Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001054.1 Hibiscus syriacus cultivar Beakdansim tig00002086_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: 38471
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35
Found at i:2151 original size:2 final size:2
Alignment explanation
Indices: 2144--2173 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2134 GATTATGTCA
2144 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
2174 TATTTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2314 original size:31 final size:32
Alignment explanation
Indices: 2279--2363 Score: 111
Period size: 31 Copynumber: 2.7 Consensus size: 32
2269 CCTAACGTTT
2279 ACTTTTTGTTTCATTTTAGTACC-CACCATTA
1 ACTTTTTGTTTCATTTTAGTACCACACCATTA
* * **
2310 ACTTTTTGTTTCATTTTAATGCCACACTGTTA
1 ACTTTTTGTTTCATTTTAGTACCACACCATTA
*
2342 A-TTTTTATTTCATTTTAGTACC
1 ACTTTTTGTTTCATTTTAGTACC
2364 TTAATTTTTA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
31 39 0.85
32 7 0.15
ACGTcount: A:0.22, C:0.19, G:0.07, T:0.52
Consensus pattern (32 bp):
ACTTTTTGTTTCATTTTAGTACCACACCATTA
Found at i:3064 original size:16 final size:16
Alignment explanation
Indices: 3043--3073 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3033 ACGATTAAAC
3043 GCTGAATGATTCAAAT
1 GCTGAATGATTCAAAT
3059 GCTGAATGATTCAAA
1 GCTGAATGATTCAAA
3074 GGCTCTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (16 bp):
GCTGAATGATTCAAAT
Found at i:3176 original size:23 final size:23
Alignment explanation
Indices: 3148--3203 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
3138 TGTACTTTGA
**
3148 TGTTGAATCATTCAACACTGTTT
1 TGTTGAATCAACCAACACTGTTT
3171 TGTTGAATCAACCAACACTGTTT
1 TGTTGAATCAACCAACACTGTTT
3194 TGTTGAATCA
1 TGTTGAATCA
3204 GTCAGCGTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (23 bp):
TGTTGAATCAACCAACACTGTTT
Found at i:5720 original size:41 final size:42
Alignment explanation
Indices: 5675--5764 Score: 148
Period size: 41 Copynumber: 2.2 Consensus size: 42
5665 TCGAAATATC
5675 GTGTTTGTTTCACGTAATTCATTTT-CGGAAAATGTTTTC-A
1 GTGTTTGTTTCACGTAATTCATTTTACGGAAAATGTTTTCTA
*
5715 TGTGTTTGTTTCACGTAATTCGTTTTACGGAAAATGTTTTCTA
1 -GTGTTTGTTTCACGTAATTCATTTTACGGAAAATGTTTTCTA
5758 GTGTTTG
1 GTGTTTG
5765 GTTGGAGGAA
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
41 24 0.52
42 21 0.46
43 1 0.02
ACGTcount: A:0.20, C:0.11, G:0.20, T:0.49
Consensus pattern (42 bp):
GTGTTTGTTTCACGTAATTCATTTTACGGAAAATGTTTTCTA
Found at i:6023 original size:22 final size:23
Alignment explanation
Indices: 5993--6039 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
5983 AAAATATATT
5993 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* *
6016 TATT-ATATTTTTAATACTATAA
1 TATTAATATTTCTAATAATATAA
6038 TA
1 TA
6040 AAATAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:6077 original size:23 final size:23
Alignment explanation
Indices: 6033--6079 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
6023 TTTTTAATAC
* *
6033 TATAATAAAATAATAAATTATAT
1 TATAATAAAATAAGAAACTATAT
* *
6056 TATAATAATATAAGATACTATAT
1 TATAATAAAATAAGAAACTATAT
6079 T
1 T
6080 TTTATTTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
TATAATAAAATAAGAAACTATAT
Found at i:6245 original size:22 final size:23
Alignment explanation
Indices: 6206--6249 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
6196 AATAATATTT
6206 TAATAAATATATTTAAAATATAC
1 TAATAAATATATTTAAAATATAC
*
6229 TAATTAATAT-TTTAAAATATA
1 TAATAAATATATTTAAAATATA
6250 ATAACACTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
TAATAAATATATTTAAAATATAC
Found at i:6349 original size:13 final size:14
Alignment explanation
Indices: 6329--6371 Score: 52
Period size: 13 Copynumber: 2.9 Consensus size: 14
6319 TTATATTTTC
6329 ATAAATAAATTATA
1 ATAAATAAATTATA
6343 A-AAATAATATTTAATA
1 ATAAATAA-A-TT-ATA
6359 ATAAATAAATTAT
1 ATAAATAAATTAT
6372 TTTAATATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
13 6 0.24
14 4 0.16
15 4 0.16
16 5 0.20
17 6 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
ATAAATAAATTATA
Found at i:6598 original size:14 final size:14
Alignment explanation
Indices: 6579--6637 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
6569 TTCAGAAATT
*
6579 AATTCATTTTTCAG
1 AATTCAATTTTCAG
* *
6593 AATTCAAATTCCAG
1 AATTCAATTTTCAG
* *
6607 TAATTCATTTTTCAT
1 -AATTCAATTTTCAG
*
6622 AATTTAATTTTCAG
1 AATTCAATTTTCAG
6636 AA
1 AA
6638 AATCAATTAC
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
14 24 0.71
15 10 0.29
ACGTcount: A:0.36, C:0.14, G:0.05, T:0.46
Consensus pattern (14 bp):
AATTCAATTTTCAG
Found at i:8744 original size:57 final size:57
Alignment explanation
Indices: 8655--8779 Score: 214
Period size: 57 Copynumber: 2.2 Consensus size: 57
8645 GATGACTTCT
* *
8655 CAGAATGCATAAGCCATATAAGAAGCTCGATAGACAAGAAAAATAAGTGTAGAGATG
1 CAGAATGCATAAGCCATATAAAAAGCTCGATAGACAAGAAAAATAAGTGTAGAGATA
*
8712 CAGAATGCATAAGCCATATAAAAAGCTGGATAGACAAGAAAAATAAGTGTAGAGATA
1 CAGAATGCATAAGCCATATAAAAAGCTCGATAGACAAGAAAAATAAGTGTAGAGATA
*
8769 CATAATGCATA
1 CAGAATGCATA
8780 TATGTTCCCA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 64 1.00
ACGTcount: A:0.49, C:0.12, G:0.21, T:0.18
Consensus pattern (57 bp):
CAGAATGCATAAGCCATATAAAAAGCTCGATAGACAAGAAAAATAAGTGTAGAGATA
Found at i:9748 original size:25 final size:25
Alignment explanation
Indices: 9704--9768 Score: 94
Period size: 25 Copynumber: 2.6 Consensus size: 25
9694 TCAGTAACTA
* *
9704 TAACCCATTCTGTTTCTGTTTATGG
1 TAACCCCTTCTGTTTATGTTTATGG
* *
9729 TAATCCCTTCTGTTTATGTTTCTGG
1 TAACCCCTTCTGTTTATGTTTATGG
9754 TAACCCCTTCTGTTT
1 TAACCCCTTCTGTTT
9769 CTAGATTGCA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.14, C:0.23, G:0.14, T:0.49
Consensus pattern (25 bp):
TAACCCCTTCTGTTTATGTTTATGG
Found at i:11004 original size:15 final size:15
Alignment explanation
Indices: 10984--11014 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
10974 CAACAAATAG
10984 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
10999 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
11014 A
1 A
11015 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:11830 original size:45 final size:45
Alignment explanation
Indices: 11781--12007 Score: 355
Period size: 45 Copynumber: 5.0 Consensus size: 45
11771 TGGAGCTCTA
*
11781 CCTCCACTTCCTAGCATGCCAACATTGCCTACCCTGCCATCCATC
1 CCTCCACTTCCTAGCATGCCAACATTGCCTACCATGCCATCCATC
* * * *
11826 CCTCCACTTCCTAGCATGCCGACAATGCCAACCATGCCATCCACC
1 CCTCCACTTCCTAGCATGCCAACATTGCCTACCATGCCATCCATC
* *
11871 CCTCCACTTCCTAGCAGGCCAACATTGCCTACCCTGCCATCCATC
1 CCTCCACTTCCTAGCATGCCAACATTGCCTACCATGCCATCCATC
* * * *
11916 CCTCCACTTCCTAGCATGCCGACAATGCCAACCATGCCATCCACC
1 CCTCCACTTCCTAGCATGCCAACATTGCCTACCATGCCATCCATC
11961 CCTCCACTTCCTAGCATGCCAACATTGCCTACCATGCCATCCATC
1 CCTCCACTTCCTAGCATGCCAACATTGCCTACCATGCCATCCATC
12006 CC
1 CC
12008 CACAATACCA
Statistics
Matches: 161, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 161 1.00
ACGTcount: A:0.22, C:0.47, G:0.10, T:0.21
Consensus pattern (45 bp):
CCTCCACTTCCTAGCATGCCAACATTGCCTACCATGCCATCCATC
Found at i:11934 original size:90 final size:90
Alignment explanation
Indices: 11781--12007 Score: 436
Period size: 90 Copynumber: 2.5 Consensus size: 90
11771 TGGAGCTCTA
11781 CCTCCACTTCCTAGCATGCCAACATTGCCTACCCTGCCATCCATCCCTCCACTTCCTAGCATGCC
1 CCTCCACTTCCTAGCATGCCAACATTGCCTACCCTGCCATCCATCCCTCCACTTCCTAGCATGCC
11846 GACAATGCCAACCATGCCATCCACC
66 GACAATGCCAACCATGCCATCCACC
*
11871 CCTCCACTTCCTAGCAGGCCAACATTGCCTACCCTGCCATCCATCCCTCCACTTCCTAGCATGCC
1 CCTCCACTTCCTAGCATGCCAACATTGCCTACCCTGCCATCCATCCCTCCACTTCCTAGCATGCC
11936 GACAATGCCAACCATGCCATCCACC
66 GACAATGCCAACCATGCCATCCACC
*
11961 CCTCCACTTCCTAGCATGCCAACATTGCCTACCATGCCATCCATCCC
1 CCTCCACTTCCTAGCATGCCAACATTGCCTACCCTGCCATCCATCCC
12008 CACAATACCA
Statistics
Matches: 134, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
90 134 1.00
ACGTcount: A:0.22, C:0.47, G:0.10, T:0.21
Consensus pattern (90 bp):
CCTCCACTTCCTAGCATGCCAACATTGCCTACCCTGCCATCCATCCCTCCACTTCCTAGCATGCC
GACAATGCCAACCATGCCATCCACC
Found at i:16562 original size:15 final size:16
Alignment explanation
Indices: 16542--16583 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 16
16532 GATGTTGGTT
16542 TTCTTTTG-TGTTTTG
1 TTCTTTTGTTGTTTTG
16557 TTCTTTTGCGTTGTTTTG
1 TTCTTTT--GTTGTTTTG
16575 TTCCTTTTG
1 TT-CTTTTG
16584 CTGGATATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 7 0.30
17 2 0.09
18 9 0.39
19 5 0.22
ACGTcount: A:0.00, C:0.12, G:0.19, T:0.69
Consensus pattern (16 bp):
TTCTTTTGTTGTTTTG
Found at i:17373 original size:18 final size:21
Alignment explanation
Indices: 17350--17393 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
17340 ATTATGGATA
17350 AATTAAT-TG-AT-TAAGGTG
1 AATTAATATGTATATAAGGTG
*
17368 AATTAATATGTGTATAAGGTG
1 AATTAATATGTATATAAGGTG
17389 AATTA
1 AATTA
17394 GGCTTATGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 7 0.32
19 2 0.09
20 1 0.05
21 12 0.55
ACGTcount: A:0.41, C:0.00, G:0.20, T:0.39
Consensus pattern (21 bp):
AATTAATATGTATATAAGGTG
Found at i:20214 original size:74 final size:76
Alignment explanation
Indices: 20124--20265 Score: 198
Period size: 74 Copynumber: 1.9 Consensus size: 76
20114 TTTTTTCTTT
* ** * *
20124 ATCTTTGTGGTTCTACTGTGAGGATCGGTGGAGAATAAGATGACC-TTTT-GGATTCTTTGATCT
1 ATCTTTGTGATTCTACTCCGAGGATAGGTGGAGAATAAGAAGACCATTTTGGGATTCTTTGATCT
20187 TTCAATCGTTG
66 TTCAATCGTTG
* * *
20198 ATCTTTGTGATTCTACTCCGAGGATAGGTGGGGAATAAGAAGACCATTTTGGGGTTGTTTGATCT
1 ATCTTTGTGATTCTACTCCGAGGATAGGTGGAGAATAAGAAGACCATTTTGGGATTCTTTGATCT
20263 TTC
66 TTC
20266 GATGTGAGCA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
74 39 0.67
75 4 0.07
76 15 0.26
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.39
Consensus pattern (76 bp):
ATCTTTGTGATTCTACTCCGAGGATAGGTGGAGAATAAGAAGACCATTTTGGGATTCTTTGATCT
TTCAATCGTTG
Found at i:21904 original size:2 final size:2
Alignment explanation
Indices: 21897--21923 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
21887 TGTATCAACA
21897 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
21924 GTGGTTCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23646 original size:69 final size:69
Alignment explanation
Indices: 23535--23668 Score: 223
Period size: 69 Copynumber: 1.9 Consensus size: 69
23525 AAGAACCAAG
* * *
23535 TTACAAAAGCATCCCACGCATACATATCTGCATACAAATATATGCATACATGCATAAATGTAAGC
1 TTACAAAAGCATCACACACATACATATCTGCATACAAATATATGCATACATGCACAAATGTAAGC
23600 GTAC
66 GTAC
* *
23604 TTACAAAAGCATCACACACATACATGTCTGCATACAAATATATGCATACATGCACAAATTTAAGC
1 TTACAAAAGCATCACACACATACATATCTGCATACAAATATATGCATACATGCACAAATGTAAGC
23669 ATATATACAA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 60 1.00
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.25
Consensus pattern (69 bp):
TTACAAAAGCATCACACACATACATATCTGCATACAAATATATGCATACATGCACAAATGTAAGC
GTAC
Found at i:23692 original size:2 final size:2
Alignment explanation
Indices: 23682--23717 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
23672 TATACAACAT
*
23682 CA CA AA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
23718 TATATATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.47, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:23722 original size:2 final size:2
Alignment explanation
Indices: 23717--23745 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
23707 ACACACACAC
23717 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
23746 AATGACAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30828 original size:2 final size:2
Alignment explanation
Indices: 30821--30867 Score: 85
Period size: 2 Copynumber: 23.0 Consensus size: 2
30811 CTTGAGCTTA
30821 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
30863 CAT AT
1 -AT AT
30868 TGAATATTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 42 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:37775 original size:3 final size:3
Alignment explanation
Indices: 37767--37836 Score: 95
Period size: 3 Copynumber: 22.7 Consensus size: 3
37757 TCATTTAAAT
**
37767 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
*
37813 TTA ATA TTA TATA TTA TTA TTA TT
1 TTA TTA TTA T-TA TTA TTA TTA TT
37837 TAATAAATAA
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
3 53 0.90
4 6 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Done.