Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2591
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: 20526
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:2434 original size:13 final size:13
Alignment explanation
Indices: 2412--2444 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
2402 GATACAATTC
2412 TACA-TGTATCGA
1 TACATTGTATCGA
2424 TACATTGTATCGA
1 TACATTGTATCGA
2437 TACATTGT
1 TACATTGT
2445 GTCATGTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.20
13 16 0.80
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.39
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:2438 original size:33 final size:33
Alignment explanation
Indices: 2396--2458 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
2386 TTTGAGGCAA
2396 TGTATCGATACAATTCT-ACATGTATCGATACAT
1 TGTATCGATAC-ATTCTGACATGTATCGATACAT
* *
2429 TGTATCGATACATTGTGTCATGTATCGATA
1 TGTATCGATACATTCTGACATGTATCGATA
2459 TAAATAGTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 4 0.15
33 23 0.85
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (33 bp):
TGTATCGATACATTCTGACATGTATCGATACAT
Found at i:2513 original size:20 final size:19
Alignment explanation
Indices: 2488--2575 Score: 71
Period size: 20 Copynumber: 4.8 Consensus size: 19
2478 TACTGCCAGT
2488 TTCATGTATCGATACATTTG
1 TTCATGTATCGATACA-TTG
* *
2508 TTCATGTAACGATACAATG
1 TTCATGTATCGATACATTG
**
2527 AACATGTATCGATACA---
1 TTCATGTATCGATACATTG
*
2543 ---ATGTATCAATACATTTG
1 TTCATGTATCGATACA-TTG
2560 TTCATGTATCGATACA
1 TTCATGTATCGATACA
2576 AAGCATAATG
Statistics
Matches: 54, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
13 12 0.22
19 15 0.28
20 27 0.50
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (19 bp):
TTCATGTATCGATACATTG
Found at i:2573 original size:52 final size:53
Alignment explanation
Indices: 2491--2595 Score: 160
Period size: 52 Copynumber: 2.0 Consensus size: 53
2481 TGCCAGTTTC
* *
2491 ATGTATCGATACATTTGTTCATGTAACGATACAATG-A-ACATGTATCGATACA
1 ATGTATCAATACATTTGTTCATGTAACGATACAAAGCATA-ATGTATCGATACA
*
2543 ATGTATCAATACATTTGTTCATGTATCGATACAAAGCATAATGTATCGATACA
1 ATGTATCAATACATTTGTTCATGTAACGATACAAAGCATAATGTATCGATACA
2596 TTTGAAAGTG
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
52 33 0.69
53 14 0.29
54 1 0.02
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.33
Consensus pattern (53 bp):
ATGTATCAATACATTTGTTCATGTAACGATACAAAGCATAATGTATCGATACA
Found at i:5096 original size:13 final size:13
Alignment explanation
Indices: 5077--5116 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
5067 ATAGTAACCC
5077 ATGTATCGATACA
1 ATGTATCGATACA
* *
5090 TTGTATCAATACA
1 ATGTATCGATACA
5103 ATGTATCGATACA
1 ATGTATCGATACA
5116 A
1 A
5117 AGAACATTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:11694 original size:23 final size:24
Alignment explanation
Indices: 11650--11698 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
11640 AACAAAAAAG
11650 AAAAAGAAAAAGAATGAAAAATGGA
1 AAAAAGAAAAAGAATG-AAAATGGA
*
11675 AAAAAGAAAAAGTATG-AAATGGA
1 AAAAAGAAAAAGAATGAAAATGGA
11698 A
1 A
11699 CAAGTGTAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.35
25 15 0.65
ACGTcount: A:0.69, C:0.00, G:0.20, T:0.10
Consensus pattern (24 bp):
AAAAAGAAAAAGAATGAAAATGGA
Found at i:11979 original size:11 final size:11
Alignment explanation
Indices: 11958--11988 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
11948 GTTGTGAAAG
11958 AGAAGAAAAAAA
1 AGAA-AAAAAAA
11970 AGAAAAAAAAA
1 AGAAAAAAAAA
11981 AGAAAAAA
1 AGAAAAAA
11989 GAGAAATGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (11 bp):
AGAAAAAAAAA
Found at i:13882 original size:47 final size:48
Alignment explanation
Indices: 13809--13931 Score: 160
Period size: 48 Copynumber: 2.6 Consensus size: 48
13799 TATACCTGGC
* *
13809 CAAACTCTTTTCCT-CCTTGTTTGACTATATT-GGGTTAAGGCCTAAT
1 CAAACTCTTTTCTTCCCTCGTTTGACTATATTAGGGTTAAGGCCTAAT
* * * *
13855 CAAACTCTTGTCTTCCCTCGTTTGACTATATTAGTGTTAGGGCCTAGT
1 CAAACTCTTTTCTTCCCTCGTTTGACTATATTAGGGTTAAGGCCTAAT
* *
13903 CAAACACTTTTCTTCCCTCATTTGACTAT
1 CAAACTCTTTTCTTCCCTCGTTTGACTAT
13932 TGTACACACC
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
46 12 0.18
47 16 0.24
48 38 0.58
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.41
Consensus pattern (48 bp):
CAAACTCTTTTCTTCCCTCGTTTGACTATATTAGGGTTAAGGCCTAAT
Done.