Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006919.1 Hibiscus syriacus cultivar Beakdansim tig00017735_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: 64530
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3041 original size:21 final size:22
Alignment explanation
Indices: 3016--3056 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
3006 ACATTGGTAC
3016 AATTTACCC-TAAAAAATTGAT
1 AATTTACCCTTAAAAAATTGAT
3037 AATTTACCCTTAAAAAATTG
1 AATTTACCCTTAAAAAATTG
3057 TGGAATATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.34
Consensus pattern (22 bp):
AATTTACCCTTAAAAAATTGAT
Found at i:9871 original size:23 final size:23
Alignment explanation
Indices: 9836--9891 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
9826 TCGAATTTTG
9836 CAGGTACCCGTAATTCTGG-TAAT
1 CAGGTACCCGTAATTC-GGATAAT
* *
9859 CGGGTACCTGTAATTCGGATAAT
1 CAGGTACCCGTAATTCGGATAAT
9882 CAGGTACCCG
1 CAGGTACCCG
9892 GTTTTTTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 2 0.07
23 26 0.93
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (23 bp):
CAGGTACCCGTAATTCGGATAAT
Found at i:10035 original size:24 final size:23
Alignment explanation
Indices: 10007--10055 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
9997 TTGATTAGTT
*
10007 TAATTTAATATATAAAATTATTAA
1 TAATTAAATATATAAAATTA-TAA
* *
10031 TAATTAAATATGTAATATTATAA
1 TAATTAAATATATAAAATTATAA
10054 TA
1 TA
10056 TATAAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TAATTAAATATATAAAATTATAA
Found at i:10662 original size:16 final size:16
Alignment explanation
Indices: 10638--10707 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
10628 TAATAAATAA
*
10638 ACGAACATAAACAAAC
1 ACGAACATAAACGAAC
*
10654 ACAAACATAAACGAAC
1 ACGAACATAAACGAAC
*
10670 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
10686 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
10702 ATGAAC
1 ACGAAC
10708 TTGGAGGCCC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.59, C:0.23, G:0.10, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:10950 original size:23 final size:24
Alignment explanation
Indices: 10896--10961 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 24
10886 AAAAATTTAA
*
10896 GAGCTCGATTAAAACTCGAGACTC
1 GAGCTCGATTAAAGCTCGAGACTC
**
10920 GAGCTCGATTAAAGCTCGATTCT-
1 GAGCTCGATTAAAGCTCGAGACTC
*
10943 GAGCTCGATTCAAGCTCGA
1 GAGCTCGATTAAAGCTCGA
10962 CATTGCTCCA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
23 18 0.47
24 20 0.53
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (24 bp):
GAGCTCGATTAAAGCTCGAGACTC
Found at i:13577 original size:22 final size:22
Alignment explanation
Indices: 13551--13593 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
13541 ACATGCTCTA
*
13551 GGGACTATTTCAGTCCATATAG
1 GGGACTACTTCAGTCCATATAG
*
13573 GGGACTGCTTCAGTCCATATA
1 GGGACTACTTCAGTCCATATA
13594 AGCCTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (22 bp):
GGGACTACTTCAGTCCATATAG
Found at i:20024 original size:31 final size:31
Alignment explanation
Indices: 19989--20057 Score: 138
Period size: 31 Copynumber: 2.2 Consensus size: 31
19979 CACTAACGCC
19989 ATCGGTCCGTCCGATTTAAGTACCTAACGTT
1 ATCGGTCCGTCCGATTTAAGTACCTAACGTT
20020 ATCGGTCCGTCCGATTTAAGTACCTAACGTT
1 ATCGGTCCGTCCGATTTAAGTACCTAACGTT
20051 ATCGGTC
1 ATCGGTC
20058 TATTCGATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (31 bp):
ATCGGTCCGTCCGATTTAAGTACCTAACGTT
Found at i:20066 original size:31 final size:31
Alignment explanation
Indices: 19989--20067 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
19979 CACTAACGCC
*
19989 ATCGGTCCGTCCGATTTAAGTACCTAACGTT
1 ATCGGTCCATCCGATTTAAGTACCTAACGTT
*
20020 ATCGGTCCGTCCGATTTAAGTACCTAACGTT
1 ATCGGTCCATCCGATTTAAGTACCTAACGTT
* *
20051 ATCGGTCTATTCGATTT
1 ATCGGTCCATCCGATTT
20068 TAGTCCCTCA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (31 bp):
ATCGGTCCATCCGATTTAAGTACCTAACGTT
Found at i:20562 original size:33 final size:33
Alignment explanation
Indices: 20525--20591 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
20515 GATCAATTAT
*
20525 TAATCGGATGATAAATTCGATTCAAAATTTTAA
1 TAATCGAATGATAAATTCGATTCAAAATTTTAA
*
20558 TAATCGAATGATAAATTCGATTCAAACTTTTAA
1 TAATCGAATGATAAATTCGATTCAAAATTTTAA
20591 T
1 T
20592 GAAAAGTTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.37
Consensus pattern (33 bp):
TAATCGAATGATAAATTCGATTCAAAATTTTAA
Found at i:25594 original size:30 final size:31
Alignment explanation
Indices: 25540--25612 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 31
25530 ATTTTTAAAA
25540 TTTATTTAAAAATTTAAAAAATAAAAATATTT
1 TTTATTTAAAAA-TTAAAAAATAAAAATATTT
* *
25572 TTTA-TTAAAAA-TAAATAAATAAATATA-TA
1 TTTATTTAAAAATTAAA-AAATAAAAATATTT
*
25601 TATATTTAAAAA
1 TTTATTTAAAAA
25613 AAATCCCTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
29 8 0.22
30 17 0.47
31 7 0.19
32 4 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (31 bp):
TTTATTTAAAAATTAAAAAATAAAAATATTT
Found at i:27329 original size:2 final size:2
Alignment explanation
Indices: 27324--27355 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
27314 AATAAAAGTT
27324 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27356 AAGTTACACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:27847 original size:15 final size:15
Alignment explanation
Indices: 27804--27843 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 15
27794 CAACTCTACT
27804 TTATTCATAATATTTAA
1 TTATT-ATAATA-TTAA
27821 TTATTATAATATTAA
1 TTATTATAATATTAA
27836 TT-TTATAA
1 TTATTATAA
27844 ATATAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.26
15 6 0.26
16 6 0.26
17 5 0.22
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
TTATTATAATATTAA
Found at i:28058 original size:15 final size:17
Alignment explanation
Indices: 28022--28058 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
28012 ATTTCAATGT
*
28022 ATTTTATCTATCTTGCA
1 ATTTAATCTATCTTGCA
28039 ATTTAATCTA-CTTG-A
1 ATTTAATCTATCTTGCA
28054 ATTTA
1 ATTTA
28059 TTATATTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 6 0.32
16 4 0.21
17 9 0.47
ACGTcount: A:0.30, C:0.14, G:0.05, T:0.51
Consensus pattern (17 bp):
ATTTAATCTATCTTGCA
Found at i:30198 original size:2 final size:2
Alignment explanation
Indices: 30191--30242 Score: 95
Period size: 2 Copynumber: 25.5 Consensus size: 2
30181 TGTATATGTG
30191 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
30233 AT AT GAT AT A
1 AT AT -AT AT A
30243 CGGGAAACAT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 47 0.96
3 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30479 original size:20 final size:20
Alignment explanation
Indices: 30450--30488 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
30440 GAGGGTTCAT
* *
30450 AGGTCCTTCGGGACATACAG
1 AGGTCATTCGAGACATACAG
30470 AGGTCATTCGAGACATACA
1 AGGTCATTCGAGACATACA
30489 TAGTCCTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.23, G:0.26, T:0.21
Consensus pattern (20 bp):
AGGTCATTCGAGACATACAG
Found at i:51866 original size:12 final size:12
Alignment explanation
Indices: 51849--51873 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
51839 TTTTTAGGAG
51849 GCTAAAGTTTGA
1 GCTAAAGTTTGA
51861 GCTAAAGTTTGA
1 GCTAAAGTTTGA
51873 G
1 G
51874 AATGGCACTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.28, T:0.32
Consensus pattern (12 bp):
GCTAAAGTTTGA
Found at i:52295 original size:2 final size:2
Alignment explanation
Indices: 52290--52336 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
52280 TTTAAATTAT
*
52290 TA TA TA TA TA TA TA TA T- TA TT TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
52331 TA TA TA
1 TA TA TA
52337 GAAAGCCTGT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:52836 original size:23 final size:23
Alignment explanation
Indices: 52805--52865 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
52795 CCAAAAGGAA
* * *
52805 GAGAAAAACGTGTCACAAAAGTT
1 GAGATAAACGTGCCACAAAAGCT
*
52828 GAGATAAACGTGCCACAAATGCT
1 GAGATAAACGTGCCACAAAAGCT
*
52851 GAGATAAACTTGCCA
1 GAGATAAACGTGCCA
52866 TAAAGGCAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.43, C:0.18, G:0.21, T:0.18
Consensus pattern (23 bp):
GAGATAAACGTGCCACAAAAGCT
Found at i:52877 original size:23 final size:23
Alignment explanation
Indices: 52798--52877 Score: 70
Period size: 23 Copynumber: 3.5 Consensus size: 23
52788 TAACTTACCA
* * *
52798 AAAGGAAGAGAAAAACGTGTCAC
1 AAAGGCAGAGATAAACGTGCCAC
* **
52821 AAAAGTTGAGATAAACGTGCCAC
1 AAAGGCAGAGATAAACGTGCCAC
* * * *
52844 AAATGCTGAGATAAACTTGCCAT
1 AAAGGCAGAGATAAACGTGCCAC
52867 AAAGGCAGAGA
1 AAAGGCAGAGA
52878 ACTTGTCACA
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.46, C:0.15, G:0.24, T:0.15
Consensus pattern (23 bp):
AAAGGCAGAGATAAACGTGCCAC
Found at i:55382 original size:26 final size:26
Alignment explanation
Indices: 55342--55420 Score: 97
Period size: 26 Copynumber: 3.0 Consensus size: 26
55332 TTTTAATTGG
*
55342 AATAAAAGAGGTAATAAATATCTTTT
1 AATAAAAGAGATAATAAATATCTTTT
* *
55368 AATAAAAGAGATAATAAATTTATTTT
1 AATAAAAGAGATAATAAATATCTTTT
* *
55394 AATAAAAGAAGA-AGTAAATCTCTTTT
1 AATAAAAG-AGATAATAAATATCTTTT
55420 A
1 A
55421 TCTTTATCCT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
26 43 0.93
27 3 0.07
ACGTcount: A:0.52, C:0.04, G:0.10, T:0.34
Consensus pattern (26 bp):
AATAAAAGAGATAATAAATATCTTTT
Found at i:58175 original size:36 final size:35
Alignment explanation
Indices: 58086--58192 Score: 153
Period size: 36 Copynumber: 3.0 Consensus size: 35
58076 TTTGTTGATA
*
58086 ATGCTCAAATTAGGTTATCCTACTAGTATTAGAAAT
1 ATGCTCAAATTAGGTTATCCCACTAGTATT-GAAAT
* *
58122 ATGCT-AAATTAGTTTATCCCACTAATATTGCAAAT
1 ATGCTCAAATTAGGTTATCCCACTAGTATTG-AAAT
58157 ATGCTCAAATTAGGTTATCCCACTAGTATTGGAAAT
1 ATGCTCAAATTAGGTTATCCCACTAGTATT-GAAAT
58193 GACGATTTTG
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
34 1 0.02
35 30 0.48
36 31 0.49
37 1 0.02
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.36
Consensus pattern (35 bp):
ATGCTCAAATTAGGTTATCCCACTAGTATTGAAAT
Found at i:59632 original size:19 final size:19
Alignment explanation
Indices: 59608--59645 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
59598 ATGCAATAAA
59608 CACTAAACCATGAAAACTG
1 CACTAAACCATGAAAACTG
59627 CACTAAACCATGAAAACTG
1 CACTAAACCATGAAAACTG
59646 TATCAGCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.26, G:0.11, T:0.16
Consensus pattern (19 bp):
CACTAAACCATGAAAACTG
Found at i:64058 original size:11 final size:12
Alignment explanation
Indices: 64033--64057 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
64023 TGTTTTATAC
64033 TTAAACAATTTT
1 TTAAACAATTTT
64045 TTAAACAATTTT
1 TTAAACAATTTT
64057 T
1 T
64058 ACAAAGTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAAACAATTTT
Found at i:64136 original size:20 final size:20
Alignment explanation
Indices: 64107--64144 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
64097 TTTAAGAGTG
64107 ATGCACCGATACACCAATCC
1 ATGCACCGATACACCAATCC
* *
64127 ATGCATCGATGCACCAAT
1 ATGCACCGATACACCAAT
64145 TAATTTTTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.34, G:0.13, T:0.18
Consensus pattern (20 bp):
ATGCACCGATACACCAATCC
Done.