Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002052.1 Hibiscus syriacus cultivar Beakdansim tig00004178_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: 72889
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:11471 original size:60 final size:59
Alignment explanation
Indices: 11375--11529 Score: 165
Period size: 59 Copynumber: 2.6 Consensus size: 59
11365 CATACATACT
* * * *
11375 CAAACTATGATATTCTTTCTAAATTAGTCCCTAAACTTCTAAATATTTTATTTTTATCCC
1 CAAACTATGATATTCATTCTAAATTAGTCCCTAAACTT-TAAACATTTTAGTTTCATCCC
* *
11435 TAAACTATGACTATT-ATTCTAAATTTA-T-CCTCAAACTTTTAACATTTTAGTTTCATCCC
1 CAAACTATGA-TATTCATTCTAAA-TTAGTCCCT-AAACTTTAAACATTTTAGTTTCATCCC
* *
11494 CAAACTAT-ATTTGTCATTCTAAATTGGTCCCTAAAC
1 CAAACTATGATAT-TCATTCTAAATTAGTCCCTAAAC
11530 GTTTCCAATA
Statistics
Matches: 79, Mismatches: 9, Indels: 15
0.77 0.09 0.15
Matches are distributed among these distances:
57 2 0.03
58 4 0.05
59 40 0.51
60 26 0.33
61 7 0.09
ACGTcount: A:0.32, C:0.21, G:0.05, T:0.43
Consensus pattern (59 bp):
CAAACTATGATATTCATTCTAAATTAGTCCCTAAACTTTAAACATTTTAGTTTCATCCC
Found at i:12225 original size:27 final size:26
Alignment explanation
Indices: 12180--12237 Score: 98
Period size: 27 Copynumber: 2.2 Consensus size: 26
12170 TTGATATATG
12180 AAAAATATTATAATGTTTTCATTTAA
1 AAAAATATTATAATGTTTTCATTTAA
*
12206 AAAAATATTATGATGTTTTTCATTTAA
1 AAAAATATTATAATG-TTTTCATTTAA
12233 AAAAA
1 AAAAA
12238 ATGTTATTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 14 0.47
27 16 0.53
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.43
Consensus pattern (26 bp):
AAAAATATTATAATGTTTTCATTTAA
Found at i:12465 original size:14 final size:14
Alignment explanation
Indices: 12448--12482 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
12438 TAAGATAAAT
12448 ATAATCAATAAAAA
1 ATAATCAATAAAAA
*
12462 ATAATTAATAAAAA
1 ATAATCAATAAAAA
*
12476 AAAATCA
1 ATAATCA
12483 GAGTGAATTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (14 bp):
ATAATCAATAAAAA
Found at i:22022 original size:21 final size:21
Alignment explanation
Indices: 21993--22041 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
21983 ACCACCACAC
* *
21993 CCACAATAGCGCCTGCGACGG
1 CCACAATAGCACCCGCGACGG
*
22014 CCGCAATAGCACCCGCGACGG
1 CCACAATAGCACCCGCGACGG
22035 CCACAAT
1 CCACAAT
22042 CACGGTAAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.27, C:0.41, G:0.24, T:0.08
Consensus pattern (21 bp):
CCACAATAGCACCCGCGACGG
Found at i:23997 original size:54 final size:54
Alignment explanation
Indices: 23925--24042 Score: 182
Period size: 54 Copynumber: 2.2 Consensus size: 54
23915 AAGAAATGCG
* * *
23925 ATACCTCTGGAGACAGTTTATACATACTTTAACGAACCTGATATAAATTATTTT
1 ATACCTCCGGAGACAGTTTATACATACTTCAACGAACATGATATAAATTATTTT
* * *
23979 ATTCCTCCGGAGACAGTTTATACATGCTTCAACGAATATGATATAAATTATTTT
1 ATACCTCCGGAGACAGTTTATACATACTTCAACGAACATGATATAAATTATTTT
24033 ATACCTCCGG
1 ATACCTCCGG
24043 GTTAACACCT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.36
Consensus pattern (54 bp):
ATACCTCCGGAGACAGTTTATACATACTTCAACGAACATGATATAAATTATTTT
Found at i:25266 original size:27 final size:26
Alignment explanation
Indices: 25236--25287 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
25226 CAATAATATT
25236 ATAAT-CTATCAAAAAATTATTTATTTG
1 ATAATACTAT-AAAAAATTA-TTATTTG
*
25263 ATAATATTATAAAAAATTATTATTT
1 ATAATACTATAAAAAATTATTATTT
25288 CACATATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 6 0.26
27 14 0.61
28 3 0.13
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (26 bp):
ATAATACTATAAAAAATTATTATTTG
Found at i:25890 original size:13 final size:13
Alignment explanation
Indices: 25872--25896 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25862 ACCTGATTCT
25872 AAATTATTTTAAA
1 AAATTATTTTAAA
25885 AAATTATTTTAA
1 AAATTATTTTAA
25897 TTAGATTATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
AAATTATTTTAAA
Found at i:29535 original size:13 final size:13
Alignment explanation
Indices: 29508--29575 Score: 54
Period size: 13 Copynumber: 5.3 Consensus size: 13
29498 ACCGTGATTT
* *
29508 TTAAAATTTAAAA
1 TTAAAATATATAA
29521 TTAAAATATATAA
1 TTAAAATATATAA
29534 TTCAAAA-ATATAA
1 TT-AAAATATATAA
29547 TCTAAAA-AT-TAA
1 T-TAAAATATATAA
*
29559 -TAAAATAGTAAAA
1 TTAAAATA-TATAA
29572 TTAA
1 TTAA
29576 TTAAAATATA
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
10 5 0.11
11 1 0.02
12 4 0.09
13 28 0.61
14 8 0.17
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (13 bp):
TTAAAATATATAA
Found at i:29945 original size:30 final size:31
Alignment explanation
Indices: 29876--29942 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
29866 TGTAATACAA
* *
29876 TCCCCCAACATTTAGTCTATTTTCATTATGG
1 TCCCCCAACATTTAGTCTATTTGCAATATGG
* *
29907 TCCCCCAACTTTTAGTCTGTTTGCAATATGG
1 TCCCCCAACATTTAGTCTATTTGCAATATGG
29938 TCCCC
1 TCCCC
29943 AACGTAACTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.19, C:0.30, G:0.12, T:0.39
Consensus pattern (31 bp):
TCCCCCAACATTTAGTCTATTTGCAATATGG
Found at i:30036 original size:29 final size:29
Alignment explanation
Indices: 29977--30036 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
29967 GCAAATGGAC
* * * *
29977 TAAAAGTTGGGGGATTCTATTGCAAGTTT
1 TAAAAGTTGGGGGATCCTAATGAAAGCTT
30006 TAAAAGTTGGGGGA-CCTAAATGAAAGCTT
1 TAAAAGTTGGGGGATCCT-AATGAAAGCTT
30035 TA
1 TA
30037 GAAAAGTTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 2 0.08
29 24 0.92
ACGTcount: A:0.33, C:0.08, G:0.27, T:0.32
Consensus pattern (29 bp):
TAAAAGTTGGGGGATCCTAATGAAAGCTT
Found at i:31053 original size:35 final size:36
Alignment explanation
Indices: 31012--31108 Score: 142
Period size: 36 Copynumber: 2.7 Consensus size: 36
31002 AACACAATCA
*
31012 TCAATTACATTTTAAACCCCAAATTCC-AAAATACT
1 TCAATTACATTCTAAACCCCAAATTCCAAAAATACT
*
31047 TCAATTACATTCTAAACCTCAAATTCCAAAAATACT
1 TCAATTACATTCTAAACCCCAAATTCCAAAAATACT
* * *
31083 TTAATTACATGCTCAACCCCAAATTC
1 TCAATTACATTCTAAACCCCAAATTC
31109 ATAATTCATT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
35 25 0.45
36 30 0.55
ACGTcount: A:0.41, C:0.27, G:0.01, T:0.31
Consensus pattern (36 bp):
TCAATTACATTCTAAACCCCAAATTCCAAAAATACT
Found at i:31950 original size:35 final size:35
Alignment explanation
Indices: 31909--31987 Score: 124
Period size: 35 Copynumber: 2.3 Consensus size: 35
31899 GGGGTTGGCA
31909 TGTAATTGAAATATTTTGGAATTTGA-GGTTTAGAG
1 TGTAATTGAAATATTTTGG-ATTTGAGGGTTTAGAG
* *
31944 TGTAATTGAAGTATTTTGGATTTTAGGGTTTAGAG
1 TGTAATTGAAATATTTTGGATTTGAGGGTTTAGAG
31979 TGTAATTGA
1 TGTAATTGA
31988 TGTCTGTGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
34 5 0.12
35 36 0.88
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (35 bp):
TGTAATTGAAATATTTTGGATTTGAGGGTTTAGAG
Found at i:53697 original size:27 final size:27
Alignment explanation
Indices: 53667--53718 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
53657 ACATAAATTG
* *
53667 ATTTTACATAATATTTGTAT-TATTTTA
1 ATTTTAAATAA-ATTTATATCTATTTTA
53694 ATTTTAAATAAATTTATATCTATTT
1 ATTTTAAATAAATTTATATCTATTT
53719 GTAAATAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.58
Consensus pattern (27 bp):
ATTTTAAATAAATTTATATCTATTTTA
Found at i:57908 original size:14 final size:13
Alignment explanation
Indices: 57889--57922 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
57879 TCTATATTAG
57889 TTATAATTCTTATA
1 TTATAATTCTTA-A
*
57903 TTATAAATCTTAA
1 TTATAATTCTTAA
57916 TTATAAT
1 TTATAAT
57923 CATTAAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (13 bp):
TTATAATTCTTAA
Found at i:58071 original size:25 final size:24
Alignment explanation
Indices: 57999--58074 Score: 70
Period size: 23 Copynumber: 3.2 Consensus size: 24
57989 TTTTAATATT
* *
57999 TATAAGTTTAATTT-ACATTTTATA
1 TATAA-TTTAATTTAAAATTTTAAA
58023 TAATAA-TTAA-TTAATAA-TTTAAA
1 T-ATAATTTAATTTAA-AATTTTAAA
58046 TATAATTTAATTTAAAATTTTAAAA
1 TATAATTTAATTTAAAATTTT-AAA
58071 TATA
1 TATA
58075 TATAAAAATG
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
22 6 0.14
23 17 0.40
24 9 0.21
25 11 0.26
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (24 bp):
TATAATTTAATTTAAAATTTTAAA
Found at i:58347 original size:25 final size:25
Alignment explanation
Indices: 58313--58370 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
58303 GCCTGAGAAG
58313 GGTTTAATGATCAATGAAATGGTTT
1 GGTTTAATGATCAATGAAATGGTTT
58338 GGTTTAATGATCAATGAAATGGTTT
1 GGTTTAATGATCAATGAAATGGTTT
*
58363 GGGTTAAT
1 GGTTTAAT
58371 TAGGTCCATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.31, C:0.03, G:0.26, T:0.40
Consensus pattern (25 bp):
GGTTTAATGATCAATGAAATGGTTT
Found at i:58639 original size:2 final size:2
Alignment explanation
Indices: 58634--58979 Score: 130
Period size: 2 Copynumber: 178.0 Consensus size: 2
58624 TACATCATAC
* * *
58634 AT AT AT ACT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AC AC AC
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
58676 AT -T AGT AT AT AT AT AT AT AT AT GT AC AT AC AT -T AT AC AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
58717 AT ACT A- AT GT AT AT ACT -T AT AT AT AT AC AT AC AC AA AT GT -T
1 AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
58758 AT AT AT ACT A- AT AT AT ACT -T AT AT AT -T AT AA AC AT A- AT -T
1 AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
*
58797 AT AT -T AT AT AT AT AT AT AT -T AT A- AGT AT A- AT GT AT ACT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT
* * ** **
58836 AT AT -T AT AT ACT -T AT AT A- AGT TT AT AT TT AT AT -T GC AT GC
1 AT AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
* * * **
58876 AT AA AT AT A- AT GT AC AT -T AT GAT AT AT AT GC AT CAT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT -AT AT AT AT
*
58917 CAT A- AC AT -T CAT CAT 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 AT AT AT
58958 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
58980 TGTTTCAATT
Statistics
Matches: 260, Mismatches: 45, Indels: 78
0.68 0.12 0.20
Matches are distributed among these distances:
1 25 0.10
2 213 0.82
3 22 0.08
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:58701 original size:79 final size:77
Alignment explanation
Indices: 58602--58751 Score: 212
Period size: 79 Copynumber: 1.9 Consensus size: 77
58592 TGTATATACT
* *
58602 TATATATATACATGTGTGTACATACATCATACATATATACTTATATATATATA-TATATATATAT
1 TATATATATACATATATGTACATACATCATACATATATAC-TA-ATATATATACT-TATATATAT
*
58666 ATATACACACATTAG
63 ACATACACACATTAG
* * *
58681 TATATATATATATATATGTACATACATTATACATATATACTAATGTATATACTTATATATATACA
1 TATATATATACATATATGTACATACATCATACATATATACTAATATATATACTTATATATATACA
58746 TACACA
66 TACACA
58752 AATGTTATAT
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
77 25 0.39
78 3 0.05
79 36 0.56
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.41
Consensus pattern (77 bp):
TATATATATACATATATGTACATACATCATACATATATACTAATATATATACTTATATATATACA
TACACACATTAG
Found at i:64032 original size:3 final size:3
Alignment explanation
Indices: 64026--64067 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
64016 TGATGATGAT
* * *
64026 GAA GAA GAA GAA GAT GAA GAA GAA GAA GAA AAA TAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
64068 TTAGAAGCCA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.67, C:0.00, G:0.29, T:0.05
Consensus pattern (3 bp):
GAA
Found at i:64043 original size:15 final size:15
Alignment explanation
Indices: 64023--64054 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
64013 GGATGATGAT
64023 GATGAAGAAGAAGAA
1 GATGAAGAAGAAGAA
64038 GATGAAGAAGAAGAA
1 GATGAAGAAGAAGAA
64053 GA
1 GA
64055 AAAATAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.34, T:0.06
Consensus pattern (15 bp):
GATGAAGAAGAAGAA
Found at i:71433 original size:3 final size:3
Alignment explanation
Indices: 71425--71481 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
71415 GAAAATTGCA
71425 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
71473 AAT AAT AAT
1 AAT AAT AAT
71482 GAAATAAGTC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Done.