Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002654.1 Hibiscus syriacus cultivar Beakdansim tig00005428_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: 61309
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:15925 original size:26 final size:26
Alignment explanation
Indices: 15894--15966 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 26
15884 AACAATTAAA
15894 TTTTAAAATACATTTTTCAAAAACAC
1 TTTTAAAATACATTTTTCAAAAACAC
** *
15920 TTTTAAAAGTAC-TTTTTTTATAACAC
1 TTTTAAAA-TACATTTTTCAAAAACAC
* *
15946 TTTTTAAAT-CAATTTTCAAAA
1 TTTTAAAATACATTTTTCAAAA
15967 GTAATATCAA
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
24 1 0.03
25 7 0.19
26 26 0.70
27 3 0.08
ACGTcount: A:0.41, C:0.12, G:0.01, T:0.45
Consensus pattern (26 bp):
TTTTAAAATACATTTTTCAAAAACAC
Found at i:16017 original size:32 final size:32
Alignment explanation
Indices: 15977--16037 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
15967 GTAATATCAA
15977 TTACTTACACCAATGTAAATAAGTTGTAACCC
1 TTACTTACACCAATGTAAATAAGTTGTAACCC
*
16009 TTACTTACACCAGTGTAAATAAGTTGTAA
1 TTACTTACACCAATGTAAATAAGTTGTAA
16038 TTTAATTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (32 bp):
TTACTTACACCAATGTAAATAAGTTGTAACCC
Found at i:16526 original size:71 final size:71
Alignment explanation
Indices: 16449--16587 Score: 215
Period size: 71 Copynumber: 2.0 Consensus size: 71
16439 GATCAAAAAT
* * * *
16449 TTCAAGCAAAGCATTGTTGTTCCTGCTACACAAAAACAAGGAGGAATAGTAAGCCATGATGAATC
1 TTCAAGCAAAGCATTATTGTTCCTGCTACACAAAAACAAGAAGAAATAGTAAGCCATAATGAATC
16514 AAAGGA
66 AAAGGA
* * *
16520 TTCAAGCAAAGCATTATTGTTCCTGCTATACAAAGACAAGAAGAAATAGTAAGCCATAATGGATC
1 TTCAAGCAAAGCATTATTGTTCCTGCTACACAAAAACAAGAAGAAATAGTAAGCCATAATGAATC
16585 AAA
66 AAA
16588 TAGTTAAAGT
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 61 1.00
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.22
Consensus pattern (71 bp):
TTCAAGCAAAGCATTATTGTTCCTGCTACACAAAAACAAGAAGAAATAGTAAGCCATAATGAATC
AAAGGA
Found at i:18812 original size:22 final size:22
Alignment explanation
Indices: 18787--18841 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
18777 TCAGGGGTTA
* *
18787 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
18809 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
18831 CGGGAGTTATA
1 CAGGAGTTATA
18842 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:24389 original size:5 final size:5
Alignment explanation
Indices: 24375--24418 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
24365 GTCCGTCCGT
* * * *
24375 CTCGT CTCGG CTCGG CACGG CACGG CACGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
24419 TGGTCGTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.07, C:0.41, G:0.36, T:0.16
Consensus pattern (5 bp):
CTCGG
Found at i:24427 original size:6 final size:6
Alignment explanation
Indices: 24416--24476 Score: 95
Period size: 6 Copynumber: 10.2 Consensus size: 6
24406 TCGGCTCGGC
* * *
24416 TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGAGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
24464 TCGTGG TCGTGG T
1 TCGTGG TCGTGG T
24477 AATACGTGTC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.05, C:0.16, G:0.49, T:0.30
Consensus pattern (6 bp):
TCGTGG
Found at i:24776 original size:22 final size:22
Alignment explanation
Indices: 24751--24805 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
24741 TCAGGAGTTA
* *
24751 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
24773 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
24795 CGGGAGTTATA
1 CAGGAGTTATA
24806 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:25841 original size:20 final size:20
Alignment explanation
Indices: 25793--25854 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 20
25783 AACTTAAATC
*
25793 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-TAATAATATAT
25813 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAATATAT
25831 AAAATAATTT-AT-ATGATAT
1 AAAATAATTTAATAAT-ATAT
25850 AAAAT
1 AAAAT
25855 TAAATATCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 5 0.14
18 13 0.35
19 11 0.30
20 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAATAATTTAATAATATAT
Found at i:25886 original size:63 final size:59
Alignment explanation
Indices: 25819--26004 Score: 157
Period size: 64 Copynumber: 3.0 Consensus size: 59
25809 ATATAAAATT
25819 TTAATAA-TATATAAAATAATTTATATGATATAAAATTAAATATCTATAATATAATATT-AAAAA
1 TTAATAATTATATAAAA-AA-TTA-AT-AT-TAAAATT-AATATCTATAATATAATATTAAAAAA
*
25882 TTAATATTTAATTTATTTAAAAAATTAATATTAAAATTAATATCTATAATATAATATTAAAAAA
1 TT-A-A--TAA-TTATATAAAAAATTAATATTAAAATTAATATCTATAATATAATATTAAAAAA
* * *
25946 TTAATATTTAATTTATTTAAAAAATTAATATTAAAAATAAAATC-A-AATATAATA-TAAAA
1 TT-A-A--TAA-TTATATAAAAAATTAATATTAAAATTAATATCTATAATATAATATTAAAA
26005 TTAAATATAA
Statistics
Matches: 113, Mismatches: 3, Indels: 16
0.86 0.02 0.12
Matches are distributed among these distances:
61 5 0.04
62 9 0.08
63 23 0.20
64 55 0.49
65 3 0.03
66 2 0.02
67 6 0.05
68 2 0.02
69 8 0.07
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.41
Consensus pattern (59 bp):
TTAATAATTATATAAAAAATTAATATTAAAATTAATATCTATAATATAATATTAAAAAA
Found at i:25918 original size:64 final size:64
Alignment explanation
Indices: 25849--26008 Score: 260
Period size: 64 Copynumber: 2.6 Consensus size: 64
25839 TTATATGATA
25849 TAAAATTAAATATCTATAATATAATATTAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
1 TAAAATTAAATATCTATAATATAATATTAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
25913 TAAAATT-AATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
1 TAAAATTAAATATCTATAATATAATATT-AAAAATTAATATTTAATTTATTTAAAAAATTAATAT
*
25977 TAAAAATAAA-ATC-A-AATATAATA-T-AAAATTAA
1 TAAAATTAAATATCTATAATATAATATTAAAAATTAA
26009 ATATAAAACC
Statistics
Matches: 93, Mismatches: 1, Indels: 9
0.90 0.01 0.09
Matches are distributed among these distances:
59 8 0.09
61 1 0.01
62 9 0.10
63 21 0.23
64 52 0.56
65 2 0.02
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (64 bp):
TAAAATTAAATATCTATAATATAATATTAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
Found at i:25948 original size:40 final size:37
Alignment explanation
Indices: 25870--25953 Score: 116
Period size: 40 Copynumber: 2.2 Consensus size: 37
25860 ATCTATAATA
*
25870 TAATATTAAAAATTAATATTTAATTTATTTAAAAAAT
1 TAATATTAAAAATTAATATTTAATTAATTTAAAAAAT
25907 TAATATT-AAAATTAATATCTATAATATAATATTAAAAAAT
1 TAATATTAAAAATTAATAT-T-TAAT-TAAT-TTAAAAAAT
25947 TAATATT
1 TAATATT
25954 TAATTTATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
36 11 0.26
37 8 0.19
38 4 0.10
39 3 0.07
40 16 0.38
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (37 bp):
TAATATTAAAAATTAATATTTAATTAATTTAAAAAAT
Found at i:25957 original size:26 final size:26
Alignment explanation
Indices: 25904--25978 Score: 95
Period size: 24 Copynumber: 3.0 Consensus size: 26
25894 TTATTTAAAA
25904 AATTAATATT--AAAATTAATATCTAT
1 AATTAATATTAAAAAATTAATAT-TAT
25929 AATATAATATTAAAAAATTAATATT-T
1 AAT-TAATATTAAAAAATTAATATTAT
*
25955 AATTTAT-TTAAAAAATTAATATTA
1 AATTAATATTAAAAAATTAATATTA
25979 AAAATAAAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
24 16 0.36
25 6 0.13
26 11 0.24
27 1 0.02
28 11 0.24
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (26 bp):
AATTAATATTAAAAAATTAATATTAT
Found at i:26004 original size:17 final size:17
Alignment explanation
Indices: 25982--26014 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
25972 AATATTAAAA
25982 ATAAAATCAAATATAAT
1 ATAAAATCAAATATAAT
*
25999 ATAAAATTAAATATAA
1 ATAAAATCAAATATAA
26015 AACCTCTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (17 bp):
ATAAAATCAAATATAAT
Found at i:29544 original size:26 final size:26
Alignment explanation
Indices: 29514--29568 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
29504 AGTAGACAAT
29514 GAGTGAGAGAGATAGAGACGTAGAGA
1 GAGTGAGAGAGATAGAGACGTAGAGA
29540 GAGTGAGAGAGATAGAGACGTAGAGA
1 GAGTGAGAGAGATAGAGACGTAGAGA
29566 GAG
1 GAG
29569 AAAAAGTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.42, C:0.04, G:0.44, T:0.11
Consensus pattern (26 bp):
GAGTGAGAGAGATAGAGACGTAGAGA
Found at i:40780 original size:12 final size:12
Alignment explanation
Indices: 40763--40796 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
40753 AAAGCAGAAG
40763 TTACAAAAGGGT
1 TTACAAAAGGGT
40775 TTACAAAAGGGT
1 TTACAAAAGGGT
40787 TTACAAAAGG
1 TTACAAAAGG
40797 TGTAGGGGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.24, T:0.24
Consensus pattern (12 bp):
TTACAAAAGGGT
Found at i:47876 original size:19 final size:19
Alignment explanation
Indices: 47837--47878 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
47827 AGATGGATGG
*
47837 TTAGGATTATAGGATATCT
1 TTAGGATTATAGGATAACT
47856 TTAGGATTATA-GACTAACT
1 TTAGGATTATAGGA-TAACT
47875 TTAG
1 TTAG
47879 TGTTTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.40
Consensus pattern (19 bp):
TTAGGATTATAGGATAACT
Found at i:52422 original size:22 final size:22
Alignment explanation
Indices: 52397--52444 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
52387 AGATGTTATC
* * *
52397 TTTATCTCCACTTAGGATGAGA
1 TTTATCTACACTGAGGATAAGA
*
52419 TTTATCTATACTGAGGATAAGA
1 TTTATCTACACTGAGGATAAGA
52441 TTTA
1 TTTA
52445 GAATAATACT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (22 bp):
TTTATCTACACTGAGGATAAGA
Found at i:60565 original size:24 final size:24
Alignment explanation
Indices: 60538--60649 Score: 77
Period size: 24 Copynumber: 4.7 Consensus size: 24
60528 TATATCAAAA
60538 ATCAAAACATAATTCAGGTCAGAT
1 ATCAAAACATAATTCAGGTCAGAT
* * *
60562 ATCATAACATAATCCATGTCAG-T
1 ATCAAAACATAATTCAGGTCAGAT
* *
60585 ATAAAAAACAGAA-TCTAGGTCA-AGT
1 AT-CAAAACATAATTC-AGGTCAGA-T
* * * * *
60610 ATCAAATCAGAATCCAGGTTAGGT
1 ATCAAAACATAATTCAGGTCAGAT
*
60634 ATCATAACATAATTCA
1 ATCAAAACATAATTCA
60650 AATCAGAAAT
Statistics
Matches: 65, Mismatches: 17, Indels: 12
0.69 0.18 0.13
Matches are distributed among these distances:
23 4 0.06
24 57 0.88
25 4 0.06
ACGTcount: A:0.45, C:0.17, G:0.12, T:0.26
Consensus pattern (24 bp):
ATCAAAACATAATTCAGGTCAGAT
Done.