Multiple sequence alignment - TraesCS6B01G345900

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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 TraesCS6B01G345900 chr6B 100.000 3671 0 0 1 3671 609847409 609843739 0.000000e+00 6780.0
1 TraesCS6B01G345900 chr6D 96.078 2932 80 19 766 3671 405587855 405584933 0.000000e+00 4745.0
2 TraesCS6B01G345900 chr6D 79.863 293 21 17 476 744 405588204 405587926 2.910000e-41 180.0
3 TraesCS6B01G345900 chr6D 95.652 92 3 1 240 330 71561915 71561824 2.950000e-31 147.0
4 TraesCS6B01G345900 chr6A 95.576 2351 68 10 787 3126 551984559 551982234 0.000000e+00 3733.0
5 TraesCS6B01G345900 chr6A 92.572 552 24 6 3123 3658 551982112 551981562 0.000000e+00 776.0
6 TraesCS6B01G345900 chr6A 83.951 243 33 5 4 242 551986687 551986447 1.030000e-55 228.0
7 TraesCS6B01G345900 chr6A 100.000 30 0 0 3641 3670 551981562 551981533 5.120000e-04 56.5
8 TraesCS6B01G345900 chr1A 94.444 108 6 0 235 342 336461512 336461619 2.270000e-37 167.0
9 TraesCS6B01G345900 chr3B 92.857 112 8 0 240 351 651411134 651411245 2.930000e-36 163.0
10 TraesCS6B01G345900 chr4A 96.471 85 3 0 267 351 673967120 673967204 1.370000e-29 141.0
11 TraesCS6B01G345900 chr4A 84.615 78 7 5 3066 3139 588933525 588933601 5.090000e-09 73.1
12 TraesCS6B01G345900 chr4A 95.455 44 2 0 240 283 673967077 673967120 1.830000e-08 71.3
13 TraesCS6B01G345900 chr7A 87.179 117 9 2 241 351 535585632 535585516 1.070000e-25 128.0
14 TraesCS6B01G345900 chr1B 93.846 65 3 1 3088 3151 174109782 174109846 3.020000e-16 97.1
15 TraesCS6B01G345900 chr1B 91.803 61 4 1 3087 3146 654813328 654813388 2.350000e-12 84.2
16 TraesCS6B01G345900 chr3A 91.935 62 3 2 3086 3145 332556231 332556292 6.530000e-13 86.1
17 TraesCS6B01G345900 chr3A 91.803 61 4 1 3087 3146 38604760 38604700 2.350000e-12 84.2
18 TraesCS6B01G345900 chr2D 91.935 62 3 2 3086 3145 427150386 427150447 6.530000e-13 86.1
19 TraesCS6B01G345900 chr3D 90.323 62 4 2 3086 3145 251316073 251316012 3.040000e-11 80.5
20 TraesCS6B01G345900 chr7B 86.154 65 4 4 451 512 425101844 425101906 8.510000e-07 65.8


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 TraesCS6B01G345900 chr6B 609843739 609847409 3670 True 6780.000 6780 100.00000 1 3671 1 chr6B.!!$R1 3670
1 TraesCS6B01G345900 chr6D 405584933 405588204 3271 True 2462.500 4745 87.97050 476 3671 2 chr6D.!!$R2 3195
2 TraesCS6B01G345900 chr6A 551981533 551986687 5154 True 1198.375 3733 93.02475 4 3670 4 chr6A.!!$R1 3666

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
348 352 0.106719 GCCCCAGCCAACAAGCTATA 60.107 55.0 0.00 0.0 42.61 1.31 F
902 2400 0.247736 CCTCTTCTCAGAACCCACCG 59.752 60.0 0.00 0.0 0.00 4.94 F
1758 3256 0.588252 GCGTGAAGAAGAAGCTGCAA 59.412 50.0 1.02 0.0 0.00 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1614 3112 0.108138 GCTTCTTCGCCAGCTTCCTA 60.108 55.000 0.0 0.0 32.87 2.94 R
1846 3344 1.168714 GGGGTGTGCTTCATCTCAAC 58.831 55.000 0.0 0.0 0.00 3.18 R
3620 5269 3.328050 AGACTGGTTTAGCTGGCTACTTT 59.672 43.478 0.0 0.0 0.00 2.66 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
19 20 2.515398 CCGCATAGGCCCATGGAA 59.485 61.111 15.22 0.00 36.38 3.53
20 21 1.601759 CCGCATAGGCCCATGGAAG 60.602 63.158 15.22 0.00 36.38 3.46
21 22 1.601759 CGCATAGGCCCATGGAAGG 60.602 63.158 15.22 0.00 36.38 3.46
57 58 3.541242 TGGGGACAAGAATGGAAATGT 57.459 42.857 0.00 0.00 37.44 2.71
63 65 5.404946 GGACAAGAATGGAAATGTGATGTG 58.595 41.667 0.00 0.00 0.00 3.21
73 75 4.260990 GGAAATGTGATGTGTTGACGACAA 60.261 41.667 0.00 0.00 40.65 3.18
95 97 1.229428 ACATGAAGCAACTCGTGTGG 58.771 50.000 0.00 0.00 42.63 4.17
96 98 0.110056 CATGAAGCAACTCGTGTGGC 60.110 55.000 8.97 8.97 43.31 5.01
97 99 1.237285 ATGAAGCAACTCGTGTGGCC 61.237 55.000 13.21 0.00 44.02 5.36
101 103 2.279851 CAACTCGTGTGGCCGTGA 60.280 61.111 0.00 0.00 0.00 4.35
102 104 1.667830 CAACTCGTGTGGCCGTGAT 60.668 57.895 0.00 0.00 0.00 3.06
108 110 1.502990 CGTGTGGCCGTGATTGTGAA 61.503 55.000 0.00 0.00 0.00 3.18
122 124 6.025280 GTGATTGTGAACACGTTGTAAAACT 58.975 36.000 0.00 0.00 0.00 2.66
133 135 3.489568 CGTTGTAAAACTTGGTTGACCCC 60.490 47.826 0.00 0.00 34.29 4.95
144 146 1.818674 GGTTGACCCCACACATGAATC 59.181 52.381 0.00 0.00 0.00 2.52
171 175 1.286248 AGGAGAACTAAATGGGGCGT 58.714 50.000 0.00 0.00 0.00 5.68
179 183 1.208535 CTAAATGGGGCGTGTAGGACA 59.791 52.381 0.00 0.00 0.00 4.02
180 184 0.623723 AAATGGGGCGTGTAGGACAT 59.376 50.000 0.00 0.00 0.00 3.06
181 185 0.180406 AATGGGGCGTGTAGGACATC 59.820 55.000 0.00 0.00 0.00 3.06
183 187 0.980754 TGGGGCGTGTAGGACATCAT 60.981 55.000 0.00 0.00 0.00 2.45
232 236 6.566141 TGCTAATATAGTTCACGTAAGCACA 58.434 36.000 0.00 0.00 45.62 4.57
236 240 9.244799 CTAATATAGTTCACGTAAGCACATCAA 57.755 33.333 0.00 0.00 45.62 2.57
239 243 9.929180 ATATAGTTCACGTAAGCACATCAATAT 57.071 29.630 0.00 0.00 45.62 1.28
242 246 7.816640 AGTTCACGTAAGCACATCAATATTTT 58.183 30.769 0.00 0.00 45.62 1.82
243 247 8.296713 AGTTCACGTAAGCACATCAATATTTTT 58.703 29.630 0.00 0.00 45.62 1.94
263 267 3.644966 TTTTGCGGAGAATCATAGGGT 57.355 42.857 0.00 0.00 36.25 4.34
266 270 4.764050 TTGCGGAGAATCATAGGGTTTA 57.236 40.909 0.00 0.00 36.25 2.01
267 271 4.974645 TGCGGAGAATCATAGGGTTTAT 57.025 40.909 0.00 0.00 36.25 1.40
268 272 5.304686 TGCGGAGAATCATAGGGTTTATT 57.695 39.130 0.00 0.00 36.25 1.40
269 273 6.428083 TGCGGAGAATCATAGGGTTTATTA 57.572 37.500 0.00 0.00 36.25 0.98
270 274 7.016153 TGCGGAGAATCATAGGGTTTATTAT 57.984 36.000 0.00 0.00 36.25 1.28
271 275 7.458397 TGCGGAGAATCATAGGGTTTATTATT 58.542 34.615 0.00 0.00 36.25 1.40
272 276 7.606456 TGCGGAGAATCATAGGGTTTATTATTC 59.394 37.037 0.00 0.00 36.25 1.75
273 277 7.065923 GCGGAGAATCATAGGGTTTATTATTCC 59.934 40.741 0.00 0.00 36.25 3.01
275 279 9.807921 GGAGAATCATAGGGTTTATTATTCCAA 57.192 33.333 0.00 0.00 36.25 3.53
284 288 8.893563 AGGGTTTATTATTCCAAAATGACAGA 57.106 30.769 0.00 0.00 0.00 3.41
285 289 8.971073 AGGGTTTATTATTCCAAAATGACAGAG 58.029 33.333 0.00 0.00 0.00 3.35
286 290 8.749354 GGGTTTATTATTCCAAAATGACAGAGT 58.251 33.333 0.00 0.00 0.00 3.24
295 299 9.927081 ATTCCAAAATGACAGAGTTATAATCCT 57.073 29.630 0.00 0.00 0.00 3.24
296 300 8.964476 TCCAAAATGACAGAGTTATAATCCTC 57.036 34.615 0.00 0.00 0.00 3.71
297 301 8.548025 TCCAAAATGACAGAGTTATAATCCTCA 58.452 33.333 6.03 2.55 0.00 3.86
298 302 8.834465 CCAAAATGACAGAGTTATAATCCTCAG 58.166 37.037 6.03 1.35 0.00 3.35
300 304 5.188327 TGACAGAGTTATAATCCTCAGCG 57.812 43.478 6.03 0.00 0.00 5.18
301 305 4.887655 TGACAGAGTTATAATCCTCAGCGA 59.112 41.667 6.03 0.00 0.00 4.93
302 306 5.189659 ACAGAGTTATAATCCTCAGCGAC 57.810 43.478 6.03 0.00 0.00 5.19
303 307 4.890581 ACAGAGTTATAATCCTCAGCGACT 59.109 41.667 6.03 0.00 0.00 4.18
304 308 6.062749 ACAGAGTTATAATCCTCAGCGACTA 58.937 40.000 6.03 0.00 0.00 2.59
305 309 6.546403 ACAGAGTTATAATCCTCAGCGACTAA 59.454 38.462 6.03 0.00 0.00 2.24
306 310 7.081349 CAGAGTTATAATCCTCAGCGACTAAG 58.919 42.308 6.03 0.00 0.00 2.18
307 311 6.773685 AGAGTTATAATCCTCAGCGACTAAGT 59.226 38.462 6.03 0.00 0.00 2.24
308 312 6.972722 AGTTATAATCCTCAGCGACTAAGTC 58.027 40.000 0.00 0.00 0.00 3.01
309 313 6.546403 AGTTATAATCCTCAGCGACTAAGTCA 59.454 38.462 0.00 0.00 32.09 3.41
310 314 3.512033 AATCCTCAGCGACTAAGTCAC 57.488 47.619 0.00 0.00 32.09 3.67
311 315 2.201921 TCCTCAGCGACTAAGTCACT 57.798 50.000 0.00 0.00 32.09 3.41
312 316 1.813178 TCCTCAGCGACTAAGTCACTG 59.187 52.381 0.00 0.00 42.10 3.66
313 317 1.813178 CCTCAGCGACTAAGTCACTGA 59.187 52.381 0.00 0.00 45.51 3.41
314 318 2.414824 CCTCAGCGACTAAGTCACTGAC 60.415 54.545 0.00 0.38 43.73 3.51
315 319 2.226674 CTCAGCGACTAAGTCACTGACA 59.773 50.000 11.80 0.00 43.73 3.58
316 320 2.031069 TCAGCGACTAAGTCACTGACAC 60.031 50.000 11.80 0.00 43.73 3.67
317 321 1.954382 AGCGACTAAGTCACTGACACA 59.046 47.619 11.80 0.00 34.60 3.72
318 322 2.361119 AGCGACTAAGTCACTGACACAA 59.639 45.455 11.80 0.00 34.60 3.33
319 323 2.726760 GCGACTAAGTCACTGACACAAG 59.273 50.000 11.80 7.69 34.60 3.16
320 324 3.309388 CGACTAAGTCACTGACACAAGG 58.691 50.000 11.80 0.24 34.60 3.61
321 325 3.004419 CGACTAAGTCACTGACACAAGGA 59.996 47.826 11.80 0.00 34.60 3.36
322 326 4.551388 GACTAAGTCACTGACACAAGGAG 58.449 47.826 11.80 2.22 34.60 3.69
323 327 2.918712 AAGTCACTGACACAAGGAGG 57.081 50.000 11.80 0.00 34.60 4.30
324 328 1.794714 AGTCACTGACACAAGGAGGT 58.205 50.000 11.80 0.00 34.60 3.85
325 329 1.414181 AGTCACTGACACAAGGAGGTG 59.586 52.381 11.80 0.00 44.35 4.00
326 330 0.758734 TCACTGACACAAGGAGGTGG 59.241 55.000 0.00 0.00 43.08 4.61
327 331 0.469917 CACTGACACAAGGAGGTGGT 59.530 55.000 0.00 0.00 43.08 4.16
328 332 1.134098 CACTGACACAAGGAGGTGGTT 60.134 52.381 0.00 0.00 43.08 3.67
329 333 1.134098 ACTGACACAAGGAGGTGGTTG 60.134 52.381 0.00 0.00 43.08 3.77
330 334 0.465460 TGACACAAGGAGGTGGTTGC 60.465 55.000 0.00 0.00 43.08 4.17
331 335 1.152756 ACACAAGGAGGTGGTTGCC 60.153 57.895 0.00 0.00 43.08 4.52
332 336 1.903404 CACAAGGAGGTGGTTGCCC 60.903 63.158 0.00 0.00 35.13 5.36
333 337 2.283173 CAAGGAGGTGGTTGCCCC 60.283 66.667 0.00 0.00 0.00 5.80
334 338 2.780924 AAGGAGGTGGTTGCCCCA 60.781 61.111 0.00 0.00 42.51 4.96
335 339 2.845345 AAGGAGGTGGTTGCCCCAG 61.845 63.158 0.00 0.00 46.45 4.45
340 344 3.615709 GTGGTTGCCCCAGCCAAC 61.616 66.667 2.29 0.00 45.65 3.77
341 345 4.149019 TGGTTGCCCCAGCCAACA 62.149 61.111 6.60 0.00 41.55 3.33
342 346 2.841988 GGTTGCCCCAGCCAACAA 60.842 61.111 6.60 0.00 38.69 2.83
343 347 2.736531 GTTGCCCCAGCCAACAAG 59.263 61.111 0.00 0.00 38.69 3.16
344 348 3.233231 TTGCCCCAGCCAACAAGC 61.233 61.111 0.00 0.00 38.69 4.01
345 349 3.754586 TTGCCCCAGCCAACAAGCT 62.755 57.895 0.00 0.00 46.45 3.74
346 350 2.035626 GCCCCAGCCAACAAGCTA 59.964 61.111 0.00 0.00 42.61 3.32
347 351 1.380380 GCCCCAGCCAACAAGCTAT 60.380 57.895 0.00 0.00 42.61 2.97
348 352 0.106719 GCCCCAGCCAACAAGCTATA 60.107 55.000 0.00 0.00 42.61 1.31
349 353 1.680338 CCCCAGCCAACAAGCTATAC 58.320 55.000 0.00 0.00 42.61 1.47
367 371 2.559998 ACTTGTTTGCGTTGGTTCTG 57.440 45.000 0.00 0.00 0.00 3.02
371 375 1.131504 TGTTTGCGTTGGTTCTGTCAC 59.868 47.619 0.00 0.00 0.00 3.67
374 378 1.745232 TGCGTTGGTTCTGTCACTTT 58.255 45.000 0.00 0.00 0.00 2.66
384 388 6.281405 TGGTTCTGTCACTTTTCTTCTAGAC 58.719 40.000 0.00 0.00 0.00 2.59
385 389 6.098409 TGGTTCTGTCACTTTTCTTCTAGACT 59.902 38.462 0.00 0.00 0.00 3.24
388 392 8.569641 GTTCTGTCACTTTTCTTCTAGACTAGA 58.430 37.037 8.17 8.17 0.00 2.43
389 393 8.871629 TCTGTCACTTTTCTTCTAGACTAGAT 57.128 34.615 12.98 0.00 34.22 1.98
390 394 9.961264 TCTGTCACTTTTCTTCTAGACTAGATA 57.039 33.333 12.98 2.35 34.22 1.98
440 444 9.614792 GTCCATACTTGTTTTGAGGAACTATAT 57.385 33.333 0.00 0.00 41.55 0.86
512 640 9.661563 CCCGTAATTTACCTGCTCATATTAATA 57.338 33.333 0.00 0.00 0.00 0.98
612 781 8.749354 GGTAATAAAAAGTGGATCAATTGAGGT 58.251 33.333 14.54 0.00 0.00 3.85
617 786 3.690460 AGTGGATCAATTGAGGTGGTTC 58.310 45.455 14.54 5.18 0.00 3.62
632 801 5.077564 AGGTGGTTCTTAGGGAAAATTGAC 58.922 41.667 0.00 0.00 35.51 3.18
633 802 4.830600 GGTGGTTCTTAGGGAAAATTGACA 59.169 41.667 0.00 0.00 35.51 3.58
685 867 2.237893 GAGGGAGGGGAAACGTATGAAA 59.762 50.000 0.00 0.00 0.00 2.69
691 873 5.429130 GAGGGGAAACGTATGAAAGAGAAT 58.571 41.667 0.00 0.00 0.00 2.40
702 884 4.188247 TGAAAGAGAATCGGACGACAAT 57.812 40.909 0.00 0.00 42.67 2.71
712 894 6.263842 AGAATCGGACGACAATACCTTACATA 59.736 38.462 0.00 0.00 0.00 2.29
820 2312 6.601613 TGTGTAATGAGTCCATTTCCATTACC 59.398 38.462 16.57 10.95 45.06 2.85
870 2362 2.757077 GCCACAGTGTTAGGCCCT 59.243 61.111 12.58 0.00 42.58 5.19
871 2363 1.675641 GCCACAGTGTTAGGCCCTG 60.676 63.158 12.58 0.86 42.58 4.45
902 2400 0.247736 CCTCTTCTCAGAACCCACCG 59.752 60.000 0.00 0.00 0.00 4.94
956 2454 2.660552 CGCCGTGTCCGTTTCAGT 60.661 61.111 0.00 0.00 0.00 3.41
968 2466 1.204941 CGTTTCAGTCTCCGAATCCCT 59.795 52.381 0.00 0.00 0.00 4.20
1443 2941 4.771356 TACGAGCACGAGCACCGC 62.771 66.667 11.40 0.00 45.49 5.68
1476 2974 0.823769 TGATCGACATCCTCTCCGGG 60.824 60.000 0.00 0.00 0.00 5.73
1614 3112 0.846693 AGAAGCACCTCACCAACCTT 59.153 50.000 0.00 0.00 0.00 3.50
1626 3124 1.026718 CCAACCTTAGGAAGCTGGCG 61.027 60.000 4.77 0.00 0.00 5.69
1695 3193 1.079127 CATCCTCCTGGACGCGTTT 60.079 57.895 15.53 0.00 46.51 3.60
1758 3256 0.588252 GCGTGAAGAAGAAGCTGCAA 59.412 50.000 1.02 0.00 0.00 4.08
1846 3344 1.339055 TGAAGGTGCTCGAGGAAATGG 60.339 52.381 15.58 0.00 0.00 3.16
1962 3460 0.041238 AGTTCATGAGGACCGAGGGA 59.959 55.000 0.00 0.00 0.00 4.20
2073 3571 8.893219 AGCTGATTTCAGATATGATTAAACGA 57.107 30.769 11.70 0.00 46.59 3.85
2223 3721 6.995686 TCACTTACAATTGCTTTCTTGAGGTA 59.004 34.615 5.05 0.00 0.00 3.08
2230 3728 5.751243 TTGCTTTCTTGAGGTACTTTGTC 57.249 39.130 0.00 0.00 41.55 3.18
2460 3958 4.286297 TGATTGTGGAAGAACGGAAGAT 57.714 40.909 0.00 0.00 0.00 2.40
2463 3961 1.071542 TGTGGAAGAACGGAAGATGCA 59.928 47.619 0.00 0.00 0.00 3.96
2935 4438 8.697846 TGTACTCTAATGTGTAGTTGTATTGC 57.302 34.615 0.00 0.00 0.00 3.56
3075 4579 0.467659 ATCTTACTCCCTCCGGTCCG 60.468 60.000 3.60 3.60 0.00 4.79
3096 4600 8.139989 GGTCCGTATTACTTGTGTGTTAGATAT 58.860 37.037 0.00 0.00 0.00 1.63
3256 4891 9.793259 ATGGATCAATATAAACGATAAACCAGT 57.207 29.630 0.00 0.00 0.00 4.00
3407 5042 9.355215 CCTACGTGGCAATAAAGATATACTAAG 57.645 37.037 0.00 0.00 0.00 2.18
3411 5046 9.477484 CGTGGCAATAAAGATATACTAAGACTT 57.523 33.333 0.00 0.00 0.00 3.01
3470 5119 3.655777 ACTCTGGAACCTGGACCAATTTA 59.344 43.478 15.32 4.67 35.67 1.40
3517 5166 6.521151 AAATCCCTTACTTGATTGCTTCTG 57.479 37.500 0.00 0.00 31.79 3.02
3526 5175 9.515020 CTTACTTGATTGCTTCTGTTTTAAACA 57.485 29.630 10.26 10.26 39.52 2.83
3603 5252 7.115805 GGCTTAATGCAAACTTAGTGTAAAACC 59.884 37.037 0.00 0.00 45.15 3.27
3620 5269 9.953697 GTGTAAAACCTATTGTTTGTGTTATGA 57.046 29.630 0.00 0.00 46.39 2.15
3632 5281 4.286297 TGTGTTATGAAAGTAGCCAGCT 57.714 40.909 0.00 0.00 0.00 4.24
3639 5288 3.674997 TGAAAGTAGCCAGCTAAACCAG 58.325 45.455 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.889692 CCATGGGCCTATGCGGGT 61.890 66.667 23.08 0.00 38.85 5.28
1 2 3.132029 TTCCATGGGCCTATGCGGG 62.132 63.158 23.08 10.49 38.85 6.13
3 4 1.601759 CCTTCCATGGGCCTATGCG 60.602 63.158 23.08 15.88 38.85 4.73
4 5 1.905354 GCCTTCCATGGGCCTATGC 60.905 63.158 23.08 8.08 43.49 3.14
5 6 4.507969 GCCTTCCATGGGCCTATG 57.492 61.111 21.68 21.68 43.49 2.23
50 51 3.249799 TGTCGTCAACACATCACATTTCC 59.750 43.478 0.00 0.00 31.20 3.13
52 53 4.891627 TTGTCGTCAACACATCACATTT 57.108 36.364 0.00 0.00 37.70 2.32
73 75 1.229428 CACGAGTTGCTTCATGTGGT 58.771 50.000 0.00 0.00 0.00 4.16
77 79 0.110056 GCCACACGAGTTGCTTCATG 60.110 55.000 1.77 0.00 33.85 3.07
82 84 4.235762 ACGGCCACACGAGTTGCT 62.236 61.111 2.24 0.00 36.68 3.91
101 103 5.802956 CCAAGTTTTACAACGTGTTCACAAT 59.197 36.000 6.88 0.00 39.87 2.71
102 104 5.154932 CCAAGTTTTACAACGTGTTCACAA 58.845 37.500 6.88 0.00 39.87 3.33
108 110 4.379708 GGTCAACCAAGTTTTACAACGTGT 60.380 41.667 6.88 0.00 39.87 4.49
115 117 3.025262 TGTGGGGTCAACCAAGTTTTAC 58.975 45.455 0.89 0.00 43.34 2.01
119 121 0.333312 TGTGTGGGGTCAACCAAGTT 59.667 50.000 0.89 0.00 43.34 2.66
122 124 0.553333 TCATGTGTGGGGTCAACCAA 59.447 50.000 0.89 0.00 43.34 3.67
133 135 9.941664 GTTCTCCTAATTTATGATTCATGTGTG 57.058 33.333 9.46 0.00 0.00 3.82
144 146 7.308589 CGCCCCATTTAGTTCTCCTAATTTATG 60.309 40.741 0.00 0.00 35.59 1.90
164 168 0.980754 ATGATGTCCTACACGCCCCA 60.981 55.000 0.00 0.00 0.00 4.96
165 169 0.532862 CATGATGTCCTACACGCCCC 60.533 60.000 0.00 0.00 0.00 5.80
171 175 4.890158 ACAACTGACATGATGTCCTACA 57.110 40.909 21.68 3.95 46.40 2.74
180 184 9.868277 AACAATAAAGAAAAACAACTGACATGA 57.132 25.926 0.00 0.00 0.00 3.07
205 209 8.385111 GTGCTTACGTGAACTATATTAGCAAAA 58.615 33.333 0.00 0.00 37.79 2.44
242 246 3.963129 ACCCTATGATTCTCCGCAAAAA 58.037 40.909 0.00 0.00 0.00 1.94
243 247 3.644966 ACCCTATGATTCTCCGCAAAA 57.355 42.857 0.00 0.00 0.00 2.44
244 248 3.644966 AACCCTATGATTCTCCGCAAA 57.355 42.857 0.00 0.00 0.00 3.68
245 249 3.644966 AAACCCTATGATTCTCCGCAA 57.355 42.857 0.00 0.00 0.00 4.85
246 250 4.974645 ATAAACCCTATGATTCTCCGCA 57.025 40.909 0.00 0.00 0.00 5.69
248 252 8.100791 TGGAATAATAAACCCTATGATTCTCCG 58.899 37.037 3.09 0.00 29.53 4.63
249 253 9.807921 TTGGAATAATAAACCCTATGATTCTCC 57.192 33.333 3.09 0.00 29.53 3.71
258 262 9.983024 TCTGTCATTTTGGAATAATAAACCCTA 57.017 29.630 0.00 0.00 0.00 3.53
259 263 8.893563 TCTGTCATTTTGGAATAATAAACCCT 57.106 30.769 0.00 0.00 0.00 4.34
260 264 8.749354 ACTCTGTCATTTTGGAATAATAAACCC 58.251 33.333 0.00 0.00 0.00 4.11
269 273 9.927081 AGGATTATAACTCTGTCATTTTGGAAT 57.073 29.630 0.00 0.00 0.00 3.01
270 274 9.396022 GAGGATTATAACTCTGTCATTTTGGAA 57.604 33.333 0.00 0.00 0.00 3.53
271 275 8.548025 TGAGGATTATAACTCTGTCATTTTGGA 58.452 33.333 5.10 0.00 34.84 3.53
272 276 8.737168 TGAGGATTATAACTCTGTCATTTTGG 57.263 34.615 5.10 0.00 34.84 3.28
273 277 8.341173 GCTGAGGATTATAACTCTGTCATTTTG 58.659 37.037 9.98 0.00 35.76 2.44
275 279 6.703607 CGCTGAGGATTATAACTCTGTCATTT 59.296 38.462 9.98 0.00 35.76 2.32
276 280 6.040955 TCGCTGAGGATTATAACTCTGTCATT 59.959 38.462 9.98 0.00 35.76 2.57
279 283 5.009210 AGTCGCTGAGGATTATAACTCTGTC 59.991 44.000 9.98 0.00 35.76 3.51
280 284 4.890581 AGTCGCTGAGGATTATAACTCTGT 59.109 41.667 9.98 0.00 35.76 3.41
281 285 5.446143 AGTCGCTGAGGATTATAACTCTG 57.554 43.478 5.10 5.53 36.23 3.35
282 286 6.773685 ACTTAGTCGCTGAGGATTATAACTCT 59.226 38.462 5.10 0.00 34.84 3.24
284 288 6.546403 TGACTTAGTCGCTGAGGATTATAACT 59.454 38.462 7.92 0.00 34.95 2.24
285 289 6.637658 GTGACTTAGTCGCTGAGGATTATAAC 59.362 42.308 17.56 0.00 39.62 1.89
286 290 6.736123 GTGACTTAGTCGCTGAGGATTATAA 58.264 40.000 17.56 0.00 39.62 0.98
288 292 5.189659 GTGACTTAGTCGCTGAGGATTAT 57.810 43.478 17.56 0.00 39.62 1.28
289 293 4.634184 GTGACTTAGTCGCTGAGGATTA 57.366 45.455 17.56 0.00 39.62 1.75
290 294 3.512033 GTGACTTAGTCGCTGAGGATT 57.488 47.619 17.56 0.00 39.62 3.01
298 302 2.417339 TGTGTCAGTGACTTAGTCGC 57.583 50.000 23.29 17.19 42.60 5.19
300 304 4.551388 CTCCTTGTGTCAGTGACTTAGTC 58.449 47.826 23.29 5.27 33.15 2.59
301 305 3.322254 CCTCCTTGTGTCAGTGACTTAGT 59.678 47.826 23.29 0.00 33.15 2.24
302 306 3.322254 ACCTCCTTGTGTCAGTGACTTAG 59.678 47.826 23.29 16.13 33.15 2.18
303 307 3.069586 CACCTCCTTGTGTCAGTGACTTA 59.930 47.826 23.29 10.01 33.15 2.24
304 308 2.119495 ACCTCCTTGTGTCAGTGACTT 58.881 47.619 23.29 0.00 33.15 3.01
305 309 1.414181 CACCTCCTTGTGTCAGTGACT 59.586 52.381 23.29 0.00 33.15 3.41
306 310 1.541233 CCACCTCCTTGTGTCAGTGAC 60.541 57.143 16.68 16.68 34.35 3.67
307 311 0.758734 CCACCTCCTTGTGTCAGTGA 59.241 55.000 0.00 0.00 34.35 3.41
308 312 0.469917 ACCACCTCCTTGTGTCAGTG 59.530 55.000 0.00 0.00 34.35 3.66
309 313 1.134098 CAACCACCTCCTTGTGTCAGT 60.134 52.381 0.00 0.00 34.35 3.41
310 314 1.597742 CAACCACCTCCTTGTGTCAG 58.402 55.000 0.00 0.00 34.35 3.51
311 315 0.465460 GCAACCACCTCCTTGTGTCA 60.465 55.000 0.00 0.00 34.35 3.58
312 316 1.172812 GGCAACCACCTCCTTGTGTC 61.173 60.000 0.00 0.00 34.35 3.67
313 317 1.152756 GGCAACCACCTCCTTGTGT 60.153 57.895 0.00 0.00 34.35 3.72
314 318 3.763671 GGCAACCACCTCCTTGTG 58.236 61.111 0.00 0.00 35.98 3.33
327 331 2.364722 TAGCTTGTTGGCTGGGGCAA 62.365 55.000 0.00 2.45 45.54 4.52
328 332 2.153898 ATAGCTTGTTGGCTGGGGCA 62.154 55.000 0.00 0.00 43.01 5.36
329 333 0.106719 TATAGCTTGTTGGCTGGGGC 60.107 55.000 0.00 0.00 43.01 5.80
330 334 1.212935 AGTATAGCTTGTTGGCTGGGG 59.787 52.381 0.00 0.00 43.01 4.96
331 335 2.717639 AGTATAGCTTGTTGGCTGGG 57.282 50.000 0.00 0.00 43.01 4.45
341 345 3.818773 ACCAACGCAAACAAGTATAGCTT 59.181 39.130 0.00 0.00 38.08 3.74
342 346 3.408634 ACCAACGCAAACAAGTATAGCT 58.591 40.909 0.00 0.00 0.00 3.32
343 347 3.824414 ACCAACGCAAACAAGTATAGC 57.176 42.857 0.00 0.00 0.00 2.97
344 348 5.049680 ACAGAACCAACGCAAACAAGTATAG 60.050 40.000 0.00 0.00 0.00 1.31
345 349 4.817464 ACAGAACCAACGCAAACAAGTATA 59.183 37.500 0.00 0.00 0.00 1.47
346 350 3.630312 ACAGAACCAACGCAAACAAGTAT 59.370 39.130 0.00 0.00 0.00 2.12
347 351 3.011119 ACAGAACCAACGCAAACAAGTA 58.989 40.909 0.00 0.00 0.00 2.24
348 352 1.816224 ACAGAACCAACGCAAACAAGT 59.184 42.857 0.00 0.00 0.00 3.16
349 353 2.159448 TGACAGAACCAACGCAAACAAG 60.159 45.455 0.00 0.00 0.00 3.16
360 364 6.098409 AGTCTAGAAGAAAAGTGACAGAACCA 59.902 38.462 0.00 0.00 0.00 3.67
408 412 4.633175 TCAAAACAAGTATGGACACGCTA 58.367 39.130 0.00 0.00 0.00 4.26
410 414 3.364964 CCTCAAAACAAGTATGGACACGC 60.365 47.826 0.00 0.00 0.00 5.34
414 418 7.923414 ATAGTTCCTCAAAACAAGTATGGAC 57.077 36.000 0.00 0.00 0.00 4.02
448 452 0.822811 ATGCCTTGTTGCAACACACA 59.177 45.000 31.17 26.40 45.84 3.72
449 453 2.791383 TATGCCTTGTTGCAACACAC 57.209 45.000 31.17 22.09 45.84 3.82
461 465 8.541234 GGCTAACCTACTAGATATTTATGCCTT 58.459 37.037 0.00 0.00 0.00 4.35
596 765 3.331889 AGAACCACCTCAATTGATCCACT 59.668 43.478 8.96 0.42 0.00 4.00
602 771 3.913799 TCCCTAAGAACCACCTCAATTGA 59.086 43.478 8.12 8.12 0.00 2.57
612 781 7.425224 TTTTGTCAATTTTCCCTAAGAACCA 57.575 32.000 0.00 0.00 32.95 3.67
654 836 1.003718 CCCTCCCTCTCGCGTTTTT 60.004 57.895 5.77 0.00 0.00 1.94
659 841 3.075005 TTTCCCCTCCCTCTCGCG 61.075 66.667 0.00 0.00 0.00 5.87
685 867 3.288964 AGGTATTGTCGTCCGATTCTCT 58.711 45.455 0.00 0.00 0.00 3.10
691 873 5.357878 ACTTATGTAAGGTATTGTCGTCCGA 59.642 40.000 4.92 0.00 37.62 4.55
771 2263 8.474025 ACACAGTTTTCCATCTTCACATAAAAA 58.526 29.630 0.00 0.00 0.00 1.94
772 2264 7.920151 CACACAGTTTTCCATCTTCACATAAAA 59.080 33.333 0.00 0.00 0.00 1.52
773 2265 7.068103 ACACACAGTTTTCCATCTTCACATAAA 59.932 33.333 0.00 0.00 0.00 1.40
774 2266 6.545666 ACACACAGTTTTCCATCTTCACATAA 59.454 34.615 0.00 0.00 0.00 1.90
775 2267 6.061441 ACACACAGTTTTCCATCTTCACATA 58.939 36.000 0.00 0.00 0.00 2.29
776 2268 4.889409 ACACACAGTTTTCCATCTTCACAT 59.111 37.500 0.00 0.00 0.00 3.21
777 2269 4.269183 ACACACAGTTTTCCATCTTCACA 58.731 39.130 0.00 0.00 0.00 3.58
778 2270 4.900635 ACACACAGTTTTCCATCTTCAC 57.099 40.909 0.00 0.00 0.00 3.18
779 2271 6.770303 TCATTACACACAGTTTTCCATCTTCA 59.230 34.615 0.00 0.00 0.00 3.02
780 2272 7.041098 ACTCATTACACACAGTTTTCCATCTTC 60.041 37.037 0.00 0.00 0.00 2.87
781 2273 6.772716 ACTCATTACACACAGTTTTCCATCTT 59.227 34.615 0.00 0.00 0.00 2.40
782 2274 6.299141 ACTCATTACACACAGTTTTCCATCT 58.701 36.000 0.00 0.00 0.00 2.90
783 2275 6.348540 GGACTCATTACACACAGTTTTCCATC 60.349 42.308 0.00 0.00 0.00 3.51
784 2276 5.473504 GGACTCATTACACACAGTTTTCCAT 59.526 40.000 0.00 0.00 0.00 3.41
785 2277 4.819630 GGACTCATTACACACAGTTTTCCA 59.180 41.667 0.00 0.00 0.00 3.53
786 2278 4.819630 TGGACTCATTACACACAGTTTTCC 59.180 41.667 0.00 0.00 0.00 3.13
787 2279 6.560253 ATGGACTCATTACACACAGTTTTC 57.440 37.500 0.00 0.00 0.00 2.29
788 2280 6.959639 AATGGACTCATTACACACAGTTTT 57.040 33.333 0.00 0.00 41.41 2.43
789 2281 6.016276 GGAAATGGACTCATTACACACAGTTT 60.016 38.462 0.00 0.00 42.29 2.66
790 2282 5.473504 GGAAATGGACTCATTACACACAGTT 59.526 40.000 0.00 0.00 42.29 3.16
791 2283 5.003804 GGAAATGGACTCATTACACACAGT 58.996 41.667 0.00 0.00 42.29 3.55
792 2284 5.003160 TGGAAATGGACTCATTACACACAG 58.997 41.667 0.00 0.00 42.29 3.66
869 2361 0.627986 AAGAGGGAAGGGGATTGCAG 59.372 55.000 0.00 0.00 0.00 4.41
870 2362 0.625849 GAAGAGGGAAGGGGATTGCA 59.374 55.000 0.00 0.00 0.00 4.08
871 2363 0.922626 AGAAGAGGGAAGGGGATTGC 59.077 55.000 0.00 0.00 0.00 3.56
902 2400 1.439679 CGGAGGGTGCTTGTTTCTAC 58.560 55.000 0.00 0.00 0.00 2.59
956 2454 0.471971 GGGGATGAGGGATTCGGAGA 60.472 60.000 0.00 0.00 0.00 3.71
968 2466 3.781307 CGAGGCAACGGGGGATGA 61.781 66.667 0.00 0.00 46.39 2.92
1107 2605 1.961277 CTGAGCGCGGTTTGAAGGT 60.961 57.895 14.00 0.00 0.00 3.50
1258 2756 1.730902 CTGTCTCTGTCACCGCGTG 60.731 63.158 4.92 3.64 34.45 5.34
1269 2767 1.309688 GGAGCCCTCCTCTGTCTCT 59.690 63.158 7.08 0.00 46.16 3.10
1443 2941 2.951884 CGATCATGTCGTTGTACGTG 57.048 50.000 0.00 0.00 45.19 4.49
1476 2974 2.505557 CGGGACTTGTACCGCGTC 60.506 66.667 11.73 0.00 43.96 5.19
1614 3112 0.108138 GCTTCTTCGCCAGCTTCCTA 60.108 55.000 0.00 0.00 32.87 2.94
1695 3193 1.971167 GACCATCCCGCACTTGCAA 60.971 57.895 0.00 0.00 42.21 4.08
1758 3256 1.482593 CTGTAGGTCTCGGCATTTCCT 59.517 52.381 0.00 0.00 0.00 3.36
1846 3344 1.168714 GGGGTGTGCTTCATCTCAAC 58.831 55.000 0.00 0.00 0.00 3.18
1962 3460 4.085733 CAGTGGGAGAGGATATCTTCGAT 58.914 47.826 9.01 0.00 38.84 3.59
2223 3721 2.103263 AGCCTTCTGAAGACGACAAAGT 59.897 45.455 18.68 0.00 0.00 2.66
2336 3834 1.193323 CCTGTGTGGCTCTCTCATCT 58.807 55.000 0.00 0.00 0.00 2.90
2362 3860 7.890127 TCTCTTGTCCATTTCAGTCCAAATATT 59.110 33.333 0.00 0.00 0.00 1.28
2460 3958 4.890158 TTCATCTAGAAGAGTGGTTGCA 57.110 40.909 0.00 0.00 0.00 4.08
2496 3994 6.361481 CGAACTTCTTGTACGACAGTTTCATA 59.639 38.462 0.00 0.00 0.00 2.15
2967 4470 3.780804 ACCACAGTATTGTAGCAACCA 57.219 42.857 0.00 0.00 35.25 3.67
3096 4600 8.631480 TGCTTAGATTTGTCTAGATACGGATA 57.369 34.615 0.00 0.00 0.00 2.59
3248 4883 5.120399 AGTCGATTGAAACACACTGGTTTA 58.880 37.500 0.00 0.00 40.85 2.01
3256 4891 9.872757 GATAAAACTAAAGTCGATTGAAACACA 57.127 29.630 0.00 0.00 0.00 3.72
3526 5175 5.675538 ACTCAGAGCTTTACAACAGAAAGT 58.324 37.500 0.00 0.00 36.47 2.66
3603 5252 8.511321 TGGCTACTTTCATAACACAAACAATAG 58.489 33.333 0.00 0.00 0.00 1.73
3606 5255 6.701145 TGGCTACTTTCATAACACAAACAA 57.299 33.333 0.00 0.00 0.00 2.83
3620 5269 3.328050 AGACTGGTTTAGCTGGCTACTTT 59.672 43.478 0.00 0.00 0.00 2.66
3632 5281 4.594062 TGGTTTAGGCAGTAGACTGGTTTA 59.406 41.667 11.51 0.00 43.94 2.01
3639 5288 4.380550 GGCAAATTGGTTTAGGCAGTAGAC 60.381 45.833 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.