Multiple sequence alignment - TraesCS2D01G335000

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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 TraesCS2D01G335000 chr2D 100.000 3087 0 0 1 3087 427959391 427956305 0.000000e+00 5701.0
1 TraesCS2D01G335000 chr2A 94.223 2354 78 17 664 2984 559620516 559622844 0.000000e+00 3541.0
2 TraesCS2D01G335000 chr2A 92.347 392 14 6 1 377 559618123 559618513 7.530000e-151 544.0
3 TraesCS2D01G335000 chr2A 95.055 182 8 1 493 673 559618513 559618694 5.040000e-73 285.0
4 TraesCS2D01G335000 chr2A 96.330 109 4 0 2979 3087 559622865 559622973 2.450000e-41 180.0
5 TraesCS2D01G335000 chr2B 97.001 1367 31 3 829 2185 512342285 512343651 0.000000e+00 2289.0
6 TraesCS2D01G335000 chr2B 92.718 1538 54 15 751 2280 504829239 504827752 0.000000e+00 2167.0
7 TraesCS2D01G335000 chr2B 86.293 839 71 14 2280 3087 512343892 512344717 0.000000e+00 872.0
8 TraesCS2D01G335000 chr2B 83.437 646 77 13 2346 2984 504787336 504786714 9.600000e-160 573.0
9 TraesCS2D01G335000 chr2B 96.026 151 5 1 2130 2280 512343710 512343859 8.550000e-61 244.0
10 TraesCS2D01G335000 chr2B 80.186 323 29 16 510 826 512341956 512342249 3.120000e-50 209.0
11 TraesCS2D01G335000 chr2B 98.214 56 1 0 2130 2185 512343653 512343708 7.040000e-17 99.0
12 TraesCS2D01G335000 chr7D 88.655 476 39 8 1311 1776 564577658 564578128 1.610000e-157 566.0
13 TraesCS2D01G335000 chr7D 89.310 290 23 5 1774 2056 563684408 563684696 1.050000e-94 357.0
14 TraesCS2D01G335000 chr7D 91.453 117 9 1 375 491 4241819 4241704 3.190000e-35 159.0
15 TraesCS2D01G335000 chr7D 89.344 122 13 0 376 497 64737352 64737231 1.480000e-33 154.0
16 TraesCS2D01G335000 chr7D 82.222 180 27 4 493 669 634884203 634884026 1.920000e-32 150.0
17 TraesCS2D01G335000 chr7D 73.803 355 80 5 2582 2923 191870537 191870183 8.990000e-26 128.0
18 TraesCS2D01G335000 chr6A 80.096 628 89 22 1148 1746 358573553 358572933 4.730000e-118 435.0
19 TraesCS2D01G335000 chr6D 83.721 344 41 7 1416 1746 263044214 263043873 8.310000e-81 311.0
20 TraesCS2D01G335000 chr7B 76.726 623 58 35 1253 1859 614282862 614282311 1.820000e-67 267.0
21 TraesCS2D01G335000 chr7B 92.949 156 11 0 1901 2056 614282312 614282157 8.610000e-56 228.0
22 TraesCS2D01G335000 chr3D 93.939 132 7 1 371 501 549125098 549125229 6.750000e-47 198.0
23 TraesCS2D01G335000 chr3D 87.417 151 17 2 493 642 298594955 298595104 4.090000e-39 172.0
24 TraesCS2D01G335000 chr7A 93.388 121 8 0 375 495 1416229 1416109 2.450000e-41 180.0
25 TraesCS2D01G335000 chr1B 87.919 149 16 2 493 640 300713431 300713284 1.140000e-39 174.0
26 TraesCS2D01G335000 chr1B 85.535 159 23 0 493 651 60389697 60389855 1.900000e-37 167.0
27 TraesCS2D01G335000 chr4D 93.103 116 7 1 376 491 400680682 400680568 5.290000e-38 169.0
28 TraesCS2D01G335000 chr4D 71.496 421 97 14 2582 2982 58258335 58257918 1.180000e-14 91.6
29 TraesCS2D01G335000 chr3B 89.922 129 13 0 493 621 394097846 394097974 1.900000e-37 167.0
30 TraesCS2D01G335000 chr3B 89.256 121 11 2 371 491 451117791 451117909 1.920000e-32 150.0
31 TraesCS2D01G335000 chr3B 87.407 135 12 5 376 509 809593097 809593227 1.920000e-32 150.0
32 TraesCS2D01G335000 chr5D 83.708 178 22 5 493 666 61793663 61793837 8.860000e-36 161.0
33 TraesCS2D01G335000 chr5B 85.093 161 20 4 493 651 438482528 438482370 8.860000e-36 161.0
34 TraesCS2D01G335000 chr5B 89.683 126 12 1 367 491 100712828 100712703 3.190000e-35 159.0
35 TraesCS2D01G335000 chr5B 81.818 99 8 2 2582 2670 91885850 91885948 1.190000e-09 75.0
36 TraesCS2D01G335000 chr1D 89.744 117 11 1 375 491 8100737 8100852 6.900000e-32 148.0
37 TraesCS2D01G335000 chr1D 93.846 65 3 1 2519 2582 61968898 61968834 2.530000e-16 97.1
38 TraesCS2D01G335000 chr4A 81.553 103 16 2 2478 2579 522261925 522261825 7.090000e-12 82.4


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 TraesCS2D01G335000 chr2D 427956305 427959391 3086 True 5701.0 5701 100.00000 1 3087 1 chr2D.!!$R1 3086
1 TraesCS2D01G335000 chr2A 559618123 559622973 4850 False 1137.5 3541 94.48875 1 3087 4 chr2A.!!$F1 3086
2 TraesCS2D01G335000 chr2B 504827752 504829239 1487 True 2167.0 2167 92.71800 751 2280 1 chr2B.!!$R2 1529
3 TraesCS2D01G335000 chr2B 512341956 512344717 2761 False 742.6 2289 91.54400 510 3087 5 chr2B.!!$F1 2577
4 TraesCS2D01G335000 chr2B 504786714 504787336 622 True 573.0 573 83.43700 2346 2984 1 chr2B.!!$R1 638
5 TraesCS2D01G335000 chr6A 358572933 358573553 620 True 435.0 435 80.09600 1148 1746 1 chr6A.!!$R1 598
6 TraesCS2D01G335000 chr7B 614282157 614282862 705 True 247.5 267 84.83750 1253 2056 2 chr7B.!!$R1 803

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
389 405 0.109412 AAAACTACTCGCTCCGTCCG 60.109 55.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2185 4244 1.212935 ACAGCCTCACTTGGTTCAACT 59.787 47.619 0.0 0.0 0.0 3.16 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
192 195 8.951243 AGCATACAGAAAAAGAAAAGATAGACC 58.049 33.333 0.00 0.00 0.00 3.85
207 210 0.685458 AGACCGGGCAATACCTACGT 60.685 55.000 11.69 0.00 39.10 3.57
264 267 8.414003 TGTATCTCGCTATAAGCTTTATATGGG 58.586 37.037 3.20 0.07 39.60 4.00
276 287 0.190069 TATATGGGGCTCGGTGGTCT 59.810 55.000 0.00 0.00 0.00 3.85
302 313 1.625818 CTTACACTCCCTCCAGTTGCT 59.374 52.381 0.00 0.00 0.00 3.91
381 397 8.684973 TCAAGTTTATAGAGAAAACTACTCGC 57.315 34.615 1.96 0.00 44.35 5.03
382 398 8.521176 TCAAGTTTATAGAGAAAACTACTCGCT 58.479 33.333 1.96 0.00 44.35 4.93
383 399 8.800031 CAAGTTTATAGAGAAAACTACTCGCTC 58.200 37.037 1.96 0.00 44.35 5.03
384 400 7.482474 AGTTTATAGAGAAAACTACTCGCTCC 58.518 38.462 0.00 0.00 43.54 4.70
385 401 2.923605 AGAGAAAACTACTCGCTCCG 57.076 50.000 0.00 0.00 39.12 4.63
386 402 2.161030 AGAGAAAACTACTCGCTCCGT 58.839 47.619 0.00 0.00 39.12 4.69
387 403 2.162008 AGAGAAAACTACTCGCTCCGTC 59.838 50.000 0.00 0.00 39.12 4.79
388 404 1.201880 AGAAAACTACTCGCTCCGTCC 59.798 52.381 0.00 0.00 0.00 4.79
389 405 0.109412 AAAACTACTCGCTCCGTCCG 60.109 55.000 0.00 0.00 0.00 4.79
390 406 1.930908 AAACTACTCGCTCCGTCCGG 61.931 60.000 0.00 0.00 0.00 5.14
391 407 2.513204 CTACTCGCTCCGTCCGGA 60.513 66.667 0.00 0.00 42.90 5.14
392 408 2.046023 TACTCGCTCCGTCCGGAA 60.046 61.111 5.23 0.00 44.66 4.30
393 409 1.651240 CTACTCGCTCCGTCCGGAAA 61.651 60.000 5.23 0.00 44.66 3.13
394 410 1.033746 TACTCGCTCCGTCCGGAAAT 61.034 55.000 5.23 0.00 44.66 2.17
395 411 1.033746 ACTCGCTCCGTCCGGAAATA 61.034 55.000 5.23 0.00 44.66 1.40
396 412 0.594284 CTCGCTCCGTCCGGAAATAC 60.594 60.000 5.23 0.00 44.66 1.89
397 413 1.033746 TCGCTCCGTCCGGAAATACT 61.034 55.000 5.23 0.00 44.66 2.12
398 414 0.179119 CGCTCCGTCCGGAAATACTT 60.179 55.000 5.23 0.00 44.66 2.24
399 415 1.287425 GCTCCGTCCGGAAATACTTG 58.713 55.000 5.23 0.00 44.66 3.16
400 416 1.405121 GCTCCGTCCGGAAATACTTGT 60.405 52.381 5.23 0.00 44.66 3.16
401 417 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
402 418 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
403 419 2.094390 TCCGTCCGGAAATACTTGTCAG 60.094 50.000 5.23 0.00 42.05 3.51
404 420 1.659098 CGTCCGGAAATACTTGTCAGC 59.341 52.381 5.23 0.00 0.00 4.26
405 421 2.007608 GTCCGGAAATACTTGTCAGCC 58.992 52.381 5.23 0.00 0.00 4.85
406 422 1.065709 TCCGGAAATACTTGTCAGCCC 60.066 52.381 0.00 0.00 0.00 5.19
407 423 1.339631 CCGGAAATACTTGTCAGCCCA 60.340 52.381 0.00 0.00 0.00 5.36
408 424 2.432444 CGGAAATACTTGTCAGCCCAA 58.568 47.619 0.00 0.00 0.00 4.12
409 425 3.016736 CGGAAATACTTGTCAGCCCAAT 58.983 45.455 0.00 0.00 0.00 3.16
410 426 3.181497 CGGAAATACTTGTCAGCCCAATG 60.181 47.826 0.00 0.00 0.00 2.82
411 427 4.016444 GGAAATACTTGTCAGCCCAATGA 58.984 43.478 0.00 0.00 0.00 2.57
412 428 4.462483 GGAAATACTTGTCAGCCCAATGAA 59.538 41.667 0.00 0.00 0.00 2.57
413 429 5.127682 GGAAATACTTGTCAGCCCAATGAAT 59.872 40.000 0.00 0.00 0.00 2.57
414 430 5.587388 AATACTTGTCAGCCCAATGAATG 57.413 39.130 0.00 0.00 0.00 2.67
415 431 2.880443 ACTTGTCAGCCCAATGAATGT 58.120 42.857 0.00 0.00 0.00 2.71
416 432 4.032960 ACTTGTCAGCCCAATGAATGTA 57.967 40.909 0.00 0.00 0.00 2.29
417 433 4.603131 ACTTGTCAGCCCAATGAATGTAT 58.397 39.130 0.00 0.00 0.00 2.29
418 434 5.754782 ACTTGTCAGCCCAATGAATGTATA 58.245 37.500 0.00 0.00 0.00 1.47
419 435 6.367983 ACTTGTCAGCCCAATGAATGTATAT 58.632 36.000 0.00 0.00 0.00 0.86
420 436 7.517320 ACTTGTCAGCCCAATGAATGTATATA 58.483 34.615 0.00 0.00 0.00 0.86
421 437 7.663081 ACTTGTCAGCCCAATGAATGTATATAG 59.337 37.037 0.00 0.00 0.00 1.31
422 438 7.315066 TGTCAGCCCAATGAATGTATATAGA 57.685 36.000 0.00 0.00 0.00 1.98
423 439 7.161404 TGTCAGCCCAATGAATGTATATAGAC 58.839 38.462 0.00 0.00 0.00 2.59
424 440 6.311445 GTCAGCCCAATGAATGTATATAGACG 59.689 42.308 0.00 0.00 0.00 4.18
425 441 6.014584 TCAGCCCAATGAATGTATATAGACGT 60.015 38.462 0.00 0.00 0.00 4.34
426 442 7.177744 TCAGCCCAATGAATGTATATAGACGTA 59.822 37.037 0.00 0.00 0.00 3.57
427 443 7.981789 CAGCCCAATGAATGTATATAGACGTAT 59.018 37.037 0.00 0.00 0.00 3.06
428 444 8.540388 AGCCCAATGAATGTATATAGACGTATT 58.460 33.333 0.00 0.00 0.00 1.89
429 445 9.162764 GCCCAATGAATGTATATAGACGTATTT 57.837 33.333 0.00 0.00 0.00 1.40
458 474 9.778741 GTTCTTAGATACATCCATTGTTATCCA 57.221 33.333 0.00 0.00 39.87 3.41
465 481 9.793252 GATACATCCATTGTTATCCATTTATGC 57.207 33.333 0.00 0.00 39.87 3.14
466 482 6.680810 ACATCCATTGTTATCCATTTATGCG 58.319 36.000 0.00 0.00 33.74 4.73
467 483 6.489700 ACATCCATTGTTATCCATTTATGCGA 59.510 34.615 0.00 0.00 33.74 5.10
468 484 6.312399 TCCATTGTTATCCATTTATGCGAC 57.688 37.500 0.00 0.00 0.00 5.19
469 485 5.825151 TCCATTGTTATCCATTTATGCGACA 59.175 36.000 0.00 0.00 0.00 4.35
470 486 6.319911 TCCATTGTTATCCATTTATGCGACAA 59.680 34.615 0.00 0.00 0.00 3.18
471 487 6.638063 CCATTGTTATCCATTTATGCGACAAG 59.362 38.462 0.00 0.00 0.00 3.16
472 488 6.751514 TTGTTATCCATTTATGCGACAAGT 57.248 33.333 0.00 0.00 0.00 3.16
473 489 7.851387 TTGTTATCCATTTATGCGACAAGTA 57.149 32.000 0.00 0.00 0.00 2.24
474 490 8.445275 TTGTTATCCATTTATGCGACAAGTAT 57.555 30.769 0.00 0.00 0.00 2.12
475 491 8.445275 TGTTATCCATTTATGCGACAAGTATT 57.555 30.769 0.00 0.00 0.00 1.89
476 492 8.898761 TGTTATCCATTTATGCGACAAGTATTT 58.101 29.630 0.00 0.00 0.00 1.40
477 493 9.382244 GTTATCCATTTATGCGACAAGTATTTC 57.618 33.333 0.00 0.00 0.00 2.17
478 494 6.371809 TCCATTTATGCGACAAGTATTTCC 57.628 37.500 0.00 0.00 0.00 3.13
479 495 5.007234 TCCATTTATGCGACAAGTATTTCCG 59.993 40.000 0.00 0.00 0.00 4.30
480 496 4.868450 TTTATGCGACAAGTATTTCCGG 57.132 40.909 0.00 0.00 0.00 5.14
481 497 2.684001 ATGCGACAAGTATTTCCGGA 57.316 45.000 0.00 0.00 0.00 5.14
482 498 2.684001 TGCGACAAGTATTTCCGGAT 57.316 45.000 4.15 0.00 0.00 4.18
483 499 2.276201 TGCGACAAGTATTTCCGGATG 58.724 47.619 4.15 0.97 0.00 3.51
484 500 1.597663 GCGACAAGTATTTCCGGATGG 59.402 52.381 4.15 0.00 0.00 3.51
485 501 2.740580 GCGACAAGTATTTCCGGATGGA 60.741 50.000 4.15 0.00 44.61 3.41
553 569 6.856938 ACTACGTCTTACGATGAATCTAATGC 59.143 38.462 6.44 0.00 46.05 3.56
626 642 9.528018 GTCAAAATTTGTGAGGTTTGAATCTTA 57.472 29.630 5.56 0.00 40.58 2.10
673 690 9.793259 ATTAGATATGGTGGGTGTATGTTTTAG 57.207 33.333 0.00 0.00 0.00 1.85
674 691 6.062095 AGATATGGTGGGTGTATGTTTTAGC 58.938 40.000 0.00 0.00 0.00 3.09
675 692 2.428491 TGGTGGGTGTATGTTTTAGCG 58.572 47.619 0.00 0.00 0.00 4.26
676 693 2.224572 TGGTGGGTGTATGTTTTAGCGT 60.225 45.455 0.00 0.00 0.00 5.07
677 694 2.160813 GGTGGGTGTATGTTTTAGCGTG 59.839 50.000 0.00 0.00 0.00 5.34
678 695 2.160813 GTGGGTGTATGTTTTAGCGTGG 59.839 50.000 0.00 0.00 0.00 4.94
679 696 1.131693 GGGTGTATGTTTTAGCGTGGC 59.868 52.381 0.00 0.00 0.00 5.01
705 2554 7.278868 CGTGGATAAGCTTTGAAGAAGACTAAT 59.721 37.037 3.20 0.00 0.00 1.73
996 2898 1.821216 GCCCAACTAGTAAAGCAGCA 58.179 50.000 0.00 0.00 0.00 4.41
1927 3867 0.940126 GCATCTCGATCGCCATGTTT 59.060 50.000 20.56 0.00 0.00 2.83
2014 3954 2.073816 CGGTTCAAGGCGTTCAACTAT 58.926 47.619 5.88 0.00 0.00 2.12
2114 4055 1.597027 CGTAGCTATTTGGCGGGGG 60.597 63.158 0.00 0.00 37.29 5.40
2166 4225 4.815269 TGAGCTTTTCAGAGAGAGCTAAC 58.185 43.478 4.72 0.00 44.88 2.34
2185 4244 5.810587 GCTAACCTTCAGTCGATTATTGACA 59.189 40.000 14.32 0.00 38.83 3.58
2271 4354 5.679734 TGCAAAAGTGAAAACTGCAAAAA 57.320 30.435 0.00 0.00 39.91 1.94
2455 4578 1.271379 ACCTTTTCAGTGGGTCATCCG 60.271 52.381 0.00 0.00 38.76 4.18
2457 4580 2.504367 CTTTTCAGTGGGTCATCCGTT 58.496 47.619 0.00 0.00 38.76 4.44
2471 4594 1.821216 TCCGTTCTCAAATTGCTCCC 58.179 50.000 0.00 0.00 0.00 4.30
2499 4622 9.908152 ATTAAGCACGCTTAACTTTAAGATTTT 57.092 25.926 22.78 3.80 46.94 1.82
2500 4623 9.738832 TTAAGCACGCTTAACTTTAAGATTTTT 57.261 25.926 17.97 3.32 41.78 1.94
2820 4945 2.648454 GCCAAATCACGGCGGTTT 59.352 55.556 13.24 6.60 40.35 3.27
2825 4950 0.606944 AAATCACGGCGGTTTAGGCA 60.607 50.000 13.24 0.00 36.37 4.75
2926 5051 3.194542 CGCCAATTTTTAGGTGGATGGAA 59.805 43.478 0.00 0.00 34.05 3.53
2956 5087 7.093945 ACACGTCTTGCCCAATCTTTAAATATT 60.094 33.333 0.00 0.00 0.00 1.28
3016 5173 2.629617 CTGCTAAATGGGCCTTTATGGG 59.370 50.000 4.53 0.00 36.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 93 7.826744 TGGTTGCTTTTCTATGGTTTTTCTTTT 59.173 29.630 0.00 0.00 0.00 2.27
92 94 7.334858 TGGTTGCTTTTCTATGGTTTTTCTTT 58.665 30.769 0.00 0.00 0.00 2.52
94 96 6.478512 TGGTTGCTTTTCTATGGTTTTTCT 57.521 33.333 0.00 0.00 0.00 2.52
95 97 7.546778 TTTGGTTGCTTTTCTATGGTTTTTC 57.453 32.000 0.00 0.00 0.00 2.29
145 147 4.430765 GGCTCGCTCGGGTTTCGA 62.431 66.667 0.00 0.00 46.77 3.71
169 171 7.553044 CCCGGTCTATCTTTTCTTTTTCTGTAT 59.447 37.037 0.00 0.00 0.00 2.29
192 195 0.249322 CCTCACGTAGGTATTGCCCG 60.249 60.000 0.00 0.00 40.94 6.13
207 210 3.460340 TGGGTGAAGTTTTTAGTCCCTCA 59.540 43.478 0.00 0.00 35.00 3.86
264 267 4.280174 TGTAAGATTATAGACCACCGAGCC 59.720 45.833 0.00 0.00 0.00 4.70
276 287 6.183360 GCAACTGGAGGGAGTGTAAGATTATA 60.183 42.308 0.00 0.00 0.00 0.98
332 343 8.030106 TGATCAACGTTTTCAAAAGGTTTACTT 58.970 29.630 16.45 4.23 42.52 2.24
333 344 7.540299 TGATCAACGTTTTCAAAAGGTTTACT 58.460 30.769 16.45 6.16 0.00 2.24
335 346 8.030106 ACTTGATCAACGTTTTCAAAAGGTTTA 58.970 29.630 16.45 10.67 0.00 2.01
368 384 1.201880 GGACGGAGCGAGTAGTTTTCT 59.798 52.381 0.00 0.00 0.00 2.52
377 393 0.594284 GTATTTCCGGACGGAGCGAG 60.594 60.000 13.64 0.00 46.06 5.03
378 394 1.033746 AGTATTTCCGGACGGAGCGA 61.034 55.000 13.64 4.95 46.06 4.93
379 395 0.179119 AAGTATTTCCGGACGGAGCG 60.179 55.000 13.64 0.00 46.06 5.03
380 396 1.287425 CAAGTATTTCCGGACGGAGC 58.713 55.000 13.64 6.15 46.06 4.70
381 397 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
382 398 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
383 399 2.268298 CTGACAAGTATTTCCGGACGG 58.732 52.381 1.83 3.96 0.00 4.79
384 400 1.659098 GCTGACAAGTATTTCCGGACG 59.341 52.381 1.83 0.00 0.00 4.79
385 401 2.007608 GGCTGACAAGTATTTCCGGAC 58.992 52.381 1.83 0.00 0.00 4.79
386 402 1.065709 GGGCTGACAAGTATTTCCGGA 60.066 52.381 0.00 0.00 0.00 5.14
387 403 1.339631 TGGGCTGACAAGTATTTCCGG 60.340 52.381 0.00 0.00 0.00 5.14
388 404 2.107950 TGGGCTGACAAGTATTTCCG 57.892 50.000 0.00 0.00 0.00 4.30
389 405 4.016444 TCATTGGGCTGACAAGTATTTCC 58.984 43.478 0.00 0.00 33.23 3.13
390 406 5.643379 TTCATTGGGCTGACAAGTATTTC 57.357 39.130 0.00 0.00 33.23 2.17
391 407 5.481473 ACATTCATTGGGCTGACAAGTATTT 59.519 36.000 0.00 0.00 33.23 1.40
392 408 5.018809 ACATTCATTGGGCTGACAAGTATT 58.981 37.500 0.00 0.00 33.23 1.89
393 409 4.603131 ACATTCATTGGGCTGACAAGTAT 58.397 39.130 0.00 0.00 33.23 2.12
394 410 4.032960 ACATTCATTGGGCTGACAAGTA 57.967 40.909 0.00 0.00 33.23 2.24
395 411 2.880443 ACATTCATTGGGCTGACAAGT 58.120 42.857 0.00 0.00 33.23 3.16
396 412 6.889301 ATATACATTCATTGGGCTGACAAG 57.111 37.500 0.00 0.00 33.23 3.16
397 413 7.661437 GTCTATATACATTCATTGGGCTGACAA 59.339 37.037 0.00 0.00 34.41 3.18
398 414 7.161404 GTCTATATACATTCATTGGGCTGACA 58.839 38.462 0.00 0.00 0.00 3.58
399 415 6.311445 CGTCTATATACATTCATTGGGCTGAC 59.689 42.308 0.00 0.00 0.00 3.51
400 416 6.014584 ACGTCTATATACATTCATTGGGCTGA 60.015 38.462 0.00 0.00 0.00 4.26
401 417 6.166279 ACGTCTATATACATTCATTGGGCTG 58.834 40.000 0.00 0.00 0.00 4.85
402 418 6.360370 ACGTCTATATACATTCATTGGGCT 57.640 37.500 0.00 0.00 0.00 5.19
403 419 8.718102 AATACGTCTATATACATTCATTGGGC 57.282 34.615 0.00 0.00 0.00 5.36
432 448 9.778741 TGGATAACAATGGATGTATCTAAGAAC 57.221 33.333 0.00 0.00 42.99 3.01
439 455 9.793252 GCATAAATGGATAACAATGGATGTATC 57.207 33.333 0.00 0.00 42.99 2.24
440 456 8.461222 CGCATAAATGGATAACAATGGATGTAT 58.539 33.333 0.00 0.00 42.99 2.29
441 457 7.663493 TCGCATAAATGGATAACAATGGATGTA 59.337 33.333 0.00 0.00 42.99 2.29
442 458 6.489700 TCGCATAAATGGATAACAATGGATGT 59.510 34.615 0.00 0.00 46.82 3.06
443 459 6.803320 GTCGCATAAATGGATAACAATGGATG 59.197 38.462 0.00 0.00 0.00 3.51
444 460 6.489700 TGTCGCATAAATGGATAACAATGGAT 59.510 34.615 0.00 0.00 0.00 3.41
445 461 5.825151 TGTCGCATAAATGGATAACAATGGA 59.175 36.000 0.00 0.00 0.00 3.41
446 462 6.070897 TGTCGCATAAATGGATAACAATGG 57.929 37.500 0.00 0.00 0.00 3.16
447 463 7.195646 ACTTGTCGCATAAATGGATAACAATG 58.804 34.615 0.00 0.00 0.00 2.82
448 464 7.333528 ACTTGTCGCATAAATGGATAACAAT 57.666 32.000 0.00 0.00 0.00 2.71
449 465 6.751514 ACTTGTCGCATAAATGGATAACAA 57.248 33.333 0.00 0.00 0.00 2.83
450 466 8.445275 AATACTTGTCGCATAAATGGATAACA 57.555 30.769 0.00 0.00 0.00 2.41
451 467 9.382244 GAAATACTTGTCGCATAAATGGATAAC 57.618 33.333 0.00 0.00 0.00 1.89
452 468 8.564574 GGAAATACTTGTCGCATAAATGGATAA 58.435 33.333 0.00 0.00 0.00 1.75
453 469 7.095397 CGGAAATACTTGTCGCATAAATGGATA 60.095 37.037 0.00 0.00 0.00 2.59
454 470 6.293407 CGGAAATACTTGTCGCATAAATGGAT 60.293 38.462 0.00 0.00 0.00 3.41
455 471 5.007234 CGGAAATACTTGTCGCATAAATGGA 59.993 40.000 0.00 0.00 0.00 3.41
456 472 5.204833 CGGAAATACTTGTCGCATAAATGG 58.795 41.667 0.00 0.00 0.00 3.16
457 473 5.007234 TCCGGAAATACTTGTCGCATAAATG 59.993 40.000 0.00 0.00 0.00 2.32
458 474 5.120399 TCCGGAAATACTTGTCGCATAAAT 58.880 37.500 0.00 0.00 0.00 1.40
459 475 4.505808 TCCGGAAATACTTGTCGCATAAA 58.494 39.130 0.00 0.00 0.00 1.40
460 476 4.126208 TCCGGAAATACTTGTCGCATAA 57.874 40.909 0.00 0.00 0.00 1.90
461 477 3.804786 TCCGGAAATACTTGTCGCATA 57.195 42.857 0.00 0.00 0.00 3.14
462 478 2.684001 TCCGGAAATACTTGTCGCAT 57.316 45.000 0.00 0.00 0.00 4.73
463 479 2.276201 CATCCGGAAATACTTGTCGCA 58.724 47.619 9.01 0.00 0.00 5.10
464 480 1.597663 CCATCCGGAAATACTTGTCGC 59.402 52.381 9.01 0.00 0.00 5.19
465 481 3.123804 CTCCATCCGGAAATACTTGTCG 58.876 50.000 9.01 0.00 42.21 4.35
466 482 3.467803 CCTCCATCCGGAAATACTTGTC 58.532 50.000 9.01 0.00 42.21 3.18
467 483 2.172717 CCCTCCATCCGGAAATACTTGT 59.827 50.000 9.01 0.00 42.21 3.16
468 484 2.438021 TCCCTCCATCCGGAAATACTTG 59.562 50.000 9.01 0.00 42.21 3.16
469 485 2.706190 CTCCCTCCATCCGGAAATACTT 59.294 50.000 9.01 0.00 42.21 2.24
470 486 2.330216 CTCCCTCCATCCGGAAATACT 58.670 52.381 9.01 0.00 42.21 2.12
471 487 1.348036 CCTCCCTCCATCCGGAAATAC 59.652 57.143 9.01 0.00 42.21 1.89
472 488 1.222039 TCCTCCCTCCATCCGGAAATA 59.778 52.381 9.01 0.00 42.21 1.40
473 489 0.030092 TCCTCCCTCCATCCGGAAAT 60.030 55.000 9.01 0.00 42.21 2.17
474 490 0.030092 ATCCTCCCTCCATCCGGAAA 60.030 55.000 9.01 0.00 42.21 3.13
475 491 0.030092 AATCCTCCCTCCATCCGGAA 60.030 55.000 9.01 0.00 42.21 4.30
476 492 0.030092 AAATCCTCCCTCCATCCGGA 60.030 55.000 6.61 6.61 39.79 5.14
477 493 1.729586 TAAATCCTCCCTCCATCCGG 58.270 55.000 0.00 0.00 0.00 5.14
478 494 7.509318 TGTATATATAAATCCTCCCTCCATCCG 59.491 40.741 0.00 0.00 0.00 4.18
479 495 8.798975 TGTATATATAAATCCTCCCTCCATCC 57.201 38.462 0.00 0.00 0.00 3.51
643 660 9.569122 AACATACACCCACCATATCTAATTTAC 57.431 33.333 0.00 0.00 0.00 2.01
658 675 2.428491 CCACGCTAAAACATACACCCA 58.572 47.619 0.00 0.00 0.00 4.51
673 690 1.644786 AAAGCTTATCCACGCCACGC 61.645 55.000 0.00 0.00 0.00 5.34
674 691 0.096976 CAAAGCTTATCCACGCCACG 59.903 55.000 0.00 0.00 0.00 4.94
675 692 1.448985 TCAAAGCTTATCCACGCCAC 58.551 50.000 0.00 0.00 0.00 5.01
676 693 2.083774 CTTCAAAGCTTATCCACGCCA 58.916 47.619 0.00 0.00 0.00 5.69
677 694 2.356135 TCTTCAAAGCTTATCCACGCC 58.644 47.619 0.00 0.00 0.00 5.68
678 695 3.684788 TCTTCTTCAAAGCTTATCCACGC 59.315 43.478 0.00 0.00 0.00 5.34
679 696 4.932200 AGTCTTCTTCAAAGCTTATCCACG 59.068 41.667 0.00 0.00 0.00 4.94
705 2554 7.147759 TGTCTCAATTTTGAAGAAACCATTGGA 60.148 33.333 10.37 0.00 36.64 3.53
996 2898 1.050988 CCGGGATCTCCACCATCTGT 61.051 60.000 0.00 0.00 37.91 3.41
1766 3699 3.532641 ACTCCCAAGAATTTCCAGCTT 57.467 42.857 0.00 0.00 0.00 3.74
2014 3954 1.751351 CGGAGCTTCCTGTAGTCATCA 59.249 52.381 0.00 0.00 33.30 3.07
2166 4225 5.869344 TCAACTGTCAATAATCGACTGAAGG 59.131 40.000 0.00 0.00 36.25 3.46
2185 4244 1.212935 ACAGCCTCACTTGGTTCAACT 59.787 47.619 0.00 0.00 0.00 3.16
2271 4354 1.444119 ATTGCCGTCGTGTTTGCACT 61.444 50.000 0.00 0.00 43.16 4.40
2367 4482 1.587946 CTTGCGTGCAACCTTCAAAAC 59.412 47.619 2.58 0.00 0.00 2.43
2455 4578 5.560966 TTAATCGGGAGCAATTTGAGAAC 57.439 39.130 0.00 0.00 0.00 3.01
2457 4580 3.627577 GCTTAATCGGGAGCAATTTGAGA 59.372 43.478 0.00 0.00 38.73 3.27
2471 4594 6.758149 TCTTAAAGTTAAGCGTGCTTAATCG 58.242 36.000 24.90 12.69 46.18 3.34
2546 4670 8.314751 CCCGACTTAATAGAAATGATAGACCAT 58.685 37.037 0.00 0.00 0.00 3.55
2777 4902 3.733960 CCACCGCTGAGACGTCGA 61.734 66.667 10.46 0.00 0.00 4.20
2820 4945 2.665000 GTGCCACTCTGCTGCCTA 59.335 61.111 0.00 0.00 0.00 3.93
2825 4950 0.395586 TTGTTTGGTGCCACTCTGCT 60.396 50.000 0.00 0.00 0.00 4.24
2926 5051 0.895100 ATTGGGCAAGACGTGTGCAT 60.895 50.000 19.38 5.11 44.07 3.96
2956 5087 1.888436 AATCCAACTCGCGAGCCTCA 61.888 55.000 34.83 17.61 0.00 3.86
3016 5173 4.423625 ACTACCATTATGCCAGGTTCTC 57.576 45.455 0.00 0.00 36.87 2.87


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

AutoCloner maintained by Alex Coulton.