Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020281.1 Corchorus olitorius cultivar O-4 contig20314, 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: 5273
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Found at i:396 original size:28 final size:27
Alignment explanation
Indices: 364--416 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
354 AACTTTTTCA
*
364 ATATAATAATAATATTTTAAAATATTCT
1 ATATAATAATAAT-TTATAAAATATTCT
* *
392 ATATATTAATACTTTATAAAATATT
1 ATATAATAATAATTTATAAAATATT
417 TAATGTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 11 0.50
28 11 0.50
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (27 bp):
ATATAATAATAATTTATAAAATATTCT
Found at i:433 original size:25 final size:27
Alignment explanation
Indices: 364--433 Score: 72
Period size: 25 Copynumber: 2.6 Consensus size: 27
354 AACTTTTTCA
* *
364 ATATAATAATAATATTTTAAAATATTCT
1 ATATATTAATAA-ATTATAAAATATTCT
**
392 ATATATTAATACTTTATAAAATATT-T
1 ATATATTAATAAATTATAAAATATTCT
*
418 A-ATGTTAATAAATTAT
1 ATATATTAATAAATTAT
434 TTCTAGTCAT
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
25 12 0.34
26 2 0.06
27 11 0.31
28 10 0.29
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (27 bp):
ATATATTAATAAATTATAAAATATTCT
Found at i:3337 original size:55 final size:55
Alignment explanation
Indices: 3286--3392 Score: 137
Period size: 55 Copynumber: 1.9 Consensus size: 55
3276 CAAAAAAATT
*
3286 TCACTGTACATACA-TGGTCAAACCTC-AAAGTTTAATAGTCAAACCACAAAAAACA
1 TCACTGTACATACACT-GTCAAACC-CAAAAGGTTAATAGTCAAACCACAAAAAACA
* * * *
3341 TCATTGTACATGCACTGTCAAACCCAAAAGGTTGATGGTCAAACCACAAAAA
1 TCACTGTACATACACTGTCAAACCCAAAAGGTTAATAGTCAAACCACAAAAA
3393 GCATTTCTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
54 1 0.02
55 43 0.96
56 1 0.02
ACGTcount: A:0.43, C:0.23, G:0.12, T:0.21
Consensus pattern (55 bp):
TCACTGTACATACACTGTCAAACCCAAAAGGTTAATAGTCAAACCACAAAAAACA
Found at i:3424 original size:37 final size:37
Alignment explanation
Indices: 3374--3456 Score: 123
Period size: 37 Copynumber: 2.3 Consensus size: 37
3364 CCAAAAGGTT
**
3374 GATGGTCAAACCACAAAAAGCATTTCTTTGTATATGC
1 GATGGTCAAACCACAAAAAGCATTTCAATGTATATGC
*
3411 GATGGTCAAACCACAAAATGCATTTCAATGTATATGC
1 GATGGTCAAACCACAAAAAGCATTTCAATGTATATGC
*
3448 -ATGATCAAA
1 GATGGTCAAA
3457 ACTCAAATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
36 8 0.19
37 34 0.81
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.28
Consensus pattern (37 bp):
GATGGTCAAACCACAAAAAGCATTTCAATGTATATGC
Found at i:3612 original size:21 final size:21
Alignment explanation
Indices: 3581--3633 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
3571 ACAACATTGT
* *
3581 ACATGCATGGTTAAACTCCAAA
1 ACATG-ATGGTCAAACCCCAAA
*
3603 GCATGATGGTCAAACCCCAAA
1 ACATGATGGTCAAACCCCAAA
*
3624 ACTTGATGGT
1 ACATGATGGT
3634 AAAATTTCGA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.23
Consensus pattern (21 bp):
ACATGATGGTCAAACCCCAAA
Found at i:3836 original size:33 final size:33
Alignment explanation
Indices: 3794--3887 Score: 172
Period size: 33 Copynumber: 2.8 Consensus size: 33
3784 TTAAAAAACC
3794 ACAAAAAACATTTTATTATATATGCATGATCAT
1 ACAAAAAACATTTTATTATATATGCATGATCAT
3827 ACAAAAAACATTTTATTATATATGCATGATCAT
1 ACAAAAAACATTTTATTATATATGCATGATCAT
3860 ACAAAAAACATTTTATTGA-ATATGCATG
1 ACAAAAAACATTTTATT-ATATATGCATG
3888 GTCAAACCCC
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
33 59 0.98
34 1 0.02
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.35
Consensus pattern (33 bp):
ACAAAAAACATTTTATTATATATGCATGATCAT
Found at i:4156 original size:75 final size:76
Alignment explanation
Indices: 4039--4210 Score: 233
Period size: 75 Copynumber: 2.3 Consensus size: 76
4029 TCAAAGTTTG
* * * *
4039 ATAGTTAAACCACAAAAAA-TTCATTGCACATGCATGGTCAAACCCCAAAGGATGATGGTCAAAC
1 ATAGTCAAACCACAAAAAACATCATTGCACATACATGGTCAAACCCCAAAGGATGATGGTAAAAC
4103 CCCAAATATT-A
66 CCCAAA-ATTCA
* * *
4114 ATAGTCAAACCATAAAAAACATCGTTGTACATACATGG-CAAACCCCAAAGGATGATGGTAAAAC
1 ATAGTCAAACCACAAAAAACATCATTGCACATACATGGTCAAACCCCAAAGGATGATGGTAAAAC
* *
4178 CCTAAAATTCG
66 CCCAAAATTCA
4189 ATAGTCAAACCACAAAAAACAT
1 ATAGTCAAACCACAAAAAACAT
4211 TTCATTCTAA
Statistics
Matches: 85, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
74 3 0.04
75 68 0.80
76 14 0.16
ACGTcount: A:0.45, C:0.22, G:0.13, T:0.20
Consensus pattern (76 bp):
ATAGTCAAACCACAAAAAACATCATTGCACATACATGGTCAAACCCCAAAGGATGATGGTAAAAC
CCCAAAATTCA
Found at i:4254 original size:132 final size:132
Alignment explanation
Indices: 4093--4372 Score: 334
Period size: 132 Copynumber: 2.1 Consensus size: 132
4083 CCAAAGGATG
* * ** *
4093 ATGGTCAAACCCCAAATATTAATAGTCAAACCATAAAAAACATCGTTGTACATACATGG-CAAAC
1 ATGGTCAAACCACAAATATTAATACTCAAACCA-AAAAAACATAATTATACATACATGGTC-AAC
** * * *
4157 -CCCAAAGGATGATGGTAAAACCCTAAAATTCGATAGTCAAACCACAAAAAACATTTCATTCTA-
64 GCCCAAAGGATGATAATAAAACCCCAAAATTCGATAGGCAAACCACAAAAAACATTTCACTCTAT
4220 ACTGC
129 A-TGC
* * * *
4225 ATGGTCAAACCTCAAAGT-TTGATACTCAAACCACAAAAACATAATTATACATGCATGGTCAACG
1 ATGGTCAAACCACAAA-TATTAATACTCAAACCAAAAAAACATAATTATACATACATGGTCAACG
* * * *
4289 CCCAAAGGATGATAATCAAACCCCAAAGTTCGATAGGCAAACCACAAAAAACATTTCGCTGTATA
65 CCCAAAGGATGATAATAAAACCCCAAAATTCGATAGGCAAACCACAAAAAACATTTCACTCTATA
4354 TGC
130 TGC
4357 ATGGTCAAACCACAAA
1 ATGGTCAAACCACAAA
4373 AACATCATTG
Statistics
Matches: 126, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
131 23 0.18
132 101 0.80
133 2 0.02
ACGTcount: A:0.43, C:0.23, G:0.12, T:0.21
Consensus pattern (132 bp):
ATGGTCAAACCACAAATATTAATACTCAAACCAAAAAAACATAATTATACATACATGGTCAACGC
CCAAAGGATGATAATAAAACCCCAAAATTCGATAGGCAAACCACAAAAAACATTTCACTCTATAT
GC
Found at i:4279 original size:207 final size:207
Alignment explanation
Indices: 3885--4342 Score: 595
Period size: 207 Copynumber: 2.2 Consensus size: 207
3875 TTGAATATGC
*
3885 ATGGTCAAACCCCAAATTTTGATAGTCAAACCACAAAAAACATCATTGTACATGCATGGTCAAAC
1 ATGGTCAAACCCCAAA-TTTGATAGTCAAACCACAAAAAACATCATTGTACATACATGGTCAAAC
* * ** * *
3950 CCCAAAGGATGATGGCCAAAGCTCATAGTTTTGATAGTCAAACCACAAAAAGCATTTCATTATAG
65 CCCAAAGGATGATGGCAAAACCTCATAAATTCGATAGTCAAACCACAAAAAACATTTCATTATAG
* * * * * *
4015 ATTCATGGTAAATCTCAAAGTTTGATAGTTAAACCACAAAAAATTCATTGCACATGCATGGTCAA
130 ATGCATGGTAAACCTCAAAGTTTGATACTCAAACCACAAAAAATTAATTACACATGCATGGTC-A
4080 AC-CCCAAAGGATG
194 ACGCCCAAAGGATG
* * *
4093 ATGGTCAAACCCCAAATATTAATAGTCAAACCATAAAAAACATCGTTGTACATACATGG-CAAAC
1 ATGGTCAAACCCCAAAT-TTGATAGTCAAACCACAAAAAACATCATTGTACATACATGGTCAAAC
* *
4157 CCCAAAGGATGATGGTAAAACC-C-TAAAATTCGATAGTCAAACCACAAAAAACATTTCATTCTA
65 CCCAAAGGATGATGGCAAAACCTCAT-AAATTCGATAGTCAAACCACAAAAAACATTTCATTATA
*
4220 -ACTGCATGGTCAAACCTCAAAGTTTGATACTCAAACCACAAAAACA-TAATTATACATGCATGG
129 GA-TGCATGGT-AAACCTCAAAGTTTGATACTCAAACCACAAAAA-ATTAATTACACATGCATGG
4283 TCAACGCCCAAAGGATG
191 TCAACGCCCAAAGGATG
** * *
4300 ATAATCAAACCCCAAAGTTCGATAGGCAAACCACAAAAAACAT
1 ATGGTCAAACCCCAAA-TTTGATAGTCAAACCACAAAAAACAT
4343 TTCGCTGTAT
Statistics
Matches: 218, Mismatches: 25, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
205 2 0.01
206 44 0.20
207 117 0.54
208 55 0.25
ACGTcount: A:0.42, C:0.22, G:0.13, T:0.22
Consensus pattern (207 bp):
ATGGTCAAACCCCAAATTTGATAGTCAAACCACAAAAAACATCATTGTACATACATGGTCAAACC
CCAAAGGATGATGGCAAAACCTCATAAATTCGATAGTCAAACCACAAAAAACATTTCATTATAGA
TGCATGGTAAACCTCAAAGTTTGATACTCAAACCACAAAAAATTAATTACACATGCATGGTCAAC
GCCCAAAGGATG
Found at i:4500 original size:21 final size:22
Alignment explanation
Indices: 4468--4516 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
4458 TAAATTTTGT
* *
4468 TCAAA-CCTCAAATTTTTATAA
1 TCAAATCCTCAAAGTTTGATAA
*
4489 TCAAATCC-CAAAGTTTGATAG
1 TCAAATCCTCAAAGTTTGATAA
4510 TCAAATC
1 TCAAATC
4517 ACGTTAAACC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33
Consensus pattern (22 bp):
TCAAATCCTCAAAGTTTGATAA
Done.