Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1132
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: 10991
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.30
Found at i:962 original size:39 final size:40
Alignment explanation
Indices: 814--1029 Score: 289
Period size: 40 Copynumber: 5.5 Consensus size: 40
804 AAGCCAAGTA
* * * * *
814 CCTTCGGGATTTA-ACCGGATATAGCT-ACTTGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
853 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
893 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
933 CCTTCGGGACTTAG-CCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
972 -CTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
1011 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
1030 TTATCATCCA
Statistics
Matches: 161, Mismatches: 11, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
38 14 0.09
39 57 0.35
40 90 0.56
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:1010 original size:78 final size:79
Alignment explanation
Indices: 814--1026 Score: 281
Period size: 78 Copynumber: 2.7 Consensus size: 79
804 AAGCCAAGTA
* * * * * *
814 CCTTCGGGATTTA-ACCGGATATAGCT-ACTTGCTCGAATGCCTTCGGGACATAGCCCGGATATA
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTAGCACAAATGCCTTCGGGACTTAG-CCGGATATA
*
877 GTAACTCGCACCAATG
64 GTAACTCGCACAAATG
*
893 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCGGATATAGT
1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCGGATATAGT
958 AACTCGCACAAATG
66 AACTCGCACAAATG
* *
972 -CTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATGCCTTCGGGACTTAGCC
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTAGCACAAATGCCTTCGGGACTTAGCC
1027 CGGTTATCAT
Statistics
Matches: 121, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
77 1 0.01
78 50 0.41
79 37 0.31
80 33 0.27
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.23
Consensus pattern (79 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCGGATATAGT
AACTCGCACAAATG
Found at i:7977 original size:16 final size:17
Alignment explanation
Indices: 7952--7985 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
7942 TTCGATTACA
*
7952 TAATTTATT-CACTATT
1 TAATTCATTCCACTATT
7968 TAATTCATTCCACTATT
1 TAATTCATTCCACTATT
7985 T
1 T
7986 TTAGTGATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.29, C:0.18, G:0.00, T:0.53
Consensus pattern (17 bp):
TAATTCATTCCACTATT
Found at i:8829 original size:40 final size:40
Alignment explanation
Indices: 8725--8938 Score: 280
Period size: 40 Copynumber: 5.5 Consensus size: 40
8715 CAGCCAAGTA
* * * *
8725 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
8764 CCTTC-GGACATAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
8803 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
8843 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
8883 CCTTC-GGACTTAGCCCGGA-ACTAGTCACTAG--TAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
8920 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
8939 TTATCATCCA
Statistics
Matches: 160, Mismatches: 10, Indels: 11
0.88 0.06 0.06
Matches are distributed among these distances:
37 10 0.06
38 20 0.12
39 53 0.33
40 77 0.48
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:8892 original size:79 final size:78
Alignment explanation
Indices: 8725--8938 Score: 276
Period size: 79 Copynumber: 2.7 Consensus size: 78
8715 CAGCCAAGTA
* * * *
8725 CCTTCGGGATTTA-ACCGGATATAGCTACTCGCTCGAATGCCTTC-GGACATAGCCCGGATATAG
1 CCTTCGGGACTTAGCCCGGATATAG-TACTCGC-CAAATGCCTTCGGGACTTAGCCCGGATATAG
*
8788 TAACTCGCACCAATG
64 TAACTCGCACAAATG
8803 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
1 CCTTCGGGACTTAGCCCGGATATAGT-ACTCGC-CAAATGCCTTCGGGACTTAGCCCGGATATAG
8868 TAACTCGCACAAATG
64 TAACTCGCACAAATG
* *
8883 CCTTC-GGACTTAGCCCGGA-ACTAGTCACTAG-TAAATGCCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGGATA-TAGT-ACTCGCCAAATGCCTTCGGGACTTAGCCCGG
8939 TTATCATCCA
Statistics
Matches: 123, Mismatches: 9, Indels: 9
0.87 0.06 0.06
Matches are distributed among these distances:
77 24 0.20
78 14 0.11
79 48 0.39
80 37 0.30
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (78 bp):
CCTTCGGGACTTAGCCCGGATATAGTACTCGCCAAATGCCTTCGGGACTTAGCCCGGATATAGTA
ACTCGCACAAATG
Found at i:10214 original size:11 final size:10
Alignment explanation
Indices: 10184--10222 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
10174 ACATGAGAGC
10184 CTTTCTTTTT
1 CTTTCTTTTT
*
10194 TTTTCTTTTT
1 CTTTCTTTTT
10204 CTTTCTCTTTT
1 CTTTCT-TTTT
10215 CTTT-TTTT
1 CTTTCTTTT
10223 CATCATCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
9 3 0.12
10 15 0.58
11 8 0.31
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (10 bp):
CTTTCTTTTT
Done.