Multiple sequence alignment - TraesCS2A01G490200

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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 TraesCS2A01G490200 chr2A 100.000 2954 0 0 1 2954 723822678 723825631 0.000000e+00 5456
1 TraesCS2A01G490200 chr2A 88.208 212 15 5 2745 2954 691568345 691568548 8.180000e-61 244
2 TraesCS2A01G490200 chr2D 91.360 2500 130 21 4 2475 589495475 589497916 0.000000e+00 3341
3 TraesCS2A01G490200 chr2D 84.232 482 34 11 2475 2954 589500020 589500461 5.850000e-117 431
4 TraesCS2A01G490200 chr2B 92.584 2144 83 21 4 2126 713674165 713676253 0.000000e+00 3009
5 TraesCS2A01G490200 chr2B 83.099 426 38 19 2502 2912 713691898 713692304 1.010000e-94 357
6 TraesCS2A01G490200 chr4B 82.713 457 46 15 474 916 149737835 149738272 2.780000e-100 375
7 TraesCS2A01G490200 chr7B 82.051 468 47 15 464 916 683287373 683287818 6.020000e-97 364
8 TraesCS2A01G490200 chr3A 82.096 458 45 16 474 916 697483767 697483332 1.010000e-94 357
9 TraesCS2A01G490200 chr3A 80.758 343 38 16 246 579 411839635 411839312 2.940000e-60 243
10 TraesCS2A01G490200 chr3A 83.230 161 25 2 51 210 67315516 67315357 2.370000e-31 147
11 TraesCS2A01G490200 chr6A 80.963 457 46 15 474 916 103973057 103972628 1.020000e-84 324
12 TraesCS2A01G490200 chr6A 88.208 212 15 4 2745 2954 36679432 36679635 8.180000e-61 244
13 TraesCS2A01G490200 chr6A 86.792 212 18 4 2745 2954 64724801 64724598 8.240000e-56 228
14 TraesCS2A01G490200 chr6A 85.849 212 20 5 2745 2954 584585046 584585249 1.780000e-52 217
15 TraesCS2A01G490200 chr4A 85.623 313 21 10 2656 2952 684980545 684980241 1.030000e-79 307
16 TraesCS2A01G490200 chr1D 80.758 343 38 16 246 579 69689443 69689120 2.940000e-60 243
17 TraesCS2A01G490200 chr1A 87.678 211 16 5 2746 2954 573145356 573145558 1.370000e-58 237
18 TraesCS2A01G490200 chr3D 83.735 166 20 5 51 210 58303471 58303307 1.830000e-32 150


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 TraesCS2A01G490200 chr2A 723822678 723825631 2953 False 5456 5456 100.000 1 2954 1 chr2A.!!$F2 2953
1 TraesCS2A01G490200 chr2D 589495475 589500461 4986 False 1886 3341 87.796 4 2954 2 chr2D.!!$F1 2950
2 TraesCS2A01G490200 chr2B 713674165 713676253 2088 False 3009 3009 92.584 4 2126 1 chr2B.!!$F1 2122

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
407 418 0.188342 AGTGCCCAGTGGGTTCAATT 59.812 50.0 29.23 8.85 46.51 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2139 2171 0.179059 ACATTCTGACGGTGTGCACA 60.179 50.0 17.42 17.42 0.0 4.57 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
129 130 3.493176 GCAGCATCAACCCTCTTTGTTTT 60.493 43.478 0.00 0.00 0.00 2.43
131 132 3.004734 AGCATCAACCCTCTTTGTTTTCG 59.995 43.478 0.00 0.00 0.00 3.46
167 171 1.860906 CTAGGGTAGGGAGAGGACCTT 59.139 57.143 0.00 0.00 39.54 3.50
168 172 1.102938 AGGGTAGGGAGAGGACCTTT 58.897 55.000 0.00 0.00 39.54 3.11
179 183 5.186942 GGAGAGGACCTTTACAATTTCTCC 58.813 45.833 0.00 0.00 41.69 3.71
253 263 2.687418 GATGATCCAGGGGCATGCGT 62.687 60.000 12.44 0.00 0.00 5.24
270 280 2.700371 TGCGTAAGATGATGATCCAGGT 59.300 45.455 0.00 0.00 43.02 4.00
285 295 0.824109 CAGGTAGTTCGCCAGATCCA 59.176 55.000 0.00 0.00 0.00 3.41
295 305 1.739067 GCCAGATCCAGCGTTTAACT 58.261 50.000 0.00 0.00 0.00 2.24
308 318 3.858238 GCGTTTAACTTCGATGTAGAGCT 59.142 43.478 4.16 0.00 0.00 4.09
345 355 5.744666 CGGATTCCGCCTAAGATTTTAAA 57.255 39.130 12.95 0.00 41.17 1.52
348 358 6.204882 CGGATTCCGCCTAAGATTTTAAATCT 59.795 38.462 12.95 13.82 41.17 2.40
350 360 8.076781 GGATTCCGCCTAAGATTTTAAATCTTC 58.923 37.037 29.12 17.60 39.01 2.87
373 384 1.868498 CTGAAAAACGTTAGGCACCGA 59.132 47.619 0.00 0.00 0.00 4.69
380 391 1.270412 ACGTTAGGCACCGATGTTTGA 60.270 47.619 0.00 0.00 0.00 2.69
392 403 4.096382 ACCGATGTTTGATAATTCCAGTGC 59.904 41.667 0.00 0.00 0.00 4.40
403 414 2.282462 CCAGTGCCCAGTGGGTTC 60.282 66.667 29.23 20.87 46.51 3.62
404 415 2.515398 CAGTGCCCAGTGGGTTCA 59.485 61.111 29.23 16.89 46.51 3.18
405 416 1.152777 CAGTGCCCAGTGGGTTCAA 60.153 57.895 29.23 10.29 46.51 2.69
406 417 0.540365 CAGTGCCCAGTGGGTTCAAT 60.540 55.000 29.23 15.98 46.51 2.57
407 418 0.188342 AGTGCCCAGTGGGTTCAATT 59.812 50.000 29.23 8.85 46.51 2.32
408 419 1.047801 GTGCCCAGTGGGTTCAATTT 58.952 50.000 29.23 0.00 46.51 1.82
409 420 2.158385 AGTGCCCAGTGGGTTCAATTTA 60.158 45.455 29.23 3.57 46.51 1.40
410 421 2.630580 GTGCCCAGTGGGTTCAATTTAA 59.369 45.455 29.23 1.76 46.51 1.52
411 422 2.896685 TGCCCAGTGGGTTCAATTTAAG 59.103 45.455 29.23 0.00 46.51 1.85
412 423 2.897326 GCCCAGTGGGTTCAATTTAAGT 59.103 45.455 29.23 0.00 46.51 2.24
413 424 3.323691 GCCCAGTGGGTTCAATTTAAGTT 59.676 43.478 29.23 0.00 46.51 2.66
414 425 4.525100 GCCCAGTGGGTTCAATTTAAGTTA 59.475 41.667 29.23 0.00 46.51 2.24
415 426 5.566032 GCCCAGTGGGTTCAATTTAAGTTAC 60.566 44.000 29.23 2.78 46.51 2.50
416 427 5.773176 CCCAGTGGGTTCAATTTAAGTTACT 59.227 40.000 21.24 0.00 38.25 2.24
417 428 6.072119 CCCAGTGGGTTCAATTTAAGTTACTC 60.072 42.308 21.24 0.00 38.25 2.59
418 429 6.715264 CCAGTGGGTTCAATTTAAGTTACTCT 59.285 38.462 0.00 0.00 0.00 3.24
419 430 7.230712 CCAGTGGGTTCAATTTAAGTTACTCTT 59.769 37.037 0.00 0.00 39.89 2.85
420 431 8.630037 CAGTGGGTTCAATTTAAGTTACTCTTT 58.370 33.333 0.00 0.00 37.56 2.52
421 432 9.197306 AGTGGGTTCAATTTAAGTTACTCTTTT 57.803 29.630 0.00 0.00 37.56 2.27
440 451 9.713713 ACTCTTTTTAGATCTGAAGTTTCTACC 57.286 33.333 5.18 0.00 0.00 3.18
451 462 1.692519 AGTTTCTACCGGAGTTGCTGT 59.307 47.619 9.46 0.00 0.00 4.40
503 514 6.714810 TGTTCAGTATTGCCTCTGTATTTTGT 59.285 34.615 0.00 0.00 33.89 2.83
504 515 6.985188 TCAGTATTGCCTCTGTATTTTGTC 57.015 37.500 0.00 0.00 33.89 3.18
527 538 4.380531 TGTGCAAGTCTTTAGACCTCTTG 58.619 43.478 6.28 6.22 45.85 3.02
603 614 4.848660 AGGGTGTATATCTGATCCAGCAAT 59.151 41.667 12.83 0.00 0.00 3.56
668 680 9.610104 TTATTAGCAATCCTATGTCTAGGGTAA 57.390 33.333 0.00 0.00 44.22 2.85
733 745 6.391227 TTTTCTTTCTTCCATCCAACTGAC 57.609 37.500 0.00 0.00 0.00 3.51
760 772 5.158494 TGTTGTAATAGCAGACACTACACG 58.842 41.667 0.00 0.00 0.00 4.49
879 902 7.336975 GTGTTAATTGTTTCATGTGCAACTTC 58.663 34.615 0.00 0.00 38.04 3.01
923 947 8.906693 CGTCTCTGTACAATTAATAGCACTATG 58.093 37.037 0.00 0.00 0.00 2.23
997 1021 2.551912 AAAGTTCAGGTTGGCGCCG 61.552 57.895 23.90 6.99 0.00 6.46
1032 1056 6.238897 CGAAGAAGATAGAGCTAGACCACAAT 60.239 42.308 0.00 0.00 0.00 2.71
1115 1139 2.301296 ACTCCACTGTGAAGATCACCAG 59.699 50.000 9.86 7.84 46.40 4.00
1409 1433 1.890979 CTGTCATCTCCATGCGGCC 60.891 63.158 0.00 0.00 0.00 6.13
1449 1473 4.481112 GCAACCATTGAGCGGGCG 62.481 66.667 0.00 0.00 0.00 6.13
1644 1668 2.681706 CACAAAGAGTGCGTGAGAGAT 58.318 47.619 0.00 0.00 42.15 2.75
1680 1704 2.677875 CTGGGCCTGGCAAAGTCC 60.678 66.667 22.05 12.43 0.00 3.85
1767 1791 0.678048 GGGAAGGAAAGCTCATGCGT 60.678 55.000 0.00 0.00 45.42 5.24
1863 1887 3.775202 CGACATAACTCTGTGGAAGGAG 58.225 50.000 0.00 0.00 35.86 3.69
1869 1893 1.248486 CTCTGTGGAAGGAGTCGTCA 58.752 55.000 0.00 0.00 0.00 4.35
1935 1959 2.502492 GCAGGAGGAGCAGGCGATA 61.502 63.158 0.00 0.00 0.00 2.92
1955 1979 1.003442 AGGAGGCCATGCAGTAGGA 59.997 57.895 5.01 0.00 0.00 2.94
1956 1980 1.053264 AGGAGGCCATGCAGTAGGAG 61.053 60.000 5.01 0.00 0.00 3.69
1957 1981 1.449353 GAGGCCATGCAGTAGGAGG 59.551 63.158 5.01 0.00 0.00 4.30
1964 1988 0.639392 ATGCAGTAGGAGGGGAGTCT 59.361 55.000 0.00 0.00 0.00 3.24
1965 1989 0.324738 TGCAGTAGGAGGGGAGTCTG 60.325 60.000 0.00 0.00 0.00 3.51
2018 2042 1.803334 TTCGTGTTTCTAGCGCCAAT 58.197 45.000 2.29 0.00 0.00 3.16
2110 2142 3.489355 TGGACAATGTCTGATTGCACTT 58.511 40.909 13.53 0.00 32.47 3.16
2163 2195 2.193447 CACACCGTCAGAATGTATCGG 58.807 52.381 0.00 0.00 45.19 4.18
2176 2208 3.120321 TGTATCGGCTGTTTGAACTGT 57.880 42.857 0.00 0.00 0.00 3.55
2189 2221 6.908825 TGTTTGAACTGTTTATATCCTGCAC 58.091 36.000 0.00 0.00 0.00 4.57
2191 2223 6.741992 TTGAACTGTTTATATCCTGCACTG 57.258 37.500 0.00 0.00 0.00 3.66
2211 2243 4.160814 ACTGGCTGTTATCGGTGTTATGTA 59.839 41.667 0.00 0.00 0.00 2.29
2229 2267 2.734606 TGTATGCTCGTGTGTGTAAAGC 59.265 45.455 0.00 0.00 0.00 3.51
2234 2272 2.688507 CTCGTGTGTGTAAAGCTCCAT 58.311 47.619 0.00 0.00 0.00 3.41
2350 2388 1.964373 GTGGTCGTGGCCGTGAAAT 60.964 57.895 0.00 0.00 35.01 2.17
2358 2396 0.322997 TGGCCGTGAAATAACCTGGG 60.323 55.000 0.00 0.00 0.00 4.45
2378 2417 1.893062 GCTGGGGACAATTCTTGCC 59.107 57.895 0.00 0.00 42.06 4.52
2380 2419 0.609131 CTGGGGACAATTCTTGCCGT 60.609 55.000 0.00 0.00 42.06 5.68
2383 2422 0.953960 GGGACAATTCTTGCCGTCGT 60.954 55.000 0.00 0.00 0.00 4.34
2409 2448 0.889186 GCTCGTGGCCCTGAAAGAAA 60.889 55.000 0.00 0.00 31.99 2.52
2425 2471 5.588648 TGAAAGAAACTGATTGTTCCTCGTT 59.411 36.000 0.00 0.00 38.03 3.85
2426 2472 5.424121 AAGAAACTGATTGTTCCTCGTTG 57.576 39.130 0.00 0.00 38.03 4.10
2437 2483 1.248486 TCCTCGTTGTCTCTCCAGTG 58.752 55.000 0.00 0.00 0.00 3.66
2439 2485 0.730834 CTCGTTGTCTCTCCAGTGCG 60.731 60.000 0.00 0.00 0.00 5.34
2443 2489 2.059541 GTTGTCTCTCCAGTGCGTTAC 58.940 52.381 0.00 0.00 0.00 2.50
2444 2490 1.617322 TGTCTCTCCAGTGCGTTACT 58.383 50.000 0.00 0.00 41.36 2.24
2445 2491 1.961394 TGTCTCTCCAGTGCGTTACTT 59.039 47.619 0.00 0.00 37.60 2.24
2446 2492 2.364324 TGTCTCTCCAGTGCGTTACTTT 59.636 45.455 0.00 0.00 37.60 2.66
2447 2493 3.181469 TGTCTCTCCAGTGCGTTACTTTT 60.181 43.478 0.00 0.00 37.60 2.27
2448 2494 3.808174 GTCTCTCCAGTGCGTTACTTTTT 59.192 43.478 0.00 0.00 37.60 1.94
2487 4637 1.446272 CGGAGAACCAGACTTCGGC 60.446 63.158 0.00 0.00 33.34 5.54
2497 4647 3.330720 ACTTCGGCCCCTCCCTTG 61.331 66.667 0.00 0.00 0.00 3.61
2499 4649 3.327404 TTCGGCCCCTCCCTTGTC 61.327 66.667 0.00 0.00 0.00 3.18
2534 4684 1.040339 ACGAGCCTCTCAGTCCATCC 61.040 60.000 0.00 0.00 0.00 3.51
2541 4691 3.083349 TCAGTCCATCCCAGGCCG 61.083 66.667 0.00 0.00 0.00 6.13
2548 4698 2.447379 ATCCCAGGCCGCATCTCT 60.447 61.111 0.00 0.00 0.00 3.10
2559 4709 2.614581 GCATCTCTGCGCTGCTTAT 58.385 52.632 9.73 0.00 38.92 1.73
2565 4715 1.048724 TCTGCGCTGCTTATACCCCT 61.049 55.000 9.73 0.00 0.00 4.79
2566 4716 0.679505 CTGCGCTGCTTATACCCCTA 59.320 55.000 9.73 0.00 0.00 3.53
2567 4717 1.276421 CTGCGCTGCTTATACCCCTAT 59.724 52.381 9.73 0.00 0.00 2.57
2568 4718 2.496070 CTGCGCTGCTTATACCCCTATA 59.504 50.000 9.73 0.00 0.00 1.31
2569 4719 2.901192 TGCGCTGCTTATACCCCTATAA 59.099 45.455 9.73 0.00 0.00 0.98
2570 4720 3.325425 TGCGCTGCTTATACCCCTATAAA 59.675 43.478 9.73 0.00 0.00 1.40
2571 4721 3.933332 GCGCTGCTTATACCCCTATAAAG 59.067 47.826 0.00 0.00 0.00 1.85
2572 4722 4.322499 GCGCTGCTTATACCCCTATAAAGA 60.322 45.833 0.00 0.00 0.00 2.52
2573 4723 5.790593 CGCTGCTTATACCCCTATAAAGAA 58.209 41.667 0.00 0.00 0.00 2.52
2574 4724 6.228258 CGCTGCTTATACCCCTATAAAGAAA 58.772 40.000 0.00 0.00 0.00 2.52
2575 4725 6.147328 CGCTGCTTATACCCCTATAAAGAAAC 59.853 42.308 0.00 0.00 0.00 2.78
2576 4726 6.996282 GCTGCTTATACCCCTATAAAGAAACA 59.004 38.462 0.00 0.00 0.00 2.83
2577 4727 7.665974 GCTGCTTATACCCCTATAAAGAAACAT 59.334 37.037 0.00 0.00 0.00 2.71
2578 4728 9.220767 CTGCTTATACCCCTATAAAGAAACATC 57.779 37.037 0.00 0.00 0.00 3.06
2579 4729 8.945193 TGCTTATACCCCTATAAAGAAACATCT 58.055 33.333 0.00 0.00 0.00 2.90
2580 4730 9.220767 GCTTATACCCCTATAAAGAAACATCTG 57.779 37.037 0.00 0.00 0.00 2.90
2583 4733 8.980481 ATACCCCTATAAAGAAACATCTGTTG 57.020 34.615 0.00 0.00 38.44 3.33
2584 4734 5.652452 ACCCCTATAAAGAAACATCTGTTGC 59.348 40.000 0.00 0.00 38.44 4.17
2585 4735 5.888161 CCCCTATAAAGAAACATCTGTTGCT 59.112 40.000 0.00 0.00 45.58 3.91
2615 4765 2.202851 ATCTCTGCGCTGCTTCGG 60.203 61.111 9.73 0.00 0.00 4.30
2652 4802 4.541648 CGTCTCCCCGGGGATCCT 62.542 72.222 42.44 0.00 44.24 3.24
2721 4871 3.971702 GGAAGGGCTGCCACCACT 61.972 66.667 22.05 5.07 0.00 4.00
2735 4885 3.086600 CACTGCCTCCTCCCTCCC 61.087 72.222 0.00 0.00 0.00 4.30
2782 4932 3.352748 TCCTCGGCACCCCTCCTA 61.353 66.667 0.00 0.00 0.00 2.94
2783 4933 2.840102 CCTCGGCACCCCTCCTAG 60.840 72.222 0.00 0.00 0.00 3.02
2784 4934 2.840102 CTCGGCACCCCTCCTAGG 60.840 72.222 0.82 0.82 34.30 3.02
2787 4937 3.164977 GGCACCCCTCCTAGGCTC 61.165 72.222 2.96 0.00 32.73 4.70
2788 4938 3.164977 GCACCCCTCCTAGGCTCC 61.165 72.222 2.96 0.00 32.73 4.70
2789 4939 2.699496 CACCCCTCCTAGGCTCCT 59.301 66.667 2.96 0.00 32.73 3.69
2790 4940 1.458588 CACCCCTCCTAGGCTCCTC 60.459 68.421 2.96 0.00 32.73 3.71
2791 4941 2.202899 CCCCTCCTAGGCTCCTCC 59.797 72.222 2.96 0.00 32.73 4.30
2793 4943 1.152355 CCCTCCTAGGCTCCTCCTG 60.152 68.421 2.96 0.00 46.98 3.86
2808 4958 4.271816 CTGCGTCGGATCCCCTCG 62.272 72.222 6.06 9.64 0.00 4.63
2840 4990 2.369394 GTGCTCCCTTGATTCCGATTT 58.631 47.619 0.00 0.00 0.00 2.17
2843 4993 2.213499 CTCCCTTGATTCCGATTTCCG 58.787 52.381 0.00 0.00 38.18 4.30
2860 5010 1.954382 TCCGAGTGTCCTCATAATCCG 59.046 52.381 0.00 0.00 37.59 4.18
2863 5013 3.372954 CGAGTGTCCTCATAATCCGTTC 58.627 50.000 0.00 0.00 37.59 3.95
2869 5019 1.202533 CCTCATAATCCGTTCGTGCCT 60.203 52.381 0.00 0.00 0.00 4.75
2876 5026 0.738975 TCCGTTCGTGCCTGATAGAG 59.261 55.000 0.00 0.00 0.00 2.43
2902 5052 5.952347 AGGGTTAACTATCCTTCGATGTT 57.048 39.130 5.42 0.00 0.00 2.71
2903 5053 5.915175 AGGGTTAACTATCCTTCGATGTTC 58.085 41.667 5.42 0.00 0.00 3.18
2904 5054 4.743644 GGGTTAACTATCCTTCGATGTTCG 59.256 45.833 5.42 0.00 42.10 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
129 130 4.058124 CCTAGCGGAATTGATTGATTCGA 58.942 43.478 0.00 0.00 36.99 3.71
131 132 4.137543 ACCCTAGCGGAATTGATTGATTC 58.862 43.478 4.45 0.00 35.71 2.52
167 171 3.546002 CGGCAAACGGAGAAATTGTAA 57.454 42.857 0.00 0.00 39.42 2.41
253 263 5.279006 GCGAACTACCTGGATCATCATCTTA 60.279 44.000 0.00 0.00 0.00 2.10
285 295 3.858238 GCTCTACATCGAAGTTAAACGCT 59.142 43.478 0.00 0.00 0.00 5.07
290 300 3.430374 GGCCAGCTCTACATCGAAGTTAA 60.430 47.826 0.00 0.00 0.00 2.01
291 301 2.100916 GGCCAGCTCTACATCGAAGTTA 59.899 50.000 0.00 0.00 0.00 2.24
292 302 1.134670 GGCCAGCTCTACATCGAAGTT 60.135 52.381 0.00 0.00 0.00 2.66
293 303 0.461961 GGCCAGCTCTACATCGAAGT 59.538 55.000 0.00 0.00 0.00 3.01
294 304 0.249657 GGGCCAGCTCTACATCGAAG 60.250 60.000 4.39 0.00 0.00 3.79
295 305 0.687757 AGGGCCAGCTCTACATCGAA 60.688 55.000 6.18 0.00 0.00 3.71
330 340 8.883731 TCAGAAGAAGATTTAAAATCTTAGGCG 58.116 33.333 0.00 0.00 38.38 5.52
344 354 6.262273 TGCCTAACGTTTTTCAGAAGAAGATT 59.738 34.615 5.91 0.00 34.71 2.40
345 355 5.763204 TGCCTAACGTTTTTCAGAAGAAGAT 59.237 36.000 5.91 0.00 34.71 2.40
348 358 4.035909 GGTGCCTAACGTTTTTCAGAAGAA 59.964 41.667 5.91 0.00 0.00 2.52
350 360 3.606153 CGGTGCCTAACGTTTTTCAGAAG 60.606 47.826 5.91 0.00 0.00 2.85
362 372 5.751243 ATTATCAAACATCGGTGCCTAAC 57.249 39.130 0.00 0.00 0.00 2.34
373 384 4.352009 TGGGCACTGGAATTATCAAACAT 58.648 39.130 0.00 0.00 0.00 2.71
380 391 1.063717 CCCACTGGGCACTGGAATTAT 60.064 52.381 0.00 0.00 35.35 1.28
414 425 9.713713 GGTAGAAACTTCAGATCTAAAAAGAGT 57.286 33.333 15.06 3.44 0.00 3.24
415 426 8.865001 CGGTAGAAACTTCAGATCTAAAAAGAG 58.135 37.037 15.06 2.95 0.00 2.85
416 427 7.817962 CCGGTAGAAACTTCAGATCTAAAAAGA 59.182 37.037 15.06 0.00 0.00 2.52
417 428 7.817962 TCCGGTAGAAACTTCAGATCTAAAAAG 59.182 37.037 0.00 2.59 0.00 2.27
418 429 7.673180 TCCGGTAGAAACTTCAGATCTAAAAA 58.327 34.615 0.00 0.00 0.00 1.94
419 430 7.039223 ACTCCGGTAGAAACTTCAGATCTAAAA 60.039 37.037 0.00 0.00 0.00 1.52
420 431 6.436532 ACTCCGGTAGAAACTTCAGATCTAAA 59.563 38.462 0.00 0.00 0.00 1.85
421 432 5.950549 ACTCCGGTAGAAACTTCAGATCTAA 59.049 40.000 0.00 0.00 0.00 2.10
436 447 1.298859 GCCAACAGCAACTCCGGTAG 61.299 60.000 0.00 0.00 42.97 3.18
451 462 5.263599 ACTGAACCAATATGAATGAGCCAA 58.736 37.500 0.00 0.00 0.00 4.52
487 498 3.253188 GCACAGACAAAATACAGAGGCAA 59.747 43.478 0.00 0.00 0.00 4.52
503 514 3.898123 AGAGGTCTAAAGACTTGCACAGA 59.102 43.478 9.84 0.00 44.20 3.41
504 515 4.264460 AGAGGTCTAAAGACTTGCACAG 57.736 45.455 9.84 0.00 44.20 3.66
527 538 5.065731 CCTTGAATCTAGTCATGGCAAAGAC 59.934 44.000 13.63 13.63 36.40 3.01
603 614 2.025037 ACTCCCAGCATTATCCTGCAAA 60.025 45.455 0.00 0.00 44.77 3.68
672 684 8.677148 ACATCAAACTTACTAGTGTCACAAAT 57.323 30.769 5.39 0.00 34.01 2.32
708 720 7.436933 GTCAGTTGGATGGAAGAAAGAAAAAT 58.563 34.615 0.00 0.00 0.00 1.82
760 772 3.892588 TCACTTTCCCACAAACCCATAAC 59.107 43.478 0.00 0.00 0.00 1.89
879 902 1.995484 ACGAACTGCATCAGACAATCG 59.005 47.619 0.29 7.43 35.18 3.34
923 947 3.926616 TCGATTCAGGAAAACAGACCTC 58.073 45.455 0.00 0.00 33.91 3.85
997 1021 5.158101 TCTATCTTCTTCGACGACATGTC 57.842 43.478 16.21 16.21 44.53 3.06
1032 1056 3.018856 GGCAGAATCATGAACCATGTCA 58.981 45.455 0.00 0.00 41.98 3.58
1115 1139 1.436336 GCAGATGCACCTCCAATGC 59.564 57.895 0.00 0.00 43.68 3.56
1146 1170 2.425592 CCAGTGAGGGTCGCAACA 59.574 61.111 0.00 0.00 0.00 3.33
1409 1433 2.544694 GCGTCACATCCTCCTGTATCAG 60.545 54.545 0.00 0.00 0.00 2.90
1428 1452 2.202388 CGCTCAATGGTTGCAGCG 60.202 61.111 16.04 16.04 44.29 5.18
1644 1668 2.927856 ACCGGTGCCCATGAGACA 60.928 61.111 6.12 0.00 0.00 3.41
1767 1791 2.282958 ACCGGAGCCTCGAAGTCA 60.283 61.111 9.46 0.00 0.00 3.41
1863 1887 2.430921 CACTGCCCGTCTGACGAC 60.431 66.667 29.93 21.02 46.05 4.34
1869 1893 2.997897 GACTCCCACTGCCCGTCT 60.998 66.667 0.00 0.00 0.00 4.18
1935 1959 1.053264 CCTACTGCATGGCCTCCTCT 61.053 60.000 3.32 0.00 0.00 3.69
1956 1980 4.101448 ATGTGGCGCAGACTCCCC 62.101 66.667 10.83 0.00 34.59 4.81
1957 1981 2.512515 GATGTGGCGCAGACTCCC 60.513 66.667 10.83 0.00 34.59 4.30
1964 1988 4.758251 CACGGGAGATGTGGCGCA 62.758 66.667 10.83 1.92 33.69 6.09
1965 1989 4.760047 ACACGGGAGATGTGGCGC 62.760 66.667 0.00 0.00 41.64 6.53
2018 2042 0.961019 GGTGAAAGCAAGTCATGGCA 59.039 50.000 0.00 0.00 0.00 4.92
2087 2119 3.442625 AGTGCAATCAGACATTGTCCATG 59.557 43.478 13.14 6.46 39.07 3.66
2139 2171 0.179059 ACATTCTGACGGTGTGCACA 60.179 50.000 17.42 17.42 0.00 4.57
2163 2195 6.030228 GCAGGATATAAACAGTTCAAACAGC 58.970 40.000 0.00 0.00 0.00 4.40
2176 2208 3.931907 ACAGCCAGTGCAGGATATAAA 57.068 42.857 0.00 0.00 41.13 1.40
2189 2221 3.531538 ACATAACACCGATAACAGCCAG 58.468 45.455 0.00 0.00 0.00 4.85
2191 2223 4.084013 GCATACATAACACCGATAACAGCC 60.084 45.833 0.00 0.00 0.00 4.85
2211 2243 2.069273 GAGCTTTACACACACGAGCAT 58.931 47.619 0.00 0.00 35.86 3.79
2229 2267 1.679680 GGTTCCACATGCATCATGGAG 59.320 52.381 22.51 3.97 45.16 3.86
2285 2323 3.451004 TGTGGCGGCCATCAATGC 61.451 61.111 26.68 11.62 35.28 3.56
2286 2324 2.491152 GTGTGGCGGCCATCAATG 59.509 61.111 26.68 0.00 35.28 2.82
2287 2325 2.755469 GGTGTGGCGGCCATCAAT 60.755 61.111 26.68 0.00 35.28 2.57
2299 2337 2.677003 GCCATCAACCGACGGTGTG 61.677 63.158 22.53 19.50 35.34 3.82
2300 2338 2.358247 GCCATCAACCGACGGTGT 60.358 61.111 22.53 8.11 35.34 4.16
2335 2373 0.445043 GGTTATTTCACGGCCACGAC 59.555 55.000 2.24 0.00 44.60 4.34
2358 2396 1.508088 CAAGAATTGTCCCCAGCGC 59.492 57.895 0.00 0.00 42.34 5.92
2378 2417 1.796355 CACGAGCACACCTACGACG 60.796 63.158 0.00 0.00 0.00 5.12
2380 2419 2.959372 CCACGAGCACACCTACGA 59.041 61.111 0.00 0.00 0.00 3.43
2409 2448 3.322254 AGAGACAACGAGGAACAATCAGT 59.678 43.478 0.00 0.00 0.00 3.41
2425 2471 1.617322 AGTAACGCACTGGAGAGACA 58.383 50.000 0.00 0.00 35.62 3.41
2426 2472 2.726832 AAGTAACGCACTGGAGAGAC 57.273 50.000 0.00 0.00 37.63 3.36
2475 2521 3.003763 GAGGGGCCGAAGTCTGGT 61.004 66.667 0.00 0.00 0.00 4.00
2477 2523 3.787001 GGGAGGGGCCGAAGTCTG 61.787 72.222 0.00 0.00 37.63 3.51
2478 2524 3.564347 AAGGGAGGGGCCGAAGTCT 62.564 63.158 0.00 0.00 37.63 3.24
2479 2525 3.009714 AAGGGAGGGGCCGAAGTC 61.010 66.667 0.00 0.00 37.63 3.01
2487 4637 3.732849 GGCCAGACAAGGGAGGGG 61.733 72.222 0.00 0.00 0.00 4.79
2509 4659 1.739562 CTGAGAGGCTCGTGGTTGC 60.740 63.158 9.22 0.00 32.35 4.17
2522 4672 1.690633 GGCCTGGGATGGACTGAGA 60.691 63.158 0.00 0.00 30.82 3.27
2548 4698 1.348064 ATAGGGGTATAAGCAGCGCA 58.652 50.000 11.47 0.00 0.00 6.09
2559 4709 6.826741 GCAACAGATGTTTCTTTATAGGGGTA 59.173 38.462 0.00 0.00 35.83 3.69
2569 4719 9.651913 TTTTTCTTAAAGCAACAGATGTTTCTT 57.348 25.926 5.00 5.00 41.84 2.52
2596 4746 1.808799 CGAAGCAGCGCAGAGATGT 60.809 57.895 11.47 0.00 38.76 3.06
2597 4747 2.523507 CCGAAGCAGCGCAGAGATG 61.524 63.158 11.47 0.00 39.70 2.90
2615 4765 3.462678 GACGGTGGGAGGGAGAGC 61.463 72.222 0.00 0.00 0.00 4.09
2618 4768 2.760385 GAGGACGGTGGGAGGGAG 60.760 72.222 0.00 0.00 0.00 4.30
2689 4839 0.239347 CTTCCAAGTTGCAAGAGCCG 59.761 55.000 0.00 0.00 41.13 5.52
2697 4847 2.653115 GCAGCCCTTCCAAGTTGC 59.347 61.111 0.00 0.00 0.00 4.17
2784 4934 3.492311 GATCCGACGCAGGAGGAGC 62.492 68.421 5.68 0.00 44.55 4.70
2785 4935 2.725008 GATCCGACGCAGGAGGAG 59.275 66.667 5.68 0.00 44.55 3.69
2786 4936 2.833582 GGATCCGACGCAGGAGGA 60.834 66.667 0.00 0.00 44.55 3.71
2787 4937 3.917760 GGGATCCGACGCAGGAGG 61.918 72.222 5.45 0.00 44.55 4.30
2788 4938 3.917760 GGGGATCCGACGCAGGAG 61.918 72.222 5.45 0.00 44.55 3.69
2789 4939 4.458829 AGGGGATCCGACGCAGGA 62.459 66.667 5.45 1.75 45.54 3.86
2790 4940 3.917760 GAGGGGATCCGACGCAGG 61.918 72.222 5.45 0.00 38.33 4.85
2791 4941 4.271816 CGAGGGGATCCGACGCAG 62.272 72.222 5.45 0.00 38.33 5.18
2808 4958 3.112709 GAGCACGGAACTCACGGC 61.113 66.667 0.00 0.00 34.18 5.68
2843 4993 3.181489 ACGAACGGATTATGAGGACACTC 60.181 47.826 0.00 0.00 44.23 3.51
2869 5019 6.254522 GGATAGTTAACCCTAGCCTCTATCA 58.745 44.000 0.88 0.00 39.79 2.15
2876 5026 3.893813 TCGAAGGATAGTTAACCCTAGCC 59.106 47.826 0.88 1.45 42.57 3.93
2887 5037 4.643784 ACTAACCGAACATCGAAGGATAGT 59.356 41.667 0.58 0.60 43.74 2.12
2902 5052 3.517602 CGTTCCATCAATCACTAACCGA 58.482 45.455 0.00 0.00 0.00 4.69
2903 5053 2.030457 GCGTTCCATCAATCACTAACCG 59.970 50.000 0.00 0.00 0.00 4.44
2904 5054 2.354821 GGCGTTCCATCAATCACTAACC 59.645 50.000 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.