Multiple sequence alignment - TraesCS3B01G210100

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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 TraesCS3B01G210100 chr3B 100.000 5264 0 0 1 5264 246153567 246148304 0.000000e+00 9721.0
1 TraesCS3B01G210100 chr3A 95.182 5189 170 24 113 5262 208241965 208236818 0.000000e+00 8124.0
2 TraesCS3B01G210100 chr3A 100.000 34 0 0 1 34 208241996 208241963 4.400000e-06 63.9
3 TraesCS3B01G210100 chr3D 95.735 4314 131 13 960 5264 170674917 170670648 0.000000e+00 6898.0
4 TraesCS3B01G210100 chr3D 94.360 922 17 10 1 890 170676149 170675231 0.000000e+00 1382.0
5 TraesCS3B01G210100 chr6A 91.148 418 20 8 152 566 61705646 61706049 7.700000e-153 551.0


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 TraesCS3B01G210100 chr3B 246148304 246153567 5263 True 9721.00 9721 100.0000 1 5264 1 chr3B.!!$R1 5263
1 TraesCS3B01G210100 chr3A 208236818 208241996 5178 True 4093.95 8124 97.5910 1 5262 2 chr3A.!!$R1 5261
2 TraesCS3B01G210100 chr3D 170670648 170676149 5501 True 4140.00 6898 95.0475 1 5264 2 chr3D.!!$R1 5263

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
860 962 0.038744 GATCTGGTATGGGCCCCATG 59.961 60.000 26.08 8.57 44.84 3.66 F
1378 1741 0.033601 AGAGGATCACGGAGCTGTCT 60.034 55.000 0.00 0.00 37.82 3.41 F
2322 2685 0.238289 GTGGGATTGCACTTGACGTG 59.762 55.000 0.00 0.00 46.58 4.49 F
2488 2851 1.546029 GGGATTTTGACAGGGCAGTTC 59.454 52.381 0.00 0.00 0.00 3.01 F
3138 3501 2.951642 CAAGGAAGCTGAACAAAGTGGA 59.048 45.455 0.00 0.00 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2373 2736 0.108945 GAAACAAGCTGCAGGCATCC 60.109 55.000 17.12 0.0 44.79 3.51 R
2545 2908 1.561076 ACATAGTGCTCCAATCAGGCA 59.439 47.619 0.00 0.0 37.29 4.75 R
3694 4057 1.354031 TGCATAGAGCCCTTTGACCAA 59.646 47.619 0.00 0.0 44.83 3.67 R
4066 4429 1.911357 TCTCTCTGTCATGGGTTGCAT 59.089 47.619 0.00 0.0 0.00 3.96 R
4994 5363 0.953960 GTTGTGGCTAACCTCACCCG 60.954 60.000 0.00 0.0 39.13 5.28 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
34 115 8.657712 AGTAACTCTGTCTAACCAAATTACCTT 58.342 33.333 0.00 0.00 0.00 3.50
35 116 9.281371 GTAACTCTGTCTAACCAAATTACCTTT 57.719 33.333 0.00 0.00 0.00 3.11
37 118 9.856162 AACTCTGTCTAACCAAATTACCTTTAA 57.144 29.630 0.00 0.00 0.00 1.52
38 119 9.856162 ACTCTGTCTAACCAAATTACCTTTAAA 57.144 29.630 0.00 0.00 0.00 1.52
40 121 9.856162 TCTGTCTAACCAAATTACCTTTAAAGT 57.144 29.630 14.03 5.22 0.00 2.66
42 123 9.070179 TGTCTAACCAAATTACCTTTAAAGTCC 57.930 33.333 14.03 0.00 0.00 3.85
43 124 9.070179 GTCTAACCAAATTACCTTTAAAGTCCA 57.930 33.333 14.03 0.00 0.00 4.02
44 125 9.643735 TCTAACCAAATTACCTTTAAAGTCCAA 57.356 29.630 14.03 5.36 0.00 3.53
46 127 8.951787 AACCAAATTACCTTTAAAGTCCAAAC 57.048 30.769 14.03 0.00 0.00 2.93
47 128 8.080363 ACCAAATTACCTTTAAAGTCCAAACA 57.920 30.769 14.03 0.00 0.00 2.83
48 129 8.710239 ACCAAATTACCTTTAAAGTCCAAACAT 58.290 29.630 14.03 0.00 0.00 2.71
49 130 8.987890 CCAAATTACCTTTAAAGTCCAAACATG 58.012 33.333 14.03 0.00 0.00 3.21
50 131 9.757227 CAAATTACCTTTAAAGTCCAAACATGA 57.243 29.630 14.03 0.00 0.00 3.07
53 134 6.590234 ACCTTTAAAGTCCAAACATGATCC 57.410 37.500 14.03 0.00 0.00 3.36
54 135 5.183140 ACCTTTAAAGTCCAAACATGATCCG 59.817 40.000 14.03 0.00 0.00 4.18
55 136 4.695217 TTAAAGTCCAAACATGATCCGC 57.305 40.909 0.00 0.00 0.00 5.54
56 137 1.086696 AAGTCCAAACATGATCCGCG 58.913 50.000 0.00 0.00 0.00 6.46
57 138 0.249120 AGTCCAAACATGATCCGCGA 59.751 50.000 8.23 0.00 0.00 5.87
58 139 1.083489 GTCCAAACATGATCCGCGAA 58.917 50.000 8.23 0.00 0.00 4.70
59 140 1.466950 GTCCAAACATGATCCGCGAAA 59.533 47.619 8.23 0.00 0.00 3.46
60 141 2.095466 GTCCAAACATGATCCGCGAAAA 60.095 45.455 8.23 0.00 0.00 2.29
61 142 2.554462 TCCAAACATGATCCGCGAAAAA 59.446 40.909 8.23 0.00 0.00 1.94
62 143 3.192422 TCCAAACATGATCCGCGAAAAAT 59.808 39.130 8.23 0.00 0.00 1.82
63 144 4.396478 TCCAAACATGATCCGCGAAAAATA 59.604 37.500 8.23 0.00 0.00 1.40
64 145 4.734854 CCAAACATGATCCGCGAAAAATAG 59.265 41.667 8.23 0.00 0.00 1.73
65 146 3.609103 ACATGATCCGCGAAAAATAGC 57.391 42.857 8.23 0.00 0.00 2.97
66 147 3.206150 ACATGATCCGCGAAAAATAGCT 58.794 40.909 8.23 0.00 0.00 3.32
67 148 4.377021 ACATGATCCGCGAAAAATAGCTA 58.623 39.130 8.23 0.00 0.00 3.32
68 149 4.997395 ACATGATCCGCGAAAAATAGCTAT 59.003 37.500 8.23 0.00 0.00 2.97
69 150 6.163476 ACATGATCCGCGAAAAATAGCTATA 58.837 36.000 8.23 0.00 0.00 1.31
70 151 6.311445 ACATGATCCGCGAAAAATAGCTATAG 59.689 38.462 8.23 0.00 0.00 1.31
71 152 6.020971 TGATCCGCGAAAAATAGCTATAGA 57.979 37.500 8.23 0.00 0.00 1.98
72 153 6.452242 TGATCCGCGAAAAATAGCTATAGAA 58.548 36.000 8.23 0.00 0.00 2.10
73 154 7.097192 TGATCCGCGAAAAATAGCTATAGAAT 58.903 34.615 8.23 0.00 0.00 2.40
74 155 7.602644 TGATCCGCGAAAAATAGCTATAGAATT 59.397 33.333 8.23 0.00 0.00 2.17
75 156 7.347508 TCCGCGAAAAATAGCTATAGAATTC 57.652 36.000 8.23 8.31 0.00 2.17
76 157 6.926826 TCCGCGAAAAATAGCTATAGAATTCA 59.073 34.615 8.23 0.00 0.00 2.57
77 158 7.439955 TCCGCGAAAAATAGCTATAGAATTCAA 59.560 33.333 8.23 0.00 0.00 2.69
78 159 8.067784 CCGCGAAAAATAGCTATAGAATTCAAA 58.932 33.333 8.23 0.00 0.00 2.69
79 160 9.096600 CGCGAAAAATAGCTATAGAATTCAAAG 57.903 33.333 6.68 2.97 0.00 2.77
80 161 9.937175 GCGAAAAATAGCTATAGAATTCAAAGT 57.063 29.630 6.68 0.00 0.00 2.66
89 170 9.360093 AGCTATAGAATTCAAAGTACGATATGC 57.640 33.333 8.44 1.49 0.00 3.14
103 184 4.920640 CGATATGCGTATCTAGGGGAAT 57.079 45.455 20.87 0.00 35.57 3.01
104 185 4.611943 CGATATGCGTATCTAGGGGAATG 58.388 47.826 20.87 1.75 35.57 2.67
105 186 4.338400 CGATATGCGTATCTAGGGGAATGA 59.662 45.833 20.87 0.00 35.57 2.57
106 187 3.963428 ATGCGTATCTAGGGGAATGAC 57.037 47.619 0.00 0.00 0.00 3.06
107 188 1.968493 TGCGTATCTAGGGGAATGACC 59.032 52.381 0.00 0.00 38.08 4.02
108 189 1.968493 GCGTATCTAGGGGAATGACCA 59.032 52.381 0.00 0.00 41.20 4.02
109 190 2.367567 GCGTATCTAGGGGAATGACCAA 59.632 50.000 0.00 0.00 41.20 3.67
110 191 3.181458 GCGTATCTAGGGGAATGACCAAA 60.181 47.826 0.00 0.00 41.20 3.28
111 192 4.377897 CGTATCTAGGGGAATGACCAAAC 58.622 47.826 0.00 0.00 41.20 2.93
112 193 3.953542 ATCTAGGGGAATGACCAAACC 57.046 47.619 0.00 0.00 41.20 3.27
113 194 1.920351 TCTAGGGGAATGACCAAACCC 59.080 52.381 0.00 0.00 41.80 4.11
114 195 2.897612 AGGGGAATGACCAAACCCT 58.102 52.632 0.00 0.00 46.67 4.34
213 297 7.057894 TCCCCAACATAATCTAAACATGTACC 58.942 38.462 0.00 0.00 32.70 3.34
215 299 7.013274 CCCCAACATAATCTAAACATGTACCAG 59.987 40.741 0.00 0.00 32.70 4.00
267 353 3.838317 AGATTTAGGGCATAGGCATACGA 59.162 43.478 0.15 0.00 43.71 3.43
499 585 0.413832 AGACCTCCTCCTTGGCTACA 59.586 55.000 0.00 0.00 35.26 2.74
502 588 0.253327 CCTCCTCCTTGGCTACAACC 59.747 60.000 0.00 0.00 35.26 3.77
520 606 0.948678 CCTCCTCGTTCCTCTCGATC 59.051 60.000 0.00 0.00 36.73 3.69
850 952 2.708325 GAGGCCCAAAGAGATCTGGTAT 59.292 50.000 0.00 0.00 0.00 2.73
851 953 2.441001 AGGCCCAAAGAGATCTGGTATG 59.559 50.000 0.00 0.00 0.00 2.39
852 954 2.487986 GGCCCAAAGAGATCTGGTATGG 60.488 54.545 0.00 3.17 0.00 2.74
853 955 3.498774 CCCAAAGAGATCTGGTATGGG 57.501 52.381 14.69 14.69 40.02 4.00
854 956 2.487986 CCCAAAGAGATCTGGTATGGGC 60.488 54.545 15.71 0.00 39.57 5.36
855 957 2.487986 CCAAAGAGATCTGGTATGGGCC 60.488 54.545 0.00 0.00 0.00 5.80
856 958 1.439543 AAGAGATCTGGTATGGGCCC 58.560 55.000 17.59 17.59 0.00 5.80
858 960 0.768221 GAGATCTGGTATGGGCCCCA 60.768 60.000 22.27 4.05 38.19 4.96
859 961 0.103715 AGATCTGGTATGGGCCCCAT 60.104 55.000 21.37 21.37 46.99 4.00
860 962 0.038744 GATCTGGTATGGGCCCCATG 59.961 60.000 26.08 8.57 44.84 3.66
861 963 0.403304 ATCTGGTATGGGCCCCATGA 60.403 55.000 26.08 14.12 44.84 3.07
862 964 1.151450 CTGGTATGGGCCCCATGAC 59.849 63.158 26.08 17.42 44.84 3.06
863 965 1.308657 TGGTATGGGCCCCATGACT 60.309 57.895 26.08 1.43 44.84 3.41
864 966 1.352622 TGGTATGGGCCCCATGACTC 61.353 60.000 26.08 12.19 44.84 3.36
865 967 1.352622 GGTATGGGCCCCATGACTCA 61.353 60.000 26.08 1.02 44.84 3.41
901 1017 1.068121 GGATACAGCCCAGCCCTAAT 58.932 55.000 0.00 0.00 0.00 1.73
904 1020 1.131638 TACAGCCCAGCCCTAATGAG 58.868 55.000 0.00 0.00 0.00 2.90
936 1052 4.093952 CTTCACTGCGGCGCTTGG 62.094 66.667 33.26 23.20 0.00 3.61
938 1054 3.899981 TTCACTGCGGCGCTTGGAT 62.900 57.895 33.26 10.68 0.00 3.41
939 1055 2.511373 CACTGCGGCGCTTGGATA 60.511 61.111 33.26 10.57 0.00 2.59
940 1056 2.511600 ACTGCGGCGCTTGGATAC 60.512 61.111 33.26 1.10 0.00 2.24
951 1067 3.006133 TGGATACAGCCCCACGCA 61.006 61.111 0.00 0.00 46.17 5.24
953 1069 2.267642 GATACAGCCCCACGCACA 59.732 61.111 0.00 0.00 41.38 4.57
955 1071 2.796483 GATACAGCCCCACGCACACA 62.796 60.000 0.00 0.00 41.38 3.72
956 1072 3.818121 TACAGCCCCACGCACACAC 62.818 63.158 0.00 0.00 41.38 3.82
1194 1557 4.335647 CGCACCCACCTCCTTGCT 62.336 66.667 0.00 0.00 32.56 3.91
1350 1713 4.146075 GCGCTGGAGCTGCTCTCT 62.146 66.667 27.09 0.00 41.60 3.10
1378 1741 0.033601 AGAGGATCACGGAGCTGTCT 60.034 55.000 0.00 0.00 37.82 3.41
1476 1839 2.492088 CGATATAATGACAGCGAGGGGA 59.508 50.000 0.00 0.00 0.00 4.81
1635 1998 0.871722 CGGTTGTGAATTTGCTCGGA 59.128 50.000 0.00 0.00 0.00 4.55
1662 2025 1.635663 GGAGAATTGGTGACGTGGCG 61.636 60.000 0.00 0.00 0.00 5.69
1820 2183 4.039004 TGTTGCAGCTGATGTGGTTAATTT 59.961 37.500 20.43 0.00 0.00 1.82
1863 2226 4.673968 TGTGTAGAGAAGGTAGTGTGGAT 58.326 43.478 0.00 0.00 0.00 3.41
1980 2343 1.418334 GGCTAGAGGATGCCTTCTCA 58.582 55.000 0.00 0.00 45.26 3.27
2038 2401 9.725019 TGGTGGATGAGTATGTATATTCAATTC 57.275 33.333 1.92 0.00 33.58 2.17
2163 2526 9.988815 AATGCAGTAATAAATGGTTTGTGTAAA 57.011 25.926 0.00 0.00 0.00 2.01
2322 2685 0.238289 GTGGGATTGCACTTGACGTG 59.762 55.000 0.00 0.00 46.58 4.49
2373 2736 7.478322 CATTATTTCTGATCAACAAGGTGGAG 58.522 38.462 0.00 0.00 0.00 3.86
2488 2851 1.546029 GGGATTTTGACAGGGCAGTTC 59.454 52.381 0.00 0.00 0.00 3.01
2545 2908 5.680619 TCTCCAGTACTGTTGTTCACAATT 58.319 37.500 21.18 0.00 38.24 2.32
2602 2965 3.128242 CACCATTGCTGATCAAGTCTTCC 59.872 47.826 0.00 0.00 38.22 3.46
2646 3009 5.905913 ACTAAGGCCTGATTCCTGTACTTAT 59.094 40.000 5.69 0.00 33.43 1.73
2732 3095 4.408182 AGACGGATGAACTAGAAATGGG 57.592 45.455 0.00 0.00 0.00 4.00
2746 3109 7.175104 ACTAGAAATGGGCTTGTTTTCATCTA 58.825 34.615 0.00 0.00 32.94 1.98
2922 3285 5.697633 GGTCGTAGAACCATTGTTAAGTGAA 59.302 40.000 0.00 0.00 39.11 3.18
3138 3501 2.951642 CAAGGAAGCTGAACAAAGTGGA 59.048 45.455 0.00 0.00 0.00 4.02
3144 3507 4.228912 AGCTGAACAAAGTGGATTTTCG 57.771 40.909 0.00 0.00 0.00 3.46
3173 3536 6.576662 TCTTGCCATGTACTCTATAGTAGC 57.423 41.667 0.00 0.00 38.89 3.58
3279 3642 6.600822 CCATTATCATCCACAACTCTGTTCTT 59.399 38.462 0.00 0.00 31.64 2.52
3280 3643 7.414873 CCATTATCATCCACAACTCTGTTCTTG 60.415 40.741 0.00 0.00 31.64 3.02
3434 3797 9.326339 CTTAGATGATGCATATGAATTGTTTCG 57.674 33.333 6.97 0.00 34.39 3.46
3694 4057 5.297776 CCAGATTTTGTCGGATTTATGAGCT 59.702 40.000 0.00 0.00 0.00 4.09
3951 4314 6.109156 TCTAATACACTTGGTCAGCTCAAA 57.891 37.500 0.00 0.00 0.00 2.69
4066 4429 0.821711 CGGAAGTTCCCAAGGCACAA 60.822 55.000 16.47 0.00 31.13 3.33
4138 4501 6.630444 AGACTGATATTGACAATGGCAATC 57.370 37.500 18.73 6.53 37.22 2.67
4285 4648 0.687920 TTGGTGACCGGTGCAATCTA 59.312 50.000 14.63 0.79 0.00 1.98
4340 4703 5.243954 TCTTCTGTAAGCAAAGCTACTCTCA 59.756 40.000 0.00 0.00 38.25 3.27
4489 4852 2.733956 TGGCAACAGAAGAAAACCAGT 58.266 42.857 0.00 0.00 46.17 4.00
4490 4853 2.426738 TGGCAACAGAAGAAAACCAGTG 59.573 45.455 0.00 0.00 46.17 3.66
4576 4940 8.926710 CACTTAAACGACTAATCAGATCAACTT 58.073 33.333 0.00 0.00 0.00 2.66
4756 5122 7.603651 TCACTTTCTAGCCCTATTCGAATATC 58.396 38.462 17.84 10.35 0.00 1.63
4811 5177 4.713814 TCTCTTGTCTCCTGCTTCACATAT 59.286 41.667 0.00 0.00 0.00 1.78
4821 5187 7.070447 TCTCCTGCTTCACATATAGATTCTGTT 59.930 37.037 0.00 0.00 0.00 3.16
4840 5206 5.878116 TCTGTTAATACATGTTAAAGCGGCT 59.122 36.000 2.30 0.00 32.86 5.52
4841 5207 7.042950 TCTGTTAATACATGTTAAAGCGGCTA 58.957 34.615 2.30 0.00 32.86 3.93
4842 5208 7.223971 TCTGTTAATACATGTTAAAGCGGCTAG 59.776 37.037 2.30 0.00 32.86 3.42
4843 5209 6.819649 TGTTAATACATGTTAAAGCGGCTAGT 59.180 34.615 2.30 0.00 0.00 2.57
4844 5210 5.986004 AATACATGTTAAAGCGGCTAGTC 57.014 39.130 2.30 0.00 0.00 2.59
4845 5211 3.611766 ACATGTTAAAGCGGCTAGTCT 57.388 42.857 1.35 0.00 0.00 3.24
4846 5212 4.730949 ACATGTTAAAGCGGCTAGTCTA 57.269 40.909 1.35 0.00 0.00 2.59
4847 5213 4.683832 ACATGTTAAAGCGGCTAGTCTAG 58.316 43.478 1.35 2.18 0.00 2.43
4889 5258 4.148838 CCCCTGTACAAACTGAAAATGGA 58.851 43.478 0.00 0.00 0.00 3.41
4907 5276 6.677781 AATGGAACCTTGTACATATGAACG 57.322 37.500 10.38 0.00 0.00 3.95
4944 5313 9.160412 ACCCTTGCTCTATACTTAGATTTATGT 57.840 33.333 0.00 0.00 33.98 2.29
4949 5318 7.016170 TGCTCTATACTTAGATTTATGTGGCCA 59.984 37.037 0.00 0.00 33.98 5.36
5107 5477 6.295039 TCAAGAAACCTACGTGTCATTTTC 57.705 37.500 0.00 0.23 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 115 3.126171 CGCGGATCATGTTTGGACTTTAA 59.874 43.478 0.00 0.00 0.00 1.52
35 116 2.675844 CGCGGATCATGTTTGGACTTTA 59.324 45.455 0.00 0.00 0.00 1.85
36 117 1.468520 CGCGGATCATGTTTGGACTTT 59.531 47.619 0.00 0.00 0.00 2.66
37 118 1.086696 CGCGGATCATGTTTGGACTT 58.913 50.000 0.00 0.00 0.00 3.01
38 119 0.249120 TCGCGGATCATGTTTGGACT 59.751 50.000 6.13 0.00 0.00 3.85
39 120 1.083489 TTCGCGGATCATGTTTGGAC 58.917 50.000 6.13 0.00 0.00 4.02
40 121 1.814793 TTTCGCGGATCATGTTTGGA 58.185 45.000 6.13 0.00 0.00 3.53
41 122 2.627863 TTTTCGCGGATCATGTTTGG 57.372 45.000 6.13 0.00 0.00 3.28
42 123 4.204978 GCTATTTTTCGCGGATCATGTTTG 59.795 41.667 6.13 0.00 0.00 2.93
43 124 4.096382 AGCTATTTTTCGCGGATCATGTTT 59.904 37.500 6.13 0.00 0.00 2.83
44 125 3.627577 AGCTATTTTTCGCGGATCATGTT 59.372 39.130 6.13 0.00 0.00 2.71
45 126 3.206150 AGCTATTTTTCGCGGATCATGT 58.794 40.909 6.13 0.00 0.00 3.21
46 127 3.885484 AGCTATTTTTCGCGGATCATG 57.115 42.857 6.13 0.00 0.00 3.07
47 128 6.631016 TCTATAGCTATTTTTCGCGGATCAT 58.369 36.000 12.39 0.00 0.00 2.45
48 129 6.020971 TCTATAGCTATTTTTCGCGGATCA 57.979 37.500 12.39 0.00 0.00 2.92
49 130 6.946229 TTCTATAGCTATTTTTCGCGGATC 57.054 37.500 12.39 0.00 0.00 3.36
50 131 7.602644 TGAATTCTATAGCTATTTTTCGCGGAT 59.397 33.333 12.39 0.00 0.00 4.18
51 132 6.926826 TGAATTCTATAGCTATTTTTCGCGGA 59.073 34.615 12.39 0.00 0.00 5.54
52 133 7.117241 TGAATTCTATAGCTATTTTTCGCGG 57.883 36.000 12.39 0.00 0.00 6.46
53 134 8.987599 TTTGAATTCTATAGCTATTTTTCGCG 57.012 30.769 12.39 0.00 0.00 5.87
54 135 9.937175 ACTTTGAATTCTATAGCTATTTTTCGC 57.063 29.630 12.39 0.00 0.00 4.70
63 144 9.360093 GCATATCGTACTTTGAATTCTATAGCT 57.640 33.333 7.05 0.00 0.00 3.32
64 145 8.314635 CGCATATCGTACTTTGAATTCTATAGC 58.685 37.037 7.05 0.33 0.00 2.97
82 163 4.338400 TCATTCCCCTAGATACGCATATCG 59.662 45.833 0.00 0.00 41.95 2.92
83 164 5.452077 GGTCATTCCCCTAGATACGCATATC 60.452 48.000 0.00 0.00 38.00 1.63
84 165 4.406003 GGTCATTCCCCTAGATACGCATAT 59.594 45.833 0.00 0.00 0.00 1.78
85 166 3.767673 GGTCATTCCCCTAGATACGCATA 59.232 47.826 0.00 0.00 0.00 3.14
86 167 2.567615 GGTCATTCCCCTAGATACGCAT 59.432 50.000 0.00 0.00 0.00 4.73
87 168 1.968493 GGTCATTCCCCTAGATACGCA 59.032 52.381 0.00 0.00 0.00 5.24
88 169 1.968493 TGGTCATTCCCCTAGATACGC 59.032 52.381 0.00 0.00 34.77 4.42
89 170 4.377897 GTTTGGTCATTCCCCTAGATACG 58.622 47.826 0.00 0.00 34.77 3.06
90 171 4.445879 GGGTTTGGTCATTCCCCTAGATAC 60.446 50.000 0.00 0.00 34.32 2.24
91 172 3.720002 GGGTTTGGTCATTCCCCTAGATA 59.280 47.826 0.00 0.00 34.32 1.98
92 173 2.514160 GGGTTTGGTCATTCCCCTAGAT 59.486 50.000 0.00 0.00 34.32 1.98
93 174 1.920351 GGGTTTGGTCATTCCCCTAGA 59.080 52.381 0.00 0.00 34.32 2.43
94 175 1.923148 AGGGTTTGGTCATTCCCCTAG 59.077 52.381 0.00 0.00 43.94 3.02
95 176 1.920351 GAGGGTTTGGTCATTCCCCTA 59.080 52.381 0.00 0.00 45.76 3.53
96 177 2.897612 AGGGTTTGGTCATTCCCCT 58.102 52.632 0.00 0.00 40.94 4.79
97 178 0.407918 TGAGGGTTTGGTCATTCCCC 59.592 55.000 0.00 0.00 40.70 4.81
98 179 2.171003 CTTGAGGGTTTGGTCATTCCC 58.829 52.381 0.00 0.00 40.16 3.97
99 180 3.084786 CTCTTGAGGGTTTGGTCATTCC 58.915 50.000 0.00 0.00 0.00 3.01
100 181 3.756117 ACTCTTGAGGGTTTGGTCATTC 58.244 45.455 2.55 0.00 0.00 2.67
101 182 3.884037 ACTCTTGAGGGTTTGGTCATT 57.116 42.857 2.55 0.00 0.00 2.57
102 183 3.884037 AACTCTTGAGGGTTTGGTCAT 57.116 42.857 2.55 0.00 0.00 3.06
103 184 3.456644 TGTAACTCTTGAGGGTTTGGTCA 59.543 43.478 0.97 0.00 0.00 4.02
104 185 4.081322 TGTAACTCTTGAGGGTTTGGTC 57.919 45.455 0.97 0.00 0.00 4.02
105 186 4.513406 TTGTAACTCTTGAGGGTTTGGT 57.487 40.909 0.97 0.00 0.00 3.67
106 187 6.405278 AAATTGTAACTCTTGAGGGTTTGG 57.595 37.500 0.97 0.00 0.00 3.28
107 188 7.716612 AGAAAATTGTAACTCTTGAGGGTTTG 58.283 34.615 0.97 0.00 0.00 2.93
108 189 7.898014 AGAAAATTGTAACTCTTGAGGGTTT 57.102 32.000 0.97 0.00 0.00 3.27
109 190 7.684428 GCAAGAAAATTGTAACTCTTGAGGGTT 60.684 37.037 13.39 1.40 44.93 4.11
110 191 6.239036 GCAAGAAAATTGTAACTCTTGAGGGT 60.239 38.462 13.39 0.00 44.93 4.34
111 192 6.152379 GCAAGAAAATTGTAACTCTTGAGGG 58.848 40.000 13.39 0.00 44.93 4.30
112 193 6.738114 TGCAAGAAAATTGTAACTCTTGAGG 58.262 36.000 13.39 0.00 44.93 3.86
113 194 8.633075 TTTGCAAGAAAATTGTAACTCTTGAG 57.367 30.769 13.39 0.00 44.93 3.02
114 195 8.250332 ACTTTGCAAGAAAATTGTAACTCTTGA 58.750 29.630 13.39 0.00 44.93 3.02
213 297 6.128172 GGACATTGTTGAGATAGTGGAAACTG 60.128 42.308 0.00 0.00 0.00 3.16
215 299 5.940470 AGGACATTGTTGAGATAGTGGAAAC 59.060 40.000 0.00 0.00 0.00 2.78
493 579 0.108281 GGAACGAGGAGGTTGTAGCC 60.108 60.000 0.00 0.00 0.00 3.93
499 585 0.037877 TCGAGAGGAACGAGGAGGTT 59.962 55.000 0.00 0.00 34.85 3.50
502 588 1.601903 CAGATCGAGAGGAACGAGGAG 59.398 57.143 0.00 0.00 42.81 3.69
850 952 0.413037 ATTTTGAGTCATGGGGCCCA 59.587 50.000 30.97 30.97 38.19 5.36
851 953 2.031870 GTATTTTGAGTCATGGGGCCC 58.968 52.381 18.17 18.17 0.00 5.80
852 954 2.733956 TGTATTTTGAGTCATGGGGCC 58.266 47.619 0.00 0.00 0.00 5.80
853 955 3.763897 ACTTGTATTTTGAGTCATGGGGC 59.236 43.478 0.00 0.00 0.00 5.80
854 956 5.009631 TCACTTGTATTTTGAGTCATGGGG 58.990 41.667 0.00 0.00 0.00 4.96
855 957 5.392380 GCTCACTTGTATTTTGAGTCATGGG 60.392 44.000 0.00 0.00 39.23 4.00
856 958 5.413833 AGCTCACTTGTATTTTGAGTCATGG 59.586 40.000 0.00 0.00 39.23 3.66
858 960 5.349817 CGAGCTCACTTGTATTTTGAGTCAT 59.650 40.000 15.40 0.00 39.23 3.06
859 961 4.686091 CGAGCTCACTTGTATTTTGAGTCA 59.314 41.667 15.40 0.00 39.23 3.41
860 962 4.092091 CCGAGCTCACTTGTATTTTGAGTC 59.908 45.833 15.40 0.00 39.23 3.36
861 963 3.997021 CCGAGCTCACTTGTATTTTGAGT 59.003 43.478 15.40 0.00 39.23 3.41
862 964 4.245660 TCCGAGCTCACTTGTATTTTGAG 58.754 43.478 15.40 0.00 39.89 3.02
863 965 4.265904 TCCGAGCTCACTTGTATTTTGA 57.734 40.909 15.40 0.00 0.00 2.69
864 966 5.580691 TGTATCCGAGCTCACTTGTATTTTG 59.419 40.000 15.40 0.00 0.00 2.44
865 967 5.730550 TGTATCCGAGCTCACTTGTATTTT 58.269 37.500 15.40 0.00 0.00 1.82
936 1052 2.106683 GTGTGCGTGGGGCTGTATC 61.107 63.158 0.00 0.00 44.05 2.24
938 1054 3.551407 TGTGTGCGTGGGGCTGTA 61.551 61.111 0.00 0.00 44.05 2.74
944 1060 2.513666 AGTGTGTGTGTGCGTGGG 60.514 61.111 0.00 0.00 0.00 4.61
946 1062 2.620459 CGAGTGTGTGTGTGCGTG 59.380 61.111 0.00 0.00 0.00 5.34
947 1063 3.261951 GCGAGTGTGTGTGTGCGT 61.262 61.111 0.00 0.00 0.00 5.24
949 1065 2.094126 GAGTGCGAGTGTGTGTGTGC 62.094 60.000 0.00 0.00 0.00 4.57
951 1067 0.806102 GTGAGTGCGAGTGTGTGTGT 60.806 55.000 0.00 0.00 0.00 3.72
953 1069 0.806102 GTGTGAGTGCGAGTGTGTGT 60.806 55.000 0.00 0.00 0.00 3.72
955 1071 1.227263 GGTGTGAGTGCGAGTGTGT 60.227 57.895 0.00 0.00 0.00 3.72
956 1072 2.302952 CGGTGTGAGTGCGAGTGTG 61.303 63.158 0.00 0.00 0.00 3.82
957 1073 2.027605 CGGTGTGAGTGCGAGTGT 59.972 61.111 0.00 0.00 0.00 3.55
1350 1713 0.817654 CGTGATCCTCTACACCAGCA 59.182 55.000 0.00 0.00 34.05 4.41
1378 1741 0.538118 CGATAGGTGGACGGGGAAAA 59.462 55.000 0.00 0.00 0.00 2.29
1476 1839 1.906824 ACGGTCGTCCACCTGACAT 60.907 57.895 0.00 0.00 44.71 3.06
1635 1998 0.040204 CACCAATTCTCCCCTGCCTT 59.960 55.000 0.00 0.00 0.00 4.35
1662 2025 2.614259 TCCATCTCCCTTATCAGCTCC 58.386 52.381 0.00 0.00 0.00 4.70
1691 2054 1.229428 CATCGCATCACCCACCATAC 58.771 55.000 0.00 0.00 0.00 2.39
1820 2183 7.345691 ACACATCCCATCAATAACAATAGTGA 58.654 34.615 0.00 0.00 40.10 3.41
1863 2226 6.672218 TCTCATCTATGAACCCCTTCACTTTA 59.328 38.462 0.00 0.00 39.28 1.85
1980 2343 7.201821 CCTGTTTGTTCAAGTTTCCTCACTATT 60.202 37.037 0.00 0.00 0.00 1.73
2038 2401 5.399301 CCTTTTTGCACAAACTGTCGATTAG 59.601 40.000 0.00 0.00 0.00 1.73
2133 2496 9.075519 CACAAACCATTTATTACTGCATTGTAG 57.924 33.333 0.00 0.00 0.00 2.74
2184 2547 1.202758 ACACCTTCAGACATTTCCGCA 60.203 47.619 0.00 0.00 0.00 5.69
2322 2685 3.930229 TGATAAGTACATTGCACGTGACC 59.070 43.478 22.23 2.42 0.00 4.02
2328 2691 9.520204 AATAATGCTTTGATAAGTACATTGCAC 57.480 29.630 0.00 0.00 31.12 4.57
2356 2719 3.276857 CATCCTCCACCTTGTTGATCAG 58.723 50.000 0.00 0.00 0.00 2.90
2373 2736 0.108945 GAAACAAGCTGCAGGCATCC 60.109 55.000 17.12 0.00 44.79 3.51
2427 2790 7.060421 TGTCTATGAGTGTATGATAGGTGACA 58.940 38.462 0.00 0.00 0.00 3.58
2488 2851 7.919690 TCTTTCTTGTACTCATCAAACAACTG 58.080 34.615 0.00 0.00 0.00 3.16
2545 2908 1.561076 ACATAGTGCTCCAATCAGGCA 59.439 47.619 0.00 0.00 37.29 4.75
2646 3009 7.894708 TGAAATTTGCATGAATCAACTTCCTA 58.105 30.769 0.00 0.00 32.49 2.94
2714 3077 3.199880 AGCCCATTTCTAGTTCATCCG 57.800 47.619 0.00 0.00 0.00 4.18
2732 3095 9.910511 CATAATTGCAAATAGATGAAAACAAGC 57.089 29.630 1.71 0.00 0.00 4.01
2922 3285 4.897076 TGCAGGCCATGAATCTTAATGAAT 59.103 37.500 5.01 0.00 0.00 2.57
3138 3501 2.214376 TGGCAAGATCCACCGAAAAT 57.786 45.000 0.00 0.00 0.00 1.82
3144 3507 2.171448 AGAGTACATGGCAAGATCCACC 59.829 50.000 0.00 0.00 39.25 4.61
3173 3536 2.964978 CTTTGCAAAGGCCCTCCG 59.035 61.111 28.12 3.94 40.13 4.63
3279 3642 2.043551 TGCTGGCACAAACCACCA 60.044 55.556 0.00 0.00 38.70 4.17
3280 3643 2.417097 GTGCTGGCACAAACCACC 59.583 61.111 19.16 0.00 45.53 4.61
3434 3797 6.208599 TCTGATACCTTTGTTGGACATTTTCC 59.791 38.462 0.00 0.00 46.13 3.13
3667 4030 6.364701 TCATAAATCCGACAAAATCTGGGAT 58.635 36.000 0.00 0.00 39.11 3.85
3681 4044 4.201950 CCTTTGACCAAGCTCATAAATCCG 60.202 45.833 0.00 0.00 0.00 4.18
3694 4057 1.354031 TGCATAGAGCCCTTTGACCAA 59.646 47.619 0.00 0.00 44.83 3.67
3951 4314 3.413846 TCATCAGTTCTCTGCAGCTTT 57.586 42.857 9.47 0.00 41.10 3.51
4015 4378 5.957842 TTGCTAGAAACATCAAAATCGGT 57.042 34.783 0.00 0.00 0.00 4.69
4066 4429 1.911357 TCTCTCTGTCATGGGTTGCAT 59.089 47.619 0.00 0.00 0.00 3.96
4116 4479 6.436261 CAGATTGCCATTGTCAATATCAGTC 58.564 40.000 0.00 5.85 34.59 3.51
4138 4501 5.596845 GTCATAGAAAGACTTCCCTAGCAG 58.403 45.833 0.00 0.00 33.29 4.24
4285 4648 2.242452 GGGCCAGAAGAACTTCCCTAAT 59.758 50.000 4.39 0.00 40.33 1.73
4340 4703 5.804639 TCTGCAAGAACATGGTGTACTTAT 58.195 37.500 0.00 0.00 42.31 1.73
4487 4850 1.918800 GCCCTCCCAGTGTACCACT 60.919 63.158 0.00 0.00 46.51 4.00
4488 4851 1.562672 ATGCCCTCCCAGTGTACCAC 61.563 60.000 0.00 0.00 34.10 4.16
4489 4852 1.229820 ATGCCCTCCCAGTGTACCA 60.230 57.895 0.00 0.00 0.00 3.25
4490 4853 1.224592 CATGCCCTCCCAGTGTACC 59.775 63.158 0.00 0.00 0.00 3.34
4631 4997 2.293122 TGTTTGCACCATTTTCTCTCGG 59.707 45.455 0.00 0.00 0.00 4.63
4756 5122 8.652810 ACATTGTCAAAGATTTCAAAGGAAAG 57.347 30.769 0.00 0.00 45.58 2.62
4788 5154 2.319844 TGTGAAGCAGGAGACAAGAGA 58.680 47.619 0.00 0.00 0.00 3.10
4790 5156 5.893824 TCTATATGTGAAGCAGGAGACAAGA 59.106 40.000 0.00 0.00 0.00 3.02
4821 5187 6.812998 AGACTAGCCGCTTTAACATGTATTA 58.187 36.000 0.00 0.00 0.00 0.98
4840 5206 5.188988 TGGAAAGGCAGACTACTAGACTA 57.811 43.478 0.00 0.00 0.00 2.59
4841 5207 4.048970 TGGAAAGGCAGACTACTAGACT 57.951 45.455 0.00 0.00 0.00 3.24
4842 5208 5.346181 AATGGAAAGGCAGACTACTAGAC 57.654 43.478 0.00 0.00 0.00 2.59
4843 5209 5.734720 CAAATGGAAAGGCAGACTACTAGA 58.265 41.667 0.00 0.00 0.00 2.43
4844 5210 4.333926 GCAAATGGAAAGGCAGACTACTAG 59.666 45.833 0.00 0.00 0.00 2.57
4845 5211 4.261801 GCAAATGGAAAGGCAGACTACTA 58.738 43.478 0.00 0.00 0.00 1.82
4846 5212 3.084786 GCAAATGGAAAGGCAGACTACT 58.915 45.455 0.00 0.00 0.00 2.57
4847 5213 2.164422 GGCAAATGGAAAGGCAGACTAC 59.836 50.000 0.00 0.00 0.00 2.73
4889 5258 5.410439 GTGTTCCGTTCATATGTACAAGGTT 59.590 40.000 12.30 0.00 0.00 3.50
4907 5276 1.541588 GAGCAAGGGTGATTGTGTTCC 59.458 52.381 0.00 0.00 32.56 3.62
4944 5313 7.582719 AGTAAAGACCATCTAATAAATGGCCA 58.417 34.615 8.56 8.56 46.38 5.36
4993 5362 2.119484 TTGTGGCTAACCTCACCCGG 62.119 60.000 0.00 0.00 39.13 5.73
4994 5363 0.953960 GTTGTGGCTAACCTCACCCG 60.954 60.000 0.00 0.00 39.13 5.28
5073 5443 9.840427 CACGTAGGTTTCTTGAAAATCATATTT 57.160 29.630 0.00 0.00 0.00 1.40
5074 5444 9.010029 ACACGTAGGTTTCTTGAAAATCATATT 57.990 29.630 0.00 0.00 0.00 1.28
5075 5445 8.561738 ACACGTAGGTTTCTTGAAAATCATAT 57.438 30.769 0.00 0.00 0.00 1.78
5076 5446 7.658167 TGACACGTAGGTTTCTTGAAAATCATA 59.342 33.333 3.62 0.00 0.00 2.15
5077 5447 6.485313 TGACACGTAGGTTTCTTGAAAATCAT 59.515 34.615 3.62 0.00 0.00 2.45
5078 5448 5.818336 TGACACGTAGGTTTCTTGAAAATCA 59.182 36.000 3.62 0.00 0.00 2.57
5079 5449 6.295039 TGACACGTAGGTTTCTTGAAAATC 57.705 37.500 3.62 0.00 0.00 2.17
5080 5450 6.877611 ATGACACGTAGGTTTCTTGAAAAT 57.122 33.333 3.62 0.00 0.00 1.82
5081 5451 6.687081 AATGACACGTAGGTTTCTTGAAAA 57.313 33.333 3.62 0.00 0.00 2.29
5082 5452 6.687081 AAATGACACGTAGGTTTCTTGAAA 57.313 33.333 3.62 0.00 0.00 2.69
5083 5453 6.510478 CGAAAATGACACGTAGGTTTCTTGAA 60.510 38.462 3.62 0.00 0.00 2.69
5084 5454 5.050634 CGAAAATGACACGTAGGTTTCTTGA 60.051 40.000 3.62 0.00 0.00 3.02
5085 5455 5.137403 CGAAAATGACACGTAGGTTTCTTG 58.863 41.667 3.62 0.00 0.00 3.02
5086 5456 4.212636 CCGAAAATGACACGTAGGTTTCTT 59.787 41.667 3.62 0.00 0.00 2.52
5087 5457 3.744426 CCGAAAATGACACGTAGGTTTCT 59.256 43.478 3.62 0.00 0.00 2.52
5088 5458 3.495753 ACCGAAAATGACACGTAGGTTTC 59.504 43.478 0.00 0.00 0.00 2.78
5089 5459 3.249080 CACCGAAAATGACACGTAGGTTT 59.751 43.478 0.00 0.00 0.00 3.27
5090 5460 2.803956 CACCGAAAATGACACGTAGGTT 59.196 45.455 0.00 0.00 0.00 3.50
5091 5461 2.224113 ACACCGAAAATGACACGTAGGT 60.224 45.455 0.00 0.00 0.00 3.08
5107 5477 7.696453 GGTTCATGATATTTCTTTACAACACCG 59.304 37.037 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.