Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001627.1 Hibiscus syriacus cultivar Beakdansim tig00003238_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: 74638
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:2088 original size:23 final size:23
Alignment explanation
Indices: 2037--2088 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
2027 CAAATAAAGA
* *
2037 ACTAAAATAAACTTAAATATACC
1 ACTAAAATAAAATTAAACATACC
2060 ACTAAAATAAAATCTAAACAT-CC
1 ACTAAAATAAAAT-TAAACATACC
*
2083 ATTAAA
1 ACTAAA
2089 CCAACCACCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.58, C:0.17, G:0.00, T:0.25
Consensus pattern (23 bp):
ACTAAAATAAAATTAAACATACC
Found at i:5758 original size:17 final size:17
Alignment explanation
Indices: 5736--5770 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
5726 AAATAGTAAA
5736 ATATCAGATCAAACTCC
1 ATATCAGATCAAACTCC
5753 ATATCAGATCAAACTCC
1 ATATCAGATCAAACTCC
5770 A
1 A
5771 CTGTCATGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.29, G:0.06, T:0.23
Consensus pattern (17 bp):
ATATCAGATCAAACTCC
Found at i:19319 original size:25 final size:26
Alignment explanation
Indices: 19267--19321 Score: 69
Period size: 25 Copynumber: 2.1 Consensus size: 26
19257 TTTAAGTATT
*
19267 TTTTATATTCTTTTATTAATTTTTTAA
1 TTTTATATTCTTTTA-TAATTTTATAA
19294 TTTTATA-TCTTTTGA-AATTTTATAA
1 TTTTATATTCTTTT-ATAATTTTATAA
19319 TTT
1 TTT
19322 CACACTTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 12 0.46
26 6 0.23
27 8 0.31
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (26 bp):
TTTTATATTCTTTTATAATTTTATAA
Found at i:20679 original size:15 final size:15
Alignment explanation
Indices: 20659--20691 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
20649 GTAATGGAAG
20659 AAAATAT-TTTATACA
1 AAAATATATTTAT-CA
20674 AAAATATATTTATCA
1 AAAATATATTTATCA
20689 AAA
1 AAA
20692 TTTTTAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (15 bp):
AAAATATATTTATCA
Found at i:22197 original size:18 final size:20
Alignment explanation
Indices: 22162--22200 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
22152 GTGTGAAAAT
*
22162 TAAATATATAGTATAATAAA
1 TAAATATATAGTAAAATAAA
22182 TAAATATA-A-TAAAATAAA
1 TAAATATATAGTAAAATAAA
22200 T
1 T
22201 CGAATAGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 1 0.06
20 8 0.44
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (20 bp):
TAAATATATAGTAAAATAAA
Found at i:23663 original size:41 final size:41
Alignment explanation
Indices: 23606--23687 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
23596 TTGCTGGGAC
*
23606 AGTAATTAGAGAAGTCACGTGGTACTGTTCTATGGCTTTGA
1 AGTAATTAGAGAAGTCACGTGGTACTGTTCTATGACTTTGA
23647 AGTAATTAGAGAAGTCACGTGGTACTGTTCTATGACTTTGA
1 AGTAATTAGAGAAGTCACGTGGTACTGTTCTATGACTTTGA
23688 GGGCTAATGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.28, C:0.12, G:0.26, T:0.34
Consensus pattern (41 bp):
AGTAATTAGAGAAGTCACGTGGTACTGTTCTATGACTTTGA
Found at i:24186 original size:13 final size:13
Alignment explanation
Indices: 24170--24195 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
24160 CACTGTAACC
24170 AACAACTGCAACT
1 AACAACTGCAACT
24183 AACAACTGCAACT
1 AACAACTGCAACT
24196 TTTGCGAGGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.31, G:0.08, T:0.15
Consensus pattern (13 bp):
AACAACTGCAACT
Found at i:27896 original size:17 final size:17
Alignment explanation
Indices: 27871--27914 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
27861 TACTGCTATA
* *
27871 TGTTTTACTATTTGTTT
1 TGTTTTACTATCTGTTC
*
27888 TGTTCTACTATCTGTTC
1 TGTTTTACTATCTGTTC
27905 TGTTTTACTA
1 TGTTTTACTA
27915 GCCCACTCCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.14, C:0.14, G:0.11, T:0.61
Consensus pattern (17 bp):
TGTTTTACTATCTGTTC
Found at i:28708 original size:54 final size:54
Alignment explanation
Indices: 28632--28739 Score: 180
Period size: 54 Copynumber: 2.0 Consensus size: 54
28622 TAAAACAAGT
* **
28632 ACTAAAAACTTCATTTTTCAATCCCAAAGACATTAGTGAGGTCCCCAAACATGC
1 ACTAAAAACTCCATTTCCCAATCCCAAAGACATTAGTGAGGTCCCCAAACATGC
*
28686 ACTAAAAACTCCATTTCCCAATCCGAAAGACATTAGTGAGGTCCCCAAACATGC
1 ACTAAAAACTCCATTTCCCAATCCCAAAGACATTAGTGAGGTCCCCAAACATGC
28740 TTAAAGTTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.37, C:0.28, G:0.12, T:0.23
Consensus pattern (54 bp):
ACTAAAAACTCCATTTCCCAATCCCAAAGACATTAGTGAGGTCCCCAAACATGC
Found at i:33869 original size:2 final size:2
Alignment explanation
Indices: 33862--33890 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
33852 TAATAAAAAT
33862 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
33891 GGATTAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34663 original size:22 final size:23
Alignment explanation
Indices: 34628--34670 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
34618 TAAATAGCAC
34628 ATGACATTTGTTTAATATAAAAAA
1 ATGACATTTGTTTAAT-TAAAAAA
34652 ATGA-ATTT-TTTAATTAAAA
1 ATGACATTTGTTTAATTAAAA
34671 TAATAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 6 0.32
23 4 0.21
24 4 0.21
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (23 bp):
ATGACATTTGTTTAATTAAAAAA
Found at i:37490 original size:2 final size:2
Alignment explanation
Indices: 37483--37508 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
37473 CTATAATTTA
37483 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
37509 GAAATAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39858 original size:2 final size:2
Alignment explanation
Indices: 39853--39883 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
39843 ATTTTTTATG
39853 AT AT AT 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 AT AT AT A
39884 ATTAAGAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53146 original size:15 final size:16
Alignment explanation
Indices: 53121--53163 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
53111 TTCAAAATTA
*
53121 AATATTATTTTA-AAT
1 AATAATATTTTACAAT
*
53136 AATTATATTTTTACAAT
1 AATAATA-TTTTACAAT
53153 AATAATATTTT
1 AATAATATTTT
53164 CTCCTCATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 5 0.22
16 9 0.39
17 9 0.39
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
AATAATATTTTACAAT
Found at i:53153 original size:17 final size:16
Alignment explanation
Indices: 53128--53163 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
53118 TTAAATATTA
*
53128 TTTTAAATAATTATAT
1 TTTTAAATAATAATAT
53144 TTTTACAATAATAATAT
1 TTTTA-AATAATAATAT
53161 TTT
1 TTT
53164 CTCCTCATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTTAAATAATAATAT
Found at i:53457 original size:20 final size:18
Alignment explanation
Indices: 53432--53470 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
53422 ATTTTAACCC
53432 TAAATTACTACTATTGATAA
1 TAAATTACTA-T-TTGATAA
*
53452 TAAATTATTATTTGATAA
1 TAAATTACTATTTGATAA
53470 T
1 T
53471 GATATTTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 1 0.06
20 9 0.50
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (18 bp):
TAAATTACTATTTGATAA
Found at i:54167 original size:20 final size:20
Alignment explanation
Indices: 54142--54199 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
54132 ATCCTATTAC
54142 CTGGTAATCTTACATTCCTA
1 CTGGTAATCTTACATTCCTA
54162 CTGGTAATCTTACATTCCTA
1 CTGGTAATCTTACATTCCTA
* *
54182 TTGGTAATTTTACATTCC
1 CTGGTAATCTTACATTCC
54200 GTGAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.43
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCTA
Found at i:62081 original size:23 final size:21
Alignment explanation
Indices: 62039--62081 Score: 50
Period size: 23 Copynumber: 2.0 Consensus size: 21
62029 ATTGAGTTAA
* *
62039 ATTTTAAATTTTTTATTAATG
1 ATTTTAAATTTTTAACTAATG
62060 ATTTTATATATTTTTAACTAAT
1 ATTTTA-A-ATTTTTAACTAAT
62082 TTTTTGTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 6 0.33
22 1 0.06
23 11 0.61
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (21 bp):
ATTTTAAATTTTTAACTAATG
Found at i:66683 original size:2 final size:2
Alignment explanation
Indices: 66678--66704 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
66668 AGTCAGGGTT
66678 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
66705 CCCTTGATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Done.