Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005586.1 Corchorus capsularis cultivar CVL-1 contig05604, whole genome shotgun sequence
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: 2107
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Found at i:1006 original size:31 final size:31
Alignment explanation
Indices: 968--1029 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
958 AGTTTTATAA
* *
968 AACTTTTGAAACGACTATTGTACCCTTATTT
1 AACTTTTGAAACGACTAGTATACCCTTATTT
* *
999 AACTTTTGAAACGCCTAGTATATCCTTATTT
1 AACTTTTGAAACGACTAGTATACCCTTATTT
1030 GTCTAACATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.42
Consensus pattern (31 bp):
AACTTTTGAAACGACTAGTATACCCTTATTT
Found at i:1591 original size:159 final size:161
Alignment explanation
Indices: 1286--1603 Score: 554
Period size: 159 Copynumber: 2.0 Consensus size: 161
1276 TAATATAAAA
*
1286 ATCAATTTTTTAATGTATTTATTTTTTAGAGAAATTCTACTCTACTAATCTTTCTTTGTTTTTTT
1 ATCAATTTTTTAATGTATTTATTTTTTAGAGAAATTCTACTCTACTAA--TTTCTTTCTTTTTTT
*
1351 TTTGCCAGTATACTCTACTAATCCGTTGACTATTTTTCTCTACTATTTTTTTTCCTTTTTCAATT
64 TTGGCCAGTATACTCTACTAATCCGTTGACTATTTTTCTCTACTATTTTTTTTCCTTTTTCAATT
*
1416 TTTCGTTTATTTAAAAAAATTATAAACTCTACT
129 TTTCATTTATTTAAAAAAATTATAAACTCTACT
1449 ATCAATTTTTTAATGTATTTATTTTTTAGAGAAATTCTACTCTACTAA-TT-TTTCTTTTTTTTT
1 ATCAATTTTTTAATGTATTTATTTTTTAGAGAAATTCTACTCTACTAATTTCTTTCTTTTTTTTT
1512 GGCCAG-AGTACTCTACTAATCCGTTGACTATTTTTCTCTACTA-TTTTTTTCCTTTTTCAATTT
66 GGCCAGTA-TACTCTACTAATCCGTTGACTATTTTTCTCTACTATTTTTTTTCCTTTTTCAATTT
1575 TTCATTTATTTAAAAAAATTATAAACTCT
130 TTCATTTATTTAAAAAAATTATAAACTCT
1604 TTATAATTTG
Statistics
Matches: 151, Mismatches: 3, Indels: 7
0.94 0.02 0.04
Matches are distributed among these distances:
158 49 0.32
159 52 0.34
160 2 0.01
163 48 0.32
ACGTcount: A:0.26, C:0.15, G:0.06, T:0.53
Consensus pattern (161 bp):
ATCAATTTTTTAATGTATTTATTTTTTAGAGAAATTCTACTCTACTAATTTCTTTCTTTTTTTTT
GGCCAGTATACTCTACTAATCCGTTGACTATTTTTCTCTACTATTTTTTTTCCTTTTTCAATTTT
TCATTTATTTAAAAAAATTATAAACTCTACT
Found at i:1667 original size:159 final size:159
Alignment explanation
Indices: 1286--1616 Score: 438
Period size: 163 Copynumber: 2.1 Consensus size: 159
1276 TAATATAAAA
** * * *
1286 ATCAATTTTTTAATGTATTTATTTTTTAGAGAAATTCTACTCTACTAATCTT-TCTTTGTTTTTT
1 ATCAATTTGCTAATGTATTTATTATGTAGAGAAATTCTACTCTACGAAT-TTGTC---G-TTTTT
*
1350 TTTTGCCAGTATACTCTACTAATCCGTTGACTATTTTTCTCTACTATTTTTTTTCCTTTTTCAAT
61 TTTGGCCAGTATACTCTACTAATCCGTTGACTATTTTTCTCTACTATTTTTTTTCCTTTTTCAAT
*
1415 TTTTCGTTTATTTAAAAAAATTATAAACTCTACT
126 TTTTCATTTATTTAAAAAAATTATAAACTCTACT
** * * * * *
1449 ATCAATTTTTTAATGTATTTATTTTTTAGAGAAATTCTACTCTACTAATTTTTCTTTTTTTTTGG
1 ATCAATTTGCTAATGTATTTATTATGTAGAGAAATTCTACTCTACGAATTTGTCGTTTTTTTTGG
1514 CCAG-AGTACTCTACTAATCCGTTGACTATTTTTCTCTACTA-TTTTTTTCCTTTTTCAATTTTT
66 CCAGTA-TACTCTACTAATCCGTTGACTATTTTTCTCTACTATTTTTTTTCCTTTTTCAATTTTT
*
1577 CATTTATTTAAAAAAATTATAAACTCT-TT
130 CATTTATTTAAAAAAATTATAAACTCTACT
1606 AT-AATTTGCTA
1 ATCAATTTGCTA
1617 GACTTCTATT
Statistics
Matches: 160, Mismatches: 6, Indels: 11
0.90 0.03 0.06
Matches are distributed among these distances:
156 7 0.04
157 3 0.02
158 49 0.31
159 48 0.30
162 2 0.01
163 51 0.32
ACGTcount: A:0.26, C:0.15, G:0.06, T:0.53
Consensus pattern (159 bp):
ATCAATTTGCTAATGTATTTATTATGTAGAGAAATTCTACTCTACGAATTTGTCGTTTTTTTTGG
CCAGTATACTCTACTAATCCGTTGACTATTTTTCTCTACTATTTTTTTTCCTTTTTCAATTTTTC
ATTTATTTAAAAAAATTATAAACTCTACT
Found at i:1901 original size:31 final size:31
Alignment explanation
Indices: 1863--1924 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
1853 AGTTTTGTAA
* *
1863 AACTTTTGAAACGTCTATTGTACCCTTATTT
1 AACTTTTGAAACGCCTATTATACCCTTATTT
*
1894 AACTTTTGAAACGCCTATTATATCCTTATTT
1 AACTTTTGAAACGCCTATTATACCCTTATTT
1925 GTAACATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.27, C:0.19, G:0.08, T:0.45
Consensus pattern (31 bp):
AACTTTTGAAACGCCTATTATACCCTTATTT
Done.