Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011385.1 Kokia drynarioides strain JFW-HI SEQ_126367, 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: 22438
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Found at i:1417 original size:120 final size:120
Alignment explanation
Indices: 1201--1451 Score: 376
Period size: 120 Copynumber: 2.1 Consensus size: 120
1191 ATATGTACAA
* * *
1201 ATACCGTATCGATGGATAGGGTACCGCATATGTTACGAGTCCTCGACAGCTTGTGTGAGCAGCAT
1 ATACCGTATCGATGGATAGGGTACCGCATATGTTACGAATCCCCGACAGCTCGTGTGAGCAGCAT
* * * *
1266 CGTATACTGGTAATAGAGTTGATACAGACATGAGAATGAAATTTAGGATTATAGC
66 CGTATACTGGAAATAGAGTTGATACAAACATGAGAATGAAATTCAAGATTATAGC
* * * * *
1321 ATACCGTATCGATGGCTGGGGTATCGCATATTTTGCGAATCCCCGACAGCTCGTGTGAGCAGCAT
1 ATACCGTATCGATGGATAGGGTACCGCATATGTTACGAATCCCCGACAGCTCGTGTGAGCAGCAT
*
1386 TGTATACTGGAAATAGAGTTGATACAAACATGAGAATGAAATTCAAGATTATAGC
66 CGTATACTGGAAATAGAGTTGATACAAACATGAGAATGAAATTCAAGATTATAGC
*
1441 ATACTGTATCG
1 ATACCGTATCG
1452 CATATGTTGT
Statistics
Matches: 117, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
120 117 1.00
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (120 bp):
ATACCGTATCGATGGATAGGGTACCGCATATGTTACGAATCCCCGACAGCTCGTGTGAGCAGCAT
CGTATACTGGAAATAGAGTTGATACAAACATGAGAATGAAATTCAAGATTATAGC
Found at i:4498 original size:17 final size:17
Alignment explanation
Indices: 4476--4510 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
4466 AGGGAAAGTC
4476 AAGATGAAGTTTGTGTT
1 AAGATGAAGTTTGTGTT
4493 AAGATGAAGTTTGTGTT
1 AAGATGAAGTTTGTGTT
4510 A
1 A
4511 CTTGATATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.29, T:0.40
Consensus pattern (17 bp):
AAGATGAAGTTTGTGTT
Found at i:12608 original size:120 final size:120
Alignment explanation
Indices: 12390--12667 Score: 351
Period size: 120 Copynumber: 2.3 Consensus size: 120
12380 ATATGTACAA
* * * * * **
12390 ATACTGTATCTATGGCTGGGGTACCGCATATGTTGCTAGTCCTCAATAGCTCGTGTGATTAGCAT
1 ATACCGTATCAATGGCTGGGGTACCGCATATGTTGCGAGTCCTCAACAGCTCGTATGAGCAGCAT
* * *
12455 CGTATATTAGTAACAAAGTTTATACAGACATGAGAATGAAATTCGGGATTAT-AG
66 CATATACTAGTAACAAAGTTGATACAGACATGAGAATGAAATTCGGGATTATAAG
* ** *
12509 CATATCGTATCAATGGCTGGGGTACCGCATATGTTGCGAGTCCTTGACAGCTCGTATGAGCAGTA
1 -ATACCGTATCAATGGCTGGGGTACCGCATATGTTGCGAGTCCTCAACAGCTCGTATGAGCAGCA
* * *
12574 TCATATGCTGGTAACAGAGTTGATACAGACATGAGAATGAAATTCGGGATTATAAG
65 TCATATACTAGTAACAAAGTTGATACAGACATGAGAATGAAATTCGGGATTATAAG
** * *
12630 ATACCGTATTGATGGCTGGAGTACCGCATATGTCGCGA
1 ATACCGTATCAATGGCTGGGGTACCGCATATGTTGCGA
12668 ATCCATGAAT
Statistics
Matches: 135, Mismatches: 22, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
120 133 0.99
121 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (120 bp):
ATACCGTATCAATGGCTGGGGTACCGCATATGTTGCGAGTCCTCAACAGCTCGTATGAGCAGCAT
CATATACTAGTAACAAAGTTGATACAGACATGAGAATGAAATTCGGGATTATAAG
Found at i:17998 original size:2 final size:2
Alignment explanation
Indices: 17991--18019 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
17981 AGCAAGCATC
17991 AT AT 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 A
18020 CTAGCATACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20230 original size:20 final size:20
Alignment explanation
Indices: 20194--20231 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
20184 CCCAAATGGA
*
20194 AATCTAATCATTTTTAATCC
1 AATCTAATCATTATTAATCC
20214 AATCTTAATCA-TATTAAT
1 AATC-TAATCATTATTAAT
20232 AAGCATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.39, C:0.16, G:0.00, T:0.45
Consensus pattern (20 bp):
AATCTAATCATTATTAATCC
Found at i:20363 original size:22 final size:23
Alignment explanation
Indices: 20337--20399 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 23
20327 GACAAATATT
20337 TTATAAAAATAAAATATTTAAAA
1 TTATAAAAATAAAATATTTAAAA
* *
20360 -TATATATATAAAA-ATTTAAAA
1 TTATAAAAATAAAATATTTAAAA
20381 TTATTTACAAAATAAAATA
1 TTA--TA-AAAATAAAATA
20400 AATACTGTGG
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
21 8 0.26
22 13 0.42
24 2 0.06
25 7 0.23
26 1 0.03
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (23 bp):
TTATAAAAATAAAATATTTAAAA
Done.