Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018460.1 Corchorus olitorius cultivar O-4 contig18493, 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: 86721
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:10708 original size:47 final size:47
Alignment explanation
Indices: 10639--10734 Score: 192
Period size: 47 Copynumber: 2.0 Consensus size: 47
10629 AGTCACAGAG
10639 TTTTTGATAGAATGTTGGATTCTTAGTTTCAGTGATCAAGATTCAAA
1 TTTTTGATAGAATGTTGGATTCTTAGTTTCAGTGATCAAGATTCAAA
10686 TTTTTGATAGAATGTTGGATTCTTAGTTTCAGTGATCAAGATTCAAA
1 TTTTTGATAGAATGTTGGATTCTTAGTTTCAGTGATCAAGATTCAAA
10733 TT
1 TT
10735 CTGATAATCT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.29, C:0.08, G:0.19, T:0.44
Consensus pattern (47 bp):
TTTTTGATAGAATGTTGGATTCTTAGTTTCAGTGATCAAGATTCAAA
Found at i:19071 original size:40 final size:40
Alignment explanation
Indices: 19016--19092 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
19006 TGATTGGTAG
* * *
19016 ACCGATGAGATTGGTTCAGTGGGAGTAAAATATATGATAA
1 ACCGATGAAATTGGTTCAATGAGAGTAAAATATATGATAA
* *
19056 ACCGATGAAATTGGTTCAATGAGAGTGAAATTTATGA
1 ACCGATGAAATTGGTTCAATGAGAGTAAAATATATGA
19093 AATATGTTAC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.38, C:0.08, G:0.26, T:0.29
Consensus pattern (40 bp):
ACCGATGAAATTGGTTCAATGAGAGTAAAATATATGATAA
Found at i:22493 original size:2 final size:2
Alignment explanation
Indices: 22486--22513 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
22476 AATCTCAAGA
22486 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
22514 TATTGAATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36970 original size:27 final size:27
Alignment explanation
Indices: 36940--36991 Score: 88
Period size: 27 Copynumber: 1.9 Consensus size: 27
36930 TGGAGAACCC
36940 TTTTCCTTTGGAGGTG-GAGGAGCTTCT
1 TTTTCCTTTGGAGGTGAG-GGAGCTTCT
36967 TTTTCCTTTGGAGGTGAGGGAGCTT
1 TTTTCCTTTGGAGGTGAGGGAGCTT
36992 TCGGCTGAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
27 23 0.96
28 1 0.04
ACGTcount: A:0.12, C:0.13, G:0.35, T:0.40
Consensus pattern (27 bp):
TTTTCCTTTGGAGGTGAGGGAGCTTCT
Found at i:41061 original size:42 final size:44
Alignment explanation
Indices: 41010--41103 Score: 115
Period size: 45 Copynumber: 2.2 Consensus size: 44
41000 AATGCATTAC
* *
41010 CTAA-ATTCTACT-T-CATCTTTAGGTAATAT-ATCAAAATAAAG
1 CTAATATTCTACTCTCCATCTCTAGATAAT-TCATCAAAATAAAG
*
41051 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAT
1 CTAATATTCTACT-CTCCATCTCTAGATAATTCATCAAAATAAAG
41096 CTAATATT
1 CTAATATT
41104 AATTGTTGTT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
41 4 0.09
42 8 0.18
44 2 0.04
45 31 0.69
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.37
Consensus pattern (44 bp):
CTAATATTCTACTCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:42085 original size:3 final size:3
Alignment explanation
Indices: 42072--42115 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
42062 TATAGTATAT
*
42072 ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
42116 TTATTATATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:46464 original size:14 final size:16
Alignment explanation
Indices: 46445--46480 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
46435 AAGATTTGGG
46445 TCCTTTTT-TTT-CTT
1 TCCTTTTTGTTTGCTT
46459 TCCTTTTTGTTTGCTT
1 TCCTTTTTGTTTGCTT
46475 TCCTTT
1 TCCTTT
46481 GCTTTTCATG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 8 0.40
15 3 0.15
16 9 0.45
ACGTcount: A:0.00, C:0.22, G:0.06, T:0.72
Consensus pattern (16 bp):
TCCTTTTTGTTTGCTT
Found at i:46903 original size:19 final size:20
Alignment explanation
Indices: 46868--46908 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
46858 TAATTTCATA
46868 TGTACAGTATCTAATCTAATC
1 TGTACAGTA-CTAATCTAATC
*
46889 TGTACAGTA-TAATCTCATC
1 TGTACAGTACTAATCTAATC
46908 T
1 T
46909 ATATAGTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
21 9 0.47
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.39
Consensus pattern (20 bp):
TGTACAGTACTAATCTAATC
Found at i:73272 original size:57 final size:57
Alignment explanation
Indices: 73184--73297 Score: 219
Period size: 57 Copynumber: 2.0 Consensus size: 57
73174 TGAGAGCCAT
73184 ATATATGACTTTGCATTCAATATACTGATCTTATAATCAAGATTTTACTAGGATTGA
1 ATATATGACTTTGCATTCAATATACTGATCTTATAATCAAGATTTTACTAGGATTGA
*
73241 ATATATGACTTTGCATTCAGTATACTGATCTTATAATCAAGATTTTACTAGGATTGA
1 ATATATGACTTTGCATTCAATATACTGATCTTATAATCAAGATTTTACTAGGATTGA
73298 GGTGCTCAAT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (57 bp):
ATATATGACTTTGCATTCAATATACTGATCTTATAATCAAGATTTTACTAGGATTGA
Done.