Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010247.1 Kokia drynarioides strain JFW-HI SEQ_125079, 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: 384304
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 26 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:310797 original size:10 final size:10
Alignment explanation
Indices: 310738--310808 Score: 58
Period size: 10 Copynumber: 7.3 Consensus size: 10
310728 AATACATAAT
310738 ATTATAAA-A
1 ATTATAAAGA
310747 ATTATAAAGTA
1 ATTATAAAG-A
**
310758 ATTATAACTA
1 ATTATAAAGA
* *
310768 TTTTTAAA-A
1 ATTATAAAGA
*
310777 A-TATTAAGA
1 ATTATAAAGA
310786 ATTATAAAGA
1 ATTATAAAGA
*
310796 ATTACAAAGA
1 ATTATAAAGA
310806 ATT
1 ATT
310809 CTTCAAAGAT
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
8 4 0.08
9 11 0.23
10 25 0.52
11 8 0.17
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.37
Consensus pattern (10 bp):
ATTATAAAGA
Found at i:310900 original size:22 final size:22
Alignment explanation
Indices: 310875--310951 Score: 75
Period size: 22 Copynumber: 3.4 Consensus size: 22
310865 TGCTAATTTT
*
310875 TTAAAAATTTATAAAAATTATG
1 TTAAAAATTTATAAAAATTATA
*
310897 TTAAAAATATA-AAAAATCTAATA
1 TTAAAAATTTATAAAAAT-T-ATA
* *
310920 TTCTAAAATATTCTAAAAATTATA
1 TT-AAAAAT-TTATAAAAATTATA
310944 TTAAAAAT
1 TTAAAAAT
310952 CTAAAAGGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
21 6 0.14
22 11 0.25
23 9 0.20
24 10 0.23
25 2 0.05
26 6 0.14
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (22 bp):
TTAAAAATTTATAAAAATTATA
Found at i:319505 original size:27 final size:25
Alignment explanation
Indices: 319475--319538 Score: 65
Period size: 27 Copynumber: 2.5 Consensus size: 25
319465 ATTACTTAAG
319475 TAATAAAAATTATTTTAAAATGATTTA
1 TAATAAAAATTATTTTAAAAT--TTTA
* * * *
319502 TAATCAATATTATTTTTAAATTTTG
1 TAATAAAAATTATTTTAAAATTTTA
*
319527 GAATAAAAATTA
1 TAATAAAAATTA
319539 AATTAATTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
25 12 0.40
27 18 0.60
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (25 bp):
TAATAAAAATTATTTTAAAATTTTA
Found at i:339407 original size:36 final size:36
Alignment explanation
Indices: 339367--339466 Score: 164
Period size: 36 Copynumber: 2.8 Consensus size: 36
339357 TGGTAACAGA
*
339367 CATGACCTTTGAGTCAACAGGGAGTAAAATGAGCAT
1 CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
339403 CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
1 CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
** *
339439 CATGACCACTGGGTCAACTGGGAGTAAA
1 CATGACCTTTGGGTCAACAGGGAGTAAA
339467 TGAATAAAGA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 60 1.00
ACGTcount: A:0.34, C:0.18, G:0.27, T:0.21
Consensus pattern (36 bp):
CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
Found at i:346948 original size:15 final size:15
Alignment explanation
Indices: 346928--346957 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
346918 CATTTTTCTA
*
346928 TTTACTTTTATTTGT
1 TTTACTTTTACTTGT
346943 TTTACTTTTACTTGT
1 TTTACTTTTACTTGT
346958 GTTGTTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.10, G:0.07, T:0.70
Consensus pattern (15 bp):
TTTACTTTTACTTGT
Found at i:349872 original size:30 final size:29
Alignment explanation
Indices: 349838--349895 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
349828 CAGTCACTTG
349838 AAAAAG-GAAAATGAGAAA-AAGAAAGAAAAA
1 AAAAAGAGAAAA-GA-AAAGAAGAAA-AAAAA
349868 AAAAAGAGAAAAGAAAAGAAGAAAAAAA
1 AAAAAGAGAAAAGAAAAGAAGAAAAAAA
349896 TGTTTGCTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
29 7 0.27
30 14 0.54
31 5 0.19
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (29 bp):
AAAAAGAGAAAAGAAAAGAAGAAAAAAAA
Found at i:349877 original size:13 final size:14
Alignment explanation
Indices: 349853--349895 Score: 56
Period size: 13 Copynumber: 3.2 Consensus size: 14
349843 GGAAAATGAG
349853 AAAAAGAA-AGAAA
1 AAAAAGAAGAGAAA
349866 AAAAA-AAGAGAAA
1 AAAAAGAAGAGAAA
349879 AGAAAAGAAGA-AAA
1 A-AAAAGAAGAGAAA
349893 AAA
1 AAA
349896 TGTTTGCTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 2 0.07
13 13 0.48
14 8 0.30
15 4 0.15
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAAGAAGAGAAA
Found at i:349879 original size:22 final size:24
Alignment explanation
Indices: 349845--349895 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
349835 TTGAAAAAGG
*
349845 AAAATGAGAAAAAG-AAAGAAAAA
1 AAAAAGAGAAAAAGAAAAGAAAAA
*
349868 AAAAAGAG-AAAAGAAAAGAAGAA
1 AAAAAGAGAAAAAGAAAAGAAAAA
349891 AAAAA
1 AAAAA
349896 TGTTTGCTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 5 0.20
23 20 0.80
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (24 bp):
AAAAAGAGAAAAAGAAAAGAAAAA
Found at i:351377 original size:14 final size:14
Alignment explanation
Indices: 351355--351384 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
351345 TGTGCATTTA
*
351355 AATATTCAACACTC
1 AATACTCAACACTC
351369 AATACTCAACACTC
1 AATACTCAACACTC
351383 AA
1 AA
351385 CACATTTGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (14 bp):
AATACTCAACACTC
Found at i:364746 original size:18 final size:18
Alignment explanation
Indices: 364717--364782 Score: 78
Period size: 18 Copynumber: 3.6 Consensus size: 18
364707 CTCATGCGAT
**
364717 CCAGTAATGCTCTTATGAG
1 CCAGT-ATGCTCAAATGAG
364736 CCAGTATGCTCAAATGAG
1 CCAGTATGCTCAAATGAG
* * *
364754 CCAATATGCCCAAACGAG
1 CCAGTATGCTCAAATGAG
364772 CCAGTATGCTC
1 CCAGTATGCTC
364783 TTTCTTTCGC
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
18 35 0.88
19 5 0.12
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (18 bp):
CCAGTATGCTCAAATGAG
Found at i:366935 original size:15 final size:15
Alignment explanation
Indices: 366915--366945 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
366905 ATAATGTTTG
366915 AATAGTGGAAACTGA
1 AATAGTGGAAACTGA
*
366930 AATAGTGGAATCTGA
1 AATAGTGGAAACTGA
366945 A
1 A
366946 TCTGATACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.26, T:0.23
Consensus pattern (15 bp):
AATAGTGGAAACTGA
Found at i:368608 original size:18 final size:18
Alignment explanation
Indices: 368585--368628 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
368575 CGGGAGGAAT
**
368585 AGCATATTGGCTCGTTTG
1 AGCATATTGGCTCGTAAG
368603 AGCATATTGGCTCGTAAG
1 AGCATATTGGCTCGTAAG
368621 AGCATATT
1 AGCATATT
368629 TAGACCGCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (18 bp):
AGCATATTGGCTCGTAAG
Found at i:372157 original size:23 final size:23
Alignment explanation
Indices: 372131--372175 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
372121 TCTTACACTT
*
372131 TTTCTTACTC-TTTTCTTTTTGTA
1 TTTC-TACTCATTTTCGTTTTGTA
372154 TTTCTACTCATTTTCGTTTTGT
1 TTTCTACTCATTTTCGTTTTGT
372176 TCTTTTCACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.09, C:0.18, G:0.07, T:0.67
Consensus pattern (23 bp):
TTTCTACTCATTTTCGTTTTGTA
Found at i:377989 original size:11 final size:10
Alignment explanation
Indices: 377973--378032 Score: 59
Period size: 10 Copynumber: 5.8 Consensus size: 10
377963 TTAATATATG
377973 AATTTTTTAAT
1 AATTTTTT-AT
377984 AA-TTTTTAT
1 AATTTTTTAT
377993 AAATTTTTTAT
1 -AATTTTTTAT
** *
378004 AGCTTGTTAT
1 AATTTTTTAT
378014 AATTGTTTTAT
1 AATT-TTTTAT
378025 AATTTTTT
1 AATTTTTT
378033 TACATTTTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
9 2 0.05
10 20 0.50
11 18 0.45
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (10 bp):
AATTTTTTAT
Found at i:377999 original size:21 final size:20
Alignment explanation
Indices: 377973--378031 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
377963 TTAATATATG
377973 AATTTTTTAATAATTTTTATA
1 AATTTTTT-ATAATTTTTATA
* *
377994 AATTTTTTATAGCTTGTTAT-
1 AATTTTTTATA-ATTTTTATA
378014 AATTGTTTTATAATTTTT
1 AATT-TTTTATAATTTTT
378032 TTACATTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 11 0.34
21 21 0.66
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.63
Consensus pattern (20 bp):
AATTTTTTATAATTTTTATA
Found at i:378138 original size:15 final size:16
Alignment explanation
Indices: 378114--378144 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
378104 GTAATATATG
378114 TTAT-ATTTTTTATTT
1 TTATAATTTTTTATTT
378129 TTATAATTTTTTATTT
1 TTATAATTTTTTATTT
378145 GTAGAATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TTATAATTTTTTATTT
Found at i:378152 original size:16 final size:16
Alignment explanation
Indices: 378118--378153 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
378108 TATATGTTAT
* *
378118 ATTTTTTATTTTTATA
1 ATTTTTTATTTGTAGA
378134 ATTTTTTATTTGTAGA
1 ATTTTTTATTTGTAGA
378150 ATTT
1 ATTT
378154 GTAGAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (16 bp):
ATTTTTTATTTGTAGA
Found at i:378172 original size:43 final size:44
Alignment explanation
Indices: 378073--378175 Score: 106
Period size: 43 Copynumber: 2.4 Consensus size: 44
378063 ATTTTTTTAT
* * *
378073 ATTTTATGACTTTATATAATTTTTTGTATTTGTAATATATGTTAT
1 ATTTTATGA-TTTTTATAATTTTTTGTATTTGTAATATATGTGAA
* *
378118 ATTTT-TTATTTTTATAA-TTTTT-TATTTGTAGA-ATTTGTAGAA
1 ATTTTATGATTTTTATAATTTTTTGTATTTGTA-ATATATGT-GAA
378160 ATTTTATGATTTTTAT
1 ATTTTATGATTTTTAT
378176 TTAAAAAATA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
41 13 0.27
42 12 0.24
43 17 0.35
44 2 0.04
45 5 0.10
ACGTcount: A:0.28, C:0.01, G:0.09, T:0.62
Consensus pattern (44 bp):
ATTTTATGATTTTTATAATTTTTTGTATTTGTAATATATGTGAA
Done.