Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002704.1 Hibiscus syriacus cultivar Beakdansim tig00005581_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: 63929
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:7622 original size:20 final size:20
Alignment explanation
Indices: 7597--7643 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
7587 CACGGAATGT
7597 AAGATTACCAGTGAAAATAA
1 AAGATTACCAGTGAAAATAA
*
7617 AAGATTACCAGTGATAATAA
1 AAGATTACCAGTGAAAATAA
7637 AAGATTA
1 AAGATTA
7644 TCAGGGAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.53, C:0.09, G:0.15, T:0.23
Consensus pattern (20 bp):
AAGATTACCAGTGAAAATAA
Found at i:15801 original size:18 final size:21
Alignment explanation
Indices: 15772--15814 Score: 65
Period size: 18 Copynumber: 2.2 Consensus size: 21
15762 ATGATTTAAA
15772 ATACTGTAAATCAGG-AA-TC
1 ATACTGTAAATCAGGTAAGTC
15791 ATACT-TAAATCAGGTAAGTC
1 ATACTGTAAATCAGGTAAGTC
15811 ATAC
1 ATAC
15815 GGTAGTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.41
19 7 0.32
20 6 0.27
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (21 bp):
ATACTGTAAATCAGGTAAGTC
Found at i:15893 original size:13 final size:13
Alignment explanation
Indices: 15875--15899 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15865 TGTGCACATG
15875 ATATTTAAAACAA
1 ATATTTAAAACAA
15888 ATATTTAAAACA
1 ATATTTAAAACA
15900 GTTATAAGGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (13 bp):
ATATTTAAAACAA
Found at i:19505 original size:23 final size:23
Alignment explanation
Indices: 19479--19565 Score: 104
Period size: 23 Copynumber: 3.8 Consensus size: 23
19469 ATAAATTGCA
19479 CCGAAGTG-CCACATAGAAATGTC
1 CCGAA-TGACCACATAGAAATGTC
* *
19502 CCGAATGACCACATAGTATTGTC
1 CCGAATGACCACATAGAAATGTC
* *
19525 CCGAATGACCGCGTAGAAATGTC
1 CCGAATGACCACATAGAAATGTC
* *
19548 TCGAATGACCACGTAGAA
1 CCGAATGACCACATAGAA
19566 TTATCCTGAA
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
22 2 0.04
23 53 0.96
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.20
Consensus pattern (23 bp):
CCGAATGACCACATAGAAATGTC
Found at i:19944 original size:22 final size:21
Alignment explanation
Indices: 19903--19945 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
19893 TGTATAACAG
*
19903 TGCATGTAACATATAGACATA
1 TGCATGTAACATATACACATA
*
19924 TGCATGTACTCATATACACATA
1 TGCATGTA-ACATATACACATA
19946 GAAATCATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.30
Consensus pattern (21 bp):
TGCATGTAACATATACACATA
Found at i:25502 original size:27 final size:25
Alignment explanation
Indices: 25461--25517 Score: 87
Period size: 27 Copynumber: 2.2 Consensus size: 25
25451 TTTTTTATAT
25461 TTTAAAATAAATTTATATTAAATAA
1 TTTAAAATAAATTTATATTAAATAA
*
25486 TTTAAAATGTAAATTTATATTAAATTA
1 TTTAAAA--TAAATTTATATTAAATAA
25513 TTTAA
1 TTTAA
25518 TTCTTAGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 7 0.24
27 22 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (25 bp):
TTTAAAATAAATTTATATTAAATAA
Found at i:27207 original size:2 final size:2
Alignment explanation
Indices: 27200--27246 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
27190 ATCTCACCTT
27200 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
27242 TA TA T
1 TA TA T
27247 GTGCGTGTGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:32477 original size:23 final size:23
Alignment explanation
Indices: 32450--32498 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
32440 AAACGTATCA
32450 AAAGACAAAGGA-AAATGTGTCAT
1 AAAGACAAA-GACAAATGTGTCAT
* *
32473 AAAGACAGAGACAAATGTGTGAT
1 AAAGACAAAGACAAATGTGTCAT
32496 AAA
1 AAA
32499 AATAAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 2 0.09
23 21 0.91
ACGTcount: A:0.53, C:0.08, G:0.22, T:0.16
Consensus pattern (23 bp):
AAAGACAAAGACAAATGTGTCAT
Found at i:33115 original size:23 final size:25
Alignment explanation
Indices: 33064--33127 Score: 69
Period size: 23 Copynumber: 2.6 Consensus size: 25
33054 TGAGCATCAT
*
33064 TAAATTAATTTATAAAACGTTAAATTA
1 TAAATT-ATTTA-AAAACATTAAATTA
33091 TAAATTATTTAAAAA-ATTAAA-TA
1 TAAATTATTTAAAAACATTAAATTA
* *
33114 TAATTTAGTTAAAA
1 TAAATTATTTAAAA
33128 TACAATATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 14 0.41
24 5 0.15
25 4 0.12
26 5 0.15
27 6 0.18
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.41
Consensus pattern (25 bp):
TAAATTATTTAAAAACATTAAATTA
Found at i:39986 original size:23 final size:23
Alignment explanation
Indices: 39957--40018 Score: 115
Period size: 23 Copynumber: 2.7 Consensus size: 23
39947 TATAACCATG
39957 TGTGATATACACATGTTTTCATA
1 TGTGATATACACATGTTTTCATA
39980 TGTGATATACACATGTTTTCATA
1 TGTGATATACACATGTTTTCATA
*
40003 TGTGATATACATATGT
1 TGTGATATACACATGT
40019 CATTTAGAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.44
Consensus pattern (23 bp):
TGTGATATACACATGTTTTCATA
Found at i:49935 original size:20 final size:20
Alignment explanation
Indices: 49907--49958 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
49897 ATAATTCTTA
49907 TTTTAAATAAAATTAGTGAT
1 TTTTAAATAAAATTAGTGAT
*
49927 TTTTGAATAAAATTAGTGA-
1 TTTTAAATAAAATTAGTGAT
*
49946 TTTTAAAAAAAAT
1 TTTTAAATAAAAT
49959 CTAATAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 11 0.38
20 18 0.62
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (20 bp):
TTTTAAATAAAATTAGTGAT
Found at i:52922 original size:51 final size:51
Alignment explanation
Indices: 52841--52939 Score: 162
Period size: 51 Copynumber: 1.9 Consensus size: 51
52831 GACGTTAATA
52841 TGTTGATTGTGATATAATAAAATATAATTCTAGAATCTTAAACAATTAGAC
1 TGTTGATTGTGATATAATAAAATATAATTCTAGAATCTTAAACAATTAGAC
* * * *
52892 TGTTGATTGTGATATGATAAATTATGATTCTATAATCTTAAACAATTA
1 TGTTGATTGTGATATAATAAAATATAATTCTAGAATCTTAAACAATTA
52940 TATAGCTCAG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.40
Consensus pattern (51 bp):
TGTTGATTGTGATATAATAAAATATAATTCTAGAATCTTAAACAATTAGAC
Found at i:58014 original size:20 final size:20
Alignment explanation
Indices: 57976--58014 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
57966 TAATTAATTC
*
57976 AATATTAATAAATATATAAA
1 AATATTAATAAAGATATAAA
57996 AATATTAA-ATAAGATATAA
1 AATATTAATA-AAGATATAA
58015 TTATATTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (20 bp):
AATATTAATAAAGATATAAA
Found at i:60191 original size:15 final size:16
Alignment explanation
Indices: 60161--60191 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
60151 GTGGGAATAA
60161 AAGATTACTAGGGAAT
1 AAGATTACTAGGGAAT
60177 AAGATTACT-GGGAAT
1 AAGATTACTAGGGAAT
60192 GTTACATTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.42, C:0.06, G:0.26, T:0.26
Consensus pattern (16 bp):
AAGATTACTAGGGAAT
Found at i:61629 original size:14 final size:15
Alignment explanation
Indices: 61563--61641 Score: 94
Period size: 14 Copynumber: 5.5 Consensus size: 15
61553 TTCCAGAAAA
61563 TGAATTACTGGAATT
1 TGAATTACTGGAATT
*
61578 TGAA-TACTGAAATT
1 TGAATTACTGGAATT
*
61592 TG-ATTACTGGAA-A
1 TGAATTACTGGAATT
61605 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
61620 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
61634 TGAATTAC
1 TGAATTAC
61642 ATTTCTGTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
13 3 0.06
14 40 0.74
15 11 0.20
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.35
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:61647 original size:20 final size:20
Alignment explanation
Indices: 61624--61693 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
61614 GGAATTTGAA
61624 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
61644 TTCTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
61664 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
61684 TTCTGGAAAA
1 TTCTGGAAAA
61694 CATCTGGAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:61935 original size:25 final size:25
Alignment explanation
Indices: 61870--61926 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
61860 GAAATATATA
61870 AATATATTCATTATTAAATAAAAAATT
1 AATATA-T-ATTATTAAATAAAAAATT
*
61897 ATTATATATTATTAAAT-AAAAATAT
1 AATATATATTATTAAATAAAAAAT-T
61922 AATAT
1 AATAT
61927 CTTATATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 6 0.22
25 15 0.56
26 1 0.04
27 5 0.19
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (25 bp):
AATATATATTATTAAATAAAAAATT
Found at i:61940 original size:18 final size:18
Alignment explanation
Indices: 61919--61996 Score: 60
Period size: 18 Copynumber: 4.7 Consensus size: 18
61909 TAAATAAAAA
*
61919 TATAATATCTTATATTAT
1 TATAATATATTATATTAT
*
61937 TATAATATATTTTATTAT
1 TATAATATATTATATTAT
* ** *
61955 T-T--TATATAATAAAAA
1 TATAATATATTATATTAT
61970 TAT-A-ATATTATATTAT
1 TATAATATATTATATTAT
61986 TATAA-ATATTA
1 TATAATATATTA
61997 ATAATATTTT
Statistics
Matches: 46, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
15 9 0.20
16 12 0.26
17 8 0.17
18 17 0.37
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (18 bp):
TATAATATATTATATTAT
Found at i:62003 original size:31 final size:31
Alignment explanation
Indices: 61943--62003 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
61933 TTATTATAAT
* * *
61943 ATATTTTATTATTTTATATAATAAAAATATA
1 ATATTATATTATTATAAATAATAAAAATATA
* *
61974 ATATTATATTATTATAAATATTAATAATAT
1 ATATTATATTATTATAAATAATAAAAATAT
62004 TTTAAATATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (31 bp):
ATATTATATTATTATAAATAATAAAAATATA
Found at i:62005 original size:49 final size:50
Alignment explanation
Indices: 61894--62007 Score: 144
Period size: 51 Copynumber: 2.3 Consensus size: 50
61884 TAAATAAAAA
* *
61894 ATTATTATATATTAT-TAAATAAAAATATAATATCTTATATTATTATAATAT
1 ATTATAATATTTTATAT-AATAAAAATATAATA-CTTATATTATTATAATAT
* *
61945 ATTTTATTATTTTATATAATAAAAATATAATA-TTATATTATTATAA-AT
1 ATTATAATATTTTATATAATAAAAATATAATACTTATATTATTATAATAT
61993 ATTAATAATATTTTA
1 ATT-ATAATATTTTA
62008 AATATTTTAA
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
48 5 0.09
49 23 0.42
51 26 0.47
52 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (50 bp):
ATTATAATATTTTATATAATAAAAATATAATACTTATATTATTATAATAT
Found at i:62009 original size:18 final size:17
Alignment explanation
Indices: 61973--62019 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
61963 ATAAAAATAT
*
61973 AATATTATATTATTATA
1 AATATTATAATATTATA
*
61990 AATATTAATAATATTTTA
1 AATATT-ATAATATTATA
*
62008 AATATTTTAATA
1 AATATTATAATA
62020 ATTAATATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
AATATTATAATATTATA
Found at i:62242 original size:42 final size:42
Alignment explanation
Indices: 62195--62313 Score: 222
Period size: 41 Copynumber: 2.9 Consensus size: 42
62185 ATGAATTACA
*
62195 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
62237 TTCCGGAAAACGAATTACGTGAAACAAACACGGG-AAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
62278 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
62314 TTCGGGAAAA
Statistics
Matches: 75, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
41 40 0.53
42 35 0.47
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.16
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Done.