Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018994.1 Corchorus olitorius cultivar O-4 contig19027, 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: 35292
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3535 original size:20 final size:21
Alignment explanation
Indices: 3487--3536 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
3477 CATCCAGAGA
3487 AAATAATAAATATTCAAATATT
1 AAAT-ATAAATATTCAAATATT
* *
3509 AAATATAAATTTTCTAA-ATT
1 AAATATAAATATTCAAATATT
*
3529 AATTATAA
1 AAATATAA
3537 TCCATTTGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 10 0.40
21 11 0.44
22 4 0.16
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (21 bp):
AAATATAAATATTCAAATATT
Found at i:3753 original size:97 final size:98
Alignment explanation
Indices: 3580--3861 Score: 433
Period size: 97 Copynumber: 2.9 Consensus size: 98
3570 TTTATTAAAT
* *
3580 TTATTATCATTTGGAAGCGGATTTAGACACGGATATGTAGTTTCCGTGTTAAATTCCGTTT-CAA
1 TTATTATCAATTAGAAGCGGATTTAGACACGGATATGTAGTTTCCGTGTTAAATTCCGTTTCCAA
3644 ATGAAATAAAAATTTATTTATAAAATAATTTTA
66 ATGAAATAAAAATTTATTTATAAAATAATTTTA
3677 TTATTATCAATTAGAAGCGGATTTAGACACGGATATGTAGTTTCCGTGTTAAATTCCGTTTCCAA
1 TTATTATCAATTAGAAGCGGATTTAGACACGGATATGTAGTTTCCGTGTTAAATTCCGTTTCCAA
* * *
3742 ATGAAAT-AAAATTTATTAATAGAATTATTTTA
66 ATGAAATAAAAATTTATTTATAAAATAATTTTA
* * * * *
3774 TTATTATCAATTTGAATCGGATTTAGACACGGATCTGCAGTTTCCGTGTTAAATTCCATTTCCAA
1 TTATTATCAATTAGAAGCGGATTTAGACACGGATATGTAGTTTCCGTGTTAAATTCCGTTTCCAA
* *
3839 GTGAAATAGAAAATTAATTTATA
66 ATGAAATA-AAAATTTATTTATA
3862 TAAGATAGTG
Statistics
Matches: 169, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
97 147 0.87
98 10 0.06
99 12 0.07
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (98 bp):
TTATTATCAATTAGAAGCGGATTTAGACACGGATATGTAGTTTCCGTGTTAAATTCCGTTTCCAA
ATGAAATAAAAATTTATTTATAAAATAATTTTA
Found at i:23772 original size:22 final size:22
Alignment explanation
Indices: 23747--23788 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
23737 GGCATTTGGG
*
23747 TTTAATC-TCATTTCAGATTTTC
1 TTTAATCAT-ATTTAAGATTTTC
23769 TTTAATCATATTTAAGATTT
1 TTTAATCATATTTAAGATTT
23789 AAGATTAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.29, C:0.12, G:0.05, T:0.55
Consensus pattern (22 bp):
TTTAATCATATTTAAGATTTTC
Found at i:24905 original size:21 final size:21
Alignment explanation
Indices: 24879--24918 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
24869 ATTTTTTTTT
24879 TTTTACTAT-ATTGGTACTTTC
1 TTTTAC-ATGATTGGTACTTTC
*
24900 TTTTACATGCTTGGTACTT
1 TTTTACATGATTGGTACTT
24919 GATTGAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.17, C:0.15, G:0.12, T:0.55
Consensus pattern (21 bp):
TTTTACATGATTGGTACTTTC
Found at i:27970 original size:14 final size:15
Alignment explanation
Indices: 27953--27982 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
27943 TATTTCATTT
27953 TAAAA-ATTTGATTA
1 TAAAACATTTGATTA
27967 TAAAACATTTGATTA
1 TAAAACATTTGATTA
27982 T
1 T
27983 TTAATAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (15 bp):
TAAAACATTTGATTA
Found at i:28310 original size:25 final size:25
Alignment explanation
Indices: 28276--28348 Score: 101
Period size: 25 Copynumber: 2.9 Consensus size: 25
28266 TAGTGCACCA
* *
28276 TAAGCATTGGGAAGAAGAACTCGAG
1 TAAGCATTGGGAAGGAGAACTAGAG
* *
28301 TAAGCTTTGGGAAGGAGAATTAGAG
1 TAAGCATTGGGAAGGAGAACTAGAG
*
28326 TAAGCCTTGGGAAGGAGAACTAG
1 TAAGCATTGGGAAGGAGAACTAG
28349 CCTATCTAGC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.37, C:0.10, G:0.34, T:0.19
Consensus pattern (25 bp):
TAAGCATTGGGAAGGAGAACTAGAG
Found at i:32092 original size:347 final size:348
Alignment explanation
Indices: 31455--32109 Score: 1170
Period size: 347 Copynumber: 1.9 Consensus size: 348
31445 TTGATAACAT
* *
31455 AAATTTTATCACATACATCTCACGTTCAACCCTATATATAACAAACAAAAAAAAACAATTATTGG
1 AAATTTTATCACATACATCCCACATTCAACCCTATATATAACAAACAAAAAAAAACAATTATTGG
* **
31520 GCTTCTTGTCATGCTATGTTTTGTGATTTACATGGATAAACGATTTATAATTAACTCACCCTTTC
66 GCTTCTTGTCAAGCTACATTTTGTGATTTACATGGATAAACGATTTATAATTAACTCACCCTTTC
*
31585 TGTATTGGAACTCCCTCTGGAGTTATGATGGGCCACAAATTAATCCCCGCCACATTCGAGCGGCC
131 TGTATCGGAACTCCCTCTGGAGTTATGATGGGCCACAAATTAATCCCCGCCACATTCGAGCGGCC
*
31650 CTCACCAATACATTTATCTTAAAAAAGTATGCTGCAAAAATGTATCTTCAATGCAATAACAACAT
196 CTCACCAAAACATTTATCTTAAAAAAGTATGCTGCAAAAATGTATCTTCAATGCAATAACAACAT
*
31715 CAATCACTTACCCATTATGTGTACCATTCAAATTGCATTTCGTACTAAAATAAGAAACCAGTGAT
261 CAATCACTAACCCATTATGTGTACCATTCAAA-TGCATTTCGTACTAAAATAAGAAACCAGTGAT
31780 AGTTTGATTCATTCATGTGATAAG
325 AGTTTGATTCATTCATGTGATAAG
31804 AAATTTTATCACATACATCCCACATTCAACCCTATATATAA-AAAC-AAAAAAAACAATTATTGG
1 AAATTTTATCACATACATCCCACATTCAACCCTATATATAACAAACAAAAAAAAACAATTATTGG
* *
31867 GCTTCTTGTCAAGCTACATTTTGTGATTTACATGGATAAACGGTTTATAATTTACTCACCCTTTC
66 GCTTCTTGTCAAGCTACATTTTGTGATTTACATGGATAAACGATTTATAATTAACTCACCCTTTC
*
31932 TGTATCGGAACTCCCTCTGGAGTTATGATGGGCCACAAATTAATCCCTGCCACATTCGAGCGGCC
131 TGTATCGGAACTCCCTCTGGAGTTATGATGGGCCACAAATTAATCCCCGCCACATTCGAGCGGCC
* *
31997 CTCACCAAAACATTTATCTTCAAAAAGTATGCTGCAAAGATGTATCTTCAATGCAATAACAACAT
196 CTCACCAAAACATTTATCTTAAAAAAGTATGCTGCAAAAATGTATCTTCAATGCAATAACAACAT
32062 CAATCACTAACCCATTATGTGTACCATTCAAATGCATTTCGTACTAAA
261 CAATCACTAACCCATTATGTGTACCATTCAAATGCATTTCGTACTAAA
32110 CTAAATTGTA
Statistics
Matches: 293, Mismatches: 13, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
346 16 0.05
347 234 0.80
348 4 0.01
349 39 0.13
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (348 bp):
AAATTTTATCACATACATCCCACATTCAACCCTATATATAACAAACAAAAAAAAACAATTATTGG
GCTTCTTGTCAAGCTACATTTTGTGATTTACATGGATAAACGATTTATAATTAACTCACCCTTTC
TGTATCGGAACTCCCTCTGGAGTTATGATGGGCCACAAATTAATCCCCGCCACATTCGAGCGGCC
CTCACCAAAACATTTATCTTAAAAAAGTATGCTGCAAAAATGTATCTTCAATGCAATAACAACAT
CAATCACTAACCCATTATGTGTACCATTCAAATGCATTTCGTACTAAAATAAGAAACCAGTGATA
GTTTGATTCATTCATGTGATAAG
Done.