Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold600
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: 23109
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Warning! 82 characters in sequence are not A, C, G, or T
Found at i:3818 original size:50 final size:50
Alignment explanation
Indices: 3759--3929 Score: 236
Period size: 50 Copynumber: 3.4 Consensus size: 50
3749 CATTTGGGTA
* *
3759 AAGAGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCATCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
*
3809 AAGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
* * * *
3859 GAGAGGTCCC-TCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATAT
1 AAGAGGTCCCAT-GTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
* **
3909 GAGAACTCCCATGTAAGACCA
1 AAGAGGTCCCATGTAAGACCA
3930 NNNNNNNNNN
Statistics
Matches: 109, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
49 1 0.01
50 107 0.98
51 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.30, T:0.20
Consensus pattern (50 bp):
AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
Found at i:7955 original size:120 final size:121
Alignment explanation
Indices: 7741--7971 Score: 403
Period size: 120 Copynumber: 1.9 Consensus size: 121
7731 ATATAGTTCT
*
7741 TATTTTACAATTTAGTCCCTTTTTTTGCAATGCCGCATCCAAAATTGACTTTATTGATATACATC
1 TATTTTACAATTTAGTCCCTTTTTTTGCAATGCCGCATCCAAAATTGACTTTAATGATATACATC
7806 AATAAGTCCTTATAATTCCTTTAAAAATTCTCTTTGTTGAACTTAAATACATTTCC
66 AATAAGTCCTTATAATTCCTTTAAAAATTCTCTTTGTTGAACTTAAATACATTTCC
* * *
7862 TATTTTACAATTTAGTCCC-TTTTTTGCAATGTCGCATCCAAAATTTATTTTAATGATAT-CTAT
1 TATTTTACAATTTAGTCCCTTTTTTTGCAATGCCGCATCCAAAATTGACTTTAATGATATAC-AT
7925 CAATAAGTCCTTATAATTCCTTTAAAAATTCTCTTTGTTGAACTTAA
65 CAATAAGTCCTTATAATTCCTTTAAAAATTCTCTTTGTTGAACTTAA
7972 TTTCAATGTT
Statistics
Matches: 105, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
119 1 0.01
120 85 0.81
121 19 0.18
ACGTcount: A:0.31, C:0.18, G:0.07, T:0.44
Consensus pattern (121 bp):
TATTTTACAATTTAGTCCCTTTTTTTGCAATGCCGCATCCAAAATTGACTTTAATGATATACATC
AATAAGTCCTTATAATTCCTTTAAAAATTCTCTTTGTTGAACTTAAATACATTTCC
Found at i:9126 original size:24 final size:25
Alignment explanation
Indices: 9069--9126 Score: 61
Period size: 24 Copynumber: 2.4 Consensus size: 25
9059 ATTTCTTCTT
9069 ATTT-TTTTTCATCTTCTTCTTTGA
1 ATTTATTTTTCATCTTCTTCTTTGA
*
9093 A-ATATGTTTTC-TCTTCATT-TTTGA
1 ATTTAT-TTTTCATCTTC-TTCTTTGA
9117 ATTTATTTTT
1 ATTTATTTTT
9127 GTTTCCTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
23 1 0.04
24 17 0.61
25 10 0.36
ACGTcount: A:0.17, C:0.12, G:0.05, T:0.66
Consensus pattern (25 bp):
ATTTATTTTTCATCTTCTTCTTTGA
Found at i:13232 original size:17 final size:16
Alignment explanation
Indices: 13210--13252 Score: 68
Period size: 17 Copynumber: 2.6 Consensus size: 16
13200 GGAATTAAAT
13210 TTATATTTATTATATAA
1 TTATATTTATTAT-TAA
13227 TTATATTTATTATTAA
1 TTATATTTATTATTAA
13243 TATATATTTA
1 T-TATATTTA
13253 GCTATAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 4 0.16
17 21 0.84
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTATATTTATTATTAA
Found at i:13246 original size:23 final size:23
Alignment explanation
Indices: 13202--13248 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
13192 ATGGCTAAGG
*
13202 AATTAAATTTATATTTATTATAT
1 AATTAAATTTATATTTAATATAT
*
13225 AATTATATTTAT-TATTAATATAT
1 AATTAAATTTATAT-TTAATATAT
13248 A
1 A
13249 TTTAGCTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 20 0.95
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
AATTAAATTTATATTTAATATAT
Found at i:22599 original size:19 final size:19
Alignment explanation
Indices: 22575--22623 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
22565 TAAATTAAAA
*
22575 TTAATTTTTATAAGTTAAT
1 TTAATTTTAATAAGTTAAT
* **
22594 TTAATTCTAATATTTTAAT
1 TTAATTTTAATAAGTTAAT
22613 TTAATTTTAAT
1 TTAATTTTAAT
22624 TTAAATGTGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (19 bp):
TTAATTTTAATAAGTTAAT
Found at i:22604 original size:25 final size:25
Alignment explanation
Indices: 22576--22624 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
22566 AAATTAAAAT
*
22576 TAATTTTTATAAGTTAA-TTTAATTC
1 TAATATTT-TAAGTTAATTTTAATTC
*
22601 TAATATTTTAATTTAATTTTAATT
1 TAATATTTTAAGTTAATTTTAATT
22625 TAAATGTGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (25 bp):
TAATATTTTAAGTTAATTTTAATTC
Done.