Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008243.1 Corchorus capsularis cultivar CVL-1 contig08264, 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: 29185
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:1088 original size:258 final size:258
Alignment explanation
Indices: 631--1406 Score: 1507
Period size: 258 Copynumber: 3.0 Consensus size: 258
621 CTCTCAACCC
* **
631 AATCTAACAATGAATCCTAAACCAAACCCAAACAATCTTGAACACTCTCGCTCGGTCTCTATGAG
1 AATCTAACAATGAATCCTAAACCAAACCCAAACAATCTTGAGCACTCTCGCTCAATCTCTATGAG
696 CACTCTCGCTCGGCCTCTGCAAACCAATCATCACATCAACAAAACCAAACATCAAACGAAACAAT
66 CACTCTCGCTCGGCCTCTGCAAACCAATCATCACATCAACAAAACCAAACATCAAACGAAACAAT
761 CTCACACACACCCATAAGGACCATCCTTTTGTCCTATGGGGTGCCTCCACCCAAATCTAACCCTT
131 CTCACACACACCCATAAGGACCATCCTTTTGTCCTATGGGGTGCCTCCACCCAAATCTAACCCTT
826 AGACTACATCTTTTCTCCAAGCATACAAAATCCTATAGAGAAACTCTCTATTTATACTAGTAT
196 AGACTACATCTTTTCTCCAAGCATACAAAATCCTATAGAGAAACTCTCTATTTATACTAGTAT
889 AATCTAACAATGAATCCTAAACCAAACCCAAACAATCTTGAGCACTCTCGCTCAATCTCTATGAG
1 AATCTAACAATGAATCCTAAACCAAACCCAAACAATCTTGAGCACTCTCGCTCAATCTCTATGAG
954 CACTCTCGCTCGGCCTCTGCAAACCAATCATCACATCAACAAAACCAAACATCAAACGAAACAAT
66 CACTCTCGCTCGGCCTCTGCAAACCAATCATCACATCAACAAAACCAAACATCAAACGAAACAAT
1019 CTCACACACACCCATAAGGACCATCCTTTTGTCCTATGGGGTGCCTCCACCCAAATCTAACCCTT
131 CTCACACACACCCATAAGGACCATCCTTTTGTCCTATGGGGTGCCTCCACCCAAATCTAACCCTT
1084 AGACTACATCTTTTCTCCAAGCATACAAAATCCTATAGAGAAACTCTCTATTTATACTAGTAT
196 AGACTACATCTTTTCTCCAAGCATACAAAATCCTATAGAGAAACTCTCTATTTATACTAGTAT
*
1147 AATCAAACAATGAATCCTAAACCAAACCCAAACAATCTTGAGCACTCTCGCTCAATCTCTATGAG
1 AATCTAACAATGAATCCTAAACCAAACCCAAACAATCTTGAGCACTCTCGCTCAATCTCTATGAG
1212 CACTCTCGCTCGGCCTCTGCAAACCAATCATCACATCAACAAAACCAAACATCAAACGAAACAAT
66 CACTCTCGCTCGGCCTCTGCAAACCAATCATCACATCAACAAAACCAAACATCAAACGAAACAAT
1277 CTCACACACACCCATAAGGACCATCCTTTTGTCCTATGGGGTGCCTCCACCCAAATCTAACCCTT
131 CTCACACACACCCATAAGGACCATCCTTTTGTCCTATGGGGTGCCTCCACCCAAATCTAACCCTT
*
1342 AGACTACATCTTTTCTCCAAGCATACAAAATCCTATAGAGAAACTCTCTATTTATACTAGCAT
196 AGACTACATCTTTTCTCCAAGCATACAAAATCCTATAGAGAAACTCTCTATTTATACTAGTAT
1405 AA
1 AA
1407 ACTTAGCCTC
Statistics
Matches: 513, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
258 513 1.00
ACGTcount: A:0.35, C:0.31, G:0.09, T:0.24
Consensus pattern (258 bp):
AATCTAACAATGAATCCTAAACCAAACCCAAACAATCTTGAGCACTCTCGCTCAATCTCTATGAG
CACTCTCGCTCGGCCTCTGCAAACCAATCATCACATCAACAAAACCAAACATCAAACGAAACAAT
CTCACACACACCCATAAGGACCATCCTTTTGTCCTATGGGGTGCCTCCACCCAAATCTAACCCTT
AGACTACATCTTTTCTCCAAGCATACAAAATCCTATAGAGAAACTCTCTATTTATACTAGTAT
Found at i:5822 original size:17 final size:17
Alignment explanation
Indices: 5776--5823 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
5766 GCTGCAATGA
*
5776 AGTGAGCTGGCCTTGTT
1 AGTGAGCTGGCTTTGTT
5793 AGTGAGCTGGCTTTGTT
1 AGTGAGCTGGCTTTGTT
* *
5810 GGTGAGCTCGCTTT
1 AGTGAGCTGGCTTT
5824 AATTCTCTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.10, C:0.17, G:0.35, T:0.38
Consensus pattern (17 bp):
AGTGAGCTGGCTTTGTT
Found at i:7844 original size:27 final size:27
Alignment explanation
Indices: 7793--7851 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
7783 TAGACTTGAG
* *
7793 ATGACCAAAATGCCCCTAAATGTGCAA
1 ATGACAAAAATGCCCCTAAACGTGCAA
* **
7820 TTGACAAAAATGCCCCTGGACGTGCAA
1 ATGACAAAAATGCCCCTAAACGTGCAA
7847 ATGAC
1 ATGAC
7852 CAGAAAGCCC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (27 bp):
ATGACAAAAATGCCCCTAAACGTGCAA
Found at i:20609 original size:19 final size:22
Alignment explanation
Indices: 20567--20618 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 22
20557 TATGATTTTC
20567 AATTATTTATTAAATTATACATT
1 AATTATTT-TTAAATTATACATT
20590 AATTATTTTT-AATT-TA-ATT
1 AATTATTTTTAAATTATACATT
*
20609 ATTTATTTTT
1 AATTATTTTT
20619 TATAGATTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 12 0.43
20 2 0.07
21 4 0.14
22 2 0.07
23 8 0.29
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
AATTATTTTTAAATTATACATT
Found at i:21167 original size:66 final size:66
Alignment explanation
Indices: 21061--21193 Score: 257
Period size: 66 Copynumber: 2.0 Consensus size: 66
21051 AATCGGGTAG
*
21061 AGGAAACTTATCTACTTCAAATGTTTAAAAATTCACAATGAGAGACATTTCTTCAGGAAAGACAG
1 AGGAAACTTATCTACTTCAAATGTTTAAAAATTCACAATGAAAGACATTTCTTCAGGAAAGACAG
21126 A
66 A
21127 AGGAAACTTATCTACTTCAAATGTTTAAAAATTCACAATGAAAGACATTTCTTCAGGAAAGACAG
1 AGGAAACTTATCTACTTCAAATGTTTAAAAATTCACAATGAAAGACATTTCTTCAGGAAAGACAG
21192 A
66 A
21193 A
1 A
21194 ACAGACATAG
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.44, C:0.15, G:0.14, T:0.27
Consensus pattern (66 bp):
AGGAAACTTATCTACTTCAAATGTTTAAAAATTCACAATGAAAGACATTTCTTCAGGAAAGACAG
A
Found at i:26272 original size:16 final size:15
Alignment explanation
Indices: 26251--26356 Score: 122
Period size: 16 Copynumber: 6.7 Consensus size: 15
26241 ACCCAATACA
26251 AATACTCACCTGGTG
1 AATACTCACCTGGTG
26266 CAATACTCACCTGGTG
1 -AATACTCACCTGGTG
*
26282 AGATACTCACCCGGTG
1 A-ATACTCACCTGGTG
** *
26298 AGATACTCACCCAGTAC
1 A-ATACTCACCTGGT-G
26315 AATACTCACCTGGTG
1 AATACTCACCTGGTG
26330 TAATACTCACCTGGTG
1 -AATACTCACCTGGTG
26346 AGATACTCACC
1 A-ATACTCACC
26357 CACACTCTCC
Statistics
Matches: 80, Mismatches: 6, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
15 2 0.03
16 77 0.96
17 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (15 bp):
AATACTCACCTGGTG
Found at i:26323 original size:48 final size:48
Alignment explanation
Indices: 26252--26358 Score: 162
Period size: 48 Copynumber: 2.2 Consensus size: 48
26242 CCCAATACAA
** *
26252 ATACTCACCTGGTGCAATACTCACCTGGTG-AGATACTCACCCGGTGAG
1 ATACTCACCCAGTACAATACTCACCTGGTGTA-ATACTCACCCGGTGAG
*
26300 ATACTCACCCAGTACAATACTCACCTGGTGTAATACTCACCTGGTGAG
1 ATACTCACCCAGTACAATACTCACCTGGTGTAATACTCACCCGGTGAG
26348 ATACTCACCCA
1 ATACTCACCCA
26359 CACTCTCCCA
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
48 53 0.98
49 1 0.02
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (48 bp):
ATACTCACCCAGTACAATACTCACCTGGTGTAATACTCACCCGGTGAG
Found at i:28294 original size:36 final size:36
Alignment explanation
Indices: 28247--28341 Score: 154
Period size: 36 Copynumber: 2.6 Consensus size: 36
28237 TGGTTGTAAT
*
28247 GCCGCTGGCCTTAGTCGCCTGATGCTTGGCTATAAC
1 GCCGCTGGCCTTAGTCGCCTAATGCTTGGCTATAAC
* *
28283 GCCGCTGGCCTTAGTCGCCCAATGTTTGGCTATAAC
1 GCCGCTGGCCTTAGTCGCCTAATGCTTGGCTATAAC
*
28319 GCCGCTGGCCTAAGTCGCCTAAT
1 GCCGCTGGCCTTAGTCGCCTAAT
28342 ACATAATTAG
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.16, C:0.32, G:0.26, T:0.26
Consensus pattern (36 bp):
GCCGCTGGCCTTAGTCGCCTAATGCTTGGCTATAAC
Done.