Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003886.1 Hibiscus syriacus cultivar Beakdansim tig00008388_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: 106545
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:23448 original size:29 final size:29
Alignment explanation
Indices: 23398--23489 Score: 150
Period size: 29 Copynumber: 3.2 Consensus size: 29
23388 TAAAGAAGTA
* *
23398 AATTTATAA-TTATTAGACAAGACGAATT
1 AATTAATAATTTATTAGAGAAGACGAATT
23426 AATTAATAATTTATTAGAGAAGACGAATT
1 AATTAATAATTTATTAGAGAAGACGAATT
*
23455 AATTAATAATTTATTAGAGAAGACAAATT
1 AATTAATAATTTATTAGAGAAGACGAATT
23484 AATTAA
1 AATTAA
23490 ATTTTATGGG
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
28 8 0.13
29 52 0.87
ACGTcount: A:0.50, C:0.04, G:0.11, T:0.35
Consensus pattern (29 bp):
AATTAATAATTTATTAGAGAAGACGAATT
Found at i:25222 original size:21 final size:21
Alignment explanation
Indices: 25196--25251 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
25186 ATCAATATAT
25196 AGGGTTATGATTTAGAGTTTA
1 AGGGTTATGATTTAGAGTTTA
25217 AGGGTTATGATTTAGAGTTTA
1 AGGGTTATGATTTAGAGTTTA
*
25238 AGGATTATGATTTA
1 AGGGTTATGATTTA
25252 TAGATAGAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.30, C:0.00, G:0.27, T:0.43
Consensus pattern (21 bp):
AGGGTTATGATTTAGAGTTTA
Found at i:25948 original size:44 final size:43
Alignment explanation
Indices: 25900--25983 Score: 105
Period size: 44 Copynumber: 1.9 Consensus size: 43
25890 TTGTGCCAAA
* * *
25900 AAACGCCGCTATATAGCATGACCTTTAGCGGCGTTTTATTATAC
1 AAACGCCGCTACATAACATGACCTTTAGCAGCG-TTTATTATAC
* * *
25944 AAACGCCGTTACATAACCTGACTTTTAGCAGCGTTTATTA
1 AAACGCCGCTACATAACATGACCTTTAGCAGCGTTTATTA
25984 GTGAAAAACG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
43 7 0.21
44 27 0.79
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.32
Consensus pattern (43 bp):
AAACGCCGCTACATAACATGACCTTTAGCAGCGTTTATTATAC
Found at i:35841 original size:3 final size:3
Alignment explanation
Indices: 35833--35864 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
35823 GGATACTATC
35833 ATT ATT ATT ATT ATT A-T ATT ATT -TT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
35865 ATAATAATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.15
3 23 0.85
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:44618 original size:7 final size:7
Alignment explanation
Indices: 44606--44663 Score: 55
Period size: 7 Copynumber: 7.7 Consensus size: 7
44596 TAAAGATAAA
44606 AAAAATG
1 AAAAATG
44613 AAAAATG
1 AAAAATG
44620 AAAAAAATGG
1 --AAAAAT-G
44630 AAAAAATG
1 -AAAAATG
44638 AAAAATG
1 AAAAATG
*
44645 AAATA-G
1 AAAAATG
44651 AAAAATAG
1 AAAAAT-G
44659 AAAAA
1 AAAAA
44664 ATGGAAAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
6 5 0.11
7 18 0.41
8 7 0.16
9 13 0.30
10 1 0.02
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.12
Consensus pattern (7 bp):
AAAAATG
Found at i:44624 original size:8 final size:8
Alignment explanation
Indices: 44605--44680 Score: 65
Period size: 9 Copynumber: 9.8 Consensus size: 8
44595 TTAAAGATAA
44605 AAAAAATG
1 AAAAAATG
44613 -AAAAATG
1 AAAAAATG
44620 AAAAAAATGG
1 -AAAAAAT-G
44630 AAAAAATG
1 AAAAAATG
44638 -AAAAATG
1 AAAAAATG
*
44645 -AAATA-G
1 AAAAAATG
44651 -AAAAATAG
1 AAAAAAT-G
44659 AAAAAATGG
1 AAAAAAT-G
44668 AAAAAAT-
1 AAAAAATG
44675 AAAAAA
1 AAAAAA
44681 AAAGAAGAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
6 5 0.08
7 24 0.41
8 2 0.03
9 27 0.46
10 1 0.02
ACGTcount: A:0.75, C:0.00, G:0.13, T:0.12
Consensus pattern (8 bp):
AAAAAATG
Found at i:44654 original size:38 final size:37
Alignment explanation
Indices: 44608--44680 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 37
44598 AAGATAAAAA
*
44608 AAATGAAAAAT-GAAAAAAATGGAAAAAATGAAAAATG
1 AAATGAAAAATAG-AAAAAATGGAAAAAATAAAAAATG
44645 AAATAGAAAAATAGAAAAAATGGAAAAAATAAAAAA
1 AAAT-GAAAAATAGAAAAAATGGAAAAAATAAAAAA
44681 AAAGAAGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
37 4 0.12
38 28 0.85
39 1 0.03
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.12
Consensus pattern (37 bp):
AAATGAAAAATAGAAAAAATGGAAAAAATAAAAAATG
Found at i:44681 original size:8 final size:9
Alignment explanation
Indices: 44604--44692 Score: 60
Period size: 9 Copynumber: 9.8 Consensus size: 9
44594 CTTAAAGATA
44604 AAAAAAATG
1 AAAAAAATG
44613 --AAAAATG
1 AAAAAAATG
44620 AAAAAAATG
1 AAAAAAATG
*
44629 GAAAAAATG
1 AAAAAAATG
44638 AAAAATGAAAT-
1 -AAAA--AAATG
*
44649 AGAAAAAT-
1 AAAAAAATG
44657 AGAAAAAATG
1 A-AAAAAATG
* *
44667 GAAAAAATA
1 AAAAAAATG
*
44676 AAAAAAAAG
1 AAAAAAATG
44685 AAGAAAAA
1 AA-AAAAA
44693 AAAAGAAGAA
Statistics
Matches: 63, Mismatches: 9, Indels: 15
0.72 0.10 0.17
Matches are distributed among these distances:
7 7 0.11
8 5 0.08
9 36 0.57
10 11 0.17
12 4 0.06
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.10
Consensus pattern (9 bp):
AAAAAAATG
Found at i:44683 original size:29 final size:29
Alignment explanation
Indices: 44606--44693 Score: 83
Period size: 29 Copynumber: 2.9 Consensus size: 29
44596 TAAAGATAAA
*
44606 AAAAATGAAAAATGAAAAAAATGGAAAAAATG
1 AAAAATG--AAAT-AAAAAAATAGAAAAAATG
*
44638 AAAAATGAAATAGAAAAATAGAAAAAATGG
1 AAAAATGAAATAAAAAAATAGAAAAAAT-G
44668 AAAAAAT-AAA-AAAAAAGA-AGAAAAAA
1 -AAAAATGAAATAAAAAA-ATAGAAAAAA
44694 AAAGAAGAAG
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
29 28 0.56
30 9 0.18
31 6 0.12
32 7 0.14
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (29 bp):
AAAAATGAAATAAAAAAATAGAAAAAATG
Found at i:44693 original size:13 final size:13
Alignment explanation
Indices: 44675--44709 Score: 61
Period size: 13 Copynumber: 2.6 Consensus size: 13
44665 TGGAAAAAAT
44675 AAAAAAAAAGAAG
1 AAAAAAAAAGAAG
44688 AAAAAAAAAGAAG
1 AAAAAAAAAGAAG
44701 AAGAAAAAA
1 AA-AAAAAA
44710 CCAAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 15 0.71
14 6 0.29
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAGAAG
Found at i:44693 original size:38 final size:38
Alignment explanation
Indices: 44605--44692 Score: 110
Period size: 38 Copynumber: 2.3 Consensus size: 38
44595 TTAAAGATAA
44605 AAAAAATGAAAAATGAAAAAAATGGAAAAAATGAAAAAT
1 AAAAAA-GAAAAATGAAAAAAATGGAAAAAATGAAAAAT
* *
44644 GAAATAGAAAAAT-AGAAAAAATGGAAAAAAT-AAAAA-
1 AAAAAAGAAAAATGA-AAAAAATGGAAAAAATGAAAAAT
44680 AAAAGAAGAAAAA
1 AAAA-AAGAAAAA
44693 AAAAGAAGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
36 3 0.07
37 13 0.30
38 23 0.53
39 4 0.09
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (38 bp):
AAAAAAGAAAAATGAAAAAAATGGAAAAAATGAAAAAT
Found at i:44694 original size:16 final size:16
Alignment explanation
Indices: 44675--44709 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
44665 TGGAAAAAAT
44675 AAAAAAAAAGAAGAAA
1 AAAAAAAAAGAAGAAA
*
44691 AAAAAAGAAGAAGAAA
1 AAAAAAAAAGAAGAAA
44707 AAA
1 AAA
44710 CCAAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAGAAGAAA
Found at i:46088 original size:55 final size:55
Alignment explanation
Indices: 46004--46232 Score: 363
Period size: 55 Copynumber: 4.2 Consensus size: 55
45994 TGAAACAAAA
*
46004 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* * *
46059 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAAGGGGCAGACGCGATTGAT
1 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* *
46114 GAAGATT-GTGGA-TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* *
46167 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTAG
1 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGT-T
46223 GAAGATTATT
1 GAAGATTATT
46233 TTTCGAGTTC
Statistics
Matches: 158, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
53 45 0.28
54 6 0.04
55 98 0.62
56 9 0.06
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.27
Consensus pattern (55 bp):
GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
Found at i:46208 original size:108 final size:110
Alignment explanation
Indices: 46004--46217 Score: 387
Period size: 108 Copynumber: 2.0 Consensus size: 110
45994 TGAAACAAAA
46004 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
46069 CGAGTCTTATACTCTCTGAAGAAATAAGGGGCAGACGCGATTGAT
66 CGAGTCTTATACTCTCTGAAGAAATAAGGGGCAGACGCGATTGAT
* *
46114 GAAGATTG-TGGA-TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
*
46177 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGAT
66 CGAGTCTTATACTCTCTGAAGAAATAAGGGGCAGACGCGAT
46218 CGTAGGAAGA
Statistics
Matches: 101, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
108 90 0.89
109 3 0.03
110 8 0.08
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (110 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
CGAGTCTTATACTCTCTGAAGAAATAAGGGGCAGACGCGATTGAT
Found at i:46284 original size:52 final size:52
Alignment explanation
Indices: 46218--46569 Score: 596
Period size: 52 Copynumber: 6.8 Consensus size: 52
46208 CAGACGCGAT
*
46218 CGTAGGAAGATTATTTTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACC
1 CGTAGGAAGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACC
* *
46270 CGTAGGAAGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCT
1 CGTAGGAAGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACC
46322 CGTAGGAAGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACC
1 CGTAGGAAGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACC
* * * *
46374 CGTAGGAAGATTATTTTTCGAGTTCTAGTCCCTGAAGAAAATTGGACAGTCT
1 CGTAGGAAGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACC
*
46426 CGTAGGAAGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGACAGACC
1 CGTAGGAAGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACC
* *
46478 CGTAGGAAGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCT
1 CGTAGGAAGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACC
* *
46530 CGTAGGAAGATTATCGTTCGAGTTCTACTCCCTGAAGAAA
1 CGTAGGAAGATTATTGTTCGAGTTCTAGTCCCTGAAGAAA
46570 TAGAGAGCGA
Statistics
Matches: 283, Mismatches: 17, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 283 1.00
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (52 bp):
CGTAGGAAGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACC
Found at i:46652 original size:55 final size:53
Alignment explanation
Indices: 46438--46640 Score: 166
Period size: 52 Copynumber: 3.8 Consensus size: 53
46428 TAGGAAGATT
* * ** **
46438 ATTGTTCGAGTTCTAGTCCCTGAAGAAAATTG-GA-C-AGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAAA-AGAGAGCGA-ACCCGTAAAAAGAAG
* * * * ** **
46490 ATTGTTCGAGTTCTAGTCCCTGAAGAAAATTG-G-GC-AGTCTCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAAA-AGAGAGCGA-ACCCGTAAAAAGAAG
* *
46542 ATCGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGAACCCGTAAAAAGAAG
1 ATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGAACCCGTAAAAAGAAG
46595 ATTGTTCGAGTTCTATACTCCCTGAAGAAAAAGAGAGCGAACCCGT
1 ATTGTTCGAGTTC--TACTCCCTGAAGAAAAAGAGAGCGAACCCGT
46641 TTGCAGAAGA
Statistics
Matches: 131, Mismatches: 14, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
51 1 0.01
52 76 0.58
53 23 0.18
54 1 0.01
55 30 0.23
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (53 bp):
ATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGAACCCGTAAAAAGAAG
Found at i:47229 original size:148 final size:148
Alignment explanation
Indices: 46961--47231 Score: 395
Period size: 148 Copynumber: 1.8 Consensus size: 148
46951 CATGGAGATT
* * * * * *
46961 GCCAATTTTGAACATGTTCTAAGCATCTTCGGTTTCTGAAGTCTTCGTAACAGTTATTCAATTAT
1 GCCAATTTTGAACATGTTCCAAACATATTCGGTGTCTGAAGTCTTAGTAACAATTATTCAATTAT
* *
47026 CTCTTAGCTTTCCAACGTACTTTGAACCGCATCAATCCGATATTTGGAGCTCGAGATATGGTTAA
66 CTCTTAGCTTTCCAACGCACTTTGAACCGCATCAATCCGATATTCGGAGCTCGAGATATGGTTAA
47091 ATTAATGAAGAATGTATC
131 ATTAATGAAGAATGTATC
* *
47109 GCCAATTTTGAACATGTTCCAAACATATTTGGATGT-TGAAGTCTTATTAACAATTATT-ACATT
1 GCCAATTTTGAACATGTTCCAAACATATTCGG-TGTCTGAAGTCTTAGTAACAATTATTCA-ATT
*
47172 ATCTCTTAGCTTTCCAACGCACTTTGAATCGCATCAATCCGATA-TCGGTAGCTCGAGATA
64 ATCTCTTAGCTTTCCAACGCACTTTGAACCGCATCAATCCGATATTCGG-AGCTCGAGATA
47232 CGCTCAGATA
Statistics
Matches: 109, Mismatches: 11, Indels: 6
0.87 0.09 0.05
Matches are distributed among these distances:
147 4 0.04
148 103 0.94
149 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (148 bp):
GCCAATTTTGAACATGTTCCAAACATATTCGGTGTCTGAAGTCTTAGTAACAATTATTCAATTAT
CTCTTAGCTTTCCAACGCACTTTGAACCGCATCAATCCGATATTCGGAGCTCGAGATATGGTTAA
ATTAATGAAGAATGTATC
Found at i:56875 original size:3 final size:3
Alignment explanation
Indices: 56867--56899 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
56857 GGATACTATC
*
56867 ATT ATT ATT ATT ATT A-T ATT ATT TTT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
56900 ATAATAATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:56889 original size:17 final size:17
Alignment explanation
Indices: 56867--56899 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
56857 GGATACTATC
56867 ATTATTATTATTATTAT
1 ATTATTATTATTATTAT
*
56884 ATTATTTTTATTATTA
1 ATTATTATTATTATTA
56900 ATAATAATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTATTATTATTATTAT
Found at i:60540 original size:3 final size:3
Alignment explanation
Indices: 60532--60563 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
60522 GGATACTATC
60532 ATT ATT ATT ATT ATT A-T ATT ATT -TT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
60564 ATAATAATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.15
3 23 0.85
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:66790 original size:26 final size:26
Alignment explanation
Indices: 66746--66798 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
66736 ATCTTTCCTG
*
66746 ATTTTGACACTTTAATTTCTGTTATTT
1 ATTTTAACACTTTAATTTCTGTT-TTT
*
66773 ATTTTAAC-CTTTTATTTCTGTTTTT
1 ATTTTAACACTTTAATTTCTGTTTTT
66798 A
1 A
66799 CCATTTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 13 0.54
27 7 0.29
ACGTcount: A:0.21, C:0.11, G:0.06, T:0.62
Consensus pattern (26 bp):
ATTTTAACACTTTAATTTCTGTTTTT
Found at i:69198 original size:88 final size:88
Alignment explanation
Indices: 69044--69217 Score: 330
Period size: 88 Copynumber: 2.0 Consensus size: 88
69034 TTAGAAATAT
*
69044 ACCAAGTGAAGCAATTAGTTAAGTTTCACATGGTTCTGCTTTGTCTGGTGCTACGCATTTTGCCC
1 ACCAAGTGAAGCAATTAGTTAAGTTTCACATGGTTCTGCTTTGTCTGGTGCTACGCATTATGCCC
69109 TACCACCTTAAAAGAAAATGGTA
66 TACCACCTTAAAAGAAAATGGTA
*
69132 ACCAGGTGAAGCAATTAGTTAAGTTTCACATGGTTCTGCTTTGTCTGGTGCTACGCATTATGCCC
1 ACCAAGTGAAGCAATTAGTTAAGTTTCACATGGTTCTGCTTTGTCTGGTGCTACGCATTATGCCC
69197 TACCACCTTAAAAGAAAATGG
66 TACCACCTTAAAAGAAAATGG
69218 CAACTTGTGA
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 84 1.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (88 bp):
ACCAAGTGAAGCAATTAGTTAAGTTTCACATGGTTCTGCTTTGTCTGGTGCTACGCATTATGCCC
TACCACCTTAAAAGAAAATGGTA
Found at i:71725 original size:12 final size:12
Alignment explanation
Indices: 71710--71741 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
71700 ATGTTTTCTT
71710 TGATTTCTATTA
1 TGATTTCTATTA
*
71722 TGATCTCTATTA
1 TGATTTCTATTA
71734 TGATTTCT
1 TGATTTCT
71742 GATCTCTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.22, C:0.12, G:0.09, T:0.56
Consensus pattern (12 bp):
TGATTTCTATTA
Found at i:71754 original size:31 final size:31
Alignment explanation
Indices: 71710--71775 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
71700 ATGTTTTCTT
* *
71710 TGATTTCTATTATGATCTCTATTATGATTTC
1 TGATCTCTATTATGATCTCTATTATGATTTA
* * * *
71741 TGATCTCTGTTATGATTTCTGTTCTGATTTA
1 TGATCTCTATTATGATCTCTATTATGATTTA
71772 TGAT
1 TGAT
71776 ATCTCTGATT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.20, C:0.12, G:0.14, T:0.55
Consensus pattern (31 bp):
TGATCTCTATTATGATCTCTATTATGATTTA
Found at i:71775 original size:19 final size:19
Alignment explanation
Indices: 71722--71761 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
71712 ATTTCTATTA
*
71722 TGATCTCTATTATGATTTC
1 TGATCTCTGTTATGATTTC
71741 TGATCTCTGTTATGATTTC
1 TGATCTCTGTTATGATTTC
71760 TG
1 TG
71762 TTCTGATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.17, C:0.15, G:0.15, T:0.53
Consensus pattern (19 bp):
TGATCTCTGTTATGATTTC
Found at i:80743 original size:36 final size:36
Alignment explanation
Indices: 80696--80768 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
80686 AAGAGAACCA
*
80696 AAGCTAAAACATTGACGAGCCATCATTCGAACTTCT
1 AAGCTAAAACATTGACGAGCCATCATTCAAACTTCT
80732 AAGCTAAAACATTGACGAGCCATCATTCAAACTTCT
1 AAGCTAAAACATTGACGAGCCATCATTCAAACTTCT
80768 A
1 A
80769 CCGTAGACAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (36 bp):
AAGCTAAAACATTGACGAGCCATCATTCAAACTTCT
Found at i:84581 original size:52 final size:52
Alignment explanation
Indices: 84503--84611 Score: 218
Period size: 52 Copynumber: 2.1 Consensus size: 52
84493 TAGATACATA
84503 TTACAGTGTATCAGAATATTTACCATCATTAGTTTATATAGTAGTATTATTT
1 TTACAGTGTATCAGAATATTTACCATCATTAGTTTATATAGTAGTATTATTT
84555 TTACAGTGTATCAGAATATTTACCATCATTAGTTTATATAGTAGTATTATTT
1 TTACAGTGTATCAGAATATTTACCATCATTAGTTTATATAGTAGTATTATTT
84607 TTACA
1 TTACA
84612 TAAAAATAAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 57 1.00
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (52 bp):
TTACAGTGTATCAGAATATTTACCATCATTAGTTTATATAGTAGTATTATTT
Found at i:85548 original size:2 final size:2
Alignment explanation
Indices: 85541--85568 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
85531 TTATCGACTA
85541 AT 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 AT
85569 GTGTGTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:86576 original size:16 final size:15
Alignment explanation
Indices: 86553--86597 Score: 58
Period size: 13 Copynumber: 3.1 Consensus size: 15
86543 ATATAAAATA
86553 TATTTTTATTATAAT
1 TATTTTTATTATAAT
*
86568 TATTTTTTATT-TTA-
1 TA-TTTTTATTATAAT
86582 TATTTTTATTATAAT
1 TATTTTTATTATAAT
86597 T
1 T
86598 TAAATTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 8 0.32
14 4 0.16
15 5 0.20
16 8 0.32
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TATTTTTATTATAAT
Found at i:86605 original size:29 final size:29
Alignment explanation
Indices: 86551--86606 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
86541 TTATATAAAA
**
86551 TATATTTTTATTATAATTATTTTTTATTT
1 TATATTTTTATTATAATTATAATTTATTT
86580 TATATTTTTATTATAATT-TAAATTTAT
1 TATATTTTTATTATAATTAT-AATTTAT
86607 ATAACTCGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 1 0.04
29 23 0.96
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (29 bp):
TATATTTTTATTATAATTATAATTTATTT
Found at i:88588 original size:27 final size:27
Alignment explanation
Indices: 88553--88634 Score: 73
Period size: 28 Copynumber: 3.0 Consensus size: 27
88543 AAAATTTGTG
*
88553 AATTAATAAATTTATATTTTTTAAAAAT
1 AATT-ATAAATTTATATATTTTAAAAAT
* *
88581 AATTAT-AATTT-TACGA-ATTAAAAGATT
1 AATTATAAATTTATA-TATTTTAAAA-A-T
88608 AATTATAAATTTAT-TATTTTAAAAAT
1 AATTATAAATTTATATATTTTAAAAAT
88634 A
1 A
88635 CTTTGATAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
25 8 0.19
26 8 0.19
27 11 0.26
28 15 0.35
29 1 0.02
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.46
Consensus pattern (27 bp):
AATTATAAATTTATATATTTTAAAAAT
Found at i:93383 original size:23 final size:23
Alignment explanation
Indices: 93334--93386 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
93324 ATTGCATCGA
* *
93334 AGTGCCACGTAGAATTATACCGG
1 AGTGCCACGTAGAATTACACAGG
* * *
93357 AGTGCCGCGTAGAATTGCACAGT
1 AGTGCCACGTAGAATTACACAGG
93380 AGTGCCA
1 AGTGCCA
93387 TATAATAATG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (23 bp):
AGTGCCACGTAGAATTACACAGG
Found at i:105017 original size:31 final size:31
Alignment explanation
Indices: 104976--105035 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
104966 TAAACTTTAT
* * *
104976 GCATTGGGGGATAGTTTCAGTTATGCATCCA
1 GCATTAGGGGATAGTATCAATTATGCATCCA
105007 GCATTAGGGGATAGTATCAATTATGCATC
1 GCATTAGGGGATAGTATCAATTATGCATC
105036 TAGAACTGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.32
Consensus pattern (31 bp):
GCATTAGGGGATAGTATCAATTATGCATCCA
Found at i:106369 original size:28 final size:28
Alignment explanation
Indices: 106337--106396 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
106327 TAGTTTACTG
*
106337 TTTCTAAAAATCCTCCGATTTATATCCA
1 TTTCTAAAAATCCTCCGATTTATACCCA
*
106365 TTTCTGAAAATCCTCCGATTTATACCCA
1 TTTCTAAAAATCCTCCGATTTATACCCA
106393 TTTC
1 TTTC
106397 ATTGCTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.28, C:0.27, G:0.05, T:0.40
Consensus pattern (28 bp):
TTTCTAAAAATCCTCCGATTTATACCCA
Done.