Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021022.1 Corchorus olitorius cultivar O-4 contig21055, 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: 33386
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Found at i:181 original size:39 final size:40
Alignment explanation
Indices: 3--189 Score: 279
Period size: 40 Copynumber: 4.7 Consensus size: 40
1 TC
* *
3 TGCCCTTCCCCACCGGAAAGTGTTGTTTAATTTCCCGTTT
1 TGCCCTTCCCCACCGGAAGGTGTTGTTTAATTTCCCATTT
43 TGCCCTTCCCCACCGGAAGGTGTTGTTTAATTTCCCATTT
1 TGCCCTTCCCCACCGGAAGGTGTTGTTTAATTTCCCATTT
* *
83 TGCCCTTCCCCATCAGAAGGTGTTGTTTAATTTCCCATTT
1 TGCCCTTCCCCACCGGAAGGTGTTGTTTAATTTCCCATTT
* * *
123 TGCCCTTCCCCACCAGAAGGTGTTGTTTAAGTTCCCAATT
1 TGCCCTTCCCCACCGGAAGGTGTTGTTTAATTTCCCATTT
*
163 TG-CCTT-CCCAGTCGGAAGGTGTTGTTT
1 TGCCCTTCCCCA-CCGGAAGGTGTTGTTT
190 TTGTCATGTT
Statistics
Matches: 137, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
38 4 0.03
39 18 0.13
40 115 0.84
ACGTcount: A:0.16, C:0.28, G:0.19, T:0.37
Consensus pattern (40 bp):
TGCCCTTCCCCACCGGAAGGTGTTGTTTAATTTCCCATTT
Found at i:1565 original size:27 final size:26
Alignment explanation
Indices: 1535--1603 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 26
1525 CTGACGAAAG
1535 AAATTTGCTTATCCTCTTTGAAAAAA
1 AAATTTGCTTATCCTCTTTGAAAAAA
1561 CAAATTTGCTTATGATCCTCTTTGAAAAAA
1 -AAATTTGC-T-T-ATCCTCTTTGAAAAAA
*
1591 AGAAATTGCTTAT
1 A-AATTTGCTTAT
1604 GAATCTCTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
27 10 0.27
28 2 0.05
29 3 0.08
30 22 0.59
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (26 bp):
AAATTTGCTTATCCTCTTTGAAAAAA
Found at i:1581 original size:30 final size:31
Alignment explanation
Indices: 1545--1628 Score: 111
Period size: 30 Copynumber: 2.8 Consensus size: 31
1535 AAATTTGCTT
*
1545 ATCCTCTTTGAAAAAACA-AATTTGCTTATG-
1 ATCCTCTTTGAAAAAA-AGAAATTGCTTATGA
1575 ATCCTCTTTGAAAAAAAGAAATTGCTTATGA
1 ATCCTCTTTGAAAAAAAGAAATTGCTTATGA
* *
1606 AT-CTCTTTCAAAAAAAAAAATTG
1 ATCCTCTTTGAAAAAAAGAAATTG
1629 ATACCGGCCA
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
29 1 0.02
30 46 0.94
31 2 0.04
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (31 bp):
ATCCTCTTTGAAAAAAAGAAATTGCTTATGA
Found at i:10669 original size:51 final size:51
Alignment explanation
Indices: 10568--10677 Score: 120
Period size: 51 Copynumber: 2.2 Consensus size: 51
10558 GTTCATCAAA
* **
10568 TTTTC-CTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCTTTTAGTGT
1 TTTTCTCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCGTACAGTGT
*
10618 TTTTCTCTTGTTTCA-ATCTTGTCTCTGGAC-ATACAAACACT-GTACACGTGT
1 TTTTCTCTTGTTT-AGATCTTGTCTCAGGACAAT-CAAACACTCGTACA-GTGT
*
10669 TTCTCTCTT
1 TTTTCTCTT
10678 AGAAATAACA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
50 9 0.18
51 41 0.80
52 1 0.02
ACGTcount: A:0.20, C:0.23, G:0.13, T:0.45
Consensus pattern (51 bp):
TTTTCTCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCGTACAGTGT
Found at i:11054 original size:2 final size:2
Alignment explanation
Indices: 11047--11076 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11037 TTTGGCGTCC
11047 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
11077 TTCTACCTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:23086 original size:15 final size:15
Alignment explanation
Indices: 23056--23097 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
23046 TTACTCTGCT
23056 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
23072 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
23087 TTGCTTTCTGT
1 TTGTTTTCTGT
23098 CAACCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:23512 original size:17 final size:16
Alignment explanation
Indices: 23478--23508 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
23468 AAATAATTTT
*
23478 TTTTTTATTTTTTGTG
1 TTTTTAATTTTTTGTG
23494 TTTTTAATTTTTTGT
1 TTTTTAATTTTTTGT
23509 TGTTGCGTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.81
Consensus pattern (16 bp):
TTTTTAATTTTTTGTG
Found at i:23556 original size:28 final size:28
Alignment explanation
Indices: 23521--23594 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 28
23511 TTGCGTTTTT
*
23521 GAAAAAAAAAGGGTTTTGTGTTTTGCGTC
1 GAAAAAAAAAGAGTTTTGT-TTTTGCGTC
**
23550 -AAGAAAAAAA-TCTGTTTGTTTTTGCGTC
1 GAA-AAAAAAAGAGT-TTTGTTTTTGCGTC
23578 GAAAAAAAAAGAGTTTT
1 GAAAAAAAAAGAGTTTT
23595 TTGAGTCATA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
28 22 0.59
29 15 0.41
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.34
Consensus pattern (28 bp):
GAAAAAAAAAGAGTTTTGTTTTTGCGTC
Found at i:26880 original size:21 final size:21
Alignment explanation
Indices: 26823--26889 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
26813 CCAAGTCATT
* *
26823 ACCGGCCATTCACCATGCCACC
1 ACCGGCCATGC-CCGTGCCACC
* * * *
26845 ACCAGTCAAGTCCGTGCCACC
1 ACCGGCCATGCCCGTGCCACC
*
26866 ACCGGCCATGCCCGTGCCATC
1 ACCGGCCATGCCCGTGCCACC
26887 ACC
1 ACC
26890 ATTCCAAGCT
Statistics
Matches: 34, Mismatches: 11, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
21 28 0.82
22 6 0.18
ACGTcount: A:0.21, C:0.48, G:0.18, T:0.13
Consensus pattern (21 bp):
ACCGGCCATGCCCGTGCCACC
Found at i:27262 original size:15 final size:14
Alignment explanation
Indices: 27242--27271 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
27232 ATCTTTTTAA
27242 TTTTCCTTGCATTAT
1 TTTTCCTTG-ATTAT
27257 TTTTCCTTGATTAT
1 TTTTCCTTGATTAT
27271 T
1 T
27272 GCTTTGATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63
Consensus pattern (14 bp):
TTTTCCTTGATTAT
Found at i:30166 original size:15 final size:15
Alignment explanation
Indices: 30136--30177 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
30126 TTACTCTGCT
30136 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
30152 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
30167 TTGCTTTCTGT
1 TTGTTTTCTGT
30178 CAACCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Done.