Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007113.1 Hibiscus syriacus cultivar Beakdansim tig00018586_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: 836039
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:781059 original size:10 final size:10
Alignment explanation
Indices: 781036--781079 Score: 58
Period size: 9 Copynumber: 4.6 Consensus size: 10
781026 TTGAATTTTA
781036 AAAAAATTAC
1 AAAAAATTAC
781046 -AAAAATTAC
1 AAAAAATTAC
781055 AAAAAA-T-C
1 AAAAAATTAC
781063 AGAAAAATTAC
1 A-AAAAATTAC
781074 AAAAAA
1 AAAAAA
781080 AAATTAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
8 2 0.07
9 15 0.50
10 11 0.37
11 2 0.07
ACGTcount: A:0.73, C:0.09, G:0.02, T:0.16
Consensus pattern (10 bp):
AAAAAATTAC
Found at i:781060 original size:19 final size:19
Alignment explanation
Indices: 781036--781079 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
781026 TTGAATTTTA
*
781036 AAAAAATTACAAAAATTAC
1 AAAAAATCACAAAAATTAC
*
781055 AAAAAATCAGAAAAATTAC
1 AAAAAATCACAAAAATTAC
781074 AAAAAA
1 AAAAAA
781080 AAATTAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.73, C:0.09, G:0.02, T:0.16
Consensus pattern (19 bp):
AAAAAATCACAAAAATTAC
Found at i:783090 original size:31 final size:31
Alignment explanation
Indices: 783049--783107 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
783039 AGAATTGTAG
* *
783049 AGGATGCTCAATTCCAAATTGCTAAAAGAAT
1 AGGATACTCAATTCCAAATTGCCAAAAGAAT
783080 AGGATACTCAATTCCAAATTGCCAAAAG
1 AGGATACTCAATTCCAAATTGCCAAAAG
783108 TGGTGCAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (31 bp):
AGGATACTCAATTCCAAATTGCCAAAAGAAT
Found at i:787819 original size:284 final size:284
Alignment explanation
Indices: 787309--787873 Score: 1040
Period size: 284 Copynumber: 2.0 Consensus size: 284
787299 GAGGGAAAAA
*
787309 ATTCCCCCCAGGGGGTACCGATTTCCCCCACTGTTCAACGGTCGAAATATTTGAATTTTACACTT
1 ATTCCCCCCAGGGGGTACCGATTCCCCCCACTGTTCAACGGTCGAAATATTTGAATTTTACACTT
*
787374 AGGGAACTGATTCCCCATGAGGGGTACCGATTCCCCCCACGCTCCAAGCAAAAATATTAATTGTT
66 AGGGAACCGATTCCCCATGAGGGGTACCGATTCCCCCCACGCTCCAAGCAAAAATATTAATTGTT
* *
787439 TTCATACTTAAACGGCTCCAAAAACTTCATTAATGATCCCCAACAATCGGAAGTGATTCAAGGTG
131 TTCACACTTAAACGGCTCCAAAAACTTCATTAATGATCCCCAACAATCAGAAGTGATTCAAGGTG
787504 TACTTAAGCAAGCTTAGAAGCCATTGATCAACAACAAGAAACAACAAACAACTAGAATCAAGAGA
196 TACTTAAGCAAGCTTAGAAGCCATTGATCAACAACAAGAAACAACAAACAACTAGAATCAAGAGA
787569 GAATCAAAGAGAAAGCATCAACCG
261 GAATCAAAGAGAAAGCATCAACCG
787593 ATTCCCCCCAGGGGGTACCGATTCCCCCCACTGTTCAACGGTCGAAATATTTGAATTTTACACTT
1 ATTCCCCCCAGGGGGTACCGATTCCCCCCACTGTTCAACGGTCGAAATATTTGAATTTTACACTT
787658 AGGGAACCGATTCCCCATGAGGGGTACCGATTCCCCCCACGCTCCAAGCAAAAATATTAATTGTT
66 AGGGAACCGATTCCCCATGAGGGGTACCGATTCCCCCCACGCTCCAAGCAAAAATATTAATTGTT
* **
787723 TTCACACTTAAACGGCTCCAAAAACTTTATTAATGATCCCCAACGTTCAGAAGTGATTCAAGGTG
131 TTCACACTTAAACGGCTCCAAAAACTTCATTAATGATCCCCAACAATCAGAAGTGATTCAAGGTG
* *
787788 TATTTAAGCAAGCTTAGAAGCCATTGATCAACAACAAGAAACAACAAGCAACTAGAATCAAGAGA
196 TACTTAAGCAAGCTTAGAAGCCATTGATCAACAACAAGAAACAACAAACAACTAGAATCAAGAGA
*
787853 GAATCAAAGAGAAATCATCAA
261 GAATCAAAGAGAAAGCATCAA
787874 ACCTCAAGTT
Statistics
Matches: 271, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
284 271 1.00
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.23
Consensus pattern (284 bp):
ATTCCCCCCAGGGGGTACCGATTCCCCCCACTGTTCAACGGTCGAAATATTTGAATTTTACACTT
AGGGAACCGATTCCCCATGAGGGGTACCGATTCCCCCCACGCTCCAAGCAAAAATATTAATTGTT
TTCACACTTAAACGGCTCCAAAAACTTCATTAATGATCCCCAACAATCAGAAGTGATTCAAGGTG
TACTTAAGCAAGCTTAGAAGCCATTGATCAACAACAAGAAACAACAAACAACTAGAATCAAGAGA
GAATCAAAGAGAAAGCATCAACCG
Found at i:795792 original size:149 final size:150
Alignment explanation
Indices: 795603--795908 Score: 551
Period size: 150 Copynumber: 2.0 Consensus size: 150
795593 GGGTAGAGGG
* *
795603 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTT-GAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
*
795667 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
*
795732 ATATGGCACTACGGTGTAAT
131 ATATGGCACTACGGTGCAAT
*
795752 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
*
795817 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTTCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
795882 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
795902 TCTACGC
1 TCTACGC
795909 AGCACTTCGG
Statistics
Matches: 150, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
149 51 0.34
150 99 0.66
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (150 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
ATATGGCACTACGGTGCAAT
Found at i:795930 original size:23 final size:23
Alignment explanation
Indices: 795887--795930 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
795877 TCATTATATG
*
795887 GCACTACGGTGCAATTCTACGCA
1 GCACTACGGTGCAATTATACGCA
* *
795910 GCACTTCGGTGCATTTATACG
1 GCACTACGGTGCAATTATACG
795931 AGCTGTGGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (23 bp):
GCACTACGGTGCAATTATACGCA
Found at i:802827 original size:149 final size:150
Alignment explanation
Indices: 802638--802941 Score: 547
Period size: 150 Copynumber: 2.0 Consensus size: 150
802628 GGGTAGAGGG
* *
802638 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTT-GAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
* *
802702 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAATATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
802767 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
*
802787 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
*
802852 TACTTGATCCCTAATATATGTATATGATTCTTAAGGAATTATATGTGGTTCTTATGGACATCATT
66 TACTTGATCCCTAATATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
802917 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
802937 TCTAC
1 TCTAC
802942 ACAGCACTTC
Statistics
Matches: 148, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
149 51 0.34
150 97 0.66
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (150 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
TACTTGATCCCTAATATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
ATATGGCACTACGGTGCAAT
Found at i:809854 original size:149 final size:150
Alignment explanation
Indices: 809666--809969 Score: 547
Period size: 150 Copynumber: 2.0 Consensus size: 150
809656 GGGTAGAGGG
* *
809666 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTT-GAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
*
809730 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
*
809795 ATATGGCATTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
*
809815 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
*
809880 TACTTGATCCCTAGTATATGTGTATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
809945 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
809965 TCTAC
1 TCTAC
809970 ACGGCACTTC
Statistics
Matches: 148, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
149 51 0.34
150 97 0.66
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (150 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
ATATGGCACTACGGTGCAAT
Found at i:812103 original size:14 final size:14
Alignment explanation
Indices: 812084--812112 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
812074 AGAGATTTTC
812084 TAAGTTAAATGAAT
1 TAAGTTAAATGAAT
812098 TAAGTTAAATGAAT
1 TAAGTTAAATGAAT
812112 T
1 T
812113 TTAAGATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (14 bp):
TAAGTTAAATGAAT
Found at i:813783 original size:29 final size:29
Alignment explanation
Indices: 813742--813814 Score: 123
Period size: 29 Copynumber: 2.6 Consensus size: 29
813732 AATGAAAATC
*
813742 AAAGTTCA--GCTATGATTGGTAAAATTA
1 AAAGTTCAGTGCTATAATTGGTAAAATTA
813769 AAAGTTCAGTGCTATAATTGGTAAAATTA
1 AAAGTTCAGTGCTATAATTGGTAAAATTA
813798 AAAGTTCAGTGCTATAA
1 AAAGTTCAGTGCTATAA
813815 ACGATATAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
27 8 0.19
29 35 0.81
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (29 bp):
AAAGTTCAGTGCTATAATTGGTAAAATTA
Found at i:818614 original size:14 final size:15
Alignment explanation
Indices: 818595--818624 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
818585 AAGACATACT
818595 ATTTTTTTC-TCTCA
1 ATTTTTTTCATCTCA
818609 ATTTTTTTCATCTCA
1 ATTTTTTTCATCTCA
818624 A
1 A
818625 CACACTCCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTTTTTCATCTCA
Found at i:821132 original size:20 final size:20
Alignment explanation
Indices: 821083--821132 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
821073 ATAGTAATGC
*
821083 ACTGTATAAATAGTACCGAT
1 ACTGTATGAATAGTACCGAT
*
821103 ACTGTATGAATAGTATCGAT
1 ACTGTATGAATAGTACCGAT
*
821123 ACTGTGTGAA
1 ACTGTATGAA
821133 CAATATCAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (20 bp):
ACTGTATGAATAGTACCGAT
Found at i:821139 original size:20 final size:20
Alignment explanation
Indices: 821099--821139 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
821089 TAAATAGTAC
* *
821099 CGATACTGTATGAATAGTAT
1 CGATACTGTATGAACAATAT
*
821119 CGATACTGTGTGAACAATAT
1 CGATACTGTATGAACAATAT
821139 C
1 C
821140 AATGCTAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.32
Consensus pattern (20 bp):
CGATACTGTATGAACAATAT
Found at i:823881 original size:20 final size:21
Alignment explanation
Indices: 823823--823881 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
823813 AATACTGTAC
823823 TGTA-TGAATAGTATCGATAT
1 TGTAGTGAATAGTATCGATAT
*
823843 TGTAG-GAAAAAGTATCGATAT
1 TGTAGTG-AATAGTATCGATAT
*
823864 TGT-GTGAATAGTACCGAT
1 TGTAGTGAATAGTATCGAT
823882 GCTCAAAAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 16 0.48
21 17 0.52
ACGTcount: A:0.36, C:0.07, G:0.24, T:0.34
Consensus pattern (21 bp):
TGTAGTGAATAGTATCGATAT
Found at i:835903 original size:26 final size:26
Alignment explanation
Indices: 835849--835912 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 26
835839 CTTCAAATCT
*
835849 CATTGAAGGAATGATTGATTTGCACG
1 CATTGAAGGAATGATTGATTTACACG
*
835875 CATTGAAGGAATGATTGATTTACATG
1 CATTGAAGGAATGATTGATTTACACG
* *
835901 CATGGAACGAAT
1 CATTGAAGGAAT
835913 CTGAGGGACA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.30
Consensus pattern (26 bp):
CATTGAAGGAATGATTGATTTACACG
Done.