Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004887.1 Kokia drynarioides strain JFW-HI SEQ_118570, 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: 43539
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1925 original size:36 final size:36
Alignment explanation
Indices: 1885--1998 Score: 106
Period size: 36 Copynumber: 3.2 Consensus size: 36
1875 AATAATGAAT
*
1885 TGTGCCCTACGCTGGCCGGTAAAATCGACAAATTGG
1 TGTGCCCTACGCTGGTCGGTAAAATCGACAAATTGG
* ** ** * *
1921 TGTGCCCGACATTGGTTAGTATAATCGA-AAACTTAG
1 TGTGCCCTACGCTGGTCGGTAAAATCGACAAA-TTGG
* *
1957 TGCGCCCTATGCTGGTCGGTAAAATCGACAAA-TGAG
1 TGTGCCCTACGCTGGTCGGTAAAATCGACAAATTG-G
1993 TGTGCC
1 TGTGCC
1999 TAATACTGAT
Statistics
Matches: 57, Mismatches: 18, Indels: 6
0.70 0.22 0.07
Matches are distributed among these distances:
35 4 0.07
36 50 0.88
37 3 0.05
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25
Consensus pattern (36 bp):
TGTGCCCTACGCTGGTCGGTAAAATCGACAAATTGG
Found at i:3510 original size:18 final size:18
Alignment explanation
Indices: 3487--3523 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
3477 TTGAAACCCT
3487 TAGTTTCGTGTATCTTTC
1 TAGTTTCGTGTATCTTTC
3505 TAGTTTCGTGTATCTTTC
1 TAGTTTCGTGTATCTTTC
3523 T
1 T
3524 TCATTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.11, C:0.16, G:0.16, T:0.57
Consensus pattern (18 bp):
TAGTTTCGTGTATCTTTC
Found at i:8664 original size:2 final size:2
Alignment explanation
Indices: 8647--8684 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
8637 ACAAAGTAAC
*
8647 AT AT A- AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8685 AGAACAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:9103 original size:22 final size:22
Alignment explanation
Indices: 9075--9119 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
9065 GAAATGTCTA
9075 GTTTTGACAACACTTAAAACAT
1 GTTTTGACAACACTTAAAACAT
* * *
9097 GTTTTGACAGCATTTGAAACAT
1 GTTTTGACAACACTTAAAACAT
9119 G
1 G
9120 CTTTAACAGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (22 bp):
GTTTTGACAACACTTAAAACAT
Found at i:9128 original size:22 final size:22
Alignment explanation
Indices: 9091--9133 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
9081 ACAACACTTA
* *
9091 AAACATGTTTTGACAGCATTTG
1 AAACATGCTTTAACAGCATTTG
9113 AAACATGCTTTAACAGCATTT
1 AAACATGCTTTAACAGCATTT
9134 AAAGCATATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (22 bp):
AAACATGCTTTAACAGCATTTG
Found at i:19036 original size:23 final size:24
Alignment explanation
Indices: 19010--19079 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
19000 AGATTGAATT
19010 TTTTA-TTTAAAAAAACAAAAGGA
1 TTTTATTTTAAAAAAACAAAAGGA
***
19033 TTTTATTTTTTTAAAACAAAAGGA
1 TTTTATTTTAAAAAAACAAAAGGA
19057 TTTTATTTTTAAAAAAA-AAAAGG
1 TTTTA-TTTTAAAAAAACAAAAGG
19080 GAATAAAAGG
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
23 5 0.13
24 26 0.67
25 8 0.21
ACGTcount: A:0.50, C:0.03, G:0.09, T:0.39
Consensus pattern (24 bp):
TTTTATTTTAAAAAAACAAAAGGA
Found at i:30844 original size:21 final size:21
Alignment explanation
Indices: 30797--30873 Score: 59
Period size: 21 Copynumber: 3.7 Consensus size: 21
30787 AATCGTGCAG
* *
30797 ACTTCTACCGATACATGTGAT
1 ACTTCTACCGATACAAGAGAT
*
30818 AGTTCTACCGATACAAGAGACT
1 ACTTCTACCGATACAAGAGA-T
* * *
30840 -CTTCTACCAAAACAAGTA-TT
1 ACTTCTACCGATACAAG-AGAT
*
30860 ACTTCTACCAATAC
1 ACTTCTACCGATAC
30874 TAAAAACTCC
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
20 1 0.02
21 42 0.93
22 2 0.04
ACGTcount: A:0.35, C:0.26, G:0.10, T:0.29
Consensus pattern (21 bp):
ACTTCTACCGATACAAGAGAT
Found at i:31053 original size:21 final size:21
Alignment explanation
Indices: 31027--31066 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
31017 TACCCTATAC
* *
31027 TTCTACCGACACATGTATGGA
1 TTCTACCGAAACAAGTATGGA
31048 TTCTACCGAAACAAGTATG
1 TTCTACCGAAACAAGTATG
31067 CAGAATCTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.28
Consensus pattern (21 bp):
TTCTACCGAAACAAGTATGGA
Done.