Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_5433
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: 10996
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.33
Found at i:5711 original size:15 final size:15
Alignment explanation
Indices: 5691--5825 Score: 101
Period size: 15 Copynumber: 9.3 Consensus size: 15
5681 GATAATCTGA
5691 AAAACCCTTAAACCT
1 AAAACCCTTAAACCT
*
5706 AAAACCCTAAAACCT
1 AAAACCCTTAAACCT
5721 -AAA-CCTTAACACCCT
1 AAAACCCTTAA-A-CCT
5736 -AAACCC-TAAA-CT
1 AAAACCCTTAAACCT
*
5748 ATAAA-CCATAAACCTT
1 A-AAACCCTTAAACC-T
5764 AAAA-CCTTAAACCT
1 AAAACCCTTAAACCT
* *
5778 TAAA-CCTAAAACCT
1 AAAACCCTTAAACCT
*
5792 AAAACCCTAAAATCCT
1 AAAACCCTTAAA-CCT
5808 -AAACCC-TAAACCCT
1 AAAACCCTTAAA-CCT
5822 AAAA
1 AAAA
5826 ACCTATGTAA
Statistics
Matches: 101, Mismatches: 8, Indels: 22
0.77 0.06 0.17
Matches are distributed among these distances:
12 2 0.02
13 7 0.07
14 34 0.34
15 51 0.50
16 7 0.07
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.19
Consensus pattern (15 bp):
AAAACCCTTAAACCT
Found at i:5721 original size:7 final size:7
Alignment explanation
Indices: 5700--5830 Score: 99
Period size: 7 Copynumber: 18.0 Consensus size: 7
5690 AAAAACCCTT
5700 AAACCTA
1 AAACCTA
5707 AAACCCTA
1 AAA-CCTA
5715 AAACCT-
1 AAACCTA
5721 AAACCTTA
1 AAACC-TA
*
5729 ACACCCTA
1 A-AACCTA
*
5737 AACCCT-
1 AAACCTA
5743 AAA-CTA
1 AAACCTA
5749 TAAACC-A
1 -AAACCTA
5756 TAAACCTTA
1 -AAACC-TA
*
5765 AAACCTT
1 AAACCTA
*
5772 AAACCTT
1 AAACCTA
5779 AAACCTA
1 AAACCTA
5786 AAACCTA
1 AAACCTA
5793 AAACCCTA
1 AAA-CCTA
5801 AAATCCTA
1 AAA-CCTA
*
5809 AACCCTA
1 AAACCTA
*
5816 AACCCTAA
1 AAACCT-A
5824 AAACCTA
1 AAACCTA
5831 TGTAAGCCAT
Statistics
Matches: 106, Mismatches: 7, Indels: 22
0.79 0.05 0.16
Matches are distributed among these distances:
5 2 0.02
6 7 0.07
7 57 0.54
8 36 0.34
9 4 0.04
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (7 bp):
AAACCTA
Found at i:5737 original size:22 final size:21
Alignment explanation
Indices: 5699--5830 Score: 126
Period size: 22 Copynumber: 6.1 Consensus size: 21
5689 GAAAAACCCT
*
5699 TAAACCTAAAACCCTAAAACC
1 TAAACCTTAAACCCTAAAACC
*
5720 TAAACCTTAACACCCTAAACCC
1 TAAACCTTAA-ACCCTAAAACC
*
5742 TAAA-CTATAAACCAT-AAACC
1 TAAACCT-TAAACCCTAAAACC
*
5762 TTAAAACCTTAAA-CCTTAAACC
1 -T-AAACCTTAAACCCTAAAACC
*
5784 TAAAACCTAAAACCCTAAAATCC
1 T-AAACCTTAAACCCTAAAA-CC
*
5807 TAAACCCTAAACCCTAAAAACC
1 TAAACCTTAAACCCT-AAAACC
5829 TA
1 TA
5831 TGTAAGCCAT
Statistics
Matches: 93, Mismatches: 9, Indels: 17
0.78 0.08 0.14
Matches are distributed among these distances:
20 4 0.04
21 29 0.31
22 51 0.55
23 9 0.10
ACGTcount: A:0.49, C:0.32, G:0.00, T:0.19
Consensus pattern (21 bp):
TAAACCTTAAACCCTAAAACC
Found at i:5760 original size:36 final size:34
Alignment explanation
Indices: 5712--5818 Score: 133
Period size: 36 Copynumber: 3.0 Consensus size: 34
5702 ACCTAAAACC
*
5712 CTAAAACCTAAACCTTAACACCCTAAACCCTAAA
1 CTAAAACCTAAACCTTAAAACCCTAAACCCTAAA
* *
5746 CTATAAACCATAAACCTTAAAACCTTAAACCTTAAA
1 CTA-AAACC-TAAACCTTAAAACCCTAAACCCTAAA
* *
5782 CCTAAAACCTAAAACCCTAAAATCCTAAACCCTAAA
1 -CTAAAACCT-AAACCTTAAAACCCTAAACCCTAAA
5818 C
1 C
5819 CCTAAAAACC
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
34 3 0.05
35 7 0.11
36 49 0.79
37 3 0.05
ACGTcount: A:0.49, C:0.32, G:0.00, T:0.20
Consensus pattern (34 bp):
CTAAAACCTAAACCTTAAAACCCTAAACCCTAAA
Found at i:5819 original size:36 final size:35
Alignment explanation
Indices: 5711--5830 Score: 129
Period size: 36 Copynumber: 3.3 Consensus size: 35
5701 AACCTAAAAC
*
5711 CCTAAAACCT-AAACCTTAACACCCTAAACCCTAAA
1 CCTAAAACCTAAAACCTTAA-AACCTAAACCCTAAA
*
5746 -CTATAAACC-ATAAACCTTAAAACCTTAAACCTTAAA
1 CCTA-AAACCTA-AAACCTTAAAACC-TAAACCCTAAA
*
5782 CCTAAAACCTAAAACCCTAAAATCCTAAACCCTAAA
1 CCTAAAACCTAAAACCTTAAAA-CCTAAACCCTAAA
5818 CCCTAAAAACCTA
1 -CCT-AAAACCTA
5831 TGTAAGCCAT
Statistics
Matches: 72, Mismatches: 4, Indels: 15
0.79 0.04 0.16
Matches are distributed among these distances:
34 3 0.04
35 8 0.11
36 44 0.61
37 9 0.12
38 8 0.11
ACGTcount: A:0.48, C:0.33, G:0.00, T:0.19
Consensus pattern (35 bp):
CCTAAAACCTAAAACCTTAAAACCTAAACCCTAAA
Found at i:7677 original size:46 final size:47
Alignment explanation
Indices: 7537--7791 Score: 172
Period size: 46 Copynumber: 5.4 Consensus size: 47
7527 TGGGCTAGTC
* ** *
7537 TAAGA-CATGTCTGGGACATGCATCGGCCAC-ATTATG-AGAGCCAGTG
1 TAAGACCATGTCTGGGACATGCATCGACTTCGA-GATGTA-AGCCAGTG
* * *
7583 TAAGACCATGTCTGGGATATGGCATC-AGCATT-GAGATG-AGTGCTAGTG
1 TAAGACCATGTCTGGGACAT-GCATCGA-C-TTCGAGATGTA-AGCCAGTG
*
7631 TAAGA-CATGTCTGGGACATGCTTCGACTTCGAGATGTAAGCCAGTG
1 TAAGACCATGTCTGGGACATGCATCGACTTCGAGATGTAAGCCAGTG
* * * * *
7677 TAAGA-CATGTCTGGGACATGAATCGGCTACGAGAGGT--GTCAGTG
1 TAAGACCATGTCTGGGACATGCATCGACTTCGAGATGTAAGCCAGTG
* * * **
7721 TAAGACCATGTCTAGGACATGGCATCGAC-ACAGATATGCTAGAGCTTGTG
1 TAAGACCATGTCTGGGACAT-GCATCGACTTC-GAGATG-TA-AGCCAGTG
*
7771 TAAGACCATGTTTGGGACATG
1 TAAGACCATGTCTGGGACATG
7792 GCATTGGCAC
Statistics
Matches: 167, Mismatches: 27, Indels: 27
0.76 0.12 0.12
Matches are distributed among these distances:
44 11 0.07
45 17 0.10
46 64 0.38
47 29 0.17
48 22 0.13
49 2 0.01
50 22 0.13
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (47 bp):
TAAGACCATGTCTGGGACATGCATCGACTTCGAGATGTAAGCCAGTG
Done.