Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3730
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: 15845
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.29
Found at i:1360 original size:27 final size:27
Alignment explanation
Indices: 1193--1370 Score: 119
Period size: 27 Copynumber: 6.6 Consensus size: 27
1183 TAAATTGTAC
*
1193 AGCACTAAGTGTGCGA-TTCTACTT-TGT
1 AGCACTAAGTGTGCGAGTT-GA-TTATGT
* ** *
1220 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAGTTGATTATGT
* * ** **
1246 ATGCACTAAGAGTGCGAATTGACCATAC
1 A-GCACTAAGTGTGCGAGTTGATTATGT
* * *
1274 GGCACTAAGTGTGCGAGTCTAACTATGT
1 AGCACTAAGTGTGCGAGT-TGATTATGT
* *
1302 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGAGTTGATTATGT
* * *
1329 GGCACTAAATGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGATTATGT
*
1356 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
1371 GGCTCAATAT
Statistics
Matches: 116, Mismatches: 30, Indels: 10
0.74 0.19 0.06
Matches are distributed among these distances:
26 1 0.01
27 93 0.80
28 22 0.19
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGATTATGT
Found at i:1361 original size:82 final size:81
Alignment explanation
Indices: 1190--1370 Score: 204
Period size: 82 Copynumber: 2.2 Consensus size: 81
1180 GATTAAATTG
* * * *
1190 TACAGCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGAGTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
1255 GAGTGCGAATTGACCA
66 GAGTGCGAATTGACCA
* ** *
1271 TACGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACT
1 TACAGCACTAAGTGTGCGAGTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
1335 AA-ATGTGCGAGTTGATTA
64 AAGA-GTGCGAATTGACCA
* *
1353 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
1371 GGCTCAATAT
Statistics
Matches: 83, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
81 23 0.28
82 60 0.72
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGAGTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GAGTGCGAATTGACCA
Found at i:9330 original size:27 final size:27
Alignment explanation
Indices: 9163--9340 Score: 119
Period size: 27 Copynumber: 6.6 Consensus size: 27
9153 TAAATTGTAC
*
9163 AGCACTAAGTGTGCGA-TTCTACTT-TGT
1 AGCACTAAGTGTGCGAGTT-GA-TTATGT
* ** *
9190 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAGTTGATTATGT
* * ** **
9216 ATGCACTAAGAGTGCGAATTGACCATAC
1 A-GCACTAAGTGTGCGAGTTGATTATGT
* * *
9244 GGCACTAAGTGTGCGAGTCTAACTATGT
1 AGCACTAAGTGTGCGAGT-TGATTATGT
* *
9272 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGAGTTGATTATGT
* * *
9299 GGCACTAAATGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGATTATGT
*
9326 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
9341 GGCTCAATAT
Statistics
Matches: 116, Mismatches: 30, Indels: 10
0.74 0.19 0.06
Matches are distributed among these distances:
26 1 0.01
27 93 0.80
28 22 0.19
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGATTATGT
Found at i:9331 original size:82 final size:81
Alignment explanation
Indices: 9160--9340 Score: 204
Period size: 82 Copynumber: 2.2 Consensus size: 81
9150 GATTAAATTG
* * * *
9160 TACAGCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGAGTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
9225 GAGTGCGAATTGACCA
66 GAGTGCGAATTGACCA
* ** *
9241 TACGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACT
1 TACAGCACTAAGTGTGCGAGTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
9305 AA-ATGTGCGAGTTGATTA
64 AAGA-GTGCGAATTGACCA
* *
9323 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
9341 GGCTCAATAT
Statistics
Matches: 83, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
81 23 0.28
82 60 0.72
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGAGTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GAGTGCGAATTGACCA
Found at i:13017 original size:29 final size:29
Alignment explanation
Indices: 12938--13047 Score: 107
Period size: 29 Copynumber: 3.8 Consensus size: 29
12928 ACCCCTCCAT
* *
12938 ACATGCATATAGCCCACTAGGCCCAA-T-
1 ACATTCATATGGCCCACTAGGCCCAATTC
* * * *
12965 ATTATTCAAATGGCCCATTTGGCCCAATTC
1 A-CATTCATATGGCCCACTAGGCCCAATTC
* *
12995 ACATTCTTATGGCTCACTAGGCCCAATTC
1 ACATTCATATGGCCCACTAGGCCCAATTC
* *
13024 ACTTTCATATGGCCCATTAGGCCC
1 ACATTCATATGGCCCACTAGGCCC
13048 GAATCATATA
Statistics
Matches: 64, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
27 1 0.02
28 19 0.30
29 43 0.67
30 1 0.02
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.28
Consensus pattern (29 bp):
ACATTCATATGGCCCACTAGGCCCAATTC
Done.