Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010154.1 Corchorus capsularis cultivar CVL-1 contig10175, 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: 4647
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Found at i:42 original size:28 final size:28
Alignment explanation
Indices: 2--57 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
1 G
2 TTAATGGGGGTAATTTTGGAATAAAGTT
1 TTAATGGGGGTAATTTTGGAATAAAGTT
30 TTAATGGGGGTAATTTTGGAATAAAGTT
1 TTAATGGGGGTAATTTTGGAATAAAGTT
58 ATTTAATAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.29, T:0.39
Consensus pattern (28 bp):
TTAATGGGGGTAATTTTGGAATAAAGTT
Found at i:116 original size:17 final size:17
Alignment explanation
Indices: 94--126 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
84 GAACGCCTTT
94 AATCATTTAATAAAAAA
1 AATCATTTAATAAAAAA
111 AATCATTTAATAAAAA
1 AATCATTTAATAAAAA
127 TGGAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (17 bp):
AATCATTTAATAAAAAA
Found at i:2709 original size:7 final size:7
Alignment explanation
Indices: 2699--2732 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
2689 ACGTACCTCG
2699 TATATAT
1 TATATAT
*
2706 TATATAA
1 TATATAT
2713 TATATA-
1 TATATAT
2719 TATATAT
1 TATATAT
2726 TATATAT
1 TATATAT
2733 AAAAAACCTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (7 bp):
TATATAT
Found at i:3214 original size:2 final size:2
Alignment explanation
Indices: 3209--3233 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3199 ACACACACAC
3209 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3234 CTACATATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3580 original size:157 final size:159
Alignment explanation
Indices: 3269--3729 Score: 459
Period size: 157 Copynumber: 2.8 Consensus size: 159
3259 GGAAATTACT
* * ** * *
3269 AAAAGATCCCCACCACGGATTAATGAGGAGCGAGAGAACTAATTTTTTTCGTCTTT-TCACACAT
1 AAAAGAT-CCCACCAAGGATTGATGTTGAGCTAGAGAACTAATTTTTTTCGTCTTTCT-ACGC--
* *** *
3333 GATCGATTACCTAAATG-CCATAACTTTTGATTCTTGAAATGATTAAAAAACTAGACTTTTTGGT
62 -A--GATTACTTAAATGTCCA-AACTTTTGATTCTTGAGGGGATTAAATAACTA-ACTTTTTGGT
* * * * * *
3397 CATTTCTCAGTTGATTTTAATGGAGTAGTGCAATTACC
122 CATTTCTCAATGGACTTGAATAGAGTAGTGCAATTAAC
* * * * *
3435 AAAAGATCCCTACCAAGGCTTGATTTTGGAGTTAGAGAACT-TTTTTTTTCGTCTTT-T-C-C-T
1 AAAAGATCCC-ACCAAGGATTGATGTT-GAGCTAGAGAACTAATTTTTTTCGTCTTTCTACGCAG
*
3495 ATTACTTAAATGTCCAAACTTTTGATTCTTGAGGGGATTAAATAAGTAATCTTTTTGGTCATTTC
64 ATTACTTAAATGTCCAAACTTTTGATTCTTGAGGGGATTAAATAACTAA-CTTTTTGGTCATTTC
* *
3560 TCAATGGACTTGAATAGAGTAGTGGAATTAAT
128 TCAATGGACTTGAATAGAGTAGTGCAATTAAC
*
3592 AAAAGATCCCATCAAGGATTGATGTTGAGCTAGAGAACTAATTTTTTTCGTCTTTACCTACTTGG
1 AAAAGATCCCACCAAGGATTGATGTTGAGCTAGAGAACTAATTTTTTTCGTCTTT--CTAC---G
* *
3657 CAGATTACTTAAATGTCCTAACTTTTGATTTTTGAGGGGATTAAATAACTAAACTTTTTGGTCAT
61 CAGATTACTTAAATGTCCAAACTTTTGATTCTTGAGGGGATTAAATAACT-AACTTTTTGGTCAT
3722 TTCTCAAT
125 TTCTCAAT
3730 TGACAAATGA
Statistics
Matches: 247, Mismatches: 33, Indels: 31
0.79 0.11 0.10
Matches are distributed among these distances:
155 12 0.05
156 28 0.11
157 87 0.35
158 3 0.01
159 1 0.00
160 1 0.00
163 1 0.00
164 2 0.01
165 67 0.27
166 34 0.14
167 11 0.04
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (159 bp):
AAAAGATCCCACCAAGGATTGATGTTGAGCTAGAGAACTAATTTTTTTCGTCTTTCTACGCAGAT
TACTTAAATGTCCAAACTTTTGATTCTTGAGGGGATTAAATAACTAACTTTTTGGTCATTTCTCA
ATGGACTTGAATAGAGTAGTGCAATTAAC
Found at i:3824 original size:14 final size:12
Alignment explanation
Indices: 3803--3835 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3793 AAGAATTAGT
3803 TTATATAT-TTA
1 TTATATATATTA
3814 TTATCATATATTA
1 TTAT-ATATATTA
3827 TTATATATA
1 TTATATATA
3836 AATGAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 4 0.20
12 9 0.45
13 7 0.35
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (12 bp):
TTATATATATTA
Done.