Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004148.1 Hibiscus syriacus cultivar Beakdansim tig00009071_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: 69717
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Found at i:9009 original size:35 final size:35
Alignment explanation
Indices: 8970--9082 Score: 145
Period size: 35 Copynumber: 3.2 Consensus size: 35
8960 ATTGGTGGTT
* * *
8970 ATATAAGCGTGAAATGGTGATAGAAGTTGGAGATG
1 ATATAGGCGTGAAATGGTGATAGAAGATGGTGATG
* *
9005 ATATAGGCGTGCAATGGTGATGGAAGATGGTGATG
1 ATATAGGCGTGAAATGGTGATAGAAGATGGTGATG
* *
9040 TTATAGGCGTAAAAATGGTGATAGAAGATGGTGATG
1 ATATAGGCGT-GAAATGGTGATAGAAGATGGTGATG
*
9076 TTATAGG
1 ATATAGG
9083 TAGTATCTTA
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
35 39 0.57
36 29 0.43
ACGTcount: A:0.34, C:0.04, G:0.35, T:0.27
Consensus pattern (35 bp):
ATATAGGCGTGAAATGGTGATAGAAGATGGTGATG
Found at i:14788 original size:20 final size:21
Alignment explanation
Indices: 14763--14804 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
14753 AGCATTTATC
*
14763 TTCATT-AAAATTATGTATTT
1 TTCATTCAAAATCATGTATTT
*
14783 TTCATTCAAAATCATGTGTTT
1 TTCATTCAAAATCATGTATTT
14804 T
1 T
14805 CAAAGGGGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.52
Consensus pattern (21 bp):
TTCATTCAAAATCATGTATTT
Found at i:14805 original size:20 final size:20
Alignment explanation
Indices: 14763--14806 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
14753 AGCATTTATC
* *
14763 TTCATTAAAATTATGTATTT
1 TTCATTAAAATCATGTAGTT
14783 TTCATTCAAAATCATGT-GTT
1 TTCATT-AAAATCATGTAGTT
14803 TTCA
1 TTCA
14807 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.32, C:0.11, G:0.07, T:0.50
Consensus pattern (20 bp):
TTCATTAAAATCATGTAGTT
Found at i:15591 original size:6 final size:6
Alignment explanation
Indices: 15580--15628 Score: 68
Period size: 6 Copynumber: 8.5 Consensus size: 6
15570 CAAAAGCAAC
15580 AAAAAG AAAAAG AAAGAAG AAAAA- AAAAA- AAAAA- AAAAAG AAAAAG
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
15626 AAA
1 AAA
15629 TACTCCTACA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
5 15 0.37
6 20 0.49
7 6 0.15
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:15601 original size:13 final size:11
Alignment explanation
Indices: 15580--15624 Score: 65
Period size: 10 Copynumber: 4.0 Consensus size: 11
15570 CAAAAGCAAC
15580 AAAAAGAAAAA
1 AAAAAGAAAAA
15591 GAAAGAAGAAAAA
1 -AAA-AAGAAAAA
15604 AAAAA-AAAAA
1 AAAAAGAAAAA
15614 AAAAAGAAAAA
1 AAAAAGAAAAA
15625 GAAATACTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
10 10 0.32
11 7 0.23
12 6 0.19
13 8 0.26
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:15886 original size:24 final size:23
Alignment explanation
Indices: 15854--15898 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
15844 TTTCATTTCC
15854 TTATTCTTTCAT-CTTTTCTTATT
1 TTATTCTTT-ATCCTTTTCTTATT
15877 TTATTACTTTATCCTTTTCTTA
1 TTATT-CTTTATCCTTTTCTTA
15899 ACCTTTTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.16, C:0.18, G:0.00, T:0.67
Consensus pattern (23 bp):
TTATTCTTTATCCTTTTCTTATT
Found at i:20227 original size:19 final size:18
Alignment explanation
Indices: 20205--20251 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
20195 AGTGAATAAT
20205 AATATAAGTAATGAAAAGA
1 AATATAAG-AATGAAAAGA
*
20224 AATAATAAGAATGAAATGA
1 AAT-ATAAGAATGAAAAGA
20243 AATA-AAGAA
1 AATATAAGAA
20252 AGGATAGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 5 0.19
18 1 0.04
19 15 0.58
20 5 0.19
ACGTcount: A:0.66, C:0.00, G:0.15, T:0.19
Consensus pattern (18 bp):
AATATAAGAATGAAAAGA
Found at i:27706 original size:19 final size:20
Alignment explanation
Indices: 27684--27747 Score: 73
Period size: 19 Copynumber: 3.4 Consensus size: 20
27674 TTTGAACTTC
27684 TCTTTTTCTT-TTCTTT-TCT
1 TCTTTTTCTTATT-TTTCTCT
27703 TC-TTTTCTTATTTTTCTCT
1 TCTTTTTCTTATTTTTCTCT
* *
27722 TC-TTTTCTGATTTTTGTCT
1 TCTTTTTCTTATTTTTCTCT
27741 TCTTTTT
1 TCTTTTT
27748 GCACTCCAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
18 10 0.25
19 26 0.65
20 4 0.10
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.75
Consensus pattern (20 bp):
TCTTTTTCTTATTTTTCTCT
Found at i:31740 original size:9 final size:9
Alignment explanation
Indices: 31728--31788 Score: 52
Period size: 11 Copynumber: 6.2 Consensus size: 9
31718 TCTTTTTGAA
31728 TTTTTC-TT
1 TTTTTCTTT
31736 TTTTTCTTT
1 TTTTTCTTT
31745 TCTTTTCTTCTT
1 T-TTTTC-T-TT
31757 TTTCTTCTTCT
1 TTT-TTCTT-T
31768 TTTTGTCTTT
1 TTTT-TCTTT
*
31778 TCTTTCTTT
1 TTTTTCTTT
31787 TT
1 TT
31789 GTACTCCAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
8 6 0.14
9 9 0.20
10 11 0.25
11 12 0.27
12 6 0.14
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:31764 original size:12 final size:11
Alignment explanation
Indices: 31731--31776 Score: 58
Period size: 12 Copynumber: 4.2 Consensus size: 11
31721 TTTTGAATTT
31731 TTCTTTTTTTC
1 TTCTTTTTTTC
*
31742 TT-TTCTTTTC
1 TTCTTTTTTTC
31752 TTCTTTTTCTTC
1 TTCTTTTT-TTC
*
31764 TTCTTTTTGTC
1 TTCTTTTTTTC
31775 TT
1 TT
31777 TTCTTTCTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 9 0.30
11 10 0.33
12 11 0.37
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (11 bp):
TTCTTTTTTTC
Found at i:31776 original size:20 final size:19
Alignment explanation
Indices: 31736--31790 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
31726 AATTTTTCTT
31736 TTTTTCTTTTCTTTTCT-TC
1 TTTTTCTTTTCTTTT-TGTC
31755 TTTTTCTTCTTCTTTTTGTC
1 TTTTTCTT-TTCTTTTTGTC
31775 -TTTTC-TTTCTTTTTGT
1 TTTTTCTTTTCTTTTTGT
31791 ACTCCAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
17 10 0.29
18 1 0.03
19 14 0.41
20 9 0.26
ACGTcount: A:0.00, C:0.18, G:0.04, T:0.78
Consensus pattern (19 bp):
TTTTTCTTTTCTTTTTGTC
Found at i:32061 original size:19 final size:18
Alignment explanation
Indices: 32039--32085 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
32029 AGTGAATAAT
32039 AATATAAGTAATGAAAAGA
1 AATATAAG-AATGAAAAGA
*
32058 AATAATAAGAATGAAATGA
1 AAT-ATAAGAATGAAAAGA
32077 AATA-AAGAA
1 AATATAAGAA
32086 ATGATAGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 5 0.19
18 1 0.04
19 15 0.58
20 5 0.19
ACGTcount: A:0.66, C:0.00, G:0.15, T:0.19
Consensus pattern (18 bp):
AATATAAGAATGAAAAGA
Found at i:39612 original size:14 final size:15
Alignment explanation
Indices: 39574--39615 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
39564 TCCAAATTCA
39574 TCATTTTCAACTCTC
1 TCATTTTCAACTCTC
39589 TCATTTTCAACTCTC
1 TCATTTTCAACTCTC
39604 TCA-TTTCAACTC
1 TCATTTTCAACTC
39616 CAACGTCTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 9 0.33
15 18 0.67
ACGTcount: A:0.21, C:0.33, G:0.00, T:0.45
Consensus pattern (15 bp):
TCATTTTCAACTCTC
Found at i:58656 original size:91 final size:91
Alignment explanation
Indices: 58500--58765 Score: 406
Period size: 91 Copynumber: 2.9 Consensus size: 91
58490 TGGTAGTTGA
* * *
58500 TGCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGAACCACATGCAAGGAACAT
1 TGCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGATCCACATGTAAGGCACAT
* *
58565 GGGGGTTGATCACATGCAAAACACAT
66 GGGGGCTGATCATATGCAAAACACAT
** *
58591 TGCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGTGCCTAAATGATCCATATGTAAGGCACAT
1 TGCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGATCCACATGTAAGGCACAT
58656 GGGGGCTGATCATATGCAAAACACAT
66 GGGGGCTGATCATATGCAAAACACAT
* * * * *
58682 GGCTTTGCCGAATAAGGAGAGAACTCTTCATCTTGGCACCTAAATGATCCACATATAAGGCACAG
1 TGCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGATCCACATGTAAGGCACAT
*
58747 GGGGGCTGGTCATATGCAA
66 GGGGGCTGATCATATGCAA
58766 GGCACATGGG
Statistics
Matches: 158, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
91 158 1.00
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (91 bp):
TGCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGATCCACATGTAAGGCACAT
GGGGGCTGATCATATGCAAAACACAT
Found at i:58886 original size:18 final size:18
Alignment explanation
Indices: 58863--58906 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
58853 GTCTCCTTCA
*
58863 AGCTAGCTTGAGTTGTTG
1 AGCTAGCTTGAGTTGTGG
58881 AGCTAGCTTGAGTTGTGG
1 AGCTAGCTTGAGTTGTGG
58899 AGCTAGCT
1 AGCTAGCT
58907 AGCAAACATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.18, C:0.14, G:0.34, T:0.34
Consensus pattern (18 bp):
AGCTAGCTTGAGTTGTGG
Found at i:63782 original size:24 final size:24
Alignment explanation
Indices: 63728--63782 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
63718 GAAAAATCAT
*
63728 AAAAG-AAGCACTCAAAATGAAGA
1 AAAAGAAAACACTCAAAATGAAGA
**
63751 AATTGAAAACACTCAAAA-GAAGAA
1 AAAAGAAAACACTCAAAATGAAG-A
63775 AAAAGAAA
1 AAAAGAAA
63783 GAAAAGTTGG
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.65, C:0.11, G:0.15, T:0.09
Consensus pattern (24 bp):
AAAAGAAAACACTCAAAATGAAGA
Found at i:68101 original size:15 final size:17
Alignment explanation
Indices: 68081--68114 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
68071 GTGCTTCAAA
68081 TTCTTT-CTTTT-TTTT
1 TTCTTTGCTTTTCTTTT
68096 TTCTTTGCTTTTCTTTT
1 TTCTTTGCTTTTCTTTT
68113 TT
1 TT
68115 TAGTGATGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 5 0.29
17 6 0.35
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (17 bp):
TTCTTTGCTTTTCTTTT
Found at i:68961 original size:91 final size:91
Alignment explanation
Indices: 68747--69019 Score: 422
Period size: 91 Copynumber: 3.0 Consensus size: 91
68737 GGTAGTTGAT
* * *
68747 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATGAACCACATGCAAGGAACAT-
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGATCCACATGCAAGGCACATG
68811 GGGGCTGATCACATGCAAAACACATG
66 GGGGCTGATCACATGCAAAACACATG
* *
68837 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGTGCCTAAATGATCCACATGTAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGATCCACATGCAAGGCACATG
*
68902 GGGGCTGATCTCATGCAAAACACATG
66 GGGGCTGATCACATGCAAAACACATG
* * *
68928 GCTTGACCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGATCCACATACAAGGCACAGG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGATCCACATGCAAGGCACATG
* * **
68993 GGGGCTGGTCATATGCAAGGCACATG
66 GGGGCTGATCACATGCAAAACACATG
69019 G
1 G
69020 GTGTTCTAGG
Statistics
Matches: 166, Mismatches: 16, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
90 59 0.36
91 107 0.64
ACGTcount: A:0.30, C:0.23, G:0.27, T:0.21
Consensus pattern (91 bp):
GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGATCCACATGCAAGGCACATG
GGGGCTGATCACATGCAAAACACATG
Done.