Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010457.1 Kokia drynarioides strain JFW-HI SEQ_125355, 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: 7237
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.31
Found at i:242 original size:7 final size:7
Alignment explanation
Indices: 230--255 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
220 AATTATTGAA
230 TTATAGC
1 TTATAGC
237 TTATAGC
1 TTATAGC
244 TTATAGC
1 TTATAGC
251 TTATA
1 TTATA
256 TGTGTTTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.46
Consensus pattern (7 bp):
TTATAGC
Found at i:1235 original size:25 final size:25
Alignment explanation
Indices: 1194--1275 Score: 73
Period size: 25 Copynumber: 3.4 Consensus size: 25
1184 AGGAACACTA
*
1194 GTGCTCTCTCTGT-TTAGCAC-GTCT
1 GTGCTCTCTAT-TATTAGCACTGTCT
*
1218 CGTGCTCTCTATTATTAGCACTGTGT
1 -GTGCTCTCTATTATTAGCACTGTCT
* * *
1244 GTGCTCTC--TGATTAGCACTTTGT
1 GTGCTCTCTATTATTAGCACTGTCT
1267 GTGCTCTCT
1 GTGCTCTCT
1276 GATTTGTACT
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
23 21 0.42
24 1 0.02
25 25 0.50
26 3 0.06
ACGTcount: A:0.11, C:0.26, G:0.21, T:0.43
Consensus pattern (25 bp):
GTGCTCTCTATTATTAGCACTGTCT
Found at i:1313 original size:69 final size:66
Alignment explanation
Indices: 1232--1371 Score: 183
Period size: 69 Copynumber: 2.0 Consensus size: 66
1222 CTCTCTATTA
* * *
1232 TTAGCACTGTGTGTGCTCTCTGATT-AGCACTTTGTGTGCTCTCTGATTTGTACTTTATGTACTC
1 TTAGCACTGTGTGTGCTCTCTG-TTCAGCAC-TTATGTGCTCTCTG-TTAGTACTTT-GGTACTC
1296 TCTGT
62 TCTGT
1301 TTAGCACTGTGTGTGCTCTCTGTTACCCAGCACTTATGTGCTCTCTGTTAGTACTTTGGTACTCT
1 TTAGCACTGTGTGTGCTCTCTGTT---CAGCACTTATGTGCTCTCTGTTAGTACTTTGGTACTCT
1366 CTGT
63 CTGT
1370 TT
1 TT
1372 GTTCCGTATA
Statistics
Matches: 64, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
68 2 0.03
69 35 0.55
70 9 0.14
71 13 0.20
72 5 0.08
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.45
Consensus pattern (66 bp):
TTAGCACTGTGTGTGCTCTCTGTTCAGCACTTATGTGCTCTCTGTTAGTACTTTGGTACTCTCTG
T
Found at i:1314 original size:46 final size:49
Alignment explanation
Indices: 1199--1349 Score: 145
Period size: 48 Copynumber: 3.2 Consensus size: 49
1189 CACTAGTGCT
* * *
1199 CTCTCTGTTTAGCAC-GTCTCGTGCTCTCT-ATTATTAGCACTGTGTGTG
1 CTCTCTGTTTAGCACTGTGT-GTGCTCTCTGATTATTAGCACTGTATGTA
* * * *
1247 CTCTCTGATTAGCACTTTGTGTGCTCTCTGA-T-TT-GTACTTTATGTA
1 CTCTCTGTTTAGCACTGTGTGTGCTCTCTGATTATTAGCACTGTATGTA
** *
1293 CTCTCTGTTTAGCACTGTGTGTGCTCTCTG-TTACCCAGCACT-TATGTG
1 CTCTCTGTTTAGCACTGTGTGTGCTCTCTGATTA-TTAGCACTGTATGTA
1341 CTCTCTGTT
1 CTCTCTGTT
1350 AGTACTTTGG
Statistics
Matches: 84, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
46 37 0.44
47 2 0.02
48 38 0.45
49 7 0.08
ACGTcount: A:0.13, C:0.25, G:0.19, T:0.44
Consensus pattern (49 bp):
CTCTCTGTTTAGCACTGTGTGTGCTCTCTGATTATTAGCACTGTATGTA
Found at i:1323 original size:23 final size:23
Alignment explanation
Indices: 1199--1371 Score: 131
Period size: 23 Copynumber: 7.4 Consensus size: 23
1189 CACTAGTGCT
*
1199 CTCTCTGTTTAGCAC-GTCTCGTG
1 CTCTCTGTTTAGCACTGTGT-GTG
*
1222 CTCTCTATTATTAGCACTGTGTGTG
1 CTCTCT-GT-TTAGCACTGTGTGTG
* *
1247 CTCTCTGATTAGCACTTTGTGTG
1 CTCTCTGTTTAGCACTGTGTGTG
* * * *
1270 CTCTCTGATTT-GTACTTTATGTA
1 CTCTCTG-TTTAGCACTGTGTGTG
1293 CTCTCTGTTTAGCACTGTGTGTG
1 CTCTCTGTTTAGCACTGTGTGTG
* *
1316 CTCTCTGTTACCCAGCACT-TATGTG
1 CTCTCTGTT---TAGCACTGTGTGTG
* * *
1341 CTCTCTG-TTAGTACTTTG-GTA
1 CTCTCTGTTTAGCACTGTGTGTG
1362 CTCTCTGTTT
1 CTCTCTGTTT
1372 GTTCCGTATA
Statistics
Matches: 121, Mismatches: 19, Indels: 21
0.75 0.12 0.13
Matches are distributed among these distances:
21 14 0.12
22 6 0.05
23 60 0.50
24 4 0.03
25 28 0.23
26 9 0.07
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.45
Consensus pattern (23 bp):
CTCTCTGTTTAGCACTGTGTGTG
Found at i:3955 original size:39 final size:39
Alignment explanation
Indices: 3911--3990 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
3901 TTGCCTGGTT
3911 TACCTCCTGAAAGAGAAGTTGAATTTGGAATTGATTTAG
1 TACCTCCTGAAAGAGAAGTTGAATTTGGAATTGATTTAG
3950 TACCTCCTGAAAGAGAAGTTGAATTTGGAATTGATTTAG
1 TACCTCCTGAAAGAGAAGTTGAATTTGGAATTGATTTAG
3989 TA
1 TA
3991 TCGGGTACTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.34, C:0.10, G:0.23, T:0.34
Consensus pattern (39 bp):
TACCTCCTGAAAGAGAAGTTGAATTTGGAATTGATTTAG
Done.