Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002619.1 Hibiscus syriacus cultivar Beakdansim tig00005327_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: 54874
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:5639 original size:18 final size:19
Alignment explanation
Indices: 5604--5640 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
5594 CACGGAATGT
5604 AAGATTATCAGTGGGAATAA
1 AAGATTATCAG-GGGAATAA
5624 AAGATTATCA-GGGAATA
1 AAGATTATCAGGGGAATA
5641 TGATTACTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.05, G:0.24, T:0.24
Consensus pattern (19 bp):
AAGATTATCAGGGGAATAA
Found at i:5863 original size:37 final size:39
Alignment explanation
Indices: 5785--5864 Score: 96
Period size: 39 Copynumber: 2.1 Consensus size: 39
5775 AACAAGTTAA
*
5785 AAAATATTTATATATTTTCTTTAAAAAAATTAAATTCAT
1 AAAATATTTATATATTTTCTTTAAAAAAATTAAAATCAT
*
5824 AAAAT-TTATATATATTTT-TTT-ACAAAATTGAAAAT-AT
1 AAAATATT-TATATATTTTCTTTAAAAAAATT-AAAATCAT
5861 AAAA
1 AAAA
5865 AAGTTTAATG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
37 13 0.35
38 9 0.24
39 15 0.41
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (39 bp):
AAAATATTTATATATTTTCTTTAAAAAAATTAAAATCAT
Found at i:13032 original size:22 final size:21
Alignment explanation
Indices: 13005--13049 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
12995 TTTTGAAAAC
*
13005 AAAATTGAAAATGTAGGTACTA
1 AAAATT-AAAATGTAGATACTA
* *
13027 AAAATTATAGTGTAGATACTA
1 AAAATTAAAATGTAGATACTA
13048 AA
1 AA
13050 TTCAAAATTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.51, C:0.04, G:0.16, T:0.29
Consensus pattern (21 bp):
AAAATTAAAATGTAGATACTA
Found at i:33740 original size:16 final size:17
Alignment explanation
Indices: 33716--33748 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
33706 TTCATAAAAT
33716 ACTAAAAAAATT-GTTA
1 ACTAAAAAAATTAGTTA
*
33732 ACTAGAAAAATTAGTTA
1 ACTAAAAAAATTAGTTA
33749 TATTGATCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.55, C:0.06, G:0.09, T:0.30
Consensus pattern (17 bp):
ACTAAAAAAATTAGTTA
Found at i:39914 original size:19 final size:20
Alignment explanation
Indices: 39876--39916 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
39866 CCAGAACGCT
*
39876 AGGGGGGAATCGATACCCCC
1 AGGGGGGAACCGATACCCCC
*
39896 AGGGGGGAACCGATTCCCCC
1 AGGGGGGAACCGATACCCCC
39916 A
1 A
39917 TAATAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.24, C:0.32, G:0.34, T:0.10
Consensus pattern (20 bp):
AGGGGGGAACCGATACCCCC
Found at i:40728 original size:103 final size:103
Alignment explanation
Indices: 40400--40720 Score: 624
Period size: 103 Copynumber: 3.1 Consensus size: 103
40390 GTAGAGGGTC
40400 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
40465 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
40503 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
40568 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
*
40606 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACACGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
40671 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
40709 TATGTGGTCCTT
1 TATGTGGTCCTT
40721 ATGGACATTA
Statistics
Matches: 216, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 216 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
Found at i:40770 original size:23 final size:23
Alignment explanation
Indices: 40737--40799 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
40727 ATTATTATAT
40737 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
40760 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
40783 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
40800 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:41598 original size:40 final size:41
Alignment explanation
Indices: 41552--41709 Score: 106
Period size: 40 Copynumber: 3.9 Consensus size: 41
41542 GTTTATAGCT
* * *
41552 CAAACGCTGGAATATAGTTGTTTATAGTGGCGTTT-TTATA
1 CAAACGCCGAAATATAGTTGTTTATAGTGGCGTTTATCATA
* ** * * * *
41592 CAAACGCCGTAATAGGGTTGCTTACAGTGGCATTTGTCCA-A
1 CAAACGCCGAAATATAGTTGTTTATAGTGGCGTTTAT-CATA
** ** ** * *
41633 CAAACGATGCTATATAGAAGTAATT-TAGCGGCGTTTATCAAA
1 CAAACGCCGAAATATAGTTGT--TTATAGTGGCGTTTATCATA
41675 CAAACGCCGAAATATAGTTGTTTATAGTGGCGTTT
1 CAAACGCCGAAATATAGTTGTTTATAGTGGCGTTT
41710 TTATACAGAT
Statistics
Matches: 84, Mismatches: 28, Indels: 11
0.68 0.23 0.09
Matches are distributed among these distances:
40 30 0.36
41 26 0.31
42 26 0.31
43 2 0.02
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.32
Consensus pattern (41 bp):
CAAACGCCGAAATATAGTTGTTTATAGTGGCGTTTATCATA
Found at i:41663 original size:123 final size:123
Alignment explanation
Indices: 41529--41806 Score: 432
Period size: 123 Copynumber: 2.3 Consensus size: 123
41519 CAATAGAGTG
** * *
41529 GTAATTTAGCGGCGTTTAT-AGCTCAAACGCTGGAATATAGTTGTTTATAGTGGCGTTTTTATAC
1 GTAATTTAGCGGCGTTTATCA-AACAAACGCCGAAATATAGTTGTTTATAGTGGCGTTTTTATAC
* * * *
41593 AAACGCCGTAATAGGGTTGCTTACAGTGGCATTTGTCCAACAAACGATGCTATATAGAA
65 AAACGCCGCAATAGGGTTGCTTACAGTGACATTTGTCCAACAAACAACGCTATATAGAA
41652 GTAATTTAGCGGCGTTTATCAAACAAACGCCGAAATATAGTTGTTTATAGTGGCGTTTTTATACA
1 GTAATTTAGCGGCGTTTATCAAACAAACGCCGAAATATAGTTGTTTATAGTGGCGTTTTTATACA
* *
41717 GATGCCGCAATAGGGTTGCTTACAGTGACATTTGTCCAACAAACAACGCTATATAGAA
66 AACGCCGCAATAGGGTTGCTTACAGTGACATTTGTCCAACAAACAACGCTATATAGAA
**
41775 GTAATTTAGCGATGTTTATCAAACAAACGCCG
1 GTAATTTAGCGGCGTTTATCAAACAAACGCCG
41807 CAATCAGTAA
Statistics
Matches: 142, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
123 141 0.99
124 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (123 bp):
GTAATTTAGCGGCGTTTATCAAACAAACGCCGAAATATAGTTGTTTATAGTGGCGTTTTTATACA
AACGCCGCAATAGGGTTGCTTACAGTGACATTTGTCCAACAAACAACGCTATATAGAA
Found at i:42132 original size:11 final size:11
Alignment explanation
Indices: 42107--42144 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
42097 TTTTTCCTTA
*
42107 TCTTCCCT-CT
1 TCTTCCCTAAT
42117 TCTTCCCTAAT
1 TCTTCCCTAAT
42128 TCTTCCCTAAT
1 TCTTCCCTAAT
42139 TCTTCC
1 TCTTCC
42145 TCGAAAAACC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 8 0.31
11 18 0.69
ACGTcount: A:0.11, C:0.42, G:0.00, T:0.47
Consensus pattern (11 bp):
TCTTCCCTAAT
Found at i:45005 original size:14 final size:14
Alignment explanation
Indices: 44986--45017 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
44976 TACCATTCGG
44986 TTACGTTGTGCACT
1 TTACGTTGTGCACT
45000 TTACGTTGTGCACT
1 TTACGTTGTGCACT
45014 TTAC
1 TTAC
45018 AGTAGTTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.44
Consensus pattern (14 bp):
TTACGTTGTGCACT
Found at i:45859 original size:83 final size:85
Alignment explanation
Indices: 45729--45928 Score: 228
Period size: 83 Copynumber: 2.4 Consensus size: 85
45719 GGCGTTTGTG
* * * *
45729 GCCGCTATAGATCTC-ACCTTTTACGACGTTTGTATCTAAAAACGCCGCTATAAATCTGACATTT
1 GCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTATCCAAAAACGCCGCTATAAATATGACATTT
* *
45793 AT-GGCGTTTGTTTC-AAAAT
66 -TCGGCGTTTGTTACAAAAAC
* * * * *
45812 GCTGCTATAGATATCGACCTTTTGCGGCGTTTGT-TCCAAAAATGCCGCTATAGATATGACCTTT
1 GCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTATCCAAAAACGCCGCTATAAATATGACATTT
45876 TGCGGCGTTTGTTACAAAAAC
66 T-CGGCGTTTGTTACAAAAAC
* * *
45897 GCCGCGATAGATCTTGACCTATTGCGGCGTTT
1 GCCGCTATAGATCTCGACCTTTTGCGGCGTTT
45929 TTTGTTCTCA
Statistics
Matches: 97, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
82 1 0.01
83 38 0.39
84 27 0.28
85 31 0.32
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (85 bp):
GCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTATCCAAAAACGCCGCTATAAATATGACATTT
TCGGCGTTTGTTACAAAAAC
Found at i:45865 original size:43 final size:43
Alignment explanation
Indices: 45729--45928 Score: 198
Period size: 42 Copynumber: 4.7 Consensus size: 43
45719 GGCGTTTGTG
* * * *
45729 GCCGCTATAGATCTC-ACCTTTTACGACGTTTGTATCTAAAAAC
1 GCCGCTATAGATATCGACCTTTTGCGGCGTTTGT-TCCAAAAAC
* * *
45772 GCCGCTATA-A-ATCTGACATTTAT--GGCGTTTGTTTC-AAAAT
1 GCCGCTATAGATATC-GACCTTT-TGCGGCGTTTGTTCCAAAAAC
* *
45812 GCTGCTATAGATATCGACCTTTTGCGGCGTTTGTTCCAAAAAT
1 GCCGCTATAGATATCGACCTTTTGCGGCGTTTGTTCCAAAAAC
*
45855 GCCGCTATAGATAT-GACCTTTTGCGGCGTTTGTTACAAAAAC
1 GCCGCTATAGATATCGACCTTTTGCGGCGTTTGTTCCAAAAAC
* * * *
45897 GCCGCGATAGATCTTGACCTATTGCGGCGTTT
1 GCCGCTATAGATATCGACCTTTTGCGGCGTTT
45929 TTTGTTCTCA
Statistics
Matches: 133, Mismatches: 15, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
40 13 0.10
41 10 0.08
42 61 0.46
43 48 0.36
44 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (43 bp):
GCCGCTATAGATATCGACCTTTTGCGGCGTTTGTTCCAAAAAC
Done.