Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015717.1 Corchorus olitorius cultivar O-4 contig15750, 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: 41136
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:9329 original size:38 final size:38
Alignment explanation
Indices: 9278--9353 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
9268 TCCTCTATGT
9278 TCTGGTTCAGAGTCACAAGCTTGATGCATCTAGGGGAA
1 TCTGGTTCAGAGTCACAAGCTTGATGCATCTAGGGGAA
9316 TCTGGTTCAGAGTCACAAGCTTGATGCATCTAGGGGAA
1 TCTGGTTCAGAGTCACAAGCTTGATGCATCTAGGGGAA
9354 ACAAATGCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.26
Consensus pattern (38 bp):
TCTGGTTCAGAGTCACAAGCTTGATGCATCTAGGGGAA
Found at i:10004 original size:24 final size:24
Alignment explanation
Indices: 9971--10056 Score: 147
Period size: 24 Copynumber: 3.6 Consensus size: 24
9961 GTACACGCAA
9971 TTTCATTTTCCGGGGCATTGCCAT
1 TTTCATTTTCCGGGGCATTGCCAT
*
9995 TTTCGA-TTTCCGGGGCGTTGCCAT
1 TTTC-ATTTTCCGGGGCATTGCCAT
10019 TTTCATTTTCCGGGGCATTGCCAT
1 TTTCATTTTCCGGGGCATTGCCAT
10043 TTTCATTTTCCGGG
1 TTTCATTTTCCGGG
10057 AATTCAGAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
23 1 0.02
24 56 0.97
25 1 0.02
ACGTcount: A:0.10, C:0.24, G:0.23, T:0.42
Consensus pattern (24 bp):
TTTCATTTTCCGGGGCATTGCCAT
Found at i:11855 original size:15 final size:15
Alignment explanation
Indices: 11835--11867 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
11825 AGGGAGTGAG
11835 ATCATAATTAATATT
1 ATCATAATTAATATT
11850 ATCATAATTAATATT
1 ATCATAATTAATATT
11865 ATC
1 ATC
11868 TAACCAGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (15 bp):
ATCATAATTAATATT
Found at i:15646 original size:19 final size:19
Alignment explanation
Indices: 15622--15662 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
15612 ACATCTTTTT
*
15622 ATAAAAGCGTTGGAGAAGG
1 ATAAAAGCATTGGAGAAGG
15641 ATAAAAGCATTGGAGAAGG
1 ATAAAAGCATTGGAGAAGG
15660 ATA
1 ATA
15663 TGAATTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.46, C:0.05, G:0.32, T:0.17
Consensus pattern (19 bp):
ATAAAAGCATTGGAGAAGG
Found at i:20266 original size:283 final size:285
Alignment explanation
Indices: 19753--20321 Score: 1070
Period size: 283 Copynumber: 2.0 Consensus size: 285
19743 AGAGGGGAGT
19753 AATGATACAAGCTGCTACGTTTTACTATAATAATTAGTTAATTTTCTTTAAGTTATTTTGTTTCA
1 AATGATACAAGCTGCTACGTTTTACTATAATAATTAGTTAATTTTCTTTAAGTTATTTTGTTTCA
19818 GTTATTTCCTTTTGCACAACTCTTGTTAGTGGCATGATTCTAGGCAATCACTCTAGGTAGTTATC
66 GTTATTTCCTTTTGCACAACTCTTGTTAGTGGCATGATTCTAGGCAATCACTCTAGGTAGTTATC
*
19883 CTTGAACACATCTCTTTATATACCCACGTTGTAAACTAGTTTGTAACAAGAAGTAATATTTTCTC
131 CTTGAACACATCTCTTTATATACCCACGTTGTAAACCAGTTTGTAACAAGAAGTAATATTTTCTC
*
19948 ATCTAAAATTTCTATTCTCTTCTTTCTTTGCTCTGTCCATCTATTTCTCCCTTTTTCTTTC-T-T
196 ATCTAAAATTTCTATTCTCTTCTTTCTTGGCTCTGTCCATCTATTTCTCCCTTTTTCTTTCTTCT
*
20011 AAATTTCCTTCATTCCTAACATTGG
261 AAATTTCCTTCATTCCAAACATTGG
*
20036 AATGATACAAGCTGCTGCGTTTTACTATAATAATTAGTTAATTTTCTTTAAGTTATTTTGTTTCA
1 AATGATACAAGCTGCTACGTTTTACTATAATAATTAGTTAATTTTCTTTAAGTTATTTTGTTTCA
20101 GTTATTTCCTTTTGCACAACTCTTGTTAGTGGCATGATTCTAGGCAATCACTCTAGGTAGTTATC
66 GTTATTTCCTTTTGCACAACTCTTGTTAGTGGCATGATTCTAGGCAATCACTCTAGGTAGTTATC
20166 CTTGAACACATCTCTTTATATACCCACGTTGTAAACCAGTTTGTAACAAGAAGTAATATTTTCTC
131 CTTGAACACATCTCTTTATATACCCACGTTGTAAACCAGTTTGTAACAAGAAGTAATATTTTCTC
*
20231 ATCTAAAATTTCTATTCTCTTCTTTCTTGGCTCTGTCCATCTATTTCTCTCTTTTTCTTTCTTCC
196 ATCTAAAATTTCTATTCTCTTCTTTCTTGGCTCTGTCCATCTATTTCTCCCTTTTTCTTTCTT-C
20296 TAAATTTCCTTCATTCCAAACATTGG
260 TAAATTTCCTTCATTCCAAACATTGG
20322 TGCTTTCATT
Statistics
Matches: 278, Mismatches: 5, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
283 252 0.91
284 1 0.00
286 25 0.09
ACGTcount: A:0.25, C:0.20, G:0.11, T:0.44
Consensus pattern (285 bp):
AATGATACAAGCTGCTACGTTTTACTATAATAATTAGTTAATTTTCTTTAAGTTATTTTGTTTCA
GTTATTTCCTTTTGCACAACTCTTGTTAGTGGCATGATTCTAGGCAATCACTCTAGGTAGTTATC
CTTGAACACATCTCTTTATATACCCACGTTGTAAACCAGTTTGTAACAAGAAGTAATATTTTCTC
ATCTAAAATTTCTATTCTCTTCTTTCTTGGCTCTGTCCATCTATTTCTCCCTTTTTCTTTCTTCT
AAATTTCCTTCATTCCAAACATTGG
Found at i:27107 original size:1 final size:1
Alignment explanation
Indices: 27096--27136 Score: 55
Period size: 1 Copynumber: 41.0 Consensus size: 1
27086 ACTCTGAAAC
* * *
27096 TTTTGTTTTTTTTTTGTTTTTGTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
27137 CAAAGGGAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (1 bp):
T
Found at i:27118 original size:17 final size:16
Alignment explanation
Indices: 27096--27136 Score: 66
Period size: 17 Copynumber: 2.6 Consensus size: 16
27086 ACTCTGAAAC
27096 TTTTGTTTTTTTTTTGT
1 TTTTGTTTTTTTTTT-T
27113 TTTTGTTTTTTTTTTT
1 TTTTGTTTTTTTTTTT
27129 TTTT-TTTT
1 TTTTGTTTT
27137 CAAAGGGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 4 0.17
16 5 0.21
17 15 0.62
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (16 bp):
TTTTGTTTTTTTTTTT
Found at i:37333 original size:2 final size:2
Alignment explanation
Indices: 37326--37364 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
37316 AGGGCGAATA
37326 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
37365 AACTTAGAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:37456 original size:13 final size:13
Alignment explanation
Indices: 37438--37469 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
37428 TGCTACATGA
37438 CCCTCCAACTTGT
1 CCCTCCAACTTGT
*
37451 CCCTCCAATTTGT
1 CCCTCCAACTTGT
37464 CCCTCC
1 CCCTCC
37470 TGACGTGTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.12, C:0.50, G:0.06, T:0.31
Consensus pattern (13 bp):
CCCTCCAACTTGT
Found at i:39348 original size:231 final size:231
Alignment explanation
Indices: 38965--39381 Score: 629
Period size: 231 Copynumber: 1.8 Consensus size: 231
38955 GAACCTTGTA
*
38965 GATCAAATTTAGCTTTCGGGGACTCCATGAAAGTCGTATATCACGCAATAACCTTTTAACCGACA
1 GATCAAATTTAGCTTTCGGGGACTCCATGAAAGTCGTAAATCACGCAATAACCTTTTAACCGACA
** * **
39030 CTTAAATAATTTTAATCGGACATGTGGATCCAAAATTATATGGTATTAAATAGACCAAAAATTGA
66 CTTAAATAACATTAATCGGACATGTGGATCCAAAATTATATGATATTAAATAGACCAAAAATCAA
*
39095 AACTACCAAATATGGGAAGCATTTTTTTCAATTGAAACATAAAAATTGGCTTTTGAACCCTTAAT
131 AACTACCAAATATCGGAAGCATTTTTTTCAATTGAAACATAAAAATTGGCTTTTGAACCCTTAAT
39160 GTTTGGCCAAAAAAAAAACCCTTAATGAAACTCATT
196 GTTTGGCCAAAAAAAAAACCCTTAATGAAACTCATT
** *
39196 GATCAAATTTAGCTTTCGGGTCCTCCATGAAAGTCGTAAATCATGCAATAACCTTTTAACCGACA
1 GATCAAATTTAGCTTTCGGGGACTCCATGAAAGTCGTAAATCACGCAATAACCTTTTAACCGACA
* * * * * ***
39261 CTTGAATAACATTAATCGGACTTGTGGATCGAAAATTATATGATATTTAATAGATCGGCAATCAA
66 CTTAAATAACATTAATCGGACATGTGGATCCAAAATTATATGATATTAAATAGACCAAAAATCAA
* * *
39326 AA-TCACCAAATTTCGGAAGCATTTTTTTGAATTGAAACATAAACATTGGCTTTTGA
131 AACT-ACCAAATATCGGAAGCATTTTTTTCAATTGAAACATAAAAATTGGCTTTTGA
39382 GTCCTTCATG
Statistics
Matches: 164, Mismatches: 21, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
230 1 0.01
231 163 0.99
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (231 bp):
GATCAAATTTAGCTTTCGGGGACTCCATGAAAGTCGTAAATCACGCAATAACCTTTTAACCGACA
CTTAAATAACATTAATCGGACATGTGGATCCAAAATTATATGATATTAAATAGACCAAAAATCAA
AACTACCAAATATCGGAAGCATTTTTTTCAATTGAAACATAAAAATTGGCTTTTGAACCCTTAAT
GTTTGGCCAAAAAAAAAACCCTTAATGAAACTCATT
Done.