Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006797.1 Hibiscus syriacus cultivar Beakdansim tig00017244_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: 62740
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1892 original size:16 final size:17
Alignment explanation
Indices: 1864--1898 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
1854 CGTATCGTCG
1864 ACAAAATTTTACTATTC
1 ACAAAATTTTACTATTC
1881 ACAAAA-TTTACTATTC
1 ACAAAATTTTACTATTC
1897 AC
1 AC
1899 GTAAACAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.37
Consensus pattern (17 bp):
ACAAAATTTTACTATTC
Found at i:10820 original size:14 final size:14
Alignment explanation
Indices: 10801--10827 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
10791 TATTAAATCC
10801 TGTACAGTTTGTCT
1 TGTACAGTTTGTCT
10815 TGTACAGTTTGTC
1 TGTACAGTTTGTC
10828 AGTAAATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.22, T:0.48
Consensus pattern (14 bp):
TGTACAGTTTGTCT
Found at i:15018 original size:37 final size:36
Alignment explanation
Indices: 14960--15078 Score: 152
Period size: 35 Copynumber: 3.3 Consensus size: 36
14950 TCCCATTATT
* *
14960 ATTTTTC-AACAAACATCTACCAAACTTTGAAAAACT
1 ATTTTTCAAAGAAACATCTACCAAACTTTG-AAAACC
* * *
14996 ATTTTTCAAAGAAACATTTACCAAAGTTTGTAAACC
1 ATTTTTCAAAGAAACATCTACCAAACTTTGAAAACC
*
15032 A-TTTTCAAAGAAACATGTACCAAACTTTGAAAACC
1 ATTTTTCAAAGAAACATCTACCAAACTTTGAAAACC
15067 ATTTTTTCAAAG
1 A-TTTTTCAAAG
15079 TTGGTTACCA
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
35 32 0.44
36 12 0.17
37 28 0.39
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (36 bp):
ATTTTTCAAAGAAACATCTACCAAACTTTGAAAACC
Found at i:17473 original size:20 final size:20
Alignment explanation
Indices: 17448--17495 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
17438 CAGACCAGTC
17448 TCATTTTCCACCATGGCCTT
1 TCATTTTCCACCATGGCCTT
17468 TCATTTTCCACCATGGCCTT
1 TCATTTTCCACCATGGCCTT
*
17488 CCATTTTC
1 TCATTTTC
17496 TGAAGGTATC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.15, C:0.35, G:0.08, T:0.42
Consensus pattern (20 bp):
TCATTTTCCACCATGGCCTT
Found at i:19620 original size:37 final size:36
Alignment explanation
Indices: 19561--19679 Score: 161
Period size: 35 Copynumber: 3.3 Consensus size: 36
19551 ATCCCATTAT
* *
19561 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAA
1 CATTTTTCAAAAAAACATTTACCAAACTTTGAAAAA
*
19596 CTATTTTTCAAAAAAACATTTACCAAACTTTGAAAAC
1 C-ATTTTTCAAAAAAACATTTACCAAACTTTGAAAAA
* *
19633 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAT
1 CATTTTTCAAAAAAACATTTACCAAACTTTGAAAAA
19668 CATTTTTTCAAA
1 CA-TTTTTCAAA
19680 GTTGGTTACC
Statistics
Matches: 75, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
35 34 0.45
36 8 0.11
37 33 0.44
ACGTcount: A:0.45, C:0.19, G:0.03, T:0.33
Consensus pattern (36 bp):
CATTTTTCAAAAAAACATTTACCAAACTTTGAAAAA
Found at i:19636 original size:21 final size:20
Alignment explanation
Indices: 19608--19672 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
19598 ATTTTTCAAA
19608 AAAACATTTACCAAACTTTG
1 AAAACATTTACCAAACTTTG
*
19628 AAAACCATTT-TCAAA----G
1 AAAA-CATTTACCAAACTTTG
19644 -AAACATTTACCAAACTTTG
1 AAAACATTTACCAAACTTTG
19663 AAAATCATTT
1 AAAA-CATTT
19673 TTTCAAAGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.14
15 7 0.20
16 1 0.03
19 1 0.03
20 11 0.31
21 10 0.29
ACGTcount: A:0.46, C:0.18, G:0.05, T:0.31
Consensus pattern (20 bp):
AAAACATTTACCAAACTTTG
Found at i:31743 original size:35 final size:35
Alignment explanation
Indices: 31704--31815 Score: 170
Period size: 35 Copynumber: 3.2 Consensus size: 35
31694 AAAACATTCA
*
31704 TCAATTTCATTCTAAACCCCAAATTCTAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCTAAAATAAT
*
31739 TCAATTTCATTCTAAACCCTAAATTCTAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCTAAAATAAT
* * * *
31774 TCAATTACATTATAAAACCCAAATTCTAAAATATT
1 TCAATTTCATTCTAAACCCCAAATTCTAAAATAAT
31809 TCAATTT
1 TCAATTT
31816 AAGGAGGAAT
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 69 1.00
ACGTcount: A:0.43, C:0.20, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCTAAAATAAT
Found at i:32937 original size:36 final size:35
Alignment explanation
Indices: 32870--32983 Score: 158
Period size: 35 Copynumber: 3.2 Consensus size: 35
32860 AAAAAAGACA
* * *
32870 GAAATTGAAGTATTTTAGAATTTAGGTTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTAGGGTTTAGAAT
*
32905 GTAATTGAATTATTTTTGGAATTTAGGGTTTAGAAT
1 GAAATTGAATTA-TTTTGGAATTTAGGGTTTAGAAT
*
32941 GAAATTGAATTACTTTGGAATTT-GTGGTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTAG-GGTTTAGAAT
32976 GAAATTGA
1 GAAATTGA
32984 GGATTGTTTT
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
34 1 0.01
35 38 0.54
36 32 0.45
ACGTcount: A:0.34, C:0.01, G:0.22, T:0.43
Consensus pattern (35 bp):
GAAATTGAATTATTTTGGAATTTAGGGTTTAGAAT
Found at i:34397 original size:21 final size:21
Alignment explanation
Indices: 34357--34417 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
34347 ATCCATGGAC
*
34357 CATATATTTCTT-TGTCTTTAT
1 CATATATTT-TTCTATCTTTAT
* * *
34378 CATGTTTTTTTTTATCTTTAT
1 CATATATTTTTCTATCTTTAT
*
34399 GATATATTTTTCTATCTTT
1 CATATATTTTTCTATCTTT
34418 TAATACGCTT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
20 2 0.06
21 30 0.94
ACGTcount: A:0.18, C:0.11, G:0.05, T:0.66
Consensus pattern (21 bp):
CATATATTTTTCTATCTTTAT
Found at i:38364 original size:15 final size:16
Alignment explanation
Indices: 38322--38364 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
38312 ATATATTATA
38322 AGAAGAA-GAAAAAAC
1 AGAAGAATGAAAAAAC
* *
38337 AGAAGAATAAAAAAAT
1 AGAAGAATGAAAAAAC
38353 AGAA-AATGAAAA
1 AGAAGAATGAAAA
38365 TGAAAACGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.74, C:0.02, G:0.16, T:0.07
Consensus pattern (16 bp):
AGAAGAATGAAAAAAC
Found at i:38376 original size:34 final size:33
Alignment explanation
Indices: 38332--38421 Score: 96
Period size: 34 Copynumber: 2.6 Consensus size: 33
38322 AGAAGAAGAA
*
38332 AAAACAGAAGAATAAAAAAATAGAAAATGA-AAATG
1 AAAAC-GAAGAAAAAAAAAATA-AAAATGAGAAA-G
38367 AAAACGAAGAAGAAAAAAAATAAAAATGAGAAAG
1 AAAACGAAGAA-AAAAAAAATAAAAATGAGAAAG
38401 AAAA-GAA-AAAGAGAAAAAATA
1 AAAACGAAGAAA-A-AAAAAATA
38422 TGAGAGATGA
Statistics
Matches: 50, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
31 1 0.02
32 3 0.06
33 11 0.22
34 18 0.36
35 17 0.34
ACGTcount: A:0.74, C:0.02, G:0.16, T:0.08
Consensus pattern (33 bp):
AAAACGAAGAAAAAAAAAATAAAAATGAGAAAG
Found at i:38386 original size:22 final size:23
Alignment explanation
Indices: 38353--38409 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
38343 ATAAAAAAAT
*
38353 AGAAAATGAAAATGAAAACGA-AGA
1 AGAAAA-GAAAATAAAAACGAGA-A
*
38377 AGAAAA-AAAATAAAAATGAGAA
1 AGAAAAGAAAATAAAAACGAGAA
38399 AGAAAAGAAAA
1 AGAAAAGAAAA
38410 AGAGAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 18 0.62
23 5 0.17
24 6 0.21
ACGTcount: A:0.74, C:0.02, G:0.18, T:0.07
Consensus pattern (23 bp):
AGAAAAGAAAATAAAAACGAGAA
Found at i:38387 original size:28 final size:27
Alignment explanation
Indices: 38355--38410 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 27
38345 AAAAAAATAG
*
38355 AAAATGAAAATGA-AAACGAAGAAGAAAA
1 AAAATAAAAATGAGAAA-GAA-AAGAAAA
38383 AAAATAAAAATGAGAAAGAAAAGAAAA
1 AAAATAAAAATGAGAAAGAAAAGAAAA
38410 A
1 A
38411 GAGAAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 8 0.31
28 15 0.58
29 3 0.12
ACGTcount: A:0.75, C:0.02, G:0.16, T:0.07
Consensus pattern (27 bp):
AAAATAAAAATGAGAAAGAAAAGAAAA
Found at i:38414 original size:17 final size:18
Alignment explanation
Indices: 38377--38419 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
38367 AAAACGAAGA
*
38377 AGAAAAAAAATAAAAATG
1 AGAAAAAAAAGAAAAATG
*
38395 AGAAAGAAAAGAAAAA-G
1 AGAAAAAAAAGAAAAATG
38412 AGAAAAAA
1 AGAAAAAA
38420 TATGAGAGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (18 bp):
AGAAAAAAAAGAAAAATG
Found at i:38416 original size:35 final size:35
Alignment explanation
Indices: 38345--38421 Score: 106
Period size: 33 Copynumber: 2.3 Consensus size: 35
38335 ACAGAAGAAT
*
38345 AAAAAAATAGAAAATGAAAATGAAAACGAAGAAGA
1 AAAAAAATAGAAAATGAAAATGAAAACGAAAAAGA
38380 AAAAAAATA-AAAATGAGAAA-GAAAA-GAAAAAGA
1 AAAAAAATAGAAAATGA-AAATGAAAACGAAAAAGA
*
38413 GAAAAAATA
1 AAAAAAATA
38422 TGAGAGATGA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
33 15 0.38
34 12 0.31
35 12 0.31
ACGTcount: A:0.75, C:0.01, G:0.16, T:0.08
Consensus pattern (35 bp):
AAAAAAATAGAAAATGAAAATGAAAACGAAAAAGA
Found at i:42011 original size:40 final size:40
Alignment explanation
Indices: 41954--42035 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
41944 TGCAGGTTTA
**
41954 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCAATGTATATGGTGGGCACGACCTTATGTG
41994 TAATACACTTCAATGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCAATGTATATGGTGGGCACGACCTTATGTG
42034 TA
1 TA
42036 GCACTACGGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (40 bp):
TAATACACTTCAATGTATATGGTGGGCACGACCTTATGTG
Found at i:42234 original size:47 final size:45
Alignment explanation
Indices: 42140--42312 Score: 249
Period size: 47 Copynumber: 3.8 Consensus size: 45
42130 GTAAGCATAC
* * * *
42140 AAATAAGCTTACGAGCTTTTGGAAT-AATGGCAAGTATATGGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATTTTGGTA
42184 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATTTTGGTA
*
42231 AAATAAGCTTACGAGCTTATGGAATTTAAATTGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATTTTGGTA
*
42278 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
42313 GGATTTTATA
Statistics
Matches: 119, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
44 23 0.19
45 10 0.08
46 1 0.01
47 85 0.71
ACGTcount: A:0.37, C:0.08, G:0.23, T:0.33
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATTTTGGTA
Found at i:43358 original size:2 final size:2
Alignment explanation
Indices: 43351--43380 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
43341 AACATTATTA
43351 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
43381 TCCTAATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44405 original size:13 final size:14
Alignment explanation
Indices: 44389--44421 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
44379 ATAAATATCG
*
44389 AATAAAAATTAA-A
1 AATAAAAATAAATA
44402 AATAAAAATAAATA
1 AATAAAAATAAATA
44416 AATAAA
1 AATAAA
44422 TCAAATGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
AATAAAAATAAATA
Found at i:46049 original size:18 final size:18
Alignment explanation
Indices: 46011--46050 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
46001 TGGAAATAAG
* *
46011 AAATAAAAATTAATAAAA
1 AAATAAAAAATAACAAAA
*
46029 AAATAAAAAATAACAATA
1 AAATAAAAAATAACAAAA
46047 AAAT
1 AAAT
46051 GAATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.20
Consensus pattern (18 bp):
AAATAAAAAATAACAAAA
Found at i:46472 original size:38 final size:36
Alignment explanation
Indices: 46100--46473 Score: 360
Period size: 38 Copynumber: 10.3 Consensus size: 36
46090 AATTATATAG
*
46100 TATATATATATATATATTCAAAAATATTTT-AAAAC
1 TATATATATATATATTTTCAAAAATATTTTCAAAAC
* * *
46135 TATACAT-TATATGTTTT-AAAAATATTTTTAAAAC
1 TATATATATATATATTTTCAAAAATATTTTCAAAAC
*
46169 TATATATTATATATATTTTTAAAAATATTTT-AAAAC
1 TATATA-TATATATATTTTCAAAAATATTTTCAAAAC
* * ** *
46205 TATATAT-TATATTTTTTTAAAAACGTTTTTAAAAC
1 TATATATATATATATTTTCAAAAATATTTTCAAAAC
** *
46240 TATATATTATATATATGTTTTTAAAAT-GTTTCAAAAAC
1 TATATA-TATATATAT-TTTCAAAAATATTTTC-AAAAC
*
46278 TATATATATTATATATATTTC-AAAATATTTTCAAGAAT
1 TATATATA-TATATAT-TTTCAAAAATATTTTCAA-AAC
*
46316 TATATATTATATATATGTTTTC-AAAATGTTTTCAAAAAC
1 TATATA-TATATATA--TTTTCAAAAATATTTTC-AAAAC
*
46355 TATATA-CTATATATTTTCAAAAATAATTTTCAAAAC
1 TATATATATATATATTTTCAAAAAT-ATTTTCAAAAC
46391 --TATA-ATATATATTTTCAAAAATCATTTTCAAAAC
1 TATATATATATATATTTTCAAAAAT-ATTTTCAAAAC
* *
46425 CATACAATATATATATTTTCAAAAATAATTTTCAAAAC
1 TATA-TATATATATATTTTCAAAAAT-ATTTTCAAAAC
46463 TATATA-ATATA
1 TATATATATATA
46474 CTTTCAAAAA
Statistics
Matches: 290, Mismatches: 27, Indels: 43
0.81 0.08 0.12
Matches are distributed among these distances:
33 11 0.04
34 69 0.24
35 24 0.08
36 38 0.13
37 42 0.14
38 79 0.27
39 24 0.08
40 3 0.01
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (36 bp):
TATATATATATATATTTTCAAAAATATTTTCAAAAC
Found at i:62633 original size:35 final size:34
Alignment explanation
Indices: 62557--62634 Score: 113
Period size: 35 Copynumber: 2.2 Consensus size: 34
62547 ATTTAGAAGT
62557 TGGTGATGATATAGGCGTGATATGGTGATAGATTA
1 TGGTGATGATATAGGCGTGATATGGTGATAGA-TA
*
62592 TGGTGATGATATAGGCGTGATAATGGTGATGGA-A
1 TGGTGATGATATAGGCGTGAT-ATGGTGATAGATA
62626 TGTGTGATG
1 TG-GTGATG
62635 GATAGATTGT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
34 3 0.08
35 27 0.68
36 10 0.25
ACGTcount: A:0.27, C:0.03, G:0.37, T:0.33
Consensus pattern (34 bp):
TGGTGATGATATAGGCGTGATATGGTGATAGATA
Done.