Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001435.1 Hibiscus syriacus cultivar Beakdansim tig00002783_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: 80381
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:10025 original size:24 final size:23
Alignment explanation
Indices: 9998--10045 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
9988 AATAACCAAG
9998 ATAAACA-TAAATATACCATTGAAA
1 ATAAACATTAAATA-ACCATT-AAA
*
10022 ATAAAGATTAAATAACCATTAAA
1 ATAAACATTAAATAACCATTAAA
10045 A
1 A
10046 CAACCACCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 4 0.18
24 12 0.55
25 6 0.27
ACGTcount: A:0.60, C:0.10, G:0.04, T:0.25
Consensus pattern (23 bp):
ATAAACATTAAATAACCATTAAA
Found at i:12604 original size:14 final size:14
Alignment explanation
Indices: 12585--12613 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
12575 AAGTCAGGAT
12585 AGCCGAAGGTGATG
1 AGCCGAAGGTGATG
12599 AGCCGAAGGTGATG
1 AGCCGAAGGTGATG
12613 A
1 A
12614 AACGAAGACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.14, G:0.41, T:0.14
Consensus pattern (14 bp):
AGCCGAAGGTGATG
Found at i:15685 original size:9 final size:9
Alignment explanation
Indices: 15673--15722 Score: 57
Period size: 9 Copynumber: 5.2 Consensus size: 9
15663 AAAAGATATA
15673 ATTATATTT
1 ATTATATTT
15682 ATTATATTT
1 ATTATATTT
15691 ATAATATATTT
1 AT--TATATTT
15702 ATTAATATTT
1 ATT-ATATTT
15712 GATTAT-TTT
1 -ATTATATTT
15721 AT
1 AT
15723 ATCTAAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
8 2 0.05
9 15 0.41
10 8 0.22
11 12 0.32
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (9 bp):
ATTATATTT
Found at i:15693 original size:21 final size:21
Alignment explanation
Indices: 15669--15711 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
15659 TTATAAAAGA
15669 TATAATTATATTTATT-ATATT
1 TATAA-TATATTTATTAATATT
15690 TATAATATATTTATTAATATT
1 TATAATATATTTATTAATATT
15711 T
1 T
15712 GATTATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATAATATATTTATTAATATT
Found at i:16602 original size:60 final size:61
Alignment explanation
Indices: 16503--16653 Score: 164
Period size: 60 Copynumber: 2.5 Consensus size: 61
16493 TTTTAGATTG
* * * * *
16503 GTCCTTAAATTTTTGAAGATTCTAATTTGA-GCCTCAAACTATGACTC-TCATTCTAAATTA
1 GTCCTTAAACTTTTGAACATTTTAATTTCATCCCTCAAACTATGAC-CATCATTCTAAATTA
* * *
16563 GTCTTTAAACTTTTGAACATTTTAATTTCATCCCT-AAACTATGACCATCTTTCTAAATTG
1 GTCCTTAAACTTTTGAACATTTTAATTTCATCCCTCAAACTATGACCATCATTCTAAATTA
** * *
16623 GTCCCCAAACTTTTGAATATTTCAATTTCAT
1 GTCCTTAAACTTTTGAACATTTTAATTTCAT
16654 TCCCAAATTC
Statistics
Matches: 76, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
59 1 0.01
60 72 0.95
61 3 0.04
ACGTcount: A:0.30, C:0.20, G:0.08, T:0.42
Consensus pattern (61 bp):
GTCCTTAAACTTTTGAACATTTTAATTTCATCCCTCAAACTATGACCATCATTCTAAATTA
Found at i:16886 original size:58 final size:59
Alignment explanation
Indices: 16809--16953 Score: 161
Period size: 60 Copynumber: 2.5 Consensus size: 59
16799 AGAATGTTCA
* * *
16809 AAAAGTTTGGGGATCAATTTAGAAT-AAAGGTCA-GTTCAAGGATAAAATTGAAATATTC
1 AAAAGTTTGAGGATCAATTTAAAATGAAA-GCCAGGTTCAAGGATAAAATTGAAATATTC
* * * *
16867 AAAAGTTTGAGGA-CTAATTTAAAATGATAGCCATGGTTTAAGGATGAAATTGAAATATTT
1 AAAAGTTTGAGGATC-AATTTAAAATGAAAGCCA-GGTTCAAGGATAAAATTGAAATATTC
* *
16927 AAAAGTTTAAGAATCAATTTAAAATGA
1 AAAAGTTTGAGGATCAATTTAAAATGA
16954 TGGTCATACT
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
57 1 0.01
58 24 0.33
59 2 0.03
60 45 0.62
61 1 0.01
ACGTcount: A:0.45, C:0.06, G:0.19, T:0.31
Consensus pattern (59 bp):
AAAAGTTTGAGGATCAATTTAAAATGAAAGCCAGGTTCAAGGATAAAATTGAAATATTC
Found at i:22826 original size:2 final size:2
Alignment explanation
Indices: 22819--22844 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
22809 TAATTAAATA
22819 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
22845 TCCAGATTAG
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:29294 original size:21 final size:21
Alignment explanation
Indices: 29268--29307 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29258 CAGAACCCCA
*
29268 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
29289 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
29308 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:29342 original size:21 final size:21
Alignment explanation
Indices: 29289--29351 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 21
29279 ATTCCCCTGT
29289 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTT-CCC-TCAA
*
29312 AGGGGGAATCGGTTCCCTC-A
1 GGGGGGAATCGGTTCCCTCAA
*
29332 GGGGCGGAATCGATTCCCTC
1 GGGG-GGAATCGGTTCCCTC
29352 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 4 0.11
21 16 0.44
22 3 0.08
23 13 0.36
ACGTcount: A:0.17, C:0.27, G:0.35, T:0.21
Consensus pattern (21 bp):
GGGGGGAATCGGTTCCCTCAA
Found at i:33182 original size:22 final size:21
Alignment explanation
Indices: 33140--33179 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
33130 TGAGTTGTTT
*
33140 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
33161 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
33180 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:35646 original size:19 final size:19
Alignment explanation
Indices: 35622--35658 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
35612 ATACATAGTA
*
35622 GTATCGATACCCTTTTTGG
1 GTATCGATACCATTTTTGG
*
35641 GTATCGGTACCATTTTTG
1 GTATCGATACCATTTTTG
35659 CATTATGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.43
Consensus pattern (19 bp):
GTATCGATACCATTTTTGG
Found at i:35731 original size:21 final size:21
Alignment explanation
Indices: 35706--35758 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
35696 TACCTAGTGA
*
35706 GTATCGATACTTTTTCAATTG
1 GTATCGATACTTGTTCAATTG
35727 GTATCGATACTTGTTCAATTG
1 GTATCGATACTTGTTCAATTG
35748 GTATCGATACT
1 GTATCGATACT
35759 GTAAGAACAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.43
Consensus pattern (21 bp):
GTATCGATACTTGTTCAATTG
Found at i:45358 original size:19 final size:20
Alignment explanation
Indices: 45319--45358 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
45309 TTTTGTTTTT
*
45319 TATTTTAAATATTAAATATA
1 TATTATAAATATTAAATATA
*
45339 TATTATAAAT-TTATATATA
1 TATTATAAATATTAAATATA
45358 T
1 T
45359 TTTACATGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TATTATAAATATTAAATATA
Found at i:46148 original size:30 final size:30
Alignment explanation
Indices: 46043--46154 Score: 111
Period size: 30 Copynumber: 3.7 Consensus size: 30
46033 AATAAAGTTA
* *
46043 TGTTCATGTTCATTTGTTTATTTTTAAAGG
1 TGTTCATGTTCGTTTATTTATTTTTAAAGG
* * *
46073 TGTTCATGTTCGTTTA--AATTTGTAATATCG
1 TGTTCATGTTCGTTTATTTATTTTTAA-A-GG
*
46103 TGTTCATGTTTGTTTATTTATTTTTAAAGG
1 TGTTCATGTTCGTTTATTTATTTTTAAAGG
** *
46133 TGTTTGTGTTCGTTTAATTATT
1 TGTTCATGTTCGTTTATTTATT
46155 GTTAGCGAAT
Statistics
Matches: 65, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
28 7 0.11
29 1 0.02
30 49 0.75
31 1 0.02
32 7 0.11
ACGTcount: A:0.20, C:0.06, G:0.17, T:0.57
Consensus pattern (30 bp):
TGTTCATGTTCGTTTATTTATTTTTAAAGG
Found at i:46186 original size:23 final size:23
Alignment explanation
Indices: 46160--46268 Score: 137
Period size: 23 Copynumber: 4.7 Consensus size: 23
46150 TTATTGTTAG
*
46160 CGAATGTGTTCATTTAATGTTCA
1 CGAACGTGTTCATTTAATGTTCA
46183 CGAACGTGTTCATTTATATGTTCA
1 CGAACGTGTTCATTTA-ATGTTCA
* *
46207 AGAACGTGTTCATTTAACGTTCA
1 CGAACGTGTTCATTTAATGTTCA
* *
46230 CGAACATGTTCATTTAGTGTTCA
1 CGAACGTGTTCATTTAATGTTCA
* * *
46253 AGAACATGTTCGTTTA
1 CGAACGTGTTCATTTA
46269 TATATTCAAT
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
23 54 0.71
24 22 0.29
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (23 bp):
CGAACGTGTTCATTTAATGTTCA
Found at i:46216 original size:47 final size:46
Alignment explanation
Indices: 46165--46268 Score: 154
Period size: 47 Copynumber: 2.2 Consensus size: 46
46155 GTTAGCGAAT
* *
46165 GTGTTCATTTAATGTTCACGAACGTGTTCATTTATATGTTCAAGAAC
1 GTGTTCATTTAACGTTCACGAACATGTTCATTTA-ATGTTCAAGAAC
*
46212 GTGTTCATTTAACGTTCACGAACATGTTCATTTAGTGTTCAAGAAC
1 GTGTTCATTTAACGTTCACGAACATGTTCATTTAATGTTCAAGAAC
* *
46258 ATGTTCGTTTA
1 GTGTTCATTTA
46269 TATATTCAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
46 20 0.38
47 32 0.62
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.40
Consensus pattern (46 bp):
GTGTTCATTTAACGTTCACGAACATGTTCATTTAATGTTCAAGAAC
Found at i:54818 original size:18 final size:19
Alignment explanation
Indices: 54789--54825 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
54779 TGAGATTTGG
*
54789 ATTTTTATTTTCCATTTCT
1 ATTTTTATTTTCAATTTCT
54808 ATTTTTA-TTTCAATTTCT
1 ATTTTTATTTTCAATTTCT
54826 TATCTGATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.68
Consensus pattern (19 bp):
ATTTTTATTTTCAATTTCT
Found at i:67422 original size:22 final size:22
Alignment explanation
Indices: 67397--67453 Score: 114
Period size: 22 Copynumber: 2.6 Consensus size: 22
67387 CTCAGAGGGA
67397 ACCGATTCCCCCCCAAGGGGGT
1 ACCGATTCCCCCCCAAGGGGGT
67419 ACCGATTCCCCCCCAAGGGGGT
1 ACCGATTCCCCCCCAAGGGGGT
67441 ACCGATTCCCCCC
1 ACCGATTCCCCCC
67454 TGTTTAACGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.14
Consensus pattern (22 bp):
ACCGATTCCCCCCCAAGGGGGT
Found at i:68366 original size:17 final size:17
Alignment explanation
Indices: 68346--68383 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
68336 ATGAAAGCTT
68346 GGATGATGATCGAGAAA
1 GGATGATGATCGAGAAA
68363 GGATGATGATCGAGAAA
1 GGATGATGATCGAGAAA
68380 GGAT
1 GGAT
68384 AATCTTCTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.39, C:0.05, G:0.37, T:0.18
Consensus pattern (17 bp):
GGATGATGATCGAGAAA
Found at i:74481 original size:18 final size:18
Alignment explanation
Indices: 74444--74484 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
74434 AGAACAACAC
*
74444 GAGGAACAAGCACGAGCA
1 GAGGAACAAGCACAAGCA
74462 GAGGAACAAGCA-AAGCCA
1 GAGGAACAAGCACAAG-CA
74480 GAGGA
1 GAGGA
74485 TCAAATGCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.46, C:0.20, G:0.34, T:0.00
Consensus pattern (18 bp):
GAGGAACAAGCACAAGCA
Found at i:75352 original size:52 final size:52
Alignment explanation
Indices: 75290--75392 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
75280 AAGTATATTT
*
75290 GATATAATTATTCGAATATCAAATTATTACTCTAAATCTTTCAAATGTCATC
1 GATATAATTATTCGAATATCAAATTATTACTCCAAATCTTTCAAATGTCATC
75342 GATATAATTATTCGAATATCAAATTATTACTCCAAATCTTTCAAATGTCAT
1 GATATAATTATTCGAATATCAAATTATTACTCCAAATCTTTCAAATGTCAT
75393 TTTTAATCCT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.39, C:0.16, G:0.06, T:0.40
Consensus pattern (52 bp):
GATATAATTATTCGAATATCAAATTATTACTCCAAATCTTTCAAATGTCATC
Done.