Multiple sequence alignment - TraesCS1D01G340900

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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 TraesCS1D01G340900 chr1D 100.000 2729 0 0 1 2729 430483152 430480424 0.000000e+00 5040
1 TraesCS1D01G340900 chr1A 91.460 2342 116 40 422 2729 528103636 528101345 0.000000e+00 3140
2 TraesCS1D01G340900 chr1A 89.161 286 23 4 1 279 528103942 528103658 1.560000e-92 350
3 TraesCS1D01G340900 chr1B 92.943 1913 74 33 396 2300 581596907 581595048 0.000000e+00 2728
4 TraesCS1D01G340900 chr1B 91.098 337 23 3 1 332 581597574 581597240 1.490000e-122 449
5 TraesCS1D01G340900 chr1B 87.037 378 23 16 2361 2729 581594624 581594264 1.180000e-108 403
6 TraesCS1D01G340900 chr3D 76.763 723 95 41 1010 1698 378529335 378530018 1.210000e-88 337
7 TraesCS1D01G340900 chr3A 76.763 723 95 41 1010 1698 502490400 502491083 1.210000e-88 337
8 TraesCS1D01G340900 chr3B 75.829 724 109 42 1010 1698 493584570 493585262 9.490000e-80 307


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 TraesCS1D01G340900 chr1D 430480424 430483152 2728 True 5040.000000 5040 100.000000 1 2729 1 chr1D.!!$R1 2728
1 TraesCS1D01G340900 chr1A 528101345 528103942 2597 True 1745.000000 3140 90.310500 1 2729 2 chr1A.!!$R1 2728
2 TraesCS1D01G340900 chr1B 581594264 581597574 3310 True 1193.333333 2728 90.359333 1 2729 3 chr1B.!!$R1 2728
3 TraesCS1D01G340900 chr3D 378529335 378530018 683 False 337.000000 337 76.763000 1010 1698 1 chr3D.!!$F1 688
4 TraesCS1D01G340900 chr3A 502490400 502491083 683 False 337.000000 337 76.763000 1010 1698 1 chr3A.!!$F1 688
5 TraesCS1D01G340900 chr3B 493584570 493585262 692 False 307.000000 307 75.829000 1010 1698 1 chr3B.!!$F1 688

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
855 1141 0.324943 ATCACCTCACGGTCAAAGGG 59.675 55.0 5.9 0.0 43.24 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2645 3388 0.327924 AAAGGTGCACCGATGATGGA 59.672 50.0 29.68 0.0 42.08 3.41 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
43 45 1.294068 TGCAATCTACCCTACCCCTCT 59.706 52.381 0.00 0.00 0.00 3.69
46 48 0.941963 ATCTACCCTACCCCTCTGCA 59.058 55.000 0.00 0.00 0.00 4.41
52 54 1.694048 CCCTACCCCTCTGCATTCTCT 60.694 57.143 0.00 0.00 0.00 3.10
57 59 2.376518 ACCCCTCTGCATTCTCTTTCAA 59.623 45.455 0.00 0.00 0.00 2.69
69 71 2.300152 TCTCTTTCAACACGCCTCTGAT 59.700 45.455 0.00 0.00 0.00 2.90
124 127 3.278574 TCATAACTGCAACCTACCATGC 58.721 45.455 0.00 0.00 42.86 4.06
205 213 6.460781 TGACTATAAATGTAATGTAGCCCGG 58.539 40.000 0.00 0.00 0.00 5.73
206 214 6.268158 TGACTATAAATGTAATGTAGCCCGGA 59.732 38.462 0.73 0.00 0.00 5.14
224 232 2.286127 GACCTCCGCCTTCTCCTTCG 62.286 65.000 0.00 0.00 0.00 3.79
248 256 1.296715 CCTCTCACGTTTCCCCTGG 59.703 63.158 0.00 0.00 0.00 4.45
251 259 0.841289 TCTCACGTTTCCCCTGGTTT 59.159 50.000 0.00 0.00 0.00 3.27
280 288 8.292448 CCAATATGATAACTTGACCATAACTGC 58.708 37.037 0.00 0.00 0.00 4.40
297 305 2.687266 CAATTTACCCCGCCCCCT 59.313 61.111 0.00 0.00 0.00 4.79
319 327 2.203252 CTCATCCACCATGCCCCG 60.203 66.667 0.00 0.00 31.70 5.73
321 329 2.516930 CATCCACCATGCCCCGAC 60.517 66.667 0.00 0.00 0.00 4.79
329 337 3.642503 ATGCCCCGACGTTTCCCA 61.643 61.111 0.00 0.00 0.00 4.37
332 340 1.974875 GCCCCGACGTTTCCCATTT 60.975 57.895 0.00 0.00 0.00 2.32
333 341 1.529152 GCCCCGACGTTTCCCATTTT 61.529 55.000 0.00 0.00 0.00 1.82
334 342 0.963225 CCCCGACGTTTCCCATTTTT 59.037 50.000 0.00 0.00 0.00 1.94
335 343 1.068125 CCCCGACGTTTCCCATTTTTC 60.068 52.381 0.00 0.00 0.00 2.29
336 344 1.068125 CCCGACGTTTCCCATTTTTCC 60.068 52.381 0.00 0.00 0.00 3.13
337 345 1.400500 CCGACGTTTCCCATTTTTCCG 60.400 52.381 0.00 0.00 0.00 4.30
338 346 1.264826 CGACGTTTCCCATTTTTCCGT 59.735 47.619 0.00 0.00 0.00 4.69
339 347 2.287129 CGACGTTTCCCATTTTTCCGTT 60.287 45.455 0.00 0.00 0.00 4.44
340 348 3.047093 GACGTTTCCCATTTTTCCGTTG 58.953 45.455 0.00 0.00 0.00 4.10
341 349 2.688958 ACGTTTCCCATTTTTCCGTTGA 59.311 40.909 0.00 0.00 0.00 3.18
342 350 3.319689 ACGTTTCCCATTTTTCCGTTGAT 59.680 39.130 0.00 0.00 0.00 2.57
343 351 3.917985 CGTTTCCCATTTTTCCGTTGATC 59.082 43.478 0.00 0.00 0.00 2.92
344 352 4.242475 GTTTCCCATTTTTCCGTTGATCC 58.758 43.478 0.00 0.00 0.00 3.36
345 353 2.088423 TCCCATTTTTCCGTTGATCCG 58.912 47.619 0.00 0.00 0.00 4.18
354 362 2.373540 CCGTTGATCCGGTAACTTGA 57.626 50.000 0.00 0.00 43.07 3.02
355 363 1.997606 CCGTTGATCCGGTAACTTGAC 59.002 52.381 0.00 0.00 43.07 3.18
356 364 2.610976 CCGTTGATCCGGTAACTTGACA 60.611 50.000 0.00 0.00 43.07 3.58
357 365 3.061322 CGTTGATCCGGTAACTTGACAA 58.939 45.455 0.00 0.00 0.00 3.18
358 366 3.682858 CGTTGATCCGGTAACTTGACAAT 59.317 43.478 0.00 0.00 0.00 2.71
359 367 4.865925 CGTTGATCCGGTAACTTGACAATA 59.134 41.667 0.00 0.00 0.00 1.90
360 368 5.005394 CGTTGATCCGGTAACTTGACAATAG 59.995 44.000 0.00 0.00 0.00 1.73
361 369 4.439057 TGATCCGGTAACTTGACAATAGC 58.561 43.478 0.00 0.00 0.00 2.97
362 370 4.161565 TGATCCGGTAACTTGACAATAGCT 59.838 41.667 0.00 0.00 0.00 3.32
363 371 3.857052 TCCGGTAACTTGACAATAGCTG 58.143 45.455 0.00 0.00 0.00 4.24
364 372 2.351726 CCGGTAACTTGACAATAGCTGC 59.648 50.000 0.00 0.00 0.00 5.25
365 373 3.000041 CGGTAACTTGACAATAGCTGCA 59.000 45.455 1.02 0.00 0.00 4.41
366 374 3.435327 CGGTAACTTGACAATAGCTGCAA 59.565 43.478 1.02 0.00 0.00 4.08
367 375 4.094887 CGGTAACTTGACAATAGCTGCAAT 59.905 41.667 1.02 0.00 0.00 3.56
368 376 5.573146 GGTAACTTGACAATAGCTGCAATC 58.427 41.667 1.02 0.00 0.00 2.67
369 377 5.355350 GGTAACTTGACAATAGCTGCAATCT 59.645 40.000 1.02 0.00 0.00 2.40
370 378 6.538742 GGTAACTTGACAATAGCTGCAATCTA 59.461 38.462 1.02 0.00 0.00 1.98
371 379 6.428385 AACTTGACAATAGCTGCAATCTAC 57.572 37.500 1.02 0.00 0.00 2.59
372 380 4.878397 ACTTGACAATAGCTGCAATCTACC 59.122 41.667 1.02 0.00 0.00 3.18
373 381 3.808728 TGACAATAGCTGCAATCTACCC 58.191 45.455 1.02 0.00 0.00 3.69
374 382 3.142174 GACAATAGCTGCAATCTACCCC 58.858 50.000 1.02 0.00 0.00 4.95
375 383 2.158608 ACAATAGCTGCAATCTACCCCC 60.159 50.000 1.02 0.00 0.00 5.40
398 406 4.821589 CCTCCGCCTTCGCCTGAC 62.822 72.222 0.00 0.00 0.00 3.51
399 407 4.821589 CTCCGCCTTCGCCTGACC 62.822 72.222 0.00 0.00 0.00 4.02
401 409 4.473520 CCGCCTTCGCCTGACCAT 62.474 66.667 0.00 0.00 0.00 3.55
402 410 3.197790 CGCCTTCGCCTGACCATG 61.198 66.667 0.00 0.00 0.00 3.66
418 695 2.288579 ACCATGCGTTCGAACTTGAGTA 60.289 45.455 24.80 10.08 0.00 2.59
459 736 6.942532 TTACAATTGATGGAAGCCAGATAC 57.057 37.500 13.59 0.00 36.75 2.24
467 744 5.127519 TGATGGAAGCCAGATACAATTTTGG 59.872 40.000 0.00 0.00 36.75 3.28
520 801 3.838317 AGTGCAGTCCTATCCTTACAACA 59.162 43.478 0.00 0.00 0.00 3.33
526 807 3.518303 GTCCTATCCTTACAACACCACCT 59.482 47.826 0.00 0.00 0.00 4.00
529 810 3.983044 ATCCTTACAACACCACCTCTC 57.017 47.619 0.00 0.00 0.00 3.20
709 992 6.072508 AGCACAACAATACCATGACAAAGTAG 60.073 38.462 0.00 0.00 0.00 2.57
713 996 8.567948 ACAACAATACCATGACAAAGTAGAAAG 58.432 33.333 0.00 0.00 0.00 2.62
723 1006 8.567948 CATGACAAAGTAGAAAGAAAAAGGCTA 58.432 33.333 0.00 0.00 0.00 3.93
787 1073 4.142049 TGAACTGAAAACCGGCAAGAAAAT 60.142 37.500 0.00 0.00 0.00 1.82
855 1141 0.324943 ATCACCTCACGGTCAAAGGG 59.675 55.000 5.90 0.00 43.24 3.95
860 1146 1.279271 CCTCACGGTCAAAGGGAGAAT 59.721 52.381 0.00 0.00 41.47 2.40
967 1256 2.461637 CCCCCTTCCTCCCTCCTT 59.538 66.667 0.00 0.00 0.00 3.36
1735 2084 2.202362 CGTCGGAGTGAGCGAGTG 60.202 66.667 0.00 0.00 0.00 3.51
1736 2085 2.677979 CGTCGGAGTGAGCGAGTGA 61.678 63.158 0.00 0.00 0.00 3.41
1737 2086 1.135731 GTCGGAGTGAGCGAGTGAG 59.864 63.158 0.00 0.00 0.00 3.51
1742 2091 1.999071 GAGTGAGCGAGTGAGCCGAT 61.999 60.000 0.00 0.00 38.01 4.18
1745 2094 3.815569 GAGCGAGTGAGCCGATCCG 62.816 68.421 0.00 0.00 36.57 4.18
1784 2137 0.316937 CGACGGCGGCGTACTATTAA 60.317 55.000 37.57 0.00 0.00 1.40
1786 2139 1.981533 GACGGCGGCGTACTATTAATC 59.018 52.381 37.57 17.43 0.00 1.75
1872 2228 2.727684 GCTCGCGAAGGAACGGAAC 61.728 63.158 11.33 0.00 0.00 3.62
1912 2268 2.041928 CTCCTCCCCTGCCCTCTT 59.958 66.667 0.00 0.00 0.00 2.85
1913 2269 2.041265 TCCTCCCCTGCCCTCTTC 59.959 66.667 0.00 0.00 0.00 2.87
1914 2270 2.041928 CCTCCCCTGCCCTCTTCT 59.958 66.667 0.00 0.00 0.00 2.85
1915 2271 2.373707 CCTCCCCTGCCCTCTTCTG 61.374 68.421 0.00 0.00 0.00 3.02
1916 2272 1.614824 CTCCCCTGCCCTCTTCTGT 60.615 63.158 0.00 0.00 0.00 3.41
1971 2332 9.601217 TGCCTAATTTACTCTCAGAATTAACTC 57.399 33.333 0.00 0.00 0.00 3.01
2030 2391 6.611613 ATTTCCCATTCCTTTCTTTCTTCC 57.388 37.500 0.00 0.00 0.00 3.46
2129 2490 4.023450 CCGCTAAGATACGAACCATCTACA 60.023 45.833 0.00 0.00 32.40 2.74
2132 2493 6.144175 GCTAAGATACGAACCATCTACAGTC 58.856 44.000 0.00 0.00 32.40 3.51
2174 2535 8.081025 GCATTCAGAATTCTTCCCAAATCTATC 58.919 37.037 4.86 0.00 0.00 2.08
2185 2546 6.708885 TCCCAAATCTATCTAAGCATCCAT 57.291 37.500 0.00 0.00 0.00 3.41
2262 2623 0.404040 AAATTCCCTGACAAGGCCGA 59.596 50.000 0.00 0.00 42.96 5.54
2360 3088 2.757314 TCAGAGAGATTGCAGTGTCGAT 59.243 45.455 0.54 0.00 0.00 3.59
2361 3089 3.114809 CAGAGAGATTGCAGTGTCGATC 58.885 50.000 0.54 6.66 0.00 3.69
2373 3101 1.986378 GTGTCGATCGAAGGAACACAG 59.014 52.381 21.31 0.00 0.00 3.66
2408 3136 0.109272 TCACATCGAGCCGTGACTTC 60.109 55.000 10.17 0.00 37.23 3.01
2438 3166 9.554724 TCGTAGAATTATTGCAACTTTGAATTC 57.445 29.630 0.00 11.84 34.82 2.17
2554 3293 0.323178 CCAGCAGCACAAGGAAGGAT 60.323 55.000 0.00 0.00 0.00 3.24
2556 3295 0.323178 AGCAGCACAAGGAAGGATGG 60.323 55.000 0.00 0.00 0.00 3.51
2557 3296 0.610232 GCAGCACAAGGAAGGATGGT 60.610 55.000 0.00 0.00 0.00 3.55
2558 3297 1.915141 CAGCACAAGGAAGGATGGTT 58.085 50.000 0.00 0.00 0.00 3.67
2560 3299 0.804989 GCACAAGGAAGGATGGTTCG 59.195 55.000 0.00 0.00 0.00 3.95
2561 3300 1.610624 GCACAAGGAAGGATGGTTCGA 60.611 52.381 0.00 0.00 0.00 3.71
2562 3301 2.350522 CACAAGGAAGGATGGTTCGAG 58.649 52.381 0.00 0.00 0.00 4.04
2563 3302 1.978580 ACAAGGAAGGATGGTTCGAGT 59.021 47.619 0.00 0.00 0.00 4.18
2564 3303 2.028020 ACAAGGAAGGATGGTTCGAGTC 60.028 50.000 0.00 0.00 0.00 3.36
2645 3388 4.740822 GCCGGCAGTCCAACCCAT 62.741 66.667 24.80 0.00 0.00 4.00
2647 3390 2.438434 CGGCAGTCCAACCCATCC 60.438 66.667 0.00 0.00 0.00 3.51
2688 3431 4.729918 CCCCAAAGCAGCTCCGCT 62.730 66.667 0.00 0.00 46.67 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 45 1.266718 GGCGTGTTGAAAGAGAATGCA 59.733 47.619 0.00 0.00 0.00 3.96
46 48 3.070018 CAGAGGCGTGTTGAAAGAGAAT 58.930 45.455 0.00 0.00 0.00 2.40
52 54 2.254546 ACATCAGAGGCGTGTTGAAA 57.745 45.000 7.65 0.00 0.00 2.69
57 59 0.321653 GGGAAACATCAGAGGCGTGT 60.322 55.000 0.00 0.00 0.00 4.49
69 71 3.284793 TCAGTCGAAAAAGGGGAAACA 57.715 42.857 0.00 0.00 0.00 2.83
205 213 1.518302 GAAGGAGAAGGCGGAGGTC 59.482 63.158 0.00 0.00 0.00 3.85
206 214 2.352032 CGAAGGAGAAGGCGGAGGT 61.352 63.158 0.00 0.00 0.00 3.85
224 232 1.557651 GGAAACGTGAGAGGTATCGC 58.442 55.000 0.00 0.00 0.00 4.58
248 256 8.220755 TGGTCAAGTTATCATATTGGCTAAAC 57.779 34.615 0.00 0.00 0.00 2.01
251 259 9.502091 GTTATGGTCAAGTTATCATATTGGCTA 57.498 33.333 0.00 0.00 0.00 3.93
280 288 1.455032 GAGGGGGCGGGGTAAATTG 60.455 63.158 0.00 0.00 0.00 2.32
297 305 0.548031 GGCATGGTGGATGAGAAGGA 59.452 55.000 0.00 0.00 33.31 3.36
305 313 4.175337 CGTCGGGGCATGGTGGAT 62.175 66.667 0.00 0.00 0.00 3.41
319 327 3.047093 CAACGGAAAAATGGGAAACGTC 58.953 45.455 0.00 0.00 32.18 4.34
321 329 3.357166 TCAACGGAAAAATGGGAAACG 57.643 42.857 0.00 0.00 0.00 3.60
336 344 2.679450 TGTCAAGTTACCGGATCAACG 58.321 47.619 9.46 0.00 0.00 4.10
337 345 5.220605 GCTATTGTCAAGTTACCGGATCAAC 60.221 44.000 9.46 9.41 0.00 3.18
338 346 4.873827 GCTATTGTCAAGTTACCGGATCAA 59.126 41.667 9.46 0.00 0.00 2.57
339 347 4.161565 AGCTATTGTCAAGTTACCGGATCA 59.838 41.667 9.46 0.00 0.00 2.92
340 348 4.508124 CAGCTATTGTCAAGTTACCGGATC 59.492 45.833 9.46 0.00 0.00 3.36
341 349 4.442706 CAGCTATTGTCAAGTTACCGGAT 58.557 43.478 9.46 0.00 0.00 4.18
342 350 3.857052 CAGCTATTGTCAAGTTACCGGA 58.143 45.455 9.46 0.00 0.00 5.14
343 351 2.351726 GCAGCTATTGTCAAGTTACCGG 59.648 50.000 0.00 0.00 0.00 5.28
344 352 3.000041 TGCAGCTATTGTCAAGTTACCG 59.000 45.455 0.00 0.00 0.00 4.02
345 353 5.355350 AGATTGCAGCTATTGTCAAGTTACC 59.645 40.000 0.00 0.00 0.00 2.85
346 354 6.428385 AGATTGCAGCTATTGTCAAGTTAC 57.572 37.500 0.00 0.00 0.00 2.50
347 355 6.538742 GGTAGATTGCAGCTATTGTCAAGTTA 59.461 38.462 0.00 0.00 0.00 2.24
348 356 5.355350 GGTAGATTGCAGCTATTGTCAAGTT 59.645 40.000 0.00 0.00 0.00 2.66
349 357 4.878397 GGTAGATTGCAGCTATTGTCAAGT 59.122 41.667 0.00 0.00 0.00 3.16
350 358 4.274459 GGGTAGATTGCAGCTATTGTCAAG 59.726 45.833 0.00 0.00 0.00 3.02
351 359 4.199310 GGGTAGATTGCAGCTATTGTCAA 58.801 43.478 0.00 0.00 0.00 3.18
352 360 3.433598 GGGGTAGATTGCAGCTATTGTCA 60.434 47.826 0.00 0.00 0.00 3.58
353 361 3.142174 GGGGTAGATTGCAGCTATTGTC 58.858 50.000 0.00 0.00 0.00 3.18
354 362 2.158608 GGGGGTAGATTGCAGCTATTGT 60.159 50.000 0.00 0.00 0.00 2.71
355 363 2.508526 GGGGGTAGATTGCAGCTATTG 58.491 52.381 0.00 0.00 0.00 1.90
356 364 2.959465 GGGGGTAGATTGCAGCTATT 57.041 50.000 0.00 0.00 0.00 1.73
392 400 2.032634 TTCGAACGCATGGTCAGGC 61.033 57.895 0.00 0.00 34.34 4.85
393 401 0.670546 AGTTCGAACGCATGGTCAGG 60.671 55.000 21.87 0.00 0.00 3.86
394 402 1.136252 CAAGTTCGAACGCATGGTCAG 60.136 52.381 21.87 2.77 0.00 3.51
395 403 0.865111 CAAGTTCGAACGCATGGTCA 59.135 50.000 21.87 0.00 0.00 4.02
396 404 1.126846 CTCAAGTTCGAACGCATGGTC 59.873 52.381 21.87 0.00 0.00 4.02
397 405 1.148310 CTCAAGTTCGAACGCATGGT 58.852 50.000 21.87 0.90 0.00 3.55
398 406 1.148310 ACTCAAGTTCGAACGCATGG 58.852 50.000 21.87 16.40 0.00 3.66
399 407 2.729360 TGTACTCAAGTTCGAACGCATG 59.271 45.455 21.87 20.35 0.00 4.06
400 408 3.021269 TGTACTCAAGTTCGAACGCAT 57.979 42.857 21.87 10.22 0.00 4.73
401 409 2.495409 TGTACTCAAGTTCGAACGCA 57.505 45.000 21.87 9.34 0.00 5.24
402 410 2.344741 GGATGTACTCAAGTTCGAACGC 59.655 50.000 21.87 0.00 0.00 4.84
450 727 4.322057 ACCTCCAAAATTGTATCTGGCT 57.678 40.909 0.00 0.00 0.00 4.75
459 736 4.916983 TCAGTGTGAACCTCCAAAATTG 57.083 40.909 0.00 0.00 0.00 2.32
467 744 4.084328 CGACTTCAAATCAGTGTGAACCTC 60.084 45.833 0.00 0.00 30.73 3.85
537 818 3.947868 AGGTGGAATTGTGAGAGATGTG 58.052 45.455 0.00 0.00 0.00 3.21
663 946 4.996758 GCTTGTGCCATGGAAAACTATTTT 59.003 37.500 18.40 0.00 35.12 1.82
709 992 5.784578 TTCTTGGGTAGCCTTTTTCTTTC 57.215 39.130 13.11 0.00 0.00 2.62
713 996 6.096673 TCATTTTCTTGGGTAGCCTTTTTC 57.903 37.500 13.11 0.00 0.00 2.29
723 1006 9.599866 CTAAAAAGTCTTTTCATTTTCTTGGGT 57.400 29.630 10.95 0.00 36.20 4.51
787 1073 4.215742 CCGTTCCGCGCTCCCATA 62.216 66.667 5.56 0.00 39.71 2.74
955 1244 2.412591 GATGGATGAAGGAGGGAGGAA 58.587 52.381 0.00 0.00 0.00 3.36
959 1248 0.401979 GGGGATGGATGAAGGAGGGA 60.402 60.000 0.00 0.00 0.00 4.20
960 1249 1.772819 CGGGGATGGATGAAGGAGGG 61.773 65.000 0.00 0.00 0.00 4.30
961 1250 0.764369 TCGGGGATGGATGAAGGAGG 60.764 60.000 0.00 0.00 0.00 4.30
964 1253 1.069765 CGTCGGGGATGGATGAAGG 59.930 63.158 0.00 0.00 0.00 3.46
967 1256 0.177141 GTTTCGTCGGGGATGGATGA 59.823 55.000 0.00 0.00 0.00 2.92
1764 2113 2.715864 TAATAGTACGCCGCCGTCGC 62.716 60.000 0.00 0.00 46.39 5.19
1784 2137 2.223829 CGAGCTACTCCGGACAATTGAT 60.224 50.000 13.59 0.00 0.00 2.57
1786 2139 1.135083 ACGAGCTACTCCGGACAATTG 60.135 52.381 0.00 3.24 0.00 2.32
1872 2228 3.664107 TCAAAGAGTGTGATCCTTTCCG 58.336 45.455 0.00 0.00 0.00 4.30
1873 2229 3.438434 GCTCAAAGAGTGTGATCCTTTCC 59.562 47.826 0.00 0.00 31.39 3.13
1874 2230 4.322567 AGCTCAAAGAGTGTGATCCTTTC 58.677 43.478 0.00 0.00 31.39 2.62
1875 2231 4.322567 GAGCTCAAAGAGTGTGATCCTTT 58.677 43.478 9.40 0.00 31.46 3.11
1912 2268 3.554960 CGATCCACCAAGAACAGAACAGA 60.555 47.826 0.00 0.00 0.00 3.41
1913 2269 2.738846 CGATCCACCAAGAACAGAACAG 59.261 50.000 0.00 0.00 0.00 3.16
1914 2270 2.549992 CCGATCCACCAAGAACAGAACA 60.550 50.000 0.00 0.00 0.00 3.18
1915 2271 2.076863 CCGATCCACCAAGAACAGAAC 58.923 52.381 0.00 0.00 0.00 3.01
1916 2272 1.697432 ACCGATCCACCAAGAACAGAA 59.303 47.619 0.00 0.00 0.00 3.02
1971 2332 2.079158 ACTGCATGATGAAACGGACAG 58.921 47.619 0.00 0.00 0.00 3.51
2129 2490 4.235079 TGCTGCAACCATTATTAGGACT 57.765 40.909 0.00 0.00 0.00 3.85
2132 2493 5.300034 TCTGAATGCTGCAACCATTATTAGG 59.700 40.000 6.36 0.00 33.34 2.69
2174 2535 3.548745 TGTGTCAGGATGGATGCTTAG 57.451 47.619 0.00 0.00 36.16 2.18
2185 2546 3.855255 TTGTTCCATCTTGTGTCAGGA 57.145 42.857 0.00 0.00 0.00 3.86
2215 2576 3.513119 CAGACACTGAGGAGAATTCTGGA 59.487 47.826 14.00 0.00 32.44 3.86
2262 2623 8.040132 CCATTGAAGAAGATACTCTGACTCTTT 58.960 37.037 0.00 0.00 29.64 2.52
2360 3088 2.833794 CTTGTTCCTGTGTTCCTTCGA 58.166 47.619 0.00 0.00 0.00 3.71
2361 3089 1.264288 GCTTGTTCCTGTGTTCCTTCG 59.736 52.381 0.00 0.00 0.00 3.79
2373 3101 0.517316 GTGACATGACGGCTTGTTCC 59.483 55.000 11.59 0.08 33.10 3.62
2408 3136 8.869897 TCAAAGTTGCAATAATTCTACGACTAG 58.130 33.333 0.59 0.00 0.00 2.57
2438 3166 9.132521 CTTCAAGGCACATAAATGTAAAAGAAG 57.867 33.333 0.00 3.54 39.39 2.85
2554 3293 0.959553 GGACAGTCTGACTCGAACCA 59.040 55.000 7.49 0.00 0.00 3.67
2556 3295 1.609555 ACTGGACAGTCTGACTCGAAC 59.390 52.381 7.49 0.00 36.92 3.95
2557 3296 1.982660 ACTGGACAGTCTGACTCGAA 58.017 50.000 7.49 0.00 36.92 3.71
2558 3297 1.609072 CAACTGGACAGTCTGACTCGA 59.391 52.381 7.49 0.00 41.58 4.04
2560 3299 3.019933 GTCAACTGGACAGTCTGACTC 57.980 52.381 24.27 0.00 46.19 3.36
2645 3388 0.327924 AAAGGTGCACCGATGATGGA 59.672 50.000 29.68 0.00 42.08 3.41
2688 3431 4.329545 GCACCACCGAGGCCAAGA 62.330 66.667 5.01 0.00 43.14 3.02


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

AutoCloner maintained by Alex Coulton.