Multiple sequence alignment - TraesCS6A01G208200

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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 TraesCS6A01G208200 chr6A 100.000 4684 0 0 1 4684 373114190 373118873 0.000000e+00 8650
1 TraesCS6A01G208200 chr6D 95.698 3928 123 26 417 4321 264443738 264447642 0.000000e+00 6276
2 TraesCS6A01G208200 chr6D 92.191 397 27 4 4291 4684 264447580 264447975 4.090000e-155 558
3 TraesCS6A01G208200 chr6D 93.377 302 14 4 6 302 264443393 264443693 4.300000e-120 442
4 TraesCS6A01G208200 chr6D 91.250 80 6 1 322 401 264443679 264443757 1.780000e-19 108
5 TraesCS6A01G208200 chr6B 97.277 2387 46 12 1942 4321 408241900 408244274 0.000000e+00 4030
6 TraesCS6A01G208200 chr6B 95.082 1525 46 10 405 1910 408240391 408241905 0.000000e+00 2374
7 TraesCS6A01G208200 chr6B 91.184 397 26 6 4291 4684 408244213 408244603 8.920000e-147 531
8 TraesCS6A01G208200 chr6B 89.262 298 19 6 6 302 408239999 408240284 1.240000e-95 361
9 TraesCS6A01G208200 chr6B 93.976 83 5 0 322 404 408240270 408240352 4.920000e-25 126


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 TraesCS6A01G208200 chr6A 373114190 373118873 4683 False 8650.0 8650 100.0000 1 4684 1 chr6A.!!$F1 4683
1 TraesCS6A01G208200 chr6D 264443393 264447975 4582 False 1846.0 6276 93.1290 6 4684 4 chr6D.!!$F1 4678
2 TraesCS6A01G208200 chr6B 408239999 408244603 4604 False 1484.4 4030 93.3562 6 4684 5 chr6B.!!$F1 4678

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
302 309 0.603975 AGCCGTTCTTGCAAGAGGAC 60.604 55.000 29.61 23.85 36.22 3.85 F
1356 1420 0.250467 TTGCAGCTCTCACTGTTCCC 60.250 55.000 0.00 0.00 39.96 3.97 F
1614 1678 1.227674 GGGCATCCTCGTCACATCC 60.228 63.158 0.00 0.00 0.00 3.51 F
3162 3237 0.978146 TGGCCCTAGAGGAGCTCAAC 60.978 60.000 17.19 8.65 38.24 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1491 1555 0.462759 GAGTCAAAGCCCCAGATCCG 60.463 60.000 0.00 0.00 0.0 4.18 R
3162 3237 0.458543 ACGCCGTAGACAATCTGCAG 60.459 55.000 7.63 7.63 0.0 4.41 R
3455 3530 2.032681 AAGACCACAGAAGCGGCC 59.967 61.111 0.00 0.00 0.0 6.13 R
4519 4599 1.066143 ACCATGGCAGGAAGTTACTCG 60.066 52.381 13.04 0.00 0.0 4.18 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
58 59 2.258591 CGGCGCCGTAGCTGATAT 59.741 61.111 39.71 0.00 45.94 1.63
59 60 1.504900 CGGCGCCGTAGCTGATATA 59.495 57.895 39.71 0.00 45.94 0.86
61 62 1.667756 CGGCGCCGTAGCTGATATAAA 60.668 52.381 39.71 0.00 45.94 1.40
63 64 1.993370 GCGCCGTAGCTGATATAAAGG 59.007 52.381 0.00 0.00 36.60 3.11
65 66 3.859627 GCGCCGTAGCTGATATAAAGGAA 60.860 47.826 0.00 0.00 36.60 3.36
66 67 4.304110 CGCCGTAGCTGATATAAAGGAAA 58.696 43.478 0.00 0.00 36.60 3.13
253 260 5.245075 TCATACACATACCACAAGACTGACA 59.755 40.000 0.00 0.00 0.00 3.58
302 309 0.603975 AGCCGTTCTTGCAAGAGGAC 60.604 55.000 29.61 23.85 36.22 3.85
305 312 1.541233 CCGTTCTTGCAAGAGGACACT 60.541 52.381 27.02 0.00 36.22 3.55
306 313 2.213499 CGTTCTTGCAAGAGGACACTT 58.787 47.619 27.02 0.00 36.22 3.16
307 314 2.614057 CGTTCTTGCAAGAGGACACTTT 59.386 45.455 27.02 0.00 36.22 2.66
308 315 3.065371 CGTTCTTGCAAGAGGACACTTTT 59.935 43.478 27.02 0.00 36.22 2.27
309 316 4.438744 CGTTCTTGCAAGAGGACACTTTTT 60.439 41.667 27.02 0.00 36.22 1.94
329 336 2.895680 TTTTTGCGGGTGCTTGCA 59.104 50.000 0.00 0.00 43.34 4.08
332 339 2.518112 TTGCGGGTGCTTGCAAGA 60.518 55.556 30.39 12.25 45.45 3.02
333 340 2.554636 TTGCGGGTGCTTGCAAGAG 61.555 57.895 30.39 14.77 45.45 2.85
334 341 3.741476 GCGGGTGCTTGCAAGAGG 61.741 66.667 30.39 13.38 38.39 3.69
335 342 2.281761 CGGGTGCTTGCAAGAGGT 60.282 61.111 30.39 0.00 0.00 3.85
336 343 2.328099 CGGGTGCTTGCAAGAGGTC 61.328 63.158 30.39 12.51 0.00 3.85
337 344 1.228245 GGGTGCTTGCAAGAGGTCA 60.228 57.895 30.39 15.08 0.00 4.02
338 345 1.518903 GGGTGCTTGCAAGAGGTCAC 61.519 60.000 30.39 24.50 0.00 3.67
343 350 3.441572 GTGCTTGCAAGAGGTCACAATAT 59.558 43.478 30.39 0.00 0.00 1.28
359 366 5.842874 TCACAATATCCATGAGATGTCCTCT 59.157 40.000 0.00 0.00 42.44 3.69
432 477 6.676950 TGTTGTTGTTGCCATCAGTAATAAG 58.323 36.000 0.00 0.00 0.00 1.73
628 682 5.962031 TCCAACTACCCTAAGAAGATGCTAA 59.038 40.000 0.00 0.00 0.00 3.09
700 754 6.090898 ACGTATTTGGATCTTGAGAAGAAACG 59.909 38.462 0.00 0.00 41.63 3.60
969 1024 3.679389 TCATCTCTTTCTTCTTGGTGCC 58.321 45.455 0.00 0.00 0.00 5.01
970 1025 3.328931 TCATCTCTTTCTTCTTGGTGCCT 59.671 43.478 0.00 0.00 0.00 4.75
971 1026 3.409026 TCTCTTTCTTCTTGGTGCCTC 57.591 47.619 0.00 0.00 0.00 4.70
1034 1089 2.234661 CTCCTTTCTTTTCCATTGCCCC 59.765 50.000 0.00 0.00 0.00 5.80
1356 1420 0.250467 TTGCAGCTCTCACTGTTCCC 60.250 55.000 0.00 0.00 39.96 3.97
1362 1426 2.190488 CTCTCACTGTTCCCCTGGCC 62.190 65.000 0.00 0.00 0.00 5.36
1491 1555 4.832608 GCCATGGGGACGTCGGTC 62.833 72.222 15.13 1.98 42.66 4.79
1500 1564 3.122250 GACGTCGGTCGGATCTGGG 62.122 68.421 0.00 0.00 44.69 4.45
1521 1585 2.454832 CTTTGACTCTCCGGCAGGCA 62.455 60.000 4.70 4.70 37.47 4.75
1525 1589 3.699894 CTCTCCGGCAGGCAGTGT 61.700 66.667 0.00 0.00 37.47 3.55
1614 1678 1.227674 GGGCATCCTCGTCACATCC 60.228 63.158 0.00 0.00 0.00 3.51
1700 1764 1.529226 TGGTTGCAGGTAACATTCCG 58.471 50.000 2.80 0.00 41.41 4.30
1721 1785 4.562757 CCGTCACAGATAACCCTTTTGAGA 60.563 45.833 0.00 0.00 0.00 3.27
1773 1837 1.559682 TCCCTTGGTTCCACTAGCATC 59.440 52.381 0.00 0.00 0.00 3.91
1774 1838 1.281867 CCCTTGGTTCCACTAGCATCA 59.718 52.381 0.00 0.00 0.00 3.07
1775 1839 2.290896 CCCTTGGTTCCACTAGCATCAA 60.291 50.000 0.00 0.00 0.00 2.57
1776 1840 3.624777 CCTTGGTTCCACTAGCATCAAT 58.375 45.455 0.00 0.00 0.00 2.57
1812 1877 5.046591 TCAAGATTCCCACAGTTTCGTCTAT 60.047 40.000 0.00 0.00 0.00 1.98
1923 1990 2.770802 AGATGCTAGTTGATGGAGTGCT 59.229 45.455 0.00 0.00 0.00 4.40
1929 1998 3.498774 AGTTGATGGAGTGCTTGAGTT 57.501 42.857 0.00 0.00 0.00 3.01
1932 2001 4.037208 AGTTGATGGAGTGCTTGAGTTTTG 59.963 41.667 0.00 0.00 0.00 2.44
2045 2116 5.116074 GCACTTGACAGATTCAAATTCAACG 59.884 40.000 0.00 0.00 43.90 4.10
2209 2280 9.614792 ATCTAAACTTTGAACAACTACTTCAGT 57.385 29.630 0.00 0.00 40.05 3.41
2252 2323 6.195600 ACAAATAGGGGTAACTGAACAGAA 57.804 37.500 8.87 0.00 0.00 3.02
2257 2328 3.826729 AGGGGTAACTGAACAGAAAATGC 59.173 43.478 8.87 0.00 0.00 3.56
2502 2574 2.769209 AGCATCTGTCTGGATTACCCT 58.231 47.619 0.00 0.00 35.38 4.34
2663 2735 6.257994 TCTTCATCATGGCTTATTTCTCCT 57.742 37.500 0.00 0.00 0.00 3.69
2749 2821 8.132995 ACTAACTTTACTTGCAACATGGTAAAC 58.867 33.333 14.38 0.00 32.85 2.01
2770 2842 6.436843 AACGAGAAAACAAGACATCTTTGT 57.563 33.333 0.00 0.00 39.32 2.83
2771 2843 5.810525 ACGAGAAAACAAGACATCTTTGTG 58.189 37.500 0.00 0.00 35.79 3.33
3080 3155 3.119316 AGCTTGGTGATCTACTGTCTTCG 60.119 47.826 0.00 0.00 0.00 3.79
3162 3237 0.978146 TGGCCCTAGAGGAGCTCAAC 60.978 60.000 17.19 8.65 38.24 3.18
3539 3614 0.767998 TTGGTGCAGTGATGGGTGTA 59.232 50.000 0.00 0.00 0.00 2.90
3581 3656 2.557924 CAGAGTCAGAGCAGAGACTGTT 59.442 50.000 9.28 0.00 44.61 3.16
3639 3714 2.813754 GTTGGTGCTTTGCTATCAGTCA 59.186 45.455 0.00 0.00 0.00 3.41
3783 3858 3.191078 ACAGTGAATAGATGAGCCAGC 57.809 47.619 0.00 0.00 0.00 4.85
3826 3901 9.347240 AGAGAAATTGAAAAGATTTGTCAGAGA 57.653 29.630 8.70 0.00 38.51 3.10
4058 4138 5.433526 TCACTACCCTTGTAATTATGCCAC 58.566 41.667 0.00 0.00 0.00 5.01
4361 4441 7.602644 TGAAGAACACACATAAGTAGGAATGTC 59.397 37.037 0.00 0.00 34.12 3.06
4377 4457 7.636150 AGGAATGTCTGAATAAATCCACAAG 57.364 36.000 0.00 0.00 0.00 3.16
4460 4540 4.943705 GGTTGTCTGAAAGGCTGATCATTA 59.056 41.667 0.00 0.00 41.06 1.90
4505 4585 5.291971 AGAAGATGGTTTTTGCACATGTTC 58.708 37.500 13.22 13.22 42.09 3.18
4506 4586 3.641648 AGATGGTTTTTGCACATGTTCG 58.358 40.909 0.00 0.00 0.00 3.95
4513 4593 3.536158 TTTGCACATGTTCGCTAACTC 57.464 42.857 9.33 0.00 36.51 3.01
4519 4599 4.026475 GCACATGTTCGCTAACTCTATGAC 60.026 45.833 0.00 0.00 36.51 3.06
4522 4602 4.274421 TGTTCGCTAACTCTATGACGAG 57.726 45.455 2.53 0.00 36.51 4.18
4530 4610 6.200808 GCTAACTCTATGACGAGTAACTTCC 58.799 44.000 0.00 0.00 43.14 3.46
4533 4613 4.096682 ACTCTATGACGAGTAACTTCCTGC 59.903 45.833 0.00 0.00 42.19 4.85
4557 4637 7.282224 TGCCATGGTATCATTCTGTTTACTAAC 59.718 37.037 14.67 0.00 34.75 2.34
4593 4674 4.169059 TCAATGGGTATGACTTGATGGG 57.831 45.455 0.00 0.00 0.00 4.00
4594 4675 3.785325 TCAATGGGTATGACTTGATGGGA 59.215 43.478 0.00 0.00 0.00 4.37
4621 4703 9.419297 CATGTTTTTCAACAATTCTCATCAGAT 57.581 29.630 0.00 0.00 46.17 2.90
4646 4729 5.620206 TGTGGACAAACTCATCAGTAACAT 58.380 37.500 0.00 0.00 30.14 2.71
4649 4732 6.874134 GTGGACAAACTCATCAGTAACATAGT 59.126 38.462 0.00 0.00 30.14 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.047034 ACCCCGCTAGACCATACCAC 61.047 60.000 0.00 0.00 0.00 4.16
1 2 1.046472 CACCCCGCTAGACCATACCA 61.046 60.000 0.00 0.00 0.00 3.25
2 3 1.746517 CACCCCGCTAGACCATACC 59.253 63.158 0.00 0.00 0.00 2.73
3 4 1.069258 GCACCCCGCTAGACCATAC 59.931 63.158 0.00 0.00 37.77 2.39
4 5 2.138179 GGCACCCCGCTAGACCATA 61.138 63.158 0.00 0.00 41.91 2.74
58 59 1.547372 CGGAGTCGGAGGTTTCCTTTA 59.453 52.381 0.00 0.00 41.67 1.85
59 60 0.320697 CGGAGTCGGAGGTTTCCTTT 59.679 55.000 0.00 0.00 41.67 3.11
61 62 0.966370 CTCGGAGTCGGAGGTTTCCT 60.966 60.000 17.69 0.00 41.67 3.36
63 64 0.170784 GTCTCGGAGTCGGAGGTTTC 59.829 60.000 23.17 10.85 36.95 2.78
65 66 0.323542 ATGTCTCGGAGTCGGAGGTT 60.324 55.000 23.17 9.19 36.95 3.50
66 67 1.032657 CATGTCTCGGAGTCGGAGGT 61.033 60.000 23.17 10.37 36.95 3.85
77 81 1.934589 TTATTGGCGTCCATGTCTCG 58.065 50.000 0.00 0.00 31.53 4.04
253 260 6.150976 TCCAAGATTCGTGCAGTTCATTTATT 59.849 34.615 0.00 0.00 0.00 1.40
312 319 0.809241 CTTGCAAGCACCCGCAAAAA 60.809 50.000 14.65 0.00 46.73 1.94
313 320 1.227205 CTTGCAAGCACCCGCAAAA 60.227 52.632 14.65 0.00 46.73 2.44
314 321 2.074230 CTCTTGCAAGCACCCGCAAA 62.074 55.000 21.99 0.00 46.73 3.68
315 322 2.518112 TCTTGCAAGCACCCGCAA 60.518 55.556 21.99 0.00 45.45 4.85
316 323 2.979676 CTCTTGCAAGCACCCGCA 60.980 61.111 21.99 1.40 42.27 5.69
317 324 3.741476 CCTCTTGCAAGCACCCGC 61.741 66.667 21.99 0.00 38.99 6.13
318 325 2.281761 ACCTCTTGCAAGCACCCG 60.282 61.111 21.99 8.74 0.00 5.28
319 326 1.228245 TGACCTCTTGCAAGCACCC 60.228 57.895 21.99 10.99 0.00 4.61
320 327 0.819259 TGTGACCTCTTGCAAGCACC 60.819 55.000 21.99 10.65 0.00 5.01
321 328 1.024271 TTGTGACCTCTTGCAAGCAC 58.976 50.000 21.99 21.53 0.00 4.40
322 329 1.985473 ATTGTGACCTCTTGCAAGCA 58.015 45.000 21.99 10.85 0.00 3.91
323 330 3.065925 GGATATTGTGACCTCTTGCAAGC 59.934 47.826 21.99 8.18 0.00 4.01
324 331 4.264253 TGGATATTGTGACCTCTTGCAAG 58.736 43.478 20.81 20.81 0.00 4.01
325 332 4.299586 TGGATATTGTGACCTCTTGCAA 57.700 40.909 0.00 0.00 0.00 4.08
326 333 3.998913 TGGATATTGTGACCTCTTGCA 57.001 42.857 0.00 0.00 0.00 4.08
327 334 4.454678 TCATGGATATTGTGACCTCTTGC 58.545 43.478 0.00 0.00 0.00 4.01
328 335 5.922053 TCTCATGGATATTGTGACCTCTTG 58.078 41.667 0.00 0.00 0.00 3.02
329 336 6.100859 ACATCTCATGGATATTGTGACCTCTT 59.899 38.462 0.00 0.00 32.64 2.85
330 337 5.605908 ACATCTCATGGATATTGTGACCTCT 59.394 40.000 0.00 0.00 32.64 3.69
331 338 5.862845 ACATCTCATGGATATTGTGACCTC 58.137 41.667 0.00 0.00 32.64 3.85
332 339 5.221803 GGACATCTCATGGATATTGTGACCT 60.222 44.000 0.00 0.00 32.64 3.85
333 340 4.999950 GGACATCTCATGGATATTGTGACC 59.000 45.833 0.00 0.00 32.64 4.02
334 341 5.862845 AGGACATCTCATGGATATTGTGAC 58.137 41.667 0.00 0.00 32.64 3.67
335 342 5.842874 AGAGGACATCTCATGGATATTGTGA 59.157 40.000 0.00 0.00 44.81 3.58
336 343 6.111669 AGAGGACATCTCATGGATATTGTG 57.888 41.667 0.00 0.00 44.81 3.33
337 344 7.015680 AGTAGAGGACATCTCATGGATATTGT 58.984 38.462 0.00 0.00 44.81 2.71
338 345 7.363705 GGAGTAGAGGACATCTCATGGATATTG 60.364 44.444 0.00 0.00 44.81 1.90
343 350 3.205282 TGGAGTAGAGGACATCTCATGGA 59.795 47.826 0.00 0.00 44.81 3.41
359 366 5.801531 ATGTAACAGAGTGTTGTGGAGTA 57.198 39.130 2.50 0.00 41.30 2.59
419 464 4.314961 TGCGCCATACTTATTACTGATGG 58.685 43.478 4.18 0.00 40.11 3.51
432 477 5.120830 CACTATAGAATTTCCTGCGCCATAC 59.879 44.000 4.18 0.00 0.00 2.39
469 518 7.435068 TTTTACTGTTCTTATTCTCACTGCC 57.565 36.000 0.00 0.00 0.00 4.85
470 519 9.334693 CATTTTTACTGTTCTTATTCTCACTGC 57.665 33.333 0.00 0.00 0.00 4.40
650 704 6.603201 TGTCTCTTCCTGTTGTTTTGATTCTT 59.397 34.615 0.00 0.00 0.00 2.52
700 754 1.687493 CTGGACCTCCCTCCACTCC 60.687 68.421 0.00 0.00 35.23 3.85
767 821 2.728007 GCCTAATCCATAATCTGGGGC 58.272 52.381 0.00 0.00 45.98 5.80
1111 1166 0.674895 AGACGGAAGCAGTGAATGGC 60.675 55.000 0.00 0.00 0.00 4.40
1266 1330 1.612726 GCCTTTGCCATCTCTGACAGT 60.613 52.381 1.59 0.00 0.00 3.55
1356 1420 4.790962 AGTGAGCGCATGGCCAGG 62.791 66.667 14.45 14.45 45.17 4.45
1491 1555 0.462759 GAGTCAAAGCCCCAGATCCG 60.463 60.000 0.00 0.00 0.00 4.18
1500 1564 1.743252 CTGCCGGAGAGTCAAAGCC 60.743 63.158 5.05 0.00 0.00 4.35
1521 1585 1.442526 GCACAGCTGCAGTCAACACT 61.443 55.000 15.27 0.00 43.62 3.55
1525 1589 0.681175 TCTAGCACAGCTGCAGTCAA 59.319 50.000 15.27 0.00 46.97 3.18
1614 1678 5.064452 CAGAGAATCATTTCCTTGGAAGACG 59.936 44.000 2.16 0.00 37.82 4.18
1700 1764 7.040409 ACAAATCTCAAAAGGGTTATCTGTGAC 60.040 37.037 0.00 0.00 0.00 3.67
1721 1785 9.631257 TCATCTGATTGACATGGTATAACAAAT 57.369 29.630 0.00 0.00 0.00 2.32
1775 1839 9.645128 TGTGGGAATCTTGAATAATTATGTGAT 57.355 29.630 0.00 0.00 0.00 3.06
1776 1840 9.123902 CTGTGGGAATCTTGAATAATTATGTGA 57.876 33.333 0.00 0.00 0.00 3.58
1878 1945 3.923017 AGTGCATAGGTTTTTGCTGTC 57.077 42.857 0.00 0.00 39.60 3.51
1990 2059 7.362142 CCCTTTGCTGGTTTCTTACTTATCTTC 60.362 40.741 0.00 0.00 0.00 2.87
2045 2116 4.202212 ACATCAACCAGGCTAAAACCAAAC 60.202 41.667 0.00 0.00 0.00 2.93
2100 2171 6.827727 TCTGCCTATAACTGGATCCTAAAAC 58.172 40.000 14.23 0.00 0.00 2.43
2209 2280 7.941431 TTTGTTGTTTCTGTACTTTCCCTAA 57.059 32.000 0.00 0.00 0.00 2.69
2265 2336 8.956426 CCACTAAAATTTCTTACTCCAGCATAA 58.044 33.333 0.00 0.00 0.00 1.90
2420 2492 8.301720 CAAGTGCATTGCTTGTGGATATATTAT 58.698 33.333 10.49 0.00 38.68 1.28
2513 2585 5.703130 GCCATAAGAGGAAGCAACCTATAAG 59.297 44.000 1.73 0.00 40.73 1.73
2645 2717 5.901413 TCAGAGGAGAAATAAGCCATGAT 57.099 39.130 0.00 0.00 0.00 2.45
2663 2735 1.196766 AGACTGCAGCACCCATCAGA 61.197 55.000 15.27 0.00 0.00 3.27
2749 2821 6.048073 TCACAAAGATGTCTTGTTTTCTCG 57.952 37.500 0.00 0.00 37.82 4.04
2770 2842 9.920133 GCTCAATAAGATGTCTGACTAATATCA 57.080 33.333 9.51 0.00 0.00 2.15
2771 2843 9.920133 TGCTCAATAAGATGTCTGACTAATATC 57.080 33.333 9.51 3.75 0.00 1.63
3068 3143 2.791655 TCTGCTTCCGAAGACAGTAGA 58.208 47.619 21.65 11.20 35.53 2.59
3080 3155 4.673841 GCTGTTGCTATCTTTTCTGCTTCC 60.674 45.833 0.00 0.00 36.03 3.46
3162 3237 0.458543 ACGCCGTAGACAATCTGCAG 60.459 55.000 7.63 7.63 0.00 4.41
3455 3530 2.032681 AAGACCACAGAAGCGGCC 59.967 61.111 0.00 0.00 0.00 6.13
3539 3614 3.181440 TGTTGAGACCTCTTGCAAATCCT 60.181 43.478 0.00 0.00 0.00 3.24
3581 3656 2.549992 CCAGGAGACCACAATTTCACGA 60.550 50.000 0.00 0.00 0.00 4.35
3754 3829 7.254590 GGCTCATCTATTCACTGTTACACATTC 60.255 40.741 0.00 0.00 0.00 2.67
3783 3858 1.078848 CTGCTGGAAACTCCCGGAG 60.079 63.158 13.31 13.31 35.03 4.63
3826 3901 8.688747 TTTGTTGCCAGGAAAATGATTATTTT 57.311 26.923 7.84 7.84 46.35 1.82
3964 4043 9.093458 ACAAGAAATTGAAATATTCCACCTTCT 57.907 29.630 0.00 0.00 0.00 2.85
4025 4105 2.233305 AGGGTAGTGAGACGAACCAT 57.767 50.000 0.00 0.00 32.53 3.55
4202 4282 8.552296 ACCAGTTCCTCTAATCTCATTGTTATT 58.448 33.333 0.00 0.00 0.00 1.40
4333 4413 8.950210 CATTCCTACTTATGTGTGTTCTTCAAT 58.050 33.333 0.00 0.00 0.00 2.57
4334 4414 7.936847 ACATTCCTACTTATGTGTGTTCTTCAA 59.063 33.333 0.00 0.00 33.90 2.69
4335 4415 7.450074 ACATTCCTACTTATGTGTGTTCTTCA 58.550 34.615 0.00 0.00 33.90 3.02
4336 4416 7.819900 AGACATTCCTACTTATGTGTGTTCTTC 59.180 37.037 0.00 0.00 35.24 2.87
4337 4417 7.604164 CAGACATTCCTACTTATGTGTGTTCTT 59.396 37.037 0.00 0.00 39.71 2.52
4338 4418 7.039011 TCAGACATTCCTACTTATGTGTGTTCT 60.039 37.037 10.75 0.00 43.00 3.01
4339 4419 7.097192 TCAGACATTCCTACTTATGTGTGTTC 58.903 38.462 10.75 0.00 43.00 3.18
4340 4420 7.004555 TCAGACATTCCTACTTATGTGTGTT 57.995 36.000 10.75 0.00 43.00 3.32
4341 4421 6.605471 TCAGACATTCCTACTTATGTGTGT 57.395 37.500 10.75 0.00 43.00 3.72
4342 4422 9.599866 TTATTCAGACATTCCTACTTATGTGTG 57.400 33.333 0.00 0.00 43.51 3.82
4348 4428 9.832445 GTGGATTTATTCAGACATTCCTACTTA 57.168 33.333 0.00 0.00 0.00 2.24
4349 4429 8.328758 TGTGGATTTATTCAGACATTCCTACTT 58.671 33.333 0.00 0.00 0.00 2.24
4350 4430 7.861629 TGTGGATTTATTCAGACATTCCTACT 58.138 34.615 0.00 0.00 0.00 2.57
4351 4431 8.506168 TTGTGGATTTATTCAGACATTCCTAC 57.494 34.615 0.00 0.00 0.00 3.18
4352 4432 7.775093 CCTTGTGGATTTATTCAGACATTCCTA 59.225 37.037 0.00 0.00 34.57 2.94
4353 4433 6.604795 CCTTGTGGATTTATTCAGACATTCCT 59.395 38.462 0.00 0.00 34.57 3.36
4354 4434 6.603201 TCCTTGTGGATTTATTCAGACATTCC 59.397 38.462 0.00 0.00 37.46 3.01
4355 4435 7.630242 TCCTTGTGGATTTATTCAGACATTC 57.370 36.000 0.00 0.00 37.46 2.67
4356 4436 8.421249 TTTCCTTGTGGATTTATTCAGACATT 57.579 30.769 0.00 0.00 42.81 2.71
4357 4437 8.421249 TTTTCCTTGTGGATTTATTCAGACAT 57.579 30.769 0.00 0.00 42.81 3.06
4358 4438 7.831691 TTTTCCTTGTGGATTTATTCAGACA 57.168 32.000 0.00 0.00 42.81 3.41
4440 4520 5.748402 ACATAATGATCAGCCTTTCAGACA 58.252 37.500 0.09 0.00 0.00 3.41
4513 4593 3.130516 TGGCAGGAAGTTACTCGTCATAG 59.869 47.826 0.00 0.00 0.00 2.23
4519 4599 1.066143 ACCATGGCAGGAAGTTACTCG 60.066 52.381 13.04 0.00 0.00 4.18
4522 4602 4.150897 TGATACCATGGCAGGAAGTTAC 57.849 45.455 13.04 0.00 0.00 2.50
4530 4610 5.824624 AGTAAACAGAATGATACCATGGCAG 59.175 40.000 13.04 0.00 39.69 4.85
4533 4613 8.964476 AGTTAGTAAACAGAATGATACCATGG 57.036 34.615 11.19 11.19 39.69 3.66
4593 4674 8.578308 TGATGAGAATTGTTGAAAAACATGTC 57.422 30.769 0.00 0.00 32.01 3.06
4594 4675 8.415553 TCTGATGAGAATTGTTGAAAAACATGT 58.584 29.630 0.00 0.00 32.01 3.21
4621 4703 5.883115 TGTTACTGATGAGTTTGTCCACAAA 59.117 36.000 0.55 0.55 42.90 2.83
4624 4706 6.874134 ACTATGTTACTGATGAGTTTGTCCAC 59.126 38.462 0.00 0.00 33.21 4.02
4646 4729 9.766766 TGTGCCCACAAAAAGGAAATCCTACTA 62.767 40.741 1.61 0.00 41.36 1.82
4649 4732 4.937612 TGTGCCCACAAAAAGGAAATCCTA 60.938 41.667 1.61 0.00 41.36 2.94


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

AutoCloner maintained by Alex Coulton.