Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 54 of 190
Found at i:15259650 original size:15 final size:15
Alignment explanation
Indices: 15259630--15259658 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
15259620 CTTTATTCCA
15259630 TTAGTTTAATTTAAC
1 TTAGTTTAATTTAAC
15259645 TTAGTTTAATTTAA
1 TTAGTTTAATTTAA
15259659 TTTCTACAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.55
Consensus pattern (15 bp):
TTAGTTTAATTTAAC
Found at i:15259831 original size:27 final size:27
Alignment explanation
Indices: 15259793--15259847 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
15259783 ATGGGAATGA
*
15259793 TCCCAGTCTCAATGATAATCCAAATTG
1 TCCCAGTCTCAATAATAATCCAAATTG
*
15259820 TCCCGGTCTCAATAATAATCCAAATTG
1 TCCCAGTCTCAATAATAATCCAAATTG
15259847 T
1 T
15259848 TAGGATGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.33, C:0.25, G:0.11, T:0.31
Consensus pattern (27 bp):
TCCCAGTCTCAATAATAATCCAAATTG
Found at i:15266958 original size:18 final size:20
Alignment explanation
Indices: 15266935--15266977 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
15266925 AAACAGTTTA
15266935 AAAATAATAAAAAT-AAAT-
1 AAAATAATAAAAATGAAATG
*
15266953 AAAAT-ATAGAAATGAAATG
1 AAAATAATAAAAATGAAATG
15266972 AAAATA
1 AAAATA
15266978 TAATATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 7 0.33
18 9 0.43
19 5 0.24
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (20 bp):
AAAATAATAAAAATGAAATG
Found at i:15267083 original size:6 final size:6
Alignment explanation
Indices: 15267059--15267121 Score: 58
Period size: 6 Copynumber: 10.5 Consensus size: 6
15267049 ATTTAAATGG
* *
15267059 ATAAAT AAAAAT ATAAAAT ATAAAT A-AAAT ATAAAT A-AATAT ATATAT
1 ATAAAT ATAAAT AT-AAAT ATAAAT ATAAAT ATAAAT ATAA-AT ATAAAT
* *
15267107 ATATAT ATATAT ATA
1 ATAAAT ATAAAT ATA
15267122 TGGAAAATAA
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
5 7 0.14
6 36 0.72
7 7 0.14
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
ATAAAT
Found at i:15267087 original size:11 final size:11
Alignment explanation
Indices: 15267059--15267103 Score: 60
Period size: 11 Copynumber: 4.3 Consensus size: 11
15267049 ATTTAAATGG
15267059 ATAAATAAAA-
1 ATAAATAAAAT
15267069 AT--ATAAAAT
1 ATAAATAAAAT
15267078 ATAAATAAAAT
1 ATAAATAAAAT
15267089 ATAAATAAATAT
1 ATAAATAAA-AT
15267101 ATA
1 ATA
15267104 TATATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
8 6 0.19
9 2 0.06
10 2 0.06
11 16 0.52
12 5 0.16
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
ATAAATAAAAT
Found at i:15267104 original size:2 final size:2
Alignment explanation
Indices: 15267087--15267122 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
15267077 TATAAATAAA
* *
15267087 AT AT AA AT AA 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
15267123 GGAAAATAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:15268600 original size:44 final size:43
Alignment explanation
Indices: 15268454--15268601 Score: 120
Period size: 44 Copynumber: 3.4 Consensus size: 43
15268444 ATTTAACTTG
* * * * **
15268454 TAGCTTTAATCTGTTCCATTGCAACTTTGGGGAGA-AAAGAGTA
1 TAGCTTTAATCTGCTCCACTGCATCTTCGGGGAGATAAA-TTTA
* ** *
15268497 GTATCTTTAATCTGCTCCACTGCATCTTCAAGGAGATAAGATTAA
1 -TAGCTTTAATCTGCTCCACTGCATCTTCGGGGAGATAA-ATTTA
** *
15268542 TA-AATTCATCCTGCTCCACTGCATCTTCGGGGAGATAAATTTTA
1 TAGCTTTAAT-CTGCTCCACTGCATCTTCGGGGAGATAAA-TTTA
15268586 TAGCTTTAATCTGCTC
1 TAGCTTTAATCTGCTC
15268602 TACTCTAACT
Statistics
Matches: 80, Mismatches: 19, Indels: 10
0.73 0.17 0.09
Matches are distributed among these distances:
43 5 0.06
44 67 0.84
45 7 0.09
46 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (43 bp):
TAGCTTTAATCTGCTCCACTGCATCTTCGGGGAGATAAATTTA
Found at i:15268657 original size:45 final size:44
Alignment explanation
Indices: 15268608--15268701 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 44
15268598 GCTCTACTCT
* * * *
15268608 AACTTTAAAGAGATAATATTTTCTATCTTCAATCTTCTCCATTGC
1 AACTTTAAAGAGATAAGA-CTTCTATCTTCAATCTGCCCCATTGC
** *
15268653 AACTTTAGGGAGATAAGACTTGTATCTTCAATCTGCCCCATTGC
1 AACTTTAAAGAGATAAGACTTCTATCTTCAATCTGCCCCATTGC
15268697 AACTT
1 AACTT
15268702 CAGGGAGATC
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
44 27 0.64
45 15 0.36
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (44 bp):
AACTTTAAAGAGATAAGACTTCTATCTTCAATCTGCCCCATTGC
Found at i:15268987 original size:44 final size:44
Alignment explanation
Indices: 15268939--15269121 Score: 160
Period size: 44 Copynumber: 4.2 Consensus size: 44
15268929 CCTCAGAGGT
* *
15268939 ATAGGATTCATCGTTTTAATCCGCTCCACTGCAACTTCAGGGAG
1 ATAGGATTTATCGCTTTAATCCGCTCCACTGCAACTTCAGGGAG
* * *
15268983 ATAGGA-TTAGCAGCTTTAATCTGCTCCACTGCAACTTTAGGGAG
1 ATAGGATTTATC-GCTTTAATCCGCTCCACTGCAACTTCAGGGAG
** *
15269027 ATCCGATTGTAT---TTTCAA-CCTGCTCCACTGCAACTTCAAGGAG
1 ATAGGATT-TATCGCTTT-AATCC-GCTCCACTGCAACTTCAGGGAG
* * * ** *
15269070 ATAGGGTTTGTCACTTTAATCTACACCACTGCAACTTCAGGGAG
1 ATAGGATTTATCGCTTTAATCCGCTCCACTGCAACTTCAGGGAG
*
15269114 ATAAGATT
1 ATAGGATT
15269122 GGTTTATTTT
Statistics
Matches: 109, Mismatches: 21, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
42 6 0.06
43 30 0.28
44 66 0.61
45 5 0.05
46 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (44 bp):
ATAGGATTTATCGCTTTAATCCGCTCCACTGCAACTTCAGGGAG
Found at i:15269070 original size:43 final size:44
Alignment explanation
Indices: 15268953--15269162 Score: 158
Period size: 44 Copynumber: 4.8 Consensus size: 44
15268943 GATTCATCGT
*
15268953 TTTAATCC-GCTCCACTGCAACTTCAGGGAGATAGGATTAGCAGC
1 TTTAA-CCTGCTCCACTGCAACTTCAGGGAGATACGATTAGCAGC
* * * * *
15268997 TTTAATCTGCTCCACTGCAACTTTAGGGAGATCCGATT-GTA-T
1 TTTAACCTGCTCCACTGCAACTTCAGGGAGATACGATTAGCAGC
* * * *
15269039 TTTCAACCTGCTCCACTGCAACTTCAAGGAGATAGGGTTTGTCA-C
1 TTT-AACCTGCTCCACTGCAACTTCAGGGAGATACGATTAG-CAGC
* * * * * * **
15269084 TTTAATCTACACCACTGCAACTTCAGGGAGATAAGATTGGTTTATT
1 TTTAACCTGCTCCACTGCAACTTCAGGGAGATACGATTAG--CAGC
* * *
15269130 TTTAACTTGTTCCACTGCAACTTTAGGGAGATA
1 TTTAACCTGCTCCACTGCAACTTCAGGGAGATA
15269163 AGGTTTGATA
Statistics
Matches: 131, Mismatches: 29, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
42 3 0.02
43 32 0.24
44 63 0.48
45 6 0.05
46 27 0.21
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.32
Consensus pattern (44 bp):
TTTAACCTGCTCCACTGCAACTTCAGGGAGATACGATTAGCAGC
Found at i:15269070 original size:87 final size:89
Alignment explanation
Indices: 15268961--15269162 Score: 257
Period size: 87 Copynumber: 2.3 Consensus size: 89
15268951 GTTTTAATCC
* * *
15268961 GCTCCACTGCAACTTCAGGGAGATAGGATTAG-CAGCTTTAATCTGCTCCACTGCAACTTTAGGG
1 GCTCCACTGCAACTTCAGGGAGATAGGATTAGTCA-CTTTAATCTACACCACTGCAACTTCAGGG
**
15269025 AGATCCGATT-G-TATTTTCAACCT
65 AGATAAGATTGGTTATTTTCAACCT
* * *
15269048 GCTCCACTGCAACTTCAAGGAGATAGGGTTTGTCACTTTAATCTACACCACTGCAACTTCAGGGA
1 GCTCCACTGCAACTTCAGGGAGATAGGATTAGTCACTTTAATCTACACCACTGCAACTTCAGGGA
* *
15269113 GATAAGATTGGTTTATTTTTAACTT
66 GATAAGATTGG-TTATTTTCAACCT
* *
15269138 GTTCCACTGCAACTTTAGGGAGATA
1 GCTCCACTGCAACTTCAGGGAGATA
15269163 AGGTTTGATA
Statistics
Matches: 98, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
87 63 0.64
88 3 0.03
90 32 0.33
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (89 bp):
GCTCCACTGCAACTTCAGGGAGATAGGATTAGTCACTTTAATCTACACCACTGCAACTTCAGGGA
GATAAGATTGGTTATTTTCAACCT
Found at i:15269188 original size:87 final size:86
Alignment explanation
Indices: 15268961--15269216 Score: 248
Period size: 87 Copynumber: 2.9 Consensus size: 86
15268951 GTTTTAATCC
* * * *
15268961 GCTCCACTGCAACTTCAGGGAGAT-AGGATTAGCAGCTTTAATCTGCTCCACTGCAACTTTAGGG
1 GCTCCACTGCAACTTCAAGGAGATAAGG-TTTGCA-CTATAATCTACTCCACTGCAACTTTAGGG
**
15269025 AGATCCGATTGTATTTTCAACCT
64 AGATAAGATTGTATTTTCAACCT
* * * *
15269048 GCTCCACTGCAACTTCAAGGAGATAGGGTTTGTCACTTTAATCTACACCACTGCAACTTCAGGGA
1 GCTCCACTGCAACTTCAAGGAGATAAGGTTTG-CACTATAATCTACTCCACTGCAACTTTAGGGA
* *
15269113 GATAAGATTGGTTTATTTTTAACTT
65 GATAAGATT-G--TATTTTCAACCT
* * * * * **
15269138 GTTCCACTGCAACTTTAGGGAGATAAGGTTTG-A-TATGATCTACTCTACTGCAACTTTAGATAG
1 GCTCCACTGCAACTTCAAGGAGATAAGGTTTGCACTATAATCTACTCCACTGCAACTTTAGGGAG
15269201 ATAAGATCTGTTATTT
66 ATAAGAT-TG-TATTT
15269217 ATAGCTTTAA
Statistics
Matches: 142, Mismatches: 21, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
86 6 0.04
87 91 0.64
88 7 0.05
90 38 0.27
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (86 bp):
GCTCCACTGCAACTTCAAGGAGATAAGGTTTGCACTATAATCTACTCCACTGCAACTTTAGGGAG
ATAAGATTGTATTTTCAACCT
Found at i:15271058 original size:17 final size:17
Alignment explanation
Indices: 15271036--15271070 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
15271026 TTCTCTTTTA
*
15271036 ATTAATTTAATATTATT
1 ATTAATCTAATATTATT
*
15271053 ATTAATCTATTATTATT
1 ATTAATCTAATATTATT
15271070 A
1 A
15271071 CTCATATCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTAATCTAATATTATT
Found at i:15271063 original size:14 final size:15
Alignment explanation
Indices: 15271045--15271084 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
15271035 AATTAATTTA
15271045 ATATTATTATTAATC
1 ATATTATTATTAATC
*
15271060 -TATTATTATTACTC
1 ATATTATTATTAATC
*
15271074 ATATCATTATT
1 ATATTATTATT
15271085 GATATTGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (15 bp):
ATATTATTATTAATC
Found at i:15273795 original size:45 final size:45
Alignment explanation
Indices: 15273729--15273973 Score: 346
Period size: 45 Copynumber: 5.4 Consensus size: 45
15273719 AGTATACAGT
* * * * *
15273729 AATCAGTAACGGTAGCAGTAACAGTATTCAACACACAAAGTGCTG
1 AATCGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
* *
15273774 AATCTGTAACAGTAACGGTAACAGTATTCGACACACAAAGTGCCG
1 AATCGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
* *
15273819 AATCGATAACAGTAACAGCAACAGTATTCGACACACAAAGTGCCG
1 AATCGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
* * *
15273864 AGTAGGTAACAGTAACAGTAATAGTATTCGACACACAAAGTGCCG
1 AATCGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
* * *
15273909 AGTCGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGTCA
1 AATCGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
*
15273954 AATCAGTAACAGTAACAGTA
1 AATCGGTAACAGTAACAGTA
15273974 GTCGGCACAT
Statistics
Matches: 179, Mismatches: 21, Indels: 0
0.89 0.10 0.00
Matches are distributed among these distances:
45 179 1.00
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.19
Consensus pattern (45 bp):
AATCGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
Found at i:15276996 original size:21 final size:21
Alignment explanation
Indices: 15276953--15276998 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
15276943 TAATTATTTT
** *
15276953 ACCTTGAACCTTAAACCTTAA
1 ACCTTGAACCCCAAACCTCAA
*
15276974 ACCTTGAACCCCAAATCTCAA
1 ACCTTGAACCCCAAACCTCAA
15276995 ACCT
1 ACCT
15276999 CGAGATTTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.35, G:0.04, T:0.24
Consensus pattern (21 bp):
ACCTTGAACCCCAAACCTCAA
Found at i:15287511 original size:39 final size:39
Alignment explanation
Indices: 15287468--15287584 Score: 198
Period size: 39 Copynumber: 3.0 Consensus size: 39
15287458 CAAACTTAGG
*
15287468 TATAATCACATAACATTTAAGCATATATCACAATACTCA
1 TATAATCACATAACATTCAAGCATATATCACAATACTCA
* *
15287507 TATAATCACATGACATTCAAGCATATATCATAATACTCA
1 TATAATCACATAACATTCAAGCATATATCACAATACTCA
*
15287546 TATAATCACATAACATTCAAGCATAAATCACAATACTCA
1 TATAATCACATAACATTCAAGCATATATCACAATACTCA
15287585 AAAACATGTT
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 72 1.00
ACGTcount: A:0.46, C:0.21, G:0.03, T:0.29
Consensus pattern (39 bp):
TATAATCACATAACATTCAAGCATATATCACAATACTCA
Found at i:15289168 original size:19 final size:20
Alignment explanation
Indices: 15289129--15289168 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
15289119 AAGTTTTGAC
15289129 TCTAGTCCTATTTTCAAAAA
1 TCTAGTCCTATTTTCAAAAA
15289149 TCTAGTCCTATTTT-AAAAA
1 TCTAGTCCTATTTTCAAAAA
15289168 T
1 T
15289169 TTTAAAATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.35, C:0.17, G:0.05, T:0.42
Consensus pattern (20 bp):
TCTAGTCCTATTTTCAAAAA
Found at i:15289178 original size:27 final size:27
Alignment explanation
Indices: 15289145--15289196 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
15289135 CCTATTTTCA
15289145 AAAATCTAGTCCTATTTTAAAAATTTT
1 AAAATCTAGTCCTATTTTAAAAATTTT
*
15289172 AAAATCTAGTCCTATTTTCAAAATT
1 AAAATCTAGTCCTATTTTAAAAATT
15289197 AAAGGTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.42
Consensus pattern (27 bp):
AAAATCTAGTCCTATTTTAAAAATTTT
Found at i:15289802 original size:23 final size:23
Alignment explanation
Indices: 15289776--15289819 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
15289766 TCAAATTTGT
15289776 TTTATTAATATATTACTTAGATA
1 TTTATTAATATATTACTTAGATA
* * *
15289799 TTTATTATTATTTTATTTAGA
1 TTTATTAATATATTACTTAGA
15289820 AAATGGTAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (23 bp):
TTTATTAATATATTACTTAGATA
Found at i:15290168 original size:12 final size:12
Alignment explanation
Indices: 15290153--15290178 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
15290143 AATATATTAA
15290153 GTTAAATATGTT
1 GTTAAATATGTT
15290165 GTTAAATATGTT
1 GTTAAATATGTT
15290177 GT
1 GT
15290179 AAGTGAGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (12 bp):
GTTAAATATGTT
Found at i:15291077 original size:2 final size:2
Alignment explanation
Indices: 15291070--15291114 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
15291060 AAATATTCTA
* *
15291070 AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT TT 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
15291112 AT A
1 AT A
15291115 AAGGATGACG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:15297726 original size:17 final size:18
Alignment explanation
Indices: 15297699--15297733 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
15297689 TATAGATAGG
*
15297699 ATTTTTAATTTTTTTTTA
1 ATTTTTAATTTTCTTTTA
15297717 ATTTTT-ATTTTCTTTTA
1 ATTTTTAATTTTCTTTTA
15297734 GGTCGTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (18 bp):
ATTTTTAATTTTCTTTTA
Found at i:15304484 original size:23 final size:22
Alignment explanation
Indices: 15304441--15304484 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
15304431 TTCTAAGTCG
15304441 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
15304464 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
15304485 TTACTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:15304594 original size:45 final size:45
Alignment explanation
Indices: 15304530--15304617 Score: 140
Period size: 45 Copynumber: 2.0 Consensus size: 45
15304520 ACAGATACTC
* * *
15304530 GGTGGATTCAGTACATAGCAACCACCTTATTAATCAATGATGTCT
1 GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCT
*
15304575 GGTGGAATCAGCACATAGCAACCACCTTACTAATTAATGATGT
1 GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
15304618 TCGGTTCACA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.28
Consensus pattern (45 bp):
GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCT
Found at i:15304686 original size:51 final size:49
Alignment explanation
Indices: 15304628--15304814 Score: 196
Period size: 51 Copynumber: 3.7 Consensus size: 49
15304618 TCGGTTCACA
* * *
15304628 TAGTAGCCTGCACATAGTACTATACATGTGACCATTACCATCCGAAACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCA-TACCATCCG-TACACG
* * * * * * * *
15304679 TAGTAGCCTACACATAGTAGTACACACGTGATCGAAACTATCTGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATACCATC-CGTACACG
* *
15304730 TAGTAGCCTGCACATAGTACTACACATGTGACC-TATCATTCCTGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATACCA-TCC-GTACACG
15304780 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
15304815 CACTTTCACT
Statistics
Matches: 109, Mismatches: 22, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
49 2 0.02
50 40 0.37
51 64 0.59
52 3 0.03
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.25
Consensus pattern (49 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATACCATCCGTACACG
Found at i:15304810 original size:101 final size:101
Alignment explanation
Indices: 15304626--15304810 Score: 284
Period size: 101 Copynumber: 1.8 Consensus size: 101
15304616 GTTCGGTTCA
*
15304626 CATAGTAGCCTGCACATAGTACTATACATGTGACCATTACCATCCGAAACACGTAGTAGCCTACA
1 CATAGTAGCCTGCACATAGTACTACACATGTGACCA-TACCATCCGAAACACGTAGTAGCCTACA
*
15304691 CATAGTAGTACACACGTGATCGAAACTATCTGGTACG
65 CATAGTACTACACACGTGATCGAAACTATCTGGTACG
* * *
15304728 CATAGTAGCCTGCACATAGTACTACACATGTGACC-TATCATTCCTG-TACACGTAGTAGCCTGC
1 CATAGTAGCCTGCACATAGTACTACACATGTGACCATACCA-TCC-GAAACACGTAGTAGCCTAC
15304791 ACATAGTACTACACACGTGA
64 ACATAGTACTACACACGTGA
15304811 CCATCACTTT
Statistics
Matches: 76, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
100 4 0.05
101 37 0.49
102 35 0.46
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.24
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGTGACCATACCATCCGAAACACGTAGTAGCCTACAC
ATAGTACTACACACGTGATCGAAACTATCTGGTACG
Found at i:15315369 original size:28 final size:27
Alignment explanation
Indices: 15315285--15315371 Score: 93
Period size: 28 Copynumber: 3.1 Consensus size: 27
15315275 CAGTAACAGA
*
15315285 ACAGAACAATGTGGGCTTTAGCCCAAT
1 ACAGAACAATGTGGGCCTTAGCCCAAT
* * * *
15315312 ATAGAAACAAGGTGAGCCTTAGCCTAAT
1 ACAG-AACAATGTGGGCCTTAGCCCAAT
* *
15315340 ACATGAACAATGTGGGCCTAAGCCCGAT
1 ACA-GAACAATGTGGGCCTTAGCCCAAT
15315368 ACAG
1 ACAG
15315372 TATCAGTATG
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
27 4 0.09
28 42 0.89
29 1 0.02
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.20
Consensus pattern (27 bp):
ACAGAACAATGTGGGCCTTAGCCCAAT
Found at i:15315760 original size:27 final size:26
Alignment explanation
Indices: 15315727--15316115 Score: 357
Period size: 27 Copynumber: 14.5 Consensus size: 26
15315717 GGGCAAAACA
**
15315727 GTCATTTTACCCTTTGAGGGTATTACG
1 GTCATTTTACCC-TACAGGGTATTACG
* *
15315754 GTTATTTTATCCTACAGGGGTATTACG
1 GTCATTTTACCCTACA-GGGTATTACG
* * *
15315781 ATTATTTTACCCTACAGGGGTATTATG
1 GTCATTTTACCCTACA-GGGTATTACG
* *
15315808 GTCATTTTACCCTATAGGGGTATTACA
1 GTCATTTTACCCTACA-GGGTATTACG
* * *
15315835 GTTATTTTACCCTACAAGGGCATTATG
1 GTCATTTTACCCTAC-AGGGTATTACG
* * * *
15315862 GTTATTTTACACTATAGGGCATTACG
1 GTCATTTTACCCTACAGGGTATTACG
* * *
15315888 ATCACTTTACCCTGCAGGGGTATTACG
1 GTCATTTTACCCTACA-GGGTATTACG
* *
15315915 ATCATTTTACCCTACAAGGGCATTACG
1 GTCATTTTACCCTAC-AGGGTATTACG
* * *
15315942 TTCACTTTACCCTACAGAGGTATTACA
1 GTCATTTTACCCTACAG-GGTATTACG
* *
15315969 GTCATTTTACCCTATAGGGGTATTATG
1 GTCATTTTACCCTACA-GGGTATTACG
* *
15315996 GTCGTTTTACCCTACAGAGGTATTACA
1 GTCATTTTACCCTACAG-GGTATTACG
* *
15316023 ATCATTTTACCCTACAGGGGAATTACG
1 GTCATTTTACCCTACA-GGGTATTACG
*
15316050 ATCATTTTACCCTACAGGGTATTACG
1 GTCATTTTACCCTACAGGGTATTACG
* * *
15316076 GTTAGTTTACCCTACAGGGGTATTATG
1 GTCATTTTACCCTACA-GGGTATTACG
15316103 GTCA-TTTACCCTA
1 GTCATTTTACCCTA
15316116 TGGGGGTCTT
Statistics
Matches: 300, Mismatches: 53, Indels: 19
0.81 0.14 0.05
Matches are distributed among these distances:
26 56 0.19
27 240 0.80
28 4 0.01
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (26 bp):
GTCATTTTACCCTACAGGGTATTACG
Found at i:15315802 original size:54 final size:54
Alignment explanation
Indices: 15315744--15316115 Score: 401
Period size: 54 Copynumber: 6.9 Consensus size: 54
15315734 TACCCTTTGA
* * *
15315744 GGGTATTACGGTTATTTTATCCTACAGGGGTATTACGATTATTTTACCCTACAG
1 GGGTATTACGGTCATTTTACCCTACAGGGGTATTACGATCATTTTACCCTACAG
* * * *
15315798 GGGTATTATGGTCATTTTACCCTATAGGGGTATTAC-AGTTATTTTACCCTACAA
1 GGGTATTACGGTCATTTTACCCTACAGGGGTATTACGA-TCATTTTACCCTACAG
* * * * * * * *
15315852 GGGCATTATGGTTATTTTACACTATA-GGGCATTACGATCACTTTACCCTGCAG
1 GGGTATTACGGTCATTTTACCCTACAGGGGTATTACGATCATTTTACCCTACAG
* * * * *
15315905 GGGTATTACGATCATTTTACCCTACAAGGGCATTACGTTCACTTTACCCTACAG
1 GGGTATTACGGTCATTTTACCCTACAGGGGTATTACGATCATTTTACCCTACAG
* * * * * *
15315959 AGGTATTACAGTCATTTTACCCTATAGGGGTATTATGGTCGTTTTACCCTACAG
1 GGGTATTACGGTCATTTTACCCTACAGGGGTATTACGATCATTTTACCCTACAG
* ** *
15316013 AGGTATTACAATCATTTTACCCTACAGGGGAATTACGATCATTTTACCCTACA-
1 GGGTATTACGGTCATTTTACCCTACAGGGGTATTACGATCATTTTACCCTACAG
* * * *
15316066 GGGTATTACGGTTAGTTTACCCTACAGGGGTATTATGGTCA-TTTACCCTA
1 GGGTATTACGGTCATTTTACCCTACAGGGGTATTACGATCATTTTACCCTA
15316116 TGGGGGTCTT
Statistics
Matches: 270, Mismatches: 45, Indels: 8
0.84 0.14 0.02
Matches are distributed among these distances:
52 9 0.03
53 74 0.27
54 187 0.69
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (54 bp):
GGGTATTACGGTCATTTTACCCTACAGGGGTATTACGATCATTTTACCCTACAG
Found at i:15315840 original size:81 final size:81
Alignment explanation
Indices: 15315727--15316100 Score: 414
Period size: 81 Copynumber: 4.6 Consensus size: 81
15315717 GGGCAAAACA
* *
15315727 GTCATTTTACCCT-TTGAGGGTATTACGGTTATTTTATCCTACAGGGGTATTACGATTATTTTAC
1 GTCATTTTACCCTATAG-GGGTATTACGGTTATTTTACCCTACAGGGGTATTACGATTATTTTAC
*
15315791 CCTACAGGGGTATTATG
65 CCTACAGGGGTATTACG
* * * * * *
15315808 GTCATTTTACCCTATAGGGGTATTACAGTTATTTTACCCTACAAGGGCATTATGGTTATTTTACA
1 GTCATTTTACCCTATAGGGGTATTACGGTTATTTTACCCTACAGGGGTATTACGATTATTTTACC
* *
15315873 CTATA-GGGCATTACG
66 CTACAGGGGTATTACG
* * ** * * * * *
15315888 ATCACTTTACCCTGCAGGGGTATTACGATCATTTTACCCTACAAGGGCATTACG-TTCACTTTAC
1 GTCATTTTACCCTATAGGGGTATTACGGTTATTTTACCCTACAGGGGTATTACGATT-ATTTTAC
* *
15315952 CCTACAGAGGTATTACA
65 CCTACAGGGGTATTACG
* ** * * *
15315969 GTCATTTTACCCTATAGGGGTATTATGGTCGTTTTACCCTACAGAGGTATTACAATCATTTTACC
1 GTCATTTTACCCTATAGGGGTATTACGGTTATTTTACCCTACAGGGGTATTACGATTATTTTACC
*
15316034 CTACAGGGGAATTACG
66 CTACAGGGGTATTACG
* * *
15316050 ATCATTTTACCCTACA-GGGTATTACGGTTAGTTTACCCTACAGGGGTATTA
1 GTCATTTTACCCTATAGGGGTATTACGGTTATTTTACCCTACAGGGGTATTA
15316101 TGGTCATTTA
Statistics
Matches: 241, Mismatches: 48, Indels: 9
0.81 0.16 0.03
Matches are distributed among these distances:
79 2 0.01
80 94 0.39
81 142 0.59
82 3 0.01
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (81 bp):
GTCATTTTACCCTATAGGGGTATTACGGTTATTTTACCCTACAGGGGTATTACGATTATTTTACC
CTACAGGGGTATTACG
Found at i:15315915 original size:134 final size:134
Alignment explanation
Indices: 15315759--15316115 Score: 457
Period size: 134 Copynumber: 2.7 Consensus size: 134
15315749 TTACGGTTAT
* * * * *
15315759 TTTATCCTACAGGGGTATTACGATTATTTTACCCTACAGGGGTATTATGGTCATTTTACCCTATA
1 TTTACCCTACAGGGGTATTACGATCATTTTACCCTACA-GGGTATTACGGTCACTTTACCCTACA
* * * *
15315824 GGGGTATTACAGTTATTTTACCCTACAAGGGCATTATGGTTATTTTACACTATAG-GGCATTACG
65 GGGGTATTACAGTCATTTTACCCTACAAGGGCATTATGGTCATTTTACACTACAGAGGCATTACA
15315888 ATCAC
130 ATCAC
* * *
15315893 TTTACCCTGCAGGGGTATTACGATCATTTTACCCTACAAGGGCATTACGTTCACTTTACCCTACA
1 TTTACCCTACAGGGGTATTACGATCATTTTACCCTAC-AGGGTATTACGGTCACTTTACCCTACA
* * * * * * *
15315958 GAGGTATTACAGTCATTTTACCCTATAGGGGTATTATGGTCGTTTTACCCTACAGAGGTATTACA
65 GGGGTATTACAGTCATTTTACCCTACAAGGGCATTATGGTCATTTTACACTACAGAGGCATTACA
*
15316023 ATCAT
130 ATCAC
* * *
15316028 TTTACCCTACAGGGGAATTACGATCATTTTACCCTACAGGGTATTACGGTTAGTTTACCCTACAG
1 TTTACCCTACAGGGGTATTACGATCATTTTACCCTACAGGGTATTACGGTCACTTTACCCTACAG
**
15316093 GGGTATTATGGTCA-TTTACCCTA
66 GGGTATTACAGTCATTTTACCCTA
15316116 TGGGGGTCTT
Statistics
Matches: 192, Mismatches: 29, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
133 9 0.05
134 136 0.71
135 47 0.24
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.35
Consensus pattern (134 bp):
TTTACCCTACAGGGGTATTACGATCATTTTACCCTACAGGGTATTACGGTCACTTTACCCTACAG
GGGTATTACAGTCATTTTACCCTACAAGGGCATTATGGTCATTTTACACTACAGAGGCATTACAA
TCAC
Found at i:15316022 original size:188 final size:188
Alignment explanation
Indices: 15315728--15316115 Score: 485
Period size: 188 Copynumber: 2.1 Consensus size: 188
15315718 GGCAAAACAG
*** * * * * *
15315728 TCATTTTACCCTTTGAGGGTATTACGGTTATTTTATCCTACAGGGGTATTACGATTATTTTACCC
1 TCATTTTACCCTACAAGGGCATTACGGTTACTTTACCCTACAGAGGTATTACGATCATTTTACCC
* * * * *
15315793 TACAGGGGTATTATGGTCATTTTACCCTATAGGGGTATTACAGTTATTTTACCCTACAAGGGCAT
66 TACAGGGGTATTATGGTCATTTTACCCTACAGAGGTATTACAATCATTTTACCCTACAAGGGAAT
* * * * *
15315858 TATGGTTATTTTACACTATAGGGCATTACGATCACTTTACCCTGCAGGGGTATTACGA
131 TACGATCATTTTACACTACAGGGCATTACGATCACTTTACCCTACAGGGGTATTACGA
15315916 TCATTTTACCCTACAAGGGCATTAC-GTTCACTTTACCCTACAGAGGTATTAC-AGTCATTTTAC
1 TCATTTTACCCTACAAGGGCATTACGGTT-ACTTTACCCTACAGAGGTATTACGA-TCATTTTAC
* * *
15315979 CCTATAGGGGTATTATGGTCGTTTTACCCTACAGAGGTATTACAATCATTTTACCCTACAGGGGA
64 CCTACAGGGGTATTATGGTCATTTTACCCTACAGAGGTATTACAATCATTTTACCCTACAAGGGA
* * * * * * *
15316044 ATTACGATCATTTTACCCTACAGGGTATTACGGTTAGTTTACCCTACAGGGGTATTATGG
129 ATTACGATCATTTTACACTACAGGGCATTACGATCACTTTACCCTACAGGGGTATTACGA
15316104 TCA-TTTACCCTA
1 TCATTTTACCCTA
15316116 TGGGGGTCTT
Statistics
Matches: 170, Mismatches: 28, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
187 13 0.08
188 157 0.92
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (188 bp):
TCATTTTACCCTACAAGGGCATTACGGTTACTTTACCCTACAGAGGTATTACGATCATTTTACCC
TACAGGGGTATTATGGTCATTTTACCCTACAGAGGTATTACAATCATTTTACCCTACAAGGGAAT
TACGATCATTTTACACTACAGGGCATTACGATCACTTTACCCTACAGGGGTATTACGA
Found at i:15318472 original size:37 final size:37
Alignment explanation
Indices: 15318417--15318658 Score: 201
Period size: 37 Copynumber: 6.6 Consensus size: 37
15318407 AGTACACAAG
* * *
15318417 TAATCCAAC-CGA-AACATGCCAATCGCTCATAAGAGC
1 TAATCC-ACTCGATAACACGCCAAACACTCATAAGAGC
*
15318453 TAATCCACTCGATAACATGCCAAACACTCATAA-ATGC
1 TAATCCACTCGATAACACGCCAAACACTCATAAGA-GC
** * **
15318490 TAATCCACTATATAACACACCAAATGCTCATAAGAGC
1 TAATCCACTCGATAACACGCCAAACACTCATAAGAGC
* * *
15318527 CAATCCAACT-GATAACATGCCAAACGCTCATAAGAGC
1 TAATCC-ACTCGATAACACGCCAAACACTCATAAGAGC
* * *
15318564 TAATTCAACT-GATAACACGCTAAACACTCATAAGAGT
1 TAA-TCCACTCGATAACACGCCAAACACTCATAAGAGC
* * * * *
15318601 TAATCCAATCGA-AACACACCAATCATTCATAAGATC
1 TAATCCACTCGATAACACGCCAAACACTCATAAGAGC
*
15318637 TAATCCAACT-AATAACACGCCA
1 TAATCC-ACTCGATAACACGCCA
15318659 TGGCACTAAC
Statistics
Matches: 167, Mismatches: 30, Indels: 17
0.78 0.14 0.08
Matches are distributed among these distances:
35 2 0.01
36 39 0.23
37 120 0.72
38 6 0.04
ACGTcount: A:0.42, C:0.28, G:0.10, T:0.20
Consensus pattern (37 bp):
TAATCCACTCGATAACACGCCAAACACTCATAAGAGC
Found at i:15318498 original size:18 final size:19
Alignment explanation
Indices: 15318429--15318498 Score: 58
Period size: 18 Copynumber: 3.8 Consensus size: 19
15318419 ATCCAACCGA
* *
15318429 AACATGCCAAT-CGCTCAT
1 AACATGCTAATCCACTCAT
*
15318447 AAGA-GCTAATCCACTCGAT
1 AACATGCTAATCCACTC-AT
* *
15318466 AACATGCCAA-ACACTCAT
1 AACATGCTAATCCACTCAT
15318484 AA-ATGCTAATCCACT
1 AACATGCTAATCCACT
15318499 ATATAACACA
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
17 11 0.28
18 15 0.38
19 10 0.25
20 4 0.10
ACGTcount: A:0.39, C:0.30, G:0.10, T:0.21
Consensus pattern (19 bp):
AACATGCTAATCCACTCAT
Found at i:15318579 original size:74 final size:75
Alignment explanation
Indices: 15318435--15318654 Score: 222
Period size: 74 Copynumber: 3.0 Consensus size: 75
15318425 CCGAAACATG
* *
15318435 CCAATCGCTCATAAGAGCTAATCC-ACTCGATAACATGCCAAACACTCATAAATGCTAATCCACT
1 CCAAACGCTCATAAGAGCTAATCCAACTCGATAACATGCCAAACACTCATAAATGCTAATCAACT
*
15318499 ATATAACACA
66 AGATAACACA
* * *
15318509 CCAAATGCTCATAAGAGCCAATCCAACT-GATAACATGCCAAACGCTCATAAGA-GCTAATTCAA
1 CCAAACGCTCATAAGAGCTAATCCAACTCGATAACATGCCAAACACTCATAA-ATGCTAA-TCAA
*
15318572 CT-GATAACACG
64 CTAGATAACACA
* * * ** * *
15318583 CTAAACACTCATAAGAGTTAATCCAA-TCGA-AACACACCAATCATTCATAAGAT-CTAATCCAA
1 CCAAACGCTCATAAGAGCTAATCCAACTCGATAACATGCCAAACACTCATAA-ATGCTAAT-CAA
15318645 CTA-ATAACAC
64 CTAGATAACAC
15318655 GCCATGGCAC
Statistics
Matches: 122, Mismatches: 17, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
72 1 0.01
73 34 0.28
74 78 0.64
75 9 0.07
ACGTcount: A:0.42, C:0.28, G:0.09, T:0.21
Consensus pattern (75 bp):
CCAAACGCTCATAAGAGCTAATCCAACTCGATAACATGCCAAACACTCATAAATGCTAATCAACT
AGATAACACA
Found at i:15321098 original size:26 final size:26
Alignment explanation
Indices: 15321068--15321144 Score: 82
Period size: 26 Copynumber: 2.9 Consensus size: 26
15321058 TTTTTCATCC
* *
15321068 CTATTTTACCCCCAGTAAATTTTTTA
1 CTATTTTACCCCCAGTAAAATTTTAA
* *
15321094 CTATTTTACTCCCGGTAAAAATTTTAA
1 CTATTTTACCCCCAGT-AAAATTTTAA
* * *
15321121 CAATTTTATCCCTAGTAAAATTTT
1 CTATTTTACCCCCAGTAAAATTTT
15321145 GAGAAAACAT
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
26 22 0.54
27 19 0.46
ACGTcount: A:0.31, C:0.19, G:0.05, T:0.44
Consensus pattern (26 bp):
CTATTTTACCCCCAGTAAAATTTTAA
Found at i:15321305 original size:12 final size:12
Alignment explanation
Indices: 15321290--15321314 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
15321280 TGCAAATAGA
15321290 TCATTTCCATTT
1 TCATTTCCATTT
15321302 TCATTTCCATTT
1 TCATTTCCATTT
15321314 T
1 T
15321315 TGGAAGCCTA
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:0.24, G:0.00, T:0.60
Consensus pattern (12 bp):
TCATTTCCATTT
Found at i:15321916 original size:16 final size:16
Alignment explanation
Indices: 15321895--15321943 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
15321885 CGACAACTTG
15321895 GCTCAAGGAAAAGCTA
1 GCTCAAGGAAAAGCTA
* *
15321911 GCTCAA-CAACAATCTA
1 GCTCAAGGAA-AAGCTA
15321927 GCTCAAGGAAAAGCTA
1 GCTCAAGGAAAAGCTA
15321943 G
1 G
15321944 ATTGCTCAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 2 0.07
16 23 0.85
17 2 0.07
ACGTcount: A:0.43, C:0.22, G:0.20, T:0.14
Consensus pattern (16 bp):
GCTCAAGGAAAAGCTA
Found at i:15334730 original size:50 final size:51
Alignment explanation
Indices: 15334664--15335003 Score: 393
Period size: 51 Copynumber: 6.7 Consensus size: 51
15334654 TATCATTCGA
* *
15334664 TACACGTAGTAACCTTCACATAGTACTACACACGTGATCAAGTTTTA-CGG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTATCGG
* *
15334714 TTCACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTA-CGG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTATCGG
* * * *
15334764 TTCACGTAGTAGCCTTCACATAGTACTATACACGTGACCAAAGCTTT-CCGG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACC-AAGTTTTATCGG
* * * *** *
15334815 TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGA
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTATCGG
* *
15334866 TTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAG-TTTATCGG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACC-AAGTTTTATCGG
* * * * * * *
15334917 TACACATTGTAGCCTTCACTTAGTACTACACATGTGACC-ATTATTTAGCGA
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGT-TTTATCGG
*
15334968 TACACGTAGTAGCCTTCACACAGTACTACACACGTG
1 TACACGTAGTAGCCTTCACATAGTACTACACACGTG
15335004 TTCATCGATA
Statistics
Matches: 247, Mismatches: 37, Indels: 11
0.84 0.13 0.04
Matches are distributed among these distances:
49 1 0.00
50 89 0.36
51 156 0.63
52 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.29
Consensus pattern (51 bp):
TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTATCGG
Found at i:15334885 original size:102 final size:101
Alignment explanation
Indices: 15334660--15335003 Score: 467
Period size: 102 Copynumber: 3.4 Consensus size: 101
15334650 CTTTTATCAT
* * * * *
15334660 TCGATACACGTAGTAACCTTCACATAGTACTACACACGTGATC-AAGTTTTACGGTTCACGTAGT
1 TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAG-TTTACGGTACACATAGT
* * * ***
15334724 AGCCTTCACATAGTACTACACACGTGATCAAGTTTTA
65 AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
* * * * *
15334761 -CGGTTCACGTAGTAGCCTTCACATAGTACTATACACGTGACCAAAGCTTTCCGGTACACATAGT
1 TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAG-TTTACGGTACACATAGT
15334825 AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
65 AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
* *
15334862 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGTTTATCGGTACACATTGT
1 TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGTTTA-CGGTACACATAGT
*
15334927 AGCCTTCACTTAGTACTACACATGTGACCATTATTTA
65 AGCCTTCACTTAGTACTACACATGTGACCATCATTTA
*
15334964 GCGATACACGTAGTAGCCTTCACACAGTACTACACACGTG
1 TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTG
15335004 TTCATCGATA
Statistics
Matches: 217, Mismatches: 23, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
100 37 0.17
101 51 0.24
102 129 0.59
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (101 bp):
TCGATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGTTTACGGTACACATAGTA
GCCTTCACTTAGTACTACACATGTGACCATCATTTA
Found at i:15341304 original size:19 final size:19
Alignment explanation
Indices: 15341280--15341327 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
15341270 TCATCCCTAC
15341280 ATCCCTCATCCTTTACTCA
1 ATCCCTCATCCTTTACTCA
15341299 ATCCCTCATCCTTTACTCA
1 ATCCCTCATCCTTTACTCA
15341318 ATCCCTCATC
1 ATCCCTCATC
15341328 TTTCATTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.21, C:0.44, G:0.00, T:0.35
Consensus pattern (19 bp):
ATCCCTCATCCTTTACTCA
Found at i:15341384 original size:8 final size:8
Alignment explanation
Indices: 15341341--15341378 Score: 76
Period size: 8 Copynumber: 4.8 Consensus size: 8
15341331 CATTTCATAT
15341341 CATTCTTC
1 CATTCTTC
15341349 CATTCTTC
1 CATTCTTC
15341357 CATTCTTC
1 CATTCTTC
15341365 CATTCTTC
1 CATTCTTC
15341373 CATTCT
1 CATTCT
15341379 CTCATTTCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.13, C:0.37, G:0.00, T:0.50
Consensus pattern (8 bp):
CATTCTTC
Found at i:15354451 original size:29 final size:29
Alignment explanation
Indices: 15354418--15354538 Score: 206
Period size: 29 Copynumber: 4.2 Consensus size: 29
15354408 ACTATCGAGC
15354418 CCATCGAATATGAAAAGGGATGGTTTCGA
1 CCATCGAATATGAAAAGGGATGGTTTCGA
*
15354447 CCATCGAATATGAAAAAGGATGGTTTCGA
1 CCATCGAATATGAAAAGGGATGGTTTCGA
*
15354476 CCATCGAATATGAAAAGGGATGGTTTTGA
1 CCATCGAATATGAAAAGGGATGGTTTCGA
* *
15354505 CCATAGAATAAGAAAAGGGATGGTTTCGA
1 CCATCGAATATGAAAAGGGATGGTTTCGA
15354534 CCATC
1 CCATC
15354539 ATTTAGCACA
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 85 1.00
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.24
Consensus pattern (29 bp):
CCATCGAATATGAAAAGGGATGGTTTCGA
Found at i:15357554 original size:24 final size:23
Alignment explanation
Indices: 15357527--15357576 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
15357517 CAATAACAAT
*
15357527 ATGCAGAAAATTCTGCCAGTAAAA
1 ATGCAGAAAA-GCTGCCAGTAAAA
* *
15357551 ATGCAGACAAGCTGCTAGTAAAA
1 ATGCAGAAAAGCTGCCAGTAAAA
15357574 ATG
1 ATG
15357577 TAATAAATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.44, C:0.16, G:0.20, T:0.20
Consensus pattern (23 bp):
ATGCAGAAAAGCTGCCAGTAAAA
Found at i:15361426 original size:15 final size:14
Alignment explanation
Indices: 15361389--15361424 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
15361379 AAAAATTTCT
15361389 AAAATTTATGATAA
1 AAAATTTATGATAA
*
15361403 AAAAGTTTATTATAA
1 AAAA-TTTATGATAA
15361418 AAAATTT
1 AAAATTT
15361425 TACATGTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.39
Consensus pattern (14 bp):
AAAATTTATGATAA
Found at i:15367721 original size:21 final size:20
Alignment explanation
Indices: 15367690--15367738 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
15367680 TCAAAAACAT
15367690 TAAAAATTATTAAATAATTA
1 TAAAAATTATTAAATAATTA
*
15367710 TAAAAATATATTAAATGATTA
1 TAAAAAT-TATTAAATAATTA
15367731 TAGAAAAT
1 TA-AAAAT
15367739 CATAAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 7 0.27
21 14 0.54
22 5 0.19
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (20 bp):
TAAAAATTATTAAATAATTA
Found at i:15367723 original size:31 final size:31
Alignment explanation
Indices: 15367688--15367751 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
15367678 ATTCAAAAAC
*
15367688 ATTAAA-AATTATTA-AATAATTATAAAAATAT
1 ATTAAATAATTA-TAGAA-AATCATAAAAATAT
*
15367719 ATTAAATGATTATAGAAAATCATAAAAATAT
1 ATTAAATAATTATAGAAAATCATAAAAATAT
15367750 AT
1 AT
15367752 GTCTTTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 23 0.79
32 6 0.21
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (31 bp):
ATTAAATAATTATAGAAAATCATAAAAATAT
Found at i:15367814 original size:25 final size:27
Alignment explanation
Indices: 15367756--15367816 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 27
15367746 ATATATGTCT
*
15367756 TTTTTAAAAATATATAAAAATATTAAA
1 TTTTAAAAAATATATAAAAATATTAAA
* *
15367783 -GTGAAAAAAT-TATAAAAATA-TAAA
1 TTTTAAAAAATATATAAAAATATTAAA
15367807 TTTTAAAAAA
1 TTTTAAAAAA
15367817 ATTTATTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
24 4 0.14
25 17 0.61
26 7 0.25
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (27 bp):
TTTTAAAAAATATATAAAAATATTAAA
Found at i:15367836 original size:26 final size:26
Alignment explanation
Indices: 15367757--15367829 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 26
15367747 TATATGTCTT
*
15367757 TTTTAAAAATA-TATAAAAATATTAAA
1 TTTTAAAAAAATTATAAAAATA-TAAA
* *
15367783 --GTGAAAAAATTATAAAAATATAAA
1 TTTTAAAAAAATTATAAAAATATAAA
15367807 TTTTAAAAAAATTTATTAAAAAT
1 TTTTAAAAAAA-TTA-TAAAAAT
15367830 GAATTTTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
24 10 0.27
25 10 0.27
26 7 0.19
27 3 0.08
28 7 0.19
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (26 bp):
TTTTAAAAAAATTATAAAAATATAAA
Found at i:15367927 original size:18 final size:19
Alignment explanation
Indices: 15367898--15367946 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
15367888 ATAAATTATG
15367898 AAAAATA-A-AAAAATG-T
1 AAAAATATAGAAAAATGTT
15367914 AAAAATATAGAAAAATGTT
1 AAAAATATAGAAAAATGTT
*
15367933 TAAAATATAGAAAA
1 AAAAATATAGAAAA
15367947 TTATTAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 7 0.24
17 1 0.03
18 7 0.24
19 14 0.48
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.22
Consensus pattern (19 bp):
AAAAATATAGAAAAATGTT
Found at i:15367947 original size:18 final size:19
Alignment explanation
Indices: 15367837--15367957 Score: 71
Period size: 18 Copynumber: 6.6 Consensus size: 19
15367827 AATGAATTTT
*
15367837 TTATATAAATTATAGAAAAA
1 TTAT-TAAAATATAGAAAAA
* *
15367857 TT-TTAAAAAAATTA-ATAAA
1 TTATT-AAAATA-TAGAAAAA
* *
15367876 TT-TT-AAATATATATAAA
1 TTATTAAAATATAGAAAAA
* *
15367893 TTATGAAAA-ATAAAAAAA
1 TTATTAAAATATAGAAAAA
15367911 TGTA--AAAATATAGAAAAA
1 T-TATTAAAATATAGAAAAA
15367929 TGT-TTAAAATATAG-AAAA
1 T-TATTAAAATATAGAAAAA
15367947 TTATTAAAATA
1 TTATTAAAATA
15367958 GAAAATTACA
Statistics
Matches: 83, Mismatches: 8, Indels: 22
0.73 0.07 0.19
Matches are distributed among these distances:
16 2 0.02
17 16 0.19
18 34 0.41
19 27 0.33
20 4 0.05
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (19 bp):
TTATTAAAATATAGAAAAA
Found at i:15368454 original size:14 final size:13
Alignment explanation
Indices: 15368435--15368467 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
15368425 TTTCATGATT
15368435 TATATTTTTTATAA
1 TATATTTTTT-TAA
15368449 TATA-TTTTTTAA
1 TATATTTTTTTAA
15368461 TATATTT
1 TATATTT
15368468 AATTTTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 7 0.39
13 7 0.39
14 4 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TATATTTTTTTAA
Found at i:15368463 original size:24 final size:24
Alignment explanation
Indices: 15368436--15368482 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
15368426 TTCATGATTT
* *
15368436 ATATTTTTTATAATATATTTTTTA
1 ATATATTTAATAATATATTTTTTA
**
15368460 ATATATTTAATTTTATATTTTTT
1 ATATATTTAATAATATATTTTTT
15368483 CATTTATAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (24 bp):
ATATATTTAATAATATATTTTTTA
Found at i:15368490 original size:26 final size:24
Alignment explanation
Indices: 15368449--15368507 Score: 57
Period size: 26 Copynumber: 2.4 Consensus size: 24
15368439 TTTTTTATAA
*
15368449 TATATTTTTTAATATATTTAA-TTT
1 TATATTTTTTAATATA-ATAATTTT
*
15368473 TATATTTTTTCATTTATAATAATTTT
1 TATATTTTTT-A-ATATAATAATTTT
*
15368499 TATAGTTTT
1 TATATTTTT
15368508 CTATATTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 10 0.34
25 4 0.14
26 15 0.52
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (24 bp):
TATATTTTTTAATATAATAATTTT
Found at i:15368621 original size:12 final size:12
Alignment explanation
Indices: 15368604--15368629 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
15368594 GTTTCTATGA
15368604 TTTTTTTATAAT
1 TTTTTTTATAAT
15368616 TTTTTTTATAAT
1 TTTTTTTATAAT
15368628 TT
1 TT
15368630 GTAACGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTTTATAAT
Found at i:15369406 original size:3 final size:3
Alignment explanation
Indices: 15369398--15369438 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
15369388 ATAACAACTT
15369398 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
15369439 TACTAGGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:15369643 original size:9 final size:9
Alignment explanation
Indices: 15369631--15369661 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
15369621 GTTAAACGAG
15369631 TCGAGTTAT
1 TCGAGTTAT
*
15369640 TCGAGTTAA
1 TCGAGTTAT
15369649 TCGAGTTAT
1 TCGAGTTAT
15369658 TCGA
1 TCGA
15369662 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:15369732 original size:9 final size:9
Alignment explanation
Indices: 15369715--15369751 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
15369705 TGAGTTTTCG
15369715 AATTCGAAT
1 AATTCGAAT
*
15369724 AACTCGAAT
1 AATTCGAAT
15369733 AATTCGAAT
1 AATTCGAAT
15369742 AATTCGAAT
1 AATTCGAAT
15369751 A
1 A
15369752 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:15374934 original size:14 final size:15
Alignment explanation
Indices: 15374915--15374945 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
15374905 AAGAAAAAAG
15374915 TTTCTTTC-TTTCTC
1 TTTCTTTCTTTTCTC
15374929 TTTCTTTCTTTTCTC
1 TTTCTTTCTTTTCTC
15374944 TT
1 TT
15374946 CATACGTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTCTTTCTTTTCTC
Found at i:15375544 original size:23 final size:23
Alignment explanation
Indices: 15375518--15375561 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
15375508 TTCTTACTGT
*
15375518 AGTAATTTTCGGGGTATTACAGC
1 AGTAATTTTCGGGATATTACAGC
15375541 AGTAATTTTCGGGATATTACA
1 AGTAATTTTCGGGATATTACA
15375562 CATATTATGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.36
Consensus pattern (23 bp):
AGTAATTTTCGGGATATTACAGC
Found at i:15376723 original size:12 final size:12
Alignment explanation
Indices: 15376706--15376733 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
15376696 GTTTTATTTA
15376706 TTTTCTTTCTTT
1 TTTTCTTTCTTT
15376718 TTTTCTTTCTTT
1 TTTTCTTTCTTT
15376730 TTTT
1 TTTT
15376734 TTTTTTGCCT
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:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTCTTTCTTT
Found at i:15376728 original size:16 final size:15
Alignment explanation
Indices: 15376706--15376739 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
15376696 GTTTTATTTA
15376706 TTTTCTTTCTTTTTT
1 TTTTCTTTCTTTTTT
15376721 TCTTTCTTT-TTTTTT
1 T-TTTCTTTCTTTTTT
15376736 TTTT
1 TTTT
15376740 GCCTTGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 3 0.17
15 8 0.44
16 7 0.39
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (15 bp):
TTTTCTTTCTTTTTT
Found at i:15377253 original size:5 final size:5
Alignment explanation
Indices: 15377239--15377290 Score: 72
Period size: 5 Copynumber: 10.8 Consensus size: 5
15377229 GGGTGAGTAT
* *
15377239 TTGA- TTGAG TTGAG TTGAG TTGAG TTGAG TTGAA TTGAG TT-AG TCGAG
1 TTGAG TTGAG TTGAG TTGAG TTGAG TTGAG TTGAG TTGAG TTGAG TTGAG
15377287 TTGA
1 TTGA
15377291 TGAATTATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
4 7 0.17
5 35 0.83
ACGTcount: A:0.23, C:0.02, G:0.35, T:0.40
Consensus pattern (5 bp):
TTGAG
Found at i:15383275 original size:9 final size:9
Alignment explanation
Indices: 15383261--15383410 Score: 68
Period size: 9 Copynumber: 16.6 Consensus size: 9
15383251 TTAAATAATT
15383261 TTTTTATAA
1 TTTTTATAA
15383270 -TTTT-T-A
1 TTTTTATAA
*
15383276 TTTTTCTAA
1 TTTTTATAA
15383285 TTTTTAATAA
1 TTTTT-ATAA
15383295 -TTTTATAA
1 TTTTTATAA
*
15383303 TTTATTA-GA
1 TTT-TTATAA
15383312 TTTTTAT--
1 TTTTTATAA
*
15383319 TATTTATAA
1 TTTTTATAA
15383328 GTTTTTATAA
1 -TTTTTATAA
**
15383338 GATTTA-AA
1 TTTTTATAA
15383346 TATTTTA-AA
1 T-TTTTATAA
15383355 TATGCTTTATTAA
1 T-T--TTTA-TAA
15383368 TTTTTTTATAA
1 --TTTTTATAA
*
15383379 TTTATTAGAA
1 TTT-TTATAA
15383389 -TTTTATAA
1 TTTTTATAA
*
15383397 ATTTTATAA
1 TTTTTATAA
15383406 TTTTT
1 TTTTT
15383411 TAAGTAAACT
Statistics
Matches: 111, Mismatches: 11, Indels: 38
0.69 0.07 0.24
Matches are distributed among these distances:
6 1 0.01
7 11 0.10
8 19 0.17
9 46 0.41
10 19 0.17
11 7 0.06
12 4 0.04
13 2 0.02
14 1 0.01
15 1 0.01
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:15383316 original size:18 final size:16
Alignment explanation
Indices: 15383261--15383337 Score: 75
Period size: 18 Copynumber: 4.6 Consensus size: 16
15383251 TTAAATAATT
15383261 TTTTTATAATTTTT-A
1 TTTTTATAATTTTTAA
*
15383276 TTTTTCTAATTTTTAA
1 TTTTTATAATTTTTAA
15383292 TAATTTTATAATTTATTAGA
1 T--TTTTATAATTT-TTA-A
* *
15383312 TTTTTATTATTTATAA
1 TTTTTATAATTTTTAA
15383328 GTTTTTATAA
1 -TTTTTATAA
15383338 GATTTAAATA
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
15 13 0.25
16 3 0.06
17 10 0.20
18 20 0.39
19 3 0.06
20 2 0.04
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (16 bp):
TTTTTATAATTTTTAA
Found at i:15383523 original size:31 final size:29
Alignment explanation
Indices: 15383455--15383526 Score: 90
Period size: 31 Copynumber: 2.4 Consensus size: 29
15383445 CTTAGGTTAT
*
15383455 ATTTTAGTCACTTATGTTTGAAATGTTAC
1 ATTTTAGTCACTTATGTTTGAAATGTAAC
* **
15383484 GTTTTAGTCACTTATGTTATCGATTTGTAAC
1 ATTTTAGTCACTTATGTT-T-GAAATGTAAC
15383515 ATTTTAGTCACT
1 ATTTTAGTCACT
15383527 GAGCCGTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
29 17 0.47
30 1 0.03
31 18 0.50
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.49
Consensus pattern (29 bp):
ATTTTAGTCACTTATGTTTGAAATGTAAC
Found at i:15383671 original size:13 final size:12
Alignment explanation
Indices: 15383653--15383696 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 12
15383643 GAGCAATTTA
15383653 ATTTTTTTCTTTT
1 ATTTTTTTC-TTT
*
15383666 ATTTTTTAACTTT
1 ATTTTTT-TCTTT
15383679 ATTTTTTTCCTTT
1 ATTTTTTT-CTTT
15383692 ATTTT
1 ATTTT
15383697 CCATTCCCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 26 0.96
14 1 0.04
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (12 bp):
ATTTTTTTCTTT
Found at i:15385660 original size:16 final size:16
Alignment explanation
Indices: 15385622--15385660 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
15385612 TGGCAGTAGC
* *
15385622 AAAGAAAGCAAAAACG
1 AAAGAAAGAAAAAACA
*
15385638 AATGAAAGAAAAAACA
1 AAAGAAAGAAAAAACA
15385654 AAAGAAA
1 AAAGAAA
15385661 AGAACTCAGC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.74, C:0.08, G:0.15, T:0.03
Consensus pattern (16 bp):
AAAGAAAGAAAAAACA
Found at i:15389732 original size:16 final size:16
Alignment explanation
Indices: 15389694--15389732 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
15389684 TGGCAGTAGC
* *
15389694 AAAGAAAGCAAAAACG
1 AAAGAAAGAAAAAACA
*
15389710 AATGAAAGAAAAAACA
1 AAAGAAAGAAAAAACA
15389726 AAAGAAA
1 AAAGAAA
15389733 AGAACTCAGC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.74, C:0.08, G:0.15, T:0.03
Consensus pattern (16 bp):
AAAGAAAGAAAAAACA
Found at i:15405785 original size:13 final size:13
Alignment explanation
Indices: 15405767--15405794 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
15405757 AGAGATAGGG
15405767 AATTAAAATTTAA
1 AATTAAAATTTAA
15405780 AATTAAAATTTAA
1 AATTAAAATTTAA
15405793 AA
1 AA
15405795 GCTGAAAGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AATTAAAATTTAA
Found at i:15406638 original size:11 final size:11
Alignment explanation
Indices: 15406622--15406728 Score: 61
Period size: 11 Copynumber: 10.4 Consensus size: 11
15406612 TTATTTTTAA
15406622 TTTTAAAATAC
1 TTTTAAAATAC
15406633 TTTTAAAATAC
1 TTTTAAAATAC
15406644 TTTTATTAAAT--
1 TTTTA--AAATAC
*
15406655 TTTTTAAAT--
1 TTTTAAAATAC
**
15406664 TTTT-AAATTT
1 TTTTAAAATAC
15406674 TTTTAAAATAC
1 TTTTAAAATAC
*
15406685 TTTTTAAAT--
1 TTTTAAAATAC
** *
15406694 TTTT--TTTAA
1 TTTTAAAATAC
*
15406703 TTTTAAAATAT
1 TTTTAAAATAC
15406714 TTTTAAAATAC
1 TTTTAAAATAC
15406725 TTTT
1 TTTT
15406729 TTTAATTTTT
Statistics
Matches: 77, Mismatches: 10, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
7 1 0.01
8 4 0.05
9 16 0.21
10 4 0.05
11 48 0.62
13 4 0.05
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:15406667 original size:10 final size:10
Alignment explanation
Indices: 15406644--15406706 Score: 60
Period size: 10 Copynumber: 6.4 Consensus size: 10
15406634 TTTAAAATAC
*
15406644 TTTTATTAAA
1 TTTTTTTAAA
15406654 -TTTTTTAAA
1 TTTTTTTAAA
15406663 --TTTTTAAA
1 TTTTTTTAAA
15406671 TTTTTTTAAAA
1 TTTTTTT-AAA
*
15406682 TACTTTTTAAA
1 T-TTTTTTAAA
*
15406693 TTTTTTTTAA
1 TTTTTTTAAA
15406703 TTTT
1 TTTT
15406707 AAAATATTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
8 8 0.18
9 8 0.18
10 16 0.36
11 8 0.18
12 5 0.11
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTTTTTAAA
Found at i:15406678 original size:41 final size:40
Alignment explanation
Indices: 15406615--15406762 Score: 181
Period size: 40 Copynumber: 3.5 Consensus size: 40
15406605 ATTTTTATTA
*
15406615 TTTTTAATTTTAAAATACTTTTAAAATACTTTTATTAAATT
1 TTTTTAATTTTAAAATATTTTTAAAATACTTTT-TTAAATT
* * *
15406656 TTTTAAATTTTTAAATTTTTTTAAAATAC-TTTTTAAATTT
1 TTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAAA-TT
*
15406696 TTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTT
1 TTTTTAATTTTAAAATATTTTTAAAATAC-TTTTTTAA-ATT
15406738 TATTTTAATTTTTAAAATAATTTTT
1 T-TTTTAA-TTTTAAAAT-ATTTTT
15406763 TGGTAATTAT
Statistics
Matches: 92, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
39 5 0.05
40 31 0.34
41 25 0.27
42 10 0.11
43 6 0.07
44 9 0.10
45 6 0.07
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (40 bp):
TTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAAATT
Found at i:15407165 original size:20 final size:21
Alignment explanation
Indices: 15407137--15407189 Score: 67
Period size: 19 Copynumber: 2.7 Consensus size: 21
15407127 AAAGTATAAA
*
15407137 TTTGGAATTTTTATAAA-TAT
1 TTTGAAATTTTTATAAATTAT
15407157 TTTGAAA-TTTTA-AAATTAT
1 TTTGAAATTTTTATAAATTAT
*
15407176 TTTGTAATTTTTAT
1 TTTGAAATTTTTAT
15407190 TGAGAGAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 3 0.11
19 14 0.50
20 11 0.39
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (21 bp):
TTTGAAATTTTTATAAATTAT
Found at i:15411337 original size:22 final size:22
Alignment explanation
Indices: 15411296--15411337 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
15411286 AGATAGGGAA
* * *
15411296 TTAAAAGGTGATAGATTAAAAT
1 TTAAAAGCTGAAAGAGTAAAAT
15411318 TTAAAAGCTGAAAGAGTAAA
1 TTAAAAGCTGAAAGAGTAAA
15411338 GGGGTTGGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.52, C:0.02, G:0.19, T:0.26
Consensus pattern (22 bp):
TTAAAAGCTGAAAGAGTAAAAT
Found at i:15418926 original size:24 final size:23
Alignment explanation
Indices: 15418866--15418926 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 23
15418856 GTAAATTACA
**
15418866 TCAGAATGAATTCATGAGAAAGG
1 TCAGAATGAATTTGTGAGAAAGG
* *
15418889 T-ATAATAAACTTTGTGAGACAAGG
1 TCAGAATGAA-TTTGTGAGA-AAGG
15418913 TCAGAATGAATTTG
1 TCAGAATGAATTTG
15418927 GGTTCCCCTG
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
22 6 0.21
23 8 0.28
24 9 0.31
25 6 0.21
ACGTcount: A:0.41, C:0.08, G:0.23, T:0.28
Consensus pattern (23 bp):
TCAGAATGAATTTGTGAGAAAGG
Found at i:15424690 original size:28 final size:29
Alignment explanation
Indices: 15424637--15424691 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
15424627 CAACAGTAGC
*
15424637 CCATGAATTTCATAAAATTTAGAATTTTT
1 CCATGAATTTCATAAAATTTACAATTTTT
* *
15424666 CCATGAATTT-ATAATATTTTCAATTT
1 CCATGAATTTCATAAAATTTACAATTT
15424692 GGTCCCTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 13 0.57
29 10 0.43
ACGTcount: A:0.36, C:0.11, G:0.05, T:0.47
Consensus pattern (29 bp):
CCATGAATTTCATAAAATTTACAATTTTT
Found at i:15428141 original size:18 final size:18
Alignment explanation
Indices: 15428118--15428157 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
15428108 TTATTATTTT
*
15428118 TAAAATTT-ACTATTAAAA
1 TAAAATTTAAATATT-AAA
15428136 TAAAATTTAAATATTAAA
1 TAAAATTTAAATATTAAA
15428154 TAAA
1 TAAA
15428158 TTATTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAAATTTAAATATTAAA
Found at i:15428164 original size:19 final size:19
Alignment explanation
Indices: 15428128--15428178 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 19
15428118 TAAAATTTAC
*
15428128 TATTAAAATAAAAT-TTAAA
1 TATT-AAATAAATTATTAAA
15428147 TATTAAATAAATTATTAAA
1 TATTAAATAAATTATTAAA
*
15428166 -AAT-AATAAATTAT
1 TATTAAATAAATTAT
15428179 ATTAATAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 10 0.34
18 10 0.34
19 9 0.31
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TATTAAATAAATTATTAAA
Found at i:15428274 original size:9 final size:9
Alignment explanation
Indices: 15428260--15428288 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
15428250 AGTTTCTATT
15428260 AATATTTTA
1 AATATTTTA
15428269 AATATTTTA
1 AATATTTTA
15428278 AATATTTTA
1 AATATTTTA
15428287 AA
1 AA
15428289 AATAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
AATATTTTA
Found at i:15435106 original size:68 final size:68
Alignment explanation
Indices: 15434994--15435181 Score: 250
Period size: 68 Copynumber: 2.8 Consensus size: 68
15434984 GTCATAGGTG
* * * * *
15434994 CATGGCACCATAATGTGTAAGACCATAGTTGGGCTATGGTAACATATAAAGTCTACTAAGACAGT
1 CATGGGACCATAATGTGTAAGACCATAGTTGGGCTATGGCAACATATGAAGTCCACCAAGACAGT
15435059 AAA
66 AAA
* * * *
15435062 CATGGGACCATAGTGTGTAAGATCATAGTTGGGCTATGGCAACATATGAAGTCCACCAGGATAGT
1 CATGGGACCATAATGTGTAAGACCATAGTTGGGCTATGGCAACATATGAAGTCCACCAAGACAGT
15435127 AAA
66 AAA
* * ** *
15435130 CATGAGATCATAATGTGTAAGACCATAGCAGGGCTATGGCCACATATGAAGT
1 CATGGGACCATAATGTGTAAGACCATAGTTGGGCTATGGCAACATATGAAGT
15435182 TCGTAAGTAC
Statistics
Matches: 104, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
68 104 1.00
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (68 bp):
CATGGGACCATAATGTGTAAGACCATAGTTGGGCTATGGCAACATATGAAGTCCACCAAGACAGT
AAA
Found at i:15443481 original size:6 final size:6
Alignment explanation
Indices: 15443415--15443495 Score: 76
Period size: 6 Copynumber: 13.3 Consensus size: 6
15443405 AAAATAAAAT
* ** *
15443415 AAAACA AAAA-A AAAACA GAAACA AAAGTA AAGACA AAAGACA AAAGACTA
1 AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA AAA-ACA AAA-AC-A
*
15443465 AAGAC- AAAACA AAAACA AAAACA AAAACA AA
1 AAAACA AAAACA AAAACA AAAACA AAAACA AA
15443496 TAAAATATAA
Statistics
Matches: 61, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
5 9 0.15
6 38 0.62
7 11 0.18
8 3 0.05
ACGTcount: A:0.77, C:0.14, G:0.07, T:0.02
Consensus pattern (6 bp):
AAAACA
Found at i:15448493 original size:37 final size:37
Alignment explanation
Indices: 15448428--15448543 Score: 146
Period size: 37 Copynumber: 3.1 Consensus size: 37
15448418 ATGTTTTGGT
* * * *
15448428 GTGTTTTCAGTTGGACTAGCTCTAATGAGCATCTGGC
1 GTGTTATCAGGTGGATTAGCTCTTATGAGCATCTGGC
*
15448465 GTGTTATC-GAGTGGATTAGGTCTTATGAGCATCTGGC
1 GTGTTATCAG-GTGGATTAGCTCTTATGAGCATCTGGC
*
15448502 GTGTTATCAGGTGGATTAGCTCTTACGAGCGAT-TGGC
1 GTGTTATCAGGTGGATTAGCTCTTATGAGC-ATCTGGC
15448539 GTGTT
1 GTGTT
15448544 CCGGTTGGAA
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
36 1 0.01
37 65 0.94
38 3 0.04
ACGTcount: A:0.18, C:0.16, G:0.31, T:0.35
Consensus pattern (37 bp):
GTGTTATCAGGTGGATTAGCTCTTATGAGCATCTGGC
Found at i:15478931 original size:21 final size:21
Alignment explanation
Indices: 15478899--15478939 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
15478889 ATTTATATAA
15478899 TCCTTATGTGATATG-TTTTTC
1 TCCTTATGTGAT-TGATTTTTC
15478920 TCCTT-TGTTGATTGATTTTT
1 TCCTTATG-TGATTGATTTTT
15478940 TGGTAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.12, C:0.12, G:0.15, T:0.61
Consensus pattern (21 bp):
TCCTTATGTGATTGATTTTTC
Found at i:15486115 original size:24 final size:25
Alignment explanation
Indices: 15486023--15486142 Score: 104
Period size: 24 Copynumber: 4.8 Consensus size: 25
15486013 ATAGCTTTTA
*
15486023 TGAGCATCCCGTTATATGGCTCGTTG
1 TGAGCTTCCCGTTA-ATGGCTCGTTG
* *
15486049 TGAGCTTCCCGATTAAAGGCTCTTTG
1 TGAGCTTCCCG-TTAATGGCTCGTTG
* * *
15486075 TGAGCTTTCCGAT-ATGGCTCGCT-
1 TGAGCTTCCCGTTAATGGCTCGTTG
* *
15486098 TGAACTTCCCGTTAATGGCT-ATTCG
1 TGAGCTTCCCGTTAATGGCTCGTT-G
*
15486123 -GAGCTTCCTGTTAATGGCTC
1 TGAGCTTCCCGTTAATGGCTC
15486143 TTCAGAGCTA
Statistics
Matches: 74, Mismatches: 15, Indels: 11
0.74 0.15 0.11
Matches are distributed among these distances:
23 11 0.15
24 30 0.41
25 1 0.01
26 29 0.39
27 3 0.04
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (25 bp):
TGAGCTTCCCGTTAATGGCTCGTTG
Found at i:15486150 original size:24 final size:24
Alignment explanation
Indices: 15486102--15486151 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
15486092 CTCGCTTGAA
*
15486102 CTTCCCGTTAATGGCTATTCGGAG
1 CTTCCCGTTAATGGCTATTCAGAG
* *
15486126 CTTCCTGTTAATGGCTCTTCAGAG
1 CTTCCCGTTAATGGCTATTCAGAG
15486150 CT
1 CT
15486152 ACCCATTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.16, C:0.26, G:0.22, T:0.36
Consensus pattern (24 bp):
CTTCCCGTTAATGGCTATTCAGAG
Found at i:15494552 original size:19 final size:19
Alignment explanation
Indices: 15494528--15494566 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
15494518 ACCCTAAAAG
15494528 AAAGAAAAATAAATTGAAA
1 AAAGAAAAATAAATTGAAA
15494547 AAAGAAAAATAAATTGAAA
1 AAAGAAAAATAAATTGAAA
15494566 A
1 A
15494567 CTAAATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.15
Consensus pattern (19 bp):
AAAGAAAAATAAATTGAAA
Found at i:15496537 original size:16 final size:17
Alignment explanation
Indices: 15496505--15496546 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
15496495 GCAAAATTAG
15496505 AATTAGATTGAGAAAATT
1 AATTA-ATTGAGAAAATT
*
15496523 ATTTAATTG-GAAAATT
1 AATTAATTGAGAAAATT
15496539 AATTAATT
1 AATTAATT
15496547 TAATAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 14 0.64
17 4 0.18
18 4 0.18
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (17 bp):
AATTAATTGAGAAAATT
Found at i:15505754 original size:20 final size:20
Alignment explanation
Indices: 15505717--15505789 Score: 64
Period size: 20 Copynumber: 3.7 Consensus size: 20
15505707 ATTGCACTTC
15505717 GGTGCCTCTATTCT-CACTCT
1 GGTGCCTCTATT-TACACTCT
*
15505737 GGTGCCTCTCTTTACACT-T
1 GGTGCCTCTATTTACACTCT
* *
15505756 CGGTGTCTCTATTTGCACTAC-
1 -GGTGCCTCTATTTACACT-CT
15505777 GGTGCCTCT-TTTA
1 GGTGCCTCTATTTA
15505790 TCACAATCGT
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
19 5 0.12
20 38 0.88
ACGTcount: A:0.11, C:0.30, G:0.18, T:0.41
Consensus pattern (20 bp):
GGTGCCTCTATTTACACTCT
Found at i:15505755 original size:40 final size:39
Alignment explanation
Indices: 15505711--15505789 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 39
15505701 TGCAGGATTG
15505711 CACTTCGGTGCCTCTATTCT-CACT-CTGGTGCCTCTCTTTA
1 CACTTCGGTGCCTCTATT-TGCACTAC-GGTGCCTCT-TTTA
*
15505751 CACTTCGGTGTCTCTATTTGCACTACGGTGCCTCTTTTA
1 CACTTCGGTGCCTCTATTTGCACTACGGTGCCTCTTTTA
15505790 TCACAATCGT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
39 5 0.14
40 30 0.83
41 1 0.03
ACGTcount: A:0.11, C:0.32, G:0.16, T:0.41
Consensus pattern (39 bp):
CACTTCGGTGCCTCTATTTGCACTACGGTGCCTCTTTTA
Found at i:15509638 original size:25 final size:25
Alignment explanation
Indices: 15509604--15509811 Score: 156
Period size: 25 Copynumber: 8.3 Consensus size: 25
15509594 AGGCTTCCAA
* *
15509604 AGAGAGTTCGCCACAAAGTCATTTC
1 AGAGAATTCGCCACAAAGGCATTTC
15509629 AGAGAATTCGCCACAAAGGCA-TTC
1 AGAGAATTCGCCACAAAGGCATTTC
* * *
15509653 TAAAGTATTCGCCACAAAGGCTTTTC
1 -AGAGAATTCGCCACAAAGGCATTTC
* *
15509679 ATAGAATTCGCCACAAA--CAAGTTCC
1 AGAGAATTCGCCACAAAGGC-A-TTTC
* * * *
15509704 AAAGAATTTGCCACAAATGCATTTT
1 AGAGAATTCGCCACAAAGGCATTTC
* *
15509729 AGAGAATTTGCCACAAAGGC-GTTC
1 AGAGAATTCGCCACAAAGGCATTTC
* * *
15509753 TAGAGAATTCACCACAAAAGG-GTTCC
1 -AGAGAATTCGCCAC-AAAGGCATTTC
* ** *
15509779 AGAGTATTCGCCACAAAGGTTTTTT
1 AGAGAATTCGCCACAAAGGCATTTC
15509804 AGAGAATT
1 AGAGAATT
15509812 TTGTGTTTAC
Statistics
Matches: 146, Mismatches: 27, Indels: 20
0.76 0.14 0.10
Matches are distributed among these distances:
23 1 0.01
24 10 0.07
25 123 0.84
26 11 0.08
27 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (25 bp):
AGAGAATTCGCCACAAAGGCATTTC
Found at i:15509669 original size:50 final size:50
Alignment explanation
Indices: 15509588--15509797 Score: 187
Period size: 50 Copynumber: 4.2 Consensus size: 50
15509578 AAGTAACACA
15509588 CCACAAAGGC-TTCCAAAGAGAGTTCGCCACAAAGTCATTTCAGAGAATTCG
1 CCACAAAGGCATTCCAAAGA-A-TTCGCCACAAAGTCATTTCAGAGAATTCG
* * * * *
15509639 CCACAAAGGCATTCTAAAGTATTCGCCACAAAGGCTTTTCATAGAATTCG
1 CCACAAAGGCATTCCAAAGAATTCGCCACAAAGTCATTTCAGAGAATTCG
* * *
15509689 CCACAAA--CAAGTTCCAAAGAATTTGCCACAAA-TGCATTTTAGAGAATTTG
1 CCACAAAGGC-A-TTCCAAAGAATTCGCCACAAAGT-CATTTCAGAGAATTCG
* * * * ** * *
15509739 CCACAAAGGCGTTCTAGAGAATTCACCACAAAAG-GGTTCCAGAGTATTCG
1 CCACAAAGGCATTCCAAAGAATTCGCCAC-AAAGTCATTTCAGAGAATTCG
15509789 CCACAAAGG
1 CCACAAAGG
15509798 TTTTTTAGAG
Statistics
Matches: 127, Mismatches: 24, Indels: 17
0.76 0.14 0.10
Matches are distributed among these distances:
48 1 0.01
49 1 0.01
50 103 0.81
51 14 0.11
52 8 0.06
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (50 bp):
CCACAAAGGCATTCCAAAGAATTCGCCACAAAGTCATTTCAGAGAATTCG
Found at i:15509804 original size:75 final size:75
Alignment explanation
Indices: 15509628--15509812 Score: 212
Period size: 75 Copynumber: 2.5 Consensus size: 75
15509618 AAAGTCATTT
* * * * * * *
15509628 CAGAGAATTCGCCACAAAGGCATTCTAAAGTATTCGCCACAAAGGCTTTTCATAGAATTCGCCAC
1 CAGAGAATTCGCCACAAAGGCATTTTAGAGAATTTGCCACAAAGGCTTCTCAGAGAATTCACCAC
15509693 AAACAAGTTC
66 AAACAAGTTC
* * *
15509703 CAAAGAATTTGCCACAAATGCATTTTAGAGAATTTGCCACAAAGGCGTTCT-AGAGAATTCACCA
1 CAGAGAATTCGCCACAAAGGCATTTTAGAGAATTTGCCACAAAGGC-TTCTCAGAGAATTCACCA
*
15509767 CAAA-AGGGTTC
65 CAAACA-AGTTC
* **
15509778 CAGAGTATTCGCCACAAAGGTTTTTTAGAGAATTT
1 CAGAGAATTCGCCACAAAGGCATTTTAGAGAATTT
15509813 TGTGTTTACC
Statistics
Matches: 91, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
74 1 0.01
75 87 0.96
76 3 0.03
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (75 bp):
CAGAGAATTCGCCACAAAGGCATTTTAGAGAATTTGCCACAAAGGCTTCTCAGAGAATTCACCAC
AAACAAGTTC
Found at i:15512825 original size:26 final size:27
Alignment explanation
Indices: 15512791--15512842 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
15512781 AGAATGTATG
*
15512791 TATATTTTAGTATTTTCTATAATTTTT
1 TATATTTTAGAATTTTCTATAATTTTT
* *
15512818 TATA-TTTAGAATTTTTTATTATTTT
1 TATATTTTAGAATTTTCTATAATTTT
15512843 AAATTTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (27 bp):
TATATTTTAGAATTTTCTATAATTTTT
Found at i:15512840 original size:17 final size:17
Alignment explanation
Indices: 15512811--15512854 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
15512801 TATTTTCTAT
15512811 AATTTTTTA-TA-TTTA
1 AATTTTTTATTATTTTA
15512826 GAATTTTTTATTATTTTA
1 -AATTTTTTATTATTTTA
15512844 AATTTTTTATT
1 AATTTTTTATT
15512855 TTTCCTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.35
17 13 0.50
18 4 0.15
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (17 bp):
AATTTTTTATTATTTTA
Found at i:15512882 original size:16 final size:16
Alignment explanation
Indices: 15512861--15512891 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
15512851 TATTTTTCCT
15512861 TTTTATTTTAAATAAA
1 TTTTATTTTAAATAAA
*
15512877 TTTTATTTTATATAA
1 TTTTATTTTAAATAA
15512892 TTTATATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTATTTTAAATAAA
Found at i:15517520 original size:23 final size:22
Alignment explanation
Indices: 15517486--15517547 Score: 79
Period size: 22 Copynumber: 2.7 Consensus size: 22
15517476 GTCCGGCTCG
*
15517486 TTTTTAATTAAAATTAAAATTATT
1 TTTTTAA-TAAAATTAAAATTA-A
15517510 TTTTTAATAAAATTAAAATTAA
1 TTTTTAATAAAATTAAAATTAA
* *
15517532 TTGTTATTAAAATTAA
1 TTTTTAATAAAATTAA
15517548 TTGTTAGTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 14 0.40
23 14 0.40
24 7 0.20
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
TTTTTAATAAAATTAAAATTAA
Found at i:15517542 original size:16 final size:16
Alignment explanation
Indices: 15517521--15517562 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
15517511 TTTTAATAAA
15517521 ATTAAAATTAATTGTT
1 ATTAAAATTAATTGTT
15517537 ATTAAAATTAATTGTT
1 ATTAAAATTAATTGTT
*
15517553 AGTAAAATTA
1 ATTAAAATTA
15517563 TCAAATTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (16 bp):
ATTAAAATTAATTGTT
Found at i:15517545 original size:22 final size:23
Alignment explanation
Indices: 15517492--15517547 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
15517482 CTCGTTTTTA
* *
15517492 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAATTATATTGTT
*
15517515 AATAAAATTAAAATTA-ATTGTT
1 ATTAAAATTAAAATTATATTGTT
15517537 ATTAAAATTAA
1 ATTAAAATTAA
15517548 TTGTTAGTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 14 0.48
23 15 0.52
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
ATTAAAATTAAAATTATATTGTT
Found at i:15517729 original size:22 final size:23
Alignment explanation
Indices: 15517684--15517727 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
15517674 AAATAAACTT
*
15517684 AAAATAAAAACTATTATATTTTA
1 AAAATAAAAACTAATATATTTTA
15517707 AAAATAAAAA-TAAATATATTT
1 AAAATAAAAACT-AATATATTT
15517728 AATATTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 1 0.05
23 18 0.95
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (23 bp):
AAAATAAAAACTAATATATTTTA
Found at i:15523180 original size:27 final size:27
Alignment explanation
Indices: 15523162--15523444 Score: 333
Period size: 27 Copynumber: 10.6 Consensus size: 27
15523152 GGTATAACAC
*
15523162 TCATTTTACCCTATGGGGGTATTTTAG
1 TCATTTTACCCTATGGGGGTATTTCAG
*
15523189 TCATTTTACCCTATGGGGGTATTTCGG
1 TCATTTTACCCTATGGGGGTATTTCAG
*
15523216 TCATTTTACCCTAT-GGGGTATTTCAA
1 TCATTTTACCCTATGGGGGTATTTCAG
*
15523242 TCATTTTACCCTATGGGGGTGTTT-AGG
1 TCATTTTACCCTATGGGGGTATTTCA-G
* * *
15523269 TCATTTTACCTTATGGGGGTTTTTCGG
1 TCATTTTACCCTATGGGGGTATTTCAG
** *
15523296 TCATTTTACCCTATAAGGGTATTTCGG
1 TCATTTTACCCTATGGGGGTATTTCAG
*
15523323 TCAATTTACCCTATGGGGGTATTTC-G
1 TCATTTTACCCTATGGGGGTATTTCAG
* *
15523349 ATCATTTTATCCTATGGGGGTATTTCGG
1 -TCATTTTACCCTATGGGGGTATTTCAG
* *
15523377 TCATTCTACCCTATGGGAGTATTTC-G
1 TCATTTTACCCTATGGGGGTATTTCAG
* * *
15523403 ATCATTTTACCCTTTGAGGGTATTTCGG
1 -TCATTTTACCCTATGGGGGTATTTCAG
*
15523431 TCA-TTTATCCTATG
1 TCATTTTACCCTATG
15523445 AAGGTACTTT
Statistics
Matches: 222, Mismatches: 27, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
26 36 0.16
27 184 0.83
28 2 0.01
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.42
Consensus pattern (27 bp):
TCATTTTACCCTATGGGGGTATTTCAG
Found at i:15523365 original size:81 final size:80
Alignment explanation
Indices: 15523162--15523444 Score: 383
Period size: 81 Copynumber: 3.5 Consensus size: 80
15523152 GGTATAACAC
* *
15523162 TCATTTTACCCTATGGGGGTATTT-TAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACC
1 TCATTTTACCCTATGGGGGTATTTCGA-TCATTTTATCCTATGGGGGTATTTCGGTCATTTTACC
*
15523226 CTATGGGGTATTTCAA
65 CTATGGGGTATTTCGA
* * * *
15523242 TCATTTTACCCTATGGGGGTGTTTAGGTCATTTTA-CCTTATGGGGGTTTTTCGGTCATTTTACC
1 TCATTTTACCCTATGGGGGTATTTCGATCATTTTATCC-TATGGGGGTATTTCGGTCATTTTACC
* *
15523306 CTATAAGGGTATTTCGG
65 CTAT-GGGGTATTTCGA
* *
15523323 TCAATTTACCCTATGGGGGTATTTCGATCATTTTATCCTATGGGGGTATTTCGGTCATTCTACCC
1 TCATTTTACCCTATGGGGGTATTTCGATCATTTTATCCTATGGGGGTATTTCGGTCATTTTACCC
15523388 TATGGGAGTATTTCGA
66 TATGGG-GTATTTCGA
* * *
15523404 TCATTTTACCCTTTGAGGGTATTTCGGTCA-TTTATCCTATG
1 TCATTTTACCCTATGGGGGTATTTCGATCATTTTATCCTATG
15523445 AAGGTACTTT
Statistics
Matches: 179, Mismatches: 19, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
79 2 0.01
80 73 0.41
81 102 0.57
82 2 0.01
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.42
Consensus pattern (80 bp):
TCATTTTACCCTATGGGGGTATTTCGATCATTTTATCCTATGGGGGTATTTCGGTCATTTTACCC
TATGGGGTATTTCGA
Found at i:15525331 original size:2 final size:2
Alignment explanation
Indices: 15525324--15525348 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15525314 TTATAAACTA
15525324 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
15525349 AGTTATAAAG
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:15532928 original size:180 final size:180
Alignment explanation
Indices: 15532622--15532976 Score: 593
Period size: 180 Copynumber: 2.0 Consensus size: 180
15532612 GGAGATTCTA
* * *
15532622 TATTCTCAAAGATTGACTTAAGGTCAGGTTATTATCAGTTGAAGGTAAAAGAAAGTGATGTATCG
1 TATTCTCAAAGACTGACTTAAGGTCAGGTTATTATCAGTTGAAGGTAAAAGAAAGTGATGTACCA
* * * * *
15532687 AAGCCAGCTTTCCGTACGAGGTAAAGCCGCTATGAGTTCTTAGTAATGCCATTTGGGTTGACAAA
66 AAGACAACTTTCCATACGAGGTAAAGCCACTATGAGTTCTTAGTAATGCCATTTAGGTTGACAAA
15532752 TGCCCCAAACACTTTTATGGATCTTATGAATCGTATTTTTCAGCCATATG
131 TGCCCCAAACACTTTTATGGATCTTATGAATCGTATTTTTCAGCCATATG
*
15532802 TATTCTCGAAGACTGACTTAAGGTCAGGTTATTATCAGTTGAAGGTAAAAGAAAGTGATGTACCA
1 TATTCTCAAAGACTGACTTAAGGTCAGGTTATTATCAGTTGAAGGTAAAAGAAAGTGATGTACCA
**
15532867 AAGACAACTTTCCATACGAGGTATGGCCACTATGAGTTCTTAGTAATGCCATTTAGGTTGACAAA
66 AAGACAACTTTCCATACGAGGTAAAGCCACTATGAGTTCTTAGTAATGCCATTTAGGTTGACAAA
**
15532932 TGCCCCAGCCACTTTTATGGATCTTATGAATCGTATTTTTCAGCC
131 TGCCCCAAACACTTTTATGGATCTTATGAATCGTATTTTTCAGCC
15532977 GTATTTAGAC
Statistics
Matches: 162, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
180 162 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (180 bp):
TATTCTCAAAGACTGACTTAAGGTCAGGTTATTATCAGTTGAAGGTAAAAGAAAGTGATGTACCA
AAGACAACTTTCCATACGAGGTAAAGCCACTATGAGTTCTTAGTAATGCCATTTAGGTTGACAAA
TGCCCCAAACACTTTTATGGATCTTATGAATCGTATTTTTCAGCCATATG
Found at i:15540281 original size:20 final size:21
Alignment explanation
Indices: 15540244--15540283 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
15540234 TCTAACCTTA
**
15540244 AAAAAAACATAATTAGAAAAC
1 AAAAAAACATAAAAAGAAAAC
15540265 AAAAAAA-ATAAAAAGAAAA
1 AAAAAAACATAAAAAGAAAA
15540284 TGGAGAATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.80, C:0.05, G:0.05, T:0.10
Consensus pattern (21 bp):
AAAAAAACATAAAAAGAAAAC
Found at i:15544791 original size:24 final size:24
Alignment explanation
Indices: 15544764--15544837 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
15544754 ATCTTGTTTA
15544764 CCATGATGCCATGGCATCTATCAC
1 CCATGATGCCATGGCATCTATCAC
* *
15544788 CCATGCT-CTTACT--CAT-TATCA-
1 CCATGATGC-CA-TGGCATCTATCAC
*
15544809 TCATGATGCCATGGCATCTATCAC
1 CCATGATGCCATGGCATCTATCAC
15544833 CCATG
1 CCATG
15544838 CTCTTACTCA
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
20 1 0.03
21 6 0.16
22 9 0.24
23 9 0.24
24 11 0.30
25 1 0.03
ACGTcount: A:0.24, C:0.32, G:0.14, T:0.30
Consensus pattern (24 bp):
CCATGATGCCATGGCATCTATCAC
Found at i:15544815 original size:45 final size:45
Alignment explanation
Indices: 15544765--15544872 Score: 198
Period size: 45 Copynumber: 2.4 Consensus size: 45
15544755 TCTTGTTTAC
15544765 CATGATGCCATGGCATCTATCACCCATGCTCTTACTCATTATCAT
1 CATGATGCCATGGCATCTATCACCCATGCTCTTACTCATTATCAT
*
15544810 CATGATGCCATGGCATCTATCACCCATGCTCTTACTCATTGTCAT
1 CATGATGCCATGGCATCTATCACCCATGCTCTTACTCATTATCAT
*
15544855 CATGATGCCATAGCATCT
1 CATGATGCCATGGCATCT
15544873 TTCAACTATG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 61 1.00
ACGTcount: A:0.24, C:0.31, G:0.13, T:0.32
Consensus pattern (45 bp):
CATGATGCCATGGCATCTATCACCCATGCTCTTACTCATTATCAT
Found at i:15544890 original size:45 final size:45
Alignment explanation
Indices: 15544765--15544894 Score: 179
Period size: 45 Copynumber: 2.9 Consensus size: 45
15544755 TCTTGTTTAC
* * *
15544765 CATGATGCCATGGCATCTATCACCCATGCTCTTACTCATTATCAT
1 CATGATGCCATAGCATCTATCAACCATGCTCTTACTCATTGTCAT
* *
15544810 CATGATGCCATGGCATCTATCACCCATGCTCTTACTCATTGTCAT
1 CATGATGCCATAGCATCTATCAACCATGCTCTTACTCATTGTCAT
* * * *
15544855 CATGATGCCATAGCATCTTTCAACTATGGTTTTACTCATT
1 CATGATGCCATAGCATCTATCAACCATGCTCTTACTCATT
15544895 TTAGGCGTAT
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 78 1.00
ACGTcount: A:0.24, C:0.28, G:0.12, T:0.35
Consensus pattern (45 bp):
CATGATGCCATAGCATCTATCAACCATGCTCTTACTCATTGTCAT
Found at i:15547096 original size:30 final size:30
Alignment explanation
Indices: 15547062--15547196 Score: 146
Period size: 30 Copynumber: 4.5 Consensus size: 30
15547052 AACCAAGGCT
15547062 ATCCCTTTTCATAATTTGATGGTCGTCACC
1 ATCCCTTTTCATAATTTGATGGTCGTCACC
** *
15547092 ATCCCTTTTCATTGTTTGATGGTCGCCACC
1 ATCCCTTTTCATAATTTGATGGTCGTCACC
* * * * *
15547122 ATCCTTTTTCGTAATTTGATAGACG-AAGCC
1 ATCCCTTTTCATAATTTGATGGTCGTCA-CC
* **
15547152 ATCCCTTTTCATAGTTCAATGGTCGTCACC
1 ATCCCTTTTCATAATTTGATGGTCGTCACC
*
15547182 ATCCCGTTTCATAAT
1 ATCCCTTTTCATAAT
15547197 CGATAGCAGA
Statistics
Matches: 83, Mismatches: 20, Indels: 4
0.78 0.19 0.04
Matches are distributed among these distances:
29 1 0.01
30 81 0.98
31 1 0.01
ACGTcount: A:0.21, C:0.27, G:0.14, T:0.39
Consensus pattern (30 bp):
ATCCCTTTTCATAATTTGATGGTCGTCACC
Found at i:15547137 original size:60 final size:60
Alignment explanation
Indices: 15547062--15547225 Score: 181
Period size: 60 Copynumber: 2.8 Consensus size: 60
15547052 AACCAAGGCT
* * * * **
15547062 ATCCCTTTTCATAATTTGATGGTCGTCA-CCATCCCTTTTCATTGTTTGATGGTCGCCACC
1 ATCCCTTTTCATAATTTGATAGACG-AAGCCATCCCTTTTCATAGTTCAATGGTCGCCACC
* * *
15547122 ATCCTTTTTCGTAATTTGATAGACGAAGCCATCCCTTTTCATAGTTCAATGGTCGTCACC
1 ATCCCTTTTCATAATTTGATAGACGAAGCCATCCCTTTTCATAGTTCAATGGTCGCCACC
* * *
15547182 ATCCCGTTTCATAA-TCGATAG-CAGAAGCTATCCCTTTTCATAGT
1 ATCCCTTTTCATAATTTGATAGAC-GAAGCCATCCCTTTTCATAGT
15547226 CGATATCTGA
Statistics
Matches: 88, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
58 1 0.01
59 27 0.31
60 60 0.68
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (60 bp):
ATCCCTTTTCATAATTTGATAGACGAAGCCATCCCTTTTCATAGTTCAATGGTCGCCACC
Found at i:15547220 original size:29 final size:29
Alignment explanation
Indices: 15547182--15547249 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
15547172 GGTCGTCACC
*
15547182 ATCCCGTTTCATAATCGATAGCAGAAGCT
1 ATCCCTTTTCATAATCGATAGCAGAAGCT
* * *
15547211 ATCCCTTTTCATAGTCGATATCTGAAGCT
1 ATCCCTTTTCATAATCGATAGCAGAAGCT
15547240 ATCCCATTTT
1 ATCCC-TTTT
15547250 ACCCATCAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 30 0.88
30 4 0.12
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.35
Consensus pattern (29 bp):
ATCCCTTTTCATAATCGATAGCAGAAGCT
Found at i:15554323 original size:16 final size:16
Alignment explanation
Indices: 15554302--15554335 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
15554292 AGCTTCCGAT
15554302 AACTACAAAACACAGA
1 AACTACAAAACACAGA
15554318 AACTACAAAACACAGA
1 AACTACAAAACACAGA
15554334 AA
1 AA
15554336 AGTAAACACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.65, C:0.24, G:0.06, T:0.06
Consensus pattern (16 bp):
AACTACAAAACACAGA
Found at i:15554691 original size:30 final size:30
Alignment explanation
Indices: 15554657--15554816 Score: 137
Period size: 30 Copynumber: 5.4 Consensus size: 30
15554647 GAAGCTATCT
15554657 CTTTTCATAATTTGATGGTCGTCACCATCC
1 CTTTTCATAATTTGATGGTCGTCACCATCC
** * **
15554687 CTTTTCATTGTTCGACAGTCGTCACCATCC
1 CTTTTCATAATTTGATGGTCGTCACCATCC
* ** ***
15554717 CTTTTTATAATTTGAT-AACCAAAGCCATCC
1 CTTTTCATAATTTGATGGTCGTCA-CCATCC
* *
15554747 CTTTTCATAGTTTGATGATCGTCACCATCC
1 CTTTTCATAATTTGATGGTCGTCACCATCC
* * *
15554777 ATTTCCATAA-TTGATGGTCATCACCA-CTC
1 CTTTTCATAATTTGATGGTCGTCACCATC-C
15554806 CTTTTCATAAT
1 CTTTTCATAAT
15554817 CGGTAGCCAA
Statistics
Matches: 98, Mismatches: 28, Indels: 8
0.73 0.21 0.06
Matches are distributed among these distances:
28 1 0.01
29 25 0.26
30 69 0.70
31 3 0.03
ACGTcount: A:0.24, C:0.27, G:0.11, T:0.39
Consensus pattern (30 bp):
CTTTTCATAATTTGATGGTCGTCACCATCC
Found at i:15554705 original size:90 final size:90
Alignment explanation
Indices: 15554592--15554776 Score: 244
Period size: 90 Copynumber: 2.1 Consensus size: 90
15554582 ATGGTTGACA
* * ** * * * *
15554592 CATCCCTTTTCTTTATTCGACAGTGGAGGCTATCCCTTTTCATAATTTAATAACCGAAGCTATCT
1 CATCCCTTTTCATTATTCGACAGTCGACACCATCCCTTTTCATAATTTAATAACCAAAGCCATCC
*
15554657 CTTTTCATAATTTGATGGTCGTCAC
66 CTTTTCATAATTTGATGATCGTCAC
* * * *
15554682 CATCCCTTTTCATTGTTCGACAGTCGTCACCATCCCTTTTTATAATTTGATAACCAAAGCCATCC
1 CATCCCTTTTCATTATTCGACAGTCGACACCATCCCTTTTCATAATTTAATAACCAAAGCCATCC
*
15554747 CTTTTCATAGTTTGATGATCGTCAC
66 CTTTTCATAATTTGATGATCGTCAC
15554772 CATCC
1 CATCC
15554777 ATTTCCATAA
Statistics
Matches: 81, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
90 81 1.00
ACGTcount: A:0.23, C:0.26, G:0.12, T:0.38
Consensus pattern (90 bp):
CATCCCTTTTCATTATTCGACAGTCGACACCATCCCTTTTCATAATTTAATAACCAAAGCCATCC
CTTTTCATAATTTGATGATCGTCAC
Found at i:15554721 original size:60 final size:60
Alignment explanation
Indices: 15554657--15554814 Score: 162
Period size: 60 Copynumber: 2.6 Consensus size: 60
15554647 GAAGCTATCT
* *
15554657 CTTTTCATAATTTGATGGTCGTCACCATCCCTTTTCATTGTTCGACAG-TCGTCACCATCC
1 CTTTTCATAATTTGATGGTCATCACCATCCCTTTTCATAGTTCGA-AGATCGTCACCATCC
* *** * * *
15554717 CTTTTTATAATTTGATAACCA-AAGCCATCCCTTTTCATAGTTTGATGATCGTCACCATCC
1 CTTTTCATAATTTGATGGTCATCA-CCATCCCTTTTCATAGTTCGAAGATCGTCACCATCC
* *
15554777 ATTTCCATAA-TTGATGGTCATCACCA-CTCCTTTTCATA
1 CTTTTCATAATTTGATGGTCATCACCATC-CCTTTTCATA
15554815 ATCGGTAGCC
Statistics
Matches: 78, Mismatches: 16, Indels: 9
0.76 0.16 0.09
Matches are distributed among these distances:
58 1 0.01
59 22 0.28
60 55 0.71
ACGTcount: A:0.23, C:0.27, G:0.11, T:0.39
Consensus pattern (60 bp):
CTTTTCATAATTTGATGGTCATCACCATCCCTTTTCATAGTTCGAAGATCGTCACCATCC
Found at i:15554791 original size:29 final size:29
Alignment explanation
Indices: 15554758--15554816 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
15554748 TTTTCATAGT
*
15554758 TTGATGATCGTCACCA-TCCATTTCCATAA
1 TTGATGATCATCACCACTCC-TTTCCATAA
* *
15554787 TTGATGGTCATCACCACTCCTTTTCATAA
1 TTGATGATCATCACCACTCCTTTCCATAA
15554816 T
1 T
15554817 CGGTAGCCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 23 0.88
30 3 0.12
ACGTcount: A:0.25, C:0.27, G:0.10, T:0.37
Consensus pattern (29 bp):
TTGATGATCATCACCACTCCTTTCCATAA
Found at i:15554839 original size:29 final size:29
Alignment explanation
Indices: 15554807--15554863 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
15554797 TCACCACTCC
*
15554807 TTTTCATAATCGGTAGCCAAAGCTATCCT
1 TTTTCATAATCGATAGCCAAAGCTATCCT
* * * *
15554836 TTTTCGTAGTCGATAGGCGAAGCTATCC
1 TTTTCATAATCGATAGCCAAAGCTATCC
15554864 CATTTCACCC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (29 bp):
TTTTCATAATCGATAGCCAAAGCTATCCT
Found at i:15556037 original size:19 final size:20
Alignment explanation
Indices: 15555993--15556040 Score: 80
Period size: 21 Copynumber: 2.4 Consensus size: 20
15555983 GGCTGTTACA
15555993 TTTGTGAACTTGATCAAACTC
1 TTTGTGAACTTGATCAAAC-C
15556014 TTTGTGAACTTGATCAAA-C
1 TTTGTGAACTTGATCAAACC
15556033 TTTGTGAA
1 TTTGTGAA
15556041 GATTCAACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 9 0.33
21 18 0.67
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.40
Consensus pattern (20 bp):
TTTGTGAACTTGATCAAACC
Found at i:15557070 original size:20 final size:20
Alignment explanation
Indices: 15557045--15557085 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
15557035 CAATTCCTGT
*
15557045 AAAGGAATTGAAGAAAGAAG
1 AAAGGAATGGAAGAAAGAAG
15557065 AAAGGAATGGAAGAAAGAAG
1 AAAGGAATGGAAGAAAGAAG
15557085 A
1 A
15557086 TTTGGGGTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.32, T:0.07
Consensus pattern (20 bp):
AAAGGAATGGAAGAAAGAAG
Done.