Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011903.1 Kokia drynarioides strain JFW-HI SEQ_126901, 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: 35841
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.34
Found at i:77 original size:14 final size:14
Alignment explanation
Indices: 39--79 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
29 CTTAAGCTCG
39 AGACCCTAA-CCCT
1 AGACCCTAAGCCCT
* *
52 AGACCGTTAGCCCT
1 AGACCCTAAGCCCT
66 AGACCCTAAGCCCT
1 AGACCCTAAGCCCT
80 CAACCTCGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
13 7 0.30
14 16 0.70
ACGTcount: A:0.27, C:0.41, G:0.15, T:0.17
Consensus pattern (14 bp):
AGACCCTAAGCCCT
Found at i:4078 original size:11 final size:11
Alignment explanation
Indices: 4062--4099 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
4052 ACACTAATCA
*
4062 CTTATCAGCTT
1 CTTATCAACTT
4073 CTTATCAACTT
1 CTTATCAACTT
*
4084 CTTACCAACTT
1 CTTATCAACTT
4095 CTTAT
1 CTTAT
4100 ATTCATGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.24, C:0.29, G:0.03, T:0.45
Consensus pattern (11 bp):
CTTATCAACTT
Found at i:11759 original size:56 final size:56
Alignment explanation
Indices: 11694--11807 Score: 228
Period size: 56 Copynumber: 2.0 Consensus size: 56
11684 AACCATGGTA
11694 ATCAAGTCTCTTAACAAGAATTAAACTCTTATTGAAGTAATTTCCCATGAAGACTG
1 ATCAAGTCTCTTAACAAGAATTAAACTCTTATTGAAGTAATTTCCCATGAAGACTG
11750 ATCAAGTCTCTTAACAAGAATTAAACTCTTATTGAAGTAATTTCCCATGAAGACTG
1 ATCAAGTCTCTTAACAAGAATTAAACTCTTATTGAAGTAATTTCCCATGAAGACTG
11806 AT
1 AT
11808 TTGTACTCAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (56 bp):
ATCAAGTCTCTTAACAAGAATTAAACTCTTATTGAAGTAATTTCCCATGAAGACTG
Found at i:12648 original size:20 final size:20
Alignment explanation
Indices: 12623--12661 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
12613 AAATACCTTT
*
12623 AGTAATCTTTCCAA-GATGGA
1 AGTAAT-TTACCAATGATGGA
12643 AGTAATTTACCAATGATGG
1 AGTAATTTACCAATGATGG
12662 TGGATACTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.31
Consensus pattern (20 bp):
AGTAATTTACCAATGATGGA
Found at i:20479 original size:24 final size:24
Alignment explanation
Indices: 20452--20497 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
20442 TCATTAACAT
*
20452 TGTTCGTAAACATGTTCAATTATA
1 TGTTCATAAACATGTTCAATTATA
* *
20476 TGTTCATGAACATGTTCGATTA
1 TGTTCATAAACATGTTCAATTA
20498 AGTTAAATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.41
Consensus pattern (24 bp):
TGTTCATAAACATGTTCAATTATA
Found at i:21381 original size:22 final size:23
Alignment explanation
Indices: 21337--21383 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
21327 TTAAATTAAA
*
21337 TTTTTATTTTAATATTTTCATAAT
1 TTTTTATTTTAATA-TTGCATAAT
*
21361 TTTTTATTTTAATA-TGGATAAT
1 TTTTTATTTTAATATTGCATAAT
21383 T
1 T
21384 AATTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 7 0.33
24 14 0.67
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (23 bp):
TTTTTATTTTAATATTGCATAAT
Found at i:23383 original size:41 final size:41
Alignment explanation
Indices: 23328--23413 Score: 102
Period size: 41 Copynumber: 2.1 Consensus size: 41
23318 AAATAATAGG
* *
23328 AAAACGCTTTCACGTG-GAAGCATTTTTCCTTGAATGAGATA
1 AAAACGCCTACACGTGAG-AGCATTTTTCCTTGAATGAGATA
* * * *
23369 AAAACGCCTACACGTTAGAGCGTTTTTCTTTGACTGAGATA
1 AAAACGCCTACACGTGAGAGCATTTTTCCTTGAATGAGATA
23410 AAAA
1 AAAA
23414 TACGCTAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 37 0.97
42 1 0.03
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (41 bp):
AAAACGCCTACACGTGAGAGCATTTTTCCTTGAATGAGATA
Found at i:26779 original size:20 final size:20
Alignment explanation
Indices: 26750--26787 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
26740 AGTTTTTTGA
*
26750 AAAAAATCAACGGTCAACCT
1 AAAAAATCAACGATCAACCT
*
26770 AAAAAGTCAACGATCAAC
1 AAAAAATCAACGATCAAC
26788 GGTCAACGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.24, G:0.11, T:0.13
Consensus pattern (20 bp):
AAAAAATCAACGATCAACCT
Found at i:29384 original size:2 final size:2
Alignment explanation
Indices: 29377--29416 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
29367 TTGTACCAAA
29377 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
29417 AATTTAAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:32825 original size:21 final size:21
Alignment explanation
Indices: 32784--32825 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
32774 AATATTTTTT
* *
32784 TGTACATTTTATATTTTAACA
1 TGTACAATTTATATTTAAACA
32805 TGTACAATTTAT-TATTAAACA
1 TGTACAATTTATAT-TTAAACA
32826 CAAATCTGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.38, C:0.10, G:0.05, T:0.48
Consensus pattern (21 bp):
TGTACAATTTATATTTAAACA
Found at i:33191 original size:5 final size:6
Alignment explanation
Indices: 33173--33202 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
33163 ATTGGTGTGA
33173 TTATTT TTATTT TTATTT TTATTT TATATT
1 TTATTT TTATTT TTATTT TTATTT T-TATT
33203 GGTGTGATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.83
7 4 0.17
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
TTATTT
Found at i:33956 original size:29 final size:30
Alignment explanation
Indices: 33923--33980 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
33913 TTGATATAAT
33923 TTGTAATGT-TATACAT-AAATTTTAATTTG
1 TTGT-ATGTATATACATCAAATTTTAATTTG
*
33952 TTGTATTTATATACATCAAATTTTAATTT
1 TTGTATGTATATACATCAAATTTTAATTT
33981 TAATTTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 3 0.12
29 11 0.42
30 12 0.46
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.53
Consensus pattern (30 bp):
TTGTATGTATATACATCAAATTTTAATTTG
Found at i:35003 original size:23 final size:23
Alignment explanation
Indices: 34930--35124 Score: 148
Period size: 23 Copynumber: 8.5 Consensus size: 23
34920 TATACGGAAC
* *
34930 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
34952 -AACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * *
34973 GGGCAACAGAGAGCACGCACAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
* * * *
34999 AAACAGAAAGTACACAAAATACT
1 AAACAGAGAGCACACAAAGTGCT
35022 AATA-AGAGAGCACACAAAGTGCT
1 AA-ACAGAGAGCACACAAAGTGCT
* *
35045 GATCAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
35068 GATCAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * * *
35091 GATCAGAGGGCACGA-AACGTGCT
1 AAACAGAGAGCAC-ACAAAGTGCT
35114 AAACAGAGAGC
1 AAACAGAGAGC
35125 GCGCTAGTGT
Statistics
Matches: 140, Mismatches: 24, Indels: 17
0.77 0.13 0.09
Matches are distributed among these distances:
21 17 0.12
23 103 0.74
24 2 0.01
25 12 0.09
26 6 0.04
ACGTcount: A:0.43, C:0.21, G:0.25, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:35052 original size:69 final size:69
Alignment explanation
Indices: 34930--35085 Score: 174
Period size: 69 Copynumber: 2.3 Consensus size: 69
34920 TATACGGAAC
* * * * *
34930 AAACAGAGAGTAC-CAAAGTACTAACAGAGAGCACATAAGTGCTGGGCAACAGAGAGCACGCACA
1 AAACAGAGAGTACACAAAATACTAAAAGAGAGCACAAAAGTGCT-GGCAACAGAGAGCACACAAA
34994 GTGCT
65 GTGCT
* *
34999 AAACAGAAAGTACACAAAATACTAATAAGAGAGCACACAAAGTGCT-G-ATCAGAGAGCACACAA
1 AAACAGAGAGTACACAAAATACTAA-AAGAGAGCACA-AAAGTGCTGGCAACAGAGAGCACACAA
35062 AGTGCT
64 AGTGCT
* * *
35068 GATCAGAGAGCACACAAA
1 AAACAGAGAGTACACAAA
35086 GTGCTGATCA
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
69 45 0.62
70 11 0.15
71 10 0.14
72 7 0.10
ACGTcount: A:0.46, C:0.21, G:0.22, T:0.12
Consensus pattern (69 bp):
AAACAGAGAGTACACAAAATACTAAAAGAGAGCACAAAAGTGCTGGCAACAGAGAGCACACAAAG
TGCT
Done.