Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010622.1 Kokia drynarioides strain JFW-HI SEQ_125555, 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: 4292
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.37
Warning! 101 characters in sequence are not A, C, G, or T
Found at i:737 original size:52 final size:52
Alignment explanation
Indices: 665--803 Score: 174
Period size: 52 Copynumber: 2.7 Consensus size: 52
655 ATGGATTATG
* * * *
665 AGGTTCGATGACTATGTGTCATCATGAGTATATGAAACTTTTACGAATTACA
1 AGGTTCGATAACTATGTGTCATCGTGAGTATATAAAACCTTTACGAATTACA
* **
717 AGG-TCTGATAACTATGTGTCATCGTGAGTATATAAAACCTTTACGGATTATG
1 AGGTTC-GATAACTATGTGTCATCGTGAGTATATAAAACCTTTACGAATTACA
* *
769 AGGTTCGATGACTATGTGTTATCGTGAGTAT-TAAA
1 AGGTTCGATAACTATGTGTCATCGTGAGTATATAAA
804 TGACAAATTA
Statistics
Matches: 76, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
51 6 0.08
52 68 0.89
53 2 0.03
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.35
Consensus pattern (52 bp):
AGGTTCGATAACTATGTGTCATCGTGAGTATATAAAACCTTTACGAATTACA
Found at i:2010 original size:7 final size:7
Alignment explanation
Indices: 1998--2027 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
1988 CTAAGTTCTT
1998 GTTTAGG
1 GTTTAGG
2005 GTTTAGG
1 GTTTAGG
*
2012 ATTTAGG
1 GTTTAGG
2019 GTTTAGG
1 GTTTAGG
2026 GT
1 GT
2028 GAGATTACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.17, C:0.00, G:0.40, T:0.43
Consensus pattern (7 bp):
GTTTAGG
Found at i:3502 original size:37 final size:36
Alignment explanation
Indices: 3452--3665 Score: 239
Period size: 37 Copynumber: 5.8 Consensus size: 36
3442 TTGCATCTAA
* *
3452 GTATTCGGGCTATGTGTCTAGCAGGCTTCGTGTCGAT
1 GTATTC-GGCTATGTGCCTAGCAGGCTTCATGTCGAT
**
3489 GTATTCAGGCTATGTGCCTAATAGGCTTCATGTCGAT
1 GTATTC-GGCTATGTGCCTAGCAGGCTTCATGTCGAT
* *
3526 GTACTCGGGCTATGTGCCTAGCAAGCTTCATGTCGAT
1 GTATTC-GGCTATGTGCCTAGCAGGCTTCATGTCGAT
* * * *
3563 GTATTCGAGCTACGTTCCTAGCAGGCTTCATGCCGGT
1 GTATTCG-GCTATGTGCCTAGCAGGCTTCATGTCGAT
* * *
3600 GTATTCAGGCTATGTGCCTAGCAAGCTTCGTGCCGAT
1 GTATTC-GGCTATGTGCCTAGCAGGCTTCATGTCGAT
* *
3637 GTATTCGAGATATGTGCCTAGAAGGCTTC
1 GTATTCG-GCTATGTGCCTAGCAGGCTTC
3666 GTCAGTGCAA
Statistics
Matches: 150, Mismatches: 24, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
36 2 0.01
37 147 0.98
38 1 0.01
ACGTcount: A:0.19, C:0.22, G:0.28, T:0.32
Consensus pattern (36 bp):
GTATTCGGCTATGTGCCTAGCAGGCTTCATGTCGAT
Found at i:3589 original size:74 final size:74
Alignment explanation
Indices: 3456--3665 Score: 280
Period size: 74 Copynumber: 2.8 Consensus size: 74
3446 ATCTAAGTAT
* *
3456 TCGGGCTATGTGTCTAGCAGGCTTCGTGTCGATGTATTC-AGGCTATGTGCCTA-ATAGGCTTCA
1 TCGGGCTATGTGCCTAGCAAGCTTCGTGTCGATGTATTCGA-GCTATGTGCCTAGA-AGGCTTCA
*
3519 TGTCGATGTAC
64 TGCCGATGTAC
* * * *
3530 TCGGGCTATGTGCCTAGCAAGCTTCATGTCGATGTATTCGAGCTACGTTCCTAGCAGGCTTCATG
1 TCGGGCTATGTGCCTAGCAAGCTTCGTGTCGATGTATTCGAGCTATGTGCCTAGAAGGCTTCATG
* *
3595 CCGGTGTAT
66 CCGATGTAC
* * *
3604 TCAGGCTATGTGCCTAGCAAGCTTCGTGCCGATGTATTCGAGATATGTGCCTAGAAGGCTTC
1 TCGGGCTATGTGCCTAGCAAGCTTCGTGTCGATGTATTCGAGCTATGTGCCTAGAAGGCTTC
3666 GTCAGTGCAA
Statistics
Matches: 118, Mismatches: 16, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
74 117 0.99
75 1 0.01
ACGTcount: A:0.19, C:0.22, G:0.28, T:0.31
Consensus pattern (74 bp):
TCGGGCTATGTGCCTAGCAAGCTTCGTGTCGATGTATTCGAGCTATGTGCCTAGAAGGCTTCATG
CCGATGTAC
Found at i:3651 original size:111 final size:111
Alignment explanation
Indices: 3452--3665 Score: 279
Period size: 111 Copynumber: 1.9 Consensus size: 111
3442 TTGCATCTAA
* * * * * *
3452 GTATTCGGGCTATGTGTCTAGCAGGCTTCGTGTCGATGTATTCAGGCTATGTGCCTAATAGGCTT
1 GTATTCGAGCTACGTGTCTAGCAGGCTTCATGCCGATGTATTCAGGCTATGTGCCTAACAAGCTT
* * *
3517 CATGTCGATGTACTCGGGCTATGTGCCTAGCAA-GCTTCATGTCGAT
66 CATGCCGATGTACTCGAGATATGTGCCTAG-AAGGCTTCATGTCGAT
* *
3563 GTATTCGAGCTACGT-TCCTAGCAGGCTTCATGCCGGTGTATTCAGGCTATGTGCCTAGCAAGCT
1 GTATTCGAGCTACGTGT-CTAGCAGGCTTCATGCCGATGTATTCAGGCTATGTGCCTAACAAGCT
* *
3627 TCGTGCCGATGTATTCGAGATATGTGCCTAGAAGGCTTC
65 TCATGCCGATGTACTCGAGATATGTGCCTAGAAGGCTTC
3666 GTCAGTGCAA
Statistics
Matches: 88, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
110 3 0.03
111 85 0.97
ACGTcount: A:0.19, C:0.22, G:0.28, T:0.32
Consensus pattern (111 bp):
GTATTCGAGCTACGTGTCTAGCAGGCTTCATGCCGATGTATTCAGGCTATGTGCCTAACAAGCTT
CATGCCGATGTACTCGAGATATGTGCCTAGAAGGCTTCATGTCGAT
Done.