Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002319.1 Hibiscus syriacus cultivar Beakdansim tig00004722_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: 53284
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:11554 original size:16 final size:15
Alignment explanation
Indices: 11521--11550 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11511 GTTAATGTCT
11521 AAACAAAAAAAAAAG
1 AAACAAAAAAAAAAG
*
11536 AAACAAAGAAAAAAG
1 AAACAAAAAAAAAAG
11551 GAAAGAGCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.07, G:0.10, T:0.00
Consensus pattern (15 bp):
AAACAAAAAAAAAAG
Found at i:14944 original size:64 final size:63
Alignment explanation
Indices: 14859--15019 Score: 175
Period size: 64 Copynumber: 2.5 Consensus size: 63
14849 TTGTTTAAGG
* * * *
14859 TGCATCGATGCACATGCAGTGCATCGATGCAT-TAATTTAAAAAGAAAACATC-AAGTAGGATTT
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCAA-TTAAAAA-AAAACATCGAA-TAGGATTT
14922 A
63 A
* * *
14923 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCAT-CCAATTAAAAAAAAACATCGAATAGGATTTA
*
14987 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
15020 ACCTTCATTA
Statistics
Matches: 84, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
63 1 0.01
64 59 0.70
65 23 0.27
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCAATTAAAAAAAAACATCGAATAGGATTTA
Found at i:16227 original size:31 final size:31
Alignment explanation
Indices: 16189--16278 Score: 89
Period size: 31 Copynumber: 3.0 Consensus size: 31
16179 TCGAGGGTTT
16189 TACCTATG-TCTTTCGAGACATATGGACAGTA
1 TACCTATGTTCTTT-GAGACATATGGACAGTA
** *
16220 TACCTATGTTCTAAG-GAACATATGGACA-TT
1 TACCTATGTTCTTTGAG-ACATATGGACAGTA
* *
16250 TACCTAGGTTCTTTG-GACCTATGGACAGT
1 TACCTATGTTCTTTGAGACATATGGACAGT
16279 TGCCGAGGTT
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
29 10 0.20
30 16 0.33
31 20 0.41
32 3 0.06
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (31 bp):
TACCTATGTTCTTTGAGACATATGGACAGTA
Found at i:16334 original size:29 final size:30
Alignment explanation
Indices: 16249--16336 Score: 99
Period size: 29 Copynumber: 3.0 Consensus size: 30
16239 ATATGGACAT
* * * *
16249 TTACCTAGGTTCTTTG-GACCTATGGACAG
1 TTACCGAGGGTCTTTGTGACCTCTGGATAG
* * *
16278 TTGCCGAGGTTCTTTATGACCTCTGGATAG
1 TTACCGAGGGTCTTTGTGACCTCTGGATAG
16308 TTACCG-GGGTCTTTGTGACCTCTGGATAG
1 TTACCGAGGGTCTTTGTGACCTCTGGATAG
16337 GTCTTTCGGG
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
29 34 0.68
30 16 0.32
ACGTcount: A:0.17, C:0.20, G:0.27, T:0.35
Consensus pattern (30 bp):
TTACCGAGGGTCTTTGTGACCTCTGGATAG
Found at i:20753 original size:16 final size:17
Alignment explanation
Indices: 20728--20761 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
20718 CTGAGGTGTC
20728 ACATTGACTTTT-CAAA
1 ACATTGACTTTTACAAA
*
20744 ACATTTACTTTTACAAA
1 ACATTGACTTTTACAAA
20761 A
1 A
20762 GAATGAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.41, C:0.18, G:0.03, T:0.38
Consensus pattern (17 bp):
ACATTGACTTTTACAAA
Found at i:21441 original size:21 final size:20
Alignment explanation
Indices: 21416--21465 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
21406 ACATAGAATT
21416 TGTCCCGAAAGACCACATATA
1 TGTCCCGAAAGACC-CATATA
*
21437 TGTCCCGAAGGACCCATATA
1 TGTCCCGAAAGACCCATATA
21457 TGTCCCGAA
1 TGTCCCGAA
21466 GAACCACTCC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.32, C:0.30, G:0.18, T:0.20
Consensus pattern (20 bp):
TGTCCCGAAAGACCCATATA
Found at i:21456 original size:20 final size:21
Alignment explanation
Indices: 21416--21573 Score: 89
Period size: 21 Copynumber: 7.9 Consensus size: 21
21406 ACATAGAATT
*
21416 TGTCCCGAAAGACCACATATA
1 TGTCCCGAAGGACCACATATA
21437 TGTCCCGAAGGACC-CATATA
1 TGTCCCGAAGGACCACATATA
*
21457 TGTCCCGAAGAACCAC-----
1 TGTCCCGAAGGACCACATATA
** *
21473 --TCCTTAAGGATCACATATA
1 TGTCCCGAAGGACCACATATA
* * * * * *
21492 TATTCCAAAGGATCAAATATG
1 TGTCCCGAAGGACCACATATA
* * *
21513 TGTTCCGAAGAACCGCATATA
1 TGTCCCGAAGGACCACATATA
* * **
21534 TGTTCCAAAGGATTACATATA
1 TGTCCCGAAGGACCACATATA
*
21555 TATCCCGAAGGACCACATA
1 TGTCCCGAAGGACCACATA
21574 GAACCCTCGA
Statistics
Matches: 101, Mismatches: 28, Indels: 16
0.70 0.19 0.11
Matches are distributed among these distances:
14 10 0.10
20 19 0.19
21 72 0.71
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (21 bp):
TGTCCCGAAGGACCACATATA
Found at i:21563 original size:42 final size:42
Alignment explanation
Indices: 21484--21573 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 42
21474 CCTTAAGGAT
* * *
21484 CACATATATATTCCAAAGGATCAAATATGTGTTCCGAAGAAC
1 CACATATATATTCCAAAGGATCAAATATATATCCCGAAGAAC
* * * * *
21526 CGCATATATGTTCCAAAGGATTACATATATATCCCGAAGGAC
1 CACATATATATTCCAAAGGATCAAATATATATCCCGAAGAAC
21568 CACATA
1 CACATA
21574 GAACCCTCGA
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.26
Consensus pattern (42 bp):
CACATATATATTCCAAAGGATCAAATATATATCCCGAAGAAC
Found at i:22379 original size:35 final size:35
Alignment explanation
Indices: 22317--22386 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
22307 CATCACAAGA
* *
22317 ATGGTATCGATACTTCCACATTGGTATCAATACCC
1 ATGGTACCGATACTTCCACATTAGTATCAATACCC
* *
22352 ATGGTACCGATACTAT-CACTTTAGTATCGATACCC
1 ATGGTACCGATACT-TCCACATTAGTATCAATACCC
22387 CATGAAGATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 29 0.97
36 1 0.03
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (35 bp):
ATGGTACCGATACTTCCACATTAGTATCAATACCC
Found at i:28292 original size:22 final size:22
Alignment explanation
Indices: 28260--28302 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
28250 ATATAAAAAA
28260 TTATTCTTTATTAAATATTTTTG
1 TTATTCTTTATTAAAT-TTTTTG
*
28283 TTATT-TTTATTTAATTTTTT
1 TTATTCTTTATTAAATTTTTT
28303 AAATAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 9 0.47
23 5 0.26
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (22 bp):
TTATTCTTTATTAAATTTTTTG
Found at i:36182 original size:14 final size:14
Alignment explanation
Indices: 36165--36215 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
36155 TGAACGTTCC
36165 GTTATGTTCGTTTG
1 GTTATGTTCGTTTG
36179 GTTATGTTCG--T-
1 GTTATGTTCGTTTG
*
36190 -TTATGTTCGTTCG
1 GTTATGTTCGTTTG
*
36203 ATTATGTTCGTTT
1 GTTATGTTCGTTT
36216 ATATTCATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
10 9 0.29
12 1 0.03
14 21 0.68
ACGTcount: A:0.10, C:0.10, G:0.24, T:0.57
Consensus pattern (14 bp):
GTTATGTTCGTTTG
Found at i:36187 original size:24 final size:25
Alignment explanation
Indices: 36160--36234 Score: 77
Period size: 24 Copynumber: 3.1 Consensus size: 25
36150 GTTCATGAAC
* *
36160 GTTCCG-TTATGTTCGTTTGGTTAT
1 GTTCCGTTTATGTTCGTTCGATTAT
36184 GTT-CGTTTATGTTCGTTCGATTAT
1 GTTCCGTTTATGTTCGTTCGATTAT
* *
36208 GTT-CGTTTATATTCATTC-ATTTAT
1 GTTCCGTTTATGTTCGTTCGA-TTAT
36232 GTT
1 GTT
36235 TAACCCAATC
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
23 3 0.07
24 42 0.93
ACGTcount: A:0.13, C:0.12, G:0.19, T:0.56
Consensus pattern (25 bp):
GTTCCGTTTATGTTCGTTCGATTAT
Found at i:36298 original size:14 final size:14
Alignment explanation
Indices: 36279--36317 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
36269 ATTTATAAGT
36279 ATCTTCTTAAACCA
1 ATCTTCTTAAACCA
*
36293 ATCTTCTTAAATCA
1 ATCTTCTTAAACCA
*
36307 ATATTCTTAAA
1 ATCTTCTTAAA
36318 TTAATCTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (14 bp):
ATCTTCTTAAACCA
Found at i:37001 original size:10 final size:10
Alignment explanation
Indices: 36986--37044 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
36976 GGGTCTCCAA
36986 CGTTTATGTT
1 CGTTTATGTT
36996 CGTTTATGTT
1 CGTTTATGTT
37006 CGTATTCAT-TT
1 CGT-TT-ATGTT
* **
37017 ATGTTCGTGTT
1 -CGTTTATGTT
37028 CGTTTATGTT
1 CGTTTATGTT
37038 CGTTTAT
1 CGTTTAT
37045 TTATTAAATG
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
10 28 0.72
11 7 0.18
12 4 0.10
ACGTcount: A:0.12, C:0.12, G:0.19, T:0.58
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:37019 original size:16 final size:15
Alignment explanation
Indices: 36998--37048 Score: 68
Period size: 16 Copynumber: 3.3 Consensus size: 15
36988 TTTATGTTCG
36998 TTTATGTTCGTATTCA
1 TTTATGTTCGT-TTCA
*
37014 TTTATGTTCGTGTTCG
1 TTTATGTTCGT-TTCA
37030 TTTATGTTCGTTT-A
1 TTTATGTTCGTTTCA
37044 TTTAT
1 TTTAT
37049 TAAATGAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
14 5 0.16
15 2 0.06
16 25 0.78
ACGTcount: A:0.14, C:0.10, G:0.16, T:0.61
Consensus pattern (15 bp):
TTTATGTTCGTTTCA
Found at i:37131 original size:16 final size:16
Alignment explanation
Indices: 37110--37142 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
37100 AAAAAAATTT
37110 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
37126 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
37142 T
1 T
37143 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:47886 original size:24 final size:24
Alignment explanation
Indices: 47851--47969 Score: 113
Period size: 24 Copynumber: 5.1 Consensus size: 24
47841 CAACTCATAT
*
47851 AATTTG-CACCGAAGTG-CCACGTAT
1 AATTTGTC-CCGAAG-GACCACGTAG
* *
47875 AATTTGTCCCGATGGACCGCGTAG
1 AATTTGTCCCGAAGGACCACGTAG
*
47899 AATTTGTCCCTAAGGACCACGTAG
1 AATTTGTCCCGAAGGACCACGTAG
* * *
47923 AA-TTATCCCGAAGGATCACATAG
1 AATTTGTCCCGAAGGACCACGTAG
*
47946 -A-TTGTCCCGAAGGACCGCGTAG
1 AATTTGTCCCGAAGGACCACGTAG
47968 AA
1 AA
47970 CCCTCAACTC
Statistics
Matches: 78, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
22 18 0.23
23 19 0.24
24 40 0.51
25 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.23
Consensus pattern (24 bp):
AATTTGTCCCGAAGGACCACGTAG
Found at i:48638 original size:20 final size:20
Alignment explanation
Indices: 48595--48646 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
48585 GCTTAAAAAT
* *
48595 GGTATCGATACCTTACTCTG
1 GGTATCGATACCTTACTATC
* *
48615 GGTATCGATACTTTCCTATC
1 GGTATCGATACCTTACTATC
*
48635 GGTATCGGTACC
1 GGTATCGATACC
48647 CCATCAATCA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.35
Consensus pattern (20 bp):
GGTATCGATACCTTACTATC
Done.