Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_325 ID=scaffold_325-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: 8175
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Found at i:1291 original size:42 final size:38
Alignment explanation
Indices: 1244--1336 Score: 123
Period size: 40 Copynumber: 2.3 Consensus size: 38
1234 AGACAAGCTT
1244 TTAGCGGCGTTTGGACAAAAAAACGCCGCTAAAAATAGAGCA
1 TTAGCGGCGTTT--AC-AAAAAACGCCGCTAAAAAT-GAGCA
**
1286 TTAGCGGCGCTTTACGTAAAACGCCGCTAAAAATGAGCA
1 TTAGCGGCG-TTTACAAAAAACGCCGCTAAAAATGAGCA
1325 TTAGCGGCGTTT
1 TTAGCGGCGTTT
1337 TTTGGAAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
38 3 0.06
39 14 0.29
40 17 0.35
41 2 0.04
42 9 0.19
43 3 0.06
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22
Consensus pattern (38 bp):
TTAGCGGCGTTTACAAAAAACGCCGCTAAAAATGAGCA
Found at i:1311 original size:40 final size:40
Alignment explanation
Indices: 1262--1358 Score: 142
Period size: 40 Copynumber: 2.4 Consensus size: 40
1252 GTTTGGACAA
1262 AAAAACGCCGCTAAAAATAGAGCATTAGCGGCG-CTTTACG
1 AAAAACGCCGCTAAAAAT-GAGCATTAGCGGCGTCTTTACG
* * **
1302 TAAAACGCCGCTAAAAATGAGCATTAGCGGCGTTTTTTGG
1 AAAAACGCCGCTAAAAATGAGCATTAGCGGCGTCTTTACG
1342 AAAAACGCCGCTAAAAA
1 AAAAACGCCGCTAAAAA
1359 CCTAAGCACA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
39 14 0.27
40 37 0.73
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.20
Consensus pattern (40 bp):
AAAAACGCCGCTAAAAATGAGCATTAGCGGCGTCTTTACG
Found at i:1465 original size:41 final size:41
Alignment explanation
Indices: 1413--1549 Score: 238
Period size: 41 Copynumber: 3.3 Consensus size: 41
1403 CGTTTTTAAA
*
1413 AAAAGCACCGCTAATGCTCAGATCTTGAGAGGCGTTTTTGG
1 AAAAGCGCCGCTAATGCTCAGATCTTGAGAGGCGTTTTTGG
1454 AAAAGCGCCGCTAATGCTCAGATCTTGAGAGGCGTTTTTGG
1 AAAAGCGCCGCTAATGCTCAGATCTTGAGAGGCGTTTTTGG
* *
1495 AAAAGCGCCGCTAATGCTCAGATCTTTAGCGGCGTTTTTGG
1 AAAAGCGCCGCTAATGCTCAGATCTTGAGAGGCGTTTTTGG
*
1536 GAAAGCGCCGCTAA
1 AAAAGCGCCGCTAA
1550 AGCCCCGAAA
Statistics
Matches: 92, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 92 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (41 bp):
AAAAGCGCCGCTAATGCTCAGATCTTGAGAGGCGTTTTTGG
Found at i:1999 original size:14 final size:15
Alignment explanation
Indices: 1970--2003 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
1960 TAAGGTTTAT
1970 AGATTATGGAATTAG
1 AGATTATGGAATTAG
1985 AGATTATGG-ATTAG
1 AGATTATGGAATTAG
1999 AGATT
1 AGATT
2004 CTGATTTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.38, C:0.00, G:0.26, T:0.35
Consensus pattern (15 bp):
AGATTATGGAATTAG
Found at i:2257 original size:7 final size:7
Alignment explanation
Indices: 2242--2287 Score: 83
Period size: 7 Copynumber: 6.6 Consensus size: 7
2232 AAGGTGTAGA
*
2242 GGTTAGG
1 GGTTTGG
2249 GGTTTGG
1 GGTTTGG
2256 GGTTTGG
1 GGTTTGG
2263 GGTTTGG
1 GGTTTGG
2270 GGTTTGG
1 GGTTTGG
2277 GGTTTGG
1 GGTTTGG
2284 GGTT
1 GGTT
2288 AAGAGTTAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.02, C:0.00, G:0.57, T:0.41
Consensus pattern (7 bp):
GGTTTGG
Found at i:2265 original size:89 final size:89
Alignment explanation
Indices: 2090--2252 Score: 256
Period size: 89 Copynumber: 1.8 Consensus size: 89
2080 TTCAGTGTTA
* *
2090 GGTTAGGGGTTAAGGTTTAGATTAATTAGTGTGTTTTAATTTATATATTAAATAATGATTAGTGG
1 GGTTAGGGGTTAAGATTTAGATTAATTAGTGTGTTTTAATTTATATATTAAATAATGATTAGAGG
2155 TTAGGGGTTAGGGATTCGGGGTCG
66 TTAGGGGTTAGGGATTCGGGGTCG
* * * *
2179 GGTTAGGGTTTATGATTTAGATTAATTAGTGTTTTTTAATTTATATATTAAATAA-GGTGTAGAG
1 GGTTAGGGGTTAAGATTTAGATTAATTAGTGTGTTTTAATTTATATATTAAATAATGAT-TAGAG
2243 GTTAGGGGTT
65 GTTAGGGGTT
2253 TGGGGTTTGG
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
88 2 0.03
89 65 0.97
ACGTcount: A:0.27, C:0.01, G:0.29, T:0.43
Consensus pattern (89 bp):
GGTTAGGGGTTAAGATTTAGATTAATTAGTGTGTTTTAATTTATATATTAAATAATGATTAGAGG
TTAGGGGTTAGGGATTCGGGGTCG
Found at i:2711 original size:17 final size:16
Alignment explanation
Indices: 2678--2711 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2668 ATATTAGATT
*
2678 TAAAAAAATTAATAAA
1 TAAAAAAATTAACAAA
2694 TAAAAAAATGTAACAAA
1 TAAAAAAAT-TAACAAA
2711 T
1 T
2712 TGATACGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (16 bp):
TAAAAAAATTAACAAA
Found at i:3095 original size:22 final size:23
Alignment explanation
Indices: 3063--3128 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 23
3053 TAAAATCCCC
3063 TCCCCCC--AAAATCCCCAACTT
1 TCCCCCCTTAAAATCCCCAACTT
* *
3084 TCCCGCC-TAAAATCCCTAA-TT
1 TCCCCCCTTAAAATCCCCAACTT
* *
3105 TCCCCCCTTGAAACCCCCAACTT
1 TCCCCCCTTAAAATCCCCAACTT
3128 T
1 T
3129 ACAAACATAC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 14 0.39
22 19 0.53
23 3 0.08
ACGTcount: A:0.26, C:0.47, G:0.03, T:0.24
Consensus pattern (23 bp):
TCCCCCCTTAAAATCCCCAACTT
Found at i:7640 original size:44 final size:43
Alignment explanation
Indices: 7424--7650 Score: 287
Period size: 43 Copynumber: 5.3 Consensus size: 43
7414 AGATTATGTT
** * *
7424 TTTAGCGGCGTTT-TGCTAGAAGCGCCGCTAAAGGT-TTGTTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* ** *
7465 TTTAGCGGCGTTTATGATAAAAGCGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* * **
7508 TATAGCGGCGTTTGTGGGGAAAGCGTTGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* * *
7551 TTTAGCGGTGTTTGTGGGGAAAGCGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
*
7594 TTTAGCGGCGTTTGTGGGAAAAAGCGCCGCTAAAGGTCTTGATC
1 TTTAGCGGCGTTTGTGGG-AAAAGCGCCGCTAAAGGTCTTGGTC
7638 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
7651 TTTCCGGCGC
Statistics
Matches: 162, Mismatches: 21, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
41 13 0.08
42 20 0.12
43 94 0.58
44 35 0.22
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.30
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
Done.