Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005368.1 Corchorus capsularis cultivar CVL-1 contig05386, 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: 16553
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:4808 original size:363 final size:363
Alignment explanation
Indices: 4143--4858 Score: 1369
Period size: 363 Copynumber: 2.0 Consensus size: 363
4133 CTCGATAGCA
4143 TTGAGGTGTGGTACTTCAAGACCAAACATATATCCTCATCAGTTTGTTTAGGACGAAACGAGTCC
1 TTGAGGTGTGGTACTTCAAGACCAAACATATATCCTCATCAGTTTGTTTAGGACGAAACGAGTCC
4208 ATTGGGGATCAAGTGACCTTACAACCATAGGGGTACTCAAAATATTTAATTTGCTTTGTGCTCAA
66 ATTGGGGATCAAGTGACCTTACAACCATAGGGGTACTCAAAATATTTAATTTGCTTTGTGCTCAA
* *
4273 ACTCTAGACCAAGGCATAATTTGGTTTTACCCAAATCCTCAAAACTCCATTTCAAATAGTTAGCA
131 ACTCTAAACAAAGGCATAATTTGGTTTTACCCAAATCCTCAAAACTCCATTTCAAATAGTTAGCA
*
4338 GTTTGGGACAACTCTTCAGGAGTTCCAAATTATATCGTCGACATAAACTGCCATTATAGCAAATC
196 GTTTGGGACAACTCTTCAGGAGTTCCAAATTATATCGTCGACATAAACTGCCACTATAGCAAATC
4403 CGGTTTCCAATTTAATAAACACACATGGGTCGATGGGATCTTTTTATACTCTTCCTTAATCAAGT
261 CGGTTTCCAATTTAATAAACACACATGGGTCGATGGGATCTTTTTATACTCTTCCTTAATCAAGT
4468 ACACGCTTTAAGCTTTGATACCACATGTCCCAAATATT
326 ACACGCTTTAAGCTTTGATACCACATGTCCCAAATATT
*
4506 TTGAGGTGTGGTACTTCAAGACCAAACATATATCCTCATCGGTTTGTTTAGGACGAAACGAGTCC
1 TTGAGGTGTGGTACTTCAAGACCAAACATATATCCTCATCAGTTTGTTTAGGACGAAACGAGTCC
4571 ATTGGGGATCAAGTGACCTTACAACCATAGGGGTACTCAAAATATTTAATTTGCTTTGTGCTCAA
66 ATTGGGGATCAAGTGACCTTACAACCATAGGGGTACTCAAAATATTTAATTTGCTTTGTGCTCAA
*
4636 GCTCTAAACAAAGGCATAATTTGGTTTTACCCAAATCCTCAAAACTCCATTTCAAATAGTTAGCA
131 ACTCTAAACAAAGGCATAATTTGGTTTTACCCAAATCCTCAAAACTCCATTTCAAATAGTTAGCA
* *
4701 GTTTGGGACAACTCTTCGGGAGTTCCAAATTATATTGTCGACATAAACTGCCACTATAGCAAATC
196 GTTTGGGACAACTCTTCAGGAGTTCCAAATTATATCGTCGACATAAACTGCCACTATAGCAAATC
4766 CGGTTTCCAATTTAATAAACACACATGGGTCGATGGGATCTTTTTATACTCTTCCTTAATCAAGT
261 CGGTTTCCAATTTAATAAACACACATGGGTCGATGGGATCTTTTTATACTCTTCCTTAATCAAGT
4831 ACACGCTTTAAGCTTTGATACCACATGT
326 ACACGCTTTAAGCTTTGATACCACATGT
4859 GGCCGGATTG
Statistics
Matches: 346, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
363 346 1.00
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (363 bp):
TTGAGGTGTGGTACTTCAAGACCAAACATATATCCTCATCAGTTTGTTTAGGACGAAACGAGTCC
ATTGGGGATCAAGTGACCTTACAACCATAGGGGTACTCAAAATATTTAATTTGCTTTGTGCTCAA
ACTCTAAACAAAGGCATAATTTGGTTTTACCCAAATCCTCAAAACTCCATTTCAAATAGTTAGCA
GTTTGGGACAACTCTTCAGGAGTTCCAAATTATATCGTCGACATAAACTGCCACTATAGCAAATC
CGGTTTCCAATTTAATAAACACACATGGGTCGATGGGATCTTTTTATACTCTTCCTTAATCAAGT
ACACGCTTTAAGCTTTGATACCACATGTCCCAAATATT
Found at i:8341 original size:32 final size:32
Alignment explanation
Indices: 8300--8361 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
8290 CAACCTCAAC
* * *
8300 GTGACAACTTCCGGTGTCAAATATTATTTATT
1 GTGACAACTTCCGGTATCAAAAATAATTTATT
*
8332 GTGACAACTTCTGGTATCAAAAATAATTTA
1 GTGACAACTTCCGGTATCAAAAATAATTTA
8362 ATATAGTGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Consensus pattern (32 bp):
GTGACAACTTCCGGTATCAAAAATAATTTATT
Found at i:9429 original size:2 final size:2
Alignment explanation
Indices: 9424--9460 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
9414 CTATACTTCC
9424 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9461 CGTAATTCCC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:10033 original size:2 final size:2
Alignment explanation
Indices: 10026--10053 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
10016 AAACATAGAA
10026 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10054 TGTTTTACCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12227 original size:74 final size:74
Alignment explanation
Indices: 12106--12254 Score: 298
Period size: 74 Copynumber: 2.0 Consensus size: 74
12096 CTGGCTGCCT
12106 AGAAAACTTGGTTTTCAATCCCAAATATGAGGGCTTCTCTGTTTGGCATTTGACATTTTGAGTAA
1 AGAAAACTTGGTTTTCAATCCCAAATATGAGGGCTTCTCTGTTTGGCATTTGACATTTTGAGTAA
12171 CTTGAAATG
66 CTTGAAATG
12180 AGAAAACTTGGTTTTCAATCCCAAATATGAGGGCTTCTCTGTTTGGCATTTGACATTTTGAGTAA
1 AGAAAACTTGGTTTTCAATCCCAAATATGAGGGCTTCTCTGTTTGGCATTTGACATTTTGAGTAA
12245 CTTGAAATG
66 CTTGAAATG
12254 A
1 A
12255 CTGTTATTGG
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (74 bp):
AGAAAACTTGGTTTTCAATCCCAAATATGAGGGCTTCTCTGTTTGGCATTTGACATTTTGAGTAA
CTTGAAATG
Done.