Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005485.1 Hibiscus syriacus cultivar Beakdansim tig00012601_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: 65763
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:6637 original size:16 final size:15
Alignment explanation
Indices: 6599--6650 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
6589 TATTATAATT
*
6599 AATTTAAAATAATAA
1 AATTTAAATTAATAA
6614 AATATTAAATTAAATAA
1 AAT-TTAAATT-AATAA
*
6631 TATTTAAA-TAATAA
1 AATTTAAATTAATAA
*
6645 ATTTTA
1 AATTTA
6651 TTAAATGTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
14 9 0.29
15 4 0.13
16 11 0.35
17 7 0.23
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AATTTAAATTAATAA
Found at i:6761 original size:48 final size:48
Alignment explanation
Indices: 6640--6761 Score: 135
Period size: 48 Copynumber: 2.5 Consensus size: 48
6630 ATATTTAAAT
* * *
6640 AATAAATTTT--ATTAAATGTAAAAATTATTTATAATAATTTGAAATTA
1 AATAAATTTTAAATTAAATATTAAAATTATTTAT-ATAATTTAAAATTA
* *
6687 TATAAAGATTTTAAATT-AATAATAAAATTATTTAT-TAATTTAAAATTA
1 AAT-AA-ATTTTAAATTAAATATTAAAATTATTTATATAATTTAAAATTA
6735 AATAAATTTTAAATTTAAATATTAAAA
1 AATAAATTTTAAA-TTAAATATTAAAA
6762 ATAATTAAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
46 8 0.13
47 6 0.10
48 25 0.40
49 5 0.08
50 15 0.24
51 3 0.05
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (48 bp):
AATAAATTTTAAATTAAATATTAAAATTATTTATATAATTTAAAATTA
Found at i:7500 original size:3 final size:3
Alignment explanation
Indices: 7488--7564 Score: 108
Period size: 3 Copynumber: 27.0 Consensus size: 3
7478 CCATATTGAT
*
7488 TTA TTA -TA TTA TTA TTT TTA TTA TTA -TA TTA TTA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
7533 TTA TT- TTA TTA TCA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
7565 AATATATAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
2 8 0.12
3 58 0.88
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:7995 original size:19 final size:19
Alignment explanation
Indices: 7971--8009 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
7961 AGAGACAGAG
7971 ACAGAGAGACAGA-AAATAC
1 ACAGAGAGA-AGAGAAATAC
7990 ACAGAGAGAAGAGAAATAC
1 ACAGAGAGAAGAGAAATAC
8009 A
1 A
8010 GAGAAACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 3 0.16
19 16 0.84
ACGTcount: A:0.59, C:0.13, G:0.23, T:0.05
Consensus pattern (19 bp):
ACAGAGAGAAGAGAAATAC
Found at i:8084 original size:16 final size:16
Alignment explanation
Indices: 8063--8095 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
8053 AACGCAGCAG
8063 AAAAGAAAGAAAAGAA
1 AAAAGAAAGAAAAGAA
*
8079 AAAAGAAAGAAGAGAA
1 AAAAGAAAGAAAAGAA
8095 A
1 A
8096 CTTACCGAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
AAAAGAAAGAAAAGAA
Found at i:9653 original size:26 final size:24
Alignment explanation
Indices: 9615--9675 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
9605 CATATATTTA
9615 ATTTATA-AT-TT-TTTTTATTA-T
1 ATTTATACATATTATTTTTA-TAGT
*
9636 ATATATACATATTATTTTTATAGT
1 ATTTATACATATTATTTTTATAGT
*
9660 ATTTATATATATTATT
1 ATTTATACATATTATT
9676 AATATTTCAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
21 6 0.18
22 2 0.06
23 4 0.12
24 21 0.64
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (24 bp):
ATTTATACATATTATTTTTATAGT
Found at i:20324 original size:10 final size:10
Alignment explanation
Indices: 20309--20342 Score: 59
Period size: 10 Copynumber: 3.3 Consensus size: 10
20299 ATGCTTGAAG
20309 AAAAAAGAAA
1 AAAAAAGAAA
20319 AAAAAAGAAA
1 AAAAAAGAAA
20329 AAAAAAGGAAA
1 AAAAAA-GAAA
20340 AAA
1 AAA
20343 GGGTGGGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 16 0.70
11 7 0.30
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:20330 original size:11 final size:11
Alignment explanation
Indices: 20309--20342 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
20299 ATGCTTGAAG
20309 AAAAAAG-AAA
1 AAAAAAGAAAA
20319 AAAAAAGAAAA
1 AAAAAAGAAAA
*
20330 AAAAAGGAAAA
1 AAAAAAGAAAA
20341 AA
1 AA
20343 GGGTGGGTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 7 0.32
11 15 0.68
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:21513 original size:82 final size:82
Alignment explanation
Indices: 21376--21886 Score: 920
Period size: 82 Copynumber: 6.2 Consensus size: 82
21366 ACCTTAACTG
21376 GAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
1 GAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
21441 AATCAATCATTGAATTT
66 AATCAATCATTGAATTT
21458 GAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
1 GAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
21523 AATCAATCATTGAATTT
66 AATCAATCATTGAATTT
21540 GAAGATGAATGTGCTC---GCCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCA
1 GAAGATGAATGTGCTCATAG-CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCA
21602 GAATCAATCATTGAATTT
65 GAATCAATCATTGAATTT
21620 GAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
1 GAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
21685 AATCAATCATTGAATTT
66 AATCAATCATTGAATTT
* *
21702 GAAGATGAATGTGCTCATAGCATATTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAG
1 GAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
21767 AATCAATCATTGAATTT
66 AATCAATCATTGAATTT
* * *
21784 GAAGATGAATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGGCAG
1 GAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
*
21849 AACCAATCATTGAATTT
66 AATCAATCATTGAATTT
*
21866 GGAAGATGAATTTGCTCATAG
1 -GAAGATGAATGTGCTCATAG
21887 TAGAAATAAG
Statistics
Matches: 414, Mismatches: 10, Indels: 9
0.96 0.02 0.02
Matches are distributed among these distances:
79 1 0.00
80 78 0.19
82 316 0.76
83 19 0.05
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (82 bp):
GAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
AATCAATCATTGAATTT
Found at i:22873 original size:113 final size:113
Alignment explanation
Indices: 22702--23128 Score: 660
Period size: 113 Copynumber: 3.8 Consensus size: 113
22692 TGGATTGACA
22702 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
*
22767 AGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGAGCAGCT
66 AGAACTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGAGCAGCT
22815 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * ** * * * * *
22880 AGAACTTGTTCAACTTTTTGTTTGAATTCATCATTTGATGGATCAACA
66 AGAACTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGAGCAGCT
* *
22928 TTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
1 TTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAAT
* *
22992 GAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGAAGGAGCAGCT
62 GAGAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGAGCAGCT
*
23044 TTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
*
23108 AGAACTTGTTCAACTTTTTGC
66 AGAACTTGTTCAACCTTTTGC
23129 ATAATTCTAT
Statistics
Matches: 281, Mismatches: 28, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
112 54 0.19
113 129 0.46
115 19 0.07
116 78 0.28
117 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (113 bp):
TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
AGAACTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGAGCAGCT
Found at i:23461 original size:3 final size:3
Alignment explanation
Indices: 23453--23527 Score: 123
Period size: 3 Copynumber: 25.0 Consensus size: 3
23443 CCATATTGAT
* *
23453 TTA TTA TTA TTA TTT TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
23501 TCA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
23528 AATATATTAA
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:23982 original size:19 final size:19
Alignment explanation
Indices: 23934--23985 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 19
23924 TCTGCAAGCA
* * *
23934 AGAGAAGAGACAGAGACAG
1 AGAGAAGAGAAATACACAG
*
23953 AGA-CAGA-AAATACACAG
1 AGAGAAGAGAAATACACAG
23970 AGAGAAGAGAAATACA
1 AGAGAAGAGAAATACA
23986 GAGAAACAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
17 10 0.38
18 6 0.23
19 10 0.38
ACGTcount: A:0.58, C:0.12, G:0.27, T:0.04
Consensus pattern (19 bp):
AGAGAAGAGAAATACACAG
Found at i:23987 original size:34 final size:36
Alignment explanation
Indices: 23934--24000 Score: 93
Period size: 34 Copynumber: 1.9 Consensus size: 36
23924 TCTGCAAGCA
* *
23934 AGAGAAGAGACAGAGACAGAGACAGAAAATACACAG
1 AGAGAAGAGACAGAGACAGAGAAACAAAATACACAG
*
23970 AGAGAAGAGA-A-ATACAGAGAAACAAAATACA
1 AGAGAAGAGACAGAGACAGAGAAACAAAATACA
24001 AAAAAAAAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 17 0.61
35 1 0.04
36 10 0.36
ACGTcount: A:0.60, C:0.12, G:0.24, T:0.04
Consensus pattern (36 bp):
AGAGAAGAGACAGAGACAGAGAAACAAAATACACAG
Found at i:24060 original size:15 final size:15
Alignment explanation
Indices: 24040--24071 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
24030 AACGCATCAG
24040 AAAAGAAAGAAAAGA
1 AAAAGAAAGAAAAGA
*
24055 AAAAGAAAGAAGAGA
1 AAAAGAAAGAAAAGA
24070 AA
1 AA
24072 CTTACTGAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAAAGAAAGAAAAGA
Found at i:24967 original size:19 final size:21
Alignment explanation
Indices: 24926--24976 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
24916 TTATGTAGTC
*
24926 ATAAATATATATATATAATAA
1 ATAAATATTTATATATAATAA
*
24947 ATAAATATTTAT-TTTAA-AA
1 ATAAATATTTATATATAATAA
24966 ATAAATTATTT
1 ATAAA-TATTT
24977 TAATATCGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 7 0.26
20 9 0.33
21 11 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATAAATATTTATATATAATAA
Found at i:30429 original size:21 final size:22
Alignment explanation
Indices: 30386--30429 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
30376 TAGCATTTTA
30386 AAATAGGAATTTGTACAGCATG
1 AAATAGGAATTTGTACAGCATG
*
30408 AAATATGG-ATTTG-ACAGTATG
1 AAATA-GGAATTTGTACAGCATG
30429 A
1 A
30430 CATTCAGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 8 0.40
22 10 0.50
23 2 0.10
ACGTcount: A:0.41, C:0.07, G:0.23, T:0.30
Consensus pattern (22 bp):
AAATAGGAATTTGTACAGCATG
Found at i:36503 original size:3 final size:3
Alignment explanation
Indices: 36495--36521 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
36485 CTGGTCCAGA
36495 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
36522 GGGATGGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:38290 original size:24 final size:22
Alignment explanation
Indices: 38244--38306 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 22
38234 GAAGGACTAT
* * **
38244 TATGTCCCGAATGACCACTATA
1 TATGTCCCGAAGGACTACTGGA
* * *
38266 TACGTCCTGTAGGACTACTGGA
1 TATGTCCCGAAGGACTACTGGA
38288 TATGTCCCGAAGGACTACT
1 TATGTCCCGAAGGACTACT
38307 ATACCCTCAA
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (22 bp):
TATGTCCCGAAGGACTACTGGA
Found at i:45027 original size:21 final size:21
Alignment explanation
Indices: 45003--45065 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 21
44993 GGACCACTAT
* * *
45003 ATACGTCTGTAGGACTATTGG
1 ATACGTCCGAAGGACTACTGG
45024 ATACGTCCCGAAGGACTACTGG
1 ATACGT-CCGAAGGACTACTGG
45046 ATACGTCCCGAAGGACTACT
1 ATACGT-CCGAAGGACTACT
45066 ATACCCTCGA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
21 6 0.16
22 32 0.84
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (21 bp):
ATACGTCCGAAGGACTACTGG
Found at i:45041 original size:22 final size:22
Alignment explanation
Indices: 45013--45065 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
45003 ATACGTCTGT
*
45013 AGGACTATTGGATACGTCCCGA
1 AGGACTACTGGATACGTCCCGA
45035 AGGACTACTGGATACGTCCCGA
1 AGGACTACTGGATACGTCCCGA
45057 AGGACTACT
1 AGGACTACT
45066 ATACCCTCGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.21
Consensus pattern (22 bp):
AGGACTACTGGATACGTCCCGA
Found at i:53183 original size:19 final size:20
Alignment explanation
Indices: 53133--53184 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
53123 GAAAGAAAGA
*
53133 GAAAAGGTAAAAGTTAAAAT
1 GAAAAGATAAAAGTTAAAAT
53153 GAAATAGA-AAAA-TTAATAAT
1 GAAA-AGATAAAAGTTAA-AAT
53173 G-AAAGATAAAAG
1 GAAAAGATAAAAG
53185 AAAAAGTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
18 3 0.11
19 10 0.37
20 12 0.44
21 2 0.07
ACGTcount: A:0.63, C:0.00, G:0.17, T:0.19
Consensus pattern (20 bp):
GAAAAGATAAAAGTTAAAAT
Found at i:59128 original size:9 final size:8
Alignment explanation
Indices: 59114--59151 Score: 67
Period size: 8 Copynumber: 4.6 Consensus size: 8
59104 TAAACTATAC
59114 AAAAAAAT
1 AAAAAAAT
59122 AAAAAAAT
1 AAAAAAAT
59130 AAAAAAAT
1 AAAAAAAT
59138 AAAAAAAAT
1 -AAAAAAAT
59147 AAAAA
1 AAAAA
59152 TGCAAAACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
8 21 0.72
9 8 0.28
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAAAAAT
Found at i:59135 original size:16 final size:17
Alignment explanation
Indices: 59114--59151 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
59104 TAAACTATAC
59114 AAAAAAAT-AAAAAAAT
1 AAAAAAATAAAAAAAAT
59130 AAAAAAATAAAAAAAAT
1 AAAAAAATAAAAAAAAT
59147 AAAAA
1 AAAAA
59152 TGCAAAACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (17 bp):
AAAAAAATAAAAAAAAT
Done.