Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022224.1 Corchorus olitorius cultivar O-4 contig22257, 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: 6610
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Found at i:401 original size:3 final size:3
Alignment explanation
Indices: 395--427 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
385 ATAACTTTAC
*
395 TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
428 AAGAAGTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:409 original size:15 final size:15
Alignment explanation
Indices: 391--423 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
381 AATAATAACT
391 TTACTATTATTATTA
1 TTACTATTATTATTA
406 TTACTATTATTATTA
1 TTACTATTATTATTA
421 TTA
1 TTA
424 TTATAAGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (15 bp):
TTACTATTATTATTA
Found at i:523 original size:15 final size:15
Alignment explanation
Indices: 503--550 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
493 GTCTTGATTA
503 ATGAAATAATTTGGG
1 ATGAAATAATTTGGG
*
518 ATG-AA-AATCTT--C
1 ATGAAATAAT-TTGGG
530 ATGAAATAATTTGGG
1 ATGAAATAATTTGGG
545 ATGAAA
1 ATGAAA
551 ATCTTTCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
12 3 0.12
13 7 0.27
14 7 0.27
15 9 0.35
ACGTcount: A:0.44, C:0.04, G:0.21, T:0.31
Consensus pattern (15 bp):
ATGAAATAATTTGGG
Found at i:533 original size:27 final size:27
Alignment explanation
Indices: 503--555 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
493 GTCTTGATTA
503 ATGAAATAATTTGGGATGAAAATCTTC
1 ATGAAATAATTTGGGATGAAAATCTTC
530 ATGAAATAATTTGGGATGAAAATCTT
1 ATGAAATAATTTGGGATGAAAATCTT
556 TCATTCTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.34
Consensus pattern (27 bp):
ATGAAATAATTTGGGATGAAAATCTTC
Found at i:705 original size:24 final size:24
Alignment explanation
Indices: 673--723 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
663 CTACTACTAA
*
673 TAATTATTATAATAATAAGAA-GTT
1 TAATAATTATAATAATAA-AATGTT
*
697 TAATAATTATAATGATAAAATGTT
1 TAATAATTATAATAATAAAATGTT
721 TAA
1 TAA
724 CGTAAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (24 bp):
TAATAATTATAATAATAAAATGTT
Found at i:1327 original size:18 final size:18
Alignment explanation
Indices: 1306--1349 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
1296 ATTAAACTTC
*
1306 TTATTATTA-TAATAATTA
1 TTATTAGTAGTAA-AATTA
1324 TTATTAGTAGTAAAATTA
1 TTATTAGTAGTAAAATTA
1342 TTATTAGT
1 TTATTAGT
1350 TGTATTATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 21 0.88
19 3 0.12
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (18 bp):
TTATTAGTAGTAAAATTA
Found at i:3422 original size:29 final size:29
Alignment explanation
Indices: 3359--3422 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
3349 AACAAACTAA
* * *
3359 AGAATTATGTAGCACGTTTATTGATAGAT
1 AGAATTATGTAGCACATATATTGATAGAC
* *
3388 AAAATTATGTAGCACATATATTGGTAGAC
1 AGAATTATGTAGCACATATATTGATAGAC
*
3417 GGAATT
1 AGAATT
3423 TTAATGATTA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.38, C:0.08, G:0.20, T:0.34
Consensus pattern (29 bp):
AGAATTATGTAGCACATATATTGATAGAC
Found at i:5455 original size:12 final size:13
Alignment explanation
Indices: 5431--5456 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5421 ACAAATAAGC
5431 AAAATTACAAAAA
1 AAAATTACAAAAA
5444 AAAATTACAAAAA
1 AAAATTACAAAAA
5457 GTATAGTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAATTACAAAAA
Done.