Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019065.1 Corchorus olitorius cultivar O-4 contig19098, 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: 47856
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:651 original size:28 final size:28
Alignment explanation
Indices: 598--651 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
588 GGGAAAATTC
*
598 CAAAAGGTATAATTTGATCATTTATAAA
1 CAAAAGGTATAATTTGATCATGTATAAA
* *
626 CAAAATGTA-AATATTGATGATGTATA
1 CAAAAGGTATAAT-TTGATCATGTATA
652 TGTTTTAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 3 0.14
28 19 0.86
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (28 bp):
CAAAAGGTATAATTTGATCATGTATAAA
Found at i:5140 original size:16 final size:16
Alignment explanation
Indices: 5119--5160 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
5109 ACTCGTTCGA
5119 ACCCGAACCCGAAATT
1 ACCCGAACCCGAAATT
5135 ACCCGAACCCGAAATT
1 ACCCGAACCCGAAATT
5151 ACCCGAACCC
1 ACCCGAACCC
5161 AACCCGAGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.36, C:0.43, G:0.12, T:0.10
Consensus pattern (16 bp):
ACCCGAACCCGAAATT
Found at i:5711 original size:31 final size:31
Alignment explanation
Indices: 5640--5711 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
5630 GTCTATCAGC
*
5640 TTTTAATTTGTTTAATTTAAGACTTTCATTT
1 TTTTAATTTGTTTAATTTAAGACTTTAATTT
*
5671 TAATT-ATTTGTTTAATTTAATG-C-TTAATTT
1 T-TTTAATTTGTTTAATTTAA-GACTTTAATTT
5701 GTTTTAATTTG
1 -TTTTAATTTG
5712 CAATAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 8 0.24
31 23 0.68
32 3 0.09
ACGTcount: A:0.26, C:0.04, G:0.08, T:0.61
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGACTTTAATTT
Found at i:5996 original size:13 final size:12
Alignment explanation
Indices: 5960--6006 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
5950 TCAATCTTTA
*
5960 TATATATTGATAA
1 TATATATT-ATAT
*
5973 TA-ATGTTATAT
1 TATATATTATAT
5984 TATATTATTATAT
1 TATA-TATTATAT
5997 TATATATTAT
1 TATATATTAT
6007 CAATAAACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 13 0.45
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:6173 original size:16 final size:17
Alignment explanation
Indices: 6152--6207 Score: 64
Period size: 16 Copynumber: 3.5 Consensus size: 17
6142 GACCCAAGCT
*
6152 CGAACCCGAAAAT-ATC
1 CGAACCCGAAAATAACC
*
6168 CGAACCCG-ACATAACC
1 CGAACCCGAAAATAACC
6184 CGAACCCGAAAA-AACC
1 CGAACCCGAAAATAACC
*
6200 TGAACCCG
1 CGAACCCG
6208 CCCCAGCCCG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
15 3 0.09
16 29 0.85
17 2 0.06
ACGTcount: A:0.41, C:0.38, G:0.14, T:0.07
Consensus pattern (17 bp):
CGAACCCGAAAATAACC
Found at i:13240 original size:32 final size:32
Alignment explanation
Indices: 13204--13268 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 32
13194 TTGTATGGCA
*
13204 TGCTTTATCA-AGTAGCATATCAGCAAAAAATC
1 TGCTTTATCACA-TAGCATATCAGAAAAAAATC
13236 TGCTTTATCACATAGCATATCAGAAAAAAATC
1 TGCTTTATCACATAGCATATCAGAAAAAAATC
13268 T
1 T
13269 AAGTGAAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 30 0.97
33 1 0.03
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (32 bp):
TGCTTTATCACATAGCATATCAGAAAAAAATC
Found at i:15760 original size:12 final size:13
Alignment explanation
Indices: 15737--15769 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
15727 TAAACTAATT
15737 ACAAACTAAACAA
1 ACAAACTAAACAA
15750 ACAAA-TAAACAA
1 ACAAACTAAACAA
15762 ACAAACTA
1 ACAAACTA
15770 TTAAACAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.70, C:0.21, G:0.00, T:0.09
Consensus pattern (13 bp):
ACAAACTAAACAA
Found at i:17248 original size:12 final size:12
Alignment explanation
Indices: 17231--17294 Score: 67
Period size: 12 Copynumber: 5.1 Consensus size: 12
17221 CAGAGGGAGT
17231 ATTATATATATA
1 ATTATATATATA
*
17243 ATTATATATATCT
1 ATTATATATAT-A
*
17256 ATTAT-TATTATT
1 ATTATATA-TATA
17268 ATTATATATATTTA
1 ATTATATATA--TA
17282 ATTATATATATA
1 ATTATATATATA
17294 A
1 A
17295 CTAAACAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
12 24 0.53
13 10 0.22
14 11 0.24
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (12 bp):
ATTATATATATA
Found at i:17262 original size:16 final size:16
Alignment explanation
Indices: 17233--17294 Score: 54
Period size: 16 Copynumber: 3.7 Consensus size: 16
17223 GAGGGAGTAT
17233 TATATATATAATTATA
1 TATATATATAATTATA
* *
17249 TATATCTATTATTATTA
1 TATATATATAATTA-TA
*
17266 TTATTATATATATTTA-A
1 -TA-TATATATAATTATA
17283 TTATATATATAA
1 -TATATATATAA
17295 CTAAACAATT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
16 20 0.54
17 6 0.16
18 2 0.05
19 9 0.24
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (16 bp):
TATATATATAATTATA
Found at i:20120 original size:20 final size:19
Alignment explanation
Indices: 20082--20122 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
20072 ATGATTTATT
*
20082 TATTAATTATTATTATTAG
1 TATTAATTATCATTATTAG
*
20101 TATTATATTATCATTTTTAG
1 TATTA-ATTATCATTATTAG
20121 TA
1 TA
20123 ACCTCACTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (19 bp):
TATTAATTATCATTATTAG
Found at i:20577 original size:17 final size:17
Alignment explanation
Indices: 20533--20579 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
20523 ATCCCATGTA
*
20533 ATCTTTGATCACCGGTG
1 ATCTTTGATCACTGGTG
*
20550 GTC-TTGCATCACTGGTG
1 ATCTTTG-ATCACTGGTG
20567 ATCTTTGATCACT
1 ATCTTTGATCACT
20580 AATGATCTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
16 3 0.12
17 19 0.76
18 3 0.12
ACGTcount: A:0.17, C:0.23, G:0.21, T:0.38
Consensus pattern (17 bp):
ATCTTTGATCACTGGTG
Found at i:29574 original size:4 final size:4
Alignment explanation
Indices: 29565--29601 Score: 67
Period size: 4 Copynumber: 9.5 Consensus size: 4
29555 AAAAAAAGTT
29565 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT- TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
29602 ATTATTAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.09
4 29 0.91
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:46926 original size:15 final size:16
Alignment explanation
Indices: 46901--46930 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
46891 AATAATTATT
46901 TTTAGATTATAATATA
1 TTTAGATTATAATATA
46917 TTTA-ATTATAATAT
1 TTTAGATTATAATAT
46931 TATTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGATTATAATATA
Done.