Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009142.1 Hibiscus syriacus cultivar Beakdansim tig00112653_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: 49462
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:3554 original size:19 final size:19
Alignment explanation
Indices: 3530--3579 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
3520 CGGCCAAGAG
*
3530 CATGTATCTTCAT-TAAAAT
1 CATGTAT-TTCATCAAAAAT
3549 CATGTATTTTCATCAAAAAT
1 CATGTA-TTTCATCAAAAAT
3569 CATGTATTTCA
1 CATGTATTTCA
3580 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.36, C:0.16, G:0.06, T:0.42
Consensus pattern (19 bp):
CATGTATTTCATCAAAAAT
Found at i:3569 original size:20 final size:19
Alignment explanation
Indices: 3530--3577 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
3520 CGGCCAAGAG
* *
3530 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATAAAAAT
3549 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCAT-AAAAAT
3569 CATGTATTT
1 CATGTATTT
3578 CAAAGGGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (19 bp):
CATGTATTTTCATAAAAAT
Found at i:9913 original size:19 final size:20
Alignment explanation
Indices: 9889--9939 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
9879 CGGCCAAGAG
* *
9889 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
9908 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
9928 CATGTATTTTCA
1 CATGTATTTTCA
9940 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:10868 original size:13 final size:13
Alignment explanation
Indices: 10850--10918 Score: 54
Period size: 13 Copynumber: 5.5 Consensus size: 13
10840 TTTAAGTGAA
**
10850 GGTGATGGACTAT
1 GGTGATGGAAGAT
10863 GGTGATGGAAGAT
1 GGTGATGGAAGAT
** *
10876 GGTGATGTTATA-
1 GGTGATGGAAGAT
* *
10888 GGCG-T-GAAAAT
1 GGTGATGGAAGAT
10899 GGTGATGGAAGAT
1 GGTGATGGAAGAT
10912 GGTGATG
1 GGTGATG
10919 TTTAGGTAGT
Statistics
Matches: 42, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
10 2 0.05
11 4 0.10
12 4 0.10
13 32 0.76
ACGTcount: A:0.28, C:0.03, G:0.42, T:0.28
Consensus pattern (13 bp):
GGTGATGGAAGAT
Found at i:11297 original size:19 final size:20
Alignment explanation
Indices: 11259--11309 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
11249 GAAACCCCTT
11259 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTTAA
11279 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
11298 TGAAGATACATG
1 TGAAAATACATG
11310 CACTCCAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:20045 original size:15 final size:16
Alignment explanation
Indices: 20022--20053 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
20012 CTTGATGAAC
20022 TCAAGCTAGTTAGCTT
1 TCAAGCTAGTTAGCTT
20038 TCAA-CTAGTTAGCTT
1 TCAAGCTAGTTAGCTT
20053 T
1 T
20054 GGTCTTCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.41
Consensus pattern (16 bp):
TCAAGCTAGTTAGCTT
Found at i:20910 original size:13 final size:12
Alignment explanation
Indices: 20886--20919 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
20876 TTTCTTTGAA
*
20886 TTTTTGTTTTTC
1 TTTTTCTTTTTC
20898 TTTATTCTTTTTC
1 TTT-TTCTTTTTC
20911 TTTTTCTTT
1 TTTTTCTTT
20920 CTTTTGCACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.03, C:0.12, G:0.03, T:0.82
Consensus pattern (12 bp):
TTTTTCTTTTTC
Found at i:20911 original size:6 final size:6
Alignment explanation
Indices: 20886--20919 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
20876 TTTCTTTGAA
*
20886 TTTTTG TTTTTC TTTATTC TTTTTC TTTTTC TTT
1 TTTTTC TTTTTC TTT-TTC TTTTTC TTTTTC TTT
20920 CTTTTGCACT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.03, C:0.12, G:0.03, T:0.82
Consensus pattern (6 bp):
TTTTTC
Found at i:20994 original size:19 final size:18
Alignment explanation
Indices: 20955--20998 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
20945 GAGTCTTTTC
*
20955 TTTCTGTTTTTTTTATTT
1 TTTCTGTTTTTTTTATCT
*
20973 TTTCTTGTTTTTTTTCTCT
1 TTTC-TGTTTTTTTTATCT
20992 TTT-TGTT
1 TTTCTGTT
20999 ACTTTTGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 4 0.17
18 4 0.17
19 15 0.65
ACGTcount: A:0.02, C:0.09, G:0.07, T:0.82
Consensus pattern (18 bp):
TTTCTGTTTTTTTTATCT
Found at i:24928 original size:16 final size:17
Alignment explanation
Indices: 24907--24947 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
24897 AAGATATGGT
*
24907 AATGAAATAATTAAA-A
1 AATGAAATAACTAAAGA
*
24923 AATGAAA-GACTAAAGA
1 AATGAAATAACTAAAGA
24939 AATGAAATA
1 AATGAAATA
24948 GTAAGAAAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.66, C:0.02, G:0.12, T:0.20
Consensus pattern (17 bp):
AATGAAATAACTAAAGA
Found at i:25188 original size:21 final size:22
Alignment explanation
Indices: 25164--25209 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
25154 TGTAGGAGTC
25164 TTTTCTT-TCTATTTTTT-TATT
1 TTTTCTTGT-TATTTTTTCTATT
*
25185 TTTTCTTGTTTTTTTTTCTATT
1 TTTTCTTGTTATTTTTTCTATT
25207 TTT
1 TTT
25210 GTTACTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.07, C:0.09, G:0.02, T:0.83
Consensus pattern (22 bp):
TTTTCTTGTTATTTTTTCTATT
Found at i:28294 original size:14 final size:14
Alignment explanation
Indices: 28253--28295 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
28243 GTTGTAGAAG
* *
28253 TCTTTTTTTTTGTT
1 TCTTTTTTTCTCTT
28267 T-TTTTTTTCTTCTT
1 TCTTTTTTTC-TCTT
28281 TCTTTTTTTCTCTT
1 TCTTTTTTTCTCTT
28295 T
1 T
28296 TTGTTACTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 7 0.28
14 10 0.40
15 8 0.32
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (14 bp):
TCTTTTTTTCTCTT
Found at i:28734 original size:13 final size:13
Alignment explanation
Indices: 28716--28784 Score: 54
Period size: 13 Copynumber: 5.5 Consensus size: 13
28706 CTGGCGTGAA
**
28716 GGTGATGGACTAT
1 GGTGATGGAAGAT
28729 GGTGATGGAAGAT
1 GGTGATGGAAGAT
** *
28742 GGTGATGTTATA-
1 GGTGATGGAAGAT
* *
28754 GG-CAT-GAAAAT
1 GGTGATGGAAGAT
28765 GGTGATGGAAGAT
1 GGTGATGGAAGAT
28778 GGTGATG
1 GGTGATG
28785 TTTAGTATCT
Statistics
Matches: 42, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
10 2 0.05
11 4 0.10
12 4 0.10
13 32 0.76
ACGTcount: A:0.29, C:0.03, G:0.41, T:0.28
Consensus pattern (13 bp):
GGTGATGGAAGAT
Found at i:33813 original size:11 final size:11
Alignment explanation
Indices: 33799--33843 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
33789 TTGCAATTCA
33799 TTTATCTT-TT
1 TTTATCTTATT
*
33809 CTTTATCTTGTT
1 -TTTATCTTATT
*
33821 TTAATCTTATT
1 TTTATCTTATT
33832 TTTATCTTATT
1 TTTATCTTATT
33843 T
1 T
33844 CCAGCACCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
11 28 0.93
12 2 0.07
ACGTcount: A:0.16, C:0.11, G:0.02, T:0.71
Consensus pattern (11 bp):
TTTATCTTATT
Found at i:34234 original size:20 final size:20
Alignment explanation
Indices: 34159--34226 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 20
34149 ATTTTTTTCA
*
34159 AAAAAAAACAAAAAAAGGAA-
1 AAAAAAAACAAAAAAA-AAAC
**
34179 AAAAAAGGCAAAAAAGGTAAAAC
1 AAAAAAAACAAAAAA---AAAAC
34202 AAAAAAAACAAAAAAAAAAC
1 AAAAAAAACAAAAAAAAAAC
34222 AAAAA
1 AAAAA
34227 TACCAAAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
20 23 0.59
22 2 0.05
23 14 0.36
ACGTcount: A:0.82, C:0.07, G:0.09, T:0.01
Consensus pattern (20 bp):
AAAAAAAACAAAAAAAAAAC
Found at i:37960 original size:40 final size:41
Alignment explanation
Indices: 37888--37987 Score: 107
Period size: 45 Copynumber: 2.4 Consensus size: 41
37878 TAGAATCAGA
* *
37888 TTTATTATTTTATTAGGAATTAAGGTGGGTTAAAACAATATTTTAG
1 TTTATTATTTTATTAGGAATT-A--TGAGTTAAAAC-AT-GTTTAG
37934 -TTATTATTTTATTAGGAA-T-TGAGTTAAAACATGTTTAG
1 TTTATTATTTTATTAGGAATTATGAGTTAAAACATGTTTAG
37972 TTTATTATATTTATTA
1 TTTATTAT-TTTATTA
37988 TTTAGTTATT
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
38 5 0.10
39 9 0.18
40 17 0.34
44 1 0.02
45 18 0.36
ACGTcount: A:0.34, C:0.02, G:0.14, T:0.50
Consensus pattern (41 bp):
TTTATTATTTTATTAGGAATTATGAGTTAAAACATGTTTAG
Found at i:38400 original size:21 final size:21
Alignment explanation
Indices: 38379--38419 Score: 73
Period size: 21 Copynumber: 1.9 Consensus size: 21
38369 CAATTCATTT
38379 ATCTTTTCTTTATCTTGTTTTA
1 ATCTTTT-TTTATCTTGTTTTA
38401 ATCTTTTTTTATCTTGTTT
1 ATCTTTTTTTATCTTGTTT
38420 CAGCACCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.12, C:0.12, G:0.05, T:0.71
Consensus pattern (21 bp):
ATCTTTTTTTATCTTGTTTTA
Found at i:38409 original size:10 final size:10
Alignment explanation
Indices: 38376--38415 Score: 53
Period size: 11 Copynumber: 3.8 Consensus size: 10
38366 TTGCAATTCA
38376 TTTATCTTTT
1 TTTATCTTTT
38386 CTTTATCTTGTT
1 -TTTATCTT-TT
*
38398 TTAATCTTTT
1 TTTATCTTTT
38408 TTTATCTT
1 TTTATCTT
38416 GTTTCAGCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
10 9 0.35
11 15 0.58
12 2 0.08
ACGTcount: A:0.12, C:0.12, G:0.03, T:0.72
Consensus pattern (10 bp):
TTTATCTTTT
Found at i:41224 original size:36 final size:35
Alignment explanation
Indices: 41172--41255 Score: 114
Period size: 36 Copynumber: 2.3 Consensus size: 35
41162 GATACTATTT
* *
41172 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATAACCATAATCCATCACCATTATCA-GCCTATA
*
41208 TCATAACCATAGTCCATCACCATTATCAGCCTATA
1 TCATAACCATAATCCATCACCATTATCAGCCTATA
41243 TCATCACACCATA
1 TCAT-A-ACCATA
41256 TCACGCCAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
35 11 0.26
36 26 0.60
37 6 0.14
ACGTcount: A:0.33, C:0.35, G:0.04, T:0.29
Consensus pattern (35 bp):
TCATAACCATAATCCATCACCATTATCAGCCTATA
Found at i:41254 original size:24 final size:24
Alignment explanation
Indices: 41225--41272 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
41215 CATAGTCCAT
* *
41225 CACCATTATCA-GCCTATATCATCA
1 CACCA-TATCACGCCAATAACATCA
41249 CACCATATCACGCCAATAACATCA
1 CACCATATCACGCCAATAACATCA
41273 TCCTTCCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.38, C:0.35, G:0.04, T:0.23
Consensus pattern (24 bp):
CACCATATCACGCCAATAACATCA
Found at i:45662 original size:35 final size:36
Alignment explanation
Indices: 45598--45708 Score: 156
Period size: 35 Copynumber: 3.2 Consensus size: 36
45588 GATACTATTT
*
45598 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
45634 TCATCACCATAGT-CATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
45669 TC-TCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
45703 ACATCA
1 TCATCA
45709 TCCTCCATTA
Statistics
Matches: 68, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
34 22 0.32
35 34 0.50
36 12 0.18
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:49414 original size:13 final size:12
Alignment explanation
Indices: 49389--49433 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
49379 CTATTTTTTC
49389 AAAAAAAACAAA
1 AAAAAAAACAAA
**
49401 AAAAAAGGCAAA
1 AAAAAAAACAAA
49413 AAAAAAAACAAA
1 AAAAAAAACAAA
49425 AACAAAAAA
1 AA-AAAAAA
49434 GCCAAAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 22 0.79
13 6 0.21
ACGTcount: A:0.87, C:0.09, G:0.04, T:0.00
Consensus pattern (12 bp):
AAAAAAAACAAA
Found at i:49415 original size:14 final size:13
Alignment explanation
Indices: 49389--49440 Score: 56
Period size: 13 Copynumber: 4.1 Consensus size: 13
49379 CTATTTTTTC
49389 AAAAAAAA-C-AA
1 AAAAAAAAGCAAA
*
49400 AAAAAAAGGCAAA
1 AAAAAAAAGCAAA
49413 AAAAAAAA-CAAA
1 AAAAAAAAGCAAA
49425 AACAAAAAAGCCAAA
1 AA-AAAAAAG-CAAA
49440 A
1 A
49441 TTTCAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
11 7 0.21
12 7 0.21
13 15 0.44
15 5 0.15
ACGTcount: A:0.83, C:0.12, G:0.06, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGCAAA
Found at i:49440 original size:24 final size:23
Alignment explanation
Indices: 49388--49440 Score: 54
Period size: 24 Copynumber: 2.2 Consensus size: 23
49378 GCTATTTTTT
*
49388 CAAAAAAAACAAAAAAAAAGGCAA
1 CAAAAAAAACAAAAAAAAAAGC-A
*
49412 AAAAAAAAACAAAAACAAAAAAGC-
1 CAAAAAAAAC-AAAA-AAAAAAGCA
49436 CAAAA
1 CAAAA
49441 TTTCAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
24 13 0.54
25 4 0.17
26 7 0.29
ACGTcount: A:0.81, C:0.13, G:0.06, T:0.00
Consensus pattern (23 bp):
CAAAAAAAACAAAAAAAAAAGCA
Done.