Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006347.1 Hibiscus syriacus cultivar Beakdansim tig00015182_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: 60991
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:3185 original size:21 final size:21
Alignment explanation
Indices: 3158--3207 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
3148 ACATTCGAAC
*
3158 AAAAAAAAGGAGCAAAAAGTTT
1 AAAAAAAAGGAG-AAAAAGATT
*
3180 CAAAAAAAGGAGAAAAAGATT
1 AAAAAAAAGGAGAAAAAGATT
3201 AAAAAAA
1 AAAAAAA
3208 GTGTGAGATG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.70, C:0.04, G:0.16, T:0.10
Consensus pattern (21 bp):
AAAAAAAAGGAGAAAAAGATT
Found at i:3186 original size:22 final size:20
Alignment explanation
Indices: 3159--3208 Score: 73
Period size: 22 Copynumber: 2.4 Consensus size: 20
3149 CATTCGAACA
*
3159 AAAAAAAGGAGCAAAAAGTTT
1 AAAAAAAGGAG-AAAAAGATT
3180 CAAAAAAAGGAGAAAAAGATT
1 -AAAAAAAGGAGAAAAAGATT
3201 AAAAAAAG
1 AAAAAAAG
3209 TGTGAGATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 8 0.30
21 8 0.30
22 11 0.41
ACGTcount: A:0.68, C:0.04, G:0.18, T:0.10
Consensus pattern (20 bp):
AAAAAAAGGAGAAAAAGATT
Found at i:4255 original size:19 final size:19
Alignment explanation
Indices: 4231--4268 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
4221 TTTAATAAAA
*
4231 GTTTTTACTTTTCTCTTTT
1 GTTTTTACTTTTCGCTTTT
4250 GTTTTTACTTTTCGCTTTT
1 GTTTTTACTTTTCGCTTTT
4269 ACGTATTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.05, C:0.16, G:0.08, T:0.71
Consensus pattern (19 bp):
GTTTTTACTTTTCGCTTTT
Found at i:11797 original size:21 final size:20
Alignment explanation
Indices: 11772--11810 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
11762 AAAAAATAAA
*
11772 AAAAAACTTAATTTATTTAT
1 AAAAAACTCAATTTATTTAT
*
11792 AAAAAACTCAATTTTTTTA
1 AAAAAACTCAATTTATTTA
11811 CTGGAACTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.44
Consensus pattern (20 bp):
AAAAAACTCAATTTATTTAT
Found at i:21136 original size:17 final size:18
Alignment explanation
Indices: 21111--21161 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
21101 TAGTTTATAA
21111 ATATTTTATACAAAATAT
1 ATATTTTATACAAAATAT
*
21129 AT-TTTTATATAAAAATAT
1 ATATTTTATA-CAAAATAT
*
21147 ATATATTATACAAAA
1 ATATTTTATACAAAA
21162 ACTATATAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 7 0.25
18 15 0.54
19 6 0.21
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATTTTATACAAAATAT
Found at i:21145 original size:18 final size:19
Alignment explanation
Indices: 21106--21169 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
21096 TAATATAGTT
* *
21106 TATAAATATTTTATACAAAA
1 TATATATATTATATA-AAAA
*
21126 TATAT-TTTTATATAAAAA
1 TATATATATTATATAAAAA
*
21144 TATATATATTATACAAAAA
1 TATATATATTATATAAAAA
21163 CTATATA
1 -TATATA
21170 AGAAATAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
18 9 0.24
19 18 0.49
20 10 0.27
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (19 bp):
TATATATATTATATAAAAA
Found at i:21162 original size:20 final size:19
Alignment explanation
Indices: 21122--21169 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
21112 TATTTTATAC
* *
21122 AAAATATAT-TTTTATATA
1 AAAATATATATATTATAAA
21140 AAAATATATATATTATACAA
1 AAAATATATATATTATA-AA
*
21160 AAACTATATA
1 AAAATATATA
21170 AGAAATAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 9 0.36
19 6 0.24
20 10 0.40
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAATATATATATTATAAA
Found at i:22803 original size:13 final size:14
Alignment explanation
Indices: 22785--22814 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
22775 TTCCATGTTA
22785 TAATATTATT-TGG
1 TAATATTATTATGG
22798 TAATATTATTATGG
1 TAATATTATTATGG
22812 TAA
1 TAA
22815 GATTTCACCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (14 bp):
TAATATTATTATGG
Found at i:29061 original size:2 final size:2
Alignment explanation
Indices: 29054--29103 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
29044 ATATAGTAAT
29054 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29096 TA TA TA TA
1 TA TA TA TA
29104 CCAACATAAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:34133 original size:15 final size:15
Alignment explanation
Indices: 34113--34151 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
34103 TAAATCCCCA
34113 TATACTTTGAGTGTT
1 TATACTTTGAGTGTT
34128 TATACTTTGAGTGTT
1 TATACTTTGAGTGTT
*
34143 TTTACTTTG
1 TATACTTTG
34152 CGCCTAATGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.18, C:0.08, G:0.18, T:0.56
Consensus pattern (15 bp):
TATACTTTGAGTGTT
Found at i:41877 original size:10 final size:10
Alignment explanation
Indices: 41864--41888 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
41854 AAAATATATA
41864 AAATTAAAAT
1 AAATTAAAAT
41874 AAATTAAAAT
1 AAATTAAAAT
41884 AAATT
1 AAATT
41889 TAATCATCCA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
AAATTAAAAT
Found at i:43788 original size:23 final size:24
Alignment explanation
Indices: 43743--43792 Score: 61
Period size: 23 Copynumber: 2.1 Consensus size: 24
43733 ATCTTTTACA
43743 TATATTTTAAAATTTTAAGTTAAAT
1 TATATTTTAAAATTTTAAGTT-AAT
43768 TATA-TTT-AAATTATTAA-TTAAT
1 TATATTTTAAAATT-TTAAGTTAAT
43790 TAT
1 TAT
43793 TATATAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 6 0.25
23 7 0.29
24 7 0.29
25 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
TATATTTTAAAATTTTAAGTTAAT
Found at i:43800 original size:23 final size:23
Alignment explanation
Indices: 43752--43800 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
43742 ATATATTTTA
*
43752 AAATTTTAAGTTAAATTATATTT
1 AAATTTTAAGTTAAATTATATAT
43775 AAATTATTAA-TT-AATTATTATAT
1 AAATT-TTAAGTTAAATTA-TATAT
43798 AAA
1 AAA
43801 AATAAATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 5 0.22
23 14 0.61
24 4 0.17
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
AAATTTTAAGTTAAATTATATAT
Found at i:43803 original size:25 final size:23
Alignment explanation
Indices: 43751--43803 Score: 54
Period size: 25 Copynumber: 2.2 Consensus size: 23
43741 CATATATTTT
*
43751 AAAATTTTAAGTTAAATTATATT
1 AAAATTTTAAGTTAAATTATATA
*
43774 TAAATTATTAA-TTAATTATTATATA
1 AAAATT-TTAAGTTAA--ATTATATA
43799 AAAAT
1 AAAAT
43804 AAATTAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
23 9 0.38
24 4 0.17
25 11 0.46
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
AAAATTTTAAGTTAAATTATATA
Found at i:44622 original size:76 final size:76
Alignment explanation
Indices: 44492--44643 Score: 277
Period size: 76 Copynumber: 2.0 Consensus size: 76
44482 TATCATTAAG
* *
44492 GACAAATAATAAATTAGCGTTTATTCTATGTGGTACGAACATCCAACCATTTTGATTTCTTTACT
1 GACAAATAATAAATTAGCGTTTATTCTACGTGGTACGAACATCCAACCACTTTGATTTCTTTACT
44557 TATTTCGAACT
66 TATTTCGAACT
*
44568 GACAAATAATAAATTAGCGTTTATTCTACGTGGTACGAACATCCTACCACTTTGATTTCTTTACT
1 GACAAATAATAAATTAGCGTTTATTCTACGTGGTACGAACATCCAACCACTTTGATTTCTTTACT
44633 TATTTCGAACT
66 TATTTCGAACT
44644 TGCATTTCTG
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 73 1.00
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (76 bp):
GACAAATAATAAATTAGCGTTTATTCTACGTGGTACGAACATCCAACCACTTTGATTTCTTTACT
TATTTCGAACT
Found at i:45263 original size:29 final size:28
Alignment explanation
Indices: 45231--45286 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
45221 TTTTAAGTAT
* *
45231 TTAAACTATTTTTTTGTCAAAATAAATAC
1 TTAAACTA-ATTTTGGTCAAAATAAATAC
*
45260 TTAAAGTAATTTTGGTCAAAATAAATA
1 TTAAACTAATTTTGGTCAAAATAAATA
45287 ATCTCGCCGC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (28 bp):
TTAAACTAATTTTGGTCAAAATAAATAC
Found at i:46895 original size:20 final size:20
Alignment explanation
Indices: 46870--46924 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
46860 TTCTCATAGG
* *
46870 ATCACATAGCTCATATATAC
1 ATCACATAACACATATATAC
46890 ATCACATAACACATATATAC
1 ATCACATAACACATATATAC
*
46910 ATCACATATCACATA
1 ATCACATAACACATA
46925 CTTCTCATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.45, C:0.25, G:0.02, T:0.27
Consensus pattern (20 bp):
ATCACATAACACATATATAC
Found at i:48694 original size:17 final size:17
Alignment explanation
Indices: 48659--48696 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
48649 TAGTTACCCC
* *
48659 TTTAATTTCCTTTTTCA
1 TTTAATTTCCTTATCCA
48676 TTTAATTTCCTTATCCA
1 TTTAATTTCCTTATCCA
48693 TTTA
1 TTTA
48697 CTCATTCACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.21, C:0.18, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTAATTTCCTTATCCA
Found at i:53869 original size:17 final size:18
Alignment explanation
Indices: 53833--53871 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
53823 ATTATACATA
*
53833 TAAAACAAATGACTAAAT
1 TAAAACAAATGACAAAAT
*
53851 TAAAATAAATG-CAAAAT
1 TAAAACAAATGACAAAAT
53868 TAAA
1 TAAA
53872 CATGTAATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.64, C:0.08, G:0.05, T:0.23
Consensus pattern (18 bp):
TAAAACAAATGACAAAAT
Found at i:55656 original size:3 final size:3
Alignment explanation
Indices: 55638--55703 Score: 78
Period size: 3 Copynumber: 21.3 Consensus size: 3
55628 TTTCTTTAAA
* * * *
55638 ATT ATT TTT AATT ATT ATT TTT ATC ATT ATT ATT ATT AAT ATAT ATT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT
55685 ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT A
55704 AATAAATAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
3 48 0.91
4 5 0.09
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:55676 original size:28 final size:28
Alignment explanation
Indices: 55638--55704 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
55628 TTTCTTTAAA
* *
55638 ATTATTTTTAAT-TATTATTTTTATCATT
1 ATTATTATTAATATA-TATTATTATCATT
*
55666 ATTATTATTAATATATATTATTATTATT
1 ATTATTATTAATATATATTATTATCATT
55694 ATTATTATTAA
1 ATTATTATTAA
55705 ATAAATAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
28 33 0.94
29 2 0.06
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (28 bp):
ATTATTATTAATATATATTATTATCATT
Found at i:55716 original size:25 final size:28
Alignment explanation
Indices: 55663--55716 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
55653 TATTTTTATC
* *
55663 ATTATTATTATTAATATATATTATTATT
1 ATTATTATTATTAATATATAATATAATT
55691 ATTATTATTATTAA-ATA-AATA-AATT
1 ATTATTATTATTAATATATAATATAATT
55716 A
1 A
55717 CAAGACCCGG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 4 0.17
26 3 0.12
27 3 0.12
28 14 0.58
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
ATTATTATTATTAATATATAATATAATT
Found at i:58131 original size:4 final size:4
Alignment explanation
Indices: 58117--58149 Score: 57
Period size: 4 Copynumber: 8.0 Consensus size: 4
58107 CAGATATTAA
58117 ATTT CATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT -ATTT ATTT ATTT ATTT ATTT ATTT ATTT
58150 GTCTGTCAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (4 bp):
ATTT
Done.