Multiple sequence alignment - TraesCS3B01G242300

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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 TraesCS3B01G242300 chr3B 100.000 3179 0 0 1 3179 382005380 382002202 0.000000e+00 5871.0
1 TraesCS3B01G242300 chr3B 97.222 36 1 0 1746 1781 810609221 810609256 9.520000e-06 62.1
2 TraesCS3B01G242300 chr3D 97.427 2060 29 3 409 2445 289840743 289838685 0.000000e+00 3489.0
3 TraesCS3B01G242300 chr3D 98.561 278 4 0 46 323 289841016 289840739 2.850000e-135 492.0
4 TraesCS3B01G242300 chr3A 94.505 2093 71 17 416 2465 380923489 380921398 0.000000e+00 3188.0
5 TraesCS3B01G242300 chr3A 93.220 118 8 0 8 125 380923690 380923573 1.170000e-39 174.0
6 TraesCS3B01G242300 chr3A 91.304 92 2 2 224 309 380923582 380923491 1.550000e-23 121.0
7 TraesCS3B01G242300 chr4B 96.117 721 23 3 2463 3179 613379003 613379722 0.000000e+00 1171.0
8 TraesCS3B01G242300 chr4B 94.678 714 35 2 2469 3179 4593520 4592807 0.000000e+00 1105.0
9 TraesCS3B01G242300 chr1B 95.549 719 28 3 2463 3179 428805102 428804386 0.000000e+00 1147.0
10 TraesCS3B01G242300 chr1B 94.708 718 37 1 2463 3179 52291245 52291962 0.000000e+00 1114.0
11 TraesCS3B01G242300 chr1B 94.505 91 5 0 318 408 467541539 467541449 1.190000e-29 141.0
12 TraesCS3B01G242300 chr1B 84.043 94 9 4 1698 1785 606319227 606319320 5.650000e-13 86.1
13 TraesCS3B01G242300 chr1B 100.000 38 0 0 1746 1783 150361185 150361222 1.580000e-08 71.3
14 TraesCS3B01G242300 chr1B 95.000 40 2 0 1745 1784 610165085 610165046 2.650000e-06 63.9
15 TraesCS3B01G242300 chr7B 94.854 719 35 2 2463 3179 456503519 456504237 0.000000e+00 1122.0
16 TraesCS3B01G242300 chr7B 93.204 103 4 1 310 409 125882175 125882277 7.100000e-32 148.0
17 TraesCS3B01G242300 chr7B 96.471 85 3 0 318 402 619059550 619059634 1.190000e-29 141.0
18 TraesCS3B01G242300 chr7B 94.505 91 5 0 319 409 619059648 619059558 1.190000e-29 141.0
19 TraesCS3B01G242300 chr5B 94.854 719 34 3 2463 3179 616724154 616723437 0.000000e+00 1120.0
20 TraesCS3B01G242300 chr5B 94.730 721 34 2 2463 3179 622465965 622465245 0.000000e+00 1118.0
21 TraesCS3B01G242300 chr5B 94.583 720 36 2 2463 3179 576157329 576158048 0.000000e+00 1110.0
22 TraesCS3B01G242300 chr5B 95.652 92 4 0 318 409 127696488 127696579 7.100000e-32 148.0
23 TraesCS3B01G242300 chr5B 94.737 95 2 1 318 409 27484740 27484834 9.190000e-31 145.0
24 TraesCS3B01G242300 chr5B 83.721 86 9 4 1701 1781 328226171 328226256 3.400000e-10 76.8
25 TraesCS3B01G242300 chr4A 94.011 718 42 1 2463 3179 423429637 423430354 0.000000e+00 1086.0
26 TraesCS3B01G242300 chr4A 94.000 100 5 1 310 409 725926685 725926783 1.980000e-32 150.0
27 TraesCS3B01G242300 chr4A 95.556 90 3 1 320 409 725926789 725926701 3.310000e-30 143.0
28 TraesCS3B01G242300 chr1D 92.381 105 3 3 320 420 461147085 461147188 9.190000e-31 145.0
29 TraesCS3B01G242300 chr6B 84.270 89 8 3 1696 1784 357124905 357124823 7.310000e-12 82.4
30 TraesCS3B01G242300 chr2D 95.122 41 2 0 1697 1737 427328433 427328473 7.360000e-07 65.8
31 TraesCS3B01G242300 chr4D 94.872 39 2 0 1746 1784 463695023 463695061 9.520000e-06 62.1


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 TraesCS3B01G242300 chr3B 382002202 382005380 3178 True 5871.0 5871 100.000000 1 3179 1 chr3B.!!$R1 3178
1 TraesCS3B01G242300 chr3D 289838685 289841016 2331 True 1990.5 3489 97.994000 46 2445 2 chr3D.!!$R1 2399
2 TraesCS3B01G242300 chr3A 380921398 380923690 2292 True 1161.0 3188 93.009667 8 2465 3 chr3A.!!$R1 2457
3 TraesCS3B01G242300 chr4B 613379003 613379722 719 False 1171.0 1171 96.117000 2463 3179 1 chr4B.!!$F1 716
4 TraesCS3B01G242300 chr4B 4592807 4593520 713 True 1105.0 1105 94.678000 2469 3179 1 chr4B.!!$R1 710
5 TraesCS3B01G242300 chr1B 428804386 428805102 716 True 1147.0 1147 95.549000 2463 3179 1 chr1B.!!$R1 716
6 TraesCS3B01G242300 chr1B 52291245 52291962 717 False 1114.0 1114 94.708000 2463 3179 1 chr1B.!!$F1 716
7 TraesCS3B01G242300 chr7B 456503519 456504237 718 False 1122.0 1122 94.854000 2463 3179 1 chr7B.!!$F2 716
8 TraesCS3B01G242300 chr5B 616723437 616724154 717 True 1120.0 1120 94.854000 2463 3179 1 chr5B.!!$R1 716
9 TraesCS3B01G242300 chr5B 622465245 622465965 720 True 1118.0 1118 94.730000 2463 3179 1 chr5B.!!$R2 716
10 TraesCS3B01G242300 chr5B 576157329 576158048 719 False 1110.0 1110 94.583000 2463 3179 1 chr5B.!!$F4 716
11 TraesCS3B01G242300 chr4A 423429637 423430354 717 False 1086.0 1086 94.011000 2463 3179 1 chr4A.!!$F1 716

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
336 343 0.251297 TGTACTCCCTCCGTTCGGAA 60.251 55.0 14.79 0.04 33.41 4.30 F
561 580 1.040339 GCATGGGATTGGCGGGTTAA 61.040 55.0 0.00 0.00 0.00 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1194 1241 0.035630 AGCAGATGAAGGGAGCACAC 60.036 55.0 0.0 0.0 0.0 3.82 R
2239 2297 0.662619 TTGTTGAGAAGTTGCCAGCG 59.337 50.0 0.0 0.0 0.0 5.18 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
39 40 3.066190 TCCGATCCGTTCAGCCGT 61.066 61.111 0.00 0.00 0.00 5.68
71 72 5.523438 TTCGCCCACTGATTTAAACTTTT 57.477 34.783 0.00 0.00 0.00 2.27
233 234 1.416401 TCTTCGGCCTGTTCTTCAGTT 59.584 47.619 0.00 0.00 42.19 3.16
239 240 2.819608 GGCCTGTTCTTCAGTTTATGCA 59.180 45.455 0.00 0.00 42.19 3.96
317 324 3.554934 TCAGTCAGGAAGCAATTGTTGT 58.445 40.909 7.40 0.00 0.00 3.32
318 325 3.316029 TCAGTCAGGAAGCAATTGTTGTG 59.684 43.478 7.40 0.64 0.00 3.33
319 326 3.067180 CAGTCAGGAAGCAATTGTTGTGT 59.933 43.478 7.40 0.00 0.00 3.72
320 327 4.275689 CAGTCAGGAAGCAATTGTTGTGTA 59.724 41.667 7.40 0.00 0.00 2.90
321 328 4.275936 AGTCAGGAAGCAATTGTTGTGTAC 59.724 41.667 7.40 0.00 0.00 2.90
322 329 4.275936 GTCAGGAAGCAATTGTTGTGTACT 59.724 41.667 7.40 0.00 0.00 2.73
323 330 4.515191 TCAGGAAGCAATTGTTGTGTACTC 59.485 41.667 7.40 0.00 0.00 2.59
324 331 3.821033 AGGAAGCAATTGTTGTGTACTCC 59.179 43.478 7.40 3.94 0.00 3.85
325 332 3.057526 GGAAGCAATTGTTGTGTACTCCC 60.058 47.826 7.40 0.00 0.00 4.30
326 333 3.508845 AGCAATTGTTGTGTACTCCCT 57.491 42.857 7.40 0.00 0.00 4.20
327 334 3.412386 AGCAATTGTTGTGTACTCCCTC 58.588 45.455 7.40 0.00 0.00 4.30
328 335 2.488153 GCAATTGTTGTGTACTCCCTCC 59.512 50.000 7.40 0.00 0.00 4.30
329 336 2.742053 CAATTGTTGTGTACTCCCTCCG 59.258 50.000 0.00 0.00 0.00 4.63
330 337 1.416243 TTGTTGTGTACTCCCTCCGT 58.584 50.000 0.00 0.00 0.00 4.69
331 338 1.416243 TGTTGTGTACTCCCTCCGTT 58.584 50.000 0.00 0.00 0.00 4.44
332 339 1.342174 TGTTGTGTACTCCCTCCGTTC 59.658 52.381 0.00 0.00 0.00 3.95
333 340 0.599558 TTGTGTACTCCCTCCGTTCG 59.400 55.000 0.00 0.00 0.00 3.95
334 341 1.246056 TGTGTACTCCCTCCGTTCGG 61.246 60.000 4.74 4.74 0.00 4.30
335 342 0.962356 GTGTACTCCCTCCGTTCGGA 60.962 60.000 13.34 13.34 0.00 4.55
336 343 0.251297 TGTACTCCCTCCGTTCGGAA 60.251 55.000 14.79 0.04 33.41 4.30
337 344 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
338 345 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
339 346 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
340 347 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
341 348 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
342 349 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
343 350 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
344 351 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
345 352 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
346 353 3.368116 CCTCCGTTCGGAATTACTTGTCT 60.368 47.826 14.79 0.00 33.41 3.41
347 354 3.841643 TCCGTTCGGAATTACTTGTCTC 58.158 45.455 11.66 0.00 0.00 3.36
348 355 2.597305 CCGTTCGGAATTACTTGTCTCG 59.403 50.000 5.19 0.00 0.00 4.04
349 356 2.597305 CGTTCGGAATTACTTGTCTCGG 59.403 50.000 0.00 0.00 0.00 4.63
350 357 3.671433 CGTTCGGAATTACTTGTCTCGGA 60.671 47.826 0.00 0.00 0.00 4.55
351 358 4.240096 GTTCGGAATTACTTGTCTCGGAA 58.760 43.478 0.00 0.00 0.00 4.30
352 359 4.524316 TCGGAATTACTTGTCTCGGAAA 57.476 40.909 0.00 0.00 0.00 3.13
353 360 5.080969 TCGGAATTACTTGTCTCGGAAAT 57.919 39.130 0.00 0.00 0.00 2.17
354 361 4.868171 TCGGAATTACTTGTCTCGGAAATG 59.132 41.667 0.00 0.00 0.00 2.32
355 362 4.034048 CGGAATTACTTGTCTCGGAAATGG 59.966 45.833 0.00 0.00 0.00 3.16
356 363 5.183228 GGAATTACTTGTCTCGGAAATGGA 58.817 41.667 0.00 0.00 0.00 3.41
357 364 5.823045 GGAATTACTTGTCTCGGAAATGGAT 59.177 40.000 0.00 0.00 0.00 3.41
358 365 6.238484 GGAATTACTTGTCTCGGAAATGGATG 60.238 42.308 0.00 0.00 0.00 3.51
359 366 3.703001 ACTTGTCTCGGAAATGGATGT 57.297 42.857 0.00 0.00 0.00 3.06
360 367 4.819105 ACTTGTCTCGGAAATGGATGTA 57.181 40.909 0.00 0.00 0.00 2.29
361 368 5.359194 ACTTGTCTCGGAAATGGATGTAT 57.641 39.130 0.00 0.00 0.00 2.29
362 369 5.360591 ACTTGTCTCGGAAATGGATGTATC 58.639 41.667 0.00 0.00 0.00 2.24
363 370 5.129485 ACTTGTCTCGGAAATGGATGTATCT 59.871 40.000 0.00 0.00 0.00 1.98
364 371 6.323996 ACTTGTCTCGGAAATGGATGTATCTA 59.676 38.462 0.00 0.00 0.00 1.98
365 372 6.332735 TGTCTCGGAAATGGATGTATCTAG 57.667 41.667 0.00 0.00 0.00 2.43
366 373 6.068670 TGTCTCGGAAATGGATGTATCTAGA 58.931 40.000 0.00 0.00 0.00 2.43
367 374 6.549736 TGTCTCGGAAATGGATGTATCTAGAA 59.450 38.462 0.00 0.00 0.00 2.10
368 375 6.864165 GTCTCGGAAATGGATGTATCTAGAAC 59.136 42.308 0.00 0.00 0.00 3.01
369 376 6.778069 TCTCGGAAATGGATGTATCTAGAACT 59.222 38.462 0.00 0.00 0.00 3.01
370 377 7.942894 TCTCGGAAATGGATGTATCTAGAACTA 59.057 37.037 0.00 0.00 0.00 2.24
371 378 8.112016 TCGGAAATGGATGTATCTAGAACTAG 57.888 38.462 0.00 2.77 34.56 2.57
372 379 7.942894 TCGGAAATGGATGTATCTAGAACTAGA 59.057 37.037 12.92 12.92 45.24 2.43
386 393 8.112016 TCTAGAACTAGATACATCCATTTCCG 57.888 38.462 7.37 0.00 37.28 4.30
387 394 6.978674 AGAACTAGATACATCCATTTCCGA 57.021 37.500 0.00 0.00 0.00 4.55
388 395 6.987386 AGAACTAGATACATCCATTTCCGAG 58.013 40.000 0.00 0.00 0.00 4.63
389 396 6.778069 AGAACTAGATACATCCATTTCCGAGA 59.222 38.462 0.00 0.00 0.00 4.04
390 397 6.334102 ACTAGATACATCCATTTCCGAGAC 57.666 41.667 0.00 0.00 0.00 3.36
391 398 5.833667 ACTAGATACATCCATTTCCGAGACA 59.166 40.000 0.00 0.00 0.00 3.41
392 399 5.614324 AGATACATCCATTTCCGAGACAA 57.386 39.130 0.00 0.00 0.00 3.18
393 400 5.605534 AGATACATCCATTTCCGAGACAAG 58.394 41.667 0.00 0.00 0.00 3.16
394 401 3.703001 ACATCCATTTCCGAGACAAGT 57.297 42.857 0.00 0.00 0.00 3.16
395 402 4.819105 ACATCCATTTCCGAGACAAGTA 57.181 40.909 0.00 0.00 0.00 2.24
396 403 5.160607 ACATCCATTTCCGAGACAAGTAA 57.839 39.130 0.00 0.00 0.00 2.24
397 404 5.745227 ACATCCATTTCCGAGACAAGTAAT 58.255 37.500 0.00 0.00 0.00 1.89
398 405 6.180472 ACATCCATTTCCGAGACAAGTAATT 58.820 36.000 0.00 0.00 0.00 1.40
399 406 6.316390 ACATCCATTTCCGAGACAAGTAATTC 59.684 38.462 0.00 0.00 0.00 2.17
400 407 5.183228 TCCATTTCCGAGACAAGTAATTCC 58.817 41.667 0.00 0.00 0.00 3.01
401 408 4.034048 CCATTTCCGAGACAAGTAATTCCG 59.966 45.833 0.00 0.00 0.00 4.30
402 409 2.953466 TCCGAGACAAGTAATTCCGG 57.047 50.000 0.00 0.00 37.08 5.14
403 410 2.449464 TCCGAGACAAGTAATTCCGGA 58.551 47.619 0.00 0.00 41.64 5.14
404 411 2.426024 TCCGAGACAAGTAATTCCGGAG 59.574 50.000 3.34 0.00 39.43 4.63
561 580 1.040339 GCATGGGATTGGCGGGTTAA 61.040 55.000 0.00 0.00 0.00 2.01
687 706 8.752005 ATTATTTGCTCAGCTAAAACTGGATA 57.248 30.769 0.00 0.00 38.26 2.59
1194 1241 1.905637 AAAACCAAGCTCCCCGTAAG 58.094 50.000 0.00 0.00 0.00 2.34
1311 1358 0.958822 AGCCATCCCGTTCAACAAAC 59.041 50.000 0.00 0.00 34.31 2.93
1547 1594 2.280628 GGAATTCGAAGCCAGGTACAG 58.719 52.381 13.34 0.00 0.00 2.74
1786 1841 5.850046 ATGGATTGGAGGGAGTATTAAGG 57.150 43.478 0.00 0.00 0.00 2.69
1819 1874 8.733458 CATCAACTATCTCAAAAGTGATTCCAA 58.267 33.333 0.00 0.00 31.85 3.53
1865 1920 6.692849 TTATTCATATGATGCACCTCCTCT 57.307 37.500 6.17 0.00 0.00 3.69
1987 2042 7.934855 ATTGATTCTCTAACTGCAATCTGTT 57.065 32.000 0.00 0.00 37.91 3.16
2030 2085 7.331687 ACACATGCTTTATTATTTTGTTGGCTC 59.668 33.333 0.00 0.00 0.00 4.70
2136 2194 6.768483 TGGAAGTTTGTCAGATGATGAACTA 58.232 36.000 11.67 0.00 40.43 2.24
2239 2297 5.994668 AGCTTTTCTGCTAGGATATGCTTAC 59.005 40.000 0.65 0.00 42.10 2.34
2449 2507 4.094887 CACATGCTCCAGGTTGTAACATAC 59.905 45.833 0.00 0.00 0.00 2.39
2609 2667 7.230108 AGTTTCCATTCTACAATATGCTGATGG 59.770 37.037 0.00 0.00 0.00 3.51
2648 2706 1.004628 ACATGACATGGCTAAGGCACA 59.995 47.619 19.39 0.00 41.84 4.57
2820 2878 6.549433 TTCAGTTACTTGGGTATACCGATT 57.451 37.500 15.80 4.98 44.64 3.34
2918 2979 5.819901 GGATAAGCTTATGTCATATGGAGGC 59.180 44.000 23.51 4.29 0.00 4.70
2971 3032 5.916661 AGTATGTCGATGTTCCTACTGTT 57.083 39.130 0.00 0.00 0.00 3.16
3040 3101 0.467290 TCCCGCTTCTTTTGGCAGTT 60.467 50.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.048724 TGGGGGAGAGCTACATTCCG 61.049 60.000 0.00 0.00 31.59 4.30
1 2 0.761802 CTGGGGGAGAGCTACATTCC 59.238 60.000 0.00 0.00 0.00 3.01
2 3 0.761802 CCTGGGGGAGAGCTACATTC 59.238 60.000 0.00 0.00 33.58 2.67
3 4 0.044855 ACCTGGGGGAGAGCTACATT 59.955 55.000 0.00 0.00 36.25 2.71
4 5 0.399233 GACCTGGGGGAGAGCTACAT 60.399 60.000 0.00 0.00 36.25 2.29
5 6 1.001760 GACCTGGGGGAGAGCTACA 59.998 63.158 0.00 0.00 36.25 2.74
6 7 1.762858 GGACCTGGGGGAGAGCTAC 60.763 68.421 0.00 0.00 36.25 3.58
39 40 3.879998 TCAGTGGGCGAATAAAATGCTA 58.120 40.909 0.00 0.00 0.00 3.49
233 234 6.439636 AGCTAAGATCCCACTAATGCATAA 57.560 37.500 0.00 0.00 0.00 1.90
239 240 3.322254 CACCGAGCTAAGATCCCACTAAT 59.678 47.826 0.00 0.00 0.00 1.73
317 324 0.251297 TTCCGAACGGAGGGAGTACA 60.251 55.000 15.34 0.00 46.06 2.90
318 325 1.109609 ATTCCGAACGGAGGGAGTAC 58.890 55.000 15.34 0.00 46.06 2.73
319 326 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
320 327 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
321 328 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
322 329 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
323 330 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
324 331 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
325 332 3.846360 AGACAAGTAATTCCGAACGGAG 58.154 45.455 15.34 5.60 46.06 4.63
326 333 3.671433 CGAGACAAGTAATTCCGAACGGA 60.671 47.826 12.04 12.04 43.52 4.69
327 334 2.597305 CGAGACAAGTAATTCCGAACGG 59.403 50.000 6.94 6.94 0.00 4.44
328 335 2.597305 CCGAGACAAGTAATTCCGAACG 59.403 50.000 0.00 0.00 0.00 3.95
329 336 3.841643 TCCGAGACAAGTAATTCCGAAC 58.158 45.455 0.00 0.00 0.00 3.95
330 337 4.524316 TTCCGAGACAAGTAATTCCGAA 57.476 40.909 0.00 0.00 0.00 4.30
331 338 4.524316 TTTCCGAGACAAGTAATTCCGA 57.476 40.909 0.00 0.00 0.00 4.55
332 339 4.034048 CCATTTCCGAGACAAGTAATTCCG 59.966 45.833 0.00 0.00 0.00 4.30
333 340 5.183228 TCCATTTCCGAGACAAGTAATTCC 58.817 41.667 0.00 0.00 0.00 3.01
334 341 6.316390 ACATCCATTTCCGAGACAAGTAATTC 59.684 38.462 0.00 0.00 0.00 2.17
335 342 6.180472 ACATCCATTTCCGAGACAAGTAATT 58.820 36.000 0.00 0.00 0.00 1.40
336 343 5.745227 ACATCCATTTCCGAGACAAGTAAT 58.255 37.500 0.00 0.00 0.00 1.89
337 344 5.160607 ACATCCATTTCCGAGACAAGTAA 57.839 39.130 0.00 0.00 0.00 2.24
338 345 4.819105 ACATCCATTTCCGAGACAAGTA 57.181 40.909 0.00 0.00 0.00 2.24
339 346 3.703001 ACATCCATTTCCGAGACAAGT 57.297 42.857 0.00 0.00 0.00 3.16
340 347 5.605534 AGATACATCCATTTCCGAGACAAG 58.394 41.667 0.00 0.00 0.00 3.16
341 348 5.614324 AGATACATCCATTTCCGAGACAA 57.386 39.130 0.00 0.00 0.00 3.18
342 349 6.068670 TCTAGATACATCCATTTCCGAGACA 58.931 40.000 0.00 0.00 0.00 3.41
343 350 6.576662 TCTAGATACATCCATTTCCGAGAC 57.423 41.667 0.00 0.00 0.00 3.36
344 351 6.778069 AGTTCTAGATACATCCATTTCCGAGA 59.222 38.462 0.00 0.00 0.00 4.04
345 352 6.987386 AGTTCTAGATACATCCATTTCCGAG 58.013 40.000 0.00 0.00 0.00 4.63
346 353 6.978674 AGTTCTAGATACATCCATTTCCGA 57.021 37.500 0.00 0.00 0.00 4.55
347 354 8.112016 TCTAGTTCTAGATACATCCATTTCCG 57.888 38.462 5.56 0.00 0.00 4.30
360 367 8.744652 CGGAAATGGATGTATCTAGTTCTAGAT 58.255 37.037 21.12 21.12 40.60 1.98
361 368 7.942894 TCGGAAATGGATGTATCTAGTTCTAGA 59.057 37.037 14.84 11.26 40.60 2.43
362 369 8.112016 TCGGAAATGGATGTATCTAGTTCTAG 57.888 38.462 14.84 10.85 40.60 2.43
363 370 7.942894 TCTCGGAAATGGATGTATCTAGTTCTA 59.057 37.037 14.84 6.27 40.60 2.10
364 371 6.778069 TCTCGGAAATGGATGTATCTAGTTCT 59.222 38.462 14.84 0.00 40.60 3.01
365 372 6.864165 GTCTCGGAAATGGATGTATCTAGTTC 59.136 42.308 9.11 9.11 40.23 3.01
366 373 6.323996 TGTCTCGGAAATGGATGTATCTAGTT 59.676 38.462 0.00 0.00 0.00 2.24
367 374 5.833667 TGTCTCGGAAATGGATGTATCTAGT 59.166 40.000 0.00 0.00 0.00 2.57
368 375 6.332735 TGTCTCGGAAATGGATGTATCTAG 57.667 41.667 0.00 0.00 0.00 2.43
369 376 6.323996 ACTTGTCTCGGAAATGGATGTATCTA 59.676 38.462 0.00 0.00 0.00 1.98
370 377 5.129485 ACTTGTCTCGGAAATGGATGTATCT 59.871 40.000 0.00 0.00 0.00 1.98
371 378 5.360591 ACTTGTCTCGGAAATGGATGTATC 58.639 41.667 0.00 0.00 0.00 2.24
372 379 5.359194 ACTTGTCTCGGAAATGGATGTAT 57.641 39.130 0.00 0.00 0.00 2.29
373 380 4.819105 ACTTGTCTCGGAAATGGATGTA 57.181 40.909 0.00 0.00 0.00 2.29
374 381 3.703001 ACTTGTCTCGGAAATGGATGT 57.297 42.857 0.00 0.00 0.00 3.06
375 382 6.238484 GGAATTACTTGTCTCGGAAATGGATG 60.238 42.308 0.00 0.00 0.00 3.51
376 383 5.823045 GGAATTACTTGTCTCGGAAATGGAT 59.177 40.000 0.00 0.00 0.00 3.41
377 384 5.183228 GGAATTACTTGTCTCGGAAATGGA 58.817 41.667 0.00 0.00 0.00 3.41
378 385 4.034048 CGGAATTACTTGTCTCGGAAATGG 59.966 45.833 0.00 0.00 0.00 3.16
379 386 4.034048 CCGGAATTACTTGTCTCGGAAATG 59.966 45.833 0.00 0.00 38.42 2.32
380 387 4.081309 TCCGGAATTACTTGTCTCGGAAAT 60.081 41.667 0.00 0.00 41.47 2.17
381 388 3.258872 TCCGGAATTACTTGTCTCGGAAA 59.741 43.478 0.00 0.00 41.47 3.13
382 389 2.827322 TCCGGAATTACTTGTCTCGGAA 59.173 45.455 0.00 0.00 41.47 4.30
383 390 2.426024 CTCCGGAATTACTTGTCTCGGA 59.574 50.000 5.23 0.00 42.04 4.55
384 391 2.481449 CCTCCGGAATTACTTGTCTCGG 60.481 54.545 5.23 0.00 37.61 4.63
385 392 2.481449 CCCTCCGGAATTACTTGTCTCG 60.481 54.545 5.23 0.00 0.00 4.04
386 393 2.764572 TCCCTCCGGAATTACTTGTCTC 59.235 50.000 5.23 0.00 34.19 3.36
387 394 2.766828 CTCCCTCCGGAATTACTTGTCT 59.233 50.000 5.23 0.00 37.86 3.41
388 395 2.500504 ACTCCCTCCGGAATTACTTGTC 59.499 50.000 5.23 0.00 37.86 3.18
389 396 2.547990 ACTCCCTCCGGAATTACTTGT 58.452 47.619 5.23 0.00 37.86 3.16
390 397 3.705072 AGTACTCCCTCCGGAATTACTTG 59.295 47.826 5.23 0.00 37.86 3.16
391 398 3.991683 AGTACTCCCTCCGGAATTACTT 58.008 45.455 5.23 0.00 37.86 2.24
392 399 3.684408 AGTACTCCCTCCGGAATTACT 57.316 47.619 5.23 2.05 37.86 2.24
393 400 4.439968 CAAAGTACTCCCTCCGGAATTAC 58.560 47.826 5.23 0.00 37.86 1.89
394 401 3.453353 CCAAAGTACTCCCTCCGGAATTA 59.547 47.826 5.23 0.00 37.86 1.40
395 402 2.238898 CCAAAGTACTCCCTCCGGAATT 59.761 50.000 5.23 0.00 37.86 2.17
396 403 1.838077 CCAAAGTACTCCCTCCGGAAT 59.162 52.381 5.23 0.00 37.86 3.01
397 404 1.203212 TCCAAAGTACTCCCTCCGGAA 60.203 52.381 5.23 0.00 37.86 4.30
398 405 0.410663 TCCAAAGTACTCCCTCCGGA 59.589 55.000 2.93 2.93 36.45 5.14
399 406 1.066358 GTTCCAAAGTACTCCCTCCGG 60.066 57.143 0.00 0.00 0.00 5.14
400 407 1.621814 TGTTCCAAAGTACTCCCTCCG 59.378 52.381 0.00 0.00 0.00 4.63
401 408 5.367060 AGATATGTTCCAAAGTACTCCCTCC 59.633 44.000 0.00 0.00 0.00 4.30
402 409 6.487299 AGATATGTTCCAAAGTACTCCCTC 57.513 41.667 0.00 0.00 0.00 4.30
403 410 6.215636 ACAAGATATGTTCCAAAGTACTCCCT 59.784 38.462 0.00 0.00 40.06 4.20
404 411 6.415573 ACAAGATATGTTCCAAAGTACTCCC 58.584 40.000 0.00 0.00 40.06 4.30
557 576 7.171848 TCGTACCACACATATGCCATAATTAAC 59.828 37.037 1.58 0.00 0.00 2.01
561 580 5.221641 ACTCGTACCACACATATGCCATAAT 60.222 40.000 1.58 0.00 0.00 1.28
608 627 4.307032 AATGTACTCCCAAACTGCATCT 57.693 40.909 0.00 0.00 0.00 2.90
687 706 6.355588 AAGGTTCCCAATTATATCCAACCT 57.644 37.500 0.00 0.00 43.20 3.50
724 743 2.936498 CCCTTCGTTGGTTACTATGCAG 59.064 50.000 0.00 0.00 0.00 4.41
1194 1241 0.035630 AGCAGATGAAGGGAGCACAC 60.036 55.000 0.00 0.00 0.00 3.82
1786 1841 8.535592 CACTTTTGAGATAGTTGATGTACGATC 58.464 37.037 0.00 0.00 32.37 3.69
1819 1874 6.877611 AATGAGTGTAAATCGGAACAAAGT 57.122 33.333 0.00 0.00 30.38 2.66
1865 1920 8.809468 AAATACCTATCAGCTCTATCGACATA 57.191 34.615 0.00 0.00 0.00 2.29
2030 2085 2.494059 CCAGTGGGTACAAGACTTGTG 58.506 52.381 27.44 11.09 45.03 3.33
2136 2194 5.840693 ACATTTCCTGAAACCCTCATTTTCT 59.159 36.000 0.00 0.00 34.58 2.52
2239 2297 0.662619 TTGTTGAGAAGTTGCCAGCG 59.337 50.000 0.00 0.00 0.00 5.18
2449 2507 1.204146 TCCCCTTACTAGCAGCCTTG 58.796 55.000 0.00 0.00 0.00 3.61
2583 2641 7.230108 CCATCAGCATATTGTAGAATGGAAACT 59.770 37.037 0.00 0.00 0.00 2.66
2609 2667 8.570488 TGTCATGTTCCATGAATAGAATAATGC 58.430 33.333 8.39 0.00 0.00 3.56
2612 2670 9.070179 CCATGTCATGTTCCATGAATAGAATAA 57.930 33.333 18.09 0.00 40.70 1.40
2820 2878 1.847328 TGGAGAGCTTACGGTGATGA 58.153 50.000 0.00 0.00 0.00 2.92
2890 2951 8.441311 TCCATATGACATAAGCTTATCCTTCT 57.559 34.615 16.21 3.64 0.00 2.85
2896 2957 5.627735 CGGCCTCCATATGACATAAGCTTAT 60.628 44.000 13.37 13.37 0.00 1.73
2918 2979 2.693591 TGAGTTAATCAGGACTAGCCGG 59.306 50.000 0.00 0.00 43.43 6.13
2971 3032 6.055588 ACTCCTTTCAGAATTTCGAAGAACA 58.944 36.000 0.00 0.00 45.90 3.18
3040 3101 0.251121 TTTCCGCTTGGCCTCATCAA 60.251 50.000 3.32 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.