Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003411.1 Hibiscus syriacus cultivar Beakdansim tig00007187_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: 75043
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:3319 original size:20 final size:22
Alignment explanation
Indices: 3277--3320 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
3267 TACTAGTAAC
*
3277 AATAATAATAGATTTTTTAAGGT
1 AATAATAATAGA-TTTATAAGGT
3300 AATAATAATAG-TTTAT-AGGT
1 AATAATAATAGATTTATAAGGT
3320 A
1 A
3321 TCATATTCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
21 4 0.20
23 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (22 bp):
AATAATAATAGATTTATAAGGT
Found at i:8911 original size:29 final size:29
Alignment explanation
Indices: 8878--8951 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
8868 ACTAAACCCG
*
8878 TCCCCATCCCCGTTTAACATAAACGGTTT
1 TCCCCATCCCCGTTTAACATAAACGATTT
* **
8907 TCCCCGTCCCCGTTTAGTATAAACGATTT
1 TCCCCATCCCCGTTTAACATAAACGATTT
*
8936 TCTCCAT-CCCGTTTAA
1 TCCCCATCCCCGTTTAA
8952 TTCGATTTTC
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 8 0.21
29 30 0.79
ACGTcount: A:0.22, C:0.34, G:0.11, T:0.34
Consensus pattern (29 bp):
TCCCCATCCCCGTTTAACATAAACGATTT
Found at i:10371 original size:2 final size:2
Alignment explanation
Indices: 10364--10388 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10354 AGTGAATTTA
10364 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
10389 ATAATAATAA
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:10435 original size:3 final size:3
Alignment explanation
Indices: 10386--10416 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
10376 ATATATATAT
10386 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
10417 ATTATTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:25921 original size:3 final size:3
Alignment explanation
Indices: 25913--25942 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
25903 CTCCCAAAGA
25913 AAG AAG AAG AAG AAG AAG AAG AAG AA- AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
25943 GGAGAAATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:27445 original size:25 final size:25
Alignment explanation
Indices: 27416--27463 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
27406 AATTGACACT
*
27416 TTATTTAATATATT-TTTACATATCA
1 TTATTAAATATATTATTTA-ATATCA
27441 TTATTAAATATATTATTTAATAT
1 TTATTAAATATATTATTTAATAT
27464 TTATAAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (25 bp):
TTATTAAATATATTATTTAATATCA
Found at i:27455 original size:12 final size:12
Alignment explanation
Indices: 27416--27467 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
27406 AATTGACACT
*
27416 TTATTTAATATA
1 TTATTAAATATA
* *
27428 TTTTTACATATCA
1 TTATTAAATAT-A
27441 TTATTAAATATA
1 TTATTAAATATA
*
27453 TTATTTAATAT-
1 TTATTAAATATA
27464 TTAT
1 TTAT
27468 AAGATTTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
11 4 0.12
12 19 0.58
13 10 0.30
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (12 bp):
TTATTAAATATA
Found at i:30259 original size:19 final size:19
Alignment explanation
Indices: 30235--30272 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
30225 TGTTAGTCAG
*
30235 TTAGGCATGCTGTTATGCA
1 TTAGGCATGCAGTTATGCA
*
30254 TTAGGCGTGCAGTTATGCA
1 TTAGGCATGCAGTTATGCA
30273 GACGGTTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.21, C:0.16, G:0.29, T:0.34
Consensus pattern (19 bp):
TTAGGCATGCAGTTATGCA
Found at i:34827 original size:19 final size:19
Alignment explanation
Indices: 34803--34840 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
34793 TGTTAGTCAG
*
34803 TTAGGCATGCTGTTATGCA
1 TTAGGCATGCAGTTATGCA
*
34822 TTAGGCGTGCAGTTATGCA
1 TTAGGCATGCAGTTATGCA
34841 GACGGTTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.21, C:0.16, G:0.29, T:0.34
Consensus pattern (19 bp):
TTAGGCATGCAGTTATGCA
Found at i:35470 original size:18 final size:18
Alignment explanation
Indices: 35447--35482 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
35437 GTGCAGTTAG
*
35447 TTTGTATTTTGTTACACC
1 TTTGTATTCTGTTACACC
35465 TTTGTATTCTGTTACACC
1 TTTGTATTCTGTTACACC
35483 AGATTACCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.19, G:0.11, T:0.53
Consensus pattern (18 bp):
TTTGTATTCTGTTACACC
Found at i:40352 original size:19 final size:19
Alignment explanation
Indices: 40328--40365 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
40318 TGTTAGTCAG
*
40328 TTAGGCATGCTGTTATGCA
1 TTAGGCATGCAGTTATGCA
*
40347 TTAGGCGTGCAGTTATGCA
1 TTAGGCATGCAGTTATGCA
40366 GACGGTTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.21, C:0.16, G:0.29, T:0.34
Consensus pattern (19 bp):
TTAGGCATGCAGTTATGCA
Found at i:40998 original size:18 final size:18
Alignment explanation
Indices: 40977--41011 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
40967 AGTTAGTTTG
*
40977 TTGTATTTTGTTACACCT
1 TTGTATTCTGTTACACCT
40995 TTGTATTCTGTTACACC
1 TTGTATTCTGTTACACC
41012 AGATTACCAG
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:0.17, C:0.20, G:0.11, T:0.51
Consensus pattern (18 bp):
TTGTATTCTGTTACACCT
Found at i:41619 original size:16 final size:16
Alignment explanation
Indices: 41598--41629 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
41588 AAATTTTTAG
41598 GATACGATTACCTCGT
1 GATACGATTACCTCGT
41614 GATACGATTACCTCGT
1 GATACGATTACCTCGT
41630 CCCTTCCATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (16 bp):
GATACGATTACCTCGT
Found at i:46700 original size:15 final size:15
Alignment explanation
Indices: 46682--46715 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
46672 AAAATATGAA
46682 AAATGAAAAGGCTAG
1 AAATGAAAAGGCTAG
* *
46697 AAATGAGAAGGCTGG
1 AAATGAAAAGGCTAG
46712 AAAT
1 AAAT
46716 TGTCGATACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.29, T:0.15
Consensus pattern (15 bp):
AAATGAAAAGGCTAG
Found at i:52664 original size:13 final size:13
Alignment explanation
Indices: 52646--52675 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
52636 ATTCCAAGGA
*
52646 TTTTTTTTTTTAC
1 TTTTTTTTTTAAC
52659 TTTTTTTTTTAAC
1 TTTTTTTTTTAAC
52672 TTTT
1 TTTT
52676 CCTCTTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.10, C:0.07, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTTTTTTAAC
Found at i:64728 original size:164 final size:160
Alignment explanation
Indices: 64493--65043 Score: 717
Period size: 157 Copynumber: 3.4 Consensus size: 160
64483 TTTAAGTTCA
* *
64493 TTTTTACCAAATTT-AAACTACATGCTCCTAAACCATAGTAGAATACATGTTTACTTTCAATTCC
1 TTTTTACCAAATTTGAATC-ACATGCTCCTAAACCATAGTAGAATACATGTGTACTTTCAATTCC
* *
64557 TCTTTTTGATAACAATAATTTTTTATTTTTCAATTTAGTCTTTCAATTTTTTCATAATCTTCTTA
65 TCTTTTTGATAACAAT--TTTTTTATTTTTCAATTTAGTCCTTCAATTTTTTCATAAT-TCCTTA
64622 TTTCTTCAATTCGTCATTTATTTTAAGTATGTTTTT
127 TTTCTTCAATTCGTCATTTATTTTAAGT-TG-TTTT
64658 TTTTTACCAAATTTGAATCACATGCTCCT-AACCATAGTAGAATACATGTGTACTTTCAATTCCT
1 TTTTTACCAAATTTGAATCACATGCTCCTAAACCATAGTAGAATACATGTGTACTTTCAATTCCT
*
64722 CTTTTTGATAACAATTTTTTTATTTTTCAATTTAATCCTTCAATTTTTT-ATAATTCCCTTATTT
66 CTTTTTGATAACAATTTTTTTATTTTTCAATTTAGTCCTTCAATTTTTTCATAATT-CCTTATTT
* *
64786 CTTCAATTCATCATTTATTTTAAGTCCG----
130 CTTCAATTCGTCATTTATTTTAAGT-TGTTTT
* * * * *
64814 TTTTTACTAAATTTGAGTCATATGCTCCTAAACCATAGTAGAATACATGTGCACTTTCAATTTCT
1 TTTTTACCAAATTTGAATCACATGCTCCTAAACCATAGTAGAATACATGTGTACTTTCAATTCCT
* * *
64879 CTTTTTGATGACAATTTTTTTATTTTTCAATTTAGTCCTTCAA-TTTTTCATAATATCCTAATTC
66 CTTTTTGATAACAATTTTTTTATTTTTCAATTTAGTCCTTCAATTTTTTCATAAT-TCCTTATTT
* *
64943 CTTCAATTTGTCATTTATTTTAAGTT-CTTT
130 CTTCAATTCGTCATTTATTTTAAGTTGTTTT
* * * * * * *
64973 TTTTTACCAAATTTAAATCACATGCTCATATACCATAATAAAATACATATGTAAC-TTCAATTGC
1 TTTTTACCAAATTTGAATCACATGCTCCTAAACCATAGTAGAATACATGTGT-ACTTTCAATTCC
*
65037 TATTTTT
65 TCTTTTT
65044 TTTACTAAAG
Statistics
Matches: 344, Mismatches: 32, Indels: 26
0.86 0.08 0.06
Matches are distributed among these distances:
156 31 0.09
157 108 0.31
158 1 0.00
159 56 0.16
160 3 0.01
161 37 0.11
162 32 0.09
164 49 0.14
165 24 0.07
166 3 0.01
ACGTcount: A:0.29, C:0.17, G:0.06, T:0.48
Consensus pattern (160 bp):
TTTTTACCAAATTTGAATCACATGCTCCTAAACCATAGTAGAATACATGTGTACTTTCAATTCCT
CTTTTTGATAACAATTTTTTTATTTTTCAATTTAGTCCTTCAATTTTTTCATAATTCCTTATTTC
TTCAATTCGTCATTTATTTTAAGTTGTTTT
Found at i:65066 original size:321 final size:319
Alignment explanation
Indices: 64461--65034 Score: 818
Period size: 321 Copynumber: 1.8 Consensus size: 319
64451 TGATTTCATG
* * *
64461 ATTTCTTCAATTCCTCCTCCATTTTAAGTTCATTTTTACCAAATTTAAACTACATGCTCCTAAAC
1 ATTTCTTCAATTCATCATCCATTTTAAGTCCATTTTTACCAAATTTAAACTACATGCTCCTAAAC
**
64526 CATAGTAGAATACATGTTTACTTTCAATTCCTCTTTTTGATAACAATAATTTTTTATTTTTCAAT
66 CATAGTAGAATACATGTGCACTTTCAATTCCTCTTTTTGATAACAAT-ATTTTTTATTTTTCAAT
* * * * * *
64591 TTAGTCTTTCAATTTTTTCATAATCTTCTTATTTCTTCAATTCGTCATTTATTTTAAGTATGTTT
130 TTAGTCCTTCAATTTTTTCATAATATCCTAATTCCTTCAATTCGTCATTTATTTTAAG-ATGTCT
* * * * * *
64656 TTTTTTTACCAAATTTGAATCACATGCTCCTAACCATAGTAGAATACATGTGTACTTTCAATTCC
194 TTTTTTTACCAAATTTAAATCACATGCTCATAACCATAATAAAATACATATGTACTTTCAATTCA
64721 TCTTTTTGATAACAATTTTTTTATTTTTCAATTTAATCCTTCAATTTTTTATAATTCCCTT
259 TCTTTTTGATAACAATTTTTTTATTTTTCAATTTAATCCTTCAATTTTTTATAATTCCCTT
** * * * * *
64782 ATTTCTTCAATTCATCATTTATTTTAAGTCCGTTTTTACTAAATTT-GAGTCATATGCTCCTAAA
1 ATTTCTTCAATTCATCATCCATTTTAAGTCCATTTTTACCAAATTTAAACT-ACATGCTCCTAAA
* *
64846 CCATAGTAGAATACATGTGCACTTTCAATTTCTCTTTTTGATGACAAT-TTTTTTATTTTTCAAT
65 CCATAGTAGAATACATGTGCACTTTCAATTCCTCTTTTTGATAACAATATTTTTTATTTTTCAAT
*
64910 TTAGTCCTTCAA-TTTTTCATAATATCCTAATTCCTTCAATTTGTCATTTATTTTAAG-T-TCTT
130 TTAGTCCTTCAATTTTTTCATAATATCCTAATTCCTTCAATTCGTCATTTATTTTAAGATGTCTT
64972 TTTTTTACCAAATTTAAATCACATGCTCATATACCATAATAAAATACATATGTAAC-TTCAATT
195 TTTTTTACCAAATTTAAATCACATGCTCATA-ACCATAATAAAATACATATGT-ACTTTCAATT
65035 GCTATTTTTT
Statistics
Matches: 224, Mismatches: 26, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
315 32 0.14
316 26 0.12
317 2 0.01
318 40 0.18
319 27 0.12
320 2 0.01
321 95 0.42
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.48
Consensus pattern (319 bp):
ATTTCTTCAATTCATCATCCATTTTAAGTCCATTTTTACCAAATTTAAACTACATGCTCCTAAAC
CATAGTAGAATACATGTGCACTTTCAATTCCTCTTTTTGATAACAATATTTTTTATTTTTCAATT
TAGTCCTTCAATTTTTTCATAATATCCTAATTCCTTCAATTCGTCATTTATTTTAAGATGTCTTT
TTTTTACCAAATTTAAATCACATGCTCATAACCATAATAAAATACATATGTACTTTCAATTCATC
TTTTTGATAACAATTTTTTTATTTTTCAATTTAATCCTTCAATTTTTTATAATTCCCTT
Found at i:68417 original size:20 final size:21
Alignment explanation
Indices: 68380--68419 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
68370 TTTTTTCTAC
68380 GGAAGAAGACACAATTTGGTG
1 GGAAGAAGACACAATTTGGTG
*
68401 GGAAGACGACA-AATTTGGT
1 GGAAGAAGACACAATTTGGT
68420 TCCTGGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.38, C:0.10, G:0.33, T:0.20
Consensus pattern (21 bp):
GGAAGAAGACACAATTTGGTG
Done.