Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018263.1 Corchorus olitorius cultivar O-4 contig18296, 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: 27379
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Found at i:155 original size:2 final size:2
Alignment explanation
Indices: 148--177 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
138 CAATAAATAA
148 AT 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 AT
178 TAAGGAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3240 original size:27 final size:27
Alignment explanation
Indices: 3187--3240 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
3177 CTCAAATACT
*
3187 TCCTCATCTCCCTCTTCCTTTCTCTCC
1 TCCTCATCTCCCTCTTCCTTTCCCTCC
* *
3214 TCCTCCTCTTCCTCTT-CTTCTCCCTCC
1 TCCTCATCTCCCTCTTCCTT-TCCCTCC
3241 AGCCGGCGGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 3 0.13
27 20 0.87
ACGTcount: A:0.02, C:0.54, G:0.00, T:0.44
Consensus pattern (27 bp):
TCCTCATCTCCCTCTTCCTTTCCCTCC
Found at i:4292 original size:22 final size:22
Alignment explanation
Indices: 4267--4317 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 22
4257 CTATTATTTA
4267 AGTATATAGGTATA-TATACTAT
1 AGTATAT-GGTATATTATACTAT
*
4289 AGTAGT-TGGTTTATTATACTAT
1 AGTA-TATGGTATATTATACTAT
*
4311 ACTATAT
1 AGTATAT
4318 TTTTTAATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
21 6 0.25
22 17 0.71
23 1 0.04
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.45
Consensus pattern (22 bp):
AGTATATGGTATATTATACTAT
Found at i:9400 original size:336 final size:336
Alignment explanation
Indices: 8793--9790 Score: 1681
Period size: 336 Copynumber: 3.0 Consensus size: 336
8783 TGCGGCCGGG
8793 ATGGTTGGATCCTGGTGATCAACATCATCTTTTCCTTGCAATTCTGGAAGGTCCACAATGGTAGA
1 ATGGTTGGATCCTGGTGATCAACATCATCTTTTCCTTGCAATTCTGGAAGGTCCACAATGGTAGA
* *
8858 ACTTTTCTTCTTGCTTTTCTTCCTTGATGACTTCTTATCCAGATTTTCTGCTTTTACCGGGCCAT
66 ACTTTTCTTCTTCCTTTTCTTCCTTGATGACTTCTTATCCAGATTTTCTGCATTTACCGGGCCAT
* *
8923 TGTTGCCTTGCTGCAAGGACTCCAGCACTTCACCAATTACATCATCAGCTCCCATATCAGTATCT
131 TGTTGCCTTGCTGCAAGGACTCCAGCACATCACCAATTACATCATCAGCTCCCATATCAGTAACT
* * *
8988 GAAGGCAAATATTCTGATGCATCCCTTTTTGATGCTTCTTTTTCGTCGGCCGTTCCATCTTTTTC
196 GAAGGCAAATATTCTGATGTATCCCTTTTTGATGCTTCTTTTCCGTCGGCTGTTCCATCTTTTTC
*
9053 AGCATTATCACTCAAGTGGTCACCAATCAAAGAGTTGGGACGCTCAAGAGGTACTATATCAATTG
261 AGCATTATCACTCAAGTGGTCACCAATCAGAGAGTTGGGACGCTCAAGAGGTACTATATCAATTG
9118 CTGCGGCCAAA
326 CTGCGGCCAAA
9129 ATGGTTGGATCCTGGTGATCAACATCATCTTTTCCTTGCAATTCTGGAAGGTCCACAATGGTAGA
1 ATGGTTGGATCCTGGTGATCAACATCATCTTTTCCTTGCAATTCTGGAAGGTCCACAATGGTAGA
*
9194 ACTTTTCTTCTTCCTTTTCTTCCTTGATGACTTCTTATCCAGATTTTCTGCATTTGCCGGGCCAT
66 ACTTTTCTTCTTCCTTTTCTTCCTTGATGACTTCTTATCCAGATTTTCTGCATTTACCGGGCCAT
* * *
9259 TATTGCCTTGCTGCAAGGACTCCAGCACATCACCAGTTACTTCATCAGCTCCCATATCAGTAACT
131 TGTTGCCTTGCTGCAAGGACTCCAGCACATCACCAATTACATCATCAGCTCCCATATCAGTAACT
* * *
9324 GAAGGCAAATATTCTGATGTATCCCTTCTTGATGTTTCTTTTCCGTCAGCTGTTCCATCTTTTTC
196 GAAGGCAAATATTCTGATGTATCCCTTTTTGATGCTTCTTTTCCGTCGGCTGTTCCATCTTTTTC
* ** *
9389 AGCAGTATCACTCAAAAGGTCACCAATCAGAGAGTTGGGACCCTCAAGAGGTACTATATCAATTG
261 AGCATTATCACTCAAGTGGTCACCAATCAGAGAGTTGGGACGCTCAAGAGGTACTATATCAATTG
***
9454 CTGCGGCCGGG
326 CTGCGGCCAAA
* *
9465 ATGGTTGGATCCTGGTGATCAACATCATCTTTTTCTTGCAATTCTGGAAGGTCCACAATGGTTGA
1 ATGGTTGGATCCTGGTGATCAACATCATCTTTTCCTTGCAATTCTGGAAGGTCCACAATGGTAGA
* *
9530 ACTTTTCTTCTTCCTTTTCTTCCTTGATGACTTCTTATCCAGATTTTCTGCATTTTCTGGGCCAT
66 ACTTTTCTTCTTCCTTTTCTTCCTTGATGACTTCTTATCCAGATTTTCTGCATTTACCGGGCCAT
* * *
9595 TGTTGCCTTGCTGCAAGGAGTCCAGCACAACACGAATTACATCATCAGCTCCCATATCAGTAACT
131 TGTTGCCTTGCTGCAAGGACTCCAGCACATCACCAATTACATCATCAGCTCCCATATCAGTAACT
* * * * *
9660 GAAGACAAATATTCGGATGTATCCCTTTTTGGTGCCTCTTTTCCGTCGGCTGTGCCATCTTTTTC
196 GAAGGCAAATATTCTGATGTATCCCTTTTTGATGCTTCTTTTCCGTCGGCTGTTCCATCTTTTTC
*
9725 AGCATTATCACTCAAGTGGTCACCAATCAGAGAGTTGGGACGCTCGAGAGGTACTATATCAATTG
261 AGCATTATCACTCAAGTGGTCACCAATCAGAGAGTTGGGACGCTCAAGAGGTACTATATCAATTG
9790 C
326 C
9791 AGGATCCTTG
Statistics
Matches: 617, Mismatches: 45, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
336 617 1.00
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (336 bp):
ATGGTTGGATCCTGGTGATCAACATCATCTTTTCCTTGCAATTCTGGAAGGTCCACAATGGTAGA
ACTTTTCTTCTTCCTTTTCTTCCTTGATGACTTCTTATCCAGATTTTCTGCATTTACCGGGCCAT
TGTTGCCTTGCTGCAAGGACTCCAGCACATCACCAATTACATCATCAGCTCCCATATCAGTAACT
GAAGGCAAATATTCTGATGTATCCCTTTTTGATGCTTCTTTTCCGTCGGCTGTTCCATCTTTTTC
AGCATTATCACTCAAGTGGTCACCAATCAGAGAGTTGGGACGCTCAAGAGGTACTATATCAATTG
CTGCGGCCAAA
Found at i:13285 original size:31 final size:31
Alignment explanation
Indices: 13250--13310 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
13240 CTTAAAATAA
*
13250 ATTATCAACGTGTAATAATTAATTTCTGAAC
1 ATTATCAACGTCTAATAATTAATTTCTGAAC
*
13281 ATTATCAATGTCTAATAATTAATTTCTGAA
1 ATTATCAACGTCTAATAATTAATTTCTGAA
13311 AAATAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.41
Consensus pattern (31 bp):
ATTATCAACGTCTAATAATTAATTTCTGAAC
Found at i:18098 original size:18 final size:18
Alignment explanation
Indices: 18075--18110 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
18065 CAGCCTTACC
18075 TAGTATACCATCAAATTA
1 TAGTATACCATCAAATTA
18093 TAGTATACCATCAAATTA
1 TAGTATACCATCAAATTA
18111 AACTCAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.33
Consensus pattern (18 bp):
TAGTATACCATCAAATTA
Found at i:22489 original size:30 final size:30
Alignment explanation
Indices: 22455--22544 Score: 76
Period size: 30 Copynumber: 3.1 Consensus size: 30
22445 TTTGTATTTC
22455 TTTGGGTAAAGTATGGTATATTTGGGCTTT
1 TTTGGGTAAAGTATGGTATATTTGGGCTTT
* * * * **
22485 TTTGGGTTAAGCATGGTGTAGTT-GAATTT
1 TTTGGGTAAAGTATGGTATATTTGGGCTTT
** * *
22514 GCTGGGCAAA-TATGGTATATTTGGGCCTT
1 TTTGGGTAAAGTATGGTATATTTGGGCTTT
22543 TT
1 TT
22545 CTTCTAAGTA
Statistics
Matches: 41, Mismatches: 18, Indels: 3
0.66 0.29 0.05
Matches are distributed among these distances:
28 9 0.22
29 13 0.32
30 19 0.46
ACGTcount: A:0.20, C:0.07, G:0.30, T:0.43
Consensus pattern (30 bp):
TTTGGGTAAAGTATGGTATATTTGGGCTTT
Found at i:24231 original size:90 final size:90
Alignment explanation
Indices: 24072--24240 Score: 293
Period size: 90 Copynumber: 1.9 Consensus size: 90
24062 GGATAGAATA
* * **
24072 CCAAAAAAAAAAATCTCACCCTGTCTATTTTAGGATTCGAACTCGAAACCTTCTATAAGAAATTT
1 CCAAAAAAAAAAATCTCACCCTGCCTATTCTAGGATTCGAACTCGAAACCTTCTATAAGAAATCC
24137 TAAGCTTCAACTAGCTGTGGTGTGT
66 TAAGCTTCAACTAGCTGTGGTGTGT
*
24162 CCAAAAAAAATAATCTCACCCTGCCTATTCTAGGATTCGAACTCGAAACCTTCTATAAGAAATCC
1 CCAAAAAAAAAAATCTCACCCTGCCTATTCTAGGATTCGAACTCGAAACCTTCTATAAGAAATCC
24227 TAAGCTTCAACTAG
66 TAAGCTTCAACTAG
24241 TTGTAGAGTG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
90 74 1.00
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.28
Consensus pattern (90 bp):
CCAAAAAAAAAAATCTCACCCTGCCTATTCTAGGATTCGAACTCGAAACCTTCTATAAGAAATCC
TAAGCTTCAACTAGCTGTGGTGTGT
Done.