Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold53
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1214666
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.30
Warning! 104343 characters in sequence are not A, C, G, or T
File 5 of 4
Found at i:1170625 original size:17 final size:17
Alignment explanation
Indices: 1170601--1170634 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1170591 CGAATTTTAC
1170601 ACTTATCTTTG-CATAT
1 ACTTATCTTTGACATAT
1170617 ACTTAATCTTTGACATAT
1 ACTT-ATCTTTGACATAT
1170635 TTACCTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 7 0.44
18 5 0.31
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.47
Consensus pattern (17 bp):
ACTTATCTTTGACATAT
Found at i:1172158 original size:17 final size:17
Alignment explanation
Indices: 1172136--1172168 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1172126 CTGGTACTGT
1172136 ACCAGTTATCGGCTAAG
1 ACCAGTTATCGGCTAAG
1172153 ACCAGTTATCGGCTAA
1 ACCAGTTATCGGCTAA
1172169 ACTGAGAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.24
Consensus pattern (17 bp):
ACCAGTTATCGGCTAAG
Found at i:1173631 original size:19 final size:19
Alignment explanation
Indices: 1173607--1173643 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1173597 AAATTTTTAC
*
1173607 ATATATTGTTTATATATAT
1 ATATATTGTTTACATATAT
1173626 ATATATTGTTTACATATA
1 ATATATTGTTTACATATA
1173644 CCTTCGAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (19 bp):
ATATATTGTTTACATATAT
Found at i:1176194 original size:11 final size:11
Alignment explanation
Indices: 1176178--1176206 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1176168 GTATATAGAG
1176178 CAATGTACACA
1 CAATGTACACA
1176189 CAATGTACACA
1 CAATGTACACA
1176200 CAATGTA
1 CAATGTA
1176207 TGATTGTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.45, C:0.24, G:0.10, T:0.21
Consensus pattern (11 bp):
CAATGTACACA
Found at i:1176698 original size:2 final size:2
Alignment explanation
Indices: 1176691--1176736 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1176681 CCTGGGATAA
1176691 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1176733 TC TC
1 TC TC
1176737 CTTGGCGTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1187742 original size:15 final size:15
Alignment explanation
Indices: 1187719--1187750 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1187709 ATAAAAATAA
*
1187719 TTTATTTTTTGCGAT
1 TTTAATTTTTGCGAT
1187734 TTTAATTTTTGCGAT
1 TTTAATTTTTGCGAT
1187749 TT
1 TT
1187751 CACTTTGACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.12, T:0.66
Consensus pattern (15 bp):
TTTAATTTTTGCGAT
Found at i:1189110 original size:15 final size:15
Alignment explanation
Indices: 1189086--1189116 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1189076 TGAAATCCAT
1189086 GATGCAGTCACAATA
1 GATGCAGTCACAATA
*
1189101 GATGCGGTCACAATA
1 GATGCAGTCACAATA
1189116 G
1 G
1189117 GGTGTTTTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.19
Consensus pattern (15 bp):
GATGCAGTCACAATA
Found at i:1190084 original size:12 final size:12
Alignment explanation
Indices: 1190067--1190091 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1190057 TATAACTTTA
1190067 TGATATCACATG
1 TGATATCACATG
1190079 TGATATCACATG
1 TGATATCACATG
1190091 T
1 T
1190092 AAAATATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (12 bp):
TGATATCACATG
Found at i:1193457 original size:24 final size:24
Alignment explanation
Indices: 1193427--1193475 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
1193417 GGTAAAATAT
1193427 TTTTGCGC-TACGCTGTTAGACATA
1 TTTTGCGCTTAC-CTGTTAGACATA
*
1193451 TTTTGCGCTTACCTGTTAGATATA
1 TTTTGCGCTTACCTGTTAGACATA
1193475 T
1 T
1193476 AAATTGATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.87
25 3 0.13
ACGTcount: A:0.20, C:0.18, G:0.18, T:0.43
Consensus pattern (24 bp):
TTTTGCGCTTACCTGTTAGACATA
Found at i:1196977 original size:13 final size:14
Alignment explanation
Indices: 1196959--1196987 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1196949 TTAATTTAAA
1196959 TTTTTTTTTA-ATT
1 TTTTTTTTTAGATT
1196972 TTTTTTTTTAGATT
1 TTTTTTTTTAGATT
1196986 TT
1 TT
1196988 GGGATATAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.83
Consensus pattern (14 bp):
TTTTTTTTTAGATT
Found at i:1203420 original size:27 final size:26
Alignment explanation
Indices: 1203364--1203420 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
1203354 ATTTTTTATT
1203364 AAAAAAATGATCGGATTGAAAATTGG
1 AAAAAAATGATCGGATTGAAAATTGG
*
1203390 AAAAAAATGATCGGATTGTAAATTGG
1 AAAAAAATGATCGGATTGAAAATTGG
1203416 AAAAA
1 AAAAA
1203421 TTATGTGGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.53, C:0.04, G:0.21, T:0.23
Consensus pattern (26 bp):
AAAAAAATGATCGGATTGAAAATTGG
Found at i:1212787 original size:4 final size:4
Alignment explanation
Indices: 1212732--1212772 Score: 57
Period size: 4 Copynumber: 10.2 Consensus size: 4
1212722 GTAGAAAGGA
*
1212732 AGAT AGAT AGAT AGAT -GAAT AGAT ATAT AGAT AGAT AGAT A
1 AGAT AGAT AGAT AGAT AG-AT AGAT AGAT AGAT AGAT AGAT A
1212773 TTCTTTAGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 1 0.03
4 31 0.94
5 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.22, T:0.27
Consensus pattern (4 bp):
AGAT
Found at i:1212827 original size:2 final size:2
Alignment explanation
Indices: 1212820--1212859 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1212810 GTGTTTGCGT
1212820 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1212860 ACTGTAAAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Done.