGCAGTCTG 59.416 66.667 12.00 0.00 46.50 3.51
925 1882 1.732355 GGTAGGGTTTGGGTTGGGGT 61.732 60.000 0.00 0.00 0.00 4.95
1386 2344 2.283821 TTGGCCATGAAGGTGCCC 60.284 61.111 6.09 0.00 44.72 5.36
1472 2430 1.642037 GAGCAGAGCAATCGCAAGCA 61.642 55.000 0.00 0.00 42.27 3.91
1480 2438 5.188751 AGGTAGAGTAAAAGAGCAGAGCAAT 59.811 40.000 0.00 0.00 0.00 3.56
1522 2483 2.666508 CGACAAACGGGACACATCTAAG 59.333 50.000 0.00 0.00 38.46 2.18
1564 2528 7.805071 GGCGATGAAATATTCAGGAAACATAAG 59.195 37.037 0.00 0.00 43.98 1.73
1757 2727 7.944729 AATCTAGAAACACCTGCAATAACAT 57.055 32.000 0.00 0.00 0.00 2.71
1759 2729 7.410485 GCTAATCTAGAAACACCTGCAATAAC 58.590 38.462 0.00 0.00 0.00 1.89
1832 2807 7.080099 CACACCTCAAAGAATCAACACATAAG 58.920 38.462 0.00 0.00 0.00 1.73
1903 2999 4.182693 TCTAGAACATACCAACCACACG 57.817 45.455 0.00 0.00 0.00 4.49
1997 3107 0.099436 GCAATCATCGAACTGCCACC 59.901 55.000 0.00 0.00 0.00 4.61
2006 3116 0.744281 TCCACGCTAGCAATCATCGA 59.256 50.000 16.45 0.00 0.00 3.59
2020 3130 1.227380 GGCAGGACTATGCTCCACG 60.227 63.158 0.00 0.00 45.75 4.94
2033 3143 1.698506 TGGTTAAACCACAAGGCAGG 58.301 50.000 0.00 0.00 44.79 4.85
2068 3178 2.154567 AGGCAATGGTGAATGCTGAT 57.845 45.000 0.00 0.00 42.20 2.90
2072 3189 1.767759 AGGTAGGCAATGGTGAATGC 58.232 50.000 0.00 0.00 41.82 3.56
2117 3239 3.126001 ACCAATAGACATATGGCACGG 57.874 47.619 12.11 7.63 0.00 4.94
2134 3546 8.158132 TCACCTACATCTACAATTTGTAAACCA 58.842 33.333 10.32 0.00 31.67 3.67
2143 3555 6.942576 AGCAAAACTCACCTACATCTACAATT 59.057 34.615 0.00 0.00 0.00 2.32
2144 3556 6.372659 CAGCAAAACTCACCTACATCTACAAT 59.627 38.462 0.00 0.00 0.00 2.71
2171 3591 6.385443 AGTAATCCTATCACATCCCAAGAGA 58.615 40.000 0.00 0.00 0.00 3.10
2194 4381 6.579145 ACTGATTACGTCGGCACTTGTAAAG 61.579 44.000 0.00 0.00 42.87 1.85
2202 4389 1.082117 CCCACTGATTACGTCGGCAC 61.082 60.000 0.00 0.00 36.64 5.01
2221 4445 5.793030 ACATACCTAGATACTGAACCAGC 57.207 43.478 0.00 0.00 34.37 4.85
2236 4460 8.133024 TGAAATCAAATTGGCTAAACATACCT 57.867 30.769 0.00 0.00 0.00 3.08
2347 4608 1.135083 ACGCACTAGAATCTGGAACGG 60.135 52.381 14.40 0.00 0.00 4.44
2349 4610 6.074544 ACTATACGCACTAGAATCTGGAAC 57.925 41.667 0.00 0.00 0.00 3.62
2350 4611 6.710597 AACTATACGCACTAGAATCTGGAA 57.289 37.500 0.00 0.00 0.00 3.53
2351 4612 6.710597 AAACTATACGCACTAGAATCTGGA 57.289 37.500 0.00 0.00 0.00 3.86
2383 4644 1.649171 GCGCACTACATATCGGAATCG 59.351 52.381 0.30 0.00 37.82 3.34
2384 4645 2.672714 TGCGCACTACATATCGGAATC 58.327 47.619 5.66 0.00 0.00 2.52
2385 4646 2.812358 TGCGCACTACATATCGGAAT 57.188 45.000 5.66 0.00 0.00 3.01
2388 4649 2.923655 CCTTATGCGCACTACATATCGG 59.076 50.000 14.90 0.75 30.42 4.18
2389 4650 2.923655 CCCTTATGCGCACTACATATCG 59.076 50.000 14.90 0.00 30.42 2.92
2391 4652 2.303022 AGCCCTTATGCGCACTACATAT 59.697 45.455 14.90 0.00 36.02 1.78
2393 4654 0.469917 AGCCCTTATGCGCACTACAT 59.530 50.000 14.90 0.00 36.02 2.29
2394 4655 0.461870 CAGCCCTTATGCGCACTACA 60.462 55.000 14.90 0.00 36.02 2.74
2395 4656 0.462047 ACAGCCCTTATGCGCACTAC 60.462 55.000 14.90 0.00 36.02 2.73
2396 4657 0.461870 CACAGCCCTTATGCGCACTA 60.462 55.000 14.90 1.83 36.02 2.74
2397 4658 1.746615 CACAGCCCTTATGCGCACT 60.747 57.895 14.90 0.00 36.02 4.40
2398 4659 1.305219 TTCACAGCCCTTATGCGCAC 61.305 55.000 14.90 0.00 36.02 5.34
2400 4661 1.723870 CTTCACAGCCCTTATGCGC 59.276 57.895 0.00 0.00 36.02 6.09
2401 4662 1.723870 GCTTCACAGCCCTTATGCG 59.276 57.895 0.00 0.00 40.61 4.73
2411 4672 1.939934 TCGTCCAAAACAGCTTCACAG 59.060 47.619 0.00 0.00 0.00 3.66
2417 5302 3.254903 GGGTTATTTCGTCCAAAACAGCT 59.745 43.478 0.00 0.00 0.00 4.24
2421 5306 5.009310 AGTTGAGGGTTATTTCGTCCAAAAC 59.991 40.000 0.00 0.00 0.00 2.43
2426 5311 3.007635 CCAGTTGAGGGTTATTTCGTCC 58.992 50.000 0.00 0.00 0.00 4.79
2437 5322 1.966451 GCCGTGAACCAGTTGAGGG 60.966 63.158 4.60 4.60 35.36 4.30
2438 5323 1.227823 TGCCGTGAACCAGTTGAGG 60.228 57.895 0.00 0.00 0.00 3.86
2439 5324 0.532862 ACTGCCGTGAACCAGTTGAG 60.533 55.000 0.00 0.00 39.11 3.02
2440 5325 0.813610 CACTGCCGTGAACCAGTTGA 60.814 55.000 1.41 0.00 43.97 3.18
2441 5326 1.648720 CACTGCCGTGAACCAGTTG 59.351 57.895 1.41 0.00 43.97 3.16
2442 5327 2.186826 GCACTGCCGTGAACCAGTT 61.187 57.895 12.93 0.00 43.97 3.16
2443 5328 2.591715 GCACTGCCGTGAACCAGT 60.592 61.111 12.93 0.00 43.97 4.00
2444 5329 2.591429 TGCACTGCCGTGAACCAG 60.591 61.111 12.93 0.00 43.97 4.00
2447 5332 3.245948 CTGCTGCACTGCCGTGAAC 62.246 63.158 12.93 0.82 43.97 3.18


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

AutoCloner maintained by Alex Coulton.