Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018247.1 Corchorus olitorius cultivar O-4 contig18280, 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: 42282
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:4809 original size:59 final size:60
Alignment explanation
Indices: 4742--4862 Score: 226
Period size: 60 Copynumber: 2.0 Consensus size: 60
4732 TATTCTTAAA
4742 AAATAAATCCTTT-AAAAATACATTCTTAAATATCCTTCAAAAATAAATCATAGGGATGC
1 AAATAAATCCTTTAAAAAATACATTCTTAAATATCCTTCAAAAATAAATCATAGGGATGC
*
4801 AAATAAATCCTTTAAAAAATACATTCTTAAATATCCTTCAAAAATAAATCCTAGGGATGC
1 AAATAAATCCTTTAAAAAATACATTCTTAAATATCCTTCAAAAATAAATCATAGGGATGC
4861 AA
1 AA
4863 GTGGGTAGTA
Statistics
Matches: 60, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
59 13 0.22
60 47 0.78
ACGTcount: A:0.48, C:0.16, G:0.07, T:0.30
Consensus pattern (60 bp):
AAATAAATCCTTTAAAAAATACATTCTTAAATATCCTTCAAAAATAAATCATAGGGATGC
Found at i:12356 original size:54 final size:54
Alignment explanation
Indices: 12290--12401 Score: 224
Period size: 54 Copynumber: 2.1 Consensus size: 54
12280 AATTAGTAAA
12290 ATGGCAAATTAAGGTGGTGTTTGGAATGGGACGATTACTTAAAAATTAAAATCC
1 ATGGCAAATTAAGGTGGTGTTTGGAATGGGACGATTACTTAAAAATTAAAATCC
12344 ATGGCAAATTAAGGTGGTGTTTGGAATGGGACGATTACTTAAAAATTAAAATCC
1 ATGGCAAATTAAGGTGGTGTTTGGAATGGGACGATTACTTAAAAATTAAAATCC
12398 ATGG
1 ATGG
12402 TAATCTACAC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.37, C:0.09, G:0.25, T:0.29
Consensus pattern (54 bp):
ATGGCAAATTAAGGTGGTGTTTGGAATGGGACGATTACTTAAAAATTAAAATCC
Found at i:15297 original size:33 final size:33
Alignment explanation
Indices: 15255--15355 Score: 202
Period size: 33 Copynumber: 3.1 Consensus size: 33
15245 TTTCTTGTAA
15255 ATTTCAGCAATTATTCATTGCTTGTGAATTGTG
1 ATTTCAGCAATTATTCATTGCTTGTGAATTGTG
15288 ATTTCAGCAATTATTCATTGCTTGTGAATTGTG
1 ATTTCAGCAATTATTCATTGCTTGTGAATTGTG
15321 ATTTCAGCAATTATTCATTGCTTGTGAATTGTG
1 ATTTCAGCAATTATTCATTGCTTGTGAATTGTG
15354 AT
1 AT
15356 ATGCTACTGT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 68 1.00
ACGTcount: A:0.25, C:0.12, G:0.18, T:0.46
Consensus pattern (33 bp):
ATTTCAGCAATTATTCATTGCTTGTGAATTGTG
Found at i:16711 original size:127 final size:127
Alignment explanation
Indices: 16485--16726 Score: 351
Period size: 127 Copynumber: 1.9 Consensus size: 127
16475 TAAAAGTTAA
* * * * *
16485 CAACATAAATTGTTAGATTTCGATTAATCAAAATCATCATAAGGAGATTTCAGAAGATTTTTTGT
1 CAACATAAATTCTAAGATTTAGATTAATCAAAATCATCATAAGGAGATTTCAGAAGAGTTTCTGT
* * * * * *
16550 TATATTTTTCTTGTTCAGGTATTCTGAGCTTTGTGCAACATATCAAGGCCGACCCTATATGG
66 TACACTGTCCTTGTTAAGGTATGCTGAGCTTTGTGCAACATATCAAGGCCGACCCTATATGG
*
16612 CAACATAAATTCTAAGATTTAGATTAATCAAAATTATCATAAGGAGATTTCA-AGAGAGTTTCTG
1 CAACATAAATTCTAAGATTTAGATTAATCAAAATCATCATAAGGAGATTTCAGA-AGAGTTTCTG
*
16676 TTACACTGTCCTTGTTAAGTTATGCTGAGCTTTGTGCAACATATCAAGGCC
65 TTACACTGTCCTTGTTAAGGTATGCTGAGCTTTGTGCAACATATCAAGGCC
16727 AATCTCATAT
Statistics
Matches: 101, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
126 1 0.01
127 100 0.99
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (127 bp):
CAACATAAATTCTAAGATTTAGATTAATCAAAATCATCATAAGGAGATTTCAGAAGAGTTTCTGT
TACACTGTCCTTGTTAAGGTATGCTGAGCTTTGTGCAACATATCAAGGCCGACCCTATATGG
Found at i:30049 original size:15 final size:15
Alignment explanation
Indices: 30029--30060 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
30019 TTACATTGTA
30029 TTTGAGCTACTTATC
1 TTTGAGCTACTTATC
30044 TTTGAGCTACTTATC
1 TTTGAGCTACTTATC
30059 TT
1 TT
30061 GCAAGTTACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.19, G:0.12, T:0.50
Consensus pattern (15 bp):
TTTGAGCTACTTATC
Found at i:30081 original size:27 final size:27
Alignment explanation
Indices: 30051--30102 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
30041 ATCTTTGAGC
* *
30051 TACTTATCTTGCAAGTTACTTTAAGAT
1 TACTTATCTTACAAGTTACTCTAAGAT
*
30078 TACTTATCTTATAAGTTACTCTAAG
1 TACTTATCTTACAAGTTACTCTAAG
30103 CCAAAATCTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (27 bp):
TACTTATCTTACAAGTTACTCTAAGAT
Found at i:33095 original size:14 final size:14
Alignment explanation
Indices: 33076--33102 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
33066 TTTTATAATT
33076 ATTTTATTTTTACC
1 ATTTTATTTTTACC
33090 ATTTTATTTTTAC
1 ATTTTATTTTTAC
33103 TATATTAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (14 bp):
ATTTTATTTTTACC
Found at i:34387 original size:41 final size:44
Alignment explanation
Indices: 34310--34393 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
34300 GCTAGAAGAA
*
34310 GCAAAATTTTCCTTTTGTTCTTTTTTTTATCGTTGCTCTTCTGG
1 GCAAAATTTTCCTTTTGTTCTTTTGTTTATCGTTGCTCTTCTGG
*
34354 GCAAAATTTTCCTTTTG-T-TTTTGTTT-TCGTTGCTTTTCTG
1 GCAAAATTTTCCTTTTGTTCTTTTGTTTATCGTTGCTCTTCTG
34394 AACTGGGTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
41 13 0.34
42 7 0.18
43 1 0.03
44 17 0.45
ACGTcount: A:0.11, C:0.17, G:0.14, T:0.58
Consensus pattern (44 bp):
GCAAAATTTTCCTTTTGTTCTTTTGTTTATCGTTGCTCTTCTGG
Found at i:35399 original size:16 final size:16
Alignment explanation
Indices: 35378--35409 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
35368 GACCTTACTC
35378 ACCTTGTGTAGCTATT
1 ACCTTGTGTAGCTATT
35394 ACCTTGTGTAGCTATT
1 ACCTTGTGTAGCTATT
35410 GCCGTGTACG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.44
Consensus pattern (16 bp):
ACCTTGTGTAGCTATT
Found at i:41157 original size:44 final size:45
Alignment explanation
Indices: 41094--41184 Score: 148
Period size: 48 Copynumber: 2.0 Consensus size: 45
41084 ATAATGAGAT
41094 TAAAATTGATGTTGC-ATATATATCACGTTAGTAATTAGTTTATA
1 TAAAATTGATGTTGCAATATATATCACGTTAGTAATTAGTTTATA
41138 TAAAATTGATGTTGCATATATATATATCACGTTAGTAATTAGTTTAT
1 TAAAATTGATGTTGC--A-ATATATATCACGTTAGTAATTAGTTTAT
41185 CATGCATATG
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
44 15 0.35
48 28 0.65
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (45 bp):
TAAAATTGATGTTGCAATATATATCACGTTAGTAATTAGTTTATA
Done.