Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002278.1 Kokia drynarioides strain JFW-HI SEQ_114302, 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: 2678
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.32
Found at i:473 original size:17 final size:17
Alignment explanation
Indices: 448--516 Score: 79
Period size: 17 Copynumber: 4.0 Consensus size: 17
438 TAGACTTTTT
*
448 TTAAATTAATTTTAAAC
1 TTAAATTAAATTTAAAC
*
465 TTAATTTAAATTTAAAC
1 TTAAATTAAATTTAAAC
482 TTAAGA--AAAGTTTAAAC
1 TTAA-ATTAAA-TTTAAAC
499 TTTAAATTAAATTTAAAC
1 -TTAAATTAAATTTAAAC
517 CCAAAATGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
16 3 0.07
17 27 0.61
18 11 0.25
19 3 0.07
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (17 bp):
TTAAATTAAATTTAAAC
Found at i:1375 original size:18 final size:18
Alignment explanation
Indices: 1352--1398 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
1342 TTACTAAAAA
1352 CTATTTTACAAAATAATC
1 CTATTTTACAAAATAATC
1370 CTATTTTACAAAATAATC
1 CTATTTTACAAAATAATC
* *
1388 GTATTTAACAA
1 CTATTTTACAA
1399 CCAAACTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.45, C:0.15, G:0.02, T:0.38
Consensus pattern (18 bp):
CTATTTTACAAAATAATC
Found at i:2174 original size:20 final size:22
Alignment explanation
Indices: 2149--2192 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
2139 TAAAAATTGT
2149 ATAATT-T-CCAAATAATATTA
1 ATAATTATGCCAAATAATATTA
2169 ATAATTGATGCCAAATAATATTA
1 ATAATT-ATGCCAAATAATATTA
2192 A
1 A
2193 AAAAAGCAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.29
22 1 0.05
23 14 0.67
ACGTcount: A:0.50, C:0.09, G:0.05, T:0.36
Consensus pattern (22 bp):
ATAATTATGCCAAATAATATTA
Found at i:2260 original size:21 final size:22
Alignment explanation
Indices: 2224--2281 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 22
2214 AACAACTGCG
*
2224 AAACATCAATAAAACAACACT-A
1 AAACATCCA-AAAACAACACTGA
*
2246 AAACATCCAAAAACAGCACTGA
1 AAACATCCAAAAACAACACTGA
2268 AAACAGTACCAAAA
1 AAACA-T-CCAAAA
2282 TGAACCAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 10 0.32
22 14 0.45
23 1 0.03
24 6 0.19
ACGTcount: A:0.60, C:0.24, G:0.05, T:0.10
Consensus pattern (22 bp):
AAACATCCAAAAACAACACTGA
Found at i:2293 original size:21 final size:21
Alignment explanation
Indices: 2267--2335 Score: 102
Period size: 21 Copynumber: 3.2 Consensus size: 21
2257 AACAGCACTG
*
2267 AAAACAGTACCAAAATGAACC
1 AAAACAGTACCAAAATGCACC
*
2288 AAAACAGTACCAAAATGCACTA
1 AAAACAGTACCAAAATGCAC-C
2310 AAAACAGTACCAAAACTGCACC
1 AAAACAGTACCAAAA-TGCACC
2332 AAAA
1 AAAA
2336 ACAACATCAA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
21 19 0.44
22 19 0.44
23 5 0.12
ACGTcount: A:0.57, C:0.25, G:0.09, T:0.10
Consensus pattern (21 bp):
AAAACAGTACCAAAATGCACC
Found at i:2299 original size:11 final size:11
Alignment explanation
Indices: 2267--2335 Score: 54
Period size: 11 Copynumber: 6.4 Consensus size: 11
2257 AACAGCACTG
2267 AAAACAGTACC
1 AAAACAGTACC
* *
2278 AAAA-TGAACC
1 AAAACAGTACC
2288 AAAACAGTACC
1 AAAACAGTACC
*
2299 AAAATGCACTA--
1 AAAA--CAGTACC
2310 AAAACAGTACC
1 AAAACAGTACC
* *
2321 AAAACTGCACC
1 AAAACAGTACC
2332 AAAA
1 AAAA
2336 ACAACATCAA
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
9 4 0.09
10 8 0.18
11 29 0.64
13 4 0.09
ACGTcount: A:0.57, C:0.25, G:0.09, T:0.10
Consensus pattern (11 bp):
AAAACAGTACC
Found at i:2335 original size:23 final size:23
Alignment explanation
Indices: 2267--2384 Score: 125
Period size: 23 Copynumber: 5.3 Consensus size: 23
2257 AACAGCACTG
*
2267 AAAACAGTACCAAAA-TGAACC-
1 AAAACAGTACCAAAACTGCACCA
*
2288 AAAACAGTACCAAAA-TGCACTA
1 AAAACAGTACCAAAACTGCACCA
2310 AAAACAGTACCAAAACTGCACCA
1 AAAACAGTACCAAAACTGCACCA
** * * * *
2333 AAAACAACATCAAATCAGCACGA
1 AAAACAGTACCAAAACTGCACCA
* *
2356 AAAATAGTACCAAATCTGCACCA
1 AAAACAGTACCAAAACTGCACCA
2379 AAAACA
1 AAAACA
2385 ACCTCCAAAA
Statistics
Matches: 79, Mismatches: 16, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
21 19 0.24
22 15 0.19
23 45 0.57
ACGTcount: A:0.55, C:0.25, G:0.08, T:0.11
Consensus pattern (23 bp):
AAAACAGTACCAAAACTGCACCA
Found at i:2560 original size:18 final size:18
Alignment explanation
Indices: 2514--2564 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
2504 ATCGAAGAAG
*
2514 CATCATTCTCATCATCCT
1 CATCATTCTCATCATCAT
*** *
2532 CATCGCCCTCATCGTCAT
1 CATCATTCTCATCATCAT
2550 CATCATTCTCATCAT
1 CATCATTCTCATCAT
2565 TCCTGCAATA
Statistics
Matches: 24, Mismatches: 9, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.22, C:0.39, G:0.04, T:0.35
Consensus pattern (18 bp):
CATCATTCTCATCATCAT
Done.