Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005258.1 Kokia drynarioides strain JFW-HI SEQ_119163, 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: 15847
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Found at i:932 original size:17 final size:18
Alignment explanation
Indices: 902--936 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
892 AATACAAAAA
902 TAGTATCGATATAAAATTT
1 TAGTATCGA-ATAAAATTT
921 TAGTATCG-ATAAAATT
1 TAGTATCGAATAAAATT
937 CAATACGCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (18 bp):
TAGTATCGAATAAAATTT
Found at i:3897 original size:15 final size:15
Alignment explanation
Indices: 3877--3916 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
3867 TAAAGGATCC
3877 ATTAAATCAAATTGA
1 ATTAAATCAAATTGA
* *
3892 ATTAAATTAAGTTGA
1 ATTAAATCAAATTGA
*
3907 ATCAAATCAA
1 ATTAAATCAA
3917 TTAAATATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (15 bp):
ATTAAATCAAATTGA
Found at i:5662 original size:27 final size:28
Alignment explanation
Indices: 5588--5665 Score: 81
Period size: 27 Copynumber: 2.8 Consensus size: 28
5578 AAATTTTAAT
*
5588 TTTTTATATATATTTTTAAAATTTTGAAAA
1 TTTTTATAAATA-TTTT-AAATTTTGAAAA
* *
5618 TTGTTTTTAAA-A-TATAAATTTTGAAAA
1 TT-TTTATAAATATTTTAAATTTTGAAAA
5645 -TTTTATAAATATTTTAAATTT
1 TTTTTATAAATATTTTAAATTT
5666 AAAAAGTTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
25 7 0.17
26 2 0.05
27 20 0.50
28 2 0.05
30 3 0.08
31 6 0.15
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (28 bp):
TTTTTATAAATATTTTAAATTTTGAAAA
Found at i:5696 original size:9 final size:9
Alignment explanation
Indices: 5675--5718 Score: 54
Period size: 10 Copynumber: 4.7 Consensus size: 9
5665 TAAAAAGTTA
5675 TTTTGAA-T
1 TTTTGAATT
5683 TTTTGAATT
1 TTTTGAATT
5692 TTTTGAATTT
1 TTTTGAA-TT
5702 TTTTGTAATT
1 TTTTG-AATT
5712 TTGTTGA
1 TT-TTGA
5719 GAGAGGCCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
8 7 0.22
9 8 0.25
10 12 0.38
11 5 0.16
ACGTcount: A:0.20, C:0.00, G:0.14, T:0.66
Consensus pattern (9 bp):
TTTTGAATT
Found at i:8872 original size:9 final size:9
Alignment explanation
Indices: 8858--8939 Score: 54
Period size: 9 Copynumber: 9.7 Consensus size: 9
8848 ATAATCACCC
8858 ATTAAAATT
1 ATTAAAATT
8867 ATTAAAATT
1 ATTAAAATT
8876 ATT----TT
1 ATTAAAATT
8881 -TTAAAATT
1 ATTAAAATT
8889 A-TAAAATTCT
1 ATTAAAA-T-T
*
8899 TTTAAATATT
1 ATTAAA-ATT
* *
8909 TTTTAAA-T
1 ATTAAAATT
8917 A-TAAAATT
1 ATTAAAATT
8925 ATTAAAATT
1 ATTAAAATT
8934 ATTAAA
1 ATTAAA
8940 TAATTTTAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 22
0.69 0.05 0.26
Matches are distributed among these distances:
4 2 0.03
5 2 0.03
7 4 0.07
8 10 0.17
9 27 0.47
10 7 0.12
11 5 0.09
12 1 0.02
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (9 bp):
ATTAAAATT
Found at i:8894 original size:30 final size:28
Alignment explanation
Indices: 8860--8936 Score: 102
Period size: 30 Copynumber: 2.7 Consensus size: 28
8850 AATCACCCAT
8860 TAAAATTATTAAAATTATTTTTTAAAATTA
1 TAAAATTATTAAAATTATTTTTT-AAA-TA
* *
8890 TAAAATTCTTTTAAA-TATTTTTTAAATA
1 TAAAATT-ATTAAAATTATTTTTTAAATA
8918 TAAAATTATTAAAATTATT
1 TAAAATTATTAAAATTATT
8937 AAATAATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 5 0.12
28 13 0.32
29 3 0.07
30 15 0.37
31 5 0.12
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (28 bp):
TAAAATTATTAAAATTATTTTTTAAATA
Found at i:8895 original size:21 final size:22
Alignment explanation
Indices: 8859--8901 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
8849 TAATCACCCA
8859 TTAAAATTATTAAAATTATTTT
1 TTAAAATTATTAAAATTATTTT
*
8881 TTAAAATTA-TAAAATTCTTTT
1 TTAAAATTATTAAAATTATTTT
8902 AAATATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAAAATTATTAAAATTATTTT
Found at i:9024 original size:35 final size:35
Alignment explanation
Indices: 8985--9053 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
8975 TATTTTTTCT
8985 CCATTTTTCCATCTAACACCACTTCTTATTCTCAC
1 CCATTTTTCCATCTAACACCACTTCTTATTCTCAC
* *
9020 CCATTTTTCCATCTAGCACCACTTCTTCTTCTCA
1 CCATTTTTCCATCTAACACCACTTCTTATTCTCA
9054 TCATCCAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.20, C:0.38, G:0.01, T:0.41
Consensus pattern (35 bp):
CCATTTTTCCATCTAACACCACTTCTTATTCTCAC
Found at i:9943 original size:51 final size:51
Alignment explanation
Indices: 9872--9971 Score: 159
Period size: 52 Copynumber: 2.0 Consensus size: 51
9862 GATGATGATG
9872 ATTTTAATAATTTTATA-TTTTAAAAAATAATTTTAAGTTAATTTTAAAATAA
1 ATTTTAATAATTTTATATTTTTAAAAAATAATTTTAA--TAATTTTAAAATAA
*
9924 ATTTT-ATATTTTTATATTTTTAAAAAATAATTTTAATAATTTTAAAAT
1 ATTTTAATAATTTTATATTTTTAAAAAATAATTTTAATAATTTTAAAAT
9972 CATTTGTTGA
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
50 12 0.26
51 10 0.22
52 24 0.52
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (51 bp):
ATTTTAATAATTTTATATTTTTAAAAAATAATTTTAATAATTTTAAAATAA
Found at i:10629 original size:3 final size:3
Alignment explanation
Indices: 10617--10664 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
10607 GTATCTCTAT
*
10617 TTC TTC -TC TTC TTC TT- TTC -TC TTT TTC TTC TTC TTC -TC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
10661 TTC T
1 TTC T
10665 ACTGCCCAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 8 0.21
3 31 0.79
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:10630 original size:8 final size:8
Alignment explanation
Indices: 10617--10661 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
10607 GTATCTCTAT
10617 TTCTTCTC
1 TTCTTCTC
10625 TTC-T-TC
1 TTCTTCTC
10631 TT-TTCTC
1 TTCTTCTC
*
10638 TTTTTCTTC
1 TTCTTC-TC
10647 TTCTTCTC
1 TTCTTCTC
10655 TTCTTCT
1 TTCTTCT
10662 TCTACTGCCC
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
6 5 0.16
7 5 0.16
8 15 0.47
9 7 0.22
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (8 bp):
TTCTTCTC
Found at i:10631 original size:11 final size:11
Alignment explanation
Indices: 10617--10664 Score: 66
Period size: 11 Copynumber: 4.6 Consensus size: 11
10607 GTATCTCTAT
10617 TTCTTCTCTTC
1 TTCTTCTCTTC
*
10628 TTCTTTTC-TC
1 TTCTTCTCTTC
10638 TT-TT-TCTTC
1 TTCTTCTCTTC
10647 TTCTTCTCTTC
1 TTCTTCTCTTC
10658 TTCTTCT
1 TTCTTCT
10665 ACTGCCCAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
8 2 0.06
9 6 0.18
10 6 0.18
11 19 0.58
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (11 bp):
TTCTTCTCTTC
Found at i:15480 original size:6 final size:6
Alignment explanation
Indices: 15469--15553 Score: 65
Period size: 6 Copynumber: 14.7 Consensus size: 6
15459 GGGCCCAACA
* * * *
15469 AAATTT AAATTT -ATTTT AAAATT AAATTT -ATTTT AAGTTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
15515 --ATTT AAAATTT AAATTT --ATTAT AAATTT AAAGTTT AAAT
1 AAATTT -AAATTT AAATTT AAATT-T AAATTT AAA-TTT AAAT
15554 ATATTTAAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
4 7 0.11
5 9 0.14
6 34 0.54
7 13 0.21
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:15515 original size:34 final size:34
Alignment explanation
Indices: 15469--15550 Score: 121
Period size: 34 Copynumber: 2.4 Consensus size: 34
15459 GGGCCCAACA
*
15469 AAATTTAAATTTATTTTAAAA-TTAAATTTATTTT
1 AAATTTAAATTTA-TTTAAAATTTAAATTTATTAT
*
15503 AAGTTTAAATTTATTTAAAATTTAAATTTATTAT
1 AAATTTAAATTTATTTAAAATTTAAATTTATTAT
15537 AAATTTAAAGTTTA
1 AAATTTAAA-TTTA
15551 AATATATTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
33 7 0.16
34 32 0.74
35 4 0.09
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (34 bp):
AAATTTAAATTTATTTAAAATTTAAATTTATTAT
Found at i:15542 original size:24 final size:23
Alignment explanation
Indices: 15515--15563 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
15505 GTTTAAATTT
*
15515 ATTTAAAATTTAAATTTATTATAA
1 ATTTAAAATTTAAATATATT-TAA
*
15539 ATTTAAAGTTTAAATATATTTAA
1 ATTTAAAATTTAAATATATTTAA
15562 AT
1 AT
15564 CAAAGTCCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
ATTTAAAATTTAAATATATTTAA
Found at i:15560 original size:34 final size:34
Alignment explanation
Indices: 15469--15563 Score: 95
Period size: 34 Copynumber: 2.8 Consensus size: 34
15459 GGGCCCAACA
** *
15469 AAATTTAAATTTATTTTAAAA-TTAAATTTATTTT
1 AAATTTAAATTTA-AATAAAATTTAAATTTATTAT
* **
15503 AAGTTTAAATTTATTTAAAATTTAAATTTATTAT
1 AAATTTAAATTTAAATAAAATTTAAATTTATTAT
*
15537 AAATTTAAAGTTTAAAT-ATATTTAAAT
1 AAATTTAAA-TTTAAATAAAATTTAAAT
15564 CAAAGTCCAA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
33 7 0.13
34 41 0.77
35 5 0.09
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (34 bp):
AAATTTAAATTTAAATAAAATTTAAATTTATTAT
Found at i:15562 original size:17 final size:16
Alignment explanation
Indices: 15469--15550 Score: 101
Period size: 17 Copynumber: 4.8 Consensus size: 16
15459 GGGCCCAACA
15469 AAATTTAAATTTATTTT
1 AAATTTAAATTTA-TTT
*
15486 AAAATTAAATTTATTTT
1 AAATTTAAATTTA-TTT
*
15503 AAGTTTAAATTTATTT
1 AAATTTAAATTTATTT
15519 AAAATTTAAATTTATTAT
1 -AAATTTAAATTTATT-T
15537 AAATTTAAAGTTTA
1 AAATTTAAA-TTTA
15551 AATATATTTA
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
16 3 0.05
17 50 0.86
18 5 0.09
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
AAATTTAAATTTATTT
Found at i:15626 original size:17 final size:17
Alignment explanation
Indices: 15604--15636 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
15594 CAAGCCCAAT
*
15604 TAAATGACCCTAATACC
1 TAAATGACCCAAATACC
15621 TAAATGACCCAAATAC
1 TAAATGACCCAAATAC
15637 TAATGGACCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.27, G:0.06, T:0.21
Consensus pattern (17 bp):
TAAATGACCCAAATACC
Done.