Multiple sequence alignment - TraesCS4A01G131000

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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 TraesCS4A01G131000 chr4A 100.000 3743 0 0 1 3743 174158495 174154753 0.000000e+00 6913.0
1 TraesCS4A01G131000 chr4D 92.531 3267 132 35 524 3725 304689710 304692929 0.000000e+00 4578.0
2 TraesCS4A01G131000 chr4D 90.451 377 24 8 1 374 304689292 304689659 1.560000e-133 486.0
3 TraesCS4A01G131000 chr4B 90.386 3079 118 51 517 3511 380652967 380655951 0.000000e+00 3882.0
4 TraesCS4A01G131000 chr4B 93.067 375 22 4 1 373 380651127 380651499 2.540000e-151 545.0
5 TraesCS4A01G131000 chr4B 97.021 235 7 0 3509 3743 380656064 380656298 2.710000e-106 396.0
6 TraesCS4A01G131000 chr2B 86.364 308 35 5 1324 1626 85177666 85177361 2.790000e-86 329.0
7 TraesCS4A01G131000 chr2B 91.724 145 12 0 1024 1168 85177910 85177766 6.340000e-48 202.0
8 TraesCS4A01G131000 chr2B 89.655 145 15 0 1024 1168 85074018 85074162 6.380000e-43 185.0
9 TraesCS4A01G131000 chr2A 86.557 305 34 5 1324 1623 54882626 54882928 2.790000e-86 329.0
10 TraesCS4A01G131000 chr2A 85.809 303 40 3 1324 1623 54955234 54954932 6.030000e-83 318.0
11 TraesCS4A01G131000 chr2A 90.604 149 14 0 1024 1172 54882382 54882530 8.200000e-47 198.0
12 TraesCS4A01G131000 chr2A 89.262 149 16 0 1024 1172 54955478 54955330 1.780000e-43 187.0
13 TraesCS4A01G131000 chr2D 86.039 308 36 5 1324 1626 54487733 54487428 1.300000e-84 324.0
14 TraesCS4A01G131000 chr2D 90.604 149 14 0 1024 1172 54487979 54487831 8.200000e-47 198.0
15 TraesCS4A01G131000 chr2D 90.345 145 14 0 1024 1168 54317524 54317668 1.370000e-44 191.0
16 TraesCS4A01G131000 chr2D 83.217 143 20 4 1024 1164 175331280 175331420 1.090000e-25 128.0
17 TraesCS4A01G131000 chr2D 84.946 93 11 1 2143 2235 54318594 54318683 1.430000e-14 91.6
18 TraesCS4A01G131000 chr1D 95.238 42 2 0 2148 2189 359665073 359665032 2.410000e-07 67.6
19 TraesCS4A01G131000 chr1A 95.238 42 2 0 2148 2189 459187451 459187410 2.410000e-07 67.6


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 TraesCS4A01G131000 chr4A 174154753 174158495 3742 True 6913.000000 6913 100.000000 1 3743 1 chr4A.!!$R1 3742
1 TraesCS4A01G131000 chr4D 304689292 304692929 3637 False 2532.000000 4578 91.491000 1 3725 2 chr4D.!!$F1 3724
2 TraesCS4A01G131000 chr4B 380651127 380656298 5171 False 1607.666667 3882 93.491333 1 3743 3 chr4B.!!$F1 3742
3 TraesCS4A01G131000 chr2B 85177361 85177910 549 True 265.500000 329 89.044000 1024 1626 2 chr2B.!!$R1 602
4 TraesCS4A01G131000 chr2A 54882382 54882928 546 False 263.500000 329 88.580500 1024 1623 2 chr2A.!!$F1 599
5 TraesCS4A01G131000 chr2A 54954932 54955478 546 True 252.500000 318 87.535500 1024 1623 2 chr2A.!!$R1 599
6 TraesCS4A01G131000 chr2D 54487428 54487979 551 True 261.000000 324 88.321500 1024 1626 2 chr2D.!!$R1 602

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
744 2147 0.035458 CGAAACCACAGAGAAGCCCT 59.965 55.0 0.00 0.0 0.0 5.19 F
944 2372 0.037232 GCCTGGTTAGCAGTCGAAGT 60.037 55.0 10.62 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2508 4008 0.533755 CTGACGAATCCATCTGCCCC 60.534 60.0 0.0 0.0 0.0 5.80 R
2928 4428 0.109458 TCGATACACACACCTGACGC 60.109 55.0 0.0 0.0 0.0 5.19 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
21 22 4.008539 GCACAAGAATAGTAGCAAGCAC 57.991 45.455 0.00 0.00 0.00 4.40
72 74 2.238942 TGAAGCTGCATATGGTACCG 57.761 50.000 7.57 0.00 0.00 4.02
94 96 3.550030 GCTACGCTTTCTTTCTTTTGCCA 60.550 43.478 0.00 0.00 0.00 4.92
137 140 7.412853 GTCCAATTTCTTGTCTGTAGCATATG 58.587 38.462 0.00 0.00 0.00 1.78
151 154 3.484407 AGCATATGCCTTTCTTAGCCAG 58.516 45.455 23.96 0.00 43.38 4.85
152 155 3.137176 AGCATATGCCTTTCTTAGCCAGA 59.863 43.478 23.96 0.00 43.38 3.86
156 159 8.720674 AGCATATGCCTTTCTTAGCCAGAAAAA 61.721 37.037 23.96 1.06 44.07 1.94
182 185 4.586841 CCAAACAAACAAATCCTACCCTCA 59.413 41.667 0.00 0.00 0.00 3.86
183 186 5.245977 CCAAACAAACAAATCCTACCCTCAT 59.754 40.000 0.00 0.00 0.00 2.90
247 250 0.902531 GCCTTGCTACTAGACCCACA 59.097 55.000 0.00 0.00 0.00 4.17
280 283 8.034215 TCAACATATTGCATACCTTCCTTTTTG 58.966 33.333 0.00 0.00 35.63 2.44
285 288 7.775053 ATTGCATACCTTCCTTTTTGTTCTA 57.225 32.000 0.00 0.00 0.00 2.10
324 334 5.467063 GCTGAAGTTGCCTATATGTTAGTCC 59.533 44.000 0.00 0.00 0.00 3.85
325 335 5.597806 TGAAGTTGCCTATATGTTAGTCCG 58.402 41.667 0.00 0.00 0.00 4.79
326 336 4.602340 AGTTGCCTATATGTTAGTCCGG 57.398 45.455 0.00 0.00 0.00 5.14
327 337 4.220724 AGTTGCCTATATGTTAGTCCGGA 58.779 43.478 0.00 0.00 0.00 5.14
328 338 4.281182 AGTTGCCTATATGTTAGTCCGGAG 59.719 45.833 3.06 0.00 0.00 4.63
329 339 3.840991 TGCCTATATGTTAGTCCGGAGT 58.159 45.455 17.68 17.68 0.00 3.85
330 340 3.825014 TGCCTATATGTTAGTCCGGAGTC 59.175 47.826 16.99 2.63 0.00 3.36
338 348 3.008813 TGTTAGTCCGGAGTCTCTACACT 59.991 47.826 16.99 3.19 0.00 3.55
356 366 2.937149 CACTCTGACTCATGCATCCTTG 59.063 50.000 0.00 0.00 0.00 3.61
358 368 1.022735 CTGACTCATGCATCCTTGGC 58.977 55.000 0.00 0.00 0.00 4.52
359 369 0.328926 TGACTCATGCATCCTTGGCA 59.671 50.000 0.00 0.00 46.66 4.92
382 392 5.545063 AAAAACCCAAGGAACGATTCATT 57.455 34.783 0.00 0.00 33.36 2.57
383 393 5.545063 AAAACCCAAGGAACGATTCATTT 57.455 34.783 0.00 0.00 30.22 2.32
384 394 6.658188 AAAACCCAAGGAACGATTCATTTA 57.342 33.333 0.00 0.00 30.22 1.40
385 395 6.850752 AAACCCAAGGAACGATTCATTTAT 57.149 33.333 0.00 0.00 30.22 1.40
386 396 5.835113 ACCCAAGGAACGATTCATTTATG 57.165 39.130 0.00 0.00 30.22 1.90
387 397 5.261216 ACCCAAGGAACGATTCATTTATGT 58.739 37.500 0.00 0.00 30.22 2.29
388 398 5.357032 ACCCAAGGAACGATTCATTTATGTC 59.643 40.000 0.00 0.00 30.22 3.06
392 402 7.812191 CCAAGGAACGATTCATTTATGTCAAAA 59.188 33.333 0.00 0.00 30.22 2.44
446 456 5.221048 GGCTGAATGAATATAAGCCGTGTTT 60.221 40.000 0.00 0.00 43.64 2.83
482 1874 8.027771 ACTATATAAGCCGTGTTATTACTCTGC 58.972 37.037 0.00 0.00 0.00 4.26
488 1880 4.708601 CCGTGTTATTACTCTGCAACAAC 58.291 43.478 0.00 0.00 33.04 3.32
489 1881 4.382831 CGTGTTATTACTCTGCAACAACG 58.617 43.478 0.00 0.00 33.04 4.10
490 1882 4.665645 CGTGTTATTACTCTGCAACAACGG 60.666 45.833 0.00 0.00 33.04 4.44
491 1883 4.212636 GTGTTATTACTCTGCAACAACGGT 59.787 41.667 0.00 0.00 33.04 4.83
492 1884 4.212425 TGTTATTACTCTGCAACAACGGTG 59.788 41.667 0.00 0.00 0.00 4.94
493 1885 2.319136 TTACTCTGCAACAACGGTGT 57.681 45.000 0.00 0.00 40.75 4.16
494 1886 1.577468 TACTCTGCAACAACGGTGTG 58.423 50.000 6.99 2.32 38.27 3.82
495 1887 1.095228 ACTCTGCAACAACGGTGTGG 61.095 55.000 6.99 4.71 38.27 4.17
496 1888 1.785041 CTCTGCAACAACGGTGTGGG 61.785 60.000 6.99 3.58 38.27 4.61
497 1889 1.821759 CTGCAACAACGGTGTGGGA 60.822 57.895 6.99 3.69 38.27 4.37
498 1890 1.152860 TGCAACAACGGTGTGGGAT 60.153 52.632 6.99 0.00 38.27 3.85
499 1891 1.169661 TGCAACAACGGTGTGGGATC 61.170 55.000 6.99 0.00 38.27 3.36
500 1892 1.862602 GCAACAACGGTGTGGGATCC 61.863 60.000 6.99 1.92 38.27 3.36
507 1899 3.644861 GGTGTGGGATCCGAAAACT 57.355 52.632 5.45 0.00 0.00 2.66
508 1900 1.905637 GGTGTGGGATCCGAAAACTT 58.094 50.000 5.45 0.00 0.00 2.66
509 1901 1.810755 GGTGTGGGATCCGAAAACTTC 59.189 52.381 5.45 0.00 0.00 3.01
510 1902 2.500229 GTGTGGGATCCGAAAACTTCA 58.500 47.619 5.45 0.00 0.00 3.02
511 1903 2.225727 GTGTGGGATCCGAAAACTTCAC 59.774 50.000 5.45 6.13 0.00 3.18
512 1904 2.158740 TGTGGGATCCGAAAACTTCACA 60.159 45.455 5.45 8.78 0.00 3.58
513 1905 2.882137 GTGGGATCCGAAAACTTCACAA 59.118 45.455 5.45 0.00 0.00 3.33
514 1906 3.316868 GTGGGATCCGAAAACTTCACAAA 59.683 43.478 5.45 0.00 0.00 2.83
515 1907 3.954904 TGGGATCCGAAAACTTCACAAAA 59.045 39.130 5.45 0.00 0.00 2.44
516 1908 4.402793 TGGGATCCGAAAACTTCACAAAAA 59.597 37.500 5.45 0.00 0.00 1.94
584 1987 1.453745 GGCCCAAATCCATCGCTCA 60.454 57.895 0.00 0.00 0.00 4.26
648 2051 4.818863 TGGCGGCCCATGTCCATG 62.819 66.667 17.97 0.14 35.79 3.66
712 2115 0.793861 CAACGATAACCACACACCCG 59.206 55.000 0.00 0.00 0.00 5.28
713 2116 0.320946 AACGATAACCACACACCCGG 60.321 55.000 0.00 0.00 0.00 5.73
714 2117 2.104253 CGATAACCACACACCCGGC 61.104 63.158 0.00 0.00 0.00 6.13
715 2118 1.747745 GATAACCACACACCCGGCC 60.748 63.158 0.00 0.00 0.00 6.13
742 2145 1.149148 GACGAAACCACAGAGAAGCC 58.851 55.000 0.00 0.00 0.00 4.35
743 2146 0.250338 ACGAAACCACAGAGAAGCCC 60.250 55.000 0.00 0.00 0.00 5.19
744 2147 0.035458 CGAAACCACAGAGAAGCCCT 59.965 55.000 0.00 0.00 0.00 5.19
745 2148 1.814793 GAAACCACAGAGAAGCCCTC 58.185 55.000 0.00 0.00 42.28 4.30
760 2163 2.285180 CTCCCTCCCTCCCTCCTG 59.715 72.222 0.00 0.00 0.00 3.86
853 2264 1.340248 TCGTCTCCAAAAGTTCGAGCT 59.660 47.619 0.00 0.00 32.34 4.09
926 2354 3.118445 AGCTACCAGATCTTCTTCCAAGC 60.118 47.826 0.00 0.00 0.00 4.01
942 2370 0.685097 AAGCCTGGTTAGCAGTCGAA 59.315 50.000 10.62 0.00 0.00 3.71
943 2371 0.247736 AGCCTGGTTAGCAGTCGAAG 59.752 55.000 10.62 0.00 0.00 3.79
944 2372 0.037232 GCCTGGTTAGCAGTCGAAGT 60.037 55.000 10.62 0.00 0.00 3.01
945 2373 1.608283 GCCTGGTTAGCAGTCGAAGTT 60.608 52.381 10.62 0.00 0.00 2.66
946 2374 2.353406 GCCTGGTTAGCAGTCGAAGTTA 60.353 50.000 10.62 0.00 0.00 2.24
947 2375 3.679083 GCCTGGTTAGCAGTCGAAGTTAT 60.679 47.826 10.62 0.00 0.00 1.89
948 2376 4.113354 CCTGGTTAGCAGTCGAAGTTATC 58.887 47.826 10.62 0.00 0.00 1.75
949 2377 4.142138 CCTGGTTAGCAGTCGAAGTTATCT 60.142 45.833 10.62 0.00 0.00 1.98
1200 2672 4.097286 TGCACCAACAGATCATGATTCATG 59.903 41.667 18.71 18.71 42.60 3.07
1214 2694 3.506067 TGATTCATGCATGCTGATGATCC 59.494 43.478 22.25 14.04 0.00 3.36
1246 2726 1.639298 CCCACTTGCGCTAGCTTCAC 61.639 60.000 18.90 0.00 45.42 3.18
1266 2746 6.951062 TCACTCTCATCTCAATAATCGTCT 57.049 37.500 0.00 0.00 0.00 4.18
1280 2760 9.653287 TCAATAATCGTCTGTTATTTCTCTTGT 57.347 29.630 0.00 0.00 31.28 3.16
1284 2764 8.608844 AATCGTCTGTTATTTCTCTTGTTTCT 57.391 30.769 0.00 0.00 0.00 2.52
1285 2765 8.608844 ATCGTCTGTTATTTCTCTTGTTTCTT 57.391 30.769 0.00 0.00 0.00 2.52
1286 2766 8.433421 TCGTCTGTTATTTCTCTTGTTTCTTT 57.567 30.769 0.00 0.00 0.00 2.52
1287 2767 9.537192 TCGTCTGTTATTTCTCTTGTTTCTTTA 57.463 29.630 0.00 0.00 0.00 1.85
1296 2776 8.956533 TTTCTCTTGTTTCTTTAATTTTGGGG 57.043 30.769 0.00 0.00 0.00 4.96
1297 2777 7.061566 TCTCTTGTTTCTTTAATTTTGGGGG 57.938 36.000 0.00 0.00 0.00 5.40
1298 2778 6.613679 TCTCTTGTTTCTTTAATTTTGGGGGT 59.386 34.615 0.00 0.00 0.00 4.95
1299 2779 7.126573 TCTCTTGTTTCTTTAATTTTGGGGGTT 59.873 33.333 0.00 0.00 0.00 4.11
1300 2780 8.320338 TCTTGTTTCTTTAATTTTGGGGGTTA 57.680 30.769 0.00 0.00 0.00 2.85
1418 2898 1.899437 CGGGCTCTGGCTACTGGAAA 61.899 60.000 0.00 0.00 38.73 3.13
1553 3033 0.809636 TCATGCACGAATACCGCCTG 60.810 55.000 0.00 0.00 43.32 4.85
1707 3190 4.658063 TGAACACCCAAAACCCTAGTATG 58.342 43.478 0.00 0.00 0.00 2.39
1719 3202 9.117183 CAAAACCCTAGTATGGAGTATAAAACC 57.883 37.037 0.00 0.00 0.00 3.27
1764 3249 3.067106 GTCTGTCAATTCGTGTCATGGT 58.933 45.455 0.00 0.00 0.00 3.55
1768 3253 4.242475 TGTCAATTCGTGTCATGGTAGTC 58.758 43.478 0.00 0.00 0.00 2.59
1829 3314 2.859806 GCACTTGCACAGCGATTTTTCT 60.860 45.455 0.00 0.00 41.59 2.52
1837 3322 0.681243 AGCGATTTTTCTGGGAGGGC 60.681 55.000 0.00 0.00 0.00 5.19
1860 3345 2.431942 GGTTCGTGTCGTCGGCAT 60.432 61.111 1.39 0.00 0.00 4.40
1866 3351 1.080772 GTGTCGTCGGCATGTCAGA 60.081 57.895 1.39 0.00 0.00 3.27
1901 3386 2.697147 ATCGGGTTGTGCAGTGGCTT 62.697 55.000 0.00 0.00 41.91 4.35
1904 3389 2.028043 GTTGTGCAGTGGCTTGCC 59.972 61.111 4.43 4.43 43.43 4.52
1906 3391 2.491897 TTGTGCAGTGGCTTGCCAG 61.492 57.895 15.31 5.56 43.43 4.85
2049 3534 3.122948 ACGCGTGTTAATGACTGATTCAC 59.877 43.478 12.93 0.00 36.92 3.18
2060 3545 0.449388 CTGATTCACCTTTCGCCTGC 59.551 55.000 0.00 0.00 0.00 4.85
2068 3553 1.167851 CCTTTCGCCTGCTTGATTGA 58.832 50.000 0.00 0.00 0.00 2.57
2198 3686 2.079925 CTACAAGAAGACCAGCCAAGC 58.920 52.381 0.00 0.00 0.00 4.01
2199 3687 0.183492 ACAAGAAGACCAGCCAAGCA 59.817 50.000 0.00 0.00 0.00 3.91
2370 3858 1.066858 CCCAAGATCCCGTCCATATCG 60.067 57.143 0.00 0.00 0.00 2.92
2388 3876 1.816835 TCGGAGTTGCTCAACGAGTAT 59.183 47.619 7.06 0.00 45.50 2.12
2494 3982 1.811965 TGAGCCAATTCCATGTGAACG 59.188 47.619 0.00 0.00 35.31 3.95
2543 4043 4.003788 AGCCTCAACGTCGGTGGG 62.004 66.667 11.00 6.85 0.00 4.61
2705 4205 2.358737 CACCTTGCAGGGGTCGTC 60.359 66.667 20.34 0.00 40.58 4.20
2709 4209 1.541310 CCTTGCAGGGGTCGTCACTA 61.541 60.000 7.05 0.00 0.00 2.74
2801 4301 6.672657 ACTATACTACTTGAACCCCATCAGTT 59.327 38.462 0.00 0.00 0.00 3.16
2847 4347 9.132521 GAACTGGTGATTTGAAGAACAATTATG 57.867 33.333 0.00 0.00 38.36 1.90
2860 4360 4.534647 ACAATTATGGGGGTCTATTGCA 57.465 40.909 0.00 0.00 31.15 4.08
2929 4429 6.866770 GGAAAAGGGATTGTACTTTTACTTGC 59.133 38.462 0.00 0.00 44.39 4.01
2930 4430 5.622770 AAGGGATTGTACTTTTACTTGCG 57.377 39.130 0.00 0.00 0.00 4.85
2931 4431 4.648651 AGGGATTGTACTTTTACTTGCGT 58.351 39.130 0.00 0.00 0.00 5.24
2932 4432 4.694037 AGGGATTGTACTTTTACTTGCGTC 59.306 41.667 0.00 0.00 0.00 5.19
2933 4433 4.453136 GGGATTGTACTTTTACTTGCGTCA 59.547 41.667 0.00 0.00 0.00 4.35
2934 4434 5.390567 GGGATTGTACTTTTACTTGCGTCAG 60.391 44.000 0.00 0.00 0.00 3.51
2943 4467 0.462375 ACTTGCGTCAGGTGTGTGTA 59.538 50.000 0.00 0.00 0.00 2.90
2952 4476 2.095415 TCAGGTGTGTGTATCGAACGAG 60.095 50.000 2.94 0.00 0.00 4.18
3132 4658 8.728088 ACAAAGATGTAAAACAGCGAAAATAG 57.272 30.769 0.00 0.00 39.90 1.73
3190 4724 8.665685 CATGTTTTACTATTGTACTCAAGGGTC 58.334 37.037 0.00 0.00 36.97 4.46
3196 4730 7.113658 ACTATTGTACTCAAGGGTCTGTATG 57.886 40.000 0.00 0.00 36.97 2.39
3227 4761 3.785486 TCAGCCATACACGAGAAGATTG 58.215 45.455 0.00 0.00 0.00 2.67
3234 4768 5.520288 CCATACACGAGAAGATTGTCGAATT 59.480 40.000 17.62 5.04 45.54 2.17
3278 4813 4.822026 AGGGACGAGAAAATCACAAGTAG 58.178 43.478 0.00 0.00 0.00 2.57
3357 4892 2.649331 ACACATAAAGGACGGACGAG 57.351 50.000 0.00 0.00 0.00 4.18
3708 5358 7.387397 CCAGAGGACAGCTCTAATTATTGATTC 59.613 40.741 0.00 0.00 0.00 2.52
3726 5376 3.443099 TTCACTGTAGCAGATCCATCG 57.557 47.619 2.91 0.00 35.18 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 7.636150 ATGAATTGTGCTTGCTACTATTCTT 57.364 32.000 19.93 15.45 39.42 2.52
14 15 6.554419 TGTCTTGTATATGAATTGTGCTTGC 58.446 36.000 0.00 0.00 0.00 4.01
151 154 5.356751 AGGATTTGTTTGTTTGGGCTTTTTC 59.643 36.000 0.00 0.00 0.00 2.29
152 155 5.260424 AGGATTTGTTTGTTTGGGCTTTTT 58.740 33.333 0.00 0.00 0.00 1.94
156 159 3.323691 GGTAGGATTTGTTTGTTTGGGCT 59.676 43.478 0.00 0.00 0.00 5.19
182 185 0.393808 ATGGCGCGGAAACAGGTTAT 60.394 50.000 8.83 0.00 0.00 1.89
183 186 1.003112 ATGGCGCGGAAACAGGTTA 60.003 52.632 8.83 0.00 0.00 2.85
247 250 9.369904 GAAGGTATGCAATATGTTGACAAATTT 57.630 29.630 6.35 0.00 37.53 1.82
280 283 7.291411 TCAGCTAGATTAACAGGGATAGAAC 57.709 40.000 0.00 0.00 0.00 3.01
285 288 6.352516 CAACTTCAGCTAGATTAACAGGGAT 58.647 40.000 0.00 0.00 0.00 3.85
324 334 2.933906 GAGTCAGAGTGTAGAGACTCCG 59.066 54.545 9.62 0.00 46.97 4.63
327 337 3.694072 GCATGAGTCAGAGTGTAGAGACT 59.306 47.826 0.00 0.00 43.50 3.24
328 338 3.441922 TGCATGAGTCAGAGTGTAGAGAC 59.558 47.826 0.00 0.00 0.00 3.36
329 339 3.690460 TGCATGAGTCAGAGTGTAGAGA 58.310 45.455 0.00 0.00 0.00 3.10
330 340 4.499526 GGATGCATGAGTCAGAGTGTAGAG 60.500 50.000 2.46 0.00 0.00 2.43
338 348 1.407851 GCCAAGGATGCATGAGTCAGA 60.408 52.381 2.46 0.00 0.00 3.27
422 432 3.815401 ACACGGCTTATATTCATTCAGCC 59.185 43.478 0.00 0.00 45.73 4.85
455 465 9.909644 CAGAGTAATAACACGGCTTATATAGTT 57.090 33.333 0.00 0.00 0.00 2.24
456 466 8.027771 GCAGAGTAATAACACGGCTTATATAGT 58.972 37.037 0.00 0.00 35.25 2.12
457 467 8.027189 TGCAGAGTAATAACACGGCTTATATAG 58.973 37.037 0.00 0.00 38.02 1.31
458 468 7.888424 TGCAGAGTAATAACACGGCTTATATA 58.112 34.615 0.00 0.00 38.02 0.86
459 469 6.755206 TGCAGAGTAATAACACGGCTTATAT 58.245 36.000 0.00 0.00 38.02 0.86
460 470 6.151663 TGCAGAGTAATAACACGGCTTATA 57.848 37.500 0.00 0.00 38.02 0.98
461 471 5.018539 TGCAGAGTAATAACACGGCTTAT 57.981 39.130 0.00 0.00 38.02 1.73
462 472 4.459390 TGCAGAGTAATAACACGGCTTA 57.541 40.909 0.00 0.00 38.02 3.09
464 474 3.000727 GTTGCAGAGTAATAACACGGCT 58.999 45.455 0.00 0.00 38.02 5.52
465 475 2.739913 TGTTGCAGAGTAATAACACGGC 59.260 45.455 0.00 0.00 37.76 5.68
468 478 4.212636 ACCGTTGTTGCAGAGTAATAACAC 59.787 41.667 7.82 0.00 33.25 3.32
471 1863 4.212425 CACACCGTTGTTGCAGAGTAATAA 59.788 41.667 0.00 0.00 31.66 1.40
473 1865 2.548057 CACACCGTTGTTGCAGAGTAAT 59.452 45.455 0.00 0.00 31.66 1.89
482 1874 1.573829 CGGATCCCACACCGTTGTTG 61.574 60.000 6.06 0.00 43.53 3.33
489 1881 1.810755 GAAGTTTTCGGATCCCACACC 59.189 52.381 6.06 0.00 0.00 4.16
490 1882 2.225727 GTGAAGTTTTCGGATCCCACAC 59.774 50.000 6.06 3.35 0.00 3.82
491 1883 2.158740 TGTGAAGTTTTCGGATCCCACA 60.159 45.455 6.06 9.04 0.00 4.17
492 1884 2.500229 TGTGAAGTTTTCGGATCCCAC 58.500 47.619 6.06 6.37 0.00 4.61
493 1885 2.940994 TGTGAAGTTTTCGGATCCCA 57.059 45.000 6.06 0.00 0.00 4.37
494 1886 4.577834 TTTTGTGAAGTTTTCGGATCCC 57.422 40.909 6.06 0.00 0.00 3.85
517 1909 0.955905 CGGAATCCCACACCGTTTTT 59.044 50.000 0.00 0.00 41.47 1.94
518 1910 2.636299 CGGAATCCCACACCGTTTT 58.364 52.632 0.00 0.00 41.47 2.43
519 1911 4.390048 CGGAATCCCACACCGTTT 57.610 55.556 0.00 0.00 41.47 3.60
610 2013 3.110178 CGTCGGCCGGTGAAACTC 61.110 66.667 27.83 5.02 36.74 3.01
643 2046 3.819652 CCGGGGATTGGGCATGGA 61.820 66.667 0.00 0.00 0.00 3.41
682 2085 6.898189 GTGTGGTTATCGTTGATTCGTTATTC 59.102 38.462 0.00 0.00 0.00 1.75
712 2115 4.024545 TTTCGTCGGGAAGGGGCC 62.025 66.667 0.00 0.00 35.70 5.80
713 2116 2.745100 GTTTCGTCGGGAAGGGGC 60.745 66.667 0.00 0.00 35.70 5.80
714 2117 2.046604 GGTTTCGTCGGGAAGGGG 60.047 66.667 0.00 0.00 35.70 4.79
715 2118 1.670083 GTGGTTTCGTCGGGAAGGG 60.670 63.158 0.00 0.00 35.70 3.95
718 2121 0.032952 CTCTGTGGTTTCGTCGGGAA 59.967 55.000 0.00 0.00 0.00 3.97
719 2122 0.824595 TCTCTGTGGTTTCGTCGGGA 60.825 55.000 0.00 0.00 0.00 5.14
720 2123 0.032952 TTCTCTGTGGTTTCGTCGGG 59.967 55.000 0.00 0.00 0.00 5.14
721 2124 1.419374 CTTCTCTGTGGTTTCGTCGG 58.581 55.000 0.00 0.00 0.00 4.79
722 2125 0.784778 GCTTCTCTGTGGTTTCGTCG 59.215 55.000 0.00 0.00 0.00 5.12
723 2126 1.149148 GGCTTCTCTGTGGTTTCGTC 58.851 55.000 0.00 0.00 0.00 4.20
724 2127 0.250338 GGGCTTCTCTGTGGTTTCGT 60.250 55.000 0.00 0.00 0.00 3.85
742 2145 3.039526 AGGAGGGAGGGAGGGAGG 61.040 72.222 0.00 0.00 0.00 4.30
743 2146 2.285180 CAGGAGGGAGGGAGGGAG 59.715 72.222 0.00 0.00 0.00 4.30
744 2147 3.368501 CCAGGAGGGAGGGAGGGA 61.369 72.222 0.00 0.00 40.01 4.20
853 2264 5.663106 AGCTTGTAGGTATGAGAAATGAGGA 59.337 40.000 0.00 0.00 0.00 3.71
926 2354 2.457366 AACTTCGACTGCTAACCAGG 57.543 50.000 0.00 0.00 46.14 4.45
1214 2694 3.861113 CGCAAGTGGGAATCAAATGAATG 59.139 43.478 0.00 0.00 0.00 2.67
1246 2726 9.689976 AATAACAGACGATTATTGAGATGAGAG 57.310 33.333 0.00 0.00 32.29 3.20
1286 2766 8.268605 GCTGGAATTAATTAACCCCCAAAATTA 58.731 33.333 0.00 0.00 0.00 1.40
1287 2767 7.116075 GCTGGAATTAATTAACCCCCAAAATT 58.884 34.615 0.00 0.00 0.00 1.82
1288 2768 6.353516 GGCTGGAATTAATTAACCCCCAAAAT 60.354 38.462 0.00 0.00 0.00 1.82
1289 2769 5.045505 GGCTGGAATTAATTAACCCCCAAAA 60.046 40.000 0.00 0.00 0.00 2.44
1290 2770 4.471747 GGCTGGAATTAATTAACCCCCAAA 59.528 41.667 0.00 0.00 0.00 3.28
1293 2773 3.648739 TGGCTGGAATTAATTAACCCCC 58.351 45.455 0.00 9.49 0.00 5.40
1294 2774 4.100963 CCTTGGCTGGAATTAATTAACCCC 59.899 45.833 0.00 11.40 0.00 4.95
1295 2775 4.442893 GCCTTGGCTGGAATTAATTAACCC 60.443 45.833 0.00 5.86 0.00 4.11
1296 2776 4.405680 AGCCTTGGCTGGAATTAATTAACC 59.594 41.667 13.99 0.00 0.00 2.85
1297 2777 5.598416 AGCCTTGGCTGGAATTAATTAAC 57.402 39.130 13.99 0.00 0.00 2.01
1298 2778 5.301805 GCTAGCCTTGGCTGGAATTAATTAA 59.698 40.000 25.72 0.00 0.00 1.40
1299 2779 4.827284 GCTAGCCTTGGCTGGAATTAATTA 59.173 41.667 25.72 1.68 0.00 1.40
1300 2780 3.638627 GCTAGCCTTGGCTGGAATTAATT 59.361 43.478 25.72 0.00 0.00 1.40
1308 2788 1.227380 CGTAGCTAGCCTTGGCTGG 60.227 63.158 23.03 20.87 41.69 4.85
1740 3223 4.869861 CCATGACACGAATTGACAGACATA 59.130 41.667 0.00 0.00 33.22 2.29
1741 3224 3.686241 CCATGACACGAATTGACAGACAT 59.314 43.478 0.00 0.00 33.22 3.06
1742 3225 3.066380 CCATGACACGAATTGACAGACA 58.934 45.455 0.00 0.00 33.22 3.41
1743 3226 3.067106 ACCATGACACGAATTGACAGAC 58.933 45.455 0.00 0.00 33.22 3.51
1744 3227 3.401033 ACCATGACACGAATTGACAGA 57.599 42.857 0.00 0.00 33.22 3.41
1745 3228 4.245660 ACTACCATGACACGAATTGACAG 58.754 43.478 0.00 0.00 33.22 3.51
1764 3249 2.813474 GTGCCACGCATGCGACTA 60.813 61.111 43.72 23.89 41.91 2.59
1860 3345 4.952071 TCCATTTTGGCAAAATCTGACA 57.048 36.364 29.98 12.91 43.31 3.58
1866 3351 3.008923 ACCCGATTCCATTTTGGCAAAAT 59.991 39.130 27.84 27.84 41.57 1.82
1901 3386 2.031012 CTCTTGCGTCCACTGGCA 59.969 61.111 0.00 0.00 37.39 4.92
1904 3389 2.675056 GCAGCTCTTGCGTCCACTG 61.675 63.158 0.00 0.00 44.09 3.66
1924 3409 1.726791 CGAGACACGCACATTAAAGCT 59.273 47.619 0.00 0.00 34.51 3.74
1925 3410 1.459592 ACGAGACACGCACATTAAAGC 59.540 47.619 0.00 0.00 46.94 3.51
1926 3411 3.788434 AACGAGACACGCACATTAAAG 57.212 42.857 0.00 0.00 46.94 1.85
1927 3412 5.654317 TTAAACGAGACACGCACATTAAA 57.346 34.783 0.00 0.00 46.94 1.52
1981 3466 1.852942 GGATCTATTGACTTCGCGCA 58.147 50.000 8.75 0.00 0.00 6.09
2049 3534 1.167851 TCAATCAAGCAGGCGAAAGG 58.832 50.000 0.00 0.00 0.00 3.11
2110 3595 4.214971 AGACGGATCGCACGTAGTATTAAT 59.785 41.667 0.00 0.00 45.68 1.40
2124 3609 3.849911 ACATATATGCCAAGACGGATCG 58.150 45.455 12.79 0.00 36.56 3.69
2258 3746 3.151710 TCGACATGGGGTAGCCGG 61.152 66.667 4.56 0.00 0.00 6.13
2261 3749 2.279517 CGCTCGACATGGGGTAGC 60.280 66.667 0.00 0.00 0.00 3.58
2370 3858 2.599082 CGAATACTCGTTGAGCAACTCC 59.401 50.000 11.16 0.00 40.33 3.85
2508 4008 0.533755 CTGACGAATCCATCTGCCCC 60.534 60.000 0.00 0.00 0.00 5.80
2788 4288 8.504005 CGTATATAATTCAAACTGATGGGGTTC 58.496 37.037 0.00 0.00 0.00 3.62
2801 4301 4.502171 TCGCCGGTCGTATATAATTCAA 57.498 40.909 16.00 0.00 39.67 2.69
2847 4347 2.736670 ATCTTGTGCAATAGACCCCC 57.263 50.000 1.43 0.00 0.00 5.40
2902 4402 9.292195 CAAGTAAAAGTACAATCCCTTTTCCTA 57.708 33.333 0.00 0.00 40.39 2.94
2906 4406 6.443792 CGCAAGTAAAAGTACAATCCCTTTT 58.556 36.000 0.00 0.00 42.07 2.27
2927 4427 0.388006 CGATACACACACCTGACGCA 60.388 55.000 0.00 0.00 0.00 5.24
2928 4428 0.109458 TCGATACACACACCTGACGC 60.109 55.000 0.00 0.00 0.00 5.19
2929 4429 1.983605 GTTCGATACACACACCTGACG 59.016 52.381 0.00 0.00 0.00 4.35
2930 4430 1.983605 CGTTCGATACACACACCTGAC 59.016 52.381 0.00 0.00 0.00 3.51
2931 4431 1.881324 TCGTTCGATACACACACCTGA 59.119 47.619 0.00 0.00 0.00 3.86
2932 4432 2.251040 CTCGTTCGATACACACACCTG 58.749 52.381 0.00 0.00 0.00 4.00
2933 4433 1.884579 ACTCGTTCGATACACACACCT 59.115 47.619 0.00 0.00 0.00 4.00
2934 4434 2.342910 ACTCGTTCGATACACACACC 57.657 50.000 0.00 0.00 0.00 4.16
2943 4467 2.220313 GGACCTAGCTACTCGTTCGAT 58.780 52.381 0.00 0.00 0.00 3.59
2952 4476 5.020132 AGTATGATCCATGGACCTAGCTAC 58.980 45.833 18.99 12.55 0.00 3.58
3278 4813 1.239347 GTTCTTGGAGCAGGTGTTCC 58.761 55.000 5.94 5.94 44.52 3.62
3357 4892 2.810767 GCCCGGGTTCCATATTCTTCTC 60.811 54.545 24.63 0.00 0.00 2.87
3497 5032 6.072728 CGGACAAGATTCTACATGGACAAAAA 60.073 38.462 0.00 0.00 0.00 1.94
3538 5188 3.700038 TGTTGATGTGCATGGCAATATCA 59.300 39.130 12.52 12.52 41.47 2.15
3539 5189 4.310357 TGTTGATGTGCATGGCAATATC 57.690 40.909 0.00 8.79 41.47 1.63
3616 5266 4.768968 CCATCCATTAATTGATCCCACTCC 59.231 45.833 0.00 0.00 0.00 3.85
3708 5358 2.099756 TGACGATGGATCTGCTACAGTG 59.900 50.000 0.00 0.00 32.61 3.66


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

AutoCloner maintained by Alex Coulton.