Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009025.1 Hibiscus syriacus cultivar Beakdansim tig00112422_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: 95271
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Found at i:22251 original size:16 final size:17
Alignment explanation
Indices: 22230--22264 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
22220 TTACTATTCA
22230 CGTGAATAGTG-AATTT
1 CGTGAATAGTGAAATTT
22246 CGTGAATAGTGAAATTT
1 CGTGAATAGTGAAATTT
22263 CG
1 CG
22265 GTCGGCGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (17 bp):
CGTGAATAGTGAAATTT
Found at i:23032 original size:15 final size:16
Alignment explanation
Indices: 23014--23046 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
23004 GTGGCAGATC
23014 AAAATCCAG-ACGGGA
1 AAAATCCAGAACGGGA
*
23029 AAAATCTAGAACGGGA
1 AAAATCCAGAACGGGA
23045 AA
1 AA
23047 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.52, C:0.15, G:0.24, T:0.09
Consensus pattern (16 bp):
AAAATCCAGAACGGGA
Found at i:34844 original size:22 final size:23
Alignment explanation
Indices: 34813--34857 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
34803 CAATATATTC
*
34813 TTTTATTG-AATTTGATTTAATTT
1 TTTTATTGAAATTT-AATTAATTT
34836 TTTTA-TGAAATTTAATTAATTT
1 TTTTATTGAAATTTAATTAATTT
34858 AGATATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (23 bp):
TTTTATTGAAATTTAATTAATTT
Found at i:37916 original size:2 final size:2
Alignment explanation
Indices: 37882--37906 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
37872 TTAAATTGCT
37882 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
37907 GAGAATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:49429 original size:12 final size:12
Alignment explanation
Indices: 49412--49451 Score: 71
Period size: 12 Copynumber: 3.2 Consensus size: 12
49402 GCAGCCCCCC
49412 CCCCCTTAGCAG
1 CCCCCTTAGCAG
49424 CCCCCTTAGCAG
1 CCCCCTTAGCAG
49436 CCCCCCTTAGCAG
1 -CCCCCTTAGCAG
49449 CCC
1 CCC
49452 ATGTGTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 15 0.56
13 12 0.44
ACGTcount: A:0.15, C:0.55, G:0.15, T:0.15
Consensus pattern (12 bp):
CCCCCTTAGCAG
Found at i:49440 original size:13 final size:13
Alignment explanation
Indices: 49411--49451 Score: 75
Period size: 13 Copynumber: 3.2 Consensus size: 13
49401 AGCAGCCCCC
49411 CCCCCCTTAGCAG
1 CCCCCCTTAGCAG
49424 -CCCCCTTAGCAG
1 CCCCCCTTAGCAG
49436 CCCCCCTTAGCAG
1 CCCCCCTTAGCAG
49449 CCC
1 CCC
49452 ATGTGTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 12 0.44
13 15 0.56
ACGTcount: A:0.15, C:0.56, G:0.15, T:0.15
Consensus pattern (13 bp):
CCCCCCTTAGCAG
Found at i:52741 original size:15 final size:16
Alignment explanation
Indices: 52713--52744 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
52703 AAAATCTTTC
52713 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
52729 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
52744 T
1 T
52745 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.25, G:0.19, T:0.50
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:53519 original size:16 final size:16
Alignment explanation
Indices: 53495--53526 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
53485 TATCGCCGAC
*
53495 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
53511 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
53527 TGTGAATAGT
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:0.34, C:0.25, G:0.06, T:0.34
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:53948 original size:13 final size:13
Alignment explanation
Indices: 53924--53969 Score: 83
Period size: 13 Copynumber: 3.5 Consensus size: 13
53914 AAAAAATTAC
53924 AGCAGCCCCCCCTT
1 AGCAG-CCCCCCTT
53938 AGCAGCCCCCCTT
1 AGCAGCCCCCCTT
53951 AGCAGCCCCCCTT
1 AGCAGCCCCCCTT
53964 AGCAGC
1 AGCAGC
53970 ACAGTGACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 27 0.84
14 5 0.16
ACGTcount: A:0.17, C:0.52, G:0.17, T:0.13
Consensus pattern (13 bp):
AGCAGCCCCCCTT
Found at i:55540 original size:2 final size:2
Alignment explanation
Indices: 55533--55567 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
55523 TCTTAGATTG
55533 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
55568 CACCATTGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:72764 original size:33 final size:33
Alignment explanation
Indices: 72727--72792 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
72717 CATCTTAATA
*
72727 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
72760 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
72793 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:72856 original size:21 final size:22
Alignment explanation
Indices: 72830--72870 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
72820 ATGCCTCTCG
72830 AGTTTCTCTACGACT-TGATCA
1 AGTTTCTCTACGACTCTGATCA
*
72851 AGTTTCTCTTCGACTCTGAT
1 AGTTTCTCTACGACTCTGAT
72871 TGTCTTGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.41
Consensus pattern (22 bp):
AGTTTCTCTACGACTCTGATCA
Found at i:74909 original size:24 final size:24
Alignment explanation
Indices: 74872--74924 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
74862 CCGTTCTATC
74872 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
74896 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
74920 TATTT
1 TATTT
74925 AATCGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:75096 original size:20 final size:20
Alignment explanation
Indices: 75067--75104 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
75057 GGTATCATTT
*
75067 TACCGTTTTTATCATTTTGA
1 TACCGGTTTTATCATTTTGA
75087 TACCGGTTTTATCATTTT
1 TACCGGTTTTATCATTTT
75105 TACCTGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.11, T:0.55
Consensus pattern (20 bp):
TACCGGTTTTATCATTTTGA
Found at i:76341 original size:21 final size:22
Alignment explanation
Indices: 76311--76354 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
76301 CAATATATTC
*
76311 TTTTATTG-AATTTGATTTAATT
1 TTTTATTGAAATTT-AATTAATT
76333 TTTTA-TGAAATTTAATTAATT
1 TTTTATTGAAATTTAATTAATT
76354 T
1 T
76355 AGATATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
TTTTATTGAAATTTAATTAATT
Found at i:79389 original size:2 final size:2
Alignment explanation
Indices: 79382--79420 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
79372 TTAAATTGCT
79382 TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA -A TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
79421 GTAACACCCC
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:79406 original size:11 final size:10
Alignment explanation
Indices: 79382--79420 Score: 64
Period size: 9 Copynumber: 4.1 Consensus size: 10
79372 TTAAATTGCT
79382 TATATATATA
1 TATATATATA
79392 TATATATAT-
1 TATATATATA
79401 TATATATATA
1 TATATATATA
79411 -ATATATATA
1 TATATATATA
79420 T
1 T
79421 GTAACACCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 18 0.67
10 9 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (10 bp):
TATATATATA
Found at i:80092 original size:30 final size:31
Alignment explanation
Indices: 80056--80238 Score: 268
Period size: 30 Copynumber: 6.0 Consensus size: 31
80046 CCGAAGGACC
* *
80056 CAGTCCATA-GATT-CGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* * *
80086 CAGTCCATATATCCCGAAGGACATAGGT-AA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
80116 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
80147 CAGTCCATATGTCCCGAA-AACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
80177 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
80208 CAGTCCATAT-TTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
80238 C
1 C
80239 CCTCGACCCT
Statistics
Matches: 139, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
30 86 0.62
31 53 0.38
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:80222 original size:91 final size:92
Alignment explanation
Indices: 80069--80238 Score: 272
Period size: 91 Copynumber: 1.9 Consensus size: 92
80059 TCCATAGATT
* * *
80069 CGAAGAACCTAGGTAATCAGTCCATATATCCCGAAGGACATAGGTAACAGTCCATATGTTCCGAA
1 CGAAGAACATAGGTAAACAGTCCATATATCCCGAAGAACATAGGTAACAGTCCATATGTTCCGAA
80134 GAACATAGGTAAACAGTCCATATGTCC
66 GAACATAGGTAAACAGTCCATATGTCC
* *
80161 CGAA-AACATAGGTAAACAGTCCATATGTTCCGAAGAACATAGGTAAACAGTCCATAT-TTCCGA
1 CGAAGAACATAGGTAAACAGTCCATATATCCCGAAGAACATAGGT-AACAGTCCATATGTTCCGA
80224 AGAACATAGGTAAAC
65 AGAACATAGGTAAAC
80239 CCTCGACCCT
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
91 56 0.78
92 16 0.22
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (92 bp):
CGAAGAACATAGGTAAACAGTCCATATATCCCGAAGAACATAGGTAACAGTCCATATGTTCCGAA
GAACATAGGTAAACAGTCCATATGTCC
Found at i:80237 original size:61 final size:62
Alignment explanation
Indices: 80056--80238 Score: 277
Period size: 61 Copynumber: 3.0 Consensus size: 62
80046 CCGAAGGACC
* * *
80056 CAGTCCATA-GATT-CGAAGAACCTAGGTAATCAGTCCATATATCCCGAAGGACATAGGT-AA
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAACAGTCCATATATCCCGAAGAACATAGGTAAA
*
80116 CAGTCCATATGTTCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAA-AACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAACAGTCCATATATCCCGAAGAACATAGGTAAA
*
80177 CAGTCCATATGTTCCGAAGAACATAGGTAAACAGTCCATAT-TTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAACAGTCCATATATCCCGAAGAACATAGGTAAA
80238 C
1 C
80239 CCTCGACCCT
Statistics
Matches: 114, Mismatches: 5, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
60 25 0.22
61 89 0.78
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (62 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAACAGTCCATATATCCCGAAGAACATAGGTAAA
Found at i:80442 original size:23 final size:24
Alignment explanation
Indices: 80416--80462 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
80406 ATATACTTGT
*
80416 TTTCACATATATA-TTTCATATCA
1 TTTCACATATACACTTTCATATCA
80439 TTTCACATATACACTTTCATATCA
1 TTTCACATATACACTTTCATATCA
80463 CATGCCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTCACATATACACTTTCATATCA
Found at i:81122 original size:21 final size:21
Alignment explanation
Indices: 81092--81136 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
81082 ATTCTGTCGT
* *
81092 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
81113 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
81134 TTG
1 TTG
81137 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:84212 original size:31 final size:31
Alignment explanation
Indices: 84174--84356 Score: 277
Period size: 31 Copynumber: 6.0 Consensus size: 31
84164 CCCGAAGGAC
* *
84174 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
84205 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
84236 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
84267 CAGTCC--ATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
84296 CAGTCC--ATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
84325 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
84356 C
1 C
84357 CCTCGACCCT
Statistics
Matches: 141, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
29 56 0.40
31 84 0.60
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:84331 original size:89 final size:90
Alignment explanation
Indices: 84187--84356 Score: 288
Period size: 89 Copynumber: 1.9 Consensus size: 90
84177 TCCATAGATT
* * *
84187 CCGAAGAACCTAGGTAATCAGTCCATATGTCCCGAAGGACATAGGTAAACAGTCCATATGTTCCG
1 CCGAAGAACATAGGTAAACAGTCCA-ATGTCCCGAAGAACATAGGTAAACAGTCCATATGTTCCG
84252 AAGAACATAGGTAAACAGTCCATGTC
65 AAGAACATAGGTAAACAGTCCATGTC
*
84278 CCGAAGAACATAGGTAAACAGTCC-ATGTTCCGAAGAACATAGGTAAACAGTCCATATGTTCCGA
1 CCGAAGAACATAGGTAAACAGTCCAATGTCCCGAAGAACATAGGTAAACAGTCCATATGTTCCGA
84342 AGAACATAGGTAAAC
66 AGAACATAGGTAAAC
84357 CCTCGACCCT
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
89 53 0.71
91 22 0.29
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.20
Consensus pattern (90 bp):
CCGAAGAACATAGGTAAACAGTCCAATGTCCCGAAGAACATAGGTAAACAGTCCATATGTTCCGA
AGAACATAGGTAAACAGTCCATGTC
Found at i:85224 original size:21 final size:21
Alignment explanation
Indices: 85194--85238 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
85184 ATTCTGTCGT
* *
85194 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
85215 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
85236 TTG
1 TTG
85239 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:86289 original size:2 final size:2
Alignment explanation
Indices: 86282--86311 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
86272 ATATTTAATA
86282 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
86312 GATGTGATTT
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
Done.