Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000814.1 Hibiscus syriacus cultivar Beakdansim tig00001574_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: 88277
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1352 original size:2 final size:2
Alignment explanation
Indices: 1345--1395 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
1335 AATATTTTTA
1345 AT AT AT AT AT AT AT AT AT A- 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
1386 AT AT AT AT AT
1 AT AT AT AT AT
1396 TTAAAATGGC
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:14741 original size:20 final size:20
Alignment explanation
Indices: 14716--14759 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
14706 ACTATTCTTC
14716 TTCTCTCTAACTTTATAAAA
1 TTCTCTCTAACTTTATAAAA
* *
14736 TTCTCTCTAGCTTTATGAAA
1 TTCTCTCTAACTTTATAAAA
14756 TTCT
1 TTCT
14760 TTCTTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.27, C:0.20, G:0.05, T:0.48
Consensus pattern (20 bp):
TTCTCTCTAACTTTATAAAA
Found at i:26783 original size:24 final size:24
Alignment explanation
Indices: 26751--26796 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
26741 AGTCTTCCTT
26751 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
26775 ATGATGTATAAAACATCTATGT
1 ATGATGTATAAAACATCTATGT
26797 TCCATGTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (24 bp):
ATGATGTATAAAACATCTATGTAC
Found at i:32724 original size:27 final size:27
Alignment explanation
Indices: 32694--32755 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
32684 TTTTCAAAGT
32694 GATGCACCGATGCCCAATCCATGCATC
1 GATGCACCGATGCCCAATCCATGCATC
32721 GATGCACCGATGCCCAATCCATGCATC
1 GATGCACCGATGCCCAATCCATGCATC
32748 GATGCACC
1 GATGCACC
32756 ATGAATTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.26, C:0.37, G:0.19, T:0.18
Consensus pattern (27 bp):
GATGCACCGATGCCCAATCCATGCATC
Found at i:35326 original size:2 final size:2
Alignment explanation
Indices: 35319--35374 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
35309 CATGAGTTAG
35319 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
35361 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
35375 TGTATAACCA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36104 original size:22 final size:22
Alignment explanation
Indices: 36075--36218 Score: 191
Period size: 22 Copynumber: 6.5 Consensus size: 22
36065 GGGTATATTA
*
36075 GTCCTTCGGGACGTATCTAGTG
1 GTCCTTCGGGACGTATCCAGTG
* *
36097 GTCATTCGGGATGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
* *
36119 GTCCTTTGGGACGTATCCAGTA
1 GTCCTTCGGGACGTATCCAGTG
*
36141 GTCCTTCGGGATGTA-CCTAGTG
1 GTCCTTCGGGACGTATCC-AGTG
*
36163 GTCCTTCGGGACATATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
* *
36185 GTCCTTCGGAACGTATCTAGTG
1 GTCCTTCGGGACGTATCCAGTG
36207 GTCCTTCGGGAC
1 GTCCTTCGGGAC
36219 ATAATAGTCC
Statistics
Matches: 104, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
21 2 0.02
22 100 0.96
23 2 0.02
ACGTcount: A:0.16, C:0.24, G:0.30, T:0.31
Consensus pattern (22 bp):
GTCCTTCGGGACGTATCCAGTG
Found at i:36180 original size:66 final size:66
Alignment explanation
Indices: 36073--36218 Score: 211
Period size: 66 Copynumber: 2.2 Consensus size: 66
36063 GAGGGTATAT
* ** * *
36073 TAGTCCTTCGGGACGTATCTAGTGGTCATTCGGGATGTATCCAGTGGTCCTTTGGGACGTATCCA
1 TAGTCCTTCGGGACGTACCTAGTGGTCATTCGGGACATATCCAGTGGTCCTTCGGAACGTATCCA
36138 G
66 G
* * *
36139 TAGTCCTTCGGGATGTACCTAGTGGTCCTTCGGGACATATCCAGTGGTCCTTCGGAACGTATCTA
1 TAGTCCTTCGGGACGTACCTAGTGGTCATTCGGGACATATCCAGTGGTCCTTCGGAACGTATCCA
36204 G
66 G
*
36205 TGGTCCTTCGGGAC
1 TAGTCCTTCGGGAC
36219 ATAATAGTCC
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
66 70 1.00
ACGTcount: A:0.16, C:0.23, G:0.29, T:0.31
Consensus pattern (66 bp):
TAGTCCTTCGGGACGTACCTAGTGGTCATTCGGGACATATCCAGTGGTCCTTCGGAACGTATCCA
G
Found at i:39872 original size:19 final size:19
Alignment explanation
Indices: 39845--39894 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
39835 ATGCCATGGA
39845 TGCATCGATGCATAAGGAG
1 TGCATCGATGCATAAGGAG
*
39864 TGTATCGATGCATAAGGAG
1 TGCATCGATGCATAAGGAG
39883 TGCATCGATGCA
1 TGCATCGATGCA
39895 CCTGCTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.24
Consensus pattern (19 bp):
TGCATCGATGCATAAGGAG
Found at i:41346 original size:13 final size:11
Alignment explanation
Indices: 41300--41389 Score: 67
Period size: 11 Copynumber: 7.5 Consensus size: 11
41290 AAGATACAAT
41300 ATATCCATCACC
1 ATAT-CATCACC
*
41312 ATTATCA-CGCC
1 A-TATCATCACC
41323 TATATCATCACC
1 -ATATCATCACC
41335 ATAGTCCATCACC
1 ATA-T-CATCACC
*
41348 ATTATCA-CGCC
1 A-TATCATCACC
41359 TATATCATCACC
1 -ATATCATCACC
41371 ATATTCCATCACC
1 ATA-T-CATCACC
41384 ATATCA
1 ATATCA
41390 CGCCTATATT
Statistics
Matches: 64, Mismatches: 4, Indels: 21
0.72 0.04 0.24
Matches are distributed among these distances:
11 24 0.38
12 16 0.25
13 22 0.34
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.03, T:0.29
Consensus pattern (11 bp):
ATATCATCACC
Found at i:41350 original size:36 final size:36
Alignment explanation
Indices: 41303--41406 Score: 183
Period size: 36 Copynumber: 2.9 Consensus size: 36
41293 ATACAATATA
41303 TCCATCACCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
41339 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
41375 TCCATCACCA-TATCACGCCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
41407 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.32
36 45 0.68
ACGTcount: A:0.31, C:0.37, G:0.04, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAG
Found at i:42010 original size:16 final size:15
Alignment explanation
Indices: 41977--42028 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
41967 GTAAGTTATC
41977 TTCATTTTTTATCAT
1 TTCATTTTTTATCAT
41992 TTCATTTCTTTATTC-T
1 TTCATTT-TTTA-TCAT
* * *
42008 TTCATCTTTTCTTAT
1 TTCATTTTTTATCAT
42023 TTCATT
1 TTCATT
42029 ACCATATCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
14 1 0.03
15 16 0.53
16 11 0.37
17 2 0.07
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.67
Consensus pattern (15 bp):
TTCATTTTTTATCAT
Found at i:45816 original size:13 final size:11
Alignment explanation
Indices: 45775--45859 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
45765 ACAATATGTC
45775 CATCACCATTAT
1 CATCACCA-TAT
*
45787 CA-CGCCTATAT
1 CATCACC-ATAT
45798 CATCACCATAGT
1 CATCACCATA-T
45810 CCATCACCATTAT
1 -CATCACCA-TAT
*
45823 CA-CGCCTATAT
1 CATCACC-ATAT
45834 CATCACCATATT
1 CATCACCATA-T
45846 CCATCACCATAT
1 -CATCACCATAT
45858 CA
1 CA
45860 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:45819 original size:36 final size:36
Alignment explanation
Indices: 45772--45876 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
45762 GATACAATAT
45772 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
45808 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
45844 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
45877 ACTTATAAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.31
36 46 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:76427 original size:7 final size:7
Alignment explanation
Indices: 76415--76440 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
76405 TAACTTGTTA
76415 AAATTTT
1 AAATTTT
76422 AAATTTT
1 AAATTTT
76429 AAATTTT
1 AAATTTT
76436 AAATT
1 AAATT
76441 CAAAACTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
AAATTTT
Found at i:76956 original size:10 final size:10
Alignment explanation
Indices: 76941--76969 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
76931 ATTAGAAGAT
76941 ATTTTTATTA
1 ATTTTTATTA
76951 ATTTTTATTA
1 ATTTTTATTA
76961 ATTTTTATT
1 ATTTTTATT
76970 TTATTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
ATTTTTATTA
Found at i:77867 original size:37 final size:38
Alignment explanation
Indices: 77815--77886 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
77805 TTTATTTTGT
*
77815 TCGGGTC-GGGTTTTTTAAGTGTGATATTTGGGTCTAG
1 TCGGGTCGGGGTTTTTTAAGTGTGATATTCGGGTCTAG
77852 TCGGGTCGGGGTTTTTTAAGTGTGATATTCGGGTC
1 TCGGGTCGGGGTTTTTTAAGTGTGATATTCGGGTC
77887 GGGTTCGGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
37 7 0.21
38 26 0.79
ACGTcount: A:0.12, C:0.10, G:0.36, T:0.42
Consensus pattern (38 bp):
TCGGGTCGGGGTTTTTTAAGTGTGATATTCGGGTCTAG
Found at i:78559 original size:25 final size:25
Alignment explanation
Indices: 78531--78584 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
78521 ATGTCTGCGA
*
78531 ACCAAACAGAATATGAAATTGGATT
1 ACCAAACAGAATATGAAATTGAATT
* * *
78556 ACCAAATAGTATATGGAATTGAATT
1 ACCAAACAGAATATGAAATTGAATT
78581 -CCAA
1 ACCAA
78585 TTCCTATAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 4 0.16
25 21 0.84
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.26
Consensus pattern (25 bp):
ACCAAACAGAATATGAAATTGAATT
Found at i:78976 original size:14 final size:15
Alignment explanation
Indices: 78946--78980 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
78936 AACATAATTA
*
78946 ATAATGTTTATATAT
1 ATAATTTTTATATAT
78961 ATAATTTTTA-ATAT
1 ATAATTTTTATATAT
78975 ATAATT
1 ATAATT
78981 ATAAAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (15 bp):
ATAATTTTTATATAT
Found at i:79009 original size:12 final size:12
Alignment explanation
Indices: 78994--79041 Score: 55
Period size: 11 Copynumber: 4.2 Consensus size: 12
78984 AAAATTATTT
78994 ATTATATTAAAA
1 ATTATATTAAAA
**
79006 ATTAT-TTAAGG
1 ATTATATTAAAA
*
79017 ATTATATAAAAA
1 ATTATATTAAAA
79029 ATTATA-TAAAA
1 ATTATATTAAAA
79040 AT
1 AT
79042 AAATATAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
11 15 0.52
12 14 0.48
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (12 bp):
ATTATATTAAAA
Found at i:80423 original size:23 final size:21
Alignment explanation
Indices: 80395--80437 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
80385 ATATAAAAAA
80395 TTAT-TTTTTATTAAATGTTTT
1 TTATATTTTTATTAAAT-TTTT
*
80416 TTATATTTTTATTTAATTTTT
1 TTATATTTTTATTAAATTTTT
80437 T
1 T
80438 AAATAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (21 bp):
TTATATTTTTATTAAATTTTT
Found at i:83443 original size:16 final size:16
Alignment explanation
Indices: 83422--83455 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
83412 GAAATTAATA
*
83422 TTTTCTTATTTTTTAT
1 TTTTCTTAATTTTTAT
83438 TTTTCTTAATTTTTAT
1 TTTTCTTAATTTTTAT
83454 TT
1 TT
83456 ATTTCTCATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTCTTAATTTTTAT
Found at i:86600 original size:30 final size:30
Alignment explanation
Indices: 86566--86629 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
86556 ATCTAATCAT
86566 AACAAAAAGAAAAAA-GAAGTAAAAAGAGAA
1 AACAAAAAGAAAAAAGGAAGTAAAAA-AGAA
86596 AAC--AAAGAAAAAAGTGAAGTAAAAAAGAA
1 AACAAAAAGAAAAAAG-GAAGTAAAAAAGAA
*
86625 GACAA
1 AACAA
86630 GACACATATG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
28 10 0.34
29 6 0.21
30 13 0.45
ACGTcount: A:0.73, C:0.05, G:0.17, T:0.05
Consensus pattern (30 bp):
AACAAAAAGAAAAAAGGAAGTAAAAAAGAA
Found at i:86608 original size:29 final size:28
Alignment explanation
Indices: 86571--86629 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
86561 ATCATAACAA
86571 AAAGAAAAA-AGAAGTAAAAAGAGAAAAC
1 AAAGAAAAAGAGAAGTAAAAA-AGAAAAC
* *
86599 AAAGAAAAAAGTGAAGTAAAAAAGAAGAC
1 AAAG-AAAAAGAGAAGTAAAAAAGAAAAC
86628 AA
1 AA
86630 GACACATATG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 4 0.15
29 13 0.48
30 10 0.37
ACGTcount: A:0.73, C:0.03, G:0.19, T:0.05
Consensus pattern (28 bp):
AAAGAAAAAGAGAAGTAAAAAAGAAAAC
Found at i:86631 original size:28 final size:28
Alignment explanation
Indices: 86571--86629 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
86561 ATCATAACAA
86571 AAAGAAAAAAGAAGTAAAAAGAGAAAAC
1 AAAGAAAAAAGAAGTAAAAAGAGAAAAC
*
86599 AAAGAAAAAAGTGAAGTAAAAA-AGAAGAC
1 AAAGAAAAAA--GAAGTAAAAAGAGAAAAC
86628 AA
1 AA
86630 GACACATATG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 10 0.36
29 8 0.29
30 10 0.36
ACGTcount: A:0.73, C:0.03, G:0.19, T:0.05
Consensus pattern (28 bp):
AAAGAAAAAAGAAGTAAAAAGAGAAAAC
Done.