Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020770.1 Corchorus olitorius cultivar O-4 contig20803, 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: 26868
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:2916 original size:28 final size:28
Alignment explanation
Indices: 2876--2931 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
2866 GAATTATTTT
2876 GAGAAAAAAGACATGAGAGGAGAGAGAA
1 GAGAAAAAAGACATGAGAGGAGAGAGAA
2904 GAGAAAAAAGACATGAGAGGAGAGAGAA
1 GAGAAAAAAGACATGAGAGGAGAGAGAA
2932 TGAATTGAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.57, C:0.04, G:0.36, T:0.04
Consensus pattern (28 bp):
GAGAAAAAAGACATGAGAGGAGAGAGAA
Found at i:4934 original size:18 final size:17
Alignment explanation
Indices: 4907--4943 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
4897 CCATGCTTTT
*
4907 CAAGATATTGAAGCCAGC
1 CAAGAAATTGAAGCC-GC
4925 CAAGAAATTGAAGCCGC
1 CAAGAAATTGAAGCCGC
4942 CA
1 CA
4944 TCACTACACG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.41, C:0.24, G:0.22, T:0.14
Consensus pattern (17 bp):
CAAGAAATTGAAGCCGC
Found at i:5356 original size:27 final size:27
Alignment explanation
Indices: 5326--5378 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
5316 AGCTAAATTT
5326 GGTGAAACCACCGAATTGCAAATCAGA
1 GGTGAAACCACCGAATTGCAAATCAGA
* * * *
5353 GGTGAGAGCTCCGAATTGCAATTCAG
1 GGTGAAACCACCGAATTGCAAATCAG
5379 GGCTCACACG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.19
Consensus pattern (27 bp):
GGTGAAACCACCGAATTGCAAATCAGA
Found at i:11462 original size:38 final size:38
Alignment explanation
Indices: 11420--11541 Score: 142
Period size: 38 Copynumber: 3.1 Consensus size: 38
11410 TAAGATAATT
11420 TTTTTTGAAATATATACTATATAAGATAAATTAATTGG
1 TTTTTTGAAATATATACTATATAAGATAAATTAATTGG
* * *
11458 TTTTTTTAAAAAATATATA-TATATACTATATAAGA-TAATT-T
1 -TTTTTT--GAAATATATACTATATA--AGATAA-ATTAATTGG
11499 TTTTTTGAAATATATACTATATAAGATAAATTAATTGG
1 TTTTTTGAAATATATACTATATAAGATAAATTAATTGG
11537 TTTTT
1 TTTTT
11542 CCAAAAAAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 17
0.75 0.07 0.18
Matches are distributed among these distances:
36 1 0.01
37 10 0.14
38 14 0.20
39 12 0.17
40 12 0.17
41 9 0.13
42 10 0.14
43 1 0.01
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.48
Consensus pattern (38 bp):
TTTTTTGAAATATATACTATATAAGATAAATTAATTGG
Found at i:11487 original size:78 final size:79
Alignment explanation
Indices: 11395--11541 Score: 287
Period size: 79 Copynumber: 1.9 Consensus size: 79
11385 AATGGGATAC
11395 TATATATATACTATATAAGATAA-TTTTTTTTGAAATATATACTATATAAGATAAATTAATTGGT
1 TATATATATACTATATAAGATAATTTTTTTTTGAAATATATACTATATAAGATAAATTAATTGGT
11459 TTTTTTAAAAAATA
66 TTTTTTAAAAAATA
11473 TATATATATACTATATAAGATAATTTTTTTTTGAAATATATACTATATAAGATAAATTAATTGGT
1 TATATATATACTATATAAGATAATTTTTTTTTGAAATATATACTATATAAGATAAATTAATTGGT
11538 TTTT
66 TTTT
11542 CCAAAAAAAA
Statistics
Matches: 68, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
78 23 0.34
79 45 0.66
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.48
Consensus pattern (79 bp):
TATATATATACTATATAAGATAATTTTTTTTTGAAATATATACTATATAAGATAAATTAATTGGT
TTTTTTAAAAAATA
Found at i:13119 original size:29 final size:29
Alignment explanation
Indices: 13077--13138 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
13067 AGACACTTGA
*
13077 GTTTTTGCTCAACTTAGGGGTGAGCAACG
1 GTTTTTGCTAAACTTAGGGGTGAGCAACG
13106 GTTTTTGCTAAACTTAGGGGTGAGCAACG
1 GTTTTTGCTAAACTTAGGGGTGAGCAACG
13135 GTTT
1 GTTT
13139 GGCGGTTCGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.21, C:0.15, G:0.31, T:0.34
Consensus pattern (29 bp):
GTTTTTGCTAAACTTAGGGGTGAGCAACG
Found at i:13234 original size:48 final size:48
Alignment explanation
Indices: 13163--13259 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
13153 GGTTTGGGAG
*
13163 ATTTTTCTAATTCCGACTAATAACTGACGGAAACATTTTGAAACCGTC
1 ATTTTTCTAATTCCGACTAATAACCGACGGAAACATTTTGAAACCGTC
13211 ATTTTTCTAATTCCGACTAATAACCGACGGAAACATTTTGAAACCGTC
1 ATTTTTCTAATTCCGACTAATAACCGACGGAAACATTTTGAAACCGTC
13259 A
1 A
13260 ACCGTCGGTT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.34, C:0.22, G:0.12, T:0.32
Consensus pattern (48 bp):
ATTTTTCTAATTCCGACTAATAACCGACGGAAACATTTTGAAACCGTC
Found at i:15689 original size:37 final size:37
Alignment explanation
Indices: 15639--15754 Score: 146
Period size: 37 Copynumber: 3.1 Consensus size: 37
15629 CACACTATAG
15639 TACCCCTCACTTCTAGGGTGTACTACCAATTTAAAAA
1 TACCCCTCACTTCTAGGGTGTACTACCAATTTAAAAA
*
15676 TACCCCTCACTTCTAGGGTGTACTGCCAATTTAAAAA
1 TACCCCTCACTTCTAGGGTGTACTACCAATTTAAAAA
* *
15713 TAACACACT-A-TAGTATAGTGGTGTACTACCAATTTAAAAA
1 T-AC-CCCTCACT--TCTAG-GGTGTACTACCAATTTAAAAA
15753 TA
1 TA
15755 ACACATTATA
Statistics
Matches: 70, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
37 38 0.54
38 3 0.04
39 8 0.11
40 21 0.30
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.30
Consensus pattern (37 bp):
TACCCCTCACTTCTAGGGTGTACTACCAATTTAAAAA
Found at i:15746 original size:40 final size:40
Alignment explanation
Indices: 15655--15772 Score: 147
Period size: 40 Copynumber: 3.0 Consensus size: 40
15645 TCACTTCTAG
* *
15655 GGTGTACTACCAATTTAAAAAT-AC-CCCTCACT--TCTAG-
1 GGTGTACTACCAATTTAAAAATAACACACT-A-TAGTATAGT
*
15692 GGTGTACTGCCAATTTAAAAATAACACACTATAGTATAGT
1 GGTGTACTACCAATTTAAAAATAACACACTATAGTATAGT
*
15732 GGTGTACTACCAATTTAAAAATAACACATTATAGTATAGT
1 GGTGTACTACCAATTTAAAAATAACACACTATAGTATAGT
15772 G
1 G
15773 TGTTGGATAT
Statistics
Matches: 71, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
37 22 0.31
38 3 0.04
39 7 0.10
40 39 0.55
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.31
Consensus pattern (40 bp):
GGTGTACTACCAATTTAAAAATAACACACTATAGTATAGT
Found at i:17549 original size:29 final size:29
Alignment explanation
Indices: 17491--17560 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 29
17481 ACTTGTTGCG
* *
17491 TTTGGACGTTTTGCTCCCTGAACTCTAAT
1 TTTGGACATTTTGCTCCATGAACTCTAAT
17520 TTTGGACATTTTG-TCCATGAACTCTCAAT
1 TTTGGACATTTTGCTCCATGAACTCT-AAT
17549 TTTGGACATTTT
1 TTTGGACATTTT
17561 ACCCCGACCC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 11 0.29
29 27 0.71
ACGTcount: A:0.20, C:0.20, G:0.16, T:0.44
Consensus pattern (29 bp):
TTTGGACATTTTGCTCCATGAACTCTAAT
Found at i:17575 original size:34 final size:29
Alignment explanation
Indices: 17491--17584 Score: 91
Period size: 29 Copynumber: 3.1 Consensus size: 29
17481 ACTTGTTGCG
* *
17491 TTTGGACGTTTTGCTCCCTGAACTCT-AAT
1 TTTGGACATTTTG-ACCCTGAACTCTCAAT
* *
17520 TTTGGACATTTTGTCCATGAACTCTCAAT
1 TTTGGACATTTTGACCCTGAACTCTCAAT
17549 TTTGGACATTTTACCCCGACCCTGAACTCTCAAT
1 TTTGGACATTTT-----GACCCTGAACTCTCAAT
17583 TT
1 TT
17585 GAACCTCTAT
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
28 11 0.20
29 27 0.49
34 17 0.31
ACGTcount: A:0.21, C:0.26, G:0.14, T:0.39
Consensus pattern (29 bp):
TTTGGACATTTTGACCCTGAACTCTCAAT
Found at i:18862 original size:16 final size:16
Alignment explanation
Indices: 18841--18877 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
18831 CAACTAGGAT
*
18841 TATTATTATTATAATA
1 TATTATTACTATAATA
*
18857 TATTATTACTATTATA
1 TATTATTACTATAATA
18873 TATTA
1 TATTA
18878 GAATTAGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTATTACTATAATA
Found at i:20375 original size:13 final size:13
Alignment explanation
Indices: 20357--20382 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20347 CATCATGTTC
20357 TTAAGAATTTCCA
1 TTAAGAATTTCCA
20370 TTAAGAATTTCCA
1 TTAAGAATTTCCA
20383 GAATGTGTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (13 bp):
TTAAGAATTTCCA
Found at i:24792 original size:36 final size:36
Alignment explanation
Indices: 24745--24821 Score: 154
Period size: 36 Copynumber: 2.1 Consensus size: 36
24735 GTCTGTTATG
24745 GATATTAAAGAACTCATATTTTCTGATCTAGTTCCT
1 GATATTAAAGAACTCATATTTTCTGATCTAGTTCCT
24781 GATATTAAAGAACTCATATTTTCTGATCTAGTTCCT
1 GATATTAAAGAACTCATATTTTCTGATCTAGTTCCT
24817 GATAT
1 GATAT
24822 AGATCATATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.42
Consensus pattern (36 bp):
GATATTAAAGAACTCATATTTTCTGATCTAGTTCCT
Done.