Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gorai.006G021000.1-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: 2433
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Found at i:485 original size:144 final size:144
Alignment explanation
Indices: 290--570 Score: 472
Period size: 144 Copynumber: 2.0 Consensus size: 144
280 AATTGGTTTA
290 TTGGTCCAATCCCATCTTCTGTCAGCAACTTAACCAATCTTGACTCGTTGTTCCTTCAAAGCAAC
1 TTGGTCCAATCCCATCTTCTGTCAGCAACTTAACCAATCTTGACTCGTTGTTCCTTCAAAGCAAC
* * *
355 CAACTTGATGGATCCATTCCAAAAGATATTGGGAGACTAACGAATTTGGTTGCATTGAATCTATC
66 CAACTTAATGGATCCATTCCAAAAGATATTGGGAGACTAACGAATTTGGTTGAATTGAAACTATC
420 CTCCAATTGTCTTG
131 CTCCAATTGTCTTG
** * *
434 TTGGTCCAATCCCATCTTCTGTCAGCAACTTAACCAATCTTTCCTCTTTGTTCCTTCAAAGCAAT
1 TTGGTCCAATCCCATCTTCTGTCAGCAACTTAACCAATCTTGACTCGTTGTTCCTTCAAAGCAAC
* * *
499 CAACTTAATGGATCCATTCCAGAAGATATTGGGGGACTAACGGATTTGGTTGAATTGAAACTATC
66 CAACTTAATGGATCCATTCCAAAAGATATTGGGAGACTAACGAATTTGGTTGAATTGAAACTATC
564 CTCCAAT
131 CTCCAAT
571 GGGCTTTTAG
Statistics
Matches: 127, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
144 127 1.00
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (144 bp):
TTGGTCCAATCCCATCTTCTGTCAGCAACTTAACCAATCTTGACTCGTTGTTCCTTCAAAGCAAC
CAACTTAATGGATCCATTCCAAAAGATATTGGGAGACTAACGAATTTGGTTGAATTGAAACTATC
CTCCAATTGTCTTG
Found at i:655 original size:72 final size:72
Alignment explanation
Indices: 536--827 Score: 413
Period size: 72 Copynumber: 3.9 Consensus size: 72
526 ATTGGGGGAC
* * * * *
536 TAACGGATTTGGTTGAATTGAAACTATCCTCCAATGGGCTTTTAGGTCACATCCCTTCCTCTCTG
1 TAACGAATTTGGTTGAATTGGATCTATCCTCCAATAGGCTTTCAGGTCACATCCCTTCCTCTCTG
601 GGCCATT
66 GGCCATT
608 TAACGAATTTGGTTGAATTGGATCTATCCTCCAATAGGCTTTCAGGTCACATCCCTTCCTCTCTG
1 TAACGAATTTGGTTGAATTGGATCTATCCTCCAATAGGCTTTCAGGTCACATCCCTTCCTCTCTG
*
673 GGCCAGT
66 GGCCATT
*
680 TAACGAATTTGGTTGAATTGGATCTATCCTCCAATAAGCTTTCAGGTCACATCCCTTCCTCTCTG
1 TAACGAATTTGGTTGAATTGGATCTATCCTCCAATAGGCTTTCAGGTCACATCCCTTCCTCTCTG
745 GGCCAGTTAACGAATTTGT
66 GG-C------C--A--T-T
764 TAACGAATTTGGTTGAATTGGATCTATCCTCCAATAGGCTTTCAGGTCACATCCCTTCCTCTCT
1 TAACGAATTTGGTTGAATTGGATCTATCCTCCAATAGGCTTTCAGGTCACATCCCTTCCTCTCT
828 AGGTCAGTTA
Statistics
Matches: 199, Mismatches: 9, Indels: 12
0.90 0.04 0.05
Matches are distributed among these distances:
72 132 0.66
73 1 0.01
79 1 0.01
81 1 0.01
84 64 0.32
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (72 bp):
TAACGAATTTGGTTGAATTGGATCTATCCTCCAATAGGCTTTCAGGTCACATCCCTTCCTCTCTG
GGCCATT
Found at i:732 original size:144 final size:149
Alignment explanation
Indices: 536--839 Score: 438
Period size: 156 Copynumber: 2.0 Consensus size: 149
526 ATTGGGGGAC
* ** *
536 TAACGGATTTGGTTGAATTGAAACTATCCTCCAATGGGCTTTTAGGTCACATCCCTTCCTCTCTG
1 TAACGAATTTGGTTGAATTGAAACTATCCTCCAATAAGCTTTCAGGTCACATCCCTTCCTCTCTG
601 GG-C-C-A-T-TTAACGAATTTGGTTGAATTGGATCTATCCTCCAATAGGCTTTCAGGTCACATC
66 GGCCACAATTGTTAACGAATTTGGTTGAATTGGATCTATCCTCCAATAGGCTTTCAGGTCACATC
*
661 CCTTCCTCTCTGGGCCAGT
131 CCTTCCTCTCTAGGCCAGT
* *
680 TAACGAATTTGGTTGAATTGGATCTATCCTCCAATAAGCTTTCAGGTCACATCCCTTCCTCTCTG
1 TAACGAATTTGGTTGAATTGAAACTATCCTCCAATAAGCTTTCAGGTCACATCCCTTCCTCTCTG
745 GGCCAGTTAACGAATTTGTTAACGAATTTGGTTGAATTGGATCTATCCTCCAATAGGCTTTCAGG
66 GGCC-----AC-AA-TTGTTAACGAATTTGGTTGAATTGGATCTATCCTCCAATAGGCTTTCAGG
*
810 TCACATCCCTTCCTCTCTAGGTCAGT
124 TCACATCCCTTCCTCTCTAGGCCAGT
836 TAAC
1 TAAC
840 AAAATTGGAA
Statistics
Matches: 140, Mismatches: 8, Indels: 12
0.88 0.05 0.08
Matches are distributed among these distances:
144 61 0.44
145 1 0.01
151 1 0.01
153 1 0.01
155 1 0.01
156 75 0.54
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.34
Consensus pattern (149 bp):
TAACGAATTTGGTTGAATTGAAACTATCCTCCAATAAGCTTTCAGGTCACATCCCTTCCTCTCTG
GGCCACAATTGTTAACGAATTTGGTTGAATTGGATCTATCCTCCAATAGGCTTTCAGGTCACATC
CCTTCCTCTCTAGGCCAGT
Found at i:767 original size:12 final size:12
Alignment explanation
Indices: 750--774 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
740 CTCTGGGCCA
750 GTTAACGAATTT
1 GTTAACGAATTT
762 GTTAACGAATTT
1 GTTAACGAATTT
774 G
1 G
775 GTTGAATTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (12 bp):
GTTAACGAATTT
Found at i:819 original size:84 final size:84
Alignment explanation
Indices: 678--839 Score: 297
Period size: 84 Copynumber: 1.9 Consensus size: 84
668 CTCTGGGCCA
678 GTTAACGAATTTGGTTGAATTGGATCTATCCTCCAATAAGCTTTCAGGTCACATCCCTTCCTCTC
1 GTTAACGAATTTGGTTGAATTGGATCTATCCTCCAATAAGCTTTCAGGTCACATCCCTTCCTCTC
*
743 TGGGCCAGTTAACGAATTT
66 TAGGCCAGTTAACGAATTT
*
762 GTTAACGAATTTGGTTGAATTGGATCTATCCTCCAATAGGCTTTCAGGTCACATCCCTTCCTCTC
1 GTTAACGAATTTGGTTGAATTGGATCTATCCTCCAATAAGCTTTCAGGTCACATCCCTTCCTCTC
*
827 TAGGTCAGTTAAC
66 TAGGCCAGTTAAC
840 AAAATTGGAA
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 75 1.00
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (84 bp):
GTTAACGAATTTGGTTGAATTGGATCTATCCTCCAATAAGCTTTCAGGTCACATCCCTTCCTCTC
TAGGCCAGTTAACGAATTT
Done.