Multiple sequence alignment - TraesCS3A01G340600

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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 TraesCS3A01G340600 chr3A 100.000 3233 0 0 1 3233 587876478 587879710 0.000000e+00 5971
1 TraesCS3A01G340600 chr3D 92.636 2784 155 18 22 2763 446063235 446066010 0.000000e+00 3960
2 TraesCS3A01G340600 chr3D 93.805 339 20 1 2894 3231 446068400 446068738 2.880000e-140 508
3 TraesCS3A01G340600 chr3D 94.776 134 5 2 2767 2899 446066424 446066556 1.180000e-49 207
4 TraesCS3A01G340600 chr3D 80.000 155 28 3 2422 2576 4321750 4321599 9.480000e-21 111
5 TraesCS3A01G340600 chr3B 91.604 2394 124 24 22 2381 584910825 584913175 0.000000e+00 3236
6 TraesCS3A01G340600 chr3B 90.382 759 45 14 2493 3228 584913171 584913924 0.000000e+00 972
7 TraesCS3A01G340600 chr2A 75.299 502 76 32 1753 2233 744449170 744448696 2.540000e-46 196
8 TraesCS3A01G340600 chr2B 75.050 497 80 29 1753 2233 747180973 747180505 1.180000e-44 191
9 TraesCS3A01G340600 chr2D 74.349 499 80 31 1753 2233 612344215 612343747 5.550000e-38 169
10 TraesCS3A01G340600 chr7B 78.761 226 42 5 2422 2646 211399806 211399586 2.600000e-31 147


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 TraesCS3A01G340600 chr3A 587876478 587879710 3232 False 5971.000000 5971 100.000 1 3233 1 chr3A.!!$F1 3232
1 TraesCS3A01G340600 chr3D 446063235 446068738 5503 False 1558.333333 3960 93.739 22 3231 3 chr3D.!!$F1 3209
2 TraesCS3A01G340600 chr3B 584910825 584913924 3099 False 2104.000000 3236 90.993 22 3228 2 chr3B.!!$F1 3206

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
135 136 0.324943 CCCTCACGGTGAATCCTTGT 59.675 55.0 12.54 0.0 36.88 3.16 F
634 640 0.537143 AGCGGTTGATCCTTGCACAA 60.537 50.0 0.00 0.0 0.00 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1166 1180 2.095252 GTCTCTTCGAGCGGCAACC 61.095 63.158 1.45 0.0 0.00 3.77 R
2314 2352 0.602638 TCTGGCAGCACGGTAAAGTG 60.603 55.000 10.34 0.0 44.47 3.16 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
17 18 4.700037 CGACGCCAGATCAGAGTC 57.300 61.111 8.86 8.86 0.00 3.36
18 19 1.064946 CGACGCCAGATCAGAGTCC 59.935 63.158 12.00 0.00 0.00 3.85
19 20 1.439644 GACGCCAGATCAGAGTCCC 59.560 63.158 7.99 0.00 0.00 4.46
20 21 2.022240 GACGCCAGATCAGAGTCCCC 62.022 65.000 7.99 0.00 0.00 4.81
28 29 3.199508 CAGATCAGAGTCCCCAATGAACT 59.800 47.826 0.00 0.00 0.00 3.01
37 38 1.550869 CCCCAATGAACTGCCCTCTTT 60.551 52.381 0.00 0.00 0.00 2.52
51 52 2.169769 CCCTCTTTACCTCATACGCCAA 59.830 50.000 0.00 0.00 0.00 4.52
52 53 3.195661 CCTCTTTACCTCATACGCCAAC 58.804 50.000 0.00 0.00 0.00 3.77
118 119 1.068055 CAGTTGATCTTTGCAGCACCC 60.068 52.381 0.00 0.00 0.00 4.61
135 136 0.324943 CCCTCACGGTGAATCCTTGT 59.675 55.000 12.54 0.00 36.88 3.16
138 139 2.496070 CCTCACGGTGAATCCTTGTAGA 59.504 50.000 12.54 0.00 36.88 2.59
161 162 2.224281 ACCTCTCTGTCGAACATTGCAA 60.224 45.455 0.00 0.00 0.00 4.08
166 167 1.333308 CTGTCGAACATTGCAACACCA 59.667 47.619 0.00 0.00 0.00 4.17
176 177 0.541392 TGCAACACCAGTGTCTGACT 59.459 50.000 9.51 0.00 44.13 3.41
198 199 3.755628 GCGTGTGGGCGACTCCTA 61.756 66.667 0.31 0.00 34.39 2.94
207 208 3.129502 CGACTCCTACGGCGACCA 61.130 66.667 16.62 0.00 0.00 4.02
208 209 2.693762 CGACTCCTACGGCGACCAA 61.694 63.158 16.62 0.00 0.00 3.67
210 211 1.870055 GACTCCTACGGCGACCAACA 61.870 60.000 16.62 0.00 0.00 3.33
213 214 1.005394 CCTACGGCGACCAACAAGT 60.005 57.895 16.62 0.00 0.00 3.16
219 220 1.165270 GGCGACCAACAAGTAGCATT 58.835 50.000 0.00 0.00 39.81 3.56
226 227 0.796312 AACAAGTAGCATTGACGCCG 59.204 50.000 3.67 0.00 34.20 6.46
321 322 2.575993 CAGTAGCAGGAGCAGCGT 59.424 61.111 0.00 0.00 45.49 5.07
324 325 2.997315 TAGCAGGAGCAGCGTGGT 60.997 61.111 8.60 8.60 45.49 4.16
326 327 4.996434 GCAGGAGCAGCGTGGTGT 62.996 66.667 0.64 0.00 41.58 4.16
356 357 0.665835 GTTGCAATGGGTCGTTGACA 59.334 50.000 0.59 0.08 32.66 3.58
360 361 0.950836 CAATGGGTCGTTGACAGCAA 59.049 50.000 0.00 0.00 32.66 3.91
381 382 2.920076 AATGGTTGTGCGGTGGGTGT 62.920 55.000 0.00 0.00 0.00 4.16
383 384 2.411290 GTTGTGCGGTGGGTGTTG 59.589 61.111 0.00 0.00 0.00 3.33
385 386 4.497984 TGTGCGGTGGGTGTTGCT 62.498 61.111 0.00 0.00 0.00 3.91
386 387 3.660111 GTGCGGTGGGTGTTGCTC 61.660 66.667 0.00 0.00 0.00 4.26
397 398 1.533033 TGTTGCTCAGGTCCTCGGA 60.533 57.895 0.00 0.00 0.00 4.55
464 465 5.191727 AGAAGGATTGAGACAGAGAGAGA 57.808 43.478 0.00 0.00 0.00 3.10
465 466 5.195940 AGAAGGATTGAGACAGAGAGAGAG 58.804 45.833 0.00 0.00 0.00 3.20
467 468 4.785301 AGGATTGAGACAGAGAGAGAGAG 58.215 47.826 0.00 0.00 0.00 3.20
468 469 4.474651 AGGATTGAGACAGAGAGAGAGAGA 59.525 45.833 0.00 0.00 0.00 3.10
469 470 4.818546 GGATTGAGACAGAGAGAGAGAGAG 59.181 50.000 0.00 0.00 0.00 3.20
470 471 5.396772 GGATTGAGACAGAGAGAGAGAGAGA 60.397 48.000 0.00 0.00 0.00 3.10
471 472 4.471904 TGAGACAGAGAGAGAGAGAGAC 57.528 50.000 0.00 0.00 0.00 3.36
472 473 3.119137 TGAGACAGAGAGAGAGAGAGACG 60.119 52.174 0.00 0.00 0.00 4.18
474 475 3.131223 AGACAGAGAGAGAGAGAGACGAG 59.869 52.174 0.00 0.00 0.00 4.18
475 476 3.096852 ACAGAGAGAGAGAGAGACGAGA 58.903 50.000 0.00 0.00 0.00 4.04
476 477 3.131223 ACAGAGAGAGAGAGAGACGAGAG 59.869 52.174 0.00 0.00 0.00 3.20
477 478 2.101582 AGAGAGAGAGAGAGACGAGAGC 59.898 54.545 0.00 0.00 0.00 4.09
478 479 1.831106 AGAGAGAGAGAGACGAGAGCA 59.169 52.381 0.00 0.00 0.00 4.26
479 480 2.236146 AGAGAGAGAGAGACGAGAGCAA 59.764 50.000 0.00 0.00 0.00 3.91
480 481 2.609459 GAGAGAGAGAGACGAGAGCAAG 59.391 54.545 0.00 0.00 0.00 4.01
508 509 3.775316 AGGATGACGAACTAGGGATGTTT 59.225 43.478 0.00 0.00 0.00 2.83
521 522 7.633789 ACTAGGGATGTTTTGTAATCACTGAT 58.366 34.615 0.00 0.00 37.15 2.90
548 549 2.118679 CCATGTGTAGGTGGAGATGGA 58.881 52.381 0.00 0.00 37.72 3.41
610 611 0.618458 AAGGGCAAATCAGACGGCTA 59.382 50.000 0.00 0.00 0.00 3.93
634 640 0.537143 AGCGGTTGATCCTTGCACAA 60.537 50.000 0.00 0.00 0.00 3.33
955 969 2.658538 CGTGATCGTCCTTCTGCAG 58.341 57.895 7.63 7.63 0.00 4.41
1005 1019 4.064768 CAGGGGCCAGCAATGGGA 62.065 66.667 4.39 0.00 0.00 4.37
1166 1180 2.579201 CCTGCACCCCTACACGAG 59.421 66.667 0.00 0.00 0.00 4.18
1389 1403 1.081242 CACGCCGCAATTTTCAGCT 60.081 52.632 0.00 0.00 0.00 4.24
1428 1445 2.584970 GAATCATCGTCGCCGCCA 60.585 61.111 0.00 0.00 0.00 5.69
1461 1478 1.444119 TTGTGGCGCCTGACTTTGAC 61.444 55.000 29.70 15.27 0.00 3.18
1464 1481 2.281484 GCGCCTGACTTTGACCCA 60.281 61.111 0.00 0.00 0.00 4.51
1553 1570 1.613630 AGAATGAGGCCACGACCCT 60.614 57.895 5.01 0.00 34.77 4.34
1667 1684 1.558756 CCACAAGAAGCTGGAGGAGAT 59.441 52.381 0.00 0.00 0.00 2.75
1683 1700 4.629122 AGGAGATGAAGGAGATGAAGGAA 58.371 43.478 0.00 0.00 0.00 3.36
1686 1703 4.039339 AGATGAAGGAGATGAAGGAAGCT 58.961 43.478 0.00 0.00 0.00 3.74
1903 1920 3.282745 GAGCTCCGCAACCTCGTCA 62.283 63.158 0.87 0.00 0.00 4.35
2111 2128 2.743928 GTTCCTGCCCTGCGACAG 60.744 66.667 0.00 0.00 0.00 3.51
2223 2240 4.101448 ATCAGGTGCCCGGTCTGC 62.101 66.667 0.00 0.00 0.00 4.26
2288 2326 2.028020 TGTCAGACTGAGAGACTCGCTA 60.028 50.000 5.10 0.00 32.35 4.26
2346 2385 0.178981 TGCCAGAGAAGCTGCCTTTT 60.179 50.000 0.00 0.00 43.50 2.27
2347 2386 0.243095 GCCAGAGAAGCTGCCTTTTG 59.757 55.000 0.00 0.00 43.50 2.44
2348 2387 0.886563 CCAGAGAAGCTGCCTTTTGG 59.113 55.000 0.00 0.00 43.50 3.28
2388 2428 6.907212 GCAATATCTTAGTTTGTTCGTGGATG 59.093 38.462 0.00 0.00 0.00 3.51
2401 2441 1.739466 CGTGGATGGATGTGTTCTTGG 59.261 52.381 0.00 0.00 0.00 3.61
2416 2456 3.194005 TCTTGGAATCGCAGTTATCCC 57.806 47.619 0.00 0.00 0.00 3.85
2438 2478 0.179000 ACCTTTCTATGCTCCAGGCG 59.821 55.000 0.00 0.00 45.43 5.52
2439 2479 1.162800 CCTTTCTATGCTCCAGGCGC 61.163 60.000 0.00 0.00 45.43 6.53
2441 2481 2.608970 TTTCTATGCTCCAGGCGCCC 62.609 60.000 26.15 7.94 45.43 6.13
2442 2482 4.976925 CTATGCTCCAGGCGCCCG 62.977 72.222 26.15 14.30 45.43 6.13
2462 2505 3.532155 CCCGGAAGAGGGCTCTCG 61.532 72.222 8.25 0.00 45.72 4.04
2563 2613 7.865706 TCTTGTATCCTGCCTATTTTCTTTC 57.134 36.000 0.00 0.00 0.00 2.62
2616 2680 5.088739 GTCTGCAAGGACGTCATTAATTTG 58.911 41.667 15.94 4.75 0.00 2.32
2704 2768 3.286353 TCTGTCTGTTTGATGTTTGCCA 58.714 40.909 0.00 0.00 0.00 4.92
2729 2793 5.574443 GCTTGGTGATTAGTTTGATTTGCTC 59.426 40.000 0.00 0.00 0.00 4.26
2785 3260 9.817809 GAGATGGTTGTTTTCATACTAGTATCA 57.182 33.333 12.62 4.91 0.00 2.15
2850 3325 2.222027 GACAGAGGACAAACCAGTTGG 58.778 52.381 0.00 0.00 41.97 3.77
2985 5311 4.634883 CAGAACCAGAAATGAGGAGACATG 59.365 45.833 0.00 0.00 0.00 3.21
3056 5382 6.757010 TCTTGCTTCTTTATCCTGATTCGTAC 59.243 38.462 0.00 0.00 0.00 3.67
3088 5415 9.555727 TTCCCGGTCTAAAATGATTATTCTAAG 57.444 33.333 0.00 0.00 0.00 2.18
3193 5520 7.012515 CGCGGAGATTCTTATAGTAGATACCAT 59.987 40.741 0.00 0.00 0.00 3.55
3231 5558 2.035066 GCAATGGACTTTGTGAACAGCT 59.965 45.455 0.00 0.00 0.00 4.24
3232 5559 3.491447 GCAATGGACTTTGTGAACAGCTT 60.491 43.478 0.00 0.00 0.00 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.064946 GGACTCTGATCTGGCGTCG 59.935 63.158 12.91 0.00 0.00 5.12
1 2 1.439644 GGGACTCTGATCTGGCGTC 59.560 63.158 11.67 11.67 0.00 5.19
2 3 2.060980 GGGGACTCTGATCTGGCGT 61.061 63.158 0.00 0.00 0.00 5.68
3 4 1.617018 TTGGGGACTCTGATCTGGCG 61.617 60.000 0.00 0.00 0.00 5.69
4 5 0.842635 ATTGGGGACTCTGATCTGGC 59.157 55.000 0.00 0.00 0.00 4.85
5 6 2.121948 TCATTGGGGACTCTGATCTGG 58.878 52.381 0.00 0.00 0.00 3.86
6 7 3.199508 AGTTCATTGGGGACTCTGATCTG 59.800 47.826 0.00 0.00 0.00 2.90
7 8 3.199508 CAGTTCATTGGGGACTCTGATCT 59.800 47.826 0.00 0.00 0.00 2.75
8 9 3.539604 CAGTTCATTGGGGACTCTGATC 58.460 50.000 0.00 0.00 0.00 2.92
9 10 2.356535 GCAGTTCATTGGGGACTCTGAT 60.357 50.000 0.00 0.00 0.00 2.90
10 11 1.003580 GCAGTTCATTGGGGACTCTGA 59.996 52.381 0.00 0.00 0.00 3.27
11 12 1.457346 GCAGTTCATTGGGGACTCTG 58.543 55.000 0.00 0.00 0.00 3.35
12 13 0.329596 GGCAGTTCATTGGGGACTCT 59.670 55.000 0.00 0.00 0.00 3.24
13 14 0.681243 GGGCAGTTCATTGGGGACTC 60.681 60.000 0.00 0.00 0.00 3.36
14 15 1.142688 AGGGCAGTTCATTGGGGACT 61.143 55.000 0.00 0.00 0.00 3.85
15 16 0.681243 GAGGGCAGTTCATTGGGGAC 60.681 60.000 0.00 0.00 0.00 4.46
16 17 0.846427 AGAGGGCAGTTCATTGGGGA 60.846 55.000 0.00 0.00 0.00 4.81
17 18 0.040204 AAGAGGGCAGTTCATTGGGG 59.960 55.000 0.00 0.00 0.00 4.96
18 19 1.928868 AAAGAGGGCAGTTCATTGGG 58.071 50.000 0.00 0.00 0.00 4.12
19 20 2.755103 GGTAAAGAGGGCAGTTCATTGG 59.245 50.000 0.00 0.00 0.00 3.16
20 21 3.690460 AGGTAAAGAGGGCAGTTCATTG 58.310 45.455 0.00 0.00 0.00 2.82
28 29 1.138266 GCGTATGAGGTAAAGAGGGCA 59.862 52.381 0.00 0.00 0.00 5.36
37 38 0.101759 GCTCGTTGGCGTATGAGGTA 59.898 55.000 9.74 0.00 39.49 3.08
51 52 2.264794 CTACCAAAGGCCGCTCGT 59.735 61.111 0.00 0.00 0.00 4.18
52 53 3.195698 GCTACCAAAGGCCGCTCG 61.196 66.667 0.00 0.00 0.00 5.03
91 92 4.497674 GCTGCAAAGATCAACTGATGGATC 60.498 45.833 0.00 0.00 40.13 3.36
138 139 2.353208 GCAATGTTCGACAGAGAGGTCT 60.353 50.000 0.00 0.00 35.63 3.85
151 152 2.358898 AGACACTGGTGTTGCAATGTTC 59.641 45.455 0.59 0.00 45.05 3.18
161 162 1.473965 CTGCAAGTCAGACACTGGTGT 60.474 52.381 6.04 6.04 45.72 4.16
166 167 0.877649 CACGCTGCAAGTCAGACACT 60.878 55.000 2.66 0.00 45.72 3.55
196 197 1.625616 CTACTTGTTGGTCGCCGTAG 58.374 55.000 0.00 0.00 0.00 3.51
198 199 1.666872 GCTACTTGTTGGTCGCCGT 60.667 57.895 0.00 0.00 0.00 5.68
207 208 0.796312 CGGCGTCAATGCTACTTGTT 59.204 50.000 0.00 0.00 34.52 2.83
208 209 1.635663 GCGGCGTCAATGCTACTTGT 61.636 55.000 9.37 0.00 34.52 3.16
210 211 2.452813 CGCGGCGTCAATGCTACTT 61.453 57.895 15.36 0.00 34.52 2.24
213 214 1.066752 ATACGCGGCGTCAATGCTA 59.933 52.632 32.91 13.20 41.54 3.49
226 227 4.228097 CGCTGGTGCTGCATACGC 62.228 66.667 5.27 7.73 36.97 4.42
248 249 1.303643 GGCAAGCCAACCACTAGCT 60.304 57.895 6.14 0.00 38.88 3.32
307 308 2.997315 ACCACGCTGCTCCTGCTA 60.997 61.111 0.00 0.00 40.48 3.49
310 311 2.281070 AACACCACGCTGCTCCTG 60.281 61.111 0.00 0.00 0.00 3.86
317 318 3.269347 GCACGACAACACCACGCT 61.269 61.111 0.00 0.00 0.00 5.07
321 322 0.449786 CAACAAGCACGACAACACCA 59.550 50.000 0.00 0.00 0.00 4.17
360 361 2.199652 CCCACCGCACAACCATTGT 61.200 57.895 0.00 0.00 46.75 2.71
363 364 2.597217 CACCCACCGCACAACCAT 60.597 61.111 0.00 0.00 0.00 3.55
364 365 3.646942 AACACCCACCGCACAACCA 62.647 57.895 0.00 0.00 0.00 3.67
367 368 3.522731 GCAACACCCACCGCACAA 61.523 61.111 0.00 0.00 0.00 3.33
368 369 4.497984 AGCAACACCCACCGCACA 62.498 61.111 0.00 0.00 0.00 4.57
372 373 2.669569 CCTGAGCAACACCCACCG 60.670 66.667 0.00 0.00 0.00 4.94
381 382 0.984230 AAATCCGAGGACCTGAGCAA 59.016 50.000 0.00 0.00 0.00 3.91
383 384 0.462759 CCAAATCCGAGGACCTGAGC 60.463 60.000 0.00 0.00 0.00 4.26
385 386 0.613260 CACCAAATCCGAGGACCTGA 59.387 55.000 0.00 0.00 0.00 3.86
386 387 0.392998 CCACCAAATCCGAGGACCTG 60.393 60.000 0.00 0.00 0.00 4.00
464 465 2.779755 TCTCTTGCTCTCGTCTCTCT 57.220 50.000 0.00 0.00 0.00 3.10
465 466 3.840890 TTTCTCTTGCTCTCGTCTCTC 57.159 47.619 0.00 0.00 0.00 3.20
467 468 3.057174 TCCTTTTCTCTTGCTCTCGTCTC 60.057 47.826 0.00 0.00 0.00 3.36
468 469 2.894126 TCCTTTTCTCTTGCTCTCGTCT 59.106 45.455 0.00 0.00 0.00 4.18
469 470 3.305398 TCCTTTTCTCTTGCTCTCGTC 57.695 47.619 0.00 0.00 0.00 4.20
470 471 3.259374 TCATCCTTTTCTCTTGCTCTCGT 59.741 43.478 0.00 0.00 0.00 4.18
471 472 3.616379 GTCATCCTTTTCTCTTGCTCTCG 59.384 47.826 0.00 0.00 0.00 4.04
472 473 3.616379 CGTCATCCTTTTCTCTTGCTCTC 59.384 47.826 0.00 0.00 0.00 3.20
474 475 3.589988 TCGTCATCCTTTTCTCTTGCTC 58.410 45.455 0.00 0.00 0.00 4.26
475 476 3.685139 TCGTCATCCTTTTCTCTTGCT 57.315 42.857 0.00 0.00 0.00 3.91
476 477 3.748568 AGTTCGTCATCCTTTTCTCTTGC 59.251 43.478 0.00 0.00 0.00 4.01
477 478 5.578727 CCTAGTTCGTCATCCTTTTCTCTTG 59.421 44.000 0.00 0.00 0.00 3.02
478 479 5.337652 CCCTAGTTCGTCATCCTTTTCTCTT 60.338 44.000 0.00 0.00 0.00 2.85
479 480 4.160626 CCCTAGTTCGTCATCCTTTTCTCT 59.839 45.833 0.00 0.00 0.00 3.10
480 481 4.159879 TCCCTAGTTCGTCATCCTTTTCTC 59.840 45.833 0.00 0.00 0.00 2.87
508 509 3.010027 TGGCTCCCAATCAGTGATTACAA 59.990 43.478 17.86 5.70 30.44 2.41
521 522 0.327924 CACCTACACATGGCTCCCAA 59.672 55.000 0.00 0.00 36.95 4.12
548 549 6.429385 ACTTGATTCTTCTCTTTCATCGCTTT 59.571 34.615 0.00 0.00 0.00 3.51
610 611 2.092968 TGCAAGGATCAACCGCTTAGAT 60.093 45.455 0.00 0.00 44.74 1.98
907 921 3.695830 TTATGGACGTGGAGCTCTTTT 57.304 42.857 14.64 0.00 0.00 2.27
914 928 2.404215 CGCCTATTTATGGACGTGGAG 58.596 52.381 0.00 0.00 0.00 3.86
1166 1180 2.095252 GTCTCTTCGAGCGGCAACC 61.095 63.158 1.45 0.00 0.00 3.77
1389 1403 2.356553 CGGAACCAACTCGGCGAA 60.357 61.111 12.13 0.00 39.03 4.70
1667 1684 3.176411 TCAGCTTCCTTCATCTCCTTCA 58.824 45.455 0.00 0.00 0.00 3.02
2162 2179 1.071605 GCACTCCTCGAACATGTCAC 58.928 55.000 0.00 0.00 0.00 3.67
2314 2352 0.602638 TCTGGCAGCACGGTAAAGTG 60.603 55.000 10.34 0.00 44.47 3.16
2346 2385 0.843309 TGCTGACCAGGAGAAAACCA 59.157 50.000 0.00 0.00 0.00 3.67
2347 2386 1.981256 TTGCTGACCAGGAGAAAACC 58.019 50.000 0.00 0.00 0.00 3.27
2348 2387 5.189180 AGATATTGCTGACCAGGAGAAAAC 58.811 41.667 0.00 0.00 0.00 2.43
2388 2428 2.083774 TGCGATTCCAAGAACACATCC 58.916 47.619 0.00 0.00 0.00 3.51
2401 2441 1.499049 GTCCGGGATAACTGCGATTC 58.501 55.000 0.00 0.00 0.00 2.52
2451 2494 1.379309 GGAGTCACGAGAGCCCTCT 60.379 63.158 0.00 0.00 43.78 3.69
2563 2613 2.290641 CACCACACGAAAGGAAAGAAGG 59.709 50.000 0.00 0.00 0.00 3.46
2666 2730 5.936956 CAGACAGAAAAATGCCTAGACTTCT 59.063 40.000 0.00 0.00 0.00 2.85
2704 2768 5.244626 AGCAAATCAAACTAATCACCAAGCT 59.755 36.000 0.00 0.00 0.00 3.74
2815 3290 6.072508 TGTCCTCTGTCAACATTTAATTGAGC 60.073 38.462 4.42 0.00 36.76 4.26
2850 3325 3.842436 TCCCTTCTTTTCCTGGGTAGTAC 59.158 47.826 0.00 0.00 40.48 2.73
2985 5311 4.319177 ACACCTCAAGCAATAACAGACTC 58.681 43.478 0.00 0.00 0.00 3.36
3056 5382 4.585879 TCATTTTAGACCGGGAAGGAAAG 58.414 43.478 6.32 0.00 45.00 2.62
3136 5463 7.489113 CAGTAATTTGTGCATTCCATTACTTCC 59.511 37.037 15.48 0.00 38.18 3.46
3193 5520 4.157656 CCATTGCGATTAAAGGTTTCTCCA 59.842 41.667 0.00 0.00 39.02 3.86


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

AutoCloner maintained by Alex Coulton.