Multiple sequence alignment - TraesCS6A01G300800

Loading Multiple Alignment...

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 TraesCS6A01G300800 chr6A 100.000 2549 0 0 1 2549 533982894 533980346 0.000000e+00 4708
1 TraesCS6A01G300800 chr6A 98.989 1978 18 2 573 2549 617222869 617220893 0.000000e+00 3541
2 TraesCS6A01G300800 chr6A 86.705 173 22 1 404 576 26878833 26879004 9.310000e-45 191
3 TraesCS6A01G300800 chr4A 98.841 1984 21 2 567 2549 36562908 36564890 0.000000e+00 3535
4 TraesCS6A01G300800 chr1B 98.643 1989 24 3 562 2549 42162349 42160363 0.000000e+00 3520
5 TraesCS6A01G300800 chr1B 98.490 1987 27 3 564 2549 7851067 7853051 0.000000e+00 3500
6 TraesCS6A01G300800 chr7A 98.735 1976 23 2 566 2539 701581933 701583908 0.000000e+00 3509
7 TraesCS6A01G300800 chr4B 98.638 1982 21 4 570 2549 578529985 578528008 0.000000e+00 3506
8 TraesCS6A01G300800 chr5B 98.587 1982 25 2 571 2549 185022642 185024623 0.000000e+00 3502
9 TraesCS6A01G300800 chr2A 98.204 2004 32 4 548 2549 751250599 751248598 0.000000e+00 3498
10 TraesCS6A01G300800 chr2A 73.966 580 133 17 5 575 39595750 39595180 4.270000e-53 219
11 TraesCS6A01G300800 chr2A 83.663 202 31 2 372 572 39775198 39775398 3.350000e-44 189
12 TraesCS6A01G300800 chr6B 98.441 1989 22 7 564 2549 645368753 645366771 0.000000e+00 3493
13 TraesCS6A01G300800 chr7D 80.058 346 59 7 202 542 23547381 23547041 5.450000e-62 248
14 TraesCS6A01G300800 chr5D 74.861 541 119 10 1 532 281517587 281517055 1.970000e-56 230
15 TraesCS6A01G300800 chr7B 73.402 579 141 10 1 575 709922886 709922317 1.200000e-48 204
16 TraesCS6A01G300800 chr2B 72.991 585 132 24 5 575 74730379 74730951 5.600000e-42 182


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 TraesCS6A01G300800 chr6A 533980346 533982894 2548 True 4708 4708 100.000 1 2549 1 chr6A.!!$R1 2548
1 TraesCS6A01G300800 chr6A 617220893 617222869 1976 True 3541 3541 98.989 573 2549 1 chr6A.!!$R2 1976
2 TraesCS6A01G300800 chr4A 36562908 36564890 1982 False 3535 3535 98.841 567 2549 1 chr4A.!!$F1 1982
3 TraesCS6A01G300800 chr1B 42160363 42162349 1986 True 3520 3520 98.643 562 2549 1 chr1B.!!$R1 1987
4 TraesCS6A01G300800 chr1B 7851067 7853051 1984 False 3500 3500 98.490 564 2549 1 chr1B.!!$F1 1985
5 TraesCS6A01G300800 chr7A 701581933 701583908 1975 False 3509 3509 98.735 566 2539 1 chr7A.!!$F1 1973
6 TraesCS6A01G300800 chr4B 578528008 578529985 1977 True 3506 3506 98.638 570 2549 1 chr4B.!!$R1 1979
7 TraesCS6A01G300800 chr5B 185022642 185024623 1981 False 3502 3502 98.587 571 2549 1 chr5B.!!$F1 1978
8 TraesCS6A01G300800 chr2A 751248598 751250599 2001 True 3498 3498 98.204 548 2549 1 chr2A.!!$R2 2001
9 TraesCS6A01G300800 chr2A 39595180 39595750 570 True 219 219 73.966 5 575 1 chr2A.!!$R1 570
10 TraesCS6A01G300800 chr6B 645366771 645368753 1982 True 3493 3493 98.441 564 2549 1 chr6B.!!$R1 1985
11 TraesCS6A01G300800 chr5D 281517055 281517587 532 True 230 230 74.861 1 532 1 chr5D.!!$R1 531
12 TraesCS6A01G300800 chr7B 709922317 709922886 569 True 204 204 73.402 1 575 1 chr7B.!!$R1 574

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
112 113 0.037590 TGGAATTACCTGCGCCACTT 59.962 50.0 4.18 0.0 39.86 3.16 F
242 244 0.250513 CCACAAGAGCTGGTAGTCCC 59.749 60.0 0.00 0.0 0.00 4.46 F
524 526 0.250901 TGCCACCAGCTTCTTCTTCC 60.251 55.0 0.00 0.0 44.23 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1118 1120 0.530744 CGGACGATTCTGGTTCCTCA 59.469 55.000 0.0 0.0 0.00 3.86 R
1160 1162 2.654863 CAATTGCCCCGATTCTTACCT 58.345 47.619 0.0 0.0 0.00 3.08 R
1830 2068 3.149005 ACGCAAGAAAACCCCTGAATA 57.851 42.857 0.0 0.0 43.62 1.75 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
21 22 1.676968 CTCATCGTCACCCCACCAA 59.323 57.895 0.00 0.00 0.00 3.67
26 27 0.256464 TCGTCACCCCACCAAAACTT 59.744 50.000 0.00 0.00 0.00 2.66
28 29 1.202359 CGTCACCCCACCAAAACTTTG 60.202 52.381 0.00 0.00 37.90 2.77
45 46 9.480053 CAAAACTTTGGAATGATGTCAGTAATT 57.520 29.630 0.00 0.00 34.59 1.40
69 70 6.432403 TTTTTGCATACTCCCTTTGGAATT 57.568 33.333 0.00 0.00 41.17 2.17
70 71 7.546250 TTTTTGCATACTCCCTTTGGAATTA 57.454 32.000 0.00 0.00 41.17 1.40
71 72 6.773976 TTTGCATACTCCCTTTGGAATTAG 57.226 37.500 0.00 0.00 41.17 1.73
75 76 6.951198 TGCATACTCCCTTTGGAATTAGAAAA 59.049 34.615 0.00 0.00 41.17 2.29
78 79 8.802267 CATACTCCCTTTGGAATTAGAAAAACA 58.198 33.333 0.00 0.00 41.17 2.83
84 85 8.150296 CCCTTTGGAATTAGAAAAACAGACATT 58.850 33.333 0.00 0.00 0.00 2.71
86 87 9.533253 CTTTGGAATTAGAAAAACAGACATTGT 57.467 29.630 0.00 0.00 43.45 2.71
96 97 8.527810 AGAAAAACAGACATTGTAAAAACTGGA 58.472 29.630 7.20 0.00 39.73 3.86
99 100 9.665719 AAAACAGACATTGTAAAAACTGGAATT 57.334 25.926 7.20 0.00 39.73 2.17
102 103 8.357402 ACAGACATTGTAAAAACTGGAATTACC 58.643 33.333 7.20 0.00 38.56 2.85
105 106 7.151976 ACATTGTAAAAACTGGAATTACCTGC 58.848 34.615 0.00 0.00 40.59 4.85
108 109 1.173913 AAACTGGAATTACCTGCGCC 58.826 50.000 4.18 0.00 40.59 6.53
111 112 0.392998 CTGGAATTACCTGCGCCACT 60.393 55.000 4.18 0.00 39.86 4.00
112 113 0.037590 TGGAATTACCTGCGCCACTT 59.962 50.000 4.18 0.00 39.86 3.16
123 124 4.705023 ACCTGCGCCACTTCTTTTAATAAT 59.295 37.500 4.18 0.00 0.00 1.28
126 127 6.126568 TGCGCCACTTCTTTTAATAATACC 57.873 37.500 4.18 0.00 0.00 2.73
132 133 8.967918 GCCACTTCTTTTAATAATACCTCCTTT 58.032 33.333 0.00 0.00 0.00 3.11
138 139 8.500238 TCTTTTAATAATACCTCCTTTCCTCCC 58.500 37.037 0.00 0.00 0.00 4.30
139 140 7.774694 TTTAATAATACCTCCTTTCCTCCCA 57.225 36.000 0.00 0.00 0.00 4.37
140 141 7.774694 TTAATAATACCTCCTTTCCTCCCAA 57.225 36.000 0.00 0.00 0.00 4.12
144 145 1.988846 ACCTCCTTTCCTCCCAAAGAG 59.011 52.381 0.00 0.00 42.83 2.85
146 147 2.238395 CCTCCTTTCCTCCCAAAGAGAG 59.762 54.545 0.00 0.00 46.50 3.20
147 148 2.909662 CTCCTTTCCTCCCAAAGAGAGT 59.090 50.000 0.00 0.00 46.50 3.24
176 178 9.447157 TTTTTCATCCATCCAACAATTATTTCC 57.553 29.630 0.00 0.00 0.00 3.13
177 179 6.729690 TCATCCATCCAACAATTATTTCCC 57.270 37.500 0.00 0.00 0.00 3.97
178 180 6.200852 TCATCCATCCAACAATTATTTCCCA 58.799 36.000 0.00 0.00 0.00 4.37
179 181 6.845446 TCATCCATCCAACAATTATTTCCCAT 59.155 34.615 0.00 0.00 0.00 4.00
183 185 8.869109 TCCATCCAACAATTATTTCCCATATTC 58.131 33.333 0.00 0.00 0.00 1.75
185 187 9.701098 CATCCAACAATTATTTCCCATATTCTG 57.299 33.333 0.00 0.00 0.00 3.02
197 199 6.312141 TCCCATATTCTGTCAATGAAGTGA 57.688 37.500 0.00 0.00 0.00 3.41
222 224 7.870509 TTAAAGCAATCACTTCTATCAGCAT 57.129 32.000 0.00 0.00 0.00 3.79
227 229 5.121105 CAATCACTTCTATCAGCATCCACA 58.879 41.667 0.00 0.00 0.00 4.17
229 231 4.763073 TCACTTCTATCAGCATCCACAAG 58.237 43.478 0.00 0.00 0.00 3.16
233 235 3.036819 TCTATCAGCATCCACAAGAGCT 58.963 45.455 0.00 0.00 37.95 4.09
236 238 2.073232 AGCATCCACAAGAGCTGGT 58.927 52.632 0.00 0.00 35.72 4.00
239 241 1.065854 GCATCCACAAGAGCTGGTAGT 60.066 52.381 0.00 0.00 0.00 2.73
242 244 0.250513 CCACAAGAGCTGGTAGTCCC 59.749 60.000 0.00 0.00 0.00 4.46
244 246 1.347707 CACAAGAGCTGGTAGTCCCAA 59.652 52.381 0.00 0.00 44.65 4.12
248 250 4.475016 ACAAGAGCTGGTAGTCCCAAATAT 59.525 41.667 0.00 0.00 44.65 1.28
251 253 6.824958 AGAGCTGGTAGTCCCAAATATTTA 57.175 37.500 0.00 0.00 44.65 1.40
254 256 7.293535 AGAGCTGGTAGTCCCAAATATTTATCT 59.706 37.037 0.00 0.60 44.65 1.98
255 257 8.506196 AGCTGGTAGTCCCAAATATTTATCTA 57.494 34.615 0.00 0.00 44.65 1.98
281 283 4.415881 TGCCTCGGTATCAATGTGTAAT 57.584 40.909 0.00 0.00 0.00 1.89
283 285 4.814234 TGCCTCGGTATCAATGTGTAATTC 59.186 41.667 0.00 0.00 0.00 2.17
284 286 5.057149 GCCTCGGTATCAATGTGTAATTCT 58.943 41.667 0.00 0.00 0.00 2.40
285 287 5.527582 GCCTCGGTATCAATGTGTAATTCTT 59.472 40.000 0.00 0.00 0.00 2.52
287 289 6.761242 CCTCGGTATCAATGTGTAATTCTTGA 59.239 38.462 0.00 0.00 32.63 3.02
288 290 7.254455 CCTCGGTATCAATGTGTAATTCTTGAC 60.254 40.741 0.00 0.00 31.00 3.18
290 292 7.768582 TCGGTATCAATGTGTAATTCTTGACAT 59.231 33.333 0.00 0.00 31.00 3.06
306 308 8.806429 TTCTTGACATATTTCATCTTTAGCCA 57.194 30.769 0.00 0.00 0.00 4.75
307 309 8.213518 TCTTGACATATTTCATCTTTAGCCAC 57.786 34.615 0.00 0.00 0.00 5.01
309 311 6.662755 TGACATATTTCATCTTTAGCCACCT 58.337 36.000 0.00 0.00 0.00 4.00
312 314 6.769822 ACATATTTCATCTTTAGCCACCTCAG 59.230 38.462 0.00 0.00 0.00 3.35
314 316 3.895232 TCATCTTTAGCCACCTCAGTC 57.105 47.619 0.00 0.00 0.00 3.51
315 317 3.173151 TCATCTTTAGCCACCTCAGTCA 58.827 45.455 0.00 0.00 0.00 3.41
317 319 3.616956 TCTTTAGCCACCTCAGTCATG 57.383 47.619 0.00 0.00 0.00 3.07
323 325 1.538047 CCACCTCAGTCATGTTTGGG 58.462 55.000 0.00 0.00 0.00 4.12
326 328 1.985159 ACCTCAGTCATGTTTGGGCTA 59.015 47.619 0.00 0.00 0.00 3.93
329 331 4.019174 CCTCAGTCATGTTTGGGCTAAAT 58.981 43.478 0.00 0.00 0.00 1.40
358 360 6.008696 ACTAGACTTAGCTCTACTCACCAT 57.991 41.667 0.00 0.00 0.00 3.55
361 363 8.053963 ACTAGACTTAGCTCTACTCACCATTTA 58.946 37.037 0.00 0.00 0.00 1.40
362 364 7.719871 AGACTTAGCTCTACTCACCATTTAA 57.280 36.000 0.00 0.00 0.00 1.52
365 367 6.212791 ACTTAGCTCTACTCACCATTTAACCA 59.787 38.462 0.00 0.00 0.00 3.67
372 374 8.335532 TCTACTCACCATTTAACCAGAATTTG 57.664 34.615 0.00 0.00 0.00 2.32
380 382 8.153550 ACCATTTAACCAGAATTTGCACAATAA 58.846 29.630 0.00 0.00 0.00 1.40
388 390 7.178274 ACCAGAATTTGCACAATAAGTATCCAA 59.822 33.333 0.00 0.00 0.00 3.53
389 391 8.199449 CCAGAATTTGCACAATAAGTATCCAAT 58.801 33.333 0.00 0.00 0.00 3.16
425 427 4.568152 AGTTGCATTTAACATATCCGCC 57.432 40.909 0.00 0.00 33.02 6.13
426 428 4.207165 AGTTGCATTTAACATATCCGCCT 58.793 39.130 0.00 0.00 33.02 5.52
440 442 3.475566 TCCGCCTTCATGAGAATTAGG 57.524 47.619 6.08 6.08 32.31 2.69
446 448 5.380043 GCCTTCATGAGAATTAGGGAATCA 58.620 41.667 11.50 0.00 32.31 2.57
448 450 6.492772 GCCTTCATGAGAATTAGGGAATCATT 59.507 38.462 11.50 0.00 32.31 2.57
470 472 8.250332 TCATTAGCAAATAAAAGGTGTGATTCC 58.750 33.333 0.00 0.00 0.00 3.01
473 475 4.857037 GCAAATAAAAGGTGTGATTCCGAC 59.143 41.667 0.00 0.00 0.00 4.79
482 484 0.802494 GTGATTCCGACGGTGCATTT 59.198 50.000 14.79 0.00 0.00 2.32
513 515 1.784358 AATCCCATCAATGCCACCAG 58.216 50.000 0.00 0.00 0.00 4.00
524 526 0.250901 TGCCACCAGCTTCTTCTTCC 60.251 55.000 0.00 0.00 44.23 3.46
529 531 3.769844 CCACCAGCTTCTTCTTCCTACTA 59.230 47.826 0.00 0.00 0.00 1.82
532 534 4.464597 ACCAGCTTCTTCTTCCTACTACAG 59.535 45.833 0.00 0.00 0.00 2.74
533 535 4.464597 CCAGCTTCTTCTTCCTACTACAGT 59.535 45.833 0.00 0.00 0.00 3.55
534 536 5.652891 CCAGCTTCTTCTTCCTACTACAGTA 59.347 44.000 0.00 0.00 0.00 2.74
535 537 6.153000 CCAGCTTCTTCTTCCTACTACAGTAA 59.847 42.308 0.00 0.00 0.00 2.24
536 538 7.309867 CCAGCTTCTTCTTCCTACTACAGTAAA 60.310 40.741 0.00 0.00 0.00 2.01
537 539 7.542824 CAGCTTCTTCTTCCTACTACAGTAAAC 59.457 40.741 0.00 0.00 0.00 2.01
538 540 7.452189 AGCTTCTTCTTCCTACTACAGTAAACT 59.548 37.037 0.00 0.00 0.00 2.66
539 541 8.738106 GCTTCTTCTTCCTACTACAGTAAACTA 58.262 37.037 0.00 0.00 0.00 2.24
553 555 9.303537 CTACAGTAAACTAGATAAACCTTCAGC 57.696 37.037 0.00 0.00 0.00 4.26
555 557 7.603024 ACAGTAAACTAGATAAACCTTCAGCAC 59.397 37.037 0.00 0.00 0.00 4.40
558 560 9.595823 GTAAACTAGATAAACCTTCAGCACATA 57.404 33.333 0.00 0.00 0.00 2.29
560 562 7.425224 ACTAGATAAACCTTCAGCACATAGT 57.575 36.000 0.00 0.00 0.00 2.12
563 565 9.817809 CTAGATAAACCTTCAGCACATAGTAAA 57.182 33.333 0.00 0.00 0.00 2.01
612 614 0.473755 TCAGTGGTGTCCATGTGCTT 59.526 50.000 0.00 0.00 35.28 3.91
698 700 1.289380 GAACTCTGCCGTCTCCGTT 59.711 57.895 0.00 0.00 0.00 4.44
953 955 3.771160 CGGCGGTGGGAAGCTAGT 61.771 66.667 0.00 0.00 0.00 2.57
1118 1120 2.317040 TCGAAGGGTTTCTCAGACACT 58.683 47.619 0.00 0.00 30.45 3.55
1160 1162 0.242555 TACGTGTGCAGCGAGAATGA 59.757 50.000 16.16 0.00 0.00 2.57
1239 1241 5.611796 TGATCTGTTTAGTGTTCATGCAC 57.388 39.130 0.00 0.00 39.51 4.57
1334 1336 4.345962 GTTGCGCATGCTGCCACA 62.346 61.111 24.60 10.14 41.12 4.17
1830 2068 2.381911 CAACTGCATCCAATTAGGCCT 58.618 47.619 11.78 11.78 37.29 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 6.951198 TCTAATTCCAAAGGGAGTATGCAAAA 59.049 34.615 0.00 0.00 46.01 2.44
56 57 7.014230 TGTCTGTTTTTCTAATTCCAAAGGGAG 59.986 37.037 0.00 0.00 46.01 4.30
60 61 9.533253 ACAATGTCTGTTTTTCTAATTCCAAAG 57.467 29.630 0.00 0.00 32.99 2.77
69 70 9.796120 CCAGTTTTTACAATGTCTGTTTTTCTA 57.204 29.630 0.00 0.00 39.64 2.10
70 71 8.527810 TCCAGTTTTTACAATGTCTGTTTTTCT 58.472 29.630 0.00 0.00 39.64 2.52
71 72 8.696410 TCCAGTTTTTACAATGTCTGTTTTTC 57.304 30.769 0.00 0.00 39.64 2.29
75 76 9.744468 GTAATTCCAGTTTTTACAATGTCTGTT 57.256 29.630 0.00 0.00 39.64 3.16
78 79 8.576442 CAGGTAATTCCAGTTTTTACAATGTCT 58.424 33.333 0.00 0.00 39.02 3.41
84 85 4.320641 GCGCAGGTAATTCCAGTTTTTACA 60.321 41.667 0.30 0.00 39.02 2.41
86 87 3.191791 GGCGCAGGTAATTCCAGTTTTTA 59.808 43.478 10.83 0.00 39.02 1.52
90 91 0.037590 TGGCGCAGGTAATTCCAGTT 59.962 50.000 10.83 0.00 39.02 3.16
93 94 0.037590 AAGTGGCGCAGGTAATTCCA 59.962 50.000 10.83 0.00 39.02 3.53
96 97 2.200373 AAGAAGTGGCGCAGGTAATT 57.800 45.000 10.83 0.00 0.00 1.40
99 100 2.843401 TAAAAGAAGTGGCGCAGGTA 57.157 45.000 10.83 0.00 0.00 3.08
100 101 1.975660 TTAAAAGAAGTGGCGCAGGT 58.024 45.000 10.83 0.00 0.00 4.00
102 103 6.038271 AGGTATTATTAAAAGAAGTGGCGCAG 59.962 38.462 10.83 0.00 0.00 5.18
105 106 6.766467 AGGAGGTATTATTAAAAGAAGTGGCG 59.234 38.462 0.00 0.00 0.00 5.69
111 112 9.916360 GGAGGAAAGGAGGTATTATTAAAAGAA 57.084 33.333 0.00 0.00 0.00 2.52
112 113 8.500238 GGGAGGAAAGGAGGTATTATTAAAAGA 58.500 37.037 0.00 0.00 0.00 2.52
123 124 3.181399 TCTCTTTGGGAGGAAAGGAGGTA 60.181 47.826 0.00 0.00 42.10 3.08
126 127 2.909662 ACTCTCTTTGGGAGGAAAGGAG 59.090 50.000 0.00 0.00 42.10 3.69
154 156 6.200852 TGGGAAATAATTGTTGGATGGATGA 58.799 36.000 0.00 0.00 0.00 2.92
169 171 9.699410 ACTTCATTGACAGAATATGGGAAATAA 57.301 29.630 0.00 0.00 0.00 1.40
170 172 9.123902 CACTTCATTGACAGAATATGGGAAATA 57.876 33.333 0.00 0.00 0.00 1.40
172 174 7.174413 TCACTTCATTGACAGAATATGGGAAA 58.826 34.615 0.00 0.00 0.00 3.13
175 177 7.578310 AATCACTTCATTGACAGAATATGGG 57.422 36.000 0.00 0.00 0.00 4.00
179 181 9.230122 TGCTTTAATCACTTCATTGACAGAATA 57.770 29.630 0.00 0.00 0.00 1.75
183 185 8.390854 GATTGCTTTAATCACTTCATTGACAG 57.609 34.615 0.00 0.00 43.79 3.51
197 199 7.870509 TGCTGATAGAAGTGATTGCTTTAAT 57.129 32.000 0.00 0.00 0.00 1.40
218 220 1.209019 CTACCAGCTCTTGTGGATGCT 59.791 52.381 0.00 0.00 38.57 3.79
222 224 1.267121 GGACTACCAGCTCTTGTGGA 58.733 55.000 0.00 0.00 38.57 4.02
251 253 7.550551 CACATTGATACCGAGGCAATATTAGAT 59.449 37.037 0.00 0.00 31.54 1.98
254 256 6.530120 ACACATTGATACCGAGGCAATATTA 58.470 36.000 0.00 0.00 31.54 0.98
255 257 5.376625 ACACATTGATACCGAGGCAATATT 58.623 37.500 0.00 0.00 31.54 1.28
259 261 2.779755 ACACATTGATACCGAGGCAA 57.220 45.000 0.00 0.00 0.00 4.52
263 265 7.277760 TGTCAAGAATTACACATTGATACCGAG 59.722 37.037 0.00 0.00 34.45 4.63
281 283 8.677300 GTGGCTAAAGATGAAATATGTCAAGAA 58.323 33.333 0.00 0.00 0.00 2.52
283 285 7.284034 AGGTGGCTAAAGATGAAATATGTCAAG 59.716 37.037 0.00 0.00 0.00 3.02
284 286 7.118723 AGGTGGCTAAAGATGAAATATGTCAA 58.881 34.615 0.00 0.00 0.00 3.18
285 287 6.662755 AGGTGGCTAAAGATGAAATATGTCA 58.337 36.000 0.00 0.00 0.00 3.58
287 289 6.662755 TGAGGTGGCTAAAGATGAAATATGT 58.337 36.000 0.00 0.00 0.00 2.29
288 290 6.769822 ACTGAGGTGGCTAAAGATGAAATATG 59.230 38.462 0.00 0.00 0.00 1.78
290 292 6.070251 TGACTGAGGTGGCTAAAGATGAAATA 60.070 38.462 0.00 0.00 0.00 1.40
300 302 3.411446 CAAACATGACTGAGGTGGCTAA 58.589 45.455 0.00 0.00 0.00 3.09
304 306 1.538047 CCCAAACATGACTGAGGTGG 58.462 55.000 0.00 0.00 0.00 4.61
305 307 0.883833 GCCCAAACATGACTGAGGTG 59.116 55.000 0.00 0.00 0.00 4.00
306 308 0.773644 AGCCCAAACATGACTGAGGT 59.226 50.000 0.00 0.00 0.00 3.85
307 309 2.787473 TAGCCCAAACATGACTGAGG 57.213 50.000 0.00 1.38 0.00 3.86
309 311 8.995027 ATATTATTTAGCCCAAACATGACTGA 57.005 30.769 0.00 0.00 0.00 3.41
338 340 7.363968 GGTTAAATGGTGAGTAGAGCTAAGTCT 60.364 40.741 0.00 0.00 0.00 3.24
341 343 6.640518 TGGTTAAATGGTGAGTAGAGCTAAG 58.359 40.000 0.00 0.00 0.00 2.18
344 346 4.777896 TCTGGTTAAATGGTGAGTAGAGCT 59.222 41.667 0.00 0.00 0.00 4.09
345 347 5.086104 TCTGGTTAAATGGTGAGTAGAGC 57.914 43.478 0.00 0.00 0.00 4.09
347 349 7.094377 GCAAATTCTGGTTAAATGGTGAGTAGA 60.094 37.037 0.00 0.00 0.00 2.59
348 350 7.029563 GCAAATTCTGGTTAAATGGTGAGTAG 58.970 38.462 0.00 0.00 0.00 2.57
349 351 6.491745 TGCAAATTCTGGTTAAATGGTGAGTA 59.508 34.615 0.00 0.00 0.00 2.59
353 355 5.295950 TGTGCAAATTCTGGTTAAATGGTG 58.704 37.500 0.00 0.00 0.00 4.17
361 363 7.178274 TGGATACTTATTGTGCAAATTCTGGTT 59.822 33.333 0.00 0.00 37.61 3.67
362 364 6.663093 TGGATACTTATTGTGCAAATTCTGGT 59.337 34.615 0.00 0.00 37.61 4.00
392 394 7.946207 TGTTAAATGCAACTTCATTACAGGAA 58.054 30.769 0.00 0.00 35.77 3.36
401 403 5.449862 GGCGGATATGTTAAATGCAACTTCA 60.450 40.000 0.00 0.00 0.00 3.02
413 415 5.545063 TTCTCATGAAGGCGGATATGTTA 57.455 39.130 0.00 0.00 0.00 2.41
422 424 3.475566 TCCCTAATTCTCATGAAGGCG 57.524 47.619 5.03 0.21 35.44 5.52
425 427 8.728833 GCTAATGATTCCCTAATTCTCATGAAG 58.271 37.037 0.00 0.00 35.44 3.02
426 428 8.219868 TGCTAATGATTCCCTAATTCTCATGAA 58.780 33.333 0.00 0.00 36.54 2.57
440 442 8.250332 TCACACCTTTTATTTGCTAATGATTCC 58.750 33.333 3.49 0.00 0.00 3.01
446 448 7.122055 TCGGAATCACACCTTTTATTTGCTAAT 59.878 33.333 0.00 0.00 0.00 1.73
448 450 5.941058 TCGGAATCACACCTTTTATTTGCTA 59.059 36.000 0.00 0.00 0.00 3.49
468 470 2.032634 GCAGAAATGCACCGTCGGA 61.033 57.895 20.51 0.00 34.41 4.55
470 472 3.252964 TGCAGAAATGCACCGTCG 58.747 55.556 0.00 0.00 40.23 5.12
482 484 1.490490 GATGGGATTAGGGTGTGCAGA 59.510 52.381 0.00 0.00 0.00 4.26
513 515 7.604549 AGTTTACTGTAGTAGGAAGAAGAAGC 58.395 38.462 0.00 0.00 28.86 3.86
529 531 7.603024 GTGCTGAAGGTTTATCTAGTTTACTGT 59.397 37.037 0.00 0.00 0.00 3.55
532 534 7.900782 TGTGCTGAAGGTTTATCTAGTTTAC 57.099 36.000 0.00 0.00 0.00 2.01
533 535 9.817809 CTATGTGCTGAAGGTTTATCTAGTTTA 57.182 33.333 0.00 0.00 0.00 2.01
534 536 8.322091 ACTATGTGCTGAAGGTTTATCTAGTTT 58.678 33.333 0.00 0.00 0.00 2.66
535 537 7.852263 ACTATGTGCTGAAGGTTTATCTAGTT 58.148 34.615 0.00 0.00 0.00 2.24
536 538 7.425224 ACTATGTGCTGAAGGTTTATCTAGT 57.575 36.000 0.00 0.00 0.00 2.57
537 539 9.817809 TTTACTATGTGCTGAAGGTTTATCTAG 57.182 33.333 0.00 0.00 0.00 2.43
539 541 9.515226 TTTTTACTATGTGCTGAAGGTTTATCT 57.485 29.630 0.00 0.00 0.00 1.98
566 568 9.150028 GGGCAAAAGGATAATTAACCCTATTTA 57.850 33.333 8.09 0.00 31.84 1.40
568 570 7.370238 AGGGCAAAAGGATAATTAACCCTATT 58.630 34.615 8.09 0.00 43.36 1.73
612 614 1.277842 TCGCATCTGAGGGCAAAACTA 59.722 47.619 5.18 0.00 0.00 2.24
1118 1120 0.530744 CGGACGATTCTGGTTCCTCA 59.469 55.000 0.00 0.00 0.00 3.86
1160 1162 2.654863 CAATTGCCCCGATTCTTACCT 58.345 47.619 0.00 0.00 0.00 3.08
1239 1241 3.558505 CCAAAGAAAGAAGCATGTCACG 58.441 45.455 0.00 0.00 0.00 4.35
1830 2068 3.149005 ACGCAAGAAAACCCCTGAATA 57.851 42.857 0.00 0.00 43.62 1.75
1932 2171 3.149005 ACCTTAATTGTTTGGCTCCGA 57.851 42.857 0.00 0.00 0.00 4.55
2127 2367 3.390639 TGTGCATTTTCCACCCTTCATTT 59.609 39.130 0.00 0.00 32.30 2.32


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

AutoCloner maintained by Alex Coulton.