Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006869.1 Hibiscus syriacus cultivar Beakdansim tig00017482_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: 73280
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.34
Found at i:1862 original size:23 final size:21
Alignment explanation
Indices: 1813--1862 Score: 55
Period size: 24 Copynumber: 2.2 Consensus size: 21
1803 TAAAACATTA
1813 AAAAAATAGATTATATAATTT
1 AAAAAATAGATTATATAATTT
* *
1834 ATAAAAATAGGATATGTATTATTT
1 A-AAAAATA-GAT-TATATAATTT
1858 AAAAA
1 AAAAA
1863 TATCAGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 1 0.04
22 7 0.29
23 7 0.29
24 9 0.38
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (21 bp):
AAAAAATAGATTATATAATTT
Found at i:2024 original size:23 final size:24
Alignment explanation
Indices: 1992--2042 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
1982 AAATATTATT
1992 TATATATATTTATAATACTAAATAAA
1 TATATAT-TTTATAATA-TAAATAAA
* *
2018 TAT-TATTTTTTTATATAAATAAA
1 TATATATTTTATAATATAAATAAA
2041 TA
1 TA
2043 ATAATAGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 10 0.43
24 7 0.30
25 3 0.13
26 3 0.13
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (24 bp):
TATATATTTTATAATATAAATAAA
Found at i:3480 original size:3 final size:3
Alignment explanation
Indices: 3427--3464 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
3417 TAATATTTAT
*
3427 TAA TAAA TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA T
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3465 TATTATATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:15889 original size:15 final size:16
Alignment explanation
Indices: 15862--15891 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
15852 CCTCTTCTCA
15862 TAATATACTTTTTTTG
1 TAATATACTTTTTTTG
15878 TAATAT-CTTTTTTT
1 TAATATACTTTTTTT
15892 TATAACATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.23, C:0.07, G:0.03, T:0.67
Consensus pattern (16 bp):
TAATATACTTTTTTTG
Found at i:15892 original size:16 final size:17
Alignment explanation
Indices: 15869--15906 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
15859 TCATAATATA
* *
15869 CTTTTTTTGTAATATCT
1 CTTTTTTTATAACATCT
15886 -TTTTTTTATAACATCT
1 CTTTTTTTATAACATCT
15902 CTTTT
1 CTTTT
15907 AACAACACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.18, C:0.13, G:0.03, T:0.66
Consensus pattern (17 bp):
CTTTTTTTATAACATCT
Found at i:16160 original size:24 final size:24
Alignment explanation
Indices: 16124--16179 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
16114 AACATGCTTG
16124 TTTATTGAGTTGTGTATAAGCTCA
1 TTTATTGAGTTGTGTATAAGCTCA
* *
16148 TTTATTGATTTGTTTATAAGCTCA
1 TTTATTGAGTTGTGTATAAGCTCA
16172 TTTATTGA
1 TTTATTGA
16180 ATCTTTTGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.25, C:0.07, G:0.16, T:0.52
Consensus pattern (24 bp):
TTTATTGAGTTGTGTATAAGCTCA
Found at i:20619 original size:18 final size:18
Alignment explanation
Indices: 20596--20630 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20586 GACCCGAACC
20596 AAAATAATATATTTATTA
1 AAAATAATATATTTATTA
* *
20614 AAAATATTATTTTTATT
1 AAAATAATATATTTATT
20631 CAATACAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AAAATAATATATTTATTA
Found at i:21392 original size:63 final size:62
Alignment explanation
Indices: 21293--21415 Score: 176
Period size: 63 Copynumber: 2.0 Consensus size: 62
21283 CACCAACAGC
* *
21293 AACAAAAAGTGATTTACATTCGATAGAACCACTCAACAACCAAA-TCAGACATATCCTCAAAAT
1 AACAAAAAGTGATTGACATTCGATAGAACCACTCAACAACCAAACCCA-ACATATCC-CAAAAT
* * *
21356 AACAAAAAGTGGTTGATATTCGATAGAACCAGTCAACAACCAAACCCAACATATCCCAAA
1 AACAAAAAGTGATTGACATTCGATAGAACCACTCAACAACCAAACCCAACATATCCCAAA
21416 TAGAAAAAAC
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
62 4 0.07
63 48 0.89
64 2 0.04
ACGTcount: A:0.47, C:0.24, G:0.10, T:0.19
Consensus pattern (62 bp):
AACAAAAAGTGATTGACATTCGATAGAACCACTCAACAACCAAACCCAACATATCCCAAAAT
Found at i:25826 original size:4 final size:4
Alignment explanation
Indices: 25817--25877 Score: 50
Period size: 4 Copynumber: 15.2 Consensus size: 4
25807 CATATAAAAA
* * * * * * * *
25817 ATAC ATAC ATAT ATAT ATAC ATAT ATAC ACAT ATAT ATAT ATAT ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
25865 ATAC ATAC ATAC A
1 ATAC ATAC ATAC A
25878 CATTTTCATT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 49 1.00
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (4 bp):
ATAC
Found at i:25830 original size:2 final size:2
Alignment explanation
Indices: 25825--25863 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
25815 AAATACATAC
* * *
25825 AT AT AT AT AT AC AT AT AT AC AC AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
25864 CATACATACA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:25842 original size:8 final size:8
Alignment explanation
Indices: 25817--25877 Score: 59
Period size: 8 Copynumber: 7.6 Consensus size: 8
25807 CATATAAAAA
*
25817 ATACATAC
1 ATACATAT
*
25825 ATATATAT
1 ATACATAT
25833 ATACATAT
1 ATACATAT
*
25841 ATACACAT
1 ATACATAT
*
25849 ATATATAT
1 ATACATAT
* *
25857 ATATATAC
1 ATACATAT
*
25865 ATACATAC
1 ATACATAT
25873 ATACA
1 ATACA
25878 CATTTTCATT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 45 1.00
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (8 bp):
ATACATAT
Found at i:25842 original size:10 final size:10
Alignment explanation
Indices: 25827--25867 Score: 59
Period size: 10 Copynumber: 4.3 Consensus size: 10
25817 ATACATACAT
25827 ATATATATAC
1 ATATATATAC
*
25837 ATATATACAC
1 ATATATATAC
25847 ATATATAT--
1 ATATATATAC
25855 ATATATATAC
1 ATATATATAC
25865 ATA
1 ATA
25868 CATACATACA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 8 0.30
10 19 0.70
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (10 bp):
ATATATATAC
Found at i:25850 original size:20 final size:20
Alignment explanation
Indices: 25821--25865 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
25811 TAAAAAATAC
*
25821 ATACATATATATATACATAT
1 ATACACATATATATACATAT
*
25841 ATACACATATATATATATAT
1 ATACACATATATATACATAT
25861 ATACA
1 ATACA
25866 TACATACATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (20 bp):
ATACACATATATATACATAT
Found at i:25852 original size:18 final size:18
Alignment explanation
Indices: 25829--25875 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
25819 ACATACATAT
25829 ATATATACATATATACAC
1 ATATATACATATATACAC
* *
25847 ATATATATATATATATAC
1 ATATATACATATATACAC
*
25865 ATACATACATA
1 ATATATACATA
25876 CACATTTTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (18 bp):
ATATATACATATATACAC
Found at i:25876 original size:12 final size:12
Alignment explanation
Indices: 25817--25877 Score: 67
Period size: 12 Copynumber: 5.4 Consensus size: 12
25807 CATATAAAAA
25817 ATACATACATAT
1 ATACATACATAT
*
25829 ATATATACATAT
1 ATACATACATAT
25841 ATAC--ACATAT
1 ATACATACATAT
*
25851 AT--ATATATAT
1 ATACATACATAT
*
25861 ATACATACATAC
1 ATACATACATAT
25873 ATACA
1 ATACA
25878 CATTTTCATT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
10 15 0.38
12 25 0.62
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (12 bp):
ATACATACATAT
Found at i:25880 original size:10 final size:10
Alignment explanation
Indices: 25821--25880 Score: 57
Period size: 10 Copynumber: 5.8 Consensus size: 10
25811 TAAAAAATAC
*
25821 ATACATATAT
1 ATACACATAT
*
25831 ATATACATAT
1 ATACACATAT
25841 ATACACATAT
1 ATACACATAT
* *
25851 ATATATATAT
1 ATACACATAT
*
25861 ATACATACATAC
1 ATAC--ACATAT
25873 ATACACAT
1 ATACACAT
25881 TTTCATTTAT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
10 32 0.80
12 8 0.20
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (10 bp):
ATACACATAT
Found at i:26262 original size:31 final size:30
Alignment explanation
Indices: 26212--26307 Score: 102
Period size: 31 Copynumber: 3.1 Consensus size: 30
26202 ATCCCAAAGG
* *
26212 ACCTATCCATATGTTCCGAATAACATAGGTA
1 ACCTGTCCATATGTCCCGAA-AACATAGGTA
* *
26243 ACCTGTCGATATGTCCCGAAGGACATAGGTA
1 ACCTGTCCATATGTCCCGAA-AACATAGGTA
* **
26274 AACTGTCCATATGTCTTGAAAGACATAGGTA
1 ACCTGTCCATATGTCCCGAAA-ACATAGGTA
26305 ACC
1 ACC
26308 CTCGACTCTT
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (30 bp):
ACCTGTCCATATGTCCCGAAAACATAGGTA
Found at i:28366 original size:2 final size:2
Alignment explanation
Indices: 28359--28429 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
28349 CATATTCATA
28359 AT AT AT 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 AT AT AT
28401 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
28430 GTATTTCCCA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28965 original size:20 final size:20
Alignment explanation
Indices: 28942--28991 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
28932 CTTACTCTTG
28942 GTATCGATAC-CTTCACATCA
1 GTATCGATACACTTCA-ATCA
28962 GTATCGATACTACTTCAATCA
1 GTATCGATAC-ACTTCAATCA
*
28983 ATATCGATA
1 GTATCGATA
28992 ATGTTCATCG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 10 0.37
21 12 0.44
22 5 0.19
ACGTcount: A:0.34, C:0.24, G:0.10, T:0.32
Consensus pattern (20 bp):
GTATCGATACACTTCAATCA
Found at i:31743 original size:16 final size:16
Alignment explanation
Indices: 31722--31755 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
31712 CAGTTTTGGT
31722 CCCTTGGCTTCATGGA
1 CCCTTGGCTTCATGGA
31738 CCCTTGGCTTCATGGA
1 CCCTTGGCTTCATGGA
31754 CC
1 CC
31756 GTTTGTTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.12, C:0.35, G:0.24, T:0.29
Consensus pattern (16 bp):
CCCTTGGCTTCATGGA
Found at i:38030 original size:24 final size:24
Alignment explanation
Indices: 37973--38030 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
37963 CCGAAGTGCC
* * *
37973 ACGTAGAATATGTCCCGAAGGATA
1 ACGTAGAATTTGTCCCGAAAGACA
*
37997 GCGTAGAATTTGTCCCGAAAGACA
1 ACGTAGAATTTGTCCCGAAAGACA
38021 ACGTAGAATT
1 ACGTAGAATT
38031 GTTCTGAAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.22
Consensus pattern (24 bp):
ACGTAGAATTTGTCCCGAAAGACA
Found at i:38286 original size:2 final size:2
Alignment explanation
Indices: 38281--38334 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
38271 CATATTCATA
38281 AT AT AT 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 AT AT AT
38323 AT AT AT AT AT AT
1 AT AT AT AT AT AT
38335 TCCCATATCA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43392 original size:20 final size:20
Alignment explanation
Indices: 43369--43418 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
43359 CTTACTCTTG
43369 GTATCGATAC-CTTCACATCA
1 GTATCGATACACTTCA-ATCA
43389 GTATCGATACTACTTCAATCA
1 GTATCGATAC-ACTTCAATCA
*
43410 ATATCGATA
1 GTATCGATA
43419 ATGTTCATCG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 10 0.37
21 12 0.44
22 5 0.19
ACGTcount: A:0.34, C:0.24, G:0.10, T:0.32
Consensus pattern (20 bp):
GTATCGATACACTTCAATCA
Found at i:46168 original size:16 final size:16
Alignment explanation
Indices: 46147--46180 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
46137 CAGTTTTGGT
*
46147 CCCTTGTCTTCATGGA
1 CCCTTGGCTTCATGGA
46163 CCCTTGGCTTCATGGA
1 CCCTTGGCTTCATGGA
46179 CC
1 CC
46181 ATTTGTTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.35, G:0.21, T:0.32
Consensus pattern (16 bp):
CCCTTGGCTTCATGGA
Found at i:52886 original size:48 final size:47
Alignment explanation
Indices: 52815--52905 Score: 139
Period size: 48 Copynumber: 1.9 Consensus size: 47
52805 CTGCTCACAT
52815 AATTTGTACCGAAGTGCCACGTAGAATATGTCCCGAAGGACCGCGTAG
1 AATTTGTACCGAAGTGCCACGTAGAAT-TGTCCCGAAGGACCGCGTAG
* *
52863 AATTTGTCCCGAAG-GACCACGTAGAATTGTCCTGAAGGACCGC
1 AATTTGTACCGAAGTG-CCACGTAGAATTGTCCCGAAGGACCGC
52906 ATACCCTCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
47 16 0.40
48 24 0.60
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (47 bp):
AATTTGTACCGAAGTGCCACGTAGAATTGTCCCGAAGGACCGCGTAG
Found at i:52899 original size:23 final size:23
Alignment explanation
Indices: 52818--52903 Score: 111
Period size: 24 Copynumber: 3.7 Consensus size: 23
52808 CTCACATAAT
*
52818 TTGTACCGAAGTG-CCACGTAGAA
1 TTGTCCCGAAG-GACCACGTAGAA
*
52841 TATGTCCCGAAGGACCGCGTAGAA
1 T-TGTCCCGAAGGACCACGTAGAA
52865 TTTGTCCCGAAGGACCACGTAGAA
1 -TTGTCCCGAAGGACCACGTAGAA
*
52889 TTGTCCTGAAGGACC
1 TTGTCCCGAAGGACC
52904 GCATACCCTC
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
23 16 0.29
24 39 0.70
25 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.27, T:0.21
Consensus pattern (23 bp):
TTGTCCCGAAGGACCACGTAGAA
Found at i:53837 original size:20 final size:20
Alignment explanation
Indices: 53812--53851 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
53802 CCGTTAGACA
*
53812 GGGGGGAATCGGTACCCCCT
1 GGGGGGAATAGGTACCCCCT
*
53832 GGGGGGAATATGTACCCCCT
1 GGGGGGAATAGGTACCCCCT
53852 AGACAATCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.28, G:0.38, T:0.17
Consensus pattern (20 bp):
GGGGGGAATAGGTACCCCCT
Found at i:54696 original size:20 final size:20
Alignment explanation
Indices: 54673--54722 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
54663 CTTACTCTTG
54673 GTATCGATAC-CTTCACATCA
1 GTATCGATACACTTCA-ATCA
54693 GTATCGATACTACTTCAATCA
1 GTATCGATAC-ACTTCAATCA
*
54714 ATATCGATA
1 GTATCGATA
54723 ATGTTCATCG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 10 0.37
21 12 0.44
22 5 0.19
ACGTcount: A:0.34, C:0.24, G:0.10, T:0.32
Consensus pattern (20 bp):
GTATCGATACACTTCAATCA
Done.