Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga03g00138.N4
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: 2942
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.33
Found at i:1691 original size:335 final size:335
Alignment explanation
Indices: 1072--1728 Score: 1224
Period size: 335 Copynumber: 2.0 Consensus size: 335
1062 AATTGAACCT
1072 CTAGCATTCCTTAACTGGGATCGTGCATACCGATTCGAAAATCGTTGAGATAGTGATTTCTGGTA
1 CTAGCATTCCTTAACTGGGATCGTGCATACCGATTCGAAAATCGTTGAGATAGTGATTTCTGGTA
*
1137 ATAGAGCTCTAGTTTAGTACCTGTTATTGCCATGTTAAATAAACTAGTCGATCCACTGATTGCAA
66 ATAAAGCTCTAGTTTAGTACCTGTTATTGCCATGTTAAATAAACTAGTCGATCCACTGATTGCAA
* *
1202 GTGTAGTTGCTTGTAATGAATTAGTTTGCATGTAGTGGTTTCTATGGTTCAAAGTCTGAAAATGG
131 GTGTAGTTGCTTGTAATCAATTAGTTTGCATGTAGTGGTTTCTATGGTGCAAAGTCTGAAAATGG
*
1267 ATTTCAAACCGATTCTTTAAGAAAGTGAGTTTTTTCTTTTGGAAATTGGAGGCCGAGTGGTTATA
196 ATTTCAAACCGATTCTTTAAGAAAGTGAGTTTTTTCTCTTGGAAATTGGAGGCCGAGTGGTTATA
1332 ATAATTGCTTGTCTCACCGCACTCTGCTCCACTATATAAAATTATCATTTTATCTTTATATAGAG
261 ATAATTGCTTGTCTCACCGCACTCTGCTCCACTATATAAAATTATCATTTTATCTTTATATAGAG
1397 CTCTGCTCCA
326 CTCTGCTCCA
*
1407 CTAGCATTCGTTAACTGGGATCGTGCATACCGATTCGAAAATCGTTGAGATAGTGATTTCTGGTA
1 CTAGCATTCCTTAACTGGGATCGTGCATACCGATTCGAAAATCGTTGAGATAGTGATTTCTGGTA
* *
1472 ATAAAGCTCTAGTTTAGTACCTGTTATTGCCATGTTAAATTAACTAGTCGATCCACTTATTGCAA
66 ATAAAGCTCTAGTTTAGTACCTGTTATTGCCATGTTAAATAAACTAGTCGATCCACTGATTGCAA
1537 GTGTAGTTGCTTGTAATCAATTAGTTTGCATGTAGTGGTTTCTATGGTGCAAAGTCTGAAAATGG
131 GTGTAGTTGCTTGTAATCAATTAGTTTGCATGTAGTGGTTTCTATGGTGCAAAGTCTGAAAATGG
*
1602 ATTTCAAACCGATTCTTTAAGAAAGTGAGTTTTTTCTCTTGGAAATTGGAGGCTGAGTGGTTATA
196 ATTTCAAACCGATTCTTTAAGAAAGTGAGTTTTTTCTCTTGGAAATTGGAGGCCGAGTGGTTATA
* *
1667 ATAATTGCTTGTCTTACTGCACTCTGCTCCACTATATAAAATTATCATTTTATCTTTATATA
261 ATAATTGCTTGTCTCACCGCACTCTGCTCCACTATATAAAATTATCATTTTATCTTTATATA
1729 TAATTATTAA
Statistics
Matches: 312, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
335 312 1.00
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.37
Consensus pattern (335 bp):
CTAGCATTCCTTAACTGGGATCGTGCATACCGATTCGAAAATCGTTGAGATAGTGATTTCTGGTA
ATAAAGCTCTAGTTTAGTACCTGTTATTGCCATGTTAAATAAACTAGTCGATCCACTGATTGCAA
GTGTAGTTGCTTGTAATCAATTAGTTTGCATGTAGTGGTTTCTATGGTGCAAAGTCTGAAAATGG
ATTTCAAACCGATTCTTTAAGAAAGTGAGTTTTTTCTCTTGGAAATTGGAGGCCGAGTGGTTATA
ATAATTGCTTGTCTCACCGCACTCTGCTCCACTATATAAAATTATCATTTTATCTTTATATAGAG
CTCTGCTCCA
Found at i:2044 original size:41 final size:41
Alignment explanation
Indices: 1999--2076 Score: 131
Period size: 41 Copynumber: 1.9 Consensus size: 41
1989 TATTGCCATC
*
1999 CCTAGTTACACTAGTTTTT-ACATTACATTGAACTAAAAGGG
1 CCTAGTTACACTAGTTTTTAAC-TTAAATTGAACTAAAAGGG
2040 CCTAGTTACACTAGTTTTTAACTTAAATTGAACTAAA
1 CCTAGTTACACTAGTTTTTAACTTAAATTGAACTAAA
2077 GGACCCAGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
41 33 0.94
42 2 0.06
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.36
Consensus pattern (41 bp):
CCTAGTTACACTAGTTTTTAACTTAAATTGAACTAAAAGGG
Done.