Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1373
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: 1895
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.34
Warning! 65 characters in sequence are not A, C, G, or T
Found at i:979 original size:27 final size:27
Alignment explanation
Indices: 941--1069 Score: 161
Period size: 27 Copynumber: 4.8 Consensus size: 27
931 CGAATAGTAC
* * *
941 AATGACCGAAATACCCTCAAAAGGTAA
1 AATGACTGAAATACCCCCAAAGGGTAA
968 AATGACTGAAATACCCCCAAAGGGTAA
1 AATGACTGAAATACCCCCAAAGGGTAA
* ** *
995 AATAACTGAAATACCCCTGAAGGGTAG
1 AATGACTGAAATACCCCCAAAGGGTAA
* *
1022 AATGA-TCGAAATACCCTCGAAGGGTAA
1 AATGACT-GAAATACCCCCAAAGGGTAA
1049 AATGACTGAAATACCCCCAAA
1 AATGACTGAAATACCCCCAAA
1070 NNNNNNNNNN
Statistics
Matches: 87, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
26 1 0.01
27 85 0.98
28 1 0.01
ACGTcount: A:0.44, C:0.22, G:0.18, T:0.16
Consensus pattern (27 bp):
AATGACTGAAATACCCCCAAAGGGTAA
Found at i:1225 original size:53 final size:54
Alignment explanation
Indices: 1136--1262 Score: 206
Period size: 53 Copynumber: 2.4 Consensus size: 54
1126 NNNNNNNNNC
* *
1136 CCCT-GAAGGGTAAAATGACCGAAATACCCTCGAAGGGTAAAATGACCGAAATA
1 CCCTCGAAGGGTAAAATGACTGAAATACCCTCAAAGGGTAAAATGACCGAAATA
1189 CCCTCGAAGGGT-AAATGACTGAAATACCCTCAAAGGGTAAAATGACCGAAATA
1 CCCTCGAAGGGTAAAATGACTGAAATACCCTCAAAGGGTAAAATGACCGAAATA
1242 CCCTC-ATAGGGTAAAATGACT
1 CCCTCGA-AGGGTAAAATGACT
1263 TTTATACTCC
Statistics
Matches: 69, Mismatches: 2, Indels: 5
0.91 0.03 0.07
Matches are distributed among these distances:
52 1 0.01
53 53 0.77
54 15 0.22
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.17
Consensus pattern (54 bp):
CCCTCGAAGGGTAAAATGACTGAAATACCCTCAAAGGGTAAAATGACCGAAATA
Found at i:1269 original size:27 final size:27
Alignment explanation
Indices: 1136--1261 Score: 204
Period size: 27 Copynumber: 4.7 Consensus size: 27
1126 NNNNNNNNNC
1136 CCCT-GAAGGGTAAAATGACCGAAATA
1 CCCTCGAAGGGTAAAATGACCGAAATA
1162 CCCTCGAAGGGTAAAATGACCGAAATA
1 CCCTCGAAGGGTAAAATGACCGAAATA
*
1189 CCCTCGAAGGGT-AAATGACTGAAATA
1 CCCTCGAAGGGTAAAATGACCGAAATA
*
1215 CCCTCAAAGGGTAAAATGACCGAAATA
1 CCCTCGAAGGGTAAAATGACCGAAATA
1242 CCCTC-ATAGGGTAAAATGAC
1 CCCTCGA-AGGGTAAAATGAC
1262 TTTTATACTC
Statistics
Matches: 94, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
26 29 0.31
27 65 0.69
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.17
Consensus pattern (27 bp):
CCCTCGAAGGGTAAAATGACCGAAATA
Found at i:1465 original size:26 final size:26
Alignment explanation
Indices: 1436--1512 Score: 82
Period size: 26 Copynumber: 3.0 Consensus size: 26
1426 TTGCTACATA
*
1436 TACTGTTATTGGCAACTTTGCTGCGT
1 TACTGTTACTGGCAACTTTGCTGCGT
* *
1462 TACTGTTACTGGCATCTTTGTTGCGT
1 TACTGTTACTGGCAACTTTGCTGCGT
* * * * *
1488 CATTATTACTGACAGCTTTGCTGCG
1 TACTGTTACTGGCAACTTTGCTGCG
1513 ATATTGGTGT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.16, C:0.21, G:0.22, T:0.42
Consensus pattern (26 bp):
TACTGTTACTGGCAACTTTGCTGCGT
Found at i:1659 original size:30 final size:31
Alignment explanation
Indices: 1618--1678 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 31
1608 ACTGCATTGT
*
1618 ACTGATTACTGTATTGGGCTAAGGCCCACAC
1 ACTGATTACTGTAATGGGCTAAGGCCCACAC
1649 ACTG-TTACTGTAATGGGCTAAGGCCCACAC
1 ACTGATTACTGTAATGGGCTAAGGCCCACAC
1679 TGTACTGATA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 25 0.86
31 4 0.14
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (31 bp):
ACTGATTACTGTAATGGGCTAAGGCCCACAC
Done.