Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005132.1 Hibiscus syriacus cultivar Beakdansim tig00011554_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: 73565
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:3423 original size:13 final size:11
Alignment explanation
Indices: 3382--3466 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
3372 ACAATCTATC
3382 CATCACCATTAT
1 CATCACCA-TAT
*
3394 CA-CGCCTATAT
1 CATCACC-ATAT
3405 CATCACCATAGT
1 CATCACCATA-T
3417 CCATCACCATTAT
1 -CATCACCA-TAT
*
3430 CA-CGCCTATAT
1 CATCACC-ATAT
3441 CATCACCATATT
1 CATCACCATA-T
3453 CCATCACCATAT
1 -CATCACCATAT
3465 CA
1 CA
3467 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:3427 original size:36 final size:36
Alignment explanation
Indices: 3380--3483 Score: 183
Period size: 36 Copynumber: 2.9 Consensus size: 36
3370 ATACAATCTA
3380 TCCATCACCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
3416 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
3452 TCCATCACCA-TATCACGCCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
3484 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.32
36 45 0.68
ACGTcount: A:0.31, C:0.37, G:0.04, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAG
Found at i:9214 original size:27 final size:28
Alignment explanation
Indices: 9184--9245 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
9174 CTTTTCTTTG
* **
9184 CTTTTCTTCTTTTTGAGTGC-TGGATTT
1 CTTTTCTTCTTTTGGAGTGCTTCAATTT
9211 C-TTTCTTTCTTTTGGAGTGCTTCAATTT
1 CTTTTC-TTCTTTTGGAGTGCTTCAATTT
9239 CTTTTCT
1 CTTTTCT
9246 GATTTTCTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
26 4 0.14
27 14 0.48
28 7 0.24
29 4 0.14
ACGTcount: A:0.08, C:0.18, G:0.15, T:0.60
Consensus pattern (28 bp):
CTTTTCTTCTTTTGGAGTGCTTCAATTT
Found at i:14968 original size:17 final size:17
Alignment explanation
Indices: 14877--14997 Score: 77
Period size: 17 Copynumber: 7.1 Consensus size: 17
14867 TTTAAACATG
* *
14877 TAGTTCATTGATTAAAT
1 TAGTTCATTAATTAAAC
* *
14894 TA-TTCATTCATTGAAC
1 TAGTTCATTAATTAAAC
* ** *
14910 TATTTCATTAAAGATTAC
1 TAGTTCATTAATTA-AAC
* *
14928 AAGTTCATTGAA-TAAAGT
1 TAGTTCATT-AATTAAA-C
14946 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
*
14963 TAGTTCATT-ATCAAAC
1 TAGTTCATTAATTAAAC
* *
14979 TAGATCATTTATTAAAC
1 TAGTTCATTAATTAAAC
14996 TA
1 TA
14998 ACTCTTAATT
Statistics
Matches: 80, Mismatches: 18, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
16 27 0.34
17 29 0.36
18 22 0.28
19 2 0.03
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:16579 original size:33 final size:33
Alignment explanation
Indices: 16542--16610 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
16532 CATCACCATA
*
16542 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
16575 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
16608 TTC
1 TTC
16611 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:21049 original size:37 final size:36
Alignment explanation
Indices: 20977--21090 Score: 167
Period size: 37 Copynumber: 3.2 Consensus size: 36
20967 GATACTATTT
*
20977 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
21013 TCATCACCATAGTCCATCACCATTTATCACGCCTATA
1 TCATCACCATAATCCATCACCA-TTATCACGCCTATA
* *
21050 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
21085 ACATCA
1 TCATCA
21091 TCCTTCCATT
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
35 17 0.24
36 20 0.28
37 35 0.49
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:21069 original size:13 final size:12
Alignment explanation
Indices: 21013--21074 Score: 56
Period size: 13 Copynumber: 5.0 Consensus size: 12
21003 CACGCCTATA
21013 TCATCACCATAGT
1 TCATCACCATA-T
*
21026 CCATCACCAT-T
1 TCATCACCATAT
*
21037 T-ATCACGCCTAT
1 TCATCAC-CATAT
21049 ATCATCACCATAT
1 -TCATCACCATAT
21062 TCCATCACCATAT
1 T-CATCACCATAT
21075 CACGCCAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
10 5 0.12
11 3 0.08
12 2 0.05
13 25 0.62
14 5 0.12
ACGTcount: A:0.31, C:0.35, G:0.03, T:0.31
Consensus pattern (12 bp):
TCATCACCATAT
Found at i:21105 original size:33 final size:33
Alignment explanation
Indices: 21061--21129 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
21051 CATCACCATA
*
21061 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
21094 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
21127 TTC
1 TTC
21130 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:24319 original size:22 final size:21
Alignment explanation
Indices: 24289--24333 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
24279 AATCTCCATT
24289 TCATCATCAACACCA-ACAACA
1 TCATCATCAACACCATA-AACA
*
24310 TCATCCATCAAGACCATAAACA
1 TCAT-CATCAACACCATAAACA
24332 TC
1 TC
24334 TTCTTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 4 0.19
22 16 0.76
23 1 0.05
ACGTcount: A:0.44, C:0.36, G:0.02, T:0.18
Consensus pattern (21 bp):
TCATCATCAACACCATAAACA
Found at i:24687 original size:19 final size:17
Alignment explanation
Indices: 24657--24699 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
24647 TTCAAAGATA
*
24657 AAAAGAA-AAAAAATCAG
1 AAAAGAAGAAAAAA-AAG
24674 AAAAGAAG-AAAAAAAG
1 AAAAGAAGAAAAAAAAG
24690 AAAAGAAGAA
1 AAAAGAAGAA
24700 TTTCAAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.02
Consensus pattern (17 bp):
AAAAGAAGAAAAAAAAG
Found at i:24691 original size:16 final size:17
Alignment explanation
Indices: 24657--24699 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
24647 TTCAAAGATA
24657 AAAAGAA-AAAAAATCAG
1 AAAAGAAGAAAAAA-CAG
24674 AAAAGAAGAAAAAA-AG
1 AAAAGAAGAAAAAACAG
24690 AAAAGAAGAA
1 AAAAGAAGAA
24700 TTTCAAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.48
17 7 0.28
18 6 0.24
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.02
Consensus pattern (17 bp):
AAAAGAAGAAAAAACAG
Found at i:35099 original size:33 final size:33
Alignment explanation
Indices: 35057--35125 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
35047 GTTGATGAAT
*
35057 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
35090 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
35123 GAA
1 GAA
35126 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:35130 original size:13 final size:12
Alignment explanation
Indices: 35111--35207 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
35101 TTATTGGCGT
35111 GATATGGTGATG
1 GATATGGTGATG
35123 GAATATGGTGAT-
1 G-ATATGGTGATG
*
35135 GATATAGGCG-T-
1 GATAT-GGTGATG
35146 GATAATGGTGATG
1 GAT-ATGGTGATG
35159 GACTATGGTGAT-
1 GA-TATGGTGATG
*
35171 GATATAGGCG-T-
1 GATAT-GGTGATG
*
35182 GATAATGGAGATG
1 GAT-ATGGTGATG
35195 GATTATGGTGATG
1 GA-TATGGTGATG
35208 AAAATAGTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
11 21 0.30
12 16 0.23
13 30 0.43
14 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:35166 original size:36 final size:36
Alignment explanation
Indices: 35096--35208 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
35086 AATGGAAGGA
* *
35096 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
35131 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
35167 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
35203 TGATGA
1 TGATGA
35209 AAATAGTATC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 16 0.22
36 56 0.78
ACGTcount: A:0.27, C:0.04, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:37395 original size:14 final size:15
Alignment explanation
Indices: 37367--37409 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
37357 TTGCTTCACT
*
37367 TTTTCTTTGCTTTTTT
1 TTTTCTTT-CTTTTTC
37383 TTATTC-TTCTTTTTC
1 TT-TTCTTTCTTTTTC
37398 TTTTCTTTCTTT
1 TTTTCTTTCTTT
37410 GCACTCCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 3 0.12
15 14 0.58
16 4 0.17
17 3 0.12
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.79
Consensus pattern (15 bp):
TTTTCTTTCTTTTTC
Found at i:37857 original size:33 final size:33
Alignment explanation
Indices: 37815--37883 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
37805 GTTGATGAAT
*
37815 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
37848 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
37881 GAA
1 GAA
37884 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:37888 original size:13 final size:12
Alignment explanation
Indices: 37869--37965 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
37859 TTATTGGCGT
37869 GATATGGTGATG
1 GATATGGTGATG
37881 GAATATGGTGAT-
1 G-ATATGGTGATG
*
37893 GATATAGGCG-T-
1 GATAT-GGTGATG
37904 GATAATGGTGATG
1 GAT-ATGGTGATG
37917 GACTATGGTGAT-
1 GA-TATGGTGATG
*
37929 GATATAGGCG-T-
1 GATAT-GGTGATG
*
37940 GATAATGGAGATG
1 GAT-ATGGTGATG
37953 GATTATGGTGATG
1 GA-TATGGTGATG
37966 AAAATAGTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
11 21 0.30
12 16 0.23
13 30 0.43
14 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:37924 original size:36 final size:36
Alignment explanation
Indices: 37854--37966 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
37844 AATGGAAGGA
* *
37854 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
37889 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
37925 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
37961 TGATGA
1 TGATGA
37967 AAATAGTATC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 16 0.22
36 56 0.78
ACGTcount: A:0.27, C:0.04, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:45033 original size:45 final size:45
Alignment explanation
Indices: 44942--45033 Score: 105
Period size: 45 Copynumber: 2.0 Consensus size: 45
44932 TTCTTCCAAA
* * * **
44942 GACACGTTCATTGAATGGAAAATGGTGTCCTTTTGCTGTTTGATG
1 GACACGTCCATTGAATGAAAAATGGTATCCTTTTGCTGTTCAATG
* *
44987 GACACGTCCTTTGAATGAAAAA-GTGTATCCTTTTGTTGTTCAATG
1 GACACGTCCATTGAATGAAAAATG-GTATCCTTTTGCTGTTCAATG
45032 GA
1 GA
45034 TATTTCTTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
44 1 0.03
45 38 0.97
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (45 bp):
GACACGTCCATTGAATGAAAAATGGTATCCTTTTGCTGTTCAATG
Found at i:47859 original size:21 final size:21
Alignment explanation
Indices: 47834--47901 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
47824 TTTTTTTTCA
*
47834 AAAAAAAAAAACAAAAAAGGC
1 AAAAAAAAAAACAAAAAAGAC
* *
47855 AAAAAAAAAAGGCAAAAAAAAC
1 AAAAAAAAAA-ACAAAAAAGAC
* ** *
47877 AAAAAAAGAGCCAAAAAAGCC
1 AAAAAAAAAAACAAAAAAGAC
47898 AAAA
1 AAAA
47902 TTTCAAACAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
21 22 0.58
22 16 0.42
ACGTcount: A:0.78, C:0.12, G:0.10, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAAACAAAAAAGAC
Found at i:47860 original size:22 final size:22
Alignment explanation
Indices: 47832--47883 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
47822 ATTTTTTTTT
**
47832 CAAAAAAAAAAAACAAAAAAGG
1 CAAAAAAAAAAAACAAAAAAAA
**
47854 CAAAAAAAAAAGGCAAAAAAAA
1 CAAAAAAAAAAAACAAAAAAAA
47876 CAAAAAAA
1 CAAAAAAA
47884 GAGCCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.83, C:0.10, G:0.08, T:0.00
Consensus pattern (22 bp):
CAAAAAAAAAAAACAAAAAAAA
Found at i:47861 original size:12 final size:13
Alignment explanation
Indices: 47841--47875 Score: 61
Period size: 13 Copynumber: 2.6 Consensus size: 13
47831 TCAAAAAAAA
47841 AAAACAAAAAAGGC
1 AAAA-AAAAAAGGC
47855 AAAAAAAAAAGGC
1 AAAAAAAAAAGGC
47868 AAAAAAAA
1 AAAAAAAA
47876 CAAAAAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 17 0.81
14 4 0.19
ACGTcount: A:0.80, C:0.09, G:0.11, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGGC
Found at i:54475 original size:117 final size:117
Alignment explanation
Indices: 54269--54494 Score: 443
Period size: 117 Copynumber: 1.9 Consensus size: 117
54259 GTCTTAAAAT
54269 GAAAAATAGATGATGCTTAGATGAGGGGAGATGTCTTTGGCCGAATGGTTCCCTTGTCTCTTCAT
1 GAAAAATAGATGATGCTTAGATGAGGGGAGATGTCTTTGGCCGAATGGTTCCCTTGTCTCTTCAT
*
54334 CTTGGCGCCAACTTGAAGCAAGATGATGGTTTGGCCGAATGGAGGGTTCAAC
66 CTTGGCACCAACTTGAAGCAAGATGATGGTTTGGCCGAATGGAGGGTTCAAC
54386 GAAAAATAGATGATGCTTAGATGAGGGGAGATGTCTTTGGCCGAATGGTTCCCTTGTCTCTTCAT
1 GAAAAATAGATGATGCTTAGATGAGGGGAGATGTCTTTGGCCGAATGGTTCCCTTGTCTCTTCAT
54451 CTTGGCACCAACTTGAAGCAAGATGATGGTTTGGCCGAATGGAG
66 CTTGGCACCAACTTGAAGCAAGATGATGGTTTGGCCGAATGGAG
54495 AGAACCCTCT
Statistics
Matches: 108, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
117 108 1.00
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (117 bp):
GAAAAATAGATGATGCTTAGATGAGGGGAGATGTCTTTGGCCGAATGGTTCCCTTGTCTCTTCAT
CTTGGCACCAACTTGAAGCAAGATGATGGTTTGGCCGAATGGAGGGTTCAAC
Done.