Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002419.1 Hibiscus syriacus cultivar Beakdansim tig00004946_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: 87779
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:5216 original size:57 final size:58
Alignment explanation
Indices: 5155--5271 Score: 182
Period size: 57 Copynumber: 2.0 Consensus size: 58
5145 AATATGTGTC
* *
5155 AAAACTATACGTCTTATTTGTTTAAAGTGTCTAAAG-TTTTTTTGTCAAATTAAATGT
1 AAAACCATACGTCTTATTTGTTTAAAGTGTCTAAAGTTTTTTTTGTCAAAGTAAATGT
* * *
5212 AAAACCATGCGTCTTATTTTTTTGAAGTGTCTAAAGTTTTTTTTGTCAAAGTAAATGT
1 AAAACCATACGTCTTATTTGTTTAAAGTGTCTAAAGTTTTTTTTGTCAAAGTAAATGT
5270 AA
1 AA
5272 TGTTTTTAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
57 32 0.59
58 22 0.41
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.44
Consensus pattern (58 bp):
AAAACCATACGTCTTATTTGTTTAAAGTGTCTAAAGTTTTTTTTGTCAAAGTAAATGT
Found at i:6061 original size:16 final size:16
Alignment explanation
Indices: 6037--6068 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
6027 GAATTAAGTC
6037 TTATACTAAATTTAAA
1 TTATACTAAATTTAAA
*
6053 TTATCCTAAATTTAAA
1 TTATACTAAATTTAAA
6069 CTATTTCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (16 bp):
TTATACTAAATTTAAA
Found at i:17196 original size:41 final size:41
Alignment explanation
Indices: 17144--17226 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
17134 TTAAATATTT
* *
17144 ATTTACAATCAATTGTCTTTGTACCATCGGGTAACAAAATA
1 ATTTACAATCAATTATCTTTGTACCATCAGGTAACAAAATA
*
17185 ATTTACAATCAATTATCTTTGTACCATCAGGTAATAAAATA
1 ATTTACAATCAATTATCTTTGTACCATCAGGTAACAAAATA
17226 A
1 A
17227 ATTATAAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.35
Consensus pattern (41 bp):
ATTTACAATCAATTATCTTTGTACCATCAGGTAACAAAATA
Found at i:20401 original size:36 final size:36
Alignment explanation
Indices: 20315--20401 Score: 129
Period size: 36 Copynumber: 2.4 Consensus size: 36
20305 AAGTTTGCAT
*
20315 CGATTAAAGTCGAAAGGAGGAAAGCATCAACACTTC
1 CGATTAAAGTCGAACGGAGGAAAGCATCAACACTTC
* **
20351 CGATTTAAGTCGAACGGAGGAAAGCATCGGCACTTC
1 CGATTAAAGTCGAACGGAGGAAAGCATCAACACTTC
*
20387 CGATTCAAGTCGAAC
1 CGATTAAAGTCGAAC
20402 TGAAGGATAT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (36 bp):
CGATTAAAGTCGAACGGAGGAAAGCATCAACACTTC
Found at i:20522 original size:36 final size:36
Alignment explanation
Indices: 20464--20603 Score: 176
Period size: 36 Copynumber: 3.9 Consensus size: 36
20454 TGAATAAGAA
* **
20464 GAACGAAAGGAAGCGTTAGCACTTTCGATTCAAAAT
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAAAT
* * *
20500 GAACGGAAGTAAGTATCGGCACTTTCGATTCAAGAA-
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAA-AAT
* *
20536 GAACGAAAGGAAGCATCGACACTTTCGATTC-AAGT
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAAAT
*
20571 GAACGAAAGGAAGCATCCGCACTTTCGATTCAA
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAA
20604 TTGTTCATCT
Statistics
Matches: 88, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
34 1 0.01
35 30 0.34
36 55 0.62
37 2 0.02
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.21
Consensus pattern (36 bp):
GAACGAAAGGAAGCATCGGCACTTTCGATTCAAAAT
Found at i:36203 original size:25 final size:25
Alignment explanation
Indices: 36175--36223 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
36165 AATAAAATCT
36175 AAAAATATAATTCAAATATAACATA
1 AAAAATATAATTCAAATATAACATA
* *
36200 AAAAGTTTAATTCAAATATAACAT
1 AAAAATATAATTCAAATATAACAT
36224 TAAAGATAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.59, C:0.08, G:0.02, T:0.31
Consensus pattern (25 bp):
AAAAATATAATTCAAATATAACATA
Found at i:41071 original size:30 final size:30
Alignment explanation
Indices: 41037--41099 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
41027 TGAAACATTG
41037 ATGAAATTGAGGTTATGCTACATTATTGGT
1 ATGAAATTGAGGTTATGCTACATTATTGGT
* *
41067 ATGAAATTGAGGTTATGTTGCATTATTGGT
1 ATGAAATTGAGGTTATGCTACATTATTGGT
41097 ATG
1 ATG
41100 TCATTACATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.29, C:0.05, G:0.25, T:0.41
Consensus pattern (30 bp):
ATGAAATTGAGGTTATGCTACATTATTGGT
Found at i:54091 original size:23 final size:23
Alignment explanation
Indices: 54065--54117 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
54055 TTAATTAATT
54065 TTAAAAATG-TTTTTAAGCACACA
1 TTAAAAATGCTTTTTAAGCA-ACA
* * * *
54088 TTAACAGTGCTTTTTAATCATCA
1 TTAAAAATGCTTTTTAAGCAACA
54111 TTAAAAA
1 TTAAAAA
54118 AAAGGCCTAA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.38
Consensus pattern (23 bp):
TTAAAAATGCTTTTTAAGCAACA
Found at i:54149 original size:4 final size:4
Alignment explanation
Indices: 54140--54164 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
54130 TTAGAAGATT
54140 GAAA GAAA GAAA GAAA GAAA GAAA G
1 GAAA GAAA GAAA GAAA GAAA GAAA G
54165 TAGCCTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:56098 original size:159 final size:159
Alignment explanation
Indices: 55802--56098 Score: 434
Period size: 159 Copynumber: 1.9 Consensus size: 159
55792 AGACAAACGC
* *
55802 TGAACAGGTAAGTTTTTCTAGTTCAAAACTATCTTTTAATTGAGACTTTCTTCTTGGGGAAAAAT
1 TGAACAGGTAAGTTTCTCCAGTTCAAAACTATCTTTTAATTGAGACTTTCTTCTTGGGGAAAAAT
* *
55867 GTGAAGCTGATGTCAAACAGATATTAGCAAATACATTTTTATCTTTGGCTTATAAAAATTTGAGT
66 GTGAAGCAGATGTCAAACAGATATTAGCAAATACATTTTTATCTTTGGCTTATAAAAAATTGAGT
**
55932 TGGGAAAAGAGATGAAACATACATTGAAT
131 TAAGAAAAGAGATGAAACATACATTGAAT
* * * * *
55961 TGAATAGGTAGGTTTCTCCAGTTCAAAGCTATCTTTTAGTTGAGCCTTTCTTCTTGGGGAAAAAA
1 TGAACAGGTAAGTTTCTCCAGTTCAAAACTATCTTTTAATTGAGACTTTCTTCTTGGGG-AAAAA
* * * * *
56026 TGTGAATCAGATGTCAAATAGATATTAGCAAATATA-TTTTATCTTTTGCTTATAAAAAATTGTG
65 TGTGAAGCAGATGTCAAACAGATATTAGCAAATACATTTTTATCTTTGGCTTATAAAAAATTGAG
56090 TTAAGAAAA
130 TTAAGAAAA
56099 CCTTCTTGAT
Statistics
Matches: 121, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
159 84 0.69
160 37 0.31
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (159 bp):
TGAACAGGTAAGTTTCTCCAGTTCAAAACTATCTTTTAATTGAGACTTTCTTCTTGGGGAAAAAT
GTGAAGCAGATGTCAAACAGATATTAGCAAATACATTTTTATCTTTGGCTTATAAAAAATTGAGT
TAAGAAAAGAGATGAAACATACATTGAAT
Found at i:59781 original size:17 final size:17
Alignment explanation
Indices: 59749--59786 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
59739 TGAAAACCAC
*
59749 AAAAATGAGAATGAAGAG
1 AAAAATGAGAAAGAAG-G
59767 AAAAATG-GAAAGAAGG
1 AAAAATGAGAAAGAAGG
59783 AAAA
1 AAAA
59787 GATTTCAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 7 0.37
18 7 0.37
ACGTcount: A:0.66, C:0.00, G:0.26, T:0.08
Consensus pattern (17 bp):
AAAAATGAGAAAGAAGG
Found at i:64017 original size:8 final size:8
Alignment explanation
Indices: 64006--64030 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
63996 TGTTCAATTG
64006 TGTATTTA
1 TGTATTTA
64014 TGTATTTA
1 TGTATTTA
64022 TGTATTTA
1 TGTATTTA
64030 T
1 T
64031 TTATACATGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (8 bp):
TGTATTTA
Found at i:80343 original size:26 final size:26
Alignment explanation
Indices: 80309--80361 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
80299 TTAAATTAGA
80309 TTTTTTACTTTCTCAAATTTATATAT
1 TTTTTTACTTTCTCAAATTTATATAT
80335 TTTTTTACTTTCTCAAATTTATATAT
1 TTTTTTACTTTCTCAAATTTATATAT
80361 T
1 T
80362 AATCAATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.62
Consensus pattern (26 bp):
TTTTTTACTTTCTCAAATTTATATAT
Found at i:85005 original size:4 final size:4
Alignment explanation
Indices: 84984--85019 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
84974 GAAAAAGATA
*
84984 AAAG AAAAG AAGG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG -AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
85020 AAGAAGCATA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
4 25 0.86
5 4 0.14
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AAAG
Done.