Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022499.1 Corchorus olitorius cultivar O-4 contig22532, 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: 44184
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:655 original size:25 final size:25
Alignment explanation
Indices: 621--670 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
611 GACATGTGCC
621 CGGTTACTAATCAATACTAATTTGT
1 CGGTTACTAATCAATACTAATTTGT
646 CGGTTACTAATCAATACTAATTTGT
1 CGGTTACTAATCAATACTAATTTGT
671 TCAAATGCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (25 bp):
CGGTTACTAATCAATACTAATTTGT
Found at i:2166 original size:28 final size:28
Alignment explanation
Indices: 2126--2234 Score: 209
Period size: 28 Copynumber: 3.9 Consensus size: 28
2116 TCTGAAATCT
2126 GAACACCGCGTTTAATAGAGCGGTGTGA
1 GAACACCGCGTTTAATAGAGCGGTGTGA
2154 GAACACCGCGTTTAATAGAGCGGTGTGA
1 GAACACCGCGTTTAATAGAGCGGTGTGA
*
2182 GAACACCGCGTTTAATAGAGCGGTGCGA
1 GAACACCGCGTTTAATAGAGCGGTGTGA
2210 GAACACCGCGTTTAATAGAGCGGTG
1 GAACACCGCGTTTAATAGAGCGGTG
2235 CGGTGCGATT
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
28 80 1.00
ACGTcount: A:0.28, C:0.19, G:0.32, T:0.20
Consensus pattern (28 bp):
GAACACCGCGTTTAATAGAGCGGTGTGA
Found at i:21602 original size:73 final size:73
Alignment explanation
Indices: 21475--21613 Score: 251
Period size: 73 Copynumber: 1.9 Consensus size: 73
21465 CGTAAGATGT
*
21475 AACTCAGAAACAAATCCCTGTTTTACTGATTAGACTATGATTTAAGGTGATTAAAATGAGAGTAC
1 AACTCAGAAACAAATCCCTGTTTTACCGATTAGACTATGATTTAAGGTGATTAAAATGAGAGTAC
21540 TTACGACG
66 TTACGACG
* *
21548 AACTTAGAAACAAATCCCTGTTTTACCGATTAGACTATGATTTAAGGTGGTTAAAATGAGAGTAC
1 AACTCAGAAACAAATCCCTGTTTTACCGATTAGACTATGATTTAAGGTGATTAAAATGAGAGTAC
21613 T
66 T
21614 GGAATAACAT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 63 1.00
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (73 bp):
AACTCAGAAACAAATCCCTGTTTTACCGATTAGACTATGATTTAAGGTGATTAAAATGAGAGTAC
TTACGACG
Found at i:28478 original size:23 final size:23
Alignment explanation
Indices: 28451--28494 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
28441 AATCCTAATC
28451 CTGGTAGGAATAGTAAAACCTTT
1 CTGGTAGGAATAGTAAAACCTTT
28474 CTGGTAGGAATAGTAAAACCT
1 CTGGTAGGAATAGTAAAACCT
28495 ACTCCTAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (23 bp):
CTGGTAGGAATAGTAAAACCTTT
Found at i:38344 original size:22 final size:22
Alignment explanation
Indices: 38316--38365 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
38306 AAGCTCAAAT
38316 TCGGCTCGTCATAAACTGGAGC
1 TCGGCTCGTCATAAACTGGAGC
38338 TCGGCTCGTCATAAACTGGAGC
1 TCGGCTCGTCATAAACTGGAGC
38360 TCGGCT
1 TCGGCT
38366 AATGAGGCTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.20, C:0.28, G:0.28, T:0.24
Consensus pattern (22 bp):
TCGGCTCGTCATAAACTGGAGC
Found at i:42354 original size:60 final size:60
Alignment explanation
Indices: 42280--42442 Score: 256
Period size: 60 Copynumber: 2.7 Consensus size: 60
42270 GCTAATTGTT
*
42280 CAAATAAAGGCCTAACGTTTGTC-AAAATGTTCAAATAAGGGTCCGATCTTTTAATTTGGC
1 CAAATAAAGGCCTAACG-TTGTCGAAAATGCTCAAATAAGGGTCCGATCTTTTAATTTGGC
* * *
42340 CAAATAAGGGCCTAATGTTGTCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAAGGCCTAACGTTGTCGAAAATGCTCAAATAAGGGTCCGATCTTTTAATTTGGC
* *
42400 CAAATAAAAGCCTAACGTTATCGAAAATGCTCAAATAAGGGTC
1 CAAATAAAGGCCTAACGTTGTCGAAAATGCTCAAATAAGGGTC
42443 TGGCGTCGAA
Statistics
Matches: 93, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
59 5 0.05
60 88 0.95
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.28
Consensus pattern (60 bp):
CAAATAAAGGCCTAACGTTGTCGAAAATGCTCAAATAAGGGTCCGATCTTTTAATTTGGC
Found at i:42579 original size:60 final size:60
Alignment explanation
Indices: 42481--42645 Score: 235
Period size: 60 Copynumber: 2.8 Consensus size: 60
42471 AAACTGACGG
42481 CAGGCCCTTATTTGAGCATTTTT-G-ATAACGTTAGGCCCTTATTTGGCCAAATTAAAAAAT
1 CAGGCCCTTATTTGAGC-TTTTTGGCA-AACGTTAGGCCCTTATTTGGCCAAATTAAAAAAT
* * * *
42541 CGGGCCCTTATTTGAGCTTTTTGGCAAACATTAAGCCCTTATTTGGCCAAATTAAAAGAT
1 CAGGCCCTTATTTGAGCTTTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAAAT
* * *
42601 CAGACTCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
1 CAGGCCCTTATTTGAGCTTTTTGGCAAACGTTAGGCCCTTATTTG
42646 AGCAATTAGC
Statistics
Matches: 93, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
59 5 0.05
60 87 0.94
61 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.35
Consensus pattern (60 bp):
CAGGCCCTTATTTGAGCTTTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAAAT
Found at i:42645 original size:31 final size:30
Alignment explanation
Indices: 42482--42649 Score: 94
Period size: 31 Copynumber: 5.6 Consensus size: 30
42472 AACTGACGGC
*
42482 AGGCCCTTATTTGAGCATTTTTGATAACGTT
1 AGGCCCTTATTTGAGCATTTTGGA-AACGTT
** * ** *
42513 AGGCCCTTATTTG-GCCAAATT-AAAAAATC
1 AGGCCCTTATTTGAG-CATTTTGGAAACGTT
* * *
42542 GGGCCCTTATTTGAGCTTTTTGGCAAACATT
1 AGGCCCTTATTTGAGCATTTTGG-AAACGTT
* ** * *
42573 AAGCCCTTATTTG-GCCAAATT--AAAAGATC
1 AGGCCCTTATTTGAG-CATTTTGGAAACG-TT
* *
42602 AGACTCTTATTTGAGCATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTTGG-AAACGTT
42633 AGGCCCTTATTTGAGCA
1 AGGCCCTTATTTGAGCA
42650 ATTAGCCTTG
Statistics
Matches: 97, Mismatches: 30, Indels: 20
0.66 0.20 0.14
Matches are distributed among these distances:
28 3 0.03
29 33 0.34
30 5 0.05
31 52 0.54
32 4 0.04
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (30 bp):
AGGCCCTTATTTGAGCATTTTGGAAACGTT
Found at i:42683 original size:23 final size:23
Alignment explanation
Indices: 42657--42700 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
42647 GCAATTAGCC
42657 TTGATTTATTGATCTTCAAACTA
1 TTGATTTATTGATCTTCAAACTA
*
42680 TTGATTTATTGGTCTTCAAAC
1 TTGATTTATTGATCTTCAAAC
42701 GAAAGTGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.14, G:0.11, T:0.48
Consensus pattern (23 bp):
TTGATTTATTGATCTTCAAACTA
Done.