Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022343.1 Corchorus olitorius cultivar O-4 contig22376, 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: 11126
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Found at i:8871 original size:35 final size:35
Alignment explanation
Indices: 8830--9132 Score: 464
Period size: 35 Copynumber: 8.7 Consensus size: 35
8820 CGAGTTCATA
* * * *
8830 TTGAAGATGCTATATCAAGTCATCCGAGATCATTT
1 TTGAAGATGCTACACCGAGTCATCCGAGGTCATTT
* **
8865 TTGAAGATGCTACACCGAGTCATCTGAATTCATTT
1 TTGAAGATGCTACACCGAGTCATCCGAGGTCATTT
8900 TTGAAGATGCTACACCGAGTCATCCGAGGTCATTT
1 TTGAAGATGCTACACCGAGTCATCCGAGGTCATTT
* *
8935 TTTAAGATGCTGCACCGAGTCATCCGAGGTCATTT
1 TTGAAGATGCTACACCGAGTCATCCGAGGTCATTT
*
8970 TTGAAGATGCTACACCGAGTCATCCGAGATCATTT
1 TTGAAGATGCTACACCGAGTCATCCGAGGTCATTT
* * *
9005 TTGAAGATGCTACACCGAGTCATCTGA-TTCATCT
1 TTGAAGATGCTACACCGAGTCATCCGAGGTCATTT
*
9039 TTGAAGATGCTACACCGAGTCATCTGAGGTCATTT
1 TTGAAGATGCTACACCGAGTCATCCGAGGTCATTT
*
9074 TTTAAGATGCTACACCGAGTCATCCGAGGTCATTT
1 TTGAAGATGCTACACCGAGTCATCCGAGGTCATTT
9109 TTGAAGATGCTACACCGAGTCATC
1 TTGAAGATGCTACACCGAGTCATC
9133 TTTGGAAAAT
Statistics
Matches: 245, Mismatches: 22, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
34 32 0.13
35 213 0.87
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (35 bp):
TTGAAGATGCTACACCGAGTCATCCGAGGTCATTT
Found at i:9075 original size:139 final size:140
Alignment explanation
Indices: 8830--9132 Score: 545
Period size: 139 Copynumber: 2.2 Consensus size: 140
8820 CGAGTTCATA
* * *
8830 TTGAAGATGCTATATCAAGTCATCCGAGATCATTTTTGAAGATGCTACACCGAGTCATCTGAATT
1 TTGAAGATGCTACACCGAGTCATCCGAGATCATTTTTGAAGATGCTACACCGAGTCATCTGAATT
* *
8895 CATTTTTGAAGATGCTACACCGAGTCATCCGAGGTCATTTTTTAAGATGCTGCACCGAGTCATCC
66 CATCTTTGAAGATGCTACACCGAGTCATCCGAGGTCATTTTTTAAGATGCTACACCGAGTCATCC
8960 GAGGTCATTT
131 GAGGTCATTT
8970 TTGAAGATGCTACACCGAGTCATCCGAGATCATTTTTGAAGATGCTACACCGAGTCATCTG-ATT
1 TTGAAGATGCTACACCGAGTCATCCGAGATCATTTTTGAAGATGCTACACCGAGTCATCTGAATT
*
9034 CATCTTTGAAGATGCTACACCGAGTCATCTGAGGTCATTTTTTAAGATGCTACACCGAGTCATCC
66 CATCTTTGAAGATGCTACACCGAGTCATCCGAGGTCATTTTTTAAGATGCTACACCGAGTCATCC
9099 GAGGTCATTT
131 GAGGTCATTT
9109 TTGAAGATGCTACACCGAGTCATC
1 TTGAAGATGCTACACCGAGTCATC
9133 TTTGGAAAAT
Statistics
Matches: 157, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
139 99 0.63
140 58 0.37
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (140 bp):
TTGAAGATGCTACACCGAGTCATCCGAGATCATTTTTGAAGATGCTACACCGAGTCATCTGAATT
CATCTTTGAAGATGCTACACCGAGTCATCCGAGGTCATTTTTTAAGATGCTACACCGAGTCATCC
GAGGTCATTT
Found at i:9771 original size:50 final size:49
Alignment explanation
Indices: 9717--9856 Score: 173
Period size: 50 Copynumber: 2.9 Consensus size: 49
9707 CTTAAATGCC
* *
9717 CTTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGGATGCAATCCTA
1 CTTTGAAAAGCGAATTTTGATCTTGGACTCA-AAATGGAAAGCAATCCTA
* **
9767 CTTTGAAAAGCGAATTTTGATCTTCGACT-----TGGAAAGCAATTTTA
1 CTTTGAAAAGCGAATTTTGATCTTGGACTCAAAATGGAAAGCAATCCTA
*
9811 CTTTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAAT
1 CTTTGAAAAGCGAATTTTGATCTTGGACTCA-AAATGGAAAGCAAT
9857 TTTATTGTAA
Statistics
Matches: 77, Mismatches: 7, Indels: 12
0.80 0.07 0.12
Matches are distributed among these distances:
44 38 0.49
50 39 0.51
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (49 bp):
CTTTGAAAAGCGAATTTTGATCTTGGACTCAAAATGGAAAGCAATCCTA
Found at i:10472 original size:5 final size:5
Alignment explanation
Indices: 10456--10521 Score: 64
Period size: 5 Copynumber: 12.6 Consensus size: 5
10446 TCAATTCTCT
*
10456 TTTGA TTTTGA TTTGA TTTGA TTTTTGA TTTTGA TTTGA TTT-T TTTGA
1 TTTGA -TTTGA TTTGA TTTGA --TTTGA -TTTGA TTTGA TTTGA TTTGA
10504 -TTGA CTTTGA TTTGA TTT
1 TTTGA -TTTGA TTTGA TTT
10522 TTTTATTTTG
Statistics
Matches: 53, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
4 7 0.13
5 26 0.49
6 15 0.28
7 5 0.09
ACGTcount: A:0.17, C:0.02, G:0.17, T:0.65
Consensus pattern (5 bp):
TTTGA
Found at i:10481 original size:23 final size:23
Alignment explanation
Indices: 10455--10535 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 23
10445 ATCAATTCTC
10455 TTTTGATTTTGATTTGATTTGAT
1 TTTTGATTTTGATTTGATTTGAT
10478 TTTTGATTTTGATTTGA-TT--T
1 TTTTGATTTTGATTTGATTTGAT
10498 TTTTGA--TTGACTTTGATTTGATT
1 TTTTGATTTTGA-TTTGATTTGA-T
*
10521 TTTTTATTTTGATTT
1 TTTTGATTTTGATTT
10536 TTTTTTTGAA
Statistics
Matches: 50, Mismatches: 1, Indels: 13
0.78 0.02 0.20
Matches are distributed among these distances:
18 4 0.08
19 5 0.10
20 9 0.18
22 2 0.04
23 23 0.46
24 3 0.06
25 4 0.08
ACGTcount: A:0.16, C:0.01, G:0.15, T:0.68
Consensus pattern (23 bp):
TTTTGATTTTGATTTGATTTGAT
Found at i:10507 original size:18 final size:19
Alignment explanation
Indices: 10461--10516 Score: 73
Period size: 18 Copynumber: 3.0 Consensus size: 19
10451 TCTCTTTTGA
10461 TTTTGATTTGATTTGA--T
1 TTTTGATTTGATTTGATTT
10478 TTTTGATTTTGATTTGATTT
1 TTTTGA-TTTGATTTGATTT
10498 TTTTGA-TTGACTTTGATTT
1 TTTTGATTTGA-TTTGATTT
10517 GATTTTTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
17 6 0.17
18 14 0.40
19 8 0.23
20 7 0.20
ACGTcount: A:0.16, C:0.02, G:0.16, T:0.66
Consensus pattern (19 bp):
TTTTGATTTGATTTGATTT
Found at i:10512 original size:24 final size:22
Alignment explanation
Indices: 10455--10525 Score: 97
Period size: 24 Copynumber: 3.1 Consensus size: 22
10445 ATCAATTCTC
*
10455 TTTTGATTTTGATTTGATTTGAT
1 TTTTGATTTTGATTTGATTT-TT
10478 TTTTGATTTTGATTTGATTTTT
1 TTTTGATTTTGATTTGATTTTT
*
10500 TTGATTGACTTTGATTTGATTTTT
1 TT--TTGATTTTGATTTGATTTTT
10524 TT
1 TT
10526 ATTTTGATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
22 3 0.07
23 20 0.45
24 21 0.48
ACGTcount: A:0.15, C:0.01, G:0.15, T:0.68
Consensus pattern (22 bp):
TTTTGATTTTGATTTGATTTTT
Found at i:10516 original size:42 final size:40
Alignment explanation
Indices: 10463--10544 Score: 121
Period size: 43 Copynumber: 2.0 Consensus size: 40
10453 TCTTTTGATT
10463 TTGATTTGATTTGA-TTTTTGATTTTGATTTGATTTTTTTGA
1 TTGATTTGATTTGATTTTTTGATTTTGATTT--TTTTTTTGA
*
10504 TTGACTTTGATTTGATTTTTTTATTTTGATTTTTTTTTTGA
1 TTGA-TTTGATTTGATTTTTTGATTTTGATTTTTTTTTTGA
10545 ATTTCTTGAT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
41 13 0.34
42 10 0.26
43 15 0.39
ACGTcount: A:0.16, C:0.01, G:0.15, T:0.68
Consensus pattern (40 bp):
TTGATTTGATTTGATTTTTTGATTTTGATTTTTTTTTTGA
Found at i:10541 original size:19 final size:18
Alignment explanation
Indices: 10467--10542 Score: 73
Period size: 18 Copynumber: 4.1 Consensus size: 18
10457 TTGATTTTGA
**
10467 TTTGATTTGATTTTTGAT
1 TTTGATTTGATTTTTTTT
*
10485 TTTGATTTGATTTTTTTG
1 TTTGATTTGATTTTTTTT
* *
10503 ATTGACTTTGATTTGATTTT
1 TTTGA-TTTGATTT-TTTTT
10523 TTT-ATTTTGATTTTTTTT
1 TTTGA-TTTGATTTTTTTT
10541 TT
1 TT
10543 GAATTTCTTG
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
18 25 0.53
19 17 0.36
20 5 0.11
ACGTcount: A:0.14, C:0.01, G:0.13, T:0.71
Consensus pattern (18 bp):
TTTGATTTGATTTTTTTT
Done.