Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01003762.1 Corchorus capsularis cultivar CVL-1 contig03770, 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, 783
Length: 1306
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:411 original size:17 final size:16
Alignment explanation
Indices: 385--418 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
375 TAGACACCCG
385 TATTTTATTATTTTTT
1 TATTTTATTATTTTTT
401 TATTATTATTATTTTTT
1 TATT-TTATTATTTTTT
418 T
1 T
419 TATAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (16 bp):
TATTTTATTATTTTTT
Found at i:644 original size:41 final size:38
Alignment explanation
Indices: 432--970 Score: 245
Period size: 41 Copynumber: 13.6 Consensus size: 38
422 AAAAAAAAAG
**
432 AAGAAGGCCAACCGATGCCAACTTTGGAAAC--TCGTT
1 AAGAAGGCCAACCGATGCCAACTTTGGAAACTTTTTTT
* * *
468 -ACAAGGCCAACCGATACCAACTTTGGAAA-TTCGATTTTA
1 AAGAAGGCCAACCGATGCCAACTTTGGAAACTT---TTTTT
* * **
507 AAGAAGGCCAACTGATGCCGACTATTATAAAACTTGATTTTT
1 AAGAAGGCCAACCGATGCCAACT-TT-GGAAACTT--TTTTT
* * * * * *
549 AGAGAAGGCCAACAGATACCGACTCTGAAAAC-ATTTTT
1 A-AGAAGGCCAACCGATGCCAACTTTGGAAACTTTTTTT
*
587 -AGAAGGCCAACCGATGCCAACATTTGGATACTTTTTCTT
1 AAGAAGGCCAACCGATGCCAAC-TTTGGAAACTTTTT-TT
* * *
626 CAAGAAGGCCAACCGATGCCAACTTTTGAAAATTCAATTTTA
1 -AAGAAGGCCAACCGATGCCAACTTTGGAAACTT---TTTTT
* * **
668 AAGAAGGCCAACTGATGCCGACTTTTATAAAACTTGATTTTT
1 AAGAAGGCCAACCGATGCCAAC-TTT-GGAAACTT--TTTTT
* * * * * *
710 AGAGAAGGCCAACAGATACCGACTCT-GAAAATATTTTT
1 A-AGAAGGCCAACCGATGCCAACTTTGGAAACTTTTTTT
* *
748 -AGAAGGCCAACCGATGCTGATA-TTTGGATACTTTTTCTT
1 AAGAAGGCCAACCGATGC-CA-ACTTTGGAAACTTTTT-TT
* * *
787 CAAGAAGGCCAACCGATGCCAACTTTTGAAAATTCGATTTTA
1 -AAGAAGGCCAACCGATGCCAACTTTGGAAACTT---TTTTT
* * ** *
829 AAGAAGGCCAACTGATGCCGACTTTTATAGAACTCGATTTTTG
1 AAGAAGGCCAACCGATGCCAAC-TTTGGA-AACT---TTTTTT
* * * * * * ** *
872 GAGAAGGTCAACAGATACCGACTCTAAAAAC-ATTTTT
1 AAGAAGGCCAACCGATGCCAACTTTGGAAACTTTTTTT
* *
909 -AGAAGGCCAATCGATGCCAACATTTGGATACTTTTTCTT
1 AAGAAGGCCAACCGATGCCAAC-TTTGGAAACTTTTT-TT
948 CAAGAAGGCCAACCGATGCCAAC
1 -AAGAAGGCCAACCGATGCCAAC
971 GCTTGAAAGA
Statistics
Matches: 384, Mismatches: 78, Indels: 77
0.71 0.14 0.14
Matches are distributed among these distances:
35 27 0.07
36 49 0.13
37 17 0.04
38 24 0.06
39 9 0.02
40 39 0.10
41 108 0.28
42 32 0.08
43 78 0.20
46 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (38 bp):
AAGAAGGCCAACCGATGCCAACTTTGGAAACTTTTTTT
Found at i:682 original size:161 final size:161
Alignment explanation
Indices: 470--970 Score: 869
Period size: 161 Copynumber: 3.1 Consensus size: 161
460 AACTCGTTAC
* * *
470 AAGGCCAACCGATACCAAC-TTTGGAAATTCGATTTTAAAGAAGGCCAACTGATGCCGACTATTA
1 AAGGCCAACCGATGCCAACTTTTGAAAATTCGATTTTAAAGAAGGCCAACTGATGCCGACTTTTA
534 TAAAACTTGATTTTTAGAGAAGGCCAACAGATACCGACTCTGAAAACATTTTTAGAAGGCCAACC
66 TAAAACTTGATTTTTAGAGAAGGCCAACAGATACCGACTCTGAAAACATTTTTAGAAGGCCAACC
599 GATGCCAACATTTGGATACTTTTTCTTCAAG
131 GATGCCAACATTTGGATACTTTTTCTTCAAG
*
630 AAGGCCAACCGATGCCAACTTTTGAAAATTCAATTTTAAAGAAGGCCAACTGATGCCGACTTTTA
1 AAGGCCAACCGATGCCAACTTTTGAAAATTCGATTTTAAAGAAGGCCAACTGATGCCGACTTTTA
*
695 TAAAACTTGATTTTTAGAGAAGGCCAACAGATACCGACTCTGAAAATATTTTTAGAAGGCCAACC
66 TAAAACTTGATTTTTAGAGAAGGCCAACAGATACCGACTCTGAAAACATTTTTAGAAGGCCAACC
** *
760 GATGCTGATATTTGGATACTTTTTCTTCAAG
131 GATGCCAACATTTGGATACTTTTTCTTCAAG
791 AAGGCCAACCGATGCCAACTTTTGAAAATTCGATTTTAAAGAAGGCCAACTGATGCCGACTTTTA
1 AAGGCCAACCGATGCCAACTTTTGAAAATTCGATTTTAAAGAAGGCCAACTGATGCCGACTTTTA
* * * * * *
856 TAGAACTCGATTTTTGGAGAAGGTCAACAGATACCGACTCTAAAAACATTTTTAGAAGGCCAATC
66 TAAAACTTGATTTTTAGAGAAGGCCAACAGATACCGACTCTGAAAACATTTTTAGAAGGCCAACC
921 GATGCCAACATTTGGATACTTTTTCTTCAAG
131 GATGCCAACATTTGGATACTTTTTCTTCAAG
952 AAGGCCAACCGATGCCAAC
1 AAGGCCAACCGATGCCAAC
971 GCTTGAAAGA
Statistics
Matches: 321, Mismatches: 19, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
160 18 0.06
161 303 0.94
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (161 bp):
AAGGCCAACCGATGCCAACTTTTGAAAATTCGATTTTAAAGAAGGCCAACTGATGCCGACTTTTA
TAAAACTTGATTTTTAGAGAAGGCCAACAGATACCGACTCTGAAAACATTTTTAGAAGGCCAACC
GATGCCAACATTTGGATACTTTTTCTTCAAG
Done.