Multiple sequence alignment - TraesCS5B01G069800

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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 TraesCS5B01G069800 chr5B 100.000 3185 0 0 1 3185 79801213 79804397 0.000000e+00 5882
1 TraesCS5B01G069800 chr5A 93.855 1790 67 18 1423 3181 67468940 67470717 0.000000e+00 2656
2 TraesCS5B01G069800 chr5A 93.882 948 40 4 410 1342 67467968 67468912 0.000000e+00 1413
3 TraesCS5B01G069800 chr5A 82.621 351 27 13 17 340 67467641 67467984 2.420000e-71 279
4 TraesCS5B01G069800 chr5D 92.599 1797 82 22 1423 3183 72900125 72901906 0.000000e+00 2534
5 TraesCS5B01G069800 chr5D 89.934 457 23 12 908 1342 72899642 72900097 4.610000e-158 568
6 TraesCS5B01G069800 chr5D 85.250 400 34 7 491 874 72899124 72899514 3.850000e-104 388
7 TraesCS5B01G069800 chr5D 100.000 56 0 0 410 465 72899069 72899124 1.560000e-18 104
8 TraesCS5B01G069800 chr3B 89.254 912 80 13 1402 2301 125783911 125783006 0.000000e+00 1125
9 TraesCS5B01G069800 chr3B 88.009 467 33 10 899 1344 125784400 125783936 6.050000e-147 531
10 TraesCS5B01G069800 chr3D 85.282 992 82 34 921 1883 79510791 79509835 0.000000e+00 965
11 TraesCS5B01G069800 chr3D 88.024 501 58 2 1880 2379 79509739 79509240 2.740000e-165 592
12 TraesCS5B01G069800 chr3D 82.624 282 32 11 2483 2761 79509162 79508895 1.910000e-57 233


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 TraesCS5B01G069800 chr5B 79801213 79804397 3184 False 5882.000000 5882 100.000000 1 3185 1 chr5B.!!$F1 3184
1 TraesCS5B01G069800 chr5A 67467641 67470717 3076 False 1449.333333 2656 90.119333 17 3181 3 chr5A.!!$F1 3164
2 TraesCS5B01G069800 chr5D 72899069 72901906 2837 False 898.500000 2534 91.945750 410 3183 4 chr5D.!!$F1 2773
3 TraesCS5B01G069800 chr3B 125783006 125784400 1394 True 828.000000 1125 88.631500 899 2301 2 chr3B.!!$R1 1402
4 TraesCS5B01G069800 chr3D 79508895 79510791 1896 True 596.666667 965 85.310000 921 2761 3 chr3D.!!$R1 1840

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
343 370 0.165944 GTGTGATCTCGGCGTTTTGG 59.834 55.0 6.85 0.0 0.0 3.28 F
345 372 0.165944 GTGATCTCGGCGTTTTGGTG 59.834 55.0 6.85 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1734 1918 1.398390 GAAGGGCACGAATGATCACAC 59.602 52.381 0.00 0.0 0.00 3.82 R
2311 2596 5.133221 AGTTTTGCAACTACTGGACTGAAT 58.867 37.500 11.53 0.0 41.81 2.57 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
68 69 1.740025 GCTCTTAACAAAGGCAGCGAT 59.260 47.619 0.00 0.00 0.00 4.58
81 82 2.432510 GGCAGCGATAGGGCTAGATTAT 59.567 50.000 0.00 0.00 42.53 1.28
82 83 3.452474 GCAGCGATAGGGCTAGATTATG 58.548 50.000 0.00 0.00 42.53 1.90
107 108 5.730568 GCCGACATGTTTGGCTTTCTATTAG 60.731 44.000 26.96 0.00 45.40 1.73
109 110 5.584649 CGACATGTTTGGCTTTCTATTAGGA 59.415 40.000 0.00 0.00 0.00 2.94
118 119 7.914427 TGGCTTTCTATTAGGACAGAGATTA 57.086 36.000 0.00 0.00 0.00 1.75
132 133 7.016072 AGGACAGAGATTATTTGTATCCCTGAG 59.984 40.741 0.00 0.00 33.16 3.35
135 136 7.989741 ACAGAGATTATTTGTATCCCTGAGTTG 59.010 37.037 0.00 0.00 33.16 3.16
165 167 8.962884 AAGTGTTTTCATTGCTAAAAAGGAAT 57.037 26.923 0.00 0.00 30.69 3.01
247 274 5.149973 TCACCAGGTAAAGTTTATGCGTA 57.850 39.130 0.00 0.00 0.00 4.42
260 287 8.822652 AAGTTTATGCGTAACAAGTACTACTT 57.177 30.769 0.00 0.53 39.39 2.24
261 288 8.458212 AGTTTATGCGTAACAAGTACTACTTC 57.542 34.615 0.00 0.00 36.03 3.01
263 290 5.656213 ATGCGTAACAAGTACTACTTCCT 57.344 39.130 0.00 0.00 36.03 3.36
265 292 6.764308 TGCGTAACAAGTACTACTTCCTAT 57.236 37.500 0.00 0.00 36.03 2.57
266 293 7.161773 TGCGTAACAAGTACTACTTCCTATT 57.838 36.000 0.00 0.00 36.03 1.73
268 295 8.739039 TGCGTAACAAGTACTACTTCCTATTAA 58.261 33.333 0.00 0.00 36.03 1.40
269 296 9.014533 GCGTAACAAGTACTACTTCCTATTAAC 57.985 37.037 0.00 0.00 36.03 2.01
270 297 9.214953 CGTAACAAGTACTACTTCCTATTAACG 57.785 37.037 0.00 0.53 36.03 3.18
295 322 7.548097 GGACTCTGTTAAATCAGTGTGATCTA 58.452 38.462 5.75 0.00 40.60 1.98
296 323 7.489757 GGACTCTGTTAAATCAGTGTGATCTAC 59.510 40.741 5.75 0.00 40.60 2.59
337 364 1.645034 AAATCAGTGTGATCTCGGCG 58.355 50.000 0.00 0.00 35.76 6.46
338 365 0.532573 AATCAGTGTGATCTCGGCGT 59.467 50.000 6.85 0.00 35.76 5.68
339 366 0.532573 ATCAGTGTGATCTCGGCGTT 59.467 50.000 6.85 0.00 29.59 4.84
340 367 0.317160 TCAGTGTGATCTCGGCGTTT 59.683 50.000 6.85 0.00 0.00 3.60
341 368 1.148310 CAGTGTGATCTCGGCGTTTT 58.852 50.000 6.85 0.00 0.00 2.43
342 369 1.136252 CAGTGTGATCTCGGCGTTTTG 60.136 52.381 6.85 0.00 0.00 2.44
343 370 0.165944 GTGTGATCTCGGCGTTTTGG 59.834 55.000 6.85 0.00 0.00 3.28
344 371 0.250124 TGTGATCTCGGCGTTTTGGT 60.250 50.000 6.85 0.00 0.00 3.67
345 372 0.165944 GTGATCTCGGCGTTTTGGTG 59.834 55.000 6.85 0.00 0.00 4.17
346 373 0.953471 TGATCTCGGCGTTTTGGTGG 60.953 55.000 6.85 0.00 0.00 4.61
347 374 2.253414 GATCTCGGCGTTTTGGTGGC 62.253 60.000 6.85 0.00 0.00 5.01
348 375 4.038080 CTCGGCGTTTTGGTGGCC 62.038 66.667 6.85 0.00 43.42 5.36
351 378 4.662961 GGCGTTTTGGTGGCCAGC 62.663 66.667 28.15 28.15 46.13 4.85
352 379 4.999939 GCGTTTTGGTGGCCAGCG 63.000 66.667 28.67 15.66 33.81 5.18
353 380 3.283684 CGTTTTGGTGGCCAGCGA 61.284 61.111 28.67 25.17 33.81 4.93
354 381 2.644992 GTTTTGGTGGCCAGCGAG 59.355 61.111 28.67 0.00 33.81 5.03
355 382 1.896660 GTTTTGGTGGCCAGCGAGA 60.897 57.895 28.67 20.26 33.81 4.04
356 383 1.600636 TTTTGGTGGCCAGCGAGAG 60.601 57.895 28.67 0.00 33.81 3.20
357 384 2.337879 TTTTGGTGGCCAGCGAGAGT 62.338 55.000 28.67 0.00 33.81 3.24
358 385 3.535629 TTGGTGGCCAGCGAGAGTG 62.536 63.158 28.67 0.00 33.81 3.51
374 401 3.997397 TGCTGCGCCGGTTGAGTA 61.997 61.111 4.18 0.00 0.00 2.59
375 402 2.740826 GCTGCGCCGGTTGAGTAA 60.741 61.111 4.18 0.00 0.00 2.24
376 403 2.106683 GCTGCGCCGGTTGAGTAAT 61.107 57.895 4.18 0.00 0.00 1.89
377 404 1.715585 CTGCGCCGGTTGAGTAATG 59.284 57.895 4.18 0.00 0.00 1.90
378 405 1.705337 CTGCGCCGGTTGAGTAATGG 61.705 60.000 4.18 0.00 0.00 3.16
379 406 1.448893 GCGCCGGTTGAGTAATGGA 60.449 57.895 1.90 0.00 0.00 3.41
380 407 1.022451 GCGCCGGTTGAGTAATGGAA 61.022 55.000 1.90 0.00 0.00 3.53
381 408 1.663695 CGCCGGTTGAGTAATGGAAT 58.336 50.000 1.90 0.00 0.00 3.01
382 409 1.597663 CGCCGGTTGAGTAATGGAATC 59.402 52.381 1.90 0.00 0.00 2.52
383 410 2.639065 GCCGGTTGAGTAATGGAATCA 58.361 47.619 1.90 0.00 0.00 2.57
384 411 3.214328 GCCGGTTGAGTAATGGAATCAT 58.786 45.455 1.90 0.00 34.56 2.45
385 412 3.632145 GCCGGTTGAGTAATGGAATCATT 59.368 43.478 1.90 0.00 44.87 2.57
386 413 4.819630 GCCGGTTGAGTAATGGAATCATTA 59.180 41.667 1.90 0.00 42.90 1.90
387 414 5.473504 GCCGGTTGAGTAATGGAATCATTAT 59.526 40.000 1.90 0.00 44.65 1.28
388 415 6.568462 GCCGGTTGAGTAATGGAATCATTATG 60.568 42.308 1.90 0.00 44.65 1.90
389 416 6.486657 CCGGTTGAGTAATGGAATCATTATGT 59.513 38.462 0.00 0.00 44.65 2.29
390 417 7.013274 CCGGTTGAGTAATGGAATCATTATGTT 59.987 37.037 0.00 0.00 44.65 2.71
391 418 8.070171 CGGTTGAGTAATGGAATCATTATGTTC 58.930 37.037 2.71 0.00 44.65 3.18
392 419 8.352942 GGTTGAGTAATGGAATCATTATGTTCC 58.647 37.037 14.98 14.98 44.65 3.62
400 427 7.773489 TGGAATCATTATGTTCCAGTTCAAA 57.227 32.000 18.38 2.72 46.59 2.69
401 428 8.187913 TGGAATCATTATGTTCCAGTTCAAAA 57.812 30.769 18.38 2.22 46.59 2.44
402 429 8.646004 TGGAATCATTATGTTCCAGTTCAAAAA 58.354 29.630 18.38 1.72 46.59 1.94
403 430 9.143631 GGAATCATTATGTTCCAGTTCAAAAAG 57.856 33.333 16.18 0.00 42.72 2.27
404 431 9.912634 GAATCATTATGTTCCAGTTCAAAAAGA 57.087 29.630 0.00 0.00 0.00 2.52
407 434 9.748708 TCATTATGTTCCAGTTCAAAAAGAAAG 57.251 29.630 0.00 0.00 38.13 2.62
408 435 9.748708 CATTATGTTCCAGTTCAAAAAGAAAGA 57.251 29.630 0.00 0.00 38.13 2.52
530 562 4.988598 CCGGCGCACAAGTCCAGT 62.989 66.667 10.83 0.00 0.00 4.00
793 837 3.426159 CGCGAATCTTAATTGCTGTGGTT 60.426 43.478 0.00 0.00 0.00 3.67
856 902 2.098280 GTCTCAGCTACGAAGAGATGCA 59.902 50.000 4.22 0.00 40.21 3.96
973 1113 0.744414 CCGTCTGCATTACCACCTGG 60.744 60.000 0.00 0.00 42.17 4.45
976 1116 0.618458 TCTGCATTACCACCTGGACC 59.382 55.000 0.00 0.00 38.94 4.46
1034 1200 1.640428 TCGTGGCGAATGACATTCTC 58.360 50.000 22.54 16.25 33.95 2.87
1206 1372 1.302511 ACTGCAACATCCACCGGTC 60.303 57.895 2.59 0.00 0.00 4.79
1388 1555 5.487433 TGTATCATGGGTTTGACAGTGTAG 58.513 41.667 0.00 0.00 0.00 2.74
1413 1580 3.974401 CACATTGTTTTACTTGTGCTCGG 59.026 43.478 0.00 0.00 33.78 4.63
1421 1588 0.593128 ACTTGTGCTCGGCATTGTTC 59.407 50.000 1.90 0.00 41.91 3.18
1460 1627 7.936847 TCTGCTTCAAGGTAGTTAAATCTGAAA 59.063 33.333 0.00 0.00 0.00 2.69
1462 1629 9.733556 TGCTTCAAGGTAGTTAAATCTGAAATA 57.266 29.630 0.00 0.00 0.00 1.40
1734 1918 4.651778 TGGTACCAAAGATCACTTGAAGG 58.348 43.478 13.60 0.00 36.39 3.46
1820 2004 3.589735 TGGTGTCTGGGTTGGTATGTTAT 59.410 43.478 0.00 0.00 0.00 1.89
1857 2042 9.410556 GATACTGCAAAGTGTTTTATCATGTTT 57.589 29.630 0.00 0.00 0.00 2.83
1860 2045 9.762933 ACTGCAAAGTGTTTTATCATGTTTATT 57.237 25.926 0.00 0.00 0.00 1.40
2037 2321 1.997256 TAAAGGGCCGTGGTGTTGGT 61.997 55.000 0.00 0.00 0.00 3.67
2070 2354 5.767168 GCAGATATTACAGAAGGCTTCCAAT 59.233 40.000 23.09 19.95 0.00 3.16
2075 2359 3.073274 ACAGAAGGCTTCCAATGGTAC 57.927 47.619 23.09 0.00 0.00 3.34
2094 2378 6.108687 TGGTACAGAACTTAATGATGCAGAG 58.891 40.000 0.00 0.00 0.00 3.35
2177 2461 1.937546 GAACCCAGCCCTGATTTGCG 61.938 60.000 0.00 0.00 0.00 4.85
2200 2484 6.087028 GCGTCTTTAGCTAGATAAGACAATCG 59.913 42.308 25.58 17.30 44.98 3.34
2311 2596 6.039717 AGCTTTTATTCAAAACTGCAGTCTCA 59.960 34.615 21.95 3.14 30.88 3.27
2346 2631 4.022849 AGTTGCAAAACTAGTGATCCTTGC 60.023 41.667 0.00 14.88 39.62 4.01
2642 2937 7.102346 CACATCCTGTATTCTTCTTCTTCAGT 58.898 38.462 0.00 0.00 0.00 3.41
2648 2944 7.279758 CCTGTATTCTTCTTCTTCAGTTGATCC 59.720 40.741 0.00 0.00 0.00 3.36
2718 3015 3.452786 TGCCTCCTTCGCTCTCCG 61.453 66.667 0.00 0.00 38.61 4.63
2740 3038 4.821805 CGTGGGTTCAGCATTTATAGGAAT 59.178 41.667 0.00 0.00 0.00 3.01
2741 3039 5.995282 CGTGGGTTCAGCATTTATAGGAATA 59.005 40.000 0.00 0.00 0.00 1.75
2742 3040 6.655003 CGTGGGTTCAGCATTTATAGGAATAT 59.345 38.462 0.00 0.00 0.00 1.28
2743 3041 7.822334 CGTGGGTTCAGCATTTATAGGAATATA 59.178 37.037 0.00 0.00 0.00 0.86
2822 3121 2.285834 CGGATAAGTTGTGCGATTCTGC 60.286 50.000 7.77 0.00 31.71 4.26
2883 3182 7.968405 GGCGAATATGATTCACTTGTAAAACTT 59.032 33.333 0.00 0.00 0.00 2.66
2884 3183 9.982291 GCGAATATGATTCACTTGTAAAACTTA 57.018 29.630 0.00 0.00 0.00 2.24
3064 3381 1.334869 CCTGTGAGTTGTTCTTGTGCC 59.665 52.381 0.00 0.00 0.00 5.01
3069 3386 3.002348 GTGAGTTGTTCTTGTGCCAGTAC 59.998 47.826 0.00 0.00 0.00 2.73
3070 3387 3.202906 GAGTTGTTCTTGTGCCAGTACA 58.797 45.455 0.00 0.00 0.00 2.90
3101 3423 6.769512 ACTGTACAGGTACAACAATCTTCAT 58.230 36.000 26.12 0.00 44.47 2.57
3183 3508 3.064931 GTGGGATATAACTTGGCTACGC 58.935 50.000 0.00 0.00 0.00 4.42
3184 3509 2.701423 TGGGATATAACTTGGCTACGCA 59.299 45.455 0.00 0.00 0.00 5.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 2.176889 GTCGGCCATAATCTAGCCCTA 58.823 52.381 2.24 0.00 44.13 3.53
118 119 7.121759 CACTTTCATCAACTCAGGGATACAAAT 59.878 37.037 0.00 0.00 39.74 2.32
122 123 5.491982 ACACTTTCATCAACTCAGGGATAC 58.508 41.667 0.00 0.00 0.00 2.24
168 170 8.666129 TTCTACAGAGAGAGAATTTTTAGGGA 57.334 34.615 0.00 0.00 31.77 4.20
169 171 9.726438 TTTTCTACAGAGAGAGAATTTTTAGGG 57.274 33.333 0.00 0.00 31.91 3.53
203 205 9.971922 GGTGAGGAATTGATATTATTTTTCAGG 57.028 33.333 0.00 0.00 0.00 3.86
206 208 9.971922 CCTGGTGAGGAATTGATATTATTTTTC 57.028 33.333 0.00 0.00 42.93 2.29
212 214 8.778059 ACTTTACCTGGTGAGGAATTGATATTA 58.222 33.333 10.23 0.00 42.93 0.98
213 215 7.643123 ACTTTACCTGGTGAGGAATTGATATT 58.357 34.615 10.23 0.00 42.93 1.28
214 216 7.213178 ACTTTACCTGGTGAGGAATTGATAT 57.787 36.000 10.23 0.00 42.93 1.63
215 217 6.636454 ACTTTACCTGGTGAGGAATTGATA 57.364 37.500 10.23 0.00 42.93 2.15
247 274 8.246871 GTCCGTTAATAGGAAGTAGTACTTGTT 58.753 37.037 20.21 10.11 38.80 2.83
260 287 8.070034 TGATTTAACAGAGTCCGTTAATAGGA 57.930 34.615 11.54 0.00 38.32 2.94
261 288 7.980099 ACTGATTTAACAGAGTCCGTTAATAGG 59.020 37.037 11.54 6.45 38.32 2.57
263 290 8.308931 ACACTGATTTAACAGAGTCCGTTAATA 58.691 33.333 11.54 5.00 38.32 0.98
265 292 6.422701 CACACTGATTTAACAGAGTCCGTTAA 59.577 38.462 7.47 7.47 39.02 2.01
266 293 5.924254 CACACTGATTTAACAGAGTCCGTTA 59.076 40.000 0.00 0.00 39.02 3.18
268 295 4.038763 TCACACTGATTTAACAGAGTCCGT 59.961 41.667 0.00 0.00 39.02 4.69
269 296 4.556233 TCACACTGATTTAACAGAGTCCG 58.444 43.478 0.00 0.00 39.02 4.79
270 297 6.402222 AGATCACACTGATTTAACAGAGTCC 58.598 40.000 0.00 0.00 39.02 3.85
319 346 0.532573 ACGCCGAGATCACACTGATT 59.467 50.000 0.00 0.00 37.20 2.57
320 347 0.532573 AACGCCGAGATCACACTGAT 59.467 50.000 0.00 0.00 40.34 2.90
321 348 0.317160 AAACGCCGAGATCACACTGA 59.683 50.000 0.00 0.00 0.00 3.41
322 349 1.136252 CAAAACGCCGAGATCACACTG 60.136 52.381 0.00 0.00 0.00 3.66
323 350 1.148310 CAAAACGCCGAGATCACACT 58.852 50.000 0.00 0.00 0.00 3.55
324 351 0.165944 CCAAAACGCCGAGATCACAC 59.834 55.000 0.00 0.00 0.00 3.82
325 352 0.250124 ACCAAAACGCCGAGATCACA 60.250 50.000 0.00 0.00 0.00 3.58
326 353 0.165944 CACCAAAACGCCGAGATCAC 59.834 55.000 0.00 0.00 0.00 3.06
327 354 0.953471 CCACCAAAACGCCGAGATCA 60.953 55.000 0.00 0.00 0.00 2.92
328 355 1.794222 CCACCAAAACGCCGAGATC 59.206 57.895 0.00 0.00 0.00 2.75
329 356 2.332654 GCCACCAAAACGCCGAGAT 61.333 57.895 0.00 0.00 0.00 2.75
330 357 2.975799 GCCACCAAAACGCCGAGA 60.976 61.111 0.00 0.00 0.00 4.04
331 358 4.038080 GGCCACCAAAACGCCGAG 62.038 66.667 0.00 0.00 31.92 4.63
332 359 4.877619 TGGCCACCAAAACGCCGA 62.878 61.111 0.00 0.00 46.12 5.54
333 360 4.341502 CTGGCCACCAAAACGCCG 62.342 66.667 0.00 0.00 46.12 6.46
334 361 4.662961 GCTGGCCACCAAAACGCC 62.663 66.667 0.00 0.00 43.32 5.68
335 362 4.999939 CGCTGGCCACCAAAACGC 63.000 66.667 0.00 0.00 30.80 4.84
336 363 3.254014 CTCGCTGGCCACCAAAACG 62.254 63.158 0.00 0.00 30.80 3.60
337 364 1.856265 CTCTCGCTGGCCACCAAAAC 61.856 60.000 0.00 0.00 30.80 2.43
338 365 1.600636 CTCTCGCTGGCCACCAAAA 60.601 57.895 0.00 0.00 30.80 2.44
339 366 2.032528 CTCTCGCTGGCCACCAAA 59.967 61.111 0.00 0.00 30.80 3.28
340 367 3.241530 ACTCTCGCTGGCCACCAA 61.242 61.111 0.00 0.00 30.80 3.67
341 368 4.007644 CACTCTCGCTGGCCACCA 62.008 66.667 0.00 0.00 0.00 4.17
343 370 4.385405 AGCACTCTCGCTGGCCAC 62.385 66.667 0.00 0.00 41.85 5.01
359 386 1.705337 CCATTACTCAACCGGCGCAG 61.705 60.000 10.83 4.65 0.00 5.18
360 387 1.743623 CCATTACTCAACCGGCGCA 60.744 57.895 10.83 0.00 0.00 6.09
361 388 1.022451 TTCCATTACTCAACCGGCGC 61.022 55.000 0.00 0.00 0.00 6.53
362 389 1.597663 GATTCCATTACTCAACCGGCG 59.402 52.381 0.00 0.00 0.00 6.46
363 390 2.639065 TGATTCCATTACTCAACCGGC 58.361 47.619 0.00 0.00 0.00 6.13
364 391 6.486657 ACATAATGATTCCATTACTCAACCGG 59.513 38.462 0.00 0.00 45.07 5.28
365 392 7.496529 ACATAATGATTCCATTACTCAACCG 57.503 36.000 0.00 0.00 45.07 4.44
366 393 8.352942 GGAACATAATGATTCCATTACTCAACC 58.647 37.037 0.00 0.00 45.07 3.77
377 404 9.143631 CTTTTTGAACTGGAACATAATGATTCC 57.856 33.333 0.00 0.00 44.08 3.01
378 405 9.912634 TCTTTTTGAACTGGAACATAATGATTC 57.087 29.630 0.00 0.00 38.20 2.52
381 408 9.748708 CTTTCTTTTTGAACTGGAACATAATGA 57.251 29.630 0.00 0.00 38.20 2.57
382 409 9.748708 TCTTTCTTTTTGAACTGGAACATAATG 57.251 29.630 0.00 0.00 38.20 1.90
384 411 9.801873 CTTCTTTCTTTTTGAACTGGAACATAA 57.198 29.630 0.00 0.00 38.20 1.90
385 412 8.966868 ACTTCTTTCTTTTTGAACTGGAACATA 58.033 29.630 0.00 0.00 38.20 2.29
386 413 7.761249 CACTTCTTTCTTTTTGAACTGGAACAT 59.239 33.333 0.00 0.00 38.20 2.71
387 414 7.090173 CACTTCTTTCTTTTTGAACTGGAACA 58.910 34.615 0.00 0.00 33.88 3.18
388 415 7.062255 CACACTTCTTTCTTTTTGAACTGGAAC 59.938 37.037 0.00 0.00 33.88 3.62
389 416 7.040062 TCACACTTCTTTCTTTTTGAACTGGAA 60.040 33.333 0.00 0.00 33.88 3.53
390 417 6.432783 TCACACTTCTTTCTTTTTGAACTGGA 59.567 34.615 0.00 0.00 33.88 3.86
391 418 6.620678 TCACACTTCTTTCTTTTTGAACTGG 58.379 36.000 0.00 0.00 33.88 4.00
392 419 8.186821 AGATCACACTTCTTTCTTTTTGAACTG 58.813 33.333 0.00 0.00 33.88 3.16
393 420 8.286191 AGATCACACTTCTTTCTTTTTGAACT 57.714 30.769 0.00 0.00 33.88 3.01
394 421 7.374491 CGAGATCACACTTCTTTCTTTTTGAAC 59.626 37.037 0.00 0.00 33.88 3.18
395 422 7.409697 CGAGATCACACTTCTTTCTTTTTGAA 58.590 34.615 0.00 0.00 0.00 2.69
396 423 6.017934 CCGAGATCACACTTCTTTCTTTTTGA 60.018 38.462 0.00 0.00 0.00 2.69
397 424 6.138761 CCGAGATCACACTTCTTTCTTTTTG 58.861 40.000 0.00 0.00 0.00 2.44
398 425 5.278022 GCCGAGATCACACTTCTTTCTTTTT 60.278 40.000 0.00 0.00 0.00 1.94
399 426 4.214332 GCCGAGATCACACTTCTTTCTTTT 59.786 41.667 0.00 0.00 0.00 2.27
400 427 3.748568 GCCGAGATCACACTTCTTTCTTT 59.251 43.478 0.00 0.00 0.00 2.52
401 428 3.330267 GCCGAGATCACACTTCTTTCTT 58.670 45.455 0.00 0.00 0.00 2.52
402 429 2.672478 CGCCGAGATCACACTTCTTTCT 60.672 50.000 0.00 0.00 0.00 2.52
403 430 1.656095 CGCCGAGATCACACTTCTTTC 59.344 52.381 0.00 0.00 0.00 2.62
404 431 1.000955 ACGCCGAGATCACACTTCTTT 59.999 47.619 0.00 0.00 0.00 2.52
405 432 0.603569 ACGCCGAGATCACACTTCTT 59.396 50.000 0.00 0.00 0.00 2.52
406 433 0.603569 AACGCCGAGATCACACTTCT 59.396 50.000 0.00 0.00 0.00 2.85
407 434 0.716108 CAACGCCGAGATCACACTTC 59.284 55.000 0.00 0.00 0.00 3.01
408 435 1.291877 GCAACGCCGAGATCACACTT 61.292 55.000 0.00 0.00 0.00 3.16
485 515 4.824515 AGTCGCCGAGGAGGAGGG 62.825 72.222 0.00 0.00 45.00 4.30
552 584 0.033228 ATGCTCTCGAGTATGGCTGC 59.967 55.000 13.13 7.29 32.46 5.25
793 837 7.386848 GCACGGCCTCTGAATAAAACTATAATA 59.613 37.037 0.00 0.00 0.00 0.98
895 941 9.553064 ACCTAGACTGTAAATTCATCATGATTC 57.447 33.333 5.16 0.00 0.00 2.52
915 1055 7.630082 ACACAAATTATTTGGAGCTACCTAGA 58.370 34.615 20.00 0.00 44.81 2.43
973 1113 1.005630 AGTGCTCACAGCTTCGGTC 60.006 57.895 2.63 0.00 42.97 4.79
976 1116 2.858868 GCAGTGCTCACAGCTTCG 59.141 61.111 8.18 0.00 42.97 3.79
1206 1372 1.674359 TGCCGTTGCCCAATGTATAG 58.326 50.000 0.15 0.00 36.33 1.31
1358 1524 7.118496 TGTCAAACCCATGATACAACTTTTT 57.882 32.000 0.00 0.00 0.00 1.94
1359 1525 6.323739 ACTGTCAAACCCATGATACAACTTTT 59.676 34.615 0.00 0.00 0.00 2.27
1360 1526 5.833131 ACTGTCAAACCCATGATACAACTTT 59.167 36.000 0.00 0.00 0.00 2.66
1361 1527 5.241506 CACTGTCAAACCCATGATACAACTT 59.758 40.000 0.00 0.00 0.00 2.66
1364 1530 4.724399 ACACTGTCAAACCCATGATACAA 58.276 39.130 0.00 0.00 0.00 2.41
1370 1536 4.024048 GTGAACTACACTGTCAAACCCATG 60.024 45.833 0.00 0.00 45.13 3.66
1371 1537 4.134563 GTGAACTACACTGTCAAACCCAT 58.865 43.478 0.00 0.00 45.13 4.00
1388 1555 5.171337 CGAGCACAAGTAAAACAATGTGAAC 59.829 40.000 15.72 9.55 44.52 3.18
1400 1567 1.890876 ACAATGCCGAGCACAAGTAA 58.109 45.000 0.50 0.00 43.04 2.24
1407 1574 2.433888 TGGGAACAATGCCGAGCA 59.566 55.556 1.01 1.01 40.61 4.26
1421 1588 5.928264 CCTTGAAGCAGAAAACTAAATTGGG 59.072 40.000 0.00 0.00 0.00 4.12
1528 1703 9.903682 CTTATTTGAGAATGTTCACAAGTTGAT 57.096 29.630 10.54 0.00 38.61 2.57
1734 1918 1.398390 GAAGGGCACGAATGATCACAC 59.602 52.381 0.00 0.00 0.00 3.82
1820 2004 6.719370 ACACTTTGCAGTATCCAAAAGGATAA 59.281 34.615 5.84 0.00 33.38 1.75
1860 2045 9.831737 GAGTGTACAAGTTAAGAAAGATACGTA 57.168 33.333 0.00 0.00 0.00 3.57
2037 2321 7.604164 GCCTTCTGTAATATCTGCTTAATGCTA 59.396 37.037 0.00 0.00 43.37 3.49
2070 2354 6.048732 TCTGCATCATTAAGTTCTGTACCA 57.951 37.500 0.00 0.00 0.00 3.25
2075 2359 6.915544 TTAGCTCTGCATCATTAAGTTCTG 57.084 37.500 0.00 0.00 0.00 3.02
2085 2369 5.424573 AGCTATATCCATTAGCTCTGCATCA 59.575 40.000 0.00 0.00 42.93 3.07
2177 2461 9.337091 GATCGATTGTCTTATCTAGCTAAAGAC 57.663 37.037 22.00 22.00 45.99 3.01
2311 2596 5.133221 AGTTTTGCAACTACTGGACTGAAT 58.867 37.500 11.53 0.00 41.81 2.57
2346 2631 2.291741 AGGAAAAGCTTGAGTTCTTGCG 59.708 45.455 0.00 0.00 0.00 4.85
2642 2937 0.846427 AACAGGGGCTCAGGGATCAA 60.846 55.000 0.00 0.00 0.00 2.57
2648 2944 1.001641 CTTCCAACAGGGGCTCAGG 60.002 63.158 0.00 0.00 37.22 3.86
2718 3015 9.515226 TTATATTCCTATAAATGCTGAACCCAC 57.485 33.333 0.00 0.00 28.93 4.61
2740 3038 7.195374 AGAGCTTATCCACACTTGGTTTATA 57.805 36.000 0.00 0.00 44.35 0.98
2741 3039 6.067217 AGAGCTTATCCACACTTGGTTTAT 57.933 37.500 0.00 0.00 44.35 1.40
2742 3040 5.499004 AGAGCTTATCCACACTTGGTTTA 57.501 39.130 0.00 0.00 44.35 2.01
2743 3041 4.373156 AGAGCTTATCCACACTTGGTTT 57.627 40.909 0.00 0.00 44.35 3.27
2822 3121 7.361799 GGGAATACCTAACAGTTTTACAAGCTG 60.362 40.741 0.00 0.00 35.85 4.24
2883 3182 4.759693 CCGCAGCATTGGAAATACCTAATA 59.240 41.667 0.00 0.00 39.86 0.98
2884 3183 3.569701 CCGCAGCATTGGAAATACCTAAT 59.430 43.478 0.00 0.00 39.86 1.73
2886 3185 2.571212 CCGCAGCATTGGAAATACCTA 58.429 47.619 0.00 0.00 39.86 3.08
2887 3186 1.392589 CCGCAGCATTGGAAATACCT 58.607 50.000 0.00 0.00 39.86 3.08
3069 3386 3.398406 TGTACCTGTACAGTTGCACATG 58.602 45.455 21.18 6.08 40.77 3.21
3070 3387 3.762407 TGTACCTGTACAGTTGCACAT 57.238 42.857 21.18 1.12 40.77 3.21
3101 3423 2.302587 GGGGGTGAAGTTTTCCATGA 57.697 50.000 0.00 0.00 0.00 3.07
3150 3475 0.322098 TATCCCACGTGCACCCAAAG 60.322 55.000 10.91 0.00 0.00 2.77
3151 3476 0.329931 ATATCCCACGTGCACCCAAA 59.670 50.000 10.91 0.00 0.00 3.28


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

AutoCloner maintained by Alex Coulton.