Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold365
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: 34181
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:5682 original size:46 final size:46
Alignment explanation
Indices: 5626--5801 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
5616 TGGTTGAGCA
*
5626 TCCGAACTCGTTGAGTTGAGTCCGAGTTTACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
5672 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
5717 CATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
5765 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
5802 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 62 0.57
47 28 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.19, G:0.30, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:5782 original size:93 final size:93
Alignment explanation
Indices: 5623--5794 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
5613 GGATGGTTGA
* *
5623 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTTACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
5688 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
5716 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGTCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
5781 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
5795 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:15614 original size:46 final size:45
Alignment explanation
Indices: 15547--15716 Score: 150
Period size: 46 Copynumber: 3.7 Consensus size: 45
15537 GTCTTAACTT
* *
15547 ATGCATGTCCCAGACATGTCTTACACTGGCTTAC-GTCTCAAGGCCG
1 ATGCATGTCCCGGACATGTCTTACACTAGC--ACTGTCTCAAGGCCG
* *
15593 ATGCATGTCCCGGACATGTCTTACACTAGCACTTGTCTCGATGCCG
1 ATGCATGTCCCGGACATGTCTTACACTAGCAC-TGTCTCAAGGCCG
* *
15639 ATGCCATGTCCCGGACATGGTCTTACA-TAG-GCTCTCAT-AATGTGGCCG
1 ATG-CATGTCCCGGACAT-GTCTTACACTAGCACTGTC-TCAA---GGCCG
* **
15687 ATGCATGTCCCAGACACATCTTACACTAGC
1 ATGCATGTCCCGGACATGTCTTACACTAGC
15717 CCACAATAAC
Statistics
Matches: 103, Mismatches: 11, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
44 2 0.02
45 4 0.04
46 50 0.49
47 32 0.31
48 15 0.15
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.26
Consensus pattern (45 bp):
ATGCATGTCCCGGACATGTCTTACACTAGCACTGTCTCAAGGCCG
Found at i:19290 original size:138 final size:138
Alignment explanation
Indices: 19042--19320 Score: 549
Period size: 138 Copynumber: 2.0 Consensus size: 138
19032 TGTCGGGTTG
19042 AATTTCAATCTCTACCGGAGAAATTACAAGTGAGGGATCCGATCTATAATGACACAACATCGACA
1 AATTTCAATCTCTACCGGAGAAATTACAAGTGAGGGATCCGATCTATAATGACACAACATCGACA
19107 CATGATACACATTATGGATCTTTTCTAATTTTGATGGCAATGCTAGCCGATATGCCACTGGTCCT
66 CATGATACACATTATGGATCTTTTCTAATTTTGATGGCAATGCTAGCCGATATGCCACTGGTCCT
19172 ATTTTTTC
131 ATTTTTTC
*
19180 AATTTCAATCTCTACCGGATAAATTACAAGTGAGGGATCCGATCTATAATGACACAACATCGACA
1 AATTTCAATCTCTACCGGAGAAATTACAAGTGAGGGATCCGATCTATAATGACACAACATCGACA
19245 CATGATACACATTATGGATCTTTTCTAATTTTGATGGCAATGCTAGCCGATATGCCACTGGTCCT
66 CATGATACACATTATGGATCTTTTCTAATTTTGATGGCAATGCTAGCCGATATGCCACTGGTCCT
19310 ATTTTTTC
131 ATTTTTTC
19318 AAT
1 AAT
19321 GATCTCATAC
Statistics
Matches: 140, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
138 140 1.00
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (138 bp):
AATTTCAATCTCTACCGGAGAAATTACAAGTGAGGGATCCGATCTATAATGACACAACATCGACA
CATGATACACATTATGGATCTTTTCTAATTTTGATGGCAATGCTAGCCGATATGCCACTGGTCCT
ATTTTTTC
Found at i:20778 original size:15 final size:17
Alignment explanation
Indices: 20760--20791 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
20750 CAGCATAATT
20760 TACCAAA-TCA-ATTCA
1 TACCAAACTCACATTCA
20775 TACCAAACTCACATTCA
1 TACCAAACTCACATTCA
20792 CAAGTATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (17 bp):
TACCAAACTCACATTCA
Found at i:21853 original size:24 final size:26
Alignment explanation
Indices: 21826--21874 Score: 75
Period size: 24 Copynumber: 1.9 Consensus size: 26
21816 AGTTCATGCA
21826 ATATTAAAGC-ATTTAA-ATACAATT
1 ATATTAAAGCTATTTAACATACAATT
21850 ATATTAAAGCTTATTTAACATACAA
1 ATATTAAAGC-TATTTAACATACAA
21875 ACTTACCTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 10 0.45
26 6 0.27
27 6 0.27
ACGTcount: A:0.49, C:0.10, G:0.04, T:0.37
Consensus pattern (26 bp):
ATATTAAAGCTATTTAACATACAATT
Found at i:27676 original size:40 final size:40
Alignment explanation
Indices: 27616--27839 Score: 281
Period size: 40 Copynumber: 5.6 Consensus size: 40
27606 TATTCGGATG
*
27616 ATATTCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
27656 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-A--AGTTACT
* * *
27699 ATACCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * * * *
27739 ATTTCCGAGCTAAGACCCGAAGGCATGTGTGCGAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * *
27779 ATATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTT-CG
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
27818 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
27840 TACTTGGTTT
Statistics
Matches: 160, Mismatches: 21, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
38 14 0.09
39 7 0.04
40 101 0.63
41 1 0.01
43 37 0.23
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:27760 original size:83 final size:80
Alignment explanation
Indices: 27621--27839 Score: 273
Period size: 83 Copynumber: 2.7 Consensus size: 80
27611 GGATGATATT
* * * *
27621 CGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGT
1 CGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGAGCTAAGACCCGAAGGCATGTGT
*
27686 GCGAGTAGTTGCTATACC
66 GC--G-AGTTACTATACC
* *
27704 CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATTTCCGAGCTAAGACCCGAAGGCATGTGT
1 CGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGAGCTAAGACCCGAAGGCATGTGT
*
27769 GCGAGTTACTATATC
66 GCGAGTTACTATACC
* * * *
27784 CGGGTTAAGTCCCGAAGGCATTTGTGCGAGT-TCGATATCCG-GCTAA-ATCCCGAAGG
1 CGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGAGCTAAGA-CCCGAAGG
27840 TACTTGGTTT
Statistics
Matches: 122, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
77 1 0.01
78 13 0.11
79 7 0.06
80 39 0.32
81 1 0.01
83 61 0.50
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (80 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGAGCTAAGACCCGAAGGCATGTGT
GCGAGTTACTATACC
Done.