Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga10g02730.F2
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: 5129
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.29
Found at i:998 original size:84 final size:81
Alignment explanation
Indices: 910--1255 Score: 355
Period size: 84 Copynumber: 4.2 Consensus size: 81
900 AGAGAAAAAG
* ***
910 AAGGCAGTTGAAGAAAGAAAACTTG-TCGATTTGGAGATGGCTAAAGCAAGCGAGTTGAGGAAGA
1 AAGGCTGTTGAAGAAAGAAAAC-TGCT-GATTTGGAGATGGCTAAAGC-AG-GAGCAAAGGAAGA
*
974 GTGCAGAAGAAACTAAGAAA
62 TTGCAGAAGAAACTAAGAAA
* * *
994 AAGGCTGTTGATGAAAGAAAATGTGCTGATTTGGAGATGGCTAAAGCAGAGAAGCAGAGGAAGAT
1 AAGGCTGTTGAAGAAAGAAAA-CTGCTGATTTGGAGATGGCTAAAGCAG-G-AGCAAAGGAAGAT
*
1059 TGCTA-AAGAAACTAAGAAG
63 TGC-AGAAGAAACTAAGAAA
* *
1078 AAGGCTGTTGAAGAAAGAAAACGTGCTGATTTAGAGATGGCTGAAGCAGTGAAGCAAAGGAAGAT
1 AAGGCTGTTGAAGAAAGAAAAC-TGCTGATTTGGAGATGGCTAAAGCAG-G-AGCAAAGGAAGAT
*
1143 TGCAGAAGAAAAC-ATGAAA
63 TGCAGAAG-AAACTAAGAAA
* * *
1162 AAGGCGGTTGAAGGAAGAAAACAAGCTGATATT-GAGATGGCTAAAGCAGAAGAGCAAAGGAAGA
1 AAGGCTGTTGAAGAAAGAAAAC-TGCTGAT-TTGGAGATGGCTAAAGCAG--GAGCAAAGGAAGA
*
1226 TTGCAGAAGAAAATAAG---
62 TTGCAGAAGAAACTAAGAAA
1243 AAGGCTGTTGAAG
1 AAGGCTGTTGAAG
1256 GGCCCAAAGT
Statistics
Matches: 227, Mismatches: 25, Indels: 23
0.83 0.09 0.08
Matches are distributed among these distances:
81 12 0.05
83 7 0.03
84 199 0.88
85 9 0.04
ACGTcount: A:0.43, C:0.09, G:0.31, T:0.17
Consensus pattern (81 bp):
AAGGCTGTTGAAGAAAGAAAACTGCTGATTTGGAGATGGCTAAAGCAGGAGCAAAGGAAGATTGC
AGAAGAAACTAAGAAA
Found at i:1201 original size:168 final size:168
Alignment explanation
Indices: 907--1245 Score: 420
Period size: 168 Copynumber: 2.0 Consensus size: 168
897 AGAAGAGAAA
* * ***
907 AAGAAGGCAGTTGAAGAAAGAAAACTTGTCGATTTGGAGATGGCTAAAGCAAGCGAGTTGAGGAA
1 AAGAAGGCAGTTGAAGAAAGAAAACGTGTCGATTTAGAGATGGCTAAAGCAAGCGAGCAAAGGAA
* * ***
972 GAGTGCAGAAGAAACTAAGAAAAAGGCTGTTGATGAAAGAAAATGTGCTGATTTGGAGATGGCTA
66 GAGTGCAGAAGAAACTAAGAAAAAGGCGGTTGAAGAAAGAAAACAAGCTGATTTGGAGATGGCTA
* *
1037 AAGCAG-AGAAGCAGAGGAAGATTGCTA-AAGAAACTAAG
131 AAGCAGAAG-AGCAAAGGAAGATTGC-AGAAGAAAATAAG
* * *
1075 AAGAAGGCTGTTGAAGAAAGAAAACGTG-CTGATTTAGAGATGGCTGAAGC-AGTGAAGCAAAGG
1 AAGAAGGCAGTTGAAGAAAGAAAACGTGTC-GATTTAGAGATGGCTAAAGCAAGCG-AGCAAAGG
* * *
1138 AAGATTGCAGAAGAAAAC-ATGAAAAAGGCGGTTGAAGGAAGAAAACAAGCTGATATT-GAGATG
64 AAGAGTGCAGAAG-AAACTAAGAAAAAGGCGGTTGAAGAAAGAAAACAAGCTGAT-TTGGAGATG
1201 GCTAAAGCAGAAGAGCAAAGGAAGATTGCAGAAGAAAATAAG
127 GCTAAAGCAGAAGAGCAAAGGAAGATTGCAGAAGAAAATAAG
1243 AAG
1 AAG
1246 GCTGTTGAAG
Statistics
Matches: 147, Mismatches: 18, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
167 5 0.03
168 134 0.91
169 8 0.05
ACGTcount: A:0.44, C:0.09, G:0.31, T:0.16
Consensus pattern (168 bp):
AAGAAGGCAGTTGAAGAAAGAAAACGTGTCGATTTAGAGATGGCTAAAGCAAGCGAGCAAAGGAA
GAGTGCAGAAGAAACTAAGAAAAAGGCGGTTGAAGAAAGAAAACAAGCTGATTTGGAGATGGCTA
AAGCAGAAGAGCAAAGGAAGATTGCAGAAGAAAATAAG
Done.