Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga13g00280.N1
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: 10707
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.35
Found at i:860 original size:38 final size:38
Alignment explanation
Indices: 818--894 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
808 ACCTTGACTT
818 TTGGTACTTAGGAAAAGTTTTAGTTTTTCTTGAATAGG
1 TTGGTACTTAGGAAAAGTTTTAGTTTTTCTTGAATAGG
856 TTGGTACTTAGGAAAAGTTTTAGTTTTTCTTGAATAGG
1 TTGGTACTTAGGAAAAGTTTTAGTTTTTCTTGAATAGG
894 T
1 T
895 ACTTCAGGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.26, C:0.05, G:0.23, T:0.45
Consensus pattern (38 bp):
TTGGTACTTAGGAAAAGTTTTAGTTTTTCTTGAATAGG
Found at i:990 original size:17 final size:19
Alignment explanation
Indices: 950--992 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
940 GACCCTGTCA
*
950 TTTCATTTTTTATACAACT
1 TTTCATTATTTATACAACT
969 TTTCATTATTTA-ACAA-T
1 TTTCATTATTTATACAACT
986 TTTCATT
1 TTTCATT
993 TAAATCTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.35
18 4 0.17
19 11 0.48
ACGTcount: A:0.28, C:0.14, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTCATTATTTATACAACT
Found at i:1860 original size:76 final size:76
Alignment explanation
Indices: 1769--1917 Score: 244
Period size: 76 Copynumber: 2.0 Consensus size: 76
1759 ATCTACATAG
** * **
1769 AAAGTAAATTGATGGATTCCTATTTCTCAAAAAATGGATCATGTCTTCATTAAAGCAATGTGTTT
1 AAAGTAAATAAATGGATTCCTATTTCTCAAAAAATGGACCATGTCTTCATTAAAGCAATGTCATT
1834 GTGCCCAACCT
66 GTGCCCAACCT
*
1845 AAAGTAAATAAATGGATTCCTATTTCTCATAAAATGGACCATGTCTTCATTAAAGCAATGTCATT
1 AAAGTAAATAAATGGATTCCTATTTCTCAAAAAATGGACCATGTCTTCATTAAAGCAATGTCATT
1910 GTGCCCAA
66 GTGCCCAA
1918 TATAAAGGGT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
76 67 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (76 bp):
AAAGTAAATAAATGGATTCCTATTTCTCAAAAAATGGACCATGTCTTCATTAAAGCAATGTCATT
GTGCCCAACCT
Found at i:5785 original size:74 final size:75
Alignment explanation
Indices: 5701--5850 Score: 284
Period size: 74 Copynumber: 2.0 Consensus size: 75
5691 CCGTGTGCCA
5701 CACACGGGCGTGTGAAAGTACCTAGTCCGTGTGGAACACTAAAATTAGCATATTTTGTCT-ATTT
1 CACACGGGCGTGTGAAAGTACCTAGTCCGTGTGGAACACTAAAATTAGCATATTTTGTCTGATTT
5765 TGTCCCGTTT
66 TGTCCCGTTT
*
5775 CACACGGGCGTGTGAAAGTACCTAGTCCGTGTGGAACACTAAAATTAGCATATTTTGTCTGTTTT
1 CACACGGGCGTGTGAAAGTACCTAGTCCGTGTGGAACACTAAAATTAGCATATTTTGTCTGATTT
5840 TGTCCCGTTT
66 TGTCCCGTTT
5850 C
1 C
5851 TTGCTCTTTT
Statistics
Matches: 74, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
74 60 0.81
75 14 0.19
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (75 bp):
CACACGGGCGTGTGAAAGTACCTAGTCCGTGTGGAACACTAAAATTAGCATATTTTGTCTGATTT
TGTCCCGTTT
Found at i:7834 original size:16 final size:17
Alignment explanation
Indices: 7813--7847 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
7803 TAATGTTTAT
7813 GAAAATTA-TTAATTGA
1 GAAAATTACTTAATTGA
7829 GAAAATTATCTTAATTGA
1 GAAAATTA-CTTAATTGA
7847 G
1 G
7848 GGGTTAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
18 9 0.53
ACGTcount: A:0.46, C:0.03, G:0.14, T:0.37
Consensus pattern (17 bp):
GAAAATTACTTAATTGA
Found at i:9013 original size:20 final size:21
Alignment explanation
Indices: 8974--9013 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
8964 CGTGTTTGTT
* *
8974 TTCCGTTTAGCTCTTATGAGC
1 TTCCGTTTAACTCATATGAGC
8995 TTCCG-TTAACTCATATGAG
1 TTCCGTTTAACTCATATGAG
9014 TTTCAGTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (21 bp):
TTCCGTTTAACTCATATGAGC
Found at i:9116 original size:39 final size:39
Alignment explanation
Indices: 9055--9155 Score: 166
Period size: 39 Copynumber: 2.6 Consensus size: 39
9045 GCTCTGATCA
9055 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
* *
9094 GTTTCAATTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
* *
9133 GCTTCAGGTAGACTTCGGGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
9156 AGATCACGAT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.14, C:0.25, G:0.24, T:0.38
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
Done.