Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3695
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: 42920
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:3156 original size:20 final size:20
Alignment explanation
Indices: 3128--3165 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3118 TATTTTCCAC
*
3128 TAAATCATTTTACAGAAAAG
1 TAAAACATTTTACAGAAAAG
*
3148 TAAAACATTTTCCAGAAA
1 TAAAACATTTTACAGAAA
3166 TCATTTTACG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.13, G:0.08, T:0.29
Consensus pattern (20 bp):
TAAAACATTTTACAGAAAAG
Found at i:3170 original size:34 final size:35
Alignment explanation
Indices: 3114--3180 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
3104 CAAACACCAG
* *
3114 AAAATATTTTCCACTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCACGAAATCATTTTACAGAAAAGT
*
3149 AAAACATTTTCCA-GAAATCATTTTACGGAAAA
1 AAAACATTTTCCACGAAATCATTTTACAGAAAA
3181 CATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCACGAAATCATTTTACAGAAAAGT
Found at i:3172 original size:14 final size:14
Alignment explanation
Indices: 3149--3188 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
3139 ACAGAAAAGT
*
3149 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
3163 AAATCATTTTACGG
1 AAAACATTTTACAG
3177 AAAACATTTTAC
1 AAAACATTTTAC
3189 TGCCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:3864 original size:40 final size:40
Alignment explanation
Indices: 3820--3903 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 40
3810 AAGCATTTAA
3820 TTAAT-ATTTTAAAGTTTTAAAAAATAA-TAATAAATATTTT
1 TTAATAATTTTAAA-TTTTAAAAAATAAGTAATAAAT-TTTT
* *
3860 TTAATAATTTTAAATTTTAAAAAATAAGTTATATATTTTT
1 TTAATAATTTTAAATTTTAAAAAATAAGTAATAAATTTTT
3900 TTAA
1 TTAA
3904 AACCTAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
40 26 0.65
41 14 0.35
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (40 bp):
TTAATAATTTTAAATTTTAAAAAATAAGTAATAAATTTTT
Found at i:4357 original size:17 final size:17
Alignment explanation
Indices: 4316--4358 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
4306 AATTCAAAAT
* * *
4316 AATTTTTAAATTTTTAA
1 AATTTATAAAATTTCAA
4333 ATATTTATAAAATTTCAA
1 A-ATTTATAAAATTTCAA
4351 AATTTATA
1 AATTTATA
4359 TTTTAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
AATTTATAAAATTTCAA
Found at i:4377 original size:25 final size:24
Alignment explanation
Indices: 4336--4384 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
4326 TTTTTAAATA
* * *
4336 TTTATAAAATTTCAAAATTTATAT
1 TTTAAAAAATTTAAAAATATATAT
4360 TTTAAAAAATTCTAAAAATATATAT
1 TTTAAAAAATT-TAAAAATATATAT
4385 AAATAAAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTAAAAAATTTAAAAATATATAT
Found at i:12551 original size:26 final size:27
Alignment explanation
Indices: 12522--12575 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
12512 TATCTACTTT
12522 CTTTAATTTGCTTCATTCATGAC-ATG
1 CTTTAATTTGCTTCATTCATGACTATG
**
12548 CTTTTCTTTGCTTCATTCATGACTATG
1 CTTTAATTTGCTTCATTCATGACTATG
12575 C
1 C
12576 AATGATTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 21 0.84
27 4 0.16
ACGTcount: A:0.19, C:0.22, G:0.11, T:0.48
Consensus pattern (27 bp):
CTTTAATTTGCTTCATTCATGACTATG
Found at i:27046 original size:38 final size:38
Alignment explanation
Indices: 26999--27094 Score: 122
Period size: 38 Copynumber: 2.6 Consensus size: 38
26989 AATAAACCAT
* * **
26999 AGTTATAAGGTAAATTTGCTATAATGCTTTTTGCTGCA
1 AGTTTTAAGGTAAATTTGCTATAATGCTGTCCGCTGCA
*
27037 AGTTTTAAGGTCAATTTGCTATAATGCTGTCCGCTGCA
1 AGTTTTAAGGTAAATTTGCTATAATGCTGTCCGCTGCA
**
27075 AGTTTTATTG-AAATTTGCTA
1 AGTTTTAAGGTAAATTTGCTA
27095 AGATGTTTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
37 9 0.18
38 41 0.82
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (38 bp):
AGTTTTAAGGTAAATTTGCTATAATGCTGTCCGCTGCA
Found at i:27629 original size:40 final size:40
Alignment explanation
Indices: 27585--27668 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 40
27575 AAGCATTTAA
27585 TTAAT-ATTTTAAAGTTTTAAAAAATAA-TAATAAATATTTT
1 TTAATAATTTTAAA-TTTTAAAAAATAAGTAATAAAT-TTTT
* *
27625 TTAATAATTTTAAATTTTAAAAAATAAGTTATATATTTTT
1 TTAATAATTTTAAATTTTAAAAAATAAGTAATAAATTTTT
27665 TTAA
1 TTAA
27669 AACCTAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
40 26 0.65
41 14 0.35
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (40 bp):
TTAATAATTTTAAATTTTAAAAAATAAGTAATAAATTTTT
Found at i:28122 original size:17 final size:17
Alignment explanation
Indices: 28081--28123 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
28071 AATTCAAAAT
* * *
28081 AATTTTTAAATTTTTAA
1 AATTTATAAAATTTCAA
28098 ATATTTATAAAATTTCAA
1 A-ATTTATAAAATTTCAA
28116 AATTTATA
1 AATTTATA
28124 TTTTAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
AATTTATAAAATTTCAA
Found at i:28142 original size:25 final size:24
Alignment explanation
Indices: 28101--28149 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
28091 TTTTTAAATA
* * *
28101 TTTATAAAATTTCAAAATTTATAT
1 TTTAAAAAATTTAAAAATATATAT
28125 TTTAAAAAATTCTAAAAATATATAT
1 TTTAAAAAATT-TAAAAATATATAT
28150 AAATAAAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTAAAAAATTTAAAAATATATAT
Found at i:34990 original size:26 final size:28
Alignment explanation
Indices: 34955--35007 Score: 92
Period size: 26 Copynumber: 2.0 Consensus size: 28
34945 GGTAATTTTC
34955 TTTCATTTGCTTCATTCATGAC-ATGCT
1 TTTCATTTGCTTCATTCATGACTATGCT
34982 TTTC-TTTGCTTCATTCATGACTATGC
1 TTTCATTTGCTTCATTCATGACTATGC
35008 AATGATTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 17 0.68
27 8 0.32
ACGTcount: A:0.17, C:0.23, G:0.11, T:0.49
Consensus pattern (28 bp):
TTTCATTTGCTTCATTCATGACTATGCT
Done.