Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001570.1 Hibiscus syriacus cultivar Beakdansim tig00003119_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: 100912
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:8262 original size:32 final size:32
Alignment explanation
Indices: 8221--8290 Score: 140
Period size: 32 Copynumber: 2.2 Consensus size: 32
8211 AGGTGTCTAG
8221 GACATAACGACCGTTAAATTCTACCATTAAAA
1 GACATAACGACCGTTAAATTCTACCATTAAAA
8253 GACATAACGACCGTTAAATTCTACCATTAAAA
1 GACATAACGACCGTTAAATTCTACCATTAAAA
8285 GACATA
1 GACATA
8291 TGTCACGTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.24
Consensus pattern (32 bp):
GACATAACGACCGTTAAATTCTACCATTAAAA
Found at i:9349 original size:18 final size:18
Alignment explanation
Indices: 9326--9360 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
9316 ACTGAATATT
9326 TGTCCCGGAA-GACCACTA
1 TGTCCC-GAATGACCACTA
9344 TGTCCCGAATGACCACT
1 TGTCCCGAATGACCACT
9361 GATAATCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.26, C:0.34, G:0.20, T:0.20
Consensus pattern (18 bp):
TGTCCCGAATGACCACTA
Found at i:20142 original size:15 final size:15
Alignment explanation
Indices: 20122--20173 Score: 79
Period size: 15 Copynumber: 3.5 Consensus size: 15
20112 TTCCAGAAAA
20122 TGAATTACTGGAATT
1 TGAATTACTGGAATT
20137 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
20152 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
20166 TGAATTAC
1 TGAATTAC
20174 ATTTCTGTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.35
15 22 0.65
ACGTcount: A:0.37, C:0.08, G:0.19, T:0.37
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:20179 original size:20 final size:20
Alignment explanation
Indices: 20156--20225 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
20146 GGAATTTGAA
20156 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
20176 TTCTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
20196 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
20216 TTCTGGAAAA
1 TTCTGGAAAA
20226 CATCTGGAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:20448 original size:28 final size:27
Alignment explanation
Indices: 20393--20457 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 27
20383 TTTACTAAAA
*
20393 TATTATTGAAATATATAAATAATATTAT
1 TATTATT-AAATATATAAAAAATATTAT
20421 TCATTATTAAATATATAAAAAA-ATTTAT
1 T-ATTATTAAATATATAAAAAATA-TTAT
20449 TATATATTA
1 TAT-TATTA
20458 TTAAAATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 3 0.09
28 24 0.73
29 6 0.18
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (27 bp):
TATTATTAAATATATAAAAAATATTAT
Found at i:20483 original size:31 final size:32
Alignment explanation
Indices: 20393--20490 Score: 84
Period size: 31 Copynumber: 3.2 Consensus size: 32
20383 TTTACTAAAA
*
20393 TATTATTGAAATATAT--AAATA-ATATTAT-T
1 TATTATT-AAATATATAAAAAAATATATTATAT
* *
20422 CATTATTAAATATATAAAAAAATTTATTATA-
1 TATTATTAAATATATAAAAAAATATATTATAT
*
20453 TATTATTAAA-ATA-AAAATATAATATCTTATAT
1 TATTATTAAATATATAAAA-A-AATATATTATAT
20485 TATTAT
1 TATTAT
20491 AATATAATTG
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
28 8 0.14
29 10 0.18
30 8 0.14
31 24 0.43
32 6 0.11
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (32 bp):
TATTATTAAATATATAAAAAAATATATTATAT
Found at i:20535 original size:22 final size:23
Alignment explanation
Indices: 20510--20553 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
20500 GATTATTTTA
20510 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
20532 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
20554 AATATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:20558 original size:22 final size:22
Alignment explanation
Indices: 20514--20570 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
20504 ATTTTATATA
* *
20514 ATATTAAAAATA-TAATATTAT
1 ATATTATAAATATTAATATAAT
20535 ATTATTATAAATATTAATA-AAT
1 A-TATTATAAATATTAATATAAT
*
20557 ATATTTTAAATATT
1 ATATTATAAATATT
20571 TTAATAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 13 0.42
22 13 0.42
23 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATTATAAATATTAATATAAT
Found at i:20569 original size:52 final size:51
Alignment explanation
Indices: 20450--20570 Score: 133
Period size: 54 Copynumber: 2.3 Consensus size: 51
20440 AAAATTTATT
**
20450 ATATATTATTAAA-A-TAAAAATATAATATCTTATATTATTATAATATAATTG
1 ATATATT-TTAAATATTAAAAATATAATA-CTTATATTATTATAATATAATAA
20501 AT-TATTTTATATAATATTAAAAATATAATA-TTATATTATTATAAATATTAATAA
1 ATATA-TTT-TA-AATATTAAAAATATAATACTTATATTATTAT-AATA-TAATAA
20555 ATATATTTTAAATATT
1 ATATATTTTAAATATT
20571 TTAATAATTA
Statistics
Matches: 60, Mismatches: 2, Indels: 15
0.78 0.03 0.19
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 20 0.33
53 7 0.12
54 22 0.37
55 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (51 bp):
ATATATTTTAAATATTAAAAATATAATACTTATATTATTATAATATAATAA
Found at i:20871 original size:42 final size:42
Alignment explanation
Indices: 20759--20872 Score: 194
Period size: 41 Copynumber: 2.7 Consensus size: 42
20749 ATGAATTACA
* *
20759 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGAAAAACGAATTACGTGAAACAAACACGGGAAAACATT
*
20801 TTCCGAAAAA-TAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGAAAAACGAATTACGTGAAACAAACACGGGAAAACATT
20842 TTCCGAAAAACGAATTACGTGAAACAAACAC
1 TTCCGAAAAACGAATTACGTGAAACAAACAC
20873 TGAAATTCGG
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
41 39 0.58
42 28 0.42
ACGTcount: A:0.46, C:0.19, G:0.17, T:0.18
Consensus pattern (42 bp):
TTCCGAAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:24343 original size:32 final size:33
Alignment explanation
Indices: 24307--24372 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 33
24297 TCAATATATA
*
24307 AGATGCAATTTTCGAACAACATATAT-TAAAAG
1 AGATGCAATATTCGAACAACATATATATAAAAG
*
24339 AGATGCAATATTCGAACAATATATATATAAAAG
1 AGATGCAATATTCGAACAACATATATATAAAAG
24372 A
1 A
24373 TGCAGTATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 24 0.77
33 7 0.23
ACGTcount: A:0.50, C:0.11, G:0.12, T:0.27
Consensus pattern (33 bp):
AGATGCAATATTCGAACAACATATATATAAAAG
Found at i:26136 original size:26 final size:26
Alignment explanation
Indices: 26100--26149 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
26090 AATCAACATG
* *
26100 AGTATTATGCAAAATTAGTATGAGCA
1 AGTATCATGCAAAATTAATATGAGCA
*
26126 AGTATCATGCATAATTAATATGAG
1 AGTATCATGCAAAATTAATATGAG
26150 TAAATATTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (26 bp):
AGTATCATGCAAAATTAATATGAGCA
Found at i:29659 original size:19 final size:19
Alignment explanation
Indices: 29635--29672 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
29625 AACTAGTCCA
29635 AAATCAATATTTTAATATT
1 AAATCAATATTTTAATATT
29654 AAATCAATATTTTAATATT
1 AAATCAATATTTTAATATT
29673 CGATTACAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (19 bp):
AAATCAATATTTTAATATT
Found at i:38222 original size:15 final size:14
Alignment explanation
Indices: 38202--38257 Score: 51
Period size: 15 Copynumber: 3.8 Consensus size: 14
38192 GATTATAATT
38202 ATTTTAAATAATTAA
1 ATTTTAAA-AATTAA
*
38217 ATTTTATAAAA-TAT
1 ATTTTA-AAAATTAA
38231 ATATTTAAAAATTAA
1 AT-TTTAAAAATTAA
*
38246 GATTTTTAAAAT
1 -ATTTTAAAAAT
38258 ATATATATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
14 8 0.24
15 22 0.65
16 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (14 bp):
ATTTTAAAAATTAA
Found at i:38253 original size:31 final size:30
Alignment explanation
Indices: 38204--38265 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 30
38194 TTATAATTAT
38204 TTTAAATAATTAAATTTTATAAA-ATATATA
1 TTTAAATAATTAAATTTTA-AAATATATATA
38234 TTTAAA-AATTAAGATTTTTAAAATATATATA
1 TTTAAATAATTAA-A-TTTTAAAATATATATA
38265 T
1 T
38266 ATATGTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
29 6 0.21
30 10 0.34
31 13 0.45
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (30 bp):
TTTAAATAATTAAATTTTAAAATATATATA
Found at i:38255 original size:29 final size:30
Alignment explanation
Indices: 38204--38263 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 30
38194 TTATAATTAT
38204 TTTAAATAATTAAATTTTATAAAATATATA
1 TTTAAATAATTAAATTTTATAAAATATATA
38234 TTTAAA-AATTAAGATTTT-TAAAATATATA
1 TTTAAATAATTAA-ATTTTATAAAATATATA
38263 T
1 T
38264 ATATATGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 18 0.62
30 11 0.38
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (30 bp):
TTTAAATAATTAAATTTTATAAAATATATA
Found at i:58976 original size:2 final size:2
Alignment explanation
Indices: 58969--58998 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
58959 TACATGGTAA
58969 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
58999 GAAGTAAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59153 original size:33 final size:33
Alignment explanation
Indices: 59105--59171 Score: 109
Period size: 33 Copynumber: 2.0 Consensus size: 33
59095 AAATGAGAAA
59105 ATATTTACTAGAAAAAACCAAAGAATTAATCTC
1 ATATTTACTAGAAAAAACCAAAGAATTAATCTC
*
59138 ATATTTACT-GAAAAAAATCAAAGAATTAATCTC
1 ATATTTACTAG-AAAAAACCAAAGAATTAATCTC
59171 A
1 A
59172 ACTTTTGATA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 1 0.03
33 31 0.97
ACGTcount: A:0.52, C:0.13, G:0.06, T:0.28
Consensus pattern (33 bp):
ATATTTACTAGAAAAAACCAAAGAATTAATCTC
Found at i:59290 original size:28 final size:28
Alignment explanation
Indices: 59250--59307 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
59240 TGAATGGCTT
59250 ATACATAATGTGACACATCAAGACACTA
1 ATACATAATGTGACACATCAAGACACTA
59278 ATACATAATGTGACACATCAAGACACTA
1 ATACATAATGTGACACATCAAGACACTA
59306 AT
1 AT
59308 GTGACTCTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.47, C:0.21, G:0.10, T:0.22
Consensus pattern (28 bp):
ATACATAATGTGACACATCAAGACACTA
Found at i:61829 original size:17 final size:17
Alignment explanation
Indices: 61807--61840 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
61797 CGTTTTCATT
61807 TTACATAATGAAAGTAA
1 TTACATAATGAAAGTAA
61824 TTACATAATGAAAGTAA
1 TTACATAATGAAAGTAA
61841 AGGCTTGTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.12, T:0.29
Consensus pattern (17 bp):
TTACATAATGAAAGTAA
Found at i:77984 original size:23 final size:23
Alignment explanation
Indices: 77899--77982 Score: 116
Period size: 23 Copynumber: 3.7 Consensus size: 23
77889 CAGCTCATAT
*
77899 AATTGCACC-TAAGTGCCACGTAG
1 AATTGCACCGT-AGTGCCGCGTAG
*
77922 AATTGCACTGTAGTGCCGCGTAG
1 AATTGCACCGTAGTGCCGCGTAG
* *
77945 AATTGCACCGGAGTGTCGCGTAG
1 AATTGCACCGTAGTGCCGCGTAG
77968 AATTGCACCGTAGTG
1 AATTGCACCGTAGTG
77983 TCATATAATA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
23 53 0.98
24 1 0.02
ACGTcount: A:0.25, C:0.23, G:0.29, T:0.24
Consensus pattern (23 bp):
AATTGCACCGTAGTGCCGCGTAG
Found at i:78624 original size:19 final size:20
Alignment explanation
Indices: 78587--78624 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
78577 CTTTTTTTTA
*
78587 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
78607 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
78625 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:83807 original size:27 final size:27
Alignment explanation
Indices: 83765--83830 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 27
83755 AAAACAGTGT
*
83765 TGAATGATTCAACACAGAAGTACATTC
1 TGAATGATTCAGCACAGAAGTACATTC
*
83792 TGAATGATTCAGCACAGAAGTACATTT
1 TGAATGATTCAGCACAGAAGTACATTC
83819 TGAATGATTCAG
1 TGAATGATTCAG
83831 AGCCATTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (27 bp):
TGAATGATTCAGCACAGAAGTACATTC
Found at i:83904 original size:15 final size:15
Alignment explanation
Indices: 83884--83921 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
83874 AGAGTCTCTG
83884 AATCATTCAACGCTT
1 AATCATTCAACGCTT
* *
83899 AATCATTCAGCGTTT
1 AATCATTCAACGCTT
83914 AATCATTC
1 AATCATTC
83922 TGAAGTAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.37
Consensus pattern (15 bp):
AATCATTCAACGCTT
Found at i:96319 original size:48 final size:48
Alignment explanation
Indices: 96208--96322 Score: 115
Period size: 48 Copynumber: 2.4 Consensus size: 48
96198 TCAGCATCTT
* * * * *
96208 CATTTATGGATG-GACTATGCATATCTTGTTCCTTAATGTCAATTCCAT
1 CATTTATGGATGAG-CTATGCACATCTTGTTACTCAATGTCAATGCCAC
* * ** * *
96256 TATTAATGGGCGAGCTATGTACATCTTGTTACTCAATGTCAGTGCCAC
1 CATTTATGGATGAGCTATGCACATCTTGTTACTCAATGTCAATGCCAC
96304 CATTTATGGATGAGCTATG
1 CATTTATGGATGAGCTATG
96323 GGCATTTTGT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
48 50 0.98
49 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.37
Consensus pattern (48 bp):
CATTTATGGATGAGCTATGCACATCTTGTTACTCAATGTCAATGCCAC
Found at i:99809 original size:2 final size:2
Alignment explanation
Indices: 99802--99845 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
99792 GAAAAATGAT
99802 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
99844 TA
1 TA
99846 GGAAGATGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:100342 original size:23 final size:23
Alignment explanation
Indices: 100312--100376 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
100302 ACAACCTTAT
100312 ATGGCACTTCGGTGCATTTCTAC
1 ATGGCACTTCGGTGCATTTCTAC
* * *
100335 ATGGCACTACGGTGTAATTCTAC
1 ATGGCACTTCGGTGCATTTCTAC
* *
100358 GTGGAACTTCGGTGCATTT
1 ATGGCACTTCGGTGCATTT
100377 ATACGAGCTG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.34
Consensus pattern (23 bp):
ATGGCACTTCGGTGCATTTCTAC
Done.