Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002288.1 Kokia drynarioides strain JFW-HI SEQ_114319, 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: 44395
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Warning! 7 characters in sequence are not A, C, G, or T
Found at i:8061 original size:9 final size:9
Alignment explanation
Indices: 8047--8113 Score: 67
Period size: 9 Copynumber: 8.0 Consensus size: 9
8037 ACAAATGATT
8047 TTAAAATTA
1 TTAAAATTA
8056 TTAAAATTA
1 TTAAAATTA
8065 TT----TT-
1 TTAAAATTA
8069 TTAAAA-TA
1 TTAAAATTA
8077 -TAAAATTA
1 TTAAAATTA
8085 TTAAAATTAA
1 TTAAAATT-A
8095 TTTAAAATTA
1 -TTAAAATTA
8105 TTAAAATTA
1 TTAAAATTA
8114 CTTTTTTGAA
Statistics
Matches: 49, Mismatches: 0, Indels: 18
0.73 0.00 0.27
Matches are distributed among these distances:
4 2 0.04
5 2 0.04
7 6 0.12
8 2 0.04
9 27 0.55
10 2 0.04
11 8 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
TTAAAATTA
Found at i:8067 original size:20 final size:20
Alignment explanation
Indices: 8039--8106 Score: 63
Period size: 20 Copynumber: 3.4 Consensus size: 20
8029 GTGGCATAAC
*
8039 AAATGATTTTAAAATTATTA
1 AAATTATTTTAAAATTATTA
8059 AAATTATTTTTTAAAA-TA-TA
1 AAATTA--TTTTAAAATTATTA
8079 AAATTA--TTAAAATTAATTTA
1 AAATTATTTTAAAATT-A-TTA
8099 AAATTATT
1 AAATTATT
8107 AAAATTACTT
Statistics
Matches: 39, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
16 6 0.15
17 1 0.03
18 1 0.03
20 21 0.54
21 2 0.05
22 8 0.21
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (20 bp):
AAATTATTTTAAAATTATTA
Found at i:8109 original size:29 final size:29
Alignment explanation
Indices: 8047--8113 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
8037 ACAAATGATT
*
8047 TTAAAATTATTAAAATTATTTTTTAAAATA
1 TTAAAATTATTAAAATTA-TATTTAAAATA
8077 -TAAAATTATTAAAATTA-ATTTAAAATTA
1 TTAAAATTATTAAAATTATATTTAAAA-TA
8105 TTAAAATTA
1 TTAAAATTA
8114 CTTTTTTGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
27 7 0.21
28 2 0.06
29 25 0.74
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
TTAAAATTATTAAAATTATATTTAAAATA
Found at i:9519 original size:11 final size:11
Alignment explanation
Indices: 9503--9541 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
9493 TTATTTCAAA
9503 AAAATAATTTT
1 AAAATAATTTT
9514 AAAATAATTTT
1 AAAATAATTTT
*
9525 AAAACAATTTT
1 AAAATAATTTT
9536 ATAAAT
1 A-AAAT
9542 TTTATATTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 22 0.88
12 3 0.12
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (11 bp):
AAAATAATTTT
Found at i:9527 original size:52 final size:49
Alignment explanation
Indices: 9471--9583 Score: 131
Period size: 49 Copynumber: 2.2 Consensus size: 49
9461 AAATTTGAAA
*
9471 TTAAAATTATTTAAT-AATTTTATTATT-TCAAAAAAATAATTTTAAAATAATT
1 TTAAAATAATTTAATAAATTTTA-TATTGT--AAAAAATAATTTT--AATAATT
* *
9523 TTAAAACAATTTTATAAATTTTATATTGTAAAAAATAATTTTAATAATT
1 TTAAAATAATTTAATAAATTTTATATTGTAAAAAATAATTTTAATAATT
*
9572 TTAAAATCATTT
1 TTAAAATAATTT
9584 GCTGACATGG
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
49 17 0.31
51 13 0.24
52 16 0.30
53 8 0.15
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.48
Consensus pattern (49 bp):
TTAAAATAATTTAATAAATTTTATATTGTAAAAAATAATTTTAATAATT
Found at i:14004 original size:20 final size:20
Alignment explanation
Indices: 13974--14023 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
13964 GTTAATGTAA
13974 AATGATTTTTAAATTATCTAT
1 AATG-TTTTTAAATTATCTAT
* * *
13995 AATGTTTTTATATTATTTTT
1 AATGTTTTTAAATTATCTAT
14015 AATGTTTTT
1 AATGTTTTT
14024 TAATATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 22 0.85
21 4 0.15
ACGTcount: A:0.30, C:0.02, G:0.06, T:0.62
Consensus pattern (20 bp):
AATGTTTTTAAATTATCTAT
Found at i:14033 original size:20 final size:20
Alignment explanation
Indices: 13994--14033 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
13984 AAATTATCTA
*
13994 TAATGTTTTTATATTATTTT
1 TAATGTTTTTATAATATTTT
14014 TAATGTTTTT-TAATATTTT
1 TAATGTTTTTATAATATTTT
14033 T
1 T
14034 GAATAGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (20 bp):
TAATGTTTTTATAATATTTT
Found at i:19201 original size:24 final size:25
Alignment explanation
Indices: 19164--19215 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
19154 CAGGATCTTT
**
19164 TTCTTCTTTCTCTTCTTCCTT-TCC
1 TTCTTCTTTCTCTTAATCCTTCTCC
19188 TTCTTCTTGT-TCTTAATCCTTCTCC
1 TTCTTCTT-TCTCTTAATCCTTCTCC
19213 TTC
1 TTC
19216 AACTGATCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.04, C:0.35, G:0.02, T:0.60
Consensus pattern (25 bp):
TTCTTCTTTCTCTTAATCCTTCTCC
Found at i:27859 original size:12 final size:12
Alignment explanation
Indices: 27842--27866 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27832 TACCTGTCGC
27842 ATACTCGACCGG
1 ATACTCGACCGG
27854 ATACTCGACCGG
1 ATACTCGACCGG
27866 A
1 A
27867 CATTTCTTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.32, G:0.24, T:0.16
Consensus pattern (12 bp):
ATACTCGACCGG
Found at i:35910 original size:2 final size:2
Alignment explanation
Indices: 35903--35928 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35893 AATTGCAAAA
35903 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
35929 CTTTTCTAGC
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37732 original size:31 final size:29
Alignment explanation
Indices: 37691--37749 Score: 82
Period size: 31 Copynumber: 2.0 Consensus size: 29
37681 TCAATCATGA
*
37691 AATTAAATAAAATTAAGAAAACTTAATAAAT
1 AATTAAATAAAACTAAGAAAA--TAATAAAT
*
37722 AATTAGATAAAACTAAGAAAATAATAAA
1 AATTAAATAAAACTAAGAAAATAATAAA
37750 GGCAATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 7 0.27
31 19 0.73
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.25
Consensus pattern (29 bp):
AATTAAATAAAACTAAGAAAATAATAAAT
Found at i:37757 original size:31 final size:30
Alignment explanation
Indices: 37691--37761 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 30
37681 TCAATCATGA
* *
37691 AATTAAATAAAATTAAGAAAACTTAATAAAT
1 AATTAAATAAAACTAAGAAAAC-TAATAAAC
*
37722 AATTAGATAAAACTAAGAAAA-TAATAAAGGC
1 AATTAAATAAAACTAAGAAAACTAATAAA--C
37753 AATTAAATA
1 AATTAAATA
37762 TAAGCTAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
29 7 0.21
31 27 0.79
ACGTcount: A:0.63, C:0.04, G:0.07, T:0.25
Consensus pattern (30 bp):
AATTAAATAAAACTAAGAAAACTAATAAAC
Found at i:39854 original size:37 final size:37
Alignment explanation
Indices: 39810--39881 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 37
39800 TGATTTTAAA
39810 ATTA-TTTTTTAAAATATAAAATTATTAATATTATTAT
1 ATTATTTTTTTAAAATATAAAATTATT-ATATTATTAT
39847 ATTATTTTTTTAAAATATAAAATTATTATATTATT
1 ATTATTTTTTTAAAATATAAAATTATTATATTATT
39882 TTAATTTCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
37 12 0.35
38 22 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (37 bp):
ATTATTTTTTTAAAATATAAAATTATTATATTATTAT
Found at i:40742 original size:13 final size:13
Alignment explanation
Indices: 40724--40749 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40714 CTCTTTAATT
40724 AAATAATTTTTTA
1 AAATAATTTTTTA
40737 AAATAATTTTTTA
1 AAATAATTTTTTA
40750 TTTATATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AAATAATTTTTTA
Found at i:40801 original size:95 final size:93
Alignment explanation
Indices: 40617--40831 Score: 331
Period size: 95 Copynumber: 2.3 Consensus size: 93
40607 TTTTATGGCA
* * * *
40617 CCACCACTTTAATTAAATAATTTTTTTAATTATTTTTTATTTATATTTTTAAAACAATTTTAATT
1 CCACCACTTTAATTAAATAATTTTTTAAATAATTTTTTATTTATATTTTTAAAAAAATTTTAAAT
40682 TTTTTTGATGATGTCATATTAAATGGTG
66 TTTTTTGATGATGTCATATTAAATGGTG
*
40710 CCACCTCTTTAATTAAATAATTTTTTAAAATAATTTTTTATTTATATTTTTAAAATAAATTTTAA
1 CCACCACTTTAATTAAATAATTTTTT-AAATAATTTTTTATTTATATTTTTAAAA-AAATTTTAA
* *
40775 ATTTTTTTGGTGGTGTCATATTAAATGGTG
64 ATTTTTTTGATGATGTCATATTAAATGGTG
*
40805 TCACCACTTTAATTAAATAAATTTTTT
1 CCACCACTTTAATTAAAT-AATTTTTT
40832 TCAACAAAAG
Statistics
Matches: 110, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
93 25 0.23
94 26 0.24
95 51 0.46
96 8 0.07
ACGTcount: A:0.33, C:0.08, G:0.07, T:0.52
Consensus pattern (93 bp):
CCACCACTTTAATTAAATAATTTTTTAAATAATTTTTTATTTATATTTTTAAAAAAATTTTAAAT
TTTTTTGATGATGTCATATTAAATGGTG
Found at i:40856 original size:95 final size:94
Alignment explanation
Indices: 40658--40857 Score: 224
Period size: 95 Copynumber: 2.1 Consensus size: 94
40648 ATTTTTTATT
* * *
40658 TATATTTTTAAAACAATTTTAATTTTTTTTGATGATGTCATATTAAATGGTGCCACCTCTTTAAT
1 TATATTTTTAAAAAAATTTTAAATTTTTTTGATGATGTCATATTAAATGGTGCCACCACTTTAAT
* ***** *
40723 TAAATAATTTTTTAAAATAATTTTTTATT
66 TAAATAATTTTTTAAAACAAAAGACTATA
* * *
40752 TATATTTTTAAAATAAATTTTAAATTTTTTTGGTGGTGTCATATTAAATGGTGTCACCACTTTAA
1 TATATTTTTAAAA-AAATTTTAAATTTTTTTGATGATGTCATATTAAATGGTGCCACCACTTTAA
**
40817 TTAAATAAATTTTTTTCAACAAAAGACTA-A
65 TTAAAT-AATTTTTTAAAACAAAAGACTATA
40847 TA-ATGTTTTAA
1 TATAT-TTTTAA
40858 TTGAATAAAA
Statistics
Matches: 88, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
94 15 0.17
95 59 0.67
96 14 0.16
ACGTcount: A:0.36, C:0.07, G:0.08, T:0.48
Consensus pattern (94 bp):
TATATTTTTAAAAAAATTTTAAATTTTTTTGATGATGTCATATTAAATGGTGCCACCACTTTAAT
TAAATAATTTTTTAAAACAAAAGACTATA
Found at i:43939 original size:18 final size:18
Alignment explanation
Indices: 43898--43939 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
43888 TAAGAGTTAC
*
43898 TTAAATATATATTTGTAT
1 TTAATTATATATTTGTAT
*
43916 TAAATTATATATGTTG-AT
1 TTAATTATATAT-TTGTAT
43934 TTAATT
1 TTAATT
43940 GTTAAAGTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (18 bp):
TTAATTATATATTTGTAT
Done.