Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008129.1 Hibiscus syriacus cultivar Beakdansim tig00110684_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: 2577775
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 10
Found at i:2521983 original size:90 final size:91
Alignment explanation
Indices: 2521829--2522010 Score: 258
Period size: 90 Copynumber: 2.0 Consensus size: 91
2521819 CCTAGAACAC
* **
2521829 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGGGCCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGACGCCAAGATG
* *
2521894 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGCTATCTCCCTATTCGGCCAAG
** * * * *
2521920 CCATGTGTTTTGCATGTGAACAG-CCCCATGTGCCTTGCATGTGGTTTATTTAGACGCCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGACGCCAAGATG
2521984 AAGAGCTATCTCCCTATTCGGCCAAG
66 AAGAGCTATCTCCCTATTCGGCCAAG
2522010 C
1 C
2522011 ATTATTTTCA
Statistics
Matches: 80, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
90 61 0.76
91 19 0.24
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGACGCCAAGATG
AAGAGCTATCTCCCTATTCGGCCAAG
Found at i:2525982 original size:16 final size:17
Alignment explanation
Indices: 2525949--2525983 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2525939 ATCTATAGTT
*
2525949 CACATCTTTATAATATG
1 CACATCATTATAATATG
2525966 CACATCATTAT-ATATG
1 CACATCATTATAATATG
2525982 CA
1 CA
2525984 TTATATAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.37
Consensus pattern (17 bp):
CACATCATTATAATATG
Found at i:2526812 original size:19 final size:21
Alignment explanation
Indices: 2526788--2526839 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
2526778 CGGCCAAGAG
*
2526788 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
2526807 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
2526828 CATGTATTTTCA
1 CATGTATTTTCA
2526840 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:2534895 original size:19 final size:21
Alignment explanation
Indices: 2534871--2534922 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
2534861 CGGCCAAGAG
*
2534871 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
2534890 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
2534911 CATGTATTTTCA
1 CATGTATTTTCA
2534923 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:2540638 original size:24 final size:24
Alignment explanation
Indices: 2540617--2540667 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
2540607 TCCTTTGACA
2540617 TTCCAACAATTATGCCACTTGAAG
1 TTCCAACAATTATGCCACTTGAAG
2540641 TTCCAACAATTATGCCACTTGAAG
1 TTCCAACAATTATGCCACTTGAAG
2540665 TTC
1 TTC
2540668 AAAAAGATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.31
Consensus pattern (24 bp):
TTCCAACAATTATGCCACTTGAAG
Found at i:2540702 original size:24 final size:24
Alignment explanation
Indices: 2540632--2540710 Score: 72
Period size: 24 Copynumber: 3.3 Consensus size: 24
2540622 ACAATTATGC
* *
2540632 CACTTGAAGTTCCAACAA-TTATGC
1 CACTTGAAGTTCC-ACAAGTTGTGT
* * *
2540656 CACTTGAAGTTCAAAAAGATGTGT
1 CACTTGAAGTTCCACAAGTTGTGT
*
2540680 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTTCCACAAGTTGTG-T
2540705 CA-TTGA
1 CACTTGA
2540711 GGCTCCAAGT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
23 3 0.07
24 38 0.86
25 3 0.07
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (24 bp):
CACTTGAAGTTCCACAAGTTGTGT
Found at i:2547993 original size:35 final size:37
Alignment explanation
Indices: 2547924--2548003 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 37
2547914 ATACTATTTC
* *
2547924 CATCACCATAATCCATCTTCCATTATCAGGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
* *
2547961 CATTACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
2547996 CATCACCA
1 CATCACCA
2548004 AATTCTCAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
35 20 0.53
36 3 0.08
37 15 0.39
ACGTcount: A:0.31, C:0.35, G:0.05, T:0.29
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:2550676 original size:33 final size:33
Alignment explanation
Indices: 2550597--2550700 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
2550587 ATACAATCTA
* *
2550597 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
2550633 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
2550666 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
2550699 TC
1 TC
2550701 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:2551143 original size:14 final size:15
Alignment explanation
Indices: 2551109--2551155 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
2551099 AACTTGGAGT
2551109 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
2551124 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
2551138 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
2551155 G
1 G
2551156 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:2554684 original size:33 final size:33
Alignment explanation
Indices: 2554605--2554708 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
2554595 ATACAATCTG
* *
2554605 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
2554641 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
2554674 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
2554707 TC
1 TC
2554709 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:2558226 original size:19 final size:20
Alignment explanation
Indices: 2558185--2558235 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
2558175 GAAACCCCTT
*
2558185 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
2558205 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
2558224 TGAAGATACATG
1 TGAAAATACATG
2558236 CTCTTAGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:2561329 original size:35 final size:37
Alignment explanation
Indices: 2561262--2561341 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
2561252 ATACTATTTC
* *
2561262 CATCACCATAATTCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
2561299 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
2561334 CATCACCA
1 CATCACCA
2561342 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 22 0.55
36 3 0.08
37 15 0.38
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.29
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:2564896 original size:36 final size:36
Alignment explanation
Indices: 2564856--2564996 Score: 201
Period size: 36 Copynumber: 3.9 Consensus size: 36
2564846 AACACCATCT
*
2564856 TCCATCTCCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
2564892 TCCATCACCATTATCACGCCTTTATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
* * *
2564928 TCCATCTCCATTATCACGCCTATATCGTCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
* * * *
2564964 TCCACCACCATTATCACACCCATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
2564997 ACTTATAAAT
Statistics
Matches: 93, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 93 1.00
ACGTcount: A:0.28, C:0.38, G:0.04, T:0.30
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAG
Found at i:2567914 original size:89 final size:91
Alignment explanation
Indices: 2567788--2567968 Score: 278
Period size: 89 Copynumber: 2.0 Consensus size: 91
2567778 CCTAGAACAC
*
2567788 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
2567853 AAGAG-T-TCTCTCCTATTCGGCCAAG
66 AAGAGCTATCTC-CCTATTCGGCCAAG
** * * *
2567878 CCATGTGTTTTGCATGTGAACAG-CCCCATGTGCCTTGCATGAGGTTTATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
2567942 AAGAGCTATCTCCCTATTCGGCCAAG
66 AAGAGCTATCTCCCTATTCGGCCAAG
2567968 C
1 C
2567969 ATCATTTCCC
Statistics
Matches: 83, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
89 44 0.53
90 35 0.42
91 4 0.05
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
AAGAGCTATCTCCCTATTCGGCCAAG
Found at i:2572288 original size:90 final size:91
Alignment explanation
Indices: 2572134--2572315 Score: 267
Period size: 90 Copynumber: 2.0 Consensus size: 91
2572124 TTCCTAGACA
*
2572134 CCATGTGCCTTGCATATGACCAGCCACCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCACCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
* * *
2572199 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGCTATCTCCCTATTCGACCAAG
** * * * *
2572225 CCATGTGTTTTGCATGTGAACAGCC-CCATGTGCCTTGCATGTGGTTTATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCACCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
2572289 AAGAGCTATCTCCCTATTCGACCAAG
66 AAGAGCTATCTCCCTATTCGACCAAG
2572315 C
1 C
2572316 ATCATTTTCC
Statistics
Matches: 81, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
90 60 0.74
91 21 0.26
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGAACAGCCACCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
AAGAGCTATCTCCCTATTCGACCAAG
Done.