Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005113.1 Hibiscus syriacus cultivar Beakdansim tig00011494_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: 75393
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:1111 original size:15 final size:15
Alignment explanation
Indices: 1082--1121 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
1072 AATCCCACAA
*
1082 TATATTAA-AATTAT
1 TATATTAATTATTAT
1096 TATATTAATTATTAT
1 TATATTAATTATTAT
1111 TATATT-ATTAT
1 TATATTAATTAT
1122 ATTCACAGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TATATTAATTATTAT
Found at i:1116 original size:8 final size:8
Alignment explanation
Indices: 1091--1124 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
1081 ATATATTAAA
1091 ATTATTAT
1 ATTATTAT
*
1099 ATTAAT-T
1 ATTATTAT
1106 ATTATTAT
1 ATTATTAT
1114 ATTATTAT
1 ATTATTAT
1122 ATT
1 ATT
1125 CACAGATGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
7 6 0.26
8 17 0.74
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
ATTATTAT
Found at i:33650 original size:17 final size:17
Alignment explanation
Indices: 33628--33663 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
33618 TTTCGTTCAA
33628 ATGTTACAAATTTTTAT
1 ATGTTACAAATTTTTAT
33645 ATGTTACAAATTTTTAT
1 ATGTTACAAATTTTTAT
33662 AT
1 AT
33664 ATCAAGATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.53
Consensus pattern (17 bp):
ATGTTACAAATTTTTAT
Found at i:41074 original size:31 final size:31
Alignment explanation
Indices: 41038--41096 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
41028 AACTTAAAAA
* *
41038 AGTTTTGCAATACTTAAATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
41069 AGTTTTATAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
41097 CCATACAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.46
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:41142 original size:22 final size:22
Alignment explanation
Indices: 41114--41166 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
41104 ATAATAATTT
41114 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
41136 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
41158 TTTTAAAAT
1 TTTTAAAAT
41167 GCTCAAACTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:41212 original size:11 final size:11
Alignment explanation
Indices: 41188--41222 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
41178 AGGTTTGATG
41188 TTTTCTCTTTGA
1 TTTTCTC-TTGA
41200 TTTTCTCTTGA
1 TTTTCTCTTGA
41211 TTTTCT-TTGA
1 TTTTCTCTTGA
41221 TT
1 TT
41223 GTTATTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 6 0.26
11 10 0.43
12 7 0.30
ACGTcount: A:0.09, C:0.14, G:0.09, T:0.69
Consensus pattern (11 bp):
TTTTCTCTTGA
Found at i:42999 original size:22 final size:21
Alignment explanation
Indices: 42973--43044 Score: 56
Period size: 22 Copynumber: 3.3 Consensus size: 21
42963 CGAAAAATAG
42973 TACAATATGATTAACATTTAAA
1 TACAATATGATT-ACATTTAAA
* * * *
42995 TACAATTTAGGGTTTCA-TTAAG
1 TACAA--TATGATTACATTTAAA
*
43017 TACAATATGATTTGCATTTAAA
1 TACAATATGA-TTACATTTAAA
43039 TACAAT
1 TACAAT
43045 TTAGGGTTTA
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
20 3 0.08
21 4 0.11
22 24 0.63
23 2 0.05
24 5 0.13
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.39
Consensus pattern (21 bp):
TACAATATGATTACATTTAAA
Found at i:43020 original size:44 final size:44
Alignment explanation
Indices: 42971--43059 Score: 151
Period size: 44 Copynumber: 2.0 Consensus size: 44
42961 GTCGAAAAAT
*
42971 AGTACAATATGATTAACATTTAAATACAATTTAGGGTTTCATTA
1 AGTACAATATGATTAACATTTAAATACAATTTAGGGTTTAATTA
**
43015 AGTACAATATGATTTGCATTTAAATACAATTTAGGGTTTAATTA
1 AGTACAATATGATTAACATTTAAATACAATTTAGGGTTTAATTA
43059 A
1 A
43060 TTTACATATA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.39
Consensus pattern (44 bp):
AGTACAATATGATTAACATTTAAATACAATTTAGGGTTTAATTA
Found at i:43059 original size:22 final size:22
Alignment explanation
Indices: 42990--43059 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
42980 TGATTAACAT
*
42990 TTAAATACAATTTAGGGTTTCA
1 TTAAATACAATTTAGGGTTTAA
* * * *
43012 TTAAGTACAA--TATGATTTGCAT
1 TTAAATACAATTTAGGGTTT--AA
43034 TTAAATACAATTTAGGGTTTAA
1 TTAAATACAATTTAGGGTTTAA
43056 TTAA
1 TTAA
43060 TTTACATATA
Statistics
Matches: 35, Mismatches: 9, Indels: 8
0.67 0.17 0.15
Matches are distributed among these distances:
20 6 0.17
22 23 0.66
24 6 0.17
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.41
Consensus pattern (22 bp):
TTAAATACAATTTAGGGTTTAA
Found at i:45851 original size:2 final size:2
Alignment explanation
Indices: 45844--45901 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
45834 CATGATCTGA
45844 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
45886 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
45902 GAAATGCCAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58225 original size:54 final size:54
Alignment explanation
Indices: 58137--58239 Score: 156
Period size: 54 Copynumber: 1.9 Consensus size: 54
58127 TGTAAGTACG
*
58137 ATTTGTAAAGTTATTTACTAAATTAAATACCATCTAAAATTATAAAATAATAAA
1 ATTTGTAAAGTTATTTAATAAATTAAATACCATCTAAAATTATAAAATAATAAA
*
58191 ATTTGTACAA-TTATTTAATAAATTATATGA-CATCTAAAATTATAAAATA
1 ATTTGTA-AAGTTATTTAATAAATTAAAT-ACCATCTAAAATTATAAAATA
58240 TATTTATAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
54 42 0.93
55 3 0.07
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (54 bp):
ATTTGTAAAGTTATTTAATAAATTAAATACCATCTAAAATTATAAAATAATAAA
Found at i:61116 original size:25 final size:25
Alignment explanation
Indices: 61077--61133 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
61067 TTTAATGTTT
* * *
61077 TTTTTTATGTTAAAGTGATTTAGGA
1 TTTTTTAAGTGAAAGCGATTTAGGA
*
61102 TTTTTTAAGTGAAAGCGATTTAGGG
1 TTTTTTAAGTGAAAGCGATTTAGGA
61127 TTTTTTA
1 TTTTTTA
61134 GGTTAATGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.26, C:0.02, G:0.21, T:0.51
Consensus pattern (25 bp):
TTTTTTAAGTGAAAGCGATTTAGGA
Found at i:61178 original size:24 final size:24
Alignment explanation
Indices: 61120--61178 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
61110 GTGAAAGCGA
*
61120 TTTAGGGTTTTTTAGGTTAATGTGG
1 TTTAGGG-TTTTTAGGTTAATGTAG
* *
61145 TTTTGAGTTTTTAGGTTAA-GTTAG
1 TTTAGGGTTTTTAGGTTAATG-TAG
61169 TTTAGGGTTT
1 TTTAGGGTTT
61179 AAAGTAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 1 0.04
24 22 0.79
25 5 0.18
ACGTcount: A:0.17, C:0.00, G:0.29, T:0.54
Consensus pattern (24 bp):
TTTAGGGTTTTTAGGTTAATGTAG
Found at i:61340 original size:27 final size:26
Alignment explanation
Indices: 61263--61376 Score: 124
Period size: 26 Copynumber: 4.3 Consensus size: 26
61253 ATTTTTTTTA
*
61263 TAGAAAATACACA-TACATTGAAAAATAT
1 TAGAAAATA-AAATTACATTG--AAATAT
* *
61291 TACAAAATATAATTACATTGAAATAT
1 TAGAAAATAAAATTACATTGAAATAT
* *
61317 TAGAAACATGAACA-TACATTGAAAAAT
1 TAGAAA-AT-AAAATTACATTGAAATAT
61344 TAGAAAATAAAATTACATTGAAATAT
1 TAGAAAATAAAATTACATTGAAATAT
61370 TAGAAAA
1 TAGAAAA
61377 CACACACATT
Statistics
Matches: 73, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
25 3 0.04
26 32 0.44
27 21 0.29
28 17 0.23
ACGTcount: A:0.57, C:0.08, G:0.08, T:0.27
Consensus pattern (26 bp):
TAGAAAATAAAATTACATTGAAATAT
Found at i:61363 original size:53 final size:55
Alignment explanation
Indices: 61273--61375 Score: 174
Period size: 53 Copynumber: 1.9 Consensus size: 55
61263 TAGAAAATAC
*
61273 ACATACATTGAAAAATATTACAAAATATAATTACATTGAAATATTAGAAACATGA
1 ACATACATTGAAAAATATTACAAAATAAAATTACATTGAAATATTAGAAACATGA
*
61328 ACATACATTG-AAAA-ATTAGAAAATAAAATTACATTGAAATATTAGAAA
1 ACATACATTGAAAAATATTACAAAATAAAATTACATTGAAATATTAGAAA
61376 ACACACACAT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
53 32 0.70
54 4 0.09
55 10 0.22
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.28
Consensus pattern (55 bp):
ACATACATTGAAAAATATTACAAAATAAAATTACATTGAAATATTAGAAACATGA
Found at i:62187 original size:6 final size:6
Alignment explanation
Indices: 62178--62230 Score: 54
Period size: 6 Copynumber: 8.8 Consensus size: 6
62168 TTTCAATGTA
* * * *
62178 AATTTG AATTTG AATTTG TATTTG TATTTC AATTTGG AA-TTG AATTTT
1 AATTTG AATTTG AATTTG AATTTG AATTTG AATTT-G AATTTG AATTTG
62226 AATTT
1 AATTT
62231 ATATTTCAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
5 3 0.08
6 35 0.88
7 2 0.05
ACGTcount: A:0.30, C:0.02, G:0.13, T:0.55
Consensus pattern (6 bp):
AATTTG
Found at i:62187 original size:18 final size:16
Alignment explanation
Indices: 62137--62188 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 16
62127 GATTAGAAGA
62137 AATGTAATTTAAGTTTC
1 AATGTAATTTAA-TTTC
62154 AATTGTAATGTTAATTTC
1 AA-TGTAAT-TTAATTTC
62172 AATGTAAATTTGAATTT
1 AATGT-AATTT-AATTT
62189 GAATTTGTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
17 7 0.23
18 20 0.65
19 4 0.13
ACGTcount: A:0.37, C:0.04, G:0.12, T:0.48
Consensus pattern (16 bp):
AATGTAATTTAATTTC
Found at i:62200 original size:18 final size:18
Alignment explanation
Indices: 62179--62242 Score: 65
Period size: 18 Copynumber: 3.6 Consensus size: 18
62169 TTCAATGTAA
*
62179 ATTTGAATTTGAATTTGT
1 ATTTGAATTTCAATTTGT
* *
62197 ATTTGTATTTCAATTTGG
1 ATTTGAATTTCAATTTGT
* * *
62215 AATTGAATTTTAATTTAT
1 ATTTGAATTTCAATTTGT
*
62233 ATTTCAATTT
1 ATTTGAATTT
62243 TATTTTTAGC
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.30, C:0.03, G:0.11, T:0.56
Consensus pattern (18 bp):
ATTTGAATTTCAATTTGT
Found at i:62221 original size:30 final size:30
Alignment explanation
Indices: 62178--62242 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
62168 TTTCAATGTA
*
62178 AATTTGAATTTGAATTTGT-ATTTGTATTTC
1 AATTTGAATTTGAATTT-TAATTTATATTTC
62208 AATTTGGAA-TTGAATTTTAATTTATATTTC
1 AATTT-GAATTTGAATTTTAATTTATATTTC
62238 AATTT
1 AATTT
62243 TATTTTTAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 1 0.03
30 28 0.88
31 3 0.09
ACGTcount: A:0.31, C:0.03, G:0.11, T:0.55
Consensus pattern (30 bp):
AATTTGAATTTGAATTTTAATTTATATTTC
Found at i:62864 original size:20 final size:20
Alignment explanation
Indices: 62839--62922 Score: 71
Period size: 20 Copynumber: 4.2 Consensus size: 20
62829 AGTAATGTTG
62839 TGTAAGGTAATGTACTCTAA
1 TGTAAGGTAATGTACTCTAA
* *
62859 TGTAAGATAATGTATTCTAA
1 TGTAAGGTAATGTACTCTAA
*** * *
62879 TGT-TTCTAATAATGCTTCTAA
1 TGTAAGGTAAT-GTAC-TCTAA
*
62900 TGTAAGGTAATGTACTGTAA
1 TGTAAGGTAATGTACTCTAA
62920 TGT
1 TGT
62923 CATGTAATTA
Statistics
Matches: 47, Mismatches: 14, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
19 4 0.09
20 29 0.62
21 10 0.21
22 4 0.09
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.40
Consensus pattern (20 bp):
TGTAAGGTAATGTACTCTAA
Found at i:66656 original size:21 final size:20
Alignment explanation
Indices: 66632--66671 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
66622 ATATAAAAAA
66632 TATTTTTATTAAATATTTTTG
1 TATTTTTATTAAAT-TTTTTG
*
66653 TATTTTTATTTAATTTTTT
1 TATTTTTATTAAATTTTTT
66672 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (20 bp):
TATTTTTATTAAATTTTTTG
Found at i:67016 original size:21 final size:21
Alignment explanation
Indices: 66992--67042 Score: 84
Period size: 22 Copynumber: 2.4 Consensus size: 21
66982 ACGGATCCAG
66992 AAATTTAAGAATAGAGATACA
1 AAATTTAAGAATAGAGATACA
*
67013 AAATTTTAAGAATAGAGATCCA
1 AAA-TTTAAGAATAGAGATACA
67035 AAATTTAA
1 AAATTTAA
67043 TTTTTTTTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 8 0.29
22 20 0.71
ACGTcount: A:0.55, C:0.06, G:0.12, T:0.27
Consensus pattern (21 bp):
AAATTTAAGAATAGAGATACA
Done.