Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_80 ID=scaffold_80-JGI_221_v2.0
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: 35213
ACGTcount: A:0.15, C:0.09, G:0.05, T:0.15
Warning! 19670 characters in sequence are not A, C, G, or T
Found at i:646 original size:142 final size:142
Alignment explanation
Indices: 390--678 Score: 578
Period size: 142 Copynumber: 2.0 Consensus size: 142
380 GATAAGATTT
390 AATTCTATATATCATTCACTCTCTAATTCATTTATACTATCCCTGGTGATTTTTCAAAGTCATGT
1 AATTCTATATATCATTCACTCTCTAATTCATTTATACTATCCCTGGTGATTTTTCAAAGTCATGT
455 CACTGCTGTTGTCCCAAAACTGTTTCATTGCAAATTTTTACACTTTCATATTTTCTAGGTATAAA
66 CACTGCTGTTGTCCCAAAACTGTTTCATTGCAAATTTTTACACTTTCATATTTTCTAGGTATAAA
520 CTATCACCTAGG
131 CTATCACCTAGG
532 AATTCTATATATCATTCACTCTCTAATTCATTTATACTATCCCTGGTGATTTTTCAAAGTCATGT
1 AATTCTATATATCATTCACTCTCTAATTCATTTATACTATCCCTGGTGATTTTTCAAAGTCATGT
597 CACTGCTGTTGTCCCAAAACTGTTTCATTGCAAATTTTTACACTTTCATATTTTCTAGGTATAAA
66 CACTGCTGTTGTCCCAAAACTGTTTCATTGCAAATTTTTACACTTTCATATTTTCTAGGTATAAA
662 CTATCACCTAGG
131 CTATCACCTAGG
674 AATTC
1 AATTC
679 ATAACACCAC
Statistics
Matches: 147, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
142 147 1.00
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.42
Consensus pattern (142 bp):
AATTCTATATATCATTCACTCTCTAATTCATTTATACTATCCCTGGTGATTTTTCAAAGTCATGT
CACTGCTGTTGTCCCAAAACTGTTTCATTGCAAATTTTTACACTTTCATATTTTCTAGGTATAAA
CTATCACCTAGG
Found at i:1031 original size:12 final size:12
Alignment explanation
Indices: 1006--1044 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
996 ACTCGCTTCT
* *
1006 TTACTTACTCAC
1 TTACTTGCTTAC
*
1018 TTACTTGTTTAC
1 TTACTTGCTTAC
1030 TTACTTGCTTAC
1 TTACTTGCTTAC
1042 TTA
1 TTA
1045 AATAACTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:2409 original size:12 final size:12
Alignment explanation
Indices: 2384--2422 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
2374 ACTCGCTTCT
* *
2384 TTACTTACTCAC
1 TTACTTGCTTAC
*
2396 TTACTTGTTTAC
1 TTACTTGCTTAC
2408 TTACTTGCTTAC
1 TTACTTGCTTAC
2420 TTA
1 TTA
2423 AATAACTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:3006 original size:12 final size:12
Alignment explanation
Indices: 2969--3019 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
2959 ATTAGAATCT
2969 TTACTTGCTT-C
1 TTACTTGCTTAC
* *
2980 TTTACTTACTCAC
1 -TTACTTGCTTAC
*
2993 TTACTTGTTTAC
1 TTACTTGCTTAC
3005 TTACTTGCTTAC
1 TTACTTGCTTAC
3017 TTA
1 TTA
3020 AATAACTCAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
12 31 0.97
13 1 0.03
ACGTcount: A:0.18, C:0.24, G:0.06, T:0.53
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:5158 original size:12 final size:12
Alignment explanation
Indices: 5133--5171 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
5123 ACTCGCTTCT
* *
5133 TTACTTACTCAC
1 TTACTTGCTTAC
*
5145 TTACTTGTTTAC
1 TTACTTGCTTAC
5157 TTACTTGCTTAC
1 TTACTTGCTTAC
5169 TTA
1 TTA
5172 AATAACTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:6724 original size:12 final size:12
Alignment explanation
Indices: 6699--6737 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
6689 ACTCGCTTCT
* *
6699 TTACTTACTCAC
1 TTACTTGCTTAC
*
6711 TTACTTGTTTAC
1 TTACTTGCTTAC
6723 TTACTTGCTTAC
1 TTACTTGCTTAC
6735 TTA
1 TTA
6738 AATAACTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:7593 original size:12 final size:12
Alignment explanation
Indices: 7568--7606 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
7558 ACTCGCTTCT
* *
7568 TTACTTACTCAC
1 TTACTTGCTTAC
*
7580 TTACTTGTTTAC
1 TTACTTGCTTAC
7592 TTACTTGCTTAC
1 TTACTTGCTTAC
7604 TTA
1 TTA
7607 AATAACTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:17612 original size:12 final size:12
Alignment explanation
Indices: 17587--17625 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
17577 ACTCGCTTCT
* *
17587 TTACTTACTCAC
1 TTACTTGCTTAC
*
17599 TTACTTGTTTAC
1 TTACTTGCTTAC
17611 TTACTTGCTTAC
1 TTACTTGCTTAC
17623 TTA
1 TTA
17626 AATAACTCAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:30111 original size:4 final size:4
Alignment explanation
Indices: 30094--30132 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
30084 ACTCCCTTCT
* **
30094 TTAC TTAC TCAC TTAC TTGT TTAC TTAC TTAC TTAC TTA
1 TTAC TTAC TTAC TTAC TTAC TTAC TTAC TTAC TTAC TTA
30133 AATAACTCTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.23, C:0.23, G:0.03, T:0.51
Consensus pattern (4 bp):
TTAC
Found at i:30118 original size:20 final size:20
Alignment explanation
Indices: 30093--30131 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
30083 TACTCCCTTC
30093 TTTACTTACTCACTTACTTG
1 TTTACTTACTCACTTACTTG
*
30113 TTTACTTACTTACTTACTT
1 TTTACTTACTCACTTACTT
30132 AAATAACTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.23, G:0.03, T:0.54
Consensus pattern (20 bp):
TTTACTTACTCACTTACTTG
Found at i:31623 original size:11 final size:11
Alignment explanation
Indices: 31607--31635 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
31597 AAATTTTTGA
31607 ACGAAATTTTC
1 ACGAAATTTTC
31618 ACGAAATTTTC
1 ACGAAATTTTC
31629 ACGAAAT
1 ACGAAAT
31636 CATTTCGTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.31
Consensus pattern (11 bp):
ACGAAATTTTC
Found at i:32119 original size:12 final size:12
Alignment explanation
Indices: 32094--32132 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
32084 ACTCGCTTCT
* *
32094 TTACTTACTCAC
1 TTACTTGCTTAC
*
32106 TTACTTGTTTAC
1 TTACTTGCTTAC
32118 TTACTTGCTTAC
1 TTACTTGCTTAC
32130 TTA
1 TTA
32133 AATAACTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:33381 original size:4 final size:4
Alignment explanation
Indices: 33364--33402 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
33354 ACTCCCTTCT
* **
33364 TTAC TTAC TCAC TTAC TTGT TTAC TTAC TTAC TTAC TTA
1 TTAC TTAC TTAC TTAC TTAC TTAC TTAC TTAC TTAC TTA
33403 AATAACTCTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.23, C:0.23, G:0.03, T:0.51
Consensus pattern (4 bp):
TTAC
Found at i:33388 original size:20 final size:20
Alignment explanation
Indices: 33363--33401 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
33353 TACTCCCTTC
33363 TTTACTTACTCACTTACTTG
1 TTTACTTACTCACTTACTTG
*
33383 TTTACTTACTTACTTACTT
1 TTTACTTACTCACTTACTT
33402 AAATAACTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.23, G:0.03, T:0.54
Consensus pattern (20 bp):
TTTACTTACTCACTTACTTG
Found at i:33727 original size:50 final size:50
Alignment explanation
Indices: 33602--33843 Score: 204
Period size: 50 Copynumber: 4.7 Consensus size: 50
33592 TGATAGTACA
* * * *
33602 TGCCAAAGCTATGTCCCAGACATAGTCTTACATGGGATGTTTTCAGTA-C--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-GTTCTCA-TATCGG
* *
33651 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
* * * ** *
33701 TGCCCATGCCATGTCTCAGACATGGTCTTAC-GGGGAACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGG-AGTTCTCATATCGG
* * ** *
33751 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCAT-A--TC---GG
* *
33807 TGCCAATGCCATCTCCCAGACATTGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
33844 TCTCATTCCC
Statistics
Matches: 157, Mismatches: 25, Indels: 15
0.80 0.13 0.08
Matches are distributed among these distances:
47 2 0.01
48 7 0.04
49 35 0.22
50 75 0.48
51 2 0.01
53 2 0.01
56 34 0.22
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGG
Done.