Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004111.1 Hibiscus syriacus cultivar Beakdansim tig00008997_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: 55070
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Found at i:9014 original size:11 final size:11
Alignment explanation
Indices: 9000--9037 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
8990 TGAAGCTTGA
9000 GATTTGAGCTC
1 GATTTGAGCTC
9011 GA-TTGAAGCTC
1 GATTTG-AGCTC
9022 GATTTTGAGCTC
1 GA-TTTGAGCTC
9034 GATT
1 GATT
9038 CAATCTCGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
10 3 0.12
11 11 0.46
12 7 0.29
13 3 0.12
ACGTcount: A:0.21, C:0.16, G:0.26, T:0.37
Consensus pattern (11 bp):
GATTTGAGCTC
Found at i:9032 original size:23 final size:23
Alignment explanation
Indices: 8981--9048 Score: 91
Period size: 23 Copynumber: 2.9 Consensus size: 23
8971 AAAAAATCAA
* *
8981 GAGCTCGATTGAAGCTTGAGATTT
1 GAGCTCGATTGAAGCTCGA-TTTT
9005 GAGCTCGATTGAAGCTCGATTTT
1 GAGCTCGATTGAAGCTCGATTTT
* *
9028 GAGCTCGATTCAATCTCGATT
1 GAGCTCGATTGAAGCTCGATT
9049 CAATCTCAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
23 22 0.55
24 18 0.45
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.34
Consensus pattern (23 bp):
GAGCTCGATTGAAGCTCGATTTT
Found at i:9047 original size:11 final size:11
Alignment explanation
Indices: 9031--9055 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
9021 CGATTTTGAG
9031 CTCGATTCAAT
1 CTCGATTCAAT
9042 CTCGATTCAAT
1 CTCGATTCAAT
9053 CTC
1 CTC
9056 AATGGGTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.32, G:0.08, T:0.36
Consensus pattern (11 bp):
CTCGATTCAAT
Found at i:10495 original size:29 final size:29
Alignment explanation
Indices: 10463--10538 Score: 134
Period size: 29 Copynumber: 2.6 Consensus size: 29
10453 TAAAGTACAT
10463 AAATAGTCTCATGGCTATTAAAAGTTATA
1 AAATAGTCTCATGGCTATTAAAAGTTATA
10492 AAATAGTCTCATGGCTATTAAAAGTTATA
1 AAATAGTCTCATGGCTATTAAAAGTTATA
* *
10521 AAATAGTCCCATGACTAT
1 AAATAGTCTCATGGCTAT
10539 AGGATGTTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (29 bp):
AAATAGTCTCATGGCTATTAAAAGTTATA
Found at i:11350 original size:14 final size:14
Alignment explanation
Indices: 11316--11365 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 14
11306 CACATAATTG
*
11316 GGTTTAGGGTTTAA
1 GGTTTAGGGATTAA
**
11330 GACTTAGGGATTAA
1 GGTTTAGGGATTAA
*
11344 GGTTTAGGGATTAG
1 GGTTTAGGGATTAA
11358 GGTTTAGG
1 GGTTTAGG
11366 TTTCATTACA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.24, C:0.02, G:0.38, T:0.36
Consensus pattern (14 bp):
GGTTTAGGGATTAA
Found at i:12637 original size:26 final size:26
Alignment explanation
Indices: 12614--12666 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
12604 AATTAAACAG
12614 TTTTTTCCTAAATTAAACAAAAACGT
1 TTTTTTCCTAAATTAAACAAAAACGT
* *
12640 TTTTTTCCTAATTTAAATAAAAACGT
1 TTTTTTCCTAAATTAAACAAAAACGT
12666 T
1 T
12667 AAGATATATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.43
Consensus pattern (26 bp):
TTTTTTCCTAAATTAAACAAAAACGT
Found at i:12643 original size:25 final size:25
Alignment explanation
Indices: 12608--12666 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 25
12598 ACCAAAAATT
12608 AAACAGTTTTTTCCTAAATTAAACAA
1 AAAC-GTTTTTTCCTAAATTAAACAA
* *
12634 AAACGTTTTTTTCCTAATTTAAATAA
1 AAACG-TTTTTTCCTAAATTAAACAA
12660 AAACGTT
1 AAACGTT
12667 AAGATATATC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 3 0.10
26 27 0.90
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.39
Consensus pattern (25 bp):
AAACGTTTTTTCCTAAATTAAACAA
Found at i:20146 original size:34 final size:33
Alignment explanation
Indices: 20095--20193 Score: 135
Period size: 33 Copynumber: 3.0 Consensus size: 33
20085 CTCATATGCA
* * *
20095 AAGTTGGTCACCTACCAAAGATGATTTTTTCAAT
1 AAGTTGGCCACCAACC-AAGATGAATTTTTCAAT
*
20129 AAGTTGGCCACCAACCAAGATGAATTTTCCAAT
1 AAGTTGGCCACCAACCAAGATGAATTTTTCAAT
* *
20162 AAGTTAGCTACCAACCAAGATGAATTTTTCAA
1 AAGTTGGCCACCAACCAAGATGAATTTTTCAA
20194 CTTACCAAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 44 0.76
34 14 0.24
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.29
Consensus pattern (33 bp):
AAGTTGGCCACCAACCAAGATGAATTTTTCAAT
Found at i:23584 original size:90 final size:89
Alignment explanation
Indices: 23463--23637 Score: 305
Period size: 90 Copynumber: 2.0 Consensus size: 89
23453 TAATCCCGAA
* *
23463 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-CCCTAATATGAT
*
23528 TAGGGTAACTTGGATATAAAATGAT
65 TAGGGTAACTTAGATATAAAATGAT
23553 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
*
23618 AGGGTAACTTAGCTATAAAA
66 AGGGTAACTTAGATATAAAA
23638 GGGTGTGTTA
Statistics
Matches: 81, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 31 0.38
90 50 0.62
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.38
Consensus pattern (89 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
AGGGTAACTTAGATATAAAATGAT
Found at i:30206 original size:90 final size:87
Alignment explanation
Indices: 30092--30263 Score: 299
Period size: 90 Copynumber: 1.9 Consensus size: 87
30082 TCTCGAATAT
*
30092 TTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGATTAG
1 TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA--CCTAATATGATTAG
30157 GGTAACTTGGATATAAAAGTATTA
64 GGTAACTTGGATATAAAAGTATTA
30181 TTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCTAATATGATTAGG
1 TTAAATTC-AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCTAATATGATTAGG
*
30246 GTAACTTGGCTATAAAAG
65 GTAACTTGGATATAAAAG
30264 GGTATGTTAG
Statistics
Matches: 80, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
88 32 0.40
89 7 0.09
90 41 0.51
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.38
Consensus pattern (87 bp):
TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCTAATATGATTAGGG
TAACTTGGATATAAAAGTATTA
Found at i:32202 original size:90 final size:88
Alignment explanation
Indices: 32088--32260 Score: 310
Period size: 90 Copynumber: 1.9 Consensus size: 88
32078 TCCCGAATAT
*
32088 TTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGATTAG
1 TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-CCCTAATATGATTAG
32153 GGTAACTTGGATATAAAAGTATTA
65 GGTAACTTGGATATAAAAGTATTA
32177 TTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAG
1 TTAAATTC-AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAG
*
32242 GGTAACTTGGCTATAAAAG
65 GGTAACTTGGATATAAAAG
32261 GGTATGTTAG
Statistics
Matches: 81, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
89 40 0.49
90 41 0.51
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.38
Consensus pattern (88 bp):
TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAGG
GTAACTTGGATATAAAAGTATTA
Found at i:34199 original size:90 final size:88
Alignment explanation
Indices: 34085--34257 Score: 310
Period size: 90 Copynumber: 1.9 Consensus size: 88
34075 TCCCGAATAT
*
34085 TTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGATTAG
1 TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-CCCTAATATGATTAG
34150 GGTAACTTGGATATAAAAGTATTA
65 GGTAACTTGGATATAAAAGTATTA
34174 TTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAG
1 TTAAATTC-AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAG
*
34239 GGTAACTTGGCTATAAAAG
65 GGTAACTTGGATATAAAAG
34258 GGTATGTTAG
Statistics
Matches: 81, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
89 40 0.49
90 41 0.51
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.38
Consensus pattern (88 bp):
TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAGG
GTAACTTGGATATAAAAGTATTA
Found at i:36198 original size:90 final size:88
Alignment explanation
Indices: 36084--36256 Score: 310
Period size: 90 Copynumber: 1.9 Consensus size: 88
36074 TCCCGAATAT
*
36084 TTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGATTAG
1 TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-CCCTAATATGATTAG
36149 GGTAACTTGGATATAAAAGTATTA
65 GGTAACTTGGATATAAAAGTATTA
36173 TTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAG
1 TTAAATTC-AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAG
*
36238 GGTAACTTGGCTATAAAAG
65 GGTAACTTGGATATAAAAG
36257 GGTATGTTAG
Statistics
Matches: 81, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
89 40 0.49
90 41 0.51
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.38
Consensus pattern (88 bp):
TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAGG
GTAACTTGGATATAAAAGTATTA
Found at i:39037 original size:33 final size:33
Alignment explanation
Indices: 38973--39071 Score: 146
Period size: 33 Copynumber: 3.0 Consensus size: 33
38963 CCCATATGCA
*
38973 AAGTTGGCCACCTACCAA-ATATGAATTTTCCAAT
1 AAGTTGGCCACCAACCAAGA-A-GAATTTTCCAAT
*
39007 AAGTTGGCCACCAACTAAGAAGAATTTTCCAAT
1 AAGTTGGCCACCAACCAAGAAGAATTTTCCAAT
*
39040 AAGTTGGCCACCAACCAAGATGAATTTTCCAA
1 AAGTTGGCCACCAACCAAGAAGAATTTTCCAA
39072 CTTGCCAAAT
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
33 42 0.70
34 17 0.28
35 1 0.02
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.25
Consensus pattern (33 bp):
AAGTTGGCCACCAACCAAGAAGAATTTTCCAAT
Found at i:53787 original size:22 final size:22
Alignment explanation
Indices: 53743--53787 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
53733 AATTAGTTTC
* *
53743 AAAATTTTAAGACATCCTAATT
1 AAAATTTTAAAACATCATAATT
*
53765 AAAATTTTAAAACATCATTATT
1 AAAATTTTAAAACATCATAATT
53787 A
1 A
53788 TATCGATCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (22 bp):
AAAATTTTAAAACATCATAATT
Done.