Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010856.1 Kokia drynarioides strain JFW-HI SEQ_125824, 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: 6914
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Found at i:359 original size:20 final size:20
Alignment explanation
Indices: 336--388 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
326 AATTATTTAA
336 ATTAATGTCCAATTACAAAC
1 ATTAATGTCCAATTACAAAC
*
356 ATTAATATCCAATTACAAAC
1 ATTAATGTCCAATTACAAAC
376 ATTAATGTCCAAT
1 ATTAATGTCCAAT
389 ACTAAAATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.45, C:0.19, G:0.04, T:0.32
Consensus pattern (20 bp):
ATTAATGTCCAATTACAAAC
Found at i:1103 original size:3 final size:3
Alignment explanation
Indices: 1090--1127 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
1080 AAAATGTATT
*
1090 TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA T
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1128 GAAAAGTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1944 original size:30 final size:30
Alignment explanation
Indices: 1908--2171 Score: 224
Period size: 30 Copynumber: 9.0 Consensus size: 30
1898 CTGAACTGTT
* *
1908 CAAAAATCACATTTTGATCCTTAAACTTTC
1 CAAAAATTACATTTTGACCCTTAAACTTTC
* *
1938 CAAAAATTACATTTTAACCCTCAAACTTTC
1 CAAAAATTACATTTTGACCCTTAAACTTTC
* *
1968 AAAAAATTACATTTTGACTCC-TAAAC-ATC
1 CAAAAATTACATTTTGAC-CCTTAAACTTTC
* ** *
1997 TAAAAATTACATTTTG-CCCCGAAACTTTT
1 CAAAAATTACATTTTGACCCTTAAACTTTC
2026 CAAAAATTACATTTTGACCCTTAAACTTTC
1 CAAAAATTACATTTTGACCCTTAAACTTTC
* * *
2056 CAAAAATTATATTTCT-ACCCCTAAA-TATC
1 CAAAAATTACATTT-TGACCCTTAAACTTTC
* *
2085 CAAAAATTCCATTTTGACCC-CAAA-TTCTC
1 CAAAAATTACATTTTGACCCTTAAACTT-TC
** * *
2114 TTAAAATTACCATTTT-AGCCTCAAAC-TTC
1 CAAAAATTA-CATTTTGACCCTTAAACTTTC
* *
2143 CAAAAATTCCATTTTTGA-CCTCAAACTTT
1 CAAAAATTACA-TTTTGACCCTTAAACTTT
2172 TCAATTCGAA
Statistics
Matches: 191, Mismatches: 30, Indels: 26
0.77 0.12 0.11
Matches are distributed among these distances:
27 2 0.01
28 12 0.06
29 83 0.43
30 91 0.48
31 3 0.02
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.35
Consensus pattern (30 bp):
CAAAAATTACATTTTGACCCTTAAACTTTC
Found at i:2011 original size:29 final size:29
Alignment explanation
Indices: 1908--2171 Score: 227
Period size: 29 Copynumber: 9.0 Consensus size: 29
1898 CTGAACTGTT
* *
1908 CAAAAATCACATTTTGATCCTTAAACTTTC
1 CAAAAATTACATTTTGA-CCCTAAACTTTC
*
1938 CAAAAATTACATTTTAACCCTCAAACTTTC
1 CAAAAATTACATTTTGACCCT-AAACTTTC
* *
1968 AAAAAATTACATTTTGACTCCTAAAC-ATC
1 CAAAAATTACATTTTGAC-CCTAAACTTTC
* * * *
1997 TAAAAATTACATTTTGCCCCGAAACTTTT
1 CAAAAATTACATTTTGACCCTAAACTTTC
2026 CAAAAATTACATTTTGACCCTTAAACTTTC
1 CAAAAATTACATTTTGACCC-TAAACTTTC
* *
2056 CAAAAATTATATTTCT-ACCCCTAAA-TATC
1 CAAAAATTACATTT-TGA-CCCTAAACTTTC
* *
2085 CAAAAATTCCATTTTGACCCCAAA-TTCTC
1 CAAAAATTACATTTTGACCCTAAACTT-TC
** *
2114 TTAAAATTACCATTTT-AGCCTCAAAC-TTC
1 CAAAAATTA-CATTTTGACCCT-AAACTTTC
*
2143 CAAAAATTCCATTTTTGA-CCTCAAACTTT
1 CAAAAATTACA-TTTTGACCCT-AAACTTT
2172 TCAATTCGAA
Statistics
Matches: 191, Mismatches: 29, Indels: 28
0.77 0.12 0.11
Matches are distributed among these distances:
28 16 0.08
29 87 0.46
30 81 0.42
31 7 0.04
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.35
Consensus pattern (29 bp):
CAAAAATTACATTTTGACCCTAAACTTTC
Found at i:2034 original size:88 final size:86
Alignment explanation
Indices: 1908--2157 Score: 272
Period size: 88 Copynumber: 2.8 Consensus size: 86
1898 CTGAACTGTT
* ** * *
1908 CAAAAATCACATTTTGATCCTTAAACTTTCCAAAAATTACATTTTAACCCTCAAACTTTCAAAAA
1 CAAAAATTACATTTTGA-CCCCAAACTTTTCAAAAATTACATTTT-ACCCTCAAACTTTCCAAAA
*
1973 ATTACATTTTGACTCCTAAACATC
64 ATTACATTTT-ACCCCTAAACATC
* *
1997 TAAAAATTACATTTTG-CCCCGAAACTTTTCAAAAATTACATTTTGACCCTTAAACTTTCCAAAA
1 CAAAAATTACATTTTGACCCC-AAACTTTTCAAAAATTACATTTT-ACCCTCAAACTTTCCAAAA
* *
2061 ATTATATTTCTACCCCTAAATATC
64 ATTACATTT-TACCCCTAAACATC
* * * *
2085 CAAAAATTCCATTTTGACCCCAAA-TTCTCTTAAAATTACCATTTTAGCCTCAAAC-TTCCAAAA
1 CAAAAATTACATTTTGACCCCAAACTTTTC-AAAAATTA-CATTTTACCCTCAAACTTTCCAAAA
*
2148 ATTCCATTTT
64 ATTACATTTT
2158 TGACCTCAAA
Statistics
Matches: 137, Mismatches: 19, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
86 1 0.01
87 21 0.15
88 90 0.66
89 25 0.18
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.35
Consensus pattern (86 bp):
CAAAAATTACATTTTGACCCCAAACTTTTCAAAAATTACATTTTACCCTCAAACTTTCCAAAAAT
TACATTTTACCCCTAAACATC
Done.