Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000660.1 Hibiscus syriacus cultivar Beakdansim tig00001285_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: 30758
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5077 original size:89 final size:89
Alignment explanation
Indices: 4967--5145 Score: 313
Period size: 89 Copynumber: 2.0 Consensus size: 89
4957 GCTAAAATCC
* *
4967 GAAGCCAAAAACACTGCAAAGTACACGACATAAGTTTAGACACAACTTACCAACACCCTCAGTAA
1 GAAGCCAAAAACACTGAAAAGTACACGACATAAGTTTAGACACAACTTACCAACACCCACAGTAA
5032 CGAGAATCACAGCAAACCTAGAGA
66 CGAGAATCACAGCAAACCTAGAGA
* * *
5056 GAAGCCAGAAACACTGAAAAGTACACGACATTAGTTTAGACACAACTTGCCAACACCCACAGTAA
1 GAAGCCAAAAACACTGAAAAGTACACGACATAAGTTTAGACACAACTTACCAACACCCACAGTAA
5121 CGAGAATCACAGCAAACCTAGAGA
66 CGAGAATCACAGCAAACCTAGAGA
5145 G
1 G
5146 TGCGGCGAAT
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
89 85 1.00
ACGTcount: A:0.44, C:0.26, G:0.16, T:0.13
Consensus pattern (89 bp):
GAAGCCAAAAACACTGAAAAGTACACGACATAAGTTTAGACACAACTTACCAACACCCACAGTAA
CGAGAATCACAGCAAACCTAGAGA
Found at i:7503 original size:15 final size:15
Alignment explanation
Indices: 7469--7506 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
7459 TTTTATCTTT
7469 TATTTTATTTTTAAAA
1 TATTTTATTTTT-AAA
7485 TATTTTAGTTTTT-AA
1 TATTTTA-TTTTTAAA
7500 TATTTTA
1 TATTTTA
7507 AATTTTGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 7 0.33
17 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (15 bp):
TATTTTATTTTTAAA
Found at i:8459 original size:20 final size:20
Alignment explanation
Indices: 8434--8476 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
8424 AACCACTCAT
8434 TATATTTTATTTCCAATCAA
1 TATATTTTATTTCCAATCAA
* *
8454 TATATTTTCTTTTCAATCAA
1 TATATTTTATTTCCAATCAA
8474 TAT
1 TAT
8477 CGTCTAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.14, G:0.00, T:0.53
Consensus pattern (20 bp):
TATATTTTATTTCCAATCAA
Found at i:9184 original size:27 final size:28
Alignment explanation
Indices: 9146--9201 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
9136 TGACTACATA
* *
9146 ACTTATCAACCAT-CAAAAACGTATATG
1 ACTTATCAACCATAAAAAAACATATATG
9173 ACTTATCAACCATAAAAAAACATATATG
1 ACTTATCAACCATAAAAAAACATATATG
9201 A
1 A
9202 TTCGTAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 13 0.50
28 13 0.50
ACGTcount: A:0.50, C:0.20, G:0.05, T:0.25
Consensus pattern (28 bp):
ACTTATCAACCATAAAAAAACATATATG
Found at i:15826 original size:9 final size:9
Alignment explanation
Indices: 15812--15857 Score: 56
Period size: 9 Copynumber: 5.0 Consensus size: 9
15802 TAAATTATCA
15812 ATAAAAAAT
1 ATAAAAAAT
*
15821 ATAAAAAAA
1 ATAAAAAAT
*
15830 ATATAAAAT
1 ATAAAAAAT
15839 ATAAAAGAAT
1 ATAAAA-AAT
*
15849 TTAAAAAAT
1 ATAAAAAAT
15858 TCAGAATACG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
9 23 0.74
10 8 0.26
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (9 bp):
ATAAAAAAT
Found at i:19282 original size:19 final size:19
Alignment explanation
Indices: 19258--19347 Score: 162
Period size: 19 Copynumber: 4.7 Consensus size: 19
19248 TGTTTATTTC
19258 ACGTAATTCGTTTTTCGGA
1 ACGTAATTCGTTTTTCGGA
*
19277 ACGTAATTCATTTTTCGGA
1 ACGTAATTCGTTTTTCGGA
19296 ACGTAATTCGTTTTTCGGA
1 ACGTAATTCGTTTTTCGGA
19315 ACGTAATTCGTTTTTCGGA
1 ACGTAATTCGTTTTTCGGA
*
19334 ACGTAATTCATTTT
1 ACGTAATTCGTTTT
19348 CCTAGTGACA
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 68 1.00
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (19 bp):
ACGTAATTCGTTTTTCGGA
Found at i:19565 original size:29 final size:28
Alignment explanation
Indices: 19532--19687 Score: 93
Period size: 27 Copynumber: 5.7 Consensus size: 28
19522 AAATATTTAA
19532 AATATATTTATTAATATTTATAATAATAT
1 AATATATTTATT-ATATTTATAATAATAT
*
19561 AATATTATATT-TT-TAGTT-TAATAATAT
1 AATA-TAT-TTATTATATTTATAATAATAT
*
19588 AATCA-ATTATATTATA---ATAATAAGAT
1 AAT-ATATT-TATTATATTTATAATAATAT
*
19614 ATTATATTT-TTAT-TTTAATAAT-ATAT
1 AATATATTTATTATATTT-ATAATAATAT
* * *
19640 AATAATTTTTTTTATATTTAATAATGA-AT
1 AAT-ATATTTATTATATTT-ATAATAATAT
19669 AATATTATTTA-TATATTTA
1 AATA-TATTTATTATATTTA
19688 AAACATATAC
Statistics
Matches: 102, Mismatches: 8, Indels: 36
0.70 0.05 0.25
Matches are distributed among these distances:
24 4 0.04
25 3 0.03
26 21 0.21
27 25 0.25
28 19 0.19
29 22 0.22
30 6 0.06
31 2 0.02
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (28 bp):
AATATATTTATTATATTTATAATAATAT
Found at i:19568 original size:26 final size:24
Alignment explanation
Indices: 19506--19568 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
19496 CATTTTCATC
19506 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
19530 AAAATATAT-TTATTAATAT-TTAT
1 AAAATATATATTATTAAAATATT-T
19553 AATAATATAATATTAT
1 AA-AATAT-ATATTAT
19569 ATTTTTAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 12 0.36
25 3 0.09
26 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:19661 original size:26 final size:28
Alignment explanation
Indices: 19595--19688 Score: 86
Period size: 28 Copynumber: 3.3 Consensus size: 28
19585 TATAATCAAT
* * *
19595 TATATTATAATAATAAGATATTA-TATTTT
1 TATATT-TAATAATGA-ATAATATTATTTA
* *
19624 TAT-TTTAATAAT-ATATAATAATTTTTTT
1 TATATTTAATAATGA-ATAAT-ATTATTTA
19652 TATATTTAATAATGAATAATATTATTTA
1 TATATTTAATAATGAATAATATTATTTA
19680 TATATTTAA
1 TATATTTAA
19689 AACATATACT
Statistics
Matches: 56, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
26 5 0.09
27 8 0.14
28 25 0.45
29 17 0.30
30 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (28 bp):
TATATTTAATAATGAATAATATTATTTA
Found at i:19722 original size:23 final size:23
Alignment explanation
Indices: 19681--19742 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
19671 TATTATTTAT
*
19681 ATATTTAAAACATATACTAGTAAAG
1 ATATTT-AAA-ATATACTAATAAAG
* *
19706 ATATTTAAAATATACTAATTAAT
1 ATATTTAAAATATACTAATAAAG
*
19729 ATTTTTAAAATATA
1 ATATTTAAAATATA
19743 ATATAACACT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 24 0.73
24 3 0.09
25 6 0.18
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (23 bp):
ATATTTAAAATATACTAATAAAG
Found at i:19861 original size:18 final size:20
Alignment explanation
Indices: 19834--19871 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
19824 TAATAAAATT
19834 ATAAAAAAA-TA-TTTAATA
1 ATAAAAAAATTATTTTAATA
*
19852 ATAAATAAATTATTTTAATA
1 ATAAAAAAATTATTTTAATA
19872 TTTTAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 2 0.12
20 7 0.41
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATAAAAAAATTATTTTAATA
Found at i:20044 original size:20 final size:20
Alignment explanation
Indices: 20019--20069 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
20009 TTTTCCAGAT
20019 ATTTTTCAGAAATGTAATTC
1 ATTTTTCAGAAATGTAATTC
*
20039 ATTTTTCAGAAATGTAATTT
1 ATTTTTCAGAAATGTAATTC
*
20059 ATTTTCCAGAA
1 ATTTTTCAGAA
20070 TTCAAATTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (20 bp):
ATTTTTCAGAAATGTAATTC
Found at i:20088 original size:15 final size:15
Alignment explanation
Indices: 20062--20133 Score: 110
Period size: 15 Copynumber: 4.9 Consensus size: 15
20052 GTAATTTATT
20062 TTCCAG-AATTCAAA
1 TTCCAGTAATTCAAA
**
20076 TTCCAGTAATTCATT
1 TTCCAGTAATTCAAA
20091 TTCCAGTAATTCAAA
1 TTCCAGTAATTCAAA
20106 TTCCAGTAATTCAAA
1 TTCCAGTAATTCAAA
*
20121 TTCCATTAATTCA
1 TTCCAGTAATTCA
20134 TTTTTCGAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
14 6 0.12
15 46 0.88
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.38
Consensus pattern (15 bp):
TTCCAGTAATTCAAA
Found at i:20104 original size:30 final size:30
Alignment explanation
Indices: 20052--20133 Score: 121
Period size: 30 Copynumber: 2.8 Consensus size: 30
20042 TTTCAGAAAT
*
20052 GTAATTTATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
20081 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
** *
20111 GTAATTCAAATTCCATTAATTCA
1 GTAATTCATTTTCCAGTAATTCA
20134 TTTTTCGAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
29 15 0.31
30 33 0.69
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.40
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:21761 original size:2 final size:2
Alignment explanation
Indices: 21756--21787 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
21746 TTTTTTTAAC
21756 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21788 TAGTGCGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22147 original size:21 final size:21
Alignment explanation
Indices: 22116--22172 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
22106 CCTAATATTG
22116 CAATG-TAAAATTAGGTGAAA
1 CAATGTTAAAATTAGGTGAAA
*
22136 CAATGTTAAAATTAGGTGCAA
1 CAATGTTAAAATTAGGTGAAA
*
22157 TAATGTTTGAAAATTA
1 CAATG-TT-AAAATTA
22173 AATGGGTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 5 0.16
21 18 0.56
22 2 0.06
23 7 0.22
ACGTcount: A:0.46, C:0.05, G:0.18, T:0.32
Consensus pattern (21 bp):
CAATGTTAAAATTAGGTGAAA
Found at i:26775 original size:21 final size:21
Alignment explanation
Indices: 26750--26797 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
26740 CCTAATATTG
26750 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
26771 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
26792 TAATGT
1 CAATGT
26798 TTGAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:27443 original size:29 final size:29
Alignment explanation
Indices: 27398--27455 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
27388 ATTGAGATAC
* *
27398 TTACCTCATACTTTAGTTGTTACATCTCA
1 TTACCTCATACTGTAGTTGTTACACCTCA
27427 TTACCTCATACTGTAGTTGTTACACCTCA
1 TTACCTCATACTGTAGTTGTTACACCTCA
27456 AAGAATCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.24, C:0.26, G:0.09, T:0.41
Consensus pattern (29 bp):
TTACCTCATACTGTAGTTGTTACACCTCA
Found at i:28281 original size:92 final size:95
Alignment explanation
Indices: 28124--28314 Score: 334
Period size: 92 Copynumber: 2.0 Consensus size: 95
28114 TATAAAAACT
* *
28124 TTGAGGTCCTCTACAACTCGTTTAGCGTAGAGAGATCTTCGTCCATTCGCCAGTTTAAACACTCT
1 TTGAGGTCCTCTACAACTCGTTTAGCATAGAGAGATCTTCGTCCATTCACCAGTTTAAACACTCT
28189 AATAATG-AAAAAAAA-A-TTAAAACTTAC
66 AATAATGAAAAAAAAATATTTAAAACTTAC
*
28216 TTGAGGTCCTCTACAACTCGTTTAGCATAGAGAGATCTTCGTCCATTCACCAGTTTAAATACTCT
1 TTGAGGTCCTCTACAACTCGTTTAGCATAGAGAGATCTTCGTCCATTCACCAGTTTAAACACTCT
28281 AATAATGAAAAAAAAATATTTAAAACTTAC
66 AATAATGAAAAAAAAATATTTAAAACTTAC
28311 TTGA
1 TTGA
28315 CCAACAAAAT
Statistics
Matches: 93, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
92 69 0.74
93 8 0.09
94 1 0.01
95 15 0.16
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (95 bp):
TTGAGGTCCTCTACAACTCGTTTAGCATAGAGAGATCTTCGTCCATTCACCAGTTTAAACACTCT
AATAATGAAAAAAAAATATTTAAAACTTAC
Found at i:29165 original size:16 final size:16
Alignment explanation
Indices: 29144--29176 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
29134 CTCCAAAATA
29144 AAACACATACATAATT
1 AAACACATACATAATT
29160 AAACACATACATAATT
1 AAACACATACATAATT
29176 A
1 A
29177 TAAAAAGCTA
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:0.58, C:0.18, G:0.00, T:0.24
Consensus pattern (16 bp):
AAACACATACATAATT
Found at i:29234 original size:9 final size:9
Alignment explanation
Indices: 29220--29290 Score: 52
Period size: 9 Copynumber: 8.7 Consensus size: 9
29210 GGTTTGTATT
29220 ATATAATTA
1 ATATAATTA
29229 ATATAA--A
1 ATATAATTA
29236 A-AT-ATT-
1 ATATAATTA
29242 ATAT-ATTA
1 ATATAATTA
29250 TATATAATTA
1 -ATATAATTA
29260 ATAT-A-TA
1 ATATAATTA
*
29267 AAAT-ATTA
1 ATATAATTA
29275 TATATAATTA
1 -ATATAATTA
29285 ATATAA
1 ATATAA
29291 AAAATAAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 18
0.72 0.03 0.25
Matches are distributed among these distances:
5 1 0.02
6 3 0.06
7 13 0.25
8 3 0.06
9 23 0.45
10 8 0.16
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
ATATAATTA
Found at i:29272 original size:25 final size:25
Alignment explanation
Indices: 29244--29296 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
29234 AAAATATTAT
*
29244 ATATTATATATAATTAATATATAAA
1 ATATTATATATAATTAATATAAAAA
29269 ATATTATATATAATTAATATAAAAA
1 ATATTATATATAATTAATATAAAAA
29294 ATA
1 ATA
29297 AAAAATATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
ATATTATATATAATTAATATAAAAA
Found at i:29304 original size:25 final size:25
Alignment explanation
Indices: 29251--29304 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
29241 TATATATTAT
* ** *
29251 ATATAATTAATATATAAAATATTAT
1 ATATAATTAATATAAAAAATAAAAA
29276 ATATAATTAATATAAAAAATAAAAA
1 ATATAATTAATATAAAAAATAAAAA
29301 ATAT
1 ATAT
29305 CATATATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (25 bp):
ATATAATTAATATAAAAAATAAAAA
Done.