Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017337.1 Corchorus olitorius cultivar O-4 contig17370, 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: 12460
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:35 original size:16 final size:15
Alignment explanation
Indices: 16--46 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
6 TCTCTCTCTC
16 TCTCTCCTTTTTTTTT
1 TCTCT-CTTTTTTTTT
32 TCTCTCTTTTTTTTT
1 TCTCTCTTTTTTTTT
47 CTTCTTCTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (15 bp):
TCTCTCTTTTTTTTT
Found at i:37 original size:18 final size:17
Alignment explanation
Indices: 16--55 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
6 TCTCTCTCTC
*
16 TCTCTCCTTTTTTTT-T
1 TCTCTCTTTTTTTTTCT
32 TCTCTCTTTTTTTTTCT
1 TCTCTCTTTTTTTTTCT
49 TCT-TCTT
1 TCTCTCTT
56 CTTCTTCCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (17 bp):
TCTCTCTTTTTTTTTCT
Found at i:52 original size:13 final size:14
Alignment explanation
Indices: 24--52 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
14 TCTCTCTCCT
24 TTTTTTTTTCTCTC
1 TTTTTTTTTCTCTC
38 TTTTTTTTTCT-TC
1 TTTTTTTTTCTCTC
51 TT
1 TT
53 CTTCTTCTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTTTTTCTCTC
Found at i:5155 original size:48 final size:50
Alignment explanation
Indices: 5085--5180 Score: 169
Period size: 48 Copynumber: 2.0 Consensus size: 50
5075 GGTAGTTGTC
5085 TTGTTTCCTATTACTTTTCACACCTCGTTTTCGTTTTACAATTCAGTTTG
1 TTGTTTCCTATTACTTTTCACACCTCGTTTTCGTTTTACAATTCAGTTTG
*
5135 TTGTTTTCTA-TA-TTTTCACACCTCGTTTTCGTTTTACAATTCAGTT
1 TTGTTTCCTATTACTTTTCACACCTCGTTTTCGTTTTACAATTCAGTT
5181 ATTTTCGTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
48 34 0.76
49 2 0.04
50 9 0.20
ACGTcount: A:0.17, C:0.21, G:0.09, T:0.53
Consensus pattern (50 bp):
TTGTTTCCTATTACTTTTCACACCTCGTTTTCGTTTTACAATTCAGTTTG
Found at i:5543 original size:16 final size:16
Alignment explanation
Indices: 5522--5552 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
5512 AGGATCACCC
5522 TTAATTAAAAGACAAT
1 TTAATTAAAAGACAAT
5538 TTAATTAAAAGACAA
1 TTAATTAAAAGACAA
5553 CTCACTGTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.29
Consensus pattern (16 bp):
TTAATTAAAAGACAAT
Found at i:8138 original size:21 final size:22
Alignment explanation
Indices: 8108--8148 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
8098 GCAAAATCTC
*
8108 TAAAACCAGGGGTCAAATTGAA
1 TAAAACCAGGGATCAAATTGAA
8130 TAAAA-CAGGGATCAAATTG
1 TAAAACCAGGGATCAAATTG
8149 CATTTAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.46, C:0.12, G:0.22, T:0.20
Consensus pattern (22 bp):
TAAAACCAGGGATCAAATTGAA
Found at i:8296 original size:41 final size:41
Alignment explanation
Indices: 8213--8304 Score: 114
Period size: 41 Copynumber: 2.2 Consensus size: 41
8203 TAAAATCTTC
* * * * *
8213 AATCAGGGGCGAAATTGAATCAATAAATAAATATTACTCTA
1 AATCAGGGACAAAATTGAATCAATAAACAAACATAACTCTA
*
8254 AATCAGGGACAAAATTGAATCAATTAACAAACATAAAC-CTA
1 AATCAGGGACAAAATTGAATCAATAAACAAACAT-AACTCTA
8295 AATCAGGGAC
1 AATCAGGGAC
8305 TAAGGTGAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
41 42 0.95
42 2 0.05
ACGTcount: A:0.49, C:0.15, G:0.14, T:0.22
Consensus pattern (41 bp):
AATCAGGGACAAAATTGAATCAATAAACAAACATAACTCTA
Found at i:9709 original size:1 final size:1
Alignment explanation
Indices: 9628--9837 Score: 96
Period size: 1 Copynumber: 210.0 Consensus size: 1
9618 TAACAACTTG
* * * * * * * * * * * * *
9628 TTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTG
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * * * * *
9693 TTTTGTTTTGTTTTTTTTTTGTTTTTGTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * * * * * *
9758 TTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
9823 TTTGTTTTTGTTTTT
1 TTTTTTTTTTTTTTT
9838 GTGCAGCCCC
Statistics
Matches: 137, Mismatches: 72, Indels: 0
0.66 0.34 0.00
Matches are distributed among these distances:
1 137 1.00
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (1 bp):
T
Found at i:9712 original size:6 final size:6
Alignment explanation
Indices: 9628--9839 Score: 312
Period size: 6 Copynumber: 38.0 Consensus size: 6
9618 TAACAACTTG
9628 TTTTG- TTTTG- TTTTG- TTTTG- TTTTG- TTTTG- TTTTG- TTTTG-
1 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT
9668 TTTTG- TTTTG- TTTTG- TTTTG- TTTTG- TTTTG- TTTTGT TTTT-T
1 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT
9709 TTTTGT TTTTG- TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT
1 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT
9756 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT
1 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT
9804 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT
1 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT
9840 GCAGCCCCAA
Statistics
Matches: 204, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
5 80 0.39
6 124 0.61
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (6 bp):
TTTTGT
Found at i:11140 original size:28 final size:27
Alignment explanation
Indices: 11109--11200 Score: 112
Period size: 28 Copynumber: 3.3 Consensus size: 27
11099 AATGACAGAG
*
11109 ATGCCCTTGAATGTGCAAAATGACCAAA
1 ATGCCCCTGAATGTGC-AAATGACCAAA
* *
11137 ATGCCCCTGGATGTGCAAATGACAAAA
1 ATGCCCCTGAATGTGCAAATGACCAAA
**
11164 ATGCCCCCTGAACATGCAAATGACCCAAA
1 ATG-CCCCTGAATGTGCAAATGA-CCAAA
11193 ATGCCCCT
1 ATGCCCCT
11201 AGATGACCTT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
27 13 0.24
28 35 0.64
29 7 0.13
ACGTcount: A:0.36, C:0.28, G:0.17, T:0.18
Consensus pattern (27 bp):
ATGCCCCTGAATGTGCAAATGACCAAA
Found at i:11463 original size:11 final size:11
Alignment explanation
Indices: 11447--11471 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
11437 TCGCAATAAA
11447 ATTGATGATGC
1 ATTGATGATGC
11458 ATTGATGATGC
1 ATTGATGATGC
11469 ATT
1 ATT
11472 TTTATCATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.08, G:0.24, T:0.40
Consensus pattern (11 bp):
ATTGATGATGC
Found at i:11753 original size:15 final size:16
Alignment explanation
Indices: 11729--11768 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
11719 AGAGGTTGAA
*
11729 AGAAATCAATTAAAC-
1 AGAAAACAATTAAACT
11744 AGAAAACAATTAAACT
1 AGAAAACAATTAAACT
11760 AGAAAACAA
1 AGAAAACAA
11769 ATCAAAGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.65, C:0.12, G:0.07, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Done.