Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010837.1 Kokia drynarioides strain JFW-HI SEQ_125804, 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: 16918
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32
Warning! 45 characters in sequence are not A, C, G, or T
Found at i:705 original size:8 final size:9
Alignment explanation
Indices: 688--776 Score: 52
Period size: 9 Copynumber: 10.2 Consensus size: 9
678 AAAATATTAA
688 AATAATTTT
1 AATAATTTT
697 AATAA-TTT
1 AATAATTTT
705 -AT-ATTTT
1 AATAATTTT
712 AAAAAATAATTTT
1 ---A-ATAATTTT
725 AAAATAATTTT
1 --AATAATTTT
736 AATAATTTT
1 AATAATTTT
745 -AT-ATTTT
1 AATAATTTT
*
752 AA-AA---A
1 AATAATTTT
757 AATAATTTT
1 AATAATTTT
766 AATAATTTT
1 AATAATTTT
775 AA
1 AA
777 AATCATTTGC
Statistics
Matches: 65, Mismatches: 2, Indels: 26
0.70 0.02 0.28
Matches are distributed among these distances:
5 2 0.03
6 3 0.05
7 10 0.15
8 7 0.11
9 25 0.38
11 8 0.12
12 5 0.08
13 5 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
AATAATTTT
Found at i:729 original size:39 final size:41
Alignment explanation
Indices: 684--776 Score: 158
Period size: 39 Copynumber: 2.4 Consensus size: 41
674 GATTAAAATA
684 TTAAAATAATTTTAATAA-TTTATATTTT-AAAAAATAATT
1 TTAAAATAATTTTAATAATTTTATATTTTAAAAAAATAATT
723 TTAAAATAATTTTAATAATTTTATATTTTAAAAAAATAATT
1 TTAAAATAATTTTAATAATTTTATATTTTAAAAAAATAATT
764 TT--AATAATTTTAA
1 TTAAAATAATTTTAA
777 AATCATTTGC
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
39 29 0.56
40 10 0.19
41 13 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (41 bp):
TTAAAATAATTTTAATAATTTTATATTTTAAAAAAATAATT
Found at i:762 original size:21 final size:23
Alignment explanation
Indices: 736--778 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
726 AAATAATTTT
736 AATAATTTT-AT-ATTTTAAAAA
1 AATAATTTTAATAATTTTAAAAA
757 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
779 TCATTTGCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 9 0.45
22 2 0.10
23 9 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AATAATTTTAATAATTTTAAAAA
Found at i:1842 original size:27 final size:27
Alignment explanation
Indices: 1804--1857 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
1794 GAAGGTATCC
1804 TACGACAGCGTTTAAGTCCGCAAATGA
1 TACGACAGCGTTTAAGTCCGCAAATGA
1831 TACGACAGCGTTTAAGTCCGCAAATGA
1 TACGACAGCGTTTAAGTCCGCAAATGA
1858 CAACAAATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (27 bp):
TACGACAGCGTTTAAGTCCGCAAATGA
Found at i:8667 original size:40 final size:40
Alignment explanation
Indices: 8623--8698 Score: 143
Period size: 40 Copynumber: 1.9 Consensus size: 40
8613 GATTGTAGAT
*
8623 AAATACCATTGTTATCATTCCATCGACAATTTAATTTTGA
1 AAATACCATTGTTATCATTCCATCGACAACTTAATTTTGA
8663 AAATACCATTGTTATCATTCCATCGACAACTTAATT
1 AAATACCATTGTTATCATTCCATCGACAACTTAATT
8699 ATCTTTCTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.38
Consensus pattern (40 bp):
AAATACCATTGTTATCATTCCATCGACAACTTAATTTTGA
Found at i:9471 original size:31 final size:29
Alignment explanation
Indices: 9436--9509 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 29
9426 TATTAAAACT
*
9436 ATAAACTTTGATCTAATATGTAATTTTATAC
1 ATAAATTTTGAT-T-ATATGTAATTTTATAC
* * *
9467 ATAAATTTTGATTTTTTGTAATTTTATAT
1 ATAAATTTTGATTATATGTAATTTTATAC
9496 ATGAAATTTTGATT
1 AT-AAATTTTGATT
9510 TGATCAAATC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 15 0.39
30 12 0.32
31 11 0.29
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.53
Consensus pattern (29 bp):
ATAAATTTTGATTATATGTAATTTTATAC
Found at i:9493 original size:29 final size:30
Alignment explanation
Indices: 9454--9510 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
9444 TGATCTAATA
9454 TGTAATTTTATACAT-AAATTTTGATTTTT
1 TGTAATTTTATACATGAAATTTTGATTTTT
*
9483 TGTAATTTTATATATGAAATTTTGATTT
1 TGTAATTTTATACATGAAATTTTGATTT
9511 GATCAAATCC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.58
Consensus pattern (30 bp):
TGTAATTTTATACATGAAATTTTGATTTTT
Found at i:9737 original size:26 final size:25
Alignment explanation
Indices: 9697--9746 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
9687 TCAAAATTTT
9697 ATATGTATAACTATATCAAATAAAAC
1 ATATGTATAACTATAT-AAATAAAAC
*
9723 ATATGTATATA-TATATAATTAAAA
1 ATATGTATA-ACTATATAAATAAAA
9747 ATTAAAACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 7 0.32
26 14 0.64
27 1 0.05
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.36
Consensus pattern (25 bp):
ATATGTATAACTATATAAATAAAAC
Found at i:16081 original size:9 final size:9
Alignment explanation
Indices: 16067--16126 Score: 53
Period size: 9 Copynumber: 7.2 Consensus size: 9
16057 ATAAATGATT
16067 TTAAAATTA
1 TTAAAATTA
16076 TTAAAATTA
1 TTAAAATTA
16085 TT----TT-
1 TTAAAATTA
16089 TTAAAA-TA
1 TTAAAATTA
16097 -TAAAATTA
1 TTAAAATTA
16105 TTTAAAAATTA
1 -TT-AAAATTA
16116 TTAAAATTA
1 TTAAAATTA
16125 TT
1 TT
16127 TTTTTAAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 18
0.70 0.00 0.30
Matches are distributed among these distances:
4 2 0.05
5 2 0.05
7 6 0.14
8 2 0.05
9 20 0.48
10 3 0.07
11 7 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
TTAAAATTA
Found at i:16087 original size:20 final size:20
Alignment explanation
Indices: 16059--16128 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
16049 TCACGTCAAT
*
16059 AAATGATTTTAAAATTATTA
1 AAATTATTTTAAAATTATTA
16079 AAATTATTTTTTAAAA-TA-TA
1 AAATTA--TTTTAAAATTATTA
*
16099 AAATTATTTAAAAATTATTA
1 AAATTATTTTAAAATTATTA
16119 AAATTATTTT
1 AAATTATTTT
16129 TTTAAATAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
18 7 0.16
19 2 0.05
20 24 0.56
21 2 0.05
22 8 0.19
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (20 bp):
AAATTATTTTAAAATTATTA
Found at i:16120 original size:40 final size:41
Alignment explanation
Indices: 16059--16159 Score: 145
Period size: 40 Copynumber: 2.5 Consensus size: 41
16049 TCACGTCAAT
* *
16059 AAATGATTTTAAAATTATTAAAATTATTTTTTAAAAT-ATA
1 AAATTATTTAAAAATTATTAAAATTATTTTTTAAAATAATA
*
16099 AAATTATTTAAAAATTATTAAAATTATTTTTTTAAATAATA
1 AAATTATTTAAAAATTATTAAAATTATTTTTTAAAATAATA
16140 AAATTA-TTAAATAATT-TTAA
1 AAATTATTTAAA-AATTATTAA
16160 TTTTCAATTT
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
40 43 0.77
41 13 0.23
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (41 bp):
AAATTATTTAAAAATTATTAAAATTATTTTTTAAAATAATA
Done.