Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008678.1 Hibiscus syriacus cultivar Beakdansim tig00111697_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: 34442
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:3172 original size:45 final size:45
Alignment explanation
Indices: 2995--3172 Score: 234
Period size: 45 Copynumber: 3.9 Consensus size: 45
2985 CTTCATACTT
* * *
2995 ATAATGCA-CCATTATGCATTTTCATTTATGGCATTCTTTCATACCA
1 ATAATGCACCCA-TATGCA-TTTCATTTATGGCATCCTTTCATGCCG
* *
3041 ATAATGCACCTATATGCATTTCAATTATGGCA-CCATTTCATGCCG
1 ATAATGCACCCATATGCATTTCATTTATGGCATCC-TTTCATGCCG
* * * *
3086 ATAATGCATCCACATGCATTTCATTTATGGAATCATTTCATGCCG
1 ATAATGCACCCATATGCATTTCATTTATGGCATCCTTTCATGCCG
3131 ATAATGCACCCATATGCATTTCATTTATGGCATCCTTTCATG
1 ATAATGCACCCATATGCATTTCATTTATGGCATCCTTTCATG
3173 TCCTTTTTTA
Statistics
Matches: 114, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
44 1 0.01
45 96 0.84
46 15 0.13
47 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.37
Consensus pattern (45 bp):
ATAATGCACCCATATGCATTTCATTTATGGCATCCTTTCATGCCG
Found at i:3239 original size:43 final size:44
Alignment explanation
Indices: 3147--3268 Score: 165
Period size: 44 Copynumber: 2.7 Consensus size: 44
3137 CACCCATATG
* *
3147 CATTTCATTTATGGCATCCTTTCATGTCCTTTTTTATACACTATTATA
1 CATTTCATTTATGACATACTTTCATG-CC---TTTATACACTATTATA
3195 CA-TTCATTTATGACATACTTTCATGCCTTTATACACTATTATA
1 CATTTCATTTATGACATACTTTCATGCCTTTATACACTATTATA
* *
3238 CATTTCATTTGTGACATATTTTCATGCCTTT
1 CATTTCATTTATGACATACTTTCATGCCTTT
3269 CATCTAACTG
Statistics
Matches: 69, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
43 18 0.26
44 26 0.38
46 2 0.03
47 21 0.30
48 2 0.03
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.48
Consensus pattern (44 bp):
CATTTCATTTATGACATACTTTCATGCCTTTATACACTATTATA
Found at i:3372 original size:68 final size:68
Alignment explanation
Indices: 3263--3659 Score: 638
Period size: 68 Copynumber: 5.9 Consensus size: 68
3253 ATATTTTCAT
* *
3263 GCCTTTCATCTAACTGGCATAATTGAAACATTTCTGTCAAATGCACAGCTAGGCCTCAAAGGCAC
1 GCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAACTAGGCCTCAAAGGCAC
3328 TTA
66 TTA
* *
3331 GCCTTTCATCTAGCTGACATAATTGACACATTTCTGTCAAATGCACAACTAGGCCTCAAAGGCAC
1 GCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAACTAGGCCTCAAAGGCAC
3396 TTA
66 TTA
*** *
3399 GCCTTTCATCTAACT-GCATAATTG--ACATTTCTGTCAAATGCACAACTAGATATCAAAGACAC
1 GCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAACTAGGCCTCAAAGGCAC
3461 TTA
66 TTA
*
3464 GCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCTCAAAGGCAC
1 GCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAACTAGGCCTCAAAGGCAC
3529 TTA
66 TTA
* * *
3532 GTCTTTCATCTAGCTGGCATAATTGCCACATTTCTGTCAAATGCACAACTAGGCCTCAAAGGCAC
1 GCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAACTAGGCCTCAAAGGCAC
3597 TTA
66 TTA
* *
3600 GCCTTTCATCTAACTGGCATAATTGACACCTTTATGTCAAATGCACAACTAGGCCATCAA
1 GCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAACTAGGCC-TCAA
3660 TATTTTATTT
Statistics
Matches: 301, Mismatches: 24, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
65 52 0.17
66 9 0.03
67 8 0.03
68 228 0.76
69 4 0.01
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (68 bp):
GCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAACTAGGCCTCAAAGGCAC
TTA
Found at i:3608 original size:201 final size:203
Alignment explanation
Indices: 3263--3651 Score: 692
Period size: 201 Copynumber: 1.9 Consensus size: 203
3253 ATATTTTCAT
*
3263 GCCTTTCATCTAACTGGCATAATTGAAACATTTCTGTCAAATGCACAGCTAGGCCTCAAAGGCAC
1 GCCTTTCATCTAACTGGCATAATTGAAACATTTCTGTCAAATGCACAACTAGGCCTCAAAGGCAC
3328 TTAGCCTTTCATCTAGCTGACATAATTGACACATTTCTGTCAAATGCACAACTAGGCCTCAAAGG
66 TTAGCCTTTCATCTAGCTGACATAATTGACACATTTCTGTCAAATGCACAACTAGGCCTCAAAGG
*
3393 CACTTAGCCTTTCATCTAACT-GCATAATTGACA-TTTCTGTCAAATGCACAACTAGATATCAAA
131 CACTTAGCCTTTCATCTAACTGGCATAATTGACACTTTATGTCAAATGCACAACTAGATATCAAA
3456 GACACTTA
196 GACACTTA
* *
3464 GCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCTCAAAGGCAC
1 GCCTTTCATCTAACTGGCATAATTGAAACATTTCTGTCAAATGCACAACTAGGCCTCAAAGGCAC
* * *
3529 TTAGTCTTTCATCTAGCTGGCATAATTGCCACATTTCTGTCAAATGCACAACTAGGCCTCAAAGG
66 TTAGCCTTTCATCTAGCTGACATAATTGACACATTTCTGTCAAATGCACAACTAGGCCTCAAAGG
3594 CACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTATGTCAAATGCACAACTAG
131 CACTTAGCCTTTCATCTAACTGGCATAATTGACA-CTTTATGTCAAATGCACAACTAG
3652 GCCATCAATA
Statistics
Matches: 178, Mismatches: 7, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
201 145 0.81
202 12 0.07
204 21 0.12
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (203 bp):
GCCTTTCATCTAACTGGCATAATTGAAACATTTCTGTCAAATGCACAACTAGGCCTCAAAGGCAC
TTAGCCTTTCATCTAGCTGACATAATTGACACATTTCTGTCAAATGCACAACTAGGCCTCAAAGG
CACTTAGCCTTTCATCTAACTGGCATAATTGACACTTTATGTCAAATGCACAACTAGATATCAAA
GACACTTA
Found at i:6543 original size:13 final size:13
Alignment explanation
Indices: 6525--6566 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
6515 TGCGTCATAA
*
6525 ATTTATGACGCGC
1 ATTTATGACGCAC
*
6538 ATTTATGACACAC
1 ATTTATGACGCAC
*
6551 ATTTATGACGCTC
1 ATTTATGACGCAC
6564 ATT
1 ATT
6567 GCGCGTCATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (13 bp):
ATTTATGACGCAC
Found at i:12911 original size:75 final size:76
Alignment explanation
Indices: 12751--12980 Score: 390
Period size: 76 Copynumber: 3.0 Consensus size: 76
12741 CTTAACAGTC
* *
12751 AATGGTGAAAAATGTTGATCAAAGGGTCACATTGAGTTTATTTTTTGAATTGGAGAGTCACATTG
1 AATGGTGAAAAACGTTGATCAAAGGGTCACATTGGGTTTATTTTTTGAATTGGAGAGTCACATTG
12816 AGAGAAAAAAT
66 AGAGAAAAAAT
*
12827 AATGGTGAAAAACGTTGATCAAAGGGTCACATTGGGTTTA-TTTTTGAATTGGAGAGTCACGTTG
1 AATGGTGAAAAACGTTGATCAAAGGGTCACATTGGGTTTATTTTTTGAATTGGAGAGTCACATTG
*
12891 AGAGAGAAAAT
66 AGAGAAAAAAT
* * *
12902 AATGGTGAAAAACATTGATCAAAGGGCCACATTTGGTTTATTTTTTGAATTGGAGAGTCACATTG
1 AATGGTGAAAAACGTTGATCAAAGGGTCACATTGGGTTTATTTTTTGAATTGGAGAGTCACATTG
12967 AGAGAAAAAAT
66 AGAGAAAAAAT
12978 AAT
1 AAT
12981 ACGATAACCA
Statistics
Matches: 144, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
75 70 0.49
76 74 0.51
ACGTcount: A:0.37, C:0.08, G:0.24, T:0.30
Consensus pattern (76 bp):
AATGGTGAAAAACGTTGATCAAAGGGTCACATTGGGTTTATTTTTTGAATTGGAGAGTCACATTG
AGAGAAAAAAT
Found at i:16154 original size:11 final size:11
Alignment explanation
Indices: 16138--16162 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
16128 GAGGTGGTGC
16138 ATGTGAAGATG
1 ATGTGAAGATG
16149 ATGTGAAGATG
1 ATGTGAAGATG
16160 ATG
1 ATG
16163 AAAAGAGACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.28
Consensus pattern (11 bp):
ATGTGAAGATG
Found at i:16765 original size:41 final size:40
Alignment explanation
Indices: 16699--16818 Score: 109
Period size: 41 Copynumber: 2.9 Consensus size: 40
16689 TTTTTAGTAA
*
16699 AAATGCCGCAATAGAGTAG-ACATTTAGCGGCGTTTTAGGC-C
1 AAATGCCGCAATAGAGT-GTA-ATTTAGCGGCGTTTTA-CCAC
* *
16740 AAATGCCGCAATATAGTGTTAATTTAGCTGCGTTTATACCAC
1 AAATGCCGCAATAGAGTG-TAATTTAGCGGCGTTT-TACCAC
* * *
16782 AAACGCCGTAATAGAGTGGTAAATTAGCGGCAGTTTT
1 AAATGCCGCAATAGAGT-GTAATTTAGCGGC-GTTTT
16819 GTCTAAAACG
Statistics
Matches: 65, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
40 1 0.02
41 30 0.46
42 29 0.45
43 5 0.08
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.28
Consensus pattern (40 bp):
AAATGCCGCAATAGAGTGTAATTTAGCGGCGTTTTACCAC
Found at i:18921 original size:81 final size:81
Alignment explanation
Indices: 18786--18952 Score: 262
Period size: 81 Copynumber: 2.1 Consensus size: 81
18776 CGAAGCCGTC
* ** * *
18786 ATCACCTACACCGTCGCTGCTTGGTACTCAACTGTTGCTGGTCGCCGCCGCTTGAAGCCGTCGTT
1 ATCACATACACCGTCGCTGCCCGGTACTCAACTGCTGCTGGTCACCGCCGCTTGAAGCCGTCGTT
*
18851 CCTGCTGCTGCTCGTT
66 CCTGCTGCTGCTCGTG
* *
18867 ATCACATACACCGTCGCTGCCCGGTACTCAACTGCTGCTGGTCATCGCCGCTTGAAGCTGTCGTT
1 ATCACATACACCGTCGCTGCCCGGTACTCAACTGCTGCTGGTCACCGCCGCTTGAAGCCGTCGTT
18932 CCTGCTGCTGCTCGTG
66 CCTGCTGCTGCTCGTG
18948 ATCAC
1 ATCAC
18953 CGCCATCGTT
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 78 1.00
ACGTcount: A:0.13, C:0.35, G:0.24, T:0.28
Consensus pattern (81 bp):
ATCACATACACCGTCGCTGCCCGGTACTCAACTGCTGCTGGTCACCGCCGCTTGAAGCCGTCGTT
CCTGCTGCTGCTCGTG
Found at i:26657 original size:21 final size:21
Alignment explanation
Indices: 26615--26657 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
26605 TTTATGGGTT
* * *
26615 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
26636 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
26657 A
1 A
26658 CGAAATGAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:26723 original size:67 final size:68
Alignment explanation
Indices: 26637--26788 Score: 234
Period size: 68 Copynumber: 2.2 Consensus size: 68
26627 ACCCATTCAA
* *
26637 GGGGAACCGATACCCCCTCAACG-AAATGAATTTCCAGAATGCTAGAGGGGAATCGGTACCCCCA
1 GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
26701 GGG
66 GGG
* * * *
26704 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
26769 GGG
66 GGG
*
26772 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
26789 ATGAGAAAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
67 22 0.29
68 55 0.71
ACGTcount: A:0.27, C:0.28, G:0.28, T:0.17
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
GGG
Found at i:27124 original size:29 final size:29
Alignment explanation
Indices: 27090--27161 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 29
27080 TATATTATGA
**
27090 TACATGACATGAATTTGTATTA-ATTGTAT
1 TACATGACATGAATTCATATTATA-TGTAT
27119 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTATATGTAT
27148 TACATGACATGAAT
1 TACATGACATGAAT
27162 ATGCAGAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
29 39 0.98
30 1 0.03
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (29 bp):
TACATGACATGAATTCATATTATATGTAT
Found at i:27218 original size:30 final size:31
Alignment explanation
Indices: 27176--27235 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
27166 AGAAAAAGTT
*
27176 ATATGCACTATGTGATAAAGGTATGTAAATG
1 ATATGCACTATGTGATAAAGGTATGGAAATG
*
27207 ATATGC-CTATGTGTTAAAGGTATGGAAAT
1 ATATGCACTATGTGATAAAGGTATGGAAAT
27236 ACTATGTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (31 bp):
ATATGCACTATGTGATAAAGGTATGGAAATG
Found at i:27515 original size:23 final size:22
Alignment explanation
Indices: 27455--27522 Score: 127
Period size: 22 Copynumber: 3.0 Consensus size: 22
27445 TTATGGACAT
27455 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
27477 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
27499 AATTCTACGGGGCACTTCGGTGC
1 AATTCTAC-GGGCACTTCGGTGC
27522 A
1 A
27523 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 30 0.67
23 15 0.33
ACGTcount: A:0.19, C:0.26, G:0.28, T:0.26
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:33686 original size:67 final size:67
Alignment explanation
Indices: 33560--33709 Score: 214
Period size: 67 Copynumber: 2.3 Consensus size: 67
33550 TACCCTTCAA
* *
33560 GGGGAACCGATA-CCCCTCAACGAAATGAATTTCCAGAATGCTAGAGGGGAATCGGTACCCCCA-
1 GGGGAACCGATACCCCCTCAACGAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCAG
33623 GG
66 GG
* * * *
33625 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACG-AAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
33690 GGG
65 GGG
*
33693 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
33710 ATGAGAAAAA
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
65 12 0.16
66 9 0.12
67 36 0.48
68 18 0.24
ACGTcount: A:0.27, C:0.28, G:0.27, T:0.17
Consensus pattern (67 bp):
GGGGAACCGATACCCCCTCAACGAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCAG
GG
Found at i:34040 original size:29 final size:29
Alignment explanation
Indices: 34008--34079 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 29
33998 TATATTATGA
**
34008 TACATGACATGAATTTGTATTA-ATTGTAT
1 TACATGACATGAATTCATATTATA-TGTAT
34037 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTATATGTAT
34066 TACATGACATGAAT
1 TACATGACATGAAT
34080 ATGCAGAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
29 39 0.98
30 1 0.03
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (29 bp):
TACATGACATGAATTCATATTATATGTAT
Found at i:34136 original size:30 final size:31
Alignment explanation
Indices: 34094--34153 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
34084 AGAAAAAGTT
*
34094 ATATGCACTATGTGATAAAGGTATGTAAATG
1 ATATGCACTATGTGATAAAGGTATGGAAATG
*
34125 ATATGC-CTATGTGTTAAAGGTATGGAAAT
1 ATATGCACTATGTGATAAAGGTATGGAAAT
34154 ACTATGTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (31 bp):
ATATGCACTATGTGATAAAGGTATGGAAATG
Found at i:34402 original size:20 final size:22
Alignment explanation
Indices: 34377--34431 Score: 87
Period size: 20 Copynumber: 2.5 Consensus size: 22
34367 ATAATTCTAC
34377 CACTTCGGTGCAATTCT-C-GG
1 CACTTCGGTGCAATTCTACGGG
34397 CACTTCGGTGCAATTCTACGGGG
1 CACTTCGGTGCAATTCTAC-GGG
34420 CACTTCGGTGCA
1 CACTTCGGTGCA
34432 TTTATACGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 17 0.53
21 1 0.03
23 14 0.44
ACGTcount: A:0.16, C:0.29, G:0.27, T:0.27
Consensus pattern (22 bp):
CACTTCGGTGCAATTCTACGGG
Found at i:34439 original size:23 final size:23
Alignment explanation
Indices: 34377--34439 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 23
34367 ATAATTCTAC
*
34377 CACTTCGGTGCAATTCT-C--GG
1 CACTTCGGTGCAATTATACGGGG
*
34397 CACTTCGGTGCAATTCTACGGGG
1 CACTTCGGTGCAATTATACGGGG
*
34420 CACTTCGGTGCATTTATACG
1 CACTTCGGTGCAATTATACG
34440 AGC
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 17 0.45
21 1 0.03
23 20 0.53
ACGTcount: A:0.17, C:0.27, G:0.25, T:0.30
Consensus pattern (23 bp):
CACTTCGGTGCAATTATACGGGG
Done.