Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016051.1 Corchorus capsularis cultivar CVL-1 contig16072, 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: 41608
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:1774 original size:29 final size:30
Alignment explanation
Indices: 1721--1783 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 30
1711 TTATTTCTAA
1721 AAGGGTTTAATGTAACAAACTAATTCTATGT
1 AAGGGTTTAATGTAACAAAC-AATTCTATGT
* *
1752 AAGGGTTTTATGTAACAAA-AATTGTATGT
1 AAGGGTTTAATGTAACAAACAATTCTATGT
1781 AAG
1 AAG
1784 TTTTTATTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 12 0.40
31 18 0.60
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.35
Consensus pattern (30 bp):
AAGGGTTTAATGTAACAAACAATTCTATGT
Found at i:1780 original size:76 final size:76
Alignment explanation
Indices: 1689--1834 Score: 283
Period size: 76 Copynumber: 1.9 Consensus size: 76
1679 TCTACGTACC
1689 AACAAAAATTCTATGTAAGTTTTTATTTCTAAAAGGGTTTAATGTAACAAACTAATTCTATGTAA
1 AACAAAAATTCTATGTAAGTTTTTATTTCTAAAAGGGTTTAATGTAACAAACTAATTCTATGTAA
1754 GGGTTTTATGT
66 GGGTTTTATGT
*
1765 AACAAAAATTGTATGTAAGTTTTTATTTCTAAAAGGGTTTAATGTAACAAACTAATTCTATGTAA
1 AACAAAAATTCTATGTAAGTTTTTATTTCTAAAAGGGTTTAATGTAACAAACTAATTCTATGTAA
1830 GGGTT
66 GGGTT
1835 CTATTGAATG
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 69 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.40
Consensus pattern (76 bp):
AACAAAAATTCTATGTAAGTTTTTATTTCTAAAAGGGTTTAATGTAACAAACTAATTCTATGTAA
GGGTTTTATGT
Found at i:3339 original size:109 final size:109
Alignment explanation
Indices: 3213--3484 Score: 440
Period size: 109 Copynumber: 2.5 Consensus size: 109
3203 GGTAAAAAAA
3213 TATAAA-ATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG
1 TATAAAGATATTAG-ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG
3276 AAAAAATTTTAATATATCCAAATTTTTTCGTAAAAATAAAGTAAT
65 AAAAAATTTTAATATATCCAAATTTTTTCGTAAAAATAAAGTAAT
3321 TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
1 TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
* *
3386 AAAAATTTTAGTATATCCAAATTTTTTGGTAAAAATAAAGTAAT
66 AAAAATTTTAATATATCCAAATTTTTTCGTAAAAATAAAGTAAT
* *
3430 TATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTAGTAGAATA
1 TATAAAGATATTAGATTTAA-TT-A---AATGAAAATAGAGTTTTTAGTAGAATA
3485 GAACTATAAT
Statistics
Matches: 153, Mismatches: 4, Indels: 8
0.93 0.02 0.05
Matches are distributed among these distances:
108 6 0.04
109 118 0.77
110 3 0.02
111 1 0.01
114 25 0.16
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.39
Consensus pattern (109 bp):
TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
AAAAATTTTAATATATCCAAATTTTTTCGTAAAAATAAAGTAAT
Found at i:3990 original size:16 final size:17
Alignment explanation
Indices: 3960--3992 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3950 TAAATTCAGT
*
3960 TAAAATTAAATTAATTA
1 TAAAAATAAATTAATTA
3977 TAAAAATAAA-TAATTA
1 TAAAAATAAATTAATTA
3993 AATCAACAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAAAATAAATTAATTA
Found at i:5890 original size:20 final size:20
Alignment explanation
Indices: 5865--5902 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5855 TTCTTCAATT
*
5865 TATAATTTATTAATTTATAA
1 TATAATTTATTAAATTATAA
*
5885 TATAATTTTTTAAATTAT
1 TATAATTTATTAAATTAT
5903 TATTGTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TATAATTTATTAAATTATAA
Found at i:6567 original size:107 final size:102
Alignment explanation
Indices: 6352--6593 Score: 322
Period size: 102 Copynumber: 2.3 Consensus size: 102
6342 AAGTAAAGAT
* * * * *
6352 TTAGTTATATATTTTATTTATAAAACCTTATAACAATATATTATTAATCATGGAATTTACCCTTA
1 TTAGTTTTATATTTTATTTCTAAAACCCTATAACAATAAATTATTAATCATAGAATTTACCCTTA
*
6417 AAATAAAGATATTAATTTGGGACTAAACTTAGTGAAA
66 AAATAAAAATATTAATTTGGGACTAAACTTAGTGAAA
* ** *
6454 TTAGTTTTGTATTTTATTTCTAAAACCCTATAACAATAAATTATTAATTTTATAATTTACCCTTA
1 TTAGTTTTATATTTTATTTCTAAAACCCTATAACAATAAATTATTAATCATAGAATTTACCCTTA
* *
6519 GAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAA
66 AAATAAAAAT---A--TTAATTTGGGACTAAACTTAGTGAAA
*
6561 TTAGTTTTATATTTTATTTCTAAAACTCTATAA
1 TTAGTTTTATATTTTATTTCTAAAACCCTATAA
6594 TAAAAAAACC
Statistics
Matches: 121, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
102 64 0.53
105 1 0.01
107 56 0.46
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.43
Consensus pattern (102 bp):
TTAGTTTTATATTTTATTTCTAAAACCCTATAACAATAAATTATTAATCATAGAATTTACCCTTA
AAATAAAAATATTAATTTGGGACTAAACTTAGTGAAA
Found at i:6574 original size:102 final size:100
Alignment explanation
Indices: 6365--6593 Score: 260
Period size: 107 Copynumber: 2.2 Consensus size: 100
6355 GTTATATATT
* * * *
6365 TTATTTATAAAACCTTATAACAATATATTATTAATCATGGAATTTACCCTTAAAATAAAGATATT
1 TTATTTATAAAACCCTATAACAATAAATTATTAATCATAGAATTTACCCTTAAAATAAAAATATT
6430 AATTTGGGACTAAACTTAGTGAAATTAGTTTTGTA
66 AATTTGGGACTAAACTTAGTGAAATTAGTTTTGTA
* ** * *
6465 TTTTATTTCTAAAACCCTATAACAATAAATTATTAATTTTATAATTTACCCTTAGAATAAAAATA
1 --TTATTTATAAAACCCTATAACAATAAATTATTAATCATAGAATTTACCCTTAAAATAAAAAT-
* *
6530 AAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATA
63 --A--TTAATTTGGGACTAAACTTAGTGAAATTAGTTTTGTA
* *
6572 TTTTATTTCTAAAACTCTATAA
1 --TTATTTATAAAACCCTATAA
6594 TAAAAAAACC
Statistics
Matches: 110, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
102 53 0.48
105 1 0.01
107 56 0.51
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.42
Consensus pattern (100 bp):
TTATTTATAAAACCCTATAACAATAAATTATTAATCATAGAATTTACCCTTAAAATAAAAATATT
AATTTGGGACTAAACTTAGTGAAATTAGTTTTGTA
Found at i:7252 original size:25 final size:25
Alignment explanation
Indices: 7214--7263 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
7204 AATCAATAAT
*
7214 AATCAATCAATAATTATTTACTTTC
1 AATCAATCAATAATGATTTACTTTC
*
7239 AATCAATCATTAATGATTTACTTTC
1 AATCAATCAATAATGATTTACTTTC
7264 CATAAACAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.16, G:0.02, T:0.44
Consensus pattern (25 bp):
AATCAATCAATAATGATTTACTTTC
Found at i:7468 original size:14 final size:13
Alignment explanation
Indices: 7434--7469 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
7424 AATCAAAATT
7434 AATTGATTTTTCA
1 AATTGATTTTTCA
*
7447 AATTGATTTTTGA
1 AATTGATTTTTCA
7460 AATTGGATTT
1 AATT-GATTT
7470 GATATGAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 16 0.76
14 5 0.24
ACGTcount: A:0.31, C:0.03, G:0.14, T:0.53
Consensus pattern (13 bp):
AATTGATTTTTCA
Found at i:8488 original size:109 final size:109
Alignment explanation
Indices: 8292--8566 Score: 455
Period size: 109 Copynumber: 2.5 Consensus size: 109
8282 ACTATTATAG
*
8292 TTTTATTCTACTAAAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT
*
8357 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
61 TATTTTTACCAAAAAATTTGGATATACTAAAAATTTTTCTAATATACAA
8406 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
*
8471 TTACCAAAAAATTTGGATATATTAAAAATTTTTCTAATATACAA
66 TTACCAAAAAATTTGGATATACTAAAAATTTTTCTAATATACAA
8515 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATAT-TTTATA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTTTATA
8567 TAGTTTTTTT
Statistics
Matches: 157, Mismatches: 3, Indels: 8
0.93 0.02 0.05
Matches are distributed among these distances:
108 7 0.04
109 123 0.78
110 3 0.02
111 2 0.01
114 22 0.14
ACGTcount: A:0.39, C:0.11, G:0.01, T:0.48
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAATTTGGATATACTAAAAATTTTTCTAATATACAA
Found at i:12298 original size:23 final size:23
Alignment explanation
Indices: 12264--12329 Score: 96
Period size: 23 Copynumber: 2.9 Consensus size: 23
12254 TGATTTGTAG
* *
12264 AGACCGAACGAGAGTGTTCATAA
1 AGACCGAGCGAGAGTGCTCATAA
* *
12287 AGACCGAGCGAGAGAGCTCATAG
1 AGACCGAGCGAGAGTGCTCATAA
12310 AGACCGAGCGAGAGTGCTCA
1 AGACCGAGCGAGAGTGCTCA
12330 AGATTATTTG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.35, C:0.21, G:0.32, T:0.12
Consensus pattern (23 bp):
AGACCGAGCGAGAGTGCTCATAA
Found at i:15214 original size:30 final size:25
Alignment explanation
Indices: 15153--15199 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
15143 TACCTTTATC
15153 CATAGCTTGGCTTTGTGTAGAAAAT
1 CATAGCTTGGCTTTGTGTAGAAAAT
*
15178 C-TAGCTTGGCTTTGTGTCGAAA
1 CATAGCTTGGCTTTGTGTAGAAA
15200 GAATCGACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.23, C:0.15, G:0.26, T:0.36
Consensus pattern (25 bp):
CATAGCTTGGCTTTGTGTAGAAAAT
Found at i:16079 original size:10 final size:11
Alignment explanation
Indices: 16055--16090 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
16045 ACCCTTAGCT
16055 AAAACTAGAAG
1 AAAACTAGAAG
16066 AAAACTAG-AG
1 AAAACTAGAAG
*
16076 AAAAATAGAAG
1 AAAACTAGAAG
16087 AAAA
1 AAAA
16091 GAAATTGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.69, C:0.06, G:0.17, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:16205 original size:29 final size:29
Alignment explanation
Indices: 16165--16251 Score: 174
Period size: 29 Copynumber: 3.0 Consensus size: 29
16155 TGGACTAATT
16165 AAACTCCATATAGACTTAGGATTAGCCTA
1 AAACTCCATATAGACTTAGGATTAGCCTA
16194 AAACTCCATATAGACTTAGGATTAGCCTA
1 AAACTCCATATAGACTTAGGATTAGCCTA
16223 AAACTCCATATAGACTTAGGATTAGCCTA
1 AAACTCCATATAGACTTAGGATTAGCCTA
16252 GGACGTTTAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 58 1.00
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.28
Consensus pattern (29 bp):
AAACTCCATATAGACTTAGGATTAGCCTA
Found at i:17414 original size:14 final size:15
Alignment explanation
Indices: 17395--17425 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
17385 AAACATGCAA
17395 TTAATAAATTTT-TT
1 TTAATAAATTTTGTT
17409 TTAATAAATTTTGTT
1 TTAATAAATTTTGTT
17424 TT
1 TT
17426 TGCCTTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (15 bp):
TTAATAAATTTTGTT
Found at i:19168 original size:6 final size:6
Alignment explanation
Indices: 19157--19203 Score: 64
Period size: 6 Copynumber: 8.2 Consensus size: 6
19147 AAGGACTATT
19157 ACAAAA ACAAAAA ACAAAA ACAAAA AC-AAA A-AAAA AC-AAA ACAAAA
1 ACAAAA AC-AAAA ACAAAA ACAAAA ACAAAA ACAAAA ACAAAA ACAAAA
19203 A
1 A
19204 ACCAACAACA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
5 13 0.35
6 18 0.49
7 6 0.16
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (6 bp):
ACAAAA
Found at i:19171 original size:7 final size:7
Alignment explanation
Indices: 19159--19205 Score: 62
Period size: 7 Copynumber: 6.9 Consensus size: 7
19149 GGACTATTAC
19159 AAAAACA
1 AAAAACA
19166 AAAAAC-
1 AAAAACA
19172 AAAAAC-
1 AAAAACA
19178 AAAAACA
1 AAAAACA
*
19185 AAAAAAA
1 AAAAACA
19192 ACAAAACA
1 A-AAAACA
19200 AAAAAC
1 AAAAAC
19206 CAACAACAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
6 12 0.33
7 18 0.50
8 6 0.17
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAACA
Found at i:19204 original size:29 final size:29
Alignment explanation
Indices: 19159--19214 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
19149 GGACTATTAC
19159 AAAAACAAAAAACAAAAACAAAAACAAAA
1 AAAAACAAAAAACAAAAACAAAAACAAAA
* *
19188 AAAAACAAAACAA-AAAACCAACAACAA
1 AAAAACAAAA-AACAAAAACAAAAACAA
19215 TAAGCAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 22 0.92
30 2 0.08
ACGTcount: A:0.82, C:0.18, G:0.00, T:0.00
Consensus pattern (29 bp):
AAAAACAAAAAACAAAAACAAAAACAAAA
Found at i:32401 original size:1 final size:1
Alignment explanation
Indices: 32397--32426 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
32387 AACAAAATTT
32397 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
32427 CACTCCATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:38747 original size:7 final size:7
Alignment explanation
Indices: 38735--38761 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
38725 GAAAATGGAC
38735 TTTCAAG
1 TTTCAAG
38742 TTTCAAG
1 TTTCAAG
38749 TTTCAAG
1 TTTCAAG
38756 TTTCAA
1 TTTCAA
38762 CTGAGTGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.44
Consensus pattern (7 bp):
TTTCAAG
Found at i:40998 original size:37 final size:37
Alignment explanation
Indices: 40957--41027 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
40947 TGGCCAAGGG
* *
40957 GAGCTTTGCGGTAAAGAGGGCGCTACCGCAGTAAAGA
1 GAGCTCTGCGGTAAAGACGGCGCTACCGCAGTAAAGA
* *
40994 GAGCTCTGCGGTAAAGACGGTGCTACCGCGGTAA
1 GAGCTCTGCGGTAAAGACGGCGCTACCGCAGTAA
41028 GGAAAGCCCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.27, C:0.21, G:0.35, T:0.17
Consensus pattern (37 bp):
GAGCTCTGCGGTAAAGACGGCGCTACCGCAGTAAAGA
Found at i:41026 original size:20 final size:19
Alignment explanation
Indices: 40964--41027 Score: 60
Period size: 20 Copynumber: 3.4 Consensus size: 19
40954 GGGGAGCTTT
*
40964 GCGGTAAAGAGGGCGCTACC
1 GCGGTAAAGA-GGAGCTACC
* *
40984 GCAGTAAAGA-GAGCT-CT
1 GCGGTAAAGAGGAGCTACC
*
41001 GCGGTAAAGACGGTGCTACC
1 GCGGTAAAGA-GGAGCTACC
41021 GCGGTAA
1 GCGGTAA
41028 GGAAAGCCCT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
17 10 0.29
18 4 0.11
19 4 0.11
20 17 0.49
ACGTcount: A:0.28, C:0.22, G:0.36, T:0.14
Consensus pattern (19 bp):
GCGGTAAAGAGGAGCTACC
Found at i:41040 original size:37 final size:37
Alignment explanation
Indices: 40963--41040 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
40953 AGGGGAGCTT
* * *
40963 TGCGGTAAAGAGGGCGCTACCGCAGTAAAGAGAGCTC
1 TGCGGTAAAGACGGCGCTACCGCAGTAAAGAAAGCCC
* * *
41000 TGCGGTAAAGACGGTGCTACCGCGGTAAGGAAAGCCC
1 TGCGGTAAAGACGGCGCTACCGCAGTAAAGAAAGCCC
41037 TGCG
1 TGCG
41041 ATGAAGAGTG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.27, C:0.23, G:0.36, T:0.14
Consensus pattern (37 bp):
TGCGGTAAAGACGGCGCTACCGCAGTAAAGAAAGCCC
Done.