Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga10g02664.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: 2619
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Found at i:1111 original size:75 final size:74
Alignment explanation
Indices: 1009--1972 Score: 770
Period size: 75 Copynumber: 13.0 Consensus size: 74
999 AACCAAACAC
* * * * ** * * *
1009 CTAAATTTCCCGAACCTGAACCCCAAGCTATATCTTGTGAACCCACTGCAATTGACGTTTTTGGT
1 CTAAATTTCCCGAACCTGAACCTCAAGC-ATACCTTGTGAACCTACTGGAATCAACATGTTTGGG
1074 AAACAGGCTT
65 AAACAGGCTT
* * * * ** *
1084 CTAAATTTCCCGAGCATGAACCTCAAGCGATGCCTTGTGAATCTGGTGGAATCAACATGTTTGGT
1 CTAAATTTCCCGAACCTGAACCTCAAGC-ATACCTTGTGAACCTACTGGAATCAACATGTTTGGG
*
1149 AAGC-GGCCTT
65 AAACAGG-CTT
* * * **
1159 CTAAATTTCCTGAACCTGAAACTCAACCAATGA-AGTGTGAACCTACTGGAATCAACATGTTTGG
1 CTAAATTTCCCGAACCTGAACCTCAAGC-AT-ACCTTGTGAACCTACTGGAATCAACATGTTTGG
*
1223 GAAACGGGCTT
64 GAAACAGGCTT
* * * * * *
1234 CTAAATTTCCTGAACCTGAACCTCAAGGCATGCCTTGTGAACGTGCTGAAATCCACATGTTTGGG
1 CTAAATTTCCCGAACCTGAACCTCAA-GCATACCTTGTGAACCTACTGGAATCAACATGTTTGGG
*
1299 AAGCAGGCTT
65 AAACAGGCTT
* * * * * * * *
1309 CTAAATTTGCTGAACCTGAACCTCGAGCCATACCTTGTGAACCCATTGGAATCGACGTGTTTGGA
1 CTAAATTTCCCGAACCTGAACCTCAAG-CATACCTTGTGAACCTACTGGAATCAACATGTTTGGG
1374 AAACAGGCTT
65 AAACAGGCTT
* *
1384 CTAAATTTCCCGAACCTGAACCTCTAAGCATGCAC-TGTGAACCTGCTGGAATCAACATGTTT-G
1 CTAAATTTCCCGAACCTGAACCTC-AAGCATAC-CTTGTGAACCTACTGGAATCAACATGTTTGG
1447 GAAAGCAGGCTT
64 GAAA-CAGGCTT
* * * * *
1459 CTAAATTTCCCGAACCTGAAACTCAACCCGTGCAC-TGTGAACCAACTGGAATCAACATGTTT-G
1 CTAAATTTCCCGAACCTGAACCTCAA-GCATAC-CTTGTGAACCTACTGGAATCAACATGTTTGG
1522 GAAAGCAGGCTT
64 GAAA-CAGGCTT
* * * * * *
1534 CTAAATTTCCTGAACCTGAAACTCAACCCATGCAC-TGTGAACCAACTGGAATCAACATTTTTGG
1 CTAAATTTCCCGAACCTGAACCTCAA-GCATAC-CTTGTGAACCTACTGGAATCAACATGTTTGG
*
1598 GAAACAGGCTA
64 GAAACAGGCTT
* * * * * * *
1609 CTAAATTTCCTGAACCCGAACCTCAAGCCATGCCTTGTGGACCAACAGGAATCAACATG-TTCGG
1 CTAAATTTCCCGAACCTGAACCTCAAG-CATACCTTGTGAACCTACTGGAATCAACATGTTTGGG
* *
1673 AAAGCAGCCAT
65 AAA-CAGGCTT
* * * *
1684 CTAAAATT------CCTGACCCTCAAGCCATGCCTTGTGAATCC-ACTGGAATCAACAAT-TTCG
1 CTAAATTTCCCGAACCTGAACCTCAAG-CATACCTTGTGAA-CCTACTGGAATCAAC-ATGTTTG
*
1741 GGAAGCAGGCTT
63 GGAAACAGGCTT
* * ** * **
1753 CTAAATTTCCCGAACCTGAACTTCGAACCATGTCTTGCGAACCTACCAGAATCAACAT-TTTCGG
1 CTAAATTTCCCGAACCTGAACCTC-AAGCATACCTTGTGAACCTACTGGAATCAACATGTTT-GG
*
1817 GAAACAAGCTT
64 GAAACAGGCTT
* * * *
1828 CTAAATTT------CCTGAACCTCAAACCATACCTTGTGAACCCACTGGACTTAACATGTTTGGG
1 CTAAATTTCCCGAACCTGAACCTC-AAGCATACCTTGTGAACCTACTGGAATCAACATGTTTGGG
*
1887 AAACAAGCTT
65 AAACAGGCTT
* ** * *
1897 CTAAGTTTCTTGAACCTGAACAC-CAAGCCATACCTTGTGAACTTACTGGACTCAACATGTTTGG
1 CTAAATTTCCCGAACCTGAAC-CTCAAG-CATACCTTGTGAACCTACTGGAATCAACATGTTTGG
*
1961 TAAACAGGCTT
64 GAAACAGGCTT
1972 C
1 C
1973 ATCTAGGCAA
Statistics
Matches: 734, Mismatches: 120, Indels: 70
0.79 0.13 0.08
Matches are distributed among these distances:
69 101 0.14
70 12 0.02
74 25 0.03
75 582 0.79
76 14 0.02
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (74 bp):
CTAAATTTCCCGAACCTGAACCTCAAGCATACCTTGTGAACCTACTGGAATCAACATGTTTGGGA
AACAGGCTT
Found at i:1401 original size:225 final size:223
Alignment explanation
Indices: 1009--1972 Score: 874
Period size: 225 Copynumber: 4.3 Consensus size: 223
999 AACCAAACAC
* * * ** * * ** * * *
1009 CTAAATTTCCCGAACCTGAACCCCAAGCTATATCTTGTGAACCCACTGCAATTGACGTTTTTGGT
1 CTAAATTTCCTGAACCTGAACCTCAAGCCATGCCTTGTGAA-CTACTGGAATCAACATGTTTGGG
* * * * * **
1074 AAACAGGCTTCTAAATTTCCCGAGCATGAACCTCAAGCGATGCCTTGTGAATCTGGTGGAATCAA
65 AAGCAGGCTTCTAAATTTCCCGAACCTGAACCTCAAGCCATGCCTTGTGAACCTACTGGAATCAA
* * *
1139 CATGTTTGGTAAGC-GGCCTTCTAAATTTCCTGAACCTGAAACTCAACCAATGAAGTGTGAACCT
130 CATGTTTGGGAAACAGG-CTTCTAAATTTCCTGAACCTGAAACTCAACC-ATGCA-TGTGAACCT
*
1203 ACTGGAATCAACATGTTTGGGAAA-CGGGCTT
192 ACTGGAATCAACATGTTTGGGAAAGCAGGCTT
* * * *
1234 CTAAATTTCCTGAACCTGAACCTCAAGGCATGCCTTGTGAACGTGCTGAAATCCACATGTTTGGG
1 CTAAATTTCCTGAACCTGAACCTCAAGCCATGCCTTGTGAAC-TACTGGAATCAACATGTTTGGG
* * * * * * *
1299 AAGCAGGCTTCTAAATTTGCTGAACCTGAACCTCGAGCCATACCTTGTGAACCCATTGGAATCGA
65 AAGCAGGCTTCTAAATTTCCCGAACCTGAACCTCAAGCCATGCCTTGTGAACCTACTGGAATCAA
* * * * * *
1364 CGTGTTTGGAAAACAGGCTTCTAAATTTCCCGAACCTGAACCTCTAAGCATGCACTGTGAACCTG
130 CATGTTTGGGAAACAGGCTTCTAAATTTCCTGAACCTGAAACTC-AACCATGCA-TGTGAACCTA
1429 CTGGAATCAACATGTTT-GGAAAGCAGGCTT
193 CTGGAATCAACATGTTTGGGAAAGCAGGCTT
* * * * *
1459 CTAAATTTCCCGAACCTGAAACTCAACCCGTGCAC-TGTGAACCAACTGGAATCAACATGTTTGG
1 CTAAATTTCCTGAACCTGAACCTCAAGCCATGC-CTTGTGAA-CTACTGGAATCAACATGTTTGG
* * * * *
1523 AAAGCAGGCTTCTAAATTTCCTGAACCTGAAACTCAACCCATGCAC-TGTGAACCAACTGGAATC
64 GAAGCAGGCTTCTAAATTTCCCGAACCTGAACCTCAAGCCATGC-CTTGTGAACCTACTGGAATC
* * * * * *
1587 AACATTTTTGGGAAACAGGCTACTAAATTTCCTGAACCCGAACCTCAAGCCATGCCTTGTGGACC
128 AACATGTTTGGGAAACAGGCTTCTAAATTTCCTGAACCTGAAACTCAA-CCATG-CATGTGAACC
* * * * *
1652 AACAGGAATCAACATG-TTCGGAAAGCAGCCAT
191 TACTGGAATCAACATGTTTGGGAAAGCAGGCTT
* * *
1684 CTAAAATTCCTG-A-C----CCTCAAGCCATGCCTTGTGAATCCACTGGAATCAACAAT-TTCGG
1 CTAAATTTCCTGAACCTGAACCTCAAGCCATGCCTTGTGAA-CTACTGGAATCAAC-ATGTTTGG
* * * **
1742 GAAGCAGGCTTCTAAATTTCCCGAACCTGAACTTCGAA-CCATGTCTTGCGAACCTACCAGAATC
64 GAAGCAGGCTTCTAAATTTCCCGAACCTGAACCTC-AAGCCATGCCTTGTGAACCTACTGGAATC
* *
1806 AACAT-TTTCGGGAAACAAGCTTCTAAATTTCCTGAACCTCAAAC-CATACC-T---TGTGAACC
128 AACATGTTT-GGGAAACAGGCTTCTAAATTTCCTGAACCTGAAACTCA-ACCATGCATGTGAACC
* * * *
1865 CACTGGACTTAACATGTTTGGGAAA-CAAGCTT
191 TACTGGAATCAACATGTTTGGGAAAGCAGGCTT
* * * *
1897 CTAAGTTTCTTGAACCTGAACAC-CAAGCCATACCTTGTGAACTTACTGGACTCAACATGTTTGG
1 CTAAATTTCCTGAACCTGAAC-CTCAAGCCATGCCTTGTGAAC-TACTGGAATCAACATGTTTGG
* *
1961 TAAACAGGCTTC
64 GAAGCAGGCTTC
1973 ATCTAGGCAA
Statistics
Matches: 604, Mismatches: 109, Indels: 58
0.78 0.14 0.08
Matches are distributed among these distances:
213 32 0.05
214 8 0.01
215 1 0.00
217 1 0.00
218 12 0.02
219 162 0.27
220 5 0.01
223 1 0.00
224 11 0.02
225 362 0.60
226 9 0.01
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (223 bp):
CTAAATTTCCTGAACCTGAACCTCAAGCCATGCCTTGTGAACTACTGGAATCAACATGTTTGGGA
AGCAGGCTTCTAAATTTCCCGAACCTGAACCTCAAGCCATGCCTTGTGAACCTACTGGAATCAAC
ATGTTTGGGAAACAGGCTTCTAAATTTCCTGAACCTGAAACTCAACCATGCATGTGAACCTACTG
GAATCAACATGTTTGGGAAAGCAGGCTT
Done.