Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002387.1 Kokia drynarioides strain JFW-HI SEQ_114470, 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: 7685
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Found at i:4626 original size:18 final size:18
Alignment explanation
Indices: 4603--4640 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
4593 ATAATCCCAC
4603 AAATTTAGGAATCTTAAT
1 AAATTTAGGAATCTTAAT
4621 AAATTTAGGAATCTTAAT
1 AAATTTAGGAATCTTAAT
4639 AA
1 AA
4641 TGACTGATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.37
Consensus pattern (18 bp):
AAATTTAGGAATCTTAAT
Found at i:5180 original size:164 final size:163
Alignment explanation
Indices: 4752--5217 Score: 772
Period size: 163 Copynumber: 2.9 Consensus size: 163
4742 TTTTTACACT
* *
4752 CCTCAAGCTGGGGTGTATATGTTATACATTCCCAGCTTGGAGTTGAA-TCATCGAAGTTGATTCT
1 CCTCAAGCT-GGGTGTATATGTTATACATTCCCAGATTGGAGTTGAATTCATCGAAGATGATTCT
* * *
4816 TGGAAAAACTTTGGTGAGAATGTCAGCAAGTTGCAGCTGTGTAGGGATGTAGCTCAGTTGGACTA
65 TGGAAGAGCTTTGGTGAGAATGTCAGCAAGTTGCAGCTGAGTAGGGATGTAGCTCAGTTGGACTA
* * *
4881 TTTCATTGTTTGGGTGTATATGTTATACACTCCC
130 TTCCATTGTTGGGGTGTATATGGTATACACTCCC
4915 CCTCAAGCTGGGTGTATATGTTATACATTCCCAGATTGGAGTTGAATTCATCGAAGATGATTCTT
1 CCTCAAGCTGGGTGTATATGTTATACATTCCCAGATTGGAGTTGAATTCATCGAAGATGATTCTT
4980 GGAAGAGCTTTGGTGAGAATGTCAGCAAGTTGCAGCTGAGTAGGGATGTAGCTCAGTTGGACTAT
66 GGAAGAGCTTTGGTGAGAATGTCAGCAAGTTGCAGCTGAGTAGGGATGTAGCTCAGTTGGACTAT
5045 TCCATTGTTGGGGTGTATATGGTATACACTCCC
131 TCCATTGTTGGGGTGTATATGGTATACACTCCC
* * * * *
5078 CCTCAAGCTGAGGTTTATGTGTTATACATTCCCAGATTGGAGTTGAATTCATTGAAGCTAATTCT
1 CCTCAAGCTG-GGTGTATATGTTATACATTCCCAGATTGGAGTTGAATTCATCGAAGATGATTCT
* *
5143 TGGAAGAGTTTTGGTGAGAATGTCAGCAAGTTGCAGCTGAGTACGGATGTAGCTCAGTTGGACTA
65 TGGAAGAGCTTTGGTGAGAATGTCAGCAAGTTGCAGCTGAGTAGGGATGTAGCTCAGTTGGACTA
5208 TTCCATTGTT
130 TTCCATTGTT
5218 AACCTTCTCT
Statistics
Matches: 286, Mismatches: 15, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
162 36 0.13
163 128 0.45
164 122 0.43
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.33
Consensus pattern (163 bp):
CCTCAAGCTGGGTGTATATGTTATACATTCCCAGATTGGAGTTGAATTCATCGAAGATGATTCTT
GGAAGAGCTTTGGTGAGAATGTCAGCAAGTTGCAGCTGAGTAGGGATGTAGCTCAGTTGGACTAT
TCCATTGTTGGGGTGTATATGGTATACACTCCC
Found at i:6189 original size:97 final size:97
Alignment explanation
Indices: 6023--6202 Score: 270
Period size: 97 Copynumber: 1.9 Consensus size: 97
6013 TATAATAATC
* * * *
6023 CCTATTCTTCTTTTGTTGCTATTATTTAAACCAACTGTTATATAATAGCACCATAGAAAGATCAA
1 CCTATTCTTCTGTTGTTGCTATTATTTAAACCAACTGTTATATAACAACACAATAGAAAGATCAA
*
6088 TAGAAGAACGAAGTAAAACTCTTTTTATTTTT
66 TAGAACAACGAAGTAAAACTCTTTTTATTTTT
* * * * *
6120 CCTATTCTTGTGTTGTTGCTATTATTTACACCAACTGTTCTATCACAACACAATAGAAAGGTCAA
1 CCTATTCTTCTGTTGTTGCTATTATTTAAACCAACTGTTATATAACAACACAATAGAAAGATCAA
6185 TAGAACAACGAAGTAAAA
66 TAGAACAACGAAGTAAAA
6203 ATTCTTTGTG
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
97 73 1.00
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (97 bp):
CCTATTCTTCTGTTGTTGCTATTATTTAAACCAACTGTTATATAACAACACAATAGAAAGATCAA
TAGAACAACGAAGTAAAACTCTTTTTATTTTT
Found at i:7525 original size:2 final size:2
Alignment explanation
Indices: 7520--7545 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
7510 TATATATATA
7520 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
7546 CCTGCTTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Done.