Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 15 of 203
Found at i:4928338 original size:26 final size:27
Alignment explanation
Indices: 4928268--4928339 Score: 92
Period size: 27 Copynumber: 2.7 Consensus size: 27
4928258 CTCAAACTGA
*
4928268 TATAAAATGATTGTTATGCCCCCACGT
1 TATAAAATGACTGTTATGCCCCCACGT
** * *
4928295 GGTAAAATGACTGTTATGCCCCTATGT
1 TATAAAATGACTGTTATGCCCCCACGT
4928322 TATAAAATGACTG-TATGC
1 TATAAAATGACTGTTATGC
4928340 TTTATGTTAT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
26 5 0.13
27 33 0.87
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (27 bp):
TATAAAATGACTGTTATGCCCCCACGT
Found at i:4931055 original size:50 final size:50
Alignment explanation
Indices: 4930945--4931056 Score: 118
Period size: 50 Copynumber: 2.2 Consensus size: 50
4930935 GGATACACCA
* * ** * * **
4930945 CAGCTCATATGAGCTTACCGATTTGTAGCTCGTGAAAGCTTACTGATTCT
1 CAGCTCGTATGAACTTACCGATTTACAGCTCATGAAAGCATACCAATTCT
* *
4930995 CAGCTAGTATGAACTTACCGATTTACAGCTCATGAGAGCATACCAATTCAT
1 CAGCTCGTATGAACTTACCGATTTACAGCTCATGAAAGCATACCAATTC-T
4931046 -AGCTCGTATGA
1 CAGCTCGTATGA
4931057 GCAAACAAGT
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
50 49 0.98
51 1 0.02
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (50 bp):
CAGCTCGTATGAACTTACCGATTTACAGCTCATGAAAGCATACCAATTCT
Found at i:4934249 original size:18 final size:19
Alignment explanation
Indices: 4934201--4934251 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 19
4934191 TCTGAATATT
4934201 TAAAGACATATTAATATAA
1 TAAAGACATATTAATATAA
* *
4934220 TAAACACA-ATTAA-ATTA
1 TAAAGACATATTAATATAA
*
4934237 TAAGGACATATTAAT
1 TAAAGACATATTAAT
4934252 GTCTAGTATC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 9 0.35
18 10 0.38
19 7 0.27
ACGTcount: A:0.55, C:0.08, G:0.06, T:0.31
Consensus pattern (19 bp):
TAAAGACATATTAATATAA
Found at i:4934698 original size:37 final size:40
Alignment explanation
Indices: 4934602--4934741 Score: 142
Period size: 40 Copynumber: 3.5 Consensus size: 40
4934592 AACACACCAG
**
4934602 TTTGGCACCCAGTGCCTCATCGGATAATTCAAAGTAATAA
1 TTTGGCACCCAGTGCCTCATCGGATAAACCAAAGTAATAA
* * * *
4934642 TTTGCCACCCAGTGTCTCATCGGCTAAACCGAAGT-A-AA
1 TTTGGCACCCAGTGCCTCATCGGATAAACCAAAGTAATAA
* * *
4934680 -TTGGCACCCAGTGCCTCATCGAATTAATCTAAAGTAATAA
1 TTTGGCACCCAGTGCCTCATCGGA-TAAACCAAAGTAATAA
* * *
4934720 ATTGACACCCAGTGTCTCATCG
1 TTTGGCACCCAGTGCCTCATCG
4934742 ACTCAAACTT
Statistics
Matches: 81, Mismatches: 15, Indels: 7
0.79 0.15 0.07
Matches are distributed among these distances:
37 19 0.23
38 10 0.12
39 2 0.02
40 31 0.38
41 19 0.23
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (40 bp):
TTTGGCACCCAGTGCCTCATCGGATAAACCAAAGTAATAA
Found at i:4934729 original size:41 final size:40
Alignment explanation
Indices: 4934607--4934742 Score: 127
Period size: 41 Copynumber: 3.5 Consensus size: 40
4934597 ACCAGTTTGG
* * *
4934607 CACCCAGTGCCTCATCGGATAAT-TCAAAGTAATAATTTGC
1 CACCCAGTGCCTCATCGAATAATCT-AAAGTAATAAATTGA
* ** * ** *
4934647 CACCCAGTGTCTCATCGGCTAAACCGAAG---TAAATTGG
1 CACCCAGTGCCTCATCGAATAATCTAAAGTAATAAATTGA
4934684 CACCCAGTGCCTCATCGAATTAATCTAAAGTAATAAATTGA
1 CACCCAGTGCCTCATCGAA-TAATCTAAAGTAATAAATTGA
*
4934725 CACCCAGTGTCTCATCGA
1 CACCCAGTGCCTCATCGA
4934743 CTCAAACTTG
Statistics
Matches: 76, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
37 22 0.29
38 7 0.09
40 23 0.30
41 24 0.32
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.25
Consensus pattern (40 bp):
CACCCAGTGCCTCATCGAATAATCTAAAGTAATAAATTGA
Found at i:4935792 original size:19 final size:20
Alignment explanation
Indices: 4935749--4935787 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
4935739 ATTAATAAGC
*
4935749 AATATATAT-TTTATTATTA
1 AATACATATGTTTATTATTA
4935768 AATACATATGTTTATTATTA
1 AATACATATGTTTATTATTA
4935788 TTACACATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (20 bp):
AATACATATGTTTATTATTA
Found at i:4947136 original size:22 final size:22
Alignment explanation
Indices: 4947112--4947288 Score: 153
Period size: 22 Copynumber: 8.0 Consensus size: 22
4947102 ATTGTATAGG
* *
4947112 ATTAGCATTATGGTGCCTACTG
1 ATTAGCACTATGGTGCCTACTA
* *
4947134 ATTTGCACTATAGTGCCTACTA
1 ATTAGCACTATGGTGCCTACTA
** *
4947156 ATTAGCACTACAGTGCGTACTA
1 ATTAGCACTATGGTGCCTACTA
* *
4947178 ATTTGCACTATAGTGCCTACTA
1 ATTAGCACTATGGTGCCTACTA
* * * *
4947200 CTCAGCACT-TCGGTACCTACTG
1 ATTAGCACTAT-GGTGCCTACTA
*
4947222 ATTTGCACTATGGTGCCTACTA
1 ATTAGCACTATGGTGCCTACTA
*
4947244 ATCAGCACT-TCGGTGCCTACTA
1 ATTAGCACTAT-GGTGCCTACTA
*
4947266 TTTAAGCACT-TCGGTGCCTACTA
1 ATT-AGCACTAT-GGTGCCTACTA
4947289 GTGTGGTGTA
Statistics
Matches: 126, Mismatches: 25, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
21 2 0.02
22 104 0.83
23 20 0.16
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (22 bp):
ATTAGCACTATGGTGCCTACTA
Found at i:4947182 original size:44 final size:44
Alignment explanation
Indices: 4947124--4947268 Score: 193
Period size: 44 Copynumber: 3.3 Consensus size: 44
4947114 TAGCATTATG
*
4947124 GTGCCTACTGATTTGCACTATAGTGCCTACTAATTAGCACTACA
1 GTGCCTACTGATTTGCACTATAGTGCCTACTAATCAGCACTACA
* * * * *
4947168 GTGCGTACTAATTTGCACTATAGTGCCTACTACTCAGCACTTCG
1 GTGCCTACTGATTTGCACTATAGTGCCTACTAATCAGCACTACA
* * * *
4947212 GTACCTACTGATTTGCACTATGGTGCCTACTAATCAGCACTTCG
1 GTGCCTACTGATTTGCACTATAGTGCCTACTAATCAGCACTACA
4947256 GTGCCTACT-ATTT
1 GTGCCTACTGATTT
4947269 AAGCACTTCG
Statistics
Matches: 89, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
43 4 0.04
44 85 0.96
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.33
Consensus pattern (44 bp):
GTGCCTACTGATTTGCACTATAGTGCCTACTAATCAGCACTACA
Found at i:4961923 original size:21 final size:21
Alignment explanation
Indices: 4961891--4961937 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 21
4961881 AGCAAAGTAG
4961891 ACACAGCCGTGTGGCTAAATC
1 ACACAGCCGTGTGGCTAAATC
4961912 ACAC-GCCTGTGTGGCTAAATC
1 ACACAGCC-GTGTGGCTAAATC
4961933 ACACA
1 ACACA
4961938 CCCATGTAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (21 bp):
ACACAGCCGTGTGGCTAAATC
Found at i:4964189 original size:30 final size:29
Alignment explanation
Indices: 4964155--4964266 Score: 116
Period size: 30 Copynumber: 3.8 Consensus size: 29
4964145 TCTAGCATCC
* *
4964155 CCATTCAGCTCCTTCAATTACATGCATGCT
1 CCATTCAGCTCCCT-AAATACATGCATGCT
* *
4964185 CCATTCAGCTCCCTAAATACATGCGTGCCC
1 CCATTCAGCTCCCTAAATACATGCATG-CT
*
4964215 CCATTCAACTCCCTAAATACATGCATGCTT
1 CCATTCAGCTCCCTAAATACATGCATGC-T
** * *
4964245 TAATTCAGCTCCATAAACACAT
1 CCATTCAGCTCCCTAAATACAT
4964267 TGGCCGAACC
Statistics
Matches: 68, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
29 12 0.18
30 56 0.82
ACGTcount: A:0.29, C:0.34, G:0.09, T:0.29
Consensus pattern (29 bp):
CCATTCAGCTCCCTAAATACATGCATGCT
Found at i:4964251 original size:60 final size:60
Alignment explanation
Indices: 4964153--4964266 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
4964143 AATCTAGCAT
* * * * * *
4964153 CCCCATTCAGCTCCTTCAATTACATGCATGCTCCATTCAGCTCCCTAAATACATGCGTGC
1 CCCCATTCAACTCCCTCAAATACATGCATGCTCAATTCAGCTCCATAAACACATGCGTGC
*
4964213 CCCCATTCAACTCCCT-AAATACATGCATGCTTTAATTCAGCTCCATAAACACAT
1 CCCCATTCAACTCCCTCAAATACATGCATGC-TCAATTCAGCTCCATAAACACAT
4964267 TGGCCGAACC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
59 13 0.28
60 33 0.72
ACGTcount: A:0.28, C:0.35, G:0.09, T:0.28
Consensus pattern (60 bp):
CCCCATTCAACTCCCTCAAATACATGCATGCTCAATTCAGCTCCATAAACACATGCGTGC
Found at i:4967045 original size:21 final size:21
Alignment explanation
Indices: 4967021--4967073 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
4967011 TGACAAAGGT
4967021 ACACGACCGTGTAAATGATA-C
1 ACACGACCGTGTAAATGA-AGC
* *
4967042 ACACGCCCGTGTAAGTGAAGC
1 ACACGACCGTGTAAATGAAGC
*
4967063 ACACGGCCGTG
1 ACACGACCGTG
4967074 CGACTGAGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.15
Consensus pattern (21 bp):
ACACGACCGTGTAAATGAAGC
Found at i:4967209 original size:21 final size:21
Alignment explanation
Indices: 4967185--4967224 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
4967175 GTAGACACGG
4967185 TCGTGTGGCT-AAATCACACAC
1 TCGTGTGGCTGAAAT-ACACAC
4967206 TCGTGTGGCTGAAATACAC
1 TCGTGTGGCTGAAATACAC
4967225 GGCCATGTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.25
Consensus pattern (21 bp):
TCGTGTGGCTGAAATACACAC
Found at i:4982582 original size:105 final size:100
Alignment explanation
Indices: 4982394--4982586 Score: 224
Period size: 105 Copynumber: 1.9 Consensus size: 100
4982384 AATTGGCGGA
* * * * * *
4982394 TAAGACCATGTTGGACCATGGTAGTGTTTAAATGTAATACCATAGCTAGGTTATGGCATTTTAAT
1 TAAGACCATGTTGGACCATGGCAGTATTTAAATGTAAGACCATAGCTAGGATATGACATTATAAT
4982459 GAAAAGACCATAACTGGGTTATGAGACCTTGAACG
66 GAAAAGACCATAACTGGGTTATGAGACCTTGAACG
* * *
4982494 TAAGACCATGGTTGGACCATGGCAGTATATATACATGTGTAAGACCATAGTTGGGATATGACATT
1 TAAGACCAT-GTTGGACCATGGCAGTAT-T-TA-A-ATGTAAGACCATAGCTAGGATATGACATT
* * * *
4982559 ATGATGATAAGATCATAATTGGGTTATG
61 ATAATGAAAAGACCATAACTGGGTTATG
4982587 GCACTACAAA
Statistics
Matches: 75, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
100 9 0.12
101 16 0.21
102 1 0.01
103 2 0.03
104 1 0.01
105 46 0.61
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (100 bp):
TAAGACCATGTTGGACCATGGCAGTATTTAAATGTAAGACCATAGCTAGGATATGACATTATAAT
GAAAAGACCATAACTGGGTTATGAGACCTTGAACG
Found at i:4984027 original size:24 final size:25
Alignment explanation
Indices: 4983990--4984036 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
4983980 ACTGGTCATA
4983990 GAGAGAATTAAGGAGAG-ATATTTG
1 GAGAGAATTAAGGAGAGAATATTTG
* *
4984014 GAGAGATTTGAGGAGAGAATATT
1 GAGAGAATTAAGGAGAGAATATT
4984037 GGGATTTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.34, T:0.26
Consensus pattern (25 bp):
GAGAGAATTAAGGAGAGAATATTTG
Found at i:4984723 original size:38 final size:38
Alignment explanation
Indices: 4984672--4984750 Score: 131
Period size: 38 Copynumber: 2.1 Consensus size: 38
4984662 TTCGAGAGGT
* *
4984672 CGATAAATGATCGAATTACCCTCATAGGATAAAATGAC
1 CGATAAATGATCGAATTACCCTCATAGGAAAAAAGGAC
*
4984710 CGATAAATGATCGAATTCCCCTCATAGGAAAAAAGGAC
1 CGATAAATGATCGAATTACCCTCATAGGAAAAAAGGAC
4984748 CGA
1 CGA
4984751 ATTCCCCCCC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (38 bp):
CGATAAATGATCGAATTACCCTCATAGGAAAAAAGGAC
Found at i:4984804 original size:26 final size:25
Alignment explanation
Indices: 4984775--4984878 Score: 84
Period size: 26 Copynumber: 4.0 Consensus size: 25
4984765 CCACAGGGTA
*
4984775 AAATGATCGAATTACCCCCACAATGG
1 AAATGATCAAATTACCCCCACAA-GG
* *
4984801 AAATTA-CTAAATTACCCTCACAAGG
1 AAATGATC-AAATTACCCCCACAAGG
* * *
4984826 TAAAATGACCAAATTACCCTCACAGGGG
1 --AAATGATCAAATTACCCCCACA-AGG
* *
4984854 AAATTATTAAATTACCCCCACAAGG
1 AAATGATCAAATTACCCCCACAAGG
4984879 TAAAATGACT
Statistics
Matches: 63, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
25 5 0.08
26 36 0.57
27 19 0.30
28 3 0.05
ACGTcount: A:0.41, C:0.25, G:0.12, T:0.21
Consensus pattern (25 bp):
AAATGATCAAATTACCCCCACAAGG
Found at i:4984839 original size:27 final size:27
Alignment explanation
Indices: 4984762--4985102 Score: 264
Period size: 27 Copynumber: 12.7 Consensus size: 27
4984752 TTCCCCCCCC
* *
4984762 CCCCCACAGGGTAAAATGATCGAATTA
1 CCCCCACAGGGTAAAATGACCAAATTA
* * *
4984789 CCCCCACAATGG--AAATTACTAAATTA
1 CCCCCAC-AGGGTAAAATGACCAAATTA
* *
4984815 CCCTCACAAGGTAAAATGACCAAATTA
1 CCCCCACAGGGTAAAATGACCAAATTA
* * * **
4984842 CCCTCACAGGG-GAAATTATTAAATTA
1 CCCCCACAGGGTAAAATGACCAAATTA
* **
4984868 CCCCCACAAGGTAAAATGACTGAATTA
1 CCCCCACAGGGTAAAATGACCAAATTA
** * *
4984895 CCTTCATAGGGTAAAATGACCGAATTA
1 CCCCCACAGGGTAAAATGACCAAATTA
* *
4984922 CCCCCACAGGGTAAAAT-AACTAATTA
1 CCCCCACAGGGTAAAATGACCAAATTA
* * *
4984948 CCCCTACATGGTAAAATAACCGAAA-TA
1 CCCCCACAGGGTAAAATGACC-AAATTA
* * *
4984975 CCCCCATAGGGTAAAATGACTAAAATA
1 CCCCCACAGGGTAAAATGACCAAATTA
* * *
4985002 CCCCCATAGGGTAAAATGATCAAAATA
1 CCCCCACAGGGTAAAATGACCAAATTA
* * * *
4985029 CCCTCATAGGGTAACATGACTGAAA-TA
1 CCCCCACAGGGTAAAATGAC-CAAATTA
* *
4985056 CCCCTATAGGGTAAAATGACCGAAA-TA
1 CCCCCACAGGGTAAAATGACC-AAATTA
*
4985083 CCCCCATAGGGTAAAATGAC
1 CCCCCACAGGGTAAAATGAC
4985103 TGTTATGGCC
Statistics
Matches: 255, Mismatches: 50, Indels: 18
0.79 0.15 0.06
Matches are distributed among these distances:
25 3 0.01
26 61 0.24
27 183 0.72
28 8 0.03
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.20
Consensus pattern (27 bp):
CCCCCACAGGGTAAAATGACCAAATTA
Found at i:4984856 original size:53 final size:53
Alignment explanation
Indices: 4984762--4984938 Score: 201
Period size: 53 Copynumber: 3.3 Consensus size: 53
4984752 TTCCCCCCCC
* * * **
4984762 CCCCCACAGGGTAAAATGATCGAATTACCCCCACAATGGAAATTACTAAATTA
1 CCCCCACAAGGTAAAATGACCGAATTACCCTCACAGGGGAAATTACTAAATTA
* * *
4984815 CCCTCACAAGGTAAAATGACCAAATTACCCTCACAGGGGAAATTATTAAATTA
1 CCCCCACAAGGTAAAATGACCGAATTACCCTCACAGGGGAAATTACTAAATTA
* * * * * **
4984868 CCCCCACAAGGTAAAATGACTGAATTACCTTCATAGGGTAAAATGACCGAATTA
1 CCCCCACAAGGTAAAATGACCGAATTACCCTCACAGGG-GAAATTACTAAATTA
*
4984922 CCCCCACAGGGTAAAAT
1 CCCCCACAAGGTAAAAT
4984939 AACTAATTAC
Statistics
Matches: 104, Mismatches: 19, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
53 78 0.75
54 26 0.25
ACGTcount: A:0.40, C:0.25, G:0.15, T:0.21
Consensus pattern (53 bp):
CCCCCACAAGGTAAAATGACCGAATTACCCTCACAGGGGAAATTACTAAATTA
Found at i:4984908 original size:80 final size:81
Alignment explanation
Indices: 4984762--4985099 Score: 328
Period size: 80 Copynumber: 4.2 Consensus size: 81
4984752 TTCCCCCCCC
* ** * * * *
4984762 CCCCCACAGGGTAAAATGATCGAATTACCCCCACAATGG--AAATTACT-AAATTACCCTCACAA
1 CCCCCACAGGGTAAAATAATTAAATTACCCCCACAA-GGTAAAATGACTGAAA-TACCCCCATAG
4984824 GGTAAAATGACCAAATTA
64 GGTAAAATGACCAAATTA
* * * * **
4984842 CCCTCACAGGG-GAAATTATTAAATTACCCCCACAAGGTAAAATGACTGAATTACCTTCATAGGG
1 CCCCCACAGGGTAAAATAATTAAATTACCCCCACAAGGTAAAATGACTGAAATACCCCCATAGGG
*
4984906 TAAAATGACCGAATTA
66 TAAAATGACCAAATTA
* * * * *
4984922 CCCCCACAGGGTAAAATAACT-AATTACCCCTACATGGTAAAATAACCGAAATACCCCCATAGGG
1 CCCCCACAGGGTAAAATAATTAAATTACCCCCACAAGGTAAAATGACTGAAATACCCCCATAGGG
* *
4984986 TAAAATGACTAAAATA
66 TAAAATGACCAAATTA
* * * * * * * * *
4985002 CCCCCATAGGGTAAAATGATCAAAATACCCTCATAGGGTAACATGACTGAAATACCCCTATAGGG
1 CCCCCACAGGGTAAAATAATTAAATTACCCCCACAAGGTAAAATGACTGAAATACCCCCATAGGG
4985067 TAAAATGACCGAAA-TA
66 TAAAATGACC-AAATTA
*
4985083 CCCCCATAGGGTAAAAT
1 CCCCCACAGGGTAAAAT
4985100 GACTGTTATG
Statistics
Matches: 213, Mismatches: 39, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
78 2 0.01
79 20 0.09
80 118 0.55
81 70 0.33
82 3 0.01
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.20
Consensus pattern (81 bp):
CCCCCACAGGGTAAAATAATTAAATTACCCCCACAAGGTAAAATGACTGAAATACCCCCATAGGG
TAAAATGACCAAATTA
Found at i:4985104 original size:54 final size:54
Alignment explanation
Indices: 4984866--4985104 Score: 302
Period size: 54 Copynumber: 4.4 Consensus size: 54
4984856 ATTATTAAAT
* * * * *
4984866 TACCCCCACAAGGTAAAATGACTGAATTA-CCTTCATAGGGTAAAATGACCGAAT
1 TACCCCCATAGGGTAAAATGACTGAAATACCCCT-ATAGGGTAAAATGACCGAAA
* * * * * *
4984920 TACCCCCACAGGGTAAAATAACT-AATTACCCCTACATGGTAAAATAACCGAAA
1 TACCCCCATAGGGTAAAATGACTGAAATACCCCTATAGGGTAAAATGACCGAAA
* * * *
4984973 TACCCCCATAGGGTAAAATGACTAAAATACCCCCATAGGGTAAAATGATCAAAA
1 TACCCCCATAGGGTAAAATGACTGAAATACCCCTATAGGGTAAAATGACCGAAA
* *
4985027 TACCCTCATAGGGTAACATGACTGAAATACCCCTATAGGGTAAAATGACCGAAA
1 TACCCCCATAGGGTAAAATGACTGAAATACCCCTATAGGGTAAAATGACCGAAA
4985081 TACCCCCATAGGGTAAAATGACTG
1 TACCCCCATAGGGTAAAATGACTG
4985105 TTATGGCCTT
Statistics
Matches: 159, Mismatches: 24, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
53 42 0.26
54 117 0.74
ACGTcount: A:0.41, C:0.23, G:0.16, T:0.20
Consensus pattern (54 bp):
TACCCCCATAGGGTAAAATGACTGAAATACCCCTATAGGGTAAAATGACCGAAA
Found at i:4985345 original size:26 final size:26
Alignment explanation
Indices: 4985297--4985383 Score: 104
Period size: 26 Copynumber: 3.3 Consensus size: 26
4985287 CCTACTGGTG
*
4985297 GCTTTGCCACATATACTATTACTGGCA
1 GCTTTGCTACA-ATACTATTACTGGCA
4985324 GCTTTGCTACAATACTGA-TACTGGCA
1 GCTTTGCTACAATACT-ATTACTGGCA
* * * *
4985350 GCTCTGCTGCAATGCTATTACTGACA
1 GCTTTGCTACAATACTATTACTGGCA
4985376 GCTTTGCT
1 GCTTTGCT
4985384 GCGATATTGG
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
25 1 0.02
26 40 0.77
27 11 0.21
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.33
Consensus pattern (26 bp):
GCTTTGCTACAATACTATTACTGGCA
Found at i:4986884 original size:40 final size:40
Alignment explanation
Indices: 4986847--4987071 Score: 260
Period size: 40 Copynumber: 5.7 Consensus size: 40
4986837 GCTACTCGTT
* *
4986847 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
4986887 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
4986927 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * * *
4986967 CCACTGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
4987006 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
4987047 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
4987072 CATCATTCGA
Statistics
Matches: 161, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
38 2 0.01
39 30 0.19
40 116 0.72
41 13 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:4987031 original size:119 final size:120
Alignment explanation
Indices: 4986851--4987071 Score: 297
Period size: 119 Copynumber: 1.9 Consensus size: 120
4986841 CTCGTTCAAA
* *
4986851 TGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTT
1 TGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATAT
*
4986916 AGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACCAC
66 AGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAATAACTCGCACCAC
* * **
4986971 TGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGAT
1 TGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGAT
* * *
4987033 ATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
4987072 CATCATTCGA
Statistics
Matches: 88, Mismatches: 10, Indels: 7
0.84 0.10 0.07
Matches are distributed among these distances:
118 4 0.05
119 66 0.75
120 18 0.20
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.25
Consensus pattern (120 bp):
TGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATAT
AGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACCAC
Found at i:4989806 original size:64 final size:64
Alignment explanation
Indices: 4989705--4989834 Score: 215
Period size: 64 Copynumber: 2.0 Consensus size: 64
4989695 CGTGACTCGA
* * *
4989705 TCCCATTTCCATTCAGGTACCATGATCGGCTGAAGTAATCCTGAAGGCACTTGATGTTCTGCTT
1 TCCCATTTCCACTCAGGTACCATGATCGGCTGAAGTAACCCTGAAGGCACTTGATGTTCCGCTT
* *
4989769 TCCCATTTCCACTCGGGTATCATGATCGGCTGAAGTAACCCTGAAGGCACTTGATGTTCCGCTT
1 TCCCATTTCCACTCAGGTACCATGATCGGCTGAAGTAACCCTGAAGGCACTTGATGTTCCGCTT
4989833 TC
1 TC
4989835 ACTTGTTGAC
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.32
Consensus pattern (64 bp):
TCCCATTTCCACTCAGGTACCATGATCGGCTGAAGTAACCCTGAAGGCACTTGATGTTCCGCTT
Found at i:4998027 original size:47 final size:47
Alignment explanation
Indices: 4997026--4998007 Score: 1779
Period size: 47 Copynumber: 20.9 Consensus size: 47
4997016 GTACAAGTAT
* * * **
4997026 ATATATGTGATAGGGCCGAGTGGCCAATGTGATGAATGTGAA-AGTAT
1 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TGC
* *
4997073 ATATATGCGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGT
1 ATATAT--GAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
* * *
4997122 GTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
1 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
4997169 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
1 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
4997216 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
1 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
4997263 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
1 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
4997310 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
1 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
4997357 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
1 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
4997404 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
1 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
4997451 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
1 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
4997498 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
1 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
4997545 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
1 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
4997592 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
1 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
4997639 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
1 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
4997686 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
1 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
4997733 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
1 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
4997780 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
1 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
4997827 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
1 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
4997874 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
1 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
* *
4997921 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGAGAA-AGTGT
1 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TGC
* * *
4997968 ATATATGTGATAATGCCGAATGGCCAATGTGATGGATGTG
1 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTG
4998008 GAAGTGTATA
Statistics
Matches: 916, Mismatches: 15, Indels: 8
0.98 0.02 0.01
Matches are distributed among these distances:
46 1 0.00
47 874 0.95
49 40 0.04
50 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.28, T:0.24
Consensus pattern (47 bp):
ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGC
Found at i:5000438 original size:56 final size:56
Alignment explanation
Indices: 5000352--5000527 Score: 334
Period size: 56 Copynumber: 3.1 Consensus size: 56
5000342 TATTAGTTTA
*
5000352 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTGATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTGATGACATGTT
5000408 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTGATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTGATGACATGTT
*
5000464 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTGATGACATGTT
5000520 TTGCCCAT
1 TTGCCCAT
5000528 CATCCCTTGT
Statistics
Matches: 118, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 118 1.00
ACGTcount: A:0.23, C:0.22, G:0.10, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTGATGACATGTT
Found at i:5000889 original size:28 final size:28
Alignment explanation
Indices: 5000848--5000936 Score: 142
Period size: 28 Copynumber: 3.2 Consensus size: 28
5000838 ATTGCACTAG
* *
5000848 ACTGTTTCTATATTGGGCTAAGGCCCAC
1 ACTGTTACTGTATTGGGCTAAGGCCCAC
*
5000876 ACTGTTACTGTATTGGGCTAAGGCTCAC
1 ACTGTTACTGTATTGGGCTAAGGCCCAC
*
5000904 ACTATTACTGTATTGGGCTAAGGCCCAC
1 ACTGTTACTGTATTGGGCTAAGGCCCAC
5000932 ACTGT
1 ACTGT
5000937 ACTACTACTA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 55 1.00
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.31
Consensus pattern (28 bp):
ACTGTTACTGTATTGGGCTAAGGCCCAC
Found at i:5004066 original size:16 final size:16
Alignment explanation
Indices: 5004047--5004082 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
5004037 ACGTTTTGAA
5004047 GGTTCTTTATTTTTCT
1 GGTTCTTTATTTTTCT
5004063 GGTTCTTTATTTTTCT
1 GGTTCTTTATTTTTCT
5004079 GGTT
1 GGTT
5004083 TCAGGGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.06, C:0.11, G:0.17, T:0.67
Consensus pattern (16 bp):
GGTTCTTTATTTTTCT
Found at i:5010023 original size:55 final size:54
Alignment explanation
Indices: 5009964--5010129 Score: 192
Period size: 55 Copynumber: 3.0 Consensus size: 54
5009954 TAATACACTG
5009964 AGAAATCTTCATACAACCCAACCAAGCCTCTGCAAAGTCATAATTTAACATATAT
1 AGAAATCTTC-TACAACCCAACCAAGCCTCTGCAAAGTCATAATTTAACATATAT
* * * *
5010019 AGAAAT-TTCTGA-ACAGCCTACCTAAGCCTCTGTAAAGCCATAATTTAACATATAT
1 AGAAATCTTCT-ACA-ACCCAACC-AAGCCTCTGCAAAGTCATAATTTAACATATAT
* * * * *
5010074 AGAAATCTCTGTACAACCGACCCAAGCCTCTACAAAGTCATAGTTTAACATATAT
1 AGAAATCT-TCTACAACCCAACCAAGCCTCTGCAAAGTCATAATTTAACATATAT
5010129 A
1 A
5010130 AGAATATCCG
Statistics
Matches: 92, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
53 2 0.02
54 10 0.11
55 71 0.77
56 6 0.07
57 3 0.03
ACGTcount: A:0.40, C:0.24, G:0.10, T:0.27
Consensus pattern (54 bp):
AGAAATCTTCTACAACCCAACCAAGCCTCTGCAAAGTCATAATTTAACATATAT
Found at i:5010165 original size:55 final size:54
Alignment explanation
Indices: 5009987--5010180 Score: 189
Period size: 55 Copynumber: 3.6 Consensus size: 54
5009977 CAACCCAACC
* * * * *
5009987 AAGCCTCTGCAAAGTCATAATTTAACATATATAGAAATTTCTGAACAGCCTACCT
1 AAGCCTCTGCAAAGCCATAATTTAACATATATAG-AATATCCGTACAGCCGACCT
* * *
5010042 AAGCCTCTGTAAAGCCATAATTTAACATATATAGAA-ATCTCTGTACAACCGACCC
1 AAGCCTCTGCAAAGCCATAATTTAACATATATAGAATATC-C-GTACAGCCGACCT
* * *
5010097 AAGCCTCTACAAAGTCATAGTTTAACATATATAAGAATATCCGTACAGTCC-ACCT
1 AAGCCTCTGCAAAGCCATAATTTAACATATAT-AGAATATCCGTACAG-CCGACCT
* *
5010152 GAA-CCTCCGCAAAGCCA-CATTTAACATAT
1 -AAGCCTCTGCAAAGCCATAATTTAACATAT
5010181 GATGCTTTTA
Statistics
Matches: 114, Mismatches: 19, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
53 2 0.02
54 12 0.11
55 88 0.77
56 9 0.08
57 3 0.03
ACGTcount: A:0.38, C:0.25, G:0.11, T:0.26
Consensus pattern (54 bp):
AAGCCTCTGCAAAGCCATAATTTAACATATATAGAATATCCGTACAGCCGACCT
Found at i:5010166 original size:110 final size:109
Alignment explanation
Indices: 5009975--5010180 Score: 265
Period size: 110 Copynumber: 1.9 Consensus size: 109
5009965 GAAATCTTCA
* * *
5009975 TACAACCCAACCAAGCCTCTGCAAAGTCATAATTTAACATATATAGAAATTTCTGAACAGCCTAC
1 TACAACCCAACCAAGCCTCTACAAAGTCATAATTTAACATATATAGAAATATCCGAACAGCCTAC
* *
5010040 CTAAGCCTCTGTAAAGCCATAATTTAACATATATAGAAATCTCTG
66 CTAAGCCTCCGCAAAGCCA-AATTTAACATATATAGAAATCTCTG
* * * *
5010085 TACAACCGACCCAAGCCTCTACAAAGTCATAGTTTAACATATATA-AGAATATCCGTACAGTCC-
1 TACAACCCAACCAAGCCTCTACAAAGTCATAATTTAACATATATAGA-AATATCCGAACAG-CCT
*
5010148 ACCTGAA-CCTCCGCAAAGCCACATTTAACATAT
64 ACCT-AAGCCTCCGCAAAGCCAAATTTAACATAT
5010181 GATGCTTTTA
Statistics
Matches: 83, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
109 12 0.14
110 67 0.81
111 4 0.05
ACGTcount: A:0.38, C:0.26, G:0.10, T:0.25
Consensus pattern (109 bp):
TACAACCCAACCAAGCCTCTACAAAGTCATAATTTAACATATATAGAAATATCCGAACAGCCTAC
CTAAGCCTCCGCAAAGCCAAATTTAACATATATAGAAATCTCTG
Found at i:5012902 original size:14 final size:14
Alignment explanation
Indices: 5012883--5012909 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5012873 GTTATGAAAA
5012883 GAACTTATCCTGAC
1 GAACTTATCCTGAC
5012897 GAACTTATCCTGA
1 GAACTTATCCTGA
5012910 TGATTCCAAG
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:0.30, C:0.26, G:0.15, T:0.30
Consensus pattern (14 bp):
GAACTTATCCTGAC
Found at i:5013316 original size:28 final size:28
Alignment explanation
Indices: 5013244--5013326 Score: 103
Period size: 28 Copynumber: 3.0 Consensus size: 28
5013234 TGTGATTGAT
* *
5013244 TAAGTGTCTTCATTTATTATGTTGGAAA
1 TAAGTGTCTACATTTATTATGTTGAAAA
* ***
5013272 TAAGTTTCCGTATTTATTATGTTGAAAA
1 TAAGTGTCTACATTTATTATGTTGAAAA
*
5013300 TAAGTGTCTACACTTATTATGTTGAAA
1 TAAGTGTCTACATTTATTATGTTGAAA
5013327 TTGAATAGGA
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.31, C:0.08, G:0.16, T:0.45
Consensus pattern (28 bp):
TAAGTGTCTACATTTATTATGTTGAAAA
Found at i:5014276 original size:19 final size:19
Alignment explanation
Indices: 5014252--5014328 Score: 73
Period size: 19 Copynumber: 4.0 Consensus size: 19
5014242 AGTAGGGTAA
*
5014252 ACTGGCACATAAAGTGCAT
1 ACTGGCACACAAAGTGCAT
*
5014271 ACTGGCGCACAAAGTGCAT
1 ACTGGCACACAAAGTGCAT
* * * **
5014290 ATTGGCATAGAAAGTATAT
1 ACTGGCACACAAAGTGCAT
*
5014309 ATCTAGCACACAAAGTGCAT
1 A-CTGGCACACAAAGTGCAT
5014329 CTTGACATAT
Statistics
Matches: 43, Mismatches: 14, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
19 31 0.72
20 12 0.28
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (19 bp):
ACTGGCACACAAAGTGCAT
Found at i:5018570 original size:42 final size:42
Alignment explanation
Indices: 5018503--5018643 Score: 196
Period size: 43 Copynumber: 3.3 Consensus size: 42
5018493 TCTTTCACAT
*
5018503 AAACGCCACTAAAGAACATGACCTTTAGCAGCACTTTTATCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCAGCACTTTT-TCAC
*
5018546 AAACGCCGCTAAA-AACATGACCTTTAGCGGCACCTTTTTCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCAGCA-CTTTTTCAC
*
5018588 AAACGCCGCTAAAGAACATGACATTTAGCGAAGC-CTTTTTCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGC--AGCACTTTTTCAC
*
5018631 AAACACCGCTAAA
1 AAACGCCGCTAAA
5018644 AGTACCGTTC
Statistics
Matches: 89, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
42 35 0.39
43 52 0.58
45 2 0.02
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.22
Consensus pattern (42 bp):
AAACGCCGCTAAAGAACATGACCTTTAGCAGCACTTTTTCAC
Found at i:5020036 original size:26 final size:26
Alignment explanation
Indices: 5020000--5020049 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
5019990 TCTTGACAAA
*
5020000 ATTATCTGAGA-CATCTAAAGCAAATT
1 ATTATCCGAGAGC-TCTAAAGCAAATT
5020026 ATTATCCGAGAGCTCTAAAGCAAA
1 ATTATCCGAGAGCTCTAAAGCAAA
5020050 CCTCTACTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 21 0.95
27 1 0.05
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (26 bp):
ATTATCCGAGAGCTCTAAAGCAAATT
Found at i:5022676 original size:26 final size:26
Alignment explanation
Indices: 5022640--5022689 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
5022630 TCTTGACAAA
*
5022640 ATTATCTGAGA-CATCTAAAGCAAATT
1 ATTATCCGAGAGC-TCTAAAGCAAATT
5022666 ATTATCCGAGAGCTCTAAAGCAAA
1 ATTATCCGAGAGCTCTAAAGCAAA
5022690 CCTCTACTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 21 0.95
27 1 0.05
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (26 bp):
ATTATCCGAGAGCTCTAAAGCAAATT
Found at i:5026305 original size:69 final size:69
Alignment explanation
Indices: 5026223--5026362 Score: 226
Period size: 69 Copynumber: 2.0 Consensus size: 69
5026213 TTTGTTGGTT
*
5026223 TGTTCTGGAAATTGTTTTGATAGTCTGCTGGAAAATGTTATTAATTTGTTAGTGAGTAGAAGATG
1 TGTTCTGGAAATTGTTTTGATAGTCTGCTGGAAAATGTTATTAATTTGTTAGTCAGTAGAAGATG
5026288 AAAC
66 AAAC
* * * * *
5026292 TGTTCTGGAAATTGTTTTGATTGTCTGCTGGAAATTGTTCTTGATTTGTTAGTCAGTAGAATATG
1 TGTTCTGGAAATTGTTTTGATAGTCTGCTGGAAAATGTTATTAATTTGTTAGTCAGTAGAAGATG
5026357 AAAC
66 AAAC
5026361 TG
1 TG
5026363 GAACTTGATT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 65 1.00
ACGTcount: A:0.27, C:0.07, G:0.24, T:0.41
Consensus pattern (69 bp):
TGTTCTGGAAATTGTTTTGATAGTCTGCTGGAAAATGTTATTAATTTGTTAGTCAGTAGAAGATG
AAAC
Found at i:5026331 original size:35 final size:35
Alignment explanation
Indices: 5026222--5026332 Score: 93
Period size: 35 Copynumber: 3.2 Consensus size: 35
5026212 TTTTGTTGGT
5026222 TTGTTCTGGAAATTGTTTTGATAGTCTGCTGGAAA
1 TTGTTCTGGAAATTGTTTTGATAGTCTGCTGGAAA
* * * * * ** *
5026257 ATGTTAT-TAATTTGTTAGTGAGTAG-AAGAT-GAAA
1 TTGTTCTGGAAATTGTT-TTGA-TAGTCTGCTGGAAA
* *
5026291 CTGTTCTGGAAATTGTTTTGATTGTCTGCTGGAAA
1 TTGTTCTGGAAATTGTTTTGATAGTCTGCTGGAAA
5026326 TTGTTCT
1 TTGTTCT
5026333 TGATTTGTTA
Statistics
Matches: 53, Mismatches: 18, Indels: 10
0.65 0.22 0.12
Matches are distributed among these distances:
33 2 0.04
34 21 0.40
35 27 0.51
36 3 0.06
ACGTcount: A:0.25, C:0.07, G:0.24, T:0.43
Consensus pattern (35 bp):
TTGTTCTGGAAATTGTTTTGATAGTCTGCTGGAAA
Found at i:5027570 original size:37 final size:37
Alignment explanation
Indices: 5027527--5027615 Score: 151
Period size: 37 Copynumber: 2.4 Consensus size: 37
5027517 ATCATAAATA
*
5027527 AATAAACTAATCAATGTTCAAACTTTGAACATGCTTT
1 AATAAACTAATCAATGTTAAAACTTTGAACATGCTTT
*
5027564 ATTAAACTAATCAATGTTAAAACTTTGAACATGCTTT
1 AATAAACTAATCAATGTTAAAACTTTGAACATGCTTT
*
5027601 AATGAACTAATCAAT
1 AATAAACTAATCAAT
5027616 ATATTTATAC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.43, C:0.15, G:0.08, T:0.35
Consensus pattern (37 bp):
AATAAACTAATCAATGTTAAAACTTTGAACATGCTTT
Found at i:5027695 original size:33 final size:33
Alignment explanation
Indices: 5027658--5027733 Score: 143
Period size: 33 Copynumber: 2.3 Consensus size: 33
5027648 TTAAAACTTG
*
5027658 AATTATACATATACCAACAATTAATTTTAGGTC
1 AATTATACATACACCAACAATTAATTTTAGGTC
5027691 AATTATACATACACCAACAATTAATTTTAGGTC
1 AATTATACATACACCAACAATTAATTTTAGGTC
5027724 AATTATACAT
1 AATTATACAT
5027734 GCTTTATAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (33 bp):
AATTATACATACACCAACAATTAATTTTAGGTC
Found at i:5030883 original size:17 final size:17
Alignment explanation
Indices: 5030858--5030891 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5030848 ATTATTTTAA
*
5030858 ATTTTATTAAATCATAT
1 ATTTAATTAAATCATAT
5030875 ATTTAATTAAATCATAT
1 ATTTAATTAAATCATAT
5030892 TTAATATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAATTAAATCATAT
Found at i:5030893 original size:15 final size:16
Alignment explanation
Indices: 5030858--5030896 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
5030848 ATTATTTTAA
*
5030858 ATTTTATTAAATCATAT
1 ATTTAATTAAATCA-AT
5030875 ATTTAATTAAATC-AT
1 ATTTAATTAAATCAAT
5030890 ATTTAAT
1 ATTTAAT
5030897 ATTAATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.43
17 12 0.57
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTTAATTAAATCAAT
Found at i:5030900 original size:17 final size:18
Alignment explanation
Indices: 5030862--5030901 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
5030852 TTTTAAATTT
*
5030862 TATTAAATCATATATTTA
1 TATTAAATCATATATTAA
5030880 -ATTAAATCATAT-TTAA
1 TATTAAATCATATATTAA
5030896 TATTAA
1 TATTAA
5030902 TTATTTGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTAAATCATATATTAA
Found at i:5030980 original size:66 final size:63
Alignment explanation
Indices: 5030917--5031098 Score: 161
Period size: 56 Copynumber: 3.0 Consensus size: 63
5030907 TGAAATTTTC
5030917 TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTCTTAAGAATTT
1 TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATT-TTAAGAATTT
* * * * * * * ** * *
5030981 TATTA-A--ATTATATATTTTAATTAT-AATATATTTA-ATAATTATGTTAA-TTT----A-TA
1 TTTTATAGTATCATATATTATGATT-TGAGTAAATTCATATAAGAATATTAATTTTAAGAATTT
5031034 TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTT
1 TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATT-TTAAGAATTT
5031098 T
1 T
5031099 ATTAAATTAT
Statistics
Matches: 83, Mismatches: 22, Indels: 26
0.63 0.17 0.20
Matches are distributed among these distances:
53 5 0.06
54 2 0.02
55 1 0.01
56 20 0.24
57 10 0.12
58 3 0.04
59 3 0.04
60 10 0.12
61 20 0.24
62 1 0.01
63 2 0.02
64 6 0.07
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (63 bp):
TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTTTAAGAATTT
Found at i:5031047 original size:117 final size:116
Alignment explanation
Indices: 5030857--5031140 Score: 448
Period size: 117 Copynumber: 2.4 Consensus size: 116
5030847 AATTATTTTA
* *
5030857 AATTTTATTAAATCATATA-TTTAATTA-AATCATATTTAATATTAATTATTTGAAATTTTCTTT
1 AATTTTATTAAATTATATATTTTAATTATAAT-ATATTT-A-A-TAATTATTT-AAATTTTATTT
*
5030920 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTCTTAAG
61 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
5030976 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATTATGTT-AATTTATATTTTAT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATTAT-TTAAATTT-TATTTTAT
5031040 AGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
64 AGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
5031093 AATTTTATTAAATTATATATTTAAATTATAATATATTTAATAATTATT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATTATT
5031141 ATGTTTAAAT
Statistics
Matches: 157, Mismatches: 4, Indels: 11
0.91 0.02 0.06
Matches are distributed among these distances:
116 6 0.04
117 112 0.71
118 3 0.02
119 19 0.12
120 14 0.09
121 3 0.02
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (116 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATTATTTAAATTTTATTTTATAG
TATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:5031374 original size:45 final size:44
Alignment explanation
Indices: 5031293--5031383 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 44
5031283 ACATCTATTC
*
5031293 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTACTATTACACCTCTATTCCATTA
*** *
5031337 CATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCCATTA
1 CATTCAACCAAACACAAGA-TTACTATTACACCTCTATTCCATTA
5031382 CA
1 CA
5031384 CCTCTATTCC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 16 0.39
45 25 0.61
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTACACCTCTATTCCATTA
Found at i:5031383 original size:16 final size:16
Alignment explanation
Indices: 5031362--5031415 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
5031352 TTGATTTGCT
5031362 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
5031378 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
* *
5031394 ATTGCGCCTCTATTCC
1 ATTACACCTCTATTCC
*
5031410 AATACA
1 ATTACA
5031416 GCAAACCAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.26, C:0.35, G:0.04, T:0.35
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:5032332 original size:18 final size:18
Alignment explanation
Indices: 5032309--5032352 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
5032299 CCTCATTAAG
*
5032309 TCATCATCTTTATCAGAT
1 TCATCATCTTTATCAAAT
5032327 TCATCATCTTTATCAAAT
1 TCATCATCTTTATCAAAT
5032345 TCATCATC
1 TCATCATC
5032353 AGATTCATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.30, C:0.25, G:0.02, T:0.43
Consensus pattern (18 bp):
TCATCATCTTTATCAAAT
Found at i:5032358 original size:12 final size:12
Alignment explanation
Indices: 5032338--5032373 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
5032328 CATCATCTTT
*
5032338 ATCAAATTCATC
1 ATCAGATTCATC
5032350 ATCAGATTCATC
1 ATCAGATTCATC
5032362 ATCAGATTCATC
1 ATCAGATTCATC
5032374 CATTGATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
ATCAGATTCATC
Found at i:5034176 original size:21 final size:21
Alignment explanation
Indices: 5034150--5034190 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5034140 GTAAGTTACG
*
5034150 TAAGTTATGATATGATATATA
1 TAAGTTATGAAATGATATATA
*
5034171 TAAGTTATTAAATGATATAT
1 TAAGTTATGAAATGATATAT
5034191 GTTATATGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (21 bp):
TAAGTTATGAAATGATATATA
Found at i:5034199 original size:35 final size:35
Alignment explanation
Indices: 5034159--5034225 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
5034149 GTAAGTTATG
*
5034159 ATATGA-TATATATAAGTTATTAAATGATATATGTT
1 ATATGAGT-TATATAAGTTATGAAATGATATATGTT
* *
5034194 ATATGAGTTATGTAAGTTATGATATGATATAT
1 ATATGAGTTATATAAGTTATGAAATGATATAT
5034226 ATATAAGTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 27 0.96
36 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (35 bp):
ATATGAGTTATATAAGTTATGAAATGATATATGTT
Found at i:5034259 original size:58 final size:58
Alignment explanation
Indices: 5034082--5034304 Score: 299
Period size: 58 Copynumber: 3.8 Consensus size: 58
5034072 AGTATAAACA
* * *
5034082 AGTTATGTAAGTTATGATATGATATATATTTAGGTATTATGTAAGTTATGTGA-GTTATGTA
1 AGTTATGTAAGTTATGATATGATATATATATAAG--TTAT-TAAGTTATGT-ATGTTATGTG
* * * * *
5034143 AGTTACGTAAGTTATGATATG--ATATATATAAGTTATTAAATGATATATGTTATATG
1 AGTTATGTAAGTTATGATATGATATATATATAAGTTATTAAGTTATGTATGTTATGTG
* *
5034199 AGTTATGTAAGTTATGATATGATATATATATAAGTTATTATGTTATGTATGTTTTGTG
1 AGTTATGTAAGTTATGATATGATATATATATAAGTTATTAAGTTATGTATGTTATGTG
5034257 AGTTATGTAAGTTATGATATGATATATATATAAGTTATTAAGTTATGT
1 AGTTATGTAAGTTATGATATGATATATATATAAGTTATTAAGTTATGT
5034305 GAATTATGAT
Statistics
Matches: 143, Mismatches: 16, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
55 1 0.01
56 33 0.23
57 4 0.03
58 76 0.53
59 9 0.06
61 20 0.14
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.46
Consensus pattern (58 bp):
AGTTATGTAAGTTATGATATGATATATATATAAGTTATTAAGTTATGTATGTTATGTG
Found at i:5034331 original size:38 final size:38
Alignment explanation
Indices: 5034128--5034369 Score: 164
Period size: 38 Copynumber: 6.3 Consensus size: 38
5034118 TTATGTAAGT
* *
5034128 TATGTGAGTTATGTAAGTTACGTAAGTTATGATATGATA
1 TATGTAAGTTAT-TAAGTTATGTAAGTTATGATATGATA
* * * * *
5034167 TATATAAGTTATTAAATGATATATG-T-T-ATATGAGT-
1 TATGTAAGTTATTAAGTTATGTAAGTTATGATATGA-TA
* *
5034202 TATGTAAGTTATGATATGATATATATATAAGTTAT--TATG-T-
1 TATGTAAGTTAT--TA--A-GT-TATGTAAGTTATGATATGATA
* * *
5034242 TATGTATGTTTTGTGAGTTATGTAAGTTATGATATGATATA
1 TATGTAAGTTAT-TAAGTTATGTAAGTTATGATATG--ATA
*
5034283 TATATAAGTTATTAAGTTATGTGAA-TTATGATATGATA
1 TATGTAAGTTATTAAGTTATGT-AAGTTATGATATGATA
*
5034321 TATGTAAGTTATTAAGTTATGTAAGTTAT-ATGTGAGT-
1 TATGTAAGTTATTAAGTTATGTAAGTTATGATATGA-TA
5034358 TATGTAAGTTAT
1 TATGTAAGTTAT
5034370 GATATACATA
Statistics
Matches: 163, Mismatches: 22, Indels: 38
0.73 0.10 0.17
Matches are distributed among these distances:
35 28 0.17
36 3 0.02
37 27 0.17
38 37 0.23
39 12 0.07
40 33 0.20
41 17 0.10
42 5 0.03
43 1 0.01
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (38 bp):
TATGTAAGTTATTAAGTTATGTAAGTTATGATATGATA
Found at i:5034338 original size:8 final size:9
Alignment explanation
Indices: 5034118--5034466 Score: 125
Period size: 9 Copynumber: 36.2 Consensus size: 9
5034108 TATTTAGGTA
5034118 TTATGTAAG
1 TTATGTAAG
*
5034127 TTATGTGAG
1 TTATGTAAG
5034136 TTATGTAAG
1 TTATGTAAG
*
5034145 TTACGTAAG
1 TTATGTAAG
*
5034154 TTATGATATG
1 TTATG-TAAG
*
5034164 ATATATATAAG
1 -T-TATGTAAG
*
5034175 TTAT-TAAA
1 TTATGTAAG
* * *
5034183 TGATATATG
1 TTATGTAAG
* *
5034192 TTATATGAG
1 TTATGTAAG
5034201 TTATGTAAG
1 TTATGTAAG
*
5034210 TTATGATATGATA
1 TTATG-TA--A-G
*
5034223 TATATATAAG
1 T-TATGTAAG
*
5034233 TTAT-TATG
1 TTATGTAAG
*
5034241 TTATGTATG
1 TTATGTAAG
* *
5034250 TTTTGTGAG
1 TTATGTAAG
5034259 TTATGTAAG
1 TTATGTAAG
*
5034268 TTATGATATGATA
1 TTATG-TA--A-G
*
5034281 TATATATAAG
1 T-TATGTAAG
5034291 TTAT-TAAG
1 TTATGTAAG
5034299 TTATGTGAA-
1 TTATGT-AAG
*
5034308 TTATGATATG
1 TTATG-TAAG
5034318 ATATATGTAAG
1 -T-TATGTAAG
5034329 TTAT-TAAG
1 TTATGTAAG
5034337 TTATGTAAG
1 TTATGTAAG
*
5034346 TTATATGTGAG
1 -T-TATGTAAG
5034357 TTATGTAAG
1 TTATGTAAG
*
5034366 TTATGATATACA
1 TTATG-TA-A-G
*
5034378 TATATATAAG
1 T-TATGTAAG
5034388 TTAT-TAAG
1 TTATGTAAG
* *
5034396 TTAAAATCGAAAA
1 TT---AT-GTAAG
* *
5034409 TTCTTTAAAG
1 TTATGT-AAG
*
5034419 TTATGTAAA
1 TTATGTAAG
5034428 TTATGTAAG
1 TTATGTAAG
*
5034437 TTATGTAAA
1 TTATGTAAG
* *
5034446 TTCTTTAAAG
1 TTATGT-AAG
5034456 TTATGTAAG
1 TTATGTAAG
5034465 TT
1 TT
5034467 TTGATTTTTA
Statistics
Matches: 254, Mismatches: 51, Indels: 70
0.68 0.14 0.19
Matches are distributed among these distances:
8 35 0.14
9 135 0.53
10 32 0.13
11 21 0.08
12 12 0.05
13 13 0.05
14 6 0.02
ACGTcount: A:0.37, C:0.01, G:0.17, T:0.45
Consensus pattern (9 bp):
TTATGTAAG
Found at i:5034458 original size:19 final size:19
Alignment explanation
Indices: 5034406--5034463 Score: 91
Period size: 19 Copynumber: 3.1 Consensus size: 19
5034396 TTAAAATCGA
5034406 AAATTCTTTAAAGTTATGT
1 AAATTCTTTAAAGTTATGT
* *
5034425 AAATTATGT-AAGTTATGT
1 AAATTCTTTAAAGTTATGT
5034443 AAATTCTTTAAAGTTATGT
1 AAATTCTTTAAAGTTATGT
5034462 AA
1 AA
5034464 GTTTTGATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
18 16 0.47
19 18 0.53
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.45
Consensus pattern (19 bp):
AAATTCTTTAAAGTTATGT
Found at i:5035493 original size:24 final size:24
Alignment explanation
Indices: 5035450--5035501 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
5035440 AAACAAAACT
*
5035450 GAAATATTAGTTTTTTTTAGGGTAA
1 GAAATATTAGTTTTTATTA-GGTAA
5035475 GAAATATTAG-TTTTATTAGGTAA
1 GAAATATTAGTTTTTATTAGGTAA
5035498 -AAAT
1 GAAAT
5035502 GTTTAAACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 4 0.15
23 5 0.19
24 7 0.27
25 10 0.38
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.44
Consensus pattern (24 bp):
GAAATATTAGTTTTTATTAGGTAA
Found at i:5037238 original size:39 final size:41
Alignment explanation
Indices: 5037167--5037251 Score: 120
Period size: 40 Copynumber: 2.1 Consensus size: 41
5037157 TGTTTATGAT
* **
5037167 TTTTTGCAGCGTTTTTTTCAAAAATGTCACTA-TTGCTTAC
1 TTTTTGCAGCGTTTTTTTAAAAAAACTCACTATTTGCTTAC
*
5037207 TTTTTGCGGCGTTTTTTTAAAAAAACT-ACTATTTGCTTAC
1 TTTTTGCAGCGTTTTTTTAAAAAAACTCACTATTTGCTTAC
5037247 TTTTT
1 TTTTT
5037252 ACTACATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 4 0.10
40 36 0.90
ACGTcount: A:0.22, C:0.15, G:0.12, T:0.51
Consensus pattern (41 bp):
TTTTTGCAGCGTTTTTTTAAAAAAACTCACTATTTGCTTAC
Found at i:5038002 original size:7 final size:7
Alignment explanation
Indices: 5037964--5038107 Score: 75
Period size: 7 Copynumber: 21.0 Consensus size: 7
5037954 TGTTTAAAAT
5037964 CCTAAAC
1 CCTAAAC
*
5037971 ACTAAAC
1 CCTAAAC
** *
5037978 TATAAAT
1 CCTAAAC
*
5037985 CCTAAGCC
1 CCTAA-AC
5037993 CCTAAAC
1 CCTAAAC
5038000 CCTAAAC
1 CCTAAAC
**
5038007 TATAAA-
1 CCTAAAC
* *
5038013 CTTTAAC
1 CCTAAAC
5038020 CCT-AAC
1 CCTAAAC
5038026 CCATAAAC
1 CC-TAAAC
5038034 CCTAAAC
1 CCTAAAC
*
5038041 ACTAAAC
1 CCTAAAC
5038048 CCTAAAC
1 CCTAAAC
*
5038055 CCTAAAT
1 CCTAAAC
*
5038062 ACTAAAC
1 CCTAAAC
**
5038069 TATAAA-
1 CCTAAAC
5038075 CCTACAA-
1 CCTA-AAC
5038082 CCTAAA-
1 CCTAAAC
5038088 CC-AAAC
1 CCTAAAC
*
5038094 ACTAAAC
1 CCTAAAC
*
5038101 TCTAAAC
1 CCTAAAC
5038108 ATTAATTATT
Statistics
Matches: 104, Mismatches: 26, Indels: 14
0.72 0.18 0.10
Matches are distributed among these distances:
5 3 0.03
6 15 0.14
7 76 0.73
8 10 0.10
ACGTcount: A:0.47, C:0.33, G:0.01, T:0.19
Consensus pattern (7 bp):
CCTAAAC
Found at i:5038527 original size:114 final size:115
Alignment explanation
Indices: 5038282--5038560 Score: 303
Period size: 114 Copynumber: 2.4 Consensus size: 115
5038272 AGATAAAATG
* * * * * * ** *
5038282 TTTTTACGGCATTTTTTACAAAGCGCCGCTAAAGCTCGATCTATAGAGGCATTTTTTAAAAAGCG
1 TTTTTGCGGCATTTTTCAAAAAGCGCCGCTAAATCTTGATCTATAGCGGCATTTTCCAAAAAGCA
* * *
5038347 CCACTAATGCCACTAAAGCTCAACCTAAAACGACGCCGTTGTGCTTAAAT
66 CCACTAATGCCACTAAAACTCAACATAAAACGACGCCGTTGTGCTTAAAC
** ** *
5038397 TTTTTGCGGCGCTTTTCAAAAAG-GCCGCTAAATCTTGATCTATAGCGGTGTTTTCCAAGAAGCA
1 TTTTTGCGGCATTTTTCAAAAAGCGCCGCTAAATCTTGATCTATAGCGGCATTTTCCAAAAAGCA
* * *
5038461 CCGCTAATGCCACTAAAACTCAACATAAAATGACGGCGTTGT-CGTTAAAC
66 CCACTAATGCCACTAAAACTCAACATAAAACGACGCCGTTGTGC-TTAAAC
** * *
5038511 TTTTTGCGGCATTTTTCATGACGCGCCGCT-AATGCTTGATATATAGCGGC
1 TTTTTGCGGCATTTTTCAAAAAGCGCCGCTAAAT-CTTGATCTATAGCGGC
5038561 GGTTTCAAAT
Statistics
Matches: 134, Mismatches: 27, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
113 1 0.01
114 95 0.71
115 38 0.28
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (115 bp):
TTTTTGCGGCATTTTTCAAAAAGCGCCGCTAAATCTTGATCTATAGCGGCATTTTCCAAAAAGCA
CCACTAATGCCACTAAAACTCAACATAAAACGACGCCGTTGTGCTTAAAC
Found at i:5051537 original size:13 final size:13
Alignment explanation
Indices: 5051521--5051550 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
5051511 ATTGTCATGT
5051521 AATTGTTTTTCTG
1 AATTGTTTTTCTG
5051534 AATTGTTTTTCTG
1 AATTGTTTTTCTG
5051547 AATT
1 AATT
5051551 TAGCTGATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.20, C:0.07, G:0.13, T:0.60
Consensus pattern (13 bp):
AATTGTTTTTCTG
Found at i:5052518 original size:82 final size:81
Alignment explanation
Indices: 5052427--5052676 Score: 186
Period size: 82 Copynumber: 3.1 Consensus size: 81
5052417 CATATAAGAA
*
5052427 TATTAATTATTAAGAATTTTATTAAATTATATATTTTAAGTATAATATATTTAATAATAATTATG
1 TATTTATTATTAAGAATTTTATTAAATTATATATTTTAA-TATAATATATTTAATAATAATTATG
5052492 TTTAAATATGATTAAAT
65 TTTAAATATGATTAAAT
* * * * * * * *
5052509 TATTTATTATT---CATATTAATAATCTTATCAAAATTTAA-ATAACA-A--TAACAATAA-TA-
1 TATTTATTATTAAGAATTTTATTAA-ATTAT-ATATTTTAATATAATATATTTAATAATAATTAT
* *
5052565 ATTTACCAA-A--A-CAAAT
64 GTTTA--AATATGATTAAAT
* *
5052581 T-TCTGGTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATGTTTAATAATAAT
1 TAT-T--T-ATTATTAAGAATTTTATTAAATTATATATTTTAA-TATAATATATTTAATAATAAT
*
5052645 TATGTTTAAATATGATTAAAA
61 TATGTTTAAATATGATTAAAT
5052666 TATTTATTATT
1 TATTTATTATT
5052677 GATAATAATA
Statistics
Matches: 121, Mismatches: 24, Indels: 46
0.63 0.13 0.24
Matches are distributed among these distances:
71 1 0.01
72 6 0.05
73 1 0.01
74 5 0.04
75 9 0.07
76 17 0.14
77 4 0.03
78 13 0.11
79 13 0.11
80 4 0.03
81 17 0.14
82 19 0.16
83 5 0.04
84 1 0.01
85 5 0.04
86 1 0.01
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (81 bp):
TATTTATTATTAAGAATTTTATTAAATTATATATTTTAATATAATATATTTAATAATAATTATGT
TTAAATATGATTAAAT
Found at i:5052596 original size:157 final size:157
Alignment explanation
Indices: 5052430--5052739 Score: 548
Period size: 157 Copynumber: 2.0 Consensus size: 157
5052420 ATAAGAATAT
*
5052430 TAATTATTAAGAATTTTATTAAATTATATATTTTAAGTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAAGTAAAATATATTTAATAATAATTATGTTT
* *
5052495 AAATATGATTAAATTATTTATTATTCATATTAATAATCTTATCAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTATTCATAATAATAATCTTATCAAAATTTAAATAACAATAACAA
5052560 TAATAATTTACCAAAACAAATTTCTGG
131 TAATAATTTACCAAAACAAATTTCTGG
* *
5052587 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATGTTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAAGTAAAATATATTTAATAATAATTATGTTT
* *
5052652 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTATTCATAATAATAATCTTATCAAAATTTAAATAACAATAACAA
*
5052717 TAATCATTTACCAAAACAAATTT
131 TAATAATTTACCAAAACAAATTT
5052740 ATGCTAAGGG
Statistics
Matches: 145, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
157 145 1.00
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAAGTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAAATATTTATTATTCATAATAATAATCTTATCAAAATTTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTCTGG
Found at i:5052896 original size:16 final size:16
Alignment explanation
Indices: 5052877--5052936 Score: 102
Period size: 16 Copynumber: 3.8 Consensus size: 16
5052867 ATTACACATT
*
5052877 TAATCTAATACACCTC
1 TAATCCAATACACCTC
*
5052893 TAATCCAATACACTTC
1 TAATCCAATACACCTC
5052909 TAATCCAATACACCTC
1 TAATCCAATACACCTC
5052925 TAATCCAATACA
1 TAATCCAATACA
5052937 GCGAACCAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.40, C:0.32, G:0.00, T:0.28
Consensus pattern (16 bp):
TAATCCAATACACCTC
Found at i:5052905 original size:32 final size:32
Alignment explanation
Indices: 5052869--5052936 Score: 111
Period size: 32 Copynumber: 2.1 Consensus size: 32
5052859 GATTTGCTAT
*
5052869 TACACATT-TAATCTAATACACCTCTAATCCAA
1 TACAC-TTCTAATCCAATACACCTCTAATCCAA
5052901 TACACTTCTAATCCAATACACCTCTAATCCAA
1 TACACTTCTAATCCAATACACCTCTAATCCAA
5052933 TACA
1 TACA
5052937 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
31 2 0.06
32 32 0.94
ACGTcount: A:0.40, C:0.31, G:0.00, T:0.29
Consensus pattern (32 bp):
TACACTTCTAATCCAATACACCTCTAATCCAA
Found at i:5060211 original size:171 final size:170
Alignment explanation
Indices: 5059902--5060238 Score: 444
Period size: 171 Copynumber: 2.0 Consensus size: 170
5059892 TGAGGAAGTC
* * * *
5059902 CATCTAAGATTTTAACTTTTGTGCATCATTGATATAATAGGCTTCTTGGGCCTTTTGGCAGTTGT
1 CATCTAAGACTTGAACTTTCGTGCATCATTGATATAATAGGCTTCTTGGGACTTTTGGCAGTTGT
** * * *
5059967 TTATTAGTTGATTGATATTCATTGTCAAGTTGATTTGATGATGTCATAACTAAAATGTAAATTTC
66 TTATTAGTTGATTGATATTCATCATCAAGTTGATTTGATGATGGCACAACTAAAATGCAAATTTC
*
5060032 TATAATTTGATCAAGTTAATGCATTGCTAGTTTGTTCTTG
131 TATAATTTGATCAAATTAATGCATTGCTAGTTTGTTCTTG
* * *
5060072 CATCTAAGACTTGATCTTTCGTGCATCATTTGATATGATGGGTCTT-TTGGGACTTTTGGCAGTT
1 CATCTAAGACTTGAACTTTCGTGCATCA-TTGATATAATAGG-CTTCTTGGGACTTTTGGCAGTT
* * * * **
5060136 GTTTATTGGTTGATTGGTGTTCATCATCAAGTTGATTTGATGATGGCACAATTAGGATGCAAATT
64 GTTTATTAGTTGATTGATATTCATCATCAAGTTGATTTGATGATGGCACAACTAAAATGCAAATT
**
5060201 T-TAGTAATTTGATCAAATTAATGCATTTTTAGTTTGTT
129 TCTA-TAATTTGATCAAATTAATGCATTGCTAGTTTGTT
5060239 TCTGAATTGT
Statistics
Matches: 143, Mismatches: 21, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
170 26 0.18
171 114 0.80
172 3 0.02
ACGTcount: A:0.25, C:0.11, G:0.20, T:0.44
Consensus pattern (170 bp):
CATCTAAGACTTGAACTTTCGTGCATCATTGATATAATAGGCTTCTTGGGACTTTTGGCAGTTGT
TTATTAGTTGATTGATATTCATCATCAAGTTGATTTGATGATGGCACAACTAAAATGCAAATTTC
TATAATTTGATCAAATTAATGCATTGCTAGTTTGTTCTTG
Found at i:5060724 original size:22 final size:22
Alignment explanation
Indices: 5060699--5060775 Score: 68
Period size: 22 Copynumber: 3.4 Consensus size: 22
5060689 CCAAAATATT
5060699 ATCTCCTAAACTTTAGCATCTA
1 ATCTCCTAAACTTTAGCATCTA
* * * *
5060721 ATCTCCT-AA-TTAAACCAAAATATT
1 ATCTCCTAAACTT-TAGC---ATCTA
5060745 ATCTCCTAAACTTTAGCATCTA
1 ATCTCCTAAACTTTAGCATCTA
5060767 ATCTCCTAA
1 ATCTCCTAA
5060776 TTAAAAGAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
20 2 0.05
21 4 0.10
22 19 0.46
24 10 0.24
25 4 0.10
26 2 0.05
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (22 bp):
ATCTCCTAAACTTTAGCATCTA
Found at i:5060738 original size:46 final size:46
Alignment explanation
Indices: 5060686--5060780 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
5060676 ACAAAGATAA
5060686 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
5060732 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
5060778 AAA
1 AAA
5060781 AGAAAATAGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.41, C:0.23, G:0.02, T:0.34
Consensus pattern (46 bp):
AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
Found at i:5065246 original size:22 final size:22
Alignment explanation
Indices: 5065221--5065297 Score: 68
Period size: 22 Copynumber: 3.4 Consensus size: 22
5065211 CCAAAATATT
5065221 ATCTCCTAAACTTTAGCATCTA
1 ATCTCCTAAACTTTAGCATCTA
* * * *
5065243 ATCTCCT-AA-TTAAACCAAAATATT
1 ATCTCCTAAACTT-TAGC---ATCTA
5065267 ATCTCCTAAACTTTAGCATCTA
1 ATCTCCTAAACTTTAGCATCTA
5065289 ATCTCCTAA
1 ATCTCCTAA
5065298 TTAAAAGAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
20 2 0.05
21 4 0.10
22 19 0.46
24 10 0.24
25 4 0.10
26 2 0.05
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (22 bp):
ATCTCCTAAACTTTAGCATCTA
Found at i:5065260 original size:46 final size:46
Alignment explanation
Indices: 5065208--5065302 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
5065198 ACAAAGATAG
5065208 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
5065254 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
5065300 AAA
1 AAA
5065303 AGAAAATAGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.41, C:0.23, G:0.02, T:0.34
Consensus pattern (46 bp):
AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
Found at i:5071810 original size:33 final size:33
Alignment explanation
Indices: 5071743--5071811 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
5071733 TTTTGACTAC
* *
5071743 TGGGGAGGGTGATGTTCAAGGGGTGGAAGTTGA
1 TGGGGAGGGTGATGATCAAGGGGTAGAAGTTGA
*
5071776 TGGGGAGGGTGATGATGAAGGGGTAGAA-TATGA
1 TGGGGAGGGTGATGATCAAGGGGTAGAAGT-TGA
5071809 TGG
1 TGG
5071812 TAAAGGTGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 1 0.03
33 31 0.97
ACGTcount: A:0.25, C:0.01, G:0.51, T:0.23
Consensus pattern (33 bp):
TGGGGAGGGTGATGATCAAGGGGTAGAAGTTGA
Found at i:5071853 original size:33 final size:33
Alignment explanation
Indices: 5071816--5071885 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
5071806 TGATGGTAAA
* * * * *
5071816 GGTGATCTGGGATAGGTAGAATCTGGTGGGGAG
1 GGTGATCTAGGAGAGGTACAAGCTGATGGGGAG
*
5071849 GGTGATGTAGGAGAGGTACAAGCTGATGGGGAG
1 GGTGATCTAGGAGAGGTACAAGCTGATGGGGAG
5071882 GGTG
1 GGTG
5071886 TGTCTGCTAC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.23, C:0.06, G:0.50, T:0.21
Consensus pattern (33 bp):
GGTGATCTAGGAGAGGTACAAGCTGATGGGGAG
Found at i:5072049 original size:51 final size:51
Alignment explanation
Indices: 5071989--5072143 Score: 265
Period size: 51 Copynumber: 3.0 Consensus size: 51
5071979 GTGAAGTTGC
*
5071989 TGCTGATGAATATGCTGGTGATTTTGCAACATTAGATAGAGTGGATAATGT
1 TGCTGATGAATATGCTGGTGATTTTGCAACATTAGATGGAGTGGATAATGT
* *
5072040 TGCTGATGAATATGTTGGTGATTTTGCAACATCAGATGGAGTGGATAATGT
1 TGCTGATGAATATGCTGGTGATTTTGCAACATTAGATGGAGTGGATAATGT
* *
5072091 TGCTGATGAATATGCTGGTGATTTTGCAACATTAAATGGACTGGATAATGT
1 TGCTGATGAATATGCTGGTGATTTTGCAACATTAGATGGAGTGGATAATGT
5072142 TG
1 TG
5072144 TTTTTGTACG
Statistics
Matches: 97, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 97 1.00
ACGTcount: A:0.28, C:0.08, G:0.28, T:0.35
Consensus pattern (51 bp):
TGCTGATGAATATGCTGGTGATTTTGCAACATTAGATGGAGTGGATAATGT
Found at i:5074665 original size:16 final size:16
Alignment explanation
Indices: 5074644--5074677 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
5074634 AGTACGGTGT
5074644 AAGGTATTTTGCCTAC
1 AAGGTATTTTGCCTAC
5074660 AAGGTATTTTGCCTAC
1 AAGGTATTTTGCCTAC
5074676 AA
1 AA
5074678 CATTCTGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (16 bp):
AAGGTATTTTGCCTAC
Found at i:5076266 original size:14 final size:13
Alignment explanation
Indices: 5076226--5076276 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
5076216 TTAAGTATAT
*
5076226 TATTATTTTATTA
1 TATTATTATATTA
* *
5076239 TATT-GTAAATTA
1 TATTATTATATTA
5076251 TATTAATTATATTA
1 TATT-ATTATATTA
5076265 TATTATTATATT
1 TATTATTATATT
5076277 TCAAATAAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
12 9 0.29
13 12 0.39
14 10 0.32
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (13 bp):
TATTATTATATTA
Found at i:5076404 original size:11 final size:11
Alignment explanation
Indices: 5076385--5076416 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
5076375 AAGTAAGTAA
5076385 TATTATATTAT
1 TATTATATTAT
*
5076396 TATTTTATTAT
1 TATTATATTAT
5076407 TATTATATTA
1 TATTATATTA
5076417 AACTAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TATTATATTAT
Found at i:5080251 original size:21 final size:23
Alignment explanation
Indices: 5080209--5080251 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
5080199 ATTTATTTCG
*
5080209 GGTGTGTTTTGGTTGGATATCCT
1 GGTGTGTTTTGGGTGGATATCCT
5080232 GGTGTG-TTTGGGTGGA-ATCC
1 GGTGTGTTTTGGGTGGATATCC
5080252 GCGTATCTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 9 0.47
23 6 0.32
ACGTcount: A:0.09, C:0.09, G:0.40, T:0.42
Consensus pattern (23 bp):
GGTGTGTTTTGGGTGGATATCCT
Found at i:5083735 original size:98 final size:97
Alignment explanation
Indices: 5083564--5083755 Score: 276
Period size: 98 Copynumber: 2.0 Consensus size: 97
5083554 TTTATAGATC
* * * * *
5083564 TATTCATTTGTGACCTTCATAGTGTGTCATACCTTAATTCTGAGTGGATGATAGACTATGTATGT
1 TATTCACTTGTGACCTTCATAGTGTGTCATACCTTAATCCTAAGTGGATAATAGACTATGTATGC
*
5083629 GTGGCTCGTATACTATGATGCAAATGAAAATTT
66 GTGACTCGTATACTATGATGCAAAT-AAAATTT
* * *
5083662 TATTCACTTGTGACGTTCATTGTGTGTCATACCTTAATCCTAAGTGGATAATGGACTATGTATGC
1 TATTCACTTGTGACCTTCATAGTGTGTCATACCTTAATCCTAAGTGGATAATAGACTATGTATGC
* *
5083727 GTGACTCGTATACTTTGATTCAAATAAAA
66 GTGACTCGTATACTATGATGCAAATAAAA
5083756 GCCTGATTTC
Statistics
Matches: 83, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
97 4 0.05
98 79 0.95
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (97 bp):
TATTCACTTGTGACCTTCATAGTGTGTCATACCTTAATCCTAAGTGGATAATAGACTATGTATGC
GTGACTCGTATACTATGATGCAAATAAAATTT
Found at i:5087236 original size:23 final size:23
Alignment explanation
Indices: 5087210--5087308 Score: 108
Period size: 23 Copynumber: 4.3 Consensus size: 23
5087200 ATAAGTGCCA
5087210 CACTGATATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCAAAGCTAC
* **
5087233 CACTGATACGTAGCCGTAGCTAC
1 CACTGATATGTAGCCAAAGCTAC
* * *
5087256 CACTGAAATATAGCCAAAGATAC
1 CACTGATATGTAGCCAAAGCTAC
* * **
5087279 CACCGATATGTAGTCGTAGCTAC
1 CACTGATATGTAGCCAAAGCTAC
5087302 CACTGAT
1 CACTGAT
5087309 CAATAAACAC
Statistics
Matches: 59, Mismatches: 17, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.22
Consensus pattern (23 bp):
CACTGATATGTAGCCAAAGCTAC
Found at i:5087280 original size:46 final size:46
Alignment explanation
Indices: 5087210--5087307 Score: 142
Period size: 46 Copynumber: 2.1 Consensus size: 46
5087200 ATAAGTGCCA
* * * *
5087210 CACTGATATGTAGCCAAAGCTACCACTGATACGTAGCCGTAGCTAC
1 CACTGAAATATAGCCAAAGATACCACCGATACGTAGCCGTAGCTAC
* *
5087256 CACTGAAATATAGCCAAAGATACCACCGATATGTAGTCGTAGCTAC
1 CACTGAAATATAGCCAAAGATACCACCGATACGTAGCCGTAGCTAC
5087302 CACTGA
1 CACTGA
5087308 TCAATAAACA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (46 bp):
CACTGAAATATAGCCAAAGATACCACCGATACGTAGCCGTAGCTAC
Found at i:5087332 original size:13 final size:14
Alignment explanation
Indices: 5087302--5087333 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
5087292 TCGTAGCTAC
5087302 CACTGATCAATAAA
1 CACTGATCAATAAA
5087316 CACTGATCAAT-AA
1 CACTGATCAATAAA
5087329 CACTG
1 CACTG
5087334 GAAATGTCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.44, C:0.25, G:0.09, T:0.22
Consensus pattern (14 bp):
CACTGATCAATAAA
Found at i:5090069 original size:30 final size:30
Alignment explanation
Indices: 5090035--5090092 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
5090025 CCTTGACTCG
5090035 AACTTTGTAAAAATTACGA-TTTTGCCCCTA
1 AACTTTGTAAAAATTAC-ACTTTTGCCCCTA
* * *
5090065 AACTTTTTCATAATTACACTTTTGCCCC
1 AACTTTGTAAAAATTACACTTTTGCCCC
5090093 AAAGCTCGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.29, C:0.24, G:0.07, T:0.40
Consensus pattern (30 bp):
AACTTTGTAAAAATTACACTTTTGCCCCTA
Found at i:5090122 original size:26 final size:27
Alignment explanation
Indices: 5090093--5090145 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
5090083 CTTTTGCCCC
5090093 AAAGCTCG-AAATTAAACTTCATCCCT
1 AAAGCTCGTAAATTAAACTTCATCCCT
5090119 AAAGCTCGTAAATTAAACTTCATCCCT
1 AAAGCTCGTAAATTAAACTTCATCCCT
5090146 TATTCTTATG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.38, C:0.26, G:0.08, T:0.28
Consensus pattern (27 bp):
AAAGCTCGTAAATTAAACTTCATCCCT
Found at i:5092401 original size:20 final size:22
Alignment explanation
Indices: 5092370--5092412 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
5092360 TTTTGGCATG
5092370 ATTTTTTATAATT-AAAATTAA
1 ATTTTTTATAATTCAAAATTAA
*
5092391 ATTTTTT-TAATTCAAAGTTAA
1 ATTTTTTATAATTCAAAATTAA
5092412 A
1 A
5092413 CAAGTCAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (22 bp):
ATTTTTTATAATTCAAAATTAA
Found at i:5102472 original size:13 final size:14
Alignment explanation
Indices: 5102443--5102479 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
5102433 ATTTAATAAA
*
5102443 TAAAAATAAAACTC
1 TAAAACTAAAACTC
5102457 TAAAACTAAAAC-C
1 TAAAACTAAAACTC
5102470 TAAAACTAAA
1 TAAAACTAAA
5102480 GTATAAAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.65, C:0.16, G:0.00, T:0.19
Consensus pattern (14 bp):
TAAAACTAAAACTC
Found at i:5102560 original size:26 final size:27
Alignment explanation
Indices: 5102526--5102592 Score: 118
Period size: 26 Copynumber: 2.5 Consensus size: 27
5102516 TCAATTAGGT
*
5102526 TAATCCGGTTAATTCGGGTAATTCGGG
1 TAATTCGGTTAATTCGGGTAATTCGGG
5102553 T-ATTCGGTTAATTCGGGTAATTCGGG
1 TAATTCGGTTAATTCGGGTAATTCGGG
5102579 TAATTCGGTTAATT
1 TAATTCGGTTAATT
5102593 TGCTCAATTC
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
26 25 0.66
27 13 0.34
ACGTcount: A:0.22, C:0.12, G:0.27, T:0.39
Consensus pattern (27 bp):
TAATTCGGTTAATTCGGGTAATTCGGG
Found at i:5102601 original size:27 final size:27
Alignment explanation
Indices: 5102526--5102610 Score: 102
Period size: 26 Copynumber: 3.2 Consensus size: 27
5102516 TCAATTAGGT
* *
5102526 TAATCCGGTTAATTCGGGTAATTCGGG
1 TAATTCGGTTAATTCGGCTAATTCGGG
*
5102553 T-ATTCGGTTAATTCGGGTAATTCGGG
1 TAATTCGGTTAATTCGGCTAATTCGGG
* *
5102579 TAATTCGGTTAATT-TGCTCAATTCGGT
1 TAATTCGGTTAATTCGGCT-AATTCGGG
5102606 TAATT
1 TAATT
5102611 TTTAACCAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
26 27 0.52
27 25 0.48
ACGTcount: A:0.22, C:0.13, G:0.25, T:0.40
Consensus pattern (27 bp):
TAATTCGGTTAATTCGGCTAATTCGGG
Found at i:5102610 original size:9 final size:9
Alignment explanation
Indices: 5102518--5102610 Score: 98
Period size: 9 Copynumber: 10.4 Consensus size: 9
5102508 TGTATGATTC
*
5102518 AATTAGGTT
1 AATTCGGTT
*
5102527 AATCCGGTT
1 AATTCGGTT
*
5102536 AATTCGGGT
1 AATTCGGTT
*
5102545 AATTCGGGT
1 AATTCGGTT
5102554 -ATTCGGTT
1 AATTCGGTT
*
5102562 AATTCGGGT
1 AATTCGGTT
*
5102571 AATTCGGGT
1 AATTCGGTT
5102580 AATTCGGTT
1 AATTCGGTT
* * *
5102589 AATTTGCTC
1 AATTCGGTT
5102598 AATTCGGTT
1 AATTCGGTT
5102607 AATT
1 AATT
5102611 TTTAACCAAA
Statistics
Matches: 70, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
8 7 0.10
9 63 0.90
ACGTcount: A:0.24, C:0.12, G:0.25, T:0.40
Consensus pattern (9 bp):
AATTCGGTT
Found at i:5102907 original size:13 final size:13
Alignment explanation
Indices: 5102889--5102921 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
5102879 TTGCTAAGAG
5102889 ATAATATCCCATA
1 ATAATATCCCATA
*
5102902 ATAATATCCTATA
1 ATAATATCCCATA
5102915 ATAATAT
1 ATAATAT
5102922 TCTAACACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.36
Consensus pattern (13 bp):
ATAATATCCCATA
Found at i:5106570 original size:28 final size:28
Alignment explanation
Indices: 5106539--5106593 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
5106529 GTTCTTGTAC
*
5106539 TATTTATAAATTTCGAAATTT-GTCCCTA
1 TATTT-TAAATTTAGAAATTTAGTCCCTA
* *
5106567 TATTTTAATTTTATAAATTTAGTCCCT
1 TATTTTAAATTTAGAAATTTAGTCCCT
5106594 CCACTTTTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.31, C:0.13, G:0.05, T:0.51
Consensus pattern (28 bp):
TATTTTAAATTTAGAAATTTAGTCCCTA
Found at i:5106983 original size:13 final size:13
Alignment explanation
Indices: 5106965--5107000 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
5106955 TTTTTAATAT
5106965 TTTAAAA-ATAGAA
1 TTTAAAACA-AGAA
5106978 TTTAAAACAAGAA
1 TTTAAAACAAGAA
5106991 TTTAAAACAA
1 TTTAAAACAA
5107001 TCTCTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 21 0.95
14 1 0.05
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.28
Consensus pattern (13 bp):
TTTAAAACAAGAA
Found at i:5107428 original size:47 final size:47
Alignment explanation
Indices: 5107359--5107453 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
5107349 AAAGGCTCAG
5107359 AAAGCCATTAAATTTCATTAATCAAACACCATCATCAATAAGAAAGT
1 AAAGCCATTAAATTTCATTAATCAAACACCATCATCAATAAGAAAGT
5107406 AAAGCCATTAAATTTCATTAATCAAACACCATCATCAATAAGAAAGT
1 AAAGCCATTAAATTTCATTAATCAAACACCATCATCAATAAGAAAGT
5107453 A
1 A
5107454 GTGGTTCTCA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.49, C:0.19, G:0.06, T:0.25
Consensus pattern (47 bp):
AAAGCCATTAAATTTCATTAATCAAACACCATCATCAATAAGAAAGT
Found at i:5108353 original size:120 final size:120
Alignment explanation
Indices: 5108212--5108452 Score: 464
Period size: 120 Copynumber: 2.0 Consensus size: 120
5108202 CAAAGACTTG
5108212 GACAATCTTGTTAACACCAAAAACGAGTTGGCAAAAAAAATTATGCTTGAAAAATTCAATACATG
1 GACAATCTTGTTAACACCAAAAACGAGTTGGCAAAAAAAATTATGCTTGAAAAATTCAATACATG
5108277 TAGCAACAAATTAGATTAAATTCTTACTGCTGGTAGAAGAGATCCAGGAAAGAGT
66 TAGCAACAAATTAGATTAAATTCTTACTGCTGGTAGAAGAGATCCAGGAAAGAGT
5108332 GACAATCTTGTTAACACCAAAAACGAGTTGGCAAAAAAAATTATGCTTGAAAAATTCAATACATG
1 GACAATCTTGTTAACACCAAAAACGAGTTGGCAAAAAAAATTATGCTTGAAAAATTCAATACATG
* *
5108397 TAGCAACAAATTAGATTAAATTCTTACTGCTGGTAGTAGAGATCCTGGAAAGAGT
66 TAGCAACAAATTAGATTAAATTCTTACTGCTGGTAGAAGAGATCCAGGAAAGAGT
5108452 G
1 G
5108453 GACTTGGATT
Statistics
Matches: 119, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 119 1.00
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (120 bp):
GACAATCTTGTTAACACCAAAAACGAGTTGGCAAAAAAAATTATGCTTGAAAAATTCAATACATG
TAGCAACAAATTAGATTAAATTCTTACTGCTGGTAGAAGAGATCCAGGAAAGAGT
Found at i:5127632 original size:17 final size:17
Alignment explanation
Indices: 5127612--5127663 Score: 104
Period size: 17 Copynumber: 3.1 Consensus size: 17
5127602 TTTCGTAGCC
5127612 TTTATGTTCTCGTGTGG
1 TTTATGTTCTCGTGTGG
5127629 TTTATGTTCTCGTGTGG
1 TTTATGTTCTCGTGTGG
5127646 TTTATGTTCTCGTGTGG
1 TTTATGTTCTCGTGTGG
5127663 T
1 T
5127664 GCATTTGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.06, C:0.12, G:0.29, T:0.54
Consensus pattern (17 bp):
TTTATGTTCTCGTGTGG
Found at i:5135628 original size:16 final size:16
Alignment explanation
Indices: 5135607--5135640 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
5135597 TTTGAGATGG
5135607 TAGCAGCTAAAATTTT
1 TAGCAGCTAAAATTTT
5135623 TAGCAGCTAAAATTTT
1 TAGCAGCTAAAATTTT
5135639 TA
1 TA
5135641 CCATCCAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (16 bp):
TAGCAGCTAAAATTTT
Found at i:5140281 original size:30 final size:29
Alignment explanation
Indices: 5140247--5140335 Score: 90
Period size: 29 Copynumber: 3.0 Consensus size: 29
5140237 AATTTACGAG
*
5140247 AATTGAATC-AAATCAAAATTTCATGTATAA
1 AATTGAA-CAAAATC-AAAGTTCATGTATAA
* *
5140277 AATTGCACAAAATCAAAGTTCATGTATAC
1 AATTGAACAAAATCAAAGTTCATGTATAA
* *
5140306 AATTGCACATTAAACCAAAGTTCATGTATA
1 AATTGAACA--AAATCAAAGTTCATGTATA
5140336 GTTTTGGGAT
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
29 23 0.44
30 11 0.21
31 18 0.35
ACGTcount: A:0.46, C:0.15, G:0.09, T:0.30
Consensus pattern (29 bp):
AATTGAACAAAATCAAAGTTCATGTATAA
Found at i:5140299 original size:29 final size:30
Alignment explanation
Indices: 5140256--5140335 Score: 108
Period size: 29 Copynumber: 2.6 Consensus size: 30
5140246 GAATTGAATC
*
5140256 AAATCAAAATTTCATGTATAAAATTGCACA-
1 AAATC-AAAGTTCATGTATAAAATTGCACAT
*
5140286 AAATCAAAGTTCATGTATACAATTGCACATT
1 AAATCAAAGTTCATGTATAAAATTGCACA-T
*
5140317 AAACCAAAGTTCATGTATA
1 AAATCAAAGTTCATGTATA
5140336 GTTTTGGGAT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
29 22 0.49
30 5 0.11
31 18 0.40
ACGTcount: A:0.46, C:0.15, G:0.09, T:0.30
Consensus pattern (30 bp):
AAATCAAAGTTCATGTATAAAATTGCACAT
Found at i:5143782 original size:37 final size:37
Alignment explanation
Indices: 5143735--5143805 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
5143725 TTGGGAAAAT
5143735 AATTCCCTTATTCTAATAAACTACTAAAAGATAAGGA
1 AATTCCCTTATTCTAATAAACTACTAAAAGATAAGGA
*
5143772 AATTCCCTTATTCTAATAAACTACTAAAGGATAA
1 AATTCCCTTATTCTAATAAACTACTAAAAGATAA
5143806 AATAAGATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.45, C:0.17, G:0.07, T:0.31
Consensus pattern (37 bp):
AATTCCCTTATTCTAATAAACTACTAAAAGATAAGGA
Found at i:5143867 original size:19 final size:19
Alignment explanation
Indices: 5143843--5143883 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
5143833 TGATTTATTC
5143843 TAAGATTTATCTACCTAAA
1 TAAGATTTATCTACCTAAA
*
5143862 TAAGATTTATCTATCTAAA
1 TAAGATTTATCTACCTAAA
5143881 TAA
1 TAA
5143884 CCTTAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.39
Consensus pattern (19 bp):
TAAGATTTATCTACCTAAA
Found at i:5146374 original size:41 final size:41
Alignment explanation
Indices: 5146280--5146361 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
5146270 AATCTAATTG
** * *
5146280 GGAAAATAATTCTTTTATTTTAGTAAACTACTAAAAGATAA
1 GGAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATAA
5146321 GGAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATAA
1 GGAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATAA
5146362 AATGAAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.48, C:0.11, G:0.09, T:0.33
Consensus pattern (41 bp):
GGAAAATAATTCCCTTATTCTAATAAACTACTAAAAGATAA
Found at i:5149492 original size:23 final size:22
Alignment explanation
Indices: 5149449--5149492 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
5149439 TTCTAAGTCG
5149449 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
5149472 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
5149493 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:5149602 original size:45 final size:45
Alignment explanation
Indices: 5149538--5149623 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
5149528 ACAGATACTC
* * *
5149538 GGTGGATTCAGCACATAGCAACCACCTTATTAATTAATGATTTCT
1 GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATTTCT
*
5149583 GGTGGAATCATCACATAGCAACCACCTTACTAATCAATGAT
1 GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGAT
5149624 GTTCGGTTCG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (45 bp):
GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATTTCT
Found at i:5149698 original size:51 final size:51
Alignment explanation
Indices: 5149636--5149870 Score: 307
Period size: 51 Copynumber: 4.6 Consensus size: 51
5149626 TCGGTTCGCA
*
5149636 TAGTAGTCTGCACATAGTACTACACATGTGACCATTATCATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATTATCATCCGATACACG
5149687 TAGTAGCCTGCACATAGTACTACACATGTGACCATTATCATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATTATCATCCGATACACG
* * * * * *
5149738 TAGTAGCCTGCACATAGTACTACACATGTGATCGA--AACTATTCGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACATGTGA-CCATTATC-ATCCGATACACG
* ** *
5149789 TAGTAGCCTGCATATAGTACTACACATACGACCTATTAT--TCCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACC-ATTATCATCCGATACACG
*
5149839 TAGTAGACTGCACATAGTACTACACATGTGAC
1 TAGTAGCCTGCACATAGTACTACACATGTGAC
5149871 AATCACTTTC
Statistics
Matches: 160, Mismatches: 19, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
50 39 0.24
51 118 0.74
52 2 0.01
53 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.26
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCATTATCATCCGATACACG
Found at i:5149736 original size:25 final size:25
Alignment explanation
Indices: 5149656--5149736 Score: 62
Period size: 25 Copynumber: 3.2 Consensus size: 25
5149646 CACATAGTAC
5149656 TACACATGTGACCATTATCATCCGA
1 TACACATGTGACCATTATCATCCGA
* * *
5149681 TACACGTAGT-AGCC-TGCA-CAT-AGTA
1 TACACAT-GTGA-CCAT-TATCATCCG-A
5149706 CTACACATGTGACCATTATCATCCGA
1 -TACACATGTGACCATTATCATCCGA
5149732 TACAC
1 TACAC
5149737 GTAGTAGCCT
Statistics
Matches: 41, Mismatches: 6, Indels: 18
0.63 0.09 0.28
Matches are distributed among these distances:
24 1 0.02
25 22 0.54
26 17 0.41
27 1 0.02
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (25 bp):
TACACATGTGACCATTATCATCCGA
Found at i:5152628 original size:18 final size:17
Alignment explanation
Indices: 5152597--5152630 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5152587 ACAAACACAG
*
5152597 TTAAAAATTTGAGGAGT
1 TTAAAAATTAGAGGAGT
5152614 TTAAAAATATAGAGGAG
1 TTAAAAAT-TAGAGGAG
5152631 AATTTGGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.47, C:0.00, G:0.24, T:0.29
Consensus pattern (17 bp):
TTAAAAATTAGAGGAGT
Found at i:5156203 original size:14 final size:14
Alignment explanation
Indices: 5156184--5156213 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5156174 AGTGGTACAT
5156184 GAGAATACCTTAAA
1 GAGAATACCTTAAA
5156198 GAGAATACCTTAAA
1 GAGAATACCTTAAA
5156212 GA
1 GA
5156214 ATTCGTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.13, G:0.17, T:0.20
Consensus pattern (14 bp):
GAGAATACCTTAAA
Found at i:5156736 original size:21 final size:21
Alignment explanation
Indices: 5156710--5156752 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
5156700 TTGAAATCCG
5156710 GAACAAGGTTCATACAACTAA
1 GAACAAGGTTCATACAACTAA
5156731 GAACAAGGTTCATACAACTAA
1 GAACAAGGTTCATACAACTAA
5156752 G
1 G
5156753 TGGTTGCAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.19, G:0.16, T:0.19
Consensus pattern (21 bp):
GAACAAGGTTCATACAACTAA
Found at i:5164342 original size:57 final size:54
Alignment explanation
Indices: 5164237--5164344 Score: 144
Period size: 57 Copynumber: 1.9 Consensus size: 54
5164227 TTAATATTAA
* * * *
5164237 ATTAATATAATATTTATCAAGATAAATATTAGATTAAATTTAACATTAAATCTT
1 ATTAATAGAATATTTATCAAGATAAACATTAAATTAAACTTAACATTAAATCTT
*
5164291 ATTAATAGAATATTTATCTACAAGATAAACATTAAATTAAACTTAATATTAAAT
1 ATTAATAGAATATTTA--T-CAAGATAAACATTAAATTAAACTTAACATTAAAT
5164345 TAATAAAATA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
54 15 0.33
56 1 0.02
57 30 0.65
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (54 bp):
ATTAATAGAATATTTATCAAGATAAACATTAAATTAAACTTAACATTAAATCTT
Found at i:5177375 original size:44 final size:44
Alignment explanation
Indices: 5177325--5177414 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
5177315 AAGATCAGAG
5177325 TAAGAAATTCTAATGAGGTAGTGAACGCAAGAAATAAGTAAAAA
1 TAAGAAATTCTAATGAGGTAGTGAACGCAAGAAATAAGTAAAAA
5177369 TAAGAAATTCTAATGAGGTAGTGAACGCAAGAAATAAGTAAAAA
1 TAAGAAATTCTAATGAGGTAGTGAACGCAAGAAATAAGTAAAAA
5177413 TA
1 TA
5177415 TAATGAAATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.52, C:0.07, G:0.20, T:0.21
Consensus pattern (44 bp):
TAAGAAATTCTAATGAGGTAGTGAACGCAAGAAATAAGTAAAAA
Found at i:5178882 original size:99 final size:100
Alignment explanation
Indices: 5178700--5178890 Score: 271
Period size: 99 Copynumber: 1.9 Consensus size: 100
5178690 CCTGATCAAC
*
5178700 ATTTTGTATTAAATGAAAAAAAGTTTTTAATGTAATTAATTCAACGATTGAACTTTCAATTCCAT
1 ATTTTGTATTAAATGAAAAAAAGTTTTTAATGTAATTAATTCAACGATTGAACTTCCAATTCCAT
** * *
5178765 TGATTATGTTTTTGTTTTTGAAGTATGGCGGCTAAA
66 CAATCATGTTTTTGTTTTT-AAATATGGCGGCTAAA
* * *
5178801 ATTTTGTATTAAATG-AAGAAAGTTTTTAA-GTCATTAATTCAGCGATTGAACTTCCAATTCCAT
1 ATTTTGTATTAAATGAAAAAAAGTTTTTAATGTAATTAATTCAACGATTGAACTTCCAATTCCAT
5178864 CAATCATGTTTTAT-TTTTTAAATATGG
66 CAATCATGTTTT-TGTTTTTAAATATGG
5178891 GGAACTCCAA
Statistics
Matches: 81, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
98 7 0.09
99 45 0.56
100 14 0.17
101 15 0.19
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (100 bp):
ATTTTGTATTAAATGAAAAAAAGTTTTTAATGTAATTAATTCAACGATTGAACTTCCAATTCCAT
CAATCATGTTTTTGTTTTTAAATATGGCGGCTAAA
Found at i:5179472 original size:22 final size:22
Alignment explanation
Indices: 5179447--5179538 Score: 112
Period size: 22 Copynumber: 4.2 Consensus size: 22
5179437 AAATTCAATA
* *
5179447 TCAATTTCTTTCAAAAATTCTC
1 TCAATTCCCTTCAAAAATTCTC
* *
5179469 TCAATTCCTTTCAAAATTTCTC
1 TCAATTCCCTTCAAAAATTCTC
* *
5179491 TCAATTCCCTTCAAAATTTCTA
1 TCAATTCCCTTCAAAAATTCTC
* *
5179513 TCAATTTCCTTCCAAAATTCTC
1 TCAATTCCCTTCAAAAATTCTC
5179535 TCAA
1 TCAA
5179539 ACTCTCAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 62 1.00
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.42
Consensus pattern (22 bp):
TCAATTCCCTTCAAAAATTCTC
Found at i:5179554 original size:52 final size:51
Alignment explanation
Indices: 5179488--5179590 Score: 129
Period size: 52 Copynumber: 2.0 Consensus size: 51
5179478 TTCAAAATTT
* * *
5179488 CTCTCAATTCCCTT-CAAAATTTCTATCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAATTCCCTTCCAAAA-TCCTATCAATTTCCTTCAAAAAATCTC-CAAA
*
5179540 CTCTCAAATT-CCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
1 CTCTC-AATTCCCTTCCAAAATCCTATCAATTTCCTTCAAAAAATCTCCAAA
5179591 TCCATATTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
51 4 0.09
52 32 0.71
53 9 0.20
ACGTcount: A:0.33, C:0.32, G:0.00, T:0.35
Consensus pattern (51 bp):
CTCTCAATTCCCTTCCAAAATCCTATCAATTTCCTTCAAAAAATCTCCAAA
Found at i:5179579 original size:21 final size:22
Alignment explanation
Indices: 5179540--5179581 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
5179530 TTCTCTCAAA
5179540 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
5179562 CTCTCAATTTCCTTCAAAAA
1 CTCTCAAATTCCTTCCAAAA
5179582 ATCTCCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Found at i:5179680 original size:28 final size:29
Alignment explanation
Indices: 5179623--5179679 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
5179613 ATTAAATTTC
5179623 ATTTTTTTAAGAAAATTTTAAAATTTTTT
1 ATTTTTTTAAGAAAATTTTAAAATTTTTT
*
5179652 ATTTTTTTAA-AATAATTTTAATATTTTT
1 ATTTTTTTAAGAA-AATTTTAAAATTTTT
5179680 AATATTTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 2 0.08
29 24 0.92
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (29 bp):
ATTTTTTTAAGAAAATTTTAAAATTTTTT
Found at i:5179687 original size:29 final size:29
Alignment explanation
Indices: 5179626--5179687 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
5179616 AAATTTCATT
* *
5179626 TTTTTAAGAAAATTTTAAAATTTTTTATT
1 TTTTTAAGAAAATTTTAAAATTTTTAATA
*
5179655 TTTTTAA-AATAATTTTAATATTTTTAATA
1 TTTTTAAGAA-AATTTTAAAATTTTTAATA
5179684 TTTT
1 TTTT
5179688 CAACAATGGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 2 0.07
29 27 0.93
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (29 bp):
TTTTTAAGAAAATTTTAAAATTTTTAATA
Found at i:5181985 original size:17 final size:18
Alignment explanation
Indices: 5181963--5181998 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5181953 TAAAATCCCT
5181963 AAACCCT-ACTTAATTAA
1 AAACCCTAACTTAATTAA
*
5181980 AAACCCTAATTTAATTAA
1 AAACCCTAACTTAATTAA
5181998 A
1 A
5181999 TTAAAAACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (18 bp):
AAACCCTAACTTAATTAA
Found at i:5181986 original size:24 final size:23
Alignment explanation
Indices: 5181951--5182040 Score: 101
Period size: 24 Copynumber: 3.8 Consensus size: 23
5181941 ACATTATTTG
*
5181951 ATTAAAATCCCTAAACCCTACTTA
1 ATTAAAAACCCT-AACCCTACTTA
** *
5181975 ATTAAAAACCCTAA-TTTAATTAA
1 ATTAAAAACCCTAACCCTACTT-A
5181998 ATTAAAAACCCTAAACCCTACTTA
1 ATTAAAAACCCT-AACCCTACTTA
*
5182022 ATTAGAAACCCTAACCCTA
1 ATTAAAAACCCTAACCCTA
5182041 ACATAATTTA
Statistics
Matches: 55, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
22 4 0.07
23 22 0.40
24 25 0.45
25 4 0.07
ACGTcount: A:0.46, C:0.26, G:0.01, T:0.28
Consensus pattern (23 bp):
ATTAAAAACCCTAACCCTACTTA
Found at i:5182069 original size:28 final size:28
Alignment explanation
Indices: 5181984--5182396 Score: 338
Period size: 28 Copynumber: 14.5 Consensus size: 28
5181974 AATTAAAAAC
5181984 CCTAATTTAATTAAATTAAAAACCCTAAA
1 CCTAATTTAATTAAATTAAAAACCCT-AA
* *****
5182013 CCCT-ACTTAATTAGAAACCCTAACCCTAA
1 -CCTAATTTAATTA-AATTAAAAACCCTAA
*
5182042 CATAATTTAATTAAATTAAAAACCCTAA
1 CCTAATTTAATTAAATTAAAAACCCTAA
*
5182070 CCTTATTTAATTAAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAATT--AAA----AACCCTAA
5182104 CCTAATTTAATTAAATTAAAAACCCTAA
1 CCTAATTTAATTAAATTAAAAACCCTAA
5182132 CCTAA--T--TT-AATTAAAAACCCTAA
1 CCTAATTTAATTAAATTAAAAACCCTAA
5182155 CCTAATTTAATTAAATTAAAAACCCTAA
1 CCTAATTTAATTAAATTAAAAACCCTAA
* *
5182183 CCCTAACCTAACCTACTTAAATTAAAAACCCTAA
1 -CCTAA--T---TTAATTAAATTAAAAACCCTAA
* *
5182217 CCTTATTTAATTTAATTAAAAACCCTAA
1 CCTAATTTAATTAAATTAAAAACCCTAA
* *
5182245 CC-----TACTTAAATTAAAAATCCTAA
1 CCTAATTTAATTAAATTAAAAACCCTAA
*
5182268 CCTTATTTAATTAAATTAAAAACCCTAA
1 CCTAATTTAATTAAATTAAAAACCCTAA
* *
5182296 CCCTAACCCTAACCTAATTAAATTAAAAATCCTAA
1 -CCTAA---T---TTAATTAAATTAAAAACCCTAA
5182331 CCTAA--T--TT-AATTAAAAACCCTAA
1 CCTAATTTAATTAAATTAAAAACCCTAA
*
5182354 CCTTATTTAATTAAATTAAAAACCCTAA
1 CCTAATTTAATTAAATTAAAAACCCTAA
5182382 CCCT-ATTTAATTAAA
1 -CCTAATTTAATTAAA
5182397 AACCCTAATT
Statistics
Matches: 314, Mismatches: 32, Indels: 76
0.74 0.08 0.18
Matches are distributed among these distances:
23 58 0.18
24 4 0.01
25 2 0.01
26 2 0.01
27 4 0.01
28 121 0.39
29 30 0.10
30 14 0.04
31 2 0.01
32 4 0.01
33 4 0.01
34 49 0.16
35 20 0.06
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.31
Consensus pattern (28 bp):
CCTAATTTAATTAAATTAAAAACCCTAA
Found at i:5182130 original size:23 final size:23
Alignment explanation
Indices: 5182104--5182182 Score: 86
Period size: 23 Copynumber: 3.2 Consensus size: 23
5182094 CTAACCCTAA
5182104 CCTAATTTAATTAAATTAAAAAC
1 CCTAATTTAATTAAATTAAAAAC
** *
5182127 CCTAACCTAATTTAATTAAAAACCC
1 CCTAATTTAATTAAATTAAAAA--C
5182152 TAACCTAATTTAATTAAATTAAAAAC
1 ---CCTAATTTAATTAAATTAAAAAC
5182178 CCTAA
1 CCTAA
5182183 CCCTAACCTA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
23 24 0.53
25 1 0.02
26 1 0.02
28 19 0.42
ACGTcount: A:0.49, C:0.19, G:0.00, T:0.32
Consensus pattern (23 bp):
CCTAATTTAATTAAATTAAAAAC
Done.