Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023111.1 Corchorus olitorius cultivar O-4 contig23144, 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: 23601
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:792 original size:23 final size:24
Alignment explanation
Indices: 765--809 Score: 83
Period size: 23 Copynumber: 1.9 Consensus size: 24
755 ATCCAAGTTT
765 AAAAAGTGAAA-CTTTTTTATCAA
1 AAAAAGTGAAATCTTTTTTATCAA
788 AAAAAGTGAAATCTTTTTTATC
1 AAAAAGTGAAATCTTTTTTATC
810 CTATGCTAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (24 bp):
AAAAAGTGAAATCTTTTTTATCAA
Found at i:3043 original size:31 final size:31
Alignment explanation
Indices: 2972--3031 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
2962 TTTTAACACA
* * *
2972 TGACATGCCACGTGTCTCTTTTTTGTATAAG
1 TGACATGCCACGTGTCCCTTTTTTATACAAG
3003 TGACATGCCACGTGTCCCTTTTTTATACA
1 TGACATGCCACGTGTCCCTTTTTTATACA
3032 CGTGGCGTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (31 bp):
TGACATGCCACGTGTCCCTTTTTTATACAAG
Found at i:3063 original size:31 final size:31
Alignment explanation
Indices: 3028--3099 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
3018 CCCTTTTTTA
*
3028 TACACGTGGCGTGCCATACATCA-TTTTTGGG
1 TACACGTGGCGTGCCACACATCACTTTTT-GG
* * **
3059 TACACATGGTGTGCCACATGTCACTTTTTGG
1 TACACGTGGCGTGCCACACATCACTTTTTGG
3090 TACACGTGGC
1 TACACGTGGC
3100 ATGTCACGTT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
31 28 0.85
32 5 0.15
ACGTcount: A:0.19, C:0.24, G:0.25, T:0.32
Consensus pattern (31 bp):
TACACGTGGCGTGCCACACATCACTTTTTGG
Found at i:4238 original size:22 final size:24
Alignment explanation
Indices: 4199--4243 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
4189 CATGTTTCTG
*
4199 TTTTATCCAACTCTACA-TATATT
1 TTTTAGCCAACTCTACATTATATT
*
4222 TTTTAGCCAAGTC-ACATTATAT
1 TTTTAGCCAACTCTACATTATAT
4244 ATTAGCATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.31, C:0.20, G:0.04, T:0.44
Consensus pattern (24 bp):
TTTTAGCCAACTCTACATTATATT
Found at i:7293 original size:23 final size:23
Alignment explanation
Indices: 7262--7305 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
7252 CTTAATTTGT
*
7262 AGTTCTTTATAAGTAGAAAGTGA
1 AGTTATTTATAAGTAGAAAGTGA
7285 AGTTATTTATAAGTAGAAAGT
1 AGTTATTTATAAGTAGAAAGT
7306 TCAGAGCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.41, C:0.02, G:0.20, T:0.36
Consensus pattern (23 bp):
AGTTATTTATAAGTAGAAAGTGA
Found at i:9093 original size:65 final size:65
Alignment explanation
Indices: 8955--9116 Score: 164
Period size: 65 Copynumber: 2.5 Consensus size: 65
8945 GTTCATAACT
* * * *
8955 GCCCTTTGAAATTTTGATAACCACTTATATTTTAATTTTGATAACCTCGATTGGAATCTTAACAA
1 GCCCTATGAAATTTTGATAACCA-TTAT-TTGTAATTTTAATAACCTCGATTGAAATCTTAACAA
*
9020 CT
64 CC
* * * * * *
9022 GCCCTAT-ATAATTATGATAACCATTCTTTGTAATTTTAATAACTTCTATTGAAATTTTGACAAC
1 GCCCTATGA-AATTTTGATAACCATTATTTGTAATTTTAATAACCTCGATTGAAATCTTAACAAC
9086 C
65 C
* * *
9087 GTCCTATGAAATTTTGATAACTATTGTTTG
1 GCCCTATGAAATTTTGATAACCATTATTTG
9117 AAAATTTGAA
Statistics
Matches: 78, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
65 54 0.69
66 5 0.06
67 19 0.24
ACGTcount: A:0.31, C:0.16, G:0.10, T:0.42
Consensus pattern (65 bp):
GCCCTATGAAATTTTGATAACCATTATTTGTAATTTTAATAACCTCGATTGAAATCTTAACAACC
Found at i:9118 original size:22 final size:22
Alignment explanation
Indices: 9031--9371 Score: 139
Period size: 22 Copynumber: 15.4 Consensus size: 22
9021 TGCCCTATAT
* *
9031 AATTATGATAACCATTC-TTTGT
1 AATTTTGATAACCA-TCATTTGA
* *
9053 AATTTTAATAA-CTTC-TATTGA
1 AATTTTGATAACCATCAT-TTGA
* * * *
9074 AATTTTGACAACCGTCCTATGA
1 AATTTTGATAACCATCATTTGA
* **
9096 AATTTTGATAACTATTGTTTGA
1 AATTTTGATAACCATCATTTGA
* * *
9118 AAATTTGAAAACCACCATTTGA
1 AATTTTGATAACCATCATTTGA
* *
9140 AATTTTGATAACCGGT-ATTTGT
1 AATTTTGATAACC-ATCATTTGA
*
9162 AATTTTGATAATC-TCGA-TTGA
1 AATTTTGATAACCATC-ATTTGA
** *
9183 AATTTTGATTGATAACTGTCCTATAT-A
1 AA--TT--TTGATAACCAT-C-ATTTGA
* * *
9210 AATTTTGATAACCACCATATGT
1 AATTTTGATAACCATCATTTGA
** *
9232 AATTTTGATAAAGA-CGCTTT-A
1 AATTTTGATAACCATC-ATTTGA
*
9253 TAATTTTGATAACCTAATCATATGA
1 -AATTTTGATAACC--ATCATTTGA
* * * *
9278 AATTTTGATAATCACCATATGT
1 AATTTTGATAACCATCATTTGA
*
9300 AATTTTGATAACC-TCATATGA
1 AATTTTGATAACCATCATTTGA
* * *
9321 AATTTCGGTAACCATCTTTTGA
1 AATTTTGATAACCATCATTTGA
*
9343 AATTTTGATAACC-TCCA-TTAA
1 AATTTTGATAACCAT-CATTTGA
9364 AATTTTGA
1 AATTTTGA
9372 AAAATACCTC
Statistics
Matches: 239, Mismatches: 58, Indels: 45
0.70 0.17 0.13
Matches are distributed among these distances:
20 4 0.02
21 52 0.22
22 139 0.58
23 11 0.05
24 15 0.06
25 11 0.05
26 1 0.00
27 5 0.02
28 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (22 bp):
AATTTTGATAACCATCATTTGA
Found at i:9284 original size:46 final size:44
Alignment explanation
Indices: 9204--9325 Score: 140
Period size: 46 Copynumber: 2.7 Consensus size: 44
9194 ATAACTGTCC
* * *
9204 TATATAAATTTTGATAACCACCATATGTAATTTTGATAAAGACGC-
1 TATAT-AATTTTGATAACCATCATATGAAATTTTGATAAACAC-CA
* *
9249 TTTATAATTTTGATAACCTAATCATATGAAATTTTGATAATCACCA
1 TATATAATTTTGATAACC--ATCATATGAAATTTTGATAAACACCA
*
9295 TATGTAATTTTGATAACC-TCATATGAAATTT
1 TATATAATTTTGATAACCATCATATGAAATTT
9326 CGGTAACCAT
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
43 13 0.19
44 13 0.19
45 5 0.07
46 36 0.54
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (44 bp):
TATATAATTTTGATAACCATCATATGAAATTTTGATAAACACCA
Found at i:9347 original size:43 final size:43
Alignment explanation
Indices: 9254--9357 Score: 118
Period size: 43 Copynumber: 2.3 Consensus size: 43
9244 GACGCTTTAT
* * *
9254 AATTTTGATAACCTAATCATATGAAATTTTGATAATCACCATATGT
1 AATTTTGATAACC---TCATATGAAATTTCGATAACCACCATATGA
* * * *
9300 AATTTTGATAACCTCATATGAAATTTCGGTAACCATCTTTTGA
1 AATTTTGATAACCTCATATGAAATTTCGATAACCACCATATGA
9343 AATTTTGATAACCTC
1 AATTTTGATAACCTC
9358 CATTAAAATT
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
43 38 0.75
46 13 0.25
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (43 bp):
AATTTTGATAACCTCATATGAAATTTCGATAACCACCATATGA
Done.