Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018553.1 Corchorus olitorius cultivar O-4 contig18586, 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: 18285
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3439 original size:83 final size:83
Alignment explanation
Indices: 3283--3439 Score: 199
Period size: 83 Copynumber: 1.9 Consensus size: 83
3273 ATATATATAT
* * * *
3283 ATATATTCTATAACGTTAAAAAATCAAACATAATGATTTAAATAGAATTTATAGATTTAAATTAA
1 ATATATTCAATAACGTTAAAAAATCAAACATAATGATTTAAATAGAATTTATAGAATGAAATGAA
**
3348 TTCCATTTAATGAAAAGC
66 TAACATTTAATGAAAAGC
* * *
3366 ATATATTCAATAACGTTACAAAATCAAACAT-ATGATTTAGATAGAATTTATCGAATGAAACTGA
1 ATATATTCAATAACGTTAAAAAATCAAACATAATGATTTAAATAGAATTTATAGAATGAAA-TGA
* *
3430 CTAATATTTA
65 ATAACATTTA
3440 GATTATTGTA
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
82 25 0.40
83 37 0.60
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.35
Consensus pattern (83 bp):
ATATATTCAATAACGTTAAAAAATCAAACATAATGATTTAAATAGAATTTATAGAATGAAATGAA
TAACATTTAATGAAAAGC
Found at i:6154 original size:22 final size:24
Alignment explanation
Indices: 6102--6154 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 24
6092 ACGTAGAGAA
* * *
6102 AATTAAATTTTAAATCTATAAATT
1 AATTATATTATAAATCTATAAAGT
*
6126 AAATATATTATAAA-CTA-AAAGT
1 AATTATATTATAAATCTATAAAGT
6148 AATTATA
1 AATTATA
6155 AAAAGTAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
22 10 0.42
23 3 0.12
24 11 0.46
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (24 bp):
AATTATATTATAAATCTATAAAGT
Found at i:6815 original size:32 final size:33
Alignment explanation
Indices: 6774--6836 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
6764 GTTTATTTAA
*
6774 CATGCATAATCTCTTC-TTCTACCTTTCTTTGT
1 CATGCATAATCTCCTCTTTCTACCTTTCTTTGT
*
6806 CATGCATAATCTCCTCTTTCTACGTTTCTTT
1 CATGCATAATCTCCTCTTTCTACCTTTCTTT
6837 ATGATTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 15 0.54
33 13 0.46
ACGTcount: A:0.16, C:0.29, G:0.06, T:0.49
Consensus pattern (33 bp):
CATGCATAATCTCCTCTTTCTACCTTTCTTTGT
Found at i:6954 original size:29 final size:29
Alignment explanation
Indices: 6912--6972 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
6902 CATCAAAAAT
* **
6912 ATAGTATCACTTTGACACCTGAAGTTGTC
1 ATAGTAACACTTTGACACCCAAAGTTGTC
*
6941 ATAGTAACATTTTGACACCCAAAGTTGTC
1 ATAGTAACACTTTGACACCCAAAGTTGTC
6970 ATA
1 ATA
6973 TTAAGGATGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.33
Consensus pattern (29 bp):
ATAGTAACACTTTGACACCCAAAGTTGTC
Found at i:8381 original size:35 final size:35
Alignment explanation
Indices: 8331--8400 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
8321 CCGGATAGTA
* *
8331 CAAATTTGATTGAAGGCTCCAGAAGAGCCAGTATT
1 CAAATTTCATCGAAGGCTCCAGAAGAGCCAGTATT
*
8366 CAAATTTCATCGAAGGCTCCAGAAGAGCTAGTATT
1 CAAATTTCATCGAAGGCTCCAGAAGAGCCAGTATT
8401 GTTTTATCTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (35 bp):
CAAATTTCATCGAAGGCTCCAGAAGAGCCAGTATT
Found at i:8684 original size:18 final size:19
Alignment explanation
Indices: 8661--8696 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
8651 TAAACTAGAA
8661 GTTTATTGATT-GCATTAT
1 GTTTATTGATTGGCATTAT
*
8679 GTTTATTGTTTGGCATTA
1 GTTTATTGATTGGCATTA
8697 CCGGTTAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.19, C:0.06, G:0.19, T:0.56
Consensus pattern (19 bp):
GTTTATTGATTGGCATTAT
Found at i:12268 original size:18 final size:18
Alignment explanation
Indices: 12247--12281 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
12237 AAAAATTTCT
12247 CAATTAAGGGTAATTTAC
1 CAATTAAGGGTAATTTAC
*
12265 CAATTAAGGGTGATTTA
1 CAATTAAGGGTAATTTA
12282 ATATAGTAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.34
Consensus pattern (18 bp):
CAATTAAGGGTAATTTAC
Found at i:12386 original size:11 final size:11
Alignment explanation
Indices: 12370--12440 Score: 79
Period size: 11 Copynumber: 6.2 Consensus size: 11
12360 TGAGCCAAAA
12370 TTTTGTTTTTC
1 TTTTGTTTTTC
**
12381 TTTTGTTCCTC
1 TTTTGTTTTTC
12392 TTTTGTTTTTC
1 TTTTGTTTTTC
*
12403 TTGTTTGTGCTTTC
1 -T-TTTGT-TTTTC
*
12417 TTTTGTTCTTC
1 TTTTGTTTTTC
12428 TTTTGTTTTTC
1 TTTTGTTTTTC
12439 TT
1 TT
12441 GTTTGTGTGT
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
11 33 0.67
12 6 0.12
13 6 0.12
14 4 0.08
ACGTcount: A:0.00, C:0.14, G:0.11, T:0.75
Consensus pattern (11 bp):
TTTTGTTTTTC
Found at i:12417 original size:36 final size:36
Alignment explanation
Indices: 12377--12447 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
12367 AAATTTTGTT
12377 TTTCTTTTGTTCCTCTTTTGTTTTTCTTGTTTGTGC
1 TTTCTTTTGTTCCTCTTTTGTTTTTCTTGTTTGTGC
*
12413 TTTCTTTTGTTCTTCTTTTGTTTTTCTTGTTTGTG
1 TTTCTTTTGTTCCTCTTTTGTTTTTCTTGTTTGTG
12448 TGTGCGCTCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.00, C:0.14, G:0.14, T:0.72
Consensus pattern (36 bp):
TTTCTTTTGTTCCTCTTTTGTTTTTCTTGTTTGTGC
Done.