Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014139.1 Corchorus olitorius cultivar O-4 contig14172, 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: 51986
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:599 original size:16 final size:15
Alignment explanation
Indices: 578--619 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
568 TTACTTTGCT
578 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
*
594 TTGTTTTATGTTTAA
1 TTGTTTTCTGTTTAA
*
609 TTATTTTCTGT
1 TTGTTTTCTGT
620 CAACCTCTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.17, C:0.05, G:0.12, T:0.67
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:18039 original size:78 final size:79
Alignment explanation
Indices: 17957--18109 Score: 220
Period size: 80 Copynumber: 1.9 Consensus size: 79
17947 TTCTTTTTTT
* * * *
17957 CTTTTAATCTTTTTTCTGTTTT-GATTT-AAAAAAAAAACAGATGATTTCATGTTTAAGAAATAG
1 CTTTTAATC-TTTTTCCGTTTTGGATTTAAAAAAAAAAACAGAGGAATTCATGTATAAGAAATAG
18020 GTTTTTCAAAATTTC
65 GTTTTTCAAAATTTC
* *
18035 CTTTTAATCTTTTTCCGTTTTGGTTTTGAAAAAAAAAAACAGAGGAATTCATGTATAAGAAATGG
1 CTTTTAATCTTTTTCCGTTTTGGATTT-AAAAAAAAAAACAGAGGAATTCATGTATAAGAAATAG
18100 GTTTTTCAAA
65 GTTTTTCAAA
18110 TCAATTTCAA
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
77 11 0.17
78 13 0.20
80 42 0.64
ACGTcount: A:0.35, C:0.09, G:0.13, T:0.42
Consensus pattern (79 bp):
CTTTTAATCTTTTTCCGTTTTGGATTTAAAAAAAAAAACAGAGGAATTCATGTATAAGAAATAGG
TTTTTCAAAATTTC
Found at i:22835 original size:13 final size:13
Alignment explanation
Indices: 22817--22841 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22807 GAATGCTTTA
22817 AATTGGTGGAATC
1 AATTGGTGGAATC
22830 AATTGGTGGAAT
1 AATTGGTGGAAT
22842 GTAGGAGAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.32, T:0.32
Consensus pattern (13 bp):
AATTGGTGGAATC
Found at i:24894 original size:11 final size:11
Alignment explanation
Indices: 24878--24907 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
24868 GAAGTTCGTG
*
24878 TTTGAAGATCA
1 TTTGAAGATAA
24889 TTTGAAGATAA
1 TTTGAAGATAA
24900 TTTGAAGA
1 TTTGAAGA
24908 CTTGAAGACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.40, C:0.03, G:0.20, T:0.37
Consensus pattern (11 bp):
TTTGAAGATAA
Found at i:26077 original size:6 final size:6
Alignment explanation
Indices: 26066--26097 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
26056 CAGGCTGCAC
*
26066 CACAAT CACAAT CACAAT CACAAT AACAAT CA
1 CACAAT CACAAT CACAAT CACAAT CACAAT CA
26098 TCCGTTAACG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.53, C:0.31, G:0.00, T:0.16
Consensus pattern (6 bp):
CACAAT
Found at i:26253 original size:39 final size:38
Alignment explanation
Indices: 26134--26274 Score: 185
Period size: 38 Copynumber: 3.7 Consensus size: 38
26124 TAGCCAACAG
26134 TTAACCCCCTGAGGCATGGGTCCACTCTTACCAAT-AGT
1 TTAACCCCCTGAGGCATGGGTCCACTCTTACC-ATCAGT
* * *
26172 TTAACCCCCTGAGGCACGGATCCACTCTTACCAACAGT
1 TTAACCCCCTGAGGCATGGGTCCACTCTTACCATCAGT
* * *
26210 TTAACCCCCTGTGGTATGAGTCCACTCTTTACCATCAGT
1 TTAACCCCCTGAGGCATGGGTCCACTC-TTACCATCAGT
* *
26249 TTAACCCCCTAAGGTATGGGTCCACT
1 TTAACCCCCTGAGGCATGGGTCCACT
26275 ATGCACAGCC
Statistics
Matches: 89, Mismatches: 12, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
37 1 0.01
38 55 0.62
39 33 0.37
ACGTcount: A:0.23, C:0.33, G:0.17, T:0.27
Consensus pattern (38 bp):
TTAACCCCCTGAGGCATGGGTCCACTCTTACCATCAGT
Found at i:32079 original size:21 final size:21
Alignment explanation
Indices: 32020--32083 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
32010 ACTACCAAGT
*
32020 CACAACCGGCCATTCACCGTGC
1 CACAACCGGCCATGC-CCGTGC
* ** *
32042 CACCACCGGTTAAGCCCGTGC
1 CACAACCGGCCATGCCCGTGC
32063 CACAACCGGCCATGCCCGTGC
1 CACAACCGGCCATGCCCGTGC
32084 TATCACCTTT
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
21 23 0.70
22 10 0.30
ACGTcount: A:0.20, C:0.45, G:0.22, T:0.12
Consensus pattern (21 bp):
CACAACCGGCCATGCCCGTGC
Found at i:36317 original size:79 final size:79
Alignment explanation
Indices: 36186--36341 Score: 303
Period size: 79 Copynumber: 2.0 Consensus size: 79
36176 GTTTGCAAGC
*
36186 TAAATCTACATTTAAACCTCATGGATTTTATACTCCTTTGCCTATTCCTCATGAACCTTGGACAC
1 TAAATCTACATTTAAACCTCATGGATTGTATACTCCTTTGCCTATTCCTCATGAACCTTGGACAC
36251 ACATTAGCATGGTT
66 ACATTAGCATGGTT
36265 TAAATCTACATTTAAACCTCATGGATTGTATACTCCTTTGCCTATTCCTCATGAACCTTGGACAC
1 TAAATCTACATTTAAACCTCATGGATTGTATACTCCTTTGCCTATTCCTCATGAACCTTGGACAC
36330 ACATTAGCATGG
66 ACATTAGCATGG
36342 ATTTTGTGTT
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 76 1.00
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.35
Consensus pattern (79 bp):
TAAATCTACATTTAAACCTCATGGATTGTATACTCCTTTGCCTATTCCTCATGAACCTTGGACAC
ACATTAGCATGGTT
Found at i:38305 original size:2 final size:2
Alignment explanation
Indices: 38298--38330 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
38288 CATACATATT
*
38298 TG TG TG TG TG TG TG TG TG AG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
38331 CTATCTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.03, C:0.00, G:0.48, T:0.48
Consensus pattern (2 bp):
TG
Found at i:38421 original size:27 final size:26
Alignment explanation
Indices: 38387--38442 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
38377 CATTTTTTTA
38387 AAATATATTTCTAA-ATTTCCATTATT
1 AAATATATTT-TAATATTTCCATTATT
* *
38413 AAATGATATTTTAATTTTTTCATTATT
1 AAAT-ATATTTTAATATTTCCATTATT
38440 AAA
1 AAA
38443 ATAATGGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 7 0.27
27 19 0.73
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (26 bp):
AAATATATTTTAATATTTCCATTATT
Found at i:44429 original size:18 final size:18
Alignment explanation
Indices: 44406--44440 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
44396 TCAAGAACAA
44406 CAAGAACATGAAAAATTG
1 CAAGAACATGAAAAATTG
*
44424 CAAGAACGTGAAAAATT
1 CAAGAACATGAAAAATT
44441 ACTAAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (18 bp):
CAAGAACATGAAAAATTG
Found at i:44538 original size:31 final size:29
Alignment explanation
Indices: 44503--44578 Score: 73
Period size: 31 Copynumber: 2.6 Consensus size: 29
44493 GCTAAATATC
*
44503 CAAATTGGGCCTAAACATTTCATTATCTGC-T
1 CAAATTGGGCCTAAACATTT-A--ATCGGCTT
* * * *
44534 CAAATTGAGCTTAAACCTTTACTCGGCTT
1 CAAATTGGGCCTAAACATTTAATCGGCTT
44563 CAAATTGGGCCTAAAC
1 CAAATTGGGCCTAAAC
44579 CTATTCGAGG
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
28 4 0.11
29 15 0.41
30 1 0.03
31 17 0.46
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (29 bp):
CAAATTGGGCCTAAACATTTAATCGGCTT
Found at i:48100 original size:21 final size:21
Alignment explanation
Indices: 48062--48107 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
48052 ACTGCCCAGC
*
48062 TGGGTCTTAAGGCGAACCACA
1 TGGGTCTCAAGGCGAACCACA
*
48083 TGGGTGCTCAAGGC-AACCATA
1 TGGGT-CTCAAGGCGAACCACA
48104 TGGG
1 TGGG
48108 CGCCCAGGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.26, C:0.22, G:0.33, T:0.20
Consensus pattern (21 bp):
TGGGTCTCAAGGCGAACCACA
Done.