Multiple sequence alignment - TraesCS2A01G169900

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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 TraesCS2A01G169900 chr2A 100.000 3452 0 0 1 3452 125201268 125197817 0.000000e+00 6375
1 TraesCS2A01G169900 chr2D 91.456 1744 78 31 511 2211 120995782 120994067 0.000000e+00 2329
2 TraesCS2A01G169900 chr2D 88.405 1147 68 25 2309 3452 120994040 120992956 0.000000e+00 1321
3 TraesCS2A01G169900 chr2D 88.355 541 44 9 1 526 120996333 120995797 1.750000e-177 632
4 TraesCS2A01G169900 chr2D 91.111 90 8 0 2224 2313 428554992 428554903 4.680000e-24 122
5 TraesCS2A01G169900 chr2B 90.699 1602 65 37 641 2211 174386796 174385248 0.000000e+00 2056
6 TraesCS2A01G169900 chr2B 89.516 1116 68 17 2343 3452 174385189 174384117 0.000000e+00 1367
7 TraesCS2A01G169900 chr2B 92.450 649 33 6 7 642 174390689 174390044 0.000000e+00 913
8 TraesCS2A01G169900 chr7B 92.222 90 7 0 2224 2313 102234366 102234455 1.010000e-25 128
9 TraesCS2A01G169900 chr3A 92.222 90 7 0 2224 2313 534181974 534181885 1.010000e-25 128
10 TraesCS2A01G169900 chr6A 93.023 86 6 0 2226 2311 577699240 577699155 3.620000e-25 126
11 TraesCS2A01G169900 chr7D 91.209 91 6 2 2224 2313 397554965 397555054 4.680000e-24 122
12 TraesCS2A01G169900 chr6D 91.111 90 8 0 2224 2313 221986441 221986530 4.680000e-24 122
13 TraesCS2A01G169900 chr3D 91.111 90 8 0 2224 2313 376343377 376343288 4.680000e-24 122
14 TraesCS2A01G169900 chr1A 91.111 90 8 0 2224 2313 567971369 567971458 4.680000e-24 122
15 TraesCS2A01G169900 chr5B 88.119 101 9 2 2224 2322 534775356 534775257 2.180000e-22 117


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 TraesCS2A01G169900 chr2A 125197817 125201268 3451 True 6375.000000 6375 100.000000 1 3452 1 chr2A.!!$R1 3451
1 TraesCS2A01G169900 chr2D 120992956 120996333 3377 True 1427.333333 2329 89.405333 1 3452 3 chr2D.!!$R2 3451
2 TraesCS2A01G169900 chr2B 174384117 174390689 6572 True 1445.333333 2056 90.888333 7 3452 3 chr2B.!!$R1 3445

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
915 4225 0.249073 CCGATCATTCTCGCGGTTCT 60.249 55.0 6.13 0.0 38.99 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2656 6013 1.202521 TCATTACAGCGTCGATGGCAT 60.203 47.619 15.82 0.0 0.0 4.4 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
230 245 7.583860 TCGACGTGATTTATTGTGAATGTTA 57.416 32.000 0.00 0.00 0.00 2.41
279 294 4.209288 CGATAAGATAGGGACAAACAAGCG 59.791 45.833 0.00 0.00 0.00 4.68
390 405 9.554395 CCTAGAATTGTGGGTTTTTGTTAAAAT 57.446 29.630 0.00 0.00 35.80 1.82
425 442 3.021695 GGTTTTGTATTACCTCAGCCCC 58.978 50.000 0.00 0.00 0.00 5.80
459 476 2.004583 TGTGCGATTCCCTCTTAACG 57.995 50.000 0.00 0.00 0.00 3.18
497 514 6.562228 TCCACCACTGCCTTAGTCTATATAT 58.438 40.000 0.00 0.00 37.60 0.86
502 519 7.616150 ACCACTGCCTTAGTCTATATATGGTAG 59.384 40.741 0.00 0.00 37.60 3.18
699 3993 2.813042 GCCAGCGCTCTCACTCAC 60.813 66.667 7.13 0.00 0.00 3.51
719 4013 2.235891 CCCTATTTAATTCGTGGGGGC 58.764 52.381 0.00 0.00 0.00 5.80
907 4217 1.202510 AGCTGCTCACCGATCATTCTC 60.203 52.381 0.00 0.00 0.00 2.87
914 4224 2.217112 CCGATCATTCTCGCGGTTC 58.783 57.895 6.13 0.00 38.99 3.62
915 4225 0.249073 CCGATCATTCTCGCGGTTCT 60.249 55.000 6.13 0.00 38.99 3.01
916 4226 0.848942 CGATCATTCTCGCGGTTCTG 59.151 55.000 6.13 0.00 0.00 3.02
917 4227 1.212616 GATCATTCTCGCGGTTCTGG 58.787 55.000 6.13 0.00 0.00 3.86
918 4228 0.811616 ATCATTCTCGCGGTTCTGGC 60.812 55.000 6.13 0.00 0.00 4.85
919 4229 1.741401 CATTCTCGCGGTTCTGGCA 60.741 57.895 6.13 0.00 0.00 4.92
920 4230 1.448540 ATTCTCGCGGTTCTGGCAG 60.449 57.895 8.58 8.58 0.00 4.85
921 4231 2.172483 ATTCTCGCGGTTCTGGCAGT 62.172 55.000 15.27 0.00 0.00 4.40
922 4232 1.529152 TTCTCGCGGTTCTGGCAGTA 61.529 55.000 15.27 1.01 0.00 2.74
923 4233 1.805945 CTCGCGGTTCTGGCAGTAC 60.806 63.158 15.27 15.18 0.00 2.73
939 4249 1.276421 AGTACTTGCGCCAATCTCACT 59.724 47.619 4.18 0.00 0.00 3.41
962 4273 0.819582 TAATTCACCGACCCTCCGAC 59.180 55.000 0.00 0.00 0.00 4.79
1029 4344 1.630244 GCTCGCTGCTGACGATGTTT 61.630 55.000 9.65 0.00 39.12 2.83
1057 4379 7.176690 ACAGTTCTTCTTCCTTTTGTTTTCTGA 59.823 33.333 0.00 0.00 0.00 3.27
1082 4409 1.596203 GTGCAGCAGCTGACTGTGA 60.596 57.895 27.39 17.56 46.30 3.58
1122 4449 0.396435 TCAACTGGGTGCAGAATCGT 59.604 50.000 0.00 0.00 0.00 3.73
1214 4541 3.114065 AGTCACTCGTTTCGTTTCACTC 58.886 45.455 0.00 0.00 0.00 3.51
1246 4575 1.699343 ACGTACGCTTTCTGAAGAGC 58.301 50.000 16.72 11.87 36.29 4.09
1304 4633 4.272245 CCGGTCCGGGAGAATAGT 57.728 61.111 23.59 0.00 44.15 2.12
1365 4694 0.178767 CATGCTCTCCATCGGAACCA 59.821 55.000 0.00 0.00 29.71 3.67
1366 4695 1.135094 ATGCTCTCCATCGGAACCAT 58.865 50.000 0.00 0.00 0.00 3.55
1367 4696 0.465705 TGCTCTCCATCGGAACCATC 59.534 55.000 0.00 0.00 0.00 3.51
1368 4697 0.598680 GCTCTCCATCGGAACCATCG 60.599 60.000 0.00 0.00 0.00 3.84
1369 4698 0.032678 CTCTCCATCGGAACCATCGG 59.967 60.000 0.00 0.00 0.00 4.18
1370 4699 0.396556 TCTCCATCGGAACCATCGGA 60.397 55.000 0.00 0.00 38.99 4.55
1371 4700 0.464036 CTCCATCGGAACCATCGGAA 59.536 55.000 0.00 0.00 38.26 4.30
1372 4701 0.177141 TCCATCGGAACCATCGGAAC 59.823 55.000 0.00 0.00 38.26 3.62
1373 4702 0.814010 CCATCGGAACCATCGGAACC 60.814 60.000 0.00 0.00 38.26 3.62
1805 5140 0.179936 CCAGCCTCAAGGATCCAGTC 59.820 60.000 15.82 0.00 37.39 3.51
1817 5152 5.223449 AGGATCCAGTCGAAACAAAACTA 57.777 39.130 15.82 0.00 0.00 2.24
1828 5163 7.437565 AGTCGAAACAAAACTAGAGAAGGTAAC 59.562 37.037 0.00 0.00 0.00 2.50
1835 5174 7.226720 ACAAAACTAGAGAAGGTAACACACATG 59.773 37.037 0.00 0.00 41.41 3.21
1898 5242 3.252974 ACCAGTGTTCACATAGCTAGC 57.747 47.619 6.62 6.62 0.00 3.42
1899 5243 2.834549 ACCAGTGTTCACATAGCTAGCT 59.165 45.455 23.12 23.12 0.00 3.32
1900 5244 4.023980 ACCAGTGTTCACATAGCTAGCTA 58.976 43.478 26.09 26.09 0.00 3.32
1901 5245 4.098654 ACCAGTGTTCACATAGCTAGCTAG 59.901 45.833 27.42 20.71 31.45 3.42
1906 5250 5.875359 GTGTTCACATAGCTAGCTAGGTTTT 59.125 40.000 33.25 14.63 40.90 2.43
1952 5296 4.766373 TGGGCGATCATGCAATAATAATGT 59.234 37.500 0.00 0.00 36.28 2.71
1955 5299 5.570206 GGCGATCATGCAATAATAATGTGTG 59.430 40.000 0.00 0.00 36.28 3.82
2065 5410 3.545624 CGTCGTCGAGGAAGTATTACCTG 60.546 52.174 9.78 0.00 39.71 4.00
2122 5467 1.454111 CCACGACGAGGAGGAGGAT 60.454 63.158 5.25 0.00 0.00 3.24
2125 5470 0.748729 ACGACGAGGAGGAGGATGAC 60.749 60.000 0.00 0.00 0.00 3.06
2126 5471 0.464735 CGACGAGGAGGAGGATGACT 60.465 60.000 0.00 0.00 0.00 3.41
2176 5527 9.736023 GACAAAACAGATTCAGATTGTAAGTTT 57.264 29.630 0.00 0.00 31.68 2.66
2214 5565 8.834749 AATTTCACTTCAGACTTAACTACTCC 57.165 34.615 0.00 0.00 0.00 3.85
2215 5566 5.979288 TCACTTCAGACTTAACTACTCCC 57.021 43.478 0.00 0.00 0.00 4.30
2216 5567 5.642165 TCACTTCAGACTTAACTACTCCCT 58.358 41.667 0.00 0.00 0.00 4.20
2218 5569 6.658391 TCACTTCAGACTTAACTACTCCCTAC 59.342 42.308 0.00 0.00 0.00 3.18
2220 5571 5.171339 TCAGACTTAACTACTCCCTACGT 57.829 43.478 0.00 0.00 0.00 3.57
2221 5572 5.564550 TCAGACTTAACTACTCCCTACGTT 58.435 41.667 0.00 0.00 0.00 3.99
2222 5573 5.645497 TCAGACTTAACTACTCCCTACGTTC 59.355 44.000 0.00 0.00 0.00 3.95
2223 5574 4.946772 AGACTTAACTACTCCCTACGTTCC 59.053 45.833 0.00 0.00 0.00 3.62
2224 5575 4.928263 ACTTAACTACTCCCTACGTTCCT 58.072 43.478 0.00 0.00 0.00 3.36
2226 5577 6.485171 ACTTAACTACTCCCTACGTTCCTAA 58.515 40.000 0.00 0.00 0.00 2.69
2227 5578 6.948309 ACTTAACTACTCCCTACGTTCCTAAA 59.052 38.462 0.00 0.00 0.00 1.85
2228 5579 7.617329 ACTTAACTACTCCCTACGTTCCTAAAT 59.383 37.037 0.00 0.00 0.00 1.40
2229 5580 9.125026 CTTAACTACTCCCTACGTTCCTAAATA 57.875 37.037 0.00 0.00 0.00 1.40
2233 5584 9.646522 ACTACTCCCTACGTTCCTAAATATAAA 57.353 33.333 0.00 0.00 0.00 1.40
2235 5586 7.440198 ACTCCCTACGTTCCTAAATATAAAGC 58.560 38.462 0.00 0.00 0.00 3.51
2237 5588 7.794041 TCCCTACGTTCCTAAATATAAAGCAA 58.206 34.615 0.00 0.00 0.00 3.91
2238 5589 8.266473 TCCCTACGTTCCTAAATATAAAGCAAA 58.734 33.333 0.00 0.00 0.00 3.68
2239 5590 8.895737 CCCTACGTTCCTAAATATAAAGCAAAA 58.104 33.333 0.00 0.00 0.00 2.44
2256 5607 8.976986 AAAGCAAAATGAATGAATCTACACTC 57.023 30.769 0.00 0.00 0.00 3.51
2257 5608 7.934855 AGCAAAATGAATGAATCTACACTCT 57.065 32.000 0.00 0.00 0.00 3.24
2258 5609 9.453572 AAGCAAAATGAATGAATCTACACTCTA 57.546 29.630 0.00 0.00 0.00 2.43
2259 5610 9.453572 AGCAAAATGAATGAATCTACACTCTAA 57.546 29.630 0.00 0.00 0.00 2.10
2265 5616 9.737427 ATGAATGAATCTACACTCTAAACTACG 57.263 33.333 0.00 0.00 0.00 3.51
2266 5617 8.737175 TGAATGAATCTACACTCTAAACTACGT 58.263 33.333 0.00 0.00 0.00 3.57
2267 5618 9.224058 GAATGAATCTACACTCTAAACTACGTC 57.776 37.037 0.00 0.00 0.00 4.34
2268 5619 7.918536 TGAATCTACACTCTAAACTACGTCT 57.081 36.000 0.00 0.00 0.00 4.18
2269 5620 9.610705 ATGAATCTACACTCTAAACTACGTCTA 57.389 33.333 0.00 0.00 0.00 2.59
2270 5621 9.610705 TGAATCTACACTCTAAACTACGTCTAT 57.389 33.333 0.00 0.00 0.00 1.98
2327 5678 6.346477 AGAATGACTACTACTTTGCACTCA 57.654 37.500 0.00 0.00 0.00 3.41
2331 5682 5.230182 TGACTACTACTTTGCACTCATGTG 58.770 41.667 0.00 0.00 46.37 3.21
2332 5683 5.215252 ACTACTACTTTGCACTCATGTGT 57.785 39.130 0.00 0.00 45.44 3.72
2356 5707 0.040058 AGACCCATGCATGCAGGAAA 59.960 50.000 32.39 5.39 0.00 3.13
2359 5710 1.483415 ACCCATGCATGCAGGAAAATC 59.517 47.619 32.39 0.00 0.00 2.17
2363 5714 3.491964 CCATGCATGCAGGAAAATCGAAT 60.492 43.478 32.39 4.96 0.00 3.34
2376 5727 2.806288 ATCGAATCGTTTCTTTGCGG 57.194 45.000 1.52 0.00 0.00 5.69
2459 5815 6.132791 TGTTCTAGAGGTGTAAAGCGATAG 57.867 41.667 0.00 0.00 0.00 2.08
2547 5904 0.377905 TCGAATTGCATGCATGGACG 59.622 50.000 27.34 22.85 0.00 4.79
2550 5907 2.542205 CGAATTGCATGCATGGACGAAT 60.542 45.455 27.34 13.01 0.00 3.34
2556 5913 2.613595 GCATGCATGGACGAATCAGTTA 59.386 45.455 27.34 0.00 0.00 2.24
2561 5918 3.873910 CATGGACGAATCAGTTAACCCT 58.126 45.455 0.88 0.00 0.00 4.34
2567 5924 5.579904 GGACGAATCAGTTAACCCTAAAGAC 59.420 44.000 0.88 0.00 0.00 3.01
2570 5927 6.171213 CGAATCAGTTAACCCTAAAGACCTT 58.829 40.000 0.88 0.00 0.00 3.50
2574 5931 6.902408 TCAGTTAACCCTAAAGACCTTCAAA 58.098 36.000 0.88 0.00 0.00 2.69
2575 5932 6.769341 TCAGTTAACCCTAAAGACCTTCAAAC 59.231 38.462 0.88 0.00 0.00 2.93
2650 6007 6.561737 TTTTGCAGATTACACGGATGTTAA 57.438 33.333 0.00 0.00 40.48 2.01
2651 6008 6.751514 TTTGCAGATTACACGGATGTTAAT 57.248 33.333 0.00 0.00 40.48 1.40
2652 6009 6.751514 TTGCAGATTACACGGATGTTAATT 57.248 33.333 0.00 0.00 40.48 1.40
2653 6010 7.851387 TTGCAGATTACACGGATGTTAATTA 57.149 32.000 0.00 0.00 40.48 1.40
2656 6013 9.549078 TGCAGATTACACGGATGTTAATTATAA 57.451 29.630 0.00 0.00 40.48 0.98
2688 6045 3.368427 CGCTGTAATGATCCCGGTGATAT 60.368 47.826 0.00 0.00 32.41 1.63
2700 6057 3.739300 CCCGGTGATATATGTTGAACGAC 59.261 47.826 0.00 0.00 0.00 4.34
2747 6104 3.005554 GGAGGACATATGATGGAATGCG 58.994 50.000 10.38 0.00 33.60 4.73
2768 6125 1.524961 AGGGTGTTGCACTGAACGA 59.475 52.632 0.00 0.00 34.40 3.85
2772 6129 0.315869 GTGTTGCACTGAACGAACGG 60.316 55.000 0.00 0.00 0.00 4.44
2829 6187 5.707764 AGGAGGAATCAGTTTTCAGCTTAAC 59.292 40.000 0.00 0.00 0.00 2.01
2980 6338 7.171678 GTGGGATACTAGATGTTGCAGTAATTC 59.828 40.741 0.00 0.00 0.00 2.17
2981 6339 6.651225 GGGATACTAGATGTTGCAGTAATTCC 59.349 42.308 0.00 0.00 0.00 3.01
2982 6340 7.445945 GGATACTAGATGTTGCAGTAATTCCT 58.554 38.462 0.00 0.00 0.00 3.36
2983 6341 8.585881 GGATACTAGATGTTGCAGTAATTCCTA 58.414 37.037 0.00 0.00 0.00 2.94
2984 6342 9.413048 GATACTAGATGTTGCAGTAATTCCTAC 57.587 37.037 0.00 0.00 0.00 3.18
2985 6343 7.425224 ACTAGATGTTGCAGTAATTCCTACT 57.575 36.000 0.00 0.00 41.87 2.57
2986 6344 8.534954 ACTAGATGTTGCAGTAATTCCTACTA 57.465 34.615 0.00 0.00 38.92 1.82
2987 6345 8.978472 ACTAGATGTTGCAGTAATTCCTACTAA 58.022 33.333 0.00 0.00 38.92 2.24
2988 6346 9.988815 CTAGATGTTGCAGTAATTCCTACTAAT 57.011 33.333 0.00 0.00 38.92 1.73
3002 6360 8.950208 ATTCCTACTAATTAGTGAAGTGAAGC 57.050 34.615 25.27 0.00 37.10 3.86
3043 6401 9.890629 TGTGCACTTTATCTTAGTCTAATCAAT 57.109 29.630 19.41 0.00 0.00 2.57
3054 6412 7.706607 TCTTAGTCTAATCAATCAATGTGGTCG 59.293 37.037 0.00 0.00 0.00 4.79
3132 6490 2.220653 ACGGTACAGCAACTAGGGTA 57.779 50.000 0.00 0.00 0.00 3.69
3144 6502 3.377253 ACTAGGGTACTCGGAACATGA 57.623 47.619 0.00 0.00 0.00 3.07
3145 6503 3.288964 ACTAGGGTACTCGGAACATGAG 58.711 50.000 0.00 0.00 39.40 2.90
3150 6508 2.186076 GTACTCGGAACATGAGAAGCG 58.814 52.381 0.00 0.00 36.93 4.68
3164 6522 2.508755 GAAGCGGCCGAAAACGGAAG 62.509 60.000 33.48 0.00 0.00 3.46
3364 6723 3.067106 ACGAGTCCATTGCAAAGTACAG 58.933 45.455 1.71 0.00 0.00 2.74
3365 6724 2.159653 CGAGTCCATTGCAAAGTACAGC 60.160 50.000 1.71 0.00 0.00 4.40
3366 6725 2.813754 GAGTCCATTGCAAAGTACAGCA 59.186 45.455 1.71 3.89 39.32 4.41
3367 6726 2.816087 AGTCCATTGCAAAGTACAGCAG 59.184 45.455 1.71 0.00 42.39 4.24
3368 6727 2.554032 GTCCATTGCAAAGTACAGCAGT 59.446 45.455 1.71 3.18 42.39 4.40
3369 6728 3.751175 GTCCATTGCAAAGTACAGCAGTA 59.249 43.478 1.71 0.00 42.39 2.74
3385 6744 6.127101 ACAGCAGTACATAGTGTATCTGGTA 58.873 40.000 16.33 0.00 38.89 3.25
3390 6749 9.326413 GCAGTACATAGTGTATCTGGTAAAAAT 57.674 33.333 15.07 0.00 35.05 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 4.941263 TCTCCCTATGTACAAATGTTGTGC 59.059 41.667 0.00 3.26 45.03 4.57
26 27 3.937079 CCGGTTGTTTTCTCCCTATGTAC 59.063 47.826 0.00 0.00 0.00 2.90
208 223 7.636359 GCTCTAACATTCACAATAAATCACGTC 59.364 37.037 0.00 0.00 0.00 4.34
230 245 5.247337 GGGAGCTTAAATATAGAGGTGCTCT 59.753 44.000 14.87 0.00 43.37 4.09
279 294 2.914838 GCGTTAATTAGGTGCAAGCAAC 59.085 45.455 0.92 0.92 36.26 4.17
351 366 7.259161 CCACAATTCTAGGACTAGTCAGTAAC 58.741 42.308 23.91 6.59 34.21 2.50
355 370 4.712337 ACCCACAATTCTAGGACTAGTCAG 59.288 45.833 23.91 13.76 34.84 3.51
390 405 2.176889 CAAAACCTCGACTCTAGGGGA 58.823 52.381 0.00 0.00 38.54 4.81
391 406 1.900486 ACAAAACCTCGACTCTAGGGG 59.100 52.381 0.00 0.00 38.54 4.79
425 442 6.399880 GGAATCGCACAAATACACAACATTTG 60.400 38.462 6.31 6.31 45.01 2.32
497 514 4.157246 TGCTGTACTTCTCCTTTCTACCA 58.843 43.478 0.00 0.00 0.00 3.25
502 519 5.578727 CAGTGTATGCTGTACTTCTCCTTTC 59.421 44.000 0.00 0.00 0.00 2.62
699 3993 2.235891 GCCCCCACGAATTAAATAGGG 58.764 52.381 0.00 0.00 36.32 3.53
907 4217 1.374252 AAGTACTGCCAGAACCGCG 60.374 57.895 0.00 0.00 0.00 6.46
918 4228 1.394917 GTGAGATTGGCGCAAGTACTG 59.605 52.381 10.83 0.00 41.68 2.74
919 4229 1.276421 AGTGAGATTGGCGCAAGTACT 59.724 47.619 10.83 0.84 41.68 2.73
920 4230 1.394917 CAGTGAGATTGGCGCAAGTAC 59.605 52.381 10.83 0.00 41.68 2.73
921 4231 1.675714 CCAGTGAGATTGGCGCAAGTA 60.676 52.381 10.83 0.00 41.68 2.24
922 4232 0.957395 CCAGTGAGATTGGCGCAAGT 60.957 55.000 10.83 0.00 41.68 3.16
923 4233 1.651240 CCCAGTGAGATTGGCGCAAG 61.651 60.000 10.83 0.00 34.26 4.01
1029 4344 9.020731 AGAAAACAAAAGGAAGAAGAACTGTAA 57.979 29.630 0.00 0.00 0.00 2.41
1057 4379 0.900421 TCAGCTGCTGCACTACTCAT 59.100 50.000 24.38 0.00 42.74 2.90
1122 4449 1.423584 TCTCCTGCTTGGTGTTCAGA 58.576 50.000 0.00 0.00 37.07 3.27
1125 4452 2.550830 TCTTCTCCTGCTTGGTGTTC 57.449 50.000 0.00 0.00 37.07 3.18
1214 4541 1.817217 CGTACGTACGCATGCATGGG 61.817 60.000 34.59 34.59 43.14 4.00
1365 4694 2.267961 GTTGCCGAGGGTTCCGAT 59.732 61.111 0.00 0.00 0.00 4.18
1366 4695 4.367023 CGTTGCCGAGGGTTCCGA 62.367 66.667 0.00 0.00 35.63 4.55
1367 4696 4.367023 TCGTTGCCGAGGGTTCCG 62.367 66.667 0.00 0.00 38.40 4.30
1476 4811 2.125512 CTTAGACTTGGCGCGCCT 60.126 61.111 45.79 30.36 36.94 5.52
1805 5140 7.010738 TGTGTTACCTTCTCTAGTTTTGTTTCG 59.989 37.037 0.00 0.00 0.00 3.46
1817 5152 4.955811 TCACATGTGTGTTACCTTCTCT 57.044 40.909 24.63 0.00 45.76 3.10
1874 5215 5.817816 GCTAGCTATGTGAACACTGGTTATT 59.182 40.000 7.70 0.00 37.36 1.40
1919 5263 3.571571 CATGATCGCCCATGCATAAAAG 58.428 45.455 0.00 0.00 37.68 2.27
1952 5296 6.750148 ACACAACAAAAGTTAGGAAAACACA 58.250 32.000 0.00 0.00 0.00 3.72
1955 5299 8.803799 CACATACACAACAAAAGTTAGGAAAAC 58.196 33.333 0.00 0.00 0.00 2.43
2065 5410 2.171003 CTTCCCATTGGTTTGTCCTCC 58.829 52.381 1.20 0.00 37.07 4.30
2103 5448 2.212794 ATCCTCCTCCTCGTCGTGGT 62.213 60.000 12.76 0.00 0.00 4.16
2122 5467 4.966965 GAAGACATCTTCTCCGTAGTCA 57.033 45.455 13.35 0.00 46.59 3.41
2176 5527 8.156820 TCTGAAGTGAAATTAATCAACTCTGGA 58.843 33.333 0.00 0.00 0.00 3.86
2211 5562 7.439381 TGCTTTATATTTAGGAACGTAGGGAG 58.561 38.462 0.00 0.00 0.00 4.30
2213 5564 8.441312 TTTGCTTTATATTTAGGAACGTAGGG 57.559 34.615 0.00 0.00 0.00 3.53
2231 5582 8.800332 AGAGTGTAGATTCATTCATTTTGCTTT 58.200 29.630 0.00 0.00 0.00 3.51
2233 5584 7.934855 AGAGTGTAGATTCATTCATTTTGCT 57.065 32.000 0.00 0.00 0.00 3.91
2239 5590 9.737427 CGTAGTTTAGAGTGTAGATTCATTCAT 57.263 33.333 0.00 0.00 0.00 2.57
2240 5591 8.737175 ACGTAGTTTAGAGTGTAGATTCATTCA 58.263 33.333 0.00 0.00 37.78 2.57
2263 5614 9.381033 GGACTACATACAGATGTATATAGACGT 57.619 37.037 19.96 9.73 45.42 4.34
2264 5615 9.379791 TGGACTACATACAGATGTATATAGACG 57.620 37.037 19.96 5.19 45.42 4.18
2296 5647 9.810545 GCAAAGTAGTAGTCATTCTAGAGATTT 57.189 33.333 0.00 0.00 0.00 2.17
2297 5648 8.972127 TGCAAAGTAGTAGTCATTCTAGAGATT 58.028 33.333 0.00 0.00 0.00 2.40
2298 5649 8.410141 GTGCAAAGTAGTAGTCATTCTAGAGAT 58.590 37.037 0.00 0.00 0.00 2.75
2299 5650 7.612244 AGTGCAAAGTAGTAGTCATTCTAGAGA 59.388 37.037 0.00 0.00 0.00 3.10
2300 5651 7.767261 AGTGCAAAGTAGTAGTCATTCTAGAG 58.233 38.462 0.00 0.00 0.00 2.43
2301 5652 7.393515 TGAGTGCAAAGTAGTAGTCATTCTAGA 59.606 37.037 0.00 0.00 30.18 2.43
2302 5653 7.539436 TGAGTGCAAAGTAGTAGTCATTCTAG 58.461 38.462 0.00 0.00 30.18 2.43
2303 5654 7.462571 TGAGTGCAAAGTAGTAGTCATTCTA 57.537 36.000 0.00 0.00 30.18 2.10
2304 5655 6.346477 TGAGTGCAAAGTAGTAGTCATTCT 57.654 37.500 0.00 0.00 30.18 2.40
2307 5658 5.871524 CACATGAGTGCAAAGTAGTAGTCAT 59.128 40.000 0.00 0.00 42.54 3.06
2327 5678 3.650281 TGCATGGGTCTGATTACACAT 57.350 42.857 0.00 0.00 44.37 3.21
2331 5682 2.292569 CTGCATGCATGGGTCTGATTAC 59.707 50.000 27.34 7.66 0.00 1.89
2332 5683 2.578786 CTGCATGCATGGGTCTGATTA 58.421 47.619 27.34 0.00 0.00 1.75
2356 5707 2.739913 TCCGCAAAGAAACGATTCGATT 59.260 40.909 13.95 7.23 40.63 3.34
2359 5710 1.782023 CGTCCGCAAAGAAACGATTCG 60.782 52.381 4.14 4.14 40.63 3.34
2363 5714 1.269206 ACTACGTCCGCAAAGAAACGA 60.269 47.619 0.00 0.00 38.44 3.85
2376 5727 9.903682 TCCATGCTTATTATTAAGTACTACGTC 57.096 33.333 0.00 0.00 37.68 4.34
2459 5815 1.953559 TCTTGACCTTGTGTGTCAGC 58.046 50.000 0.00 0.00 43.14 4.26
2547 5904 7.166167 TGAAGGTCTTTAGGGTTAACTGATTC 58.834 38.462 5.42 0.00 0.00 2.52
2550 5907 6.503560 TTGAAGGTCTTTAGGGTTAACTGA 57.496 37.500 5.42 0.00 0.00 3.41
2556 5913 5.701224 TGATGTTTGAAGGTCTTTAGGGTT 58.299 37.500 0.00 0.00 0.00 4.11
2561 5918 7.639113 AACTGTTGATGTTTGAAGGTCTTTA 57.361 32.000 0.00 0.00 0.00 1.85
2567 5924 6.867662 ACTCTAACTGTTGATGTTTGAAGG 57.132 37.500 2.69 0.00 31.30 3.46
2570 5927 7.870954 ACGATAACTCTAACTGTTGATGTTTGA 59.129 33.333 2.69 0.00 0.00 2.69
2574 5931 5.577164 GCACGATAACTCTAACTGTTGATGT 59.423 40.000 2.69 0.00 0.00 3.06
2575 5932 5.005779 GGCACGATAACTCTAACTGTTGATG 59.994 44.000 2.69 0.00 0.00 3.07
2650 6007 3.664107 ACAGCGTCGATGGCATTATAAT 58.336 40.909 15.82 0.00 0.00 1.28
2651 6008 3.106242 ACAGCGTCGATGGCATTATAA 57.894 42.857 15.82 0.00 0.00 0.98
2652 6009 2.812358 ACAGCGTCGATGGCATTATA 57.188 45.000 15.82 0.00 0.00 0.98
2653 6010 2.812358 TACAGCGTCGATGGCATTAT 57.188 45.000 15.82 0.00 0.00 1.28
2656 6013 1.202521 TCATTACAGCGTCGATGGCAT 60.203 47.619 15.82 0.00 0.00 4.40
2688 6045 3.061073 CGTTCAACACGTCGTTCAACATA 60.061 43.478 14.27 0.00 38.41 2.29
2747 6104 1.827789 TTCAGTGCAACACCCTGGC 60.828 57.895 0.00 0.00 41.43 4.85
2768 6125 1.597027 CTTGGCTTGTCGACCCGTT 60.597 57.895 14.12 0.00 0.00 4.44
2772 6129 2.151202 TCAAATCTTGGCTTGTCGACC 58.849 47.619 14.12 0.00 0.00 4.79
2780 6137 3.083122 ACAGCAGATCAAATCTTGGCT 57.917 42.857 0.00 0.00 38.68 4.75
2829 6187 5.361571 GGAAGGAAAGAGGGAGTAAGACTAG 59.638 48.000 0.00 0.00 0.00 2.57
2950 6308 4.469586 TGCAACATCTAGTATCCCACAGAA 59.530 41.667 0.00 0.00 0.00 3.02
2980 6338 8.547967 TTTGCTTCACTTCACTAATTAGTAGG 57.452 34.615 17.62 12.44 34.13 3.18
2981 6339 9.209175 ACTTTGCTTCACTTCACTAATTAGTAG 57.791 33.333 17.62 14.50 34.13 2.57
2983 6341 9.555727 TTACTTTGCTTCACTTCACTAATTAGT 57.444 29.630 12.50 12.50 36.90 2.24
2986 6344 9.516314 GTTTTACTTTGCTTCACTTCACTAATT 57.484 29.630 0.00 0.00 0.00 1.40
2987 6345 8.135529 GGTTTTACTTTGCTTCACTTCACTAAT 58.864 33.333 0.00 0.00 0.00 1.73
2988 6346 7.338449 AGGTTTTACTTTGCTTCACTTCACTAA 59.662 33.333 0.00 0.00 0.00 2.24
2989 6347 6.826741 AGGTTTTACTTTGCTTCACTTCACTA 59.173 34.615 0.00 0.00 0.00 2.74
2990 6348 5.652452 AGGTTTTACTTTGCTTCACTTCACT 59.348 36.000 0.00 0.00 0.00 3.41
2991 6349 5.891451 AGGTTTTACTTTGCTTCACTTCAC 58.109 37.500 0.00 0.00 0.00 3.18
2992 6350 5.650266 TGAGGTTTTACTTTGCTTCACTTCA 59.350 36.000 0.00 0.00 0.00 3.02
3002 6360 5.186996 AGTGCACATGAGGTTTTACTTTG 57.813 39.130 21.04 0.00 0.00 2.77
3043 6401 4.686972 GATCTTGAGATCGACCACATTGA 58.313 43.478 5.32 0.00 41.15 2.57
3132 6490 0.108615 CCGCTTCTCATGTTCCGAGT 60.109 55.000 0.00 0.00 0.00 4.18
3304 6663 0.877213 CTTTGCCAAAGGTGCACAGC 60.877 55.000 20.43 12.98 38.72 4.40
3364 6723 8.712285 TTTTTACCAGATACACTATGTACTGC 57.288 34.615 0.00 0.00 35.42 4.40
3368 6727 9.621629 CCCAATTTTTACCAGATACACTATGTA 57.378 33.333 0.00 0.00 37.24 2.29
3369 6728 8.333235 TCCCAATTTTTACCAGATACACTATGT 58.667 33.333 0.00 0.00 0.00 2.29
3370 6729 8.746052 TCCCAATTTTTACCAGATACACTATG 57.254 34.615 0.00 0.00 0.00 2.23
3371 6730 9.762381 TTTCCCAATTTTTACCAGATACACTAT 57.238 29.630 0.00 0.00 0.00 2.12
3372 6731 9.589461 TTTTCCCAATTTTTACCAGATACACTA 57.411 29.630 0.00 0.00 0.00 2.74
3374 6733 9.150348 CATTTTCCCAATTTTTACCAGATACAC 57.850 33.333 0.00 0.00 0.00 2.90
3375 6734 7.821846 GCATTTTCCCAATTTTTACCAGATACA 59.178 33.333 0.00 0.00 0.00 2.29
3376 6735 7.279981 GGCATTTTCCCAATTTTTACCAGATAC 59.720 37.037 0.00 0.00 0.00 2.24
3377 6736 7.334858 GGCATTTTCCCAATTTTTACCAGATA 58.665 34.615 0.00 0.00 0.00 1.98
3378 6737 6.179756 GGCATTTTCCCAATTTTTACCAGAT 58.820 36.000 0.00 0.00 0.00 2.90
3380 6739 4.699735 GGGCATTTTCCCAATTTTTACCAG 59.300 41.667 0.00 0.00 45.82 4.00
3381 6740 4.657013 GGGCATTTTCCCAATTTTTACCA 58.343 39.130 0.00 0.00 45.82 3.25


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

AutoCloner maintained by Alex Coulton.