Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000588.1 Hibiscus syriacus cultivar Beakdansim tig00001144_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: 67674
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:549 original size:63 final size:64
Alignment explanation
Indices: 482--636 Score: 162
Period size: 63 Copynumber: 2.5 Consensus size: 64
472 TTGAAGGTGT
**
482 ATCGATGCA-CAGGTAGTGCATCGATGCACTCTTTAA-AATAGA-A-ACATCGAATGCA-ATTAG
1 ATCGATGCATCAGGTAGTGCATCGATGCA-TC-CCAATAATA-ATACACATCGAATGCATATTA-
542 TGC
62 TGC
* * * *
545 ATCGATGCATAAGG-AATGCATCGATGCATCCCAATAATAATACACATCGAATGTATTTTATGC
1 ATCGATGCATCAGGTAGTGCATCGATGCATCCCAATAATAATACACATCGAATGCATATTATGC
*
608 ACCGATGCATCA-GTAGTGCATCGATGCAT
1 ATCGATGCATCAGGTAGTGCATCGATGCAT
637 ACCCTTATTG
Statistics
Matches: 77, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
61 3 0.04
62 8 0.10
63 60 0.78
64 6 0.08
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.26
Consensus pattern (64 bp):
ATCGATGCATCAGGTAGTGCATCGATGCATCCCAATAATAATACACATCGAATGCATATTATGC
Found at i:1818 original size:32 final size:31
Alignment explanation
Indices: 1779--1906 Score: 125
Period size: 32 Copynumber: 4.1 Consensus size: 31
1769 AGAGTTGAGG
*
1779 GTATACCTATGTTCTAAGGAACATATGGATA
1 GTATACCTATGTTCTAAGGAACATATGGACA
***
1810 -TAATTACCTATG-TCTTTCGAGACATATGGACA
1 GT-A-TACCTATGTTCTAAGGA-ACATATGGACA
1842 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTATACCTATGTTCTAAGGAACATATGGACA
* * ** *
1873 GTTTACCTAGGTTTCTTCGGAACCTATGGACA
1 GTATACCTATG-TTCTAAGGAACATATGGACA
1905 GT
1 GT
1907 TGTCGAGGAT
Statistics
Matches: 79, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
30 1 0.01
31 34 0.43
32 43 0.54
33 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (31 bp):
GTATACCTATGTTCTAAGGAACATATGGACA
Found at i:1852 original size:31 final size:31
Alignment explanation
Indices: 1779--1881 Score: 111
Period size: 31 Copynumber: 3.3 Consensus size: 31
1769 AGAGTTGAGG
* *
1779 GTATACCTATGTTCTAAGGAACATATGGATA
1 GTATACCTATGTTCTAACGAACATATGGACA
**
1810 -TAATTACCTATG-TCTTTCGAGACATATGGACA
1 GT-A-TACCTATGTTCTAACGA-ACATATGGACA
*
1842 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTATACCTATGTTCTAACGAACATATGGACA
*
1873 GTTTACCTA
1 GTATACCTA
1882 GGTTTCTTCG
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
30 1 0.02
31 33 0.56
32 24 0.41
33 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (31 bp):
GTATACCTATGTTCTAACGAACATATGGACA
Found at i:1901 original size:63 final size:62
Alignment explanation
Indices: 1779--1906 Score: 170
Period size: 63 Copynumber: 2.0 Consensus size: 62
1769 AGAGTTGAGG
* *
1779 GTATACCTATGTTCTAAGGAACATATGGATATAATTACCTATGTCTTTCGAGACATATGGACA
1 GTATACCTATGTTCTAAGGAACATATGGACAT-ATTACCTAGGTCTTTCGAGACATATGGACA
* *
1842 GTATACCTATGTTCTAAGGAACATATGGACAGT-TTACCTAGGTTTCTTCG-GAACCTATGGACA
1 GTATACCTATGTTCTAAGGAACATATGGACA-TATTACCTAGGTCT-TTCGAG-ACATATGGACA
1905 GT
1 GT
1907 TGTCGAGGAT
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
62 11 0.19
63 46 0.79
64 1 0.02
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (62 bp):
GTATACCTATGTTCTAAGGAACATATGGACATATTACCTAGGTCTTTCGAGACATATGGACA
Found at i:6247 original size:31 final size:31
Alignment explanation
Indices: 6174--6300 Score: 123
Period size: 31 Copynumber: 4.1 Consensus size: 31
6164 AGAGTTGAGG
* *
6174 GTATACCTATGTTCTAAGGAACATATGGATA
1 GTATACCTATGTTCTAACGAACATATGGACA
* **
6205 GAATTACCTATG-TCTTTCGAGACATATGGACA
1 GTA-TACCTATGTTCTAACGA-ACATATGGACA
*
6237 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTATACCTATGTTCTAACGAACATATGGACA
* * * *
6268 GTTTACCTAGGTTCT-TCGGAACCTATGGACA
1 GTATACCTATGTTCTAAC-GAACATATGGACA
6299 GT
1 GT
6301 TGCCGAGGAT
Statistics
Matches: 78, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
31 53 0.68
32 25 0.32
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31
Consensus pattern (31 bp):
GTATACCTATGTTCTAACGAACATATGGACA
Found at i:7250 original size:13 final size:14
Alignment explanation
Indices: 7232--7260 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
7222 CATATGTAAT
7232 TTAAGTG-ATTTAA
1 TTAAGTGCATTTAA
7245 TTAAGTGCATTTAA
1 TTAAGTGCATTTAA
7259 TT
1 TT
7261 TAATTTAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.48
Consensus pattern (14 bp):
TTAAGTGCATTTAA
Found at i:15851 original size:29 final size:29
Alignment explanation
Indices: 15811--15991 Score: 299
Period size: 29 Copynumber: 6.2 Consensus size: 29
15801 CGGTGGAGCT
* *
15811 TGAAATTAATGGTTTATTCAACGGAGAGGA
1 TGAAA-TAATGGTTTATTCAATGGAGCGGA
15841 TGAAATAATGGTTTATTCAATGGAGCGGA
1 TGAAATAATGGTTTATTCAATGGAGCGGA
*
15870 TGAAATAATGGTTTATTCAACGGAGCGGA
1 TGAAATAATGGTTTATTCAATGGAGCGGA
*
15899 TGAAATAATGGTTTATTCAATGGAGCGTA
1 TGAAATAATGGTTTATTCAATGGAGCGGA
15928 TGAAATAATGGTTTATTCAATGGAGCGGA
1 TGAAATAATGGTTTATTCAATGGAGCGGA
* *
15957 TGAAATAATGGTTTATTCAGTGGAGCAGA
1 TGAAATAATGGTTTATTCAATGGAGCGGA
15986 TGAAAT
1 TGAAAT
15992 TTCAATTTCA
Statistics
Matches: 143, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
29 138 0.97
30 5 0.03
ACGTcount: A:0.35, C:0.07, G:0.27, T:0.31
Consensus pattern (29 bp):
TGAAATAATGGTTTATTCAATGGAGCGGA
Found at i:21760 original size:111 final size:112
Alignment explanation
Indices: 21557--21788 Score: 394
Period size: 111 Copynumber: 2.1 Consensus size: 112
21547 TCGCTCGGAT
* * * *
21557 AGAAATAATATATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAAT
1 AGAATTAATATATCTCGACACTTTGCTGATACAGTAACATTTTAACCTTTTAATTTAATTTAAAT
* * *
21622 TATTAGTAATATTTAGTTGATTTATTTAATGCATGATTATTATATTA
66 TATTAGTAATAATTAGTTGATTCATTTAATGCATGATTATTAGATTA
21669 AGAATTAA-ATATCTCGACACTTTGCTGATACAGTAACATTTTAACCTTTTAATTTAATTTAAAT
1 AGAATTAATATATCTCGACACTTTGCTGATACAGTAACATTTTAACCTTTTAATTTAATTTAAAT
21733 TATTAGTAATAATTAGTTGATTCATTTAATGCATGATTATTAGATTA
66 TATTAGTAATAATTAGTTGATTCATTTAATGCATGATTATTAGATTA
21780 AGAATTAAT
1 AGAATTAAT
21789 TTTTGTAATT
Statistics
Matches: 112, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
111 105 0.94
112 7 0.06
ACGTcount: A:0.37, C:0.09, G:0.10, T:0.44
Consensus pattern (112 bp):
AGAATTAATATATCTCGACACTTTGCTGATACAGTAACATTTTAACCTTTTAATTTAATTTAAAT
TATTAGTAATAATTAGTTGATTCATTTAATGCATGATTATTAGATTA
Found at i:23652 original size:21 final size:21
Alignment explanation
Indices: 23628--23667 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
23618 ACCTGCTCAG
23628 GACGACGACGATGACGATGGT
1 GACGACGACGATGACGATGGT
23649 GACGACGACGATGACGATG
1 GACGACGACGATGACGATG
23668 ACAGCGAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.20, G:0.38, T:0.12
Consensus pattern (21 bp):
GACGACGACGATGACGATGGT
Found at i:23922 original size:35 final size:33
Alignment explanation
Indices: 23883--23967 Score: 82
Period size: 35 Copynumber: 2.5 Consensus size: 33
23873 ATATTTTAGT
23883 TAATTTTGTT-TATTACAATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACAATTTAAT-TC--TTATTG
* *
23918 TAATTTGGTTATCATTTACCATTTAATTCTTATTG
1 TAATTTTGTTAT-A-TTACAATTTAATTCTTATTG
* *
23953 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
23968 TAAATATCAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.57
36 1 0.02
37 3 0.07
38 11 0.26
ACGTcount: A:0.27, C:0.07, G:0.11, T:0.55
Consensus pattern (33 bp):
TAATTTTGTTATATTACAATTTAATTCTTATTG
Found at i:27633 original size:50 final size:49
Alignment explanation
Indices: 27572--27687 Score: 133
Period size: 49 Copynumber: 2.3 Consensus size: 49
27562 CTCTACGTGG
* * * * * *
27572 CGTATAGCGCGGATCAAGGGGCGCGCTATACCAACGTGGCGCCACATCAC
1 CGTATATCGCGGAGC-AGGGGAGCGCTATACCAACGTGACGCCAAATCAA
* *
27622 CGTATATCGCGGGGCAGGGGAGCGCTATACCCACGTGACGCCAAATCAA
1 CGTATATCGCGGAGCAGGGGAGCGCTATACCAACGTGACGCCAAATCAA
* *
27671 CATATATCGCGGTGCAG
1 CGTATATCGCGGAGCAG
27688 AGGGCGCACT
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
49 44 0.79
50 12 0.21
ACGTcount: A:0.25, C:0.29, G:0.30, T:0.16
Consensus pattern (49 bp):
CGTATATCGCGGAGCAGGGGAGCGCTATACCAACGTGACGCCAAATCAA
Found at i:27648 original size:49 final size:49
Alignment explanation
Indices: 27588--27687 Score: 137
Period size: 49 Copynumber: 2.0 Consensus size: 49
27578 GCGCGGATCA
* * * * *
27588 AGGGGCGCGCTATACCAACGTGGCGCCACATCACCGTATATCGCGGGGC
1 AGGGGAGCGCTATACCAACGTGACGCCAAATCAACATATATCGCGGGGC
* *
27637 AGGGGAGCGCTATACCCACGTGACGCCAAATCAACATATATCGCGGTGC
1 AGGGGAGCGCTATACCAACGTGACGCCAAATCAACATATATCGCGGGGC
27686 AG
1 AG
27688 AGGGCGCACT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.25, C:0.30, G:0.30, T:0.15
Consensus pattern (49 bp):
AGGGGAGCGCTATACCAACGTGACGCCAAATCAACATATATCGCGGGGC
Found at i:44129 original size:49 final size:49
Alignment explanation
Indices: 44076--44177 Score: 195
Period size: 49 Copynumber: 2.1 Consensus size: 49
44066 CATAGTTACC
*
44076 ATTACTCTCTTTTCTTCTTCATTTTTGTTCATTATTTTTCATTTACTTT
1 ATTACTCTCTTTTCTTCTTCATTTTTATTCATTATTTTTCATTTACTTT
44125 ATTACTCTCTTTTCTTCTTCATTTTTATTCATTATTTTTCATTTACTTT
1 ATTACTCTCTTTTCTTCTTCATTTTTATTCATTATTTTTCATTTACTTT
44174 ATTA
1 ATTA
44178 TAGCATATAT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.17, C:0.18, G:0.01, T:0.65
Consensus pattern (49 bp):
ATTACTCTCTTTTCTTCTTCATTTTTATTCATTATTTTTCATTTACTTT
Found at i:45687 original size:2 final size:2
Alignment explanation
Indices: 45680--45710 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
45670 TTTAGGCAAA
45680 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
45711 ATGGGAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:48494 original size:2 final size:2
Alignment explanation
Indices: 48487--48529 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
48477 TTCTTTGGAA
48487 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48529 A
1 A
48530 ATTCGATATC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:49399 original size:26 final size:27
Alignment explanation
Indices: 49352--49407 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
49342 TCAATATTTA
* *
49352 TTTTATATTTATATGAATTTAT-TATT
1 TTTTATATTTATATAAAATTATATATT
49378 TTTTATATTGTATA-AAAATTATATATT
1 TTTTATATT-TATATAAAATTATATATT
49405 TTT
1 TTT
49408 GATCTATCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 15 0.58
27 11 0.42
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (27 bp):
TTTTATATTTATATAAAATTATATATT
Found at i:50953 original size:13 final size:13
Alignment explanation
Indices: 50935--50982 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
50925 ACCAGAAGAT
50935 AAAAAAATCCTCA
1 AAAAAAATCCTCA
**
50948 AAAAAAATCCAGAA
1 AAAAAAATCC-TCA
50962 GATAAAAAATCCTCA
1 -A-AAAAAATCCTCA
50977 AAAAAA
1 AAAAAA
50983 CAACAACCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
13 15 0.54
14 2 0.07
15 2 0.07
16 9 0.32
ACGTcount: A:0.67, C:0.17, G:0.04, T:0.12
Consensus pattern (13 bp):
AAAAAAATCCTCA
Found at i:50978 original size:29 final size:30
Alignment explanation
Indices: 50926--50982 Score: 107
Period size: 29 Copynumber: 1.9 Consensus size: 30
50916 ACTTAAACAA
50926 CCAGAAGATAAAAAAATCCTCAAAAAAAAT
1 CCAGAAGATAAAAAAATCCTCAAAAAAAAT
50956 CCAGAAGAT-AAAAAATCCTCAAAAAAA
1 CCAGAAGATAAAAAAATCCTCAAAAAAA
50983 CAACAACCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
29 18 0.67
30 9 0.33
ACGTcount: A:0.63, C:0.18, G:0.07, T:0.12
Consensus pattern (30 bp):
CCAGAAGATAAAAAAATCCTCAAAAAAAAT
Found at i:60549 original size:5 final size:5
Alignment explanation
Indices: 60539--60564 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
60529 TATTTATGAG
60539 TTAAT TTAAT TTAAT TTAAT TTAAT T
1 TTAAT TTAAT TTAAT TTAAT TTAAT T
60565 GACATTGTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTAAT
Done.