Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019442.1 Corchorus olitorius cultivar O-4 contig19475, 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: 23441
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:3225 original size:21 final size:21
Alignment explanation
Indices: 3201--3247 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
3191 TTTGAAAAAG
* *
3201 TAGAAAAAGTGCTATAACGGC
1 TAGAAAAAGAGCTACAACGGC
*
3222 TAG-AAAAGAGCTCCAACGGC
1 TAGAAAAAGAGCTACAACGGC
3242 TAGAAA
1 TAGAAA
3248 CTTGTGAGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (21 bp):
TAGAAAAAGAGCTACAACGGC
Found at i:4630 original size:31 final size:29
Alignment explanation
Indices: 4560--4630 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
4550 ATTGAAATTG
** *
4560 AGGGGGCAAAACGTTTAAAATTAAAGTTC
1 AGGGGGCAAAACGTCCAAAAGTAAAGTTC
* *
4589 ATGGGACAAAACGTCCAAATAGTACAAGTTC
1 AGGGGGCAAAACGTCCAAA-AGTA-AAGTTC
4620 AGGGGGCAAAA
1 AGGGGGCAAAA
4631 AGGGCATTAA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
29 15 0.45
30 3 0.09
31 15 0.45
ACGTcount: A:0.42, C:0.14, G:0.25, T:0.18
Consensus pattern (29 bp):
AGGGGGCAAAACGTCCAAAAGTAAAGTTC
Found at i:6815 original size:31 final size:30
Alignment explanation
Indices: 6769--6848 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 30
6759 GGCTAAATAT
*
6769 CAAAAAAATCCCTTATGTTTTTCTTTTGGGA
1 CAAAATAATCCCTTATGTTTTT-TTTTGGGA
*
6800 CAAAATAATCTCTTATG-TTTTTTTTGGGA
1 CAAAATAATCCCTTATGTTTTTTTTTGGGA
* *
6829 CAAATTAATCCCTTACGTTT
1 CAAAATAATCCCTTATGTTT
6849 CAAAATTGAG
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 22 0.51
30 6 0.14
31 15 0.35
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.44
Consensus pattern (30 bp):
CAAAATAATCCCTTATGTTTTTTTTTGGGA
Found at i:8125 original size:15 final size:15
Alignment explanation
Indices: 8093--8141 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
8083 TCAATTGGAG
8093 AAGAAGAAGAAGAAATA
1 AAGAAGAA-AA-AAATA
*
8110 AGGAA-AAAGAAAATA
1 AAGAAGAAA-AAAATA
8125 AAGAAGAAAAAAATA
1 AAGAAGAAAAAAATA
8140 AA
1 AA
8142 AATAAAGAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
15 18 0.64
16 6 0.21
17 4 0.14
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (15 bp):
AAGAAGAAAAAAATA
Found at i:10640 original size:6 final size:6
Alignment explanation
Indices: 10591--10645 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
10581 TTGATCTCCA
* * * * *
10591 CCGTCT CCGTTT CCTTCT CGGTCT CGGTCT CGGTCT CCGTCT CCGTCT
1 CCGTCT CCGTCT CCGTCT CCGTCT CCGTCT CCGTCT CCGTCT CCGTCT
*
10639 CCTTCT C
1 CCGTCT C
10646 GTACTCGTTG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.00, C:0.44, G:0.18, T:0.38
Consensus pattern (6 bp):
CCGTCT
Found at i:10645 original size:18 final size:18
Alignment explanation
Indices: 10591--10645 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
10581 TTGATCTCCA
*
10591 CCGTCTCCGTTTCCTTCT
1 CCGTCTCCGTCTCCTTCT
* * **
10609 CGGTCTCGGTCTCGGTCT
1 CCGTCTCCGTCTCCTTCT
10627 CCGTCTCCGTCTCCTTCT
1 CCGTCTCCGTCTCCTTCT
10645 C
1 C
10646 GTACTCGTTG
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.00, C:0.44, G:0.18, T:0.38
Consensus pattern (18 bp):
CCGTCTCCGTCTCCTTCT
Found at i:11148 original size:26 final size:27
Alignment explanation
Indices: 11111--11169 Score: 84
Period size: 26 Copynumber: 2.2 Consensus size: 27
11101 AGGTTTGCTC
**
11111 CAAAATGCAATTTGGGATATAACGTTA
1 CAAAATGCAATTAAGGATATAACGTTA
11138 CAAAA-GCAATTAAGGATATAACGTTA
1 CAAAATGCAATTAAGGATATAACGTTA
11164 CGAAAA
1 C-AAAA
11170 ACGAGCAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 20 0.69
27 9 0.31
ACGTcount: A:0.47, C:0.12, G:0.17, T:0.24
Consensus pattern (27 bp):
CAAAATGCAATTAAGGATATAACGTTA
Found at i:11344 original size:31 final size:31
Alignment explanation
Indices: 11307--11447 Score: 153
Period size: 31 Copynumber: 4.6 Consensus size: 31
11297 TCCTAACTGA
11307 TTATATCCTTAATTGCTTGAAATCGAAAACG
1 TTATATCCTTAATTGCTTGAAATCGAAAACG
* * *
11338 TCATATCCCTAATTGCTTGAAATCAAAAACG
1 TTATATCCTTAATTGCTTGAAATCGAAAACG
** * *
11369 TTATATCCTTAATTGCTTG-TTTTG-TAACG
1 TTATATCCTTAATTGCTTGAAATCGAAAACG
***
11398 TTATATCCTTAATTGCTT-ACGGCAGAAAACG
1 TTATATCCTTAATTGCTTGAAATC-GAAAACG
*
11429 TTATATCCTAAATTGCTTG
1 TTATATCCTTAATTGCTTG
11448 CTTATCCTCT
Statistics
Matches: 90, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
29 22 0.24
30 2 0.02
31 66 0.73
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (31 bp):
TTATATCCTTAATTGCTTGAAATCGAAAACG
Found at i:11414 original size:60 final size:62
Alignment explanation
Indices: 11307--11447 Score: 162
Period size: 60 Copynumber: 2.3 Consensus size: 62
11297 TCCTAACTGA
*
11307 TTATATCCTTAATTGCTTGAAATCGAAAACGTCATATCCCTAATTGCTTGAAATCA-AAAACG
1 TTATATCCTTAATTGCTTGAAATCGAAAACGTCATATCCCTAATTGCTT-AAAGCAGAAAACG
** * * * * **
11369 TTATATCCTTAATTGCTTG-TTTTG-TAACGTTATATCCTTAATTGCTTACGGCAGAAAACG
1 TTATATCCTTAATTGCTTGAAATCGAAAACGTCATATCCCTAATTGCTTAAAGCAGAAAACG
*
11429 TTATATCCTAAATTGCTTG
1 TTATATCCTTAATTGCTTG
11448 CTTATCCTCT
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
59 3 0.04
60 44 0.65
61 2 0.03
62 19 0.28
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (62 bp):
TTATATCCTTAATTGCTTGAAATCGAAAACGTCATATCCCTAATTGCTTAAAGCAGAAAACG
Found at i:12502 original size:60 final size:62
Alignment explanation
Indices: 12428--12565 Score: 145
Period size: 60 Copynumber: 2.3 Consensus size: 62
12418 GTCAAATAAT
* * *
12428 CAATTTAGGATATAATGTTTGTTGCCACAAGCAATTAAGGATATAACG-TTAC-AAAACAAG
1 CAATTAAGGATATAATATTTGTTACCACAAGCAATTAAGGATATAACGTTTACGAAAACAAG
* * *** * * ***
12488 CAATTAAGGATATAACATTTTTTATTTCAAGCAATTAAGGATATGACGTTTTCGATTTCAAG
1 CAATTAAGGATATAATATTTGTTACCACAAGCAATTAAGGATATAACGTTTACGAAAACAAG
12550 CAATTAAGGATATAAT
1 CAATTAAGGATATAAT
12566 CAGTTAAGGC
Statistics
Matches: 62, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
60 39 0.63
61 3 0.05
62 20 0.32
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (62 bp):
CAATTAAGGATATAATATTTGTTACCACAAGCAATTAAGGATATAACGTTTACGAAAACAAG
Found at i:12522 original size:31 final size:31
Alignment explanation
Indices: 12484--12564 Score: 126
Period size: 31 Copynumber: 2.6 Consensus size: 31
12474 CGTTACAAAA
**
12484 CAAGCAATTAAGGATATAACATTTTTTATTT
1 CAAGCAATTAAGGATATAACATTTTCGATTT
* *
12515 CAAGCAATTAAGGATATGACGTTTTCGATTT
1 CAAGCAATTAAGGATATAACATTTTCGATTT
12546 CAAGCAATTAAGGATATAA
1 CAAGCAATTAAGGATATAA
12565 TCAGTTAAGG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.35
Consensus pattern (31 bp):
CAAGCAATTAAGGATATAACATTTTCGATTT
Found at i:12607 original size:11 final size:11
Alignment explanation
Indices: 12590--12626 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
12580 TTAATTGATG
12590 ACGTGGCATCC
1 ACGTGGCATCC
*
12601 GCGTGGCATCC
1 ACGTGGCATCC
*
12612 ACGTGGTATCC
1 ACGTGGCATCC
12623 ACGT
1 ACGT
12627 AGATGACACG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.16, C:0.32, G:0.30, T:0.22
Consensus pattern (11 bp):
ACGTGGCATCC
Found at i:12768 original size:29 final size:31
Alignment explanation
Indices: 12694--12760 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
12684 CATAACAGAC
12694 TATATCCTTAATTGCTCGCTTTTCGTAACGT
1 TATATCCTTAATTGCTCGCTTTTCGTAACGT
*
12725 TATATCCTTAATTGCTTG-TTTT-GTAACGT
1 TATATCCTTAATTGCTCGCTTTTCGTAACGT
12754 TATATCC
1 TATATCC
12761 CAAATTGCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 14 0.40
30 4 0.11
31 17 0.49
ACGTcount: A:0.21, C:0.19, G:0.12, T:0.48
Consensus pattern (31 bp):
TATATCCTTAATTGCTCGCTTTTCGTAACGT
Found at i:13986 original size:17 final size:17
Alignment explanation
Indices: 13964--13999 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
13954 GGTGATCTTA
*
13964 ATCACCAGTGATGAAAG
1 ATCACCAGTGATCAAAG
*
13981 ATCACCGGTGATCAAAG
1 ATCACCAGTGATCAAAG
13998 AT
1 AT
14000 TACATGGGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.19, G:0.22, T:0.19
Consensus pattern (17 bp):
ATCACCAGTGATCAAAG
Found at i:22056 original size:13 final size:13
Alignment explanation
Indices: 22038--22063 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
22028 CTTGGCATGA
22038 GTGATGATTTTTG
1 GTGATGATTTTTG
22051 GTGATGATTTTTG
1 GTGATGATTTTTG
22064 TTGAGATCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (13 bp):
GTGATGATTTTTG
Done.