Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019699.1 Corchorus olitorius cultivar O-4 contig19732, 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: 25292
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:102 original size:38 final size:40
Alignment explanation
Indices: 35--119 Score: 120
Period size: 38 Copynumber: 2.2 Consensus size: 40
25 TAGCGGATCG
* *
35 CGACCCGGGTCCATGGCCAGGTTGCGACGCGGGTCGCGCA
1 CGACCCGAGTCCATGGCCAGGTCGCGACGCGGGTCGCGCA
* *
75 CGACCCGAG-CCATGG-CGGGTCGCGACGCGGGTCGCGCG
1 CGACCCGAGTCCATGGCCAGGTCGCGACGCGGGTCGCGCA
113 CGACCCG
1 CGACCCG
120 CTATTTTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
38 27 0.66
39 6 0.15
40 8 0.20
ACGTcount: A:0.12, C:0.38, G:0.41, T:0.09
Consensus pattern (40 bp):
CGACCCGAGTCCATGGCCAGGTCGCGACGCGGGTCGCGCA
Found at i:7623 original size:10 final size:10
Alignment explanation
Indices: 7608--7656 Score: 57
Period size: 9 Copynumber: 4.9 Consensus size: 10
7598 TGGACATCAG
7608 ATTTTTTTTA
1 ATTTTTTTTA
7618 A-TTTTTTTA
1 ATTTTTTTTA
7627 A-TTTTTTTA
1 ATTTTTTTTA
*
7636 ATTTTTATTTT
1 ATTTTT-TTTA
7647 ATTTTATTTT
1 ATTTT-TTTT
7657 TTGCAGTTGA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
9 18 0.51
10 5 0.14
11 11 0.31
12 1 0.03
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (10 bp):
ATTTTTTTTA
Found at i:7624 original size:9 final size:9
Alignment explanation
Indices: 7610--7641 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
7600 GACATCAGAT
7610 TTTTTTTAA
1 TTTTTTTAA
7619 TTTTTTTAA
1 TTTTTTTAA
7628 TTTTTTTAA
1 TTTTTTTAA
7637 TTTTT
1 TTTTT
7642 ATTTTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:13987 original size:36 final size:36
Alignment explanation
Indices: 13940--14009 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
13930 TTCAATAACC
* *
13940 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
13976 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
14010 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:14934 original size:201 final size:203
Alignment explanation
Indices: 14528--14936 Score: 727
Period size: 201 Copynumber: 2.0 Consensus size: 203
14518 GCTTAATAAC
14528 TTTATCAATGGTGAATGTTATTAATTTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATA
1 TTTATCAATGGTGAATGTTATTAATTTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATA
*
14593 AGATACAACACATTATTATTATATATAAAACTATACAAAGAAAAATTAGTTGAACATTAGTGGTT
66 AGATACAACACATTACTATTATATATAAAACTATACAAAGAAAAATTAGTTGAACATTAGTGGTT
*
14658 GAATTATTAAATTAAATTAGATCAGTGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGAT
131 GAATTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGAT
14723 CCGATTTA
196 CCGATTTA
14731 TTTATCAATGGTGAATGTTATTAA-TTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATA
1 TTTATCAATGGTGAATGTTATTAATTTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATA
*
14795 AGATACAACACATTACTATTATATATAGAACTATACCAAA-AAAAATTAG-TGAACATTAGTGGT
66 AGATACAACACATTACTATTATATATAAAACTATA-CAAAGAAAAATTAGTTGAACATTAGTGGT
*
14858 TG-ATTCATTAAATTAAATTAGATTAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAG
130 TGAATT-ATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAG
*
14922 ATCTGATTTA
194 ATCCGATTTA
14932 TTTAT
1 TTTAT
14937 TATTAAGGAA
Statistics
Matches: 199, Mismatches: 5, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
200 3 0.02
201 86 0.43
202 82 0.41
203 28 0.14
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.36
Consensus pattern (203 bp):
TTTATCAATGGTGAATGTTATTAATTTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATA
AGATACAACACATTACTATTATATATAAAACTATACAAAGAAAAATTAGTTGAACATTAGTGGTT
GAATTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGAT
CCGATTTA
Found at i:15099 original size:39 final size:40
Alignment explanation
Indices: 15045--15125 Score: 110
Period size: 39 Copynumber: 2.0 Consensus size: 40
15035 CTACCTAAGA
* * *
15045 ATTTAATTAATGTAAGTATTTCGGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGCATTTCAGTTATTATATATATTAC
* *
15084 ATTTAATTGATGTAAGCATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGCATTTCAGTTATTATATATATTAC
15124 AT
1 AT
15126 AGGAATTAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
39 28 0.78
40 8 0.22
ACGTcount: A:0.35, C:0.05, G:0.11, T:0.49
Consensus pattern (40 bp):
ATTTAATTAATGTAAGCATTTCAGTTATTATATATATTAC
Found at i:15299 original size:103 final size:103
Alignment explanation
Indices: 15183--15390 Score: 398
Period size: 103 Copynumber: 2.0 Consensus size: 103
15173 ATTTTAATAT
*
15183 AATAATATATTTAATTTAATTGATAAATGAAATTACATATTAAACCTTAAAAGTTTTATTTGATA
1 AATAATATATTTAATTTAATTGATAAATGAAATTACATATTAAACCTTAAAAGTTTAATTTGATA
15248 AATACATGTTTACCCTTTAAATGAATACTAAACTTTTA
66 AATACATGTTTACCCTTTAAATGAATACTAAACTTTTA
*
15286 AATAATATATTTAATTTAATTGATAAATGAAATTACATATTGAACCTTAAAAGTTTAATTTGATA
1 AATAATATATTTAATTTAATTGATAAATGAAATTACATATTAAACCTTAAAAGTTTAATTTGATA
15351 AATACATGTTTACCCTTTAAATGAATACTAAACTTTTA
66 AATACATGTTTACCCTTTAAATGAATACTAAACTTTTA
15389 AA
1 AA
15391 ATTAAAAAGG
Statistics
Matches: 103, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 103 1.00
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (103 bp):
AATAATATATTTAATTTAATTGATAAATGAAATTACATATTAAACCTTAAAAGTTTAATTTGATA
AATACATGTTTACCCTTTAAATGAATACTAAACTTTTA
Found at i:15806 original size:20 final size:21
Alignment explanation
Indices: 15773--15811 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
15763 GGATTTGCTA
*
15773 ATTGATTTACTAAA-ATTGGG
1 ATTGATATACTAAATATTGGG
*
15793 ATTGATATAGTAAATATTG
1 ATTGATATACTAAATATTG
15812 AACAGAAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (21 bp):
ATTGATATACTAAATATTGGG
Found at i:24604 original size:39 final size:40
Alignment explanation
Indices: 24548--24628 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
24538 TTTAGTTCCT
24548 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
24588 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
24627 AT
1 AT
24629 TCTTAGGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:25100 original size:203 final size:203
Alignment explanation
Indices: 24709--25119 Score: 720
Period size: 203 Copynumber: 2.0 Consensus size: 203
24699 TTCCTTAATA
*
24709 ATAAATAAATTGGATCTTTAATATCTTTAATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCGGATCTTTAATATCTTTAATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
*
24774 AATTTAATAAATTAACCACTAATATTCAACTAATTTTTTTTTGGTATAGTTCTATATATAATAGT
66 AATTTAATAAATTAACCACTAATATTCAACTAATTTTTTTTTGGTATAGTTCTATATATAATAAT
*
24839 AATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATT
131 AATGTGTTGTATCTTATTCACTACAACTTTATTAGTAATCTTAGACTTAAAAAATTAATAACATT
*
24904 CACCATTG
196 CACCAATG
*
24912 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCGGATCTTTAATATCTTTAATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
*
24977 AATTTAAT-AATTCAACCACTAATGTTCAACTAA-TTTTTTTTGGTATAGTT-TAATATATAATA
66 AATTTAATAAATT-AACCACTAATATTCAACTAATTTTTTTTTGGTATAGTTCT-ATATATAATA
25039 ATAATGTGTTGTATCTTATTCACTACAACTTTATTAGTAATCTTAGACTTAAAAGAATTAATAAC
129 ATAATGTGTTGTATCTTATTCACTACAACTTTATTAGTAATCTTAGACTTAAAA-AATTAATAAC
25104 ATTCACCAATG
193 ATTCACCAATG
25115 ATAAA
1 ATAAA
25120 GTTATTAAGC
Statistics
Matches: 199, Mismatches: 6, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
201 1 0.01
202 83 0.42
203 115 0.58
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.44
Consensus pattern (203 bp):
ATAAATAAATCGGATCTTTAATATCTTTAATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
AATTTAATAAATTAACCACTAATATTCAACTAATTTTTTTTTGGTATAGTTCTATATATAATAAT
AATGTGTTGTATCTTATTCACTACAACTTTATTAGTAATCTTAGACTTAAAAAATTAATAACATT
CACCAATG
Done.