Multiple sequence alignment - TraesCS6B01G211000

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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 TraesCS6B01G211000 chr6B 100.000 2990 0 0 1 2990 279034565 279031576 0.000000e+00 5522.0
1 TraesCS6B01G211000 chr6D 96.100 1718 44 13 587 2289 156438536 156436827 0.000000e+00 2780.0
2 TraesCS6B01G211000 chr6D 97.035 371 8 3 7 376 156441978 156441610 3.270000e-174 621.0
3 TraesCS6B01G211000 chr6A 93.653 1733 53 23 534 2231 209843068 209841358 0.000000e+00 2538.0
4 TraesCS6B01G211000 chr6A 92.790 319 20 2 7 325 209892132 209891817 2.720000e-125 459.0
5 TraesCS6B01G211000 chr6A 91.045 67 2 1 2223 2289 209840934 209840872 1.480000e-13 87.9
6 TraesCS6B01G211000 chr7B 93.848 699 40 2 2291 2988 657549521 657550217 0.000000e+00 1050.0
7 TraesCS6B01G211000 chr7B 84.600 500 69 6 1496 1993 480276708 480277201 9.630000e-135 490.0
8 TraesCS6B01G211000 chr1B 93.705 699 43 1 2291 2988 407249625 407248927 0.000000e+00 1046.0
9 TraesCS6B01G211000 chr4B 89.255 698 69 5 2293 2988 481521338 481520645 0.000000e+00 869.0
10 TraesCS6B01G211000 chr7D 86.119 706 77 17 2292 2988 48268194 48268887 0.000000e+00 741.0
11 TraesCS6B01G211000 chr7D 84.000 500 72 6 1496 1993 458521498 458521991 9.700000e-130 473.0
12 TraesCS6B01G211000 chr7D 89.873 79 7 1 86 163 102581615 102581693 1.900000e-17 100.0
13 TraesCS6B01G211000 chr1D 86.037 709 77 18 2289 2988 77841433 77842128 0.000000e+00 741.0
14 TraesCS6B01G211000 chr1D 91.045 67 6 0 433 499 425263104 425263038 1.140000e-14 91.6
15 TraesCS6B01G211000 chr5D 85.694 706 83 15 2290 2988 515271355 515272049 0.000000e+00 728.0
16 TraesCS6B01G211000 chr2B 85.633 703 86 13 2293 2988 396929169 396929863 0.000000e+00 725.0
17 TraesCS6B01G211000 chr7A 84.758 702 92 13 2291 2987 34343624 34344315 0.000000e+00 689.0
18 TraesCS6B01G211000 chr7A 84.770 499 68 6 1496 1992 541454501 541454009 7.450000e-136 494.0
19 TraesCS6B01G211000 chr7A 80.804 448 74 8 995 1433 541455049 541454605 1.030000e-89 340.0
20 TraesCS6B01G211000 chr7A 91.489 47 4 0 433 479 533039992 533040038 6.920000e-07 65.8
21 TraesCS6B01G211000 chr5B 86.879 564 69 5 2293 2854 523671096 523670536 7.040000e-176 627.0
22 TraesCS6B01G211000 chr5B 86.585 82 10 1 90 170 415799705 415799786 4.110000e-14 89.8
23 TraesCS6B01G211000 chr5A 92.537 67 5 0 101 167 389716417 389716351 2.450000e-16 97.1


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 TraesCS6B01G211000 chr6B 279031576 279034565 2989 True 5522.00 5522 100.0000 1 2990 1 chr6B.!!$R1 2989
1 TraesCS6B01G211000 chr6D 156436827 156441978 5151 True 1700.50 2780 96.5675 7 2289 2 chr6D.!!$R1 2282
2 TraesCS6B01G211000 chr6A 209840872 209843068 2196 True 1312.95 2538 92.3490 534 2289 2 chr6A.!!$R2 1755
3 TraesCS6B01G211000 chr7B 657549521 657550217 696 False 1050.00 1050 93.8480 2291 2988 1 chr7B.!!$F2 697
4 TraesCS6B01G211000 chr1B 407248927 407249625 698 True 1046.00 1046 93.7050 2291 2988 1 chr1B.!!$R1 697
5 TraesCS6B01G211000 chr4B 481520645 481521338 693 True 869.00 869 89.2550 2293 2988 1 chr4B.!!$R1 695
6 TraesCS6B01G211000 chr7D 48268194 48268887 693 False 741.00 741 86.1190 2292 2988 1 chr7D.!!$F1 696
7 TraesCS6B01G211000 chr1D 77841433 77842128 695 False 741.00 741 86.0370 2289 2988 1 chr1D.!!$F1 699
8 TraesCS6B01G211000 chr5D 515271355 515272049 694 False 728.00 728 85.6940 2290 2988 1 chr5D.!!$F1 698
9 TraesCS6B01G211000 chr2B 396929169 396929863 694 False 725.00 725 85.6330 2293 2988 1 chr2B.!!$F1 695
10 TraesCS6B01G211000 chr7A 34343624 34344315 691 False 689.00 689 84.7580 2291 2987 1 chr7A.!!$F1 696
11 TraesCS6B01G211000 chr7A 541454009 541455049 1040 True 417.00 494 82.7870 995 1992 2 chr7A.!!$R1 997
12 TraesCS6B01G211000 chr5B 523670536 523671096 560 True 627.00 627 86.8790 2293 2854 1 chr5B.!!$R1 561

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
284 285 0.178975 TTTCCCCGGTTCAGTGCATT 60.179 50.0 0.0 0.0 0.0 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2247 5616 0.252197 ATACTTCTCCCACAACCGGC 59.748 55.0 0.0 0.0 0.0 6.13 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
44 45 1.981256 AAACCTGACATTCGCTGGTT 58.019 45.000 0.00 0.00 45.69 3.67
269 270 7.755373 GCTTCATTAAGTCCTAATGTTGTTTCC 59.245 37.037 1.94 0.00 44.99 3.13
278 279 1.616159 ATGTTGTTTCCCCGGTTCAG 58.384 50.000 0.00 0.00 0.00 3.02
284 285 0.178975 TTTCCCCGGTTCAGTGCATT 60.179 50.000 0.00 0.00 0.00 3.56
296 297 5.335127 GTTCAGTGCATTTGCTTAGTATGG 58.665 41.667 3.94 0.00 42.66 2.74
321 322 6.980978 GCTGAGTAGTGCAATACTTCATTAGA 59.019 38.462 26.03 5.90 40.89 2.10
393 395 9.612620 AAAAATCTTGTTATTCTAGCGAAACAG 57.387 29.630 0.00 1.63 31.91 3.16
394 396 6.910536 ATCTTGTTATTCTAGCGAAACAGG 57.089 37.500 0.00 6.66 31.91 4.00
395 397 6.032956 TCTTGTTATTCTAGCGAAACAGGA 57.967 37.500 9.88 9.88 29.12 3.86
396 398 6.460781 TCTTGTTATTCTAGCGAAACAGGAA 58.539 36.000 10.91 0.00 28.87 3.36
397 399 7.103641 TCTTGTTATTCTAGCGAAACAGGAAT 58.896 34.615 10.91 0.00 28.87 3.01
399 401 6.403049 TGTTATTCTAGCGAAACAGGAATGA 58.597 36.000 0.00 0.00 31.91 2.57
402 404 1.936547 CTAGCGAAACAGGAATGAGCC 59.063 52.381 0.00 0.00 0.00 4.70
403 405 0.326264 AGCGAAACAGGAATGAGCCT 59.674 50.000 0.00 0.00 39.37 4.58
409 411 4.751431 AGGAATGAGCCTGGCAAC 57.249 55.556 22.65 14.69 36.76 4.17
411 413 0.610232 AGGAATGAGCCTGGCAACAC 60.610 55.000 22.65 9.60 46.17 3.32
412 414 1.503542 GAATGAGCCTGGCAACACG 59.496 57.895 22.65 0.00 46.17 4.49
418 420 3.049674 CCTGGCAACACGCGTCAT 61.050 61.111 9.86 0.00 46.17 3.06
420 422 2.280457 TGGCAACACGCGTCATCA 60.280 55.556 9.86 0.43 46.17 3.07
421 423 1.840630 CTGGCAACACGCGTCATCAA 61.841 55.000 9.86 0.00 46.17 2.57
422 424 1.440353 GGCAACACGCGTCATCAAC 60.440 57.895 9.86 0.00 43.84 3.18
437 439 6.755461 GTCATCAACGATCTACTGGTAATG 57.245 41.667 0.00 0.00 0.00 1.90
438 440 6.273825 GTCATCAACGATCTACTGGTAATGT 58.726 40.000 0.00 0.00 0.00 2.71
439 441 6.418226 GTCATCAACGATCTACTGGTAATGTC 59.582 42.308 0.00 0.00 0.00 3.06
440 442 6.321435 TCATCAACGATCTACTGGTAATGTCT 59.679 38.462 0.00 0.00 0.00 3.41
441 443 6.132791 TCAACGATCTACTGGTAATGTCTC 57.867 41.667 0.00 0.00 0.00 3.36
442 444 5.650703 TCAACGATCTACTGGTAATGTCTCA 59.349 40.000 0.00 0.00 0.00 3.27
443 445 6.152154 TCAACGATCTACTGGTAATGTCTCAA 59.848 38.462 0.00 0.00 0.00 3.02
444 446 6.716934 ACGATCTACTGGTAATGTCTCAAT 57.283 37.500 0.00 0.00 0.00 2.57
445 447 6.740110 ACGATCTACTGGTAATGTCTCAATC 58.260 40.000 0.00 0.00 0.00 2.67
446 448 5.853810 CGATCTACTGGTAATGTCTCAATCG 59.146 44.000 0.00 0.00 0.00 3.34
448 450 6.961360 TCTACTGGTAATGTCTCAATCGAT 57.039 37.500 0.00 0.00 0.00 3.59
449 451 6.739112 TCTACTGGTAATGTCTCAATCGATG 58.261 40.000 0.00 0.00 0.00 3.84
450 452 4.122776 ACTGGTAATGTCTCAATCGATGC 58.877 43.478 0.00 0.00 0.00 3.91
451 453 4.141846 ACTGGTAATGTCTCAATCGATGCT 60.142 41.667 0.00 0.00 0.00 3.79
452 454 5.069119 ACTGGTAATGTCTCAATCGATGCTA 59.931 40.000 0.00 0.00 0.00 3.49
453 455 6.101650 TGGTAATGTCTCAATCGATGCTAT 57.898 37.500 0.00 0.00 0.00 2.97
454 456 7.039714 ACTGGTAATGTCTCAATCGATGCTATA 60.040 37.037 0.00 0.00 0.00 1.31
456 458 7.761249 TGGTAATGTCTCAATCGATGCTATATG 59.239 37.037 0.00 0.00 0.00 1.78
457 459 6.659361 AATGTCTCAATCGATGCTATATGC 57.341 37.500 0.00 0.00 43.25 3.14
458 460 4.498241 TGTCTCAATCGATGCTATATGCC 58.502 43.478 0.00 0.00 42.00 4.40
459 461 4.221482 TGTCTCAATCGATGCTATATGCCT 59.779 41.667 0.00 0.00 42.00 4.75
460 462 5.174395 GTCTCAATCGATGCTATATGCCTT 58.826 41.667 0.00 0.00 42.00 4.35
461 463 5.641209 GTCTCAATCGATGCTATATGCCTTT 59.359 40.000 0.00 0.00 42.00 3.11
463 465 5.550290 TCAATCGATGCTATATGCCTTTGA 58.450 37.500 0.00 0.00 42.00 2.69
464 466 5.997129 TCAATCGATGCTATATGCCTTTGAA 59.003 36.000 0.00 0.00 42.00 2.69
466 468 4.960938 TCGATGCTATATGCCTTTGAACT 58.039 39.130 0.00 0.00 42.00 3.01
467 469 5.368145 TCGATGCTATATGCCTTTGAACTT 58.632 37.500 0.00 0.00 42.00 2.66
469 471 4.637483 TGCTATATGCCTTTGAACTTGC 57.363 40.909 0.00 0.00 42.00 4.01
470 472 4.015764 TGCTATATGCCTTTGAACTTGCA 58.984 39.130 0.00 0.00 42.00 4.08
471 473 4.646040 TGCTATATGCCTTTGAACTTGCAT 59.354 37.500 0.00 0.00 45.67 3.96
472 474 4.980434 GCTATATGCCTTTGAACTTGCATG 59.020 41.667 6.12 0.00 43.76 4.06
474 476 1.702182 TGCCTTTGAACTTGCATGGA 58.298 45.000 4.44 0.00 0.00 3.41
475 477 1.614903 TGCCTTTGAACTTGCATGGAG 59.385 47.619 4.44 0.00 0.00 3.86
476 478 1.888512 GCCTTTGAACTTGCATGGAGA 59.111 47.619 4.44 0.00 0.00 3.71
477 479 2.494870 GCCTTTGAACTTGCATGGAGAT 59.505 45.455 4.44 0.00 0.00 2.75
478 480 3.056322 GCCTTTGAACTTGCATGGAGATT 60.056 43.478 4.44 0.00 0.00 2.40
479 481 4.491676 CCTTTGAACTTGCATGGAGATTG 58.508 43.478 4.44 0.00 0.00 2.67
480 482 4.219070 CCTTTGAACTTGCATGGAGATTGA 59.781 41.667 4.44 0.00 0.00 2.57
481 483 5.105473 CCTTTGAACTTGCATGGAGATTGAT 60.105 40.000 4.44 0.00 0.00 2.57
482 484 4.976224 TGAACTTGCATGGAGATTGATG 57.024 40.909 4.44 0.00 0.00 3.07
491 493 6.431198 GCATGGAGATTGATGCAAAATTTT 57.569 33.333 0.00 0.00 43.75 1.82
493 495 6.315393 GCATGGAGATTGATGCAAAATTTTCT 59.685 34.615 0.00 0.00 43.75 2.52
494 496 7.148306 GCATGGAGATTGATGCAAAATTTTCTT 60.148 33.333 0.00 0.00 43.75 2.52
496 498 7.673180 TGGAGATTGATGCAAAATTTTCTTCT 58.327 30.769 0.00 0.00 0.00 2.85
541 1162 9.841880 TTATATAATATGTCGCTTGTCTCAGTC 57.158 33.333 0.00 0.00 0.00 3.51
564 1185 1.324740 TAAGACGTAGCCGCACCCAT 61.325 55.000 0.00 0.00 37.70 4.00
570 3140 1.755395 TAGCCGCACCCATAGACGT 60.755 57.895 0.00 0.00 0.00 4.34
571 3141 2.011741 TAGCCGCACCCATAGACGTG 62.012 60.000 0.00 0.00 0.00 4.49
580 3152 3.374058 CACCCATAGACGTGCCTAAAAAG 59.626 47.826 0.00 0.00 0.00 2.27
593 3458 7.608761 ACGTGCCTAAAAAGAGTAATTATGGAA 59.391 33.333 0.00 0.00 0.00 3.53
598 3463 9.462606 CCTAAAAAGAGTAATTATGGAAGTGGT 57.537 33.333 0.00 0.00 0.00 4.16
706 3573 2.433491 TCCGCACGTCCATTTCCG 60.433 61.111 0.00 0.00 0.00 4.30
770 3649 2.744062 CCAATTGGCACACCCTTCA 58.256 52.632 12.53 0.00 39.29 3.02
773 3652 0.188342 AATTGGCACACCCTTCACCT 59.812 50.000 0.00 0.00 39.29 4.00
774 3653 0.540365 ATTGGCACACCCTTCACCTG 60.540 55.000 0.00 0.00 39.29 4.00
798 3681 1.078848 ATCTCTCGTTGCCACAGCC 60.079 57.895 0.00 0.00 38.69 4.85
864 3747 3.692576 CTCTCACGACGGACGAATTAAT 58.307 45.455 6.90 0.00 45.77 1.40
1992 4929 2.547642 GCTCTTGAGCGGCAGATAGATT 60.548 50.000 6.88 0.00 0.00 2.40
2029 4966 4.319046 CGGTGAATTGATTGATCGATGACC 60.319 45.833 0.54 10.22 34.05 4.02
2060 4997 2.627699 GCCTCCATCGATCTCTTCTTCT 59.372 50.000 0.00 0.00 0.00 2.85
2073 5010 0.953727 TTCTTCTGCGCTGCATGTTT 59.046 45.000 9.73 0.00 38.13 2.83
2092 5029 7.807433 GCATGTTTTTGATGTATGTGTTGTCTA 59.193 33.333 0.00 0.00 0.00 2.59
2246 5615 8.608185 AAATATTTAAATTCCCTCTTGAGCCA 57.392 30.769 5.91 0.00 0.00 4.75
2247 5616 7.830099 ATATTTAAATTCCCTCTTGAGCCAG 57.170 36.000 5.91 0.00 0.00 4.85
2248 5617 1.844687 AAATTCCCTCTTGAGCCAGC 58.155 50.000 0.00 0.00 0.00 4.85
2249 5618 0.033699 AATTCCCTCTTGAGCCAGCC 60.034 55.000 0.00 0.00 0.00 4.85
2349 5724 7.172019 ACTTTCATAACGGAAATACAACGTCTT 59.828 33.333 0.00 0.00 40.31 3.01
2364 5739 2.294074 CGTCTTGGGAACTGAAACCAA 58.706 47.619 0.00 0.00 41.66 3.67
2512 5889 4.451629 ACACCTACGGAAAGTATCACAG 57.548 45.455 0.00 0.00 34.34 3.66
2560 5937 1.211709 GCCACAACCGCCATAACAC 59.788 57.895 0.00 0.00 0.00 3.32
2565 5942 1.338655 ACAACCGCCATAACACCAAAC 59.661 47.619 0.00 0.00 0.00 2.93
2605 5983 3.117552 ACCCTCCTACCAAGGTCTAAG 57.882 52.381 0.00 0.00 44.09 2.18
2725 6112 1.734047 CGCCTTCTTCCTCAGTTCTCG 60.734 57.143 0.00 0.00 0.00 4.04
2755 6143 1.351017 TCTTTAGCTGGAACTGGTGGG 59.649 52.381 0.00 0.00 38.70 4.61
2893 6281 4.687483 GCTGTGAAAACAATCTCAAATGGG 59.313 41.667 0.00 0.00 0.00 4.00
2947 6335 1.076485 CCTGGCCAGCCAAATAGCT 60.076 57.895 28.39 0.00 46.63 3.32
2988 6376 4.506288 GCCAACAGTGTAAATTTTGTCCAC 59.494 41.667 0.00 0.00 0.00 4.02
2989 6377 5.047188 CCAACAGTGTAAATTTTGTCCACC 58.953 41.667 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.209019 AGCAATCTCAGCGAACATCCT 59.791 47.619 0.00 0.00 37.01 3.24
1 2 1.661341 AGCAATCTCAGCGAACATCC 58.339 50.000 0.00 0.00 37.01 3.51
2 3 4.864916 TTAAGCAATCTCAGCGAACATC 57.135 40.909 0.00 0.00 37.01 3.06
4 5 5.431420 TTTTTAAGCAATCTCAGCGAACA 57.569 34.783 0.00 0.00 37.01 3.18
28 29 2.002586 CACTAACCAGCGAATGTCAGG 58.997 52.381 0.00 0.00 0.00 3.86
44 45 7.107542 ACATTATCGTTAAAAGGAAGCCACTA 58.892 34.615 0.00 0.00 0.00 2.74
262 263 1.104577 GCACTGAACCGGGGAAACAA 61.105 55.000 6.32 0.00 0.00 2.83
269 270 1.080569 GCAAATGCACTGAACCGGG 60.081 57.895 6.32 0.00 41.59 5.73
278 279 3.378112 TCAGCCATACTAAGCAAATGCAC 59.622 43.478 8.28 0.00 45.16 4.57
284 285 4.680708 GCACTACTCAGCCATACTAAGCAA 60.681 45.833 0.00 0.00 0.00 3.91
296 297 6.980978 TCTAATGAAGTATTGCACTACTCAGC 59.019 38.462 16.20 9.97 36.04 4.26
376 378 6.510317 GCTCATTCCTGTTTCGCTAGAATAAC 60.510 42.308 0.00 0.00 36.09 1.89
378 380 5.050490 GCTCATTCCTGTTTCGCTAGAATA 58.950 41.667 0.00 0.00 36.09 1.75
379 381 3.873952 GCTCATTCCTGTTTCGCTAGAAT 59.126 43.478 0.00 0.00 36.09 2.40
380 382 3.262420 GCTCATTCCTGTTTCGCTAGAA 58.738 45.455 0.00 0.00 33.98 2.10
381 383 2.418746 GGCTCATTCCTGTTTCGCTAGA 60.419 50.000 0.00 0.00 0.00 2.43
383 385 1.555075 AGGCTCATTCCTGTTTCGCTA 59.445 47.619 0.00 0.00 34.56 4.26
385 387 0.449388 CAGGCTCATTCCTGTTTCGC 59.551 55.000 1.80 0.00 46.59 4.70
392 394 0.610232 GTGTTGCCAGGCTCATTCCT 60.610 55.000 14.15 0.00 36.78 3.36
393 395 1.885871 GTGTTGCCAGGCTCATTCC 59.114 57.895 14.15 0.00 0.00 3.01
394 396 1.503542 CGTGTTGCCAGGCTCATTC 59.496 57.895 14.15 0.93 0.00 2.67
395 397 2.629656 GCGTGTTGCCAGGCTCATT 61.630 57.895 14.15 0.00 46.36 2.57
396 398 3.058160 GCGTGTTGCCAGGCTCAT 61.058 61.111 14.15 0.00 46.36 2.90
402 404 1.840630 TTGATGACGCGTGTTGCCAG 61.841 55.000 20.70 0.00 42.08 4.85
403 405 1.889573 TTGATGACGCGTGTTGCCA 60.890 52.632 20.70 8.60 42.08 4.92
404 406 1.440353 GTTGATGACGCGTGTTGCC 60.440 57.895 20.70 1.01 42.08 4.52
405 407 1.788203 CGTTGATGACGCGTGTTGC 60.788 57.895 20.70 1.49 45.86 4.17
406 408 4.398113 CGTTGATGACGCGTGTTG 57.602 55.556 20.70 0.00 45.86 3.33
414 416 6.273825 ACATTACCAGTAGATCGTTGATGAC 58.726 40.000 0.00 0.00 0.00 3.06
415 417 6.321435 AGACATTACCAGTAGATCGTTGATGA 59.679 38.462 0.00 0.00 0.00 2.92
416 418 6.507900 AGACATTACCAGTAGATCGTTGATG 58.492 40.000 0.00 0.00 0.00 3.07
417 419 6.321435 TGAGACATTACCAGTAGATCGTTGAT 59.679 38.462 0.00 0.00 0.00 2.57
418 420 5.650703 TGAGACATTACCAGTAGATCGTTGA 59.349 40.000 0.00 0.00 0.00 3.18
420 422 6.525578 TTGAGACATTACCAGTAGATCGTT 57.474 37.500 0.00 0.00 0.00 3.85
421 423 6.513556 CGATTGAGACATTACCAGTAGATCGT 60.514 42.308 0.00 0.00 0.00 3.73
422 424 5.853810 CGATTGAGACATTACCAGTAGATCG 59.146 44.000 0.00 0.00 0.00 3.69
423 425 6.971602 TCGATTGAGACATTACCAGTAGATC 58.028 40.000 0.00 0.00 0.00 2.75
425 427 6.735968 GCATCGATTGAGACATTACCAGTAGA 60.736 42.308 0.00 0.00 0.00 2.59
428 430 4.122776 GCATCGATTGAGACATTACCAGT 58.877 43.478 0.00 0.00 0.00 4.00
429 431 4.375272 AGCATCGATTGAGACATTACCAG 58.625 43.478 0.00 0.00 0.00 4.00
434 436 6.659361 GCATATAGCATCGATTGAGACATT 57.341 37.500 0.00 0.00 44.79 2.71
446 448 8.468992 CATGCAAGTTCAAAGGCATATAGCATC 61.469 40.741 0.00 0.00 44.55 3.91
448 450 5.450826 CATGCAAGTTCAAAGGCATATAGCA 60.451 40.000 0.00 0.00 44.55 3.49
449 451 4.637483 TGCAAGTTCAAAGGCATATAGC 57.363 40.909 0.00 0.00 44.65 2.97
450 452 5.300034 TCCATGCAAGTTCAAAGGCATATAG 59.700 40.000 0.00 0.00 44.55 1.31
451 453 5.199723 TCCATGCAAGTTCAAAGGCATATA 58.800 37.500 0.00 0.00 44.55 0.86
452 454 4.025360 TCCATGCAAGTTCAAAGGCATAT 58.975 39.130 0.00 0.00 44.55 1.78
453 455 3.429492 TCCATGCAAGTTCAAAGGCATA 58.571 40.909 0.00 0.00 44.55 3.14
456 458 1.888512 TCTCCATGCAAGTTCAAAGGC 59.111 47.619 0.00 0.00 0.00 4.35
457 459 4.219070 TCAATCTCCATGCAAGTTCAAAGG 59.781 41.667 0.00 0.00 0.00 3.11
458 460 5.381174 TCAATCTCCATGCAAGTTCAAAG 57.619 39.130 0.00 0.00 0.00 2.77
459 461 5.716094 CATCAATCTCCATGCAAGTTCAAA 58.284 37.500 0.00 0.00 0.00 2.69
460 462 4.381185 GCATCAATCTCCATGCAAGTTCAA 60.381 41.667 0.00 0.00 44.18 2.69
461 463 3.129813 GCATCAATCTCCATGCAAGTTCA 59.870 43.478 0.00 0.00 44.18 3.18
463 465 3.795623 GCATCAATCTCCATGCAAGTT 57.204 42.857 0.00 0.00 44.18 2.66
469 471 7.843490 AGAAAATTTTGCATCAATCTCCATG 57.157 32.000 8.47 0.00 0.00 3.66
470 472 8.319146 AGAAGAAAATTTTGCATCAATCTCCAT 58.681 29.630 8.47 0.00 0.00 3.41
471 473 7.673180 AGAAGAAAATTTTGCATCAATCTCCA 58.327 30.769 8.47 0.00 0.00 3.86
472 474 8.543862 AAGAAGAAAATTTTGCATCAATCTCC 57.456 30.769 8.47 0.00 0.00 3.71
515 1136 9.841880 GACTGAGACAAGCGACATATTATATAA 57.158 33.333 0.00 0.00 0.00 0.98
522 1143 2.683362 TCGACTGAGACAAGCGACATAT 59.317 45.455 0.00 0.00 0.00 1.78
524 1145 0.881796 TCGACTGAGACAAGCGACAT 59.118 50.000 0.00 0.00 0.00 3.06
528 1149 2.159824 TCTTAGTCGACTGAGACAAGCG 59.840 50.000 30.05 9.58 43.24 4.68
537 1158 2.455295 GGCTACGTCTTAGTCGACTG 57.545 55.000 28.12 12.46 0.00 3.51
564 1185 9.309516 CATAATTACTCTTTTTAGGCACGTCTA 57.690 33.333 0.00 0.00 0.00 2.59
570 3140 8.956426 CACTTCCATAATTACTCTTTTTAGGCA 58.044 33.333 0.00 0.00 0.00 4.75
571 3141 8.406297 CCACTTCCATAATTACTCTTTTTAGGC 58.594 37.037 0.00 0.00 0.00 3.93
574 3144 8.736244 GCACCACTTCCATAATTACTCTTTTTA 58.264 33.333 0.00 0.00 0.00 1.52
580 3152 4.335594 GTGGCACCACTTCCATAATTACTC 59.664 45.833 12.66 0.00 43.12 2.59
598 3463 3.932580 GATGTCTCGCACGGTGGCA 62.933 63.158 10.60 0.00 0.00 4.92
763 3642 1.203364 AGATGAGGACAGGTGAAGGGT 60.203 52.381 0.00 0.00 0.00 4.34
766 3645 2.098934 CGAGAGATGAGGACAGGTGAAG 59.901 54.545 0.00 0.00 0.00 3.02
767 3646 2.095461 CGAGAGATGAGGACAGGTGAA 58.905 52.381 0.00 0.00 0.00 3.18
768 3647 1.004862 ACGAGAGATGAGGACAGGTGA 59.995 52.381 0.00 0.00 0.00 4.02
770 3649 1.821753 CAACGAGAGATGAGGACAGGT 59.178 52.381 0.00 0.00 35.71 4.00
773 3652 0.532573 GGCAACGAGAGATGAGGACA 59.467 55.000 0.00 0.00 35.71 4.02
774 3653 0.532573 TGGCAACGAGAGATGAGGAC 59.467 55.000 0.00 0.00 42.51 3.85
798 3681 3.194116 AGCACAGCATTACAAATTCAGGG 59.806 43.478 0.00 0.00 0.00 4.45
852 3735 6.021596 GCTTATGGCATTATTAATTCGTCCG 58.978 40.000 4.78 0.00 41.35 4.79
1551 4488 1.039233 CCCCCGTCACCGTGTAGTAT 61.039 60.000 0.00 0.00 0.00 2.12
2016 4953 4.616143 CGAACGGATAGGTCATCGATCAAT 60.616 45.833 0.00 0.00 35.97 2.57
2029 4966 0.387367 CGATGGAGGCGAACGGATAG 60.387 60.000 0.00 0.00 0.00 2.08
2060 4997 1.269673 ACATCAAAAACATGCAGCGCA 60.270 42.857 11.47 5.73 44.86 6.09
2073 5010 7.450074 AGGAACTAGACAACACATACATCAAA 58.550 34.615 0.00 0.00 36.02 2.69
2163 5100 7.980662 CACTTCTGATCTGATCTATGACAAGTT 59.019 37.037 17.82 1.89 0.00 2.66
2164 5101 7.123997 ACACTTCTGATCTGATCTATGACAAGT 59.876 37.037 17.82 12.46 0.00 3.16
2165 5102 7.490840 ACACTTCTGATCTGATCTATGACAAG 58.509 38.462 17.82 11.96 0.00 3.16
2166 5103 7.415592 ACACTTCTGATCTGATCTATGACAA 57.584 36.000 17.82 0.00 0.00 3.18
2168 5105 8.629158 AGTAACACTTCTGATCTGATCTATGAC 58.371 37.037 17.82 5.02 0.00 3.06
2169 5106 8.759481 AGTAACACTTCTGATCTGATCTATGA 57.241 34.615 17.82 10.72 0.00 2.15
2170 5107 9.814899 AAAGTAACACTTCTGATCTGATCTATG 57.185 33.333 17.82 10.95 37.47 2.23
2173 5110 8.474025 CCTAAAGTAACACTTCTGATCTGATCT 58.526 37.037 17.82 0.00 37.47 2.75
2219 5156 9.317936 GGCTCAAGAGGGAATTTAAATATTTTG 57.682 33.333 5.91 1.46 0.00 2.44
2220 5157 9.045745 TGGCTCAAGAGGGAATTTAAATATTTT 57.954 29.630 5.91 0.00 0.00 1.82
2246 5615 0.834687 TACTTCTCCCACAACCGGCT 60.835 55.000 0.00 0.00 0.00 5.52
2247 5616 0.252197 ATACTTCTCCCACAACCGGC 59.748 55.000 0.00 0.00 0.00 6.13
2248 5617 1.406887 CCATACTTCTCCCACAACCGG 60.407 57.143 0.00 0.00 0.00 5.28
2249 5618 2.012051 GCCATACTTCTCCCACAACCG 61.012 57.143 0.00 0.00 0.00 4.44
2316 5690 9.621629 TGTATTTCCGTTATGAAAGTAATGGAT 57.378 29.630 8.07 0.00 44.85 3.41
2349 5724 2.383855 CCTTGTTGGTTTCAGTTCCCA 58.616 47.619 0.00 0.00 0.00 4.37
2364 5739 5.568620 TTCCTCTTTCTTTCTAGCCTTGT 57.431 39.130 0.00 0.00 0.00 3.16
2560 5937 5.534654 TCTGGTAGTTCTTTTGGATGTTTGG 59.465 40.000 0.00 0.00 0.00 3.28
2565 5942 4.459337 GGGTTCTGGTAGTTCTTTTGGATG 59.541 45.833 0.00 0.00 0.00 3.51
2725 6112 1.521681 AGCTAAAGATGGGCGCGAC 60.522 57.895 12.10 6.99 0.00 5.19
2893 6281 8.360390 ACTTTTGAACTCAAATGGATTAACTCC 58.640 33.333 17.46 0.00 44.30 3.85
2947 6335 2.092484 TGGCTTGGCTGCTATATGTTGA 60.092 45.455 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.