Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014106.1 Corchorus capsularis cultivar CVL-1 contig14127, 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: 22740
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Found at i:3145 original size:37 final size:37
Alignment explanation
Indices: 3104--3486 Score: 642
Period size: 37 Copynumber: 10.4 Consensus size: 37
3094 ACTCAAGATG
3104 ATTAAGTAAAAGCAGTTAAAGAACTTAATTCAGGGTA
1 ATTAAGTAAAAGCAGTTAAAGAACTTAATTCAGGGTA
3141 ATTAAGTAAAAGCAGTTAAAGAACTTAATTCAGGGTA
1 ATTAAGTAAAAGCAGTTAAAGAACTTAATTCAGGGTA
3178 ATTAAGTAAAAGCAGTTAAAGAACTTAATTCAGGGTA
1 ATTAAGTAAAAGCAGTTAAAGAACTTAATTCAGGGTA
*
3215 ATTAAGTAAAAGCAGTTAAAGAACTTAGTTCAGGGTA
1 ATTAAGTAAAAGCAGTTAAAGAACTTAATTCAGGGTA
* *
3252 ATTAAGTAAAAGCAGTTAAAGGACTTAATTTAGGGTA
1 ATTAAGTAAAAGCAGTTAAAGAACTTAATTCAGGGTA
*
3289 ATTAAGTAAAAGCAGTTAAAGAACTTAGTTCAGGGTA
1 ATTAAGTAAAAGCAGTTAAAGAACTTAATTCAGGGTA
*
3326 ATTAAGTAAAAGTAGTTAAAGAACTTAATTCAGGGTA
1 ATTAAGTAAAAGCAGTTAAAGAACTTAATTCAGGGTA
3363 ATTAAGTAAAAGCAGTTAAAGAACTTAATTCAGGGTA
1 ATTAAGTAAAAGCAGTTAAAGAACTTAATTCAGGGTA
* *
3400 ATTAAGTAAAAGTAGTTAAAGGACTTAATTCAGGGTA
1 ATTAAGTAAAAGCAGTTAAAGAACTTAATTCAGGGTA
** * * *
3437 ATTAAGTAAAATTAG-TCAAGGAGTTAATTCAGGGTA
1 ATTAAGTAAAAGCAGTTAAAGAACTTAATTCAGGGTA
*
3473 ATTGAGTAAAAGCA
1 ATTAAGTAAAAGCA
3487 AGCACAAACT
Statistics
Matches: 328, Mismatches: 18, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
36 30 0.09
37 298 0.91
ACGTcount: A:0.45, C:0.07, G:0.20, T:0.28
Consensus pattern (37 bp):
ATTAAGTAAAAGCAGTTAAAGAACTTAATTCAGGGTA
Found at i:3565 original size:41 final size:41
Alignment explanation
Indices: 3486--3665 Score: 263
Period size: 41 Copynumber: 4.4 Consensus size: 41
3476 GAGTAAAAGC
*
3486 AAGCACAAACTTAATTTCAAGGAAGGAAATTAGATAAAGAA
1 AAGCACAAACTTAATTTCAAGGAAGGAAATTAGGTAAAGAA
3527 ACAGCACAAACTTAATTTCAA-GAAGGAAATTAGGTAAAGAA
1 A-AGCACAAACTTAATTTCAAGGAAGGAAATTAGGTAAAGAA
* * *
3568 TAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAC
1 AAGCACAAACTTAATTTCAAGGAAGGAAATTAGGTAAAGAA
* * **
3609 AAGCACAGACTTAATTTCAATGAAGGAAATTAGGTAAAGGC
1 AAGCACAAACTTAATTTCAAGGAAGGAAATTAGGTAAAGAA
*
3650 AAGCACATACTTAATT
1 AAGCACAAACTTAATT
3666 CAGGGTAATT
Statistics
Matches: 129, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
40 18 0.14
41 92 0.71
42 19 0.15
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.22
Consensus pattern (41 bp):
AAGCACAAACTTAATTTCAAGGAAGGAAATTAGGTAAAGAA
Found at i:3748 original size:36 final size:36
Alignment explanation
Indices: 3672--3775 Score: 88
Period size: 36 Copynumber: 2.9 Consensus size: 36
3662 AATTCAGGGT
* * *
3672 AATTAAGT-AAATTAGCCAAGACTTAATCTCACAAG
1 AATTAAGTAAAATCATCAAAGACTTAATCTCACAAG
*
3707 AATTAATTAAAATCATCAAAGACTTAATC-CA-AAG
1 AATTAAGTAAAATCATCAAAGACTTAATCTCACAAG
* * * *
3741 ATGATTAAGTAAGATCAGACAAAAACTTAACCTCA
1 A--ATTAAGTAAAATCA-TCAAAGACTTAATCTCA
3776 GGGGATTAAG
Statistics
Matches: 55, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
34 4 0.07
35 9 0.16
36 29 0.53
37 11 0.20
38 2 0.04
ACGTcount: A:0.49, C:0.16, G:0.10, T:0.25
Consensus pattern (36 bp):
AATTAAGTAAAATCATCAAAGACTTAATCTCACAAG
Found at i:3840 original size:37 final size:37
Alignment explanation
Indices: 3803--4170 Score: 523
Period size: 37 Copynumber: 10.1 Consensus size: 37
3793 AATGAATTAG
* *
3803 TTCCAAGGAAGGGAATTAAGTAGAGTTAAGGACTTAG
1 TTCCAAGGAAGGAAATTAAGTAGAGTTAAGGACTTAA
*
3840 TTCCAAGGAAGGAAATTAAGTAGAGTAAAGGACTTAA
1 TTCCAAGGAAGGAAATTAAGTAGAGTTAAGGACTTAA
* * *
3877 TTTCAAGGAAGGAAATTAAGTAGAGTAAAGGACTTGA
1 TTCCAAGGAAGGAAATTAAGTAGAGTTAAGGACTTAA
*
3914 TTCCAAGGAAGGGAATTAAGTAGAGTTAAGGACTTAA
1 TTCCAAGGAAGGAAATTAAGTAGAGTTAAGGACTTAA
**
3951 TTTAAAGGAAGGAAATTAAGTAGAGTTAAGGACTTAA
1 TTCCAAGGAAGGAAATTAAGTAGAGTTAAGGACTTAA
*
3988 TTCCAAGGAAGGGAATTAAGTAGAGTTAAGGACTTAA
1 TTCCAAGGAAGGAAATTAAGTAGAGTTAAGGACTTAA
*
4025 TTCCAAGGAAGGGAATTAAGTAGAGTTAAGGACTTAA
1 TTCCAAGGAAGGAAATTAAGTAGAGTTAAGGACTTAA
** *
4062 TTTTAAGGAAGGAAATTAAGT--AG---AGGACTTGA
1 TTCCAAGGAAGGAAATTAAGTAGAGTTAAGGACTTAA
* *
4094 TTCCAAGGAAGGGAATTAGGTAGAGTTAAGGACTTAA
1 TTCCAAGGAAGGAAATTAAGTAGAGTTAAGGACTTAA
* *
4131 TTTCAAGGAAGGAAATTAAGTCA-AGTTAGGGACTTAA
1 TTCCAAGGAAGGAAATTAAGT-AGAGTTAAGGACTTAA
4168 TTC
1 TTC
4171 AGGGTAATTA
Statistics
Matches: 296, Mismatches: 29, Indels: 12
0.88 0.09 0.04
Matches are distributed among these distances:
32 25 0.08
34 2 0.01
35 2 0.01
37 266 0.90
38 1 0.00
ACGTcount: A:0.41, C:0.07, G:0.27, T:0.25
Consensus pattern (37 bp):
TTCCAAGGAAGGAAATTAAGTAGAGTTAAGGACTTAA
Found at i:3907 original size:19 final size:19
Alignment explanation
Indices: 3848--3908 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
3838 AGTTCCAAGG
3848 AAGGAAATTAAGTAGAGTA
1 AAGGAAATTAAGTAGAGTA
* * *
3867 AAGG-ACTTAATTTCA-AG-G
1 AAGGAAATTAA-GT-AGAGTA
3885 AAGGAAATTAAGTAGAGTA
1 AAGGAAATTAAGTAGAGTA
3904 AAGGA
1 AAGGA
3909 CTTGATTCCA
Statistics
Matches: 31, Mismatches: 6, Indels: 10
0.66 0.13 0.21
Matches are distributed among these distances:
17 1 0.03
18 12 0.39
19 17 0.55
20 1 0.03
ACGTcount: A:0.49, C:0.03, G:0.26, T:0.21
Consensus pattern (19 bp):
AAGGAAATTAAGTAGAGTA
Found at i:3981 original size:19 final size:19
Alignment explanation
Indices: 3922--3982 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
3912 GATTCCAAGG
*
3922 AAGGGAATTAAGTAGAGTT
1 AAGGAAATTAAGTAGAGTT
* * * *
3941 AAGG-ACTTAATTTAAAG-G
1 AAGGAAATTAA-GTAGAGTT
3959 AAGGAAATTAAGTAGAGTT
1 AAGGAAATTAAGTAGAGTT
3978 AAGGA
1 AAGGA
3983 CTTAATTCCA
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
18 13 0.42
19 18 0.58
ACGTcount: A:0.46, C:0.02, G:0.28, T:0.25
Consensus pattern (19 bp):
AAGGAAATTAAGTAGAGTT
Found at i:3999 original size:18 final size:18
Alignment explanation
Indices: 3978--4036 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
3968 AAGTAGAGTT
3978 AAGGACTTAATTCCAAGG
1 AAGGACTTAATTCCAAGG
* * *
3996 AAGGGAATTAAGT--AGAGTT
1 AA-GGACTTAATTCCA-AG-G
4015 AAGGACTTAATTCCAAGG
1 AAGGACTTAATTCCAAGG
4033 AAGG
1 AAGG
4037 GAATTAAGTA
Statistics
Matches: 30, Mismatches: 6, Indels: 10
0.65 0.13 0.22
Matches are distributed among these distances:
17 1 0.03
18 16 0.53
19 12 0.40
20 1 0.03
ACGTcount: A:0.41, C:0.10, G:0.27, T:0.22
Consensus pattern (18 bp):
AAGGACTTAATTCCAAGG
Found at i:4191 original size:37 final size:37
Alignment explanation
Indices: 4150--4291 Score: 141
Period size: 37 Copynumber: 3.9 Consensus size: 37
4140 AGGAAATTAA
*
4150 GTCAAGTTAGGGACTTAATTCAGGGTAATTAAGTAGC
1 GTCAAGTAAGGGACTTAATTCAGGGTAATTAAGTAGC
* * *
4187 GTCAAGTCAGGGACTTAATTCAAGGTAATTAACTAGC
1 GTCAAGTAAGGGACTTAATTCAGGGTAATTAAGTAGC
* * * *
4224 ATCAA-TAAAAGG-CTTAATTCAGGGTAATTAAG-GGA
1 GTCAAGT-AAGGGACTTAATTCAGGGTAATTAAGTAGC
* *
4259 GTCAA-TAAAAGG-CTTAATTCGGGGTAATTAAGT
1 GTCAAGT-AAGGGACTTAATTCAGGGTAATTAAGT
4292 GGAGTCAATA
Statistics
Matches: 91, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
35 31 0.34
36 19 0.21
37 41 0.45
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.28
Consensus pattern (37 bp):
GTCAAGTAAGGGACTTAATTCAGGGTAATTAAGTAGC
Found at i:4303 original size:36 final size:36
Alignment explanation
Indices: 4163--4303 Score: 162
Period size: 36 Copynumber: 3.9 Consensus size: 36
4153 AAGTTAGGGA
* * * *
4163 CTTAATTCAGGGTAATTAAGTAGCGTCAAGT-CAGGG
1 CTTAATTCAGGGTAATTAAGTGGAGTCAA-TAAAAGG
* * *
4199 ACTTAATTCAAGGTAATTAACTAGCA-TCAATAAAAGG
1 -CTTAATTCAGGGTAATTAAGT-GGAGTCAATAAAAGG
4236 CTTAATTCAGGGTAATTAAG-GGAGTCAATAAAAGG
1 CTTAATTCAGGGTAATTAAGTGGAGTCAATAAAAGG
*
4271 CTTAATTCGGGGTAATTAAGTGGAGTCAATAAA
1 CTTAATTCAGGGTAATTAAGTGGAGTCAATAAA
4304 GAACTTAATC
Statistics
Matches: 89, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
34 2 0.02
35 30 0.34
36 31 0.35
37 26 0.29
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (36 bp):
CTTAATTCAGGGTAATTAAGTGGAGTCAATAAAAGG
Found at i:9948 original size:15 final size:15
Alignment explanation
Indices: 9928--9980 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
9918 AATCCTGCGA
9928 ATTGGATTGTGATTG
1 ATTGGATTGTGATTG
9943 ATTGGA-T-TG--TG
1 ATTGGATTGTGATTG
9954 A--GGATTGTGATTG
1 ATTGGATTGTGATTG
9967 ATTGGATTGTGATT
1 ATTGGATTGTGATT
9981 CTCTTTTAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
9 3 0.09
10 1 0.03
11 5 0.16
13 5 0.16
14 1 0.03
15 17 0.53
ACGTcount: A:0.21, C:0.00, G:0.34, T:0.45
Consensus pattern (15 bp):
ATTGGATTGTGATTG
Found at i:9963 original size:24 final size:24
Alignment explanation
Indices: 9931--9978 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
9921 CCTGCGAATT
9931 GGATTGTGATTGATTGGATTGTGA
1 GGATTGTGATTGATTGGATTGTGA
9955 GGATTGTGATTGATTGGATTGTGA
1 GGATTGTGATTGATTGGATTGTGA
9979 TTCTCTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.38, T:0.42
Consensus pattern (24 bp):
GGATTGTGATTGATTGGATTGTGA
Found at i:10041 original size:21 final size:21
Alignment explanation
Indices: 10015--10060 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
10005 ATAGTGTAGC
*
10015 TCCTGTCCTTTGAGAGGGAGG
1 TCCTGTCCTTTGAGAGGGAGA
*
10036 TCCTGTCCTTTGGGAGGGAGA
1 TCCTGTCCTTTGAGAGGGAGA
10057 TCCT
1 TCCT
10061 ATGAGAGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.13, C:0.22, G:0.35, T:0.30
Consensus pattern (21 bp):
TCCTGTCCTTTGAGAGGGAGA
Found at i:10152 original size:28 final size:28
Alignment explanation
Indices: 10112--10168 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
10102 GATCTTCTTT
10112 TAGTTTCTGTTCTTCATGTACATAGAAG
1 TAGTTTCTGTTCTTCATGTACATAGAAG
10140 TAGTTTCTGTTCTTCATGTACATAGAAG
1 TAGTTTCTGTTCTTCATGTACATAGAAG
10168 T
1 T
10169 GCAAACATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.44
Consensus pattern (28 bp):
TAGTTTCTGTTCTTCATGTACATAGAAG
Found at i:11704 original size:41 final size:40
Alignment explanation
Indices: 11648--11733 Score: 154
Period size: 41 Copynumber: 2.1 Consensus size: 40
11638 ATCTCACACT
*
11648 TTCACTTTTGTAAGATGATAGTTGGTAGGTAATGGTTTTG
1 TTCACTTTTGTAAGATGATAGTTGGTAGATAATGGTTTTG
11688 TTCACTTTTTGTAAGATGATAGTTGGTAGATAATGGTTTTG
1 TTCAC-TTTTGTAAGATGATAGTTGGTAGATAATGGTTTTG
11729 TTCAC
1 TTCAC
11734 AACATGGGGC
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 5 0.11
41 39 0.89
ACGTcount: A:0.23, C:0.07, G:0.24, T:0.45
Consensus pattern (40 bp):
TTCACTTTTGTAAGATGATAGTTGGTAGATAATGGTTTTG
Found at i:17473 original size:14 final size:13
Alignment explanation
Indices: 17448--17497 Score: 52
Period size: 14 Copynumber: 4.0 Consensus size: 13
17438 TCGTTTGGCA
*
17448 TCGTTTTCGTTTT
1 TCGTTTTTGTTTT
17461 TCGTTTTTTGTTTT
1 TCG-TTTTTGTTTT
*
17475 TTGTTTTTG--TT
1 TCGTTTTTGTTTT
17486 TCG-TTTTGTTTT
1 TCGTTTTTGTTTT
17498 CATTACGCTG
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
10 5 0.16
11 4 0.13
12 2 0.06
13 9 0.29
14 11 0.35
ACGTcount: A:0.00, C:0.08, G:0.16, T:0.76
Consensus pattern (13 bp):
TCGTTTTTGTTTT
Found at i:18735 original size:1 final size:1
Alignment explanation
Indices: 18729--18762 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
18719 GGAGGAAAGG
18729 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
18763 GGAAGCTAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:21892 original size:15 final size:15
Alignment explanation
Indices: 21854--21893 Score: 64
Period size: 14 Copynumber: 2.7 Consensus size: 15
21844 CGGAAAAAGG
21854 CATTTCAGAATTTTT
1 CATTTCAGAATTTTT
*
21869 C-TTTAAGAATTTTT
1 CATTTCAGAATTTTT
21883 CATTTCAGAAT
1 CATTTCAGAAT
21894 CATCCCATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.30, C:0.12, G:0.07, T:0.50
Consensus pattern (15 bp):
CATTTCAGAATTTTT
Done.