Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002526.1 Kokia drynarioides strain JFW-HI SEQ_114695, 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: 60437
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 36 characters in sequence are not A, C, G, or T
Found at i:10274 original size:13 final size:13
Alignment explanation
Indices: 10256--10281 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10246 AGCTTTGCTT
10256 TTATTTTTAATTA
1 TTATTTTTAATTA
10269 TTATTTTTAATTA
1 TTATTTTTAATTA
10282 ATAAATATAT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTATTTTTAATTA
Found at i:18201 original size:19 final size:19
Alignment explanation
Indices: 18177--18213 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
18167 AAACAAAATT
*
18177 GTTTATACTATGAGTTTTG
1 GTTTATACTATGAATTTTG
*
18196 GTTTATAGTATGAATTTT
1 GTTTATACTATGAATTTT
18214 TTAATATTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.03, G:0.19, T:0.54
Consensus pattern (19 bp):
GTTTATACTATGAATTTTG
Found at i:18890 original size:20 final size:20
Alignment explanation
Indices: 18867--18914 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
18857 CAATCTCTTT
18867 CTTTGTGTTTCTCTGTTTTC
1 CTTTGTGTTTCTCTGTTTTC
18887 CTTTGTGTTTCTCTGTTTTC
1 CTTTGTGTTTCTCTGTTTTC
*
18907 CTGTGTGT
1 CTTTGTGT
18915 CATCAATGGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.00, C:0.19, G:0.19, T:0.62
Consensus pattern (20 bp):
CTTTGTGTTTCTCTGTTTTC
Found at i:38012 original size:30 final size:29
Alignment explanation
Indices: 37927--38012 Score: 113
Period size: 29 Copynumber: 3.0 Consensus size: 29
37917 TAAAATTTAA
37927 TTAA-AAAAATCAAATTTAAGGGTAAAAG
1 TTAATAAAAATCAAATTTAAGGGTAAAAG
* *
37955 TTAGTAAAAATCAAATTTGAGGGTAAAAG
1 TTAATAAAAATCAAATTTAAGGGTAAAAG
*
37984 TTAATAAAATTCAAAGTTT-AGTGGTAAAA
1 TTAATAAAAATCAAA-TTTAAG-GGTAAAA
38013 TCTAATCACG
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.06
29 38 0.75
30 10 0.20
ACGTcount: A:0.51, C:0.03, G:0.16, T:0.29
Consensus pattern (29 bp):
TTAATAAAAATCAAATTTAAGGGTAAAAG
Found at i:41035 original size:24 final size:24
Alignment explanation
Indices: 40955--41023 Score: 102
Period size: 24 Copynumber: 2.9 Consensus size: 24
40945 AATTTTTGAG
* * *
40955 TTAAACTTTGTTTAATTCTTTCAA
1 TTAAACTCTGTTTATTTGTTTCAA
*
40979 TTAAACTCAGTTTATTTGTTTCAA
1 TTAAACTCTGTTTATTTGTTTCAA
41003 TTAAACTCTGTTTATTTGTTT
1 TTAAACTCTGTTTATTTGTTT
41024 GAGTCAAACT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.26, C:0.12, G:0.07, T:0.55
Consensus pattern (24 bp):
TTAAACTCTGTTTATTTGTTTCAA
Found at i:42983 original size:24 final size:23
Alignment explanation
Indices: 42950--43022 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 23
42940 AGAAATAATC
*
42950 TTTCAGTTAAACTTTGTTTAATTG
1 TTTCAATTAAAC-TTGTTTAATTG
42974 TTTCAATTAAACTCTGTTT-ATGTG
1 TTTCAATTAAACT-TGTTTAAT-TG
* *
42998 TTTTAATTAAAC-TGTTTATTTG
1 TTTCAATTAAACTTGTTTAATTG
43020 TTT
1 TTT
43023 GAGTCAACTT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
22 10 0.23
23 4 0.09
24 29 0.67
ACGTcount: A:0.25, C:0.08, G:0.11, T:0.56
Consensus pattern (23 bp):
TTTCAATTAAACTTGTTTAATTG
Found at i:56287 original size:363 final size:363
Alignment explanation
Indices: 55622--56346 Score: 1227
Period size: 363 Copynumber: 2.0 Consensus size: 363
55612 AAGAAGTATC
** *
55622 ATGATTGAAAACACCTTGTTGTATACTCTTTACGGAAGCAATTCATCCAACTGCTTTATCCAATG
1 ATGATTGAAAACACCTAATTGTATACTCTTTACGAAAGCAATTCATCCAACTGCTTTATCCAATG
55687 ACCTCGTCATATGTGTTACCCTCATATGATATCCTTAATTCCTTTGAGTTAAATTCGTTCACTCA
66 ACCTCGTCATATGTGTTACCCTCATATGATATCCTTAATTCCTTTGAGTTAAATTCGTTCACTCA
*
55752 ATACAATCATATTTTATCTCATTGTCACCATTGTGTCTTCTTAATGATTAATATGATCACTGTCA
131 ATACAATCATATTTTATCTCATTCTCACCATTGTGTCTTCTTAATGATTAATATGATCACTGTCA
* *
55817 ACAAATGACTGTGGTAAATTGCTCGTTCTAGAACAAGCAACCCGTGGTCACGTTCCACATTTATC
196 ACAAATGACTATGGTAAATTGCTCGTTCGAGAACAAGCAACCCGTGGTCACGTTCCACATTTATC
* *
55882 AATCCACACAATACCAATAAGAGGATATCATTAACTCTTTAATTGAGCTATGAATTCCACTATTG
261 AATCCACACAATACCAATAAGAGAATATCATTAACTCTTTAATTGAACTATGAATTCCACTATTG
* *
55947 CTAGTAAAGCTATGCCATACATAAGTCATGTACCCAAT
326 CTAGTAAAGCCATGCCATACACAAGTCATGTACCCAAT
*
55985 ATGATTGAAAACACCTAATTGTATACTCTTTACGAAAGCAATTCATCCAACTGCTTTATTCAATG
1 ATGATTGAAAACACCTAATTGTATACTCTTTACGAAAGCAATTCATCCAACTGCTTTATCCAATG
* * * *
56050 ACCTCGTCATGTGTGTTACCCTTATATGATATCCTTGATTCCTTTGAGTTAAGTAT-GTTCACTC
66 ACCTCGTCATATGTGTTACCCTCATATGATATCCTTAATTCCTTTGAGTTAAAT-TCGTTCACTC
*
56114 AATACAATCTTATTTTATCTCATTCTCACCATTGTGTCTTCTTAATGATTAATATGATCACTGTC
130 AATACAATCATATTTTATCTCATTCTCACCATTGTGTCTTCTTAATGATTAATATGATCACTGTC
* *
56179 AACAAATGACTATGGTAAATTGCTCGTTCGAGAATAAGCAACCCGTGGTCACGTTCCATATTTAT
195 AACAAATGACTATGGTAAATTGCTCGTTCGAGAACAAGCAACCCGTGGTCACGTTCCACATTTAT
* * * *
56244 CAATCCACACAGTGCCAATAAGAGAATATCATTAACTCTTTAATTGAATTTTGAATTCCACTATT
260 CAATCCACACAATACCAATAAGAGAATATCATTAACTCTTTAATTGAACTATGAATTCCACTATT
*
56309 GCTAGTAAAGCCATGTCATACACAAGTCATGTACCCAA
325 GCTAGTAAAGCCATGCCATACACAAGTCATGTACCCAA
56347 CATACCGGCT
Statistics
Matches: 338, Mismatches: 23, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
363 337 1.00
364 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.35
Consensus pattern (363 bp):
ATGATTGAAAACACCTAATTGTATACTCTTTACGAAAGCAATTCATCCAACTGCTTTATCCAATG
ACCTCGTCATATGTGTTACCCTCATATGATATCCTTAATTCCTTTGAGTTAAATTCGTTCACTCA
ATACAATCATATTTTATCTCATTCTCACCATTGTGTCTTCTTAATGATTAATATGATCACTGTCA
ACAAATGACTATGGTAAATTGCTCGTTCGAGAACAAGCAACCCGTGGTCACGTTCCACATTTATC
AATCCACACAATACCAATAAGAGAATATCATTAACTCTTTAATTGAACTATGAATTCCACTATTG
CTAGTAAAGCCATGCCATACACAAGTCATGTACCCAAT
Found at i:59613 original size:69 final size:69
Alignment explanation
Indices: 59484--59657 Score: 210
Period size: 69 Copynumber: 2.5 Consensus size: 69
59474 TATACGAAAC
* * *
59484 AAACAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACATAAGTGTTGGGCAGCAAAAAACACACAA
1 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACAAAAGTGCT--GAAGCAAAAAACACACAA
59547 AGTGCT
64 AGTGCT
* * * *
59553 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT-AATCAGAGAGCACACAAA
1 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACA-AAAGTGCTGAAGCAAAAAACACACAAA
59617 GTGCT
65 GTGCT
* * *
59622 AATCAGAGAGCACACAAAGTGCTAATCAGAGAGCAC
1 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCAC
59658 GAGACGTGCT
Statistics
Matches: 92, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
69 64 0.70
70 11 0.12
71 11 0.12
72 6 0.07
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.13
Consensus pattern (69 bp):
AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACAAAAGTGCTGAAGCAAAAAACACACAAAG
TGCT
Found at i:59667 original size:46 final size:44
Alignment explanation
Indices: 59540--59678 Score: 188
Period size: 46 Copynumber: 3.0 Consensus size: 44
59530 CAGCAAAAAA
* *
59540 CACACAAAGTGCTAAACAGAGAGTACACAAAGTACTAATCAGAGAG
1 CACACAAAGTGCTAATCAGAGAG--CACAAAGTGCTAATCAGAGAG
59586 CACACAAAGTGCTAATCAGAGAGCACACAAAGTGCTAATCAGAGAG
1 CACACAAAGTGCTAATCAGAGAG--CACAAAGTGCTAATCAGAGAG
* *
59632 CACACAAAGTGCTAATCAGAGAGCACGAGACGTGCTAAACAGAGAG
1 CACACAAAGTGCTAATCAGAGAGCAC-A-AAGTGCTAATCAGAGAG
59678 C
1 C
59679 GCGCTAGTGT
Statistics
Matches: 86, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
44 3 0.03
45 1 0.01
46 82 0.95
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (44 bp):
CACACAAAGTGCTAATCAGAGAGCACAAAGTGCTAATCAGAGAG
Found at i:59667 original size:69 final size:69
Alignment explanation
Indices: 59540--59678 Score: 208
Period size: 69 Copynumber: 2.0 Consensus size: 69
59530 CAGCAAAAAA
* *
59540 CACACAAAGTGCTAAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCTAATCAG
1 CACACAAAGTGCTAAACAGAGAGCACACAAAGTACTAATCAGAGAGCACACAAAGTGCTAAACAG
59605 AGAG
66 AGAG
* * * *
59609 CACACAAAGTGCTAATCAGAGAGCACACAAAGTGCTAATCAGAGAGCACGA-GACGTGCTAAACA
1 CACACAAAGTGCTAAACAGAGAGCACACAAAGTACTAATCAGAGAGCAC-ACAAAGTGCTAAACA
59673 GAGAG
65 GAGAG
59678 C
1 C
59679 GCGCTAGTGT
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
69 62 0.98
70 1 0.02
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (69 bp):
CACACAAAGTGCTAAACAGAGAGCACACAAAGTACTAATCAGAGAGCACACAAAGTGCTAAACAG
AGAG
Found at i:59678 original size:23 final size:23
Alignment explanation
Indices: 59540--59657 Score: 209
Period size: 23 Copynumber: 5.1 Consensus size: 23
59530 CAGCAAAAAA
*
59540 CACACAAAGTGCTAAACAGAGAG
1 CACACAAAGTGCTAATCAGAGAG
* *
59563 TACACAAAGTACTAATCAGAGAG
1 CACACAAAGTGCTAATCAGAGAG
59586 CACACAAAGTGCTAATCAGAGAG
1 CACACAAAGTGCTAATCAGAGAG
59609 CACACAAAGTGCTAATCAGAGAG
1 CACACAAAGTGCTAATCAGAGAG
59632 CACACAAAGTGCTAATCAGAGAG
1 CACACAAAGTGCTAATCAGAGAG
59655 CAC
1 CAC
59658 GAGACGTGCT
Statistics
Matches: 90, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 90 1.00
ACGTcount: A:0.45, C:0.22, G:0.20, T:0.13
Consensus pattern (23 bp):
CACACAAAGTGCTAATCAGAGAG
Done.