Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001282.1 Hibiscus syriacus cultivar Beakdansim tig00002516_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: 180784
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:154414 original size:39 final size:39
Alignment explanation
Indices: 154371--154457 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
154361 ATTAAAAATG
* *
154371 ATAGTTAACGATTAAGATTACCGTTACAAATTTTAATAA
1 ATAGTTAACGATTAAGATTACAGTTAAAAATTTTAATAA
154410 ATAGTTAACGATTAAGATTACAGTTAAAAATTTTAATAA
1 ATAGTTAACGATTAAGATTACAGTTAAAAATTTTAATAA
154449 ATAGTTAAC
1 ATAGTTAAC
154458 TGTTAATAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (39 bp):
ATAGTTAACGATTAAGATTACAGTTAAAAATTTTAATAA
Found at i:154752 original size:51 final size:50
Alignment explanation
Indices: 154683--154793 Score: 150
Period size: 51 Copynumber: 2.2 Consensus size: 50
154673 TTGTGAGATG
** *
154683 TATTTACTTACATCGGTGTAAGTATGTATTAAGTGTTATATTTTTTTATTT
1 TATTTACTTACATCGGTGTAAGTATGTATTAAGTACTATA-CTTTTTATTT
* * *
154734 TATTTACTTTCATTGGTGTAAGTATGTGTTAAGTACTATACTTTTTATTT
1 TATTTACTTACATCGGTGTAAGTATGTATTAAGTACTATACTTTTTATTT
*
154784 TATTCACTTA
1 TATTTACTTA
154794 TACCGAAGTA
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
50 17 0.33
51 35 0.67
ACGTcount: A:0.25, C:0.08, G:0.13, T:0.54
Consensus pattern (50 bp):
TATTTACTTACATCGGTGTAAGTATGTATTAAGTACTATACTTTTTATTT
Found at i:154833 original size:2 final size:2
Alignment explanation
Indices: 154826--154869 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
154816 GTAGAAACAC
154826 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
154867 AT A
1 AT A
154870 GATTACTCAG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:159705 original size:139 final size:139
Alignment explanation
Indices: 159440--160243 Score: 987
Period size: 139 Copynumber: 5.8 Consensus size: 139
159430 ATAATTTGGG
* * *
159440 GACAACACGGTTCCTACGTGATGAGGAAGTCT-AGTTATCTGAGGATGATGCTACTCCTACGTGT
1 GACAACACAGTTCCTACGTGATGAGGAAGTCTGA-TTATCTGAGGATGACGCTGCTCCTACGTGT
* * * *
159504 TGAGGAGATCTGGTCGGTGGACGACATTGTTCCTACGTGACGAGGATGTATAGCCGTCTTTAGGG
65 TGAGGAGATCTGGTCGGTGGACGACATTGTTCCTACGTGATGAGGACGTCTAGCCGTATTTAGGG
*
159569 ATAAATTGGA
130 ATAAATTGAA
* * * *
159579 GACAACACAGTTTCTACATGATGAGGAAGTTTGATTATCTGAGGATGACGTTGCTCCTACGTGTT
1 GACAACACAGTTCCTACGTGATGAGGAAGTCTGATTATCTGAGGATGACGCTGCTCCTACGTGTT
* * * *
159644 GAGGAGATATGGTCGGTGGATGACATTGTTCTTACGTGATGAGGACGTCTAGACGTATTTAGGGA
66 GAGGAGATCTGGTCGGTGGACGACATTGTTCCTACGTGATGAGGACGTCTAGCCGTATTTAGGGA
**
159709 TAAATCAAA
131 TAAATTGAA
* * * * * *
159718 GACAACACGGTTCCTACGTGATGATGAGGTCTGGTTATATGAGGATGACACTGCTCCTACGTGTT
1 GACAACACAGTTCCTACGTGATGAGGAAGTCTGATTATCTGAGGATGACGCTGCTCCTACGTGTT
* *
159783 GAGGAGATCTGGTCGGTGGATGACATTGTTCCTACATGATGAGGACGTCTAGCCGTATTTAGGGA
66 GAGGAGATCTGGTCGGTGGACGACATTGTTCCTACGTGATGAGGACGTCTAGCCGTATTTAGGGA
**
159848 TAAATCAAA
131 TAAATTGAA
* * * * * * **
159857 GATAACACGGTTCCTACGTGATGATGAGGTCTGGTTATATGAGGATGAAACTGCTCCTACGTGTT
1 GACAACACAGTTCCTACGTGATGAGGAAGTCTGATTATCTGAGGATGACGCTGCTCCTACGTGTT
* * * * * *
159922 AAGGAGATCTGGTCTGTGGA-TAGCATTGCTCCTACATGATGAGGACGTCTAGCCGTCTTTAGGG
66 GAGGAGATCTGGTCGGTGGACGA-CATTGTTCCTACGTGATGAGGACGTCTAGCCGTATTTAGGG
159986 ATAAATTGAA
130 ATAAATTGAA
* * *
159996 GACAACACAGTTCCTACATGATGAGGAAGTCT-ACTTATCCGAGGATGATGCTGCTCCTACGTGT
1 GACAACACAGTTCCTACGTGATGAGGAAGTCTGA-TTATCTGAGGATGACGCTGCTCCTACGTGT
* * * * ** *
160060 TGAGAAGATATGGTCGGTGGACGACATTATTCCTACGTGATGAGGATGTCTAGCTATCTTTAGGG
65 TGAGGAGATCTGGTCGGTGGACGACATTGTTCCTACGTGATGAGGACGTCTAGCCGTATTTAGGG
*
160125 ATAAATTGGA
130 ATAAATTGAA
* * * *
160135 GAC-A-ACA----CTACGTGATGAGGAAGTCTGGTTATCTGAGGATGTCGTTGCTCCTACGTGAT
1 GACAACACAGTTCCTACGTGATGAGGAAGTCTGATTATCTGAGGATGACGCTGCTCCTACGTGTT
* *
160194 GAGGAGATCTGGTCGGTGGACGACATTGTTCCTATGTGATGAGGAAGTCT
66 GAGGAGATCTGGTCGGTGGACGACATTGTTCCTACGTGATGAGGACGTCT
160244 GGTTATCTGA
Statistics
Matches: 585, Mismatches: 75, Indels: 16
0.87 0.11 0.02
Matches are distributed among these distances:
133 89 0.15
137 3 0.01
138 2 0.00
139 489 0.84
140 2 0.00
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (139 bp):
GACAACACAGTTCCTACGTGATGAGGAAGTCTGATTATCTGAGGATGACGCTGCTCCTACGTGTT
GAGGAGATCTGGTCGGTGGACGACATTGTTCCTACGTGATGAGGACGTCTAGCCGTATTTAGGGA
TAAATTGAA
Found at i:160205 original size:43 final size:43
Alignment explanation
Indices: 160142--160289 Score: 171
Period size: 43 Copynumber: 3.5 Consensus size: 43
160132 GGAGACAACA
160142 CTACGTGATGAGGAAGTCTGGTTATCTGAGGATGTCGTTGCTC
1 CTACGTGATGAGGAAGTCTGGTTATCTGAGGATGTCGTTGCTC
* * * * * *
160185 CTACGTGATGAGG-AGATCTGG---TCGGTGGACGACATTGTTC
1 CTACGTGATGAGGAAG-TCTGGTTATCTGAGGATGTCGTTGCTC
*
160225 CTATGTGATGAGGAAGTCTGGTTATCTGAGGATGTCGTTGCTC
1 CTACGTGATGAGGAAGTCTGGTTATCTGAGGATGTCGTTGCTC
*
160268 CTACGTTATGAGG-AGATCTGGT
1 CTACGTGATGAGGAAG-TCTGGT
160290 CGGTGGACGA
Statistics
Matches: 84, Mismatches: 15, Indels: 12
0.76 0.14 0.11
Matches are distributed among these distances:
40 30 0.36
41 2 0.02
42 4 0.05
43 48 0.57
ACGTcount: A:0.20, C:0.16, G:0.33, T:0.32
Consensus pattern (43 bp):
CTACGTGATGAGGAAGTCTGGTTATCTGAGGATGTCGTTGCTC
Found at i:160238 original size:40 final size:40
Alignment explanation
Indices: 160183--160321 Score: 145
Period size: 40 Copynumber: 3.4 Consensus size: 40
160173 ATGTCGTTGC
160183 TCCTACGTGATGAGGAGATCTGGTCGGTGGACGACATTGT
1 TCCTACGTGATGAGGAGATCTGGTCGGTGGACGACATTGT
* * * * * * *
160223 TCCTATGTGATGAGGA-AGTCTGGTTATCTGAGGATGTCGTTGC
1 TCCTACGTGATGAGGAGA-TCTGG---TCGGTGGACGACATTGT
*
160266 TCCTACGTTATGAGGAGATCTGGTCGGTGGACGACATTGT
1 TCCTACGTGATGAGGAGATCTGGTCGGTGGACGACATTGT
* *
160306 TTCTATGTGATGAGGA
1 TCCTACGTGATGAGGA
160322 CGTCTAGTCG
Statistics
Matches: 76, Mismatches: 18, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
39 1 0.01
40 44 0.58
43 30 0.39
44 1 0.01
ACGTcount: A:0.20, C:0.15, G:0.33, T:0.32
Consensus pattern (40 bp):
TCCTACGTGATGAGGAGATCTGGTCGGTGGACGACATTGT
Found at i:160285 original size:83 final size:83
Alignment explanation
Indices: 160146--160326 Score: 335
Period size: 83 Copynumber: 2.2 Consensus size: 83
160136 ACAACACTAC
160146 GTGATGAGGAAGTCTGGTTATCTGAGGATGTCGTTGCTCCTACGTGATGAGGAGATCTGGTCGGT
1 GTGATGAGGAAGTCTGGTTATCTGAGGATGTCGTTGCTCCTACGTGATGAGGAGATCTGGTCGGT
160211 GGACGACATTGTTCCTAT
66 GGACGACATTGTTCCTAT
*
160229 GTGATGAGGAAGTCTGGTTATCTGAGGATGTCGTTGCTCCTACGTTATGAGGAGATCTGGTCGGT
1 GTGATGAGGAAGTCTGGTTATCTGAGGATGTCGTTGCTCCTACGTGATGAGGAGATCTGGTCGGT
*
160294 GGACGACATTGTTTCTAT
66 GGACGACATTGTTCCTAT
*
160312 GTGATGAGGACGTCT
1 GTGATGAGGAAGTCT
160327 AGTCGTCTTT
Statistics
Matches: 95, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
83 95 1.00
ACGTcount: A:0.19, C:0.15, G:0.34, T:0.32
Consensus pattern (83 bp):
GTGATGAGGAAGTCTGGTTATCTGAGGATGTCGTTGCTCCTACGTGATGAGGAGATCTGGTCGGT
GGACGACATTGTTCCTAT
Found at i:162319 original size:28 final size:28
Alignment explanation
Indices: 162272--162334 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
162262 AATTTATACC
*
162272 TAAAAATATAAAATTATATGATT-AAAT
1 TAAAAATATAAAATTATATGATTGAAAA
*
162299 TAAAAAGTAATAAAATT-TATGGTTGAAAA
1 TAAAAA-T-ATAAAATTATATGATTGAAAA
162328 TAAAAAT
1 TAAAAAT
162335 TATTTAAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 6 0.19
28 8 0.26
29 17 0.55
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (28 bp):
TAAAAATATAAAATTATATGATTGAAAA
Found at i:163174 original size:19 final size:19
Alignment explanation
Indices: 163147--163189 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
163137 GGGCGGTCTT
*
163147 CGGTTAGTCACCAAAACTA
1 CGGTGAGTCACCAAAACTA
163166 CGGTGAGTCACCAAAACTA
1 CGGTGAGTCACCAAAACTA
163185 CGGTG
1 CGGTG
163190 GTGACTCATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.19
Consensus pattern (19 bp):
CGGTGAGTCACCAAAACTA
Found at i:163549 original size:3 final size:3
Alignment explanation
Indices: 163541--163598 Score: 93
Period size: 3 Copynumber: 19.7 Consensus size: 3
163531 TTTGGGCCTG
163541 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TTAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
163586 -AA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
163599 TTATTAAAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.08
3 45 0.87
4 3 0.06
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:170593 original size:37 final size:36
Alignment explanation
Indices: 170552--170834 Score: 173
Period size: 37 Copynumber: 8.1 Consensus size: 36
170542 TGTTTATGTT
170552 TCAAGAGAGACAAAACTTTATTTCAAGAGAAACTATC
1 TCAAGAGAGACAAAA-TTTATTTCAAGAGAAACTATC
* * *
170589 TCAAGCGAGACAAAACTTTTTTTCAAGAGAAACTGTC
1 TCAAGAGAGACAAAA-TTTATTTCAAGAGAAACTATC
* * * *
170626 TCAAGCGAGACAAAATTTGTTTCAAGGGAAACAATC
1 TCAAGAGAGACAAAATTTATTTCAAGAGAAACTATC
** *** * *
170662 TC-A-ATTG--TTTATGT-TTT-AAGAGAAAATATC
1 TCAAGAGAGACAAAATTTATTTCAAGAGAAACTATC
* *
170692 TCAAGAGAGACAAACTTTGTTTCAAGAGAAACTATC
1 TCAAGAGAGACAAAATTTATTTCAAGAGAAACTATC
* *
170728 TCAA-AG-G------TTTATGTTTCAAGATAAACTGTC
1 TCAAGAGAGACAAAATTTA--TTTCAAGAGAAACTATC
* * * *
170758 TCAAGCGAGACAAAATTTGTTTCAAGAAAAACTGTC
1 TCAAGAGAGACAAAATTTATTTCAAGAGAAACTATC
* * **
170794 TCAAGCGAGATAAAACTTTATTTTGAGAGAAAC-AGTC
1 TCAAGAGAGACAAAA-TTTATTTCAAGAGAAACTA-TC
170831 TCAA
1 TCAA
170835 AGGTTTATCA
Statistics
Matches: 191, Mismatches: 37, Indels: 36
0.72 0.14 0.14
Matches are distributed among these distances:
28 3 0.02
30 31 0.16
31 5 0.03
32 6 0.03
34 4 0.02
35 6 0.03
36 65 0.34
37 68 0.36
38 3 0.02
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.28
Consensus pattern (36 bp):
TCAAGAGAGACAAAATTTATTTCAAGAGAAACTATC
Found at i:170657 original size:36 final size:36
Alignment explanation
Indices: 170552--170834 Score: 200
Period size: 36 Copynumber: 8.1 Consensus size: 36
170542 TGTTTATGTT
* *
170552 TCAAGAGAGACAAAACTTTATTTCAAGAGAAACTATC
1 TCAAGCGAGACAAAA-TTTGTTTCAAGAGAAACTATC
* *
170589 TCAAGCGAGACAAAACTTTTTTTCAAGAGAAACTGTC
1 TCAAGCGAGACAAAA-TTTGTTTCAAGAGAAACTATC
* *
170626 TCAAGCGAGACAAAATTTGTTTCAAGGGAAACAATC
1 TCAAGCGAGACAAAATTTGTTTCAAGAGAAACTATC
** * * *
170662 TCAA--TTG-----TTTATGTTTTAAGAGAAAATATC
1 TCAAGCGAGACAAAATT-TGTTTCAAGAGAAACTATC
* *
170692 TCAAGAGAGACAAACTTTGTTTCAAGAGAAACTATC
1 TCAAGCGAGACAAAATTTGTTTCAAGAGAAACTATC
** * *
170728 TCAA---AG----GTTTATGTTTCAAGATAAACTGTC
1 TCAAGCGAGACAAAATT-TGTTTCAAGAGAAACTATC
* *
170758 TCAAGCGAGACAAAATTTGTTTCAAGAAAAACTGTC
1 TCAAGCGAGACAAAATTTGTTTCAAGAGAAACTATC
* * **
170794 TCAAGCGAGATAAAACTTTATTTTGAGAGAAAC-AGTC
1 TCAAGCGAGACAAAA-TTTGTTTCAAGAGAAACTA-TC
170831 TCAA
1 TCAA
170835 AGGTTTATCA
Statistics
Matches: 196, Mismatches: 32, Indels: 36
0.74 0.12 0.14
Matches are distributed among these distances:
29 4 0.02
30 40 0.20
32 1 0.01
33 4 0.02
34 1 0.01
36 74 0.38
37 72 0.37
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.28
Consensus pattern (36 bp):
TCAAGCGAGACAAAATTTGTTTCAAGAGAAACTATC
Found at i:170790 original size:66 final size:66
Alignment explanation
Indices: 170609--170797 Score: 270
Period size: 66 Copynumber: 2.9 Consensus size: 66
170599 CAAAACTTTT
* * **
170609 TTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCAAGGGAAACAATCTCAATTGTTTAT
1 TTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACTATCTCAAAGGTTTAT
170674 G
66 G
* * * * *
170675 TTTTAAGAGAAAATATCTCAAGAGAGACAAACTTTGTTTCAAGAGAAACTATCTCAAAGGTTTAT
1 TTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACTATCTCAAAGGTTTAT
170740 G
66 G
* * *
170741 TTTCAAGATAAACTGTCTCAAGCGAGACAAAATTTGTTTCAAGAAAAACTGTCTCAA
1 TTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACTATCTCAA
170798 GCGAGATAAA
Statistics
Matches: 106, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
66 106 1.00
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (66 bp):
TTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACTATCTCAAAGGTTTAT
G
Found at i:171653 original size:33 final size:32
Alignment explanation
Indices: 171606--171684 Score: 131
Period size: 33 Copynumber: 2.4 Consensus size: 32
171596 ACAAAGTTTA
* *
171606 CGATAATTGAAATACTTAAATACTTCCAAGTT
1 CGATAATTCAAATACTTAAAAACTTCCAAGTT
171638 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
1 CGAT-AATTCAAATACTTAAAAACTTCCAAGTT
171671 CGATAATTCAAATA
1 CGATAATTCAAATA
171685 AAGTTTAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
32 14 0.32
33 30 0.68
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (32 bp):
CGATAATTCAAATACTTAAAAACTTCCAAGTT
Found at i:179689 original size:25 final size:25
Alignment explanation
Indices: 179655--179729 Score: 141
Period size: 25 Copynumber: 3.0 Consensus size: 25
179645 GTACCTAACA
179655 AGTAAGATCTGAGTTAGTCATCCAT
1 AGTAAGATCTGAGTTAGTCATCCAT
*
179680 AGTAAAATCTGAGTTAGTCATCCAT
1 AGTAAGATCTGAGTTAGTCATCCAT
179705 AGTAAGATCTGAGTTAGTCATCCAT
1 AGTAAGATCTGAGTTAGTCATCCAT
179730 GCATAGGATG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 48 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (25 bp):
AGTAAGATCTGAGTTAGTCATCCAT
Done.