Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011857.1 Corchorus olitorius cultivar O-4 contig11890, 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: 17430
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:3799 original size:130 final size:130
Alignment explanation
Indices: 3595--3845 Score: 375
Period size: 130 Copynumber: 1.9 Consensus size: 130
3585 TCATTTATCC
* * *
3595 AAATTCTAATATATCTAAGTTTTTAATTAAATTAGTAAAATGATAAAAATAAATTAGGTATAAGG
1 AAATTCTAATATATATAAATTTTTAATTAAATTAGTAAAATGATAAAAATAAATTAGGTATAAAG
*
3660 ATATAAGATTTAATTAAACAAAAAATAGAGTTTTTAGTTGAGTAAAACT-ATAAAAGTATATTTA
66 ATATAAGATTTAAGTAAA-AAAAAATAGAGTTTTTAGTTGAGTAAAA-TAATAAAAGTATATTTA
3724 AA
129 AA
*
3726 AAATTCTAATATATATAAATTTTTAATTAGAA-TA-TAAAATGATAAAAATTAAA-TAGTTATAA
1 AAATTCTAATATATATAAATTTTTAATTA-AATTAGTAAAATGATAAAAA-TAAATTAGGTATAA
* *
3788 AGATATTAGATTTAAGTAAATAAAAATAGAGTTTTTAGTTGAGTAAAATAATAAAAGT
64 AGATATAAGATTTAAGTAAAAAAAAATAGAGTTTTTAGTTGAGTAAAATAATAAAAGT
3846 TTAAATAATG
Statistics
Matches: 110, Mismatches: 7, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
128 1 0.01
129 35 0.32
130 39 0.35
131 33 0.30
132 2 0.02
ACGTcount: A:0.51, C:0.02, G:0.10, T:0.36
Consensus pattern (130 bp):
AAATTCTAATATATATAAATTTTTAATTAAATTAGTAAAATGATAAAAATAAATTAGGTATAAAG
ATATAAGATTTAAGTAAAAAAAAATAGAGTTTTTAGTTGAGTAAAATAATAAAAGTATATTTAAA
Found at i:3871 original size:129 final size:131
Alignment explanation
Indices: 3595--3871 Score: 332
Period size: 129 Copynumber: 2.1 Consensus size: 131
3585 TCATTTATCC
* * * * *
3595 AAATTCTAATATATCTAAGTTTTTAATTAAATTAGTAAAATGATAAAAATAAATTAGGTATAAGG
1 AAATTCTAAGAAATATAAATTTTTAATTAAATTAGTAAAATGATAAAAATAAATTAGGTATAAAG
* **
3660 ATATAAGATTTAATTAAACAAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATATTTAA
66 ATATAAGATTTAAGTAAACAAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATAAATAA
3725 A
131 A
* * *
3726 AAATTCTAATATATATAAATTTTTAATTAGAA-TA-TAAAATGATAAAAATTAAA-TAGTTATAA
1 AAATTCTAAGAAATATAAATTTTTAATTA-AATTAGTAAAATGATAAAAA-TAAATTAGGTATAA
* * *
3788 AGATATTAGATTTAAGTAAA-TAAAAATAGAGTTTTTAGTTGAGTAAAA-TAATAAAAGTTTAAA
64 AGATATAAGATTTAAGTAAACAAAAAATAGAGTTTTTAGTTGAGTAAAACT-ATAAAAGTATAAA
*
3851 TAATG
128 TAA-A
*
3856 ACATT-TAAGAAATATA
1 AAATTCTAAGAAATATA
3872 TTCGAAAAAT
Statistics
Matches: 128, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
128 1 0.01
129 49 0.38
130 43 0.34
131 33 0.26
132 2 0.02
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.36
Consensus pattern (131 bp):
AAATTCTAAGAAATATAAATTTTTAATTAAATTAGTAAAATGATAAAAATAAATTAGGTATAAAG
ATATAAGATTTAAGTAAACAAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATAAATAA
A
Found at i:3952 original size:15 final size:15
Alignment explanation
Indices: 3932--3975 Score: 79
Period size: 15 Copynumber: 2.9 Consensus size: 15
3922 TACTTTTTAA
*
3932 TATAGAGATAGATAG
1 TATAGATATAGATAG
3947 TATAGATATAGATAG
1 TATAGATATAGATAG
3962 TATAGATATAGATA
1 TATAGATATAGATA
3976 TAGATGATCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (15 bp):
TATAGATATAGATAG
Found at i:3955 original size:21 final size:23
Alignment explanation
Indices: 3931--3979 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
3921 GTACTTTTTA
3931 ATATAGAGATAG-ATAG-TATAG
1 ATATAGAGATAGTATAGATATAG
3952 ATAT--AGATAGTATAGATATAG
1 ATATAGAGATAGTATAGATATAG
3973 ATATAGA
1 ATATAGA
3980 TGATCTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
19 6 0.25
20 4 0.17
21 13 0.54
23 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.20, T:0.31
Consensus pattern (23 bp):
ATATAGAGATAGTATAGATATAG
Found at i:9347 original size:6 final size:6
Alignment explanation
Indices: 9333--9376 Score: 70
Period size: 6 Copynumber: 7.3 Consensus size: 6
9323 CCACAGAGAT
* *
9333 GACACG GACAGG GACAGG GACAGG GACAGG GTCAGG GACAGG GA
1 GACAGG GACAGG GACAGG GACAGG GACAGG GACAGG GACAGG GA
9377 GGGCTTCTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.32, C:0.18, G:0.48, T:0.02
Consensus pattern (6 bp):
GACAGG
Found at i:10388 original size:17 final size:17
Alignment explanation
Indices: 10368--10402 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
10358 ATTTCTCCCC
*
10368 TTCTCCGTATTCTCTTA
1 TTCTCCATATTCTCTTA
*
10385 TTCTCTATATTCTCTTA
1 TTCTCCATATTCTCTTA
10402 T
1 T
10403 CCTTTTTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.14, C:0.26, G:0.03, T:0.57
Consensus pattern (17 bp):
TTCTCCATATTCTCTTA
Found at i:10586 original size:31 final size:31
Alignment explanation
Indices: 10548--10607 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
10538 CAAAAAGATC
10548 GAGATTGAAAGTTCAATCATACAAGTCTACG
1 GAGATTGAAAGTTCAATCATACAAGTCTACG
* *
10579 GAGATTGAAAGTTGAATCATGCAAGTCTA
1 GAGATTGAAAGTTCAATCATACAAGTCTA
10608 AGGTTAGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.27
Consensus pattern (31 bp):
GAGATTGAAAGTTCAATCATACAAGTCTACG
Found at i:13007 original size:23 final size:23
Alignment explanation
Indices: 12974--13047 Score: 103
Period size: 23 Copynumber: 3.2 Consensus size: 23
12964 GTGCAAATTT
*
12974 TATTAAAGGCTCCATAAGAGCTAG
1 TATT-AAGGCTCCAGAAGAGCTAG
*
12998 TATTAAGGCTCCAGAAGAGCTAA
1 TATTAAGGCTCCAGAAGAGCTAG
**
13021 TATTAAGGCTCTGGAAGAGCTAG
1 TATTAAGGCTCCAGAAGAGCTAG
13044 TATT
1 TATT
13048 GTTTTTTATC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 41 0.91
24 4 0.09
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (23 bp):
TATTAAGGCTCCAGAAGAGCTAG
Done.