Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005884.1 Hibiscus syriacus cultivar Beakdansim tig00013817_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: 63431
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:10908 original size:21 final size:21
Alignment explanation
Indices: 10878--10938 Score: 95
Period size: 21 Copynumber: 2.9 Consensus size: 21
10868 ACTATTTAGC
*
10878 CTTTTTACTTTTTCCATCAAT
1 CTTTTAACTTTTTCCATCAAT
10899 CTTTTAACTTTTTCCATCAAT
1 CTTTTAACTTTTTCCATCAAT
* *
10920 CTTTTAATTTTTTCAATCA
1 CTTTTAACTTTTTCCATCA
10939 CACCACATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.23, C:0.21, G:0.00, T:0.56
Consensus pattern (21 bp):
CTTTTAACTTTTTCCATCAAT
Found at i:15780 original size:20 final size:20
Alignment explanation
Indices: 15758--15835 Score: 56
Period size: 20 Copynumber: 3.9 Consensus size: 20
15748 TATAAGATAA
15758 TTATT-AAAT-TTATTAAA-
1 TTATTAAAATATTATTAAAT
*
15775 ATATTACAAAATATATATTAAAT
1 TTATTA--AAATAT-TATTAAAT
* *
15798 TTTTTAAAATATTATTATAT
1 TTATTAAAATATTATTAAAT
*
15818 TTA-TAAAAAATTGATTAA
1 TTATTAAAATATT-ATTAA
15836 TTTGATATAA
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
17 4 0.09
19 8 0.17
20 17 0.36
21 7 0.15
22 7 0.15
23 4 0.09
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (20 bp):
TTATTAAAATATTATTAAAT
Found at i:15824 original size:19 final size:18
Alignment explanation
Indices: 15782--15838 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 18
15772 AAAATATTAC
*
15782 AAAATATATATTAAATTTTTT
1 AAAATAT-TATT-AA-TTTAT
15803 AAAATATTATTATATTTAT
1 AAAATATTATTA-ATTTAT
*
15822 AAAAAATTGATTAATTT
1 AAAATATT-ATTAATTT
15839 GATATAAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 16 0.50
20 9 0.28
21 7 0.22
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
AAAATATTATTAATTTAT
Found at i:20893 original size:6 final size:6
Alignment explanation
Indices: 20882--20908 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
20872 TAGAACATAC
20882 ATTCAT ATTCAT ATTCAT ATTCAT ATT
1 ATTCAT ATTCAT ATTCAT ATTCAT ATT
20909 ACGTGTTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.52
Consensus pattern (6 bp):
ATTCAT
Found at i:21737 original size:20 final size:20
Alignment explanation
Indices: 21699--21738 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
21689 TAATTCAAAT
*
21699 TAATTATAAACCAAATATTA
1 TAATTATAAACAAAATATTA
21719 TAATTATAAA-AAAATTATTA
1 TAATTATAAACAAAA-TATTA
21739 ATTATTTCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
TAATTATAAACAAAATATTA
Found at i:21742 original size:18 final size:20
Alignment explanation
Indices: 21697--21743 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
21687 CTTAATTCAA
21697 ATTAATTATAAACCAAATATT
1 ATTAATTATAAA-CAAATATT
21718 A-TAATTATAAA-AAA-ATT
1 ATTAATTATAAACAAATATT
21735 ATTAATTAT
1 ATTAATTAT
21744 TTCCTTGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 4 0.16
18 10 0.40
20 10 0.40
21 1 0.04
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (20 bp):
ATTAATTATAAACAAATATT
Found at i:22044 original size:36 final size:36
Alignment explanation
Indices: 21994--22069 Score: 118
Period size: 37 Copynumber: 2.1 Consensus size: 36
21984 AAAATAACGT
*
21994 TAAATTTTGAACGGG-TATTAAAATGAAACAAAAAC
1 TAAATTTTGAACGGGATACTAAAATGAAACAAAAAC
*
22029 TAAAGTTTTTAACGGGATACTAAAATGAAACAAAAAC
1 TAAA-TTTTGAACGGGATACTAAAATGAAACAAAAAC
22066 TAAA
1 TAAA
22070 CTTTAGATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 4 0.11
36 10 0.27
37 23 0.62
ACGTcount: A:0.53, C:0.09, G:0.13, T:0.25
Consensus pattern (36 bp):
TAAATTTTGAACGGGATACTAAAATGAAACAAAAAC
Found at i:24111 original size:158 final size:156
Alignment explanation
Indices: 23677--24143 Score: 632
Period size: 158 Copynumber: 3.0 Consensus size: 156
23667 CATGATAATA
* ** *
23677 AATTTTTTATTTTTCAATTTAGTCCTTAATTTTTCATAATTTCGTTATTTAGTCAATACATCATT
1 AATTTTTTATTTTTCAATTTAGTCCTTAATTTTTCATAATTTCCTTATTTCTTCAATTCATCATT
* * * * *
23742 TATTTTAAGTCCCCTTTTTACCAAATTTGAATCACATGCTCATATACCACAATAGAATACCTATG
66 TATTTTAAGTCGCTTTTTTACCAAATTTGAACCACATGCTCATATACAACAATAGAATAACTATG
* * *
23807 TAACTTCAATTCATCTTTTTGATAAT
131 TAACTTCAATTCCTCTTTTTAACAAT
* * *
23833 AATTTTTTATTTTTCAATTTAGTCCCTTAATTTTTTTATAATTTCTTTATTTCTTCAATTCATCC
1 AATTTTTTATTTTTCAATTTAGT-CCTTAA-TTTTTCATAATTTCCTTATTTCTTCAATTCATCA
* **
23898 TTTATTTTAAGTTTG-TTCTTTTACCAAATTTGAACTGCATGCTCATATACAACAATAGAATAAC
64 TTTATTTTAAG-TCGCTT-TTTTACCAAATTTGAACCACATGCTCATATACAACAATAGAATAAC
23962 TATGTAACTTCAATTCCTCTTTTTAACAAT
127 TATGTAACTTCAATTCCTCTTTTTAACAAT
* * *
23992 AGTTTTTTATTTTTCAATTTAGTCTCTCAAATTTTCATAATTTCCTTATTTCTTCAATTCATCAT
1 AATTTTTTATTTTTCAATTTAGTC-CTTAATTTTTCATAATTTCCTTATTTCTTCAATTCATCAT
* * *
24057 TTATTTTCAGTACGCTTTTTTACCAAATTTGAACCACATGCTCATATACTACAATAGAAT-ATTA
65 TTATTTTAAGT-CGCTTTTTTACCAAATTTGAACCACATGCTCATATACAACAATAGAATAACTA
*
24121 TGTAACTTCAATTTCTACTTTTT
129 TGTAACTTCAATTCCT-CTTTTT
24144 TTAAAAAAAT
Statistics
Matches: 273, Mismatches: 30, Indels: 14
0.86 0.09 0.04
Matches are distributed among these distances:
156 23 0.08
157 25 0.09
158 128 0.47
159 97 0.36
ACGTcount: A:0.29, C:0.17, G:0.05, T:0.48
Consensus pattern (156 bp):
AATTTTTTATTTTTCAATTTAGTCCTTAATTTTTCATAATTTCCTTATTTCTTCAATTCATCATT
TATTTTAAGTCGCTTTTTTACCAAATTTGAACCACATGCTCATATACAACAATAGAATAACTATG
TAACTTCAATTCCTCTTTTTAACAAT
Found at i:24349 original size:2 final size:2
Alignment explanation
Indices: 24342--24380 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
24332 TATGAAACGA
24342 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 A
24381 GAAAAAGTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:31739 original size:17 final size:18
Alignment explanation
Indices: 31702--31742 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
31692 ATATTATGTA
*
31702 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
31720 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
31737 TTTACT
1 TTTACT
31743 AATATAGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:34020 original size:26 final size:25
Alignment explanation
Indices: 33934--34020 Score: 67
Period size: 25 Copynumber: 3.5 Consensus size: 25
33924 ATAGATTTTT
* *
33934 TTTTATTATATTT-ATATTTACTTTA
1 TTTTGTTAAATTTAATA-TTACTTTA
33959 TTTTGTTAAATTGTAAT-TT--TTTA
1 TTTTGTTAAATT-TAATATTACTTTA
* *
33982 TTATT-TCACATTTAATACTTACTTTA
1 TT-TTGTTAAATTTAATA-TTACTTTA
34008 TTTTGTTAAATTT
1 TTTTGTTAAATTT
34021 GTTAGACTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 15
0.70 0.09 0.22
Matches are distributed among these distances:
22 4 0.08
23 11 0.23
24 4 0.08
25 14 0.29
26 13 0.27
27 2 0.04
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.63
Consensus pattern (25 bp):
TTTTGTTAAATTTAATATTACTTTA
Found at i:37730 original size:40 final size:41
Alignment explanation
Indices: 37669--37777 Score: 166
Period size: 41 Copynumber: 2.7 Consensus size: 41
37659 CGCGATCGCA
**
37669 CTATAGCCCTACGTGGGGTATAGCGCGG-CCCTGATCCGCG
1 CTATAGCCCTACGTGACGTATAGCGCGGCCCCTGATCCGCG
* *
37709 CTATAGCCCTACATGACGTATAGTGCGGCCCCTGATCCGCG
1 CTATAGCCCTACGTGACGTATAGCGCGGCCCCTGATCCGCG
*
37750 CTATACCCCTACGTGACGTATAGCGCGG
1 CTATAGCCCTACGTGACGTATAGCGCGG
37778 ATCAGGGGGC
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
40 24 0.39
41 37 0.61
ACGTcount: A:0.18, C:0.33, G:0.28, T:0.21
Consensus pattern (41 bp):
CTATAGCCCTACGTGACGTATAGCGCGGCCCCTGATCCGCG
Found at i:41322 original size:18 final size:19
Alignment explanation
Indices: 41288--41323 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
41278 ATTTGGGAAT
*
41288 AAAATTAATTGAGTTTAAA
1 AAAATTAATGGAGTTTAAA
41307 AAAATTAATGGA-TTTAA
1 AAAATTAATGGAGTTTAA
41324 GGTTAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.36
Consensus pattern (19 bp):
AAAATTAATGGAGTTTAAA
Done.