Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013916.1 Corchorus capsularis cultivar CVL-1 contig13937, 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: 34425
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:11 original size:2 final size:2
Alignment explanation
Indices: 5--40 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1 TATG
5 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
41 TACGTCTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4893 original size:31 final size:31
Alignment explanation
Indices: 4855--4916 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
4845 AGTTTTGTAA
* *
4855 AACTTTTGAAATACCTATTGTATCCTTATTT
1 AACTTTTGAAACACCTATTATATCCTTATTT
* *
4886 AACTTTTGAAACGCCTATTATATCTTTATTT
1 AACTTTTGAAACACCTATTATATCCTTATTT
4917 TTCTAACATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.29, C:0.16, G:0.06, T:0.48
Consensus pattern (31 bp):
AACTTTTGAAACACCTATTATATCCTTATTT
Found at i:5172 original size:138 final size:137
Alignment explanation
Indices: 4938--5213 Score: 507
Period size: 138 Copynumber: 2.0 Consensus size: 137
4928 TTCTAAACTG
*
4938 CCATTATATAATTATTTTTTTAATTTTGTTAATTTACATTTAATTAAATCTACGAAATATATATC
1 CCATTATATAATTATTTTTTTAATTTTGTTAATTTACATTTAATTAAATCTACGAAATATATATA
*
5003 TCAAATTTAGTTTTTATAGATTTCAACTTCTTGAACCAAACGTTTCTAATAGACTAATAACATTT
66 TCAAATTTAGTTTCTATAGATTTCAACTTCTTGAACCAAA-GTTTCTAATAGACTAATAACATTT
5068 AATTAAAT
130 AATTAAAT
5076 CCATTATATAATTATTTTTTTAATTTTGTTAATTTACATTTAATTAAATCTACGAAATATATATA
1 CCATTATATAATTATTTTTTTAATTTTGTTAATTTACATTTAATTAAATCTACGAAATATATATA
* *
5141 TCAAATTTAGTTTCTATAGATTTCAATTTCTTGAACCAAAGTTTCTAATAGACTAATAGCATTTA
66 TCAAATTTAGTTTCTATAGATTTCAACTTCTTGAACCAAAGTTTCTAATAGACTAATAACATTTA
5206 ATTAAAT
131 ATTAAAT
5213 C
1 C
5214 TACGAAATAT
Statistics
Matches: 134, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
137 32 0.24
138 102 0.76
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (137 bp):
CCATTATATAATTATTTTTTTAATTTTGTTAATTTACATTTAATTAAATCTACGAAATATATATA
TCAAATTTAGTTTCTATAGATTTCAACTTCTTGAACCAAAGTTTCTAATAGACTAATAACATTTA
ATTAAAT
Found at i:7543 original size:25 final size:26
Alignment explanation
Indices: 7514--7565 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 26
7504 TCTGAAGAAG
*
7514 GAAAAAGAAA-ATAAAAAGAAAATAA
1 GAAAAAGAAAGAGAAAAAGAAAATAA
* *
7539 G-AAAAGAAAGAGGAAGAGAAAATAA
1 GAAAAAGAAAGAGAAAAAGAAAATAA
7564 GA
1 GA
7566 GGGTTAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.73, C:0.00, G:0.21, T:0.06
Consensus pattern (26 bp):
GAAAAAGAAAGAGAAAAAGAAAATAA
Found at i:18800 original size:6 final size:6
Alignment explanation
Indices: 18791--18817 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
18781 AAAGCAAAGC
18791 AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAA
18818 GCAGATTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:19782 original size:10 final size:10
Alignment explanation
Indices: 19767--19802 Score: 72
Period size: 10 Copynumber: 3.6 Consensus size: 10
19757 GAGGACTCTA
19767 GAATTTTCTG
1 GAATTTTCTG
19777 GAATTTTCTG
1 GAATTTTCTG
19787 GAATTTTCTG
1 GAATTTTCTG
19797 GAATTT
1 GAATTT
19803 GGCAGCAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.22, C:0.08, G:0.19, T:0.50
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:25647 original size:23 final size:23
Alignment explanation
Indices: 25603--25658 Score: 78
Period size: 25 Copynumber: 2.4 Consensus size: 23
25593 GGAAAAAACC
*
25603 TTTTTTTTATCGATGCAAAAACAAT
1 TTTTTTTTATCGACGC-AAAAC-AT
25628 TTTTTTTTATCGACGC-AAACAT
1 TTTTTTTTATCGACGCAAAACAT
25650 TTTTTTTTA
1 TTTTTTTTA
25659 AAGAAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 11 0.37
23 4 0.13
25 15 0.50
ACGTcount: A:0.29, C:0.12, G:0.07, T:0.52
Consensus pattern (23 bp):
TTTTTTTTATCGACGCAAAACAT
Found at i:26065 original size:17 final size:17
Alignment explanation
Indices: 26035--26067 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
26025 GATTAATAAG
26035 ACAAATTAATAAAGCAA
1 ACAAATTAATAAAGCAA
26052 ACAATATTAA-AAAGCA
1 ACAA-ATTAATAAAGCA
26068 TACTTCTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.64, C:0.12, G:0.06, T:0.18
Consensus pattern (17 bp):
ACAAATTAATAAAGCAA
Found at i:26985 original size:10 final size:10
Alignment explanation
Indices: 26970--26997 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
26960 GAGGACTCTA
26970 GAATTTTCTG
1 GAATTTTCTG
26980 GAATTTTCTG
1 GAATTTTCTG
26990 GAATTTTC
1 GAATTTTC
26998 CAGCAACTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.21, C:0.11, G:0.18, T:0.50
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:28191 original size:7 final size:7
Alignment explanation
Indices: 28171--28211 Score: 73
Period size: 7 Copynumber: 5.7 Consensus size: 7
28161 ATCTATAACA
28171 TTATATT
1 TTATATT
28178 ATTATATT
1 -TTATATT
28186 TTATATT
1 TTATATT
28193 TTATATT
1 TTATATT
28200 TTATATT
1 TTATATT
28207 TTATA
1 TTATA
28212 AGAGAAGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 26 0.79
8 7 0.21
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
TTATATT
Found at i:28470 original size:150 final size:150
Alignment explanation
Indices: 28199--28502 Score: 545
Period size: 150 Copynumber: 2.0 Consensus size: 150
28189 TATTTTATAT
* *
28199 TTTATATTTTATAAGAGAAGTAAAAGTACTAAAAAACCAGTTGAAAAACCTCACCACATTCACCC
1 TTTATATATAATAAGAGAAGTAAAAGTACTAAAAAACCAGTTGAAAAACCTCACCACATTCACCC
* * *
28264 AAGAACAACTTATCAGGGGTATTTCGGTACTTTTGTGCTCGGTTTCTTTGTTATTTGAGTTGATG
66 AAGAACAAATTATCAGGGGTATTTCGGTACTTTTATGCTCGATTTCTTTGTTATTTGAGTTGATG
28329 GTTGAGGGCGTTTCTAGAAC
131 GTTGAGGGCGTTTCTAGAAC
* *
28349 TTTATATATAATAAGAGAAGTAAAAGTACTAAAAAACCAGTTGAGAAAGCTCACCACATTCACCC
1 TTTATATATAATAAGAGAAGTAAAAGTACTAAAAAACCAGTTGAAAAACCTCACCACATTCACCC
28414 AAGAACAAATTATCAGGGGTATTTCGGTACTTTTATGCTCGATTTCTTTGTTATTTGAGTTGATG
66 AAGAACAAATTATCAGGGGTATTTCGGTACTTTTATGCTCGATTTCTTTGTTATTTGAGTTGATG
28479 GTTGAGGGCGTTTCTAGAAC
131 GTTGAGGGCGTTTCTAGAAC
28499 TTTA
1 TTTA
28503 GAAAAATGTT
Statistics
Matches: 147, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
150 147 1.00
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (150 bp):
TTTATATATAATAAGAGAAGTAAAAGTACTAAAAAACCAGTTGAAAAACCTCACCACATTCACCC
AAGAACAAATTATCAGGGGTATTTCGGTACTTTTATGCTCGATTTCTTTGTTATTTGAGTTGATG
GTTGAGGGCGTTTCTAGAAC
Found at i:29403 original size:86 final size:86
Alignment explanation
Indices: 29256--29413 Score: 201
Period size: 86 Copynumber: 1.8 Consensus size: 86
29246 GGTCCATCTG
* * *** * * * *
29256 TCCGATTGAGATTGTTCAAGTGTCGGTTAAAAGGTTATTGTGTGATTTGCGACTTTCATGAAGGA
1 TCCGATTGAGATTATTAAAGTGTCGGTTAAAAGGTTATTACATAATCTACGACTTTCATGAAGCA
29321 CCCGAAAGTTAAATTTGATTC
66 CCCGAAAGTTAAATTTGATTC
*
29342 TCCGATTGA-AGTTATTAAAGTGTCGGTTAAAAGGTTATTACATAATCTACGACTTTTATGAAGC
1 TCCGATTGAGA-TTATTAAAGTGTCGGTTAAAAGGTTATTACATAATCTACGACTTTCATGAAGC
*
29406 ACCTGAAA
65 ACCCGAAA
29414 TCCTAATTTA
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
85 1 0.02
86 59 0.98
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (86 bp):
TCCGATTGAGATTATTAAAGTGTCGGTTAAAAGGTTATTACATAATCTACGACTTTCATGAAGCA
CCCGAAAGTTAAATTTGATTC
Found at i:30106 original size:2 final size:2
Alignment explanation
Indices: 30099--30125 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
30089 GTGATTAAAC
30099 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
30126 CTAAACACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31455 original size:38 final size:38
Alignment explanation
Indices: 31397--31581 Score: 309
Period size: 38 Copynumber: 4.9 Consensus size: 38
31387 CACAATTTAG
31397 CCAACAG-TTAACCCCCTGAGGCACGGGTCCACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
*
31434 CCAACAGTTTAACCCCATGAGGCACGGGTCCACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
*
31472 CCAACAGTTTAACCCCCTGAGGCACGGGTCTACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
* *
31510 CGAACAGTTTAACCCCCTGAGGCACGGGTCCACTTTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
* *
31548 CCATCAGTTTAACCCCCTGAGGCGCGGGTCCACT
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACT
31582 ATGCACAGTC
Statistics
Matches: 138, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
37 7 0.05
38 131 0.95
ACGTcount: A:0.23, C:0.35, G:0.20, T:0.22
Consensus pattern (38 bp):
CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
Found at i:33832 original size:37 final size:38
Alignment explanation
Indices: 33779--34001 Score: 333
Period size: 38 Copynumber: 5.9 Consensus size: 38
33769 CACAATTTAG
33779 CCAACAG-TTAACCCCCTGAGGCACGGGTCCACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
*
33816 CCAACAGTTTAA-CCCCTGAGGCACGGGTCCATTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
*
33853 CCAACAGTTTAACCCCCTGAGGCACGAGTCCACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
* * *
33891 CCAACCAGTTTAACCCCCTGAGGCACGAGTCTATTCTTA
1 CCAA-CAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
*
33930 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTTTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
* * * *
33968 CCATCAGTTGAACCCCCTGAGGCGCGTGTCCACT
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACT
34002 ATGCACAGCC
Statistics
Matches: 170, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
37 43 0.25
38 91 0.54
39 36 0.21
ACGTcount: A:0.24, C:0.35, G:0.18, T:0.22
Consensus pattern (38 bp):
CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
Found at i:33943 original size:77 final size:76
Alignment explanation
Indices: 33779--33999 Score: 347
Period size: 77 Copynumber: 2.9 Consensus size: 76
33769 CACAATTTAG
*
33779 CCAACAG-TTAACCCCCTGAGGCACGGGTCCACTCTTACCAACAGTTTAA-CCCCTGAGGCACGG
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCACGA
33842 GTCCATTCTTA
66 GTCCATTCTTA
*
33853 CCAACAGTTTAACCCCCTGAGGCACGAGTCCACTCTTACCAACCAGTTTAACCCCCTGAGGCACG
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACCAA-CAGTTTAACCCCCTGAGGCACG
*
33918 AGTCTATTCTTA
65 AGTCCATTCTTA
* * * * *
33930 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTTTTACCATCAGTTGAACCCCCTGAGGCGCGT
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCACGA
33995 GTCCA
66 GTCCA
34000 CTATGCACAG
Statistics
Matches: 134, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
74 7 0.05
75 33 0.25
76 32 0.24
77 62 0.46
ACGTcount: A:0.24, C:0.35, G:0.19, T:0.22
Consensus pattern (76 bp):
CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCACGA
GTCCATTCTTA
Done.