Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001853.1 Hibiscus syriacus cultivar Beakdansim tig00003752_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: 54680
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Found at i:9993 original size:29 final size:29
Alignment explanation
Indices: 9951--10009 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
9941 ATTTTCACCT
*
9951 AACTAAATTGATGTAAGCAGTGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
9980 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
10009 A
1 A
10010 TTAATTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.47, C:0.14, G:0.15, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:13272 original size:31 final size:31
Alignment explanation
Indices: 13237--13379 Score: 268
Period size: 31 Copynumber: 4.6 Consensus size: 31
13227 TCTATAGATT
* *
13237 CCGAAGAACCTAGGTAATCAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
13268 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
13299 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
13330 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
13361 CCGAAGAACATAGGTAAAC
1 CCGAAGAACATAGGTAAAC
13380 CCTCGACCCT
Statistics
Matches: 110, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 110 1.00
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACAGTCCATATGTC
Found at i:13985 original size:18 final size:18
Alignment explanation
Indices: 13962--13996 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
13952 TTCATTTAGG
13962 GGGGAATCGATACCCCCA
1 GGGGAATCGATACCCCCA
13980 GGGGAATCGATACCCCC
1 GGGGAATCGATACCCCC
13997 TGAACATACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.34, G:0.29, T:0.11
Consensus pattern (18 bp):
GGGGAATCGATACCCCCA
Found at i:17165 original size:19 final size:17
Alignment explanation
Indices: 17140--17184 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
17130 GAGGCATATA
*
17140 AAACATATAATATTTCAT
1 AAACATATAATA-TACAT
*
17158 ATAACATAAAATATACAT
1 A-AACATATAATATACAT
17176 AAACATATA
1 AAACATATA
17185 CCATCATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 7 0.30
18 6 0.26
19 10 0.43
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.31
Consensus pattern (17 bp):
AAACATATAATATACAT
Found at i:17573 original size:31 final size:31
Alignment explanation
Indices: 17550--17721 Score: 308
Period size: 31 Copynumber: 5.5 Consensus size: 31
17540 CATAGATTCT
* *
17550 GAAGAACCTAGGTAATCAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
17581 GAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
*
17612 GAAGAACATAGGTAAACAATCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
17643 GAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
*
17674 GAAGAACATAGGTAAACGGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
17705 GAAGAACATAGGTAAAC
1 GAAGAACATAGGTAAAC
17722 CCTCGACCCT
Statistics
Matches: 136, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 136 1.00
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (31 bp):
GAAGAACATAGGTAAACAGTCCATATGTCCC
Found at i:21271 original size:29 final size:29
Alignment explanation
Indices: 21229--21287 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
21219 ATTTTCACCT
21229 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
21258 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
21287 A
1 A
21288 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:27030 original size:16 final size:16
Alignment explanation
Indices: 27006--27039 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
26996 TATCGCCGAC
*
27006 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
27022 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
27038 CG
1 CG
27040 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:30699 original size:26 final size:26
Alignment explanation
Indices: 30670--30721 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
30660 AATAGCTAAG
30670 ATAAATTATAAAATAATATTATTTTA
1 ATAAATTATAAAATAATATTATTTTA
30696 ATAAATTATAAAATAATATTATTTTA
1 ATAAATTATAAAATAATATTATTTTA
30722 TAACTCAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
ATAAATTATAAAATAATATTATTTTA
Found at i:34588 original size:60 final size:60
Alignment explanation
Indices: 34441--34624 Score: 187
Period size: 60 Copynumber: 3.1 Consensus size: 60
34431 GTATTTTATG
* * * *
34441 TCCCCAAACTATAACCCTCATTTTAAATTGGTCCTTAAACTTTTGAATATTATAATTTCA
1 TCCCTAAACTATGACCCTCATTTTAAATTGGCCCTTAAACTTTTGAATATTCTAATTTCA
* * * * * *
34501 T-CATCAAATTATGA-CTTCCATTCTAAATTAGCCCTTAAACTTTTGAACATTCTAATTTCA
1 TCCCT-AAACTATGACCCT-CATTTTAAATTGGCCCTTAAACTTTTGAATATTCTAATTTCA
* * *
34561 TCCCTAAACTATGACCCTCTTTTTAAATTGGTCTCC--AAACTTTTGAATATTCCAATTCCA
1 TCCCTAAACTATGACCCTCATTTTAAATTGG-C-CCTTAAACTTTTGAATATTCTAATTTCA
34621 TCCC
1 TCCC
34625 CAAATTCATC
Statistics
Matches: 99, Mismatches: 19, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
59 3 0.03
60 89 0.90
61 5 0.05
62 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.05, T:0.39
Consensus pattern (60 bp):
TCCCTAAACTATGACCCTCATTTTAAATTGGCCCTTAAACTTTTGAATATTCTAATTTCA
Found at i:34932 original size:60 final size:60
Alignment explanation
Indices: 34816--34937 Score: 140
Period size: 60 Copynumber: 2.0 Consensus size: 60
34806 TCATTGTTTG
* *
34816 GGGATGAAATTGAAATGTTCAAAAGTTTGAGAACTAATTTAGAATGACAATTATAATTTA
1 GGGATGAAATTGAAATGTTCAAAAGTTTAAGAACTAATTTAGAATGACAATCATAATTTA
* * * ***
34876 GGGATGAAATTAGAATAT-TT-AAAATTTTAAGGACTAATTTATAATGATGGTCATAATTTA
1 GGGATGAAATT-GAA-ATGTTCAAAAGTTTAAGAACTAATTTAGAATGACAATCATAATTTA
34936 GG
1 GG
34938 AACATGTGAT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
60 45 0.87
61 5 0.10
62 2 0.04
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.35
Consensus pattern (60 bp):
GGGATGAAATTGAAATGTTCAAAAGTTTAAGAACTAATTTAGAATGACAATCATAATTTA
Found at i:35390 original size:21 final size:21
Alignment explanation
Indices: 35366--35451 Score: 111
Period size: 21 Copynumber: 4.1 Consensus size: 21
35356 CAACAATCCC
*
35366 TACGGGTATTACAGAAACCCG
1 TACGGATATTACAGAAACCCG
35387 TACGGATATTACA-ACAACCCG
1 TACGGATATTACAGA-AACCCG
* *
35408 TCCGGGTATTACAGAAACCCG
1 TACGGATATTACAGAAACCCG
* *
35429 TACGGATATTCCAGCAACCCG
1 TACGGATATTACAGAAACCCG
35450 TA
1 TA
35452 ATCTGGTTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
20 1 0.02
21 54 0.96
22 1 0.02
ACGTcount: A:0.33, C:0.28, G:0.20, T:0.20
Consensus pattern (21 bp):
TACGGATATTACAGAAACCCG
Found at i:35414 original size:42 final size:42
Alignment explanation
Indices: 35368--35450 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
35358 ACAATCCCTA
35368 CGGGTATTACAGAAACCCGTACGGATATTACAACAACCCGTC
1 CGGGTATTACAGAAACCCGTACGGATATTACAACAACCCGTC
* *
35410 CGGGTATTACAGAAACCCGTACGGATATTCCAGCAACCCGT
1 CGGGTATTACAGAAACCCGTACGGATATTACAACAACCCGT
35451 AATCTGGTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.19
Consensus pattern (42 bp):
CGGGTATTACAGAAACCCGTACGGATATTACAACAACCCGTC
Found at i:35714 original size:2 final size:2
Alignment explanation
Indices: 35707--35753 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
35697 ATTGTAAAAC
35707 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35749 TA TA T
1 TA TA T
35754 TCCCAATAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:38049 original size:2 final size:2
Alignment explanation
Indices: 38042--38078 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
38032 TTTATTTATT
38042 TA 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 TA T
38079 TAATTTTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:42027 original size:16 final size:16
Alignment explanation
Indices: 42006--42039 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
41996 TTACTATTCA
*
42006 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
42022 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
42038 CG
1 CG
42040 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:42806 original size:15 final size:16
Alignment explanation
Indices: 42788--42820 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
42778 GTGGCAGATC
42788 AAAATCCAG-ACGGGA
1 AAAATCCAGAACGGGA
*
42803 AAAATCTAGAACGGGA
1 AAAATCCAGAACGGGA
42819 AA
1 AA
42821 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
Done.