Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1482
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: 30732
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:8431 original size:11 final size:11
Alignment explanation
Indices: 8415--8441 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
8405 TAACATGAAT
8415 AATTTTTTATA
1 AATTTTTTATA
8426 AATTTTTTATA
1 AATTTTTTATA
8437 AATTT
1 AATTT
8442 ATTTTGAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
AATTTTTTATA
Found at i:9104 original size:19 final size:19
Alignment explanation
Indices: 9080--9125 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 19
9070 ATTAATATAT
9080 TAATATTGAATATTTTAAA
1 TAATATTGAATATTTTAAA
*
9099 TAATATT---TATTTTCAA
1 TAATATTGAATATTTTAAA
9115 TAATATGTGAA
1 TAATAT-TGAA
9126 GAATCTTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 7
0.73 0.03 0.23
Matches are distributed among these distances:
16 14 0.64
17 1 0.05
19 7 0.32
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (19 bp):
TAATATTGAATATTTTAAA
Found at i:9116 original size:25 final size:27
Alignment explanation
Indices: 9061--9116 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
9051 AATTGTAATA
* * *
9061 AATATTTTTATTAATATATTAATATTG
1 AATATTTTAAATAATATATTAATATTC
*
9088 AATATTTTAAATAATAT-TT-ATTTTC
1 AATATTTTAAATAATATATTAATATTC
9113 AATA
1 AATA
9117 ATATGTGAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 8 0.32
26 2 0.08
27 15 0.60
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (27 bp):
AATATTTTAAATAATATATTAATATTC
Found at i:18053 original size:18 final size:18
Alignment explanation
Indices: 18030--18071 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
18020 ACCAGGTGAA
*
18030 TATCCTAGCCCTTATATG
1 TATCCTAACCCTTATATG
18048 TATCCTAACCCTTATATG
1 TATCCTAACCCTTATATG
*
18066 TTTCCT
1 TATCCT
18072 TTTCCCAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.21, C:0.29, G:0.07, T:0.43
Consensus pattern (18 bp):
TATCCTAACCCTTATATG
Found at i:29467 original size:20 final size:20
Alignment explanation
Indices: 29442--29503 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
29432 ATATACATGC
29442 TTTTATTATTGTATTTTTTA
1 TTTTATTATTGTATTTTTTA
* *
29462 TTTTATTATCGTCA-TTATTA
1 TTTTATTATTGT-ATTTTTTA
* *
29482 TTTTATT-TTATTTTTTTTA
1 TTTTATTATTGTATTTTTTA
29501 TTT
1 TTT
29504 GTTATTTTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
19 10 0.29
20 23 0.68
21 1 0.03
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.74
Consensus pattern (20 bp):
TTTTATTATTGTATTTTTTA
Found at i:29510 original size:21 final size:21
Alignment explanation
Indices: 29442--29523 Score: 76
Period size: 21 Copynumber: 3.8 Consensus size: 21
29432 ATATACATGC
* *
29442 TTTTATTATT-GTATTTTTTA
1 TTTTATTATTCTTATTTGTTA
*
29462 TTTTATTATCGTCATTATTATTTTA
1 TTTTATTAT--TC-TTATT-TGTTA
* *
29487 TTTTATTTTTTTTATTTGTTA
1 TTTTATTATTCTTATTTGTTA
29508 TTTTATTATTCTTATT
1 TTTTATTATTCTTATT
29524 AGTTGGGCAC
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
20 9 0.18
21 18 0.35
22 6 0.12
23 1 0.02
24 4 0.08
25 13 0.25
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.73
Consensus pattern (21 bp):
TTTTATTATTCTTATTTGTTA
Found at i:29522 original size:9 final size:8
Alignment explanation
Indices: 29453--29524 Score: 55
Period size: 8 Copynumber: 9.2 Consensus size: 8
29443 TTTATTATTG
29453 TATTTT-T
1 TATTTTAT
29460 TATTTTAT
1 TATTTTAT
* *
29468 TATCGTCAT
1 TAT-TTTAT
29477 TATTATT-T
1 TATT-TTAT
29485 TATTTTAT
1 TATTTTAT
29493 T-TTTT-T
1 TATTTTAT
*
29499 TA-TTTGT
1 TATTTTAT
29506 TATTTTAT
1 TATTTTAT
29514 TATTCTTAT
1 TATT-TTAT
29523 TA
1 TA
29525 GTTGGGCACT
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
6 5 0.10
7 15 0.29
8 19 0.37
9 13 0.25
ACGTcount: A:0.21, C:0.04, G:0.03, T:0.72
Consensus pattern (8 bp):
TATTTTAT
Done.