Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008353.1 Hibiscus syriacus cultivar Beakdansim tig00111088_pilon, 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: 2583621
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 13 of 13
Found at i:2552792 original size:37 final size:36
Alignment explanation
Indices: 2552721--2552862 Score: 121
Period size: 36 Copynumber: 3.9 Consensus size: 36
2552711 CAAAGCGTCA
*
2552721 TCTCGCTTGAGACAATTT-TCTTAAAAA-AGAATTTTG
1 TCTCACTTGAGACAATTTCTC-TAAAAACA-AATTTTG
* * *
2552757 TCTCTCTTAAGACAGATTTCTCTAAAAACAAATTTTA
1 TCTCACTTGAGACA-ATTTCTCTAAAAACAAATTTTG
* ** *
2552794 TCTCACTTGAGATAATTTCTCTCCAAATAAA--TTG
1 TCTCACTTGAGACAATTTCTCTAAAAACAAATTTTG
* *
2552828 TCTCGCTTGAGACAATTTTCTTTAAAACACAAATT
1 TCTCACTTGAGACAA-TTTCTCTAAAA-ACAAATT
2552863 CTGAAGTTGT
Statistics
Matches: 83, Mismatches: 16, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
34 15 0.18
35 8 0.10
36 30 0.36
37 27 0.33
38 3 0.04
ACGTcount: A:0.35, C:0.18, G:0.09, T:0.38
Consensus pattern (36 bp):
TCTCACTTGAGACAATTTCTCTAAAAACAAATTTTG
Found at i:2556518 original size:24 final size:23
Alignment explanation
Indices: 2556489--2556560 Score: 75
Period size: 24 Copynumber: 3.3 Consensus size: 23
2556479 AAACATATTA
2556489 ATATTTTCAAATAATTAAAATAAT
1 ATATTTTCAAATAATT-AAATAAT
*
2556513 ATATTTTCTAAA-AATT---TATT
1 ATATTTTC-AAATAATTAAATAAT
2556533 ATATTTT--AATAATTAAATAAT
1 ATATTTTCAAATAATTAAATAAT
2556554 ATATTTT
1 ATATTTT
2556561 AATACTATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
17 2 0.05
18 4 0.10
20 10 0.24
21 10 0.24
24 12 0.29
25 3 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (23 bp):
ATATTTTCAAATAATTAAATAAT
Found at i:2556575 original size:21 final size:21
Alignment explanation
Indices: 2556489--2556564 Score: 68
Period size: 21 Copynumber: 3.5 Consensus size: 21
2556479 AAACATATTA
2556489 ATATTTTCAAATAATTAAAATAAT
1 ATATTTT--AATAATT-AAATAAT
* *
2556513 ATATTTT-CTAA--AAATTTATT
1 ATATTTTAATAATTAAA--TAAT
2556533 ATATTTTAATAATTAAATAAT
1 ATATTTTAATAATTAAATAAT
2556554 ATATTTTAATA
1 ATATTTTAATA
2556565 CTATAAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 13
0.72 0.07 0.22
Matches are distributed among these distances:
18 3 0.07
20 10 0.23
21 20 0.47
23 3 0.07
24 7 0.16
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (21 bp):
ATATTTTAATAATTAAATAAT
Found at i:2558029 original size:35 final size:35
Alignment explanation
Indices: 2557956--2558030 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
2557946 AACCCCCAAC
* **
2557956 AGTAAGGCCCTGAGCACATAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
2557991 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
2558026 AGTAA
1 AGTAA
2558031 TCTTCCTCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.33, C:0.28, G:0.28, T:0.11
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:2558135 original size:24 final size:23
Alignment explanation
Indices: 2558112--2558193 Score: 91
Period size: 24 Copynumber: 3.7 Consensus size: 23
2558102 ATTCAAGTCA
2558112 AGTATCATATCAGAATCCAGGTC
1 AGTATCATATCAGAATCCAGGTC
* *
2558135 ATGTATCAGATCAGAATCCATGTC
1 A-GTATCATATCAGAATCCAGGTC
2558159 A--ATC--ATCAGAATCCAGGTC
1 AGTATCATATCAGAATCCAGGTC
* *
2558178 AGGATCATAACAGAAT
1 AGTATCATATCAGAAT
2558194 TCAAGTCGGA
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
19 15 0.30
21 6 0.12
23 8 0.16
24 21 0.42
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (23 bp):
AGTATCATATCAGAATCCAGGTC
Found at i:2560526 original size:12 final size:12
Alignment explanation
Indices: 2560509--2560533 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2560499 CGGTCAACGA
2560509 TCAACGGGTCGG
1 TCAACGGGTCGG
2560521 TCAACGGGTCGG
1 TCAACGGGTCGG
2560533 T
1 T
2560534 TCGGGTCGGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.40, T:0.20
Consensus pattern (12 bp):
TCAACGGGTCGG
Found at i:2575061 original size:2 final size:2
Alignment explanation
Indices: 2575056--2575087 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2575046 AGGGGATTTC
2575056 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2575088 CTAAAGTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Done.