Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold47
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: 4828
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3041 original size:16 final size:16
Alignment explanation
Indices: 3020--3050 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3010 TTTATTATTC
*
3020 CAACGTTGAGAAATGT
1 CAACGTTAAGAAATGT
3036 CAACGTTAAGAAATG
1 CAACGTTAAGAAATG
3051 CGCGGAGAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.13, G:0.23, T:0.23
Consensus pattern (16 bp):
CAACGTTAAGAAATGT
Left flanking sequence: Indices 2520 -- 3019
ACTTAGTACTCGTAACCTTGATGCTCCTTGCGACTTGCCTCCTTTTGCCCTACTCTTCACCTTGA
AGGTGTGTCAGATTATGAGGATCTGAGTCGTTTTTACACTGCTTTCAGCGCTATCTGCTCTGATT
GCATTTACTACATTTTGGGTAGATAAAACTTACCCATGGGCACATACCGACGGTCAAACTCCAAA
GAGCTAAATCGAATTTGCTATCAATGGGGTACCCCTCCACGGCAGGAACTCCGAATCCATTACCC
AAAATGATGATACACCTCCATGTGAGACGGCTAGCTAAACCTTGAACTACCTATTTTCATCGTTA
CTACGATCTTTTGCGTATTAACACTGAATACGAATGCAGGAGAACGACATGAATATAGGCAAATT
TTCCGCTCACTACTGCTGAAATGTTTTCCGCCAACGATGTAATTACCTTTTGCGATTAAACGTTT
CTCTCCTGATCATATTACTCCGGCTCAAGGGTAAATTTATTATTC
Right flanking sequence: Indices 3051 -- 3550
CGCGGAGAAATTTCCGCATTAAGTGTAAAAGCGGGATTGTTGTCAAGAAACTCAATCAGAAGTCA
AATAACGTGATCGCTCAGTAGCTCACAATTCTAGTTTGAACTTATCCACAATTCCGCAGTTTTCT
ACCAAAGCTCCAGTCGATCGACCTATAGTACGAATTTAAGAGTGATTCGGAATGAAGACAGACGG
CTGTAGTAGACAAACCGTAGAATTAGTTTCATGCCTAAAACCGGCCTAAAACCGGTAATTACTAT
CAGCTATCATCCGAAAATTGGTTACCGCATTGATCAGTGCATATGATACGAAACTGGAGGCAGCG
GCAGCTTCTCCCACGTATGACTAGGGATGTGTCTGGGTGTGTTGCGGCCATTCGCGCTACTTCAG
TGACTCCAAACTCGCGTAACATGCAATAAATTAGGCCCTTTCGCACCTAATAAAAGGATACAATA
AACCTGATAACTAGACAAAACTAATAAAGACTGATAAGAAAACCG
Found at i:4772 original size:188 final size:187
Alignment explanation
Indices: 4455--4828 Score: 730
Period size: 188 Copynumber: 2.0 Consensus size: 187
4445 CGGTGTTTTT
4455 TGAGATCGACGGCAAATGAAGATGTTGCCTATTTCCAGTGACTGCTTAAAAATTGGTCAACACGC
1 TGAGATCGACGGCAAATGAAGATGTTGCCTATTTCCAGTGACTGCTTAAAAATTGGTCAACACGC
*
4520 AGAAAGTGACCGAATACGGAGGCCCGCCCTCGAGGTCAGAAGCCAAGGGACCGAAGGTGCCGTTG
66 AGAAAGTGACCGAATACGGAGACCCGCCCTCGAGGTCAGAAGCCAAGGGACCGAAGGTGCCGTTG
4585 GAAAGCTCCATGTCGTTTTTAACCATGGTGGATTTCTTACTCAATTCGAAGGGTACA
131 GAAAGCTCCATGTCGTTTTTAACCATGGTGGATTTCTTACTCAATTCGAAGGGTACA
4642 NTGAGATCGACGGCAAATGAAGATGTTGCCTATTTCCAGTGACTGCTTAAAAATTGGTCAACACG
1 -TGAGATCGACGGCAAATGAAGATGTTGCCTATTTCCAGTGACTGCTTAAAAATTGGTCAACACG
4707 CAGAAAGTGACCGAATACGGAGACCCGCCCTCGAGGTCAGAAGCCAAGGGACCGAAGGTGCCGTT
65 CAGAAAGTGACCGAATACGGAGACCCGCCCTCGAGGTCAGAAGCCAAGGGACCGAAGGTGCCGTT
4772 GGAAAGCTCCATGTCGTTTTTAACCATGGTGGATTTCTTACTCAATTCGAAGGGTAC
130 GGAAAGCTCCATGTCGTTTTTAACCATGGTGGATTTCTTACTCAATTCGAAGGGTAC
Statistics
Matches: 185, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
188 185 1.00
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.23
Consensus pattern (187 bp):
TGAGATCGACGGCAAATGAAGATGTTGCCTATTTCCAGTGACTGCTTAAAAATTGGTCAACACGC
AGAAAGTGACCGAATACGGAGACCCGCCCTCGAGGTCAGAAGCCAAGGGACCGAAGGTGCCGTTG
GAAAGCTCCATGTCGTTTTTAACCATGGTGGATTTCTTACTCAATTCGAAGGGTACA
Left flanking sequence: Indices 3955 -- 4454
GAACAAATTGTATGGGTATACTCTCACAGATTTTCTCGACCTGTGAATTACAATTGTTTAGTTTA
TACCGATTGTTACGAAAACTTTTTAGAAGCCGAACCCTCTATTTCCATATCCTGAGTCATTCAAG
CGAACTTTAACTGCTAACGACTCCATTTAAGACTGAAATAATGCAACTGACTAGTTACTAAACGA
ACTATTAATGTCCGTGGAGTTTATCGAGAAAAGTTAAAATCGCTAACTCCAACGCCAACGTGAAT
GACTACGTTTCTGCGGGTGAATGCTCTCCTGGCGAATCTACTAGCCAGAATTCCTCATTCTAACG
GCTCTTAAGAGAATTGTGGGTCTGCTATGGTTGAGAGTACATTTACCCCATAATCACTAATCTAC
TTTTCAGTATTCAACTGGCTGTCTGATTCACAGCACTATTTGTGGCGCCAGTACGTCTATAAACT
AGGGATAAAATAATCGGTAAACTCAGATGAATGGTCGGTGTTTTT
Right flanking sequence: None
Done.