Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023077.1 Corchorus olitorius cultivar O-4 contig23110, 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: 48059
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:5851 original size:43 final size:42
Alignment explanation
Indices: 5804--6091 Score: 409
Period size: 43 Copynumber: 6.8 Consensus size: 42
5794 ACAAGGAGAA
* * *
5804 ATGCCTCTGTTTTATATATGTGTTTGAGGACTTTGTAATAGAG
1 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTG-AATAGAG
*
5847 ATGCCCCTGTGTTATATATGTGTTTGGGGAC-TTGAATATAG
1 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGAATAGAG
* * * *
5888 ATGTCACTGTGTTATATATGTGTTTGAGAACTTTGATATAGAG
1 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGA-ATAGAG
5931 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGATATAGAG
1 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGA-ATAGAG
* *
5974 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTG-ATATAT
1 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGAATAGAG
* * *
6015 ATGCCTCTATGTTATATATGTGTTTGAGGACTTTGGAATAGAG
1 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTT-GAATAGAG
6058 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTT
1 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTT
6092 TGGTCATTGG
Statistics
Matches: 218, Mismatches: 23, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
41 68 0.31
42 8 0.04
43 142 0.65
ACGTcount: A:0.22, C:0.11, G:0.25, T:0.42
Consensus pattern (42 bp):
ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGAATAGAG
Found at i:5921 original size:84 final size:84
Alignment explanation
Indices: 5804--6091 Score: 409
Period size: 84 Copynumber: 3.4 Consensus size: 84
5794 ACAAGGAGAA
* *
5804 ATGCCTCTGTTTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATGTG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTG-AATAGAGATGCCCCTGTGTTATATATGTG
*
5869 TTTGGGGAC-TTGAATATAG
65 TTTGGGGACTTTGAATAGAG
* * *
5888 ATGTCACTGTGTTATATATGTGTTTGAGAACTTTGATATAGAGATGCCCCTGTGTTATATATGTG
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGA-ATAGAGATGCCCCTGTGTTATATATGTG
5953 TTTGGGGACTTTGATATAGAG
65 TTTGGGGACTTTGA-ATAGAG
* * * * *
5974 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTG-ATATATATGCCTCTATGTTATATATGTGT
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGAATAGAGATGCCCCTGTGTTATATATGTGT
*
6038 TTGAGGACTTTGGAATAGAG
66 TTGGGGACTTT-GAATAGAG
*
6058 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTT
1 ATGCCCCTGTGTTATATATGTGTTTGAGGACTTT
6092 TGGTCATTGG
Statistics
Matches: 186, Mismatches: 14, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
83 1 0.01
84 143 0.77
85 6 0.03
86 36 0.19
ACGTcount: A:0.22, C:0.11, G:0.25, T:0.42
Consensus pattern (84 bp):
ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGAATAGAGATGCCCCTGTGTTATATATGTGT
TTGGGGACTTTGAATAGAG
Found at i:6001 original size:127 final size:127
Alignment explanation
Indices: 5804--6091 Score: 456
Period size: 127 Copynumber: 2.3 Consensus size: 127
5794 ACAAGGAGAA
* * *
5804 ATGCCTCTGTTTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATGTG
1 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGTAATAGAGATGCCCCTGTGTTATATATGTG
* *
5869 TTTGGGGAC-TTGAATATAGATGTCACTGTGTTATATATGTGTTTGAGAACTTT-GATATAGAG
66 TTTGGGGACTTTG-ATATAGATGCCACTATGTTATATATGTGTTTGAGAACTTTGGA-ATAGAG
5931 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTG-ATATAGAGATGCCCCTGTGTTATATATGT
1 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGTA-ATAGAGATGCCCCTGTGTTATATATGT
* * *
5995 GTTTGGGGACTTTGATATATATGCCTCTATGTTATATATGTGTTTGAGGACTTTGGAATAGAG
65 GTTTGGGGACTTTGATATAGATGCCACTATGTTATATATGTGTTTGAGAACTTTGGAATAGAG
6058 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTT
1 ATGCCCCTGTGTTATATATGTGTTTGGGGACTTT
6092 TGGTCATTGG
Statistics
Matches: 150, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
126 1 0.01
127 144 0.96
128 5 0.03
ACGTcount: A:0.22, C:0.11, G:0.25, T:0.42
Consensus pattern (127 bp):
ATGCCCCTGTGTTATATATGTGTTTGGGGACTTTGTAATAGAGATGCCCCTGTGTTATATATGTG
TTTGGGGACTTTGATATAGATGCCACTATGTTATATATGTGTTTGAGAACTTTGGAATAGAG
Found at i:8260 original size:15 final size:17
Alignment explanation
Indices: 8240--8272 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
8230 CGCTCAAATG
8240 TCGGGTC-ATT-TGGGT
1 TCGGGTCAATTCTGGGT
8255 TCGGGTCAATTCTGGGT
1 TCGGGTCAATTCTGGGT
8272 T
1 T
8273 GGGCCGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 3 0.19
17 6 0.38
ACGTcount: A:0.09, C:0.15, G:0.36, T:0.39
Consensus pattern (17 bp):
TCGGGTCAATTCTGGGT
Found at i:11393 original size:2 final size:2
Alignment explanation
Indices: 11386--11422 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
11376 TTTGTGCAAA
11386 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11423 AAGGAAGTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:13678 original size:25 final size:25
Alignment explanation
Indices: 13627--13683 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 25
13617 GCGGATTGTA
*
13627 AAATAAATTGAATAATAAAGACATT
1 AAATAAATTGAAGAATAAAGACATT
* *
13652 AAATAAATTTAAGAATTAA-ACATT
1 AAATAAATTGAAGAATAAAGACATT
*
13676 TAA-AAATT
1 AAATAAATT
13684 CAAGGTTGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 5 0.18
24 7 0.25
25 16 0.57
ACGTcount: A:0.60, C:0.04, G:0.05, T:0.32
Consensus pattern (25 bp):
AAATAAATTGAAGAATAAAGACATT
Found at i:15475 original size:15 final size:15
Alignment explanation
Indices: 15455--15485 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
15445 ATAATACATT
15455 AACTATCAAATAGAA
1 AACTATCAAATAGAA
15470 AACTATCAAATAGAA
1 AACTATCAAATAGAA
15485 A
1 A
15486 CAGGTTAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.13, G:0.06, T:0.19
Consensus pattern (15 bp):
AACTATCAAATAGAA
Found at i:15532 original size:14 final size:14
Alignment explanation
Indices: 15513--15547 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
15503 CCTTTTAAAT
15513 TAAAATAGTAAAAA
1 TAAAATAGTAAAAA
*
15527 TAAAATGGTAAAAA
1 TAAAATAGTAAAAA
15541 TAAAATA
1 TAAAATA
15548 ATTATAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.23
Consensus pattern (14 bp):
TAAAATAGTAAAAA
Found at i:16010 original size:15 final size:15
Alignment explanation
Indices: 15990--16020 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
15980 ATAATACATT
15990 AACTATCAAATAGAA
1 AACTATCAAATAGAA
16005 AACTATCAAATAGAA
1 AACTATCAAATAGAA
16020 A
1 A
16021 CAGGTTAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.13, G:0.06, T:0.19
Consensus pattern (15 bp):
AACTATCAAATAGAA
Found at i:16067 original size:14 final size:14
Alignment explanation
Indices: 16048--16082 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
16038 CCTTTTAAAT
16048 TAAAATAGTAAAAA
1 TAAAATAGTAAAAA
*
16062 TAAAATGGTAAAAA
1 TAAAATAGTAAAAA
16076 TAAAATA
1 TAAAATA
16083 ATTATAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.23
Consensus pattern (14 bp):
TAAAATAGTAAAAA
Found at i:16253 original size:535 final size:535
Alignment explanation
Indices: 15244--16311 Score: 2136
Period size: 535 Copynumber: 2.0 Consensus size: 535
15234 ACCCATATGA
15244 CCCGAAATTTCCTTAACCCGAAACTGTTCGAACCAAAATTCAACCTGACCTCCCATTTGCATATA
1 CCCGAAATTTCCTTAACCCGAAACTGTTCGAACCAAAATTCAACCTGACCTCCCATTTGCATATA
15309 CATAGGGTTTTACTATCAAAGGAACAAAAGAAATTATTCCACATAAATAAAAATATTAACAAAGT
66 CATAGGGTTTTACTATCAAAGGAACAAAAGAAATTATTCCACATAAATAAAAATATTAACAAAGT
15374 AAAATATAACGTACTTTATCTAGCAATAATTGAAATTAATTATAAGTTAAATAAAATAATAAATT
131 AAAATATAACGTACTTTATCTAGCAATAATTGAAATTAATTATAAGTTAAATAAAATAATAAATT
15439 ATAATCATAATACATTAACTATCAAATAGAAAACTATCAAATAGAAACAGGTTAATCACAATAAC
196 ATAATCATAATACATTAACTATCAAATAGAAAACTATCAAATAGAAACAGGTTAATCACAATAAC
15504 CTTTTAAATTAAAATAGTAAAAATAAAATGGTAAAAATAAAATAATTATAAAAATATTTAATTTA
261 CTTTTAAATTAAAATAGTAAAAATAAAATGGTAAAAATAAAATAATTATAAAAATATTTAATTTA
15569 ATTAAATGCAAATAGAGTTTTCAGTTGAATAAAATTGTATATTAAAAGTTTTTAATATATCCAAG
326 ATTAAATGCAAATAGAGTTTTCAGTTGAATAAAATTGTATATTAAAAGTTTTTAATATATCCAAG
15634 TTTTTAATGAAAAATAGTAAAATAGTAAAAATAAAGTAATTATAAAGATATTAGATTTCATTAAA
391 TTTTTAATGAAAAATAGTAAAATAGTAAAAATAAAGTAATTATAAAGATATTAGATTTCATTAAA
15699 TAAAAATAGAGTTTTTAGTAGAATAAAACTATAATAGTTTAAGTAATGGTATTTAAGAAATATAT
456 TAAAAATAGAGTTTTTAGTAGAATAAAACTATAATAGTTTAAGTAATGGTATTTAAGAAATATAT
15764 TCGAAAAATAAGGGT
521 TCGAAAAATAAGGGT
15779 CCCGAAATTTCCTTAACCCGAAACTGTTCGAACCAAAATTCAACCTGACCTCCCATTTGCATATA
1 CCCGAAATTTCCTTAACCCGAAACTGTTCGAACCAAAATTCAACCTGACCTCCCATTTGCATATA
15844 CATAGGGTTTTACTATCAAAGGAACAAAAGAAATTATTCCACATAAATAAAAATATTAACAAAGT
66 CATAGGGTTTTACTATCAAAGGAACAAAAGAAATTATTCCACATAAATAAAAATATTAACAAAGT
15909 AAAATATAACGTACTTTATCTAGCAATAATTGAAATTAATTATAAGTTAAATAAAATAATAAATT
131 AAAATATAACGTACTTTATCTAGCAATAATTGAAATTAATTATAAGTTAAATAAAATAATAAATT
15974 ATAATCATAATACATTAACTATCAAATAGAAAACTATCAAATAGAAACAGGTTAATCACAATAAC
196 ATAATCATAATACATTAACTATCAAATAGAAAACTATCAAATAGAAACAGGTTAATCACAATAAC
16039 CTTTTAAATTAAAATAGTAAAAATAAAATGGTAAAAATAAAATAATTATAAAAATATTTAATTTA
261 CTTTTAAATTAAAATAGTAAAAATAAAATGGTAAAAATAAAATAATTATAAAAATATTTAATTTA
16104 ATTAAATGCAAATAGAGTTTTCAGTTGAATAAAATTGTATATTAAAAGTTTTTAATATATCCAAG
326 ATTAAATGCAAATAGAGTTTTCAGTTGAATAAAATTGTATATTAAAAGTTTTTAATATATCCAAG
16169 TTTTTAATGAAAAATAGTAAAATAGTAAAAATAAAGTAATTATAAAGATATTAGATTTCATTAAA
391 TTTTTAATGAAAAATAGTAAAATAGTAAAAATAAAGTAATTATAAAGATATTAGATTTCATTAAA
16234 TAAAAATAGAGTTTTTAGTAGAATAAAACTATAATAGTTTAAGTAATGGTATTTAAGAAATATAT
456 TAAAAATAGAGTTTTTAGTAGAATAAAACTATAATAGTTTAAGTAATGGTATTTAAGAAATATAT
16299 TCGAAAAATAAGG
521 TCGAAAAATAAGG
16312 ATATAATGGG
Statistics
Matches: 533, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
535 533 1.00
ACGTcount: A:0.49, C:0.10, G:0.09, T:0.32
Consensus pattern (535 bp):
CCCGAAATTTCCTTAACCCGAAACTGTTCGAACCAAAATTCAACCTGACCTCCCATTTGCATATA
CATAGGGTTTTACTATCAAAGGAACAAAAGAAATTATTCCACATAAATAAAAATATTAACAAAGT
AAAATATAACGTACTTTATCTAGCAATAATTGAAATTAATTATAAGTTAAATAAAATAATAAATT
ATAATCATAATACATTAACTATCAAATAGAAAACTATCAAATAGAAACAGGTTAATCACAATAAC
CTTTTAAATTAAAATAGTAAAAATAAAATGGTAAAAATAAAATAATTATAAAAATATTTAATTTA
ATTAAATGCAAATAGAGTTTTCAGTTGAATAAAATTGTATATTAAAAGTTTTTAATATATCCAAG
TTTTTAATGAAAAATAGTAAAATAGTAAAAATAAAGTAATTATAAAGATATTAGATTTCATTAAA
TAAAAATAGAGTTTTTAGTAGAATAAAACTATAATAGTTTAAGTAATGGTATTTAAGAAATATAT
TCGAAAAATAAGGGT
Found at i:16409 original size:25 final size:25
Alignment explanation
Indices: 16359--16409 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
16349 GTACTTTTTA
*
16359 ATATAGTATAAATAGATACTTTTAT
1 ATATAGTATAAATAGATACTTATAT
* *
16384 ATATAGTATAGATATATA--TATAT
1 ATATAGTATAAATAGATACTTATAT
16407 ATA
1 ATA
16410 GCTTTGGAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 7 0.30
25 16 0.70
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43
Consensus pattern (25 bp):
ATATAGTATAAATAGATACTTATAT
Found at i:19137 original size:13 final size:13
Alignment explanation
Indices: 19119--19144 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19109 TTTTGGCTTT
19119 ATAATTAGTATAG
1 ATAATTAGTATAG
19132 ATAATTAGTATAG
1 ATAATTAGTATAG
19145 GCTATGTTAA
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:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (13 bp):
ATAATTAGTATAG
Found at i:45569 original size:102 final size:102
Alignment explanation
Indices: 45389--45585 Score: 277
Period size: 102 Copynumber: 1.9 Consensus size: 102
45379 ATAAGTATAG
* *
45389 CTGTTCAAGGGTCAGGCTACCCGCCCAAACCCGTAAGCCCGCCCGATATTTTAAAGAGCTTAGAC
1 CTGTTCAAGGGCCAGGCTACCCGCCCAAACCCGTAAGCCCGCCCGATATTTGAAAGAGCTTAGAC
* * * *
45454 AAGAATTTTAAGCCCATTGGATGGGTTTGGGCTAGAT
66 AAAAATTTGAAGCCCATTGGACGGGCTTGGGCTAGAT
* * ** * *
45491 CTGTTCAAGGGCCGGGCTACCCGCCCAAGCCCGTAAGCCCGCCCGATATTTGGGAGGGCTTGGAC
1 CTGTTCAAGGGCCAGGCTACCCGCCCAAACCCGTAAGCCCGCCCGATATTTGAAAGAGCTTAGAC
*
45556 AAAAATTTGAAGCCCGTTGGACGGGCTTGG
66 AAAAATTTGAAGCCCATTGGACGGGCTTGG
45586 ACAAAATTTG
Statistics
Matches: 82, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
102 82 1.00
ACGTcount: A:0.23, C:0.26, G:0.28, T:0.22
Consensus pattern (102 bp):
CTGTTCAAGGGCCAGGCTACCCGCCCAAACCCGTAAGCCCGCCCGATATTTGAAAGAGCTTAGAC
AAAAATTTGAAGCCCATTGGACGGGCTTGGGCTAGAT
Found at i:45595 original size:31 final size:31
Alignment explanation
Indices: 45546--45636 Score: 146
Period size: 31 Copynumber: 2.9 Consensus size: 31
45536 ATATTTGGGA
45546 GGGCTTGGACAAAAATTTGAAGCCCGTTGGAC
1 GGGCTTGGAC-AAAATTTGAAGCCCGTTGGAC
*
45578 GGGCTTGGACAAAATTTGAAGCCCGTTTGAC
1 GGGCTTGGACAAAATTTGAAGCCCGTTGGAC
*
45609 GGGCTTGGACAAAATTTTAAGGCCCGTT
1 GGGCTTGGACAAAATTTGAA-GCCCGTT
45637 TACAAAATGG
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
31 39 0.70
32 17 0.30
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (31 bp):
GGGCTTGGACAAAATTTGAAGCCCGTTGGAC
Done.