Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007827.1 Kokia drynarioides strain JFW-HI SEQ_122463, 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: 14404
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Found at i:101 original size:12 final size:12
Alignment explanation
Indices: 84--166 Score: 67
Period size: 12 Copynumber: 6.8 Consensus size: 12
74 ATAACATTCA
*
84 AACAACCAAAAT
1 AACAACAAAAAT
* *
96 AACAACCAAAAC
1 AACAACAAAAAT
* *
108 AGCAGCAAAAAT
1 AACAACAAAAAT
* *
120 AATAATAAAAAAT
1 AACAA-CAAAAAT
*
133 AGCAACAAAAAT
1 AACAACAAAAAT
*
145 AACAATAAAAAT
1 AACAACAAAAAT
*
157 AACACCAAAA
1 AACAACAAAA
167 CAGTAAAAAA
Statistics
Matches: 54, Mismatches: 16, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
12 45 0.83
13 9 0.17
ACGTcount: A:0.69, C:0.18, G:0.04, T:0.10
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:141 original size:25 final size:25
Alignment explanation
Indices: 86--155 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 25
76 AACATTCAAA
* **
86 CAACCAAAATAACAA-CCAAAACAG
1 CAACAAAAATAACAATAAAAAACAG
* * *
110 CAGCAAAAATAATAATAAAAAATAG
1 CAACAAAAATAACAATAAAAAACAG
135 CAACAAAAATAACAATAAAAA
1 CAACAAAAATAACAATAAAAA
156 TAACACCAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
24 12 0.32
25 25 0.68
ACGTcount: A:0.69, C:0.17, G:0.04, T:0.10
Consensus pattern (25 bp):
CAACAAAAATAACAATAAAAAACAG
Found at i:234 original size:33 final size:33
Alignment explanation
Indices: 163--234 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
153 AAATAACACC
* *
163 AAAACAGTAAAAAAACAGCACCAAAACAACAAT
1 AAAACAGTAAAAAAACAACACCAAAACAACAAA
* * *
196 CAAACAGTAAAAACACAACACCAAAACAGCAAA
1 AAAACAGTAAAAAAACAACACCAAAACAACAAA
229 AAAACA
1 AAAACA
235 ATATAATTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.67, C:0.24, G:0.06, T:0.04
Consensus pattern (33 bp):
AAAACAGTAAAAAAACAACACCAAAACAACAAA
Found at i:6298 original size:6 final size:6
Alignment explanation
Indices: 6287--6311 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
6277 TAACATACAA
6287 GAGATG GAGATG GAGATG GAGATG G
1 GAGATG GAGATG GAGATG GAGATG G
6312 CAGAGGATAT
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:0.32, C:0.00, G:0.52, T:0.16
Consensus pattern (6 bp):
GAGATG
Found at i:6363 original size:6 final size:6
Alignment explanation
Indices: 6356--6402 Score: 76
Period size: 6 Copynumber: 7.8 Consensus size: 6
6346 AAATGATGCT
* *
6356 GTTGCT GTTACG GTTGCG GTTGCG GTTGCG GTTGCG GTTGCG GTTGC
1 GTTGCG GTTGCG GTTGCG GTTGCG GTTGCG GTTGCG GTTGCG GTTGC
6403 ACTTGTTTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.02, C:0.17, G:0.45, T:0.36
Consensus pattern (6 bp):
GTTGCG
Found at i:6662 original size:13 final size:13
Alignment explanation
Indices: 6644--6669 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6634 AGTTTTAACA
6644 AAATTTTAGGTTT
1 AAATTTTAGGTTT
6657 AAATTTTAGGTTT
1 AAATTTTAGGTTT
6670 GATCCGAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (13 bp):
AAATTTTAGGTTT
Found at i:7040 original size:12 final size:12
Alignment explanation
Indices: 7006--7111 Score: 65
Period size: 12 Copynumber: 9.1 Consensus size: 12
6996 ATAACATCAA
* *
7006 AACAACCAAAAT
1 AACAACAAAAAC
**
7018 AACAATTAAAAC
1 AACAACAAAAAC
* *
7030 AACAGCAAAAAT
1 AACAACAAAAAC
*
7042 AATAAC-AAAAC
1 AACAACAAAAAC
*
7053 AAC-ACAAAAAT
1 AACAACAAAAAC
* *
7064 AGCAATAAAAAC
1 AACAACAAAAAC
*
7076 AACAGCAAAAAC
1 AACAACAAAAAC
*
7088 AAC-ACCAAAAC
1 AACAACAAAAAC
* *
7099 AATAAAAAAAAC
1 AACAACAAAAAC
7111 A
1 A
7112 GCATCAAAAC
Statistics
Matches: 68, Mismatches: 23, Indels: 6
0.70 0.24 0.06
Matches are distributed among these distances:
10 2 0.03
11 20 0.29
12 46 0.68
ACGTcount: A:0.70, C:0.20, G:0.03, T:0.08
Consensus pattern (12 bp):
AACAACAAAAAC
Found at i:7051 original size:23 final size:22
Alignment explanation
Indices: 6992--7100 Score: 105
Period size: 23 Copynumber: 4.9 Consensus size: 22
6982 AAAAACGCAT
*
6992 AAAAATAACATCAAAACAAC-C
1 AAAAATAACAACAAAACAACAC
*
7013 -AAAATAACAATTAAAACAACAGC
1 AAAAATAACAA-CAAAACAACA-C
*
7036 AAAAATAATAACAAAACAACAC
1 AAAAATAACAACAAAACAACAC
* *
7058 AAAAATAGCAATAAAAACAACAGC
1 AAAAATAACAA-CAAAACAACA-C
* *
7082 AAAAACAACACCAAAACAA
1 AAAAATAACAACAAAACAA
7101 TAAAAAAAAC
Statistics
Matches: 71, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
20 9 0.13
21 8 0.11
22 10 0.14
23 26 0.37
24 18 0.25
ACGTcount: A:0.69, C:0.20, G:0.03, T:0.08
Consensus pattern (22 bp):
AAAAATAACAACAAAACAACAC
Found at i:7080 original size:46 final size:44
Alignment explanation
Indices: 6992--7100 Score: 146
Period size: 46 Copynumber: 2.4 Consensus size: 44
6982 AAAAACGCAT
* *
6992 AAAAATAACATCAAAACAACCAAAATAACAATTAAAACAACAGC
1 AAAAATAACAACAAAACAACCAAAATAACAATAAAAACAACAGC
* *
7036 AAAAATAATAACAAAACAACACAAAAATAGCAATAAAAACAACAGC
1 AAAAATAACAACAAAACAAC-C-AAAATAACAATAAAAACAACAGC
* *
7082 AAAAACAACACCAAAACAA
1 AAAAATAACAACAAAACAA
7101 TAAAAAAAAC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 18 0.32
45 1 0.02
46 37 0.66
ACGTcount: A:0.69, C:0.20, G:0.03, T:0.08
Consensus pattern (44 bp):
AAAAATAACAACAAAACAACCAAAATAACAATAAAAACAACAGC
Found at i:7092 original size:35 final size:32
Alignment explanation
Indices: 7048--7114 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 32
7038 AAATAATAAC
*
7048 AAAACAACACAAAAATAGCAATAAAAACAACAGCA
1 AAAACAACAC-AAAA-A-CAATAAAAAAAACAGCA
*
7083 AAAACAACACCAAAACAATAAAAAAAACAGCA
1 AAAACAACACAAAAACAATAAAAAAAACAGCA
7115 TCAAAACAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
32 16 0.53
33 1 0.03
34 3 0.10
35 10 0.33
ACGTcount: A:0.70, C:0.21, G:0.04, T:0.04
Consensus pattern (32 bp):
AAAACAACACAAAAACAATAAAAAAAACAGCA
Found at i:7108 original size:23 final size:23
Alignment explanation
Indices: 7082--7131 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
7072 AAACAACAGC
7082 AAAAACAACACCAAAACAATAAA
1 AAAAACAACACCAAAACAATAAA
* * *
7105 AAAAACAGCATCAAAACAGTAAA
1 AAAAACAACACCAAAACAATAAA
7128 AAAA
1 AAAA
7132 GCATCAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.72, C:0.18, G:0.04, T:0.06
Consensus pattern (23 bp):
AAAAACAACACCAAAACAATAAA
Found at i:7121 original size:46 final size:46
Alignment explanation
Indices: 7020--7122 Score: 118
Period size: 46 Copynumber: 2.2 Consensus size: 46
7010 ACCAAAATAA
* * * * * *
7020 CAATTAAAACAACAGCAAAAATAATAACAAAACAACACAAAAATAG
1 CAATAAAAACAACAGCAAAAACAACAACAAAACAAAAAAAAAACAG
*
7066 CAATAAAAACAACAGCAAAAACAACACCAAAACAATAAAAAAAACAG
1 CAATAAAAACAACAGCAAAAACAACAACAAAACAA-AAAAAAAACAG
*
7113 C-ATCAAAACA
1 CAATAAAAACA
7123 GTAAAAAAAG
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
46 39 0.81
47 9 0.19
ACGTcount: A:0.68, C:0.20, G:0.04, T:0.08
Consensus pattern (46 bp):
CAATAAAAACAACAGCAAAAACAACAACAAAACAAAAAAAAAACAG
Found at i:7128 original size:20 final size:20
Alignment explanation
Indices: 7104--7204 Score: 94
Period size: 20 Copynumber: 4.8 Consensus size: 20
7094 AAAACAATAA
7104 AAAAAACAGCATCAAAACAGT
1 AAAAAA-AGCATCAAAACAGT
*
7125 AAAAAAAGCATCAAAATAGT
1 AAAAAAAGCATCAAAACAGT
** *
7145 AAAAAAAAAATACCAAAACTGT
1 AAAAAAAGCAT--CAAAACAGT
**
7167 AAAAAATAGCAATCAAATTAGT
1 AAAAAA-AGC-ATCAAAACAGT
*
7189 AAAAAAAGCACCAAAA
1 AAAAAAAGCATCAAAA
7205 TAACGACATA
Statistics
Matches: 64, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
20 27 0.42
21 9 0.14
22 25 0.39
23 1 0.02
24 2 0.03
ACGTcount: A:0.65, C:0.14, G:0.08, T:0.13
Consensus pattern (20 bp):
AAAAAAAGCATCAAAACAGT
Found at i:7140 original size:43 final size:42
Alignment explanation
Indices: 7076--7183 Score: 101
Period size: 43 Copynumber: 2.5 Consensus size: 42
7066 CAATAAAAAC
* * * *
7076 AACAGCAAAAACAA-CACCAAAACAATAAAAAAAACAGCATCAA
1 AACAGTAAAAA-AAGCATCAAAACAATAAAAAAAA-AACACCAA
* * *
7119 AACAGTAAAAAAAGCATCAAAATAGTAAAAAAAAAATACCAA
1 AACAGTAAAAAAAGCATCAAAACAATAAAAAAAAAACACCAA
*
7161 AACTGTAAAAAATAGCAATCAAA
1 AACAGTAAAAAA-AGC-ATCAAA
7184 TTAGTAAAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
42 18 0.33
43 30 0.56
44 6 0.11
ACGTcount: A:0.67, C:0.17, G:0.06, T:0.10
Consensus pattern (42 bp):
AACAGTAAAAAAAGCATCAAAACAATAAAAAAAAAACACCAA
Found at i:7152 original size:44 final size:44
Alignment explanation
Indices: 7101--7195 Score: 122
Period size: 44 Copynumber: 2.2 Consensus size: 44
7091 ACCAAAACAA
* *
7101 TAAAAAAAACAGCATCAAAACAGTAAAAAA-AGC-ATCAAAATAG
1 TAAAAAAAA-AACACCAAAACAGTAAAAAATAGCAATCAAAATAG
* * *
7144 TAAAAAAAAAATACCAAAACTGTAAAAAATAGCAATCAAATTAG
1 TAAAAAAAAAACACCAAAACAGTAAAAAATAGCAATCAAAATAG
7188 TAAAAAAA
1 TAAAAAAA
7196 GCACCAAAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
42 16 0.36
43 12 0.27
44 17 0.38
ACGTcount: A:0.66, C:0.12, G:0.07, T:0.15
Consensus pattern (44 bp):
TAAAAAAAAAACACCAAAACAGTAAAAAATAGCAATCAAAATAG
Found at i:7202 original size:42 final size:41
Alignment explanation
Indices: 7103--7204 Score: 116
Period size: 42 Copynumber: 2.4 Consensus size: 41
7093 CAAAACAATA
*
7103 AAAAAAACAGCATCAAAACAGTAAAAAAAGCATCAAAATAGT
1 AAAAAAA-AGCACCAAAACAGTAAAAAAAGCATCAAAATAGT
** * *
7145 AAAAAAAAAATACCAAAACTGTAAAAAATAGCAATCAAATTAGT
1 -AAAAAAAAGCACCAAAACAGTAAAAAA-AGC-ATCAAAATAGT
7189 -AAAAAAAGCACCAAAA
1 AAAAAAAAGCACCAAAA
7205 TAACGACATA
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
42 30 0.60
43 10 0.20
44 10 0.20
ACGTcount: A:0.66, C:0.14, G:0.08, T:0.13
Consensus pattern (41 bp):
AAAAAAAAGCACCAAAACAGTAAAAAAAGCATCAAAATAGT
Found at i:7944 original size:20 final size:19
Alignment explanation
Indices: 7903--7950 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
7893 AAATGTGGAT
* *
7903 TATATTTCATTATTAAAAA
1 TATATTTTATTATCAAAAA
*
7922 TATATTTTATTTATCAAACA
1 TATATTTTA-TTATCAAAAA
*
7942 TATTTTTTA
1 TATATTTTA
7951 ATTTGAAAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (19 bp):
TATATTTTATTATCAAAAA
Found at i:13979 original size:15 final size:15
Alignment explanation
Indices: 13961--13997 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
13951 ATTATTTTTC
*
13961 TTAAATATAAAATTT
1 TTAAATATAAAATTA
13976 TTAAATATAAAATTA
1 TTAAATATAAAATTA
13991 TTAAATA
1 TTAAATA
13998 ATTTTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TTAAATATAAAATTA
Done.