Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020827.1 Corchorus olitorius cultivar O-4 contig20860, 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: 36660
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Found at i:12111 original size:60 final size:60
Alignment explanation
Indices: 12044--12261 Score: 312
Period size: 60 Copynumber: 3.6 Consensus size: 60
12034 GCTAATTGCT
* **
12044 CAAATAAGGACCTAACGTT-TGCCAAAATGCTCAAATAAGGATCCGATCTTTTAATTTGAC
1 CAAATAAGGACCTAACGTTAT-CGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGAC
* * *
12104 CAAATAAGGGCCTAATGTTATCGAAAATGCTCAAATAGGGGCCCGATCTTTTAATTTGAC
1 CAAATAAGGACCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGAC
* ** * *
12164 CAAATAAGGGCCTAATATTATCGAAAATGCTCAAATAGGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGACCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGAC
*
12224 CAAATAAGGATCTAACGTTATCGAAAATGCTCAAATAA
1 CAAATAAGGACCTAACGTTATCGAAAATGCTCAAATAA
12262 AGACCTGGCG
Statistics
Matches: 144, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
60 143 0.99
61 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (60 bp):
CAAATAAGGACCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGAC
Found at i:12146 original size:31 final size:31
Alignment explanation
Indices: 12104--12206 Score: 95
Period size: 31 Copynumber: 3.4 Consensus size: 31
12094 TTAATTTGAC
*
12104 CAAATAAGGGCCTAATGTTATCGAAAATGCT
1 CAAATAAGGGCCTAATATTATCGAAAATGCT
* ** * * **
12135 CAAATAGGGGCCCGATCTT-T-TAATTTGAC-
1 CAAATAAGGGCCTAATATTATCGAAAATG-CT
12164 CAAATAAGGGCCTAATATTATCGAAAATGCT
1 CAAATAAGGGCCTAATATTATCGAAAATGCT
*
12195 CAAATAGGGGCC
1 CAAATAAGGGCC
12207 CGATCTTTTA
Statistics
Matches: 53, Mismatches: 15, Indels: 8
0.70 0.20 0.11
Matches are distributed among these distances:
29 19 0.36
30 4 0.08
31 30 0.57
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.25
Consensus pattern (31 bp):
CAAATAAGGGCCTAATATTATCGAAAATGCT
Found at i:12174 original size:29 final size:28
Alignment explanation
Indices: 12075--12232 Score: 91
Period size: 29 Copynumber: 5.3 Consensus size: 28
12065 CCAAAATGCT
**
12075 CAAATAAGGATCCGATCTTTTAATTTGAC
1 CAAATAAGGGCCCGATCTTTTAATTTG-C
** * * **
12104 CAAATAAGGGCCTAATGTTATCGAAAATGC
1 CAAATAAGGGCCCGATCTT-T-TAATTTGC
*
12134 TCAAATAGGGGCCCGATCTTTTAATTTGAC
1 -CAAATAAGGGCCCGATCTTTTAATTTG-C
** * * **
12164 CAAATAAGGGCCTAATATTATCGAAAATGC
1 CAAATAAGGGCCCGATCTT-T-TAATTTGC
*
12194 TCAAATAGGGGCCCGATCTTTTAATTTGGC
1 -CAAATAAGGGCCCGATCTTTTAATTT-GC
12224 CAAATAAGG
1 CAAATAAGG
12233 ATCTAACGTT
Statistics
Matches: 91, Mismatches: 30, Indels: 16
0.66 0.22 0.12
Matches are distributed among these distances:
29 44 0.48
30 9 0.10
31 38 0.42
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (28 bp):
CAAATAAGGGCCCGATCTTTTAATTTGC
Found at i:12344 original size:31 final size:30
Alignment explanation
Indices: 12306--12473 Score: 89
Period size: 31 Copynumber: 5.6 Consensus size: 30
12296 TTTCGATGCC
12306 AGACCCTTATTTGAGCATTTTGGCAAACGTT
1 AGACCCTTATTTGAGCATTTT-GCAAACGTT
** * *
12337 AGACCCTTATTTG-GCCAAATT--AAAAGAT
1 AGACCCTTATTTGAG-CATTTTGCAAACGTT
* *
12365 CGAGCCCTTATTTGAACATTTTGACAAACGTT
1 AGA-CCCTTATTTGAGCATTTTG-CAAACGTT
* ** * *
12397 AGGCCCTTATTTG-GCCAAATT--AAAAGATC
1 AGACCCTTATTTGAG-CATTTTGCAAACG-TT
* * *
12426 ATG-TCCTTATTTAAACATTTTGACAAACGTT
1 A-GACCCTTATTTGAGCATTTTG-CAAACGTT
12457 AGACCCTTATTTGAGCA
1 AGACCCTTATTTGAGCA
12474 ATTAGCCAAC
Statistics
Matches: 96, Mismatches: 27, Indels: 28
0.64 0.18 0.19
Matches are distributed among these distances:
28 11 0.11
29 28 0.29
30 3 0.03
31 44 0.46
32 10 0.10
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (30 bp):
AGACCCTTATTTGAGCATTTTGCAAACGTT
Found at i:12404 original size:60 final size:60
Alignment explanation
Indices: 12309--12469 Score: 261
Period size: 60 Copynumber: 2.7 Consensus size: 60
12299 CGATGCCAGA
* *
12309 CCCTTATTTGAGCATTTTGGCAAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCGA-G
1 CCCTTATTTGAACATTTTGACAAACGTTAGACCCTTATTTGGCCAAATTAAAAGATC-ATG
*
12369 CCCTTATTTGAACATTTTGACAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCATG
1 CCCTTATTTGAACATTTTGACAAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCATG
* *
12429 TCCTTATTTAAACATTTTGACAAACGTTAGACCCTTATTTG
1 CCCTTATTTGAACATTTTGACAAACGTTAGACCCTTATTTG
12470 AGCAATTAGC
Statistics
Matches: 94, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
59 1 0.01
60 93 0.99
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (60 bp):
CCCTTATTTGAACATTTTGACAAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCATG
Found at i:12547 original size:2 final size:2
Alignment explanation
Indices: 12497--12530 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12487 TTCTGATGAC
12497 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12531 CCATACAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14838 original size:12 final size:12
Alignment explanation
Indices: 14779--14839 Score: 70
Period size: 12 Copynumber: 5.1 Consensus size: 12
14769 CTAAAATTCA
*
14779 AGTTCGAGCTCA
1 AGTTCGAGCTCG
14791 AGTTCGAGCTCG
1 AGTTCGAGCTCG
* *
14803 AATTCGATAC-CG
1 AGTTCGA-GCTCG
14815 AGTTCGAGCTCG
1 AGTTCGAGCTCG
*
14827 AGCTCGAGCTCG
1 AGTTCGAGCTCG
14839 A
1 A
14840 CAGGTATATA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
11 1 0.02
12 39 0.95
13 1 0.02
ACGTcount: A:0.23, C:0.26, G:0.28, T:0.23
Consensus pattern (12 bp):
AGTTCGAGCTCG
Found at i:16535 original size:20 final size:20
Alignment explanation
Indices: 16510--16548 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
16500 CATATAAAAT
*
16510 AATAATAACTAATTTTTAAA
1 AATAATAACTAATTATTAAA
16530 AATAATAACTAATTATTAA
1 AATAATAACTAATTATTAA
16549 TTTTTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
AATAATAACTAATTATTAAA
Found at i:19831 original size:21 final size:21
Alignment explanation
Indices: 19805--19848 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
19795 TTCTCTCACA
*
19805 GCGCCACATCATCCTCCCTAT
1 GCGCCACATCAGCCTCCCTAT
*
19826 GCGCCACATTAGCCTCCCTAT
1 GCGCCACATCAGCCTCCCTAT
19847 GC
1 GC
19849 ACAAGGTCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.45, G:0.14, T:0.23
Consensus pattern (21 bp):
GCGCCACATCAGCCTCCCTAT
Found at i:20650 original size:20 final size:20
Alignment explanation
Indices: 20625--20666 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
20615 TTAGGCTTTT
20625 AACAATTTCAACGGTTTAAA
1 AACAATTTCAACGGTTTAAA
20645 AACAATTTCAACGGTTTAAA
1 AACAATTTCAACGGTTTAAA
20665 AA
1 AA
20667 GTATAATCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.48, C:0.14, G:0.10, T:0.29
Consensus pattern (20 bp):
AACAATTTCAACGGTTTAAA
Found at i:20904 original size:27 final size:26
Alignment explanation
Indices: 20829--20919 Score: 150
Period size: 26 Copynumber: 3.5 Consensus size: 26
20819 TAATCTAAAC
20829 AAGCCCAAGAACCC-AATCTT-AAAAA
1 AAGCCCAA-AACCCGAATCTTAAAAAA
20854 AAGCCCAAAACCCGAATCTTAAAAAA
1 AAGCCCAAAACCCGAATCTTAAAAAA
20880 AAGCCCAAAACCCGAATCTTAAAAAAA
1 AAGCCCAAAACCCGAATCTT-AAAAAA
20907 AAGCCCAAAACCC
1 AAGCCCAAAACCC
20920 CAAATGAAAA
Statistics
Matches: 63, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
24 5 0.08
25 14 0.22
26 25 0.40
27 19 0.30
ACGTcount: A:0.53, C:0.30, G:0.08, T:0.10
Consensus pattern (26 bp):
AAGCCCAAAACCCGAATCTTAAAAAA
Found at i:20929 original size:26 final size:26
Alignment explanation
Indices: 20849--20932 Score: 98
Period size: 27 Copynumber: 3.2 Consensus size: 26
20839 ACCCAATCTT
* *
20849 AAAAAAAGCCCAAAA-CCCGAATCTTA
1 AAAAAAAGCCCAAAACCCCAAAT-TAA
* *
20875 AAAAAAAGCCCAAAACCCGAATCTTAA
1 AAAAAAAGCCCAAAACCCCAA-ATTAA
*
20902 AAAAAAAGCCCAAAACCCCAAATGAA
1 AAAAAAAGCCCAAAACCCCAAATTAA
20928 AAAAA
1 AAAAA
20933 CAAACAAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
26 23 0.47
27 25 0.51
28 1 0.02
ACGTcount: A:0.60, C:0.25, G:0.07, T:0.08
Consensus pattern (26 bp):
AAAAAAAGCCCAAAACCCCAAATTAA
Found at i:27295 original size:14 final size:14
Alignment explanation
Indices: 27276--27303 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
27266 AAAATTTTGA
27276 GAGAGAGAAGAGCT
1 GAGAGAGAAGAGCT
27290 GAGAGAGAAGAGCT
1 GAGAGAGAAGAGCT
27304 AAGCTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.43, T:0.07
Consensus pattern (14 bp):
GAGAGAGAAGAGCT
Done.