Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002552.1 Kokia drynarioides strain JFW-HI SEQ_114742, 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: 144937
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Warning! 96 characters in sequence are not A, C, G, or T
Found at i:4791 original size:5 final size:5
Alignment explanation
Indices: 4781--4808 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
4771 TCAATGACGT
4781 TTTTC TTTTC TTTTC TTTTC TTTTC TTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTT
4809 CAACTCAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:8842 original size:74 final size:74
Alignment explanation
Indices: 8730--8877 Score: 251
Period size: 74 Copynumber: 2.0 Consensus size: 74
8720 CTAAGTTTAA
** *
8730 CTCAGTGACTAATAAAGTTGTGTGTAGTTGCAAGTTAACTAATGATATCTCTCTAGAAGGTGGTG
1 CTCAGTGACTAATAAAAATGTGTGTAGTTGCAAGTTAACTAATGATATCTCTCTAGAAGGTGGTA
8795 TAAGTGATT
66 TAAGTGATT
* *
8804 CTCAGTGACTAATAAAAATGTGTGTATTTGCAAGTTAACTAATGATATCTGTCTAGAAGGTGGTA
1 CTCAGTGACTAATAAAAATGTGTGTAGTTGCAAGTTAACTAATGATATCTCTCTAGAAGGTGGTA
8869 TAAGTGATT
66 TAAGTGATT
8878 TCCTAAAAAA
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
74 69 1.00
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.35
Consensus pattern (74 bp):
CTCAGTGACTAATAAAAATGTGTGTAGTTGCAAGTTAACTAATGATATCTCTCTAGAAGGTGGTA
TAAGTGATT
Found at i:18418 original size:20 final size:20
Alignment explanation
Indices: 18395--18435 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
18385 TTTTTATATA
*
18395 TATTGATGGGGTTTTATTTT
1 TATTGACGGGGTTTTATTTT
* *
18415 TATTGACGGGTTTTTGTTTT
1 TATTGACGGGGTTTTATTTT
18435 T
1 T
18436 TTATCAAGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.12, C:0.02, G:0.24, T:0.61
Consensus pattern (20 bp):
TATTGACGGGGTTTTATTTT
Found at i:24906 original size:38 final size:38
Alignment explanation
Indices: 24855--24931 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
24845 ATAAGTATGT
*
24855 TAATATCACGCTTATACTCGATCCATGAGCACCTTTAG
1 TAATATCACGCTTATACCCGATCCATGAGCACCTTTAG
24893 TAATATCACGCTTATACCCGATCCATGAGCACCTTTAG
1 TAATATCACGCTTATACCCGATCCATGAGCACCTTTAG
24931 T
1 T
24932 GATAACATTG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (38 bp):
TAATATCACGCTTATACCCGATCCATGAGCACCTTTAG
Found at i:41072 original size:17 final size:17
Alignment explanation
Indices: 41050--41103 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
41040 GTCCCTTTGA
41050 ATTTATTTTTAAATATT
1 ATTTATTTTTAAATATT
41067 ATTTATTTAATTAAAATATT
1 ATTTATTT--TT-AAATATT
* *
41087 -TTTATGTATAAATATT
1 ATTTATTTTTAAATATT
41103 A
1 A
41104 AAAATGCCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
16 7 0.23
17 9 0.29
19 8 0.26
20 7 0.23
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
ATTTATTTTTAAATATT
Found at i:49600 original size:23 final size:22
Alignment explanation
Indices: 49552--49600 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
49542 ATTTAAATTT
* * *
49552 TAAATTTAAAAAATAATAAGAT
1 TAAATTTAAAAAATAAAAACAA
*
49574 TAAATTTTTAAAAATAAAAACAA
1 TAAA-TTTAAAAAATAAAAACAA
49597 TAAA
1 TAAA
49601 CCGAAATTCC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (22 bp):
TAAATTTAAAAAATAAAAACAA
Found at i:60039 original size:2 final size:2
Alignment explanation
Indices: 60032--60064 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
60022 GTACATATTT
60032 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
60065 TAATTTTATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:73156 original size:7 final size:7
Alignment explanation
Indices: 73144--73174 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
73134 ACAAAACAGT
73144 ATTTATA
1 ATTTATA
73151 ATTTATA
1 ATTTATA
73158 ATTTATA
1 ATTTATA
73165 ATTTATA
1 ATTTATA
73172 ATT
1 ATT
73175 AATTTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
ATTTATA
Found at i:76676 original size:4 final size:4
Alignment explanation
Indices: 76667--76721 Score: 58
Period size: 4 Copynumber: 13.2 Consensus size: 4
76657 AAACACACAA
* *
76667 ATAC ATAC ATAC ATAC ACTGAC ATAC ATAC ATGC ATAC ATGC ATAC GA-AC
1 ATAC ATAC ATAC ATAC A-T-AC ATAC ATAC ATAC ATAC ATAC ATAC -ATAC
76717 ATAC A
1 ATAC A
76722 CGCACACAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
3 1 0.02
4 36 0.84
5 3 0.07
6 3 0.07
ACGTcount: A:0.45, C:0.25, G:0.07, T:0.22
Consensus pattern (4 bp):
ATAC
Found at i:76684 original size:22 final size:22
Alignment explanation
Indices: 76659--76705 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
76649 ACACACGAAA
76659 ACACACAAATACATACATACAT
1 ACACACAAATACATACATACAT
** * *
76681 ACACTGACATACATACATGCAT
1 ACACACAAATACATACATACAT
76703 ACA
1 ACA
76706 TGCATACGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.28, G:0.04, T:0.19
Consensus pattern (22 bp):
ACACACAAATACATACATACAT
Found at i:78875 original size:106 final size:106
Alignment explanation
Indices: 78690--78904 Score: 376
Period size: 106 Copynumber: 2.0 Consensus size: 106
78680 ATGCAAGAGG
* *
78690 GGAGAATAATTGTGGTGGTGGAGAGAAGATAAAATTCAAGTCGAGACAACAACAGTTATAGTTAT
1 GGAGAATAATTGTGGTGGTGGAGAGAAGATAAAACTCAAGTCGAGACAACAACAATTATAGTTAT
78755 TAATAAGTTTTTTAATCACAGCAATCATTGTCAGCTCGAAA
66 TAATAAGTTTTTTAATCACAGCAATCATTGTCAGCTCGAAA
* * *
78796 GGAGAGTAATTGTGGTGGTGGAGAGAAGATAAAACTCAAGTCGAGACAATAACAATTGTAGTTAT
1 GGAGAATAATTGTGGTGGTGGAGAGAAGATAAAACTCAAGTCGAGACAACAACAATTATAGTTAT
*
78861 TAATAAGTTTTTTAATCACAGCAATCATTGTCGGCTCGAAA
66 TAATAAGTTTTTTAATCACAGCAATCATTGTCAGCTCGAAA
78902 GGA
1 GGA
78905 CTTTCATCTT
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
106 103 1.00
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (106 bp):
GGAGAATAATTGTGGTGGTGGAGAGAAGATAAAACTCAAGTCGAGACAACAACAATTATAGTTAT
TAATAAGTTTTTTAATCACAGCAATCATTGTCAGCTCGAAA
Found at i:79966 original size:3 final size:3
Alignment explanation
Indices: 79958--79982 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
79948 TTTTGAGAAG
79958 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
79983 GAACCATCTA
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:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:83987 original size:31 final size:31
Alignment explanation
Indices: 83952--84020 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
83942 CTTTACAGTC
* *
83952 TAATGATTTAAATAAAAACTTTTGAATTGTT
1 TAATGATTTAAATAAAAACTTTCGAATAGTT
* *
83983 TAATGACTTAAATGAAAACTTTCGAATAGTT
1 TAATGATTTAAATAAAAACTTTCGAATAGTT
84014 TAATGAT
1 TAATGAT
84021 ATTTTTAACT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.41
Consensus pattern (31 bp):
TAATGATTTAAATAAAAACTTTCGAATAGTT
Found at i:92391 original size:23 final size:22
Alignment explanation
Indices: 92361--92403 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
92351 ATCTAAATTT
92361 TAAATTTTAAAAAATAGAAAGAC
1 TAAATTTTAAAAAATA-AAAGAC
*
92384 TAAATTTTTAAAAATAAAAG
1 TAAATTTTAAAAAATAAAAG
92404 TACAATGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.30
Consensus pattern (22 bp):
TAAATTTTAAAAAATAAAAGAC
Found at i:93400 original size:15 final size:16
Alignment explanation
Indices: 93370--93407 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
93360 AGGGGTTATG
93370 ATTTTTTCAGAGTTTAA
1 ATTTTTTCAGAGTTT-A
93387 ATTTTTTCA-A-TTTA
1 ATTTTTTCAGAGTTTA
93401 ATTTTTT
1 ATTTTTT
93408 GTAAATTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.38
15 3 0.14
16 1 0.05
17 9 0.43
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.63
Consensus pattern (16 bp):
ATTTTTTCAGAGTTTA
Found at i:96574 original size:14 final size:14
Alignment explanation
Indices: 96541--96571 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
96531 TTAAAGATCA
96541 AATTAAAGTAAATG
1 AATTAAAGTAAATG
96555 AATTAAAGT-AATG
1 AATTAAAGTAAATG
96568 AATT
1 AATT
96572 TAAGCAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (14 bp):
AATTAAAGTAAATG
Found at i:101365 original size:6 final size:7
Alignment explanation
Indices: 101338--101364 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
101328 TTTTTCAATA
101338 ATTTTTT
1 ATTTTTT
101345 ATTTTTT
1 ATTTTTT
101352 ATTTTTT
1 ATTTTTT
101359 ATTTTT
1 ATTTTT
101365 AAAATTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
ATTTTTT
Found at i:101912 original size:24 final size:22
Alignment explanation
Indices: 101868--101914 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 22
101858 TTATTCTTAT
*
101868 ATCATAAAAAATTAAAAAATTA
1 ATCATAAAAAAATAAAAAATTA
101890 ATCATAAAATTAAATAAAAAATTA
1 ATCATAAAA--AAATAAAAAATTA
101914 A
1 A
101915 AATCCGATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 9 0.41
24 13 0.59
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (22 bp):
ATCATAAAAAAATAAAAAATTA
Found at i:115113 original size:18 final size:19
Alignment explanation
Indices: 115092--115129 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
115082 TATTAAAAAA
115092 TGAAAATTT-ATTCAAATG
1 TGAAAATTTAATTCAAATG
* *
115110 TGAATATTTAATTGAAATG
1 TGAAAATTTAATTCAAATG
115129 T
1 T
115130 TTCAATTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.42, C:0.03, G:0.13, T:0.42
Consensus pattern (19 bp):
TGAAAATTTAATTCAAATG
Found at i:115991 original size:42 final size:42
Alignment explanation
Indices: 115932--116023 Score: 175
Period size: 42 Copynumber: 2.2 Consensus size: 42
115922 TGTCCACTTT
*
115932 TCAGCCCAAGTGAACCACAGTTCATGGCTTACAGATATAATC
1 TCAGCCCAAGTGAACCACAGTTCATGGCTTACAGATAAAATC
115974 TCAGCCCAAGTGAACCACAGTTCATGGCTTACAGATAAAATC
1 TCAGCCCAAGTGAACCACAGTTCATGGCTTACAGATAAAATC
116016 TCAGCCCA
1 TCAGCCCA
116024 TCTCACTAAG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.22
Consensus pattern (42 bp):
TCAGCCCAAGTGAACCACAGTTCATGGCTTACAGATAAAATC
Found at i:116893 original size:5 final size:5
Alignment explanation
Indices: 116879--116908 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
116869 AAATGTGATT
116879 AATT- AATTA AATTA AATTA AATTA AATTA A
1 AATTA AATTA AATTA AATTA AATTA AATTA A
116909 TAAACAAGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATTA
Found at i:116901 original size:15 final size:14
Alignment explanation
Indices: 116876--116909 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
116866 TTAAAATGTG
116876 ATTAATT-AATTAA
1 ATTAATTAAATTAA
116889 ATTAAATTAAATTAA
1 ATT-AATTAAATTAA
116904 ATTAAT
1 ATTAAT
116910 AAACAAGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 3 0.16
14 7 0.37
15 9 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATTAATTAAATTAA
Found at i:120108 original size:4 final size:4
Alignment explanation
Indices: 120099--120126 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
120089 TTGAAAATCC
120099 TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG
120127 CGTATGTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:121438 original size:2 final size:2
Alignment explanation
Indices: 121433--121460 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
121423 TTCTCTTTCA
121433 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
121461 ATATATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:121465 original size:2 final size:2
Alignment explanation
Indices: 121460--121490 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
121450 TCTCTCTCTC
121460 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
121491 GAAGCTATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:125258 original size:15 final size:15
Alignment explanation
Indices: 125238--125267 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
125228 TAAATATAAC
125238 TCTTTTCTCTTTCTT
1 TCTTTTCTCTTTCTT
*
125253 TCTTTTCTTTTTCTT
1 TCTTTTCTCTTTCTT
125268 ATAAAATCTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (15 bp):
TCTTTTCTCTTTCTT
Found at i:127130 original size:36 final size:36
Alignment explanation
Indices: 127090--127160 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
127080 ATATTTTATC
*
127090 TTCTTAAAATCACTTTTAACAACAATGGTAAACTAT
1 TTCTTAAAATCACTTTTAACAACAATGATAAACTAT
127126 TTCTTAAAATCACTTTTAACAACAATGATAAACTA
1 TTCTTAAAATCACTTTTAACAACAATGATAAACTA
127161 ATCCTTAGTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.44, C:0.17, G:0.04, T:0.35
Consensus pattern (36 bp):
TTCTTAAAATCACTTTTAACAACAATGATAAACTAT
Done.