Multiple sequence alignment - TraesCS1D01G120500

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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 TraesCS1D01G120500 chr1D 100.000 3242 0 0 1 3242 119011895 119008654 0.000000e+00 5987.0
1 TraesCS1D01G120500 chr1B 95.433 2693 68 20 578 3242 181218790 181216125 0.000000e+00 4241.0
2 TraesCS1D01G120500 chr1B 93.913 230 6 4 289 512 181220324 181220097 1.110000e-89 340.0
3 TraesCS1D01G120500 chr1B 90.840 131 9 1 1 131 255515186 255515059 4.300000e-39 172.0
4 TraesCS1D01G120500 chr1B 91.489 47 4 0 201 247 263784452 263784498 7.510000e-07 65.8
5 TraesCS1D01G120500 chr1A 96.659 2275 50 11 597 2865 131522080 131519826 0.000000e+00 3757.0
6 TraesCS1D01G120500 chr1A 96.310 271 10 0 2864 3134 131519570 131519300 2.290000e-121 446.0
7 TraesCS1D01G120500 chr1A 91.429 210 14 3 275 482 131522577 131522370 5.290000e-73 285.0
8 TraesCS1D01G120500 chr1A 94.118 136 8 0 141 276 131522836 131522701 1.180000e-49 207.0
9 TraesCS1D01G120500 chr1A 99.091 110 1 0 3133 3242 131519062 131518953 7.090000e-47 198.0
10 TraesCS1D01G120500 chr3D 83.349 1045 153 17 1112 2144 75355778 75356813 0.000000e+00 946.0
11 TraesCS1D01G120500 chr3D 78.628 889 166 21 1123 1999 291765482 291766358 4.690000e-158 568.0
12 TraesCS1D01G120500 chr3B 82.901 1041 165 12 1112 2144 121575940 121576975 0.000000e+00 924.0
13 TraesCS1D01G120500 chr3B 77.562 927 181 20 1151 2065 384909917 384910828 4.760000e-148 534.0
14 TraesCS1D01G120500 chr3A 82.762 1050 158 19 1113 2149 88854736 88855775 0.000000e+00 915.0
15 TraesCS1D01G120500 chr3A 77.862 926 182 18 1150 2065 384319987 384320899 1.310000e-153 553.0
16 TraesCS1D01G120500 chr6D 79.197 971 165 34 1135 2088 60168256 60167306 9.810000e-180 640.0
17 TraesCS1D01G120500 chr4A 93.893 131 8 0 1 131 571477678 571477808 7.090000e-47 198.0
18 TraesCS1D01G120500 chr4A 87.586 145 16 2 156 299 677356620 677356763 2.000000e-37 167.0
19 TraesCS1D01G120500 chr5A 77.811 338 60 14 1152 1481 619098999 619098669 9.180000e-46 195.0
20 TraesCS1D01G120500 chr2B 81.579 76 13 1 195 269 30555192 30555117 9.710000e-06 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 TraesCS1D01G120500 chr1D 119008654 119011895 3241 True 5987.0 5987 100.0000 1 3242 1 chr1D.!!$R1 3241
1 TraesCS1D01G120500 chr1B 181216125 181220324 4199 True 2290.5 4241 94.6730 289 3242 2 chr1B.!!$R2 2953
2 TraesCS1D01G120500 chr1A 131518953 131522836 3883 True 978.6 3757 95.5214 141 3242 5 chr1A.!!$R1 3101
3 TraesCS1D01G120500 chr3D 75355778 75356813 1035 False 946.0 946 83.3490 1112 2144 1 chr3D.!!$F1 1032
4 TraesCS1D01G120500 chr3D 291765482 291766358 876 False 568.0 568 78.6280 1123 1999 1 chr3D.!!$F2 876
5 TraesCS1D01G120500 chr3B 121575940 121576975 1035 False 924.0 924 82.9010 1112 2144 1 chr3B.!!$F1 1032
6 TraesCS1D01G120500 chr3B 384909917 384910828 911 False 534.0 534 77.5620 1151 2065 1 chr3B.!!$F2 914
7 TraesCS1D01G120500 chr3A 88854736 88855775 1039 False 915.0 915 82.7620 1113 2149 1 chr3A.!!$F1 1036
8 TraesCS1D01G120500 chr3A 384319987 384320899 912 False 553.0 553 77.8620 1150 2065 1 chr3A.!!$F2 915
9 TraesCS1D01G120500 chr6D 60167306 60168256 950 True 640.0 640 79.1970 1135 2088 1 chr6D.!!$R1 953

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
42 43 0.033504 ATAGCACGTCCGCCATAAGG 59.966 55.0 0.0 0.0 38.23 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2321 3838 0.160182 CGTACTTTTGTGACGGCGAC 59.84 55.0 16.62 8.59 33.01 5.19 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
22 23 4.394729 GTTATTGTCCCAACCTCTCAACA 58.605 43.478 0.00 0.00 0.00 3.33
23 24 3.593442 ATTGTCCCAACCTCTCAACAA 57.407 42.857 0.00 0.00 0.00 2.83
24 25 3.593442 TTGTCCCAACCTCTCAACAAT 57.407 42.857 0.00 0.00 0.00 2.71
25 26 4.715534 TTGTCCCAACCTCTCAACAATA 57.284 40.909 0.00 0.00 0.00 1.90
26 27 4.286297 TGTCCCAACCTCTCAACAATAG 57.714 45.455 0.00 0.00 0.00 1.73
27 28 3.010420 GTCCCAACCTCTCAACAATAGC 58.990 50.000 0.00 0.00 0.00 2.97
28 29 2.642311 TCCCAACCTCTCAACAATAGCA 59.358 45.455 0.00 0.00 0.00 3.49
29 30 2.749621 CCCAACCTCTCAACAATAGCAC 59.250 50.000 0.00 0.00 0.00 4.40
30 31 2.416547 CCAACCTCTCAACAATAGCACG 59.583 50.000 0.00 0.00 0.00 5.34
31 32 3.067106 CAACCTCTCAACAATAGCACGT 58.933 45.455 0.00 0.00 0.00 4.49
32 33 2.960819 ACCTCTCAACAATAGCACGTC 58.039 47.619 0.00 0.00 0.00 4.34
33 34 2.271800 CCTCTCAACAATAGCACGTCC 58.728 52.381 0.00 0.00 0.00 4.79
34 35 1.920574 CTCTCAACAATAGCACGTCCG 59.079 52.381 0.00 0.00 0.00 4.79
35 36 0.370273 CTCAACAATAGCACGTCCGC 59.630 55.000 0.00 0.00 0.00 5.54
36 37 1.017177 TCAACAATAGCACGTCCGCC 61.017 55.000 0.00 0.00 0.00 6.13
37 38 1.004320 AACAATAGCACGTCCGCCA 60.004 52.632 0.00 0.00 0.00 5.69
38 39 0.392461 AACAATAGCACGTCCGCCAT 60.392 50.000 0.00 0.00 0.00 4.40
39 40 0.462375 ACAATAGCACGTCCGCCATA 59.538 50.000 0.00 0.00 0.00 2.74
40 41 1.134640 ACAATAGCACGTCCGCCATAA 60.135 47.619 0.00 0.00 0.00 1.90
41 42 1.526887 CAATAGCACGTCCGCCATAAG 59.473 52.381 0.00 0.00 0.00 1.73
42 43 0.033504 ATAGCACGTCCGCCATAAGG 59.966 55.000 0.00 0.00 38.23 2.69
43 44 1.038681 TAGCACGTCCGCCATAAGGA 61.039 55.000 0.00 0.00 36.89 3.36
44 45 1.227556 GCACGTCCGCCATAAGGAT 60.228 57.895 0.00 0.00 40.30 3.24
45 46 1.222115 GCACGTCCGCCATAAGGATC 61.222 60.000 0.00 0.00 40.30 3.36
46 47 0.389391 CACGTCCGCCATAAGGATCT 59.611 55.000 0.00 0.00 40.30 2.75
47 48 1.120530 ACGTCCGCCATAAGGATCTT 58.879 50.000 0.00 0.00 40.30 2.40
48 49 1.202533 ACGTCCGCCATAAGGATCTTG 60.203 52.381 0.00 0.00 40.30 3.02
49 50 1.230324 GTCCGCCATAAGGATCTTGC 58.770 55.000 0.00 0.00 40.30 4.01
50 51 0.249868 TCCGCCATAAGGATCTTGCG 60.250 55.000 0.95 0.95 41.51 4.85
51 52 0.532862 CCGCCATAAGGATCTTGCGT 60.533 55.000 6.54 0.00 40.34 5.24
52 53 1.299541 CGCCATAAGGATCTTGCGTT 58.700 50.000 0.00 0.00 37.44 4.84
53 54 1.003545 CGCCATAAGGATCTTGCGTTG 60.004 52.381 0.00 0.00 37.44 4.10
54 55 1.268743 GCCATAAGGATCTTGCGTTGC 60.269 52.381 0.00 0.00 36.89 4.17
55 56 2.016318 CCATAAGGATCTTGCGTTGCA 58.984 47.619 0.00 0.00 36.89 4.08
56 57 2.423185 CCATAAGGATCTTGCGTTGCAA 59.577 45.455 0.00 0.00 41.29 4.08
63 64 2.650196 TTGCGTTGCAAGGCCATC 59.350 55.556 33.93 13.31 43.99 3.51
64 65 2.929903 TTGCGTTGCAAGGCCATCC 61.930 57.895 33.93 12.98 43.99 3.51
65 66 3.372730 GCGTTGCAAGGCCATCCA 61.373 61.111 29.12 0.00 33.94 3.41
66 67 2.879907 CGTTGCAAGGCCATCCAG 59.120 61.111 5.01 0.00 33.74 3.86
67 68 1.675310 CGTTGCAAGGCCATCCAGA 60.675 57.895 5.01 0.00 33.74 3.86
68 69 1.651240 CGTTGCAAGGCCATCCAGAG 61.651 60.000 5.01 0.00 33.74 3.35
69 70 0.322816 GTTGCAAGGCCATCCAGAGA 60.323 55.000 5.01 0.00 33.74 3.10
70 71 0.405198 TTGCAAGGCCATCCAGAGAA 59.595 50.000 5.01 0.00 33.74 2.87
71 72 0.405198 TGCAAGGCCATCCAGAGAAA 59.595 50.000 5.01 0.00 33.74 2.52
72 73 1.101331 GCAAGGCCATCCAGAGAAAG 58.899 55.000 5.01 0.00 33.74 2.62
73 74 1.340405 GCAAGGCCATCCAGAGAAAGA 60.340 52.381 5.01 0.00 33.74 2.52
74 75 2.686118 GCAAGGCCATCCAGAGAAAGAT 60.686 50.000 5.01 0.00 33.74 2.40
75 76 3.212685 CAAGGCCATCCAGAGAAAGATC 58.787 50.000 5.01 0.00 33.74 2.75
76 77 2.774173 AGGCCATCCAGAGAAAGATCT 58.226 47.619 5.01 0.00 34.66 2.75
77 78 3.121688 AGGCCATCCAGAGAAAGATCTT 58.878 45.455 5.01 0.88 32.88 2.40
78 79 3.117963 AGGCCATCCAGAGAAAGATCTTG 60.118 47.826 9.17 0.00 32.88 3.02
79 80 2.617774 GCCATCCAGAGAAAGATCTTGC 59.382 50.000 9.17 7.11 35.54 4.01
80 81 3.882444 CCATCCAGAGAAAGATCTTGCA 58.118 45.455 16.08 0.00 35.54 4.08
81 82 4.462133 CCATCCAGAGAAAGATCTTGCAT 58.538 43.478 16.08 0.75 35.54 3.96
82 83 4.888239 CCATCCAGAGAAAGATCTTGCATT 59.112 41.667 16.08 0.09 35.54 3.56
83 84 5.360144 CCATCCAGAGAAAGATCTTGCATTT 59.640 40.000 16.08 0.00 35.54 2.32
84 85 5.892160 TCCAGAGAAAGATCTTGCATTTG 57.108 39.130 16.08 9.89 35.54 2.32
85 86 4.703575 TCCAGAGAAAGATCTTGCATTTGG 59.296 41.667 16.08 17.39 35.54 3.28
86 87 4.421948 CAGAGAAAGATCTTGCATTTGGC 58.578 43.478 16.08 0.00 38.56 4.52
105 106 4.247380 GGAGCCCATCCTCGCCAG 62.247 72.222 0.00 0.00 45.64 4.85
106 107 3.157252 GAGCCCATCCTCGCCAGA 61.157 66.667 0.00 0.00 0.00 3.86
107 108 3.453070 GAGCCCATCCTCGCCAGAC 62.453 68.421 0.00 0.00 0.00 3.51
108 109 3.785859 GCCCATCCTCGCCAGACA 61.786 66.667 0.00 0.00 0.00 3.41
109 110 2.187946 CCCATCCTCGCCAGACAC 59.812 66.667 0.00 0.00 0.00 3.67
110 111 2.362369 CCCATCCTCGCCAGACACT 61.362 63.158 0.00 0.00 0.00 3.55
111 112 1.153489 CCATCCTCGCCAGACACTG 60.153 63.158 0.00 0.00 0.00 3.66
112 113 1.593787 CATCCTCGCCAGACACTGT 59.406 57.895 0.00 0.00 0.00 3.55
113 114 0.036952 CATCCTCGCCAGACACTGTT 60.037 55.000 0.00 0.00 0.00 3.16
114 115 0.036952 ATCCTCGCCAGACACTGTTG 60.037 55.000 0.00 0.00 0.00 3.33
115 116 2.320587 CCTCGCCAGACACTGTTGC 61.321 63.158 0.00 0.00 0.00 4.17
116 117 1.595109 CTCGCCAGACACTGTTGCA 60.595 57.895 0.00 0.00 0.00 4.08
117 118 0.952497 CTCGCCAGACACTGTTGCAT 60.952 55.000 0.00 0.00 0.00 3.96
118 119 0.320050 TCGCCAGACACTGTTGCATA 59.680 50.000 0.00 0.00 0.00 3.14
119 120 1.066215 TCGCCAGACACTGTTGCATAT 60.066 47.619 0.00 0.00 0.00 1.78
120 121 2.167487 TCGCCAGACACTGTTGCATATA 59.833 45.455 0.00 0.00 0.00 0.86
121 122 2.541346 CGCCAGACACTGTTGCATATAG 59.459 50.000 0.00 0.00 0.00 1.31
122 123 2.874701 GCCAGACACTGTTGCATATAGG 59.125 50.000 0.00 0.00 0.00 2.57
123 124 3.432186 GCCAGACACTGTTGCATATAGGA 60.432 47.826 0.00 0.00 0.00 2.94
124 125 4.375272 CCAGACACTGTTGCATATAGGAG 58.625 47.826 0.00 0.00 0.00 3.69
125 126 4.100035 CCAGACACTGTTGCATATAGGAGA 59.900 45.833 0.00 0.00 0.00 3.71
126 127 5.221601 CCAGACACTGTTGCATATAGGAGAT 60.222 44.000 0.00 0.00 0.00 2.75
127 128 6.286758 CAGACACTGTTGCATATAGGAGATT 58.713 40.000 0.00 0.00 0.00 2.40
128 129 6.765036 CAGACACTGTTGCATATAGGAGATTT 59.235 38.462 0.00 0.00 0.00 2.17
129 130 6.765036 AGACACTGTTGCATATAGGAGATTTG 59.235 38.462 0.00 0.00 0.00 2.32
130 131 6.653020 ACACTGTTGCATATAGGAGATTTGA 58.347 36.000 0.00 0.00 0.00 2.69
131 132 6.540189 ACACTGTTGCATATAGGAGATTTGAC 59.460 38.462 0.00 0.00 0.00 3.18
132 133 6.765036 CACTGTTGCATATAGGAGATTTGACT 59.235 38.462 0.00 0.00 0.00 3.41
133 134 6.765036 ACTGTTGCATATAGGAGATTTGACTG 59.235 38.462 0.00 0.00 0.00 3.51
134 135 6.057533 TGTTGCATATAGGAGATTTGACTGG 58.942 40.000 0.00 0.00 0.00 4.00
135 136 6.126796 TGTTGCATATAGGAGATTTGACTGGA 60.127 38.462 0.00 0.00 0.00 3.86
136 137 6.106648 TGCATATAGGAGATTTGACTGGAG 57.893 41.667 0.00 0.00 0.00 3.86
137 138 5.012458 TGCATATAGGAGATTTGACTGGAGG 59.988 44.000 0.00 0.00 0.00 4.30
138 139 5.247110 GCATATAGGAGATTTGACTGGAGGA 59.753 44.000 0.00 0.00 0.00 3.71
139 140 6.696411 CATATAGGAGATTTGACTGGAGGAC 58.304 44.000 0.00 0.00 0.00 3.85
140 141 1.827969 AGGAGATTTGACTGGAGGACG 59.172 52.381 0.00 0.00 0.00 4.79
141 142 1.550976 GGAGATTTGACTGGAGGACGT 59.449 52.381 0.00 0.00 0.00 4.34
142 143 2.417515 GGAGATTTGACTGGAGGACGTC 60.418 54.545 7.13 7.13 0.00 4.34
163 164 5.333513 GTCCTCTATTCAGTGTTGTACTCG 58.666 45.833 0.00 0.00 37.60 4.18
186 187 3.191669 TCCGTTTCATAATGTAGTGCGG 58.808 45.455 0.00 0.00 38.20 5.69
248 249 8.702163 ACAAAGTTTGTGGAGAAAACTATTTG 57.298 30.769 20.26 6.87 44.93 2.32
548 841 2.159057 GGATGAATGTGCCCCAACAATC 60.159 50.000 0.00 0.00 32.81 2.67
555 848 2.038295 TGTGCCCCAACAATCCAAATTC 59.962 45.455 0.00 0.00 0.00 2.17
608 2095 0.455410 GCTTTGGATTATGCACGCCA 59.545 50.000 0.00 0.00 0.00 5.69
610 2097 0.814457 TTTGGATTATGCACGCCACC 59.186 50.000 0.00 0.00 0.00 4.61
648 2150 1.691976 CCAGTACAGTCCACTGAACCA 59.308 52.381 13.75 0.00 46.59 3.67
649 2151 2.548067 CCAGTACAGTCCACTGAACCAC 60.548 54.545 13.75 5.77 46.59 4.16
650 2152 2.365617 CAGTACAGTCCACTGAACCACT 59.634 50.000 13.75 7.69 46.59 4.00
651 2153 2.365617 AGTACAGTCCACTGAACCACTG 59.634 50.000 13.75 0.00 46.59 3.66
652 2154 1.496060 ACAGTCCACTGAACCACTGA 58.504 50.000 13.75 0.00 46.59 3.41
653 2155 1.837439 ACAGTCCACTGAACCACTGAA 59.163 47.619 13.75 0.00 46.59 3.02
654 2156 2.213499 CAGTCCACTGAACCACTGAAC 58.787 52.381 0.00 0.00 46.59 3.18
655 2157 1.141053 AGTCCACTGAACCACTGAACC 59.859 52.381 0.00 0.00 0.00 3.62
751 2259 2.135189 TCCTCTCCCCCACCATAAATG 58.865 52.381 0.00 0.00 0.00 2.32
855 2363 1.190643 CTGTCTTCCTCTCCCCACTC 58.809 60.000 0.00 0.00 0.00 3.51
873 2381 3.330720 CCACCTCCACCTCCACCC 61.331 72.222 0.00 0.00 0.00 4.61
1045 2553 2.047274 TCCTCTGCCTTTTCGCCG 60.047 61.111 0.00 0.00 0.00 6.46
1110 2618 2.444895 GAGGGGATCAGGGCGACT 60.445 66.667 0.00 0.00 0.00 4.18
2252 3769 4.625742 ACGTTACCGATGATTCTTTGACAG 59.374 41.667 0.00 0.00 37.88 3.51
2257 3774 3.309138 CCGATGATTCTTTGACAGCAGAG 59.691 47.826 0.00 0.00 0.00 3.35
2321 3838 3.393970 TGGAAGAGCCAGCGGAGG 61.394 66.667 0.00 0.00 43.33 4.30
2546 4063 5.527214 GGAAATTTGAAAGGTGGGAACAAAG 59.473 40.000 0.00 0.00 46.06 2.77
2549 4066 3.374042 TGAAAGGTGGGAACAAAGTGA 57.626 42.857 0.00 0.00 46.06 3.41
2566 4083 1.404391 GTGAGCTTGGATTGATGGCTG 59.596 52.381 0.00 0.00 33.13 4.85
2567 4084 0.384669 GAGCTTGGATTGATGGCTGC 59.615 55.000 0.00 0.00 33.13 5.25
2568 4085 0.033405 AGCTTGGATTGATGGCTGCT 60.033 50.000 0.00 0.00 31.68 4.24
2576 4093 2.824689 TTGATGGCTGCTAATTGGGA 57.175 45.000 0.00 0.00 0.00 4.37
2661 4178 3.990092 TGTGATGCGGGATGTATAGAAC 58.010 45.455 0.00 0.00 0.00 3.01
2664 4181 3.509967 TGATGCGGGATGTATAGAACGAT 59.490 43.478 0.00 0.00 0.00 3.73
2665 4182 4.703093 TGATGCGGGATGTATAGAACGATA 59.297 41.667 0.00 0.00 0.00 2.92
2666 4183 4.430137 TGCGGGATGTATAGAACGATAC 57.570 45.455 0.00 0.00 33.60 2.24
2823 4350 7.820044 GAGAATGTTGTCTCCTAACTGTTAG 57.180 40.000 18.46 18.46 38.51 2.34
2832 4361 5.184287 GTCTCCTAACTGTTAGTCTGCTCTT 59.816 44.000 22.27 0.00 0.00 2.85
2833 4362 6.374894 GTCTCCTAACTGTTAGTCTGCTCTTA 59.625 42.308 22.27 0.00 0.00 2.10
2834 4363 6.600032 TCTCCTAACTGTTAGTCTGCTCTTAG 59.400 42.308 22.27 6.76 0.00 2.18
3059 4850 6.650390 GGTGCCAAAATTGTGTAGAATGAAAT 59.350 34.615 0.00 0.00 0.00 2.17
3077 4868 5.663456 TGAAATAGAATGGCTGCCAAAATC 58.337 37.500 27.24 22.24 36.95 2.17
3088 4879 3.313526 GCTGCCAAAATCGTGTATCTGAT 59.686 43.478 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.010420 GCTATTGTTGAGAGGTTGGGAC 58.990 50.000 0.00 0.00 0.00 4.46
7 8 2.642311 TGCTATTGTTGAGAGGTTGGGA 59.358 45.455 0.00 0.00 0.00 4.37
8 9 2.749621 GTGCTATTGTTGAGAGGTTGGG 59.250 50.000 0.00 0.00 0.00 4.12
9 10 2.416547 CGTGCTATTGTTGAGAGGTTGG 59.583 50.000 0.00 0.00 0.00 3.77
10 11 3.067106 ACGTGCTATTGTTGAGAGGTTG 58.933 45.455 0.00 0.00 0.00 3.77
11 12 3.326747 GACGTGCTATTGTTGAGAGGTT 58.673 45.455 0.00 0.00 0.00 3.50
12 13 2.353803 GGACGTGCTATTGTTGAGAGGT 60.354 50.000 0.00 0.00 0.00 3.85
13 14 2.271800 GGACGTGCTATTGTTGAGAGG 58.728 52.381 0.00 0.00 0.00 3.69
14 15 1.920574 CGGACGTGCTATTGTTGAGAG 59.079 52.381 5.27 0.00 0.00 3.20
15 16 1.990799 CGGACGTGCTATTGTTGAGA 58.009 50.000 5.27 0.00 0.00 3.27
16 17 0.370273 GCGGACGTGCTATTGTTGAG 59.630 55.000 5.27 0.00 0.00 3.02
17 18 1.017177 GGCGGACGTGCTATTGTTGA 61.017 55.000 5.27 0.00 34.52 3.18
18 19 1.295357 TGGCGGACGTGCTATTGTTG 61.295 55.000 5.27 0.00 34.52 3.33
19 20 0.392461 ATGGCGGACGTGCTATTGTT 60.392 50.000 5.27 0.00 31.33 2.83
20 21 0.462375 TATGGCGGACGTGCTATTGT 59.538 50.000 5.27 0.00 37.28 2.71
21 22 1.526887 CTTATGGCGGACGTGCTATTG 59.473 52.381 5.27 0.00 37.28 1.90
22 23 1.540363 CCTTATGGCGGACGTGCTATT 60.540 52.381 5.27 0.00 37.28 1.73
23 24 0.033504 CCTTATGGCGGACGTGCTAT 59.966 55.000 5.27 3.63 39.55 2.97
24 25 1.038681 TCCTTATGGCGGACGTGCTA 61.039 55.000 5.27 0.00 34.52 3.49
25 26 1.686325 ATCCTTATGGCGGACGTGCT 61.686 55.000 5.27 0.00 32.41 4.40
26 27 1.222115 GATCCTTATGGCGGACGTGC 61.222 60.000 0.00 0.00 32.41 5.34
27 28 0.389391 AGATCCTTATGGCGGACGTG 59.611 55.000 0.00 0.00 32.41 4.49
28 29 1.120530 AAGATCCTTATGGCGGACGT 58.879 50.000 0.00 0.00 32.41 4.34
29 30 1.502231 CAAGATCCTTATGGCGGACG 58.498 55.000 0.00 0.00 32.41 4.79
30 31 1.230324 GCAAGATCCTTATGGCGGAC 58.770 55.000 0.00 0.00 32.41 4.79
31 32 0.249868 CGCAAGATCCTTATGGCGGA 60.250 55.000 0.00 0.00 40.70 5.54
32 33 2.238353 CGCAAGATCCTTATGGCGG 58.762 57.895 0.00 0.00 40.70 6.13
34 35 1.268743 GCAACGCAAGATCCTTATGGC 60.269 52.381 0.00 0.00 43.62 4.40
35 36 2.016318 TGCAACGCAAGATCCTTATGG 58.984 47.619 0.00 0.00 43.62 2.74
36 37 3.763097 TTGCAACGCAAGATCCTTATG 57.237 42.857 0.00 0.00 43.99 1.90
46 47 2.650196 GATGGCCTTGCAACGCAA 59.350 55.556 19.80 10.96 46.80 4.85
47 48 3.372730 GGATGGCCTTGCAACGCA 61.373 61.111 19.80 8.41 36.47 5.24
48 49 3.346631 CTGGATGGCCTTGCAACGC 62.347 63.158 13.88 11.47 34.31 4.84
49 50 1.651240 CTCTGGATGGCCTTGCAACG 61.651 60.000 13.88 3.90 34.31 4.10
50 51 0.322816 TCTCTGGATGGCCTTGCAAC 60.323 55.000 13.88 0.00 34.31 4.17
51 52 0.405198 TTCTCTGGATGGCCTTGCAA 59.595 50.000 13.88 0.00 34.31 4.08
52 53 0.405198 TTTCTCTGGATGGCCTTGCA 59.595 50.000 12.39 12.39 34.31 4.08
53 54 1.101331 CTTTCTCTGGATGGCCTTGC 58.899 55.000 3.32 3.07 34.31 4.01
54 55 2.795231 TCTTTCTCTGGATGGCCTTG 57.205 50.000 3.32 0.00 34.31 3.61
55 56 3.121688 AGATCTTTCTCTGGATGGCCTT 58.878 45.455 3.32 0.00 34.31 4.35
56 57 2.774173 AGATCTTTCTCTGGATGGCCT 58.226 47.619 3.32 0.00 34.31 5.19
57 58 3.212685 CAAGATCTTTCTCTGGATGGCC 58.787 50.000 4.86 0.00 0.00 5.36
58 59 2.617774 GCAAGATCTTTCTCTGGATGGC 59.382 50.000 4.86 0.00 0.00 4.40
59 60 3.882444 TGCAAGATCTTTCTCTGGATGG 58.118 45.455 4.86 0.00 0.00 3.51
60 61 6.266323 CAAATGCAAGATCTTTCTCTGGATG 58.734 40.000 4.86 0.00 0.00 3.51
61 62 5.360144 CCAAATGCAAGATCTTTCTCTGGAT 59.640 40.000 4.86 0.00 0.00 3.41
62 63 4.703575 CCAAATGCAAGATCTTTCTCTGGA 59.296 41.667 4.86 0.00 0.00 3.86
63 64 4.677250 GCCAAATGCAAGATCTTTCTCTGG 60.677 45.833 4.86 10.12 40.77 3.86
64 65 4.421948 GCCAAATGCAAGATCTTTCTCTG 58.578 43.478 4.86 0.00 40.77 3.35
65 66 4.715527 GCCAAATGCAAGATCTTTCTCT 57.284 40.909 4.86 0.00 40.77 3.10
88 89 4.247380 CTGGCGAGGATGGGCTCC 62.247 72.222 0.00 0.00 45.33 4.70
89 90 3.157252 TCTGGCGAGGATGGGCTC 61.157 66.667 0.00 0.00 40.91 4.70
90 91 3.474570 GTCTGGCGAGGATGGGCT 61.475 66.667 0.00 0.00 40.91 5.19
91 92 3.785859 TGTCTGGCGAGGATGGGC 61.786 66.667 0.00 0.00 40.63 5.36
92 93 2.187946 GTGTCTGGCGAGGATGGG 59.812 66.667 0.00 0.00 0.00 4.00
93 94 1.153489 CAGTGTCTGGCGAGGATGG 60.153 63.158 0.00 0.00 0.00 3.51
94 95 0.036952 AACAGTGTCTGGCGAGGATG 60.037 55.000 0.00 0.00 35.51 3.51
95 96 0.036952 CAACAGTGTCTGGCGAGGAT 60.037 55.000 0.00 0.00 35.51 3.24
96 97 1.367471 CAACAGTGTCTGGCGAGGA 59.633 57.895 0.00 0.00 35.51 3.71
97 98 2.320587 GCAACAGTGTCTGGCGAGG 61.321 63.158 0.00 0.00 35.51 4.63
98 99 0.952497 ATGCAACAGTGTCTGGCGAG 60.952 55.000 0.00 0.00 35.51 5.03
99 100 0.320050 TATGCAACAGTGTCTGGCGA 59.680 50.000 0.00 0.00 35.51 5.54
100 101 1.372582 ATATGCAACAGTGTCTGGCG 58.627 50.000 0.00 0.00 35.51 5.69
101 102 2.874701 CCTATATGCAACAGTGTCTGGC 59.125 50.000 0.00 1.66 35.51 4.85
102 103 4.100035 TCTCCTATATGCAACAGTGTCTGG 59.900 45.833 0.00 0.00 35.51 3.86
103 104 5.268118 TCTCCTATATGCAACAGTGTCTG 57.732 43.478 0.00 0.00 37.52 3.51
104 105 6.491714 AATCTCCTATATGCAACAGTGTCT 57.508 37.500 0.00 0.00 0.00 3.41
105 106 6.763135 TCAAATCTCCTATATGCAACAGTGTC 59.237 38.462 0.00 0.00 0.00 3.67
106 107 6.540189 GTCAAATCTCCTATATGCAACAGTGT 59.460 38.462 0.00 0.00 0.00 3.55
107 108 6.765036 AGTCAAATCTCCTATATGCAACAGTG 59.235 38.462 0.00 0.00 0.00 3.66
108 109 6.765036 CAGTCAAATCTCCTATATGCAACAGT 59.235 38.462 0.00 0.00 0.00 3.55
109 110 6.204301 CCAGTCAAATCTCCTATATGCAACAG 59.796 42.308 0.00 0.00 0.00 3.16
110 111 6.057533 CCAGTCAAATCTCCTATATGCAACA 58.942 40.000 0.00 0.00 0.00 3.33
111 112 6.291377 TCCAGTCAAATCTCCTATATGCAAC 58.709 40.000 0.00 0.00 0.00 4.17
112 113 6.464892 CCTCCAGTCAAATCTCCTATATGCAA 60.465 42.308 0.00 0.00 0.00 4.08
113 114 5.012458 CCTCCAGTCAAATCTCCTATATGCA 59.988 44.000 0.00 0.00 0.00 3.96
114 115 5.247110 TCCTCCAGTCAAATCTCCTATATGC 59.753 44.000 0.00 0.00 0.00 3.14
115 116 6.571344 CGTCCTCCAGTCAAATCTCCTATATG 60.571 46.154 0.00 0.00 0.00 1.78
116 117 5.478679 CGTCCTCCAGTCAAATCTCCTATAT 59.521 44.000 0.00 0.00 0.00 0.86
117 118 4.827835 CGTCCTCCAGTCAAATCTCCTATA 59.172 45.833 0.00 0.00 0.00 1.31
118 119 3.639094 CGTCCTCCAGTCAAATCTCCTAT 59.361 47.826 0.00 0.00 0.00 2.57
119 120 3.024547 CGTCCTCCAGTCAAATCTCCTA 58.975 50.000 0.00 0.00 0.00 2.94
120 121 1.827969 CGTCCTCCAGTCAAATCTCCT 59.172 52.381 0.00 0.00 0.00 3.69
121 122 1.550976 ACGTCCTCCAGTCAAATCTCC 59.449 52.381 0.00 0.00 0.00 3.71
122 123 2.417515 GGACGTCCTCCAGTCAAATCTC 60.418 54.545 27.64 0.00 39.21 2.75
123 124 1.550976 GGACGTCCTCCAGTCAAATCT 59.449 52.381 27.64 0.00 39.21 2.40
124 125 1.550976 AGGACGTCCTCCAGTCAAATC 59.449 52.381 31.69 1.07 44.77 2.17
125 126 1.645710 AGGACGTCCTCCAGTCAAAT 58.354 50.000 31.69 5.48 44.77 2.32
126 127 3.143010 AGGACGTCCTCCAGTCAAA 57.857 52.632 31.69 0.00 44.77 2.69
127 128 4.945645 AGGACGTCCTCCAGTCAA 57.054 55.556 31.69 0.00 44.77 3.18
136 137 3.056749 ACAACACTGAATAGAGGACGTCC 60.057 47.826 27.67 27.67 0.00 4.79
137 138 4.175787 ACAACACTGAATAGAGGACGTC 57.824 45.455 7.13 7.13 0.00 4.34
138 139 4.765856 AGTACAACACTGAATAGAGGACGT 59.234 41.667 0.00 0.00 35.62 4.34
139 140 5.312120 AGTACAACACTGAATAGAGGACG 57.688 43.478 0.00 0.00 35.62 4.79
140 141 5.333513 CGAGTACAACACTGAATAGAGGAC 58.666 45.833 0.00 0.00 37.72 3.85
141 142 4.142447 GCGAGTACAACACTGAATAGAGGA 60.142 45.833 0.00 0.00 37.72 3.71
142 143 4.106197 GCGAGTACAACACTGAATAGAGG 58.894 47.826 0.00 0.00 37.72 3.69
143 144 4.987832 AGCGAGTACAACACTGAATAGAG 58.012 43.478 0.00 0.00 37.72 2.43
144 145 4.142447 GGAGCGAGTACAACACTGAATAGA 60.142 45.833 0.00 0.00 37.72 1.98
145 146 4.106197 GGAGCGAGTACAACACTGAATAG 58.894 47.826 0.00 0.00 37.72 1.73
163 164 3.302480 CGCACTACATTATGAAACGGAGC 60.302 47.826 0.00 0.00 0.00 4.70
378 505 8.275187 TCCCTCTATTCCATAATGTTGTGTAT 57.725 34.615 0.00 0.00 0.00 2.29
379 506 7.347222 ACTCCCTCTATTCCATAATGTTGTGTA 59.653 37.037 0.00 0.00 0.00 2.90
380 507 6.158695 ACTCCCTCTATTCCATAATGTTGTGT 59.841 38.462 0.00 0.00 0.00 3.72
506 753 9.917129 TCATCCATATATGAATTTTGCACATTC 57.083 29.630 14.54 9.90 32.97 2.67
518 765 5.222296 TGGGGCACATTCATCCATATATGAA 60.222 40.000 14.54 2.65 46.81 2.57
519 766 4.291777 TGGGGCACATTCATCCATATATGA 59.708 41.667 14.54 1.10 34.07 2.15
522 769 4.141065 TGTTGGGGCACATTCATCCATATA 60.141 41.667 0.00 0.00 0.00 0.86
534 807 1.727062 ATTTGGATTGTTGGGGCACA 58.273 45.000 0.00 0.00 0.00 4.57
548 841 7.693969 AGTAAGAGTGAAATCTGGAATTTGG 57.306 36.000 0.00 0.00 0.00 3.28
580 874 6.363626 CGTGCATAATCCAAAGCTAGTAGTAG 59.636 42.308 0.00 0.00 0.00 2.57
648 2150 1.302511 GTGATGGCGTGGGTTCAGT 60.303 57.895 0.00 0.00 0.00 3.41
649 2151 2.040544 GGTGATGGCGTGGGTTCAG 61.041 63.158 0.00 0.00 0.00 3.02
650 2152 2.033448 GGTGATGGCGTGGGTTCA 59.967 61.111 0.00 0.00 0.00 3.18
651 2153 3.124921 CGGTGATGGCGTGGGTTC 61.125 66.667 0.00 0.00 0.00 3.62
655 2157 3.748660 TATGGCGGTGATGGCGTGG 62.749 63.158 0.00 0.00 37.19 4.94
855 2363 3.330720 GGTGGAGGTGGAGGTGGG 61.331 72.222 0.00 0.00 0.00 4.61
873 2381 4.824515 AGGAGCGAGGACGAGGGG 62.825 72.222 0.00 0.00 42.66 4.79
953 2461 1.834263 CGGAGAAGAATCCAGGGAACT 59.166 52.381 0.00 0.00 46.44 3.01
2321 3838 0.160182 CGTACTTTTGTGACGGCGAC 59.840 55.000 16.62 8.59 33.01 5.19
2374 3891 2.497107 TTACGCCGGTAGCTATCAAC 57.503 50.000 1.90 0.00 40.39 3.18
2546 4063 1.404391 CAGCCATCAATCCAAGCTCAC 59.596 52.381 0.00 0.00 0.00 3.51
2549 4066 0.033405 AGCAGCCATCAATCCAAGCT 60.033 50.000 0.00 0.00 0.00 3.74
2566 4083 9.683069 CAGTTTATTATTCACATCCCAATTAGC 57.317 33.333 0.00 0.00 0.00 3.09
2568 4085 9.707957 ACCAGTTTATTATTCACATCCCAATTA 57.292 29.630 0.00 0.00 0.00 1.40
2576 4093 9.388506 CTCTCTCAACCAGTTTATTATTCACAT 57.611 33.333 0.00 0.00 0.00 3.21
2661 4178 8.801913 CCTTTTACCGAACTAAAAGTAGTATCG 58.198 37.037 13.99 9.50 39.79 2.92
2664 4181 7.962441 ACCCTTTTACCGAACTAAAAGTAGTA 58.038 34.615 13.99 0.00 39.79 1.82
2665 4182 6.830912 ACCCTTTTACCGAACTAAAAGTAGT 58.169 36.000 13.99 10.28 42.66 2.73
2666 4183 6.930722 TGACCCTTTTACCGAACTAAAAGTAG 59.069 38.462 13.99 9.89 40.15 2.57
2901 4689 5.336372 GGCTAAATTAACAAGCACACCATGA 60.336 40.000 0.00 0.00 38.01 3.07
3059 4850 2.423185 CACGATTTTGGCAGCCATTCTA 59.577 45.455 17.09 0.00 31.53 2.10
3077 4868 3.623060 CCTTTGTCCCAATCAGATACACG 59.377 47.826 0.00 0.00 0.00 4.49
3088 4879 0.741915 GACGCAAACCTTTGTCCCAA 59.258 50.000 0.00 0.00 40.24 4.12


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

AutoCloner maintained by Alex Coulton.