Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CotAD_44477
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: 1746
ACGTcount: A:0.50, C:0.07, G:0.31, T:0.12
Found at i:668 original size:30 final size:30
Alignment explanation
Indices: 634--741 Score: 76
Period size: 30 Copynumber: 3.3 Consensus size: 30
624 GAAGAAAAAG
634 GATAAAGAGAAAAAGAAGGAAAAGAAGACA
1 GATAAAGAGAAAAAGAAGGAAAAGAAGACA
664 GATAACGAGGATGAACAAAAGAAGGACAAGAAGAAGA-A
1 GATAA--A-GA-G-A-AAAAGAAGG--AA-AAGAAGACA
* * *
702 GGATAAGGAGAAAAAGGAA-GAAGAGAAGTCA
1 -GATAAAGAGAAAAA-GAAGGAAAAGAAGACA
733 GATAAAGAG
1 GATAAAGAG
742 GATGATGTAG
Statistics
Matches: 62, Mismatches: 4, Indels: 24
0.69 0.04 0.27
Matches are distributed among these distances:
30 18 0.29
31 3 0.05
32 1 0.02
33 7 0.11
34 5 0.08
35 2 0.03
36 11 0.18
38 3 0.05
39 12 0.19
ACGTcount: A:0.59, C:0.05, G:0.31, T:0.06
Consensus pattern (30 bp):
GATAAAGAGAAAAAGAAGGAAAAGAAGACA
Found at i:902 original size:27 final size:27
Alignment explanation
Indices: 863--918 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
853 GTCGAAGAGG
* *
863 AGGAGAAGAAGAAGAAGAAAGATAAGA
1 AGGAGAAGAAGAAAAAGAAAGAAAAGA
* *
890 AGGATAAGGAGAAAAAGAAAGAAAAGA
1 AGGAGAAGAAGAAAAAGAAAGAAAAGA
917 AG
1 AG
919 TCGGACGAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.32, T:0.04
Consensus pattern (27 bp):
AGGAGAAGAAGAAAAAGAAAGAAAAGA
Found at i:909 original size:93 final size:92
Alignment explanation
Indices: 697--1232 Score: 617
Period size: 93 Copynumber: 5.8 Consensus size: 92
687 GGACAAGAAG
* * *
697 AAGAAGGATAAGGAGAAAAAGGAAGAAGAGAAGTCAGATAAAGAGGATGATGTAGAAGATGCCAA
1 AAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGT-GGATAAAGAGGATGATGTAGAAGATGCC-A
762 AGAGAAGGAGAAGAAGAAGAAGAAGAAAGAT
64 A-AG-AGGAGAAGAAGAAGAAGAAGAAAGAT
* ** * * * * *
793 AATAAGGATAAGGAGAAAAAGAAAGACCAGAAGTGTGATAAAGAGGATGAGGAAGAAAATGTCGA
1 AAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTG-GATAAAGAGGATGATGTAGAAGATGCCAA
*
858 AGAGGAGGAGAAGAAGAAGAAGAAAGAT
65 AGAGGAGAAGAAGAAGAAGAAGAAAGAT
**
886 AAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTCGGACGAAGAGGATGATGTAGAAGATGCCAA
1 AAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGT-GGATAAAGAGGATGATGTAGAAGATGCCAA
*
951 AGAGGCA-AAGGAGAAGAAGAAGAAAGAT
65 AGAGG-AGAAGAAGAAGAAGAAGAAAGAT
* *
979 AACAAGGATAAGGAGAAAAAGAAAGATAAGAAGTGCGATAAAGAGGATGATGTAGAAGATGCC--
1 AAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTG-GATAAAGAGGATGATGTAGAAGATGCCAA
1042 A-A--AG-AG--G-AGAAGAAGAAAGAT
65 AGAGGAGAAGAAGAAGAAGAAGAAAGAT
* * * *
1063 AAGAAGGATAAGGAGAAGAAGAAAGATAAGAAGTCGGATGAAGAGGATGGA-GTAGAAGATGACA
1 AAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGT-GGATAAAGAGGAT-GATGTAGAAGATGCCA
* * *
1127 AAGAGGAGAAAAAGAAGAAAAAGAAAGAG
64 AAGAGGAGAAGAAGAAGAAGAAGAAAGAT
* ** * * *
1156 AAGAAGGATAAGGAGAAAAAGAAAGAACAGAAGTCCAATAAAGAGGATGATGTAAAAGATGACGA
1 AAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGT-GGATAAAGAGGATGATGTAGAAGATGCCAA
*
1221 AGAGAAGAAGAA
65 AGAGGAGAAGAA
1233 AGATAAGAAG
Statistics
Matches: 379, Mismatches: 44, Indels: 37
0.82 0.10 0.08
Matches are distributed among these distances:
84 68 0.18
85 4 0.01
86 1 0.00
87 4 0.01
89 2 0.01
90 2 0.01
91 1 0.00
92 4 0.01
93 235 0.62
94 4 0.01
95 1 0.00
96 53 0.14
ACGTcount: A:0.55, C:0.04, G:0.32, T:0.09
Consensus pattern (92 bp):
AAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTGGATAAAGAGGATGATGTAGAAGATGCCAAA
GAGGAGAAGAAGAAGAAGAAGAAAGAT
Found at i:1068 original size:12 final size:12
Alignment explanation
Indices: 1051--1095 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 12
1041 CAAAGAGGAG
1051 AAGAAGAAAGAT
1 AAGAAGAAAGAT
*
1063 AAGAAGGATAAGGAG
1 AAGAA-GA-AA-GAT
1078 AAGAAGAAAGAT
1 AAGAAGAAAGAT
1090 AAGAAG
1 AAGAAG
1096 TCGGATGAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
12 13 0.46
13 4 0.14
14 4 0.14
15 7 0.25
ACGTcount: A:0.62, C:0.00, G:0.31, T:0.07
Consensus pattern (12 bp):
AAGAAGAAAGAT
Found at i:1132 original size:177 final size:174
Alignment explanation
Indices: 697--1268 Score: 711
Period size: 177 Copynumber: 3.2 Consensus size: 174
687 GGACAAGAAG
* * *
697 AAGAAGGATAAGGAGAAAAAGGAAGAAGAGAAGTCAGATAAAGAGGATGATGTAGAAGATGCCAA
1 AAGAAGGATAAGGAGAAAAAGAAAGAA-AGAAGTCGGATGAAGAGGATGATGTAGAAGATGCC-A
* *
762 AGAGAAGGAGAAGAAGAAGAAGAAGAAAGATAATAAGGATAAGGAGAAAAAGAAAGACCAGAAGT
64 A-AG-AGGAGAAGAAGAAGAAGAAGAAAGATAACAAGGATAAGGAGAAAAAGAAAGA-AAGAAGT
* * * *
827 GTGATAAAGAGGATGAGGAAGAAAATGTCGAAGAGGAGGAGAAGAAGAAGAAGAAAGAT
126 GCGATAAAGAGGATGATGTAGAAGATG-C--A-A--A-GAG--G-AGAAGAAGAAAGAT
*
886 AAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTCGGACGAAGAGGATGATGTAGAAGATGCCAA
1 AAGAAGGATAAGGAGAAAAAGAAAG-AAAGAAGTCGGATGAAGAGGATGATGTAGAAGATGCCAA
*
951 AGAGGCA-AAGGAGAAGAAGAAGAAAGATAACAAGGATAAGGAGAAAAAGAAAGATAAGAAGTGC
65 AGAGG-AGAAGAAGAAGAAGAAGAAAGATAACAAGGATAAGGAGAAAAAGAAAGA-AAGAAGTGC
1015 GATAAAGAGGATGATGTAGAAGATGCCAAAGAGGAGAAGAAGAAAGAT
128 GATAAAGAGGATGATGTAGAAGATG-CAAAGAGGAGAAGAAGAAAGAT
* *
1063 AAGAAGGATAAGGAGAAGAAGAAAGATAAGAAGTCGGATGAAGAGGATGGA-GTAGAAGATGACA
1 AAGAAGGATAAGGAGAAAAAGAAAGA-AAGAAGTCGGATGAAGAGGAT-GATGTAGAAGATGCCA
* * * * *
1127 AAGAGGAGAAAAAGAAGAAAAAGAAAGAGAAGAAGGATAAGGAGAAAAAGAAAGAACAGAAGTCC
64 AAGAGGAGAAGAAGAAGAAGAAGAAAGATAACAAGGATAAGGAGAAAAAGAAAGAA-AGAAGTGC
* * * *
1192 AATAAAGAGGATGATGTAAAAGATG--ACGAAGAGAAGAAGAAAGAT
128 GATAAAGAGGATGATGTAGAAGATGCAAAGAGGAGAAGAAGAAAGAT
1237 AAGAAGGATAAGGAGAAAAAGAAAGAGAAGAA
1 AAGAAGGATAAGGAGAAAAAGAAAGA-AAGAA
1269 ACACGAGGAT
Statistics
Matches: 349, Mismatches: 28, Indels: 27
0.86 0.07 0.07
Matches are distributed among these distances:
174 48 0.14
176 3 0.01
177 148 0.42
178 3 0.01
180 3 0.01
181 1 0.00
183 1 0.00
184 1 0.00
186 78 0.22
187 3 0.01
188 2 0.01
189 56 0.16
190 2 0.01
ACGTcount: A:0.55, C:0.04, G:0.32, T:0.09
Consensus pattern (174 bp):
AAGAAGGATAAGGAGAAAAAGAAAGAAAGAAGTCGGATGAAGAGGATGATGTAGAAGATGCCAAA
GAGGAGAAGAAGAAGAAGAAGAAAGATAACAAGGATAAGGAGAAAAAGAAAGAAAGAAGTGCGAT
AAAGAGGATGATGTAGAAGATGCAAAGAGGAGAAGAAGAAAGAT
Found at i:1235 original size:12 final size:12
Alignment explanation
Indices: 1220--1268 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
1210 AAAGATGACG
1220 AAGAGAAGAAGA
1 AAGAGAAGAAGA
*
1232 AAGATAAGAAGGA
1 AAGAGAAGAA-GA
*
1245 TAAGGAGAAAAAGA
1 -AA-GAGAAGAAGA
1259 AAGAGAAGAA
1 AAGAGAAGAA
1269 ACACGAGGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
12 16 0.53
13 4 0.13
14 4 0.13
15 6 0.20
ACGTcount: A:0.65, C:0.00, G:0.31, T:0.04
Consensus pattern (12 bp):
AAGAGAAGAAGA
Done.