Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000395.1 Hibiscus syriacus cultivar Beakdansim tig00000728_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: 72626
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:3011 original size:21 final size:21
Alignment explanation
Indices: 2969--3012 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2959 ACCCCGGGAG
* *
2969 CTAGTTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
2990 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
3011 CT
1 CT
3013 CCTCATCCGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.39, G:0.16, T:0.36
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:4035 original size:20 final size:20
Alignment explanation
Indices: 4006--4043 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3996 TTTCAAAGTG
*
4006 ATGCACCGATGTACCAATCC
1 ATGCACCGATGCACCAATCC
*
4026 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
4044 TAATTTTTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.21
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:6999 original size:28 final size:28
Alignment explanation
Indices: 6946--6999 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
6936 TGATTTATTA
* * *
6946 TTTTAATATTTTTATTAATAATATTAGT
1 TTTTAATATTGTGATTAATAAAATTAGT
6974 TTTTAATATTGTGA-TAATATAAATTA
1 TTTTAATATTGTGATTAATA-AAATTA
7000 TGCAGTATGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (28 bp):
TTTTAATATTGTGATTAATAAAATTAGT
Found at i:7056 original size:21 final size:22
Alignment explanation
Indices: 7024--7065 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
7014 TGTTTCTGAA
7024 AAAATGAATTTTT-TAAGTATTG
1 AAAATGAATTTTTATAA-TATTG
7046 AAAAT-AATTTTTATAATATT
1 AAAATGAATTTTTATAATATT
7066 AATATTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (22 bp):
AAAATGAATTTTTATAATATTG
Found at i:7057 original size:22 final size:21
Alignment explanation
Indices: 7024--7065 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
7014 TGTTTCTGAA
*
7024 AAAATGAATTTTTTAAGTATTG
1 AAAATGAATTTTATAA-TATTG
7046 AAAAT-AATTTTTATAATATT
1 AAAATGAA-TTTTATAATATT
7066 AATATTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (21 bp):
AAAATGAATTTTATAATATTG
Found at i:7143 original size:24 final size:24
Alignment explanation
Indices: 7115--7160 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
7105 TAAAAAATAT
**
7115 TATAATAAATTATTTTATTTATAA
1 TATAATAAATTAAATTATTTATAA
*
7139 TATAATAATTTAAATTATTTAT
1 TATAATAAATTAAATTATTTAT
7161 CTTACTTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TATAATAAATTAAATTATTTATAA
Found at i:7223 original size:2 final size:2
Alignment explanation
Indices: 7216--7250 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
7206 CACATTCCTA
* *
7216 AT AT AT AT GT GT 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 AT AT A
7251 ATTCAGTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11035 original size:22 final size:22
Alignment explanation
Indices: 11010--11051 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
11000 TTCATGTAAC
11010 ACACTGATGCACACTACTAAAT
1 ACACTGATGCACACTACTAAAT
11032 ACACTGATGCACACTACTAA
1 ACACTGATGCACACTACTAA
11052 CTAACTTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.29, G:0.10, T:0.21
Consensus pattern (22 bp):
ACACTGATGCACACTACTAAAT
Found at i:15433 original size:150 final size:150
Alignment explanation
Indices: 15162--15457 Score: 565
Period size: 150 Copynumber: 2.0 Consensus size: 150
15152 AAGATTCATC
*
15162 ATCTTCTTTTACTAATAAAATAGATGCAACATAAGGTTACTAACAAGTAGCAAGACCTGCATGAA
1 ATCTTCTTTTACTAATAAAATAGATGCAACATAAGGTTACTAACAAGTAGCAAGACCTGCATAAA
*
15227 ATAAAATGCATGCTTTTGAAGTGAAACCTAAGAAAAGTATGAATGATACTTTTAACAAGCTCACC
66 ATAAAATGCATGCTTTTGAAGTGAAACCTAAGAAAAGTATGAATGACACTTTTAACAAGCTCACC
15292 CTCCCAACACCTGAAAGTGA
131 CTCCCAACACCTGAAAGTGA
*
15312 ATCTTCTTTTACTAATAAAATAGATGCAACATAAGGTTACTAACATGTAGCAAGACCTGCATAAA
1 ATCTTCTTTTACTAATAAAATAGATGCAACATAAGGTTACTAACAAGTAGCAAGACCTGCATAAA
15377 ATAAAATGCATGCTTTTGAAGTGAAACCTAAGAAAAGTATGAATGACACTTTTAACAAGCTCACC
66 ATAAAATGCATGCTTTTGAAGTGAAACCTAAGAAAAGTATGAATGACACTTTTAACAAGCTCACC
15442 CTCCCAACACCTGAAA
131 CTCCCAACACCTGAAA
15458 ACTTTCACTT
Statistics
Matches: 143, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
150 143 1.00
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.26
Consensus pattern (150 bp):
ATCTTCTTTTACTAATAAAATAGATGCAACATAAGGTTACTAACAAGTAGCAAGACCTGCATAAA
ATAAAATGCATGCTTTTGAAGTGAAACCTAAGAAAAGTATGAATGACACTTTTAACAAGCTCACC
CTCCCAACACCTGAAAGTGA
Found at i:31959 original size:59 final size:59
Alignment explanation
Indices: 31883--31995 Score: 190
Period size: 59 Copynumber: 1.9 Consensus size: 59
31873 AATAGATGAA
* *
31883 TAAGTGTCCTATTGAACCCTCCTAGTCGCAATGAAAAGGAAAACTCGATAATATATCTC
1 TAAGTGTCCTATCGAACCCTCCTAATCGCAATGAAAAGGAAAACTCGATAATATATCTC
* *
31942 TAAGTGTCCTATCGAACCCTCCTAATTGCAATGAAAAGGCAAACTCGATAATAT
1 TAAGTGTCCTATCGAACCCTCCTAATCGCAATGAAAAGGAAAACTCGATAATAT
31996 GGCTCTAACC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 50 1.00
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (59 bp):
TAAGTGTCCTATCGAACCCTCCTAATCGCAATGAAAAGGAAAACTCGATAATATATCTC
Found at i:35955 original size:17 final size:17
Alignment explanation
Indices: 35933--36001 Score: 93
Period size: 17 Copynumber: 3.9 Consensus size: 17
35923 AACGGTCAAC
*
35933 GGTCAATGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
35950 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
35967 GGTCAACAGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
35984 AGTCAGACGGGTCGGGTC
1 GGTCA-AC-GGTCGGGTC
36002 AGACCGATCA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
17 36 0.78
18 2 0.04
19 8 0.17
ACGTcount: A:0.14, C:0.22, G:0.45, T:0.19
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:36024 original size:19 final size:19
Alignment explanation
Indices: 36000--36040 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
35990 ACGGGTCGGG
36000 TCAGACCGATCAAACCGGT
1 TCAGACCGATCAAACCGGT
36019 TCAGACCGATCAAACCGGT
1 TCAGACCGATCAAACCGGT
36038 TCA
1 TCA
36041 AAACTGGTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.20, T:0.17
Consensus pattern (19 bp):
TCAGACCGATCAAACCGGT
Found at i:36041 original size:10 final size:10
Alignment explanation
Indices: 36009--36058 Score: 50
Period size: 9 Copynumber: 5.1 Consensus size: 10
35999 GTCAGACCGA
36009 TCAAACCGGT
1 TCAAACCGGT
* *
36019 TCAGACC-GA
1 TCAAACCGGT
36028 TCAAACCGGT
1 TCAAACCGGT
*
36038 TCAAAACTGG-
1 TC-AAACCGGT
36048 TCAAACCGGT
1 TCAAACCGGT
36058 T
1 T
36059 TTCCAGCAGC
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
9 13 0.42
10 12 0.39
11 6 0.19
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.20
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:36053 original size:20 final size:19
Alignment explanation
Indices: 36004--36058 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
35994 GTCGGGTCAG
*
36004 ACCGATCAAACCGGTTCAG
1 ACCGATCAAACCGGTTCAA
36023 ACCGATCAAACCGGTTCAAA
1 ACCGATCAAACCGGTTC-AA
* *
36043 ACTGGTCAAACCGGTT
1 ACCGATCAAACCGGTT
36059 TTCCAGCAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.33, C:0.29, G:0.20, T:0.18
Consensus pattern (19 bp):
ACCGATCAAACCGGTTCAA
Found at i:39411 original size:3 final size:3
Alignment explanation
Indices: 39398--39454 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
39388 GAAACCACAC
*
39398 TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
39446 TAT TAT TAT
1 TAT TAT TAT
39455 ACATCATAAG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:39561 original size:6 final size:6
Alignment explanation
Indices: 39550--39585 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
39540 TATGGTGCAA
*
39550 TGGGAT TGGGAT TGGGAT TGGGAT TGAGATT TGGGA
1 TGGGAT TGGGAT TGGGAT TGGGAT TGGGA-T TGGGA
39586 AAGGTCAGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 22 0.81
7 5 0.19
ACGTcount: A:0.19, C:0.00, G:0.47, T:0.33
Consensus pattern (6 bp):
TGGGAT
Found at i:42659 original size:2 final size:2
Alignment explanation
Indices: 42652--42688 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
42642 TTAGAGAATA
42652 AT AT AT 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 AT AT AT A
42689 ATAACTCATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:44102 original size:149 final size:149
Alignment explanation
Indices: 43832--44132 Score: 548
Period size: 149 Copynumber: 2.0 Consensus size: 149
43822 CTTTGCAGCA
*
43832 ATCCTCGTCCTACCAAAGTGCCCTCCACACAGGGATGTATGGAAATGAAATATAATATCATTTTG
1 ATCCTCGTCCTACCAAAGTGCCCTCCACACAGGGATGTATGGAAATGAAATAGAATATCATTTTG
43897 TTATTCTTCAGGGACGCATCTCTGGATTATTTGATCCCCACATTGTTTGAATAAGAATTGTTCAT
66 TTATTCTTCAGGGACGCATCTCTGGATTATTTGATCCCCACATTGTTTGAATAAGAATTGTTCAT
43962 CCCAATAATAATGTCGCAC
131 CCCAATAATAATGTCGCAC
* * *
43981 ATCCTCGTCCTATCAAAGTGTCCTCCACACAGGGATGTATGGAAATGAAATAGAATATCCTTTTG
1 ATCCTCGTCCTACCAAAGTGCCCTCCACACAGGGATGTATGGAAATGAAATAGAATATCATTTTG
* *
44046 TTCTTCTTCAGGGACGCATCTCTGGATTATTTGATCCCCACATTGTTTGAATAAGAATTTTTCAT
66 TTATTCTTCAGGGACGCATCTCTGGATTATTTGATCCCCACATTGTTTGAATAAGAATTGTTCAT
44111 CCCAATAATAATGTCGCAC
131 CCCAATAATAATGTCGCAC
44130 ATC
1 ATC
44133 ATGTCTAAAC
Statistics
Matches: 146, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
149 146 1.00
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (149 bp):
ATCCTCGTCCTACCAAAGTGCCCTCCACACAGGGATGTATGGAAATGAAATAGAATATCATTTTG
TTATTCTTCAGGGACGCATCTCTGGATTATTTGATCCCCACATTGTTTGAATAAGAATTGTTCAT
CCCAATAATAATGTCGCAC
Found at i:50331 original size:12 final size:12
Alignment explanation
Indices: 50314--50342 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
50304 GTCATTTTCT
50314 ATCACATGCATC
1 ATCACATGCATC
50326 ATCACATGCATC
1 ATCACATGCATC
50338 A-CACA
1 ATCACA
50343 ACCTTTCTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.38, C:0.34, G:0.07, T:0.21
Consensus pattern (12 bp):
ATCACATGCATC
Found at i:58897 original size:138 final size:138
Alignment explanation
Indices: 58645--58899 Score: 393
Period size: 138 Copynumber: 1.8 Consensus size: 138
58635 CACCGAAGTG
* *
58645 TCGAAATGGAAATTCACAAACTCATTATGAATTCCATGGATGCACACATAGTGTCGAAAGTACAC
1 TCGAAATGGAAATTCAAAAACTCATTATGAATACCATGGATGCACACATAGTGTCGAAAGTACAC
* *
58710 ATAGTACTGATACGAAAATGCATCGTTATGCATTAAACAAAATCAATCGATACCTTTTATACATA
66 ATAGTACTGATACAAAAATGCACCGTTATGCATTAAACAAAATCAATCGATACCTTTTATACATA
58775 ATTGTATA
131 ATTGTATA
* * * *
58783 TCGAAATGGTAATTCAAAAACTCATTATGAATACCATGGTTGCACATATAGTGTCGAAAGTACGC
1 TCGAAATGGAAATTCAAAAACTCATTATGAATACCATGGATGCACACATAGTGTCGAAAGTACAC
* * * **
58848 ATAGTATTGATACAAAAATGTACCGTTATGCATTAAACCAAATTGATCGATA
66 ATAGTACTGATACAAAAATGCACCGTTATGCATTAAACAAAATCAATCGATA
58900 ACCATTACAT
Statistics
Matches: 104, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
138 104 1.00
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (138 bp):
TCGAAATGGAAATTCAAAAACTCATTATGAATACCATGGATGCACACATAGTGTCGAAAGTACAC
ATAGTACTGATACAAAAATGCACCGTTATGCATTAAACAAAATCAATCGATACCTTTTATACATA
ATTGTATA
Found at i:65593 original size:19 final size:19
Alignment explanation
Indices: 65558--65594 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
65548 ACACTTAGTG
**
65558 CATCGGTGCACGTAGTGTA
1 CATCGGTGCACCAAGTGTA
65577 CATCGGTGCACCAAGTGT
1 CATCGGTGCACCAAGTGT
65595 GCACCGATGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.24, G:0.30, T:0.24
Consensus pattern (19 bp):
CATCGGTGCACCAAGTGTA
Found at i:65678 original size:64 final size:64
Alignment explanation
Indices: 65593--65751 Score: 185
Period size: 64 Copynumber: 2.5 Consensus size: 64
65583 TGCACCAAGT
* * * ** * * ***
65593 GTGCACCGATGCATAAAATGCATTCGATGTTTGAA-AATAGCCTGAGTGCATCGGTGCATTGCTT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTGAATAA-AACCCAAGTGCATCGATGCATAGAGA
* * *
65657 GTGCATTGATTCATGAAATGCATTCGATGTTTTAATAAAACCCAAGTGCATCGATGCATAGAGA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAAACCCAAGTGCATCGATGCATAGAGA
65721 GTGCATCGATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATGAAATGCATTCGATGTT
65752 CAATTTATTC
Statistics
Matches: 79, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
64 77 0.97
65 2 0.03
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAAACCCAAGTGCATCGATGCATAGAGA
Found at i:68480 original size:21 final size:21
Alignment explanation
Indices: 68451--68524 Score: 60
Period size: 21 Copynumber: 3.4 Consensus size: 21
68441 CAAGGCGTGC
*
68451 ATCGGTGCATCAACATGATGA
1 ATCGATGCATCAACATGATGA
* * * *
68472 ATCAATGCA-CATTCAAGGCATGT
1 ATCGATGCATCA-AC-ATG-ATGA
*
68495 ATCGTTGCATCAACATGATGA
1 ATCGATGCATCAACATGATGA
68516 ATCGATGCA
1 ATCGATGCA
68525 CATTCAAAGG
Statistics
Matches: 38, Mismatches: 11, Indels: 8
0.67 0.19 0.14
Matches are distributed among these distances:
20 2 0.05
21 19 0.50
22 4 0.11
23 11 0.29
24 2 0.05
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (21 bp):
ATCGATGCATCAACATGATGA
Found at i:68487 original size:44 final size:44
Alignment explanation
Indices: 68456--68548 Score: 125
Period size: 44 Copynumber: 2.1 Consensus size: 44
68446 CGTGCATCGG
* * *
68456 TGCATCAACATGATGAATCAATGCACATTCAAGGCATGTATCGT
1 TGCATCAACATGATGAATCAATGCACATTCAAGGCGTGCATCGA
*
68500 TGCATCAACATGATGAATCGATGCACATTCAAAGG-GATGCATCGA
1 TGCATCAACATGATGAATCAATGCACATTC-AAGGCG-TGCATCGA
68545 TGCA
1 TGCA
68549 CTATTAAGTG
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
44 29 0.67
45 14 0.33
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.25
Consensus pattern (44 bp):
TGCATCAACATGATGAATCAATGCACATTCAAGGCGTGCATCGA
Done.