Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010489.1 Kokia drynarioides strain JFW-HI SEQ_125397, 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: 80515
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:10187 original size:2 final size:2
Alignment explanation
Indices: 10180--10218 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
10170 TATTGTTGAA
10180 AT AT AT AT AT AT 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 AT AT AT AT AT AT A
10219 ATTTTGTCCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12023 original size:17 final size:17
Alignment explanation
Indices: 12011--12049 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
12001 ACCTTTAATC
*
12011 TTTCATCTTCTTTAACA
1 TTTCATATTCTTTAACA
12028 TTTCATATTCTTGTAACTA
1 TTTCATATTCTT-TAAC-A
12047 TTT
1 TTT
12050 TTTCTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 11 0.58
18 4 0.21
19 4 0.21
ACGTcount: A:0.23, C:0.18, G:0.03, T:0.56
Consensus pattern (17 bp):
TTTCATATTCTTTAACA
Found at i:34473 original size:28 final size:28
Alignment explanation
Indices: 34437--34493 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
34427 TATATGTGTG
* *
34437 TGTGTATTTAATACTAATATATCTCAAA
1 TGTGCATTTAATACTAAGATATCTCAAA
34465 TGTGCATTTAATACTAAGATATCTCAAA
1 TGTGCATTTAATACTAAGATATCTCAAA
34493 T
1 T
34494 TCATATTTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (28 bp):
TGTGCATTTAATACTAAGATATCTCAAA
Found at i:34813 original size:29 final size:28
Alignment explanation
Indices: 34781--34839 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
34771 TAATGGGTGT
*
34781 TATTCAATTTTTTT-TATTAAAATTTCATC
1 TATTCAATTTTTTTATA-T-AAATTTAATC
*
34810 TATTTAATTTTTTTATATAAATTTAATC
1 TATTCAATTTTTTTATATAAATTTAATC
34838 TA
1 TA
34840 ATAATAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 11 0.41
29 14 0.52
30 2 0.07
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (28 bp):
TATTCAATTTTTTTATATAAATTTAATC
Found at i:34844 original size:27 final size:28
Alignment explanation
Indices: 34789--34855 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 28
34779 GTTATTCAAT
* *
34789 TTTTTTTATTAAAATTTCATCTATTTAA
1 TTTTTTTATTAAAATTTAATCTATATAA
34817 TTTTTTTA-TATAAATTTAATCTAATAATAAA
1 TTTTTTTATTA-AAATTTAATCT-AT-AT-AA
34848 TTTTTTTA
1 TTTTTTTA
34856 CATATGTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
27 2 0.06
28 18 0.55
29 2 0.06
30 1 0.03
31 10 0.30
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (28 bp):
TTTTTTTATTAAAATTTAATCTATATAA
Found at i:36063 original size:49 final size:52
Alignment explanation
Indices: 36003--36099 Score: 137
Period size: 49 Copynumber: 1.9 Consensus size: 52
35993 CTTAAACATC
* *
36003 AAATATTAAATTTAAAATTTTT-TTA-T-TTCGAGTTCAGCTCAATTATATA
1 AAATATCAAATTTAAAATTTTTATTATTGTTCGAGTTCAGCTAAATTATATA
* *
36052 AAATATCAAATTTAAATTTTTTATTATTGTTGGAGTTCAGCTAAATTA
1 AAATATCAAATTTAAAATTTTTATTATTGTTCGAGTTCAGCTAAATTA
36100 CAACTCTACT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
49 20 0.49
50 3 0.07
51 1 0.02
52 17 0.41
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.46
Consensus pattern (52 bp):
AAATATCAAATTTAAAATTTTTATTATTGTTCGAGTTCAGCTAAATTATATA
Found at i:40695 original size:12 final size:12
Alignment explanation
Indices: 40678--40712 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
40668 GTGAGGAGGG
40678 AATAAAAAATAT
1 AATAAAAAATAT
*
40690 AATAAAAATTAT
1 AATAAAAAATAT
40702 ATATAAAAAAT
1 A-ATAAAAAAT
40713 TTGAGAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AATAAAAAATAT
Found at i:47352 original size:23 final size:24
Alignment explanation
Indices: 47316--47365 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
47306 ATTGTGGTAG
*
47316 TATTAAGTTTTTATAAAAGATAAT
1 TATTAAGTTATTATAAAAGATAAT
* *
47340 TATT-AGTTATTATTAAATATAAT
1 TATTAAGTTATTATAAAAGATAAT
47363 TAT
1 TAT
47366 GTTCTTTGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (24 bp):
TATTAAGTTATTATAAAAGATAAT
Found at i:47439 original size:21 final size:22
Alignment explanation
Indices: 47393--47445 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
47383 TTTATTTTTT
*
47393 ATTTTTGATATTATTAATATGA
1 ATTTTTGATATTATTAAGATGA
*
47415 ATTTTT-ATATTATTTCAGATG-
1 ATTTTTGATATTA-TTAAGATGA
*
47436 ATTTTAGATA
1 ATTTTTGATA
47446 ATAAAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.34, C:0.02, G:0.09, T:0.55
Consensus pattern (22 bp):
ATTTTTGATATTATTAAGATGA
Found at i:54374 original size:7 final size:7
Alignment explanation
Indices: 54362--54387 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
54352 TTTTCCCCTT
54362 ATTTTAC
1 ATTTTAC
54369 ATTTTAC
1 ATTTTAC
54376 ATTTTAC
1 ATTTTAC
54383 ATTTT
1 ATTTT
54388 GATTTCTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.62
Consensus pattern (7 bp):
ATTTTAC
Found at i:61648 original size:29 final size:29
Alignment explanation
Indices: 61616--61679 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
61606 TCCGTGCCAT
* *
61616 TTTGTTCTAATATTGCACTTCGATGTTAC
1 TTTGTACTAATACTGCACTTCGATGTTAC
**
61645 TTTGTACTGTTACTGCACTTCGATGTTAC
1 TTTGTACTAATACTGCACTTCGATGTTAC
*
61674 TCTGTA
1 TTTGTA
61680 TTATTTTTGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.19, C:0.19, G:0.16, T:0.47
Consensus pattern (29 bp):
TTTGTACTAATACTGCACTTCGATGTTAC
Found at i:71121 original size:18 final size:18
Alignment explanation
Indices: 71098--71135 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
71088 TAATATTACT
*
71098 AAATACTTTTGAGATAAA
1 AAATACTTTTAAGATAAA
*
71116 AAATACTTTTAATATAAA
1 AAATACTTTTAAGATAAA
71134 AA
1 AA
71136 CATTGCTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.34
Consensus pattern (18 bp):
AAATACTTTTAAGATAAA
Found at i:75563 original size:24 final size:27
Alignment explanation
Indices: 75536--75588 Score: 76
Period size: 24 Copynumber: 2.1 Consensus size: 27
75526 AATTTTTTAA
75536 AAATATTAATTAA-AATT-AATA-ATG
1 AAATATTAATTAAGAATTAAATACATG
*
75560 AAATATTTATTAAGAATTAAATACATG
1 AAATATTAATTAAGAATTAAATACATG
75587 AA
1 AA
75589 TATGATCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 12 0.48
25 4 0.16
26 4 0.16
27 5 0.20
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.36
Consensus pattern (27 bp):
AAATATTAATTAAGAATTAAATACATG
Done.