Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2612
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: 33087
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:3669 original size:26 final size:26
Alignment explanation
Indices: 3640--3695 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
3630 AACTTTAAGA
3640 AGCTCTTAAAAAAGATGAAGAACATG
1 AGCTCTTAAAAAAGATGAAGAACATG
*
3666 AGCTCTTAAAGAAGATGAAGAACATG
1 AGCTCTTAAAAAAGATGAAGAACATG
3692 AGCT
1 AGCT
3696 AACTCAAACC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.46, C:0.12, G:0.21, T:0.20
Consensus pattern (26 bp):
AGCTCTTAAAAAAGATGAAGAACATG
Found at i:5767 original size:47 final size:48
Alignment explanation
Indices: 5680--5786 Score: 117
Period size: 47 Copynumber: 2.2 Consensus size: 48
5670 TTTGCTCAAA
* * * *
5680 GTATCGATACTTCTGGAATTTTTCAGAATGTATCGATACAAGGCAAAAT
1 GTATCGATACATCTGG-AGTTTTCAGAATGTATCAATACAAAGCAAAAT
* * **
5729 GTATCGATACATCTGG-GTTTTCAGATTGTATTAATACAAAGCAATTT
1 GTATCGATACATCTGGAGTTTTCAGAATGTATCAATACAAAGCAAAAT
*
5776 GTATCAATACA
1 GTATCGATACA
5787 ATGTACTGAT
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
47 34 0.69
49 15 0.31
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.35
Consensus pattern (48 bp):
GTATCGATACATCTGGAGTTTTCAGAATGTATCAATACAAAGCAAAAT
Found at i:8384 original size:33 final size:33
Alignment explanation
Indices: 8328--8394 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
8318 CATGCAGATA
* *
8328 TATCGATACCAGTTGCTAAGTATCGATACATTG
1 TATCGATACAAATTGCTAAGTATCGATACATTG
* *
8361 TATCGATACAAATTTCTATGTATCGATACATTG
1 TATCGATACAAATTGCTAAGTATCGATACATTG
8394 T
1 T
8395 GAAATTATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.37
Consensus pattern (33 bp):
TATCGATACAAATTGCTAAGTATCGATACATTG
Found at i:8491 original size:21 final size:19
Alignment explanation
Indices: 8457--8515 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 19
8447 TACAACCTTG
*
8457 AAATTGTATTGATACATTA
1 AAATTATATTGATACATTA
* *
8476 TTAAATTATATCGATACATCA
1 --AAATTATATTGATACATTA
8497 AGAATTATATTGATACATT
1 A-AATTATATTGATACATT
8516 TGGCCTAATG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
19 1 0.03
20 15 0.47
21 16 0.50
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.41
Consensus pattern (19 bp):
AAATTATATTGATACATTA
Found at i:10522 original size:17 final size:17
Alignment explanation
Indices: 10502--10537 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
10492 TTAAAAAAAA
10502 AACCTATTGAAAACTAT
1 AACCTATTGAAAACTAT
10519 AACCTATTGAAAACTAT
1 AACCTATTGAAAACTAT
10536 AA
1 AA
10538 GATTATCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.17, G:0.06, T:0.28
Consensus pattern (17 bp):
AACCTATTGAAAACTAT
Found at i:14084 original size:20 final size:21
Alignment explanation
Indices: 14055--14137 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 21
14045 CCCTATATCG
14055 ATACAATGTATCGATACAAAGA
1 ATAC-ATGTATCGATACAAAGA
**
14077 ATA-ATGTATCGATACATTGA
1 ATACATGTATCGATACAAAGA
* *
14097 ATTTCCAGATGTATCGATACACAGA
1 A--T--ACATGTATCGATACAAAGA
14122 A-ACATGTATCGATACA
1 ATACATGTATCGATACA
14138 TTTTGGAAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
20 30 0.59
22 4 0.08
24 1 0.02
25 16 0.31
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (21 bp):
ATACATGTATCGATACAAAGA
Found at i:22468 original size:17 final size:16
Alignment explanation
Indices: 22446--22499 Score: 67
Period size: 17 Copynumber: 3.4 Consensus size: 16
22436 TATTTAAAAT
22446 ATTTTATATTTATATAA
1 ATTTTATA-TTATATAA
22463 ATTTTA-A-TATATAA
1 ATTTTATATTATATAA
*
22477 TAATTTATATTATATAA
1 -ATTTTATATTATATAA
22494 ATTTTA
1 ATTTTA
22500 AAAAAGGTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
14 7 0.22
15 5 0.16
16 7 0.22
17 13 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTTTATATTATATAA
Found at i:22475 original size:14 final size:14
Alignment explanation
Indices: 22456--22500 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 14
22446 ATTTTATATT
22456 TATATAAATTTTAA
1 TATATAAATTTTAA
*
22470 TATATAATAATTTATAT
1 TATAT-A-AATTT-TAA
22487 TATATAAATTTTAA
1 TATATAAATTTTAA
22501 AAAAGGTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 7 0.27
15 6 0.23
16 6 0.23
17 7 0.27
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TATATAAATTTTAA
Found at i:25617 original size:18 final size:18
Alignment explanation
Indices: 25594--25628 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
25584 ATATTATTTT
25594 ATTTAAAAATAAATTTAA
1 ATTTAAAAATAAATTTAA
* *
25612 ATTTAATAATATATTTA
1 ATTTAAAAATAAATTTA
25629 TTAAATATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTTAAAAATAAATTTAA
Found at i:25716 original size:14 final size:14
Alignment explanation
Indices: 25699--25803 Score: 56
Period size: 14 Copynumber: 7.1 Consensus size: 14
25689 TTTTATAAAA
25699 TAAATTTAAATATT
1 TAAATTTAAATATT
*
25713 TAAA-TTAATTATT
1 TAAATTTAAATATT
*
25726 TATATTATATAAATAAATT
1 TA-A--ATTTAAAT--ATT
*
25745 TAAATAATAAATATT
1 TAAAT-TTAAATATT
* *
25760 TAAAATTAATTCA-T
1 TAAATTTAAAT-ATT
25774 TATAA-TTATAATATT
1 TA-AATTTA-AATATT
25789 TAAATTTAAAT-TT
1 TAAATTTAAATATT
25802 TA
1 TA
25804 TTTAAATTTA
Statistics
Matches: 72, Mismatches: 7, Indels: 25
0.69 0.07 0.24
Matches are distributed among these distances:
13 14 0.19
14 21 0.29
15 18 0.25
16 3 0.04
17 10 0.14
18 1 0.01
19 5 0.07
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (14 bp):
TAAATTTAAATATT
Found at i:30582 original size:30 final size:30
Alignment explanation
Indices: 30548--30610 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
30538 TATACTTTTA
* * *
30548 TTGCATACAAATAAGCTCTTAACCTTTAAT
1 TTGCACACAAATAAACCCTTAACCTTTAAT
* *
30578 TTGCACCCAAATAAACCCTTAACTTTTAAT
1 TTGCACACAAATAAACCCTTAACCTTTAAT
30608 TTG
1 TTG
30611 TACTCAATCT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.35, C:0.22, G:0.06, T:0.37
Consensus pattern (30 bp):
TTGCACACAAATAAACCCTTAACCTTTAAT
Done.