Multiple sequence alignment - TraesCS2D01G520300

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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 TraesCS2D01G520300 chr2D 100.000 2627 0 0 1 2627 609516782 609514156 0.000000e+00 4852.0
1 TraesCS2D01G520300 chr2A 87.606 2243 149 62 20 2187 742294571 742292383 0.000000e+00 2483.0
2 TraesCS2D01G520300 chr2A 87.179 429 32 9 2221 2627 742292384 742291957 1.420000e-127 466.0
3 TraesCS2D01G520300 chr2A 77.536 138 16 6 541 663 334112530 334112667 4.690000e-08 69.4
4 TraesCS2D01G520300 chr2B 91.179 1213 52 12 738 1921 744058707 744057521 0.000000e+00 1596.0
5 TraesCS2D01G520300 chr2B 89.163 406 35 5 22 426 744059205 744058808 5.050000e-137 497.0
6 TraesCS2D01G520300 chr2B 86.161 448 38 10 2201 2627 743922414 743921970 1.840000e-126 462.0
7 TraesCS2D01G520300 chr2B 84.594 357 30 9 2154 2488 744057392 744057039 5.420000e-87 331.0
8 TraesCS2D01G520300 chr2B 82.440 336 24 10 2201 2502 743926085 743925751 7.210000e-66 261.0
9 TraesCS2D01G520300 chr2B 86.547 223 20 5 1707 1921 743922862 743922642 1.220000e-58 237.0
10 TraesCS2D01G520300 chr2B 87.432 183 15 4 1707 1881 743926304 743926122 1.230000e-48 204.0
11 TraesCS2D01G520300 chr2B 80.645 124 18 3 544 661 799382781 799382904 1.000000e-14 91.6
12 TraesCS2D01G520300 chr7D 82.873 181 27 4 1022 1200 611135689 611135867 2.710000e-35 159.0
13 TraesCS2D01G520300 chr7D 80.645 186 28 8 1022 1203 91143766 91143585 1.270000e-28 137.0
14 TraesCS2D01G520300 chr7B 82.320 181 28 4 1022 1200 700184178 700184356 1.260000e-33 154.0
15 TraesCS2D01G520300 chr7B 85.385 130 17 2 1075 1203 43754557 43754429 1.640000e-27 134.0
16 TraesCS2D01G520300 chr7A 81.768 181 29 4 1022 1200 701149419 701149597 5.860000e-32 148.0
17 TraesCS2D01G520300 chr7A 81.421 183 26 8 1022 1200 93081906 93082084 2.730000e-30 143.0
18 TraesCS2D01G520300 chr3A 83.333 120 14 3 548 661 41236386 41236505 3.580000e-19 106.0
19 TraesCS2D01G520300 chr3A 76.978 139 17 5 540 663 327161319 327161181 6.070000e-07 65.8
20 TraesCS2D01G520300 chr1A 79.032 124 19 5 547 664 56922629 56922507 7.800000e-11 78.7
21 TraesCS2D01G520300 chr1A 77.536 138 16 5 541 663 79355123 79354986 4.690000e-08 69.4
22 TraesCS2D01G520300 chr1A 77.536 138 16 5 541 663 92253855 92253718 4.690000e-08 69.4
23 TraesCS2D01G520300 chr1A 77.536 138 16 5 541 663 164112003 164111866 4.690000e-08 69.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G520300 chr2D 609514156 609516782 2626 True 4852.0 4852 100.0000 1 2627 1 chr2D.!!$R1 2626
1 TraesCS2D01G520300 chr2A 742291957 742294571 2614 True 1474.5 2483 87.3925 20 2627 2 chr2A.!!$R1 2607
2 TraesCS2D01G520300 chr2B 744057039 744059205 2166 True 808.0 1596 88.3120 22 2488 3 chr2B.!!$R2 2466
3 TraesCS2D01G520300 chr2B 743921970 743926304 4334 True 291.0 462 85.6450 1707 2627 4 chr2B.!!$R1 920

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
776 797 0.517316 GTGCTGGCTTTAACAGTCCG 59.483 55.0 0.0 0.0 38.22 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1674 1713 0.032952 ACAAAGCAGCAGCCACAATG 59.967 50.0 0.0 0.0 43.56 2.82 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
103 104 2.490217 CCCCGTCGAGCACACTAG 59.510 66.667 0.00 0.00 0.00 2.57
112 113 2.093106 CGAGCACACTAGACCCTACTT 58.907 52.381 0.00 0.00 0.00 2.24
122 123 2.169330 AGACCCTACTTCCGTTGTCTC 58.831 52.381 0.00 0.00 0.00 3.36
136 138 4.214437 CGTTGTCTCAAAATGCAAGACTC 58.786 43.478 14.78 8.37 40.07 3.36
149 152 7.516198 AATGCAAGACTCTTTTGACACTATT 57.484 32.000 0.00 0.00 0.00 1.73
162 165 7.759489 TTTGACACTATTAGGCAACAAATCT 57.241 32.000 0.00 0.00 41.41 2.40
172 175 5.551760 AGGCAACAAATCTAACATTCTCG 57.448 39.130 0.00 0.00 41.41 4.04
176 179 6.305638 GGCAACAAATCTAACATTCTCGAAAC 59.694 38.462 0.00 0.00 0.00 2.78
225 228 4.223923 ACCCTTCAGGAGTGTTAATCTCAG 59.776 45.833 11.04 5.18 39.89 3.35
250 253 7.918033 AGTCGAATCAATGTTAGTCATGTCTAG 59.082 37.037 0.04 0.00 36.81 2.43
389 392 2.784347 GGTGAGCTAAAGAAAGGCTGT 58.216 47.619 0.00 0.00 36.37 4.40
411 414 2.483583 TGCGTGTTTTGAACCACATC 57.516 45.000 0.00 0.00 0.00 3.06
423 426 3.648067 TGAACCACATCAGTTCCTCTTCT 59.352 43.478 1.53 0.00 42.41 2.85
426 429 5.053978 ACCACATCAGTTCCTCTTCTTTT 57.946 39.130 0.00 0.00 0.00 2.27
430 433 7.175641 ACCACATCAGTTCCTCTTCTTTTAATG 59.824 37.037 0.00 0.00 0.00 1.90
431 434 7.362401 CCACATCAGTTCCTCTTCTTTTAATGG 60.362 40.741 0.00 0.00 0.00 3.16
433 436 7.391833 ACATCAGTTCCTCTTCTTTTAATGGAC 59.608 37.037 0.00 0.00 0.00 4.02
434 437 6.837312 TCAGTTCCTCTTCTTTTAATGGACA 58.163 36.000 0.00 0.00 0.00 4.02
435 438 7.287061 TCAGTTCCTCTTCTTTTAATGGACAA 58.713 34.615 0.00 0.00 0.00 3.18
436 439 7.944554 TCAGTTCCTCTTCTTTTAATGGACAAT 59.055 33.333 0.00 0.00 0.00 2.71
438 441 9.981460 AGTTCCTCTTCTTTTAATGGACAATAT 57.019 29.630 0.00 0.00 0.00 1.28
440 443 9.973661 TTCCTCTTCTTTTAATGGACAATATGA 57.026 29.630 0.00 0.00 0.00 2.15
441 444 9.396022 TCCTCTTCTTTTAATGGACAATATGAC 57.604 33.333 0.00 0.00 0.00 3.06
516 529 0.978146 CGGTGATGGTTCCTCCCTCT 60.978 60.000 0.00 0.00 33.02 3.69
526 539 2.879026 GTTCCTCCCTCTGTGTTTGAAC 59.121 50.000 0.00 0.00 0.00 3.18
540 553 0.828022 TTGAACTGGCCGACGGATAT 59.172 50.000 20.50 0.00 0.00 1.63
560 574 7.064371 CGGATATCGTTATATATACTCCCTCCG 59.936 44.444 11.38 11.38 0.00 4.63
563 577 5.431765 TCGTTATATATACTCCCTCCGTCC 58.568 45.833 0.00 0.00 0.00 4.79
564 578 4.272018 CGTTATATATACTCCCTCCGTCCG 59.728 50.000 0.00 0.00 0.00 4.79
576 590 2.268298 CTCCGTCCGGAAATAGTTGTG 58.732 52.381 5.23 0.00 44.66 3.33
594 608 5.653769 AGTTGTGGGAAAATGGATGTATCTG 59.346 40.000 0.00 0.00 0.00 2.90
595 609 5.191727 TGTGGGAAAATGGATGTATCTGT 57.808 39.130 0.00 0.00 0.00 3.41
598 612 7.353525 TGTGGGAAAATGGATGTATCTGTATT 58.646 34.615 0.00 0.00 0.00 1.89
599 613 7.838696 TGTGGGAAAATGGATGTATCTGTATTT 59.161 33.333 0.00 0.00 0.00 1.40
600 614 8.695456 GTGGGAAAATGGATGTATCTGTATTTT 58.305 33.333 0.00 0.00 32.84 1.82
601 615 9.928618 TGGGAAAATGGATGTATCTGTATTTTA 57.071 29.630 0.00 0.00 31.68 1.52
656 670 6.662414 TGACAATTATTTTAGGACAGAGCG 57.338 37.500 0.00 0.00 0.00 5.03
697 711 5.485209 AAAAAGATCGTTCTAGGGACTGT 57.515 39.130 0.00 0.00 41.52 3.55
762 783 2.617308 CCCATAATCTGAAGCTGTGCTG 59.383 50.000 0.00 0.00 39.62 4.41
776 797 0.517316 GTGCTGGCTTTAACAGTCCG 59.483 55.000 0.00 0.00 38.22 4.79
835 856 2.100584 TCACCATGTGTGTTGAAAAGCC 59.899 45.455 12.26 0.00 45.61 4.35
970 991 5.104193 TCCTCCTACTATAAACCTCACGACT 60.104 44.000 0.00 0.00 0.00 4.18
1474 1513 4.710695 CGCCAGGTACGACGTGCA 62.711 66.667 17.84 0.00 33.03 4.57
1634 1673 0.706433 AACCCCAACTGATCCATGCT 59.294 50.000 0.00 0.00 0.00 3.79
1668 1707 2.413796 GCAATTGTTCATGCATGGTGTG 59.586 45.455 25.97 15.60 42.12 3.82
1699 1753 1.507141 GGCTGCTGCTTTGTACGTGT 61.507 55.000 15.64 0.00 39.59 4.49
1705 1759 0.528901 TGCTTTGTACGTGTGCTCGT 60.529 50.000 0.00 4.75 45.97 4.18
1807 1869 0.602638 TTGCGCGGTCTGTGATTCTT 60.603 50.000 8.83 0.00 0.00 2.52
1809 1871 0.645868 GCGCGGTCTGTGATTCTTAC 59.354 55.000 8.83 0.00 0.00 2.34
1877 5404 5.585390 ACATTTCTTTGCACTCTGTTTCAG 58.415 37.500 0.00 0.00 0.00 3.02
1921 5448 5.547465 TGTTTCAGTCGTCATTCTTGGTAT 58.453 37.500 0.00 0.00 0.00 2.73
1923 5450 6.147164 TGTTTCAGTCGTCATTCTTGGTATTC 59.853 38.462 0.00 0.00 0.00 1.75
1924 5451 4.755411 TCAGTCGTCATTCTTGGTATTCC 58.245 43.478 0.00 0.00 0.00 3.01
1925 5452 4.221924 TCAGTCGTCATTCTTGGTATTCCA 59.778 41.667 0.00 0.00 42.66 3.53
1946 5475 4.502016 CAAGAATGCAGAGCAGAAGTAGA 58.498 43.478 0.00 0.00 43.65 2.59
1947 5476 4.815533 AGAATGCAGAGCAGAAGTAGAA 57.184 40.909 0.00 0.00 43.65 2.10
1948 5477 4.757594 AGAATGCAGAGCAGAAGTAGAAG 58.242 43.478 0.00 0.00 43.65 2.85
1950 5479 4.550076 ATGCAGAGCAGAAGTAGAAGTT 57.450 40.909 0.00 0.00 43.65 2.66
1951 5480 3.919216 TGCAGAGCAGAAGTAGAAGTTC 58.081 45.455 0.00 0.00 33.32 3.01
1952 5481 3.321968 TGCAGAGCAGAAGTAGAAGTTCA 59.678 43.478 5.50 0.00 33.32 3.18
1953 5482 3.677596 GCAGAGCAGAAGTAGAAGTTCAC 59.322 47.826 5.50 1.76 30.04 3.18
1954 5483 4.560513 GCAGAGCAGAAGTAGAAGTTCACT 60.561 45.833 5.50 4.08 30.04 3.41
1968 5497 3.463944 AGTTCACTTGTCCGAAATCGTT 58.536 40.909 1.79 0.00 37.74 3.85
1970 5499 1.529438 TCACTTGTCCGAAATCGTTGC 59.471 47.619 1.79 0.00 37.74 4.17
2001 5531 3.085533 TGGAAGTAGCTGACTGACTCTC 58.914 50.000 0.00 0.00 38.87 3.20
2020 5553 3.324846 TCTCTTGTAGTGGTTGCTCACAT 59.675 43.478 7.82 0.00 39.93 3.21
2030 5563 3.006940 GGTTGCTCACATCCGTAATTGA 58.993 45.455 0.00 0.00 0.00 2.57
2041 5574 4.201208 TCCGTAATTGACTCGATCGTAC 57.799 45.455 15.94 7.32 0.00 3.67
2063 5596 2.464865 GTTGGATCGATCAGGACGAAG 58.535 52.381 25.93 0.00 42.80 3.79
2107 5640 1.610522 ACATTGACAAAGAGCAGCACC 59.389 47.619 0.00 0.00 0.00 5.01
2149 5682 2.158813 AGAAACCAGAAACGAAGGAGCA 60.159 45.455 0.00 0.00 0.00 4.26
2171 5704 4.389890 AAACTGCTCAAAATGCAACAGA 57.610 36.364 0.00 0.00 40.13 3.41
2183 5716 2.513753 TGCAACAGATCGGGATTTTGT 58.486 42.857 0.00 0.00 0.00 2.83
2184 5717 2.890311 TGCAACAGATCGGGATTTTGTT 59.110 40.909 0.00 6.65 32.71 2.83
2185 5718 3.244976 GCAACAGATCGGGATTTTGTTG 58.755 45.455 22.35 22.35 42.72 3.33
2186 5719 3.836949 CAACAGATCGGGATTTTGTTGG 58.163 45.455 20.61 10.42 39.84 3.77
2187 5720 1.818674 ACAGATCGGGATTTTGTTGGC 59.181 47.619 0.00 0.00 0.00 4.52
2188 5721 1.818060 CAGATCGGGATTTTGTTGGCA 59.182 47.619 0.00 0.00 0.00 4.92
2189 5722 1.818674 AGATCGGGATTTTGTTGGCAC 59.181 47.619 0.00 0.00 0.00 5.01
2190 5723 0.894835 ATCGGGATTTTGTTGGCACC 59.105 50.000 0.00 0.00 0.00 5.01
2191 5724 0.468214 TCGGGATTTTGTTGGCACCA 60.468 50.000 0.00 0.00 0.00 4.17
2192 5725 0.607620 CGGGATTTTGTTGGCACCAT 59.392 50.000 0.00 0.00 0.00 3.55
2193 5726 1.821753 CGGGATTTTGTTGGCACCATA 59.178 47.619 0.00 0.00 0.00 2.74
2194 5727 2.430332 CGGGATTTTGTTGGCACCATAT 59.570 45.455 0.00 0.00 0.00 1.78
2195 5728 3.634448 CGGGATTTTGTTGGCACCATATA 59.366 43.478 0.00 0.00 0.00 0.86
2196 5729 4.098654 CGGGATTTTGTTGGCACCATATAA 59.901 41.667 0.00 0.00 0.00 0.98
2197 5730 5.221422 CGGGATTTTGTTGGCACCATATAAT 60.221 40.000 0.00 0.00 0.00 1.28
2198 5731 6.015856 CGGGATTTTGTTGGCACCATATAATA 60.016 38.462 0.00 0.00 0.00 0.98
2199 5732 7.309744 CGGGATTTTGTTGGCACCATATAATAT 60.310 37.037 0.00 0.00 0.00 1.28
2282 5847 2.141517 CAGTTCAGTGTTCTGCCTGAG 58.858 52.381 8.13 0.00 39.97 3.35
2287 5852 2.036475 TCAGTGTTCTGCCTGAGAGTTC 59.964 50.000 0.00 0.00 41.10 3.01
2290 5855 6.537012 CAGTGTTCTGCCTGAGAGTTCAGT 62.537 50.000 4.09 0.00 39.76 3.41
2305 5886 0.317160 TCAGTGTCCTGCTGGTAACG 59.683 55.000 9.73 6.33 38.66 3.18
2343 5932 4.234574 CACTGTTGTACGAGATAACTGCA 58.765 43.478 0.00 0.00 33.22 4.41
2479 6071 2.372264 TGTGTGTCGGATAGTAGGTCC 58.628 52.381 0.00 0.00 0.00 4.46
2508 6100 5.644644 ACGTTATTACAGTTAGGAACCTCG 58.355 41.667 0.00 0.00 0.00 4.63
2546 6138 7.279313 TGAACTGAAAAACTAACTGGACTACAC 59.721 37.037 0.00 0.00 0.00 2.90
2550 6142 7.925993 TGAAAAACTAACTGGACTACACAATG 58.074 34.615 0.00 0.00 0.00 2.82
2586 6178 5.959618 AAAAAGGAGCGCAGTATAAAACT 57.040 34.783 11.47 0.00 39.81 2.66
2618 6210 9.283768 GTGAAACATATGTTCATGATATACCCA 57.716 33.333 21.02 0.00 37.25 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 113 3.003275 GTCTTGCATTTTGAGACAACGGA 59.997 43.478 10.02 0.00 39.59 4.69
122 123 6.038356 AGTGTCAAAAGAGTCTTGCATTTTG 58.962 36.000 6.06 12.59 41.67 2.44
136 138 8.299570 AGATTTGTTGCCTAATAGTGTCAAAAG 58.700 33.333 0.00 0.00 0.00 2.27
149 152 6.403049 TCGAGAATGTTAGATTTGTTGCCTA 58.597 36.000 0.00 0.00 0.00 3.93
162 165 6.202188 GGTGAAACTCTGTTTCGAGAATGTTA 59.798 38.462 15.46 0.00 36.74 2.41
213 216 7.295952 ACATTGATTCGACTGAGATTAACAC 57.704 36.000 0.00 0.00 0.00 3.32
225 228 6.893958 AGACATGACTAACATTGATTCGAC 57.106 37.500 0.00 0.00 37.07 4.20
250 253 9.798994 ATTGCATGATTTCTCTCATTTCTAAAC 57.201 29.630 0.00 0.00 33.59 2.01
344 347 2.224917 ACCCTTGAAGAGACTCTCGAGT 60.225 50.000 13.13 0.00 45.84 4.18
389 392 4.036852 TGATGTGGTTCAAAACACGCAATA 59.963 37.500 6.45 0.00 40.39 1.90
411 414 7.510549 TTGTCCATTAAAAGAAGAGGAACTG 57.489 36.000 0.00 0.00 41.55 3.16
490 503 0.515564 GGAACCATCACCGACAAACG 59.484 55.000 0.00 0.00 42.18 3.60
516 529 1.433053 CGTCGGCCAGTTCAAACACA 61.433 55.000 2.24 0.00 0.00 3.72
540 553 5.431765 GGACGGAGGGAGTATATATAACGA 58.568 45.833 0.00 0.00 0.00 3.85
544 557 4.040047 TCCGGACGGAGGGAGTATATATA 58.960 47.826 9.76 0.00 39.76 0.86
545 558 2.848694 TCCGGACGGAGGGAGTATATAT 59.151 50.000 9.76 0.00 39.76 0.86
547 560 1.070604 TCCGGACGGAGGGAGTATAT 58.929 55.000 9.76 0.00 39.76 0.86
548 561 0.846015 TTCCGGACGGAGGGAGTATA 59.154 55.000 13.64 0.00 46.06 1.47
556 570 2.268298 CACAACTATTTCCGGACGGAG 58.732 52.381 13.64 3.57 46.06 4.63
560 574 2.773993 TCCCACAACTATTTCCGGAC 57.226 50.000 1.83 0.00 0.00 4.79
563 577 4.461081 TCCATTTTCCCACAACTATTTCCG 59.539 41.667 0.00 0.00 0.00 4.30
564 578 5.993748 TCCATTTTCCCACAACTATTTCC 57.006 39.130 0.00 0.00 0.00 3.13
633 647 6.403049 TCGCTCTGTCCTAAAATAATTGTCA 58.597 36.000 0.00 0.00 0.00 3.58
646 660 3.510531 TCCATATACTCGCTCTGTCCT 57.489 47.619 0.00 0.00 0.00 3.85
697 711 7.309920 GCCGTAAAAGGAGTAAAATTCAATCA 58.690 34.615 0.00 0.00 0.00 2.57
719 733 5.449999 GGGTAAACAATCTTTTCTATGGCCG 60.450 44.000 0.00 0.00 0.00 6.13
762 783 7.278424 TGTGTAATAATACGGACTGTTAAAGCC 59.722 37.037 0.00 0.00 34.60 4.35
776 797 6.403878 ACCAGTGGTGAGTGTGTAATAATAC 58.596 40.000 15.86 0.00 32.98 1.89
937 958 6.610425 GGTTTATAGTAGGAGGAGTGGAGAAA 59.390 42.308 0.00 0.00 0.00 2.52
970 991 1.939934 CTTCGCTTTGTTGGTGACTCA 59.060 47.619 0.00 0.00 0.00 3.41
1231 1267 2.439883 GGCGGAGGAGGACGTACT 60.440 66.667 0.00 0.00 0.00 2.73
1574 1613 1.442857 CACTGGACAGTCTCGTCGC 60.443 63.158 1.21 0.00 40.20 5.19
1578 1617 0.898320 ATTCCCACTGGACAGTCTCG 59.102 55.000 1.21 0.00 41.57 4.04
1579 1618 1.677217 GCATTCCCACTGGACAGTCTC 60.677 57.143 1.21 0.00 41.57 3.36
1580 1619 0.326264 GCATTCCCACTGGACAGTCT 59.674 55.000 1.21 0.00 41.57 3.24
1582 1621 1.136329 AGGCATTCCCACTGGACAGT 61.136 55.000 0.00 0.00 41.57 3.55
1583 1622 0.679002 CAGGCATTCCCACTGGACAG 60.679 60.000 0.00 0.00 41.57 3.51
1584 1623 1.379916 CAGGCATTCCCACTGGACA 59.620 57.895 0.00 0.00 41.57 4.02
1634 1673 0.958091 CAATTGCTTGGTCGTTCCCA 59.042 50.000 0.00 0.00 34.77 4.37
1673 1712 0.669318 CAAAGCAGCAGCCACAATGG 60.669 55.000 0.00 0.00 43.56 3.16
1674 1713 0.032952 ACAAAGCAGCAGCCACAATG 59.967 50.000 0.00 0.00 43.56 2.82
1689 1743 1.542272 GCGACGAGCACACGTACAAA 61.542 55.000 0.00 0.00 46.52 2.83
1723 1777 4.576463 ACCGCATTTATTCAGAGGATGTTC 59.424 41.667 0.00 0.00 0.00 3.18
1807 1869 8.543839 GAACTGAGGGTTGCCATAAGATGGTA 62.544 46.154 7.31 0.00 44.46 3.25
1809 1871 5.463504 GAACTGAGGGTTGCCATAAGATGG 61.464 50.000 0.83 0.83 44.97 3.51
1897 5424 4.196193 ACCAAGAATGACGACTGAAACAA 58.804 39.130 0.00 0.00 0.00 2.83
1921 5448 2.865119 TCTGCTCTGCATTCTTGGAA 57.135 45.000 0.00 0.00 38.13 3.53
1923 5450 2.434428 ACTTCTGCTCTGCATTCTTGG 58.566 47.619 0.00 0.00 38.13 3.61
1924 5451 4.502016 TCTACTTCTGCTCTGCATTCTTG 58.498 43.478 0.00 0.00 38.13 3.02
1925 5452 4.815533 TCTACTTCTGCTCTGCATTCTT 57.184 40.909 0.00 0.00 38.13 2.52
1926 5453 4.222588 ACTTCTACTTCTGCTCTGCATTCT 59.777 41.667 0.00 0.00 38.13 2.40
1927 5454 4.502962 ACTTCTACTTCTGCTCTGCATTC 58.497 43.478 0.00 0.00 38.13 2.67
1946 5475 3.463944 ACGATTTCGGACAAGTGAACTT 58.536 40.909 4.84 0.00 44.95 2.66
1947 5476 3.107642 ACGATTTCGGACAAGTGAACT 57.892 42.857 4.84 0.00 44.95 3.01
1948 5477 3.541711 CAACGATTTCGGACAAGTGAAC 58.458 45.455 4.84 0.00 44.95 3.18
1950 5479 1.529438 GCAACGATTTCGGACAAGTGA 59.471 47.619 4.84 0.00 44.95 3.41
1951 5480 1.262950 TGCAACGATTTCGGACAAGTG 59.737 47.619 4.84 0.00 44.95 3.16
1952 5481 1.263217 GTGCAACGATTTCGGACAAGT 59.737 47.619 4.84 0.00 44.95 3.16
1953 5482 1.262950 TGTGCAACGATTTCGGACAAG 59.737 47.619 4.84 0.00 42.39 3.16
1954 5483 1.300481 TGTGCAACGATTTCGGACAA 58.700 45.000 4.84 0.00 42.39 3.18
1968 5497 4.455533 CAGCTACTTCCAACTTTATGTGCA 59.544 41.667 0.00 0.00 0.00 4.57
1970 5499 5.934625 AGTCAGCTACTTCCAACTTTATGTG 59.065 40.000 0.00 0.00 33.35 3.21
2001 5531 2.744202 GGATGTGAGCAACCACTACAAG 59.256 50.000 0.00 0.00 37.48 3.16
2020 5553 3.302675 CGTACGATCGAGTCAATTACGGA 60.303 47.826 24.34 0.00 31.28 4.69
2030 5563 1.332997 GATCCAACCGTACGATCGAGT 59.667 52.381 24.34 10.40 0.00 4.18
2041 5574 0.595053 CGTCCTGATCGATCCAACCG 60.595 60.000 22.31 14.90 0.00 4.44
2063 5596 1.069358 CCGATCAGGAAAGGTAGAGCC 59.931 57.143 0.00 0.00 45.00 4.70
2149 5682 4.757594 TCTGTTGCATTTTGAGCAGTTTT 58.242 34.783 0.00 0.00 43.75 2.43
2163 5696 2.513753 ACAAAATCCCGATCTGTTGCA 58.486 42.857 0.00 0.00 0.00 4.08
2171 5704 0.894835 GGTGCCAACAAAATCCCGAT 59.105 50.000 0.00 0.00 0.00 4.18
2194 5727 8.272866 CGACTGATGTAAAATCGCAACATATTA 58.727 33.333 0.00 0.00 34.09 0.98
2195 5728 7.125755 CGACTGATGTAAAATCGCAACATATT 58.874 34.615 0.00 0.00 34.09 1.28
2196 5729 6.292865 CCGACTGATGTAAAATCGCAACATAT 60.293 38.462 0.00 0.00 34.09 1.78
2197 5730 5.006261 CCGACTGATGTAAAATCGCAACATA 59.994 40.000 0.00 0.00 34.09 2.29
2198 5731 4.201812 CCGACTGATGTAAAATCGCAACAT 60.202 41.667 0.00 0.00 36.57 2.71
2199 5732 3.124466 CCGACTGATGTAAAATCGCAACA 59.876 43.478 0.00 0.00 0.00 3.33
2261 5826 1.486310 TCAGGCAGAACACTGAACTGT 59.514 47.619 15.84 0.00 40.51 3.55
2290 5855 1.301401 GCACGTTACCAGCAGGACA 60.301 57.895 0.35 0.00 38.69 4.02
2292 5857 1.292223 GAGCACGTTACCAGCAGGA 59.708 57.895 0.35 0.00 38.69 3.86
2293 5858 1.005037 TGAGCACGTTACCAGCAGG 60.005 57.895 0.00 0.00 42.21 4.85
2294 5859 0.319900 ACTGAGCACGTTACCAGCAG 60.320 55.000 7.50 0.00 0.00 4.24
2295 5860 0.963225 TACTGAGCACGTTACCAGCA 59.037 50.000 7.50 0.00 0.00 4.41
2305 5886 1.873591 CAGTGGTGGTTTACTGAGCAC 59.126 52.381 0.00 0.00 45.46 4.40
2343 5932 4.766375 TCGTCTTCACAAAAGTTTCCTCT 58.234 39.130 0.00 0.00 0.00 3.69
2479 6071 5.969423 TCCTAACTGTAATAACGTCCCTTG 58.031 41.667 0.00 0.00 0.00 3.61
2492 6084 1.188863 GGCCGAGGTTCCTAACTGTA 58.811 55.000 0.00 0.00 0.00 2.74
2508 6100 3.281727 TTCAGTTCAGTGATATGGGCC 57.718 47.619 0.00 0.00 0.00 5.80
2586 6178 7.742556 TCATGAACATATGTTTCACTGTCAA 57.257 32.000 21.63 0.00 38.56 3.18


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

AutoCloner maintained by Alex Coulton.