Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006976.1 Hibiscus syriacus cultivar Beakdansim tig00017964_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: 63238
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:2853 original size:64 final size:64
Alignment explanation
Indices: 2708--2898 Score: 178
Period size: 64 Copynumber: 3.0 Consensus size: 64
2698 ATGTACCAAT
* ** * * *
2708 CCAT-GCATCGATGCACCATGAATTAAATTGAAA-ATCGAATGCATTTCATGCATCGATGCACTT
1 CCATGGCACCGATGCACC-TGAA-TATTTTGAAACATCGAATGCACTTGATGCATCGATGCACTC
2771 A
64 A
* *
2772 CCATGGCACCGATGCA-CTGAATATTTTATGAAAACATTGAATGCA-TTGATGTATCGATGCAC-
1 CCATGGCACCGATGCACCTGAATA-TTT-TG-AAACATCGAATGCACTTGATGCATCGATGCACT
2834 CA
63 CA
* **
2836 GCCAT-GCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTGATGCATCGATGCACT
1 -CCATGGCACCGATGCAC-CTGAATATTTTGAAACATCGAATGCACTTGATGCATCGATGCACT
2899 AAGGGTCCAA
Statistics
Matches: 105, Mismatches: 12, Indels: 19
0.77 0.09 0.14
Matches are distributed among these distances:
62 2 0.02
63 18 0.17
64 36 0.34
65 35 0.33
66 14 0.13
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (64 bp):
CCATGGCACCGATGCACCTGAATATTTTGAAACATCGAATGCACTTGATGCATCGATGCACTCA
Found at i:11496 original size:46 final size:45
Alignment explanation
Indices: 11438--11544 Score: 126
Period size: 45 Copynumber: 2.4 Consensus size: 45
11428 TGCACTTACC
* * * *
11438 ATGCACCGATGCACTGAAGAT-TTTATGAAAACATTGAATGCATTTG
1 ATGCATCGATGCACTCAAGATATTT-TG-AAACATCGAATGCACTTG
** *
11484 ATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTG
1 ATGCATCGATGCACTCAAGATATTTTGAAACATCGAATGCACTTG
11529 ATGCATCGATGCACTC
1 ATGCATCGATGCACTC
11545 TTAGTGCACC
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
45 32 0.60
46 18 0.34
47 3 0.06
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.30
Consensus pattern (45 bp):
ATGCATCGATGCACTCAAGATATTTTGAAACATCGAATGCACTTG
Found at i:11542 original size:17 final size:19
Alignment explanation
Indices: 11514--11562 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
11504 TATTTTGAAA
11514 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
11532 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
11551 CACCGATGCACT
1 CATCGATGCACT
11563 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:13088 original size:18 final size:18
Alignment explanation
Indices: 13062--13097 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
13052 GAGGGATTAT
13062 TAGTGGTCCTTCGGGACA
1 TAGTGGTCCTTCGGGACA
*
13080 TAGTTGTCCTTCGGGACA
1 TAGTGGTCCTTCGGGACA
13098 AATTTTAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.22, G:0.31, T:0.31
Consensus pattern (18 bp):
TAGTGGTCCTTCGGGACA
Found at i:17557 original size:17 final size:17
Alignment explanation
Indices: 17535--17569 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
17525 TCTTTCTTTA
*
17535 TTCAAAGAATGGATTAC
1 TTCAAAGAATGGAATAC
*
17552 TTCAAATAATGGAATAC
1 TTCAAAGAATGGAATAC
17569 T
1 T
17570 ACAATAACTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.31
Consensus pattern (17 bp):
TTCAAAGAATGGAATAC
Found at i:20658 original size:29 final size:29
Alignment explanation
Indices: 20562--20660 Score: 76
Period size: 29 Copynumber: 3.3 Consensus size: 29
20552 TTTAAATTGG
* *
20562 TCCCTAAACTTTT-AAATATTTTAATTTTA
1 TCCCCAAACTTTTGAAA-ATTTTAATTTAA
* * * *
20591 TCCCTAAAC-TATGACTATAAATTTAAATTAA
1 TCCCCAAACTTTTGA--A-AATTTTAATTTAA
* *
20622 TCCTCAAACTTTTGAAAATTTTAATTTCA
1 TCCCCAAACTTTTGAAAATTTTAATTTAA
20651 TCCCCAAACT
1 TCCCCAAACT
20661 ATGATCCCTA
Statistics
Matches: 54, Mismatches: 11, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
28 2 0.04
29 29 0.54
30 1 0.02
31 17 0.31
32 5 0.09
ACGTcount: A:0.37, C:0.19, G:0.02, T:0.41
Consensus pattern (29 bp):
TCCCCAAACTTTTGAAAATTTTAATTTAA
Found at i:20678 original size:60 final size:59
Alignment explanation
Indices: 20552--20694 Score: 146
Period size: 60 Copynumber: 2.4 Consensus size: 59
20542 CGAGATGGAT
** * * * *
20552 TTTAAATTGGTCCCTAAACTTTTAAATATTTTAATTTTATCCCTAAACTATGACTATAAA
1 TTTAAATTAATCCCCAAACTTTTAAATATTTTAATTTCATCCCCAAACTATGACCAT-AA
* *
20612 TTTAAATTAATCCTCAAACTTTTGAAA-ATTTTAATTTCATCCCCAAACTATGATCCCT-A
1 TTTAAATTAATCCCCAAACTTTT-AAATATTTTAATTTCATCCCCAAACTATGA-CCATAA
**
20671 TTCTAAATTGGTCCCCAAACTTTT
1 TT-TAAATTAATCCCCAAACTTTT
20695 TGATCATTCA
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
59 3 0.04
60 61 0.88
61 5 0.07
ACGTcount: A:0.34, C:0.20, G:0.05, T:0.41
Consensus pattern (59 bp):
TTTAAATTAATCCCCAAACTTTTAAATATTTTAATTTCATCCCCAAACTATGACCATAA
Found at i:25615 original size:2 final size:2
Alignment explanation
Indices: 25608--25702 Score: 190
Period size: 2 Copynumber: 47.5 Consensus size: 2
25598 TCACTAAAAT
25608 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25650 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25692 TA TA TA TA TA T
1 TA TA TA TA TA T
25703 GATTGTCAAT
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 93 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:30028 original size:19 final size:19
Alignment explanation
Indices: 30004--30063 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 19
29994 GTTTCGCTAC
30004 TGGGTATCGGTACTCAAGA
1 TGGGTATCGGTACTCAAGA
*
30023 TGGGTATC-G--CT--A-C
1 TGGGTATCGGTACTCAAGA
*
30036 TGGGTATCGGTACTCAAGG
1 TGGGTATCGGTACTCAAGA
30055 TGGGTATCG
1 TGGGTATCG
30064 ATGCTAAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
13 8 0.24
14 2 0.06
16 4 0.12
18 2 0.06
19 17 0.52
ACGTcount: A:0.20, C:0.17, G:0.35, T:0.28
Consensus pattern (19 bp):
TGGGTATCGGTACTCAAGA
Found at i:30038 original size:32 final size:32
Alignment explanation
Indices: 29997--30063 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
29987 TCACCAAGTT
29997 TCGCTACTGGGTATCGGTACTCAAGATGGGTA
1 TCGCTACTGGGTATCGGTACTCAAGATGGGTA
*
30029 TCGCTACTGGGTATCGGTACTCAAGGTGGGTA
1 TCGCTACTGGGTATCGGTACTCAAGATGGGTA
30061 TCG
1 TCG
30064 ATGCTAAGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.19, C:0.19, G:0.33, T:0.28
Consensus pattern (32 bp):
TCGCTACTGGGTATCGGTACTCAAGATGGGTA
Found at i:33073 original size:2 final size:2
Alignment explanation
Indices: 33066--33092 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
33056 TTATATTTAC
33066 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 A
33093 CACACACACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34843 original size:31 final size:31
Alignment explanation
Indices: 34805--34869 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
34795 GGATTCCTTT
* *
34805 CGGTCTCACACATATGGCAACAATAATCTCC
1 CGGTCTCACACATATCGCAACAATAATATCC
34836 CGGTCTCACACATATCGCAACAATAATATCC
1 CGGTCTCACACATATCGCAACAATAATATCC
34867 CGG
1 CGG
34870 GTCATCTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.32, G:0.14, T:0.22
Consensus pattern (31 bp):
CGGTCTCACACATATCGCAACAATAATATCC
Found at i:36910 original size:8 final size:8
Alignment explanation
Indices: 36895--36934 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
36885 TAGTATTATT
36895 ATTAAATA
1 ATTAAATA
*
36903 AATAAATA
1 ATTAAATA
36911 ATTAAATA
1 ATTAAATA
36919 ATTAAA-A
1 ATTAAATA
36926 ATTACAATA
1 ATTA-AATA
36935 GACCCGGAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
7 5 0.18
8 22 0.79
9 1 0.04
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (8 bp):
ATTAAATA
Found at i:40491 original size:3 final size:3
Alignment explanation
Indices: 40479--40509 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
40469 TGTCTTTTAA
40479 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
40510 ATTTACATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:48612 original size:5 final size:5
Alignment explanation
Indices: 48602--48626 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
48592 CTCATGTTTA
48602 TGATT TGATT TGATT TGATT TGATT
1 TGATT TGATT TGATT TGATT TGATT
48627 GTGTGCCTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (5 bp):
TGATT
Found at i:50213 original size:79 final size:79
Alignment explanation
Indices: 50078--50241 Score: 213
Period size: 79 Copynumber: 2.1 Consensus size: 79
50068 GCATGATGAT
* * * * **
50078 CAAATCCATCTGTAAGTCTTTCGAGCATGATGCTTAAATCATTTGGGCCATCTTAAGCCTTCACC
1 CAAATTCATCAGTAAGCCTTTCGAGCATGATGATTAAATCATCCGGGCCATCTTAAGCCTTCACC
*
50143 GAAGTATAGTGAAG
66 GAAGAATAGTGAAG
* * *
50157 CAAATTCATCAGTAAGCC-TTCTGAGCATGATGATTAAGTCCTCCGGGCCATTTTAAGCCTTCAC
1 CAAATTCATCAGTAAGCCTTTC-GAGCATGATGATTAAATCATCCGGGCCATCTTAAGCCTTCAC
*
50221 GGAAGAATAGTGAAG
65 CGAAGAATAGTGAAG
50236 CAAATT
1 CAAATT
50242 ATCTATCTGA
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
78 3 0.04
79 70 0.96
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (79 bp):
CAAATTCATCAGTAAGCCTTTCGAGCATGATGATTAAATCATCCGGGCCATCTTAAGCCTTCACC
GAAGAATAGTGAAG
Found at i:50454 original size:111 final size:111
Alignment explanation
Indices: 50246--50784 Score: 801
Period size: 111 Copynumber: 4.9 Consensus size: 111
50236 CAAATTATCT
* * * * * * * *
50246 ATCTGATATTCCCTTCAGAAGAAGTGAAACAGATCACTCTCTTGCAATATTTGATATTACATGAG
1 ATCTGATATTCCC-TCAGAGGAAGCGGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAG
50311 TGACAGCGGAACAAGTCTACCCTGATTCAATGAATCAACTTTCCCAG
65 TGACAGCGGAACAAGTCTACCCTGATTCAATGAATCAACTTTCCCAG
*
50358 ATCTGATATTCCCTCAGAGGAAGCGGAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGT
1 ATCTGATATTCCCTCAGAGGAAGCGGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGT
*
50423 GACAGCGGAACAAGTCTACCCTGATTTAATGAATCAACTTTCCCAG
66 GACAGCGGAACAAGTCTACCCTGATTCAATGAATCAACTTTCCCAG
* * *
50469 ATCTGATATTCCCTCAGAGAAAGCGGAACAGATCACTCTCTTTCAAGATTTGATATTCTCTGAGT
1 ATCTGATATTCCCTCAGAGGAAGCGGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGT
*
50534 GACAGCGGAACAAGTCTACCCTGATTCAATGAATCAACTTTCCTAG
66 GACAGCGGAACAAGTCTACCCTGATTCAATGAATCAACTTTCCCAG
* * * *
50580 ATATGATATTCCCACAGAGAAAGCGGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTAAGT
1 ATCTGATATTCCCTCAGAGGAAGCGGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGT
* *
50645 GACAACGGAACAAGTCTACCCTGATTCAATGGATCAACTTTCCCAG
66 GACAGCGGAACAAGTCTACCCTGATTCAATGAATCAACTTTCCCAG
* * * * * *
50691 ATCTGATATTCCCT-AGAAGAAGTGGAACATATCCTTCTCTTTCAAGATTTGATATTACATGAGT
1 ATCTGATATTCCCTCAGAGGAAGCGGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGT
* **
50755 GATAATGGAACAAGTCTACCCTGATTCAAT
66 GACAGCGGAACAAGTCTACCCTGATTCAAT
50785 CTTCCCTGCA
Statistics
Matches: 391, Mismatches: 36, Indels: 2
0.91 0.08 0.00
Matches are distributed among these distances:
110 70 0.18
111 308 0.79
112 13 0.03
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.29
Consensus pattern (111 bp):
ATCTGATATTCCCTCAGAGGAAGCGGAACAGATCCCTCTCTTTCAAGATTTGATATTCCCTGAGT
GACAGCGGAACAAGTCTACCCTGATTCAATGAATCAACTTTCCCAG
Found at i:51004 original size:3 final size:3
Alignment explanation
Indices: 50992--51026 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
50982 TGTCTTTTAA
50992 TAT T-T TAT TAT TAT TAT TAT TAAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TA
51027 ATTTACATGC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.83
4 3 0.10
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:51019 original size:13 final size:13
Alignment explanation
Indices: 50988--51029 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
50978 GTCATGTCTT
50988 TTAA-TATT-TTA
1 TTAATTATTATTA
50999 TT-ATTATTATTA
1 TTAATTATTATTA
51011 TTAATTATTATTA
1 TTAATTATTATTA
51024 TTAATT
1 TTAATT
51030 TACATGCAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.04
11 6 0.21
12 5 0.18
13 16 0.57
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTAATTATTATTA
Found at i:58609 original size:33 final size:36
Alignment explanation
Indices: 58567--58661 Score: 146
Period size: 33 Copynumber: 2.8 Consensus size: 36
58557 GTCTTACTAA
58567 GATTCAAACTCCTAAAAATA-GATAGAA-TTT-TAG
1 GATTCAAACTCCTAAAAATAGGATAGAATTTTCTAG
58600 GATTCAAACTCCT-AAAATAGGATA-AATTTTGCTAG
1 GATTCAAACTCCTAAAAATAGGATAGAATTTT-CTAG
58635 GATTCAAACTCCTAAAAATAGGATAGA
1 GATTCAAACTCCTAAAAATAGGATAGA
58662 GTTCTACTAT
Statistics
Matches: 56, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
32 8 0.14
33 20 0.36
35 16 0.29
36 11 0.20
37 1 0.02
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (36 bp):
GATTCAAACTCCTAAAAATAGGATAGAATTTTCTAG
Found at i:59069 original size:15 final size:15
Alignment explanation
Indices: 59051--59085 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
59041 ATATGGATAT
* *
59051 TTATTCATTTTTTTA
1 TTATTCATGTTATTA
59066 TTATTCATGTTATTA
1 TTATTCATGTTATTA
59081 TTATT
1 TTATT
59086 ATATATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.23, C:0.06, G:0.03, T:0.69
Consensus pattern (15 bp):
TTATTCATGTTATTA
Found at i:59168 original size:22 final size:22
Alignment explanation
Indices: 59130--59201 Score: 53
Period size: 22 Copynumber: 3.3 Consensus size: 22
59120 TGATTTTTAC
*
59130 TATATTT-TATTATTATTATATA
1 TATATTTCT-TTAATATTATATA
*
59152 TATATTTCTTTAATATTTTACT-
1 TATATTTCTTTAATATTATA-TA
**
59174 TATAAGTC--TAATATTACTATA
1 TATATTTCTTTAATATTA-TATA
59195 TATATTT
1 TATATTT
59202 AATTATCTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 9
0.71 0.13 0.16
Matches are distributed among these distances:
20 8 0.21
21 7 0.18
22 22 0.56
23 2 0.05
ACGTcount: A:0.35, C:0.06, G:0.01, T:0.58
Consensus pattern (22 bp):
TATATTTCTTTAATATTATATA
Done.