Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01000153.1 Corchorus olitorius cultivar O-4 contig00153, 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: 14926
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:501 original size:202 final size:202
Alignment explanation
Indices: 148--557 Score: 793
Period size: 202 Copynumber: 2.0 Consensus size: 202
138 CCAGTAAATT
148 ACTTTTGTAATGGCACTCTTATTGTGTGATGAAACATGGACCAGGTAAAGGCTCTTCACTGCTCC
1 ACTTTTGTAATGGCACTCTTATTGTGTGATGAAACATGGACCAGGTAAAGGCTCTTCACTGCTCC
213 AATTCTTCTGATATACAACCATGAAAATAAATGAGTCTATGCTTGATTTTCTGGTTAAGAATCTT
66 AATTCTTCTGATATACAACCATGAAAATAAATGAGTCTATGCTTGATTTTCTGGTTAAGAATCTT
278 TTGTTATTCTCATGCATGGTGACTTTGTTCGATACATTCTGTGATTATAAAGCAAATTTCTCACT
131 TTGTTATTCTCATGCATGGTGACTTTGTTCGATACATTCTGTGATTATAAAGCAAATTTCTCACT
343 ATTAACA
196 ATTAACA
350 ACTTTTGTAATGGCACTCTTATTGTGTGATGAAACATGGACCAGGTAAAGGCTCTTCACTGCTCC
1 ACTTTTGTAATGGCACTCTTATTGTGTGATGAAACATGGACCAGGTAAAGGCTCTTCACTGCTCC
415 AATTCTTCTGATATACAACCATGAAAATAAATGAGTCTATGCTTGATTTTCTGGTTAAGAATCTT
66 AATTCTTCTGATATACAACCATGAAAATAAATGAGTCTATGCTTGATTTTCTGGTTAAGAATCTT
* *
480 TTGTTATTTTCATGTATGGTGACTTTGTTCGATACATTCTGTGATTATAAAGCAAATTTCTCACT
131 TTGTTATTCTCATGCATGGTGACTTTGTTCGATACATTCTGTGATTATAAAGCAAATTTCTCACT
545 ATTAACA
196 ATTAACA
*
552 GCTTTT
1 ACTTTT
558 TGCTTAAAGC
Statistics
Matches: 205, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
202 205 1.00
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (202 bp):
ACTTTTGTAATGGCACTCTTATTGTGTGATGAAACATGGACCAGGTAAAGGCTCTTCACTGCTCC
AATTCTTCTGATATACAACCATGAAAATAAATGAGTCTATGCTTGATTTTCTGGTTAAGAATCTT
TTGTTATTCTCATGCATGGTGACTTTGTTCGATACATTCTGTGATTATAAAGCAAATTTCTCACT
ATTAACA
Found at i:3388 original size:13 final size:13
Alignment explanation
Indices: 3370--3394 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3360 TTTTCAACTA
3370 AAATTGAAAACAT
1 AAATTGAAAACAT
3383 AAATTGAAAACA
1 AAATTGAAAACA
3395 GGAAAAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.08, G:0.08, T:0.20
Consensus pattern (13 bp):
AAATTGAAAACAT
Found at i:12312 original size:13 final size:13
Alignment explanation
Indices: 12294--12352 Score: 82
Period size: 13 Copynumber: 4.5 Consensus size: 13
12284 TTAATTATTA
*
12294 GGAGGGTTAAGTT
1 GGAGGGTTAAATT
*
12307 GGAGGGATAAATT
1 GGAGGGTTAAATT
*
12320 GGAGGGTTAAGTT
1 GGAGGGTTAAATT
*
12333 GGAGGGATAAATT
1 GGAGGGTTAAATT
12346 GGAGGGT
1 GGAGGGT
12353 CAAAAAGATT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 39 1.00
ACGTcount: A:0.29, C:0.00, G:0.46, T:0.25
Consensus pattern (13 bp):
GGAGGGTTAAATT
Found at i:12323 original size:26 final size:26
Alignment explanation
Indices: 12294--12352 Score: 118
Period size: 26 Copynumber: 2.3 Consensus size: 26
12284 TTAATTATTA
12294 GGAGGGTTAAGTTGGAGGGATAAATT
1 GGAGGGTTAAGTTGGAGGGATAAATT
12320 GGAGGGTTAAGTTGGAGGGATAAATT
1 GGAGGGTTAAGTTGGAGGGATAAATT
12346 GGAGGGT
1 GGAGGGT
12353 CAAAAAGATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.29, C:0.00, G:0.46, T:0.25
Consensus pattern (26 bp):
GGAGGGTTAAGTTGGAGGGATAAATT
Found at i:13185 original size:60 final size:60
Alignment explanation
Indices: 13117--13280 Score: 220
Period size: 60 Copynumber: 2.7 Consensus size: 60
13107 GCTAATTGCT
* ** *
13117 CAAATAAGGGTCTAACGTTTGTTAAAATGCTTAAATAAGGGTCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGC
* * * *
13177 CAAATAAGGGCCTAACATTTGCCAAAATGCACAAATAAGGGCCTTATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGC
* * * *
13237 CAAATTAGGGCCTAATGTTTACCAAAATGCTCAAATGAGGGTCT
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCT
13281 AACATTGAAA
Statistics
Matches: 89, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 89 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGC
Found at i:13397 original size:58 final size:59
Alignment explanation
Indices: 13323--13457 Score: 184
Period size: 58 Copynumber: 2.3 Consensus size: 59
13313 GACACCAGAC
13323 CCTTATTTGAGT-ATTTTCGATAACGTTAGCCCCTTATCTGGCCAAATTAAAAGATCGGG
1 CCTTATTTGA-TCATTTTCGATAACGTTAGCCCCTTATCTGGCCAAATTAAAAGATCGGG
* ** * *
13382 -CTTATTTGATCATTTTCGATAATGTTAGGTCCTTATTTGGCCAAATTAAAAGATTGGG
1 CCTTATTTGATCATTTTCGATAACGTTAGCCCCTTATCTGGCCAAATTAAAAGATCGGG
*
13440 CCCTTATTTGAACATTTT
1 -CCTTATTTGATCATTTT
13458 GGAAAATATT
Statistics
Matches: 67, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
57 1 0.01
58 51 0.76
60 15 0.22
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (59 bp):
CCTTATTTGATCATTTTCGATAACGTTAGCCCCTTATCTGGCCAAATTAAAAGATCGGG
Found at i:13476 original size:60 final size:58
Alignment explanation
Indices: 13324--13480 Score: 170
Period size: 58 Copynumber: 2.7 Consensus size: 58
13314 ACACCAGACC
** * ** * *
13324 CTTATTTGAGTATTTTCGATAACGTTAGCCCCTTATCTGGCCAAATTAAAAGATCGGG
1 CTTATTTGAACATTTTCGAAAATATTAGACCCTTATTTGGCCAAATTAAAAGATCGGG
* * * ** *
13382 CTTATTTGATCATTTTCGATAATGTTAGGTCCTTATTTGGCCAAATTAAAAGATTGGG
1 CTTATTTGAACATTTTCGAAAATATTAGACCCTTATTTGGCCAAATTAAAAGATCGGG
*
13440 CCCTTATTTGAACATTTTGGAAAATATTAGACCCTTATTTG
1 --CTTATTTGAACATTTTCGAAAATATTAGACCCTTATTTG
13481 AGCAATTAGT
Statistics
Matches: 84, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
58 51 0.61
60 33 0.39
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (58 bp):
CTTATTTGAACATTTTCGAAAATATTAGACCCTTATTTGGCCAAATTAAAAGATCGGG
Done.