Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006434.1 Kokia drynarioides strain JFW-HI SEQ_121016, 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: 9206
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.35
Found at i:463 original size:23 final size:23
Alignment explanation
Indices: 433--478 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
423 TAATCATATA
433 ACTTCTAGATTTGTTTCCTAATG
1 ACTTCTAGATTTGTTTCCTAATG
456 ACTTCTAGATTTGTTTCCTAATG
1 ACTTCTAGATTTGTTTCCTAATG
479 TAATGATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.17, G:0.13, T:0.48
Consensus pattern (23 bp):
ACTTCTAGATTTGTTTCCTAATG
Found at i:3452 original size:24 final size:22
Alignment explanation
Indices: 3390--3458 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
3380 GAATTAAATC
**
3390 TTATATTTTTATAATAGTAAAA
1 TTATATTTTTATAATTTTAAAA
* * *
3412 TTATAATTTTATTATTTTAATAGT
1 TTATATTTTTATAATTTTAA-A-A
3436 TTATATTTTTATAATTTTTAAAA
1 TTATATTTTTATAA-TTTTAAAA
3459 ATTTAAATCA
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
22 16 0.44
23 1 0.03
24 13 0.36
25 6 0.17
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (22 bp):
TTATATTTTTATAATTTTAAAA
Found at i:5518 original size:2 final size:2
Alignment explanation
Indices: 5511--5537 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5501 AATAAATAAA
5511 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
5538 AATAGAAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9047 original size:30 final size:29
Alignment explanation
Indices: 9005--9166 Score: 145
Period size: 29 Copynumber: 5.5 Consensus size: 29
8995 CCATTTTACT
9005 CCCGAACTTCCAAAAATCCCATATTTGAC
1 CCCGAACTTCCAAAAATCCCATATTTGAC
* *
9034 CCCGAACCTTCCAAAAAT--TATCATTTTAC
1 CCCGAA-CTTCCAAAAATCCCAT-ATTTGAC
9063 CCTCGAACTTCCAAAAATCCCAT-TTTGAC
1 CC-CGAACTTCCAAAAATCCCATATTTGAC
* * * *
9092 CCCGAACCTTTCGAAAAT--TATCATTTTAC
1 CCCGAA-CTTCCAAAAATCCCAT-ATTTGAC
* *
9121 CTTCGAACTTCCAAAAATCCCATTTTTGAC
1 C-CCGAACTTCCAAAAATCCCATATTTGAC
*
9151 TCCGAATCTTCCAAAA
1 CCCGAA-CTTCCAAAA
9167 CTACCATTTT
Statistics
Matches: 105, Mismatches: 16, Indels: 23
0.73 0.11 0.16
Matches are distributed among these distances:
27 2 0.02
28 6 0.06
29 60 0.57
30 33 0.31
31 4 0.04
ACGTcount: A:0.33, C:0.31, G:0.06, T:0.30
Consensus pattern (29 bp):
CCCGAACTTCCAAAAATCCCATATTTGAC
Found at i:9116 original size:58 final size:58
Alignment explanation
Indices: 8996--9166 Score: 263
Period size: 58 Copynumber: 2.9 Consensus size: 58
8986 ATATATACTC
8996 CATTTTACTCC-CGAACTTCCAAAAATCCCATATTTGACCCCGAACCTTCCAAAAATTAT
1 CATTTTAC-CCTCGAACTTCCAAAAATCCCAT-TTTGACCCCGAACCTTCCAAAAATTAT
* *
9055 CATTTTACCCTCGAACTTCCAAAAATCCCATTTTGACCCCGAACCTTTCGAAAATTAT
1 CATTTTACCCTCGAACTTCCAAAAATCCCATTTTGACCCCGAACCTTCCAAAAATTAT
* * *
9113 CATTTTACCTTCGAACTTCCAAAAATCCCATTTTTGACTCCGAATCTTCCAAAA
1 CATTTTACCCTCGAACTTCCAAAAATCCCA-TTTTGACCCCGAACCTTCCAAAA
9167 CTACCATTTT
Statistics
Matches: 103, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
58 56 0.54
59 47 0.46
ACGTcount: A:0.32, C:0.31, G:0.06, T:0.31
Consensus pattern (58 bp):
CATTTTACCCTCGAACTTCCAAAAATCCCATTTTGACCCCGAACCTTCCAAAAATTAT
Found at i:9176 original size:29 final size:28
Alignment explanation
Indices: 8995--9181 Score: 166
Period size: 30 Copynumber: 6.5 Consensus size: 28
8985 TATATATACT
*
8995 CCATTTT-ACTCCCGAACTTCCAAAAATC
1 CCATTTTGAC-CCCGAACTTCCAAAAATA
9023 CCATATTTGACCCCGAACCTTCCAAAAATTA
1 CCAT-TTTGACCCCGAA-CTTCCAAAAA-TA
* *
9054 TCATTTT-ACCCTCGAACTTCCAAAAATC
1 CCATTTTGACCC-CGAACTTCCAAAAATA
* *
9082 CCATTTTGACCCCGAACCTTTCGAAAATTA
1 CCATTTTGACCCCGAA-C-TTCCAAAAATA
* * *
9112 TCATTTT-ACCTTCGAACTTCCAAAAATC
1 CCATTTTGACC-CCGAACTTCCAAAAATA
* *
9140 CCATTTTTGACTCCGAATCTTCCAAAACTA
1 CCA-TTTTGACCCCGAA-CTTCCAAAAATA
9170 CCATTTTG-CCCC
1 CCATTTTGACCCC
9182 TGTGCATCCG
Statistics
Matches: 129, Mismatches: 18, Indels: 24
0.75 0.11 0.14
Matches are distributed among these distances:
28 28 0.22
29 45 0.35
30 52 0.40
31 4 0.03
ACGTcount: A:0.30, C:0.33, G:0.06, T:0.31
Consensus pattern (28 bp):
CCATTTTGACCCCGAACTTCCAAAAATA
Done.