Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2455
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: 24525
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:820 original size:20 final size:20
Alignment explanation
Indices: 782--851 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
772 TTACAATTTG
782 TATCGATATAAAT-AGTAAATA
1 TATCGATAT--ATGAGTAAATA
*
803 TATCGATATATGAGTAAATG
1 TATCGATATATGAGTAAATA
* **
823 TATCGATACATGCCTGAAATA
1 TATCGATATATGAGT-AAATA
844 TATCGATA
1 TATCGATA
852 GAAAACCACC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 2 0.05
20 19 0.45
21 21 0.50
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (20 bp):
TATCGATATATGAGTAAATA
Found at i:6626 original size:20 final size:19
Alignment explanation
Indices: 6577--6635 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 19
6567 GCTACCCTAA
*
6577 GTGAAATGTATCGATATAT
1 GTGAAATGTATCGATACAT
* *
6596 GGGACATTGTATCGATACAT
1 GTGA-AATGTATCGATACAT
6616 GATGAAATGTATCGATACAT
1 G-TGAAATGTATCGATACAT
6636 TGTGCCCAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
19 3 0.09
20 28 0.85
21 2 0.06
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.32
Consensus pattern (19 bp):
GTGAAATGTATCGATACAT
Found at i:8055 original size:27 final size:27
Alignment explanation
Indices: 8016--8079 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
8006 AACAGGATTG
*
8016 GAGTATCCTCTCGGAGGAATGGGGTTA
1 GAGTATCCCCTCGGAGGAATGGGGTTA
*
8043 GAGTATCCCCTCGGAGGAATGGGGTTG
1 GAGTATCCCCTCGGAGGAATGGGGTTA
8070 GAGTATCCCC
1 GAGTATCCCC
8080 GTTGATGACA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.20, C:0.20, G:0.36, T:0.23
Consensus pattern (27 bp):
GAGTATCCCCTCGGAGGAATGGGGTTA
Found at i:16751 original size:21 final size:20
Alignment explanation
Indices: 16727--16774 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
16717 CAAATCCTTT
16727 TCAAAATTCATC-ATTTTCACA
1 TCAAAATT-ATCTATTTT-ACA
* *
16748 TCAAAACTATCTATTTTTCA
1 TCAAAATTATCTATTTTACA
16768 TCAAAAT
1 TCAAAAT
16775 ATTTTTCAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.40, C:0.21, G:0.00, T:0.40
Consensus pattern (20 bp):
TCAAAATTATCTATTTTACA
Found at i:19268 original size:13 final size:13
Alignment explanation
Indices: 19246--19298 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
19236 GATACATGGG
19246 ACATTGTATCGAT
1 ACATTGTATCGAT
*
19259 ACATTTTATCGAT
1 ACATTGTATCGAT
19272 ACA-TG-AT-GA-
1 ACATTGTATCGAT
19281 A-A-TGTATCGAT
1 ACATTGTATCGAT
19292 ACATTGT
1 ACATTGT
19299 GCCCAACGAC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
8 3 0.09
9 3 0.09
10 4 0.12
11 3 0.09
12 2 0.06
13 18 0.55
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:19274 original size:33 final size:33
Alignment explanation
Indices: 19232--19296 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
19222 AAGTGAAATG
*
19232 TATCGATACATG-GGACATTGTATCGATACATTT
1 TATCGATACATGAGGA-AATGTATCGATACATTT
*
19265 TATCGATACATGATGAAATGTATCGATACATT
1 TATCGATACATGAGGAAATGTATCGATACATT
19297 GTGCCCAACG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 27 0.93
34 2 0.07
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (33 bp):
TATCGATACATGAGGAAATGTATCGATACATTT
Found at i:19355 original size:20 final size:20
Alignment explanation
Indices: 19326--19374 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
19316 TCAAATGCAT
*
19326 GTATCGATACATTATGAAAA
1 GTATCAATACATTATGAAAA
19346 GTATCAATACATTATGAAAA
1 GTATCAATACATTATGAAAA
19366 GTATCAATA
1 GTATCAATA
19375 TATAGTAACG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.31
Consensus pattern (20 bp):
GTATCAATACATTATGAAAA
Found at i:20240 original size:95 final size:94
Alignment explanation
Indices: 20056--20241 Score: 264
Period size: 95 Copynumber: 2.0 Consensus size: 94
20046 GAGCTTATAG
* * *
20056 ATGACAATTTAGGAAAATTAAGATTTAAATCTTGACAAGTTTAAAAATGGGGTTGGAGTATCCCA
1 ATGACAATTTAGCAAAAATAAGATTTAAATCTTGACAAGTTTAAAAATAGGGTTGGAGTATCCCA
** * **
20121 TCGGAAGAATGGGGTTGGAGTATCCCGAT
66 TAAGAAAAATGGGGTTAAAGTATCCCGAT
* *
20150 ATGACAATTTAAGCAAAAATATGATTTAAATCTTGACGAGTTTAAAAATAGGGTTGGAGTATCCC
1 ATGACAATTT-AGCAAAAATAAGATTTAAATCTTGACAAGTTTAAAAATAGGGTTGGAGTATCCC
*
20215 TTAAGAAAAATGGGGTTAAAGTATCCC
65 ATAAGAAAAATGGGGTTAAAGTATCCC
20242 CATGAATAAT
Statistics
Matches: 80, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
94 10 0.12
95 70 0.88
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.29
Consensus pattern (94 bp):
ATGACAATTTAGCAAAAATAAGATTTAAATCTTGACAAGTTTAAAAATAGGGTTGGAGTATCCCA
TAAGAAAAATGGGGTTAAAGTATCCCGAT
Found at i:22887 original size:20 final size:21
Alignment explanation
Indices: 22862--22914 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 21
22852 ATTTCAAGCA
**
22862 TGTATCGATACATTCTCTTG-
1 TGTATCGATACATTAACTTGT
22882 TGTATCGATACATTAACTTGT
1 TGTATCGATACATTAACTTGT
22903 TGTATCGATACA
1 TGTATCGATACA
22915 AATTGTAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (21 bp):
TGTATCGATACATTAACTTGT
Done.