Multiple sequence alignment - TraesCS4A01G336200

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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 TraesCS4A01G336200 chr4A 100.000 3535 0 0 1 3535 618531057 618527523 0.000000e+00 6529.0
1 TraesCS4A01G336200 chr4A 87.891 1792 163 37 1248 3012 618464557 618462793 0.000000e+00 2058.0
2 TraesCS4A01G336200 chr4A 83.278 1214 164 25 1607 2803 618412602 618411411 0.000000e+00 1081.0
3 TraesCS4A01G336200 chr4A 86.649 764 96 5 2034 2791 618418233 618417470 0.000000e+00 841.0
4 TraesCS4A01G336200 chr4A 92.628 529 26 2 3008 3535 618462752 618462236 0.000000e+00 749.0
5 TraesCS4A01G336200 chr4A 81.738 909 90 41 1089 1955 618419215 618418341 0.000000e+00 689.0
6 TraesCS4A01G336200 chr4A 86.611 239 28 4 24 260 618550216 618549980 9.730000e-66 261.0
7 TraesCS4A01G336200 chr4A 85.294 102 13 2 422 521 58822186 58822287 1.740000e-18 104.0
8 TraesCS4A01G336200 chr5B 90.403 2459 151 40 455 2859 691943781 691941354 0.000000e+00 3155.0
9 TraesCS4A01G336200 chr5B 86.582 1811 150 43 1082 2859 691825490 691823740 0.000000e+00 1912.0
10 TraesCS4A01G336200 chr5B 83.448 1740 218 45 1048 2762 691798693 691796999 0.000000e+00 1554.0
11 TraesCS4A01G336200 chr5B 90.764 563 37 5 2858 3419 691941306 691940758 0.000000e+00 737.0
12 TraesCS4A01G336200 chr5B 82.415 853 101 27 1113 1955 691773892 691773079 0.000000e+00 699.0
13 TraesCS4A01G336200 chr5B 91.853 491 31 4 3033 3514 691823159 691822669 0.000000e+00 676.0
14 TraesCS4A01G336200 chr5B 91.870 246 18 2 117 360 691950745 691950500 3.380000e-90 342.0
15 TraesCS4A01G336200 chr5B 92.188 128 10 0 2876 3003 691823545 691823418 7.800000e-42 182.0
16 TraesCS4A01G336200 chr5B 92.233 103 7 1 1 103 691950995 691950894 1.020000e-30 145.0
17 TraesCS4A01G336200 chr5B 98.592 71 0 1 3444 3514 691940763 691940694 1.330000e-24 124.0
18 TraesCS4A01G336200 chr5D 90.862 2331 131 41 570 2859 547926991 547924702 0.000000e+00 3049.0
19 TraesCS4A01G336200 chr5D 86.743 1569 152 38 1248 2790 547892870 547891332 0.000000e+00 1694.0
20 TraesCS4A01G336200 chr5D 82.243 1881 241 62 1022 2859 547841428 547839598 0.000000e+00 1537.0
21 TraesCS4A01G336200 chr5D 87.406 802 91 8 2034 2827 547883302 547882503 0.000000e+00 913.0
22 TraesCS4A01G336200 chr5D 84.211 703 69 24 1268 1955 547884085 547883410 0.000000e+00 645.0
23 TraesCS4A01G336200 chr5D 82.396 676 76 21 2858 3514 547924654 547924003 1.850000e-152 549.0
24 TraesCS4A01G336200 chr5D 83.831 402 46 15 21 412 547927386 547926994 7.210000e-97 364.0
25 TraesCS4A01G336200 chr5D 80.380 158 22 9 415 564 441796802 441796646 1.040000e-20 111.0
26 TraesCS4A01G336200 chr5D 88.043 92 10 1 431 521 386859440 386859349 1.340000e-19 108.0
27 TraesCS4A01G336200 chr2B 83.448 145 18 4 426 564 756614333 756614189 2.860000e-26 130.0
28 TraesCS4A01G336200 chr6A 81.879 149 21 3 415 557 21574730 21574582 1.720000e-23 121.0
29 TraesCS4A01G336200 chr6D 85.577 104 14 1 415 517 83012175 83012278 1.340000e-19 108.0
30 TraesCS4A01G336200 chr5A 83.761 117 16 3 406 521 708724315 708724429 1.340000e-19 108.0
31 TraesCS4A01G336200 chr6B 79.487 156 26 4 415 564 715747574 715747419 4.830000e-19 106.0
32 TraesCS4A01G336200 chr1A 84.906 106 15 1 417 521 144861401 144861506 4.830000e-19 106.0
33 TraesCS4A01G336200 chr2A 100.000 31 0 0 3505 3535 681252274 681252244 1.370000e-04 58.4


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 TraesCS4A01G336200 chr4A 618527523 618531057 3534 True 6529.000000 6529 100.000000 1 3535 1 chr4A.!!$R2 3534
1 TraesCS4A01G336200 chr4A 618462236 618464557 2321 True 1403.500000 2058 90.259500 1248 3535 2 chr4A.!!$R5 2287
2 TraesCS4A01G336200 chr4A 618411411 618412602 1191 True 1081.000000 1081 83.278000 1607 2803 1 chr4A.!!$R1 1196
3 TraesCS4A01G336200 chr4A 618417470 618419215 1745 True 765.000000 841 84.193500 1089 2791 2 chr4A.!!$R4 1702
4 TraesCS4A01G336200 chr5B 691796999 691798693 1694 True 1554.000000 1554 83.448000 1048 2762 1 chr5B.!!$R2 1714
5 TraesCS4A01G336200 chr5B 691940694 691943781 3087 True 1338.666667 3155 93.253000 455 3514 3 chr5B.!!$R4 3059
6 TraesCS4A01G336200 chr5B 691822669 691825490 2821 True 923.333333 1912 90.207667 1082 3514 3 chr5B.!!$R3 2432
7 TraesCS4A01G336200 chr5B 691773079 691773892 813 True 699.000000 699 82.415000 1113 1955 1 chr5B.!!$R1 842
8 TraesCS4A01G336200 chr5D 547891332 547892870 1538 True 1694.000000 1694 86.743000 1248 2790 1 chr5D.!!$R4 1542
9 TraesCS4A01G336200 chr5D 547839598 547841428 1830 True 1537.000000 1537 82.243000 1022 2859 1 chr5D.!!$R3 1837
10 TraesCS4A01G336200 chr5D 547924003 547927386 3383 True 1320.666667 3049 85.696333 21 3514 3 chr5D.!!$R6 3493
11 TraesCS4A01G336200 chr5D 547882503 547884085 1582 True 779.000000 913 85.808500 1268 2827 2 chr5D.!!$R5 1559

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
19 20 0.037605 GATTGCTTGCAGCTTGCCTT 60.038 50.0 9.12 0.0 44.23 4.35 F
226 234 0.107800 CAGACATCAGTGGAGCTGGG 60.108 60.0 0.00 0.0 45.08 4.45 F
1206 1242 0.110486 TCTTCTTGTTCCCACCAGCC 59.890 55.0 0.00 0.0 0.00 4.85 F
1421 1498 0.250513 GGGGAGCTAGTGTTGACCTG 59.749 60.0 0.00 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1044 1077 0.886938 TGTTGAAATTGGCGAGGCGA 60.887 50.000 0.00 0.0 0.00 5.54 R
1930 2136 1.067295 ACATCTTGTCCTTGGAGGCA 58.933 50.000 0.00 0.0 34.61 4.75 R
2501 2770 1.003355 CTGGCTGGCCTTCTCGAAA 60.003 57.895 13.05 0.0 36.94 3.46 R
3392 4176 1.268079 GGCCAAGAGCAAACTCAACTC 59.732 52.381 0.00 0.0 46.09 3.01 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
17 18 4.180496 GATTGCTTGCAGCTTGCC 57.820 55.556 9.12 0.00 44.23 4.52
18 19 1.590147 GATTGCTTGCAGCTTGCCT 59.410 52.632 9.12 0.00 44.23 4.75
19 20 0.037605 GATTGCTTGCAGCTTGCCTT 60.038 50.000 9.12 0.00 44.23 4.35
42 49 0.537188 ATACCCCGCTGTTGTGAGAG 59.463 55.000 0.00 0.00 0.00 3.20
48 55 1.946768 CCGCTGTTGTGAGAGGAAAAA 59.053 47.619 0.00 0.00 35.00 1.94
49 56 2.031682 CCGCTGTTGTGAGAGGAAAAAG 60.032 50.000 0.00 0.00 35.00 2.27
84 91 8.162878 AGTGAATTATGTAATCCAATGCTCTG 57.837 34.615 0.00 0.00 0.00 3.35
89 96 7.801716 TTATGTAATCCAATGCTCTGTAACC 57.198 36.000 0.00 0.00 0.00 2.85
93 100 3.616956 TCCAATGCTCTGTAACCTGAG 57.383 47.619 0.00 0.00 39.09 3.35
125 132 2.689983 CTCAGGGGGTTTGCAATATGAC 59.310 50.000 0.00 0.00 0.00 3.06
127 134 1.360852 AGGGGGTTTGCAATATGACCA 59.639 47.619 17.58 0.00 33.81 4.02
130 137 3.964031 GGGGGTTTGCAATATGACCAATA 59.036 43.478 17.58 0.00 33.81 1.90
132 139 5.511202 GGGGGTTTGCAATATGACCAATATG 60.511 44.000 17.58 0.00 31.49 1.78
181 188 1.141019 CGACACCGGTAGGACATGG 59.859 63.158 6.87 0.00 41.02 3.66
212 220 0.884259 CACGGCAACACCATCAGACA 60.884 55.000 0.00 0.00 39.03 3.41
215 223 1.825090 GGCAACACCATCAGACATCA 58.175 50.000 0.00 0.00 38.86 3.07
226 234 0.107800 CAGACATCAGTGGAGCTGGG 60.108 60.000 0.00 0.00 45.08 4.45
256 268 1.153628 CAGCGTTAGAGGGGGTTCG 60.154 63.158 0.00 0.00 0.00 3.95
257 269 1.608627 AGCGTTAGAGGGGGTTCGT 60.609 57.895 0.00 0.00 0.00 3.85
268 280 0.175989 GGGGTTCGTTGAGGCTAGAG 59.824 60.000 0.00 0.00 0.00 2.43
278 290 1.063567 TGAGGCTAGAGGAGGAAGACC 60.064 57.143 0.00 0.00 0.00 3.85
281 293 1.476477 GCTAGAGGAGGAAGACCGTT 58.524 55.000 0.00 0.00 41.83 4.44
290 302 1.153804 GAAGACCGTTCGGAGGAGC 60.154 63.158 18.28 2.23 0.00 4.70
295 307 2.646175 CCGTTCGGAGGAGCAGGAA 61.646 63.158 5.19 0.00 0.00 3.36
321 333 0.471617 CGGCCCTCAGATTTCCATCT 59.528 55.000 0.00 0.00 40.79 2.90
346 358 2.028930 GGTCCACTCTGATTTGACGAGT 60.029 50.000 0.00 0.00 38.47 4.18
350 362 4.021104 TCCACTCTGATTTGACGAGTTCAT 60.021 41.667 0.00 0.00 35.95 2.57
377 389 8.897872 TTTTATTTCGAGACTATTACCCCATC 57.102 34.615 0.00 0.00 0.00 3.51
378 390 4.950205 TTTCGAGACTATTACCCCATCC 57.050 45.455 0.00 0.00 0.00 3.51
379 391 3.605726 TCGAGACTATTACCCCATCCA 57.394 47.619 0.00 0.00 0.00 3.41
380 392 3.228453 TCGAGACTATTACCCCATCCAC 58.772 50.000 0.00 0.00 0.00 4.02
381 393 3.117246 TCGAGACTATTACCCCATCCACT 60.117 47.826 0.00 0.00 0.00 4.00
394 406 5.208121 CCCCATCCACTTGTTTAATGGTAT 58.792 41.667 0.00 0.00 36.04 2.73
397 409 5.890985 CCATCCACTTGTTTAATGGTATGGA 59.109 40.000 13.11 8.36 40.24 3.41
398 410 6.039717 CCATCCACTTGTTTAATGGTATGGAG 59.960 42.308 13.11 4.38 40.24 3.86
399 411 4.947388 TCCACTTGTTTAATGGTATGGAGC 59.053 41.667 0.00 0.00 34.89 4.70
400 412 4.201910 CCACTTGTTTAATGGTATGGAGCG 60.202 45.833 0.00 0.00 0.00 5.03
412 424 0.872388 ATGGAGCGGTCGTTTTGAAC 59.128 50.000 8.77 0.00 0.00 3.18
413 425 0.462225 TGGAGCGGTCGTTTTGAACA 60.462 50.000 8.77 0.00 32.01 3.18
414 426 0.872388 GGAGCGGTCGTTTTGAACAT 59.128 50.000 8.77 0.00 32.01 2.71
415 427 2.070783 GGAGCGGTCGTTTTGAACATA 58.929 47.619 8.77 0.00 32.01 2.29
416 428 2.159747 GGAGCGGTCGTTTTGAACATAC 60.160 50.000 8.77 0.00 32.01 2.39
417 429 2.735134 GAGCGGTCGTTTTGAACATACT 59.265 45.455 0.00 0.00 32.01 2.12
418 430 3.135994 AGCGGTCGTTTTGAACATACTT 58.864 40.909 0.00 0.00 32.01 2.24
419 431 3.185797 AGCGGTCGTTTTGAACATACTTC 59.814 43.478 0.00 0.00 32.01 3.01
420 432 3.666111 GCGGTCGTTTTGAACATACTTCC 60.666 47.826 0.00 0.00 32.01 3.46
421 433 3.744426 CGGTCGTTTTGAACATACTTCCT 59.256 43.478 0.00 0.00 32.01 3.36
422 434 4.212636 CGGTCGTTTTGAACATACTTCCTT 59.787 41.667 0.00 0.00 32.01 3.36
423 435 5.277634 CGGTCGTTTTGAACATACTTCCTTT 60.278 40.000 0.00 0.00 32.01 3.11
424 436 5.912955 GGTCGTTTTGAACATACTTCCTTTG 59.087 40.000 0.00 0.00 33.12 2.77
425 437 6.459161 GGTCGTTTTGAACATACTTCCTTTGT 60.459 38.462 0.00 0.00 33.12 2.83
426 438 6.970613 GTCGTTTTGAACATACTTCCTTTGTT 59.029 34.615 0.00 0.00 36.34 2.83
427 439 7.486870 GTCGTTTTGAACATACTTCCTTTGTTT 59.513 33.333 0.00 0.00 33.92 2.83
428 440 8.030106 TCGTTTTGAACATACTTCCTTTGTTTT 58.970 29.630 0.00 0.00 33.92 2.43
429 441 8.652463 CGTTTTGAACATACTTCCTTTGTTTTT 58.348 29.630 0.00 0.00 33.92 1.94
495 507 9.624373 ATGAAGCAAAATGAGTGAATCTATACT 57.376 29.630 0.00 0.00 0.00 2.12
530 549 9.825109 TGTCTAAATACATCCGTTCATATCAAA 57.175 29.630 0.00 0.00 0.00 2.69
564 583 8.640033 AAAAGAGTTATATTTAGGGAGGGAGT 57.360 34.615 0.00 0.00 0.00 3.85
565 584 9.739737 AAAAGAGTTATATTTAGGGAGGGAGTA 57.260 33.333 0.00 0.00 0.00 2.59
566 585 8.959676 AAGAGTTATATTTAGGGAGGGAGTAG 57.040 38.462 0.00 0.00 0.00 2.57
567 586 8.071235 AGAGTTATATTTAGGGAGGGAGTAGT 57.929 38.462 0.00 0.00 0.00 2.73
568 587 9.192129 AGAGTTATATTTAGGGAGGGAGTAGTA 57.808 37.037 0.00 0.00 0.00 1.82
641 660 2.230266 GCGACTTGGAAAATAAGCCCAA 59.770 45.455 0.00 0.00 37.60 4.12
645 664 6.626302 CGACTTGGAAAATAAGCCCAAAATA 58.374 36.000 0.00 0.00 39.22 1.40
702 721 5.118990 AGTTGGATATTGGAACATGACGAG 58.881 41.667 0.00 0.00 39.30 4.18
706 725 2.496899 ATTGGAACATGACGAGGCTT 57.503 45.000 0.00 0.00 39.30 4.35
846 865 3.009723 CAGCCGCATAGAAAAAGAAGGA 58.990 45.455 0.00 0.00 0.00 3.36
847 866 3.064545 CAGCCGCATAGAAAAAGAAGGAG 59.935 47.826 0.00 0.00 0.00 3.69
856 875 5.619625 AGAAAAAGAAGGAGATGAAAGCG 57.380 39.130 0.00 0.00 0.00 4.68
939 966 1.134037 TCGCCATTTATTTACCCCGCT 60.134 47.619 0.00 0.00 0.00 5.52
976 1008 1.134280 CATCCATCACCTCACCTCACC 60.134 57.143 0.00 0.00 0.00 4.02
977 1009 0.117140 TCCATCACCTCACCTCACCT 59.883 55.000 0.00 0.00 0.00 4.00
978 1010 0.539051 CCATCACCTCACCTCACCTC 59.461 60.000 0.00 0.00 0.00 3.85
979 1011 1.269958 CATCACCTCACCTCACCTCA 58.730 55.000 0.00 0.00 0.00 3.86
980 1012 1.066573 CATCACCTCACCTCACCTCAC 60.067 57.143 0.00 0.00 0.00 3.51
981 1013 0.832135 TCACCTCACCTCACCTCACC 60.832 60.000 0.00 0.00 0.00 4.02
982 1014 1.536662 ACCTCACCTCACCTCACCC 60.537 63.158 0.00 0.00 0.00 4.61
983 1015 1.536418 CCTCACCTCACCTCACCCA 60.536 63.158 0.00 0.00 0.00 4.51
984 1016 1.548357 CCTCACCTCACCTCACCCAG 61.548 65.000 0.00 0.00 0.00 4.45
985 1017 2.177594 CTCACCTCACCTCACCCAGC 62.178 65.000 0.00 0.00 0.00 4.85
1044 1077 2.029290 CCCTATTTATACGGCACTCGCT 60.029 50.000 0.00 0.00 43.89 4.93
1206 1242 0.110486 TCTTCTTGTTCCCACCAGCC 59.890 55.000 0.00 0.00 0.00 4.85
1383 1460 2.288334 CCTCTCTCTCAATCGCCATGAG 60.288 54.545 0.00 5.81 44.53 2.90
1391 1468 3.673902 TCAATCGCCATGAGTTCTGAAA 58.326 40.909 0.00 0.00 0.00 2.69
1394 1471 5.183713 TCAATCGCCATGAGTTCTGAAATTT 59.816 36.000 0.00 0.00 0.00 1.82
1412 1489 4.803329 ATTTTCATCATGGGGAGCTAGT 57.197 40.909 0.00 0.00 0.00 2.57
1421 1498 0.250513 GGGGAGCTAGTGTTGACCTG 59.749 60.000 0.00 0.00 0.00 4.00
1425 1502 2.561419 GGAGCTAGTGTTGACCTGTGTA 59.439 50.000 0.00 0.00 0.00 2.90
1597 1692 2.095053 GCTCTGCTTTTTCCATCTCGTC 59.905 50.000 0.00 0.00 0.00 4.20
1598 1693 3.594134 CTCTGCTTTTTCCATCTCGTCT 58.406 45.455 0.00 0.00 0.00 4.18
1655 1833 4.454678 TGAAATGCTGTTCTGTCTTCTGT 58.545 39.130 2.35 0.00 0.00 3.41
1801 2005 9.529325 CATGCACTTGATTCATTCTATTTTGAT 57.471 29.630 0.00 0.00 0.00 2.57
1930 2136 0.694771 TGCAGCTCTGGATCAACCTT 59.305 50.000 0.00 0.00 39.86 3.50
1992 2260 5.812642 ACTATCAATCTTCTTTACACGGCAG 59.187 40.000 0.00 0.00 0.00 4.85
2150 2419 4.810184 GGGGAGGCCTTCGGGGTA 62.810 72.222 6.77 0.00 37.43 3.69
2354 2623 4.554036 GGGGATGGGCTCAGCGTC 62.554 72.222 0.00 0.00 0.00 5.19
2374 2643 4.814294 GAATCGGTCCGGCGCACT 62.814 66.667 12.29 0.00 0.00 4.40
2469 2738 2.993008 GTGCCCAGATCCAGCAGA 59.007 61.111 2.39 0.00 37.15 4.26
2551 2820 2.428530 CCTGATTCTCATCGGTGTCTCA 59.571 50.000 0.00 0.00 34.26 3.27
2772 3048 9.761504 TGATTGTTTCATCATAAAAGAGCAAAA 57.238 25.926 0.00 0.00 0.00 2.44
2826 3104 4.202599 TGGGAAATGATGGGTGGATATCAG 60.203 45.833 4.83 0.00 36.81 2.90
2829 3107 4.377762 AATGATGGGTGGATATCAGGTG 57.622 45.455 4.83 0.00 36.81 4.00
2869 3197 2.136298 TTTCAAGTGAGCCACCAACA 57.864 45.000 2.18 0.00 34.49 3.33
3067 3801 3.093814 TGGACTTCGGTCAGCTTACATA 58.906 45.455 0.00 0.00 46.11 2.29
3137 3912 4.729227 TCAGAGTGCCATTATCGTGTAA 57.271 40.909 0.00 0.00 0.00 2.41
3147 3922 5.514914 GCCATTATCGTGTAACATTGTTTGG 59.485 40.000 7.45 7.00 35.74 3.28
3315 4098 4.498009 GCTGAGCTGCTGTAAAAGTTTCAA 60.498 41.667 7.01 0.00 0.00 2.69
3318 4101 6.393990 TGAGCTGCTGTAAAAGTTTCAAAAA 58.606 32.000 7.01 0.00 0.00 1.94
3372 4156 9.807921 ATTTTCCTAATTGACTGTCCTAAAAGA 57.192 29.630 5.17 0.00 0.00 2.52
3384 4168 6.971726 TGTCCTAAAAGACTGACAGACTTA 57.028 37.500 18.38 5.51 37.66 2.24
3385 4169 7.540474 TGTCCTAAAAGACTGACAGACTTAT 57.460 36.000 18.38 8.10 37.66 1.73
3423 4207 4.174704 TGCTCTTGGCCATCTTAATGAT 57.825 40.909 6.09 0.00 40.92 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.405463 GGGTATGTTAAGGCAAGCTGC 59.595 52.381 0.00 0.00 44.08 5.25
9 10 2.024414 GGGGTATGTTAAGGCAAGCTG 58.976 52.381 0.00 0.00 0.00 4.24
10 11 1.408266 CGGGGTATGTTAAGGCAAGCT 60.408 52.381 0.00 0.00 0.00 3.74
11 12 1.021968 CGGGGTATGTTAAGGCAAGC 58.978 55.000 0.00 0.00 0.00 4.01
12 13 1.021968 GCGGGGTATGTTAAGGCAAG 58.978 55.000 0.00 0.00 0.00 4.01
13 14 0.621609 AGCGGGGTATGTTAAGGCAA 59.378 50.000 0.00 0.00 0.00 4.52
14 15 0.107410 CAGCGGGGTATGTTAAGGCA 60.107 55.000 0.00 0.00 0.00 4.75
15 16 0.107361 ACAGCGGGGTATGTTAAGGC 60.107 55.000 0.00 0.00 0.00 4.35
16 17 2.014128 CAACAGCGGGGTATGTTAAGG 58.986 52.381 0.00 0.00 37.54 2.69
17 18 2.418628 CACAACAGCGGGGTATGTTAAG 59.581 50.000 0.00 0.00 37.54 1.85
18 19 2.038689 TCACAACAGCGGGGTATGTTAA 59.961 45.455 0.00 0.00 37.54 2.01
19 20 1.624312 TCACAACAGCGGGGTATGTTA 59.376 47.619 0.00 0.00 37.54 2.41
66 73 6.992123 CAGGTTACAGAGCATTGGATTACATA 59.008 38.462 0.00 0.00 0.00 2.29
70 77 5.674525 CTCAGGTTACAGAGCATTGGATTA 58.325 41.667 0.00 0.00 0.00 1.75
73 80 3.616956 CTCAGGTTACAGAGCATTGGA 57.383 47.619 0.00 0.00 0.00 3.53
82 89 2.485426 CACAACATGGCTCAGGTTACAG 59.515 50.000 0.00 0.00 36.20 2.74
84 91 1.200020 GCACAACATGGCTCAGGTTAC 59.800 52.381 0.00 0.00 36.20 2.50
93 100 2.345760 CCCCTGAGCACAACATGGC 61.346 63.158 0.00 0.00 0.00 4.40
94 101 1.679977 CCCCCTGAGCACAACATGG 60.680 63.158 0.00 0.00 0.00 3.66
108 115 1.859302 TGGTCATATTGCAAACCCCC 58.141 50.000 14.07 6.99 0.00 5.40
132 139 3.249091 TGACAACAAAACATGTGTGCAC 58.751 40.909 10.75 10.75 42.99 4.57
169 176 4.201679 TCGCGCCATGTCCTACCG 62.202 66.667 0.00 0.00 0.00 4.02
194 202 0.036732 ATGTCTGATGGTGTTGCCGT 59.963 50.000 0.00 0.00 41.21 5.68
197 205 2.161012 CACTGATGTCTGATGGTGTTGC 59.839 50.000 0.00 0.00 0.00 4.17
203 211 1.485480 AGCTCCACTGATGTCTGATGG 59.515 52.381 0.00 0.00 0.00 3.51
236 245 0.108281 GAACCCCCTCTAACGCTGAC 60.108 60.000 0.00 0.00 0.00 3.51
237 246 1.601419 CGAACCCCCTCTAACGCTGA 61.601 60.000 0.00 0.00 0.00 4.26
244 256 1.262640 GCCTCAACGAACCCCCTCTA 61.263 60.000 0.00 0.00 0.00 2.43
256 268 2.429250 GTCTTCCTCCTCTAGCCTCAAC 59.571 54.545 0.00 0.00 0.00 3.18
257 269 2.624557 GGTCTTCCTCCTCTAGCCTCAA 60.625 54.545 0.00 0.00 0.00 3.02
268 280 1.511768 CTCCGAACGGTCTTCCTCC 59.488 63.158 12.93 0.00 36.47 4.30
278 290 1.153745 CTTCCTGCTCCTCCGAACG 60.154 63.158 0.00 0.00 0.00 3.95
281 293 3.077556 GCCTTCCTGCTCCTCCGA 61.078 66.667 0.00 0.00 0.00 4.55
321 333 3.617288 CGTCAAATCAGAGTGGACCATCA 60.617 47.826 0.00 0.00 0.00 3.07
324 336 1.967779 TCGTCAAATCAGAGTGGACCA 59.032 47.619 0.00 0.00 0.00 4.02
361 373 4.409247 ACAAGTGGATGGGGTAATAGTCTC 59.591 45.833 0.00 0.00 0.00 3.36
363 375 4.772886 ACAAGTGGATGGGGTAATAGTC 57.227 45.455 0.00 0.00 0.00 2.59
364 376 5.530176 AAACAAGTGGATGGGGTAATAGT 57.470 39.130 0.00 0.00 0.00 2.12
365 377 7.014230 CCATTAAACAAGTGGATGGGGTAATAG 59.986 40.741 0.00 0.00 34.89 1.73
366 378 6.836527 CCATTAAACAAGTGGATGGGGTAATA 59.163 38.462 0.00 0.00 34.89 0.98
367 379 5.660864 CCATTAAACAAGTGGATGGGGTAAT 59.339 40.000 0.00 0.00 34.89 1.89
368 380 5.020132 CCATTAAACAAGTGGATGGGGTAA 58.980 41.667 0.00 0.00 34.89 2.85
370 382 3.181412 ACCATTAAACAAGTGGATGGGGT 60.181 43.478 5.74 0.00 41.18 4.95
372 384 5.068987 CCATACCATTAAACAAGTGGATGGG 59.931 44.000 5.74 0.00 41.18 4.00
374 386 6.460123 GCTCCATACCATTAAACAAGTGGATG 60.460 42.308 0.00 0.18 36.82 3.51
375 387 5.594317 GCTCCATACCATTAAACAAGTGGAT 59.406 40.000 0.00 0.00 36.82 3.41
376 388 4.947388 GCTCCATACCATTAAACAAGTGGA 59.053 41.667 0.00 1.49 36.82 4.02
377 389 4.201910 CGCTCCATACCATTAAACAAGTGG 60.202 45.833 0.00 0.00 38.96 4.00
378 390 4.201910 CCGCTCCATACCATTAAACAAGTG 60.202 45.833 0.00 0.00 0.00 3.16
379 391 3.945285 CCGCTCCATACCATTAAACAAGT 59.055 43.478 0.00 0.00 0.00 3.16
380 392 3.945285 ACCGCTCCATACCATTAAACAAG 59.055 43.478 0.00 0.00 0.00 3.16
381 393 3.942748 GACCGCTCCATACCATTAAACAA 59.057 43.478 0.00 0.00 0.00 2.83
394 406 0.462225 TGTTCAAAACGACCGCTCCA 60.462 50.000 0.00 0.00 0.00 3.86
397 409 2.762745 AGTATGTTCAAAACGACCGCT 58.237 42.857 0.00 0.00 0.00 5.52
398 410 3.476181 GAAGTATGTTCAAAACGACCGC 58.524 45.455 0.00 0.00 0.00 5.68
399 411 3.744426 AGGAAGTATGTTCAAAACGACCG 59.256 43.478 0.00 0.00 0.00 4.79
400 412 5.684550 AAGGAAGTATGTTCAAAACGACC 57.315 39.130 0.00 0.00 0.00 4.79
469 481 9.624373 AGTATAGATTCACTCATTTTGCTTCAT 57.376 29.630 0.00 0.00 0.00 2.57
511 523 9.559732 TGAGATTTTTGATATGAACGGATGTAT 57.440 29.630 0.00 0.00 0.00 2.29
564 583 7.333323 TGATAGCCGCATACAGTACTATACTA 58.667 38.462 0.00 0.00 37.23 1.82
565 584 6.178324 TGATAGCCGCATACAGTACTATACT 58.822 40.000 0.00 0.00 40.28 2.12
566 585 6.315642 TCTGATAGCCGCATACAGTACTATAC 59.684 42.308 0.00 0.00 0.00 1.47
567 586 6.412214 TCTGATAGCCGCATACAGTACTATA 58.588 40.000 0.00 0.00 0.00 1.31
568 587 5.254115 TCTGATAGCCGCATACAGTACTAT 58.746 41.667 0.00 0.00 0.00 2.12
574 593 4.143242 CGAATTTCTGATAGCCGCATACAG 60.143 45.833 0.00 0.00 0.00 2.74
620 639 1.816224 TGGGCTTATTTTCCAAGTCGC 59.184 47.619 0.00 0.00 0.00 5.19
664 683 2.435069 TCCAACTACTCCCGTTTTCACA 59.565 45.455 0.00 0.00 0.00 3.58
665 684 3.116079 TCCAACTACTCCCGTTTTCAC 57.884 47.619 0.00 0.00 0.00 3.18
666 685 5.687166 ATATCCAACTACTCCCGTTTTCA 57.313 39.130 0.00 0.00 0.00 2.69
679 698 5.097742 TCGTCATGTTCCAATATCCAACT 57.902 39.130 0.00 0.00 0.00 3.16
939 966 1.344438 GATGATGGTGGATGCGAGGTA 59.656 52.381 0.00 0.00 0.00 3.08
1044 1077 0.886938 TGTTGAAATTGGCGAGGCGA 60.887 50.000 0.00 0.00 0.00 5.54
1206 1242 3.111838 CGAGGAAGACGAAGACATGATG 58.888 50.000 0.00 0.00 0.00 3.07
1383 1460 6.284891 TCCCCATGATGAAAATTTCAGAAC 57.715 37.500 14.10 8.52 43.98 3.01
1391 1468 4.079558 ACACTAGCTCCCCATGATGAAAAT 60.080 41.667 0.00 0.00 0.00 1.82
1394 1471 2.481441 ACACTAGCTCCCCATGATGAA 58.519 47.619 0.00 0.00 0.00 2.57
1412 1489 4.588951 AGAAGAGACATACACAGGTCAACA 59.411 41.667 0.00 0.00 37.94 3.33
1421 1498 4.033817 GCAGCATCAAGAAGAGACATACAC 59.966 45.833 0.00 0.00 0.00 2.90
1425 1502 3.271729 CAGCAGCATCAAGAAGAGACAT 58.728 45.455 0.00 0.00 0.00 3.06
1513 1598 3.012722 GGGTGGTCGGGGAATCCA 61.013 66.667 0.09 0.00 34.36 3.41
1585 1680 4.039245 ACAGAACAGAAGACGAGATGGAAA 59.961 41.667 0.00 0.00 0.00 3.13
1597 1692 5.675575 GCAGGCAATATCAACAGAACAGAAG 60.676 44.000 0.00 0.00 0.00 2.85
1598 1693 4.156556 GCAGGCAATATCAACAGAACAGAA 59.843 41.667 0.00 0.00 0.00 3.02
1801 2005 5.478407 TCAGATGCGATGTTAGTTCTCAAA 58.522 37.500 0.00 0.00 0.00 2.69
1891 2097 2.266055 CCCTTCTGCACTCCGTCC 59.734 66.667 0.00 0.00 0.00 4.79
1930 2136 1.067295 ACATCTTGTCCTTGGAGGCA 58.933 50.000 0.00 0.00 34.61 4.75
2150 2419 2.620112 CGTGTAGACCGGTGACCGT 61.620 63.158 23.73 11.07 46.80 4.83
2439 2708 1.815421 GGGCACGCGAGTTCATGAT 60.815 57.895 15.93 0.00 46.40 2.45
2469 2738 3.434739 CCGTAGTAGTAGTCCTCCATGGT 60.435 52.174 12.58 0.00 37.07 3.55
2501 2770 1.003355 CTGGCTGGCCTTCTCGAAA 60.003 57.895 13.05 0.00 36.94 3.46
2576 2845 2.796031 CAATGTTTTGCACGACAATGCT 59.204 40.909 5.52 0.00 46.28 3.79
2765 3041 7.437267 CCCAAATCTATGATGAACATTTTGCTC 59.563 37.037 0.00 0.00 40.07 4.26
2772 3048 6.989155 ATTGCCCAAATCTATGATGAACAT 57.011 33.333 0.00 0.00 42.39 2.71
2869 3197 5.684704 TGGACTGAGAAGATCAAACAAAGT 58.315 37.500 0.00 0.00 37.52 2.66
3067 3801 7.287810 ACTTTGTACATTGTTTTAGAGGACCT 58.712 34.615 0.00 0.00 0.00 3.85
3108 3844 6.703607 ACGATAATGGCACTCTGAATTTCTAG 59.296 38.462 0.00 0.00 0.00 2.43
3318 4101 8.137437 CACATCTTCTAAACCAACAGTCAATTT 58.863 33.333 0.00 0.00 0.00 1.82
3319 4102 7.285401 ACACATCTTCTAAACCAACAGTCAATT 59.715 33.333 0.00 0.00 0.00 2.32
3320 4103 6.772716 ACACATCTTCTAAACCAACAGTCAAT 59.227 34.615 0.00 0.00 0.00 2.57
3384 4168 6.107901 AGAGCAAACTCAACTCTGACTAAT 57.892 37.500 0.00 0.00 46.09 1.73
3385 4169 5.537300 AGAGCAAACTCAACTCTGACTAA 57.463 39.130 0.00 0.00 46.09 2.24
3392 4176 1.268079 GGCCAAGAGCAAACTCAACTC 59.732 52.381 0.00 0.00 46.09 3.01


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

AutoCloner maintained by Alex Coulton.