Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004091.1 Hibiscus syriacus cultivar Beakdansim tig00008948_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: 67757
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1086 original size:33 final size:29
Alignment explanation
Indices: 1017--1090 Score: 96
Period size: 33 Copynumber: 2.4 Consensus size: 29
1007 TTCCGCAAAA
1017 ATTAATATTTCTATTGTCAATTCTCATCG
1 ATTAATATTTCTATTGTCAATTCTCATCG
1046 ATTAATATTTCGTATTGTCAATTTGTTCTCA-CG
1 ATTAATATTTC-TATTGTCAA----TTCTCATCG
1079 ATTAATATTTCT
1 ATTAATATTTCT
1091 GTTATATGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
29 11 0.28
30 9 0.22
32 1 0.03
33 13 0.32
34 6 0.15
ACGTcount: A:0.27, C:0.15, G:0.08, T:0.50
Consensus pattern (29 bp):
ATTAATATTTCTATTGTCAATTCTCATCG
Found at i:1371 original size:34 final size:36
Alignment explanation
Indices: 1297--1380 Score: 129
Period size: 34 Copynumber: 2.4 Consensus size: 36
1287 AATTACATCC
* *
1297 ACTTTAGC-TTAGGTAAAAGCTTAAACGTAATATGA
1 ACTTTAGCTTTAGGTAAAAGCTAAAACATAATATGA
1332 ACTTTAGCTTTAGGTAAAAGCTAAAACAT-A-ATGA
1 ACTTTAGCTTTAGGTAAAAGCTAAAACATAATATGA
1366 ACTTTAGCTTTAGGT
1 ACTTTAGCTTTAGGT
1381 TAACTAAATT
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
34 19 0.41
35 9 0.20
36 18 0.39
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (36 bp):
ACTTTAGCTTTAGGTAAAAGCTAAAACATAATATGA
Found at i:6001 original size:16 final size:17
Alignment explanation
Indices: 5969--6002 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
5959 ACGAGACGGT
5969 CTGTTGATGACTTGTCA
1 CTGTTGATGACTTGTCA
5986 CTGTTGATGA-TTGTCA
1 CTGTTGATGACTTGTCA
6002 C
1 C
6003 CTCAAAGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.41
Consensus pattern (17 bp):
CTGTTGATGACTTGTCA
Found at i:6348 original size:32 final size:32
Alignment explanation
Indices: 6213--6348 Score: 100
Period size: 32 Copynumber: 4.2 Consensus size: 32
6203 TAACATAAAC
*
6213 ATTTTACTTGTTA-CCGAAACATACAAATGCAG
1 ATTTTACTTGTTATCC-AAACATACAAGTGCAG
* **
6245 ATTTTACTTTGATTATCCAAA-GTA-AAGTGACCTTT
1 ATTTTAC-TTG-TTATCCAAACATACAAGTG--C-AG
* * * * *
6280 AATTTA-TTATTATCCAAAGAAACAAGTGCAC
1 ATTTTACTTGTTATCCAAACATACAAGTGCAG
*
6311 CTTTTACTTGTTATCCAAACATACAAGTGCAG
1 ATTTTACTTGTTATCCAAACATACAAGTGCAG
6343 ATTTTA
1 ATTTTA
6349 TTTAACATAA
Statistics
Matches: 78, Mismatches: 17, Indels: 18
0.69 0.15 0.16
Matches are distributed among these distances:
31 4 0.05
32 47 0.60
33 8 0.10
34 12 0.15
35 7 0.09
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (32 bp):
ATTTTACTTGTTATCCAAACATACAAGTGCAG
Found at i:20564 original size:16 final size:17
Alignment explanation
Indices: 20538--20572 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
20528 GGGATATATG
20538 TGATCTTTGATTTTCTT
1 TGATCTTTGATTTTCTT
20555 TGAT-TTTGATTTTCTT
1 TGATCTTTGATTTTCTT
20571 TG
1 TG
20573 TAAGTAGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.11, C:0.09, G:0.14, T:0.66
Consensus pattern (17 bp):
TGATCTTTGATTTTCTT
Found at i:22255 original size:15 final size:15
Alignment explanation
Indices: 22232--22261 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
22222 TGTTTAAATC
*
22232 AATTTATTAATTTTA
1 AATTAATTAATTTTA
22247 AATTAATTAATTTTA
1 AATTAATTAATTTTA
22262 TTAAAAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
AATTAATTAATTTTA
Found at i:24729 original size:23 final size:22
Alignment explanation
Indices: 24697--24746 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
24687 TAAAATTGTA
*
24697 TTAAAAAT-AAATCAAATTAATG
1 TTAAAAATAAAAT-AAAATAATG
24719 TTAAACAATAAAATAAAATAATG
1 TTAAA-AATAAAATAAAATAATG
24742 TTAAA
1 TTAAA
24747 TAAATGGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 5 0.20
23 16 0.64
24 4 0.16
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (22 bp):
TTAAAAATAAAATAAAATAATG
Found at i:25856 original size:16 final size:16
Alignment explanation
Indices: 25835--25877 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
25825 AAAATAAATA
*
25835 AATAAATAAACATATT
1 AATAAATAAACATAAT
*
25851 AATAAATATAACTTAAT
1 AATAAATA-AACATAAT
25868 AATAATATAA
1 AATAA-ATAA
25878 TATATATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 8 0.35
17 12 0.52
18 3 0.13
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (16 bp):
AATAAATAAACATAAT
Found at i:25984 original size:15 final size:15
Alignment explanation
Indices: 25964--25993 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
25954 AAAACTATAA
25964 TATGTTTTCAAAAAT
1 TATGTTTTCAAAAAT
*
25979 TATGTTTTTAAAAAT
1 TATGTTTTCAAAAAT
25994 ATAATAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (15 bp):
TATGTTTTCAAAAAT
Found at i:26011 original size:34 final size:35
Alignment explanation
Indices: 25942--26017 Score: 100
Period size: 34 Copynumber: 2.2 Consensus size: 35
25932 AGTAACCTAC
**
25942 ATTATATTTTCAAAAACTATAATATGTTTTCAAAA
1 ATTATATTTTCAAAAACTATAATAAATTTTCAAAA
* * *
25977 ATTATGTTTTTAAAAA-TATAATAAATTTTTAAAA
1 ATTATATTTTCAAAAACTATAATAAATTTTCAAAA
26011 ATTATAT
1 ATTATAT
26018 ATATTATGTG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
34 21 0.60
35 14 0.40
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (35 bp):
ATTATATTTTCAAAAACTATAATAAATTTTCAAAA
Found at i:26095 original size:18 final size:18
Alignment explanation
Indices: 26068--26108 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
26058 CCATACATAT
* *
26068 TATATGTTTTCAAAACTA
1 TATATATTTTCAAAACCA
26086 TATATATTTTCAAAACCA
1 TATATATTTTCAAAACCA
26104 TATAT
1 TATAT
26109 TATATACATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.41, C:0.12, G:0.02, T:0.44
Consensus pattern (18 bp):
TATATATTTTCAAAACCA
Found at i:29057 original size:6 final size:7
Alignment explanation
Indices: 29035--29064 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
29025 GTCAAAGGAA
29035 GTCAACG
1 GTCAACG
29042 GTCAACG
1 GTCAACG
29049 GTC-ACG
1 GTCAACG
29055 GTCAACG
1 GTCAACG
29062 GTC
1 GTC
29065 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:29057 original size:13 final size:13
Alignment explanation
Indices: 29039--29064 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29029 AAGGAAGTCA
29039 ACGGTCAACGGTC
1 ACGGTCAACGGTC
29052 ACGGTCAACGGTC
1 ACGGTCAACGGTC
29065 GGGTCGGGTC
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:0.23, C:0.31, G:0.31, T:0.15
Consensus pattern (13 bp):
ACGGTCAACGGTC
Found at i:29081 original size:14 final size:14
Alignment explanation
Indices: 29062--29090 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
29052 ACGGTCAACG
29062 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
29076 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
29090 G
1 G
29091 ACCGGTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.21, G:0.52, T:0.21
Consensus pattern (14 bp):
GTCGGGTCGGGTCA
Found at i:29113 original size:10 final size:9
Alignment explanation
Indices: 29085--29134 Score: 73
Period size: 9 Copynumber: 5.3 Consensus size: 9
29075 AGTCGGGTCG
*
29085 GGTCAGACC
1 GGTCAAACC
29094 GGTCAAACC
1 GGTCAAACC
29103 GGTCGAAACC
1 GGTC-AAACC
29113 GGTCAGAACC
1 GGTCA-AACC
29123 GGTCAAACC
1 GGTCAAACC
29132 GGT
1 GGT
29135 TTCCAGCCCT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
9 20 0.53
10 18 0.47
ACGTcount: A:0.28, C:0.30, G:0.30, T:0.12
Consensus pattern (9 bp):
GGTCAAACC
Found at i:29115 original size:19 final size:19
Alignment explanation
Indices: 29085--29134 Score: 75
Period size: 19 Copynumber: 2.6 Consensus size: 19
29075 AGTCGGGTCG
*
29085 GGTCAGACCGGTCA-AACC
1 GGTCAAACCGGTCAGAACC
29103 GGTCGAAACCGGTCAGAACC
1 GGTC-AAACCGGTCAGAACC
29123 GGTCAAACCGGT
1 GGTCAAACCGGT
29135 TTCCAGCCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 4 0.14
19 17 0.59
20 8 0.28
ACGTcount: A:0.28, C:0.30, G:0.30, T:0.12
Consensus pattern (19 bp):
GGTCAAACCGGTCAGAACC
Found at i:36289 original size:19 final size:20
Alignment explanation
Indices: 36265--36309 Score: 74
Period size: 19 Copynumber: 2.3 Consensus size: 20
36255 TCGGGTCAGT
36265 CGGTTCAGACCGGCCA-AAC
1 CGGTTCAGACCGGCCAGAAC
*
36284 CGGTTCAGACCGGTCAGAAC
1 CGGTTCAGACCGGCCAGAAC
36304 CGGTTC
1 CGGTTC
36310 GAACTTGTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.22, C:0.33, G:0.29, T:0.16
Consensus pattern (20 bp):
CGGTTCAGACCGGCCAGAAC
Found at i:36374 original size:20 final size:21
Alignment explanation
Indices: 36329--36367 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
36319 GAAACCGGTC
36329 AAACCGATCAGAACCGGTTGA
1 AAACCGATCAGAACCGGTTGA
36350 AAACCGATCA-AACCGGTT
1 AAACCGATCAGAACCGGTT
36368 TCCAACCCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.38, C:0.26, G:0.21, T:0.15
Consensus pattern (21 bp):
AAACCGATCAGAACCGGTTGA
Found at i:39707 original size:14 final size:14
Alignment explanation
Indices: 39683--39716 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
39673 AATCTGATTG
39683 AAAATTTAAATTTAT
1 AAAA-TTAAATTTAT
*
39698 TAAATTAAATTTAT
1 AAAATTAAATTTAT
39712 AAAAT
1 AAAAT
39717 ATGTAAGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 14 0.82
15 3 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AAAATTAAATTTAT
Found at i:41983 original size:19 final size:19
Alignment explanation
Indices: 41959--41996 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
41949 AACTAGTCCA
41959 AAATCAACATTTTAATATT
1 AAATCAACATTTTAATATT
* *
41978 AAATCAATATTTTACTATT
1 AAATCAACATTTTAATATT
41997 TGATTCCAAT
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:0.45, C:0.11, G:0.00, T:0.45
Consensus pattern (19 bp):
AAATCAACATTTTAATATT
Found at i:46270 original size:19 final size:19
Alignment explanation
Indices: 46246--46283 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
46236 AACTAGTCCA
46246 AAATCAACATTTCAATATT
1 AAATCAACATTTCAATATT
* *
46265 AAATCAATATTTTAATATT
1 AAATCAACATTTCAATATT
46284 CGATTCCAAT
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:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATCAACATTTCAATATT
Found at i:46772 original size:31 final size:30
Alignment explanation
Indices: 46737--46794 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
46727 TTAAGTCTCT
* *
46737 ACTTTTTCATAATATACAATTTAGTCCACAA
1 ACTTTATCA-AATATACAAATTAGTCCACAA
* *
46768 ACTTTATCAAATTTCCAAATTAGTCCA
1 ACTTTATCAAATATACAAATTAGTCCA
46795 ATTTCACATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 15 0.65
31 8 0.35
ACGTcount: A:0.38, C:0.21, G:0.03, T:0.38
Consensus pattern (30 bp):
ACTTTATCAAATATACAAATTAGTCCACAA
Found at i:57228 original size:19 final size:21
Alignment explanation
Indices: 57173--57229 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 21
57163 ATAAGGCAGA
57173 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCCTT-AAG
* * *
57195 GGGAACCAATTCCCCC-T-AG
1 GGGAATCGATACCCCCTTAAG
57214 GGGAATCGATACCCCC
1 GGGAATCGATACCCCC
57230 CTGGGGTTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 15 0.52
21 1 0.03
22 13 0.45
ACGTcount: A:0.26, C:0.33, G:0.25, T:0.16
Consensus pattern (21 bp):
GGGAATCGATACCCCCTTAAG
Found at i:61569 original size:60 final size:59
Alignment explanation
Indices: 61485--61598 Score: 156
Period size: 60 Copynumber: 1.9 Consensus size: 59
61475 GGTCCCTCGA
*
61485 CTATAGGGTGTTACTTTGTGGAGTCTCTCAACTATCAAAAGTTACAAAATGATCATTTTT
1 CTATAGGATGTTACTTTGTGGAGTCTCTCAACTAT-AAAAGTTACAAAATGATCATTTTT
** * * * *
61545 CTATAGGATGTTGTTTTGTTGAGTCTCTCGACTATTAAAGTTACAAAATTATCA
1 CTATAGGATGTTACTTTGTGGAGTCTCTCAACTATAAAAGTTACAAAATGATCA
61599 CCCAATTATT
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
59 17 0.36
60 30 0.64
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (59 bp):
CTATAGGATGTTACTTTGTGGAGTCTCTCAACTATAAAAGTTACAAAATGATCATTTTT
Done.