Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1471
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: 32164
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Found at i:7261 original size:27 final size:28
Alignment explanation
Indices: 7177--7274 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
7167 CATGAGATTG
* * * *
7177 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
7206 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
7234 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
7261 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
7275 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:7285 original size:27 final size:27
Alignment explanation
Indices: 7205--7287 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
7195 TAAATTGTAC
* *
7205 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
7233 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
7260 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
7287 A
1 A
7288 TTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:7288 original size:29 final size:27
Alignment explanation
Indices: 7177--7288 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
7167 CATGAGATTG
** * *
7177 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
7206 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
7234 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
7261 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
7289 TTTTGAATCA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 23 0.32
28 28 0.39
29 21 0.29
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:9393 original size:39 final size:39
Alignment explanation
Indices: 9350--9478 Score: 125
Period size: 39 Copynumber: 3.3 Consensus size: 39
9340 TAGAATTTAA
* *
9350 ACATACTTAAAAGCATGTATTAAAGATGTCCAAACTATG
1 ACATAATTAAAAACATGTATTAAAGATGTCCAAACTATG
* * * * **
9389 ACATAATTAAAAACTTTTATTAATGATGTTCAAGTTATG
1 ACATAATTAAAAACATGTATTAAAGATGTCCAAACTATG
* * * * *
9428 ACATAATTAAAAAC-TCTTATTAATGATGTTCAGATTATG
1 ACATAATTAAAAACAT-GTATTAAAGATGTCCAAACTATG
9467 ACATAATTAAAA
1 ACATAATTAAAA
9479 CTCATATTAA
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
38 1 0.01
39 78 0.99
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.35
Consensus pattern (39 bp):
ACATAATTAAAAACATGTATTAAAGATGTCCAAACTATG
Found at i:9488 original size:38 final size:39
Alignment explanation
Indices: 9367--9515 Score: 210
Period size: 39 Copynumber: 3.8 Consensus size: 39
9357 TAAAAGCATG
* * * *
9367 TATTAAAGATGTCCAAACTATGACATAATTAAAAACTTT
1 TATTAATGATGTTCAAATTATGACATAATTAAAAACTCT
*
9406 TATTAATGATGTTCAAGTTATGACATAATTAAAAACTCT
1 TATTAATGATGTTCAAATTATGACATAATTAAAAACTCT
* *
9445 TATTAATGATGTTCAGATTATGACATAATT-AAAACTCA
1 TATTAATGATGTTCAAATTATGACATAATTAAAAACTCT
* *
9483 TATTAATGATGTTAAAATTATGATATAATTAAA
1 TATTAATGATGTTCAAATTATGACATAATTAAA
9516 GACTTAAAAC
Statistics
Matches: 98, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
38 34 0.35
39 64 0.65
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (39 bp):
TATTAATGATGTTCAAATTATGACATAATTAAAAACTCT
Found at i:9514 original size:77 final size:78
Alignment explanation
Indices: 9367--9515 Score: 210
Period size: 77 Copynumber: 1.9 Consensus size: 78
9357 TAAAAGCATG
** * *
9367 TATTAAAGATGTCCAAACTATGACATAATTAAAAACTTTTATTAATGATGTTCAAGTTATGACAT
1 TATTAAAGATGTCCAAACTATGACATAATTAAAAACTCATATTAATGATGTTAAAATTATGACAT
9432 AATTAAAAACTCT
66 AATTAAAAACTCT
* * * * *
9445 TATTAATGATGTTCAGATTATGACATAATT-AAAACTCATATTAATGATGTTAAAATTATGATAT
1 TATTAAAGATGTCCAAACTATGACATAATTAAAAACTCATATTAATGATGTTAAAATTATGACAT
9509 AATTAAA
66 AATTAAA
9516 GACTTAAAAC
Statistics
Matches: 62, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
77 36 0.58
78 26 0.42
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (78 bp):
TATTAAAGATGTCCAAACTATGACATAATTAAAAACTCATATTAATGATGTTAAAATTATGACAT
AATTAAAAACTCT
Found at i:10207 original size:18 final size:20
Alignment explanation
Indices: 10159--10207 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 20
10149 AAAATAAGTT
10159 AAAAATAAAAGAAATTGAGAG
1 AAAAA-AAAAGAAATTGAGAG
10180 AAGAAAAAAAGAAA-TGAGAG
1 AA-AAAAAAAGAAATTGAGAG
10200 AAAAAAAA
1 AAAAAAAA
10208 TTGAAAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.22
20 8 0.30
21 10 0.37
22 3 0.11
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.08
Consensus pattern (20 bp):
AAAAAAAAAGAAATTGAGAG
Found at i:10213 original size:20 final size:21
Alignment explanation
Indices: 10165--10207 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
10155 AGTTAAAAAT
10165 AAAAGAAATTGAGAGAAGAAA
1 AAAAGAAATTGAGAGAAGAAA
10186 AAAAGAAA-TGAGAGAA-AAA
1 AAAAGAAATTGAGAGAAGAAA
10205 AAA
1 AAA
10208 TTGAAAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.27
20 8 0.36
21 8 0.36
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.07
Consensus pattern (21 bp):
AAAAGAAATTGAGAGAAGAAA
Found at i:12203 original size:50 final size:52
Alignment explanation
Indices: 12146--12277 Score: 189
Period size: 50 Copynumber: 2.6 Consensus size: 52
12136 ATGTGTTTTG
*
12146 CATTAAATAAAGTCATGCATTATGTAACTCTCATGTTAGTT-AAGTTTA-CAT
1 CATTAAATTAAGTCATGCATTATGTAACTCTCATGTTAGTTAAAG-TTAGCAT
* * *
12197 CA-TAAATTATGACATGCTTTATGTAACTCTCATGTTAGTTAAAGTTAGCAT
1 CATTAAATTAAGTCATGCATTATGTAACTCTCATGTTAGTTAAAGTTAGCAT
*
12248 CATTAAATTAAGTCATGCATTAAGTAACTC
1 CATTAAATTAAGTCATGCATTATGTAACTC
12278 ATCTATTCAT
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
50 37 0.53
51 10 0.14
52 23 0.33
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (52 bp):
CATTAAATTAAGTCATGCATTATGTAACTCTCATGTTAGTTAAAGTTAGCAT
Found at i:16546 original size:40 final size:40
Alignment explanation
Indices: 16482--16739 Score: 396
Period size: 40 Copynumber: 6.5 Consensus size: 40
16472 CGGATGATAA
16482 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * * *
16522 CCGGGCTAAGTCCCAAAGGAATTTGTGTGAGTTA-TGATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAT
16562 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
16602 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACGATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
16642 CCGGGCTAAGTCCCAAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
16682 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
16722 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
16740 TACTTGGGTT
Statistics
Matches: 199, Mismatches: 16, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
39 17 0.09
40 181 0.91
41 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:22489 original size:27 final size:27
Alignment explanation
Indices: 22317--22489 Score: 211
Period size: 27 Copynumber: 6.4 Consensus size: 27
22307 TGGATAAGTT
* * *
22317 GTAGAATTACTGAAATTCCCCTGTAGG
1 GTAGAATTACCGAAATACCCTTGTAGG
** *
22344 GTAGAATTATTGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCTTGTAGG
**
22371 GTAGAATTACTAAAATACCCTTGTAGG
1 GTAGAATTACCGAAATACCCTTGTAGG
* *
22398 ATAGAATTACCGAAATACTCTTGTAGG
1 GTAGAATTACCGAAATACCCTTGTAGG
* *
22425 GTAGAAATACCGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCTTGTAGG
* *
22452 GTAGAATTACCGAGATACCCTTGTGGG
1 GTAGAATTACCGAAATACCCTTGTAGG
*
22479 GTAAAATTACC
1 GTAGAATTACC
22490 ATTTTGCCCC
Statistics
Matches: 128, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 128 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.27
Consensus pattern (27 bp):
GTAGAATTACCGAAATACCCTTGTAGG
Found at i:29854 original size:27 final size:27
Alignment explanation
Indices: 29814--29985 Score: 211
Period size: 27 Copynumber: 6.4 Consensus size: 27
29804 TGGATAAGTT
* *
29814 GTAGAATTATCGAAATTCCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
*
29841 GTAGAATTACCGAAATTCCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
**
29868 GTAGAATTATTGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* * *
29895 GTAGAATTACAGAAATACCCTTATAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* * *
29922 GTAGAAATACCGAAATAACCCTATAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* * *
29949 GTAGAATTACCGAGATACCCTTGTGGG
1 GTAGAATTACCGAAATACCCCTGTAGG
29976 GTA-AATTACC
1 GTAGAATTACC
29986 ATTTTGCCCC
Statistics
Matches: 127, Mismatches: 18, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
26 7 0.06
27 120 0.94
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (27 bp):
GTAGAATTACCGAAATACCCCTGTAGG
Done.