Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018783.1 Corchorus olitorius cultivar O-4 contig18816, 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: 14515
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Found at i:6976 original size:31 final size:30
Alignment explanation
Indices: 6938--7038 Score: 98
Period size: 31 Copynumber: 3.3 Consensus size: 30
6928 ATTATGGGCT
6938 AAATAAGGGCCTAATGTTTGCCAAAATGCTC
1 AAATAAGGGCCTAATGTTTG-CAAAATGCTC
** * * **
6969 AAATAAGGGCCCGATCTTT-TAATTTGGC-C
1 AAATAAGGGCCTAATGTTTGCAAAAT-GCTC
*
6998 AAATAAGGGCCTAACGTTTGACAAAATGCTC
1 AAATAAGGGCCTAATGTTTG-CAAAATGCTC
7029 AAATAAGGGC
1 AAATAAGGGC
7039 TTGGTTCGAA
Statistics
Matches: 53, Mismatches: 13, Indels: 8
0.72 0.18 0.11
Matches are distributed among these distances:
29 19 0.36
30 4 0.08
31 30 0.57
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.25
Consensus pattern (30 bp):
AAATAAGGGCCTAATGTTTGCAAAATGCTC
Found at i:7117 original size:31 final size:31
Alignment explanation
Indices: 7078--7276 Score: 157
Period size: 31 Copynumber: 6.5 Consensus size: 31
7068 AACCGATGGC
7078 AGGCCCTTATTTGAGCATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTTGGCAAACGTT
* *
7109 AGGTCCTTATTTAAGCATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTTGGCAAACGTT
** * *
7140 AGGCCCTTATTTG-GTCAAATT---AAAAGATC
1 AGGCCCTTATTTGAG-CATTTTGGCAAACG-TT
*
7169 GGGCCCTTATTTGAGCATTTT--CAATAACGTT
1 AGGCCCTTATTTGAGCATTTTGGC-A-AACGTT
** * *
7200 AGGCCCTTATTTG-GCCAAATT---AAAAGATC
1 AGGCCCTTATTTGAG-CATTTTGGCAAACG-TT
* *
7229 AGACCCTTATTTGAGCATTTTGACAAACGTT
1 AGGCCCTTATTTGAGCATTTTGGCAAACGTT
7260 AGGCCCTTATTTGAGCA
1 AGGCCCTTATTTGAGCA
7277 ATTAGCCACA
Statistics
Matches: 132, Mismatches: 24, Indels: 24
0.73 0.13 0.13
Matches are distributed among these distances:
28 7 0.05
29 35 0.27
30 4 0.03
31 79 0.60
32 7 0.05
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (31 bp):
AGGCCCTTATTTGAGCATTTTGGCAAACGTT
Found at i:7177 original size:29 final size:28
Alignment explanation
Indices: 7140--7241 Score: 98
Period size: 29 Copynumber: 3.5 Consensus size: 28
7130 GGCAAACGTT
7140 AGGCCCTTATTTGGTCAAATTAAAAGATC
1 AGGCCCTTATTTGG-CAAATTAAAAGATC
* ** *
7169 GGGCCCTTATTTGAGCATTTTCAATAACG-TT
1 AGGCCCTTATTTG-GCAAATT-AA-AA-GATC
7200 AGGCCCTTATTTGGCCAAATTAAAAGATC
1 AGGCCCTTATTTGG-CAAATTAAAAGATC
*
7229 AGACCCTTATTTG
1 AGGCCCTTATTTG
7242 AGCATTTTGA
Statistics
Matches: 58, Mismatches: 9, Indels: 12
0.73 0.11 0.15
Matches are distributed among these distances:
28 1 0.02
29 31 0.53
30 6 0.10
31 19 0.33
32 1 0.02
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (28 bp):
AGGCCCTTATTTGGCAAATTAAAAGATC
Found at i:7186 original size:60 final size:59
Alignment explanation
Indices: 7113--7272 Score: 241
Period size: 60 Copynumber: 2.7 Consensus size: 59
7103 AACGTTAGGT
* * * *
7113 CCTTATTTAAGCATTTTGGCAAACGTTAGGCCCTTATTTGGTCAAATTAAAAGATCGGGC
1 CCTTATTTGAGCATTTT-GCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGAC
7173 CCTTATTTGAGCATTTT-CAATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGAC
1 CCTTATTTGAGCATTTTGC-A-AACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGAC
7233 CCTTATTTGAGCATTTTGACAAACGTTAGGCCCTTATTTG
1 CCTTATTTGAGCATTTTG-CAAACGTTAGGCCCTTATTTG
7273 AGCAATTAGC
Statistics
Matches: 92, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
58 1 0.01
59 1 0.01
60 88 0.96
61 1 0.01
62 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.35
Consensus pattern (59 bp):
CCTTATTTGAGCATTTTGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGAC
Found at i:7416 original size:19 final size:18
Alignment explanation
Indices: 7383--7418 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
7373 TTGAAATAAT
7383 TCTTCAAAAATCTTCAAG
1 TCTTCAAAAATCTTCAAG
*
7401 TCTTCAAATTATCTTCAA
1 TCTTCAAA-AATCTTCAA
7419 ATGATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (18 bp):
TCTTCAAAAATCTTCAAG
Found at i:7417 original size:11 final size:11
Alignment explanation
Indices: 7401--7430 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
7391 AATCTTCAAG
*
7401 TCTTCAAATTA
1 TCTTCAAATGA
7412 TCTTCAAATGA
1 TCTTCAAATGA
7423 TCTTCAAA
1 TCTTCAAA
7431 CACGAACTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.37, C:0.20, G:0.03, T:0.40
Consensus pattern (11 bp):
TCTTCAAATGA
Found at i:10823 original size:18 final size:18
Alignment explanation
Indices: 10800--10835 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
10790 GAAAAGGAAT
10800 GGCGGC-ATCTATCTTGTC
1 GGCGGCAATCT-TCTTGTC
10818 GGCGGCAATCTTCTTGTC
1 GGCGGCAATCTTCTTGTC
10836 TATCCCCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.11, C:0.28, G:0.28, T:0.33
Consensus pattern (18 bp):
GGCGGCAATCTTCTTGTC
Found at i:11501 original size:33 final size:32
Alignment explanation
Indices: 11423--11503 Score: 85
Period size: 30 Copynumber: 2.6 Consensus size: 32
11413 AGATCACAAG
**
11423 GATACAGAAAATCACCACCAAGTGTTTGAATC
1 GATACAGAAAATCACCACCAAGTGTTCAAATC
* ** *
11455 GGT-C-GAAGCTCACCACCAAGTGATTCAAATT
1 GATACAGAAAATCACCACCAAGTG-TTCAAATC
11486 GATACAGAAAATCACCAC
1 GATACAGAAAATCACCAC
11504 AACTTGAAAT
Statistics
Matches: 37, Mismatches: 9, Indels: 5
0.73 0.18 0.10
Matches are distributed among these distances:
30 16 0.43
31 8 0.22
32 3 0.08
33 10 0.27
ACGTcount: A:0.40, C:0.25, G:0.16, T:0.20
Consensus pattern (32 bp):
GATACAGAAAATCACCACCAAGTGTTCAAATC
Done.