Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008223.1 Kokia drynarioides strain JFW-HI SEQ_122887, 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: 69535
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 161 characters in sequence are not A, C, G, or T
Found at i:3384 original size:31 final size:30
Alignment explanation
Indices: 3349--3406 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
3339 GTTTCAAAAT
*
3349 AATTATTGAATTATTTAAAAATT-TTATTTTA
1 AATTATCGAATTA-TT-AAAATTATTATTTTA
3380 AATTATCGAATTATTAAAATTATTATT
1 AATTATCGAATTATTAAAATTATTATT
3407 GTATAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 6 0.24
30 7 0.28
31 12 0.48
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (30 bp):
AATTATCGAATTATTAAAATTATTATTTTA
Found at i:7599 original size:18 final size:19
Alignment explanation
Indices: 7558--7593 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
7548 ATTTTGGGTT
7558 AATAATATATATTAAATAC
1 AATAATATATATTAAATAC
7577 AATAATATA-ATTAAATA
1 AATAATATATATTAAATA
7594 ATATAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (19 bp):
AATAATATATATTAAATAC
Found at i:11695 original size:17 final size:15
Alignment explanation
Indices: 11675--11714 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
11665 TATAATTCTT
11675 TAAAATTTATAAATATA
1 TAAAATTTA-AAATA-A
11692 TAAAATATTAAAATAA
1 TAAAAT-TTAAAATAA
11708 TAAAATT
1 TAAAATT
11715 ACATTTATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 1 0.05
16 7 0.32
17 11 0.50
18 3 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TAAAATTTAAAATAA
Found at i:16941 original size:19 final size:19
Alignment explanation
Indices: 16919--16963 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
16909 TTTTATTAGG
16919 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
16938 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
16957 ATTTAAT
1 ATTTAAT
16964 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:19005 original size:21 final size:21
Alignment explanation
Indices: 18981--19024 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
18971 GAATTTCAGT
*
18981 AGCAATCTATAAATTTTCAAA
1 AGCAAACTATAAATTTTCAAA
* *
19002 AGCAAACTGTAGATTTTCAAA
1 AGCAAACTATAAATTTTCAAA
19023 AG
1 AG
19025 AAAATTAAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.30
Consensus pattern (21 bp):
AGCAAACTATAAATTTTCAAA
Found at i:22949 original size:6 final size:6
Alignment explanation
Indices: 22938--22970 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
22928 GGTAACCCAA
22938 TTAATT TTAATT TTAATT TTAATT TTAATT TTA
1 TTAATT TTAATT TTAATT TTAATT TTAATT TTA
22971 TAATTATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTAATT
Found at i:22980 original size:14 final size:13
Alignment explanation
Indices: 22939--22991 Score: 56
Period size: 12 Copynumber: 4.1 Consensus size: 13
22929 GTAACCCAAT
*
22939 TAATTT-TAATTT
1 TAATTTATAATTA
*
22951 TAATTT-TAATTT
1 TAATTTATAATTA
22963 TAATTTTATAATTA
1 TAA-TTTATAATTA
22977 TAATTTATTAATTA
1 TAATTTA-TAATTA
22991 T
1 T
22992 TTTTTATTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
12 15 0.41
13 7 0.19
14 15 0.41
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TAATTTATAATTA
Found at i:25581 original size:13 final size:13
Alignment explanation
Indices: 25563--25588 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25553 CTAATCGGGT
25563 AAAAAAAGAGAAA
1 AAAAAAAGAGAAA
25576 AAAAAAAGAGAAA
1 AAAAAAAGAGAAA
25589 TAAATAAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAGAAA
Found at i:25899 original size:20 final size:20
Alignment explanation
Indices: 25874--25913 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
25864 AGGTGTCTTG
25874 GTAAGTTTGGTAAATTACCT
1 GTAAGTTTGGTAAATTACCT
25894 GTAAGTTTGGTAAATTACCT
1 GTAAGTTTGGTAAATTACCT
25914 AACTTTCATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (20 bp):
GTAAGTTTGGTAAATTACCT
Found at i:27227 original size:15 final size:16
Alignment explanation
Indices: 27209--27241 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
27199 CACCTCTATT
27209 TTCTA-TTTCTTTTAA
1 TTCTATTTTCTTTTAA
27224 TTCTATTTTCTTTTAA
1 TTCTATTTTCTTTTAA
27240 TT
1 TT
27242 TTCCCCAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.18, C:0.12, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCTATTTTCTTTTAA
Found at i:32502 original size:20 final size:20
Alignment explanation
Indices: 32477--32515 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
32467 TAAACAATTA
*
32477 ACTTTTGAAAGAA-ATTTTTG
1 ACTTTTCAAA-AACATTTTTG
32497 ACTTTTCAAAAACATTTTT
1 ACTTTTCAAAAACATTTTT
32516 TCTTAGATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.46
Consensus pattern (20 bp):
ACTTTTCAAAAACATTTTTG
Found at i:36641 original size:18 final size:18
Alignment explanation
Indices: 36591--36655 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 18
36581 TCCTCAAATG
*
36591 CAGCAACCACAGCAACATCA
1 CAGCAACAACAGCAAC-T-A
*
36611 GCAGCAGCAACAGCAACTA
1 -CAGCAACAACAGCAACTA
* *
36630 CTGCAACAACAGCAGCTA
1 CAGCAACAACAGCAACTA
36648 CAGCAACA
1 CAGCAACA
36656 TGCTCAACAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
18 22 0.58
19 1 0.03
20 1 0.03
21 14 0.37
ACGTcount: A:0.43, C:0.35, G:0.15, T:0.06
Consensus pattern (18 bp):
CAGCAACAACAGCAACTA
Found at i:36650 original size:27 final size:27
Alignment explanation
Indices: 36612--36667 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
36602 GCAACATCAG
36612 CAGCAGCAACAGCAAC-TACTGCAACAA
1 CAGCAGCAACAGCAACATACT-CAACAA
* *
36639 CAGCAGCTACAGCAACATGCTCAACAA
1 CAGCAGCAACAGCAACATACTCAACAA
36666 CA
1 CA
36668 ATTACAACCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 23 0.88
28 3 0.12
ACGTcount: A:0.43, C:0.34, G:0.14, T:0.09
Consensus pattern (27 bp):
CAGCAGCAACAGCAACATACTCAACAA
Found at i:39578 original size:39 final size:40
Alignment explanation
Indices: 39518--39594 Score: 129
Period size: 39 Copynumber: 1.9 Consensus size: 40
39508 GCTGAACTTC
*
39518 CCTAAAGACATAGTTCGATTCTGTCTTAAATCATACTACGT
1 CCTAAAGACA-AGTTCAATTCTGTCTTAAATCATACTACGT
39559 CCTAAAGAC-AGTTCAATTCTGTCTTAAATCATACTA
1 CCTAAAGACAAGTTCAATTCTGTCTTAAATCATACTA
39595 TGATGTCCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
39 26 0.74
41 9 0.26
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.34
Consensus pattern (40 bp):
CCTAAAGACAAGTTCAATTCTGTCTTAAATCATACTACGT
Found at i:52304 original size:43 final size:45
Alignment explanation
Indices: 52204--52304 Score: 109
Period size: 44 Copynumber: 2.3 Consensus size: 45
52194 AGGTAGCATT
* *
52204 ATATCATCATATACTTCCATCAAAATAGTAAACCAATAACTGAAC
1 ATATCATCATATTCTTCCATCAAAACAGTAAACCAATAACTGAAC
*** **
52249 ATATTGCCATATTCTT-CATCCGAACAGTAAA-CAGATAACT-AAC
1 ATATCATCATATTCTTCCATCAAAACAGTAAACCA-ATAACTGAAC
52292 ATATCATCATATT
1 ATATCATCATATT
52305 GTTTTATTGA
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
43 15 0.33
44 18 0.40
45 12 0.27
ACGTcount: A:0.43, C:0.22, G:0.06, T:0.30
Consensus pattern (45 bp):
ATATCATCATATTCTTCCATCAAAACAGTAAACCAATAACTGAAC
Found at i:55228 original size:17 final size:17
Alignment explanation
Indices: 55203--55248 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
55193 TGTTGAGAAA
55203 TATATATTTTAATGT-T
1 TATATATTTTAATGTAT
*
55219 TTTAATATTTTTAATGTAT
1 TAT-ATA-TTTTAATGTAT
55238 TATATATTTTA
1 TATATATTTTA
55249 TTTTTTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
16 2 0.08
17 8 0.32
18 12 0.48
19 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (17 bp):
TATATATTTTAATGTAT
Found at i:55259 original size:18 final size:18
Alignment explanation
Indices: 55202--55259 Score: 50
Period size: 17 Copynumber: 3.3 Consensus size: 18
55192 TTGTTGAGAA
55202 ATATATATTTTAATGTTTTT
1 ATATATATTTT-AT-TTTTT
* * *
55222 A-ATAT-TTTTAATGTAT
1 ATATATATTTTATTTTTT
55238 -TATATATTTTATTTTTT
1 ATATATATTTTATTTTTT
55255 ATATA
1 ATATA
55260 AAAAATAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
16 7 0.24
17 9 0.31
18 8 0.28
19 4 0.14
20 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
ATATATATTTTATTTTTT
Found at i:56714 original size:18 final size:18
Alignment explanation
Indices: 56693--56727 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
56683 GAGAAAAACA
* *
56693 AATGAATAAACAAAAGAG
1 AATGAAAAAAAAAAAGAG
56711 AATGAAAAAAAAAAAGA
1 AATGAAAAAAAAAAAGA
56728 ACATAAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.03, G:0.14, T:0.09
Consensus pattern (18 bp):
AATGAAAAAAAAAAAGAG
Found at i:60970 original size:2 final size:2
Alignment explanation
Indices: 60963--60989 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
60953 TGCGTGTATG
60963 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
60990 GAGAGAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:60994 original size:2 final size:2
Alignment explanation
Indices: 60989--61025 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
60979 ATATATATAT
* *
60989 AG AG AG AG AG AG AG AG AG AG AG AC AG AG AC AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
61026 TATAACATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.05, G:0.43, T:0.00
Consensus pattern (2 bp):
AG
Found at i:63498 original size:2 final size:2
Alignment explanation
Indices: 63491--63526 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
63481 GCTTGAAATT
63491 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
63527 CAGCTTTCCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:65506 original size:3 final size:3
Alignment explanation
Indices: 65498--65528 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
65488 TATATAACAT
65498 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
65529 CAAATATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:67037 original size:30 final size:29
Alignment explanation
Indices: 66988--67089 Score: 118
Period size: 29 Copynumber: 3.4 Consensus size: 29
66978 ATTAAAATTA
66988 TTTAATAATTTTATTATTTTTAAAAAATAAT
1 TTTAATAATTTTA-TA-TTTTAAAAAATAAT
*
67019 TTTAATAATTTTACATTTTAAAAAATAA-
1 TTTAATAATTTTATATTTTAAAAAATAAT
* * *
67047 ATTAAAAATAATTTATATTTT-AAAAATAGT
1 TTTAATAAT--TTTATATTTTAAAAAATAAT
67077 TTTAATAATTTTA
1 TTTAATAATTTTA
67090 AAAATATTTG
Statistics
Matches: 61, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
28 11 0.18
29 20 0.33
30 17 0.28
31 13 0.21
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (29 bp):
TTTAATAATTTTATATTTTAAAAAATAAT
Found at i:67071 original size:18 final size:21
Alignment explanation
Indices: 67048--67095 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
67038 AAAAAATAAA
67048 TTAAAAATA-ATTT-AT-ATT
1 TTAAAAATAGATTTAATAATT
*
67066 TTAAAAATAGTTTTAATAATT
1 TTAAAAATAGATTTAATAATT
67087 TTAAAAATA
1 TTAAAAATA
67096 TTTGTTGACA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 9 0.35
19 3 0.12
20 2 0.08
21 12 0.46
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
TTAAAAATAGATTTAATAATT
Done.