Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023459.1 Corchorus olitorius cultivar O-4 contig23492, 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: 28041
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:891 original size:19 final size:19
Alignment explanation
Indices: 841--891 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
831 TGTGGGATTT
841 TTAATAA-TAATTATTCAA
1 TTAATAATTAATTATTCAA
* *
859 TAAAATAATT-ATTATTTAA
1 T-TAATAATTAATTATTCAA
878 TTAATAATTAATTA
1 TTAATAATTAATTA
892 ATTTCAGCCC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 8 0.30
19 18 0.67
20 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAATAATTAATTATTCAA
Found at i:1931 original size:129 final size:127
Alignment explanation
Indices: 1798--2042 Score: 301
Period size: 127 Copynumber: 1.9 Consensus size: 127
1788 TTTTCACTCC
* * * * * * *
1798 TCATAATTCCTTAGTGATTAACCTTAACCCTAAATAAATTATGAAATTAGCCGAGGTTTATTTTC
1 TCATAATTACTTAGTAATAAACCTTAACCCTAAATAAATTATGAAA-TAACCAAGATTTATTTCC
* * *
1863 TAAAGGGTCCAAATTAACTTTAATTAGACCTAGATACTTAATTATCTCTTAAATCTAATTATTG
65 TAAA-GGTCCAAATTAACTTTAATTAAACCTAAATACTTAACTATCTCTTAAATCTAATTATTG
* * ** * *
1927 TCATAGTTACTTAGTAATAAACTTTAATTCTAAGTATATTATGAAATAACCAAGATTTATTTCCT
1 TCATAATTACTTAGTAATAAACCTTAACCCTAAATAAATTATGAAATAACCAAGATTTATTTCCT
** *
1992 AAAGGTTTAAATTAACTTTAATTAAACCTAAATATTTAACTATCTCTTAAA
66 AAAGGTCCAAATTAACTTTAATTAAACCTAAATACTTAACTATCTCTTAAA
2043 ATCCCATTAT
Statistics
Matches: 97, Mismatches: 19, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
127 42 0.43
128 18 0.19
129 37 0.38
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (127 bp):
TCATAATTACTTAGTAATAAACCTTAACCCTAAATAAATTATGAAATAACCAAGATTTATTTCCT
AAAGGTCCAAATTAACTTTAATTAAACCTAAATACTTAACTATCTCTTAAATCTAATTATTG
Found at i:6421 original size:177 final size:177
Alignment explanation
Indices: 6125--6462 Score: 651
Period size: 177 Copynumber: 1.9 Consensus size: 177
6115 AAAAACAACT
*
6125 TTTTCCAAACTGATGTTTTTCAATTGATAGAAAAATATTTTCCACATGATCATCCAAACGATAGA
1 TTTTCCAAACTGAAGTTTTTCAATTGATAGAAAAATATTTTCCACATGATCATCCAAACGATAGA
6190 AAATATCAAATTTTCCAGAGCTTATTACCCATCCCCCCTTACAACCAAAAAAAATTCTAAAAGTG
66 AAATATCAAATTTTCCAGAGCTTATTACCCATCCCCCCTTACAACCAAAAAAAATTCTAAAAGTG
6255 ACACTTTCCTCCGTAAAGTTTTTTTGTCCATCCAATTGAAACTGATG
131 ACACTTTCCTCCGTAAAGTTTTTTTGTCCATCCAATTGAAACTGATG
6302 TTTTCCAAACTGAAGTTTTTCAATTGATAGAAAAATATTTTCCACATGATCATCCAAACGATAGA
1 TTTTCCAAACTGAAGTTTTTCAATTGATAGAAAAATATTTTCCACATGATCATCCAAACGATAGA
6367 AAATATCAAATTTTTCCAGAGCTTATTACCCATCCCCCCTTACAACC-AAAAAAATTCTAAAAGT
66 AAATATCAAA-TTTTCCAGAGCTTATTACCCATCCCCCCTTACAACCAAAAAAAATTCTAAAAGT
6431 GACACTTTCCTCCGTAAAGTTTTTTTGTCCAT
130 GACACTTTCCTCCGTAAAGTTTTTTTGTCCAT
6463 ACCCCCCCCC
Statistics
Matches: 159, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
177 123 0.77
178 36 0.23
ACGTcount: A:0.36, C:0.22, G:0.09, T:0.33
Consensus pattern (177 bp):
TTTTCCAAACTGAAGTTTTTCAATTGATAGAAAAATATTTTCCACATGATCATCCAAACGATAGA
AAATATCAAATTTTCCAGAGCTTATTACCCATCCCCCCTTACAACCAAAAAAAATTCTAAAAGTG
ACACTTTCCTCCGTAAAGTTTTTTTGTCCATCCAATTGAAACTGATG
Found at i:7242 original size:21 final size:21
Alignment explanation
Indices: 7213--7256 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
7203 TTGTGTGGAG
7213 AAGAAAGAGAGAAAAAGGAAA
1 AAGAAAGAGAGAAAAAGGAAA
* * *
7234 AAGAGAGAGAGTAAAAGTAAA
1 AAGAAAGAGAGAAAAAGGAAA
7255 AA
1 AA
7257 TAAAATTGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.27, T:0.05
Consensus pattern (21 bp):
AAGAAAGAGAGAAAAAGGAAA
Found at i:7684 original size:3 final size:3
Alignment explanation
Indices: 7676--7732 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
7666 CAAATTATTT
7676 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
7724 ATA ATA ATA
1 ATA ATA ATA
7733 TATTTCCAAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:14910 original size:28 final size:28
Alignment explanation
Indices: 14867--14920 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
14857 CATTTATAAT
* * *
14867 GAATATTGTGATTATTTATGAATCAAAA
1 GAATATTGTAAATATTCATGAATCAAAA
*
14895 GAATATTGTAAATATTCATGAGTCAA
1 GAATATTGTAAATATTCATGAATCAA
14921 GAGTTCTCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.43, C:0.06, G:0.15, T:0.37
Consensus pattern (28 bp):
GAATATTGTAAATATTCATGAATCAAAA
Found at i:27239 original size:107 final size:105
Alignment explanation
Indices: 27067--27324 Score: 412
Period size: 107 Copynumber: 2.5 Consensus size: 105
27057 AGTTTAGCCT
*
27067 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
27132 AATAATTTATTGTTATAGGCTTTTAGAAATAAAATATAAAAC
66 AATAA--TATTGTTATAGGCTTTTAGAAATAAAATATAAAAC
* *
27174 TAATTTCACTAAGTTTAGCCCCAAATTTAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
* *
27239 AATAATATTGTTATAGGGTTTTAGAAATAAAATATATAAC
66 AATAATATTGTTATAGGCTTTTAGAAATAAAATATAAAAC
** *
27279 TAA-TTCACTAAGTTTAG-CCCAAATTAAAATTAAAATTTTATTTTAA
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAA
27325 AGGTTAGAAA
Statistics
Matches: 142, Mismatches: 9, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
103 25 0.18
104 14 0.10
105 36 0.25
107 67 0.47
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (105 bp):
TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
AATAATATTGTTATAGGCTTTTAGAAATAAAATATAAAAC
Found at i:27544 original size:31 final size:31
Alignment explanation
Indices: 27509--27567 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
27499 AAAATTATTA
* *
27509 ATGAATATTGTGATTATTCATGAATCAAAAG
1 ATGAATATTGTAAATATTCATGAATCAAAAG
*
27540 ATGAATATTGTAAATATTCATTAATCAA
1 ATGAATATTGTAAATATTCATGAATCAA
27568 GAGTTCTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (31 bp):
ATGAATATTGTAAATATTCATGAATCAAAAG
Done.