Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004873.1 Hibiscus syriacus cultivar Beakdansim tig00010984_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: 63049
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:223 original size:20 final size:20
Alignment explanation
Indices: 180--234 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
170 CTCTGTATAG
*
180 TAGTATCGATACCAT-GGTA
1 TAGTATCGATACCATAGGCA
199 TAGTATCGATACCATAGGCA
1 TAGTATCGATACCATAGGCA
219 TAGTATCGATACCATA
1 TAGTATCGATACCATA
235 AGGCCCCAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 15 0.44
20 19 0.56
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (20 bp):
TAGTATCGATACCATAGGCA
Found at i:3040 original size:17 final size:18
Alignment explanation
Indices: 3013--3049 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
3003 TTTTCCTCTG
3013 AGAGAAATAGAATTCAGT
1 AGAGAAATAGAATTCAGT
3031 AGAG-AATAGAATTCAGT
1 AGAGAAATAGAATTCAGT
3048 AG
1 AG
3050 CACGTTTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.49, C:0.05, G:0.24, T:0.22
Consensus pattern (18 bp):
AGAGAAATAGAATTCAGT
Found at i:3933 original size:13 final size:13
Alignment explanation
Indices: 3915--3957 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
3905 CATAAAGCAC
3915 GTCATAAATGCGT
1 GTCATAAATGCGT
*
3928 GTCATAAATGTGT
1 GTCATAAATGCGT
* *
3941 CATCATAAATTCGT
1 -GTCATAAATGCGT
3955 GTC
1 GTC
3958 GGTGGCTTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
13 14 0.58
14 10 0.42
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (13 bp):
GTCATAAATGCGT
Found at i:22218 original size:20 final size:20
Alignment explanation
Indices: 22193--22256 Score: 92
Period size: 20 Copynumber: 3.2 Consensus size: 20
22183 TATGTTTTTG
* *
22193 AGTATCGGTATTGTTCACAC
1 AGTATCGGTATTATTCATAC
* *
22213 AGTATCGATACTATTCATAC
1 AGTATCGGTATTATTCATAC
22233 AGTATCGGTATTATTCATAC
1 AGTATCGGTATTATTCATAC
22253 AGTA
1 AGTA
22257 CAATACTATT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (20 bp):
AGTATCGGTATTATTCATAC
Found at i:22255 original size:40 final size:39
Alignment explanation
Indices: 22193--22270 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
22183 TATGTTTTTG
* *
22193 AGTATCGGTATTGTTCACACAGTATCGATACTATTCATAC
1 AGTATCGGTATTATTCACACAGTA-CAATACTATTCATAC
*
22233 AGTATCGGTATTATTCATACAGTACAATACTATTCATA
1 AGTATCGGTATTATTCACACAGTACAATACTATTCATA
22271 AAAATATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 13 0.37
40 22 0.63
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (39 bp):
AGTATCGGTATTATTCACACAGTACAATACTATTCATAC
Found at i:24817 original size:11 final size:11
Alignment explanation
Indices: 24801--24825 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
24791 TAAAATGCAG
24801 AAAAATAAAAT
1 AAAAATAAAAT
24812 AAAAATAAAAT
1 AAAAATAAAAT
24823 AAA
1 AAA
24826 CAAACAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:25578 original size:16 final size:16
Alignment explanation
Indices: 25557--25589 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
25547 TAATAAATAA
25557 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
25573 ACGAACATGAACGAAC
1 ACGAACATAAACGAAC
25589 A
1 A
25590 AAAAAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.24, G:0.15, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:25638 original size:10 final size:10
Alignment explanation
Indices: 25623--25700 Score: 77
Period size: 10 Copynumber: 7.6 Consensus size: 10
25613 CATTTAAATG
25623 ATAAACGAAC
1 ATAAACGAAC
*
25633 ATAAACAAAC
1 ATAAACGAAC
*
25643 ACAAACGAAC
1 ATAAACGAAC
*
25653 ATAAACAAAC
1 ATAAACGAAC
*
25663 ATAATAAATGAAC
1 ---ATAAACGAAC
25676 ATAAACGAAC
1 ATAAACGAAC
25686 ATAAAC-AAC
1 ATAAACGAAC
*
25695 ACAAAC
1 ATAAAC
25701 ACAAAAAACA
Statistics
Matches: 56, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
9 8 0.14
10 40 0.71
13 8 0.14
ACGTcount: A:0.64, C:0.21, G:0.05, T:0.10
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:25976 original size:14 final size:14
Alignment explanation
Indices: 25957--25984 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
25947 CCTCTGTTCG
25957 AACATAAATGAACA
1 AACATAAATGAACA
25971 AACATAAATGAACA
1 AACATAAATGAACA
25985 TATAATCGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.14, G:0.07, T:0.14
Consensus pattern (14 bp):
AACATAAATGAACA
Found at i:30129 original size:19 final size:20
Alignment explanation
Indices: 30107--30145 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
30097 TTTTTAATGT
*
30107 ATTTTTTAT-TAAAATTTTA
1 ATTTTATATCTAAAATTTTA
30126 ATTTTATATCTAAAATTTTA
1 ATTTTATATCTAAAATTTTA
30146 TAATTTGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTTATATCTAAAATTTTA
Found at i:40047 original size:31 final size:30
Alignment explanation
Indices: 39974--40050 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 30
39964 TCAAATGGTC
*
39974 GGGGACCATGTTGCAAACAGACTAAATGTT
1 GGGGACCATATTGCAAACAGACTAAATGTT
**
40004 GGGGACCATATTGCAAATGGACTAAATGTT
1 GGGGACCATATTGCAAACAGACTAAATGTT
**
40034 GAGGGACTGTATTGCAA
1 G-GGGACCATATTGCAA
40051 GTTTAAAAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 28 0.68
31 13 0.32
ACGTcount: A:0.32, C:0.14, G:0.29, T:0.25
Consensus pattern (30 bp):
GGGGACCATATTGCAAACAGACTAAATGTT
Found at i:41599 original size:19 final size:20
Alignment explanation
Indices: 41575--41625 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
41565 AATGACCAAT
41575 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
41594 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
41614 AAAATCGCAACG
1 AAAATCGCAACG
41626 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:41635 original size:20 final size:20
Alignment explanation
Indices: 41612--41665 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
41602 AACGCGATTT
*
41612 AGAAAATCGCAACGTTAAAA
1 AGAAAATCGCAACGGTAAAA
*
41632 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAACGGTAAAA
41652 AGAAAATCGCAACG
1 AGAAAATCGCAACG
41666 CGAGCTTCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.52, C:0.19, G:0.19, T:0.11
Consensus pattern (20 bp):
AGAAAATCGCAACGGTAAAA
Found at i:41725 original size:20 final size:20
Alignment explanation
Indices: 41700--41827 Score: 238
Period size: 20 Copynumber: 6.4 Consensus size: 20
41690 TTTAGAAGAA
41700 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
41720 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
41740 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
41760 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
41780 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
*
41800 AATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGATAG
*
41820 AGTCGCAA
1 AATCGCAA
41828 AGAAGAGAAT
Statistics
Matches: 106, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 106 1.00
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.23
Consensus pattern (20 bp):
AATCGCAATGCGATTGATAG
Found at i:41844 original size:35 final size:35
Alignment explanation
Indices: 41798--41877 Score: 115
Period size: 35 Copynumber: 2.3 Consensus size: 35
41788 TGCGATTGAT
* *
41798 AGAATCGCAATGCGATTGAGAGAGTCGCAAAGAAG
1 AGAATCGCAATGCGACTGAGAGAATCGCAAAGAAG
* **
41833 AGAATCGCAATGCGACTGAGAGAATCGCAACGTTG
1 AGAATCGCAATGCGACTGAGAGAATCGCAAAGAAG
41868 AGAATCGCAA
1 AGAATCGCAA
41878 CGGTCAAAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.39, C:0.17, G:0.29, T:0.15
Consensus pattern (35 bp):
AGAATCGCAATGCGACTGAGAGAATCGCAAAGAAG
Found at i:41978 original size:6 final size:6
Alignment explanation
Indices: 41971--42000 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
41961 CGTATTACCA
*
41971 CGACCA CGACCC CGACCC CGACCC CGACCC
1 CGACCC CGACCC CGACCC CGACCC CGACCC
42001 GAGACGGCGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.20, C:0.63, G:0.17, T:0.00
Consensus pattern (6 bp):
CGACCC
Found at i:42694 original size:6 final size:6
Alignment explanation
Indices: 42683--42841 Score: 318
Period size: 6 Copynumber: 26.5 Consensus size: 6
42673 TCTCGTCTCG
42683 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
42731 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
42779 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
42827 GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGT
42842 AATACGTGTC
Statistics
Matches: 153, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 153 1.00
ACGTcount: A:0.00, C:0.16, G:0.50, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:42944 original size:20 final size:20
Alignment explanation
Indices: 42919--42962 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
42909 TTTTTAACTA
*
42919 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
*
42939 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
42959 TTCT
1 TTCT
42963 AAATCGCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.16, T:0.55
Consensus pattern (20 bp):
TTCTTTTGAACGTTGCGATT
Found at i:42972 original size:20 final size:20
Alignment explanation
Indices: 42949--43225 Score: 182
Period size: 20 Copynumber: 13.6 Consensus size: 20
42939 TTCTTTTTAA
42949 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
42969 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
42989 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * *
43009 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
43029 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
* * *
43052 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
43072 CATTGCGATTATATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
43092 CATTGCGATTCTATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
43112 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
* *
43135 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
43153 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
43175 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
43195 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
43214 CGTTGCGATTTT
1 CGTTGCGATTTT
43226 ATTGGTCATT
Statistics
Matches: 214, Mismatches: 33, Indels: 21
0.80 0.12 0.08
Matches are distributed among these distances:
18 2 0.01
19 17 0.08
20 158 0.74
21 3 0.01
22 6 0.03
23 28 0.13
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.40
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:42995 original size:40 final size:40
Alignment explanation
Indices: 42951--43144 Score: 244
Period size: 40 Copynumber: 4.7 Consensus size: 40
42941 CTTTTTAACG
42951 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
* * * * *
42991 TTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
*
43031 TTGCGATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCA
1 TTGCGA--TT-TTCTAAATCGCGTTGCGATTCTCTCAATCGCA
* * * *
43074 TTGCGATTATATAAATCGCATTGCGATTCTATCAATCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
43114 TTGCGATTTTCTTCTAAATCGCGTTGCGATT
1 TTGCGA--TT-TTCTAAATCGCGTTGCGATT
43145 TTCTTTTGAC
Statistics
Matches: 129, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
40 74 0.57
41 2 0.02
42 4 0.03
43 49 0.38
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.38
Consensus pattern (40 bp):
TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
Found at i:43164 original size:83 final size:83
Alignment explanation
Indices: 42959--43142 Score: 305
Period size: 83 Copynumber: 2.2 Consensus size: 83
42949 CGTTGCGATT
* * * * * *
42959 TTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTCTC
1 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTATATAAATCGCATTGCGATTCTATC
*
43024 AGTCGCATTGCGATTTTC
66 AATCGCATTGCGATTTTC
43042 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTATATAAATCGCATTGCGATTCTATC
1 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTATATAAATCGCATTGCGATTCTATC
43107 AATCGCATTGCGATTTTC
66 AATCGCATTGCGATTTTC
43125 TTCTAAATCGCGTTGCGA
1 TTCTAAATCGCGTTGCGA
43143 TTTTCTTTTG
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
83 94 1.00
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (83 bp):
TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTATATAAATCGCATTGCGATTCTATC
AATCGCATTGCGATTTTC
Found at i:43215 original size:19 final size:20
Alignment explanation
Indices: 43175--43225 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
43165 TTCTTTTTAA
*
43175 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
43195 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
43214 CGTTGCGATTTT
1 CGTTGCGATTTT
43226 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:45934 original size:20 final size:20
Alignment explanation
Indices: 45891--45938 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
45881 TCGGTTCACC
*
45891 CCGGTTTTTCCGGTTTTCAG
1 CCGGTTCTTCCGGTTTTCAG
*
45911 CCGGTTCTTCCGGTTCTTTA-
1 CCGGTTCTTCCGGTT-TTCAG
45931 CCGGTTCT
1 CCGGTTCT
45939 GTACTAATCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 22 0.88
21 3 0.12
ACGTcount: A:0.04, C:0.29, G:0.23, T:0.44
Consensus pattern (20 bp):
CCGGTTCTTCCGGTTTTCAG
Found at i:62292 original size:27 final size:27
Alignment explanation
Indices: 62261--62315 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
62251 GCTTTGCTGA
62261 AGGATTTGGGTATTCAACGGTGTAAGG
1 AGGATTTGGGTATTCAACGGTGTAAGG
62288 AGGATTTGGGTATTCAACGGTGTAAGG
1 AGGATTTGGGTATTCAACGGTGTAAGG
62315 A
1 A
62316 ACCGGTTGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.27, C:0.07, G:0.36, T:0.29
Consensus pattern (27 bp):
AGGATTTGGGTATTCAACGGTGTAAGG
Done.