Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002932.1 Kokia drynarioides strain JFW-HI SEQ_115376, 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: 4450
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Found at i:2778 original size:139 final size:140
Alignment explanation
Indices: 2528--2937 Score: 506
Period size: 139 Copynumber: 2.9 Consensus size: 140
2518 AATATTTAGG
** * *
2528 AAAGTGTTGGCATAGTGTT-GGACAAAGACAACACTTATTTAAGCGTTGCCTTAAGCATGCATAT
1 AAAGTGTCAGCATAGTGTTGGGA-AAAGACAACTCTTATTTAAGCGTTGCCTTAGGCATGCATAT
* * *** *
2592 TCCAACTCTTATACAAAGAGTTGGGCAAAGTGTATTTCGGTTAGTTTATCCTAACACTTAGGAAA
65 TCCAACTCTTATACAAAGAGTTGGGTAAAGCGTATTTCGACAAGTTTATCCCAACACTTAGGAAA
* *
2657 GTGTAGTG-TA
130 GTGTAGGGCCA
* * * *
2667 AAAGTGTCAGCATAGTGTTGGGTAAAGTCGACTCTTATTTAAGCGTTGCCTTAGGTATGCATATT
1 AAAGTGTCAGCATAGTGTTGGGAAAAGACAACTCTTATTTAAGCGTTGCCTTAGGCATGCATATT
* *
2732 CCAACTCTTATATAAATAGTTGGGTAAAGCGTATTTCGACAAGTTTATCCCAACACTTAGGAAAG
66 CCAACTCTTATACAAAGAGTTGGGTAAAGCGTATTTCGACAAGTTTATCCCAACACTTAGGAAAG
*
2797 TGTTGGGCCA
131 TGTAGGGCCA
* * *
2807 AAAGTGTCAGCATAGTGTTGGGAAAAGCCAACTCTTATTTAAGCGTTGCCTTAGGGACGCATA-T
1 AAAGTGTCAGCATAGTGTTGGGAAAAGACAACTCTTATTTAAGCGTTGCCTTAGGCATGCATATT
* * * * *
2871 CCTAA-TCCTTATACAAAGAGTT-GATCAAAGCATATGTCAACAACTTTATCCCAACACTTAGGA
66 CC-AACT-CTTATACAAAGAGTTGGGT-AAAGCGTATTTCGACAAGTTTATCCCAACACTTAGGA
2934 AAGT
128 AAGT
2938 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:2882 original size:140 final size:139
Alignment explanation
Indices: 2528--3158 Score: 508
Period size: 140 Copynumber: 4.6 Consensus size: 139
2518 AATATTTAGG
** * *
2528 AAAGTGTTGGCATAGTGTT-GGACAAAGACAACACTTATTTAAGCGTTGCCTTAAGCATGCATAT
1 AAAGTGTCAGCATAGTGTTGGGA-AAAGACAACTCTTATTTAAGCGTTGCCTTAGGCATGCATAT
* * *** *
2592 TCCAACTCTTATACAAAGAGTTGGGCAAAGTGTATTTCGGTTAGTTTATCCTAACACTTAGGAAA
65 TCCAACTCTTATACAAAGAGTTGGGTAAAGCGTATTTCGACAAGTTTATCCCAACACTTAGGAAA
* *
2657 GTGTAGTGTA
130 GTGTAGGGCA
* * * *
2667 AAAGTGTCAGCATAGTGTTGGGTAAAGTCGACTCTTATTTAAGCGTTGCCTTAGGTATGCATATT
1 AAAGTGTCAGCATAGTGTTGGGAAAAGACAACTCTTATTTAAGCGTTGCCTTAGGCATGCATATT
* *
2732 CCAACTCTTATATAAATAGTTGGGTAAAGCGTATTTCGACAAGTTTATCCCAACACTTAGGAAAG
66 CCAACTCTTATACAAAGAGTTGGGTAAAGCGTATTTCGACAAGTTTATCCCAACACTTAGGAAAG
*
2797 TGTTGGGCCA
131 TGTAGGG-CA
* * *
2807 AAAGTGTCAGCATAGTGTTGGGAAAAGCCAACTCTTATTTAAGCGTTGCCTTAGGGACGCATA-T
1 AAAGTGTCAGCATAGTGTTGGGAAAAGACAACTCTTATTTAAGCGTTGCCTTAGGCATGCATATT
* * * * *
2871 CCTAA-TCCTTATACAAAGAGTT-GATCAAAGCATATGTCAACAACTTTATCCCAACACTTAGGA
66 CC-AACT-CTTATACAAAGAGTTGGGT-AAAGCGTATTTCGACAAGTTTATCCCAACACTTAGGA
2934 AA--GT------
128 AAGTGTAGGGCA
* * * *
2938 --A-T-CCA-CATACTGTT-GAACAAAG-CAAAC-CTTATTTAAGCGTTTCCTTAGGCATGCATA
1 AAAGTGTCAGCATAGTGTTGGGA-AAAGAC-AACTCTTATTTAAGCGTTGCCTTAGGCATGCATA
** * * * *
2995 -TCACAA-TCCTTATACAAAAGAGTTGGCAAAAGCGTATGTTGGTA-AA-TCTATCTCAACACAT
64 TTC-CAACT-CTTATAC-AAAGAGTTGGGTAAAGCGTAT-TTCG-ACAAGTTTATCCCAACACTT
* ***
3056 AGGAAAGTGACACCTCA
124 AGGAAAGTG-TAGGGCA
* *
3073 AAAGTG-CTAGCATAATGTT-GGATAAAGCCAACTCTTATTTAAGCGTTGCCTTTA-GCATGCAT
1 AAAGTGTC-AGCATAGTGTTGGGA-AAAGACAACTCTTATTTAAGCGTTGCC-TTAGGCATGCAT
* *
3135 ATCCCAAAC-CTTATGCAAAGAGTT
63 ATTCC-AACTCTTATACAAAGAGTT
3159 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:3059 original size:126 final size:126
Alignment explanation
Indices: 2830--3063 Score: 294
Period size: 126 Copynumber: 1.9 Consensus size: 126
2820 AGTGTTGGGA
* *
2830 AAAGCCAACTCTTATTTAAGCGTTGCCTTAGGGACGCATATCCTAATCCTTATACAAAGAGTTGA
1 AAAGCAAACTCTTATTTAAGCGTTGCCTTAGGCACGCATATCCTAATCCTTATACAAAGAGTTGA
* * * *
2895 TCAAAGCATATGTCAACAACTTTATCCCAACACTTAGGAAAGTATCCACATACTGTTGAAC
66 GCAAAGCATATGTCAACAAATCTATCCCAACACATAGGAAAGTATCCACATACTGTTGAAC
* *
2956 AAAGCAAAC-CTTATTTAAGCGTTTCCTTAGGCATGCATATCAC-AATCCTTATACAAAAGAGTT
1 AAAGCAAACTCTTATTTAAGCGTTGCCTTAGGCACGCATATC-CTAATCCTTATAC-AAAGAGTT
* **** *
3019 G-GCAAAAGCGTATGTTGGTAAATCTATCTCAACACATAGGAAAGT
64 GAGC-AAAGCATATGTCAACAAATCTATCCCAACACATAGGAAAGT
3064 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.