Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014373.1 Corchorus olitorius cultivar O-4 contig14406, 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: 30772
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:5585 original size:45 final size:46
Alignment explanation
Indices: 5534--5622 Score: 135
Period size: 46 Copynumber: 2.0 Consensus size: 46
5524 ACAAATATTA
* * *
5534 ACCATTTGACT-TAAGAATATAGATCAATGTAGAACAATTCAACAT
1 ACCATTTGACTAAAAAAATATAGATCAACGTAGAACAATTCAACAT
*
5579 ACCATTTGACTAAAAAAATATAGTTCAACGTAGAACAATTCAAC
1 ACCATTTGACTAAAAAAATATAGATCAACGTAGAACAATTCAAC
5623 TATATATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 11 0.28
46 28 0.72
ACGTcount: A:0.46, C:0.17, G:0.10, T:0.27
Consensus pattern (46 bp):
ACCATTTGACTAAAAAAATATAGATCAACGTAGAACAATTCAACAT
Found at i:6495 original size:31 final size:31
Alignment explanation
Indices: 6457--6518 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
6447 CGGATGGGAT
6457 AAAAAAAATCTTGATTAAAATACTCCATATA
1 AAAAAAAATCTTGATTAAAATACTCCATATA
6488 AAAAAAAATCTTGATTAAAATACTCCATATA
1 AAAAAAAATCTTGATTAAAATACTCCATATA
6519 TATATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.55, C:0.13, G:0.03, T:0.29
Consensus pattern (31 bp):
AAAAAAAATCTTGATTAAAATACTCCATATA
Found at i:13001 original size:31 final size:30
Alignment explanation
Indices: 12958--13064 Score: 103
Period size: 31 Copynumber: 3.5 Consensus size: 30
12948 ATTGGCTAAT
12958 TGCTCAAATAAGGGCCTAACGTTTGTCAAAA
1 TGCTCAAATAAGGGCCTAAC-TTTGTCAAAA
* * * **
12989 TGCTAAAATAAGGGCCCGATCTTT-T-AATT
1 TGCTCAAATAAGGG-CCTAACTTTGTCAAAA
*
13018 TGGC-CAAATAAGGGCCTAACTTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAAC-TTTGTCAAAA
13049 TGCTCAAATAAGGGCC
1 TGCTCAAATAAGGGCC
13065 CGATCTTTTA
Statistics
Matches: 59, Mismatches: 11, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
28 4 0.07
29 15 0.25
30 5 0.08
31 31 0.53
32 4 0.07
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.26
Consensus pattern (30 bp):
TGCTCAAATAAGGGCCTAACTTTGTCAAAA
Found at i:13033 original size:29 final size:29
Alignment explanation
Indices: 12994--13093 Score: 114
Period size: 29 Copynumber: 3.4 Consensus size: 29
12984 CAAAATGCTA
12994 AAATAAGGGCCCGATCTTTTAATTTGGCC
1 AAATAAGGGCCCGATCTTTTAATTTGGCC
* * **
13023 AAATAAGGG-CCTAACTTTTGCCAAAAT-GCTC
1 AAATAAGGGCCCGATCTTTT---AATTTGGC-C
13054 AAATAAGGGCCCGATCTTTTAATTTGGCC
1 AAATAAGGGCCCGATCTTTTAATTTGGCC
13083 AAATAAGGGCC
1 AAATAAGGGCC
13094 TAGCATCAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
28 8 0.14
29 24 0.42
30 4 0.07
31 13 0.23
32 8 0.14
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (29 bp):
AAATAAGGGCCCGATCTTTTAATTTGGCC
Found at i:13058 original size:60 final size:60
Alignment explanation
Indices: 12962--13095 Score: 241
Period size: 60 Copynumber: 2.2 Consensus size: 60
12952 GCTAATTGCT
*
12962 CAAATAAGGGCCTAACGTTTGTCAAAATGCTAAAATAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTAAAATAAGGGCCCGATCTTTTAATTTGGC
* *
13022 CAAATAAGGGCCTAACTTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTAAAATAAGGGCCCGATCTTTTAATTTGGC
13082 CAAATAAGGGCCTA
1 CAAATAAGGGCCTA
13096 GCATCAAAAA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 71 1.00
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTAAAATAAGGGCCCGATCTTTTAATTTGGC
Found at i:13170 original size:31 final size:29
Alignment explanation
Indices: 13135--13300 Score: 138
Period size: 31 Copynumber: 5.5 Consensus size: 29
13125 CTGACGCTAT
*
13135 GCCCTTATTTGAGCATTTTGGCAAACATTAG
1 GCCCTTATTTGAGCATTTT--AAAACATTAG
** * *
13166 GCCCTTATTTG-GCCAAATTAAAAGATTGG
1 GCCCTTATTTGAG-CATTTTAAAACATTAG
* * *
13195 GCCTTTATTTGAGCATTTTTGATAACGTTAG
1 GCCCTTATTTGAGCA-TTTT-AAAACATTAG
** * *
13226 GCCCTTATTTG-GCCAAATTAAAAGATCAG
1 GCCCTTATTTGAG-CATTTTAAAACATTAG
13255 GCCCTTATTTGAGCATTTTGACAAACATTAG
1 GCCCTTATTTGAGCATTTT-A-AAACATTAG
13286 GCCCTTATTTGAGCA
1 GCCCTTATTTGAGCA
13301 ATTAGCCATT
Statistics
Matches: 104, Mismatches: 23, Indels: 16
0.73 0.16 0.11
Matches are distributed among these distances:
29 40 0.38
30 9 0.09
31 55 0.53
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (29 bp):
GCCCTTATTTGAGCATTTTAAAACATTAG
Found at i:13212 original size:60 final size:60
Alignment explanation
Indices: 13135--13296 Score: 254
Period size: 60 Copynumber: 2.7 Consensus size: 60
13125 CTGACGCTAT
**
13135 GCCCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGGCCAAATTAAAAGATTGG
1 GCCCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGGCCAAATTAAAAGATCAG
* * *
13195 GCCTTTATTTGAGCATTTTTG-ATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAG
1 GCCCTTATTTGAGCATTTTGGCA-AACATTAGGCCCTTATTTGGCCAAATTAAAAGATCAG
*
13255 GCCCTTATTTGAGCATTTTGACAAACATTAGGCCCTTATTTG
1 GCCCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTG
13297 AGCAATTAGC
Statistics
Matches: 91, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
59 1 0.01
60 89 0.98
61 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (60 bp):
GCCCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGGCCAAATTAAAAGATCAG
Found at i:13259 original size:29 final size:29
Alignment explanation
Indices: 13161--13296 Score: 107
Period size: 29 Copynumber: 4.6 Consensus size: 29
13151 TTTGGCAAAC
13161 ATTAGGCCCTTATTTGGCCAAATTAAAAG
1 ATTAGGCCCTTATTTGGCCAAATTAAAAG
* * ** *
13190 ATTGGGCCTTTATTTGAG-CATTTTTGATAACG
1 ATTAGGCCCTTATTTG-GCCA-AATT-A-AAAG
13222 -TTAGGCCCTTATTTGGCCAAATTAAAAG
1 ATTAGGCCCTTATTTGGCCAAATTAAAAG
* ** *
13250 ATCAGGCCCTTATTTGAG-CATTTTGACAAAC
1 ATTAGGCCCTTATTTG-GCCAAATT-A-AAAG
13281 ATTAGGCCCTTATTTG
1 ATTAGGCCCTTATTTG
13297 AGCAATTAGC
Statistics
Matches: 83, Mismatches: 15, Indels: 16
0.73 0.13 0.14
Matches are distributed among these distances:
28 3 0.04
29 35 0.42
30 8 0.10
31 34 0.41
32 3 0.04
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (29 bp):
ATTAGGCCCTTATTTGGCCAAATTAAAAG
Found at i:18777 original size:6 final size:6
Alignment explanation
Indices: 18766--18812 Score: 94
Period size: 6 Copynumber: 7.8 Consensus size: 6
18756 TTTTTTATGC
18766 TTCAGT TTCAGT TTCAGT TTCAGT TTCAGT TTCAGT TTCAGT TTCAG
1 TTCAGT TTCAGT TTCAGT TTCAGT TTCAGT TTCAGT TTCAGT TTCAG
18813 GCGCACATCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.49
Consensus pattern (6 bp):
TTCAGT
Done.