Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: C10587
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 5467
ACGTcount: A:0.24, C:0.31, G:0.21, T:0.24
Found at i:1044 original size:15 final size:15
Alignment explanation
Indices: 1024--1094 Score: 115
Period size: 15 Copynumber: 4.7 Consensus size: 15
1014 CAGATCATAC
*
1024 GGTAACAACTCGTCT
1 GGTAACAACTCGTAT
1039 GGTAACAACTCGTAT
1 GGTAACAACTCGTAT
1054 GGTAACAACTCGTAT
1 GGTAACAACTCGTAT
*
1069 GGCAACAACTCGTAT
1 GGTAACAACTCGTAT
*
1084 GGCAACAACTC
1 GGTAACAACTC
1095 CTCTGGCAAC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 54 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (15 bp):
GGTAACAACTCGTAT
Left flanking sequence: Indices 524 -- 1023
CTGAGATCAACAACACCGACGCGAAACTCAAGTACCAACTTGACGCAACCATTGTCCTGTATGTG
AGGCTTCACAACCCCACTTTGACTTTTGACCCCACTCTTCGTGTACGTGAGTACGTCGCTAAAGC
ACGTCTGGCTTTAATGGATTCCCACAGAATGTTTGAGTACTACGTTGCAGCAATTGATCGGAGCC
CTCTCAAGATGGCCATACTTCACAATAACTCATGGTTCGATAAATTCTCAATCACCCTTACCGAG
CTTCTGGATGACATCCGTTACATGAGCCCCACAAAGGCTCATGCCATTGGTAACACTCTCTTTGC
ACACCGTCATTCACTTTCCATGGAACTCAAGTTTGAACTCCTCCAGCCCCTTTCCTTCTTCAACG
ACTGCAACATGAAAACACAAGAGACCATCAGTGCCCAAGCTCCTGGCATGATCACGTCAGTCGTT
CGAGGCGTCACCACTATCCGGGACAACCTCCCGCGCAGATCATAC
Right flanking sequence: Indices 1095 -- 1594
CTCTGGCAACGAAAACTCCAACAAACAGAATCGTTCTTACAACCCTGGCGCAAAATCATCCATCG
GTTACAGCCGTGGAGGATCTAACCAACTGAGAGGTGGCCAGCGTAACACGAACTTATCTCTGGAA
TATGCTCTGGAGTATGTGCAGGAGGAGGACGGCCCGTTCTACGACGAGGAGGATGGAGTGAACGC
TCCAGACGAGGAACAGCGTGCACTACCTTACTACGCGTAAATTTAGTGATGAGCTCTTTGCTCTA
GGCCCCCTCGCCTACTATGACACTGCTGCTGATTTCCCCATTGCCCTGACTGATACTATTTTGAC
TGATTTTACCCCAGAACCACACCACTACGATGCCACCAATGGCGCGCCCATCCTCGCCACCGGCT
ACGGCACTCTCACCATCTGTGATACAAAGGGGCACAAGGCCCAATTCGAAACTGCTCTTGTTCCT
CACACACCTGGTTTCCAGAGTGCTGCCGACGCTGTCATCAACCCG
Found at i:1058 original size:30 final size:30
Alignment explanation
Indices: 1024--1104 Score: 126
Period size: 30 Copynumber: 2.7 Consensus size: 30
1014 CAGATCATAC
*
1024 GGTAACAACTCGTCTGGTAACAACTCGTAT
1 GGTAACAACTCGTCTGGCAACAACTCGTAT
*
1054 GGTAACAACTCGTATGGCAACAACTCGTAT
1 GGTAACAACTCGTCTGGCAACAACTCGTAT
* *
1084 GGCAACAACTCCTCTGGCAAC
1 GGTAACAACTCGTCTGGCAAC
1105 GAAAACTCCA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (30 bp):
GGTAACAACTCGTCTGGCAACAACTCGTAT
Left flanking sequence: Indices 524 -- 1023
CTGAGATCAACAACACCGACGCGAAACTCAAGTACCAACTTGACGCAACCATTGTCCTGTATGTG
AGGCTTCACAACCCCACTTTGACTTTTGACCCCACTCTTCGTGTACGTGAGTACGTCGCTAAAGC
ACGTCTGGCTTTAATGGATTCCCACAGAATGTTTGAGTACTACGTTGCAGCAATTGATCGGAGCC
CTCTCAAGATGGCCATACTTCACAATAACTCATGGTTCGATAAATTCTCAATCACCCTTACCGAG
CTTCTGGATGACATCCGTTACATGAGCCCCACAAAGGCTCATGCCATTGGTAACACTCTCTTTGC
ACACCGTCATTCACTTTCCATGGAACTCAAGTTTGAACTCCTCCAGCCCCTTTCCTTCTTCAACG
ACTGCAACATGAAAACACAAGAGACCATCAGTGCCCAAGCTCCTGGCATGATCACGTCAGTCGTT
CGAGGCGTCACCACTATCCGGGACAACCTCCCGCGCAGATCATAC
Right flanking sequence: Indices 1105 -- 1604
GAAAACTCCAACAAACAGAATCGTTCTTACAACCCTGGCGCAAAATCATCCATCGGTTACAGCCG
TGGAGGATCTAACCAACTGAGAGGTGGCCAGCGTAACACGAACTTATCTCTGGAATATGCTCTGG
AGTATGTGCAGGAGGAGGACGGCCCGTTCTACGACGAGGAGGATGGAGTGAACGCTCCAGACGAG
GAACAGCGTGCACTACCTTACTACGCGTAAATTTAGTGATGAGCTCTTTGCTCTAGGCCCCCTCG
CCTACTATGACACTGCTGCTGATTTCCCCATTGCCCTGACTGATACTATTTTGACTGATTTTACC
CCAGAACCACACCACTACGATGCCACCAATGGCGCGCCCATCCTCGCCACCGGCTACGGCACTCT
CACCATCTGTGATACAAAGGGGCACAAGGCCCAATTCGAAACTGCTCTTGTTCCTCACACACCTG
GTTTCCAGAGTGCTGCCGACGCTGTCATCAACCCGGTGTACTTGC
Found at i:1101 original size:15 final size:15
Alignment explanation
Indices: 1027--1104 Score: 111
Period size: 15 Copynumber: 5.2 Consensus size: 15
1017 ATCATACGGT
* *
1027 AACAACTCGTCTGGT
1 AACAACTCGTATGGC
*
1042 AACAACTCGTATGGT
1 AACAACTCGTATGGC
1057 AACAACTCGTATGGC
1 AACAACTCGTATGGC
1072 AACAACTCGTATGGC
1 AACAACTCGTATGGC
* *
1087 AACAACTCCTCTGGC
1 AACAACTCGTATGGC
1102 AAC
1 AAC
1105 GAAAACTCCA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 59 1.00
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (15 bp):
AACAACTCGTATGGC
Left flanking sequence: Indices 527 -- 1026
AGATCAACAACACCGACGCGAAACTCAAGTACCAACTTGACGCAACCATTGTCCTGTATGTGAGG
CTTCACAACCCCACTTTGACTTTTGACCCCACTCTTCGTGTACGTGAGTACGTCGCTAAAGCACG
TCTGGCTTTAATGGATTCCCACAGAATGTTTGAGTACTACGTTGCAGCAATTGATCGGAGCCCTC
TCAAGATGGCCATACTTCACAATAACTCATGGTTCGATAAATTCTCAATCACCCTTACCGAGCTT
CTGGATGACATCCGTTACATGAGCCCCACAAAGGCTCATGCCATTGGTAACACTCTCTTTGCACA
CCGTCATTCACTTTCCATGGAACTCAAGTTTGAACTCCTCCAGCCCCTTTCCTTCTTCAACGACT
GCAACATGAAAACACAAGAGACCATCAGTGCCCAAGCTCCTGGCATGATCACGTCAGTCGTTCGA
GGCGTCACCACTATCCGGGACAACCTCCCGCGCAGATCATACGGT
Right flanking sequence: Indices 1105 -- 1604
GAAAACTCCAACAAACAGAATCGTTCTTACAACCCTGGCGCAAAATCATCCATCGGTTACAGCCG
TGGAGGATCTAACCAACTGAGAGGTGGCCAGCGTAACACGAACTTATCTCTGGAATATGCTCTGG
AGTATGTGCAGGAGGAGGACGGCCCGTTCTACGACGAGGAGGATGGAGTGAACGCTCCAGACGAG
GAACAGCGTGCACTACCTTACTACGCGTAAATTTAGTGATGAGCTCTTTGCTCTAGGCCCCCTCG
CCTACTATGACACTGCTGCTGATTTCCCCATTGCCCTGACTGATACTATTTTGACTGATTTTACC
CCAGAACCACACCACTACGATGCCACCAATGGCGCGCCCATCCTCGCCACCGGCTACGGCACTCT
CACCATCTGTGATACAAAGGGGCACAAGGCCCAATTCGAAACTGCTCTTGTTCCTCACACACCTG
GTTTCCAGAGTGCTGCCGACGCTGTCATCAACCCGGTGTACTTGC
Done.