Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006243.1 Hibiscus syriacus cultivar Beakdansim tig00014884_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: 98989
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2341 original size:29 final size:30
Alignment explanation
Indices: 2264--2341 Score: 79
Period size: 29 Copynumber: 2.6 Consensus size: 30
2254 TTTAGAGATT
* * * *
2264 GTTCAAATACGAGTCTAATATTTTTAGATT
1 GTTCAAATAAGAGTCTAATATTTTAAAATG
* *
2294 ATTCAAATAAG-GATTTAATA-TTTAAAATG
1 GTTCAAATAAGAG-TCTAATATTTTAAAATG
2323 GTTCAAATAAGAGTCTAAT
1 GTTCAAATAAGAGTCTAAT
2342 CTATAACCCT
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
29 22 0.58
30 16 0.42
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38
Consensus pattern (30 bp):
GTTCAAATAAGAGTCTAATATTTTAAAATG
Found at i:13902 original size:20 final size:20
Alignment explanation
Indices: 13879--13921 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
13869 ATTCCACCAC
*
13879 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
13899 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
13919 ATG
1 ATG
13922 GGCTTTTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:21138 original size:2 final size:2
Alignment explanation
Indices: 21131--21156 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21121 TGATAAAATA
21131 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
21157 GAAGATATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25004 original size:15 final size:15
Alignment explanation
Indices: 24984--25017 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
24974 CTTAGCCTAT
24984 ATATGATTAAAAGAA
1 ATATGATTAAAAGAA
24999 ATATGATTAAAAGAA
1 ATATGATTAAAAGAA
25014 ATAT
1 ATAT
25018 CTTTTCATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.29
Consensus pattern (15 bp):
ATATGATTAAAAGAA
Found at i:38922 original size:3 final size:3
Alignment explanation
Indices: 38910--38944 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
38900 TCTAATTTTT
*
38910 TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
38945 TGGCTCAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:40285 original size:6 final size:6
Alignment explanation
Indices: 40278--40312 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
40268 CGTATTACCA
* *
40278 CGACCA CGACCT CAACCT CGACCT CGACCT CGACC
1 CGACCT CGACCT CGACCT CGACCT CGACCT CGACC
40313 ATGGCCATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.23, C:0.51, G:0.14, T:0.11
Consensus pattern (6 bp):
CGACCT
Found at i:45788 original size:22 final size:22
Alignment explanation
Indices: 45763--45821 Score: 100
Period size: 22 Copynumber: 2.7 Consensus size: 22
45753 TCAGCTGTTA
45763 TAACTCCTGAAATTATATCATG
1 TAACTCCTGAAATTATATCATG
45785 TAACTCCTGAAATTATATCATG
1 TAACTCCTGAAATTATATCATG
* *
45807 TAACACCTGATATTA
1 TAACTCCTGAAATTA
45822 GCCTTAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.36
Consensus pattern (22 bp):
TAACTCCTGAAATTATATCATG
Found at i:46514 original size:28 final size:28
Alignment explanation
Indices: 46483--46575 Score: 107
Period size: 28 Copynumber: 3.3 Consensus size: 28
46473 GTTAATAATT
* **
46483 TAAAATTTTTGATTGAAGTAGGTATAAA
1 TAAAATTTTTGAATGAAGTAAATATAAA
*
46511 TAAATTTTTTGAATGAAGTAAATATAAA
1 TAAAATTTTTGAATGAAGTAAATATAAA
* * *
46539 TAAAATTTTTAAAT-AAGGTCAATGTAAA
1 TAAAATTTTTGAATGAA-GTAAATATAAA
46567 TAAAATTTT
1 TAAAATTTT
46576 AGGATAAATA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
27 2 0.04
28 54 0.96
ACGTcount: A:0.47, C:0.01, G:0.12, T:0.40
Consensus pattern (28 bp):
TAAAATTTTTGAATGAAGTAAATATAAA
Found at i:47054 original size:15 final size:15
Alignment explanation
Indices: 47033--47067 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
47023 AATTCTAATT
47033 GAATTTTCTTGAATC
1 GAATTTTCTTGAATC
*
47048 TAATTTTCTTGAATC
1 GAATTTTCTTGAATC
47063 GAATT
1 GAATT
47068 AAATGGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (15 bp):
GAATTTTCTTGAATC
Found at i:49776 original size:2 final size:2
Alignment explanation
Indices: 49769--49847 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
49759 ATACTTCCAC
49769 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
49811 AT AT AT AT 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 AT AT AT AT A
49848 ACTTGTCAGG
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:60911 original size:17 final size:17
Alignment explanation
Indices: 60862--60926 Score: 85
Period size: 17 Copynumber: 3.8 Consensus size: 17
60852 GTTTCTGATA
*
60862 GAATTGGAATCTGTGAAG
1 GAATTGGAATCTGT-CAG
* *
60880 GCATTGGAATATGTCAG
1 GAATTGGAATCTGTCAG
*
60897 GAATTGAAATCTGTCAG
1 GAATTGGAATCTGTCAG
60914 GAATTGGAATCTG
1 GAATTGGAATCTG
60927 AATCTGAAAC
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
17 28 0.70
18 12 0.30
ACGTcount: A:0.32, C:0.09, G:0.29, T:0.29
Consensus pattern (17 bp):
GAATTGGAATCTGTCAG
Found at i:62300 original size:64 final size:63
Alignment explanation
Indices: 62214--62374 Score: 200
Period size: 64 Copynumber: 2.5 Consensus size: 63
62204 ATTGTTTAAG
* * *
62214 ATGCATCGATGCACATGCAGTGCATCGATGCAT-GAATTTAAATAGAAAACATCGAATAGGA-TT
1 ATGCATCGATGCACAAGCAGTGCATCGATGCATCCAA-TTAAATA-AAAACATCGAAT-GCATTT
62277 T
63 T
* * *
62278 ATGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAAAAACATCGAATGCATTTT
1 ATGCATCGATGCACAAGCAGTGCATCGATGCAT-CCAATTAAATAAAAACATCGAATGCATTTT
* *
62342 ATGCACCGATGCACAAGTAGTGCATCGATGCAT
1 ATGCATCGATGCACAAGCAGTGCATCGATGCAT
62375 ACATTCATTG
Statistics
Matches: 85, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
63 2 0.02
64 75 0.88
65 7 0.08
66 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.25
Consensus pattern (63 bp):
ATGCATCGATGCACAAGCAGTGCATCGATGCATCCAATTAAATAAAAACATCGAATGCATTTT
Found at i:63469 original size:36 final size:36
Alignment explanation
Indices: 63428--63500 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
63418 GGGTATAGTG
63428 ATATATGTGTTATAAGATGAGTATATGGTAAGTGGA
1 ATATATGTGTTATAAGATGAGTATATGGTAAGTGGA
*
63464 ATATATGTGTTATATGATGAGTATATGGTAAGTGGA
1 ATATATGTGTTATAAGATGAGTATATGGTAAGTGGA
63500 A
1 A
63501 AGGATTATTG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.00, G:0.27, T:0.37
Consensus pattern (36 bp):
ATATATGTGTTATAAGATGAGTATATGGTAAGTGGA
Found at i:66563 original size:64 final size:63
Alignment explanation
Indices: 66477--66637 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 63
66467 ATTGTTTAAG
* * *
66477 ATGCATCGATGCACATGCAGTGCATCGATGCAT-GAATTTAAATAGAAAACATCGAATAGGA-TT
1 ATGCATCGATGCACAAGCAGTGCATCGATGCATCCAA-TTAAATA-AAAACATCGAAT-GCATTT
66540 T
63 T
* * * *
66541 ATGTATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAAAAACATCGAATGCATTTT
1 ATGCATCGATGCACAAGCAGTGCATCGATGCAT-CCAATTAAATAAAAACATCGAATGCATTTT
* *
66605 ATGCACCGATGCACAAGTAGTGCATCGATGCAT
1 ATGCATCGATGCACAAGCAGTGCATCGATGCAT
66638 ACATTCATTG
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
63 2 0.02
64 73 0.88
65 7 0.08
66 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (63 bp):
ATGCATCGATGCACAAGCAGTGCATCGATGCATCCAATTAAATAAAAACATCGAATGCATTTT
Found at i:67352 original size:30 final size:30
Alignment explanation
Indices: 67316--67379 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
67306 AAGGAACATA
* *
67316 TGGATAGTTGCCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
* * *
67346 TGGATAGTTACCGGGGTTCTTTGTAACCTC
1 TGGATAGTTACCGAGGATCTTTATAACCTC
67376 TGGA
1 TGGA
67380 CAGGTCCTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATAACCTC
Found at i:82132 original size:19 final size:20
Alignment explanation
Indices: 82110--82149 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
82100 TTTCAAATTC
82110 GTTG-CGATAGTCTACAGTT
1 GTTGTCGATAGTCTACAGTT
82129 GTTGTTACGATAGTCTACAGT
1 GTTG-T-CGATAGTCTACAGT
82150 CGTAGTTGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
22 14 0.78
ACGTcount: A:0.23, C:0.15, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGTCGATAGTCTACAGTT
Found at i:83153 original size:3 final size:3
Alignment explanation
Indices: 83145--83171 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
83135 TTTTAAAAAT
83145 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
83172 GATATTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:89315 original size:48 final size:48
Alignment explanation
Indices: 89262--89365 Score: 120
Period size: 50 Copynumber: 2.1 Consensus size: 48
89252 TAGTAGGAAA
* * * * *
89262 GCGCCCTG-CACCGCGTTATATGTTGATTTGGCGTCACGTAGGTATAAC
1 GCGCCCTGTC-CCGCGATATACGGTGATCTGGCATCACGTAGGTATAAC
*
89310 GCGCCCCCTGTCCCGCGATATACGGTGATCTGGCATCACGTGGGTATAAC
1 GCG--CCCTGTCCCGCGATATACGGTGATCTGGCATCACGTAGGTATAAC
89360 GCGCCC
1 GCGCCC
89366 CCGATCCGCG
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
48 6 0.13
50 40 0.85
51 1 0.02
ACGTcount: A:0.17, C:0.31, G:0.28, T:0.24
Consensus pattern (48 bp):
GCGCCCTGTCCCGCGATATACGGTGATCTGGCATCACGTAGGTATAAC
Found at i:93052 original size:35 final size:34
Alignment explanation
Indices: 92967--93053 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
92957 ATTTGATATT
*
92967 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
93001 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
93039 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
93054 ACTAAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:93274 original size:6 final size:6
Alignment explanation
Indices: 93258--93328 Score: 64
Period size: 6 Copynumber: 12.8 Consensus size: 6
93248 ACTCCTCGTT
* *
93258 GTCATC ATCATC GTCATC GTCGTC GTCA-C --CATC GTCATC G---TC
1 GTCATC GTCATC GTCATC GTCATC GTCATC GTCATC GTCATC GTCATC
* *
93300 GTCATC ATCATC GTCATC GTCATT GTCAT
1 GTCATC GTCATC GTCATC GTCATC GTCAT
93329 GAGCAGTACA
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
3 5 0.10
4 1 0.02
5 1 0.02
6 45 0.87
ACGTcount: A:0.18, C:0.32, G:0.15, T:0.34
Consensus pattern (6 bp):
GTCATC
Found at i:93277 original size:21 final size:21
Alignment explanation
Indices: 93253--93320 Score: 109
Period size: 21 Copynumber: 3.2 Consensus size: 21
93243 TTCTGACTCC
*
93253 TCGTTGTCATCATCATCGTCA
1 TCGTCGTCATCATCATCGTCA
* *
93274 TCGTCGTCGTCACCATCGTCA
1 TCGTCGTCATCATCATCGTCA
93295 TCGTCGTCATCATCATCGTCA
1 TCGTCGTCATCATCATCGTCA
93316 TCGTC
1 TCGTC
93321 ATTGTCATGA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.16, C:0.34, G:0.16, T:0.34
Consensus pattern (21 bp):
TCGTCGTCATCATCATCGTCA
Found at i:93316 original size:9 final size:9
Alignment explanation
Indices: 93280--93322 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
93270 GTCATCGTCG
*
93280 TCGTCACCA
1 TCGTCATCA
*
93289 TCGTCATCG
1 TCGTCATCA
93298 TCGTCATCA
1 TCGTCATCA
* *
93307 TCATCGTCA
1 TCGTCATCA
93316 TCGTCAT
1 TCGTCAT
93323 TGTCATGAGC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.19, C:0.35, G:0.14, T:0.33
Consensus pattern (9 bp):
TCGTCATCA
Found at i:93322 original size:15 final size:15
Alignment explanation
Indices: 93271--93317 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
93261 ATCATCATCG
*
93271 TCATCGTCGTCGTCA
1 TCATCGTCATCGTCA
* *
93286 CCATCGTCATCGTCG
1 TCATCGTCATCGTCA
*
93301 TCATCATCATCGTCA
1 TCATCGTCATCGTCA
93316 TC
1 TC
93318 GTCATTGTCA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.17, C:0.36, G:0.15, T:0.32
Consensus pattern (15 bp):
TCATCGTCATCGTCA
Found at i:95305 original size:111 final size:111
Alignment explanation
Indices: 95168--95389 Score: 399
Period size: 111 Copynumber: 2.0 Consensus size: 111
95158 ATTACAAAAA
* *
95168 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
* *
95233 AATTAAAACGTTAAAATGTTACCGTATTAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
95279 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
95344 AATTAAAACGTTCAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
95390 ATGATTTCCA
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 106 1.00
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:95706 original size:50 final size:49
Alignment explanation
Indices: 95652--95771 Score: 132
Period size: 50 Copynumber: 2.4 Consensus size: 49
95642 AGCTATCCAG
* * * *
95652 GTATAGCGCGGATCAGGGGGCACGCTATACCCACATGGCGCCAGATCACC
1 GTATAACGCGG-TCAGGGGGCACGATATACCCACATGGCGCCAAATCAAC
* * * *
95702 GTATATCGCGGGGCAGGGGGCGCGATATACCCACGTGGCGCCAAATCAAC
1 GTATAACGC-GGTCAGGGGGCACGATATACCCACATGGCGCCAAATCAAC
*
95752 ATATAACGCGGTGCAGGGGG
1 GTATAACGCGGT-CAGGGGG
95772 AACGTTTTCC
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
49 2 0.03
50 54 0.93
51 2 0.03
ACGTcount: A:0.24, C:0.28, G:0.34, T:0.14
Consensus pattern (49 bp):
GTATAACGCGGTCAGGGGGCACGATATACCCACATGGCGCCAAATCAAC
Done.