Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold4465.1
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: 58772
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:10404 original size:27 final size:26
Alignment explanation
Indices: 10384--10544 Score: 142
Period size: 27 Copynumber: 6.1 Consensus size: 26
10374 ATTTTACCCT
*
10384 ACAGGGGTATTTCGGTAATTTTACACT
1 ACAGGGGTATTTCGGTAATTTTACA-A
** * *
10411 ACAAAGGTATCTAGGTAATTTTACAA
1 ACAGGGGTATTTCGGTAATTTTACAA
* * *
10437 ACTGGGGTATGTCGATAATTTTACAA
1 ACAGGGGTATTTCGGTAATTTTACAA
* *
10463 ATCGGGGGTATTTCGGTAATTTTATAA
1 A-CAGGGGTATTTCGGTAATTTTACAA
* * * **
10490 TCTGAGGTATTTTAGTAATTTTACAA
1 ACAGGGGTATTTCGGTAATTTTACAA
**
10516 ACTAATGGTATTTCGGTAATTTTACAA
1 AC-AGGGGTATTTCGGTAATTTTACAA
10543 AC
1 AC
10545 CGTGGTCTTC
Statistics
Matches: 105, Mismatches: 27, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
26 42 0.40
27 63 0.60
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (26 bp):
ACAGGGGTATTTCGGTAATTTTACAA
Found at i:10499 original size:53 final size:53
Alignment explanation
Indices: 10389--10544 Score: 140
Period size: 53 Copynumber: 2.9 Consensus size: 53
10379 ACCCTACAGG
* * * * *
10389 GGTATTTCG-GTAATTTTACACTAC-AAAGGTATCTAGGTAATTTTACAAACTGG
1 GGTA-TTCGAGTAATTTTACA-AACTAAGGGTATTTCGGTAATTTTACAAACTGA
** * *
10442 GGTATGTCGA-TAATTTTACAAA-TCGGGGGTATTTCGGTAATTTTATAATCTGA
1 GGTAT-TCGAGTAATTTTACAAACT-AAGGGTATTTCGGTAATTTTACAAACTGA
** *
10495 GGTATTTTAGTAATTTTACAAACTAATGGTATTTCGGTAATTTTACAAAC
1 GGTATTCGAGTAATTTTACAAACTAAGGGTATTTCGGTAATTTTACAAAC
10545 CGTGGTCTTC
Statistics
Matches: 81, Mismatches: 16, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
52 4 0.05
53 76 0.94
54 1 0.01
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (53 bp):
GGTATTCGAGTAATTTTACAAACTAAGGGTATTTCGGTAATTTTACAAACTGA
Found at i:14232 original size:40 final size:40
Alignment explanation
Indices: 14177--14283 Score: 187
Period size: 40 Copynumber: 2.7 Consensus size: 40
14167 AGCATTGGAT
14177 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATGA
*
14217 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATGA
* *
14257 TATGTCCGGGTTAAGACCCGAAGGCAA
1 TATATCCGGGCTAAGACCCGAAGGCAA
14284 ATGTGTTTGC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 64 1.00
ACGTcount: A:0.31, C:0.21, G:0.28, T:0.21
Consensus pattern (40 bp):
TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATGA
Found at i:16861 original size:2 final size:2
Alignment explanation
Indices: 16854--16886 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
16844 AGGAAAAAGG
16854 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
16887 GGGGTAAGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:17394 original size:90 final size:90
Alignment explanation
Indices: 17238--17404 Score: 219
Period size: 90 Copynumber: 1.9 Consensus size: 90
17228 CAAATAGGGT
* * * * *
17238 GCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCACACATTGATGCCATATCTCAGATATG
1 GCCAAAGCCATGTACCAGACATGATCTTACACGGGACCACACATCGATGCCATATCTCAGACATG
17303 GTCTTATACGAAGTCTGGAATCAGC
66 GTCTTATACGAAGTCTGGAATCAGC
* * * * * *
17328 GCCAACGCCATGTACCAGACATGATCTTATACGGGACCTCATATCGATGCCATGTC-CTGGACAT
1 GCCAAAGCCATGTACCAGACATGATCTTACACGGGACCACACATCGATGCCATATCTC-AGACAT
17392 GGTCTTATACGAA
65 GGTCTTATACGAA
17405 ATCATTTATT
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
89 1 0.02
90 64 0.98
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (90 bp):
GCCAAAGCCATGTACCAGACATGATCTTACACGGGACCACACATCGATGCCATATCTCAGACATG
GTCTTATACGAAGTCTGGAATCAGC
Found at i:17645 original size:33 final size:33
Alignment explanation
Indices: 17603--17669 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
17593 TTATTAAATC
17603 ATTTCATATAACATCAAGCATTAAATACACGAT
1 ATTTCATATAACATCAAGCATTAAATACACGAT
17636 ATTTCATATAACATCAAGCATTAAATACACGAT
1 ATTTCATATAACATCAAGCATTAAATACACGAT
17669 A
1 A
17670 ATGAAATTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.46, C:0.18, G:0.06, T:0.30
Consensus pattern (33 bp):
ATTTCATATAACATCAAGCATTAAATACACGAT
Found at i:40320 original size:42 final size:42
Alignment explanation
Indices: 40273--40357 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
40263 CGACGACTGC
* *
40273 TACTGAGATCTCTTTCGATGTCCTACAATTGATTAGTACAGT
1 TACTGAGATCTCTTGCGATGTCCTACAATTGATTAGCACAGT
40315 TACTGAGATCTCTTGCGATGTCCTACAATTGATTAGCACAGT
1 TACTGAGATCTCTTGCGATGTCCTACAATTGATTAGCACAGT
40357 T
1 T
40358 CTTATTTACA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (42 bp):
TACTGAGATCTCTTGCGATGTCCTACAATTGATTAGCACAGT
Found at i:44781 original size:26 final size:26
Alignment explanation
Indices: 44752--44806 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
44742 TCCAAAGTTG
44752 CCTTATGCTTGGTCAACCAATCCATC
1 CCTTATGCTTGGTCAACCAATCCATC
44778 CCTTATGCTTGGTCAACCAATCCATC
1 CCTTATGCTTGGTCAACCAATCCATC
44804 CCT
1 CCT
44807 AGTATCAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.22, C:0.36, G:0.11, T:0.31
Consensus pattern (26 bp):
CCTTATGCTTGGTCAACCAATCCATC
Found at i:58733 original size:7 final size:7
Alignment explanation
Indices: 58721--58745 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
58711 ATTCATATAA
58721 ATGAAAT
1 ATGAAAT
58728 ATGAAAT
1 ATGAAAT
58735 ATGAAAT
1 ATGAAAT
58742 ATGA
1 ATGA
58746 TAGTTGAGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.16, T:0.28
Consensus pattern (7 bp):
ATGAAAT
Done.