Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013950.1 Kokia drynarioides strain JFW-HI SEQ_128980, 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: 41090
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33
Found at i:990 original size:21 final size:21
Alignment explanation
Indices: 965--1011 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
955 TGAATTGAAT
965 TTGAATGATTTGTGATCAAAA
1 TTGAATGATTTGTGATCAAAA
986 TTGAATGATTTGTGATCAAAA
1 TTGAATGATTTGTGATCAAAA
1007 TTGAA
1 TTGAA
1012 AGTGAAAGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.38, C:0.04, G:0.19, T:0.38
Consensus pattern (21 bp):
TTGAATGATTTGTGATCAAAA
Found at i:1017 original size:27 final size:25
Alignment explanation
Indices: 957--1011 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 25
947 AGTATATTTG
957 AATTGAATTTGAATGATTTGTGATCAA
1 AATTGAA--TGAATGATTTGTGATCAA
984 AA-T---TGAATGATTTGTGATCAA
1 AATTGAATGAATGATTTGTGATCAA
1005 AATTGAA
1 AATTGAA
1012 AGTGAAAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
21 20 0.83
22 1 0.04
26 1 0.04
27 2 0.08
ACGTcount: A:0.40, C:0.04, G:0.18, T:0.38
Consensus pattern (25 bp):
AATTGAATGAATGATTTGTGATCAA
Found at i:1019 original size:6 final size:6
Alignment explanation
Indices: 1008--1036 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
998 TGATCAAAAT
1008 TGAAAG TGAAAG TGAAAG TGAAAG TGAAA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAA
1037 TTGGAGTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.31, T:0.17
Consensus pattern (6 bp):
TGAAAG
Found at i:1047 original size:18 final size:19
Alignment explanation
Indices: 1007--1052 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
997 GTGATCAAAA
1007 TTGAAAGTGAAAGTGAAAG
1 TTGAAAGTGAAAGTGAAAG
* *
1026 -TGAAAGTGAAATTG-GAG
1 TTGAAAGTGAAAGTGAAAG
1043 TTGAAAGTGA
1 TTGAAAGTGA
1053 TATGAATTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 2 0.08
18 22 0.92
ACGTcount: A:0.43, C:0.00, G:0.33, T:0.24
Consensus pattern (19 bp):
TTGAAAGTGAAAGTGAAAG
Found at i:3009 original size:18 final size:20
Alignment explanation
Indices: 2977--3014 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
2967 TTTTAAAACT
2977 AATTATAAATCAAATAAATA
1 AATTATAAATCAAATAAATA
2997 AATTA-AAAT-AAATAAATA
1 AATTATAAATCAAATAAATA
3015 TTAATTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.50
19 4 0.22
20 5 0.28
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (20 bp):
AATTATAAATCAAATAAATA
Found at i:3733 original size:3 final size:3
Alignment explanation
Indices: 3725--3751 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3715 GAACTCCAAC
3725 ACT ACT ACT ACT ACT ACT ACT ACT ACT
1 ACT ACT ACT ACT ACT ACT ACT ACT ACT
3752 GCCGTCGCCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ACT
Found at i:5352 original size:3 final size:3
Alignment explanation
Indices: 5344--5368 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5334 GGTTTGTTGG
5344 TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA T
5369 AGGGTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TGA
Found at i:23939 original size:24 final size:23
Alignment explanation
Indices: 23912--23959 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
23902 TTTAATATTT
23912 AATTAA-T-ATTTTTGTT-AAAA
1 AATTAATTCATTTTTGTTCAAAA
23932 AATTAATTCATTTTTGTTCAAAA
1 AATTAATTCATTTTTGTTCAAAA
23955 AATTA
1 AATTA
23960 CTCATTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 6 0.24
21 1 0.04
22 9 0.36
23 9 0.36
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (23 bp):
AATTAATTCATTTTTGTTCAAAA
Found at i:23964 original size:22 final size:22
Alignment explanation
Indices: 23912--23965 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
23902 TTTAATATTT
23912 AATTAA-T-ATTTTTGTTAAAA
1 AATTAACTCATTTTTGTTAAAA
*
23932 AATTAATTCATTTTTGTTCAAAA
1 AATTAACTCATTTTTGTT-AAAA
23955 AATT-ACTCATT
1 AATTAACTCATT
23966 AAATTTGACT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 6 0.20
21 1 0.03
22 15 0.50
23 8 0.27
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (22 bp):
AATTAACTCATTTTTGTTAAAA
Found at i:25298 original size:31 final size:31
Alignment explanation
Indices: 25237--25307 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
25227 GATTTGGTTA
*
25237 AATTATATACATAAAATTTGAATTACGATTC
1 AATTGTATACATAAAATTTGAATTACGATTC
**
25268 -ATATGTATACATAAAAATTTG-ATTTTGATTC
1 AAT-TGTATACAT-AAAATTTGAATTACGATTC
25299 AATTGTATA
1 AATTGTATA
25308 TATTTAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
30 2 0.06
31 22 0.65
32 10 0.29
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.42
Consensus pattern (31 bp):
AATTGTATACATAAAATTTGAATTACGATTC
Found at i:30607 original size:2 final size:2
Alignment explanation
Indices: 30600--30635 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
30590 TATGTTTAAG
30600 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT A
30636 ACTGATGAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:33161 original size:29 final size:29
Alignment explanation
Indices: 33119--33175 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
33109 TCCTCCTCTC
33119 TATATGTTGGATTGAAATGAATAAAATTT
1 TATATGTTGGATTGAAATGAATAAAATTT
33148 TATATGTTGGATTGAAATGAATAAAATT
1 TATATGTTGGATTGAAATGAATAAAATT
33176 AAAAAAAGCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.00, G:0.18, T:0.40
Consensus pattern (29 bp):
TATATGTTGGATTGAAATGAATAAAATTT
Found at i:37055 original size:21 final size:20
Alignment explanation
Indices: 37034--37073 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
37024 AAGAGAAAGA
37034 AAGAAA-GAAGGAAGAAGGAG
1 AAGAAAGGAAGG-AGAAGGAG
37054 AAGAAAGGGAAGGAGAAGGA
1 AAGAAA-GGAAGGAGAAGGA
37074 AAAAATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 7 0.39
22 5 0.28
ACGTcount: A:0.57, C:0.00, G:0.42, T:0.00
Consensus pattern (20 bp):
AAGAAAGGAAGGAGAAGGAG
Found at i:37453 original size:20 final size:21
Alignment explanation
Indices: 37414--37456 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
37404 TAATTTATTT
*
37414 TAATTTAATTTTTTTAGTTAG
1 TAATTTAATTTTGTTAGTTAG
*
37435 TAATTTTATTTTGTT-GTTAG
1 TAATTTAATTTTGTTAGTTAG
37455 TA
1 TA
37457 GTAGTCAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.26, C:0.00, G:0.12, T:0.63
Consensus pattern (21 bp):
TAATTTAATTTTGTTAGTTAG
Found at i:37978 original size:16 final size:16
Alignment explanation
Indices: 37933--37982 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
37923 TAAACCTAGC
37933 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
37949 T-A-TAA-TA-CAAAAAA
1 TAATTAATTATC--AAAA
37963 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
37979 TAAT
1 TAAT
37983 ATCCCCATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
12 1 0.04
13 2 0.07
14 8 0.29
15 2 0.07
16 12 0.43
17 2 0.07
18 1 0.04
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:39361 original size:43 final size:43
Alignment explanation
Indices: 39279--39363 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
39269 ATTAACATGT
* *
39279 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTTAC
1 TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
* *
39322 TAAATTATATTACTTTACTCTTATTAATAT-CTTGACATGTTA
1 TAAATTATATTACTTGACTCGTATTAATATGCTTG-CATGTTA
39364 TCAATTGTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 3 0.08
43 34 0.92
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.47
Consensus pattern (43 bp):
TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
Found at i:39981 original size:45 final size:44
Alignment explanation
Indices: 39917--40053 Score: 166
Period size: 45 Copynumber: 3.0 Consensus size: 44
39907 GCATAGCTCA
*
39917 TCAAGCCAAGGATATCAGCCTTAGTTTGACGAGCCACTGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACT-CAATAC
* * *
39962 TCAAGCCAAGTATATCAGCCTCAATTTGACGAGCCACCTCGATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCA-CTCAATAC
** * * *
40007 TCAAGGGAAGGATATCAGGCTGAGTTTGACGAGCCACCACAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCA-CTCAATAC
40052 TC
1 TC
40054 TATTCCTCTC
Statistics
Matches: 79, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
45 77 0.97
46 2 0.03
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.21
Consensus pattern (44 bp):
TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACTCAATAC
Found at i:40090 original size:21 final size:21
Alignment explanation
Indices: 40046--40086 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
40036 CGAGCCACCA
*
40046 CAATACTCTATTCCTCTCGGG
1 CAATACTCTACTCCTCTCGGG
40067 CAATACTCTACTCCTC-CGGG
1 CAATACTCTACTCCTCTCGGG
40087 GCAAATGGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.20, C:0.37, G:0.15, T:0.29
Consensus pattern (21 bp):
CAATACTCTACTCCTCTCGGG
Found at i:40355 original size:28 final size:29
Alignment explanation
Indices: 40310--40389 Score: 103
Period size: 28 Copynumber: 2.8 Consensus size: 29
40300 TTTCATAACA
*
40310 TTAAACCTTAAA-ACCTAGACTTGAAAC-C
1 TTAAACCGTAAACA-CTAGACTTGAAACTC
40338 TTAAACCGTAAACACTAGACTTGAAACTC
1 TTAAACCGTAAACACTAGACTTGAAACTC
**
40367 CAAAACCGTAAACACTAGA-TTGA
1 TTAAACCGTAAACACTAGACTTGA
40390 TTAAGGAGAG
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
28 28 0.60
29 19 0.40
ACGTcount: A:0.44, C:0.24, G:0.10, T:0.23
Consensus pattern (29 bp):
TTAAACCGTAAACACTAGACTTGAAACTC
Found at i:40381 original size:29 final size:28
Alignment explanation
Indices: 40320--40389 Score: 99
Period size: 29 Copynumber: 2.5 Consensus size: 28
40310 TTAAACCTTA
**
40320 AAAC-CTAGACTTGAAACCTTAAACCGT
1 AAACACTAGACTTGAAACCCAAAACCGT
40347 AAACACTAGACTTGAAACTCCAAAACCGT
1 AAACACTAGACTTGAAAC-CCAAAACCGT
40376 AAACACTAGA-TTGA
1 AAACACTAGACTTGA
40390 TTAAGGAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
27 4 0.10
28 17 0.44
29 18 0.46
ACGTcount: A:0.44, C:0.24, G:0.11, T:0.20
Consensus pattern (28 bp):
AAACACTAGACTTGAAACCCAAAACCGT
Done.