Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2728
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: 16331
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Found at i:1094 original size:22 final size:24
Alignment explanation
Indices: 1068--1113 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
1058 TGTCCATCTT
1068 TTTAATAGAATC-T-ATATATATA
1 TTTAATAGAATCTTAATATATATA
*
1090 TTTAATATAATCTTAATATATATA
1 TTTAATAGAATCTTAATATATATA
1114 AGACATCCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 11 0.52
23 1 0.05
24 9 0.43
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (24 bp):
TTTAATAGAATCTTAATATATATA
Found at i:4108 original size:18 final size:18
Alignment explanation
Indices: 4079--4156 Score: 120
Period size: 18 Copynumber: 4.3 Consensus size: 18
4069 GTCACGATCG
*
4079 ATATCGTCACTATCATCA
1 ATATCGTCACTAGCATCA
* *
4097 ATAGCTTCACTAGCATCA
1 ATATCGTCACTAGCATCA
4115 ATATCGTCACTAGCATCA
1 ATATCGTCACTAGCATCA
*
4133 ATATCGTCACTATCATCA
1 ATATCGTCACTAGCATCA
4151 ATATCG
1 ATATCG
4157 ATATCATCAA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 54 1.00
ACGTcount: A:0.33, C:0.27, G:0.09, T:0.31
Consensus pattern (18 bp):
ATATCGTCACTAGCATCA
Found at i:4126 original size:36 final size:36
Alignment explanation
Indices: 4079--4168 Score: 123
Period size: 36 Copynumber: 2.6 Consensus size: 36
4069 GTCACGATCG
*
4079 ATATCGTCACTATCATCAATAGCTTCACTAGCATCA
1 ATATCGTCACTATCATCAATAGCGTCACTAGCATCA
* * *
4115 ATATCGTCACTAGCATCAATATCGTCACTATCATCA
1 ATATCGTCACTATCATCAATAGCGTCACTAGCATCA
4151 ATATCG--A-TATCATCAATA
1 ATATCGTCACTATCATCAATA
4169 AGAAAACCTT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
33 10 0.20
34 1 0.02
36 38 0.78
ACGTcount: A:0.36, C:0.26, G:0.08, T:0.31
Consensus pattern (36 bp):
ATATCGTCACTATCATCAATAGCGTCACTAGCATCA
Found at i:4155 original size:9 final size:9
Alignment explanation
Indices: 4079--4155 Score: 55
Period size: 9 Copynumber: 8.6 Consensus size: 9
4069 GTCACGATCG
*
4079 ATATCGTCA
1 ATATCATCA
*
4088 CTATCATCA
1 ATATCATCA
* *
4097 ATAGCTTCA
1 ATATCATCA
* *
4106 CTAGCATCA
1 ATATCATCA
*
4115 ATATCGTCA
1 ATATCATCA
* *
4124 CTAGCATCA
1 ATATCATCA
*
4133 ATATCGTCA
1 ATATCATCA
*
4142 CTATCATCA
1 ATATCATCA
4151 ATATC
1 ATATC
4156 GATATCATCA
Statistics
Matches: 49, Mismatches: 19, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
9 49 1.00
ACGTcount: A:0.34, C:0.27, G:0.08, T:0.31
Consensus pattern (9 bp):
ATATCATCA
Found at i:4161 original size:15 final size:17
Alignment explanation
Indices: 4079--4168 Score: 94
Period size: 18 Copynumber: 5.2 Consensus size: 17
4069 GTCACGATCG
4079 ATATCGTCACTATCATCA
1 ATATCG-CACTATCATCA
* * *
4097 ATAGCTTCACTAGCATCA
1 ATATC-GCACTATCATCA
*
4115 ATATCGTCACTAGCATCA
1 ATATCG-CACTATCATCA
4133 ATATCGTCACTATCATCA
1 ATATCG-CACTATCATCA
4151 ATATCG-A-TATCATCA
1 ATATCGCACTATCATCA
4166 ATA
1 ATA
4169 AGAAAACCTT
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
15 11 0.17
16 1 0.02
18 52 0.81
ACGTcount: A:0.36, C:0.26, G:0.08, T:0.31
Consensus pattern (17 bp):
ATATCGCACTATCATCA
Found at i:6564 original size:21 final size:21
Alignment explanation
Indices: 6534--6622 Score: 90
Period size: 21 Copynumber: 4.1 Consensus size: 21
6524 CTCACAAAGA
* *
6534 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTAGAC
* *
6554 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTAGAC
*
6575 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTAGAC
*
6596 AAAAAGAAACGAAGTGACTTAGAC
1 AAAAAG--A-GAAGTAACTTAGAC
6620 AAA
1 AAA
6623 TCTTTTTTGT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
20 6 0.10
21 36 0.62
23 1 0.02
24 15 0.26
ACGTcount: A:0.54, C:0.10, G:0.24, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTAGAC
Found at i:6615 original size:24 final size:21
Alignment explanation
Indices: 6534--6602 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
6524 CTCACAAAGA
* * *
6534 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTGGAC
*
6554 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
6575 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
6596 AAAAAGA
1 AAAAAGA
6603 AACGAAGTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 6 0.14
21 37 0.86
ACGTcount: A:0.55, C:0.09, G:0.25, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTGGAC
Found at i:10796 original size:14 final size:14
Alignment explanation
Indices: 10777--10807 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
10767 TACAATATAT
10777 ATAAGAATTATACG
1 ATAAGAATTATACG
10791 ATAAGAATTATACG
1 ATAAGAATTATACG
10805 ATA
1 ATA
10808 TATATCCATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.52, C:0.06, G:0.13, T:0.29
Consensus pattern (14 bp):
ATAAGAATTATACG
Found at i:11437 original size:14 final size:14
Alignment explanation
Indices: 11420--11472 Score: 70
Period size: 14 Copynumber: 3.6 Consensus size: 14
11410 ATATTTATAT
11420 TAAATATTATTAAA
1 TAAATATTATTAAA
11434 TAAATATTATTAAA
1 TAAATATTATTAAA
* *
11448 TTATTATTATTAAAA
1 TAAATATTATT-AAA
11463 TGAAATATTA
1 T-AAATATTA
11473 AAAAAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
14 23 0.70
15 4 0.12
16 6 0.18
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (14 bp):
TAAATATTATTAAA
Found at i:13142 original size:19 final size:19
Alignment explanation
Indices: 13097--13147 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 19
13087 CAGTTCTAAA
13097 TTCTATAAGGAAATTCTAT
1 TTCTATAAGGAAATTCTAT
13116 TTC--T----AAATTCTAT
1 TTCTATAAGGAAATTCTAT
13129 TTCTATAAGGAAATTCTAT
1 TTCTATAAGGAAATTCTAT
13148 AAGGTTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 12
0.68 0.00 0.32
Matches are distributed among these distances:
13 12 0.46
15 1 0.04
17 1 0.04
19 12 0.46
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.45
Consensus pattern (19 bp):
TTCTATAAGGAAATTCTAT
Done.