Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold955
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: 11733
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Found at i:1880 original size:14 final size:14
Alignment explanation
Indices: 1861--1895 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
1851 GTACTCGCAT
1861 AAATGGCTTCCTTC
1 AAATGGCTTCCTTC
*
1875 AAATGGCTTCTTTC
1 AAATGGCTTCCTTC
1889 AAATGGC
1 AAATGGC
1896 CACGTCACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (14 bp):
AAATGGCTTCCTTC
Found at i:6058 original size:42 final size:40
Alignment explanation
Indices: 5970--6139 Score: 277
Period size: 40 Copynumber: 4.2 Consensus size: 40
5960 GCTCTCGATA
*
5970 TAATATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTAG
1 TAATATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGG
*
6010 TAATATATATCCGAGTTAAATCCCGCAGGCTTCGTGCTGG
1 TAATATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGG
*
6050 TAATATATATCTGGGTTAAATCCCGCAGGCTTCGTGCTGG
1 TAATATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGG
*
6090 TAATATATATATCCGGGTTAAATCCCGCAGGCTTAGTGCTGG
1 T-A-ATATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGG
*
6132 TACTATAT
1 TAATATAT
6140 CCGGACTTAG
Statistics
Matches: 121, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
40 82 0.68
41 2 0.02
42 37 0.31
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (40 bp):
TAATATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGG
Found at i:6079 original size:80 final size:82
Alignment explanation
Indices: 5970--6139 Score: 281
Period size: 82 Copynumber: 2.1 Consensus size: 82
5960 GCTCTCGATA
5970 TAATATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTAGT-A-ATATATATCCGAGTTAAATCC
1 TAATATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTAGTAATATATATATCCGAGTTAAATCC
*
6033 CGCAGGCTTCGTGCTGG
66 CGCAGGCTTAGTGCTGG
* * *
6050 TAATATATATCTGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATATATATATCCGGGTTAAATCC
1 TAATATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTAGTAATATATATATCCGAGTTAAATCC
6115 CGCAGGCTTAGTGCTGG
66 CGCAGGCTTAGTGCTGG
*
6132 TACTATAT
1 TAATATAT
6140 CCGGACTTAG
Statistics
Matches: 83, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
80 39 0.47
81 1 0.01
82 43 0.52
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (82 bp):
TAATATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTAGTAATATATATATCCGAGTTAAATCC
CGCAGGCTTAGTGCTGG
Found at i:6416 original size:70 final size:70
Alignment explanation
Indices: 6331--6471 Score: 264
Period size: 70 Copynumber: 2.0 Consensus size: 70
6321 TTGCAAAGTG
*
6331 AGTCATTACTATTAAACAATGATATAATTATGTGAATGATTAATATATCCATGAAATAGAGAAAT
1 AGTCATTACTATTAAACAACGATATAATTATGTGAATGATTAATATATCCATGAAATAGAGAAAT
6396 GACCT
66 GACCT
*
6401 AGTCATTACTATTAAACAACGATATAATTATGTGAATGATTAATATATCTATGAAATAGAGAAAT
1 AGTCATTACTATTAAACAACGATATAATTATGTGAATGATTAATATATCCATGAAATAGAGAAAT
6466 GACCT
66 GACCT
6471 A
1 A
6472 TTCGATCGAT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.33
Consensus pattern (70 bp):
AGTCATTACTATTAAACAACGATATAATTATGTGAATGATTAATATATCCATGAAATAGAGAAAT
GACCT
Found at i:9588 original size:29 final size:27
Alignment explanation
Indices: 9570--9639 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
9560 ATATTAAGTC
9570 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
9597 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
9625 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
9640 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:9633 original size:28 final size:28
Alignment explanation
Indices: 9570--9667 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
9560 ATATTAAGTC
*
9570 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
9597 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
9625 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
9654 CGCACACTTAGTGC
1 CGCACACTTAGTGC
9668 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Done.