Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015021.1 Kokia drynarioides strain JFW-HI SEQ_130065, 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: 16793
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Found at i:1084 original size:19 final size:21
Alignment explanation
Indices: 1044--1090 Score: 71
Period size: 19 Copynumber: 2.3 Consensus size: 21
1034 ATATGGAATT
*
1044 AAAAAATAACTCTTAATCTAA
1 AAAAAATAACTCTTAATATAA
1065 AAAAAATAA-TCTT-ATATAA
1 AAAAAATAACTCTTAATATAA
1084 AAAAAAT
1 AAAAAAT
1091 CACTTACCCG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 12 0.48
20 4 0.16
21 9 0.36
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.28
Consensus pattern (21 bp):
AAAAAATAACTCTTAATATAA
Found at i:1191 original size:25 final size:25
Alignment explanation
Indices: 1163--1244 Score: 80
Period size: 25 Copynumber: 3.3 Consensus size: 25
1153 ATAAGTGATG
* *
1163 AATATTTTATATTTGAAATTTATTT
1 AATATTTTATATTTGATATTTATTA
* *
1188 AATATTATT-CATTTGATATTT-GTA
1 AATATT-TTATATTTGATATTTATTA
*
1212 AATATATTTATATAT-ATATTTATTA
1 AATAT-TTTATATTTGATATTTATTA
1237 AATATTTT
1 AATATTTT
1245 TTTAGAAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
24 17 0.37
25 27 0.59
26 2 0.04
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (25 bp):
AATATTTTATATTTGATATTTATTA
Found at i:1220 original size:12 final size:12
Alignment explanation
Indices: 1203--1241 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1193 TATTCATTTG
*
1203 ATATTTGTAAAT
1 ATATTTATAAAT
*
1215 ATATTTATATAT
1 ATATTTATAAAT
1227 ATATTTATTAAAT
1 ATATTTA-TAAAT
1240 AT
1 AT
1242 TTTTTTAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 17 0.74
13 6 0.26
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (12 bp):
ATATTTATAAAT
Found at i:6072 original size:20 final size:22
Alignment explanation
Indices: 6047--6087 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
6037 ATATTTTTTA
6047 TAAAATT-AATAAAA-CATATT
1 TAAAATTGAATAAAAGCATATT
*
6067 TAAAATTGGATAAAAGCATAT
1 TAAAATTGAATAAAAGCATAT
6088 AAAATTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 6 0.33
22 5 0.28
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (22 bp):
TAAAATTGAATAAAAGCATATT
Found at i:6090 original size:20 final size:18
Alignment explanation
Indices: 6045--6093 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 18
6035 TAATATTTTT
6045 TATAAAATTAATAAAACA
1 TATAAAATTAATAAAACA
*
6063 TATTTAAAATTGGATAAAAGCA
1 TA--TAAAATT-AATAAAA-CA
6085 TATAAAATT
1 TATAAAATT
6094 TCTTTAAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 2 0.08
20 14 0.54
21 6 0.23
22 4 0.15
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (18 bp):
TATAAAATTAATAAAACA
Found at i:6159 original size:28 final size:30
Alignment explanation
Indices: 6128--6187 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 30
6118 AATTTGATAT
*
6128 AAACTTATAAA-AATATAAAAAA-AAAATA
1 AAACTTACAAATAATATAAAAAATAAAATA
* *
6156 AAACTTACAAATATTATAAAAAATCAAATA
1 AAACTTACAAATAATATAAAAAATAAAATA
6186 AA
1 AA
6188 TTATTAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 10 0.37
29 10 0.37
30 7 0.26
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (30 bp):
AAACTTACAAATAATATAAAAAATAAAATA
Found at i:6295 original size:21 final size:20
Alignment explanation
Indices: 6239--6309 Score: 60
Period size: 21 Copynumber: 3.6 Consensus size: 20
6229 ATTTAATATT
*
6239 TTATAAAAACA-TATAAAAA
1 TTATAAAAAAATTATAAAAA
**
6258 TTCAT--AAAACCTATAAATAA
1 TT-ATAAAAAAATTATAAA-AA
6278 -TATAAAATAAATTATAAAAA
1 TTATAAAA-AAATTATAAAAA
6298 TTATAAAAAAAT
1 TTATAAAAAAAT
6310 CCTTTAAACC
Statistics
Matches: 41, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
18 5 0.12
19 9 0.22
20 12 0.29
21 15 0.37
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.30
Consensus pattern (20 bp):
TTATAAAAAAATTATAAAAA
Found at i:6298 original size:9 final size:9
Alignment explanation
Indices: 6239--6306 Score: 55
Period size: 10 Copynumber: 7.0 Consensus size: 9
6229 ATTTAATATT
6239 TTATAAAAA
1 TTATAAAAA
*
6248 CATATAAAAA
1 -TTATAAAAA
*
6258 TTCATAAAAC
1 TT-ATAAAAA
*
6268 CTATAAATAA
1 TTATAAA-AA
*
6278 TATAAAATAAA
1 T-TATAA-AAA
6289 TTATAAAAA
1 TTATAAAAA
6298 TTATAAAAA
1 TTATAAAAA
6307 AATCCTTTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
9 18 0.39
10 20 0.43
11 7 0.15
12 1 0.02
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (9 bp):
TTATAAAAA
Found at i:6303 original size:30 final size:29
Alignment explanation
Indices: 6239--6306 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
6229 ATTTAATATT
* *
6239 TTATAAAAACATATAAAAATTCATAAAAC
1 TTATAAAAACATAAAAAAATTCATAAAAA
* *
6268 CTATAAATAATATAAAATAAATT-ATAAAAA
1 TTATAAA-AACATAAAA-AAATTCATAAAAA
6298 TTATAAAAA
1 TTATAAAAA
6307 AATCCTTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
29 8 0.25
30 19 0.59
31 5 0.16
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (29 bp):
TTATAAAAACATAAAAAAATTCATAAAAA
Found at i:7431 original size:12 final size:11
Alignment explanation
Indices: 7410--7489 Score: 51
Period size: 11 Copynumber: 7.4 Consensus size: 11
7400 TTTTTTGTAA
7410 TTTTTAT-TTT
1 TTTTTATATTT
*
7420 TTTCTATATTT
1 TTTTTATATTT
**
7431 TTTTTATAGAT
1 TTTTTATATTT
*
7442 TTTTTA-A-TA
1 TTTTTATATTT
*
7451 TTTTAATATTT
1 TTTTTATATTT
*
7462 TTATTGAT-TTT
1 TT-TTTATATTT
7473 TATTTTATCATTT
1 T-TTTTAT-ATTT
7486 TTTT
1 TTTT
7490 CACATATCAT
Statistics
Matches: 53, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
9 5 0.09
10 8 0.15
11 28 0.53
12 8 0.15
13 4 0.08
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (11 bp):
TTTTTATATTT
Done.