Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012829.1 Corchorus olitorius cultivar O-4 contig12862, 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: 34898
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Found at i:870 original size:11 final size:11
Alignment explanation
Indices: 850--884 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
840 TTGACAGCGC
850 AACAAAAACAA
1 AACAAAAACAA
*
861 AACGAAAACAA
1 AACAAAAACAA
872 AACAAAAACAA
1 AACAAAAACAA
883 AA
1 AA
885 AACAGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.80, C:0.17, G:0.03, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:3557 original size:2 final size:2
Alignment explanation
Indices: 3552--3576 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3542 ATTGTTTCAC
3552 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3577 ATCATCATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5939 original size:39 final size:40
Alignment explanation
Indices: 5864--5941 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 40
5854 AGCTACCATA
*
5864 TAGAGAATTCTTTTCTGAAGATGGGTGCTCATATAAGAGC
1 TAGAGAATTCTTTTCTGAAGATGGGTGCTCACATAAGAGC
* *
5904 TAGAGTATTCTTTT-TGAAGATGGGTGTTCACATAAGAG
1 TAGAGAATTCTTTTCTGAAGATGGGTGCTCACATAAGAG
5942 TTACTGCATA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 22 0.63
40 13 0.37
ACGTcount: A:0.29, C:0.10, G:0.26, T:0.35
Consensus pattern (40 bp):
TAGAGAATTCTTTTCTGAAGATGGGTGCTCACATAAGAGC
Found at i:6026 original size:48 final size:46
Alignment explanation
Indices: 5904--6139 Score: 287
Period size: 46 Copynumber: 5.1 Consensus size: 46
5894 ATATAAGAGC
* * * * * ***
5904 TAGAGTATTCTTTTTGAAGATGGGTGTTCACATAAGAGTTACTGCA
1 TAGAGTATTCTTTCTGAAAAAGGGTGCTCACATAAGAGCTACCATA
* *
5950 TAGAGTATTCTTTCT-AAAGAAGGGTGCTCACATAGGAGCTACCGTA
1 TAGAGTATTCTTTCTGAAA-AAGGGTGCTCACATAAGAGCTACCATA
* * * *
5996 TAGACTTTTTTTTTTTCGAAGAAA-GGTGCTCACATAAGAGCTACCATA
1 TAGA-GTATTCTTTCT-GAA-AAAGGGTGCTCACATAAGAGCTACCATA
*
6044 TAGAGTATTCTTTCTGAAAAATGGTGCTCACATAAGAGCTACCATA
1 TAGAGTATTCTTTCTGAAAAAGGGTGCTCACATAAGAGCTACCATA
6090 TAGAGTATTCTTTCTGAAAAAGGGTGCTCACATAAGAGCTACCATA
1 TAGAGTATTCTTTCTGAAAAAGGGTGCTCACATAAGAGCTACCATA
6136 TAGA
1 TAGA
6140 TTTCAAAAAT
Statistics
Matches: 165, Mismatches: 19, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
45 5 0.03
46 115 0.70
47 14 0.08
48 26 0.16
49 4 0.02
50 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (46 bp):
TAGAGTATTCTTTCTGAAAAAGGGTGCTCACATAAGAGCTACCATA
Found at i:6083 original size:94 final size:92
Alignment explanation
Indices: 5904--6139 Score: 287
Period size: 94 Copynumber: 2.5 Consensus size: 92
5894 ATATAAGAGC
* * * * * ***
5904 TAGAGTATTCTTTTTGAAGATGGGTGTTCACATAAGAGTTACTGCATAGAGTATTCTTTCTAAAG
1 TAGAGTATTCTTTCTGAAAAAGGGTGCTCACATAAGAGCTACCATATAGAGTATTCTTTCTAAAG
* *
5969 AAGGGTGCTCACATAGGAGCTACCGTA
66 AAGGGTGCTCACATAAGAGCTACCATA
* * * *
5996 TAGACTTTTTTTTTTTCGAAGAAA-GGTGCTCACATAAGAGCTACCATATAGAGTATTCTTTCTG
1 TAGA-GTATTCTTTCT-GAA-AAAGGGTGCTCACATAAGAGCTACCATATAGAGTATTCTTTCT-
*
6060 AAA-AATGGTGCTCACATAAGAGCTACCATA
62 AAAGAAGGGTGCTCACATAAGAGCTACCATA
6090 TAGAGTATTCTTTCTGAAAAAGGGTGCTCACATAAGAGCTACCATATAGA
1 TAGAGTATTCTTTCTGAAAAAGGGTGCTCACATAAGAGCTACCATATAGA
6140 TTTCAAAAAT
Statistics
Matches: 122, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
91 3 0.02
92 35 0.29
93 15 0.12
94 65 0.53
95 4 0.03
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (92 bp):
TAGAGTATTCTTTCTGAAAAAGGGTGCTCACATAAGAGCTACCATATAGAGTATTCTTTCTAAAG
AAGGGTGCTCACATAAGAGCTACCATA
Found at i:6646 original size:77 final size:78
Alignment explanation
Indices: 6536--6680 Score: 238
Period size: 77 Copynumber: 1.9 Consensus size: 78
6526 AGACTTCGTG
* * **
6536 AACACCATATGCTTTTGACATTGAAAGAGGGTGATAGTTTCGCGAACATTATATGCCTTTGACAT
1 AACACCATATGCTTTTAACATTGAAAGAAGGTGATAGTTTCGCGAACACCATATGCCTTTGACAT
6601 TGAAAGAGGCACA
66 TGAAAGAGGCACA
*
6614 AACACCATATG-TTTTAACGTTGAAAGAAGGTGATAGTTTCGCGAACACCATATGCCTTTGACAT
1 AACACCATATGCTTTTAACATTGAAAGAAGGTGATAGTTTCGCGAACACCATATGCCTTTGACAT
6678 TGA
66 TGA
6681 CATTGAAAGA
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
77 51 0.82
78 11 0.18
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (78 bp):
AACACCATATGCTTTTAACATTGAAAGAAGGTGATAGTTTCGCGAACACCATATGCCTTTGACAT
TGAAAGAGGCACA
Found at i:6919 original size:42 final size:42
Alignment explanation
Indices: 6873--7003 Score: 201
Period size: 42 Copynumber: 3.1 Consensus size: 42
6863 TTGACGCCAA
* *
6873 ATGCCTTTA-CTATCGCGAATACCATACCATAGCGCGAGTACC
1 ATGCCTTTAGC-ATCGCGAATACCATACCACATCGCGAGTACC
* *
6915 ATGCCTTTAGCATCACGAATACCATACCACATTGCGAGTACC
1 ATGCCTTTAGCATCGCGAATACCATACCACATCGCGAGTACC
*
6957 ATGCCTTTAGCGTCGCGAATACCATACCACATCGCGAGTACC
1 ATGCCTTTAGCATCGCGAATACCATACCACATCGCGAGTACC
6999 ATGCC
1 ATGCC
7004 ACATGCCACT
Statistics
Matches: 81, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
42 80 0.99
43 1 0.01
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.23
Consensus pattern (42 bp):
ATGCCTTTAGCATCGCGAATACCATACCACATCGCGAGTACC
Found at i:6937 original size:23 final size:23
Alignment explanation
Indices: 6873--6981 Score: 74
Period size: 23 Copynumber: 5.1 Consensus size: 23
6863 TTGACGCCAA
6873 ATGCCTTTA-CTATCGCGAATACC
1 ATGCCTTTAGC-ATCGCGAATACC
* * *
6896 ATACC-ATAG---CGCGAGTACC
1 ATGCCTTTAGCATCGCGAATACC
*
6915 ATGCCTTTAGCATCACGAATACC
1 ATGCCTTTAGCATCGCGAATACC
* * *
6938 ATACC---A-CATTGCGAGTACC
1 ATGCCTTTAGCATCGCGAATACC
*
6957 ATGCCTTTAGCGTCGCGAATACC
1 ATGCCTTTAGCATCGCGAATACC
6980 AT
1 AT
6982 ACCACATCGC
Statistics
Matches: 62, Mismatches: 15, Indels: 18
0.65 0.16 0.19
Matches are distributed among these distances:
19 27 0.44
20 4 0.06
22 3 0.05
23 28 0.45
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (23 bp):
ATGCCTTTAGCATCGCGAATACC
Found at i:6958 original size:19 final size:19
Alignment explanation
Indices: 6884--7007 Score: 77
Period size: 19 Copynumber: 6.1 Consensus size: 19
6874 TGCCTTTACT
* *
6884 ATCGCGAATACCATACCAT
1 ATCGCGAGTACCATACCAC
* *
6903 AGCGCGAGTACCATGCCTTTAGC
1 ATCGCGAGTACCATACC---A-C
* *
6926 ATCACGAATACCATACCAC
1 ATCGCGAGTACCATACCAC
* *
6945 ATTGCGAGTACCATGCCTTTAGC
1 ATCGCGAGTACCATACC---A-C
* *
6968 GTCGCGAATACCATACCAC
1 ATCGCGAGTACCATACCAC
*
6987 ATCGCGAGTACCATGCCAC
1 ATCGCGAGTACCATACCAC
7006 AT
1 AT
7008 GCCACTGTAC
Statistics
Matches: 78, Mismatches: 19, Indels: 16
0.69 0.17 0.14
Matches are distributed among these distances:
19 47 0.60
20 2 0.03
22 2 0.03
23 27 0.35
ACGTcount: A:0.30, C:0.32, G:0.17, T:0.21
Consensus pattern (19 bp):
ATCGCGAGTACCATACCAC
Found at i:7069 original size:14 final size:14
Alignment explanation
Indices: 7052--7122 Score: 79
Period size: 14 Copynumber: 4.9 Consensus size: 14
7042 ATACTATATC
*
7052 GCGAATGCCACATT
1 GCGAATACCACATT
*
7066 GCGAATACCACATC
1 GCGAATACCACATT
* *
7080 GCGTATGCCACATT
1 GCGAATACCACATT
7094 GCGCGAATACCACATT
1 --GCGAATACCACATT
*
7110 GCAAATACCACAT
1 GCGAATACCACAT
7123 GCCTTTGATG
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
14 35 0.74
16 12 0.26
ACGTcount: A:0.32, C:0.31, G:0.17, T:0.20
Consensus pattern (14 bp):
GCGAATACCACATT
Found at i:7102 original size:30 final size:28
Alignment explanation
Indices: 7040--7122 Score: 94
Period size: 28 Copynumber: 2.9 Consensus size: 28
7030 TTGGAAGAAG
* *
7040 GAATACTATATCGCGAATGCCACATTGC
1 GAATACCACATCGCGAATGCCACATTGC
*
7068 GAATACCACATCGCGTATGCCACATTGCGC
1 GAATACCACATCGCGAATGCCACATT--GC
* * *
7098 GAATACCACATTGCAAATACCACAT
1 GAATACCACATCGCGAATGCCACAT
7123 GCCTTTGATG
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
28 23 0.50
30 23 0.50
ACGTcount: A:0.34, C:0.29, G:0.16, T:0.22
Consensus pattern (28 bp):
GAATACCACATCGCGAATGCCACATTGC
Found at i:7175 original size:25 final size:26
Alignment explanation
Indices: 7108--7176 Score: 68
Period size: 29 Copynumber: 2.6 Consensus size: 26
7098 GAATACCACA
7108 TTGCAAATACCACATGCCTTTGATGT
1 TTGCAAATACCACATGCCTTTGATGT
* ** *
7134 TTGAAGCGAACGCCACATGCTTTTGATG-
1 TT---GCAAATACCACATGCCTTTGATGT
7162 TTGCAAATACCACAT
1 TTGCAAATACCACAT
7177 CGCAAATACC
Statistics
Matches: 33, Mismatches: 7, Indels: 7
0.70 0.15 0.15
Matches are distributed among these distances:
25 10 0.30
26 2 0.06
28 2 0.06
29 19 0.58
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.30
Consensus pattern (26 bp):
TTGCAAATACCACATGCCTTTGATGT
Found at i:7183 original size:14 final size:14
Alignment explanation
Indices: 7164--7204 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
7154 TTTTGATGTT
7164 GCAAATACCACATC
1 GCAAATACCACATC
*
7178 GCAAATACCATATC
1 GCAAATACCACATC
* *
7192 GCGAATGCCACAT
1 GCAAATACCACAT
7205 GCCTTTGACG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.39, C:0.32, G:0.12, T:0.17
Consensus pattern (14 bp):
GCAAATACCACATC
Found at i:7212 original size:53 final size:53
Alignment explanation
Indices: 7139--7339 Score: 294
Period size: 53 Copynumber: 3.8 Consensus size: 53
7129 GATGTTTGAA
* * * * * *
7139 GCGAACGCCACATGCTTTTGATGTTGCAAATACCACATCGCAAATACCATATC
1 GCGAATGCCACATGCCTTTGACGTCGCGAATACCACATTGCAAATACCATATC
* * *
7192 GCGAATGCCACATGCCTTTGACGTCGCGAGTACCATATTGCAAATACCACATC
1 GCGAATGCCACATGCCTTTGACGTCGCGAATACCACATTGCAAATACCATATC
*
7245 GCGAATGCCACATGCCTTTTGACGTCGCGAATACCACATTGCAAATACTATATC
1 GCGAATGCCACATGCC-TTTGACGTCGCGAATACCACATTGCAAATACCATATC
*
7299 GTGAATGCCACATGCCTTTGACGTCGCGAATACCACATTGC
1 GCGAATGCCACATGCCTTTGACGTCGCGAATACCACATTGC
7340 GAATGCCACA
Statistics
Matches: 133, Mismatches: 14, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
53 85 0.64
54 48 0.36
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (53 bp):
GCGAATGCCACATGCCTTTGACGTCGCGAATACCACATTGCAAATACCATATC
Found at i:7289 original size:107 final size:106
Alignment explanation
Indices: 7139--7350 Score: 316
Period size: 107 Copynumber: 2.0 Consensus size: 106
7129 GATGTTTGAA
* *
7139 GCGAACGCCACATGCTTTTGATGTTGCAAATACCACATCGCAAATACCATATCGCGAATGCCACA
1 GCGAACGCCACATGCTTTTGACGTCGCAAATACCACATCGCAAATACCATATCGCGAATGCCACA
* *
7204 TGCCTTTGACGTCGCGAGTACCATATTGCAAATACCACATC
66 TGCCTTTGACGTCGCGAATACCACATTGCAAATACCACATC
* * * * *
7245 GCGAATGCCACATGCCTTTTGACGTCGCGAATACCACATTGCAAATACTATATCGTGAATGCCAC
1 GCGAACGCCACATG-CTTTTGACGTCGCAAATACCACATCGCAAATACCATATCGCGAATGCCAC
* *
7310 ATGCCTTTGACGTCGCGAATACCACATTGCGAATGCCACAT
65 ATGCCTTTGACGTCGCGAATACCACATTGCAAATACCACAT
7351 GCCTTTGACG
Statistics
Matches: 94, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
106 13 0.14
107 81 0.86
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (106 bp):
GCGAACGCCACATGCTTTTGACGTCGCAAATACCACATCGCAAATACCATATCGCGAATGCCACA
TGCCTTTGACGTCGCGAATACCACATTGCAAATACCACATC
Found at i:7344 original size:39 final size:39
Alignment explanation
Indices: 7301--7387 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
7291 ACTATATCGT
7301 GAATGCCACATGCCTTTGACGTCGCGAATACCACATTGC
1 GAATGCCACATGCCTTTGACGTCGCGAATACCACATTGC
*
7340 GAATGCCACATGCCTTTGACGTCTCGAATACCACATTGC
1 GAATGCCACATGCCTTTGACGTCGCGAATACCACATTGC
* *
7379 AAATACCAC
1 GAATGCCAC
7388 CACATGCCTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (39 bp):
GAATGCCACATGCCTTTGACGTCGCGAATACCACATTGC
Found at i:12653 original size:13 final size:13
Alignment explanation
Indices: 12630--12660 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
12620 AAGTTTATTG
12630 ATAAT-ATATAAT
1 ATAATAATATAAT
12642 ATAATAATATAAT
1 ATAATAATATAAT
12655 ATAATA
1 ATAATA
12661 TTATTATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
ATAATAATATAAT
Found at i:14465 original size:15 final size:15
Alignment explanation
Indices: 14445--14473 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
14435 ATTTCATGTA
14445 TTTAATTAATTATAC
1 TTTAATTAATTATAC
14460 TTTAATTAATTATA
1 TTTAATTAATTATA
14474 AGGTACTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTAATTAATTATAC
Found at i:14738 original size:17 final size:17
Alignment explanation
Indices: 14713--14757 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
14703 TATTTCGAGT
*
14713 TCGGGCTCGGGTCGGGA
1 TCGGGCTCGGGTCAGGA
* *
14730 TCGGTCTCGGGTCAGGT
1 TCGGGCTCGGGTCAGGA
14747 TCGGGCTCGGG
1 TCGGGCTCGGG
14758 CTGTCTCGGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.04, C:0.24, G:0.49, T:0.22
Consensus pattern (17 bp):
TCGGGCTCGGGTCAGGA
Found at i:14782 original size:16 final size:16
Alignment explanation
Indices: 14763--14805 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
14753 TCGGGCTGTC
*
14763 TCGGGTTCGGGTATTT
1 TCGGGTTCGGGTAATT
**
14779 TCGGACTCGGGTAATT
1 TCGGGTTCGGGTAATT
14795 TCGGGTTCGGG
1 TCGGGTTCGGG
14806 ACGTTGATTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.09, C:0.16, G:0.40, T:0.35
Consensus pattern (16 bp):
TCGGGTTCGGGTAATT
Found at i:18175 original size:2 final size:2
Alignment explanation
Indices: 18170--18204 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
18160 TTTTTTCCCT
*
18170 TC TC TC TC TC TC TC TC TC TC TC TC TC TC CC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
18205 ACCATATTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Done.