Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016810.1 Corchorus olitorius cultivar O-4 contig16843, 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: 9953
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:794 original size:27 final size:29
Alignment explanation
Indices: 763--840 Score: 97
Period size: 29 Copynumber: 2.8 Consensus size: 29
753 ATGTGAACTT
763 AAAATGACCAAAATGCCCCT-GAAT-GTG
1 AAAATGACCAAAATGCCCCTAGAATCGTG
* * * * *
790 CAAATGACTAAAATGCCCATAGATTCTTG
1 AAAATGACCAAAATGCCCCTAGAATCGTG
819 AAAATGACCAAAATGCCCCTAG
1 AAAATGACCAAAATGCCCCTAG
841 GTGATCCTAA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
27 17 0.41
28 3 0.07
29 21 0.51
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.21
Consensus pattern (29 bp):
AAAATGACCAAAATGCCCCTAGAATCGTG
Found at i:4092 original size:28 final size:27
Alignment explanation
Indices: 4061--4151 Score: 101
Period size: 27 Copynumber: 3.3 Consensus size: 27
4051 AATGACCGAG
* *
4061 ATGCCCTTGAATGTGCAAAATAACCAAA
1 ATGCCCCTGAACGTGC-AAATAACCAAA
* * *
4089 ATGCCCCTGGACGTGCAAATGACAAAA
1 ATGCCCCTGAACGTGCAAATAACCAAA
* *
4116 ATGCCCCTGAACATGCAAATGACCCAAA
1 ATGCCCCTGAACGTGCAAAT-AACCAAA
4144 ATGCCCCT
1 ATGCCCCT
4152 AGATGACCTT
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
27 27 0.52
28 25 0.48
ACGTcount: A:0.37, C:0.29, G:0.16, T:0.18
Consensus pattern (27 bp):
ATGCCCCTGAACGTGCAAATAACCAAA
Found at i:5948 original size:6 final size:6
Alignment explanation
Indices: 5937--5969 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
5927 CAATTCAAAT
5937 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGA
5970 GAAATAATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:7465 original size:19 final size:18
Alignment explanation
Indices: 7432--7467 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
7422 TTGAAATAAT
7432 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
7450 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
7468 TGAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:7475 original size:11 final size:10
Alignment explanation
Indices: 7432--7478 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
7422 TTGAAATAAT
7432 TCTTCAATGA
1 TCTTCAATGA
7442 TCTTCAA--A
1 TCTTCAATGA
*
7450 TCTTCAAATTA
1 TCTTC-AATGA
7461 TCTTCAATGA
1 TCTTCAATGA
7471 GTCTTCAA
1 -TCTTCAA
7479 GCACGAGCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
8 6 0.19
9 2 0.06
10 11 0.34
11 13 0.41
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.40
Consensus pattern (10 bp):
TCTTCAATGA
Found at i:9037 original size:49 final size:49
Alignment explanation
Indices: 8938--9069 Score: 218
Period size: 49 Copynumber: 2.8 Consensus size: 49
8928 AGCAACAATT
* *
8938 AATATTAGCTTTATTTTGATGAATTATCT--A-A-AGATGGAGGAGTAG
1 AATATCAGCTTTATTTTGATGAATTACCTAGAGATAGATGGAGGAGTAG
8983 AATATCAGCTTTATTTTGATGAATTACCTAGAGATAGATGGAGGAGTAG
1 AATATCAGCTTTATTTTGATGAATTACCTAGAGATAGATGGAGGAGTAG
9032 AATATCAGCTTTATTTTGATGAATTACCTAGAGATAGA
1 AATATCAGCTTTATTTTGATGAATTACCTAGAGATAGA
9070 GTAGAATTTA
Statistics
Matches: 81, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
45 27 0.33
47 1 0.01
48 1 0.01
49 52 0.64
ACGTcount: A:0.36, C:0.08, G:0.21, T:0.36
Consensus pattern (49 bp):
AATATCAGCTTTATTTTGATGAATTACCTAGAGATAGATGGAGGAGTAG
Found at i:9357 original size:26 final size:27
Alignment explanation
Indices: 9281--9350 Score: 140
Period size: 27 Copynumber: 2.6 Consensus size: 27
9271 CTCTTATTTA
9281 GCATTTTGGTCATTTTTACATTCAGGG
1 GCATTTTGGTCATTTTTACATTCAGGG
9308 GCATTTTGGTCATTTTTACATTCAGGG
1 GCATTTTGGTCATTTTTACATTCAGGG
9335 GCATTTTGGTCATTTT
1 GCATTTTGGTCATTTT
9351 AAGTTCACAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.47
Consensus pattern (27 bp):
GCATTTTGGTCATTTTTACATTCAGGG
Done.