Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010004.1 Corchorus capsularis cultivar CVL-1 contig10025, 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: 48508
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Found at i:27194 original size:31 final size:31
Alignment explanation
Indices: 27152--27239 Score: 131
Period size: 31 Copynumber: 2.8 Consensus size: 31
27142 CATGATTACT
* *
27152 CACCAAAAGGTATATCGTAAATACTCCCTACC
1 CACC-AAAGGTATACCGTAAATACTCCATACC
27184 CACCAAAGGTATACCGTAAATACTCCATACC
1 CACCAAAGGTATACCGTAAATACTCCATACC
* *
27215 CACCAAAGGTATAGCGTAAACACTC
1 CACCAAAGGTATACCGTAAATACTC
27240 ACCAAGTATT
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
31 48 0.92
32 4 0.08
ACGTcount: A:0.39, C:0.31, G:0.11, T:0.19
Consensus pattern (31 bp):
CACCAAAGGTATACCGTAAATACTCCATACC
Found at i:29710 original size:7 final size:7
Alignment explanation
Indices: 29698--29724 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
29688 AGTTGAGGAG
29698 TGTATCA
1 TGTATCA
29705 TGTATCA
1 TGTATCA
29712 TGTATCA
1 TGTATCA
29719 TGTATC
1 TGTATC
29725 TACAGCTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (7 bp):
TGTATCA
Found at i:32039 original size:60 final size:60
Alignment explanation
Indices: 31946--32105 Score: 216
Period size: 60 Copynumber: 2.7 Consensus size: 60
31936 CTAATTGCTT
* *
31946 AAATAAGAACCTAACATTTGTC-AAAATGCTCAAATAAGGGCCCT-ATCTTTGAATTTGGAC
1 AAATAAGAGCCTAACA-TTATCGAAAATGCTCAAATAAGGG-CCTGATCTTTGAATTTGGAC
* * *
32006 AAATAAGCGCCTAACATTATCGAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGCC
1 AAATAAGAGCCTAACATTATCGAAAATGCTCAAATAAGGGCCTGATCTTTGAATTTGGAC
* * *
32066 GAATAAGAGCCGAACGTTATCGAAAATGCTCAAATAAGGG
1 AAATAAGAGCCTAACATTATCGAAAATGCTCAAATAAGGG
32106 TCTGGTGTCA
Statistics
Matches: 89, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
59 7 0.08
60 82 0.92
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (60 bp):
AAATAAGAGCCTAACATTATCGAAAATGCTCAAATAAGGGCCTGATCTTTGAATTTGGAC
Found at i:32209 original size:60 final size:60
Alignment explanation
Indices: 32135--32360 Score: 310
Period size: 60 Copynumber: 3.8 Consensus size: 60
32125 ACGCGTGAGA
* * * *
32135 CAGGCCCTTATTTGAGCATTTTGGTAAACATTATG-CCCTTATTTGGCCAAATTCAAAGAT
1 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTA-GACCCTTATTTGACCAAATTAAAAGAT
* * *
32195 GAGGCCCTTATTTGAGTATTTTGGCAAACGTTAGACCCTTATTTGATCAAATTAAAAGAT
1 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGACCCTTATTTGACCAAATTAAAAGAT
* *
32255 CAGACCCTTATTTGAGCATTTTGGCAAATGTTAGACCCTTATTTGACCAAATTAAAAGAT
1 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGACCCTTATTTGACCAAATTAAAAGAT
* ** * *
32315 CATGTTCTTATTTGAACATTTTAGCAAACGTTAGACCCTTATTTGA
1 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGACCCTTATTTGA
32361 ACAATTAGCC
Statistics
Matches: 146, Mismatches: 19, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
59 1 0.01
60 145 0.99
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.36
Consensus pattern (60 bp):
CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGACCCTTATTTGACCAAATTAAAAGAT
Found at i:32266 original size:29 final size:29
Alignment explanation
Indices: 32227--32316 Score: 92
Period size: 29 Copynumber: 3.0 Consensus size: 29
32217 GGCAAACGTT
*
32227 AGACCCTTATTTGATCAAATTAAAAGATC
1 AGACCCTTATTTGACCAAATTAAAAGATC
* ** * *
32256 AGACCCTTATTTGAGCATTTTGGCAAATG-TT
1 AGACCCTTATTTGACCAAATT---AAAAGATC
32287 AGACCCTTATTTGACCAAATTAAAAGATC
1 AGACCCTTATTTGACCAAATTAAAAGATC
32316 A
1 A
32317 TGTTCTTATT
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
28 4 0.09
29 20 0.43
31 19 0.40
32 4 0.09
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (29 bp):
AGACCCTTATTTGACCAAATTAAAAGATC
Found at i:32359 original size:31 final size:30
Alignment explanation
Indices: 32199--32363 Score: 106
Period size: 31 Copynumber: 5.5 Consensus size: 30
32189 AAAGATGAGG
** *
32199 CCCTTATTTGAGTATTTTGGCAAACGTTAGA
1 CCCTTATTTGAACATTTTAGCAAA-GTTAGA
* ** *
32230 CCCTTATTTGATCAAATTA--AAAGATCAGA
1 CCCTTATTTGAACATTTTAGCAAAG-TTAGA
* *
32259 CCCTTATTTGAGCATTTTGGCAAATGTTAGA
1 CCCTTATTTGAACATTTTAGCAAA-GTTAGA
* ** *
32290 CCCTTATTTGACCAAATTA--AAAGATCATG-
1 CCCTTATTTGAACATTTTAGCAAAG-TTA-GA
**
32319 TTCTTATTTGAACATTTTAGCAAACGTTAGA
1 CCCTTATTTGAACATTTTAGCAAA-GTTAGA
32350 CCCTTATTTGAACA
1 CCCTTATTTGAACA
32364 ATTAGCCAAA
Statistics
Matches: 100, Mismatches: 24, Indels: 20
0.69 0.17 0.14
Matches are distributed among these distances:
28 2 0.02
29 41 0.41
30 2 0.02
31 53 0.53
32 2 0.02
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (30 bp):
CCCTTATTTGAACATTTTAGCAAAGTTAGA
Found at i:44363 original size:17 final size:17
Alignment explanation
Indices: 44338--44389 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 17
44328 TTTTAAATAC
44338 TTTTCTTTTATGATTAA
1 TTTTCTTTTATGATTAA
* * **
44355 TTTTTTTTTCTGAAGAA
1 TTTTCTTTTATGATTAA
44372 TTTTCTTTTATGATTAA
1 TTTTCTTTTATGATTAA
44389 T
1 T
44390 GATTAAATAA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.23, C:0.06, G:0.08, T:0.63
Consensus pattern (17 bp):
TTTTCTTTTATGATTAA
Found at i:44899 original size:2 final size:2
Alignment explanation
Indices: 44892--44921 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
44882 AGAAGAAGAA
44892 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44922 TTGATTAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.