Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold822
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: 5764
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.28
Warning! 580 characters in sequence are not A, C, G, or T
Found at i:1532 original size:8 final size:8
Alignment explanation
Indices: 1519--1552 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
1509 GGACTAACTG
1519 AACAAATA
1 AACAAATA
*
1527 AACAAACA
1 AACAAATA
1535 AACAAATA
1 AACAAATA
*
1543 AACGAATA
1 AACAAATA
1551 AA
1 AA
1553 TCGACCACAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.74, C:0.15, G:0.03, T:0.09
Consensus pattern (8 bp):
AACAAATA
Found at i:1553 original size:12 final size:12
Alignment explanation
Indices: 1487--1553 Score: 53
Period size: 12 Copynumber: 5.4 Consensus size: 12
1477 ACACCACATT
1487 TAAATAAACAAA
1 TAAATAAACAAA
* *
1499 TAAATGAAACGGAC
1 TAAAT-AAAC-AAA
* *
1513 TAACTGAACAAA
1 TAAATAAACAAA
*
1525 TAAACAAACAAA
1 TAAATAAACAAA
* *
1537 CAAATAAACGAA
1 TAAATAAACAAA
1549 TAAAT
1 TAAAT
1554 CGACCACACC
Statistics
Matches: 40, Mismatches: 13, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
12 28 0.70
13 7 0.17
14 5 0.12
ACGTcount: A:0.64, C:0.13, G:0.07, T:0.15
Consensus pattern (12 bp):
TAAATAAACAAA
Found at i:1835 original size:15 final size:15
Alignment explanation
Indices: 1804--1837 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1794 TTTCTTTATT
*
1804 AAAAATAAAAGACAA
1 AAAAATAAAAAACAA
*
1819 AAAAATAAAAAATAA
1 AAAAATAAAAAACAA
1834 AAAA
1 AAAA
1838 GGTTAATGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.85, C:0.03, G:0.03, T:0.09
Consensus pattern (15 bp):
AAAAATAAAAAACAA
Found at i:4055 original size:18 final size:18
Alignment explanation
Indices: 4034--4113 Score: 106
Period size: 18 Copynumber: 4.4 Consensus size: 18
4024 TTTTTCATCA
*
4034 TCTTTTTCAATTTCTTTT
1 TCTTTTTCAATTTCTATT
* *
4052 TCTTTTGCAATTTCTTTT
1 TCTTTTTCAATTTCTATT
**
4070 TCTTTTTCGTTTTCTATT
1 TCTTTTTCAATTTCTATT
*
4088 TCTTTTTCACTTTCTATT
1 TCTTTTTCAATTTCTATT
4106 TCTTTTTC
1 TCTTTTTC
4114 TTCTTTTTTG
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 55 1.00
ACGTcount: A:0.09, C:0.19, G:0.03, T:0.70
Consensus pattern (18 bp):
TCTTTTTCAATTTCTATT
Found at i:4082 original size:7 final size:6
Alignment explanation
Indices: 4020--4115 Score: 75
Period size: 6 Copynumber: 16.0 Consensus size: 6
4010 TTTTCTTTCG
* ** ** * **
4020 TTTCTT TTTCAT CATCTT TTTCAA TTTCTT TTTCTT TTGCAA TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
* * ** *
4068 TTTCTT TTTCGT TTTCTA TTTCTT TTTCAC TTTCTA TTTCTT TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
4116 CTTTTTTGTT
Statistics
Matches: 65, Mismatches: 25, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
6 65 1.00
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (6 bp):
TTTCTT
Found at i:4955 original size:18 final size:18
Alignment explanation
Indices: 4932--4974 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
4922 ATACTTCACT
*
4932 TTTTTTTTACTCGTACTC
1 TTTTTTTTACTCGAACTC
4950 TTTTTTTTACTCGAACTC
1 TTTTTTTTACTCGAACTC
4968 TTTTTTT
1 TTTTTTT
4975 CTCAATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.12, C:0.19, G:0.05, T:0.65
Consensus pattern (18 bp):
TTTTTTTTACTCGAACTC
Done.