Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1612
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, 888
Length: 1480
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.27
Found at i:114 original size:12 final size:12
Alignment explanation
Indices: 99--142 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
89 AAAAATATAT
99 AAAAAAATTTGA
1 AAAAAAATTTGA
111 AAAAAAATTTTGA
1 AAAAAAA-TTTGA
* *
124 AAAAAAAATTCA
1 AAAAAAATTTGA
136 AAAAAAA
1 AAAAAAA
143 AGTTTGTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 17 0.59
13 12 0.41
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (12 bp):
AAAAAAATTTGA
Found at i:115 original size:13 final size:13
Alignment explanation
Indices: 99--148 Score: 66
Period size: 13 Copynumber: 3.8 Consensus size: 13
89 AAAAATATAT
99 AAAAAAATTTGAA
1 AAAAAAATTTGAA
*
112 AAAAAATTTTGAA
1 AAAAAAATTTGAA
*
125 AAAAAAA-TTCAA
1 AAAAAAATTTGAA
137 AAAAAAAGTTTG
1 AAAAAAA-TTTG
149 TATTCAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
12 11 0.35
13 18 0.58
14 2 0.06
ACGTcount: A:0.66, C:0.02, G:0.08, T:0.24
Consensus pattern (13 bp):
AAAAAAATTTGAA
Found at i:226 original size:31 final size:31
Alignment explanation
Indices: 188--260 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
178 AGTATTGAAG
* * **
188 AAAAAAAAAGAAGAAGAAAAATTCGGAATTA
1 AAAAAAAAAGAAGAAAAAAAAATCAAAATTA
*
219 AAAAAAAAAGAAGAAAAAAAAATCAAAATTG
1 AAAAAAAAAGAAGAAAAAAAAATCAAAATTA
250 AAAAAAAAAGA
1 AAAAAAAAAGA
261 GTGATTGAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.75, C:0.03, G:0.12, T:0.10
Consensus pattern (31 bp):
AAAAAAAAAGAAGAAAAAAAAATCAAAATTA
Found at i:1105 original size:21 final size:21
Alignment explanation
Indices: 1081--1132 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
1071 GAGAGAAGAA
1081 AAAAAGAAAAAGAAATAAAAG
1 AAAAAGAAAAAGAAATAAAAG
1102 AAAAAGAAAAAGAAATAAAAG
1 AAAAAGAAAAAGAAATAAAAG
1123 AAAAAGAAAA
1 AAAAAGAAAA
1133 TGAGAGTGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (21 bp):
AAAAAGAAAAAGAAATAAAAG
Found at i:1130 original size:15 final size:14
Alignment explanation
Indices: 1076--1127 Score: 70
Period size: 15 Copynumber: 3.6 Consensus size: 14
1066 AAATTGAGAG
1076 AAGAAAAAAAGAAA
1 AAGAAAAAAAGAAA
1090 AAGAAATAAAAGAAA
1 AAGAAA-AAAAGAAA
1105 AAGAAAAAGAA-ATAA
1 AAGAAAAA-AAGA-AA
1120 AAGAAAAA
1 AAGAAAAA
1128 GAAAATGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.26
15 26 0.74
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (14 bp):
AAGAAAAAAAGAAA
Found at i:1131 original size:15 final size:15
Alignment explanation
Indices: 1103--1131 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1093 AAATAAAAGA
1103 AAAAGAAAAAGAAAT
1 AAAAGAAAAAGAAAT
1118 AAAAGAAAAAGAAA
1 AAAAGAAAAAGAAA
1132 ATGAGAGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (15 bp):
AAAAGAAAAAGAAAT
Found at i:1152 original size:6 final size:6
Alignment explanation
Indices: 1081--1132 Score: 50
Period size: 6 Copynumber: 7.7 Consensus size: 6
1071 GAGAGAAGAA
1081 AAAAAG AAAAAG AAATAAAAG AAAAAG AAAAAG AAATAAAAG AAAAAG
1 AAAAAG AAAAAG --A-AAAAG AAAAAG AAAAAG --A-AAAAG AAAAAG
1129 AAAA
1 AAAA
1133 TGAGAGTGAG
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
6 26 0.65
7 2 0.05
8 2 0.05
9 10 0.25
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (6 bp):
AAAAAG
Done.