Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006791.1 Kokia drynarioides strain JFW-HI SEQ_121390, 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: 56717
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:6614 original size:20 final size:20
Alignment explanation
Indices: 6572--6615 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
6562 AAAATTTTTG
* * * *
6572 AAAATTTTAGTTATACTTTT
1 AAAATTTTAATTAAACCTCT
6592 AAAATTTTAATTAAACCTCT
1 AAAATTTTAATTAAACCTCT
6612 AAAA
1 AAAA
6616 GTTATTAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.43
Consensus pattern (20 bp):
AAAATTTTAATTAAACCTCT
Found at i:7573 original size:21 final size:21
Alignment explanation
Indices: 7549--7594 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
7539 AATTCTTTTC
* *
7549 ATTTAAAAATATAATTTATAT
1 ATTTAAAAATAAAATTTAAAT
**
7570 ATTTTTAAATAAAATTTAAAT
1 ATTTAAAAATAAAATTTAAAT
7591 ATTT
1 ATTT
7595 TATTAAAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTTAAAAATAAAATTTAAAT
Found at i:7576 original size:23 final size:22
Alignment explanation
Indices: 7554--7605 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 22
7544 TTTTCATTTA
*
7554 AAAATATAATTTATATATTTTT
1 AAAATATAATTTAAATATTTTT
*
7576 -AAATAAAATTTAAATATTTTATT
1 AAAATATAATTTAAATA-TTT-TT
7599 AAAATAT
1 AAAATAT
7606 TTTTACTAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 14 0.58
22 3 0.12
23 2 0.08
24 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAAATATAATTTAAATATTTTT
Found at i:7595 original size:21 final size:21
Alignment explanation
Indices: 7555--7595 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
7545 TTTCATTTAA
* *
7555 AAATATAATTTATATATTTTT
1 AAATAAAATTTAAATATTTTT
7576 AAATAAAATTTAAATATTTT
1 AAATAAAATTTAAATATTTT
7596 ATTAAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AAATAAAATTTAAATATTTTT
Found at i:23568 original size:50 final size:50
Alignment explanation
Indices: 23509--23611 Score: 197
Period size: 50 Copynumber: 2.1 Consensus size: 50
23499 CTCATATGAT
23509 AAGAAAGCTAAAATTAAGAAATGAATCAAAATGTGATAATAGTTCAAACA
1 AAGAAAGCTAAAATTAAGAAATGAATCAAAATGTGATAATAGTTCAAACA
*
23559 AAGAAAGCTAAAATTAATAAATGAATCAAAATGTGATAATAGTTCAAACA
1 AAGAAAGCTAAAATTAAGAAATGAATCAAAATGTGATAATAGTTCAAACA
23609 AAG
1 AAG
23612 CACGTGAAAT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.56, C:0.08, G:0.14, T:0.22
Consensus pattern (50 bp):
AAGAAAGCTAAAATTAAGAAATGAATCAAAATGTGATAATAGTTCAAACA
Found at i:23968 original size:11 final size:12
Alignment explanation
Indices: 23939--23969 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
23929 AAGCATATGG
23939 TTTGTTGGTAGA
1 TTTGTTGGTAGA
23951 TTTGTTGGTAGA
1 TTTGTTGGTAGA
23963 -TTGTTGG
1 TTTGTTGG
23970 ACTCTTAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.37
12 12 0.63
ACGTcount: A:0.13, C:0.00, G:0.35, T:0.52
Consensus pattern (12 bp):
TTTGTTGGTAGA
Found at i:29987 original size:70 final size:70
Alignment explanation
Indices: 29874--30004 Score: 253
Period size: 70 Copynumber: 1.9 Consensus size: 70
29864 GCCAGCCAAA
29874 AAGCTAAATGATAAGTCAATAAGGTTAATATATCACCAGGATGCCCATAGAAATAGTAGTCAATA
1 AAGCTAAATGATAAGTCAATAAGGTTAATATATCACCAGGATGCCCATAGAAATAGTAGTCAATA
29939 AGGTT
66 AGGTT
*
29944 AAGCTAAATGATAAGTCAATAAGGTTAATATATCACCAGGATGCCCGTAGAAATAGTAGTC
1 AAGCTAAATGATAAGTCAATAAGGTTAATATATCACCAGGATGCCCATAGAAATAGTAGTC
30005 CTCATAAGCC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
70 60 1.00
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (70 bp):
AAGCTAAATGATAAGTCAATAAGGTTAATATATCACCAGGATGCCCATAGAAATAGTAGTCAATA
AGGTT
Found at i:33313 original size:17 final size:19
Alignment explanation
Indices: 33268--33314 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
33258 TATATGTTGT
33268 AAATTATATAATATGTCAAA
1 AAATTATAT-ATATGTCAAA
*
33288 AAATAATATA-ATGT-AAA
1 AAATTATATATATGTCAAA
*
33305 ATATTATATA
1 AAATTATATA
33315 CTTAAAAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 11 0.46
18 4 0.17
19 1 0.04
20 8 0.33
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.36
Consensus pattern (19 bp):
AAATTATATATATGTCAAA
Found at i:33813 original size:36 final size:35
Alignment explanation
Indices: 33773--33843 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 35
33763 CCATAATGAT
* *
33773 TTATTTTATCTTTTAATATTTTTTAA-AAATAAAAAG
1 TTATTTTAACTTTT--TATTTATTAATAAATAAAAAG
33809 TTATTTTAACTTTTTATTTATTAATTAAATAAAAA
1 TTATTTTAACTTTTTATTTATTAA-TAAATAAAAA
33844 AATTAGATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
34 9 0.29
36 22 0.71
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (35 bp):
TTATTTTAACTTTTTATTTATTAATAAATAAAAAG
Found at i:36978 original size:25 final size:25
Alignment explanation
Indices: 36944--36993 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
36934 TGATCCTTTC
36944 TTCATCATTC-CTAAAACTATTTACA
1 TTCATCATTCTC-AAAACTATTTACA
36969 TTCATCATTCTCAAAACTATTTACA
1 TTCATCATTCTCAAAACTATTTACA
36994 GGCAAAGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 23 0.96
26 1 0.04
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.40
Consensus pattern (25 bp):
TTCATCATTCTCAAAACTATTTACA
Found at i:39624 original size:94 final size:93
Alignment explanation
Indices: 39463--39643 Score: 292
Period size: 94 Copynumber: 1.9 Consensus size: 93
39453 TTAGCCTGAG
39463 TGCTTCCTCTTTCATTGCCTCTGCATGCTTCCCTTTTTGTTTTTGAAGTTCTAGAGCTGGCAATA
1 TGCTTCCTCTTTCATTGCCTCTGCA-GCTTCCCTTTTTGTTTTTGAAGTTCTAGAGCTGGCAATA
39528 CCACTCTTGCGGTAGGTACTTTGTTCTCA
65 CCACTCTTGCGGTAGGTACTTTGTTCTCA
* **
39557 TGCTTCCTCTTTCATTGCCTCTAAGC-GCTTCCCTTTTTGTTTTTGAAGTTCTAGAGTTGGTGAT
1 TGCTTCCTCTTTCATTGCCTCT--GCAGCTTCCCTTTTTGTTTTTGAAGTTCTAGAGCTGGCAAT
*
39621 ACCATTCTTGCGGTAGGTACTTT
64 ACCACTCTTGCGGTAGGTACTTT
39644 TTTTCTCAAT
Statistics
Matches: 81, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
94 79 0.98
96 2 0.02
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.44
Consensus pattern (93 bp):
TGCTTCCTCTTTCATTGCCTCTGCAGCTTCCCTTTTTGTTTTTGAAGTTCTAGAGCTGGCAATAC
CACTCTTGCGGTAGGTACTTTGTTCTCA
Found at i:50026 original size:21 final size:21
Alignment explanation
Indices: 50002--50150 Score: 65
Period size: 21 Copynumber: 6.8 Consensus size: 21
49992 AAAAATATAT
*
50002 AAAAACTAAC-ATCCAAACAAC
1 AAAAA-TAACAATCAAAACAAC
**
50023 AAAAATAACAATCAAAACAGTTGT
1 AAAAATAACAATCAAAACA---AC
*
50047 AAAAATAACAGT-AAAACAAC
1 AAAAATAACAATCAAAACAAC
*
50067 ATTAAA-AACAA-CAAAAACGGTAAC
1 A-AAAATAACAATC-AAAAC---AAC
* *
50091 AAAAATAACAGTAAAAACAAC
1 AAAAATAACAATCAAAACAAC
* * *
50112 ACGAAAACAACAATCAAAATAAT
1 A--AAAATAACAATCAAAACAAC
*
50135 AAAAA-AACCATCAAAA
1 AAAAATAACAATCAAAA
50151 TAGTAAAAAA
Statistics
Matches: 97, Mismatches: 17, Indels: 29
0.68 0.12 0.20
Matches are distributed among these distances:
20 19 0.20
21 29 0.30
23 25 0.26
24 24 0.25
ACGTcount: A:0.66, C:0.17, G:0.05, T:0.12
Consensus pattern (21 bp):
AAAAATAACAATCAAAACAAC
Found at i:50064 original size:44 final size:45
Alignment explanation
Indices: 50016--50130 Score: 119
Period size: 44 Copynumber: 2.5 Consensus size: 45
50006 ACTAACATCC
***
50016 AAACAACA-AAAATAACAATCAAAACAGTTGTAAAAATAACAGT-A
1 AAACAACACAAAA-AACAATCAAAACAGTAACAAAAATAACAGTAA
** *
50060 AAACAACATTAAAAACAA-CAAAAACGGTAACAAAAATAACAGTAA
1 AAACAACACAAAAAACAATC-AAAACAGTAACAAAAATAACAGTAA
50105 AAACAACACGAAAACAACAATCAAAA
1 AAACAACAC-AAAA-AACAATCAAAA
50131 TAATAAAAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 9
0.78 0.09 0.12
Matches are distributed among these distances:
43 1 0.02
44 32 0.55
45 12 0.21
46 3 0.05
47 9 0.16
48 1 0.02
ACGTcount: A:0.66, C:0.17, G:0.06, T:0.11
Consensus pattern (45 bp):
AAACAACACAAAAAACAATCAAAACAGTAACAAAAATAACAGTAA
Found at i:50163 original size:21 final size:20
Alignment explanation
Indices: 50115--50161 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
50105 AAACAACACG
*
50115 AAAACAACAATCAAAATAAT
1 AAAAAAACAATCAAAATAAT
* *
50135 AAAAAAACCATCAAAATAGT
1 AAAAAAACAATCAAAATAAT
50155 AAAAAAA
1 AAAAAAA
50162 ACAGCAACCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.72, C:0.13, G:0.02, T:0.13
Consensus pattern (20 bp):
AAAAAAACAATCAAAATAAT
Found at i:50191 original size:20 final size:21
Alignment explanation
Indices: 50154--50199 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
50144 ATCAAAATAG
50154 TAAAAAAAACAGCAACCAAAA
1 TAAAAAAAACAGCAACCAAAA
*
50175 TAAAAAAAATAGC-ACCAAAA
1 TAAAAAAAACAGCAACCAAAA
*
50195 CAAAA
1 TAAAA
50200 TATAAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.72, C:0.17, G:0.04, T:0.07
Consensus pattern (21 bp):
TAAAAAAAACAGCAACCAAAA
Found at i:54466 original size:28 final size:28
Alignment explanation
Indices: 54406--54475 Score: 83
Period size: 27 Copynumber: 2.5 Consensus size: 28
54396 ATTCCTGACA
*
54406 AATTT-AAAATTTAATTTTTATATTTTT
1 AATTTCAAAATTTAATTCTTATATTTTT
*
54433 ATTTTCAAGAATTTAA-TCTTAT-TTTTT
1 AATTTCAA-AATTTAATTCTTATATTTTT
54460 AGATTTCAAAATTTAA
1 A-ATTTCAAAATTTAA
54476 ATGTATTGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
27 17 0.46
28 13 0.35
29 7 0.19
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.56
Consensus pattern (28 bp):
AATTTCAAAATTTAATTCTTATATTTTT
Done.