Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017174.1 Corchorus olitorius cultivar O-4 contig17207, 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: 23117
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:4489 original size:14 final size:15
Alignment explanation
Indices: 4470--4498 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4460 TTTTTTTTTC
4470 AAAAAT-AAAATTAT
1 AAAAATAAAAATTAT
4484 AAAAATAAAAATTAT
1 AAAAATAAAAATTAT
4499 CCCATCTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AAAAATAAAAATTAT
Found at i:7071 original size:24 final size:24
Alignment explanation
Indices: 7039--7088 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
7029 AACTGTTTCT
7039 TGGTGATTGTGATATAGTTAAAAA
1 TGGTGATTGTGATATAGTTAAAAA
7063 TGGTGATTGTGATATAGTTAAAAA
1 TGGTGATTGTGATATAGTTAAAAA
7087 TG
1 TG
7089 ACACGGAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.26, T:0.38
Consensus pattern (24 bp):
TGGTGATTGTGATATAGTTAAAAA
Found at i:12362 original size:14 final size:13
Alignment explanation
Indices: 12343--12379 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
12333 CATTTAAATC
12343 TATGTATATATAT
1 TATGTATATATAT
12356 GTATGTATATATAT
1 -TATGTATATATAT
*
12370 TATATATATA
1 TATGTATATA
12380 GGGTAGGGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (13 bp):
TATGTATATATAT
Found at i:13982 original size:5 final size:5
Alignment explanation
Indices: 13924--13971 Score: 51
Period size: 5 Copynumber: 9.6 Consensus size: 5
13914 GCCGGGGCCG
* * * * *
13924 GGGCA GGGCA GGGCA GGGCA TGGCA AGCCA AGGCA GAGCA GGGCA GGG
1 GGGCA GGGCA GGGCA GGGCA GGGCA GGGCA GGGCA GGGCA GGGCA GGG
13972 GCGCAGGGCA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.25, C:0.21, G:0.52, T:0.02
Consensus pattern (5 bp):
GGGCA
Found at i:14225 original size:57 final size:57
Alignment explanation
Indices: 14134--14477 Score: 582
Period size: 57 Copynumber: 6.0 Consensus size: 57
14124 ATCTAAATTA
* * ** * * *
14134 CAAATAA-CTATTTCCATTTGACAATTTATTATCAATTCTGTTTTGTTCAGATCAGAC
1 CAAATAATC-ATTTTCATATGACAATTTACGATCAATTATGTTTTATTCAGATCGGAC
14191 CAAATAATCATTTTCATATGACAATTTACGATCAATTATGTTTTATTCAGATCGGAC
1 CAAATAATCATTTTCATATGACAATTTACGATCAATTATGTTTTATTCAGATCGGAC
*
14248 CAAATAATCATTTTCATATGACAATTTACGATCAATTATGTTTTGTTCAGATCGGAC
1 CAAATAATCATTTTCATATGACAATTTACGATCAATTATGTTTTATTCAGATCGGAC
14305 CAAATAATCATTTTCATATGACAATTTACGATCAATTATGTTTTATTCAGATCGGAC
1 CAAATAATCATTTTCATATGACAATTTACGATCAATTATGTTTTATTCAGATCGGAC
14362 CAAATAATCATTTTCATATGACAATTTACGATCAATTATGTTTTATTCAGATCGGAC
1 CAAATAATCATTTTCATATGACAATTTACGATCAATTATGTTTTATTCAGATCGGAC
* *
14419 CAAATAATCATTTTCATATGACAATTTACGATTAATCATGTTTTATTCAGATCGGAC
1 CAAATAATCATTTTCATATGACAATTTACGATCAATTATGTTTTATTCAGATCGGAC
14476 CA
1 CA
14478 CTACATGGGT
Statistics
Matches: 275, Mismatches: 11, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
57 274 1.00
58 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.39
Consensus pattern (57 bp):
CAAATAATCATTTTCATATGACAATTTACGATCAATTATGTTTTATTCAGATCGGAC
Found at i:19394 original size:13 final size:13
Alignment explanation
Indices: 19376--19400 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19366 AAAGAATATA
19376 AAAAGAAAGAAAC
1 AAAAGAAAGAAAC
19389 AAAAGAAAGAAA
1 AAAAGAAAGAAA
19401 ACAATGAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.04, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAAGAAAGAAAC
Found at i:19877 original size:3 final size:3
Alignment explanation
Indices: 19869--19900 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
19859 TAGCTATTAG
19869 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
19901 AAGAAACCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Done.