Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015027.1 Corchorus olitorius cultivar O-4 contig15060, 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: 38169
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:3591 original size:32 final size:32
Alignment explanation
Indices: 3550--3612 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
3540 TGAATTTCTT
3550 AAAATTAAAAAGT-CATGTTCATACAATTGCCG
1 AAAATT-AAAAGTCCATGTTCATACAATTGCCG
* *
3582 AAAATTAAAATTCCATGTTCATACAGTTGCC
1 AAAATTAAAAGTCCATGTTCATACAATTGCC
3613 AGCACCTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 5 0.18
32 23 0.82
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.30
Consensus pattern (32 bp):
AAAATTAAAAGTCCATGTTCATACAATTGCCG
Found at i:16627 original size:22 final size:22
Alignment explanation
Indices: 16602--16644 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
16592 TTTCTTTTTT
*
16602 TTTTTAGTTTGACTTT-ATTTAG
1 TTTTAAGTTTGA-TTTGATTTAG
16624 TTTTAAGTTTGATTTGATTTA
1 TTTTAAGTTTGATTTGATTTA
16645 CTGAGTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.21, C:0.02, G:0.14, T:0.63
Consensus pattern (22 bp):
TTTTAAGTTTGATTTGATTTAG
Found at i:16708 original size:25 final size:27
Alignment explanation
Indices: 16664--16725 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 27
16654 TTATGTAAAT
16664 TTATATAATAATATAAATAT-ATT-TATTA
1 TTATAT-ATAATAT-AATATGATTATA-TA
16692 TTATATATAATAT-ATATGATTATCATA
1 TTATATATAATATAATATGATTAT-ATA
16719 TTATATA
1 TTATATA
16726 CTTAATGTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
25 4 0.13
26 3 0.10
27 17 0.55
28 7 0.23
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (27 bp):
TTATATATAATATAATATGATTATATA
Found at i:16713 original size:22 final size:20
Alignment explanation
Indices: 16674--16719 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
16664 TTATATAATA
* *
16674 ATATAAATATATTTATTATT
1 ATATAAATATATTGATTATC
16694 ATATATAATATATATGATTATC
1 ATATA-AATATAT-TGATTATC
16716 ATAT
1 ATAT
16720 TATATACTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 5 0.23
21 7 0.32
22 10 0.45
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (20 bp):
ATATAAATATATTGATTATC
Found at i:22636 original size:109 final size:109
Alignment explanation
Indices: 22443--22662 Score: 327
Period size: 109 Copynumber: 2.0 Consensus size: 109
22433 ACTTACGCAT
*
22443 TTAAGGTGCCTTGCATACTCGTAATTTTGGATAGTGACTGACGCGACAGTTGATATTTGTGATAC
1 TTAAGGTGCCTTGCATACTCATAATTTTGGATAGTGACTGACGCGACAGTTGATATTTGTGATAC
*
22508 CGAACCCCGTGTGCTCCACTTCCCAAAAACAGAGGAGTAATTTA
66 CGAACCCCGAGTGCTCCACTTCCCAAAAACAGAGGAGTAATTTA
* * * *
22552 TTAAGGTGCTTTGCATACTCATAATTTTGGGTCGTGACTGACGCGGA-TGTTGATATTTGTGATA
1 TTAAGGTGCCTTGCATACTCATAATTTTGGATAGTGACTGACGC-GACAGTTGATATTTGTGATA
* * *
22616 CCGAACCCCGAGT-ATCCCACTTCCCAAAAACAGCGGAGTAGTTTA
65 CCGAACCCCGAGTGCT-CCACTTCCCAAAAACAGAGGAGTAATTTA
22661 TT
1 TT
22663 GAATTCCCTC
Statistics
Matches: 100, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
108 1 0.01
109 97 0.97
110 2 0.02
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.30
Consensus pattern (109 bp):
TTAAGGTGCCTTGCATACTCATAATTTTGGATAGTGACTGACGCGACAGTTGATATTTGTGATAC
CGAACCCCGAGTGCTCCACTTCCCAAAAACAGAGGAGTAATTTA
Found at i:29986 original size:16 final size:16
Alignment explanation
Indices: 29967--30018 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
29957 AATTAAATTC
29967 AAAATATATGAAATAA
1 AAAATATATGAAATAA
* * **
29983 AAAA-ATTTTAAATTC
1 AAAATATATGAAATAA
29998 AAAATATATGAAATAA
1 AAAATATATGAAATAA
30014 AAAAT
1 AAAAT
30019 TTTAAATTCA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
15 11 0.41
16 16 0.59
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (16 bp):
AAAATATATGAAATAA
Found at i:30001 original size:14 final size:14
Alignment explanation
Indices: 29984--30032 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
29974 ATGAAATAAA
29984 AAAATTTTAAATTC
1 AAAATTTTAAATTC
* **
29998 AAAATATATGAAATAA
1 AAAAT-T-TTAAATTC
30014 AAAATTTTAAATTC
1 AAAATTTTAAATTC
30028 AAAAT
1 AAAAT
30033 ATAGCCATTT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
14 15 0.56
15 2 0.07
16 10 0.37
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (14 bp):
AAAATTTTAAATTC
Found at i:30018 original size:30 final size:31
Alignment explanation
Indices: 29959--30035 Score: 147
Period size: 30 Copynumber: 2.5 Consensus size: 31
29949 AGTTAATTAA
29959 TTAAATTCAAAATATATGAAATAAAAAAATT
1 TTAAATTCAAAATATATGAAATAAAAAAATT
29990 TTAAATTCAAAATATATGAAAT-AAAAAATT
1 TTAAATTCAAAATATATGAAATAAAAAAATT
30020 TTAAATTCAAAATATA
1 TTAAATTCAAAATATA
30036 GCCATTTAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
30 24 0.52
31 22 0.48
ACGTcount: A:0.60, C:0.04, G:0.03, T:0.34
Consensus pattern (31 bp):
TTAAATTCAAAATATATGAAATAAAAAAATT
Found at i:32181 original size:48 final size:48
Alignment explanation
Indices: 32121--32216 Score: 167
Period size: 48 Copynumber: 2.0 Consensus size: 48
32111 GCATTCTGAT
32121 GATCATTGTTTCAATGATGTTCTGTTCTGTCGTACT-AATCATTGGGAA
1 GATCATTGTTTCAATGATGTTCTGTTCTGTCGTACTGAA-CATTGGGAA
*
32169 GATCGTTGTTTCAATGATGTTCTGTTCTGTCGTACTGAACATTGGGAA
1 GATCATTGTTTCAATGATGTTCTGTTCTGTCGTACTGAACATTGGGAA
32217 AGTTTCTGTT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
48 44 0.96
49 2 0.04
ACGTcount: A:0.22, C:0.15, G:0.23, T:0.41
Consensus pattern (48 bp):
GATCATTGTTTCAATGATGTTCTGTTCTGTCGTACTGAACATTGGGAA
Done.