Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000602.1 Hibiscus syriacus cultivar Beakdansim tig00001171_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: 61885
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:15886 original size:17 final size:17
Alignment explanation
Indices: 15866--15993 Score: 107
Period size: 18 Copynumber: 7.4 Consensus size: 17
15856 ATATGATATC
15866 TGTAAATATCTGATAAA
1 TGTAAATATCTGATAAA
15883 TGT-AATCATCTGATAAA
1 TGTAAAT-ATCTGATAAA
* *
15900 TGAAAATCATCTGATAAC
1 TGTAAAT-ATCTGATAAA
* *
15918 TGTAAATATCTAATAAC
1 TGTAAATATCTGATAAA
* * *
15935 TGAAAATAATTTGATAAT
1 TGTAAAT-ATCTGATAAA
*
15953 TGTAAATATCTAATAACA
1 TGTAAATATCTGATAA-A
* *
15971 -GTGAAATGTCTGATAAC
1 TGT-AAATATCTGATAAA
15988 TGTAAA
1 TGTAAA
15994 CATTTAGAAT
Statistics
Matches: 90, Mismatches: 15, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
16 3 0.03
17 42 0.47
18 45 0.50
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.34
Consensus pattern (17 bp):
TGTAAATATCTGATAAA
Found at i:15921 original size:52 final size:52
Alignment explanation
Indices: 15839--15992 Score: 150
Period size: 52 Copynumber: 2.9 Consensus size: 52
15829 TTAATTTGTT
* * * * *
15839 TCTGATAACTGTAAAA-CATATGATATCTGTAAATATCTGATAAATGTAATCA
1 TCTGATAAATG-AAAATCATCTGATAACTGTAAATATCTGATAACTGTAATAA
* *
15891 TCTGATAAATGAAAATCATCTGATAACTGTAAATATCTAATAACTGAAAATAA
1 TCTGATAAATGAAAATCATCTGATAACTGTAAATATCTGATAACTG-TAATAA
* * * * * *
15944 TTTGATAATTGTAAAT-ATCTAATAACAGTGAAATGTCTGATAACTGTAA
1 TCTGATAAATGAAAATCATCTGATAACTGT-AAATATCTGATAACTGTAA
15993 ACATTTAGAA
Statistics
Matches: 84, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
51 4 0.05
52 49 0.58
53 31 0.37
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (52 bp):
TCTGATAAATGAAAATCATCTGATAACTGTAAATATCTGATAACTGTAATAA
Found at i:15957 original size:70 final size:69
Alignment explanation
Indices: 15839--15996 Score: 169
Period size: 70 Copynumber: 2.3 Consensus size: 69
15829 TTAATTTGTT
* * * *
15839 TCTGATAACTGTAAAACATATGATATCTGTAAATATCTGATAAATGT-AATCATCTGATAA-A-T
1 TCTGATAACTGT-AAACATATAATAACTGAAAATATCTGATAAATGTAAAT-ATCTAATAACAGT
15901 GAAAATCA
64 G-AAAT-A
* * * *
15909 TCTGATAACTGTAAATATCTAATAACTGAAAATAATTTGATAATTGTAAATATCTAATAACAGTG
1 TCTGATAACTGTAAACATATAATAACTGAAAAT-ATCTGATAAATGTAAATATCTAATAACAGTG
*
15974 AAATG
65 AAATA
15979 TCTGATAACTGTAAACAT
1 TCTGATAACTGTAAACAT
15997 TTAGAATTCA
Statistics
Matches: 74, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
69 16 0.22
70 48 0.65
71 8 0.11
72 2 0.03
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (69 bp):
TCTGATAACTGTAAACATATAATAACTGAAAATATCTGATAAATGTAAATATCTAATAACAGTGA
AATA
Found at i:15985 original size:35 final size:35
Alignment explanation
Indices: 15839--15993 Score: 138
Period size: 35 Copynumber: 4.4 Consensus size: 35
15829 TTAATTTGTT
* * * * *
15839 TCTGATAACTGTAAAACATATGATATCTGTAAAT-A
1 TCTGATAACTGT-AAATATCTAATAACTGAAAATAA
* * * *
15874 TCTGATAAATGT-AATCATCTGATAAATGAAAATCA
1 TCTGATAACTGTAAAT-ATCTAATAACTGAAAATAA
15909 TCTGATAACTGTAAATATCTAATAACTGAAAATAA
1 TCTGATAACTGTAAATATCTAATAACTGAAAATAA
* * *
15944 TTTGATAATTGTAAATATCTAATAACAGTG-AAAT-G
1 TCTGATAACTGTAAATATCTAATAAC--TGAAAATAA
15979 TCTGATAACTGTAAA
1 TCTGATAACTGTAAA
15994 CATTTAGAAT
Statistics
Matches: 100, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
33 2 0.02
34 13 0.13
35 76 0.76
36 7 0.07
37 2 0.02
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.34
Consensus pattern (35 bp):
TCTGATAACTGTAAATATCTAATAACTGAAAATAA
Found at i:16520 original size:18 final size:18
Alignment explanation
Indices: 16497--16539 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
16487 TCTATTTTAA
16497 ACGAATCTAGATTGACAT
1 ACGAATCTAGATTGACAT
16515 ACGAATCTAGATTGACAT
1 ACGAATCTAGATTGACAT
16533 ACGAATC
1 ACGAATC
16540 AACGGTGTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.26
Consensus pattern (18 bp):
ACGAATCTAGATTGACAT
Found at i:24377 original size:2 final size:2
Alignment explanation
Indices: 24370--24395 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
24360 ATCCAATCTA
24370 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
24396 TAGGTAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24791 original size:21 final size:21
Alignment explanation
Indices: 24767--24818 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
24757 AAAAATTATG
*
24767 TTTTAAGTAAAAATGATAACA
1 TTTTAAGTAAAAATAATAACA
* *
24788 TTTTAGGTAAAAATAATAATA
1 TTTTAAGTAAAAATAATAACA
24809 TTTTAAGTAA
1 TTTTAAGTAA
24819 CTTTTTATCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (21 bp):
TTTTAAGTAAAAATAATAACA
Found at i:25938 original size:36 final size:36
Alignment explanation
Indices: 25885--26080 Score: 293
Period size: 36 Copynumber: 5.4 Consensus size: 36
25875 GTGCGATACA
** *
25885 TCCTTCCGTTCAACTTGAATCGGAAGTGTTGATGCT
1 TCCTTCCGTTCGTCTTGAATCGGAAGTGCTGATGCT
* *
25921 TCCTTCCGTTCGTCTTGAATAGGAAGTGCTGATGAT
1 TCCTTCCGTTCGTCTTGAATCGGAAGTGCTGATGCT
25957 TCCTTCCGTTCGTCTTGAATCGGAAGTGCTGATGCT
1 TCCTTCCGTTCGTCTTGAATCGGAAGTGCTGATGCT
* * *
25993 TCATTCCGTTCGTCTTGAATTGGAAGTTCTGATGCT
1 TCCTTCCGTTCGTCTTGAATCGGAAGTGCTGATGCT
* *
26029 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCT
1 TCCTTCCGTTCGTCTTGAATCGGAAGTGCTGATGCT
*
26065 TCCTTCCGTTCTTCTT
1 TCCTTCCGTTCGTCTT
26081 ATTCACAATA
Statistics
Matches: 143, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 143 1.00
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (36 bp):
TCCTTCCGTTCGTCTTGAATCGGAAGTGCTGATGCT
Found at i:28486 original size:20 final size:20
Alignment explanation
Indices: 28457--28499 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
28447 ATTTCACCAC
* *
28457 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCAAA
*
28477 ATGCATCTATATGATCCAAA
1 ATGCAACTATATGATCCAAA
28497 ATG
1 ATG
28500 GGCTTTTAGA
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:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (20 bp):
ATGCAACTATATGATCCAAA
Found at i:31590 original size:29 final size:29
Alignment explanation
Indices: 31529--31602 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
31519 GTCTGCAAAA
* ** *
31529 AAAATTAATTAAATAAAATATTTAGCAATT
1 AAAA-TAATTAAATAAAATATTAAAAAACT
*
31559 AAAATAATTAAATAAATTATTAAAAAACT
1 AAAATAATTAAATAAAATATTAAAAAACT
*
31588 AAATATAATAAAATA
1 AAA-ATAATTAAATA
31603 TACCTTAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 23 0.62
30 14 0.38
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (29 bp):
AAAATAATTAAATAAAATATTAAAAAACT
Found at i:32562 original size:16 final size:17
Alignment explanation
Indices: 32533--32564 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
32523 TGTTTTTATC
32533 TTTTGTTCAAGTTTTTG
1 TTTTGTTCAAGTTTTTG
32550 TTTTGTT-AAGTTTTT
1 TTTTGTTCAAGTTTTT
32565 AACATTTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.12, C:0.03, G:0.16, T:0.69
Consensus pattern (17 bp):
TTTTGTTCAAGTTTTTG
Found at i:41261 original size:45 final size:46
Alignment explanation
Indices: 41206--41307 Score: 147
Period size: 47 Copynumber: 2.2 Consensus size: 46
41196 TTTTAAGTAA
* *
41206 TTTTTT-ACTGAAAATGTT-AAAAAATAACATTTCT-AGTAGTGTAT
1 TTTTTTAACTGAAAATATTAAAAAAATAACATTTCTGA-TAGCGTAT
41250 TTTTTTAACTGAAAATATTAAAAAAAATAACATTTCTGATAGCGTAT
1 TTTTTTAACTGAAAATATT-AAAAAAATAACATTTCTGATAGCGTAT
41297 TTTTTTAACTG
1 TTTTTTAACTG
41308 TATATTAAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
44 6 0.12
45 11 0.21
47 34 0.65
48 1 0.02
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.43
Consensus pattern (46 bp):
TTTTTTAACTGAAAATATTAAAAAAATAACATTTCTGATAGCGTAT
Found at i:41313 original size:45 final size:46
Alignment explanation
Indices: 41224--41317 Score: 138
Period size: 47 Copynumber: 2.0 Consensus size: 46
41214 TGAAAATGTT
*
41224 AAAAAATAACATTTCTAGTAGTGTATTTTTTTAACTGAAAATATTAA
1 AAAAAATAACATTTCTAGTAGCGTATTTTTTTAACTG-AAATATTAA
*
41271 AAAAAATAACATTTCT-GATAGCGTATTTTTTTAACTG-TATATTAA
1 AAAAAATAACATTTCTAG-TAGCGTATTTTTTTAACTGAAATATTAA
41316 AA
1 AA
41318 CCGTCGTACC
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
45 9 0.20
46 1 0.02
47 34 0.77
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (46 bp):
AAAAAATAACATTTCTAGTAGCGTATTTTTTTAACTGAAATATTAA
Found at i:59132 original size:39 final size:42
Alignment explanation
Indices: 59055--59143 Score: 103
Period size: 39 Copynumber: 2.2 Consensus size: 42
59045 TATTTTAGAT
*
59055 ATTATAATAAATATATTAAATCGATTTAAAAAATTAAATA-TA
1 ATTAT-ATAAATATATTAAATCGAATTAAAAAATTAAATATTA
* ** *
59097 ATTATATAAATATATT-TATC-AATTAAATTATTAAATATTG
1 ATTATATAAATATATTAAATCGAATTAAAAAATTAAATATTA
59137 ATTATAT
1 ATTATAT
59144 TAAAATTTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
39 14 0.34
40 11 0.27
41 11 0.27
42 5 0.12
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (42 bp):
ATTATATAAATATATTAAATCGAATTAAAAAATTAAATATTA
Found at i:59277 original size:2 final size:2
Alignment explanation
Indices: 59270--59299 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
59260 CATTCTTTTA
59270 AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
59300 ATGAATTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:59288 original size:15 final size:15
Alignment explanation
Indices: 59268--59301 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
59258 TCCATTCTTT
59268 TAATATATATATATA
1 TAATATATATATATA
59283 TAATATATATATATA
1 TAATATATATATATA
59298 TAAT
1 TAAT
59302 GAATTTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TAATATATATATATA
Found at i:59290 original size:13 final size:13
Alignment explanation
Indices: 59272--59297 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
59262 TTCTTTTAAT
59272 ATATATATATATA
1 ATATATATATATA
59285 ATATATATATATA
1 ATATATATATATA
59298 TAATGAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATATATATA
Done.