Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000339.1 Hibiscus syriacus cultivar Beakdansim tig00000629_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: 74918
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Found at i:10626 original size:13 final size:13
Alignment explanation
Indices: 10608--10632 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10598 CACATGGATT
10608 CCTCATCCCAACC
1 CCTCATCCCAACC
10621 CCTCATCCCAAC
1 CCTCATCCCAAC
10633 AATACCCACG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.60, G:0.00, T:0.16
Consensus pattern (13 bp):
CCTCATCCCAACC
Found at i:13833 original size:139 final size:131
Alignment explanation
Indices: 13607--13879 Score: 393
Period size: 139 Copynumber: 2.0 Consensus size: 131
13597 AATTTATTAG
* *
13607 TTTATTAAATTTATTGTACTAATTTTTATTACTTTTTGCAGTATAAATGGAATGCAAGCTACTAC
1 TTTATTAAATTTATTGTACTAATTTTTATTAATTTTTGCAGTATAAATGGAAGGCAAGCTACTAC
*
13672 GTTTAGATGAGAATCATATCTCGAGGCATTTTGTCGATATGATAACAATTTTAAATTGTGTTGTT
66 GTTTAGATGAGAATCATATCTCGAGGCATTTTGTCAATATGATAACAATTTTAAATTGTGTTGTT
13737 A
131 A
*
13738 TTTATTAAATTTTATTGTACTAATTTTTTTATTTATTATTTTTGCAGTTATAAAATGGAAGGCAT
1 TTTATTAAA-TTTATTGTACTAA--TTTTTA-TTA--ATTTTTGCAG-TAT-AAATGGAAGGCAA
* * * * *
13803 GTTGCTACGTTTAGATGAGAATCATTTCTCGAGGTATTTTGTCAATATGGTAACAATTTTAAATT
58 GCTACTACGTTTAGATGAGAATCATATCTCGAGGCATTTTGTCAATATGATAACAATTTTAAATT
13868 GTGTTGTTA
123 GTGTTGTTA
13877 TTT
1 TTT
13880 TAATTATTGT
Statistics
Matches: 125, Mismatches: 9, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
131 9 0.07
132 13 0.10
134 6 0.05
135 3 0.02
137 9 0.07
138 3 0.02
139 82 0.66
ACGTcount: A:0.30, C:0.08, G:0.15, T:0.47
Consensus pattern (131 bp):
TTTATTAAATTTATTGTACTAATTTTTATTAATTTTTGCAGTATAAATGGAAGGCAAGCTACTAC
GTTTAGATGAGAATCATATCTCGAGGCATTTTGTCAATATGATAACAATTTTAAATTGTGTTGTT
A
Found at i:15547 original size:21 final size:21
Alignment explanation
Indices: 15508--15547 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
15498 ACCATTTCAT
*
15508 ATGCCACCGCAGCTAGGTTAG
1 ATGCCACCGCAGCGAGGTTAG
* *
15529 ATGCCACCGCCGCGGGGTT
1 ATGCCACCGCAGCGAGGTT
15548 TTATGACCCC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.33, G:0.33, T:0.17
Consensus pattern (21 bp):
ATGCCACCGCAGCGAGGTTAG
Found at i:17170 original size:142 final size:137
Alignment explanation
Indices: 16918--17200 Score: 449
Period size: 142 Copynumber: 2.0 Consensus size: 137
16908 AATTTATTAG
16918 TTTATTAAATTTTATTGTACTAATTTTTTTATTACTTTTTGCAGTAATAAAATGGAAGGCAAGCT
1 TTTATTAAATTTTATTGTACTAATTTTTTTATTACTTTTTGCAGTAATAAAATGGAAGGCAAGCT
*
16983 ACTACGTTTAGATGAGAATCATATCTCGAGGCATTTTGTCGATATGATAACAATTTTAAATTGTG
66 ACTACGTTTAGATGAGAATCATATCTCGAGGCATTTTGTCAATATGATAACAATTTTAAATTGTG
17048 TTGTTAT
131 TTGTTAT
*
17055 TTTATTAAATTTTATTGTACTAATTTTATTTATTTATTACTTTTTGCAGTTATAAAATGGAAGGC
1 TTTATTAAATTTTATTGTACTAA---T-TTT-TTTATTACTTTTTGCAGTAATAAAATGGAAGGC
* * * * * *
17120 ATGTTGCTACGTTTAGATGAGAATCATTTCTCGAGGCATTTTGTCAATATGGTAATAATTTTAAA
61 AAGCTACTACGTTTAGATGAGAATCATATCTCGAGGCATTTTGTCAATATGATAACAATTTTAAA
17185 TTGTGTTGTTAT
126 TTGTGTTGTTAT
17197 TTTA
1 TTTA
17201 ATTATTGTAA
Statistics
Matches: 133, Mismatches: 8, Indels: 5
0.91 0.05 0.03
Matches are distributed among these distances:
137 23 0.17
140 1 0.01
141 3 0.02
142 106 0.80
ACGTcount: A:0.30, C:0.08, G:0.15, T:0.46
Consensus pattern (137 bp):
TTTATTAAATTTTATTGTACTAATTTTTTTATTACTTTTTGCAGTAATAAAATGGAAGGCAAGCT
ACTACGTTTAGATGAGAATCATATCTCGAGGCATTTTGTCAATATGATAACAATTTTAAATTGTG
TTGTTAT
Found at i:23101 original size:65 final size:63
Alignment explanation
Indices: 23027--23184 Score: 192
Period size: 65 Copynumber: 2.5 Consensus size: 63
23017 TTAAATTGAT
* *
23027 CATCAAATGCATTTCATGCATCGATGCACATACCATGCATCGATGCACTAAGGAT-TTTATGAAA
1 CATCGAATGCATTTGATGCATCGATGCACA-ACCATGCATCGATGCACTAAGGATATTT-TG-AA
23091 A
63 A
* * ** *
23092 CATCGAATGCATTTGATGCATCGATGCACCAGCTATGCATCGATGCACTCTGGCTATTTTGAAA
1 CATCGAATGCATTTGATGCATCGATGCA-CAACCATGCATCGATGCACTAAGGATATTTTGAAA
* *
23156 CATCGAATTCACTTGATGCATCGATGCAC
1 CATCGAATGCATTTGATGCATCGATGCAC
23185 TCTTAGTGCA
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
63 1 0.01
64 29 0.35
65 47 0.57
66 5 0.06
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.28
Consensus pattern (63 bp):
CATCGAATGCATTTGATGCATCGATGCACAACCATGCATCGATGCACTAAGGATATTTTGAAA
Found at i:28869 original size:30 final size:30
Alignment explanation
Indices: 28810--28906 Score: 115
Period size: 30 Copynumber: 3.2 Consensus size: 30
28800 CCCGAAGGAC
*
28810 CTATCCAGAGGTCACAAAG-ACCCCGGTAA
1 CTATCCAGAGGTCACAAAGAACCTCGGTAA
*
28839 CTATCTAGAGGTCACAAAGAACCTCGGTAA
1 CTATCCAGAGGTCACAAAGAACCTCGGTAA
* * * * *
28869 CTGTCCATAGGTCTCGAAGAACCTAGGTAAA
1 CTATCCAGAGGTCACAAAGAACCTCGGT-AA
28900 CTATCCA
1 CTATCCA
28907 TATGTCTCGA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
29 18 0.32
30 31 0.54
31 8 0.14
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.20
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGAACCTCGGTAA
Found at i:28914 original size:31 final size:31
Alignment explanation
Indices: 28837--28931 Score: 102
Period size: 31 Copynumber: 3.1 Consensus size: 31
28827 AGACCCCGGT
* * * * *
28837 AACTATCTAGAGGTCACAAAGAACCTCGGT-
1 AACTATCCATAGGTCTCGAAGAACCTAGGTA
*
28867 AACTGTCCATAGGTCTCGAAGAACCTAGGTA
1 AACTATCCATAGGTCTCGAAGAACCTAGGTA
* * *
28898 AACTATCCATATGTCTCGAAAAACATAGGTA
1 AACTATCCATAGGTCTCGAAGAACCTAGGTA
28929 AAC
1 AAC
28932 CCTCGACTCT
Statistics
Matches: 54, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 24 0.44
31 30 0.56
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (31 bp):
AACTATCCATAGGTCTCGAAGAACCTAGGTA
Found at i:29851 original size:20 final size:20
Alignment explanation
Indices: 29826--29863 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
29816 TTCCCCTTGA
29826 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
29846 AGTGCATCGATGCATTCT
1 AGTGCATCGATGCATTCT
29864 TTAACATATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:29880 original size:24 final size:20
Alignment explanation
Indices: 29828--29883 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 20
29818 CCCCTTGAAG
*
29828 TGCATCGATGCATTCTACAG
1 TGCATCGATGCATTCTACAA
29848 TGCATCGATGCATTCTTTAACATA
1 TGCATCGATGCATTC--T-ACA-A
29872 TGCATCGATGCA
1 TGCATCGATGCA
29884 CTACCCATGC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 15 0.48
22 1 0.03
23 3 0.10
24 12 0.39
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (20 bp):
TGCATCGATGCATTCTACAA
Found at i:29980 original size:64 final size:64
Alignment explanation
Indices: 29871--30011 Score: 155
Period size: 64 Copynumber: 2.2 Consensus size: 64
29861 TCTTTAACAT
* * * *
29871 ATGCATCGATGCACTACCCATGCATTGATACACAAATTACCTTCGATGTTTTCAT-TTTAAGGGG
1 ATGCATCGATGCACTACCCATGCATCGATACACAAATTACATTCGATG-TTTCATCTTTAAAGAG
* * * *
29935 ATGCATCGATGCACT-CCTTATGCATCGATGCATC-AATTGCATTCGATGTTTCTTCTTTAAAGA
1 ATGCATCGATGCACTACC-CATGCATCGATACA-CAAATTACATTCGATGTTTCATCTTTAAAGA
29998 G
64 G
29999 -TGCATCGATGCAC
1 ATGCATCGATGCAC
30012 ATTGAATATG
Statistics
Matches: 66, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
63 20 0.30
64 45 0.68
65 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACCCATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGAG
Found at i:33157 original size:31 final size:31
Alignment explanation
Indices: 33089--33183 Score: 104
Period size: 31 Copynumber: 3.1 Consensus size: 31
33079 AGACCCCGAT
* * * * *
33089 AACTATCCATAGGTCACAAAGAACCTCGG-C
1 AACTGTCCATAGGTCTCGAAGAACCTAGGTA
33119 AACTGTCCATAGGTCTCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCTCGAAGAACCTAGGTA
* *
33150 AACTGTCCATATGTCTCGAA-AGACATAGGTA
1 AACTGTCCATAGGTCTCGAAGA-ACCTAGGTA
33181 AAC
1 AAC
33184 CCTCGACTCT
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
30 26 0.46
31 30 0.54
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (31 bp):
AACTGTCCATAGGTCTCGAAGAACCTAGGTA
Found at i:34100 original size:20 final size:22
Alignment explanation
Indices: 34075--34132 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
34065 TTCCCCTTGA
34075 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
34095 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
34118 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
34133 CTACCCATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:34211 original size:64 final size:63
Alignment explanation
Indices: 34120--34260 Score: 153
Period size: 64 Copynumber: 2.2 Consensus size: 63
34110 TCTTTAACAT
* * *
34120 GTGCATCGATGCACTACCCATGCATCGATACA-CAAATTACCTTCGATGTTTTCAT-TTTAAGGG
1 GTGCATCGATGCACTACCCATGCATCGATACATC-AATTACATTCGATG-TTTCATCTTTAAAGA
* * * * *
34183 GATGCATCGATGCACT-CCTTATGTATCGATGCATCAATTGCATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTACC-CATGCATCGATACATCAATTACATTCGATGTTTCATCTTTAAAGA
34247 GTGCATCGATGCAC
1 GTGCATCGATGCAC
34261 ATTGAATATG
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
63 21 0.32
64 44 0.67
65 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTACCCATGCATCGATACATCAATTACATTCGATGTTTCATCTTTAAAGA
Found at i:34274 original size:21 final size:21
Alignment explanation
Indices: 34248--34298 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
34238 CTTTAAAGAG
34248 TGCATCGATGCACATTGAATA
1 TGCATCGATGCACATTGAATA
34269 TGCATCGATGCACATTGAATA
1 TGCATCGATGCACATTGAATA
34290 TGCATCGAT
1 TGCATCGAT
34299 ACACCTTGCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (21 bp):
TGCATCGATGCACATTGAATA
Found at i:38670 original size:65 final size:64
Alignment explanation
Indices: 38543--38743 Score: 223
Period size: 65 Copynumber: 3.1 Consensus size: 64
38533 TTTTCAAAGT
* * *
38543 GATGCACCAATCCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATTGAATGCATTTCATGC
1 GATGCACCAA-CCATGCATCGATGCACTCAGGATATT---TTGAAACATCGAATGCATTTGATGC
38605 ATC
62 ATC
* *
38608 GATGTA-CATACCATGCATCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCATTTGATGCA
1 GATGCACCA-ACCATGCATCGATGCACTCAGGATATTT-TG-AAACATCGAATGCATTTGATGCA
38671 TC
63 TC
* * * *
38673 GATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTGATGCATC
1 GATGCACCAACCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATTTGATGCATC
38737 GATGCAC
1 GATGCAC
38744 TCTTAGTGCA
Statistics
Matches: 117, Mismatches: 11, Indels: 17
0.81 0.08 0.12
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 49 0.42
65 60 0.51
66 5 0.04
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (64 bp):
GATGCACCAACCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATTTGATGCATC
Found at i:66463 original size:20 final size:21
Alignment explanation
Indices: 66426--66467 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
66416 GTCATGCAAC
66426 TAATAATAGTTGCATAATGCA
1 TAATAATAGTTGCATAATGCA
*
66447 TAATAATGGTT-CATAATGCA
1 TAATAATAGTTGCATAATGCA
66467 T
1 T
66468 TGGAAGTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (21 bp):
TAATAATAGTTGCATAATGCA
Found at i:73797 original size:30 final size:30
Alignment explanation
Indices: 73763--73819 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
73753 ACCGTGTTAC
*
73763 GTTGGATAAACAAATAAGAGTAAACTACAA
1 GTTGGAAAAACAAATAAGAGTAAACTACAA
73793 GTTGGAAAAACAAATAAGAGTAAACTA
1 GTTGGAAAAACAAATAAGAGTAAACTA
73820 TATGTTTAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.54, C:0.09, G:0.18, T:0.19
Consensus pattern (30 bp):
GTTGGAAAAACAAATAAGAGTAAACTACAA
Done.