Multiple sequence alignment - TraesCS5A01G026000

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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 TraesCS5A01G026000 chr5A 100.000 5387 0 0 1 5387 21407052 21412438 0.000000e+00 9949.0
1 TraesCS5A01G026000 chr5B 95.739 4741 113 31 688 5387 24096830 24101522 0.000000e+00 7553.0
2 TraesCS5A01G026000 chr5B 88.703 717 48 10 4685 5387 24094653 24095350 0.000000e+00 845.0
3 TraesCS5A01G026000 chr5D 97.281 4156 90 9 765 4900 32691943 32696095 0.000000e+00 7027.0
4 TraesCS5A01G026000 chr5D 88.160 549 61 2 1577 2124 483514874 483515419 0.000000e+00 651.0
5 TraesCS5A01G026000 chr5D 86.503 489 22 12 4912 5387 32696275 32696732 1.040000e-136 497.0
6 TraesCS5A01G026000 chr5D 91.525 354 24 4 372 722 32691144 32691494 2.920000e-132 483.0
7 TraesCS5A01G026000 chr5D 92.517 147 10 1 32 177 32688571 32688717 5.470000e-50 209.0
8 TraesCS5A01G026000 chr5D 88.690 168 17 2 223 388 32690962 32691129 2.540000e-48 204.0
9 TraesCS5A01G026000 chr5D 85.075 134 7 2 5050 5183 32696156 32696276 2.040000e-24 124.0
10 TraesCS5A01G026000 chrUn 98.775 408 5 0 3983 4390 477032214 477031807 0.000000e+00 726.0
11 TraesCS5A01G026000 chr2D 85.915 71 8 2 36 105 491953802 491953871 2.080000e-09 75.0
12 TraesCS5A01G026000 chr6B 97.561 41 0 1 1 40 96152748 96152788 9.680000e-08 69.4
13 TraesCS5A01G026000 chr6B 95.000 40 1 1 2 40 158047141 158047180 1.620000e-05 62.1
14 TraesCS5A01G026000 chr6B 95.000 40 1 1 3 41 301071348 301071387 1.620000e-05 62.1
15 TraesCS5A01G026000 chr3A 95.122 41 1 1 1 40 229617204 229617244 4.500000e-06 63.9
16 TraesCS5A01G026000 chr3A 95.000 40 0 2 3 40 210535117 210535078 1.620000e-05 62.1
17 TraesCS5A01G026000 chr1A 95.122 41 1 1 1 40 302328713 302328673 4.500000e-06 63.9
18 TraesCS5A01G026000 chr1A 94.872 39 1 1 3 40 125929055 125929017 5.830000e-05 60.2
19 TraesCS5A01G026000 chr7A 97.297 37 0 1 5 40 283287778 283287742 1.620000e-05 62.1
20 TraesCS5A01G026000 chr4A 95.000 40 0 2 3 40 293008124 293008085 1.620000e-05 62.1


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 TraesCS5A01G026000 chr5A 21407052 21412438 5386 False 9949 9949 100.000000 1 5387 1 chr5A.!!$F1 5386
1 TraesCS5A01G026000 chr5B 24094653 24101522 6869 False 4199 7553 92.221000 688 5387 2 chr5B.!!$F1 4699
2 TraesCS5A01G026000 chr5D 32688571 32696732 8161 False 1424 7027 90.265167 32 5387 6 chr5D.!!$F2 5355
3 TraesCS5A01G026000 chr5D 483514874 483515419 545 False 651 651 88.160000 1577 2124 1 chr5D.!!$F1 547

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
595 2830 0.173481 TAGTTGTCGCTAGCTGCCTG 59.827 55.000 13.93 0.00 38.78 4.85 F
1702 4355 1.022451 CCTTGCCACATTTGCCATGC 61.022 55.000 0.00 0.00 0.00 4.06 F
1828 4481 1.722751 GCGTGCATGCGTTATATCTGC 60.723 52.381 16.43 2.42 0.00 4.26 F
2058 4711 2.267324 GTGCTCTGCCTGGAGGTC 59.733 66.667 0.00 0.00 37.57 3.85 F
2943 5596 1.681264 CTCTGCCGGGAAACAGTTTTT 59.319 47.619 2.18 0.00 35.37 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1828 4481 0.457035 AACAGCACTGGCACAAACAG 59.543 50.000 2.21 0.00 44.61 3.16 R
2711 5364 0.883833 CAAGATCCAAGCGGCTTTGT 59.116 50.000 13.53 1.53 0.00 2.83 R
2718 5371 2.670414 GAGACAAGTCAAGATCCAAGCG 59.330 50.000 2.72 0.00 0.00 4.68 R
3798 6451 3.149196 TCTCTTGATGGTGAAAGTTGGC 58.851 45.455 0.00 0.00 0.00 4.52 R
4696 7359 0.106708 AAAAGACCACTCTCAGCGCA 59.893 50.000 11.47 0.00 0.00 6.09 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
24 25 7.534085 TGTGACGTGATCCAAATAGTTATTC 57.466 36.000 0.00 0.00 0.00 1.75
25 26 7.327975 TGTGACGTGATCCAAATAGTTATTCT 58.672 34.615 0.00 0.00 0.00 2.40
26 27 8.471609 TGTGACGTGATCCAAATAGTTATTCTA 58.528 33.333 0.00 0.00 0.00 2.10
27 28 9.309516 GTGACGTGATCCAAATAGTTATTCTAA 57.690 33.333 0.00 0.00 31.94 2.10
30 31 9.490379 ACGTGATCCAAATAGTTATTCTAATCC 57.510 33.333 0.00 0.00 31.94 3.01
31 32 8.936864 CGTGATCCAAATAGTTATTCTAATCCC 58.063 37.037 0.00 0.00 31.94 3.85
32 33 8.936864 GTGATCCAAATAGTTATTCTAATCCCG 58.063 37.037 0.00 0.00 31.94 5.14
124 125 1.207791 CCATGGTTACAGAGGCCTCT 58.792 55.000 30.40 30.40 41.37 3.69
133 134 0.827368 CAGAGGCCTCTACCTTGGAC 59.173 60.000 34.67 3.49 41.32 4.02
146 147 1.732259 CCTTGGACAAGAATCCGTTCG 59.268 52.381 13.35 0.00 42.24 3.95
167 168 8.823818 CGTTCGTAGGATTATTAAAACCTTCAT 58.176 33.333 9.66 0.00 38.68 2.57
207 2369 9.866655 AAGAAGATCTATCTACATCTCAAGACT 57.133 33.333 0.00 0.00 35.76 3.24
212 2374 9.453572 GATCTATCTACATCTCAAGACTCATCT 57.546 37.037 0.00 0.00 36.42 2.90
213 2375 9.812347 ATCTATCTACATCTCAAGACTCATCTT 57.188 33.333 0.00 0.00 46.63 2.40
226 2427 6.441088 AGACTCATCTTTCCTAAAGGTTGT 57.559 37.500 0.00 0.00 39.01 3.32
233 2434 9.177608 TCATCTTTCCTAAAGGTTGTATTCATG 57.822 33.333 0.00 0.00 39.01 3.07
244 2445 9.733556 AAAGGTTGTATTCATGTGTATCTTGTA 57.266 29.630 0.00 0.00 0.00 2.41
246 2447 9.547753 AGGTTGTATTCATGTGTATCTTGTATC 57.452 33.333 0.00 0.00 0.00 2.24
286 2487 6.561614 GGAGTATCTTCGTGTGAATCTTGTA 58.438 40.000 0.00 0.00 32.61 2.41
287 2488 7.203910 GGAGTATCTTCGTGTGAATCTTGTAT 58.796 38.462 0.00 0.00 32.61 2.29
288 2489 7.707035 GGAGTATCTTCGTGTGAATCTTGTATT 59.293 37.037 0.00 0.00 32.61 1.89
328 2530 9.528018 TGATTTTCCTTTATGTTCTTTGTGTTC 57.472 29.630 0.00 0.00 0.00 3.18
331 2533 5.701224 TCCTTTATGTTCTTTGTGTTCCCT 58.299 37.500 0.00 0.00 0.00 4.20
346 2548 2.305927 GTTCCCTCTCAAATCCACCTCA 59.694 50.000 0.00 0.00 0.00 3.86
348 2550 3.192944 TCCCTCTCAAATCCACCTCAAT 58.807 45.455 0.00 0.00 0.00 2.57
374 2577 1.668826 AGTTCAGGCCACCAATAGGA 58.331 50.000 5.01 0.00 38.69 2.94
377 2580 3.011708 AGTTCAGGCCACCAATAGGATTT 59.988 43.478 5.01 0.00 38.69 2.17
388 2591 6.484288 CACCAATAGGATTTGCCCTATATCA 58.516 40.000 0.00 0.00 46.06 2.15
389 2592 6.947733 CACCAATAGGATTTGCCCTATATCAA 59.052 38.462 0.00 0.00 46.06 2.57
395 2629 4.213482 GGATTTGCCCTATATCAACGTGTC 59.787 45.833 0.00 0.00 0.00 3.67
422 2656 8.915057 ATAGATTTGATCCATCCAAACTACAG 57.085 34.615 0.00 0.00 36.48 2.74
457 2691 2.036571 CGATTGCTGCTCTGGTGCA 61.037 57.895 0.00 0.00 41.05 4.57
460 2694 0.538977 ATTGCTGCTCTGGTGCACTT 60.539 50.000 17.98 0.00 38.12 3.16
496 2730 8.025445 GGTCTTAACACGATGACTTTCTAACTA 58.975 37.037 0.00 0.00 0.00 2.24
526 2760 1.964223 ACAAAGTTCTCTCAGCTCCGA 59.036 47.619 0.00 0.00 0.00 4.55
527 2761 2.288518 ACAAAGTTCTCTCAGCTCCGAC 60.289 50.000 0.00 0.00 0.00 4.79
573 2808 1.423395 CTTCAACTCGCTCCAGTGAC 58.577 55.000 0.00 0.00 0.00 3.67
592 2827 1.272781 CTGTAGTTGTCGCTAGCTGC 58.727 55.000 13.93 5.80 38.57 5.25
594 2829 0.173708 GTAGTTGTCGCTAGCTGCCT 59.826 55.000 13.93 4.03 38.78 4.75
595 2830 0.173481 TAGTTGTCGCTAGCTGCCTG 59.827 55.000 13.93 0.00 38.78 4.85
596 2831 1.374758 GTTGTCGCTAGCTGCCTGT 60.375 57.895 13.93 0.00 38.78 4.00
597 2832 1.374631 TTGTCGCTAGCTGCCTGTG 60.375 57.895 13.93 0.00 38.78 3.66
638 2874 4.873827 TGTTACTTCTTGTGTTCTGTCACC 59.126 41.667 0.00 0.00 37.51 4.02
639 2875 2.550978 ACTTCTTGTGTTCTGTCACCG 58.449 47.619 0.00 0.00 37.51 4.94
663 2899 7.134815 CGAAGTTGATGAACAAATCAGAAGTT 58.865 34.615 0.00 0.00 42.53 2.66
664 2900 7.645340 CGAAGTTGATGAACAAATCAGAAGTTT 59.355 33.333 0.00 0.00 42.53 2.66
665 2901 9.305925 GAAGTTGATGAACAAATCAGAAGTTTT 57.694 29.630 0.00 0.00 42.53 2.43
980 3624 1.101635 GCAAAACCCTAGATCCCGGC 61.102 60.000 0.00 0.00 0.00 6.13
1085 3738 4.148825 CTTCTCCTCCACCCGCGG 62.149 72.222 21.04 21.04 0.00 6.46
1140 3793 2.284699 AACTCCACCTCCTCCCCG 60.285 66.667 0.00 0.00 0.00 5.73
1392 4045 2.348998 CAGGGCGCCTTCTTCACT 59.651 61.111 28.56 10.17 0.00 3.41
1702 4355 1.022451 CCTTGCCACATTTGCCATGC 61.022 55.000 0.00 0.00 0.00 4.06
1821 4474 2.739704 GAGCTGCGTGCATGCGTTA 61.740 57.895 25.05 7.81 45.94 3.18
1828 4481 1.722751 GCGTGCATGCGTTATATCTGC 60.723 52.381 16.43 2.42 0.00 4.26
2058 4711 2.267324 GTGCTCTGCCTGGAGGTC 59.733 66.667 0.00 0.00 37.57 3.85
2319 4972 7.122204 GGTTATTATGTGGCAAGGTTCTTTACT 59.878 37.037 0.00 0.00 0.00 2.24
2385 5038 3.572255 GCTTGATGGTCCTTTGGTTTGTA 59.428 43.478 0.00 0.00 0.00 2.41
2397 5050 7.120726 GTCCTTTGGTTTGTAGTGCATAACTAT 59.879 37.037 0.00 0.00 43.30 2.12
2601 5254 5.039920 TCTTCAACTATGCTGCCATGTAT 57.960 39.130 0.00 0.00 32.85 2.29
2943 5596 1.681264 CTCTGCCGGGAAACAGTTTTT 59.319 47.619 2.18 0.00 35.37 1.94
3615 6268 1.893315 TGTTGGCTATAGAAGGGGCT 58.107 50.000 3.21 0.00 0.00 5.19
3651 6304 6.439636 TTGGGTCTCTATGCTGCTATATTT 57.560 37.500 0.00 0.00 0.00 1.40
3798 6451 3.933742 CGGAGATCTCATGCTGCG 58.066 61.111 23.85 12.96 39.45 5.18
4035 6688 6.434340 ACTTCCCTGTGACAATTTCTATTTCC 59.566 38.462 0.00 0.00 0.00 3.13
4161 6814 3.708890 TGCTGTGAAAAATGTTGCTCTG 58.291 40.909 0.00 0.00 0.00 3.35
4673 7336 7.687005 TGCGTTTTCAGTCGAATTTTTAAAT 57.313 28.000 0.00 0.00 0.00 1.40
4676 7339 7.426169 CGTTTTCAGTCGAATTTTTAAATCGG 58.574 34.615 9.21 0.00 0.00 4.18
4684 7347 5.031578 CGAATTTTTAAATCGGCGGATCAA 58.968 37.500 7.21 2.57 30.81 2.57
4696 7359 2.945668 GGCGGATCAAGTGCTAAGATTT 59.054 45.455 0.00 0.00 0.00 2.17
4722 7385 4.636249 CTGAGAGTGGTCTTTTTGTAGCT 58.364 43.478 0.00 0.00 30.97 3.32
4729 7392 1.154225 CTTTTTGTAGCTGGGCGCG 60.154 57.895 0.00 0.00 45.59 6.86
4749 7412 3.948719 TGTCTTTTCGGGCCGCCT 61.949 61.111 23.83 0.00 0.00 5.52
4779 7443 1.004394 CCGTTAGCTTTTCCCCTCCTT 59.996 52.381 0.00 0.00 0.00 3.36
4786 7450 3.898123 AGCTTTTCCCCTCCTTTCTTTTC 59.102 43.478 0.00 0.00 0.00 2.29
4787 7451 3.006967 GCTTTTCCCCTCCTTTCTTTTCC 59.993 47.826 0.00 0.00 0.00 3.13
4811 7475 7.020602 CCGCTGTTGTTTTGAATTTTCTTTTT 58.979 30.769 0.00 0.00 0.00 1.94
4812 7476 7.007277 CCGCTGTTGTTTTGAATTTTCTTTTTG 59.993 33.333 0.00 0.00 0.00 2.44
4887 7551 0.395036 TGAGCGGAAGGGAGAGAGAG 60.395 60.000 0.00 0.00 0.00 3.20
4900 7564 3.264450 GGAGAGAGAGATAGAGGAGGGAG 59.736 56.522 0.00 0.00 0.00 4.30
4905 7569 0.783850 AGATAGAGGAGGGAGAGGCC 59.216 60.000 0.00 0.00 0.00 5.19
4924 7756 2.368548 GCCCTTCCTTGGTGATTTGTTT 59.631 45.455 0.00 0.00 0.00 2.83
4925 7757 3.803368 GCCCTTCCTTGGTGATTTGTTTG 60.803 47.826 0.00 0.00 0.00 2.93
4939 7771 0.251121 TGTTTGGCGATGTCCATGGT 60.251 50.000 12.58 0.00 35.77 3.55
4988 7821 3.243234 CCTGAGGTCTAACGCTATGAGTG 60.243 52.174 0.00 0.00 0.00 3.51
4992 7825 2.159226 GGTCTAACGCTATGAGTGCTGT 60.159 50.000 0.00 0.00 0.00 4.40
5005 7838 0.321653 GTGCTGTGGATTCGGTTCCT 60.322 55.000 6.19 0.00 36.68 3.36
5058 7891 2.818130 TTTCCTTTGGATGTTGCTGC 57.182 45.000 0.00 0.00 0.00 5.25
5077 7910 4.737054 CTGCTTGTGTTCTGTTGTTCTTT 58.263 39.130 0.00 0.00 0.00 2.52
5097 7930 9.152595 GTTCTTTATCTAGTTCTCCGATTTGTT 57.847 33.333 0.00 0.00 0.00 2.83
5114 7947 1.913419 TGTTGACTGGGTTCCTATCCC 59.087 52.381 0.00 0.00 44.81 3.85
5119 7952 3.135814 GGGTTCCTATCCCGTCCG 58.864 66.667 0.00 0.00 35.27 4.79
5120 7953 2.420466 GGTTCCTATCCCGTCCGC 59.580 66.667 0.00 0.00 0.00 5.54
5121 7954 2.428925 GGTTCCTATCCCGTCCGCA 61.429 63.158 0.00 0.00 0.00 5.69
5122 7955 1.518774 GTTCCTATCCCGTCCGCAA 59.481 57.895 0.00 0.00 0.00 4.85
5123 7956 0.106149 GTTCCTATCCCGTCCGCAAT 59.894 55.000 0.00 0.00 0.00 3.56
5124 7957 1.342174 GTTCCTATCCCGTCCGCAATA 59.658 52.381 0.00 0.00 0.00 1.90
5125 7958 1.933021 TCCTATCCCGTCCGCAATAT 58.067 50.000 0.00 0.00 0.00 1.28
5126 7959 1.822990 TCCTATCCCGTCCGCAATATC 59.177 52.381 0.00 0.00 0.00 1.63
5127 7960 1.134788 CCTATCCCGTCCGCAATATCC 60.135 57.143 0.00 0.00 0.00 2.59
5167 8000 2.302733 GGTTTGTGATTTTCCCATGGCT 59.697 45.455 6.09 0.00 0.00 4.75
5174 8007 4.081476 GTGATTTTCCCATGGCTAGCTTTT 60.081 41.667 15.72 0.00 0.00 2.27
5227 8072 6.959639 TTGCTATGACTATTTTGGGGATTC 57.040 37.500 0.00 0.00 0.00 2.52
5251 8096 9.866655 TTCTTGGCATATGTTATTTAGGATTCT 57.133 29.630 4.29 0.00 0.00 2.40
5338 8189 5.514274 TGTTTGAAAAGGAAGCTTACCAG 57.486 39.130 4.63 0.00 0.00 4.00
5354 8205 0.254178 CCAGTGCTGGTGCTAGGAAT 59.746 55.000 9.96 0.00 45.53 3.01
5355 8206 1.486310 CCAGTGCTGGTGCTAGGAATA 59.514 52.381 9.96 0.00 45.53 1.75
5356 8207 2.484417 CCAGTGCTGGTGCTAGGAATAG 60.484 54.545 9.96 0.00 45.53 1.73
5357 8208 1.765314 AGTGCTGGTGCTAGGAATAGG 59.235 52.381 0.00 0.00 40.48 2.57
5379 8230 6.522054 AGGTAGGAATGTGGTATATGTTTCG 58.478 40.000 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.327975 AGAATAACTATTTGGATCACGTCACA 58.672 34.615 0.00 0.00 0.00 3.58
4 5 9.490379 GGATTAGAATAACTATTTGGATCACGT 57.510 33.333 0.00 0.00 0.00 4.49
5 6 8.936864 GGGATTAGAATAACTATTTGGATCACG 58.063 37.037 0.00 0.00 0.00 4.35
6 7 8.936864 CGGGATTAGAATAACTATTTGGATCAC 58.063 37.037 0.00 0.00 0.00 3.06
7 8 8.100791 CCGGGATTAGAATAACTATTTGGATCA 58.899 37.037 0.00 0.00 0.00 2.92
8 9 7.553044 CCCGGGATTAGAATAACTATTTGGATC 59.447 40.741 18.48 0.00 0.00 3.36
9 10 7.018249 ACCCGGGATTAGAATAACTATTTGGAT 59.982 37.037 32.02 0.00 0.00 3.41
11 12 6.540083 ACCCGGGATTAGAATAACTATTTGG 58.460 40.000 32.02 0.00 0.00 3.28
13 14 9.162733 TCTAACCCGGGATTAGAATAACTATTT 57.837 33.333 32.02 7.34 36.06 1.40
14 15 8.731591 TCTAACCCGGGATTAGAATAACTATT 57.268 34.615 32.02 8.08 36.06 1.73
15 16 8.175431 TCTCTAACCCGGGATTAGAATAACTAT 58.825 37.037 32.02 0.00 38.02 2.12
16 17 7.449704 GTCTCTAACCCGGGATTAGAATAACTA 59.550 40.741 32.02 11.64 38.02 2.24
17 18 6.267242 GTCTCTAACCCGGGATTAGAATAACT 59.733 42.308 32.02 0.00 38.02 2.24
18 19 6.267242 AGTCTCTAACCCGGGATTAGAATAAC 59.733 42.308 32.02 26.09 38.02 1.89
19 20 6.379579 AGTCTCTAACCCGGGATTAGAATAA 58.620 40.000 32.02 18.69 38.02 1.40
20 21 5.961897 AGTCTCTAACCCGGGATTAGAATA 58.038 41.667 32.02 20.81 38.02 1.75
22 23 4.261411 AGTCTCTAACCCGGGATTAGAA 57.739 45.455 32.02 20.28 38.02 2.10
24 25 3.958798 TCAAGTCTCTAACCCGGGATTAG 59.041 47.826 32.02 27.54 0.00 1.73
25 26 3.958798 CTCAAGTCTCTAACCCGGGATTA 59.041 47.826 32.02 20.07 0.00 1.75
26 27 2.766828 CTCAAGTCTCTAACCCGGGATT 59.233 50.000 32.02 20.02 0.00 3.01
27 28 2.024273 TCTCAAGTCTCTAACCCGGGAT 60.024 50.000 32.02 20.40 0.00 3.85
29 30 1.751924 CTCTCAAGTCTCTAACCCGGG 59.248 57.143 22.25 22.25 0.00 5.73
30 31 2.685897 CTCTCTCAAGTCTCTAACCCGG 59.314 54.545 0.00 0.00 0.00 5.73
31 32 2.098443 GCTCTCTCAAGTCTCTAACCCG 59.902 54.545 0.00 0.00 0.00 5.28
32 33 3.361786 AGCTCTCTCAAGTCTCTAACCC 58.638 50.000 0.00 0.00 0.00 4.11
116 117 1.208293 CTTGTCCAAGGTAGAGGCCTC 59.792 57.143 26.22 26.22 38.03 4.70
124 125 3.615592 CGAACGGATTCTTGTCCAAGGTA 60.616 47.826 7.16 0.00 38.21 3.08
133 134 8.583810 TTAATAATCCTACGAACGGATTCTTG 57.416 34.615 16.65 0.00 45.68 3.02
179 180 9.859152 TCTTGAGATGTAGATAGATCTTCTTCA 57.141 33.333 0.00 8.37 36.57 3.02
182 183 9.507329 GAGTCTTGAGATGTAGATAGATCTTCT 57.493 37.037 0.00 6.60 36.57 2.85
184 185 9.812347 ATGAGTCTTGAGATGTAGATAGATCTT 57.188 33.333 0.00 0.00 36.57 2.40
185 186 9.453572 GATGAGTCTTGAGATGTAGATAGATCT 57.546 37.037 0.00 0.00 38.81 2.75
207 2369 9.177608 CATGAATACAACCTTTAGGAAAGATGA 57.822 33.333 2.06 0.00 41.02 2.92
212 2374 9.747898 ATACACATGAATACAACCTTTAGGAAA 57.252 29.630 0.00 0.00 38.94 3.13
213 2375 9.391006 GATACACATGAATACAACCTTTAGGAA 57.609 33.333 0.00 0.00 38.94 3.36
226 2427 8.178313 AGGTCGATACAAGATACACATGAATA 57.822 34.615 0.00 0.00 0.00 1.75
308 2510 5.701224 AGGGAACACAAAGAACATAAAGGA 58.299 37.500 0.00 0.00 0.00 3.36
311 2513 6.361433 TGAGAGGGAACACAAAGAACATAAA 58.639 36.000 0.00 0.00 0.00 1.40
314 2516 4.437682 TGAGAGGGAACACAAAGAACAT 57.562 40.909 0.00 0.00 0.00 2.71
319 2521 4.022849 GTGGATTTGAGAGGGAACACAAAG 60.023 45.833 0.00 0.00 35.15 2.77
322 2524 2.224769 GGTGGATTTGAGAGGGAACACA 60.225 50.000 0.00 0.00 0.00 3.72
328 2530 3.659183 ATTGAGGTGGATTTGAGAGGG 57.341 47.619 0.00 0.00 0.00 4.30
331 2533 4.002982 CACGAATTGAGGTGGATTTGAGA 58.997 43.478 0.00 0.00 0.00 3.27
346 2548 1.880027 GTGGCCTGAACTTCACGAATT 59.120 47.619 3.32 0.00 0.00 2.17
348 2550 0.534203 GGTGGCCTGAACTTCACGAA 60.534 55.000 3.32 0.00 0.00 3.85
374 2577 5.036117 AGACACGTTGATATAGGGCAAAT 57.964 39.130 0.00 0.00 0.00 2.32
377 2580 6.243148 TCTATAGACACGTTGATATAGGGCA 58.757 40.000 0.00 0.00 30.98 5.36
388 2591 7.155328 GGATGGATCAAATCTATAGACACGTT 58.845 38.462 4.10 0.00 29.98 3.99
389 2592 6.267699 TGGATGGATCAAATCTATAGACACGT 59.732 38.462 4.10 0.00 29.98 4.49
448 2682 1.669115 CGGGACAAGTGCACCAGAG 60.669 63.158 14.63 3.44 0.00 3.35
496 2730 7.039363 AGCTGAGAGAACTTTGTTGTACTAGAT 60.039 37.037 0.00 0.00 0.00 1.98
510 2744 0.321741 TCGTCGGAGCTGAGAGAACT 60.322 55.000 0.00 0.00 0.00 3.01
526 2760 1.824329 ATCATCGTCCCTCGCTCGT 60.824 57.895 0.00 0.00 39.67 4.18
527 2761 1.371022 CATCATCGTCCCTCGCTCG 60.371 63.158 0.00 0.00 39.67 5.03
573 2808 1.272781 GCAGCTAGCGACAACTACAG 58.727 55.000 9.55 0.00 0.00 2.74
592 2827 8.455903 ACAATGATTATATCCAGTTTCACAGG 57.544 34.615 0.00 0.00 0.00 4.00
614 2850 5.353123 GGTGACAGAACACAAGAAGTAACAA 59.647 40.000 0.00 0.00 41.88 2.83
638 2874 6.662616 ACTTCTGATTTGTTCATCAACTTCG 58.337 36.000 0.00 0.00 35.61 3.79
639 2875 8.862550 AAACTTCTGATTTGTTCATCAACTTC 57.137 30.769 0.00 0.00 35.61 3.01
737 2974 1.210478 ACTGCCACGGATGCTTAGATT 59.790 47.619 0.00 0.00 0.00 2.40
738 2975 0.833287 ACTGCCACGGATGCTTAGAT 59.167 50.000 0.00 0.00 0.00 1.98
740 2977 1.134818 TGTACTGCCACGGATGCTTAG 60.135 52.381 0.00 0.00 0.00 2.18
941 3585 0.041982 GGGGGCTATGGTTTGGGAAA 59.958 55.000 0.00 0.00 0.00 3.13
942 3586 1.700985 GGGGGCTATGGTTTGGGAA 59.299 57.895 0.00 0.00 0.00 3.97
1140 3793 2.286502 AAGGGGAGGAGGGGCTTC 60.287 66.667 0.00 0.00 0.00 3.86
1702 4355 3.383185 ACGGAGAAGAGCCAATAGAAGAG 59.617 47.826 0.00 0.00 0.00 2.85
1821 4474 2.751259 CACTGGCACAAACAGCAGATAT 59.249 45.455 0.00 0.00 38.70 1.63
1828 4481 0.457035 AACAGCACTGGCACAAACAG 59.543 50.000 2.21 0.00 44.61 3.16
2058 4711 3.806316 AAAGCGTGAAATACAACTCGG 57.194 42.857 0.00 0.00 0.00 4.63
2319 4972 7.334421 GTGAAGTATGATGACAGGCTTTTCTTA 59.666 37.037 0.00 0.00 0.00 2.10
2397 5050 6.098124 CAGCAACCCAAATATTTAGATCCCAA 59.902 38.462 0.00 0.00 0.00 4.12
2601 5254 3.842007 TCGTCCTCAAACCCAAAGTAA 57.158 42.857 0.00 0.00 0.00 2.24
2664 5317 3.861840 TCTTCTTACAAGAGCCAATCCG 58.138 45.455 0.00 0.00 36.22 4.18
2711 5364 0.883833 CAAGATCCAAGCGGCTTTGT 59.116 50.000 13.53 1.53 0.00 2.83
2718 5371 2.670414 GAGACAAGTCAAGATCCAAGCG 59.330 50.000 2.72 0.00 0.00 4.68
2775 5428 3.376636 TGAAACCCATACCACCGATCTA 58.623 45.455 0.00 0.00 0.00 1.98
2943 5596 3.211045 GTTCCACCACTGTAAAGCTTCA 58.789 45.455 0.00 0.00 0.00 3.02
3253 5906 3.309954 GCTGCTAATGTAAGTACCACTGC 59.690 47.826 0.00 0.00 0.00 4.40
3615 6268 3.260884 AGAGACCCAAAAGCGACATTCTA 59.739 43.478 0.00 0.00 0.00 2.10
3798 6451 3.149196 TCTCTTGATGGTGAAAGTTGGC 58.851 45.455 0.00 0.00 0.00 4.52
4090 6743 2.124403 CCATCCTCCACTGCCAGC 60.124 66.667 0.00 0.00 0.00 4.85
4233 6886 2.370189 AGGCAGTGTCAGAAGTAGCTTT 59.630 45.455 0.00 0.00 0.00 3.51
4626 7289 9.777843 CGCATTAAAATTAGTCAAGTGAAAAAC 57.222 29.630 0.00 0.00 0.00 2.43
4650 7313 6.935209 CGATTTAAAAATTCGACTGAAAACGC 59.065 34.615 4.09 0.00 37.71 4.84
4673 7336 0.179111 CTTAGCACTTGATCCGCCGA 60.179 55.000 0.00 0.00 0.00 5.54
4676 7339 3.790123 GCAAATCTTAGCACTTGATCCGC 60.790 47.826 0.00 0.00 0.00 5.54
4684 7347 2.005451 CTCAGCGCAAATCTTAGCACT 58.995 47.619 11.47 0.00 0.00 4.40
4696 7359 0.106708 AAAAGACCACTCTCAGCGCA 59.893 50.000 11.47 0.00 0.00 6.09
4729 7392 4.084888 CGGCCCGAAAAGACACGC 62.085 66.667 0.00 0.00 0.00 5.34
4749 7412 2.934886 AAGCTAACGGGTGGTAAACA 57.065 45.000 0.00 0.00 0.00 2.83
4779 7443 4.442375 TCAAAACAACAGCGGAAAAGAA 57.558 36.364 0.00 0.00 0.00 2.52
4786 7450 5.717038 AAGAAAATTCAAAACAACAGCGG 57.283 34.783 0.00 0.00 0.00 5.52
4787 7451 7.007277 CCAAAAAGAAAATTCAAAACAACAGCG 59.993 33.333 0.00 0.00 0.00 5.18
4812 7476 2.600470 AAAAGGCTGAACCGGGCC 60.600 61.111 11.19 11.19 46.52 5.80
4887 7551 3.374318 GGCCTCTCCCTCCTCTATC 57.626 63.158 0.00 0.00 0.00 2.08
4905 7569 3.803368 GCCAAACAAATCACCAAGGAAGG 60.803 47.826 0.00 0.00 0.00 3.46
4906 7570 3.392882 GCCAAACAAATCACCAAGGAAG 58.607 45.455 0.00 0.00 0.00 3.46
4907 7571 2.223923 CGCCAAACAAATCACCAAGGAA 60.224 45.455 0.00 0.00 0.00 3.36
4908 7572 1.339610 CGCCAAACAAATCACCAAGGA 59.660 47.619 0.00 0.00 0.00 3.36
4924 7756 0.255604 AATCACCATGGACATCGCCA 59.744 50.000 21.47 0.00 43.23 5.69
4925 7757 0.664761 CAATCACCATGGACATCGCC 59.335 55.000 21.47 0.00 0.00 5.54
4988 7821 0.321653 ACAGGAACCGAATCCACAGC 60.322 55.000 8.83 0.00 42.27 4.40
4992 7825 0.613260 CTCCACAGGAACCGAATCCA 59.387 55.000 8.83 0.00 42.27 3.41
5005 7838 1.534697 GGGGTCAAACCACTCCACA 59.465 57.895 0.00 0.00 39.07 4.17
5025 7858 9.415544 CATCCAAAGGAAAAATCTAGACAAAAG 57.584 33.333 0.00 0.00 34.34 2.27
5026 7859 8.923270 ACATCCAAAGGAAAAATCTAGACAAAA 58.077 29.630 0.00 0.00 34.34 2.44
5027 7860 8.477419 ACATCCAAAGGAAAAATCTAGACAAA 57.523 30.769 0.00 0.00 34.34 2.83
5028 7861 8.359642 CAACATCCAAAGGAAAAATCTAGACAA 58.640 33.333 0.00 0.00 34.34 3.18
5029 7862 7.523709 GCAACATCCAAAGGAAAAATCTAGACA 60.524 37.037 0.00 0.00 34.34 3.41
5030 7863 6.808704 GCAACATCCAAAGGAAAAATCTAGAC 59.191 38.462 0.00 0.00 34.34 2.59
5031 7864 6.721208 AGCAACATCCAAAGGAAAAATCTAGA 59.279 34.615 0.00 0.00 34.34 2.43
5032 7865 6.810182 CAGCAACATCCAAAGGAAAAATCTAG 59.190 38.462 0.00 0.00 34.34 2.43
5033 7866 6.690530 CAGCAACATCCAAAGGAAAAATCTA 58.309 36.000 0.00 0.00 34.34 1.98
5034 7867 5.544650 CAGCAACATCCAAAGGAAAAATCT 58.455 37.500 0.00 0.00 34.34 2.40
5035 7868 4.152938 GCAGCAACATCCAAAGGAAAAATC 59.847 41.667 0.00 0.00 34.34 2.17
5036 7869 4.067192 GCAGCAACATCCAAAGGAAAAAT 58.933 39.130 0.00 0.00 34.34 1.82
5037 7870 3.134442 AGCAGCAACATCCAAAGGAAAAA 59.866 39.130 0.00 0.00 34.34 1.94
5041 7874 1.614903 CAAGCAGCAACATCCAAAGGA 59.385 47.619 0.00 0.00 35.55 3.36
5058 7891 9.046296 ACTAGATAAAGAACAACAGAACACAAG 57.954 33.333 0.00 0.00 0.00 3.16
5077 7910 7.258441 CAGTCAACAAATCGGAGAACTAGATA 58.742 38.462 0.00 0.00 43.58 1.98
5114 7947 0.179056 AACCCTGGATATTGCGGACG 60.179 55.000 0.00 0.00 0.00 4.79
5115 7948 1.676006 CAAACCCTGGATATTGCGGAC 59.324 52.381 0.00 0.00 0.00 4.79
5116 7949 1.283613 ACAAACCCTGGATATTGCGGA 59.716 47.619 0.00 0.00 0.00 5.54
5117 7950 1.405105 CACAAACCCTGGATATTGCGG 59.595 52.381 0.00 0.00 0.00 5.69
5118 7951 2.091541 ACACAAACCCTGGATATTGCG 58.908 47.619 0.00 0.00 0.00 4.85
5119 7952 3.088532 TCACACAAACCCTGGATATTGC 58.911 45.455 0.00 0.00 0.00 3.56
5120 7953 5.185635 ACATTCACACAAACCCTGGATATTG 59.814 40.000 0.00 0.00 0.00 1.90
5121 7954 5.332743 ACATTCACACAAACCCTGGATATT 58.667 37.500 0.00 0.00 0.00 1.28
5122 7955 4.934356 ACATTCACACAAACCCTGGATAT 58.066 39.130 0.00 0.00 0.00 1.63
5123 7956 4.380843 ACATTCACACAAACCCTGGATA 57.619 40.909 0.00 0.00 0.00 2.59
5124 7957 3.243359 ACATTCACACAAACCCTGGAT 57.757 42.857 0.00 0.00 0.00 3.41
5125 7958 2.746279 ACATTCACACAAACCCTGGA 57.254 45.000 0.00 0.00 0.00 3.86
5126 7959 2.819608 CCTACATTCACACAAACCCTGG 59.180 50.000 0.00 0.00 0.00 4.45
5127 7960 3.486383 ACCTACATTCACACAAACCCTG 58.514 45.455 0.00 0.00 0.00 4.45
5167 8000 6.760770 CCAGGAAACAAACAAATCAAAAGCTA 59.239 34.615 0.00 0.00 0.00 3.32
5174 8007 5.186797 ACAGAACCAGGAAACAAACAAATCA 59.813 36.000 0.00 0.00 0.00 2.57
5227 8072 8.517878 CCAGAATCCTAAATAACATATGCCAAG 58.482 37.037 1.58 0.00 0.00 3.61
5251 8096 2.171840 GAGCTCAACTCTACCTCACCA 58.828 52.381 9.40 0.00 42.62 4.17
5338 8189 1.486726 ACCTATTCCTAGCACCAGCAC 59.513 52.381 0.00 0.00 45.49 4.40
5354 8205 7.256048 CCGAAACATATACCACATTCCTACCTA 60.256 40.741 0.00 0.00 0.00 3.08
5355 8206 6.463897 CCGAAACATATACCACATTCCTACCT 60.464 42.308 0.00 0.00 0.00 3.08
5356 8207 5.699458 CCGAAACATATACCACATTCCTACC 59.301 44.000 0.00 0.00 0.00 3.18
5357 8208 6.285990 ACCGAAACATATACCACATTCCTAC 58.714 40.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.