Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004791.1 Hibiscus syriacus cultivar Beakdansim tig00010801_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: 55631
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:6354 original size:18 final size:19
Alignment explanation
Indices: 6333--6371 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
6323 GAATAAATAA
6333 AAAATA-TCTAATATTTTC
1 AAAATATTCTAATATTTTC
6351 AAAATATTCTAATATTTTC
1 AAAATATTCTAATATTTTC
6370 AA
1 AA
6372 TTAAAGAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (19 bp):
AAAATATTCTAATATTTTC
Found at i:6939 original size:19 final size:19
Alignment explanation
Indices: 6917--6960 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
6907 TTTTCTAAAT
*
6917 ATAATATTTAATATAAAAC
1 ATAATATCTAATATAAAAC
* *
6936 ATAATATCTATTATAAAAT
1 ATAATATCTAATATAAAAC
6955 ATAATA
1 ATAATA
6961 AGATGTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (19 bp):
ATAATATCTAATATAAAAC
Found at i:11023 original size:3 final size:3
Alignment explanation
Indices: 11017--11071 Score: 83
Period size: 3 Copynumber: 17.3 Consensus size: 3
11007 CACCCCCAGG
11017 TCT TCT TCT TCCT TCTT TCTT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT T-CT TC-T TC-T TCT TCT TCT TCT TCT TCT TCT TCT TCT
11065 TCT TCT T
1 TCT TCT T
11072 TGAGACAAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
3 40 0.80
4 10 0.20
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:17319 original size:161 final size:161
Alignment explanation
Indices: 16959--17439 Score: 821
Period size: 161 Copynumber: 3.0 Consensus size: 161
16949 AAAGATGATC
*
16959 AAAATACTCGAATCTAAAGAATCTCGACCCGACCTTACAAAAGCAGTTTTTTTAAAATTTTAAAA
1 AAAATACTCGAATCTAACGAATCTCGACCCGACCTTACAAAAGCAGTTTTTTTAAAATTTTAAAA
17024 AATCAATCCGACCCAACCTGGTATAAATTATTATTCTATC--TATATATATACACGTATATACCC
66 AATCAATCCGACCCAACCTGGTATAAATTATTATTCTATCTATATATATATACACGTATATACCC
17087 GGCTCCGTCCCACCCTGATCCCTAAAATTTT
131 GGCTCCGTCCCACCCTGATCCCTAAAATTTT
* * * *
17118 AAAATACTTGAATCTAACAAATCTTGACCCGACCTTACAAAAGTAGTTTTTTTAAAATTTTAAAA
1 AAAATACTCGAATCTAACGAATCTCGACCCGACCTTACAAAAGCAGTTTTTTTAAAATTTTAAAA
17183 AATCAATCCGACCCAACCTGGTATAAATTATTATTCTATCTATATATATATACACGTATATACCC
66 AATCAATCCGACCCAACCTGGTATAAATTATTATTCTATCTATATATATATACACGTATATACCC
* *
17248 AGTTCCGTCCCACCCTGATCCCTAAAATTTT
131 GGCTCCGTCCCACCCTGATCCCTAAAATTTT
* *
17279 AAAATACTCGAATCTTACGAATCTCGACCCGACCTTACAAAAGCAGTTTTTTTTAAATTTTAAAA
1 AAAATACTCGAATCTAACGAATCTCGACCCGACCTTACAAAAGCAGTTTTTTTAAAATTTTAAAA
17344 AATCAATCCGACCCAACCTGGTATAAATTATTA---T-TCTATATATATATACACGTATATACCC
66 AATCAATCCGACCCAACCTGGTATAAATTATTATTCTATCTATATATATATACACGTATATACCC
* *
17405 GGCTACGTCCCACCCTGAACCCTAAAATTTT
131 GGCTCCGTCCCACCCTGATCCCTAAAATTTT
17436 AAAA
1 AAAA
17440 AAAATTACTT
Statistics
Matches: 303, Mismatches: 17, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
157 58 0.19
158 1 0.00
159 100 0.33
161 144 0.48
ACGTcount: A:0.37, C:0.23, G:0.08, T:0.32
Consensus pattern (161 bp):
AAAATACTCGAATCTAACGAATCTCGACCCGACCTTACAAAAGCAGTTTTTTTAAAATTTTAAAA
AATCAATCCGACCCAACCTGGTATAAATTATTATTCTATCTATATATATATACACGTATATACCC
GGCTCCGTCCCACCCTGATCCCTAAAATTTT
Found at i:17883 original size:49 final size:49
Alignment explanation
Indices: 17820--17976 Score: 140
Period size: 50 Copynumber: 3.1 Consensus size: 49
17810 GCCCCTGCAC
** *
17820 CGCGCTATACCCCACGTG-T-CAGAT-ATCCAGGTATAGCGCGTTGCAGGGGT
1 CGCGCTATA-CCCACGTGATCCAGATCA-CC--GTATAGCGCGGGGCAGGGGG
17870 CGCGCTATACCCACGTGTATGCCAGATCACCGTATAGCGCGGGGCAGGGGG
1 CGCGCTATACCCACGTG-AT-CCAGATCACCGTATAGCGCGGGGCAGGGGG
** * * * * *
17921 CGCGCTATACCCACGTGGCGCCAAATCAACGTATAGCGCGGTGCATGCGG
1 CGCGCTATACCCACGT-GATCCAGATCACCGTATAGCGCGGGGCAGGGGG
17971 CGCGCT
1 CGCGCT
17977 TTACTGCTAA
Statistics
Matches: 91, Mismatches: 10, Indels: 12
0.81 0.09 0.11
Matches are distributed among these distances:
49 8 0.09
50 40 0.44
51 34 0.37
52 1 0.01
53 7 0.08
54 1 0.01
ACGTcount: A:0.20, C:0.31, G:0.32, T:0.18
Consensus pattern (49 bp):
CGCGCTATACCCACGTGATCCAGATCACCGTATAGCGCGGGGCAGGGGG
Found at i:17917 original size:51 final size:50
Alignment explanation
Indices: 17850--17976 Score: 155
Period size: 51 Copynumber: 2.5 Consensus size: 50
17840 AGATATCCAG
** * * * *
17850 GTATAGCGCGTTGCAGGGGTCGCGCTATACCCACGTGTATGCCAGATCACC
1 GTATAGCGCGGGGCAGGGGGCGCGCTATACCCACGTG-ACGCCAAATCAAC
*
17901 GTATAGCGCGGGGCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCAAC
1 GTATAGCGCGGGGCAGGGGGCGCGCTATACCCACGTGACGCCAAATCAAC
* * *
17951 GTATAGCGCGGTGCATGCGGCGCGCT
1 GTATAGCGCGGGGCAGGGGGCGCGCT
17977 TTACTGCTAA
Statistics
Matches: 66, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
50 32 0.48
51 34 0.52
ACGTcount: A:0.19, C:0.29, G:0.35, T:0.17
Consensus pattern (50 bp):
GTATAGCGCGGGGCAGGGGGCGCGCTATACCCACGTGACGCCAAATCAAC
Found at i:17973 original size:50 final size:50
Alignment explanation
Indices: 17850--17976 Score: 157
Period size: 50 Copynumber: 2.5 Consensus size: 50
17840 AGATATCCAG
* * * *
17850 GTATAGCGCGTTGCAGGGGTCGCGCTATACCCACGTGTATGCCAGATCACC
1 GTATAGCGCGGTGCAGGGG-CGCGCTATACCCACGTGTACGCCAAATCAAC
* *
17901 GTATAGCGCGGGGCAGGGGGCGCGCTATACCCACGTG-GCGCCAAATCAAC
1 GTATAGCGCGGTGCA-GGGGCGCGCTATACCCACGTGTACGCCAAATCAAC
*
17951 GTATAGCGCGGTGCATGCGGCGCGCT
1 GTATAGCGCGGTGCA-GGGGCGCGCT
17977 TTACTGCTAA
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
50 32 0.48
51 30 0.45
52 4 0.06
ACGTcount: A:0.19, C:0.29, G:0.35, T:0.17
Consensus pattern (50 bp):
GTATAGCGCGGTGCAGGGGCGCGCTATACCCACGTGTACGCCAAATCAAC
Found at i:19235 original size:10 final size:10
Alignment explanation
Indices: 19220--19245 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
19210 AACGATTTTT
19220 TATAATTATA
1 TATAATTATA
19230 TATAATTATA
1 TATAATTATA
19240 TATAAT
1 TATAAT
19246 CTTTTGGGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
TATAATTATA
Found at i:20548 original size:29 final size:31
Alignment explanation
Indices: 20512--20569 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 31
20502 AATATACATT
**
20512 ATAATAATCTTTTATTCCT-TT-AACCAAAC
1 ATAATAATCTTACATTCCTGTTAAACCAAAC
20541 ATAATAATCTTACATTCCTGTTAAACCAA
1 ATAATAATCTTACATTCCTGTTAAACCAA
20570 CCAAACACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 17 0.68
30 2 0.08
31 6 0.24
ACGTcount: A:0.40, C:0.21, G:0.02, T:0.38
Consensus pattern (31 bp):
ATAATAATCTTACATTCCTGTTAAACCAAAC
Found at i:21167 original size:47 final size:47
Alignment explanation
Indices: 21106--21199 Score: 170
Period size: 47 Copynumber: 2.0 Consensus size: 47
21096 GATACTCTAA
*
21106 TTTAAACGATTTTTTATAATTATATATAATATGCATTTATACTTCTT
1 TTTAAACGACTTTTTATAATTATATATAATATGCATTTATACTTCTT
*
21153 TTTAAATGACTTTTTATAATTATATATAATATGCATTTATACTTCTT
1 TTTAAACGACTTTTTATAATTATATATAATATGCATTTATACTTCTT
21200 CATAAGTGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.34, C:0.09, G:0.04, T:0.53
Consensus pattern (47 bp):
TTTAAACGACTTTTTATAATTATATATAATATGCATTTATACTTCTT
Found at i:21193 original size:23 final size:23
Alignment explanation
Indices: 21118--21193 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 23
21108 TAAACGATTT
21118 TTTATAATTATATATAATATGCA
1 TTTATAATTATATATAATATGCA
* * * * *
21141 TTTATACTTCTTTTTAA-ATGACTT
1 TTTATAATTATATATAATATG-C-A
21165 TTTATAATTATATATAATATGCA
1 TTTATAATTATATATAATATGCA
21188 TTTATA
1 TTTATA
21194 CTTCTTCATA
Statistics
Matches: 40, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
22 3 0.08
23 20 0.50
24 14 0.35
25 3 0.08
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.53
Consensus pattern (23 bp):
TTTATAATTATATATAATATGCA
Found at i:21204 original size:23 final size:22
Alignment explanation
Indices: 21130--21204 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 22
21120 TATAATTATA
21130 TATAATATGCATTTATACTTCTT
1 TATAATATGCATTTATACTTC-T
* * * *
21153 TTTAA-ATGACTTTTTATAATTAT
1 TATAATATG-C-ATTTATACTTCT
21176 ATATAATATGCATTTATACTTCT
1 -TATAATATGCATTTATACTTCT
21199 TCATAA
1 T-ATAA
21205 GTGATACATA
Statistics
Matches: 39, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
22 4 0.10
23 19 0.49
24 13 0.33
25 3 0.08
ACGTcount: A:0.35, C:0.11, G:0.04, T:0.51
Consensus pattern (22 bp):
TATAATATGCATTTATACTTCT
Found at i:27079 original size:2 final size:2
Alignment explanation
Indices: 27072--27136 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
27062 AAATTTATCA
27072 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
27114 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
27137 AGTATAAAAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30939 original size:14 final size:14
Alignment explanation
Indices: 30920--30948 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
30910 TGCATGCAGC
30920 TAATGTAATTAATG
1 TAATGTAATTAATG
30934 TAATGTAATTAATG
1 TAATGTAATTAATG
30948 T
1 T
30949 TTTTTTACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (14 bp):
TAATGTAATTAATG
Found at i:50353 original size:35 final size:34
Alignment explanation
Indices: 50268--50354 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 34
50258 AAAATAATTT
* *
50268 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGA
* *
50302 TAAATGATAACCAAATTACAATAACTGATATTAAATGA
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAATGA
50340 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
50355 ACTTAAATAC
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.55
36 1 0.02
37 4 0.09
38 10 0.23
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGA
Found at i:52624 original size:16 final size:16
Alignment explanation
Indices: 52600--52675 Score: 80
Period size: 16 Copynumber: 4.4 Consensus size: 16
52590 TATATCTGCA
* *
52600 AAAAAATTAAATAAGT
1 AAAATATTAAATAAAT
52616 AAAATATTAAATAAAT
1 AAAATATTAAATAAAT
*
52632 TAAATATTTAAATAAATT
1 AAAATA-TTAAATAAA-T
52650 AAAAATATTAAAATATAAT
1 -AAAATATT-AAATA-AAT
52669 AAAATAT
1 AAAATAT
52676 ACCTTAGAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
16 19 0.37
17 9 0.18
18 10 0.20
19 11 0.22
20 2 0.04
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (16 bp):
AAAATATTAAATAAAT
Found at i:52633 original size:9 final size:9
Alignment explanation
Indices: 52603--52661 Score: 54
Period size: 8 Copynumber: 6.9 Consensus size: 9
52593 ATCTGCAAAA
52603 AAATTAAAT
1 AAATTAAAT
*
52612 -AAGTAAA-
1 AAATTAAAT
*
52619 ATATTAAAT
1 AAATTAAAT
52628 AAATTAAAT
1 AAATTAAAT
*
52637 -ATTTAAAT
1 AAATTAAAT
52645 AAATTAAA-
1 AAATTAAAT
52653 AATATTAAA
1 AA-ATTAAA
52662 ATATAATAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
8 20 0.50
9 20 0.50
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (9 bp):
AAATTAAAT
Found at i:52643 original size:25 final size:24
Alignment explanation
Indices: 52600--52675 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 24
52590 TATATCTGCA
52600 AAAAAATTAAATA-AGTAAAATATT
1 AAAAAATTAAATATA-TAAAATATT
* *
52624 AAATAAATTAAATATTTAAATAAATT
1 AAA-AAATTAAATATATAAA-ATATT
52650 AAAAATATTAAAATATAATAAAATAT
1 AAAAA-ATT-AAATAT-ATAAAATAT
52676 ACCTTAGAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
24 3 0.07
25 16 0.38
26 10 0.24
27 9 0.21
28 4 0.10
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (24 bp):
AAAAAATTAAATATATAAAATATT
Found at i:53403 original size:16 final size:16
Alignment explanation
Indices: 53384--53414 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53374 ATTTATGCTT
53384 TAATTTATAATATTAA
1 TAATTTATAATATTAA
*
53400 TAATTTGTAATATTA
1 TAATTTATAATATTA
53415 TAAGTATTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (16 bp):
TAATTTATAATATTAA
Found at i:54408 original size:21 final size:20
Alignment explanation
Indices: 54384--54455 Score: 60
Period size: 21 Copynumber: 3.5 Consensus size: 20
54374 TTTTAAATAC
54384 TATTTTAATAAATATATTAA
1 TATTTTAATAAATATATTAA
*
54404 T-TATTAA-AACATATTTATTAA
1 TATTTTAATAA-ATA--TATTAA
54425 TAGTTTTAATAAATAATATT-A
1 TA-TTTTAATAAAT-ATATTAA
54446 TACTTTTAAT
1 TA-TTTTAAT
54456 GCTTTAATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 13
0.72 0.05 0.22
Matches are distributed among these distances:
18 2 0.05
19 8 0.19
20 1 0.02
21 17 0.40
22 4 0.10
23 7 0.17
24 3 0.07
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (20 bp):
TATTTTAATAAATATATTAA
Found at i:54773 original size:20 final size:20
Alignment explanation
Indices: 54748--54797 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
54738 TAAAAATTTT
54748 GAAACCATTGAAATTAAGTC
1 GAAACCATTGAAATTAAGTC
54768 GAAACCATTGAAATTAAGTC
1 GAAACCATTGAAATTAAGTC
**
54788 TTAACCATTG
1 GAAACCATTG
54798 TTAATAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (20 bp):
GAAACCATTGAAATTAAGTC
Done.