Multiple sequence alignment - TraesCS5A01G047000

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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 TraesCS5A01G047000 chr5A 100.000 3542 0 0 1 3542 42258372 42261913 0.000000e+00 6541.0
1 TraesCS5A01G047000 chr5D 90.773 2612 130 45 644 3212 54097284 54099827 0.000000e+00 3386.0
2 TraesCS5A01G047000 chr5D 93.782 386 24 0 1727 2112 321998712 321999097 6.590000e-162 580.0
3 TraesCS5A01G047000 chr5D 83.272 544 31 17 13 525 54096420 54096934 2.510000e-121 446.0
4 TraesCS5A01G047000 chr5D 84.470 264 37 3 1172 1433 455614355 455614616 1.260000e-64 257.0
5 TraesCS5A01G047000 chr5D 80.278 360 42 14 3205 3542 54099847 54100199 9.820000e-61 244.0
6 TraesCS5A01G047000 chr5B 89.082 2134 132 42 13 2096 56978261 56980343 0.000000e+00 2556.0
7 TraesCS5A01G047000 chr5B 88.063 1399 89 38 2173 3542 56980420 56981769 0.000000e+00 1587.0
8 TraesCS5A01G047000 chr5B 93.363 889 52 6 1382 2263 460971339 460970451 0.000000e+00 1308.0
9 TraesCS5A01G047000 chr5B 89.934 914 62 7 915 1812 56915527 56916426 0.000000e+00 1151.0
10 TraesCS5A01G047000 chr5B 83.548 620 37 17 316 905 56696039 56696623 1.460000e-143 520.0
11 TraesCS5A01G047000 chr5B 84.381 525 35 19 429 926 56912533 56913037 4.140000e-129 472.0
12 TraesCS5A01G047000 chr5B 78.759 419 64 15 1020 1433 557354523 557354921 1.260000e-64 257.0
13 TraesCS5A01G047000 chr3B 92.408 843 55 9 1429 2263 813200986 813200145 0.000000e+00 1194.0
14 TraesCS5A01G047000 chr7A 93.160 731 50 0 1382 2112 17262277 17263007 0.000000e+00 1074.0
15 TraesCS5A01G047000 chr2B 95.717 537 22 1 1382 1918 723045638 723046173 0.000000e+00 863.0
16 TraesCS5A01G047000 chr2B 94.434 539 28 2 1382 1918 785072157 785072695 0.000000e+00 828.0
17 TraesCS5A01G047000 chr7B 94.786 537 28 0 1382 1918 17357308 17356772 0.000000e+00 837.0
18 TraesCS5A01G047000 chrUn 84.470 264 37 3 1172 1433 63675115 63675376 1.260000e-64 257.0
19 TraesCS5A01G047000 chr3D 93.023 43 3 0 15 57 452228509 452228551 2.950000e-06 63.9


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 TraesCS5A01G047000 chr5A 42258372 42261913 3541 False 6541.000000 6541 100.000000 1 3542 1 chr5A.!!$F1 3541
1 TraesCS5A01G047000 chr5D 54096420 54100199 3779 False 1358.666667 3386 84.774333 13 3542 3 chr5D.!!$F3 3529
2 TraesCS5A01G047000 chr5B 56978261 56981769 3508 False 2071.500000 2556 88.572500 13 3542 2 chr5B.!!$F4 3529
3 TraesCS5A01G047000 chr5B 460970451 460971339 888 True 1308.000000 1308 93.363000 1382 2263 1 chr5B.!!$R1 881
4 TraesCS5A01G047000 chr5B 56912533 56916426 3893 False 811.500000 1151 87.157500 429 1812 2 chr5B.!!$F3 1383
5 TraesCS5A01G047000 chr5B 56696039 56696623 584 False 520.000000 520 83.548000 316 905 1 chr5B.!!$F1 589
6 TraesCS5A01G047000 chr3B 813200145 813200986 841 True 1194.000000 1194 92.408000 1429 2263 1 chr3B.!!$R1 834
7 TraesCS5A01G047000 chr7A 17262277 17263007 730 False 1074.000000 1074 93.160000 1382 2112 1 chr7A.!!$F1 730
8 TraesCS5A01G047000 chr2B 723045638 723046173 535 False 863.000000 863 95.717000 1382 1918 1 chr2B.!!$F1 536
9 TraesCS5A01G047000 chr2B 785072157 785072695 538 False 828.000000 828 94.434000 1382 1918 1 chr2B.!!$F2 536
10 TraesCS5A01G047000 chr7B 17356772 17357308 536 True 837.000000 837 94.786000 1382 1918 1 chr7B.!!$R1 536

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
213 214 0.029035 CAAGATACGGACGGAGGTCG 59.971 60.0 0.00 0.0 44.39 4.79 F
214 215 0.107508 AAGATACGGACGGAGGTCGA 60.108 55.0 0.00 0.0 44.39 4.20 F
311 312 0.179020 CCAATAAGCATCGGCCTCCA 60.179 55.0 0.00 0.0 42.56 3.86 F
445 482 0.517742 GTCCGTGCAATTACGCGAAC 60.518 55.0 15.93 0.0 46.13 3.95 F
2143 5022 0.693049 ATTCTTGCCGTCTCCCTTGT 59.307 50.0 0.00 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1821 4681 1.648720 CTTGTTGTGCAGGACGTGG 59.351 57.895 0.00 0.00 0.00 4.94 R
2131 5010 2.032924 GTGTTTGAAACAAGGGAGACGG 59.967 50.000 12.89 0.00 44.16 4.79 R
2151 5032 2.095364 CCAGTAACTCGTCGCTGTTAGT 60.095 50.000 9.73 10.11 33.95 2.24 R
2226 5107 4.778143 ATCGCCACCACCTTCCGC 62.778 66.667 0.00 0.00 0.00 5.54 R
3236 6158 1.326245 CAAACACTTTCGAGCGTGTCA 59.674 47.619 18.24 0.00 43.05 3.58 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 0.736053 AAAAGTGCTCGGCGTTTGAA 59.264 45.000 6.85 0.00 0.00 2.69
32 33 0.038618 GCGTTTGAAGGGCCGAATTT 60.039 50.000 0.00 0.00 0.00 1.82
33 34 1.200484 GCGTTTGAAGGGCCGAATTTA 59.800 47.619 0.00 0.00 0.00 1.40
34 35 2.159296 GCGTTTGAAGGGCCGAATTTAT 60.159 45.455 0.00 0.00 0.00 1.40
35 36 3.691498 CGTTTGAAGGGCCGAATTTATC 58.309 45.455 0.00 0.00 0.00 1.75
47 48 2.286418 CGAATTTATCAAGTCCGGCTGC 60.286 50.000 0.00 0.00 0.00 5.25
57 58 2.895865 CCGGCTGCAGATGCTCTG 60.896 66.667 20.43 3.81 46.90 3.35
58 59 2.895865 CGGCTGCAGATGCTCTGG 60.896 66.667 20.43 0.00 44.43 3.86
63 64 2.191641 GCAGATGCTCTGGGTCCC 59.808 66.667 0.00 0.00 44.43 4.46
75 76 0.978907 TGGGTCCCTTTTACCTCGAC 59.021 55.000 10.00 0.00 37.18 4.20
92 93 2.142292 GACCACCCAGCTGGACCAAT 62.142 60.000 34.91 14.97 37.39 3.16
159 160 3.443976 TGCGTACTACAGCATACACATG 58.556 45.455 0.00 0.00 38.59 3.21
194 195 1.268946 GCATGCGTACGCGTAGAAC 59.731 57.895 32.55 18.86 45.51 3.01
205 206 2.107178 CGCGTAGAACAAGATACGGAC 58.893 52.381 0.00 0.00 43.75 4.79
206 207 2.107178 GCGTAGAACAAGATACGGACG 58.893 52.381 6.85 0.00 43.75 4.79
207 208 2.713011 CGTAGAACAAGATACGGACGG 58.287 52.381 0.00 0.00 40.74 4.79
208 209 2.352651 CGTAGAACAAGATACGGACGGA 59.647 50.000 0.00 0.00 40.74 4.69
209 210 3.545624 CGTAGAACAAGATACGGACGGAG 60.546 52.174 0.00 0.00 40.74 4.63
210 211 1.749634 AGAACAAGATACGGACGGAGG 59.250 52.381 0.00 0.00 0.00 4.30
211 212 1.475682 GAACAAGATACGGACGGAGGT 59.524 52.381 0.00 0.00 0.00 3.85
212 213 1.101331 ACAAGATACGGACGGAGGTC 58.899 55.000 0.00 0.00 42.66 3.85
213 214 0.029035 CAAGATACGGACGGAGGTCG 59.971 60.000 0.00 0.00 44.39 4.79
214 215 0.107508 AAGATACGGACGGAGGTCGA 60.108 55.000 0.00 0.00 44.39 4.20
215 216 0.813210 AGATACGGACGGAGGTCGAC 60.813 60.000 7.13 7.13 44.39 4.20
236 237 2.631984 TCGATCATCGACGGAGCG 59.368 61.111 17.43 17.43 44.82 5.03
237 238 3.094058 CGATCATCGACGGAGCGC 61.094 66.667 12.63 0.00 43.74 5.92
238 239 3.094058 GATCATCGACGGAGCGCG 61.094 66.667 0.00 0.00 0.00 6.86
255 256 1.803519 CGCAGAGACGCAAGAGGAC 60.804 63.158 0.00 0.00 43.62 3.85
260 261 0.803740 GAGACGCAAGAGGACGTACT 59.196 55.000 0.00 0.00 43.71 2.73
262 263 1.736681 AGACGCAAGAGGACGTACTAC 59.263 52.381 0.00 0.00 43.71 2.73
268 269 3.003482 GCAAGAGGACGTACTACGATGAT 59.997 47.826 15.49 0.00 46.05 2.45
269 270 4.528504 CAAGAGGACGTACTACGATGATG 58.471 47.826 15.49 3.30 46.05 3.07
270 271 4.069300 AGAGGACGTACTACGATGATGA 57.931 45.455 15.49 0.00 46.05 2.92
281 282 0.857287 CGATGATGAGTGGCACATCG 59.143 55.000 21.41 19.82 44.64 3.84
291 292 2.404789 GCACATCGCATTGGGTCG 59.595 61.111 0.24 0.00 41.79 4.79
311 312 0.179020 CCAATAAGCATCGGCCTCCA 60.179 55.000 0.00 0.00 42.56 3.86
329 353 0.588730 CAATAACCATGAACGCGGCG 60.589 55.000 22.36 22.36 0.00 6.46
353 390 3.296709 AACTCCACAGCCTACCGCG 62.297 63.158 0.00 0.00 44.76 6.46
359 396 2.026301 CAGCCTACCGCGCTAGAC 59.974 66.667 10.03 0.00 44.76 2.59
445 482 0.517742 GTCCGTGCAATTACGCGAAC 60.518 55.000 15.93 0.00 46.13 3.95
525 562 1.043116 CCGGCCAGGTCACTCTGATA 61.043 60.000 2.24 0.00 36.93 2.15
529 566 2.667470 GCCAGGTCACTCTGATACCTA 58.333 52.381 6.27 0.00 41.75 3.08
530 567 3.235200 GCCAGGTCACTCTGATACCTAT 58.765 50.000 6.27 0.00 41.75 2.57
531 568 3.257127 GCCAGGTCACTCTGATACCTATC 59.743 52.174 6.27 0.21 41.75 2.08
532 569 4.735369 CCAGGTCACTCTGATACCTATCT 58.265 47.826 6.27 0.00 41.75 1.98
533 570 4.522405 CCAGGTCACTCTGATACCTATCTG 59.478 50.000 6.27 0.00 41.75 2.90
534 571 5.380900 CAGGTCACTCTGATACCTATCTGA 58.619 45.833 6.27 2.88 41.75 3.27
535 572 6.009589 CAGGTCACTCTGATACCTATCTGAT 58.990 44.000 6.27 0.00 41.75 2.90
539 576 4.397730 CACTCTGATACCTATCTGATCCCG 59.602 50.000 0.00 0.00 39.09 5.14
638 689 4.996434 GCTCCATGCCCCGATCCG 62.996 72.222 0.00 0.00 35.15 4.18
837 1169 2.047560 GCGGGTTTGGCTCGTACT 60.048 61.111 0.00 0.00 44.37 2.73
847 1179 2.781923 TGGCTCGTACTGTACTGTACA 58.218 47.619 30.54 18.77 41.92 2.90
954 3793 5.221742 GGGAGAGTAAATAAGGACATCCCAG 60.222 48.000 0.00 0.00 40.79 4.45
999 3848 1.227674 GCCATTACTCCCTGCTCCG 60.228 63.158 0.00 0.00 0.00 4.63
1065 3914 2.031157 GCTGAGCTACGAGATCTTCTCC 60.031 54.545 0.00 0.00 40.34 3.71
1095 3944 1.140252 AGCAAGTTCTTGTACGGTGGT 59.860 47.619 13.04 0.00 0.00 4.16
1102 3960 2.495366 CTTGTACGGTGGTGGCGCTA 62.495 60.000 7.64 0.00 0.00 4.26
1515 4373 1.212229 GAGGTCGTCGGACAAGTCC 59.788 63.158 9.22 9.22 45.28 3.85
2136 5015 2.677228 CCCCCATTCTTGCCGTCT 59.323 61.111 0.00 0.00 0.00 4.18
2137 5016 1.452108 CCCCCATTCTTGCCGTCTC 60.452 63.158 0.00 0.00 0.00 3.36
2138 5017 1.452108 CCCCATTCTTGCCGTCTCC 60.452 63.158 0.00 0.00 0.00 3.71
2139 5018 1.452108 CCCATTCTTGCCGTCTCCC 60.452 63.158 0.00 0.00 0.00 4.30
2142 5021 1.089920 CATTCTTGCCGTCTCCCTTG 58.910 55.000 0.00 0.00 0.00 3.61
2143 5022 0.693049 ATTCTTGCCGTCTCCCTTGT 59.307 50.000 0.00 0.00 0.00 3.16
2151 5032 2.294074 CCGTCTCCCTTGTTTCAAACA 58.706 47.619 0.00 0.00 40.21 2.83
2181 5062 0.736325 CGAGTTACTGGTTCCAGGCG 60.736 60.000 20.88 12.61 38.30 5.52
2533 5414 2.202362 CGTCGACGCAGGACTCAG 60.202 66.667 26.59 0.00 32.24 3.35
2595 5476 3.923645 TGGACGGGTCACCCTCCT 61.924 66.667 24.27 3.93 42.67 3.69
2596 5477 2.606826 GGACGGGTCACCCTCCTT 60.607 66.667 19.36 0.00 42.67 3.36
2597 5478 2.657066 GGACGGGTCACCCTCCTTC 61.657 68.421 19.36 7.81 42.67 3.46
2598 5479 2.606826 ACGGGTCACCCTCCTTCC 60.607 66.667 12.38 0.00 42.67 3.46
2599 5480 3.400054 CGGGTCACCCTCCTTCCC 61.400 72.222 12.38 0.00 42.67 3.97
2600 5481 3.015753 GGGTCACCCTCCTTCCCC 61.016 72.222 5.22 0.00 41.34 4.81
2612 5493 3.245264 CCTCCTTCCCCAGTTTTGTACAT 60.245 47.826 0.00 0.00 0.00 2.29
2621 5502 1.960689 AGTTTTGTACATTTGCCCGCT 59.039 42.857 0.00 0.00 0.00 5.52
2636 5517 1.293924 CCGCTTATGCAACAGAGGAG 58.706 55.000 11.55 0.00 39.64 3.69
2645 5526 1.129437 GCAACAGAGGAGTCGAAATGC 59.871 52.381 0.00 0.00 0.00 3.56
2648 5529 2.966050 ACAGAGGAGTCGAAATGCTTC 58.034 47.619 0.00 0.00 0.00 3.86
2653 5534 2.753452 AGGAGTCGAAATGCTTCTACGA 59.247 45.455 0.00 0.00 33.54 3.43
2654 5535 3.109619 GGAGTCGAAATGCTTCTACGAG 58.890 50.000 0.00 0.00 33.54 4.18
2657 5538 4.660105 AGTCGAAATGCTTCTACGAGTAC 58.340 43.478 0.00 0.00 35.41 2.73
2659 5540 5.583854 AGTCGAAATGCTTCTACGAGTACTA 59.416 40.000 0.00 0.00 35.41 1.82
2661 5542 6.744537 GTCGAAATGCTTCTACGAGTACTAAA 59.255 38.462 0.00 0.00 33.82 1.85
2662 5543 6.965500 TCGAAATGCTTCTACGAGTACTAAAG 59.035 38.462 0.00 0.00 0.00 1.85
2663 5544 6.746364 CGAAATGCTTCTACGAGTACTAAAGT 59.254 38.462 0.00 0.00 0.00 2.66
2664 5545 7.272948 CGAAATGCTTCTACGAGTACTAAAGTT 59.727 37.037 0.00 0.00 0.00 2.66
2665 5546 8.828688 AAATGCTTCTACGAGTACTAAAGTTT 57.171 30.769 0.00 0.00 0.00 2.66
2666 5547 9.918630 AAATGCTTCTACGAGTACTAAAGTTTA 57.081 29.630 0.00 0.00 0.00 2.01
2697 5578 0.894141 TCTGCTCTCCTCTGTTCTGC 59.106 55.000 0.00 0.00 0.00 4.26
2766 5647 9.941325 CCTATGAAGTCAAGCTGATTCTATTAT 57.059 33.333 0.00 0.00 0.00 1.28
2771 5652 9.418045 GAAGTCAAGCTGATTCTATTATACTCC 57.582 37.037 0.00 0.00 0.00 3.85
2772 5653 7.598278 AGTCAAGCTGATTCTATTATACTCCG 58.402 38.462 0.00 0.00 0.00 4.63
2787 5668 1.893137 ACTCCGTAGCTCACATCACAA 59.107 47.619 0.00 0.00 0.00 3.33
2817 5703 1.136252 CACTTTGTCGAGTGGCATTCG 60.136 52.381 24.25 24.25 42.58 3.34
2837 5723 0.736053 AAAAGCAGTTCACCGCGAAA 59.264 45.000 8.23 0.00 34.69 3.46
2838 5724 0.951558 AAAGCAGTTCACCGCGAAAT 59.048 45.000 8.23 0.00 34.69 2.17
2839 5725 1.803334 AAGCAGTTCACCGCGAAATA 58.197 45.000 8.23 0.00 34.69 1.40
2840 5726 1.076332 AGCAGTTCACCGCGAAATAC 58.924 50.000 8.23 0.00 34.69 1.89
2841 5727 1.076332 GCAGTTCACCGCGAAATACT 58.924 50.000 8.23 2.53 34.69 2.12
3048 5935 6.444633 GCTGACAGACGGCTAATAAATAGTA 58.555 40.000 6.65 0.00 46.39 1.82
3049 5936 6.362820 GCTGACAGACGGCTAATAAATAGTAC 59.637 42.308 6.65 0.00 46.39 2.73
3135 6025 1.924524 GCATCATGCATGTTGCTGAAC 59.075 47.619 37.86 20.07 45.38 3.18
3178 6071 3.313007 CTGATTGTGTGGCGTGCGG 62.313 63.158 0.00 0.00 0.00 5.69
3212 6105 2.058057 GCAATTTCAACGCGGTTCATT 58.942 42.857 12.47 0.00 0.00 2.57
3225 6146 3.701532 GGTTCATTGAAACGGACACAA 57.298 42.857 0.00 0.00 0.00 3.33
3226 6147 3.628017 GGTTCATTGAAACGGACACAAG 58.372 45.455 0.00 0.00 0.00 3.16
3236 6158 7.033530 TGAAACGGACACAAGAAATATTGTT 57.966 32.000 0.00 0.00 41.41 2.83
3243 6165 5.212194 ACACAAGAAATATTGTTGACACGC 58.788 37.500 14.72 0.00 41.41 5.34
3251 6173 1.647346 TTGTTGACACGCTCGAAAGT 58.353 45.000 0.00 0.00 0.00 2.66
3262 6184 2.659757 CGCTCGAAAGTGTTTGTCGATA 59.340 45.455 0.00 0.00 42.42 2.92
3310 6232 8.927675 AAACCTATACACCAAAATGTCTGTTA 57.072 30.769 0.00 0.00 33.85 2.41
3353 6287 2.165030 GCCAAATGTCTGCTATGCAACT 59.835 45.455 0.00 0.00 38.41 3.16
3354 6288 3.733077 GCCAAATGTCTGCTATGCAACTC 60.733 47.826 0.00 0.00 38.41 3.01
3357 6291 2.391616 TGTCTGCTATGCAACTCCAG 57.608 50.000 0.00 0.00 38.41 3.86
3404 6349 7.186804 ACATTTGAATCCTAATAAAAGCGTCG 58.813 34.615 0.00 0.00 0.00 5.12
3407 6352 4.807304 TGAATCCTAATAAAAGCGTCGGAC 59.193 41.667 0.00 0.00 0.00 4.79
3410 6355 2.533129 CCTAATAAAAGCGTCGGACGTC 59.467 50.000 28.75 20.99 44.73 4.34
3425 6370 6.962678 CGTCGGACGTCCAATAAAATTTTAAT 59.037 34.615 32.80 3.71 36.74 1.40
3426 6371 7.482428 CGTCGGACGTCCAATAAAATTTTAATT 59.518 33.333 32.80 7.13 36.74 1.40
3463 6408 7.497909 TCGGTTCCAAATTTAATCATACTCCTC 59.502 37.037 0.00 0.00 0.00 3.71
3498 6443 5.419542 TCATTTCAAACTATCACTCCTCGG 58.580 41.667 0.00 0.00 0.00 4.63
3506 6451 0.984230 ATCACTCCTCGGGCTTGAAA 59.016 50.000 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.991770 CAAACGCCGAGCACTTTTCG 60.992 55.000 0.00 0.00 37.78 3.46
1 2 0.306533 TCAAACGCCGAGCACTTTTC 59.693 50.000 0.00 0.00 0.00 2.29
2 3 0.736053 TTCAAACGCCGAGCACTTTT 59.264 45.000 0.00 0.00 0.00 2.27
3 4 0.307760 CTTCAAACGCCGAGCACTTT 59.692 50.000 0.00 0.00 0.00 2.66
4 5 1.507141 CCTTCAAACGCCGAGCACTT 61.507 55.000 0.00 0.00 0.00 3.16
5 6 1.961277 CCTTCAAACGCCGAGCACT 60.961 57.895 0.00 0.00 0.00 4.40
6 7 2.556287 CCTTCAAACGCCGAGCAC 59.444 61.111 0.00 0.00 0.00 4.40
7 8 2.668212 CCCTTCAAACGCCGAGCA 60.668 61.111 0.00 0.00 0.00 4.26
8 9 4.103103 GCCCTTCAAACGCCGAGC 62.103 66.667 0.00 0.00 0.00 5.03
9 10 3.431725 GGCCCTTCAAACGCCGAG 61.432 66.667 0.00 0.00 31.92 4.63
21 22 2.745152 CGGACTTGATAAATTCGGCCCT 60.745 50.000 0.00 0.00 0.00 5.19
28 29 2.684881 CTGCAGCCGGACTTGATAAATT 59.315 45.455 5.05 0.00 0.00 1.82
32 33 1.123077 ATCTGCAGCCGGACTTGATA 58.877 50.000 9.47 0.00 0.00 2.15
33 34 0.463295 CATCTGCAGCCGGACTTGAT 60.463 55.000 9.47 0.00 0.00 2.57
34 35 1.078918 CATCTGCAGCCGGACTTGA 60.079 57.895 9.47 0.00 0.00 3.02
35 36 2.758089 GCATCTGCAGCCGGACTTG 61.758 63.158 9.47 0.18 41.59 3.16
57 58 0.251354 GGTCGAGGTAAAAGGGACCC 59.749 60.000 0.59 0.59 40.97 4.46
58 59 0.978907 TGGTCGAGGTAAAAGGGACC 59.021 55.000 1.68 1.68 45.75 4.46
63 64 1.944430 GCTGGGTGGTCGAGGTAAAAG 60.944 57.143 0.00 0.00 0.00 2.27
75 76 1.679977 CATTGGTCCAGCTGGGTGG 60.680 63.158 32.23 8.31 39.19 4.61
92 93 0.038067 CGATCACGTACAACCACCCA 60.038 55.000 0.00 0.00 34.56 4.51
97 98 1.408474 GCGGTCGATCACGTACAACC 61.408 60.000 0.00 0.00 40.69 3.77
98 99 0.730155 TGCGGTCGATCACGTACAAC 60.730 55.000 0.00 0.00 40.69 3.32
99 100 0.730155 GTGCGGTCGATCACGTACAA 60.730 55.000 18.00 0.00 43.55 2.41
180 181 1.542544 ATCTTGTTCTACGCGTACGC 58.457 50.000 29.83 29.83 45.53 4.42
182 183 3.031812 CCGTATCTTGTTCTACGCGTAC 58.968 50.000 16.41 9.51 39.42 3.67
183 184 2.935849 TCCGTATCTTGTTCTACGCGTA 59.064 45.455 19.40 19.40 39.42 4.42
194 195 0.029035 CGACCTCCGTCCGTATCTTG 59.971 60.000 0.00 0.00 35.40 3.02
237 238 1.803519 GTCCTCTTGCGTCTCTGCG 60.804 63.158 0.00 0.00 37.81 5.18
238 239 1.803519 CGTCCTCTTGCGTCTCTGC 60.804 63.158 0.00 0.00 0.00 4.26
240 241 0.803740 GTACGTCCTCTTGCGTCTCT 59.196 55.000 0.00 0.00 41.77 3.10
241 242 0.803740 AGTACGTCCTCTTGCGTCTC 59.196 55.000 0.00 0.00 41.77 3.36
244 245 0.445436 CGTAGTACGTCCTCTTGCGT 59.555 55.000 14.62 0.00 44.02 5.24
255 256 2.032924 TGCCACTCATCATCGTAGTACG 59.967 50.000 16.65 16.65 44.19 3.67
260 261 2.543653 CGATGTGCCACTCATCATCGTA 60.544 50.000 15.17 0.00 43.45 3.43
262 263 0.857287 CGATGTGCCACTCATCATCG 59.143 55.000 10.94 10.94 43.22 3.84
268 269 1.307355 CCAATGCGATGTGCCACTCA 61.307 55.000 0.00 0.00 45.60 3.41
269 270 1.430632 CCAATGCGATGTGCCACTC 59.569 57.895 0.00 0.00 45.60 3.51
270 271 2.048023 CCCAATGCGATGTGCCACT 61.048 57.895 0.00 0.00 45.60 4.00
311 312 1.711060 CCGCCGCGTTCATGGTTATT 61.711 55.000 12.58 0.00 0.00 1.40
329 353 1.135170 GTAGGCTGTGGAGTTCGTACC 60.135 57.143 0.00 0.00 0.00 3.34
345 377 1.226888 GTTGGTCTAGCGCGGTAGG 60.227 63.158 36.60 22.23 0.00 3.18
353 390 3.258971 AGCTTGATCAGTTGGTCTAGC 57.741 47.619 17.33 17.33 41.44 3.42
426 463 0.517742 GTTCGCGTAATTGCACGGAC 60.518 55.000 5.77 1.87 42.18 4.79
427 464 1.628447 GGTTCGCGTAATTGCACGGA 61.628 55.000 5.77 0.00 42.18 4.69
483 520 0.804156 CCTTTCTTCCTCGCTCGCTC 60.804 60.000 0.00 0.00 0.00 5.03
519 556 3.245264 TGCGGGATCAGATAGGTATCAGA 60.245 47.826 0.00 0.00 35.17 3.27
525 562 1.476007 GGCTGCGGGATCAGATAGGT 61.476 60.000 0.00 0.00 36.19 3.08
529 566 2.769621 TGGGCTGCGGGATCAGAT 60.770 61.111 0.00 0.00 36.19 2.90
530 567 3.785859 GTGGGCTGCGGGATCAGA 61.786 66.667 0.00 0.00 36.19 3.27
531 568 4.864334 GGTGGGCTGCGGGATCAG 62.864 72.222 0.00 0.00 37.15 2.90
532 569 3.993865 TAGGTGGGCTGCGGGATCA 62.994 63.158 0.00 0.00 0.00 2.92
533 570 3.161450 TAGGTGGGCTGCGGGATC 61.161 66.667 0.00 0.00 0.00 3.36
534 571 3.480133 GTAGGTGGGCTGCGGGAT 61.480 66.667 0.00 0.00 0.00 3.85
582 619 1.002624 CCGGCCAGCTAAGTTTCCA 60.003 57.895 2.24 0.00 0.00 3.53
620 660 3.564218 GGATCGGGGCATGGAGCT 61.564 66.667 0.00 0.00 44.79 4.09
856 1194 0.997932 AGAGACGACGCTACAGTACG 59.002 55.000 0.00 0.00 0.00 3.67
857 1195 1.327156 GGAGAGACGACGCTACAGTAC 59.673 57.143 0.00 0.00 0.00 2.73
932 3771 5.301555 GCTGGGATGTCCTTATTTACTCTC 58.698 45.833 0.00 0.00 36.20 3.20
954 3793 1.578206 GAGTGGGAGCTTTCGTTGGC 61.578 60.000 0.00 0.00 0.00 4.52
981 3820 1.227674 CGGAGCAGGGAGTAATGGC 60.228 63.158 0.00 0.00 0.00 4.40
1380 4238 1.947642 GTCCGCGGCCGTATACTTG 60.948 63.158 28.70 7.61 0.00 3.16
1515 4373 2.504244 GAGGACGCCGACAACGAG 60.504 66.667 0.00 0.00 42.66 4.18
1821 4681 1.648720 CTTGTTGTGCAGGACGTGG 59.351 57.895 0.00 0.00 0.00 4.94
2079 4940 3.626996 TTGGCTGACCTGGATGCGG 62.627 63.158 0.00 0.00 36.63 5.69
2131 5010 2.032924 GTGTTTGAAACAAGGGAGACGG 59.967 50.000 12.89 0.00 44.16 4.79
2136 5015 4.097286 GCTGTTAGTGTTTGAAACAAGGGA 59.903 41.667 12.89 0.00 44.16 4.20
2137 5016 4.359706 GCTGTTAGTGTTTGAAACAAGGG 58.640 43.478 12.89 2.06 44.16 3.95
2138 5017 4.035017 CGCTGTTAGTGTTTGAAACAAGG 58.965 43.478 12.89 1.41 44.16 3.61
2139 5018 4.728608 GTCGCTGTTAGTGTTTGAAACAAG 59.271 41.667 12.89 7.29 44.16 3.16
2142 5021 3.000523 TCGTCGCTGTTAGTGTTTGAAAC 59.999 43.478 0.14 0.14 0.00 2.78
2143 5022 3.188492 TCGTCGCTGTTAGTGTTTGAAA 58.812 40.909 0.00 0.00 0.00 2.69
2151 5032 2.095364 CCAGTAACTCGTCGCTGTTAGT 60.095 50.000 9.73 10.11 33.95 2.24
2226 5107 4.778143 ATCGCCACCACCTTCCGC 62.778 66.667 0.00 0.00 0.00 5.54
2533 5414 3.036084 CGTGTCGTGTCAGTGCCC 61.036 66.667 0.00 0.00 0.00 5.36
2595 5476 3.070302 GGCAAATGTACAAAACTGGGGAA 59.930 43.478 0.00 0.00 0.00 3.97
2596 5477 2.630580 GGCAAATGTACAAAACTGGGGA 59.369 45.455 0.00 0.00 0.00 4.81
2597 5478 2.289382 GGGCAAATGTACAAAACTGGGG 60.289 50.000 0.00 0.00 0.00 4.96
2598 5479 2.609244 CGGGCAAATGTACAAAACTGGG 60.609 50.000 0.00 0.00 0.00 4.45
2599 5480 2.671596 CGGGCAAATGTACAAAACTGG 58.328 47.619 0.00 0.00 0.00 4.00
2600 5481 2.058057 GCGGGCAAATGTACAAAACTG 58.942 47.619 0.00 0.00 0.00 3.16
2621 5502 3.953712 TTCGACTCCTCTGTTGCATAA 57.046 42.857 0.00 0.00 0.00 1.90
2636 5517 4.660105 AGTACTCGTAGAAGCATTTCGAC 58.340 43.478 0.00 0.00 38.38 4.20
2661 5542 9.785982 GGAGAGCAGAGGATAAATAAATAAACT 57.214 33.333 0.00 0.00 0.00 2.66
2662 5543 9.785982 AGGAGAGCAGAGGATAAATAAATAAAC 57.214 33.333 0.00 0.00 0.00 2.01
2664 5545 9.386122 AGAGGAGAGCAGAGGATAAATAAATAA 57.614 33.333 0.00 0.00 0.00 1.40
2665 5546 8.811017 CAGAGGAGAGCAGAGGATAAATAAATA 58.189 37.037 0.00 0.00 0.00 1.40
2666 5547 7.292120 ACAGAGGAGAGCAGAGGATAAATAAAT 59.708 37.037 0.00 0.00 0.00 1.40
2697 5578 3.827898 GGCGACTCGTGGAGGGAG 61.828 72.222 0.00 0.00 37.54 4.30
2766 5647 2.718563 TGTGATGTGAGCTACGGAGTA 58.281 47.619 0.00 0.00 45.11 2.59
2769 5650 1.893137 AGTTGTGATGTGAGCTACGGA 59.107 47.619 0.00 0.00 0.00 4.69
2771 5652 2.663602 GACAGTTGTGATGTGAGCTACG 59.336 50.000 0.00 0.00 0.00 3.51
2772 5653 2.996621 GGACAGTTGTGATGTGAGCTAC 59.003 50.000 0.00 0.00 0.00 3.58
2787 5668 0.249322 CGACAAAGTGGACGGACAGT 60.249 55.000 0.00 0.00 0.00 3.55
2811 5697 2.319472 GGTGAACTGCTTTTCGAATGC 58.681 47.619 14.31 14.31 0.00 3.56
2817 5703 0.306533 TTCGCGGTGAACTGCTTTTC 59.693 50.000 6.13 0.00 45.75 2.29
2839 5725 9.914834 TTTCAATTTTGGGCAGTATAGTATAGT 57.085 29.630 0.00 0.00 0.00 2.12
3048 5935 5.299531 TGCAATCGATCAAGCTACTAGTAGT 59.700 40.000 26.76 13.66 35.65 2.73
3049 5936 5.763088 TGCAATCGATCAAGCTACTAGTAG 58.237 41.667 23.25 23.25 36.29 2.57
3135 6025 2.757868 ACGAGAAGAAGAGGAGACCATG 59.242 50.000 0.00 0.00 0.00 3.66
3178 6071 2.693267 AATTGCCCTTACTCCTCGAC 57.307 50.000 0.00 0.00 0.00 4.20
3212 6105 6.627395 ACAATATTTCTTGTGTCCGTTTCA 57.373 33.333 0.00 0.00 37.93 2.69
3225 6146 4.242475 TCGAGCGTGTCAACAATATTTCT 58.758 39.130 0.00 0.00 0.00 2.52
3226 6147 4.577687 TCGAGCGTGTCAACAATATTTC 57.422 40.909 0.00 0.00 0.00 2.17
3236 6158 1.326245 CAAACACTTTCGAGCGTGTCA 59.674 47.619 18.24 0.00 43.05 3.58
3243 6165 4.432503 CCGTTATCGACAAACACTTTCGAG 60.433 45.833 11.72 0.00 44.43 4.04
3251 6173 4.202080 CCTCCTATCCGTTATCGACAAACA 60.202 45.833 11.72 0.00 39.71 2.83
3262 6184 3.547513 GCCGCCCTCCTATCCGTT 61.548 66.667 0.00 0.00 0.00 4.44
3332 6266 2.165030 AGTTGCATAGCAGACATTTGGC 59.835 45.455 0.00 0.00 40.61 4.52
3342 6276 3.138884 TCAAACTGGAGTTGCATAGCA 57.861 42.857 0.00 0.00 38.44 3.49
3353 6287 5.491070 AGTTGATCGATGATTCAAACTGGA 58.509 37.500 0.54 0.00 0.00 3.86
3354 6288 5.808042 AGTTGATCGATGATTCAAACTGG 57.192 39.130 0.54 0.00 0.00 4.00
3385 6330 4.085210 CGTCCGACGCTTTTATTAGGATTC 60.085 45.833 8.21 0.00 33.65 2.52
3388 6333 2.801063 CGTCCGACGCTTTTATTAGGA 58.199 47.619 8.21 0.00 33.65 2.94
3440 6385 8.433421 TCGAGGAGTATGATTAAATTTGGAAC 57.567 34.615 0.00 0.00 0.00 3.62
3450 6395 3.552273 GCCGCTTTCGAGGAGTATGATTA 60.552 47.826 0.00 0.00 38.10 1.75
3463 6408 2.261037 TGAAATGAATGCCGCTTTCG 57.739 45.000 12.80 0.00 31.73 3.46
3498 6443 5.531634 TGTGTTGATGAAGAATTTCAAGCC 58.468 37.500 0.00 0.00 45.82 4.35


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

AutoCloner maintained by Alex Coulton.