Multiple sequence alignment - TraesCS5D01G428300

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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 TraesCS5D01G428300 chr5D 100.000 3008 0 0 1 3008 486099303 486102310 0.000000e+00 5555.0
1 TraesCS5D01G428300 chr5D 95.798 595 21 2 2418 3008 502513212 502512618 0.000000e+00 957.0
2 TraesCS5D01G428300 chr5D 95.286 594 22 3 2419 3008 177374270 177374861 0.000000e+00 937.0
3 TraesCS5D01G428300 chr5D 95.286 594 21 4 2419 3008 351409677 351410267 0.000000e+00 935.0
4 TraesCS5D01G428300 chr5D 94.399 607 26 7 2406 3008 254316785 254317387 0.000000e+00 926.0
5 TraesCS5D01G428300 chr5D 93.750 48 3 0 2258 2305 552996640 552996687 4.160000e-09 73.1
6 TraesCS5D01G428300 chr5A 88.816 2432 125 60 1 2383 606840214 606842547 0.000000e+00 2848.0
7 TraesCS5D01G428300 chr5A 82.153 353 36 16 1965 2312 606842694 606843024 8.210000e-71 278.0
8 TraesCS5D01G428300 chr5B 92.009 1389 64 15 972 2332 597146608 597147977 0.000000e+00 1906.0
9 TraesCS5D01G428300 chr5B 87.843 510 32 11 1 491 597145748 597146246 3.360000e-159 571.0
10 TraesCS5D01G428300 chr5B 93.085 188 12 1 691 877 597146348 597146535 1.060000e-69 274.0
11 TraesCS5D01G428300 chr5B 92.391 92 4 1 541 632 597146244 597146332 8.750000e-26 128.0
12 TraesCS5D01G428300 chr6D 95.318 598 22 3 2415 3008 303546077 303546672 0.000000e+00 944.0
13 TraesCS5D01G428300 chr6D 94.966 596 24 2 2419 3008 86923433 86922838 0.000000e+00 929.0
14 TraesCS5D01G428300 chrUn 95.159 599 22 3 2415 3008 30249263 30249859 0.000000e+00 939.0
15 TraesCS5D01G428300 chr4D 95.134 596 22 4 2419 3008 291814196 291814790 0.000000e+00 933.0
16 TraesCS5D01G428300 chr4D 94.958 595 25 2 2418 3008 280595429 280596022 0.000000e+00 928.0
17 TraesCS5D01G428300 chr4B 93.305 239 10 3 1557 1795 26331078 26330846 6.170000e-92 348.0


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 TraesCS5D01G428300 chr5D 486099303 486102310 3007 False 5555.00 5555 100.0000 1 3008 1 chr5D.!!$F4 3007
1 TraesCS5D01G428300 chr5D 502512618 502513212 594 True 957.00 957 95.7980 2418 3008 1 chr5D.!!$R1 590
2 TraesCS5D01G428300 chr5D 177374270 177374861 591 False 937.00 937 95.2860 2419 3008 1 chr5D.!!$F1 589
3 TraesCS5D01G428300 chr5D 351409677 351410267 590 False 935.00 935 95.2860 2419 3008 1 chr5D.!!$F3 589
4 TraesCS5D01G428300 chr5D 254316785 254317387 602 False 926.00 926 94.3990 2406 3008 1 chr5D.!!$F2 602
5 TraesCS5D01G428300 chr5A 606840214 606843024 2810 False 1563.00 2848 85.4845 1 2383 2 chr5A.!!$F1 2382
6 TraesCS5D01G428300 chr5B 597145748 597147977 2229 False 719.75 1906 91.3320 1 2332 4 chr5B.!!$F1 2331
7 TraesCS5D01G428300 chr6D 303546077 303546672 595 False 944.00 944 95.3180 2415 3008 1 chr6D.!!$F1 593
8 TraesCS5D01G428300 chr6D 86922838 86923433 595 True 929.00 929 94.9660 2419 3008 1 chr6D.!!$R1 589
9 TraesCS5D01G428300 chrUn 30249263 30249859 596 False 939.00 939 95.1590 2415 3008 1 chrUn.!!$F1 593
10 TraesCS5D01G428300 chr4D 291814196 291814790 594 False 933.00 933 95.1340 2419 3008 1 chr4D.!!$F2 589
11 TraesCS5D01G428300 chr4D 280595429 280596022 593 False 928.00 928 94.9580 2418 3008 1 chr4D.!!$F1 590

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
742 772 0.030638 ACGCGGGCAAATATGAATGC 59.969 50.0 12.47 0.92 41.82 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2348 2445 0.107361 ACTTTTTATCCTCGCGGGGG 60.107 55.0 28.04 18.66 35.33 5.4 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
118 121 3.461061 CACATCCCATATATGCCGCTAG 58.539 50.000 7.24 0.00 0.00 3.42
119 122 2.158900 ACATCCCATATATGCCGCTAGC 60.159 50.000 4.06 4.06 44.14 3.42
169 189 3.610911 GAGTGGGTAACTAAAGCAGCAT 58.389 45.455 0.00 0.00 40.07 3.79
344 369 8.993121 CCTTAATCATTAAGCACTACCATGTAG 58.007 37.037 11.24 0.00 40.96 2.74
345 370 8.902540 TTAATCATTAAGCACTACCATGTAGG 57.097 34.615 6.25 0.00 45.67 3.18
352 377 3.700038 AGCACTACCATGTAGGAGTACAC 59.300 47.826 6.25 0.00 42.06 2.90
381 407 0.889994 TCCATGACATTGCTGCAACC 59.110 50.000 18.51 10.39 0.00 3.77
387 413 2.115052 ATTGCTGCAACCGTGGGA 59.885 55.556 18.51 0.00 0.00 4.37
404 430 3.253432 GTGGGATGGTGAAAAGAAGTGAC 59.747 47.826 0.00 0.00 0.00 3.67
405 431 3.117701 TGGGATGGTGAAAAGAAGTGACA 60.118 43.478 0.00 0.00 0.00 3.58
406 432 4.082125 GGGATGGTGAAAAGAAGTGACAT 58.918 43.478 0.00 0.00 0.00 3.06
407 433 4.524328 GGGATGGTGAAAAGAAGTGACATT 59.476 41.667 0.00 0.00 0.00 2.71
408 434 5.335976 GGGATGGTGAAAAGAAGTGACATTC 60.336 44.000 0.00 0.00 0.00 2.67
409 435 5.474876 GGATGGTGAAAAGAAGTGACATTCT 59.525 40.000 0.00 0.00 41.31 2.40
410 436 5.756195 TGGTGAAAAGAAGTGACATTCTG 57.244 39.130 0.00 0.00 39.47 3.02
434 460 2.675889 GCCTGGCATTCTCAAAACCATG 60.676 50.000 15.17 0.00 0.00 3.66
455 481 5.247507 TGTGTCAAAATTGTGTTCAGGAG 57.752 39.130 0.00 0.00 0.00 3.69
456 482 4.097741 TGTGTCAAAATTGTGTTCAGGAGG 59.902 41.667 0.00 0.00 0.00 4.30
480 506 3.493176 GGCATTGCAGGTTTTCAGAGTTT 60.493 43.478 11.39 0.00 0.00 2.66
525 551 6.715280 ACACTTTCAGAGTTGGTGATGATAT 58.285 36.000 0.00 0.00 36.10 1.63
605 631 2.805099 GGAGTGCTCTTGACAGTTGAAG 59.195 50.000 0.00 0.00 0.00 3.02
606 632 3.493350 GGAGTGCTCTTGACAGTTGAAGA 60.493 47.826 0.00 0.00 0.00 2.87
607 633 4.122776 GAGTGCTCTTGACAGTTGAAGAA 58.877 43.478 0.00 0.00 0.00 2.52
649 675 1.251251 AAAGGTGCACAGAATGGCTC 58.749 50.000 20.43 0.00 43.62 4.70
650 676 0.403271 AAGGTGCACAGAATGGCTCT 59.597 50.000 20.43 0.00 43.62 4.09
670 700 8.587608 TGGCTCTGAGAAAATAAAACATGAAAT 58.412 29.630 9.28 0.00 0.00 2.17
710 740 8.819015 GTTTTTAATTACTTTGCGGGAGAAAAA 58.181 29.630 0.00 0.00 36.82 1.94
729 759 1.804601 AGTAGAAAAGGAAACGCGGG 58.195 50.000 12.47 0.00 0.00 6.13
742 772 0.030638 ACGCGGGCAAATATGAATGC 59.969 50.000 12.47 0.92 41.82 3.56
745 775 1.925946 GCGGGCAAATATGAATGCGAC 60.926 52.381 0.00 0.00 43.47 5.19
774 804 4.893424 TCGGAAAAGGTGAAAGTTTGAG 57.107 40.909 0.00 0.00 0.00 3.02
847 878 5.429957 AGCTAAAAGCAGTCAAAACAGAG 57.570 39.130 1.22 0.00 45.56 3.35
852 883 7.043788 GCTAAAAGCAGTCAAAACAGAGAAAAG 60.044 37.037 0.00 0.00 41.89 2.27
882 915 0.111253 AGCAAGTTGGTAGCTTGGCT 59.889 50.000 5.60 0.00 42.44 4.75
883 916 1.351017 AGCAAGTTGGTAGCTTGGCTA 59.649 47.619 5.60 0.00 42.44 3.93
884 917 2.025887 AGCAAGTTGGTAGCTTGGCTAT 60.026 45.455 5.60 0.00 43.30 2.97
885 918 2.098117 GCAAGTTGGTAGCTTGGCTATG 59.902 50.000 4.75 0.00 43.30 2.23
886 919 3.347216 CAAGTTGGTAGCTTGGCTATGT 58.653 45.455 0.00 0.00 43.30 2.29
887 920 4.513442 CAAGTTGGTAGCTTGGCTATGTA 58.487 43.478 0.00 0.00 43.30 2.29
888 921 4.837093 AGTTGGTAGCTTGGCTATGTAA 57.163 40.909 0.00 0.00 43.30 2.41
889 922 4.770795 AGTTGGTAGCTTGGCTATGTAAG 58.229 43.478 0.00 0.00 43.30 2.34
903 936 2.403252 TGTAAGCTTTGAGCCTAGCC 57.597 50.000 3.20 0.00 43.77 3.93
904 937 1.628340 TGTAAGCTTTGAGCCTAGCCA 59.372 47.619 3.20 0.00 43.77 4.75
905 938 2.284190 GTAAGCTTTGAGCCTAGCCAG 58.716 52.381 3.20 0.00 43.77 4.85
906 939 0.987294 AAGCTTTGAGCCTAGCCAGA 59.013 50.000 0.00 0.00 43.77 3.86
907 940 0.540923 AGCTTTGAGCCTAGCCAGAG 59.459 55.000 0.00 0.00 43.77 3.35
908 941 0.463474 GCTTTGAGCCTAGCCAGAGG 60.463 60.000 0.00 0.00 39.88 3.69
930 963 2.662866 CGTTGGTAGGGAGGAGTGATA 58.337 52.381 0.00 0.00 0.00 2.15
931 964 3.231818 CGTTGGTAGGGAGGAGTGATAT 58.768 50.000 0.00 0.00 0.00 1.63
932 965 3.005897 CGTTGGTAGGGAGGAGTGATATG 59.994 52.174 0.00 0.00 0.00 1.78
933 966 2.609747 TGGTAGGGAGGAGTGATATGC 58.390 52.381 0.00 0.00 0.00 3.14
934 967 2.090775 TGGTAGGGAGGAGTGATATGCA 60.091 50.000 0.00 0.00 0.00 3.96
990 1045 1.179152 CCTGCATTGCACTCCATCAA 58.821 50.000 7.38 0.00 33.79 2.57
992 1047 2.089201 CTGCATTGCACTCCATCAAGA 58.911 47.619 7.38 0.00 33.79 3.02
1021 1076 4.790962 ATCACGGGCAGCAGCAGG 62.791 66.667 2.65 0.00 44.61 4.85
1261 1316 2.811101 CGCTCTGGCTCTACCTGG 59.189 66.667 0.00 0.00 40.22 4.45
1269 1324 2.799371 CTCTACCTGGTCGCCGTC 59.201 66.667 0.63 0.00 0.00 4.79
1869 1924 3.294214 GGATTACTTCTGGTCCGTCCTA 58.706 50.000 0.00 0.00 37.07 2.94
1872 1927 2.305858 ACTTCTGGTCCGTCCTACTT 57.694 50.000 0.00 0.00 37.07 2.24
1873 1928 2.606378 ACTTCTGGTCCGTCCTACTTT 58.394 47.619 0.00 0.00 37.07 2.66
1896 1958 4.466370 TCCCTCTACTTCGTTCATGTCAAT 59.534 41.667 0.00 0.00 0.00 2.57
1928 1994 7.878477 CCATTTGCATGGTATACATTCATTC 57.122 36.000 5.01 0.00 44.81 2.67
1948 2018 7.428020 TCATTCATTTGCTTACTTATCCATGC 58.572 34.615 0.00 0.00 0.00 4.06
1949 2019 5.422666 TCATTTGCTTACTTATCCATGCG 57.577 39.130 0.00 0.00 0.00 4.73
2006 2081 4.701651 TGGCCACAGAGAACAAATCTATTG 59.298 41.667 0.00 0.00 38.96 1.90
2022 2101 2.503895 ATTGACTCAAGCCTCCTTGG 57.496 50.000 3.86 0.00 46.69 3.61
2033 2121 1.826385 CCTCCTTGGTTCACATGGTC 58.174 55.000 0.00 0.00 43.18 4.02
2053 2141 4.074647 GTGGTTCCCACGGAAAGG 57.925 61.111 0.00 0.00 44.95 3.11
2054 2142 1.602605 GTGGTTCCCACGGAAAGGG 60.603 63.158 0.00 0.00 44.95 3.95
2055 2143 2.035155 GGTTCCCACGGAAAGGGG 59.965 66.667 0.00 0.00 43.86 4.79
2160 2250 5.178797 AGAGTTTGCTCCACATGTATGTAC 58.821 41.667 0.00 0.00 42.59 2.90
2231 2327 3.570926 ATGTGTGTCGTCGTGTATTCT 57.429 42.857 0.00 0.00 0.00 2.40
2232 2328 2.657184 TGTGTGTCGTCGTGTATTCTG 58.343 47.619 0.00 0.00 0.00 3.02
2235 2331 4.221342 GTGTGTCGTCGTGTATTCTGTTA 58.779 43.478 0.00 0.00 0.00 2.41
2270 2367 8.644619 CATCTACAAAAATTCAAGCTGACAATG 58.355 33.333 0.00 0.00 0.00 2.82
2272 2369 5.916318 ACAAAAATTCAAGCTGACAATGGA 58.084 33.333 0.00 0.00 0.00 3.41
2306 2403 2.408565 GGTATTGGACTCTCATCCCCA 58.591 52.381 0.00 0.00 38.06 4.96
2321 2418 4.873129 CCATCCCCGCGACAGTCG 62.873 72.222 19.10 19.10 43.89 4.18
2334 2431 1.079405 CAGTCGCACCATACCCGTT 60.079 57.895 0.00 0.00 0.00 4.44
2335 2432 0.173935 CAGTCGCACCATACCCGTTA 59.826 55.000 0.00 0.00 0.00 3.18
2338 2435 1.218585 CGCACCATACCCGTTACCA 59.781 57.895 0.00 0.00 0.00 3.25
2340 2437 1.589803 GCACCATACCCGTTACCATC 58.410 55.000 0.00 0.00 0.00 3.51
2345 2442 1.761500 ATACCCGTTACCATCCCCGC 61.761 60.000 0.00 0.00 0.00 6.13
2346 2443 3.788145 CCCGTTACCATCCCCGCA 61.788 66.667 0.00 0.00 0.00 5.69
2347 2444 2.512974 CCGTTACCATCCCCGCAC 60.513 66.667 0.00 0.00 0.00 5.34
2348 2445 2.512974 CGTTACCATCCCCGCACC 60.513 66.667 0.00 0.00 0.00 5.01
2349 2446 2.124445 GTTACCATCCCCGCACCC 60.124 66.667 0.00 0.00 0.00 4.61
2383 2480 5.728637 AAAAAGTTTCACATCCTCATCCC 57.271 39.130 0.00 0.00 0.00 3.85
2384 2481 4.387026 AAAGTTTCACATCCTCATCCCA 57.613 40.909 0.00 0.00 0.00 4.37
2388 2503 1.206878 TCACATCCTCATCCCAGTGG 58.793 55.000 0.63 0.63 0.00 4.00
2411 2526 5.003804 GGGAGAACCATATACGCAATCAAT 58.996 41.667 0.00 0.00 39.85 2.57
2554 2688 3.085443 GCAGTAGCGCTCTAGATGAAA 57.915 47.619 16.34 0.00 0.00 2.69
2577 2714 4.276678 ACGCTACTACTATAATTGCCACGA 59.723 41.667 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 18 1.424403 TCTTTCGTGCGTGTGTATGG 58.576 50.000 0.00 0.00 0.00 2.74
118 121 2.535574 GCAGCAGTAAACACAAAAGTGC 59.464 45.455 0.00 0.00 39.38 4.40
119 122 3.768406 TGCAGCAGTAAACACAAAAGTG 58.232 40.909 0.00 0.00 0.00 3.16
120 123 3.181487 CCTGCAGCAGTAAACACAAAAGT 60.181 43.478 21.26 0.00 0.00 2.66
169 189 0.605319 CGCCCTGTTGCTTTACCTCA 60.605 55.000 0.00 0.00 0.00 3.86
344 369 4.829588 GCCTTAGGCGTGTACTCC 57.170 61.111 7.77 0.00 39.62 3.85
381 407 2.226437 CACTTCTTTTCACCATCCCACG 59.774 50.000 0.00 0.00 0.00 4.94
387 413 6.064060 TCAGAATGTCACTTCTTTTCACCAT 58.936 36.000 0.00 0.00 37.40 3.55
404 430 1.030457 GAATGCCAGGCCTCAGAATG 58.970 55.000 9.64 0.00 37.54 2.67
405 431 0.924823 AGAATGCCAGGCCTCAGAAT 59.075 50.000 9.64 0.00 0.00 2.40
406 432 0.254178 GAGAATGCCAGGCCTCAGAA 59.746 55.000 9.64 0.00 0.00 3.02
407 433 0.911045 TGAGAATGCCAGGCCTCAGA 60.911 55.000 9.64 0.00 32.51 3.27
408 434 0.034767 TTGAGAATGCCAGGCCTCAG 60.035 55.000 15.95 0.00 37.04 3.35
409 435 0.405198 TTTGAGAATGCCAGGCCTCA 59.595 50.000 9.64 11.90 34.25 3.86
410 436 1.203287 GTTTTGAGAATGCCAGGCCTC 59.797 52.381 9.64 9.15 0.00 4.70
434 460 4.610945 CCTCCTGAACACAATTTTGACAC 58.389 43.478 0.00 0.00 0.00 3.67
455 481 1.737735 GAAAACCTGCAATGCCGCC 60.738 57.895 1.53 0.00 0.00 6.13
456 482 1.006337 TGAAAACCTGCAATGCCGC 60.006 52.632 1.53 0.00 0.00 6.53
537 563 9.140286 GCAACGCTAAATCTTCATATCATAGTA 57.860 33.333 0.00 0.00 0.00 1.82
539 565 8.021955 TGCAACGCTAAATCTTCATATCATAG 57.978 34.615 0.00 0.00 0.00 2.23
684 714 7.933728 TTTCTCCCGCAAAGTAATTAAAAAC 57.066 32.000 0.00 0.00 0.00 2.43
689 719 6.887626 ACTTTTTCTCCCGCAAAGTAATTA 57.112 33.333 0.00 0.00 38.65 1.40
710 740 1.804601 CCCGCGTTTCCTTTTCTACT 58.195 50.000 4.92 0.00 0.00 2.57
729 759 7.552848 AATTATTCGTCGCATTCATATTTGC 57.447 32.000 0.00 0.00 35.50 3.68
847 878 6.256539 CCAACTTGCTTCTCTTTTTCCTTTTC 59.743 38.462 0.00 0.00 0.00 2.29
852 883 4.655762 ACCAACTTGCTTCTCTTTTTCC 57.344 40.909 0.00 0.00 0.00 3.13
882 915 3.454447 TGGCTAGGCTCAAAGCTTACATA 59.546 43.478 18.18 0.00 41.99 2.29
883 916 2.239654 TGGCTAGGCTCAAAGCTTACAT 59.760 45.455 18.18 0.00 41.99 2.29
884 917 1.628340 TGGCTAGGCTCAAAGCTTACA 59.372 47.619 18.18 0.00 41.99 2.41
885 918 2.093447 TCTGGCTAGGCTCAAAGCTTAC 60.093 50.000 18.18 0.00 41.99 2.34
886 919 2.169352 CTCTGGCTAGGCTCAAAGCTTA 59.831 50.000 18.18 0.00 41.99 3.09
887 920 0.987294 TCTGGCTAGGCTCAAAGCTT 59.013 50.000 18.18 0.00 41.99 3.74
888 921 0.540923 CTCTGGCTAGGCTCAAAGCT 59.459 55.000 18.18 0.00 41.99 3.74
889 922 0.463474 CCTCTGGCTAGGCTCAAAGC 60.463 60.000 18.18 0.00 41.46 3.51
890 923 3.776616 CCTCTGGCTAGGCTCAAAG 57.223 57.895 18.18 6.44 0.00 2.77
902 935 2.584608 CCTACCAACGGCCTCTGG 59.415 66.667 16.44 16.44 38.77 3.86
903 936 1.961180 CTCCCTACCAACGGCCTCTG 61.961 65.000 0.00 0.00 0.00 3.35
904 937 1.686110 CTCCCTACCAACGGCCTCT 60.686 63.158 0.00 0.00 0.00 3.69
905 938 2.732619 CCTCCCTACCAACGGCCTC 61.733 68.421 0.00 0.00 0.00 4.70
906 939 2.687566 CCTCCCTACCAACGGCCT 60.688 66.667 0.00 0.00 0.00 5.19
907 940 2.686106 TCCTCCCTACCAACGGCC 60.686 66.667 0.00 0.00 0.00 6.13
908 941 1.988406 ACTCCTCCCTACCAACGGC 60.988 63.158 0.00 0.00 0.00 5.68
909 942 0.613853 TCACTCCTCCCTACCAACGG 60.614 60.000 0.00 0.00 0.00 4.44
910 943 1.486211 ATCACTCCTCCCTACCAACG 58.514 55.000 0.00 0.00 0.00 4.10
911 944 3.244249 GCATATCACTCCTCCCTACCAAC 60.244 52.174 0.00 0.00 0.00 3.77
912 945 2.972713 GCATATCACTCCTCCCTACCAA 59.027 50.000 0.00 0.00 0.00 3.67
913 946 2.090775 TGCATATCACTCCTCCCTACCA 60.091 50.000 0.00 0.00 0.00 3.25
914 947 2.300437 GTGCATATCACTCCTCCCTACC 59.700 54.545 0.00 0.00 42.38 3.18
915 948 3.669251 GTGCATATCACTCCTCCCTAC 57.331 52.381 0.00 0.00 42.38 3.18
932 965 4.104417 GCTGCTGCTGCTCAGTGC 62.104 66.667 22.10 9.17 44.66 4.40
933 966 3.789858 CGCTGCTGCTGCTCAGTG 61.790 66.667 25.43 17.64 44.66 3.66
956 992 2.359230 AGGTTTGCTCGAGCTGCC 60.359 61.111 35.27 30.20 42.66 4.85
969 1005 1.180029 GATGGAGTGCAATGCAGGTT 58.820 50.000 14.92 0.00 40.08 3.50
990 1045 3.813443 CCCGTGATTCATCCTGAATTCT 58.187 45.455 7.05 0.00 46.20 2.40
992 1047 2.301346 GCCCGTGATTCATCCTGAATT 58.699 47.619 4.03 0.00 46.20 2.17
1021 1076 1.301401 TGTTGCTCAGGTGGTACGC 60.301 57.895 0.00 0.00 38.67 4.42
1188 1243 1.737201 GAGCGAGACTAGGAAGGCC 59.263 63.158 0.00 0.00 0.00 5.19
1261 1316 3.519930 GAGGAGGAGGACGGCGAC 61.520 72.222 16.62 7.58 0.00 5.19
1269 1324 1.671901 GGAAGAGCACGAGGAGGAGG 61.672 65.000 0.00 0.00 0.00 4.30
1851 1906 3.446442 AGTAGGACGGACCAGAAGTAA 57.554 47.619 0.00 0.00 42.04 2.24
1869 1924 4.283722 ACATGAACGAAGTAGAGGGAAAGT 59.716 41.667 0.00 0.00 45.00 2.66
1872 1927 3.830178 TGACATGAACGAAGTAGAGGGAA 59.170 43.478 0.00 0.00 45.00 3.97
1873 1928 3.427573 TGACATGAACGAAGTAGAGGGA 58.572 45.455 0.00 0.00 45.00 4.20
1928 1994 5.422666 TCGCATGGATAAGTAAGCAAATG 57.577 39.130 0.00 0.00 0.00 2.32
1948 2018 7.330454 CCTTGACCTGATTCATACATAGATTCG 59.670 40.741 0.00 0.00 0.00 3.34
1949 2019 8.153550 ACCTTGACCTGATTCATACATAGATTC 58.846 37.037 0.00 0.00 0.00 2.52
2006 2081 1.072331 TGAACCAAGGAGGCTTGAGTC 59.928 52.381 0.00 0.00 43.14 3.36
2021 2100 0.110486 ACCACCAGACCATGTGAACC 59.890 55.000 0.00 0.00 34.37 3.62
2022 2101 1.880027 GAACCACCAGACCATGTGAAC 59.120 52.381 0.00 0.00 34.37 3.18
2053 2141 4.034410 TCCAAACCAATAATTAAGCCCCC 58.966 43.478 0.00 0.00 0.00 5.40
2054 2142 5.685520 TTCCAAACCAATAATTAAGCCCC 57.314 39.130 0.00 0.00 0.00 5.80
2055 2143 7.609918 ACAAATTCCAAACCAATAATTAAGCCC 59.390 33.333 0.00 0.00 0.00 5.19
2056 2144 8.560355 ACAAATTCCAAACCAATAATTAAGCC 57.440 30.769 0.00 0.00 0.00 4.35
2065 2153 8.970859 TTTGTTCATACAAATTCCAAACCAAT 57.029 26.923 0.00 0.00 46.46 3.16
2133 2221 6.540189 ACATACATGTGGAGCAAACTCTTATC 59.460 38.462 9.11 0.00 40.03 1.75
2160 2250 3.239026 CACGTACTTTACTTGATACGCGG 59.761 47.826 12.47 0.00 43.19 6.46
2250 2346 6.218019 TCTCCATTGTCAGCTTGAATTTTTG 58.782 36.000 0.00 0.00 0.00 2.44
2321 2418 1.589803 GATGGTAACGGGTATGGTGC 58.410 55.000 0.00 0.00 42.51 5.01
2323 2420 1.134228 GGGATGGTAACGGGTATGGT 58.866 55.000 0.00 0.00 42.51 3.55
2348 2445 0.107361 ACTTTTTATCCTCGCGGGGG 60.107 55.000 28.04 18.66 35.33 5.40
2349 2446 1.746470 AACTTTTTATCCTCGCGGGG 58.254 50.000 22.26 22.26 35.33 5.73
2353 2450 5.123979 AGGATGTGAAACTTTTTATCCTCGC 59.876 40.000 0.00 0.00 40.10 5.03
2360 2457 6.310941 TGGGATGAGGATGTGAAACTTTTTA 58.689 36.000 0.00 0.00 38.04 1.52
2383 2480 2.548067 GCGTATATGGTTCTCCCCACTG 60.548 54.545 0.00 0.00 37.31 3.66
2384 2481 1.692519 GCGTATATGGTTCTCCCCACT 59.307 52.381 0.00 0.00 37.31 4.00
2388 2503 4.002906 TGATTGCGTATATGGTTCTCCC 57.997 45.455 0.00 0.00 0.00 4.30
2392 2507 7.589954 GGTTGTTATTGATTGCGTATATGGTTC 59.410 37.037 0.00 0.00 0.00 3.62
2394 2509 6.544197 TGGTTGTTATTGATTGCGTATATGGT 59.456 34.615 0.00 0.00 0.00 3.55
2411 2526 5.608015 AGGTTTTCCCTAGTAGTGGTTGTTA 59.392 40.000 0.00 0.00 43.87 2.41
2444 2559 1.676006 ACAACGCTGCTGCTAAGTTTT 59.324 42.857 14.03 1.33 36.97 2.43
2447 2562 1.308998 AAACAACGCTGCTGCTAAGT 58.691 45.000 14.03 5.99 36.97 2.24
2502 2635 2.922740 AGTAGCACGGTTTCCTGAAA 57.077 45.000 0.00 0.00 0.00 2.69
2550 2684 6.477688 GTGGCAATTATAGTAGTAGCGTTTCA 59.522 38.462 0.00 0.00 0.00 2.69
2551 2685 6.345565 CGTGGCAATTATAGTAGTAGCGTTTC 60.346 42.308 0.00 0.00 0.00 2.78
2554 2688 4.276678 TCGTGGCAATTATAGTAGTAGCGT 59.723 41.667 0.00 0.00 0.00 5.07
2900 3056 9.734620 AACATCAAAAATATACATTGGTCATCG 57.265 29.630 0.00 0.00 0.00 3.84


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

AutoCloner maintained by Alex Coulton.