Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2506
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: 30737
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:14524 original size:18 final size:20
Alignment explanation
Indices: 14501--14538 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
14491 ACGTGGCAGT
14501 CCAAC-TAGATTT-TAAATG
1 CCAACTTAGATTTCTAAATG
*
14519 CCAACTTGGATTTCTAAATG
1 CCAACTTAGATTTCTAAATG
14539 AGATAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 6 0.35
20 6 0.35
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.34
Consensus pattern (20 bp):
CCAACTTAGATTTCTAAATG
Found at i:15852 original size:18 final size:18
Alignment explanation
Indices: 15816--15854 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
15806 ACCAGTTTAA
*
15816 TTAAAAATTATTAAGATT
1 TTAAAAATTATTAAAATT
*
15834 TTAAAAATT-TTAAAAAT
1 TTAAAAATTATTAAAATT
15851 TTAA
1 TTAA
15855 TCATCTATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (18 bp):
TTAAAAATTATTAAAATT
Found at i:21620 original size:30 final size:30
Alignment explanation
Indices: 21568--21625 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
21558 CATGGCCATG
* *
21568 ACACACGGGTGTGTGGTCTACCCGTGTGTC
1 ACACACGGGCGTGTGGTCTACCCATGTGTC
*
21598 ACACATGGGCGTGTGGAT-TACCCATGTG
1 ACACACGGGCGTGTGG-TCTACCCATGTG
21626 GAACTGCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 23 0.96
31 1 0.04
ACGTcount: A:0.17, C:0.24, G:0.33, T:0.26
Consensus pattern (30 bp):
ACACACGGGCGTGTGGTCTACCCATGTGTC
Found at i:24346 original size:13 final size:13
Alignment explanation
Indices: 24328--24458 Score: 61
Period size: 13 Copynumber: 9.5 Consensus size: 13
24318 TAAAAATGAC
24328 ATAATAATATAAA
1 ATAATAATATAAA
*
24341 ATAAT-ATATATA
1 ATAATAATATAAA
*
24353 AT-ATGTATATAAAA
1 ATAAT-AATAT-AAA
* *
24367 ATAATGTATAGTATAT
1 ATAAT-AATA-TA-AA
* *
24383 ATATTAATATATA
1 ATAATAATATAAA
* *
24396 AT-ATAAGCACAAA
1 ATAATAA-TATAAA
24409 TATAATAACCATATATAA
1 -ATAATAA---TATA-AA
*
24427 ATAATAATGTAAA
1 ATAATAATATAAA
24440 ATAATAATATAAA
1 ATAATAATATAAA
24453 ATAATA
1 ATAATA
24459 TATTTAAAAC
Statistics
Matches: 90, Mismatches: 16, Indels: 24
0.69 0.12 0.18
Matches are distributed among these distances:
11 2 0.02
12 11 0.12
13 34 0.38
14 11 0.12
15 15 0.17
16 6 0.07
17 9 0.10
18 2 0.02
ACGTcount: A:0.59, C:0.03, G:0.04, T:0.34
Consensus pattern (13 bp):
ATAATAATATAAA
Found at i:24400 original size:24 final size:22
Alignment explanation
Indices: 24346--24400 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 22
24336 ATAAAATAAT
24346 ATATATAATAT-GTATATAAAA
1 ATATATAATATAGTATATAAAA
* *
24367 ATA-AT-GTATAGTATATATATTA
1 ATATATAATATAGTATATA-A-AA
24389 ATATATAATATA
1 ATATATAATATA
24401 AGCACAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 7
0.72 0.08 0.19
Matches are distributed among these distances:
19 3 0.12
20 9 0.35
21 4 0.15
22 4 0.15
23 2 0.08
24 4 0.15
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (22 bp):
ATATATAATATAGTATATAAAA
Found at i:24583 original size:25 final size:25
Alignment explanation
Indices: 24549--24602 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
24539 ATAATATATG
24549 ATAAAAATATAAGTAGTA-TTTTTTA
1 ATAAAAATATAAGTA-TAGTTTTTTA
* *
24574 ATAATAATATATGTATAGTTTTTT-
1 ATAAAAATATAAGTATAGTTTTTTA
24598 ATAAA
1 ATAAA
24603 TAGATTATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 6 0.24
25 19 0.76
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (25 bp):
ATAAAAATATAAGTATAGTTTTTTA
Found at i:27780 original size:18 final size:18
Alignment explanation
Indices: 27759--27801 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
27749 ATAATTTAAA
27759 ATATAAATTTATTAATAT
1 ATATAAATTTATTAATAT
27777 ATATAAATTTATTAATAT
1 ATATAAATTTATTAATAT
*
27795 ATGTAAA
1 ATATAAA
27802 AACAGCTTTT
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:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
ATATAAATTTATTAATAT
Found at i:27903 original size:19 final size:20
Alignment explanation
Indices: 27879--27921 Score: 79
Period size: 19 Copynumber: 2.2 Consensus size: 20
27869 TCCAAACATG
27879 GAAAAGTAAATCATTTTC-A
1 GAAAAGTAAATCATTTTCTA
27898 GAAAAGTAAATCATTTTCTA
1 GAAAAGTAAATCATTTTCTA
27918 GAAA
1 GAAA
27922 TTATTTTCCG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.49, C:0.09, G:0.12, T:0.30
Consensus pattern (20 bp):
GAAAAGTAAATCATTTTCTA
Done.