Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009417.1 Kokia drynarioides strain JFW-HI SEQ_124124, 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: 99449
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 96 characters in sequence are not A, C, G, or T
Found at i:5059 original size:78 final size:79
Alignment explanation
Indices: 4930--5091 Score: 245
Period size: 78 Copynumber: 2.1 Consensus size: 79
4920 ATTCTAGAGT
* * * * *
4930 TAAAATTGATATTGTATTTATATCATATCTCATGTCATAATCGAGTTTAACA-TAAAATATATTC
1 TAAAATTGATATCGTATTTAAATCACATATCATATCATAATCGAGTTTAACAGTAAAATATATTC
4994 ATATTTTTATTAGA
66 ATATTTTTATTAGA
5008 TAAAATTGATATCGTATTTAAATCACATATCATATCATAATCGAGTTTAACATGTAAAATATATT
1 TAAAATTGATATCGTATTTAAATCACATATCATATCATAATCGAGTTTAACA-GTAAAATATATT
* *
5073 CATGTTTTTATTATA
65 CATATTTTTATTAGA
5088 TAAA
1 TAAA
5092 TTTTAATACA
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
78 47 0.63
80 28 0.37
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.43
Consensus pattern (79 bp):
TAAAATTGATATCGTATTTAAATCACATATCATATCATAATCGAGTTTAACAGTAAAATATATTC
ATATTTTTATTAGA
Found at i:7871 original size:13 final size:13
Alignment explanation
Indices: 7855--7880 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7845 ATATAATTTA
7855 TATATATTTAAAT
1 TATATATTTAAAT
7868 TATATATTTAAAT
1 TATATATTTAAAT
7881 GATAAATCCT
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):
TATATATTTAAAT
Found at i:7876 original size:23 final size:22
Alignment explanation
Indices: 7821--7877 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
7811 CATATTATTC
* *
7821 TATATTATTAATATATTTTAATT
1 TATA-TATTTATATATTTTAAAT
7844 TATATAATTTATATATATTTAAAT
1 TATAT-ATTTATATAT-TTTAAAT
7868 TATATATTTA
1 TATATATTTA
7878 AATGATAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 1 0.03
23 18 0.60
24 11 0.37
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TATATATTTATATATTTTAAAT
Found at i:8019 original size:21 final size:20
Alignment explanation
Indices: 7993--8031 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
7983 AAATCACGGA
7993 TAAATCCAAGCGATTCTTTCT
1 TAAATCCAAGCGA-TCTTTCT
8014 TAAATCCAAGCGATCTTT
1 TAAATCCAAGCGATCTTT
8032 TTGCAGGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (20 bp):
TAAATCCAAGCGATCTTTCT
Found at i:9861 original size:15 final size:16
Alignment explanation
Indices: 9841--9876 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
9831 ATAAAATTAT
9841 AATAAAATA-TTAAAA
1 AATAAAATATTTAAAA
9856 AAT-AAATATTTAAAA
1 AATAAAATATTTAAAA
9871 AA-AAAA
1 AATAAAA
9877 ACATGTCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (16 bp):
AATAAAATATTTAAAA
Found at i:10007 original size:23 final size:26
Alignment explanation
Indices: 9955--10016 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 26
9945 TAAATATCTG
*
9955 TTTTTCTAATATATATATATTGAAT-
1 TTTTTCTAATATATATATATTAAATA
*
9980 TTTTTTTAATATATAT-T-TTAAATA
1 TTTTTCTAATATATATATATTAAATA
* *
10004 TTTTACTATTATA
1 TTTTTCTAATATA
10017 CACTAACAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 5 0.16
24 11 0.35
25 15 0.48
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (26 bp):
TTTTTCTAATATATATATATTAAATA
Found at i:12182 original size:21 final size:21
Alignment explanation
Indices: 12156--12198 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
12146 CTTGGTGGTA
12156 AGCATAAGTATAACATACGGG
1 AGCATAAGTATAACATACGGG
12177 AGCATAAGTATAACATACGGG
1 AGCATAAGTATAACATACGGG
12198 A
1 A
12199 TTCCTATCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.44, C:0.14, G:0.23, T:0.19
Consensus pattern (21 bp):
AGCATAAGTATAACATACGGG
Found at i:17738 original size:10 final size:10
Alignment explanation
Indices: 17725--17763 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
17715 TTTAGAAAAT
17725 TTTAAAATTC
1 TTTAAAATTC
17735 TTTAAATATTC
1 TTTAAA-ATTC
* *
17746 TTTAGAATTT
1 TTTAAAATTC
17756 TTTAAAAT
1 TTTAAAAT
17764 ATAAATTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (10 bp):
TTTAAAATTC
Found at i:17797 original size:18 final size:19
Alignment explanation
Indices: 17776--17811 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
17766 AAATTTTGCA
*
17776 ATTTTTATAAA-TATTTTT
1 ATTTTTAAAAATTATTTTT
17794 ATTTTTAAAAATTATTTT
1 ATTTTTAAAAATTATTTT
17812 GAAATTTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTTTTAAAAATTATTTTT
Found at i:19779 original size:4 final size:4
Alignment explanation
Indices: 19770--19799 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
19760 TCATATATCA
19770 TATG TATG TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TA
19800 AACAAATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:20912 original size:19 final size:20
Alignment explanation
Indices: 20871--20917 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
20861 TTTCCCTCTC
*
20871 ATTAGATATTCTAGCTTTGTA
1 ATTAGATATTCTA-CTTTCTA
*
20892 ATTATATATTCTA-TTTCTA
1 ATTAGATATTCTACTTTCTA
20911 ATT-GATA
1 ATTAGATA
20918 CCCTTGTGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 3 0.13
19 8 0.35
21 12 0.52
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.51
Consensus pattern (20 bp):
ATTAGATATTCTACTTTCTA
Found at i:32101 original size:29 final size:29
Alignment explanation
Indices: 32038--32449 Score: 432
Period size: 30 Copynumber: 13.8 Consensus size: 29
32028 AAAGGTCCCC
*
32038 AAACCTTTCCAAAATTACATTTTAACCACT
1 AAACTTTTCCAAAATTACATTTTAACC-CT
* *
32068 AAACTTTTCCAAAATTACATTTTGACCCC
1 AAACTTTTCCAAAATTACATTTTAACCCT
32097 AAACTTTTCCAAAATTACATTTTAACCCTT
1 AAACTTTTCCAAAATTACATTTTAACCC-T
*
32127 AAAC-TTTCCAAAATTACATTTTAACTTCT
1 AAACTTTTCCAAAATTACATTTTAAC-CCT
* *
32156 AAACTTTT-AAAAATTACATTTTGACCCTT
1 AAACTTTTCCAAAATTACATTTTAACCC-T
32185 AAACTTTTCCAAAATTACATTTTAACCTCT
1 AAACTTTTCCAAAATTACATTTTAACC-CT
* * *
32215 AAGCTTTTCCAAAATCATATTTTAACCCTT
1 AAACTTTTCCAAAATTACATTTTAACCC-T
32245 AAACTTTTCCAAAATTACATTTTAACCCCCT
1 AAACTTTTCCAAAATTACATTTTAA--CCCT
* * * *
32276 AAACTTTTTCAAAATCATATTTTGACCCCT
1 AAACTTTTCCAAAATTACATTTT-AACCCT
** *
32306 AAACTTTTCCAAAATTACATTTTGATGCCA
1 AAACTTTTCCAAAATTACATTTT-AACCCT
* * * *
32336 AAACTTTTCCAAAATCATATTTTGACCCCC
1 AAACTTTTCCAAAATTACATTTT-AACCCT
* * *
32366 AAACTTTTCCAAAATCATATTTTAACCTTCC
1 AAACTTTTCCAAAATTACATTTTAACC--CT
* *
32397 GAACTTTTCCAAAATCACATTTTAACCTCT
1 AAACTTTTCCAAAATTACATTTTAACC-CT
* * *
32427 AAACTTCTCTAAAATTTCATTTT
1 AAACTTTTCCAAAATTACATTTT
32450 CATCCTGAGT
Statistics
Matches: 329, Mismatches: 41, Indels: 24
0.84 0.10 0.06
Matches are distributed among these distances:
28 1 0.00
29 82 0.25
30 193 0.59
31 49 0.15
32 4 0.01
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.38
Consensus pattern (29 bp):
AAACTTTTCCAAAATTACATTTTAACCCT
Found at i:32258 original size:60 final size:60
Alignment explanation
Indices: 32038--32449 Score: 467
Period size: 61 Copynumber: 6.9 Consensus size: 60
32028 AAAGGTCCCC
* * * *
32038 AAACCTTTCCAAAATTACATTTTAACCAC-TAAACTTTTCCAAAATTACATTTTGACC-CC
1 AAACTTTTCCAAAATCACATTTTAACC-CTTAAACTTTTCCAAAATTACATTTTAACCTCT
* *
32097 AAACTTTTCCAAAATTACATTTTAACCCTTAAAC-TTTCCAAAATTACATTTTAACTTCT
1 AAACTTTTCCAAAATCACATTTTAACCCTTAAACTTTTCCAAAATTACATTTTAACCTCT
* * *
32156 AAACTTTT-AAAAATTACATTTTGACCCTTAAACTTTTCCAAAATTACATTTTAACCTCT
1 AAACTTTTCCAAAATCACATTTTAACCCTTAAACTTTTCCAAAATTACATTTTAACCTCT
* * *
32215 AAGCTTTTCCAAAATCATATTTTAACCCTTAAACTTTTCCAAAATTACATTTTAACCCCCT
1 AAACTTTTCCAAAATCACATTTTAACCCTTAAACTTTTCCAAAATTACATTTTAA-CCTCT
* * * * ** *
32276 AAACTTTTTCAAAATCATATTTTGACCCCTAAACTTTTCCAAAATTACATTTTGATGC-CA
1 AAACTTTTCCAAAATCACATTTTAACCCTTAAACTTTTCCAAAATTACATTTT-AACCTCT
* * ** * * *
32336 AAACTTTTCCAAAATCATATTTTGACCCCCAAACTTTTCCAAAATCATATTTTAACCTTCC
1 AAACTTTTCCAAAATCACATTTTAACCCTTAAACTTTTCCAAAATTACATTTTAACC-TCT
* * * *
32397 GAACTTTTCCAAAATCACATTTTAA-CCTCTAAACTTCTCTAAAATTTCATTTT
1 AAACTTTTCCAAAATCACATTTTAACCCT-TAAACTTTTCCAAAATTACATTTT
32450 CATCCTGAGT
Statistics
Matches: 307, Mismatches: 37, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
58 44 0.14
59 73 0.24
60 94 0.31
61 95 0.31
62 1 0.00
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.38
Consensus pattern (60 bp):
AAACTTTTCCAAAATCACATTTTAACCCTTAAACTTTTCCAAAATTACATTTTAACCTCT
Found at i:39010 original size:20 final size:21
Alignment explanation
Indices: 38953--39017 Score: 71
Period size: 20 Copynumber: 3.0 Consensus size: 21
38943 GTTTTTCTAT
38953 TGAGTTATTTTTTTAAA-TAA
1 TGAGTTATTTTTTTAAATTAA
*
38973 TTACGTTTATTTTCTTTAAATTAA
1 TGA-G-TTATTTT-TTTAAATTAA
*
38997 -GAGTTATTTTTTTAATTTAA
1 TGAGTTATTTTTTTAAATTAA
39017 T
1 T
39018 TTATTATTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
20 11 0.30
21 8 0.22
22 8 0.22
23 7 0.19
24 3 0.08
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.58
Consensus pattern (21 bp):
TGAGTTATTTTTTTAAATTAA
Found at i:40850 original size:6 final size:6
Alignment explanation
Indices: 40839--40863 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
40829 TCGAATATTG
40839 GTGTGA GTGTGA GTGTGA GTGTGA G
1 GTGTGA GTGTGA GTGTGA GTGTGA G
40864 ATTTATGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.52, T:0.32
Consensus pattern (6 bp):
GTGTGA
Found at i:51060 original size:42 final size:42
Alignment explanation
Indices: 51008--51091 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
50998 CAAATATTTT
* *
51008 TAAACCCAAATGTAATTTCATTATTCAGA-AACACTCATAAAC
1 TAAACCCAAATATAATTTCATTATT-AAATAACACTCATAAAC
* * *
51050 TAAACTCAAATATAATTTTATTCTTAAATAACACTCATAAAC
1 TAAACCCAAATATAATTTCATTATTAAATAACACTCATAAAC
51092 AACTCTTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
41 2 0.06
42 34 0.94
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.32
Consensus pattern (42 bp):
TAAACCCAAATATAATTTCATTATTAAATAACACTCATAAAC
Found at i:51923 original size:28 final size:27
Alignment explanation
Indices: 51873--51952 Score: 106
Period size: 28 Copynumber: 2.9 Consensus size: 27
51863 CTTGTTATCA
* *
51873 ATTTTTTATTCTTAAATGCCAATTCTCG
1 ATTTTTTAATC-TAAATTCCAATTCTCG
*
51901 ATTTTTTAATCTAAATTCTCAATTCTTG
1 ATTTTTTAATCTAAATTC-CAATTCTCG
51929 ATTTTTTAATCTAAATTCCCAATT
1 ATTTTTTAATCTAAATT-CCAATT
51953 TAAATTAATT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
27 6 0.13
28 40 0.85
29 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.04, T:0.51
Consensus pattern (27 bp):
ATTTTTTAATCTAAATTCCAATTCTCG
Found at i:54265 original size:11 final size:12
Alignment explanation
Indices: 54242--54270 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
54232 AAAGATTCAA
54242 TCCTTTCCCCCT
1 TCCTTTCCCCCT
54254 TCCTTT-CCCCT
1 TCCTTTCCCCCT
54265 TCCTTT
1 TCCTTT
54271 TCTTCCACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (12 bp):
TCCTTTCCCCCT
Found at i:62817 original size:6 final size:7
Alignment explanation
Indices: 62800--62824 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
62790 TCACTGAATT
62800 TTTTTTA
1 TTTTTTA
62807 TTTTTTA
1 TTTTTTA
62814 TTTTTTA
1 TTTTTTA
62821 TTTT
1 TTTT
62825 GATAATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:91233 original size:18 final size:16
Alignment explanation
Indices: 91206--91257 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 16
91196 GTTTCTTGAC
91206 TTTTAATTTTTCATCT
1 TTTTAATTTTTCATCT
*
91222 TCTTTAATTTTTACATGAT
1 T-TTTAATTTTT-CAT-CT
91241 TTTTAATTTTTCATCT
1 TTTTAATTTTTCATCT
91257 T
1 T
91258 ACTCAATCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
16 3 0.10
17 13 0.42
18 13 0.42
19 2 0.06
ACGTcount: A:0.21, C:0.12, G:0.02, T:0.65
Consensus pattern (16 bp):
TTTTAATTTTTCATCT
Found at i:96627 original size:24 final size:24
Alignment explanation
Indices: 96595--96644 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
96585 ATGGATGTTC
*
96595 AACCTTTCATCTTCCTTGACTTTT
1 AACCTTTCATCTTCCTTAACTTTT
*
96619 AACCTTTCATCTTCTTTAACTTTT
1 AACCTTTCATCTTCCTTAACTTTT
96643 AA
1 AA
96645 TATTCTTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.26, G:0.02, T:0.50
Consensus pattern (24 bp):
AACCTTTCATCTTCCTTAACTTTT
Done.