Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000194.1 Hibiscus syriacus cultivar Beakdansim tig00000344_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: 74466
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:7083 original size:20 final size:21
Alignment explanation
Indices: 7044--7084 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
7034 TTAAGGTTTT
*
7044 TTCATTTCATGACTTTTCGAGC
1 TTCAGTTCATGAC-TTTCGAGC
7066 TTCAGTTCATGA-TTTCGAG
1 TTCAGTTCATGACTTTCGAG
7085 TTCGAGTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.44
Consensus pattern (21 bp):
TTCAGTTCATGACTTTCGAGC
Found at i:9199 original size:50 final size:49
Alignment explanation
Indices: 9051--9228 Score: 223
Period size: 50 Copynumber: 3.6 Consensus size: 49
9041 AATTCATACT
* *
9051 ACAAAAAATGTAGCACTTAACACATACTTATACCGATGTAAATGAATAAA
1 ACAAAAAATGTAGCACTTAACACATAC-TACACCGATGTAAGTGAATAAA
* * * *
9101 ATAAACAAATGTAGCAATTAACACATACT-CACTGGTGTAAGTGAATAAA
1 ACAAA-AAATGTAGCACTTAACACATACTACACCGATGTAAGTGAATAAA
* *
9150 ACAAAAAAGTGTAGCACTTAACACGTACTACACCAATGTAAGTGAATAAA
1 ACAAAAAA-TGTAGCACTTAACACATACTACACCGATGTAAGTGAATAAA
* *
9200 ATAAAAAAGTGTAGCACTTAACATATACT
1 ACAAAAAA-TGTAGCACTTAACACATACT
9229 TACAACTAGG
Statistics
Matches: 110, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
48 3 0.03
49 38 0.35
50 48 0.44
51 21 0.19
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.24
Consensus pattern (49 bp):
ACAAAAAATGTAGCACTTAACACATACTACACCGATGTAAGTGAATAAA
Found at i:18556 original size:7 final size:7
Alignment explanation
Indices: 18546--18571 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
18536 AGGAAACTAG
18546 AAAGTGA
1 AAAGTGA
18553 AAAGTGA
1 AAAGTGA
18560 AAAGTGA
1 AAAGTGA
18567 AAAGT
1 AAAGT
18572 AAGTGGGGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.27, T:0.15
Consensus pattern (7 bp):
AAAGTGA
Found at i:26292 original size:20 final size:20
Alignment explanation
Indices: 26269--26311 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
26259 AATCCACCAC
*
26269 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* *
26289 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
26309 ATG
1 ATG
26312 GGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:30783 original size:29 final size:30
Alignment explanation
Indices: 30741--30812 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
30731 CCCGAAGGAC
*
30741 CTATCCAGAGGTCACACAGA-CCCCGGTAA
1 CTATCCAGAGGTCACAAAGATCCCCGGTAA
* *
30770 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGATCCCCGGTAA
* *
30800 CTGTCCACAGGTC
1 CTATCCAGAGGTC
30813 CCGAATAACC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 18 0.49
30 19 0.51
ACGTcount: A:0.29, C:0.31, G:0.21, T:0.19
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGATCCCCGGTAA
Found at i:31569 original size:64 final size:65
Alignment explanation
Indices: 31458--31608 Score: 191
Period size: 64 Copynumber: 2.3 Consensus size: 65
31448 TCTTTCAATG
* * * * * *
31458 AAGGTATGCATCGATGCACTA-CTTGTGCATCGGTGCATAAAATGCATTCGATGTTTTTATTTTA
1 AAGGAATGCATCGATGCATTATCTTATGCATCGATGCATAAAAGGCATTCGATGTTCTTATTTT-
31522 A
65 A
* *
31523 AAGG-ATGCATCGATGCATTATC-TATGCATCGATGCATCAAAGGCATTCGATGTTCTTCTTTTA
1 AAGGAATGCATCGATGCATTATCTTATGCATCGATGCATAAAAGGCATTCGATGTTCTTATTTTA
31586 AAGGAATGCATCGATGCACTTAT
1 AAGGAATGCATCGATGCA-TTAT
31609 GAATGTGCAT
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
63 5 0.07
64 62 0.82
65 9 0.12
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.34
Consensus pattern (65 bp):
AAGGAATGCATCGATGCATTATCTTATGCATCGATGCATAAAAGGCATTCGATGTTCTTATTTTA
Found at i:34561 original size:19 final size:20
Alignment explanation
Indices: 34537--34585 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
34527 TTTATGTTTT
34537 TCACATATACACA-TTCATA
1 TCACATATACACATTTCATA
*
34556 TCACATAGT-CATATTTTCATA
1 TCACATA-TACACA-TTTCATA
34577 TCACATATA
1 TCACATATA
34586 TCATGTAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
19 10 0.40
20 2 0.08
21 13 0.52
ACGTcount: A:0.39, C:0.22, G:0.02, T:0.37
Consensus pattern (20 bp):
TCACATATACACATTTCATA
Found at i:41980 original size:21 final size:21
Alignment explanation
Indices: 41951--41990 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
41941 AACTTTTAAG
* *
41951 ATAATATTTTGAAGGACAATT
1 ATAAAATTTTGAAAGACAATT
41972 ATAAAATTTTGAAAGACAA
1 ATAAAATTTTGAAAGACAA
41991 ATATTTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.05, G:0.12, T:0.33
Consensus pattern (21 bp):
ATAAAATTTTGAAAGACAATT
Found at i:44150 original size:2 final size:2
Alignment explanation
Indices: 44143--44191 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
44133 AAACAATCTT
44143 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
44185 TA TA TA T
1 TA TA TA T
44192 TAATGGTTGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:44599 original size:2 final size:2
Alignment explanation
Indices: 44592--44620 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
44582 GTTAAGTTGT
44592 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
44621 TAGGATCCAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44804 original size:21 final size:21
Alignment explanation
Indices: 44779--44839 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
44769 TAGGGTTATA
44779 ATTTAGGAA-TTAGAGTTTAAG
1 ATTTA-GAATTTAGAGTTTAAG
*
44800 ATTTAGAATTTAGGGTTTAA-
1 ATTTAGAATTTAGAGTTTAAG
* *
44820 AGTTTAGTATTTAGGGTTTA
1 A-TTTAGAATTTAGAGTTTA
44840 GAGTGTAGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.11
21 32 0.89
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.44
Consensus pattern (21 bp):
ATTTAGAATTTAGAGTTTAAG
Found at i:44946 original size:22 final size:22
Alignment explanation
Indices: 44861--44938 Score: 79
Period size: 22 Copynumber: 3.6 Consensus size: 22
44851 ATAAGATGTA
*
44861 GGGTTTAGAA-TTTGA-GTTTG
1 GGGTTTAGAATTTTAAGGTTTG
* * *
44881 GAGTTTAGAATTTCAAGTTTTG
1 GGGTTTAGAATTTTAAGGTTTG
* **
44903 GGATTTAGGTTTTTAAGGTTTG
1 GGGTTTAGAATTTTAAGGTTTG
44925 GGGTTTAGAATTTT
1 GGGTTTAGAATTTT
44939 TAAATTTGAG
Statistics
Matches: 43, Mismatches: 13, Indels: 2
0.74 0.22 0.03
Matches are distributed among these distances:
20 9 0.21
21 3 0.07
22 31 0.72
ACGTcount: A:0.22, C:0.01, G:0.29, T:0.47
Consensus pattern (22 bp):
GGGTTTAGAATTTTAAGGTTTG
Found at i:46033 original size:12 final size:12
Alignment explanation
Indices: 46018--46064 Score: 58
Period size: 12 Copynumber: 3.7 Consensus size: 12
46008 CCGGTTTTTT
*
46018 AACCGGATAAAA
1 AACCGGTTAAAA
46030 AACCGGTTTGAAAAA
1 AACCGG-TT--AAAA
46045 AACCGGTTAAAA
1 AACCGGTTAAAA
46057 AACCGGTT
1 AACCGGTT
46065 TTTATCCGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
12 18 0.58
13 1 0.03
14 2 0.06
15 10 0.32
ACGTcount: A:0.47, C:0.17, G:0.19, T:0.17
Consensus pattern (12 bp):
AACCGGTTAAAA
Found at i:48371 original size:21 final size:21
Alignment explanation
Indices: 48347--48386 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
48337 TTTATTTTAT
48347 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
48368 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
48387 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:48434 original size:33 final size:33
Alignment explanation
Indices: 48381--48479 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
48371 TTTGTTTCAA
48381 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
48413 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
48446 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
48479 T
1 T
48480 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:48508 original size:13 final size:13
Alignment explanation
Indices: 48465--48519 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
48455 TTGGAAGTAT
48465 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
48478 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
48492 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
48505 TTAAGTATTTGAA
1 TTAAGTATTTCAA
48518 TT
1 TT
48520 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:48921 original size:15 final size:15
Alignment explanation
Indices: 48896--48951 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
48886 ATCTGGAATA
*
48896 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
48911 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
48926 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
48943 TTAAAACCG
1 TTAAAACCG
48952 AAACCAGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 21 0.62
17 13 0.38
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:48935 original size:17 final size:18
Alignment explanation
Indices: 48915--48948 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
48905 GTTTTTTTAT
48915 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
48932 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
48949 CCGAAACCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:55152 original size:2 final size:2
Alignment explanation
Indices: 55147--55212 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
55137 GAATCAATTT
55147 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
55189 TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
55213 AAAATAAAAC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:56560 original size:2 final size:2
Alignment explanation
Indices: 56553--56577 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
56543 TTAAAAATTA
56553 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 A
56578 AAAAACCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:56944 original size:22 final size:22
Alignment explanation
Indices: 56917--56984 Score: 136
Period size: 22 Copynumber: 3.1 Consensus size: 22
56907 TCAATACTTA
56917 AAAGTTGAAGGACTAAATTTAT
1 AAAGTTGAAGGACTAAATTTAT
56939 AAAGTTGAAGGACTAAATTTAT
1 AAAGTTGAAGGACTAAATTTAT
56961 AAAGTTGAAGGACTAAATTTAT
1 AAAGTTGAAGGACTAAATTTAT
56983 AA
1 AA
56985 TTAAACCAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.47, C:0.04, G:0.18, T:0.31
Consensus pattern (22 bp):
AAAGTTGAAGGACTAAATTTAT
Found at i:57299 original size:30 final size:29
Alignment explanation
Indices: 57263--57370 Score: 101
Period size: 30 Copynumber: 3.6 Consensus size: 29
57253 TACCCCTATA
*
57263 TTTGTTTCTTTGTTTTTGTTGTGATGGGCT
1 TTTGTTTCTTTG-TTTTGTTGTGATGGGTT
* *
57293 TTTGTTTCCTTTGCTTCTGCTGTGA-GGGTT
1 TTTGTTT-CTTTG-TTTTGTTGTGATGGGTT
* *
57323 TTTGTTTTCTTTGGTTTGTTGTGGTGGGTT
1 TTTG-TTTCTTTGTTTTGTTGTGATGGGTT
* *
57353 TCTTCTTTCTTTGGTTTG
1 T-TTGTTTCTTTGTTTTG
57371 CTTTCATGGG
Statistics
Matches: 65, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
29 7 0.11
30 39 0.60
31 19 0.29
ACGTcount: A:0.02, C:0.10, G:0.27, T:0.61
Consensus pattern (29 bp):
TTTGTTTCTTTGTTTTGTTGTGATGGGTT
Found at i:59919 original size:24 final size:24
Alignment explanation
Indices: 59868--59919 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
59858 ATGATAAATG
** *
59868 AACACAAACGAATGAACGTTAACG
1 AACACAAACGAATGAACGCAAACA
* *
59892 AACACACATGAATGAACGCAAACA
1 AACACAAACGAATGAACGCAAACA
59916 AACA
1 AACA
59920 TAATCAAACA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.54, C:0.23, G:0.13, T:0.10
Consensus pattern (24 bp):
AACACAAACGAATGAACGCAAACA
Found at i:60437 original size:2 final size:2
Alignment explanation
Indices: 60430--60472 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
60420 TCTTTAATTT
60430 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
60472 T
1 T
60473 GAGAATTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:60873 original size:2 final size:2
Alignment explanation
Indices: 60868--60944 Score: 147
Period size: 2 Copynumber: 39.0 Consensus size: 2
60858 AAAACAAAAA
60868 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60909 AT AT 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 AT AT
60945 GGTTGGCATG
Statistics
Matches: 74, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 73 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:65006 original size:35 final size:36
Alignment explanation
Indices: 64940--65008 Score: 86
Period size: 35 Copynumber: 1.9 Consensus size: 36
64930 CCTTATGTCT
* * * *
64940 ATAAGGAATTACTAGTTTGATCAGTGTTGAACCTAC
1 ATAAGGAATTACCAGCTTGATCAGAGCTGAACCTAC
*
64976 ATAAGG-ATTACCAGCTTGATCGGAGCTGAACCT
1 ATAAGGAATTACCAGCTTGATCAGAGCTGAACCT
65009 GCAGAGACTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
35 22 0.79
36 6 0.21
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (36 bp):
ATAAGGAATTACCAGCTTGATCAGAGCTGAACCTAC
Found at i:66684 original size:20 final size:20
Alignment explanation
Indices: 66661--66700 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
66651 ACTCAATTTA
66661 CTAATTTAAAAATCTAACAG
1 CTAATTTAAAAATCTAACAG
66681 CTAATTTAAAAATCTAACAG
1 CTAATTTAAAAATCTAACAG
66701 TGGCATAACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.05, T:0.30
Consensus pattern (20 bp):
CTAATTTAAAAATCTAACAG
Done.