Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga10g02689.F1
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: 3586
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Found at i:759 original size:135 final size:133
Alignment explanation
Indices: 512--934 Score: 436
Period size: 135 Copynumber: 3.1 Consensus size: 133
502 GGCTACCGTG
** * * ** * ** * *
512 TTTATGAACATTAAAAAGCGGAGCAAACGTAGAAATTTGGACAGTAAGATGACCGAAAGAATCCC
1 TTTATGAACATTAAAGCGCAGAGCAAGCACAGAAACTTGGACAGTGCGATGACAGAAAGAAGCCC
* * *
577 TCAGGAGAATAAGAAGGATGCAATGAGTGAAAGAAGCTCTGAAGAGACTAAGAAGGAAAACTGCG
66 TCAGGAGAATAAGAAGGATGCAATGA-TGAAAGAAGCCCTCAGGAGACTAAGAAGGAAAACTGCG
642 ATCGT
130 ATC-T
* * * * ***
647 TTTATGAACGTTAAAGTGCGGAGCAAAG-GCAGAAACTTGGTTGGTGCGATGACAGAAAGAAGCC
1 TTTATGAACATTAAAGCGCAGAGC-AAGCACAGAAACTTGGACAGTGCGATGACAGAAAGAAGCC
* * * * * *
711 CTCAGGAGAGTGAGGAGAATGCAATGACTGAAAGTAGCCCTCAGGAGACTAAGAAGGAAAACTGT
65 CTCAGGAGAATAAGAAGGATGCAATGA-TGAAAGAAGCCCTCAGGAGACTAAGAAGGAAAACTGC
776 GATCTT
129 GATC-T
* * * *
782 TTTGTGAACATTAAAGCGCAGAGCAAGCACAGGAATTTGGACAGTGCTATGA-ATGAAAGAAGCC
1 TTTATGAACATTAAAGCGCAGAGCAAGCACAGAAACTTGGACAGTGCGATGACA-GAAAGAAGCC
* * * *
846 CTCGGGAGACTAAGAAGGATGCAATGATCGAAAGAAGCCCTCAGGAGACTAAAAAGGAAAATTGC
65 CTCAGGAGAATAAGAAGGATGCAATGAT-GAAAGAAGCCCTCAGGAGACTAAGAAGGAAAACTGC
*
911 TATCT
129 GATCT
916 TTCTATGAACATTAAAGCG
1 TT-TATGAACATTAAAGCG
935 AATCTGGACA
Statistics
Matches: 237, Mismatches: 46, Indels: 10
0.81 0.16 0.03
Matches are distributed among these distances:
134 8 0.03
135 227 0.96
136 2 0.01
ACGTcount: A:0.39, C:0.15, G:0.27, T:0.19
Consensus pattern (133 bp):
TTTATGAACATTAAAGCGCAGAGCAAGCACAGAAACTTGGACAGTGCGATGACAGAAAGAAGCCC
TCAGGAGAATAAGAAGGATGCAATGATGAAAGAAGCCCTCAGGAGACTAAGAAGGAAAACTGCGA
TCT
Found at i:1153 original size:96 final size:95
Alignment explanation
Indices: 935--1156 Score: 239
Period size: 96 Copynumber: 2.3 Consensus size: 95
925 CATTAAAGCG
* * * * *
935 AATCTGGACAGTGCTATGACTGAAAGAAGCCAGCAGGAGACTATGAAGGAAAACTGCGCTCTTTT
1 AATCTGGACAGTGCAATGACTGAAAGAAGCCAG-AGGAGACTAAGAAGAAAAACTGCGATCTTTC
* *
1000 TATGAACATTAAAGCACGGAGCAAACGTAGA
65 TATAAACATTAAAGCACGGAGCAAACGCAGA
* ** ** * * *
1031 AATCTGGACAGTGCGACAACCAAAAGAAGTCCTTG-TGAGACTAAGAAGAAAAACTGTGATCTTT
1 AATCTGGACAGTGCAATGACTGAAAGAAG-CC-AGAGGAGACTAAGAAGAAAAACTGCGATCTTT
** *
1095 CTATAAACATTAAAGGGCGGAGCAAAGGCAGA
64 CTATAAACATTAAAGCACGGAGCAAACGCAGA
*
1127 AATTTGGACAGTGCAATGACTGAAAGAAGC
1 AATCTGGACAGTGCAATGACTGAAAGAAGC
1157 GGCAATGATA
Statistics
Matches: 101, Mismatches: 23, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
95 1 0.01
96 97 0.96
97 2 0.02
98 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.19
Consensus pattern (95 bp):
AATCTGGACAGTGCAATGACTGAAAGAAGCCAGAGGAGACTAAGAAGAAAAACTGCGATCTTTCT
ATAAACATTAAAGCACGGAGCAAACGCAGA
Found at i:3462 original size:83 final size:84
Alignment explanation
Indices: 3368--3527 Score: 243
Period size: 84 Copynumber: 1.9 Consensus size: 84
3358 TCGCTCGGAC
* * * *
3368 AATTGTCAGAGA-TATCCGGGCTGGGAATTTCTTTACTTTTCCCCGGGG-CATAGCTTGACCTTT
1 AATTGTCAGAGACCATCCGGGATGGGAATTTATTTACTTTTCCCCGGGGTC-TAACTTGACCTTT
3431 TTGTATGCAACTTCATTTGG
65 TTGTATGCAACTTCATTTGG
* *
3451 AATTGTTAGAGACCATCCGGGATGGGAATTTATTTATTTTTCCCCGGGGTCTAACTTGACCTTTT
1 AATTGTCAGAGACCATCCGGGATGGGAATTTATTTACTTTTCCCCGGGGTCTAACTTGACCTTTT
3516 TGTATGCAACTT
66 TGTATGCAACTT
3528 TTGGAGCACA
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
83 11 0.16
84 57 0.83
85 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (84 bp):
AATTGTCAGAGACCATCCGGGATGGGAATTTATTTACTTTTCCCCGGGGTCTAACTTGACCTTTT
TGTATGCAACTTCATTTGG
Done.