Multiple sequence alignment - TraesCS5D01G123100

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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 TraesCS5D01G123100 chr5D 100.000 5263 0 0 1 5263 179943248 179948510 0.000000e+00 9720.0
1 TraesCS5D01G123100 chr5A 97.604 4757 70 15 35 4754 212222965 212218216 0.000000e+00 8113.0
2 TraesCS5D01G123100 chr5A 93.466 352 9 7 4769 5109 212218121 212217773 1.310000e-140 510.0
3 TraesCS5D01G123100 chr5A 98.113 53 1 0 5018 5070 212217794 212217742 5.610000e-15 93.5
4 TraesCS5D01G123100 chr5B 97.802 2320 29 12 2442 4754 157385432 157383128 0.000000e+00 3982.0
5 TraesCS5D01G123100 chr5B 95.444 2063 34 20 113 2149 157395004 157392976 0.000000e+00 3234.0
6 TraesCS5D01G123100 chr5B 95.806 310 13 0 2145 2454 157390786 157390477 7.870000e-138 501.0
7 TraesCS5D01G123100 chr5B 91.228 114 7 3 5105 5216 588879899 588880011 9.130000e-33 152.0
8 TraesCS5D01G123100 chr3B 90.678 118 9 2 5100 5216 681095184 681095068 7.060000e-34 156.0
9 TraesCS5D01G123100 chr7A 91.892 111 6 3 5108 5216 539298654 539298763 9.130000e-33 152.0
10 TraesCS5D01G123100 chr7A 90.517 116 8 3 5103 5216 689286612 689286498 3.280000e-32 150.0
11 TraesCS5D01G123100 chr6D 90.598 117 8 3 5102 5216 410169236 410169351 9.130000e-33 152.0
12 TraesCS5D01G123100 chr4D 92.523 107 6 2 5111 5216 413012195 413012090 9.130000e-33 152.0
13 TraesCS5D01G123100 chr2D 90.598 117 8 3 5102 5216 508728621 508728736 9.130000e-33 152.0
14 TraesCS5D01G123100 chr2D 100.000 28 0 0 1 28 107564856 107564883 1.000000e-02 52.8
15 TraesCS5D01G123100 chr7B 88.618 123 10 4 5104 5223 45642850 45642971 4.250000e-31 147.0
16 TraesCS5D01G123100 chr7B 89.130 46 2 3 1 46 639902196 639902238 3.000000e-03 54.7
17 TraesCS5D01G123100 chr4B 89.256 121 8 5 5108 5225 568449108 568449226 4.250000e-31 147.0
18 TraesCS5D01G123100 chr6B 100.000 34 0 0 1 34 6880604 6880571 4.400000e-06 63.9
19 TraesCS5D01G123100 chr6B 94.595 37 1 1 3 39 558924706 558924741 7.360000e-04 56.5
20 TraesCS5D01G123100 chr6B 92.308 39 2 1 1 39 346812472 346812435 3.000000e-03 54.7
21 TraesCS5D01G123100 chr3A 100.000 31 0 0 2 32 435212 435182 2.050000e-04 58.4
22 TraesCS5D01G123100 chr3A 86.000 50 6 1 1 50 51464772 51464820 1.000000e-02 52.8
23 TraesCS5D01G123100 chr3D 94.595 37 1 1 3 39 23152045 23152010 7.360000e-04 56.5
24 TraesCS5D01G123100 chr2A 100.000 28 0 0 1 28 754445536 754445563 1.000000e-02 52.8


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 TraesCS5D01G123100 chr5D 179943248 179948510 5262 False 9720.0 9720 100.000000 1 5263 1 chr5D.!!$F1 5262
1 TraesCS5D01G123100 chr5A 212217742 212222965 5223 True 2905.5 8113 96.394333 35 5109 3 chr5A.!!$R1 5074
2 TraesCS5D01G123100 chr5B 157383128 157385432 2304 True 3982.0 3982 97.802000 2442 4754 1 chr5B.!!$R1 2312
3 TraesCS5D01G123100 chr5B 157390477 157395004 4527 True 1867.5 3234 95.625000 113 2454 2 chr5B.!!$R2 2341

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
395 416 0.174389 CCTCCGCCATATCGATCTGG 59.826 60.000 22.18 22.18 35.53 3.86 F
475 496 1.278238 GGTCGTATTTGCTCTCCGTG 58.722 55.000 0.00 0.00 0.00 4.94 F
785 822 1.892209 AACTTGGGGTTCTAAGTGCG 58.108 50.000 0.00 0.00 42.66 5.34 F
2044 2092 3.239449 CAGTGATATGTGCTACCCCCTA 58.761 50.000 0.00 0.00 0.00 3.53 F
2366 4608 7.308229 GCATGCCTAAGATGAACTATTTCGAAT 60.308 37.037 6.36 0.00 34.04 3.34 F
4046 6288 3.181470 TGTTGTGTGAGAATCGGACTGAA 60.181 43.478 0.00 0.00 38.61 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1831 1879 5.897250 TGTCTTATCAGCCCTATCAACTGTA 59.103 40.000 0.0 0.0 33.12 2.74 R
2252 4494 6.300354 GTAATGCACCACATCCTAATGTAC 57.700 41.667 0.0 0.0 44.41 2.90 R
2631 4873 5.248380 AGCCCTGAGTACAAAGAAAGAAT 57.752 39.130 0.0 0.0 0.00 2.40 R
2947 5189 3.327757 TGTTGCTGATACCTCCTTCAACT 59.672 43.478 0.0 0.0 34.95 3.16 R
4232 6474 3.008049 CCCCGATCTTCGAAAATATCCCT 59.992 47.826 0.0 0.0 43.74 4.20 R
4955 7299 1.921243 CTGGAACACGCATCATACGA 58.079 50.000 0.0 0.0 0.00 3.43 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
25 26 8.745464 GCTCTTATATTAGTTTACGGAGGAAG 57.255 38.462 0.00 0.00 0.00 3.46
26 27 8.358895 GCTCTTATATTAGTTTACGGAGGAAGT 58.641 37.037 0.00 0.00 0.00 3.01
34 35 8.814038 TTAGTTTACGGAGGAAGTAGATTAGT 57.186 34.615 0.00 0.00 0.00 2.24
35 36 9.905713 TTAGTTTACGGAGGAAGTAGATTAGTA 57.094 33.333 0.00 0.00 0.00 1.82
36 37 8.814038 AGTTTACGGAGGAAGTAGATTAGTAA 57.186 34.615 0.00 0.00 0.00 2.24
37 38 8.681806 AGTTTACGGAGGAAGTAGATTAGTAAC 58.318 37.037 0.00 0.00 0.00 2.50
38 39 8.462016 GTTTACGGAGGAAGTAGATTAGTAACA 58.538 37.037 0.00 0.00 0.00 2.41
39 40 8.757982 TTACGGAGGAAGTAGATTAGTAACAT 57.242 34.615 0.00 0.00 0.00 2.71
40 41 9.851686 TTACGGAGGAAGTAGATTAGTAACATA 57.148 33.333 0.00 0.00 0.00 2.29
41 42 8.937207 ACGGAGGAAGTAGATTAGTAACATAT 57.063 34.615 0.00 0.00 0.00 1.78
42 43 9.364653 ACGGAGGAAGTAGATTAGTAACATATT 57.635 33.333 0.00 0.00 0.00 1.28
68 69 5.266709 AGTCTGTAAGTTACTCCCCACTA 57.733 43.478 14.00 0.00 33.76 2.74
371 392 2.190578 CGGCAGATCTTCCACCCC 59.809 66.667 12.14 0.00 0.00 4.95
395 416 0.174389 CCTCCGCCATATCGATCTGG 59.826 60.000 22.18 22.18 35.53 3.86
404 425 3.119673 CCATATCGATCTGGTTCTCCTCG 60.120 52.174 19.12 0.00 32.54 4.63
475 496 1.278238 GGTCGTATTTGCTCTCCGTG 58.722 55.000 0.00 0.00 0.00 4.94
785 822 1.892209 AACTTGGGGTTCTAAGTGCG 58.108 50.000 0.00 0.00 42.66 5.34
853 890 4.214119 GCAGCAACTTTTGAGTATGTCTGA 59.786 41.667 0.00 0.00 0.00 3.27
1330 1378 3.274288 GCAGCTAAACTTGATGTAGCCT 58.726 45.455 0.00 0.00 40.96 4.58
2044 2092 3.239449 CAGTGATATGTGCTACCCCCTA 58.761 50.000 0.00 0.00 0.00 3.53
2366 4608 7.308229 GCATGCCTAAGATGAACTATTTCGAAT 60.308 37.037 6.36 0.00 34.04 3.34
2947 5189 3.696051 GGCAGTAATCAGCTTCCAATGAA 59.304 43.478 0.00 0.00 0.00 2.57
3551 5793 8.103935 CCTTTTCTTGAAGGTCTAGTTAGGATT 58.896 37.037 0.00 0.00 41.06 3.01
4046 6288 3.181470 TGTTGTGTGAGAATCGGACTGAA 60.181 43.478 0.00 0.00 38.61 3.02
4232 6474 3.966979 TGATAAGCTGCCCAATTTCTCA 58.033 40.909 0.00 0.00 0.00 3.27
4598 6840 1.421480 CCTGAGCCCATCTGATCTCA 58.579 55.000 7.17 7.17 34.74 3.27
4601 6843 2.435069 CTGAGCCCATCTGATCTCAGTT 59.565 50.000 19.25 0.00 44.43 3.16
4668 6920 5.757886 CATGTCTGTACCAATTTTCAACGT 58.242 37.500 0.00 0.00 0.00 3.99
4748 7000 6.883744 ACTGTTTCACATACCACCAATTTTT 58.116 32.000 0.00 0.00 0.00 1.94
4808 7141 4.433186 TTATTTTGCTGTTCATGGTCGG 57.567 40.909 0.00 0.00 0.00 4.79
4821 7165 0.250234 TGGTCGGGAGCTCTCATTTG 59.750 55.000 15.40 0.00 0.00 2.32
4829 7173 2.158449 GGAGCTCTCATTTGTGTGTTCG 59.842 50.000 14.64 0.00 0.00 3.95
4831 7175 3.987868 GAGCTCTCATTTGTGTGTTCGTA 59.012 43.478 6.43 0.00 0.00 3.43
4876 7220 6.327154 GTTGAAACCCGAAAGAGAAAGAAAA 58.673 36.000 0.00 0.00 0.00 2.29
4877 7221 6.131544 TGAAACCCGAAAGAGAAAGAAAAG 57.868 37.500 0.00 0.00 0.00 2.27
4878 7222 5.883673 TGAAACCCGAAAGAGAAAGAAAAGA 59.116 36.000 0.00 0.00 0.00 2.52
4884 7228 6.139435 CCGAAAGAGAAAGAAAAGAAGCTTC 58.861 40.000 19.11 19.11 0.00 3.86
4894 7238 3.427161 AAAGAAGCTTCTGCACACAAC 57.573 42.857 29.09 0.00 42.74 3.32
4955 7299 2.943036 ACGGGAGTGTGTTATGGTTT 57.057 45.000 0.00 0.00 44.82 3.27
5114 7458 9.249053 TGTGCAATCTTTAATTAAGTATTCCCA 57.751 29.630 0.00 1.08 35.28 4.37
5119 7463 9.862149 AATCTTTAATTAAGTATTCCCATCCGT 57.138 29.630 0.00 0.00 35.28 4.69
5121 7465 9.689501 TCTTTAATTAAGTATTCCCATCCGTTT 57.310 29.630 0.00 0.00 35.28 3.60
5122 7466 9.946165 CTTTAATTAAGTATTCCCATCCGTTTC 57.054 33.333 0.00 0.00 0.00 2.78
5123 7467 9.689501 TTTAATTAAGTATTCCCATCCGTTTCT 57.310 29.630 0.00 0.00 0.00 2.52
5126 7470 9.689501 AATTAAGTATTCCCATCCGTTTCTAAA 57.310 29.630 0.00 0.00 0.00 1.85
5127 7471 9.862149 ATTAAGTATTCCCATCCGTTTCTAAAT 57.138 29.630 0.00 0.00 0.00 1.40
5131 7475 9.862149 AGTATTCCCATCCGTTTCTAAATATTT 57.138 29.630 5.89 5.89 0.00 1.40
5132 7476 9.893305 GTATTCCCATCCGTTTCTAAATATTTG 57.107 33.333 11.05 1.65 0.00 2.32
5134 7478 7.562454 TCCCATCCGTTTCTAAATATTTGTC 57.438 36.000 11.05 0.00 0.00 3.18
5135 7479 7.343357 TCCCATCCGTTTCTAAATATTTGTCT 58.657 34.615 11.05 0.00 0.00 3.41
5136 7480 7.832187 TCCCATCCGTTTCTAAATATTTGTCTT 59.168 33.333 11.05 0.00 0.00 3.01
5137 7481 8.466798 CCCATCCGTTTCTAAATATTTGTCTTT 58.533 33.333 11.05 0.00 0.00 2.52
5171 7515 9.996554 TTCAAATGAACTATCATATACGGATGT 57.003 29.630 0.00 0.00 45.60 3.06
5211 7555 8.976986 AAAGTGTAGATTCATTCATTTTGCTC 57.023 30.769 0.00 0.00 0.00 4.26
5212 7556 7.093322 AGTGTAGATTCATTCATTTTGCTCC 57.907 36.000 0.00 0.00 0.00 4.70
5213 7557 5.967674 GTGTAGATTCATTCATTTTGCTCCG 59.032 40.000 0.00 0.00 0.00 4.63
5214 7558 5.647658 TGTAGATTCATTCATTTTGCTCCGT 59.352 36.000 0.00 0.00 0.00 4.69
5215 7559 6.821160 TGTAGATTCATTCATTTTGCTCCGTA 59.179 34.615 0.00 0.00 0.00 4.02
5216 7560 6.369059 AGATTCATTCATTTTGCTCCGTAG 57.631 37.500 0.00 0.00 0.00 3.51
5228 7572 3.006659 GCTCCGTAGCTGTCATCTAAG 57.993 52.381 0.00 0.00 45.85 2.18
5229 7573 2.860582 GCTCCGTAGCTGTCATCTAAGC 60.861 54.545 0.00 0.00 45.85 3.09
5230 7574 2.359214 CTCCGTAGCTGTCATCTAAGCA 59.641 50.000 0.00 0.00 42.06 3.91
5231 7575 2.758423 TCCGTAGCTGTCATCTAAGCAA 59.242 45.455 0.00 0.00 42.06 3.91
5232 7576 3.194755 TCCGTAGCTGTCATCTAAGCAAA 59.805 43.478 0.00 0.00 42.06 3.68
5233 7577 3.932710 CCGTAGCTGTCATCTAAGCAAAA 59.067 43.478 0.00 0.00 42.06 2.44
5234 7578 4.391830 CCGTAGCTGTCATCTAAGCAAAAA 59.608 41.667 0.00 0.00 42.06 1.94
5235 7579 5.316770 CGTAGCTGTCATCTAAGCAAAAAC 58.683 41.667 0.00 0.00 42.06 2.43
5236 7580 5.120830 CGTAGCTGTCATCTAAGCAAAAACT 59.879 40.000 0.00 0.00 42.06 2.66
5237 7581 6.347725 CGTAGCTGTCATCTAAGCAAAAACTT 60.348 38.462 0.00 0.00 42.06 2.66
5238 7582 6.396829 AGCTGTCATCTAAGCAAAAACTTT 57.603 33.333 0.00 0.00 42.06 2.66
5239 7583 6.809869 AGCTGTCATCTAAGCAAAAACTTTT 58.190 32.000 0.00 0.00 42.06 2.27
5243 7587 8.578308 TGTCATCTAAGCAAAAACTTTTGATG 57.422 30.769 17.07 11.38 44.98 3.07
5244 7588 8.196771 TGTCATCTAAGCAAAAACTTTTGATGT 58.803 29.630 17.07 6.23 44.98 3.06
5245 7589 8.482429 GTCATCTAAGCAAAAACTTTTGATGTG 58.518 33.333 17.07 8.57 44.98 3.21
5246 7590 8.412456 TCATCTAAGCAAAAACTTTTGATGTGA 58.588 29.630 17.07 12.65 44.98 3.58
5247 7591 7.985634 TCTAAGCAAAAACTTTTGATGTGAC 57.014 32.000 17.07 0.72 44.98 3.67
5248 7592 7.542890 TCTAAGCAAAAACTTTTGATGTGACA 58.457 30.769 17.07 0.00 44.98 3.58
5249 7593 8.031864 TCTAAGCAAAAACTTTTGATGTGACAA 58.968 29.630 17.07 0.00 44.98 3.18
5250 7594 7.064060 AAGCAAAAACTTTTGATGTGACAAG 57.936 32.000 17.07 0.00 44.98 3.16
5251 7595 6.650390 AAGCAAAAACTTTTGATGTGACAAGT 59.350 30.769 17.07 0.00 44.98 3.16
5252 7596 7.360269 AAGCAAAAACTTTTGATGTGACAAGTG 60.360 33.333 17.07 0.00 44.98 3.16
5255 7599 8.687824 AAAAACTTTTGATGTGACAAGTGTAG 57.312 30.769 0.00 0.00 0.00 2.74
5256 7600 7.391148 AAACTTTTGATGTGACAAGTGTAGT 57.609 32.000 0.00 0.00 0.00 2.73
5257 7601 6.363577 ACTTTTGATGTGACAAGTGTAGTG 57.636 37.500 0.00 0.00 0.00 2.74
5258 7602 6.112734 ACTTTTGATGTGACAAGTGTAGTGA 58.887 36.000 0.00 0.00 0.00 3.41
5259 7603 5.984233 TTTGATGTGACAAGTGTAGTGAC 57.016 39.130 0.00 0.00 0.00 3.67
5260 7604 3.990092 TGATGTGACAAGTGTAGTGACC 58.010 45.455 0.00 0.00 0.00 4.02
5261 7605 2.902705 TGTGACAAGTGTAGTGACCC 57.097 50.000 0.00 0.00 0.00 4.46
5262 7606 2.394632 TGTGACAAGTGTAGTGACCCT 58.605 47.619 0.00 0.00 0.00 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.358895 ACTTCCTCCGTAAACTAATATAAGAGC 58.641 37.037 0.00 0.00 0.00 4.09
14 15 8.757982 ATGTTACTAATCTACTTCCTCCGTAA 57.242 34.615 0.00 0.00 0.00 3.18
16 17 8.937207 ATATGTTACTAATCTACTTCCTCCGT 57.063 34.615 0.00 0.00 0.00 4.69
38 39 9.585369 GGGGAGTAACTTACAGACTACTAATAT 57.415 37.037 1.79 0.00 0.00 1.28
39 40 8.560039 TGGGGAGTAACTTACAGACTACTAATA 58.440 37.037 1.79 0.00 0.00 0.98
40 41 7.341512 GTGGGGAGTAACTTACAGACTACTAAT 59.658 40.741 1.79 0.00 0.00 1.73
41 42 6.660949 GTGGGGAGTAACTTACAGACTACTAA 59.339 42.308 1.79 0.00 0.00 2.24
42 43 6.012157 AGTGGGGAGTAACTTACAGACTACTA 60.012 42.308 1.79 0.00 0.00 1.82
43 44 5.015515 GTGGGGAGTAACTTACAGACTACT 58.984 45.833 1.79 0.00 0.00 2.57
44 45 5.015515 AGTGGGGAGTAACTTACAGACTAC 58.984 45.833 1.79 0.05 0.00 2.73
45 46 5.266709 AGTGGGGAGTAACTTACAGACTA 57.733 43.478 1.79 0.00 0.00 2.59
46 47 4.129317 AGTGGGGAGTAACTTACAGACT 57.871 45.455 1.79 0.00 0.00 3.24
47 48 5.990120 TTAGTGGGGAGTAACTTACAGAC 57.010 43.478 1.79 0.00 0.00 3.51
48 49 7.416731 AGTATTAGTGGGGAGTAACTTACAGA 58.583 38.462 1.79 0.00 0.00 3.41
49 50 7.657023 AGTATTAGTGGGGAGTAACTTACAG 57.343 40.000 1.79 0.00 0.00 2.74
50 51 8.339247 ACTAGTATTAGTGGGGAGTAACTTACA 58.661 37.037 0.00 0.00 38.69 2.41
51 52 8.759481 ACTAGTATTAGTGGGGAGTAACTTAC 57.241 38.462 0.00 0.00 38.69 2.34
52 53 8.785859 AGACTAGTATTAGTGGGGAGTAACTTA 58.214 37.037 2.15 0.00 40.21 2.24
53 54 7.650660 AGACTAGTATTAGTGGGGAGTAACTT 58.349 38.462 2.15 0.00 40.21 2.66
54 55 7.223472 AGACTAGTATTAGTGGGGAGTAACT 57.777 40.000 2.15 0.00 40.21 2.24
55 56 7.894753 AAGACTAGTATTAGTGGGGAGTAAC 57.105 40.000 0.00 0.00 40.21 2.50
68 69 8.113173 GGATTCAGACCGATAAGACTAGTATT 57.887 38.462 8.02 8.02 0.00 1.89
371 392 2.657237 GATATGGCGGAGGGGTCG 59.343 66.667 0.00 0.00 0.00 4.79
475 496 1.001158 CGGAGAGGAATTAGTCGCTCC 60.001 57.143 12.50 12.50 41.61 4.70
853 890 2.378547 TCACCCTAAAGCCAGGAAATGT 59.621 45.455 0.00 0.00 38.00 2.71
969 1007 9.612879 ATTCAGAGGGAAGAAATCAGAGATATA 57.387 33.333 0.00 0.00 39.30 0.86
970 1008 7.927683 TTCAGAGGGAAGAAATCAGAGATAT 57.072 36.000 0.00 0.00 0.00 1.63
971 1009 7.927683 ATTCAGAGGGAAGAAATCAGAGATA 57.072 36.000 0.00 0.00 39.30 1.98
972 1010 6.828307 ATTCAGAGGGAAGAAATCAGAGAT 57.172 37.500 0.00 0.00 39.30 2.75
1330 1378 8.098286 TGAATTCTCGGAAGTTAAGGATTTACA 58.902 33.333 7.05 0.00 0.00 2.41
1831 1879 5.897250 TGTCTTATCAGCCCTATCAACTGTA 59.103 40.000 0.00 0.00 33.12 2.74
2044 2092 8.388484 AGAAGCAAATTAATGAGAATATCGCT 57.612 30.769 0.00 0.00 0.00 4.93
2252 4494 6.300354 GTAATGCACCACATCCTAATGTAC 57.700 41.667 0.00 0.00 44.41 2.90
2631 4873 5.248380 AGCCCTGAGTACAAAGAAAGAAT 57.752 39.130 0.00 0.00 0.00 2.40
2947 5189 3.327757 TGTTGCTGATACCTCCTTCAACT 59.672 43.478 0.00 0.00 34.95 3.16
3551 5793 3.967326 AGATAAATGTGATCCGGGAGACA 59.033 43.478 12.62 12.62 0.00 3.41
4046 6288 4.146075 GCTCTCTGCCTCAGCGCT 62.146 66.667 2.64 2.64 44.31 5.92
4232 6474 3.008049 CCCCGATCTTCGAAAATATCCCT 59.992 47.826 0.00 0.00 43.74 4.20
4668 6920 5.453567 TCTTTCTCTCAGATGTTCGAACA 57.546 39.130 31.41 31.41 44.06 3.18
4803 7136 0.250513 ACAAATGAGAGCTCCCGACC 59.749 55.000 10.93 0.00 0.00 4.79
4808 7141 2.158449 CGAACACACAAATGAGAGCTCC 59.842 50.000 10.93 2.40 0.00 4.70
4821 7165 7.751047 ATGTATGATTACAGTACGAACACAC 57.249 36.000 0.00 0.00 41.49 3.82
4831 7175 9.733556 TTCAACCAACTTATGTATGATTACAGT 57.266 29.630 0.00 0.00 41.49 3.55
4861 7205 6.850317 CAGAAGCTTCTTTTCTTTCTCTTTCG 59.150 38.462 26.44 5.62 34.74 3.46
4876 7220 2.042686 TGTTGTGTGCAGAAGCTTCT 57.957 45.000 23.49 23.49 42.74 2.85
4877 7221 2.849880 TTGTTGTGTGCAGAAGCTTC 57.150 45.000 19.11 19.11 42.74 3.86
4878 7222 3.806625 ATTTGTTGTGTGCAGAAGCTT 57.193 38.095 0.00 0.00 42.74 3.74
4884 7228 6.645700 AACTACAAAATTTGTTGTGTGCAG 57.354 33.333 22.25 12.29 46.18 4.41
4955 7299 1.921243 CTGGAACACGCATCATACGA 58.079 50.000 0.00 0.00 0.00 3.43
5109 7453 7.832187 AGACAAATATTTAGAAACGGATGGGAA 59.168 33.333 0.00 0.00 0.00 3.97
5111 7455 7.568199 AGACAAATATTTAGAAACGGATGGG 57.432 36.000 0.00 0.00 0.00 4.00
5112 7456 9.855021 AAAAGACAAATATTTAGAAACGGATGG 57.145 29.630 0.00 0.00 0.00 3.51
5145 7489 9.996554 ACATCCGTATATGATAGTTCATTTGAA 57.003 29.630 0.00 0.00 42.61 2.69
5186 7530 8.031277 GGAGCAAAATGAATGAATCTACACTTT 58.969 33.333 0.00 0.00 0.00 2.66
5187 7531 7.542025 GGAGCAAAATGAATGAATCTACACTT 58.458 34.615 0.00 0.00 0.00 3.16
5188 7532 6.183360 CGGAGCAAAATGAATGAATCTACACT 60.183 38.462 0.00 0.00 0.00 3.55
5189 7533 5.967674 CGGAGCAAAATGAATGAATCTACAC 59.032 40.000 0.00 0.00 0.00 2.90
5190 7534 5.647658 ACGGAGCAAAATGAATGAATCTACA 59.352 36.000 0.00 0.00 0.00 2.74
5191 7535 6.124088 ACGGAGCAAAATGAATGAATCTAC 57.876 37.500 0.00 0.00 0.00 2.59
5192 7536 7.482654 CTACGGAGCAAAATGAATGAATCTA 57.517 36.000 0.00 0.00 0.00 1.98
5193 7537 6.369059 CTACGGAGCAAAATGAATGAATCT 57.631 37.500 0.00 0.00 0.00 2.40
5209 7553 2.359214 TGCTTAGATGACAGCTACGGAG 59.641 50.000 0.00 0.00 36.92 4.63
5210 7554 2.375146 TGCTTAGATGACAGCTACGGA 58.625 47.619 0.00 0.00 36.92 4.69
5211 7555 2.871182 TGCTTAGATGACAGCTACGG 57.129 50.000 0.00 0.00 36.92 4.02
5212 7556 5.120830 AGTTTTTGCTTAGATGACAGCTACG 59.879 40.000 0.00 0.00 36.92 3.51
5213 7557 6.487689 AGTTTTTGCTTAGATGACAGCTAC 57.512 37.500 0.00 0.00 36.92 3.58
5214 7558 7.510549 AAAGTTTTTGCTTAGATGACAGCTA 57.489 32.000 0.00 0.00 36.92 3.32
5215 7559 6.396829 AAAGTTTTTGCTTAGATGACAGCT 57.603 33.333 0.00 0.00 36.92 4.24
5216 7560 6.697019 TCAAAAGTTTTTGCTTAGATGACAGC 59.303 34.615 11.50 0.00 45.35 4.40
5217 7561 8.697067 CATCAAAAGTTTTTGCTTAGATGACAG 58.303 33.333 14.43 0.00 45.35 3.51
5218 7562 8.196771 ACATCAAAAGTTTTTGCTTAGATGACA 58.803 29.630 21.60 0.00 45.35 3.58
5219 7563 8.482429 CACATCAAAAGTTTTTGCTTAGATGAC 58.518 33.333 21.60 0.00 45.35 3.06
5220 7564 8.412456 TCACATCAAAAGTTTTTGCTTAGATGA 58.588 29.630 21.60 7.05 45.35 2.92
5221 7565 8.482429 GTCACATCAAAAGTTTTTGCTTAGATG 58.518 33.333 16.57 16.57 45.35 2.90
5222 7566 8.196771 TGTCACATCAAAAGTTTTTGCTTAGAT 58.803 29.630 11.50 0.00 45.35 1.98
5223 7567 7.542890 TGTCACATCAAAAGTTTTTGCTTAGA 58.457 30.769 11.50 5.71 45.35 2.10
5224 7568 7.754069 TGTCACATCAAAAGTTTTTGCTTAG 57.246 32.000 11.50 5.11 45.35 2.18
5225 7569 7.816995 ACTTGTCACATCAAAAGTTTTTGCTTA 59.183 29.630 11.50 0.00 45.35 3.09
5226 7570 6.650390 ACTTGTCACATCAAAAGTTTTTGCTT 59.350 30.769 11.50 1.00 45.35 3.91
5227 7571 6.091169 CACTTGTCACATCAAAAGTTTTTGCT 59.909 34.615 11.50 0.83 45.35 3.91
5228 7572 6.128580 ACACTTGTCACATCAAAAGTTTTTGC 60.129 34.615 11.50 0.00 45.35 3.68
5229 7573 7.350110 ACACTTGTCACATCAAAAGTTTTTG 57.650 32.000 10.35 10.35 46.70 2.44
5230 7574 8.303876 ACTACACTTGTCACATCAAAAGTTTTT 58.696 29.630 0.00 0.00 30.59 1.94
5231 7575 7.754924 CACTACACTTGTCACATCAAAAGTTTT 59.245 33.333 0.00 0.00 30.59 2.43
5232 7576 7.120579 TCACTACACTTGTCACATCAAAAGTTT 59.879 33.333 0.00 0.00 30.59 2.66
5233 7577 6.597672 TCACTACACTTGTCACATCAAAAGTT 59.402 34.615 0.00 0.00 30.59 2.66
5234 7578 6.037172 GTCACTACACTTGTCACATCAAAAGT 59.963 38.462 0.00 0.00 33.20 2.66
5235 7579 6.422223 GTCACTACACTTGTCACATCAAAAG 58.578 40.000 0.00 0.00 0.00 2.27
5236 7580 5.295787 GGTCACTACACTTGTCACATCAAAA 59.704 40.000 0.00 0.00 0.00 2.44
5237 7581 4.814234 GGTCACTACACTTGTCACATCAAA 59.186 41.667 0.00 0.00 0.00 2.69
5238 7582 4.377021 GGTCACTACACTTGTCACATCAA 58.623 43.478 0.00 0.00 0.00 2.57
5239 7583 3.244078 GGGTCACTACACTTGTCACATCA 60.244 47.826 0.00 0.00 0.00 3.07
5240 7584 3.006967 AGGGTCACTACACTTGTCACATC 59.993 47.826 0.00 0.00 35.04 3.06
5241 7585 2.972713 AGGGTCACTACACTTGTCACAT 59.027 45.455 0.00 0.00 35.04 3.21
5242 7586 2.394632 AGGGTCACTACACTTGTCACA 58.605 47.619 0.00 0.00 35.04 3.58


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

AutoCloner maintained by Alex Coulton.