Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015962.1 Corchorus olitorius cultivar O-4 contig15995, 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: 12549
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.31
Found at i:819 original size:28 final size:28
Alignment explanation
Indices: 755--829 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 28
745 TCCGGCATTT
* *
755 AAGGGCAAAATTGTAA-TTTAGTTAACC
1 AAGGGCAAAATAGTAATTTTAGCTAACC
* * * *
782 AGGGGTAAAATGGTAATTTTAGCTGACC
1 AAGGGCAAAATAGTAATTTTAGCTAACC
810 AAGGGCAAAATAGTAATTTT
1 AAGGGCAAAATAGTAATTTT
830 GACATCTTAA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
27 13 0.33
28 26 0.67
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.29
Consensus pattern (28 bp):
AAGGGCAAAATAGTAATTTTAGCTAACC
Found at i:1752 original size:23 final size:23
Alignment explanation
Indices: 1723--1777 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
1713 GCTAGCCCAG
* *
1723 GCGCTGGGCC-ATGCGCTGGCCC
1 GCGCTGGGCCTAGGCACTGGCCC
*
1745 GCGCCT-GGCCTAGGCACTGGGCC
1 GCG-CTGGGCCTAGGCACTGGCCC
1768 GCGCTGGGCC
1 GCGCTGGGCC
1778 GCGTGCCTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
22 9 0.33
23 18 0.67
ACGTcount: A:0.05, C:0.40, G:0.42, T:0.13
Consensus pattern (23 bp):
GCGCTGGGCCTAGGCACTGGCCC
Found at i:1806 original size:25 final size:25
Alignment explanation
Indices: 1772--1829 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
1762 TGGGCCGCGC
1772 TGGGCCGCGTGCCTAGCCTTGTGTT
1 TGGGCCGCGTGCCTAGCCTTGTGTT
1797 TGGGCCGCGTGCCTAGCCTTGTGTT
1 TGGGCCGCGTGCCTAGCCTTGTGTT
1822 TGGGCCGC
1 TGGGCCGC
1830 ACCAGGCTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.03, C:0.29, G:0.38, T:0.29
Consensus pattern (25 bp):
TGGGCCGCGTGCCTAGCCTTGTGTT
Found at i:2977 original size:14 final size:15
Alignment explanation
Indices: 2958--2988 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
2948 TCCTTTAACC
2958 ATATCATA-ATCATA
1 ATATCATATATCATA
2972 ATATCATATATCATA
1 ATATCATATATCATA
2987 AT
1 AT
2989 CATAATACTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (15 bp):
ATATCATATATCATA
Found at i:4309 original size:2 final size:2
Alignment explanation
Indices: 4304--4335 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4294 CTCACACAAT
4304 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
4336 AAACTAAGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:8627 original size:16 final size:18
Alignment explanation
Indices: 8601--8633 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
8591 GATATTGCGT
8601 TTTATTTTTTCT-TTTTC
1 TTTATTTTTTCTATTTTC
8618 TTTA-TTTTTCTATTTT
1 TTTATTTTTTCTATTTT
8634 AATTTGCACT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTATTTTTTCTATTTTC
Found at i:12152 original size:21 final size:22
Alignment explanation
Indices: 12128--12171 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
12118 CATCTTGAAG
12128 ATTTTAAAG-CCATCGGAGATC
1 ATTTTAAAGCCCATCGGAGATC
* *
12149 A-TTTGAAGCCCATTGGAGATC
1 ATTTTAAAGCCCATCGGAGATC
12170 AT
1 AT
12172 CAACAAAGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (22 bp):
ATTTTAAAGCCCATCGGAGATC
Done.