Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold459
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: 19810
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.33
Found at i:255 original size:15 final size:15
Alignment explanation
Indices: 235--264 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
225 TATTGTAAGA
235 AATTTTTAACATTAT
1 AATTTTTAACATTAT
250 AATTTTTAACATTAT
1 AATTTTTAACATTAT
265 TGTAAGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (15 bp):
AATTTTTAACATTAT
Found at i:1742 original size:40 final size:39
Alignment explanation
Indices: 1679--1764 Score: 118
Period size: 40 Copynumber: 2.2 Consensus size: 39
1669 TAACGACTTA
**
1679 TCGGCTAAAATGGCACTTAGTGTGCGGTTCGAAATAGCT
1 TCGGCTAAAATGGCACTTAGTGTGCAATTCGAAATAGCT
* * *
1718 TCGGCTAAAAGTGGCACTTGGTGTGCAATTTGAGATAGCT
1 TCGGCTAAAA-TGGCACTTAGTGTGCAATTCGAAATAGCT
1758 TCGGCTA
1 TCGGCTA
1765 TATATATATA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 10 0.24
40 31 0.76
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.29
Consensus pattern (39 bp):
TCGGCTAAAATGGCACTTAGTGTGCAATTCGAAATAGCT
Found at i:4562 original size:50 final size:50
Alignment explanation
Indices: 4498--4632 Score: 148
Period size: 50 Copynumber: 2.7 Consensus size: 50
4488 CAATACATGT
* *
4498 GAGCTAGTGTAAGACCATGTTTGGGACATGGCATCAG-CAC-AAAAAGAGGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCACGAAAAA-A-GA
* * * * * * *
4548 GAGCCAGTGTAAGACCATGTCTGGGATATGACGTCGGCCTCGATATAAGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCACGAAAAAAGA
*
4598 GAGTCAGTGTAAGACCATGTCTGGGACATGGCATC
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATC
4633 GACTCGATAT
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
50 64 0.91
51 3 0.04
52 3 0.04
ACGTcount: A:0.30, C:0.19, G:0.30, T:0.21
Consensus pattern (50 bp):
GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCACGAAAAAAGA
Found at i:4732 original size:43 final size:43
Alignment explanation
Indices: 4605--4748 Score: 132
Period size: 43 Copynumber: 3.3 Consensus size: 43
4595 AGAGAGTCAG
4605 TGTAAGACCATGTCTGGGACA-TGGCATCGACTCGATATGTGATTAAA
1 TGTAAGACCATGTCTGGGACAGTGG---C-A-TCGATATGTGATTAAA
* * * ***
4652 TGTAATACCATGTCTGGGACATTGGCATTG-TATTGTGATTTTG
1 TGTAAGACCATGTCTGGGACAGTGGCATCGATA-TGTGATTAAA
* *
4695 TGTAAGACCCTGTGTGGGACAGTGGCATCGATATGTGA-TAACA
1 TGTAAGACCATGTCTGGGACAGTGGCATCGATATGTGATTAA-A
4738 TGTAAGACCAT
1 TGTAAGACCAT
4749 ATCTAGGATA
Statistics
Matches: 79, Mismatches: 14, Indels: 12
0.75 0.13 0.11
Matches are distributed among these distances:
42 3 0.04
43 49 0.62
44 3 0.04
45 1 0.01
47 20 0.25
48 3 0.04
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.31
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACAGTGGCATCGATATGTGATTAAA
Found at i:8747 original size:40 final size:39
Alignment explanation
Indices: 8669--8747 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 39
8659 TTAATGACTT
**
8669 ATCAGCTAAAATGGCACTTAGTGTGCGGTTCGAAATAGC
1 ATCAGCTAAAATGGCACTTAGTGTGCAATTCGAAATAGC
* * *
8708 ATCAGCTAAAAGTGGCACTTGGTGTGCAATTTGAGATAGC
1 ATCAGCTAAAA-TGGCACTTAGTGTGCAATTCGAAATAGC
8748 TTCGGCTATA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
39 11 0.32
40 23 0.68
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (39 bp):
ATCAGCTAAAATGGCACTTAGTGTGCAATTCGAAATAGC
Found at i:8828 original size:40 final size:40
Alignment explanation
Indices: 8773--8853 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
8763 GTAAATGGAA
8773 CTGTGACAGCCCTAAATTGACCCTAGACGGGAAGTGGTTT
1 CTGTGACAGCCCTAAATTGACCCTAGACGGGAAGTGGTTT
*
8813 CTGTGACAGCCCTAAATTGACCCTAGTCGGGAAGTGGTTT
1 CTGTGACAGCCCTAAATTGACCCTAGACGGGAAGTGGTTT
8853 C
1 C
8854 GGGGTCGCTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
CTGTGACAGCCCTAAATTGACCCTAGACGGGAAGTGGTTT
Found at i:10491 original size:40 final size:40
Alignment explanation
Indices: 10385--10560 Score: 279
Period size: 40 Copynumber: 4.5 Consensus size: 40
10375 CGGATGACAA
10385 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
10425 CCGGGCTAAGT--CGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
10463 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* **
10503 CCGGGCTAAGTCCCGAAGGCAGTTGAACGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
10543 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
10561 TACTGGTTTG
Statistics
Matches: 129, Mismatches: 4, Indels: 7
0.92 0.03 0.05
Matches are distributed among these distances:
38 38 0.29
39 17 0.13
40 74 0.57
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:10514 original size:78 final size:79
Alignment explanation
Indices: 10385--10560 Score: 277
Period size: 78 Copynumber: 2.2 Consensus size: 79
10375 CGGATGACAA
* *
10385 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGT-CGAAGGCATTTGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCGAAGGCAGTTGA
*
10449 GCGAGTTA-CTATAT
66 ACGAG-TAGCTATAT
10463 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCAGTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGT-CCGAAGGCAGTTG
10528 AACGAGTAGCTATAT
65 AACGAGTAGCTATAT
*
10543 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
10561 TACTGGTTTG
Statistics
Matches: 91, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
78 51 0.56
79 17 0.19
80 23 0.25
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.24
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCGAAGGCAGTTGA
ACGAGTAGCTATAT
Found at i:18347 original size:40 final size:40
Alignment explanation
Indices: 18292--18546 Score: 412
Period size: 40 Copynumber: 6.5 Consensus size: 40
18282 CGGATGATAA
18292 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
18332 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
18372 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
18412 CCGGGCTAAGT--CGAAGGCATTTGCGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
18450 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* **
18490 CCGGGCTAAGT-CCGAAGGCAGTTGAACGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
18529 CC-GGCTAAATCTCGAAGG
1 CCGGGCTAAGTCCCGAAGG
18547 TACTGGTTTG
Statistics
Matches: 204, Mismatches: 7, Indels: 9
0.93 0.03 0.04
Matches are distributed among these distances:
38 46 0.23
39 30 0.15
40 128 0.63
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:18474 original size:78 final size:79
Alignment explanation
Indices: 18292--18546 Score: 417
Period size: 78 Copynumber: 3.2 Consensus size: 79
18282 CGGATGATAA
18292 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGT-CCGAAGGCATTTG
*
18357 TGCGAGTTACTATAT
65 AGCGAGTTACTATAT
*
18372 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGT-CGAAGGCATTTGC
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCGAAGGCATTTGA
18436 GCGAGTTACTATAT
66 GCGAGTTACTATAT
*
18450 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCGAAGGCAGTTGA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCGAAGGCATTTGA
*
18515 ACGAG-TAGCTATAT
66 GCGAGTTA-CTATAT
* *
18529 CC-GGCTAAATCTCGAAGG
1 CCGGGCTAAGTCCCGAAGG
18547 TACTGGTTTG
Statistics
Matches: 167, Mismatches: 6, Indels: 6
0.93 0.03 0.03
Matches are distributed among these distances:
78 93 0.56
79 23 0.14
80 51 0.31
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCGAAGGCATTTGA
GCGAGTTACTATAT
Found at i:18544 original size:118 final size:120
Alignment explanation
Indices: 18292--18546 Score: 403
Period size: 118 Copynumber: 2.2 Consensus size: 120
18282 CGGATGATAA
* * *
18292 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAATCTCGAAGGCATTTGCGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
* **
18357 TGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
66 TGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCAGTTGAACGAGTTACTATAT
*
18412 CCGGGCT-AA-GTCGAAGGCATTTGCGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAATCTCGAAGGCATTTGCGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
18475 TGCGAGTTACTATATCCGGGCTAAGT-CCGAAGGCAGTTGAACGAG-TAGCTATAT
66 TGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCAGTTGAACGAGTTA-CTATAT
18529 CC-GGCTAAATCTCGAAGG
1 CCGGGCTAAATCTCGAAGG
18547 TACTGGTTTG
Statistics
Matches: 124, Mismatches: 8, Indels: 8
0.89 0.06 0.06
Matches are distributed among these distances:
116 6 0.05
117 26 0.21
118 84 0.68
119 1 0.01
120 7 0.06
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (120 bp):
CCGGGCTAAATCTCGAAGGCATTTGCGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCAGTTGAACGAGTTACTATAT
Done.