Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_498 ID=scaffold_498-JGI_221_v2.0
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: 7655
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.27
Warning! 1238 characters in sequence are not A, C, G, or T
Found at i:2069 original size:16 final size:16
Alignment explanation
Indices: 2048--2111 Score: 92
Period size: 16 Copynumber: 3.9 Consensus size: 16
2038 CGGACTTGCA
*
2048 TAACTTATATAATACT
1 TAACTTACATAATACT
2064 TAACTTACATAACTTACT
1 TAACTTACATAA--TACT
*
2082 TAACTTACATAATACA
1 TAACTTACATAATACT
2098 TAACTTACATAATA
1 TAACTTACATAATA
2112 ACATAATAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
16 28 0.64
18 16 0.36
ACGTcount: A:0.45, C:0.17, G:0.00, T:0.38
Consensus pattern (16 bp):
TAACTTACATAATACT
Found at i:2106 original size:9 final size:9
Alignment explanation
Indices: 2041--2406 Score: 80
Period size: 9 Copynumber: 41.3 Consensus size: 9
2031 AACTTGTCGG
*
2041 ACTTGCATA
1 ACTTACATA
*
2050 ACTTATATA
1 ACTTACATA
*
2059 A--TACTTA
1 ACTTACATA
2066 ACTTACATA
1 ACTTACATA
*
2075 ACTTACTTA
1 ACTTACATA
2084 ACTTACATA
1 ACTTACATA
2093 A--TACATA
1 ACTTACATA
2100 ACTTACATA
1 ACTTACATA
*
2109 A-TAACATAATA
1 ACTTAC---ATA
*
2120 AGTTACATAA
1 ACTTACAT-A
*
2130 TATTATACATA
1 -ACT-TACATA
*
2141 ACTCACATA
1 ACTTACATA
*
2150 AC-TAAATGA
1 ACTTACAT-A
2159 A-TTA-AT-
1 ACTTACATA
*
2165 ATTATACATTA
1 ACT-TACA-TA
* **
2176 ACTTGTC-GG
1 ACTT-ACATA
*
2185 ACTTGCATA
1 ACTTACATA
*
2194 ACTTATATA
1 ACTTACATA
*
2203 A--TACTTA
1 ACTTACATA
*
2210 ACTTTCATA
1 ACTTACATA
2219 ACTTACATA
1 ACTTACATA
2228 ACTTACATA
1 ACTTACATA
*
2237 A--TACAGA
1 ACTTACATA
2244 ACTTACATA
1 ACTTACATA
*
2253 A-TAACATAATA
1 ACTTAC---ATA
*
2264 AGTTACATAA
1 ACTTACAT-A
*
2274 TATTATACATA
1 -ACT-TACATA
*
2285 ACTCACATA
1 ACTTACATA
*
2294 AC-TAAATTA
1 ACTTACA-TA
* * *
2303 ATTTATATT
1 ACTTACATA
2312 A--TACATTA
1 ACTTACA-TA
* **
2320 ACTTGTC-GG
1 ACTT-ACATA
* *
2329 ACTTGCGTA
1 ACTTACATA
*
2338 ACTTATATA
1 ACTTACATA
*
2347 A--TACTTA
1 ACTTACATA
2354 ACTTACATA
1 ACTTACATA
2363 ACTTACATA
1 ACTTACATA
2372 A--TACATA
1 ACTTACATA
*
2379 ACTTACGTA
1 ACTTACATA
2388 A--TACATA
1 ACTTACATA
2395 ACTTACATA
1 ACTTACATA
2404 ACT
1 ACT
2407 CATATATACT
Statistics
Matches: 257, Mismatches: 56, Indels: 88
0.64 0.14 0.22
Matches are distributed among these distances:
6 1 0.00
7 45 0.18
8 19 0.07
9 146 0.57
10 12 0.05
11 18 0.07
12 16 0.06
ACGTcount: A:0.44, C:0.17, G:0.04, T:0.36
Consensus pattern (9 bp):
ACTTACATA
Found at i:2213 original size:16 final size:16
Alignment explanation
Indices: 2190--2261 Score: 81
Period size: 16 Copynumber: 4.3 Consensus size: 16
2180 GTCGGACTTG
*
2190 CATAACTTATATAATA
1 CATAACTTACATAATA
* *
2206 CTTAACTTTCATAACTTA
1 CATAACTTACATAA--TA
2224 CATAACTTACATAATA
1 CATAACTTACATAATA
*
2240 CAGAACTTACATAATAA
1 CATAACTTACATAAT-A
2257 CATAA
1 CATAA
2262 TAAGTTACAT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
16 27 0.59
17 5 0.11
18 14 0.30
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.33
Consensus pattern (16 bp):
CATAACTTACATAATA
Found at i:2291 original size:144 final size:144
Alignment explanation
Indices: 2031--2379 Score: 630
Period size: 144 Copynumber: 2.4 Consensus size: 144
2021 NNNNNNNNNN
*
2031 AACTTGTCGGACTTGCATAACTTATATAATACTTAACTTACATAACTTACTTAACTTACATAATA
1 AACTTGTCGGACTTGCATAACTTATATAATACTTAACTTACATAACTTACATAACTTACATAATA
*
2096 CATAACTTACATAATAACATAATAAGTTACATAATATTATACATAACTCACATAACTAAATGAAT
66 CAGAACTTACATAATAACATAATAAGTTACATAATATTATACATAACTCACATAACTAAATGAAT
2161 TAATATTATACATT
131 TAATATTATACATT
*
2175 AACTTGTCGGACTTGCATAACTTATATAATACTTAACTTTCATAACTTACATAACTTACATAATA
1 AACTTGTCGGACTTGCATAACTTATATAATACTTAACTTACATAACTTACATAACTTACATAATA
*
2240 CAGAACTTACATAATAACATAATAAGTTACATAATATTATACATAACTCACATAACTAAATTAAT
66 CAGAACTTACATAATAACATAATAAGTTACATAATATTATACATAACTCACATAACTAAATGAAT
*
2305 TTATATTATACATT
131 TAATATTATACATT
*
2319 AACTTGTCGGACTTGCGTAACTTATATAATACTTAACTTACATAACTTACATAA--TACATAA
1 AACTTGTCGGACTTGCATAACTTATATAATACTTAACTTACATAACTTACATAACTTACATAA
2380 CTTACGTAAT
Statistics
Matches: 198, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
142 7 0.04
144 191 0.96
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (144 bp):
AACTTGTCGGACTTGCATAACTTATATAATACTTAACTTACATAACTTACATAACTTACATAATA
CAGAACTTACATAATAACATAATAAGTTACATAATATTATACATAACTCACATAACTAAATGAAT
TAATATTATACATT
Found at i:2364 original size:25 final size:25
Alignment explanation
Indices: 2336--2406 Score: 83
Period size: 25 Copynumber: 2.8 Consensus size: 25
2326 CGGACTTGCG
* *
2336 TAACTTATATAATACTTAACTTACA
1 TAACTTACATAATACATAACTTACA
*
2361 TAACTTACATAATACATAACTTACG
1 TAACTTACATAATACATAACTTACA
2386 TAA--TACATAACTTACATAACT
1 TAACTTACATAA--TACATAACT
2407 CATATATACT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
23 7 0.17
25 34 0.83
ACGTcount: A:0.45, C:0.18, G:0.01, T:0.35
Consensus pattern (25 bp):
TAACTTACATAATACATAACTTACA
Found at i:2410 original size:16 final size:16
Alignment explanation
Indices: 2357--2404 Score: 87
Period size: 16 Copynumber: 3.0 Consensus size: 16
2347 ATACTTAACT
2357 TACATAACTTACATAA
1 TACATAACTTACATAA
*
2373 TACATAACTTACGTAA
1 TACATAACTTACATAA
2389 TACATAACTTACATAA
1 TACATAACTTACATAA
2405 CTCATATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.48, C:0.19, G:0.02, T:0.31
Consensus pattern (16 bp):
TACATAACTTACATAA
Done.