Multiple sequence alignment - TraesCS2B01G540300

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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 TraesCS2B01G540300 chr2B 100.000 2951 0 0 1 2951 736758288 736755338 0.000000e+00 5450.0
1 TraesCS2B01G540300 chr2B 89.474 76 7 1 5 80 39872646 39872720 8.710000e-16 95.3
2 TraesCS2B01G540300 chr2D 93.401 2576 98 28 405 2951 605911022 605908490 0.000000e+00 3749.0
3 TraesCS2B01G540300 chr2D 88.053 226 18 5 85 301 605911364 605911139 2.920000e-65 259.0
4 TraesCS2B01G540300 chr2A 93.452 1909 88 20 997 2892 737341792 737339908 0.000000e+00 2798.0
5 TraesCS2B01G540300 chr2A 91.667 444 21 9 495 928 737342264 737341827 4.210000e-168 601.0
6 TraesCS2B01G540300 chr2A 95.946 74 3 0 2878 2951 737339894 737339821 1.440000e-23 121.0
7 TraesCS2B01G540300 chr2A 88.506 87 9 1 1 86 600518580 600518666 1.450000e-18 104.0
8 TraesCS2B01G540300 chr7B 88.235 85 9 1 1 84 138467344 138467428 1.870000e-17 100.0
9 TraesCS2B01G540300 chr7A 85.556 90 12 1 1 89 516839482 516839571 3.130000e-15 93.5
10 TraesCS2B01G540300 chr5A 87.952 83 5 4 5 84 649254878 649254798 3.130000e-15 93.5
11 TraesCS2B01G540300 chr3D 85.393 89 13 0 1 89 378044689 378044601 3.130000e-15 93.5
12 TraesCS2B01G540300 chr7D 96.296 54 2 0 1349 1402 579339586 579339533 4.050000e-14 89.8
13 TraesCS2B01G540300 chr4D 85.227 88 12 1 1 87 125073280 125073193 4.050000e-14 89.8
14 TraesCS2B01G540300 chr5D 85.714 84 10 1 1 82 472403360 472403277 1.460000e-13 87.9
15 TraesCS2B01G540300 chr3A 86.420 81 10 1 5 84 489637649 489637569 1.460000e-13 87.9


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 TraesCS2B01G540300 chr2B 736755338 736758288 2950 True 5450.000000 5450 100.000000 1 2951 1 chr2B.!!$R1 2950
1 TraesCS2B01G540300 chr2D 605908490 605911364 2874 True 2004.000000 3749 90.727000 85 2951 2 chr2D.!!$R1 2866
2 TraesCS2B01G540300 chr2A 737339821 737342264 2443 True 1173.333333 2798 93.688333 495 2951 3 chr2A.!!$R1 2456

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
403 420 0.095245 CGCTTGTAGGAATGTGCGTG 59.905 55.000 0.0 0.0 38.81 5.34 F
535 612 1.065636 CAGACCATGATGACACCAGCT 60.066 52.381 0.0 0.0 0.00 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1557 1638 0.108424 CGGAGAAGAGCAGGTTCTGG 60.108 60.0 0.40 0.0 34.3 3.86 R
2423 2524 0.029567 CCCGATGACAGCGACTCTAC 59.970 60.0 15.87 0.0 0.0 2.59 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
24 25 7.519347 TGGGGAGAAAAGTAAATATAGGTGT 57.481 36.000 0.00 0.00 0.00 4.16
25 26 7.571025 TGGGGAGAAAAGTAAATATAGGTGTC 58.429 38.462 0.00 0.00 0.00 3.67
26 27 7.404980 TGGGGAGAAAAGTAAATATAGGTGTCT 59.595 37.037 0.00 0.00 0.00 3.41
27 28 7.932491 GGGGAGAAAAGTAAATATAGGTGTCTC 59.068 40.741 0.00 0.00 0.00 3.36
28 29 8.483758 GGGAGAAAAGTAAATATAGGTGTCTCA 58.516 37.037 0.00 0.00 31.49 3.27
29 30 9.886132 GGAGAAAAGTAAATATAGGTGTCTCAA 57.114 33.333 0.00 0.00 31.49 3.02
65 66 4.558226 TGGGACATCTGTATCCATATGC 57.442 45.455 0.00 0.00 36.65 3.14
66 67 4.170449 TGGGACATCTGTATCCATATGCT 58.830 43.478 0.00 0.00 36.65 3.79
67 68 5.341169 TGGGACATCTGTATCCATATGCTA 58.659 41.667 0.00 0.00 36.65 3.49
68 69 5.187772 TGGGACATCTGTATCCATATGCTAC 59.812 44.000 0.00 2.27 36.65 3.58
69 70 5.395768 GGGACATCTGTATCCATATGCTACC 60.396 48.000 0.00 0.00 36.65 3.18
70 71 5.187772 GGACATCTGTATCCATATGCTACCA 59.812 44.000 0.00 0.00 34.87 3.25
71 72 6.126940 GGACATCTGTATCCATATGCTACCAT 60.127 42.308 0.00 0.00 34.87 3.55
72 73 7.262990 ACATCTGTATCCATATGCTACCATT 57.737 36.000 0.00 0.00 30.42 3.16
73 74 7.108194 ACATCTGTATCCATATGCTACCATTG 58.892 38.462 0.00 2.51 30.42 2.82
74 75 6.686484 TCTGTATCCATATGCTACCATTGT 57.314 37.500 0.00 0.00 32.85 2.71
75 76 7.790782 TCTGTATCCATATGCTACCATTGTA 57.209 36.000 0.00 0.00 32.85 2.41
76 77 7.611770 TCTGTATCCATATGCTACCATTGTAC 58.388 38.462 0.00 0.00 32.85 2.90
77 78 7.234577 TCTGTATCCATATGCTACCATTGTACA 59.765 37.037 0.00 0.00 32.85 2.90
78 79 7.917003 TGTATCCATATGCTACCATTGTACAT 58.083 34.615 0.00 0.00 32.85 2.29
79 80 7.823799 TGTATCCATATGCTACCATTGTACATG 59.176 37.037 0.00 0.00 32.85 3.21
80 81 5.003160 TCCATATGCTACCATTGTACATGC 58.997 41.667 0.00 0.00 32.85 4.06
81 82 4.156556 CCATATGCTACCATTGTACATGCC 59.843 45.833 0.00 0.00 32.85 4.40
82 83 2.051334 TGCTACCATTGTACATGCCC 57.949 50.000 0.00 0.00 0.00 5.36
83 84 1.563879 TGCTACCATTGTACATGCCCT 59.436 47.619 0.00 0.00 0.00 5.19
105 106 2.191128 AAGAGCACATCAACAGGGTC 57.809 50.000 0.00 0.00 0.00 4.46
136 137 6.153340 CACTCCAATCCTAACAAATCAACCAT 59.847 38.462 0.00 0.00 0.00 3.55
181 182 4.771577 TGCCATCATGTGTTAACTCCAATT 59.228 37.500 7.22 0.00 0.00 2.32
209 210 2.203294 AAACTTTGTCGGCCCGCT 60.203 55.556 0.00 0.00 0.00 5.52
225 235 2.092882 GCTACGGGTCAAGTCGCAC 61.093 63.158 0.00 0.00 31.65 5.34
226 236 1.585006 CTACGGGTCAAGTCGCACT 59.415 57.895 0.00 0.00 0.00 4.40
233 243 1.137513 GTCAAGTCGCACTGGTGTAC 58.862 55.000 2.64 2.22 0.00 2.90
245 255 2.159014 ACTGGTGTACGCACTTTTCTGA 60.159 45.455 8.97 0.00 44.65 3.27
246 256 2.869801 CTGGTGTACGCACTTTTCTGAA 59.130 45.455 8.97 0.00 44.65 3.02
252 262 6.128391 GGTGTACGCACTTTTCTGAATTGATA 60.128 38.462 8.97 0.00 44.65 2.15
254 264 7.962918 GTGTACGCACTTTTCTGAATTGATATT 59.037 33.333 0.39 0.00 42.13 1.28
257 267 6.150976 ACGCACTTTTCTGAATTGATATTGGA 59.849 34.615 0.00 0.00 0.00 3.53
265 275 7.880160 TCTGAATTGATATTGGATTTTCGGT 57.120 32.000 0.00 0.00 0.00 4.69
272 282 7.403312 TGATATTGGATTTTCGGTGATGTTT 57.597 32.000 0.00 0.00 0.00 2.83
274 284 3.296322 TGGATTTTCGGTGATGTTTGC 57.704 42.857 0.00 0.00 0.00 3.68
298 308 6.677781 TCAATGAGAGAAGACGTTTTTGTT 57.322 33.333 0.00 0.00 0.00 2.83
301 311 8.335356 TCAATGAGAGAAGACGTTTTTGTTAAG 58.665 33.333 0.00 0.00 0.00 1.85
307 324 4.888038 AGACGTTTTTGTTAAGTCACCC 57.112 40.909 0.00 0.00 34.56 4.61
310 327 4.187694 ACGTTTTTGTTAAGTCACCCGTA 58.812 39.130 0.00 0.00 0.00 4.02
313 330 5.847515 CGTTTTTGTTAAGTCACCCGTATTC 59.152 40.000 0.00 0.00 0.00 1.75
323 340 3.680937 GTCACCCGTATTCATTTCGTCAA 59.319 43.478 0.00 0.00 0.00 3.18
324 341 4.331717 GTCACCCGTATTCATTTCGTCAAT 59.668 41.667 0.00 0.00 0.00 2.57
325 342 4.569162 TCACCCGTATTCATTTCGTCAATC 59.431 41.667 0.00 0.00 0.00 2.67
326 343 4.570772 CACCCGTATTCATTTCGTCAATCT 59.429 41.667 0.00 0.00 0.00 2.40
327 344 4.809426 ACCCGTATTCATTTCGTCAATCTC 59.191 41.667 0.00 0.00 0.00 2.75
328 345 4.808895 CCCGTATTCATTTCGTCAATCTCA 59.191 41.667 0.00 0.00 0.00 3.27
329 346 5.293324 CCCGTATTCATTTCGTCAATCTCAA 59.707 40.000 0.00 0.00 0.00 3.02
330 347 6.017934 CCCGTATTCATTTCGTCAATCTCAAT 60.018 38.462 0.00 0.00 0.00 2.57
331 348 7.170828 CCCGTATTCATTTCGTCAATCTCAATA 59.829 37.037 0.00 0.00 0.00 1.90
332 349 8.712363 CCGTATTCATTTCGTCAATCTCAATAT 58.288 33.333 0.00 0.00 0.00 1.28
333 350 9.521179 CGTATTCATTTCGTCAATCTCAATATG 57.479 33.333 0.00 0.00 0.00 1.78
338 355 9.558648 TCATTTCGTCAATCTCAATATGTTTTG 57.441 29.630 0.00 0.00 0.00 2.44
339 356 7.795431 TTTCGTCAATCTCAATATGTTTTGC 57.205 32.000 0.00 0.00 0.00 3.68
340 357 6.741992 TCGTCAATCTCAATATGTTTTGCT 57.258 33.333 0.00 0.00 0.00 3.91
341 358 6.545508 TCGTCAATCTCAATATGTTTTGCTG 58.454 36.000 0.00 0.00 0.00 4.41
342 359 6.371271 TCGTCAATCTCAATATGTTTTGCTGA 59.629 34.615 0.00 0.00 0.00 4.26
343 360 7.066163 TCGTCAATCTCAATATGTTTTGCTGAT 59.934 33.333 0.00 0.00 0.00 2.90
344 361 7.699391 CGTCAATCTCAATATGTTTTGCTGATT 59.301 33.333 0.00 0.00 33.75 2.57
345 362 9.017669 GTCAATCTCAATATGTTTTGCTGATTC 57.982 33.333 0.00 0.00 32.51 2.52
346 363 8.963725 TCAATCTCAATATGTTTTGCTGATTCT 58.036 29.630 0.00 0.00 32.51 2.40
347 364 9.234384 CAATCTCAATATGTTTTGCTGATTCTC 57.766 33.333 0.00 0.00 32.51 2.87
348 365 8.749026 ATCTCAATATGTTTTGCTGATTCTCT 57.251 30.769 0.00 0.00 0.00 3.10
349 366 8.571461 TCTCAATATGTTTTGCTGATTCTCTT 57.429 30.769 0.00 0.00 0.00 2.85
350 367 8.671921 TCTCAATATGTTTTGCTGATTCTCTTC 58.328 33.333 0.00 0.00 0.00 2.87
351 368 8.571461 TCAATATGTTTTGCTGATTCTCTTCT 57.429 30.769 0.00 0.00 0.00 2.85
352 369 9.017509 TCAATATGTTTTGCTGATTCTCTTCTT 57.982 29.630 0.00 0.00 0.00 2.52
353 370 9.635520 CAATATGTTTTGCTGATTCTCTTCTTT 57.364 29.630 0.00 0.00 0.00 2.52
357 374 9.688592 ATGTTTTGCTGATTCTCTTCTTTAAAG 57.311 29.630 9.04 9.04 0.00 1.85
358 375 8.137437 TGTTTTGCTGATTCTCTTCTTTAAAGG 58.863 33.333 15.13 0.40 0.00 3.11
359 376 7.823745 TTTGCTGATTCTCTTCTTTAAAGGT 57.176 32.000 15.13 0.00 0.00 3.50
360 377 6.808008 TGCTGATTCTCTTCTTTAAAGGTG 57.192 37.500 15.13 8.40 0.00 4.00
361 378 5.182001 TGCTGATTCTCTTCTTTAAAGGTGC 59.818 40.000 15.13 5.86 0.00 5.01
362 379 5.414144 GCTGATTCTCTTCTTTAAAGGTGCT 59.586 40.000 15.13 0.00 0.00 4.40
363 380 6.403092 GCTGATTCTCTTCTTTAAAGGTGCTC 60.403 42.308 15.13 4.73 0.00 4.26
364 381 6.533730 TGATTCTCTTCTTTAAAGGTGCTCA 58.466 36.000 15.13 6.91 0.00 4.26
365 382 6.998074 TGATTCTCTTCTTTAAAGGTGCTCAA 59.002 34.615 15.13 0.47 0.00 3.02
366 383 7.502226 TGATTCTCTTCTTTAAAGGTGCTCAAA 59.498 33.333 15.13 0.00 0.00 2.69
367 384 6.867662 TCTCTTCTTTAAAGGTGCTCAAAG 57.132 37.500 15.13 9.28 0.00 2.77
368 385 5.765182 TCTCTTCTTTAAAGGTGCTCAAAGG 59.235 40.000 15.13 4.69 0.00 3.11
369 386 4.827284 TCTTCTTTAAAGGTGCTCAAAGGG 59.173 41.667 15.13 0.00 0.00 3.95
370 387 4.447138 TCTTTAAAGGTGCTCAAAGGGA 57.553 40.909 15.13 0.00 0.00 4.20
371 388 4.142038 TCTTTAAAGGTGCTCAAAGGGAC 58.858 43.478 15.13 0.00 0.00 4.46
397 414 1.060937 GCGTGCGCTTGTAGGAATG 59.939 57.895 9.73 0.00 38.26 2.67
398 415 1.635663 GCGTGCGCTTGTAGGAATGT 61.636 55.000 9.73 0.00 38.26 2.71
400 417 0.179189 GTGCGCTTGTAGGAATGTGC 60.179 55.000 9.73 0.00 36.59 4.57
403 420 0.095245 CGCTTGTAGGAATGTGCGTG 59.905 55.000 0.00 0.00 38.81 5.34
410 481 2.173382 GAATGTGCGTGCGTCACC 59.827 61.111 13.35 0.00 33.71 4.02
422 493 2.031157 GTGCGTCACCTAAAATGCAACT 60.031 45.455 0.00 0.00 39.00 3.16
432 503 7.450014 TCACCTAAAATGCAACTCCTCAATTTA 59.550 33.333 0.00 0.00 0.00 1.40
433 504 8.087750 CACCTAAAATGCAACTCCTCAATTTAA 58.912 33.333 0.00 0.00 0.00 1.52
434 505 8.815912 ACCTAAAATGCAACTCCTCAATTTAAT 58.184 29.630 0.00 0.00 0.00 1.40
435 506 9.305925 CCTAAAATGCAACTCCTCAATTTAATC 57.694 33.333 0.00 0.00 0.00 1.75
436 507 9.859427 CTAAAATGCAACTCCTCAATTTAATCA 57.141 29.630 0.00 0.00 0.00 2.57
448 519 9.904198 TCCTCAATTTAATCACAATGTCAGATA 57.096 29.630 0.00 0.00 0.00 1.98
485 556 5.824429 AGTTTCATTCATTCACACACACAG 58.176 37.500 0.00 0.00 0.00 3.66
486 557 5.589855 AGTTTCATTCATTCACACACACAGA 59.410 36.000 0.00 0.00 0.00 3.41
487 558 5.678132 TTCATTCATTCACACACACAGAG 57.322 39.130 0.00 0.00 0.00 3.35
488 559 4.067192 TCATTCATTCACACACACAGAGG 58.933 43.478 0.00 0.00 0.00 3.69
489 560 1.882912 TCATTCACACACACAGAGGC 58.117 50.000 0.00 0.00 0.00 4.70
490 561 1.140652 TCATTCACACACACAGAGGCA 59.859 47.619 0.00 0.00 0.00 4.75
491 562 1.534163 CATTCACACACACAGAGGCAG 59.466 52.381 0.00 0.00 0.00 4.85
514 585 2.701780 CGTCCTCCTCTGACACCCG 61.702 68.421 0.00 0.00 32.91 5.28
517 594 2.575993 CTCCTCTGACACCCGCAG 59.424 66.667 0.00 0.00 34.71 5.18
535 612 1.065636 CAGACCATGATGACACCAGCT 60.066 52.381 0.00 0.00 0.00 4.24
536 613 1.632409 AGACCATGATGACACCAGCTT 59.368 47.619 0.00 0.00 0.00 3.74
537 614 2.040813 AGACCATGATGACACCAGCTTT 59.959 45.455 0.00 0.00 0.00 3.51
549 627 1.130613 CAGCTTTGAGCACGTACGC 59.869 57.895 16.72 0.00 45.56 4.42
810 891 1.281925 TTCCTCCCCCAATCTGAGCC 61.282 60.000 0.00 0.00 0.00 4.70
837 918 4.400109 TGCGTCGACCGAGCAGTC 62.400 66.667 10.58 0.00 39.56 3.51
881 962 1.662686 CTGACCTTTCCCCTCTCCTT 58.337 55.000 0.00 0.00 0.00 3.36
1128 1209 1.746220 CTCACCTTCCTCTACACCTCG 59.254 57.143 0.00 0.00 0.00 4.63
1792 1873 1.821061 CTTCGAGGTGGAGCAGGTGT 61.821 60.000 0.00 0.00 0.00 4.16
1935 2016 4.388499 GCCACGCCCGAGGAGAAA 62.388 66.667 8.32 0.00 0.00 2.52
2120 2204 4.142881 GCTCCTTCGATCAAAAGTGTAACC 60.143 45.833 0.00 0.00 37.80 2.85
2132 2216 6.429692 TCAAAAGTGTAACCATCAATCGTGAT 59.570 34.615 0.00 0.00 45.80 3.06
2337 2437 3.005554 GTGGGATCATATTCATCTGCCG 58.994 50.000 0.00 0.00 0.00 5.69
2343 2443 2.888414 TCATATTCATCTGCCGGTCGTA 59.112 45.455 1.90 0.00 0.00 3.43
2364 2465 8.621286 GTCGTAATTTTGGTCATTAATGAGGAT 58.379 33.333 18.47 5.90 37.51 3.24
2412 2513 1.202582 CAAGAAGTGTCTCGGATCGGT 59.797 52.381 0.00 0.00 30.70 4.69
2419 2520 1.088340 GTCTCGGATCGGTCGTCAGA 61.088 60.000 0.00 0.00 0.00 3.27
2423 2524 0.040870 CGGATCGGTCGTCAGATCAG 60.041 60.000 20.04 14.29 43.54 2.90
2425 2526 2.219458 GGATCGGTCGTCAGATCAGTA 58.781 52.381 20.04 0.00 43.54 2.74
2578 2693 0.034756 ATGTGCAGTCTACGTGGCAA 59.965 50.000 0.00 0.00 38.10 4.52
2581 2696 0.673333 TGCAGTCTACGTGGCAATGG 60.673 55.000 0.00 0.00 32.54 3.16
2585 2700 1.555075 AGTCTACGTGGCAATGGTCAT 59.445 47.619 0.00 0.00 0.00 3.06
2638 2754 6.728089 ACATGTGTGATCTCTGATACTCAT 57.272 37.500 0.00 0.00 0.00 2.90
2639 2755 6.747125 ACATGTGTGATCTCTGATACTCATC 58.253 40.000 0.00 0.00 0.00 2.92
2640 2756 6.323225 ACATGTGTGATCTCTGATACTCATCA 59.677 38.462 0.00 0.00 38.90 3.07
2646 2762 8.162746 TGTGATCTCTGATACTCATCACTAGAT 58.837 37.037 10.74 7.15 39.41 1.98
2647 2763 9.665719 GTGATCTCTGATACTCATCACTAGATA 57.334 37.037 0.00 0.00 38.13 1.98
2657 2773 9.771534 ATACTCATCACTAGATAAAAGGAAAGC 57.228 33.333 0.00 0.00 31.88 3.51
2658 2774 7.624549 ACTCATCACTAGATAAAAGGAAAGCA 58.375 34.615 0.00 0.00 31.88 3.91
2663 2779 9.771534 ATCACTAGATAAAAGGAAAGCAGATAC 57.228 33.333 0.00 0.00 31.14 2.24
2665 2781 9.255304 CACTAGATAAAAGGAAAGCAGATACTC 57.745 37.037 0.00 0.00 0.00 2.59
2666 2782 8.425703 ACTAGATAAAAGGAAAGCAGATACTCC 58.574 37.037 0.00 0.00 0.00 3.85
2667 2783 7.444703 AGATAAAAGGAAAGCAGATACTCCT 57.555 36.000 0.00 0.00 40.10 3.69
2670 2786 5.360649 AAAGGAAAGCAGATACTCCTACC 57.639 43.478 0.00 0.00 37.31 3.18
2672 2788 2.036089 GGAAAGCAGATACTCCTACCGG 59.964 54.545 0.00 0.00 0.00 5.28
2674 2790 0.851469 AGCAGATACTCCTACCGGGA 59.149 55.000 6.32 0.00 42.77 5.14
2675 2791 0.960286 GCAGATACTCCTACCGGGAC 59.040 60.000 6.32 0.00 39.58 4.46
2677 2793 2.877866 CAGATACTCCTACCGGGACAT 58.122 52.381 6.32 0.00 39.58 3.06
2678 2794 2.820787 CAGATACTCCTACCGGGACATC 59.179 54.545 6.32 0.00 39.58 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.404980 AGACACCTATATTTACTTTTCTCCCCA 59.595 37.037 0.00 0.00 0.00 4.96
1 2 7.803131 AGACACCTATATTTACTTTTCTCCCC 58.197 38.462 0.00 0.00 0.00 4.81
2 3 8.483758 TGAGACACCTATATTTACTTTTCTCCC 58.516 37.037 0.00 0.00 0.00 4.30
3 4 9.886132 TTGAGACACCTATATTTACTTTTCTCC 57.114 33.333 0.00 0.00 0.00 3.71
35 36 7.581814 TGGATACAGATGTCCCATGATAAAAA 58.418 34.615 0.00 0.00 46.17 1.94
36 37 7.147958 TGGATACAGATGTCCCATGATAAAA 57.852 36.000 0.00 0.00 46.17 1.52
37 38 6.762077 TGGATACAGATGTCCCATGATAAA 57.238 37.500 0.00 0.00 46.17 1.40
54 55 7.201644 GCATGTACAATGGTAGCATATGGATAC 60.202 40.741 8.04 7.27 37.65 2.24
55 56 6.823182 GCATGTACAATGGTAGCATATGGATA 59.177 38.462 8.04 4.80 0.00 2.59
56 57 5.649395 GCATGTACAATGGTAGCATATGGAT 59.351 40.000 8.04 0.00 0.00 3.41
57 58 5.003160 GCATGTACAATGGTAGCATATGGA 58.997 41.667 8.04 3.13 0.00 3.41
58 59 4.156556 GGCATGTACAATGGTAGCATATGG 59.843 45.833 8.04 3.90 0.00 2.74
59 60 4.156556 GGGCATGTACAATGGTAGCATATG 59.843 45.833 8.04 8.82 0.00 1.78
60 61 4.043310 AGGGCATGTACAATGGTAGCATAT 59.957 41.667 8.04 2.39 0.00 1.78
61 62 3.394274 AGGGCATGTACAATGGTAGCATA 59.606 43.478 8.04 0.00 0.00 3.14
62 63 2.175499 AGGGCATGTACAATGGTAGCAT 59.825 45.455 0.00 0.40 0.00 3.79
63 64 1.563879 AGGGCATGTACAATGGTAGCA 59.436 47.619 0.00 0.00 0.00 3.49
64 65 2.348411 AGGGCATGTACAATGGTAGC 57.652 50.000 0.00 0.00 0.00 3.58
65 66 6.119536 TCTTTTAGGGCATGTACAATGGTAG 58.880 40.000 0.00 0.00 0.00 3.18
66 67 6.068461 TCTTTTAGGGCATGTACAATGGTA 57.932 37.500 0.00 0.00 0.00 3.25
67 68 4.929479 TCTTTTAGGGCATGTACAATGGT 58.071 39.130 0.00 0.00 0.00 3.55
68 69 4.202050 GCTCTTTTAGGGCATGTACAATGG 60.202 45.833 0.00 0.00 0.00 3.16
69 70 4.398988 TGCTCTTTTAGGGCATGTACAATG 59.601 41.667 0.00 0.12 0.00 2.82
70 71 4.399303 GTGCTCTTTTAGGGCATGTACAAT 59.601 41.667 4.33 0.00 38.27 2.71
71 72 3.756434 GTGCTCTTTTAGGGCATGTACAA 59.244 43.478 4.33 0.00 38.27 2.41
72 73 3.244735 TGTGCTCTTTTAGGGCATGTACA 60.245 43.478 4.33 0.00 38.27 2.90
73 74 3.343617 TGTGCTCTTTTAGGGCATGTAC 58.656 45.455 4.33 0.00 38.27 2.90
74 75 3.712016 TGTGCTCTTTTAGGGCATGTA 57.288 42.857 4.33 0.00 38.27 2.29
75 76 2.584835 TGTGCTCTTTTAGGGCATGT 57.415 45.000 4.33 0.00 38.27 3.21
76 77 3.018856 TGATGTGCTCTTTTAGGGCATG 58.981 45.455 4.33 0.00 38.27 4.06
77 78 3.370840 TGATGTGCTCTTTTAGGGCAT 57.629 42.857 4.33 0.00 38.27 4.40
78 79 2.819608 GTTGATGTGCTCTTTTAGGGCA 59.180 45.455 0.00 0.00 0.00 5.36
79 80 2.819608 TGTTGATGTGCTCTTTTAGGGC 59.180 45.455 0.00 0.00 0.00 5.19
80 81 3.441572 CCTGTTGATGTGCTCTTTTAGGG 59.558 47.826 0.00 0.00 0.00 3.53
81 82 3.441572 CCCTGTTGATGTGCTCTTTTAGG 59.558 47.826 0.00 0.00 0.00 2.69
82 83 4.074970 ACCCTGTTGATGTGCTCTTTTAG 58.925 43.478 0.00 0.00 0.00 1.85
83 84 4.072131 GACCCTGTTGATGTGCTCTTTTA 58.928 43.478 0.00 0.00 0.00 1.52
105 106 3.270027 TGTTAGGATTGGAGTGCAATCG 58.730 45.455 25.38 0.00 39.30 3.34
136 137 6.594937 GGCAAAATTGGAATGCTTATTTCTCA 59.405 34.615 0.00 0.00 39.94 3.27
181 182 4.553156 GCCGACAAAGTTTCGATGTTGTAA 60.553 41.667 0.00 0.00 38.85 2.41
209 210 1.287815 CAGTGCGACTTGACCCGTA 59.712 57.895 0.00 0.00 0.00 4.02
233 243 6.554419 TCCAATATCAATTCAGAAAAGTGCG 58.446 36.000 0.00 0.00 0.00 5.34
245 255 8.010733 ACATCACCGAAAATCCAATATCAATT 57.989 30.769 0.00 0.00 0.00 2.32
246 256 7.587037 ACATCACCGAAAATCCAATATCAAT 57.413 32.000 0.00 0.00 0.00 2.57
252 262 4.021192 AGCAAACATCACCGAAAATCCAAT 60.021 37.500 0.00 0.00 0.00 3.16
254 264 2.890311 AGCAAACATCACCGAAAATCCA 59.110 40.909 0.00 0.00 0.00 3.41
257 267 4.582701 TTGAGCAAACATCACCGAAAAT 57.417 36.364 0.00 0.00 0.00 1.82
262 272 2.743664 TCTCATTGAGCAAACATCACCG 59.256 45.455 8.89 0.00 0.00 4.94
265 275 5.410746 GTCTTCTCTCATTGAGCAAACATCA 59.589 40.000 8.89 0.00 42.38 3.07
272 282 3.667497 AACGTCTTCTCTCATTGAGCA 57.333 42.857 8.89 0.00 42.38 4.26
274 284 6.292389 ACAAAAACGTCTTCTCTCATTGAG 57.708 37.500 7.38 7.38 43.96 3.02
287 297 3.063861 ACGGGTGACTTAACAAAAACGTC 59.936 43.478 0.00 0.00 0.00 4.34
293 303 7.513371 AAATGAATACGGGTGACTTAACAAA 57.487 32.000 0.00 0.00 0.00 2.83
298 308 5.075858 ACGAAATGAATACGGGTGACTTA 57.924 39.130 0.00 0.00 0.00 2.24
301 311 3.255725 TGACGAAATGAATACGGGTGAC 58.744 45.455 0.00 0.00 0.00 3.67
307 324 9.521179 CATATTGAGATTGACGAAATGAATACG 57.479 33.333 0.00 0.00 0.00 3.06
313 330 8.316046 GCAAAACATATTGAGATTGACGAAATG 58.684 33.333 0.00 0.00 31.84 2.32
323 340 8.749026 AGAGAATCAGCAAAACATATTGAGAT 57.251 30.769 0.00 0.00 37.82 2.75
324 341 8.571461 AAGAGAATCAGCAAAACATATTGAGA 57.429 30.769 0.00 0.00 37.82 3.27
325 342 8.675504 AGAAGAGAATCAGCAAAACATATTGAG 58.324 33.333 0.00 0.00 37.82 3.02
326 343 8.571461 AGAAGAGAATCAGCAAAACATATTGA 57.429 30.769 0.00 0.00 37.82 2.57
327 344 9.635520 AAAGAAGAGAATCAGCAAAACATATTG 57.364 29.630 0.00 0.00 37.82 1.90
331 348 9.688592 CTTTAAAGAAGAGAATCAGCAAAACAT 57.311 29.630 9.77 0.00 37.82 2.71
332 349 8.137437 CCTTTAAAGAAGAGAATCAGCAAAACA 58.863 33.333 16.98 0.00 37.82 2.83
333 350 8.138074 ACCTTTAAAGAAGAGAATCAGCAAAAC 58.862 33.333 16.98 0.00 37.82 2.43
334 351 8.137437 CACCTTTAAAGAAGAGAATCAGCAAAA 58.863 33.333 16.98 0.00 37.82 2.44
335 352 7.651808 CACCTTTAAAGAAGAGAATCAGCAAA 58.348 34.615 16.98 0.00 37.82 3.68
336 353 6.294176 GCACCTTTAAAGAAGAGAATCAGCAA 60.294 38.462 16.98 0.00 37.82 3.91
337 354 5.182001 GCACCTTTAAAGAAGAGAATCAGCA 59.818 40.000 16.98 0.00 37.82 4.41
338 355 5.414144 AGCACCTTTAAAGAAGAGAATCAGC 59.586 40.000 16.98 5.32 37.82 4.26
339 356 6.652481 TGAGCACCTTTAAAGAAGAGAATCAG 59.348 38.462 16.98 0.00 37.82 2.90
340 357 6.533730 TGAGCACCTTTAAAGAAGAGAATCA 58.466 36.000 16.98 8.16 37.82 2.57
341 358 7.440523 TTGAGCACCTTTAAAGAAGAGAATC 57.559 36.000 16.98 5.93 0.00 2.52
342 359 7.040132 CCTTTGAGCACCTTTAAAGAAGAGAAT 60.040 37.037 16.98 0.00 33.18 2.40
343 360 6.263168 CCTTTGAGCACCTTTAAAGAAGAGAA 59.737 38.462 16.98 0.00 33.18 2.87
344 361 5.765182 CCTTTGAGCACCTTTAAAGAAGAGA 59.235 40.000 16.98 0.00 33.18 3.10
345 362 5.048434 CCCTTTGAGCACCTTTAAAGAAGAG 60.048 44.000 16.98 2.35 33.18 2.85
346 363 4.827284 CCCTTTGAGCACCTTTAAAGAAGA 59.173 41.667 16.98 0.00 33.18 2.87
347 364 4.827284 TCCCTTTGAGCACCTTTAAAGAAG 59.173 41.667 16.98 9.65 33.18 2.85
348 365 4.583073 GTCCCTTTGAGCACCTTTAAAGAA 59.417 41.667 16.98 0.00 33.18 2.52
349 366 4.142038 GTCCCTTTGAGCACCTTTAAAGA 58.858 43.478 16.98 0.00 33.18 2.52
350 367 3.888930 TGTCCCTTTGAGCACCTTTAAAG 59.111 43.478 8.32 8.32 0.00 1.85
351 368 3.888930 CTGTCCCTTTGAGCACCTTTAAA 59.111 43.478 0.00 0.00 0.00 1.52
352 369 3.137544 TCTGTCCCTTTGAGCACCTTTAA 59.862 43.478 0.00 0.00 0.00 1.52
353 370 2.708861 TCTGTCCCTTTGAGCACCTTTA 59.291 45.455 0.00 0.00 0.00 1.85
354 371 1.494721 TCTGTCCCTTTGAGCACCTTT 59.505 47.619 0.00 0.00 0.00 3.11
355 372 1.140312 TCTGTCCCTTTGAGCACCTT 58.860 50.000 0.00 0.00 0.00 3.50
356 373 1.140312 TTCTGTCCCTTTGAGCACCT 58.860 50.000 0.00 0.00 0.00 4.00
357 374 1.815003 CATTCTGTCCCTTTGAGCACC 59.185 52.381 0.00 0.00 0.00 5.01
358 375 2.227388 CACATTCTGTCCCTTTGAGCAC 59.773 50.000 0.00 0.00 0.00 4.40
359 376 2.507484 CACATTCTGTCCCTTTGAGCA 58.493 47.619 0.00 0.00 0.00 4.26
360 377 1.200948 GCACATTCTGTCCCTTTGAGC 59.799 52.381 0.00 0.00 0.00 4.26
361 378 1.466167 CGCACATTCTGTCCCTTTGAG 59.534 52.381 0.00 0.00 0.00 3.02
362 379 1.202758 ACGCACATTCTGTCCCTTTGA 60.203 47.619 0.00 0.00 0.00 2.69
363 380 1.069022 CACGCACATTCTGTCCCTTTG 60.069 52.381 0.00 0.00 0.00 2.77
364 381 1.238439 CACGCACATTCTGTCCCTTT 58.762 50.000 0.00 0.00 0.00 3.11
365 382 1.237285 GCACGCACATTCTGTCCCTT 61.237 55.000 0.00 0.00 0.00 3.95
366 383 1.672356 GCACGCACATTCTGTCCCT 60.672 57.895 0.00 0.00 0.00 4.20
367 384 2.870372 GCACGCACATTCTGTCCC 59.130 61.111 0.00 0.00 0.00 4.46
368 385 2.476051 CGCACGCACATTCTGTCC 59.524 61.111 0.00 0.00 0.00 4.02
369 386 2.175184 AAGCGCACGCACATTCTGTC 62.175 55.000 18.24 0.00 44.88 3.51
370 387 2.253758 AAGCGCACGCACATTCTGT 61.254 52.632 18.24 0.00 44.88 3.41
371 388 1.794785 CAAGCGCACGCACATTCTG 60.795 57.895 18.24 0.89 44.88 3.02
397 414 0.515564 ATTTTAGGTGACGCACGCAC 59.484 50.000 8.45 8.45 34.83 5.34
398 415 0.515127 CATTTTAGGTGACGCACGCA 59.485 50.000 4.33 0.00 34.83 5.24
400 417 0.515127 TGCATTTTAGGTGACGCACG 59.485 50.000 4.33 0.00 34.83 5.34
403 420 2.414161 GGAGTTGCATTTTAGGTGACGC 60.414 50.000 0.00 0.00 0.00 5.19
410 481 9.859427 TGATTAAATTGAGGAGTTGCATTTTAG 57.141 29.630 0.00 0.00 0.00 1.85
422 493 8.812513 ATCTGACATTGTGATTAAATTGAGGA 57.187 30.769 0.00 0.00 0.00 3.71
432 503 6.816136 TCATACGGTATCTGACATTGTGATT 58.184 36.000 0.00 0.00 0.00 2.57
433 504 6.405278 TCATACGGTATCTGACATTGTGAT 57.595 37.500 0.00 0.00 0.00 3.06
434 505 5.845391 TCATACGGTATCTGACATTGTGA 57.155 39.130 0.00 0.00 0.00 3.58
435 506 6.144563 GTCATCATACGGTATCTGACATTGTG 59.855 42.308 23.00 8.31 34.57 3.33
436 507 6.216569 GTCATCATACGGTATCTGACATTGT 58.783 40.000 23.00 0.00 34.57 2.71
448 519 3.861276 TGAAACTCGTCATCATACGGT 57.139 42.857 0.00 0.00 43.05 4.83
485 556 4.863925 GAGGACGCGCTCTGCCTC 62.864 72.222 5.73 15.52 42.08 4.70
488 559 4.863925 GAGGAGGACGCGCTCTGC 62.864 72.222 5.73 9.56 41.47 4.26
489 560 3.137459 AGAGGAGGACGCGCTCTG 61.137 66.667 5.73 0.00 0.00 3.35
490 561 3.137459 CAGAGGAGGACGCGCTCT 61.137 66.667 5.73 6.71 0.00 4.09
491 562 3.134792 TCAGAGGAGGACGCGCTC 61.135 66.667 5.73 5.46 0.00 5.03
514 585 1.376543 CTGGTGTCATCATGGTCTGC 58.623 55.000 0.00 0.00 0.00 4.26
517 594 2.119801 AAGCTGGTGTCATCATGGTC 57.880 50.000 0.00 0.00 0.00 4.02
535 612 1.373748 GAGGGCGTACGTGCTCAAA 60.374 57.895 17.90 0.00 38.00 2.69
536 613 2.260434 GAGGGCGTACGTGCTCAA 59.740 61.111 17.90 0.00 38.00 3.02
537 614 2.825075 TAGGAGGGCGTACGTGCTCA 62.825 60.000 17.90 0.00 38.00 4.26
549 627 1.221021 GTTCGGCCTTGTAGGAGGG 59.779 63.158 0.00 0.00 37.67 4.30
835 916 1.636340 GTGTGTGTGTGTGCTCGAC 59.364 57.895 0.00 0.00 0.00 4.20
836 917 1.876263 CGTGTGTGTGTGTGCTCGA 60.876 57.895 0.00 0.00 0.00 4.04
837 918 1.811217 CTCGTGTGTGTGTGTGCTCG 61.811 60.000 0.00 0.00 0.00 5.03
838 919 1.490693 CCTCGTGTGTGTGTGTGCTC 61.491 60.000 0.00 0.00 0.00 4.26
839 920 1.521457 CCTCGTGTGTGTGTGTGCT 60.521 57.895 0.00 0.00 0.00 4.40
840 921 3.014036 CCTCGTGTGTGTGTGTGC 58.986 61.111 0.00 0.00 0.00 4.57
1068 1149 2.659610 GAGGCGAAGACCAGCAGT 59.340 61.111 0.00 0.00 31.70 4.40
1101 1182 0.968393 AGAGGAAGGTGAGGAGCGTC 60.968 60.000 0.00 0.00 0.00 5.19
1251 1332 2.087009 CGTCGCGTTGGAGAAGGAC 61.087 63.158 5.77 0.00 0.00 3.85
1557 1638 0.108424 CGGAGAAGAGCAGGTTCTGG 60.108 60.000 0.40 0.00 34.30 3.86
1687 1768 2.737376 GGTGGTGAAGACGGACGC 60.737 66.667 0.00 0.00 0.00 5.19
1693 1774 3.041940 CACGGCGGTGGTGAAGAC 61.042 66.667 16.16 0.00 40.58 3.01
1792 1873 1.815408 GCACAGGAACTCCTTGCTCAA 60.815 52.381 18.13 0.00 46.09 3.02
1924 2005 2.436115 GCGGGTTTTCTCCTCGGG 60.436 66.667 0.00 0.00 0.00 5.14
1935 2016 2.104253 CGATTACTTGCGGCGGGTT 61.104 57.895 9.78 0.00 0.00 4.11
2132 2216 1.408702 TCGAGGCGATCAATCATGTCA 59.591 47.619 0.00 0.00 0.00 3.58
2337 2437 7.066525 TCCTCATTAATGACCAAAATTACGACC 59.933 37.037 14.23 0.00 32.50 4.79
2343 2443 6.408434 GGCCATCCTCATTAATGACCAAAATT 60.408 38.462 14.23 0.00 32.50 1.82
2364 2465 2.565391 TCAGATCAAAGTAACGAGGCCA 59.435 45.455 5.01 0.00 0.00 5.36
2412 2513 1.934525 GCGACTCTACTGATCTGACGA 59.065 52.381 6.60 1.69 0.00 4.20
2419 2520 2.289274 CGATGACAGCGACTCTACTGAT 59.711 50.000 7.46 0.00 37.35 2.90
2423 2524 0.029567 CCCGATGACAGCGACTCTAC 59.970 60.000 15.87 0.00 0.00 2.59
2425 2526 3.069980 GCCCGATGACAGCGACTCT 62.070 63.158 15.87 0.00 0.00 3.24
2503 2613 2.588034 GATACGCCCCCAGTTCGC 60.588 66.667 0.00 0.00 0.00 4.70
2581 2696 0.101759 GCATGATGGTGGTGCATGAC 59.898 55.000 0.00 0.00 41.35 3.06
2585 2700 1.679641 CTGGCATGATGGTGGTGCA 60.680 57.895 0.00 0.00 40.53 4.57
2631 2747 9.771534 GCTTTCCTTTTATCTAGTGATGAGTAT 57.228 33.333 0.00 0.00 34.32 2.12
2632 2748 8.758829 TGCTTTCCTTTTATCTAGTGATGAGTA 58.241 33.333 0.00 0.00 34.32 2.59
2633 2749 7.624549 TGCTTTCCTTTTATCTAGTGATGAGT 58.375 34.615 0.00 0.00 34.32 3.41
2634 2750 7.984050 TCTGCTTTCCTTTTATCTAGTGATGAG 59.016 37.037 0.00 0.00 34.32 2.90
2635 2751 7.851228 TCTGCTTTCCTTTTATCTAGTGATGA 58.149 34.615 0.00 0.00 34.32 2.92
2636 2752 8.674263 ATCTGCTTTCCTTTTATCTAGTGATG 57.326 34.615 0.00 0.00 34.32 3.07
2637 2753 9.771534 GTATCTGCTTTCCTTTTATCTAGTGAT 57.228 33.333 0.00 0.00 36.74 3.06
2638 2754 8.982723 AGTATCTGCTTTCCTTTTATCTAGTGA 58.017 33.333 0.00 0.00 0.00 3.41
2639 2755 9.255304 GAGTATCTGCTTTCCTTTTATCTAGTG 57.745 37.037 0.00 0.00 0.00 2.74
2640 2756 8.425703 GGAGTATCTGCTTTCCTTTTATCTAGT 58.574 37.037 0.00 0.00 33.73 2.57
2646 2762 6.406624 CGGTAGGAGTATCTGCTTTCCTTTTA 60.407 42.308 0.00 0.00 40.43 1.52
2647 2763 5.627040 CGGTAGGAGTATCTGCTTTCCTTTT 60.627 44.000 0.00 0.00 40.43 2.27
2651 2767 2.036089 CCGGTAGGAGTATCTGCTTTCC 59.964 54.545 0.00 0.48 41.02 3.13
2656 2772 3.434053 TCCCGGTAGGAGTATCTGC 57.566 57.895 0.00 0.00 40.93 4.26
2665 2781 2.483014 TGTTTTGATGTCCCGGTAGG 57.517 50.000 0.00 0.00 37.24 3.18
2666 2782 5.385509 AAAATGTTTTGATGTCCCGGTAG 57.614 39.130 0.00 0.00 0.00 3.18
2667 2783 5.533482 CAAAAATGTTTTGATGTCCCGGTA 58.467 37.500 0.00 0.00 0.00 4.02
2670 2786 3.186205 GGCAAAAATGTTTTGATGTCCCG 59.814 43.478 15.74 0.00 0.00 5.14
2672 2788 4.133078 TGGGCAAAAATGTTTTGATGTCC 58.867 39.130 15.74 9.98 34.70 4.02
2674 2790 5.192176 AGTTGGGCAAAAATGTTTTGATGT 58.808 33.333 15.74 0.00 0.00 3.06
2675 2791 5.754543 AGTTGGGCAAAAATGTTTTGATG 57.245 34.783 15.74 1.45 0.00 3.07
2677 2793 5.248640 TCAAGTTGGGCAAAAATGTTTTGA 58.751 33.333 15.74 0.00 0.00 2.69
2678 2794 5.557891 TCAAGTTGGGCAAAAATGTTTTG 57.442 34.783 2.34 8.72 0.00 2.44


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

AutoCloner maintained by Alex Coulton.