Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000316.1 Hibiscus syriacus cultivar Beakdansim tig00000595_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: 144220
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2071 original size:124 final size:126
Alignment explanation
Indices: 1851--2106 Score: 453
Period size: 124 Copynumber: 2.0 Consensus size: 126
1841 AAAAATTCAA
1851 TTTTTTTCCTAAATAATGGGGATGCACTTAACCCCTAGGGGCTTAGTGCATCTGCCTCTGCCTGT
1 TTTTTTTCCTAAATAATGGGGATGCACTTAACCCCTAGGGGCTTAG-G---CTGCCTCTGCCTGT
*
1916 ATCATGCTATTATTTTAAATATATAAAACTTATTATATCAATAATAAATATTAACTATTAATTAG
62 ATCATGCTATTATTTTAAATATATAAAACTTATCATATCAATAATAAATATTAACTATTAATTAG
1981 TTTTTTTCCTAAATAATGGGGATGCACTTAACCCCTAGGGGCTTA-G-TGCCTCTGCCTGTATCA
1 TTTTTTTCCTAAATAATGGGGATGCACTTAACCCCTAGGGGCTTAGGCTGCCTCTGCCTGTATCA
2044 TGCTATTATTTTAAATATATAAAACTTATCATATCAATAATAAATATTAACTATTAATTAG
66 TGCTATTATTTTAAATATATAAAACTTATCATATCAATAATAAATATTAACTATTAATTAG
2105 TT
1 TT
2107 AATAATTTTC
Statistics
Matches: 125, Mismatches: 1, Indels: 6
0.95 0.01 0.05
Matches are distributed among these distances:
124 79 0.63
128 1 0.01
130 45 0.36
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.39
Consensus pattern (126 bp):
TTTTTTTCCTAAATAATGGGGATGCACTTAACCCCTAGGGGCTTAGGCTGCCTCTGCCTGTATCA
TGCTATTATTTTAAATATATAAAACTTATCATATCAATAATAAATATTAACTATTAATTAG
Found at i:6599 original size:21 final size:21
Alignment explanation
Indices: 6575--6617 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
6565 TTAACTTTTG
6575 TTTTAATT-TTATATAATTTAA
1 TTTTAATTCTTA-ATAATTTAA
*
6596 TTTTAATTCTTAATATTTTAA
1 TTTTAATTCTTAATAATTTAA
6617 T
1 T
6618 ATTACATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTAATTCTTAATAATTTAA
Found at i:7154 original size:35 final size:35
Alignment explanation
Indices: 7099--7171 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
7089 CATAGGATGC
* *
7099 AACCTTACTAGCATATACCATATTCTACAAACCAG
1 AACCTTACTAGCATAAACCATATTCCACAAACCAG
* *
7134 AACCTTGCTAGTATAAACCATATTCCACAAACCAG
1 AACCTTACTAGCATAAACCATATTCCACAAACCAG
7169 AAC
1 AAC
7172 GGAGGTCGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.41, C:0.29, G:0.07, T:0.23
Consensus pattern (35 bp):
AACCTTACTAGCATAAACCATATTCCACAAACCAG
Found at i:7277 original size:12 final size:12
Alignment explanation
Indices: 7260--7287 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
7250 GTTGACCAAT
7260 TTCACAAATATG
1 TTCACAAATATG
7272 TTCACAAATATG
1 TTCACAAATATG
7284 TTCA
1 TTCA
7288 ATTGTTATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (12 bp):
TTCACAAATATG
Found at i:14302 original size:26 final size:26
Alignment explanation
Indices: 14273--14322 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
14263 ATGGGTTAAT
14273 AGACGTGTGTTAGAATTGAAGATGCA
1 AGACGTGTGTTAGAATTGAAGATGCA
*
14299 AGACTTGTGTTAGAATTGAAGATG
1 AGACGTGTGTTAGAATTGAAGATG
14323 TAATGTATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.34, C:0.06, G:0.30, T:0.30
Consensus pattern (26 bp):
AGACGTGTGTTAGAATTGAAGATGCA
Found at i:15709 original size:26 final size:26
Alignment explanation
Indices: 15676--15745 Score: 95
Period size: 26 Copynumber: 2.7 Consensus size: 26
15666 GCCAACAACT
15676 GTATGCATGAACAATATGCAATAACA
1 GTATGCATGAACAATATGCAATAACA
* * * *
15702 TTATGCATTAGCAATATGTAATAACA
1 GTATGCATGAACAATATGCAATAACA
*
15728 GTATGCATGAAGAATATG
1 GTATGCATGAACAATATG
15746 TATTACCAAG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.29
Consensus pattern (26 bp):
GTATGCATGAACAATATGCAATAACA
Found at i:17686 original size:45 final size:45
Alignment explanation
Indices: 17622--17738 Score: 180
Period size: 45 Copynumber: 2.6 Consensus size: 45
17612 CTATCCTAAC
* *
17622 CTCAGCAGGTTCTGGTTCATCAATTTCAGGTTCATTAATTTCTGG
1 CTCAGCAGGTTCTGGTTCATTAATTTCAGGTTCATTAATTTCTAG
*
17667 CTCAGCAGGTTCTGGTTCATTAATTCCAGGTTCATTAATTTCTAG
1 CTCAGCAGGTTCTGGTTCATTAATTTCAGGTTCATTAATTTCTAG
* **
17712 CTCAACTTGTTCTGGTTCATTAATTTC
1 CTCAGCAGGTTCTGGTTCATTAATTTC
17739 TGGCTTAGCT
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 65 1.00
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.42
Consensus pattern (45 bp):
CTCAGCAGGTTCTGGTTCATTAATTTCAGGTTCATTAATTTCTAG
Found at i:17739 original size:15 final size:15
Alignment explanation
Indices: 17631--17778 Score: 87
Period size: 15 Copynumber: 10.3 Consensus size: 15
17621 CCTCAGCAGG
*
17631 TTCTGGTTCATCAAT
1 TTCTGGTTCATTAAT
*
17646 TTCAGGTTCATTAAT
1 TTCTGGTTCATTAAT
* ** **
17661 TTCTGGCTCAGCAGG
1 TTCTGGTTCATTAAT
17676 TTCTGGTTCATTAAT
1 TTCTGGTTCATTAAT
* *
17691 TCCAGGTTCATTAAT
1 TTCTGGTTCATTAAT
* * *
17706 TTCTAGCTCAACTT--G
1 TTCTGGTTC-A-TTAAT
17721 TTCTGGTTCATTAAT
1 TTCTGGTTCATTAAT
17736 TTCTGG--C-TT-A-
1 TTCTGGTTCATTAAT
*
17746 -GCTGGTTCATTAAT
1 TTCTGGTTCATTAAT
* *
17760 TTCGGGTTCAGTAAT
1 TTCTGGTTCATTAAT
17775 TTCT
1 TTCT
17779 TGTTGAACTG
Statistics
Matches: 95, Mismatches: 28, Indels: 20
0.66 0.20 0.14
Matches are distributed among these distances:
9 4 0.04
11 2 0.02
12 4 0.04
13 4 0.04
14 1 0.01
15 77 0.81
16 1 0.01
17 2 0.02
ACGTcount: A:0.20, C:0.18, G:0.18, T:0.45
Consensus pattern (15 bp):
TTCTGGTTCATTAAT
Found at i:17775 original size:69 final size:69
Alignment explanation
Indices: 17678--17807 Score: 179
Period size: 69 Copynumber: 1.9 Consensus size: 69
17668 TCAGCAGGTT
* * * *
17678 CTGGTTCATTAATTCCAGGTTCATTAATTTCTAGCTCAACTTGTTCTGGTTCATTAATTTCTGGC
1 CTGGTTCATTAATTCCAGGTTCAGTAATTTCTAGCTCAACTGGTTCTGCTTCATCAATTTCTGGC
17743 TTAG
66 TTAG
* * * * *
17747 CTGGTTCATTAATTTCGGGTTCAGTAATTTCTTGTTGAACTGGTTCTGCTTCATCAATTTC
1 CTGGTTCATTAATTCCAGGTTCAGTAATTTCTAGCTCAACTGGTTCTGCTTCATCAATTTC
17808 AGGTTCATTA
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
69 52 1.00
ACGTcount: A:0.19, C:0.18, G:0.17, T:0.45
Consensus pattern (69 bp):
CTGGTTCATTAATTCCAGGTTCAGTAATTTCTAGCTCAACTGGTTCTGCTTCATCAATTTCTGGC
TTAG
Found at i:19035 original size:24 final size:24
Alignment explanation
Indices: 19000--19066 Score: 98
Period size: 24 Copynumber: 2.8 Consensus size: 24
18990 ACGGGGAGGT
*
19000 TGAAGGCGAATGAATTTTCTGCGA
1 TGAAGGCGAATGAGTTTTCTGCGA
* * *
19024 TGAAGGCTAATGGGTTTTCTTCGA
1 TGAAGGCGAATGAGTTTTCTGCGA
19048 TGAAGGCGAATGAGTTTTC
1 TGAAGGCGAATGAGTTTTC
19067 AGACGAAATC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.25, C:0.12, G:0.30, T:0.33
Consensus pattern (24 bp):
TGAAGGCGAATGAGTTTTCTGCGA
Found at i:19153 original size:88 final size:88
Alignment explanation
Indices: 19024--19341 Score: 440
Period size: 88 Copynumber: 3.5 Consensus size: 88
19014 TTTTCTGCGA
* * * *
19024 TGAAGGCTAATGGGTTTTCTTCGATGAAGGCGAATGAGTTTTCAGACGAAATCTCTCTAAAGTGC
1 TGAAGGCGAATGAGTTTTCTGCGATGAAGGCGAATGGGTTTTCAGACGAAATCTCTCTAAAGTGC
*
19089 GAAGGATTTTTAGACGAGGAGGT
66 GAAGGATTTTCAGACGAGGAGGT
*
19112 TGAAGGCGAATGAGTTTTCTGTGATGAAGGCGAATGGGTTTTCAGACGAAATCTCTCTAAAGTGC
1 TGAAGGCGAATGAGTTTTCTGCGATGAAGGCGAATGGGTTTTCAGACGAAATCTCTCTAAAGTGC
*
19177 GAAGGATTTTCAAACGAGGAGGT
66 GAAGGATTTTCAGACGAGGAGGT
19200 TGAAGGCGAACTGA-TTTTCTGCGATGAAGGCGAATGGGTTTTCAGACGAAATCTCTCGAAATCT
1 TGAAGGCGAA-TGAGTTTTCTGCGATGAAGGCGAATGGGTTTTC--A-G--A-----CGAAATCT
19264 CTCTAAAGTGCGAAGGATTTTCAGACGAGGAGGT
55 CTCTAAAGTGCGAAGGATTTTCAGACGAGGAGGT
* * *
19298 TGAAGGCGAATGGGTTTTATGCGATGAAGGCGAATGTGTTTTCA
1 TGAAGGCGAATGAGTTTTCTGCGATGAAGGCGAATGGGTTTTCA
19342 CTCTTTCAAC
Statistics
Matches: 206, Mismatches: 12, Indels: 16
0.88 0.05 0.07
Matches are distributed among these distances:
88 119 0.58
89 3 0.01
90 1 0.00
91 1 0.00
93 1 0.00
96 1 0.00
97 2 0.01
98 78 0.38
ACGTcount: A:0.28, C:0.13, G:0.30, T:0.28
Consensus pattern (88 bp):
TGAAGGCGAATGAGTTTTCTGCGATGAAGGCGAATGGGTTTTCAGACGAAATCTCTCTAAAGTGC
GAAGGATTTTCAGACGAGGAGGT
Found at i:19327 original size:98 final size:98
Alignment explanation
Indices: 19158--19341 Score: 316
Period size: 98 Copynumber: 1.9 Consensus size: 98
19148 GGTTTTCAGA
*
19158 CGAAATCTCTCTAAAGTGCGAAGGATTTTCAAACGAGGAGGTTGAAGGCGAACTGATTTTCTGCG
1 CGAAATCTCTCTAAAGTGCGAAGGATTTTCAAACGAGGAGGTTGAAGGCGAACTGATTTTATGCG
19223 ATGAAGGCGAATGGGTTTTCAGACGAAATCTCT
66 ATGAAGGCGAATGGGTTTTCAGACGAAATCTCT
* *
19256 CGAAATCTCTCTAAAGTGCGAAGGATTTTCAGACGAGGAGGTTGAAGGCGAA-TGGGTTTTATGC
1 CGAAATCTCTCTAAAGTGCGAAGGATTTTCAAACGAGGAGGTTGAAGGCGAACT-GATTTTATGC
*
19320 GATGAAGGCGAATGTGTTTTCA
65 GATGAAGGCGAATGGGTTTTCA
19342 CTCTTTCAAC
Statistics
Matches: 81, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
97 1 0.01
98 80 0.99
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (98 bp):
CGAAATCTCTCTAAAGTGCGAAGGATTTTCAAACGAGGAGGTTGAAGGCGAACTGATTTTATGCG
ATGAAGGCGAATGGGTTTTCAGACGAAATCTCT
Found at i:25610 original size:3 final size:3
Alignment explanation
Indices: 25602--25626 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
25592 AATATGATAC
25602 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
25627 CAAAATCATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:26241 original size:5 final size:5
Alignment explanation
Indices: 26231--26261 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
26221 TTAAAAAACT
*
26231 CGACC CGACC CGACC CGACC CGACC CAACC C
1 CGACC CGACC CGACC CGACC CGACC CGACC C
26262 CAAAATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.23, C:0.61, G:0.16, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:26844 original size:15 final size:15
Alignment explanation
Indices: 26824--26870 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
26814 GCTAAACTCT
26824 AAACTCTAAATCTTA
1 AAACTCTAAATCTTA
* *
26839 AAACTCCAAATCCT-
1 AAACTCTAAATCTTA
**
26853 AAACAATAAATCTTA
1 AAACTCTAAATCTTA
26868 AAA
1 AAA
26871 TTTTAAAATC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.53, C:0.21, G:0.00, T:0.26
Consensus pattern (15 bp):
AAACTCTAAATCTTA
Found at i:27028 original size:2 final size:2
Alignment explanation
Indices: 27021--27056 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
27011 CGTCACGGTA
27021 AT AT AT AT 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 AT AT AT AT
27057 GAGAAAATAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27815 original size:3 final size:3
Alignment explanation
Indices: 27807--27840 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
27797 GGTGTATACC
27807 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
27841 TGTACTGGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:37686 original size:3 final size:3
Alignment explanation
Indices: 37680--37715 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
37670 AAAAAGAAAG
37680 AGA AGA ATG- AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA A-GA AGA AGA AGA AGA AGA AGA AGA AGA AGA
37716 GATCAAATGA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 1 0.03
3 29 0.94
4 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.33, T:0.03
Consensus pattern (3 bp):
AGA
Found at i:37691 original size:9 final size:8
Alignment explanation
Indices: 37677--37717 Score: 55
Period size: 9 Copynumber: 4.8 Consensus size: 8
37667 ATAAAAAAGA
37677 AAGAGAAG
1 AAGAGAAG
37685 AATGAGAAG
1 AA-GAGAAG
37694 AAGAAGAAG
1 AAG-AGAAG
37703 AAGAAGAAG
1 AAG-AGAAG
37712 AAGAGA
1 AAGAGA
37718 TCAAATGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
8 6 0.19
9 25 0.81
ACGTcount: A:0.63, C:0.00, G:0.34, T:0.02
Consensus pattern (8 bp):
AAGAGAAG
Found at i:38454 original size:2 final size:2
Alignment explanation
Indices: 38449--38473 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38439 ATTTTTTTAA
38449 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 A
38474 ATTATTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39703 original size:22 final size:21
Alignment explanation
Indices: 39668--39709 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
39658 CATAATTATT
39668 TAAAAAATTAAATAAAAATAC
1 TAAAAAATTAAATAAAAATAC
*
39689 TAAAAATATTTAATAAAAATA
1 TAAAAA-ATTAAATAAAAATA
39710 ATTTTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAAAAATTAAATAAAAATAC
Found at i:40684 original size:2 final size:2
Alignment explanation
Indices: 40672--40704 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
40662 ACATACATAC
40672 AT AT A- 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 AT AT AT
40705 TGTCACGCCC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:44687 original size:17 final size:17
Alignment explanation
Indices: 44667--44699 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
44657 TTCAAAATAA
*
44667 TTAAAATAGTATATTTT
1 TTAAAATAATATATTTT
44684 TTAAAATAATATATTT
1 TTAAAATAATATATTT
44700 ATAAGCATTA
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:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (17 bp):
TTAAAATAATATATTTT
Found at i:45000 original size:51 final size:51
Alignment explanation
Indices: 44937--45045 Score: 173
Period size: 51 Copynumber: 2.1 Consensus size: 51
44927 CAATTACAAT
* *
44937 AAAAATATTATATTTTTTATAATATTTTTAACTGTAATCGAAAAAAATACA
1 AAAAATAATATATTTTTTATAATATTTTTAACTATAATCGAAAAAAATACA
* * *
44988 AAAAATAATATATTTTTTATAATATTTTTAATTATAATCGAAAATAATGCA
1 AAAAATAATATATTTTTTATAATATTTTTAACTATAATCGAAAAAAATACA
45039 AAAAATA
1 AAAAATA
45046 TTTTTAATTA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.40
Consensus pattern (51 bp):
AAAAATAATATATTTTTTATAATATTTTTAACTATAATCGAAAAAAATACA
Found at i:46796 original size:27 final size:27
Alignment explanation
Indices: 46766--46823 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
46756 TAACCTGCAC
* *
46766 TTGAATGGTTTTTTAATGGTAGCTGAA
1 TTGAATGGTTGTTTAATGGTAACTGAA
46793 TTGAATGGTTGTTTAATGGTAACTGAA
1 TTGAATGGTTGTTTAATGGTAACTGAA
46820 TTGA
1 TTGA
46824 CTTCTTGTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.28, C:0.03, G:0.26, T:0.43
Consensus pattern (27 bp):
TTGAATGGTTGTTTAATGGTAACTGAA
Found at i:46831 original size:27 final size:27
Alignment explanation
Indices: 46766--46832 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 27
46756 TAACCTGCAC
* * *
46766 TTGAATGGTTTTTTAATGGTAGCTGAA
1 TTGAATGCTTGTTTAATGGTAACTGAA
*
46793 TTGAATGGTTGTTTAATGGTAACTGAA
1 TTGAATGCTTGTTTAATGGTAACTGAA
* *
46820 TTGACTTCTTGTT
1 TTGAATGCTTGTT
46833 CTTTGCCTAG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.24, C:0.06, G:0.24, T:0.46
Consensus pattern (27 bp):
TTGAATGCTTGTTTAATGGTAACTGAA
Found at i:47823 original size:2 final size:2
Alignment explanation
Indices: 47818--47864 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
47808 TATGAATTGC
47818 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
47860 AT AT A
1 AT AT A
47865 AAGTCTAGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:57502 original size:29 final size:29
Alignment explanation
Indices: 57445--57502 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
57435 GTGTTGGTCG
*
57445 TAGGTCGCCATGCCTTCCGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCGGGCAACCTAC
* * *
57474 TAGGTCGCCATGTCTTCCTGGCAAGCTAC
1 TAGGTCGCCATGCCTTCCGGGCAACCTAC
57503 AAGAGATTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.16, C:0.34, G:0.26, T:0.24
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCGGGCAACCTAC
Found at i:57564 original size:14 final size:14
Alignment explanation
Indices: 57545--57572 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
57535 CGCTGGGCAT
57545 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
57559 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
57573 ACGAACTATG
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:0.21, C:0.43, G:0.29, T:0.07
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:57615 original size:33 final size:33
Alignment explanation
Indices: 57569--57643 Score: 107
Period size: 33 Copynumber: 2.3 Consensus size: 33
57559 CCGAGGCCAT
* * *
57569 CCGAACGAACTATGCGAGGGCATCCGAGGGTAA-
1 CCGAGCGAGCTATGCGAGGGAATCCGAGGG-AAG
57602 CCGAGCGAGCTATGCGAGGGAATCCGAGGGAAG
1 CCGAGCGAGCTATGCGAGGGAATCCGAGGGAAG
57635 CCGAGCGAG
1 CCGAGCGAG
57644 GGTAGGTCGC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 2 0.05
33 36 0.95
ACGTcount: A:0.28, C:0.24, G:0.39, T:0.09
Consensus pattern (33 bp):
CCGAGCGAGCTATGCGAGGGAATCCGAGGGAAG
Found at i:57680 original size:29 final size:29
Alignment explanation
Indices: 57647--57731 Score: 143
Period size: 29 Copynumber: 2.9 Consensus size: 29
57637 GAGCGAGGGT
* *
57647 AGGTCGCCCAGAGTGCATGGCGATCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
57676 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
*
57705 AGGTCGCCCGGAGGGCATGGCGACCTA
1 AGGTCGCCCGGAGTGCATGGCGACCTA
57732 TGTGTTGGGA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.21, C:0.29, G:0.35, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGAGTGCATGGCGACCTACA
Found at i:57777 original size:12 final size:12
Alignment explanation
Indices: 57760--57784 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
57750 TACCATGCAA
57760 CACGTTCATTCT
1 CACGTTCATTCT
57772 CACGTTCATTCT
1 CACGTTCATTCT
57784 C
1 C
57785 TCTGTTTGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.36, G:0.08, T:0.40
Consensus pattern (12 bp):
CACGTTCATTCT
Found at i:57844 original size:29 final size:29
Alignment explanation
Indices: 57802--57887 Score: 163
Period size: 29 Copynumber: 3.0 Consensus size: 29
57792 GAGCAAGGGT
57802 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
57831 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
*
57860 AGGTCGCCCGGAGTACATGGCGACCTAC
1 AGGTCGCCCGGAGTGCATGGCGACCTAC
57888 GGCCAACATT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 56 1.00
ACGTcount: A:0.21, C:0.31, G:0.34, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGAGTGCATGGCGACCTACA
Found at i:61900 original size:76 final size:76
Alignment explanation
Indices: 61771--61979 Score: 294
Period size: 76 Copynumber: 2.8 Consensus size: 76
61761 TCGTTGTACA
* * * *
61771 AGGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAG
** *
61835 CAAAACTGTTT
66 CAAAACCATTC
* *
61846 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAG
*
61911 CCAAACCATTC
66 CAAAACCATTC
* * *
61922 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCAGTTCCCTCTGAGCAATCTGGAATT
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATT
61980 TTTGGCTTTG
Statistics
Matches: 119, Mismatches: 14, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
75 19 0.16
76 100 0.84
ACGTcount: A:0.20, C:0.24, G:0.33, T:0.23
Consensus pattern (76 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAG
CAAAACCATTC
Found at i:62590 original size:17 final size:17
Alignment explanation
Indices: 62568--62611 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
62558 TTCATAAATC
62568 CAAAATCCAACAATCCA
1 CAAAATCCAACAATCCA
*
62585 CAAAATCAAACAATCCA
1 CAAAATCCAACAATCCA
62602 -AAATATCCAA
1 CAAA-ATCCAA
62612 AATGTTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.14
Consensus pattern (17 bp):
CAAAATCCAACAATCCA
Found at i:62603 original size:9 final size:8
Alignment explanation
Indices: 62563--62613 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 8
62553 CACTATTCAT
62563 AAATCC-A
1 AAATCCAA
62570 AAATCCAA
1 AAATCCAA
*
62578 CAATCCACA
1 AAATCCA-A
62587 AAAT-CAA
1 AAATCCAA
62594 ACAATCCAA
1 A-AATCCAA
62603 AATATCCAA
1 AA-ATCCAA
62612 AA
1 AA
62614 TGTTGAAACA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
7 8 0.22
8 13 0.35
9 16 0.43
ACGTcount: A:0.59, C:0.27, G:0.00, T:0.14
Consensus pattern (8 bp):
AAATCCAA
Found at i:85476 original size:6 final size:6
Alignment explanation
Indices: 85465--85490 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
85455 CTATATGCTG
85465 TTGTAT TTGTAT TTGTAT TTGTAT TT
1 TTGTAT TTGTAT TTGTAT TTGTAT TT
85491 TTTCATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.69
Consensus pattern (6 bp):
TTGTAT
Found at i:100168 original size:6 final size:6
Alignment explanation
Indices: 100157--100190 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
100147 AATCATTCAA
100157 AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG AGAG
1 AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG AGAG
100191 AGAAGGGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (6 bp):
AGAGGG
Found at i:105008 original size:64 final size:65
Alignment explanation
Indices: 104861--105016 Score: 169
Period size: 64 Copynumber: 2.4 Consensus size: 65
104851 GAAGGTGTAT
* ** *
104861 CGATGCACAGGTAGTGCATCGATGCA-CTCTTTTAAAATAAAAAAGATCGAATGCAATTAGTGCA
1 CGATGCACAAGTAGTGCATCGATGCATCTCCATTAAAAT-AAAAACATCGAATGCAATTAGTGCA
*
104925 T
65 C
* * *
104926 CGATGCATAAGGCA-TGCATCGATGCATC-CCATTAATAAT-AAAACATCGAATGCATTTTA-TG
1 CGATGCACAA-GTAGTGCATCGATGCATCTCCATTAA-AATAAAAACATCGAATGCA-ATTAGTG
104987 CAC
63 CAC
104990 CGATGCACAAGTAGTGCATCGATGCAT
1 CGATGCACAAGTAGTGCATCGATGCAT
105017 ACCTTCATTA
Statistics
Matches: 76, Mismatches: 10, Indels: 11
0.78 0.10 0.11
Matches are distributed among these distances:
63 2 0.03
64 40 0.53
65 28 0.37
66 6 0.08
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (65 bp):
CGATGCACAAGTAGTGCATCGATGCATCTCCATTAAAATAAAAACATCGAATGCAATTAGTGCAC
Found at i:105430 original size:29 final size:29
Alignment explanation
Indices: 105390--105470 Score: 119
Period size: 29 Copynumber: 2.8 Consensus size: 29
105380 TATGTGATAT
105390 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
* *
105420 TAGATATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
*
105449 GAGAAATAACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
105471 ACATATGAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 7 0.15
29 36 0.78
30 3 0.07
ACGTcount: A:0.44, C:0.16, G:0.20, T:0.20
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:105602 original size:15 final size:15
Alignment explanation
Indices: 105555--105603 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
105545 AAGGGTATAA
105555 TAGTCCTTCAGGG-CG
1 TAGTCCTTC-GGGACG
*
105570 TAGTCCTTCGGAACG
1 TAGTCCTTCGGGACG
*
105585 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
105600 TAGT
1 TAGT
105604 GGTCCTACGA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
14 2 0.07
15 28 0.93
ACGTcount: A:0.16, C:0.22, G:0.31, T:0.31
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Found at i:107218 original size:2 final size:2
Alignment explanation
Indices: 107211--107267 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
107201 AATGCTTAGT
107211 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
107253 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
107268 GTAGTGTAGT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:111700 original size:13 final size:13
Alignment explanation
Indices: 111682--111706 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
111672 CACCTTTTGT
111682 ATTTGCATTTGCC
1 ATTTGCATTTGCC
111695 ATTTGCATTTGC
1 ATTTGCATTTGC
111707 ATTACATGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.20, G:0.16, T:0.48
Consensus pattern (13 bp):
ATTTGCATTTGCC
Found at i:116229 original size:216 final size:215
Alignment explanation
Indices: 115846--116383 Score: 902
Period size: 216 Copynumber: 2.5 Consensus size: 215
115836 GTGAAGCAAA
*
115846 CCATCCATAAGACCTTCGGGTAAGATGTTTTCAAAAGAATTTGAAAAT-AAAAAATGATGTTTTA
1 CCATCCATAAAACCTTCGGGTAAGATGTTTTCAAAAGAATTTGAAAATGAAAAAATGATGTTTTA
* * *
115910 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCG
66 AGAAGATGAAATTTTTGAAAACGAAGAATGTGATTTTCAAAATTTCACAATTTATAAGTCATTCG
*
115975 GGCCATCAGTAAGTCTTTCGAGCATAATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
131 GGCCATCAATAAGTCTTTCGAGCATAATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
116040 AAGATGATAAGTCCTTCGGG
196 AAGATGATAAGTCCTTCGGG
* *
116060 CCATCCGTAAAACCTTCGGGTATGATGTTTTCAAAAGAATTTGAAAATGAAAAAAATGATGTTTT
1 CCATCCATAAAACCTTCGGGTAAGATGTTTTCAAAAGAATTTGAAAATG-AAAAAATGATGTTTT
* *
116125 GAGAAGATGAAATTTTTGAAAACAAAGAATGTGATTTTCAAAATTTCACAATTTATAAGTCATTC
65 AAGAAGATGAAATTTTTGAAAACGAAGAATGTGATTTTCAAAATTTCACAATTTATAAGTCATTC
*
116190 GGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAG
130 GGGCCATCAATAAGTCTTTCGAGCATAATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAG
116255 CAAGATGATAAGTCCTTCGGG
195 CAAGATGATAAGTCCTTCGGG
* * * * * *
116276 CCATCCATAAAACCTTCGGGTAGGATGTTTTTACATGAATTTGAAAATG--AAACTTATGTTTTA
1 CCATCCATAAAACCTTCGGGTAAGATGTTTTCAAAAGAATTTGAAAATGAAAAAATGATGTTTTA
116339 AGAAGATGAAATTTTTGAAAACGAAGAATGTGATTTTCAAAATTT
66 AGAAGATGAAATTTTTGAAAACGAAGAATGTGATTTTCAAAATTT
116384 TATAATCAGT
Statistics
Matches: 303, Mismatches: 19, Indels: 5
0.93 0.06 0.02
Matches are distributed among these distances:
213 55 0.18
214 45 0.15
216 203 0.67
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (215 bp):
CCATCCATAAAACCTTCGGGTAAGATGTTTTCAAAAGAATTTGAAAATGAAAAAATGATGTTTTA
AGAAGATGAAATTTTTGAAAACGAAGAATGTGATTTTCAAAATTTCACAATTTATAAGTCATTCG
GGCCATCAATAAGTCTTTCGAGCATAATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
AAGATGATAAGTCCTTCGGG
Found at i:116256 original size:42 final size:41
Alignment explanation
Indices: 116187--116280 Score: 107
Period size: 42 Copynumber: 2.3 Consensus size: 41
116177 TTATAAGTCA
** * * * *
116187 TTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCC
1 TTCGGGCCATCTGTAAGCCTTTAGAGCAAGATG-ATAAATCC
* *
116229 TTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCC
1 TTCGGGCCATCTGTAAGCCTTTAGAGCAAGATGATAAATCC
116270 TTCGGGCCATC
1 TTCGGGCCATC
116281 CATAAAACCT
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
41 16 0.37
42 27 0.63
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.30
Consensus pattern (41 bp):
TTCGGGCCATCTGTAAGCCTTTAGAGCAAGATGATAAATCC
Found at i:116931 original size:53 final size:53
Alignment explanation
Indices: 116868--117180 Score: 405
Period size: 53 Copynumber: 5.9 Consensus size: 53
116858 ATCAAACCAT
116868 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * *
116921 AAGATTGTTCGAGTTTTACTCCCTGAAGCAAGAGGGAGCAAACCCGTAGACAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * *
116974 AAGATTGTTTGAGTTCTACTCCTTGAAGCAAGAGGGAGCGAACCCGCT-GGTAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCG-TAGGCAG
* * *
117027 AAGATTATTCGAGTTCTACCCCCTGAAGCAAGAGGGAGCGAACCCGTAAGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * * ****
117080 AAGATTATTCGAGTTCTACTCCCTGAAGCAATAGGGAGCGAACCCATTTTTAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * * *
117133 AAGATTGTTCGAGTTCCTTAATCCCGGAA-CAAGAGAGAGCGGACCCGT
1 AAGATTGTTCGAGTT-C-TACTCCCTGAAGCAAGAGGGAGCGAACCCGT
117181 CATTTGAAGA
Statistics
Matches: 227, Mismatches: 29, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
52 1 0.00
53 200 0.88
54 17 0.07
55 9 0.04
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.22
Consensus pattern (53 bp):
AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
Found at i:118864 original size:2 final size:2
Alignment explanation
Indices: 118857--118945 Score: 178
Period size: 2 Copynumber: 44.5 Consensus size: 2
118847 AATGCTTAGT
118857 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
118899 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
118941 TA TA T
1 TA TA T
118946 GTAGTGTAGT
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 87 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:122460 original size:41 final size:41
Alignment explanation
Indices: 122405--122766 Score: 390
Period size: 41 Copynumber: 8.7 Consensus size: 41
122395 CAAAATACTA
* * *
122405 TACTTTAGTGGCGTTTGTATAAAAACGCCGCTAAAGAATCG
1 TACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGAATCG
* * *
122446 TAATGTAGTGGCGTTTTTATACAAACGCCGCTATA-AACTAG
1 TACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGAA-TCG
* *
122487 TATTTTAGTGGCGTTTTTATACAAACGCTGCTATAGACA-CG
1 TACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGA-ATCG
* * * * * *
122528 TACTTTTGTGGCGTTTTAATACCAAACGACGTTATAGACTCA
1 TACTTTAGTGGCGTTTTTATA-CAAACGCCGCTATAGAATCG
** *
122570 TACTTTAGTGGTATTTTTACACAAACGCCGCTATAGACA-CG
1 TACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGA-ATCG
* * *
122611 TACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGATTCG
1 TACTTTAGTGGCGTTTTTATA-CAAACGCCGCTATAGAATCG
*
122653 TACTTTAGTGGCGTTTTTACACAAACGCCGCTATAGACA-CG
1 TACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGA-ATCG
* * * *
122694 TATTTTTGTGGCGTTTTAATAACAAACGCCGCTATAGACTCG
1 TACTTTAGTGGCGTTTTTAT-ACAAACGCCGCTATAGAATCG
*
122736 TACTTTAGTGGCGTTTTAATACCAAACGCCG
1 TACTTTAGTGGCGTTTTTATA-CAAACGCCG
122767 TAATTGTCAT
Statistics
Matches: 265, Mismatches: 44, Indels: 23
0.80 0.13 0.07
Matches are distributed among these distances:
40 2 0.01
41 149 0.56
42 113 0.43
43 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (41 bp):
TACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGAATCG
Found at i:122587 original size:83 final size:83
Alignment explanation
Indices: 122404--122766 Score: 480
Period size: 83 Copynumber: 4.4 Consensus size: 83
122394 GCAAAATACT
* * * * * * *
122404 ATACTTTAGTGGCGTTTGTATAAAAACGCCGCTAAAGA-ATCGTAATGTAGTGGCGTTTTTATA-
1 ATACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACA-CGTACTTTTGTGGCGTTTTAATAC
*
122467 CAAACGCCGCTATAAACT-
65 CAAACGCCGCTATAGACTC
* *
122485 AGTATTTTAGTGGCGTTTTTATACAAACGCTGCTATAGACACGTACTTTTGTGGCGTTTTAATAC
1 A-TACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATAC
* *
122550 CAAACGACGTTATAGACTC
65 CAAACGCCGCTATAGACTC
** *
122569 ATACTTTAGTGGTATTTTTACACAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACC
1 ATACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACC
*
122634 AAACGCCGCTATAGATTC
66 AAACGCCGCTATAGACTC
* * * *
122652 GTACTTTAGTGGCGTTTTTACACAAACGCCGCTATAGACACGTATTTTTGTGGCGTTTTAATAAC
1 ATACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACC
122717 AAACGCCGCTATAGACTC
66 AAACGCCGCTATAGACTC
* *
122735 GTACTTTAGTGGCGTTTTAATACCAAACGCCG
1 ATACTTTAGTGGCGTTTTTATA-CAAACGCCG
122767 TAATTGTCAT
Statistics
Matches: 249, Mismatches: 28, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
81 1 0.00
82 51 0.20
83 187 0.75
84 10 0.04
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (83 bp):
ATACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACC
AAACGCCGCTATAGACTC
Found at i:127546 original size:21 final size:21
Alignment explanation
Indices: 127504--127562 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
127494 TGATTTATTA
**
127504 TTATGGATTTCATTTTTCTTG
1 TTATGGATTTCAAGTTTCTTG
* *
127525 TTATGGATTTTAAGTTTGTTG
1 TTATGGATTTCAAGTTTCTTG
* *
127546 TTATCGATGTCAAGTTT
1 TTATGGATTTCAAGTTT
127563 ATTGGAAAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.19, C:0.07, G:0.19, T:0.56
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTCTTG
Found at i:127762 original size:43 final size:43
Alignment explanation
Indices: 127715--127939 Score: 283
Period size: 43 Copynumber: 5.3 Consensus size: 43
127705 ACCAGATCTT
* *
127715 TTGCGGTGTTTGTGGGAAAAACGCCGCTAAATATCAAGACCTA
1 TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATATCAACACCTA
*
127758 TTGCGGCGTTTAT-GGACAAAACGCCGCTAAATATCAACACCTA
1 TTGCGGCGTTTGTGGGA-AAAACGCCGCTAAATATCAACACCTA
** * *
127801 TTGCGGCGTTTGTGTAAAAAACGCCGCTAAATCTCAACACATA
1 TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATATCAACACCTA
* * *
127844 TTGCGGCGTTTGTTGGAAAAA-GCCACCAAATATCAACACCTA
1 TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATATCAACACCTA
* * * ***
127886 TTGCGGCGTTTGTTGGACAAACGCCGCTATATATCGTTACCTA
1 TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATATCAACACCTA
127929 TTGCGGCGTTT
1 TTGCGGCGTTT
127940 TTTGTTACTA
Statistics
Matches: 157, Mismatches: 22, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
42 40 0.25
43 116 0.74
44 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (43 bp):
TTGCGGCGTTTGTGGGAAAAACGCCGCTAAATATCAACACCTA
Found at i:127896 original size:85 final size:86
Alignment explanation
Indices: 127715--127939 Score: 276
Period size: 85 Copynumber: 2.6 Consensus size: 86
127705 ACCAGATCTT
* * * *
127715 TTGCGGTGTTTGTGGGAAAAACGCCGCTAAATATCAAGACCTATTGCGGCGTTTATGGACAAAAC
1 TTGCGGCGTTTGTGGAAAAAACGCCGCTAAATATCAACACATATTGCGGCGTTTATGGACAAAAC
* *
127780 GCCGCTAAATATCAACACCTA
66 GCCACCAAATATCAACACCTA
* * *
127801 TTGCGGCGTTTGTGTAAAAAACGCCGCTAAATCTCAACACATATTGCGGCGTTTGTTGGA-AAAA
1 TTGCGGCGTTTGTGGAAAAAACGCCGCTAAATATCAACACATATTGCGGCGTTT-ATGGACAAAA
127865 -GCCACCAAATATCAACACCTA
65 CGCCACCAAATATCAACACCTA
* * *** *
127886 TTGCGGCGTTTGTTGG-ACAAACGCCGCTATATATCGTTACCTATTGCGGCGTTT
1 TTGCGGCGTTTG-TGGAAAAAACGCCGCTAAATATCAACACATATTGCGGCGTTT
127940 TTTGTTACTA
Statistics
Matches: 120, Mismatches: 17, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
85 62 0.52
86 54 0.45
87 4 0.03
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (86 bp):
TTGCGGCGTTTGTGGAAAAAACGCCGCTAAATATCAACACATATTGCGGCGTTTATGGACAAAAC
GCCACCAAATATCAACACCTA
Found at i:128689 original size:22 final size:21
Alignment explanation
Indices: 128624--128683 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
128614 GATTTCTGGG
128624 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAATCGGTACCCATT
128645 CAA-GGGAATCGGTACCCATT
1 CAAGGGGAATCGGTACCCATT
*
128665 CAATGGGGAATCGATACCC
1 CAA-GGGGAATCGGTACCC
128684 CCTCAAACGA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 20 0.56
21 3 0.08
22 13 0.36
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.18
Consensus pattern (21 bp):
CAAGGGGAATCGGTACCCATT
Found at i:130255 original size:103 final size:103
Alignment explanation
Indices: 130035--130247 Score: 381
Period size: 103 Copynumber: 2.1 Consensus size: 103
130025 GGGTCTACGC
*
130035 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTATTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* * *
130100 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATATATATGATTCTTAAGGAATGATATGT
130138 GGTCCTTCGGGACATATATGTATTATTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTATTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
*
130203 CCCTAGTATATATATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATATATATGATTCTTAAGGAATGATATGT
130241 GGTCCTT
1 GGTCCTT
130248 ATGGACATTA
Statistics
Matches: 105, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (103 bp):
GGTCCTTCGGGACATATATGTATTATTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
CCCTAGCATATATATATGATTCTTAAGGAATGATATGT
Found at i:130297 original size:23 final size:23
Alignment explanation
Indices: 130264--130354 Score: 137
Period size: 23 Copynumber: 4.0 Consensus size: 23
130254 ATTATTATAT
*
130264 GGCACTACGGTGCAATTCTACGC
1 GGCACTCCGGTGCAATTCTACGC
*
130287 GGCACTCCGGTACAATTCTACGC
1 GGCACTCCGGTGCAATTCTACGC
*
130310 GGCACTCCGGTGCAATTCTACGT
1 GGCACTCCGGTGCAATTCTACGC
* *
130333 GGCACTTCGGTGCAATTATACG
1 GGCACTCCGGTGCAATTCTACG
130355 AGCTGTGGTG
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 62 1.00
ACGTcount: A:0.21, C:0.30, G:0.25, T:0.24
Consensus pattern (23 bp):
GGCACTCCGGTGCAATTCTACGC
Found at i:131845 original size:202 final size:201
Alignment explanation
Indices: 131565--131994 Score: 511
Period size: 202 Copynumber: 2.1 Consensus size: 201
131555 GAATATAACC
* * *
131565 ATATTTGGCTAAACTTAAAGAAAAGTTACAATACTAGGCCTCTAAGCTTACAAATTACGAAAAAT
1 ATATTAGGCTCAACTTAAAGATAAGTTACAATACTAGGCCTCTAAGCTTACAAATTACGAAAAAT
* * ** * *
131630 ATGTTATTTACAACCCGAAAATAATACTCGAACACGCCTATGAAGTCATGTTGCCTTAAAACTTT
66 ATGCTATTTACAACCCGAAAATAATAATCGAACACGCCTATGAAACCATGTTACCTT-AAACTTG
* * * * ** *
131695 ATGA-CGAAAAGCATTCTTCCTAACCATTTCCAGGGTGTTTTTTACCCCGCTTAGAATGTCTCGA
130 ATGATC-AAAAGCATGCTTCCGAACCATTTCCAGGATGATTTTTACCCAACTTAGAATGTCTCAA
131759 ATGTGGCA
194 ATGTGGCA
* * * * *
131767 ATATTATGCTCAACTTAAAGATAAGTTACAATACTAGGTCTTTATGCTTATAAATTACGAAAAAT
1 ATATTAGGCTCAACTTAAAGATAAGTTACAATACTAGGCCTCTAAGCTTACAAATTACGAAAAAT
* * * * * * *
131832 CTGCTGTTTACAACTCGGAAATAATAATCGAACATGCCTATGAAACCATTTTACCTTACACTTGA
66 ATGCTATTTACAACCCGAAAATAATAATCGAACACGCCTATGAAACCATGTTACCTTAAACTTGA
* * * * *
131897 TGATCAAAATCATGCTTTCGATCCATTTTCAGGATGATTTTTATCCAACTTAGAATGTCTCAAAT
131 TGATCAAAAGCATGCTTCCGAACCATTTCCAGGATGATTTTTACCCAACTTAGAATGTCTCAAAT
**
131962 GTGGTG
196 GTGGCA
*
131968 ATATTAGGCTCAAATTAAAGATAAGTT
1 ATATTAGGCTCAACTTAAAGATAAGTT
131995 GCGGTATCTC
Statistics
Matches: 190, Mismatches: 37, Indels: 3
0.83 0.16 0.01
Matches are distributed among these distances:
201 86 0.45
202 104 0.55
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (201 bp):
ATATTAGGCTCAACTTAAAGATAAGTTACAATACTAGGCCTCTAAGCTTACAAATTACGAAAAAT
ATGCTATTTACAACCCGAAAATAATAATCGAACACGCCTATGAAACCATGTTACCTTAAACTTGA
TGATCAAAAGCATGCTTCCGAACCATTTCCAGGATGATTTTTACCCAACTTAGAATGTCTCAAAT
GTGGCA
Found at i:132025 original size:201 final size:201
Alignment explanation
Indices: 131565--132031 Score: 476
Period size: 201 Copynumber: 2.3 Consensus size: 201
131555 GAATATAACC
* * ** *
131565 ATATTTGGCT-AAACTTAAAGAAAAGTTACAATACTAGGCCTCTAAGCTTACAAATTACGAAAAA
1 ATATTAGGCTCAAA-TTAAAGATAAGTTACAATACTA-GTATCTAAGCTTATAAATTACGAAAAA
* * ** *
131629 TATGTTATTTACAACCCGAAAATAATACTCGAACACGCCTATGAAGTCATGTTGCCTTAAAACTT
64 TATGCTATTTACAACCCGAAAATAATAATCGAACACGCCTATGAAACCATGTTACCTTAAAACTT
* * * * * ** *
131694 TATGACGAAAAGCATTCTTCCTAACCATTTCCAGGGTGTTTTTTACCCCGCTTAGAATGTCTCGA
129 GATGACGAAAAGCATGCTTCCGAACCATTTCCAGGATGATTTTTACCCAACTTAGAATGTCTCAA
131759 ATGTGGCA
194 ATGTGGCA
* * * * *
131767 ATATTATGCTCAACTTAAAGATAAGTTACAATACTAGGTCTTTATGCTTATAAATTACGAAAAAT
1 ATATTAGGCTCAAATTAAAGATAAGTTACAATACTA-GTATCTAAGCTTATAAATTACGAAAAAT
* * * * * * *
131832 CTGCTGTTTACAACTCGGAAATAATAATCGAACATGCCTATGAAACCATTTTACCTT-ACACTTG
65 ATGCTATTTACAACCCGAAAATAATAATCGAACACGCCTATGAAACCATGTTACCTTAAAACTTG
* * * * *
131896 ATGATC-AAAATCATGCTTTCGATCCATTTTCAGGATGATTTTTATCCAACTTAGAATGTCTCAA
130 ATGA-CGAAAAGCATGCTTCCGAACCATTTCCAGGATGATTTTTACCCAACTTAGAATGTCTCAA
**
131960 ATGTGGTG
194 ATGTGGCA
* ** *
131968 ATATTAGGCTCAAATTAAAGATAAGTTGCGGTATCTCA-TATCTACGCTTATAAATTAC-AAAAA
1 ATATTAGGCTCAAATTAAAGATAAGTTACAATA-CT-AGTATCTAAGCTTATAAATTACGAAAAA
132031 T
64 T
132032 TTTGCAGTTT
Statistics
Matches: 218, Mismatches: 43, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
200 6 0.03
201 106 0.49
202 103 0.47
203 3 0.01
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (201 bp):
ATATTAGGCTCAAATTAAAGATAAGTTACAATACTAGTATCTAAGCTTATAAATTACGAAAAATA
TGCTATTTACAACCCGAAAATAATAATCGAACACGCCTATGAAACCATGTTACCTTAAAACTTGA
TGACGAAAAGCATGCTTCCGAACCATTTCCAGGATGATTTTTACCCAACTTAGAATGTCTCAAAT
GTGGCA
Found at i:141347 original size:21 final size:22
Alignment explanation
Indices: 141301--141347 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
141291 TTATGTTTCT
*
141301 TTGTTTAGGCAATCTTTTGTAA
1 TTGTTTAGGCAATCTTATGTAA
*
141323 -TGTTT-GGTAATCTTATGTAA
1 TTGTTTAGGCAATCTTATGTAA
141343 TTGTT
1 TTGTT
141348 GGTTATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.21, C:0.06, G:0.19, T:0.53
Consensus pattern (22 bp):
TTGTTTAGGCAATCTTATGTAA
Done.