Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1760
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: 16869
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Found at i:70 original size:19 final size:19
Alignment explanation
Indices: 48--93 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
38 AAAAAAATTT
48 AATATTTTTT-ATATCTTTA
1 AATATTTTTTAAT-TCTTTA
*
67 AATATTATTTTAATTTTTTA
1 AATATT-TTTTAATTCTTTA
87 AATATTT
1 AATATTT
94 ATATAATGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 7 0.29
20 15 0.62
21 2 0.08
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
AATATTTTTTAATTCTTTA
Found at i:1611 original size:16 final size:16
Alignment explanation
Indices: 1590--1624 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1580 CTCATTCAAG
**
1590 AATAGTTATTATTTAA
1 AATAGTTAGCATTTAA
1606 AATAGTTAGCATTTAA
1 AATAGTTAGCATTTAA
1622 AAT
1 AAT
1625 GACTCTTAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.43
Consensus pattern (16 bp):
AATAGTTAGCATTTAA
Found at i:10681 original size:129 final size:128
Alignment explanation
Indices: 10446--10683 Score: 298
Period size: 129 Copynumber: 1.9 Consensus size: 128
10436 AACCAAGATT
* *
10446 TAAGTTTTCCTTAGCTTTATTCAACAAACGATAAAACTTGTAGCATCGCCATTAGGTTTTTCAAA
1 TAAGTTTTCCTTAGCTTTATACAACAAACGATAAAACTTGTAGCATCGCCATTAAGTTTTTCAAA
* * ***
10511 TGTCACATTTGAATTGATGTCACTAGATTCAGTTGACATAGTAATAGATACACTGTCAGGATA
66 TGTCACATTTAAATTAATGTCACTAGATTCAGCAAACATAGTAATAGATACACTGTCAGGATA
* * * * *
10574 TAAGTTTTCCTTAGCTTTGTACAACAAATGATAAAAGTTTGTAGCTTTGCCATTAAGTTCTTT-A
1 TAAGTTTTCCTTAGCTTTATACAACAAACGATAAAA-CTTGTAGCATCGCCATTAAGTT-TTTCA
* * * * *
10638 ATTGTCGCATTTAAATTAATGTTAGTAGATTTAGCAAACATAGTAA
64 AATGTCACATTTAAATTAATGTCACTAGATTCAGCAAACATAGTAA
10684 CGACACATTT
Statistics
Matches: 91, Mismatches: 17, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
128 33 0.36
129 55 0.60
130 3 0.03
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.37
Consensus pattern (128 bp):
TAAGTTTTCCTTAGCTTTATACAACAAACGATAAAACTTGTAGCATCGCCATTAAGTTTTTCAAA
TGTCACATTTAAATTAATGTCACTAGATTCAGCAAACATAGTAATAGATACACTGTCAGGATA
Found at i:14910 original size:58 final size:58
Alignment explanation
Indices: 14848--15218 Score: 315
Period size: 58 Copynumber: 6.6 Consensus size: 58
14838 GATTTTTTAC
* * *
14848 ATTTTGATGTCATTTAGTTCATTTACCATGATATAGGGACTTAGATGTAATTTTATGA
1 ATTTTGATGTCATTTAGGTCATTTTCCATGATCTAGGGACTTAGATGTAATTTTATGA
* * * * * * *
14906 ATTTTGATG-CTATTTAGGTCATTTTTCATCATCTAAGGACTGT-TATGTTATTTAATGC
1 ATTTTGATGTC-ATTTAGGTCATTTTCCATGATCTAGGGACT-TAGATGTAATTTTATGA
* * * * *
14964 ATTTTGATATCATTTAGGTTATTTTTCATGATCTAGGGACTTAGATGCAATTTTGTGA
1 ATTTTGATGTCATTTAGGTCATTTTCCATGATCTAGGGACTTAGATGTAATTTTATGA
* * * ** * * *
15022 ATTTTGATGCCATTTAGGTCATTTT-CATGATCCAAGGACTTTTATATCATTTCAT-A
1 ATTTTGATGTCATTTAGGTCATTTTCCATGATCTAGGGACTTAGATGTAATTTTATGA
* * *
15078 ATTTTGATGTCATTTAGGGT-ATTTTCCATAATCTAGGGA-TCTGGATGTAATTTTGTGA
1 ATTTTGATGTCATTTA-GGTCATTTTCCATGATCTAGGGACT-TAGATGTAATTTTATGA
* *
15136 ATTTT--TGTCATTTAGGTCATTTACCATGATCT-GGG----A-A--TAATTTTGTGA
1 ATTTTGATGTCATTTAGGTCATTTTCCATGATCTAGGGACTTAGATGTAATTTTATGA
* * *
15184 ATTTTGATGCCATTTAGGTTATTTTTCATGATCTA
1 ATTTTGATGTCATTTAGGTCATTTTCCATGATCTA
15219 AAAACTTTTC
Statistics
Matches: 252, Mismatches: 49, Indels: 31
0.76 0.15 0.09
Matches are distributed among these distances:
48 16 0.06
50 24 0.10
55 6 0.02
56 43 0.17
57 45 0.18
58 116 0.46
59 2 0.01
ACGTcount: A:0.26, C:0.11, G:0.17, T:0.46
Consensus pattern (58 bp):
ATTTTGATGTCATTTAGGTCATTTTCCATGATCTAGGGACTTAGATGTAATTTTATGA
Found at i:14932 original size:116 final size:115
Alignment explanation
Indices: 14808--15167 Score: 345
Period size: 116 Copynumber: 3.1 Consensus size: 115
14798 GGTCATTCTA
* * ** *
14808 GTCATTTTCATGAT-TTATGACCATTCATATGATTTTTTACATTTTGATGTCATTTA-GTTCATT
1 GTCATTTTCATGATCTAAGGACCATT-ATATGATTTAATACATTTTGATATCATTTAGGTT-ATT
* *
14871 TACCATGATATAGGGACTTAGATGTAATTTTATGAATTTTGATGCTATTTAG
64 TACCATGATATAGGGACTTAGATGCAATTTTATGAATTTTGATGCCATTTAG
* ** * * *
14923 GTCATTTTTCATCATCTAAGGACTGTTATGTTATTTAATGCATTTTGATATCATTTAGGTTATTT
1 GTCA-TTTTCATGATCTAAGGACCATTATATGATTTAATACATTTTGATATCATTTAGGTTATTT
** * *
14988 TTCATGATCTAGGGACTTAGATGCAATTTTGTGAATTTTGATGCCATTTAG
65 ACCATGATATAGGGACTTAGATGCAATTTTATGAATTTTGATGCCATTTAG
* ** * * * * *
15039 GTCATTTTCATGATCCAAGGACTTTTATATCATTTCATA-ATTTTGATGTCATTTAGGGTATTTT
1 GTCATTTTCATGATCTAAGGACCATTATATGATTTAATACATTTTGATATCATTTAGGTTATTTA
* * * * * *
15103 CCATAATCTAGGGA-TCTGGATGTAATTTTGTGAATTTT--TGTCATTTAG
66 CCATGATATAGGGACT-TAGATGCAATTTTATGAATTTTGATGCCATTTAG
*
15151 GTCATTTACCATGATCT
1 GTCATTT-TCATGATCT
15168 GGGAATAATT
Statistics
Matches: 207, Mismatches: 33, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
112 16 0.08
113 8 0.04
114 55 0.27
115 32 0.15
116 86 0.42
117 10 0.05
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.47
Consensus pattern (115 bp):
GTCATTTTCATGATCTAAGGACCATTATATGATTTAATACATTTTGATATCATTTAGGTTATTTA
CCATGATATAGGGACTTAGATGCAATTTTATGAATTTTGATGCCATTTAG
Done.