Multiple sequence alignment - TraesCS3B01G148000

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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 TraesCS3B01G148000 chr3B 100.000 2330 0 0 1 2330 139224214 139226543 0.000000e+00 4303.0
1 TraesCS3B01G148000 chr3B 96.748 123 4 0 404 526 139224496 139224618 3.030000e-49 206.0
2 TraesCS3B01G148000 chr3B 96.748 123 4 0 283 405 139224617 139224739 3.030000e-49 206.0
3 TraesCS3B01G148000 chr3D 94.589 1848 64 20 499 2330 89803175 89805002 0.000000e+00 2826.0
4 TraesCS3B01G148000 chr3D 94.286 210 11 1 1 210 89802982 89803190 1.040000e-83 320.0
5 TraesCS3B01G148000 chr3D 100.000 28 0 0 378 405 89803175 89803202 4.000000e-03 52.8
6 TraesCS3B01G148000 chr3A 94.065 1668 72 12 683 2330 106404172 106405832 0.000000e+00 2507.0
7 TraesCS3B01G148000 chr3A 94.045 403 21 3 1 403 106403414 106403813 1.980000e-170 608.0
8 TraesCS3B01G148000 chr7B 87.640 89 7 3 1527 1614 721089415 721089500 1.470000e-17 100.0
9 TraesCS3B01G148000 chr7B 92.453 53 3 1 1545 1597 595676721 595676670 8.930000e-10 75.0
10 TraesCS3B01G148000 chr1D 86.957 69 4 4 1545 1611 335394627 335394562 3.210000e-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 TraesCS3B01G148000 chr3B 139224214 139226543 2329 False 1571.666667 4303 97.832000 1 2330 3 chr3B.!!$F1 2329
1 TraesCS3B01G148000 chr3D 89802982 89805002 2020 False 1066.266667 2826 96.291667 1 2330 3 chr3D.!!$F1 2329
2 TraesCS3B01G148000 chr3A 106403414 106405832 2418 False 1557.500000 2507 94.055000 1 2330 2 chr3A.!!$F1 2329

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
990 1192 0.03467 CCAGAAGAAGGGCAGGGAAG 60.035 60.0 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2298 2519 1.156736 CACCAGAACCGCTAAACCTG 58.843 55.0 0.0 0.0 0.0 4.0 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
114 115 6.351711 TCCATGGCTTGCAGATATCATATAC 58.648 40.000 6.96 0.00 0.00 1.47
200 201 2.053244 CCCTGGATCATGCTTAGGTCT 58.947 52.381 0.00 0.00 0.00 3.85
201 202 2.224475 CCCTGGATCATGCTTAGGTCTG 60.224 54.545 0.00 0.00 0.00 3.51
205 206 2.492012 GATCATGCTTAGGTCTGCTGG 58.508 52.381 0.00 0.00 0.00 4.85
243 244 5.452078 TTAGTTTTCTTGGTTGCTCCATG 57.548 39.130 2.36 5.35 46.60 3.66
305 306 5.199723 TGGCAAGCAAAACTATCATGGATA 58.800 37.500 0.00 0.00 0.00 2.59
306 307 5.834742 TGGCAAGCAAAACTATCATGGATAT 59.165 36.000 0.00 0.00 0.00 1.63
307 308 6.154445 GGCAAGCAAAACTATCATGGATATG 58.846 40.000 0.00 0.00 35.57 1.78
308 309 6.239120 GGCAAGCAAAACTATCATGGATATGT 60.239 38.462 0.00 0.00 35.73 2.29
309 310 6.860023 GCAAGCAAAACTATCATGGATATGTC 59.140 38.462 0.00 0.00 35.73 3.06
310 311 7.255381 GCAAGCAAAACTATCATGGATATGTCT 60.255 37.037 0.00 0.00 35.73 3.41
311 312 7.741027 AGCAAAACTATCATGGATATGTCTG 57.259 36.000 0.00 0.00 35.73 3.51
312 313 7.285566 AGCAAAACTATCATGGATATGTCTGT 58.714 34.615 0.00 0.00 35.73 3.41
313 314 7.776969 AGCAAAACTATCATGGATATGTCTGTT 59.223 33.333 0.00 0.00 35.73 3.16
314 315 8.072567 GCAAAACTATCATGGATATGTCTGTTC 58.927 37.037 0.00 0.00 35.73 3.18
315 316 8.562892 CAAAACTATCATGGATATGTCTGTTCC 58.437 37.037 0.00 0.00 35.73 3.62
316 317 7.379059 AACTATCATGGATATGTCTGTTCCA 57.621 36.000 0.00 0.00 43.37 3.53
317 318 7.002250 ACTATCATGGATATGTCTGTTCCAG 57.998 40.000 0.00 0.00 42.53 3.86
318 319 4.077300 TCATGGATATGTCTGTTCCAGC 57.923 45.455 0.00 0.00 42.53 4.85
319 320 3.455543 TCATGGATATGTCTGTTCCAGCA 59.544 43.478 0.00 0.00 42.53 4.41
320 321 4.103627 TCATGGATATGTCTGTTCCAGCAT 59.896 41.667 0.00 0.00 42.53 3.79
321 322 5.307716 TCATGGATATGTCTGTTCCAGCATA 59.692 40.000 0.00 9.28 42.53 3.14
322 323 5.830799 TGGATATGTCTGTTCCAGCATAT 57.169 39.130 14.97 14.97 40.34 1.78
323 324 5.798132 TGGATATGTCTGTTCCAGCATATC 58.202 41.667 23.06 23.06 44.78 1.63
325 326 6.047511 GATATGTCTGTTCCAGCATATCCT 57.952 41.667 21.95 7.79 42.89 3.24
326 327 3.827008 TGTCTGTTCCAGCATATCCTC 57.173 47.619 0.00 0.00 0.00 3.71
327 328 3.378512 TGTCTGTTCCAGCATATCCTCT 58.621 45.455 0.00 0.00 0.00 3.69
328 329 3.133542 TGTCTGTTCCAGCATATCCTCTG 59.866 47.826 0.00 0.00 0.00 3.35
329 330 3.133721 GTCTGTTCCAGCATATCCTCTGT 59.866 47.826 0.00 0.00 0.00 3.41
330 331 3.133542 TCTGTTCCAGCATATCCTCTGTG 59.866 47.826 0.00 0.00 0.00 3.66
331 332 3.106827 TGTTCCAGCATATCCTCTGTGA 58.893 45.455 0.00 0.00 0.00 3.58
332 333 3.713248 TGTTCCAGCATATCCTCTGTGAT 59.287 43.478 0.00 0.00 0.00 3.06
333 334 4.202295 TGTTCCAGCATATCCTCTGTGATC 60.202 45.833 0.00 0.00 0.00 2.92
334 335 2.560105 TCCAGCATATCCTCTGTGATCG 59.440 50.000 0.00 0.00 0.00 3.69
335 336 2.353505 CCAGCATATCCTCTGTGATCGG 60.354 54.545 0.00 0.00 0.00 4.18
336 337 1.898472 AGCATATCCTCTGTGATCGGG 59.102 52.381 0.00 0.00 0.00 5.14
337 338 1.895798 GCATATCCTCTGTGATCGGGA 59.104 52.381 0.00 0.00 0.00 5.14
338 339 2.094286 GCATATCCTCTGTGATCGGGAG 60.094 54.545 0.00 3.39 0.00 4.30
339 340 2.294449 TATCCTCTGTGATCGGGAGG 57.706 55.000 17.20 17.20 45.65 4.30
340 341 4.686695 CCTCTGTGATCGGGAGGA 57.313 61.111 18.00 0.00 46.82 3.71
341 342 2.119886 CCTCTGTGATCGGGAGGAC 58.880 63.158 18.00 0.00 46.82 3.85
342 343 0.396417 CCTCTGTGATCGGGAGGACT 60.396 60.000 18.00 0.00 46.82 3.85
343 344 1.479709 CTCTGTGATCGGGAGGACTT 58.520 55.000 0.00 0.00 0.00 3.01
344 345 1.135915 CTCTGTGATCGGGAGGACTTG 59.864 57.143 0.00 0.00 0.00 3.16
345 346 1.186200 CTGTGATCGGGAGGACTTGA 58.814 55.000 0.00 0.00 0.00 3.02
346 347 1.759445 CTGTGATCGGGAGGACTTGAT 59.241 52.381 0.00 0.00 0.00 2.57
347 348 1.757118 TGTGATCGGGAGGACTTGATC 59.243 52.381 0.00 0.00 38.14 2.92
348 349 1.757118 GTGATCGGGAGGACTTGATCA 59.243 52.381 0.00 0.00 43.50 2.92
349 350 2.034878 TGATCGGGAGGACTTGATCAG 58.965 52.381 0.00 0.00 41.53 2.90
350 351 1.342819 GATCGGGAGGACTTGATCAGG 59.657 57.143 2.78 2.78 37.70 3.86
351 352 0.687757 TCGGGAGGACTTGATCAGGG 60.688 60.000 9.90 3.17 0.00 4.45
352 353 1.529309 GGGAGGACTTGATCAGGGC 59.471 63.158 9.90 5.87 0.00 5.19
353 354 0.985490 GGGAGGACTTGATCAGGGCT 60.985 60.000 10.93 0.00 0.00 5.19
354 355 0.179936 GGAGGACTTGATCAGGGCTG 59.820 60.000 10.93 0.00 0.00 4.85
355 356 0.179936 GAGGACTTGATCAGGGCTGG 59.820 60.000 10.93 0.00 0.00 4.85
356 357 0.548682 AGGACTTGATCAGGGCTGGT 60.549 55.000 10.93 0.00 0.00 4.00
357 358 0.329596 GGACTTGATCAGGGCTGGTT 59.670 55.000 10.93 0.00 0.00 3.67
358 359 1.559682 GGACTTGATCAGGGCTGGTTA 59.440 52.381 10.93 0.00 0.00 2.85
359 360 2.420687 GGACTTGATCAGGGCTGGTTAG 60.421 54.545 10.93 0.00 0.00 2.34
360 361 1.561542 ACTTGATCAGGGCTGGTTAGG 59.438 52.381 9.90 0.00 0.00 2.69
361 362 0.918983 TTGATCAGGGCTGGTTAGGG 59.081 55.000 0.00 0.00 0.00 3.53
362 363 0.253160 TGATCAGGGCTGGTTAGGGT 60.253 55.000 0.00 0.00 0.00 4.34
363 364 1.009060 TGATCAGGGCTGGTTAGGGTA 59.991 52.381 0.00 0.00 0.00 3.69
364 365 1.694696 GATCAGGGCTGGTTAGGGTAG 59.305 57.143 0.00 0.00 0.00 3.18
365 366 0.326238 TCAGGGCTGGTTAGGGTAGG 60.326 60.000 0.00 0.00 0.00 3.18
366 367 0.620700 CAGGGCTGGTTAGGGTAGGT 60.621 60.000 0.00 0.00 0.00 3.08
367 368 1.021275 AGGGCTGGTTAGGGTAGGTA 58.979 55.000 0.00 0.00 0.00 3.08
368 369 1.126488 GGGCTGGTTAGGGTAGGTAC 58.874 60.000 0.00 0.00 0.00 3.34
369 370 1.623279 GGGCTGGTTAGGGTAGGTACA 60.623 57.143 0.00 0.00 0.00 2.90
370 371 2.190538 GGCTGGTTAGGGTAGGTACAA 58.809 52.381 0.00 0.00 0.00 2.41
371 372 2.573009 GGCTGGTTAGGGTAGGTACAAA 59.427 50.000 0.00 0.00 0.00 2.83
372 373 3.201487 GGCTGGTTAGGGTAGGTACAAAT 59.799 47.826 0.00 0.00 0.00 2.32
373 374 4.449131 GCTGGTTAGGGTAGGTACAAATC 58.551 47.826 0.00 0.00 0.00 2.17
374 375 4.080751 GCTGGTTAGGGTAGGTACAAATCA 60.081 45.833 0.00 0.00 0.00 2.57
375 376 5.572066 GCTGGTTAGGGTAGGTACAAATCAA 60.572 44.000 0.00 0.00 0.00 2.57
376 377 6.451292 TGGTTAGGGTAGGTACAAATCAAA 57.549 37.500 0.00 0.00 0.00 2.69
377 378 7.034967 TGGTTAGGGTAGGTACAAATCAAAT 57.965 36.000 0.00 0.00 0.00 2.32
378 379 7.471890 TGGTTAGGGTAGGTACAAATCAAATT 58.528 34.615 0.00 0.00 0.00 1.82
379 380 7.394923 TGGTTAGGGTAGGTACAAATCAAATTG 59.605 37.037 0.00 0.00 36.37 2.32
380 381 7.147966 GGTTAGGGTAGGTACAAATCAAATTGG 60.148 40.741 0.00 0.00 34.56 3.16
381 382 5.899278 AGGGTAGGTACAAATCAAATTGGT 58.101 37.500 0.00 0.00 34.56 3.67
382 383 6.319715 AGGGTAGGTACAAATCAAATTGGTT 58.680 36.000 0.00 0.00 34.56 3.67
383 384 6.785466 AGGGTAGGTACAAATCAAATTGGTTT 59.215 34.615 0.00 0.00 34.56 3.27
393 394 4.933505 TCAAATTGGTTTGATGTGCTGA 57.066 36.364 0.00 0.00 46.49 4.26
394 395 5.471556 TCAAATTGGTTTGATGTGCTGAT 57.528 34.783 0.00 0.00 46.49 2.90
395 396 5.231702 TCAAATTGGTTTGATGTGCTGATG 58.768 37.500 0.00 0.00 46.49 3.07
396 397 5.010820 TCAAATTGGTTTGATGTGCTGATGA 59.989 36.000 0.00 0.00 46.49 2.92
397 398 5.670792 AATTGGTTTGATGTGCTGATGAT 57.329 34.783 0.00 0.00 0.00 2.45
398 399 4.443913 TTGGTTTGATGTGCTGATGATG 57.556 40.909 0.00 0.00 0.00 3.07
399 400 2.164827 TGGTTTGATGTGCTGATGATGC 59.835 45.455 0.00 0.00 0.00 3.91
400 401 2.426024 GGTTTGATGTGCTGATGATGCT 59.574 45.455 0.00 0.00 0.00 3.79
401 402 3.628942 GGTTTGATGTGCTGATGATGCTA 59.371 43.478 0.00 0.00 0.00 3.49
402 403 4.261072 GGTTTGATGTGCTGATGATGCTAG 60.261 45.833 0.00 0.00 0.00 3.42
403 404 3.832615 TGATGTGCTGATGATGCTAGT 57.167 42.857 0.00 0.00 0.00 2.57
404 405 3.463944 TGATGTGCTGATGATGCTAGTG 58.536 45.455 0.00 0.00 0.00 2.74
405 406 2.320745 TGTGCTGATGATGCTAGTGG 57.679 50.000 0.00 0.00 0.00 4.00
406 407 0.942962 GTGCTGATGATGCTAGTGGC 59.057 55.000 0.00 0.00 42.22 5.01
419 420 4.021191 GCTAGTGGCAAGCAAAACTATC 57.979 45.455 6.30 0.00 39.83 2.08
420 421 3.440173 GCTAGTGGCAAGCAAAACTATCA 59.560 43.478 6.30 0.00 39.83 2.15
421 422 4.096984 GCTAGTGGCAAGCAAAACTATCAT 59.903 41.667 6.30 0.00 39.83 2.45
422 423 4.445452 AGTGGCAAGCAAAACTATCATG 57.555 40.909 0.00 0.00 0.00 3.07
423 424 3.194116 AGTGGCAAGCAAAACTATCATGG 59.806 43.478 0.00 0.00 0.00 3.66
424 425 3.193267 GTGGCAAGCAAAACTATCATGGA 59.807 43.478 0.00 0.00 0.00 3.41
425 426 4.025360 TGGCAAGCAAAACTATCATGGAT 58.975 39.130 0.00 0.00 0.00 3.41
426 427 5.067674 GTGGCAAGCAAAACTATCATGGATA 59.932 40.000 0.00 0.00 0.00 2.59
427 428 5.834742 TGGCAAGCAAAACTATCATGGATAT 59.165 36.000 0.00 0.00 0.00 1.63
435 436 9.023967 GCAAAACTATCATGGATATGTTTGTTC 57.976 33.333 15.62 4.98 33.72 3.18
436 437 9.520204 CAAAACTATCATGGATATGTTTGTTCC 57.480 33.333 0.00 0.00 33.72 3.62
444 445 6.942532 TGGATATGTTTGTTCCAGCTTATC 57.057 37.500 0.00 0.00 34.65 1.75
455 456 2.101415 TCCAGCTTATCCTGTGTGATCG 59.899 50.000 0.00 0.00 0.00 3.69
469 470 1.757118 GTGATCGGGAGGACTTGATCA 59.243 52.381 0.00 0.00 43.50 2.92
475 476 0.179936 GGAGGACTTGATCAGGGCTG 59.820 60.000 10.93 0.00 0.00 4.85
490 491 1.623279 GGGCTGGTTAGGGTAGGTACA 60.623 57.143 0.00 0.00 0.00 2.90
495 496 4.080751 GCTGGTTAGGGTAGGTACAAATCA 60.081 45.833 0.00 0.00 0.00 2.57
521 522 2.480759 GGTTTGATGTGCTGATGATGCC 60.481 50.000 0.00 0.00 0.00 4.40
553 554 4.095483 GCAATAGCAGCATATATTCGCCTT 59.905 41.667 0.00 0.00 41.58 4.35
620 621 3.686691 GCTTGAGGGCCATATTCAGAAGT 60.687 47.826 6.18 0.00 0.00 3.01
668 672 5.050159 TGTGACGATCATGTTTTCACTCAAG 60.050 40.000 15.28 0.00 37.94 3.02
716 917 7.936584 TCAAGTTTGAAATTCTACCGATGTTT 58.063 30.769 0.00 0.00 33.55 2.83
773 974 2.224499 TGCTTCATGCCAACTCAGTGTA 60.224 45.455 0.00 0.00 42.00 2.90
775 976 2.078849 TCATGCCAACTCAGTGTACG 57.921 50.000 0.00 0.00 0.00 3.67
816 1017 7.561722 GCATCCTAATCCTCACCAGTATCTATA 59.438 40.741 0.00 0.00 0.00 1.31
850 1051 2.039418 CCATCGTCTGACCCTTATCCA 58.961 52.381 1.55 0.00 0.00 3.41
851 1052 2.036475 CCATCGTCTGACCCTTATCCAG 59.964 54.545 1.55 0.00 0.00 3.86
852 1053 1.112113 TCGTCTGACCCTTATCCAGC 58.888 55.000 1.55 0.00 0.00 4.85
990 1192 0.034670 CCAGAAGAAGGGCAGGGAAG 60.035 60.000 0.00 0.00 0.00 3.46
1422 1625 7.190191 GTCCATCGAGTATATACATGCTACTG 58.810 42.308 15.18 3.50 0.00 2.74
1437 1640 2.610727 GCTACTGCCTCCGTTCCATATC 60.611 54.545 0.00 0.00 0.00 1.63
1470 1673 8.230486 CACTGATTTAGTACAACACTTGATTCC 58.770 37.037 0.00 0.00 37.60 3.01
1532 1735 6.096673 TCCCCAGTTTTATTTTCTGCTTTC 57.903 37.500 0.00 0.00 0.00 2.62
1566 1769 1.079612 GGCTGGTTGATGGCTTTGC 60.080 57.895 0.00 0.00 0.00 3.68
1602 1805 3.577649 CTCTGTCTCGAGCCTTTGTTA 57.422 47.619 7.81 0.00 0.00 2.41
1657 1860 6.517013 TGAGGGAGTAGTACTCAGTGATAT 57.483 41.667 27.41 8.28 46.79 1.63
1849 2054 5.468072 GCTGCAGCACATATCTTGTATAAGT 59.532 40.000 33.36 0.00 41.59 2.24
1892 2097 7.815840 TGTTTTCATTTGGTTCTGTATCTGA 57.184 32.000 0.00 0.00 0.00 3.27
2203 2424 8.406297 GTTGAGAATTGTTACCAAAGAGAAGTT 58.594 33.333 0.00 0.00 33.44 2.66
2221 2442 7.011857 AGAGAAGTTGTTGAGAATTTGAGTGAC 59.988 37.037 0.00 0.00 0.00 3.67
2222 2443 6.599244 AGAAGTTGTTGAGAATTTGAGTGACA 59.401 34.615 0.00 0.00 0.00 3.58
2298 2519 1.659954 CGATGCCTAGACTGCGAGC 60.660 63.158 0.00 0.00 0.00 5.03
2319 2540 1.583495 GGTTTAGCGGTTCTGGTGGC 61.583 60.000 0.00 0.00 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
162 163 2.852449 AGGGGCTAATTCATCAACCTGA 59.148 45.455 0.00 0.00 0.00 3.86
205 206 0.807496 CTAAAACTCAGCCAGCAGCC 59.193 55.000 0.00 0.00 45.47 4.85
310 311 3.106827 TCACAGAGGATATGCTGGAACA 58.893 45.455 0.00 0.00 36.47 3.18
311 312 3.827008 TCACAGAGGATATGCTGGAAC 57.173 47.619 0.00 0.00 36.47 3.62
312 313 3.006217 CGATCACAGAGGATATGCTGGAA 59.994 47.826 0.00 0.00 36.47 3.53
313 314 2.560105 CGATCACAGAGGATATGCTGGA 59.440 50.000 0.00 0.00 36.47 3.86
314 315 2.353505 CCGATCACAGAGGATATGCTGG 60.354 54.545 0.00 0.00 36.47 4.85
315 316 2.353505 CCCGATCACAGAGGATATGCTG 60.354 54.545 0.00 0.00 38.10 4.41
316 317 1.898472 CCCGATCACAGAGGATATGCT 59.102 52.381 0.00 0.00 0.00 3.79
317 318 1.895798 TCCCGATCACAGAGGATATGC 59.104 52.381 0.00 0.00 0.00 3.14
318 319 3.865011 CTCCCGATCACAGAGGATATG 57.135 52.381 0.00 0.00 0.00 1.78
324 325 1.135915 CAAGTCCTCCCGATCACAGAG 59.864 57.143 0.00 0.00 0.00 3.35
325 326 1.186200 CAAGTCCTCCCGATCACAGA 58.814 55.000 0.00 0.00 0.00 3.41
326 327 1.186200 TCAAGTCCTCCCGATCACAG 58.814 55.000 0.00 0.00 0.00 3.66
327 328 1.757118 GATCAAGTCCTCCCGATCACA 59.243 52.381 0.00 0.00 35.42 3.58
328 329 1.757118 TGATCAAGTCCTCCCGATCAC 59.243 52.381 0.00 0.00 39.37 3.06
329 330 2.034878 CTGATCAAGTCCTCCCGATCA 58.965 52.381 0.00 0.00 41.39 2.92
330 331 1.342819 CCTGATCAAGTCCTCCCGATC 59.657 57.143 0.00 0.00 35.81 3.69
331 332 1.418334 CCTGATCAAGTCCTCCCGAT 58.582 55.000 0.00 0.00 0.00 4.18
332 333 0.687757 CCCTGATCAAGTCCTCCCGA 60.688 60.000 0.00 0.00 0.00 5.14
333 334 1.826024 CCCTGATCAAGTCCTCCCG 59.174 63.158 0.00 0.00 0.00 5.14
334 335 0.985490 AGCCCTGATCAAGTCCTCCC 60.985 60.000 0.00 0.00 0.00 4.30
335 336 0.179936 CAGCCCTGATCAAGTCCTCC 59.820 60.000 0.00 0.00 0.00 4.30
336 337 0.179936 CCAGCCCTGATCAAGTCCTC 59.820 60.000 0.00 0.00 0.00 3.71
337 338 0.548682 ACCAGCCCTGATCAAGTCCT 60.549 55.000 0.00 0.00 0.00 3.85
338 339 0.329596 AACCAGCCCTGATCAAGTCC 59.670 55.000 0.00 0.00 0.00 3.85
339 340 2.420687 CCTAACCAGCCCTGATCAAGTC 60.421 54.545 0.00 0.00 0.00 3.01
340 341 1.561542 CCTAACCAGCCCTGATCAAGT 59.438 52.381 0.00 0.00 0.00 3.16
341 342 1.133976 CCCTAACCAGCCCTGATCAAG 60.134 57.143 0.00 0.00 0.00 3.02
342 343 0.918983 CCCTAACCAGCCCTGATCAA 59.081 55.000 0.00 0.00 0.00 2.57
343 344 0.253160 ACCCTAACCAGCCCTGATCA 60.253 55.000 0.00 0.00 0.00 2.92
344 345 1.694696 CTACCCTAACCAGCCCTGATC 59.305 57.143 0.00 0.00 0.00 2.92
345 346 1.695989 CCTACCCTAACCAGCCCTGAT 60.696 57.143 0.00 0.00 0.00 2.90
346 347 0.326238 CCTACCCTAACCAGCCCTGA 60.326 60.000 0.00 0.00 0.00 3.86
347 348 0.620700 ACCTACCCTAACCAGCCCTG 60.621 60.000 0.00 0.00 0.00 4.45
348 349 1.021275 TACCTACCCTAACCAGCCCT 58.979 55.000 0.00 0.00 0.00 5.19
349 350 1.126488 GTACCTACCCTAACCAGCCC 58.874 60.000 0.00 0.00 0.00 5.19
350 351 1.870064 TGTACCTACCCTAACCAGCC 58.130 55.000 0.00 0.00 0.00 4.85
351 352 3.986996 TTTGTACCTACCCTAACCAGC 57.013 47.619 0.00 0.00 0.00 4.85
352 353 5.687166 TGATTTGTACCTACCCTAACCAG 57.313 43.478 0.00 0.00 0.00 4.00
353 354 6.451292 TTTGATTTGTACCTACCCTAACCA 57.549 37.500 0.00 0.00 0.00 3.67
354 355 7.147966 CCAATTTGATTTGTACCTACCCTAACC 60.148 40.741 0.00 0.00 0.00 2.85
355 356 7.395206 ACCAATTTGATTTGTACCTACCCTAAC 59.605 37.037 0.00 0.00 0.00 2.34
356 357 7.471890 ACCAATTTGATTTGTACCTACCCTAA 58.528 34.615 0.00 0.00 0.00 2.69
357 358 7.034967 ACCAATTTGATTTGTACCTACCCTA 57.965 36.000 0.00 0.00 0.00 3.53
358 359 5.899278 ACCAATTTGATTTGTACCTACCCT 58.101 37.500 0.00 0.00 0.00 4.34
359 360 6.599356 AACCAATTTGATTTGTACCTACCC 57.401 37.500 0.00 0.00 0.00 3.69
373 374 5.231702 TCATCAGCACATCAAACCAATTTG 58.768 37.500 0.00 0.00 45.67 2.32
374 375 5.471556 TCATCAGCACATCAAACCAATTT 57.528 34.783 0.00 0.00 0.00 1.82
375 376 5.416083 CATCATCAGCACATCAAACCAATT 58.584 37.500 0.00 0.00 0.00 2.32
376 377 4.679639 GCATCATCAGCACATCAAACCAAT 60.680 41.667 0.00 0.00 0.00 3.16
377 378 3.367600 GCATCATCAGCACATCAAACCAA 60.368 43.478 0.00 0.00 0.00 3.67
378 379 2.164827 GCATCATCAGCACATCAAACCA 59.835 45.455 0.00 0.00 0.00 3.67
379 380 2.426024 AGCATCATCAGCACATCAAACC 59.574 45.455 0.00 0.00 0.00 3.27
380 381 3.777465 AGCATCATCAGCACATCAAAC 57.223 42.857 0.00 0.00 0.00 2.93
381 382 4.334481 CACTAGCATCATCAGCACATCAAA 59.666 41.667 0.00 0.00 0.00 2.69
382 383 3.875134 CACTAGCATCATCAGCACATCAA 59.125 43.478 0.00 0.00 0.00 2.57
383 384 3.463944 CACTAGCATCATCAGCACATCA 58.536 45.455 0.00 0.00 0.00 3.07
384 385 2.806818 CCACTAGCATCATCAGCACATC 59.193 50.000 0.00 0.00 0.00 3.06
385 386 2.847441 CCACTAGCATCATCAGCACAT 58.153 47.619 0.00 0.00 0.00 3.21
386 387 1.744798 GCCACTAGCATCATCAGCACA 60.745 52.381 0.00 0.00 42.97 4.57
387 388 0.942962 GCCACTAGCATCATCAGCAC 59.057 55.000 0.00 0.00 42.97 4.40
388 389 3.391736 GCCACTAGCATCATCAGCA 57.608 52.632 0.00 0.00 42.97 4.41
398 399 3.440173 TGATAGTTTTGCTTGCCACTAGC 59.560 43.478 0.00 0.00 44.14 3.42
399 400 5.449588 CCATGATAGTTTTGCTTGCCACTAG 60.450 44.000 0.00 0.00 0.00 2.57
400 401 4.398988 CCATGATAGTTTTGCTTGCCACTA 59.601 41.667 0.00 0.00 0.00 2.74
401 402 3.194116 CCATGATAGTTTTGCTTGCCACT 59.806 43.478 0.00 0.00 0.00 4.00
402 403 3.193267 TCCATGATAGTTTTGCTTGCCAC 59.807 43.478 0.00 0.00 0.00 5.01
403 404 3.429492 TCCATGATAGTTTTGCTTGCCA 58.571 40.909 0.00 0.00 0.00 4.92
404 405 4.660789 ATCCATGATAGTTTTGCTTGCC 57.339 40.909 0.00 0.00 0.00 4.52
405 406 6.742109 ACATATCCATGATAGTTTTGCTTGC 58.258 36.000 0.00 0.00 35.96 4.01
406 407 9.027129 CAAACATATCCATGATAGTTTTGCTTG 57.973 33.333 0.00 0.00 35.96 4.01
407 408 8.752187 ACAAACATATCCATGATAGTTTTGCTT 58.248 29.630 14.26 1.96 35.67 3.91
408 409 8.297470 ACAAACATATCCATGATAGTTTTGCT 57.703 30.769 14.26 5.61 35.67 3.91
409 410 8.931385 AACAAACATATCCATGATAGTTTTGC 57.069 30.769 14.26 0.00 35.67 3.68
410 411 9.520204 GGAACAAACATATCCATGATAGTTTTG 57.480 33.333 0.00 13.44 36.86 2.44
411 412 9.253832 TGGAACAAACATATCCATGATAGTTTT 57.746 29.630 0.00 0.00 38.30 2.43
412 413 8.821686 TGGAACAAACATATCCATGATAGTTT 57.178 30.769 0.00 0.00 38.30 2.66
413 414 7.013655 GCTGGAACAAACATATCCATGATAGTT 59.986 37.037 0.00 0.00 42.12 2.24
414 415 6.488006 GCTGGAACAAACATATCCATGATAGT 59.512 38.462 0.00 0.00 42.12 2.12
415 416 6.713903 AGCTGGAACAAACATATCCATGATAG 59.286 38.462 0.00 0.00 42.12 2.08
416 417 6.604171 AGCTGGAACAAACATATCCATGATA 58.396 36.000 0.00 0.00 42.12 2.15
417 418 5.452255 AGCTGGAACAAACATATCCATGAT 58.548 37.500 0.00 0.00 42.12 2.45
418 419 4.858850 AGCTGGAACAAACATATCCATGA 58.141 39.130 0.00 0.00 42.12 3.07
419 420 5.587388 AAGCTGGAACAAACATATCCATG 57.413 39.130 0.00 0.00 42.12 3.66
420 421 6.491403 GGATAAGCTGGAACAAACATATCCAT 59.509 38.462 8.30 0.00 41.23 3.41
421 422 5.827797 GGATAAGCTGGAACAAACATATCCA 59.172 40.000 8.30 0.00 41.23 3.41
422 423 6.016777 CAGGATAAGCTGGAACAAACATATCC 60.017 42.308 5.87 5.87 41.56 2.59
423 424 6.543831 ACAGGATAAGCTGGAACAAACATATC 59.456 38.462 0.00 0.00 38.70 1.63
424 425 6.319658 CACAGGATAAGCTGGAACAAACATAT 59.680 38.462 0.00 0.00 38.70 1.78
425 426 5.647658 CACAGGATAAGCTGGAACAAACATA 59.352 40.000 0.00 0.00 38.70 2.29
426 427 4.460382 CACAGGATAAGCTGGAACAAACAT 59.540 41.667 0.00 0.00 38.70 2.71
427 428 3.820467 CACAGGATAAGCTGGAACAAACA 59.180 43.478 0.00 0.00 38.70 2.83
435 436 2.477825 CGATCACACAGGATAAGCTGG 58.522 52.381 0.00 0.00 0.00 4.85
436 437 2.477825 CCGATCACACAGGATAAGCTG 58.522 52.381 0.00 0.00 0.00 4.24
444 445 0.972983 AGTCCTCCCGATCACACAGG 60.973 60.000 0.00 0.00 0.00 4.00
455 456 0.985490 AGCCCTGATCAAGTCCTCCC 60.985 60.000 0.00 0.00 0.00 4.30
469 470 1.021275 TACCTACCCTAACCAGCCCT 58.979 55.000 0.00 0.00 0.00 5.19
475 476 7.147966 CCAATTTGATTTGTACCTACCCTAACC 60.148 40.741 0.00 0.00 0.00 2.85
495 496 5.471556 TCATCAGCACATCAAACCAATTT 57.528 34.783 0.00 0.00 0.00 1.82
521 522 2.285977 TGCTGCTATTGCTCATCACTG 58.714 47.619 0.00 0.00 40.48 3.66
553 554 5.793817 TGTACTGCTGCAGATTCTTTTCTA 58.206 37.500 34.28 11.27 35.18 2.10
620 621 5.003804 GGCATCTCCTCAACTTGTTTTCTA 58.996 41.667 0.00 0.00 0.00 2.10
668 672 8.083462 TGAACACTACTGATGTGTGTAATTTC 57.917 34.615 10.06 5.29 46.46 2.17
733 934 7.160049 TGAAGCAATCATTGAGGCAAAAATAA 58.840 30.769 0.00 0.00 31.50 1.40
775 976 0.727398 GATGCTTACAAGACGTGGCC 59.273 55.000 0.00 0.00 0.00 5.36
782 983 5.163301 GGTGAGGATTAGGATGCTTACAAGA 60.163 44.000 0.00 0.00 40.50 3.02
852 1053 4.036498 TGGTTGGAAAATGCAGCAAAATTG 59.964 37.500 0.00 0.00 0.00 2.32
1422 1625 2.213499 CACTTGATATGGAACGGAGGC 58.787 52.381 0.00 0.00 0.00 4.70
1437 1640 7.224753 AGTGTTGTACTAAATCAGTGACACTTG 59.775 37.037 5.04 2.11 45.18 3.16
1470 1673 2.268280 CAGAGGTGGGCAGCTGAG 59.732 66.667 20.43 0.00 39.57 3.35
1532 1735 4.589908 ACCAGCCAGGAAATTACAACTAG 58.410 43.478 0.00 0.00 41.22 2.57
1566 1769 1.672881 CAGAGCCCGGCTTTGAATTAG 59.327 52.381 22.73 0.00 42.32 1.73
1657 1860 2.204237 CTGCATGCAACTATACGAGCA 58.796 47.619 22.88 0.00 41.73 4.26
1723 1926 6.545666 TCAAGTGGTAGAGAAATCAGCAAAAA 59.454 34.615 0.00 0.00 0.00 1.94
1849 2054 3.860641 ACATCATGTTCATGTACAGCGA 58.139 40.909 11.03 9.89 32.48 4.93
2055 2263 6.959366 TCATATGGAAGGGAGGAAAACATTTT 59.041 34.615 2.13 0.00 0.00 1.82
2065 2273 7.008941 AGATGAAAAATCATATGGAAGGGAGG 58.991 38.462 2.13 0.00 0.00 4.30
2066 2274 7.722728 TGAGATGAAAAATCATATGGAAGGGAG 59.277 37.037 2.13 0.00 0.00 4.30
2156 2377 2.175499 CCTAGAATCCCATCCCAAGCAA 59.825 50.000 0.00 0.00 0.00 3.91
2163 2384 5.574970 ATTCTCAACCTAGAATCCCATCC 57.425 43.478 0.00 0.00 41.34 3.51
2203 2424 6.318396 TGTTCATGTCACTCAAATTCTCAACA 59.682 34.615 0.00 0.00 0.00 3.33
2221 2442 7.544566 ACTTTACCTACGTAATCAGTGTTCATG 59.455 37.037 0.00 0.00 34.44 3.07
2222 2443 7.544566 CACTTTACCTACGTAATCAGTGTTCAT 59.455 37.037 0.00 0.00 37.94 2.57
2298 2519 1.156736 CACCAGAACCGCTAAACCTG 58.843 55.000 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.