Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005576.1 Kokia drynarioides strain JFW-HI SEQ_119695, 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: 15190
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.37
Found at i:1301 original size:27 final size:27
Alignment explanation
Indices: 1263--1317 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
1253 TCCCTAACCT
1263 ACCCAAAACAGAATTAGTTGGTTTTGC
1 ACCCAAAACAGAATTAGTTGGTTTTGC
1290 ACCCAAAACAGAATTAGTTGGTTTTGC
1 ACCCAAAACAGAATTAGTTGGTTTTGC
1317 A
1 A
1318 GATACAGGGT
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:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (27 bp):
ACCCAAAACAGAATTAGTTGGTTTTGC
Found at i:2054 original size:17 final size:17
Alignment explanation
Indices: 2032--2064 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2022 TCTCTTGAGC
2032 TTTAACCTTTCATATTT
1 TTTAACCTTTCATATTT
2049 TTTAACCTTTCATATT
1 TTTAACCTTTCATATT
2065 CTTGTAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.18, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTAACCTTTCATATTT
Found at i:3385 original size:15 final size:16
Alignment explanation
Indices: 3351--3386 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
3341 AATTTTATAC
3351 TTTTTTATATATTGAAA
1 TTTTTTATATATTG-AA
3368 TTTTTTATATATTG-A
1 TTTTTTATATATTGAA
3383 TTTT
1 TTTT
3387 AACATTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.26
17 14 0.74
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.67
Consensus pattern (16 bp):
TTTTTTATATATTGAA
Found at i:8659 original size:30 final size:30
Alignment explanation
Indices: 8616--8695 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 30
8606 TAAATTTTTT
* *
8616 AAAAATTATAATTTTATCT-TTGAACTTTAC
1 AAAAATTA-AATTTTACCTATCGAACTTTAC
* *
8646 AAAAATATAAATTTTACCTATCGAATTTTCC
1 AAAAAT-TAAATTTTACCTATCGAACTTTAC
*
8677 AAAAATTTAAATTTGACCT
1 AAAAA-TTAAATTTTACCT
8696 TAAAATTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
30 15 0.36
31 26 0.62
32 1 0.02
ACGTcount: A:0.42, C:0.12, G:0.04, T:0.41
Consensus pattern (30 bp):
AAAAATTAAATTTTACCTATCGAACTTTAC
Found at i:8711 original size:30 final size:29
Alignment explanation
Indices: 8677--8859 Score: 129
Period size: 30 Copynumber: 6.2 Consensus size: 29
8667 CGAATTTTCC
*
8677 AAAAATTTAAATTTGACCTTAAAATTTTTT
1 AAAAATTTAAATTTGACCCT-AAATTTTTT
* * * **
8707 AAAAATTCAAATTAGACCACTAAACTTTCC
1 AAAAATTTAAATTTGACC-CTAAATTTTTT
* * *
8737 AAATATTTGAATTTGACCC-AAACCTTTTT
1 AAAAATTTAAATTTGACCCTAAA-TTTTTT
* * *
8766 -AAAATTTGAATTTAACCCTAAATTTTCTA
1 AAAAATTTAAATTTGACCCTAAATTTT-TT
*
8795 AAAAATTCTAAA-TTGACCCTTGAATTTTTT
1 AAAAATT-TAAATTTGACCC-TAAATTTTTT
* * * * *
8825 GAAAATTCAAATTTGACCCCAAACTTTTC
1 AAAAATTTAAATTTGACCCTAAATTTTTT
8854 AAAAAT
1 AAAAAT
8860 ACCAATTTGG
Statistics
Matches: 118, Mismatches: 27, Indels: 17
0.73 0.17 0.10
Matches are distributed among these distances:
28 22 0.19
29 23 0.19
30 62 0.53
31 11 0.09
ACGTcount: A:0.42, C:0.16, G:0.05, T:0.38
Consensus pattern (29 bp):
AAAAATTTAAATTTGACCCTAAATTTTTT
Found at i:8751 original size:60 final size:58
Alignment explanation
Indices: 8672--8859 Score: 166
Period size: 59 Copynumber: 3.2 Consensus size: 58
8662 CCTATCGAAT
8672 TTTCCAAAAATTTAAATTTGACCTTAAAATTTTTTAAAAATTCAAATTAGACCACTAAAC
1 TTTCCAAAAATTT-AATTTGACCTTAAAATTTTTTAAAAATTCAAATTAGACC-CTAAAC
* * ** * * * *
8732 TTTCCAAATATTTGAATTTGACC-CAAACCTTTTTAAAATTTGAATTTA-ACCCTAAAT
1 TTTCCAAAAATTT-AATTTGACCTTAAAATTTTTTAAAAATTCAAATTAGACCCTAAAC
* * * * * *
8789 TTTCTAAAAAATTCTAAATTGACCCTT-GAATTTTTTGAAAATTCAAATTTGACCCCAAAC
1 TTTC-CAAAAATT-TAATTTGA-CCTTAAAATTTTTTAAAAATTCAAATTAGACCCTAAAC
*
8849 TTTTCAAAAAT
1 TTTCCAAAAAT
8860 ACCAATTTGG
Statistics
Matches: 98, Mismatches: 25, Indels: 11
0.73 0.19 0.08
Matches are distributed among these distances:
57 9 0.09
58 15 0.15
59 43 0.44
60 31 0.32
ACGTcount: A:0.40, C:0.16, G:0.05, T:0.38
Consensus pattern (58 bp):
TTTCCAAAAATTTAATTTGACCTTAAAATTTTTTAAAAATTCAAATTAGACCCTAAAC
Found at i:9780 original size:26 final size:28
Alignment explanation
Indices: 9737--9811 Score: 66
Period size: 26 Copynumber: 2.7 Consensus size: 28
9727 TTATGTATTA
* * *
9737 AATATTTTACAATAAAATTTATTAGTAAT
1 AATATTTTA-ATTGAAATTTATTAATAAT
*
9766 AAT-TTTTAATT-AAATAT-TTAATAAT
1 AATATTTTAATTGAAATTTATTAATAAT
*
9791 ATTATTTTAATTGATAATTTA
1 AATATTTTAATTGA-AATTTA
9812 AAAATTATTA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
25 9 0.24
26 13 0.35
27 3 0.08
28 9 0.24
29 3 0.08
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (28 bp):
AATATTTTAATTGAAATTTATTAATAAT
Found at i:9797 original size:27 final size:27
Alignment explanation
Indices: 9769--9837 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
9759 TAGTAATAAT
*
9769 TTTTAATTAA-ATATTTAATAA-TATTA
1 TTTTAATTAATA-ATTTAAAAATTATTA
*
9795 TTTTAATTGATAATTTAAAAATTATTA
1 TTTTAATTAATAATTTAAAAATTATTA
*
9822 TTTTAATTTATAATTT
1 TTTTAATTAATAATTT
9838 TAATTGAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
26 17 0.45
27 21 0.55
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (27 bp):
TTTTAATTAATAATTTAAAAATTATTA
Found at i:9810 original size:13 final size:13
Alignment explanation
Indices: 9794--9844 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
9784 TAATAATATT
9794 ATTTTAATTGATA
1 ATTTTAATTGATA
* *
9807 ATTTAAAAATT-ATT
1 ATTT--TAATTGATA
*
9821 ATTTTAATTTATA
1 ATTTTAATTGATA
9834 ATTTTAATTGA
1 ATTTTAATTGA
9845 AAATAAAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
12 4 0.13
13 16 0.53
14 6 0.20
15 4 0.13
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (13 bp):
ATTTTAATTGATA
Found at i:11489 original size:20 final size:21
Alignment explanation
Indices: 11466--11510 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
11456 TTTTATTTTT
*
11466 ATATATGATATAAAAAT-TAA
1 ATATATAATATAAAAATATAA
* *
11486 ATATATAATATTATAATATAA
1 ATATATAATATAAAAATATAA
11507 ATAT
1 ATAT
11511 TAAAAAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
ATATATAATATAAAAATATAA
Found at i:12655 original size:22 final size:22
Alignment explanation
Indices: 12628--12673 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
12618 TATTTATATT
12628 ATATATTGATTAAATGAAATAAAA
1 ATATA-TGATTAAAT-AAATAAAA
*
12652 ATATATTATTAAATAAATAAAA
1 ATATATGATTAAATAAATAAAA
12674 TAATTAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.38
23 8 0.38
24 5 0.24
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (22 bp):
ATATATGATTAAATAAATAAAA
Done.