Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009490.1 Hibiscus syriacus cultivar Beakdansim tig00114598_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: 62997
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:1791 original size:24 final size:23
Alignment explanation
Indices: 1764--1832 Score: 93
Period size: 24 Copynumber: 2.9 Consensus size: 23
1754 TTCCACCAAA
*
1764 GCTCTGATTACCGCTTGATGTATG
1 GCTCTGA-TACCACTTGATGTATG
*
1788 GCTCGGATACCACTTGATGTATG
1 GCTCTGATACCACTTGATGTATG
*
1811 GCTTCTGATGCCACTTGATGTA
1 GC-TCTGATACCACTTGATGTA
1833 AGGTAATTCT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 17 0.43
24 23 0.57
ACGTcount: A:0.19, C:0.22, G:0.25, T:0.35
Consensus pattern (23 bp):
GCTCTGATACCACTTGATGTATG
Found at i:1798 original size:23 final size:24
Alignment explanation
Indices: 1772--1832 Score: 88
Period size: 23 Copynumber: 2.6 Consensus size: 24
1762 AAGCTCTGAT
*
1772 TACCGCTTGATGTATGGC-TCGGA
1 TACCACTTGATGTATGGCTTCGGA
*
1795 TACCACTTGATGTATGGCTTCTGA
1 TACCACTTGATGTATGGCTTCGGA
*
1819 TGCCACTTGATGTA
1 TACCACTTGATGTA
1833 AGGTAATTCT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
23 17 0.50
24 17 0.50
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.34
Consensus pattern (24 bp):
TACCACTTGATGTATGGCTTCGGA
Found at i:2668 original size:90 final size:90
Alignment explanation
Indices: 2488--2653 Score: 251
Period size: 90 Copynumber: 1.8 Consensus size: 90
2478 TGGAAATGAT
* *
2488 GCTTGGCCGAATAGGGAGAGAGCTCTTCATCTTGGCGCCTAAATAAACCACATGCAATGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACATG
*
2553 GGGCTGTTCACACGCAAAACACATG
66 GGGCTGGTCACACGCAAAACACATG
* * * * *
2578 GCTTGGCCGAATAGGGAGATAACTCTTCATCTTGGTGCCTAAATGATCCTCATGCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACAT-
2643 GGGGCTGGTCA
65 GGGGCTGGTCA
2654 TATCAAGGCA
Statistics
Matches: 67, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
90 57 0.85
91 10 0.15
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (90 bp):
GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACATG
GGGCTGGTCACACGCAAAACACATG
Found at i:10515 original size:11 final size:11
Alignment explanation
Indices: 10499--10547 Score: 62
Period size: 11 Copynumber: 4.5 Consensus size: 11
10489 TATTTTTTTC
10499 AAAAAAACAAA
1 AAAAAAACAAA
10510 AAAAAAACAAA
1 AAAAAAACAAA
**
10521 AAAAAGGCAAA
1 AAAAAAACAAA
**
10532 AAAAAGCCAAA
1 AAAAAAACAAA
10543 AAAAA
1 AAAAA
10548 GCCAAAAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 35 1.00
ACGTcount: A:0.84, C:0.10, G:0.06, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:10531 original size:22 final size:21
Alignment explanation
Indices: 10499--10556 Score: 73
Period size: 22 Copynumber: 2.8 Consensus size: 21
10489 TATTTTTTTC
10499 AAAAAAA-CAAAAAAAAAACA
1 AAAAAAAGCAAAAAAAAAACA
**
10519 AAAAAAAGGCAAAAAAAAGCCA
1 AAAAAAA-GCAAAAAAAAAACA
*
10541 AAAAAAAGCCAAAAAA
1 AAAAAAAGCAAAAAAA
10557 GCCAAAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 8 0.24
22 18 0.55
ACGTcount: A:0.81, C:0.12, G:0.07, T:0.00
Consensus pattern (21 bp):
AAAAAAAGCAAAAAAAAAACA
Found at i:10548 original size:11 final size:11
Alignment explanation
Indices: 10506--10556 Score: 75
Period size: 11 Copynumber: 4.6 Consensus size: 11
10496 TTCAAAAAAA
**
10506 CAAAAAAAAAA
1 CAAAAAAAAGC
*
10517 CAAAAAAAAGG
1 CAAAAAAAAGC
10528 CAAAAAAAAGC
1 CAAAAAAAAGC
10539 CAAAAAAAAGC
1 CAAAAAAAAGC
10550 CAAAAAA
1 CAAAAAA
10557 GCCAAAATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
11 37 1.00
ACGTcount: A:0.78, C:0.14, G:0.08, T:0.00
Consensus pattern (11 bp):
CAAAAAAAAGC
Found at i:10554 original size:20 final size:22
Alignment explanation
Indices: 10499--10563 Score: 75
Period size: 20 Copynumber: 3.1 Consensus size: 22
10489 TATTTTTTTC
**
10499 AAAAAAA--CAAAAAAAAAACA
1 AAAAAAAGGCAAAAAAAAGCCA
10519 AAAAAAAGGCAAAAAAAAGCCA
1 AAAAAAAGGCAAAAAAAAGCCA
*
10541 AAAAAAA-GC-CAAAAAAGCCA
1 AAAAAAAGGCAAAAAAAAGCCA
10561 AAA
1 AAA
10564 TTTCAAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
20 20 0.50
21 2 0.05
22 18 0.45
ACGTcount: A:0.78, C:0.14, G:0.08, T:0.00
Consensus pattern (22 bp):
AAAAAAAGGCAAAAAAAAGCCA
Found at i:15677 original size:19 final size:21
Alignment explanation
Indices: 15653--15704 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
15643 CGGCCAAGAG
*
15653 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
15672 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
15693 CATGTATTTTCA
1 CATGTATTTTCA
15705 CGGGGATTCA
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:24048 original size:36 final size:36
Alignment explanation
Indices: 23996--24108 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
23986 GATACTATTT
*
23996 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
24032 TCATCACCATAGTCCATCACCATTATCACACCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
24068 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
24103 ACATCA
1 TCATCA
24109 TCCTTCCATT
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 16 0.23
36 54 0.77
ACGTcount: A:0.34, C:0.36, G:0.03, T:0.27
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:24069 original size:11 final size:11
Alignment explanation
Indices: 23996--24094 Score: 76
Period size: 13 Copynumber: 8.3 Consensus size: 11
23986 GATACTATTT
23996 TCATCACCATAA
1 TCATCACCAT-A
*
24008 TCCATCTCCATTA
1 T-CATCACCA-TA
*
24021 TCA-CGCCTATA
1 TCATCACC-ATA
24032 TCATCACCATA
1 TCATCACCATA
24043 GTCCATCACCATTA
1 -T-CATCACCA-TA
24057 TCA-CACCTATA
1 TCATCACC-ATA
24068 TCATCACCATA
1 TCATCACCATA
24079 TTCCATCACCATA
1 -T-CATCACCATA
24092 TCA
1 TCA
24095 CGCCAATAAC
Statistics
Matches: 73, Mismatches: 3, Indels: 23
0.74 0.03 0.23
Matches are distributed among these distances:
11 25 0.34
12 17 0.23
13 28 0.38
14 3 0.04
ACGTcount: A:0.32, C:0.36, G:0.02, T:0.29
Consensus pattern (11 bp):
TCATCACCATA
Found at i:24123 original size:33 final size:33
Alignment explanation
Indices: 24079--24147 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
24069 CATCACCATA
*
24079 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
24112 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
24145 TTC
1 TTC
24148 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:31017 original size:19 final size:17
Alignment explanation
Indices: 30950--31020 Score: 66
Period size: 13 Copynumber: 4.4 Consensus size: 17
30940 ATTTTTTTTT
30950 CAAAAAAACAAAAAAA--
1 CAAAAAAA-AAAAAAAGG
30966 -AAAAAAAAAAAAAAGG
1 CAAAAAAAAAAAAAAGG
30982 C----AAAAAAAAAAGG
1 CAAAAAAAAAAAAAAGG
30995 CAAAAAAAAAAAAAAGAG
1 CAAAAAAAAAAAAAAG-G
31013 CCAAAAAA
1 -CAAAAAA
31021 GACAAAATTT
Statistics
Matches: 46, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
13 13 0.28
14 7 0.15
15 7 0.15
17 11 0.24
18 1 0.02
19 7 0.15
ACGTcount: A:0.83, C:0.08, G:0.08, T:0.00
Consensus pattern (17 bp):
CAAAAAAAAAAAAAAGG
Found at i:31020 original size:1 final size:1
Alignment explanation
Indices: 30951--31009 Score: 55
Period size: 1 Copynumber: 59.0 Consensus size: 1
30941 TTTTTTTTTC
* *** ***
30951 AAAAAAACAAAAAAAAAAAAAAAAAAAAAGGCAAAAAAAAAAGGCAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
31010 GAGCCAAAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.88, C:0.05, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:35192 original size:15 final size:15
Alignment explanation
Indices: 35160--35198 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
35150 CTTTATTATC
35160 TTATTTCATCTTCCGT
1 TTATTT-ATCTTCCGT
**
35176 TTATTTATCTTTTGT
1 TTATTTATCTTCCGT
35191 TTATTTAT
1 TTATTTAT
35199 TCTAATCTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.15, C:0.13, G:0.05, T:0.67
Consensus pattern (15 bp):
TTATTTATCTTCCGT
Found at i:35451 original size:36 final size:36
Alignment explanation
Indices: 35399--35511 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
35389 GATACTATTT
*
35399 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
35435 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
35471 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
35506 ACATCA
1 TCATCA
35512 TCCTTCCATT
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 17 0.24
36 55 0.76
ACGTcount: A:0.33, C:0.36, G:0.04, T:0.27
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:35454 original size:13 final size:11
Alignment explanation
Indices: 35399--35497 Score: 67
Period size: 13 Copynumber: 8.3 Consensus size: 11
35389 GATACTATTT
35399 TCATCACCATAA
1 TCATCACCAT-A
*
35411 TCCATCTCCATTA
1 T-CATCACCA-TA
*
35424 TCA-CGCCTATA
1 TCATCACC-ATA
35435 TCATCACCATA
1 TCATCACCATA
35446 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
35460 TCA-CGCCTATA
1 TCATCACC-ATA
35471 TCATCACCATA
1 TCATCACCATA
35482 TTCCATCACCATA
1 -T-CATCACCATA
35495 TCA
1 TCA
35498 CGCCAATAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.34
12 16 0.23
13 28 0.39
14 3 0.04
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.29
Consensus pattern (11 bp):
TCATCACCATA
Found at i:35526 original size:33 final size:33
Alignment explanation
Indices: 35400--35526 Score: 112
Period size: 36 Copynumber: 3.6 Consensus size: 33
35390 ATACTATTTT
* * *
35400 CATCACCATAATCCATCTCCATTATCACGCCTATAT
1 CATCACCAT--TCCATCACCA-TATCACGCCAATAA
* *
35436 CATCACCATAGTCCATCACCATTATCACGCCTATAT
1 CATCACCAT--TCCATCACCA-TATCACGCCAATAA
35472 CATCACCATATTCCATCACCATATCACGCCAATAA
1 CATCACC--ATTCCATCACCATATCACGCCAATAA
*
35507 CATCATCC-TTCCATTACCAT
1 CATCA-CCATTCCATCACCAT
35527 TACATCACCA
Statistics
Matches: 83, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
33 11 0.13
35 17 0.20
36 53 0.64
38 2 0.02
ACGTcount: A:0.31, C:0.37, G:0.03, T:0.28
Consensus pattern (33 bp):
CATCACCATTCCATCACCATATCACGCCAATAA
Found at i:37445 original size:22 final size:23
Alignment explanation
Indices: 37414--37464 Score: 86
Period size: 22 Copynumber: 2.3 Consensus size: 23
37404 TTAGAAGTTT
*
37414 GTGATAATATAGGCGTGAT-ATG
1 GTGATGATATAGGCGTGATAATG
37436 GTGATGATATAGGCGTGATAATG
1 GTGATGATATAGGCGTGATAATG
37459 GTGATG
1 GTGATG
37465 GACAGATTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 18 0.67
23 9 0.33
ACGTcount: A:0.29, C:0.04, G:0.35, T:0.31
Consensus pattern (23 bp):
GTGATGATATAGGCGTGATAATG
Found at i:46558 original size:25 final size:22
Alignment explanation
Indices: 46529--46586 Score: 62
Period size: 25 Copynumber: 2.4 Consensus size: 22
46519 CTTGGCTTGC
46529 TTTCTTTTGAATTTCTTTTTCTTT
1 TTTCTTTTG-ATTT-TTTTTCTTT
46553 TCTTCTATTCTGATTTTTTTTCTTT
1 T-TTCT-TT-TGATTTTTTTTCTTT
46578 TTGTCTTTT
1 TT-TCTTTT
46587 CTTTCTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
23 1 0.03
24 4 0.13
25 17 0.57
26 6 0.20
27 2 0.07
ACGTcount: A:0.07, C:0.14, G:0.05, T:0.74
Consensus pattern (22 bp):
TTTCTTTTGATTTTTTTTCTTT
Found at i:56675 original size:35 final size:35
Alignment explanation
Indices: 56623--56732 Score: 150
Period size: 35 Copynumber: 3.1 Consensus size: 35
56613 GTAATGGAAG
* *
56623 GATGTTATTGGCGTGATATGGTGATGGAATATGGT
1 GATGATATAGGCGTGATATGGTGATGGAATATGGT
*
56658 GATGATATAGGCGTGATAATGGTGATGGACTATGGT
1 GATGATATAGGCGTGAT-ATGGTGATGGAATATGGT
* * *
56694 GAT-ATATAGGCGTGATAAGGAGATGGATTATGGT
1 GATGATATAGGCGTGATATGGTGATGGAATATGGT
56728 GATGA
1 GATGA
56733 AAATAGTATC
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
34 18 0.27
35 29 0.43
36 20 0.30
ACGTcount: A:0.28, C:0.04, G:0.36, T:0.32
Consensus pattern (35 bp):
GATGATATAGGCGTGATATGGTGATGGAATATGGT
Found at i:56694 original size:13 final size:11
Alignment explanation
Indices: 56636--56732 Score: 56
Period size: 13 Copynumber: 8.3 Consensus size: 11
56626 GTTATTGGCG
56636 TGATATGGTGA
1 TGATATGGTGA
56647 TGGAATATGGTGA
1 T-G-ATATGGTGA
*
56660 TGATATAGGCG-
1 TGATAT-GGTGA
56671 TGATAATGGTGA
1 TGAT-ATGGTGA
56683 TGGACTATGGTGA
1 T-GA-TATGGTGA
*
56696 T-ATATAGGCG-
1 TGATAT-GGTGA
* *
56706 TGATAAGGAGA
1 TGATATGGTGA
56717 TGGATTATGGTGA
1 T-GA-TATGGTGA
56730 TGA
1 TGA
56733 AAATAGTATC
Statistics
Matches: 67, Mismatches: 7, Indels: 23
0.69 0.07 0.24
Matches are distributed among these distances:
10 7 0.10
11 20 0.30
12 12 0.18
13 27 0.40
14 1 0.01
ACGTcount: A:0.30, C:0.03, G:0.36, T:0.31
Consensus pattern (11 bp):
TGATATGGTGA
Found at i:61006 original size:33 final size:33
Alignment explanation
Indices: 60964--61032 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
60954 GTTGATGAAT
*
60964 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
60997 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
61030 GAA
1 GAA
61033 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:61037 original size:13 final size:12
Alignment explanation
Indices: 61018--61114 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
61008 TTATTGGCGT
61018 GATATGGTGATG
1 GATATGGTGATG
61030 GAATATGGTGAT-
1 G-ATATGGTGATG
*
61042 GATATAGGCG-T-
1 GATAT-GGTGATG
61053 GATAATGGTGATG
1 GAT-ATGGTGATG
61066 GACTATGGTGAT-
1 GA-TATGGTGATG
*
61078 GATATAGGCG-T-
1 GATAT-GGTGATG
*
61089 GATAATGGAGATG
1 GAT-ATGGTGATG
61102 GATTATGGTGATG
1 GA-TATGGTGATG
61115 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:61073 original size:36 final size:36
Alignment explanation
Indices: 61003--61115 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
60993 AATGGAAGGA
* *
61003 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
61038 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
61074 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
61110 TGATGA
1 TGATGA
61116 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
Done.