Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015983.1 Corchorus olitorius cultivar O-4 contig16016, 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: 88175
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:99 original size:59 final size:60
Alignment explanation
Indices: 4--134 Score: 194
Period size: 59 Copynumber: 2.2 Consensus size: 60
1 TTG
* *
4 GGCCCTTATTTGGCCAAATTAAAAGATCAGATCCTTA-TTGAGCATTTTTGA-TAACATTA
1 GGCCCTTATTTGGCCAAATTAAAAGATCAGACCCTTATTTGAGCA-TTTTGACAAACATTA
* *
63 GGCCCTTATTTGGCCAAATTAAAAGATCGGGCCCTTATTTGAGCATTTTGACAAACATTA
1 GGCCCTTATTTGGCCAAATTAAAAGATCAGACCCTTATTTGAGCATTTTGACAAACATTA
*
123 GACCCTTATTTG
1 GGCCCTTATTTG
135 AACAATTAGC
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
59 40 0.62
60 25 0.38
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (60 bp):
GGCCCTTATTTGGCCAAATTAAAAGATCAGACCCTTATTTGAGCATTTTGACAAACATTA
Found at i:4994 original size:24 final size:25
Alignment explanation
Indices: 4967--5025 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
4957 ACTTACTAAT
*
4967 AAAAAGAGAACT-CTAAAA-AGAAAG
1 AAAAA-AGAACTACAAAAAGAGAAAG
*
4991 AAAAAAAAACTAACAAAAAGAGAAAG
1 AAAAAAGAACT-ACAAAAAGAGAAAG
5017 AAAAAAGAA
1 AAAAAAGAA
5026 AGACTGTAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 5 0.17
24 5 0.17
25 5 0.17
26 14 0.48
ACGTcount: A:0.75, C:0.07, G:0.14, T:0.05
Consensus pattern (25 bp):
AAAAAAGAACTACAAAAAGAGAAAG
Found at i:15990 original size:3 final size:3
Alignment explanation
Indices: 15975--16005 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
15965 TTGAATTTTA
15975 TAT TAT ATAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT
16006 CATAATATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:20186 original size:74 final size:75
Alignment explanation
Indices: 20014--20205 Score: 332
Period size: 75 Copynumber: 2.6 Consensus size: 75
20004 TCTGTATTAA
* * *
20014 TATTTGTCATGATGAATTGATATTTTACATTCAGGAAAGGAAATAATCACTACCTTAATCAACCT
1 TATTTGTCATGATGAATTGACATTTTACATTCATGAAAGAAAATAATCACTACCTTAATCAACCT
20079 TTTGTTGCTG
66 TTTGTTGCTG
*
20089 TATTTGTCATGATGAATTGACATTTTACATTCATTAAAGAAAATAATCACTACCTTAATCAA-CT
1 TATTTGTCATGATGAATTGACATTTTACATTCATGAAAGAAAATAATCACTACCTTAATCAACCT
*
20153 TTTGTTTCTG
66 TTTGTTGCTG
20163 TATTTGTCATGATGAATTGACATTTTACATTCATGAAAGAAAA
1 TATTTGTCATGATGAATTGACATTTTACATTCATGAAAGAAAA
20206 AAACTTCTTA
Statistics
Matches: 111, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
74 53 0.48
75 58 0.52
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.40
Consensus pattern (75 bp):
TATTTGTCATGATGAATTGACATTTTACATTCATGAAAGAAAATAATCACTACCTTAATCAACCT
TTTGTTGCTG
Found at i:27999 original size:13 final size:13
Alignment explanation
Indices: 27981--28006 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27971 TTGAATCTCC
27981 ACAAATCTCTATT
1 ACAAATCTCTATT
27994 ACAAATCTCTATT
1 ACAAATCTCTATT
28007 GGTGTACAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.38
Consensus pattern (13 bp):
ACAAATCTCTATT
Found at i:44166 original size:16 final size:19
Alignment explanation
Indices: 44141--44177 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
44131 CTCCGCCACG
44141 TCACCACTCCG-ACA-CTC
1 TCACCACTCCGTACAGCTC
44158 TCACC-CTCCGTACAGCTC
1 TCACCACTCCGTACAGCTC
44176 TC
1 TC
44178 CAAGCTACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.28
17 8 0.44
18 5 0.28
ACGTcount: A:0.19, C:0.51, G:0.08, T:0.22
Consensus pattern (19 bp):
TCACCACTCCGTACAGCTC
Found at i:61032 original size:10 final size:10
Alignment explanation
Indices: 61017--61051 Score: 70
Period size: 10 Copynumber: 3.5 Consensus size: 10
61007 CAATAGTATT
61017 TAACTTTGCC
1 TAACTTTGCC
61027 TAACTTTGCC
1 TAACTTTGCC
61037 TAACTTTGCC
1 TAACTTTGCC
61047 TAACT
1 TAACT
61052 AGGCAAACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.23, C:0.29, G:0.09, T:0.40
Consensus pattern (10 bp):
TAACTTTGCC
Found at i:61676 original size:7 final size:7
Alignment explanation
Indices: 61664--61688 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
61654 ATGCTTTTTG
61664 TTTGGAC
1 TTTGGAC
61671 TTTGGAC
1 TTTGGAC
61678 TTTGGAC
1 TTTGGAC
61685 TTTG
1 TTTG
61689 TTCAACCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.28, T:0.48
Consensus pattern (7 bp):
TTTGGAC
Found at i:64866 original size:24 final size:24
Alignment explanation
Indices: 64839--64886 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
64829 GAGCTAATAA
*
64839 TGGTGGTGATACTTGTGCTGACAC
1 TGGTGGTGATACTTGCGCTGACAC
*
64863 TGGTGGTGCTACTTGCGCTGACAC
1 TGGTGGTGATACTTGCGCTGACAC
64887 AGGGGGCAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.15, C:0.21, G:0.33, T:0.31
Consensus pattern (24 bp):
TGGTGGTGATACTTGCGCTGACAC
Found at i:67324 original size:11 final size:11
Alignment explanation
Indices: 67307--67342 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
67297 GTCTAAAGTG
67307 AAAGTAAAATC
1 AAAGTAAAATC
*
67318 AAGGTAAAATC
1 AAAGTAAAATC
67329 AAAGTAAAATC
1 AAAGTAAAATC
67340 AAA
1 AAA
67343 ATATAGAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.64, C:0.08, G:0.11, T:0.17
Consensus pattern (11 bp):
AAAGTAAAATC
Found at i:71178 original size:21 final size:20
Alignment explanation
Indices: 71136--71178 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
71126 ATTCAGAATG
* **
71136 AAAATAGCTTTTGAGTTTCA
1 AAAATAGCTTTTGAATGCCA
71156 AAAATTAGCTTTTGAATGCCA
1 AAAA-TAGCTTTTGAATGCCA
71177 AA
1 AA
71179 CAGTAACCAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.35
Consensus pattern (20 bp):
AAAATAGCTTTTGAATGCCA
Found at i:73153 original size:14 final size:13
Alignment explanation
Indices: 73134--73172 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
73124 AAATTGTAAA
73134 ATTTAAAAAATTT
1 ATTTAAAAAATTT
* *
73147 CATTTAAGAAATAT
1 -ATTTAAAAAATTT
73161 ATTTAAAAAATT
1 ATTTAAAAAATT
73173 CTAATATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (13 bp):
ATTTAAAAAATTT
Found at i:73400 original size:123 final size:127
Alignment explanation
Indices: 73158--73412 Score: 410
Period size: 131 Copynumber: 2.0 Consensus size: 127
73148 ATTTAAGAAA
*
73158 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAA
1 TATATTTAAAAAATTCTAATATACATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT---A
* *
73223 TAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAA
63 TA-GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTAAGTAAAACTATAAAA
73288 G
127 G
73289 TATATTTAAAAAATTCTAATATACATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT-TA-
1 TATATTTAAAAAATTCTAATATACATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAG
*
73352 TA-AA-GATATTTGATTTAATTAAATAAAAATAGAGTTTTTAGTTAAGTAAAACTATAAAAG
66 TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTAAGTAAAACTATAAAAG
73412 T
1 T
73413 TTAAACAATG
Statistics
Matches: 120, Mismatches: 4, Indels: 8
0.91 0.03 0.06
Matches are distributed among these distances:
123 54 0.45
124 2 0.02
125 2 0.02
127 2 0.02
131 60 0.50
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.38
Consensus pattern (127 bp):
TATATTTAAAAAATTCTAATATACATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAG
TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTAAGTAAAACTATAAAAG
Found at i:74281 original size:94 final size:95
Alignment explanation
Indices: 74119--74499 Score: 703
Period size: 94 Copynumber: 4.0 Consensus size: 95
74109 ATTTACATTT
* *
74119 TCCTTTAATTTTTTTTATTACAATCGGTAATTTATCACCCAGCTAATTATTGTTTTTTTTATCCC
1 TCCTTTAATTTTTTTTATTACAATCGGTAATTTATCACCTAGCTAGTTATTGTTTTTTTTATCCC
* * *
74184 ATCCGGTATCCAAAGTTTTGCTTTGACTAA
66 ATCCGGTATCTAAGGTTTTGCTCTGACTAA
74214 TCCTTTAA-TTTTTTTATTACAATCGGTAATTTATCACCTAGCTAGTTATTGTTTTTTTTATCCC
1 TCCTTTAATTTTTTTTATTACAATCGGTAATTTATCACCTAGCTAGTTATTGTTTTTTTTATCCC
74278 ATCCGGTATCTAAGGTTTTGCTCTGACTAA
66 ATCCGGTATCTAAGGTTTTGCTCTGACTAA
74308 TCCTTTAA-TTTTTTTATTACAATCGGTAATTTATCACCTAGCTAGTTATTGTTTTTTTTATCCC
1 TCCTTTAATTTTTTTTATTACAATCGGTAATTTATCACCTAGCTAGTTATTGTTTTTTTTATCCC
74372 ATCCGGTATCTAAGGTTTTGCTCTGACTAA
66 ATCCGGTATCTAAGGTTTTGCTCTGACTAA
74402 TCCTTTAATTTTTTTTATTACAATCGGTAATTTATCACCTAGCTAGTTATTGTTTTTTTTATCCC
1 TCCTTTAATTTTTTTTATTACAATCGGTAATTTATCACCTAGCTAGTTATTGTTTTTTTTATCCC
74467 ATCCGGTATCTAAGGTTTTGCTCTGACTAA
66 ATCCGGTATCTAAGGTTTTGCTCTGACTAA
74497 TCC
1 TCC
74500 GGATTCCATC
Statistics
Matches: 280, Mismatches: 5, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
94 183 0.65
95 97 0.35
ACGTcount: A:0.23, C:0.19, G:0.11, T:0.48
Consensus pattern (95 bp):
TCCTTTAATTTTTTTTATTACAATCGGTAATTTATCACCTAGCTAGTTATTGTTTTTTTTATCCC
ATCCGGTATCTAAGGTTTTGCTCTGACTAA
Found at i:74441 original size:189 final size:189
Alignment explanation
Indices: 74119--74499 Score: 701
Period size: 189 Copynumber: 2.0 Consensus size: 189
74109 ATTTACATTT
74119 TCCTTTAATTTTTTTTATTACAATCGGTAATTTATCACCCAGCTAATTATTGTTTTTTTTATCCC
1 TCCTTTAATTTTTTTTATTACAATCGGTAATTTATCACCCAGCTAATTATTGTTTTTTTTATCCC
*
74184 ATCCGGTATCCAAAGTTTTGCTTTGACTAATCCTTTAATTTTTTTATTACAATCGGTAATTTATC
66 ATCCGGTATCCAAAGTTTTGCTCTGACTAATCCTTTAATTTTTTTATTACAATCGGTAATTTATC
74249 ACCTAGCTAGTTATTGTTTTTTTTATCCCATCCGGTATCTAAGGTTTTGCTCTGACTAA
131 ACCTAGCTAGTTATTGTTTTTTTTATCCCATCCGGTATCTAAGGTTTTGCTCTGACTAA
* *
74308 TCCTTTAA-TTTTTTTATTACAATCGGTAATTTATCACCTAGCTAGTTATTGTTTTTTTTATCCC
1 TCCTTTAATTTTTTTTATTACAATCGGTAATTTATCACCCAGCTAATTATTGTTTTTTTTATCCC
* *
74372 ATCCGGTATCTAAGGTTTTGCTCTGACTAATCCTTTAATTTTTTTTATTACAATCGGTAATTTAT
66 ATCCGGTATCCAAAGTTTTGCTCTGACTAATCCTTTAA-TTTTTTTATTACAATCGGTAATTTAT
74437 CACCTAGCTAGTTATTGTTTTTTTTATCCCATCCGGTATCTAAGGTTTTGCTCTGACTAA
130 CACCTAGCTAGTTATTGTTTTTTTTATCCCATCCGGTATCTAAGGTTTTGCTCTGACTAA
74497 TCC
1 TCC
74500 GGATTCCATC
Statistics
Matches: 186, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
188 89 0.48
189 97 0.52
ACGTcount: A:0.23, C:0.19, G:0.11, T:0.48
Consensus pattern (189 bp):
TCCTTTAATTTTTTTTATTACAATCGGTAATTTATCACCCAGCTAATTATTGTTTTTTTTATCCC
ATCCGGTATCCAAAGTTTTGCTCTGACTAATCCTTTAATTTTTTTATTACAATCGGTAATTTATC
ACCTAGCTAGTTATTGTTTTTTTTATCCCATCCGGTATCTAAGGTTTTGCTCTGACTAA
Found at i:81915 original size:3 final size:3
Alignment explanation
Indices: 81907--82006 Score: 182
Period size: 3 Copynumber: 32.7 Consensus size: 3
81897 CTCCTTTCAG
81907 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
81955 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA -TTA
82002 TTA TT
1 TTA TT
82007 TACTTCTGGG
Statistics
Matches: 95, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
3 89 0.94
4 6 0.06
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:86706 original size:13 final size:12
Alignment explanation
Indices: 86674--86716 Score: 54
Period size: 13 Copynumber: 3.7 Consensus size: 12
86664 TTATTGCTGA
86674 TTTATATCTTA-
1 TTTATATCTTAT
*
86685 TCT-TATCTTAT
1 TTTATATCTTAT
86696 TTTACTATCTTAT
1 TTTA-TATCTTAT
86709 TTTATATC
1 TTTATATC
86717 AAAAATTCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 7 0.26
11 4 0.15
12 4 0.15
13 12 0.44
ACGTcount: A:0.23, C:0.14, G:0.00, T:0.63
Consensus pattern (12 bp):
TTTATATCTTAT
Found at i:87342 original size:18 final size:19
Alignment explanation
Indices: 87305--87344 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
87295 ATTAATTTCA
87305 TTTTCCTGCATCCCATTTT
1 TTTTCCTGCATCCCATTTT
*
87324 TTTTCCTGCATCTCATTTT
1 TTTTCCTGCATCCCATTTT
87343 TT
1 TT
87345 CTTTCTCATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.10, C:0.28, G:0.05, T:0.57
Consensus pattern (19 bp):
TTTTCCTGCATCCCATTTT
Found at i:88094 original size:54 final size:54
Alignment explanation
Indices: 88024--88129 Score: 194
Period size: 54 Copynumber: 2.0 Consensus size: 54
88014 TCATAGTACT
*
88024 TTCGAAATTTCTTACGTATCAAACAATTTAATTCGAATAGAAAATTGTTCAAGC
1 TTCGAAATTTCCTACGTATCAAACAATTTAATTCGAATAGAAAATTGTTCAAGC
*
88078 TTCGAAATTTCCTACGTATCAAACAATTTAATTCGAATTGAAAATTGTTCAA
1 TTCGAAATTTCCTACGTATCAAACAATTTAATTCGAATAGAAAATTGTTCAA
88130 AGAAGTAGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (54 bp):
TTCGAAATTTCCTACGTATCAAACAATTTAATTCGAATAGAAAATTGTTCAAGC
Done.