Multiple sequence alignment - TraesCS5A01G092800

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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 TraesCS5A01G092800 chr5A 100.000 5307 0 0 1 5307 129106233 129111539 0.000000e+00 9801.0
1 TraesCS5A01G092800 chr5A 80.882 340 58 7 16 351 704580547 704580883 1.470000e-65 261.0
2 TraesCS5A01G092800 chr5A 89.024 82 6 3 4516 4595 129110669 129110749 1.220000e-16 99.0
3 TraesCS5A01G092800 chr5A 89.024 82 6 3 4437 4517 129110748 129110827 1.220000e-16 99.0
4 TraesCS5A01G092800 chr5D 96.528 4205 110 11 1110 5307 119000915 119005090 0.000000e+00 6924.0
5 TraesCS5A01G092800 chr5D 90.400 750 52 5 7 752 118998187 118998920 0.000000e+00 968.0
6 TraesCS5A01G092800 chr5D 91.923 260 11 5 859 1109 119000625 119000883 6.540000e-94 355.0
7 TraesCS5A01G092800 chr5D 89.024 82 6 3 4516 4595 119004220 119004300 1.220000e-16 99.0
8 TraesCS5A01G092800 chr5D 88.889 81 8 1 4437 4517 119004299 119004378 1.220000e-16 99.0
9 TraesCS5A01G092800 chr5B 94.633 4211 142 37 1110 5307 131314880 131319019 0.000000e+00 6447.0
10 TraesCS5A01G092800 chr5B 90.777 759 53 8 7 759 131313716 131314463 0.000000e+00 998.0
11 TraesCS5A01G092800 chr5B 93.617 376 10 5 744 1109 131314477 131314848 2.790000e-152 549.0
12 TraesCS5A01G092800 chr5B 87.805 82 7 3 4516 4595 131318168 131318248 5.660000e-15 93.5
13 TraesCS5A01G092800 chr2D 81.686 344 53 6 7 349 603393932 603393598 1.460000e-70 278.0
14 TraesCS5A01G092800 chr2D 80.769 338 53 9 16 351 600412841 600413168 2.450000e-63 254.0
15 TraesCS5A01G092800 chr2D 86.017 236 29 3 7 239 151990353 151990587 3.170000e-62 250.0
16 TraesCS5A01G092800 chr6B 80.938 341 48 11 14 351 633552537 633552211 2.450000e-63 254.0
17 TraesCS5A01G092800 chr6B 78.371 356 71 6 7 358 707915606 707915959 5.350000e-55 226.0
18 TraesCS5A01G092800 chr6B 91.667 60 5 0 16 75 477692964 477692905 3.410000e-12 84.2
19 TraesCS5A01G092800 chr3A 78.512 363 52 14 18 355 614470314 614470675 1.160000e-51 215.0


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 TraesCS5A01G092800 chr5A 129106233 129111539 5306 False 3333.000 9801 92.682667 1 5307 3 chr5A.!!$F2 5306
1 TraesCS5A01G092800 chr5D 118998187 119005090 6903 False 1689.000 6924 91.352800 7 5307 5 chr5D.!!$F1 5300
2 TraesCS5A01G092800 chr5B 131313716 131319019 5303 False 2021.875 6447 91.708000 7 5307 4 chr5B.!!$F1 5300

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
378 380 0.171455 ACTAGCGAAGGAAGTGAGCG 59.829 55.000 0.00 0.0 0.00 5.03 F
1857 3562 0.029567 CGTCCGAGGTATCAGCTCAC 59.970 60.000 6.23 0.0 42.53 3.51 F
2509 4214 0.180642 TTACCACCAGGCGTTGTCAA 59.819 50.000 0.00 0.0 39.06 3.18 F
3149 4856 1.985159 TGGTACCATCTTGCCTGTTCT 59.015 47.619 11.60 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2215 3920 0.323178 CATTGACAAGCCTCAGCCCT 60.323 55.000 0.0 0.0 41.25 5.19 R
3204 4921 1.271108 TGCTGACCTGCCAACGAATTA 60.271 47.619 0.0 0.0 0.00 1.40 R
4249 5967 1.757118 CTATGCAGACCCCTTCTCGAA 59.243 52.381 0.0 0.0 28.96 3.71 R
5058 6778 0.098200 CTCGTCTGTGCATGGCATTG 59.902 55.000 0.0 0.0 41.91 2.82 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
51 52 1.202498 TCGACGCGAAGATAGAGGAGA 60.202 52.381 15.93 0.00 31.06 3.71
53 54 2.031807 CGACGCGAAGATAGAGGAGAAA 59.968 50.000 15.93 0.00 0.00 2.52
66 67 2.680352 AGAAAGAGGCCGGAGCGA 60.680 61.111 5.05 0.00 41.24 4.93
170 171 2.734606 CGACGAGGAGTAGCTAGATCTG 59.265 54.545 5.18 0.00 0.00 2.90
174 175 3.676172 CGAGGAGTAGCTAGATCTGTACG 59.324 52.174 5.18 0.00 0.00 3.67
202 204 4.920927 GCGTAGGTTTTGTTATTTGCATGT 59.079 37.500 0.00 0.00 0.00 3.21
207 209 9.432077 GTAGGTTTTGTTATTTGCATGTTTTTG 57.568 29.630 0.00 0.00 0.00 2.44
282 284 0.755698 AGTGTCCGGTCACTGTCTGT 60.756 55.000 29.70 8.24 45.40 3.41
289 291 1.067416 GTCACTGTCTGTGGACGCA 59.933 57.895 9.69 0.00 46.20 5.24
338 340 7.126573 TGAGGGGTTATATTTATCATATGCGGA 59.873 37.037 0.00 0.00 0.00 5.54
378 380 0.171455 ACTAGCGAAGGAAGTGAGCG 59.829 55.000 0.00 0.00 0.00 5.03
382 384 1.289066 CGAAGGAAGTGAGCGGACA 59.711 57.895 0.00 0.00 0.00 4.02
391 393 2.447443 AGTGAGCGGACAGTTCAGATA 58.553 47.619 0.00 0.00 40.77 1.98
440 442 0.877649 CCATGAACCGATCCGCTCAG 60.878 60.000 0.00 0.00 0.00 3.35
636 639 2.153645 TGTACATTGAGCTGCCTGTTG 58.846 47.619 0.00 0.00 0.00 3.33
668 673 8.117813 ACTACAAAGGAAAGAAGAACAACAAA 57.882 30.769 0.00 0.00 0.00 2.83
760 798 4.032703 ACAATCACAAGTCAAGTGTTGC 57.967 40.909 0.00 0.00 38.16 4.17
770 808 3.035942 GTCAAGTGTTGCACTAAAAGCG 58.964 45.455 1.97 0.00 44.62 4.68
791 829 2.721231 GCAACTCAAACGCTGCCA 59.279 55.556 0.00 0.00 0.00 4.92
793 831 1.369209 CAACTCAAACGCTGCCACG 60.369 57.895 0.00 0.00 39.50 4.94
803 2431 0.248458 CGCTGCCACGTCTTGTTTTT 60.248 50.000 0.00 0.00 0.00 1.94
805 2433 1.838913 CTGCCACGTCTTGTTTTTGG 58.161 50.000 0.00 0.00 0.00 3.28
807 2435 0.874175 GCCACGTCTTGTTTTTGGCC 60.874 55.000 0.00 0.00 45.95 5.36
827 2455 1.793414 GGGGCTTGGATTATTTGCCT 58.207 50.000 0.00 0.00 42.84 4.75
846 2474 2.500229 CTGTTTTACTTTGGCCCGAGA 58.500 47.619 0.00 0.00 0.00 4.04
874 2502 0.596577 GTCTTGGCCCGAGAAAAACC 59.403 55.000 1.07 0.00 0.00 3.27
901 2531 5.487131 AGAAGCTGAGATTAGGGAACTTTCT 59.513 40.000 0.00 0.00 43.67 2.52
1231 2909 0.111253 AGTGTTTGGCTTCAGAGGGG 59.889 55.000 0.00 0.00 0.00 4.79
1235 2913 0.850100 TTTGGCTTCAGAGGGGTCAA 59.150 50.000 0.00 0.00 0.00 3.18
1388 3090 4.533707 TCTGATGACTGTGAAGGAAGGATT 59.466 41.667 0.00 0.00 0.00 3.01
1407 3109 5.072329 AGGATTCTTCAGAGAAACTGTTCCA 59.928 40.000 0.00 0.00 44.61 3.53
1453 3155 7.540745 GCCTATTATTCATTTGTGAAACGTTGT 59.459 33.333 0.00 0.00 42.39 3.32
1734 3439 3.827302 TCAAGTAGGTCTCACTGGTCTTC 59.173 47.826 0.00 0.00 0.00 2.87
1736 3441 3.845860 AGTAGGTCTCACTGGTCTTCAA 58.154 45.455 0.00 0.00 0.00 2.69
1737 3442 3.829601 AGTAGGTCTCACTGGTCTTCAAG 59.170 47.826 0.00 0.00 0.00 3.02
1738 3443 2.683768 AGGTCTCACTGGTCTTCAAGT 58.316 47.619 0.00 0.00 0.00 3.16
1739 3444 3.845860 AGGTCTCACTGGTCTTCAAGTA 58.154 45.455 0.00 0.00 0.00 2.24
1740 3445 3.829601 AGGTCTCACTGGTCTTCAAGTAG 59.170 47.826 0.00 0.00 0.00 2.57
1857 3562 0.029567 CGTCCGAGGTATCAGCTCAC 59.970 60.000 6.23 0.00 42.53 3.51
2215 3920 4.040461 ACAAGCACTAAGAAGTTCAGGCTA 59.960 41.667 5.50 0.00 31.90 3.93
2304 4009 3.712907 GCGCAGGGTGGAGGGTAA 61.713 66.667 0.30 0.00 0.00 2.85
2318 4023 3.566351 GAGGGTAATGCCTATTTGCCTT 58.434 45.455 0.00 0.00 37.43 4.35
2324 4029 6.215845 GGTAATGCCTATTTGCCTTACATTG 58.784 40.000 11.43 0.00 41.35 2.82
2502 4207 4.796495 GGGGCTTACCACCAGGCG 62.796 72.222 0.00 0.00 42.91 5.52
2509 4214 0.180642 TTACCACCAGGCGTTGTCAA 59.819 50.000 0.00 0.00 39.06 3.18
2544 4249 7.827819 TGATACTGTGCAGAAGTTATTACAC 57.172 36.000 7.26 0.00 0.00 2.90
2600 4305 9.141400 GAAGGTAAAGGCTCTATGTTTATATCG 57.859 37.037 0.00 0.00 0.00 2.92
2601 4306 7.612677 AGGTAAAGGCTCTATGTTTATATCGG 58.387 38.462 0.00 0.00 0.00 4.18
2602 4307 7.453752 AGGTAAAGGCTCTATGTTTATATCGGA 59.546 37.037 0.00 0.00 0.00 4.55
2603 4308 7.760340 GGTAAAGGCTCTATGTTTATATCGGAG 59.240 40.741 0.00 0.00 0.00 4.63
2610 4315 9.771915 GCTCTATGTTTATATCGGAGTACTAAC 57.228 37.037 0.00 0.00 0.00 2.34
2638 4343 5.389859 AATACTGCATGCTGCTTTTGTAA 57.610 34.783 22.92 0.00 45.31 2.41
3056 4763 4.002906 TGATCAACAACTGTCCTGTACC 57.997 45.455 0.00 0.00 0.00 3.34
3058 4765 3.188159 TCAACAACTGTCCTGTACCAC 57.812 47.619 0.00 0.00 0.00 4.16
3101 4808 2.162408 GTGCTTCTGGGTTGAGTAATGC 59.838 50.000 0.00 0.00 0.00 3.56
3148 4855 2.489938 TGGTACCATCTTGCCTGTTC 57.510 50.000 11.60 0.00 0.00 3.18
3149 4856 1.985159 TGGTACCATCTTGCCTGTTCT 59.015 47.619 11.60 0.00 0.00 3.01
3150 4857 3.178046 TGGTACCATCTTGCCTGTTCTA 58.822 45.455 11.60 0.00 0.00 2.10
3151 4858 3.780294 TGGTACCATCTTGCCTGTTCTAT 59.220 43.478 11.60 0.00 0.00 1.98
3152 4859 4.130118 GGTACCATCTTGCCTGTTCTATG 58.870 47.826 7.15 0.00 0.00 2.23
3153 4860 4.141711 GGTACCATCTTGCCTGTTCTATGA 60.142 45.833 7.15 0.00 0.00 2.15
3154 4861 4.148128 ACCATCTTGCCTGTTCTATGAG 57.852 45.455 0.00 0.00 0.00 2.90
3155 4862 3.521126 ACCATCTTGCCTGTTCTATGAGT 59.479 43.478 0.00 0.00 0.00 3.41
3156 4863 4.018960 ACCATCTTGCCTGTTCTATGAGTT 60.019 41.667 0.00 0.00 0.00 3.01
3157 4864 4.574013 CCATCTTGCCTGTTCTATGAGTTC 59.426 45.833 0.00 0.00 0.00 3.01
3169 4886 7.907389 TGTTCTATGAGTTCCATTCACTAACT 58.093 34.615 0.00 0.00 36.71 2.24
3171 4888 6.341316 TCTATGAGTTCCATTCACTAACTGC 58.659 40.000 0.00 0.00 36.71 4.40
3179 4896 8.462016 AGTTCCATTCACTAACTGCAATAATTC 58.538 33.333 0.00 0.00 32.38 2.17
3189 4906 9.515226 ACTAACTGCAATAATTCCTTAAGAACA 57.485 29.630 3.36 0.00 37.29 3.18
3196 4913 9.173939 GCAATAATTCCTTAAGAACATCAATCG 57.826 33.333 3.36 0.00 37.29 3.34
3282 4999 7.502060 AGGACTTCAATCAAAGGAGAGATTA 57.498 36.000 0.00 0.00 33.41 1.75
3294 5011 8.163408 TCAAAGGAGAGATTATGTTCTTTCCAA 58.837 33.333 14.77 0.88 45.24 3.53
3314 5031 5.700832 TCCAACAAGCAACTGATGTAAGTAG 59.299 40.000 0.00 0.00 0.00 2.57
3326 5043 8.709386 ACTGATGTAAGTAGTAATGCTTCAAG 57.291 34.615 0.00 0.00 0.00 3.02
3327 5044 7.278868 ACTGATGTAAGTAGTAATGCTTCAAGC 59.721 37.037 1.04 1.04 42.82 4.01
3373 5091 8.540507 AGAAACATATAGAGGTTGCTCTAAGA 57.459 34.615 0.00 0.00 28.60 2.10
3376 5094 3.719173 ATAGAGGTTGCTCTAAGACGC 57.281 47.619 0.00 0.00 39.13 5.19
3466 5184 5.172687 TGTTAGCCATCAAATAGTCACCA 57.827 39.130 0.00 0.00 0.00 4.17
3468 5186 5.414454 TGTTAGCCATCAAATAGTCACCAAC 59.586 40.000 0.00 0.00 0.00 3.77
3472 5190 5.047802 AGCCATCAAATAGTCACCAACAAAG 60.048 40.000 0.00 0.00 0.00 2.77
3647 5365 2.189594 TTTGGTCAGCATGGACAGAG 57.810 50.000 0.00 0.00 39.59 3.35
3922 5640 4.627467 AGCAGCAGTAATTACTCTGAAACG 59.373 41.667 29.52 15.95 35.44 3.60
3974 5692 3.228188 TGGTGACTTGCTTTGGATCTT 57.772 42.857 0.00 0.00 0.00 2.40
4049 5767 4.085733 ACTATGCAATGGCCAAACACTAA 58.914 39.130 10.96 0.00 40.13 2.24
4189 5907 3.236618 GACACCTTTGTCGCCACGC 62.237 63.158 0.00 0.00 42.86 5.34
4249 5967 1.927569 TAGGGCGACTCTCCAGAGCT 61.928 60.000 3.33 0.00 45.79 4.09
4331 6049 4.813161 CCTGCTGAATAGTGTGGATAACAG 59.187 45.833 0.00 0.00 40.26 3.16
4627 6346 4.899502 ACAGGAGTCAGACCATGTAAAAG 58.100 43.478 7.35 0.00 0.00 2.27
4628 6347 4.593206 ACAGGAGTCAGACCATGTAAAAGA 59.407 41.667 7.35 0.00 0.00 2.52
4665 6384 5.012046 TCACTCTTGCTCCTGAAGTTCATTA 59.988 40.000 5.91 0.00 0.00 1.90
4862 6582 7.331193 GGTACAACAGTAATTTCTAGTGTGGAG 59.669 40.741 8.99 0.00 32.01 3.86
5018 6738 5.762179 TCCAAGGAGCTTCAAGAAGATAA 57.238 39.130 13.70 0.00 40.79 1.75
5058 6778 0.599558 TTGCTCTGATTTGCCAGCAC 59.400 50.000 0.00 0.00 41.56 4.40
5071 6791 1.290639 CAGCACAATGCCATGCACA 59.709 52.632 0.00 0.00 46.52 4.57
5162 6882 4.277515 TGGAGTTCTTCTTCCATCTGTG 57.722 45.455 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.465512 CGCATTGGTCGCAGTGGC 62.466 66.667 0.00 0.00 0.00 5.01
51 52 2.266055 CTTCGCTCCGGCCTCTTT 59.734 61.111 0.00 0.00 34.44 2.52
174 175 5.566395 GCAAATAACAAAACCTACGCACTAC 59.434 40.000 0.00 0.00 0.00 2.73
230 232 5.072741 AGCACAACTGTATTTGGACATCTT 58.927 37.500 0.00 0.00 0.00 2.40
282 284 4.429212 CACGTCCGGATGCGTCCA 62.429 66.667 23.85 3.09 45.37 4.02
378 380 6.660722 CGACTAGTACATATCTGAACTGTCC 58.339 44.000 0.00 0.00 0.00 4.02
382 384 4.815308 ACGCGACTAGTACATATCTGAACT 59.185 41.667 15.93 0.00 0.00 3.01
418 420 2.189257 CGGATCGGTTCATGGCCA 59.811 61.111 8.56 8.56 0.00 5.36
429 431 2.890847 AAGGTTCGCTGAGCGGATCG 62.891 60.000 27.65 0.00 46.45 3.69
440 442 2.671963 GTGGTGGGGAAGGTTCGC 60.672 66.667 0.00 0.00 39.19 4.70
515 518 1.823169 GACGCTGGACCCCTGTTACA 61.823 60.000 0.00 0.00 0.00 2.41
636 639 5.751990 TCTTCTTTCCTTTGTAGTTGACGAC 59.248 40.000 0.00 0.00 0.00 4.34
760 798 3.064207 TGAGTTGCCTACGCTTTTAGTG 58.936 45.455 0.00 0.00 35.36 2.74
770 808 0.110192 GCAGCGTTTGAGTTGCCTAC 60.110 55.000 0.00 0.00 41.53 3.18
791 829 1.730451 CCCGGCCAAAAACAAGACGT 61.730 55.000 2.24 0.00 0.00 4.34
793 831 1.365999 CCCCGGCCAAAAACAAGAC 59.634 57.895 2.24 0.00 0.00 3.01
796 834 2.066999 AAGCCCCGGCCAAAAACAA 61.067 52.632 2.24 0.00 43.17 2.83
797 835 2.444895 AAGCCCCGGCCAAAAACA 60.445 55.556 2.24 0.00 43.17 2.83
799 837 3.237741 CCAAGCCCCGGCCAAAAA 61.238 61.111 2.24 0.00 43.17 1.94
803 2431 1.943730 AATAATCCAAGCCCCGGCCA 61.944 55.000 2.24 0.00 43.17 5.36
805 2433 0.389025 CAAATAATCCAAGCCCCGGC 59.611 55.000 0.00 0.00 42.33 6.13
807 2435 0.389025 GGCAAATAATCCAAGCCCCG 59.611 55.000 0.00 0.00 39.42 5.73
827 2455 2.642154 TCTCGGGCCAAAGTAAAACA 57.358 45.000 4.39 0.00 0.00 2.83
846 2474 1.304962 GGGCCAAGACGGGGATTTT 60.305 57.895 4.39 0.00 34.06 1.82
874 2502 5.495640 AGTTCCCTAATCTCAGCTTCTTTG 58.504 41.667 0.00 0.00 0.00 2.77
1231 2909 2.305927 TCATGAACTCCTCCCCTTTGAC 59.694 50.000 0.00 0.00 0.00 3.18
1235 2913 1.290134 GGTCATGAACTCCTCCCCTT 58.710 55.000 2.64 0.00 0.00 3.95
1353 3055 5.126222 CACAGTCATCAGAAGTTCTAGCCTA 59.874 44.000 4.74 0.00 0.00 3.93
1388 3090 4.408921 TCCTTGGAACAGTTTCTCTGAAGA 59.591 41.667 1.79 0.00 46.27 2.87
1407 3109 3.574396 GGCCTTTCTTTTAGCTGTTCCTT 59.426 43.478 0.00 0.00 0.00 3.36
1453 3155 4.860072 GATATATCTATCGCGGCATGTCA 58.140 43.478 6.13 0.00 0.00 3.58
1479 3181 5.656416 TGCTTGGCCTTTAGCTGTTATAAAT 59.344 36.000 20.55 0.00 43.05 1.40
1566 3268 6.403527 CGAAACCTGAAATATGCAGATGTGAA 60.404 38.462 0.00 0.00 35.39 3.18
1638 3340 2.281970 TTGGAGGTGCTGCTGCTG 60.282 61.111 17.00 0.77 40.48 4.41
1639 3341 2.033757 CTTGGAGGTGCTGCTGCT 59.966 61.111 17.00 0.00 40.48 4.24
1640 3342 3.060615 CCTTGGAGGTGCTGCTGC 61.061 66.667 8.89 8.89 40.20 5.25
1734 3439 5.460419 GCAGCTTAGCATGTACTACTACTTG 59.540 44.000 7.07 0.00 33.20 3.16
1736 3441 4.645136 TGCAGCTTAGCATGTACTACTACT 59.355 41.667 7.07 0.00 40.11 2.57
1737 3442 4.933330 TGCAGCTTAGCATGTACTACTAC 58.067 43.478 7.07 0.00 40.11 2.73
1857 3562 7.133891 ACAGGTTTTAGATCATTCAAGAACG 57.866 36.000 0.00 0.00 0.00 3.95
2215 3920 0.323178 CATTGACAAGCCTCAGCCCT 60.323 55.000 0.00 0.00 41.25 5.19
2318 4023 8.729805 AAAACCAAATGAAAAGCTTCAATGTA 57.270 26.923 0.00 0.00 44.64 2.29
2365 4070 2.628178 TCTCAGCTCCAAACGAAGAAGA 59.372 45.455 0.00 0.00 0.00 2.87
2467 4172 3.838317 GCCCCTTTCCTACCAATCTTTTT 59.162 43.478 0.00 0.00 0.00 1.94
2502 4207 6.857964 CAGTATCAATTCCACTGTTTGACAAC 59.142 38.462 0.00 0.00 35.91 3.32
2544 4249 9.598517 AGCTTCTCTTCATTCTTTACATAAGAG 57.401 33.333 0.00 0.00 40.69 2.85
2627 4332 6.090628 TCAGCAACTTTGTTTTACAAAAGCAG 59.909 34.615 17.97 13.37 46.15 4.24
2634 4339 7.064016 GTCCAATTTCAGCAACTTTGTTTTACA 59.936 33.333 0.00 0.00 0.00 2.41
2638 4343 5.733676 AGTCCAATTTCAGCAACTTTGTTT 58.266 33.333 0.00 0.00 0.00 2.83
3031 4738 6.823689 GGTACAGGACAGTTGTTGATCATAAT 59.176 38.462 0.00 0.00 0.00 1.28
3039 4746 3.194005 AGTGGTACAGGACAGTTGTTG 57.806 47.619 0.00 0.00 41.80 3.33
3046 4753 5.818678 AACTTATGAAGTGGTACAGGACA 57.181 39.130 0.00 0.00 41.91 4.02
3056 4763 5.865552 CCCTTTGCATGAAACTTATGAAGTG 59.134 40.000 0.00 0.00 41.91 3.16
3058 4765 5.865552 CACCCTTTGCATGAAACTTATGAAG 59.134 40.000 0.00 0.00 0.00 3.02
3101 4808 7.606858 TTCAGTATCTGCTGATTTTGAAGAG 57.393 36.000 19.33 3.77 43.99 2.85
3148 4855 6.108687 TGCAGTTAGTGAATGGAACTCATAG 58.891 40.000 0.00 0.00 34.44 2.23
3149 4856 6.048732 TGCAGTTAGTGAATGGAACTCATA 57.951 37.500 0.00 0.00 34.44 2.15
3150 4857 4.910195 TGCAGTTAGTGAATGGAACTCAT 58.090 39.130 0.00 0.00 37.79 2.90
3151 4858 4.350368 TGCAGTTAGTGAATGGAACTCA 57.650 40.909 0.00 0.00 31.04 3.41
3152 4859 5.886960 ATTGCAGTTAGTGAATGGAACTC 57.113 39.130 0.00 0.00 31.04 3.01
3153 4860 7.944729 ATTATTGCAGTTAGTGAATGGAACT 57.055 32.000 0.00 0.00 33.71 3.01
3154 4861 7.702348 GGAATTATTGCAGTTAGTGAATGGAAC 59.298 37.037 0.00 0.00 0.00 3.62
3155 4862 7.615365 AGGAATTATTGCAGTTAGTGAATGGAA 59.385 33.333 0.00 0.00 0.00 3.53
3156 4863 7.118723 AGGAATTATTGCAGTTAGTGAATGGA 58.881 34.615 0.00 0.00 0.00 3.41
3157 4864 7.338800 AGGAATTATTGCAGTTAGTGAATGG 57.661 36.000 0.00 0.00 0.00 3.16
3194 4911 3.498777 TGCCAACGAATTAACATCAACGA 59.501 39.130 0.00 0.00 0.00 3.85
3196 4913 4.165779 CCTGCCAACGAATTAACATCAAC 58.834 43.478 0.00 0.00 0.00 3.18
3204 4921 1.271108 TGCTGACCTGCCAACGAATTA 60.271 47.619 0.00 0.00 0.00 1.40
3250 4967 6.043243 TCCTTTGATTGAAGTCCTTGACTAGT 59.957 38.462 0.00 0.00 42.59 2.57
3282 4999 4.402155 TCAGTTGCTTGTTGGAAAGAACAT 59.598 37.500 0.00 0.00 35.77 2.71
3294 5011 7.148407 GCATTACTACTTACATCAGTTGCTTGT 60.148 37.037 0.00 0.00 0.00 3.16
3343 5061 8.928448 AGAGCAACCTCTATATGTTTCTTATCA 58.072 33.333 0.00 0.00 46.45 2.15
3365 5083 2.568696 TGATGACAGCGTCTTAGAGC 57.431 50.000 9.49 0.00 33.15 4.09
3373 5091 3.057386 TGCATGAAAATTGATGACAGCGT 60.057 39.130 0.00 0.00 0.00 5.07
3376 5094 3.863424 GCCTGCATGAAAATTGATGACAG 59.137 43.478 0.00 4.14 31.42 3.51
3466 5184 7.362920 GCTTGGATCATATGGTGTAACTTTGTT 60.363 37.037 2.13 0.00 36.74 2.83
3468 5186 6.460123 GGCTTGGATCATATGGTGTAACTTTG 60.460 42.308 2.13 0.00 36.74 2.77
3472 5190 4.460263 TGGCTTGGATCATATGGTGTAAC 58.540 43.478 2.13 0.00 0.00 2.50
3554 5272 3.614092 TCAGCATCTGGACCAAAATCTC 58.386 45.455 0.00 0.00 31.51 2.75
3647 5365 5.633830 TTGTTCAGAGAAATGAGAATGGC 57.366 39.130 0.00 0.00 0.00 4.40
3903 5621 6.589139 AGGTAACGTTTCAGAGTAATTACTGC 59.411 38.462 22.68 13.45 46.39 4.40
3922 5640 8.959705 ATCAGGTAATTAGCAGTAAAGGTAAC 57.040 34.615 16.53 0.00 34.67 2.50
3974 5692 6.463472 CCTGCAGATGTCATCCAGAACTAATA 60.463 42.308 17.39 0.00 0.00 0.98
4049 5767 7.520937 GCCAGCAAAAACTTGATTTGATTGATT 60.521 33.333 3.37 0.00 39.56 2.57
4189 5907 3.420893 TGCCTTGATCTTAACCCACTTG 58.579 45.455 0.00 0.00 0.00 3.16
4249 5967 1.757118 CTATGCAGACCCCTTCTCGAA 59.243 52.381 0.00 0.00 28.96 3.71
4331 6049 2.375110 CGCACATTGTTCTGTCACAAC 58.625 47.619 0.00 0.00 39.48 3.32
4604 6323 5.778241 TCTTTTACATGGTCTGACTCCTGTA 59.222 40.000 7.85 9.87 0.00 2.74
4627 6346 4.620184 GCAAGAGTGAAGAAATTGCATGTC 59.380 41.667 3.51 0.00 44.32 3.06
4628 6347 4.280174 AGCAAGAGTGAAGAAATTGCATGT 59.720 37.500 10.44 0.00 46.66 3.21
4665 6384 9.354673 TCACTTCATTTTAAAAGGATTGTCTCT 57.645 29.630 15.37 0.00 0.00 3.10
4766 6486 4.394300 CAGGCTAGCCATGTTTATAGCATC 59.606 45.833 34.70 2.35 41.92 3.91
5018 6738 7.819644 AGCAACAAAAAGCTTTTCAAAAGAAT 58.180 26.923 24.04 3.83 38.01 2.40
5058 6778 0.098200 CTCGTCTGTGCATGGCATTG 59.902 55.000 0.00 0.00 41.91 2.82
5071 6791 1.489481 TTCTGCCATCATCCTCGTCT 58.511 50.000 0.00 0.00 0.00 4.18
5103 6823 8.970691 AACACTGTAAAGTAATGAATCAATGC 57.029 30.769 0.00 0.00 0.00 3.56
5162 6882 1.933181 GGCAAACAACTTTTGAGTGGC 59.067 47.619 0.91 0.00 36.80 5.01


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

AutoCloner maintained by Alex Coulton.