Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002331.1 Hibiscus syriacus cultivar Beakdansim tig00004761_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: 57554
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Found at i:6668 original size:2 final size:2
Alignment explanation
Indices: 6661--6685 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6651 TTAATTTAAT
6661 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 T
6686 TACTTTAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8353 original size:20 final size:20
Alignment explanation
Indices: 8328--8367 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
8318 GGACGACCGG
8328 ATTTTTTA-CCGGATAAAAAA
1 ATTTTTTATCCGGA-AAAAAA
8348 ATTTTTTATCCGGAAAAAAA
1 ATTTTTTATCCGGAAAAAAA
8368 TCCGGTCTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (20 bp):
ATTTTTTATCCGGAAAAAAA
Found at i:13256 original size:18 final size:17
Alignment explanation
Indices: 13233--13282 Score: 59
Period size: 15 Copynumber: 3.0 Consensus size: 17
13223 AATTTAATAT
13233 TATATTATAATAATAAAA
1 TATATTAT-ATAATAAAA
13251 TATATTAT-T-ATAAAA
1 TATATTATATAATAAAA
**
13266 TATAAAATATAATAAAA
1 TATATTATATAATAAAA
13283 ATAATTTTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
15 12 0.43
16 2 0.07
17 6 0.21
18 8 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TATATTATATAATAAAA
Found at i:13256 original size:23 final size:22
Alignment explanation
Indices: 13235--13276 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
13225 TTTAATATTA
*
13235 TATTATAATA-ATAAAATATAT
1 TATTATAAAATATAAAATATAT
13256 TATTATAAAATATAAAATATA
1 TATTATAAAATATAAAATATA
13277 ATAAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TATTATAAAATATAAAATATAT
Found at i:31020 original size:124 final size:124
Alignment explanation
Indices: 30800--31049 Score: 401
Period size: 124 Copynumber: 2.0 Consensus size: 124
30790 GTTCAGTTGG
*
30800 TAGAGCGTGAGATTTTTAATCTTGTGATCGTAAGATCGAGTCCTACGATGGCAATTCATAAATTC
1 TAGAGCGTAAGATTTTTAATCTTGTGATCGTAAGATCGAGTCCTACGATGGCAATTCATAAATTC
* * * * * *
30865 TGACTGTCGAATGTCTCCTATGGAAACTACTCTCAACCTGGCCGGATAGCCTACTACTT
66 TAACTGTCGAAGGTCTCCCATAGAAACTACTCTCAACCTAGCCGGATAGCCTACTAATT
* * *
30924 TAGAGCGTAAGGTTTTTAATTTTGTGATCGTAAGATCGAGTCCTACGGTGGCAATTCATAAATTC
1 TAGAGCGTAAGATTTTTAATCTTGTGATCGTAAGATCGAGTCCTACGATGGCAATTCATAAATTC
*
30989 TAACTGTCGAAGGTCTCCCATAGAAACTACTCTCAACCTAGCCGGGTAGCCTACTAATT
66 TAACTGTCGAAGGTCTCCCATAGAAACTACTCTCAACCTAGCCGGATAGCCTACTAATT
31048 TA
1 TA
31050 CCTCTCTCTC
Statistics
Matches: 115, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
124 115 1.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (124 bp):
TAGAGCGTAAGATTTTTAATCTTGTGATCGTAAGATCGAGTCCTACGATGGCAATTCATAAATTC
TAACTGTCGAAGGTCTCCCATAGAAACTACTCTCAACCTAGCCGGATAGCCTACTAATT
Found at i:32143 original size:21 final size:21
Alignment explanation
Indices: 32098--32144 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
32088 AGTGCCCAAC
* *
32098 AATAACAAAATCGGTAGAAAA
1 AATAACAAAACCGATAGAAAA
32119 AATAACAAAACCGATA-AAAA
1 AATAACAAAACCGATAGAAAA
32139 TAATAA
1 -AATAA
32145 TGTTTTCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.66, C:0.11, G:0.09, T:0.15
Consensus pattern (21 bp):
AATAACAAAACCGATAGAAAA
Found at i:33718 original size:18 final size:19
Alignment explanation
Indices: 33695--33737 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
33685 GACCAGACCC
*
33695 AAAAAAA-TATTTTTATTA
1 AAAAAAATTATTTCTATTA
33713 AAAAAAATTATTTCTATTA
1 AAAAAAATTATTTCTATTA
33732 AAAAAA
1 AAAAAA
33738 GGATTTGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAAAAATTATTTCTATTA
Found at i:35361 original size:37 final size:37
Alignment explanation
Indices: 35288--35362 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 37
35278 GTTGAAAAAT
* *
35288 ATTTATATATTTTCTTTAAAAGATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAGATTGAAAATCATAAA
*
35325 ATTTATATAATTTTTTTTACAAA-ATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTA-AAAGATTGAAAATCATAAA
35362 A
1 A
35363 ATGTTTAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 14 0.42
38 16 0.48
39 3 0.09
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAGATTGAAAATCATAAA
Found at i:38900 original size:24 final size:24
Alignment explanation
Indices: 38847--38905 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
38837 TTTATTAAAA
38847 TATTATTTAAATATATAATATTATT
1 TATTA-TTAAATATATAATATTATT
*
38872 CATTATTAAATATATAA-ATT-TT
1 TATTATTAAATATATAATATTATT
*
38894 T-TTATTATATAT
1 TATTATTAAATAT
38906 TATTAAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 10 0.32
22 2 0.06
23 3 0.10
24 12 0.39
25 4 0.13
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (24 bp):
TATTATTAAATATATAATATTATT
Found at i:38973 original size:17 final size:17
Alignment explanation
Indices: 38929--38986 Score: 64
Period size: 17 Copynumber: 3.2 Consensus size: 17
38919 ATATAATATC
38929 TTATATTATTATAATATAA
1 TTATATTATTATAA-AT-A
38948 TTGATTATT-TTATATAATA
1 TT-A-TATTATTATA-AATA
38967 TTATATTATTATAAATA
1 TTATATTATTATAAATA
38984 TTA
1 TTA
38987 ATAAATAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
17 11 0.31
18 6 0.17
19 5 0.14
20 8 0.23
21 5 0.14
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
TTATATTATTATAAATA
Found at i:39234 original size:42 final size:42
Alignment explanation
Indices: 39176--39289 Score: 210
Period size: 42 Copynumber: 2.7 Consensus size: 42
39166 ATGAATTACA
* *
39176 TTCCGGAAAACTAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACACT
39218 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACACT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACACT
39260 TTCCGGAAAACGAATTACGTGAAACAAACA
1 TTCCGGAAAACGAATTACGTGAAACAAACA
39290 AGAGAATTCG
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.46, C:0.20, G:0.18, T:0.17
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACACT
Found at i:39450 original size:15 final size:15
Alignment explanation
Indices: 39426--39496 Score: 60
Period size: 15 Copynumber: 4.8 Consensus size: 15
39416 ATACTATTAA
*
39426 ATTAATTTATAAAAT
1 ATTAAATTATAAAAT
39441 ATTAAATTATAAAAT
1 ATTAAATTATAAAAT
* *
39456 ACTAAATGTAT-AATT
1 ATTAAAT-TATAAAAT
39471 A-TAAATTAGTTAAAAT
1 ATTAAATTA--TAAAAT
39487 -TTAAA-TATAA
1 ATTAAATTATAA
39497 TTTAATTAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
13 5 0.11
14 5 0.11
15 27 0.57
16 10 0.21
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (15 bp):
ATTAAATTATAAAAT
Found at i:47933 original size:22 final size:23
Alignment explanation
Indices: 47891--47933 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
47881 GCCAAGAAAA
*
47891 CAAACTGTTGTATCCATTTTAAT
1 CAAACTGTTGTATCAATTTTAAT
47914 CAAA-TGTTGT-TCAATGTTTA
1 CAAACTGTTGTATCAAT-TTTA
47934 CAAACTAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 4 0.22
22 10 0.56
23 4 0.22
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (23 bp):
CAAACTGTTGTATCAATTTTAAT
Found at i:52256 original size:22 final size:21
Alignment explanation
Indices: 52227--52272 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 21
52217 CCAAGAAAAG
*
52227 ATTCTTGCTAAGGAGTCTATC
1 ATTCTTGCTAAGGAGTCTAAC
52248 ATTCATTGCTAAGGAGTCTAAC
1 ATTC-TTGCTAAGGAGTCTAAC
52270 ATT
1 ATT
52273 TAGCAAAGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.37
Consensus pattern (21 bp):
ATTCTTGCTAAGGAGTCTAAC
Found at i:57011 original size:19 final size:19
Alignment explanation
Indices: 56987--57057 Score: 90
Period size: 19 Copynumber: 3.8 Consensus size: 19
56977 TCAACTATGA
**
56987 TCAAAGTCAACGGGTCATG
1 TCAAAGTCAACGGGTCGGG
*
57006 TCAAAGTCAATGGGTCGGG
1 TCAAAGTCAACGGGTCGGG
* *
57025 TC-AAGTTAACAGGTCGGG
1 TCAAAGTCAACGGGTCGGG
57043 TCAAAGTCAACGGGT
1 TCAAAGTCAACGGGT
57058 AAGTTCAGTT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
18 15 0.35
19 28 0.65
ACGTcount: A:0.30, C:0.18, G:0.31, T:0.21
Consensus pattern (19 bp):
TCAAAGTCAACGGGTCGGG
Done.