Multiple sequence alignment - TraesCS6B01G243800

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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 TraesCS6B01G243800 chr6B 100.000 3503 0 0 1 3503 433707396 433710898 0.000000e+00 6469.0
1 TraesCS6B01G243800 chr6B 97.273 110 3 0 400 509 136094553 136094662 1.660000e-43 187.0
2 TraesCS6B01G243800 chr6B 92.373 118 9 0 399 516 686311595 686311478 6.010000e-38 169.0
3 TraesCS6B01G243800 chr6B 89.412 85 8 1 33 117 93453116 93453033 4.780000e-19 106.0
4 TraesCS6B01G243800 chr6B 100.000 43 0 0 3453 3495 546088092 546088050 2.900000e-11 80.5
5 TraesCS6B01G243800 chr6A 96.482 3013 86 19 504 3503 389244263 389247268 0.000000e+00 4959.0
6 TraesCS6B01G243800 chr6A 96.766 402 10 3 1 402 389243869 389244267 0.000000e+00 667.0
7 TraesCS6B01G243800 chr6A 86.526 475 63 1 2976 3449 155748675 155748201 4.010000e-144 521.0
8 TraesCS6B01G243800 chr6A 79.744 469 90 4 2976 3442 137136362 137136827 5.600000e-88 335.0
9 TraesCS6B01G243800 chr6A 91.129 124 9 2 401 522 64543175 64543052 2.160000e-37 167.0
10 TraesCS6B01G243800 chr6D 97.464 2248 29 7 512 2743 272646495 272648730 0.000000e+00 3810.0
11 TraesCS6B01G243800 chr6D 93.554 574 36 1 2931 3503 272649554 272650127 0.000000e+00 854.0
12 TraesCS6B01G243800 chr6D 96.269 402 11 2 1 402 272646097 272646494 0.000000e+00 656.0
13 TraesCS6B01G243800 chr6D 89.723 253 10 3 2743 2979 272649307 272649559 3.400000e-80 309.0
14 TraesCS6B01G243800 chr6D 89.506 162 13 3 2817 2976 431160670 431160829 5.930000e-48 202.0
15 TraesCS6B01G243800 chr2A 85.683 461 64 2 2976 3435 348048624 348049083 5.260000e-133 484.0
16 TraesCS6B01G243800 chr2A 90.062 161 14 2 2817 2975 578387557 578387717 1.270000e-49 207.0
17 TraesCS6B01G243800 chr2A 89.441 161 15 2 2817 2975 713931596 713931436 5.930000e-48 202.0
18 TraesCS6B01G243800 chr2A 89.441 161 14 3 2817 2975 342647401 342647560 2.130000e-47 200.0
19 TraesCS6B01G243800 chr2A 83.636 110 17 1 2976 3084 550171684 550171793 6.190000e-18 102.0
20 TraesCS6B01G243800 chr2D 82.590 471 80 2 2982 3451 57196487 57196018 7.000000e-112 414.0
21 TraesCS6B01G243800 chr2D 82.353 476 76 6 2982 3451 650975416 650974943 1.170000e-109 407.0
22 TraesCS6B01G243800 chr2D 80.294 477 80 6 2976 3451 241695204 241695667 7.200000e-92 348.0
23 TraesCS6B01G243800 chr2D 90.968 155 12 2 2823 2975 133271194 133271348 1.270000e-49 207.0
24 TraesCS6B01G243800 chr2D 92.373 118 9 0 401 518 43919052 43918935 6.010000e-38 169.0
25 TraesCS6B01G243800 chr2D 93.103 87 4 2 33 118 72781251 72781336 3.670000e-25 126.0
26 TraesCS6B01G243800 chr7D 81.624 468 81 5 2976 3442 274685678 274686141 1.970000e-102 383.0
27 TraesCS6B01G243800 chr7D 89.571 163 13 4 2817 2975 213758517 213758679 1.650000e-48 204.0
28 TraesCS6B01G243800 chr7D 91.954 87 6 1 31 117 167359519 167359604 1.710000e-23 121.0
29 TraesCS6B01G243800 chr1B 92.593 162 9 3 2817 2976 673969369 673969209 2.720000e-56 230.0
30 TraesCS6B01G243800 chr3A 94.690 113 6 0 400 512 614468533 614468421 3.590000e-40 176.0
31 TraesCS6B01G243800 chr4D 93.220 118 8 0 399 516 24299709 24299592 1.290000e-39 174.0
32 TraesCS6B01G243800 chr5B 92.437 119 9 0 393 511 622393560 622393442 1.670000e-38 171.0
33 TraesCS6B01G243800 chr5B 92.373 118 9 0 399 516 415033319 415033436 6.010000e-38 169.0
34 TraesCS6B01G243800 chr4B 92.437 119 9 0 399 517 161785223 161785105 1.670000e-38 171.0
35 TraesCS6B01G243800 chr7A 91.954 87 7 0 31 117 168872247 168872333 4.750000e-24 122.0
36 TraesCS6B01G243800 chr3B 91.954 87 4 2 33 118 654652707 654652791 6.140000e-23 119.0
37 TraesCS6B01G243800 chr3B 89.412 85 9 0 33 117 672866956 672866872 1.330000e-19 108.0
38 TraesCS6B01G243800 chr5A 90.805 87 8 0 31 117 622203850 622203936 2.210000e-22 117.0
39 TraesCS6B01G243800 chr5A 92.593 54 4 0 3450 3503 92207179 92207232 1.040000e-10 78.7


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 TraesCS6B01G243800 chr6B 433707396 433710898 3502 False 6469.00 6469 100.0000 1 3503 1 chr6B.!!$F2 3502
1 TraesCS6B01G243800 chr6A 389243869 389247268 3399 False 2813.00 4959 96.6240 1 3503 2 chr6A.!!$F2 3502
2 TraesCS6B01G243800 chr6D 272646097 272650127 4030 False 1407.25 3810 94.2525 1 3503 4 chr6D.!!$F2 3502

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
461 464 1.134280 AGACAGTGTGCAAAGCAGTCT 60.134 47.619 0.00 5.98 40.08 3.24 F
1164 1168 0.809241 CAGCGCAGATCAGGAGTTCC 60.809 60.000 11.47 0.00 0.00 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2001 2005 0.033504 ACAGATAGCCCGCATTACCG 59.966 55.0 0.00 0.00 0.0 4.02 R
2537 2541 0.174389 ACGCTATCAGCTGACCACTG 59.826 55.0 20.97 10.72 39.6 3.66 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
402 405 6.348950 CGACAGGATCCAGAGATAATGAGTAC 60.349 46.154 15.82 0.00 30.90 2.73
403 406 6.619464 ACAGGATCCAGAGATAATGAGTACT 58.381 40.000 15.82 0.00 30.90 2.73
404 407 6.719370 ACAGGATCCAGAGATAATGAGTACTC 59.281 42.308 16.32 16.32 30.90 2.59
405 408 6.152661 CAGGATCCAGAGATAATGAGTACTCC 59.847 46.154 20.11 4.25 30.90 3.85
406 409 5.420739 GGATCCAGAGATAATGAGTACTCCC 59.579 48.000 20.11 4.99 30.90 4.30
407 410 5.671463 TCCAGAGATAATGAGTACTCCCT 57.329 43.478 20.11 9.47 0.00 4.20
408 411 5.636123 TCCAGAGATAATGAGTACTCCCTC 58.364 45.833 20.11 16.13 0.00 4.30
409 412 5.374154 TCCAGAGATAATGAGTACTCCCTCT 59.626 44.000 20.11 17.76 32.50 3.69
410 413 5.476599 CCAGAGATAATGAGTACTCCCTCTG 59.523 48.000 27.44 27.44 43.39 3.35
411 414 6.068010 CAGAGATAATGAGTACTCCCTCTGT 58.932 44.000 26.82 17.88 40.61 3.41
412 415 6.549364 CAGAGATAATGAGTACTCCCTCTGTT 59.451 42.308 26.82 15.38 40.61 3.16
413 416 6.775629 AGAGATAATGAGTACTCCCTCTGTTC 59.224 42.308 20.11 9.62 32.50 3.18
414 417 6.436027 AGATAATGAGTACTCCCTCTGTTCA 58.564 40.000 20.11 0.00 32.50 3.18
415 418 4.810191 AATGAGTACTCCCTCTGTTCAC 57.190 45.455 20.11 0.00 32.50 3.18
416 419 3.527507 TGAGTACTCCCTCTGTTCACT 57.472 47.619 20.11 0.00 32.50 3.41
417 420 3.845860 TGAGTACTCCCTCTGTTCACTT 58.154 45.455 20.11 0.00 32.50 3.16
418 421 4.223953 TGAGTACTCCCTCTGTTCACTTT 58.776 43.478 20.11 0.00 32.50 2.66
419 422 4.654262 TGAGTACTCCCTCTGTTCACTTTT 59.346 41.667 20.11 0.00 32.50 2.27
420 423 5.836898 TGAGTACTCCCTCTGTTCACTTTTA 59.163 40.000 20.11 0.00 32.50 1.52
421 424 6.497259 TGAGTACTCCCTCTGTTCACTTTTAT 59.503 38.462 20.11 0.00 32.50 1.40
422 425 7.672660 TGAGTACTCCCTCTGTTCACTTTTATA 59.327 37.037 20.11 0.00 32.50 0.98
423 426 8.431910 AGTACTCCCTCTGTTCACTTTTATAA 57.568 34.615 0.00 0.00 0.00 0.98
424 427 8.532819 AGTACTCCCTCTGTTCACTTTTATAAG 58.467 37.037 0.00 0.00 37.40 1.73
425 428 7.317722 ACTCCCTCTGTTCACTTTTATAAGT 57.682 36.000 0.00 0.00 45.40 2.24
426 429 7.387643 ACTCCCTCTGTTCACTTTTATAAGTC 58.612 38.462 0.00 0.00 42.67 3.01
427 430 6.708285 TCCCTCTGTTCACTTTTATAAGTCC 58.292 40.000 0.00 0.00 42.67 3.85
428 431 6.500751 TCCCTCTGTTCACTTTTATAAGTCCT 59.499 38.462 0.00 0.00 42.67 3.85
429 432 7.017254 TCCCTCTGTTCACTTTTATAAGTCCTT 59.983 37.037 0.00 0.00 42.67 3.36
430 433 7.119846 CCCTCTGTTCACTTTTATAAGTCCTTG 59.880 40.741 0.00 0.00 42.67 3.61
431 434 7.878127 CCTCTGTTCACTTTTATAAGTCCTTGA 59.122 37.037 0.00 0.00 42.67 3.02
432 435 9.273016 CTCTGTTCACTTTTATAAGTCCTTGAA 57.727 33.333 0.00 0.00 42.67 2.69
433 436 9.273016 TCTGTTCACTTTTATAAGTCCTTGAAG 57.727 33.333 0.00 0.00 42.67 3.02
434 437 9.273016 CTGTTCACTTTTATAAGTCCTTGAAGA 57.727 33.333 0.00 0.00 42.67 2.87
435 438 9.052759 TGTTCACTTTTATAAGTCCTTGAAGAC 57.947 33.333 0.00 0.00 42.67 3.01
436 439 9.052759 GTTCACTTTTATAAGTCCTTGAAGACA 57.947 33.333 0.00 0.00 42.67 3.41
437 440 9.793259 TTCACTTTTATAAGTCCTTGAAGACAT 57.207 29.630 0.00 0.00 42.67 3.06
438 441 9.793259 TCACTTTTATAAGTCCTTGAAGACATT 57.207 29.630 0.00 0.00 42.67 2.71
446 449 7.736447 AAGTCCTTGAAGACATTTTAGACAG 57.264 36.000 0.00 0.00 39.34 3.51
447 450 6.831976 AGTCCTTGAAGACATTTTAGACAGT 58.168 36.000 0.00 0.00 39.34 3.55
448 451 6.708054 AGTCCTTGAAGACATTTTAGACAGTG 59.292 38.462 0.00 0.00 39.34 3.66
449 452 6.483640 GTCCTTGAAGACATTTTAGACAGTGT 59.516 38.462 0.00 0.00 36.73 3.55
450 453 6.483307 TCCTTGAAGACATTTTAGACAGTGTG 59.517 38.462 0.00 0.00 0.00 3.82
451 454 5.673337 TGAAGACATTTTAGACAGTGTGC 57.327 39.130 0.00 0.00 0.00 4.57
452 455 5.122519 TGAAGACATTTTAGACAGTGTGCA 58.877 37.500 0.00 0.00 0.00 4.57
453 456 5.588246 TGAAGACATTTTAGACAGTGTGCAA 59.412 36.000 0.00 0.00 0.00 4.08
454 457 6.094742 TGAAGACATTTTAGACAGTGTGCAAA 59.905 34.615 0.00 0.00 0.00 3.68
455 458 6.064846 AGACATTTTAGACAGTGTGCAAAG 57.935 37.500 0.00 0.00 0.00 2.77
456 459 4.610945 ACATTTTAGACAGTGTGCAAAGC 58.389 39.130 0.00 0.00 0.00 3.51
457 460 4.097741 ACATTTTAGACAGTGTGCAAAGCA 59.902 37.500 0.00 0.00 35.60 3.91
458 461 3.969117 TTTAGACAGTGTGCAAAGCAG 57.031 42.857 0.00 0.00 40.08 4.24
459 462 2.620251 TAGACAGTGTGCAAAGCAGT 57.380 45.000 0.00 0.00 40.08 4.40
460 463 1.303309 AGACAGTGTGCAAAGCAGTC 58.697 50.000 0.00 0.00 40.08 3.51
461 464 1.134280 AGACAGTGTGCAAAGCAGTCT 60.134 47.619 0.00 5.98 40.08 3.24
462 465 2.103094 AGACAGTGTGCAAAGCAGTCTA 59.897 45.455 0.00 0.00 38.14 2.59
463 466 3.070018 GACAGTGTGCAAAGCAGTCTAT 58.930 45.455 0.00 0.00 40.08 1.98
464 467 3.480470 ACAGTGTGCAAAGCAGTCTATT 58.520 40.909 0.00 0.00 40.08 1.73
465 468 3.885297 ACAGTGTGCAAAGCAGTCTATTT 59.115 39.130 0.00 0.00 40.08 1.40
466 469 4.339247 ACAGTGTGCAAAGCAGTCTATTTT 59.661 37.500 0.00 0.00 40.08 1.82
467 470 4.913924 CAGTGTGCAAAGCAGTCTATTTTC 59.086 41.667 0.00 0.00 40.08 2.29
468 471 4.580167 AGTGTGCAAAGCAGTCTATTTTCA 59.420 37.500 0.00 0.00 40.08 2.69
469 472 4.913924 GTGTGCAAAGCAGTCTATTTTCAG 59.086 41.667 0.00 0.00 40.08 3.02
470 473 4.580167 TGTGCAAAGCAGTCTATTTTCAGT 59.420 37.500 0.00 0.00 40.08 3.41
471 474 5.067674 TGTGCAAAGCAGTCTATTTTCAGTT 59.932 36.000 0.00 0.00 40.08 3.16
472 475 5.400485 GTGCAAAGCAGTCTATTTTCAGTTG 59.600 40.000 0.00 0.00 40.08 3.16
473 476 5.067674 TGCAAAGCAGTCTATTTTCAGTTGT 59.932 36.000 0.00 0.00 33.32 3.32
474 477 5.626955 GCAAAGCAGTCTATTTTCAGTTGTC 59.373 40.000 0.00 0.00 0.00 3.18
475 478 6.514048 GCAAAGCAGTCTATTTTCAGTTGTCT 60.514 38.462 0.00 0.00 0.00 3.41
476 479 6.551385 AAGCAGTCTATTTTCAGTTGTCTG 57.449 37.500 0.00 0.00 42.54 3.51
494 497 6.102006 TGTCTGAAACGACTTACAAAAGTG 57.898 37.500 0.00 0.00 46.09 3.16
495 498 5.870433 TGTCTGAAACGACTTACAAAAGTGA 59.130 36.000 0.00 0.00 46.09 3.41
496 499 6.369340 TGTCTGAAACGACTTACAAAAGTGAA 59.631 34.615 0.00 0.00 46.09 3.18
497 500 6.681599 GTCTGAAACGACTTACAAAAGTGAAC 59.318 38.462 0.00 0.00 46.09 3.18
498 501 5.552807 TGAAACGACTTACAAAAGTGAACG 58.447 37.500 0.00 0.00 46.09 3.95
499 502 4.525411 AACGACTTACAAAAGTGAACGG 57.475 40.909 0.00 0.00 46.09 4.44
500 503 3.784338 ACGACTTACAAAAGTGAACGGA 58.216 40.909 0.00 0.00 46.09 4.69
501 504 3.800506 ACGACTTACAAAAGTGAACGGAG 59.199 43.478 0.00 0.00 46.09 4.63
502 505 3.183775 CGACTTACAAAAGTGAACGGAGG 59.816 47.826 0.00 0.00 46.09 4.30
503 506 3.473625 ACTTACAAAAGTGAACGGAGGG 58.526 45.455 0.00 0.00 44.40 4.30
504 507 3.135167 ACTTACAAAAGTGAACGGAGGGA 59.865 43.478 0.00 0.00 44.40 4.20
505 508 2.256117 ACAAAAGTGAACGGAGGGAG 57.744 50.000 0.00 0.00 0.00 4.30
506 509 1.489230 ACAAAAGTGAACGGAGGGAGT 59.511 47.619 0.00 0.00 0.00 3.85
507 510 2.701951 ACAAAAGTGAACGGAGGGAGTA 59.298 45.455 0.00 0.00 0.00 2.59
512 515 4.635699 AGTGAACGGAGGGAGTATTTTT 57.364 40.909 0.00 0.00 0.00 1.94
539 542 2.378507 AAAGGCGTTTCGTTTTCTCG 57.621 45.000 0.00 0.00 29.27 4.04
815 819 1.342819 GAGACTCTGTGTTGAGCTGGT 59.657 52.381 0.00 0.00 37.58 4.00
950 954 8.721478 GCTGCTGTTAGCTATTATTATTTAGCA 58.279 33.333 0.00 0.00 42.97 3.49
986 990 1.359130 ACCCAGGCTGGCTAATTTCTT 59.641 47.619 28.51 0.00 35.79 2.52
1094 1098 9.817809 ATTATCGTTATCATCAGTTACACACTT 57.182 29.630 0.00 0.00 30.92 3.16
1164 1168 0.809241 CAGCGCAGATCAGGAGTTCC 60.809 60.000 11.47 0.00 0.00 3.62
1305 1309 4.985538 ACTGGAAATCTGCTTTTGGTCTA 58.014 39.130 0.00 0.00 0.00 2.59
2001 2005 5.296813 ACAATTCCTTGATTAACGTGCTC 57.703 39.130 0.00 0.00 36.20 4.26
2217 2221 3.243201 GGCCACTTCTCAGACTGTTTTTG 60.243 47.826 0.00 0.00 0.00 2.44
2610 2630 5.451039 CAATGCTTTAAAACATTTGTGCCC 58.549 37.500 12.96 0.00 34.32 5.36
2620 2640 4.893424 ACATTTGTGCCCATTATACGAC 57.107 40.909 0.00 0.00 0.00 4.34
2823 3435 2.445525 GTCATCTACTCCCTCTCCCTCT 59.554 54.545 0.00 0.00 0.00 3.69
2824 3436 3.653836 GTCATCTACTCCCTCTCCCTCTA 59.346 52.174 0.00 0.00 0.00 2.43
3106 3763 0.304705 CGCAACTCAGAGTGCGTTTT 59.695 50.000 26.32 2.55 39.27 2.43
3111 3768 0.040067 CTCAGAGTGCGTTTTTGCCC 60.040 55.000 0.00 0.00 0.00 5.36
3147 3804 9.712305 ATTACAGACAATATCTTAGTGGCATAC 57.288 33.333 0.00 0.00 33.38 2.39
3201 3858 2.404559 TGGTAAAGAGGGTCTGTGTGT 58.595 47.619 0.00 0.00 0.00 3.72
3259 3916 5.782845 AGTAGAGTGGTCTTTTCTGAAGGAT 59.217 40.000 0.00 0.00 33.84 3.24
3317 3974 9.248291 GGGTAAATTTAATCATGCAATGTGTAG 57.752 33.333 0.00 0.00 46.80 2.74
3393 4050 0.252881 ACCAGAGGATTGAGGCAGGA 60.253 55.000 0.00 0.00 0.00 3.86
3475 4132 6.307776 TCAAATGTGGGTATGGACAAAAGTA 58.692 36.000 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
188 189 9.363763 CTTGCATGATCATATTCGTACTCTTAT 57.636 33.333 8.15 0.00 0.00 1.73
189 190 8.360390 ACTTGCATGATCATATTCGTACTCTTA 58.640 33.333 8.15 0.00 0.00 2.10
195 196 8.141268 TGAACTACTTGCATGATCATATTCGTA 58.859 33.333 8.15 7.28 0.00 3.43
355 358 6.969473 GTCGTCCAAATTACTACTAGGTACAC 59.031 42.308 0.00 0.00 0.00 2.90
402 405 6.819146 GGACTTATAAAAGTGAACAGAGGGAG 59.181 42.308 0.00 0.00 46.09 4.30
403 406 6.500751 AGGACTTATAAAAGTGAACAGAGGGA 59.499 38.462 0.00 0.00 46.09 4.20
404 407 6.712276 AGGACTTATAAAAGTGAACAGAGGG 58.288 40.000 0.00 0.00 46.09 4.30
405 408 7.878127 TCAAGGACTTATAAAAGTGAACAGAGG 59.122 37.037 0.00 0.00 46.09 3.69
406 409 8.833231 TCAAGGACTTATAAAAGTGAACAGAG 57.167 34.615 0.00 0.00 46.09 3.35
407 410 9.273016 CTTCAAGGACTTATAAAAGTGAACAGA 57.727 33.333 0.00 0.00 46.09 3.41
408 411 9.273016 TCTTCAAGGACTTATAAAAGTGAACAG 57.727 33.333 0.00 0.00 46.09 3.16
409 412 9.052759 GTCTTCAAGGACTTATAAAAGTGAACA 57.947 33.333 0.00 0.00 46.09 3.18
410 413 9.052759 TGTCTTCAAGGACTTATAAAAGTGAAC 57.947 33.333 0.00 0.00 46.09 3.18
411 414 9.793259 ATGTCTTCAAGGACTTATAAAAGTGAA 57.207 29.630 0.00 0.00 46.09 3.18
412 415 9.793259 AATGTCTTCAAGGACTTATAAAAGTGA 57.207 29.630 0.00 0.00 46.09 3.41
420 423 9.442047 CTGTCTAAAATGTCTTCAAGGACTTAT 57.558 33.333 0.00 0.00 37.16 1.73
421 424 8.429641 ACTGTCTAAAATGTCTTCAAGGACTTA 58.570 33.333 0.00 0.00 37.16 2.24
422 425 7.227512 CACTGTCTAAAATGTCTTCAAGGACTT 59.772 37.037 0.00 0.00 37.16 3.01
423 426 6.708054 CACTGTCTAAAATGTCTTCAAGGACT 59.292 38.462 0.00 0.00 37.16 3.85
424 427 6.483640 ACACTGTCTAAAATGTCTTCAAGGAC 59.516 38.462 0.00 0.00 36.81 3.85
425 428 6.483307 CACACTGTCTAAAATGTCTTCAAGGA 59.517 38.462 0.00 0.00 0.00 3.36
426 429 6.662616 CACACTGTCTAAAATGTCTTCAAGG 58.337 40.000 0.00 0.00 0.00 3.61
427 430 6.138761 GCACACTGTCTAAAATGTCTTCAAG 58.861 40.000 0.00 0.00 0.00 3.02
428 431 5.588246 TGCACACTGTCTAAAATGTCTTCAA 59.412 36.000 0.00 0.00 0.00 2.69
429 432 5.122519 TGCACACTGTCTAAAATGTCTTCA 58.877 37.500 0.00 0.00 0.00 3.02
430 433 5.673337 TGCACACTGTCTAAAATGTCTTC 57.327 39.130 0.00 0.00 0.00 2.87
431 434 6.449635 TTTGCACACTGTCTAAAATGTCTT 57.550 33.333 0.00 0.00 0.00 3.01
432 435 5.506317 GCTTTGCACACTGTCTAAAATGTCT 60.506 40.000 0.00 0.00 0.00 3.41
433 436 4.676924 GCTTTGCACACTGTCTAAAATGTC 59.323 41.667 0.00 0.00 0.00 3.06
434 437 4.097741 TGCTTTGCACACTGTCTAAAATGT 59.902 37.500 0.00 0.00 31.71 2.71
435 438 4.609947 TGCTTTGCACACTGTCTAAAATG 58.390 39.130 0.00 0.00 31.71 2.32
436 439 4.339247 ACTGCTTTGCACACTGTCTAAAAT 59.661 37.500 0.00 0.00 33.79 1.82
437 440 3.694072 ACTGCTTTGCACACTGTCTAAAA 59.306 39.130 0.00 0.00 33.79 1.52
438 441 3.278574 ACTGCTTTGCACACTGTCTAAA 58.721 40.909 0.00 0.00 33.79 1.85
439 442 2.872245 GACTGCTTTGCACACTGTCTAA 59.128 45.455 10.67 0.00 33.79 2.10
440 443 2.103094 AGACTGCTTTGCACACTGTCTA 59.897 45.455 16.07 0.00 38.14 2.59
441 444 1.134280 AGACTGCTTTGCACACTGTCT 60.134 47.619 13.36 13.36 36.17 3.41
442 445 1.303309 AGACTGCTTTGCACACTGTC 58.697 50.000 10.19 10.19 33.79 3.51
443 446 2.620251 TAGACTGCTTTGCACACTGT 57.380 45.000 0.00 0.00 33.79 3.55
444 447 4.494350 AAATAGACTGCTTTGCACACTG 57.506 40.909 0.00 0.00 33.79 3.66
445 448 4.580167 TGAAAATAGACTGCTTTGCACACT 59.420 37.500 0.00 0.00 33.79 3.55
446 449 4.858935 TGAAAATAGACTGCTTTGCACAC 58.141 39.130 0.00 0.00 33.79 3.82
447 450 4.580167 ACTGAAAATAGACTGCTTTGCACA 59.420 37.500 0.00 0.00 33.79 4.57
448 451 5.113502 ACTGAAAATAGACTGCTTTGCAC 57.886 39.130 0.00 0.00 33.79 4.57
449 452 5.067674 ACAACTGAAAATAGACTGCTTTGCA 59.932 36.000 0.00 0.00 36.92 4.08
450 453 5.523369 ACAACTGAAAATAGACTGCTTTGC 58.477 37.500 0.00 0.00 0.00 3.68
451 454 6.854892 CAGACAACTGAAAATAGACTGCTTTG 59.145 38.462 0.00 0.00 46.03 2.77
452 455 6.963796 CAGACAACTGAAAATAGACTGCTTT 58.036 36.000 0.00 0.00 46.03 3.51
453 456 6.551385 CAGACAACTGAAAATAGACTGCTT 57.449 37.500 0.00 0.00 46.03 3.91
467 470 5.712217 TTGTAAGTCGTTTCAGACAACTG 57.288 39.130 0.00 0.00 43.24 3.16
468 471 6.370718 ACTTTTGTAAGTCGTTTCAGACAACT 59.629 34.615 0.00 0.00 40.60 3.16
469 472 6.464834 CACTTTTGTAAGTCGTTTCAGACAAC 59.535 38.462 0.00 0.00 42.67 3.32
470 473 6.369340 TCACTTTTGTAAGTCGTTTCAGACAA 59.631 34.615 0.00 0.00 42.67 3.18
471 474 5.870433 TCACTTTTGTAAGTCGTTTCAGACA 59.130 36.000 0.00 0.00 42.67 3.41
472 475 6.340537 TCACTTTTGTAAGTCGTTTCAGAC 57.659 37.500 0.00 0.00 42.67 3.51
473 476 6.454583 CGTTCACTTTTGTAAGTCGTTTCAGA 60.455 38.462 0.00 0.00 42.67 3.27
474 477 5.671140 CGTTCACTTTTGTAAGTCGTTTCAG 59.329 40.000 0.00 0.00 42.67 3.02
475 478 5.446206 CCGTTCACTTTTGTAAGTCGTTTCA 60.446 40.000 0.00 0.00 42.67 2.69
476 479 4.959757 CCGTTCACTTTTGTAAGTCGTTTC 59.040 41.667 0.00 0.00 42.67 2.78
477 480 4.630940 TCCGTTCACTTTTGTAAGTCGTTT 59.369 37.500 0.00 0.00 42.67 3.60
478 481 4.183101 TCCGTTCACTTTTGTAAGTCGTT 58.817 39.130 0.00 0.00 42.67 3.85
479 482 3.784338 TCCGTTCACTTTTGTAAGTCGT 58.216 40.909 0.00 0.00 42.67 4.34
480 483 3.183775 CCTCCGTTCACTTTTGTAAGTCG 59.816 47.826 0.00 0.00 42.67 4.18
481 484 3.497262 CCCTCCGTTCACTTTTGTAAGTC 59.503 47.826 0.00 0.00 42.67 3.01
482 485 3.135167 TCCCTCCGTTCACTTTTGTAAGT 59.865 43.478 0.00 0.00 45.40 2.24
483 486 3.735591 TCCCTCCGTTCACTTTTGTAAG 58.264 45.455 0.00 0.00 37.40 2.34
484 487 3.135167 ACTCCCTCCGTTCACTTTTGTAA 59.865 43.478 0.00 0.00 0.00 2.41
485 488 2.701951 ACTCCCTCCGTTCACTTTTGTA 59.298 45.455 0.00 0.00 0.00 2.41
486 489 1.489230 ACTCCCTCCGTTCACTTTTGT 59.511 47.619 0.00 0.00 0.00 2.83
487 490 2.256117 ACTCCCTCCGTTCACTTTTG 57.744 50.000 0.00 0.00 0.00 2.44
488 491 4.635699 AATACTCCCTCCGTTCACTTTT 57.364 40.909 0.00 0.00 0.00 2.27
489 492 4.635699 AAATACTCCCTCCGTTCACTTT 57.364 40.909 0.00 0.00 0.00 2.66
490 493 4.635699 AAAATACTCCCTCCGTTCACTT 57.364 40.909 0.00 0.00 0.00 3.16
491 494 4.635699 AAAAATACTCCCTCCGTTCACT 57.364 40.909 0.00 0.00 0.00 3.41
530 533 3.059868 TCAAAGTTAGCAGCGAGAAAACG 60.060 43.478 0.00 0.00 0.00 3.60
539 542 1.807142 GGTGGACTCAAAGTTAGCAGC 59.193 52.381 0.00 0.00 0.00 5.25
950 954 3.614092 CTGGGTGCTGAATATCACAGTT 58.386 45.455 10.24 0.00 37.64 3.16
986 990 0.040646 AGACATCCGGTGGTAGGACA 59.959 55.000 0.00 0.00 41.10 4.02
1046 1050 4.755411 TCTACAAGGAAGGAGTAATTGCG 58.245 43.478 0.00 0.00 0.00 4.85
1094 1098 7.921214 GGTCAATACTGTTAAGATCTCGATTCA 59.079 37.037 0.00 0.00 0.00 2.57
1305 1309 2.233271 CTCAACTGTGCCCACTGAAAT 58.767 47.619 11.50 0.00 34.80 2.17
1587 1591 6.913132 GTGCTACTTCAACCTTCTTTTCTTTC 59.087 38.462 0.00 0.00 0.00 2.62
1971 1975 8.287503 ACGTTAATCAAGGAATTGTAGAACAAC 58.712 33.333 0.00 0.00 41.40 3.32
2001 2005 0.033504 ACAGATAGCCCGCATTACCG 59.966 55.000 0.00 0.00 0.00 4.02
2217 2221 1.827969 TCAGCTTGGCCTCTTCTACTC 59.172 52.381 3.32 0.00 0.00 2.59
2471 2475 9.180678 CAGAAATACCAAAACAAGACATGTAAC 57.819 33.333 0.00 0.00 42.99 2.50
2537 2541 0.174389 ACGCTATCAGCTGACCACTG 59.826 55.000 20.97 10.72 39.60 3.66
2610 2630 9.902196 TTATAGTGTGTGGTATGTCGTATAATG 57.098 33.333 0.00 0.00 0.00 1.90
2620 2640 7.987458 AGGAACTCAATTATAGTGTGTGGTATG 59.013 37.037 0.00 0.00 0.00 2.39
2747 3344 2.810767 GCCCGATCCTGATCTTTTACCC 60.811 54.545 5.66 0.00 35.72 3.69
2847 3459 9.273016 CCGTATGTAGTCATTTATTGGAATCTT 57.727 33.333 0.00 0.00 35.70 2.40
2860 3472 9.261180 CATTCATTTTACTCCGTATGTAGTCAT 57.739 33.333 0.00 0.00 38.00 3.06
3106 3763 1.066071 TGTAATCATTCGTCCGGGCAA 60.066 47.619 6.96 0.00 0.00 4.52
3111 3768 6.863645 AGATATTGTCTGTAATCATTCGTCCG 59.136 38.462 0.00 0.00 35.31 4.79
3177 3834 3.910627 ACACAGACCCTCTTTACCATTCT 59.089 43.478 0.00 0.00 0.00 2.40
3201 3858 7.701539 ACTTTGTGCATATCCAGTTTAATGA 57.298 32.000 0.00 0.00 0.00 2.57
3317 3974 2.722201 CCCGGTACTCCACTGAGGC 61.722 68.421 0.00 0.00 43.29 4.70
3376 4033 1.836166 TCTTCCTGCCTCAATCCTCTG 59.164 52.381 0.00 0.00 0.00 3.35
3393 4050 4.618378 AAGTATGGAGAGAGAGGGTCTT 57.382 45.455 0.00 0.00 34.71 3.01


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

AutoCloner maintained by Alex Coulton.