Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008927.1 Kokia drynarioides strain JFW-HI SEQ_123618, 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: 16183
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:529 original size:168 final size:168
Alignment explanation
Indices: 225--743 Score: 698
Period size: 168 Copynumber: 3.1 Consensus size: 168
215 GAAGATGATG
** * *
225 GTTGTCCTCCTGTCACCCCTGGCATTGGACATGGTCTGGACTCTGGAAGATAAACTATTTGAATG
1 GTTGTCCTCCAATCACCCCTGGCATTGGACA-----TGG--TCTGGAAGATGAACTATTTGGATG
*
290 ACCTGTAAAATTGAAGTCTAAGCCAGCC-GTGAGCTGGTCAACTGCTGATCGTTATTCATTGGTG
59 ACCTGTAAAATTGAAGTCTAAGCCAGCCTGTGAGCTGGTCAACTGCTGATTGTTATTCATTGGTG
*
354 CTGAATTTGTATGCGGAGCTGATGCTTGAATCTATTGTGATGGAT
124 CTGAATTTGTATGCGGAGCTGATGCTTGAATCTGTTGTGATGGAT
* * * * *
399 TTTGTCCTTCAATCACCCCTGGCATTGGACATGGTCTGGAAGATGAACTATTCGGACGACCTATA
1 GTTGTCCTCCAATCACCCCTGGCATTGGACATGGTCTGGAAGATGAACTATTTGGATGACCTGTA
* * * *
464 AAATAGAAGTCTAAGCCAGCCTGCGAGCTGGTCAACTGCTGATTGTTACTCATTGGTTCTGAATT
66 AAATTGAAGTCTAAGCCAGCCTGTGAGCTGGTCAACTGCTGATTGTTATTCATTGGTGCTGAATT
*
529 TGTATGCGGAGCTGATGCTTGAATTTGTTGTGATGGAT
131 TGTATGCGGAGCTGATGCTTGAATCTGTTGTGATGGAT
* * * * * *
567 GTTGTCCTCCTATCACCCCTGGTATTGGACATTGTCTAGAAGATGTACTATTTAGATGACCTGTA
1 GTTGTCCTCCAATCACCCCTGGCATTGGACATGGTCTGGAAGATGAACTATTTGGATGACCTGTA
* * * * * * *
632 AAATTGAAGTCTAATCCAGCCTGTAAGCTGGTCAACTTCTGATTGTTATTTATTTGTGCCGAATA
66 AAATTGAAGTCTAAGCCAGCCTGTGAGCTGGTCAACTGCTGATTGTTATTCATTGGTGCTGAATT
*
697 TGTATGCAGAGCTGATGCTTGAATCTGTTGTGATGGAT
131 TGTATGCGGAGCTGATGCTTGAATCTGTTGTGATGGAT
735 GTTGTCCTC
1 GTTGTCCTC
744 TTATCCTTGA
Statistics
Matches: 304, Mismatches: 40, Indels: 8
0.86 0.11 0.02
Matches are distributed among these distances:
167 46 0.15
168 228 0.75
169 3 0.01
174 27 0.09
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (168 bp):
GTTGTCCTCCAATCACCCCTGGCATTGGACATGGTCTGGAAGATGAACTATTTGGATGACCTGTA
AAATTGAAGTCTAAGCCAGCCTGTGAGCTGGTCAACTGCTGATTGTTATTCATTGGTGCTGAATT
TGTATGCGGAGCTGATGCTTGAATCTGTTGTGATGGAT
Found at i:2326 original size:16 final size:16
Alignment explanation
Indices: 2305--2338 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2295 GACTTATTTG
*
2305 ATAACATAGATTGAGA
1 ATAACATAGATTAAGA
2321 ATAACATAGATTAAGA
1 ATAACATAGATTAAGA
2337 AT
1 AT
2339 TTTCAATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.15, T:0.26
Consensus pattern (16 bp):
ATAACATAGATTAAGA
Found at i:12664 original size:52 final size:52
Alignment explanation
Indices: 12603--12707 Score: 156
Period size: 52 Copynumber: 2.0 Consensus size: 52
12593 AAACGGAGCA
* * * * *
12603 CTCCACTTTGCCGACGGTAACATATAATCCTTCGATTGTAGCAATTAGGTTC
1 CTCCACTTTGCCGACGGCAACACAGAATCCTTCGATTGCACCAATTAGGTTC
*
12655 CTCCACTTTGCCGACGGCAACACAGAATCTTTCGATTGCACCAATTAGGTTC
1 CTCCACTTTGCCGACGGCAACACAGAATCCTTCGATTGCACCAATTAGGTTC
12707 C
1 C
12708 ACTTGCATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.30
Consensus pattern (52 bp):
CTCCACTTTGCCGACGGCAACACAGAATCCTTCGATTGCACCAATTAGGTTC
Found at i:14532 original size:21 final size:21
Alignment explanation
Indices: 14506--14574 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 21
14496 GGACATACCA
14506 ATGCCTAGGGTACTCCCATGG
1 ATGCCTAGGGTACTCCCATGG
* *
14527 ATGCCT-GTGGAAGACATACCA---
1 ATGCCTAG-GG--TAC-TCCCATGG
14548 ATGCCTAGGGTACTCCCATGG
1 ATGCCTAGGGTACTCCCATGG
14569 ATGCCT
1 ATGCCT
14575 GTGGAATATA
Statistics
Matches: 36, Mismatches: 4, Indels: 16
0.64 0.07 0.29
Matches are distributed among these distances:
18 4 0.11
19 2 0.06
20 1 0.03
21 22 0.61
22 1 0.03
23 2 0.06
24 4 0.11
ACGTcount: A:0.23, C:0.28, G:0.26, T:0.23
Consensus pattern (21 bp):
ATGCCTAGGGTACTCCCATGG
Found at i:14544 original size:42 final size:42
Alignment explanation
Indices: 14497--14580 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
14487 CCATTGTTTG
14497 GACATACCAATGCCTAGGGTACTCCCATGGATGCCTGTGGAA
1 GACATACCAATGCCTAGGGTACTCCCATGGATGCCTGTGGAA
14539 GACATACCAATGCCTAGGGTACTCCCATGGATGCCTGTGGAA
1 GACATACCAATGCCTAGGGTACTCCCATGGATGCCTGTGGAA
14581 TATACATCTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.21
Consensus pattern (42 bp):
GACATACCAATGCCTAGGGTACTCCCATGGATGCCTGTGGAA
Done.