Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004669.1 Kokia drynarioides strain JFW-HI SEQ_118217, 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: 99781
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:5948 original size:64 final size:63
Alignment explanation
Indices: 5847--5975 Score: 240
Period size: 64 Copynumber: 2.0 Consensus size: 63
5837 TTCCGACTAG
5847 TCAGGTATATAATTTGGTTGATCAGTGGTGTTCGCCAGAAATATTTGGTTCACTATTCTATTTA
1 TCAGGTATATAATTTGGTTGATCAGTGGTGTTCGCCAGAAATATTT-GTTCACTATTCTATTTA
*
5911 TCAGGTATATAATTTGGTTGATCGGTGGTGTTCGCCAGAAATATTTGTTCACTATTCTATTTA
1 TCAGGTATATAATTTGGTTGATCAGTGGTGTTCGCCAGAAATATTTGTTCACTATTCTATTTA
5974 TC
1 TC
5976 TGAACATGAT
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
63 19 0.30
64 45 0.70
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.43
Consensus pattern (63 bp):
TCAGGTATATAATTTGGTTGATCAGTGGTGTTCGCCAGAAATATTTGTTCACTATTCTATTTA
Found at i:11841 original size:4 final size:4
Alignment explanation
Indices: 11832--11857 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
11822 ACCGTCATCC
11832 TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TA
11858 TATATTACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:13998 original size:21 final size:21
Alignment explanation
Indices: 13958--13998 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
13948 TCGTGTGGAT
*
13958 ATATTTTTTTTTTTATTTTGA
1 ATATTTTTTTTTTTAGTTTGA
13979 ATATTTTTTTTGTTT-GTTTG
1 ATATTTTTTTT-TTTAGTTTG
13999 TTTGAAAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.15, C:0.00, G:0.10, T:0.76
Consensus pattern (21 bp):
ATATTTTTTTTTTTAGTTTGA
Found at i:15080 original size:21 final size:20
Alignment explanation
Indices: 15056--15103 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
15046 ATAAAATATG
15056 ATTAATAT-ATTTTTATATAAA
1 ATTAATATCA-TTTTAT-TAAA
15077 ATTAA-ATCATTTTATTAAA
1 ATTAATATCATTTTATTAAA
15096 A-TAATATC
1 ATTAATATC
15104 TTAACTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 3 0.12
19 8 0.32
20 8 0.32
21 6 0.24
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (20 bp):
ATTAATATCATTTTATTAAA
Found at i:20094 original size:24 final size:25
Alignment explanation
Indices: 20042--20093 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 25
20032 TTATGTATAT
20042 TAAAATAAAAATATATAAAACATAA
1 TAAAATAAAAATATATAAAACATAA
20067 TAAAATAAAACTTATATATAAAA-ATAA
1 TAAAATAAAA---ATATATAAAACATAA
20094 AGCCTTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 10 0.42
27 4 0.17
28 10 0.42
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (25 bp):
TAAAATAAAAATATATAAAACATAA
Found at i:20102 original size:20 final size:19
Alignment explanation
Indices: 20068--20114 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
20058 AAAACATAAT
20068 AAAATAAAACTTATATATA
1 AAAATAAAACTTATATATA
*
20087 AAAATAAAGCCTTATATATA
1 AAAATAAA-ACTTATATATA
*
20107 AAAGTAAA
1 AAAATAAA
20115 TTTAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.62, C:0.06, G:0.04, T:0.28
Consensus pattern (19 bp):
AAAATAAAACTTATATATA
Found at i:20699 original size:31 final size:31
Alignment explanation
Indices: 20631--20714 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 31
20621 TTTTAATTTA
* * * *
20631 ATCACTAATGTTTTAGATCATTTTTATGTTG
1 ATCACTCATGTGTTAGATTATTTCTATGTTG
* *
20662 GTCACTCATGTGTTAGATTATTTCTATTTTG
1 ATCACTCATGTGTTAGATTATTTCTATGTTG
*
20693 ATCACTC-TCTGTTAGATTATTT
1 ATCACTCATGTGTTAGATTATTT
20715 TTATAATTAC
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 14 0.31
31 31 0.69
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.51
Consensus pattern (31 bp):
ATCACTCATGTGTTAGATTATTTCTATGTTG
Found at i:23633 original size:43 final size:43
Alignment explanation
Indices: 23580--23683 Score: 115
Period size: 42 Copynumber: 2.4 Consensus size: 43
23570 CTATTGCTTC
*
23580 ACCTCTAGCGGCATTTTTCCCATAAAAGCCGCTAATGCTCTT-T
1 ACCTTTAGCGGCATTTTTCCCATAAAAGCCGCTAATGCT-TTGT
* * * *
23623 ACCTTTAGCGGC-GTTTTCCCATAAACGCTGCTATTGCTTTGT
1 ACCTTTAGCGGCATTTTTCCCATAAAAGCCGCTAATGCTTTGT
*
23665 ACCTTTTA-CAGCATTTTTC
1 ACC-TTTAGCGGCATTTTTC
23684 AAATAAACTC
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
41 2 0.04
42 29 0.57
43 20 0.39
ACGTcount: A:0.20, C:0.28, G:0.14, T:0.38
Consensus pattern (43 bp):
ACCTTTAGCGGCATTTTTCCCATAAAAGCCGCTAATGCTTTGT
Found at i:25891 original size:201 final size:191
Alignment explanation
Indices: 25542--25895 Score: 451
Period size: 201 Copynumber: 1.8 Consensus size: 191
25532 TATCATAAAT
* * *
25542 TGTTCCCTAACGATGCTACTCACACGAGTTGTCGAGAGTATGCAATAAGCATAGTCCCAGCCATC
1 TGTTCCCTAACGATGCTACTCACACGAGCTGTCGAGAATATGCAATAAGCATAATCCCAGCCATC
* * *
25607 GTAGGGCTTGTAATCCATTTAAGATCCATACCTCTTTCTCGAGTCACGATGCTACTCACACGAGC
66 GTAGGGCCTGCAATCCATTTAAGATCCATACCTCTTTCTCGACTCACGATGCTACTCACACGAGC
25672 TATCGAGGACTCGCAACATATGCGATACCTTAGCCATCGATACAGTATTTGTGCATATAAC
131 TATCGAGGACTCGCAACATATGCGATACCTTAGCCATCGATACAGTATTTGTGCATATAAC
* * *
25733 TGTTCCCTAACGATGCTGCTCACACGAGCTGTCGAGAATATGCACTTATA-CATAAATCTCAGCC
1 TGTTCCCTAACGATGCTACTCACACGAGCTGTCGAGAATATGCA-ATA-AGCAT-AATCCCAGCC
* * *
25797 ATTGTAGGGCCTGCAATCCATTTAGGATTCATATTTCTTTTCTCATTT-TCTGACTCACGATGCT
63 ATCGTAGGGCCTGCAATCCATTTAAGATCCATA---C----CTC-TTTCTC-GACTCACGATGCT
* * *
25861 GCTCACACGAGCTGTCGAGGACTTGCAACATATGC
119 ACTCACACGAGCTATCGAGGACTCGCAACATATGC
25896 TGTAGCTCAG
Statistics
Matches: 136, Mismatches: 15, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
191 41 0.30
192 5 0.04
193 37 0.27
196 1 0.01
200 5 0.04
201 47 0.35
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (191 bp):
TGTTCCCTAACGATGCTACTCACACGAGCTGTCGAGAATATGCAATAAGCATAATCCCAGCCATC
GTAGGGCCTGCAATCCATTTAAGATCCATACCTCTTTCTCGACTCACGATGCTACTCACACGAGC
TATCGAGGACTCGCAACATATGCGATACCTTAGCCATCGATACAGTATTTGTGCATATAAC
Found at i:28919 original size:40 final size:40
Alignment explanation
Indices: 28867--28951 Score: 116
Period size: 40 Copynumber: 2.1 Consensus size: 40
28857 CAAACGTCGT
* **
28867 TATTGCTTTACCTTTTGCAGCGTTTACGTAAAAATGCCGC
1 TATTGCTTTACCTTTTGCAGCGTTTACGGAAAAACACCGC
* * *
28907 TATTGTTTTACCTTTTGCTGCGTTTATGGAAAAACACCGC
1 TATTGCTTTACCTTTTGCAGCGTTTACGGAAAAACACCGC
28947 TATTG
1 TATTG
28952 ATCTATTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (40 bp):
TATTGCTTTACCTTTTGCAGCGTTTACGGAAAAACACCGC
Found at i:29711 original size:29 final size:29
Alignment explanation
Indices: 29679--29738 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
29669 AGGATAATTT
* *
29679 AATTAGAAAAATGTAAA-ATATTTTTTAAA
1 AATTAGAAAAAT-TAAATAAATTATTTAAA
* *
29708 AATTATAGAAATTAAATAAATTATTTAAA
1 AATTAGAAAAATTAAATAAATTATTTAAA
29737 AA
1 AA
29739 AACTATAGAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 4 0.15
29 22 0.85
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (29 bp):
AATTAGAAAAATTAAATAAATTATTTAAA
Found at i:35349 original size:10 final size:10
Alignment explanation
Indices: 35334--35384 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
35324 AATATAAAAA
35334 TAAAAAATAT
1 TAAAAAATAT
35344 T-AAAAATGAT
1 TAAAAAAT-AT
*
35354 AAAAAAATAT
1 TAAAAAATAT
* *
35364 ATATAAAATAC
1 -TAAAAAATAT
35375 TAAAAAATAT
1 TAAAAAATAT
35385 ATTTAAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
9 6 0.19
10 13 0.41
11 13 0.41
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (10 bp):
TAAAAAATAT
Found at i:35401 original size:23 final size:22
Alignment explanation
Indices: 35335--35402 Score: 70
Period size: 23 Copynumber: 3.1 Consensus size: 22
35325 ATATAAAAAT
35335 AAAAAATAT-T-AAAAATGATA
1 AAAAAATATATAAAAAATGATA
*
35355 AAAAAATATATATAAAAT-ACTA
1 AAAAAATATATAAAAAATGA-TA
* *
35377 AAAAATATATTTAAAAAATGTTA
1 AAAAA-ATATATAAAAAATGATA
35400 AAA
1 AAA
35403 TTTAATATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
20 9 0.23
21 2 0.05
22 12 0.31
23 16 0.41
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.28
Consensus pattern (22 bp):
AAAAAATATATAAAAAATGATA
Found at i:37773 original size:15 final size:16
Alignment explanation
Indices: 37747--37776 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
37737 TCTTAAGCAT
37747 CTCAGTGAAGATGACA
1 CTCAGTGAAGATGACA
37763 CTCAG-GAAGATGAC
1 CTCAGTGAAGATGAC
37777 GAGACCTCGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.37, C:0.20, G:0.27, T:0.17
Consensus pattern (16 bp):
CTCAGTGAAGATGACA
Found at i:60477 original size:5 final size:5
Alignment explanation
Indices: 60467--60492 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
60457 GGACCACCTT
60467 CTCTC CTCTC CTCTC CTCTC CTCTC C
1 CTCTC CTCTC CTCTC CTCTC CTCTC C
60493 ACATTAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (5 bp):
CTCTC
Found at i:75890 original size:18 final size:18
Alignment explanation
Indices: 75867--75902 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
75857 TTTCCTAAAT
*
75867 AAAGCAGTAGAATCCAAG
1 AAAGCAGCAGAATCCAAG
75885 AAAGCAGCAGAATCCAAG
1 AAAGCAGCAGAATCCAAG
75903 TTTAAACATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.50, C:0.19, G:0.22, T:0.08
Consensus pattern (18 bp):
AAAGCAGCAGAATCCAAG
Found at i:79804 original size:2 final size:2
Alignment explanation
Indices: 79797--79821 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
79787 AGACAAAGTT
79797 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
79822 AGCAAAAGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:83219 original size:29 final size:29
Alignment explanation
Indices: 83187--83280 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 29
83177 GGTTATTGAT
83187 GAGTATGGTGACCCAACTAGGTTGCTAAC
1 GAGTATGGTGACCCAACTAGGTTGCTAAC
* * ** * * * *
83216 GAGTAAGGCGACCTGA-TCAAGTTACTGAG
1 GAGTATGGTGACCCAACT-AGGTTGCTAAC
* *
83245 GAGTATGGTGACTCAACTAGGTTGCTAGC
1 GAGTATGGTGACCCAACTAGGTTGCTAAC
*
83274 AAGTATG
1 GAGTATG
83281 ACAAGCCAGT
Statistics
Matches: 44, Mismatches: 19, Indels: 4
0.66 0.28 0.06
Matches are distributed among these distances:
28 1 0.02
29 42 0.95
30 1 0.02
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.24
Consensus pattern (29 bp):
GAGTATGGTGACCCAACTAGGTTGCTAAC
Found at i:85184 original size:12 final size:12
Alignment explanation
Indices: 85136--85186 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
85126 TCGCCTTCCT
85136 CTTCTTCCTCTG
1 CTTCTTCCTCTG
* *
85148 TTTCTT-CTGCTT
1 CTTCTTCCT-CTG
*
85160 CTTCTTCATCTG
1 CTTCTTCCTCTG
85172 CTTCTTCCTCTG
1 CTTCTTCCTCTG
85184 CTT
1 CTT
85187 TGTCTCTCTC
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
11 2 0.06
12 28 0.90
13 1 0.03
ACGTcount: A:0.02, C:0.35, G:0.08, T:0.55
Consensus pattern (12 bp):
CTTCTTCCTCTG
Found at i:94434 original size:6 final size:6
Alignment explanation
Indices: 94423--94448 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
94413 AAAAATGTAA
94423 ACGCAC ACGCAC ACGCAC ACGCAC AC
1 ACGCAC ACGCAC ACGCAC ACGCAC AC
94449 AAACAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.50, G:0.15, T:0.00
Consensus pattern (6 bp):
ACGCAC
Found at i:97517 original size:14 final size:14
Alignment explanation
Indices: 97498--97528 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
97488 ACAATAATGA
97498 TTAAATTAAAAATT
1 TTAAATTAAAAATT
*
97512 TTAAATTAAAACTT
1 TTAAATTAAAAATT
97526 TTA
1 TTA
97529 TAATGTACTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (14 bp):
TTAAATTAAAAATT
Found at i:98762 original size:11 final size:11
Alignment explanation
Indices: 98748--98795 Score: 60
Period size: 11 Copynumber: 4.4 Consensus size: 11
98738 GCCTTTTTTT
*
98748 AATTTATTTTA
1 AATTTAATTTA
*
98759 AATTTGATTTA
1 AATTTAATTTA
* *
98770 AATTTAAATTG
1 AATTTAATTTA
98781 AATTTAATTTA
1 AATTTAATTTA
98792 AATT
1 AATT
98796 AAAAAGTCCA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (11 bp):
AATTTAATTTA
Done.