Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000541.1 Hibiscus syriacus cultivar Beakdansim tig00001047_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: 72817
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Found at i:10925 original size:29 final size:29
Alignment explanation
Indices: 10893--10976 Score: 150
Period size: 29 Copynumber: 2.9 Consensus size: 29
10883 AATAAGATCT
* *
10893 TATCCCTATAATTATTCTTAATATCTGTC
1 TATCCCTATGATTATTCTTATTATCTGTC
10922 TATCCCTATGATTATTCTTATTATCTGTC
1 TATCCCTATGATTATTCTTATTATCTGTC
10951 TATCCCTATGATTATTCTTATTATCT
1 TATCCCTATGATTATTCTTATTATCT
10977 ATATAAGGTA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.24, C:0.20, G:0.05, T:0.51
Consensus pattern (29 bp):
TATCCCTATGATTATTCTTATTATCTGTC
Found at i:26053 original size:19 final size:17
Alignment explanation
Indices: 26024--26078 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 17
26014 CATGATTTCC
*
26024 TTTTATTTATTTTTTAA
1 TTTTTTTTATTTTTTAA
*
26041 TTTCTATTTTATTTCTTATA
1 TTT-T-TTTTATTTTTTA-A
26061 TTTTTTTTATTTTTTAA
1 TTTTTTTTATTTTTTAA
26078 T
1 T
26079 CAATTTTCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
17 5 0.16
18 12 0.38
19 11 0.34
20 4 0.12
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTTTTATTTTTTAA
Found at i:28138 original size:12 final size:12
Alignment explanation
Indices: 28121--28149 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
28111 CAATACAGAT
28121 AATACGATTATA
1 AATACGATTATA
28133 AATACGATTATA
1 AATACGATTATA
28145 AATAC
1 AATAC
28150 TTATCGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.52, C:0.10, G:0.07, T:0.31
Consensus pattern (12 bp):
AATACGATTATA
Found at i:29124 original size:23 final size:23
Alignment explanation
Indices: 29098--29142 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
29088 CACCACAGCT
* *
29098 CGTATAATTGCACTGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
29121 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
29143 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:29385 original size:147 final size:148
Alignment explanation
Indices: 29118--29422 Score: 558
Period size: 147 Copynumber: 2.1 Consensus size: 148
29108 CACTGAAGTG
*
29118 CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAG
1 CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAG
* *
29183 AATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTTCACAGAAT
66 AATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAAT
29248 AT-ATATATCCCGAAGGA
131 ATAATATATCCCGAAGGA
29265 CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAG
1 CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAG
29330 AATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAAT
66 AATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAAT
*
29395 ATACATATGTCCCGAAGGA
131 ATA-ATATATCCCGAAGGA
29414 CCGCGTAGA
1 CCGCGTAGA
29423 CCCTCGACTC
Statistics
Matches: 152, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
147 129 0.85
149 23 0.15
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (148 bp):
CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAG
AATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAAT
ATAATATATCCCGAAGGA
Found at i:30499 original size:21 final size:21
Alignment explanation
Indices: 30475--30519 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
30465 TATTGTTCGT
* *
30475 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
30496 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
30517 TTG
1 TTG
30520 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:33680 original size:23 final size:23
Alignment explanation
Indices: 33654--33698 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
33644 CACCACAGCT
* *
33654 CGTATAATTGCACTGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
33677 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
33699 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:33917 original size:149 final size:149
Alignment explanation
Indices: 33674--33980 Score: 560
Period size: 149 Copynumber: 2.1 Consensus size: 149
33664 CACTGAAGTG
*
33674 CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAG
1 CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAG
* *
33739 AATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTTCACAGAAT
66 AATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAAT
*
33804 ATATATATATCCCGAAGGA
131 ATACATATATCCCGAAGGA
33823 CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAG
1 CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAG
33888 AATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAAT
66 AATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAAT
*
33953 ATACATATGTCCCGAAGGA
131 ATACATATATCCCGAAGGA
*
33972 CCGCATAGA
1 CCGCGTAGA
33981 CCCTCGACTC
Statistics
Matches: 152, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
149 152 1.00
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (149 bp):
CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAG
AATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAAT
ATACATATATCCCGAAGGA
Found at i:34707 original size:5 final size:5
Alignment explanation
Indices: 34697--34726 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
34687 ATTCATATAA
34697 TTCAT TTCAT TTCAT TTCAT TTCAT TTCAT
1 TTCAT TTCAT TTCAT TTCAT TTCAT TTCAT
34727 ATCTATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (5 bp):
TTCAT
Found at i:34920 original size:22 final size:21
Alignment explanation
Indices: 34895--34938 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
34885 TAATTCAATT
34895 TCATATAAC-TCATATAATCTTC
1 TCATATAACTTCATA-AAT-TTC
34917 TCATATAACTTCATAAATTTC
1 TCATATAACTTCATAAATTTC
34938 T
1 T
34939 ATCATACAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 4 0.19
22 12 0.57
23 5 0.24
ACGTcount: A:0.36, C:0.20, G:0.00, T:0.43
Consensus pattern (21 bp):
TCATATAACTTCATAAATTTC
Found at i:35649 original size:21 final size:21
Alignment explanation
Indices: 35607--35651 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
35597 TATTGTTCGT
* *
35607 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
* *
35628 TTGAATGGGTACCGATTGCCC
1 TTGAAGGGGTACCGATTCCCC
35649 TTG
1 TTG
35652 CCCAGAAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.22, G:0.31, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:40100 original size:24 final size:24
Alignment explanation
Indices: 40070--40133 Score: 110
Period size: 24 Copynumber: 2.7 Consensus size: 24
40060 CACATAAACA
*
40070 AACATAAACGACCATAAATGAATG
1 AACATAAACGAACATAAATGAATG
*
40094 AATATAAACGAACATAAATGAATG
1 AACATAAACGAACATAAATGAATG
40118 AACATAAACGAACATA
1 AACATAAACGAACATA
40134 TTATCGAACG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.58, C:0.14, G:0.11, T:0.17
Consensus pattern (24 bp):
AACATAAACGAACATAAATGAATG
Found at i:47630 original size:46 final size:47
Alignment explanation
Indices: 47559--47670 Score: 176
Period size: 46 Copynumber: 2.4 Consensus size: 47
47549 ACTATGATGC
47559 ACTTGTGCTTATATAGG-TTAGTATAGGAAGGCACCATCATGCTTGA
1 ACTTGTGCTTATATAGGTTTAGTATAGGAAGGCACCATCATGCTTGA
* *
47605 ACTTGTGCTTATATAGGTTTA-TATAGGAAGGTATCATCATGCTTGA
1 ACTTGTGCTTATATAGGTTTAGTATAGGAAGGCACCATCATGCTTGA
*
47651 ACTTGGGCTTATATA-GTTTA
1 ACTTGTGCTTATATAGGTTTA
47671 ACTACTCTGC
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
45 5 0.08
46 54 0.87
47 3 0.05
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (47 bp):
ACTTGTGCTTATATAGGTTTAGTATAGGAAGGCACCATCATGCTTGA
Found at i:53135 original size:23 final size:23
Alignment explanation
Indices: 53109--53160 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
53099 AACATTTCAC
53109 TTATCAAAAGAAAAACATATATA
1 TTATCAAAAGAAAAACATATATA
53132 TTATCAAAAGAAAAACATATATA
1 TTATCAAAAGAAAAACATATATA
53155 TTATCA
1 TTATCA
53161 TCTAGAATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.58, C:0.10, G:0.04, T:0.29
Consensus pattern (23 bp):
TTATCAAAAGAAAAACATATATA
Found at i:53247 original size:41 final size:36
Alignment explanation
Indices: 53150--53253 Score: 199
Period size: 36 Copynumber: 2.9 Consensus size: 36
53140 AGAAAAACAT
*
53150 ATATATTATCATCTAGAATTCAGTTCAATCAAGCAC
1 ATATATTATCATCTAGAATTCAATTCAATCAAGCAC
53186 ATATATTATCATCTAGAATTCAATTCAATCAAGCAC
1 ATATATTATCATCTAGAATTCAATTCAATCAAGCAC
53222 ATATATTATCATCTAGAATTCAATTCAATCAA
1 ATATATTATCATCTAGAATTCAATTCAATCAA
53254 ACATGGAAAC
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
36 67 1.00
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (36 bp):
ATATATTATCATCTAGAATTCAATTCAATCAAGCAC
Found at i:53855 original size:11 final size:11
Alignment explanation
Indices: 53827--53863 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
53817 CGTCTGGTTT
53827 GAGGGAAA-AG
1 GAGGGAAAGAG
*
53837 GAGAGAAAGAG
1 GAGGGAAAGAG
53848 GAGGGAAAG-G
1 GAGGGAAAGAG
53858 GAGGGA
1 GAGGGA
53864 GAGTTTGGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 14 0.58
11 10 0.42
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (11 bp):
GAGGGAAAGAG
Found at i:56679 original size:3 final size:3
Alignment explanation
Indices: 56673--56750 Score: 156
Period size: 3 Copynumber: 26.0 Consensus size: 3
56663 TAGTAGTTAC
56673 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
56721 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
56751 CAAATTTAGT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:59171 original size:2 final size:2
Alignment explanation
Indices: 59164--59192 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
59154 AACCCACATA
59164 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 A
59193 AAATAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:60271 original size:20 final size:20
Alignment explanation
Indices: 60248--60285 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
60238 AAATTATTAT
* *
60248 AATAATATTAATTATAATTG
1 AATAATAATAATAATAATTG
60268 AATAATAATAATAATAAT
1 AATAATAATAATAATAAT
60286 AGAAACAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (20 bp):
AATAATAATAATAATAATTG
Found at i:64851 original size:12 final size:12
Alignment explanation
Indices: 64787--64856 Score: 54
Period size: 12 Copynumber: 5.8 Consensus size: 12
64777 ACAGAGATAT
*
64787 CAGAAATCAAAA
1 CAGAAATCAGAA
*
64799 CAGAATTCAGAA
1 CAGAAATCAGAA
* * *
64811 GAGATATCATAA
1 CAGAAATCAGAA
64823 CAG-AATCCAGATA
1 CAGAAAT-CAGA-A
64836 -AGAAATCAGAA
1 CAGAAATCAGAA
*
64847 CAGAATTCAG
1 CAGAAATCAG
64857 GTCATGTATC
Statistics
Matches: 44, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
11 3 0.07
12 37 0.84
13 4 0.09
ACGTcount: A:0.53, C:0.16, G:0.16, T:0.16
Consensus pattern (12 bp):
CAGAAATCAGAA
Found at i:64867 original size:48 final size:48
Alignment explanation
Indices: 64788--64893 Score: 117
Period size: 48 Copynumber: 2.2 Consensus size: 48
64778 CAGAGATATC
* * *
64788 AGAAATCAAAACAGAATTCAGAAGAGATATCATAACAGAATCC-AGATA
1 AGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCAAG-TA
** * *
64836 AGAAATCAGAACAGAATTCAGGTCATG-TATCAGAACAGAATTCAAGTC
1 AGAAATCAGAACAGAATTCAGAACA-GATATCAGAACAGAATCCAAGTA
64884 AGAAATCAGA
1 AGAAATCAGA
64894 TAAAATATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
48 46 0.94
49 3 0.06
ACGTcount: A:0.50, C:0.15, G:0.17, T:0.18
Consensus pattern (48 bp):
AGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCAAGTA
Found at i:64891 original size:24 final size:24
Alignment explanation
Indices: 64786--64893 Score: 89
Period size: 24 Copynumber: 4.5 Consensus size: 24
64776 AACAGAGATA
*
64786 TCAGAAATCAAAACAGAATTCAGAAG
1 TCAGAAATCAGAACAGAATTC--AAG
* * *
64812 --AGATATCATAACAGAA-TCCAG
1 TCAGAAATCAGAACAGAATTCAAG
* *
64833 ATAAGAAATCAGAACAGAATTCAGG
1 -TCAGAAATCAGAACAGAATTCAAG
*
64858 TCATG-TATCAGAACAGAATTCAAG
1 TCA-GAAATCAGAACAGAATTCAAG
64882 TCAGAAATCAGA
1 TCAGAAATCAGA
64894 TAAAATATTT
Statistics
Matches: 65, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
21 2 0.03
23 3 0.05
24 56 0.86
25 4 0.06
ACGTcount: A:0.49, C:0.16, G:0.17, T:0.19
Consensus pattern (24 bp):
TCAGAAATCAGAACAGAATTCAAG
Found at i:66485 original size:17 final size:18
Alignment explanation
Indices: 66448--66486 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
66438 AAGTAAAACT
*
66448 AATATTTTTATGCACATC
1 AATAGTTTTATGCACATC
*
66466 AATAGTTTTAT-CAGATC
1 AATAGTTTTATGCACATC
66483 AATA
1 AATA
66487 TGTCTCTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (18 bp):
AATAGTTTTATGCACATC
Done.