Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007723.1 Corchorus capsularis cultivar CVL-1 contig07744, 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: 25326
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4981 original size:27 final size:27
Alignment explanation
Indices: 4943--4998 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
4933 AAGTTGTAAT
*
4943 TAAAATATGATTGGACAATACGTGGTG
1 TAAAATATGATTGGACAATACATGGTG
*
4970 TAAAATATGATTGGACAATTCATGGTG
1 TAAAATATGATTGGACAATACATGGTG
4997 TA
1 TA
4999 GTAGGATGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.32
Consensus pattern (27 bp):
TAAAATATGATTGGACAATACATGGTG
Found at i:5175 original size:6 final size:6
Alignment explanation
Indices: 5164--5197 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
5154 TGGATCATAA
5164 ATCTAT ATCTAT ATCTAT ATCTAT A-CTAT A-CTAT
1 ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT
5198 CTTTCTATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 9 0.32
6 19 0.68
ACGTcount: A:0.35, C:0.18, G:0.00, T:0.47
Consensus pattern (6 bp):
ATCTAT
Found at i:8489 original size:12 final size:12
Alignment explanation
Indices: 8457--8495 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
8447 ATGGAATTAA
8457 ATATCCGTCG--
1 ATATCCGTCGAT
8467 ATA-CC-TCGAT
1 ATATCCGTCGAT
8477 ATATCCGTCGAT
1 ATATCCGTCGAT
8489 ATATCCG
1 ATATCCG
8496 ATATCTGTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
8 3 0.12
9 2 0.08
10 6 0.24
11 2 0.08
12 12 0.48
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (12 bp):
ATATCCGTCGAT
Found at i:9663 original size:16 final size:16
Alignment explanation
Indices: 9644--9683 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
9634 GGTGGTCTCG
*
9644 GGTTCGGGTATTTTCA
1 GGTTCGGGTAATTTCA
*
9660 GGTTCGGGTAATTTCG
1 GGTTCGGGTAATTTCA
9676 GGTTCGGG
1 GGTTCGGG
9684 ACGTTGACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.10, C:0.12, G:0.40, T:0.38
Consensus pattern (16 bp):
GGTTCGGGTAATTTCA
Found at i:13822 original size:18 final size:20
Alignment explanation
Indices: 13801--13839 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
13791 TCGATGTCTC
13801 CGCCACCG-G-ACCACCGTG
1 CGCCACCGCGAACCACCGTG
13819 CGCCACCGCGAACCACCGTG
1 CGCCACCGCGAACCACCGTG
13839 C
1 C
13840 CGGAGGGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.42
19 1 0.05
20 10 0.53
ACGTcount: A:0.18, C:0.51, G:0.26, T:0.05
Consensus pattern (20 bp):
CGCCACCGCGAACCACCGTG
Found at i:15730 original size:22 final size:22
Alignment explanation
Indices: 15702--15997 Score: 89
Period size: 22 Copynumber: 13.4 Consensus size: 22
15692 TCATTGAAGT
* * *
15702 AAATTGAAGCGTTGACATATTG
1 AAATTGAAGCATTGAAAAATTG
*
15724 AAATTGAAACATTGAAAAATTG
1 AAATTGAAGCATTGAAAAATTG
* *
15746 AATTTGAAGAATTG--AAATTG
1 AAATTGAAGCATTGAAAAATTG
**
15766 AAGCATTGAAATATTG--AAATTG
1 AA--ATTGAAGCATTGAAAAATTG
* *
15788 AAACATTGAAGAATTGAAATATTG
1 -AA-ATTGAAGCATTGAAAAATTG
* *
15812 AAGCATTGAA--ATTTG-GAATTTG
1 AA--ATTGAAGCA-TTGAAAAATTG
*
15834 AAGGATTGAA--ATT-AAAGTATTG
1 AA--ATTGAAGCATTGAAA-AATTG
**
15856 AAATATGGAA--ATTGAAGTATTG
1 AAAT-T-GAAGCATTGAAAAATTG
* **
15878 AAGAATCGAA--ATTGAATCATTG
1 -A-AATTGAAGCATTGAAAAATTG
* *
15900 AAGAATTGAAACATTGAAGAATTG
1 AA-A-TTGAAGCATTGAAAAATTG
* * *
15924 AGATTGAAGCATTGGAATATTG
1 AAATTGAAGCATTGAAAAATTG
* *
15946 AAATTGAAACATTGAAGAATTG
1 AAATTGAAGCATTGAAAAATTG
* * * *
15968 AATTTGGAGAATTGAAATATTG
1 AAATTGAAGCATTGAAAAATTG
15990 AAATTGAA
1 AAATTGAA
15998 ACATAGAAGG
Statistics
Matches: 211, Mismatches: 45, Indels: 36
0.72 0.15 0.12
Matches are distributed among these distances:
20 11 0.05
21 6 0.03
22 157 0.74
23 11 0.05
24 26 0.12
ACGTcount: A:0.45, C:0.04, G:0.20, T:0.31
Consensus pattern (22 bp):
AAATTGAAGCATTGAAAAATTG
Found at i:15737 original size:8 final size:7
Alignment explanation
Indices: 15720--16096 Score: 118
Period size: 8 Copynumber: 51.0 Consensus size: 7
15710 GCGTTGACAT
15720 ATTG-AA
1 ATTGAAA
15726 ATTGAAA
1 ATTGAAA
15733 CATTGAAAA
1 -ATTG-AAA
15742 ATTG-AA
1 ATTGAAA
*
15748 TTTGAAGA
1 ATTGAA-A
15756 ATTG-AA
1 ATTGAAA
*
15762 ATTGAAGC
1 ATTGAA-A
15770 ATTGAAA
1 ATTGAAA
15777 TATTG-AA
1 -ATTGAAA
15784 ATTGAAA
1 ATTGAAA
15791 CATTGAAGA
1 -ATTGAA-A
15800 ATTGAAA
1 ATTGAAA
*
15807 TATTGAAGC
1 -ATTGAA-A
15816 ATTGAAA
1 ATTGAAA
* *
15823 TTTGGAA
1 ATTGAAA
* *
15830 TTTGAAGG
1 ATTGAA-A
15838 ATTG-AA
1 ATTGAAA
15844 ATT-AAA
1 ATTGAAA
15850 GTATTG-AA
1 --ATTGAAA
*
15858 ATATGGAA
1 AT-TGAAA
*
15866 ATTGAAGT
1 ATTGAA-A
15874 ATTGAAGA
1 ATTGAA-A
*
15882 ATCG-AA
1 ATTGAAA
*
15888 ATTGAATC
1 ATTGAA-A
15896 ATTGAAGA
1 ATTGAA-A
15904 ATTGAAA
1 ATTGAAA
15911 CATTGAAGA
1 -ATTGAA-A
*
15920 ATTG-AG
1 ATTGAAA
*
15926 ATTGAAGC
1 ATTGAA-A
*
15934 ATTGGAAT
1 ATT-GAAA
15942 ATTG-AA
1 ATTGAAA
15948 ATTGAAA
1 ATTGAAA
15955 CATTGAAGA
1 -ATTGAA-A
15964 ATTG-AA
1 ATTGAAA
* *
15970 TTTGGAGA
1 ATT-GAAA
15978 ATTGAAA
1 ATTGAAA
15985 TATTG-AA
1 -ATTGAAA
15992 ATTGAAA
1 ATTGAAA
* *
15999 CATAGAAGG
1 -ATTGAA-A
*
16008 ACTG-AA
1 ATTGAAA
*
16014 CTTGAAGA
1 ATTGAA-A
16022 ATTG-AA
1 ATTGAAA
* **
16028 ATCGGATC
1 AT-TGAAA
16036 ATTGAAA
1 ATTGAAA
16043 CATTGAAGA
1 -ATTGAA-A
16052 ATTGAAA
1 ATTGAAA
16059 CATTGAAA
1 -ATTGAAA
16067 TATTG-AA
1 -ATTGAAA
*
16074 ATTGAAGC
1 ATTGAA-A
16082 ATTGAAA
1 ATTGAAA
16089 TATTGAAA
1 -ATTGAAA
16097 CTGAAGCATT
Statistics
Matches: 279, Mismatches: 45, Indels: 92
0.67 0.11 0.22
Matches are distributed among these distances:
6 54 0.19
7 53 0.19
8 162 0.58
9 10 0.04
ACGTcount: A:0.46, C:0.05, G:0.20, T:0.30
Consensus pattern (7 bp):
ATTGAAA
Found at i:15842 original size:104 final size:100
Alignment explanation
Indices: 15756--16141 Score: 366
Period size: 104 Copynumber: 3.7 Consensus size: 100
15746 AATTTGAAGA
*
15756 ATTGAAATTGAAGCATTGAAATATTGAAATTGAAACATTGAAGAATTGAAATATTGAAGCATTGA
1 ATTGAAATTGAAGCATTGAAATATTGAAATTGAAACATTGAAGAATTGAAA-ATTGAAGAATTGA
* *
15821 AATTTGGAATTTGAAGGATTGAAATT-AAAGTATTGAAAT
65 AA-TTGG-ATTTGAA-CATTGAAATTGAAA-CATTGAAAT
* * * *
15860 ATGGAAATTGAAGTATTGAAGA-ATCGAAATTGAATCATTGAAGAATTGAAACATTGAAGAATTG
1 ATTGAAATTGAAGCATTGAA-ATATTGAAATTGAAACATTGAAGAATTGAAA-ATTGAAGAATTG
* * *
15924 AGATTGAAGCATTGGAATATTGAAATTGAAACATTGAAGA-
64 AAATTG--G-ATTTGAACATTGAAATTGAAACATTGAA-AT
* * * * * * *
15964 ATTGAATTTGGAGAATTGAAATATTGAAATTGAAACATAGAAGGACTG-AACTTGAAGAATTGAA
1 ATTGAAATTGAAGCATTGAAATATTGAAATTGAAACATTGAAGAATTGAAAATTGAAGAATTGAA
*
16028 ATCGGATCATTGAAACATTGAAGAATTGAAACATTGAAAT
66 ATTGGAT--TTG-AACATTG-A-AATTGAAACATTGAAAT
* * *
16068 ATTGAAATTGAAGCATTGAAATATTGAAACTGAAGCATTAAAGAATTGAAAGAAATGTTGAAGAA
1 ATTGAAATTGAAGCATTGAAATATTGAAATTGAAACATTGAAGAATTG--A-AAA--TTGAAGAA
16133 TTGAAATTG
61 TTGAAATTG
16142 AAGCATTGGA
Statistics
Matches: 228, Mismatches: 36, Indels: 30
0.78 0.12 0.10
Matches are distributed among these distances:
99 2 0.01
100 1 0.00
101 2 0.01
102 21 0.09
103 8 0.04
104 164 0.72
105 12 0.05
108 2 0.01
110 16 0.07
ACGTcount: A:0.46, C:0.05, G:0.20, T:0.29
Consensus pattern (100 bp):
ATTGAAATTGAAGCATTGAAATATTGAAATTGAAACATTGAAGAATTGAAAATTGAAGAATTGAA
ATTGGATTTGAACATTGAAATTGAAACATTGAAAT
Found at i:15993 original size:44 final size:43
Alignment explanation
Indices: 15703--16149 Score: 250
Period size: 44 Copynumber: 10.3 Consensus size: 43
15693 CATTGAAGTA
** * *
15703 AATTGAAGCGTTGACATATTGAAATTGAAACATTGAAAAATTG
1 AATTGAAGAATTGAAATATTGAAATTGAAACATTGAAGAATTG
*
15746 AATTTGAAGAATTG-AA-ATTGAAGCATTGAAATATTG-A-AATTG
1 AA-TTGAAGAATTGAAATATTGAA--ATTGAAACATTGAAGAATTG
* *
15788 AAACATTGAAGAATTGAAATATTGAAGCATTGAAATTTGGAATTTGAAGGATTG
1 --A-ATTGAAGAATTGAAATATTGAA--ATTGAAA-----CA-TTGAAGAATTG
* * * ** *
15842 AAATTAAAGTATTGAAATATGGAAATTGAAGTATTGAAGAATCG
1 -AATTGAAGAATTGAAATATTGAAATTGAAACATTGAAGAATTG
**
15886 AAATTGAATCATTG--A-A--G-AATTGAAACATTGAAGAATTG
1 -AATTGAAGAATTGAAATATTGAAATTGAAACATTGAAGAATTG
* *
15924 AGATTGAAGCATTGGAATATTGAAATTGAAACATTGAAGAATTG
1 A-ATTGAAGAATTGAAATATTGAAATTGAAACATTGAAGAATTG
* * * *
15968 AATTTGGAGAATTGAAATATTGAAATTGAAACATAGAAGGACTG
1 AA-TTGAAGAATTGAAATATTGAAATTGAAACATTGAAGAATTG
** *
16012 AACTTGAAGAATTGAAAT-CGGATCATTGAAACATTGAAGAATTG
1 AA-TTGAAGAATTGAAATATTGA-AATTGAAACATTGAAGAATTG
* *
16056 -A---AA-CATTGAAATATTGAAATTGAAGCATTGAA-ATATTG
1 AATTGAAGAATTGAAATATTGAAATTGAAACATTGAAGA-ATTG
* * * **
16094 AAACTGAAGCATT-AAAGAATTGAAA--GAAATGTTGAAGAATTG
1 -AATTGAAGAATTGAAA-TATTGAAATTGAAACATTGAAGAATTG
*
16136 AAATTGAAGCATTG
1 -AATTGAAGAATTG
16150 GAGATTTGGA
Statistics
Matches: 324, Mismatches: 44, Indels: 72
0.74 0.10 0.16
Matches are distributed among these distances:
37 2 0.01
38 54 0.17
39 5 0.02
40 2 0.01
41 2 0.01
42 36 0.11
43 15 0.05
44 153 0.47
45 4 0.01
46 15 0.05
50 6 0.02
51 1 0.00
52 22 0.07
53 3 0.01
54 4 0.01
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.29
Consensus pattern (43 bp):
AATTGAAGAATTGAAATATTGAAATTGAAACATTGAAGAATTG
Found at i:16079 original size:22 final size:22
Alignment explanation
Indices: 16035--16173 Score: 108
Period size: 22 Copynumber: 6.3 Consensus size: 22
16025 GAAATCGGAT
* *
16035 CATTGAAACATTGAAGAATTGAAA
1 CATTGAAATATTG-A-AATTGAAG
16059 CATTGAAATATTGAAATTGAAG
1 CATTGAAATATTGAAATTGAAG
*
16081 CATTGAAATATTGAAACTGAAG
1 CATTGAAATATTGAAATTGAAG
* *
16103 CATT-AAAGAATTGAAA--GAAA
1 CATTGAAA-TATTGAAATTGAAG
**
16123 TGTTGAAGA-ATTGAAATTGAAG
1 CATTGAA-ATATTGAAATTGAAG
* * *
16145 CATTGGAGAT-TTGGAATTGAGG
1 CATT-GAAATATTGAAATTGAAG
16167 CATTGAA
1 CATTGAA
16174 TAATTAAGGA
Statistics
Matches: 94, Mismatches: 14, Indels: 17
0.75 0.11 0.14
Matches are distributed among these distances:
20 12 0.13
21 7 0.07
22 60 0.64
23 3 0.03
24 12 0.13
ACGTcount: A:0.45, C:0.06, G:0.22, T:0.28
Consensus pattern (22 bp):
CATTGAAATATTGAAATTGAAG
Found at i:16116 original size:30 final size:31
Alignment explanation
Indices: 15852--16118 Score: 110
Period size: 30 Copynumber: 9.0 Consensus size: 31
15842 AAATTAAAGT
*
15852 ATTGAAATA-TGGAA-ATTGAAGTATTGAAGA-
1 ATTGAAATACT-GAACATTGAAGAATTGAA-AC
*
15882 ATCGAAAT--TGAATCATTGAAGAATTGAAAC
1 ATTGAAATACTGAA-CATTGAAGAATTGAAAC
* * * * *
15912 ATTGAAGA-ATTG-AGATTGAAGCATTGGAAT
1 ATTGAA-ATACTGAACATTGAAGAATTGAAAC
15942 ATTGAAAT--TGAAACATTGAAGAATTG-AA-
1 ATTGAAATACTG-AACATTGAAGAATTGAAAC
* *
15970 TTTGGAGAAT--TGAAATATTG-A-AATTGAAAC
1 ATT-GA-AATACTG-AACATTGAAGAATTGAAAC
* **
16000 ATAGAAGGACTGAAC-TTGAAGAATTG-AA-
1 ATTGAAATACTGAACATTGAAGAATTGAAAC
* * *
16028 ATCG-GATCATTGAAACATTGAAGAATTGAAAC
1 ATTGAAAT-ACTG-AACATTGAAGAATTGAAAC
* * *
16060 ATTGAAATATTGAA-ATTGAAGCATTGAAAT
1 ATTGAAATACTGAACATTGAAGAATTGAAAC
*
16090 ATTG-AA-ACTGAAGCATTAAAGAATTGAAA
1 ATTGAAATACTGAA-CATTGAAGAATTGAAA
16119 GAAATGTTGA
Statistics
Matches: 184, Mismatches: 28, Indels: 50
0.70 0.11 0.19
Matches are distributed among these distances:
28 27 0.15
29 22 0.12
30 118 0.64
31 6 0.03
32 9 0.05
33 2 0.01
ACGTcount: A:0.46, C:0.06, G:0.20, T:0.28
Consensus pattern (31 bp):
ATTGAAATACTGAACATTGAAGAATTGAAAC
Found at i:16238 original size:16 final size:18
Alignment explanation
Indices: 16207--16240 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
16197 CACCATGTAT
16207 CATTGAAGCAAATTGAAG
1 CATTGAAGCAAATTGAAG
16225 CATTGAA-C-AATTGAAG
1 CATTGAAGCAAATTGAAG
16241 AGACGAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 1 0.06
18 7 0.44
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.24
Consensus pattern (18 bp):
CATTGAAGCAAATTGAAG
Found at i:16287 original size:8 final size:8
Alignment explanation
Indices: 16274--16377 Score: 54
Period size: 8 Copynumber: 13.0 Consensus size: 8
16264 TCATTAAAAT
16274 GAATTGAA
1 GAATTGAA
16282 GAATTGAA
1 GAATTGAA
* *
16290 GCATT-TA
1 GAATTGAA
*
16297 GTAACTGAA
1 G-AATTGAA
*
16306 TAATTGAA
1 GAATTGAA
16314 GCAA-T-AA
1 G-AATTGAA
16321 GTAATTGAA
1 G-AATTGAA
*
16330 TAATTGAA
1 GAATTGAA
16338 -ATATTGAA
1 GA-ATTGAA
* *
16346 TAATTGGA
1 GAATTGAA
16354 GAATTGAA
1 GAATTGAA
* *
16362 CAATGGAA
1 GAATTGAA
*
16370 GAGTTGAA
1 GAATTGAA
16378 TCTTTAAAGA
Statistics
Matches: 71, Mismatches: 18, Indels: 14
0.69 0.17 0.14
Matches are distributed among these distances:
7 8 0.11
8 57 0.80
9 6 0.08
ACGTcount: A:0.46, C:0.04, G:0.21, T:0.29
Consensus pattern (8 bp):
GAATTGAA
Found at i:16305 original size:24 final size:24
Alignment explanation
Indices: 16278--16337 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
16268 TAAAATGAAT
* * *
16278 TGAAGAATTGAAGCATTTAGTAAC
1 TGAATAATTGAAGCAATAAGTAAC
*
16302 TGAATAATTGAAGCAATAAGTAAT
1 TGAATAATTGAAGCAATAAGTAAC
16326 TGAATAATTGAA
1 TGAATAATTGAA
16338 ATATTGAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.47, C:0.05, G:0.18, T:0.30
Consensus pattern (24 bp):
TGAATAATTGAAGCAATAAGTAAC
Found at i:16648 original size:17 final size:18
Alignment explanation
Indices: 16626--16659 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16616 CTCATGATGC
16626 AATGCAA-AATGCATGAT
1 AATGCAATAATGCATGAT
*
16643 AATGCAATTATGCATGA
1 AATGCAATAATGCATGA
16660 CATGCTTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.44, C:0.12, G:0.18, T:0.26
Consensus pattern (18 bp):
AATGCAATAATGCATGAT
Found at i:17684 original size:6 final size:6
Alignment explanation
Indices: 17675--17719 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
17665 TCACTTTCAC
* *
17675 TTTTGA TTTTGA TTTTGG TTTTGA TTTTGA TATTGA -TTTGA TTTT
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTT
17720 TTTTTTTGCA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
5 4 0.12
6 30 0.88
ACGTcount: A:0.16, C:0.00, G:0.18, T:0.67
Consensus pattern (6 bp):
TTTTGA
Found at i:18076 original size:33 final size:34
Alignment explanation
Indices: 18028--18093 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 34
18018 TGCAAAACAT
*
18028 TTTTGAAAAAACATTTTTGAAAATCATGACTCTC
1 TTTTGAAAAAACATTTTTGAAAACCATGACTCTC
18062 TTTTG-AAAAACATTTTTGAAAACCATGACTCT
1 TTTTGAAAAAACATTTTTGAAAACCATGACTCT
18094 ACTATTCCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 26 0.84
34 5 0.16
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (34 bp):
TTTTGAAAAAACATTTTTGAAAACCATGACTCTC
Done.