Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020148.1 Corchorus olitorius cultivar O-4 contig20181, 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: 24768
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:2854 original size:26 final size:26
Alignment explanation
Indices: 2825--2874 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
2815 ACTATATAGC
*
2825 TTTTTAAGT-AATTTTAAATAAGAAT
1 TTTTTAAATCAATTTTAAATAAGAAT
*
2850 TTTTTAAATCAATTTTAAATTAGAA
1 TTTTTAAATCAATTTTAAATAAGAA
2875 AATTGACTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (26 bp):
TTTTTAAATCAATTTTAAATAAGAAT
Found at i:7283 original size:26 final size:26
Alignment explanation
Indices: 7254--7305 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
7244 GAAATTACCT
7254 TGATTTATAGTCATCAGCAAATCGAA
1 TGATTTATAGTCATCAGCAAATCGAA
7280 TGATTTATAGTCATCAGCAAATCGAA
1 TGATTTATAGTCATCAGCAAATCGAA
7306 CAGAAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (26 bp):
TGATTTATAGTCATCAGCAAATCGAA
Found at i:18481 original size:21 final size:21
Alignment explanation
Indices: 18457--18523 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
18447 AGTTCTCTGT
18457 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
* * ** *
18478 AAATCATAGAAA-ATTC-TTTGT
1 AAATTA-AGAAATACTCAACT-C
18499 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
18520 AAAT
1 AAAT
18524 CCTGATCCTT
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
20 6 0.19
21 20 0.62
22 6 0.19
ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28
Consensus pattern (21 bp):
AAATTAAGAAATACTCAACTC
Found at i:18513 original size:42 final size:42
Alignment explanation
Indices: 18444--18524 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
18434 ACTAAGTCTT
*
18444 GAAAGTTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
*
18486 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATC
18525 CTGATCCTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.46, C:0.16, G:0.09, T:0.30
Consensus pattern (42 bp):
GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
Found at i:18843 original size:7 final size:7
Alignment explanation
Indices: 18831--18874 Score: 74
Period size: 7 Copynumber: 6.6 Consensus size: 7
18821 AAATAATATG
18831 TATAGTA
1 TATAGTA
18838 TATAGTA
1 TATAGTA
18845 TATAGTA
1 TATAGTA
18852 TATAGTA
1 TATAGTA
18859 TATA-TA
1 TATAGTA
18865 TATA-TA
1 TATAGTA
18871 TATA
1 TATA
18875 TATGTATGGA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 12 0.32
7 25 0.68
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (7 bp):
TATAGTA
Found at i:18848 original size:2 final size:2
Alignment explanation
Indices: 18826--18877 Score: 59
Period size: 2 Copynumber: 24.0 Consensus size: 2
18816 GTTTCAAATA
*
18826 AT AT GT AT AGT AT AT AGT AT AT AGT AT AT AGT AT AT AT AT AT AT
1 AT AT AT AT A-T AT AT A-T AT AT A-T AT AT A-T AT AT AT AT AT AT
18870 AT AT AT AT
1 AT AT AT AT
18878 GTATGGAGAA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 36 0.82
3 8 0.18
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (2 bp):
AT
Found at i:22334 original size:20 final size:21
Alignment explanation
Indices: 22297--22340 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
22287 AAAACTTTAC
*
22297 TTTTATTTCTTTTATTTT-CT
1 TTTTATTTATTTTATTTTCCT
22317 TTTTATTTA-TTTATTTTTCCT
1 TTTTATTTATTTTA-TTTTCCT
22338 TTT
1 TTT
22341 CTTTTCCTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 4 0.19
20 12 0.57
21 5 0.24
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTATTTATTTTATTTTCCT
Found at i:22507 original size:35 final size:35
Alignment explanation
Indices: 22437--22530 Score: 136
Period size: 35 Copynumber: 2.7 Consensus size: 35
22427 TGGGGCCCAA
** * *
22437 GCCTGGCCTAGGCGCT-GGCCGCATTGGCCCGCGC
1 GCCTGGCCTAGGCGCTGGGCCGCGCTAGCCCACGC
*
22471 GCCTGGCCTGGGCGCTGGGCCGCGCTAGCCCACGC
1 GCCTGGCCTAGGCGCTGGGCCGCGCTAGCCCACGC
22506 GCCTGGCCTAGGCGCTGGGCCGCGC
1 GCCTGGCCTAGGCGCTGGGCCGCGC
22531 GCCAGGCCGG
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 15 0.28
35 38 0.72
ACGTcount: A:0.05, C:0.41, G:0.40, T:0.13
Consensus pattern (35 bp):
GCCTGGCCTAGGCGCTGGGCCGCGCTAGCCCACGC
Found at i:22576 original size:3 final size:3
Alignment explanation
Indices: 22570--22604 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
22560 TTTTTTTTCT
22570 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
22605 TTTTTTATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Done.