Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008326.1 Hibiscus syriacus cultivar Beakdansim tig00111030_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: 69586
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:2912 original size:20 final size:21
Alignment explanation
Indices: 2887--2935 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
2877 ATCCTATTCC
2887 CTGGTAATATTTTA-TTCCCA
1 CTGGTAATATTTTATTTCCCA
* *
2907 CTGGTAATCTTTTATTTCTCA
1 CTGGTAATATTTTATTTCCCA
2928 CTGGTAAT
1 CTGGTAAT
2936 CTTACATTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.22, C:0.18, G:0.12, T:0.47
Consensus pattern (21 bp):
CTGGTAATATTTTATTTCCCA
Found at i:2931 original size:21 final size:20
Alignment explanation
Indices: 2887--2938 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 20
2877 ATCCTATTCC
*
2887 CTGGTAATATTTTATTCCCA
1 CTGGTAATCTTTTATTCCCA
*
2907 CTGGTAATCTTTTATTTCTCA
1 CTGGTAATCTTTTA-TTCCCA
2928 CTGGTAATCTT
1 CTGGTAATCTT
2939 ACATTCCGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.21, C:0.19, G:0.12, T:0.48
Consensus pattern (20 bp):
CTGGTAATCTTTTATTCCCA
Found at i:14918 original size:64 final size:64
Alignment explanation
Indices: 14850--14971 Score: 165
Period size: 64 Copynumber: 1.9 Consensus size: 64
14840 ATTGTTCAAG
* * * *
14850 GTGTATCGATGCACATGAAGT-CTATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATCA
1 GTGTATCGATGAACAAGAAGTGC-ATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCATCA
* * *
14914 GTGTATCGATGAACAAGTAGTGCGTCGATGCACCCCCTTAAAATACAAACATCGAATG
1 GTGTATCGATGAACAAGAAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATG
14972 ATATTTATGT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
64 49 0.98
65 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (64 bp):
GTGTATCGATGAACAAGAAGTGCATCGATGCACCCCCTTAAAATAAAAACATCGAATGCCATCA
Found at i:14988 original size:64 final size:64
Alignment explanation
Indices: 14873--15012 Score: 160
Period size: 64 Copynumber: 2.2 Consensus size: 64
14863 CATGAAGTCT
* * * *
14873 ATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATCAGTGTATCGATGAACA-AG-TAGTG
1 ATCGATGCACCCCCTTAAAATAAAAACATCGAATGACATCAGTGTACCGATG--CATAGATAGTG
14936 C
64 C
* * * *
14937 GTCGATGCACCCCCTTAAAATACAAACATCGAATGATATTTA-TGTACCGATGCATAGATAGTGC
1 ATCGATGCACCCCCTTAAAATAAAAACATCGAATGACA-TCAGTGTACCGATGCATAGATAGTGC
15001 ATCGATGCACCC
1 ATCGATGCACCC
15013 GTCAAGGGAT
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
62 2 0.03
63 2 0.03
64 58 0.91
65 2 0.03
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (64 bp):
ATCGATGCACCCCCTTAAAATAAAAACATCGAATGACATCAGTGTACCGATGCATAGATAGTGC
Found at i:15691 original size:23 final size:23
Alignment explanation
Indices: 15656--15714 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
15646 ATCTTATATA
* *
15656 GCACTACGATGCAATTCTACGTG
1 GCACTTCGGTGCAATTCTACGTG
15679 GCACTTCGGTGCAATTCTACGTG
1 GCACTTCGGTGCAATTCTACGTG
15702 GCACTTCGGTGCA
1 GCACTTCGGTGCA
15715 TTTATATGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.27
Consensus pattern (23 bp):
GCACTTCGGTGCAATTCTACGTG
Found at i:21901 original size:64 final size:64
Alignment explanation
Indices: 21833--21995 Score: 170
Period size: 64 Copynumber: 2.5 Consensus size: 64
21823 ATTGTTCAAG
* * *
21833 GTGTATCGATGCACATGAAGTGTATCGATGCA-CTACTATAAAATAAAAACATCGAATGCCATCA
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCCACT-TAAAATAAAAACATCGAATGCCATCA
* * * * ** *
21897 GTGTATCGATGCTCAAGTAGTGCATCGATGCACCCCCTTAAAATACAAACATCGAATGGGATTTA
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCCACTTAAAATAAAAACATCGAATGCCA-TCA
* *
21962 -TGTACCGATGCA-TAGATAGTGCATCGATGCACCC
1 GTGTATCGATGCACAAGA-AGTGCATCGATGCACCC
21996 GTCAAGGGAT
Statistics
Matches: 82, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
63 2 0.02
64 75 0.91
65 5 0.06
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (64 bp):
GTGTATCGATGCACAAGAAGTGCATCGATGCACCCACTTAAAATAAAAACATCGAATGCCATCA
Found at i:22672 original size:23 final size:23
Alignment explanation
Indices: 22646--22690 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
22636 ATAGCACTAC
*
22646 GGTGCAATTCTATGTGGCACTTT
1 GGTGCAATTCTACGTGGCACTTT
22669 GGTGCAATTCTACGTGGCACTT
1 GGTGCAATTCTACGTGGCACTT
22691 CAGTGCATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.36
Consensus pattern (23 bp):
GGTGCAATTCTACGTGGCACTTT
Found at i:22696 original size:23 final size:23
Alignment explanation
Indices: 22647--22697 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
22637 TAGCACTACG
* **
22647 GTGCAATTCTATGTGGCACTTTG
1 GTGCAATTCTACGTGGCACTTCA
22670 GTGCAATTCTACGTGGCACTTCA
1 GTGCAATTCTACGTGGCACTTCA
22693 GTGCA
1 GTGCA
22698 TTTATGTGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.33
Consensus pattern (23 bp):
GTGCAATTCTACGTGGCACTTCA
Found at i:27692 original size:20 final size:20
Alignment explanation
Indices: 27652--27718 Score: 80
Period size: 20 Copynumber: 3.3 Consensus size: 20
27642 ATGCTCACTA
* **
27652 ATTTTTCAAATTGGTCATTT
1 ATTTTTTAAATTGACCATTT
*
27672 ATTTTTTAAATTGACCTTTT
1 ATTTTTTAAATTGACCATTT
*
27692 AATTTTTTAAATTGACCACTT
1 -ATTTTTTAAATTGACCATTT
27713 ATTTTT
1 ATTTTT
27719 CCTTTTCAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
20 22 0.55
21 18 0.45
ACGTcount: A:0.27, C:0.10, G:0.06, T:0.57
Consensus pattern (20 bp):
ATTTTTTAAATTGACCATTT
Found at i:44688 original size:8 final size:8
Alignment explanation
Indices: 44653--44690 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
44643 TTATTTCACT
44653 TATATGT-
1 TATATGTA
44660 TATAT-TA
1 TATATGTA
*
44667 TATATATA
1 TATATGTA
44675 TATATGTA
1 TATATGTA
44683 TATATGTA
1 TATATGTA
44691 CACATTTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
6 1 0.04
7 10 0.36
8 17 0.61
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (8 bp):
TATATGTA
Found at i:44926 original size:184 final size:197
Alignment explanation
Indices: 44539--44932 Score: 580
Period size: 206 Copynumber: 2.0 Consensus size: 197
44529 TTCTCGGGAT
*
44539 ATTAGTTTTAATTATCTTTTTATATTACATTATAATATTTATATATATTTTATATTATTATTTTT
1 ATTAGTTTTAATTATCTTTTTATATTACATTATAATATTTATATATATTTTATATTACTA----T
* * *
44604 TTTTTTACACATTCGTATATATTTATTATTAGTATATTATTATTTCACTTATATGTTATATTATA
62 TTTTTTA-ACATTCGTATACATTTATTATTAGTATAGTATTATTTCACTTATA--TTATAGTATA
44669 TATATATATATGTATATATGTACACATTTTGTATTTTACCCTATTTTTTTACTTCTTTATTATTA
124 TATATATATA-GTATATATGTACACATTTTGTATTTTACCCTA-TTTTTTACTTCTTTATTATTA
44734 TATTTATTTAC
187 TATTTATTTAC
44745 ATTAGTTTTAATTATCTTTTTATATTACATTATAATATTTATATATA-TTT-TA-TACTA-TTTT
1 ATTAGTTTTAATTATCTTTTTATATTACATTATAATATTTATATATATTTTATATTACTATTTTT
44806 TT-ACATTCGTATACATTTATTATTAGTATAGTATTATTTCA-TT-TA-TAT-GT-TATAT-TAT
66 TTAACATTCGTATACATTTATTATTAGTATAGTATTATTTCACTTATATTATAGTATATATATAT
44864 ATA-TATATATGTACACATTTTGTATTTTACCCTA-TTTTTACTTCTTTATTATTATATTTATTT
131 ATAGTATATATGTACACATTTTGTATTTTACCCTATTTTTTACTTCTTTATTATTATATTTATTT
44927 AC
196 AC
44929 ATTA
1 ATTA
44933 TTTATTTTTT
Statistics
Matches: 184, Mismatches: 4, Indels: 22
0.88 0.02 0.10
Matches are distributed among these distances:
184 35 0.19
186 31 0.17
188 6 0.03
189 5 0.03
190 1 0.01
191 3 0.02
194 2 0.01
195 2 0.01
196 37 0.20
198 6 0.03
203 4 0.02
204 2 0.01
205 3 0.02
206 47 0.26
ACGTcount: A:0.30, C:0.08, G:0.04, T:0.58
Consensus pattern (197 bp):
ATTAGTTTTAATTATCTTTTTATATTACATTATAATATTTATATATATTTTATATTACTATTTTT
TTAACATTCGTATACATTTATTATTAGTATAGTATTATTTCACTTATATTATAGTATATATATAT
ATAGTATATATGTACACATTTTGTATTTTACCCTATTTTTTACTTCTTTATTATTATATTTATTT
AC
Found at i:56663 original size:105 final size:105
Alignment explanation
Indices: 56481--57250 Score: 1270
Period size: 105 Copynumber: 7.4 Consensus size: 105
56471 CAGGTTTTAC
56481 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
*
56546 GACGAAAGGACCGCTGGTTGTCAACGAACATTTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATT
56586 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
56651 GACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATT
56691 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
56756 GACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATT
56796 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
56861 GACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATT
* *
56901 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
* * * *
56966 GACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCCAATC
66 GACGAAGGGACCGCTGGTTGTCAACGAAC-ATTTCTCAATT
* *
57006 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
* * *
57071 GACGAAGGGACCGCTGCTTGTC-AC-AACGACTTCCCAATCT
66 GACGAAGGGACCGCTGGTTGTCAACGAAC-ATTTCTCAAT-T
* *
57111 T-AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTTAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
* *
57175 GACGAAGGGACCGCTGCTTGTCAAC-AA-AATT-TC-A-T
66 GACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATT
** * *
57210 TCAGATTCAATTTCAACTTCACAACGAAGGACATCGGACTC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
57251 GGAACAACAC
Statistics
Matches: 642, Mismatches: 19, Indels: 13
0.95 0.03 0.02
Matches are distributed among these distances:
99 2 0.00
100 35 0.05
101 1 0.00
102 1 0.00
103 3 0.00
104 101 0.16
105 499 0.78
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (105 bp):
TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
GACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATT
Found at i:58760 original size:8 final size:8
Alignment explanation
Indices: 58725--58762 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
58715 TTATTTCACT
58725 TATATGT-
1 TATATGTA
58732 TATAT-TA
1 TATATGTA
*
58739 TATATATA
1 TATATGTA
58747 TATATGTA
1 TATATGTA
58755 TATATGTA
1 TATATGTA
58763 CACATTTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
6 1 0.04
7 10 0.36
8 17 0.61
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (8 bp):
TATATGTA
Found at i:59023 original size:19 final size:20
Alignment explanation
Indices: 58977--59038 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 20
58967 CTATTTTTAC
58977 TTCT-TTATTATTATATTTAT
1 TTCTATTATTATTATATTT-T
58997 TTAC-ATTATTTATT-T-TTTT
1 TT-CTATTA-TTATTATATTTT
59016 TTCTATTATTATTATATTTT
1 TTCTATTATTATTATATTTT
59036 TTC
1 TTC
59039 CTCCCTCTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
18 6 0.17
19 8 0.22
20 12 0.33
21 5 0.14
22 5 0.14
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (20 bp):
TTCTATTATTATTATATTTT
Found at i:59035 original size:22 final size:22
Alignment explanation
Indices: 58968--59037 Score: 69
Period size: 22 Copynumber: 3.4 Consensus size: 22
58958 TATTTTACCC
*
58968 TATTTTTACTTCT-TTATTATTA
1 TATTTTT-TTTCTATTATTATTA
* *
58990 TATTTATTTAC-ATTA-T-TTA
1 TATTTTTTTTCTATTATTATTA
59009 T-TTTTTTTTCTATTATTATTA
1 TATTTTTTTTCTATTATTATTA
59030 TATTTTTT
1 TATTTTTT
59038 CCTCCCTCTT
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
18 7 0.18
19 8 0.21
20 2 0.05
21 9 0.24
22 12 0.32
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (22 bp):
TATTTTTTTTCTATTATTATTA
Done.