Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018945.1 Corchorus olitorius cultivar O-4 contig18978, 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: 21973
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:4825 original size:4 final size:4
Alignment explanation
Indices: 4816--4841 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
4806 AGTTGGCGGT
4816 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
4842 CACATTTCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:9095 original size:1 final size:1
Alignment explanation
Indices: 9089--9124 Score: 63
Period size: 1 Copynumber: 36.0 Consensus size: 1
9079 AGATACGAGA
*
9089 TTTTTTTTTTTTTTTATTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
9125 AAATTTATGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.03, C:0.00, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:15468 original size:15 final size:15
Alignment explanation
Indices: 15448--15478 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
15438 CATGAAGTTG
15448 AGGTTTTAGGCTTTA
1 AGGTTTTAGGCTTTA
15463 AGGTTTTAGGCTTTA
1 AGGTTTTAGGCTTTA
15478 A
1 A
15479 AGAAAACTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.06, G:0.26, T:0.45
Consensus pattern (15 bp):
AGGTTTTAGGCTTTA
Found at i:15614 original size:31 final size:31
Alignment explanation
Indices: 15576--15634 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
15566 GATCATTTTC
15576 AAATAAATAATGTTTCACGCACAAACGCATA
1 AAATAAATAATGTTTCACGCACAAACGCATA
**
15607 AAATAAATAATGTTTCGTGCACAAACGC
1 AAATAAATAATGTTTCACGCACAAACGC
15635 GCAAAATTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.24
Consensus pattern (31 bp):
AAATAAATAATGTTTCACGCACAAACGCATA
Found at i:15641 original size:31 final size:31
Alignment explanation
Indices: 15576--15641 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
15566 GATCATTTTC
*
15576 AAATAAATAATGTTTCACGCACAAACGCATA
1 AAATAAATAATGTTTCACGCACAAACGCACA
** *
15607 AAATAAATAATGTTTCGTGCACAAACGCGCA
1 AAATAAATAATGTTTCACGCACAAACGCACA
15638 AAAT
1 AAAT
15642 TGTAAATTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.23
Consensus pattern (31 bp):
AAATAAATAATGTTTCACGCACAAACGCACA
Found at i:16161 original size:22 final size:22
Alignment explanation
Indices: 16130--16362 Score: 168
Period size: 22 Copynumber: 10.6 Consensus size: 22
16120 TCCAACGTAG
*
16130 AAATATTGATAACCACACTGTGA
1 AAAT-TTGATAACCACACTATGA
* ** *
16153 AAATCTGATAACCTTATTAT-A
1 AAATTTGATAACCACACTATGA
**
16174 AAATTTCGATAACTTCACTATGA
1 AAATTT-GATAACCACACTATGA
* *
16197 AAATTTGATAACCACATTGTGA
1 AAATTTGATAACCACACTATGA
*
16219 AATTTTGATAACCACACTATGA
1 AAATTTGATAACCACACTATGA
* * * *
16241 AATTTTGATAACCTCAGTGTGA
1 AAATTTGATAACCACACTATGA
* * * *
16263 AATTTTGATAATCTCTCTATGA
1 AAATTTGATAACCACACTATGA
* **
16285 AATTTTGATAATTACACTAT--
1 AAATTTGATAACCACACTATGA
* * * *
16305 AAAGTTGGTAATCGCACTATGA
1 AAATTTGATAACCACACTATGA
*
16327 AAATTTTGATAACCACACCATG-
1 AAA-TTTGATAACCACACTATGA
16349 AAATTTCGATAACC
1 AAATTT-GATAACC
16363 TCCTAATTAT
Statistics
Matches: 168, Mismatches: 36, Indels: 13
0.77 0.17 0.06
Matches are distributed among these distances:
20 15 0.09
21 9 0.05
22 120 0.71
23 24 0.14
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (22 bp):
AAATTTGATAACCACACTATGA
Found at i:16244 original size:66 final size:64
Alignment explanation
Indices: 16130--16362 Score: 198
Period size: 66 Copynumber: 3.5 Consensus size: 64
16120 TCCAACGTAG
* * * ** *
16130 AAATATTGATAACCACACTGTGAAAATCTGATAACCTTATTATAAAATTTCGATAACTTCACTAT
1 AAAT-TTGATAACCACACTATGAAATTTTGATAACCACACTAT-AAATTT-GATAACTTCACTAT
16195 GA
63 GA
* * * * *
16197 AAATTTGATAACCACATTGTGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCAGTGTG
1 AAATTTGATAACCACACTATGAAATTTTGATAACCACACTAT-AAA-TTTGATAACTTCACTATG
16262 A
64 A
* * * * ** * * *
16263 AATTTTGATAATCTCTCTATGAAATTTTGATAATTACACTATAAAGTTGGTAA-TCGCACTATGA
1 AAATTTGATAACCACACTATGAAATTTTGATAACCACACTATAAATTTGATAACT-TCACTATGA
* *
16327 AAATTTTGATAACCACACCATGAAATTTCGATAACC
1 AAA-TTTGATAACCACACTATGAAATTTTGATAACC
16363 TCCTAATTAT
Statistics
Matches: 131, Mismatches: 32, Indels: 8
0.77 0.19 0.05
Matches are distributed among these distances:
64 14 0.11
65 28 0.21
66 82 0.63
67 7 0.05
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (64 bp):
AAATTTGATAACCACACTATGAAATTTTGATAACCACACTATAAATTTGATAACTTCACTATGA
Found at i:16582 original size:22 final size:22
Alignment explanation
Indices: 16507--16715 Score: 88
Period size: 22 Copynumber: 9.5 Consensus size: 22
16497 CCTCCCTCCC
* * **
16507 TATGAAATTTTGTTTACCTTTT
1 TATGAAATTTTGATAACCTTCA
* * *
16529 TATAAAATTTTGAAAACC-ACA
1 TATGAAATTTTGATAACCTTCA
*
16550 CTAT-AAATTTTGATAACCTTCG
1 -TATGAAATTTTGATAACCTTCA
* *
16572 TATGAAATTTTGTTAACCCCTC-
1 TATGAAATTTTGATAA-CCTTCA
* * * *
16594 TAAGAAATTTCGATAACTTTTA
1 TATGAAATTTTGATAACCTTCA
* ** * **
16616 TGTGAAATTTTGGCAACATTTG
1 TATGAAATTTTGATAACCTTCA
* * *
16638 TATGAAATCTTGATAATCTCCA
1 TATGAAATTTTGATAACCTTCA
*
16660 TATGAAACTTTTG-TAACC-ACA
1 TATGAAA-TTTTGATAACCTTCA
* *
16681 CTATGAAATTTT-ACTGACCTTCC
1 -TATGAAATTTTGA-TAACCTTCA
*
16704 TATGTAATTTTG
1 TATGAAATTTTG
16716 GTTTGATTGT
Statistics
Matches: 135, Mismatches: 41, Indels: 21
0.69 0.21 0.11
Matches are distributed among these distances:
21 24 0.18
22 102 0.76
23 9 0.07
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCA
Found at i:20498 original size:41 final size:41
Alignment explanation
Indices: 20435--20514 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
20425 ACTTGAGCCT
*
20435 CCTAATAATTAAGGAAATAAATTAAATCCAGGTTTAGCCCC
1 CCTAATAATTAAGGAAAGAAATTAAATCCAGGTTTAGCCCC
*
20476 CCTAATAATTAAGGTAAGAAATTAAATCCAGGTTTAGCC
1 CCTAATAATTAAGGAAAGAAATTAAATCCAGGTTTAGCC
20515 ACTAGTTATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (41 bp):
CCTAATAATTAAGGAAAGAAATTAAATCCAGGTTTAGCCCC
Done.