Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006752.1 Corchorus capsularis cultivar CVL-1 contig06773, 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: 12621
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Found at i:6066 original size:3 final size:3
Alignment explanation
Indices: 6053--6087 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
6043 TATATTTTAA
6053 TAT TA- TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
6088 CTTTTCAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.13
3 26 0.87
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:6082 original size:23 final size:22
Alignment explanation
Indices: 6045--6087 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
6035 ATGTAGTATA
6045 TATTTTAATATTATATTATTAT
1 TATTTTAATATTATATTATTAT
*
6067 TATTATTATTATTATATTATT
1 TATT-TTAATATTATATTATT
6088 CTTTTCAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TATTTTAATATTATATTATTAT
Found at i:6606 original size:85 final size:85
Alignment explanation
Indices: 6502--6669 Score: 309
Period size: 85 Copynumber: 2.0 Consensus size: 85
6492 TAATCAGAAC
*
6502 AAAATTAAACATGATTGATGATGAAAACAAAATAATAAAATGTTTGTTGGTACAAACTAAATCTC
1 AAAATTAAACATGATTGATGATGAAAACAAAATAAGAAAATGTTTGTTGGTACAAACTAAATCTC
*
6567 ATGTTTAAAGAACAAAATAA
66 ATGATTAAAGAACAAAATAA
*
6587 AAAATTAAACATGATTGATGATGAAAACAAAATAAGAAAATGTTTGTTGGTACAAATTAAATCTC
1 AAAATTAAACATGATTGATGATGAAAACAAAATAAGAAAATGTTTGTTGGTACAAACTAAATCTC
6652 ATGATTAAAGAACAAAAT
66 ATGATTAAAGAACAAAAT
6670 CAACACCCAA
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
85 80 1.00
ACGTcount: A:0.52, C:0.08, G:0.12, T:0.28
Consensus pattern (85 bp):
AAAATTAAACATGATTGATGATGAAAACAAAATAAGAAAATGTTTGTTGGTACAAACTAAATCTC
ATGATTAAAGAACAAAATAA
Found at i:6743 original size:82 final size:83
Alignment explanation
Indices: 6531--6767 Score: 232
Period size: 85 Copynumber: 2.8 Consensus size: 83
6521 GATGAAAACA
* * * * * ***
6531 AAATAATAAAATGTTTGTTGGTACAAACTAAATCTCATGTTTAAAGAACAAAATAAAAAATTAAA
1 AAATAAGAAAATGTTTGTTGGTACAAATTAAATCTCATGATTAAAGAACAAAATCAACACCCAAA
** ** *
6596 -CATGATTGATGATGAAAA-CA
66 TCAT-A---AAAAACAAAATCC
6616 AAATAAGAAAATGTTTGTTGGTACAAATTAAATCTCATGATTAAAGAACAAAATCAACACCCAAA
1 AAATAAGAAAATGTTTGTTGGTACAAATTAAATCTCATGATTAAAGAACAAAATCAACACCCAAA
6681 TCATAAAAAACAAAATCC
66 TCATAAAAAACAAAATCC
* * * *
6699 AAATAAG-AAATGCTTT-TTGGTACAAATTAAATTTC-TTATCTAAAGAATAAAATCAATACCCA
1 AAATAAGAAAATG-TTTGTTGGTACAAATTAAATCTCATGAT-TAAAGAACAAAATCAACACCCA
6761 AATCATA
64 AATCATA
6768 TAAACTAATC
Statistics
Matches: 131, Mismatches: 17, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
81 3 0.02
82 56 0.43
83 11 0.08
85 58 0.44
86 3 0.02
ACGTcount: A:0.51, C:0.12, G:0.09, T:0.27
Consensus pattern (83 bp):
AAATAAGAAAATGTTTGTTGGTACAAATTAAATCTCATGATTAAAGAACAAAATCAACACCCAAA
TCATAAAAAACAAAATCC
Found at i:7235 original size:33 final size:33
Alignment explanation
Indices: 7193--7259 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
7183 AACCCATAAT
7193 TGTAAAGGATTAAATAGCATAAAGCATAAAAAG
1 TGTAAAGGATTAAATAGCATAAAGCATAAAAAG
7226 TGTAAAGGATTAAATAGCATAAAGCATAAAAAG
1 TGTAAAGGATTAAATAGCATAAAGCATAAAAAG
7259 T
1 T
7260 ATGAGGATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.54, C:0.06, G:0.18, T:0.22
Consensus pattern (33 bp):
TGTAAAGGATTAAATAGCATAAAGCATAAAAAG
Found at i:7248 original size:17 final size:17
Alignment explanation
Indices: 7195--7249 Score: 67
Period size: 17 Copynumber: 3.3 Consensus size: 17
7185 CCCATAATTG
7195 TAAAGGATTAAATAGCA
1 TAAAGGATTAAATAGCA
* * **
7212 TAAAGCA-TAAAAAGTG
1 TAAAGGATTAAATAGCA
7228 TAAAGGATTAAATAGCA
1 TAAAGGATTAAATAGCA
7245 TAAAG
1 TAAAG
7250 CATAAAAAGT
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
16 12 0.41
17 17 0.59
ACGTcount: A:0.55, C:0.05, G:0.18, T:0.22
Consensus pattern (17 bp):
TAAAGGATTAAATAGCA
Found at i:9816 original size:2 final size:2
Alignment explanation
Indices: 9811--9852 Score: 50
Period size: 2 Copynumber: 21.0 Consensus size: 2
9801 GCATACATAC
* *
9811 AT AT AT AT AT AT AT AT AT AT AC AT AC AT AT -T AT AT ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
9853 GTTTCTGTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
1 1 0.03
2 31 0.91
3 2 0.06
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:10314 original size:57 final size:57
Alignment explanation
Indices: 10251--10369 Score: 238
Period size: 57 Copynumber: 2.1 Consensus size: 57
10241 TAGTCACCAA
10251 AGTGGCCTAGTTTGAAAAGAATTTAGACATCTAATAAATTAAGCAATTGTTCAAATT
1 AGTGGCCTAGTTTGAAAAGAATTTAGACATCTAATAAATTAAGCAATTGTTCAAATT
10308 AGTGGCCTAGTTTGAAAAGAATTTAGACATCTAATAAATTAAGCAATTGTTCAAATT
1 AGTGGCCTAGTTTGAAAAGAATTTAGACATCTAATAAATTAAGCAATTGTTCAAATT
10365 AGTGG
1 AGTGG
10370 ATGCTATTAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 62 1.00
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (57 bp):
AGTGGCCTAGTTTGAAAAGAATTTAGACATCTAATAAATTAAGCAATTGTTCAAATT
Done.