Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006216.1 Hibiscus syriacus cultivar Beakdansim tig00014808_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: 82255
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1523 original size:14 final size:14
Alignment explanation
Indices: 1499--1532 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
1489 AAAATTTGGT
1499 TAAAT-AATAAATA
1 TAAATAAATAAATA
1512 TAAATAAATAAATA
1 TAAATAAATAAATA
1526 T-AATAAA
1 TAAATAAA
1533 GATTTTACCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
TAAATAAATAAATA
Found at i:2721 original size:83 final size:82
Alignment explanation
Indices: 2568--2725 Score: 201
Period size: 83 Copynumber: 1.9 Consensus size: 82
2558 TGATTTTGTC
* * * *
2568 AAGATCCAAACTTACTCACAAATATTTTCAGAAAGTTAGAGAAATTACATAGGGCCCATTAAGAA
1 AAGATCCAAACTTACCCACAAATATTTTCAGAAAGTTAGAGAAATTACATAAGACCCATCAAGAA
2633 AAAGAAGAAGTTTTATG
66 AAAGAAGAAGTTTTATG
* * * * *
2650 AAGATTCAATCTTACCCAACAAATATTTTCATAAAGTTGGAGAAATTACA-AAGACTCCATCATG
1 AAGATCCAAACTTACCC-ACAAATATTTTCAGAAAGTTAGAGAAATTACATAAGAC-CCATCAAG
*
2714 AAGAAGAAGAAG
64 AAAAAGAAGAAG
2726 ATTCAAACTT
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
82 17 0.27
83 47 0.73
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.25
Consensus pattern (82 bp):
AAGATCCAAACTTACCCACAAATATTTTCAGAAAGTTAGAGAAATTACATAAGACCCATCAAGAA
AAAGAAGAAGTTTTATG
Found at i:12079 original size:24 final size:24
Alignment explanation
Indices: 12047--12103 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
12037 ACAAACAACA
*
12047 TGCCCTCAAACCTAAGATGTGAAT
1 TGCCCTCAAACCTAAGATGCGAAT
*
12071 TGCCCTCAAACCTAAGATGCGCAT
1 TGCCCTCAAACCTAAGATGCGAAT
12095 TGCCCTCAA
1 TGCCCTCAA
12104 TGCATGTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.30, C:0.32, G:0.16, T:0.23
Consensus pattern (24 bp):
TGCCCTCAAACCTAAGATGCGAAT
Found at i:22490 original size:39 final size:37
Alignment explanation
Indices: 22386--22495 Score: 105
Period size: 39 Copynumber: 2.8 Consensus size: 37
22376 TATAAAAAGT
* *
22386 AATTTAGAATTTAATGCGAAATAGTTTAAGAAATTAAG
1 AATTTAGAATTTAA-GTGAAATAATTTAAGAAATTAAG
* * *
22424 AATTTAGAATATTATAATGGCAA-AATTTAAGAAATTAGG
1 AATTTAGAAT-TTA-AGT-GAAATAATTTAAGAAATTAAG
*
22463 AATTTAGAATGTTAGAGTGAAATAATTTGAGAA
1 AATTTAGAAT-TTA-AGTGAAATAATTTAAGAA
22496 GTCTGAATAA
Statistics
Matches: 58, Mismatches: 10, Indels: 7
0.77 0.13 0.09
Matches are distributed among these distances:
38 13 0.22
39 41 0.71
40 4 0.07
ACGTcount: A:0.47, C:0.02, G:0.17, T:0.34
Consensus pattern (37 bp):
AATTTAGAATTTAAGTGAAATAATTTAAGAAATTAAG
Found at i:25697 original size:41 final size:41
Alignment explanation
Indices: 25604--25792 Score: 185
Period size: 41 Copynumber: 4.8 Consensus size: 41
25594 CCGAGAAAGT
* * *
25604 TCAATGGATTCACCATTCGGGATGAATTTCACATT-AAAACA
1 TCAATGGATTCACCCTTCGGGATGAATTTCAC-TTCGAAATA
* ** * *
25645 CCGGTGTATTCACCCTTCGAGATGAATTTCACTTCGAAATA
1 TCAATGGATTCACCCTTCGGGATGAATTTCACTTCGAAATA
*
25686 TCAATGGATTCACCCTTTGGGATGAATTTCACTTCGAAATA
1 TCAATGGATTCACCCTTCGGGATGAATTTCACTTCGAAATA
* * *
25727 TCAATGGA-T----CTTCAGGATGAATTTCAATTTGAAATA
1 TCAATGGATTCACCCTTCGGGATGAATTTCACTTCGAAATA
* * *
25763 TCAACGGGTTCA-CCTTTGGGATGAATTTCA
1 TCAATGGATTCACCCTTCGGGATGAATTTCA
25793 TTTTTGATTA
Statistics
Matches: 121, Mismatches: 22, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
36 29 0.24
37 1 0.01
40 18 0.15
41 73 0.60
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (41 bp):
TCAATGGATTCACCCTTCGGGATGAATTTCACTTCGAAATA
Found at i:26707 original size:63 final size:67
Alignment explanation
Indices: 26631--26758 Score: 192
Period size: 68 Copynumber: 2.0 Consensus size: 67
26621 TAAATATAAT
*
26631 TATATATTTTGAATATTTCAAATT-AAAG-TA-A-TATCTATTTAATTTTGAATACTAAAAGATG
1 TATATATTTTGAATATTTCAAATTAAAAGATATAGTATCTATTTAAATTTGAATACTAAAAGATG
26692 TC
66 TC
* *
26694 TATATCTTTTGAATATTTCAAATTAAAAGATATTAGTATCTGTTTAAATTTGAATACTAAAAGAT
1 TATATATTTTGAATATTTCAAATTAAAAGATA-TAGTATCTATTTAAATTTGAATACTAAAAGAT
26759 ATCTGATTGG
Statistics
Matches: 57, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
63 23 0.40
64 4 0.07
65 2 0.04
67 1 0.02
68 27 0.47
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (67 bp):
TATATATTTTGAATATTTCAAATTAAAAGATATAGTATCTATTTAAATTTGAATACTAAAAGATG
TC
Found at i:26721 original size:34 final size:33
Alignment explanation
Indices: 26630--26734 Score: 87
Period size: 34 Copynumber: 3.2 Consensus size: 33
26620 GTAAATATAA
*
26630 TTATATATTTTGAATATTTCAAATT--AA-A-G
1 TTATATCTTTTGAATATTTCAAATTAAAAGATG
* * *
26659 TAATATCTATTT-AAT-TTTGAATACTAAAAGATG
1 TTATATCT-TTTGAATATTTCAA-ATTAAAAGATG
*
26692 TCTATATCTTTTGAATATTTCAAATTAAAAGATA
1 T-TATATCTTTTGAATATTTCAAATTAAAAGATG
26726 TTAGTATCT
1 TTA-TATCT
26735 GTTTAAATTT
Statistics
Matches: 58, Mismatches: 8, Indels: 15
0.72 0.10 0.19
Matches are distributed among these distances:
28 5 0.09
29 11 0.19
30 3 0.05
31 2 0.03
32 1 0.02
33 7 0.12
34 24 0.41
35 5 0.09
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.46
Consensus pattern (33 bp):
TTATATCTTTTGAATATTTCAAATTAAAAGATG
Found at i:26755 original size:34 final size:33
Alignment explanation
Indices: 26661--26762 Score: 109
Period size: 34 Copynumber: 3.0 Consensus size: 33
26651 AATTAAAGTA
* *
26661 ATATCTATTTAATTTTGAATACTAAAAGATGTCT
1 ATATCT-TTTAAATTTGAATACTAAAAGATATCT
* *
26695 ATATCTTTTGAATATTTCAA-ATTAAAAGATAT-T
1 ATATCTTTT-AA-ATTTGAATACTAAAAGATATCT
26728 AGTATCTGTTTAAATTTGAATACTAAAAGATATCT
1 A-TATCT-TTTAAATTTGAATACTAAAAGATATCT
26763 GATTGGACTA
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
33 11 0.20
34 36 0.64
35 9 0.16
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.43
Consensus pattern (33 bp):
ATATCTTTTAAATTTGAATACTAAAAGATATCT
Found at i:27262 original size:15 final size:15
Alignment explanation
Indices: 27242--27274 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
27232 AATGATGATG
27242 ATTATTTT-TATAATT
1 ATTATTTTCTAT-ATT
27257 ATTATTTTCTATATT
1 ATTATTTTCTATATT
27272 ATT
1 ATT
27275 CTCTTATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 14 0.82
16 3 0.18
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTATTTTCTATATT
Found at i:41938 original size:50 final size:51
Alignment explanation
Indices: 41883--41986 Score: 138
Period size: 50 Copynumber: 2.0 Consensus size: 51
41873 TTGATAGATT
* * *
41883 TATATTCAATATTTTAATTCTATTCGTCATTTAT-ACAAAAATATTGTTTG
1 TATATTCAACATCTTAATTCTATTCGTCATTTATAAAAAAAATATTGTTTG
* **
41933 TATATTCAACATCTTAATTCTATTCTTTTTTTATAAAAAAAAATATTGTTTG
1 TATATTCAACATCTTAATTCTATTCGTCATTTAT-AAAAAAAATATTGTTTG
41985 TA
1 TA
41987 AAATCATTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
50 29 0.63
52 17 0.37
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.50
Consensus pattern (51 bp):
TATATTCAACATCTTAATTCTATTCGTCATTTATAAAAAAAATATTGTTTG
Found at i:43007 original size:46 final size:48
Alignment explanation
Indices: 42934--43034 Score: 152
Period size: 48 Copynumber: 2.1 Consensus size: 48
42924 TATAGCTAAG
* * *
42934 CCTTGCATTATTAGTTATGTCTTT-A-ATATTCAACGGTCAGTGCTTT
1 CCTTGAATTATTAGCTATGTCTTTAATATATTCAACGATCAGTGCTTT
*
42980 TCTTGAATTATTAGCTATGTCTTTAATATATTCAACGATCAGTGCTTT
1 CCTTGAATTATTAGCTATGTCTTTAATATATTCAACGATCAGTGCTTT
43028 CCTTGAA
1 CCTTGAA
43035 GATTCAAAGG
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
46 21 0.44
47 1 0.02
48 26 0.54
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.45
Consensus pattern (48 bp):
CCTTGAATTATTAGCTATGTCTTTAATATATTCAACGATCAGTGCTTT
Found at i:43593 original size:2 final size:2
Alignment explanation
Indices: 43586--43614 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
43576 GATGTTCTCA
43586 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
43615 CAGTCTATTG
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:49566 original size:14 final size:15
Alignment explanation
Indices: 49547--49584 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
49537 AAGTCAATGG
*
49547 GTTGACTCGGA-CGA
1 GTTGACTCAGACCGA
49561 GTTGACTCAGACCGA
1 GTTGACTCAGACCGA
49576 GTTGACTCA
1 GTTGACTCA
49585 AACGGGTAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.24
Consensus pattern (15 bp):
GTTGACTCAGACCGA
Found at i:51549 original size:15 final size:16
Alignment explanation
Indices: 51526--51558 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
51516 ATAATTACCA
51526 TTTGTCATTAAAATAT
1 TTTGTCATTAAAATAT
51542 TTTG-CATTAAAATAT
1 TTTGTCATTAAAATAT
51557 TT
1 TT
51559 CATAGACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52
Consensus pattern (16 bp):
TTTGTCATTAAAATAT
Found at i:56660 original size:18 final size:19
Alignment explanation
Indices: 56637--56680 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
56627 CCAGTAATCC
*
56637 TATTCC-CTGGCAATCTTT
1 TATTCCACTGGCAATCTTA
*
56655 TATTCCCACTGGTAATCTTA
1 TATT-CCACTGGCAATCTTA
56675 TATTCC
1 TATTCC
56681 GTGAACCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 4 0.18
19 4 0.18
20 14 0.64
ACGTcount: A:0.20, C:0.27, G:0.09, T:0.43
Consensus pattern (19 bp):
TATTCCACTGGCAATCTTA
Found at i:56671 original size:20 final size:20
Alignment explanation
Indices: 56643--56680 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
56633 ATCCTATTCC
*
56643 CTGGCAATCTTTTATTCCCA
1 CTGGCAATCTTATATTCCCA
*
56663 CTGGTAATCTTATATTCC
1 CTGGCAATCTTATATTCC
56681 GTGAACCAAA
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:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGCAATCTTATATTCCCA
Found at i:65477 original size:25 final size:23
Alignment explanation
Indices: 65444--65495 Score: 68
Period size: 25 Copynumber: 2.2 Consensus size: 23
65434 TTTATTTAAT
*
65444 ATTAATATATTTTAAATTTTAAATA
1 ATTAATATATATTAAA-TTTAAA-A
*
65469 ATTAATATATATTACATTTAAAA
1 ATTAATATATATTAAATTTAAAA
65492 ATTA
1 ATTA
65496 TAGATGTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 5 0.20
24 6 0.24
25 14 0.56
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
ATTAATATATATTAAATTTAAAA
Found at i:68117 original size:21 final size:20
Alignment explanation
Indices: 68091--68171 Score: 58
Period size: 21 Copynumber: 3.8 Consensus size: 20
68081 AGTCAAGGGT
68091 TTATGTGGTC-CTTCGGGACAA
1 TTATGTGG-CACTTCGGGA-AA
*
68112 TTATGTGGCACTACGGTGTAAA
1 TTATGTGGCACTTCGG-G-AAA
**
68134 TCTATGTGGTC-CTTTAGGATAA
1 T-TATGTGG-CACTTCGGGA-AA
68156 TTATGTGGCACTTCGG
1 TTATGTGGCACTTCGG
68172 TGCAAATTAC
Statistics
Matches: 47, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
20 2 0.04
21 25 0.53
22 8 0.17
23 11 0.23
24 1 0.02
ACGTcount: A:0.21, C:0.16, G:0.27, T:0.36
Consensus pattern (20 bp):
TTATGTGGCACTTCGGGAAA
Found at i:68144 original size:44 final size:44
Alignment explanation
Indices: 68092--68178 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
68082 GTCAAGGGTT
* *
68092 TATGTGGTCCTTCGGGACAATTATGTGGCACTACGGTGTAAATC
1 TATGTGGTCCTTCAGGACAATTATGTGGCACTACGGTGCAAATC
* * *
68136 TATGTGGTCCTTTAGGATAATTATGTGGCACTTCGGTGCAAAT
1 TATGTGGTCCTTCAGGACAATTATGTGGCACTACGGTGCAAAT
68179 TACGAGTTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.34
Consensus pattern (44 bp):
TATGTGGTCCTTCAGGACAATTATGTGGCACTACGGTGCAAATC
Found at i:73361 original size:20 final size:21
Alignment explanation
Indices: 73324--73363 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
73314 ACTGCAGGAA
*
73324 TTTATGGCCTCGACAAAAGAT
1 TTTATGGCCTCGAAAAAAGAT
*
73345 TTTATGGCTTC-AAAAAAGA
1 TTTATGGCCTCGAAAAAAGA
73364 CCTTGATACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (21 bp):
TTTATGGCCTCGAAAAAAGAT
Found at i:79526 original size:21 final size:21
Alignment explanation
Indices: 79500--79543 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
79490 CAATTAAGAA
* *
79500 TCAAGGAGCTTTACTTCATAG
1 TCAAGGAGCCTTACTTCAAAG
*
79521 TCAAGGCGCCTTACTTCAAAG
1 TCAAGGAGCCTTACTTCAAAG
79542 TC
1 TC
79544 CTAGCTCGTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (21 bp):
TCAAGGAGCCTTACTTCAAAG
Done.