Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008766.1 Kokia drynarioides strain JFW-HI SEQ_123449, 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: 16116
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:5257 original size:25 final size:23
Alignment explanation
Indices: 5216--5261 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
5206 CCAATTAGGG
5216 AATTATTATTTAGATTTAATTCA
1 AATTATTATTTAGATTTAATTCA
*
5239 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TATTTAG-ATTTAATT
5262 TGGATCTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (23 bp):
AATTATTATTTAGATTTAATTCA
Found at i:6336 original size:6 final size:6
Alignment explanation
Indices: 6325--6377 Score: 52
Period size: 6 Copynumber: 8.5 Consensus size: 6
6315 ACTTTAGCCA
* * * *
6325 TTTATT TTTATT TTTATT TTCATT TTTAAT TTAACTT TTCTATT TTAATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTA-TT TT-TATT TTTATT
6375 TTT
1 TTT
6378 TTCCCTTTTG
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
6 29 0.78
7 7 0.19
8 1 0.03
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (6 bp):
TTTATT
Found at i:6342 original size:12 final size:12
Alignment explanation
Indices: 6325--6377 Score: 61
Period size: 12 Copynumber: 4.2 Consensus size: 12
6315 ACTTTAGCCA
*
6325 TTTATTTTTATT
1 TTTATTTTAATT
*
6337 TTTATTTTCATT
1 TTTATTTTAATT
*
6349 TTTAATTTAACTT
1 TTTATTTTAA-TT
6362 TTCTATTTTAATT
1 TT-TATTTTAATT
6375 TTT
1 TTT
6378 TTCCCTTTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
12 20 0.57
13 8 0.23
14 7 0.20
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTATTTTAATT
Found at i:6356 original size:19 final size:20
Alignment explanation
Indices: 6328--6377 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
6318 TTAGCCATTT
6328 ATTTTT-ATTTTTA-TTTTC
1 ATTTTTAATTTTTACTTTTC
*
6346 ATTTTTAA-TTTAACTTTTC
1 ATTTTTAATTTTTACTTTTC
6365 -TATTTTAATTTTT
1 AT-TTTTAATTTTT
6378 TTCCCTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 11 0.42
19 12 0.46
20 3 0.12
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (20 bp):
ATTTTTAATTTTTACTTTTC
Found at i:9260 original size:5 final size:5
Alignment explanation
Indices: 9239--9281 Score: 50
Period size: 6 Copynumber: 7.8 Consensus size: 5
9229 AAATAGTATA
9239 TTTATT TTTAGT TTTAT TTTAT TTTATT TTTAAT TTTAT TTTA
1 TTTA-T TTTA-T TTTAT TTTAT TTTA-T TTT-AT TTTAT TTTA
9282 ATTATGCAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
5 16 0.47
6 17 0.50
7 1 0.03
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (5 bp):
TTTAT
Found at i:9261 original size:17 final size:18
Alignment explanation
Indices: 9239--9280 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
9229 AAATAGTATA
9239 TTTATTTTTAGTTTT-AT
1 TTTATTTTTAGTTTTAAT
*
9256 TTTA-TTTTATTTTTAAT
1 TTTATTTTTAGTTTTAAT
9273 TTTATTTT
1 TTTATTTT
9281 AATTATGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 9 0.41
17 10 0.45
18 3 0.14
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (18 bp):
TTTATTTTTAGTTTTAAT
Found at i:9265 original size:22 final size:22
Alignment explanation
Indices: 9239--9281 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
9229 AAATAGTATA
*
9239 TTTATTTTTAGTTTTATTTTAT
1 TTTATTTTTAATTTTATTTTAT
9261 TTTATTTTTAATTTTATTTTA
1 TTTATTTTTAATTTTATTTTA
9282 ATTATGCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (22 bp):
TTTATTTTTAATTTTATTTTAT
Found at i:10224 original size:13 final size:13
Alignment explanation
Indices: 10202--10269 Score: 73
Period size: 14 Copynumber: 4.8 Consensus size: 13
10192 TTATTGTTTA
10202 GAAAAAAAAAATT
1 GAAAAAAAAAATT
10215 GAAAAGAAAAAAATT
1 G-AAA-AAAAAAATT
10230 GAAAAAAAAAATT
1 GAAAAAAAAAATT
**
10243 GAGAAAATAAAAAAA
1 GA-AAAA-AAAAATT
10258 GAAAAAAGAAAA
1 GAAAAAA-AAAA
10270 AAAAGACAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
13 13 0.27
14 18 0.38
15 17 0.35
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (13 bp):
GAAAAAAAAAATT
Found at i:10226 original size:16 final size:15
Alignment explanation
Indices: 10203--10271 Score: 74
Period size: 15 Copynumber: 4.7 Consensus size: 15
10193 TATTGTTTAG
10203 AAAAAAAAAATTGAA
1 AAAAAAAAAATTGAA
*
10218 AAGAAAAAAATTG--
1 AAAAAAAAAATTGAA
10231 AAAAAAAAAATTGAGA
1 AAAAAAAAAATTGA-A
10247 AAATAAAAAAA--GAA
1 AAA-AAAAAAATTGAA
10261 AAAAGAAAAAA
1 AAAA-AAAAAA
10272 AAGACAAAAG
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
13 13 0.28
14 10 0.21
15 14 0.30
16 3 0.06
17 7 0.15
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (15 bp):
AAAAAAAAAATTGAA
Found at i:10233 original size:28 final size:28
Alignment explanation
Indices: 10201--10269 Score: 88
Period size: 28 Copynumber: 2.4 Consensus size: 28
10191 TTTATTGTTT
10201 AGAAAAAAAAAATTGA-AAAGA-AAAAAA
1 AGAAAAAAAAAATTGAGAAA-ATAAAAAA
*
10228 TTGAAAAAAAAAATTGAGAAAATAAAAAA
1 -AGAAAAAAAAAATTGAGAAAATAAAAAA
10257 AGAAAAAAGAAAA
1 AGAAAAAA-AAAA
10270 AAAAGACAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
28 23 0.64
29 13 0.36
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (28 bp):
AGAAAAAAAAAATTGAGAAAATAAAAAA
Found at i:10272 original size:16 final size:16
Alignment explanation
Indices: 10251--10281 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
10241 TTGAGAAAAT
10251 AAAAAAAGAAAAAAGA
1 AAAAAAAGAAAAAAGA
*
10267 AAAAAAAGACAAAAG
1 AAAAAAAGAAAAAAG
10282 TGTGTTTGAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.84, C:0.03, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAAAAAGAAAAAAGA
Done.