Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006399.1 Hibiscus syriacus cultivar Beakdansim tig00015422_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: 58845
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1804 original size:28 final size:28
Alignment explanation
Indices: 1772--1826 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
1762 GATATTATTG
1772 CATAAAGCATGCAAGACAGTTATGGAAT
1 CATAAAGCATGCAAGACAGTTATGGAAT
**
1800 CATAAAGCATGCAAGATGGTTATGGAA
1 CATAAAGCATGCAAGACAGTTATGGAA
1827 ACAAAGTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.22
Consensus pattern (28 bp):
CATAAAGCATGCAAGACAGTTATGGAAT
Found at i:13658 original size:37 final size:41
Alignment explanation
Indices: 13612--13701 Score: 109
Period size: 43 Copynumber: 2.2 Consensus size: 41
13602 TTGAAAGAAT
13612 ATAAAATAA-T-AAGATATTTT-AC-TATTAAA-ATATAAGA
1 ATAAAATAAGTAAAGATATTTTAACTTATTAAATA-ATAAGA
*
13649 ATAAAATAATAGTAAATATATTTTAACTTATTAAATAATAAGA
1 ATAAAAT-A-AGTAAAGATATTTTAACTTATTAAATAATAAGA
13692 ATAAAATAAG
1 ATAAAATAAG
13702 ATACAATATA
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
37 7 0.16
38 1 0.02
39 1 0.02
40 1 0.02
41 11 0.24
42 3 0.07
43 20 0.44
44 1 0.02
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34
Consensus pattern (41 bp):
ATAAAATAAGTAAAGATATTTTAACTTATTAAATAATAAGA
Found at i:13690 original size:43 final size:41
Alignment explanation
Indices: 13625--13747 Score: 134
Period size: 43 Copynumber: 3.0 Consensus size: 41
13615 AAATAATAAG
*
13625 ATATTTTACTATTAAAATATAAGAATAAAATAATAGTA-AAT
1 ATATTTTACTATTAAAATATAAGAATAAAATAAGA-TACAAT
13666 ATATTTTAACTTATT-AAATAATAAGAATAAAATAAGATACAAT
1 ATATTTT-AC-TATTAAAAT-ATAAGAATAAAATAAGATACAAT
13709 ATA-TTTAC--TTAAAAGT-TAAG-ATAATAATAAGATACAAT
1 ATATTTTACTATTAAAA-TATAAGAATAA-AATAAGATACAAT
13747 A
1 A
13748 AATATATTTT
Statistics
Matches: 74, Mismatches: 1, Indels: 17
0.80 0.01 0.18
Matches are distributed among these distances:
37 4 0.05
38 20 0.27
39 3 0.04
40 1 0.01
41 9 0.12
42 11 0.15
43 26 0.35
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.35
Consensus pattern (41 bp):
ATATTTTACTATTAAAATATAAGAATAAAATAAGATACAAT
Found at i:14301 original size:14 final size:14
Alignment explanation
Indices: 14282--14308 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
14272 TGCAACCACT
14282 TTGATTTTATTGGG
1 TTGATTTTATTGGG
14296 TTGATTTTATTGG
1 TTGATTTTATTGG
14309 TGAAAAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.26, T:0.59
Consensus pattern (14 bp):
TTGATTTTATTGGG
Found at i:20090 original size:2 final size:2
Alignment explanation
Indices: 20051--20077 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20041 AGATATATTC
20051 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 A
20078 CACTCTCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24022 original size:60 final size:58
Alignment explanation
Indices: 23944--24126 Score: 158
Period size: 60 Copynumber: 3.1 Consensus size: 58
23934 ATCCTCAAAT
* * * * * *
23944 TATGACCTTCATTTTAAATTGGTCTATAAATTTTTTAATA-TTCAAAATTT-ATCTCTAAAC
1 TATGA-CTTCATTCTAAATTGGTCT-CAAACTTTTAAACATTTC--AATTTCATCCCTAAAC
*
24004 TATGACTATCATTCTAAATTAGTCCTCAAACTTTTAAACATTTCAATTTCATCCCTAAAC
1 TATGACT-TCATTCTAAATTGGT-CTCAAACTTTTAAACATTTCAATTTCATCCCTAAAC
* * *
24064 TATAACTTTCATTCTAAATTGGTCCCCAAACTTTTTGAACA-TTCTAATTTCATCCC-AAAC
1 TATGAC-TTCATTCTAAATTGGT-CTCAAAC-TTTTAAACATTTC-AATTTCATCCCTAAAC
24124 TAT
1 TAT
24127 ATGTATATAC
Statistics
Matches: 105, Mismatches: 11, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
59 7 0.07
60 73 0.70
61 25 0.24
ACGTcount: A:0.34, C:0.20, G:0.04, T:0.42
Consensus pattern (58 bp):
TATGACTTCATTCTAAATTGGTCTCAAACTTTTAAACATTTCAATTTCATCCCTAAAC
Found at i:24127 original size:60 final size:60
Alignment explanation
Indices: 23989--24127 Score: 185
Period size: 60 Copynumber: 2.3 Consensus size: 60
23979 TAATATTCAA
* * *
23989 AATTT-ATCTCTAAACTATGACTATCATTCTAAATTAGTCCTCAAACTTTTAAACATTTC
1 AATTTCATCCCTAAACTATAACTATCATTCTAAATTAGTCCCCAAACTTTTAAACATTTC
* * *
24048 AATTTCATCCCTAAACTATAACTTTCATTCTAAATTGGTCCCCAAACTTTTTGAACA-TTC
1 AATTTCATCCCTAAACTATAACTATCATTCTAAATTAGTCCCCAAAC-TTTTAAACATTTC
24108 TAATTTCATCCC-AAACTATA
1 -AATTTCATCCCTAAACTATA
24128 TGTATATACA
Statistics
Matches: 71, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
59 5 0.07
60 47 0.66
61 19 0.27
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.39
Consensus pattern (60 bp):
AATTTCATCCCTAAACTATAACTATCATTCTAAATTAGTCCCCAAACTTTTAAACATTTC
Found at i:24353 original size:60 final size:60
Alignment explanation
Indices: 24256--24412 Score: 199
Period size: 60 Copynumber: 2.6 Consensus size: 60
24246 AATTTGGGGG
* * * * *
24256 TGAAATTAGAATATTCAAAAGTTTAAAGATTAGTTTAGAAAGAGGGTCATGGTTT-AGGGA
1 TGAAATTAGAATATTCAAAAGTTTAAAGACTAATTTAGAAAGAGAGTCATAGTTTGA-AGA
* * *
24316 TGAAATTAGAATGTTCAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTTTGAAGA
1 TGAAATTAGAATATTCAAAAGTTTAAAGACTAATTTAGAAAGAGAGTCATAGTTTGAAGA
* * *
24376 TGAAATTAGAATATTTAAAAGTTTAATGACCAATTTA
1 TGAAATTAGAATATTCAAAAGTTTAAAGACTAATTTA
24413 AAATAAAAAT
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
60 83 0.99
61 1 0.01
ACGTcount: A:0.42, C:0.04, G:0.20, T:0.33
Consensus pattern (60 bp):
TGAAATTAGAATATTCAAAAGTTTAAAGACTAATTTAGAAAGAGAGTCATAGTTTGAAGA
Found at i:24674 original size:10 final size:10
Alignment explanation
Indices: 24659--24710 Score: 95
Period size: 10 Copynumber: 5.2 Consensus size: 10
24649 ACACCAACAG
24659 TACCATATCA
1 TACCATATCA
24669 TACCATATCA
1 TACCATATCA
24679 TACCATATCA
1 TACCATATCA
24689 TACCATATCA
1 TACCATATCA
*
24699 TACCATACCA
1 TACCATATCA
24709 TA
1 TA
24711 TTAATCTTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
10 41 1.00
ACGTcount: A:0.40, C:0.31, G:0.00, T:0.29
Consensus pattern (10 bp):
TACCATATCA
Found at i:24675 original size:5 final size:5
Alignment explanation
Indices: 24659--24710 Score: 68
Period size: 5 Copynumber: 10.4 Consensus size: 5
24649 ACACCAACAG
* * * *
24659 TACCA TATCA TACCA TATCA TACCA TATCA TACCA TATCA TACCA TACCA
1 TACCA TACCA TACCA TACCA TACCA TACCA TACCA TACCA TACCA TACCA
24709 TA
1 TA
24711 TTAATCTTAT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.40, C:0.31, G:0.00, T:0.29
Consensus pattern (5 bp):
TACCA
Found at i:33383 original size:24 final size:24
Alignment explanation
Indices: 33356--33427 Score: 101
Period size: 24 Copynumber: 3.0 Consensus size: 24
33346 AAACGAAGAT
33356 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* *
33380 ATCA-AATATCAAAACATAATCCAG
1 ATCAGAA-ATCAAAACAGAATTCAG
*
33404 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
33428 GTAATGTATC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
23 2 0.05
24 37 0.90
25 2 0.05
ACGTcount: A:0.53, C:0.18, G:0.11, T:0.18
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:33460 original size:48 final size:48
Alignment explanation
Indices: 33356--33464 Score: 123
Period size: 48 Copynumber: 2.3 Consensus size: 48
33346 AAACGAAGAT
* * *
33356 ATCAGAAATCAAAACAGAATTCAGATCAAATATCAAAACATAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAAATATCAAAACAGAATCAAG
* * *
33404 ATCAGAAATCAGAACAGAATTCAGGT-AATGTATCATAACAGAATTCAAG
1 ATCAGAAATCAGAACAGAATTCAGATCAA-ATATCAAAACAGAA-TCAAG
*
33453 -TCGGAAATCAGA
1 ATCAGAAATCAGA
33465 TAAAATATTT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
47 2 0.04
48 46 0.88
49 4 0.08
ACGTcount: A:0.50, C:0.17, G:0.14, T:0.20
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAAATATCAAAACAGAATCAAG
Found at i:35080 original size:31 final size:31
Alignment explanation
Indices: 35042--35197 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
35032 CCCGAAGGAC
* * *
35042 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
35073 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
35104 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
35135 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
35166 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
35197 C
1 C
35198 CCTCGACCCT
Statistics
Matches: 117, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
31 116 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:36092 original size:21 final size:21
Alignment explanation
Indices: 36066--36111 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
36056 AATTCTGTCG
* *
36066 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
36087 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
36108 CTTG
1 CTTG
36112 CCCAGAACTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:39299 original size:31 final size:31
Alignment explanation
Indices: 39261--39416 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
39251 CCCGAAGGAC
* * *
39261 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
39292 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
39323 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
39354 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
39385 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
39416 C
1 C
39417 CCTCGACCCT
Statistics
Matches: 117, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
31 116 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:40310 original size:21 final size:21
Alignment explanation
Indices: 40284--40329 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
40274 AATTCTGTCG
* *
40284 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
40305 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
40326 CTTG
1 CTTG
40330 CCCAGAACTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:46935 original size:29 final size:29
Alignment explanation
Indices: 46877--46937 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
46867 GAGAGTCAAA
* * *
46877 TTATAATTTTATATAAATTAATATCTATT
1 TTATAATTTTAAAAAAATTAAAATCTATT
*
46906 TTATCATTTTAAAAAAATTAAAAATC-ATT
1 TTATAATTTTAAAAAAATT-AAAATCTATT
46935 TTA
1 TTA
46938 GCATATAGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (29 bp):
TTATAATTTTAAAAAAATTAAAATCTATT
Found at i:50955 original size:12 final size:12
Alignment explanation
Indices: 50920--50958 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
50910 AAAGTGATTG
*
50920 TGATGAGTTTGG
1 TGATGAGTTTGA
50932 TGATGAGTTTGA
1 TGATGAGTTTGA
*
50944 TGATGGGTTTGA
1 TGATGAGTTTGA
50956 TGA
1 TGA
50959 AGGGGGGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.21, C:0.00, G:0.38, T:0.41
Consensus pattern (12 bp):
TGATGAGTTTGA
Found at i:56663 original size:72 final size:72
Alignment explanation
Indices: 56546--56682 Score: 247
Period size: 72 Copynumber: 1.9 Consensus size: 72
56536 CGTAATCTCA
* *
56546 GCTTAATTTAGATAGGATTTCTCTGCTTTAAACTCTTAGGTAGCAGAAACCTTAAATTTGACCAT
1 GCTTAATTTAGATAGAATTTCTCTGCTTGAAACTCTTAGGTAGCAGAAACCTTAAATTTGACCAT
56611 TATTTAT
66 TATTTAT
*
56618 GCTTAATTTAGATAGAATTTCTCTTCTTGAAACTCTTAGGTAGCAGAAACCTTAAATTTGACCAT
1 GCTTAATTTAGATAGAATTTCTCTGCTTGAAACTCTTAGGTAGCAGAAACCTTAAATTTGACCAT
56683 CTTTTGGTCA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 62 1.00
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (72 bp):
GCTTAATTTAGATAGAATTTCTCTGCTTGAAACTCTTAGGTAGCAGAAACCTTAAATTTGACCAT
TATTTAT
Found at i:58728 original size:16 final size:16
Alignment explanation
Indices: 58709--58740 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
58699 TGCCTTGGTT
58709 ATCTTATTACCTTTTC
1 ATCTTATTACCTTTTC
58725 ATCTTATTACCTTTTC
1 ATCTTATTACCTTTTC
58741 TTTCTCTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.25, G:0.00, T:0.56
Consensus pattern (16 bp):
ATCTTATTACCTTTTC
Done.