Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gorai.001G094000.1-JGI_221_v2.1
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: 2072
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Found at i:508 original size:15 final size:15
Alignment explanation
Indices: 488--527 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
478 CTAAACCACC
488 GAAGCCACCGGTGGT
1 GAAGCCACCGGTGGT
503 GAAGCCACCGGTGGT
1 GAAGCCACCGGTGGT
518 GAAGCCACCG
1 GAAGCCACCG
528 TATCACCCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.23, C:0.30, G:0.38, T:0.10
Consensus pattern (15 bp):
GAAGCCACCGGTGGT
Found at i:550 original size:42 final size:42
Alignment explanation
Indices: 504--586 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
494 ACCGGTGGTG
* *
504 AAGCCACCGGTGGTGAAGCCACCGTATCACCCTAAACCACCT
1 AAGCCACCGGTGGTGAAACCACCATATCACCCTAAACCACCT
* * *
546 AAGCCTCCGGTGGTGAAACCCCCATATCACCCTAAGCCACC
1 AAGCCACCGGTGGTGAAACCACCATATCACCCTAAACCACC
587 AAAACATCCC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.28, C:0.40, G:0.18, T:0.14
Consensus pattern (42 bp):
AAGCCACCGGTGGTGAAACCACCATATCACCCTAAACCACCT
Found at i:697 original size:36 final size:36
Alignment explanation
Indices: 652--931 Score: 488
Period size: 36 Copynumber: 7.8 Consensus size: 36
642 AAGCCACCTA
* * * *
652 TTGTAAAGCCTCCACCGTATACACCCAAACCACCGG
1 TTGTGAAGCCTCCGCCATATACACCCAAACCGCCGG
688 TTGTGAAGCCTCCGCCATATACACCCAAACCGCCGG
1 TTGTGAAGCCTCCGCCATATACACCCAAACCGCCGG
724 TTGTGAAGCCTCCGCCATATACACCCAAACCGCCGG
1 TTGTGAAGCCTCCGCCATATACACCCAAACCGCCGG
760 TTGTGAAGCCTCCGCCATATACACCCAAACCGCCGG
1 TTGTGAAGCCTCCGCCATATACACCCAAACCGCCGG
*
796 TTGTGAAGCCTCCGCCATATGCACCCAAACCGCCGG
1 TTGTGAAGCCTCCGCCATATACACCCAAACCGCCGG
*
832 TTGTGAAGCCTCCGCCATATGCACCCAAACCGCCGG
1 TTGTGAAGCCTCCGCCATATACACCCAAACCGCCGG
*
868 TTGTGAAGCCTCCGCCATATGCACCCAAACCGCCGG
1 TTGTGAAGCCTCCGCCATATACACCCAAACCGCCGG
*
904 TTGTGAAGCCTCCACCATATACACCCAA
1 TTGTGAAGCCTCCGCCATATACACCCAA
932 GCCACCTTAC
Statistics
Matches: 237, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 237 1.00
ACGTcount: A:0.25, C:0.39, G:0.19, T:0.17
Consensus pattern (36 bp):
TTGTGAAGCCTCCGCCATATACACCCAAACCGCCGG
Found at i:955 original size:144 final size:142
Alignment explanation
Indices: 673--1099 Score: 460
Period size: 144 Copynumber: 3.0 Consensus size: 142
663 CCACCGTATA
*
673 CACCCAAACCACCGGTTGTGAAGCCTCCGCCATATACACCCAAACCGCCGGTTGTGAAGCCTCCG
1 CACCCAAACCGCCGGTTGTGAAGCCTCCGCCATAT-CACCCAAACCGCCGGTTGTGAAGCCTCCG
* * *
738 CCATATACACCCAAACCGCCGGTTGTGAAGCCTCCGCCATATACACCCAAACCGCCGGTT-GTGA
65 CCATATACACCCAAACCGCCGGTTGTGAAGCCTCCGCCATATACACCCAAGCCACC--TTACT--
*
802 AGCC--T-CCGCCATAT
126 ATCCAATACCGCCATAT
816 GCACCCAAACCGCCGGTTGTGAAGCCTCCGCCATATGCACCCAAACCGCCGGTTGTGAAGCCTCC
1 -CACCCAAACCGCCGGTTGTGAAGCCTCCGCCATAT-CACCCAAACCGCCGGTTGTGAAGCCTCC
* *
881 GCCATATGCACCCAAACCGCCGGTTGTGAAGCCTCCACCATATACACCCAAGCCACCTTACTATC
64 GCCATATACACCCAAACCGCCGGTTGTGAAGCCTCCGCCATATACACCCAAGCCACCTTACTATC
946 CAATACCGCCGGTCATAT
129 CAATACCG-C---CATAT
* *** * * ** * ** * *
964 CACCACCAACACTGCC---TCCAAAGCCACCAGTC-TA-C-CCCAGTCCACCAATAGTGAACCCT
1 CA-C-CCAA-ACCGCCGGTTGTGAAGCCTCC-GCCATATCACCCAAACCGCCGGTTGTGAAGCCT
*
1023 CCACCATATACACCCAAACCGCCGGTTGTGAAGCCTCCGCCATATACACCCAAGCCACCTTACTA
62 CCGCCATATACACCCAAACCGCCGGTTGTGAAGCCTCCGCCATATACACCCAAGCCACCTTACTA
1088 TCCAATACCGCC
127 TCCAATACCGCC
1100 GGTCATATCA
Statistics
Matches: 247, Mismatches: 24, Indels: 28
0.83 0.08 0.09
Matches are distributed among these distances:
140 1 0.00
141 3 0.01
142 2 0.01
143 3 0.01
144 207 0.84
145 2 0.01
147 12 0.05
148 8 0.03
149 4 0.02
150 5 0.02
ACGTcount: A:0.26, C:0.41, G:0.16, T:0.17
Consensus pattern (142 bp):
CACCCAAACCGCCGGTTGTGAAGCCTCCGCCATATCACCCAAACCGCCGGTTGTGAAGCCTCCGC
CATATACACCCAAACCGCCGGTTGTGAAGCCTCCGCCATATACACCCAAGCCACCTTACTATCCA
ATACCGCCATAT
Found at i:1130 original size:144 final size:144
Alignment explanation
Indices: 870--1165 Score: 556
Period size: 144 Copynumber: 2.1 Consensus size: 144
860 ACCGCCGGTT
* * *
870 GTGAAGCCTCCGCCATATGCACCCAAACCGCCGGTTGTGAAGCCTCCACCATATACACCCAAGCC
1 GTGAACCCTCCACCATATACACCCAAACCGCCGGTTGTGAAGCCTCCACCATATACACCCAAGCC
935 ACCTTACTATCCAATACCGCCGGTCATATCACCACCAACACTGCCTCCAAAGCCACCAGTCTACC
66 ACCTTACTATCCAATACCGCCGGTCATATCACCACCAACACTGCCTCCAAAGCCACCAGTCTACC
1000 CCAGTCCACCAATA
131 CCAGTCCACCAATA
*
1014 GTGAACCCTCCACCATATACACCCAAACCGCCGGTTGTGAAGCCTCCGCCATATACACCCAAGCC
1 GTGAACCCTCCACCATATACACCCAAACCGCCGGTTGTGAAGCCTCCACCATATACACCCAAGCC
1079 ACCTTACTATCCAATACCGCCGGTCATATCACCACCAACACTGCCTCCAAAGCCACCAGTCTACC
66 ACCTTACTATCCAATACCGCCGGTCATATCACCACCAACACTGCCTCCAAAGCCACCAGTCTACC
1144 CCAGTCCACCAATA
131 CCAGTCCACCAATA
1158 GTGAACCC
1 GTGAACCC
1166 ACCAACACCG
Statistics
Matches: 148, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
144 148 1.00
ACGTcount: A:0.29, C:0.42, G:0.13, T:0.17
Consensus pattern (144 bp):
GTGAACCCTCCACCATATACACCCAAACCGCCGGTTGTGAAGCCTCCACCATATACACCCAAGCC
ACCTTACTATCCAATACCGCCGGTCATATCACCACCAACACTGCCTCCAAAGCCACCAGTCTACC
CCAGTCCACCAATA
Found at i:1254 original size:24 final size:24
Alignment explanation
Indices: 1186--1279 Score: 82
Period size: 24 Copynumber: 3.9 Consensus size: 24
1176 CCGATTCTGC
*
1186 CACCTCCTATTGTGAATCCACCAA
1 CACCTCCTATTGTGAACCCACCAA
* * * * *
1210 CACCGCCGATTCT-ACCACCACCAT
1 CACCTCCTATTGTGAAC-CCACCAA
*
1234 CACCACCTATTGTGAACCCACCAA
1 CACCTCCTATTGTGAACCCACCAA
* * *
1258 CGCCTCCTATCGTGAAGCCACC
1 CACCTCCTATTGTGAACCCACC
1280 TTCACCGGGA
Statistics
Matches: 53, Mismatches: 15, Indels: 4
0.74 0.21 0.06
Matches are distributed among these distances:
23 1 0.02
24 50 0.94
25 2 0.04
ACGTcount: A:0.27, C:0.44, G:0.11, T:0.19
Consensus pattern (24 bp):
CACCTCCTATTGTGAACCCACCAA
Found at i:1878 original size:6 final size:6
Alignment explanation
Indices: 1867--1905 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
1857 TGAACTTCGC
1867 TTTATT TTTATT TTTATT TTTATT TTTA-T TTTATT TTTA
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTA
1906 CACTCCAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTATT
Found at i:1890 original size:18 final size:17
Alignment explanation
Indices: 1867--1905 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 17
1857 TGAACTTCGC
1867 TTTATTTTTATTTTTATT
1 TTTATTTTTA-TTTTATT
1885 TTTATTTTTATTTTATT
1 TTTATTTTTATTTTATT
1902 TTTA
1 TTTA
1906 CACTCCAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTATTTTTATTTTATT
Done.