Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000177.1 Hibiscus syriacus cultivar Beakdansim tig00000311_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: 69199
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:8837 original size:15 final size:15
Alignment explanation
Indices: 8813--8864 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
8803 TTGAGACATT
8813 ACCC-CCCCGCATCC
1 ACCCGCCCCGCATCC
8827 ACCCGCCCCGCATCC
1 ACCCGCCCCGCATCC
* *
8842 GCCCGCCCCACATCC
1 ACCCGCCCCGCATCC
*
8857 GCCCGCCC
1 ACCCGCCC
8865 AGTTAAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
14 4 0.11
15 31 0.89
ACGTcount: A:0.12, C:0.69, G:0.13, T:0.06
Consensus pattern (15 bp):
ACCCGCCCCGCATCC
Found at i:12465 original size:3 final size:3
Alignment explanation
Indices: 12457--12481 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12447 AATAAAGATT
12457 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
12482 GCAGCTTTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:18415 original size:19 final size:20
Alignment explanation
Indices: 18377--18415 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
18367 TTTTATAATT
**
18377 GTATTTAGAGATTTATAAAA
1 GTATTTAGAGATCAATAAAA
18397 GTATTTAGAGA-CAATAAAA
1 GTATTTAGAGATCAATAAAA
18416 AGCTTATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.49, C:0.03, G:0.15, T:0.33
Consensus pattern (20 bp):
GTATTTAGAGATCAATAAAA
Found at i:19134 original size:31 final size:31
Alignment explanation
Indices: 19092--19181 Score: 135
Period size: 31 Copynumber: 2.9 Consensus size: 31
19082 GTTCATTTAT
* *
19092 GTTATCATTTTATTAAGTTTTAGTCACTTCC
1 GTTATCGTTTTATTAAGTTTTAGTCACTTAC
19123 GTTATCGTTTTATTAAGTTTTAGTCACTTAC
1 GTTATCGTTTTATTAAGTTTTAGTCACTTAC
* * *
19154 GTGATCGTTTTATTAAATTTTGGTCACT
1 GTTATCGTTTTATTAAGTTTTAGTCACT
19182 CGGACGTTAA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 54 1.00
ACGTcount: A:0.22, C:0.13, G:0.13, T:0.51
Consensus pattern (31 bp):
GTTATCGTTTTATTAAGTTTTAGTCACTTAC
Found at i:19957 original size:31 final size:31
Alignment explanation
Indices: 19919--19992 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
19909 CCTCATTTCC
19919 AAGTGACCAAAACTTAATAAAACAATAACGT
1 AAGTGACCAAAACTTAATAAAACAATAACGT
* *
19950 AAGTGACCAAAATTTAATAAAACGATAACGT
1 AAGTGACCAAAACTTAATAAAACAATAACGT
* *
19981 AAATGATCAAAA
1 AAGTGACCAAAA
19993 GTGTACAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.55, C:0.14, G:0.11, T:0.20
Consensus pattern (31 bp):
AAGTGACCAAAACTTAATAAAACAATAACGT
Found at i:27724 original size:63 final size:63
Alignment explanation
Indices: 27574--27764 Score: 247
Period size: 63 Copynumber: 3.0 Consensus size: 63
27564 TAAAGATAAT
* * ** * * *
27574 TATATATTTTTTGAATATTTTAAAGCAAAATAATATCTTTTAAAGTTTGAATAGTAAAAGGTG
1 TATATATATTTTGAATATTTCAAATTAAAATAATATTTTTTTAAGTTTGAATAATAAAAGGTG
27637 TATATATATTTTGAATATTTCAAATTAAAATAATATTTTTTTAAGTTTGAATAATAAAAGGTG
1 TATATATATTTTGAATATTTCAAATTAAAATAATATTTTTTTAAGTTTGAATAATAAAAGGTG
* * *
27700 TATATATCTTTTGAATATTTCAAATTAAAATATATTATTAATTGTTTAAATTTGAATATTAAAAG
1 TATATATATTTTGAATATTTCAAATTAAAATA-A-TATT--TT-TTTAAGTTTGAATAATAAAAG
27765 ATATTTGATT
Statistics
Matches: 113, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
63 87 0.77
64 1 0.01
65 4 0.04
67 2 0.02
68 19 0.17
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (63 bp):
TATATATATTTTGAATATTTCAAATTAAAATAATATTTTTTTAAGTTTGAATAATAAAAGGTG
Found at i:34664 original size:31 final size:30
Alignment explanation
Indices: 34600--34665 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
34590 ATGACATCTA
* *
34600 TTAATAACTCAAATTTATTTTATTAATATT
1 TTAATAACTCAAATTTAATTAATTAATATT
*
34630 TTAATAACTCAAAGTTTAAATTAATT-TTATT
1 TTAATAACTCAAA-TTT-AATTAATTAATATT
34661 TTAAT
1 TTAAT
34666 GTATTTGCCT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 13 0.42
31 12 0.39
32 6 0.19
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.52
Consensus pattern (30 bp):
TTAATAACTCAAATTTAATTAATTAATATT
Found at i:38797 original size:15 final size:15
Alignment explanation
Indices: 38777--38808 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
38767 TTAGTTAAAA
38777 ATTTAAAGGTAAATT
1 ATTTAAAGGTAAATT
*
38792 ATTTAAGGGTAAATT
1 ATTTAAAGGTAAATT
38807 AT
1 AT
38809 ACCATTGGCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.41
Consensus pattern (15 bp):
ATTTAAAGGTAAATT
Found at i:44869 original size:315 final size:314
Alignment explanation
Indices: 44324--45217 Score: 1520
Period size: 315 Copynumber: 2.8 Consensus size: 314
44314 TCTTTCACGT
44324 TCGACGAGCAACGATGAGTACCACTAACGATGAGCG-TCGATAAATTAATTTATAAAACATTAAA
1 TCGACGAGCAACGATGAGTACCACTAACGATGAGCGCT-GATAAATTAATTTATAAAACATTAAA
* * *
44388 ATTATAAAGTATTCAATGTATAATTATAAATTAGCTAAAATTTTAAATGTAAATTATTTAAGGGT
65 ATTATAAAGTACTCAATGTATAATTATAAATTAGTTAAAAATTTAAATGTAAATTATTTAAGGGT
* *
44453 AAACTATATCATTAACCACTCAACTATTGAGAATTTTTTACTTTTATCATCAATCTTTCAATTTT
130 AAACTATATCATTAACCACTCAACTATTTAG-ATTTTTTACTTTTATCATCGATCTTTCAATTTT
*
44518 GTCAATCAGACCACTTAACTATTTGATTATATTCAATTAAGCCAGCAGTCGTTAATATTTAATAG
194 GTCAATCAGACCACTTAACTATTTGATTATATTCAATTAAGCCAACAGTCGTTAATATTTAATAG
* *
44583 AAGTGCTGATGTGACAGTTAATAAAATTGTTTATTTAAATTATGAGTCTTCCACAC
259 AAGTGCTGATGTGACAGTTAATAAAATTGCTTATTTAAATGATGAGTCTTCCACAC
44639 TCGACGAGCAACGATGAGTACCACTAACGATGAGCGCTGATAAATTAATTTATAAAACATTAAAA
1 TCGACGAGCAACGATGAGTACCACTAACGATGAGCGCTGATAAATTAATTTATAAAACATTAAAA
*
44704 TTATAAAGTACTCAATGTATAATTATAAATTAGTTAAAAATTTAAATGTAAATTTTTTAAGGGTA
66 TTATAAAGTACTCAATGTATAATTATAAATTAGTTAAAAATTTAAATGTAAATTATTTAAGGGTA
*
44769 AACTATATCATTAACCACTCAACTATTTAGATTTTTTTACTTTTATCATCGATTTTTCAATTTTG
131 AACTATATCATTAACCACTCAACTATTTAGA-TTTTTTACTTTTATCATCGATCTTTCAATTTTG
* * *
44834 TCAATCAGACCATTTAACTATTTGATTATATTCAATTAAGCCAACAGTTGCTAATATTTAATAGA
195 TCAATCAGACCACTTAACTATTTGATTATATTCAATTAAGCCAACAGTCGTTAATATTTAATAGA
*
44899 AGTCCTGATGTGACAGTTAATAAAATTGCTTATTTAAATGATGAGTCTTCCACAC
260 AGTGCTGATGTGACAGTTAATAAAATTGCTTATTTAAATGATGAGTCTTCCACAC
* * *
44954 TCGACGAGCAGCGATGAGTACCACTAACGATGAGTGCCGATAAATTAATTTATAAAACATTAAAA
1 TCGACGAGCAACGATGAGTACCACTAACGATGAGCGCTGATAAATTAATTTATAAAACATTAAAA
* * *
45019 TTATAAAATACTCAACGTATAATTATAAATTAGTTAAAAATTTAAAGGTAAATTATTTAAGGGTA
66 TTATAAAGTACTCAATGTATAATTATAAATTAGTTAAAAATTTAAATGTAAATTATTTAAGGGTA
* * *
45084 AACTATACCATTGACCACTCAACTATTTAGCATTTTTTACTTTTATCATCGATCTTTCAATTTTC
131 AACTATATCATTAACCACTCAACTATTTAG-ATTTTTTACTTTTATCATCGATCTTTCAATTTTG
* *
45149 TCAATCAGACCACTTAACTATTTAATTATATTCAATTAAGCCACCAGTCGTTAATATTTAATAGA
195 TCAATCAGACCACTTAACTATTTGATTATATTCAATTAAGCCAACAGTCGTTAATATTTAATAGA
45214 AGTG
260 AGTG
45218 TCGATATGGC
Statistics
Matches: 545, Mismatches: 31, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
314 1 0.00
315 542 0.99
316 2 0.00
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.36
Consensus pattern (314 bp):
TCGACGAGCAACGATGAGTACCACTAACGATGAGCGCTGATAAATTAATTTATAAAACATTAAAA
TTATAAAGTACTCAATGTATAATTATAAATTAGTTAAAAATTTAAATGTAAATTATTTAAGGGTA
AACTATATCATTAACCACTCAACTATTTAGATTTTTTACTTTTATCATCGATCTTTCAATTTTGT
CAATCAGACCACTTAACTATTTGATTATATTCAATTAAGCCAACAGTCGTTAATATTTAATAGAA
GTGCTGATGTGACAGTTAATAAAATTGCTTATTTAAATGATGAGTCTTCCACAC
Found at i:49010 original size:31 final size:31
Alignment explanation
Indices: 48975--49044 Score: 122
Period size: 31 Copynumber: 2.3 Consensus size: 31
48965 ATTTCAAAAC
*
48975 TAACAAATTGATCACTAATATTATTGATTTA
1 TAACAAATTAATCACTAATATTATTGATTTA
49006 TAACAAATTAATCACTAATATTATTGATTTA
1 TAACAAATTAATCACTAATATTATTGATTTA
*
49037 TAATAAAT
1 TAACAAAT
49045 CGGTCACTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (31 bp):
TAACAAATTAATCACTAATATTATTGATTTA
Found at i:50628 original size:31 final size:31
Alignment explanation
Indices: 50593--50662 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
50583 TAAGTGATCG
* *
50593 ATTTATTATAAATTAATAATATTAATAATTA
1 ATTTATTATAAATTAATAACATTAATAACTA
* *
50624 ATTTATTATAAATTTATAACATTAATGACTA
1 ATTTATTATAAATTAATAACATTAATAACTA
50655 ATTTATTA
1 ATTTATTA
50663 ATCATGATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (31 bp):
ATTTATTATAAATTAATAACATTAATAACTA
Found at i:59741 original size:7 final size:7
Alignment explanation
Indices: 59720--59789 Score: 88
Period size: 7 Copynumber: 10.1 Consensus size: 7
59710 TTAGAGGTAA
59720 TAGGG-T
1 TAGGGTT
*
59726 TATGGTT
1 TAGGGTT
59733 TAGGGTT
1 TAGGGTT
59740 TAGGGTT
1 TAGGGTT
*
59747 TAAGGTT
1 TAGGGTT
*
59754 TAGAGTT
1 TAGGGTT
59761 TAGGGTT
1 TAGGGTT
*
59768 TAAGGTT
1 TAGGGTT
*
59775 TAAGGTT
1 TAGGGTT
59782 TAGGGTT
1 TAGGGTT
59789 T
1 T
59790 TAAGTTAAGG
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
6 4 0.07
7 51 0.93
ACGTcount: A:0.20, C:0.00, G:0.36, T:0.44
Consensus pattern (7 bp):
TAGGGTT
Found at i:59755 original size:21 final size:21
Alignment explanation
Indices: 59720--59789 Score: 106
Period size: 21 Copynumber: 3.4 Consensus size: 21
59710 TTAGAGGTAA
*
59720 TAGGG-TTATGGTTTAGGGTT
1 TAGGGTTTAAGGTTTAGGGTT
*
59740 TAGGGTTTAAGGTTTAGAGTT
1 TAGGGTTTAAGGTTTAGGGTT
*
59761 TAGGGTTTAAGGTTTAAGGTT
1 TAGGGTTTAAGGTTTAGGGTT
59782 TAGGGTTT
1 TAGGGTTT
59790 TAAGTTAAGG
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
20 5 0.11
21 40 0.89
ACGTcount: A:0.20, C:0.00, G:0.36, T:0.44
Consensus pattern (21 bp):
TAGGGTTTAAGGTTTAGGGTT
Found at i:62432 original size:22 final size:22
Alignment explanation
Indices: 62407--62453 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
62397 CTACGGCGAC
*
62407 ATCCGTCCCCATCTCCGACGTA
1 ATCCGTCCCCATCTCCGACGAA
62429 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
62451 ATC
1 ATC
62454 TGTCTATCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.21, C:0.45, G:0.13, T:0.21
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:62875 original size:20 final size:20
Alignment explanation
Indices: 62850--62935 Score: 145
Period size: 20 Copynumber: 4.3 Consensus size: 20
62840 GCGAATTTAG
62850 TTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
62870 TTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
*
62890 GTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
* *
62910 GTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
62930 TTTCGC
1 TTTCGC
62936 ATTGTGAATT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.09, C:0.20, G:0.22, T:0.49
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTCAT
Found at i:64916 original size:4 final size:4
Alignment explanation
Indices: 64907--64956 Score: 64
Period size: 4 Copynumber: 12.5 Consensus size: 4
64897 TTTTTTGGCA
* * * *
64907 TTAT TTAT TTAT TTAT TTAT TTAT TTAC TGAT TTAT GTAT TAAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
64955 TT
1 TT
64957 TCAGCAGCCC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (4 bp):
TTAT
Found at i:65133 original size:21 final size:21
Alignment explanation
Indices: 65100--65175 Score: 93
Period size: 21 Copynumber: 3.6 Consensus size: 21
65090 GATGCACCTG
* *
65100 TCATCATTTAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
65121 TCATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
65142 TCATCGTTC-AGTAGGCCCCT-
1 TCATCGTTCAAG-AGGCCCCTC
*
65162 TCAACCGTTCAAGA
1 TC-ATCGTTCAAGA
65176 TCCCGATTCA
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
20 4 0.08
21 43 0.88
22 2 0.04
ACGTcount: A:0.22, C:0.34, G:0.17, T:0.26
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:66788 original size:21 final size:20
Alignment explanation
Indices: 66729--66803 Score: 87
Period size: 20 Copynumber: 3.7 Consensus size: 20
66719 TTTTGTTGTT
* *
66729 GTGATAGTCAAATTCACAAC
1 GTGAAAGTCAAATTCGCAAC
*
66749 GTGAAAGTCAAATTTGCAAC
1 GTGAAAGTCAAATTCGCAAC
*
66769 GTTAAAGTCAAAATTCGCAAC
1 GTGAAAGTC-AAATTCGCAAC
* *
66790 GCGAAAGTTAAATT
1 GTGAAAGTCAAATT
66804 TGCGTTGCGA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 30 0.65
21 16 0.35
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.25
Consensus pattern (20 bp):
GTGAAAGTCAAATTCGCAAC
Done.