Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023757.1 Corchorus olitorius cultivar O-4 contig23790, 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: 14003
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Found at i:2361 original size:3 final size:3
Alignment explanation
Indices: 2353--2435 Score: 166
Period size: 3 Copynumber: 27.7 Consensus size: 3
2343 TTATAAGCTA
2353 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2401 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2436 CTACTACTAC
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 80 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:4046 original size:15 final size:16
Alignment explanation
Indices: 4022--4061 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
4012 AGAGGTTGAA
*
4022 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
4037 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
4053 AGAAAACAA
1 AGAAAACAA
4062 AACAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:11081 original size:28 final size:28
Alignment explanation
Indices: 11038--11111 Score: 130
Period size: 28 Copynumber: 2.6 Consensus size: 28
11028 AGTTCGTGTA
11038 TGAAGACCATTTGAAGATAAATTGGAGATT
1 TGAAGA-C-TTTGAAGATAAATTGGAGATT
11068 TGAAGACTTTGAAGATAAATTGGAGATT
1 TGAAGACTTTGAAGATAAATTGGAGATT
11096 TGAAGACTTTGAAGAT
1 TGAAGACTTTGAAGAT
11112 TTATTTCAAG
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
28 37 0.84
29 1 0.02
30 6 0.14
ACGTcount: A:0.39, C:0.05, G:0.24, T:0.31
Consensus pattern (28 bp):
TGAAGACTTTGAAGATAAATTGGAGATT
Found at i:11113 original size:17 final size:17
Alignment explanation
Indices: 11063--11113 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
11053 GATAAATTGG
11063 AGATTTGAAGACTTTGA
1 AGATTTGAAGACTTTGA
*
11080 AGA--T-AA-A--TTGG
1 AGATTTGAAGACTTTGA
11091 AGATTTGAAGACTTTGA
1 AGATTTGAAGACTTTGA
11108 AGATTT
1 AGATTT
11114 ATTTCAAGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 12
0.65 0.05 0.30
Matches are distributed among these distances:
11 6 0.23
13 2 0.08
14 4 0.15
15 2 0.08
17 12 0.46
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.35
Consensus pattern (17 bp):
AGATTTGAAGACTTTGA
Found at i:12524 original size:15 final size:16
Alignment explanation
Indices: 12493--12532 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
12483 TTACTTTGCT
12493 TTGTTTTCTAATTTAA
1 TTGTTTTCTAATTTAA
*
12509 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAATTTAA
12524 TTGTTTTCT
1 TTGTTTTCT
12533 TTCAACCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.15, C:0.07, G:0.10, T:0.68
Consensus pattern (16 bp):
TTGTTTTCTAATTTAA
Found at i:12810 original size:30 final size:30
Alignment explanation
Indices: 12774--12860 Score: 85
Period size: 31 Copynumber: 3.0 Consensus size: 30
12764 TTCTTAGTCT
12774 CTGCGTTTTCTCTAAAA-AAAAAAAAATTTC
1 CTGCGTTTTCTC-AAAATAAAAAAAAATTTC
*
12804 CTGCGTTTTTTCAAAATTAAAAAAAAA-TTC
1 CTGCGTTTTCTCAAAA-TAAAAAAAAATTTC
* *
12834 TTTGCGTTTT-T--AATTAAAAAAAAATTT
1 -CTGCGTTTTCTCAAAATAAAAAAAAATTT
12861 GTTTTGTGTT
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
27 10 0.20
28 4 0.08
29 4 0.08
30 15 0.30
31 17 0.34
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (30 bp):
CTGCGTTTTCTCAAAATAAAAAAAAATTTC
Found at i:12829 original size:31 final size:32
Alignment explanation
Indices: 12771--12860 Score: 97
Period size: 30 Copynumber: 3.0 Consensus size: 32
12761 TGTTTCTTAG
*
12771 TCTCTGCGTTTTCTCTAAAA--AAAAAAAAATT
1 TCTCTGCGTTTTTTC-AAAATTAAAAAAAAATT
12802 TC-CTGCGTTTTTTCAAAATTAAAAAAAAA-T
1 TCTCTGCGTTTTTTCAAAATTAAAAAAAAATT
*
12832 TCTTTGCG-TTTTT---AATTAAAAAAAAATT
1 TCTCTGCGTTTTTTCAAAATTAAAAAAAAATT
12860 T
1 T
12861 GTTTTGTGTT
Statistics
Matches: 53, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
27 13 0.25
28 2 0.04
29 4 0.08
30 19 0.36
31 15 0.28
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.40
Consensus pattern (32 bp):
TCTCTGCGTTTTTTCAAAATTAAAAAAAAATT
Found at i:12897 original size:32 final size:34
Alignment explanation
Indices: 12834--12903 Score: 90
Period size: 32 Copynumber: 2.1 Consensus size: 34
12824 AAAAAAATTC
** *
12834 TTTGCGTTTTTAATTAAAAAAAAATTTGTTTTGTG
1 TTTGCGTTTTTAA-TAAAAAAAAATCGGTTTTGCG
12869 TTTGCG-TTTTAA-AAAAAAAAATCGGTTTTGCG
1 TTTGCGTTTTTAATAAAAAAAAATCGGTTTTGCG
12901 TTT
1 TTT
12904 TCGAAAAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 20 0.62
34 6 0.19
35 6 0.19
ACGTcount: A:0.31, C:0.06, G:0.16, T:0.47
Consensus pattern (34 bp):
TTTGCGTTTTTAATAAAAAAAAATCGGTTTTGCG
Found at i:12910 original size:28 final size:27
Alignment explanation
Indices: 12869--12942 Score: 80
Period size: 26 Copynumber: 2.7 Consensus size: 27
12859 TTGTTTTGTG
*
12869 TTTGCGTTTT-AAAAAAAAAAATCGGT
1 TTTGCGTTTTCAAAAAAAAAAATCGCT
* * *
12895 TTTGCGTTTTC-GAAAAACAATTCTTGCT
1 TTTGCGTTTTCAAAAAAAAAAATC--GCT
12923 TTTGCGTTTTCAAAAAAAAA
1 TTTGCGTTTTCAAAAAAAAA
12943 GAAAAAAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
26 19 0.50
28 13 0.34
29 6 0.16
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (27 bp):
TTTGCGTTTTCAAAAAAAAAAATCGCT
Done.