Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold12595.1
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: 2158
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.34
Found at i:1030 original size:33 final size:33
Alignment explanation
Indices: 992--1054 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
982 GATTACTCAC
992 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
1025 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
1055 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:1087 original size:13 final size:12
Alignment explanation
Indices: 1071--1190 Score: 72
Period size: 12 Copynumber: 10.0 Consensus size: 12
1061 TTTTTTTGCT
1071 TTTTCTTTTTCAA
1 TTTTCTTTTTC-A
1084 TTTTCTTTTCTTCA
1 TTTTC-TTT-TTCA
1098 TTTTCTTTTTC-
1 TTTTCTTTTTCA
**
1109 TCTCACTTTTTCGA
1 T-TTTCTTTTTC-A
1123 -TTTCTTTTTC-
1 TTTTCTTTTTCA
** *
1133 TTTTGCAATTTCT
1 TTTT-CTTTTTCA
*
1146 TTTTCTTTTTCG
1 TTTTCTTTTTCA
*
1158 TTTTCTTTTT-G
1 TTTTCTTTTTCA
1169 TTTTC--TTTCA
1 TTTTCTTTTTCA
*
1179 ATTTCTTTTTCA
1 TTTTCTTTTTCA
1191 ATCTCTTTCT
Statistics
Matches: 85, Mismatches: 11, Indels: 23
0.71 0.09 0.19
Matches are distributed among these distances:
9 3 0.04
10 4 0.05
11 10 0.12
12 44 0.52
13 12 0.14
14 9 0.11
15 3 0.04
ACGTcount: A:0.08, C:0.18, G:0.03, T:0.70
Consensus pattern (12 bp):
TTTTCTTTTTCA
Found at i:1100 original size:14 final size:13
Alignment explanation
Indices: 1051--1107 Score: 53
Period size: 14 Copynumber: 4.2 Consensus size: 13
1041 TCAAGCTCTC
*
1051 TTTCAATTTCTTTT
1 TTTCATTTTC-TTT
*
1065 TTTGCTTTTTC-TT
1 TTT-CATTTTCTTT
1078 TTTCAATTTTCTTT
1 TTTC-ATTTTCTTT
1092 TCTTCATTTTCTTT
1 T-TTCATTTTCTTT
1106 TT
1 TT
1108 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
12 1 0.03
13 11 0.31
14 16 0.44
15 8 0.22
ACGTcount: A:0.09, C:0.16, G:0.02, T:0.74
Consensus pattern (13 bp):
TTTCATTTTCTTT
Found at i:1107 original size:15 final size:15
Alignment explanation
Indices: 1052--1109 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 15
1042 CAAGCTCTCT
*
1052 TTCAATTTCTTTTT-
1 TTCATTTTCTTTTTC
*
1066 TTGCTTTTTCTTTTTC
1 TT-CATTTTCTTTTTC
*
1082 --AATTTTC-TTTTC
1 TTCATTTTCTTTTTC
1094 TTCATTTTCTTTTTC
1 TTCATTTTCTTTTTC
1109 T
1 T
1110 CTCACTTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
12 5 0.15
13 5 0.15
14 8 0.24
15 16 0.47
ACGTcount: A:0.09, C:0.17, G:0.02, T:0.72
Consensus pattern (15 bp):
TTCATTTTCTTTTTC
Found at i:1167 original size:18 final size:18
Alignment explanation
Indices: 1064--1172 Score: 85
Period size: 18 Copynumber: 5.8 Consensus size: 18
1054 CAATTTCTTT
1064 TTTTGCTTTTTCTTTTTCAA
1 TTTT-CTTTTTCTTTTTC-A
* *
1084 TTTTCTTTTCTTCATTTTCT
1 TTTTC-TTT-TTCTTTTTCA
* **
1104 TTTTCTCTCACTTTTTCGA
1 TTTTCTTTTTCTTTTTC-A
*
1123 -TTTCTTTTTCTTTTGCA
1 TTTTCTTTTTCTTTTTCA
* *
1140 ATTTCTTTTTCTTTTTCG
1 TTTTCTTTTTCTTTTTCA
*
1158 TTTTCTTTTTGTTTT
1 TTTTCTTTTTCTTTT
1173 CTTTCAATTT
Statistics
Matches: 70, Mismatches: 15, Indels: 10
0.74 0.16 0.11
Matches are distributed among these distances:
17 1 0.01
18 46 0.66
19 3 0.04
20 12 0.17
21 8 0.11
ACGTcount: A:0.06, C:0.17, G:0.05, T:0.72
Consensus pattern (18 bp):
TTTTCTTTTTCTTTTTCA
Found at i:1189 original size:6 final size:6
Alignment explanation
Indices: 1063--1176 Score: 77
Period size: 6 Copynumber: 18.5 Consensus size: 6
1053 TCAATTTCTT
* * * **
1063 TTTTTGC TTTTTC TTTTTC AATTTTC TTTTCTTC ATTTTC TTTTTC TCTCAC
1 TTTTT-C TTTTTC TTTTTC -TTTTTC -TTT-TTC TTTTTC TTTTTC TTTTTC
** * ** *
1115 TTTTTC GATTTC TTTTTC TTTTGC AATTTC TTTTTC TTTTTC GTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
*
1163 TTTTT- GTTTTC TTT
1 TTTTTC TTTTTC TTT
1177 CAATTTCTTT
Statistics
Matches: 79, Mismatches: 25, Indels: 7
0.71 0.23 0.06
Matches are distributed among these distances:
5 4 0.05
6 58 0.73
7 14 0.18
8 3 0.04
ACGTcount: A:0.06, C:0.18, G:0.04, T:0.72
Consensus pattern (6 bp):
TTTTTC
Found at i:1208 original size:81 final size:83
Alignment explanation
Indices: 1054--1208 Score: 181
Period size: 81 Copynumber: 1.9 Consensus size: 83
1044 AGCTCTCTTT
* * ** *
1054 CAATTTCTTTTTTTGCTTTTTCTTTTTCAATTTTCTTTTCTTCATTTTCTTTTTCTCTCACTTTT
1 CAATTTC-TTTTTTGCTTTTTCGTTTTCAATTTTCTTTTCTTCAATTTCTTTTTCAATCACTTTC
*
1119 TCGATTTCTTTTTCTTTTG
65 TCCATTTCTTTTTCTTTTG
* * *
1138 CAATTTC-TTTTT-CTTTTTCGTTTTC-TTTTTGTTTTCTTTCAATTTCTTTTTCAATCTCTTTC
1 CAATTTCTTTTTTGCTTTTTCGTTTTCAATTTTCTTTTC-TTCAATTTCTTTTTCAATCACTTTC
*
1200 TCCTTTTCT
65 TCCATTTCT
1209 CGCTCAATGG
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
80 9 0.15
81 39 0.65
82 5 0.08
84 7 0.12
ACGTcount: A:0.08, C:0.20, G:0.03, T:0.68
Consensus pattern (83 bp):
CAATTTCTTTTTTGCTTTTTCGTTTTCAATTTTCTTTTCTTCAATTTCTTTTTCAATCACTTTCT
CCATTTCTTTTTCTTTTG
Done.