Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000286.1 Hibiscus syriacus cultivar Beakdansim tig00000528_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: 57966
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32
Found at i:7053 original size:9 final size:9
Alignment explanation
Indices: 7035--7108 Score: 66
Period size: 9 Copynumber: 8.7 Consensus size: 9
7025 TTGCTTGAAG
*
7035 AAAAATAGA
1 AAAAAAAGA
7044 AAAAAAAGA
1 AAAAAAAGA
7053 AAAAAAA-A
1 AAAAAAAGA
*
7061 AAAAGAAGA
1 AAAAAAAGA
* *
7070 ATAAGAAG-
1 AAAAAAAGA
*
7078 AAAAGAA-A
1 AAAAAAAGA
*
7086 AAAGAAAG-
1 AAAAAAAGA
7094 AAAAAAAGA
1 AAAAAAAGA
7103 AAAAAA
1 AAAAAA
7109 GTACATAAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
8 25 0.46
9 29 0.54
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.03
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:7058 original size:12 final size:12
Alignment explanation
Indices: 7035--7108 Score: 78
Period size: 12 Copynumber: 6.2 Consensus size: 12
7025 TTGCTTGAAG
*
7035 AAAAATAGAAAA
1 AAAAAAAGAAAA
*
7047 AAAAGAA-AAAA
1 AAAAAAAGAAAA
*
7058 AAAAAAAGAAGA
1 AAAAAAAGAAAA
* *
7070 ATAAGAAGAAAA
1 AAAAAAAGAAAA
* *
7082 GAAAAAAGAAAG
1 AAAAAAAGAAAA
7094 AAAAAAAGAAAA
1 AAAAAAAGAAAA
7106 AAA
1 AAA
7109 GTACATAAAA
Statistics
Matches: 48, Mismatches: 13, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
11 10 0.21
12 38 0.79
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.03
Consensus pattern (12 bp):
AAAAAAAGAAAA
Found at i:7101 original size:8 final size:8
Alignment explanation
Indices: 7032--7109 Score: 77
Period size: 8 Copynumber: 9.4 Consensus size: 8
7022 ATTTTGCTTG
7032 AAGAAAAA
1 AAGAAAAA
*
7040 TAGAAAAAA
1 AAG-AAAAA
7049 AAGAAAAA
1 AAGAAAAA
*
7057 AAAAAAAA
1 AAGAAAAA
*
7065 GAAGAATAAG
1 -AAGAA-AAA
7075 AAGAAAAGA
1 AAGAAAA-A
*
7084 AA-AAAGA
1 AAGAAAAA
7091 AAGAAAAA
1 AAGAAAAA
7099 AAGAAAAA
1 AAGAAAAA
7107 AAG
1 AAG
7110 TACATAAAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
7 3 0.05
8 34 0.60
9 18 0.32
10 2 0.04
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (8 bp):
AAGAAAAA
Found at i:8421 original size:115 final size:114
Alignment explanation
Indices: 8215--8673 Score: 588
Period size: 114 Copynumber: 4.0 Consensus size: 114
8205 TATTAAAGAC
* * *
8215 AAGTAGAACAAGT-TTGCCTCGATTCAATGGATCAAACTCCTTCAGATCTGATATTCCCTTCAGA
1 AAGTGGAACAAGTCTT-CCCCGATTCAATGGATCAAACTCCTCCAGATCTGATATTCCCTTCAGA
* *
8279 GTAAGTGGAACATGTCTCTCTTTCCCAAGATTTGATATTCCCTTTAGAGT
65 GTAAGCGGAACATGTCTCTCTTTCCCAAGATTTGATATTCCCTTCAGAGT
* * *
8329 AAGTGGAACAAGTCTTCCCCGATTTAATGGATCAAACTTCTCCAAGATCTGATATTCCCTTTAGA
1 AAGTGGAACAAGTCTTCCCCGATTCAATGGATCAAACTCCTCC-AGATCTGATATTCCCTTCAGA
* * *
8394 GTAAGCGGAACAGGTCCCTCTTTCCCAAGATTTGATATTCCCTTTAGAGT
65 GTAAGCGGAACATGTCTCTCTTTCCCAAGATTTGATATTCCCTTCAGAGT
* * * * *
8444 AAGTGGAACAAGTCTGCCCCGATTCAATGGATTAAAAC-CCTTCAGATCTGATATTCCTTTCAAA
1 AAGTGGAACAAGTCTTCCCCGATTCAATGGA-TCAAACTCCTCCAGATCTGATATTCCCTTCAGA
* * *
8508 GTAAACGGAACAAGTCTCTCTTTTCCAAGATTTGATATTCCCTTCAGAGT
65 GTAAGCGGAACATGTCTCTCTTTCCCAAGATTTGATATTCCCTTCAGAGT
***
8558 AAGTGGAAC-AGTCTAT-TTTGATTCAATGGATCAAACTCCTCCAAGATCTGATATTCCCTTCAG
1 AAGTGGAACAAGTCT-TCCCCGATTCAATGGATCAAACTCCTCC-AGATCTGATATTCCCTTCAG
* * * *
8621 CGTAAGC-GAACATGTCTCTC-TCCTCCAAGATCTGATATTCCCTTCAGCGT
64 AGTAAGCGGAACATGTCTCTCTTTC-CCAAGATTTGATATTCCCTTCAGAGT
8671 AAG
1 AAG
8674 CAGAACAGGT
Statistics
Matches: 301, Mismatches: 37, Indels: 15
0.85 0.10 0.04
Matches are distributed among these distances:
112 6 0.02
113 59 0.20
114 130 0.43
115 101 0.34
116 5 0.02
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.31
Consensus pattern (114 bp):
AAGTGGAACAAGTCTTCCCCGATTCAATGGATCAAACTCCTCCAGATCTGATATTCCCTTCAGAG
TAAGCGGAACATGTCTCTCTTTCCCAAGATTTGATATTCCCTTCAGAGT
Found at i:8662 original size:47 final size:48
Alignment explanation
Indices: 8593--8715 Score: 176
Period size: 47 Copynumber: 2.6 Consensus size: 48
8583 ATGGATCAAA
*
8593 CTCCTCCAAGATCTGATATTCCCTTCAGCGTAAGC-GAACATGTCTCT
1 CTCCTCCAAGATCTGATATTCCCTTCAGCGTAAGCAGAACAGGTCTCT
*
8640 CTCCTCCAAGATCTGATATTCCCTTCAGCGTAAGCAGAACAGGTCTTT
1 CTCCTCCAAGATCTGATATTCCCTTCAGCGTAAGCAGAACAGGTCTCT
** * * *
8688 CTGTTCTAAGATTTGATATTCACTTCAG
1 CTCCTCCAAGATCTGATATTCCCTTCAG
8716 AGAAAGTGGA
Statistics
Matches: 68, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
47 35 0.51
48 33 0.49
ACGTcount: A:0.24, C:0.28, G:0.15, T:0.33
Consensus pattern (48 bp):
CTCCTCCAAGATCTGATATTCCCTTCAGCGTAAGCAGAACAGGTCTCT
Found at i:14808 original size:54 final size:54
Alignment explanation
Indices: 14745--15407 Score: 790
Period size: 54 Copynumber: 12.3 Consensus size: 54
14735 TTACCAAATA
* *** *
14745 GGCACTAAGTGTACAAACCACGAAATTCATCCTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * *
14799 AGCACTAAGTGTGCATTTCACAGAATTCATCATATATGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * * *
14853 GGCACTAAATGTGCATTTCATGGAATTCATCCTAGGTTGATGAATAACGGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * * * *
14907 AGCACTAAGTGTGCTTTTCAAGGAATTCATCTTATGTGAATGAATAATCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * *
14961 GACACTATGTGTGCATTTCACGGAATTCATCATATGTGGATGAATAACCGTTTT
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
*
15015 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTT
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * * *
15069 GGCACTAATTGTGCATTTCACGAAATTCATTCTAGGTGGATGAATAATCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
15123 GGCACTAAGTGTACATTTCACGGAATTCATCCTATATGGATGAATAACGGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * * * *
15177 AGCACTGAGTGTACATTTCTCGAAATTCATCCTAGGTGGATGAATAACCGTTT-
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* *
15230 GGCACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAATCGTTT-
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * *
15283 GGCACTAAGTGTGCATTTCACGAAATTCATCATATGTTGATGAATAACTGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *** ** ** * *
15337 GGCACTAGGTGTACAAACCACGGAATTCATAATATGTTTATGAATAACCGTATG
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* *
15391 GGCACTACGGGTGCATT
1 GGCACTAAGTGTGCATT
15408 ATAAGAAATG
Statistics
Matches: 519, Mismatches: 89, Indels: 2
0.85 0.15 0.00
Matches are distributed among these distances:
53 94 0.18
54 425 0.82
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
Found at i:23274 original size:14 final size:13
Alignment explanation
Indices: 23242--23276 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
23232 ATTATGCTTG
*
23242 AAGAAAAAAATAA
1 AAGAAAAAAAGAA
23255 AAGAAAAAAAGAA
1 AAGAAAAAAAGAA
23268 AATGAAAAA
1 AA-GAAAAA
23277 GGGGGTCAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 14 0.70
14 6 0.30
ACGTcount: A:0.83, C:0.00, G:0.11, T:0.06
Consensus pattern (13 bp):
AAGAAAAAAAGAA
Found at i:24673 original size:139 final size:139
Alignment explanation
Indices: 24409--24798 Score: 539
Period size: 139 Copynumber: 2.8 Consensus size: 139
24399 ATCAATGAAC
* * * * *
24409 ATTTCTAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAATGAGAAAAAGTTCATAGTTAG
1 ATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGGAGAAGAAGTTCATAATGAG
* *
24474 AAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAAACAGTGACACCTTACTCAA
66 AAGAACTTGTTCAACCTTAACTCGATTCATCACATATGGAGTTGAAACAGCGACACCTTACTCAA
24539 GGGATCAAT
131 GGGATCAAT
* *
24548 ATTTCCAGTGGAGAATTCATAATGAGAAGAACTCATCCGATGAAGGAGAAGATGTTCATAATGAG
1 ATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGGAGAAGAAGTTCATAATGAG
* * * *
24613 AAGAACTTGTTCAACCTTAACTCGATTCATCGCATATGGAGTTGAATCAGCGACATCTTACTCGA
66 AAGAACTTGTTCAACCTTAACTCGATTCATCACATATGGAGTTGAAACAGCGACACCTTACTCAA
24678 GGGATCAAT
131 GGGATCAAT
* * *
24687 ATTTCCAATGGAAGAGTTCATAATGAGAAGAACTCGTCCGA-GGAGGAAGAAGAAGTTCATAATG
1 ATTTCCAGTGG-AGAGTTCATAATGAGAAGAACTCATCCGATGAAGG-AGAAGAAGTTCATAATG
* * * * * *
24751 AGAAGAACATGTTCGACCTTTTACTAGATTCTATCACAGAAGGAGTTG
64 AGAAGAACTTGTTCAACC-TTAACTCGATTC-ATCACATATGGAGTTG
24799 GATCAACATT
Statistics
Matches: 222, Mismatches: 25, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
139 140 0.63
140 59 0.27
141 10 0.05
142 13 0.06
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (139 bp):
ATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAAGGAGAAGAAGTTCATAATGAG
AAGAACTTGTTCAACCTTAACTCGATTCATCACATATGGAGTTGAAACAGCGACACCTTACTCAA
GGGATCAAT
Found at i:24816 original size:119 final size:119
Alignment explanation
Indices: 24679--24914 Score: 355
Period size: 119 Copynumber: 2.0 Consensus size: 119
24669 CTTACTCGAG
* * **
24679 GGATCAATATTTCCAATGGAAGAGTTCATAATGAGAAGAACTCGTCCGAGGAGGAAGAAGAAGTT
1 GGATCAACATTTCCAATGGAAGAGTTCATAATGAGAAGAACTCGTCCAAAAAGGAAGAAGAAGTT
* * *
24744 CATAATGAGAAGAACATGTTCGACCTTTTACTAGATTCTATCACAGAAGGAGTT
66 CATAATGAGAAAAACATGTTCAACCTTTTACTAGACTCTATCACAGAAGGAGTT
* * *
24798 GGATCAACATTTCCAATGGAAGTGTTCATAATGAGAAGAACTCGTCCAAAAAGGGAGAAGAATTT
1 GGATCAACATTTCCAATGGAAGAGTTCATAATGAGAAGAACTCGTCCAAAAAGGAAGAAGAAGTT
* * *
24863 CATAATGAGAAAAACATGTTCAACCTTTTGCTTGACTCTATCGCAGAAGGAG
66 CATAATGAGAAAAACATGTTCAACCTTTTACTAGACTCTATCACAGAAGGAG
24915 ATAGATCAGC
Statistics
Matches: 104, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
119 104 1.00
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.25
Consensus pattern (119 bp):
GGATCAACATTTCCAATGGAAGAGTTCATAATGAGAAGAACTCGTCCAAAAAGGAAGAAGAAGTT
CATAATGAGAAAAACATGTTCAACCTTTTACTAGACTCTATCACAGAAGGAGTT
Found at i:25043 original size:43 final size:43
Alignment explanation
Indices: 24988--25090 Score: 118
Period size: 43 Copynumber: 2.4 Consensus size: 43
24978 TTACTCGGTC
*
24988 CTTCAGAGAAGGAGTTGGATTAGT-AACAAAATTTCACTTAATT
1 CTTCACAGAAGGAGTTGGATTAGTGAA-AAAATTTCACTTAATT
* * ** * **
25031 CTTCATAGAAGGATTTGGATTAGTGAAAATCTTTCGCTTGGTT
1 CTTCACAGAAGGAGTTGGATTAGTGAAAAAATTTCACTTAATT
25074 CTTCACAGAAGGAGTTG
1 CTTCACAGAAGGAGTTG
25091 AATCAGCGTC
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
43 48 0.96
44 2 0.04
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.34
Consensus pattern (43 bp):
CTTCACAGAAGGAGTTGGATTAGTGAAAAAATTTCACTTAATT
Found at i:27298 original size:19 final size:19
Alignment explanation
Indices: 27274--27313 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
27264 TTAGTCTTAA
27274 GCGTATTATTATTGTCAAT
1 GCGTATTATTATTGTCAAT
*
27293 GCGTATTATTATTGTCCAT
1 GCGTATTATTATTGTCAAT
27312 GC
1 GC
27314 CCATAATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.23, C:0.15, G:0.17, T:0.45
Consensus pattern (19 bp):
GCGTATTATTATTGTCAAT
Found at i:30606 original size:20 final size:20
Alignment explanation
Indices: 30577--30619 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
30567 AAATTGAAAG
*
30577 AAAATGTAACTTA-AAAAATT
1 AAAATGTAAC-AACAAAAATT
*
30597 AAAATTTAACAACAAAAATT
1 AAAATGTAACAACAAAAATT
30617 AAA
1 AAA
30620 GGAGATACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 19 0.95
ACGTcount: A:0.65, C:0.07, G:0.02, T:0.26
Consensus pattern (20 bp):
AAAATGTAACAACAAAAATT
Found at i:43795 original size:19 final size:19
Alignment explanation
Indices: 43771--43817 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
43761 TCACATGCTT
43771 GTAGGACACTCTCCCACAC
1 GTAGGACACTCTCCCACAC
*
43790 GTAGGACACTCTCCCACGC
1 GTAGGACACTCTCCCACAC
43809 GTAGGACAC
1 GTAGGACAC
43818 CTTTGAGCTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.26, C:0.38, G:0.21, T:0.15
Consensus pattern (19 bp):
GTAGGACACTCTCCCACAC
Found at i:48317 original size:64 final size:65
Alignment explanation
Indices: 48205--48327 Score: 171
Period size: 64 Copynumber: 1.9 Consensus size: 65
48195 CGATGCACAT
* *
48205 ACCATGCATCGATGCACTCCATGTATTATTAAAACATCGAATTGATTTTATGCATCGATACAAAG
1 ACCATGCATCGATGCACTCCAGGTAGTATTAAAACATCGAATTGATTTTATGCATCGATACAAAG
* *
48270 ACCATGCATCGATGCA-TTCAGGTTAGT-TTGAAACATCGAA-TGCATTTTATGCATCGAT
1 ACCATGCATCGATGCACTCCAGG-TAGTATTAAAACATCGAATTG-ATTTTATGCATCGAT
48328 GCATCCTTAG
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
63 2 0.04
64 31 0.60
65 19 0.37
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.32
Consensus pattern (65 bp):
ACCATGCATCGATGCACTCCAGGTAGTATTAAAACATCGAATTGATTTTATGCATCGATACAAAG
Found at i:48565 original size:10 final size:10
Alignment explanation
Indices: 48550--48574 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
48540 GCCATTGATC
48550 AACAACAAGA
1 AACAACAAGA
48560 AACAACAAGA
1 AACAACAAGA
48570 AACAA
1 AACAA
48575 GAAACTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.72, C:0.20, G:0.08, T:0.00
Consensus pattern (10 bp):
AACAACAAGA
Found at i:50987 original size:15 final size:15
Alignment explanation
Indices: 50967--50999 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
50957 TGAGACATTA
*
50967 CCCGCCCCGCATCCG
1 CCCGCCCCACATCCG
50982 CCCGCCCCACATCCG
1 CCCGCCCCACATCCG
50997 CCC
1 CCC
51000 ACCTAGCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.70, G:0.15, T:0.06
Consensus pattern (15 bp):
CCCGCCCCACATCCG
Found at i:52759 original size:15 final size:15
Alignment explanation
Indices: 52732--52781 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
52722 AGACATTACT
52732 CGCCCCACATCTGCC
1 CGCCCCACATCTGCC
* *
52747 CGGCCCGCATCTGCC
1 CGCCCCACATCTGCC
*
52762 CGCCCCACATCCGCC
1 CGCCCCACATCTGCC
52777 CGCCC
1 CGCCC
52782 AGCTAAATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.10, C:0.62, G:0.18, T:0.10
Consensus pattern (15 bp):
CGCCCCACATCTGCC
Done.