Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003670.1 Kokia drynarioides strain JFW-HI SEQ_116587, 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: 71438
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:6510 original size:19 final size:18
Alignment explanation
Indices: 6488--6536 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
6478 ATATATTATC
*
6488 AATTCGGTTAATTTTGATT
1 AATTCGGTTAA-TTTAATT
6507 AATTCCGGTTAATTTAATT
1 AATT-CGGTTAATTTAATT
*
6526 AATTTGGTTAA
1 AATTCGGTTAA
6537 CCAAAAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 6 0.22
19 14 0.52
20 7 0.26
ACGTcount: A:0.31, C:0.06, G:0.14, T:0.49
Consensus pattern (18 bp):
AATTCGGTTAATTTAATT
Found at i:9801 original size:20 final size:20
Alignment explanation
Indices: 9776--9813 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
9766 TCCCATAATT
*
9776 TTAAACTTAAATCTTGAACC
1 TTAAACCTAAATCTTGAACC
9796 TTAAACCTAAATCTTGAA
1 TTAAACCTAAATCTTGAA
9814 TATCAAATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.18, G:0.05, T:0.34
Consensus pattern (20 bp):
TTAAACCTAAATCTTGAACC
Found at i:16598 original size:21 final size:21
Alignment explanation
Indices: 16574--16619 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
16564 CTGTTTCGCA
*
16574 CTTCGATACTCGGTGATTTGC
1 CTTCGATACTCAGTGATTTGC
* *
16595 CTTCGATGCTTAGTGATTTGC
1 CTTCGATACTCAGTGATTTGC
16616 CTTC
1 CTTC
16620 AGTGCCTAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.13, C:0.24, G:0.22, T:0.41
Consensus pattern (21 bp):
CTTCGATACTCAGTGATTTGC
Found at i:16629 original size:21 final size:21
Alignment explanation
Indices: 16586--16630 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
16576 TCGATACTCG
*
16586 GTGATTTGCCTTCGATGCTTA
1 GTGATTTGCCTTCGATGCCTA
16607 GTGATTTGCCTTC-AGTGCCTA
1 GTGATTTGCCTTCGA-TGCCTA
16628 GTG
1 GTG
16631 TTCTATTAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.13, C:0.20, G:0.27, T:0.40
Consensus pattern (21 bp):
GTGATTTGCCTTCGATGCCTA
Found at i:17226 original size:22 final size:22
Alignment explanation
Indices: 17201--17243 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
17191 TTCTGTGTAA
*
17201 TTAT-TAATAAGAAAATTTTAAG
1 TTATGTAA-AAGAAAATATTAAG
*
17223 TTATGTAAATGAAAATATTAA
1 TTATGTAAAAGAAAATATTAA
17244 TTAAATTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (22 bp):
TTATGTAAAAGAAAATATTAAG
Found at i:29535 original size:16 final size:16
Alignment explanation
Indices: 29514--29544 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29504 TTTTATAATT
*
29514 TTATTAATATAAAATA
1 TTATTAAAATAAAATA
29530 TTATTAAAATAAAAT
1 TTATTAAAATAAAAT
29545 TGAATTTTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TTATTAAAATAAAATA
Found at i:36723 original size:117 final size:116
Alignment explanation
Indices: 36506--36739 Score: 319
Period size: 117 Copynumber: 2.0 Consensus size: 116
36496 ACAAATTGAA
* * *
36506 ATCCAAACTAAGAACACGCATTAGAAAAAAATCTAGACTTAGAACACCCATCAATCCATTAAGAA
1 ATCCAAACTAAGAACACGAATTAGAAAAAAATCCAGACTTAGAACACCCATAAATCCATTAAGAA
** *
36571 AGTCAGAAACTTAACATCACAAATAAAACCCTAAAAAATAACATATCAAAC
66 AACCAAAAACTTAACATCACAAATAAAACCCTAAAAAATAACATATCAAAC
* *
36622 ATCCAAACTTAGAACATC-AATTAGAAAAAAAAGTCCATACTTAGAACACCCATAAATCCATTAA
1 ATCCAAACTAAGAACA-CGAATTAG-AAAAAAA-TCCAGACTTAGAACACCCATAAATCCATTAA
* * * *
36686 -AAAACCAAAAAGTTAACATCATAAATAAAATCCTAAAAATTAACATATCAAAC
63 GAAAACCAAAAACTTAACATCACAAATAAAACCCTAAAAAATAACATATCAAAC
36739 A
1 A
36740 AAACCCATCA
Statistics
Matches: 103, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
116 20 0.19
117 55 0.53
118 28 0.27
ACGTcount: A:0.54, C:0.21, G:0.06, T:0.20
Consensus pattern (116 bp):
ATCCAAACTAAGAACACGAATTAGAAAAAAATCCAGACTTAGAACACCCATAAATCCATTAAGAA
AACCAAAAACTTAACATCACAAATAAAACCCTAAAAAATAACATATCAAAC
Found at i:49785 original size:21 final size:19
Alignment explanation
Indices: 49758--49802 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
49748 GAAAAGAAAA
* *
49758 GAAAAATTAAATGGAAATGG
1 GAAAAAATAAAAGGAAA-GG
*
49778 GAAAAAATAAAAGGGAAGG
1 GAAAAAATAAAAGGAAAGG
49797 GAAAAA
1 GAAAAA
49803 CGAGAAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.62, C:0.00, G:0.27, T:0.11
Consensus pattern (19 bp):
GAAAAAATAAAAGGAAAGG
Found at i:53276 original size:24 final size:24
Alignment explanation
Indices: 53225--53278 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
53215 TTCGTAGGTC
* * *
53225 AAATAAATTATGCTAATAAATGCA
1 AAATATATTATACTAATAAATACA
*
53249 AAATATATTATACTAATAAATACT
1 AAATATATTATACTAATAAATACA
53273 AAATAT
1 AAATAT
53279 TCTAGAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.56, C:0.07, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACA
Found at i:55241 original size:24 final size:24
Alignment explanation
Indices: 55190--55241 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
55180 TTCGTAGGTC
* *
55190 AAATAAATTATGCTAATAAATGCA
1 AAATAAATTATACTAATAAATACA
* *
55214 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACA
55238 AAAT
1 AAAT
55242 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACA
Found at i:61400 original size:215 final size:213
Alignment explanation
Indices: 61003--61430 Score: 802
Period size: 215 Copynumber: 2.0 Consensus size: 213
60993 AAGGAAGAGG
61003 TAGAAGGTTATTTGCCATACGAATATGATCTTTCAGGTCACTTTGTAGGACATATTATAATTGGA
1 TAGAAGGTTATTTGCCATACGAATATGATCTTTCAGGTCACTTTGTAGGACATATTATAATTGGA
61068 ACGATACATACATAGAAGATTAGCATGACCCCGTGGAAGCATGACATGCACAAATCAAGAAACGA
66 ACGATACATACATAGAAGATTAGCATGACCCCGTGGAAGCATGACATGCACAAATCAAGAAACGA
* *
61133 TCCAAATTTTATTACTAAAGACATGCCTCTTTAATTGATATAAAAAGAACCAGTACTCAGAAATG
131 TCCAAAATTTATTACTAAAGACATGCCTCTTTAACTGATATAAAAAGAACCAGTACTCAGAAATG
*
61198 GTCTGGTTTTGCTTGAGA
196 GTCTGGTTTTGATTGAGA
61216 TAGAAGGTTATTTGCCATACGAATATGATCTTTCAGGTCACTTTGTAGGACATATTATAATTGGA
1 TAGAAGGTTATTTGCCATACGAATATGATCTTTCAGGTCACTTTGTAGGACATATTATAATTGGA
*
61281 ACGATACATACATAGAAGATTAGCATATGACCCTGTGGAAGCATGACATGCACAAATCAAGAAAC
66 ACGATACATACATAGAAGATTAGC--ATGACCCCGTGGAAGCATGACATGCACAAATCAAGAAAC
61346 GATCCAAAATTTATTACTAAAGACATGCCTCTTTAACTGATATAAAAAGAACCAGTACTCAGAAA
129 GATCCAAAATTTATTACTAAAGACATGCCTCTTTAACTGATATAAAAAGAACCAGTACTCAGAAA
61411 TGGTCTGGTTTTGATTGAGA
194 TGGTCTGGTTTTGATTGAGA
61431 AATTCACAAC
Statistics
Matches: 209, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
213 89 0.43
215 120 0.57
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (213 bp):
TAGAAGGTTATTTGCCATACGAATATGATCTTTCAGGTCACTTTGTAGGACATATTATAATTGGA
ACGATACATACATAGAAGATTAGCATGACCCCGTGGAAGCATGACATGCACAAATCAAGAAACGA
TCCAAAATTTATTACTAAAGACATGCCTCTTTAACTGATATAAAAAGAACCAGTACTCAGAAATG
GTCTGGTTTTGATTGAGA
Found at i:70152 original size:19 final size:19
Alignment explanation
Indices: 70107--70156 Score: 61
Period size: 17 Copynumber: 2.8 Consensus size: 19
70097 AAAAAAAATA
* *
70107 ATAATAAAA-AGAAAATTT
1 ATAATAAAATAAAAAAGTT
70125 AT-A-AAAATAAAAAAGTT
1 ATAATAAAATAAAAAAGTT
70142 ATAATAAAATAAAAA
1 ATAATAAAATAAAAA
70157 TATTAAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 4 0.15
17 10 0.37
18 3 0.11
19 10 0.37
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (19 bp):
ATAATAAAATAAAAAAGTT
Found at i:70165 original size:18 final size:18
Alignment explanation
Indices: 70100--70165 Score: 52
Period size: 19 Copynumber: 3.8 Consensus size: 18
70090 AAATCATAAA
*
70100 AAAAATAAT-AATAAAA-
1 AAAAATATTAAATAAAAT
*
70116 AGAAAAT-TTATA-AAAAT
1 A-AAAATATTAAATAAAAT
70133 AAAAA-AGTTATAATAAAAT
1 AAAAATA-TTA-AATAAAAT
70152 AAAAATATTAAATA
1 AAAAATATTAAATA
70166 TTAAATTTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
16 10 0.26
17 10 0.26
18 5 0.13
19 13 0.33
20 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATTAAATAAAAT
Found at i:70230 original size:17 final size:19
Alignment explanation
Indices: 70202--70240 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
70192 TTATAAAAAA
*
70202 AAAACTTATAAATATT-AT
1 AAAACTTATAAAAATTAAT
70220 AAAAC-TATAAAAATTAAT
1 AAAACTTATAAAAATTAAT
70238 AAA
1 AAA
70241 TTAATAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAACTTATAAAAATTAAT
Found at i:70747 original size:19 final size:19
Alignment explanation
Indices: 70723--70781 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
70713 AGTCTCATTC
70723 AAGTTTTTATAATTTTTAT
1 AAGTTTTTATAATTTTTAT
* *
70742 AAGTTTATATCAATTTTAAT
1 AAGTTTTTAT-AATTTTTAT
*
70762 -ATTTTTTATAATTTTTAT
1 AAGTTTTTATAATTTTTAT
70780 AA
1 AA
70782 AATTTTAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
18 8 0.24
19 17 0.52
20 8 0.24
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (19 bp):
AAGTTTTTATAATTTTTAT
Found at i:70768 original size:29 final size:28
Alignment explanation
Indices: 70721--70791 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 28
70711 CCAGTCTCAT
*
70721 TCAAGTTTTTATAATTTTTATAAGTTTATA
1 TCAA-TTTTAATAATTTTTATAA-TTTATA
* *
70751 TCAATTTTAATATTTTTTATAATTTTTA
1 TCAATTTTAATAATTTTTATAATTTATA
*
70779 TAAAATTTTAATA
1 T-CAATTTTAATA
70792 CGTTTTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 6 0.17
29 26 0.72
30 4 0.11
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (28 bp):
TCAATTTTAATAATTTTTATAATTTATA
Found at i:70867 original size:10 final size:9
Alignment explanation
Indices: 70726--70854 Score: 78
Period size: 9 Copynumber: 13.0 Consensus size: 9
70716 CTCATTCAAG
70726 TTTTTATAA
1 TTTTTATAA
70735 TTTTTATAA
1 TTTTTATAA
*
70744 GTTTATATCAA
1 -TTTTTAT-AA
* *
70755 TTTTAATAT
1 TTTTTATAA
70764 TTTTTATAA
1 TTTTTATAA
70773 TTTTTATAAAA
1 TTTTTAT--AA
* *
70784 TTTTAATACGT
1 TTTTTATA--A
*
70795 TTTTTTTAA
1 TTTTTATAA
*
70804 TGTTTTAAATA
1 T-TTTTATA-A
70815 TATTTTATTAA
1 T-TTTTA-TAA
*
70826 TTTTATTAGAA
1 -TTT-TTATAA
70837 TTTTTATAA
1 TTTTTATAA
70846 TTTTTATAA
1 TTTTTATAA
70855 ATTTATATCA
Statistics
Matches: 92, Mismatches: 17, Indels: 22
0.70 0.13 0.17
Matches are distributed among these distances:
9 40 0.43
10 19 0.21
11 28 0.30
12 5 0.05
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Done.