Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007210.1 Hibiscus syriacus cultivar Beakdansim tig00019059_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: 54558
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:11693 original size:27 final size:28
Alignment explanation
Indices: 11663--11724 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
11653 AACAATAAGT
* *
11663 AATAAAGTCCCATGA-GCCATAGAGAAA-
1 AATAAAGTCCCATAAGGCCATA-AAAAAC
*
11690 AATAATGTCCCATAAGGCCATAAAAAAC
1 AATAAAGTCCCATAAGGCCATAAAAAAC
11718 AATAAAG
1 AATAAAG
11725 CAGTAAATAG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 17 0.59
28 12 0.41
ACGTcount: A:0.52, C:0.18, G:0.15, T:0.16
Consensus pattern (28 bp):
AATAAAGTCCCATAAGGCCATAAAAAAC
Found at i:12758 original size:3 final size:3
Alignment explanation
Indices: 12750--12779 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
12740 ATCCACTTAA
12750 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12780 TTAAACCCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:14523 original size:15 final size:17
Alignment explanation
Indices: 14503--14535 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
14493 AAAATTTTAA
14503 AATAAAA-A-TATAATT
1 AATAAAATACTATAATT
14518 AATAAAATACTATAATT
1 AATAAAATACTATAATT
14535 A
1 A
14536 TGTACTTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 1 0.06
17 8 0.50
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
AATAAAATACTATAATT
Found at i:18219 original size:2 final size:2
Alignment explanation
Indices: 18212--18252 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
18202 AGGTAACAAA
18212 AT AT 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 AT AT A
18253 AATTTAGGGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:23937 original size:29 final size:29
Alignment explanation
Indices: 23902--23983 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
23892 AAACTAAATT
*
23902 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
23931 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
23960 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
23984 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:28702 original size:29 final size:29
Alignment explanation
Indices: 28667--28748 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
28657 AAACTAAATT
*
28667 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
28696 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
28725 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
28749 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:30402 original size:90 final size:89
Alignment explanation
Indices: 30247--30423 Score: 300
Period size: 90 Copynumber: 2.0 Consensus size: 89
30237 CCTAACACAC
30247 CCTTTTATAGCCAAGTTACCCTAATCATATTAAAGTTTTATTATTTCAAATTAATTAAATCTATA
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAAAGTTTTATTATTTCAAATTAATTAAATCTATA
* *
30312 TTTAATTAATTGAAATTTAATAAT
66 TTTAATTAATTAAAATTAAATAAT
* **
30336 CCTTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAAAG-TTTTATTATTTCAAATTAATTAAATCTAT
30401 ATTTAATTAATTAAAATTAAATA
65 ATTTAATTAATTAAAATTAAATA
30424 TTCGGGATTA
Statistics
Matches: 82, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
89 32 0.39
90 50 0.61
ACGTcount: A:0.40, C:0.11, G:0.05, T:0.45
Consensus pattern (89 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAAAGTTTTATTATTTCAAATTAATTAAATCTATA
TTTAATTAATTAAAATTAAATAAT
Found at i:32877 original size:65 final size:64
Alignment explanation
Indices: 32679--32888 Score: 196
Period size: 65 Copynumber: 3.2 Consensus size: 64
32669 TGCACTAAGA
* * * *
32679 GTGCATCGATGCATCAAGTGCATTTGATGTTTCAAAAT-AGTCATAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTTGATGTTTCAATATAATTCAT-GTGCATCGATGCATGGTTG
* * * *
32743 GTGCATCGATGCATCAAATGCATTTGATGTTTTC-ATAAAATCCTCA-ATGCATCGGTGCACGGT
1 GTGCATCGATGCATCAAATGCATTTGATG-TTTCAATATAAT--TCATGTGCATCGATGCATGGT
32806 AT-
63 -TG
* * * *
32808 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCATCGATACATGGATT
1 GTGCATCGATGCATCAAATGCATTTGATGTTTCAATATAATTCAT-GTGCATCGATGCATGG-TT
32872 G
64 G
* *
32873 GTGCATTGGTGCATCA
1 GTGCATCGATGCATCA
32889 CACTAAAAAT
Statistics
Matches: 117, Mismatches: 19, Indels: 19
0.75 0.12 0.12
Matches are distributed among these distances:
62 3 0.03
63 3 0.03
64 48 0.41
65 59 0.50
66 1 0.01
67 3 0.03
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTTGATGTTTCAATATAATTCATGTGCATCGATGCATGGTTG
Found at i:33355 original size:2 final size:2
Alignment explanation
Indices: 33344--33388 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
33334 TAGCCAATTG
33344 AT AT -T 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
33385 AT AT
1 AT AT
33389 CTTAAGCTGC
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:41562 original size:64 final size:64
Alignment explanation
Indices: 41448--41636 Score: 217
Period size: 64 Copynumber: 3.0 Consensus size: 64
41438 TGCACTAAGA
* *
41448 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGTCAGAGTGCATCGATGCATGGT-T
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATACTCAGAGTGCATCGATGCATGGTAT
* * *
41511 GGTGTATCGATGCATCAAATGCATTCGATGTTTCATAAAATCCTCA-A-TGCATCGGTGCATGGT
1 -GTGCATCGATGCATCAAATGCATTCGATGTTTC--AAAATACTCAGAGTGCATCGATGCATGGT
41574 AT
63 AT
* ** *
41576 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATG-GTGCATCGATGCATGG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAAT-ACTCA-GAGTGCATCGATGCATGG
41637 ATTGGTGCAT
Statistics
Matches: 106, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
61 3 0.03
62 3 0.03
63 3 0.03
64 87 0.82
65 2 0.02
66 8 0.08
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATACTCAGAGTGCATCGATGCATGGTAT
Done.