Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019479.1 Corchorus olitorius cultivar O-4 contig19512, 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: 40464
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Found at i:1132 original size:18 final size:20
Alignment explanation
Indices: 1111--1159 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
1101 ATTTTACCAC
1111 TAATAATAA-TTAAT-ATAA
1 TAATAATAAGTTAATAATAA
*
1129 TAATAATAAGTTTAATAATTA
1 TAATAATAAG-TTAATAATAA
1150 TAATAATAAG
1 TAATAATAAG
1160 AGGTTTAACG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 9 0.33
20 5 0.19
21 13 0.48
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (20 bp):
TAATAATAAGTTAATAATAA
Found at i:1144 original size:15 final size:14
Alignment explanation
Indices: 1111--1154 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
1101 ATTTTACCAC
1111 TAATAATAATTAATA
1 TAATAATAA-TAATA
*
1126 TAATAATAATAAGTT
1 TAATAATAATAA-TA
*
1141 TAATAATTATAATA
1 TAATAATAATAATA
1155 ATAAGAGGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 4 0.16
15 21 0.84
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (14 bp):
TAATAATAATAATA
Found at i:1508 original size:63 final size:64
Alignment explanation
Indices: 1433--1556 Score: 207
Period size: 63 Copynumber: 2.0 Consensus size: 64
1423 AGTTTAGACT
*
1433 TATATAGTATATAGATATAG-ATATAATTACATATTCAATTACACAAAACCATTTGATTAATATA
1 TATATAGTATATAGATAT-GTATATAATGACATATTCAATTACACAAAACCATTTGATTAATATA
*
1497 TATATA-TATATATATATGTATATAATGACATATTCAATTACACAAAACCATTTGATTAAT
1 TATATAGTATATAGATATGTATATAATGACATATTCAATTACACAAAACCATTTGATTAAT
1557 TAGCTATAGC
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
62 1 0.02
63 50 0.88
64 6 0.11
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.39
Consensus pattern (64 bp):
TATATAGTATATAGATATGTATATAATGACATATTCAATTACACAAAACCATTTGATTAATATA
Found at i:4160 original size:36 final size:36
Alignment explanation
Indices: 4114--4182 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
4104 TCAATAACCT
* **
4114 TACATCTTTTGTGATTTTGGTTATCATATTTCTTAC
1 TACATCTTTTGTAATTTTGAATATCATATTTCTTAC
*
4150 TACATTTTTTGTAATTTTGAATATCATATTTCT
1 TACATCTTTTGTAATTTTGAATATCATATTTCT
4183 CCAAAATCTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.23, C:0.12, G:0.09, T:0.57
Consensus pattern (36 bp):
TACATCTTTTGTAATTTTGAATATCATATTTCTTAC
Found at i:5082 original size:206 final size:201
Alignment explanation
Indices: 4695--5106 Score: 727
Period size: 206 Copynumber: 2.0 Consensus size: 201
4685 GCTTAATAAC
4695 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
*
4760 CATACAACACATTATTATTATATATATAACTATACAAAAAAAAAGTAGTTGAACATTAGTGGTTG
66 CATACAACACATTATTATTATATATATAACTATACAAAAAAAAAGTAGTTGAACATTAGTGATTG
4825 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATC
131 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT-AAGATC
4890 CGATTTA
195 CGATTTA
4897 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
* * *
4962 GATACAACACATTACTATTATTATATATATAGAACTATAC-CAAAAAAATTAGTTGAACATTAGT
66 CATACAACACA-T--TATTATTATATATAT--AACTATACAAAAAAAAAGTAGTTGAACATTAGT
5026 GATTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAA
126 GATTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAA
5091 GATCCGATTTA
191 GATCCGATTTA
5102 TTTAT
1 TTTAT
5107 TATTAAGGAA
Statistics
Matches: 201, Mismatches: 4, Indels: 7
0.95 0.02 0.03
Matches are distributed among these distances:
202 75 0.37
203 1 0.00
205 33 0.16
206 84 0.42
207 8 0.04
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (201 bp):
TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
CATACAACACATTATTATTATATATATAACTATACAAAAAAAAAGTAGTTGAACATTAGTGATTG
ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCC
GATTTA
Found at i:5212 original size:25 final size:24
Alignment explanation
Indices: 5178--5224 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
5168 ACGTTTGCAC
5178 AAATACCTAAGAATTTGAATTAAAA
1 AAATACCTAAGAATTT-AATTAAAA
5203 AAATACCTAAGAATTTAATTAA
1 AAATACCTAAGAATTTAATTAA
5225 TGTAAGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (24 bp):
AAATACCTAAGAATTTAATTAAAA
Found at i:5274 original size:42 final size:40
Alignment explanation
Indices: 5215--5298 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 40
5205 ATACCTAAGA
*
5215 ATTTAATTAATGTAAGTATTTCAGTTATTATAGTATTATTAC
1 ATTTAATTAATCTAAGTATTTCAGTTATTATA-TA-TATTAC
*
5257 ATTTAATTAATCTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATCTAAGTATTTCAGTTATTATATATATTAC
5297 AT
1 AT
5299 AGGAATTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
40 8 0.20
41 2 0.05
42 30 0.75
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATCTAAGTATTTCAGTTATTATATATATTAC
Found at i:6696 original size:27 final size:27
Alignment explanation
Indices: 6647--6743 Score: 131
Period size: 29 Copynumber: 3.4 Consensus size: 27
6637 AACATATGCA
* *
6647 TATGTACTTTGTTTTCTGAGTGATATATG
1 TATGTACTTT-TTTTTTG-GTGAAATATG
6676 TATGTACTTTTTTTTTGGTGAAAGATATG
1 TATGTACTTTTTTTTTGGTG-AA-ATATG
*
6705 TATGTACTTTTTTTTTGGTGAAAAATG
1 TATGTACTTTTTTTTTGGTGAAATATG
6732 TATGTACTTTTT
1 TATGTACTTTTT
6744 GAAACCAAGA
Statistics
Matches: 63, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
27 19 0.30
28 9 0.14
29 35 0.56
ACGTcount: A:0.23, C:0.05, G:0.19, T:0.54
Consensus pattern (27 bp):
TATGTACTTTTTTTTTGGTGAAATATG
Found at i:6758 original size:26 final size:26
Alignment explanation
Indices: 6729--6793 Score: 130
Period size: 26 Copynumber: 2.5 Consensus size: 26
6719 TTGGTGAAAA
6729 ATGTATGTACTTTTTGAAACCAAGAT
1 ATGTATGTACTTTTTGAAACCAAGAT
6755 ATGTATGTACTTTTTGAAACCAAGAT
1 ATGTATGTACTTTTTGAAACCAAGAT
6781 ATGTATGTACTTT
1 ATGTATGTACTTT
6794 ATTACTAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (26 bp):
ATGTATGTACTTTTTGAAACCAAGAT
Found at i:24460 original size:29 final size:29
Alignment explanation
Indices: 24404--24504 Score: 112
Period size: 30 Copynumber: 3.4 Consensus size: 29
24394 TTAATACCAT
* *
24404 TTTTACCCCCTGAACTTGTAGTGTTTGGACG
1 TTTTACCCCCTGAACTT-CAAT-TTTGGACG
* *
24435 TTTTACCCTCTGAACTTCAATTTTGGACA
1 TTTTACCCCCTGAACTTCAATTTTGGACG
* *
24464 TTTTGCCCCCTGAACTCTCAATCTTGGACG
1 TTTTACCCCCTGAACT-TCAATTTTGGACG
*
24494 TTTTGCCCCCT
1 TTTTACCCCCT
24505 CTCAAATGAT
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
29 21 0.34
30 24 0.39
31 16 0.26
ACGTcount: A:0.17, C:0.29, G:0.16, T:0.39
Consensus pattern (29 bp):
TTTTACCCCCTGAACTTCAATTTTGGACG
Found at i:24650 original size:17 final size:17
Alignment explanation
Indices: 24628--24663 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
24618 CGACATGACA
24628 ATGCCGTTAGCGTAATC
1 ATGCCGTTAGCGTAATC
*
24645 ATGCCGTTAGCTTAATC
1 ATGCCGTTAGCGTAATC
24662 AT
1 AT
24664 TTGGAAGGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.33
Consensus pattern (17 bp):
ATGCCGTTAGCGTAATC
Found at i:28004 original size:31 final size:31
Alignment explanation
Indices: 27967--28094 Score: 150
Period size: 31 Copynumber: 4.1 Consensus size: 31
27957 GGCATGTCAC
27967 GTGTACCAAAAAGCGACATGTGACACGCCAT
1 GTGTACCAAAAAGCGACATGTGACACGCCAT
* * *
27998 GTGTACCAAAAAACGATATGTGACACGCCAC
1 GTGTACCAAAAAGCGACATGTGACACGCCAT
*
28029 GTGTACCAAAAAGTGACATGT-ATCACGCCAT
1 GTGTACCAAAAAGCGACATGTGA-CACGCCAT
* * * * * *
28060 GTTTACCCAAAAGTGACACGTGGCATGCCAT
1 GTGTACCAAAAAGCGACATGTGACACGCCAT
28091 GTGT
1 GTGT
28095 TTCAAAAAAG
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
30 1 0.01
31 81 0.99
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20
Consensus pattern (31 bp):
GTGTACCAAAAAGCGACATGTGACACGCCAT
Found at i:28101 original size:62 final size:62
Alignment explanation
Indices: 27964--28109 Score: 159
Period size: 62 Copynumber: 2.3 Consensus size: 62
27954 CATGGCATGT
* * *
27964 CACGTGTACCAAAAAGCGACATGTGACACGCCATGTGTACCAAAAAACGATATGTGACACGC
1 CACGTGTACCAAAAAGTGACATGTGACACGCCATGTGTACCAAAAAACGACACGTGACACGC
* * ** * *
28026 CACGTGTACCAAAAAGTGACATGT-ATCACGCCATGTTTACCCAAAAGTGACACGTGGCATGC
1 CACGTGTACCAAAAAGTGACATGTGA-CACGCCATGTGTACCAAAAAACGACACGTGACACGC
* * *
28088 CATGTGTTTCAAAAAAGTGACA
1 CACGTG-TACCAAAAAGTGACA
28110 CATGGCATGT
Statistics
Matches: 70, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
61 1 0.01
62 56 0.80
63 13 0.19
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.20
Consensus pattern (62 bp):
CACGTGTACCAAAAAGTGACATGTGACACGCCATGTGTACCAAAAAACGACACGTGACACGC
Found at i:33319 original size:72 final size:72
Alignment explanation
Indices: 33199--33336 Score: 204
Period size: 72 Copynumber: 1.9 Consensus size: 72
33189 GAGTTACATA
* * * *
33199 TGCACCGTCAACTGGATCACCAAAATTTGAATATATGTTATGCTTCTTGACATTAAACTTTGGTT
1 TGCACCGCCAACTGGATCACCAAAATTTGAATATATGTTATGCATCTTGAAATGAAACTTTGGTT
33264 TCATAAG
66 TCATAAG
** * *
33271 TGCACCGCCAACTGGATCAGGAAAATTTGAATATGTGTTATGCATCTTGAAATGAAAGTTTGGTT
1 TGCACCGCCAACTGGATCACCAAAATTTGAATATATGTTATGCATCTTGAAATGAAACTTTGGTT
33336 T
66 T
33337 TATAGAGGGT
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
72 58 1.00
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (72 bp):
TGCACCGCCAACTGGATCACCAAAATTTGAATATATGTTATGCATCTTGAAATGAAACTTTGGTT
TCATAAG
Found at i:37141 original size:2 final size:2
Alignment explanation
Indices: 37130--37165 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
37120 ATTTCGTGTT
37130 TA TA -A TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
37166 GGAGTATCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:39055 original size:122 final size:128
Alignment explanation
Indices: 38802--39064 Score: 394
Period size: 122 Copynumber: 2.1 Consensus size: 128
38792 TAAGTTTATA
*
38802 TATAAGAAATATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTA
1 TATAA-AAGTATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGT-
* *
38867 AAAATAAAATAGATATAAGGATATTAGGTTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAA
64 --AATAAAATACATATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAA
38932 AC
127 AC
* *
38934 TGTAAAAGTATATTT-AAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGT-A
1 TATAAAAGTATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAA
*
38997 -AAAAT-CATA-AA-GATATTAGATTTAATTAAATAAAATTAGAGTTTTTAGTTGAGTAAAAC
66 TAAAATACATATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAAC
39056 TATAAAAGT
1 TATAAAAGT
39065 TTAAACAATG
Statistics
Matches: 124, Mismatches: 7, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
122 54 0.44
123 2 0.02
124 3 0.02
125 5 0.04
126 1 0.01
130 46 0.37
131 9 0.07
132 4 0.03
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37
Consensus pattern (128 bp):
TATAAAAGTATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAA
TAAAATACATATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAAC
Found at i:39669 original size:23 final size:22
Alignment explanation
Indices: 39636--39678 Score: 77
Period size: 23 Copynumber: 1.9 Consensus size: 22
39626 ACTCAGAATC
39636 AAACTAACTGACTCAAAAAAAG
1 AAACTAACTGACTCAAAAAAAG
39658 AAACTGAACTGACTCAAAAAA
1 AAACT-AACTGACTCAAAAAA
39679 CTGACTAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.58, C:0.19, G:0.09, T:0.14
Consensus pattern (22 bp):
AAACTAACTGACTCAAAAAAAG
Found at i:40168 original size:129 final size:130
Alignment explanation
Indices: 40016--40277 Score: 386
Period size: 129 Copynumber: 2.0 Consensus size: 130
40006 TTGTTTAAAC
* * * *
40016 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATT-TAATTAAATCTAATATCCTTATAACT
1 TTTTATAATTTTACTCAACTAAAAACTCAATTTCTATTGT-ATAAAATCTAATATCCTTATAACT
* *
40080 ATTTTATTTTTACCATTTTACTATTTTAATTAAAAAAACTT-ATATATTAGAATTTTT-TAATAT
65 ATTTTATTTTTACCATTTTACTAATTTAATT-AAAAAACTTAATATATTAGAATTTTTAAAATAT
40143 AT
129 AT
* *
40145 TTTTATAATTTTACTCAACTAAAAACTCAATTTCTATTGTATAAAATCTAATATCTTTATACCTA
1 TTTTATAATTTTACTCAACTAAAAACTCAATTTCTATTGTATAAAATCTAATATCCTTATAACTA
* *
40210 TTTTATTTTTACCATTTTATTAATTTAATTAAAAAATTTAGATATATTAGAATTTTTAAAATATA
66 TTTTATTTTTACCATTTTACTAATTTAATTAAAAAACTTA-ATATATTAGAATTTTTAAAATATA
40275 T
130 T
40276 TT
1 TT
40278 CTTAAATGAC
Statistics
Matches: 119, Mismatches: 10, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
128 8 0.07
129 85 0.71
130 17 0.14
131 9 0.08
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (130 bp):
TTTTATAATTTTACTCAACTAAAAACTCAATTTCTATTGTATAAAATCTAATATCCTTATAACTA
TTTTATTTTTACCATTTTACTAATTTAATTAAAAAACTTAATATATTAGAATTTTTAAAATATAT
Done.