Multiple sequence alignment - TraesCS6B01G268100

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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 TraesCS6B01G268100 chr6B 100.000 2654 0 0 1 2654 481845615 481842962 0.000000e+00 4902.0
1 TraesCS6B01G268100 chr6D 96.880 1827 42 6 366 2189 338513371 338515185 0.000000e+00 3044.0
2 TraesCS6B01G268100 chr6D 93.902 328 19 1 1 327 338513043 338513370 6.600000e-136 494.0
3 TraesCS6B01G268100 chr6A 94.438 1744 55 18 453 2189 479042112 479043820 0.000000e+00 2645.0
4 TraesCS6B01G268100 chr6A 86.416 346 40 2 2316 2654 479044027 479044372 3.230000e-99 372.0
5 TraesCS6B01G268100 chr6A 85.507 69 7 3 2181 2247 530043918 530043851 4.740000e-08 69.4
6 TraesCS6B01G268100 chr3D 86.441 177 14 7 273 441 83492073 83491899 4.510000e-43 185.0
7 TraesCS6B01G268100 chr7D 86.127 173 18 4 273 443 566988861 566989029 5.840000e-42 182.0
8 TraesCS6B01G268100 chr2D 84.483 174 20 5 275 441 606924711 606924884 5.880000e-37 165.0
9 TraesCS6B01G268100 chr2D 83.766 154 23 1 2 155 56293003 56292852 7.660000e-31 145.0
10 TraesCS6B01G268100 chr2D 79.882 169 32 2 273 441 590937827 590937993 3.590000e-24 122.0
11 TraesCS6B01G268100 chr5A 83.243 185 19 9 265 441 487808125 487808305 2.730000e-35 159.0
12 TraesCS6B01G268100 chr1D 83.626 171 22 4 273 441 414276745 414276579 3.540000e-34 156.0
13 TraesCS6B01G268100 chr1A 84.667 150 23 0 2 151 84628396 84628545 1.650000e-32 150.0
14 TraesCS6B01G268100 chr2A 82.659 173 19 8 275 441 251254074 251253907 2.750000e-30 143.0
15 TraesCS6B01G268100 chr2A 84.667 150 12 7 301 441 713142115 713142262 3.560000e-29 139.0
16 TraesCS6B01G268100 chr2A 79.389 131 15 8 280 409 65663647 65663528 6.090000e-12 82.4
17 TraesCS6B01G268100 chr4A 84.783 138 16 3 304 441 596675284 596675152 1.660000e-27 134.0
18 TraesCS6B01G268100 chr7A 81.699 153 24 3 1 151 531069751 531069901 9.970000e-25 124.0
19 TraesCS6B01G268100 chr3B 81.699 153 18 5 2 154 720269739 720269597 4.640000e-23 119.0
20 TraesCS6B01G268100 chr5B 75.000 272 55 10 1107 1367 492619510 492619779 2.160000e-21 113.0
21 TraesCS6B01G268100 chr4D 92.308 78 6 0 2 79 502705555 502705478 7.770000e-21 111.0
22 TraesCS6B01G268100 chr4D 91.549 71 5 1 2 71 50978188 50978118 2.170000e-16 97.1
23 TraesCS6B01G268100 chr3A 88.889 90 10 0 2 91 27046866 27046777 7.770000e-21 111.0
24 TraesCS6B01G268100 chr7B 87.671 73 9 0 3 75 321320202 321320274 4.710000e-13 86.1


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 TraesCS6B01G268100 chr6B 481842962 481845615 2653 True 4902.0 4902 100.000 1 2654 1 chr6B.!!$R1 2653
1 TraesCS6B01G268100 chr6D 338513043 338515185 2142 False 1769.0 3044 95.391 1 2189 2 chr6D.!!$F1 2188
2 TraesCS6B01G268100 chr6A 479042112 479044372 2260 False 1508.5 2645 90.427 453 2654 2 chr6A.!!$F1 2201

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
244 245 0.031994 GTGCCGAGTGTGCCATTTTT 59.968 50.0 0.0 0.0 0.0 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2115 2122 0.251916 CAAGGGATCGGTTAGGTGCA 59.748 55.0 0.0 0.0 0.0 4.57 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
32 33 6.038170 TGGATATAGGGGATCGGATATGAA 57.962 41.667 0.00 0.00 0.00 2.57
59 60 2.221749 CGGATGTGGACGATGCTATTTG 59.778 50.000 0.00 0.00 0.00 2.32
91 92 3.731136 ACTGCATGTGAACGCGTT 58.269 50.000 26.97 26.97 0.00 4.84
116 117 2.644992 GTTGGCAGGCGTTTGAGG 59.355 61.111 0.00 0.00 0.00 3.86
205 206 7.340232 TGGAGAATGTTAAAAATCTGATCCCTG 59.660 37.037 0.00 0.00 0.00 4.45
243 244 1.659794 GTGCCGAGTGTGCCATTTT 59.340 52.632 0.00 0.00 0.00 1.82
244 245 0.031994 GTGCCGAGTGTGCCATTTTT 59.968 50.000 0.00 0.00 0.00 1.94
267 269 2.394708 CCGACCGCAGATACTTGTATG 58.605 52.381 0.00 0.00 0.00 2.39
288 290 5.934402 TGAAGAAAGGGTATGACTAGGTC 57.066 43.478 0.00 0.00 0.00 3.85
290 292 5.657302 TGAAGAAAGGGTATGACTAGGTCTC 59.343 44.000 0.00 0.00 33.15 3.36
299 301 4.909696 ATGACTAGGTCTCAATCGACTG 57.090 45.455 0.00 0.00 34.38 3.51
309 311 4.075682 TCTCAATCGACTGAGACTTCACT 58.924 43.478 21.83 0.00 45.45 3.41
327 329 6.266558 ACTTCACTAAGTCTCTGTCAAGTGAT 59.733 38.462 4.03 0.00 42.42 3.06
328 330 7.448777 ACTTCACTAAGTCTCTGTCAAGTGATA 59.551 37.037 4.03 0.00 42.42 2.15
329 331 7.946381 TCACTAAGTCTCTGTCAAGTGATAT 57.054 36.000 0.00 0.00 38.64 1.63
330 332 9.462606 TTCACTAAGTCTCTGTCAAGTGATATA 57.537 33.333 4.03 0.00 41.94 0.86
331 333 9.114952 TCACTAAGTCTCTGTCAAGTGATATAG 57.885 37.037 0.00 0.00 38.64 1.31
332 334 8.898761 CACTAAGTCTCTGTCAAGTGATATAGT 58.101 37.037 0.00 0.00 37.18 2.12
337 339 9.634021 AGTCTCTGTCAAGTGATATAGTATTCA 57.366 33.333 0.00 0.00 0.00 2.57
425 427 5.640783 TCGACTGAGACATAACGAAGTCTTA 59.359 40.000 0.00 0.00 45.00 2.10
426 428 5.960683 CGACTGAGACATAACGAAGTCTTAG 59.039 44.000 11.33 11.33 45.00 2.18
429 431 5.866075 TGAGACATAACGAAGTCTTAGTCG 58.134 41.667 0.00 0.00 45.00 4.18
430 432 5.640783 TGAGACATAACGAAGTCTTAGTCGA 59.359 40.000 0.00 0.00 45.00 4.20
431 433 5.867166 AGACATAACGAAGTCTTAGTCGAC 58.133 41.667 7.70 7.70 45.00 4.20
432 434 5.642919 AGACATAACGAAGTCTTAGTCGACT 59.357 40.000 23.66 23.66 45.00 4.18
433 435 5.629097 ACATAACGAAGTCTTAGTCGACTG 58.371 41.667 28.12 12.46 45.00 3.51
434 436 5.410746 ACATAACGAAGTCTTAGTCGACTGA 59.589 40.000 28.12 19.13 45.00 3.41
964 969 2.528818 CCACCTGCTTCCACTCCCA 61.529 63.158 0.00 0.00 0.00 4.37
1386 1391 1.915228 GGGTGCTAGCCCTGATGAA 59.085 57.895 13.29 0.00 45.22 2.57
1500 1505 2.511600 CAGTTCGCCGGTGATCCC 60.512 66.667 20.33 10.02 0.00 3.85
1674 1679 2.730183 TACGCGCATTTGAGTTATGC 57.270 45.000 5.73 0.00 43.80 3.14
1762 1769 2.258286 GCATGGTTGCCGTTCCAC 59.742 61.111 0.00 0.00 43.38 4.02
1881 1888 0.390603 CACGCTTGTCGGGTTATGGA 60.391 55.000 0.00 0.00 43.86 3.41
1990 1997 3.862845 GGTGTTTGGTTAAGCAAAGTGTG 59.137 43.478 28.14 0.00 0.00 3.82
2115 2122 7.490657 AAAACCAGGTTTTCTCCTTAAAACT 57.509 32.000 22.74 0.00 41.11 2.66
2171 2184 9.127277 AGTACAACTTTGGAAGTGCTAAAAATA 57.873 29.630 0.00 0.00 41.91 1.40
2216 2265 4.324402 CGCAAGGATGACAAATTTAGTTGC 59.676 41.667 0.00 0.00 35.52 4.17
2218 2267 4.701956 AGGATGACAAATTTAGTTGCCG 57.298 40.909 0.00 0.00 31.29 5.69
2223 2272 3.505680 TGACAAATTTAGTTGCCGAGCAT 59.494 39.130 0.00 0.00 38.76 3.79
2233 2282 0.955428 TGCCGAGCATGACACTTTCC 60.955 55.000 0.00 0.00 31.71 3.13
2235 2284 1.405526 GCCGAGCATGACACTTTCCTA 60.406 52.381 0.00 0.00 0.00 2.94
2238 2287 2.675032 CGAGCATGACACTTTCCTAGCA 60.675 50.000 0.00 0.00 0.00 3.49
2267 2316 1.686052 TGTTTTGAGTTGGACCATGCC 59.314 47.619 0.00 0.00 0.00 4.40
2284 2333 1.953686 TGCCTGTCAACTAAACTTGCC 59.046 47.619 0.00 0.00 0.00 4.52
2287 2336 2.293399 CCTGTCAACTAAACTTGCCACC 59.707 50.000 0.00 0.00 0.00 4.61
2292 2341 2.955660 CAACTAAACTTGCCACCCTTGA 59.044 45.455 0.00 0.00 0.00 3.02
2293 2342 3.306472 ACTAAACTTGCCACCCTTGAA 57.694 42.857 0.00 0.00 0.00 2.69
2296 2345 3.990959 AAACTTGCCACCCTTGAAAAA 57.009 38.095 0.00 0.00 0.00 1.94
2302 2351 2.896685 TGCCACCCTTGAAAAACATAGG 59.103 45.455 0.00 0.00 0.00 2.57
2303 2352 2.233676 GCCACCCTTGAAAAACATAGGG 59.766 50.000 0.00 0.00 44.65 3.53
2304 2353 2.233676 CCACCCTTGAAAAACATAGGGC 59.766 50.000 5.95 0.00 43.82 5.19
2305 2354 2.233676 CACCCTTGAAAAACATAGGGCC 59.766 50.000 5.95 0.00 43.82 5.80
2306 2355 1.831106 CCCTTGAAAAACATAGGGCCC 59.169 52.381 16.46 16.46 38.79 5.80
2308 2357 2.442413 CTTGAAAAACATAGGGCCCGA 58.558 47.619 18.44 13.02 0.00 5.14
2309 2358 1.828979 TGAAAAACATAGGGCCCGAC 58.171 50.000 18.44 0.00 0.00 4.79
2310 2359 1.353022 TGAAAAACATAGGGCCCGACT 59.647 47.619 18.44 0.39 0.00 4.18
2311 2360 2.224917 TGAAAAACATAGGGCCCGACTT 60.225 45.455 18.44 3.17 0.00 3.01
2313 2362 3.724732 AAAACATAGGGCCCGACTTAA 57.275 42.857 18.44 0.00 0.00 1.85
2314 2363 3.724732 AAACATAGGGCCCGACTTAAA 57.275 42.857 18.44 0.00 0.00 1.52
2328 2424 5.704053 CCCGACTTAAATTTTACTCCACTGT 59.296 40.000 0.00 0.00 0.00 3.55
2329 2425 6.348213 CCCGACTTAAATTTTACTCCACTGTG 60.348 42.308 0.00 0.00 0.00 3.66
2333 2429 1.165270 ATTTTACTCCACTGTGCGCC 58.835 50.000 4.18 0.00 0.00 6.53
2334 2430 0.887387 TTTTACTCCACTGTGCGCCC 60.887 55.000 4.18 0.00 0.00 6.13
2335 2431 2.741486 TTTACTCCACTGTGCGCCCC 62.741 60.000 4.18 0.00 0.00 5.80
2354 2450 5.686650 CGCCCCACTCTTAAATATACTTGGT 60.687 44.000 0.00 0.00 0.00 3.67
2359 2455 5.175126 CACTCTTAAATATACTTGGTCGCCG 59.825 44.000 0.00 0.00 0.00 6.46
2360 2456 4.624015 TCTTAAATATACTTGGTCGCCGG 58.376 43.478 0.00 0.00 0.00 6.13
2361 2457 4.341806 TCTTAAATATACTTGGTCGCCGGA 59.658 41.667 5.05 0.00 0.00 5.14
2376 2478 2.099098 CGCCGGAGCAATAAAATTTCCT 59.901 45.455 5.05 0.00 39.83 3.36
2382 2484 5.123820 CGGAGCAATAAAATTTCCTCTCACA 59.876 40.000 0.00 0.00 0.00 3.58
2385 2487 5.774690 AGCAATAAAATTTCCTCTCACACCA 59.225 36.000 0.00 0.00 0.00 4.17
2398 2500 2.424956 CTCACACCACTCGATCTCATCA 59.575 50.000 0.00 0.00 0.00 3.07
2404 2506 4.269603 CACCACTCGATCTCATCAATTCAC 59.730 45.833 0.00 0.00 0.00 3.18
2407 2509 3.452264 ACTCGATCTCATCAATTCACCCA 59.548 43.478 0.00 0.00 0.00 4.51
2410 2512 2.806945 TCTCATCAATTCACCCACCC 57.193 50.000 0.00 0.00 0.00 4.61
2488 2591 1.607612 CAAATGGCTAGGTCCCCGT 59.392 57.895 0.00 0.00 0.00 5.28
2496 2599 0.384669 CTAGGTCCCCGTTGTCGATC 59.615 60.000 0.00 0.00 39.71 3.69
2503 2606 1.413767 CCCGTTGTCGATCAGAAGCG 61.414 60.000 0.00 0.00 39.71 4.68
2563 2666 0.905357 CTCATCCCGGTTCCTTGACT 59.095 55.000 0.00 0.00 0.00 3.41
2570 2673 0.535102 CGGTTCCTTGACTTGCCACT 60.535 55.000 0.00 0.00 0.00 4.00
2571 2674 0.954452 GGTTCCTTGACTTGCCACTG 59.046 55.000 0.00 0.00 0.00 3.66
2573 2676 0.823356 TTCCTTGACTTGCCACTGCC 60.823 55.000 0.00 0.00 36.33 4.85
2612 2715 0.748367 TACCTTGGCGTGCAACAACA 60.748 50.000 0.00 0.00 35.74 3.33
2616 2719 2.052237 GGCGTGCAACAACAGTCG 60.052 61.111 0.00 0.00 35.74 4.18
2619 2722 1.713246 CGTGCAACAACAGTCGTGT 59.287 52.632 0.00 0.00 39.19 4.49
2633 2736 2.032634 CGTGTGGGATTGGGTGACG 61.033 63.158 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 2.821546 CATCGTCCACATCCGTGTATT 58.178 47.619 0.00 0.00 41.93 1.89
51 52 1.824852 TCGAGCACTCCTCAAATAGCA 59.175 47.619 0.00 0.00 40.78 3.49
59 60 0.527385 GCAGTGATCGAGCACTCCTC 60.527 60.000 32.02 19.80 45.54 3.71
101 102 4.659172 CCCCTCAAACGCCTGCCA 62.659 66.667 0.00 0.00 0.00 4.92
116 117 1.519758 CGCGTACGACAAATATGACCC 59.480 52.381 21.65 0.00 43.93 4.46
167 168 2.375174 ACATTCTCCAGCAAACCCTACA 59.625 45.455 0.00 0.00 0.00 2.74
169 170 3.806949 AACATTCTCCAGCAAACCCTA 57.193 42.857 0.00 0.00 0.00 3.53
172 173 7.116805 CAGATTTTTAACATTCTCCAGCAAACC 59.883 37.037 0.00 0.00 0.00 3.27
205 206 4.454847 GCACCTAGGACCTGTTTCTTTAAC 59.545 45.833 17.98 0.00 37.26 2.01
243 244 0.974010 AAGTATCTGCGGTCGGGGAA 60.974 55.000 0.00 0.00 0.00 3.97
244 245 1.380785 AAGTATCTGCGGTCGGGGA 60.381 57.895 0.00 0.00 0.00 4.81
267 269 5.657302 TGAGACCTAGTCATACCCTTTCTTC 59.343 44.000 0.00 0.00 34.60 2.87
288 290 4.433186 AGTGAAGTCTCAGTCGATTGAG 57.567 45.455 27.00 27.00 44.74 3.02
290 292 5.704888 ACTTAGTGAAGTCTCAGTCGATTG 58.295 41.667 0.68 0.68 42.50 2.67
306 308 8.898761 ACTATATCACTTGACAGAGACTTAGTG 58.101 37.037 0.00 0.00 35.51 2.74
398 400 6.483974 AGACTTCGTTATGTCTCAGTCGATAT 59.516 38.462 0.00 0.00 39.04 1.63
403 405 6.844254 ACTAAGACTTCGTTATGTCTCAGTC 58.156 40.000 0.00 0.00 37.24 3.51
425 427 7.390996 TCTTTATCAGTTAAGTCTCAGTCGACT 59.609 37.037 13.58 13.58 45.73 4.18
426 428 7.528307 TCTTTATCAGTTAAGTCTCAGTCGAC 58.472 38.462 7.70 7.70 0.00 4.20
428 430 8.744008 TTTCTTTATCAGTTAAGTCTCAGTCG 57.256 34.615 0.00 0.00 0.00 4.18
432 434 9.996554 TCACATTTCTTTATCAGTTAAGTCTCA 57.003 29.630 0.00 0.00 0.00 3.27
434 436 8.940952 GCTCACATTTCTTTATCAGTTAAGTCT 58.059 33.333 0.00 0.00 0.00 3.24
964 969 2.955881 GCGAGTGTAAGCTGGGGGT 61.956 63.158 0.00 0.00 0.00 4.95
1500 1505 2.497675 CCCATCGTCCATCCCATAGTAG 59.502 54.545 0.00 0.00 0.00 2.57
1611 1616 4.470170 CCGTCATCGTCGCCGTCA 62.470 66.667 0.00 0.00 35.01 4.35
1756 1763 6.685527 AGTTCAGAAAAGAGAAAGTGGAAC 57.314 37.500 0.00 0.00 34.02 3.62
1762 1769 6.204495 CCCAGAGAAGTTCAGAAAAGAGAAAG 59.796 42.308 5.50 0.00 0.00 2.62
1881 1888 2.035449 TCGGAGTTCGAACACTCACAAT 59.965 45.455 28.78 6.59 45.86 2.71
2025 2032 6.600032 GGATCGGTTAGATTAGAGATGCTCTA 59.400 42.308 0.22 0.22 39.64 2.43
2026 2033 5.417580 GGATCGGTTAGATTAGAGATGCTCT 59.582 44.000 2.22 2.22 40.98 4.09
2027 2034 5.393678 GGGATCGGTTAGATTAGAGATGCTC 60.394 48.000 0.00 0.00 40.26 4.26
2028 2035 4.464597 GGGATCGGTTAGATTAGAGATGCT 59.535 45.833 0.00 0.00 40.26 3.79
2029 2036 4.464597 AGGGATCGGTTAGATTAGAGATGC 59.535 45.833 0.00 0.00 40.26 3.91
2030 2037 6.597832 AAGGGATCGGTTAGATTAGAGATG 57.402 41.667 0.00 0.00 40.26 2.90
2031 2038 9.992442 TTATAAGGGATCGGTTAGATTAGAGAT 57.008 33.333 0.00 0.00 40.26 2.75
2032 2039 9.818270 TTTATAAGGGATCGGTTAGATTAGAGA 57.182 33.333 0.00 0.00 40.26 3.10
2034 2041 8.529476 GCTTTATAAGGGATCGGTTAGATTAGA 58.471 37.037 0.00 0.00 40.26 2.10
2035 2042 8.532819 AGCTTTATAAGGGATCGGTTAGATTAG 58.467 37.037 0.00 0.00 40.26 1.73
2036 2043 8.431910 AGCTTTATAAGGGATCGGTTAGATTA 57.568 34.615 0.00 0.00 40.26 1.75
2037 2044 7.317722 AGCTTTATAAGGGATCGGTTAGATT 57.682 36.000 0.00 0.00 40.26 2.40
2038 2045 6.936968 AGCTTTATAAGGGATCGGTTAGAT 57.063 37.500 0.00 0.00 43.51 1.98
2097 2104 4.341235 GGTGCAGTTTTAAGGAGAAAACCT 59.659 41.667 7.87 0.00 46.15 3.50
2099 2106 5.515797 AGGTGCAGTTTTAAGGAGAAAAC 57.484 39.130 4.04 4.04 45.60 2.43
2110 2117 2.433436 GGATCGGTTAGGTGCAGTTTT 58.567 47.619 0.00 0.00 0.00 2.43
2115 2122 0.251916 CAAGGGATCGGTTAGGTGCA 59.748 55.000 0.00 0.00 0.00 4.57
2171 2184 5.343860 GCGCCAACTAAAAATTTAACGTCAT 59.656 36.000 0.00 0.00 0.00 3.06
2189 2202 1.255882 ATTTGTCATCCTTGCGCCAA 58.744 45.000 4.18 0.00 0.00 4.52
2190 2203 1.255882 AATTTGTCATCCTTGCGCCA 58.744 45.000 4.18 0.00 0.00 5.69
2191 2204 2.368655 AAATTTGTCATCCTTGCGCC 57.631 45.000 4.18 0.00 0.00 6.53
2192 2205 4.096732 ACTAAATTTGTCATCCTTGCGC 57.903 40.909 0.00 0.00 0.00 6.09
2193 2206 4.324402 GCAACTAAATTTGTCATCCTTGCG 59.676 41.667 0.00 0.00 0.00 4.85
2216 2265 2.544685 CTAGGAAAGTGTCATGCTCGG 58.455 52.381 0.00 0.00 0.00 4.63
2218 2267 2.977914 TGCTAGGAAAGTGTCATGCTC 58.022 47.619 0.00 0.00 0.00 4.26
2246 2295 2.299867 GGCATGGTCCAACTCAAAACAT 59.700 45.455 0.00 0.00 0.00 2.71
2251 2300 0.478072 ACAGGCATGGTCCAACTCAA 59.522 50.000 2.31 0.00 0.00 3.02
2252 2301 0.036732 GACAGGCATGGTCCAACTCA 59.963 55.000 2.31 0.00 0.00 3.41
2255 2304 0.598065 GTTGACAGGCATGGTCCAAC 59.402 55.000 14.33 14.33 34.36 3.77
2256 2305 0.478072 AGTTGACAGGCATGGTCCAA 59.522 50.000 2.31 1.05 34.36 3.53
2259 2308 3.412386 AGTTTAGTTGACAGGCATGGTC 58.588 45.455 2.31 0.00 35.83 4.02
2260 2309 3.508845 AGTTTAGTTGACAGGCATGGT 57.491 42.857 2.31 0.00 0.00 3.55
2267 2316 2.293399 GGGTGGCAAGTTTAGTTGACAG 59.707 50.000 6.09 0.00 46.33 3.51
2284 2333 2.233676 GGCCCTATGTTTTTCAAGGGTG 59.766 50.000 8.02 0.00 41.82 4.61
2287 2336 1.476488 CGGGCCCTATGTTTTTCAAGG 59.524 52.381 22.43 0.00 0.00 3.61
2292 2341 2.597578 AAGTCGGGCCCTATGTTTTT 57.402 45.000 22.43 1.37 0.00 1.94
2293 2342 3.724732 TTAAGTCGGGCCCTATGTTTT 57.275 42.857 22.43 8.05 0.00 2.43
2296 2345 3.945640 AATTTAAGTCGGGCCCTATGT 57.054 42.857 22.43 5.07 0.00 2.29
2302 2351 4.011698 TGGAGTAAAATTTAAGTCGGGCC 58.988 43.478 0.00 0.00 0.00 5.80
2303 2352 4.698780 AGTGGAGTAAAATTTAAGTCGGGC 59.301 41.667 0.00 0.00 0.00 6.13
2304 2353 5.704053 ACAGTGGAGTAAAATTTAAGTCGGG 59.296 40.000 0.00 0.00 0.00 5.14
2305 2354 6.599437 CACAGTGGAGTAAAATTTAAGTCGG 58.401 40.000 0.00 0.00 0.00 4.79
2306 2355 6.077838 GCACAGTGGAGTAAAATTTAAGTCG 58.922 40.000 1.84 0.00 0.00 4.18
2308 2357 5.562113 GCGCACAGTGGAGTAAAATTTAAGT 60.562 40.000 0.30 0.00 0.00 2.24
2309 2358 4.851558 GCGCACAGTGGAGTAAAATTTAAG 59.148 41.667 0.30 0.00 0.00 1.85
2310 2359 4.320641 GGCGCACAGTGGAGTAAAATTTAA 60.321 41.667 10.83 0.00 0.00 1.52
2311 2360 3.189702 GGCGCACAGTGGAGTAAAATTTA 59.810 43.478 10.83 0.00 0.00 1.40
2313 2362 1.539827 GGCGCACAGTGGAGTAAAATT 59.460 47.619 10.83 0.00 0.00 1.82
2314 2363 1.165270 GGCGCACAGTGGAGTAAAAT 58.835 50.000 10.83 0.00 0.00 1.82
2328 2424 3.389983 AGTATATTTAAGAGTGGGGCGCA 59.610 43.478 10.83 0.00 0.00 6.09
2329 2425 4.004196 AGTATATTTAAGAGTGGGGCGC 57.996 45.455 0.00 0.00 0.00 6.53
2333 2429 5.465724 GCGACCAAGTATATTTAAGAGTGGG 59.534 44.000 0.00 0.00 0.00 4.61
2334 2430 5.465724 GGCGACCAAGTATATTTAAGAGTGG 59.534 44.000 0.00 0.00 0.00 4.00
2335 2431 5.175126 CGGCGACCAAGTATATTTAAGAGTG 59.825 44.000 0.00 0.00 0.00 3.51
2354 2450 2.098443 GGAAATTTTATTGCTCCGGCGA 59.902 45.455 9.30 0.00 42.25 5.54
2359 2455 6.325596 GTGTGAGAGGAAATTTTATTGCTCC 58.674 40.000 5.15 0.00 45.68 4.70
2360 2456 6.071952 TGGTGTGAGAGGAAATTTTATTGCTC 60.072 38.462 0.00 0.92 45.11 4.26
2361 2457 5.774690 TGGTGTGAGAGGAAATTTTATTGCT 59.225 36.000 0.00 0.00 33.28 3.91
2376 2478 2.200373 TGAGATCGAGTGGTGTGAGA 57.800 50.000 0.00 0.00 0.00 3.27
2382 2484 4.437239 GTGAATTGATGAGATCGAGTGGT 58.563 43.478 0.00 0.00 0.00 4.16
2385 2487 3.452264 TGGGTGAATTGATGAGATCGAGT 59.548 43.478 0.00 0.00 0.00 4.18
2398 2500 1.384191 GCTCAGGGGTGGGTGAATT 59.616 57.895 0.00 0.00 0.00 2.17
2404 2506 2.608988 AGAGTGCTCAGGGGTGGG 60.609 66.667 1.82 0.00 0.00 4.61
2407 2509 1.908340 GATGCAGAGTGCTCAGGGGT 61.908 60.000 0.00 0.00 45.31 4.95
2410 2512 1.153208 GGGATGCAGAGTGCTCAGG 60.153 63.158 0.00 0.00 45.31 3.86
2488 2591 1.014044 GTGGCGCTTCTGATCGACAA 61.014 55.000 7.64 0.00 46.07 3.18
2496 2599 3.175240 CGTCGAGTGGCGCTTCTG 61.175 66.667 7.64 0.00 40.61 3.02
2534 2637 3.195698 GGGATGAGGACGCGTTGC 61.196 66.667 15.53 6.60 0.00 4.17
2539 2642 2.202892 GAACCGGGATGAGGACGC 60.203 66.667 6.32 0.00 0.00 5.19
2547 2650 0.322546 GCAAGTCAAGGAACCGGGAT 60.323 55.000 6.32 0.00 0.00 3.85
2612 2715 1.125093 TCACCCAATCCCACACGACT 61.125 55.000 0.00 0.00 0.00 4.18
2616 2719 1.674322 CCGTCACCCAATCCCACAC 60.674 63.158 0.00 0.00 0.00 3.82
2619 2722 0.620410 ATCTCCGTCACCCAATCCCA 60.620 55.000 0.00 0.00 0.00 4.37


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

AutoCloner maintained by Alex Coulton.