Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016623.1 Corchorus olitorius cultivar O-4 contig16656, 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: 73753
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:22756 original size:107 final size:105
Alignment explanation
Indices: 22532--22793 Score: 393
Period size: 107 Copynumber: 2.5 Consensus size: 105
22522 AATTTTTCTA
**
22532 ACCCTTAAAATAAAATTTTAATTTTAATTT-GGGTTAAACTTAGT-AAATTAGTTATATATTTTA
1 ACCCTTAAAATAAAATTAAAATTTTAATTTGGGGTTAAACTTAGTGAAATTAGTTATATATTTTA
* *
22595 TTTCTAAAACCCTATAAAAATATTATTAATTATGGAATTT
66 TTTCTAAAACCCTATAAAAAAATTATTAATTATGAAATTT
* * * *
22635 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGTTAAACTTAGTGAAATTCGTTTTGTATTTTA
1 ACCCTTAAAATAAAATTAAAATTTTAATTTGGGGTTAAACTTAGTGAAATTAGTTATATATTTTA
*
22700 TTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
66 TTTCTAAAACCCTATAA-AA-AAATTATTAATTATGAAATTT
* *
22742 ACCCTTCAAATAAAATTAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
1 ACCCTTAAAATAAAATTAAAATTTTAATTTGGGGTTAAACTTAGTGAAATTA
22794 AGGTTAAACT
Statistics
Matches: 142, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
103 27 0.19
104 14 0.10
105 33 0.23
106 2 0.01
107 66 0.46
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (105 bp):
ACCCTTAAAATAAAATTAAAATTTTAATTTGGGGTTAAACTTAGTGAAATTAGTTATATATTTTA
TTTCTAAAACCCTATAAAAAAATTATTAATTATGAAATTT
Found at i:22824 original size:11 final size:11
Alignment explanation
Indices: 22808--22838 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
22798 TAAACTTAAT
*
22808 AAAAAGAATAA
1 AAAAAGAAAAA
22819 AAAAAGAAAAA
1 AAAAAGAAAAA
22830 AAAAAGAAA
1 AAAAAGAAA
22839 GGAAGAGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.87, C:0.00, G:0.10, T:0.03
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:28278 original size:102 final size:102
Alignment explanation
Indices: 28167--28351 Score: 318
Period size: 102 Copynumber: 1.8 Consensus size: 102
28157 CTATGGGTTC
28167 ATACCAAATTAAATATTACTCCAAATTAGTAAATATTCGGTACTAATTAATTACAGATCTT-TAT
1 ATACCAAATTAAATATTACTCCAAATTAGTAAATATTCGGTACTAATTAATTACAGAT-TTATAT
*
28231 TTTTGAAGTATCTATGCAATACTATGGACGTCGTTCAT
65 TTTTCAAGTATCTATGCAATACTATGGACGTCGTTCAT
** *
28269 ATACCAAATTAAATATTACTGTAAATTAGTAAATATTCGGTACTAATTAATTATAGATTTATATT
1 ATACCAAATTAAATATTACTCCAAATTAGTAAATATTCGGTACTAATTAATTACAGATTTATATT
28334 TTTCAAGTATCTATGCAA
66 TTTCAAGTATCTATGCAA
28352 CAATATATAT
Statistics
Matches: 78, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
101 2 0.03
102 76 0.97
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.39
Consensus pattern (102 bp):
ATACCAAATTAAATATTACTCCAAATTAGTAAATATTCGGTACTAATTAATTACAGATTTATATT
TTTCAAGTATCTATGCAATACTATGGACGTCGTTCAT
Found at i:35429 original size:54 final size:53
Alignment explanation
Indices: 35347--35454 Score: 198
Period size: 54 Copynumber: 2.0 Consensus size: 53
35337 ATTCTTAAGC
35347 GTAAAGCTCAATTTTTTTATGAAACAAGAACCACTGTTATTTACCTCAGAAAA
1 GTAAAGCTCAATTTTTTTATGAAACAAGAACCACTGTTATTTACCTCAGAAAA
*
35400 GTAAAGCTCAATTTTTTTTATGAAACAAGAACCACTGTTATTTATCTCAGAAAA
1 GTAAAGCTCAA-TTTTTTTATGAAACAAGAACCACTGTTATTTACCTCAGAAAA
35454 G
1 G
35455 AACCAATGTT
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
53 11 0.21
54 42 0.79
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (53 bp):
GTAAAGCTCAATTTTTTTATGAAACAAGAACCACTGTTATTTACCTCAGAAAA
Found at i:35443 original size:24 final size:24
Alignment explanation
Indices: 35362--35444 Score: 60
Period size: 24 Copynumber: 3.2 Consensus size: 24
35352 GCTCAATTTT
35362 TTTATGAAACAAGAACCACTGTTA
1 TTTATGAAACAAGAACCACTGTTA
* * * *
35386 TTTACCTCAGAA-AAGTAAAGCTCAATTTTT
1 TTTA--TGA-AACAAG--AA-C-CACTGTTA
35416 TTTATGAAACAAGAACCACTGTTA
1 TTTATGAAACAAGAACCACTGTTA
35440 TTTAT
1 TTTAT
35445 CTCAGAAAAG
Statistics
Matches: 43, Mismatches: 8, Indels: 16
0.64 0.12 0.24
Matches are distributed among these distances:
24 14 0.33
25 1 0.02
26 7 0.16
27 4 0.09
28 7 0.16
29 1 0.02
30 9 0.21
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.35
Consensus pattern (24 bp):
TTTATGAAACAAGAACCACTGTTA
Found at i:35958 original size:32 final size:32
Alignment explanation
Indices: 35919--35982 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
35909 TTAATTATAA
35919 ATAAATCAAAGGAAATAATTTTATGTTAGCGT
1 ATAAATCAAAGGAAATAATTTTATGTTAGCGT
35951 ATAAATCAAAGGAAATAATTTTATGTTAGCGT
1 ATAAATCAAAGGAAATAATTTTATGTTAGCGT
35983 TCTTTTATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.34
Consensus pattern (32 bp):
ATAAATCAAAGGAAATAATTTTATGTTAGCGT
Found at i:36343 original size:44 final size:46
Alignment explanation
Indices: 36285--36374 Score: 132
Period size: 44 Copynumber: 2.0 Consensus size: 46
36275 AAAAAGTCTC
**
36285 CAATTTTTTAAAATTAAAATGGTAAAAA-AATTTATTTA-AAAAAT
1 CAATTTTTTAAAATTAAAATGGTAAAAATAAAATATTTATAAAAAT
36329 CAATTTATTT-AAATTAAAATGGTAAAAATAAAATATTTATAAAAAT
1 CAATTT-TTTAAAATTAAAATGGTAAAAATAAAATATTTATAAAAAT
36375 ATTGAATTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
44 24 0.59
45 11 0.27
46 6 0.15
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (46 bp):
CAATTTTTTAAAATTAAAATGGTAAAAATAAAATATTTATAAAAAT
Found at i:36390 original size:49 final size:44
Alignment explanation
Indices: 36295--36397 Score: 116
Period size: 44 Copynumber: 2.2 Consensus size: 44
36285 CAATTTTTTA
** *
36295 AAATTAAAATGGTAAAAAAATTTATTTAAAAAATCAATTTATTT
1 AAATTAAAATGGTAAAAAAAAATATTTAAAAAATCAATTTAATT
*
36339 AAATTAAAATGGTAAAAATAAAATATTTATAAAAATATTGAATTTAATT
1 AAATTAAAATGGTAAAAA-AAAATA-TT-TAAAAA-A-TCAATTTAATT
*
36388 AAATAAAAAT
1 AAATTAAAAT
36398 AGAGTTTGTA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
44 18 0.37
45 4 0.08
46 2 0.04
47 6 0.12
48 1 0.02
49 18 0.37
ACGTcount: A:0.58, C:0.01, G:0.05, T:0.36
Consensus pattern (44 bp):
AAATTAAAATGGTAAAAAAAAATATTTAAAAAATCAATTTAATT
Found at i:36560 original size:84 final size:83
Alignment explanation
Indices: 36469--36628 Score: 268
Period size: 84 Copynumber: 1.9 Consensus size: 83
36459 AAATTATAAT
36469 ATATATCTAAG-TTATGTAATTAAAATAGTAAAAATGGTAAAAATAAAATAGTTATAAAGAGATT
1 ATATATCTAAGTTTATGTAATTAAAATAGT-AAAATGGTAAAAATAAAATAGTTATAAAGA-ATT
*
36533 AGATTTAATTAAAAGTTCTA
64 ACATTTAATTAAAAGTTCTA
* *
36553 ATATATCTAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAAGAATTAC
1 ATATATCTAAGTTTATGTAATTAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAAGAATTAC
36618 ATTTAATTAAA
66 ATTTAATTAAA
36629 TAAAAATAGA
Statistics
Matches: 72, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
83 15 0.21
84 41 0.57
85 16 0.22
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.36
Consensus pattern (83 bp):
ATATATCTAAGTTTATGTAATTAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAAGAATTAC
ATTTAATTAAAAGTTCTA
Found at i:43064 original size:18 final size:17
Alignment explanation
Indices: 43025--43061 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
43015 GGACTGTCAC
43025 TTTATACCCAATTTTTT
1 TTTATACCCAATTTTTT
43042 TTTATACCCAATTTTTT
1 TTTATACCCAATTTTTT
43059 TTT
1 TTT
43062 TATTTTGATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.22, C:0.16, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTATACCCAATTTTTT
Found at i:43255 original size:31 final size:31
Alignment explanation
Indices: 43218--43376 Score: 201
Period size: 31 Copynumber: 5.1 Consensus size: 31
43208 GATACATGTT
* * *
43218 ACGTGTCACTTTTTGGTACACATGGTGTGAC
1 ACGTGTCACTTTTTGGTACACGTGGCGTGCC
* *
43249 ACGTGTCACTTTTTGGTACATGTGACGTGCC
1 ACGTGTCACTTTTTGGTACACGTGGCGTGCC
*
43280 ACGTGTCACTTTTTGGTACATGTGGCGTGCC
1 ACGTGTCACTTTTTGGTACACGTGGCGTGCC
* * * * *
43311 ACATGTCGCTTTTTTGTATACGTGGCGTGTC
1 ACGTGTCACTTTTTGGTACACGTGGCGTGCC
* *
43342 ACATGTCACTTTTTGGTACACGTGGCATGCC
1 ACGTGTCACTTTTTGGTACACGTGGCGTGCC
43373 ACGT
1 ACGT
43377 CAGACATCGT
Statistics
Matches: 110, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 110 1.00
ACGTcount: A:0.16, C:0.22, G:0.26, T:0.36
Consensus pattern (31 bp):
ACGTGTCACTTTTTGGTACACGTGGCGTGCC
Found at i:43783 original size:11 final size:11
Alignment explanation
Indices: 43767--43791 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
43757 AATTGAACTT
43767 TTTATTTAGAG
1 TTTATTTAGAG
43778 TTTATTTAGAG
1 TTTATTTAGAG
43789 TTT
1 TTT
43792 GATGTGACTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.16, T:0.60
Consensus pattern (11 bp):
TTTATTTAGAG
Found at i:48536 original size:19 final size:19
Alignment explanation
Indices: 48512--48553 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
48502 GATTCTAACA
48512 CTGGCTGACCCAAAGCAGT
1 CTGGCTGACCCAAAGCAGT
*
48531 CTGGCTGAGCCAAAGCAGT
1 CTGGCTGACCCAAAGCAGT
48550 CTGG
1 CTGG
48554 TTTCTTGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.24, C:0.29, G:0.31, T:0.17
Consensus pattern (19 bp):
CTGGCTGACCCAAAGCAGT
Found at i:52070 original size:6 final size:6
Alignment explanation
Indices: 52055--52084 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
52045 ATCTCACCTG
*
52055 GATTTT GATTTC GATTTC GATTTC GATTTC
1 GATTTC GATTTC GATTTC GATTTC GATTTC
52085 TCTGCCCAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.13, G:0.17, T:0.53
Consensus pattern (6 bp):
GATTTC
Found at i:66668 original size:27 final size:25
Alignment explanation
Indices: 66637--66692 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 25
66627 TAAAAAAATA
66637 TTAGTATTATTTCAGTTTGTTCCCTCT
1 TTAGTATTA--TCAGTTTGTTCCCTCT
66664 TTAG---TATCAGTTTGTTCCCTCT
1 TTAGTATTATCAGTTTGTTCCCTCT
66686 TTAGTAT
1 TTAGTAT
66693 CAGTTTCTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
22 20 0.77
24 2 0.08
27 4 0.15
ACGTcount: A:0.16, C:0.18, G:0.12, T:0.54
Consensus pattern (25 bp):
TTAGTATTATCAGTTTGTTCCCTCT
Found at i:66676 original size:22 final size:22
Alignment explanation
Indices: 66648--66698 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
66638 TAGTATTATT
66648 TCAGTTTGTTCCCTCTTTAGTA
1 TCAGTTTGTTCCCTCTTTAGTA
66670 TCAGTTTGTTCCCTCTTTAGTA
1 TCAGTTTGTTCCCTCTTTAGTA
66692 TCAGTTT
1 TCAGTTT
66699 CTGAGCAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.14, C:0.22, G:0.14, T:0.51
Consensus pattern (22 bp):
TCAGTTTGTTCCCTCTTTAGTA
Found at i:67904 original size:51 final size:51
Alignment explanation
Indices: 67822--67920 Score: 135
Period size: 51 Copynumber: 1.9 Consensus size: 51
67812 GAAAATCACT
* *
67822 TGGGTGGTGAAATTTTCAAAAGAAATCATCTTGGGAACTTCTTTTTCTGAG
1 TGGGTGATGAAATCTTCAAAAGAAATCATCTTGGGAACTTCTTTTTCTGAG
* * * * *
67873 TGGGTGATGAAATCTTCGAGAGAATTTATCTTGGGATCTTCTTTTTCT
1 TGGGTGATGAAATCTTCAAAAGAAATCATCTTGGGAACTTCTTTTTCT
67921 TGGTCTTCCT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 41 1.00
ACGTcount: A:0.24, C:0.12, G:0.23, T:0.40
Consensus pattern (51 bp):
TGGGTGATGAAATCTTCAAAAGAAATCATCTTGGGAACTTCTTTTTCTGAG
Found at i:70160 original size:31 final size:29
Alignment explanation
Indices: 70122--70228 Score: 81
Period size: 31 Copynumber: 3.6 Consensus size: 29
70112 TTCCGTCAAA
** *
70122 TTTAGGCTCAAATTGGTTGCTTTTGTAAACG
1 TTTAGGCTCAAATTGG-TGCACTT-CAAACG
* * *
70153 TTTAGGCTCTATTTGGTGCACTTCAAAGG
1 TTTAGGCTCAAATTGGTGCACTTCAAACG
* *
70182 TTTAGGCTCAAATTGAT-CAACTCGACAAACG
1 TTTAGGCTCAAATTGGTGC-ACT--TCAAACG
*
70213 TTTAGGCCCAAATTGG
1 TTTAGGCTCAAATTGG
70229 ATATTTGGCC
Statistics
Matches: 60, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
28 1 0.02
29 21 0.35
30 5 0.08
31 33 0.55
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (29 bp):
TTTAGGCTCAAATTGGTGCACTTCAAACG
Found at i:72217 original size:17 final size:17
Alignment explanation
Indices: 72197--72229 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
72187 CTTAGAGATT
72197 AGATCACCATCGTGATG
1 AGATCACCATCGTGATG
*
72214 AGATCACCATGGTGAT
1 AGATCACCATCGTGAT
72230 CTCGAAAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.24
Consensus pattern (17 bp):
AGATCACCATCGTGATG
Done.