Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005958.1 Kokia drynarioides strain JFW-HI SEQ_120353, 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: 60352
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 29 characters in sequence are not A, C, G, or T
Found at i:9713 original size:80 final size:80
Alignment explanation
Indices: 9572--9958 Score: 494
Period size: 80 Copynumber: 4.8 Consensus size: 80
9562 TTTGATGAAT
* * * * * *
9572 ATATGTTGTCAGTTTAACTGACTCGAGCTGGGCTCACAATTACGGTTTATTCGCTAGGCACTGGG
1 ATAT-TTGTCGGTTTAACTGACTAGAGCTGGGCTCACATTTGCGGTTTATCCGCTAAGCACTGGG
* *
9637 TGCCAAGATGTGACGG
65 TGCTAAGATTTGACGG
* *
9653 ATATTTGTCGATTTAACCGACTAGAGCTGGGCTCACATTTGCGGTTTATCCGCTAAGCACTGGGT
1 ATATTTGTCGGTTTAACTGACTAGAGCTGGGCTCACATTTGCGGTTTATCCGCTAAGCACTGGGT
*
9718 GCTAAGATTTGACAG
66 GCTAAGATTTGACGG
* * * * *
9733 ATATTTGTTGGTTTAACTGAGTAGAGTTTGGCTCACATTTG-GGTTTATCTGCTAAGCACTGGGT
1 ATATTTGTCGGTTTAACTGACTAGAGCTGGGCTCACATTTGCGGTTTATCCGCTAAGCACTGGGT
9797 GCTAAGATTTGACGG
66 GCTAAGATTTGACGG
* * *
9812 ATATTTTTCGGTTTAACTTACTAGAGCTGGACTCACATTTGCGGTTTATCCGCTAAGCACTGGGT
1 ATATTTGTCGGTTTAACTGACTAGAGCTGGGCTCACATTTGCGGTTTATCCGCTAAGCACTGGGT
9877 GCTAAGATTTGACGG
66 GCTAAGATTTGACGG
* ** * *
9892 ATATTTGTTGG-TTAATCCAACTAGAGTTGGGCTCAC-TTTCGCGG-TTATTCCGCTAGGCACTG
1 ATATTTGTCGGTTTAA-CTGACTAGAGCTGGGCTCACATTT-GCGGTTTA-TCCGCTAAGCACTG
9954 GGTGC
63 GGTGC
9959 CATAATTGTC
Statistics
Matches: 268, Mismatches: 34, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
79 80 0.30
80 184 0.69
81 4 0.01
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (80 bp):
ATATTTGTCGGTTTAACTGACTAGAGCTGGGCTCACATTTGCGGTTTATCCGCTAAGCACTGGGT
GCTAAGATTTGACGG
Found at i:9904 original size:159 final size:160
Alignment explanation
Indices: 9583--9960 Score: 496
Period size: 159 Copynumber: 2.4 Consensus size: 160
9573 TATGTTGTCA
* *
9583 GTTTAACTGACTCGAGCTGGGCTCACAATTACGGTTTATTCGCTAGGCACTGGGTGCCAAGATGT
1 GTTTAACTGACTAGAGCTGGGCTCACAATTACGGTTTATTCGCTAAGCACTGGGTGCCAAGATGT
*
9648 GACGGATATTTGTCGATTTAACCGACTAGAGCTGGGCTCACATTTGCGGTTTATCCGCTAAGCAC
66 GACGGATATTTGTCGATTTAACCGACTAGAGCTGGACTCACATTTGCGGTTTATCCGCTAAGCAC
9713 TGGGTGCTAAGATTTGACAGATATTTGTTG
131 TGGGTGCTAAGATTTGACAGATATTTGTTG
* * * ** * *
9743 GTTTAACTGAGTAGAGTTTGGCTCAC-ATTTGGGTTTA-TCTGCTAAGCACTGGGTGCTAAGATT
1 GTTTAACTGACTAGAGCTGGGCTCACAATTACGGTTTATTC-GCTAAGCACTGGGTGCCAAGATG
* * **
9806 TGACGGATATTTTTCGGTTTAACTTACTAGAGCTGGACTCACATTTGCGGTTTATCCGCTAAGCA
65 TGACGGATATTTGTCGATTTAACCGACTAGAGCTGGACTCACATTTGCGGTTTATCCGCTAAGCA
*
9871 CTGGGTGCTAAGATTTGACGGATATTTGTTG
130 CTGGGTGCTAAGATTTGACAGATATTTGTTG
** * * * *
9902 G-TTAATCCAACTAGAGTTGGGCTCAC--TTTCGCGGTTATTCCGCTAGGCACTGGGTGCCA
1 GTTTAA-CTGACTAGAGCTGGGCTCACAATTACG-GTTTATT-CGCTAAGCACTGGGTGCCA
9961 TAATTGTCGG
Statistics
Matches: 190, Mismatches: 23, Indels: 10
0.85 0.10 0.04
Matches are distributed among these distances:
158 10 0.05
159 140 0.74
160 39 0.21
161 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (160 bp):
GTTTAACTGACTAGAGCTGGGCTCACAATTACGGTTTATTCGCTAAGCACTGGGTGCCAAGATGT
GACGGATATTTGTCGATTTAACCGACTAGAGCTGGACTCACATTTGCGGTTTATCCGCTAAGCAC
TGGGTGCTAAGATTTGACAGATATTTGTTG
Found at i:11604 original size:95 final size:95
Alignment explanation
Indices: 11441--11630 Score: 371
Period size: 95 Copynumber: 2.0 Consensus size: 95
11431 AAAAAACGAG
*
11441 GAGATTGTTAGCTTTTATCTCCCAAGATTTTGATACAACAACATTTAAGATAAACTTCAATTATT
1 GAGATTGTTAGCTTTTATCTCCCAAGATTTTGATACAAAAACATTTAAGATAAACTTCAATTATT
11506 TATTTCCTAAGTCATTTACTGATCAAACAT
66 TATTTCCTAAGTCATTTACTGATCAAACAT
11536 GAGATTGTTAGCTTTTATCTCCCAAGATTTTGATACAAAAACATTTAAGATAAACTTCAATTATT
1 GAGATTGTTAGCTTTTATCTCCCAAGATTTTGATACAAAAACATTTAAGATAAACTTCAATTATT
11601 TATTTCCTAAGTCATTTACTGATCAAACAT
66 TATTTCCTAAGTCATTTACTGATCAAACAT
11631 TTCCAAAGTC
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 94 1.00
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.39
Consensus pattern (95 bp):
GAGATTGTTAGCTTTTATCTCCCAAGATTTTGATACAAAAACATTTAAGATAAACTTCAATTATT
TATTTCCTAAGTCATTTACTGATCAAACAT
Found at i:16498 original size:19 final size:19
Alignment explanation
Indices: 16471--16548 Score: 102
Period size: 19 Copynumber: 4.1 Consensus size: 19
16461 AGCGATATAT
* *
16471 GATACTGGCTTGTAAGAGC
1 GATACTAGCTCGTAAGAGC
* *
16490 GATAATGGCTCGTAAGAGC
1 GATACTAGCTCGTAAGAGC
*
16509 AATACTAGCTCGTAAGAGC
1 GATACTAGCTCGTAAGAGC
*
16528 AATACTAGCTCGTAAGAGC
1 GATACTAGCTCGTAAGAGC
16547 GA
1 GA
16549 ATTACTGACT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 53 1.00
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.22
Consensus pattern (19 bp):
GATACTAGCTCGTAAGAGC
Found at i:18670 original size:3 final size:3
Alignment explanation
Indices: 18662--18758 Score: 98
Period size: 3 Copynumber: 34.0 Consensus size: 3
18652 TTCCATTTTC
* * *
18662 TCT TCT TCT TC- TCC TCT TAT TAT T-T TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* *
18708 TCT TCT TCT TC- TCT AT-T TCT TC- TCT TAT TCT TCT TTT TC- TCT
1 TCT TCT TCT TCT TCT -TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
18750 TCT TCT TCT
1 TCT TCT TCT
18759 ACTACCCATG
Statistics
Matches: 81, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
2 11 0.14
3 69 0.85
4 1 0.01
ACGTcount: A:0.04, C:0.30, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:18756 original size:28 final size:28
Alignment explanation
Indices: 18657--18758 Score: 118
Period size: 28 Copynumber: 3.6 Consensus size: 28
18647 ACTCCTTCCA
* * *
18657 TTTTCTCTTCTTCTTCTCCTCTTATT-A
1 TTTTCTCTTCTTCTTCTCTTCTTCTTCT
18684 TTTTCTTCTTCTTCTTCTTCTTCTTCTTCT
1 TTTTC-TCTTCTTCTTC-TCTTCTTCTTCT
* *
18714 TCTTCTCTAT-TTCTTCTCTTATTCTTCT
1 TTTTCTCT-TCTTCTTCTCTTCTTCTTCT
18742 TTTTCTCTTCTTCTTCT
1 TTTTCTCTTCTTCTTCT
18759 ACTACCCATG
Statistics
Matches: 64, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
27 6 0.09
28 36 0.56
29 17 0.27
30 5 0.08
ACGTcount: A:0.04, C:0.29, G:0.00, T:0.67
Consensus pattern (28 bp):
TTTTCTCTTCTTCTTCTCTTCTTCTTCT
Found at i:19038 original size:20 final size:19
Alignment explanation
Indices: 18993--19040 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
18983 TATTTTTCTT
* *
18993 TAAAATTTTGAAATATTAT
1 TAAAATTTTAAAATATTAA
*
19012 TATAAATTTTAAAATGTTAAA
1 TA-AAATTTTAAAATATT-AA
19033 TAAAATTT
1 TAAAATTT
19041 AAATTTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (19 bp):
TAAAATTTTAAAATATTAA
Found at i:21446 original size:241 final size:241
Alignment explanation
Indices: 21006--21480 Score: 801
Period size: 241 Copynumber: 2.0 Consensus size: 241
20996 TATATATATA
* *
21006 TATATTTCCCAACAGATTTATTCAATATCCTCCTTTTATTTCATTATTTCGACAATAATATTGCA
1 TATATTTCCCAACAGATTTATTCAATATCCTCCTTTTATTTCACTATTTCCACAATAATATTGCA
*
21071 TGCAAAACCATTGTCGACCACTTTTATTATTGGTTCAACATTTTCTCAAATTGACATAACTTATC
66 TGCAAAACCATTGTCAACCACTTTTATTATTGGTTCAACATTTTCTCAAATTGACATAACTTATC
* *
21136 GAGATATATTATTTTCACTATTTTAATCTTCAGTTTCAAGTACCCATCTCTTCTTATTAGTTATG
131 GAGATATATTATTTTCACTATTTTAATCTTCAGTTTCAAATACCAATCTCTTCTTATTAGTTATG
21201 TCTTGGGTCTCTTCTGGAGCACCCGCCTTCACTATATGACCACATC
196 TCTTGGGTCTCTTCTGGAGCACCCGCCTTCACTATATGACCACATC
*
21247 TATATTTCCCAATAGATTTATTCAATATCCTCCTTTTATTTCACTATTTCCACAATAATATTGCA
1 TATATTTCCCAACAGATTTATTCAATATCCTCCTTTTATTTCACTATTTCCACAATAATATTGCA
* * *
21312 TGCAAAACGATTGTCAACCATTTTTATTATTGGTTCGACATTTTCTCAAATTGACATAACTTATC
66 TGCAAAACCATTGTCAACCACTTTTATTATTGGTTCAACATTTTCTCAAATTGACATAACTTATC
* * *
21377 GAGATCTCTTATTTTCATTATTTTAATCTTCAGTTTCAAATACCTGAATCTCTTCTTATTAG-T-
131 GAGATATATTATTTTCACTATTTTAATCTTCAGTTTCAAATACC--AATCTCTTCTTATTAGTTA
*
21440 TGTCTTGGGTCTCTTCTGGAGCACCCGCCTTCCCTATATGA
194 TGTCTTGGGTCTCTTCTGGAGCACCCGCCTTCACTATATGA
21481 TCATTTAGAT
Statistics
Matches: 219, Mismatches: 13, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
241 203 0.93
242 1 0.00
243 15 0.07
ACGTcount: A:0.27, C:0.22, G:0.10, T:0.42
Consensus pattern (241 bp):
TATATTTCCCAACAGATTTATTCAATATCCTCCTTTTATTTCACTATTTCCACAATAATATTGCA
TGCAAAACCATTGTCAACCACTTTTATTATTGGTTCAACATTTTCTCAAATTGACATAACTTATC
GAGATATATTATTTTCACTATTTTAATCTTCAGTTTCAAATACCAATCTCTTCTTATTAGTTATG
TCTTGGGTCTCTTCTGGAGCACCCGCCTTCACTATATGACCACATC
Found at i:42541 original size:3 final size:3
Alignment explanation
Indices: 42535--42575 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
42525 AAGCTTTAAA
42535 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
42576 ATAAATGGGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:43080 original size:6 final size:6
Alignment explanation
Indices: 43069--43094 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
43059 CACACACCTC
43069 TCATCT TCATCT TCATCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TC
43095 TTCCTTTTTT
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:0.15, C:0.35, G:0.00, T:0.50
Consensus pattern (6 bp):
TCATCT
Found at i:47847 original size:23 final size:23
Alignment explanation
Indices: 47821--47908 Score: 81
Period size: 23 Copynumber: 3.7 Consensus size: 23
47811 CGCTCTCCGA
47821 TTAGCACTGTGTGTGCTTTCTGT
1 TTAGCACTGTGTGTGCTTTCTGT
* * *
47844 TTAGCAC-GTCTCGTTCTCTCTGTT
1 TTAGCACTGTGT-GTGCTTTCTG-T
*
47868 ATTAGCACTGTGTGTGCTCTT-TGA
1 -TTAGCACTGTGTGTGCT-TTCTGT
*
47892 TTAGCACTTTGTGTGCT
1 TTAGCACTGTGTGTGCT
47909 CAGTAGTACT
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
22 3 0.06
23 31 0.60
24 1 0.02
25 13 0.25
26 4 0.08
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.45
Consensus pattern (23 bp):
TTAGCACTGTGTGTGCTTTCTGT
Found at i:47909 original size:23 final size:22
Alignment explanation
Indices: 47861--47952 Score: 91
Period size: 23 Copynumber: 4.2 Consensus size: 22
47851 GTCTCGTTCT
*
47861 CTCTGTTATTAGCACTGTGTGTG
1 CTCT-TTATTAGCACTTTGTGTG
47884 CTCTTTGATTAGCACTTTGTGTG
1 CTCTTT-ATTAGCACTTTGTGTG
* * *
47907 CTC---AGTAGTACTTTGTGTA
1 CTCTTTATTAGCACTTTGTGTG
*
47926 CTCTTTTTTTAGCACTTTGTGTG
1 CTC-TTTATTAGCACTTTGTGTG
47949 CTCT
1 CTCT
47953 CTGTTGCCCA
Statistics
Matches: 56, Mismatches: 8, Indels: 11
0.75 0.11 0.15
Matches are distributed among these distances:
19 16 0.29
22 3 0.05
23 37 0.66
ACGTcount: A:0.13, C:0.18, G:0.21, T:0.48
Consensus pattern (22 bp):
CTCTTTATTAGCACTTTGTGTG
Found at i:48743 original size:14 final size:13
Alignment explanation
Indices: 48721--48763 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 13
48711 TTAAGTCTTG
48721 ATTTTAATTATAC
1 ATTTTAATTATAC
*
48734 ATTATTAATTTAAGAC
1 ATT-TTAA-TT-ATAC
48750 ATTTTAATTATAC
1 ATTTTAATTATAC
48763 A
1 A
48764 AGGTTAAGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 7 0.28
14 6 0.24
15 6 0.24
16 6 0.24
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (13 bp):
ATTTTAATTATAC
Found at i:48919 original size:26 final size:26
Alignment explanation
Indices: 48887--48938 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
48877 ATTTCTTGGT
48887 TTATTATTAATGATGAGTTAATCAGA
1 TTATTATTAATGATGAGTTAATCAGA
48913 TTATTATTAATGATGAGTTAATCAGA
1 TTATTATTAATGATGAGTTAATCAGA
48939 ATAGAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.04, G:0.15, T:0.42
Consensus pattern (26 bp):
TTATTATTAATGATGAGTTAATCAGA
Done.