Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3119
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: 15483
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.31
Found at i:897 original size:13 final size:13
Alignment explanation
Indices: 879--904 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
869 CAGGGCCGGA
879 GACACACTCGTGT
1 GACACACTCGTGT
892 GACACACTCGTGT
1 GACACACTCGTGT
905 CTTGGCCGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.31, G:0.23, T:0.23
Consensus pattern (13 bp):
GACACACTCGTGT
Found at i:1361 original size:22 final size:24
Alignment explanation
Indices: 1327--1370 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
1317 CATCATAATA
*
1327 TCATCCATTTCAT-ATCACAAAAC
1 TCATCCATATCATCATCACAAAAC
*
1350 TCAT-CATATCATCATCTCAAA
1 TCATCCATATCATCATCACAAA
1371 CCAAACCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.39, C:0.30, G:0.00, T:0.32
Consensus pattern (24 bp):
TCATCCATATCATCATCACAAAAC
Found at i:5430 original size:39 final size:39
Alignment explanation
Indices: 5338--5593 Score: 372
Period size: 40 Copynumber: 6.5 Consensus size: 39
5328 TGGATGATAA
* * *
5338 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TT
5378 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATT
5417 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAGTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TT
5457 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATT
5496 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT-T
* * * *
5536 CCGGGCTATGTCCCGAAGGTATTCGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTAT-T
* *
5576 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
5594 TACTTGGCTT
Statistics
Matches: 203, Mismatches: 10, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
39 94 0.46
40 109 0.54
ACGTcount: A:0.21, C:0.23, G:0.29, T:0.26
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATT
Found at i:5469 original size:79 final size:79
Alignment explanation
Indices: 5338--5593 Score: 383
Period size: 79 Copynumber: 3.2 Consensus size: 79
5328 TGGATGATAA
* * *
5338 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGTTCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAGTTCCGGGCTAAGTCCCGAAGGCATTTG
5403 TGCGAGTTACTATT
66 TGCGAGTTACTATT
5417 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAGTTCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAGTTCCGGGCTAAGTCCCGAAGGCATTTG
5482 TGCGAGTTACTATT
66 TGCGAGTTACTATT
* * *
5496 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TATCCGGGCTATGTCCCGAAGGTATTC
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAGT-TCCGGGCTAAGTCCCGAAGGCATTT
*
5560 GAGCGAG-TAGCTATAT
65 GTGCGAGTTA-CTAT-T
* *
5576 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
5594 TACTTGGCTT
Statistics
Matches: 165, Mismatches: 9, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
78 3 0.02
79 159 0.96
80 3 0.02
ACGTcount: A:0.21, C:0.23, G:0.29, T:0.26
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAGTTCCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGTTACTATT
Found at i:13708 original size:40 final size:39
Alignment explanation
Indices: 13653--13909 Score: 315
Period size: 40 Copynumber: 6.5 Consensus size: 39
13643 TGGATGATAA
*
13653 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGT-ACTA-TAT
*
13693 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTACTATAT
*
13732 CCGGGCTAAGTCCTGAAGGCATTTGTG-TGAGCTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCT-AG-TACTATAT
13772 CCGGGCTAAGTCCCGAAGGCATTTGTG-TGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCT-AG-TACTATAT
* *
13812 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TACTATAT
* * * *
13852 CCGGGCTATGTCCCGAAGGCATTCGAGCAAGTAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTA-CTATAT
* *
13892 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
13910 TACTTGGCTT
Statistics
Matches: 197, Mismatches: 15, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
38 1 0.01
39 48 0.24
40 148 0.75
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTACTATAT
Found at i:13848 original size:80 final size:79
Alignment explanation
Indices: 13653--13909 Score: 347
Period size: 79 Copynumber: 3.2 Consensus size: 79
13643 TGGATGATAA
* * *
13653 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-TCCGGGCTAAGTCCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TATCCGGGCTAAGTCCCGAAGGCATTT
13717 GTGCGAGTACTATAT
65 GTGCGAGTACTATAT
* * *
13732 CCGGGCTAAGTCCTGAAGGCATTTGTGTGAGCTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
*
13797 TGTGAGTTACTATAT
66 TGCGAG-TACTATAT
* * *
13812 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATATCCGGGCTATGTCCCGAAGGCATTCG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
* *
13877 AGCAAGTAGCTATAT
66 TGCGAGTA-CTATAT
* *
13892 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
13910 TACTTGGCTT
Statistics
Matches: 157, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
78 1 0.01
79 78 0.50
80 78 0.50
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGTACTATAT
Found at i:13905 original size:119 final size:119
Alignment explanation
Indices: 13653--13909 Score: 342
Period size: 119 Copynumber: 2.2 Consensus size: 119
13643 TGGATGATAA
* *
13653 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGTTCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAATCCCGAAGGCATTTGCGCTAGTGACTAGTTCCGGGCTAAGTCCCGAAGGCATTGG
* * * **
13718 TGCGAGTACTATATCCGGGCTAAGTCCTGAAGGCATTTGTGTGAGCTACTATAT
66 TGCGAGTACTATATCCGGGCTAAGTCCCGAAGGCATTCGAGCAAGCTACTATAT
* * *
13772 CCGGGCTAAGTCCCGAAGGCATTTGTG-TGAGTTACTA-TATCCGGGCTAAGTCCCGAAGGCATT
1 CCGGGCTAAATCCCGAAGGCATTTGCGCT-AGTGACTAGT-TCCGGGCTAAGTCCCGAAGGCATT
*
13835 GGTGCGAGTTACTATATCCGGGCTATGTCCCGAAGGCATTCGAGCAAG-TAGCTATAT
64 GGTGCGAG-TACTATATCCGGGCTAAGTCCCGAAGGCATTCGAGCAAGCTA-CTATAT
*
13892 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAATCCCGAAGG
13910 TACTTGGCTT
Statistics
Matches: 123, Mismatches: 11, Indels: 8
0.87 0.08 0.06
Matches are distributed among these distances:
118 2 0.02
119 80 0.65
120 41 0.33
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (119 bp):
CCGGGCTAAATCCCGAAGGCATTTGCGCTAGTGACTAGTTCCGGGCTAAGTCCCGAAGGCATTGG
TGCGAGTACTATATCCGGGCTAAGTCCCGAAGGCATTCGAGCAAGCTACTATAT
Done.