Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007330.1 Hibiscus syriacus cultivar Beakdansim tig00019604_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: 58553
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1368 original size:8 final size:8
Alignment explanation
Indices: 1357--1395 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
1347 TTTTTGGGTT
*
1357 TTTTTTTA
1 TTTTATTA
1365 TTTT-TTA
1 TTTTATTA
1372 TTTTATTA
1 TTTTATTA
*
1380 TTTTATTT
1 TTTTATTA
1388 TTTTATTA
1 TTTTATTA
1396 ATTTGTGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 7 0.25
8 21 0.75
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTATTA
Found at i:1697 original size:16 final size:17
Alignment explanation
Indices: 1670--1701 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1660 CATCTTTAGA
1670 GTAGAGGTAGAGATGCT
1 GTAGAGGTAGAGATGCT
1687 GTAGA-GTAGAGATGC
1 GTAGAGGTAGAGATGC
1702 GGGCTGGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.31, C:0.06, G:0.41, T:0.22
Consensus pattern (17 bp):
GTAGAGGTAGAGATGCT
Found at i:18629 original size:2 final size:2
Alignment explanation
Indices: 18622--18709 Score: 176
Period size: 2 Copynumber: 44.0 Consensus size: 2
18612 TTTTTGTGTT
18622 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
18664 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
18706 TA TA
1 TA TA
18710 AAGTTTATAC
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 86 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25729 original size:22 final size:23
Alignment explanation
Indices: 25703--25786 Score: 77
Period size: 22 Copynumber: 3.7 Consensus size: 23
25693 TTGGTGCAGA
*
25703 GGGAATCGATCCCCCCTCATGA-
1 GGGAACCGATCCCCCCTCATGAG
* *
25725 GGGAACCGATTCCCCCT-TTGAAG
1 GGGAACCGATCCCCCCTCATG-AG
*
25748 GGGAACCGATTCCCCC-CAT-AG
1 GGGAACCGATCCCCCCTCATGAG
*
25769 GGGAATCGATACCCCCCT
1 GGGAACCGAT-CCCCCCT
25787 GGGGTTCTGT
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
21 13 0.25
22 21 0.41
23 17 0.33
ACGTcount: A:0.23, C:0.36, G:0.24, T:0.18
Consensus pattern (23 bp):
GGGAACCGATCCCCCCTCATGAG
Found at i:25772 original size:21 final size:21
Alignment explanation
Indices: 25703--25785 Score: 69
Period size: 21 Copynumber: 3.8 Consensus size: 21
25693 TTGGTGCAGA
* *
25703 GGGAATCGATCCCCCCTCAT-G
1 GGGAACCGATTCCCCC-CATAG
**
25724 AGGGAACCGATTCCCCCTTTGAAG
1 -GGGAACCGATTCCCCCCAT--AG
25748 GGGAACCGATTCCCCCCATAG
1 GGGAACCGATTCCCCCCATAG
* *
25769 GGGAATCGATACCCCCC
1 GGGAACCGATTCCCCCC
25786 TGGGGTTCTG
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
21 18 0.36
22 14 0.28
23 17 0.34
24 1 0.02
ACGTcount: A:0.23, C:0.36, G:0.24, T:0.17
Consensus pattern (21 bp):
GGGAACCGATTCCCCCCATAG
Found at i:33909 original size:2 final size:2
Alignment explanation
Indices: 33902--33930 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
33892 ATGCAAATAC
33902 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
33931 GGGAAATGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33910 original size:89 final size:89
Alignment explanation
Indices: 33759--33922 Score: 319
Period size: 89 Copynumber: 1.8 Consensus size: 89
33749 TGACATATTT
33759 ATTAGAAAGATGGCATAAAAATATAGATCTACATATCAAGACAAATGCAAATACATACATATATA
1 ATTAGAAAGATGGCATAAAAATATAGATCTACATATCAAGACAAATGCAAATACATACATATATA
33824 TATATATATAGGGAAATGTCGAGG
66 TATATATATAGGGAAATGTCGAGG
*
33848 ATTAGAAAGATGGCATAAAAATATAGATCTACATATCAAGACAAATGCAAATACATATATATATA
1 ATTAGAAAGATGGCATAAAAATATAGATCTACATATCAAGACAAATGCAAATACATACATATATA
33913 TATATATATA
66 TATATATATA
33923 TATATATAGG
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
89 74 1.00
ACGTcount: A:0.50, C:0.10, G:0.13, T:0.27
Consensus pattern (89 bp):
ATTAGAAAGATGGCATAAAAATATAGATCTACATATCAAGACAAATGCAAATACATACATATATA
TATATATATAGGGAAATGTCGAGG
Found at i:34092 original size:2 final size:2
Alignment explanation
Indices: 34085--34143 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
34075 AATGAAAAGA
34085 AT AT AT AT AT AT AT AT 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 AT
34127 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
34144 AAAGCTAAAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:35346 original size:23 final size:23
Alignment explanation
Indices: 35302--35347 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
35292 TTGTTGCTTC
* * *
35302 ATGATCTTTTTTCTTCCGTTTTT
1 ATGATATTTTTTCTCCCATTTTT
*
35325 ATGATATTTTTTGTCCCATTTTT
1 ATGATATTTTTTCTCCCATTTTT
35348 GCTTGATGGC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.13, C:0.15, G:0.09, T:0.63
Consensus pattern (23 bp):
ATGATATTTTTTCTCCCATTTTT
Found at i:35682 original size:2 final size:2
Alignment explanation
Indices: 35675--35840 Score: 241
Period size: 2 Copynumber: 84.5 Consensus size: 2
35665 AATCCCATTA
* *
35675 AT AT AT AT AT AT AT AT GT AT GT 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 AT
* *
35717 AT AT AT AT AT AT AT AT AT GT AT GT 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 AT
* *
35759 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AC 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 AT
35801 AT AT AT AT AT AT AT AT A- AT -T ACT -T AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
35840 A
1 A
35841 CATACATACA
Statistics
Matches: 147, Mismatches: 12, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
1 4 0.03
2 142 0.97
3 1 0.01
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:36474 original size:128 final size:127
Alignment explanation
Indices: 36301--36612 Score: 346
Period size: 128 Copynumber: 2.4 Consensus size: 127
36291 AGACTAAAAA
* * * * * *
36301 AAAATGTTGATCCACTTCGCTGCTCTGTAGGGAAGATTGAATCAAACTTGATTTTCTTTGTTTCT
1 AAAATTTTGATTCACTTCGCTGCTCTTTAGGGAAGATTGAATCAAACTTGATTTCCTTCGTTGCT
* ** * * * *
36366 CTTT-AGGTAGACCAAA-T-TCG-A-AAGAATCTGCTTCACATTTCTTTAGGGTAGATCAGACTC
66 -TTTCAGGGAGACCAAACTAAAGAAGAAGAATCTGATCCAC-TAT-TTT-GGGTA-ATCA-AATC
36426 AAG
125 AAG
* *
36429 AAAATTTTGATTCACTTCACTGCTCTTTAGGGAAGATTGAGTCAAACTTGATTTCCTTCGTTGCT
1 AAAATTTTGATTCACTTCGCTGCTCTTTAGGGAAGATTGAATCAAACTTGATTTCCTTCGTTGCT
**
36494 TTTCAGGGAGACCAAACCTGAAAGAAGAAGAATCTGATCCACTATTTTGGGTAATCAAATCTTG
66 TTTCAGGGAGACCAAA-CT-AAAGAAGAAGAATCTGATCCACTATTTTGGGTAATCAAATCAAG
*
36558 AAAATTATTGATTCACTTCGCTGCTCTTCAGGGAAGATTGAATCAAACTTGATTT
1 AAAATT-TTGATTCACTTCGCTGCTCTTTAGGGAAGATTGAATCAAACTTGATTT
36613 GTTTCAGTGC
Statistics
Matches: 156, Mismatches: 20, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
127 3 0.02
128 68 0.44
129 10 0.06
130 50 0.32
131 5 0.03
132 4 0.03
133 3 0.02
134 13 0.08
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (127 bp):
AAAATTTTGATTCACTTCGCTGCTCTTTAGGGAAGATTGAATCAAACTTGATTTCCTTCGTTGCT
TTTCAGGGAGACCAAACTAAAGAAGAAGAATCTGATCCACTATTTTGGGTAATCAAATCAAG
Found at i:46987 original size:19 final size:19
Alignment explanation
Indices: 46935--46987 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
46925 GAATCAATAT
*
46935 AATGTAATGCAAAAGATAA
1 AATGCAATGCAAAAGATAA
* *
46954 AATGCATTGTGAAAAG-TAA
1 AATGCAATG-CAAAAGATAA
46973 AATGCACATGCAAAA
1 AATGCA-ATGCAAAA
46988 TGCAAGGTGT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
19 20 0.74
20 7 0.26
ACGTcount: A:0.53, C:0.09, G:0.17, T:0.21
Consensus pattern (19 bp):
AATGCAATGCAAAAGATAA
Found at i:48836 original size:55 final size:55
Alignment explanation
Indices: 48790--49305 Score: 757
Period size: 55 Copynumber: 9.4 Consensus size: 55
48780 TATTTTGTTT
*
48790 ATGAATTTCCGTATGGGCACTTAATGTGTAAACTTAAGAAATTCATACTAAGTGG
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
* * *
48845 ATGAATTTCCGTATGGGCACTTTATATGCAAACTTAAGAAATTCATACTAAGTGA
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
* *
48900 ATGAATTTCCATATGGGCACTTTATGTGTAAATTTAAGAAATTCATACTAAGTGG
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
* * *
48955 ATGAATTTTCGTATGGGCACTTTATATGGAAACTTAAGAAATTCATACTAAGTGG
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
49010 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
* *
49065 ATGAATTTCCGTATGGGCACTTTATGTATAAACTTAAGAAATTCATACCAAGTGG
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
* * * * *
49120 ATGAATTTTCATATGGGCACTTTATGTGTAAATTTAAGAAATTCATTAC-ATGTAG
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCA-TACTAAGTGG
*
49175 ATGAATTTCCGTATGGGCACTTTATGCGTAAACTTAAGAAATTCATACTAAGTGG
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
** * * * * **
49230 ATGAATTTATGTATGGGCACTTTGTATGTAAAAC-TAAGAAATGCATAATAAGTTT
1 ATGAATTTCCGTATGGGCACTTTATGTGT-AAACTTAAGAAATTCATACTAAGTGG
* *
49285 ATGAATTTCAGTATTGGCACT
1 ATGAATTTCCGTATGGGCACT
49306 GTGTGTGGAA
Statistics
Matches: 415, Mismatches: 43, Indels: 6
0.89 0.09 0.01
Matches are distributed among these distances:
54 3 0.01
55 405 0.98
56 7 0.02
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35
Consensus pattern (55 bp):
ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
Found at i:53152 original size:16 final size:17
Alignment explanation
Indices: 53133--53174 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
53123 CAAAATATTT
*
53133 TTTAATTTTAATAAG-A
1 TTTAATTTTAAAAAGTA
53149 TTTAATTTTAAAAAGTA
1 TTTAATTTTAAAAAGTA
53166 TTTAATTTT
1 TTTAATTTT
53175 TTTTAAGGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (17 bp):
TTTAATTTTAAAAAGTA
Found at i:53546 original size:21 final size:22
Alignment explanation
Indices: 53522--53567 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
53512 AAATTAAATT
53522 AAAAAA-TACCAATCCTATTAA
1 AAAAAATTACCAATCCTATTAA
53543 AAAAAATTACCAATCCTATTAA
1 AAAAAATTACCAATCCTATTAA
53565 AAA
1 AAA
53568 GAAGAAGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.59, C:0.17, G:0.00, T:0.24
Consensus pattern (22 bp):
AAAAAATTACCAATCCTATTAA
Done.