Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008627.1 Hibiscus syriacus cultivar Beakdansim tig00111594_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: 1073793
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
File 6 of 6
Found at i:1038595 original size:21 final size:21
Alignment explanation
Indices: 1038544--1038596 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 21
1038534 CAACATAATT
1038544 ATAAATTAGTTAAAAATTTAAAG
1 ATAAATTA-TTAAAAA-TTAAAG
* *
1038567 ATAGATTATTTAAAA-TAAAGG
1 ATAAATTATTAAAAATTAAA-G
1038588 ATAAATTAT
1 ATAAATTAT
1038597 ACAAGTGACC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 4 0.15
21 9 0.35
22 6 0.23
23 7 0.27
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (21 bp):
ATAAATTATTAAAAATTAAAG
Found at i:1039098 original size:18 final size:18
Alignment explanation
Indices: 1039072--1039119 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
1039062 TTTATATATT
*
1039072 TTAACTTAAATTCACATA
1 TTAAATTAAATTCACATA
* *
1039090 TTAAATT-AATTTACATC
1 TTAAATTAAATTCACATA
1039107 TTAACATTAAATT
1 TTAA-ATTAAATT
1039120 TTTTTTATCT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 12 0.48
18 9 0.36
19 4 0.16
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAAATTAAATTCACATA
Found at i:1039132 original size:22 final size:23
Alignment explanation
Indices: 1039104--1039151 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
1039094 ATTAATTTAC
* *
1039104 ATCTTAAC-ATTAAATTTTTTTT
1 ATCTTAACTATTAAATATATTTT
1039126 ATCTTAACTTATTAAATATATTTT
1 ATCTTAAC-TATTAAATATATTTT
1039150 AT
1 AT
1039152 TCTTTTCGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 8 0.36
24 14 0.64
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.56
Consensus pattern (23 bp):
ATCTTAACTATTAAATATATTTT
Found at i:1039203 original size:29 final size:29
Alignment explanation
Indices: 1039139--1039275 Score: 114
Period size: 29 Copynumber: 4.6 Consensus size: 29
1039129 TTAACTTATT
* * *
1039139 AAATATATTTTATTCTT-TTCGTAACTTGA
1 AAATATATTTTATTCTTATT-TTAATTTAA
* *
1039168 AAGTATATTTCATTCTTATTTTAATTTAA
1 AAATATATTTTATTCTTATTTTAATTTAA
* * *
1039197 AAATATATTTTAATCTTATCTTAAATTAAA
1 AAATATATTTTATTCTTAT-TTTAATTTAA
* *
1039227 AAATATATAATTTATGCTTATCTTAATTTAA
1 AAATATAT--TTTATTCTTATTTTAATTTAA
*
1039258 ATATTTATATTTTATTCT
1 A-A-ATATATTTTATTCT
1039276 GATAATATTT
Statistics
Matches: 85, Mismatches: 17, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
29 37 0.44
30 18 0.21
31 15 0.18
32 10 0.12
33 5 0.06
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.53
Consensus pattern (29 bp):
AAATATATTTTATTCTTATTTTAATTTAA
Found at i:1039247 original size:32 final size:30
Alignment explanation
Indices: 1039124--1039258 Score: 96
Period size: 29 Copynumber: 4.5 Consensus size: 30
1039114 TAAATTTTTT
* ** *
1039124 TTATCTTAACTTATTAAATATATTTTATTC
1 TTATCTTAAATTAAAAAATATATTTTAATC
* * * * * * *
1039154 TTTTCGTAACTT-GAAAGTATATTTCATTC
1 TTATCTTAAATTAAAAAATATATTTTAATC
* *
1039183 TTAT-TTTAATTTAAAAATATATTTTAATC
1 TTATCTTAAATTAAAAAATATATTTTAATC
1039212 TTATCTTAAATTAAAAAATATATAATTT-ATGC
1 TTATCTTAAATTAAAAAATATAT--TTTAAT-C
*
1039244 TTATCTTAATTTAAA
1 TTATCTTAAATTAAA
1039259 TATTTATATT
Statistics
Matches: 83, Mismatches: 17, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
28 4 0.05
29 33 0.40
30 26 0.31
31 2 0.02
32 18 0.22
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (30 bp):
TTATCTTAAATTAAAAAATATATTTTAATC
Found at i:1039587 original size:30 final size:28
Alignment explanation
Indices: 1039493--1039606 Score: 113
Period size: 28 Copynumber: 3.9 Consensus size: 28
1039483 AATAAGGATA
* *
1039493 AAGACTAAAATATATTTTTATGTTAAAAT
1 AAGAATAAAATATA-TTTTAAGTTAAAAT
* *
1039522 AAGAATAAAATATATTTTAGGTTAAGAT
1 AAGAATAAAATATATTTTAAGTTAAAAT
*
1039550 AAGAATAAAATATATTTAATAAGTTAATAT
1 AAGAATAAAATATATTT--TAAGTTAAAAT
*
1039580 GAA-AATAAAATTTATTTTTAATGTTAA
1 -AAGAATAAAATATA-TTTTAA-GTTAA
1039607 GATGTAAAAT
Statistics
Matches: 74, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
28 29 0.39
29 16 0.22
30 24 0.32
31 5 0.07
ACGTcount: A:0.51, C:0.01, G:0.09, T:0.39
Consensus pattern (28 bp):
AAGAATAAAATATATTTTAAGTTAAAAT
Found at i:1039637 original size:18 final size:18
Alignment explanation
Indices: 1039596--1039643 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
1039586 AAAATTTATT
1039596 TTTAATGTTAAGATGTAAA
1 TTTAAT-TTAAGATGTAAA
* * *
1039615 ATTAATTTAATATGTGAA
1 TTTAATTTAAGATGTAAA
*
1039633 TTTAAGTTAAG
1 TTTAATTTAAG
1039644 GTAAATAAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.44
Consensus pattern (18 bp):
TTTAATTTAAGATGTAAA
Found at i:1044047 original size:20 final size:20
Alignment explanation
Indices: 1044022--1044071 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
1044012 GGCCGTTTTT
1044022 AGCCGTTGGGAGTGATTTGG
1 AGCCGTTGGGAGTGATTTGG
*
1044042 AGCCGTTGGAAGTGATTTGG
1 AGCCGTTGGGAGTGATTTGG
*
1044062 AGTCGTTGGG
1 AGCCGTTGGG
1044072 GATGTTTTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.16, C:0.10, G:0.44, T:0.30
Consensus pattern (20 bp):
AGCCGTTGGGAGTGATTTGG
Found at i:1044374 original size:40 final size:40
Alignment explanation
Indices: 1044324--1044408 Score: 134
Period size: 40 Copynumber: 2.1 Consensus size: 40
1044314 CTTACCTTTG
* *
1044324 GTATCGGTACCACATGAACAATATCGGTACTGTTCATATA
1 GTATCAGTACCACATGAACAATATCGATACTGTTCATATA
* *
1044364 TTATCAGTACCACATGAACAATATCGATACTGTTTATATA
1 GTATCAGTACCACATGAACAATATCGATACTGTTCATATA
1044404 GTATC
1 GTATC
1044409 GATATTGTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (40 bp):
GTATCAGTACCACATGAACAATATCGATACTGTTCATATA
Found at i:1045840 original size:52 final size:49
Alignment explanation
Indices: 1045760--1045899 Score: 142
Period size: 52 Copynumber: 2.8 Consensus size: 49
1045750 TACGTAGAGA
* * *
1045760 TAACTAGTTCTAATAAAAAATATTTTTATTTAAACTCGTCACATCGAGG
1 TAACGAGTTCTAATAAAAAATATTTTTATTAAAACTCATCACATCGAGG
* * *
1045809 TAACGAGTTCTAATGAAATATAATATTTTTATTAAAATTTATCACATCGAGA
1 TAACGAGTTCTAAT-AAA-A-AATATTTTTATTAAAACTCATCACATCGAGG
** *
1045861 TAAAAAGTT-TCAAT--AAAATATTTTTATTAAAATTCATCA
1 TAACGAGTTCT-AATAAAAAATATTTTTATTAAAACTCATCA
1045900 TCTTAATATG
Statistics
Matches: 78, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
47 22 0.28
48 1 0.01
49 14 0.18
50 3 0.04
51 2 0.03
52 36 0.46
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.39
Consensus pattern (49 bp):
TAACGAGTTCTAATAAAAAATATTTTTATTAAAACTCATCACATCGAGG
Found at i:1051037 original size:24 final size:21
Alignment explanation
Indices: 1050993--1051036 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 21
1050983 ATTATATATT
1050993 TTATTTTTATTTTTTAAAAAA
1 TTATTTTTATTTTTTAAAAAA
1051014 TTATTTTATATATTTTTAAAAAA
1 TTATTTT-TAT-TTTTTAAAAAA
1051037 AATTAAGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 7 0.33
22 3 0.14
23 11 0.52
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTATTTTTATTTTTTAAAAAA
Found at i:1052718 original size:7 final size:7
Alignment explanation
Indices: 1052706--1052730 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1052696 TTAATTTTGT
1052706 GGATTTA
1 GGATTTA
1052713 GGATTTA
1 GGATTTA
1052720 GGATTTA
1 GGATTTA
1052727 GGAT
1 GGAT
1052731 GAGTTTTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.32, T:0.40
Consensus pattern (7 bp):
GGATTTA
Found at i:1053529 original size:19 final size:20
Alignment explanation
Indices: 1053490--1053530 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1053480 TTCAGAAAGG
*
1053490 TTTTGATAAAATTATTATTA
1 TTTTGATAAAATTAATATTA
*
1053510 TTTTGATAAATTTAAT-TTA
1 TTTTGATAAAATTAATATTA
1053529 TT
1 TT
1053531 ATCCAAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (20 bp):
TTTTGATAAAATTAATATTA
Found at i:1073352 original size:18 final size:18
Alignment explanation
Indices: 1073316--1073352 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1073306 GAAAGTCATT
*
1073316 TTAGTATCGATACCCTAG
1 TTAGTATCGATACCATAG
*
1073334 TTAGTATCGATACTATAG
1 TTAGTATCGATACCATAG
1073352 T
1 T
1073353 ATGGAAGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (18 bp):
TTAGTATCGATACCATAG
Found at i:1073469 original size:20 final size:19
Alignment explanation
Indices: 1073421--1073470 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1073411 TTTTTCCTTG
1073421 AGTATCGATACCCAAAATA
1 AGTATCGATACCCAAAATA
* * *
1073440 AGTA-CGATACTCCATAGTT
1 AGTATCGATAC-CCAAAATA
1073459 AGTATCGATACC
1 AGTATCGATACC
1073471 ATATTCTTGG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 6 0.23
19 14 0.54
20 6 0.23
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (19 bp):
AGTATCGATACCCAAAATA
Done.