Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006871.1 Kokia drynarioides strain JFW-HI SEQ_121471, 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: 63703
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:5674 original size:34 final size:34
Alignment explanation
Indices: 5631--5706 Score: 116
Period size: 34 Copynumber: 2.2 Consensus size: 34
5621 CATAAACTAA
* *
5631 ACCCAAATATTTTTAATTTTTTACCTTTTATCTT
1 ACCCAAATATTATTAATTTTTTACCTTTTACCTT
*
5665 ACCCAAATATTATTAATTTTTTACTTTTTACCTT
1 ACCCAAATATTATTAATTTTTTACCTTTTACCTT
*
5699 ATCCAAAT
1 ACCCAAAT
5707 GTTGTTTACT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.30, C:0.18, G:0.00, T:0.51
Consensus pattern (34 bp):
ACCCAAATATTATTAATTTTTTACCTTTTACCTT
Found at i:6614 original size:45 final size:45
Alignment explanation
Indices: 6575--6678 Score: 156
Period size: 45 Copynumber: 2.3 Consensus size: 45
6565 TCTTTCAATC
6575 ATGGTCTTACTCATT-TCCATCATGATGCCATAACATCTTTCAGCT
1 ATGGTCTTACTCATTAT-CATCATGATGCCATAACATCTTTCAGCT
* * * *
6620 ATAGTCTTACTCATTATCGTCATGATGTCATAGCATCTTTCAGCT
1 ATGGTCTTACTCATTATCATCATGATGCCATAACATCTTTCAGCT
6665 ATGGTCTTACTCAT
1 ATGGTCTTACTCAT
6679 CTTACGCATA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
45 52 0.98
46 1 0.02
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.39
Consensus pattern (45 bp):
ATGGTCTTACTCATTATCATCATGATGCCATAACATCTTTCAGCT
Found at i:7565 original size:7 final size:6
Alignment explanation
Indices: 7526--7574 Score: 53
Period size: 6 Copynumber: 7.8 Consensus size: 6
7516 CATTTCCCAT
* * *
7526 TTTCCC TTTCCC TTCCCC TTCCCC TTCCCCC TTTCTCC TTTCCC TTTCC
1 TTTCCC TTTCCC TTTCCC TTTCCC TT-TCCC TTTC-CC TTTCCC TTTCC
7575 TCGCCACCCC
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
6 27 0.69
7 12 0.31
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (6 bp):
TTTCCC
Found at i:7986 original size:24 final size:24
Alignment explanation
Indices: 7928--7989 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
7918 GAAATAATCA
*
7928 TTCAGTTAAACTCTGTTTATTTGT
1 TTCAGTTAAACTCTGTTTATTTAT
* *
7952 TTTAATTAAACTC-GATTTATTTAT
1 TTCAGTTAAACTCTG-TTTATTTAT
*
7976 TTCAGTCAAACTCT
1 TTCAGTTAAACTCT
7990 TATTAGTTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
23 1 0.03
24 29 0.97
ACGTcount: A:0.27, C:0.15, G:0.08, T:0.50
Consensus pattern (24 bp):
TTCAGTTAAACTCTGTTTATTTAT
Found at i:13730 original size:20 final size:21
Alignment explanation
Indices: 13705--13746 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
13695 GTGACAAGGA
13705 AAGGGAAAGGAGAAA-GGGGG
1 AAGGGAAAGGAGAAATGGGGG
*
13725 AAGGGAAGGGAGAAATGGGGG
1 AAGGGAAAGGAGAAATGGGGG
13746 A
1 A
13747 GAGACTTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.43, C:0.00, G:0.55, T:0.02
Consensus pattern (21 bp):
AAGGGAAAGGAGAAATGGGGG
Found at i:15038 original size:65 final size:66
Alignment explanation
Indices: 14924--15052 Score: 147
Period size: 65 Copynumber: 2.0 Consensus size: 66
14914 GGGCAGAATT
* * ** *
14924 TACCCAAACCCCATTCCAGACTTGACACTTTGATTAAGCGAAGTGGCCATTCTTAACAAA-ATGC
1 TACCCAAACCCCATT-CAGACCTAACACTTAAATTAAGCCAAGTGGCCATTCTTAA-AAATATGC
14988 GTG
64 GTG
* *
14991 TACCCAAACCCCATT-ATACCTAACACTTAAATTAAGCCAAGCT-GCCATTTTTAAAAATATGC
1 TACCCAAACCCCATTCAGACCTAACACTTAAATTAAGCCAAG-TGGCCATTCTTAAAAATATGC
15053 ATGCACACAT
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
64 3 0.06
65 34 0.64
66 1 0.02
67 15 0.28
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.26
Consensus pattern (66 bp):
TACCCAAACCCCATTCAGACCTAACACTTAAATTAAGCCAAGTGGCCATTCTTAAAAATATGCGT
G
Found at i:19563 original size:152 final size:153
Alignment explanation
Indices: 19334--19614 Score: 420
Period size: 152 Copynumber: 1.8 Consensus size: 153
19324 GGTAAGATCC
* * *
19334 ATCTAAGTTTCTCCATGTGGAGGACCCCTGTAGGTCGTACCTCCATATCCAGGTGCCGGATATGA
1 ATCTAAGTTTCTCCATGTGGAGGACCCCTGCAGGTCGTACCTCCATATCCAAGCGCCGGATATGA
* * * * *
19399 GTGTCAGACACAAATACCTAAAGAAAAATGAAGATTCGGAGCAACAAAGTCTAAATATGCATCAC
66 ATGCCAAACACAAATACCTAAAGAAAAATGAAGATTCAGAGCAACAAAATCTAAATATGCATCAC
19464 GATATATAACAAAGTATGGTAAG
131 GATATATAACAAAGTATGGTAAG
* * * * *
19487 ATCTAAGTTTTTCCATGTGGAGGATCCCTGCA-GTCTTACCTCTATATCCAAGCGTCGGATATGA
1 ATCTAAGTTTCTCCATGTGGAGGACCCCTGCAGGTCGTACCTCCATATCCAAGCGCCGGATATGA
* *
19551 ATGCCAAACACAAATACCTTAAGAAAAATGAAGATTCAGAGCAACAAAATCTAGATATGCATCA
66 ATGCCAAACACAAATACCTAAAGAAAAATGAAGATTCAGAGCAACAAAATCTAAATATGCATCA
19615 TAACATATAA
Statistics
Matches: 113, Mismatches: 15, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
152 84 0.74
153 29 0.26
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (153 bp):
ATCTAAGTTTCTCCATGTGGAGGACCCCTGCAGGTCGTACCTCCATATCCAAGCGCCGGATATGA
ATGCCAAACACAAATACCTAAAGAAAAATGAAGATTCAGAGCAACAAAATCTAAATATGCATCAC
GATATATAACAAAGTATGGTAAG
Found at i:24232 original size:16 final size:16
Alignment explanation
Indices: 24211--24249 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
24201 GAAGGCTTCG
*
24211 GGCAGAGAAAGCGTTA
1 GGCAGAGAAAGCATTA
* *
24227 GGCAGAGGAAGCATTG
1 GGCAGAGAAAGCATTA
24243 GGCAGAG
1 GGCAGAG
24250 TAGTCTCGGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.33, C:0.13, G:0.44, T:0.10
Consensus pattern (16 bp):
GGCAGAGAAAGCATTA
Found at i:33978 original size:20 final size:20
Alignment explanation
Indices: 33953--33991 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
33943 CTGTTTCTCA
33953 GAAATACAA-ATTTGAGGAGG
1 GAAATA-AACATTTGAGGAGG
33973 GAAATAAAGCATTTGAGGA
1 GAAATAAA-CATTTGAGGA
33992 TCTTAACCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 2 0.12
20 6 0.35
21 9 0.53
ACGTcount: A:0.46, C:0.05, G:0.28, T:0.21
Consensus pattern (20 bp):
GAAATAAACATTTGAGGAGG
Found at i:35742 original size:5 final size:6
Alignment explanation
Indices: 35727--35751 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
35717 ACATTATATC
35727 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
35752 TTCCATATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:40138 original size:27 final size:25
Alignment explanation
Indices: 40101--40156 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
40091 TTTTACTTAA
*
40101 AAAAAACTAAAATTAATTCTAAAAAAT
1 AAAAAACT-AAATTAAAT-TAAAAAAT
* *
40128 AAAAAATTAAATTAAATTAAAAGAT
1 AAAAAACTAAATTAAATTAAAAAAT
40153 AAAA
1 AAAA
40157 TGATGTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 11 0.42
26 8 0.31
27 7 0.27
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.25
Consensus pattern (25 bp):
AAAAAACTAAATTAAATTAAAAAAT
Found at i:41333 original size:6 final size:6
Alignment explanation
Indices: 41324--41350 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
41314 GGCGATACCG
41324 ATCCCT ATCCCT ATCCCT ATCCCT ATC
1 ATCCCT ATCCCT ATCCCT ATCCCT ATC
41351 TCTGTCTCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.48, G:0.00, T:0.33
Consensus pattern (6 bp):
ATCCCT
Found at i:50861 original size:8 final size:8
Alignment explanation
Indices: 50850--50881 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
50840 GTTTATTAGT
50850 TTTATATA
1 TTTATATA
50858 TTTATATA
1 TTTATATA
50866 TTTATATA
1 TTTATATA
*
50874 TTTTTATA
1 TTTATATA
50882 ATTTTTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (8 bp):
TTTATATA
Found at i:50892 original size:16 final size:17
Alignment explanation
Indices: 50850--50959 Score: 64
Period size: 16 Copynumber: 6.4 Consensus size: 17
50840 GTTTATTAGT
*
50850 TTTATATATTTATAT-A
1 TTTATATATTTTTATAA
50866 TTTATATATTTTTATAA
1 TTTATATATTTTTATAA
* *
50883 TTTTTA-ATTTTCATAAA
1 TTTATATATTTTTAT-AA
* * * *
50900 CTTATAAATTTTAATTA
1 TTTATATATTTTTATAA
* * *
50917 TTTA-AAAATATTATAA
1 TTTATATATTTTTATAA
*
50933 GCATTATATATTTTTATAAA
1 --TTTATATATTTTTAT-AA
50953 TTTATAT
1 TTTATAT
50960 TTCATATATT
Statistics
Matches: 70, Mismatches: 17, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
16 29 0.41
17 16 0.23
18 16 0.23
19 7 0.10
20 2 0.03
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (17 bp):
TTTATATATTTTTATAA
Found at i:53131 original size:14 final size:14
Alignment explanation
Indices: 53087--53137 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
53077 CAGTCAAATG
53087 GAAAAGAAAATTAA
1 GAAAAGAAAATTAA
*
53101 -AAAA-AAAA-GAA
1 GAAAAGAAAATTAA
53112 TCGAAAAGAAAATTAA
1 --GAAAAGAAAATTAA
53128 GAAAAGAAAA
1 GAAAAGAAAA
53138 AAGATGAACG
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
11 2 0.07
12 4 0.13
13 4 0.13
14 14 0.47
15 4 0.13
16 2 0.07
ACGTcount: A:0.75, C:0.02, G:0.14, T:0.10
Consensus pattern (14 bp):
GAAAAGAAAATTAA
Found at i:53938 original size:18 final size:19
Alignment explanation
Indices: 53915--53958 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 19
53905 CCAAAATTTA
53915 ATTTTAATATTT-TTAT-AC
1 ATTTTAAT-TTTATTATCAC
53933 ATTTTAATTTTATTATGCAC
1 ATTTTAATTTTATTAT-CAC
53953 ATTTTA
1 ATTTTA
53959 TTACTTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.13
18 12 0.52
20 8 0.35
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.59
Consensus pattern (19 bp):
ATTTTAATTTTATTATCAC
Found at i:61472 original size:19 final size:19
Alignment explanation
Indices: 61445--61497 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
61435 ATCATTAAGG
* * *
61445 TTAAGTTAATTAGGTTTAA
1 TTAAATTAATTAAGATTAA
61464 TTAAATTAATTAAGATTAA
1 TTAAATTAATTAAGATTAA
*
61483 TTAGATTTAATTAAG
1 TTA-AATTAATTAAG
61498 GTATAAAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 19 0.66
20 10 0.34
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.45
Consensus pattern (19 bp):
TTAAATTAATTAAGATTAA
Found at i:62226 original size:2 final size:2
Alignment explanation
Indices: 62219--62244 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
62209 TTTTAATGTG
62219 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
62245 CACGAGTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.