Multiple sequence alignment - TraesCS1D01G430600

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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 TraesCS1D01G430600 chr1D 100.000 7962 0 0 1 7962 481412998 481420959 0.000000e+00 14704.0
1 TraesCS1D01G430600 chr1D 100.000 907 0 0 1 907 150066722 150065816 0.000000e+00 1676.0
2 TraesCS1D01G430600 chr1D 100.000 907 0 0 1 907 481265947 481265041 0.000000e+00 1676.0
3 TraesCS1D01G430600 chr1D 99.669 907 3 0 1 907 62993949 62994855 0.000000e+00 1659.0
4 TraesCS1D01G430600 chr1A 96.334 6547 178 31 909 7440 577921155 577927654 0.000000e+00 10704.0
5 TraesCS1D01G430600 chr1A 86.172 499 34 13 7473 7957 577927764 577928241 2.560000e-139 507.0
6 TraesCS1D01G430600 chr1B 97.285 5673 105 15 911 6575 669896444 669902075 0.000000e+00 9577.0
7 TraesCS1D01G430600 chr1B 89.720 642 34 20 6812 7440 669902074 669902696 0.000000e+00 791.0
8 TraesCS1D01G430600 chr1B 84.156 486 42 17 7490 7957 669902788 669903256 9.490000e-119 438.0
9 TraesCS1D01G430600 chr1B 88.060 67 8 0 6843 6909 669907206 669907272 6.620000e-11 80.5
10 TraesCS1D01G430600 chr2B 95.044 1251 32 9 909 2149 335374696 335375926 0.000000e+00 1940.0
11 TraesCS1D01G430600 chr2B 96.218 238 7 2 1223 1459 657784819 657784583 9.690000e-104 388.0
12 TraesCS1D01G430600 chr2B 97.468 79 2 0 1444 1522 657783095 657783017 1.390000e-27 135.0
13 TraesCS1D01G430600 chr6D 99.669 907 3 0 1 907 129198054 129197148 0.000000e+00 1659.0
14 TraesCS1D01G430600 chr6D 90.909 154 14 0 5865 6018 413800362 413800209 2.910000e-49 207.0
15 TraesCS1D01G430600 chr6D 100.000 28 0 0 4873 4900 413800387 413800360 1.400000e-02 52.8
16 TraesCS1D01G430600 chr3D 99.669 907 3 0 1 907 373900143 373899237 0.000000e+00 1659.0
17 TraesCS1D01G430600 chr2D 99.669 907 3 0 1 907 35222024 35222930 0.000000e+00 1659.0
18 TraesCS1D01G430600 chr2D 99.669 907 3 0 1 907 224638484 224639390 0.000000e+00 1659.0
19 TraesCS1D01G430600 chr2D 99.669 907 3 0 1 907 535125550 535124644 0.000000e+00 1659.0
20 TraesCS1D01G430600 chr5D 99.560 909 2 1 1 907 520925104 520924196 0.000000e+00 1655.0


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 TraesCS1D01G430600 chr1D 481412998 481420959 7961 False 14704.000 14704 100.00000 1 7962 1 chr1D.!!$F2 7961
1 TraesCS1D01G430600 chr1D 150065816 150066722 906 True 1676.000 1676 100.00000 1 907 1 chr1D.!!$R1 906
2 TraesCS1D01G430600 chr1D 481265041 481265947 906 True 1676.000 1676 100.00000 1 907 1 chr1D.!!$R2 906
3 TraesCS1D01G430600 chr1D 62993949 62994855 906 False 1659.000 1659 99.66900 1 907 1 chr1D.!!$F1 906
4 TraesCS1D01G430600 chr1A 577921155 577928241 7086 False 5605.500 10704 91.25300 909 7957 2 chr1A.!!$F1 7048
5 TraesCS1D01G430600 chr1B 669896444 669907272 10828 False 2721.625 9577 89.80525 911 7957 4 chr1B.!!$F1 7046
6 TraesCS1D01G430600 chr2B 335374696 335375926 1230 False 1940.000 1940 95.04400 909 2149 1 chr2B.!!$F1 1240
7 TraesCS1D01G430600 chr2B 657783017 657784819 1802 True 261.500 388 96.84300 1223 1522 2 chr2B.!!$R1 299
8 TraesCS1D01G430600 chr6D 129197148 129198054 906 True 1659.000 1659 99.66900 1 907 1 chr6D.!!$R1 906
9 TraesCS1D01G430600 chr3D 373899237 373900143 906 True 1659.000 1659 99.66900 1 907 1 chr3D.!!$R1 906
10 TraesCS1D01G430600 chr2D 35222024 35222930 906 False 1659.000 1659 99.66900 1 907 1 chr2D.!!$F1 906
11 TraesCS1D01G430600 chr2D 224638484 224639390 906 False 1659.000 1659 99.66900 1 907 1 chr2D.!!$F2 906
12 TraesCS1D01G430600 chr2D 535124644 535125550 906 True 1659.000 1659 99.66900 1 907 1 chr2D.!!$R1 906
13 TraesCS1D01G430600 chr5D 520924196 520925104 908 True 1655.000 1655 99.56000 1 907 1 chr5D.!!$R1 906

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
925 928 3.704800 AAAAGACTGGACTTAGCTCCC 57.295 47.619 0.00 0.0 0.00 4.30 F
1630 3147 1.191535 CACCTGATAAGGACGGACCA 58.808 55.000 1.89 0.0 42.04 4.02 F
1793 3310 4.698201 TCAGAACATTGGGTGTCTTACA 57.302 40.909 0.00 0.0 41.14 2.41 F
3060 4582 3.349927 GGTATTTCTGTACACCCCCAAC 58.650 50.000 0.00 0.0 0.00 3.77 F
4074 5596 3.740832 TGTTTGCTGTGTATTCTGTCTCG 59.259 43.478 0.00 0.0 0.00 4.04 F
5183 6712 4.451096 TCCGAGACAAACTTTAAGTGCATC 59.549 41.667 0.00 0.0 0.00 3.91 F
6567 8101 1.202359 GCACACACATTTCCGGTTGTT 60.202 47.619 0.00 0.0 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2071 3592 1.680735 GTGTTCATCAAGGTGCCAACA 59.319 47.619 0.00 0.00 0.00 3.33 R
3060 4582 0.737219 GCAGCTATCTTGCCACAAGG 59.263 55.000 7.44 0.00 38.23 3.61 R
3581 5103 3.424703 ACCAGACATTTCAAGTGGATGG 58.575 45.455 4.63 4.63 34.40 3.51 R
4155 5677 3.544684 CATTGTATCTGCTGTGGGCTTA 58.455 45.455 0.00 0.00 42.39 3.09 R
5211 6740 1.662629 CCATCAACAGCAGCGAAGTAG 59.337 52.381 0.00 0.00 0.00 2.57 R
6850 8385 0.454620 CGAGTTCGAACGCTAGCTGT 60.455 55.000 25.97 9.71 43.02 4.40 R
7773 9411 0.247736 TGCGCCTTCTTCTTCTCCTC 59.752 55.000 4.18 0.00 0.00 3.71 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
925 928 3.704800 AAAAGACTGGACTTAGCTCCC 57.295 47.619 0.00 0.00 0.00 4.30
950 953 7.206687 CAGTAGGTTGTTTGCTTCCATTTTAA 58.793 34.615 0.00 0.00 0.00 1.52
990 1001 5.324409 TCAGGGCATCAGAAATTTTACTGT 58.676 37.500 6.74 0.00 35.84 3.55
995 1006 5.402398 GCATCAGAAATTTTACTGTGACCC 58.598 41.667 6.74 0.00 35.84 4.46
1027 1038 6.984740 TTCAAGTTTGCGATGAAATTGTAC 57.015 33.333 0.00 0.00 30.60 2.90
1039 1050 7.438459 GCGATGAAATTGTACAAGGTAGAGTAT 59.562 37.037 14.65 0.88 0.00 2.12
1040 1051 9.961265 CGATGAAATTGTACAAGGTAGAGTATA 57.039 33.333 14.65 0.00 0.00 1.47
1061 1072 3.637911 TTATTGGCCGATGGTTGTAGT 57.362 42.857 16.45 0.00 0.00 2.73
1081 1092 7.833786 TGTAGTCGGATTATACCATGGAATAC 58.166 38.462 21.47 7.81 0.00 1.89
1082 1093 6.928348 AGTCGGATTATACCATGGAATACA 57.072 37.500 21.47 0.00 0.00 2.29
1083 1094 7.496346 AGTCGGATTATACCATGGAATACAT 57.504 36.000 21.47 3.22 41.57 2.29
1168 1180 7.789273 TTGAAATATGGCCAGCAATTTTATG 57.211 32.000 13.05 0.00 0.00 1.90
1178 1190 5.578336 GCCAGCAATTTTATGAAGTCTTTCC 59.422 40.000 0.00 0.00 32.09 3.13
1193 1205 3.796717 GTCTTTCCGAAAGTTGCCAAAAG 59.203 43.478 18.32 0.00 39.52 2.27
1217 1229 6.500049 AGAGAAAGGCTATACATATCAAGGCT 59.500 38.462 0.00 0.00 45.75 4.58
1244 1257 9.369904 GATTTATATTGCAGTCACACCATTTTT 57.630 29.630 0.00 0.00 0.00 1.94
1609 3126 4.715297 ACAGATCTTTGGTACTCCCGTATT 59.285 41.667 0.00 0.00 35.15 1.89
1630 3147 1.191535 CACCTGATAAGGACGGACCA 58.808 55.000 1.89 0.00 42.04 4.02
1793 3310 4.698201 TCAGAACATTGGGTGTCTTACA 57.302 40.909 0.00 0.00 41.14 2.41
2071 3592 8.302438 GCTTAGCTGCAAAATATCCAAGATAAT 58.698 33.333 1.02 0.00 0.00 1.28
2973 4495 7.182060 ACCAAAAGCCCTTAATTCTTCTATGA 58.818 34.615 0.00 0.00 0.00 2.15
3060 4582 3.349927 GGTATTTCTGTACACCCCCAAC 58.650 50.000 0.00 0.00 0.00 3.77
3770 5292 5.922739 TTGGCATACTAAATACATCAGCG 57.077 39.130 0.00 0.00 0.00 5.18
4074 5596 3.740832 TGTTTGCTGTGTATTCTGTCTCG 59.259 43.478 0.00 0.00 0.00 4.04
4155 5677 9.624373 ATTTTCTCACTTGATTATGTCAGCTAT 57.376 29.630 0.00 0.00 38.29 2.97
4864 6391 6.231211 TGAAGTCTGGGATTTTCTAAGTGTC 58.769 40.000 0.00 0.00 0.00 3.67
5183 6712 4.451096 TCCGAGACAAACTTTAAGTGCATC 59.549 41.667 0.00 0.00 0.00 3.91
5482 7011 6.053005 TCTGGTTGTTTCTACAAATTCTCGT 58.947 36.000 0.00 0.00 45.33 4.18
5763 7293 4.286297 TGAACCCGTTTGATCTTGATCT 57.714 40.909 11.31 0.00 0.00 2.75
5841 7371 4.891756 GGAATGGGAGACACATTTGATGAT 59.108 41.667 0.82 0.00 38.57 2.45
6018 7548 8.574737 GCAATTAGCCAATTAGATGAATTCTCT 58.425 33.333 7.05 9.37 35.45 3.10
6069 7599 4.103153 CCCTGATTAAGGCTGTATCTTCCA 59.897 45.833 9.63 0.00 45.89 3.53
6125 7655 5.246656 TGGAATTTTCATGACAAAGCATCCT 59.753 36.000 19.16 0.00 0.00 3.24
6438 7972 1.202582 CTAGTGAGTCTGGTTGGTCGG 59.797 57.143 0.00 0.00 0.00 4.79
6551 8085 3.253921 CCATTTCATCAACAGTCTGCACA 59.746 43.478 0.00 0.00 0.00 4.57
6558 8092 3.016031 TCAACAGTCTGCACACACATTT 58.984 40.909 0.00 0.00 0.00 2.32
6567 8101 1.202359 GCACACACATTTCCGGTTGTT 60.202 47.619 0.00 0.00 0.00 2.83
6601 8135 5.063880 TGAAAGCTCCTAGTTTTCTCCAAC 58.936 41.667 14.58 0.00 43.17 3.77
6632 8166 9.112725 CACTCTTGAAACATCACCATTATATCA 57.887 33.333 0.00 0.00 0.00 2.15
6633 8167 9.857656 ACTCTTGAAACATCACCATTATATCAT 57.142 29.630 0.00 0.00 0.00 2.45
6661 8195 7.758076 GTCATCTTCATCTCATTTTTGCATTCA 59.242 33.333 0.00 0.00 0.00 2.57
6739 8274 7.577616 CGGAAGATCATACTGGTCATTATGCTA 60.578 40.741 0.00 0.00 27.47 3.49
6810 8345 9.736414 CAATGGAATGATCCTTAGACTGATATT 57.264 33.333 0.00 0.00 46.70 1.28
6850 8385 0.106419 AGTCCCCGGTTTGCTTGAAA 60.106 50.000 0.00 0.00 0.00 2.69
6953 8488 2.867855 AAGCACGAGTTCTCCGCCA 61.868 57.895 0.00 0.00 0.00 5.69
6979 8514 2.139917 TGATTCTTTCGGACGGTTGTG 58.860 47.619 0.00 0.00 0.00 3.33
6981 8516 1.574134 TTCTTTCGGACGGTTGTGTC 58.426 50.000 0.00 0.00 38.17 3.67
6984 8519 1.260561 CTTTCGGACGGTTGTGTCTTG 59.739 52.381 0.00 0.00 38.91 3.02
7125 8661 0.544223 TGCCATACAGTATGCCGGTT 59.456 50.000 14.41 0.00 42.53 4.44
7223 8762 4.688770 TTTTTGGTTCCGCCCTGT 57.311 50.000 0.00 0.00 36.04 4.00
7254 8793 1.070443 TGCTAGCGTGCGTTTGTAAAC 60.070 47.619 10.77 0.00 35.36 2.01
7321 8862 8.862325 TGATGATGATGATGATGAATGAATGA 57.138 30.769 0.00 0.00 0.00 2.57
7325 8866 9.295825 TGATGATGATGATGAATGAATGAATGA 57.704 29.630 0.00 0.00 0.00 2.57
7328 8869 9.912634 TGATGATGATGAATGAATGAATGAATG 57.087 29.630 0.00 0.00 0.00 2.67
7353 8894 1.747355 GAGTCGATCGGTTCCTGGTTA 59.253 52.381 16.41 0.00 0.00 2.85
7354 8895 1.749634 AGTCGATCGGTTCCTGGTTAG 59.250 52.381 16.41 0.00 0.00 2.34
7355 8896 0.458669 TCGATCGGTTCCTGGTTAGC 59.541 55.000 16.41 0.00 0.00 3.09
7357 8898 1.404986 CGATCGGTTCCTGGTTAGCAA 60.405 52.381 7.38 0.00 0.00 3.91
7398 8943 7.440255 TCTGTGTGATAAGATGCTTCATGTATG 59.560 37.037 2.07 0.00 0.00 2.39
7399 8944 7.274447 TGTGTGATAAGATGCTTCATGTATGA 58.726 34.615 2.07 0.00 34.44 2.15
7400 8945 7.440255 TGTGTGATAAGATGCTTCATGTATGAG 59.560 37.037 2.07 0.00 38.19 2.90
7401 8946 6.932960 TGTGATAAGATGCTTCATGTATGAGG 59.067 38.462 2.07 0.09 38.19 3.86
7402 8947 7.157347 GTGATAAGATGCTTCATGTATGAGGA 58.843 38.462 8.02 0.00 38.19 3.71
7412 8957 3.748568 TCATGTATGAGGAGTCGATCGAG 59.251 47.826 20.09 1.70 32.11 4.04
7415 8960 0.816018 ATGAGGAGTCGATCGAGCGT 60.816 55.000 23.61 14.92 0.00 5.07
7432 8977 3.517602 AGCGTGTCGTTGCTGAATATTA 58.482 40.909 0.00 0.00 40.62 0.98
7436 8981 5.401376 GCGTGTCGTTGCTGAATATTATAGA 59.599 40.000 3.94 0.00 0.00 1.98
7470 9064 2.949447 ACTCCAGTTTTGGCAGTTGAT 58.051 42.857 0.00 0.00 44.63 2.57
7505 9129 1.334054 CAGTACGCGTCTGTTGGTAC 58.666 55.000 18.63 5.56 36.40 3.34
7573 9197 3.842923 CGGGCGGTGCATCTCTCT 61.843 66.667 0.00 0.00 0.00 3.10
7578 9202 1.342819 GGCGGTGCATCTCTCTAATCT 59.657 52.381 0.00 0.00 0.00 2.40
7579 9203 2.558795 GGCGGTGCATCTCTCTAATCTA 59.441 50.000 0.00 0.00 0.00 1.98
7580 9204 3.570559 GCGGTGCATCTCTCTAATCTAC 58.429 50.000 0.00 0.00 0.00 2.59
7581 9205 3.254657 GCGGTGCATCTCTCTAATCTACT 59.745 47.826 0.00 0.00 0.00 2.57
7776 9414 2.202932 CCATGGCGAAGACGGAGG 60.203 66.667 0.00 0.00 41.59 4.30
7777 9415 2.721167 CCATGGCGAAGACGGAGGA 61.721 63.158 0.00 0.00 41.59 3.71
7780 9418 0.970937 ATGGCGAAGACGGAGGAGAA 60.971 55.000 0.00 0.00 41.59 2.87
7787 9425 3.426963 CGAAGACGGAGGAGAAGAAGAAG 60.427 52.174 0.00 0.00 35.72 2.85
7788 9426 2.452505 AGACGGAGGAGAAGAAGAAGG 58.547 52.381 0.00 0.00 0.00 3.46
7789 9427 0.899019 ACGGAGGAGAAGAAGAAGGC 59.101 55.000 0.00 0.00 0.00 4.35
7790 9428 0.179124 CGGAGGAGAAGAAGAAGGCG 60.179 60.000 0.00 0.00 0.00 5.52
7791 9429 0.461163 GGAGGAGAAGAAGAAGGCGC 60.461 60.000 0.00 0.00 0.00 6.53
7792 9430 0.247736 GAGGAGAAGAAGAAGGCGCA 59.752 55.000 10.83 0.00 0.00 6.09
7793 9431 0.248843 AGGAGAAGAAGAAGGCGCAG 59.751 55.000 10.83 0.00 0.00 5.18
7794 9432 0.742635 GGAGAAGAAGAAGGCGCAGG 60.743 60.000 10.83 0.00 0.00 4.85
7957 9612 1.077644 TCCTCGAGACCCTTCTCCG 60.078 63.158 15.71 0.00 45.06 4.63
7959 9614 3.114647 CTCGAGACCCTTCTCCGCG 62.115 68.421 6.58 0.00 45.06 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
907 910 2.183679 CTGGGAGCTAAGTCCAGTCTT 58.816 52.381 13.59 0.00 42.17 3.01
925 928 4.853924 AATGGAAGCAAACAACCTACTG 57.146 40.909 0.00 0.00 0.00 2.74
990 1001 2.278245 ACTTGAATCATCCTGGGGTCA 58.722 47.619 0.00 0.00 0.00 4.02
995 1006 2.749076 TCGCAAACTTGAATCATCCTGG 59.251 45.455 0.00 0.00 0.00 4.45
1027 1038 6.931838 TCGGCCAATAATATACTCTACCTTG 58.068 40.000 2.24 0.00 0.00 3.61
1039 1050 5.298989 ACTACAACCATCGGCCAATAATA 57.701 39.130 2.24 0.00 0.00 0.98
1040 1051 4.134563 GACTACAACCATCGGCCAATAAT 58.865 43.478 2.24 0.00 0.00 1.28
1041 1052 3.537580 GACTACAACCATCGGCCAATAA 58.462 45.455 2.24 0.00 0.00 1.40
1046 1057 4.104143 CGACTACAACCATCGGCC 57.896 61.111 0.00 0.00 32.22 6.13
1061 1072 7.489239 TGATGTATTCCATGGTATAATCCGA 57.511 36.000 12.58 1.92 32.56 4.55
1081 1092 6.536582 CCTTGTCTTTAGACTACACCATGATG 59.463 42.308 10.92 0.00 44.99 3.07
1082 1093 6.213600 ACCTTGTCTTTAGACTACACCATGAT 59.786 38.462 10.92 0.00 44.99 2.45
1083 1094 5.542635 ACCTTGTCTTTAGACTACACCATGA 59.457 40.000 10.92 0.00 44.99 3.07
1168 1180 2.616842 TGGCAACTTTCGGAAAGACTTC 59.383 45.455 31.26 18.99 41.02 3.01
1178 1190 4.044426 CCTTTCTCTTTTGGCAACTTTCG 58.956 43.478 0.00 0.00 37.61 3.46
1193 1205 6.593382 CAGCCTTGATATGTATAGCCTTTCTC 59.407 42.308 0.00 0.00 0.00 2.87
1217 1229 7.643569 AATGGTGTGACTGCAATATAAATCA 57.356 32.000 0.00 0.00 0.00 2.57
1609 3126 2.291735 TGGTCCGTCCTTATCAGGTGTA 60.292 50.000 0.00 0.00 41.69 2.90
1630 3147 6.798427 TTAACTATGCTGATGAGTTCCTCT 57.202 37.500 0.00 0.00 35.17 3.69
1793 3310 7.127339 TCCCTGCATAAGGTAGATAAAGTCTTT 59.873 37.037 2.81 2.81 45.78 2.52
2071 3592 1.680735 GTGTTCATCAAGGTGCCAACA 59.319 47.619 0.00 0.00 0.00 3.33
2973 4495 6.185511 ACTCAAGTGGATGTGAATCATTGAT 58.814 36.000 0.00 0.00 36.83 2.57
3060 4582 0.737219 GCAGCTATCTTGCCACAAGG 59.263 55.000 7.44 0.00 38.23 3.61
3581 5103 3.424703 ACCAGACATTTCAAGTGGATGG 58.575 45.455 4.63 4.63 34.40 3.51
3770 5292 3.561725 GTCCATCCGTCCTTGAATCATTC 59.438 47.826 0.00 0.00 0.00 2.67
4074 5596 6.113411 ACTATTACTGTTGGCATCAGTTACC 58.887 40.000 29.98 0.00 42.50 2.85
4155 5677 3.544684 CATTGTATCTGCTGTGGGCTTA 58.455 45.455 0.00 0.00 42.39 3.09
4787 6314 6.758886 AGAAGATTCTGTAGAATTAACAGGCG 59.241 38.462 16.46 0.00 44.14 5.52
4864 6391 6.961359 TTTAATACACTGACCTGTGAATCG 57.039 37.500 12.85 0.00 40.12 3.34
5211 6740 1.662629 CCATCAACAGCAGCGAAGTAG 59.337 52.381 0.00 0.00 0.00 2.57
5482 7011 7.414873 GCTTGAGCAGACATAAAGAATTGATGA 60.415 37.037 0.00 0.00 41.59 2.92
5755 7285 6.695278 CGCCTACAAAAACAAAAAGATCAAGA 59.305 34.615 0.00 0.00 0.00 3.02
5763 7293 4.327627 GCTTGACGCCTACAAAAACAAAAA 59.672 37.500 0.00 0.00 0.00 1.94
5841 7371 3.960102 ACTGGATTTTCTCAACAAGCCAA 59.040 39.130 0.00 0.00 37.98 4.52
6018 7548 5.559991 CGATCACGAACCAAGATTTGACAAA 60.560 40.000 2.48 2.48 42.66 2.83
6125 7655 1.597742 GAGCAGCTGGTTTTCTGTCA 58.402 50.000 21.18 0.00 33.09 3.58
6438 7972 3.851098 AGCACATCTTTCGTACTCCTTC 58.149 45.455 0.00 0.00 0.00 3.46
6551 8085 3.634910 AGCTAAAACAACCGGAAATGTGT 59.365 39.130 9.46 2.08 0.00 3.72
6558 8092 2.843401 TGCTAGCTAAAACAACCGGA 57.157 45.000 17.23 0.00 0.00 5.14
6601 8135 3.058914 GGTGATGTTTCAAGAGTGTTCCG 60.059 47.826 0.00 0.00 32.48 4.30
6632 8166 8.515695 TGCAAAAATGAGATGAAGATGACTAT 57.484 30.769 0.00 0.00 0.00 2.12
6633 8167 7.926674 TGCAAAAATGAGATGAAGATGACTA 57.073 32.000 0.00 0.00 0.00 2.59
6810 8345 4.142138 ACTGCACGGGAAACAAATTGTTAA 60.142 37.500 12.11 0.00 40.14 2.01
6850 8385 0.454620 CGAGTTCGAACGCTAGCTGT 60.455 55.000 25.97 9.71 43.02 4.40
6953 8488 2.418746 CCGTCCGAAAGAATCAGTCCAT 60.419 50.000 0.00 0.00 0.00 3.41
6979 8514 2.408704 CGAAACAGATCGACACCAAGAC 59.591 50.000 0.00 0.00 45.48 3.01
6981 8516 1.126846 GCGAAACAGATCGACACCAAG 59.873 52.381 0.24 0.00 45.48 3.61
6984 8519 0.716108 CAGCGAAACAGATCGACACC 59.284 55.000 0.24 0.00 45.48 4.16
7233 8772 0.509499 TTACAAACGCACGCTAGCAC 59.491 50.000 16.45 2.22 0.00 4.40
7254 8793 2.902846 TGTGACCAAAACGGCCGG 60.903 61.111 31.76 13.93 39.03 6.13
7321 8862 4.060900 CCGATCGACTCCATTCATTCATT 58.939 43.478 18.66 0.00 0.00 2.57
7323 8864 2.430694 ACCGATCGACTCCATTCATTCA 59.569 45.455 18.66 0.00 0.00 2.57
7324 8865 3.099267 ACCGATCGACTCCATTCATTC 57.901 47.619 18.66 0.00 0.00 2.67
7325 8866 3.458189 GAACCGATCGACTCCATTCATT 58.542 45.455 18.66 0.00 0.00 2.57
7326 8867 2.224066 GGAACCGATCGACTCCATTCAT 60.224 50.000 23.03 0.00 0.00 2.57
7327 8868 1.136305 GGAACCGATCGACTCCATTCA 59.864 52.381 23.03 0.00 0.00 2.57
7328 8869 1.409427 AGGAACCGATCGACTCCATTC 59.591 52.381 27.08 16.03 0.00 2.67
7329 8870 1.137086 CAGGAACCGATCGACTCCATT 59.863 52.381 27.08 12.39 0.00 3.16
7330 8871 0.747255 CAGGAACCGATCGACTCCAT 59.253 55.000 27.08 15.19 0.00 3.41
7331 8872 1.320344 CCAGGAACCGATCGACTCCA 61.320 60.000 27.08 0.00 0.00 3.86
7353 8894 2.366266 AGATGTTGGCATTGTTGTTGCT 59.634 40.909 0.00 0.00 40.03 3.91
7354 8895 2.477375 CAGATGTTGGCATTGTTGTTGC 59.523 45.455 0.00 0.00 39.41 4.17
7355 8896 3.491639 CACAGATGTTGGCATTGTTGTTG 59.508 43.478 0.00 0.00 35.07 3.33
7357 8898 2.694628 ACACAGATGTTGGCATTGTTGT 59.305 40.909 0.00 0.00 34.46 3.32
7398 8943 1.010574 CACGCTCGATCGACTCCTC 60.011 63.158 15.15 0.42 0.00 3.71
7399 8944 1.707239 GACACGCTCGATCGACTCCT 61.707 60.000 15.15 0.00 0.00 3.69
7400 8945 1.297745 GACACGCTCGATCGACTCC 60.298 63.158 15.15 4.69 0.00 3.85
7401 8946 1.648756 CGACACGCTCGATCGACTC 60.649 63.158 15.15 8.10 46.14 3.36
7402 8947 1.909141 AACGACACGCTCGATCGACT 61.909 55.000 15.15 0.00 46.14 4.18
7412 8957 2.806288 AATATTCAGCAACGACACGC 57.194 45.000 0.00 0.00 0.00 5.34
7432 8977 8.152023 ACTGGAGTTGATAGTCCTTTTTCTAT 57.848 34.615 0.00 0.00 43.29 1.98
7436 8981 7.201911 CCAAAACTGGAGTTGATAGTCCTTTTT 60.202 37.037 0.00 0.00 43.29 1.94
7447 9040 2.426738 CAACTGCCAAAACTGGAGTTGA 59.573 45.455 16.49 0.00 42.66 3.18
7470 9064 3.813443 GTACTGGTGGAGGTACGATCTA 58.187 50.000 0.00 0.00 30.85 1.98
7493 9117 4.929211 TCAATCTGATTGTACCAACAGACG 59.071 41.667 25.08 4.65 41.16 4.18
7505 9129 6.074623 CGATTCGGTTACTCTCAATCTGATTG 60.075 42.308 21.51 21.51 41.57 2.67
7515 9139 6.478344 TCTTCTACTACGATTCGGTTACTCTC 59.522 42.308 11.29 0.00 0.00 3.20
7578 9202 9.922477 ATCGGATGGATAGATCATACTTAAGTA 57.078 33.333 17.41 17.41 32.17 2.24
7579 9203 8.830915 ATCGGATGGATAGATCATACTTAAGT 57.169 34.615 13.68 13.68 32.17 2.24
7580 9204 8.356657 GGATCGGATGGATAGATCATACTTAAG 58.643 40.741 0.00 0.00 41.71 1.85
7581 9205 7.839200 TGGATCGGATGGATAGATCATACTTAA 59.161 37.037 0.00 0.00 41.71 1.85
7773 9411 0.247736 TGCGCCTTCTTCTTCTCCTC 59.752 55.000 4.18 0.00 0.00 3.71
7774 9412 0.248843 CTGCGCCTTCTTCTTCTCCT 59.751 55.000 4.18 0.00 0.00 3.69
7776 9414 1.365368 GCCTGCGCCTTCTTCTTCTC 61.365 60.000 4.18 0.00 0.00 2.87
7777 9415 1.376553 GCCTGCGCCTTCTTCTTCT 60.377 57.895 4.18 0.00 0.00 2.85
7780 9418 2.046507 CTGCCTGCGCCTTCTTCT 60.047 61.111 4.18 0.00 0.00 2.85
7791 9429 4.498520 ATCGTCGGTCGCTGCCTG 62.499 66.667 0.00 0.00 39.67 4.85
7792 9430 4.498520 CATCGTCGGTCGCTGCCT 62.499 66.667 0.00 0.00 39.67 4.75
7794 9432 4.796231 ACCATCGTCGGTCGCTGC 62.796 66.667 0.00 0.00 39.67 5.25
7795 9433 2.880879 CACCATCGTCGGTCGCTG 60.881 66.667 0.00 0.00 37.07 5.18


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

AutoCloner maintained by Alex Coulton.