Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002933.1 Kokia drynarioides strain JFW-HI SEQ_115377, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 9454
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Found at i:6138 original size:37 final size:36
Alignment explanation
Indices: 6027--6367 Score: 211
Period size: 36 Copynumber: 9.4 Consensus size: 36
6017 AAAGCAATCA
* * * *
6027 TAAAAAAGTTAGGATTGATCTTGTCTAAGGTAACT-T
1 TAAAAAGGTTGGGATAGA-CTTGTTTAAGGTAACTCT
* * * * * *
6063 TATAAATGTTGGGATAGACTTGTCTAATG-CATTCT
1 TAAAAAGGTTGGGATAGACTTGTTTAAGGTAACTCT
* *
6098 TAAAAAGGTTGTGATAGACATTGTTTAAGGGAACTCT
1 TAAAAAGGTTGGGATAGAC-TTGTTTAAGGTAACTCT
* * *
6135 TAAAAAGGTTAGGGTTGGGCTT-TCTTAAGGTAACT-T
1 TAAAAAGGTT-GGGATAGACTTGT-TTAAGGTAACTCT
** *
6171 TAAAAAGGTTCGAAATAAACTTTGTTTAAGGTAA-TCT
1 TAAAAAGGTT-GGGATAGAC-TTGTTTAAGGTAACTCT
* *
6208 TAAAAAGATTGGGATAGATCTTGTTTGAGGTAAC-CTT
1 TAAAAAGGTTGGGATAGA-CTTGTTTAAGGTAACTC-T
* * * *
6245 TAAAAAAGGTAGGGATGGA-TTCGTCTAAGGTAAC-CA
1 T-AAAAAGGTTGGGATAGACTT-GTTTAAGGTAACTCT
* * * *
6281 TAAAAAGGTTGAGAT-GAACTTTGTCTAAAGAAAC-CT
1 TAAAAAGGTTGGGATAG-AC-TTGTTTAAGGTAACTCT
* *
6317 TAAAAAGATTGGGATTGACTTGTTTAA-GTAAACT-T
1 TAAAAAGGTTGGGATAGACTTGTTTAAGGT-AACTCT
6352 TAAAAAGGTTGGGATA
1 TAAAAAGGTTGGGATA
6368 TATCGGTGTA
Statistics
Matches: 238, Mismatches: 48, Indels: 39
0.73 0.15 0.12
Matches are distributed among these distances:
34 4 0.02
35 65 0.27
36 85 0.36
37 64 0.27
38 20 0.08
ACGTcount: A:0.36, C:0.09, G:0.23, T:0.33
Consensus pattern (36 bp):
TAAAAAGGTTGGGATAGACTTGTTTAAGGTAACTCT
Found at i:6850 original size:28 final size:28
Alignment explanation
Indices: 6810--6867 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
6800 ATTTTACCCT
*
6810 AAACCTAAAACTTTAAATCTTGAA-CTCA
1 AAACCTAAAAC-TTAAATCTTAAACCTCA
*
6838 AAACCTAAAACTTAATTCTTAAACCTCA
1 AAACCTAAAACTTAAATCTTAAACCTCA
6866 AA
1 AA
6868 CATCAAGGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 10 0.37
28 17 0.63
ACGTcount: A:0.48, C:0.22, G:0.02, T:0.28
Consensus pattern (28 bp):
AAACCTAAAACTTAAATCTTAAACCTCA
Found at i:7782 original size:139 final size:140
Alignment explanation
Indices: 7532--7941 Score: 506
Period size: 139 Copynumber: 2.9 Consensus size: 140
7522 AATATTTAGG
** * *
7532 AAAGTGTTGGCATAGTGTT-GGACAAAGACAACACTTATTTAAGCGTTGCCTTAAGCATGCATAT
1 AAAGTGTCAGCATAGTGTTGGGA-AAAGACAACTCTTATTTAAGCGTTGCCTTAGGCATGCATAT
* * *** *
7596 TCCAACTCTTATACAAAGAGTTGGGCAAAGTGTATTTCGGTTAGTTTATCCTAACACTTAGGAAA
65 TCCAACTCTTATACAAAGAGTTGGGTAAAGCGTATTTCGACAAGTTTATCCCAACACTTAGGAAA
* *
7661 GTGTAGTG-TA
130 GTGTAGGGCCA
* * * *
7671 AAAGTGTCAGCATAGTGTTGGGTAAAGTCGACTCTTATTTAAGCGTTGCCTTAGGTATGCATATT
1 AAAGTGTCAGCATAGTGTTGGGAAAAGACAACTCTTATTTAAGCGTTGCCTTAGGCATGCATATT
* *
7736 CCAACTCTTATATAAATAGTTGGGTAAAGCGTATTTCGACAAGTTTATCCCAACACTTAGGAAAG
66 CCAACTCTTATACAAAGAGTTGGGTAAAGCGTATTTCGACAAGTTTATCCCAACACTTAGGAAAG
*
7801 TGTTGGGCCA
131 TGTAGGGCCA
* * *
7811 AAAGTGTCAGCATAGTGTTGGGAAAAGCCAACTCTTATTTAAGCGTTGCCTTAGGGACGCATA-T
1 AAAGTGTCAGCATAGTGTTGGGAAAAGACAACTCTTATTTAAGCGTTGCCTTAGGCATGCATATT
* * * * *
7875 CCTAA-TCCTTATACAAAGAGTT-GATCAAAGCATATGTCAACAACTTTATCCCAACACTTAGGA
66 CC-AACT-CTTATACAAAGAGTTGGGT-AAAGCGTATTTCGACAAGTTTATCCCAACACTTAGGA
7938 AAGT
128 AAGT
7942 ATCCACATAC
Statistics
Matches: 235, Mismatches: 31, Indels: 9
0.85 0.11 0.03
Matches are distributed among these distances:
139 122 0.52
140 113 0.48
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (140 bp):
AAAGTGTCAGCATAGTGTTGGGAAAAGACAACTCTTATTTAAGCGTTGCCTTAGGCATGCATATT
CCAACTCTTATACAAAGAGTTGGGTAAAGCGTATTTCGACAAGTTTATCCCAACACTTAGGAAAG
TGTAGGGCCA
Found at i:7886 original size:140 final size:139
Alignment explanation
Indices: 7532--8162 Score: 508
Period size: 140 Copynumber: 4.6 Consensus size: 139
7522 AATATTTAGG
** * *
7532 AAAGTGTTGGCATAGTGTT-GGACAAAGACAACACTTATTTAAGCGTTGCCTTAAGCATGCATAT
1 AAAGTGTCAGCATAGTGTTGGGA-AAAGACAACTCTTATTTAAGCGTTGCCTTAGGCATGCATAT
* * *** *
7596 TCCAACTCTTATACAAAGAGTTGGGCAAAGTGTATTTCGGTTAGTTTATCCTAACACTTAGGAAA
65 TCCAACTCTTATACAAAGAGTTGGGTAAAGCGTATTTCGACAAGTTTATCCCAACACTTAGGAAA
* *
7661 GTGTAGTGTA
130 GTGTAGGGCA
* * * *
7671 AAAGTGTCAGCATAGTGTTGGGTAAAGTCGACTCTTATTTAAGCGTTGCCTTAGGTATGCATATT
1 AAAGTGTCAGCATAGTGTTGGGAAAAGACAACTCTTATTTAAGCGTTGCCTTAGGCATGCATATT
* *
7736 CCAACTCTTATATAAATAGTTGGGTAAAGCGTATTTCGACAAGTTTATCCCAACACTTAGGAAAG
66 CCAACTCTTATACAAAGAGTTGGGTAAAGCGTATTTCGACAAGTTTATCCCAACACTTAGGAAAG
*
7801 TGTTGGGCCA
131 TGTAGGG-CA
* * *
7811 AAAGTGTCAGCATAGTGTTGGGAAAAGCCAACTCTTATTTAAGCGTTGCCTTAGGGACGCATA-T
1 AAAGTGTCAGCATAGTGTTGGGAAAAGACAACTCTTATTTAAGCGTTGCCTTAGGCATGCATATT
* * * * *
7875 CCTAA-TCCTTATACAAAGAGTT-GATCAAAGCATATGTCAACAACTTTATCCCAACACTTAGGA
66 CC-AACT-CTTATACAAAGAGTTGGGT-AAAGCGTATTTCGACAAGTTTATCCCAACACTTAGGA
7938 AA--GT------
128 AAGTGTAGGGCA
* * * *
7942 --A-T-CCA-CATACTGTT-GAACAAAG-CAAAC-CTTATTTAAGCGTTTCCTTAGGCATGCATA
1 AAAGTGTCAGCATAGTGTTGGGA-AAAGAC-AACTCTTATTTAAGCGTTGCCTTAGGCATGCATA
** * * * *
7999 -TCACAA-TCCTTATACAAAAGAGTTGGCAAAAGCGTATGTTGGTA-AA-TCTATCTCAACACAT
64 TTC-CAACT-CTTATAC-AAAGAGTTGGGTAAAGCGTAT-TTCG-ACAAGTTTATCCCAACACTT
* ***
8060 AGGAAAGTGACACCTCA
124 AGGAAAGTG-TAGGGCA
* *
8077 AAAGTG-CTAGCATAATGTT-GGATAAAGCCAACTCTTATTTAAGCGTTGCCTTTA-GCATGCAT
1 AAAGTGTC-AGCATAGTGTTGGGA-AAAGACAACTCTTATTTAAGCGTTGCC-TTAGGCATGCAT
* *
8139 ATCCCAAAC-CTTATGCAAAGAGTT
63 ATTCC-AACTCTTATACAAAGAGTT
8163 AGCCATAGTG
Statistics
Matches: 406, Mismatches: 53, Indels: 65
0.77 0.10 0.12
Matches are distributed among these distances:
125 43 0.11
126 50 0.12
127 6 0.01
128 3 0.01
129 1 0.00
137 1 0.00
138 4 0.01
139 123 0.30
140 136 0.33
141 33 0.08
142 6 0.01
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (139 bp):
AAAGTGTCAGCATAGTGTTGGGAAAAGACAACTCTTATTTAAGCGTTGCCTTAGGCATGCATATT
CCAACTCTTATACAAAGAGTTGGGTAAAGCGTATTTCGACAAGTTTATCCCAACACTTAGGAAAG
TGTAGGGCA
Found at i:8063 original size:126 final size:126
Alignment explanation
Indices: 7834--8067 Score: 294
Period size: 126 Copynumber: 1.9 Consensus size: 126
7824 AGTGTTGGGA
* *
7834 AAAGCCAACTCTTATTTAAGCGTTGCCTTAGGGACGCATATCCTAATCCTTATACAAAGAGTTGA
1 AAAGCAAACTCTTATTTAAGCGTTGCCTTAGGCACGCATATCCTAATCCTTATACAAAGAGTTGA
* * * *
7899 TCAAAGCATATGTCAACAACTTTATCCCAACACTTAGGAAAGTATCCACATACTGTTGAAC
66 GCAAAGCATATGTCAACAAATCTATCCCAACACATAGGAAAGTATCCACATACTGTTGAAC
* *
7960 AAAGCAAAC-CTTATTTAAGCGTTTCCTTAGGCATGCATATCAC-AATCCTTATACAAAAGAGTT
1 AAAGCAAACTCTTATTTAAGCGTTGCCTTAGGCACGCATATC-CTAATCCTTATAC-AAAGAGTT
* **** *
8023 G-GCAAAAGCGTATGTTGGTAAATCTATCTCAACACATAGGAAAGT
64 GAGC-AAAGCATATGTCAACAAATCTATCCCAACACATAGGAAAGT
8068 GACACCTCAA
Statistics
Matches: 91, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
125 41 0.45
126 50 0.55
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (126 bp):
AAAGCAAACTCTTATTTAAGCGTTGCCTTAGGCACGCATATCCTAATCCTTATACAAAGAGTTGA
GCAAAGCATATGTCAACAAATCTATCCCAACACATAGGAAAGTATCCACATACTGTTGAAC
Done.