Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006720.1 Hibiscus syriacus cultivar Beakdansim tig00016807_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: 59845
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Found at i:124 original size:17 final size:17
Alignment explanation
Indices: 94--126 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
84 TTAATTAAAA
94 ATATAAAAATATTTAAT
1 ATATAAAAATATTTAAT
111 ATATATAAAA-ATTTAA
1 ATATA-AAAATATTTAA
127 AATTTTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATATAAAAATATTTAAT
Found at i:507 original size:23 final size:24
Alignment explanation
Indices: 481--525 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
471 TAATTTTAAA
*
481 AAAATTATTTA-AAATTTAAAATT
1 AAAATTATATATAAATTTAAAATT
*
504 AAAATTATATATATATTTAAAA
1 AAAATTATATATAAATTTAAAA
526 AAAACACCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
AAAATTATATATAAATTTAAAATT
Found at i:2605 original size:60 final size:60
Alignment explanation
Indices: 2536--2710 Score: 167
Period size: 60 Copynumber: 2.9 Consensus size: 60
2526 GTATATACAT
* *
2536 ATAGTTT-GGGATGAAATTGGAATATTAAAAAAGTTTAGGGATCAAATTAGAATGAAAGTG
1 ATAGTTTAGGGATAAAATTGGAATATT-AAAAAGTTTAGGGATCAAATTAGAATGAAAGTC
* ** * * * * *
2596 ATAGTTTGGGGATAAAATTAAAATCTTCAAAAGTCT-GAGGA-CTAAGTTAGAATGATAGTC
1 ATAGTTTAGGGATAAAATTGGAATATTAAAAAGTTTAG-GGATC-AAATTAGAATGAAAGTC
* ** * *
2656 ATAGTTTAGGGATAAAATTGGAACATTGGAAAGTTTAAGGATCAATTTAGAATGA
1 ATAGTTTAGGGATAAAATTGGAATATTAAAAAGTTTAGGGATCAAATTAGAATGA
2711 GGGTCATACT
Statistics
Matches: 91, Mismatches: 19, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
59 2 0.02
60 73 0.80
61 16 0.18
ACGTcount: A:0.42, C:0.05, G:0.23, T:0.30
Consensus pattern (60 bp):
ATAGTTTAGGGATAAAATTGGAATATTAAAAAGTTTAGGGATCAAATTAGAATGAAAGTC
Found at i:6633 original size:18 final size:18
Alignment explanation
Indices: 6607--6649 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
6597 AACCCGACTC
*
6607 TATTCAAAATATTATATT
1 TATTAAAAATATTATATT
*
6625 TATTAAAAATATTATTTT
1 TATTAAAAATATTATATT
6643 TAATTAA
1 T-ATTAA
6650 TAAAAATAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTAAAAATATTATATT
Found at i:12334 original size:24 final size:23
Alignment explanation
Indices: 12273--12342 Score: 56
Period size: 24 Copynumber: 3.1 Consensus size: 23
12263 ATTATCTCCT
* *
12273 TTTTCTAATG-AATATTTTATTA
1 TTTTCTAATGTAATATCTTATCA
* * *
12295 TTTTTTACTGTGAATATCTTCTCA
1 TTTTCTAATGT-AATATCTTATCA
12319 TTTTCTAATGTTAATA--TTATCA
1 TTTTCTAATG-TAATATCTTATCA
12341 TT
1 TT
12343 CTACTGTCAC
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
22 15 0.41
24 21 0.57
25 1 0.03
ACGTcount: A:0.27, C:0.10, G:0.06, T:0.57
Consensus pattern (23 bp):
TTTTCTAATGTAATATCTTATCA
Found at i:22812 original size:19 final size:18
Alignment explanation
Indices: 22778--22813 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
22768 TATATAAAGA
*
22778 AAACACAAATTTTGAAAT
1 AAACACAAACTTTGAAAT
22796 AAACACAAAACTTTGAAA
1 AAACAC-AAACTTTGAAA
22814 ACCTTCATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.58, C:0.14, G:0.06, T:0.22
Consensus pattern (18 bp):
AAACACAAACTTTGAAAT
Found at i:23072 original size:29 final size:29
Alignment explanation
Indices: 23030--23099 Score: 113
Period size: 29 Copynumber: 2.4 Consensus size: 29
23020 AACTTTCTAC
* *
23030 TTTGGTAACTAAACATTCAAAATTTATGT
1 TTTGGTCACTAAACATTCAAAATTTACGT
*
23059 TTTGGTCACTAAACTTTCAAAATTTACGT
1 TTTGGTCACTAAACATTCAAAATTTACGT
23088 TTTGGTCACTAA
1 TTTGGTCACTAA
23100 CCAAAATTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.41
Consensus pattern (29 bp):
TTTGGTCACTAAACATTCAAAATTTACGT
Found at i:36644 original size:21 final size:21
Alignment explanation
Indices: 36618--36662 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
36608 GATTTCTGGG
* *
36618 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
36639 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
36660 CAA
1 CAA
36663 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:38527 original size:23 final size:23
Alignment explanation
Indices: 38483--38527 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
38473 ATCATTATAT
*
38483 GGCACTACAGTGCAATTCTACGC
1 GGCACTACAGTGCAATTATACGC
* * *
38506 GGCACTTCGGTGCATTTATACG
1 GGCACTACAGTGCAATTATACG
38528 AGCTGTGGTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (23 bp):
GGCACTACAGTGCAATTATACGC
Found at i:39936 original size:8 final size:8
Alignment explanation
Indices: 39923--39951 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
39913 ATTATTATAA
39923 TAAAAAAT
1 TAAAAAAT
39931 T-AAAAAT
1 TAAAAAAT
39938 TAAAAAAT
1 TAAAAAAT
39946 TAAAAA
1 TAAAAA
39952 TAAAATGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
TAAAAAAT
Found at i:39941 original size:15 final size:14
Alignment explanation
Indices: 39921--39956 Score: 63
Period size: 15 Copynumber: 2.5 Consensus size: 14
39911 TTATTATTAT
39921 AATAAAAAATTAAA
1 AATAAAAAATTAAA
39935 AATTAAAAAATTAAA
1 AA-TAAAAAATTAAA
39950 AATAAAA
1 AATAAAA
39957 TGAAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
AATAAAAAATTAAA
Found at i:41387 original size:20 final size:20
Alignment explanation
Indices: 41362--41495 Score: 124
Period size: 20 Copynumber: 6.6 Consensus size: 20
41352 GTTGCGAAAA
* *
41362 TCGCGTTACGATTTTCCATT
1 TCGCGTTGCGATTTTCCAAT
*
41382 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAAT
* ** *
41402 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCAAT
* * ** *
41423 TCGCGTTACGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCAAT
*
41444 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAAT
*
41464 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAAT
41484 TCGCGTTGCGAT
1 TCGCGTTGCGAT
41496 AGTTGAAAAT
Statistics
Matches: 98, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
20 64 0.65
21 34 0.35
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCAAT
Found at i:41428 original size:21 final size:21
Alignment explanation
Indices: 41402--41519 Score: 123
Period size: 21 Copynumber: 5.7 Consensus size: 21
41392 ATTTTCCAGT
41402 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
*
41423 TCGCGTTACGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
41444 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
* ** **
41464 TCGCGTTGCGAT-TTTCCAGT
1 TCGCGTTGCGATAGTTGAAAA
41484 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
41505 TCGCGTTGCGATAGT
1 TCGCGTTGCGATAGT
41520 CTACAGTTGT
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
20 34 0.41
21 49 0.59
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:41494 original size:82 final size:82
Alignment explanation
Indices: 41357--41519 Score: 308
Period size: 82 Copynumber: 2.0 Consensus size: 82
41347 AATTCGTTGC
41357 GAAAATCGCGTTACGATTTTCCATTTCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAA
1 GAAAATCGCGTTACGATTTTCCATTTCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAA
41422 ATCGCGTTACGATAGTT
66 ATCGCGTTACGATAGTT
*
41439 GAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAA
1 GAAAATCGCGTTACGATTTTCCATTTCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAA
*
41504 ATCGCGTTGCGATAGT
66 ATCGCGTTACGATAGT
41520 CTACAGTTGT
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 79 1.00
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.35
Consensus pattern (82 bp):
GAAAATCGCGTTACGATTTTCCATTTCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAA
ATCGCGTTACGATAGTT
Found at i:41553 original size:82 final size:81
Alignment explanation
Indices: 41357--41560 Score: 277
Period size: 82 Copynumber: 2.5 Consensus size: 81
41347 AATTCGTTGC
* *
41357 GAAAATCGCGTTACGATTTTCCATTTCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAA
1 GAAAATCGCGTTGCGATTTTCCAATTC-CGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAA
41422 ATCGCGTTACGATAGTT
65 ATCGCGTTACGATAGTT
*
41439 GAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAA
1 GAAAATCGCGTTGCGATTTTCCAATTC-CGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAA
*
41504 ATCGCGTTGCGATAGTCT
65 ATCGCGTTACGATAGT-T
* * * *
41522 -ACAGTTGTCGTTGTGATTTTCCAAATT-CGTTGCGATTTT
1 GAAAATCG-CGTTGCGATTTTCC-AATTCCGTTGCGATTTT
41561 ACATTGTAGA
Statistics
Matches: 112, Mismatches: 7, Indels: 6
0.90 0.06 0.05
Matches are distributed among these distances:
82 95 0.85
83 14 0.12
84 3 0.03
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (81 bp):
GAAAATCGCGTTGCGATTTTCCAATTCCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAA
TCGCGTTACGATAGTT
Found at i:51819 original size:30 final size:31
Alignment explanation
Indices: 51739--51821 Score: 148
Period size: 31 Copynumber: 2.6 Consensus size: 31
51729 TTTTTTTTAA
51739 AGTTTAAGTACTAAAATATATCAAAATTGAT
1 AGTTTAAGTACTAAAATATATCAAAATTGAT
*
51770 AGTTTAAGTATTAAAATATATCAAAATTGAT
1 AGTTTAAGTACTAAAATATATCAAAATTGAT
51801 AGTTTAAGTACTAAATATATA
1 AGTTTAAGTACTAAA-ATATA
51822 ATTTACCCTA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
31 44 0.90
32 5 0.10
ACGTcount: A:0.48, C:0.05, G:0.10, T:0.37
Consensus pattern (31 bp):
AGTTTAAGTACTAAAATATATCAAAATTGAT
Found at i:52020 original size:72 final size:72
Alignment explanation
Indices: 51930--52064 Score: 261
Period size: 72 Copynumber: 1.9 Consensus size: 72
51920 ATATATGAAT
*
51930 AATTTTGCACACGTGATATTTTATTTTATGTTCTATGTCAACAAATAATTTAAATATTAAAAAAA
1 AATTTTGCACACGTGATATTTTATTTCATGTTCTATGTCAACAAATAATTTAAATATTAAAAAAA
51995 TAAACTA
66 TAAACTA
52002 AATTTTGCACACGTGATATTTTATTTCATGTTCTATGTCAACAAATAATTTAAATATTAAAAA
1 AATTTTGCACACGTGATATTTTATTTCATGTTCTATGTCAACAAATAATTTAAATATTAAAAA
52065 TAAAATAAAA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
72 62 1.00
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.41
Consensus pattern (72 bp):
AATTTTGCACACGTGATATTTTATTTCATGTTCTATGTCAACAAATAATTTAAATATTAAAAAAA
TAAACTA
Found at i:59208 original size:2 final size:2
Alignment explanation
Indices: 59203--59241 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
59193 TGTGCGTAAT
*
59203 TA TA TA TA TA TA TA TA AA TA T- TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59242 GTAAAAGTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:59626 original size:14 final size:14
Alignment explanation
Indices: 59588--59618 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
59578 AACCTATTGG
59588 ATTAAAATAAATTT
1 ATTAAAATAAATTT
59602 ATTAAAATAAATTT
1 ATTAAAATAAATTT
59616 ATT
1 ATT
59619 GAATTAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTAAAATAAATTT
Done.