Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006182.1 Hibiscus syriacus cultivar Beakdansim tig00014706_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: 76789
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:12234 original size:15 final size:15
Alignment explanation
Indices: 12214--12244 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
12204 ACAGATGAGA
12214 CCTCTTCATGAATAC
1 CCTCTTCATGAATAC
12229 CCTCTTCATGAATAC
1 CCTCTTCATGAATAC
12244 C
1 C
12245 AGGCTCTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.35, G:0.06, T:0.32
Consensus pattern (15 bp):
CCTCTTCATGAATAC
Found at i:21420 original size:9 final size:9
Alignment explanation
Indices: 21406--21430 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
21396 AGCATAACAA
21406 CTTCATCAT
1 CTTCATCAT
21415 CTTCATCAT
1 CTTCATCAT
21424 CTTCATC
1 CTTCATC
21431 TACAAGGTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.36, G:0.00, T:0.44
Consensus pattern (9 bp):
CTTCATCAT
Found at i:22565 original size:15 final size:15
Alignment explanation
Indices: 22545--22578 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
22535 CTCTTTTGAG
22545 TATTTACTCTTCCTC
1 TATTTACTCTTCCTC
22560 TATTTACTCTTCCTC
1 TATTTACTCTTCCTC
22575 TATT
1 TATT
22579 CATCAGAAGT
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:0.15, C:0.29, G:0.00, T:0.56
Consensus pattern (15 bp):
TATTTACTCTTCCTC
Found at i:24124 original size:57 final size:57
Alignment explanation
Indices: 24029--24160 Score: 169
Period size: 61 Copynumber: 2.3 Consensus size: 57
24019 CTGTGATTAT
* * *
24029 CAAGAACAGACTCATACGCAAACGAATAACTGCATACTT-AAA-AAAGGAAAAAAAA
1 CAAGAACAGACACATACGAAAACGAATAACTGCATACTTAAAAGAAAAGAAAAAAAA
*
24084 CAAGAACAGACACATACGAAATTACGAATAACTGTATACTTAGAAAAGAAAAGAAAAAAAA
1 CAAGAACAGACACATACGAAA--ACGAATAACTGCATACTT--AAAAGAAAAGAAAAAAAA
*
24145 CAAGAACAAACACATA
1 CAAGAACAGACACATA
24161 AGCACGAATT
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
55 19 0.29
57 17 0.26
60 3 0.05
61 27 0.41
ACGTcount: A:0.58, C:0.17, G:0.12, T:0.13
Consensus pattern (57 bp):
CAAGAACAGACACATACGAAAACGAATAACTGCATACTTAAAAGAAAAGAAAAAAAA
Found at i:24652 original size:21 final size:21
Alignment explanation
Indices: 24628--24667 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
24618 TATAATGTAA
* *
24628 ATTTCAGAATAATTAAATTAG
1 ATTTCAAAATAAATAAATTAG
24649 ATTTCAAAATAAATAAATT
1 ATTTCAAAATAAATAAATT
24668 TAATTATTTT
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:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (21 bp):
ATTTCAAAATAAATAAATTAG
Found at i:31182 original size:24 final size:24
Alignment explanation
Indices: 31155--31201 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
31145 TCGGAAAATA
* *
31155 AACTACTTTCCCCCTTTCTCTCAC
1 AACTACTCTCCCCCTCTCTCTCAC
* *
31179 AACTTCTCTCTCCCTCTCTCTCA
1 AACTACTCTCCCCCTCTCTCTCA
31202 TCCTTGACAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.15, C:0.47, G:0.00, T:0.38
Consensus pattern (24 bp):
AACTACTCTCCCCCTCTCTCTCAC
Found at i:31394 original size:38 final size:38
Alignment explanation
Indices: 31343--31423 Score: 162
Period size: 38 Copynumber: 2.1 Consensus size: 38
31333 CCTTATCCCT
31343 AATTAACTCAATAATCTCAGTCAACAACGAACGCTCAG
1 AATTAACTCAATAATCTCAGTCAACAACGAACGCTCAG
31381 AATTAACTCAATAATCTCAGTCAACAACGAACGCTCAG
1 AATTAACTCAATAATCTCAGTCAACAACGAACGCTCAG
31419 AATTA
1 AATTA
31424 GGACAACCAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.43, C:0.25, G:0.10, T:0.22
Consensus pattern (38 bp):
AATTAACTCAATAATCTCAGTCAACAACGAACGCTCAG
Found at i:40879 original size:2 final size:2
Alignment explanation
Indices: 40874--40915 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
40864 GAGTTGTGTG
40874 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
40916 ATGTGATAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41496 original size:32 final size:31
Alignment explanation
Indices: 41426--41575 Score: 171
Period size: 32 Copynumber: 4.8 Consensus size: 31
41416 GAGTCGAGGG
*
41426 TTACCTATG-TCTTTCGGAACATAT-AGATAGA
1 TTACCTATGTTC-TTCGGAACATATGACAT-GA
41457 TTACCTATGTTCTTCGGAACATATGAACATGA
1 TTACCTATGTTCTTCGGAACATATG-ACATGA
* *
41489 TTACCTATGTTCTTTGGAACATATGGACAGGA
1 TTACCTATGTTCTTCGGAACATAT-GACATGA
* * * * *
41521 TTACTTATGTTCTCCAGAACATATG-GATAA
1 TTACCTATGTTCTTCGGAACATATGACATGA
41551 TTACCTATGTTCTTCGGAACATATG
1 TTACCTATGTTCTTCGGAACATATG
41576 GATAGGTCAT
Statistics
Matches: 102, Mismatches: 13, Indels: 9
0.82 0.10 0.07
Matches are distributed among these distances:
30 24 0.24
31 22 0.22
32 52 0.51
33 4 0.04
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGAACATATGACATGA
Found at i:41573 original size:62 final size:62
Alignment explanation
Indices: 41426--41577 Score: 191
Period size: 62 Copynumber: 2.4 Consensus size: 62
41416 GAGTCGAGGG
* * * * *
41426 TTACCTATG-TCTTTCGGAACATATAGATAGATTACCTATGTTCTTCGGAACATATGAACATGA
1 TTACCTATGTTC-TTCGGAACATATGGACAGATTACCTATGTTCTCCAGAACATATG-ACATAA
* * *
41489 TTACCTATGTTCTTTGGAACATATGGACAGGATTACTTATGTTCTCCAGAACATATG-GATAA
1 TTACCTATGTTCTTCGGAACATATGGACA-GATTACCTATGTTCTCCAGAACATATGACATAA
41551 TTACCTATGTTCTTCGGAACATATGGA
1 TTACCTATGTTCTTCGGAACATATGGA
41578 TAGGTCATTC
Statistics
Matches: 78, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
62 29 0.37
63 23 0.29
64 26 0.33
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (62 bp):
TTACCTATGTTCTTCGGAACATATGGACAGATTACCTATGTTCTCCAGAACATATGACATAA
Found at i:46113 original size:32 final size:31
Alignment explanation
Indices: 46041--46192 Score: 211
Period size: 32 Copynumber: 4.9 Consensus size: 31
46031 GAGTCGAGGG
* *
46041 TTACCTATG-TCTTTCAGAACATATGGATAGA
1 TTACCTATGTTC-TTCGGAACATATGGACAGA
*
46072 TTACATATGTTCTTCGGAACATATGGACAGGA
1 TTACCTATGTTCTTCGGAACATATGGACA-GA
46104 TTACCTATGTTCTTCGGAACATATGGACATGA
1 TTACCTATGTTCTTCGGAACATATGGACA-GA
46136 TTACCTATGTTC-TCTGGAACATATGGACAG-
1 TTACCTATGTTCTTC-GGAACATATGGACAGA
*
46166 TTACCTATGTTATTCGGAACATATGGA
1 TTACCTATGTTCTTCGGAACATATGGA
46193 TAGGTCCTTC
Statistics
Matches: 111, Mismatches: 6, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
30 23 0.21
31 28 0.25
32 60 0.54
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGAACATATGGACAGA
Found at i:56360 original size:14 final size:15
Alignment explanation
Indices: 56328--56364 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
56318 TCGTTTAACT
56328 TATCATTTATATCTA
1 TATCATTTATATCTA
*
56343 TATCATTTAT-TTTA
1 TATCATTTATATCTA
56357 TATCATTT
1 TATCATTT
56365 TCTCTTGCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.30, C:0.11, G:0.00, T:0.59
Consensus pattern (15 bp):
TATCATTTATATCTA
Found at i:57053 original size:64 final size:64
Alignment explanation
Indices: 56920--57076 Score: 162
Period size: 64 Copynumber: 2.5 Consensus size: 64
56910 TAATGAAGGT
* * ** *
56920 ATGCATCGATGCAC-CACTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATTATTGGG
1 ATGCATCGATGCACTC-CTAATGCATCGATGCATAAAATGCATTCGATGTTGTATTATTAAAGAG
* * *
56984 ATGCATCGATGCACTCCTTATGCATCGATGCATTAATTGCATTCGATGTT-T-TTATCTTAAA-A
1 ATGCATCGATGCACTCCTAATGCATCGATGCATAAAATGCATTCGATGTTGTATTA--TTAAAGA
57046 G
64 G
57047 AGTGCATCGATGCACTACC-AATGCATCGAT
1 A-TGCATCGATGCACT-CCTAATGCATCGAT
57077 ACACCTTCAA
Statistics
Matches: 80, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
62 3 0.04
63 3 0.04
64 71 0.89
65 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTCCTAATGCATCGATGCATAAAATGCATTCGATGTTGTATTATTAAAGAG
Found at i:60143 original size:26 final size:25
Alignment explanation
Indices: 60114--60165 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 25
60104 TTTTATTTTT
*
60114 AATA-TTTTTAAATAATAATATTAAAA
1 AATAGTTTTTAAAAAAT-ATA-TAAAA
60140 AATAGTTTTTAAAAAATATATAAAA
1 AATAGTTTTTAAAAAATATATAAAA
60165 A
1 A
60166 TTCATAATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 6 0.25
26 7 0.29
27 11 0.46
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (25 bp):
AATAGTTTTTAAAAAATATATAAAA
Done.