Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005357.1 Kokia drynarioides strain JFW-HI SEQ_119336, 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: 3826
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Found at i:2562 original size:24 final size:21
Alignment explanation
Indices: 2534--2585 Score: 61
Period size: 24 Copynumber: 2.4 Consensus size: 21
2524 TTTTAGATTT
2534 TATATTTTTTTCTGAATTTTTCTA
1 TATATTTTTTTCT--ATTTTT-TA
*
2558 TATATTTATTTCTATTTTTTA
1 TATATTTTTTTCTATTTTTTA
2579 TAT-TTTT
1 TATATTTT
2586 AATGTGTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 3 0.12
21 5 0.19
22 6 0.23
24 12 0.46
ACGTcount: A:0.21, C:0.06, G:0.02, T:0.71
Consensus pattern (21 bp):
TATATTTTTTTCTATTTTTTA
Found at i:2985 original size:31 final size:31
Alignment explanation
Indices: 2949--3028 Score: 115
Period size: 31 Copynumber: 2.6 Consensus size: 31
2939 TTTTTTGTCC
**
2949 AATTTGGTATTTAAACTTGAGACTTTTTCTT
1 AATTTGGTACCTAAACTTGAGACTTTTTCTT
* *
2980 AATTTGGTACCTAAGCTTGATACTTTTTCTT
1 AATTTGGTACCTAAACTTGAGACTTTTTCTT
*
3011 AATTTGATACCTAAACTT
1 AATTTGGTACCTAAACTT
3029 TTTGGGGTCT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.28, C:0.14, G:0.11, T:0.47
Consensus pattern (31 bp):
AATTTGGTACCTAAACTTGAGACTTTTTCTT
Found at i:3058 original size:90 final size:89
Alignment explanation
Indices: 2914--3083 Score: 232
Period size: 90 Copynumber: 1.9 Consensus size: 89
2904 AACTTGACAT
* * *** * * *
2914 TTTTTCTTAATTTGGTATCTAAATTTTTTTTGTCCAATTTGGTATTTAAACTTGAGACTTTTTCT
1 TTTTTCTTAATTTGATACCTAAATTTTTGGGGTCCAATTTGGTACTTAAACTTGACACTTTTTCC
2979 TAATTTGGTACCTAAGCTTGATAC
66 TAATTTGGTACCTAAGCTTGATAC
* **
3003 TTTTTCTTAATTTGATACCTAAACTTTTTGGGGTCTAATTTGGTACTTAAACTTGACTGTTTTTC
1 TTTTTCTTAATTTGATACCTAAA-TTTTTGGGGTCCAATTTGGTACTTAAACTTGACACTTTTTC
3068 CTAATTTGGTACCTAA
65 CTAATTTGGTACCTAA
3084 TTTTTTTTAA
Statistics
Matches: 69, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
89 21 0.30
90 48 0.70
ACGTcount: A:0.24, C:0.14, G:0.13, T:0.50
Consensus pattern (89 bp):
TTTTTCTTAATTTGATACCTAAATTTTTGGGGTCCAATTTGGTACTTAAACTTGACACTTTTTCC
TAATTTGGTACCTAAGCTTGATAC
Found at i:3292 original size:60 final size:61
Alignment explanation
Indices: 3199--3330 Score: 167
Period size: 60 Copynumber: 2.2 Consensus size: 61
3189 TTAATATAAT
** * * *
3199 ATTTGGTATTTGAACTTGGTACTTTTTCCTAATTTGGTACCTAA-ACTTTTTTTGGACCCA
1 ATTTGGTACCTGAACTTGGCACTTTTTCCTAATTTGGCACCTAATACTTTTTTTAGACCCA
* * **
3259 ATTTGGTACCTGAACTTGGCATTTTTTCCTAATTTGGCACCTAATATTTTTTTTAGATTCA
1 ATTTGGTACCTGAACTTGGCACTTTTTCCTAATTTGGCACCTAATACTTTTTTTAGACCCA
*
3320 ATTTGATACCT
1 ATTTGGTACCT
3331 AAATTTATTA
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
60 39 0.64
61 22 0.36
ACGTcount: A:0.23, C:0.17, G:0.14, T:0.47
Consensus pattern (61 bp):
ATTTGGTACCTGAACTTGGCACTTTTTCCTAATTTGGCACCTAATACTTTTTTTAGACCCA
Found at i:3522 original size:31 final size:31
Alignment explanation
Indices: 3487--3675 Score: 124
Period size: 31 Copynumber: 6.2 Consensus size: 31
3477 GATTAGGTAT
*
3487 CAAATTAGAAAAAAGAGTCAAGTTCAAGTAC
1 CAAATTAGAAAAAAGAGTCAAGTTTAAGTAC
*** *
3518 CAAATTAGACTCCAA-A---AAGCTTAAGTAC
1 CAAATTAGA-AAAAAGAGTCAAGTTTAAGTAC
* *
3546 CAACCTTA-AAAAAAGTGTCAAGTTTAAGTAC
1 CAA-ATTAGAAAAAAGAGTCAAGTTTAAGTAC
* * * *
3577 CAAATTAGGAAAATGGGTCAAGTTTGAGTAC
1 CAAATTAGAAAAAAGAGTCAAGTTTAAGTAC
* **
3608 TAAATTAGACAAAAA-A-AAAAGTTTAAGTAC
1 CAAATTAGA-AAAAAGAGTCAAGTTTAAGTAC
* *
3638 CAAATTAAAAAAAAAAATGTCAAGTTT-AGATAC
1 CAAATT-AGAAAAAAGA-GTCAAGTTTAAG-TAC
3671 CAAAT
1 CAAAT
3676 GTTATATTAA
Statistics
Matches: 118, Mismatches: 27, Indels: 24
0.70 0.16 0.14
Matches are distributed among these distances:
27 2 0.02
28 14 0.12
29 3 0.03
30 24 0.20
31 53 0.45
32 8 0.07
33 14 0.12
ACGTcount: A:0.50, C:0.13, G:0.14, T:0.23
Consensus pattern (31 bp):
CAAATTAGAAAAAAGAGTCAAGTTTAAGTAC
Found at i:3637 original size:30 final size:28
Alignment explanation
Indices: 3596--3654 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 28
3586 AAAATGGGTC
* *
3596 AAGTTTGAGTACTAAATTAGACAAAAAAAA
1 AAGTTTAAGTACCAAATTA-A-AAAAAAAA
3626 AAGTTTAAGTACCAAATTAAAAAAAAAA
1 AAGTTTAAGTACCAAATTAAAAAAAAAA
3654 A
1 A
3655 TGTCAAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 9 0.33
29 1 0.04
30 17 0.63
ACGTcount: A:0.61, C:0.07, G:0.10, T:0.22
Consensus pattern (28 bp):
AAGTTTAAGTACCAAATTAAAAAAAAAA
Found at i:3662 original size:27 final size:30
Alignment explanation
Indices: 3603--3662 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
3593 GTCAAGTTTG
* *
3603 AGTACTAAATTAGACAAAAAAAAAAGTTTA
1 AGTACCAAATTAGACAAAAAAAAAAGTTCA
*
3633 AGTACCAAATTA-A-AAAAAAAAATG-TCA
1 AGTACCAAATTAGACAAAAAAAAAAGTTCA
3660 AGT
1 AGT
3663 TTAGATACCA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 5 0.19
28 10 0.37
29 1 0.04
30 11 0.41
ACGTcount: A:0.60, C:0.08, G:0.10, T:0.22
Consensus pattern (30 bp):
AGTACCAAATTAGACAAAAAAAAAAGTTCA
Done.