Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005052.1 Hibiscus syriacus cultivar Beakdansim tig00011341_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: 60710
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:11543 original size:2 final size:2
Alignment explanation
Indices: 11536--11568 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
11526 CATACCCAGA
11536 AT AT 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 AT AT A
11569 CACACACACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12966 original size:36 final size:37
Alignment explanation
Indices: 12908--13032 Score: 139
Period size: 36 Copynumber: 3.4 Consensus size: 37
12898 GTTGTCACCT
* * *
12908 TTGAGACAATTTCTTTTAAAAACATATTTTATCTCGC
1 TTGAGACAATTTCTCTTAAAAACATATTGTATCTCAC
* * *
12945 TTGAGACAGTTT-TCTTAAAAACAAATTGTGTCTCAC
1 TTGAGACAATTTCTCTTAAAAACATATTGTATCTCAC
* *
12981 TTGAGACAATTTCTCTCAAAACAAATATTGTA--TCAC
1 TTGAGACAATTTCTCTTAAAA-ACATATTGTATCTCAC
*
13017 TTGAGACATTTTCTCT
1 TTGAGACAATTTCTCT
13033 CATAATACAA
Statistics
Matches: 74, Mismatches: 12, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
36 49 0.66
37 18 0.24
38 7 0.09
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.39
Consensus pattern (37 bp):
TTGAGACAATTTCTCTTAAAAACATATTGTATCTCAC
Found at i:13043 original size:38 final size:36
Alignment explanation
Indices: 12944--13045 Score: 127
Period size: 36 Copynumber: 2.8 Consensus size: 36
12934 TTTTATCTCG
* *
12944 CTTGAGACAGTTTTCT-TAAAAACAAATTGTGTCTCA
1 CTTGAGACA-TTTTCTCTCAAAACAAATTGTGTATCA
*
12980 CTTGAGACAATTTCTCTCAAAACAAATAT-TGTATCA
1 CTTGAGACATTTTCTCTCAAAACAAAT-TGTGTATCA
13016 CTTGAGACATTTTCTCTCATAATACAAATT
1 CTTGAGACATTTTCTCTCA-AA-ACAAATT
13046 TCAAAGTTGT
Statistics
Matches: 58, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
35 5 0.09
36 43 0.74
37 4 0.07
38 6 0.10
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.36
Consensus pattern (36 bp):
CTTGAGACATTTTCTCTCAAAACAAATTGTGTATCA
Found at i:13369 original size:64 final size:64
Alignment explanation
Indices: 13174--13369 Score: 214
Period size: 64 Copynumber: 3.0 Consensus size: 64
13164 TAAAGTTTAT
* * * * * * * *
13174 AATCTTTGAGTCTGTTTCTTTTGAAACATATCTTGTCTCCCTTTAGACAGATTCTCATAAAATAC
1 AATCTTTGAGTTTGTTTCTCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTC-CATTAAA-AC
*
13239 C
64 A
* * ** * *
13240 AATCTTTGAGTTTATTTCTCTTAAAACAAACTTTGTCTTACTTGAGACAGTCTT-CTTTAAGACA
1 AATCTTTGAGTTTGTTTCTCTTAAAACAAATTTTGTCTCCCTTGAGACAGT-TTCCATTAAAACA
*
13304 AATCTTTGAGTTTGTTTCTCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTAAAACA
1 AATCTTTGAGTTTGTTTCTCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCCATTAAAACA
13368 AA
1 AA
13370 ATCATTTTTG
Statistics
Matches: 107, Mismatches: 21, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
63 2 0.02
64 59 0.55
65 4 0.04
66 40 0.37
67 2 0.02
ACGTcount: A:0.29, C:0.19, G:0.11, T:0.41
Consensus pattern (64 bp):
AATCTTTGAGTTTGTTTCTCTTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCCATTAAAACA
Found at i:13709 original size:131 final size:131
Alignment explanation
Indices: 13466--13719 Score: 355
Period size: 131 Copynumber: 1.9 Consensus size: 131
13456 TTGAAACATA
* * * *
13466 ATCCCTAAATATGGCCTGCCATCCTCATCACATAGGAACCGTGTCATCCTCCGAACAGACCTCCT
1 ATCCCTAAAGATGGCCTACCATCCTCATCACATAGGAACCATGTCATCCACCGAACAGACCTCCT
* * *
13531 CATCACTTAGGAGCTGTGTCAACCCTAGATAACAAGCCATCCACATCACGTAGGAACCATGTTAT
66 CATCACGTAGGAGCCGTGTCAACCCTAGATAACAAGACATCCACATCACGTAGGAACCATGTTAT
13596 C
131 C
* * *
13597 ATCCCTAAAGATGGCCTACCATCCTCATCACGTAGGAACTATGTCATCCACCGACCAGACCTCCT
1 ATCCCTAAAGATGGCCTACCATCCTCATCACATAGGAACCATGTCATCCACCGAACAGACCTCCT
* * * * * * *
13662 GATCACGTAGGATCCGTGTCACCCCTAGATAACCATACGTCCTCATCACGTAGGAACC
66 CATCACGTAGGAGCCGTGTCAACCCTAGATAACAAGACATCCACATCACGTAGGAACC
13720 TTGTCATCCC
Statistics
Matches: 106, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
131 106 1.00
ACGTcount: A:0.28, C:0.34, G:0.16, T:0.22
Consensus pattern (131 bp):
ATCCCTAAAGATGGCCTACCATCCTCATCACATAGGAACCATGTCATCCACCGAACAGACCTCCT
CATCACGTAGGAGCCGTGTCAACCCTAGATAACAAGACATCCACATCACGTAGGAACCATGTTAT
C
Found at i:15608 original size:2 final size:2
Alignment explanation
Indices: 15536--15597 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
15526 TTATAATTTC
15536 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
15578 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
15598 GCATGTATAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16598 original size:18 final size:18
Alignment explanation
Indices: 16556--16598 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
16546 TTACTATTTT
*
16556 ATTTTATTTTAAATTAAA
1 ATTTTATTTTAAATAAAA
16574 ATATTTATTTT-AATAAAAA
1 AT-TTTATTTTAAAT-AAAA
16593 ATTTTA
1 ATTTTA
16599 ATTAATTAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTTATTTTAAATAAAA
Found at i:16720 original size:18 final size:18
Alignment explanation
Indices: 16699--16755 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
16689 TGCATGCACC
16699 ATTATCTACATTAATAAA
1 ATTATCTACATTAATAAA
16717 ATTAAT-TA-ATTAATAAA
1 ATT-ATCTACATTAATAAA
* *
16734 A-AATACTACATTAATGAA
1 ATTAT-CTACATTAATAAA
16752 ATTA
1 ATTA
16756 AGATTTAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
15 2 0.06
17 12 0.39
18 14 0.45
19 3 0.10
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (18 bp):
ATTATCTACATTAATAAA
Found at i:20292 original size:2 final size:2
Alignment explanation
Indices: 20285--20321 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
20275 AGAACATTAA
20285 AT AT AT AT 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 AT AT AT AT A
20322 CAAATAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21933 original size:2 final size:2
Alignment explanation
Indices: 21926--21955 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
21916 AACCTCATGA
21926 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
21956 TGTAAAGGAG
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:22987 original size:28 final size:25
Alignment explanation
Indices: 22951--23017 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 25
22941 TAATGATAAT
*
22951 TATTTAATTTATTTTTAGTAAATTGTA
1 TATTTAATTTATTTATA-TAAATT-TA
22978 TATTGTAATTATAATTTATATAAATTTA
1 TATT-TAATT-T-ATTTATATAAATTTA
23006 TATTTTAATTTA
1 TA-TTTAATTTA
23018 ATGAAGACAC
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
26 1 0.03
27 5 0.14
28 14 0.40
29 9 0.26
30 6 0.17
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.58
Consensus pattern (25 bp):
TATTTAATTTATTTATATAAATTTA
Found at i:24649 original size:23 final size:23
Alignment explanation
Indices: 24623--24667 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
24613 AAAAACCATA
*
24623 AAATCAAGTAAAACAAAATATTC
1 AAATCAACTAAAACAAAATATTC
* *
24646 AAATCAACTACAACATAATATT
1 AAATCAACTAAAACAAAATATT
24668 TAGGTAAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.58, C:0.16, G:0.02, T:0.24
Consensus pattern (23 bp):
AAATCAACTAAAACAAAATATTC
Found at i:27839 original size:21 final size:21
Alignment explanation
Indices: 27815--27867 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
27805 TCATGTCTTA
27815 TTTAGAGTTTAAAATTATAAT
1 TTTAGAGTTTAAAATTATAAT
* *
27836 TTTA-ATATTTAAGATTATAAT
1 TTTAGA-GTTTAAAATTATAAT
*
27857 TTTAGGGTTTA
1 TTTAGAGTTTA
27868 TCATGATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 1 0.04
21 25 0.96
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (21 bp):
TTTAGAGTTTAAAATTATAAT
Found at i:28045 original size:31 final size:30
Alignment explanation
Indices: 27993--28065 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 30
27983 AATAAAATAA
* *
27993 TAAATATATAATAATTGATAATGTAAGTAAT
1 TAAA-ATATAATAATCGATAATATAAGTAAT
* *
28024 TAAAATTTAATAAGTCGATAATATAAGTGAT
1 TAAAATATAATAA-TCGATAATATAAGTAAT
*
28055 TGAAATATAAT
1 TAAAATATAAT
28066 TTTTTTAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 8 0.23
31 27 0.77
ACGTcount: A:0.51, C:0.01, G:0.11, T:0.37
Consensus pattern (30 bp):
TAAAATATAATAATCGATAATATAAGTAAT
Found at i:34771 original size:20 final size:19
Alignment explanation
Indices: 34727--34771 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
34717 GTTTGTGGCC
* *
34727 GTTTCTAGCCGTTGGGTAT
1 GTTTTTAGCCGTTGGGGAT
34746 GATTTTTAGCCGTTTGGGGAT
1 G-TTTTTAGCCG-TTGGGGAT
34767 GTTTT
1 GTTTT
34772 CTCTACAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 13 0.59
21 8 0.36
ACGTcount: A:0.11, C:0.11, G:0.31, T:0.47
Consensus pattern (19 bp):
GTTTTTAGCCGTTGGGGAT
Found at i:39728 original size:20 final size:20
Alignment explanation
Indices: 39691--39733 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
39681 TTTCCACTAC
39691 ATGCAACTAAATGCTTCTAA
1 ATGCAACTAAATGCTTCTAA
* * *
39711 ATGCATCTACATGGTTCTAA
1 ATGCAACTAAATGCTTCTAA
39731 ATG
1 ATG
39734 AGCTCTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (20 bp):
ATGCAACTAAATGCTTCTAA
Found at i:45797 original size:9 final size:9
Alignment explanation
Indices: 45783--45815 Score: 66
Period size: 9 Copynumber: 3.7 Consensus size: 9
45773 TTGAATTATT
45783 TTTGAAAAC
1 TTTGAAAAC
45792 TTTGAAAAC
1 TTTGAAAAC
45801 TTTGAAAAC
1 TTTGAAAAC
45810 TTTGAA
1 TTTGAA
45816 TAAATTCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.36
Consensus pattern (9 bp):
TTTGAAAAC
Found at i:47599 original size:3 final size:3
Alignment explanation
Indices: 47584--47621 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
47574 TCCTACCTCA
* *
47584 TTC TTC TTG TTC TTC TT- TTC TTC ATC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
47622 ATTTATCATC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.03, C:0.29, G:0.03, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:48864 original size:20 final size:21
Alignment explanation
Indices: 48839--48885 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
48829 GTTTGTGGTC
48839 ATTTCTAGCCG-TTGGGGATG
1 ATTTCTAGCCGTTTGGGGATG
*
48859 ATTTCTAGTCGTTTGGGGATG
1 ATTTCTAGCCGTTTGGGGATG
*
48880 TTTTCT
1 ATTTCT
48886 CTGCAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.13, C:0.13, G:0.30, T:0.45
Consensus pattern (21 bp):
ATTTCTAGCCGTTTGGGGATG
Found at i:49133 original size:20 final size:20
Alignment explanation
Indices: 49104--49163 Score: 111
Period size: 20 Copynumber: 3.0 Consensus size: 20
49094 CAAGCTGGTA
*
49104 GTATCGATACTACCTTGAGC
1 GTATCAATACTACCTTGAGC
49124 GTATCAATACTACCTTGAGC
1 GTATCAATACTACCTTGAGC
49144 GTATCAATACTACCTTGAGC
1 GTATCAATACTACCTTGAGC
49164 ATATTGATAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (20 bp):
GTATCAATACTACCTTGAGC
Found at i:50919 original size:2 final size:2
Alignment explanation
Indices: 50912--50939 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
50902 TAATTTACAA
50912 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
50940 CTAACCAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.