Multiple sequence alignment - TraesCS2A01G315900

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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 TraesCS2A01G315900 chr2A 100.000 2624 0 0 1 2624 541837902 541835279 0.000000e+00 4846.0
1 TraesCS2A01G315900 chr2B 89.268 2171 117 52 12 2116 477596935 477594815 0.000000e+00 2612.0
2 TraesCS2A01G315900 chr2B 88.476 807 64 13 456 1255 574921922 574922706 0.000000e+00 948.0
3 TraesCS2A01G315900 chr2B 93.199 544 25 5 2082 2624 477594816 477594284 0.000000e+00 789.0
4 TraesCS2A01G315900 chr2D 91.888 1467 53 18 451 1887 403486849 403485419 0.000000e+00 1989.0
5 TraesCS2A01G315900 chr2D 95.588 544 17 4 2082 2624 403484458 403483921 0.000000e+00 865.0
6 TraesCS2A01G315900 chr2D 84.755 387 19 9 4 377 403487283 403486924 4.160000e-93 351.0
7 TraesCS2A01G315900 chr2D 93.642 173 10 1 1944 2116 403484661 403484490 9.320000e-65 257.0
8 TraesCS2A01G315900 chr4B 89.193 805 63 13 456 1255 351297538 351296753 0.000000e+00 983.0
9 TraesCS2A01G315900 chr4B 88.865 467 30 11 460 921 257300444 257300893 2.950000e-154 555.0
10 TraesCS2A01G315900 chr1B 92.500 40 3 0 374 413 14142932 14142893 1.010000e-04 58.4
11 TraesCS2A01G315900 chr1D 100.000 29 0 0 376 404 83942038 83942066 1.000000e-03 54.7


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 TraesCS2A01G315900 chr2A 541835279 541837902 2623 True 4846.0 4846 100.00000 1 2624 1 chr2A.!!$R1 2623
1 TraesCS2A01G315900 chr2B 477594284 477596935 2651 True 1700.5 2612 91.23350 12 2624 2 chr2B.!!$R1 2612
2 TraesCS2A01G315900 chr2B 574921922 574922706 784 False 948.0 948 88.47600 456 1255 1 chr2B.!!$F1 799
3 TraesCS2A01G315900 chr2D 403483921 403487283 3362 True 865.5 1989 91.46825 4 2624 4 chr2D.!!$R1 2620
4 TraesCS2A01G315900 chr4B 351296753 351297538 785 True 983.0 983 89.19300 456 1255 1 chr4B.!!$R1 799

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
922 1033 0.171903 GGCTCAATTGCGCATTGTCT 59.828 50.0 21.09 0.0 42.79 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2520 3455 0.605589 GGCCGACACCTTTAAGCACT 60.606 55.0 0.0 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
23 24 2.819595 CCATCGGTGGTTGGCGAG 60.820 66.667 6.53 0.00 40.83 5.03
43 44 3.044305 GACAGAGCACCACACGCC 61.044 66.667 0.00 0.00 0.00 5.68
96 108 2.761208 TGCCGAAAAAGGAAACAGGAAA 59.239 40.909 0.00 0.00 0.00 3.13
97 109 3.195825 TGCCGAAAAAGGAAACAGGAAAA 59.804 39.130 0.00 0.00 0.00 2.29
98 110 3.802139 GCCGAAAAAGGAAACAGGAAAAG 59.198 43.478 0.00 0.00 0.00 2.27
99 111 4.440940 GCCGAAAAAGGAAACAGGAAAAGA 60.441 41.667 0.00 0.00 0.00 2.52
100 112 5.281727 CCGAAAAAGGAAACAGGAAAAGAG 58.718 41.667 0.00 0.00 0.00 2.85
101 113 5.067283 CCGAAAAAGGAAACAGGAAAAGAGA 59.933 40.000 0.00 0.00 0.00 3.10
102 114 6.405397 CCGAAAAAGGAAACAGGAAAAGAGAA 60.405 38.462 0.00 0.00 0.00 2.87
103 115 7.203218 CGAAAAAGGAAACAGGAAAAGAGAAT 58.797 34.615 0.00 0.00 0.00 2.40
104 116 7.168135 CGAAAAAGGAAACAGGAAAAGAGAATG 59.832 37.037 0.00 0.00 0.00 2.67
105 117 6.410942 AAAGGAAACAGGAAAAGAGAATGG 57.589 37.500 0.00 0.00 0.00 3.16
106 118 3.829026 AGGAAACAGGAAAAGAGAATGGC 59.171 43.478 0.00 0.00 0.00 4.40
129 141 0.942252 AAACCGACGGAAAAGCAGAC 59.058 50.000 23.38 0.00 0.00 3.51
246 270 3.100671 TCTTTAGCTTCCTCTGTCTCCC 58.899 50.000 0.00 0.00 0.00 4.30
256 280 3.775316 TCCTCTGTCTCCCCATCTTTAAC 59.225 47.826 0.00 0.00 0.00 2.01
266 290 6.099845 TCTCCCCATCTTTAACTAATCTGGAC 59.900 42.308 0.00 0.00 0.00 4.02
324 348 3.810941 GGGATTTCAAACACGTGTCACTA 59.189 43.478 23.61 7.28 0.00 2.74
325 349 4.454504 GGGATTTCAAACACGTGTCACTAT 59.545 41.667 23.61 11.83 0.00 2.12
326 350 5.640357 GGGATTTCAAACACGTGTCACTATA 59.360 40.000 23.61 6.73 0.00 1.31
327 351 6.315393 GGGATTTCAAACACGTGTCACTATAT 59.685 38.462 23.61 11.31 0.00 0.86
328 352 7.493320 GGGATTTCAAACACGTGTCACTATATA 59.507 37.037 23.61 3.52 0.00 0.86
329 353 9.042008 GGATTTCAAACACGTGTCACTATATAT 57.958 33.333 23.61 8.24 0.00 0.86
371 395 2.574006 TCTGAGCAGAGGCAAACAAT 57.426 45.000 0.00 0.00 44.61 2.71
372 396 2.156917 TCTGAGCAGAGGCAAACAATG 58.843 47.619 0.00 0.00 44.61 2.82
373 397 3.711278 TCTGAGCAGAGGCAAACAATGC 61.711 50.000 0.00 0.00 42.71 3.56
385 409 3.558505 CAAACAATGCTCTCGAAACAGG 58.441 45.455 0.00 0.00 0.00 4.00
386 410 1.160137 ACAATGCTCTCGAAACAGGC 58.840 50.000 0.00 0.00 0.00 4.85
387 411 1.271054 ACAATGCTCTCGAAACAGGCT 60.271 47.619 0.00 0.00 0.00 4.58
388 412 1.808945 CAATGCTCTCGAAACAGGCTT 59.191 47.619 0.00 0.00 0.00 4.35
389 413 2.191128 ATGCTCTCGAAACAGGCTTT 57.809 45.000 0.00 0.00 0.00 3.51
390 414 1.512926 TGCTCTCGAAACAGGCTTTC 58.487 50.000 0.00 0.00 0.00 2.62
391 415 1.202639 TGCTCTCGAAACAGGCTTTCA 60.203 47.619 0.33 0.00 0.00 2.69
392 416 1.195674 GCTCTCGAAACAGGCTTTCAC 59.804 52.381 0.33 0.00 0.00 3.18
393 417 1.801178 CTCTCGAAACAGGCTTTCACC 59.199 52.381 0.33 0.00 0.00 4.02
394 418 0.875059 CTCGAAACAGGCTTTCACCC 59.125 55.000 0.33 0.00 0.00 4.61
395 419 0.536460 TCGAAACAGGCTTTCACCCC 60.536 55.000 0.33 0.00 0.00 4.95
396 420 1.852067 CGAAACAGGCTTTCACCCCG 61.852 60.000 0.33 0.00 0.00 5.73
397 421 0.822121 GAAACAGGCTTTCACCCCGT 60.822 55.000 0.00 0.00 0.00 5.28
398 422 0.396556 AAACAGGCTTTCACCCCGTT 60.397 50.000 0.00 0.00 0.00 4.44
399 423 0.396556 AACAGGCTTTCACCCCGTTT 60.397 50.000 0.00 0.00 0.00 3.60
400 424 0.396556 ACAGGCTTTCACCCCGTTTT 60.397 50.000 0.00 0.00 0.00 2.43
401 425 1.133730 ACAGGCTTTCACCCCGTTTTA 60.134 47.619 0.00 0.00 0.00 1.52
402 426 2.167662 CAGGCTTTCACCCCGTTTTAT 58.832 47.619 0.00 0.00 0.00 1.40
403 427 3.244981 ACAGGCTTTCACCCCGTTTTATA 60.245 43.478 0.00 0.00 0.00 0.98
404 428 3.128068 CAGGCTTTCACCCCGTTTTATAC 59.872 47.826 0.00 0.00 0.00 1.47
405 429 3.083293 GGCTTTCACCCCGTTTTATACA 58.917 45.455 0.00 0.00 0.00 2.29
406 430 3.697542 GGCTTTCACCCCGTTTTATACAT 59.302 43.478 0.00 0.00 0.00 2.29
412 436 2.240160 ACCCCGTTTTATACATGAGGCA 59.760 45.455 0.00 0.00 0.00 4.75
413 437 2.878406 CCCCGTTTTATACATGAGGCAG 59.122 50.000 0.00 0.00 0.00 4.85
429 454 1.374190 CAGGCAGTGCTCTGGAAGT 59.626 57.895 16.11 0.00 41.57 3.01
441 480 3.251972 GCTCTGGAAGTTGGAAGTGAAAG 59.748 47.826 0.00 0.00 33.76 2.62
443 482 5.310409 TCTGGAAGTTGGAAGTGAAAGAT 57.690 39.130 0.00 0.00 33.76 2.40
462 504 2.584835 TCAACACATTCCCAAGGGAG 57.415 50.000 8.06 0.24 46.06 4.30
482 524 6.667414 AGGGAGGTGATGAATATGATCTAGAC 59.333 42.308 0.00 0.00 0.00 2.59
576 672 0.179100 CAGGGACGATCATTGACGCT 60.179 55.000 0.00 0.00 0.00 5.07
607 705 7.718272 TTTATAAGCGGCTAATCACGTTTAT 57.282 32.000 1.35 10.13 44.57 1.40
661 759 0.721718 CCGTGGCTAAAGAGAAAGCG 59.278 55.000 0.00 0.00 39.71 4.68
788 886 5.385509 TCCTTTTCCGAGGCTTAAAAATG 57.614 39.130 0.00 0.00 36.71 2.32
801 900 5.515270 GGCTTAAAAATGGCTTAATCACGAC 59.485 40.000 0.00 0.00 0.00 4.34
922 1033 0.171903 GGCTCAATTGCGCATTGTCT 59.828 50.000 21.09 0.00 42.79 3.41
923 1034 1.265568 GCTCAATTGCGCATTGTCTG 58.734 50.000 12.75 12.77 42.79 3.51
924 1035 1.401931 GCTCAATTGCGCATTGTCTGT 60.402 47.619 12.75 0.00 42.79 3.41
925 1036 2.512885 CTCAATTGCGCATTGTCTGTC 58.487 47.619 12.75 0.00 42.79 3.51
933 1044 0.445436 GCATTGTCTGTCCTCTTGCG 59.555 55.000 0.00 0.00 0.00 4.85
989 1100 4.468689 GGGAACGGAGGAAGGGCG 62.469 72.222 0.00 0.00 0.00 6.13
991 1102 4.468689 GAACGGAGGAAGGGCGGG 62.469 72.222 0.00 0.00 0.00 6.13
1247 1358 2.827642 GAGGCTGCACTCCATGGC 60.828 66.667 6.96 0.00 0.00 4.40
1437 1551 4.436998 GCCGTGGACAGGAGGACG 62.437 72.222 0.00 0.00 0.00 4.79
1660 1781 1.811266 ATGTCCGCGTGTGCATCTC 60.811 57.895 4.92 0.00 42.97 2.75
1665 1786 1.226295 CGCGTGTGCATCTCTCGTA 60.226 57.895 0.00 0.00 42.97 3.43
1700 1821 0.476771 AACGGGGAAGTGTGATGGTT 59.523 50.000 0.00 0.00 0.00 3.67
1701 1822 1.354101 ACGGGGAAGTGTGATGGTTA 58.646 50.000 0.00 0.00 0.00 2.85
1702 1823 1.700739 ACGGGGAAGTGTGATGGTTAA 59.299 47.619 0.00 0.00 0.00 2.01
1703 1824 2.307686 ACGGGGAAGTGTGATGGTTAAT 59.692 45.455 0.00 0.00 0.00 1.40
1704 1825 3.245122 ACGGGGAAGTGTGATGGTTAATT 60.245 43.478 0.00 0.00 0.00 1.40
1705 1826 3.761752 CGGGGAAGTGTGATGGTTAATTT 59.238 43.478 0.00 0.00 0.00 1.82
1706 1827 4.219725 CGGGGAAGTGTGATGGTTAATTTT 59.780 41.667 0.00 0.00 0.00 1.82
1707 1828 5.478407 GGGGAAGTGTGATGGTTAATTTTG 58.522 41.667 0.00 0.00 0.00 2.44
1708 1829 5.011635 GGGGAAGTGTGATGGTTAATTTTGT 59.988 40.000 0.00 0.00 0.00 2.83
1790 1926 3.118738 CCTATCTTGGGCAAGTTACGTCT 60.119 47.826 0.00 0.00 39.38 4.18
1807 1943 5.824243 ACGTCTTGTATATATTTCGCTGC 57.176 39.130 0.00 0.00 0.00 5.25
1904 2042 5.890334 TGAGTTTGTTTGTCTGATTGAACC 58.110 37.500 0.00 0.00 0.00 3.62
1905 2043 5.652014 TGAGTTTGTTTGTCTGATTGAACCT 59.348 36.000 0.00 0.00 0.00 3.50
1906 2044 6.152661 TGAGTTTGTTTGTCTGATTGAACCTT 59.847 34.615 0.00 0.00 0.00 3.50
1939 2077 4.318332 CGGCATACACATCCATGAATACT 58.682 43.478 0.00 0.00 0.00 2.12
1940 2078 5.478407 CGGCATACACATCCATGAATACTA 58.522 41.667 0.00 0.00 0.00 1.82
1967 2832 3.820557 ACAGAGCCAATAGTGTGTTGTT 58.179 40.909 0.00 0.00 0.00 2.83
1976 2841 5.280011 CCAATAGTGTGTTGTTACTCCCTCT 60.280 44.000 0.00 0.00 0.00 3.69
1997 2862 6.368791 CCTCTGTTCGAAAATAACTGACATGA 59.631 38.462 0.00 0.00 33.14 3.07
2017 2882 8.408043 ACATGATTTTAGTTTGAGACCATCAA 57.592 30.769 0.00 0.00 46.31 2.57
2123 3054 4.326826 TCTGAATGCCAACCTTACAAGAG 58.673 43.478 0.00 0.00 0.00 2.85
2134 3065 6.349777 CCAACCTTACAAGAGTTGTTTTCACA 60.350 38.462 15.76 0.00 42.22 3.58
2417 3348 3.705604 ACGCACATTTTGAACAGGAAAG 58.294 40.909 0.00 0.00 0.00 2.62
2505 3440 9.515226 TGATTTATTCCTTGCTTTTGTACTACT 57.485 29.630 0.00 0.00 0.00 2.57
2519 3454 7.528996 TTTGTACTACTAGTTCCTGTTGCTA 57.471 36.000 0.00 0.00 0.00 3.49
2520 3455 7.528996 TTGTACTACTAGTTCCTGTTGCTAA 57.471 36.000 0.00 0.00 0.00 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 3.044305 GTGTGGTGCTCTGTCGCC 61.044 66.667 0.00 0.00 37.15 5.54
43 44 2.072298 GAGCAAGCTGGTAGAGTGTTG 58.928 52.381 0.00 0.00 0.00 3.33
96 108 2.814336 GTCGGTTTCTTGCCATTCTCTT 59.186 45.455 0.00 0.00 0.00 2.85
97 109 2.427506 GTCGGTTTCTTGCCATTCTCT 58.572 47.619 0.00 0.00 0.00 3.10
98 110 1.128692 CGTCGGTTTCTTGCCATTCTC 59.871 52.381 0.00 0.00 0.00 2.87
99 111 1.156736 CGTCGGTTTCTTGCCATTCT 58.843 50.000 0.00 0.00 0.00 2.40
100 112 0.168128 CCGTCGGTTTCTTGCCATTC 59.832 55.000 2.08 0.00 0.00 2.67
101 113 0.250553 TCCGTCGGTTTCTTGCCATT 60.251 50.000 11.88 0.00 0.00 3.16
102 114 0.250553 TTCCGTCGGTTTCTTGCCAT 60.251 50.000 11.88 0.00 0.00 4.40
103 115 0.464013 TTTCCGTCGGTTTCTTGCCA 60.464 50.000 11.88 0.00 0.00 4.92
104 116 0.664224 TTTTCCGTCGGTTTCTTGCC 59.336 50.000 11.88 0.00 0.00 4.52
105 117 1.924629 GCTTTTCCGTCGGTTTCTTGC 60.925 52.381 11.88 6.13 0.00 4.01
106 118 1.332375 TGCTTTTCCGTCGGTTTCTTG 59.668 47.619 11.88 0.00 0.00 3.02
129 141 4.225497 CTTTAGCAAGCTCCCCCG 57.775 61.111 0.00 0.00 0.00 5.73
246 270 5.986135 CCGAGTCCAGATTAGTTAAAGATGG 59.014 44.000 0.00 0.00 0.00 3.51
256 280 3.829601 AGCCTAATCCGAGTCCAGATTAG 59.170 47.826 20.79 20.79 46.07 1.73
266 290 0.178929 ACCCCCTAGCCTAATCCGAG 60.179 60.000 0.00 0.00 0.00 4.63
277 301 6.234177 CAAAATCTAGATTAGCACCCCCTAG 58.766 44.000 18.23 0.00 0.00 3.02
364 388 3.558505 CCTGTTTCGAGAGCATTGTTTG 58.441 45.455 0.00 0.00 0.00 2.93
365 389 2.030805 GCCTGTTTCGAGAGCATTGTTT 60.031 45.455 0.00 0.00 0.00 2.83
366 390 1.537202 GCCTGTTTCGAGAGCATTGTT 59.463 47.619 0.00 0.00 0.00 2.83
367 391 1.160137 GCCTGTTTCGAGAGCATTGT 58.840 50.000 0.00 0.00 0.00 2.71
368 392 1.446907 AGCCTGTTTCGAGAGCATTG 58.553 50.000 0.00 0.00 0.00 2.82
369 393 2.191128 AAGCCTGTTTCGAGAGCATT 57.809 45.000 0.00 0.00 0.00 3.56
370 394 2.079925 GAAAGCCTGTTTCGAGAGCAT 58.920 47.619 0.00 0.00 0.00 3.79
371 395 1.202639 TGAAAGCCTGTTTCGAGAGCA 60.203 47.619 0.00 0.00 0.00 4.26
372 396 1.195674 GTGAAAGCCTGTTTCGAGAGC 59.804 52.381 0.00 0.00 0.00 4.09
373 397 1.801178 GGTGAAAGCCTGTTTCGAGAG 59.199 52.381 0.00 0.00 0.00 3.20
374 398 1.878953 GGTGAAAGCCTGTTTCGAGA 58.121 50.000 0.00 0.00 0.00 4.04
385 409 4.396790 TCATGTATAAAACGGGGTGAAAGC 59.603 41.667 0.00 0.00 0.00 3.51
386 410 5.065988 CCTCATGTATAAAACGGGGTGAAAG 59.934 44.000 0.00 0.00 0.00 2.62
387 411 4.944930 CCTCATGTATAAAACGGGGTGAAA 59.055 41.667 0.00 0.00 0.00 2.69
388 412 4.519213 CCTCATGTATAAAACGGGGTGAA 58.481 43.478 0.00 0.00 0.00 3.18
389 413 3.683281 GCCTCATGTATAAAACGGGGTGA 60.683 47.826 0.00 0.00 0.00 4.02
390 414 2.616842 GCCTCATGTATAAAACGGGGTG 59.383 50.000 0.00 0.00 0.00 4.61
391 415 2.240160 TGCCTCATGTATAAAACGGGGT 59.760 45.455 0.00 0.00 0.00 4.95
392 416 2.878406 CTGCCTCATGTATAAAACGGGG 59.122 50.000 0.00 0.00 0.00 5.73
393 417 2.878406 CCTGCCTCATGTATAAAACGGG 59.122 50.000 0.00 0.00 0.00 5.28
394 418 2.290641 GCCTGCCTCATGTATAAAACGG 59.709 50.000 0.00 0.00 0.00 4.44
395 419 2.942376 TGCCTGCCTCATGTATAAAACG 59.058 45.455 0.00 0.00 0.00 3.60
396 420 3.947834 ACTGCCTGCCTCATGTATAAAAC 59.052 43.478 0.00 0.00 0.00 2.43
397 421 3.947196 CACTGCCTGCCTCATGTATAAAA 59.053 43.478 0.00 0.00 0.00 1.52
398 422 3.544684 CACTGCCTGCCTCATGTATAAA 58.455 45.455 0.00 0.00 0.00 1.40
399 423 2.746142 GCACTGCCTGCCTCATGTATAA 60.746 50.000 0.00 0.00 40.42 0.98
400 424 1.202687 GCACTGCCTGCCTCATGTATA 60.203 52.381 0.00 0.00 40.42 1.47
401 425 0.465097 GCACTGCCTGCCTCATGTAT 60.465 55.000 0.00 0.00 40.42 2.29
402 426 1.078214 GCACTGCCTGCCTCATGTA 60.078 57.895 0.00 0.00 40.42 2.29
403 427 2.360852 GCACTGCCTGCCTCATGT 60.361 61.111 0.00 0.00 40.42 3.21
412 436 0.250640 CAACTTCCAGAGCACTGCCT 60.251 55.000 5.52 0.00 42.25 4.75
413 437 1.239968 CCAACTTCCAGAGCACTGCC 61.240 60.000 5.52 0.00 42.25 4.85
425 449 6.183360 TGTGTTGATCTTTCACTTCCAACTTC 60.183 38.462 0.00 0.00 36.02 3.01
429 454 6.239008 GGAATGTGTTGATCTTTCACTTCCAA 60.239 38.462 21.97 0.00 38.15 3.53
441 480 3.019564 CTCCCTTGGGAATGTGTTGATC 58.980 50.000 9.93 0.00 0.00 2.92
443 482 1.075374 CCTCCCTTGGGAATGTGTTGA 59.925 52.381 9.93 0.00 0.00 3.18
482 524 4.153958 CGTCCTCGGATGAATCTAGAAG 57.846 50.000 0.00 0.00 33.22 2.85
576 672 8.065407 CGTGATTAGCCGCTTATAAAATTGTAA 58.935 33.333 0.00 0.00 0.00 2.41
607 705 4.005650 GGATCAGCTCACTTGTCAAATCA 58.994 43.478 0.00 0.00 0.00 2.57
661 759 4.819783 TGGCATCTCCAACACACC 57.180 55.556 0.00 0.00 43.21 4.16
750 848 2.759839 AGGAGGAGGGTAAGTAGAGC 57.240 55.000 0.00 0.00 0.00 4.09
788 886 3.365969 CCTTTTGGTGTCGTGATTAAGCC 60.366 47.826 0.00 0.00 34.07 4.35
933 1044 1.647084 GTTGTCCTGTCGTGCAACC 59.353 57.895 0.00 0.00 36.25 3.77
945 1056 0.243907 TCTGCTCTGCTACGTTGTCC 59.756 55.000 0.00 0.00 0.00 4.02
974 1085 4.468689 CCCGCCCTTCCTCCGTTC 62.469 72.222 0.00 0.00 0.00 3.95
991 1102 3.567797 GAAGTGCATCGCCGCTCC 61.568 66.667 0.00 0.00 0.00 4.70
1392 1506 4.421479 ACGCACGGCTTCCTCTCG 62.421 66.667 0.00 0.00 0.00 4.04
1437 1551 4.828296 TCCTCCCGGGGCTCGTAC 62.828 72.222 23.50 0.00 37.11 3.67
1660 1781 1.353804 GAGGCTGCGAGAGTACGAG 59.646 63.158 0.00 0.00 35.09 4.18
1665 1786 3.684990 TTGCGAGGCTGCGAGAGT 61.685 61.111 9.91 0.00 37.81 3.24
1700 1821 7.600375 TGAGCAACACTGTTTGAAACAAAATTA 59.400 29.630 12.26 0.00 41.61 1.40
1701 1822 6.426328 TGAGCAACACTGTTTGAAACAAAATT 59.574 30.769 12.26 3.72 41.61 1.82
1702 1823 5.931146 TGAGCAACACTGTTTGAAACAAAAT 59.069 32.000 12.26 0.00 41.61 1.82
1703 1824 5.292765 TGAGCAACACTGTTTGAAACAAAA 58.707 33.333 12.26 0.00 41.61 2.44
1704 1825 4.876125 TGAGCAACACTGTTTGAAACAAA 58.124 34.783 12.26 0.00 41.61 2.83
1705 1826 4.484236 CTGAGCAACACTGTTTGAAACAA 58.516 39.130 12.26 0.00 41.61 2.83
1706 1827 3.673052 GCTGAGCAACACTGTTTGAAACA 60.673 43.478 10.65 10.65 39.52 2.83
1707 1828 2.854185 GCTGAGCAACACTGTTTGAAAC 59.146 45.455 0.00 0.14 0.00 2.78
1708 1829 2.491298 TGCTGAGCAACACTGTTTGAAA 59.509 40.909 3.81 0.00 34.76 2.69
1782 1918 7.114529 AGCAGCGAAATATATACAAGACGTAAC 59.885 37.037 0.00 0.00 32.59 2.50
1790 1926 9.051679 ACATAACAAGCAGCGAAATATATACAA 57.948 29.630 0.00 0.00 0.00 2.41
1807 1943 8.833231 ATAGGTTCGGATATCAACATAACAAG 57.167 34.615 4.83 0.00 0.00 3.16
1904 2042 2.931325 TGTATGCCGGCGTAACTAAAAG 59.069 45.455 29.44 0.00 0.00 2.27
1905 2043 2.672381 GTGTATGCCGGCGTAACTAAAA 59.328 45.455 29.44 5.31 0.00 1.52
1906 2044 2.270047 GTGTATGCCGGCGTAACTAAA 58.730 47.619 29.44 6.15 0.00 1.85
1939 2077 7.655521 ACACACTATTGGCTCTGTAATACTA 57.344 36.000 0.00 0.00 0.00 1.82
1940 2078 6.546428 ACACACTATTGGCTCTGTAATACT 57.454 37.500 0.00 0.00 0.00 2.12
1967 2832 6.209986 TCAGTTATTTTCGAACAGAGGGAGTA 59.790 38.462 0.00 0.00 0.00 2.59
2092 2957 4.461781 AGGTTGGCATTCAGAATTCAAGAG 59.538 41.667 8.44 0.00 0.00 2.85
2142 3073 9.337396 ACAAACATTGTTGTACAATTCTCTAGA 57.663 29.630 12.26 0.00 45.80 2.43
2252 3183 6.216801 ACATGAATCTTGATGATTGTTGGG 57.783 37.500 0.00 0.00 44.70 4.12
2519 3454 1.235724 GCCGACACCTTTAAGCACTT 58.764 50.000 0.00 0.00 0.00 3.16
2520 3455 0.605589 GGCCGACACCTTTAAGCACT 60.606 55.000 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.