Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003307.1 Hibiscus syriacus cultivar Beakdansim tig00006957_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: 54858
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:3110 original size:29 final size:29
Alignment explanation
Indices: 3048--3119 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 29
3038 TTTAAAGTAA
3048 AGACTAAATTGAAATAAAATAAAAACATG
1 AGACTAAATTGAAATAAAATAAAAACATG
* * * *
3077 A-ACTAAATTGCAATAAATTTAAAA-TTAG
1 AGACTAAATTGAAATAAAATAAAAACAT-G
3105 AGACTAAATTGAAAT
1 AGACTAAATTGAAAT
3120 TTATAGGAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 1 0.03
28 22 0.61
29 13 0.36
ACGTcount: A:0.57, C:0.07, G:0.10, T:0.26
Consensus pattern (29 bp):
AGACTAAATTGAAATAAAATAAAAACATG
Found at i:7251 original size:18 final size:20
Alignment explanation
Indices: 7223--7259 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
7213 CCCTCTTATT
7223 TTTACTTTAATTG-CTTTTA
1 TTTACTTTAATTGTCTTTTA
7242 TTTA-TTTAATTGTCTTTT
1 TTTACTTTAATTGTCTTTT
7260 TGACTATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.19, C:0.08, G:0.05, T:0.68
Consensus pattern (20 bp):
TTTACTTTAATTGTCTTTTA
Found at i:13753 original size:14 final size:14
Alignment explanation
Indices: 13734--13762 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
13724 ATTACACGAG
13734 TTCTTGGAGGTTTC
1 TTCTTGGAGGTTTC
13748 TTCTTGGAGGTTTC
1 TTCTTGGAGGTTTC
13762 T
1 T
13763 CTAATTATTC
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:0.14, G:0.28, T:0.52
Consensus pattern (14 bp):
TTCTTGGAGGTTTC
Found at i:19651 original size:15 final size:16
Alignment explanation
Indices: 19631--19664 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
19621 TATATTTAGT
19631 TTTTTTA-TTAATTTA
1 TTTTTTATTTAATTTA
19646 TTTTTTATTTAATTTA
1 TTTTTTATTTAATTTA
19662 TTT
1 TTT
19665 AATCTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTTATTTAATTTA
Found at i:19651 original size:16 final size:17
Alignment explanation
Indices: 19624--19664 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
19614 AATAATATAT
19624 ATTTAGTTTTTTTA-TTA
1 ATTTA-TTTTTTTATTTA
19641 ATTTA-TTTTTTATTTA
1 ATTTATTTTTTTATTTA
19657 ATTTATTT
1 ATTTATTT
19665 AATCTTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 7 0.32
16 8 0.36
17 7 0.32
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (17 bp):
ATTTATTTTTTTATTTA
Found at i:24233 original size:24 final size:24
Alignment explanation
Indices: 24156--24238 Score: 73
Period size: 24 Copynumber: 3.5 Consensus size: 24
24146 AGGGTGTCGG
*
24156 GATAAAGACAATGACTGAGGCTGC
1 GATAAAGACAATGACTGAGGCTGA
** * *
24180 GA-ATTG-CGATGACGGAGGCTGA
1 GATAAAGACAATGACTGAGGCTGA
*
24202 GATGAAGACAATGACTGAGGCT-A
1 GATAAAGACAATGACTGAGGCTGA
*
24225 GGATAAAGAGAATG
1 -GATAAAGACAATG
24239 CTAATTCTGA
Statistics
Matches: 44, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
22 15 0.34
23 4 0.09
24 25 0.57
ACGTcount: A:0.37, C:0.12, G:0.34, T:0.17
Consensus pattern (24 bp):
GATAAAGACAATGACTGAGGCTGA
Found at i:41523 original size:26 final size:26
Alignment explanation
Indices: 41437--41503 Score: 125
Period size: 26 Copynumber: 2.6 Consensus size: 26
41427 AGCTCCCAAT
*
41437 CGCCGCTGCTTCCAGAATATCTCAGC
1 CGCCGCTGCTTCCAAAATATCTCAGC
41463 CGCCGCTGCTTCCAAAATATCTCAGC
1 CGCCGCTGCTTCCAAAATATCTCAGC
41489 CGCCGCTGCTTCCAA
1 CGCCGCTGCTTCCAA
41504 GGGATTCCAG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.19, C:0.40, G:0.18, T:0.22
Consensus pattern (26 bp):
CGCCGCTGCTTCCAAAATATCTCAGC
Found at i:46188 original size:20 final size:21
Alignment explanation
Indices: 46163--46202 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
46153 ATTCTGACTA
46163 TTGCGATTTTCC-AATTCACG
1 TTGCGATTTTCCTAATTCACG
46183 TTGCGATTTTCCTAATTCAC
1 TTGCGATTTTCCTAATTCAC
46203 AATGCGAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.20, C:0.25, G:0.12, T:0.42
Consensus pattern (21 bp):
TTGCGATTTTCCTAATTCACG
Found at i:46208 original size:21 final size:20
Alignment explanation
Indices: 46164--46209 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
46154 TTCTGACTAT
**
46164 TGCGATTTTCCAATTCACGT
1 TGCGATTTTCCAATTCACAA
46184 TGCGATTTTCCTAATTCACAA
1 TGCGATTTTCC-AATTCACAA
46205 TGCGA
1 TGCGA
46210 AACATAAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (20 bp):
TGCGATTTTCCAATTCACAA
Found at i:46239 original size:20 final size:20
Alignment explanation
Indices: 46202--46290 Score: 144
Period size: 20 Copynumber: 4.5 Consensus size: 20
46192 TCCTAATTCA
*
46202 CAATGCGAA-ACATAAATCG
1 CAATGCGAATACGTAAATCG
46221 CAATGCGAATACGTAAATCG
1 CAATGCGAATACGTAAATCG
46241 CAATGCGAATACGTAAATCG
1 CAATGCGAATACGTAAATCG
*
46261 CAATGTGAATACGTAAATCG
1 CAATGCGAATACGTAAATCG
*
46281 CAACGCGAAT
1 CAATGCGAAT
46291 CTGACTATCG
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
19 9 0.14
20 56 0.86
ACGTcount: A:0.42, C:0.20, G:0.19, T:0.19
Consensus pattern (20 bp):
CAATGCGAATACGTAAATCG
Found at i:46385 original size:31 final size:31
Alignment explanation
Indices: 46342--46403 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
46332 TGACTATCAC
46342 AACGCGATTCTGACTATCGCAACGAGATTCT
1 AACGCGATTCTGACTATCGCAACGAGATTCT
* * *
46373 AACGTGATTCTGACTATCGCAATGCGATTCT
1 AACGCGATTCTGACTATCGCAACGAGATTCT
46404 GACTATCGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.29
Consensus pattern (31 bp):
AACGCGATTCTGACTATCGCAACGAGATTCT
Found at i:46415 original size:20 final size:20
Alignment explanation
Indices: 46277--46414 Score: 150
Period size: 20 Copynumber: 7.3 Consensus size: 20
46267 GAATACGTAA
*
46277 ATCGCAACGCGAATCTGACT
1 ATCGCAACGCGATTCTGACT
46297 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* *
46317 ATCGCAATGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
46337 ATCACAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
46357 ATCGCAA--CGA----GA-T
1 ATCGCAACGCGATTCTGACT
* *
46370 -TC-TAACGTGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
46388 ATCGCAATGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
46408 ATCGCAA
1 ATCGCAA
46415 TACTAAATTT
Statistics
Matches: 97, Mismatches: 12, Indels: 18
0.76 0.09 0.14
Matches are distributed among these distances:
11 2 0.02
12 2 0.02
13 3 0.03
14 2 0.02
17 2 0.02
18 4 0.04
19 2 0.02
20 80 0.82
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:46604 original size:22 final size:22
Alignment explanation
Indices: 46576--46627 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
46566 CTCCGGCGAT
46576 ATCCGTTCCTATATCCAACGAC
1 ATCCGTTCCTATATCCAACGAC
46598 ATCCGTTCCTATATCCAACGAC
1 ATCCGTTCCTATATCCAACGAC
46620 ATCC-TTCC
1 ATCCGTTCC
46628 CCATCCGGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 4 0.13
22 26 0.87
ACGTcount: A:0.25, C:0.38, G:0.08, T:0.29
Consensus pattern (22 bp):
ATCCGTTCCTATATCCAACGAC
Found at i:47308 original size:23 final size:24
Alignment explanation
Indices: 47270--47321 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 24
47260 GTATTCGAAA
*
47270 TTTGATCTTGGTCAATACTCGGAC
1 TTTGATCTTGGTCAATACTCAGAC
*
47294 TTTGATC-TGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACTCAGAC
47317 TTTGA
1 TTTGA
47322 GATTTTTCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 19 0.73
24 7 0.27
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.40
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACTCAGAC
Found at i:49698 original size:20 final size:19
Alignment explanation
Indices: 49673--49741 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 19
49663 CAACGCGGAA
49673 ATCGCAACGCGAATATGACT
1 ATCGCAACGCGAA-ATGACT
*
49693 ATCGCAACACGGAAATGACT
1 ATCGCAACGC-GAAATGACT
*
49713 ATCGTAACGCCGAAATGACT
1 ATCGCAACG-CGAAATGACT
49733 ATCGCAACG
1 ATCGCAACG
49742 AGAGAATCGC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
20 39 0.91
21 4 0.09
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.17
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:49770 original size:33 final size:34
Alignment explanation
Indices: 49733--49806 Score: 123
Period size: 33 Copynumber: 2.2 Consensus size: 34
49723 CGAAATGACT
*
49733 ATCGCAACGAGAGAATCGCAATGC-AAAATGAAA
1 ATCGCAACGAGAGAATCACAATGCAAAAATGAAA
*
49766 ATCGCAACGAGAGAATCACAGTGCAAAAATGAAA
1 ATCGCAACGAGAGAATCACAATGCAAAAATGAAA
49800 ATCGCAA
1 ATCGCAA
49807 TGCGAATTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 22 0.58
34 16 0.42
ACGTcount: A:0.49, C:0.19, G:0.20, T:0.12
Consensus pattern (34 bp):
ATCGCAACGAGAGAATCACAATGCAAAAATGAAA
Found at i:49868 original size:34 final size:34
Alignment explanation
Indices: 49825--49918 Score: 127
Period size: 33 Copynumber: 2.8 Consensus size: 34
49815 TAGTTTTGCG
49825 TTGCAATTTTCATTTTCGCATTGCGATTCTCTCA
1 TTGCAATTTTCATTTTCGCATTGCGATTCTCTCA
*
49859 TTGCAATTTTCA-TTTCGCATTGCGATTCTCTCG
1 TTGCAATTTTCATTTTCGCATTGCGATTCTCTCA
* ** * *
49892 TTGCGATAGTCATTTCCGCGTTGCGAT
1 TTGCAATTTTCATTTTCGCATTGCGAT
49919 AGTCTGTTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 29 0.55
34 24 0.45
ACGTcount: A:0.16, C:0.23, G:0.17, T:0.44
Consensus pattern (34 bp):
TTGCAATTTTCATTTTCGCATTGCGATTCTCTCA
Found at i:50036 original size:14 final size:14
Alignment explanation
Indices: 50017--50053 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
50007 CATCAATTAA
50017 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
50031 ACAAATCATCTTTT
1 ACAAATCAACATTT
50045 ACAAATCAA
1 ACAAATCAA
50054 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:52059 original size:19 final size:20
Alignment explanation
Indices: 51975--52046 Score: 117
Period size: 20 Copynumber: 3.6 Consensus size: 20
51965 GAAACTTAAA
* **
51975 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAATTTGACT
51995 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAATTTGACT
52015 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAATTTGACT
52035 ATCGCAATGCGA
1 ATCGCAATGCGA
52047 TTTTCATTTC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGAATTTGACT
Found at i:52174 original size:33 final size:34
Alignment explanation
Indices: 52093--52184 Score: 105
Period size: 33 Copynumber: 2.7 Consensus size: 34
52083 TCAAATTCGT
* * *
52093 ATTGCGATAGTCATTTTCGCGTTGCAATTTTGTT
1 ATTGCGATAGTCATTTTCGCGTTGCAATTCTCTC
* ** * *
52127 GTTGCGATTTTCA-TTTCGCATTGCGATTCTCTC
1 ATTGCGATAGTCATTTTCGCGTTGCAATTCTCTC
52160 ATTGCGATAGTCATTTTCGCGTTGC
1 ATTGCGATAGTCATTTTCGCGTTGC
52185 CATAGTCATT
Statistics
Matches: 45, Mismatches: 12, Indels: 2
0.76 0.20 0.03
Matches are distributed among these distances:
33 25 0.56
34 20 0.44
ACGTcount: A:0.15, C:0.20, G:0.21, T:0.45
Consensus pattern (34 bp):
ATTGCGATAGTCATTTTCGCGTTGCAATTCTCTC
Found at i:52189 original size:20 final size:20
Alignment explanation
Indices: 52159--52210 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
52149 GCGATTCTCT
52159 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
* *
52179 CGTTGCCATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
52199 CATTGCGATAGT
1 CATTGCGATAGT
52211 AAACTATTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.38
Consensus pattern (20 bp):
CATTGCGATAGTCATTTTCG
Found at i:52190 original size:87 final size:87
Alignment explanation
Indices: 52042--52204 Score: 245
Period size: 87 Copynumber: 1.9 Consensus size: 87
52032 ACTATCGCAA
* * * *
52042 TGCGATTTTCATTTCGCATTGCGATTCTTTCGTTACGATAGTCAAATTCGTATTGCGATAGTCAT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCATTACGATAGTCAAATTCGCATTGCCATAGTCAT
*
52107 TTTCGCGTTGCAATTTTGTTGT
66 TTTCGCATTGCAATTTTGTTGT
* ** *
52129 TGCGATTTTCATTTCGCATTGCGATTCTCTCATTGCGATAGTCATTTTCGCGTTGCCATAGTCAT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCATTACGATAGTCAAATTCGCATTGCCATAGTCAT
52194 TTTCGCATTGC
66 TTTCGCATTGC
52205 GATAGTAAAC
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 67 1.00
ACGTcount: A:0.17, C:0.20, G:0.19, T:0.44
Consensus pattern (87 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCATTACGATAGTCAAATTCGCATTGCCATAGTCAT
TTTCGCATTGCAATTTTGTTGT
Found at i:54085 original size:20 final size:20
Alignment explanation
Indices: 54070--54112 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
54060 TTAAAATCTT
54070 AACACGAAAATGAAAATCGC
1 AACACGAAAATGAAAATCGC
**
54090 AACACGAAAATGACTATCGC
1 AACACGAAAATGAAAATCGC
54110 AAC
1 AAC
54113 GCAAGAATCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.23, G:0.14, T:0.12
Consensus pattern (20 bp):
AACACGAAAATGAAAATCGC
Found at i:54760 original size:20 final size:20
Alignment explanation
Indices: 54730--54858 Score: 217
Period size: 20 Copynumber: 6.5 Consensus size: 20
54720 CGATAGTCAG
*
54730 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
54750 ATTTGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
54770 ATTCACATT--GATTTACGT
1 ATTCGCATTGCGATTTACGT
54788 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
54808 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
54828 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
54848 ATTCGCATTGC
1 ATTCGCATTGC
Statistics
Matches: 102, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
18 17 0.17
20 85 0.83
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.41
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Done.