Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga09g00208.F4
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: 2737
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.32
Found at i:591 original size:72 final size:72
Alignment explanation
Indices: 486--680 Score: 241
Period size: 72 Copynumber: 2.7 Consensus size: 72
476 CTTGAAGAGT
** * * *
486 TTGAAACTGTTGGACCTATC-ACATAATCAAATTACTGGTCCTATTCCTTCTACCCTGTGCAACT
1 TTGAAACTGTTGGACCTATCTGGA-AACCAAATTACTGGTCCTATCCCTTCTACCCTGGGCAACT
550 TAACAAAC
65 TAACAAAC
* * * *
558 TTGAAACAGTTGGACCTATCTGGAAACCAAATTATTGGCCCTATCCCTTCTACCTTGGGCAACTT
1 TTGAAACTGTTGGACCTATCTGGAAACCAAATTACTGGTCCTATCCCTTCTACCCTGGGCAACTT
*
623 AACCAAC
66 AACAAAC
* * *
630 TT-AGAATTGTTGAACCTATCTGGAAACGAAATTACTGGTCCTATCCCTTCT
1 TTGA-AACTGTTGGACCTATCTGGAAACCAAATTACTGGTCCTATCCCTTCT
681 GCCTTGGGTA
Statistics
Matches: 105, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
71 1 0.01
72 103 0.98
73 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (72 bp):
TTGAAACTGTTGGACCTATCTGGAAACCAAATTACTGGTCCTATCCCTTCTACCCTGGGCAACTT
AACAAAC
Found at i:686 original size:72 final size:72
Alignment explanation
Indices: 513--700 Score: 243
Period size: 72 Copynumber: 2.6 Consensus size: 72
503 ATCACATAAT
* * * * *
513 CAAATTACTGGTCCTATTCCTTCTACCCTGTGCAACTTAACAAACTTGAAACAGTTGGACCTATC
1 CAAATTACTGGTCCTATCCCTTCTACCTTGGGCAACTTAACCAACTTGAAACAGTTGAACCTATC
578 TGGAAAC
66 TGGAAAC
* * **
585 CAAATTATTGGCCCTATCCCTTCTACCTTGGGCAACTTAACCAACTT-AGAATTGTTGAACCTAT
1 CAAATTACTGGTCCTATCCCTTCTACCTTGGGCAACTTAACCAACTTGA-AACAGTTGAACCTAT
649 CTGGAAAC
65 CTGGAAAC
* * * *
657 GAAATTACTGGTCCTATCCCTTCTGCCTTGGGTAAATTAACCAA
1 CAAATTACTGGTCCTATCCCTTCTACCTTGGGCAACTTAACCAA
701 TTTAAAAGAG
Statistics
Matches: 100, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
71 1 0.01
72 99 0.99
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.30
Consensus pattern (72 bp):
CAAATTACTGGTCCTATCCCTTCTACCTTGGGCAACTTAACCAACTTGAAACAGTTGAACCTATC
TGGAAAC
Found at i:1156 original size:144 final size:144
Alignment explanation
Indices: 896--1174 Score: 332
Period size: 144 Copynumber: 1.9 Consensus size: 144
886 CAATCCCTCA
* * * *
896 TGAAATTGGAAACTTAAAGAATTTGGTTGCATTGAATTTAAGTAACAACAATCTCAAGCATCGGA
1 TGAAATTGGAAACTTAAAGAATTTGGTTGAATTGAATCTAAGTAAAAACAAGCTCAAGCATCGGA
* * * *
961 TTCCTCAATCCCTAACTACTTTATCCAAATTGAGCTACTTGTACTTGGATTCAAAT-TTTCTACA
66 TCCCTCAATCACTAACTAATTTATCCAAATTGAGCTACTTGTACTTGGATTCAAATCTTT-TAAA
1025 AGGTCCAATTCCTAG
130 AGGTCCAATTCCTAG
* * * **
1040 TGAAATTGGAAACTTGAAGAATTTGTTTGAATTGAATCTAAGTAAAAACAAGCTCAATG-GTTTG
1 TGAAATTGGAAACTTAAAGAATTTGGTTGAATTGAATCTAAGTAAAAACAAGCTCAA-GCATCGG
* * * * *
1104 ATCCCTTC-ATCACTAGCTAATTTATCTAGATTGAGCTATTTGTTCCTT-GATTCAAATCTTTTA
65 ATCCC-TCAATCACTAACTAATTTATCCAAATTGAGCTACTTG-TACTTGGATTCAAATCTTTTA
1167 AAAGGTCC
128 AAAGGTCC
1175 CTTACCATCT
Statistics
Matches: 113, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
144 103 0.91
145 10 0.09
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (144 bp):
TGAAATTGGAAACTTAAAGAATTTGGTTGAATTGAATCTAAGTAAAAACAAGCTCAAGCATCGGA
TCCCTCAATCACTAACTAATTTATCCAAATTGAGCTACTTGTACTTGGATTCAAATCTTTTAAAA
GGTCCAATTCCTAG
Done.