Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga03g00233.F3
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: 5114
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.31
Found at i:1607 original size:42 final size:42
Alignment explanation
Indices: 1561--1719 Score: 153
Period size: 42 Copynumber: 3.8 Consensus size: 42
1551 TCATGCAAGG
* **
1561 TCAAGATCCAAATCAAAATCACCCCTTAGTTATCGGAGAAGA
1 TCAAGATCCAAATCAAGATCACCAATTAGTTATCGGAGAAGA
* *
1603 TCAAGAT-CAAAGTCTAGATCACCAATTAGTTATCGGCGAAGA
1 TCAAGATCCAAA-TCAAGATCACCAATTAGTTATCGGAGAAGA
* * * * * *
1645 TCAAGGTCCAAGTCAAGATCACCAATCATTTATAGGCGAA-A
1 TCAAGATCCAAATCAAGATCACCAATTAGTTATCGGAGAAGA
* *
1686 GTCAAGGT-CAAAGTCAAGATCACCAATCAGTTAT
1 -TCAAGATCCAAA-TCAAGATCACCAATTAGTTAT
1720 AGGCGAAGGA
Statistics
Matches: 100, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
41 8 0.08
42 89 0.89
43 3 0.03
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23
Consensus pattern (42 bp):
TCAAGATCCAAATCAAGATCACCAATTAGTTATCGGAGAAGA
Found at i:1720 original size:42 final size:43
Alignment explanation
Indices: 1599--1726 Score: 188
Period size: 42 Copynumber: 3.0 Consensus size: 43
1589 GTTATCGGAG
* * * *
1599 AAGATCAAGATCAAAGTCTAGATCACCAATTAGTTATCGGCG-
1 AAGATCAAGGTCAAAGTCAAGATCACCAATCAGTTATAGGCGA
* *
1641 AAGATCAAGGTCCAAGTCAAGATCACCAATCATTTATAGGCGA
1 AAGATCAAGGTCAAAGTCAAGATCACCAATCAGTTATAGGCGA
1684 AAG-TCAAGGTCAAAGTCAAGATCACCAATCAGTTATAGGCGA
1 AAGATCAAGGTCAAAGTCAAGATCACCAATCAGTTATAGGCGA
1726 A
1 A
1727 GGAGGAGATC
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
42 74 0.96
43 3 0.04
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.21
Consensus pattern (43 bp):
AAGATCAAGGTCAAAGTCAAGATCACCAATCAGTTATAGGCGA
Found at i:2528 original size:45 final size:45
Alignment explanation
Indices: 2455--2551 Score: 140
Period size: 45 Copynumber: 2.2 Consensus size: 45
2445 TAAGAAATCT
* * **
2455 AAGCATCGGGATAGAAGGCGGTTGAGGTCAAGATCTGCTGATGGC
1 AAGCATCGGGATAGAAAGAGGTCAAGGTCAAGATCTGCTGATGGC
**
2500 AAGCATCGGGATAGAAAGAGGTCAAGGTCAAGATCTTTTGATGGC
1 AAGCATCGGGATAGAAAGAGGTCAAGGTCAAGATCTGCTGATGGC
2545 AAGCATC
1 AAGCATC
2552 ACAGAGGAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.31, C:0.15, G:0.33, T:0.21
Consensus pattern (45 bp):
AAGCATCGGGATAGAAAGAGGTCAAGGTCAAGATCTGCTGATGGC
Found at i:3966 original size:12 final size:11
Alignment explanation
Indices: 3947--3988 Score: 66
Period size: 11 Copynumber: 3.7 Consensus size: 11
3937 TTTGCTTGTA
3947 TTTTTTTTTCT
1 TTTTTTTTTCT
*
3958 TTCTTTTTTCT
1 TTTTTTTTTCT
3969 CTTTTTTTTTCT
1 -TTTTTTTTTCT
3981 TTTTTTTT
1 TTTTTTTT
3989 CCCTTTTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TTTTTTTTTCT
Found at i:3966 original size:13 final size:12
Alignment explanation
Indices: 3947--3997 Score: 63
Period size: 11 Copynumber: 4.5 Consensus size: 12
3937 TTTGCTTGTA
3947 TTTTTTTTTCT-
1 TTTTTTTTTCTC
*
3958 TTCTTTTTTCTC
1 TTTTTTTTTCTC
3970 -TTTTTTTT-TC
1 TTTTTTTTTCTC
*
3980 TTTTTTTTTCCC
1 TTTTTTTTTCTC
3992 TTTTTT
1 TTTTTT
3998 CGTCATTTCC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
10 2 0.06
11 25 0.74
12 7 0.21
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTTTTTCTC
Found at i:3977 original size:23 final size:22
Alignment explanation
Indices: 3947--3997 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
3937 TTTGCTTGTA
*
3947 TTTTTTTTTCTTTCTTTTTTCTC
1 TTTTTTTTTCTTT-TTTTTTCCC
3970 TTTTTTTTTCTTTTTTTTTCCC
1 TTTTTTTTTCTTTTTTTTTCCC
3992 TTTTTT
1 TTTTTT
3998 CGTCATTTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 14 0.52
23 13 0.48
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (22 bp):
TTTTTTTTTCTTTTTTTTTCCC
Found at i:3987 original size:10 final size:10
Alignment explanation
Indices: 3947--3989 Score: 59
Period size: 10 Copynumber: 4.0 Consensus size: 10
3937 TTTGCTTGTA
3947 TTTTTTTTTC
1 TTTTTTTTTC
3957 TTTCTTTTTTCTC
1 -TT-TTTTTT-TC
3970 TTTTTTTTTC
1 TTTTTTTTTC
3980 TTTTTTTTTC
1 TTTTTTTTTC
3990 CCTTTTTTCG
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
10 12 0.40
11 8 0.27
12 8 0.27
13 2 0.07
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:4822 original size:16 final size:16
Alignment explanation
Indices: 4777--4822 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
4767 ATCTTCGGTC
4777 TTCCTCTTTCTTTCTT
1 TTCCTCTTTCTTTCTT
* * *
4793 TTCTTTTTTTTTTCTT
1 TTCCTCTTTCTTTCTT
*
4809 TTCCCCTTTCTTTC
1 TTCCTCTTTCTTTC
4823 CAGATTTTTT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (16 bp):
TTCCTCTTTCTTTCTT
Done.