Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014564.1 Kokia drynarioides strain JFW-HI SEQ_129603, 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: 2350
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.31
Found at i:2225 original size:86 final size:85
Alignment explanation
Indices: 1984--2350 Score: 535
Period size: 84 Copynumber: 4.3 Consensus size: 85
1974 ATTTAAAATT
* * *
1984 AATTTAACATTATTTAAAT-AAAAAATTATTATTATATTACAATTTATATCAAATATTGTGTTCA
1 AATTTAA-A-TATTTAAATAAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGA
2048 TTTGACAATACATTATTTA-TCA
64 TTTGACAATACATTATTTACT-A
** *
2070 AATTTTCATATTTAAAGT-ACAAAA-TATTATTATATTACAATTTTTATCAAATAATGTGTTGAT
1 AATTTAAATATTTAAA-TAAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGAT
2133 TTGACAATACATTATTTACTA
65 TTGACAATACATTATTTACTA
* *
2154 AATTTATATATTTAAATAAAAAAATTTATTATTATATTTCAATTTTTATCAAATAATGTGTTGAT
1 AATTTAAATATTTAAATAAAAAAA-TTATTATTATATTACAATTTTTATCAAATAATGTGTTGAT
*
2219 TGGACAATACATTATTTACTA
65 TTGACAATACATTATTTACTA
*
2240 AATTTAAATATTTAAATAAAAAATATTATTATTATTATATTATAATTTTTATCAAATAATGTGTT
1 AATTTAAATATTTAAAT-AAAAA-A--ATTATTATTATATTACAATTTTTATCAAATAATGTGTT
2305 GATTTGACAATACATTATTTACTA
62 GATTTGACAATACATTATTTACTA
2329 AATTTAAATATTTAAATAAAAA
1 AATTTAAATATTTAAATAAAAA
Statistics
Matches: 257, Mismatches: 15, Indels: 16
0.89 0.05 0.06
Matches are distributed among these distances:
83 1 0.00
84 82 0.32
85 8 0.03
86 79 0.31
87 5 0.02
88 6 0.02
89 75 0.29
90 1 0.00
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.46
Consensus pattern (85 bp):
AATTTAAATATTTAAATAAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATT
TGACAATACATTATTTACTA
Found at i:2316 original size:175 final size:169
Alignment explanation
Indices: 1984--2350 Score: 533
Period size: 175 Copynumber: 2.1 Consensus size: 169
1974 ATTTAAAATT
*
1984 AATTTAACATTATTTAAAT-AAAAAATTATTATTATATTACAATTTATATCAAATATTGTGTTCA
1 AATTTAA-A-TATTTAAATAAAAAAATTATTATTATATTACAATTTATATCAAATAATGTGTTCA
* ** *
2048 TTTGACAATACATTATTTATCAAATTTTCATATTTAAAGTACAAAATATTATTATATTACAATTT
64 TTGGACAATACATTATTTATCAAATTTAAATATTTAAAGTAAAAAATATTATTATATTACAATTT
2113 TTATCAAATAATGTGTTGATTTGACAATACATTATTTACTA
129 TTATCAAATAATGTGTTGATTTGACAATACATTATTTACTA
* * * *
2154 AATTTATATATTTAAATAAAAAAATTTATTATTATATTTCAATTTTTATCAAATAATGTGTTGAT
1 AATTTAAATATTTAAATAAAAAAA-TTATTATTATATTACAATTTATATCAAATAATGTGTTCAT
2219 TGGACAATACATTATTTA-CTAAATTTAAATATTTAAA-TAAAAAATATTATTATTATTATATTA
65 TGGACAATACATTATTTATC-AAATTTAAATATTTAAAGT--AAAA-A--A-TATTATTATATTA
*
2282 TAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACTA
123 CAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACTA
2329 AATTTAAATATTTAAATAAAAA
1 AATTTAAATATTTAAATAAAAA
Statistics
Matches: 177, Mismatches: 11, Indels: 13
0.88 0.05 0.06
Matches are distributed among these distances:
168 9 0.05
169 9 0.05
170 74 0.42
171 3 0.02
172 1 0.01
174 1 0.01
175 80 0.45
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.46
Consensus pattern (169 bp):
AATTTAAATATTTAAATAAAAAAATTATTATTATATTACAATTTATATCAAATAATGTGTTCATT
GGACAATACATTATTTATCAAATTTAAATATTTAAAGTAAAAAATATTATTATATTACAATTTTT
ATCAAATAATGTGTTGATTTGACAATACATTATTTACTA
Found at i:2321 original size:89 final size:87
Alignment explanation
Indices: 1984--2350 Score: 527
Period size: 86 Copynumber: 4.3 Consensus size: 87
1974 ATTTAAAATT
* *
1984 AATTTAACATTATTTAAAT--AAAAA-ATTATTATTATATTACAATTTATATCAAATATTGTGTT
1 AATTTAA-A-TATTTAAATAAAAAAATATTATTATTATATTACAATTTTTATCAAATAATGTGTT
*
2046 CATTTGACAATACATTATTTA-TCA
64 GATTTGACAATACATTATTTACT-A
** *
2070 AATTTTCATATTTAAAGT--ACAAA-A-TATTATTATATTACAATTTTTATCAAATAATGTGTTG
1 AATTTAAATATTTAAA-TAAAAAAATATTATTATTATATTACAATTTTTATCAAATAATGTGTTG
2131 ATTTGACAATACATTATTTACTA
65 ATTTGACAATACATTATTTACTA
* *
2154 AATTTATATATTTAAATAAAAAAAT-TTATTATTATATTTCAATTTTTATCAAATAATGTGTTGA
1 AATTTAAATATTTAAATAAAAAAATATTATTATTATATTACAATTTTTATCAAATAATGTGTTGA
*
2218 TTGGACAATACATTATTTACTA
66 TTTGACAATACATTATTTACTA
*
2240 AATTTAAATATTTAAATAAAAAATATTATTATTATTATATTATAATTTTTATCAAATAATGTGTT
1 AATTTAAATATTTAAATAAAAAA-A-TATTATTATTATATTACAATTTTTATCAAATAATGTGTT
2305 GATTTGACAATACATTATTTACTA
64 GATTTGACAATACATTATTTACTA
2329 AATTTAAATATTTAAATAAAAA
1 AATTTAAATATTTAAATAAAAA
Statistics
Matches: 257, Mismatches: 15, Indels: 15
0.90 0.05 0.05
Matches are distributed among these distances:
83 1 0.00
84 77 0.30
85 12 0.05
86 85 0.33
87 1 0.00
88 1 0.00
89 80 0.31
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.46
Consensus pattern (87 bp):
AATTTAAATATTTAAATAAAAAAATATTATTATTATATTACAATTTTTATCAAATAATGTGTTGA
TTTGACAATACATTATTTACTA
Done.