Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000851.1 Hibiscus syriacus cultivar Beakdansim tig00001644_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: 7304151
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 31 of 31
Found at i:7239031 original size:22 final size:23
Alignment explanation
Indices: 7239001--7239045 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
7238991 ATATATATAT
7239001 AAACGAACGATAAACAAACACTA
1 AAACGAACGATAAACAAACACTA
*
7239024 AAAC-AACGCTAAACAAACACTA
1 AAACGAACGATAAACAAACACTA
7239046 TGAACGCTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.60, C:0.24, G:0.07, T:0.09
Consensus pattern (23 bp):
AAACGAACGATAAACAAACACTA
Found at i:7239155 original size:23 final size:23
Alignment explanation
Indices: 7239123--7239190 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
7239113 AAACGAACGC
7239123 TAAACGAACATGTT-GTGAACAT
1 TAAACGAACATGTTCGTGAACAT
* * *
7239145 ATAAACAAACACGTTCTTGAACAT
1 -TAAACGAACATGTTCGTGAACAT
*
7239169 TAAATGAACATGTTCGTGAACA
1 TAAACGAACATGTTCGTGAACA
7239191 ATACATAAAC
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
23 30 0.81
24 7 0.19
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.26
Consensus pattern (23 bp):
TAAACGAACATGTTCGTGAACAT
Found at i:7239229 original size:30 final size:30
Alignment explanation
Indices: 7239190--7239301 Score: 122
Period size: 30 Copynumber: 3.7 Consensus size: 30
7239180 GTTCGTGAAC
*
7239190 AATACATAAACGAACACAAACACCTTTAAA
1 AATAAATAAACGAACACAAACACCTTTAAA
* *
7239220 AATAAATAAACGAACACGAACACAATATTAAA
1 AATAAATAAACGAACACAAACAC-CT-TTAAA
* *
7239252 AACT---TAAATGAACACAAACACCTTCAAA
1 AA-TAAATAAACGAACACAAACACCTTTAAA
*
7239280 AATAAATAAACGAACACGAACA
1 AATAAATAAACGAACACAAACA
7239302 TAACCTTGTT
Statistics
Matches: 67, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
27 1 0.01
28 6 0.09
29 1 0.01
30 50 0.75
31 1 0.01
32 7 0.10
33 1 0.01
ACGTcount: A:0.59, C:0.21, G:0.05, T:0.15
Consensus pattern (30 bp):
AATAAATAAACGAACACAAACACCTTTAAA
Found at i:7252115 original size:25 final size:26
Alignment explanation
Indices: 7252087--7252142 Score: 96
Period size: 25 Copynumber: 2.2 Consensus size: 26
7252077 TAAATTAATT
*
7252087 AAATCTTTTTTTAAAAT-AAAATAAA
1 AAATATTTTTTTAAAATGAAAATAAA
7252112 AAATATTTTTTTAAAATGAAAATAAA
1 AAATATTTTTTTAAAATGAAAATAAA
7252138 AAATA
1 AAATA
7252143 AAAAAAGTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 16 0.55
26 13 0.45
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (26 bp):
AAATATTTTTTTAAAATGAAAATAAA
Found at i:7253205 original size:20 final size:20
Alignment explanation
Indices: 7253180--7253217 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
7253170 AACAGTGGTT
7253180 CTTTAATAT-ATATTCTGACC
1 CTTTAATATGA-ATTCTGACC
7253200 CTTTAATATGAATTCTGA
1 CTTTAATATGAATTCTGA
7253218 TTTCTAAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.45
Consensus pattern (20 bp):
CTTTAATATGAATTCTGACC
Found at i:7268998 original size:25 final size:24
Alignment explanation
Indices: 7268960--7269007 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
7268950 TGAAAATAAA
*
7268960 ATAAAAATTGCATAACATACATAC
1 ATAAAAATTACATAACATACATAC
*
7268984 ATAAAAATGTACATACCATACATA
1 ATAAAAAT-TACATAACATACATA
7269008 AAATAGTAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.54, C:0.17, G:0.04, T:0.25
Consensus pattern (24 bp):
ATAAAAATTACATAACATACATAC
Found at i:7271094 original size:55 final size:54
Alignment explanation
Indices: 7271035--7271233 Score: 143
Period size: 55 Copynumber: 3.6 Consensus size: 54
7271025 GATAAGTGAG
7271035 ACTTGAAAAATTCTTC-AAAATCGGGTTCGCTCCCTATCGTTTCAGGGAACATAGA
1 ACTTGAAAAA-TCTTCGAAAA-CGGGTTCGCTCCCTATCGTTTCAGGGAACATAGA
* *** * **
7271090 ACTTGAAGAATCTTCTGGGGACGGGTTCGCTCCCTATTGTTTCAGGGAGTATAGA
1 ACTTGAAAAATCTTC-GAAAACGGGTTCGCTCCCTATCGTTTCAGGGAACATAGA
* * ** * * * **
7271145 ACTCGAATAATCTTCTGCTAACTGGTTCGCTCCCTCT-TTCTTCAGGGAGTATAGA
1 ACTTGAAAAATCTTC-GAAAACGGGTTCGCTCCCTATCGT-TTCAGGGAACATAGA
* * **
7271200 ACTCG-AACATCTTCTTCAAACGGGTTCGCTCCCT
1 ACTTGAAAAATCTTC-GAAAACGGGTTCGCTCCCT
7271234 CTTTCTTCAG
Statistics
Matches: 121, Mismatches: 20, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
54 30 0.25
55 90 0.74
56 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (54 bp):
ACTTGAAAAATCTTCGAAAACGGGTTCGCTCCCTATCGTTTCAGGGAACATAGA
Found at i:7271292 original size:55 final size:53
Alignment explanation
Indices: 7271119--7271711 Score: 515
Period size: 55 Copynumber: 10.9 Consensus size: 53
7271109 GACGGGTTCG
* ** * *
7271119 CTCCCTATTGT-TTCAGGGAGTATAGAACTCGAATAATCTTCTGCTAA-CTGGTTCG
1 CTCCCTATT-TCTTCAGGGAGTAT-GAACTCGAACAATCTTCAAC-AATC-GGGTCT
* ** * *
7271174 CTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAC-ATCTTCTTCAAACGGGTTCG
1 CTCCCTATTTCTTCAGGGAGTAT-GAACTCGAACAATCTTCAACAATCGGG-TCT
* ** *
7271228 CTCCCTCTTTCTTCAGGGAGTATGGAACTCGAACAATCTTCTGCAAGCGGGT-T
1 CTCCCTATTTCTTCAGGGAGTAT-GAACTCGAACAATCTTCAACAATCGGGTCT
* * * * * *
7271281 CATTCCCTCTTT-ATCTAGGGAGTGTGGAACTCGAAC-GTCTT-TA-AA-CGGGTTCA
1 C--TCCCTATTTCTTC-AGGGAGTAT-GAACTCGAACAATCTTCAACAATCGGG-TCT
* * * ** * *
7271334 CTCCCTCTTTCTTCAGGGAGAATAGAACTCGAA-TATCTTCTTCAAACGGGTTT
1 CTCCCTATTTCTTCAGGGAGTAT-GAACTCGAACAATCTTCAACAATCGGGTCT
* *
7271387 GCTCCCTCTTTC-TCTAGGGAGTATGAAACTCGAACAATCTTCAACAATCGTGTCT
1 -CTCCCTATTTCTTC-AGGGAGTATG-AACTCGAACAATCTTCAACAATCGGGTCT
* *
7271442 GCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCT
1 -CTCCCTATTTCTTCAGGGAGTATGA-ACTCGAACAATCTTCAACAATCGGGTCT
* *
7271497 GCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCT
1 -CTCCCTATTTCTTCAGGGAGTATGA-ACTCGAACAATCTTCAACAATCGGGTCT
* * *
7271552 GCTCCCTATTTCTTCAGAGAGTATAGGACTCGAACAATCTTCAACAATCGTGTCT
1 -CTCCCTATTTCTTCAGGGAGTAT-GAACTCGAACAATCTTCAACAATCGGGTCT
* *
7271607 GCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCT
1 -CTCCCTATTTCTTCAGGGAGTATGA-ACTCGAACAATCTTCAACAATCGGGTCT
* *
7271662 GCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCG
1 -CTCCCTATTTCTTCAGGGAGTATGA-ACTCGAACAATCTTCAACAATCG
7271712 TTGGGAAATC
Statistics
Matches: 483, Mismatches: 33, Indels: 44
0.86 0.06 0.08
Matches are distributed among these distances:
51 33 0.07
52 6 0.01
53 13 0.03
54 86 0.18
55 342 0.71
56 3 0.01
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (53 bp):
CTCCCTATTTCTTCAGGGAGTATGAACTCGAACAATCTTCAACAATCGGGTCT
Found at i:7271475 original size:160 final size:164
Alignment explanation
Indices: 7271118--7271703 Score: 603
Period size: 165 Copynumber: 3.6 Consensus size: 164
7271108 GGACGGGTTC
* * ** *
7271118 GCTCCCTATTGT-TTCAGGGAGTAT-AGAACTCGAATAATCTTCTGCTAA-CTGGTTCGCTCCCT
1 GCTCCCTATT-TCTTCAGAGAGTATGAG-ACTCGAACAATCTTCAAC-AATCGGGTTCGCTCCCT
* *
7271180 CTTTCTTCAGGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGG
63 CTTTCTTCAGGGAGTATAGAACTCGAAAATCTTCTTCAAACGGGTTTGCTCCCTCTTTCTTCAGG
* ** * *
7271245 GAGTATGGAACTCGAACAATCTTCTGCAAGCGGGT-T
128 GAGTATGAAACTCGAACAATCTTCAACAATCGTGTCT
* * * * * * *
7271281 -CATTCCCTCTTT-ATCTAGGGAGTGTG-GAACTCGAAC-GTCTT-TA-AA-CGGGTTCACTCCC
1 GC--TCCCTATTTCTTC-AGAGAGTATGAG-ACTCGAACAATCTTCAACAATCGGGTTCGCTCCC
* *
7271339 TCTTTCTTCAGGGAGAATAGAACTCGAATATCTTCTTCAAACGGGTTTGCTCCCTCTTTC-TCTA
62 TCTTTCTTCAGGGAGTATAGAACTCGAAAATCTTCTTCAAACGGGTTTGCTCCCTCTTTCTTC-A
7271403 GGGAGTATGAAACTCGAACAATCTTCAACAATCGTGTCT
126 GGGAGTATGAAACTCGAACAATCTTCAACAATCGTGTCT
* *
7271442 GCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTG-TCTGCTCCCTAT
1 GCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGGGTTC-GCTCCCTCT
* ** * * * * *
7271506 TTCTTCAGAGAGTAT-GAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGA
65 TTCTTCAGGGAGTATAGA-ACTCGAA-AATCTTCTTCAAACGGGTTTGCTCCCTCTTTCTTCAGG
*
7271570 GAGTAT-AGGACTCGAACAATCTTCAACAATCGTGTCT
128 GAGTATGA-AACTCGAACAATCTTCAACAATCGTGTCT
* *
7271607 GCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTG-TCTGCTCCCTAT
1 GCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGGGTTC-GCTCCCTCT
*
7271671 TTCTTCAGAGAGTAT-GAGACTCGAACAATCTTC
65 TTCTTCAGGGAGTATAGA-ACTCGAA-AATCTTC
7271704 AATAATCGTT
Statistics
Matches: 369, Mismatches: 36, Indels: 34
0.84 0.08 0.08
Matches are distributed among these distances:
159 2 0.01
160 127 0.34
161 8 0.02
162 4 0.01
163 13 0.04
164 55 0.15
165 158 0.43
166 2 0.01
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (164 bp):
GCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGGGTTCGCTCCCTCTT
TCTTCAGGGAGTATAGAACTCGAAAATCTTCTTCAAACGGGTTTGCTCCCTCTTTCTTCAGGGAG
TATGAAACTCGAACAATCTTCAACAATCGTGTCT
Found at i:7271712 original size:55 final size:55
Alignment explanation
Indices: 7271334--7271712 Score: 586
Period size: 55 Copynumber: 6.9 Consensus size: 55
7271324 AACGGGTTCA
* * * * ** * * *
7271334 CTCCCTCTTTCTTCAGGGAGAAT-AGAACTCGAA-TATCTTCTTCAAACGGGTTTG
1 CTCCCTATTTCTTCAGAGAGTATGAG-ACTCGAACAATCTTCAACAATCGTGTCTG
* * *
7271388 CTCCCTCTTTC-TCTAGGGAGTATGAAACTCGAACAATCTTCAACAATCGTGTCTG
1 CTCCCTATTTCTTC-AGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTG
7271443 CTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTG
1 CTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTG
7271498 CTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTG
1 CTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTG
7271553 CTCCCTATTTCTTCAGAGAGTAT-AGGACTCGAACAATCTTCAACAATCGTGTCTG
1 CTCCCTATTTCTTCAGAGAGTATGA-GACTCGAACAATCTTCAACAATCGTGTCTG
7271608 CTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTG
1 CTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTG
*
7271663 CTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGT
1 CTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGT
7271713 TGGGAAATCT
Statistics
Matches: 307, Mismatches: 12, Indels: 11
0.93 0.04 0.03
Matches are distributed among these distances:
53 2 0.01
54 27 0.09
55 275 0.90
56 3 0.01
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.31
Consensus pattern (55 bp):
CTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTG
Found at i:7283809 original size:25 final size:24
Alignment explanation
Indices: 7283771--7283818 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
7283761 TGAAAATAAA
*
7283771 ATAAAAATTGCATAACATACATAC
1 ATAAAAATTACATAACATACATAC
*
7283795 ATAAAAATGTACATACCATACATA
1 ATAAAAAT-TACATAACATACATA
7283819 AAATAGTAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.54, C:0.17, G:0.04, T:0.25
Consensus pattern (24 bp):
ATAAAAATTACATAACATACATAC
Found at i:7286811 original size:31 final size:31
Alignment explanation
Indices: 7286776--7286837 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
7286766 GTGAGAAGCC
* *
7286776 ACCTCTCATTTATTGATATGCACACAATTTG
1 ACCTCTCATGTATTGATATCCACACAATTTG
*
7286807 ACCTCTCATGTATTGATCTCCACACAATTTG
1 ACCTCTCATGTATTGATATCCACACAATTTG
7286838 GCCATGTCTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.27, C:0.26, G:0.10, T:0.37
Consensus pattern (31 bp):
ACCTCTCATGTATTGATATCCACACAATTTG
Found at i:7287463 original size:18 final size:18
Alignment explanation
Indices: 7287440--7287474 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
7287430 GGTTAAATAA
7287440 TATATTTATAATAATTTT
1 TATATTTATAATAATTTT
*
7287458 TATATTTGTAATAATTT
1 TATATTTATAATAATTT
7287475 GGGGAGAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (18 bp):
TATATTTATAATAATTTT
Found at i:7288515 original size:3 final size:3
Alignment explanation
Indices: 7288509--7288534 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
7288499 GTCTAATAGC
7288509 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
7288535 TGGTTAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:7288894 original size:22 final size:22
Alignment explanation
Indices: 7288853--7288900 Score: 80
Period size: 23 Copynumber: 2.2 Consensus size: 22
7288843 CCAATCCCAT
7288853 TAGTAATTTAAATAATATTTTG
1 TAGTAATTTAAATAATATTTTG
7288875 ATAGTAATTTAAA-AATATTTTG
1 -TAGTAATTTAAATAATATTTTG
7288897 TAGT
1 TAGT
7288901 CTCTCTAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 4 0.16
22 9 0.36
23 12 0.48
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (22 bp):
TAGTAATTTAAATAATATTTTG
Found at i:7294665 original size:25 final size:25
Alignment explanation
Indices: 7294635--7294684 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
7294625 ATAAATGGAG
7294635 ACGAACTCGATTTTTTAATACCACT
1 ACGAACTCGATTTTTTAATACCACT
7294660 ACGAACTCGATTTTTTAATACCACT
1 ACGAACTCGATTTTTTAATACCACT
7294685 CTCAGTTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.36
Consensus pattern (25 bp):
ACGAACTCGATTTTTTAATACCACT
Found at i:7300792 original size:3 final size:3
Alignment explanation
Indices: 7300784--7300812 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
7300774 CTAACCCTCT
7300784 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
7300813 GAAATGGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:7301786 original size:16 final size:15
Alignment explanation
Indices: 7301765--7301794 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
7301755 TAATTTTATA
7301765 AAAGGGACATGACATT
1 AAAGGGACA-GACATT
7301781 AAAGGGACAGACAT
1 AAAGGGACAGACAT
7301795 GATTTCATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.47, C:0.13, G:0.27, T:0.13
Consensus pattern (15 bp):
AAAGGGACAGACATT
Done.