Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009629.1 Kokia drynarioides strain JFW-HI SEQ_124345, 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: 68809
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 26 characters in sequence are not A, C, G, or T
Found at i:5547 original size:11 final size:11
Alignment explanation
Indices: 5520--5549 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
5510 TCAGTCTTTA
5520 ATGATTTTTCT
1 ATGATTTTTCT
5531 AT-ATTTTTCT
1 ATGATTTTTCT
5541 ATGATTTTT
1 ATGATTTTT
5550 TAAAGTCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.67
Consensus pattern (11 bp):
ATGATTTTTCT
Found at i:13083 original size:18 final size:18
Alignment explanation
Indices: 13060--13095 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
13050 TAGATGAAAA
13060 CGTGCCATAAAACAGAAG
1 CGTGCCATAAAACAGAAG
*
13078 CGTGCCATAAGACAGAAG
1 CGTGCCATAAAACAGAAG
13096 AAAAGCATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.22, G:0.25, T:0.11
Consensus pattern (18 bp):
CGTGCCATAAAACAGAAG
Found at i:14475 original size:13 final size:12
Alignment explanation
Indices: 14453--14491 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
14443 TAAGTGTCAC
14453 ATTTATTTATAT
1 ATTTATTTATAT
14465 ATTTAATTTATAT
1 ATTT-ATTTATAT
14478 ATTT-TTTACTAT
1 ATTTATTTA-TAT
14490 AT
1 AT
14492 CCTATAAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.16
12 9 0.36
13 12 0.48
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTTATTTATAT
Found at i:19613 original size:30 final size:30
Alignment explanation
Indices: 19548--19606 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
19538 TGAATAATGT
* *
19548 TGTACATC-AACTTTAATTTGGTGCATTTG
1 TGTATATCAAACTTTAATTTGATGCATTTG
*
19577 TGTATATCAAACTTTAAATTTGATTCATTT
1 TGTATATCAAACTTT-AATTTGATGCATTT
19607 TTTATATGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 7 0.28
30 6 0.24
31 12 0.48
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (30 bp):
TGTATATCAAACTTTAATTTGATGCATTTG
Found at i:22353 original size:65 final size:65
Alignment explanation
Indices: 22278--22401 Score: 221
Period size: 65 Copynumber: 1.9 Consensus size: 65
22268 AATTATATAT
* *
22278 ATTTTTTGAATTGATTACTTAACTAAAAGAGATTATTATTTTTTGGTCCATTATCATTATAAGAC
1 ATTTTTTGAATTGATTACTTAACTAAAAGAGATTATTATTTTTTGATCCATTACCATTATAAGAC
*
22343 ATTTTTTGAATTGGTTACTTAACTAAAAGAGATTATTATTTTTTGATCCATTACCATTA
1 ATTTTTTGAATTGATTACTTAACTAAAAGAGATTATTATTTTTTGATCCATTACCATTA
22402 AGACTCTGAC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 56 1.00
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.47
Consensus pattern (65 bp):
ATTTTTTGAATTGATTACTTAACTAAAAGAGATTATTATTTTTTGATCCATTACCATTATAAGAC
Found at i:22691 original size:30 final size:29
Alignment explanation
Indices: 22651--22707 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
22641 CTCGTGTAAT
*
22651 TTTTTAAAATTTTATAATT-TTTTTGAATA
1 TTTTTAAAATTTTA-AATTATTTGTGAATA
22680 TTTTTATAAATTTTAAATTATTTGTGAA
1 TTTTTA-AAATTTTAAATTATTTGTGAA
22708 CGTAATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (29 bp):
TTTTTAAAATTTTAAATTATTTGTGAATA
Found at i:24754 original size:27 final size:28
Alignment explanation
Indices: 24696--24752 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
24686 CGTATACTTT
* **
24696 AATAAAAAAAATATAAGTACTTAATTAA
1 AATAAAAAAAATATAAATACCAAATTAA
*
24724 AATAAAAAAAATTTAAATACCAAATTAA
1 AATAAAAAAAATATAAATACCAAATTAA
24752 A
1 A
24753 TATTAAAACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (28 bp):
AATAAAAAAAATATAAATACCAAATTAA
Found at i:24829 original size:23 final size:23
Alignment explanation
Indices: 24777--24822 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
24767 TTTTGTACTT
* * *
24777 AATTGAAAAAATTTCATATATCA
1 AATTAAAAAAATCTCAAATATCA
24800 AATTAAAAAAATCTCAAATATCA
1 AATTAAAAAAATCTCAAATATCA
24823 TAATAAACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (23 bp):
AATTAAAAAAATCTCAAATATCA
Found at i:27360 original size:2 final size:2
Alignment explanation
Indices: 27355--27384 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
27345 GAGCAGAAAG
27355 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27385 CTGTAAGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32683 original size:22 final size:21
Alignment explanation
Indices: 32649--32689 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
32639 TTAATTAAGT
*
32649 TTATGATTGAATTTGGAATTAA
1 TTATGATTAAATTT-GAATTAA
*
32671 TTATGTTTAAATTTGAATT
1 TTATGATTAAATTTGAATT
32690 TATTTAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (21 bp):
TTATGATTAAATTTGAATTAA
Found at i:32686 original size:28 final size:28
Alignment explanation
Indices: 32635--32716 Score: 80
Period size: 28 Copynumber: 3.0 Consensus size: 28
32625 TTTTTCTGTC
* *
32635 GGAATTAATTAAGTTTATGA-TTGAATTT
1 GGAATTAATTATGTTTA-AATTTGAATTT
32663 GGAATTAATTATGTTTAAATTTGAATTT
1 GGAATTAATTATGTTTAAATTTGAATTT
* * * *
32691 --ATTTAATAATTTTTATATTTGAATTT
1 GGAATTAATTATGTTTAAATTTGAATTT
32717 ATTTAATGAG
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 22 0.47
27 1 0.02
28 24 0.51
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.52
Consensus pattern (28 bp):
GGAATTAATTATGTTTAAATTTGAATTT
Found at i:32705 original size:26 final size:26
Alignment explanation
Indices: 32667--32723 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
32657 GAATTTGGAA
*
32667 TTAATTATGTTTAAATTTGAATTTAT
1 TTAATAATGTTTAAATTTGAATTTAT
* *
32693 TTAATAATTTTTATATTTGAATTTAT
1 TTAATAATGTTTAAATTTGAATTTAT
32719 TTAAT
1 TTAAT
32724 GAGGTTTAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (26 bp):
TTAATAATGTTTAAATTTGAATTTAT
Found at i:32731 original size:26 final size:26
Alignment explanation
Indices: 32675--32731 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
32665 AATTAATTAT
*
32675 GTTTAAATTTGAATTTATTTAATAAT
1 GTTTAAATTTGAATTTATTTAATAAG
* * *
32701 TTTTATATTTGAATTTATTTAATGAG
1 GTTTAAATTTGAATTTATTTAATAAG
32727 GTTTA
1 GTTTA
32732 GCAAATGACA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (26 bp):
GTTTAAATTTGAATTTATTTAATAAG
Found at i:32807 original size:6 final size:6
Alignment explanation
Indices: 32796--32836 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
32786 ATATTTGCAT
*
32796 ACATAA ACATAA ATA-AGA ACATAA ACATAA ACATAA ACATA
1 ACATAA ACATAA ACATA-A ACATAA ACATAA ACATAA ACATA
32837 TTTAATTCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 1 0.03
6 29 0.94
7 1 0.03
ACGTcount: A:0.66, C:0.15, G:0.02, T:0.17
Consensus pattern (6 bp):
ACATAA
Found at i:35170 original size:25 final size:24
Alignment explanation
Indices: 35121--35170 Score: 57
Period size: 25 Copynumber: 2.0 Consensus size: 24
35111 TACTTTTTAA
35121 AAAATAATAATATTTTTTTAATATT
1 AAAATAATAATATTTTTTT-ATATT
*
35146 AAAATAATTACTATTATTTTT-TATT
1 AAAATAA-TAATATT-TTTTTATATT
35171 TTTTTCTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 11 0.50
26 6 0.27
27 5 0.23
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (24 bp):
AAAATAATAATATTTTTTTATATT
Found at i:36458 original size:15 final size:16
Alignment explanation
Indices: 36438--36468 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
36428 GGGATTAAAT
36438 GTAATTTT-AATTTTA
1 GTAATTTTAAATTTTA
36453 GTAATTTTAAATTTTA
1 GTAATTTTAAATTTTA
36469 AAAGACTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (16 bp):
GTAATTTTAAATTTTA
Found at i:36884 original size:2 final size:2
Alignment explanation
Indices: 36877--36901 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
36867 AATTACTTGT
36877 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
36902 TTATTTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:47905 original size:43 final size:43
Alignment explanation
Indices: 47844--47932 Score: 178
Period size: 43 Copynumber: 2.1 Consensus size: 43
47834 GTTGTGATCC
47844 AATATGCAGTAACTAAAATTTGATAGGATAATCATGTATCCTG
1 AATATGCAGTAACTAAAATTTGATAGGATAATCATGTATCCTG
47887 AATATGCAGTAACTAAAATTTGATAGGATAATCATGTATCCTG
1 AATATGCAGTAACTAAAATTTGATAGGATAATCATGTATCCTG
47930 AAT
1 AAT
47933 GATTACGTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (43 bp):
AATATGCAGTAACTAAAATTTGATAGGATAATCATGTATCCTG
Found at i:68109 original size:34 final size:33
Alignment explanation
Indices: 68069--68134 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
68059 AATATTTCAG
*
68069 AATTTATCAATTTAAAAATATTT-TAAACTTTTAA
1 AATTTATCAA-TTAAAAAAATTTAT-AACTTTTAA
**
68103 AATTTATTTATTAAAAAAATTTATAACTTTTA
1 AATTTATCAATTAAAAAAATTTATAACTTTTA
68135 CAAACCTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 19 0.68
34 9 0.32
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (33 bp):
AATTTATCAATTAAAAAAATTTATAACTTTTAA
Done.