Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000757.1 Kokia drynarioides strain JFW-HI SEQ_111804, 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: 21388
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.36
Found at i:975 original size:62 final size:62
Alignment explanation
Indices: 905--1028 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
895 TTGATGAAAG
905 AAAGTGCATCTTTTTTATTGAAAATAAAAAGCCAATGAACATATGTCCTTTACAAAAAGATC
1 AAAGTGCATCTTTTTTATTGAAAATAAAAAGCCAATGAACATATGTCCTTTACAAAAAGATC
967 AAAGTGCATCTTTTTTATTGAAAATAAAAAGCCAATGAACATATGTCCTTTACAAAAAGATC
1 AAAGTGCATCTTTTTTATTGAAAATAAAAAGCCAATGAACATATGTCCTTTACAAAAAGATC
1029 CCAATTGCTC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.31
Consensus pattern (62 bp):
AAAGTGCATCTTTTTTATTGAAAATAAAAAGCCAATGAACATATGTCCTTTACAAAAAGATC
Found at i:1499 original size:93 final size:92
Alignment explanation
Indices: 1318--1501 Score: 325
Period size: 91 Copynumber: 2.0 Consensus size: 92
1308 TGGCTTGCTT
1318 TTGATCTCTTCCCCACTTATTCTAGCCCTTCTCTTGTCTTGTTTTTTCTGTAGCTCTTCTTTTCT
1 TTGATCTCTTCCCCACTTATTCTAGCCCTTCTC-TGTCTTGTTTTTTCTGTAGCTCTTCTTTTCT
1383 CTGCTTCATGTTTGGGTAGTTTTTTTTA
65 CTGCTTCATGTTTGGGTAGTTTTTTTTA
* * *
1411 TTGATCTCTTCGCCACTTATTCTAGCCCTTCTC-GTCTTGTTTTTTTTGTAGCTCTTCTTTTCTT
1 TTGATCTCTTCCCCACTTATTCTAGCCCTTCTCTGTCTTGTTTTTTCTGTAGCTCTTCTTTTCTC
1475 TGCTTCATGTTTGGGTAGTTTTTTTTA
66 TGCTTCATGTTTGGGTAGTTTTTTTTA
1502 AAAGGTATTT
Statistics
Matches: 88, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
91 56 0.64
93 32 0.36
ACGTcount: A:0.09, C:0.22, G:0.14, T:0.55
Consensus pattern (92 bp):
TTGATCTCTTCCCCACTTATTCTAGCCCTTCTCTGTCTTGTTTTTTCTGTAGCTCTTCTTTTCTC
TGCTTCATGTTTGGGTAGTTTTTTTTA
Found at i:1956 original size:30 final size:29
Alignment explanation
Indices: 1916--1972 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
1906 GCTAAAAAAT
* *
1916 TAAGTATTGAATTTTTATTGATAAAATTTA
1 TAAGTATTGAATTTATATT-AAAAAATTTA
*
1946 TAAGTGTTGAATTTATATTAAAAAATT
1 TAAGTATTGAATTTATATTAAAAAATT
1973 ATTTGGTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 7 0.29
30 17 0.71
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (29 bp):
TAAGTATTGAATTTATATTAAAAAATTTA
Found at i:1969 original size:28 final size:30
Alignment explanation
Indices: 1908--1974 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
1898 AATTAAGTGC
* *
1908 TAAAAAAT-TAAGTATTGAATTTTTATTGA
1 TAAAAATTATAAGTATTGAATTTATATTGA
* *
1937 TAAAATTTATAAGTGTTGAATTTATATT-A
1 TAAAAATTATAAGTATTGAATTTATATTGA
1966 -AAAAATTAT
1 TAAAAATTAT
1975 TTGGTAAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
28 8 0.25
29 7 0.22
30 17 0.53
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.45
Consensus pattern (30 bp):
TAAAAATTATAAGTATTGAATTTATATTGA
Found at i:2070 original size:17 final size:17
Alignment explanation
Indices: 2032--2066 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
2022 TAAAAGTAAA
2032 TATTTATTTTAAAAATT
1 TATTTATTTTAAAAATT
*
2049 TATTTA-TTTAAAATTT
1 TATTTATTTTAAAAATT
2065 TA
1 TA
2067 ATTTTATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTTATTTTAAAAATT
Found at i:2196 original size:28 final size:28
Alignment explanation
Indices: 2144--2198 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
2134 AATATCTAAT
* * *
2144 TTTTTTAAAAAAATATAATTTATTTTAA
1 TTTTTTAAAAAAATAAAAATAATTTTAA
*
2172 TTTTTTAATAAAATAAAAATAATTTTA
1 TTTTTTAAAAAAATAAAAATAATTTTA
2199 CATCTTGTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
TTTTTTAAAAAAATAAAAATAATTTTAA
Found at i:6623 original size:19 final size:19
Alignment explanation
Indices: 6599--6637 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
6589 GGAACTAGAT
6599 CAAGTGGTACTACGCTTCC
1 CAAGTGGTACTACGCTTCC
*
6618 CAAGTGGTACTATGCTTCC
1 CAAGTGGTACTACGCTTCC
6637 C
1 C
6638 CATAATGACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.31, G:0.21, T:0.28
Consensus pattern (19 bp):
CAAGTGGTACTACGCTTCC
Found at i:21018 original size:12 final size:12
Alignment explanation
Indices: 21001--21025 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20991 TGACCCGTTT
21001 TCCTATAATCTA
1 TCCTATAATCTA
21013 TCCTATAATCTA
1 TCCTATAATCTA
21025 T
1 T
21026 AATATAGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.44
Consensus pattern (12 bp):
TCCTATAATCTA
Done.