Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004165.1 Hibiscus syriacus cultivar Beakdansim tig00009107_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: 72971
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:5134 original size:21 final size:21
Alignment explanation
Indices: 5083--5135 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
5073 GATGGATTGC
5083 CACGTCAGCATTATGGACCGT
1 CACGTCAGCATTATGGACCGT
* * * *
5104 CACATTAGCATTGTGGATCGT
1 CACGTCAGCATTATGGACCGT
5125 CACGTCAGCAT
1 CACGTCAGCAT
5136 CGTGAATTGA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (21 bp):
CACGTCAGCATTATGGACCGT
Found at i:8502 original size:36 final size:36
Alignment explanation
Indices: 8448--8536 Score: 151
Period size: 36 Copynumber: 2.5 Consensus size: 36
8438 TTGGTCAACC
* * *
8448 TCAAGCTATGTCCGCTGGTATGACTTCCCTTTCGCA
1 TCAATCTATGCCCACTGGTATGACTTCCCTTTCGCA
8484 TCAATCTATGCCCACTGGTATGACTTCCCTTTCGCA
1 TCAATCTATGCCCACTGGTATGACTTCCCTTTCGCA
8520 TCAATCTATGCCCACTG
1 TCAATCTATGCCCACTG
8537 CTGCAACTGG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.19, C:0.33, G:0.16, T:0.33
Consensus pattern (36 bp):
TCAATCTATGCCCACTGGTATGACTTCCCTTTCGCA
Found at i:9920 original size:46 final size:46
Alignment explanation
Indices: 9862--9953 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
9852 TTTGAAATAT
*
9862 TTCCTTGGTCGGTCCTGCTGGAATGCAGACCATTGTTATTCTGGTA
1 TTCCATGGTCGGTCCTGCTGGAATGCAGACCATTGTTATTCTGGTA
9908 TTCCATGGTCGGTCCTGCTGGAATGCAGACCATTGTTATTCTGGTA
1 TTCCATGGTCGGTCCTGCTGGAATGCAGACCATTGTTATTCTGGTA
9954 AACATGTTTA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.16, C:0.22, G:0.26, T:0.36
Consensus pattern (46 bp):
TTCCATGGTCGGTCCTGCTGGAATGCAGACCATTGTTATTCTGGTA
Found at i:10343 original size:18 final size:18
Alignment explanation
Indices: 10316--10368 Score: 97
Period size: 18 Copynumber: 2.9 Consensus size: 18
10306 CGGACAGCAG
*
10316 CCAGGAATGGGTGCCCAA
1 CCAGGGATGGGTGCCCAA
10334 CCAGGGATGGGTGCCCAA
1 CCAGGGATGGGTGCCCAA
10352 CCAGGGATGGGTGCCCA
1 CCAGGGATGGGTGCCCA
10369 GCCGATTACT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.23, C:0.28, G:0.38, T:0.11
Consensus pattern (18 bp):
CCAGGGATGGGTGCCCAA
Found at i:10600 original size:6 final size:6
Alignment explanation
Indices: 10589--10743 Score: 268
Period size: 6 Copynumber: 26.8 Consensus size: 6
10579 TGCTCAAATA
10589 CTCACT CTCACT CTCA-- CTCACT CTCACT CTCACT CTCACT CTCACT
1 CTCACT CTCACT CTCACT CTCACT CTCACT CTCACT CTCACT CTCACT
10635 CTCACT CTCACT CTCACT CTCA-- CTCACT CTCACT CTCACT CTCACT
1 CTCACT CTCACT CTCACT CTCACT CTCACT CTCACT CTCACT CTCACT
10681 CTCACT CTCACT CTCACT CTCACT CTCACT CTCA-- CTCACT CTCACT
1 CTCACT CTCACT CTCACT CTCACT CTCACT CTCACT CTCACT CTCACT
10727 CTCACT CTCACT CTCAC
1 CTCACT CTCACT CTCAC
10744 ACACACACAC
Statistics
Matches: 143, Mismatches: 0, Indels: 12
0.92 0.00 0.08
Matches are distributed among these distances:
4 12 0.08
6 131 0.92
ACGTcount: A:0.17, C:0.50, G:0.00, T:0.32
Consensus pattern (6 bp):
CTCACT
Found at i:10667 original size:52 final size:52
Alignment explanation
Indices: 10589--10743 Score: 292
Period size: 52 Copynumber: 3.0 Consensus size: 52
10579 TGCTCAAATA
10589 CTCACTCTCACTCTCACTCACTCTCACTCTCACTCTCACTCTCACTCTCACT
1 CTCACTCTCACTCTCACTCACTCTCACTCTCACTCTCACTCTCACTCTCACT
10641 CTCACTCTCACTCTCACTCACTCTCACTCTCACTCTCACTCTCACTCTCACT
1 CTCACTCTCACTCTCACTCACTCTCACTCTCACTCTCACTCTCACTCTCACT
* *
10693 CTCACTCTCACTCTCACTCTCACTCACTCTCACTCTCACTCTCACTCTCAC
1 CTCACTCTCACTCTCACTCACTCTCACTCTCACTCTCACTCTCACTCTCAC
10744 ACACACACAC
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 101 1.00
ACGTcount: A:0.17, C:0.50, G:0.00, T:0.32
Consensus pattern (52 bp):
CTCACTCTCACTCTCACTCACTCTCACTCTCACTCTCACTCTCACTCTCACT
Found at i:10760 original size:22 final size:22
Alignment explanation
Indices: 10735--10776 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
10725 CTCTCACTCT
*
10735 CACTCTCACACACACACACAAA
1 CACTCGCACACACACACACAAA
* *
10757 CACTGGCACATACACACACA
1 CACTCGCACACACACACACA
10777 TGTGGGCATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.43, G:0.05, T:0.10
Consensus pattern (22 bp):
CACTCGCACACACACACACAAA
Found at i:24825 original size:12 final size:13
Alignment explanation
Indices: 24798--24826 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
24788 TTATTTAAAT
24798 AATAAAATCGAAA
1 AATAAAATCGAAA
24811 AATAAAATC-AAA
1 AATAAAATCGAAA
24823 AATA
1 AATA
24827 TTATTAAACG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.72, C:0.07, G:0.03, T:0.17
Consensus pattern (13 bp):
AATAAAATCGAAA
Found at i:26603 original size:15 final size:16
Alignment explanation
Indices: 26571--26602 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
26561 TTCAAACTTG
*
26571 ACTCGAACTCAAAAAA
1 ACTCAAACTCAAAAAA
26587 ACTCAAACTCAAAAAA
1 ACTCAAACTCAAAAAA
26603 CAATATCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.25, G:0.03, T:0.12
Consensus pattern (16 bp):
ACTCAAACTCAAAAAA
Found at i:37580 original size:31 final size:31
Alignment explanation
Indices: 37544--37668 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
37534 CCCAAAGGAT
* * *
37544 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
37575 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
37606 CAGTCCATATGTCCCAAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
37637 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
37668 C
1 C
37669 CCTCGACCCT
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:39434 original size:13 final size:13
Alignment explanation
Indices: 39401--39445 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
39391 GTCATAACCC
39401 GACCCGACCCGTT
1 GACCCGACCCGTT
* * *
39414 TACTCGACCTGTT
1 GACCCGACCCGTT
39427 GACCCGACCCGTT
1 GACCCGACCCGTT
39440 GACCCG
1 GACCCG
39446 TTGACCGTTG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.16, C:0.42, G:0.22, T:0.20
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:39455 original size:15 final size:17
Alignment explanation
Indices: 39435--39468 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
39425 TTGACCCGAC
39435 CCGTTGACC-C-GTTGA
1 CCGTTGACCGCTGTTGA
39450 CCGTTGACCGCTGTTGA
1 CCGTTGACCGCTGTTGA
39467 CC
1 CC
39469 AAAACTTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 1 0.06
17 7 0.41
ACGTcount: A:0.12, C:0.35, G:0.26, T:0.26
Consensus pattern (17 bp):
CCGTTGACCGCTGTTGA
Found at i:41917 original size:12 final size:12
Alignment explanation
Indices: 41902--41970 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
41892 GATACATTAC
41902 CTGAATTCTGTT
1 CTGAATTCTGTT
*
41914 CTG-ATTCTGAT
1 CTGAATTCTGTT
* *
41925 CTGGATTCTATT
1 CTGAATTCTGTT
*
41937 CTG-ATATCTGAT
1 CTGAAT-TCTGTT
*
41949 ATGAATTCTGTT
1 CTGAATTCTGTT
* *
41961 TTGATTTCTG
1 CTGAATTCTG
41971 ATATCTCCGT
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
11 12 0.27
12 31 0.69
13 2 0.04
ACGTcount: A:0.19, C:0.14, G:0.17, T:0.49
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:41956 original size:24 final size:23
Alignment explanation
Indices: 41879--41974 Score: 93
Period size: 24 Copynumber: 4.0 Consensus size: 23
41869 ATTTCCAAAT
* * **
41879 TGAATTCTGTTCTGATACATTACC
1 TGAATTCTGTTCTGATTC-TGATA
*
41903 TGAATTCTGTTCTGATTCTGATC
1 TGAATTCTGTTCTGATTCTGATA
* *
41926 TGGATTCTATTCTGATATCTGATA
1 TGAATTCTGTTCTGAT-TCTGATA
*
41950 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTCTGA-TTCTGATA
41974 T
1 T
41975 CTCCGTTTAC
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
23 17 0.28
24 43 0.70
25 1 0.02
ACGTcount: A:0.22, C:0.15, G:0.16, T:0.48
Consensus pattern (23 bp):
TGAATTCTGTTCTGATTCTGATA
Found at i:44080 original size:13 final size:13
Alignment explanation
Indices: 44062--44104 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
44052 ACCGGTCATA
*
44062 ACCCGACCCGTTT
1 ACCCGACCCGTTG
*
44075 ACCCGACCTGTTG
1 ACCCGACCCGTTG
44088 ACCCGACCCG-TG
1 ACCCGACCCGTTG
44100 ACCCG
1 ACCCG
44105 TTGACCGTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 7 0.26
13 20 0.74
ACGTcount: A:0.16, C:0.47, G:0.21, T:0.16
Consensus pattern (13 bp):
ACCCGACCCGTTG
Found at i:46618 original size:24 final size:23
Alignment explanation
Indices: 46563--46632 Score: 77
Period size: 24 Copynumber: 3.0 Consensus size: 23
46553 ACGTTACCTT
* *
46563 AATTTTGTTCTGATTCTGATCTG
1 AATTATGTTCTGATTCTGATATG
* *
46586 GATTCTGTTCTGATATCTGATATG
1 AATTATGTTCTGAT-TCTGATATG
*
46610 AATTATGTTTTGATTTCTGATAT
1 AATTATGTTCTGA-TTCTGATAT
46633 CTCCGTTTAC
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
23 12 0.31
24 26 0.67
25 1 0.03
ACGTcount: A:0.21, C:0.10, G:0.17, T:0.51
Consensus pattern (23 bp):
AATTATGTTCTGATTCTGATATG
Found at i:50898 original size:23 final size:25
Alignment explanation
Indices: 50872--50922 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 25
50862 AAACGTTAAG
50872 TATAAT-TTAAAAA-A-AATAAAAAT
1 TATAATATTAAAAAGACAA-AAAAAT
50895 TAT-ATATTAAAAAGACAAAAAAAT
1 TATAATATTAAAAAGACAAAAAAAT
50919 TATA
1 TATA
50923 GTGTATGTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
22 2 0.08
23 10 0.42
24 10 0.42
25 2 0.08
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (25 bp):
TATAATATTAAAAAGACAAAAAAAT
Found at i:57924 original size:37 final size:36
Alignment explanation
Indices: 57849--57924 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
57839 TTTTTATATT
*
57849 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
57885 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
57922 TTT
1 TTT
57925 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:57949 original size:18 final size:18
Alignment explanation
Indices: 57901--57949 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
57891 TTTTTAAAGA
*
57901 AAATATATAAATATTTTAC
1 AAATATAT-AATATTATAC
* *
57920 -AATTTGTAATATTATAC
1 AAATATATAATATTATAC
57937 AAATATATAATAT
1 AAATATATAATAT
57950 GGACAATTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
AAATATATAATATTATAC
Found at i:58770 original size:27 final size:26
Alignment explanation
Indices: 58727--58777 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
58717 AAATTTATGT
*
58727 TTTTTTAAAAAATATATATAATTTTA
1 TTTTTTAAAAAATATATAAAATTTTA
**
58753 TTTTTTAAAATTTAATATAAAATTT
1 TTTTTTAAAAAAT-ATATAAAATTT
58778 AAAAATTACC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 11 0.52
27 10 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
TTTTTTAAAAAATATATAAAATTTTA
Found at i:67324 original size:39 final size:39
Alignment explanation
Indices: 67275--67358 Score: 141
Period size: 39 Copynumber: 2.2 Consensus size: 39
67265 AAAGAGAAAA
* *
67275 AGGTGTTTGGGTGAGTTTGAGGTTGTTCCTACAACTACT
1 AGGTGCTTGGGTGAGCTTGAGGTTGTTCCTACAACTACT
*
67314 AGGTGCTTGGGTGAGCTTGAGGTTGTTCCTACAACTATT
1 AGGTGCTTGGGTGAGCTTGAGGTTGTTCCTACAACTACT
67353 AGGTGC
1 AGGTGC
67359 AAGGTAACAC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.18, C:0.14, G:0.32, T:0.36
Consensus pattern (39 bp):
AGGTGCTTGGGTGAGCTTGAGGTTGTTCCTACAACTACT
Found at i:68842 original size:2 final size:2
Alignment explanation
Indices: 68835--68871 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
68825 AATACCATGC
68835 AT AT AT 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 AT AT AT A
68872 CACCCCCCCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:70451 original size:30 final size:30
Alignment explanation
Indices: 70407--70465 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
70397 AAAATATGTT
70407 TTCGACCCTCTTAAATTTTACAAGTTCAAA
1 TTCGACCCTCTTAAATTTTACAAGTTCAAA
* * *
70437 TTCGCCCCTTTTAAATTTTATAAGTTCAA
1 TTCGACCCTCTTAAATTTTACAAGTTCAA
70466 GTTATCTCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.41
Consensus pattern (30 bp):
TTCGACCCTCTTAAATTTTACAAGTTCAAA
Done.