Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003584.1 Hibiscus syriacus cultivar Beakdansim tig00007560_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: 66831
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3167 original size:16 final size:16
Alignment explanation
Indices: 3143--3180 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
3133 CTGCTGCTAT
*
3143 AATCCCAGTGAGTTCA
1 AATCTCAGTGAGTTCA
*
3159 AATCTCAGTGAGTTTA
1 AATCTCAGTGAGTTCA
3175 AATCTC
1 AATCTC
3181 TATGGCCCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.32
Consensus pattern (16 bp):
AATCTCAGTGAGTTCA
Found at i:5804 original size:2 final size:2
Alignment explanation
Indices: 5797--5830 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5787 CAAAAGACTG
5797 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
5831 CATTATTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6971 original size:21 final size:21
Alignment explanation
Indices: 6947--6990 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
6937 CAATTGTCTT
6947 ATTCCCTT-TTCTTCTCTTCTC
1 ATTCCCTTATT-TTCTCTTCTC
*
6968 ATTCTCTTATTTTCTCTTCTC
1 ATTCCCTTATTTTCTCTTCTC
6989 AT
1 AT
6991 CAGTGGCAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.09, C:0.32, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTCCCTTATTTTCTCTTCTC
Found at i:9588 original size:45 final size:46
Alignment explanation
Indices: 9539--9630 Score: 150
Period size: 45 Copynumber: 2.0 Consensus size: 46
9529 TCAAACATCA
* * *
9539 AATGCATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTC
1 AATGCATTTGATGCACCGATGCACAAGACCATGCATCGATGCACTC
9584 AATGCATTTGATGCACCGATGCACAAGACCATGCATCGATGCACTC
1 AATGCATTTGATGCACCGATGCACAAGACCATGCATCGATGCACTC
9630 A
1 A
9631 GGCTTTTTCA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
45 22 0.51
46 21 0.49
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.25
Consensus pattern (46 bp):
AATGCATTTGATGCACCGATGCACAAGACCATGCATCGATGCACTC
Found at i:17147 original size:21 final size:21
Alignment explanation
Indices: 17105--17148 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
17095 ACCCCAGGAG
* *
17105 CTAGTTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
17126 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
17147 CT
1 CT
17149 CCTCCTCCGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.39, G:0.16, T:0.36
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:17504 original size:14 final size:15
Alignment explanation
Indices: 17479--17507 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
17469 TTATTTTTGA
17479 TGTTTCTGGATTGTT
1 TGTTTCTGGATTGTT
17494 TGTTT-TGGATTGTT
1 TGTTTCTGGATTGTT
17508 AATTGCTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.07, C:0.03, G:0.28, T:0.62
Consensus pattern (15 bp):
TGTTTCTGGATTGTT
Found at i:18274 original size:17 final size:19
Alignment explanation
Indices: 18237--18274 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
18227 CATTTTATGT
*
18237 ATCGATGCACATGCCATGC
1 ATCGATGCACATGCAATGC
18256 ATCGATGCAC-T-CAATGC
1 ATCGATGCACATGCAATGC
18273 AT
1 AT
18275 TTTATTCATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 1 0.06
19 10 0.56
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (19 bp):
ATCGATGCACATGCAATGC
Found at i:18285 original size:26 final size:26
Alignment explanation
Indices: 18252--18317 Score: 105
Period size: 26 Copynumber: 2.5 Consensus size: 26
18242 TGCACATGCC
*
18252 ATGCATCGATGCACTCAATGCATTTT
1 ATGCATCGATGCACTCAATGCATTTG
*
18278 ATTCATCGATGCACTCAATGCATTTG
1 ATGCATCGATGCACTCAATGCATTTG
*
18304 ATGCATTGATGCAC
1 ATGCATCGATGCAC
18318 AAGACCATGC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (26 bp):
ATGCATCGATGCACTCAATGCATTTG
Found at i:23410 original size:12 final size:12
Alignment explanation
Indices: 23390--23483 Score: 59
Period size: 12 Copynumber: 7.8 Consensus size: 12
23380 GATACATTAC
*
23390 CTGAATTCTGTT
1 CTGATTTCTGTT
*
23402 CTGATTTCTGAT
1 CTGATTTCTGTT
23414 CTGGA-TTCTGTT
1 CT-GATTTCTGTT
* *
23426 CTTATATCT-TAT
1 CTGATTTCTGT-T
23438 CTGGA-TTCTGTT
1 CT-GATTTCTGTT
* * *
23450 ATGATATCTGAT
1 CTGATTTCTGTT
*
23462 CTGAATTCTGTT
1 CTGATTTCTGTT
*
23474 TTGATTTCTG
1 CTGATTTCTG
23484 ATATCTCCGT
Statistics
Matches: 60, Mismatches: 16, Indels: 12
0.68 0.18 0.14
Matches are distributed among these distances:
11 4 0.07
12 52 0.87
13 4 0.07
ACGTcount: A:0.17, C:0.15, G:0.17, T:0.51
Consensus pattern (12 bp):
CTGATTTCTGTT
Found at i:23421 original size:24 final size:24
Alignment explanation
Indices: 23394--23485 Score: 121
Period size: 24 Copynumber: 3.8 Consensus size: 24
23384 CATTACCTGA
*
23394 ATTCTGTTCTGATTTCTGATCTGG
1 ATTCTGTTCTGATATCTGATCTGG
* *
23418 ATTCTGTTCTTATATCTTATCTGG
1 ATTCTGTTCTGATATCTGATCTGG
* *
23442 ATTCTGTTATGATATCTGATCTGA
1 ATTCTGTTCTGATATCTGATCTGG
* *
23466 ATTCTGTTTTGATTTCTGAT
1 ATTCTGTTCTGATATCTGAT
23486 ATCTCCGTTT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.17, C:0.14, G:0.16, T:0.52
Consensus pattern (24 bp):
ATTCTGTTCTGATATCTGATCTGG
Found at i:25621 original size:18 final size:18
Alignment explanation
Indices: 25571--25621 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
25561 CCCGTTTACC
* *
25571 CGACACGTTGACCCAACT
1 CGACCCGTTGACCCGACT
*
25589 CAACCCGTTGACCCGACT
1 CGACCCGTTGACCCGACT
25607 CGACCCGTTGACCCG
1 CGACCCGTTGACCCG
25622 TTGACCACTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.22, C:0.43, G:0.20, T:0.16
Consensus pattern (18 bp):
CGACCCGTTGACCCGACT
Found at i:28656 original size:20 final size:22
Alignment explanation
Indices: 28617--28656 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
28607 TTTAATTAAG
*
28617 TTTTACAATATATGATTATGCA
1 TTTTACAATATATAATTATGCA
28639 TTTT-CAATAT-TAATTATG
1 TTTTACAATATATAATTATG
28657 TATAATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 6 0.35
22 4 0.24
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.50
Consensus pattern (22 bp):
TTTTACAATATATAATTATGCA
Found at i:29331 original size:20 final size:19
Alignment explanation
Indices: 29280--29332 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
29270 GTTCAAAGAG
29280 AAATTAAAA-TAAATTAAA
1 AAATTAAAATTAAATTAAA
* * *
29298 AAATTTATATTTAAATTACA
1 AAA-TTAAAATTAAATTAAA
29318 AAATTAAAAATTAAA
1 AAATT-AAAATTAAA
29333 ATAGTGTTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
18 3 0.11
19 6 0.22
20 18 0.67
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (19 bp):
AAATTAAAATTAAATTAAA
Found at i:31930 original size:35 final size:35
Alignment explanation
Indices: 31881--31961 Score: 108
Period size: 35 Copynumber: 2.3 Consensus size: 35
31871 AACACATTCA
* **
31881 TCAATTTACATTCTAAACCCCAAATTCCAAAATGTT
1 TCAA-TTATATTCTAAACCCCAAATTCCAAAATACT
* *
31917 TCAATTATATTCTAAACCTCAAATTCCAAGATACT
1 TCAATTATATTCTAAACCCCAAATTCCAAAATACT
31952 TCAATTATAT
1 TCAATTATAT
31962 GCCCAACCCC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
35 36 0.90
36 4 0.10
ACGTcount: A:0.40, C:0.22, G:0.02, T:0.36
Consensus pattern (35 bp):
TCAATTATATTCTAAACCCCAAATTCCAAAATACT
Found at i:34825 original size:12 final size:12
Alignment explanation
Indices: 34808--34843 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
34798 TTGGAATAGA
34808 AGGAGGATTTGG
1 AGGAGGATTTGG
*
34820 ATGAGGATTTGG
1 AGGAGGATTTGG
*
34832 AGGTGGATTTGG
1 AGGAGGATTTGG
34844 TTGACGACTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.22, C:0.00, G:0.47, T:0.31
Consensus pattern (12 bp):
AGGAGGATTTGG
Found at i:42495 original size:35 final size:35
Alignment explanation
Indices: 42456--42530 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
42446 GTTGGGCATA
* *
42456 TAATTAAAGTATTTTAG-AATTTGATATTTAGAATG
1 TAATTAAAGCATTTT-GTAATTTGAGATTTAGAATG
* * *
42491 TAATTGAAGCATTTTGTAATTTGGGGTTTAGAATG
1 TAATTAAAGCATTTTGTAATTTGAGATTTAGAATG
42526 TAATT
1 TAATT
42531 GATGATCGTG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 1 0.03
35 33 0.97
ACGTcount: A:0.35, C:0.01, G:0.19, T:0.45
Consensus pattern (35 bp):
TAATTAAAGCATTTTGTAATTTGAGATTTAGAATG
Found at i:47461 original size:3 final size:3
Alignment explanation
Indices: 47453--47480 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
47443 ACCAAAATGT
47453 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
47481 ACGCAGAGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:61865 original size:26 final size:25
Alignment explanation
Indices: 61836--61916 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 25
61826 TTAATTTAAA
61836 CTAAACTACTTAGTAGTTATCCTTAT
1 CTAAACTACTTAGTAGTTAT-CTTAT
* * *
61862 CT-AACTTTCTAAG-AGTTAAT-TTAAA
1 CTAAAC-TACTTAGTAGTT-ATCTT-AT
61887 CTAAACTACTTAGTAGTTATCTTTAT
1 CTAAACTACTTAGTAGTTATC-TTAT
61913 CTAA
1 CTAA
61917 CTTTCTAAGA
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
24 2 0.05
25 17 0.40
26 21 0.50
27 2 0.05
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.42
Consensus pattern (25 bp):
CTAAACTACTTAGTAGTTATCTTAT
Found at i:61878 original size:25 final size:24
Alignment explanation
Indices: 61850--61930 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 24
61840 ACTACTTAGT
61850 AGTTATCCTTATCTAACTTTCTAAG
1 AGTTAT-CTTATCTAACTTTCTAAG
* * *
61875 AGTTAAT-TTAAACTAAAC-TACTTAG
1 AGTT-ATCTT-ATCT-AACTTTCTAAG
61900 TAGTTATCTTTATCTAACTTTCTAAG
1 -AGTTATC-TTATCTAACTTTCTAAG
61926 AGTTA
1 AGTTA
61931 GTGTTATATT
Statistics
Matches: 43, Mismatches: 6, Indels: 14
0.68 0.10 0.22
Matches are distributed among these distances:
24 2 0.05
25 22 0.51
26 17 0.40
27 2 0.05
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (24 bp):
AGTTATCTTATCTAACTTTCTAAG
Found at i:61902 original size:51 final size:51
Alignment explanation
Indices: 61826--61967 Score: 203
Period size: 51 Copynumber: 2.8 Consensus size: 51
61816 GAATAAGTAT
61826 TTAATTTAAACTAAACTACTTAGTAGTTATCCTTATCTAACTTTCTAAGAG
1 TTAATTTAAACTAAACTACTTAGTAGTTATCCTTATCTAACTTTCTAAGAG
*
61877 TTAATTTAAACTAAACTACTTAGTAGTTATCTTTATCTAACTTTCTAAGAG
1 TTAATTTAAACTAAACTACTTAGTAGTTATCCTTATCTAACTTTCTAAGAG
* * * * * * *
61928 TTAGTGTTATATTAAAATACTAATTAATTATCCTTATCTA
1 TTAAT-TTAAACTAAACTACTTAGTAGTTATCCTTATCTA
61968 TCGCATAACC
Statistics
Matches: 81, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
51 54 0.67
52 27 0.33
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.44
Consensus pattern (51 bp):
TTAATTTAAACTAAACTACTTAGTAGTTATCCTTATCTAACTTTCTAAGAG
Found at i:66131 original size:48 final size:48
Alignment explanation
Indices: 66058--66153 Score: 158
Period size: 48 Copynumber: 2.0 Consensus size: 48
66048 GAACAAGTAT
66058 TTAATTTAAACTAACTACTTAGTAGTTATCCTTAT-AACTTTCTAAGA
1 TTAATTTAAACTAACTACTTAGTAGTTATCCTTATCAACTTTCTAAGA
* *
66105 TTAATTTAAACTAAACTACTTAGTAGTTATCTTTATCTACTTTCTAAGA
1 TTAATTTAAACT-AACTACTTAGTAGTTATCCTTATCAACTTTCTAAGA
66154 GTTAGTGTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
47 12 0.27
48 22 0.49
49 11 0.24
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (48 bp):
TTAATTTAAACTAACTACTTAGTAGTTATCCTTATCAACTTTCTAAGA
Found at i:66193 original size:51 final size:49
Alignment explanation
Indices: 66058--66194 Score: 134
Period size: 51 Copynumber: 2.8 Consensus size: 49
66048 GAACAAGTAT
* * * *
66058 TTAATTTAAACT-AACTACTTAGTAGTTATCCTTAT-AACTTTCTAAGA
1 TTAATTTAAACTAAAATACTAAGTAATTATCCTTATCTACTTTCTAAGA
* * * *
66105 TTAATTTAAACTAAACTACTTAGTAGTTATCTTTATCTACTTTCTAAGA
1 TTAATTTAAACTAAAATACTAAGTAATTATCCTTATCTACTTTCTAAGA
* * * *
66154 GTTAGTGTTATATTAAAATACTAATTAATTATCCTTATCTA
1 -TTAAT-TTAAACTAAAATACTAAGTAATTATCCTTATCTA
66195 TCGGTAACCT
Statistics
Matches: 76, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
47 12 0.16
48 22 0.29
49 11 0.14
50 4 0.05
51 27 0.36
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.45
Consensus pattern (49 bp):
TTAATTTAAACTAAAATACTAAGTAATTATCCTTATCTACTTTCTAAGA
Done.