Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021146.1 Corchorus olitorius cultivar O-4 contig21179, 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: 12242
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:114 original size:16 final size:15
Alignment explanation
Indices: 76--117 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
66 ACAGAGATTG
*
76 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
91 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
106 ACTAGAAAACAA
1 AC-AGAAAACAA
118 AGCAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:5128 original size:14 final size:14
Alignment explanation
Indices: 5109--5144 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
5099 ATGCATTAAT
5109 CATAATTTCAATGC
1 CATAATTTCAATGC
*
5123 CATAATTTCGATGC
1 CATAATTTCAATGC
5137 CATAATTT
1 CATAATTT
5145 TTTCGAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.19, G:0.08, T:0.39
Consensus pattern (14 bp):
CATAATTTCAATGC
Found at i:6423 original size:29 final size:30
Alignment explanation
Indices: 6376--6435 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
6366 GAAGTTCGTG
* *
6376 TTTGAAGACTCATTGAAGACTTATTTGAAGA
1 TTTGAAGAC-CATTGAAGAATTATTTCAAGA
6407 TTTGAAGA-CATTGAAGAATTATTTCAAGA
1 TTTGAAGACCATTGAAGAATTATTTCAAGA
6436 GCAAGAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 19 0.70
31 8 0.30
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.35
Consensus pattern (30 bp):
TTTGAAGACCATTGAAGAATTATTTCAAGA
Found at i:10439 original size:333 final size:332
Alignment explanation
Indices: 9802--11128 Score: 1907
Period size: 333 Copynumber: 4.0 Consensus size: 332
9792 ACGACCGATC
*
9802 AAAAACTTAGCCACGTTGCGTTTAACGA-TT-TTTTTACGAGCATTTGAATCTTGTTTCGATTTA
1 AAAAACTTAGCCACGTTGCATTTAACGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTA
9865 ATTAGAAATTAATTCAAAAAAATATGAAAAACGATATTAAAAGCATGAAAAGTCCTCCAATGTTT
66 ATTAGAAATTAATTCAAAAAAATATGAAAAACGATATTAAAAGCATGAAAAGTCCTCCAATGTTT
* * *
9930 TTGGCGTTAAATTATATATATCTTATGAGTATTTTATCTAAAAATTGAGGAAAAATTTTTCCCGG
131 TTGGCGTTAAATTATATATATTTTATGAGTATTTTATCCAAAAATTGAGGAAAAATTTTTCGCGG
* * *
9995 TAATTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACCATCAAGATTTTTGGCTTAAAACGCG
196 TAATTTTTTGCAAAATTTTAGCCAAAATCGTATACTAACCATCACGATTTTTGGCTAAAAACGCG
* * *
10060 TTTCGGGGTCCCAG-CGCAGTTTTGCACGATTTTTATCGTCAAGACTCCTTGATATATCTATATT
261 TTTCGGGGTCCC-GTCTCAGTTTTGCATGATTTTTATCGTCAAGACTCCTTGAAATATCTATATT
10124 CATCTAAT
325 CATCTAAT
* * * *
10132 AAAAAATTAGTCACGTTGCATTTAA-GAATTTGTTTTTACGAGCATTTGAATCTTGTTTCTAGTT
1 AAAAACTTAGCCACGTTGCATTTAACG-ATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTT
*
10196 AATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCTTGAAAAGTCCTCCAATGT
65 AATTAGAAATTAATTCA-AAAAAATATGAAAAACGATATTAAAAGCATGAAAAGTCCTCCAATGT
* * *
10261 TTATGGCGTTAATTTATGTATATTTTATGAGTATTTTATCCAAAAATTGAGGAAAAATTTTTCGC
129 TTTTGGCGTTAAATTATATATATTTTATGAGTATTTTATCCAAAAATTGAGGAAAAATTTTTCGC
* *
10326 GGTAATTTTTTGAAAAATTTTAGCCAAAATCGTATACTAACCATTACGATTTTTGGCTAAAAACG
194 GGTAATTTTTTGCAAAATTTTAGCCAAAATCGTATACTAACCATCACGATTTTTGGCTAAAAACG
* **
10391 CGTTTCGGGGTCCCGTCTCAGTTTTGTATGATTTTTGGCAGT-AAGACTCCTTGAAATATCTATA
259 CGTTTCGGGGTCCCGTCTCAGTTTTGCATGATTTTTATC-GTCAAGACTCCTTGAAATATCTATA
*
10455 TTCATTTAAT
323 TTCATCTAAT
* * **
10465 AAAAACTTAGCCACGTTGCGTTTAACGATTTTTTTTTTTGAGCATTTGAATCTTGTTTCGATTTA
1 AAAAACTTAGCCACGTTGCATTTAACGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTA
*
10530 ATTAGAAATTAATTCAAAACAATATGAAAAACGATATTAAAAGCATGAAAAGTCCTCCAATGTTT
66 ATTAGAAATTAATTCAAAAAAATATGAAAAACGATATTAAAAGCATGAAAAGTCCTCCAATGTTT
* * *
10595 TTGGCATTAAATTATATATATTTTATGAGTATTTTATCCAAAAATTAAGGAAACAA-TTTTCACG
131 TTGGCGTTAAATTATATATATTTTATGAGTATTTTATCCAAAAATTGAGGAAA-AATTTTTCGCG
* * *
10659 GTAATTTTTTGCAAAATTTTAGCCATAATCGTGA-ACCAACCATCACGGTCTTTTTGGCTAAAAA
195 GTAATTTTTTGCAAAATTTTAGCCAAAATCGT-ATACTAACCATCAC-G-ATTTTTGGCTAAAAA
* * * * *
10723 CGCGTTTAGGGGTCCAAGT-ACAGTTTTGCATGATTTTTATCGTCAAGACACCTTGAAATATATA
257 CGCGTTTCGGGGTCC-CGTCTCAGTTTTGCATGATTTTTATCGTCAAGACTCCTTGAAATATCTA
*
10787 TATTCATCTCAT
321 TATTCATCTAAT
* ** *
10799 AAAAACTTAGTCACACTGCATTTAAGGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTA
1 AAAAACTTAGCCACGTTGCATTTAACGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTA
* *
10864 ATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCTTGAAAAGTCCTCCAATGTTT
66 ATTAGAAATTAATTCAAAAAAATATGAAAAACGATATTAAAAGCATGAAAAGTCCTCCAATGTTT
* * *
10929 TTGACGTTAAATTATGTATATTTTATGATTATTTTATCCAAAAATTGAGGAAAAATTTTTCGCGG
131 TTGGCGTTAAATTATATATATTTTATGAGTATTTTATCCAAAAATTGAGGAAAAATTTTTCGCGG
* * * * *
10994 TAATTTTTTGCAAAATTTTTGCCAAAATCG--T-GT----A--GCGGTTTTAGGCTAAAAACGCG
196 TAATTTTTTGCAAAATTTTAGCCAAAATCGTATACTAACCATCACGATTTTTGGCTAAAAACGCG
** *
11050 TTTCGGGGTCCCAACTCAGTTTTGCATGATTTTTGA-CGTTAAGACTCCTTGAAATATCTATATT
261 TTTCGGGGTCCCGTCTCAGTTTTGCATGATTTTT-ATCGTCAAGACTCCTTGAAATATCTATATT
*
11114 CATTTAAT
325 CATCTAAT
11122 AAAAACT
1 AAAAACT
11129 GATCGAGCTA
Statistics
Matches: 891, Mismatches: 89, Indels: 41
0.87 0.09 0.04
Matches are distributed among these distances:
323 83 0.09
324 2 0.00
325 1 0.00
327 1 0.00
329 1 0.00
330 23 0.03
331 2 0.00
332 190 0.21
333 306 0.34
334 280 0.31
335 2 0.00
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.38
Consensus pattern (332 bp):
AAAAACTTAGCCACGTTGCATTTAACGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTA
ATTAGAAATTAATTCAAAAAAATATGAAAAACGATATTAAAAGCATGAAAAGTCCTCCAATGTTT
TTGGCGTTAAATTATATATATTTTATGAGTATTTTATCCAAAAATTGAGGAAAAATTTTTCGCGG
TAATTTTTTGCAAAATTTTAGCCAAAATCGTATACTAACCATCACGATTTTTGGCTAAAAACGCG
TTTCGGGGTCCCGTCTCAGTTTTGCATGATTTTTATCGTCAAGACTCCTTGAAATATCTATATTC
ATCTAAT
Done.