Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004768.1 Hibiscus syriacus cultivar Beakdansim tig00010751_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: 84118
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:2135 original size:23 final size:24
Alignment explanation
Indices: 2092--2136 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
2082 TTTTGGCCGT
*
2092 TTTCTATTTTGAATAAATTAATGA
1 TTTCTATTTTGAAAAAATTAATGA
2116 TTTCT-TTTT-AAAAAAGTTAAT
1 TTTCTATTTTGAAAAAA-TTAAT
2137 ATCAATATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 5 0.26
23 9 0.47
24 5 0.26
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.51
Consensus pattern (24 bp):
TTTCTATTTTGAAAAAATTAATGA
Found at i:11492 original size:23 final size:25
Alignment explanation
Indices: 11448--11493 Score: 62
Period size: 23 Copynumber: 1.9 Consensus size: 25
11438 ATTTGGCCGT
11448 TTTCTATTTTGAATAAAATTAATGA
1 TTTCTATTTTGAATAAAATTAATGA
11473 TTTCT-TTTT-AA-AAAAGTTAAT
1 TTTCTATTTTGAATAAAA-TTAAT
11494 ATCAATATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 4 0.20
23 7 0.35
24 4 0.20
25 5 0.25
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (25 bp):
TTTCTATTTTGAATAAAATTAATGA
Found at i:12064 original size:12 final size:13
Alignment explanation
Indices: 12039--12067 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
12029 ATATTTATTT
12039 ATATAAAAATATA
1 ATATAAAAATATA
12052 ATATAAAAA-ATA
1 ATATAAAAATATA
12064 ATAT
1 ATAT
12068 TATAATTTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
ATATAAAAATATA
Found at i:23525 original size:3 final size:3
Alignment explanation
Indices: 23519--23623 Score: 194
Period size: 3 Copynumber: 35.3 Consensus size: 3
23509 CATACAACAA
23519 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
23566 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ACT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
23614 ATT ATT ATT A
1 ATT ATT ATT A
23624 GTTTTTGGCC
Statistics
Matches: 99, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
2 2 0.02
3 97 0.98
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:25498 original size:2 final size:2
Alignment explanation
Indices: 25491--25530 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
25481 AACTTGAGCA
*
25491 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25531 GTATTGCCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32661 original size:15 final size:15
Alignment explanation
Indices: 32641--32676 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
32631 GAGAGACTGA
32641 TGTTGCATCAAGGCT
1 TGTTGCATCAAGGCT
32656 TGTTGCATCAAGGCT
1 TGTTGCATCAAGGCT
32671 TGTTGC
1 TGTTGC
32677 TGTAGCTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.17, C:0.19, G:0.28, T:0.36
Consensus pattern (15 bp):
TGTTGCATCAAGGCT
Found at i:33479 original size:21 final size:21
Alignment explanation
Indices: 33453--33496 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
33443 ACCTAAATTA
* *
33453 TTACCTAAAATATTATTATTT
1 TTACCTAAAATATCAATATTT
33474 TTACCTAAAATATCAATATTT
1 TTACCTAAAATATCAATATTT
33495 TT
1 TT
33497 TAATATTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (21 bp):
TTACCTAAAATATCAATATTT
Found at i:33560 original size:21 final size:21
Alignment explanation
Indices: 33522--33568 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
33512 AGTTTCTAAC
*
33522 AATAACAAAATCAGTAGAAAA
1 AATAACAAAACCAGTAGAAAA
*
33543 AATAACAAAACC-GATAGAAAT
1 AATAACAAAACCAG-TAGAAAA
33564 AATAA
1 AATAA
33569 TATTTTTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.66, C:0.11, G:0.09, T:0.15
Consensus pattern (21 bp):
AATAACAAAACCAGTAGAAAA
Found at i:35680 original size:25 final size:25
Alignment explanation
Indices: 35646--35695 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
35636 AGCATTTCGG
35646 TGTCAAATACCGTTGTTAGAGACAT
1 TGTCAAATACCGTTGTTAGAGACAT
*
35671 TGTCAAATACTGTTGTTAGAGACAT
1 TGTCAAATACCGTTGTTAGAGACAT
35696 ATTCGTGTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (25 bp):
TGTCAAATACCGTTGTTAGAGACAT
Found at i:42772 original size:31 final size:31
Alignment explanation
Indices: 42734--42828 Score: 102
Period size: 31 Copynumber: 3.1 Consensus size: 31
42724 GAACCTCGGC
* *
42734 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* ** *
42765 AACTGTCCATATGTTCCTTATAACATAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* *
42796 TACTGTCCATATGTCTCGAAAG-ACATAGGTA
1 AACTGTCCATATGTC-CCAAAGAACATAGGTA
42827 AA
1 AA
42829 ACCCTCGACT
Statistics
Matches: 50, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
31 48 0.96
32 2 0.04
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTCCCAAAGAACATAGGTA
Found at i:42994 original size:17 final size:19
Alignment explanation
Indices: 42962--42997 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
42952 CATATATCTC
42962 ATATCATATCACATGTATT
1 ATATCATATCACATGTATT
42981 ATAT-ATAT-ACATGTATT
1 ATATCATATCACATGTATT
42998 CATGTAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (19 bp):
ATATCATATCACATGTATT
Found at i:46912 original size:31 final size:31
Alignment explanation
Indices: 46844--46968 Score: 103
Period size: 31 Copynumber: 4.1 Consensus size: 31
46834 AGACCCCGGT
* * *
46844 AACTATCCATAGGTCCCAAAGAACCTCA-G-C
1 AACTGTCCATAGGTCCCAAAGAACAT-AGGTA
*
46874 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATAGGTCCCAAAGAACATAGGTA
* * **
46905 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATAGGTCCCAAAGAACATAGGTA
* * * *
46936 TATTGTCCATATGTCTCGAAAG-ACATAGGTA
1 AACTGTCCATAGGTC-CCAAAGAACATAGGTA
46967 AA
1 AA
46969 ACCCTCGACT
Statistics
Matches: 78, Mismatches: 14, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
29 1 0.01
30 26 0.33
31 48 0.62
32 3 0.04
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (31 bp):
AACTGTCCATAGGTCCCAAAGAACATAGGTA
Found at i:47134 original size:17 final size:19
Alignment explanation
Indices: 47102--47137 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
47092 CATATATCTC
47102 ATATCATATCACATGTATT
1 ATATCATATCACATGTATT
47121 ATAT-ATAT-ACATGTATT
1 ATATCATATCACATGTATT
47138 CATGTAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (19 bp):
ATATCATATCACATGTATT
Found at i:47815 original size:64 final size:63
Alignment explanation
Indices: 47717--47877 Score: 200
Period size: 64 Copynumber: 2.5 Consensus size: 63
47707 TAATGAAGGT
* *
47717 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAAT--
*
47780 GG
62 GC
*
47782 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATGC
* *
47846 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
47878 CCTTAAACAA
Statistics
Matches: 86, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
63 1 0.01
64 58 0.67
65 24 0.28
66 3 0.03
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATGC
Found at i:48433 original size:10 final size:10
Alignment explanation
Indices: 48420--48448 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
48410 GAAAGGAGAA
48420 GAGAATTCTG
1 GAGAATTCTG
48430 GAGAATTCTG
1 GAGAATTCTG
48440 GAGAATTCT
1 GAGAATTCT
48449 CTCCCTCTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.31, C:0.10, G:0.28, T:0.31
Consensus pattern (10 bp):
GAGAATTCTG
Found at i:56087 original size:12 final size:12
Alignment explanation
Indices: 56072--56107 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
56062 AGGCTGTTGT
56072 TGTAGCTGCTGC
1 TGTAGCTGCTGC
*
56084 TGTAGTTGCTGC
1 TGTAGCTGCTGC
*
56096 TGTGGCTGCTGC
1 TGTAGCTGCTGC
56108 ATTTGAGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.06, C:0.22, G:0.36, T:0.36
Consensus pattern (12 bp):
TGTAGCTGCTGC
Found at i:58109 original size:191 final size:189
Alignment explanation
Indices: 57787--58140 Score: 573
Period size: 191 Copynumber: 1.9 Consensus size: 189
57777 AATTCCAACT
* * ** **
57787 TTAGCTAACGGAAAGATCTCGAGGACAAATGTAACTCGCTTAAATCCCTTACTAAAGCATGCACA
1 TTAGCTAACAGAAAGATCTCAAGGACAAATGTAACAAGCTTAAATCCCTTACTAAAAAATGCACA
* **
57852 GGAAAAACTTGAATCCAAAATGCATGAGATAGTATTTGGAGACTTGGGTTTTTAAAGATGGATTT
66 GGAAAAACTTGAATCCAAAATGCATGAGATAGTATTTGGAGACTTGGATTTCGAAAGATGGATTT
57917 AGATTTCAAAAATAGTGGAGTTGTGTGGTAGAAATATAAAATTCATGATTCTTTCTCAA
131 AGATTTCAAAAATAGTGGAGTTGTGTGGTAGAAATATAAAATTCATGATTCTTTCTCAA
* * *
57976 TTAGCTAACAGCAAGATCTCAAGGACAAATGTAACAAGCTTAAATCCCTTGCTAAAAAAAATTCA
1 TTAGCTAACAGAAAGATCTCAAGGACAAATGTAACAAGCTTAAATCCCTTACT--AAAAAATGCA
*
58041 CAGGAAAAACTTGAATCCAAAATGTATGAGATAGTATTTGGAGACTTGGATTTCGAAAGATGGAT
64 CAGGAAAAACTTGAATCCAAAATGCATGAGATAGTATTTGGAGACTTGGATTTCGAAAGATGGAT
58106 TTAGATTTCAAAAATAGTGGAGTTGTGTGGTAGAA
129 TTAGATTTCAAAAATAGTGGAGTTGTGTGGTAGAA
58141 CACATATAAA
Statistics
Matches: 150, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
189 47 0.31
191 103 0.69
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (189 bp):
TTAGCTAACAGAAAGATCTCAAGGACAAATGTAACAAGCTTAAATCCCTTACTAAAAAATGCACA
GGAAAAACTTGAATCCAAAATGCATGAGATAGTATTTGGAGACTTGGATTTCGAAAGATGGATTT
AGATTTCAAAAATAGTGGAGTTGTGTGGTAGAAATATAAAATTCATGATTCTTTCTCAA
Found at i:61999 original size:20 final size:20
Alignment explanation
Indices: 61955--62000 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
61945 TTGGTTTGGA
* *
61955 TTTTAAATTATTTTTTATTT
1 TTTTAAAATATTTTTAATTT
61975 TTTTAAAATA-TTTTAATTT
1 TTTTAAAATATTTTTAATTT
61994 TCTTTAA
1 T-TTTAA
62001 TAGTTTGAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTAAAATATTTTTAATTT
Found at i:64725 original size:43 final size:43
Alignment explanation
Indices: 64664--64748 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 43
64654 AGCTTTGTTT
* *
64664 CCTCTGTAGTCAACTTGTAGGATGTATTTGTCTATATATTTTG
1 CCTCTGTAGTCAACTTGTAGGATCTATATGTCTATATATTTTG
* * *
64707 CCTCTGTAGTTAACTTGTAGGGTCTATATGTCTATATGTTTT
1 CCTCTGTAGTCAACTTGTAGGATCTATATGTCTATATATTTT
64749 ACTGGTAACA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.20, C:0.14, G:0.19, T:0.47
Consensus pattern (43 bp):
CCTCTGTAGTCAACTTGTAGGATCTATATGTCTATATATTTTG
Found at i:68332 original size:19 final size:19
Alignment explanation
Indices: 68308--68346 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
68298 AGGCATGTAG
68308 GGAGAGCATGCACCTCTTT
1 GGAGAGCATGCACCTCTTT
68327 GGAGAGCATGCACCTCTTT
1 GGAGAGCATGCACCTCTTT
68346 G
1 G
68347 CAGTGCATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.26, G:0.28, T:0.26
Consensus pattern (19 bp):
GGAGAGCATGCACCTCTTT
Found at i:68354 original size:19 final size:19
Alignment explanation
Indices: 68310--68354 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
68300 GCATGTAGGG
*
68310 AGAGCATGCACCTCTTTGG
1 AGAGCATGCACCTCTTTGC
68329 AGAGCATGCACCTCTTTGC
1 AGAGCATGCACCTCTTTGC
*
68348 AGTGCAT
1 AGAGCAT
68355 TTTGAGATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (19 bp):
AGAGCATGCACCTCTTTGC
Found at i:76412 original size:30 final size:31
Alignment explanation
Indices: 76378--76449 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 31
76368 TGACCCTTAT
* * * *
76378 ATTTTAGATATACTACTAATTTGA-CTCTAA
1 ATTTTAGATAAAATACTAAGTTGATCCCTAA
*
76408 ATTTTAGATAAAATATTAAGTTGATCCCTAA
1 ATTTTAGATAAAATACTAAGTTGATCCCTAA
76439 ATTTTAGATAA
1 ATTTTAGATAA
76450 GATATCAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 20 0.56
31 16 0.44
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (31 bp):
ATTTTAGATAAAATACTAAGTTGATCCCTAA
Found at i:76442 original size:31 final size:31
Alignment explanation
Indices: 76378--76464 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 31
76368 TGACCCTTAT
* * * *
76378 ATTTTAGATATACTACTAATTTGA-CTCTAA
1 ATTTTAGATAAAATATTAATTTGATCCCTAA
*
76408 ATTTTAGATAAAATATTAAGTTGATCCCTAA
1 ATTTTAGATAAAATATTAATTTGATCCCTAA
* *
76439 ATTTTAGATAAGATATCAATTTGATC
1 ATTTTAGATAAAATATTAATTTGATC
76465 ATTGAATCAT
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 20 0.42
31 28 0.58
ACGTcount: A:0.39, C:0.10, G:0.09, T:0.41
Consensus pattern (31 bp):
ATTTTAGATAAAATATTAATTTGATCCCTAA
Found at i:78639 original size:28 final size:28
Alignment explanation
Indices: 78582--78639 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
78572 AGTTCCGTTT
* *
78582 TTTTGAGAAAGAGATTTTTTTATAGGAA
1 TTTTGAGAAAGAGATTTTTGTAGAGGAA
* *
78610 TTTTGAG-AAGAGATTTATTGTGGAGTAA
1 TTTTGAGAAAGAGATTT-TTGTAGAGGAA
78638 TT
1 TT
78640 GGTTATTAGC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
27 9 0.36
28 16 0.64
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.43
Consensus pattern (28 bp):
TTTTGAGAAAGAGATTTTTGTAGAGGAA
Found at i:81597 original size:30 final size:30
Alignment explanation
Indices: 81561--81623 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
81551 GCTCTATAGG
81561 TGTGCTTGCTGCCTTGCATCTAAGATTGCA
1 TGTGCTTGCTGCCTTGCATCTAAGATTGCA
81591 TGTGCTTGCTGCCTTGCATCTAAGATTGCA
1 TGTGCTTGCTGCCTTGCATCTAAGATTGCA
81621 TGT
1 TGT
81624 TCTTTAATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (30 bp):
TGTGCTTGCTGCCTTGCATCTAAGATTGCA
Done.