Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 142 of 310
Found at i:46395056 original size:9 final size:9
Alignment explanation
Indices: 46395029--46395076 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
46395019 TAAATTTTAC
46395029 AATTCGAAT
1 AATTCGAAT
*
46395038 AACTT-AAAT
1 AA-TTCGAAT
46395047 AATTCGAAT
1 AATTCGAAT
*
46395056 AACTCGAAT
1 AATTCGAAT
*
46395065 AATTCAAAT
1 AATTCGAAT
46395074 AAT
1 AAT
46395077 AGATTGGTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
8 2 0.06
9 28 0.88
10 2 0.06
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.31
Consensus pattern (9 bp):
AATTCGAAT
Found at i:46395208 original size:20 final size:20
Alignment explanation
Indices: 46395159--46395210 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
46395149 TACAAAAAAA
* *
46395159 AAAAATTCAAAATTTTTTTT
1 AAAAATTCAAAATTATTTAT
46395179 AAAGAATTCAAAA-TATTTAT
1 AAA-AATTCAAAATTATTTAT
46395199 AAAAATTTCAAA
1 AAAAA-TTCAAA
46395211 TTTTATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 2 0.07
20 17 0.61
21 9 0.32
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (20 bp):
AAAAATTCAAAATTATTTAT
Found at i:46395895 original size:3 final size:3
Alignment explanation
Indices: 46395889--46395915 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
46395879 TCCCATACAA
46395889 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
46395916 TTCAAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:46398603 original size:31 final size:31
Alignment explanation
Indices: 46398561--46398644 Score: 141
Period size: 31 Copynumber: 2.7 Consensus size: 31
46398551 TCGGTTTGCT
* *
46398561 GGTGTTCTTCACTGAGTGTTTTCTATTTTTG
1 GGTGTTTTTCACTGAATGTTTTCTATTTTTG
46398592 GGTGTTTTTCACTGAATGTTTTCTATTTTTG
1 GGTGTTTTTCACTGAATGTTTTCTATTTTTG
*
46398623 GGTGTTTTTCACTGATTGTTTT
1 GGTGTTTTTCACTGAATGTTTT
46398645 TTTGCGTTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 50 1.00
ACGTcount: A:0.11, C:0.11, G:0.21, T:0.57
Consensus pattern (31 bp):
GGTGTTTTTCACTGAATGTTTTCTATTTTTG
Found at i:46400839 original size:25 final size:25
Alignment explanation
Indices: 46400811--46400978 Score: 158
Period size: 25 Copynumber: 6.8 Consensus size: 25
46400801 GTTCCAACCC
*
46400811 ACAGCTCGTGTGAGCATACCAATTT
1 ACAGCTCGTGTGAGCATACCGATTT
** *
46400836 ACAGCTCGTAAGAGCATACCGATCT
1 ACAGCTCGTGTGAGCATACCGATTT
* *
46400861 ACAGCTCGTGAGAGCATACTGATTT
1 ACAGCTCGTGTGAGCATACCGATTT
* **
46400886 ACAGCTTGTGTGAGCATATTGATTT
1 ACAGCTCGTGTGAGCATACCGATTT
* * * *
46400911 ACAGCTTGTGAGATCATACCGATCT
1 ACAGCTCGTGTGAGCATACCGATTT
* * * * *
46400936 ATAGCTCGAGTGAACATA-CAATTC
1 ACAGCTCGTGTGAGCATACCGATTT
*
46400960 ACAGCTCGTATGAGCATAC
1 ACAGCTCGTGTGAGCATAC
46400979 ATGTAGAGGA
Statistics
Matches: 115, Mismatches: 27, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
24 17 0.15
25 98 0.85
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (25 bp):
ACAGCTCGTGTGAGCATACCGATTT
Found at i:46400954 original size:75 final size:74
Alignment explanation
Indices: 46400810--46400978 Score: 203
Period size: 75 Copynumber: 2.3 Consensus size: 74
46400800 CGTTCCAACC
* *
46400810 CACAGCTCGTGTGAGCATACCAATTTACAGCTCGTAAGAGCATACCGATCTACAGCTCGTGAGAG
1 CACAGCTCGTGTGAGCATACCAATTTACAGCTCGTAAGAGCATACCGATCTACAGCTCGAGAGAA
*
46400875 CATACTGATT
66 CATAC-AATT
* * *** * * * * *
46400885 TACAGCTTGTGTGAGCATATTGATTTACAGCTTGTGAGATCATACCGATCTATAGCTCGAGTGAA
1 CACAGCTCGTGTGAGCATACCAATTTACAGCTCGTAAGAGCATACCGATCTACAGCTCGAGAGAA
46400950 CATACAATT
66 CATACAATT
*
46400959 CACAGCTCGTATGAGCATAC
1 CACAGCTCGTGTGAGCATAC
46400979 ATGTAGAGGA
Statistics
Matches: 77, Mismatches: 17, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
74 19 0.25
75 58 0.75
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (74 bp):
CACAGCTCGTGTGAGCATACCAATTTACAGCTCGTAAGAGCATACCGATCTACAGCTCGAGAGAA
CATACAATT
Found at i:46402104 original size:20 final size:20
Alignment explanation
Indices: 46402071--46402109 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
46402061 GCCATATGGT
46402071 TTGGCTTGTGTTATGGTATC
1 TTGGCTTGTGTTATGGTATC
46402091 TTGG-TTGTGATTATGGTAT
1 TTGGCTTGTG-TTATGGTAT
46402110 TTTTGAATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.13, C:0.05, G:0.31, T:0.51
Consensus pattern (20 bp):
TTGGCTTGTGTTATGGTATC
Found at i:46402129 original size:14 final size:15
Alignment explanation
Indices: 46402104--46402133 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
46402094 GTTGTGATTA
46402104 TGGTATTTTTGAATG
1 TGGTATTTTTGAATG
46402119 TGGTA-TTTTGAATG
1 TGGTATTTTTGAATG
46402133 T
1 T
46402134 TGACAAAGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.53
Consensus pattern (15 bp):
TGGTATTTTTGAATG
Found at i:46406067 original size:16 final size:16
Alignment explanation
Indices: 46406045--46406085 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
46406035 TAACCCAAAT
46406045 TGAATTAAGTTAGATTA
1 TGAATTAA-TTAGATTA
*
46406062 -GAATTAATTATATTA
1 TGAATTAATTAGATTA
46406077 TGAATTAAT
1 TGAATTAAT
46406086 ACACATAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (16 bp):
TGAATTAATTAGATTA
Found at i:46410133 original size:13 final size:13
Alignment explanation
Indices: 46410115--46410139 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46410105 CAGGGGACAC
46410115 ACGGCCAAACCAT
1 ACGGCCAAACCAT
46410128 ACGGCCAAACCA
1 ACGGCCAAACCA
46410140 CACGCTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.40, G:0.16, T:0.04
Consensus pattern (13 bp):
ACGGCCAAACCAT
Found at i:46411903 original size:7 final size:7
Alignment explanation
Indices: 46411861--46411887 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
46411851 AAGTAACATC
46411861 TTTATCA
1 TTTATCA
46411868 TTTATCA
1 TTTATCA
46411875 TTTATCA
1 TTTATCA
46411882 TTTATC
1 TTTATC
46411888 GGGCATTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.00, T:0.59
Consensus pattern (7 bp):
TTTATCA
Found at i:46411913 original size:19 final size:19
Alignment explanation
Indices: 46411876--46411923 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
46411866 CATTTATCAT
*
46411876 TTATCATTTA--TCGGGCA
1 TTATCATTTATTTCAGGCA
46411893 TTATCATTTATTTCAGGCA
1 TTATCATTTATTTCAGGCA
46411912 TTATCATTTATT
1 TTATCATTTATT
46411924 GGGCTTTGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
17 10 0.36
19 18 0.64
ACGTcount: A:0.25, C:0.15, G:0.10, T:0.50
Consensus pattern (19 bp):
TTATCATTTATTTCAGGCA
Found at i:46414523 original size:10 final size:10
Alignment explanation
Indices: 46414502--46414531 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
46414492 AAAAATAGTA
46414502 GGCCCGAGCCC
1 GGCCC-AGCCC
46414513 GGCCCAGCCC
1 GGCCCAGCCC
46414523 GGCCCAGCC
1 GGCCCAGCC
46414532 ATATTAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 14 0.74
11 5 0.26
ACGTcount: A:0.10, C:0.57, G:0.33, T:0.00
Consensus pattern (10 bp):
GGCCCAGCCC
Found at i:46421188 original size:50 final size:46
Alignment explanation
Indices: 46421117--46421238 Score: 136
Period size: 46 Copynumber: 2.6 Consensus size: 46
46421107 TGTCTTCGAC
** * *
46421117 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATCTATATATCTAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAG-C--C-ATATATCTAAT
* * *
46421167 ATGGGCTTACATGGCTCATTCCTGTTTCCAAAGCCATATATCTGAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATATCTAAT
*
46421213 ATGGACTTACATGGCTCATTTCTGTC
1 ATGGACTTACATGGCTCATTCCTGTC
46421239 CTGTCCTGTC
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
46 33 0.53
47 1 0.02
49 1 0.02
50 27 0.44
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (46 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATATCTAAT
Found at i:46424842 original size:40 final size:38
Alignment explanation
Indices: 46424787--46424863 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 38
46424777 AAATCATGTC
46424787 TGGGACATTGCCATCA-ACTTGTGATTTACGTGTAAGACCA
1 TGGGACATTGCCATCATA-TT-TGATTT-CGTGTAAGACCA
*
46424827 TGGGACATTGGCATCATATTTGATTTCGTGTAAGACC
1 TGGGACATTGCCATCATATTTGATTTCGTGTAAGACC
46424864 CTATCTGGGA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
38 11 0.31
39 6 0.17
40 17 0.49
41 1 0.03
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.32
Consensus pattern (38 bp):
TGGGACATTGCCATCATATTTGATTTCGTGTAAGACCA
Found at i:46428338 original size:40 final size:39
Alignment explanation
Indices: 46428301--46428392 Score: 132
Period size: 39 Copynumber: 2.3 Consensus size: 39
46428291 GCTACTCGTT
*
46428301 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGG-CATAGCCCGGAAT-TAGTAACTCGCA
* *
46428341 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCATAGCCCGGAATTAGTAACTCGCA
46428380 CAAATGCCTTCGG
1 CAAATGCCTTCGG
46428393 ATCTTAGTCC
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
39 33 0.69
40 15 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGCATAGCCCGGAATTAGTAACTCGCA
Found at i:46428372 original size:39 final size:40
Alignment explanation
Indices: 46428282--46428445 Score: 176
Period size: 40 Copynumber: 4.1 Consensus size: 40
46428272 CGGAATTTAA
** *
46428282 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
*
46428322 CCGGTTATAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
46428361 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
46428401 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
46428441 CCGGA
1 CCGGA
46428446 CATCATTCAA
Statistics
Matches: 105, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
38 3 0.03
39 32 0.30
40 58 0.55
41 12 0.11
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:46432138 original size:81 final size:81
Alignment explanation
Indices: 46432050--46432213 Score: 319
Period size: 81 Copynumber: 2.0 Consensus size: 81
46432040 GGCAAGGAGG
46432050 TCCAGGGTTCGAAACTCATGGCAATCAAAGAGCATTTATTTTGCTAACAGGGGGTGGCAAGAGTT
1 TCCAGGGTTCGAAACTCATGGCAATCAAAGAGCATTTATTTTGCTAACAGGGGGTGGCAAGAGTT
46432115 GGTGTTGAATTTAAAC
66 GGTGTTGAATTTAAAC
*
46432131 TCCAGGGTTCGACACTCATGGCAATCAAAGAGCATTTATTTTGCTAACAGGGGGTGGCAAGAGTT
1 TCCAGGGTTCGAAACTCATGGCAATCAAAGAGCATTTATTTTGCTAACAGGGGGTGGCAAGAGTT
46432196 GGTGTTGAATTTAAAC
66 GGTGTTGAATTTAAAC
46432212 TC
1 TC
46432214 TGATGTTGGA
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.29
Consensus pattern (81 bp):
TCCAGGGTTCGAAACTCATGGCAATCAAAGAGCATTTATTTTGCTAACAGGGGGTGGCAAGAGTT
GGTGTTGAATTTAAAC
Found at i:46432707 original size:27 final size:27
Alignment explanation
Indices: 46432677--46432874 Score: 281
Period size: 27 Copynumber: 7.3 Consensus size: 27
46432667 TACTGAAATG
**
46432677 CCCTCGATTTGTAGAATTACCATTTTA
1 CCCTCGATTTACAGAATTACCATTTTA
* *
46432704 CCCTCGATTTATAGAATTACCATTTCA
1 CCCTCGATTTACAGAATTACCATTTTA
* *
46432731 CCCTCGATTTACAAAATTACCGTTTTA
1 CCCTCGATTTACAGAATTACCATTTTA
*
46432758 CCCTCGATTTATAGAATTACCATTTTA
1 CCCTCGATTTACAGAATTACCATTTTA
*
46432785 CCCTCGATTTACAGAATTACCGTTTTA
1 CCCTCGATTTACAGAATTACCATTTTA
*
46432812 CCCTCGATTTACAAAATTACCATTTTA
1 CCCTCGATTTACAGAATTACCATTTTA
* *
46432839 CCCTC-AGTTTACAAAATTACCGTTTTA
1 CCCTCGA-TTTACAGAATTACCATTTTA
46432866 CCCTCGATT
1 CCCTCGATT
46432875 GTGAAATTAC
Statistics
Matches: 155, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
26 1 0.01
27 153 0.99
28 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.08, T:0.38
Consensus pattern (27 bp):
CCCTCGATTTACAGAATTACCATTTTA
Found at i:46432896 original size:27 final size:26
Alignment explanation
Indices: 46432866--46433056 Score: 147
Period size: 27 Copynumber: 7.1 Consensus size: 26
46432856 TACCGTTTTA
* **
46432866 CCCTCGATTGTGAAATTACTGAAATAC
1 CCCT-GATTGTAAAATTACCAAAATAC
* *
46432893 CCCTG-TAGGATAGAATTACCAAAATAC
1 CCCTGAT-TG-TAAAATTACCAAAATAC
*
46432920 CCCTAGTTTGTAAAATTACCAAAATAC
1 CCCT-GATTGTAAAATTACCAAAATAC
*
46432947 CCCTAGTTTGTAAAATTACCAAAATAC
1 CCCT-GATTGTAAAATTACCAAAATAC
* * * *
46432974 CACTGGTTTGTGAAATTACCGAAATA-
1 CCCT-GATTGTAAAATTACCAAAATAC
*
46433000 CCCTCAATTTGTAAAATTACCAAAATAC
1 CCCT-GA-TTGTAAAATTACCAAAATAC
46433028 CCCTGATT-TACAAAATTA-CAGAAATAC
1 CCCTGATTGT--AAAATTACCA-AAATAC
46433055 CC
1 CC
46433057 TTGACTTTCT
Statistics
Matches: 137, Mismatches: 18, Indels: 18
0.79 0.10 0.10
Matches are distributed among these distances:
25 2 0.01
26 9 0.07
27 119 0.87
28 6 0.04
29 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.10, T:0.28
Consensus pattern (26 bp):
CCCTGATTGTAAAATTACCAAAATAC
Found at i:46432947 original size:54 final size:54
Alignment explanation
Indices: 46432873--46433028 Score: 181
Period size: 54 Copynumber: 2.9 Consensus size: 54
46432863 TTACCCTCGA
* * *
46432873 TTGTGAAATTACTGAAATACCCCT-GTAGGATAGAATTACCAAAATACCCCTAGT
1 TTGTGAAATTACCGAAATACCCCTAGTAGG-TAAAATTACCAAAATACCACTAGT
* * ** *
46432927 TTGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCACTGGT
1 TTGTGAAATTACCGAAATACCCCTAGTAGGTAAAATTACCAAAATACCACTAGT
* **
46432981 TTGTGAAATTACCGAAATA-CCCTCAATTTGTAAAATTACCAAAATACC
1 TTGTGAAATTACCGAAATACCCCT-AGTAGGTAAAATTACCAAAATACC
46433029 CCTGATTTAC
Statistics
Matches: 89, Mismatches: 11, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
53 4 0.04
54 82 0.92
55 3 0.03
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.29
Consensus pattern (54 bp):
TTGTGAAATTACCGAAATACCCCTAGTAGGTAAAATTACCAAAATACCACTAGT
Found at i:46433043 original size:81 final size:81
Alignment explanation
Indices: 46432906--46433055 Score: 216
Period size: 81 Copynumber: 1.9 Consensus size: 81
46432896 TGTAGGATAG
* **
46432906 AATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCA-AA
1 AATTACCAAAATACCCCTAATTTGTAAAATTACCAAAATACCCCTAGTTTACAAAATTA-CAGAA
46432970 ATACCACTGGTTTGTGA
65 ATACCACTGGTTTGTGA
*
46432987 AATTACCGAAATA-CCCTCAATTTGTAAAATTACCAAAATACCCCT-GATTTACAAAATTACAGA
1 AATTACCAAAATACCCCT-AATTTGTAAAATTACCAAAATACCCCTAG-TTTACAAAATTACAGA
46433050 AATACC
64 AATACC
46433056 CTTGACTTTC
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
80 7 0.11
81 55 0.89
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.28
Consensus pattern (81 bp):
AATTACCAAAATACCCCTAATTTGTAAAATTACCAAAATACCCCTAGTTTACAAAATTACAGAAA
TACCACTGGTTTGTGA
Found at i:46433044 original size:54 final size:54
Alignment explanation
Indices: 46432906--46433113 Score: 188
Period size: 54 Copynumber: 3.8 Consensus size: 54
46432896 TGTAGGATAG
* ** * *
46432906 AATTACCAAAATACCCCT-AGTTTGTAAAATTACCAAAATACCC-CTAGTTTGTAA
1 AATTACCAAAATACCACTGA-TTTACAAAATTACCGAAATACCCTC-AATTTGTAA
* ***
46432960 AATTACCAAAATACCACTGGTTTGTGAAATTACCGAAATACCCTCAATTTGTAA
1 AATTACCAAAATACCACTGATTTACAAAATTACCGAAATACCCTCAATTTGTAA
* * * * *
46433014 AATTACCAAAATACCCCTGATTTACAAAATTACAGAAATACCCTTGACTTTCTAAA
1 AATTACCAAAATACCACTGATTTACAAAATTACCGAAATACCC-TCAATTTGT-AA
* * * *
46433070 AATTA-TAGAAATACCATTGGTTTACAAAATTACTGAAATACCCT
1 AATTACCA-AAATACCACTGATTTACAAAATTACCGAAATACCCT
46433114 TGGTTTGTAG
Statistics
Matches: 130, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
54 83 0.64
55 9 0.07
56 38 0.29
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.30
Consensus pattern (54 bp):
AATTACCAAAATACCACTGATTTACAAAATTACCGAAATACCCTCAATTTGTAA
Found at i:46433107 original size:27 final size:27
Alignment explanation
Indices: 46433012--46433119 Score: 103
Period size: 27 Copynumber: 3.9 Consensus size: 27
46433002 CTCAATTTGT
** * *
46433012 AAAATTACCAAAATACCCCTGATTTAC
1 AAAATTACTGAAATACCCTTGGTTTAC
* *
46433039 AAAATTACAGAAATACCCTTGACTTT-C
1 AAAATTACTGAAATACCCTTG-GTTTAC
*
46433066 TAAAAATTA-TAGAAATACCATTGGTTTAC
1 --AAAATTACT-GAAATACCCTTGGTTTAC
46433095 AAAATTACTGAAATACCCTTGGTTT
1 AAAATTACTGAAATACCCTTGGTTT
46433120 GTAGATTTAC
Statistics
Matches: 67, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
27 41 0.61
28 7 0.10
29 19 0.28
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (27 bp):
AAAATTACTGAAATACCCTTGGTTTAC
Found at i:46433203 original size:27 final size:27
Alignment explanation
Indices: 46433160--46433233 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
46433150 AAATGACTAA
*
46433160 AATACCCCTAATA-GGTAAAAAGACCGT
1 AATACCCCT-GTAGGGTAAAAAGACCGT
**
46433187 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTGTAGGGTAAAAAGACCGT
* *
46433214 AATACCCTTGTATGGTAAAA
1 AATACCCCTGTAGGGTAAAA
46433234 TGACGAATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
26 3 0.08
27 34 0.89
28 1 0.03
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (27 bp):
AATACCCCTGTAGGGTAAAAAGACCGT
Found at i:46433237 original size:27 final size:27
Alignment explanation
Indices: 46433173--46433237 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
46433163 ACCCCTAATA
*
46433173 GGTAAAAAGACCGTAAAGCCCCTGTAG
1 GGTAAAATGACCGTAAAGCCCCTGTAG
* * *
46433200 GGTAAAGTGACCGTAATA-CCCTTGTAT
1 GGTAAAATGACCGTAA-AGCCCCTGTAG
46433227 GGTAAAATGAC
1 GGTAAAATGAC
46433238 GAATATGCCC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (27 bp):
GGTAAAATGACCGTAAAGCCCCTGTAG
Found at i:46434116 original size:24 final size:25
Alignment explanation
Indices: 46434040--46434109 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
46434030 AGGAAGTGCT
* * * *
46434040 AAAAGGGCTATGCCCTAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTATCA
46434065 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTATCA
46434090 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
46434110 ATTAAAAGAG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTATCA
Found at i:46434122 original size:24 final size:24
Alignment explanation
Indices: 46434065--46434136 Score: 76
Period size: 25 Copynumber: 3.0 Consensus size: 24
46434055 TAGTTTACCG
46434065 AAAAG-GGCTTTGCCCCAGTTTATC
1 AAAAGAGGCTTTGCCCCAG-TTATC
*
46434089 AAAA-AGGGCTTTGCCCCAGTTATT
1 AAAAGA-GGCTTTGCCCCAGTTATC
**
46434113 AAAAGAGGCTAGGCCTCCAGTTAT
1 AAAAGAGGCTTTGCC-CCAGTTAT
46434137 ATGATAAAGC
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
24 19 0.46
25 22 0.54
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (24 bp):
AAAAGAGGCTTTGCCCCAGTTATC
Found at i:46437877 original size:72 final size:74
Alignment explanation
Indices: 46437693--46437878 Score: 199
Period size: 72 Copynumber: 2.6 Consensus size: 74
46437683 GCCCGCATTT
* * *
46437693 GAGCTACTCACGGGTCTG-TACACAAAGTCAGCACCTAGA-CCCAAAAGTATTATCATGTAATGC
1 GAGCTACTCACGGGTCTGATACACAAAGTCAGCACCTGGACCCCAAAAGCATTAACATGTAATGC
* **
46437756 CTGCTCATT
66 CTACTCAGC
* * *
46437765 GAGCTACTCACGGGT-TTATACACAAAGTCAGTACCCGGACCCCAAAA-CATTAACATG-ATATG
1 GAGCTACTCACGGGTCTGATACACAAAGTCAGCACCTGGACCCCAAAAGCATTAACATGTA-ATG
46437827 -CTCACTCAGC
65 CCT-ACTCAGC
*
46437837 GAGTTACTCACGGGTCTGAT-CACATAA-TCAGCACCTGGACCC
1 GAGCTACTCACGGGTCTGATACACA-AAGTCAGCACCTGGACCC
46437879 ACATTACATA
Statistics
Matches: 95, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
71 4 0.04
72 79 0.83
73 12 0.13
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (74 bp):
GAGCTACTCACGGGTCTGATACACAAAGTCAGCACCTGGACCCCAAAAGCATTAACATGTAATGC
CTACTCAGC
Found at i:46438579 original size:20 final size:20
Alignment explanation
Indices: 46438554--46438592 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
46438544 AAAATTTCAA
46438554 TTATTTCAC-ACATTTACAAC
1 TTATTTCACAAC-TTTACAAC
*
46438574 TTATTTTACAACTTTACAA
1 TTATTTCACAACTTTACAA
46438593 AATAGCCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.44
Consensus pattern (20 bp):
TTATTTCACAACTTTACAAC
Found at i:46443902 original size:15 final size:15
Alignment explanation
Indices: 46443867--46443911 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
46443857 CAAACATAAC
*
46443867 AAGAAAACCAAG-TA
1 AAGAAATCCAAGATA
46443881 AAGAAATCCAAGATA
1 AAGAAATCCAAGATA
*
46443896 GAGAAATCCTAAGATA
1 AAGAAATCC-AAGATA
46443912 CTATACTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
14 11 0.41
15 10 0.37
16 6 0.22
ACGTcount: A:0.58, C:0.13, G:0.16, T:0.13
Consensus pattern (15 bp):
AAGAAATCCAAGATA
Found at i:46447779 original size:72 final size:72
Alignment explanation
Indices: 46447678--46447886 Score: 204
Period size: 72 Copynumber: 2.9 Consensus size: 72
46447668 ATGCTCGCAT
* * * ** * *
46447678 TTGAGCTACTCACGGGTCTGTACCCAAAGTCAGCACCCGGACCTGAAAGCATTATCATG-TAATG
1 TTGAGCTACTCACGGGTTTATACACAAAGTCAGCACCCGGACCCCAAAACATTAACATGAT-ATG
*
46447742 CCCGCTCA
65 CCCACTCA
** * * *
46447750 TTGAGCTACTCACATGTTTATACACAAAGTCAGTACCTGGACCCCAAAATATTAACATGATATGC
1 TTGAGCTACTCACGGGTTTATACACAAAGTCAGCACCCGGACCCCAAAACATTAACATGATATGC
*
46447815 TCACTCA
66 CCACTCA
** * **** *
46447822 GCGAGTTACTCACGGGTTTATACACAAAGTCAGCACTTAAATCCCAAAACATTAACATGATATGC
1 TTGAGCTACTCACGGGTTTATACACAAAGTCAGCACCCGGACCCCAAAACATTAACATGATATGC
46447887 TCGCTCAGCG
Statistics
Matches: 111, Mismatches: 25, Indels: 2
0.80 0.18 0.01
Matches are distributed among these distances:
72 110 0.99
73 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (72 bp):
TTGAGCTACTCACGGGTTTATACACAAAGTCAGCACCCGGACCCCAAAACATTAACATGATATGC
CCACTCA
Found at i:46447887 original size:72 final size:72
Alignment explanation
Indices: 46447756--46447907 Score: 223
Period size: 72 Copynumber: 2.1 Consensus size: 72
46447746 CTCATTGAGC
** * ** *
46447756 TACTCACATGTTTATACACAAAGTCAGTACCTGGACCCCAAAATATTAACATGATATGCTCACTC
1 TACTCACGGGTTTATACACAAAGTCAGCACCTAAACCCCAAAACATTAACATGATATGCTCACTC
46447821 AGCGAGT
66 AGCGAGT
* * *
46447828 TACTCACGGGTTTATACACAAAGTCAGCACTTAAATCCCAAAACATTAACATGATATGCTCGCTC
1 TACTCACGGGTTTATACACAAAGTCAGCACCTAAACCCCAAAACATTAACATGATATGCTCACTC
46447893 AGCGAGT
66 AGCGAGT
46447900 TACTCACG
1 TACTCACG
46447908 AGCCTGATCA
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (72 bp):
TACTCACGGGTTTATACACAAAGTCAGCACCTAAACCCCAAAACATTAACATGATATGCTCACTC
AGCGAGT
Found at i:46447928 original size:72 final size:72
Alignment explanation
Indices: 46447792--46447930 Score: 192
Period size: 72 Copynumber: 1.9 Consensus size: 72
46447782 GTACCTGGAC
* ** * *
46447792 CCCAAAATATTAACATGATATGCTCACTCAGCGAGTTACTCACGGGTTTATACACAAAGTCAGCA
1 CCCAAAACATTAACATGATATGCTCACTCAGCGAGTTACTCACGGCCTGATACACAAAGCCAGCA
46447857 CTTAAAT
66 CTTAAAT
*
46447864 CCCAAAACATTAACATGATATGCTCGCTCAGCGAGTTACTCACGAGCCTGAT-CACATAA-CCAG
1 CCCAAAACATTAACATGATATGCTCACTCAGCGAGTTACTCACG-GCCTGATACACA-AAGCCAG
46447927 CACT
64 CACT
46447931 CGGACCCACA
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
72 53 0.90
73 6 0.10
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.24
Consensus pattern (72 bp):
CCCAAAACATTAACATGATATGCTCACTCAGCGAGTTACTCACGGCCTGATACACAAAGCCAGCA
CTTAAAT
Found at i:46451230 original size:37 final size:37
Alignment explanation
Indices: 46451189--46451284 Score: 97
Period size: 37 Copynumber: 2.6 Consensus size: 37
46451179 TCTTCAGAGT
*
46451189 ATTTGGCATGTTATCGGTTGGATTAGCTCT-TTGAAGC
1 ATTTGGCATGTTATCGGTTGGATTAGCTCTCATG-AGC
** *
46451226 ATTTGAAATGCTATCGGTTTGG-TTAGCTCTCATGAGC
1 ATTTGGCATGTTATCGG-TTGGATTAGCTCTCATGAGC
* * *
46451263 ATTTGGCGTGTTTTCTGTTGGA
1 ATTTGGCATGTTATCGGTTGGA
46451285 CTACTGTGCT
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
36 4 0.09
37 36 0.78
38 6 0.13
ACGTcount: A:0.18, C:0.14, G:0.27, T:0.42
Consensus pattern (37 bp):
ATTTGGCATGTTATCGGTTGGATTAGCTCTCATGAGC
Found at i:46452339 original size:50 final size:50
Alignment explanation
Indices: 46452258--46452442 Score: 156
Period size: 50 Copynumber: 3.7 Consensus size: 50
46452248 CCAAACCAAG
*
46452258 CCTTTGTGGCGAATTGTCTAGGAAGCCTTTGTGGTAAGTCATCTGTCAAA-
1 CCTTTGTGGCGAATTGTCTAGAAAGCCTTTGTGGTAAGTCATCTGT-AAAT
* * * * * *
46452308 CCTTTTTGGCAAATTGTCTATAAAGCTTTTGTGGTGAGTCATTTGTAAAT
1 CCTTTGTGGCGAATTGTCTAGAAAGCCTTTGTGGTAAGTCATCTGTAAAT
* * * * * ** * **
46452358 CCTTTGTGGCGAATTGTTTGGGAAGCTTTTGCGGCGAGTAATCTGTAAGG
1 CCTTTGTGGCGAATTGTCTAGAAAGCCTTTGTGGTAAGTCATCTGTAAAT
* * * * *
46452408 CCTTTGGGGCGAATTTTTTGGGAAGCCTTTGTGGT
1 CCTTTGTGGCGAATTGTCTAGAAAGCCTTTGTGGT
46452443 GAATTGTTTG
Statistics
Matches: 110, Mismatches: 24, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
49 3 0.03
50 107 0.97
ACGTcount: A:0.19, C:0.15, G:0.28, T:0.38
Consensus pattern (50 bp):
CCTTTGTGGCGAATTGTCTAGAAAGCCTTTGTGGTAAGTCATCTGTAAAT
Found at i:46452388 original size:25 final size:25
Alignment explanation
Indices: 46452358--46452465 Score: 101
Period size: 25 Copynumber: 4.3 Consensus size: 25
46452348 ATTTGTAAAT
46452358 CCTTTGTGGCGAATTGTTTGGGAAG
1 CCTTTGTGGCGAATTGTTTGGGAAG
* * * ** * *
46452383 CTTTTGCGGCGAGTAATCT-GTAAGG
1 CCTTTGTGGCGAATTGTTTGGGAA-G
* *
46452408 CCTTTGGGGCGAATTTTTTGGGAAG
1 CCTTTGTGGCGAATTGTTTGGGAAG
* *
46452433 CCTTTGTGGTGAATTGTTTGGTAAG
1 CCTTTGTGGCGAATTGTTTGGGAAG
46452458 CCTTTGTG
1 CCTTTGTG
46452466 CCGAGTCATC
Statistics
Matches: 63, Mismatches: 18, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
24 3 0.05
25 57 0.90
26 3 0.05
ACGTcount: A:0.16, C:0.13, G:0.33, T:0.38
Consensus pattern (25 bp):
CCTTTGTGGCGAATTGTTTGGGAAG
Found at i:46452483 original size:25 final size:25
Alignment explanation
Indices: 46452455--46452508 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
46452445 ATTGTTTGGT
46452455 AAGCCTTTGTGCCGAGTCATCTATA
1 AAGCCTTTGTGCCGAGTCATCTATA
* *
46452480 AAGCCTTTGTGGCGAGTCATCTGTA
1 AAGCCTTTGTGCCGAGTCATCTATA
46452505 AAGC
1 AAGC
46452509 TTTTATGATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (25 bp):
AAGCCTTTGTGCCGAGTCATCTATA
Found at i:46452521 original size:75 final size:75
Alignment explanation
Indices: 46452324--46452549 Score: 236
Period size: 75 Copynumber: 3.0 Consensus size: 75
46452314 TGGCAAATTG
* * * * *
46452324 TCTATAAAGCTTTTGTGGTGAGTCATTTGTAAATCCTTTGTGGCGAATTGTTTGGGAAGCTTTTG
1 TCTATAAAGCCTTTGTGGCGAGTCATTTGTAAAGCCTTTGTGGTGAATTGTTTGGGAAGCCTTTG
* * *
46452389 CGGCGAGTAA
66 TGACGAGTCA
* * * * ** ** *
46452399 TCTGTAAGGCCTTTGGGGCGAATTTTTTGGGAAGCCTTTGTGGTGAATTGTTTGGTAAGCCTTTG
1 TCTATAAAGCCTTTGTGGCGAGTCATTTGTAAAGCCTTTGTGGTGAATTGTTTGGGAAGCCTTTG
*
46452464 TGCCGAGTCA
66 TGACGAGTCA
* * * * * *
46452474 TCTATAAAGCCTTTGTGGCGAGTCATCTGTAAAGCTTTTATGATGAATTATTTGGGAAGCCCTTG
1 TCTATAAAGCCTTTGTGGCGAGTCATTTGTAAAGCCTTTGTGGTGAATTGTTTGGGAAGCCTTTG
46452539 TGACGAGTCA
66 TGACGAGTCA
46452549 T
1 T
46452550 GTAGGAAGCC
Statistics
Matches: 118, Mismatches: 33, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
75 118 1.00
ACGTcount: A:0.21, C:0.14, G:0.28, T:0.37
Consensus pattern (75 bp):
TCTATAAAGCCTTTGTGGCGAGTCATTTGTAAAGCCTTTGTGGTGAATTGTTTGGGAAGCCTTTG
TGACGAGTCA
Found at i:46454701 original size:46 final size:48
Alignment explanation
Indices: 46454629--46454896 Score: 159
Period size: 46 Copynumber: 5.7 Consensus size: 48
46454619 TTATTTGTGT
* * *
46454629 GCCAATGTAAGA-CGTGTGTGGGACAT-GCATCGGCCTCGTGACGTAA
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGTGACGTAA
* * *
46454675 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCAG-CTACGAGAGGT--
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCT-CGTGACGTAA
** * *
46454719 GTTAGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-AGAT-ATGTGAGA
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-CTCG-TGACGT-A-A
* * *
46454769 GCTAGTGTAAGACCATGTCTGGGACATGGCGTCGGCCTCGAAT-TCG-ATA
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCG--TGACGTA-A
* * * * * * *
46454818 GTCATTGTAAGACCATGCCTGGGACGTGGCATC-GACT--TGATGGATGA
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGTGA-CG-TAA
*
46454865 GCCAGTGTAAGACCATGTCTGGAACATGGCAT
1 GCCAGTGTAAGACCATGTCTGGGACATGGCAT
46454897 TGGCATTATA
Statistics
Matches: 173, Mismatches: 33, Indels: 31
0.73 0.14 0.13
Matches are distributed among these distances:
44 11 0.06
45 16 0.09
46 46 0.27
47 28 0.16
48 4 0.02
49 30 0.17
50 35 0.20
51 3 0.02
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.23
Consensus pattern (48 bp):
GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGTGACGTAA
Found at i:46454744 original size:45 final size:48
Alignment explanation
Indices: 46454678--46454796 Score: 140
Period size: 50 Copynumber: 2.5 Consensus size: 48
46454668 GACGTAAGCC
* *
46454678 AGTGTAAGA-CATGTCTGGGACATGCATCAGCTAC-G-A-GAG-GTGTT
1 AGTGTAAGACCATGTCTGGGACATGCATCAGC-ACAGAATGAGAGAGCT
* *
46454722 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGATATGTGAGAGCT
1 AGTGTAAGACCATGTCTGGGACAT-GCATCAGCACAGA-ATGAGAGAGCT
46454772 AGTGTAAGACCATGTCTGGGACATG
1 AGTGTAAGACCATGTCTGGGACATG
46454797 GCGTCGGCCT
Statistics
Matches: 64, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
44 9 0.14
45 16 0.25
46 8 0.12
48 1 0.02
49 3 0.05
50 27 0.42
ACGTcount: A:0.28, C:0.17, G:0.32, T:0.24
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGCATCAGCACAGAATGAGAGAGCT
Found at i:46454785 original size:50 final size:49
Alignment explanation
Indices: 46454721--46454901 Score: 169
Period size: 50 Copynumber: 3.7 Consensus size: 49
46454711 CGAGAGGTGT
46454721 TAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGATATGTGAGAGC
1 TAGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-GATATGTGAGAGC
* * *
46454771 TAGTGTAAGACCATGTCTGGGACATGGCGTCGGCCTCGA-AT-TCGATAG-
1 TAGTGTAAGACCATGTCTGGGACATGGCATCGG-CACGATATGT-GAGAGC
* * * *
46454819 TCATTGTAAGACCATGCCTGGGACGTGGCATC-G-AC-TTGATG-GATGAGC
1 T-AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGAT-ATGTGA-GAGC
* * *
46454867 CAGTGTAAGACCATGTCTGGAACATGGCATTGGCA
1 TAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
46454902 TTATACCTTA
Statistics
Matches: 105, Mismatches: 16, Indels: 21
0.74 0.11 0.15
Matches are distributed among these distances:
46 3 0.03
47 29 0.28
48 4 0.04
49 33 0.31
50 34 0.32
51 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (49 bp):
TAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGATATGTGAGAGC
Found at i:46456664 original size:46 final size:48
Alignment explanation
Indices: 46456592--46456859 Score: 159
Period size: 46 Copynumber: 5.7 Consensus size: 48
46456582 TTATTTGTGT
* * *
46456592 GCCAATGTAAGA-CGTGTGTGGGACAT-GCATCGGCCTCGTGACGTAA
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGTGACGTAA
* * *
46456638 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCAG-CTACGAGAGGT--
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCT-CGTGACGTAA
** * *
46456682 GTTAGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-AGAT-ATGTGAGA
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-CTCG-TGACGT-A-A
* * *
46456732 GCTAGTGTAAGACCATGTCTGGGACATGGCGTCGGCCTCGAAT-TCG-ATA
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCG--TGACGTA-A
* * * * * * *
46456781 GTCATTGTAAGACCATGCCTGGGACGTGGCATC-GACT--TGATGGATGA
1 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGTGA-CG-TAA
*
46456828 GCCAGTGTAAGACCATGTCTGGAACATGGCAT
1 GCCAGTGTAAGACCATGTCTGGGACATGGCAT
46456860 TGGCATTATA
Statistics
Matches: 173, Mismatches: 33, Indels: 31
0.73 0.14 0.13
Matches are distributed among these distances:
44 11 0.06
45 16 0.09
46 46 0.27
47 28 0.16
48 4 0.02
49 30 0.17
50 35 0.20
51 3 0.02
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.23
Consensus pattern (48 bp):
GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGTGACGTAA
Found at i:46456707 original size:45 final size:48
Alignment explanation
Indices: 46456641--46456759 Score: 140
Period size: 50 Copynumber: 2.5 Consensus size: 48
46456631 GACGTAAGCC
* *
46456641 AGTGTAAGA-CATGTCTGGGACATGCATCAGCTAC-G-A-GAG-GTGTT
1 AGTGTAAGACCATGTCTGGGACATGCATCAGC-ACAGAATGAGAGAGCT
* *
46456685 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGATATGTGAGAGCT
1 AGTGTAAGACCATGTCTGGGACAT-GCATCAGCACAGA-ATGAGAGAGCT
46456735 AGTGTAAGACCATGTCTGGGACATG
1 AGTGTAAGACCATGTCTGGGACATG
46456760 GCGTCGGCCT
Statistics
Matches: 64, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
44 9 0.14
45 16 0.25
46 8 0.12
48 1 0.02
49 3 0.05
50 27 0.42
ACGTcount: A:0.28, C:0.17, G:0.32, T:0.24
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGCATCAGCACAGAATGAGAGAGCT
Found at i:46456748 original size:50 final size:49
Alignment explanation
Indices: 46456684--46456864 Score: 169
Period size: 50 Copynumber: 3.7 Consensus size: 49
46456674 CGAGAGGTGT
46456684 TAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGATATGTGAGAGC
1 TAGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-GATATGTGAGAGC
* * *
46456734 TAGTGTAAGACCATGTCTGGGACATGGCGTCGGCCTCGA-AT-TCGATAG-
1 TAGTGTAAGACCATGTCTGGGACATGGCATCGG-CACGATATGT-GAGAGC
* * * *
46456782 TCATTGTAAGACCATGCCTGGGACGTGGCATC-G-AC-TTGATG-GATGAGC
1 T-AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGAT-ATGTGA-GAGC
* * *
46456830 CAGTGTAAGACCATGTCTGGAACATGGCATTGGCA
1 TAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
46456865 TTATACCTTA
Statistics
Matches: 105, Mismatches: 16, Indels: 21
0.74 0.11 0.15
Matches are distributed among these distances:
46 3 0.03
47 29 0.28
48 4 0.04
49 33 0.31
50 34 0.32
51 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (49 bp):
TAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGATATGTGAGAGC
Found at i:46458058 original size:20 final size:21
Alignment explanation
Indices: 46458019--46458058 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
46458009 AGCACAGCCA
* *
46458019 TCACAGGGGCGTGTTGCCCTT
1 TCACACGGGCATGTTGCCCTT
46458040 TCACACGGGCATG-TGCCCT
1 TCACACGGGCATGTTGCCCT
46458059 GTTTCAAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.12, C:0.33, G:0.30, T:0.25
Consensus pattern (21 bp):
TCACACGGGCATGTTGCCCTT
Found at i:46462910 original size:46 final size:46
Alignment explanation
Indices: 46462857--46463220 Score: 211
Period size: 46 Copynumber: 7.8 Consensus size: 46
46462847 TTATTTGTCT
*
46462857 GCCAGTGTAAGA-CATGTTTGGGACATGCATCGGCCACACTATGAGA
1 GCCAGTGTAAGACCATGTCTGGGACATGCATCGG-CACACTATGAGA
* *
46462903 GCCAGTGTAAGACCATGTCTGGGACATGGCATC-G-ACATTGAGACGAGA
1 GCCAGTGTAAGACCATGTCTGGGACAT-GCATCGGCACACT---ATGAGA
* *
46462951 GCTAGTGTAAGA-CATGTCTGGGACATGCATCGGC-CTCGTGACAT-A-A
1 GCCAGTGTAAGACCATGTCTGGGACATGCATCGGCACAC-T---ATGAGA
* * * * *
46462997 GGCAATGTAAGA-CATGTCTGAGACATGCATCGGC-TACTA-GATGT
1 GCCAGTGTAAGACCATGTCTGGGACATGCATCGGCACACTATGA-GA
* *
46463041 GTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGATATGTGAGA
1 GCCAGTGTAAGACCATGTCTGGGACAT-GCATCGGCACA-CTA--TGAGA
* * * * * *
46463091 GCTAGTGTAAGACCATGTCTGGGACATGGCGTCAGC-CTCGAATTCGATA
1 GCCAGTGTAAGACCATGTCTGGGACAT-GCATCGGCACAC-TA-T-GAGA
* * **
46463140 GTCAGTGTAAGACCATGTCTAGGACATGGCAT---CA-ACT-TGATTTT
1 GCCAGTGTAAGACCATGTCTGGGACAT-GCATCGGCACACTATGA--GA
*
46463184 GACAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
1 GCCAGTGTAAGACCATGTCTGGGACAT-GCATCGGCA
46463221 TTATACCCTA
Statistics
Matches: 253, Mismatches: 39, Indels: 51
0.74 0.11 0.15
Matches are distributed among these distances:
42 4 0.02
43 1 0.00
44 41 0.16
45 18 0.07
46 59 0.23
47 34 0.13
48 28 0.11
49 33 0.13
50 33 0.13
51 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.23
Consensus pattern (46 bp):
GCCAGTGTAAGACCATGTCTGGGACATGCATCGGCACACTATGAGA
Found at i:46463098 original size:140 final size:140
Alignment explanation
Indices: 46462862--46463220 Score: 385
Period size: 143 Copynumber: 2.5 Consensus size: 140
46462852 TGTCTGCCAG
* * * *
46462862 TGTAAGACATGTTTGGGACATGCATCGGCCACACTATGA-GAGCCAGTGTAAGACCATGTCTGGG
1 TGTAAGACATGTCTGAGACATGCATCGG-CA-ACTA-GATGTGACAGTGTAAGACCATGTCTGGG
* ** *
46462926 ACATGGCATCGACATTGAGACGAGAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCG
63 ACATGGCATCGGCACAGAGACGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCG
46462989 -TGAC-ATAAGGCAA
128 AT-ACGAT-AGGCAA
* *
46463002 TGTAAGACATGTCTGAGACATGCATCGGCTACTAGATGTGTCAGTGTAAGACCATGTCTGGGACA
1 TGTAAGACATGTCTGAGACATGCATCGGCAACTAGATGTGACAGTGTAAGACCATGTCTGGGACA
* * *
46463067 TGGCATCGGCACAGATATGTGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCGTCAGCCTCGA
66 TGGCATCGGCACAGAGA--CGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCG-
* * *
46463132 ATTCGATAGTCAG
128 ATACGATAGGCAA
* *
46463145 TGTAAGACCATGTCT-AGGACATGGCAT---CAACTTGATTTTGACAGTGTAAGACCATGTCTGG
1 TGTAAGA-CATGTCTGA-GACAT-GCATCGGCAACTAGA-TGTGACAGTGTAAGACCATGTCTGG
46463206 GACATGGCATCGGCA
62 GACATGGCATCGGCA
46463221 TTATACCCTA
Statistics
Matches: 188, Mismatches: 19, Indels: 21
0.82 0.08 0.09
Matches are distributed among these distances:
137 2 0.01
138 43 0.23
139 1 0.01
140 42 0.22
141 14 0.07
142 16 0.09
143 51 0.27
144 15 0.08
145 4 0.02
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.24
Consensus pattern (140 bp):
TGTAAGACATGTCTGAGACATGCATCGGCAACTAGATGTGACAGTGTAAGACCATGTCTGGGACA
TGGCATCGGCACAGAGACGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCGATA
CGATAGGCAA
Found at i:46463102 original size:94 final size:89
Alignment explanation
Indices: 46462859--46463220 Score: 265
Period size: 93 Copynumber: 3.9 Consensus size: 89
46462849 ATTTGTCTGC
* *
46462859 CAGTGTAAGACATGTTTGGGACATGCATCGGCCACACTATGAGAGCCAGTGTAAGACCATGTCTG
1 CAGTGTAAGACATGTCTGGGACATGCATCGG-CACAGTATGAGAG-CAGTGTAAGACCATGTCTG
* * * * *
46462924 GGACATGGCATCGACATTGAGACGAGAG
64 GGACATGGCATCGGCACT-AGATGTG-T
* * *
46462952 CTAGTGTAAGACATGTCTGGGACATGCATCGGC-CTCGTGACATAAG-GCAATGTAAGA-CATGT
1 C-AGTGTAAGACATGTCTGGGACATGCATCGGCAC-AGT---ATGAGAGCAGTGTAAGACCATGT
*
46463014 CTGAGACAT-GCATCGGCTACTAGATGTGT
61 CTGGGACATGGCATCGGC-ACTAGATGTGT
46463043 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGATATGTGAGAGCTAGTGTAAGACCATG
1 CAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCACAG-TA--TGAGAGC-AGTGTAAGACCATG
* * *
46463108 TCTGGGACATGGCGTCAGC-CTCGAATTCGATAGT
60 TCTGGGACATGGCATCGGCACTAG-A-T-G-T-GT
* * * **
46463142 CAGTGTAAGACCATGTCTAGGACATGGCATC--AAC-TTGATTTTGA-CAGTGTAAGACCATGTC
1 CAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCACAGT-A-TGAGAGCAGTGTAAGACCATGTC
46463203 TGGGACATGGCATCGGCA
62 TGGGACATGGCATCGGCA
46463221 TTATACCCTA
Statistics
Matches: 220, Mismatches: 26, Indels: 45
0.76 0.09 0.15
Matches are distributed among these distances:
90 10 0.05
91 15 0.07
92 25 0.11
93 53 0.24
94 50 0.23
95 19 0.09
96 12 0.05
97 3 0.01
98 1 0.00
99 32 0.15
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (89 bp):
CAGTGTAAGACATGTCTGGGACATGCATCGGCACAGTATGAGAGCAGTGTAAGACCATGTCTGGG
ACATGGCATCGGCACTAGATGTGT
Found at i:46463166 original size:49 final size:50
Alignment explanation
Indices: 46463041--46463216 Score: 176
Period size: 49 Copynumber: 3.7 Consensus size: 50
46463031 TACTAGATGT
*
46463041 GTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGATATGTGAGA
1 GTCAGTGTAAGACCATGTCTGGGACATGGCATCAGCACAGATATGTGAGA
* * *
46463091 G-CTAGTGTAAGACCATGTCTGGGACATGGCGTCAGC-CTCGA-AT-TCGATA
1 GTC-AGTGTAAGACCATGTCTGGGACATGGCATCAGCAC-AGATATGT-GAGA
* * *
46463140 GTCAGTGTAAGACCATGTCTAGGACATGGCATCA--ACTTGAT-T-T-TGA
1 GTCAGTGTAAGACCATGTCTGGGACATGGCATCAGCAC-AGATATGTGAGA
46463186 --CAGTGTAAGACCATGTCTGGGACATGGCATC
1 GTCAGTGTAAGACCATGTCTGGGACATGGCATC
46463217 GGCATTATAC
Statistics
Matches: 110, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
44 30 0.27
46 1 0.01
48 7 0.06
49 37 0.34
50 35 0.32
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (50 bp):
GTCAGTGTAAGACCATGTCTGGGACATGGCATCAGCACAGATATGTGAGA
Found at i:46464377 original size:21 final size:20
Alignment explanation
Indices: 46464352--46464391 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
46464342 GTTATAATGA
* *
46464352 CCACAGGGGTGTGTTGCCCTT
1 CCACACGGGCGTG-TGCCCTT
46464373 CCACACGGGCGTGTGCCCT
1 CCACACGGGCGTGTGCCCT
46464392 GTTTCAAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.10, C:0.35, G:0.33, T:0.23
Consensus pattern (20 bp):
CCACACGGGCGTGTGCCCTT
Found at i:46469945 original size:38 final size:38
Alignment explanation
Indices: 46469903--46469978 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
46469893 TGATACTTAG
*
46469903 CCACCCTACCTTTTCCATGATTTTTTTTACATTTTACT
1 CCACCCTACCTTTTCCATGATTATTTTTACATTTTACT
46469941 CCACCCTACCTTTTCCATGATTATTTTTACATTTTACT
1 CCACCCTACCTTTTCCATGATTATTTTTACATTTTACT
46469979 TATTACTCAG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.20, C:0.29, G:0.03, T:0.49
Consensus pattern (38 bp):
CCACCCTACCTTTTCCATGATTATTTTTACATTTTACT
Found at i:46470123 original size:50 final size:48
Alignment explanation
Indices: 46470062--46470177 Score: 135
Period size: 50 Copynumber: 2.4 Consensus size: 48
46470052 TTTTGCTGAC
* *
46470062 AGACTTGTTTTATCATTTCAATCAAAAGGCTTCCATCAAATCATGT-AG
1 AGACTTATTTTATCATCTCAATCAAAAGGCTTCCATCAAATCAT-TCAG
* ** * *
46470110 AGAGTCTTATTTTATCATCTCAGTCATCAGGCTTCTATCAACTCATTCAG
1 AGA--CTTATTTTATCATCTCAATCAAAAGGCTTCCATCAAATCATTCAG
46470160 AGACTTATTTTATCATCT
1 AGACTTATTTTATCATCT
46470178 TATTCTTCCA
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
48 18 0.31
49 1 0.02
50 39 0.67
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39
Consensus pattern (48 bp):
AGACTTATTTTATCATCTCAATCAAAAGGCTTCCATCAAATCATTCAG
Found at i:46471078 original size:16 final size:15
Alignment explanation
Indices: 46471052--46471088 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
46471042 GCCTAAGAAG
46471052 TAAATTGAATTGAAT
1 TAAATTGAATTGAAT
*
46471067 TAAATATGAATTGTAT
1 TAAAT-TGAATTGAAT
46471083 TAAATT
1 TAAATT
46471089 CAGCTGAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (15 bp):
TAAATTGAATTGAAT
Found at i:46472262 original size:15 final size:15
Alignment explanation
Indices: 46472242--46472299 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
46472232 TGCATAATAG
*
46472242 AACAATAATAATGAA
1 AACAATAATAATAAA
46472257 AACAATAAT-ATAAA
1 AACAATAATAATAAA
** *
46472271 TAACAACGATAAAAAA
1 -AACAATAATAATAAA
46472287 AACAATAATAATA
1 AACAATAATAATA
46472300 GCAATACTAC
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
14 4 0.12
15 26 0.76
16 4 0.12
ACGTcount: A:0.69, C:0.09, G:0.03, T:0.19
Consensus pattern (15 bp):
AACAATAATAATAAA
Found at i:46472442 original size:24 final size:24
Alignment explanation
Indices: 46472415--46472464 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
46472405 CAAGCTAATT
* *
46472415 GTAAATAAATAATAA-TAATAATAA
1 GTAAAAAAATAAAAACTAATAA-AA
46472439 GTAAAAAAATAAAAACTAATAAAA
1 GTAAAAAAATAAAAACTAATAAAA
46472463 GT
1 GT
46472465 TTAATTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.68, C:0.02, G:0.06, T:0.24
Consensus pattern (24 bp):
GTAAAAAAATAAAAACTAATAAAA
Found at i:46472539 original size:3 final size:3
Alignment explanation
Indices: 46472531--46472591 Score: 70
Period size: 3 Copynumber: 20.7 Consensus size: 3
46472521 AACAGTTAAA
* * * * *
46472531 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAC GAT GAT ATT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
46472579 AAT AAT -AT AAT AA
1 AAT AAT AAT AAT AA
46472592 AAATTTGAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:46472742 original size:29 final size:29
Alignment explanation
Indices: 46472688--46472758 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
46472678 AAAAAATAAT
* *
46472688 AATGAAAATAATATTAATATATAAATAGA
1 AATGAAAATAATAATAATATAGAAATAGA
* *
46472717 AATGGAAAT-ATAATAATAGTAGAAATATA
1 AATGAAAATAATAATAATA-TAGAAATAGA
46472746 AATAGATAAATAA
1 AAT-GA-AAATAA
46472759 AAAATAGACA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
28 8 0.24
29 19 0.58
30 1 0.03
31 4 0.12
32 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (29 bp):
AATGAAAATAATAATAATATAGAAATAGA
Found at i:46472748 original size:23 final size:20
Alignment explanation
Indices: 46472697--46472757 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 20
46472687 TAATGAAAAT
*
46472697 AATATTAATATATAAATAGA
1 AATATAAATATATAAATAGA
**
46472717 AATGGAAATATAATAATAGTAGA
1 AATATAAATAT-ATAA-A-TAGA
*
46472740 AATATAAATAGATAAATA
1 AATATAAATATATAAATA
46472758 AAAAATAGAC
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
20 10 0.31
21 5 0.16
22 5 0.16
23 12 0.38
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.30
Consensus pattern (20 bp):
AATATAAATATATAAATAGA
Found at i:46477111 original size:58 final size:57
Alignment explanation
Indices: 46476963--46477111 Score: 158
Period size: 57 Copynumber: 2.6 Consensus size: 57
46476953 ATCATATAAC
* * * * * *
46476963 AGGATTGCCAGTCCAAGCTAAATCCTGTCTCTAACATATGCTCAGAAGAGCTTAATT
1 AGGATTACCAGTCTAGGCTAAATCCTATCTGTAACATATGCTCAGAAGAGATTAATT
* *
46477020 AGGATTACCAGTCTAGGCTAAATCCTAAT-TGTAACGTATGCTCA-AGAGGGATTATATT
1 AGGATTACCAGTCTAGGCTAAATCCT-ATCTGTAACATATGCTCAGA-AGAGATTA-ATT
* * *
46477078 AGGATTACCCGTCTGGGCTAAATCCTTTCTGTAA
1 AGGATTACCAGTCTAGGCTAAATCCTATCTGTAA
46477112 TGAGGTCAAT
Statistics
Matches: 77, Mismatches: 11, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
56 1 0.01
57 43 0.56
58 33 0.43
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.30
Consensus pattern (57 bp):
AGGATTACCAGTCTAGGCTAAATCCTATCTGTAACATATGCTCAGAAGAGATTAATT
Found at i:46478654 original size:42 final size:42
Alignment explanation
Indices: 46478602--46478740 Score: 224
Period size: 42 Copynumber: 3.3 Consensus size: 42
46478592 TTGGACAAAG
*
46478602 ACACGGGCGTGTATCTCAGCCGTGTGTAGCACACGGCCTGGC
1 ACACGGGCGTGTGTCTCAGCCGTGTGTAGCACACGGCCTGGC
* * *
46478644 ACACGAGCGTGTGTCTCAGCCGTGTGTAGCACAAGTCCTGGC
1 ACACGGGCGTGTGTCTCAGCCGTGTGTAGCACACGGCCTGGC
*
46478686 ACACGGGCGTGTGTCTCAGCCATGTGTAGCACACGGCCTGGC
1 ACACGGGCGTGTGTCTCAGCCGTGTGTAGCACACGGCCTGGC
*
46478728 ACACGGGCATGTG
1 ACACGGGCGTGTG
46478741 ACTTGACCAT
Statistics
Matches: 88, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 88 1.00
ACGTcount: A:0.18, C:0.29, G:0.33, T:0.19
Consensus pattern (42 bp):
ACACGGGCGTGTGTCTCAGCCGTGTGTAGCACACGGCCTGGC
Found at i:46482387 original size:20 final size:20
Alignment explanation
Indices: 46482359--46482400 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
46482349 GATAATTAAC
* *
46482359 CTTAGTTTAATTATATAATA
1 CTTAATTTAATTAAATAATA
46482379 CTTAATTTAATTAAATAATA
1 CTTAATTTAATTAAATAATA
46482399 CT
1 CT
46482401 CACATAACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (20 bp):
CTTAATTTAATTAAATAATA
Found at i:46487683 original size:13 final size:13
Alignment explanation
Indices: 46487665--46487689 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46487655 TGTATCTTTT
46487665 TTTTTAATATTTA
1 TTTTTAATATTTA
46487678 TTTTTAATATTT
1 TTTTTAATATTT
46487690 TACTATATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTAATATTTA
Found at i:46488842 original size:17 final size:18
Alignment explanation
Indices: 46488815--46488849 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
46488805 CAATTCACTT
46488815 TTTTTTACTTTTTTTTTG
1 TTTTTTACTTTTTTTTTG
46488833 TTTTTT-CTTTTTTTTTG
1 TTTTTTACTTTTTTTTTG
46488850 GGGGGGGGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.03, C:0.06, G:0.06, T:0.86
Consensus pattern (18 bp):
TTTTTTACTTTTTTTTTG
Found at i:46488883 original size:1 final size:1
Alignment explanation
Indices: 46488879--46488915 Score: 74
Period size: 1 Copynumber: 37.0 Consensus size: 1
46488869 CATTGATTTC
46488879 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
46488916 GGGGGGGGGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:46490690 original size:71 final size:71
Alignment explanation
Indices: 46490615--46490749 Score: 270
Period size: 71 Copynumber: 1.9 Consensus size: 71
46490605 TGTCAAAATT
46490615 CAATCAAATTTGAAGTTTAATGGTAAAAATTCAATCATAAAAAAATAATTAATAGACAAATTTAC
1 CAATCAAATTTGAAGTTTAATGGTAAAAATTCAATCATAAAAAAATAATTAATAGACAAATTTAC
46490680 AAAGTG
66 AAAGTG
46490686 CAATCAAATTTGAAGTTTAATGGTAAAAATTCAATCATAAAAAAATAATTAATAGACAAATTTA
1 CAATCAAATTTGAAGTTTAATGGTAAAAATTCAATCATAAAAAAATAATTAATAGACAAATTTA
46490750 TCTATATTCT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 64 1.00
ACGTcount: A:0.53, C:0.08, G:0.09, T:0.30
Consensus pattern (71 bp):
CAATCAAATTTGAAGTTTAATGGTAAAAATTCAATCATAAAAAAATAATTAATAGACAAATTTAC
AAAGTG
Found at i:46492136 original size:55 final size:55
Alignment explanation
Indices: 46492052--46492163 Score: 215
Period size: 55 Copynumber: 2.0 Consensus size: 55
46492042 AATGAATCTC
46492052 TTACGTATATTCACCCTCAAATATACTACGGTCTAACTTTTTTTTTTATAATAGT
1 TTACGTATATTCACCCTCAAATATACTACGGTCTAACTTTTTTTTTTATAATAGT
*
46492107 TTACGTATATTCACCCTCAAATTTACTACGGTCTAACTTTTTTTTTTATAATAGT
1 TTACGTATATTCACCCTCAAATATACTACGGTCTAACTTTTTTTTTTATAATAGT
46492162 TT
1 TT
46492164 CATTTGTTTT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.28, C:0.18, G:0.07, T:0.47
Consensus pattern (55 bp):
TTACGTATATTCACCCTCAAATATACTACGGTCTAACTTTTTTTTTTATAATAGT
Found at i:46498857 original size:18 final size:18
Alignment explanation
Indices: 46498834--46498870 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
46498824 AAACTCTTAT
46498834 ATTCATCTACCAGCAGCA
1 ATTCATCTACCAGCAGCA
46498852 ATTCATCTACCAGCAGCA
1 ATTCATCTACCAGCAGCA
46498870 A
1 A
46498871 GTTTAACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.32, G:0.11, T:0.22
Consensus pattern (18 bp):
ATTCATCTACCAGCAGCA
Found at i:46502607 original size:16 final size:17
Alignment explanation
Indices: 46502586--46502620 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
46502576 GAATTCAAAA
*
46502586 AATAATAA-TATAAATT
1 AATAATAATTAGAAATT
46502602 AATAATAATTAGAAATT
1 AATAATAATTAGAAATT
46502619 AA
1 AA
46502621 AAGAAGATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
AATAATAATTAGAAATT
Found at i:46517806 original size:38 final size:38
Alignment explanation
Indices: 46517745--46517948 Score: 257
Period size: 38 Copynumber: 5.3 Consensus size: 38
46517735 ATTTGATGTG
* * *
46517745 TATCCGGGCTTAAAGACCCGCAGGCTAT-ATGCTGGAATTA
1 TATCCGGG-TTAAA-TCCCGCAGGCT-TCGTGCTGGTATTA
46517785 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTA
46517823 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTA
* *
46517861 TATCCGGGTTAAATCCCGCAGGCCTAGTGCTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTA
* * * *
46517899 TATCTGAGTTTAAAGTCCCGTAGGCTTCGTGCTGGTGTTA
1 TATCCG-GGTTAAA-TCCCGCAGGCTTCGTGCTGGTATTA
* *
46517939 TGTTCGGGTT
1 TATCCGGGTT
46517949 TTATACCTCG
Statistics
Matches: 146, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
37 1 0.01
38 99 0.68
39 14 0.10
40 32 0.22
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.32
Consensus pattern (38 bp):
TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTA
Found at i:46522021 original size:11 final size:11
Alignment explanation
Indices: 46522005--46522052 Score: 60
Period size: 11 Copynumber: 4.2 Consensus size: 11
46521995 CTTTATATAC
46522005 TAATAAAATAA
1 TAATAAAATAA
46522016 TAATAAAATATA
1 TAATAAAATA-A
* *
46522028 TTATTAAAATAT
1 -TAATAAAATAA
46522040 TAATAAAATAA
1 TAATAAAATAA
46522051 TA
1 TA
46522053 TTTATCTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
11 21 0.68
12 1 0.03
13 9 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:46522035 original size:24 final size:24
Alignment explanation
Indices: 46521999--46522054 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
46521989 TTCTTTCTTT
*
46521999 ATATACTAATAAAATAATAATAAA
1 ATATATTAATAAAATAATAATAAA
* *
46522023 ATATATTATTAAAATATTAATAAA
1 ATATATTAATAAAATAATAATAAA
46522047 ATAATATT
1 AT-ATATT
46522055 TATCTAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 23 0.82
25 5 0.18
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (24 bp):
ATATATTAATAAAATAATAATAAA
Found at i:46523140 original size:16 final size:17
Alignment explanation
Indices: 46523109--46523141 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
46523099 TTCATAAGTA
46523109 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
46523126 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
46523142 GCTCCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:46531845 original size:105 final size:105
Alignment explanation
Indices: 46531678--46531888 Score: 287
Period size: 105 Copynumber: 2.0 Consensus size: 105
46531668 TGTCCATCTG
* *
46531678 TGTCATAGTCACTAAATTATTTATATCTGGAGCTATAGAACTCCAAATTAAGATCCGATAATTTT
1 TGTCATAGTCACAAAATTATTTATATCTGGAGCTAAAGAACTCCAAATTAAGATCCGATAATTTT
** * * *
46531743 TTATGAAACTAGACTTATATATATTATTATCATAATATTT
66 CCATGAAACTAGACTCACATATATTATTATCATAAAATTT
* * * * *
46531783 TGTCATAGTCACAAAATTATTTTTATCTTGAGCTAAAGAACTCCAAATTAGGATCTGCTAATTTT
1 TGTCATAGTCACAAAATTATTTATATCTGGAGCTAAAGAACTCCAAATTAAGATCCGATAATTTT
* * *
46531848 CCATGAAACTATAGTCACATATATTCTTATCATAAAATTT
66 CCATGAAACTAGACTCACATATATTATTATCATAAAATTT
46531888 T
1 T
46531889 CAGAATTTTT
Statistics
Matches: 91, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
105 91 1.00
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.40
Consensus pattern (105 bp):
TGTCATAGTCACAAAATTATTTATATCTGGAGCTAAAGAACTCCAAATTAAGATCCGATAATTTT
CCATGAAACTAGACTCACATATATTATTATCATAAAATTT
Found at i:46532574 original size:266 final size:266
Alignment explanation
Indices: 46532100--46532633 Score: 1050
Period size: 266 Copynumber: 2.0 Consensus size: 266
46532090 CCAATTTTTT
* *
46532100 ATGATTTTCCAAAGTCAGAACAGGGGAACCCTAATTCATTCTGACTTTGTCTCACAAAATTTATT
1 ATGATTTTCCAAAGTCAGAACAGGGGAACCCGAATTCATTCTGACTTTGTCTCACAAAATTCATT
46532165 ATATCTCATGATTTACAAATCCATTGCTTACACCGTTTCTTCTATGAGAAAATAGACTCAATAAG
66 ATATCTCATGATTTACAAATCCATTGCTTACACCGTTTCTTCTATGAGAAAATAGACTCAATAAG
46532230 CTTTAATTTAATGTTTTTTTCATCTTCTAATTATATTTCTACAATTTATGGTGATTTTTCAAAGT
131 CTTTAATTTAATGTTTTTTTCATCTTCTAATTATATTTCTACAATTTATGGTGATTTTTCAAAGT
46532295 TACTCTACTGCTGCTGTCCAATATTGTTTTAGTGCAAGCTGTTTATTACCATTTTTTTCCCTTAA
196 TACTCTACTGCTGCTGTCCAATATTGTTTTAGTGCAAGCTGTTTATTACCATTTTTTTCCCTTAA
46532360 GCTTTA
261 GCTTTA
46532366 ATGATTTTCCAAAGTCAGAACAGGGGAACCCGAATTCATTCTGACTTTGTCTCACAAAATTCATT
1 ATGATTTTCCAAAGTCAGAACAGGGGAACCCGAATTCATTCTGACTTTGTCTCACAAAATTCATT
46532431 ATATCTCATGATTTACAAATCCATTGCTTACACCGTTTCTTCTATGAGAAAATAGACTCAATAAG
66 ATATCTCATGATTTACAAATCCATTGCTTACACCGTTTCTTCTATGAGAAAATAGACTCAATAAG
46532496 CTTTAATTTAATGTTTTTTTCATCTTCTAATTATATTTCTACAATTTATGGTGATTTTTCAAAGT
131 CTTTAATTTAATGTTTTTTTCATCTTCTAATTATATTTCTACAATTTATGGTGATTTTTCAAAGT
46532561 TACTCTACTGCTGCTGTCCAATATTGTTTTAGTGCAAGCTGTTTATTACCATTTTTTTCCCTTAA
196 TACTCTACTGCTGCTGTCCAATATTGTTTTAGTGCAAGCTGTTTATTACCATTTTTTTCCCTTAA
46532626 GCTTTA
261 GCTTTA
46532632 AT
1 AT
46532634 AAATAACAAT
Statistics
Matches: 266, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
266 266 1.00
ACGTcount: A:0.28, C:0.18, G:0.11, T:0.42
Consensus pattern (266 bp):
ATGATTTTCCAAAGTCAGAACAGGGGAACCCGAATTCATTCTGACTTTGTCTCACAAAATTCATT
ATATCTCATGATTTACAAATCCATTGCTTACACCGTTTCTTCTATGAGAAAATAGACTCAATAAG
CTTTAATTTAATGTTTTTTTCATCTTCTAATTATATTTCTACAATTTATGGTGATTTTTCAAAGT
TACTCTACTGCTGCTGTCCAATATTGTTTTAGTGCAAGCTGTTTATTACCATTTTTTTCCCTTAA
GCTTTA
Found at i:46533451 original size:18 final size:18
Alignment explanation
Indices: 46533403--46533451 Score: 53
Period size: 21 Copynumber: 2.5 Consensus size: 18
46533393 ATAATATAAT
46533403 TATTTAATTAATAAATATC
1 TATTTAA-TAATAAATATC
*
46533422 TTTTATAAAATAATAAATATC
1 TATT-T--AATAATAAATATC
46533443 TATTTAATA
1 TATTTAATA
46533452 TCTAATACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
18 4 0.16
19 3 0.12
20 2 0.08
21 14 0.56
22 2 0.08
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTTAATAATAAATATC
Found at i:46533740 original size:48 final size:48
Alignment explanation
Indices: 46533684--46533779 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
46533674 TGCTAAATGG
46533684 CATAATTTGAATTTTGGTCCATTTTATTTTCTTTTAATCTATAATTAA
1 CATAATTTGAATTTTGGTCCATTTTATTTTCTTTTAATCTATAATTAA
46533732 CATAATTTGAATTTTGGTCCATTTTATTTTCTTTTAATCTATAATTAA
1 CATAATTTGAATTTTGGTCCATTTTATTTTCTTTTAATCTATAATTAA
46533780 ACTTTCACAC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.29, C:0.10, G:0.06, T:0.54
Consensus pattern (48 bp):
CATAATTTGAATTTTGGTCCATTTTATTTTCTTTTAATCTATAATTAA
Found at i:46534682 original size:113 final size:117
Alignment explanation
Indices: 46534536--46534911 Score: 336
Period size: 117 Copynumber: 3.2 Consensus size: 117
46534526 AATCCACAGC
* *
46534536 TAAAATGACGATGTTTCCATTCAATT-AAAAAA-A-TACGG-TGTTTTT-TAAAAAGCGCTGCTA
1 TAAAATGACGACGTTTCCATTCAATTAAAAAAATACTACGGCT-TTTTTATAAAAAGCGCCGCTA
* *
46534596 ATTCTTATCTATTGCGGCGTTTATTAGCTAGGGCCGCTAATTCCACAAAGCAT
65 ATTCTTATATATTGCGGCGTTTATTAGCTAGCGCCGCTAATTCCACAAAGCAT
* * *
46534649 TAAAATGGCGACGTTTCCATTCAATTACAAAAATACTACGGCTTTTTTATAAAAAGCGCCGCTAG
1 TAAAATGACGACGTTTCCATTCAATTAAAAAAATACTACGGCTTTTTTATAAAAAGCGCCGCTAA
* * *
46534714 TTCTTATATATTGCGGCGTTTATTAGCTAGCGTCGCTAATTTCACGAAGCAT
66 TTCTTATATATTGCGGCGTTTATTAGCTAGCGCCGCTAATTCCACAAAGCAT
* * * * * *** ** * * *
46534766 TAAAA-CAGCGTCCTTTTCATTCAGTTAAAATTTTTTTA-GG-TGTTTTACAGAAAGCGCCGCTA
1 TAAAATGA-CGACGTTTCCATTCAATTAAAAAAATACTACGGCTTTTTTATAAAAAGCGCCGCTA
* * * * * * * * *
46534828 ATACTGATCTATTTCGGCATTTATAATCTAGCGTCGCTAATTCCACTAAACCCACACT
65 ATTCTTATATATTGCGGCGTTTATTAGCTAGCGCCGCTAATTCCAC-AAA---GCA-T
*
46534886 TAAAATGACGTCGTTTCCATTCAATT
1 TAAAATGACGACGTTTCCATTCAATT
46534912 GAATTTCTTT
Statistics
Matches: 211, Mismatches: 40, Indels: 17
0.79 0.15 0.06
Matches are distributed among these distances:
113 24 0.11
114 5 0.02
115 57 0.27
116 14 0.07
117 87 0.41
119 2 0.01
120 21 0.10
121 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.34
Consensus pattern (117 bp):
TAAAATGACGACGTTTCCATTCAATTAAAAAAATACTACGGCTTTTTTATAAAAAGCGCCGCTAA
TTCTTATATATTGCGGCGTTTATTAGCTAGCGCCGCTAATTCCACAAAGCAT
Found at i:46534734 original size:117 final size:113
Alignment explanation
Indices: 46534536--46534770 Score: 337
Period size: 117 Copynumber: 2.0 Consensus size: 113
46534526 AATCCACAGC
* *
46534536 TAAAATGACGATGTTTCCATTCAATTAAAAAAATACGGTGTTTTTTAAAAAGCGCTGCTAATTCT
1 TAAAATGACGACGTTTCCATTCAATTAAAAAAATACGGTGTTTTTTAAAAAGCGCCGCTAATTCT
* *
46534601 TATCTATTGCGGCGTTTATTAGCTAGGGCCGCTAATTCCACAAAGCAT
66 TATATATTGCGGCGTTTATTAGCTAGCGCCGCTAATTCCACAAAGCAT
*
46534649 TAAAATGGCGACGTTTCCATTCAATTACAAAAATACTACGGCT-TTTTTATAAAAAGCGCCGCTA
1 TAAAATGACGACGTTTCCATTCAATTA-AAAAA-A-TACGG-TGTTTTT-TAAAAAGCGCCGCTA
* * * *
46534713 GTTCTTATATATTGCGGCGTTTATTAGCTAGCGTCGCTAATTTCACGAAGCAT
61 ATTCTTATATATTGCGGCGTTTATTAGCTAGCGCCGCTAATTCCACAAAGCAT
46534766 TAAAA
1 TAAAA
46534771 CAGCGTCCTT
Statistics
Matches: 108, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
113 25 0.23
114 5 0.05
115 1 0.01
116 10 0.09
117 67 0.62
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (113 bp):
TAAAATGACGACGTTTCCATTCAATTAAAAAAATACGGTGTTTTTTAAAAAGCGCCGCTAATTCT
TATATATTGCGGCGTTTATTAGCTAGCGCCGCTAATTCCACAAAGCAT
Found at i:46535176 original size:14 final size:14
Alignment explanation
Indices: 46535156--46535197 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
46535146 CAAATTTTAT
46535156 CCTTAAACCCTAAA
1 CCTTAAACCCTAAA
* *
46535170 GCTTAAACTCTAAA
1 CCTTAAACCCTAAA
46535184 CCTTAAACCCTAAA
1 CCTTAAACCCTAAA
46535198 ATCTAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.43, C:0.31, G:0.02, T:0.24
Consensus pattern (14 bp):
CCTTAAACCCTAAA
Found at i:46535197 original size:21 final size:21
Alignment explanation
Indices: 46535159--46535203 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
46535149 ATTTTATCCT
* * *
46535159 TAAACCCTAAAGCTTAAACTC
1 TAAACCCTAAACCCTAAAATC
*
46535180 TAAACCTTAAACCCTAAAATC
1 TAAACCCTAAACCCTAAAATC
46535201 TAA
1 TAA
46535204 CTCAAAAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.47, C:0.27, G:0.02, T:0.24
Consensus pattern (21 bp):
TAAACCCTAAACCCTAAAATC
Found at i:46535299 original size:15 final size:15
Alignment explanation
Indices: 46535279--46535323 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
46535269 TACCCTTAAA
*
46535279 CCCTAATATCCTAAC
1 CCCTAAAATCCTAAC
*
46535294 CCCTAAAATCCTAAA
1 CCCTAAAATCCTAAC
* *
46535309 CACTAAAACCCTAAC
1 CCCTAAAATCCTAAC
46535324 TATAAAATAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.42, C:0.38, G:0.00, T:0.20
Consensus pattern (15 bp):
CCCTAAAATCCTAAC
Found at i:46535309 original size:30 final size:29
Alignment explanation
Indices: 46535275--46535340 Score: 69
Period size: 30 Copynumber: 2.2 Consensus size: 29
46535265 TAATTACCCT
* * * *
46535275 TAAACCCTAATATCCTAACCCCTAAAATCC
1 TAAACCCTAAAACCCTAA-CCATAAAATAC
* *
46535305 TAAACACTAAAACCCTAACTATAAAATAC
1 TAAACCCTAAAACCCTAACCATAAAATAC
46535334 TAAACCC
1 TAAACCC
46535341 CAAATCATAA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
29 14 0.48
30 15 0.52
ACGTcount: A:0.47, C:0.32, G:0.00, T:0.21
Consensus pattern (29 bp):
TAAACCCTAAAACCCTAACCATAAAATAC
Found at i:46535539 original size:40 final size:40
Alignment explanation
Indices: 46535475--46535577 Score: 125
Period size: 40 Copynumber: 2.5 Consensus size: 40
46535465 TGCTTGATCT
* *
46535475 TTTGCGGCGTTTTTTTCATAAACGCCGCTAATGTTTGACC
1 TTTGCGGCATTTTTTTCATAAACGCCGCCAATGTTTGACC
* * *
46535515 TTTGTGGCATTTTTTTCGTAAACGCTGCCAATGTTTGACC
1 TTTGCGGCATTTTTTTCATAAACGCCGCCAATGTTTGACC
** *
46535555 TTTTGCGGTGTTTTTATCATAAA
1 -TTTGCGGCATTTTTTTCATAAA
46535578 TGTTGCTAAT
Statistics
Matches: 52, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
40 35 0.67
41 17 0.33
ACGTcount: A:0.18, C:0.18, G:0.19, T:0.44
Consensus pattern (40 bp):
TTTGCGGCATTTTTTTCATAAACGCCGCCAATGTTTGACC
Found at i:46535569 original size:41 final size:41
Alignment explanation
Indices: 46535468--46535601 Score: 162
Period size: 41 Copynumber: 3.3 Consensus size: 41
46535458 TAGCGTTTGC
* *
46535468 TTGATCTTTTGCGGCGTTTTTTTCATAAACGCCGCTAATGT
1 TTGACCTTTTGCGGCGTTTTTTTCATAAACGCTGCTAATGT
* * * *
46535509 TTGACC-TTTGTGGCATTTTTTTCGTAAACGCTGCCAATGT
1 TTGACCTTTTGCGGCGTTTTTTTCATAAACGCTGCTAATGT
* * * * *
46535549 TTGACCTTTTGCGGTGTTTTTATCATAAATGTTGCTAATGC
1 TTGACCTTTTGCGGCGTTTTTTTCATAAACGCTGCTAATGT
46535590 TTGACCTTTTGC
1 TTGACCTTTTGC
46535602 AAACGCCGCT
Statistics
Matches: 77, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
40 35 0.45
41 42 0.55
ACGTcount: A:0.17, C:0.19, G:0.19, T:0.45
Consensus pattern (41 bp):
TTGACCTTTTGCGGCGTTTTTTTCATAAACGCTGCTAATGT
Found at i:46550488 original size:5 final size:5
Alignment explanation
Indices: 46550480--46550507 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
46550470 TTTAGAAGGC
46550480 AAATA AAATA AAATA AAATA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAA
46550508 CAAACCCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:46553144 original size:43 final size:43
Alignment explanation
Indices: 46553044--46553153 Score: 109
Period size: 43 Copynumber: 2.6 Consensus size: 43
46553034 TGTGTTATCG
* * *
46553044 TGTAAGACCACGTCTGGGA-TGTTGGAATCGTACTTAATTTCG
1 TGTAAGACCACGTCTGGGACAGTTGGAATCGTACTTAATTACA
** * * *
46553086 TGTAAGACCTTGTCTGGGACAG-TGGCATCGATATTTCATTACA
1 TGTAAGACCACGTCTGGGACAGTTGGAATCG-TACTTAATTACA
*
46553129 TGTAAGACCACGTCTGAGACA-TTGG
1 TGTAAGACCACGTCTGGGACAGTTGG
46553154 TATTGTACGA
Statistics
Matches: 54, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
42 24 0.44
43 30 0.56
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACAGTTGGAATCGTACTTAATTACA
Found at i:46556673 original size:21 final size:22
Alignment explanation
Indices: 46556636--46556727 Score: 109
Period size: 23 Copynumber: 4.2 Consensus size: 22
46556626 ACATATATAT
*
46556636 ATATA-AATAATAGTATTAGAA
1 ATATACAATAATAATATTAGAA
46556657 ATATACAAT-ATAATATTAGAA
1 ATATACAATAATAATATTAGAA
* *
46556678 ATATACATATAATAGTATTAAAA
1 ATATACA-ATAATAATATTAGAA
*
46556701 ATATATAACTAATAATATTA-AA
1 ATATACAA-TAATAATATTAGAA
46556723 ATATA
1 ATATA
46556728 ATATTGAAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
21 23 0.37
22 13 0.21
23 26 0.42
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.35
Consensus pattern (22 bp):
ATATACAATAATAATATTAGAA
Found at i:46556682 original size:44 final size:45
Alignment explanation
Indices: 46556634--46556727 Score: 129
Period size: 44 Copynumber: 2.1 Consensus size: 45
46556624 GCACATATAT
* *
46556634 ATATATAAATAATAGTATTAGAAATATACAA-T-ATAATATTAGAA
1 ATATACAAATAATAGTATTAAAAATATACAACTAATAATATTA-AA
* *
46556678 ATATACATATAATAGTATTAAAAATATATAACTAATAATATTAAA
1 ATATACAAATAATAGTATTAAAAATATACAACTAATAATATTAAA
46556723 ATATA
1 ATATA
46556728 ATATTGAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
44 27 0.61
45 8 0.18
46 9 0.20
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.35
Consensus pattern (45 bp):
ATATACAAATAATAGTATTAAAAATATACAACTAATAATATTAAA
Found at i:46557005 original size:21 final size:22
Alignment explanation
Indices: 46556968--46557070 Score: 115
Period size: 23 Copynumber: 4.8 Consensus size: 22
46556958 ACATATATAT
*
46556968 ATATA-AATAATAGTATTAGAA
1 ATATACAATAATAATATTAGAA
46556989 ATATACAAT-ATAATATTAGAA
1 ATATACAATAATAATATTAGAA
* *
46557010 ATATACATATAATAGTATTAAAA
1 ATATACA-ATAATAATATTAGAA
*
46557033 ATATATAACTAATAATATTA-AA
1 ATATACAA-TAATAATATTAGAA
*
46557055 ATATA-TATAATAATAT
1 ATATACAATAATAATAT
46557071 ATAAAAAATA
Statistics
Matches: 72, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.12
21 24 0.33
22 13 0.18
23 26 0.36
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.36
Consensus pattern (22 bp):
ATATACAATAATAATATTAGAA
Found at i:46557081 original size:21 final size:21
Alignment explanation
Indices: 46556966--46557085 Score: 111
Period size: 23 Copynumber: 5.5 Consensus size: 21
46556956 GCACATATAT
*
46556966 ATATATAAATAATAGTATTAGAA
1 ATATAT-AATAATA-TATTAAAA
* *
46556989 ATATACAAT-ATAATATTAGAA
1 ATATATAATAAT-ATATTAAAA
*
46557010 ATATACATATAATAGTATTAAAA
1 ATATATA-ATAATA-TATTAAAA
46557033 ATATATAACTAATAATATTAAAA
1 ATATATAA-TAAT-ATATTAAAA
46557056 TATATATAATAATATA-TAAAA
1 -ATATATAATAATATATTAAAA
46557077 A-ATATAATA
1 ATATATAATA
46557086 TTGAAAACAT
Statistics
Matches: 87, Mismatches: 3, Indels: 18
0.81 0.03 0.17
Matches are distributed among these distances:
19 8 0.09
20 1 0.01
21 22 0.25
22 11 0.13
23 36 0.41
24 9 0.10
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (21 bp):
ATATATAATAATATATTAAAA
Found at i:46557310 original size:17 final size:16
Alignment explanation
Indices: 46557284--46557315 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
46557274 CTATATATAA
46557284 ATATATATACATACAT
1 ATATATATACATACAT
46557300 ATATAATATACATACA
1 ATAT-ATATACATACA
46557316 CTAATATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (16 bp):
ATATATATACATACAT
Found at i:46557417 original size:3 final size:3
Alignment explanation
Indices: 46557389--46557476 Score: 58
Period size: 3 Copynumber: 29.7 Consensus size: 3
46557379 ATTAATATGT
* * * * *
46557389 TAA TAA AAA TAA TAG TAA TGAA -AA TAA TAC TAA CAG TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
* *
46557434 -AGA TAA TAA TAGA -AA TAA -AA TAA TAG TAA TAA TAT TAA TAA TA
1 TA-A TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
46557477 TGTAAAAAAA
Statistics
Matches: 64, Mismatches: 14, Indels: 14
0.70 0.15 0.15
Matches are distributed among these distances:
2 6 0.09
3 54 0.84
4 4 0.06
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:46557519 original size:3 final size:3
Alignment explanation
Indices: 46557511--46557667 Score: 60
Period size: 3 Copynumber: 52.3 Consensus size: 3
46557501 AAAAGGACTA
*
46557511 AAT AAT AAT AAT AA- AACT AGA- AAT AAT AAT AATT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AA-T A-AT AAT AAT AAT AA-T AAT AAT AAT AAT
* * * ** * *
46557557 ACGT TAG AA- AAT AATT AAT -AT GTT AAT AAA AAT AAT AGT AAT GAA-
1 A-AT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
* * *
46557602 AAT AAT ACT AAC AGT AAT AAT AA- AGAT AAT AAT AGA- AAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT A-AT AAT AAT AAT
** *
46557646 AAT CGT AAT AAT ATT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT A
46557668 TGTAAAAAAA
Statistics
Matches: 112, Mismatches: 26, Indels: 32
0.66 0.15 0.19
Matches are distributed among these distances:
2 13 0.12
3 87 0.78
4 11 0.10
5 1 0.01
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:46557560 original size:191 final size:189
Alignment explanation
Indices: 46557323--46557703 Score: 717
Period size: 191 Copynumber: 2.0 Consensus size: 189
46557313 ACACTAATAT
*
46557323 TAATAATAATAAAACTAGAAAAATAATAATTAGTGATAATAATACGTTAGAAAATAATTAATATG
1 TAATAATAATAAAACTAGAAAAATAATAATTAGTAATAATAATACGTTAGAAAATAATTAATATG
46557388 TTAATAAAAATAATAGTAATGAAAATAATACTAACAGTAATAATAAAGATAATAATAGAAATAAA
66 TTAATAAAAATAATAGTAATGAAAATAATACTAACAGTAATAATAAAGATAATAATAGAAATAAA
46557453 ATAATAGTAATAATATTAATAATATGTAAAAAAATGGAAAATAAACGAAAAAGGACTAAA
131 ATAATAGTAATAATATTAATAATATGTAAAAAAAT-GAAAATAAACGAAAAAGGACTAAA
46557513 TAATAATAATAAAACTAGAAATAATAATAATTAGTAATAATAATACGTTAGAAAATAATTAATAT
1 TAATAATAATAAAACTAGAAA-AATAATAATTAGTAATAATAATACGTTAGAAAATAATTAATAT
46557578 GTTAATAAAAATAATAGTAATGAAAATAATACTAACAGTAATAATAAAGATAATAATAGAAATAA
65 GTTAATAAAAATAATAGTAATGAAAATAATACTAACAGTAATAATAAAGATAATAATAGAAATAA
* *
46557643 AATAATCGTAATAATATTAATAATATGTAAAAAAATGAAAATAAACTAAAAAGGACTAAA
130 AATAATAGTAATAATATTAATAATATGTAAAAAAATGAAAATAAACGAAAAAGGACTAAA
46557703 T
1 T
46557704 CGAACTAAGA
Statistics
Matches: 187, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
190 45 0.24
191 142 0.76
ACGTcount: A:0.60, C:0.03, G:0.09, T:0.28
Consensus pattern (189 bp):
TAATAATAATAAAACTAGAAAAATAATAATTAGTAATAATAATACGTTAGAAAATAATTAATATG
TTAATAAAAATAATAGTAATGAAAATAATACTAACAGTAATAATAAAGATAATAATAGAAATAAA
ATAATAGTAATAATATTAATAATATGTAAAAAAATGAAAATAAACGAAAAAGGACTAAA
Found at i:46559170 original size:14 final size:15
Alignment explanation
Indices: 46559151--46559180 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
46559141 AATTGCATTT
46559151 TAAATATT-ATTTTA
1 TAAATATTAATTTTA
46559165 TAAATATTAATTTTA
1 TAAATATTAATTTTA
46559180 T
1 T
46559181 TCATAGTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TAAATATTAATTTTA
Found at i:46562462 original size:24 final size:24
Alignment explanation
Indices: 46562433--46562569 Score: 116
Period size: 23 Copynumber: 6.0 Consensus size: 24
46562423 TAAAAAAAAT
46562433 TTTACATGGAAAAAAATAA-TTAAA
1 TTTACATGG-AAAAAATAATTTAAA
46562457 TTTACATGGAAAAAATAATTTAAA
1 TTTACATGGAAAAAATAATTTAAA
* * *
46562481 -TGAAAT--AAGAAAA-AA-ATAAA
1 TTTACATGGAA-AAAATAATTTAAA
46562501 TTTACATGGAAAAAATAATTTAAA
1 TTTACATGGAAAAAATAATTTAAA
* * *
46562525 -TGAAAT--AAGAAAA-AA-ATAAA
1 TTTACATGGAA-AAAATAATTTAAA
46562545 TTTACATGGAAAAAATAATTTAAA
1 TTTACATGGAAAAAATAATTTAAA
46562569 T
1 T
46562570 GAAATAAGAA
Statistics
Matches: 88, Mismatches: 12, Indels: 26
0.70 0.10 0.21
Matches are distributed among these distances:
20 8 0.09
21 16 0.18
22 16 0.18
23 25 0.28
24 23 0.26
ACGTcount: A:0.61, C:0.03, G:0.09, T:0.28
Consensus pattern (24 bp):
TTTACATGGAAAAAATAATTTAAA
Found at i:46562478 original size:18 final size:18
Alignment explanation
Indices: 46562455--46562566 Score: 62
Period size: 18 Copynumber: 5.3 Consensus size: 18
46562445 AAAATAATTA
46562455 AATTTACATGGAAAAAAT
1 AATTTACATGGAAAAAAT
*
46562473 AATTTAAATGAAATAAGAAAAAAAT
1 AATTTACATG------GA-AAAAAT
46562498 AAATTTACATGGAAAAAAT
1 -AATTTACATGGAAAAAAT
*
46562517 AATTTAAATGAAATAAGAAAAAAAT
1 AATTTACATG------G-AAAAAAT
46562542 AAATTTACATGGAAAAAAT
1 -AATTTACATGGAAAAAAT
46562561 AATTTA
1 AATTTA
46562567 AATGAAATAA
Statistics
Matches: 74, Mismatches: 4, Indels: 32
0.67 0.04 0.29
Matches are distributed among these distances:
18 24 0.32
19 13 0.18
20 3 0.04
24 3 0.04
25 13 0.18
26 18 0.24
ACGTcount: A:0.62, C:0.03, G:0.09, T:0.27
Consensus pattern (18 bp):
AATTTACATGGAAAAAAT
Found at i:46562507 original size:44 final size:44
Alignment explanation
Indices: 46562444--46562592 Score: 271
Period size: 44 Copynumber: 3.3 Consensus size: 44
46562434 TTACATGGAA
46562444 AAAAATAATTAAATTTACATGGAAAAAATAATTTAAATGAAATAAG
1 AAAAA-AA-TAAATTTACATGGAAAAAATAATTTAAATGAAATAAG
46562490 AAAAAAATAAATTTACATGGAAAAAATAATTTAAATGAAATAAG
1 AAAAAAATAAATTTACATGGAAAAAATAATTTAAATGAAATAAG
46562534 AAAAAAATAAATTTACATGGAAAAAATAATTTAAATGAAATAAG
1 AAAAAAATAAATTTACATGGAAAAAATAATTTAAATGAAATAAG
*
46562578 AAAAAATTAAATTTA
1 AAAAAAATAAATTTA
46562593 AATGAAATGA
Statistics
Matches: 102, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
44 95 0.93
45 2 0.02
46 5 0.05
ACGTcount: A:0.63, C:0.02, G:0.08, T:0.27
Consensus pattern (44 bp):
AAAAAAATAAATTTACATGGAAAAAATAATTTAAATGAAATAAG
Found at i:46562589 original size:20 final size:20
Alignment explanation
Indices: 46562476--46562589 Score: 70
Period size: 21 Copynumber: 5.3 Consensus size: 20
46562466 AAAAAATAAT
46562476 TTAAATGAAATAAGAAAAAA
1 TTAAATGAAATAAGAAAAAA
* * *
46562496 ATAAATTTACATGGAA-AAAATAA
1 TTAAA-TGAAAT--AAGAAAA-AA
46562519 TTTAAATGAAATAAGAAAAAA
1 -TTAAATGAAATAAGAAAAAA
* * *
46562540 ATAAATTTACATGGAA-AAAATAA
1 TTAAA-TGAAAT--AAGAAAA-AA
46562563 TTTAAATGAAATAAGAAAAAA
1 -TTAAATGAAATAAGAAAAAA
46562584 TTAAAT
1 TTAAAT
46562590 TTAAATGAAA
Statistics
Matches: 70, Mismatches: 12, Indels: 24
0.66 0.11 0.23
Matches are distributed among these distances:
20 14 0.20
21 16 0.23
22 16 0.23
23 16 0.23
24 8 0.11
ACGTcount: A:0.64, C:0.02, G:0.09, T:0.25
Consensus pattern (20 bp):
TTAAATGAAATAAGAAAAAA
Found at i:46562590 original size:26 final size:26
Alignment explanation
Indices: 46562553--46562697 Score: 133
Period size: 26 Copynumber: 5.7 Consensus size: 26
46562543 AATTTACATG
46562553 GAAAAAAT-AATTTAAATGAAAT-AA
1 GAAAAAATAAATTTAAATGAAATGAA
46562577 GAAAAAATTAAATTTAAATGAAATGACA
1 GAAAAAA-TAAATTTAAATGAAATGA-A
* * *
46562605 AAAAAAATTAAATTAAAATG---GGAA
1 GAAAAAA-TAAATTTAAATGAAATGAA
46562629 G-AAAAAT-AATTTAAATGAAATGAGAA
1 GAAAAAATAAATTTAAATGAAAT--GAA
* * *
46562655 AAAAAAATAAACTTAAATGAAATAAA
1 GAAAAAATAAATTTAAATGAAATGAA
*
46562681 GAAAAAATAAAGTTAAA
1 GAAAAAATAAATTTAAA
46562698 ACGGAAAGAA
Statistics
Matches: 99, Mismatches: 11, Indels: 20
0.76 0.08 0.15
Matches are distributed among these distances:
21 9 0.09
22 1 0.01
23 5 0.05
24 8 0.08
25 3 0.03
26 34 0.34
27 7 0.07
28 32 0.32
ACGTcount: A:0.66, C:0.01, G:0.10, T:0.22
Consensus pattern (26 bp):
GAAAAAATAAATTTAAATGAAATGAA
Found at i:46562704 original size:28 final size:26
Alignment explanation
Indices: 46562651--46562710 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
46562641 AAATGAAATG
*
46562651 AGAAA-AAAAAATAAACTTAAATGAA
1 AGAAAGAAAAAATAAACTTAAAGGAA
* *
46562676 ATAAAGAAAAAATAAAGTTAAAACGGAA
1 AGAAAGAAAAAATAAACTT-AAA-GGAA
46562704 AGAAAGA
1 AGAAAGA
46562711 TAACTTGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
25 4 0.14
26 12 0.43
27 3 0.11
28 9 0.32
ACGTcount: A:0.70, C:0.03, G:0.13, T:0.13
Consensus pattern (26 bp):
AGAAAGAAAAAATAAACTTAAAGGAA
Found at i:46562783 original size:21 final size:20
Alignment explanation
Indices: 46562731--46562786 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
46562721 CTAGTTATGA
*
46562731 TTAATATGAAAAAATAAAATT
1 TTAA-ATGAAAAAATAAAAAT
* *
46562752 TGTATAGGAAAAAATAATAAAT
1 T-TAAATGAAAAAATAA-AAAT
46562774 TTAAATGAAAAAA
1 TTAAATGAAAAAA
46562787 ATTAATGAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
21 22 0.79
22 6 0.21
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.29
Consensus pattern (20 bp):
TTAAATGAAAAAATAAAAAT
Found at i:46562802 original size:23 final size:22
Alignment explanation
Indices: 46562760--46562802 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
46562750 TTTGTATAGG
*
46562760 AAAAAATAATAAATTTAAATGA
1 AAAAAATAATAAATTGAAATGA
46562782 AAAAAATTAATGAAA-TGAAAT
1 AAAAAA-TAAT-AAATTGAAAT
46562803 ATGAATATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 6 0.33
23 9 0.50
24 3 0.17
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (22 bp):
AAAAAATAATAAATTGAAATGA
Found at i:46563241 original size:25 final size:26
Alignment explanation
Indices: 46563195--46563244 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
46563185 ATGAGAAATT
* *
46563195 TTTTTTAATTTAAGTGAAATTTAAAA
1 TTTTGTAATGTAAGTGAAATTTAAAA
*
46563221 TTTTGTAATGTAA-TGATATTTAAA
1 TTTTGTAATGTAAGTGAAATTTAAA
46563245 TTGAAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (26 bp):
TTTTGTAATGTAAGTGAAATTTAAAA
Found at i:46563355 original size:14 final size:14
Alignment explanation
Indices: 46563326--46563357 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
46563316 GAAAAAATAT
46563326 AAAATGAATTGAAA
1 AAAATGAATTGAAA
46563340 AAAATTGAATTGAAA
1 AAAA-TGAATTGAAA
46563355 AAA
1 AAA
46563358 GATAACTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.66, C:0.00, G:0.12, T:0.22
Consensus pattern (14 bp):
AAAATGAATTGAAA
Found at i:46563519 original size:28 final size:28
Alignment explanation
Indices: 46563461--46563521 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
46563451 TAAATGAGAT
** *
46563461 ATGAATATCAAATGAAATGTAATTTGTA
1 ATGAATATCAAATGAAATAAAATTTGAA
*
46563489 ATGAATATGAAATGAAATAAAAGTTT-AA
1 ATGAATATCAAATGAAATAAAA-TTTGAA
46563517 ATGAA
1 ATGAA
46563522 AAAAATTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 25 0.89
29 3 0.11
ACGTcount: A:0.52, C:0.02, G:0.15, T:0.31
Consensus pattern (28 bp):
ATGAATATCAAATGAAATAAAATTTGAA
Found at i:46563600 original size:5 final size:5
Alignment explanation
Indices: 46563590--46563641 Score: 50
Period size: 5 Copynumber: 9.6 Consensus size: 5
46563580 AAATAAATTT
* *
46563590 AAATG AAATG AAATG TAAACG AAATG AAATGG AAATTA AAATGG AAATG
1 AAATG AAATG AAATG -AAATG AAATG AAAT-G AAA-TG AAAT-G AAATG
46563639 AAA
1 AAA
46563642 AAAAATAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
5 23 0.59
6 15 0.38
7 1 0.03
ACGTcount: A:0.60, C:0.02, G:0.19, T:0.19
Consensus pattern (5 bp):
AAATG
Found at i:46563608 original size:16 final size:16
Alignment explanation
Indices: 46563564--46563625 Score: 65
Period size: 16 Copynumber: 3.9 Consensus size: 16
46563554 GAAATGAAAA
*
46563564 AAATGAAATTATAAAT-
1 AAATGAAA-TGTAAATG
*
46563580 AAAT-AAATTTAAATG
1 AAATGAAATGTAAATG
*
46563595 AAATGAAATGTAAACG
1 AAATGAAATGTAAATG
*
46563611 AAATGAAATGGAAAT
1 AAATGAAATGTAAAT
46563626 TAAAATGGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
14 6 0.15
15 7 0.18
16 26 0.67
ACGTcount: A:0.60, C:0.02, G:0.13, T:0.26
Consensus pattern (16 bp):
AAATGAAATGTAAATG
Found at i:46563624 original size:11 final size:11
Alignment explanation
Indices: 46563590--46563641 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
46563580 AAATAAATTT
46563590 AAATGAAAT-G
1 AAATGAAATGG
*
46563600 AAATGTAAA-CG
1 AAATG-AAATGG
46563611 AAATGAAATGG
1 AAATGAAATGG
*
46563622 AAATTAAAATGG
1 AAA-TGAAATGG
46563634 AAATGAAA
1 AAATGAAA
46563642 AAAAATAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
10 8 0.23
11 17 0.49
12 10 0.29
ACGTcount: A:0.60, C:0.02, G:0.19, T:0.19
Consensus pattern (11 bp):
AAATGAAATGG
Found at i:46564859 original size:104 final size:104
Alignment explanation
Indices: 46564640--46564906 Score: 288
Period size: 104 Copynumber: 2.6 Consensus size: 104
46564630 ACACATATTT
* * * * *
46564640 ATGTCCTTACCTGTGTGGCTCACACGGCTTAGGCACACGCCTATG-TCGTCTGCCCGTGTGGTTC
1 ATGTCCTTACCTGTGTGGCTCACACGGCCTGGGCACACGCCCATGTTC--CTGGCCATGTGGTTC
* *
46564704 TAAATCATAAACAGTGAGTTATACGGCCCGAACACACGCCA
64 TAAATCATAAACAGTGAGTTACACAGCCCGAACACACGCCA
* * *
46564745 ATGTCCTTACCTGTGTGACTCACACGGCCTGGGCACACACCCATGTTCCTGGTCATGTGGTTCTA
1 ATGTCCTTACCTGTGTGGCTCACACGGCCTGGGCACACGCCCATGTTCCTGGCCATGTGGTTCTA
* * * * * *
46564810 TAGT-GTAAATAGTGAGTTACACAGCCTGGACACACGCCC
66 -AATCATAAACAGTGAGTTACACAGCCCGAACACACGCCA
* * * * *
46564849 ATGTCTTTACCCGTGTGGCTCACATGGCCTAGGG-ACACGCCCATGTCCCTGGCTATGT
1 ATGTCCTTACCTGTGTGGCTCACACGGCCT-GGGCACACGCCCATGTTCCTGGCCATGT
46564907 TGCTTCAACA
Statistics
Matches: 135, Mismatches: 24, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
104 88 0.65
105 45 0.33
106 2 0.01
ACGTcount: A:0.21, C:0.30, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGTCCTTACCTGTGTGGCTCACACGGCCTGGGCACACGCCCATGTTCCTGGCCATGTGGTTCTA
AATCATAAACAGTGAGTTACACAGCCCGAACACACGCCA
Found at i:46566407 original size:20 final size:20
Alignment explanation
Indices: 46566379--46566416 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
46566369 TAATTTTGAG
*
46566379 ACTTCTACTGACACAAGTCC
1 ACTTATACTGACACAAGTCC
*
46566399 ACTTATACTGATACAAGT
1 ACTTATACTGACACAAGT
46566417 ATATCTGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (20 bp):
ACTTATACTGACACAAGTCC
Found at i:46567221 original size:13 final size:14
Alignment explanation
Indices: 46567195--46567223 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
46567185 TAAGTTCATT
46567195 TATAAAATAATTAA
1 TATAAAATAATTAA
46567209 TATAAAA-AATTAA
1 TATAAAATAATTAA
46567222 TA
1 TA
46567224 AGATACAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
TATAAAATAATTAA
Found at i:46569395 original size:7 final size:7
Alignment explanation
Indices: 46569379--46569408 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
46569369 AGATTTTTCA
*
46569379 TTATTTT
1 TTATTAT
46569386 TTATTAT
1 TTATTAT
46569393 TTATTAT
1 TTATTAT
46569400 TTATTAT
1 TTATTAT
46569407 TT
1 TT
46569409 TATAAATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (7 bp):
TTATTAT
Found at i:46577974 original size:30 final size:30
Alignment explanation
Indices: 46577940--46577999 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
46577930 CCTTAATACG
46577940 AACTTTGGCAAAATTAC-CATTTTACCCCTA
1 AACTTTGGCAAAATTACAC-TTTTACCCCTA
* * *
46577970 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTACCCCTA
46578000 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.37
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTACCCCTA
Found at i:46579657 original size:18 final size:18
Alignment explanation
Indices: 46579634--46579670 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
46579624 GCTAGGGCAA
*
46579634 ATGGAGAAGGAAGAAGAG
1 ATGGAGAAAGAAGAAGAG
46579652 ATGGAGAAAGAAGAAGAG
1 ATGGAGAAAGAAGAAGAG
46579670 A
1 A
46579671 AGCAAAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.41, T:0.05
Consensus pattern (18 bp):
ATGGAGAAAGAAGAAGAG
Found at i:46586401 original size:25 final size:24
Alignment explanation
Indices: 46586373--46586429 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
46586363 TAATATAATA
*
46586373 ATATTATCTGATATT-TTATTAATTT
1 ATATTATCT-ATATTACTATT-ATTT
46586398 ATATTCATCTATATTACTATTATTT
1 ATATT-ATCTATATTACTATTATTT
*
46586423 AAATTAT
1 ATATTAT
46586430 TTAAAACTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 2 0.07
25 18 0.64
26 8 0.29
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.56
Consensus pattern (24 bp):
ATATTATCTATATTACTATTATTT
Found at i:46589414 original size:36 final size:36
Alignment explanation
Indices: 46589374--46589444 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
46589364 TTTAAGTTAA
*
46589374 TTAAATTATCTATCAAATATTCAAATATGTTAAATG
1 TTAAATTATCTATCAAATATTCAAATATGCTAAATG
* ***
46589410 TTAAATTATCTGTTGGATATTCAAATATGCTAAAT
1 TTAAATTATCTATCAAATATTCAAATATGCTAAAT
46589445 ATTTGTATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.42
Consensus pattern (36 bp):
TTAAATTATCTATCAAATATTCAAATATGCTAAATG
Found at i:46597688 original size:24 final size:23
Alignment explanation
Indices: 46597648--46597694 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
46597638 TTTTAATGTA
* *
46597648 TTAAGTATAATTCTTAAATATTT
1 TTAAGTATAAATATTAAATATTT
*
46597671 TTAAGTAATAAATATTAATTATTT
1 TTAAGT-ATAAATATTAAATATTT
46597695 ATAAAATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (23 bp):
TTAAGTATAAATATTAAATATTT
Found at i:46600726 original size:29 final size:28
Alignment explanation
Indices: 46600677--46600750 Score: 69
Period size: 29 Copynumber: 2.5 Consensus size: 28
46600667 ATTTAATTAA
* * *
46600677 ATAAA-TTTAATAATATTAAAATTTAAAT
1 ATAAATTTTAA-AATATAAAAAATAAAAT
*
46600705 TTAAATTTTAAAATATAAAAAAATAAAAT
1 ATAAATTTTAAAATAT-AAAAAATAAAAT
46600734 ATAAATTCTTTAAAATA
1 ATAAA-T-TTTAAAATA
46600751 AAATTGAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
28 9 0.24
29 18 0.49
30 1 0.03
31 9 0.24
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (28 bp):
ATAAATTTTAAAATATAAAAAATAAAAT
Done.