Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007470.1 Kokia drynarioides strain JFW-HI SEQ_122092, 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: 74262
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:822 original size:31 final size:27
Alignment explanation
Indices: 757--811 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
747 TAGAAAAAAT
757 AATAATAATAAAGAGAGAGAATTTAAC
1 AATAATAATAAAGAGAGAGAATTTAAC
784 AATAATAATAAAGAGAGAGAATTTAAC
1 AATAATAATAAAGAGAGAGAATTTAAC
811 A
1 A
812 GTGTTTAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.60, C:0.04, G:0.15, T:0.22
Consensus pattern (27 bp):
AATAATAATAAAGAGAGAGAATTTAAC
Found at i:1650 original size:33 final size:34
Alignment explanation
Indices: 1613--1676 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
1603 AATTTTTATA
*
1613 ATATTATTAATGC-TTTTTAATTTTTAAAAAAAT
1 ATATTATTAATGCATTTTTAAATTTTAAAAAAAT
* **
1646 ATATTTTTTTTGCATTTTTAAATTTTAAAAA
1 ATATTATTAATGCATTTTTAAATTTTAAAAA
1677 TTAATTAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 10 0.38
34 16 0.62
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (34 bp):
ATATTATTAATGCATTTTTAAATTTTAAAAAAAT
Found at i:6937 original size:30 final size:30
Alignment explanation
Indices: 6883--6943 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
6873 AATAGTCTAT
*
6883 ATTTTTATAATTTTTAAAAAATTAAATTAC
1 ATTTTTATAATTTTTAAAAAATTAAAATAC
* ***
6913 ATTTTTATCATTTTTAAGGGATTAAAATAC
1 ATTTTTATAATTTTTAAAAAATTAAAATAC
6943 A
1 A
6944 AATTTTTTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (30 bp):
ATTTTTATAATTTTTAAAAAATTAAAATAC
Found at i:8683 original size:20 final size:20
Alignment explanation
Indices: 8658--8699 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
8648 GCTTCTCATT
8658 ATCACCACTCAGGTACTAAA
1 ATCACCACTCAGGTACTAAA
8678 ATCACCACTCAGGTACTAAA
1 ATCACCACTCAGGTACTAAA
8698 AT
1 AT
8700 AACTTAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.29, G:0.10, T:0.21
Consensus pattern (20 bp):
ATCACCACTCAGGTACTAAA
Found at i:9957 original size:29 final size:29
Alignment explanation
Indices: 9915--9972 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
9905 TAAGGTTTTA
* *
9915 ACCCTTATCTTTCAAGTACCAACGAAGTG
1 ACCCTCATCTTTCAAGTACCAACCAAGTG
* *
9944 ACCCTCATTTTTCAAGTGCCAACCAAGTG
1 ACCCTCATCTTTCAAGTACCAACCAAGTG
9973 TACGACACCG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.28
Consensus pattern (29 bp):
ACCCTCATCTTTCAAGTACCAACCAAGTG
Found at i:11386 original size:16 final size:15
Alignment explanation
Indices: 11365--11420 Score: 67
Period size: 16 Copynumber: 3.5 Consensus size: 15
11355 GTGTAACATT
11365 ATTAAATTTAATTTTA
1 ATTAAATTT-ATTTTA
*
11381 ATTAAATATTTTTTTA
1 ATTAAAT-TTATTTTA
*
11397 ATTTAATTTGATTTTA
1 ATTAAATTT-ATTTTA
11413 ATTAAATT
1 ATTAAATT
11421 ACTTAAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
15 2 0.06
16 30 0.88
17 2 0.06
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (15 bp):
ATTAAATTTATTTTA
Found at i:16772 original size:20 final size:21
Alignment explanation
Indices: 16733--16772 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
16723 AAATTAAAAT
16733 AAATTATATATTAAAAAATTC
1 AAATTATATATTAAAAAATTC
* *
16754 AAATTA-ATTTTAAATAATT
1 AAATTATATATTAAAAAATT
16773 GTAATTCTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (21 bp):
AAATTATATATTAAAAAATTC
Found at i:29253 original size:16 final size:16
Alignment explanation
Indices: 29210--29255 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
29200 CAAATGATTT
*
29210 TAAAATTATTAAAAT-
1 TAAATTTATTAAAATA
* *
29225 T-ATTTTTTTAAAATA
1 TAAATTTATTAAAATA
29240 TAAATTTATTAAAATA
1 TAAATTTATTAAAATA
29256 ATTTTAAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
14 10 0.42
15 2 0.08
16 12 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TAAATTTATTAAAATA
Found at i:35996 original size:20 final size:20
Alignment explanation
Indices: 35973--36011 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
35963 TATTTTATAA
*
35973 AAATTAAAATAAATTTTAAT
1 AAATGAAAATAAATTTTAAT
* *
35993 AAATGAAATTACATTTTAA
1 AAATGAAAATAAATTTTAA
36012 AATTTTATTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (20 bp):
AAATGAAAATAAATTTTAAT
Found at i:37802 original size:82 final size:82
Alignment explanation
Indices: 37702--37866 Score: 276
Period size: 82 Copynumber: 2.0 Consensus size: 82
37692 ATCCTAAAAG
* *
37702 AGGTATTATCTCCTCTTCTTCTGCTACATATTTTTGTTACAATGATTTAGAATCAGTTCAACACT
1 AGGTATTATCTCCGCTTCTTCTACTACATATTTTTGTTACAATGATTTAGAATCAGTTCAACACT
*
37767 TATTCTTCACATGTGAT
66 TATTCTTCACACGTGAT
* * *
37784 AGGTATTATCTCCGCTTCTTCTACTACATGTTTTTGTTACTATGATTTAGAATTAGTTCAACACT
1 AGGTATTATCTCCGCTTCTTCTACTACATATTTTTGTTACAATGATTTAGAATCAGTTCAACACT
37849 TATTCTTCACACGTGAT
66 TATTCTTCACACGTGAT
37866 A
1 A
37867 AGGCTTGAAG
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
82 77 1.00
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.44
Consensus pattern (82 bp):
AGGTATTATCTCCGCTTCTTCTACTACATATTTTTGTTACAATGATTTAGAATCAGTTCAACACT
TATTCTTCACACGTGAT
Found at i:39579 original size:20 final size:20
Alignment explanation
Indices: 39537--39579 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
39527 TCATATCAAC
*
39537 AAATAATTTAAAAATTATAA
1 AAATAATTTAAAAATTAAAA
39557 AAAT-ATTTAAAAAATTAAAA
1 AAATAATTT-AAAAATTAAAA
39577 AAA
1 AAA
39580 AAAATTCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
AAATAATTTAAAAATTAAAA
Found at i:50384 original size:1 final size:1
Alignment explanation
Indices: 50380--50405 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
50370 NNNNNNNNNN
50380 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
50406 ACGTAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:60610 original size:26 final size:26
Alignment explanation
Indices: 60563--60628 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 26
60553 ATCAATCTGT
*
60563 TTACTTAGCTTG--ATGAGTAATAGGA
1 TTACTTAG-TTGTTATGAGCAATAGGA
60588 TTACTTAGTTGTTATGAGCAATAGGA
1 TTACTTAGTTGTTATGAGCAATAGGA
*
60614 TTACTTAGTAGTTAT
1 TTACTTAGTTGTTAT
60629 AAACCTATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
24 3 0.08
25 8 0.22
26 26 0.70
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.41
Consensus pattern (26 bp):
TTACTTAGTTGTTATGAGCAATAGGA
Done.