Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold448
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: 1056520
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 4 of 7
Found at i:512680 original size:33 final size:32
Alignment explanation
Indices: 512619--512686 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 32
512609 CCTTAACTGT
512619 TTGTATCGATACATACAAGATGTATCGATACA
1 TTGTATCGATACATACAAGATGTATCGATACA
512651 TTGTATCGATACATGACCAA-ATGTATCGATACA
1 TTGTATCGATACAT-A-CAAGATGTATCGATACA
512684 TTG
1 TTG
512687 GTTTGTAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
32 14 0.41
33 17 0.50
34 3 0.09
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (32 bp):
TTGTATCGATACATACAAGATGTATCGATACA
Found at i:514806 original size:21 final size:21
Alignment explanation
Indices: 514782--514834 Score: 90
Period size: 20 Copynumber: 2.6 Consensus size: 21
514772 TTTTATAATT
514782 TGTATCGATACAATAAGTGAA
1 TGTATCGATACAATAAGTGAA
*
514803 TGTATCAATAC-ATAAGTGAA
1 TGTATCGATACAATAAGTGAA
514823 TGTATCGATACA
1 TGTATCGATACA
514835 GGATCATGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 19 0.66
21 10 0.34
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (21 bp):
TGTATCGATACAATAAGTGAA
Found at i:519980 original size:13 final size:13
Alignment explanation
Indices: 519962--520013 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
519952 AGCTTTATAG
519962 CGATACATTGTAT
1 CGATACATTGTAT
519975 CGATACAACACTTCTGTAT
1 CGAT---ACA-TT--GTAT
519994 CGATACATTGTAT
1 CGATACATTGTAT
520007 CGATACA
1 CGATACA
520014 AATTGTTGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 15 0.45
15 2 0.06
16 6 0.18
17 2 0.06
19 8 0.24
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:520780 original size:53 final size:52
Alignment explanation
Indices: 520613--520850 Score: 189
Period size: 52 Copynumber: 4.6 Consensus size: 52
520603 GATAAAGGGA
* * *
520613 CCAATATGCTGATTCACGGCCAACGATATTGGGTTTCAAAGATGTA-AAAATG
1 CCAATATGCTGATTCAAGGCCAACGACATTGGGTTTTAAAGATG-AGAAAATG
* * * * * * * *
520665 TCAATGTGCTGATTCACGGTCAGCGACATT-AGTCTTGAAGATGAGAAAAATG
1 CCAATATGCTGATTCAAGGCCAACGACATTGGGTTTTAAAGATGAG-AAAATG
* * * *
520717 CCAATGTGCTGATTCAAGGCCAACGGCATTGGGTTTTAAAGATGACGAAGACG
1 CCAATATGCTGATTCAAGGCCAACGACATTGGGTTTTAAAGATGA-GAAAATG
* * ** **
520770 CCAATATGCTGATTCAAGGCCAGCGATATT-GGACTTAAAGAT--GAAGGTG
1 CCAATATGCTGATTCAAGGCCAACGACATTGGGTTTTAAAGATGAGAAAATG
* * **
520819 CCAATGTGCTGAATCAAGGCCAGTGACATTGG
1 CCAATATGCTGATTCAAGGCCAACGACATTGG
520851 ACTTAAAGAT
Statistics
Matches: 150, Mismatches: 31, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
49 31 0.21
50 2 0.01
51 9 0.06
52 66 0.44
53 41 0.27
54 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.25
Consensus pattern (52 bp):
CCAATATGCTGATTCAAGGCCAACGACATTGGGTTTTAAAGATGAGAAAATG
Found at i:520840 original size:49 final size:48
Alignment explanation
Indices: 520613--520903 Score: 178
Period size: 52 Copynumber: 5.9 Consensus size: 48
520603 GATAAAGGGA
* * * ** *
520613 CCAATATGCTGATTCACGGCCAACGATATTGGGTTTCAAAGATGTAAAAATG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTT-AAAGATG---AAGTG
* * * * * * * *
520665 TCAATGTGCTGATTCACGGTCAGCGACATTAGTCTTGAAGATGAGAAAAATG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT--G--AAGTG
* * * ** *
520717 CCAATGTGCTGATTCAAGGCCAACGGCATTGGGTTTTAAAGATGACGAAGACG
1 CCAATATGCTGATTCAAGGCCAGCGACATT-GGACTTAAAGAT---GAAG-TG
*
520770 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAA-GTG
* * *
520819 CCAATGTGCTGAATCAAGGCCAGTGACATTGGACTT-AA-A-G-A-TG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGTG
* *
520862 CCAATATGCTGGTTCAAGGCCAGCGATATTGGACTTAGAAGA
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTA-AAGA
520904 AGATGCCACC
Statistics
Matches: 193, Mismatches: 37, Indels: 24
0.76 0.15 0.09
Matches are distributed among these distances:
43 33 0.17
45 3 0.02
46 2 0.01
47 1 0.01
48 2 0.01
49 36 0.19
50 1 0.01
51 5 0.03
52 72 0.37
53 37 0.19
54 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (48 bp):
CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGTG
Found at i:520879 original size:43 final size:43
Alignment explanation
Indices: 520764--520903 Score: 163
Period size: 43 Copynumber: 3.1 Consensus size: 43
520754 AAAGATGACG
*
520764 AAGACGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAA
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-A
* * * *
520808 AGATGAAGGTGCCAATGTGCTGAATCAAGGCCAGTGACATTGGACTTA
1 A-A-G-A--TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA
*
520856 AAGATGCCAATATGCTGGTTCAAGGCCAGCGATATTGGACTTA
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA
520899 GAAGA
1 -AAGA
520904 AGATGCCACC
Statistics
Matches: 80, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
43 34 0.43
44 5 0.06
45 2 0.03
46 2 0.03
47 2 0.03
48 2 0.03
49 33 0.41
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.23
Consensus pattern (43 bp):
AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA
Found at i:520977 original size:28 final size:30
Alignment explanation
Indices: 520920--521043 Score: 168
Period size: 29 Copynumber: 4.3 Consensus size: 30
520910 CACCAACTTG
* *
520920 TGTGGGCTTTTGAAAGGGTTG-CACCAACT
1 TGTGGGCTTTTGAAAGGGGTGCCACCGACT
* *
520949 TGTGTGCTTTTG-AA-GGTTGCCACCGACT
1 TGTGGGCTTTTGAAAGGGGTGCCACCGACT
520977 TGTGGGC-TTTGAAAGGGGTGCCACCGACT
1 TGTGGGCTTTTGAAAGGGGTGCCACCGACT
*
521006 TGTGGGC-CTTGAAAGGGGTGCCACCGACT
1 TGTGGGCTTTTGAAAGGGGTGCCACCGACT
521035 TGTGGGCTT
1 TGTGGGCTT
521044 ACAGGAAAAA
Statistics
Matches: 85, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
27 9 0.11
28 17 0.20
29 59 0.69
ACGTcount: A:0.16, C:0.20, G:0.35, T:0.29
Consensus pattern (30 bp):
TGTGGGCTTTTGAAAGGGGTGCCACCGACT
Found at i:521007 original size:57 final size:57
Alignment explanation
Indices: 520920--521043 Score: 162
Period size: 57 Copynumber: 2.2 Consensus size: 57
520910 CACCAACTTG
* * * *
520920 TGTGGGCTTTTGAAAGGGTTGCACCAACTTGTGTGCTTTTG-AA-GGTTGCCACCGACT
1 TGTGGGC-TTTGAAAGGGGTGCACCAACTTGTGGGC-CTTGAAAGGGGTGCCACCGACT
*
520977 TGTGGGCTTTGAAAGGGGTGCCACCGACTTGTGGGCCTTGAAAGGGGTGCCACCGACT
1 TGTGGGCTTTGAAAGGGGTG-CACCAACTTGTGGGCCTTGAAAGGGGTGCCACCGACT
521035 TGTGGGCTT
1 TGTGGGCTT
521044 ACAGGAAAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
56 15 0.25
57 22 0.37
58 22 0.37
ACGTcount: A:0.16, C:0.20, G:0.35, T:0.29
Consensus pattern (57 bp):
TGTGGGCTTTGAAAGGGGTGCACCAACTTGTGGGCCTTGAAAGGGGTGCCACCGACT
Found at i:521088 original size:34 final size:32
Alignment explanation
Indices: 521058--521205 Score: 99
Period size: 35 Copynumber: 4.6 Consensus size: 32
521048 GAAAAAGGGA
* *
521058 TGCCACGGAGGTGTGGGCTTAAAAAGAAAAGG
1 TGCCACAGAGGTGTGGACTTAAAAAGAAAAGG
*
521090 TGCCACAGAGTTGTGGACTT-AAAAG----GG
1 TGCCACAGAGGTGTGGACTTAAAAAGAAAAGG
* *
521117 TGCCACAGAGTTATGGACTTAAAAAAGAAGAAGAG
1 TGCCACAGAGGTGTGGACTT-AAAAAGAA-AAG-G
* * * * *
521152 TGCCACAAAGTTGTGGGCTTTCAAAAGAAAAATG
1 TGCCACAGAGGTGTGGAC-TTAAAAAG-AAAAGG
* **
521186 TGCCACTGACTTGTGGACTT
1 TGCCACAGAGGTGTGGACTT
521206 TTGAAGGTTG
Statistics
Matches: 93, Mismatches: 13, Indels: 19
0.74 0.10 0.15
Matches are distributed among these distances:
27 21 0.23
29 5 0.05
31 5 0.05
32 17 0.18
33 2 0.02
34 16 0.17
35 23 0.25
36 4 0.04
ACGTcount: A:0.34, C:0.15, G:0.29, T:0.22
Consensus pattern (32 bp):
TGCCACAGAGGTGTGGACTTAAAAAGAAAAGG
Found at i:521121 original size:27 final size:26
Alignment explanation
Indices: 521084--521140 Score: 96
Period size: 27 Copynumber: 2.2 Consensus size: 26
521074 GCTTAAAAAG
*
521084 AAAAGGTGCCACAGAGTTGTGGACTT
1 AAAAGGTGCCACAGAGTTATGGACTT
521110 AAAAGGGTGCCACAGAGTTATGGACTT
1 AAAA-GGTGCCACAGAGTTATGGACTT
521137 AAAA
1 AAAA
521141 AAGAAGAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 4 0.14
27 25 0.86
ACGTcount: A:0.37, C:0.14, G:0.28, T:0.21
Consensus pattern (26 bp):
AAAAGGTGCCACAGAGTTATGGACTT
Found at i:521166 original size:62 final size:60
Alignment explanation
Indices: 521050--521167 Score: 157
Period size: 59 Copynumber: 1.9 Consensus size: 60
521040 GCTTACAGGA
* * * *
521050 AAAAGGGATGCCACGGAGGTGTGGGCTTAAAAAGAAAAGGTGCCACAGAGTTGTGGACTT
1 AAAAGGGATGCCACAGAGGTATGGACTTAAAAAGAAAAGGTGCCACAAAGTTGTGGACTT
*
521110 AAAAGGG-TGCCACAGAGTTATGGACTTAAAAAAGAAGAAGAGTGCCACAAAGTTGTGG
1 AAAAGGGATGCCACAGAGGTATGGACTT-AAAAAGAA-AAG-GTGCCACAAAGTTGTGG
521168 GCTTTCAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
59 16 0.32
60 15 0.30
61 3 0.06
62 16 0.32
ACGTcount: A:0.37, C:0.13, G:0.32, T:0.18
Consensus pattern (60 bp):
AAAAGGGATGCCACAGAGGTATGGACTTAAAAAGAAAAGGTGCCACAAAGTTGTGGACTT
Found at i:521226 original size:28 final size:28
Alignment explanation
Indices: 521186--521325 Score: 165
Period size: 28 Copynumber: 5.0 Consensus size: 28
521176 AAGAAAAATG
* * *
521186 TGCCACTGACTTGTGGACTTTTGAAGGT
1 TGCCACTGACTTGTGGGCTTTTGAAAGA
*
521214 TGCCACTGACTTGTGGGCTTTGGAAAAGA
1 TGCCACTGACTTGTGGGCTTTTG-AAAGA
* * * *
521243 TGCCACTAACTTGTGGACTTTTGAAGGT
1 TGCCACTGACTTGTGGGCTTTTGAAAGA
*
521271 TGCCACTGACTTGTGGGCTTTGGAAAAGA
1 TGCCACTGACTTGTGGGCTTTTG-AAAGA
*
521300 TG-CACTAACTTGTGGGCTTTTGAAAG
1 TGCCACTGACTTGTGGGCTTTTGAAAG
521326 GTGAGGAACG
Statistics
Matches: 94, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
27 4 0.04
28 62 0.66
29 28 0.30
ACGTcount: A:0.22, C:0.17, G:0.29, T:0.32
Consensus pattern (28 bp):
TGCCACTGACTTGTGGGCTTTTGAAAGA
Found at i:521327 original size:57 final size:57
Alignment explanation
Indices: 521186--521323 Score: 251
Period size: 57 Copynumber: 2.4 Consensus size: 57
521176 AAGAAAAATG
*
521186 TGCCACTGACTTGTGGACTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGA
1 TGCCACTAACTTGTGGACTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGA
521243 TGCCACTAACTTGTGGACTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGA
1 TGCCACTAACTTGTGGACTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGA
*
521300 TG-CACTAACTTGTGGGCTTTTGAA
1 TGCCACTAACTTGTGGACTTTTGAA
521324 AGGTGAGGAA
Statistics
Matches: 79, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
56 21 0.27
57 58 0.73
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (57 bp):
TGCCACTAACTTGTGGACTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGA
Found at i:522777 original size:14 final size:15
Alignment explanation
Indices: 522763--522843 Score: 58
Period size: 15 Copynumber: 5.2 Consensus size: 15
522753 CTTTTTATTG
522763 TTTTTTTTTGTTTGT
1 TTTTTTTTTGTTTGT
522778 TTTTTTTTTGTTT-T
1 TTTTTTTTTGTTTGT
* *
522792 TTGTTTTATT-TTTCT
1 TT-TTTTTTTGTTTGT
* *
522807 TCTTCTCCTTTTTTTTTGG
1 T-TT-T--TTTTTGTTTGT
*
522826 TTTTTTTTTGTTTAT
1 TTTTTTTTTGTTTGT
522841 TTT
1 TTT
522844 GTGGAGGACG
Statistics
Matches: 52, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
14 6 0.12
15 33 0.63
16 2 0.04
17 1 0.02
18 6 0.12
19 4 0.08
ACGTcount: A:0.02, C:0.06, G:0.09, T:0.83
Consensus pattern (15 bp):
TTTTTTTTTGTTTGT
Found at i:522786 original size:18 final size:19
Alignment explanation
Indices: 522763--522804 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
522753 CTTTTTATTG
522763 TTTTTT-TTTGTTTGTTTT-
1 TTTTTTGTTT-TTTGTTTTA
522781 TTTTTTGTTTTTTGTTTTA
1 TTTTTTGTTTTTTGTTTTA
522800 TTTTT
1 TTTTT
522805 CTTCTTCTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.02, C:0.00, G:0.10, T:0.88
Consensus pattern (19 bp):
TTTTTTGTTTTTTGTTTTA
Found at i:522803 original size:11 final size:10
Alignment explanation
Indices: 522754--522843 Score: 65
Period size: 11 Copynumber: 8.6 Consensus size: 10
522744 ATCCGGACCC
*
522754 TTTTTATTGT
1 TTTTTTTTGT
522764 TTTTTTTTGT
1 TTTTTTTTGT
*
522774 TTGTTTTTTTT
1 TT-TTTTTTGT
522785 TTGTTTTTTGT
1 TT-TTTTTTGT
*
522796 TTTATTTTTCT
1 TTT-TTTTTGT
* **
522807 TCTTCTCCT-T
1 T-TTTTTTTGT
*
522817 TTTTTTTGGT
1 TTTTTTTTGT
522827 TTTTTTTTGT
1 TTTTTTTTGT
522837 TTATTTT
1 TT-TTTT
522844 GTGGAGGACG
Statistics
Matches: 63, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
9 3 0.05
10 26 0.41
11 32 0.51
12 2 0.03
ACGTcount: A:0.03, C:0.06, G:0.09, T:0.82
Consensus pattern (10 bp):
TTTTTTTTGT
Found at i:535521 original size:13 final size:13
Alignment explanation
Indices: 535503--535528 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
535493 TTTGGGATGA
535503 TGAAACAGCCCGT
1 TGAAACAGCCCGT
535516 TGAAACAGCCCGT
1 TGAAACAGCCCGT
535529 GGTATAAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.31, G:0.23, T:0.15
Consensus pattern (13 bp):
TGAAACAGCCCGT
Found at i:536610 original size:80 final size:80
Alignment explanation
Indices: 536519--536997 Score: 427
Period size: 80 Copynumber: 6.0 Consensus size: 80
536509 ACCAACCCCC
* * * * * ** **
536519 CGTTTTCACTTCTAAAACATCGAATTTTTCATTTTTGGGGATACTCTTACCCCAACATTTTCGAA
1 CGTTTTTACTTCTAAAACACCAAAATTTTCATCTCAGGGGATACTCCAACCCCAACATTTTCGAA
536584 GGGATACTCCAACCT
66 GGGATACTCCAACCT
* * *
536599 TGTTTTTACTTCTAAAACACC-AAATTTCTCATCTCAGGGGATACTCCAACCCCACCATTTCCG-
1 CGTTTTTACTTCTAAAACACCAAAATTT-TCATCTCAGGGGATACTCCAACCCCAACATTTTCGA
536662 AGGGCATACTCCAATCC-
65 AGGG-ATACTCCAA-CCT
* * * *
536679 CATTTTTACTTCTAAAACACCAAAATTTTCATTTCAAGGAATACTCCAACCCC-ACAATTTTCGA
1 CGTTTTTACTTCTAAAACACCAAAATTTTCATCTCAGGGGATACTCCAACCCCAAC-ATTTTCGA
*
536743 AGGGATACTCTAA-CT
65 AGGGATACTCCAACCT
* ** * * * * * *
536758 ACGTTTTTATTTCCCAAACACCAAAATTTTGATCTCTA-GGGATACTCCAACTCCATC-GTCTCC
1 -CGTTTTTACTTCTAAAACACCAAAATTTTCATCTC-AGGGGATACTCCAACCCCAACATTTTCG
*
536821 AAGGGGATACTCCAACCC
64 AA-GGGATACTCCAACCT
* * * * * * * *
536839 CATTTTTACTTGTAAAACATCAAAATTTTCATCTCAGGAGATACTCTAGCCCCATCATTTTTG-A
1 CGTTTTTACTTCTAAAACACCAAAATTTTCATCTCAGGGGATACTCCAACCCCAACATTTTCGAA
*
536903 GAGGATAATCCAACCT
66 G-GGATACTCCAACCT
* * * * *
536919 CGTTTTTACTTCCAAAACACCAAAATTTACATCTTC-GAGGATACTCCAACCCCACCATCTTCGA
1 CGTTTTTACTTCTAAAACACCAAAATTTTCATC-TCAGGGGATACTCCAACCCCAACATTTTCGA
* *
536983 GGGGATACTTCAACC
65 AGGGATACTCCAACC
536998 CTGATTTTCA
Statistics
Matches: 317, Mismatches: 65, Indels: 34
0.76 0.16 0.08
Matches are distributed among these distances:
78 1 0.00
79 17 0.05
80 279 0.88
81 20 0.06
ACGTcount: A:0.30, C:0.28, G:0.11, T:0.31
Consensus pattern (80 bp):
CGTTTTTACTTCTAAAACACCAAAATTTTCATCTCAGGGGATACTCCAACCCCAACATTTTCGAA
GGGATACTCCAACCT
Found at i:536710 original size:160 final size:159
Alignment explanation
Indices: 536516--536998 Score: 539
Period size: 160 Copynumber: 3.0 Consensus size: 159
536506 TACACCAACC
* * * * **
536516 CCCCGTTTTCACTTCTAAAACATCGAATTTTTCATTTTTGGGGATACTCTTACCCCAACATTTTC
1 CCCCATTTTTACTTCTAAAACATCAAAATTTTCATTTCAGGGGATACTC-TACCCCAACATTTTC
* *
536581 GAAGGGATACTCCAACCTTGTTTTTACTTCTAAAACACC-AAATTTCTCATCTCAGGGGATACTC
65 GAAGGGATACTCCAACCTCGTTTTTACTTCCAAAACACCAAAATTT-TCATCTCAGGGGATACTC
*
536645 CAACCCCACCATTTCCGAGGGCATACTCCAA
129 CAACCCCACCATTTCCGAGGGGATACTCCAA
* * * * *
536676 TCCCATTTTTACTTCTAAAACACCAAAATTTTCATTTCAAGGAATACTCCAACCCC-ACAATTTT
1 CCCCATTTTTACTTCTAAAACATCAAAATTTTCATTTCAGGGGATACT-CTACCCCAAC-ATTTT
* * * *
536740 CGAAGGGATACTCTAA-CTACGTTTTTATTTCCCAAACACCAAAATTTTGATCTCTA-GGGATAC
64 CGAAGGGATACTCCAACCT-CGTTTTTACTTCCAAAACACCAAAATTTTCATCTC-AGGGGATAC
* * * * *
536803 TCCAACTCCATCGTCTCCAAGGGGATACTCCAA
127 TCCAACCCCACCATTTCCGAGGGGATACTCCAA
* * * * *
536836 CCCCATTTTTACTTGTAAAACATCAAAATTTTCATCTCAGGAGATACTCTAGCCCCATCATTTTT
1 CCCCATTTTTACTTCTAAAACATCAAAATTTTCATTTCAGGGGATACTCTA-CCCCAACATTTTC
* * *
536901 G-AGAGGATAATCCAACCTCGTTTTTACTTCCAAAACACCAAAATTTACATCTTC-GAGGATACT
65 GAAG-GGATACTCCAACCTCGTTTTTACTTCCAAAACACCAAAATTTTCATC-TCAGGGGATACT
*
536964 CCAACCCCACCATCTT-CGAGGGGATACTTCAA
128 CCAACCCCACCAT-TTCCGAGGGGATACTCCAA
536996 CCC
1 CCC
536999 TGATTTTCAC
Statistics
Matches: 265, Mismatches: 46, Indels: 24
0.79 0.14 0.07
Matches are distributed among these distances:
159 8 0.03
160 243 0.92
161 14 0.05
ACGTcount: A:0.30, C:0.29, G:0.11, T:0.31
Consensus pattern (159 bp):
CCCCATTTTTACTTCTAAAACATCAAAATTTTCATTTCAGGGGATACTCTACCCCAACATTTTCG
AAGGGATACTCCAACCTCGTTTTTACTTCCAAAACACCAAAATTTTCATCTCAGGGGATACTCCA
ACCCCACCATTTCCGAGGGGATACTCCAA
Found at i:541986 original size:24 final size:24
Alignment explanation
Indices: 541953--542038 Score: 82
Period size: 24 Copynumber: 3.6 Consensus size: 24
541943 TTATGTTGCG
* * *
541953 GGAGTCATGCCAAAGGAAGTTCCA
1 GGAGTTATGCCAAAAGATGTTCCA
* *
541977 GGAGTTATGCCAAAAGTTGTTGCA
1 GGAGTTATGCCAAAAGATGTTCCA
** * *
542001 TAAGTTGTGCCAAAAGATGTTTCA
1 GGAGTTATGCCAAAAGATGTTCCA
*
542025 AGAGTTATGCCAAA
1 GGAGTTATGCCAAA
542039 GGTTGTCTTA
Statistics
Matches: 49, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.26
Consensus pattern (24 bp):
GGAGTTATGCCAAAAGATGTTCCA
Found at i:542030 original size:48 final size:48
Alignment explanation
Indices: 541960--542089 Score: 129
Period size: 48 Copynumber: 2.7 Consensus size: 48
541950 GCGGGAGTCA
* * * * *
541960 TGCCAAAGGAAGTTCCAGGAGTTATGCCAAAAGTTGT-TGCATAAGTTG
1 TGCCAAAAGATGTTTCAAGAGTTATGCCAAAAGTTGTCT-CAGAAGTTG
* *
542008 TGCCAAAAGATGTTTCAAGAGTTATGCCAAAGGTTGTCTTAGAAGTTG
1 TGCCAAAAGATGTTTCAAGAGTTATGCCAAAAGTTGTCTCAGAAGTTG
* * * *
542056 TGCCAAATGTTGGGTT-AAGAGTTATGCTAAAAGT
1 TGCCAAAAGAT-GTTTCAAGAGTTATGCCAAAAGT
542090 ACTAGGAGCT
Statistics
Matches: 68, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
48 64 0.94
49 4 0.06
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (48 bp):
TGCCAAAAGATGTTTCAAGAGTTATGCCAAAAGTTGTCTCAGAAGTTG
Found at i:542078 original size:24 final size:24
Alignment explanation
Indices: 542024--542082 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
542014 AAGATGTTTC
*
542024 AAGAGTTATGCCAAAGGTTGTCTT
1 AAGAGTTATGCCAAAGGTTGGCTT
* * *
542048 -AGAAGTTGTGCCAAATGTTGGGTT
1 AAG-AGTTATGCCAAAGGTTGGCTT
542072 AAGAGTTATGC
1 AAGAGTTATGC
542083 TAAAAGTACT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
23 2 0.07
24 24 0.86
25 2 0.07
ACGTcount: A:0.29, C:0.10, G:0.29, T:0.32
Consensus pattern (24 bp):
AAGAGTTATGCCAAAGGTTGGCTT
Found at i:544945 original size:15 final size:15
Alignment explanation
Indices: 544905--544946 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
544895 ATTAAATTAG
*
544905 TATATATGTTTTAAA
1 TATATATTTTTTAAA
*
544920 T-TAATAATTTTTAAA
1 TAT-ATATTTTTTAAA
544935 TATATATTTTTT
1 TATATATTTTTT
544947 TAAAAATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
14 1 0.05
15 20 0.91
16 1 0.05
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (15 bp):
TATATATTTTTTAAA
Found at i:545601 original size:45 final size:45
Alignment explanation
Indices: 545510--545611 Score: 125
Period size: 45 Copynumber: 2.3 Consensus size: 45
545500 TGGATATTGC
* * *
545510 CTCGCGAGTAATATCTTGCATTAAAAAATACATAGCAGATATTAT
1 CTCGCGAGTAATACCCTGCATTAAAAAATACATAGCAGATAATAT
* * **
545555 CTCGCGAATAATACCCTGCATTAAATAATACCAT-GTGGATAATAT
1 CTCGCGAGTAATACCCTGCATTAAAAAATA-CATAGCAGATAATAT
545600 CTCGCGAGTAAT
1 CTCGCGAGTAAT
545612 GCCTTGCAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
45 45 0.94
46 3 0.06
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (45 bp):
CTCGCGAGTAATACCCTGCATTAAAAAATACATAGCAGATAATAT
Found at i:545853 original size:4 final size:4
Alignment explanation
Indices: 545839--545882 Score: 61
Period size: 4 Copynumber: 10.5 Consensus size: 4
545829 CTCTATACTT
*
545839 TTTA TTTTA TTTA TTTA TTTA TTTA TTTA TTATG TTTA TTTA TT
1 TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TT-TA TTTA TTTA TT
545883 ATTATTATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
4 29 0.81
5 7 0.19
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:545857 original size:13 final size:13
Alignment explanation
Indices: 545839--545892 Score: 67
Period size: 13 Copynumber: 4.2 Consensus size: 13
545829 CTCTATACTT
545839 TTTATTTTATTTA
1 TTTATTTTATTTA
545852 TTTA-TTTATTTA
1 TTTATTTTATTTA
* *
545864 TTTATTATGTTTA
1 TTTATTTTATTTA
545877 TTTATTATTA-TTA
1 TTTATT-TTATTTA
545890 TTT
1 TTT
545893 CATTCAATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
12 12 0.34
13 22 0.63
14 1 0.03
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:549443 original size:21 final size:21
Alignment explanation
Indices: 549418--549461 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
549408 CAATTAATAT
* *
549418 CATGTCTGAATGGTCAAAAGC
1 CATGTCAGAATGATCAAAAGC
*
549439 CATGTCAGGATGATCAAAAGC
1 CATGTCAGAATGATCAAAAGC
549460 CA
1 CA
549462 CATTAACAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.20
Consensus pattern (21 bp):
CATGTCAGAATGATCAAAAGC
Found at i:550914 original size:2 final size:2
Alignment explanation
Indices: 550909--550954 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
550899 ATATTACACG
550909 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
550951 GA GA
1 GA GA
550955 AGCTAGGTCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:552298 original size:2 final size:2
Alignment explanation
Indices: 552291--552321 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
552281 TATATTTTAT
552291 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
552322 GGAAATTTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:558497 original size:16 final size:16
Alignment explanation
Indices: 558476--558528 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
558466 TAAGGTTCTG
558476 ATCATTTTAAATTCGA
1 ATCATTTTAAATTCGA
*
558492 ATCATTTTAAATTCGG
1 ATCATTTTAAATTCGA
** *
558508 ATCATTTCGAATTTGA
1 ATCATTTTAAATTCGA
558524 ATCAT
1 ATCAT
558529 ATGGATTGTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.43
Consensus pattern (16 bp):
ATCATTTTAAATTCGA
Found at i:560738 original size:3 final size:3
Alignment explanation
Indices: 560730--560758 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
560720 ATGCTGCAGA
560730 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
560759 AGAAAGAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:561106 original size:3 final size:3
Alignment explanation
Indices: 561100--561134 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
561090 TTATGATAGC
561100 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
561135 ATTGAAGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:561253 original size:16 final size:16
Alignment explanation
Indices: 561232--561283 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 16
561222 TTTATATAAA
561232 TTAAATAAAAATTTAT
1 TTAAATAAAAATTTAT
*
561248 TTAAAT-ATAA---A-
1 TTAAATAAAAATTTAT
561259 TTAAATAAAAATTTAT
1 TTAAATAAAAATTTAT
561275 TT-AATAAAA
1 TTAAATAAAA
561284 TTAAATATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 11
0.69 0.05 0.26
Matches are distributed among these distances:
11 6 0.21
12 4 0.14
15 11 0.38
16 8 0.28
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TTAAATAAAAATTTAT
Found at i:561258 original size:27 final size:26
Alignment explanation
Indices: 561219--561290 Score: 119
Period size: 27 Copynumber: 2.8 Consensus size: 26
561209 TATGAATTTA
*
561219 TATTTTATATAAATTAAATAAAAATT
1 TATTTAATATAAATTAAATAAAAATT
561245 TATTTAAATATAAATTAAATAAAAATT
1 TATTT-AATATAAATTAAATAAAAATT
561272 TATTTAATA-AAATTAAATA
1 TATTTAATATAAATTAAATA
561291 TTAAACATAT
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
25 10 0.23
26 9 0.20
27 25 0.57
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
TATTTAATATAAATTAAATAAAAATT
Found at i:565425 original size:9 final size:9
Alignment explanation
Indices: 565413--565497 Score: 51
Period size: 9 Copynumber: 10.0 Consensus size: 9
565403 GTAATTAAAA
*
565413 TAATCTATT
1 TAATATATT
565422 TAATATATT
1 TAATATATT
565431 T-ATAT-TT
1 TAATATATT
565438 ATATATATATT
1 -TA-ATATATT
*
565449 ATATTATATT
1 -TAATATATT
565459 T--T-TATT
1 TAATATATT
*
565465 TAAAAT-TT
1 TAATATATT
565473 TAATATATT
1 TAATATATT
565482 T--TATATT
1 TAATATATT
*
565489 TACTATATT
1 TAATATATT
565498 GATATAAAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
6 5 0.08
7 10 0.16
8 12 0.19
9 20 0.32
10 10 0.16
11 5 0.08
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (9 bp):
TAATATATT
Found at i:565436 original size:6 final size:6
Alignment explanation
Indices: 565425--565466 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
565415 ATCTATTTAA
* *
565425 TATATT TATATT TATATA TATA-T TATA-T TATATT TTTATT TA
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TA
565467 AAATTTTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
5 9 0.29
6 22 0.71
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
TATATT
Found at i:565503 original size:24 final size:23
Alignment explanation
Indices: 565421--565490 Score: 68
Period size: 28 Copynumber: 2.8 Consensus size: 23
565411 AATAATCTAT
*
565421 TTAATATATTTATATTTATATATATA
1 TTAATATATTTTTATTTA-A-A-ATA
*
565447 TTATATTATATTTTTATTTAAAATT
1 TTA-A-TATATTTTTATTTAAAATA
565472 TTAATATATTTTATATTTA
1 TTAATATATTTT-TATTTA
565491 CTATATTGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
23 8 0.21
24 7 0.18
25 5 0.13
26 4 0.10
27 2 0.05
28 13 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
TTAATATATTTTTATTTAAAATA
Found at i:566690 original size:2 final size:2
Alignment explanation
Indices: 566683--566707 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
566673 TATTGCCTAC
566683 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
566708 CATGTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:567307 original size:6 final size:6
Alignment explanation
Indices: 567296--567320 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
567286 TTAAAATATT
567296 TTAATA TTAATA TTAATA TTAATA T
1 TTAATA TTAATA TTAATA TTAATA T
567321 ATTATTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTAATA
Found at i:570939 original size:52 final size:52
Alignment explanation
Indices: 570848--570982 Score: 150
Period size: 52 Copynumber: 2.6 Consensus size: 52
570838 AAAAAAGATG
* * * *
570848 TATCGATACATT-TTTATTGTATTGATACATTTTAGGTTTTTGA-TCCAAATA
1 TATCGATACATTCTTCATTTTATAGATACATTTTAGGTTTTTAACT-CAAATA
* *
570899 TATCGATACATTCTTCATTTTATCGATACATTTT-GAGTTTTTAACTCAAATG
1 TATCGATACATTCTTCATTTTATAGATACATTTTAG-GTTTTTAACTCAAATA
* * *
570951 TATCGATATATTCTTCAATTTATAAATACATT
1 TATCGATACATTCTTCATTTTATAGATACATT
570983 CAGTTAAATT
Statistics
Matches: 72, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
51 13 0.18
52 58 0.81
53 1 0.01
ACGTcount: A:0.31, C:0.13, G:0.09, T:0.47
Consensus pattern (52 bp):
TATCGATACATTCTTCATTTTATAGATACATTTTAGGTTTTTAACTCAAATA
Found at i:573258 original size:3 final size:3
Alignment explanation
Indices: 573247--573288 Score: 75
Period size: 3 Copynumber: 13.7 Consensus size: 3
573237 AAAATAAAAA
573247 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
573289 CAAGTGATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:586573 original size:13 final size:12
Alignment explanation
Indices: 586555--586608 Score: 54
Period size: 12 Copynumber: 4.2 Consensus size: 12
586545 TACTATGCTT
586555 AAAAAAAGTAAAAA
1 AAAAAAAG--AAAA
586569 AAAAAAAGAAAGA
1 AAAAAAAGAAA-A
**
586582 AAAAAATTAAAA
1 AAAAAAAGAAAA
*
586594 AAAGAAAGAAAA
1 AAAAAAAGAAAA
586606 AAA
1 AAA
586609 TCAGATGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
12 16 0.47
13 10 0.29
14 8 0.24
ACGTcount: A:0.85, C:0.00, G:0.09, T:0.06
Consensus pattern (12 bp):
AAAAAAAGAAAA
Found at i:586595 original size:21 final size:21
Alignment explanation
Indices: 586569--586609 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
586559 AAAGTAAAAA
586569 AAAAAAAGAAAGAAAAAAATT
1 AAAAAAAGAAAGAAAAAAATT
586590 AAAAAAAGAAAGAAAAAAAT
1 AAAAAAAGAAAGAAAAAAAT
586610 CAGATGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (21 bp):
AAAAAAAGAAAGAAAAAAATT
Found at i:588307 original size:42 final size:42
Alignment explanation
Indices: 588159--589080 Score: 488
Period size: 42 Copynumber: 22.1 Consensus size: 42
588149 AACCTTCTTA
* ** * * * *
588159 TTTACCCTTTGTCTGTCGGTCGGCTTAGACTTGGGAGACTTC
1 TTTACCCTTTGTCTGCCCATCGGATTTGACTCGAGAGACTTC
* * * * * * * *
588201 TTTACCTTTTGTCTACCCATAGAATTTAACTTGGGAGACTAC
1 TTTACCCTTTGTCTGCCCATCGGATTTGACTCGAGAGACTTC
* * * *
588243 TTTACCCTTTCTTTGCCTATCGGATTTGACTTGAGAGACTTC
1 TTTACCCTTTGTCTGCCCATCGGATTTGACTCGAGAGACTTC
* * * * * *
588285 TTTACCCCTTGTCTGCCCATCGGCTTTGACCCAAAAGA-TTT
1 TTTACCCTTTGTCTGCCCATCGGATTTGACTCGAGAGACTTC
* * * *
588326 TTTACCCTTTTTTTGCCCATCGGCTTTGAC-CTGAAAGACTTC
1 TTTACCCTTTGTCTGCCCATCGGATTTGACTC-GAGAGACTTC
* * ** * * *
588368 TTTACCGTTTGTCTACTTATTGGCTTTGACTCGAAAGACTTC
1 TTTACCCTTTGTCTGCCCATCGGATTTGACTCGAGAGACTTC
* * * * * *
588410 TTTACCTTTTGTCAG-CTATCAGCTTTGAC-CCAGGAGACTTC
1 TTTACCCTTTGTCTGCCCATCGGATTTGACTCGA-GAGACTTC
* * * * * *
588451 TTTACCCCTTATTTGCCCATC-AATTTTGAC-CCAGGAGACTTA
1 TTTACCCTTTGTCTGCCCATCGGA-TTTGACTCGA-GAGACTTC
* * * * *
588493 TTTACCCTTTGTCTACCCGTCGGCTTTCA-TCCGGGAGACTTC
1 TTTACCCTTTGTCTGCCCATCGGATTTGACT-CGAGAGACTTC
* * * * * * *
588535 TTTGCCCTTTGTCTACTCGTC-AACTTTGA-TCCAG-GAATTTC
1 TTTACCCTTTGTCTGCCCATCGGA-TTTGACTCGAGAG-ACTTC
* * * *
588576 TTTA-CC-TTGTCTGCCCGTCGGCTTTGACCCGAGAGACTTT
1 TTTACCCTTTGTCTGCCCATCGGATTTGACTCGAGAGACTTC
* ** ** * *
588616 TTTACCTTTTGTCTGCCTGT-TAACTTTGACCCGAGAGATTTC
1 TTTACCCTTTGTCTGCCCATCGGA-TTTGACTCGAGAGACTTC
* * * *
588658 TTTACCCTTTGTCTGCCCATCAGCTTTGACTCG-GAAGATTTT
1 TTTACCCTTTGTCTGCCCATCGGATTTGACTCGAG-AGACTTC
* *
588700 TTTACCCTTTATCTGCCCGTC-GACTTTGACTCGAGAGACTTC
1 TTTACCCTTTGTCTGCCCATCGGA-TTTGACTCGAGAGACTTC
* *
588742 TTTACCCCTTGTCTGCCTATC-GACTTTGACTCGAGAGACTTC
1 TTTACCCTTTGTCTGCCCATCGGA-TTTGACTCGAGAGACTTC
* * *
588784 TTTACCCCTTGTTTGCCCATC-GACTTTGACCCTG-GAGACTTC
1 TTTACCCTTTGTCTGCCCATCGGA-TTTGACTC-GAGAGACTTC
* ** * *
588826 TTTACTCTTTGTCTGCCTGTCGGCTTTGAC-CTAGGAGACTTC
1 TTTACCCTTTGTCTGCCCATCGGATTTGACTCGA-GAGACTTC
* *** * * *
588868 TTTACCCTTTGTCTACTTGT-TGACTTTGACTAGAAAGACTTC
1 TTTACCCTTTGTCTGCCCATCGGA-TTTGACTCGAGAGACTTC
* * * *
588910 TTTACCTTTTGTCTGCTCAT-TGACTTTGAC-CTAGGAGACTTC
1 TTTACCCTTTGTCTGCCCATCGGA-TTTGACTCGA-GAGACTTC
* * * *
588952 TTTACCTTTTGTCTGCCCATC-GACTTTGACCCGAGAAACTTT
1 TTTACCCTTTGTCTGCCCATCGGA-TTTGACTCGAGAGACTTC
* * * *
588994 TTTACCCCTTGTCTACCCATC-AATTTTGACTCGAGAGACTTT
1 TTTACCCTTTGTCTGCCCATCGGA-TTTGACTCGAGAGACTTC
* * * * * * *
589036 TTTTCTCTTTATCTGCCCGTCGGCTTAGACTCGAGAGACTCC
1 TTTACCCTTTGTCTGCCCATCGGATTTGACTCGAGAGACTTC
589078 TTT
1 TTT
589081 CTCTTTTGCT
Statistics
Matches: 690, Mismatches: 159, Indels: 62
0.76 0.17 0.07
Matches are distributed among these distances:
39 16 0.02
40 16 0.02
41 78 0.11
42 572 0.83
43 8 0.01
ACGTcount: A:0.17, C:0.27, G:0.17, T:0.39
Consensus pattern (42 bp):
TTTACCCTTTGTCTGCCCATCGGATTTGACTCGAGAGACTTC
Found at i:588746 original size:126 final size:125
Alignment explanation
Indices: 588192--589053 Score: 691
Period size: 126 Copynumber: 6.9 Consensus size: 125
588182 CTTAGACTTG
* * * * * * * * * *
588192 GGAGACTTCTTTACCTTTTGTCTACCCATAGAATTTAACTTGGGAGACTACTTTACCCTTTCTTT
1 GGAGACTTCTTTACCCTTTGTCTGCCCATCGACTTTGAC-CGAGAGACTTCTTTACCCTTTGTCT
* * * * * *
588257 GCCTATCGGA-TTTGACTTGAGAGACTTCTTTACCCCTTGTCTGCCCATCGGCTTTGACCCA
65 ACCTGT-TGACTTTGACTCGAGAGACTTCTTTACCCTTTGTCTGCCCATCAGCTTTGACCCA
** * * * * * *
588318 AAAGA-TTTTTTACCCTTTTTTTGCCCATCGGCTTTGACCTGAAAGACTTCTTTACCGTTTGTCT
1 GGAGACTTCTTTACCCTTTGTCTGCCCATCGACTTTGACC-GAGAGACTTCTTTACCCTTTGTCT
* * * * * * *
588382 ACTTATTGGCTTTGACTCGAAAGACTTCTTTACCTTTTGTCAG-CTATCAGCTTTGACCCA
65 ACCTGTTGACTTTGACTCGAGAGACTTCTTTACCCTTTGTCTGCCCATCAGCTTTGACCCA
* * * * * * *
588442 GGAGACTTCTTTACCCCTTATTTGCCCATCAATTTTGACCCAGGAGACTTATTTACCCTTTGTCT
1 GGAGACTTCTTTACCCTTTGTCTGCCCATCGACTTTGACCGA-GAGACTTCTTTACCCTTTGTCT
* * * * * * * * * * *
588507 ACCCGTCGGCTTTCA-TCCGGGAGACTTCTTTGCCCTTTGTCTACTCGTCAACTTTGATCCA
65 ACCTGTTGACTTTGACT-CGAGAGACTTCTTTACCCTTTGTCTGCCCATCAGCTTTGACCCA
* * * * *
588568 GGA-ATTTCTTTA-CC-TTGTCTGCCCGTCGGCTTTGACCCGAGAGACTTTTTTACCTTTTGTCT
1 GGAGACTTCTTTACCCTTTGTCTGCCCATCGACTTTGA-CCGAGAGACTTCTTTACCCTTTGTCT
* * * * *
588630 GCCTGTTAACTTTGACCCGAGAGATTTCTTTACCCTTTGTCTGCCCATCAGCTTTGACTC-
65 ACCTGTTGACTTTGACTCGAGAGACTTCTTTACCCTTTGTCTGCCCATCAGCTTTGACCCA
* * * * *
588690 GGAAGATTTTTTTACCCTTTATCTGCCCGTCGACTTTGACTCGAGAGACTTCTTTACCCCTTGTC
1 GG-AGACTTCTTTACCCTTTGTCTGCCCATCGACTTTGAC-CGAGAGACTTCTTTACCCTTTGTC
* * * * * *
588755 TGCCTATCGACTTTGACTCGAGAGACTTCTTTACCCCTTGTTTGCCCATC-GACTTTGACCCT
64 TACCTGTTGACTTTGACTCGAGAGACTTCTTTACCCTTTGTCTGCCCATCAG-CTTTGACCCA
* ** * *
588817 GGAGACTTCTTTACTCTTTGTCTGCCTGTCGGCTTTGACCTAGGAGACTTCTTTACCCTTTGTCT
1 GGAGACTTCTTTACCCTTTGTCTGCCCATCGACTTTGACCGA-GAGACTTCTTTACCCTTTGTCT
* * * * * * *
588882 ACTTGTTGACTTTGACTAGAAAGACTTCTTTACCTTTTGTCTGCTCAT-TGACTTTGACCTA
65 ACCTGTTGACTTTGACTCGAGAGACTTCTTTACCCTTTGTCTGCCCATCAG-CTTTGACCCA
* * * *
588943 GGAGACTTCTTTACCTTTTGTCTGCCCATCGACTTTGACCCGAGAAACTTTTTTACCCCTTGTCT
1 GGAGACTTCTTTACCCTTTGTCTGCCCATCGACTTTGA-CCGAGAGACTTCTTTACCCTTTGTCT
** ** * * * * *
589008 ACCCATCAATTTTGACTCGAGAGACTTTTTTTCTCTTTATCTGCCC
65 ACCTGTTGACTTTGACTCGAGAGACTTCTTTACCCTTTGTCTGCCC
589054 GTCGGCTTAG
Statistics
Matches: 578, Mismatches: 140, Indels: 36
0.77 0.19 0.05
Matches are distributed among these distances:
122 2 0.00
123 79 0.14
124 34 0.06
125 165 0.29
126 293 0.51
127 5 0.01
ACGTcount: A:0.18, C:0.27, G:0.16, T:0.39
Consensus pattern (125 bp):
GGAGACTTCTTTACCCTTTGTCTGCCCATCGACTTTGACCGAGAGACTTCTTTACCCTTTGTCTA
CCTGTTGACTTTGACTCGAGAGACTTCTTTACCCTTTGTCTGCCCATCAGCTTTGACCCA
Found at i:589032 original size:84 final size:84
Alignment explanation
Indices: 588159--589080 Score: 598
Period size: 84 Copynumber: 11.0 Consensus size: 84
588149 AACCTTCTTA
* ** * * * * * *
588159 TTTACCCTTTGTCTGTCGGTCGGCTTAGACTTGGGAGACTTCTTTACCTTTTGTCTACCCATAGA
1 TTTACCCTTTGTCTGCCCATCGGCTTTGACTCGAGAGACTTCTTTACCCTTTGTCTGCCCATCGA
* * ** * * *
588224 ATTTAACTTGGGAGACTAC
66 CTTTGACCCGAGAAACTTC
* * * * * * *
588243 TTTACCCTTTCTTTGCCTATCGGATTTGACTTGAGAGACTTCTTTACCCCTTGTCTGCCCATCGG
1 TTTACCCTTTGTCTGCCCATCGGCTTTGACTCGAGAGACTTCTTTACCCTTTGTCTGCCCATCGA
* *
588308 CTTTGACCC-A-AAAGATTT
66 CTTTGACCCGAGAAA-CTTC
* * * * * ** *
588326 TTTACCCTTTTTTTGCCCATCGGCTTTGAC-CTGAAAGACTTCTTTACCGTTTGTCTACTTATTG
1 TTTACCCTTTGTCTGCCCATCGGCTTTGACTC-GAGAGACTTCTTTACCCTTTGTCTGCCCATCG
* *
588390 GCTTTGACTCGA-AAGACTTC
65 ACTTTGACCCGAGAA-ACTTC
* * * * * * * * *
588410 TTTACCTTTTGTCAG-CTATCAGCTTTGAC-CCAGGAGACTTCTTTACCCCTTATTTGCCCATCA
1 TTTACCCTTTGTCTGCCCATCGGCTTTGACTCGA-GAGACTTCTTTACCCTTTGTCTGCCCATCG
* * *
588473 ATTTTGACCC-AGGAGACTTA
65 ACTTTGACCCGA-GAAACTTC
* * * * * * * * *
588493 TTTACCCTTTGTCTACCCGTCGGCTTTCA-TCCGGGAGACTTCTTTGCCCTTTGTCTACTCGTCA
1 TTTACCCTTTGTCTGCCCATCGGCTTTGACT-CGAGAGACTTCTTTACCCTTTGTCTGCCCATCG
* * *
588557 ACTTTGATCC-AGGAATTTC
65 ACTTTGACCCGAGAAACTTC
* * * * ** **
588576 TTTA-CC-TTGTCTGCCCGTCGGCTTTGACCCGAGAGACTTTTTTACCTTTTGTCTGCCTGTTAA
1 TTTACCCTTTGTCTGCCCATCGGCTTTGACTCGAGAGACTTCTTTACCCTTTGTCTGCCCATCGA
* *
588639 CTTTGACCCGAGAGATTTC
66 CTTTGACCCGAGAAACTTC
* * * * *
588658 TTTACCCTTTGTCTGCCCATCAGCTTTGACTCG-GAAGATTTTTTTACCCTTTATCTGCCCGTCG
1 TTTACCCTTTGTCTGCCCATCGGCTTTGACTCGAG-AGACTTCTTTACCCTTTGTCTGCCCATCG
* *
588722 ACTTTGACTCGAGAGACTTC
65 ACTTTGACCCGAGAAACTTC
* * * * *
588742 TTTACCCCTTGTCTGCCTATCGACTTTGACTCGAGAGACTTCTTTACCCCTTGTTTGCCCATCGA
1 TTTACCCTTTGTCTGCCCATCGGCTTTGACTCGAGAGACTTCTTTACCCTTTGTCTGCCCATCGA
*
588807 CTTTGACCCTG-GAGACTTC
66 CTTTGACCC-GAGAAACTTC
* ** * * *** *
588826 TTTACTCTTTGTCTGCCTGTCGGCTTTGAC-CTAGGAGACTTCTTTACCCTTTGTCTACTTGTTG
1 TTTACCCTTTGTCTGCCCATCGGCTTTGACTCGA-GAGACTTCTTTACCCTTTGTCTGCCCATCG
**
588890 ACTTTGACTAGA-AAGACTTC
65 ACTTTGACCCGAGAA-ACTTC
* * * * * *
588910 TTTACCTTTTGTCTGCTCATTGACTTTGAC-CTAGGAGACTTCTTTACCTTTTGTCTGCCCATCG
1 TTTACCCTTTGTCTGCCCATCGGCTTTGACTCGA-GAGACTTCTTTACCCTTTGTCTGCCCATCG
*
588974 ACTTTGACCCGAGAAACTTT
65 ACTTTGACCCGAGAAACTTC
* * *** * * * * * *
588994 TTTACCCCTTGTCTACCCATCAATTTTGACTCGAGAGACTTTTTTTCTCTTTATCTGCCCGTCGG
1 TTTACCCTTTGTCTGCCCATCGGCTTTGACTCGAGAGACTTCTTTACCCTTTGTCTGCCCATCGA
* * * *
589059 CTTAGACTCGAGAGACTCC
66 CTTTGACCCGAGAAACTTC
589078 TTT
1 TTT
589081 CTCTTTTGCT
Statistics
Matches: 649, Mismatches: 167, Indels: 44
0.75 0.19 0.05
Matches are distributed among these distances:
81 53 0.08
82 17 0.03
83 133 0.20
84 438 0.67
85 8 0.01
ACGTcount: A:0.17, C:0.27, G:0.17, T:0.39
Consensus pattern (84 bp):
TTTACCCTTTGTCTGCCCATCGGCTTTGACTCGAGAGACTTCTTTACCCTTTGTCTGCCCATCGA
CTTTGACCCGAGAAACTTC
Found at i:592005 original size:165 final size:161
Alignment explanation
Indices: 591572--592045 Score: 572
Period size: 165 Copynumber: 2.9 Consensus size: 161
591562 ATTTTTGTTT
* * * *
591572 TTTTTTTCTTGAAGTTCACATTTTTTTGAAATACAGAGTTTTTTACTTTGTAATTTTTTCGG-GG
1 TTTTTTCCTTGAAATTC-CCTTTTTTTGAAATACGGAG-TTTTTACTTTGTAA-TTTTTCGGAGG
* * * * * * * *
591636 GGTTTCTATTGATTTTTAATTTTTAAAAGTCATCAAATACTATTATTTATTTTATATTAATACAT
63 GATTTTTCTTGTTTTTTAATTTTTAAAAGTTATAAAATATTATTATTTATTTTATATTAAT-TAT
* *
591701 TTTTC-AAAATTCATTCATTTTCATAAGTTTTAAA
127 TTTTCAAAAATTCATTCATTTCCATAAGATTTAAA
* * *
591735 TTTTTTCCTTGAAATTCCCTTTTGTTCT-AAGATAGGGAGTTTTTAC----TCA-TATT-GGAGG
1 TTTTTTCCTTGAAATTCCCTTTT-TT-TGAA-ATACGGAGTTTTTACTTTGTAATTTTTCGGAGG
* *
591793 GATTTTTCTTGTTGTTTAATTTTTAAAAGTTATAAAATATTATTATTTATTTTATATTAATTTTG
63 GATTTTTCTTGTTTTTTAATTTTTAAAAGTTATAAAATATTATTATTTATTTTATATTAATTAT-
591858 TTTTCAAAAATTCATTCATTTCCATAA-ATTTAGAA
127 TTTTCAAAAATTCATTCATTTCCATAAGATTTA-AA
591893 TTTTTTCCTTGAAATTCCTCTTTTTTTGAAATACGGAGTTTTTACTTTGTAAATTCTTTCGGAGG
1 TTTTTTCCTTGAAATTCC-CTTTTTTTGAAATACGGAGTTTTTACTTTGT-AATT-TTTCGGAGG
*
591958 GATTTTTCTTGTTTTTTAATTTTTAAAAGTTATAAAATATTATTATTTATTTTATATTCATTCAT
63 GATTTTTCTTGTTTTTTAATTTTTAAAAGTTATAAAATATTATTATTTATTTTATATTAATT-AT
*
592023 TTTTCAAAAATTTATTCATTTCC
127 TTTTCAAAAATTCATTCATTTCC
592046 GTGAATTTTT
Statistics
Matches: 267, Mismatches: 26, Indels: 34
0.82 0.08 0.10
Matches are distributed among these distances:
156 3 0.01
157 82 0.31
158 44 0.16
159 7 0.03
161 1 0.00
162 6 0.02
163 27 0.10
164 9 0.03
165 87 0.33
166 1 0.00
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.53
Consensus pattern (161 bp):
TTTTTTCCTTGAAATTCCCTTTTTTTGAAATACGGAGTTTTTACTTTGTAATTTTTCGGAGGGAT
TTTTCTTGTTTTTTAATTTTTAAAAGTTATAAAATATTATTATTTATTTTATATTAATTATTTTT
CAAAAATTCATTCATTTCCATAAGATTTAAA
Found at i:592672 original size:13 final size:12
Alignment explanation
Indices: 592646--592693 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
592636 TTAGAAAAAA
*
592646 AAAAGAAGAGAG
1 AAAAGAAGAAAG
592658 AAAAGAGAGAAAG
1 AAAAGA-AGAAAG
*
592671 AAAAAAAGAAA-
1 AAAAGAAGAAAG
592682 AAATAGAAGAAA
1 AAA-AGAAGAAA
592694 ATATAGAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
11 3 0.10
12 18 0.58
13 10 0.32
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (12 bp):
AAAAGAAGAAAG
Found at i:592689 original size:21 final size:22
Alignment explanation
Indices: 592656--592712 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
592646 AAAAGAAGAG
* *
592656 AGAAAAGAGAGAAAGAAAA-AA
1 AGAAAAAATAGAAAGAAAATAA
*
592677 AGAAAAAATAG-AAGAAAATAT
1 AGAAAAAATAGAAAGAAAATAA
592698 AGAAAAAAATAGAAA
1 AG-AAAAAATAGAAA
592713 AGCTAAGCTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 7 0.23
21 12 0.40
22 9 0.30
23 2 0.07
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.07
Consensus pattern (22 bp):
AGAAAAAATAGAAAGAAAATAA
Found at i:592691 original size:12 final size:12
Alignment explanation
Indices: 592637--592711 Score: 52
Period size: 12 Copynumber: 6.4 Consensus size: 12
592627 TTTTGAAGTT
592637 TAGAA-AAAAAA
1 TAGAAGAAAAAA
* *
592648 AAGAAGAGAGAAA
1 TAGAAGA-AAAAA
592661 -AGAGAGAAAGAAA
1 TAGA-AGAAA-AAA
*
592674 -AAAAGAAAAAA
1 TAGAAGAAAAAA
*
592685 TAGAAGAAAATA
1 TAGAAGAAAAAA
592697 TAG-A-AAAAAA
1 TAGAAGAAAAAA
592707 TAGAA
1 TAGAA
592712 AAGCTAAGCT
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
10 8 0.16
11 9 0.18
12 22 0.43
13 12 0.24
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.07
Consensus pattern (12 bp):
TAGAAGAAAAAA
Found at i:593870 original size:128 final size:128
Alignment explanation
Indices: 593631--593972 Score: 485
Period size: 128 Copynumber: 2.7 Consensus size: 128
593621 CCCATTAATT
* * *
593631 TAAACAAATATTAATCATTTTTAATCTTTTATATTCCTATGGATAT-TCGTAGGGGTATAAAAGA
1 TAAATAAATATTAATCATTTTTAATCTTTTATATTTCTATGGGTATCT-GTAGGGGTATAAAAGA
* *
593695 TTTCAAAAACTTTTCGTATCTTTTCGGGTATTCATTAAGGTACGAAATGATTTTTTTCCAAACA
65 TTTCAAAAACTTTTCGTATCTTTTCGGGTATTCATTAAGATACGAAATGATTTTTTTCCAAAAA
* **
593759 TAAATAAATATTAATCATTTTTAATTTTTTATATTTCTATGGGTATCTGTAAAGGTATAAAAGAT
1 TAAATAAATATTAATCATTTTTAATCTTTTATATTTCTATGGGTATCTGTAGGGGTATAAAAGAT
* * *
593824 TTCAAAAACTTTTTGTATCTTTTCGGGT-TTCTATTAAGATATGAAATGATTTTTTTTCAAAAA
66 TTCAAAAACTTTTCGTATCTTTTCGGGTATTC-ATTAAGATACGAAATGATTTTTTTCCAAAAA
* * *
593887 TAAATAAATATTAATCATTTTTTAATCTTTTATATTTCTATAGGTATCCGCAGGGGTATTAAAAG
1 TAAATAAATATTAATCA-TTTTTAATCTTTTATATTTCTATGGGTATCTGTAGGGGTA-TAAAAG
*
593952 ATTTC--AAATTTTTCGTATCTT
64 ATTTCAAAAACTTTTCGTATCTT
593973 GGCGGGTTTC
Statistics
Matches: 191, Mismatches: 19, Indels: 8
0.88 0.09 0.04
Matches are distributed among these distances:
127 3 0.02
128 142 0.74
129 35 0.18
130 11 0.06
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.45
Consensus pattern (128 bp):
TAAATAAATATTAATCATTTTTAATCTTTTATATTTCTATGGGTATCTGTAGGGGTATAAAAGAT
TTCAAAAACTTTTCGTATCTTTTCGGGTATTCATTAAGATACGAAATGATTTTTTTCCAAAAA
Found at i:599663 original size:158 final size:157
Alignment explanation
Indices: 599253--599732 Score: 485
Period size: 158 Copynumber: 3.1 Consensus size: 157
599243 TTCCCCAATG
* * * **
599253 GTGAAAAATCGATGTTTTGAAAATAAAAT-AGTGGTTAGAGTATCCCCTTGGAAATAACGAGGTT
1 GTGAAAAATCGGTGTTTGGGAAATAAAATCAG-GGTTAGAGTATCCCCTTAAAAATAACGAGGTT
* * * * *
599317 GGAGTATCCCCGATTGTGGAAAATCGATGTTTTAGAAATAAAGTTGGGGTTGGAGCATCTTCC-C
65 GGAGTATCCCTGATTGTGAAAAATCGATGTTTTAGAAATAAAGATGGGGTTGGAGTAT-TCCCTC
* * *
599381 -GAAATAATGGGGTTAGATTATCCCCAATT
129 AAAAATAATGGGGTTAGAGTAT-CCCGATT
* * * * * *
599410 GTGAAAAATCGGTATTTTGGG-AAT--AACCGGGGTTGGAGTAT-CCCTTAAGAAATAATGGGGT
1 GTGAAAAATCGGT-GTTTGGGAAATAAAATCAGGGTTAGAGTATCCCCTTAA-AAATAACGAGGT
* * * * *
599471 TGGAGTATCCCTGATTATGAAAAATTGATGTTTTAGAAGTAAAGCTGGGGTTAGAGTATTCCCTC
64 TGGAGTATCCCTGATTGTGAAAAATCGATGTTTTAGAAATAAAGATGGGGTTGGAGTATTCCCTC
* *
599536 AAAAATAACGGGGTTGGAGTATCCTCGATT
129 AAAAATAATGGGGTTAGAGTATCC-CGATT
** * *
599566 GTGAAAAATCGGTGTTTGGGAAATAAAATCAGGGTTAGAGTATCCCCTCCAAAATAACAAGGTTA
1 GTGAAAAATCGGTGTTTGGGAAATAAAATCAGGGTTAGAGTATCCCCTTAAAAATAACGAGGTTG
* * * *
599631 GAGTATCCGTGATGGTGAAAAATCGGTATTTTAGAAATAAA-ATCGGGGTTGGAGTA-TCCCTTT
66 GAGTATCCCTGATTGTGAAAAATCGATGTTTTAGAAATAAAGAT-GGGGTTGGAGTATTCCC--T
*
599694 GAAAAA-AATGGGGTTAGAGTATCCCTGATT
128 CAAAAATAATGGGGTTAGAGTATCCC-GATT
599724 GTGAAAAAT
1 GTGAAAAAT
599733 TGATATTTTA
Statistics
Matches: 262, Mismatches: 47, Indels: 27
0.78 0.14 0.08
Matches are distributed among these distances:
154 8 0.03
155 82 0.31
156 38 0.15
157 21 0.08
158 102 0.39
159 11 0.04
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (157 bp):
GTGAAAAATCGGTGTTTGGGAAATAAAATCAGGGTTAGAGTATCCCCTTAAAAATAACGAGGTTG
GAGTATCCCTGATTGTGAAAAATCGATGTTTTAGAAATAAAGATGGGGTTGGAGTATTCCCTCAA
AAATAATGGGGTTAGAGTATCCCGATT
Found at i:599747 original size:79 final size:78
Alignment explanation
Indices: 599253--599769 Score: 395
Period size: 79 Copynumber: 6.6 Consensus size: 78
599243 TTCCCCAATG
* * * * * *
599253 GTGAAAAATCGATGTTTT-GAAAATAAAATAGTGGTTAGAGTATCCCCTTGGAAATAACGAGGTT
1 GTGAAAAATCGATGTTTTAG-AAATAAAATCGGGGTTGGAGTAT-CCCTTGAAAAAAACGGGGTT
* *
599317 GGAGTATCCCCGATT
64 AGAGTATCCCTGATT
* * * * * * *
599332 GTGGAAAATCGATGTTTTAGAAATAAAGTTGGGGTTGGAGCATCTTCC-CG-AAATAATGGGGTT
1 GTGAAAAATCGATGTTTTAGAAATAAAATCGGGGTTGGAGTATC--CCTTGAAAAAAACGGGGTT
* **
599395 AGATTATCCCCAATT
64 AGAGTATCCCTGATT
* * * * * *
599410 GTGAAAAATCGGTATTTTGGGAAT--AACCGGGGTTGGAGTATCCCTT-AAGAAATAATGGGGTT
1 GTGAAAAATCGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCTTGAA-AAA-AACGGGGTT
*
599472 GGAGTATCCCTGATT
64 AGAGTATCCCTGATT
* * * * * *
599487 ATGAAAAATTGATGTTTTAGAAGT-AAAGCTGGGGTTAGAGTATTCCC-TCAAAAATAACGGGGT
1 GTGAAAAATCGATGTTTTAGAAATAAAATC-GGGGTTGGAGTA-TCCCTTGAAAAA-AACGGGGT
*
599550 TGGAGTAT-CCTCGATT
63 TAGAGTATCCCT-GATT
* ** * * ** * **
599566 GTGAAAAATCGGTGTTTGGGAAATAAAATCAGGGTTAGAGTATCCCCTCCAAAATAACAAGGTTA
1 GTGAAAAATCGATGTTTTAGAAATAAAATCGGGGTTGGAGTAT-CCCTTGAAAAAAACGGGGTTA
* *
599631 GAGTATCCGTGATG
65 GAGTATCCCTGATT
* * *
599645 GTGAAAAATCGGTATTTTAGAAATAAAATCGGGGTTGGAGTATCCCTTTGAAAAAAATGGGGTTA
1 GTGAAAAATCGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCCC-TTGAAAAAAACGGGGTTA
599710 GAGTATCCCTGATT
65 GAGTATCCCTGATT
* * ***
599724 GTGAAAAATTGATATTTTAGAAATAAGGCCGGGGTTGGAGTATCCC
1 GTGAAAAATCGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCCC
599770 CAATTATGAA
Statistics
Matches: 351, Mismatches: 70, Indels: 34
0.77 0.15 0.07
Matches are distributed among these distances:
74 2 0.01
75 1 0.00
76 16 0.05
77 37 0.11
78 53 0.15
79 222 0.63
80 20 0.06
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (78 bp):
GTGAAAAATCGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCTTGAAAAAAACGGGGTTAG
AGTATCCCTGATT
Found at i:599759 original size:209 final size:209
Alignment explanation
Indices: 599544--599958 Score: 505
Period size: 209 Copynumber: 2.0 Consensus size: 209
599534 TCAAAAATAA
* * * * *
599544 CGGGGTTGGAGTATCCTCGATTGTGAAAAATCGGTGTTTGGGAAATAAAATCAGGGTTAGAGTAT
1 CGGGGTTGGAGTATCCCCAATTATGAAAAATCGATGTTTGGGAAATAAAATCAGGGTTAGAGTAC
*
599609 CCCCTCCAAAATAACAAGGTTAG-AGTATC-CGTGATGGTGAAAAATCGGTATTTTAGAAATAAA
66 CCCCTCCAAAATAACAAGGTT-GCAGTATCTC-TGATGGTG-AAAATCGATATTTTAGAAATAAA
* * * * * *
599672 ATCGGGGTTGGAGTATCCCTTTGAAAAAAATGGGGTTAGAGTATCCCTGATTG-TG-AAAAATTG
128 ACCGGGGTTAGAGTATCCCCTCGAAAAAAACGGGGTTAGAGTATCCCTGA-TGATGAAAAAATCG
599735 ATATTTTAGAAATAAGGC
192 ATATTTTAGAAATAAGGC
* ** *
599753 CGGGGTTGGAGTATCCCCAATTATGAAAAATCGATGTTTTGGAAATAAAATTGGGGTTGGAGTAC
1 CGGGGTTGGAGTATCCCCAATTATGAAAAATCGATGTTTGGGAAATAAAATCAGGGTTAGAGTAC
* ** * * * **
599818 CCCCTCGAAAATAACGGGGTTGCAGTATCTCTGATGTTGAAAATTGATATTTTAGGAATAATGCC
66 CCCCTCCAAAATAACAAGGTTGCAGTATCTCTGATGGTGAAAATCGATATTTTAGAAATAAAACC
* * * *
599883 GGGGTTAGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCTTGATGATGAAAAAATCGATGT
131 GGGGTTAGAGTATCCCCTCGAAAAAAACGGGGTTAGAGTATCCCTGATGATGAAAAAATCGATAT
*
599948 TTTGGAAATAA
196 TTTAGAAATAA
599959 AAAACATCGA
Statistics
Matches: 173, Mismatches: 29, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
207 2 0.01
208 63 0.36
209 107 0.62
210 1 0.01
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (209 bp):
CGGGGTTGGAGTATCCCCAATTATGAAAAATCGATGTTTGGGAAATAAAATCAGGGTTAGAGTAC
CCCCTCCAAAATAACAAGGTTGCAGTATCTCTGATGGTGAAAATCGATATTTTAGAAATAAAACC
GGGGTTAGAGTATCCCCTCGAAAAAAACGGGGTTAGAGTATCCCTGATGATGAAAAAATCGATAT
TTTAGAAATAAGGC
Found at i:599765 original size:130 final size:129
Alignment explanation
Indices: 599626--599899 Score: 345
Period size: 130 Copynumber: 2.1 Consensus size: 129
599616 AAAATAACAA
*** * * *
599626 GGTTAGAGTATCCGTGATGGTGAAAAATCGGTATTTTAGAAATAAAATCGGGGTTGGAGTATCCC
1 GGTTAGAGTATCCCCAATGATGAAAAATCGATATTTTAGAAATAAAATCGGGGTTGGAGTACCCC
* * *
599691 TTTGAAAAAAATGGGGTTAG-AGTATCCCTGAT-TGTGAAAAATTGATATTTTAGAAATAAGGCC
66 CTCGAAAAAAACGGGGTT-GCAGTATCCCTGATGT-TG-AAAATTGATATTTTAGAAATAAGGCC
599754 GG
128 GG
* * * * *
599756 GGTTGGAGTATCCCCAATTATGAAAAATCGATGTTTTGGAAATAAAATTGGGGTTGGAGTACCCC
1 GGTTAGAGTATCCCCAATGATGAAAAATCGATATTTTAGAAATAAAATCGGGGTTGGAGTACCCC
* * * *
599821 CTCGAAAATAACGGGGTTGCAGTATCTCTGATGTTGAAAATTGATATTTTAGGAATAATGCCGG
66 CTCGAAAAAAACGGGGTTGCAGTATCCCTGATGTTGAAAATTGATATTTTAGAAATAAGGCCGG
599885 GGTTAGAGTATCCCC
1 GGTTAGAGTATCCCC
599900 TCGAAAATAA
Statistics
Matches: 123, Mismatches: 19, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
129 41 0.33
130 81 0.66
131 1 0.01
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (129 bp):
GGTTAGAGTATCCCCAATGATGAAAAATCGATATTTTAGAAATAAAATCGGGGTTGGAGTACCCC
CTCGAAAAAAACGGGGTTGCAGTATCCCTGATGTTGAAAATTGATATTTTAGAAATAAGGCCGG
Found at i:599780 original size:51 final size:51
Alignment explanation
Indices: 599703--599800 Score: 133
Period size: 51 Copynumber: 1.9 Consensus size: 51
599693 TGAAAAAAAT
** * *
599703 GGGGTTAGAGTATCCCTGATTGTGAAAAATTGATATTTTAGAAATAAGGCC
1 GGGGTTAGAGTATCCCCAATTATGAAAAATCGATATTTTAGAAATAAGGCC
* * *
599754 GGGGTTGGAGTATCCCCAATTATGAAAAATCGATGTTTTGGAAATAA
1 GGGGTTAGAGTATCCCCAATTATGAAAAATCGATATTTTAGAAATAA
599801 AATTGGGGTT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 40 1.00
ACGTcount: A:0.34, C:0.10, G:0.26, T:0.31
Consensus pattern (51 bp):
GGGGTTAGAGTATCCCCAATTATGAAAAATCGATATTTTAGAAATAAGGCC
Found at i:599809 original size:51 final size:50
Alignment explanation
Indices: 599694--599821 Score: 132
Period size: 51 Copynumber: 2.5 Consensus size: 50
599684 GTATCCCTTT
* ** * *
599694 GAAA-AAAATGGGGTTAGAGTATCCCTGATTGTGAAAAATTGATATTTTA
1 GAAATAAAATGGGGTTGGAGTATCCCCAATTATGAAAAATCGATATTTTA
*** * *
599743 GAAATAAGGCCGGGGTTGGAGTATCCCCAATTATGAAAAATCGATGTTTTG
1 GAAATAA-AATGGGGTTGGAGTATCCCCAATTATGAAAAATCGATATTTTA
*
599794 GAAATAAAATTGGGGTTGGAGTACCCCC
1 GAAATAAAA-TGGGGTTGGAGTATCCCC
599822 TCGAAAATAA
Statistics
Matches: 62, Mismatches: 14, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
49 4 0.06
50 2 0.03
51 56 0.90
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.28
Consensus pattern (50 bp):
GAAATAAAATGGGGTTGGAGTATCCCCAATTATGAAAAATCGATATTTTA
Found at i:599836 original size:79 final size:79
Alignment explanation
Indices: 599753--599960 Score: 242
Period size: 78 Copynumber: 2.6 Consensus size: 79
599743 GAAATAAGGC
** ** *
599753 CGGGGTTGGAGTATCCCCAATTATGAAAAATCGATGTTTTGGAAATAAAATTGGGGTTGGAGTAC
1 CGGGGTTGGAGTATCCCTGATTATGAAAAATCGATGTTTTGGAAATAAAACCGGGGTTAGAGTAC
599818 CCCCTCGAAAATAA
66 CCCCTCGAAAATAA
* * * * **
599832 CGGGGTTGCAGTATCTCTGATGT-TG-AAAATTGATATTTTAGG-AATAATGCCGGGGTTAGAGT
1 CGGGGTTGGAGTATCCCTGAT-TATGAAAAATCGATGTTTT-GGAAATAAAACCGGGGTTAGAGT
*
599894 ATCCCCTCGAAAATAA
64 ACCCCCTCGAAAATAA
* *
599910 CGGGGTTGGAGTATCCTTGATGATGAAAAAATCGATGTTTTGGAAATAAAA
1 CGGGGTTGGAGTATCCCTGATTATG-AAAAATCGATGTTTTGGAAATAAAA
599961 AACATCGATG
Statistics
Matches: 103, Mismatches: 20, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
78 62 0.60
79 23 0.22
80 18 0.17
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCTGATTATGAAAAATCGATGTTTTGGAAATAAAACCGGGGTTAGAGTAC
CCCCTCGAAAATAA
Found at i:610658 original size:20 final size:20
Alignment explanation
Indices: 610633--610687 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
610623 CTGCCAAGGA
610633 AATGTATCGATACATT-ATTC
1 AATGTATCGATACATTGA-TC
610653 AATGTATCGATACATTGATC
1 AATGTATCGATACATTGATC
**
610673 TTTGTATCGATACAT
1 AATGTATCGATACAT
610688 GCAGGCAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.40
Consensus pattern (20 bp):
AATGTATCGATACATTGATC
Found at i:617163 original size:54 final size:54
Alignment explanation
Indices: 617082--617203 Score: 156
Period size: 54 Copynumber: 2.3 Consensus size: 54
617072 TACTATGCAT
* * * * *
617082 AAAAAAA-TGAATGGCAATGCTTAGATGAAAACTCGAAAGGGCATTCAAGTAAG
1 AAAAAAATTGAATGACAATGCTTAGATGAAAACCCAAAAAGGCATTCAAGTAAA
** * *
617135 AAAAATTTTGAATGACAATGCTTGGATGAAAACCCAAAAAGGCGTTCAAGTAAA
1 AAAAAAATTGAATGACAATGCTTAGATGAAAACCCAAAAAGGCATTCAAGTAAA
617189 AAAAAAATTGAATGA
1 AAAAAAATTGAATGA
617204 AAACCCAAAA
Statistics
Matches: 57, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
53 5 0.09
54 52 0.91
ACGTcount: A:0.49, C:0.11, G:0.20, T:0.20
Consensus pattern (54 bp):
AAAAAAATTGAATGACAATGCTTAGATGAAAACCCAAAAAGGCATTCAAGTAAA
Found at i:618777 original size:42 final size:44
Alignment explanation
Indices: 618713--618813 Score: 109
Period size: 42 Copynumber: 2.3 Consensus size: 44
618703 CTCCTCACCC
* * *
618713 ATCGTCTTCCCGTTGACATAGACTTGGGAGAC-T-CCTTTAT-T
1 ATCGTCTACCCGTCGACATAGACCTGGGAGACTTCCCTTTATCT
* *
618754 AATCGTCTACCCGTCGACCTAGACCTGGGGGACTTCCCTTTATCT
1 -ATCGTCTACCCGTCGACATAGACCTGGGAGACTTCCCTTTATCT
* *
618799 TTCGTCTGCCCGTCG
1 ATCGTCTACCCGTCG
618814 GTTCATACCT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
42 27 0.55
43 1 0.02
44 20 0.41
45 1 0.02
ACGTcount: A:0.16, C:0.31, G:0.21, T:0.33
Consensus pattern (44 bp):
ATCGTCTACCCGTCGACATAGACCTGGGAGACTTCCCTTTATCT
Found at i:618804 original size:44 final size:42
Alignment explanation
Indices: 618651--618813 Score: 105
Period size: 42 Copynumber: 3.9 Consensus size: 42
618641 ATTAGTTCAA
* ** * * * *
618651 ACCTGGGAGACTTCTCCATCAATCATCTGCCCGTCGACGTAG
1 ACCTGGGAGACTCCTTTATTAATCGTCTACCCGTCGACATAG
* * * *** * *
618693 ACCCGAGAGACTCC-TCACCCATCGTCTTCCCGTTGACATAG
1 ACCTGGGAGACTCCTTTATTAATCGTCTACCCGTCGACATAG
* *
618734 ACTTGGGAGACTCCTTTATTAATCGTCTACCCGTCGACCTAG
1 ACCTGGGAGACTCCTTTATTAATCGTCTACCCGTCGACATAG
* * *
618776 ACCTGGGGGACTTCCCTTTATCT-TTCGTCTGCCCGTCG
1 ACCTGGGAGAC-T-CCTTTAT-TAATCGTCTACCCGTCG
618814 GTTCATACCT
Statistics
Matches: 93, Mismatches: 24, Indels: 6
0.76 0.20 0.05
Matches are distributed among these distances:
41 31 0.33
42 40 0.43
43 1 0.01
44 20 0.22
45 1 0.01
ACGTcount: A:0.18, C:0.34, G:0.20, T:0.28
Consensus pattern (42 bp):
ACCTGGGAGACTCCTTTATTAATCGTCTACCCGTCGACATAG
Found at i:619082 original size:43 final size:43
Alignment explanation
Indices: 618884--619182 Score: 147
Period size: 43 Copynumber: 7.0 Consensus size: 43
618874 CTTCACCCAT
* * * *
618884 CATCTGCCCATCGACTCAATCCCAGAAGACTTCCTTTATCAAT
1 CATCTGCCCATCGGCTCAGTCCCAGGAGACTTCCTTTATCAAC
* *** ** * * * ***
618927 CGTCTGCTTGTTAGCTTAGGCCGA-GAGACTT-CTTTATCCTT
1 CATCTGCCCATCGGCTCAGTCCCAGGAGACTTCCTTTATCAAC
* * * * * * *
618968 CGTCTGCTCGTCGGCTCATTCCCAAGAGACTTTCTTTATCAAT
1 CATCTGCCCATCGGCTCAGTCCCAGGAGACTTCCTTTATCAAC
** * * * * * * *
619011 TGTTTGCCTATCGACTCAATCTCGGGAGAATTCCTTTATCAAC
1 CATCTGCCCATCGGCTCAGTCCCAGGAGACTTCCTTTATCAAC
* * ***
619054 CATCTGCCCATCGGCTTAGGCCCAGGAGACTT-CTTTATCCTT
1 CATCTGCCCATCGGCTCAGTCCCAGGAGACTTCCTTTATCAAC
* * ** *
619096 CATCTGCCCATCGGCTGAGTCTC-GAGAGACTTTTTTTATCAAT
1 CATCTGCCCATCGGCTCAGTCCCAG-GAGACTTCCTTTATCAAC
* * * *
619139 CGTCTGCTCATCAGCTCAGTCCCAAGAGACTTCCTTTATCAAC
1 CATCTGCCCATCGGCTCAGTCCCAGGAGACTTCCTTTATCAAC
619182 C
1 C
619183 GTTTGCCCGT
Statistics
Matches: 186, Mismatches: 65, Indels: 10
0.71 0.25 0.04
Matches are distributed among these distances:
41 26 0.14
42 47 0.25
43 113 0.61
ACGTcount: A:0.21, C:0.30, G:0.16, T:0.33
Consensus pattern (43 bp):
CATCTGCCCATCGGCTCAGTCCCAGGAGACTTCCTTTATCAAC
Found at i:619173 original size:128 final size:127
Alignment explanation
Indices: 618886--619276 Score: 315
Period size: 128 Copynumber: 3.1 Consensus size: 127
618876 TCACCCATCA
* * * * *** ** *
618886 TCTGCCCATCGACTCAATCCC-AGAAGACTTCCTTTATCAATCGTCTGCTTGTTAGCTTAGGCCG
1 TCTGCCTATCGACTCAATCCCAAG-AGAATTCCTTTATCAACCATCTGCCCATCGGCTTAGGCCC
* * * * *
618950 AGAGACTTCTTTATCCTTCGTCTGCTCGTCGGCTCATTCCCAAGAGACTTTCTTTATCAATTG
65 AGAGACTTCTTTATCCTTCATCTGCCCATCGGCTCAGTCCCAAGAGACTTTCTTTATCAATCG
* * **
619013 TTTGCCTATCGACTCAATCTCGGGAGAATTCCTTTATCAACCATCTGCCCATCGGCTTAGGCCCA
1 TCTGCCTATCGACTCAATCCCAAGAGAATTCCTTTATCAACCATCTGCCCATCGGCTTAGGCCCA
* * * *
619078 GGAGACTTCTTTATCCTTCATCTGCCCATCGGCTGAGTCTCGAGAGACTTTTTTTATCAATCG
66 -GAGACTTCTTTATCCTTCATCTGCCCATCGGCTCAGTCCCAAGAGACTTTCTTTATCAATCG
* * * * * ** *
619141 TCTG-CTCATC-AGCTCAGTCCCAAGAGACTTCCTTTATCAACCGTTTGCCCGTTAGCTCAGGCC
1 TCTGCCT-ATCGA-CTCAATCCCAAGAGAATTCCTTTATCAACCATCTGCCCATCGGCTTAGGCC
* * * * * * ** * * *
619204 TGAGAGGCTTCTTCATCCATT-GTCTGCACGTTTGCTCAGTCTCGAGAGACTTT-TTTATCAATT
64 -CAGAGACTTCTTTATCC-TTCATCTGCCCATCGGCTCAGTCCCAAGAGACTTTCTTTATCAATC
619267 G
127 G
619268 TCTGCCTAT
1 TCTGCCTAT
619277 TGGCTCAGAC
Statistics
Matches: 213, Mismatches: 44, Indels: 14
0.79 0.16 0.05
Matches are distributed among these distances:
127 69 0.32
128 141 0.66
129 3 0.01
ACGTcount: A:0.19, C:0.29, G:0.18, T:0.34
Consensus pattern (127 bp):
TCTGCCTATCGACTCAATCCCAAGAGAATTCCTTTATCAACCATCTGCCCATCGGCTTAGGCCCA
GAGACTTCTTTATCCTTCATCTGCCCATCGGCTCAGTCCCAAGAGACTTTCTTTATCAATCG
Found at i:619268 original size:42 final size:42
Alignment explanation
Indices: 618910--619272 Score: 142
Period size: 43 Copynumber: 8.5 Consensus size: 42
618900 CAATCCCAGA
** * *
618910 AGACTTCCTTTATCAATCGTCTGCTTGTTAGCTTAGGC-CGAG
1 AGACTT-CTTTATCAATCGTCTGCACGTTAGCTCAGTCTCGAG
** * ** * * *
618952 AGACTTCTTTATCCTTCGTCTGCTCGTCGGCTCATTCCCAAG
1 AGACTTCTTTATCAATCGTCTGCACGTTAGCTCAGTCTCGAG
* * * * *
618994 AGACTTTCTTTATCAATTGTTTGC-C-TATCGACTCAATCTCGGG
1 AGAC-TTCTTTATCAATCGTCTGCACGT-TAG-CTCAGTCTCGAG
* * * * * ** * * *
619037 AGAATTCCTTTATCAACCATCTGCCCATCGGCTTAGGC-CCAGG
1 AGACTT-CTTTATCAATCGTCTGCACGTTAGCTCAGTCTCGA-G
** * * * ** *
619080 AGACTTCTTTATCCTTCATCTGCCCATCGGCTGAGTCTCGAG
1 AGACTTCTTTATCAATCGTCTGCACGTTAGCTCAGTCTCGAG
* * * * * *
619122 AGACTTTTTTTATCAATCGTCTGCTCATCAGCTCAGTCCCAAG
1 AGAC-TTCTTTATCAATCGTCTGCACGTTAGCTCAGTCTCGAG
* * * *
619165 AGACTTCCTTTATCAACCGTTTGCCCGTTAGCTCAGGC-CTGAG
1 AGACTT-CTTTATCAATCGTCTGCACGTTAGCTCAGTCTC-GAG
* * * * *
619208 AGGCTTCTTCATCCATTGTCTGCACGTTTGCTCAGTCTCGAG
1 AGACTTCTTTATCAATCGTCTGCACGTTAGCTCAGTCTCGAG
* *
619250 AGACTTTTTTATCAATTGTCTGC
1 AGACTTCTTTATCAATCGTCTGC
619273 CTATTGGCTC
Statistics
Matches: 240, Mismatches: 68, Indels: 26
0.72 0.20 0.08
Matches are distributed among these distances:
41 24 0.10
42 97 0.40
43 116 0.48
44 2 0.01
45 1 0.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (42 bp):
AGACTTCTTTATCAATCGTCTGCACGTTAGCTCAGTCTCGAG
Found at i:620700 original size:163 final size:162
Alignment explanation
Indices: 620226--620827 Score: 605
Period size: 158 Copynumber: 3.7 Consensus size: 162
620216 CCTCATCAAA
* * *** * ** *
620226 TCAGTTTTGCAAAATTCTTTCATTTTCATGAATCTTTGGTTTTTTCCTTGAAGTTCTCTTTTTTT
1 TCAGTTTT-CAAAATTCATTCATTTCCATGAAT-TTTAAATTTTTCCTTGAA-ATC-CCCTTTTC
** * * * *
620291 CTTAAATACGGAGTTTTCTACTTCGTAAATTTTTTTGGAGAGATTTTTTTTAGTTTTTAATTTTT
62 CCAAAATACGGAGTTTTCTACTCCGTAAATTTTTTCGGAGGGATTTTTCTT-GTTTTTAATTTTT
* ** *
620356 AAAATTTGTCAAATATTATTATTTATTTTTTATTAAAT
126 AAAAGTCATCAAATATTATTATTTATTTTATATT-AAT
* * * * ** * **
620394 T-AATTCTCAAAGATTCATTCATTTTCATAAATTTTTTATTTTTACCTTGAAAT---TTTTTTTC
1 TCAGTTTTCAAA-ATTCATTCATTTCCATGAATTTTAAATTTTT-CCTTGAAATCCCCTTTTCCC
* * **
620455 GAAATACGGAGTTTTTTACTCCGT-AA-TTTTT-GG-GGGGGTTTTCTTGATTTTTAATTTTTAA
64 AAAATACGGAGTTTTCTACTCCGTAAATTTTTTCGGAGGGATTTTTCTTG-TTTTTAATTTTTAA
*
620516 AAGTCATCAAATATTATTATTTATTTTGTATTAAT
128 AAGTCATCAAATATTATTATTTATTTTATATTAAT
620551 TCAGTTTTCAAAACTTCATTCATTTCCATGAATTTTAAATTTTTCCTTGAAATCCCCTTTTCCCA
1 TCAGTTTTCAAAA-TTCATTCATTTCCATGAATTTTAAATTTTTCCTTGAAATCCCCTTTTCCCA
* *
620616 AAATACAGAGTTTT-TACTCCGTAAATTCTTTCGGAGGGATTTTTCTTGCTTTTTAATTTTTAAA
65 AAATACGGAGTTTTCTACTCCGTAAATTTTTTCGGAGGGATTTTTCTTG-TTTTTAATTTTTAAA
*
620680 AGTCATCAAATATTATTATTTATTTCATATTAAT
129 AGTCATCAAATATTATTATTTATTTTATATTAAT
*
620714 TCAGTTTTCAAAAATTCATTCATTTCCCATGAATTTTGAATTTTTTCCTTGAAATCCCCTTTCTC
1 TCAGTTTTC-AAAATTCATTCATTT-CCATGAATTTT-AAATTTTTCCTTGAAATCCCCTTT-TC
* * * * *
620779 CGAAAA-ATC-GAGTTTTCTATTCCATAAATTTTTTCAGAGGAATTTTTCT
62 CCAAAATA-CGGAGTTTTCTACTCCGTAAATTTTTTCGGAGGGATTTTTCT
620828 CAATTTAAAA
Statistics
Matches: 371, Mismatches: 45, Indels: 38
0.82 0.10 0.08
Matches are distributed among these distances:
157 15 0.04
158 84 0.23
159 10 0.03
160 25 0.07
161 6 0.02
162 29 0.08
163 78 0.21
164 15 0.04
165 31 0.08
166 48 0.13
167 29 0.08
168 1 0.00
ACGTcount: A:0.27, C:0.13, G:0.09, T:0.50
Consensus pattern (162 bp):
TCAGTTTTCAAAATTCATTCATTTCCATGAATTTTAAATTTTTCCTTGAAATCCCCTTTTCCCAA
AATACGGAGTTTTCTACTCCGTAAATTTTTTCGGAGGGATTTTTCTTGTTTTTAATTTTTAAAAG
TCATCAAATATTATTATTTATTTTATATTAAT
Found at i:620919 original size:166 final size:164
Alignment explanation
Indices: 620507--620925 Score: 450
Period size: 163 Copynumber: 2.5 Consensus size: 164
620497 CTTGATTTTT
* * ** *** *
620507 AATTTTTAAAAGTCATCAAATATTATTATTTATTTTGTATTAATTCAGTTTTCAAAACTTCATTC
1 AATTTTTAAAAGTCATCAAATATTATCATTGAACTCACATTAATTCAGTTTTCAAAAATTCATTC
* *
620572 ATTTCCATGAATTTT-AAATTTTTCCTTGAAATCCCCTTTTCCCAAAATACAGAGTTTTTACTCC
66 ATTTCCATGAATTTTGAATTTTTTCCTTGAAATCCCCTTTTCCAAAAATACAGAGTTTTTACTCC
* * * *** **
620636 GTAAATTCTTTCGGAGGGATTTTTCTTGCTTTTT
131 ATAAATTCTTTCAGAGGAATTTTTCTCAATTTAA
* * ** *
620670 AATTTTTAAAAGTCATCAAATATTATTATTTATTTCATATTAATTCAGTTTTCAAAAATTCATTC
1 AATTTTTAAAAGTCATCAAATATTATCATTGAACTCACATTAATTCAGTTTTCAAAAATTCATTC
620735 ATTTCCCATGAATTTTGAATTTTTTCCTTGAAATCCCCTTTCTCCGAAAAAT-C-GAGTTTTCTA
66 ATTT-CCATGAATTTTGAATTTTTTCCTTGAAATCCCCTTT-TCC-AAAAATACAGAGTTTT-TA
* *
620798 TTCCATAAATTTTTTCAGAGGAATTTTTCTCAATTTAA
127 CTCCATAAATTCTTTCAGAGGAATTTTTCTCAATTTAA
* * * * * * *
620836 AATTTTTAAAAATTCATCTAATATTGTCATTGAACTCCCATTAATTCAGTTTTGAAAATTTTAAT
1 AATTTTT-AAAAGTCATCAAATATTATCATTGAACTCACATTAATTCAGTTTTCAAAA-ATTCAT
* *
620901 TTATTT-CATTAATTTTGAATTTTTT
64 TCATTTCCATGAATTTTGAATTTTTT
620926 TTTGTATATA
Statistics
Matches: 220, Mismatches: 29, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
163 66 0.30
164 11 0.05
165 30 0.14
166 59 0.27
167 45 0.20
168 9 0.04
ACGTcount: A:0.31, C:0.15, G:0.07, T:0.47
Consensus pattern (164 bp):
AATTTTTAAAAGTCATCAAATATTATCATTGAACTCACATTAATTCAGTTTTCAAAAATTCATTC
ATTTCCATGAATTTTGAATTTTTTCCTTGAAATCCCCTTTTCCAAAAATACAGAGTTTTTACTCC
ATAAATTCTTTCAGAGGAATTTTTCTCAATTTAA
Found at i:621418 original size:20 final size:19
Alignment explanation
Indices: 621392--621460 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 19
621382 AGTTCAGCAA
* *
621392 AAAAGAAAAGAGAAAAGAG
1 AAAAGAAAAAAGAAAAAAG
621411 AGAAAGAAAAAAGAAAAAAG
1 A-AAAGAAAAAAGAAAAAAG
621431 AAGAAGAAAATATAGAAAAAA-
1 AA-AAGAAAA-A-AGAAAAAAG
*
621452 AATAGAAAA
1 AAAAGAAAA
621461 GCTAGGCTAG
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
19 2 0.05
20 30 0.70
21 3 0.07
22 8 0.19
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (19 bp):
AAAAGAAAAAAGAAAAAAG
Found at i:621422 original size:15 final size:14
Alignment explanation
Indices: 621390--621432 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 14
621380 GAAGTTCAGC
621390 AAAAA-AGAAAAGA
1 AAAAAGAGAAAAGA
*
621403 GAAAAGAGAGAAAGA
1 AAAAAGAGA-AAAGA
*
621418 AAAAAGAAAAAAGA
1 AAAAAGAGAAAAGA
621432 A
1 A
621433 GAAGAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 4 0.16
14 9 0.36
15 12 0.48
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAAAGAGAAAAGA
Found at i:621428 original size:33 final size:33
Alignment explanation
Indices: 621391--621460 Score: 81
Period size: 33 Copynumber: 2.1 Consensus size: 33
621381 AAGTTCAGCA
621391 AAAAAGAAAAG-AGAAAAGAGAGAAAGAAAAA-AG
1 AAAAA-AAAAGAAGAAAAGAGAGAAA-AAAAATAG
* * *
621424 AAAAAAGAAGAAGAAAATATAGAAAAAAAATAG
1 AAAAAAAAAGAAGAAAAGAGAGAAAAAAAATAG
621457 AAAA
1 AAAA
621461 GCTAGGCTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
32 9 0.28
33 23 0.72
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (33 bp):
AAAAAAAAAGAAGAAAAGAGAGAAAAAAAATAG
Found at i:621432 original size:7 final size:7
Alignment explanation
Indices: 621390--621451 Score: 56
Period size: 7 Copynumber: 8.9 Consensus size: 7
621380 GAAGTTCAGC
621390 AAAAAAG
1 AAAAAAG
*
621397 AAAAGAG
1 AAAAAAG
*
621404 AAAAGAG
1 AAAAAAG
*
621411 -AGAAAG
1 AAAAAAG
621417 AAAAAAG
1 AAAAAAG
621424 AAAAAAG
1 AAAAAAG
*
621431 -AAGAAG
1 AAAAAAG
621437 AAAATATAG
1 AAAA-A-AG
621446 AAAAAA
1 AAAAAA
621452 AATAGAAAAG
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
6 9 0.20
7 28 0.62
8 2 0.04
9 6 0.13
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.03
Consensus pattern (7 bp):
AAAAAAG
Found at i:621437 original size:13 final size:12
Alignment explanation
Indices: 621390--621461 Score: 60
Period size: 11 Copynumber: 6.0 Consensus size: 12
621380 GAAGTTCAGC
621390 AAAAAAGAAAAG
1 AAAAAAGAAAAG
* *
621402 AGAAAAG-AGAG
1 AAAAAAGAAAAG
*
621413 AAAGAA-AAAAG
1 AAAAAAGAAAAG
621424 AAAAAAGAAGAAG
1 AAAAAAGAA-AAG
621437 AAAATATAGAAAA-
1 AAAA-A-AGAAAAG
*
621450 AAAATAGAAAAG
1 AAAAAAGAAAAG
621462 CTAGGCTAGT
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
11 21 0.45
12 8 0.17
13 11 0.23
14 3 0.06
15 4 0.09
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.04
Consensus pattern (12 bp):
AAAAAAGAAAAG
Found at i:622118 original size:43 final size:43
Alignment explanation
Indices: 622057--622144 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
622047 CATGATGGAA
622057 TTGTATTTTGGATGTTTTGCGATAAAATTGCAAATTTTGAAAG
1 TTGTATTTTGGATGTTTTGCGATAAAATTGCAAATTTTGAAAG
622100 TTGTATTTTGGATGTTTTGCGATAAAATTGCAAATTTTGAAAG
1 TTGTATTTTGGATGTTTTGCGATAAAATTGCAAATTTTGAAAG
622143 TT
1 TT
622145 TAGGATAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (43 bp):
TTGTATTTTGGATGTTTTGCGATAAAATTGCAAATTTTGAAAG
Found at i:622618 original size:128 final size:126
Alignment explanation
Indices: 622377--622650 Score: 383
Period size: 128 Copynumber: 2.2 Consensus size: 126
622367 CCCGTTAATT
* *
622377 TAAACAAATATTAATCATTTTTAATCTTTTATATTCCTATGGGTATCCGTAGAGGTATAAAAGAT
1 TAAAAAAATATTAATCATTTTTAATCTTTTATATTCCTATGGGTATCCATAGAGGTATAAAAGAT
622442 TTCAAAAACTTTTCGTATCTTTTCGAGTATCCATTAAGGTACGAAATAATTTTTTTCCATAAAA
66 TTCAAAAACTTTTCGTATCTTTTCGAGTATCCATTAAGGTACGAAATAA-TTTTTT-CA-AAAA
* * * *
622506 TAAATAAATA-TAATCATTTTTAATTTTTTATATTCCTATGGGTATCTATAGGGGTATAAAAGAT
1 TAAAAAAATATTAATCATTTTTAATCTTTTATATTCCTATGGGTATCCATAGAGGTATAAAAGAT
* * * * * *
622570 TTTAGAAACTTTTCTTATCTTTTCAGGGTTTTCATTAAGGTACG-AATAATTTTTTCAAAAA
66 TTCAAAAACTTTTCGTATCTTTTC-GAGTATCCATTAAGGTACGAAATAATTTTTTCAAAAA
622631 TAAAAAAATATTAATC-TTTT
1 TAAAAAAATATTAATCATTTT
622651 ATATTCCTAT
Statistics
Matches: 131, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
125 17 0.13
126 7 0.05
127 6 0.05
128 76 0.58
129 25 0.19
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.43
Consensus pattern (126 bp):
TAAAAAAATATTAATCATTTTTAATCTTTTATATTCCTATGGGTATCCATAGAGGTATAAAAGAT
TTCAAAAACTTTTCGTATCTTTTCGAGTATCCATTAAGGTACGAAATAATTTTTTCAAAAA
Found at i:622695 original size:116 final size:123
Alignment explanation
Indices: 622382--622706 Score: 348
Period size: 128 Copynumber: 2.6 Consensus size: 123
622372 TAATTTAAAC
622382 AAATATTAATCATTTTTAATCTTTTATATTCCTATGGGTATCCGTA-GAGGTATAAAAGATTTCA
1 AAATA-TAATCA--TTTAATCTTTTATATTCCTATGGGTATCCGTATG-GGTATAAAAGATTTC-
*
622446 AAAACTTTTCGTATCTTTTCGAGTATCCATTAAGGTACGAAATAATTTTTTTCCATAAAATAAAT
61 -AAACTTTTCCTATCTTTTCGAGTATCCATTAAGGTACGAAATAATTTTTTTCCATAAAAT-AAT
* ** * *
622511 AAATATAATCATTTTTAATTTTTTATATTCCTATGGGTATCTATAGGGGTATAAAAGATTTTAGA
1 AAATATAATCA--TTTAATCTTTTATATTCCTATGGGTATCCGTATGGGTATAAAAGA-TTT-CA
* * * *
622576 AACTTTTCTTATCTTTTCAGGGTTTTCATTAAGGTACG-AATAA-TTTTTT-CA-AAAAT-A-
62 AACTTTTCCTATCTTTTC-GAGTATCCATTAAGGTACGAAATAATTTTTTTCCATAAAATAAT
*
622633 AAA-A-AAT-A-TTAATCTTTTATATTCCTATAGGTATCCGTATGGGATATTAAAAGATTTCAAA
1 AAATATAATCATTTAATCTTTTATATTCCTATGGGTATCCGTATGGG-TA-TAAAAGATTTCAAA
622694 CTTTTCCTATCTT
64 CTTTTCCTATCTT
622707 GGCGGGTTTG
Statistics
Matches: 175, Mismatches: 15, Indels: 25
0.81 0.07 0.12
Matches are distributed among these distances:
116 45 0.26
117 5 0.03
118 7 0.04
119 1 0.01
120 3 0.02
121 1 0.01
122 3 0.02
123 1 0.01
125 5 0.03
126 2 0.01
127 6 0.03
128 71 0.41
129 25 0.14
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.43
Consensus pattern (123 bp):
AAATATAATCATTTAATCTTTTATATTCCTATGGGTATCCGTATGGGTATAAAAGATTTCAAACT
TTTCCTATCTTTTCGAGTATCCATTAAGGTACGAAATAATTTTTTTCCATAAAATAAT
Found at i:624653 original size:53 final size:53
Alignment explanation
Indices: 624553--624657 Score: 158
Period size: 53 Copynumber: 2.0 Consensus size: 53
624543 CTAAGTGTAC
* * *
624553 GATCGATGGAGTAGGTGTTTAGTGTCAAGTCCTCTTCATTTGATTATGTGGAT
1 GATCAATGGAGTAGGTGTTTAGTGTCAAGTCCTCCTCATTAGATTATGTGGAT
*
624606 GATCAATGGAGTAGGTGTTTAGTGTTAAGTCCTCCTCATTCAG-TTATGTGGA
1 GATCAATGGAGTAGGTGTTTAGTGTCAAGTCCTCCTCATT-AGATTATGTGGA
624658 AGATTGGTGG
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
53 46 0.98
54 1 0.02
ACGTcount: A:0.22, C:0.12, G:0.28, T:0.38
Consensus pattern (53 bp):
GATCAATGGAGTAGGTGTTTAGTGTCAAGTCCTCCTCATTAGATTATGTGGAT
Found at i:624785 original size:59 final size:58
Alignment explanation
Indices: 624683--624814 Score: 144
Period size: 59 Copynumber: 2.2 Consensus size: 58
624673 ACATTCTTGT
*
624683 TAAGTCCACTCTAGTCAAGTATTTGGAAGATCGGAAGAATTAGCAATTTAGTTTTCAGC
1 TAAGTCCACTCTAGTCAAGTATATGGAAGATCGGAAG-ATTAGCAATTTAGTTTTCAGC
* * * *
624742 TAAGTCTACTCTAGT-AAGTTATATGGAAGATTGGTTAAG-TTAGCAATTTGGTTTT-ATGT
1 TAAGTCCACTCTAGTCAAG-TATATGGAAGATCGG--AAGATTAGCAATTTAGTTTTCA-GC
*
624801 TAAATCCACTCTAG
1 TAAGTCCACTCTAG
624815 AGTTGAGAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
58 4 0.06
59 55 0.89
61 3 0.05
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (58 bp):
TAAGTCCACTCTAGTCAAGTATATGGAAGATCGGAAGATTAGCAATTTAGTTTTCAGC
Found at i:624897 original size:95 final size:95
Alignment explanation
Indices: 624727--624909 Score: 235
Period size: 95 Copynumber: 1.9 Consensus size: 95
624717 AAGAATTAGC
** *
624727 AATTTAGTTTTCAGCTAAGTCTACTCTAGTAAGTTATATGGAAGATTGGTTAAGTTAGCAATTTG
1 AATTTAGTTTTCAGCTAAGTCTACTCTAGTAAGTTATATGGAAGACCGGTTAAGTTAGCAATTTA
*
624792 GTTTTATGTTAAATCCACTCTAGAGTTGAG
66 GTTTCATGTTAAATCCACTCTAGAGTTGAG
* * * * *
624822 AATTTAG-TTTCTAGTTAAGTCTACTCTAGTTAGTTATGTGGAAGACCGG-TAGAGTTGGCAGTT
1 AATTTAGTTTTC-AGCTAAGTCTACTCTAGTAAGTTATATGGAAGACCGGTTA-AGTTAGCAATT
* *
624885 TAGTTTCCTGTTAAGTCCACTCTAG
64 TAGTTTCATGTTAAATCCACTCTAG
624910 TTAGTTATGT
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
94 6 0.08
95 69 0.92
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (95 bp):
AATTTAGTTTTCAGCTAAGTCTACTCTAGTAAGTTATATGGAAGACCGGTTAAGTTAGCAATTTA
GTTTCATGTTAAATCCACTCTAGAGTTGAG
Found at i:625062 original size:119 final size:118
Alignment explanation
Indices: 624822--625079 Score: 320
Period size: 119 Copynumber: 2.2 Consensus size: 118
624812 TAGAGTTGAG
* * * * * *
624822 AATTTAG-TTTCTAGTTAAGTCTACTCTAGTTAGTTATGTGGAAGACCGGTAGAGTTGGCAGTTT
1 AATTTAGTTTTCT-GTTAAGTCTACTCTAATCAATTATGTAGAAGACCGATAGAGTTAGCAGTTT
* * * *
624886 AGTTTCCTGTTAAGTCCACTCTAGTTAGTTATGTAGAAGACCGATAGAGTTCAC
65 AGTTTCCTATTAAGTCCACTCTAGTTAGTTACGTAGAAGACCAATAAAGTTCAC
*
624940 AATTTAGTTTTCTGTTAAGTCTACTCTAATCAATTATGTAGAAGACCTGATAGAGTTAGTAGTTT
1 AATTTAGTTTTCTGTTAAGTCTACTCTAATCAATTATGTAGAAGACC-GATAGAGTTAGCAGTTT
** * * * **
625005 AGTTTTGTATTAATTCCACTCTAGTTGGTTACGTGGAAGACCAATAAAGTTGGC
65 AGTTTCCTATTAAGTCCACTCTAGTTAGTTACGTAGAAGACCAATAAAGTTCAC
*
625059 AATTTAGTTTTTTGTTAAGTC
1 AATTTAGTTTTCTGTTAAGTC
625080 CGCTCTAGTT
Statistics
Matches: 119, Mismatches: 19, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
118 37 0.31
119 82 0.69
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.39
Consensus pattern (118 bp):
AATTTAGTTTTCTGTTAAGTCTACTCTAATCAATTATGTAGAAGACCGATAGAGTTAGCAGTTTA
GTTTCCTATTAAGTCCACTCTAGTTAGTTACGTAGAAGACCAATAAAGTTCAC
Found at i:625093 original size:59 final size:59
Alignment explanation
Indices: 624812--625089 Score: 299
Period size: 59 Copynumber: 4.7 Consensus size: 59
624802 AAATCCACTC
* * *
624812 TAGAGTTGAG-AATTTAG-TTTCTAGTTAAGTCTACTCTAGTTAGTTATGTGGAAGACCGG
1 TAGAGTTG-GCAATTTAGTTTTCT-GTTAAGTCCACTCTAGTTAGTTATGTAGAAGACCGA
* *
624871 TAGAGTTGGCAGTTTAGTTTCCTGTTAAGTCCACTCTAGTTAGTTATGTAGAAGACCGA
1 TAGAGTTGGCAATTTAGTTTTCTGTTAAGTCCACTCTAGTTAGTTATGTAGAAGACCGA
** * * * *
624930 TAGAGTTCACAATTTAGTTTTCTGTTAAGTCTACTCTAATCAATTATGTAGAAGACCTGA
1 TAGAGTTGGCAATTTAGTTTTCTGTTAAGTCCACTCTAGTTAGTTATGTAGAAGACC-GA
* * * * * * * * * *
624990 TAGAGTTAGTAGTTTAGTTTTGTATTAATTCCACTCTAGTTGGTTACGTGGAAGACCAA
1 TAGAGTTGGCAATTTAGTTTTCTGTTAAGTCCACTCTAGTTAGTTATGTAGAAGACCGA
* * *
625049 TAAAGTTGGCAATTTAGTTTTTTGTTAAGTCCGCTCTAGTT
1 TAGAGTTGGCAATTTAGTTTTCTGTTAAGTCCACTCTAGTT
625090 GGTTTTCAAT
Statistics
Matches: 180, Mismatches: 36, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
58 1 0.01
59 130 0.72
60 49 0.27
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (59 bp):
TAGAGTTGGCAATTTAGTTTTCTGTTAAGTCCACTCTAGTTAGTTATGTAGAAGACCGA
Found at i:626915 original size:23 final size:23
Alignment explanation
Indices: 626889--626944 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
626879 TAGCTGCTCA
* * *
626889 TTCTTTTCTTCTTTTTCTGCTTG
1 TTCTTCTCTTCATTTGCTGCTTG
*
626912 TTCTTCTCCTCATTTGCTGCTTG
1 TTCTTCTCTTCATTTGCTGCTTG
626935 TTCTTCTCTT
1 TTCTTCTCTT
626945 TTACTGCCCC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.02, C:0.27, G:0.09, T:0.62
Consensus pattern (23 bp):
TTCTTCTCTTCATTTGCTGCTTG
Found at i:626951 original size:20 final size:19
Alignment explanation
Indices: 626894--626951 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 19
626884 GCTCATTCTT
626894 TTCTTCT-TTTTCTGCTTG
1 TTCTTCTCTTTTCTGCTTG
626912 TTCTTCTCCTCATTTGCTGCTTG
1 TTCTTCT-CT--TTT-CTGCTTG
626935 TTCTTCTCTTTTACTGC
1 TTCTTCTCTTTT-CTGC
626952 CCCTTCCTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
18 7 0.21
20 8 0.24
22 5 0.15
23 14 0.41
ACGTcount: A:0.03, C:0.28, G:0.10, T:0.59
Consensus pattern (19 bp):
TTCTTCTCTTTTCTGCTTG
Found at i:627730 original size:19 final size:18
Alignment explanation
Indices: 627706--627750 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
627696 ATATGAATGT
627706 ATGAAATGAAAGCAATCC
1 ATGAAATGAAAGCAATCC
* *
627724 AATGAAATGAATGCAATGC
1 -ATGAAATGAAAGCAATCC
627743 ATGAAATG
1 ATGAAATG
627751 TTTCTTCGGC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.49, C:0.11, G:0.20, T:0.20
Consensus pattern (18 bp):
ATGAAATGAAAGCAATCC
Found at i:627802 original size:22 final size:20
Alignment explanation
Indices: 627770--627831 Score: 54
Period size: 22 Copynumber: 3.0 Consensus size: 20
627760 CTTTCCTCCC
*
627770 TTTTTTAATTAATTATTTTT
1 TTTTTTTATTAATTATTTTT
*
627790 TATTTTTTGATTATTTAAATTTTT
1 T-TTTTTT-ATTAATT--ATTTTT
*
627814 TTGTTTTATT-ATTATTTT
1 TTTTTTTATTAATTATTTT
627832 AATTTTATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
19 5 0.15
20 1 0.03
21 7 0.21
22 9 0.26
23 5 0.15
24 7 0.21
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (20 bp):
TTTTTTTATTAATTATTTTT
Found at i:627820 original size:25 final size:25
Alignment explanation
Indices: 627785--627837 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
627775 TAATTAATTA
627785 TTTTTTATTTT-TTGATTATTTAAAT
1 TTTTTTATTTTATT-ATTATTTAAAT
* *
627810 TTTTTTGTTTTATTATTATTTTAAT
1 TTTTTTATTTTATTATTATTTAAAT
627835 TTT
1 TTT
627838 ATATAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 23 0.92
26 2 0.08
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (25 bp):
TTTTTTATTTTATTATTATTTAAAT
Found at i:648138 original size:51 final size:52
Alignment explanation
Indices: 648024--648161 Score: 190
Period size: 52 Copynumber: 2.7 Consensus size: 52
648014 ATTTAACTAG
* * * * *
648024 ATGTATCGATATATTGAAAAATGTATTAATAAATTTAGGTCAAAAACTCAAA
1 ATGTATCGATACAATGAAAAATGTATCAATACATTTAGGTCAAAAACCCAAA
* *
648076 ATGTATTGATACAATGAAAAATGTATCAATACATTTGGGTC-AAAACCCAAA
1 ATGTATCGATACAATGAAAAATGTATCAATACATTTAGGTCAAAAACCCAAA
*
648127 ATGTATCGATACAAT-AAAAATGTATCGATACATTT
1 ATGTATCGATACAATGAAAAATGTATCAATACATTT
648162 TTTTCCAAAA
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
50 19 0.25
51 23 0.30
52 35 0.45
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.31
Consensus pattern (52 bp):
ATGTATCGATACAATGAAAAATGTATCAATACATTTAGGTCAAAAACCCAAA
Found at i:648226 original size:20 final size:20
Alignment explanation
Indices: 648198--648250 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
648188 AACAGGTCCA
* *
648198 GTATTGATACATTTACTCAT
1 GTATCGATACATTCACTCAT
*
648218 GTATCGATACATTCACTTAT
1 GTATCGATACATTCACTCAT
*
648238 GTATCAATACATT
1 GTATCGATACATT
648251 AACTTGTTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.32, C:0.17, G:0.09, T:0.42
Consensus pattern (20 bp):
GTATCGATACATTCACTCAT
Found at i:649163 original size:51 final size:51
Alignment explanation
Indices: 649103--649221 Score: 161
Period size: 51 Copynumber: 2.3 Consensus size: 51
649093 TACATTGAAG
* *
649103 AATGTATCAATAAATTT-AGGTCAAAAACCCAAAATATATTGAT-TCAATAAA
1 AATGTATCAATACATTTGA-GTCAAAAACCCAAAATATATCGATAT-AATAAA
* *
649154 AATGTATCAATACATTTGAGTCAAAAACCCAGAATGTATCGATATAATAAA
1 AATGTATCAATACATTTGAGTCAAAAACCCAAAATATATCGATATAATAAA
*
649205 AATGTATCGATACATTT
1 AATGTATCAATACATTT
649222 TTTTTCCAGA
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
51 59 0.97
52 2 0.03
ACGTcount: A:0.47, C:0.13, G:0.10, T:0.30
Consensus pattern (51 bp):
AATGTATCAATACATTTGAGTCAAAAACCCAAAATATATCGATATAATAAA
Found at i:649324 original size:21 final size:20
Alignment explanation
Indices: 649259--649330 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
649249 ACCAGGTCCA
* * *
649259 GTATCGATATATTTACTCTT
1 GTATCGATACATTAACTTTT
* *
649279 GTATCGATACATTTACTTAT
1 GTATCGATACATTAACTTTT
*
649299 GTATCAATACATTAACTTGTT
1 GTATCGATACATTAACTT-TT
649320 GTATCGATACA
1 GTATCGATACA
649331 AGTAGCAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
20 33 0.75
21 11 0.25
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (20 bp):
GTATCGATACATTAACTTTT
Found at i:650409 original size:26 final size:26
Alignment explanation
Indices: 650307--650407 Score: 93
Period size: 25 Copynumber: 3.9 Consensus size: 26
650297 TATTATATAG
* *
650307 AATAATATAATAAAATAGATAAAT-T
1 AATAATATTATAAAATATATAAATGT
*
650332 -ATAATATTCATAAAGATA-ATAAATATTT
1 AATAATATT-ATAAA-ATATAT-AA-ATGT
*
650360 AATAATATTATCAAATATATAAATGT
1 AATAATATTATAAAATATATAAATGT
*
650386 AATAATA-TATAAAATATTTAAA
1 AATAATATTATAAAATATATAAA
650408 ATATACAGTA
Statistics
Matches: 64, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
24 7 0.11
25 20 0.31
26 15 0.23
27 7 0.11
28 7 0.11
29 8 0.12
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (26 bp):
AATAATATTATAAAATATATAAATGT
Found at i:650610 original size:10 final size:10
Alignment explanation
Indices: 650592--650758 Score: 98
Period size: 10 Copynumber: 16.3 Consensus size: 10
650582 ACTTAATAAT
*
650592 ATATATTAAA
1 ATATTTTAAA
*
650602 ATATTTTAAT
1 ATATTTTAAA
*
650612 ATATTTTCAA
1 ATATTTTAAA
*
650622 ATATTTTAGTA
1 ATATTTTA-AA
650633 ATA-TTTAATA
1 ATATTTTAA-A
*
650643 TTATTTTAAA
1 ATATTTTAAA
**
650653 A-ATAAT-AA
1 ATATTTTAAA
650661 ATAATTTTTAAA
1 AT-A-TTTTAAA
*
650673 A-ACTCTTAATA
1 ATA-TTTTAA-A
650684 ATA-TTTAATA
1 ATATTTTAA-A
650694 A-ATTATTAAA
1 ATATT-TTAAA
650704 ATATTTTAAA
1 ATATTTTAAA
650714 ATA-TTTAATA
1 ATATTTTAA-A
650724 ATATATTT-AA
1 ATAT-TTTAAA
650734 ATATTTTAATA
1 ATATTTTAA-A
650745 ATATTTTAACA
1 ATATTTTAA-A
650756 ATA
1 ATA
650759 ATTATATTAT
Statistics
Matches: 123, Mismatches: 17, Indels: 33
0.71 0.10 0.19
Matches are distributed among these distances:
8 3 0.02
9 12 0.10
10 66 0.54
11 35 0.28
12 7 0.06
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (10 bp):
ATATTTTAAA
Found at i:650611 original size:20 final size:20
Alignment explanation
Indices: 650524--650808 Score: 102
Period size: 20 Copynumber: 14.1 Consensus size: 20
650514 TCTAATAACA
*
650524 ATATATTCAAATTATTTTAATT
1 ATATATT-AAAATATTTTAA-T
*
650546 ATTATATTTATAA-ATTTTAAT
1 A-TATA-TTAAAATATTTTAAT
* *
650567 GATATATTACACAAAACTTAATAAT
1 -ATATATTA-A-AATA-TT-TTAAT
650592 ATATATTAAAATATTTTAAT
1 ATATATTAAAATATTTTAAT
* * *
650612 ATATTTTCAAATATTTTAGT
1 ATATATTAAAATATTTTAAT
*
650632 A-ATATTTAATATTATTTTAA-
1 ATATA-TTAA-AATATTTTAAT
* *
650652 AAATAAT-AAATAATTTTTAA-
1 ATATATTAAAAT-A-TTTTAAT
* *
650672 AAACTCTTAATAATA-TTTAAT
1 ATA-TATTAA-AATATTTTAAT
* *
650693 AAATTATTAAAATATTTTAAA
1 ATA-TATTAAAATATTTTAAT
650714 ATAT-TTAATAATATATTTAA-
1 ATATATTAA-AATAT-TTTAAT
* *
650734 ATATTTTAATAATATTTTAAC
1 ATATATTAA-AATATTTTAAT
650755 A-ATAATT---ATATTATTAA-
1 ATAT-ATTAAAATATT-TTAAT
650772 ATATATT----TA-TTTAAT
1 ATATATTAAAATATTTTAAT
650787 AATATATTAAAATATTTTAAT
1 -ATATATTAAAATATTTTAAT
650808 A
1 A
650809 ATAATAATCA
Statistics
Matches: 209, Mismatches: 22, Indels: 66
0.70 0.07 0.22
Matches are distributed among these distances:
14 4 0.02
15 1 0.00
16 9 0.04
17 9 0.04
18 8 0.04
19 8 0.04
20 68 0.33
21 59 0.28
22 16 0.08
23 11 0.05
24 12 0.06
25 4 0.02
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (20 bp):
ATATATTAAAATATTTTAAT
Found at i:650656 original size:21 final size:21
Alignment explanation
Indices: 650592--650811 Score: 126
Period size: 20 Copynumber: 10.6 Consensus size: 21
650582 ACTTAATAAT
*
650592 ATATATTAA-AATATTTT-AAT
1 ATAT-TTAATAATATTTTAAAA
* **
650612 ATATTTTCA-AATATTTTAGTA
1 ATA-TTTAATAATATTTTAAAA
*
650633 ATATTTAATATTATTTTAAAA
1 ATATTTAATAATATTTTAAAA
* *
650654 ATAATAAATAAT-TTTTAAAA
1 ATATTTAATAATATTTTAAAA
*
650674 ACT-CTTAATAATA-TTTAATAA
1 A-TATTTAATAATATTTTAA-AA
650695 AT-TATTAA-AATATTTT-AAA
1 ATAT-TTAATAATATTTTAAAA
*
650714 ATATTTAATAATATATTTAAAT
1 ATATTTAATAATAT-TTTAAAA
*
650736 AT-TTTAATAATATTTTAACA
1 ATATTTAATAATATTTTAAAA
* *
650756 ATAATT-AT-AT-TATTAAATA
1 ATATTTAATAATATTTTAAA-A
*
650775 TATTTATTTAATAATATATT-AAA
1 -A--TATTTAATAATATTTTAAAA
650798 ATATTTTAATAATA
1 ATA-TTTAATAATA
650812 ATAATCAATA
Statistics
Matches: 158, Mismatches: 21, Indels: 41
0.72 0.10 0.19
Matches are distributed among these distances:
18 5 0.03
19 11 0.07
20 63 0.40
21 59 0.37
22 9 0.06
23 3 0.02
24 4 0.03
25 4 0.03
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
ATATTTAATAATATTTTAAAA
Found at i:650717 original size:30 final size:30
Alignment explanation
Indices: 650644--650811 Score: 144
Period size: 30 Copynumber: 5.4 Consensus size: 30
650634 TATTTAATAT
* * * *
650644 TATTTTAAAAATAATAAATAATTTTTAAAA
1 TATTTTAATAATATTTAATAATTATTAAAA
*
650674 -ACTCTTAATAATATTTAATAAATTATTAAAA
1 TA-TTTTAATAATATTTAAT-AATTATTAAAA
*
650705 TATTTTAA-AATATTTAATAATATATTTAAA
1 TATTTTAATAATATTTAATAAT-TATTAAAA
* * * *
650735 TATTTTAATAATATTTTAACAATAATTATAT
1 TATTTTAATAATA-TTTAATAATTATTAAAA
*
650766 TA-TTAAATATATTTATTTAATAATATATTAAAA
1 TATTTTAATA-A--TATTTAATAAT-TATTAAAA
650799 TATTTTAATAATA
1 TATTTTAATAATA
650812 ATAATCAATA
Statistics
Matches: 109, Mismatches: 18, Indels: 21
0.74 0.12 0.14
Matches are distributed among these distances:
29 4 0.04
30 44 0.40
31 28 0.26
32 17 0.16
33 10 0.09
34 6 0.06
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (30 bp):
TATTTTAATAATATTTAATAATTATTAAAA
Found at i:650762 original size:64 final size:64
Alignment explanation
Indices: 650644--650811 Score: 156
Period size: 64 Copynumber: 2.7 Consensus size: 64
650634 TATTTAATAT
* * * * *
650644 TATTTTAAAAATAATAAATAAT-T-TTTAAAAACTCTTAATAATATTTAATAAA-T-TATTA-AA
1 TATTTT-AAAATATTTAATAATATATTTAAATA-TTTTAATAATATTTAAAAAATTATATTATAA
650704 A
64 A
650705 TATTTTAAAATATTTAATAATATATTTAAATATTTTAATAATATTTTAACAATAATTATATTATT
1 TATTTTAAAATATTTAATAATATATTTAAATATTTTAATAATA-TTTAA-AA-AATTATATTA-T
650770 AAA
62 AAA
* *
650773 TATATT----TATTTAATAATATATTAAAATATTTTAATAATA
1 TATTTTAAAATATTTAATAATATATTTAAATATTTTAATAATA
650812 ATAATCAATA
Statistics
Matches: 91, Mismatches: 7, Indels: 15
0.81 0.06 0.13
Matches are distributed among these distances:
60 13 0.14
61 17 0.19
62 12 0.13
63 1 0.01
64 34 0.37
65 1 0.01
66 5 0.05
68 8 0.09
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (64 bp):
TATTTTAAAATATTTAATAATATATTTAAATATTTTAATAATATTTAAAAAATTATATTATAAA
Found at i:650821 original size:21 final size:21
Alignment explanation
Indices: 650678--650811 Score: 113
Period size: 21 Copynumber: 6.4 Consensus size: 21
650668 TTAAAAACTC
650678 TTAATAATAT-TTAATAA-ATT
1 TTAATAATATATTAA-AATATT
*
650698 ATTAA-AATATTTTAAAATA-T
1 -TTAATAATATATTAAAATATT
*
650718 TTAATAATATATTTAAATATT
1 TTAATAATATATTAAAATATT
* *
650739 TTAATAATATTTTAACAATA-A
1 TTAATAATATATTAA-AATATT
650760 TT-AT-AT-TATTAAATATATTTAT
1 TTAATAATATATTAAA-ATA--T-T
650782 TTAATAATATATTAAAATATT
1 TTAATAATATATTAAAATATT
650803 TTAATAATA
1 TTAATAATA
650812 ATAATCAATA
Statistics
Matches: 93, Mismatches: 7, Indels: 26
0.74 0.06 0.21
Matches are distributed among these distances:
17 1 0.01
18 8 0.09
19 6 0.06
20 22 0.24
21 35 0.38
22 7 0.08
23 2 0.02
24 5 0.05
25 7 0.08
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (21 bp):
TTAATAATATATTAAAATATT
Found at i:654285 original size:26 final size:26
Alignment explanation
Indices: 654255--654307 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
654245 ATAGTGATTG
*
654255 ATCCAAAAGAGGGAGTTAATGTCGTA
1 ATCCAAAAGAAGGAGTTAATGTCGTA
654281 ATCCAAAAGAAGGAGTTAATGTCGTA
1 ATCCAAAAGAAGGAGTTAATGTCGTA
654307 A
1 A
654308 CTCTCACTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.11, G:0.25, T:0.23
Consensus pattern (26 bp):
ATCCAAAAGAAGGAGTTAATGTCGTA
Found at i:661049 original size:114 final size:113
Alignment explanation
Indices: 660849--661075 Score: 282
Period size: 114 Copynumber: 2.0 Consensus size: 113
660839 TTAAGTAAGG
* * * **
660849 TCATAAATTATTTAATTTTAGACTATGTCTTATAAAAATATATATTAGATAAAATAGATTCCACG
1 TCATAAATTATTTAATTTAAGACTAAGCCTTATAAAAATATATATTAGATAAAATAGAGCCCACG
* **
660914 TGCTTATTTAATTAAGTTATTT-GAGTTTATTTTATTTAATTATATTAGA
66 T-CATATTTAATTAAGTTATTTAG-GCCTATTTTATTTAATTATATTAGA
* *
660963 TCATAAATTATTTAATTTAAG-GTCAAGCCTTATAAAAAATATATATTGGATAAAATAGAGCCAC
1 TCATAAATTATTTAATTTAAGACT-AAGCCTTAT-AAAAATATATATTAGATAAAATAGAGCC-C
661027 ACGT-ATATTTAATTAA-TATATTTAGGCCTATTTTATTTAATTATATTAG
63 ACGTCATATTTAATTAAGT-TATTTAGGCCTATTTTATTTAATTATATTAG
661076 GCTAATTTTT
Statistics
Matches: 98, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
113 2 0.02
114 65 0.66
115 26 0.27
116 5 0.05
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.44
Consensus pattern (113 bp):
TCATAAATTATTTAATTTAAGACTAAGCCTTATAAAAATATATATTAGATAAAATAGAGCCCACG
TCATATTTAATTAAGTTATTTAGGCCTATTTTATTTAATTATATTAGA
Found at i:661066 original size:24 final size:23
Alignment explanation
Indices: 661033--661094 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 23
661023 CCACACGTAT
*
661033 ATTTAATTAATATATTTAGGCCTA
1 ATTTATTTAATATATTTAGG-CTA
*
661057 TTTTATTTAAT-TATATTAGGCTA
1 ATTTATTTAATATAT-TTAGGCTA
661080 ATTT-TTTAA-ATATTT
1 ATTTATTTAATATATTT
661095 TAAATTTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
21 2 0.06
22 8 0.24
23 9 0.27
24 14 0.42
ACGTcount: A:0.34, C:0.05, G:0.06, T:0.55
Consensus pattern (23 bp):
ATTTATTTAATATATTTAGGCTA
Found at i:663682 original size:22 final size:22
Alignment explanation
Indices: 663657--663700 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
663647 ATGCAATAAT
663657 ATCAAA-TTATTATTTTACAAAA
1 ATCAAATTTATTATTTT-CAAAA
663679 ATCAAATTTATTATTTTCAAAA
1 ATCAAATTTATTATTTTCAAAA
663701 TTCATGCATC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (22 bp):
ATCAAATTTATTATTTTCAAAA
Found at i:664902 original size:2 final size:2
Alignment explanation
Indices: 664895--664922 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
664885 TAATTTGGTA
664895 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
664923 GAATTTAGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:665583 original size:2 final size:2
Alignment explanation
Indices: 665576--665601 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
665566 GAAGAAATAG
665576 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
665602 TAAAGGTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:666660 original size:24 final size:23
Alignment explanation
Indices: 666608--666663 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 23
666598 AAATTTTGAC
*
666608 ATATTTATTTGTGTTATATTTATA
1 ATATTT-TTTGTGTGATATTTATA
*
666632 TTATTTTTTCGTGTGATATTT-TAA
1 ATATTTTTT-GTGTGATATTTAT-A
666656 ATATTTTT
1 ATATTTTT
666664 CTTGAATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 4 0.15
24 23 0.85
ACGTcount: A:0.25, C:0.02, G:0.09, T:0.64
Consensus pattern (23 bp):
ATATTTTTTGTGTGATATTTATA
Found at i:667392 original size:21 final size:21
Alignment explanation
Indices: 667359--667399 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
667349 CTAAGTAAAA
667359 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
667380 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
667400 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:667561 original size:53 final size:53
Alignment explanation
Indices: 667479--667615 Score: 229
Period size: 53 Copynumber: 2.6 Consensus size: 53
667469 AGATTGCATA
* *
667479 GTATCGATGCACACAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
1 GTATCGATACACAC-AATATGTATCGATACAGGACACTGGCAGTAGCCAAATTT
*
667533 GTATCGATACACACAATATGTATCGATACAGGTCACTGGCAGTAGCCAAATTT
1 GTATCGATACACACAATATGTATCGATACAGGACACTGGCAGTAGCCAAATTT
*
667586 GTATCGATACACAAAATATGTATCGATACA
1 GTATCGATACACACAATATGTATCGATACA
667616 TTGGTAGTAG
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
53 66 0.84
54 13 0.16
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.26
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAGGACACTGGCAGTAGCCAAATTT
Found at i:667658 original size:10 final size:10
Alignment explanation
Indices: 667639--667679 Score: 64
Period size: 10 Copynumber: 4.1 Consensus size: 10
667629 AATCTCATTT
*
667639 TCACTGTTCA
1 TCACTATTCA
667649 TCACTATTCA
1 TCACTATTCA
667659 TCACTATTCA
1 TCACTATTCA
*
667669 TCACTGTTCA
1 TCACTATTCA
667679 T
1 T
667680 GTATCGATAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.24, C:0.29, G:0.05, T:0.41
Consensus pattern (10 bp):
TCACTATTCA
Found at i:667693 original size:22 final size:23
Alignment explanation
Indices: 667667--667723 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 23
667657 CATCACTATT
667667 CATCACTGTTCATGTATCGAT-A
1 CATCACTGTTCATGTATCGATAA
*
667689 CATCACT-TTCATGTATCGTTAA
1 CATCACTGTTCATGTATCGATAA
*
667711 AATCACTGTTCAT
1 CATCACTGTTCAT
667724 AGGTCATTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 12 0.39
22 14 0.45
23 5 0.16
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.39
Consensus pattern (23 bp):
CATCACTGTTCATGTATCGATAA
Found at i:669548 original size:13 final size:13
Alignment explanation
Indices: 669530--669557 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
669520 AAATTCAATT
669530 TATATATATATAA
1 TATATATATATAA
669543 TATATATATATAA
1 TATATATATATAA
669556 TA
1 TA
669558 CAGTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TATATATATATAA
Found at i:669578 original size:114 final size:109
Alignment explanation
Indices: 669419--669652 Score: 312
Period size: 111 Copynumber: 2.1 Consensus size: 109
669409 GGCTATAAAC
* * *
669419 ATATCTATATAATATATATAAAATATAGTTTTTTTTGCATAAATGCTAATATTTATTATTAGTTT
1 ATATATATATAATATATATAAAATACAGTTTTTTTTGCATAAATGCTAATATTTATTATGAG--T
*
669484 TTTTAAAACAAATTTCATATATTATAATAATTCATTAAATTCAATTT
64 TTTTAAAA-AAATTTCATATATTATAATAATTCATTAAATTCAATAT
669531 ATATATATATAATATATATATATAATACAG-TTTTTTTGACATAAATGCTAATATTTATTATGAG
1 ATATATATATAATATATATA-A-AATACAGTTTTTTTTG-CATAAATGCTAATATTTATTATGAG
* ** * *
669595 TTTTTCAAAATTTTTTATGTATTATAATAATTCATTAAATTCAATAT
63 TTTTTAAAAAAATTTCATATATTATAATAATTCATTAAATTCAATAT
669642 ATA-ATAT-TAAT
1 ATATATATATAAT
669653 TTAACTAATT
Statistics
Matches: 110, Mismatches: 9, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
109 4 0.04
110 4 0.04
111 36 0.33
112 27 0.25
113 9 0.08
114 30 0.27
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (109 bp):
ATATATATATAATATATATAAAATACAGTTTTTTTTGCATAAATGCTAATATTTATTATGAGTTT
TTAAAAAAATTTCATATATTATAATAATTCATTAAATTCAATAT
Found at i:669732 original size:47 final size:43
Alignment explanation
Indices: 669660--669756 Score: 108
Period size: 47 Copynumber: 2.2 Consensus size: 43
669650 AATTTAACTA
*
669660 ATTAATTTTATCTCATTCATCTTCATTCATTATGTATAATATAATAT
1 ATTAATTTTATCTCATGCATCTTCATTCA--AT-T-TAATATAATAT
* *
669707 ATTAATTTTATCTCA-GCCTCATTCATTGAATTTAATATAATAT
1 ATTAATTTTATCTCATGCATC-TTCATTCAATTTAATATAATAT
669750 A-TAATTT
1 ATTAATTT
669757 CATTAATTAC
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
42 6 0.13
43 12 0.26
44 1 0.02
45 2 0.04
46 3 0.07
47 22 0.48
ACGTcount: A:0.35, C:0.12, G:0.03, T:0.49
Consensus pattern (43 bp):
ATTAATTTTATCTCATGCATCTTCATTCAATTTAATATAATAT
Found at i:669798 original size:60 final size:60
Alignment explanation
Indices: 669731--669850 Score: 206
Period size: 60 Copynumber: 2.0 Consensus size: 60
669721 AGCCTCATTC
* *
669731 ATTGAATTTAATATAATATA-TAATTTCATTAATTACTTTTTAAATTATATTTTAATTCTT
1 ATTGAATTTAATATAATATATTAAGTTCATTAATTA-ATTTTAAATTATATTTTAATTCTT
669791 ATTGAATTTAATATAATATATTAAGTTCATTAATTAATTTTAAATTATATTTTAATTCTT
1 ATTGAATTTAATATAATATATTAAGTTCATTAATTAATTTTAAATTATATTTTAATTCTT
669851 TTTAGTAGAA
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
60 43 0.75
61 14 0.25
ACGTcount: A:0.39, C:0.04, G:0.03, T:0.54
Consensus pattern (60 bp):
ATTGAATTTAATATAATATATTAAGTTCATTAATTAATTTTAAATTATATTTTAATTCTT
Found at i:669830 original size:31 final size:31
Alignment explanation
Indices: 669725--669848 Score: 100
Period size: 31 Copynumber: 4.1 Consensus size: 31
669715 TATCTCAGCC
*
669725 TCATTCATTGAATTTAATATAATATA-TAATT
1 TCATTAATTGAATTTAATATAATATATTAA-T
* * *
669756 TCATTAATT-ACTTTTTAA-ATTATATTTTAAT
1 TCATTAATTGA--ATTTAATATAATATATTAAT
669787 TC-TT-ATTGAATTTAATATAATATATTAAGT
1 TCATTAATTGAATTTAATATAATATATTAA-T
* *
669817 TCATTAATT-AATTTTAA-ATTATATTTTAAT
1 TCATTAATTGAA-TTTAATATAATATATTAAT
669847 TC
1 TC
669849 TTTTTAGTAG
Statistics
Matches: 75, Mismatches: 9, Indels: 19
0.73 0.09 0.18
Matches are distributed among these distances:
28 5 0.07
29 13 0.17
30 10 0.13
31 31 0.41
32 16 0.21
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (31 bp):
TCATTAATTGAATTTAATATAATATATTAAT
Found at i:671403 original size:21 final size:20
Alignment explanation
Indices: 671376--671429 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
671366 ATTTTCAAAA
*
671376 AGATATAATTTT-ATATTTTT
1 AGATATAATTTTCA-AATTTT
*
671396 AGCATATATTTTTCAAATTTT
1 AG-ATATAATTTTCAAATTTT
671417 AGATATTAATTTT
1 AGATA-TAATTTT
671430 TTAAAAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 5 0.18
21 22 0.79
22 1 0.04
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.56
Consensus pattern (20 bp):
AGATATAATTTTCAAATTTT
Found at i:671446 original size:30 final size:30
Alignment explanation
Indices: 671411--671474 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 30
671401 ATATTTTTCA
671411 AATTTTAGATATT-AAT-TTTTTAAAAATAAT
1 AATTTTA-ATATTCAATATTTTT-AAAATAAT
* *
671441 AATTTTAATATTCTATATTTTTAAAATATT
1 AATTTTAATATTCAATATTTTTAAAATAAT
671471 AATT
1 AATT
671475 AAAACATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 5 0.17
30 20 0.67
31 5 0.17
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (30 bp):
AATTTTAATATTCAATATTTTTAAAATAAT
Found at i:671864 original size:2 final size:2
Alignment explanation
Indices: 671857--671881 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
671847 CTTTCTGTAC
671857 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
671882 TGTACAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:672587 original size:28 final size:29
Alignment explanation
Indices: 672555--672610 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
672545 TTAATCAAAT
* *
672555 ATTAATTTAAT-TATTAAAATAAATAAAA
1 ATTAATATAATATAATAAAATAAATAAAA
*
672583 ATTAATATAATATAATAATATAAATAAA
1 ATTAATATAATATAATAAAATAAATAAA
672611 TAAAAACGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 10 0.42
29 14 0.58
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (29 bp):
ATTAATATAATATAATAAAATAAATAAAA
Found at i:672989 original size:2 final size:2
Alignment explanation
Indices: 672982--673018 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
672972 GGTTAATGTT
672982 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
673019 TATTTGAGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:675752 original size:18 final size:18
Alignment explanation
Indices: 675709--675753 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
675699 ATTTAATTTT
* * *
675709 AATTATAAAATATATTAA
1 AATTAAAAAAAATATAAA
675727 AATGTAAAAAAAATATAAA
1 AAT-TAAAAAAAATATAAA
675746 AATTAAAA
1 AATTAAAA
675754 TTTTTTTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (18 bp):
AATTAAAAAAAATATAAA
Found at i:678970 original size:3 final size:3
Alignment explanation
Indices: 678964--678989 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
678954 GGGAGGAGGA
678964 GGT GGT GGT GGT GGT GGT GGT GGT GG
1 GGT GGT GGT GGT GGT GGT GGT GGT GG
678990 AATTTGAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.69, T:0.31
Consensus pattern (3 bp):
GGT
Found at i:681304 original size:17 final size:20
Alignment explanation
Indices: 681267--681310 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 20
681257 TTGATTCAGC
681267 TTAATTATTCTTTATAATTA
1 TTAATTATTCTTTATAATTA
681287 TTAA-TATT-TTTA-AATTA
1 TTAATTATTCTTTATAATTA
681304 -TAATTAT
1 TTAATTAT
681311 AAATCTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 4 0.17
19 4 0.17
20 4 0.17
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (20 bp):
TTAATTATTCTTTATAATTA
Done.