Multiple sequence alignment - TraesCS2B01G201100

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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 TraesCS2B01G201100 chr2B 100.000 2684 0 0 1 2684 180538897 180541580 0.000000e+00 4957.0
1 TraesCS2B01G201100 chr2B 76.730 679 126 21 1025 1696 180546256 180546909 1.530000e-92 350.0
2 TraesCS2B01G201100 chr2B 88.764 89 7 3 461 548 76491455 76491369 3.650000e-19 106.0
3 TraesCS2B01G201100 chr2D 95.293 2167 59 17 541 2684 126946181 126948327 0.000000e+00 3397.0
4 TraesCS2B01G201100 chr2D 77.071 676 131 17 1025 1696 126958614 126959269 4.220000e-98 368.0
5 TraesCS2B01G201100 chr2D 81.818 264 25 11 127 368 126945842 126946104 1.630000e-47 200.0
6 TraesCS2B01G201100 chr2D 87.179 78 10 0 382 459 126946090 126946167 3.680000e-14 89.8
7 TraesCS2B01G201100 chr2A 95.966 1859 63 8 830 2684 133472925 133474775 0.000000e+00 3007.0
8 TraesCS2B01G201100 chr2A 92.143 280 20 2 550 829 133472236 133472513 6.960000e-106 394.0
9 TraesCS2B01G201100 chr2A 76.271 649 126 18 1025 1668 133484907 133485532 1.200000e-83 320.0
10 TraesCS2B01G201100 chr6B 90.110 91 8 1 461 550 183378843 183378933 1.690000e-22 117.0
11 TraesCS2B01G201100 chr3D 90.698 86 8 0 463 548 21587139 21587224 6.070000e-22 115.0
12 TraesCS2B01G201100 chr7D 87.912 91 11 0 461 551 51417392 51417302 1.020000e-19 108.0
13 TraesCS2B01G201100 chr7D 87.097 93 10 2 461 552 538167431 538167340 1.310000e-18 104.0
14 TraesCS2B01G201100 chr7A 88.506 87 10 0 461 547 585471747 585471833 3.650000e-19 106.0
15 TraesCS2B01G201100 chr1D 86.458 96 10 3 461 553 479598725 479598630 4.730000e-18 102.0
16 TraesCS2B01G201100 chr1A 86.957 92 11 1 461 552 11807550 11807640 4.730000e-18 102.0
17 TraesCS2B01G201100 chr5A 84.848 99 13 2 461 559 554301836 554301740 6.120000e-17 99.0
18 TraesCS2B01G201100 chr5B 83.133 83 11 3 279 360 510809841 510809761 3.710000e-09 73.1


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 TraesCS2B01G201100 chr2B 180538897 180541580 2683 False 4957.000000 4957 100.000000 1 2684 1 chr2B.!!$F1 2683
1 TraesCS2B01G201100 chr2B 180546256 180546909 653 False 350.000000 350 76.730000 1025 1696 1 chr2B.!!$F2 671
2 TraesCS2B01G201100 chr2D 126945842 126948327 2485 False 1228.933333 3397 88.096667 127 2684 3 chr2D.!!$F2 2557
3 TraesCS2B01G201100 chr2D 126958614 126959269 655 False 368.000000 368 77.071000 1025 1696 1 chr2D.!!$F1 671
4 TraesCS2B01G201100 chr2A 133472236 133474775 2539 False 1700.500000 3007 94.054500 550 2684 2 chr2A.!!$F2 2134
5 TraesCS2B01G201100 chr2A 133484907 133485532 625 False 320.000000 320 76.271000 1025 1668 1 chr2A.!!$F1 643

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
290 312 0.034337 CCCGAGAAAAGTGGAACGGA 59.966 55.0 0.0 0.0 45.86 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1805 2267 1.067846 GCTGTACACGACATGGACTCA 60.068 52.381 0.0 0.0 43.47 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
30 31 9.715121 AATAGATTGTGCATTGTGAGAAAAATT 57.285 25.926 0.00 0.00 0.00 1.82
31 32 9.715121 ATAGATTGTGCATTGTGAGAAAAATTT 57.285 25.926 0.00 0.00 0.00 1.82
33 34 9.545105 AGATTGTGCATTGTGAGAAAAATTTAA 57.455 25.926 0.00 0.00 0.00 1.52
99 100 9.508642 AAAAAGAAAGACAATAAACCAAAACCA 57.491 25.926 0.00 0.00 0.00 3.67
100 101 9.508642 AAAAGAAAGACAATAAACCAAAACCAA 57.491 25.926 0.00 0.00 0.00 3.67
101 102 9.508642 AAAGAAAGACAATAAACCAAAACCAAA 57.491 25.926 0.00 0.00 0.00 3.28
102 103 9.508642 AAGAAAGACAATAAACCAAAACCAAAA 57.491 25.926 0.00 0.00 0.00 2.44
103 104 9.508642 AGAAAGACAATAAACCAAAACCAAAAA 57.491 25.926 0.00 0.00 0.00 1.94
104 105 9.549509 GAAAGACAATAAACCAAAACCAAAAAC 57.450 29.630 0.00 0.00 0.00 2.43
105 106 7.618502 AGACAATAAACCAAAACCAAAAACC 57.381 32.000 0.00 0.00 0.00 3.27
106 107 6.314152 AGACAATAAACCAAAACCAAAAACCG 59.686 34.615 0.00 0.00 0.00 4.44
107 108 5.354513 ACAATAAACCAAAACCAAAAACCGG 59.645 36.000 0.00 0.00 0.00 5.28
108 109 3.420300 AAACCAAAACCAAAAACCGGT 57.580 38.095 0.00 0.00 38.85 5.28
109 110 2.676632 ACCAAAACCAAAAACCGGTC 57.323 45.000 8.04 0.00 34.99 4.79
110 111 1.207570 ACCAAAACCAAAAACCGGTCC 59.792 47.619 8.04 0.00 34.99 4.46
111 112 1.562017 CAAAACCAAAAACCGGTCCG 58.438 50.000 8.04 3.60 34.99 4.79
216 229 2.496111 TGCCTGGTTGGTTAGTAAACG 58.504 47.619 0.00 0.00 36.39 3.60
218 231 3.070734 TGCCTGGTTGGTTAGTAAACGTA 59.929 43.478 0.00 0.00 36.39 3.57
232 245 4.180496 CGTAAGTTGGAGGTCGCC 57.820 61.111 0.00 0.00 0.00 5.54
238 251 3.235481 TTGGAGGTCGCCGGTTCA 61.235 61.111 1.90 0.00 0.00 3.18
240 253 2.031465 GGAGGTCGCCGGTTCAAA 59.969 61.111 1.90 0.00 0.00 2.69
241 254 1.376812 GGAGGTCGCCGGTTCAAAT 60.377 57.895 1.90 0.00 0.00 2.32
242 255 1.366854 GGAGGTCGCCGGTTCAAATC 61.367 60.000 1.90 0.00 0.00 2.17
249 270 1.982073 GCCGGTTCAAATCTCAGCCG 61.982 60.000 1.90 0.00 38.99 5.52
257 278 1.308069 AAATCTCAGCCGCGCATGTT 61.308 50.000 8.75 0.00 0.00 2.71
261 282 1.339235 CTCAGCCGCGCATGTTTTTG 61.339 55.000 8.75 0.00 0.00 2.44
262 283 2.734346 AGCCGCGCATGTTTTTGC 60.734 55.556 8.75 0.00 39.29 3.68
263 284 3.034923 GCCGCGCATGTTTTTGCA 61.035 55.556 8.75 0.00 42.91 4.08
264 285 2.381967 GCCGCGCATGTTTTTGCAT 61.382 52.632 8.75 0.00 42.91 3.96
273 295 5.726413 GCGCATGTTTTTGCATATTAAACCC 60.726 40.000 0.30 2.01 42.91 4.11
276 298 6.237808 GCATGTTTTTGCATATTAAACCCGAG 60.238 38.462 0.00 0.00 42.31 4.63
287 309 5.700722 ATTAAACCCGAGAAAAGTGGAAC 57.299 39.130 0.00 0.00 0.00 3.62
290 312 0.034337 CCCGAGAAAAGTGGAACGGA 59.966 55.000 0.00 0.00 45.86 4.69
361 384 1.080093 CCGGCGTCTGAAGTGCTAA 60.080 57.895 6.01 0.00 0.00 3.09
362 385 0.669318 CCGGCGTCTGAAGTGCTAAA 60.669 55.000 6.01 0.00 0.00 1.85
363 386 0.716108 CGGCGTCTGAAGTGCTAAAG 59.284 55.000 0.00 0.00 0.00 1.85
364 387 1.668919 CGGCGTCTGAAGTGCTAAAGA 60.669 52.381 0.00 0.00 0.00 2.52
365 388 1.996191 GGCGTCTGAAGTGCTAAAGAG 59.004 52.381 0.00 0.00 0.00 2.85
366 389 1.996191 GCGTCTGAAGTGCTAAAGAGG 59.004 52.381 0.00 0.00 0.00 3.69
367 390 2.352814 GCGTCTGAAGTGCTAAAGAGGA 60.353 50.000 0.00 0.00 0.00 3.71
368 391 3.861131 GCGTCTGAAGTGCTAAAGAGGAA 60.861 47.826 0.00 0.00 0.00 3.36
369 392 4.307432 CGTCTGAAGTGCTAAAGAGGAAA 58.693 43.478 0.00 0.00 0.00 3.13
370 393 4.750098 CGTCTGAAGTGCTAAAGAGGAAAA 59.250 41.667 0.00 0.00 0.00 2.29
371 394 5.236478 CGTCTGAAGTGCTAAAGAGGAAAAA 59.764 40.000 0.00 0.00 0.00 1.94
372 395 6.073003 CGTCTGAAGTGCTAAAGAGGAAAAAT 60.073 38.462 0.00 0.00 0.00 1.82
373 396 7.520614 CGTCTGAAGTGCTAAAGAGGAAAAATT 60.521 37.037 0.00 0.00 0.00 1.82
374 397 8.138074 GTCTGAAGTGCTAAAGAGGAAAAATTT 58.862 33.333 0.00 0.00 0.00 1.82
375 398 8.352942 TCTGAAGTGCTAAAGAGGAAAAATTTC 58.647 33.333 0.00 0.00 36.46 2.17
376 399 8.006298 TGAAGTGCTAAAGAGGAAAAATTTCA 57.994 30.769 8.06 0.00 38.92 2.69
377 400 8.474025 TGAAGTGCTAAAGAGGAAAAATTTCAA 58.526 29.630 8.06 0.00 38.92 2.69
378 401 9.313118 GAAGTGCTAAAGAGGAAAAATTTCAAA 57.687 29.630 8.06 0.00 38.92 2.69
379 402 9.665719 AAGTGCTAAAGAGGAAAAATTTCAAAA 57.334 25.926 8.06 0.00 38.92 2.44
380 403 9.665719 AGTGCTAAAGAGGAAAAATTTCAAAAA 57.334 25.926 8.06 0.00 38.92 1.94
405 428 6.276832 AGTACTAAATAGGAAACGCTGTCA 57.723 37.500 0.00 0.00 0.00 3.58
407 430 7.156673 AGTACTAAATAGGAAACGCTGTCAAA 58.843 34.615 0.00 0.00 0.00 2.69
413 436 2.158957 AGGAAACGCTGTCAAAGTCTCA 60.159 45.455 0.00 0.00 0.00 3.27
414 437 2.612212 GGAAACGCTGTCAAAGTCTCAA 59.388 45.455 0.00 0.00 0.00 3.02
421 444 6.970484 ACGCTGTCAAAGTCTCAATAAATTT 58.030 32.000 0.00 0.00 0.00 1.82
455 478 8.830580 CCGACTAAGACATGTCAATAAAATCAT 58.169 33.333 27.02 0.00 33.18 2.45
462 485 9.466497 AGACATGTCAATAAAATCATAAGGTGT 57.534 29.630 27.02 0.00 0.00 4.16
467 490 9.747898 TGTCAATAAAATCATAAGGTGTAAGGT 57.252 29.630 0.00 0.00 0.00 3.50
473 496 8.706322 AAAATCATAAGGTGTAAGGTCTTTGT 57.294 30.769 0.00 0.00 0.00 2.83
474 497 7.687941 AATCATAAGGTGTAAGGTCTTTGTG 57.312 36.000 0.00 0.00 0.00 3.33
475 498 6.428083 TCATAAGGTGTAAGGTCTTTGTGA 57.572 37.500 0.00 0.00 0.00 3.58
476 499 6.833041 TCATAAGGTGTAAGGTCTTTGTGAA 58.167 36.000 0.00 0.00 0.00 3.18
477 500 7.458397 TCATAAGGTGTAAGGTCTTTGTGAAT 58.542 34.615 0.00 0.00 0.00 2.57
478 501 8.598916 TCATAAGGTGTAAGGTCTTTGTGAATA 58.401 33.333 0.00 0.00 0.00 1.75
479 502 9.226606 CATAAGGTGTAAGGTCTTTGTGAATAA 57.773 33.333 0.00 0.00 0.00 1.40
480 503 9.975218 ATAAGGTGTAAGGTCTTTGTGAATAAT 57.025 29.630 0.00 0.00 0.00 1.28
481 504 8.706322 AAGGTGTAAGGTCTTTGTGAATAATT 57.294 30.769 0.00 0.00 0.00 1.40
482 505 9.802039 AAGGTGTAAGGTCTTTGTGAATAATTA 57.198 29.630 0.00 0.00 0.00 1.40
483 506 9.802039 AGGTGTAAGGTCTTTGTGAATAATTAA 57.198 29.630 0.00 0.00 0.00 1.40
518 541 1.336125 GCATCACCTAAATGCAGAGGC 59.664 52.381 11.12 1.80 46.93 4.70
519 542 1.952296 CATCACCTAAATGCAGAGGCC 59.048 52.381 11.12 0.00 40.13 5.19
520 543 0.107703 TCACCTAAATGCAGAGGCCG 60.108 55.000 11.12 4.48 40.13 6.13
521 544 1.097547 CACCTAAATGCAGAGGCCGG 61.098 60.000 11.12 0.00 40.13 6.13
522 545 1.224592 CCTAAATGCAGAGGCCGGT 59.775 57.895 1.90 0.00 40.13 5.28
523 546 1.097547 CCTAAATGCAGAGGCCGGTG 61.098 60.000 1.90 0.00 40.13 4.94
524 547 0.392998 CTAAATGCAGAGGCCGGTGT 60.393 55.000 1.90 0.00 40.13 4.16
525 548 0.037590 TAAATGCAGAGGCCGGTGTT 59.962 50.000 1.90 0.00 40.13 3.32
526 549 1.244019 AAATGCAGAGGCCGGTGTTC 61.244 55.000 1.90 0.00 40.13 3.18
527 550 2.410322 AATGCAGAGGCCGGTGTTCA 62.410 55.000 1.90 0.70 40.13 3.18
528 551 2.045926 GCAGAGGCCGGTGTTCAT 60.046 61.111 1.90 0.00 0.00 2.57
529 552 2.109126 GCAGAGGCCGGTGTTCATC 61.109 63.158 1.90 0.00 0.00 2.92
530 553 1.450312 CAGAGGCCGGTGTTCATCC 60.450 63.158 1.90 0.00 0.00 3.51
531 554 1.613630 AGAGGCCGGTGTTCATCCT 60.614 57.895 1.90 0.00 0.00 3.24
532 555 1.201429 AGAGGCCGGTGTTCATCCTT 61.201 55.000 1.90 0.00 0.00 3.36
533 556 0.744771 GAGGCCGGTGTTCATCCTTC 60.745 60.000 1.90 0.00 0.00 3.46
534 557 1.201429 AGGCCGGTGTTCATCCTTCT 61.201 55.000 1.90 0.00 0.00 2.85
535 558 0.322546 GGCCGGTGTTCATCCTTCTT 60.323 55.000 1.90 0.00 0.00 2.52
536 559 1.087501 GCCGGTGTTCATCCTTCTTC 58.912 55.000 1.90 0.00 0.00 2.87
537 560 1.339151 GCCGGTGTTCATCCTTCTTCT 60.339 52.381 1.90 0.00 0.00 2.85
538 561 2.622436 CCGGTGTTCATCCTTCTTCTC 58.378 52.381 0.00 0.00 0.00 2.87
539 562 2.234908 CCGGTGTTCATCCTTCTTCTCT 59.765 50.000 0.00 0.00 0.00 3.10
617 640 7.900782 TCTAGCTCCAACACTTTTATGTAAC 57.099 36.000 0.00 0.00 30.75 2.50
627 651 9.184062 CAACACTTTTATGTAACGAGTACAGTA 57.816 33.333 9.08 0.00 45.88 2.74
628 652 9.748708 AACACTTTTATGTAACGAGTACAGTAA 57.251 29.630 9.08 4.24 45.88 2.24
670 694 7.128234 AGATTCCATTGGACCCAAAAATATG 57.872 36.000 4.45 0.00 39.55 1.78
671 695 6.902416 AGATTCCATTGGACCCAAAAATATGA 59.098 34.615 4.45 0.00 39.55 2.15
701 725 0.655733 CAAGTTCGTGACACACACCC 59.344 55.000 6.37 0.00 45.73 4.61
799 823 1.194781 ACGAATGGGCCTCTGACAGT 61.195 55.000 4.53 0.00 0.00 3.55
807 831 2.650116 CCTCTGACAGTGGACCCCG 61.650 68.421 17.06 0.00 30.66 5.73
844 1279 2.568623 AACCACAAGATCCAGTCACC 57.431 50.000 0.00 0.00 0.00 4.02
898 1333 1.047801 GAGCTCCCTTCCATCTCTCC 58.952 60.000 0.87 0.00 0.00 3.71
899 1334 0.641601 AGCTCCCTTCCATCTCTCCT 59.358 55.000 0.00 0.00 0.00 3.69
918 1357 2.556766 CTCCCCCTTTCTTCTTCCTCT 58.443 52.381 0.00 0.00 0.00 3.69
1792 2254 8.494433 AGCTTATTTATTACTTGGTGATGAGGA 58.506 33.333 0.00 0.00 0.00 3.71
1793 2255 9.120538 GCTTATTTATTACTTGGTGATGAGGAA 57.879 33.333 0.00 0.00 0.00 3.36
1799 2261 1.276421 CTTGGTGATGAGGAAGTCCGT 59.724 52.381 0.00 0.00 42.08 4.69
1805 2267 3.104512 TGATGAGGAAGTCCGTGGTTAT 58.895 45.455 0.00 0.00 42.08 1.89
1824 2286 3.510388 ATGAGTCCATGTCGTGTACAG 57.490 47.619 0.00 0.00 42.70 2.74
1846 2308 4.527944 GCAAGAAGCCTTATTACCTCCTT 58.472 43.478 0.00 0.00 37.23 3.36
1847 2309 5.681639 GCAAGAAGCCTTATTACCTCCTTA 58.318 41.667 0.00 0.00 37.23 2.69
1921 2391 5.300792 GGGAAGATTTTAGTTCACCACAACA 59.699 40.000 0.00 0.00 0.00 3.33
2035 2505 1.029681 TCATTGATGATGCAGGCAGC 58.970 50.000 1.98 1.98 45.96 5.25
2067 2537 2.280797 TGCTGTCGGTGGTTCTGC 60.281 61.111 0.00 0.00 0.00 4.26
2072 2542 0.981183 TGTCGGTGGTTCTGCCTATT 59.019 50.000 0.00 0.00 38.35 1.73
2117 2587 1.516821 CCCAATGGTGCGCGAATTG 60.517 57.895 12.10 17.72 0.00 2.32
2309 2779 1.518903 GCAGGGCGTCAAAGCTTCTT 61.519 55.000 0.00 0.00 37.29 2.52
2399 2869 4.457496 CACCGCAGATGCTCCCGT 62.457 66.667 2.95 0.00 39.32 5.28
2532 3005 0.770557 AGTGGGGGTAGCTGGTTTGA 60.771 55.000 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.715121 AATTTTTCTCACAATGCACAATCTATT 57.285 25.926 0.00 0.00 0.00 1.73
5 6 9.715121 AAATTTTTCTCACAATGCACAATCTAT 57.285 25.926 0.00 0.00 0.00 1.98
7 8 9.545105 TTAAATTTTTCTCACAATGCACAATCT 57.455 25.926 0.00 0.00 0.00 2.40
73 74 9.508642 TGGTTTTGGTTTATTGTCTTTCTTTTT 57.491 25.926 0.00 0.00 0.00 1.94
74 75 9.508642 TTGGTTTTGGTTTATTGTCTTTCTTTT 57.491 25.926 0.00 0.00 0.00 2.27
75 76 9.508642 TTTGGTTTTGGTTTATTGTCTTTCTTT 57.491 25.926 0.00 0.00 0.00 2.52
76 77 9.508642 TTTTGGTTTTGGTTTATTGTCTTTCTT 57.491 25.926 0.00 0.00 0.00 2.52
77 78 9.508642 TTTTTGGTTTTGGTTTATTGTCTTTCT 57.491 25.926 0.00 0.00 0.00 2.52
78 79 9.549509 GTTTTTGGTTTTGGTTTATTGTCTTTC 57.450 29.630 0.00 0.00 0.00 2.62
79 80 8.516234 GGTTTTTGGTTTTGGTTTATTGTCTTT 58.484 29.630 0.00 0.00 0.00 2.52
80 81 7.148390 CGGTTTTTGGTTTTGGTTTATTGTCTT 60.148 33.333 0.00 0.00 0.00 3.01
81 82 6.314152 CGGTTTTTGGTTTTGGTTTATTGTCT 59.686 34.615 0.00 0.00 0.00 3.41
82 83 6.457122 CCGGTTTTTGGTTTTGGTTTATTGTC 60.457 38.462 0.00 0.00 0.00 3.18
83 84 5.354513 CCGGTTTTTGGTTTTGGTTTATTGT 59.645 36.000 0.00 0.00 0.00 2.71
84 85 5.354513 ACCGGTTTTTGGTTTTGGTTTATTG 59.645 36.000 0.00 0.00 35.82 1.90
85 86 5.498393 ACCGGTTTTTGGTTTTGGTTTATT 58.502 33.333 0.00 0.00 35.82 1.40
86 87 5.100344 ACCGGTTTTTGGTTTTGGTTTAT 57.900 34.783 0.00 0.00 35.82 1.40
87 88 4.502016 GACCGGTTTTTGGTTTTGGTTTA 58.498 39.130 9.42 0.00 40.63 2.01
88 89 3.336468 GACCGGTTTTTGGTTTTGGTTT 58.664 40.909 9.42 0.00 40.63 3.27
89 90 2.354906 GGACCGGTTTTTGGTTTTGGTT 60.355 45.455 9.42 0.00 40.63 3.67
90 91 1.207570 GGACCGGTTTTTGGTTTTGGT 59.792 47.619 9.42 0.00 40.63 3.67
91 92 1.803252 CGGACCGGTTTTTGGTTTTGG 60.803 52.381 9.42 0.00 40.63 3.28
92 93 1.562017 CGGACCGGTTTTTGGTTTTG 58.438 50.000 9.42 0.00 40.63 2.44
93 94 0.460722 CCGGACCGGTTTTTGGTTTT 59.539 50.000 25.54 0.00 42.73 2.43
94 95 2.117257 CCGGACCGGTTTTTGGTTT 58.883 52.632 25.54 0.00 42.73 3.27
95 96 3.844741 CCGGACCGGTTTTTGGTT 58.155 55.556 25.54 0.00 42.73 3.67
114 115 7.234661 TCTTCTACTTTTGTTGTGGGTTTTT 57.765 32.000 0.00 0.00 0.00 1.94
115 116 6.844097 TCTTCTACTTTTGTTGTGGGTTTT 57.156 33.333 0.00 0.00 0.00 2.43
116 117 6.844097 TTCTTCTACTTTTGTTGTGGGTTT 57.156 33.333 0.00 0.00 0.00 3.27
117 118 6.844097 TTTCTTCTACTTTTGTTGTGGGTT 57.156 33.333 0.00 0.00 0.00 4.11
118 119 6.844097 TTTTCTTCTACTTTTGTTGTGGGT 57.156 33.333 0.00 0.00 0.00 4.51
184 190 2.291209 ACCAGGCAAATGACACATCA 57.709 45.000 0.00 0.00 39.83 3.07
185 191 2.353011 CCAACCAGGCAAATGACACATC 60.353 50.000 0.00 0.00 0.00 3.06
187 193 1.039068 CCAACCAGGCAAATGACACA 58.961 50.000 0.00 0.00 0.00 3.72
192 198 5.227152 GTTTACTAACCAACCAGGCAAATG 58.773 41.667 0.00 0.00 43.14 2.32
193 199 4.022676 CGTTTACTAACCAACCAGGCAAAT 60.023 41.667 0.00 0.00 43.14 2.32
216 229 1.447314 CCGGCGACCTCCAACTTAC 60.447 63.158 9.30 0.00 0.00 2.34
218 231 2.726822 GAACCGGCGACCTCCAACTT 62.727 60.000 9.30 0.00 0.00 2.66
229 242 1.425428 GCTGAGATTTGAACCGGCG 59.575 57.895 0.00 0.00 0.00 6.46
232 245 1.425428 GCGGCTGAGATTTGAACCG 59.575 57.895 0.00 0.00 43.37 4.44
238 251 1.308069 AACATGCGCGGCTGAGATTT 61.308 50.000 8.83 0.00 0.00 2.17
240 253 1.308069 AAAACATGCGCGGCTGAGAT 61.308 50.000 8.83 0.00 0.00 2.75
241 254 1.514678 AAAAACATGCGCGGCTGAGA 61.515 50.000 8.83 0.00 0.00 3.27
242 255 1.081242 AAAAACATGCGCGGCTGAG 60.081 52.632 8.83 0.00 0.00 3.35
257 278 7.596995 CACTTTTCTCGGGTTTAATATGCAAAA 59.403 33.333 0.00 0.00 0.00 2.44
261 282 5.355910 TCCACTTTTCTCGGGTTTAATATGC 59.644 40.000 0.00 0.00 0.00 3.14
262 283 6.995511 TCCACTTTTCTCGGGTTTAATATG 57.004 37.500 0.00 0.00 0.00 1.78
263 284 6.093082 CGTTCCACTTTTCTCGGGTTTAATAT 59.907 38.462 0.00 0.00 0.00 1.28
264 285 5.409214 CGTTCCACTTTTCTCGGGTTTAATA 59.591 40.000 0.00 0.00 0.00 0.98
273 295 1.145803 GGTCCGTTCCACTTTTCTCG 58.854 55.000 0.00 0.00 0.00 4.04
276 298 1.848932 GCCGGTCCGTTCCACTTTTC 61.849 60.000 11.06 0.00 0.00 2.29
378 401 8.387190 ACAGCGTTTCCTATTTAGTACTTTTT 57.613 30.769 0.00 0.00 0.00 1.94
379 402 7.658575 TGACAGCGTTTCCTATTTAGTACTTTT 59.341 33.333 0.00 0.00 0.00 2.27
380 403 7.156673 TGACAGCGTTTCCTATTTAGTACTTT 58.843 34.615 0.00 0.00 0.00 2.66
381 404 6.694447 TGACAGCGTTTCCTATTTAGTACTT 58.306 36.000 0.00 0.00 0.00 2.24
382 405 6.276832 TGACAGCGTTTCCTATTTAGTACT 57.723 37.500 0.00 0.00 0.00 2.73
383 406 6.956299 TTGACAGCGTTTCCTATTTAGTAC 57.044 37.500 0.00 0.00 0.00 2.73
384 407 7.156673 ACTTTGACAGCGTTTCCTATTTAGTA 58.843 34.615 0.00 0.00 0.00 1.82
385 408 5.995897 ACTTTGACAGCGTTTCCTATTTAGT 59.004 36.000 0.00 0.00 0.00 2.24
386 409 6.369065 AGACTTTGACAGCGTTTCCTATTTAG 59.631 38.462 0.00 0.00 0.00 1.85
387 410 6.228258 AGACTTTGACAGCGTTTCCTATTTA 58.772 36.000 0.00 0.00 0.00 1.40
388 411 5.063880 AGACTTTGACAGCGTTTCCTATTT 58.936 37.500 0.00 0.00 0.00 1.40
389 412 4.642429 AGACTTTGACAGCGTTTCCTATT 58.358 39.130 0.00 0.00 0.00 1.73
396 419 6.560253 ATTTATTGAGACTTTGACAGCGTT 57.440 33.333 0.00 0.00 0.00 4.84
401 424 7.173218 AGAGCGAAATTTATTGAGACTTTGACA 59.827 33.333 0.00 0.00 0.00 3.58
405 428 6.317857 GCAGAGCGAAATTTATTGAGACTTT 58.682 36.000 0.00 0.00 0.00 2.66
407 430 4.333926 GGCAGAGCGAAATTTATTGAGACT 59.666 41.667 0.00 0.00 0.00 3.24
413 436 3.270877 AGTCGGCAGAGCGAAATTTATT 58.729 40.909 0.00 0.00 0.00 1.40
414 437 2.906354 AGTCGGCAGAGCGAAATTTAT 58.094 42.857 0.00 0.00 0.00 1.40
421 444 0.958876 TGTCTTAGTCGGCAGAGCGA 60.959 55.000 0.00 0.00 0.00 4.93
455 478 9.802039 AATTATTCACAAAGACCTTACACCTTA 57.198 29.630 0.00 0.00 0.00 2.69
492 515 3.380479 GCATTTAGGTGATGCATGCAT 57.620 42.857 32.66 32.66 46.96 3.96
493 516 2.875087 GCATTTAGGTGATGCATGCA 57.125 45.000 25.04 25.04 46.96 3.96
499 522 1.952296 GGCCTCTGCATTTAGGTGATG 59.048 52.381 0.00 0.00 40.13 3.07
500 523 1.475751 CGGCCTCTGCATTTAGGTGAT 60.476 52.381 0.00 0.00 40.13 3.06
501 524 0.107703 CGGCCTCTGCATTTAGGTGA 60.108 55.000 0.00 0.00 40.13 4.02
502 525 1.097547 CCGGCCTCTGCATTTAGGTG 61.098 60.000 0.00 5.11 40.13 4.00
503 526 1.224592 CCGGCCTCTGCATTTAGGT 59.775 57.895 0.00 0.00 40.13 3.08
504 527 1.097547 CACCGGCCTCTGCATTTAGG 61.098 60.000 0.00 5.70 40.13 2.69
505 528 0.392998 ACACCGGCCTCTGCATTTAG 60.393 55.000 0.00 0.00 40.13 1.85
506 529 0.037590 AACACCGGCCTCTGCATTTA 59.962 50.000 0.00 0.00 40.13 1.40
507 530 1.228552 AACACCGGCCTCTGCATTT 60.229 52.632 0.00 0.00 40.13 2.32
508 531 1.675641 GAACACCGGCCTCTGCATT 60.676 57.895 0.00 0.00 40.13 3.56
509 532 2.045926 GAACACCGGCCTCTGCAT 60.046 61.111 0.00 0.00 40.13 3.96
510 533 2.803155 GATGAACACCGGCCTCTGCA 62.803 60.000 0.00 0.00 40.13 4.41
511 534 2.045926 ATGAACACCGGCCTCTGC 60.046 61.111 0.00 0.00 0.00 4.26
512 535 1.450312 GGATGAACACCGGCCTCTG 60.450 63.158 0.00 0.00 0.00 3.35
513 536 1.201429 AAGGATGAACACCGGCCTCT 61.201 55.000 0.00 0.00 0.00 3.69
514 537 0.744771 GAAGGATGAACACCGGCCTC 60.745 60.000 0.00 0.00 0.00 4.70
515 538 1.201429 AGAAGGATGAACACCGGCCT 61.201 55.000 0.00 0.00 0.00 5.19
516 539 0.322546 AAGAAGGATGAACACCGGCC 60.323 55.000 0.00 0.00 0.00 6.13
517 540 1.087501 GAAGAAGGATGAACACCGGC 58.912 55.000 0.00 0.00 0.00 6.13
518 541 2.234908 AGAGAAGAAGGATGAACACCGG 59.765 50.000 0.00 0.00 0.00 5.28
519 542 3.601443 AGAGAAGAAGGATGAACACCG 57.399 47.619 0.00 0.00 0.00 4.94
520 543 7.745620 TTTTTAGAGAAGAAGGATGAACACC 57.254 36.000 0.00 0.00 0.00 4.16
587 610 6.502136 AAAAGTGTTGGAGCTAGAAATAGC 57.498 37.500 0.00 0.00 43.12 2.97
598 621 6.780706 ACTCGTTACATAAAAGTGTTGGAG 57.219 37.500 0.00 0.00 33.62 3.86
617 640 0.459063 GGCCGGGTTTACTGTACTCG 60.459 60.000 2.18 0.00 39.16 4.18
627 651 3.230990 GCTGTTTGGGCCGGGTTT 61.231 61.111 2.18 0.00 0.00 3.27
670 694 0.519077 CGAACTTGCAAGGCTCCTTC 59.481 55.000 29.18 20.65 33.42 3.46
671 695 0.179018 ACGAACTTGCAAGGCTCCTT 60.179 50.000 29.18 14.60 36.60 3.36
730 754 1.982958 GCCCGGAGATATTTTAGGGGA 59.017 52.381 0.73 0.00 39.24 4.81
807 831 0.664166 TTTACGTGTTCCCGTCGAGC 60.664 55.000 0.00 0.00 42.00 5.03
898 1333 2.503765 GAGAGGAAGAAGAAAGGGGGAG 59.496 54.545 0.00 0.00 0.00 4.30
899 1334 2.552367 GAGAGGAAGAAGAAAGGGGGA 58.448 52.381 0.00 0.00 0.00 4.81
976 1421 2.009424 CTCCTCCTGCTGCGATTCGA 62.009 60.000 10.88 0.00 0.00 3.71
1792 2254 2.253610 TGGACTCATAACCACGGACTT 58.746 47.619 0.00 0.00 0.00 3.01
1793 2255 1.933021 TGGACTCATAACCACGGACT 58.067 50.000 0.00 0.00 0.00 3.85
1799 2261 2.565391 ACACGACATGGACTCATAACCA 59.435 45.455 0.00 0.00 40.57 3.67
1805 2267 1.067846 GCTGTACACGACATGGACTCA 60.068 52.381 0.00 0.00 43.47 3.41
1824 2286 4.157849 AGGAGGTAATAAGGCTTCTTGC 57.842 45.455 1.30 3.72 41.94 4.01
1881 2345 1.449601 CCCGGGGTTCAGAACGATG 60.450 63.158 14.71 0.00 0.00 3.84
1882 2346 1.196104 TTCCCGGGGTTCAGAACGAT 61.196 55.000 23.50 0.00 0.00 3.73
1921 2391 5.878406 AACCCTATCTGAAGATTCGATGT 57.122 39.130 0.00 0.00 36.05 3.06
2067 2537 4.779993 AGGCCCTTGAGAAAGTAATAGG 57.220 45.455 0.00 0.00 0.00 2.57
2072 2542 5.250774 AGTTATGAAGGCCCTTGAGAAAGTA 59.749 40.000 0.00 0.00 0.00 2.24
2377 2847 2.358615 AGCATCTGCGGTGCGAAA 60.359 55.556 12.44 0.00 46.86 3.46
2403 2873 2.756042 TTGGGATCATCGGCAGGGG 61.756 63.158 0.00 0.00 0.00 4.79
2444 2917 2.371259 GGAAGCCACCTCCTCCTCC 61.371 68.421 0.00 0.00 0.00 4.30
2445 2918 2.371259 GGGAAGCCACCTCCTCCTC 61.371 68.421 0.00 0.00 0.00 3.71
2446 2919 2.285743 GGGAAGCCACCTCCTCCT 60.286 66.667 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.