Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A04
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: 82679320
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4050000 characters in sequence are not A, C, G, or T
File 10 of 255
Found at i:2911349 original size:26 final size:26
Alignment explanation
Indices: 2911320--2911427 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
2911310 TTATACAAAT
2911320 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
2911346 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
2911372 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
2911398 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
2911424 TGAT
1 TGAT
2911428 GGGAATTTCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:2913004 original size:22 final size:21
Alignment explanation
Indices: 2912977--2913017 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
2912967 CATGTTTGAC
2912977 TGTTGTTATTTACTGCATGCCA
1 TGTTGTTATTTACTG-ATGCCA
*
2912999 TGTTGTTATTTTCTGATGC
1 TGTTGTTATTTACTGATGC
2913018 ATGGGATTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.15, C:0.15, G:0.20, T:0.51
Consensus pattern (21 bp):
TGTTGTTATTTACTGATGCCA
Found at i:2917618 original size:44 final size:43
Alignment explanation
Indices: 2917531--2917651 Score: 197
Period size: 44 Copynumber: 2.8 Consensus size: 43
2917521 TTTATTGGAA
* *
2917531 AAAAACGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGG
1 AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCGCTTGTGGG
* *
2917574 AGATGCGCCGCTAAAGGTCAAGGCTTTTTAGCGGCGCTTGTGGG
1 AAAAGCGCCGCTAAAGGTCAAGGC-TTTTAGCGGCGCTTGTGGG
2917618 AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGC
1 AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGC
2917652 CCTTTTTTTA
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
43 31 0.44
44 40 0.56
ACGTcount: A:0.24, C:0.21, G:0.33, T:0.22
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCGCTTGTGGG
Found at i:2917670 original size:43 final size:42
Alignment explanation
Indices: 2917532--2917675 Score: 164
Period size: 43 Copynumber: 3.3 Consensus size: 42
2917522 TTATTGGAAA
*
2917532 AAAACGCCGCTAAAGGTCAAGGCTTTTAGCGG-CGTTTGTGGG
1 AAAACGCCGCTAAAGGTCAAGGCTTTTAGCGGCCCTTT-TGGG
** * *
2917574 AGATGCGCCGCTAAAGGTCAAGGCTTTTTAGCGGCGCTTGTGGG
1 A-AAACGCCGCTAAAGGTCAAGGC-TTTTAGCGGCCCTTTTGGG
***
2917618 AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCCCTTTTTTT
1 AAAA-CGCCGCTAAAGGTCAAGGCTTTTAGCGGCCCTTTTGGG
2917661 ACAAACGCCGCTAAA
1 A-AAACGCCGCTAAA
2917676 TTTGGCAGAT
Statistics
Matches: 85, Mismatches: 12, Indels: 9
0.80 0.11 0.08
Matches are distributed among these distances:
42 1 0.01
43 46 0.54
44 36 0.42
45 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.24
Consensus pattern (42 bp):
AAAACGCCGCTAAAGGTCAAGGCTTTTAGCGGCCCTTTTGGG
Found at i:2917762 original size:31 final size:31
Alignment explanation
Indices: 2917727--2917810 Score: 96
Period size: 31 Copynumber: 2.6 Consensus size: 31
2917717 CTTCCTGCAT
* * *
2917727 TAAAATCCAACCAAATACAACAAATATAATA
1 TAAAATACAACCAAAAACAACAAATATAACA
* *
2917758 TAAAATACAGCCAAAAACAACAAATTTAACA
1 TAAAATACAACCAAAAACAACAAATATAACA
2917789 TAAAAAAATACAACCAAAAACA
1 T---AAAATACAACCAAAAACA
2917811 TTAATTCTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
31 27 0.61
34 17 0.39
ACGTcount: A:0.64, C:0.19, G:0.01, T:0.15
Consensus pattern (31 bp):
TAAAATACAACCAAAAACAACAAATATAACA
Found at i:2923832 original size:9 final size:9
Alignment explanation
Indices: 2923721--2923822 Score: 134
Period size: 9 Copynumber: 11.4 Consensus size: 9
2923711 TATTTAAGTA
2923721 TTATATAAG
1 TTATATAAG
*
2923730 TTATGTAAG
1 TTATATAAG
*
2923739 TTATAT-AT
1 TTATATAAG
*
2923747 TTATCTAAG
1 TTATATAAG
2923756 TTATATAAG
1 TTATATAAG
2923765 TTATATAAG
1 TTATATAAG
* *
2923774 TTATGTATG
1 TTATATAAG
2923783 TTATATAAG
1 TTATATAAG
*
2923792 TTATGTAAG
1 TTATATAAG
*
2923801 TTATATATG
1 TTATATAAG
2923810 TTATATAAG
1 TTATATAAG
2923819 TTAT
1 TTAT
2923823 GTAAATTATG
Statistics
Matches: 78, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
8 6 0.08
9 72 0.92
ACGTcount: A:0.37, C:0.01, G:0.13, T:0.49
Consensus pattern (9 bp):
TTATATAAG
Found at i:2923957 original size:15 final size:15
Alignment explanation
Indices: 2923937--2923992 Score: 73
Period size: 15 Copynumber: 3.8 Consensus size: 15
2923927 AAGTAGCGGG
2923937 ATTAAATAATATTTA
1 ATTAAATAATATTTA
2923952 ATTAAATAATATTT-
1 ATTAAATAATATTTA
2923966 A-TAAA-AATTATTTTA
1 ATTAAATAA-TA-TTTA
2923981 ATTAAATAATAT
1 ATTAAATAATAT
2923993 ACATGTTGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
12 2 0.06
13 6 0.17
14 4 0.11
15 16 0.44
16 6 0.17
17 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
ATTAAATAATATTTA
Found at i:2924196 original size:24 final size:24
Alignment explanation
Indices: 2924169--2924236 Score: 111
Period size: 24 Copynumber: 2.8 Consensus size: 24
2924159 ACTTAAATGG
2924169 TAAAACGGACGATAATATTTGTGA
1 TAAAACGGACGATAATATTTGTGA
2924193 TAAAACGGA-GAATAATATTTGTGA
1 TAAAACGGACG-ATAATATTTGTGA
*
2924217 TAAAACGGACGAGAATATTT
1 TAAAACGGACGATAATATTT
2924237 CAATAATAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
23 1 0.02
24 39 0.95
25 1 0.02
ACGTcount: A:0.44, C:0.07, G:0.21, T:0.28
Consensus pattern (24 bp):
TAAAACGGACGATAATATTTGTGA
Found at i:2928860 original size:14 final size:14
Alignment explanation
Indices: 2928825--2928867 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
2928815 ATAATAATAT
2928825 ACCTTAAACTTT-A
1 ACCTTAAACTTTAA
2928838 ACCTTAAACTTTAA
1 ACCTTAAACTTTAA
* *
2928852 ACCTCAAACTATAA
1 ACCTTAAACTTTAA
2928866 AC
1 AC
2928868 TTACACTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 12 0.44
14 15 0.56
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.30
Consensus pattern (14 bp):
ACCTTAAACTTTAA
Found at i:2929124 original size:15 final size:15
Alignment explanation
Indices: 2929104--2929135 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2929094 AAATAATAAT
*
2929104 TTATATATATTTATC
1 TTATATACATTTATC
2929119 TTATATACATTTATC
1 TTATATACATTTATC
2929134 TT
1 TT
2929136 CTACATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATATACATTTATC
Found at i:2929578 original size:18 final size:18
Alignment explanation
Indices: 2929555--2929603 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
2929545 TTACACCCTA
2929555 AATATATATTATAA-TCTT
1 AATATATATTATAAGT-TT
*
2929573 AATATATATTAGAAGTTT
1 AATATATATTATAAGTTT
2929591 AATATATA-TATAA
1 AATATATATTATAA
2929604 CAAGGGACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 23 0.82
19 1 0.04
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (18 bp):
AATATATATTATAAGTTT
Found at i:2929956 original size:41 final size:41
Alignment explanation
Indices: 2929910--2930181 Score: 391
Period size: 41 Copynumber: 6.6 Consensus size: 41
2929900 TTACTTTTTT
* * *
2929910 GCGGCGTTTTTCCATAAGCGCCGCTAAAACATCGGCCTATA
1 GCGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCGACCTATA
* * *
2929951 GCGGCGTTTTTCCATAAGCGCCGCTAAAACATCGGCCTATA
1 GCGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCGACCTATA
* *
2929992 GCGGCGTTTTTCCAAAAGCCCCGCTAAAACCTCGGCCTATA
1 GCGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCGACCTATA
*
2930033 GCGGCGTTTTTCCAAAAGCACCGCTAAAACCTCGACCTATA
1 GCGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCGACCTATA
* *
2930074 GCGTCATTTTTCCAAAAGCGCCGCTAAAACCTCGACCTATA
1 GCGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCGACCTATA
* * * *
2930115 GCAGCGTTTTTGCAGAAGCGCCACTAAAACCTCGACCTATA
1 GCGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCGACCTATA
**
2930156 GCGGCGTTTTTCCAAAAAAGCCGCTA
1 GCGGCGTTTTTCCAAAAGCGCCGCTA
2930182 TTGTACAGTT
Statistics
Matches: 211, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 211 1.00
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (41 bp):
GCGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCGACCTATA
Found at i:2930221 original size:41 final size:41
Alignment explanation
Indices: 2930167--2930247 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 41
2930157 CGGCGTTTTT
2930167 CCAAAAAAGCCGCTATTG-TACAGTTTTTAGCGGCATTTGGG
1 CCAAAAAAGCCGCTATTGCT-CAGTTTTTAGCGGCATTTGGG
*
2930208 CCAAAAACA-CCGCTATTGCTCAGTTTTTAGCGGCGTTTGG
1 CCAAAAA-AGCCGCTATTGCTCAGTTTTTAGCGGCATTTGG
2930248 ATCTATTGCT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
41 35 0.95
42 2 0.05
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (41 bp):
CCAAAAAAGCCGCTATTGCTCAGTTTTTAGCGGCATTTGGG
Found at i:2930256 original size:30 final size:30
Alignment explanation
Indices: 2930220--2930276 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
2930210 AAAAACACCG
2930220 CTATTGCTCAGTTTTTAGCGGCGTTTGGAT
1 CTATTGCTCAGTTTTTAGCGGCGTTTGGAT
* *
2930250 CTATTGCTCTGTTTTTTGCGGCGTTTG
1 CTATTGCTCAGTTTTTAGCGGCGTTTG
2930277 CAATGTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.09, C:0.18, G:0.26, T:0.47
Consensus pattern (30 bp):
CTATTGCTCAGTTTTTAGCGGCGTTTGGAT
Found at i:2943448 original size:22 final size:22
Alignment explanation
Indices: 2943417--2943474 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 22
2943407 TTTTTATTGT
2943417 TCTTTCTCTTCCATTTT-TTTTCC
1 TCTTT-TCTTCC-TTTTCTTTTCC
*
2943440 TCTTTTCTT-CTTTTCTTTTTC
1 TCTTTTCTTCCTTTTCTTTTCC
2943461 -CTTTTCTTCTCTTT
1 TCTTTTCTTC-CTTT
2943475 CCTTGGGTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 12 0.39
21 6 0.19
22 8 0.26
23 5 0.16
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.71
Consensus pattern (22 bp):
TCTTTTCTTCCTTTTCTTTTCC
Found at i:2945810 original size:14 final size:14
Alignment explanation
Indices: 2945779--2945819 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
2945769 ATTAAGATTG
2945779 TAAAAAAT-ATAAA
1 TAAAAAATAATAAA
*
2945792 T-AAAAATAATTAA
1 TAAAAAATAATAAA
*
2945805 TAAAAAATAAAAAA
1 TAAAAAATAATAAA
2945819 T
1 T
2945820 TATTTTTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
12 6 0.26
13 6 0.26
14 11 0.48
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
TAAAAAATAATAAA
Found at i:2945977 original size:11 final size:11
Alignment explanation
Indices: 2945956--2946022 Score: 57
Period size: 11 Copynumber: 6.2 Consensus size: 11
2945946 AAATTTTGAA
2945956 TATTGTAAAAAT
1 TATT-TAAAAAT
2945968 TATTTAAAAAT
1 TATTTAAAAAT
2945979 TA-TTAAAAAT
1 TATTTAAAAAT
* **
2945989 GATAAAAAAAT
1 TATTTAAAAAT
* *
2946000 TA-TGAATAAT
1 TATTTAAAAAT
*
2946010 TATTAAAAAAT
1 TATTTAAAAAT
2946021 TA
1 TA
2946023 ATATATATAT
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
10 16 0.36
11 24 0.55
12 4 0.09
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.37
Consensus pattern (11 bp):
TATTTAAAAAT
Found at i:2945984 original size:10 final size:10
Alignment explanation
Indices: 2945961--2946018 Score: 62
Period size: 10 Copynumber: 5.6 Consensus size: 10
2945951 TTGAATATTG
2945961 TAAAAATTATT
1 TAAAAATTA-T
2945972 TAAAAATTAT
1 TAAAAATTAT
*
2945982 TAAAAATGAT
1 TAAAAATTAT
*
2945992 AAAAAAATTAT
1 -TAAAAATTAT
* *
2946003 GAATAATTAT
1 TAAAAATTAT
2946013 TAAAAA
1 TAAAAA
2946019 ATTAATATAT
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
10 22 0.56
11 17 0.44
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:2945985 original size:21 final size:21
Alignment explanation
Indices: 2945961--2946022 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
2945951 TTGAATATTG
*
2945961 TAAAAATTATTTAAAAATTAT
1 TAAAAATTATTAAAAAATTAT
* *
2945982 TAAAAATGATAAAAAAATTAT
1 TAAAAATTATTAAAAAATTAT
* *
2946003 GAATAATTATTAAAAAATTA
1 TAAAAATTATTAAAAAATTA
2946023 ATATATATAT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (21 bp):
TAAAAATTATTAAAAAATTAT
Found at i:2952663 original size:126 final size:126
Alignment explanation
Indices: 2952438--2952672 Score: 443
Period size: 126 Copynumber: 1.9 Consensus size: 126
2952428 TAGCCTTAAA
*
2952438 AGGATATTTGAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATTCTTC
1 AGGATATTCGAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATTCTTC
*
2952503 GAATTCTTTAAATACCGAACATTTCCTTTATTTTGAAAATTTTTTAGAGTGAACTGGTAAG
66 GAATTCTTTAAATACCGAACATTGCCTTTATTTTGAAAATTTTTTAGAGTGAACTGGTAAG
*
2952564 AGGATATTCGAATATTCAAGACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATTCTTC
1 AGGATATTCGAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATTCTTC
2952629 GAATTCTTTAAATACCGAACATTGCCTTTATTTTGAAAATTTTT
66 GAATTCTTTAAATACCGAACATTGCCTTTATTTTGAAAATTTTT
2952673 GAAAGAAGAT
Statistics
Matches: 106, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
126 106 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (126 bp):
AGGATATTCGAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATTCTTC
GAATTCTTTAAATACCGAACATTGCCTTTATTTTGAAAATTTTTTAGAGTGAACTGGTAAG
Found at i:2952791 original size:13 final size:13
Alignment explanation
Indices: 2952758--2952808 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
2952748 CTAACCATAT
* *
2952758 ATAAATAATAAAA
1 ATAATTAATAGAA
2952771 ATAA-TAATA-ATA
1 ATAATTAATAGA-A
*
2952783 GTAATTAATAGAA
1 ATAATTAATAGAA
2952796 ATAATTAATAGAA
1 ATAATTAATAGAA
2952809 CAACAGTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
11 1 0.03
12 9 0.27
13 22 0.67
14 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (13 bp):
ATAATTAATAGAA
Found at i:2953127 original size:15 final size:15
Alignment explanation
Indices: 2953107--2953152 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
2953097 AAAAATATAT
2953107 ATATATACAT-AATAA
1 ATATATA-ATAAATAA
2953122 ATATATAATAAATAA
1 ATATATAATAAATAA
*
2953137 ATAAATAATATAATAA
1 ATATATAATA-AATAA
2953153 TATGAAACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 2 0.07
15 21 0.75
16 5 0.18
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (15 bp):
ATATATAATAAATAA
Found at i:2953563 original size:18 final size:19
Alignment explanation
Indices: 2953540--2953576 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2953530 ATAACAAGTA
*
2953540 GGGTGAT-GGAGTTAGTGG
1 GGGTGATGGGAGGTAGTGG
2953558 GGGTGATGGGAGGTAGTGG
1 GGGTGATGGGAGGTAGTGG
2953577 ATGGTTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.16, C:0.00, G:0.59, T:0.24
Consensus pattern (19 bp):
GGGTGATGGGAGGTAGTGG
Found at i:2954012 original size:85 final size:85
Alignment explanation
Indices: 2953858--2954245 Score: 611
Period size: 85 Copynumber: 4.6 Consensus size: 85
2953848 AACGAAGATA
* *
2953858 AGATCTG-CAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTGCTC
1 AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTACTC
* **
2953922 TACCACTGCTCGAAGAG-CC
66 CACCACTGCTCGGCGAGCCC
* *
2953941 AGGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGTGAGTCTTTGACCTACT
1 A-GATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTACT
*
2954006 CCACCACTGCTCGGTGAGCCC
65 CCACCACTGCTCGGCGAGCCC
* * * *
2954027 A-AGTCTGTAAACTTTAGCCTGTTACCCTACTGCTTTGGGGGTTAAGACGAGTCTTCGACCTATT
1 AGA-TCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTACT
2954091 CCACCACTGCTCGGCGAGCCC
65 CCACCACTGCTCGGCGAGCCC
*
2954112 AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTGCTC
1 AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTACTC
*
2954177 CGCCACTGCTCGGCGAGCCC
66 CACCACTGCTCGGCGAGCCC
2954197 AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCG
1 AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCG
2954246 TGTATCTTTG
Statistics
Matches: 280, Mismatches: 20, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
83 1 0.00
84 7 0.03
85 268 0.96
86 4 0.01
ACGTcount: A:0.20, C:0.27, G:0.24, T:0.29
Consensus pattern (85 bp):
AGATCTGTAAATTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCGAGTCTTCGACCTACTC
CACCACTGCTCGGCGAGCCC
Found at i:2954316 original size:44 final size:44
Alignment explanation
Indices: 2954267--2954411 Score: 145
Period size: 44 Copynumber: 3.3 Consensus size: 44
2954257 TCTGCTCCAA
2954267 TATTGCTTAGGGAGATAAGATCTATAATCTTCAGCTTGTTACCC
1 TATTGCTTAGGGAGATAAGATCTATAATCTTCAGCTTGTTACCC
* * * * * * *
2954311 GATTGCTTAGGGAGTTAA-AGC-ATGTATCTT-TGATCTGCT-CCAC
1 TATTGCTTAGGGAGATAAGATCTAT-AATCTTCAGCT-TGTTACC-C
* *
2954354 TATTACTTAGGGAGATAAGATCTATAATTTTCAGCTTGTTACCC
1 TATTGCTTAGGGAGATAAGATCTATAATCTTCAGCTTGTTACCC
*
2954398 TATTGCTTAAGGAG
1 TATTGCTTAGGGAG
2954412 TTAAAGCCTG
Statistics
Matches: 76, Mismatches: 18, Indels: 14
0.70 0.17 0.13
Matches are distributed among these distances:
42 6 0.08
43 26 0.34
44 38 0.50
45 6 0.08
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.37
Consensus pattern (44 bp):
TATTGCTTAGGGAGATAAGATCTATAATCTTCAGCTTGTTACCC
Found at i:2954328 original size:87 final size:87
Alignment explanation
Indices: 2954216--2954418 Score: 325
Period size: 87 Copynumber: 2.3 Consensus size: 87
2954206 AATTTTAGCC
* * * * *
2954216 TGTTACCCTACTGCTTAGGGGGTTAAGGCGTGTATCTTTGATCTGCTCCAATATTGCTTAGGGAG
1 TGTTACCCTATTGCTTAGGGAGTTAAAGCATGTATCTTTGATCTGCTCCAATATTACTTAGGGAG
2954281 ATAAGATCTATAATCTTCAGCT
66 ATAAGATCTATAATCTTCAGCT
* *
2954303 TGTTACCCGATTGCTTAGGGAGTTAAAGCATGTATCTTTGATCTGCTCCACTATTACTTAGGGAG
1 TGTTACCCTATTGCTTAGGGAGTTAAAGCATGTATCTTTGATCTGCTCCAATATTACTTAGGGAG
*
2954368 ATAAGATCTATAATTTTCAGCT
66 ATAAGATCTATAATCTTCAGCT
*
2954390 TGTTACCCTATTGCTTAAGGAGTTAAAGC
1 TGTTACCCTATTGCTTAGGGAGTTAAAGC
2954419 CTGCTGAAAT
Statistics
Matches: 106, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 106 1.00
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (87 bp):
TGTTACCCTATTGCTTAGGGAGTTAAAGCATGTATCTTTGATCTGCTCCAATATTACTTAGGGAG
ATAAGATCTATAATCTTCAGCT
Found at i:2954364 original size:43 final size:43
Alignment explanation
Indices: 2954227--2954367 Score: 117
Period size: 43 Copynumber: 3.3 Consensus size: 43
2954217 GTTACCCTAC
* * * *
2954227 TGCTTAGGGGGTTAAGGCGTGTATCTTTGATCTGCTCCAATAT
1 TGCTTAGGGAGTTAAAGCATGTATCTTTGATCTGCTCCACTAT
* * * * * * *
2954270 TGCTTAGGGAGAT-AAG-ATCTATAATCTTCAGCTTGTTACC-CGAT
1 TGCTTAGGGAGTTAAAGCATGTAT-CT-TTGATC-TGCT-CCACTAT
2954314 TGCTTAGGGAGTTAAAGCATGTATCTTTGATCTGCTCCACTAT
1 TGCTTAGGGAGTTAAAGCATGTATCTTTGATCTGCTCCACTAT
*
2954357 TACTTAGGGAG
1 TGCTTAGGGAG
2954368 ATAAGATCTA
Statistics
Matches: 72, Mismatches: 19, Indels: 14
0.69 0.18 0.13
Matches are distributed among these distances:
41 4 0.06
42 5 0.07
43 31 0.43
44 21 0.29
45 6 0.08
46 5 0.07
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.35
Consensus pattern (43 bp):
TGCTTAGGGAGTTAAAGCATGTATCTTTGATCTGCTCCACTAT
Found at i:2962132 original size:21 final size:21
Alignment explanation
Indices: 2962106--2962150 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
2962096 ACTGGCTCAT
*
2962106 CATGTTGTTCTGTGACTCCAG
1 CATGTTGTTCTGGGACTCCAG
*
2962127 CATGTTTTTCTGGGACTCCAG
1 CATGTTGTTCTGGGACTCCAG
2962148 CAT
1 CAT
2962151 TTGATCCCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (21 bp):
CATGTTGTTCTGGGACTCCAG
Found at i:2965427 original size:11 final size:11
Alignment explanation
Indices: 2965411--2965435 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2965401 CGAGGAAGAT
2965411 TTGGTACTTGA
1 TTGGTACTTGA
2965422 TTGGTACTTGA
1 TTGGTACTTGA
2965433 TTG
1 TTG
2965436 ATTATTTAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.08, G:0.28, T:0.48
Consensus pattern (11 bp):
TTGGTACTTGA
Found at i:2965885 original size:126 final size:126
Alignment explanation
Indices: 2965650--2965889 Score: 428
Period size: 126 Copynumber: 1.9 Consensus size: 126
2965640 TAGCCTTAAA
*
2965650 AGGATATTCGAATATTCAAAACAAACAAAGAGAGCGAAACCCAGTACGTTAGGGCACGATTCTTC
1 AGGATATTCGAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATTCTTC
2965715 GAATTCTTTAAATACCAAACATTGCCTTTATTTTAAAAATTTTTGAGAGTGAACTGGTAAG
66 GAATTCTTTAAATACCAAACATTGCCTTTATTTTAAAAATTTTTGAGAGTGAACTGGTAAG
* *
2965776 AGGATCTTCGAATATTCAAGACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATTCTTC
1 AGGATATTCGAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATTCTTC
*
2965841 GAATTCTTTAAATACCGAACATTGCCTTTATTTTGAAAAA-TTTTGAGAG
66 GAATTCTTTAAATACCAAACATTGCCTTTATTTT-AAAAATTTTTGAGAG
2965890 AAGATCAATG
Statistics
Matches: 109, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
126 104 0.95
127 5 0.05
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (126 bp):
AGGATATTCGAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATTCTTC
GAATTCTTTAAATACCAAACATTGCCTTTATTTTAAAAATTTTTGAGAGTGAACTGGTAAG
Found at i:2966004 original size:13 final size:13
Alignment explanation
Indices: 2965971--2966021 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
2965961 CTAACCATAT
* *
2965971 ATAAATAATAAAA
1 ATAATTAATAGAA
2965984 ATAA-TAATA-ATA
1 ATAATTAATAGA-A
*
2965996 GTAATTAATAGAA
1 ATAATTAATAGAA
2966009 ATAATTAATAGAA
1 ATAATTAATAGAA
2966022 CAACAGTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
11 1 0.03
12 9 0.27
13 22 0.67
14 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (13 bp):
ATAATTAATAGAA
Found at i:2966779 original size:18 final size:18
Alignment explanation
Indices: 2966756--2966791 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2966746 ATAACAAGTA
*
2966756 GGGTGATGGAGTTAGTGG
1 GGGTGATGGAGGTAGTGG
2966774 GGGTGATGGAGGTAGTGG
1 GGGTGATGGAGGTAGTGG
2966792 ATGGTTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.58, T:0.25
Consensus pattern (18 bp):
GGGTGATGGAGGTAGTGG
Found at i:2966807 original size:29 final size:29
Alignment explanation
Indices: 2966774--2966836 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
2966764 GAGTTAGTGG
*
2966774 GGGTGATGGAGGTAGTGGAT-GGTTTAGTA
1 GGGTGATGGAGGTAGT-GATCGATTTAGTA
* *
2966803 GGGTGATGGAGTTAGTGATCGATTTAGTG
1 GGGTGATGGAGGTAGTGATCGATTTAGTA
2966832 GGGTG
1 GGGTG
2966837 TTTAATTTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 3 0.10
29 27 0.90
ACGTcount: A:0.19, C:0.02, G:0.48, T:0.32
Consensus pattern (29 bp):
GGGTGATGGAGGTAGTGATCGATTTAGTA
Found at i:2967458 original size:19 final size:19
Alignment explanation
Indices: 2967434--2967531 Score: 146
Period size: 19 Copynumber: 5.2 Consensus size: 19
2967424 AATCTTTAAG
* *
2967434 GATATGTAATCTTAAATAT
1 GATATGCAATCTTAGATAT
2967453 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
2967472 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
2967489 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
2967508 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
2967529 GAT
1 GAT
2967532 CTTGTAATCT
Statistics
Matches: 73, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
17 17 0.23
19 47 0.64
21 9 0.12
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:2967464 original size:36 final size:36
Alignment explanation
Indices: 2967424--2967511 Score: 112
Period size: 36 Copynumber: 2.5 Consensus size: 36
2967414 ATGGAAATAT
2967424 AATCTTTAAGGATATG-T-AATCTTAAATATGATATGC
1 AATCTTT-A-GATATGATAAATCTTAAATATGATATGC
*
2967460 AATC-TTAGATATGATACAATCTTAGATATGATATGC
1 AATCTTTAGATATGATA-AATCTTAAATATGATATGC
2967496 AATC-TTAGATATGATA
1 AATCTTTAGATATGATA
2967512 TGCAATCTTG
Statistics
Matches: 48, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
33 6 0.12
34 2 0.04
35 2 0.04
36 38 0.79
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.38
Consensus pattern (36 bp):
AATCTTTAGATATGATAAATCTTAAATATGATATGC
Found at i:2967470 original size:14 final size:15
Alignment explanation
Indices: 2967453--2967509 Score: 53
Period size: 17 Copynumber: 3.5 Consensus size: 15
2967443 TCTTAAATAT
2967453 GATATG-CAATCTTA
1 GATATGACAATCTTA
2967467 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
2967484 GATATGATATGCAATCTTA
1 GATATG--A--CAATCTTA
2967503 GATATGA
1 GATATGA
2967510 TATGCAATCT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
14 6 0.16
17 18 0.47
19 14 0.37
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.35
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:2967944 original size:16 final size:15
Alignment explanation
Indices: 2967916--2967967 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 15
2967906 TCTATGCATG
2967916 TATATAT-ATTATAT
1 TATATATCATTATAT
2967930 TATATATCATGTATAT
1 TATATATCAT-TATAT
2967946 CGTATATCATCTATTATAT
1 --TATAT-ATC-ATTATAT
2967965 TAT
1 TAT
2967968 TTATGTTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
14 7 0.22
15 2 0.06
16 5 0.16
17 3 0.09
18 5 0.16
19 8 0.25
20 2 0.06
ACGTcount: A:0.37, C:0.08, G:0.04, T:0.52
Consensus pattern (15 bp):
TATATATCATTATAT
Found at i:2973340 original size:7 final size:7
Alignment explanation
Indices: 2973328--2973393 Score: 52
Period size: 7 Copynumber: 9.7 Consensus size: 7
2973318 TCTATTTCAA
2973328 AAAAAAG
1 AAAAAAG
2973335 AAAAAAG
1 AAAAAAG
2973342 --AAAAG
1 AAAAAAG
2973347 -AAAAAG
1 AAAAAAG
2973353 AAAAAA-
1 AAAAAAG
* *
2973359 ATAATAAT
1 A-AAAAAG
2973367 AAAAATA-
1 AAAAA-AG
2973374 AAAAAGAG
1 AAAAA-AG
2973382 AAAAAAG
1 AAAAAAG
2973389 AAAAA
1 AAAAA
2973394 TGGAGAGGCC
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
5 5 0.10
6 6 0.12
7 32 0.64
8 7 0.14
ACGTcount: A:0.83, C:0.00, G:0.11, T:0.06
Consensus pattern (7 bp):
AAAAAAG
Found at i:2973350 original size:11 final size:12
Alignment explanation
Indices: 2973326--2973392 Score: 54
Period size: 11 Copynumber: 5.8 Consensus size: 12
2973316 CTTCTATTTC
2973326 AAAA-AAAAGAA
1 AAAAGAAAAGAA
2973337 AAAAGAAAAG-A
1 AAAAGAAAAGAA
2973348 AAAAGAAAA-AA
1 AAAAGAAAAGAA
* *
2973359 ATAATAATAA-AA
1 AAAAGAA-AAGAA
2973371 ATAAA-AAAGAGAA
1 A-AAAGAAA-AGAA
2973384 AAAAGAAAA
1 AAAAGAAAA
2973393 ATGGAGAGGC
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
11 21 0.46
12 17 0.37
13 8 0.17
ACGTcount: A:0.84, C:0.00, G:0.10, T:0.06
Consensus pattern (12 bp):
AAAAGAAAAGAA
Found at i:2974338 original size:44 final size:44
Alignment explanation
Indices: 2974286--2974463 Score: 191
Period size: 44 Copynumber: 4.0 Consensus size: 44
2974276 CAAGATTTGG
2974286 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGA
1 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGA
* * * * ** *
2974330 CATTCCTGTGCTTACAGCGAAGCAGATCGAAGATTTCAG--CATGG
1 CATCCCTGTGTTTATAGGGAA-CAGATCGAAGATAGCAGATC-TGA
* * * * *
2974374 TATCCCTGTATTTATAGGGAACA-AGTTGAAGATAGCAGATTTGG
1 CATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAGCAGATCTGA
*
2974418 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAACAGATCTGA
1 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGA
2974462 CA
1 CA
2974464 CTTCTGTGCT
Statistics
Matches: 105, Mismatches: 23, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
42 1 0.01
43 13 0.12
44 75 0.71
45 16 0.15
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.26
Consensus pattern (44 bp):
CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGA
Found at i:2974543 original size:44 final size:44
Alignment explanation
Indices: 2974488--2974719 Score: 170
Period size: 44 Copynumber: 5.3 Consensus size: 44
2974478 GCAAAGCAGA
*
2974488 TGGCATCCCTGTGTTTATAGGGAACA-AGTTGAAGATAGCAGATT
1 TGGCATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAGCAGATT
* * *
2974532 TGGTATCCCTGTGTTTATAGGGAACAGATCGAAGATAACAGATC
1 TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATT
* * * * * * **
2974576 TGACA-CTTCTGTGCTTACAGTGAAGCAGATCGAGGATTTCAGCA--
1 TGGCATC-CCTGTGTTTATAGGGAA-CAGATCGAAGATAGCAG-ATT
**
2974620 TGGCATCCCTGTGTTTATAGGGAACA-AGTTAAAGATAGCAGATT
1 TGGCATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAGCAGATT
* * * * ** *
2974664 TGGCATCTCTGTATTGT-CAGAGAGTAGATCGAAGATACCAGATT
1 TGGCATCCCTGTGTT-TATAGGGAACAGATCGAAGATAGCAGATT
*
2974708 TGGCATCTCTGT
1 TGGCATCCCTGT
2974720 ATTGGAGGAG
Statistics
Matches: 146, Mismatches: 32, Indels: 20
0.74 0.16 0.10
Matches are distributed among these distances:
42 2 0.01
43 11 0.08
44 114 0.78
45 18 0.12
46 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (44 bp):
TGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATT
Found at i:2974581 original size:117 final size:117
Alignment explanation
Indices: 2974370--2974605 Score: 427
Period size: 117 Copynumber: 2.0 Consensus size: 117
2974360 AGATTTCAGC
*
2974370 ATGGTATCCCTGTATTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCATCCCTGTGTTTATAG
1 ATGGCATCCCTGTATTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCATCCCTGTGTTTATAG
2974435 GGAACAGATCGAAGATAACAGATCTGACACTTCTGTGCTTACAGCAAAGCAG
66 GGAACAGATCGAAGATAACAGATCTGACACTTCTGTGCTTACAGCAAAGCAG
* *
2974487 ATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTTGGTATCCCTGTGTTTATAG
1 ATGGCATCCCTGTATTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCATCCCTGTGTTTATAG
**
2974552 GGAACAGATCGAAGATAACAGATCTGACACTTCTGTGCTTACAGTGAAGCAG
66 GGAACAGATCGAAGATAACAGATCTGACACTTCTGTGCTTACAGCAAAGCAG
2974604 AT
1 AT
2974606 CGAGGATTTC
Statistics
Matches: 114, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
117 114 1.00
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.28
Consensus pattern (117 bp):
ATGGCATCCCTGTATTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCATCCCTGTGTTTATAG
GGAACAGATCGAAGATAACAGATCTGACACTTCTGTGCTTACAGCAAAGCAG
Found at i:2974720 original size:44 final size:44
Alignment explanation
Indices: 2974651--2974742 Score: 141
Period size: 44 Copynumber: 2.1 Consensus size: 44
2974641 GAACAAGTTA
* *
2974651 AAGATAGCAGATTTGGCATCTCTGTATTGTCA-GAGAGTAGATCG
1 AAGATACCAGATTTGGCATCTCTGTATTG-CAGGAGAGCAGATCG
*
2974695 AAGATACCAGATTTGGCATCTCTGTATTGGAGGAGAGCAGATCG
1 AAGATACCAGATTTGGCATCTCTGTATTGCAGGAGAGCAGATCG
2974739 AAGA
1 AAGA
2974743 CATAGCTGAT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
43 1 0.02
44 43 0.98
ACGTcount: A:0.32, C:0.14, G:0.28, T:0.26
Consensus pattern (44 bp):
AAGATACCAGATTTGGCATCTCTGTATTGCAGGAGAGCAGATCG
Found at i:2975362 original size:205 final size:205
Alignment explanation
Indices: 2974729--2975437 Score: 1233
Period size: 204 Copynumber: 3.5 Consensus size: 205
2974719 TATTGGAGGA
* * *
2974729 GAGCAGATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAATCTAAGATGAT
1 GAGCAAATCAAAGACATAGCTGATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGAT
*
2974794 TTGGCATCTTTGTATTGTCAGAGAACAAATCAAAGTCTGGCATCTCCACTTCGACGGAGGGCAGA
66 TTGGCATCTCTGTATTGTCAGAGAACAAATCAAAGTCTGGCATCTCCACTTCGACGGAGGGCAGA
2974859 CACATAGCAGATCCAACCTTCAGATGTTTATACT-AAGTAGATCCAAGATGGTTTGGCATCCTTG
131 CACATAGCAGATCCAACCTTCAGATGTTTATACTGAAGTAGATCCAAGATGGTTTGGCATCCTTG
2974923 TGCTTACAAG
196 TGCTTACAAG
* * *
2974933 GAGCAAATCAAAGACATAACTGATTTGGCTTTCACGTGCTTACGTTGAAACAAATCTATGATGAT
1 GAGCAAATCAAAGACATAGCTGATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGAT
*
2974998 TTGGCATCTCTGTATTGTCAGAGAACAAATCAAAGTCTGGCATCTCCACTTCGACGGAGAGCA-A
66 TTGGCATCTCTGTATTGTCAGAGAACAAATCAAAGTCTGGCATCTCCACTTCGACGGAGGGCAGA
* *
2975062 CACATAGCAGATCCAAACTTTAGATGTTTATACTGAAGTAGATCCAAGATGGTTTGGCATCCTTG
131 CACATAGCAGATCCAACCTTCAGATGTTTATACTGAAGTAGATCCAAGATGGTTTGGCATCCTTG
2975127 TGCTTACAAG
196 TGCTTACAAG
**
2975137 GAGCAAATTGAAGACATAGCTGATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGAT
1 GAGCAAATCAAAGACATAGCTGATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGAT
* * * *
2975202 TTGGCATCTCTGTATTATCAGAGAACAAATCGAAGTCTAGCATCTCCACTTCGATGGAGGGCAGA
66 TTGGCATCTCTGTATTGTCAGAGAACAAATCAAAGTCTGGCATCTCCACTTCGACGGAGGGCAGA
*
2975267 CACATAGCAGATCCAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGGTTTGGCATCCTTG
131 CACATAGCAGATCCAACCTTCAGATGTTTATACTGAAGTAGATCCAAGATGGTTTGGCATCCTTG
2975332 TGCTTACAAG
196 TGCTTACAAG
*
2975342 GAGCAAATCAAAGACATAGCTGATTTGGCTTTCACGTGCTTACGTTAAAGCAAATCTAAGATGAT
1 GAGCAAATCAAAGACATAGCTGATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGAT
*
2975407 TTGGCATCTCTGTATTGTCAGGGAACAAATC
66 TTGGCATCTCTGTATTGTCAGAGAACAAATC
2975438 GAAGCAGCAG
Statistics
Matches: 475, Mismatches: 28, Indels: 3
0.94 0.06 0.01
Matches are distributed among these distances:
203 33 0.07
204 278 0.59
205 164 0.35
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.28
Consensus pattern (205 bp):
GAGCAAATCAAAGACATAGCTGATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGAT
TTGGCATCTCTGTATTGTCAGAGAACAAATCAAAGTCTGGCATCTCCACTTCGACGGAGGGCAGA
CACATAGCAGATCCAACCTTCAGATGTTTATACTGAAGTAGATCCAAGATGGTTTGGCATCCTTG
TGCTTACAAG
Found at i:2975596 original size:45 final size:45
Alignment explanation
Indices: 2975517--2975626 Score: 116
Period size: 45 Copynumber: 2.5 Consensus size: 45
2975507 GTTTGCAATG
* * * *
2975517 AGCAGATTAAAGA-AGCAAATTTAGCGTCTTTGTATTAGACGGTG-
1 AGCAGATCAAAGATAACAGATTTAGCGTCTCTGTATTAGACGG-GA
* * *
2975561 AGCAGATCGAAGATAACAGATTTGGCGTCTCTGTATTAGCCGGGA
1 AGCAGATCAAAGATAACAGATTTAGCGTCTCTGTATTAGACGGGA
* *
2975606 AGTAGATCAAAGATAGCAGAT
1 AGCAGATCAAAGATAACAGAT
2975627 ATCGCCTTCC
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
44 12 0.22
45 42 0.78
ACGTcount: A:0.35, C:0.14, G:0.26, T:0.25
Consensus pattern (45 bp):
AGCAGATCAAAGATAACAGATTTAGCGTCTCTGTATTAGACGGGA
Found at i:2976006 original size:19 final size:19
Alignment explanation
Indices: 2975982--2976060 Score: 126
Period size: 19 Copynumber: 4.2 Consensus size: 19
2975972 AATGTTTAAG
2975982 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
2976001 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
2976020 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
2976037 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
2976058 GAT
1 GAT
2976061 CTTGTAATCT
Statistics
Matches: 56, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.30
19 30 0.54
21 9 0.16
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:2976029 original size:36 final size:37
Alignment explanation
Indices: 2975988--2976060 Score: 130
Period size: 36 Copynumber: 2.0 Consensus size: 37
2975978 TAAGGATATG
2975988 CAATCTTAGATATGATATGCAATCTT-AGATATGATA
1 CAATCTTAGATATGATATGCAATCTTAAGATATGATA
2976024 CAATCTTAGATATGATATGCAATCTTGAAGATATGAT
1 CAATCTTAGATATGATATGCAATCTT-AAGATATGAT
2976061 CTTGTAATCT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
36 26 0.74
38 9 0.26
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (37 bp):
CAATCTTAGATATGATATGCAATCTTAAGATATGATA
Found at i:2983165 original size:28 final size:28
Alignment explanation
Indices: 2983129--2983183 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
2983119 AAGTACTGAA
*
2983129 AGCGTGTCCAACTAGAAGCGTTTTTTGT
1 AGCGCGTCCAACTAGAAGCGTTTTTTGT
2983157 AGCGCGTCCAACTAGAAGCGTTTTTTG
1 AGCGCGTCCAACTAGAAGCGTTTTTTG
2983184 CTAGGTTGGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (28 bp):
AGCGCGTCCAACTAGAAGCGTTTTTTGT
Found at i:2986533 original size:16 final size:16
Alignment explanation
Indices: 2986456--2986708 Score: 65
Period size: 16 Copynumber: 15.7 Consensus size: 16
2986446 AATCTAACCC
2986456 TATATA-TATTTAT-T
1 TATATATTATTTATAT
*
2986470 TCTATTATTA-TTATA-
1 TATA-TATTATTTATAT
* *
2986485 TATATATAAATT-T-T
1 TATATATTATTTATAT
* *
2986499 TATATTGTTATTTGT-T
1 TATA-TATTATTTATAT
2986515 TATATAGTTATTT-TAT
1 TATATA-TTATTTATAT
*
2986531 TATGTATTATTTATAT
1 TATATATTATTTATAT
2986547 TATTATATTA-TTAT-T
1 TA-TATATTATTTATAT
*
2986562 TTTCACTAATTA-TTATTAT
1 TAT-A-T-ATTATTTA-TAT
* *
2986581 TTTACATTA-TTAT-T
1 TATATATTATTTATAT
2986595 TATATATTATTGT-TA-
1 TATATATTATT-TATAT
* * *
2986610 TAT-TTTTACTTGTAT
1 TATATATTATTTATAT
*
2986625 TATATATTTATTAATTATT
1 TATATA-TTATTTA-TA-T
*
2986644 TATATGTATTATATATAT
1 TATA--TATTATTTATAT
*
2986662 TCACATATATACTTTCATAT
1 T-ATATAT-TA-TTT-ATAT
2986682 TATATATTATAATTAT-T
1 TATATATTAT--TTATAT
2986699 T-TATATTATT
1 TATATATTATT
2986709 ATGTCATTTT
Statistics
Matches: 182, Mismatches: 24, Indels: 66
0.67 0.09 0.24
Matches are distributed among these distances:
13 1 0.01
14 29 0.16
15 36 0.20
16 47 0.26
17 23 0.13
18 12 0.07
19 22 0.12
20 10 0.05
21 2 0.01
ACGTcount: A:0.33, C:0.04, G:0.03, T:0.61
Consensus pattern (16 bp):
TATATATTATTTATAT
Found at i:2986541 original size:3 final size:3
Alignment explanation
Indices: 2986522--2986610 Score: 53
Period size: 3 Copynumber: 29.3 Consensus size: 3
2986512 GTTTATATAG
*
2986522 TTA TT- TTA TTA TGTA TTA TT- TATA TTA TTA -TA TTA TTA TTT TTCA
1 TTA TTA TTA TTA T-TA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TT-A
* * *
2986567 CTAA TTA TTA TTA TT- TTA -CA TTA TTA TTTA TATA TTA TTG TTA T
1 -TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA T-TA TTA TTA TTA T
2986611 ATTTTTACTT
Statistics
Matches: 67, Mismatches: 8, Indels: 22
0.69 0.08 0.23
Matches are distributed among these distances:
2 8 0.12
3 47 0.70
4 11 0.16
5 1 0.01
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:2986549 original size:19 final size:19
Alignment explanation
Indices: 2986522--2986710 Score: 79
Period size: 19 Copynumber: 9.6 Consensus size: 19
2986512 GTTTATATAG
* *
2986522 TTATTTTATTATGTATTAT
1 TTATATTATTATTTATTAT
2986541 TTATATTATTATATTATTAT
1 TTATATTATTAT-TTATTAT
* *
2986561 TTTTCACTAATTA-TTATTATT
1 TTAT-A-TTATTATTTATTA-T
*
2986582 TTACATTATTATTTA-TAT
1 TTATATTATTATTTATTAT
* *
2986600 ATTATTGTTA-TATTT-TTAC
1 -TTA-TATTATTATTTATTAT
* *
2986619 TTGTATTATATATTTATTAA
1 TTATATTAT-TATTTATTAT
*
2986639 TTAT-TTA-TATGTATTAT
1 TTATATTATTATTTATTAT
* * *
2986656 ATATATTCA-CATATA-TACT
1 TTATATT-ATTATTTATTA-T
2986675 TTCATATTATATATTATAATTATT
1 TT-ATATTAT-TATT-T-ATTA-T
2986699 TTATATTATTAT
1 TTATATTATTAT
2986711 GTCATTTTTT
Statistics
Matches: 127, Mismatches: 23, Indels: 37
0.68 0.12 0.20
Matches are distributed among these distances:
17 15 0.12
18 7 0.06
19 44 0.35
20 33 0.26
21 6 0.05
22 9 0.07
23 8 0.06
24 5 0.04
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (19 bp):
TTATATTATTATTTATTAT
Found at i:2986557 original size:17 final size:17
Alignment explanation
Indices: 2986517--2986748 Score: 71
Period size: 17 Copynumber: 13.2 Consensus size: 17
2986507 TATTTGTTTA
2986517 TATAGTTATTT-TATTA-
1 TATA-TTATTTATATTAT
*
2986533 TGTATTATTTATATTAT
1 TATATTATTTATATTAT
2986550 TATATTA-TTAT-TT-T
1 TATATTATTTATATTAT
2986564 TCACTAATTA-TTATTATT-T
1 T-A-T-ATTATTTA-TATTAT
*
2986583 TACATTA-TTAT-TTA-
1 TATATTATTTATATTAT
*
2986597 TATATTATTGTTATATTTT
1 TATATTA-T-TTATATTAT
2986616 TACT-TGTATTATATATTTAT
1 TA-TAT-TATT-TATA-TTAT
2986636 TA-ATTATTTATATGTAT
1 TATATTATTTATAT-TAT
* *
2986653 TATATATATTCACA-TA-
1 TATAT-TATTTATATTAT
2986669 TATACTTTCATATTATA-TAT
1 TATA--TT-AT-TTATATTAT
2986689 TATAATTATTTTATATTAT
1 TAT-ATTA-TTTATATTAT
* *
2986708 TATGTCATTTTTTTATACTAT
1 TA--T-A-TTATTTATATTAT
* *
2986729 TATATTTTTTATCTTAT
1 TATATTATTTATATTAT
2986746 TAT
1 TAT
2986749 CATTTAAGTT
Statistics
Matches: 169, Mismatches: 15, Indels: 63
0.68 0.06 0.26
Matches are distributed among these distances:
14 10 0.06
15 10 0.06
16 25 0.15
17 43 0.25
18 21 0.12
19 33 0.20
20 11 0.07
21 14 0.08
22 2 0.01
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (17 bp):
TATATTATTTATATTAT
Found at i:2986591 original size:13 final size:14
Alignment explanation
Indices: 2986573--2986605 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2986563 TTCACTAATT
2986573 ATTATTATTT-TAC
1 ATTATTATTTATAC
*
2986586 ATTATTATTTATAT
1 ATTATTATTTATAC
2986600 ATTATT
1 ATTATT
2986606 GTTATATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTATTATTTATAC
Found at i:2986627 original size:53 final size:55
Alignment explanation
Indices: 2986458--2986632 Score: 155
Period size: 57 Copynumber: 3.1 Consensus size: 55
2986448 TCTAACCCTA
* * * * * *
2986458 TATATATTTATTTCTATTATTATTATATATATATAAATTTTTATATTGTTATTTGT-T
1 TATATA-TTATTT-TATCATTATTATTTATATAT-TATTATTATATTTTTACTTGTAT
* *
2986515 TATATAGTTATTTTATTATGTATTATTTATATTATTA-TATTATTATTTTTCAC-T-AAT
1 TATATA-TTATTTTATCAT-TATTATTTATA-TATTATTATTA-TATTTTT-ACTTGTAT
*
2986572 TAT-TATTATTTTA-CATTATTATTTATATATTATTGTTATATTTTTACTTGTAT
1 TATATATTATTTTATCATTATTATTTATATATTATTATTATATTTTTACTTGTAT
2986625 TATATATT
1 TATATATT
2986633 TATTAATTAT
Statistics
Matches: 99, Mismatches: 10, Indels: 21
0.76 0.08 0.16
Matches are distributed among these distances:
51 2 0.02
52 13 0.13
53 20 0.20
54 6 0.06
55 8 0.08
56 12 0.12
57 34 0.34
58 4 0.04
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (55 bp):
TATATATTATTTTATCATTATTATTTATATATTATTATTATATTTTTACTTGTAT
Found at i:2986704 original size:18 final size:17
Alignment explanation
Indices: 2986681--2986753 Score: 51
Period size: 21 Copynumber: 3.9 Consensus size: 17
2986671 TACTTTCATA
2986681 TTATA-TATTATAATTATT
1 TTATACTATTAT-ATT-TT
*
2986699 TTATATTATTATGTCATTTTT
1 TTATACTATTA--T-AT-TTT
2986720 TTATACTATTATATTTT
1 TTATACTATTATATTTT
2986737 TTAT-CTTATTATCATTT
1 TTATAC-TATTAT-ATTT
2986754 AAGTTTTAGC
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
16 1 0.02
17 13 0.28
18 11 0.23
19 6 0.13
21 15 0.32
22 1 0.02
ACGTcount: A:0.29, C:0.05, G:0.01, T:0.64
Consensus pattern (17 bp):
TTATACTATTATATTTT
Found at i:2987052 original size:17 final size:17
Alignment explanation
Indices: 2986995--2987052 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 17
2986985 TCTAAACCAT
*
2986995 TATATTTTATATTTTTA
1 TATATTATATATTTTTA
*
2987012 TATAATTAT-TATTCTTA
1 TAT-ATTATATATTTTTA
2987029 TA-A--ATATATTTTTA
1 TATATTATATATTTTTA
2987043 TATATTATAT
1 TATATTATAT
2987053 CATTAAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
13 2 0.06
14 9 0.27
15 2 0.06
17 16 0.48
18 4 0.12
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
TATATTATATATTTTTA
Found at i:2989060 original size:33 final size:33
Alignment explanation
Indices: 2989018--2989090 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 33
2989008 TTAAACCTAA
*
2989018 TTTT-AACTAGTTTTAAACATCAAAACCTTCTT
1 TTTTAAACTAGTTTTAAACATCAAAACCCTCTT
*
2989050 TTTTAAACTAGTTTTAAACGTCAAAACCCTCTT
1 TTTTAAACTAGTTTTAAACATCAAAACCCTCTT
2989083 TTTTAAAC
1 TTTTAAAC
2989091 ATAATAACTC
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 4 0.11
33 34 0.89
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.42
Consensus pattern (33 bp):
TTTTAAACTAGTTTTAAACATCAAAACCCTCTT
Found at i:2989938 original size:37 final size:37
Alignment explanation
Indices: 2989894--2990056 Score: 274
Period size: 37 Copynumber: 4.4 Consensus size: 37
2989884 CTTGTCCCTA
2989894 ATCAGATAAGTGTAGCCACCTATCACTTTGTTTCTTG
1 ATCAGATAAGTGTAGCCACCTATCACTTTGTTTCTTG
2989931 ATCAGATAAGTGTAGCCACCTATCACTTTGTTTCTTG
1 ATCAGATAAGTGTAGCCACCTATCACTTTGTTTCTTG
*
2989968 ATCAGATAAGTGTAGCCACTTATCACTTTGTTTCTTG
1 ATCAGATAAGTGTAGCCACCTATCACTTTGTTTCTTG
* * *
2990005 GTCAGATAAGTGTAGCCACTTATCAC-TTGTCTCTTG
1 ATCAGATAAGTGTAGCCACCTATCACTTTGTTTCTTG
*
2990041 ATCAGATAAGTATAGC
1 ATCAGATAAGTGTAGC
2990057 TAAAGCTATC
Statistics
Matches: 121, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
36 23 0.19
37 98 0.81
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (37 bp):
ATCAGATAAGTGTAGCCACCTATCACTTTGTTTCTTG
Found at i:2990099 original size:52 final size:52
Alignment explanation
Indices: 2990021--2990386 Score: 468
Period size: 52 Copynumber: 7.2 Consensus size: 52
2990011 TAAGTGTAGC
* * **
2990021 CACTTATCACTTGTCTCTTGATCAGATAAGTATAGCTAAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
*
2990073 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
*
2990125 CAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
* * ** *
2990171 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
*
2990223 CAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
2990269 CACTTTCCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
* * ** *
2990321 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
2990373 CACTTTGTCACTTG
1 CACTTT-TCACTTG
2990387 ATCAGAAGTA
Statistics
Matches: 275, Mismatches: 26, Indels: 25
0.84 0.08 0.08
Matches are distributed among these distances:
46 83 0.30
49 1 0.00
52 185 0.67
53 6 0.02
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:2990151 original size:98 final size:98
Alignment explanation
Indices: 2990021--2990378 Score: 520
Period size: 98 Copynumber: 3.6 Consensus size: 98
2990011 TAAGTGTAGC
* * *
2990021 CACTTATCAC-TTGTCTCTTGATCAGATAAGTATAGCTAAAGCTATCACTTATCACTTTTCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTCCACTT
2990085 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
66 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
2990118 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTCCACTT
** *
2990183 GTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
66 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
2990216 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTCCACTT
*
2990281 GTCACTTGATCAGATAAGTATAGCCGAAGCTAT
66 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* * * *
2990314 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTT
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTT
2990379 GTCACTTGAT
Statistics
Matches: 236, Mismatches: 18, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
97 10 0.04
98 182 0.77
100 1 0.00
104 43 0.18
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTCCACTT
GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:2990387 original size:150 final size:144
Alignment explanation
Indices: 2990028--2990392 Score: 577
Period size: 150 Copynumber: 2.5 Consensus size: 144
2990018 AGCCACTTAT
* * *
2990028 CACTTGTCTCTTGATCAGATAAGTATAGCTAAAGCTATCACTTATCACTTTTCACTTGTCACTTG
1 CACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC---T---TTGTCACTTG
*
2990093 ATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGA
60 ATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGA
2990158 AGCTATTACTTATCACTTTC
125 AGCTATTACTTATCACTTTC
2990178 CACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGA
1 CACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGA
*
2990243 TAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTATAGCCGA
66 TAAGTATAGCCGAAGCTATCACTTATCAC--T----TTGTCACTTGATCAGATAAGTATAGCCGA
2990308 AGCTATTACTTATCACTTTC
125 AGCTATTACTTATCACTTTC
2990328 CACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGA
1 CACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGA
2990393 AGTACTCAAA
Statistics
Matches: 204, Mismatches: 5, Indels: 12
0.92 0.02 0.05
Matches are distributed among these distances:
144 43 0.21
146 1 0.00
147 1 0.00
150 159 0.78
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.34
Consensus pattern (144 bp):
CACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGA
TAAGTATAGCCGAAGCTATCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
TACTTATCACTTTC
Found at i:2996792 original size:15 final size:14
Alignment explanation
Indices: 2996762--2996788 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2996752 AAATGTGTTT
2996762 TTTTTTAATATTTA
1 TTTTTTAATATTTA
2996776 TTTTTTAATATTT
1 TTTTTTAATATTT
2996789 TATTATACTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTTTAATATTTA
Found at i:2997061 original size:39 final size:37
Alignment explanation
Indices: 2997003--2997087 Score: 136
Period size: 39 Copynumber: 2.3 Consensus size: 37
2996993 TGCCGTCAAA
*
2997003 TAATGTAAC-TTATTTAATCACAAATGGATATTTTTG
1 TAATGTAACGTTATTTAATCACAAAAGGATATTTTTG
2997039 TAATGTAACGTCTCATTTAATCACAAAAGGATATTTTTG
1 TAATGTAACGT-T-ATTTAATCACAAAAGGATATTTTTG
2997078 TAATGTAACG
1 TAATGTAACG
2997088 CCTCGAAATT
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
36 9 0.20
37 1 0.02
38 1 0.02
39 34 0.76
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (37 bp):
TAATGTAACGTTATTTAATCACAAAAGGATATTTTTG
Found at i:2999819 original size:19 final size:18
Alignment explanation
Indices: 2999797--2999840 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
2999787 AAATAATTAT
2999797 TAAAAAAC-TAAAAGATATA
1 TAAAAAACTTAAAA-A-ATA
2999816 TAAAAAACTTAAAAAATA
1 TAAAAAACTTAAAAAATA
2999834 TAAAAAA
1 TAAAAAA
2999841 AAAACTCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.42
19 9 0.38
20 5 0.21
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.20
Consensus pattern (18 bp):
TAAAAAACTTAAAAAATA
Found at i:2999841 original size:20 final size:19
Alignment explanation
Indices: 2999798--2999842 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
2999788 AATAATTATT
* *
2999798 AAAAAACTAAAAGATATAT
1 AAAAAACTAAAAAATATAA
2999817 AAAAAACTTAAAAAATATAA
1 AAAAAAC-TAAAAAATATAA
2999837 AAAAAA
1 AAAAAA
2999843 AACTCTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (19 bp):
AAAAAACTAAAAAATATAA
Found at i:3001394 original size:14 final size:14
Alignment explanation
Indices: 3001375--3001422 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
3001365 AAGTTAATTA
3001375 TTTATATTAAAAAT
1 TTTATATTAAAAAT
**
3001389 TTTATAAGTTAATTA-
1 TTTAT-A-TTAAAAAT
3001404 TTTATATTAAAAAT
1 TTTATATTAAAAAT
3001418 TTTAT
1 TTTAT
3001423 GCATATGTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
13 5 0.19
14 11 0.41
15 6 0.22
16 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (14 bp):
TTTATATTAAAAAT
Found at i:3001397 original size:29 final size:29
Alignment explanation
Indices: 3001364--3001422 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
3001354 GATTAAAGAG
3001364 TAAGTTAATTATTTATATTAAAAATTTTA
1 TAAGTTAATTATTTATATTAAAAATTTTA
3001393 TAAGTTAATTATTTATATTAAAAATTTTA
1 TAAGTTAATTATTTATATTAAAAATTTTA
3001422 T
1 T
3001423 GCATATGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (29 bp):
TAAGTTAATTATTTATATTAAAAATTTTA
Found at i:3003319 original size:49 final size:49
Alignment explanation
Indices: 3003255--3003351 Score: 194
Period size: 49 Copynumber: 2.0 Consensus size: 49
3003245 TAAATTAGTT
3003255 CTTATACGTTAAATAAGAGAGTAAACATGTCATTCTATTAAAAATTCAA
1 CTTATACGTTAAATAAGAGAGTAAACATGTCATTCTATTAAAAATTCAA
3003304 CTTATACGTTAAATAAGAGAGTAAACATGTCATTCTATTAAAAATTCA
1 CTTATACGTTAAATAAGAGAGTAAACATGTCATTCTATTAAAAATTCA
3003352 TCTATTTTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.33
Consensus pattern (49 bp):
CTTATACGTTAAATAAGAGAGTAAACATGTCATTCTATTAAAAATTCAA
Found at i:3004026 original size:14 final size:15
Alignment explanation
Indices: 3004009--3004038 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
3003999 TAAATTTGAT
3004009 TAAATAAAA-TAAAA
1 TAAATAAAATTAAAA
3004023 TAAATAAAATTAAAA
1 TAAATAAAATTAAAA
3004038 T
1 T
3004039 TGAGTTAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
TAAATAAAATTAAAA
Found at i:3006365 original size:3 final size:3
Alignment explanation
Indices: 3006357--3006386 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3006347 TAATTATTTC
3006357 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3006387 TTTGCTAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3006855 original size:28 final size:28
Alignment explanation
Indices: 3006824--3006879 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
3006814 AACCCATGTA
* *
3006824 ATTTTTGTCCATTTTGGTAATTGTACTT
1 ATTTTGGTCCATTTTGGTAATTGAACTT
* *
3006852 ATTTTGGTCCGTTTTGGTACTTGAACTT
1 ATTTTGGTCCATTTTGGTAATTGAACTT
3006880 GACAAATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.16, C:0.12, G:0.18, T:0.54
Consensus pattern (28 bp):
ATTTTGGTCCATTTTGGTAATTGAACTT
Found at i:3014347 original size:27 final size:27
Alignment explanation
Indices: 3014306--3014357 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
3014296 ACAAGTGAGG
3014306 AAAAAGAGAAAGAGAATGAAAAAGAGC
1 AAAAAGAGAAAGAGAATGAAAAAGAGC
** *
3014333 AAAAAGAGATTGAGAGTGAAAAAGA
1 AAAAAGAGAAAGAGAATGAAAAAGA
3014358 AATTGAAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.63, C:0.02, G:0.27, T:0.08
Consensus pattern (27 bp):
AAAAAGAGAAAGAGAATGAAAAAGAGC
Found at i:3023301 original size:40 final size:38
Alignment explanation
Indices: 3023114--3023304 Score: 265
Period size: 38 Copynumber: 5.0 Consensus size: 38
3023104 AGCACCCGAT
* **
3023114 ATATATCCGGGTTAAGTCCTGCAGGCTTCGTGCTGGTA
1 ATATATCCGGGTTAAATCCCACAGGCTTCGTGCTGGTA
* * *
3023152 ATATATCTGGGTTAAGTCCCGCAGGCTTCGTGCTGGTA
1 ATATATCCGGGTTAAATCCCACAGGCTTCGTGCTGGTA
3023190 ATATATCCGGGTTAAATCCCACAGGCTTCGTGCTGGTA
1 ATATATCCGGGTTAAATCCCACAGGCTTCGTGCTGGTA
* *
3023228 ATATATCCAGGTTAAATCCCACAGGCTTAGTGCTGGTA
1 ATATATCCGGGTTAAATCCCACAGGCTTCGTGCTGGTA
* * *
3023266 TTATATCCGAGCTTAAAGTCCCACAGGCTTTGTGCTGGT
1 ATATATCCG-GGTTAAA-TCCCACAGGCTTCGTGCTGGT
3023305 GACTGGATTC
Statistics
Matches: 140, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
38 114 0.81
39 6 0.04
40 20 0.14
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (38 bp):
ATATATCCGGGTTAAATCCCACAGGCTTCGTGCTGGTA
Found at i:3030490 original size:79 final size:80
Alignment explanation
Indices: 3030314--3030538 Score: 271
Period size: 79 Copynumber: 2.8 Consensus size: 80
3030304 TTGAATGATG
* * * *
3030314 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATATCCGGACTAAGATCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTATATCCGGGCTAAGACCCGAAGGCAT
3030377 TTGTGCGAGATACTAAA
64 TTGTGCGAGATACTAAA
*
3030394 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATTCCGGGCTAAG-CCCGAAGGCAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTATA-TCCGGGCTAAGACCCGAAGGCAT
* *
3030456 TTGTGTGAGTTACTAAA
64 TTGTGCGAGATACTAAA
* * * * *
3030473 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATATCCGGGCTAAGACCCGAAGGCATTT
3030538 G
66 G
3030539 AATGAGTAGC
Statistics
Matches: 126, Mismatches: 12, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
78 1 0.01
79 68 0.54
80 46 0.37
81 10 0.08
82 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATATCCGGGCTAAGACCCGAAGGCATTT
GTGCGAGATACTAAA
Found at i:3030506 original size:40 final size:40
Alignment explanation
Indices: 3030314--3030538 Score: 271
Period size: 40 Copynumber: 5.7 Consensus size: 40
3030304 TTGAATGATG
* * * *
3030314 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
3030354 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
3030394 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
3030434 TCCGGGCTAAG-CCCGAAGGCATTTGTGTGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
3030473 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
3030514 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
3030539 AATGAGTAGC
Statistics
Matches: 165, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
39 34 0.21
40 121 0.73
41 10 0.06
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:3030530 original size:119 final size:120
Alignment explanation
Indices: 3030314--3030538 Score: 298
Period size: 119 Copynumber: 1.9 Consensus size: 120
3030304 TTGAATGATG
*
3030314 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
3030379 GTGCGAGATACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
66 GTGCGAGATACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
* * * **
3030434 TCCGGGCTAAG-CCCGAAGGCATTTGTG-TGAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * *
3030496 TTGTGCGAGTTACTATAA-CCGGGCTATG-TCCCGAAGGCATTTG
64 TTGTGCGAGATACTA-AATCCGGACTAAGAT-CCGAAGGCATTTG
3030539 AATGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
118 2 0.02
119 71 0.77
120 19 0.21
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:3030560 original size:79 final size:79
Alignment explanation
Indices: 3030321--3030571 Score: 262
Period size: 79 Copynumber: 3.2 Consensus size: 79
3030311 ATGTCCGGGC
* * * * *
3030321 TAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATTTGTGCG
1 TAAGTCCCGAAGGCATTTGTGC-GAGTTACTATATCCGGGCTAAG-TCCCGAAGGCATTTGTGTG
*
3030384 AGATACTAAATCCGGAC
64 AGATACTAAATCCGG-T
*
3030401 TAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATTCCGGGCTAAG-CCCGAAGGCATTTGTGTG
1 TAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGTCCCGAAGGCATTTGTGTG
*
3030463 AGTTACTAAATCCGGGT
64 AGATACTAAATCC-GGT
* * **
3030480 TAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTTGAATGAG
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGTGAG
*
3030545 -TAGCTATATCCGGT
66 ATA-CTAAATCCGGT
* *
3030559 TAAATTCCGAAGG
1 TAAGTCCCGAAGG
3030572 TACGTGATTT
Statistics
Matches: 146, Mismatches: 16, Indels: 19
0.81 0.09 0.10
Matches are distributed among these distances:
78 1 0.01
79 82 0.56
80 55 0.38
81 8 0.05
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.26
Consensus pattern (79 bp):
TAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGTGAG
ATACTAAATCCGGT
Found at i:3049913 original size:39 final size:39
Alignment explanation
Indices: 3049868--3049949 Score: 155
Period size: 39 Copynumber: 2.1 Consensus size: 39
3049858 ATGCAAGACA
3049868 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
*
3049907 CTGGAAATGTATCCGGGCTAAAGTCTCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
3049946 CTGG
1 CTGG
3049950 TAATATAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.20, C:0.24, G:0.32, T:0.24
Consensus pattern (39 bp):
CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
Found at i:3054414 original size:15 final size:14
Alignment explanation
Indices: 3054381--3054421 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
3054371 ACAGTTTTTG
3054381 ATTTGGGGAAAAAA
1 ATTTGGGGAAAAAA
*
3054395 GTTTGGGGAAAAAA
1 ATTTGGGGAAAAAA
*
3054409 TATTTGGAGAAAA
1 -ATTTGGGGAAAA
3054422 TGTTGGGGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.46, C:0.00, G:0.29, T:0.24
Consensus pattern (14 bp):
ATTTGGGGAAAAAA
Found at i:3054952 original size:125 final size:124
Alignment explanation
Indices: 3054712--3055116 Score: 449
Period size: 125 Copynumber: 3.2 Consensus size: 124
3054702 TGCACCTAGC
** ** * ** * * **
3054712 GCCGCTAAAGCTTGACCTATTGCGATGTTTTTAACCTAGCATCGCTAATGCCA-TAAAAATTCCA
1 GCCGCTATTGCTT-ACCTATTGCGGCGTTTTTCACCTAGCGCCACTAATGCCACTATAAACACCA
* * * ** **
3054776 TTAAAAACGACGCCGTTTTGTTTAAAGGAAAACGATTTTTTATGGCATTTTTATGAAAAAT
65 CTAAAAACGACGCCATTTTGTTTAAAGTAAAATTATTTTTTGCGGCATTTTTAT-AAAAAT
* * *
3054837 GCCTCTATTG--TAGTCTTTTTGCGGAC-TTTTTCACCTAGCGCCACTAATGCCACTATAAACAC
1 GCCGCTATTGCTTA--CCTATTGCGG-CGTTTTTCACCTAGCGCCACTAATGCCACTATAAACAC
* *
3054899 CACTAAAAACGGCGCCATTTTGTTTAAAGTAAAATTATTTTTTGCGGCGTTTTTATCAAAAAT
63 CACTAAAAACGACGCCATTTTGTTTAAAGTAAAATTATTTTTTGCGGCATTTTTAT-AAAAAT
* *
3054962 GCCGCTATTGCTTACCTATTGCGGCGTTTTTCACCTAGCGCCGCTAATGCCACTATAAACGCCAC
1 GCCGCTATTGCTTACCTATTGCGGCGTTTTTCACCTAGCGCCACTAATGCCACTATAAACACCAC
* *
3055027 TAAAAACGACGCTATTTTGTTTAAAGTAAAATTATTTTTTGCGGCATTTTTGATAAAAAC
66 TAAAAACGACGCCATTTTGTTTAAAGTAAAATTATTTTTTGCGGCATTTTT-ATAAAAAT
* * *
3055087 ACCGCTATTGCTTACCTTTTGTGGCGTTTT
1 GCCGCTATTGCTTACCTATTGCGGCGTTTT
3055117 CTCATAAATG
Statistics
Matches: 236, Mismatches: 36, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
122 1 0.00
123 1 0.00
124 30 0.13
125 200 0.85
126 2 0.01
127 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (124 bp):
GCCGCTATTGCTTACCTATTGCGGCGTTTTTCACCTAGCGCCACTAATGCCACTATAAACACCAC
TAAAAACGACGCCATTTTGTTTAAAGTAAAATTATTTTTTGCGGCATTTTTATAAAAAT
Found at i:3056351 original size:3 final size:3
Alignment explanation
Indices: 3056343--3056410 Score: 50
Period size: 3 Copynumber: 23.0 Consensus size: 3
3056333 CCTTTAACAG
* * * * *
3056343 AGA AGA AGA AGA A-A CAGC AGC AGC AGC AGA AGA AGA A-A AAA AGA
1 AGA AGA AGA AGA AGA -AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* *
3056387 AGA AGA AGA AGA AGC AGA AAA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA
3056411 TTAAAGAGCT
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
2 3 0.05
3 52 0.95
ACGTcount: A:0.63, C:0.09, G:0.28, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:3057406 original size:30 final size:31
Alignment explanation
Indices: 3057335--3057398 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
3057325 GGAAACCGTT
*
3057335 AGTTAGTGACTGTTTTGTCACTTTTTTATAA
1 AGTTAGTGACTGTTTTGTCACTTTTTCATAA
* *
3057366 CGTTAGTGACTGTTTTGTTA-TTTTTCA-AA
1 AGTTAGTGACTGTTTTGTCACTTTTTCATAA
3057395 AGTT
1 AGTT
3057399 GGGTGACTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 5 0.17
30 6 0.21
31 18 0.62
ACGTcount: A:0.22, C:0.09, G:0.17, T:0.52
Consensus pattern (31 bp):
AGTTAGTGACTGTTTTGTCACTTTTTCATAA
Found at i:3057607 original size:15 final size:15
Alignment explanation
Indices: 3057588--3057630 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
3057578 ACCCTTAAAC
3057588 ACTAAACCATAAAAT
1 ACTAAACCATAAAAT
*
3057603 CCTAAACCATAAAAT
1 ACTAAACCATAAAAT
3057618 ACTAAACCATAAA
1 ACTAAACCATAAA
3057631 CCATAAATCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.58, C:0.23, G:0.00, T:0.19
Consensus pattern (15 bp):
ACTAAACCATAAAAT
Found at i:3057716 original size:22 final size:21
Alignment explanation
Indices: 3057690--3057763 Score: 69
Period size: 22 Copynumber: 3.5 Consensus size: 21
3057680 ACATAAATAG
* *
3057690 TAAACCCTAAGCTATAAACCG
1 TAAACCCTAAACTATAAACCA
* *
3057711 TAAAACACTAAACCATAAACCA
1 T-AAACCCTAAACTATAAACCA
* **
3057733 TAAACCATAAACTAT-AATGA
1 TAAACCCTAAACTATAAACCA
3057753 TAAACCCTAAA
1 TAAACCCTAAA
3057764 ATAAATTTTT
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
20 13 0.31
21 12 0.29
22 17 0.40
ACGTcount: A:0.53, C:0.24, G:0.04, T:0.19
Consensus pattern (21 bp):
TAAACCCTAAACTATAAACCA
Found at i:3057763 original size:7 final size:7
Alignment explanation
Indices: 3057590--3057749 Score: 64
Period size: 7 Copynumber: 22.4 Consensus size: 7
3057580 CCTTAAACAC
3057590 TAAACCA
1 TAAACCA
3057597 TAAAATCC-
1 T-AAA-CCA
3057605 TAAACCA
1 TAAACCA
**
3057612 TAAAATA
1 TAAACCA
3057619 CTAAACCA
1 -TAAACCA
3057627 TAAACCA
1 TAAACCA
3057634 TAAATCC-
1 TAAA-CCA
3057641 TAAA-CA
1 TAAACCA
3057647 CTAAACTC-
1 -TAAAC-CA
*
3057655 TAAAACA
1 TAAACCA
3057662 TAAATTCC-
1 TAAA--CCA
* *
3057670 -AACCCT
1 TAAACCA
*
3057676 TAAAACA
1 TAAACCA
*
3057683 TAAA-TA
1 TAAACCA
*
3057689 GTAAACCC
1 -TAAACCA
* *
3057697 TAAGCTA
1 TAAACCA
*
3057704 TAAACCG
1 TAAACCA
*
3057711 TAAAACA
1 TAAACCA
3057718 CTAAACCA
1 -TAAACCA
3057726 TAAACCA
1 TAAACCA
3057733 TAAACCA
1 TAAACCA
*
3057740 TAAACTA
1 TAAACCA
3057747 TAA
1 TAA
3057750 TGATAAACCC
Statistics
Matches: 113, Mismatches: 23, Indels: 34
0.66 0.14 0.20
Matches are distributed among these distances:
5 3 0.03
6 4 0.04
7 85 0.75
8 17 0.15
9 4 0.04
ACGTcount: A:0.54, C:0.24, G:0.02, T:0.20
Consensus pattern (7 bp):
TAAACCA
Found at i:3076822 original size:27 final size:27
Alignment explanation
Indices: 3076790--3076968 Score: 153
Period size: 27 Copynumber: 6.5 Consensus size: 27
3076780 AAACTTCCAG
* * *
3076790 GAAAAGAATAGCCTGTGTGGCAAACTCC
1 GAAAAGAAT-GCCTTTATGGCAAACTCT
* * *
3076818 GAAAGGAATTCCTTTATGGAAAACTCT
1 GAAAAGAATGCCTTTATGGCAAACTCT
* *
3076845 GAAAAGAATAACCTTTGTGGCAAACT-T
1 GAAAAGAAT-GCCTTTATGGCAAACTCT
* * *
3076872 GAAAGGAATGTCTTTATGGAAAACTCT
1 GAAAAGAATGCCTTTATGGCAAACTCT
*
3076899 GAAAAAAATAGCCCTTTATGGCAAACTCT
1 GAAAAGAAT-G-CCTTTATGGCAAACTCT
* * * *
3076928 GAAAAGAATGCCTGTGTGGGAAAGTCT
1 GAAAAGAATGCCTTTATGGCAAACTCT
**
3076955 GAATGGAATGCCTT
1 GAAAAGAATGCCTT
3076969 GATGACACAT
Statistics
Matches: 120, Mismatches: 27, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
26 12 0.10
27 62 0.52
28 23 0.19
29 23 0.19
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (27 bp):
GAAAAGAATGCCTTTATGGCAAACTCT
Found at i:3076894 original size:54 final size:56
Alignment explanation
Indices: 3076790--3076937 Score: 203
Period size: 55 Copynumber: 2.7 Consensus size: 56
3076780 AAACTTCCAG
* * *
3076790 GAAAAGAATAGCCTGTGTGGCAAACTCCGAAAGGAAT-TCCTTTATGGAAAACTCT
1 GAAAAGAATAACCTTTGTGGCAAACTCTGAAAGGAATGTCCTTTATGGAAAACTCT
3076845 GAAAAGAATAACCTTTGTGGCAAACT-TGAAAGGAATGT-CTTTATGGAAAACTCT
1 GAAAAGAATAACCTTTGTGGCAAACTCTGAAAGGAATGTCCTTTATGGAAAACTCT
* * * *
3076899 GAAAAAAATAGCCCTTTATGGCAAACTCTGAAAAGAATG
1 GAAAAGAATA-ACCTTTGTGGCAAACTCTGAAAGGAATG
3076938 CCTGTGTGGG
Statistics
Matches: 83, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
54 34 0.41
55 39 0.47
56 10 0.12
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (56 bp):
GAAAAGAATAACCTTTGTGGCAAACTCTGAAAGGAATGTCCTTTATGGAAAACTCT
Found at i:3078341 original size:16 final size:17
Alignment explanation
Indices: 3078320--3078355 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
3078310 ATATCATTAT
*
3078320 AAATAA-TATTTAAATA
1 AAATAATTATTAAAATA
3078336 AAATAATTATTAAAATA
1 AAATAATTATTAAAATA
3078353 AAA
1 AAA
3078356 AGAATCCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATAATTATTAAAATA
Found at i:3087098 original size:4 final size:4
Alignment explanation
Indices: 3087089--3087133 Score: 90
Period size: 4 Copynumber: 11.2 Consensus size: 4
3087079 TTACTACTAA
3087089 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG T
3087134 TGTTGTTGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:3091483 original size:21 final size:21
Alignment explanation
Indices: 3091459--3091509 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
3091449 AATTTAAATT
3091459 GCAATAAAATAAATGGCTAAA
1 GCAATAAAATAAATGGCTAAA
3091480 GCAATAAAATAAATGGCTAAA
1 GCAATAAAATAAATGGCTAAA
**
3091501 TTAATAAAA
1 GCAATAAAA
3091510 ATTAAGTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.59, C:0.08, G:0.12, T:0.22
Consensus pattern (21 bp):
GCAATAAAATAAATGGCTAAA
Found at i:3093028 original size:19 final size:19
Alignment explanation
Indices: 3093004--3093043 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
3092994 TCAGAATAGT
3093004 TAGCAGGATTACCAGACTA
1 TAGCAGGATTACCAGACTA
*
3093023 TAGCAGGATTACTAGACTA
1 TAGCAGGATTACCAGACTA
3093042 TA
1 TA
3093044 CCTCTTGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (19 bp):
TAGCAGGATTACCAGACTA
Found at i:3096302 original size:18 final size:18
Alignment explanation
Indices: 3096279--3096314 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3096269 GTTGGTTGGG
3096279 TTTAGGGGAAACTCAAGA
1 TTTAGGGGAAACTCAAGA
3096297 TTTAGGGGAAACTCAAGA
1 TTTAGGGGAAACTCAAGA
3096315 AACGAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.28, T:0.22
Consensus pattern (18 bp):
TTTAGGGGAAACTCAAGA
Found at i:3097116 original size:20 final size:20
Alignment explanation
Indices: 3097079--3097116 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3097069 TGATGGGGAG
*
3097079 CAAGAATATCAAGTTGGATT
1 CAAGAATATCAAGCTGGATT
3097099 CAAGAA-ATCGAAGCTGGA
1 CAAGAATATC-AAGCTGGA
3097117 GGAGAGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.21
Consensus pattern (20 bp):
CAAGAATATCAAGCTGGATT
Found at i:3099031 original size:46 final size:46
Alignment explanation
Indices: 3098960--3099278 Score: 489
Period size: 46 Copynumber: 7.0 Consensus size: 46
3098950 AGTGTGCTCT
* *
3098960 CTGATATGAAATGTGTAAGATCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
3099006 CTAATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
3099052 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
3099098 CTGATATG-AATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
3099143 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* ***
3099189 GTGATATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
3099235 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
3099279 TCATGTCAAA
Statistics
Matches: 254, Mismatches: 17, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
45 45 0.18
46 209 0.82
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:3099215 original size:137 final size:138
Alignment explanation
Indices: 3098960--3099278 Score: 489
Period size: 137 Copynumber: 2.3 Consensus size: 138
3098950 AGTGTGCTCT
* *
3098960 CTGATATGAAATGTGTAAGATCATGGTTGAAAGATACCATGGCAGCCTAATATGAAATGTGTAAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTAATATGAAATGTGTAAG
***
3099025 ACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACC
66 ACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGAACAAGACCATGGTTGAAAGATACC
*
3099090 ATGGCAGC
131 ATGGCAAC
*
3099098 CTGATATG-AATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTAATATGAAATGTGTAAG
*
3099162 ACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGAACAAGACCATGGTTGAAAGATACC
66 ACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGAACAAGACCATGGTTGAAAGATACC
3099227 ATGGCAAC
131 ATGGCAAC
* * * * * *
3099235 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
3099279 TCATGTCAAA
Statistics
Matches: 165, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
136 1 0.01
137 125 0.76
138 39 0.24
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (138 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTAATATGAAATGTGTAAG
ACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGAACAAGACCATGGTTGAAAGATACC
ATGGCAAC
Found at i:3101330 original size:18 final size:18
Alignment explanation
Indices: 3101307--3101341 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3101297 ATGCAAATGT
3101307 ATAAAAACAAAAAATAAC
1 ATAAAAACAAAAAATAAC
* *
3101325 ATAAAAATAACAAATAA
1 ATAAAAACAAAAAATAA
3101342 TTTACGAGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.77, C:0.09, G:0.00, T:0.14
Consensus pattern (18 bp):
ATAAAAACAAAAAATAAC
Found at i:3101741 original size:12 final size:12
Alignment explanation
Indices: 3101710--3101819 Score: 61
Period size: 12 Copynumber: 9.0 Consensus size: 12
3101700 ATAAATAGTT
*
3101710 TATAATAAAATGA
1 TATAAT-AAATAA
3101723 TAT-ATAAATAA
1 TATAATAAATAA
3101734 TATAATAAATAA
1 TATAATAAATAA
*
3101746 TAAATATAATATAA
1 TATA-ATAA-ATAA
*
3101760 TATGTAATAATTTACA
1 TA--TAATAA-ATA-A
*
3101776 TATAA-ATATAA
1 TATAATAAATAA
3101787 -A-AATAAATAA
1 TATAATAAATAA
3101797 TAT-ATAAAGT-A
1 TATAATAAA-TAA
*
3101808 TTTAATAAATAA
1 TATAATAAATAA
3101820 ATTATGCAAA
Statistics
Matches: 77, Mismatches: 8, Indels: 25
0.70 0.07 0.23
Matches are distributed among these distances:
9 2 0.03
10 6 0.08
11 19 0.25
12 22 0.29
13 8 0.10
14 9 0.12
15 7 0.09
16 4 0.05
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (12 bp):
TATAATAAATAA
Found at i:3101769 original size:21 final size:21
Alignment explanation
Indices: 3101696--3101761 Score: 64
Period size: 21 Copynumber: 3.0 Consensus size: 21
3101686 CAAAATTTTT
*
3101696 AATAATAAATAGT-TTATAATAA
1 AATAATAAATA-TAATATAAT-A
3101718 AATGATATATAA-ATAATATAATA
1 AAT-A-ATA-AATATAATATAATA
3101741 AATAATAAATATAATATAATA
1 AATAATAAATATAATATAATA
3101762 TGTAATAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
20 2 0.05
21 14 0.37
22 4 0.11
23 6 0.16
24 10 0.26
25 2 0.05
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (21 bp):
AATAATAAATATAATATAATA
Found at i:3101820 original size:39 final size:40
Alignment explanation
Indices: 3101731--3101821 Score: 93
Period size: 38 Copynumber: 2.3 Consensus size: 40
3101721 GATATATAAA
* *
3101731 TAATATAATAAATAATAAATATAATATAATATGTAATAATT
1 TAATA-AATAAATAATAAAAATAATATAATATATAATAATT
3101772 TACAT--ATAAAT-ATAAAAATAA-ATAATATATAA-AGTATT
1 TA-ATAAATAAATAATAAAAATAATATAATATATAATA--ATT
3101810 TAATAAATAAAT
1 TAATAAATAAAT
3101822 TATGCAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
36 1 0.02
37 12 0.28
38 14 0.33
39 12 0.28
41 2 0.05
42 2 0.05
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.36
Consensus pattern (40 bp):
TAATAAATAAATAATAAAAATAATATAATATATAATAATT
Found at i:3103301 original size:132 final size:132
Alignment explanation
Indices: 3103105--3103552 Score: 637
Period size: 132 Copynumber: 3.4 Consensus size: 132
3103095 TACAGAGATG
* ** * * * *
3103105 CCAAATCTGCTATCTTCAATTTG-TATCTTCCAATACAGAGACGCCAAATTTGCTATCTTTGATC
1 CCAAATCTGCTATCTTCAATCTGCTATCTGGCAATACAGAGACACCAAATCTGTTATCTTCGATC
* * *
3103169 TGCTCTCTGACAATACAGAGACACTAAATCTGTTATCTTCGATCTGCTCTCTGACAATATAGAGA
66 TGCTCTCTGACAATATAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGACAATATAGAGA
3103234 CA
131 CA
* * * **
3103236 CCAAATCTGTTATCTTCAATCTGCTATCTGTCAATGCAGAGATGCCAAATCTGTTATCTTCGATC
1 CCAAATCTGCTATCTTCAATCTGCTATCTGGCAATACAGAGACACCAAATCTGTTATCTTCGATC
* *
3103301 TGCTCTCTGACAATATAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGGCAATATAGAGA
66 TGCTCTCTGACAATATAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGACAATATAGAGA
3103366 CA
131 CA
* * *
3103368 CCAAATCTTCTATCTTCAATCTGCTCTCTGGAAATACAGAGACACCAAATCTGTTATCTTCGATC
1 CCAAATCTGCTATCTTCAATCTGCTATCTGGCAATACAGAGACACCAAATCTGTTATCTTCGATC
* * *
3103433 TGCTCTCTGACAATATAGAGACGCCAAATCTGTTATCTTCGATCTGCTATTTGACAATACAGAGA
66 TGCTCTCTGACAATATAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGACAATATAGAGA
*
3103498 CG
131 CA
* * * *
3103500 CCAAATCTGCTGTGTTCGATCTGCTCTCTGGCAATACAGAGACACCAAATCTG
1 CCAAATCTGCTATCTTCAATCTGCTATCTGGCAATACAGAGACACCAAATCTG
3103553 CCACCGGTGA
Statistics
Matches: 283, Mismatches: 33, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
131 21 0.07
132 262 0.93
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (132 bp):
CCAAATCTGCTATCTTCAATCTGCTATCTGGCAATACAGAGACACCAAATCTGTTATCTTCGATC
TGCTCTCTGACAATATAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGACAATATAGAGA
CA
Found at i:3103565 original size:44 final size:44
Alignment explanation
Indices: 3103092--3103552 Score: 568
Period size: 44 Copynumber: 10.5 Consensus size: 44
3103082 TGCACCCCGC
** * * * * **
3103092 CAATACAGAGATGCCAAATCTGCTATCTTCAATTTG-TATCTTC
1 CAATACAGAGACACCAAATCTGTTATCTTCGATCTGCTCTCTGA
* * * *
3103135 CAATACAGAGACGCCAAATTTGCTATCTTTGATCTGCTCTCTGA
1 CAATACAGAGACACCAAATCTGTTATCTTCGATCTGCTCTCTGA
*
3103179 CAATACAGAGACACTAAATCTGTTATCTTCGATCTGCTCTCTGA
1 CAATACAGAGACACCAAATCTGTTATCTTCGATCTGCTCTCTGA
* * * *
3103223 CAATATAGAGACACCAAATCTGTTATCTTCAATCTGCTATCTGT
1 CAATACAGAGACACCAAATCTGTTATCTTCGATCTGCTCTCTGA
* **
3103267 CAATGCAGAGATGCCAAATCTGTTATCTTCGATCTGCTCTCTGA
1 CAATACAGAGACACCAAATCTGTTATCTTCGATCTGCTCTCTGA
* * * *
3103311 CAATATAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGG
1 CAATACAGAGACACCAAATCTGTTATCTTCGATCTGCTCTCTGA
* *
3103355 CAATATAGAGACACCAAATCT-TCTATCTTCAATCTGCTCTCTGGA
1 CAATACAGAGACACCAAATCTGT-TATCTTCGATCTGCTCTCT-GA
3103400 -AATACAGAGACACCAAATCTGTTATCTTCGATCTGCTCTCTGA
1 CAATACAGAGACACCAAATCTGTTATCTTCGATCTGCTCTCTGA
* * * *
3103443 CAATATAGAGACGCCAAATCTGTTATCTTCGATCTGCTATTTGA
1 CAATACAGAGACACCAAATCTGTTATCTTCGATCTGCTCTCTGA
* * * * *
3103487 CAATACAGAGACGCCAAATCTGCTGTGTTCGATCTGCTCTCTGG
1 CAATACAGAGACACCAAATCTGTTATCTTCGATCTGCTCTCTGA
3103531 CAATACAGAGACACCAAATCTG
1 CAATACAGAGACACCAAATCTG
3103553 CCACCGGTGA
Statistics
Matches: 365, Mismatches: 48, Indels: 9
0.86 0.11 0.02
Matches are distributed among these distances:
43 33 0.09
44 330 0.90
45 2 0.01
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (44 bp):
CAATACAGAGACACCAAATCTGTTATCTTCGATCTGCTCTCTGA
Found at i:3115596 original size:12 final size:12
Alignment explanation
Indices: 3115565--3115674 Score: 61
Period size: 11 Copynumber: 9.0 Consensus size: 12
3115555 ATAAATAGTT
*
3115565 TATAATAAAATGA
1 TATAAT-AAATAA
3115578 TAT-ATAAATAA
1 TATAATAAATAA
3115589 TATAATAAATAA
1 TATAATAAATAA
*
3115601 TAAAAATAATATAA
1 T-ATAATAA-ATAA
*
3115615 TATGTAATAATTTACA
1 TA--TAATAA-ATA-A
*
3115631 TATAA-ATATAA
1 TATAATAAATAA
3115642 -AT-ATAAATAA
1 TATAATAAATAA
3115652 TAT-ATAAAGT-A
1 TATAATAAA-TAA
*
3115663 TTTAATAAATAA
1 TATAATAAATAA
3115675 ATTATGCAAA
Statistics
Matches: 78, Mismatches: 8, Indels: 23
0.72 0.07 0.21
Matches are distributed among these distances:
9 1 0.01
10 7 0.09
11 20 0.26
12 20 0.26
13 11 0.14
14 8 0.10
15 8 0.10
16 3 0.04
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (12 bp):
TATAATAAATAA
Found at i:3115607 original size:21 final size:23
Alignment explanation
Indices: 3115565--3115616 Score: 72
Period size: 21 Copynumber: 2.3 Consensus size: 23
3115555 ATAAATAGTT
*
3115565 TATAATAAAATGATATATAAATAA
1 TATAAT-AAATGATATAAAAATAA
3115589 TATAATAAAT-A-ATAAAAATAA
1 TATAATAAATGATATAAAAATAA
3115610 TATAATA
1 TATAATA
3115617 TGTAATAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 16 0.59
22 1 0.04
23 4 0.15
24 6 0.22
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (23 bp):
TATAATAAATGATATAAAAATAA
Found at i:3115651 original size:16 final size:18
Alignment explanation
Indices: 3115632--3115673 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
3115622 TAATTTACAT
3115632 ATAAATATAAA-TA-TAA
1 ATAAATATAAAGTATTAA
*
3115648 ATAATATATAAAGTATTTA
1 ATAA-ATATAAAGTATTAA
3115667 ATAAATA
1 ATAAATA
3115674 AATTATGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 4 0.18
17 7 0.32
18 5 0.23
19 6 0.27
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
ATAAATATAAAGTATTAA
Found at i:3115654 original size:21 final size:20
Alignment explanation
Indices: 3115579--3115655 Score: 66
Period size: 21 Copynumber: 3.7 Consensus size: 20
3115569 ATAAAATGAT
*
3115579 ATATAAATAATATAATAAATA
1 ATATAAATAATATAATATA-A
* *
3115600 ATAAAAATAATATAATATGTA
1 ATATAAATAATATAATAT-AA
**
3115621 ATA-ATTTACATATAAATATAA
1 ATATAAATA-ATAT-AATATAA
3115642 ATATAAATAATATA
1 ATATAAATAATATA
3115656 TAAAGTATTT
Statistics
Matches: 44, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
20 4 0.09
21 32 0.73
22 8 0.18
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (20 bp):
ATATAAATAATATAATATAA
Found at i:3122369 original size:24 final size:24
Alignment explanation
Indices: 3122342--3122398 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
3122332 ATCACAAACA
3122342 TGCCAAAAGACCATACATTTCAAT
1 TGCCAAAAGACCATACATTTCAAT
*
3122366 TGCCAAAAGACCATACATTTGAAT
1 TGCCAAAAGACCATACATTTCAAT
*
3122390 TACCAAAAG
1 TGCCAAAAG
3122399 GCGGTCAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.44, C:0.23, G:0.11, T:0.23
Consensus pattern (24 bp):
TGCCAAAAGACCATACATTTCAAT
Found at i:3127621 original size:46 final size:46
Alignment explanation
Indices: 3127568--3127740 Score: 201
Period size: 46 Copynumber: 3.7 Consensus size: 46
3127558 TGGTTGAGCA
3127568 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAATG
* * * *
3127614 TCCGAACTCGTTGAGTTGAGTCTGAGTTC-GTGA-A-ATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAA-T--G
* *
3127659 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAATG
* *
3127707 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
3127741 GGGGCGGGTT
Statistics
Matches: 106, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 3 0.03
46 60 0.57
47 28 0.26
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAATG
Found at i:3127724 original size:93 final size:93
Alignment explanation
Indices: 3127565--3127735 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
3127555 GGATGGTTGA
* *
3127565 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAACGCCCGAACTCGTTGAGT
*
3127630 TGAGTCTGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* *
3127658 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAACGCCCGAACTCGTTGAGT
3127723 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
3127736 ACTTAGGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:3140918 original size:6 final size:5
Alignment explanation
Indices: 3140909--3140949 Score: 55
Period size: 5 Copynumber: 7.6 Consensus size: 5
3140899 TTTTGTGTTC
3140909 TTTAT CTTTAT CTTTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT -TTTAT -T-TTAT TTTAT TTTAT TTTAT TTTAT TTT
3140950 TCACATGTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
5 22 0.65
6 8 0.24
7 4 0.12
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTAT
Found at i:3140931 original size:5 final size:5
Alignment explanation
Indices: 3140921--3140949 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
3140911 TATCTTTATC
3140921 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
3140950 TCACATGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:3141073 original size:18 final size:18
Alignment explanation
Indices: 3141050--3141085 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3141040 GTTAGCTGGG
3141050 TTTAGGGGAAACTCAAGA
1 TTTAGGGGAAACTCAAGA
3141068 TTTAGGGGAAACTCAAGA
1 TTTAGGGGAAACTCAAGA
3141086 AACGAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.28, T:0.22
Consensus pattern (18 bp):
TTTAGGGGAAACTCAAGA
Found at i:3178161 original size:12 final size:12
Alignment explanation
Indices: 3178137--3178220 Score: 66
Period size: 12 Copynumber: 7.1 Consensus size: 12
3178127 GGAAAGGCAT
3178137 ATATAATATAATA
1 ATATAA-ATAATA
3178150 ATATAAATAATA
1 ATATAAATAATA
* * *
3178162 ATATACACTGAGA
1 ATATA-AATAATA
3178175 A-AT-AATAATA
1 ATATAAATAATA
3178185 ATATAAATAATA
1 ATATAAATAATA
* * *
3178197 GTAAAAATAAAA
1 ATATAAATAATA
*
3178209 ATA-AAAAAATA
1 ATATAAATAATA
3178220 A
1 A
3178221 AACAAAGCTC
Statistics
Matches: 56, Mismatches: 12, Indels: 8
0.74 0.16 0.11
Matches are distributed among these distances:
10 5 0.09
11 9 0.16
12 31 0.55
13 11 0.20
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (12 bp):
ATATAAATAATA
Found at i:3178649 original size:13 final size:13
Alignment explanation
Indices: 3178631--3178690 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 13
3178621 GGGTGGTTTA
3178631 GGTGGCCAAGGTG
1 GGTGGCCAAGGTG
***
3178644 GGTGGCCAACAAG
1 GGTGGCCAAGGTG
*** *
3178657 GGTGGTGGA-GTA
1 GGTGGCCAAGGTG
3178669 GGTGGCCAAGGTG
1 GGTGGCCAAGGTG
3178682 GGTGGCCAA
1 GGTGGCCAA
3178691 CAAGGGTGGT
Statistics
Matches: 33, Mismatches: 13, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
12 6 0.18
13 27 0.82
ACGTcount: A:0.20, C:0.15, G:0.50, T:0.15
Consensus pattern (13 bp):
GGTGGCCAAGGTG
Found at i:3178671 original size:38 final size:38
Alignment explanation
Indices: 3178629--3178711 Score: 157
Period size: 38 Copynumber: 2.2 Consensus size: 38
3178619 TGGGGTGGTT
*
3178629 TAGGTGGCCAAGGTGGGTGGCCAACAAGGGTGGTGGAG
1 TAGGTGGCCAAGGTGGGTGGCCAACAAGGGTGGTGAAG
3178667 TAGGTGGCCAAGGTGGGTGGCCAACAAGGGTGGTGAAG
1 TAGGTGGCCAAGGTGGGTGGCCAACAAGGGTGGTGAAG
3178705 TAGGTGG
1 TAGGTGG
3178712 GATTAGGGTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 44 1.00
ACGTcount: A:0.22, C:0.12, G:0.49, T:0.17
Consensus pattern (38 bp):
TAGGTGGCCAAGGTGGGTGGCCAACAAGGGTGGTGAAG
Found at i:3178772 original size:12 final size:12
Alignment explanation
Indices: 3178755--3178779 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3178745 TTGGCTTAGT
3178755 GTTTTGGGCTAA
1 GTTTTGGGCTAA
3178767 GTTTTGGGCTAA
1 GTTTTGGGCTAA
3178779 G
1 G
3178780 GGTTTTGGGT
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:0.08, G:0.36, T:0.40
Consensus pattern (12 bp):
GTTTTGGGCTAA
Found at i:3179127 original size:21 final size:21
Alignment explanation
Indices: 3179103--3179167 Score: 51
Period size: 21 Copynumber: 3.1 Consensus size: 21
3179093 TCCACTGAAA
3179103 CTTCAAGGAGATCTGCTGTAG
1 CTTCAAGGAGATCTGCTGTAG
* ** ** * *
3179124 CTTCGATTA-ATCCACTGAAA
1 CTTCAAGGAGATCTGCTGTAG
*
3179144 CTTCAAGGAGATCTGCTGTGG
1 CTTCAAGGAGATCTGCTGTAG
3179165 CTT
1 CTT
3179168 TTAGCTGCTC
Statistics
Matches: 28, Mismatches: 15, Indels: 2
0.62 0.33 0.04
Matches are distributed among these distances:
20 13 0.46
21 15 0.54
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.31
Consensus pattern (21 bp):
CTTCAAGGAGATCTGCTGTAG
Found at i:3179392 original size:87 final size:87
Alignment explanation
Indices: 3179214--3179555 Score: 442
Period size: 87 Copynumber: 4.0 Consensus size: 87
3179204 TGATTTTCAA
* ** * *
3179214 CCTGTTACCCTACTGCTTAGGGGGTTAAGGTTGTCATCA--TT-GATCTGTTTCCCTACTGCTGA
1 CCTGTTACCCTACTGCTTAGGGGTTTAA-G-ACTCATCACCTTCAATCTGTTTCCCTACTGCTTA
** * *
3179276 -GGTTTTAAGATCTTGTAAAATGAG
64 GGGGGTTAAGATC-TGTAAATTTAG
* * *
3179300 CCTGTTACCCTACTGCTTAGGGGTTTAAGGCTCATCGCCTTCGATCTGTTTCCCTACTGCTTAGG
1 CCTGTTACCCTACTGCTTAGGGGTTTAAGACTCATCACCTTCAATCTGTTTCCCTACTGCTTAGG
3179365 GGGTTAAGATCTGTAAATTTAG
66 GGGTTAAGATCTGTAAATTTAG
* * * *
3179387 TCTGTTACCCTACTGCTTAGGGTTTTAAGACTCATCATCTTCAATCTGCTTCCCTACTGCTTAGG
1 CCTGTTACCCTACTGCTTAGGGGTTTAAGACTCATCACCTTCAATCTGTTTCCCTACTGCTTAGG
* *
3179452 GGGTTGAGGTCTGTAAATTTAG
66 GGGTTAAGATCTGTAAATTTAG
*
3179474 CCTGTTACCCTACTGCTTAGGGGTTTAAGACTCATCATCTTCAAT-TGTTTCCCTACTGCTTAGG
1 CCTGTTACCCTACTGCTTAGGGGTTTAAGACTCATCACCTTCAATCTGTTTCCCTACTGCTTAGG
*
3179538 GGGTTGAGATCTGTAAAT
66 GGGTTAAGATCTGTAAAT
3179556 CTTCAATCTG
Statistics
Matches: 230, Mismatches: 22, Indels: 8
0.88 0.08 0.03
Matches are distributed among these distances:
84 5 0.02
85 1 0.00
86 64 0.28
87 150 0.65
88 10 0.04
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.37
Consensus pattern (87 bp):
CCTGTTACCCTACTGCTTAGGGGTTTAAGACTCATCACCTTCAATCTGTTTCCCTACTGCTTAGG
GGGTTAAGATCTGTAAATTTAG
Found at i:3179405 original size:43 final size:43
Alignment explanation
Indices: 3179215--3179555 Score: 207
Period size: 43 Copynumber: 7.9 Consensus size: 43
3179205 GATTTTCAAC
* * *
3179215 CTGTTACCCTACTGCTTAGGGGGTTAAGGT-TGTCATCATTGA-T
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGT-A-AATTTAGT
* * ** * * *
3179258 CTGTTTCCCTACTGCTGA-GGTTTTAAGATCTTGTAAAATGAGC
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATC-TGTAAATTTAGT
* * * **** *
3179301 CTGTTACCCTACTGCTTAGGGGTTTAAG-GCTCATCGCCTTCGAT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCT-GTAAATTTAG-T
*
3179345 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATTTAGT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTTAGT
** * * *
3179388 CTGTTACCCTACTGCTTAGGGTTTTAAGA-CT-CATCATCTTCAAT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTA-AAT-TT-AGT
* * *
3179432 CTGCTT-CCCTACTGCTTAGGGGGTTGAGGTCTGTAAATTTAGC
1 CTG-TTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTTAGT
* * * *
3179475 CTGTTACCCTACTGCTTAGGGGTTTAAGA-CT-CATCATCTTCAAT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTA-AAT-TT-AGT
* *
3179519 -TGTTTCCCTACTGCTTAGGGGGTTGAGATCTGTAAAT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAAT
3179556 CTTCAATCTG
Statistics
Matches: 224, Mismatches: 55, Indels: 37
0.71 0.17 0.12
Matches are distributed among these distances:
41 2 0.01
42 23 0.10
43 117 0.52
44 72 0.32
45 9 0.04
46 1 0.00
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.37
Consensus pattern (43 bp):
CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTTAGT
Found at i:3179788 original size:86 final size:85
Alignment explanation
Indices: 3179693--3179863 Score: 245
Period size: 86 Copynumber: 2.0 Consensus size: 85
3179683 GTAAATTTGG
* * *
3179693 CTTGTTACCCTACTGCTTAGGGGGTTAAAGGTCATT-ATTTTATCTGTTTCCCTACTGCTTATGG
1 CTTGTTACCCTACTGCTTAGGGGGTTAAAGCTCATTCATTTGATCTGTTCCCCTACTGCTTATGG
3179757 TGATAAGATCTATGAACTTCAA
66 -GATAAGATCTATGAA-TTCAA
* *
3179779 CTTGTTACCCTACTGCTTAGGGGGTTAAAGCTCGTTGCCTTTGATCTGTTCCCCTACTGCTTATG
1 CTTGTTACCCTACTGCTTAGGGGGTTAAAGCTCATT-CATTTGATCTGTTCCCCTACTGCTTATG
* *
3179844 GGGTAAGATCTGTGAATTCA
65 GGATAAGATCTATGAATTCA
3179864 CTGATTCTAG
Statistics
Matches: 76, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
86 38 0.50
87 13 0.17
88 25 0.33
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.38
Consensus pattern (85 bp):
CTTGTTACCCTACTGCTTAGGGGGTTAAAGCTCATTCATTTGATCTGTTCCCCTACTGCTTATGG
GATAAGATCTATGAATTCAA
Found at i:3187893 original size:19 final size:19
Alignment explanation
Indices: 3187851--3187897 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
3187841 AGTGAAAGTT
*
3187851 TAATGCAAATGTTTCAATG
1 TAATGCAAATGTTGCAATG
*
3187870 TAATGCAAATGTATGGAATG
1 TAATGCAAATGT-TGCAATG
3187890 -AATGCAAA
1 TAATGCAAA
3187898 AGAAAGGAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 20 0.80
20 5 0.20
ACGTcount: A:0.43, C:0.09, G:0.19, T:0.30
Consensus pattern (19 bp):
TAATGCAAATGTTGCAATG
Done.