Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005252.1 Hibiscus syriacus cultivar Beakdansim tig00011876_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: 79024
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:667 original size:16 final size:17
Alignment explanation
Indices: 648--693 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
638 ATTAGTTTAT
648 AATAAATA-TAAAATAA
1 AATAAATACTAAAATAA
**
664 AAT-AATAGAAAAATAA
1 AATAAATACTAAAATAA
680 AA-AAATACTAAAAT
1 AATAAATACTAAAAT
694 CTAAATAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
15 4 0.16
16 21 0.84
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (17 bp):
AATAAATACTAAAATAA
Found at i:12852 original size:44 final size:43
Alignment explanation
Indices: 12778--12866 Score: 133
Period size: 44 Copynumber: 2.0 Consensus size: 43
12768 AGCAATAACA
* * * *
12778 TACATAAAACTTAAAACATCCCCTGGCATAAAAGCCTTTACAG
1 TACATAAAACTTAAAACACCCCCTGCCATAAAAACCTTCACAG
12821 TACATAAAACTTAAAAACACCCCCTGCCATAAAAACCTTCACAG
1 TACATAAAACTT-AAAACACCCCCTGCCATAAAAACCTTCACAG
12865 TA
1 TA
12867 GAATAGAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
43 12 0.29
44 29 0.71
ACGTcount: A:0.44, C:0.28, G:0.07, T:0.21
Consensus pattern (43 bp):
TACATAAAACTTAAAACACCCCCTGCCATAAAAACCTTCACAG
Found at i:35077 original size:26 final size:26
Alignment explanation
Indices: 35046--35105 Score: 111
Period size: 26 Copynumber: 2.3 Consensus size: 26
35036 TTTGGTTCTC
35046 TGGAATCCCTTGGAATTAGGGGGAAT
1 TGGAATCCCTTGGAATTAGGGGGAAT
35072 TGGAATCCCTTGGAATTAGGGGGAAT
1 TGGAATCCCTTGGAATTAGGGGGAAT
*
35098 TAGAATCC
1 TGGAATCC
35106 AATTACACCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.28, C:0.13, G:0.32, T:0.27
Consensus pattern (26 bp):
TGGAATCCCTTGGAATTAGGGGGAAT
Found at i:35869 original size:16 final size:17
Alignment explanation
Indices: 35848--35895 Score: 80
Period size: 18 Copynumber: 2.8 Consensus size: 17
35838 GTTTAAGTTT
35848 CAGATTCTAATTCTT-A
1 CAGATTCTAATTCTTCA
35864 CAGATTCTAATTCCTTCA
1 CAGATTCTAATT-CTTCA
35882 CAGATTCTAATTCT
1 CAGATTCTAATTCT
35896 CTCAGAAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
16 12 0.40
17 5 0.17
18 13 0.43
ACGTcount: A:0.29, C:0.23, G:0.06, T:0.42
Consensus pattern (17 bp):
CAGATTCTAATTCTTCA
Found at i:52051 original size:25 final size:25
Alignment explanation
Indices: 52017--52077 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
52007 TGGGATTTGA
52017 AGAAGAAGAAGAAGAAATAACCGGG
1 AGAAGAAGAAGAAGAAATAACCGGG
* * *
52042 AGAAGAAGAAAAAGGAATAACCTGG
1 AGAAGAAGAAGAAGAAATAACCGGG
52067 AGAAGAAGAAG
1 AGAAGAAGAAG
52078 GGATAAAAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.57, C:0.07, G:0.31, T:0.05
Consensus pattern (25 bp):
AGAAGAAGAAGAAGAAATAACCGGG
Found at i:52734 original size:36 final size:36
Alignment explanation
Indices: 52667--52736 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
52657 GATATCTTTA
* * *
52667 AATTATATTATATAATTATTAATGTTTTTAAAAATT
1 AATTATATTATATAATTACTAATATTATTAAAAATT
*
52703 AATTATATTTTATATATTACT-ATATTATTAAAAA
1 AATTATATTATATA-ATTACTAATATTATTAAAAA
52737 AATGTGATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 24 0.83
37 5 0.17
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (36 bp):
AATTATATTATATAATTACTAATATTATTAAAAATT
Found at i:53428 original size:24 final size:24
Alignment explanation
Indices: 53394--53439 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
53384 TTCCAGGAAA
53394 ATGGGGCTGAT-TTCGGGTATTTTG
1 ATGGGGCTGATCTTCGGG-ATTTTG
*
53418 ATGGGGTTGATCTTCGGGATTT
1 ATGGGGCTGATCTTCGGGATTT
53440 CGTTAATGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.13, C:0.09, G:0.37, T:0.41
Consensus pattern (24 bp):
ATGGGGCTGATCTTCGGGATTTTG
Found at i:55162 original size:28 final size:28
Alignment explanation
Indices: 55122--55178 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
55112 CTTATTCAAC
55122 TCTTTTGATGTTTTTTTAATTGAAATAG
1 TCTTTTGATGTTTTTTTAATTGAAATAG
55150 TCTTTTGATGTTTTTTTAATTGAAATAG
1 TCTTTTGATGTTTTTTTAATTGAAATAG
55178 T
1 T
55179 TTTACTTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.25, C:0.04, G:0.14, T:0.58
Consensus pattern (28 bp):
TCTTTTGATGTTTTTTTAATTGAAATAG
Found at i:55188 original size:27 final size:28
Alignment explanation
Indices: 55129--55190 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
55119 AACTCTTTTG
**
55129 ATGTTTTTTTAATTGAAATAGTCTTTTG
1 ATGTTTTTTTAATTGAAATAGTCTTTAC
55157 ATGTTTTTTTAATTGAAATAGT-TTTAC
1 ATGTTTTTTTAATTGAAATAGTCTTTAC
*
55184 TTGTTTT
1 ATGTTTT
55191 ATATGCAACT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
27 9 0.29
28 22 0.71
ACGTcount: A:0.24, C:0.03, G:0.13, T:0.60
Consensus pattern (28 bp):
ATGTTTTTTTAATTGAAATAGTCTTTAC
Found at i:64014 original size:23 final size:22
Alignment explanation
Indices: 63983--64042 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
63973 AAGTGAAAAT
63983 TAAATAAAAACATTACAAACTAAA
1 TAAATAAAAACATTA-AAA-TAAA
* *
64007 T-AATAAAAACAATAAAATAAT
1 TAAATAAAAACATTAAAATAAA
*
64028 TAAATATAAACATTA
1 TAAATAAAAACATTA
64043 GATACAAACG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 4 0.13
22 14 0.45
23 12 0.39
24 1 0.03
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (22 bp):
TAAATAAAAACATTAAAATAAA
Found at i:64176 original size:44 final size:44
Alignment explanation
Indices: 64066--64277 Score: 316
Period size: 44 Copynumber: 4.8 Consensus size: 44
64056 CAATTCAAAC
* *
64066 AATAAAAATATTAAGAAACAAAATAAATAAAAAGTCCATAATTAAA
1 AATAAAAACATTAAGAAACAAAATAAATAAAAAATCCATAATT--A
* *
64112 TAATAAAAACATTAAGAAACAAAATAAATAAAAAATCTATGATTA
1 -AATAAAAACATTAAGAAACAAAATAAATAAAAAATCCATAATTA
** *
64157 AATAAAAACATTAAGAAACAAAATAAATAAAAAATTTATAGTTA
1 AATAAAAACATTAAGAAACAAAATAAATAAAAAATCCATAATTA
* *
64201 AATAAAAAAATTAAGAAACAAAATAAATAAAAAGTCCATAATTA
1 AATAAAAACATTAAGAAACAAAATAAATAAAAAATCCATAATTA
64245 AATAAAAACATTAAGAAACAAAATAAATAAAAA
1 AATAAAAACATTAAGAAACAAAATAAATAAAAA
64278 CAAGTCTATC
Statistics
Matches: 152, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
44 112 0.74
45 1 0.01
47 39 0.26
ACGTcount: A:0.68, C:0.06, G:0.04, T:0.22
Consensus pattern (44 bp):
AATAAAAACATTAAGAAACAAAATAAATAAAAAATCCATAATTA
Found at i:64891 original size:15 final size:15
Alignment explanation
Indices: 64843--64891 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
64833 TAAGAAATTG
64843 TAATTTAAATATTATT
1 TAATTTAAA-ATTATT
*
64859 T--TTT-TAATTATAT
1 TAATTTAAAATTAT-T
64872 TAATTTAAAATTATT
1 TAATTTAAAATTATT
64887 TAATT
1 TAATT
64892 ATTTAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 9
0.71 0.05 0.24
Matches are distributed among these distances:
12 5 0.19
13 3 0.11
14 3 0.11
15 9 0.33
16 7 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TAATTTAAAATTATT
Found at i:69579 original size:14 final size:14
Alignment explanation
Indices: 69560--69587 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
69550 ATTGAATGAA
69560 TATAAATAAAATTT
1 TATAAATAAAATTT
69574 TATAAATAAAATTT
1 TATAAATAAAATTT
69588 CAAACAGGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TATAAATAAAATTT
Found at i:74491 original size:39 final size:38
Alignment explanation
Indices: 74408--74503 Score: 131
Period size: 38 Copynumber: 2.5 Consensus size: 38
74398 TCTAAATCTG
*
74408 GTTTCCATATGAAAAATCATATTGAAACCAAAAATCCC
1 GTTTCTATATGAAAAATCATATTGAAACCAAAAATCCC
* *
74446 GTTTCTATATGAAAAATCATGTTGCAACCTAAAAA-CCC
1 GTTTCTATATGAAAAATCATATTGAAACC-AAAAATCCC
*
74484 GATTTCTATGTGAAAAATCA
1 G-TTTCTATATGAAAAATCA
74504 AGCCTAAAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
38 30 0.58
39 22 0.42
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (38 bp):
GTTTCTATATGAAAAATCATATTGAAACCAAAAATCCC
Found at i:77218 original size:16 final size:14
Alignment explanation
Indices: 77198--77249 Score: 50
Period size: 16 Copynumber: 3.4 Consensus size: 14
77188 TATCTTAAAT
*
77198 TTAAATACAAAAGTA
1 TTAAATACAAAA-AA
77213 TATAAATATTCAAAAAA
1 T-TAAATA--CAAAAAA
77230 TTAAATACAAAAATA
1 TTAAATACAAAAA-A
77245 TTAAA
1 TTAAA
77250 ATAAAATTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
14 6 0.19
15 7 0.22
16 12 0.38
17 2 0.06
18 5 0.16
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (14 bp):
TTAAATACAAAAAA
Found at i:77251 original size:16 final size:16
Alignment explanation
Indices: 77200--77252 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 16
77190 TCTTAAATTT
*
77200 AAATACAAAAGTATATA
1 AAATACAAAAATAT-TA
*
77217 AATATTCAAAAA-ATT-
1 AA-ATACAAAAATATTA
77232 AAATACAAAAATATTA
1 AAATACAAAAATATTA
77248 AAATA
1 AAATA
77253 AAATTAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
14 8 0.27
15 5 0.17
16 6 0.20
17 4 0.13
18 7 0.23
ACGTcount: A:0.66, C:0.06, G:0.02, T:0.26
Consensus pattern (16 bp):
AAATACAAAAATATTA
Found at i:77728 original size:16 final size:18
Alignment explanation
Indices: 77693--77729 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
77683 ATTAATAGTA
*
77693 TTTTTAATATATATACTT
1 TTTTTAATATATATAATT
77711 TTTTTAATA-AT-TAATT
1 TTTTTAATATATATAATT
77727 TTT
1 TTT
77730 ATTTTTTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 2 0.11
18 9 0.50
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTTAATATATATAATT
Done.