Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1168
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: 10131
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.31
Found at i:1006 original size:49 final size:49
Alignment explanation
Indices: 934--1031 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
924 GTGGAGATGG
934 AGGAATTGTTATATAAAGCTATCAAGGTAGAAAGGCAATTGAAGTGTAA
1 AGGAATTGTTATATAAAGCTATCAAGGTAGAAAGGCAATTGAAGTGTAA
*
983 AGGAATTGTTGTATAAAGCTATCAAGGTAGAAAGGCAATTGAAGTGTAA
1 AGGAATTGTTATATAAAGCTATCAAGGTAGAAAGGCAATTGAAGTGTAA
1032 GGGCACTTCC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.42, C:0.06, G:0.26, T:0.27
Consensus pattern (49 bp):
AGGAATTGTTATATAAAGCTATCAAGGTAGAAAGGCAATTGAAGTGTAA
Found at i:5907 original size:21 final size:21
Alignment explanation
Indices: 5881--5945 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
5871 TATGCCTAGA
5881 AGTAGAAGAAGTAGAAGCATT
1 AGTAGAAGAAGTAGAAGCATT
* *
5902 AGTAGAATTAA-AAGAAGCA-T
1 AGTAGAA-GAAGTAGAAGCATT
5922 --TAGAAGAAGTAGAAGCATT
1 AGTAGAAGAAGTAGAAGCATT
5941 AGTAG
1 AGTAG
5946 GATTTCTTAC
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
17 2 0.06
18 12 0.34
19 1 0.03
20 1 0.03
21 17 0.49
22 2 0.06
ACGTcount: A:0.49, C:0.05, G:0.26, T:0.20
Consensus pattern (21 bp):
AGTAGAAGAAGTAGAAGCATT
Found at i:5935 original size:18 final size:18
Alignment explanation
Indices: 5883--5942 Score: 75
Period size: 18 Copynumber: 3.2 Consensus size: 18
5873 TGCCTAGAAG
5883 TAGAAGAAGTAGAAGCAT
1 TAGAAGAAGTAGAAGCAT
* *
5901 TAGTAGAATTAAAAGAAGCAT
1 TAGAAGAAGT---AGAAGCAT
5922 TAGAAGAAGTAGAAGCAT
1 TAGAAGAAGTAGAAGCAT
5940 TAG
1 TAG
5943 TAGGATTTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
18 19 0.54
21 16 0.46
ACGTcount: A:0.50, C:0.05, G:0.25, T:0.20
Consensus pattern (18 bp):
TAGAAGAAGTAGAAGCAT
Found at i:6144 original size:20 final size:20
Alignment explanation
Indices: 6119--6158 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
6109 TACATAGGGA
*
6119 TGGAGTTCCACTGTGTCACG
1 TGGAGTTCCACTATGTCACG
6139 TGGAGTTCCACTATGTCACG
1 TGGAGTTCCACTATGTCACG
6159 GATATCATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.17, C:0.25, G:0.28, T:0.30
Consensus pattern (20 bp):
TGGAGTTCCACTATGTCACG
Found at i:6590 original size:18 final size:18
Alignment explanation
Indices: 6567--6631 Score: 51
Period size: 18 Copynumber: 3.3 Consensus size: 18
6557 ATCTTCTTCT
6567 CTCCTCCTTCTATCATCC
1 CTCCTCCTTCTATCATCC
*
6585 CTCCT-CTCTCTATTATCTC
1 CTCCTCCT-TCTATCATC-C
6604 TCTTATCTCTCCTTCTATCATCC
1 -C---TC-CTCCTTCTATCATCC
6627 CTCCT
1 CTCCT
6632 ATCTCTACTA
Statistics
Matches: 37, Mismatches: 2, Indels: 16
0.67 0.04 0.29
Matches are distributed among these distances:
17 2 0.05
18 15 0.41
19 3 0.08
20 1 0.03
22 1 0.03
23 3 0.08
24 10 0.27
25 2 0.05
ACGTcount: A:0.11, C:0.45, G:0.00, T:0.45
Consensus pattern (18 bp):
CTCCTCCTTCTATCATCC
Found at i:6609 original size:9 final size:9
Alignment explanation
Indices: 6598--6658 Score: 65
Period size: 9 Copynumber: 7.1 Consensus size: 9
6588 CTCTCTCTAT
*
6598 TATCTCTCT
1 TATCTCTCC
6607 TATCTCTCC
1 TATCTCTCC
*
6616 T-TCTAT-C
1 TATCTCTCC
*
6623 -ATCCCTCC
1 TATCTCTCC
*
6631 TATCTCTAC
1 TATCTCTCC
6640 TATCTCTCC
1 TATCTCTCC
6649 TATCTCTCC
1 TATCTCTCC
6658 T
1 T
6659 CCTATCAGCC
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
7 4 0.10
8 5 0.12
9 33 0.79
ACGTcount: A:0.13, C:0.41, G:0.00, T:0.46
Consensus pattern (9 bp):
TATCTCTCC
Found at i:6619 original size:42 final size:42
Alignment explanation
Indices: 6557--6688 Score: 176
Period size: 42 Copynumber: 3.1 Consensus size: 42
6547 TCACTCTTCC
* * *
6557 ATCT-TCTTCTCTCCTCCTTCTATCATCCCTCCTCTCTCTATT
1 ATCTCTCTTATCT-CTCCTTCTATCATCCCTCCTATCTCTACT
6599 ATCTCTCTTATCTCTCCTTCTATCATCCCTCCTATCTCTACT
1 ATCTCTCTTATCTCTCCTTCTATCATCCCTCCTATCTCTACT
* * * *
6641 ATCTCTCCTATCTCTCCTCCTATCAGCCCTCCTATCTCTTCT
1 ATCTCTCTTATCTCTCCTTCTATCATCCCTCCTATCTCTACT
*
6683 TTCTCT
1 ATCTCT
6689 TTAAGAGCTA
Statistics
Matches: 81, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
42 74 0.91
43 7 0.09
ACGTcount: A:0.11, C:0.42, G:0.01, T:0.45
Consensus pattern (42 bp):
ATCTCTCTTATCTCTCCTTCTATCATCCCTCCTATCTCTACT
Found at i:6633 original size:12 final size:11
Alignment explanation
Indices: 6607--6678 Score: 53
Period size: 12 Copynumber: 6.5 Consensus size: 11
6597 TTATCTCTCT
*
6607 TATCTCTCCTTC
1 TATCTC-CCTCC
6619 TATCATCCCTCC
1 TATC-TCCCTCC
*
6631 TATCT--CTAC
1 TATCTCCCTCC
6640 TATCT--CTCC
1 TATCTCCCTCC
6649 TATCTCTCCTCC
1 TATCTC-CCTCC
*
6661 TATCAGCCCTCC
1 TATC-TCCCTCC
6673 TATCTC
1 TATCTC
6679 TTCTTTCTCT
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
9 16 0.32
11 2 0.04
12 29 0.58
13 3 0.06
ACGTcount: A:0.14, C:0.44, G:0.01, T:0.40
Consensus pattern (11 bp):
TATCTCCCTCC
Done.