Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024053.1 Corchorus olitorius cultivar O-4 contig24086, 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: 25922
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.29
Found at i:566 original size:15 final size:16
Alignment explanation
Indices: 542--581 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
532 AGTGGTTGAA
*
542 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
557 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
573 AGAAAACAA
1 AGAAAACAA
582 AACAAACAAA
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:13341 original size:11 final size:11
Alignment explanation
Indices: 13325--13372 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
13315 GAAGTTCGTG
13325 TTTGAAGACCA
1 TTTGAAGACCA
**
13336 TTTGAAGATAA
1 TTTGAAGACCA
13347 TTTGAAGA-C-
1 TTTGAAGACCA
13356 -TTGAAGACCA
1 TTTGAAGACCA
13366 -TTGAAGA
1 TTTGAAGA
13373 TTTATTTCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
8 7 0.22
9 1 0.03
10 7 0.22
11 17 0.53
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (11 bp):
TTTGAAGACCA
Found at i:14783 original size:15 final size:15
Alignment explanation
Indices: 14753--14794 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
14743 TTACTTTGTT
14753 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
14769 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
14784 TTGTTTTCTGT
1 TTGTTTTCTGT
14795 CAACCTCTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:19265 original size:11 final size:11
Alignment explanation
Indices: 19249--19296 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
19239 GAAATTCGTG
19249 TTTGAAGACCA
1 TTTGAAGACCA
**
19260 TTTGAAGATAA
1 TTTGAAGACCA
19271 TTTGAAGA-C-
1 TTTGAAGACCA
19280 -TTGAAGACCA
1 TTTGAAGACCA
19290 -TTGAAGA
1 TTTGAAGA
19297 TTTATTTCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
8 7 0.22
9 1 0.03
10 7 0.22
11 17 0.53
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (11 bp):
TTTGAAGACCA
Found at i:20708 original size:15 final size:15
Alignment explanation
Indices: 20678--20719 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
20668 TTACTTTGTT
20678 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
20694 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
20709 TTGTTTTCTGT
1 TTGTTTTCTGT
20720 CAACCTATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:23711 original size:50 final size:50
Alignment explanation
Indices: 23651--23977 Score: 582
Period size: 50 Copynumber: 6.5 Consensus size: 50
23641 ACCAGATTTC
23651 AAGATTGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTT
1 AAGATTGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTT
*
23701 AGGATTGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTT
1 AAGATTGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTT
23751 AAGATTGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTT
1 AAGATTGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTT
*
23801 AAGATTGAATTGGAAGACACTTCGAAGGATAAGCGGAAGACGGTCCTTTT
1 AAGATTGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTT
* * *
23851 AAGATTGAATTGGAAGATAGTTCGAGGGATAAGCGGAAGACGTTCCTTTT
1 AAGATTGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTT
*
23901 AAGATTGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCTTTTT
1 AAGATTGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTT
* *
23951 AAGATGGAATTGGAAGACAATTCGAAG
1 AAGATTGAATTGGAAGACAGTTCGAAG
23978 AAGTTGATCG
Statistics
Matches: 264, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 264 1.00
ACGTcount: A:0.34, C:0.11, G:0.30, T:0.24
Consensus pattern (50 bp):
AAGATTGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCTTTT
Found at i:23739 original size:23 final size:23
Alignment explanation
Indices: 23662--23791 Score: 73
Period size: 23 Copynumber: 5.3 Consensus size: 23
23652 AGATTGAATT
23662 GGAAGACAGTTCGAAGGATAAGC
1 GGAAGACAGTTCGAAGGATAAGC
* *** **
23685 GGAAGACGGTCCTTTTAGGATTGAATT
1 GGAAGACAGT--TCGAAGGA-T-AAGC
23712 GGAAGACAGTTCGAAGGATAAGC
1 GGAAGACAGTTCGAAGGATAAGC
* ** **
23735 GGAAGACGGTCCTTTTAA-GATTGAATT
1 GGAAGACAG---TTCGAAGGA-T-AAGC
23762 GGAAGACAGTTCGAAGGATAAGC
1 GGAAGACAGTTCGAAGGATAAGC
23785 GGAAGAC
1 GGAAGAC
23792 GGTCCTTTTA
Statistics
Matches: 75, Mismatches: 22, Indels: 20
0.64 0.19 0.17
Matches are distributed among these distances:
23 28 0.37
24 6 0.08
25 14 0.19
26 6 0.08
27 21 0.28
ACGTcount: A:0.35, C:0.12, G:0.32, T:0.21
Consensus pattern (23 bp):
GGAAGACAGTTCGAAGGATAAGC
Found at i:24237 original size:28 final size:28
Alignment explanation
Indices: 24197--24294 Score: 187
Period size: 28 Copynumber: 3.5 Consensus size: 28
24187 ATTCACTTCT
*
24197 CATTTTGGTCATTTTTCATCTCCTGGGG
1 CATTTTGGTCATTTTTCATCTCCAGGGG
24225 CATTTTGGTCATTTTTCATCTCCAGGGG
1 CATTTTGGTCATTTTTCATCTCCAGGGG
24253 CATTTTGGTCATTTTTCATCTCCAGGGG
1 CATTTTGGTCATTTTTCATCTCCAGGGG
24281 CATTTTGGTCATTT
1 CATTTTGGTCATTT
24295 CGAGTGCACT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
28 69 1.00
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.46
Consensus pattern (28 bp):
CATTTTGGTCATTTTTCATCTCCAGGGG
Found at i:24325 original size:14 final size:14
Alignment explanation
Indices: 24306--24333 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
24296 GAGTGCACTT
24306 TTAACTTTTATCAA
1 TTAACTTTTATCAA
24320 TTAACTTTTATCAA
1 TTAACTTTTATCAA
24334 AAAATCTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (14 bp):
TTAACTTTTATCAA
Found at i:24373 original size:13 final size:13
Alignment explanation
Indices: 24355--24379 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24345 ATGAGCACCT
24355 TTATTATTTTTTA
1 TTATTATTTTTTA
24368 TTATTATTTTTT
1 TTATTATTTTTT
24380 TTGCACATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTATTATTTTTTA
Done.