Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_190 ID=scaffold_190-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: 9650
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Found at i:1364 original size:40 final size:40
Alignment explanation
Indices: 1234--1345 Score: 138
Period size: 40 Copynumber: 2.8 Consensus size: 40
1224 CGTTTGGACA
** * *
1234 AAAAACGCCGCTAAAAATTAAGCGTTAGCGGCGC-TTCACG
1 AAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTTC-CT
* * *
1274 CAAAACTCCGCTAAAGATCGAGCATTAGCGGCGCTTTCCT
1 AAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTTCCT
1314 AAAAACGCCGCTAAAAAT-GAGCATTAGCGGCG
1 AAAAACGCCGCTAAAAATCGAGCATTAGCGGCG
1346 TTTTTTAGAA
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
39 14 0.23
40 44 0.72
41 3 0.05
ACGTcount: A:0.34, C:0.26, G:0.22, T:0.18
Consensus pattern (40 bp):
AAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTTCCT
Found at i:1484 original size:41 final size:41
Alignment explanation
Indices: 1407--1518 Score: 188
Period size: 41 Copynumber: 2.7 Consensus size: 41
1397 CCTTTCGGGG
*
1407 CTTTAGCGGCGTTTTTAAAAAAAGCACCGCTAATGCTCAGAT
1 CTTTAGCGGCGTTTTT-GAAAAAGCACCGCTAATGCTCAGAT
*
1449 CTTTAGCGGCGTTTTTGAAGAAGCACCGCTAATGCTCAGAT
1 CTTTAGCGGCGTTTTTGAAAAAGCACCGCTAATGCTCAGAT
*
1490 CTTTAGCGGCGTTTTTGAAAAAGCGCCGC
1 CTTTAGCGGCGTTTTTGAAAAAGCACCGC
1519 AAAAACATTT
Statistics
Matches: 66, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
41 50 0.76
42 16 0.24
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGAAAAAGCACCGCTAATGCTCAGAT
Found at i:1956 original size:14 final size:15
Alignment explanation
Indices: 1923--1956 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1913 TAAGGTTTAT
1923 AGATTATGGAATTAG
1 AGATTATGGAATTAG
1938 AGATTATGG-ATTAG
1 AGATTATGGAATTAG
*
1952 GGATT
1 AGATT
1957 CTTATTTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.35, C:0.00, G:0.29, T:0.35
Consensus pattern (15 bp):
AGATTATGGAATTAG
Found at i:2199 original size:88 final size:89
Alignment explanation
Indices: 2044--2217 Score: 271
Period size: 88 Copynumber: 2.0 Consensus size: 89
2034 TCGGTGTCAT
* * *
2044 GTTAGGGTTTAGGGTTTAGATTAATTAGTGTGTTTTAATTTATATATTAAATAATGTTTAGGGGT
1 GTTAGGGTTTAGGATTTAGATTAATTAGTGTGTTTTAATTTATATATTAAATAAGGTTTAAGGGT
*
2109 TAG-GGATTAGGGATTTGGGGTCGG
66 TAGTGG-TTAGGGATTAGGGGTCGG
*
2133 GTTAGGGTTTATGATTTAGATTAATTAGTGT-TTTTAATTTATATATTAAATAAGGTTTAAGGGT
1 GTTAGGGTTTAGGATTTAGATTAATTAGTGTGTTTTAATTTATATATTAAATAAGGTTTAAGGGT
*
2197 TAGTGGTTAGGGGTTAGGGGT
66 TAGTGGTTAGGGATTAGGGGT
2218 TTGGGGTTAA
Statistics
Matches: 78, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
88 47 0.60
89 31 0.40
ACGTcount: A:0.26, C:0.01, G:0.30, T:0.44
Consensus pattern (89 bp):
GTTAGGGTTTAGGATTTAGATTAATTAGTGTGTTTTAATTTATATATTAAATAAGGTTTAAGGGT
TAGTGGTTAGGGATTAGGGGTCGG
Found at i:2204 original size:7 final size:7
Alignment explanation
Indices: 2193--2226 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
2183 TAAGGTTTAA
2193 GGGTTAG
1 GGGTTAG
*
2200 TGGTTAG
1 GGGTTAG
2207 GGGTTAG
1 GGGTTAG
*
2214 GGGTTTG
1 GGGTTAG
2221 GGGTTA
1 GGGTTA
2227 AGAGTTAGTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.12, C:0.00, G:0.53, T:0.35
Consensus pattern (7 bp):
GGGTTAG
Found at i:3309 original size:146 final size:143
Alignment explanation
Indices: 3071--3360 Score: 424
Period size: 146 Copynumber: 2.0 Consensus size: 143
3061 ATGATTTAGC
*
3071 ATAGCAAAACAGTGTCATTTTATTCCAAATGAAATAAGTTTTTGCGGCGTTTTTTATAAAAACGC
1 ATAGCAAAACAGTGTCATTTTATTCCAAATAAAATAAGTTTTTGCGGCGTTTTTTATAAAAACGC
* * *
3136 CGCAAAAGATAAGCAATCGCGGCGTTTTTATAAAAAACGCCACAAAAAATAATTTTACTTTAAAA
66 CGCAAAAGATAAGCAATAGCGGAGTTTTTATAAAAAACGCCAC--AAAA-AA-TTTACTTAAAAA
3201 AAATAGCACCATTTTAT
127 AAATAGCACCATTTTAT
* *
3218 ATAGCAAAACAGTGTCGTTTTATTCCAAATAAAAT-ATTTTTTGCGGCG-TTTTTATGAAAAACG
1 ATAGCAAAACAGTGTCATTTTATTCCAAATAAAATAAGTTTTTGCGGCGTTTTTTAT-AAAAACG
* *
3281 CCGCAAAA-AGTAAGCAATAGCGGAGTTTTTGTTAAAAACGCCACAAAAAATTTACTTAAAAAAA
65 CCGCAAAAGA-TAAGCAATAGCGGAGTTTTTATAAAAAACGCCACAAAAAATTTACTTAAAAAAA
*
3345 ATAGCGCCATTTTAT
129 ATAGCACCATTTTAT
3360 A
1 A
3361 AAATCCCCTC
Statistics
Matches: 132, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
142 28 0.21
143 2 0.02
144 4 0.03
145 8 0.06
146 57 0.43
147 33 0.25
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (143 bp):
ATAGCAAAACAGTGTCATTTTATTCCAAATAAAATAAGTTTTTGCGGCGTTTTTTATAAAAACGC
CGCAAAAGATAAGCAATAGCGGAGTTTTTATAAAAAACGCCACAAAAAATTTACTTAAAAAAAAT
AGCACCATTTTAT
Found at i:3401 original size:22 final size:22
Alignment explanation
Indices: 3369--3434 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
3359 TAAAATCCCC
3369 TCCCCCC-AAAATCCCCAACTT
1 TCCCCCCTAAAATCCCCAACTT
* *
3390 TCCCCCCTAAAATCCCTAATTT
1 TCCCCCCTAAAATCCCCAACTT
* * *
3412 TCCCCCTTGAAACCCCCAACTT
1 TCCCCCCTAAAATCCCCAACTT
3434 T
1 T
3435 ACAAACATAC
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
21 7 0.19
22 30 0.81
ACGTcount: A:0.26, C:0.47, G:0.02, T:0.26
Consensus pattern (22 bp):
TCCCCCCTAAAATCCCCAACTT
Found at i:7041 original size:43 final size:43
Alignment explanation
Indices: 6992--7295 Score: 448
Period size: 43 Copynumber: 7.1 Consensus size: 43
6982 ATGTTTTAGT
* * *
6992 GGCGTTTTTGCGAGAAGCGCCGCTAAAGGTCGTGGTCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCGTGGTCTATAGC
** *
7035 GGCGTTTGTAAGAAAAGCGCCGCTAAAGGTCGTGGTCCATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCGTGGTCTATAGC
* *
7078 GGCGTTTGTGGGAAAAGCGTCGCTAAAGGGCGTGGTCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCGTGGTCTATAGC
** * *
7121 GGCGTTTGTAAGAAAAGCGCCGCTAAAGGTCGTGGTCCAAAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCGTGGTCTATAGC
*
7164 GGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCGTGGTCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCGTGGTCTATAGC
* *
7207 GGCGTTTGTGGGAAAAGCACCGCTAAAGGTCATGGTCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCGTGGTCTATAGC
* *
7250 GGCGTTTGTGGG-AAAGCGCCGCTAAAGGTCTTGGTCTTTAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCGTGGTCTATAGC
7292 GGCG
1 GGCG
7296 ATTTTTTCTA
Statistics
Matches: 234, Mismatches: 27, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
42 31 0.13
43 203 0.87
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.23
Consensus pattern (43 bp):
GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCGTGGTCTATAGC
Found at i:7419 original size:22 final size:22
Alignment explanation
Indices: 7392--7434 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
7382 TAGTGGCGTT
*
7392 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
*
7414 AAAAAGTGCCGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
7435 GTTTTGGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.26, G:0.21, T:0.12
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Done.