Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012108.1 Kokia drynarioides strain JFW-HI SEQ_127107, 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: 265239
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 112 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:235844 original size:24 final size:24
Alignment explanation
Indices: 235800--235845 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
235790 GTTTGACTGC
235800 AACAAATAAACAGAGTTTAATTAA
1 AACAAATAAACAGAGTTTAATTAA
*
235824 AACAAATAGACAGAGTTTAATT
1 AACAAATAAACAGAGTTTAATT
235846 GAAATATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.54, C:0.09, G:0.11, T:0.26
Consensus pattern (24 bp):
AACAAATAAACAGAGTTTAATTAA
Found at i:237798 original size:24 final size:24
Alignment explanation
Indices: 237770--237844 Score: 132
Period size: 24 Copynumber: 3.1 Consensus size: 24
237760 AATTTGACTC
237770 AAACAAATAAATAGAGTTTAATTG
1 AAACAAATAAATAGAGTTTAATTG
237794 AAACAAATAAATAGAGTTTAATTG
1 AAACAAATAAATAGAGTTTAATTG
* *
237818 AAACAATTAAACAGAGTTTAATTG
1 AAACAAATAAATAGAGTTTAATTG
237842 AAA
1 AAA
237845 TATTATTTCT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.55, C:0.05, G:0.12, T:0.28
Consensus pattern (24 bp):
AAACAAATAAATAGAGTTTAATTG
Found at i:245938 original size:22 final size:22
Alignment explanation
Indices: 245910--245953 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
245900 ACATTAGAGT
* *
245910 ATTCATCTTTAATTTCATCATG
1 ATTCATCTCTAATTTCAACATG
245932 ATTCATCTCTAATTTCAACATG
1 ATTCATCTCTAATTTCAACATG
245954 GCATTAGAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (22 bp):
ATTCATCTCTAATTTCAACATG
Found at i:248519 original size:29 final size:29
Alignment explanation
Indices: 248486--248541 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
248476 TTGAATATGA
248486 TAAATGTGAGCATTTGTGACTGATTTTAT
1 TAAATGTGAGCATTTGTGACTGATTTTAT
* *
248515 TAAATGTGAGCCTTTGTGGCTGATTTT
1 TAAATGTGAGCATTTGTGACTGATTTT
248542 GTAAATGACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.23, C:0.09, G:0.23, T:0.45
Consensus pattern (29 bp):
TAAATGTGAGCATTTGTGACTGATTTTAT
Found at i:248608 original size:26 final size:26
Alignment explanation
Indices: 248578--248634 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
248568 AATGGAAAAG
* *
248578 CCTTTGTGACTATCTCTGATTGGACA
1 CCTTTGTGACCATCTCTAATTGGACA
* *
248604 CCTTTGTGGCCATCTCTAATTGGACG
1 CCTTTGTGACCATCTCTAATTGGACA
248630 CCTTT
1 CCTTT
248635 ACGACTACCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.16, C:0.26, G:0.19, T:0.39
Consensus pattern (26 bp):
CCTTTGTGACCATCTCTAATTGGACA
Found at i:248689 original size:28 final size:28
Alignment explanation
Indices: 248658--248711 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
248648 GTTTGATGAT
*
248658 GCCT-TCTAGCTATCTATTGTTCAAGGAC
1 GCCTCTCTAGCTATCTA-TGTTAAAGGAC
* *
248686 GCCTCTGTAGTTATCTATGTTAAAGG
1 GCCTCTCTAGCTATCTATGTTAAAGG
248712 GAAGACTTCG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
28 12 0.55
29 10 0.45
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.37
Consensus pattern (28 bp):
GCCTCTCTAGCTATCTATGTTAAAGGAC
Found at i:250243 original size:18 final size:19
Alignment explanation
Indices: 250204--250250 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
250194 AAAGAGAAAG
250204 TTTTAATTTAATCCCTAAC
1 TTTTAATTTAATCCCTAAC
*
250223 TTTTAATTTAATCTC-AAC
1 TTTTAATTTAATCCCTAAC
250241 TTTTAATTTA
1 TTTTAATTTA
250251 TTTCAATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.32, C:0.15, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTAATTTAATCCCTAAC
Found at i:262591 original size:24 final size:24
Alignment explanation
Indices: 262564--262611 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
262554 AAAAGAGCAA
* *
262564 GGACAGAGACAGGGAAAGGGAGAG
1 GGACAGAGAAAGAGAAAGGGAGAG
*
262588 GGACAGAGAAAGAGACAGGGAGAG
1 GGACAGAGAAAGAGAAAGGGAGAG
262612 AGCAAAGGCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.44, C:0.08, G:0.48, T:0.00
Consensus pattern (24 bp):
GGACAGAGAAAGAGAAAGGGAGAG
Found at i:262598 original size:18 final size:18
Alignment explanation
Indices: 262564--262619 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
262554 AAAAGAGCAA
* *
262564 GGACAGAGACAGGGAAAG
1 GGACAGGGACAGAGAAAG
*
262582 GGAGAGGGACAGAGAAAG
1 GGACAGGGACAGAGAAAG
* *
262600 AGACAGGGAGAGAGCAAAG
1 GGACAGGGACAGAG-AAAG
262619 G
1 G
262620 CCCGGGATCG
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
18 26 0.87
19 4 0.13
ACGTcount: A:0.45, C:0.09, G:0.46, T:0.00
Consensus pattern (18 bp):
GGACAGGGACAGAGAAAG
Done.