Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002240.1 Kokia drynarioides strain JFW-HI SEQ_114244, 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: 23042
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Found at i:7865 original size:3 final size:3
Alignment explanation
Indices: 7815--7851 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
7805 TTTAAGGAAG
7815 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
7852 AATAATTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:8539 original size:19 final size:18
Alignment explanation
Indices: 8490--8542 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
8480 TAAAAATAAT
*
8490 TATTTAAATTTCAAAA-A
1 TATTTAAATTTTAAAATA
**
8507 TATTTAAAAATTAAAATA
1 TATTTAAATTTTAAAATA
8525 TCATTTAAATTTTAAAAT
1 T-ATTTAAATTTTAAAAT
8543 TATAAAAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
17 13 0.45
18 2 0.07
19 14 0.48
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (18 bp):
TATTTAAATTTTAAAATA
Found at i:10646 original size:23 final size:23
Alignment explanation
Indices: 10616--10660 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
10606 GGTAAATAGT
10616 TATCTATCTTGGTCCATCTGTGC
1 TATCTATCTTGGTCCATCTGTGC
10639 TATCTATCTTGGTCCATCTGTG
1 TATCTATCTTGGTCCATCTGTG
10661 GAGATTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.44
Consensus pattern (23 bp):
TATCTATCTTGGTCCATCTGTGC
Found at i:17138 original size:30 final size:31
Alignment explanation
Indices: 17063--17138 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
17053 TTGATCTAAT
* *
17063 TTGGTACTCAAACTTAACACTTTTTCTTAAT
1 TTGGTACTTAAACTTAACACTTTTTCTTAAG
* * *
17094 TTGATACCTAAACTTGACACTTTTT-TTAAG
1 TTGGTACTTAAACTTAACACTTTTTCTTAAG
17124 TTGGTACTTAAACTT
1 TTGGTACTTAAACTT
17139 TTTGGGGTCC
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 17 0.45
31 21 0.55
ACGTcount: A:0.29, C:0.17, G:0.09, T:0.45
Consensus pattern (31 bp):
TTGGTACTTAAACTTAACACTTTTTCTTAAG
Found at i:17154 original size:89 final size:90
Alignment explanation
Indices: 17017--17193 Score: 214
Period size: 89 Copynumber: 2.0 Consensus size: 90
17007 GTATCTGAAT
* ** * *
17017 TTGACACATTTTCTTAATTTAGTACTTAAACTTTTTTTGATCTAATTTGGTA-CTCAAACTTAAC
1 TTGACACATTTTCTTAAGTTAGTACTTAAACTTTTTGGGATCCAATTTGATACCT-AAACTTAAC
* **
17081 ACTTTTTCTTAATTTGATACCTAAAC
65 ACTATTTCCCAATTTGATACCTAAAC
* * * *
17107 TTGACAC-TTTTTTTAAGTTGGTACTTAAACTTTTTGGGGTCCAATTTGATACCTAAACTTAACT
1 TTGACACATTTTCTTAAGTTAGTACTTAAACTTTTTGGGATCCAATTTGATACCTAAACTTAACA
*
17171 CTATTTCCCAATTTGGTACCTAA
66 CTATTTCCCAATTTGATACCTAA
17194 TCTTTTTTTA
Statistics
Matches: 73, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
89 64 0.88
90 9 0.12
ACGTcount: A:0.28, C:0.18, G:0.10, T:0.45
Consensus pattern (90 bp):
TTGACACATTTTCTTAAGTTAGTACTTAAACTTTTTGGGATCCAATTTGATACCTAAACTTAACA
CTATTTCCCAATTTGATACCTAAAC
Found at i:17469 original size:59 final size:58
Alignment explanation
Indices: 17335--17508 Score: 178
Period size: 59 Copynumber: 3.0 Consensus size: 58
17325 TAATATTTAA
17335 TAAA-TTTAG-TACCAAATTGAATCTAAAAAAAAAGTTTAGGTACCAAATTAGGAAAAA-TG
1 TAAAGTTTAGATACCAAATTGAATC--AAAAAAAA-TTTAGGTACCAAATTA-GAAAAATTG
* * ** *
17394 TCAAGTTCA-AGTACCAAATTGGGTCAAAAAAAATTTAGGTCCCAAATTAGAAGAAATTG
1 TAAAGTTTAGA-TACCAAATTGAATCAAAAAAAATTTAGGTACCAAATTAGAA-AAATTG
* * * *
17453 TAAAGTTTAGATACCAAATTGATTTAAAAAAAA-TTAGATACCAAATTAAAAAAATT
1 TAAAGTTTAGATACCAAATTGAATCAAAAAAAATTTAGGTACCAAATTAGAAAAATT
17509 ATCAAATTTA
Statistics
Matches: 96, Mismatches: 13, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
57 8 0.08
58 33 0.34
59 39 0.41
60 4 0.04
61 12 0.12
ACGTcount: A:0.50, C:0.10, G:0.13, T:0.28
Consensus pattern (58 bp):
TAAAGTTTAGATACCAAATTGAATCAAAAAAAATTTAGGTACCAAATTAGAAAAATTG
Found at i:22497 original size:60 final size:60
Alignment explanation
Indices: 22432--22582 Score: 178
Period size: 60 Copynumber: 2.5 Consensus size: 60
22422 TTAATATAAC
* * * * *
22432 ATTTGATACTTGAACTTGATATTTTTTCCTAATTTGGTACCTAAATATTTTTTGGACCTA
1 ATTTGATACTTGAACTTGATATTTTTTCCTAATTTAGTACCTAAAAACTTTTTGAACCCA
* * * *
22492 ATTTGATACTTAAACTTGACACTTTTTCTTAATTTAGTACCTAAAAACTTTTTGAACCCA
1 ATTTGATACTTGAACTTGATATTTTTTCCTAATTTAGTACCTAAAAACTTTTTGAACCCA
* *
22552 ATTTGGTACATGAACTTCGCAT-TTTTTTCCT
1 ATTTGATACTTGAACTT-G-ATATTTTTTCCT
22583 GTACCTAAGC
Statistics
Matches: 74, Mismatches: 15, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
60 65 0.88
61 8 0.11
62 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.10, T:0.46
Consensus pattern (60 bp):
ATTTGATACTTGAACTTGATATTTTTTCCTAATTTAGTACCTAAAAACTTTTTGAACCCA
Found at i:22932 original size:90 final size:90
Alignment explanation
Indices: 22767--22950 Score: 244
Period size: 90 Copynumber: 2.0 Consensus size: 90
22757 TTAAAAAAAA
* *
22767 TTAGGTATCAAATTAGGAAAAAGAGTCAAATTCAGGTACCAAATTGGATCATAAAAAGTTTAAGT
1 TTAGGTACCAAATTAGGAAAAAGAGTCAAATTCAGGTACCAAATTGGATCAAAAAAAGTTTAAGT
* *
22832 ACCAACTTAAAAAAAAGTGTCAAGC
66 ACCAAATTAAAAAAAAATGTCAAGC
* * * * * *
22857 TTAGGTACCAAATTAGGAAAGAGTGTCAAGTT-TGAGTATCAAATTGGATCAAAAAAAGTTTAGG
1 TTAGGTACCAAATTAGGAAAAAGAGTCAAATTCAG-GTACCAAATTGGATCAAAAAAAGTTTAAG
* *
22921 TATCAAATTAAAAAAAAATGTCAAGT
65 TACCAAATTAAAAAAAAATGTCAAGC
22947 TTAG
1 TTAG
22951 ATATCAAAAT
Statistics
Matches: 81, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
89 1 0.01
90 80 0.99
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.27
Consensus pattern (90 bp):
TTAGGTACCAAATTAGGAAAAAGAGTCAAATTCAGGTACCAAATTGGATCAAAAAAAGTTTAAGT
ACCAAATTAAAAAAAAATGTCAAGC
Found at i:22950 original size:31 final size:31
Alignment explanation
Indices: 22822--22958 Score: 95
Period size: 31 Copynumber: 4.5 Consensus size: 31
22812 GGATCATAAA
* * * *
22822 AAGTTTAAGTACCAACTTAAAAAAAAGTGTC
1 AAGTTTAGGTATCAAATTAAAAAAAAATGTC
* * ** * *
22853 AAGCTTAGGTACCAAATTAGGAAAGAGTGTC
1 AAGTTTAGGTATCAAATTAAAAAAAAATGTC
* **
22884 AAGTTT-GAGTATCAAATTGGATCAAAAA----
1 AAGTTTAG-GTATCAAATT-AAAAAAAAATGTC
22912 AAGTTTAGGTATCAAATTAAAAAAAAATGTC
1 AAGTTTAGGTATCAAATTAAAAAAAAATGTC
*
22943 AAGTTTAGATATCAAA
1 AAGTTTAGGTATCAAA
22959 ATATTATATT
Statistics
Matches: 81, Mismatches: 18, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
27 6 0.07
28 16 0.20
29 1 0.01
30 1 0.01
31 54 0.67
32 3 0.04
ACGTcount: A:0.47, C:0.09, G:0.17, T:0.27
Consensus pattern (31 bp):
AAGTTTAGGTATCAAATTAAAAAAAAATGTC
Done.