Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008648.1 Corchorus capsularis cultivar CVL-1 contig08669, 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: 35674
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:6103 original size:6 final size:6
Alignment explanation
Indices: 6092--6116 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
6082 TAACAAAGAC
6092 ATCACA ATCACA ATCACA ATCACA A
1 ATCACA ATCACA ATCACA ATCACA A
6117 ACATGTTCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.32, G:0.00, T:0.16
Consensus pattern (6 bp):
ATCACA
Found at i:14804 original size:2 final size:2
Alignment explanation
Indices: 14797--14831 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
14787 CCCTTGTTGG
14797 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
14832 TCTATAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:20998 original size:15 final size:13
Alignment explanation
Indices: 20978--21055 Score: 72
Period size: 15 Copynumber: 5.8 Consensus size: 13
20968 AAAAATAATG
20978 AACTAATTAATTATA
1 AACTAATTAA--ATA
20993 AACTAATTAAAT-
1 AACTAATTAAATA
21005 -ACTAATTAAACATA
1 AACTAATT-AA-ATA
*
21019 AACTAA-TAAACA
1 AACTAATTAAATA
*
21031 AACTAATTTTAATA
1 AACTAA-TTAAATA
21045 AACTAATTAAA
1 AACTAATTAAA
21056 ATTAATCATC
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
11 7 0.13
12 10 0.19
13 10 0.19
14 11 0.21
15 15 0.28
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.32
Consensus pattern (13 bp):
AACTAATTAAATA
Found at i:21012 original size:26 final size:26
Alignment explanation
Indices: 20978--21056 Score: 90
Period size: 26 Copynumber: 3.0 Consensus size: 26
20968 AAAAATAATG
20978 AACTAATTAATTATAAACTAATTAAA
1 AACTAATTAATTATAAACTAATTAAA
* ** *
21004 TACTAATTAAACATAAACTAATAAACA
1 AACTAATTAATTATAAACTAATTAA-A
21031 AACTAATT--TTAATAAACTAATTAAA
1 AACTAATTAATT-ATAAACTAATTAAA
21056 A
1 A
21057 TTAATCATCA
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
25 2 0.05
26 33 0.77
27 8 0.19
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.32
Consensus pattern (26 bp):
AACTAATTAATTATAAACTAATTAAA
Found at i:21060 original size:18 final size:18
Alignment explanation
Indices: 20924--21061 Score: 67
Period size: 18 Copynumber: 7.9 Consensus size: 18
20914 ATCATAAATT
*
20924 AACTAATTAAAACTAATA
1 AACTAATTAAAATTAATA
* *
20942 TACTAAGTAATAATTAATA
1 AACTAATTAA-AATTAATA
* ** * *
20961 AA-AAAACAAAAATAATG
1 AACTAATTAAAATTAATA
20978 AACTAATT--AATT-ATA
1 AACTAATTAAAATTAATA
*
20993 AACTAATTAAATACTAATTA
1 AACTAATTAAA-ATTAA-TA
*
21013 AAC--A-T-AAACTAATA
1 AACTAATTAAAATTAATA
* * **
21027 AACAAACTAATTTTAATA
1 AACTAATTAAAATTAATA
21045 AACTAATTAAAATTAAT
1 AACTAATTAAAATTAAT
21062 CATCAAAATT
Statistics
Matches: 87, Mismatches: 22, Indels: 22
0.66 0.17 0.17
Matches are distributed among these distances:
14 5 0.06
15 15 0.17
16 6 0.07
17 11 0.13
18 36 0.41
19 9 0.10
20 5 0.06
ACGTcount: A:0.59, C:0.09, G:0.01, T:0.30
Consensus pattern (18 bp):
AACTAATTAAAATTAATA
Found at i:21249 original size:15 final size:15
Alignment explanation
Indices: 21229--21278 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
21219 AAAAATAATG
**
21229 AACTAATTAATTATA
1 AACTAATTAAACATA
21244 AACTAATTAAACATA
1 AACTAATTAAACATA
21259 AACTAA-TAAAC--A
1 AACTAATTAAACATA
21271 AACTAATT
1 AACTAATT
21279 TTAATAAACT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 7 0.22
13 1 0.03
14 5 0.16
15 19 0.59
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (15 bp):
AACTAATTAAACATA
Found at i:21609 original size:25 final size:25
Alignment explanation
Indices: 21560--21643 Score: 118
Period size: 25 Copynumber: 3.4 Consensus size: 25
21550 AAATGAAGGA
*
21560 AAATG-AGTTTGAAG-ATTTGTTAG
1 AAATGAAGTTTGAAGAAGTTGTTAG
*
21583 AAATGAAGTTTGGAGAAGTTGTTAG
1 AAATGAAGTTTGAAGAAGTTGTTAG
*
21608 AAATGAAGTTTGAAGAAGTTATTAG
1 AAATGAAGTTTGAAGAAGTTGTTAG
*
21633 GAATGAAGTTT
1 AAATGAAGTTT
21644 AGGGTTTGAA
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
23 5 0.09
24 8 0.15
25 41 0.76
ACGTcount: A:0.38, C:0.00, G:0.27, T:0.35
Consensus pattern (25 bp):
AAATGAAGTTTGAAGAAGTTGTTAG
Found at i:21750 original size:20 final size:21
Alignment explanation
Indices: 21722--21765 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
21712 CAAAAGTGTA
*
21722 AAAAGGGGGGCGGTATTTAGC
1 AAAAGGGGGGAGGTATTTAGC
21743 AAAAGGGGGGAGGTATTTAGC
1 AAAAGGGGGGAGGTATTTAGC
21764 AA
1 AA
21766 TCCAGTACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.34, C:0.07, G:0.41, T:0.18
Consensus pattern (21 bp):
AAAAGGGGGGAGGTATTTAGC
Found at i:24791 original size:13 final size:14
Alignment explanation
Indices: 24764--24809 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
24754 TGCTAAGTAA
*
24764 ATATGATGATTAATG
1 ATAT-ATGATGAATG
24779 ATAT-TGATGAATG
1 ATATATGATGAATG
24792 A-ATATGATGAAT-
1 ATATATGATGAATG
24804 ATATAT
1 ATATAT
24810 ATATATATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
12 3 0.11
13 21 0.75
15 4 0.14
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.39
Consensus pattern (14 bp):
ATATATGATGAATG
Found at i:24809 original size:2 final size:2
Alignment explanation
Indices: 24802--24828 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
24792 AATATGATGA
24802 AT 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 AT A
24829 ACATATGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30180 original size:19 final size:18
Alignment explanation
Indices: 30156--30191 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
30146 TGAAGATTTC
30156 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
30175 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
30192 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Done.