Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006004.1 Kokia drynarioides strain JFW-HI SEQ_120435, 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: 23211
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Warning! 37 characters in sequence are not A, C, G, or T
Found at i:2000 original size:12 final size:12
Alignment explanation
Indices: 1983--2019 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
1973 TTGATTGCTG
1983 TAGTTGACACAA
1 TAGTTGACACAA
1995 TAGTTGACACAA
1 TAGTTGACACAA
2007 TAGTTGACACAA
1 TAGTTGACACAA
2019 T
1 T
2020 CAGCATTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (12 bp):
TAGTTGACACAA
Found at i:14977 original size:68 final size:70
Alignment explanation
Indices: 14905--15055 Score: 207
Period size: 68 Copynumber: 2.2 Consensus size: 70
14895 ATTTTAATAG
* * * * * * *
14905 TTTTAATATTAAATTTAATTTTATATTTATTTTGAT-AGTATTTTATTAATTTAATATTAAAGTA
1 TTTTAATATTAAATATAATATAATATTTATCTTGATAACTATTCTATTAACTTAATATTAAAGTA
14969 ATT-A
66 ATTAA
*
14973 TTTTAATATTAAATATAATATAATATTTATCTTGATAACTATTCTATTAACTTAATATTAAAGTG
1 TTTTAATATTAAATATAATATAATATTTATCTTGATAACTATTCTATTAACTTAATATTAAAGTA
15038 ATTAA
66 ATTAA
*
15043 GTTTAATATTAAA
1 TTTTAATATTAAA
15056 GAAATAATAT
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
68 32 0.44
69 27 0.38
70 13 0.18
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.52
Consensus pattern (70 bp):
TTTTAATATTAAATATAATATAATATTTATCTTGATAACTATTCTATTAACTTAATATTAAAGTA
ATTAA
Found at i:18291 original size:23 final size:23
Alignment explanation
Indices: 18261--18305 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
18251 GGGGTCAAAT
18261 TTTTTA-TTTATTACTAATATATG
1 TTTTTATTTTATT-CTAATATATG
*
18284 TTTTTATTTTATTGTAATATAT
1 TTTTTATTTTATTCTAATATAT
18306 TTTATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.64
Consensus pattern (23 bp):
TTTTTATTTTATTCTAATATATG
Found at i:18598 original size:29 final size:29
Alignment explanation
Indices: 18537--18595 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
18527 TTTTTTAAAA
**
18537 TTATGTTTTTTATAAGTTTTTAAGAATTT
1 TTATGTTTTTTATAAAATTTTAAGAATTT
18566 TTATG-TTTTTATAAAATTTTAA-ATATTT
1 TTATGTTTTTTATAAAATTTTAAGA-ATTT
18594 TT
1 TT
18596 TATTAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 1 0.04
28 21 0.78
29 5 0.19
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.63
Consensus pattern (29 bp):
TTATGTTTTTTATAAAATTTTAAGAATTT
Found at i:18633 original size:9 final size:9
Alignment explanation
Indices: 18543--18636 Score: 59
Period size: 9 Copynumber: 10.0 Consensus size: 9
18533 AAAATTATGT
18543 TTTTTATAA
1 TTTTTATAA
*
18552 GTTTTTAAGAA
1 -TTTTT-ATAA
*
18563 TTTTTAT-G
1 TTTTTATAA
18571 TTTTTATAAAA
1 TTTTTAT--AA
* *
18582 TTTTAAATAT
1 TTTT-TATAA
18592 TTTTTATTAA
1 TTTTTA-TAA
18602 -TTTTATAA
1 TTTTTATAA
18610 TTTATTAT-A
1 TTT-TTATAA
18619 TTTTTATAA
1 TTTTTATAA
*
18628 TATTTATAA
1 TTTTTATAA
18637 GTTCCTATTA
Statistics
Matches: 66, Mismatches: 9, Indels: 19
0.70 0.10 0.20
Matches are distributed among these distances:
8 14 0.21
9 22 0.33
10 21 0.32
11 7 0.11
12 2 0.03
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:18782 original size:27 final size:28
Alignment explanation
Indices: 18739--18810 Score: 76
Period size: 29 Copynumber: 2.6 Consensus size: 28
18729 AATGATTTTT
* *
18739 TTTATATTTTAATAAATTTA-TA-ATTG
1 TTTATAATTTAATAAATTTATTATATTA
*
18765 TTTATAATTTATTAAAATTTATTATATTA
1 TTTATAATTTAAT-AAATTTATTATATTA
*
18794 TTTATAAGTTTTATAAA
1 TTTATAA-TTTAATAAA
18811 ATATTAAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
26 11 0.30
27 7 0.19
28 2 0.05
29 13 0.35
30 4 0.11
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (28 bp):
TTTATAATTTAATAAATTTATTATATTA
Found at i:18816 original size:38 final size:39
Alignment explanation
Indices: 18754--18831 Score: 97
Period size: 38 Copynumber: 2.0 Consensus size: 39
18744 ATTTTAATAA
* ** *
18754 ATTTATAATTGTTTATAATTTATTAAA-ATTTATTATATT
1 ATTTATAAGTGTTTATAAAATATTAAATATATATT-TATT
18793 ATTTATAAGT-TTTATAAAATATTAAATATATATTTATT
1 ATTTATAAGTGTTTATAAAATATTAAATATATATTTATT
18831 A
1 A
18832 GTTTTAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
38 19 0.56
39 15 0.44
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (39 bp):
ATTTATAAGTGTTTATAAAATATTAAATATATATTTATT
Found at i:18979 original size:10 final size:10
Alignment explanation
Indices: 18956--18987 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
18946 TTTTAAATTT
18956 TTTTATAATA
1 TTTTATAATA
18966 -TTTATAATA
1 TTTTATAATA
18975 TTTTATAATA
1 TTTTATAATA
18985 TTT
1 TTT
18988 GTATGCTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TTTTATAATA
Found at i:19050 original size:18 final size:18
Alignment explanation
Indices: 19029--19090 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 18
19019 TTTTGATAAG
*
19029 TTTTATGATTTCTTATG-T
1 TTTTATGAATT-TTATGAT
19047 TTTTAATGAATTTTATGAT
1 TTTT-ATGAATTTTATGAT
*
19066 TTTTAT-AACTTTTTAAGAT
1 TTTTATGAA--TTTTATGAT
19085 TTTTAT
1 TTTTAT
19091 ATATTTTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
17 2 0.05
18 11 0.29
19 25 0.66
ACGTcount: A:0.26, C:0.03, G:0.08, T:0.63
Consensus pattern (18 bp):
TTTTATGAATTTTATGAT
Found at i:19051 original size:101 final size:100
Alignment explanation
Indices: 18865--19052 Score: 297
Period size: 101 Copynumber: 1.9 Consensus size: 100
18855 TTATTAGAAT
* * *
18865 TTTATAATTTTTTATAATATTTATATGCTTATATCAATTTTAATGTTTTTAAGTTTGATAAGTTT
1 TTTATAATATTTTATAATATTTATATGCTTATATCAATCTTAATGATTTTAAGTTTGATAAGTTT
18930 TATGATTTCTTATTAATTTTAAATTTTTTTATAATA
66 TATGATTTCTTATT-ATTTTAAATTTTTTTATAATA
* *
18966 TTTATAATATTTTATAATATTTGTATGCTTATATCAATCTTAATGCATTTTAATTTTGATAAGTT
1 TTTATAATATTTTATAATATTTATATGCTTATATCAATCTTAATG-ATTTTAAGTTTGATAAGTT
19031 TTATGATTTCTTATGT-TTTTAA
65 TTATGATTTCTTAT-TATTTTAA
19053 TGAATTTTAT
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
101 48 0.60
102 31 0.39
103 1 0.01
ACGTcount: A:0.31, C:0.04, G:0.07, T:0.58
Consensus pattern (100 bp):
TTTATAATATTTTATAATATTTATATGCTTATATCAATCTTAATGATTTTAAGTTTGATAAGTTT
TATGATTTCTTATTATTTTAAATTTTTTTATAATA
Found at i:19061 original size:101 final size:100
Alignment explanation
Indices: 18843--19073 Score: 290
Period size: 101 Copynumber: 2.3 Consensus size: 100
18833 TTTTAAAAAT
* * * *
18843 TTATTTTATA-AATTATTAGAAT-TTTATAATTTTTTATAATATTTATATGCTTATATCAATTTT
1 TTATTTTAAATAATT-TTATAATATTTATAATATTTTATAATATTTATATGCTTATATCAATCTT
*
18906 AATGTTTTTAAGTTTGATAAGTTTTATGATTTCTTA
65 AATGATTTTAAGTTTGATAAGTTTTATGATTTCTTA
** *
18942 TTAATTTTAAATTTTTTTATAATATTTATAATATTTTATAATATTTGTATGCTTATATCAATCTT
1 TT-ATTTTAAATAATTTTATAATATTTATAATATTTTATAATATTTATATGCTTATATCAATCTT
*
19007 AATGCATTTTAATTTTGATAAGTTTTATGATTTCTTA
65 AATG-ATTTTAAGTTTGATAAGTTTTATGATTTCTTA
* *
19044 TGT-TTTT-AATGAATTTTATGATTTTTATAA
1 T-TATTTTAAAT-AATTTTATAATATTTATAA
19074 CTTTTTAAGA
Statistics
Matches: 113, Mismatches: 13, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
99 2 0.02
100 16 0.14
101 63 0.56
102 31 0.27
103 1 0.01
ACGTcount: A:0.32, C:0.03, G:0.07, T:0.58
Consensus pattern (100 bp):
TTATTTTAAATAATTTTATAATATTTATAATATTTTATAATATTTATATGCTTATATCAATCTTA
ATGATTTTAAGTTTGATAAGTTTTATGATTTCTTA
Found at i:19069 original size:9 final size:9
Alignment explanation
Indices: 19029--19100 Score: 65
Period size: 9 Copynumber: 7.7 Consensus size: 9
19019 TTTTGATAAG
19029 TTTTATGAT
1 TTTTATGAT
19038 TTCTTATG-T
1 TT-TTATGAT
*
19047 TTTTAATGAA
1 TTTT-ATGAT
19057 TTTTATGAT
1 TTTTATGAT
*
19066 TTTTATAACT
1 TTTTATGA-T
*
19076 TTTTAAGAT
1 TTTTATGAT
*
19085 TTTTATATAT
1 TTTTAT-GAT
19095 TTTTAT
1 TTTTAT
19101 AAAAGTTTAA
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
8 2 0.04
9 25 0.49
10 24 0.47
ACGTcount: A:0.26, C:0.03, G:0.07, T:0.64
Consensus pattern (9 bp):
TTTTATGAT
Found at i:19079 original size:19 final size:19
Alignment explanation
Indices: 19036--19100 Score: 64
Period size: 19 Copynumber: 3.4 Consensus size: 19
19026 AAGTTTTATG
19036 ATTTCTTATG-TTTTTA-AT
1 ATTT-TTATGATTTTTATAT
*
19054 GAATTTTATGATTTTTATA-
1 -ATTTTTATGATTTTTATAT
*
19073 ACTTTTTAAGATTTTTATAT
1 A-TTTTTATGATTTTTATAT
19093 ATTTTTAT
1 ATTTTTAT
19101 AAAAGTTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
18 6 0.16
19 30 0.79
20 2 0.05
ACGTcount: A:0.28, C:0.03, G:0.06, T:0.63
Consensus pattern (19 bp):
ATTTTTATGATTTTTATAT
Found at i:19101 original size:10 final size:9
Alignment explanation
Indices: 19016--19102 Score: 54
Period size: 9 Copynumber: 9.3 Consensus size: 9
19006 TAATGCATTT
*
19016 TAATTTTGA
1 TAATTTTTA
*
19025 TAAGTTTTA
1 TAATTTTTA
*
19034 TGATTTCTTA
1 TAATTT-TTA
*
19044 T-GTTTTTAA
1 TAATTTTT-A
19053 TGAA-TTTTA
1 T-AATTTTTA
*
19062 TGATTTTTA
1 TAATTTTTA
19071 TAACTTTTTA
1 TAA-TTTTTA
19081 -AGATTTTTA
1 TA-ATTTTTA
19090 TATATTTTTA
1 TA-ATTTTTA
19100 TAA
1 TAA
19103 AAGTTTAAAT
Statistics
Matches: 61, Mismatches: 9, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
8 3 0.05
9 33 0.54
10 25 0.41
ACGTcount: A:0.30, C:0.02, G:0.08, T:0.60
Consensus pattern (9 bp):
TAATTTTTA
Found at i:19215 original size:19 final size:17
Alignment explanation
Indices: 19173--19223 Score: 59
Period size: 16 Copynumber: 2.9 Consensus size: 17
19163 TTTTATAATA
19173 TTTATAATTTTTTTA-G
1 TTTATAATTTTTTTATG
*
19189 TTTTTAATTTTTTTATG
1 TTTATAATTTTTTTATG
*
19206 ACTTTATAATATTTTTAT
1 --TTTATAATTTTTTTAT
19224 AAAAAATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
16 14 0.48
17 1 0.03
19 14 0.48
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (17 bp):
TTTATAATTTTTTTATG
Found at i:19409 original size:1 final size:1
Alignment explanation
Indices: 19405--19434 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
19395 ATTTTTAAGG
19405 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
19435 NNNNNNNNNN
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:21471 original size:12 final size:12
Alignment explanation
Indices: 21454--21490 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
21444 TTGATTGCTG
21454 TAGTTGACACAA
1 TAGTTGACACAA
21466 TAGTTGACACAA
1 TAGTTGACACAA
21478 TAGTTGACACAA
1 TAGTTGACACAA
21490 T
1 T
21491 CAGCATTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (12 bp):
TAGTTGACACAA
Done.