Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
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: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 90 of 311
Found at i:28848815 original size:34 final size:36
Alignment explanation
Indices: 28848767--28848833 Score: 95
Period size: 34 Copynumber: 1.9 Consensus size: 36
28848757 TTAATAAAAA
*
28848767 TAATATATAATTTAATAA-CATTATTAATATAATTAT
1 TAATATATAATTTAATAATAATT-TTAATATAATTAT
28848803 TAATA-AT-ATTTAATAATAATTTTAATATAAT
1 TAATATATAATTTAATAATAATTTTAATATAAT
28848834 AATATTATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 19 0.66
35 5 0.17
36 5 0.17
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (36 bp):
TAATATATAATTTAATAATAATTTTAATATAATTAT
Found at i:28853715 original size:15 final size:16
Alignment explanation
Indices: 28853690--28853726 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
28853680 TATGAATTTG
28853690 ATTTTTATACT-TTATT
1 ATTTTTATACTCTTA-T
28853706 ATTTTT-TACTCTTAT
1 ATTTTTATACTCTTAT
28853721 ATTTTT
1 ATTTTT
28853727 CAAATTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.70
Consensus pattern (16 bp):
ATTTTTATACTCTTAT
Found at i:28857501 original size:26 final size:25
Alignment explanation
Indices: 28857451--28857512 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 25
28857441 TTATTAATAA
28857451 AATAAAAATATTATGATTAAATTATT
1 AATAAAAATATTATGATTAAATTA-T
*
28857477 AATAAAAAT-TTATAAGA-TAATTTAT
1 AATAAAAATATTAT--GATTAAATTAT
*
28857502 AATTAAAATAT
1 AATAAAAATAT
28857513 ATTAAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
25 13 0.42
26 16 0.52
27 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.40
Consensus pattern (25 bp):
AATAAAAATATTATGATTAAATTAT
Found at i:28859296 original size:16 final size:15
Alignment explanation
Indices: 28859275--28859322 Score: 64
Period size: 16 Copynumber: 3.3 Consensus size: 15
28859265 ATAAAAGTAT
28859275 AAAAGAAAAAGATAA
1 AAAAGAAAAAGATAA
*
28859290 GAAAAGAAAAAAATAA
1 -AAAAGAAAAAGATAA
28859306 AAAA-AAAAAGA-AA
1 AAAAGAAAAAGATAA
28859319 AAAA
1 AAAA
28859323 TTTACCTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
13 6 0.20
14 6 0.20
15 4 0.13
16 14 0.47
ACGTcount: A:0.85, C:0.00, G:0.10, T:0.04
Consensus pattern (15 bp):
AAAAGAAAAAGATAA
Found at i:28860076 original size:14 final size:14
Alignment explanation
Indices: 28860053--28860093 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
28860043 TATTGTTATC
28860053 TTTA-TTTTTTGTT
1 TTTATTTTTTTGTT
*
28860066 TTTATTTTTTTATT
1 TTTATTTTTTTGTT
28860080 TTTATTTTTATTGT
1 TTTATTTTT-TTGT
28860094 CGTCATTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 4 0.17
14 17 0.71
15 3 0.12
ACGTcount: A:0.12, C:0.00, G:0.05, T:0.83
Consensus pattern (14 bp):
TTTATTTTTTTGTT
Found at i:28860091 original size:12 final size:13
Alignment explanation
Indices: 28860048--28860088 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
28860038 ATTAGTATTG
*
28860048 TTATCTTTATTTT
1 TTATTTTTATTTT
*
28860061 TTGTTTTTATTTTT
1 TTATTTTTA-TTTT
28860075 TTATTTTTATTTT
1 TTATTTTTATTTT
28860088 T
1 T
28860089 ATTGTCGTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.12, C:0.02, G:0.02, T:0.83
Consensus pattern (13 bp):
TTATTTTTATTTT
Found at i:28860427 original size:24 final size:24
Alignment explanation
Indices: 28860387--28860432 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
28860377 AATATTATAT
28860387 TATATATATCTATATAT-TTTTCG
1 TATATATATCTATATATGTTTTCG
*
28860410 TATATATTATGTATATATGTTTT
1 TATATA-TATCTATATATGTTTT
28860433 TAATATTGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 10 0.50
25 4 0.20
ACGTcount: A:0.30, C:0.04, G:0.07, T:0.59
Consensus pattern (24 bp):
TATATATATCTATATATGTTTTCG
Found at i:28862232 original size:30 final size:30
Alignment explanation
Indices: 28862198--28862257 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
28862188 ACTTAACAAG
*
28862198 CAAATACCTCTAAAATAATAATAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
** *
28862228 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
28862258 TAAAAAATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.28
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAACAAAATTAA
Found at i:28863883 original size:31 final size:31
Alignment explanation
Indices: 28863848--28863906 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
28863838 TAAAAATAGG
* *
28863848 TAGGGACTAATTT-GAAATAATTCTAAAAGTT
1 TAGGG-CTAATTTCAAAAAAATTCTAAAAGTT
*
28863879 TAGGGCTATTTTCAAAAAAATTCTAAAA
1 TAGGGCTAATTTCAAAAAAATTCTAAAA
28863907 ATAGGGGACA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 6 0.25
31 18 0.75
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34
Consensus pattern (31 bp):
TAGGGCTAATTTCAAAAAAATTCTAAAAGTT
Found at i:28867316 original size:20 final size:19
Alignment explanation
Indices: 28867280--28867330 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
28867270 AAAGGCTATT
*
28867280 TTGTAAA-GTTGTAAAATAA
1 TTGTAAATG-TGTGAAATAA
28867299 GTTGTAAATGTGTGAAATAA
1 -TTGTAAATGTGTGAAATAA
28867319 TTG-AAAT-TGTGA
1 TTGTAAATGTGTGA
28867331 GTTGCTATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 5 0.17
18 4 0.14
19 3 0.10
20 16 0.55
21 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37
Consensus pattern (19 bp):
TTGTAAATGTGTGAAATAA
Found at i:28868749 original size:63 final size:62
Alignment explanation
Indices: 28868659--28868830 Score: 186
Period size: 63 Copynumber: 2.8 Consensus size: 62
28868649 GTACATCATT
* * *
28868659 AACAGAAGCTCGAA-AGCTGAACAGAAGCTCATAAGAGCTAGACAGAAACCCATAAGGGTTG
1 AACAGAAGCTCGAAGAGCTGAACGGAAGCTCATAAGAGATAGACAGAAACCCATAAGAGTTG
* * * *
28868720 AACAAAAGCTCGTAAGAGCTGAATGGAAGCTCATAAGAGAT-GAATAGAAACTCATAAGAGTTG
1 AACAGAAGCTCG-AAGAGCTGAACGGAAGCTCATAAGAGATAG-ACAGAAACCCATAAGAGTTG
* * * * * * *
28868783 AATAGAAGCTCAAAGAGCTAAACGGAAACTCATATGAGTTAAACAGAA
1 AACAGAAGCTCGAAGAGCTGAACGGAAGCTCATAAGAGATAGACAGAA
28868831 GCTCGTAAGA
Statistics
Matches: 90, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
61 11 0.12
62 31 0.34
63 48 0.53
ACGTcount: A:0.45, C:0.16, G:0.23, T:0.16
Consensus pattern (62 bp):
AACAGAAGCTCGAAGAGCTGAACGGAAGCTCATAAGAGATAGACAGAAACCCATAAGAGTTG
Found at i:28868755 original size:42 final size:42
Alignment explanation
Indices: 28868676--28868841 Score: 131
Period size: 42 Copynumber: 4.0 Consensus size: 42
28868666 GCTCGAAAGC
* * * * * *
28868676 TGAACAGAAGCTCATAAGAGCT-AGACAGAAACCCATAAGGGT
1 TGAACAGAAACTCATAAGAGCTGA-ATAGAAGCTCATAAGAGA
* *
28868718 TGAACA-AAAGCTCGTAAGAGCTGAATGGAAGCTCATAAGAGA
1 TGAACAGAAA-CTCATAAGAGCTGAATAGAAGCTCATAAGAGA
* * *
28868760 TGAATAGAAACTCATAAGAGTTGAATAGAAGCTCA-AAGAGC
1 TGAACAGAAACTCATAAGAGCTGAATAGAAGCTCATAAGAGA
* * * * * * *
28868801 TAAACGGAAACTCATATGAGTTAAACAGAAGCTCGTAAGAG
1 TGAACAGAAACTCATAAGAGCTGAATAGAAGCTCATAAGAG
28868842 CTTAACAAAA
Statistics
Matches: 100, Mismatches: 20, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
41 35 0.35
42 61 0.61
43 4 0.04
ACGTcount: A:0.44, C:0.15, G:0.23, T:0.17
Consensus pattern (42 bp):
TGAACAGAAACTCATAAGAGCTGAATAGAAGCTCATAAGAGA
Found at i:28868811 original size:41 final size:41
Alignment explanation
Indices: 28868732--28868848 Score: 117
Period size: 41 Copynumber: 2.8 Consensus size: 41
28868722 CAAAAGCTCG
* * * * *
28868732 TAAGAGCTGAATGGAAGCTCATAAGAGATGAATAGAAACTCA
1 TAAGAGTTGAATAGAAGCTCA-AAGAGCTAAACAGAAACTCA
*
28868774 TAAGAGTTGAATAGAAGCTCAAAGAGCTAAACGGAAACTCA
1 TAAGAGTTGAATAGAAGCTCAAAGAGCTAAACAGAAACTCA
* * * * *
28868815 TATGAGTTAAACAGAAGCTCGTAAGAGCTTAACA
1 TAAGAGTTGAATAGAAGCTC-AAAGAGCTAAACA
28868849 AAAAGTAAAA
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
41 33 0.53
42 29 0.47
ACGTcount: A:0.44, C:0.14, G:0.22, T:0.20
Consensus pattern (41 bp):
TAAGAGTTGAATAGAAGCTCAAAGAGCTAAACAGAAACTCA
Found at i:28868848 original size:21 final size:21
Alignment explanation
Indices: 28868657--28868848 Score: 119
Period size: 21 Copynumber: 9.3 Consensus size: 21
28868647 GAGTACATCA
*
28868657 TTAACAGAAGCTC-GAA-AGC
1 TTAACAGAAGCTCATAAGAGC
*
28868676 TGAACAGAAGCTCATAAGAGC
1 TTAACAGAAGCTCATAAGAGC
* * *
28868697 -TAGACAGAAACCCATAAG-GG
1 TTA-ACAGAAGCTCATAAGAGC
* *
28868717 TTGAACAAAAGCTCGTAAGAGC
1 TT-AACAGAAGCTCATAAGAGC
* ** *
28868739 TGAATGGAAGCTCATAAGAGA
1 TTAACAGAAGCTCATAAGAGC
* * *
28868760 TGAATAGAAACTCATAAGAG-
1 TTAACAGAAGCTCATAAGAGC
*
28868780 TTGAATAGAAGCTCA-AAGAGC
1 TT-AACAGAAGCTCATAAGAGC
* * * *
28868801 TAAACGGAAACTCATATGAG-
1 TTAACAGAAGCTCATAAGAGC
*
28868821 TTAAACAGAAGCTCGTAAGAGC
1 TT-AACAGAAGCTCATAAGAGC
28868843 TTAACA
1 TTAACA
28868849 AAAAGTAAAA
Statistics
Matches: 131, Mismatches: 31, Indels: 20
0.72 0.17 0.11
Matches are distributed among these distances:
19 12 0.09
20 20 0.15
21 94 0.72
22 5 0.04
ACGTcount: A:0.44, C:0.16, G:0.22, T:0.18
Consensus pattern (21 bp):
TTAACAGAAGCTCATAAGAGC
Found at i:28888265 original size:20 final size:20
Alignment explanation
Indices: 28888242--28888279 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28888232 CACATCCAAA
*
28888242 TACAAAATTTTAAAAATCTT
1 TACAAAATATTAAAAATCTT
*
28888262 TACAAAATATTGAAAATC
1 TACAAAATATTAAAAATC
28888280 GCGAGTAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.34
Consensus pattern (20 bp):
TACAAAATATTAAAAATCTT
Found at i:28892664 original size:50 final size:50
Alignment explanation
Indices: 28892589--28892782 Score: 241
Period size: 50 Copynumber: 3.9 Consensus size: 50
28892579 AATGCTAGGG
* *
28892589 AGATATGTGAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTCC
1 AGATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCC
* * *
28892639 AGATATGAGAGCTAGTGTAAGACCATGTCTGGAACATGGCATC-GACACC
1 AGATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCC
* * *
28892688 -GATAGATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATTGGCCTCG
1 AGAT--ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCC
* * *
28892739 ATATACGAGAG-TCAGTGTAAGACTATGTCTGGGACATGGCATCG
1 AGATATGAGAGCT-AGTGTAAGACCATGTCTGGGACATGGCATCG
28892783 ACTTTGATGT
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
48 3 0.02
49 4 0.03
50 111 0.90
51 3 0.02
52 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (50 bp):
AGATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCC
Found at i:28892776 original size:100 final size:98
Alignment explanation
Indices: 28892597--28892823 Score: 285
Period size: 100 Copynumber: 2.3 Consensus size: 98
28892587 GGAGATATGT
* * *
28892597 GAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTCCAGATATGAGAGCTAGTGTAAGAC
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCCAGATACGAGAGCTAGTGTAAGAC
28892662 CATGTCTGGAACATGGCATCGACACCGATAGATGA
66 CATGTCTGGAACATGGCATCGACACCGAT-G-TGA
* * *
28892697 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATTGGCCTCGATATACGAGAG-TCAGTGTAAGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCCAGATACGAGAGCT-AGTGTAAGA
* * *** *
28892761 CTATGTCTGGGACATGGCATCGACTTTGATGTGT
65 CCATGTCTGGAACATGGCATCGACACCGATGTGA
* * *
28892795 GAACCAGTGTAAGACCATGACCGGGACAT
1 GAGCCAGTGTAAGACCATGTCTGGGACAT
28892824 AGCGTCAGCA
Statistics
Matches: 111, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
98 28 0.25
99 2 0.02
100 81 0.73
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.23
Consensus pattern (98 bp):
GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCCAGATACGAGAGCTAGTGTAAGAC
CATGTCTGGAACATGGCATCGACACCGATGTGA
Found at i:28904791 original size:40 final size:40
Alignment explanation
Indices: 28904645--28904829 Score: 198
Period size: 40 Copynumber: 4.7 Consensus size: 40
28904635 TTGAATGATG
* * * *
28904645 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * *
28904685 TCCGGACTAAAAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCT-AAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
28904725 TTCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
28904764 TCCGAGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
28904805 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28904830 AATGAGTAGC
Statistics
Matches: 119, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
39 35 0.29
40 72 0.61
41 12 0.10
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:28904852 original size:79 final size:79
Alignment explanation
Indices: 28904694--28904862 Score: 184
Period size: 79 Copynumber: 2.2 Consensus size: 79
28904684 ATCCGGACTA
* ** **
28904694 AAAT-CCGAAGGCATTTGTGCGAGATACTAATTTCGGGCTAAGCCCGAAGGCATTTGTGCGAGTT
1 AAATCCCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTT
28904758 ACTAAATCCGAGTT
66 ACTAAATCCGAGTT
* * * *
28904772 AAGTCCCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAATGAG
1 AAATCCCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAG
*
28904836 -TAGCTATATCCG-GTT
64 TTA-CTAAATCCGAGTT
*
28904851 AAATTCCGAAGG
1 AAATCCCGAAGG
28904863 TACGTGATTT
Statistics
Matches: 75, Mismatches: 12, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
78 5 0.07
79 45 0.60
80 25 0.33
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (79 bp):
AAATCCCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTT
ACTAAATCCGAGTT
Found at i:28914483 original size:50 final size:50
Alignment explanation
Indices: 28914359--28914542 Score: 177
Period size: 50 Copynumber: 3.8 Consensus size: 50
28914349 GGCTTGGCTA
* * **
28914359 ATGAGAGCTAGTGTAAGACCATGTGTGGGACATGGTATCAGC-TTG--AC
1 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCACCGATAC
* * * *
28914406 ATGTG-TC-AGTGTAAGACCATGCCTGGGACATGGCATCAGCACCGATAG
1 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCACCGATAC
* * *
28914454 ATGAGAGCTAGTGTAAGACCATGTTTGGGACATGGCAT-TG-ACCTCGATAT
1 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCA-C-CGATAC
*
28914504 ACGAGAG-TCAGTGTAAGACCATGTCTGGGACATGGCATC
1 ATGAGAGCT-AGTGTAAGACCATGTCTGGGACATGGCATC
28914543 GACTTTGATG
Statistics
Matches: 112, Mismatches: 16, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
45 30 0.27
46 2 0.02
47 4 0.04
48 6 0.05
49 4 0.04
50 66 0.59
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (50 bp):
ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCACCGATAC
Found at i:28931109 original size:30 final size:30
Alignment explanation
Indices: 28931075--28931133 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
28931065 ACATGTTTAT
*
28931075 CTCAATTTAATTTTTAACAGACTATATCAC
1 CTCAATTTAATTTTCAACAGACTATATCAC
*
28931105 CTCAATTTAATTTTCAACATACTATATCA
1 CTCAATTTAATTTTCAACAGACTATATCA
28931134 TCACATTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.37, C:0.20, G:0.02, T:0.41
Consensus pattern (30 bp):
CTCAATTTAATTTTCAACAGACTATATCAC
Found at i:28931218 original size:14 final size:14
Alignment explanation
Indices: 28931199--28931228 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28931189 CAATAATCAT
28931199 ATATGTATATATGC
1 ATATGTATATATGC
*
28931213 ATATGTATTTATGC
1 ATATGTATATATGC
28931227 AT
1 AT
28931229 TGAGCTCGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (14 bp):
ATATGTATATATGC
Found at i:28934280 original size:48 final size:48
Alignment explanation
Indices: 28934158--28934390 Score: 304
Period size: 48 Copynumber: 4.8 Consensus size: 48
28934148 AAAGGGTAAG
* *
28934158 ATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATATCG
1 ATGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATA--A
* * *
28934208 GTGTCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTTATATAA
1 ATGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAA
* * * * * **
28934256 ATGCCGATGCCATGTTCCAAACATGGTCTTACACTAGCCCACATGTCG
1 ATGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAA
* *
28934304 AGGCCGATGCTATGTCCCAGACATGGTCTTACACTAGCTCTCATATAA
1 ATGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAA
* *
28934352 ATGCCGATGCCATGTTCCAAACATGGTCTTACACTAGCT
1 ATGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCT
28934391 TACATAACCT
Statistics
Matches: 155, Mismatches: 28, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
48 112 0.72
50 43 0.28
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (48 bp):
ATGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATAA
Found at i:28934338 original size:96 final size:98
Alignment explanation
Indices: 28934158--28934390 Score: 364
Period size: 96 Copynumber: 2.4 Consensus size: 98
28934148 AAAGGGTAAG
* * * * *
28934158 ATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATATCGGTGTCGATGCCATGT
1 ATGCCGATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCACATATCGGTGCCGATGCCATGT
*
28934223 CCCAGACATGGTCTTACACTAGCTCTTATATAA
66 CCCAGACATGGTCTTACACTAGCTCTCATATAA
* *
28934256 ATGCCGATGCCATGTTCCAAACATGGTCTTACACTAGC-C-CACATGTCGAG-GCCGATGCTATG
1 ATGCCGATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCACATATCG-GTGCCGATGCCATG
28934318 TCCCAGACATGGTCTTACACTAGCTCTCATATAA
65 TCCCAGACATGGTCTTACACTAGCTCTCATATAA
28934352 ATGCCGATGCCATGTTCCAAACATGGTCTTACACTAGCT
1 ATGCCGATGCCATGTTCCAAACATGGTCTTACACTAGCT
28934391 TACATAACCT
Statistics
Matches: 125, Mismatches: 8, Indels: 5
0.91 0.06 0.04
Matches are distributed among these distances:
96 88 0.70
97 2 0.02
98 35 0.28
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (98 bp):
ATGCCGATGCCATGTTCCAAACATGGTCTTACACTAGCTCTCACATATCGGTGCCGATGCCATGT
CCCAGACATGGTCTTACACTAGCTCTCATATAA
Found at i:28935926 original size:25 final size:24
Alignment explanation
Indices: 28935891--28935942 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
28935881 ACAAACACAA
28935891 CTCTTTATGAGCGTCCTGATATAGG
1 CTCTTTATGAGCGTCCTGATAT-GG
* * *
28935916 CTCTTTTTGAGCTTCTTGATATGG
1 CTCTTTATGAGCGTCCTGATATGG
28935940 CTC
1 CTC
28935943 GCTTGAACTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.42
Consensus pattern (24 bp):
CTCTTTATGAGCGTCCTGATATGG
Found at i:28939023 original size:42 final size:43
Alignment explanation
Indices: 28938910--28939023 Score: 158
Period size: 43 Copynumber: 2.7 Consensus size: 43
28938900 GGAATTAAAA
* *
28938910 AATCCGAGCTCGTTGAGTGGTCCGAGCTCGTGATATATGTGAG
1 AATCTGAGCTCGTTGAGTGGTCCGAGTTCGTGATATATGTGAG
* * *
28938953 AATCTGAACTTGTTGAGTGGTCCAAGTTCGTGATATATGT-AG
1 AATCTGAGCTCGTTGAGTGGTCCGAGTTCGTGATATATGTGAG
* *
28938995 CATCTGAGCTCGTTGAGTGGTTCGAGTTC
1 AATCTGAGCTCGTTGAGTGGTCCGAGTTC
28939024 ATAATGGATG
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
42 26 0.43
43 35 0.57
ACGTcount: A:0.21, C:0.17, G:0.30, T:0.32
Consensus pattern (43 bp):
AATCTGAGCTCGTTGAGTGGTCCGAGTTCGTGATATATGTGAG
Found at i:28939058 original size:51 final size:51
Alignment explanation
Indices: 28938982--28939094 Score: 163
Period size: 51 Copynumber: 2.2 Consensus size: 51
28938972 GTCCAAGTTC
* * * * *
28938982 GTGATATATGTAGCATCTGAGCTCGTTGAGTGGTTCGAGTTCATAATGGAT
1 GTGATACATGTAACATCCGAGCTCGTTGAGAGGTCCGAGTTCATAATGGAT
*
28939033 GTGATACATGTAACATCCGAGCTCGTTGAGAGGTCCGAGTTCATTATGGAT
1 GTGATACATGTAACATCCGAGCTCGTTGAGAGGTCCGAGTTCATAATGGAT
*
28939084 GTGTTACATGT
1 GTGATACATGT
28939095 TATAAGGTAG
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (51 bp):
GTGATACATGTAACATCCGAGCTCGTTGAGAGGTCCGAGTTCATAATGGAT
Found at i:28940684 original size:30 final size:30
Alignment explanation
Indices: 28940650--28940708 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
28940640 TATTTTATTA
28940650 TTAATTTTGTTATTATTTTAAAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
* *
28940680 TTAATTTTGTTATTATTTTAGAGGTATTT
1 TTAATTTTGTTATTATTTTAAAGGCATTT
28940709 ACTTGTTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.25, C:0.02, G:0.14, T:0.59
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGGCATTTG
Found at i:28940859 original size:11 final size:11
Alignment explanation
Indices: 28940828--28940860 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
28940818 TATTATATAT
*
28940828 ATATAAAAATT
1 ATATAAAAATA
28940839 ATAT-AAAATA
1 ATATAAAAATA
28940849 ATATAAAAATA
1 ATATAAAAATA
28940860 A
1 A
28940861 ATACGGGCGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
ATATAAAAATA
Found at i:28944699 original size:20 final size:18
Alignment explanation
Indices: 28944674--28944710 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
28944664 ATTGCTAAGT
28944674 TGTAAAATGAGTTGTAAATG
1 TGTAAAAT-AGTTG-AAATG
28944694 TGTAAAATAGTTGAAAT
1 TGTAAAATAGTTGAAAT
28944711 TATGAGTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (18 bp):
TGTAAAATAGTTGAAATG
Found at i:28949257 original size:48 final size:50
Alignment explanation
Indices: 28949183--28949313 Score: 140
Period size: 48 Copynumber: 2.6 Consensus size: 50
28949173 GAAACCAAAC
* * *
28949183 AAGCCTTTGTGGTTAGTTATCCAAAAAGCCTATGT-G-ACATTATCTAGG
1 AAGCCTTTGTGGCTAATTATCTAAAAAGCCTATGTGGCACATTATCTAGG
** * * *
28949231 AAGCCTTTGTGGCTAATTATCTAAAAAAACTATGTGGCATATTATTTGGG
1 AAGCCTTTGTGGCTAATTATCTAAAAAGCCTATGTGGCACATTATCTAGG
* * *
28949281 AAGCCTTAGTGGCAAAGTTATCTGAAAAGCCTA
1 AAGCCTTTGTGGCTAA-TTATCTAAAAAGCCTA
28949314 GATGGTGAAC
Statistics
Matches: 67, Mismatches: 13, Indels: 3
0.81 0.16 0.04
Matches are distributed among these distances:
48 30 0.45
49 1 0.01
50 23 0.34
51 13 0.19
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (50 bp):
AAGCCTTTGTGGCTAATTATCTAAAAAGCCTATGTGGCACATTATCTAGG
Found at i:28952548 original size:40 final size:40
Alignment explanation
Indices: 28952476--28952847 Score: 358
Period size: 40 Copynumber: 9.3 Consensus size: 40
28952466 TCTTTGGGAT
* *
28952476 TTAG-CCGGATATAA-CTACTTGCAC-AAGGCCTTCGGGTC
1 TTAGCCCGGATATAATC-ACTAGCACAAATGCCTTCGGGTC
* ** * *
28952514 TTAGCCCGGATGTGGTCACTAGCATAAATGCCTTCGGGAC
1 TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGTC
* * *
28952554 TTAGCCCGGATATAATCGCTAGCACAAATGCCTTCGAGTT
1 TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGTC
* * * * *
28952594 TTAGCCCGGATATAATCGCTAGCACAAATTCCTTTGAGTT
1 TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGTC
* *
28952634 TTATCCCGGATATAATCGCTAGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGTC
* * * *
28952674 TTAGCCCGGATAT-AGCAACTCGCACGAATGCCTTCGGATC
1 TTAGCCCGGATATAATC-ACTAGCACAAATGCCTTCGGGTC
* * *
28952714 TTAGTCCGGTTATAATCGCTAGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGTC
* * * * *
28952754 TTAGCCTGGATAT-AGCAACTCGCACGAATGCCTTCGGATC
1 TTAGCCCGGATATAATC-ACTAGCACAAATGCCTTCGGGTC
* * * * *
28952794 TTAGTCCGGTTATAGTCACCTAGCACAAAAGCCTTCGGGAC
1 TTAGCCCGGATATAATCA-CTAGCACAAATGCCTTCGGGTC
*
28952835 TTAACCCGGATAT
1 TTAGCCCGGATAT
28952848 CATTCGAATA
Statistics
Matches: 270, Mismatches: 56, Indels: 13
0.80 0.17 0.04
Matches are distributed among these distances:
38 4 0.01
39 17 0.06
40 219 0.81
41 30 0.11
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (40 bp):
TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGTC
Found at i:28961627 original size:48 final size:48
Alignment explanation
Indices: 28961363--28961629 Score: 206
Period size: 48 Copynumber: 5.6 Consensus size: 48
28961353 AGCTCCTGTA
* * * ** *
28961363 TAAGACCATATCTGGGATATGGCTTTGGTAGT-GACATGTGATCCCATG
1 TAAGACCATATCTGGGACATGGCATTGGCA-TCGTTATGTGGTCCCATG
* * * *
28961411 TAAGACCATGTCTGGGACATGACTTTGGCATCGTTATGTGATCCCATG
1 TAAGACCATATCTGGGACATGGCATTGGCATCGTTATGTGGTCCCATG
* * * * * * * *
28961459 TAAGACCATGTCTAGGACATGGCATTGGCATCATAATG-AGACATCGTG
1 TAAGACCATATCTGGGACATGGCATTGGCATCGTTATGTGGTC-CCATG
* * * *
28961507 TAAGACCATAGCTGGG-C-T---ATCGGCTTCGATATGTGTGATCCCATG
1 TAAGACCATATCTGGGACATGGCATTGGCATCGTTATGTG-G-TCCCATG
* * *
28961552 TAATACCATGTCTGGGACATGGAATTGGCATCGTTATGTGGTCCCATG
1 TAAGACCATATCTGGGACATGGCATTGGCATCGTTATGTGGTCCCATG
* *
28961600 TAAGATCATATCTGGGATATGGCATTGGCA
1 TAAGACCATATCTGGGACATGGCATTGGCA
28961630 CCCTACCTTG
Statistics
Matches: 170, Mismatches: 39, Indels: 20
0.74 0.17 0.09
Matches are distributed among these distances:
43 10 0.06
45 17 0.10
46 3 0.02
47 4 0.02
48 121 0.71
49 1 0.01
50 14 0.08
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (48 bp):
TAAGACCATATCTGGGACATGGCATTGGCATCGTTATGTGGTCCCATG
Found at i:28968603 original size:39 final size:39
Alignment explanation
Indices: 28968551--28968641 Score: 121
Period size: 39 Copynumber: 2.3 Consensus size: 39
28968541 GGCGTTTGAA
*
28968551 TGAAAAACGCCGCTAAAGAAT-GAGCATTAGCGGCGCTTG
1 TGAAAAACACCGCTAAAG-ATCGAGCATTAGCGGCGCTTG
* * *
28968590 TGAAAAATACCGCTAAAGATCGAGTATTAGCGGCGCTTT
1 TGAAAAACACCGCTAAAGATCGAGCATTAGCGGCGCTTG
*
28968629 TTAAAAACACCGC
1 TGAAAAACACCGC
28968642 CATATTTACA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
38 2 0.04
39 43 0.96
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (39 bp):
TGAAAAACACCGCTAAAGATCGAGCATTAGCGGCGCTTG
Found at i:28970411 original size:27 final size:26
Alignment explanation
Indices: 28970367--28970418 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
28970357 CTCGTTGCAA
*
28970367 TCTGGTGGCGTCGCCACATATATCTGT
1 TCTGGTGACGTCGCCACA-ATATCTGT
* *
28970394 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACGTCGCCACAATATCTG
28970419 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.35
Consensus pattern (26 bp):
TCTGGTGACGTCGCCACAATATCTGT
Found at i:28977752 original size:48 final size:48
Alignment explanation
Indices: 28977700--28977792 Score: 150
Period size: 48 Copynumber: 1.9 Consensus size: 48
28977690 TAGCATTGAC
* * *
28977700 ATGTGATCCCAAGTAAGACCATGTCTGGGACATGGCTTTGGCATCTTT
1 ATGTGATCCCAAGTAAGACCATGTCCGGGACATGGCATTAGCATCTTT
*
28977748 ATGTGATCCCATGTAAGACCATGTCCGGGACATGGCATTAGCATC
1 ATGTGATCCCAAGTAAGACCATGTCCGGGACATGGCATTAGCATC
28977793 ATAATAAGAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.28
Consensus pattern (48 bp):
ATGTGATCCCAAGTAAGACCATGTCCGGGACATGGCATTAGCATCTTT
Found at i:28979786 original size:21 final size:22
Alignment explanation
Indices: 28979747--28979787 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
28979737 ATTTCGCAAT
28979747 CATTTCATAGTCAAAAGTCATA
1 CATTTCATAGTCAAAAGTCATA
28979769 CATTATCATA-TC-AAAGTCA
1 CATT-TCATAGTCAAAAGTCA
28979788 AATATCAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 6 0.33
23 5 0.28
ACGTcount: A:0.41, C:0.20, G:0.07, T:0.32
Consensus pattern (22 bp):
CATTTCATAGTCAAAAGTCATA
Found at i:28981223 original size:42 final size:42
Alignment explanation
Indices: 28981127--28981283 Score: 140
Period size: 43 Copynumber: 3.7 Consensus size: 42
28981117 GCCAACGTCT
* * * * *
28981127 CAGACGTGGTCTTACATGTAATCAAATATCAATGCCATTGTCC
1 CAGACATGGTCTTACACGAAATCAAATA-CGATGCCACTGTCC
*
28981170 CAGACAGGGTCTTACACGAAATCAAATACGATGCCGA-TGTCC
1 CAGACATGGTCTTACACGAAATCAAATACGATGCC-ACTGTCC
* * *
28981212 CGGACATGGTCTTACACATAAATCTCAAAT-CGATGCAAACT-TCC
1 CAGACATGGTCTTACAC-GAAA--TCAAATACGATGC-CACTGTCC
* *
28981256 CAGACGTGGTCTTAGACGAAATCAAATA
1 CAGACATGGTCTTACACGAAATCAAATA
28981284 TCAGAATCCT
Statistics
Matches: 94, Mismatches: 13, Indels: 15
0.77 0.11 0.12
Matches are distributed among these distances:
41 6 0.06
42 26 0.28
43 31 0.33
44 24 0.26
45 7 0.07
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (42 bp):
CAGACATGGTCTTACACGAAATCAAATACGATGCCACTGTCC
Found at i:28983642 original size:71 final size:71
Alignment explanation
Indices: 28983501--28983645 Score: 166
Period size: 71 Copynumber: 2.0 Consensus size: 71
28983491 TACAAGCTTT
* * * ** * *
28983501 ATTCGATGCTACTCACTCAAGCTGTCGAGAATTCACAACATATGTTAGATCTCTATAATCGATAA
1 ATTCCATGCTACTCACTCAAGCTATCGAAAACCCACAACATATGTTAGATCTCTACAATCAATAA
*
28983566 GGAATA
66 AGAATA
* * * *
28983572 ATTCCATGCTACTCACTCAAGCTATCGAAAACCCAGAATATATGTTGGATCT-TAGCCATCAATA
1 ATTCCATGCTACTCACTCAAGCTATCGAAAACCCACAACATATGTTAGATCTCTA-CAATCAATA
28983636 AAGAATA
65 AAGAATA
28983643 ATT
1 ATT
28983646 TGTATTCAAA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
70 2 0.03
71 59 0.97
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.29
Consensus pattern (71 bp):
ATTCCATGCTACTCACTCAAGCTATCGAAAACCCACAACATATGTTAGATCTCTACAATCAATAA
AGAATA
Found at i:28985835 original size:28 final size:28
Alignment explanation
Indices: 28985798--28985900 Score: 133
Period size: 27 Copynumber: 3.8 Consensus size: 28
28985788 GCTAGAACAT
*
28985798 ATAA-TGTGGCAGAGTCACCAGATACAG
1 ATAATTGTGGCAGAGCCACCAGATACAG
*
28985825 ATAATCGTGGCAGAGCCACCAGA-ACAG
1 ATAATTGTGGCAGAGCCACCAGATACAG
*
28985852 A-AATATGTGGCAGAGCCACCAAAT-CAG
1 ATAAT-TGTGGCAGAGCCACCAGATACAG
*
28985879 ATAATTGTGGCATAGCCACCAG
1 ATAATTGTGGCAGAGCCACCAG
28985901 GACACTTCCT
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
26 3 0.05
27 44 0.67
28 19 0.29
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.17
Consensus pattern (28 bp):
ATAATTGTGGCAGAGCCACCAGATACAG
Found at i:28986053 original size:28 final size:28
Alignment explanation
Indices: 28986006--28986070 Score: 105
Period size: 28 Copynumber: 2.3 Consensus size: 28
28985996 AAATTAACCC
*
28986006 TAGGGGTATAGAGGTTATTTTGCATACA
1 TAGGGGTATAGAGGTAATTTTGCATACA
28986034 TAGGGGTATA-ATGGTAATTTTGCATACA
1 TAGGGGTATAGA-GGTAATTTTGCATACA
28986062 TAGGGGTAT
1 TAGGGGTAT
28986071 TCTAGTAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 1 0.03
28 34 0.97
ACGTcount: A:0.29, C:0.06, G:0.29, T:0.35
Consensus pattern (28 bp):
TAGGGGTATAGAGGTAATTTTGCATACA
Found at i:28986345 original size:8 final size:8
Alignment explanation
Indices: 28986318--28986348 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
28986308 CCAAAATACT
28986318 GGCTTTTC
1 GGCTTTTC
*
28986326 GGCATTTC
1 GGCTTTTC
28986334 GGCTTTTC
1 GGCTTTTC
28986342 GGCTTTT
1 GGCTTTT
28986349 GCCGATCTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.03, C:0.23, G:0.26, T:0.48
Consensus pattern (8 bp):
GGCTTTTC
Found at i:28992874 original size:40 final size:41
Alignment explanation
Indices: 28992815--28993073 Score: 315
Period size: 40 Copynumber: 6.6 Consensus size: 41
28992805 TTATTGAATG
*
28992815 ATAT-CGGGCTAAG-TCCCGAAGGCTTTTATGCTAGTGACT
1 ATATCCGGGCTAAGATCCCGAAGGCATTTATGCTAGTGACT
* * *
28992854 ATATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGATCCCGAAGGCATTTATGCTAG-TGACT
* *
28992894 ATATCCGGGCTAAGA-CCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATCCCGAAGGCATTTATGCTAGTGACT
* *
28992934 ATATCCGGGCTAAG-TCCCAAAGGCTTTTATGCTAGTGACT
1 ATATCCGGGCTAAGATCCCGAAGGCATTTATGCTAGTGACT
*
28992974 ATATCCGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGATCCCGAAGGCATTTATGCTAGTGACT
* * * *
28993014 ATATCCGGGCTAAGA-CCCGAAGGC-CTTGTGCGAGTGGCT
1 ATATCCGGGCTAAGATCCCGAAGGCATTTATGCTAGTGACT
28993053 ATATCC-GGCTAA-ATCCCGAAG
1 ATATCCGGGCTAAGATCCCGAAG
28993074 ATACTTGGGT
Statistics
Matches: 193, Mismatches: 19, Indels: 17
0.84 0.08 0.07
Matches are distributed among these distances:
37 1 0.01
38 13 0.07
39 21 0.11
40 155 0.80
41 3 0.02
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (41 bp):
ATATCCGGGCTAAGATCCCGAAGGCATTTATGCTAGTGACT
Found at i:28993032 original size:120 final size:119
Alignment explanation
Indices: 28992815--28993069 Score: 365
Period size: 120 Copynumber: 2.2 Consensus size: 119
28992805 TTATTGAATG
*
28992815 ATAT-CGGGCTAAGTCCCGAAGGCTTTTATGCTAGTGACTATATCCGGACTAAGATCCGAAGGCA
1 ATATCCGGGCTAAGTCCCAAAGGCTTTTATGCTAGTGACTATATCCGGACTAAGATCCGAAGGCA
* * * *
28992879 TTTGTGCGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
66 TTTATGCGAGTTGCCATATCCGGGCTAAGACCCGAAGGC-CTTGTGCGAGCGACT
*
28992934 ATATCCGGGCTAAGTCCCAAAGGCTTTTATGCTAGTGACTATATCCGGGCTAAG-TCCCGAAGGC
1 ATATCCGGGCTAAGTCCCAAAGGCTTTTATGCTAGTGACTATATCCGGACTAAGAT-CCGAAGGC
* * *
28992998 ATTTATGCTAG-TGACCATATCCGGGCTAAGACCCGAAGGCCTTGTGCGAGTGGCT
65 ATTTATGCGAGTTG-CCATATCCGGGCTAAGACCCGAAGGCCTTGTGCGAGCGACT
*
28993053 ATATCC-GGCTAAATCCC
1 ATATCCGGGCTAAGTCCC
28993070 GAAGATACTT
Statistics
Matches: 123, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
118 10 0.08
119 24 0.20
120 89 0.72
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (119 bp):
ATATCCGGGCTAAGTCCCAAAGGCTTTTATGCTAGTGACTATATCCGGACTAAGATCCGAAGGCA
TTTATGCGAGTTGCCATATCCGGGCTAAGACCCGAAGGCCTTGTGCGAGCGACT
Found at i:29001065 original size:40 final size:40
Alignment explanation
Indices: 29001002--29001261 Score: 319
Period size: 40 Copynumber: 6.5 Consensus size: 40
29000992 TATTCGAATG
*
29001002 ATATCCGGGCTAAGTCCCGAAGGCTTTTATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACT
* * * * **
29001042 ATATCCGGACTAAGAT-CCAAAGGCATTTGTGCAAGTTTCT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACT
* * *
29001082 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACT
*
29001122 ATATCCGGGCTAAGTCCCGAAGGCTTTTATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACT
*
29001162 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACT
* * * * *
29001202 ATATCCGGGCTAAGACCCGAAGGC-CTTGTGCGAGTGGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACT
* *
29001241 ATATCC-GGCTAAATCTCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
29001262 ATACTTGGGT
Statistics
Matches: 189, Mismatches: 29, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
38 12 0.06
39 16 0.08
40 160 0.85
41 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACT
Found at i:29001215 original size:120 final size:119
Alignment explanation
Indices: 29001002--29001261 Score: 371
Period size: 120 Copynumber: 2.2 Consensus size: 119
29000992 TATTCGAATG
29001002 ATATCCGGGCTAAGTCCCGAAGGCTTTTATGCTAGTGACTATATCCGGACTAAGATCCAAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCTTTTATGCTAGTGACTATATCCGGACTAAGATCCAAAGGCA
* ** * * *
29001067 TTTGTGCAAGTTTCTATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
66 TTTATGCAAGTGACCATATCCGGGCTAAGACCCGAAGGC-CTTGTGCGAGCGACT
* *
29001122 ATATCCGGGCTAAGTCCCGAAGGCTTTTATGCTAGTGACTATATCCGGGCTAAG-TCCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGCTTTTATGCTAGTGACTATATCCGGACTAAGAT-CCAAAGGC
* * *
29001186 ATTTATGCTAGTGACCATATCCGGGCTAAGACCCGAAGGCCTTGTGCGAGTGGCT
65 ATTTATGCAAGTGACCATATCCGGGCTAAGACCCGAAGGCCTTGTGCGAGCGACT
* *
29001241 ATATCC-GGCTAAATCTCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
29001262 ATACTTGGGT
Statistics
Matches: 126, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
118 13 0.10
119 18 0.14
120 95 0.75
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.26
Consensus pattern (119 bp):
ATATCCGGGCTAAGTCCCGAAGGCTTTTATGCTAGTGACTATATCCGGACTAAGATCCAAAGGCA
TTTATGCAAGTGACCATATCCGGGCTAAGACCCGAAGGCCTTGTGCGAGCGACT
Found at i:29005325 original size:28 final size:27
Alignment explanation
Indices: 29005269--29005380 Score: 129
Period size: 27 Copynumber: 4.1 Consensus size: 27
29005259 AGCATGGCTG
** *
29005269 CCAGAACAGATAA-TGTGATAGAGTCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
*
29005295 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAATTGTGGCAGAGCCA
29005323 CCAGAACAGA-AATATGTGGCAGAGCCA
1 CCAGAACAGATAAT-TGTGGCAGAGCCA
* * *
29005350 CTAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
29005377 CCAG
1 CCAG
29005381 GACGCTTCCT
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
26 8 0.11
27 48 0.66
28 17 0.23
ACGTcount: A:0.38, C:0.21, G:0.24, T:0.17
Consensus pattern (27 bp):
CCAGAACAGATAATTGTGGCAGAGCCA
Found at i:29005332 original size:54 final size:54
Alignment explanation
Indices: 29005269--29005380 Score: 145
Period size: 54 Copynumber: 2.1 Consensus size: 54
29005259 AGCATGGCTG
* * *
29005269 CCAGAACAGATA-ATGTGATAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGAAATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * *
29005323 CCAGAACAGAAATATGTGGCAGAGCCACTAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGAAATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
29005377 CCAG
1 CCAG
29005381 GACGCTTCCT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
54 34 0.68
55 16 0.32
ACGTcount: A:0.38, C:0.21, G:0.24, T:0.17
Consensus pattern (54 bp):
CCAGAACAGAAATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:29005533 original size:28 final size:28
Alignment explanation
Indices: 29005486--29005550 Score: 105
Period size: 28 Copynumber: 2.3 Consensus size: 28
29005476 AAATTAACCC
*
29005486 TAGGGGTATAGAGGTCATTTTGCATACA
1 TAGGGGTATAGAGGTAATTTTGCATACA
29005514 TAGGGGTATA-ATGGTAATTTTGCATACA
1 TAGGGGTATAGA-GGTAATTTTGCATACA
29005542 TAGGGGTAT
1 TAGGGGTAT
29005551 TCTAGTAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 1 0.03
28 34 0.97
ACGTcount: A:0.29, C:0.08, G:0.29, T:0.34
Consensus pattern (28 bp):
TAGGGGTATAGAGGTAATTTTGCATACA
Found at i:29010752 original size:18 final size:18
Alignment explanation
Indices: 29010715--29010753 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
29010705 TTGGAAATCA
*
29010715 AAATTATTAAAAGATGAT
1 AAATTATTAAAAGATAAT
29010733 AAATTATTAAATAGA-AAT
1 AAATTATTAAA-AGATAAT
29010751 AAA
1 AAA
29010754 AATCATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (18 bp):
AAATTATTAAAAGATAAT
Found at i:29013881 original size:24 final size:24
Alignment explanation
Indices: 29013849--29013896 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
29013839 AATGTTCGAG
29013849 TAAAAATGTTGCTTATGATAAAAA
1 TAAAAATGTTGCTTATGATAAAAA
29013873 TAAAAATGTTGCTTATGATAAAAA
1 TAAAAATGTTGCTTATGATAAAAA
29013897 GGGTACTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.04, G:0.12, T:0.33
Consensus pattern (24 bp):
TAAAAATGTTGCTTATGATAAAAA
Found at i:29017473 original size:18 final size:18
Alignment explanation
Indices: 29017422--29017474 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
29017412 GGCTAAGGGG
29017422 TAAATTAGAAATGAAAATTAT
1 TAAA-TAGAAAT--AAATTAT
*
29017443 TAAA-AGATGATAAATTAT
1 TAAATAGA-AATAAATTAT
29017461 TAAATAGAAATAAA
1 TAAATAGAAATAAA
29017475 AATCATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
18 16 0.57
19 6 0.21
20 2 0.07
21 4 0.14
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.30
Consensus pattern (18 bp):
TAAATAGAAATAAATTAT
Found at i:29018900 original size:57 final size:56
Alignment explanation
Indices: 29018765--29018901 Score: 143
Period size: 56 Copynumber: 2.4 Consensus size: 56
29018755 TACAGAAAAA
* * * * * *
29018765 GATTTAGCCTAGACGGGTAATCCTGATATAAGTCCTGTCGAGCACATGTTATAGATTG
1 GATTTAGCCTGGAC-GGTAATCC-GAAATAAGTCCTGTAGAGCACATGTCATAAATAG
* *
29018823 GATTTAGCCCGGACGGTAATCC-AAATCAAGCTCCT-TAGAGCATATGTCATAAATAG
1 GATTTAGCCTGGACGGTAATCCGAAAT-AAG-TCCTGTAGAGCACATGTCATAAATAG
29018879 GATTTAGCCTGGACTGGTAATCC
1 GATTTAGCCTGGAC-GGTAATCC
29018902 TATTGTATAC
Statistics
Matches: 67, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
55 3 0.04
56 32 0.48
57 20 0.30
58 12 0.18
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (56 bp):
GATTTAGCCTGGACGGTAATCCGAAATAAGTCCTGTAGAGCACATGTCATAAATAG
Found at i:29025623 original size:28 final size:27
Alignment explanation
Indices: 29025602--29025680 Score: 97
Period size: 28 Copynumber: 2.9 Consensus size: 27
29025592 TAAGCCTATC
*
29025602 GGGACAATAAACACAAGGTAAGTTCGTT
1 GGGACAATAAACACAAGGTAAG-TCCTT
* *
29025630 GGGACAGTAAACACAAGGTAAGTCCGT
1 GGGACAATAAACACAAGGTAAGTCCTT
*
29025657 GAGAACAATAAACACAA-GTAAGTC
1 G-GGACAATAAACACAAGGTAAGTC
29025681 TGCTAGGACA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
27 11 0.24
28 34 0.76
ACGTcount: A:0.43, C:0.16, G:0.24, T:0.16
Consensus pattern (27 bp):
GGGACAATAAACACAAGGTAAGTCCTT
Found at i:29025691 original size:27 final size:27
Alignment explanation
Indices: 29025603--29025691 Score: 92
Period size: 28 Copynumber: 3.2 Consensus size: 27
29025593 AAGCCTATCG
*
29025603 GGACAATAAACACAAGGTAAGT-TCGTTG
1 GGACAATAAACACAAGGTAAGTCT-G-TA
* *
29025631 GGACAGTAAACACAAGGTAAGTCCGTGA
1 GGACAATAAACACAAGGTAAGTCTGT-A
*
29025659 GAACAATAAACACAA-GTAAGTCTGCTA
1 GGACAATAAACACAAGGTAAGTCTG-TA
29025686 GGACAA
1 GGACAA
29025692 GAGAAAATAG
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
27 15 0.29
28 36 0.71
ACGTcount: A:0.43, C:0.17, G:0.24, T:0.17
Consensus pattern (27 bp):
GGACAATAAACACAAGGTAAGTCTGTA
Found at i:29028695 original size:48 final size:47
Alignment explanation
Indices: 29028637--29028787 Score: 136
Period size: 48 Copynumber: 3.2 Consensus size: 47
29028627 TGTGATCCTA
29028637 TGTAAGACCATGTCTAGGACATGGCATTGGCATCAATATGAGACATCG
1 TGTAAGACCATGTCTAGGACATGGCA-TGGCATCAATATGAGACATCG
* * * * * *
29028685 TGTAAGACCATAG-CT-GGGCTAT--CA--GCTTCGATATGCATTAC-CCA
1 TGTAAGACCAT-GTCTAGGAC-ATGGCATGGCATCAATATG-A-GACATCG
*
29028729 TGTAAGACCATGTCTAGGACATGGTACTGGCATCAATATGAGACATCG
1 TGTAAGACCATGTCTAGGACATGGCA-TGGCATCAATATGAGACATCG
29028777 TGTAAGACCAT
1 TGTAAGACCAT
29028788 AGCTGGGCTA
Statistics
Matches: 78, Mismatches: 13, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
43 10 0.13
44 17 0.22
45 5 0.06
46 3 0.04
47 5 0.06
48 28 0.36
49 10 0.13
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (47 bp):
TGTAAGACCATGTCTAGGACATGGCATGGCATCAATATGAGACATCG
Found at i:29028739 original size:44 final size:44
Alignment explanation
Indices: 29028685--29028832 Score: 140
Period size: 44 Copynumber: 3.3 Consensus size: 44
29028675 TGAGACATCG
29028685 TGTAAGACCATAGCTGGGCTATCAGCTTCGATATGCATTACCCA
1 TGTAAGACCATAGCTGGGCTATCAGCTTCGATATGCATTACCCA
* * * * * * * *
29028729 TGTAAGACCAT-GTCTAGGACATGGTACTGGCATCAATATG-A-GACATCG
1 TGTAAGACCATAG-CT-GGGC-T-AT-C-AGCTTCGATATGCATTAC-CCA
29028777 TGTAAGACCATAGCTGGGCTATCAGCTTCGATATGCATTACCCA
1 TGTAAGACCATAGCTGGGCTATCAGCTTCGATATGCATTACCCA
29028821 TGTAAGACCATA
1 TGTAAGACCATA
29028833 ACTAGGATAT
Statistics
Matches: 78, Mismatches: 16, Indels: 20
0.68 0.14 0.18
Matches are distributed among these distances:
43 10 0.13
44 28 0.36
45 6 0.08
46 2 0.03
47 6 0.08
48 16 0.21
49 10 0.13
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (44 bp):
TGTAAGACCATAGCTGGGCTATCAGCTTCGATATGCATTACCCA
Found at i:29028793 original size:92 final size:92
Alignment explanation
Indices: 29028636--29028854 Score: 393
Period size: 92 Copynumber: 2.4 Consensus size: 92
29028626 GTGTGATCCT
29028636 ATGTAAGACCATGTCTAGGACATGGCATTGGCATCAATATGAGACATCGTGTAAGACCATAGCTG
1 ATGTAAGACCATGTCTAGGACATGGCATTGGCATCAATATGAGACATCGTGTAAGACCATAGCTG
29028701 GGCTATCAGCTTCGATATGCATTACCC
66 GGCTATCAGCTTCGATATGCATTACCC
* *
29028728 ATGTAAGACCATGTCTAGGACATGGTACTGGCATCAATATGAGACATCGTGTAAGACCATAGCTG
1 ATGTAAGACCATGTCTAGGACATGGCATTGGCATCAATATGAGACATCGTGTAAGACCATAGCTG
29028793 GGCTATCAGCTTCGATATGCATTACCC
66 GGCTATCAGCTTCGATATGCATTACCC
** *
29028820 ATGTAAGACCATAACTAGGATATGGCATTGGCATC
1 ATGTAAGACCATGTCTAGGACATGGCATTGGCATC
29028855 TTACTATGTG
Statistics
Matches: 120, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
92 120 1.00
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (92 bp):
ATGTAAGACCATGTCTAGGACATGGCATTGGCATCAATATGAGACATCGTGTAAGACCATAGCTG
GGCTATCAGCTTCGATATGCATTACCC
Found at i:29029758 original size:26 final size:26
Alignment explanation
Indices: 29029704--29029760 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
29029694 TATGAAGGTT
29029704 TAAGTG-CATGAAATTATGTCATGTG
1 TAAGTGCCATGAAATTATGTCATGTG
* *
29029729 -AAGTGCCATTGAAGTTATGT-TTGTG
1 TAAGTGCCA-TGAAATTATGTCATGTG
29029754 TAAGTGC
1 TAAGTGC
29029761 AATTAAGGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 5 0.19
25 6 0.22
26 16 0.59
ACGTcount: A:0.28, C:0.09, G:0.26, T:0.37
Consensus pattern (26 bp):
TAAGTGCCATGAAATTATGTCATGTG
Found at i:29034295 original size:27 final size:27
Alignment explanation
Indices: 29034264--29034332 Score: 129
Period size: 27 Copynumber: 2.6 Consensus size: 27
29034254 AAGTTAGGGG
29034264 TAAATTGAGTCCATTAAGCCTAGGACA
1 TAAATTGAGTCCATTAAGCCTAGGACA
29034291 TAAATTGAGTCCATTAAGCCTAGGACA
1 TAAATTGAGTCCATTAAGCCTAGGACA
*
29034318 TAAGTTGAGTCCATT
1 TAAATTGAGTCCATT
29034333 TAAATATGAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (27 bp):
TAAATTGAGTCCATTAAGCCTAGGACA
Found at i:29036331 original size:43 final size:43
Alignment explanation
Indices: 29036161--29036331 Score: 156
Period size: 43 Copynumber: 4.0 Consensus size: 43
29036151 CTCGTACAAT
* * *
29036161 GCCAACATCCTAGACATGGTCTTACATGTAATCAAATATCGATA
1 GCCAACGTCCCAGACATGGTCTTACACGTAATCAAATATCGA-A
* * * *
29036205 -CC-ACTGTCCCAGACAGGGTCTTACATGAAATCAAATAT-GAT
1 GCCAAC-GTCCCAGACATGGTCTTACACGTAATCAAATATCGAA
* *
29036246 GCCAACGTCCCAAACGTGGTCTTACACGTAAATC--ATAGTCGAA
1 GCCAACGTCCCAGACATGGTCTTACACGT-AATCAAATA-TCGAA
* *
29036289 GCCAACGTCCTAGACATGGTCTTACACGATAAT-ACATATCGAA
1 GCCAACGTCCCAGACATGGTCTTACACG-TAATCAAATATCGAA
29036332 ATCCTATATC
Statistics
Matches: 104, Mismatches: 14, Indels: 19
0.76 0.10 0.14
Matches are distributed among these distances:
41 3 0.03
42 25 0.24
43 72 0.69
44 4 0.04
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.24
Consensus pattern (43 bp):
GCCAACGTCCCAGACATGGTCTTACACGTAATCAAATATCGAA
Found at i:29047114 original size:40 final size:39
Alignment explanation
Indices: 29046926--29047149 Score: 263
Period size: 40 Copynumber: 5.6 Consensus size: 39
29046916 TTGAATGATG
* * * *
29046926 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
29046966 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
29047006 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
*
29047046 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
29047085 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
29047126 -CCGGGCTATGTCCGAAGGCATTTG
1 TCCGGGCTAAGTCCGAAGGCATTTG
29047150 AACGAGTAGC
Statistics
Matches: 165, Mismatches: 15, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
39 48 0.29
40 107 0.65
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:29047156 original size:79 final size:78
Alignment explanation
Indices: 29046926--29047168 Score: 276
Period size: 79 Copynumber: 3.1 Consensus size: 78
29046916 TTGAATGATG
* * * *
29046926 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATATCCGGGCTAAG-TCCGAAGGCATT
*
29046990 TGTGCGAGATACTAAT
64 TGTGCGAG-TACTAAA
* * *
29047006 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATTCCGGGCTAAGCCCGAAGGCATT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGTCCGAAGGCATT
29047069 TGTGCGAGTTACTAAA
64 TGTGCGAG-TACTAAA
* * *
29047085 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCGAAGGCATTTG
** *
29047150 AACGAGTAGCTATA
66 TGCGAGTA-CTAAA
29047164 TCCGG
1 TCCGG
29047169 TTAAATTCCG
Statistics
Matches: 139, Mismatches: 18, Indels: 13
0.82 0.11 0.08
Matches are distributed among these distances:
78 3 0.02
79 94 0.68
80 34 0.24
81 8 0.06
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (78 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCGAAGGCATTTG
TGCGAGTACTAAA
Found at i:29047179 original size:39 final size:40
Alignment explanation
Indices: 29046939--29047182 Score: 184
Period size: 40 Copynumber: 6.2 Consensus size: 40
29046929 GGGCTAAGTC
* * * **
29046939 CCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGA-T
1 CCGAAGGCATTTGTGC-GAGTTACTATATCCGGGTTAA-ATT
* **
29046979 CCGAAGGCATTTGTGCGAGATACTA-ATTCCGGACTAAGA-T
1 CCGAAGGCATTTGTGCGAGTTACTATA-TCCGGGTTAA-ATT
* * **
29047019 CCGAAGGCATTTGTGCGAGATACTA-ATTCCGGGCT-AAGC
1 CCGAAGGCATTTGTGCGAGTTACTATA-TCCGGGTTAAATT
* * *
29047058 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGTTAAATT
* *
29047098 CCGAAGGCATTTGTGCGAGTTACTATAACCGGGCT--ATGT
1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGTTAAAT-T
**
29047137 CCGAAGGCATTTGAACGAG-TAGCTATATCC-GGTTAAATT
1 CCGAAGGCATTTGTGCGAGTTA-CTATATCCGGGTTAAATT
29047176 CCGAAGG
1 CCGAAGG
29047183 TACGTGATTT
Statistics
Matches: 176, Mismatches: 19, Indels: 19
0.82 0.09 0.09
Matches are distributed among these distances:
38 7 0.04
39 65 0.37
40 97 0.55
41 7 0.04
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGTTACTATATCCGGGTTAAATT
Found at i:29054894 original size:36 final size:38
Alignment explanation
Indices: 29054851--29055035 Score: 200
Period size: 40 Copynumber: 4.8 Consensus size: 38
29054841 GGACTAAGAT
* *
29054851 CCGAAGGCATTTGTGCGAG-ATCTAATTCC-GGCTAAG-
1 CCGAAGGCATTTGTGCGAGTA-CTAAATCCGGGTTAAGC
29054887 CCGAAGGCATTTGTGCGAGTACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTACTAAATCCGGGTTAAG-C
29054926 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAG-TACTAAATCCGGGTTAAG-C
* *
29054966 CCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATG-
1 CCGAAGGCATTTGTGCGAG-TACTA-AATCCGGGTTAAGC
* ** *
29055004 TCGAAGGCATTTGAACGAGTAGCTATATCCGG
1 CCGAAGGCATTTGTGCGAGTA-CTAAATCCGG
29055036 TAAATTCCGA
Statistics
Matches: 133, Mismatches: 8, Indels: 14
0.86 0.05 0.09
Matches are distributed among these distances:
36 26 0.20
37 10 0.08
38 23 0.17
39 19 0.14
40 53 0.40
41 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (38 bp):
CCGAAGGCATTTGTGCGAGTACTAAATCCGGGTTAAGC
Found at i:29054961 original size:40 final size:39
Alignment explanation
Indices: 29054799--29055016 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 39
29054789 TTGAATGATG
* * * *
29054799 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
29054839 T-CGGACTAAGATCCGAAGGCATTTGTGCGAGAT-CTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
29054877 TCC-GGCTAAG-CCGAAGGCATTTGTGCGAG-TACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
29054913 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTAAA
*
29054953 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
29054994 -CCGGGCTATGT-CGAAGGCATTTG
1 TCCGGGCTAAGTCCGAAGGCATTTG
29055017 AACGAGTAGC
Statistics
Matches: 157, Mismatches: 12, Indels: 20
0.83 0.06 0.11
Matches are distributed among these distances:
35 1 0.01
36 26 0.17
37 6 0.04
38 21 0.13
39 38 0.24
40 63 0.40
41 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:29055035 original size:78 final size:78
Alignment explanation
Indices: 29054799--29055023 Score: 214
Period size: 75 Copynumber: 2.9 Consensus size: 78
29054789 TTGAATGATG
* * * * *
29054799 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT-CGGACTAAGATCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGT-ACTAAATCCGGGCTAAG-TCCGAAGGCATT
** * *
29054862 TGTGCGAGAT-CTAAT
63 TGAACGAGTTACTAAA
* *
29054877 TCC-GGCTAAG--CCGAAGGCATTTGTGCGAGTACTAAATCCGGGTTAAGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTACTAAATCCGGGCTAAGT-CCGAAGGCATTTG
**
29054939 TGCGAGTTACTAAA
65 AACGAGTTACTAAA
*
29054953 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGT-CGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAG-TACTA-AATCCGGGCTAAGTCCGAAGGCATTT
29055016 GAACGAGT
64 GAACGAGT
29055024 AGCTATATCC
Statistics
Matches: 126, Mismatches: 12, Indels: 18
0.81 0.08 0.12
Matches are distributed among these distances:
74 6 0.05
75 38 0.30
76 14 0.11
77 13 0.10
78 20 0.16
79 19 0.15
80 14 0.11
81 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (78 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTACTAAATCCGGGCTAAGTCCGAAGGCATTTGA
ACGAGTTACTAAA
Found at i:29058811 original size:14 final size:13
Alignment explanation
Indices: 29058792--29058829 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
29058782 CATGAGAGCT
29058792 TTTCTTCTTCTTTC
1 TTTCTTCTT-TTTC
*
29058806 TTTCTTCTTTTTT
1 TTTCTTCTTTTTC
29058819 TTTC-TCTTTTT
1 TTTCTTCTTTTT
29058830 TTTTTTGGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 7 0.30
13 7 0.30
14 9 0.39
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTCTTCTTTTTC
Found at i:29059013 original size:56 final size:56
Alignment explanation
Indices: 29058905--29059078 Score: 325
Period size: 55 Copynumber: 3.1 Consensus size: 56
29058895 TATTAGTTTA
29058905 TTGCCCATGCTTCTTATTTTATTCTT-CATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
29058960 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
29059016 TTGCCCATGC-TCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
29059071 TTGCCCAT
1 TTGCCCAT
29059079 CATCCCTGTC
Statistics
Matches: 117, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
55 78 0.67
56 39 0.33
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:29060322 original size:46 final size:46
Alignment explanation
Indices: 29060272--29060447 Score: 182
Period size: 46 Copynumber: 3.8 Consensus size: 46
29060262 TGGTTGAGCA
* *
29060272 TCCGAACTCATTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
29060318 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
29060363 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
*
29060411 -CTCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TC-CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
29060448 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 12, Indels: 20
0.77 0.09 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 4 0.04
46 62 0.57
47 28 0.26
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:29060428 original size:93 final size:93
Alignment explanation
Indices: 29060269--29060439 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
29060259 GGATGGTTGA
* *
29060269 GCATCCGAACTCATTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
29060334 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* * *
29060362 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CTCGAGCTCGTTGAG
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTC-CGAACTCGTTGAG
29060426 TTGAGTCCGAGTTC
65 TTGAGTCCGAGTTC
29060440 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 1 0.01
93 71 0.99
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:29067562 original size:50 final size:50
Alignment explanation
Indices: 29067487--29067589 Score: 161
Period size: 50 Copynumber: 2.1 Consensus size: 50
29067477 AATTTCGGTT
* * * *
29067487 GTTAGGGGGATTTGGAGAGTGTTTTGTGGAGGAAAATTTGGATAGAAGAA
1 GTTAGGGAGATTTGGAGAGTGTTTTGTGGAGAAAAAATTAGATAGAAGAA
*
29067537 GTTAGGGAGATTTGGGGAGTGTTTTGTGGAGAAAAAATTAGATAGAAGAA
1 GTTAGGGAGATTTGGAGAGTGTTTTGTGGAGAAAAAATTAGATAGAAGAA
29067587 GTT
1 GTT
29067590 GTGTGGAATT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.32, C:0.00, G:0.38, T:0.30
Consensus pattern (50 bp):
GTTAGGGAGATTTGGAGAGTGTTTTGTGGAGAAAAAATTAGATAGAAGAA
Found at i:29067697 original size:15 final size:15
Alignment explanation
Indices: 29067677--29067714 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
29067667 CGAAATAGGA
29067677 TTCTTGCTTCTCAGG
1 TTCTTGCTTCTCAGG
29067692 TTCTTGCTTCTCAGG
1 TTCTTGCTTCTCAGG
29067707 TTC-TGCTT
1 TTCTTGCTT
29067715 TGGTTGGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 5 0.22
15 18 0.78
ACGTcount: A:0.05, C:0.26, G:0.18, T:0.50
Consensus pattern (15 bp):
TTCTTGCTTCTCAGG
Found at i:29069395 original size:34 final size:32
Alignment explanation
Indices: 29069349--29069412 Score: 83
Period size: 34 Copynumber: 1.9 Consensus size: 32
29069339 GCTACTGAAT
* *
29069349 TGGGCTAAGGCCCTCACTGATATTGATACTATAA
1 TGGGCTAAGGCCCTAACT-AAATTGA-ACTATAA
*
29069383 TGGGCTAGGGCCCTAACTAAATTGAACTAT
1 TGGGCTAAGGCCCTAACTAAATTGAACTAT
29069413 TACTGAAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 5 0.19
33 6 0.22
34 16 0.59
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (32 bp):
TGGGCTAAGGCCCTAACTAAATTGAACTATAA
Found at i:29073037 original size:27 final size:26
Alignment explanation
Indices: 29072981--29073037 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
29072971 CAACCTTAAC
* * *
29072981 CCTAGGGGTATATCAGTAATTTTGCT
1 CCTAGGGGTAAATCAGTAATTTTCCA
*
29073007 CCTAGGGGTAAATCTGTAAATTTTCCA
1 CCTAGGGGTAAATCAGT-AATTTTCCA
29073034 CCTA
1 CCTA
29073038 TAAAGGTGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 15 0.58
27 11 0.42
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (26 bp):
CCTAGGGGTAAATCAGTAATTTTCCA
Found at i:29080924 original size:27 final size:26
Alignment explanation
Indices: 29080869--29080924 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 26
29080859 AACCTTAACT
* *
29080869 CTAGGGGTATATCAGTAATTTTCCTC
1 CTAGGGGTAAATCAGTAATTTTCCAC
29080895 CTAGGGGTAAATCTA-TAAATTTTCCAC
1 CTAGGGGTAAATC-AGT-AATTTTCCAC
29080922 CTA
1 CTA
29080925 TAAAGGTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 13 0.50
27 13 0.50
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.36
Consensus pattern (26 bp):
CTAGGGGTAAATCAGTAATTTTCCAC
Found at i:29083533 original size:23 final size:23
Alignment explanation
Indices: 29083507--29083556 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
29083497 TGTTAGGGCA
29083507 AAGAAAGCCATGAAAATGATTTG
1 AAGAAAGCCATGAAAATGATTTG
** *
29083530 AAGAAAGTGATGAAAATGGTTTG
1 AAGAAAGCCATGAAAATGATTTG
29083553 AAGA
1 AAGA
29083557 TTCAGCCAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.48, C:0.04, G:0.26, T:0.22
Consensus pattern (23 bp):
AAGAAAGCCATGAAAATGATTTG
Found at i:29084324 original size:44 final size:43
Alignment explanation
Indices: 29084250--29084351 Score: 107
Period size: 44 Copynumber: 2.3 Consensus size: 43
29084240 TAATTATGCC
* **
29084250 CACTTAGTGTGCGAAATCGAGACAGTTTCGGATATGTATATTT-G
1 CACTTAGTGTGCGAGATCGAGACAACTTCGGATAT-T-TATTTGG
* * *
29084294 CACTTAGTGTGCGAGATTGATACAACTTCGGCTATTTATTTGG
1 CACTTAGTGTGCGAGATCGAGACAACTTCGGATATTTATTTGG
* *
29084337 CACTAAGTGTACGAG
1 CACTTAGTGTGCGAG
29084352 TTTTTTGAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
42 5 0.10
43 15 0.31
44 29 0.59
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (43 bp):
CACTTAGTGTGCGAGATCGAGACAACTTCGGATATTTATTTGG
Found at i:29087360 original size:16 final size:17
Alignment explanation
Indices: 29087328--29087361 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
29087318 CGGGATGGCG
29087328 TTTGTTTGATGTTTATT
1 TTTGTTTGATGTTTATT
*
29087345 TTTGTTT-ATTTTTATT
1 TTTGTTTGATGTTTATT
29087361 T
1 T
29087362 CATAAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (17 bp):
TTTGTTTGATGTTTATT
Found at i:29090119 original size:46 final size:45
Alignment explanation
Indices: 29090063--29090238 Score: 212
Period size: 46 Copynumber: 3.8 Consensus size: 45
29090053 TATTTGGGCA
29090063 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *** * *
29090109 TCTGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
29090156 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
29090202 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
29090239 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 67 0.61
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:29090218 original size:93 final size:93
Alignment explanation
Indices: 29090059--29090230 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
29090049 AGGATATTTG
* * *
29090059 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCTGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
29090124 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
*
29090152 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
29090217 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
29090231 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.22, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:29093211 original size:15 final size:15
Alignment explanation
Indices: 29093191--29093246 Score: 87
Period size: 15 Copynumber: 3.7 Consensus size: 15
29093181 GTATCTTGGG
29093191 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
29093206 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
29093221 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
29093236 TTTCTTTATTC
1 TTTCTTTATTC
29093247 GGTTTCCTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
14 2 0.05
15 33 0.89
16 2 0.05
ACGTcount: A:0.12, C:0.16, G:0.11, T:0.61
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:29095229 original size:46 final size:45
Alignment explanation
Indices: 29095173--29095348 Score: 212
Period size: 46 Copynumber: 3.8 Consensus size: 45
29095163 TATTTGGGCA
29095173 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *** * *
29095219 TCTGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
29095266 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
29095312 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
29095349 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 67 0.61
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:29095328 original size:93 final size:93
Alignment explanation
Indices: 29095169--29095340 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
29095159 AGGATATTTG
* * *
29095169 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCTGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
29095234 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
*
29095262 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
29095327 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
29095341 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.22, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:29107438 original size:40 final size:40
Alignment explanation
Indices: 29107381--29107584 Score: 243
Period size: 40 Copynumber: 5.1 Consensus size: 40
29107371 CGGGTGATAA
* *
29107381 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
* *
29107421 CCGGGCTAAG-CCTCGAAGGCATTTGTCCGAGTTACTATAA
1 CCGGGCTAAGTCC-CGAAGGCATTTGTGCGAGTTACTATAT
* * *
29107461 CCGGGCTATGTCCCGAAGGCCTTCGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
29107501 CCGGGCTAAGCCCCGAAGGCATTTGTGCGAGTTACCATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
29107541 CCGGGCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
29107581 CCGG
1 CCGG
29107585 TTAAATTCCG
Statistics
Matches: 139, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
39 4 0.03
40 132 0.95
41 3 0.02
ACGTcount: A:0.22, C:0.26, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:29107510 original size:80 final size:80
Alignment explanation
Indices: 29107377--29107584 Score: 303
Period size: 80 Copynumber: 2.6 Consensus size: 80
29107367 TATTCGGGTG
* * * * *
29107377 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCCGGGCTAAGCCTCGAAGGC
1 ATAACCGGGCTATGTCCCGAAGGCATTCGTGCGAGTTACTATA-TCCGGGCTAAGCCCCGAAGGC
*
29107441 ATTTGTCCGAGTTACT
65 ATTTGTCCGAGTTACC
*
29107457 ATAACCGGGCTATGTCCCGAAGGCCTTCGTGCGAGTTACTATATCCGGGCTAAGCCCCGAAGGCA
1 ATAACCGGGCTATGTCCCGAAGGCATTCGTGCGAGTTACTATATCCGGGCTAAGCCCCGAAGGCA
*
29107522 TTTGTGCGAGTTACC
66 TTTGTCCGAGTTACC
*
29107537 ATAACCGGGCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATATCCGG
1 ATAACCGGGCTATGTCCCGAAGGCATTCGTGCGAGTTA-CTATATCCGG
29107585 TTAAATTCCG
Statistics
Matches: 116, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
79 2 0.02
80 113 0.97
81 1 0.01
ACGTcount: A:0.23, C:0.25, G:0.27, T:0.24
Consensus pattern (80 bp):
ATAACCGGGCTATGTCCCGAAGGCATTCGTGCGAGTTACTATATCCGGGCTAAGCCCCGAAGGCA
TTTGTCCGAGTTACC
Found at i:29112925 original size:15 final size:15
Alignment explanation
Indices: 29112905--29112935 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
29112895 AAAATGAAAG
29112905 ATATGTGTTGGGTTA
1 ATATGTGTTGGGTTA
29112920 ATATGTGTTGGGTTA
1 ATATGTGTTGGGTTA
29112935 A
1 A
29112936 ATGAGAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.32, T:0.45
Consensus pattern (15 bp):
ATATGTGTTGGGTTA
Found at i:29113578 original size:42 final size:44
Alignment explanation
Indices: 29113463--29113600 Score: 119
Period size: 44 Copynumber: 3.2 Consensus size: 44
29113453 GGTGTGATAT
* * *
29113463 CGTGTAAG-ACCATGTTTGAGACATTGGCATCGACT-TGA-GATATA
1 CGTGTAAGAACCATGTCTAAGACATCGGCATCGA-TAT-ATGAT-TA
* *
29113507 CGTGTAAG-ACCATGTCTAGGACATCGGCATCG-TATATGATTT
1 CGTGTAAGAACCATGTCTAAGACATCGGCATCGATATATGATTA
* *
29113549 CGTGTAAGAACC-TTTCTAAGACAGT-GGCATCGATATTTGATTA
1 CGTGTAAGAACCATGTCTAAGACA-TCGGCATCGATATATGATTA
*
29113592 CATGTAAGA
1 CGTGTAAGA
29113601 CCACATCCGA
Statistics
Matches: 79, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
42 27 0.34
43 24 0.30
44 28 0.35
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (44 bp):
CGTGTAAGAACCATGTCTAAGACATCGGCATCGATATATGATTA
Found at i:29126638 original size:15 final size:15
Alignment explanation
Indices: 29126619--29126658 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
29126609 ATGAGTCTTC
*
29126619 AAAAATAAATAGAAAT
1 AAAAATAAACA-AAAT
*
29126635 AAAAGTAAACAAAAT
1 AAAAATAAACAAAAT
29126650 AAAAATAAA
1 AAAAATAAA
29126659 ACGAGTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.15
Consensus pattern (15 bp):
AAAAATAAACAAAAT
Found at i:29134445 original size:41 final size:41
Alignment explanation
Indices: 29134394--29134494 Score: 132
Period size: 41 Copynumber: 2.5 Consensus size: 41
29134384 TGGCATTACT
*
29134394 TGACAGCTTGTGTGATCAGCATCATGTAGCTACATCTTGAC
1 TGACAGCTTGTGTGATCAGCACCATGTAGCTACATCTTGAC
* * **
29134435 TGACAGCTTGTGTGAGT-AGCACCGTGTAGCTACATTTTGGT
1 TGACAGCTTGTGTGA-TCAGCACCATGTAGCTACATCTTGAC
*
29134476 TGATAGCTTGTGTGATCAG
1 TGACAGCTTGTGTGATCAG
29134495 GCCCGTTGAT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
40 1 0.02
41 50 0.96
42 1 0.02
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.34
Consensus pattern (41 bp):
TGACAGCTTGTGTGATCAGCACCATGTAGCTACATCTTGAC
Found at i:29145027 original size:47 final size:47
Alignment explanation
Indices: 29144911--29145116 Score: 184
Period size: 47 Copynumber: 4.3 Consensus size: 47
29144901 ATAGTAAAAT
** * *
29144911 TATGGTCTTGCACA-TAGTCACATATCACATACCGAGGCCATAGCCCAGC
1 TATGGTCTTATACAGTAG-CACATATCAC--ACCGATGCCATAGCCCAGA
* * * *
29144960 CATGGTCTTATAC-G-ATCACATATCACACTGATGCCATATCCCAGA
1 TATGGTCTTATACAGTAGCACATATCACACCGATGCCATAGCCCAGA
* *
29145005 TATGGTCTTATACAGTAGCACATATCACACCGATGCCATATCCCGGA
1 TATGGTCTTATACAGTAGCACATATCACACCGATGCCATAGCCCAGA
* * * * *
29145052 TATGGTCTTATACGGAAGCACAAATCACATTTCTCCGAAGCCATAGCCCAGC
1 TATGGTCTTATACAGTAGCACATATCACA-----CCGATGCCATAGCCCAGA
29145104 TATGGTCTTATAC
1 TATGGTCTTATAC
29145117 GGAAATCACA
Statistics
Matches: 130, Mismatches: 19, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
45 27 0.21
46 1 0.01
47 64 0.49
48 1 0.01
49 10 0.08
52 27 0.21
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (47 bp):
TATGGTCTTATACAGTAGCACATATCACACCGATGCCATAGCCCAGA
Found at i:29146991 original size:40 final size:40
Alignment explanation
Indices: 29146897--29147118 Score: 209
Period size: 40 Copynumber: 5.5 Consensus size: 40
29146887 TATTCGAATG
*
29146897 ATATCCGGGCTAAG-TCCCGAAGGCTTTTGTGCTAGGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCTA-GTGACT
* * * *
29146938 ATAACCGGACTAAGATCCGAAGGCATTCGTGCGAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAG-TGACT
* * * *
29146978 ATATCCGGGCTAAGACCCGTAGGCATTTGTGCTAGCGATT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
* * *
29147018 ATATCCGGGCTAA-AACTCGAAGGCATTTGTGCTAGCGATT
1 ATATCCGGGCTAAGATC-CGAAGGCATTTGTGCTAGTGACT
* * * *
29147058 ATATCTGGGCTAAG-TCCCGAAGGTATTTATGCTAGTGACC
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCTAGTGACT
* *
29147098 ACATCCGGGCTAAGACCCGAA
1 ATATCCGGGCTAAGATCCGAA
29147119 AGCCTTGTGC
Statistics
Matches: 149, Mismatches: 25, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
39 3 0.02
40 115 0.77
41 30 0.20
42 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
Found at i:29147071 original size:80 final size:80
Alignment explanation
Indices: 29146897--29147157 Score: 242
Period size: 80 Copynumber: 3.3 Consensus size: 80
29146887 TATTCGAATG
* * * *
29146897 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACTATAACCGGACTAAGATCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTA-GTGACTATATCCGGGCTAAAATCCGAAGGC
*
29146962 ATTCGTGCGAGTTGCT
65 ATTCGTGCGAGTCGCT
* * * *
29146978 ATATCCGGGCTAAGACCCGTAGGCATTTGTGCTAGCGATTATATCCGGGCTAAAA-CTCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAAATC-CGAAGGC
* * *
29147042 ATTTGTGCTAG-CGATT
65 ATTCGTGCGAGTCG-CT
* * * * * * * * *
29147058 ATATCTGGGCTAAGTCCCGAAGGTATTTATGCTAGTGACCACATCCGGGCTAAGACCCGAAAGCC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAAATCCGAAGGCA
* * *
29147123 TT-GTGCAAGTAGTT
66 TTCGTGCGAGTCGCT
*
29147137 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
29147158 ATTACTTGAG
Statistics
Matches: 148, Mismatches: 28, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
78 14 0.09
79 15 0.10
80 87 0.59
81 32 0.22
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (80 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAAATCCGAAGGCA
TTCGTGCGAGTCGCT
Found at i:29151486 original size:27 final size:27
Alignment explanation
Indices: 29151455--29151666 Score: 271
Period size: 27 Copynumber: 7.9 Consensus size: 27
29151445 CACTGCGATC
*
29151455 AATGCCCTTGTAGGATAAAATGACCGT
1 AATGCCCTTGTAGGGTAAAATGACCGT
*
29151482 AATGCCCATGTAGGGTAAAATGACCGT
1 AATGCCCTTGTAGGGTAAAATGACCGT
* * **
29151509 AATGCCCCTGTAGGGTAAAATAATTGT
1 AATGCCCTTGTAGGGTAAAATGACCGT
* *
29151536 AATACCCTTGTAGGTTAAAATGACCGT
1 AATGCCCTTGTAGGGTAAAATGACCGT
* *
29151563 AATGCCCTTGTAGGGTAAAATAATCGT
1 AATGCCCTTGTAGGGTAAAATGACCGT
* *
29151590 AATACCCTTGTAAGGTAAAATGACCGT
1 AATGCCCTTGTAGGGTAAAATGACCGT
*
29151617 AATGCCCGTGTAGGGTAAAATGACCGT
1 AATGCCCTTGTAGGGTAAAATGACCGT
* * * *
29151644 AATACCCCTATATGGTAAAATGA
1 AATGCCCTTGTAGGGTAAAATGA
29151667 TAATTATGCC
Statistics
Matches: 158, Mismatches: 27, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 158 1.00
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.26
Consensus pattern (27 bp):
AATGCCCTTGTAGGGTAAAATGACCGT
Found at i:29152062 original size:27 final size:27
Alignment explanation
Indices: 29152022--29152082 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
29152012 CACTATACTG
* *
29152022 ATACTGTATTGGGCTTAGG-CCACACT
1 ATACTGTATAGGGCTAAGGCCCACACT
*
29152048 ATTACTGTATAGGGCTAAGGCCCAGACT
1 A-TACTGTATAGGGCTAAGGCCCACACT
29152076 ATACTGT
1 ATACTGT
29152083 TACTGAATAG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 1 0.03
27 22 0.73
28 7 0.23
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (27 bp):
ATACTGTATAGGGCTAAGGCCCACACT
Found at i:29156498 original size:30 final size:30
Alignment explanation
Indices: 29156464--29156523 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
29156454 ATTTAATACG
29156464 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
29156494 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
29156524 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:29160870 original size:13 final size:13
Alignment explanation
Indices: 29160852--29160880 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
29160842 TTTAGTTTAA
29160852 TTAGTTAATTAGT
1 TTAGTTAATTAGT
29160865 TTAGTTAATTAGT
1 TTAGTTAATTAGT
29160878 TTA
1 TTA
29160881 ATAAACAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (13 bp):
TTAGTTAATTAGT
Found at i:29169646 original size:13 final size:13
Alignment explanation
Indices: 29169628--29169653 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29169618 CTATGCACCC
29169628 TTAGTTTAGATAA
1 TTAGTTTAGATAA
29169641 TTAGTTTAGATAA
1 TTAGTTTAGATAA
29169654 ACAAATCCCT
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:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (13 bp):
TTAGTTTAGATAA
Found at i:29172925 original size:40 final size:40
Alignment explanation
Indices: 29172880--29173112 Score: 371
Period size: 40 Copynumber: 5.8 Consensus size: 40
29172870 TCATTTGATG
*
29172880 TGGAATTGTATCCGGGCTTAAAGACCCACAGGCTTCGTGC
1 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
* *
29172920 TGGAATTGTATCCGGGTTTAAAGACCCTCAGGCTTCGTGC
1 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
*
29172960 TGGAATTGTATCCGGGCTTAAAGACCTGCAGGCTTCGTGC
1 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
29173000 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
1 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
*
29173040 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTAGTGC
1 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
* * *
29173080 TGGAA-TGACATCCGGG-TTAAAAACCTGCAGGCT
1 TGGAATTG-TATCCGGGCTTAAAGACCCGCAGGCT
29173113 GTGCTAGATA
Statistics
Matches: 182, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
39 17 0.09
40 165 0.91
ACGTcount: A:0.22, C:0.23, G:0.29, T:0.26
Consensus pattern (40 bp):
TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
Found at i:29181085 original size:40 final size:40
Alignment explanation
Indices: 29181027--29181139 Score: 149
Period size: 40 Copynumber: 2.9 Consensus size: 40
29181017 TTATATGATG
* *
29181027 TGGAATTGTATCCAGGCTTAAAGACCCGCAGGCTTCGTGC
1 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTAGTGC
*
29181067 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTAGTGT
1 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTAGTGC
* * *
29181107 TGGAA-TGACATCCGGG-TTAAAAACCTGCAGGCT
1 TGGAATTG-TATCCGGGCTTAAAGACCCGCAGGCT
29181140 GTGCTAGATA
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
39 17 0.26
40 49 0.74
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTAGTGC
Found at i:29194873 original size:49 final size:50
Alignment explanation
Indices: 29194796--29195033 Score: 268
Period size: 49 Copynumber: 4.8 Consensus size: 50
29194786 TAGCCGAAGC
* * *
29194796 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGATC-AAT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCGAAT
* * * * *
29194845 TATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAAC
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCGAAT
* * * * *
29194895 CATCTGATGCACGTAGTAGCCTACACTTAGTACTACAC--GCATGATCGAAGT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGC--GACCGAA-T
* * * *
29194946 TTTCAGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC-AAT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCGAAT
29194995 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACA
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACA
29195034 CGTGACCTCA
Statistics
Matches: 154, Mismatches: 29, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
48 1 0.01
49 76 0.49
50 42 0.27
51 33 0.21
53 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.26
Consensus pattern (50 bp):
TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCGAAT
Found at i:29194982 original size:101 final size:98
Alignment explanation
Indices: 29194809--29195032 Score: 290
Period size: 101 Copynumber: 2.3 Consensus size: 98
29194799 CTGGTACGCA
* *
29194809 TAGTAGCCTGCACTTAGTACTACA-CATGCGATCAATTATCCGGTACACGTAGTAGCCTGCACTT
1 TAGTAGCCTGCACTTAGTACTACACCAT-CGATCAATTATCAGGTACACATAGTAGCCTGCACTT
* *
29194873 AGTACTACACACGTGACCTAACCATCTGATGCACG
65 AGTACTACACACGCGACC-AACCATCTGATACACG
* * *
29194908 TAGTAGCCTACACTTAGTACTACACGCAT-GATCGAAGTTTTCAGGTACGCATAGTAGCCTGCAC
1 TAGTAGCCTGCACTTAGTACTACAC-CATCGATC-AA-TTATCAGGTACACATAGTAGCCTGCAC
* ** *
29194972 TTAGTACTACACATGCGACCAATTATCTGGTACACG
63 TTAGTACTACACACGCGACCAACCATCTGATACACG
29195008 TAGTAGCCTGCACTTAGTACTACAC
1 TAGTAGCCTGCACTTAGTACTACAC
29195033 ACGTGACCTC
Statistics
Matches: 109, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
99 27 0.25
100 38 0.35
101 44 0.40
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (98 bp):
TAGTAGCCTGCACTTAGTACTACACCATCGATCAATTATCAGGTACACATAGTAGCCTGCACTTA
GTACTACACACGCGACCAACCATCTGATACACG
Found at i:29195722 original size:30 final size:30
Alignment explanation
Indices: 29195688--29195747 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
29195678 CTTTAATACG
29195688 AACTTTGACAAAATTAC-CATTTTGCCCCTA
1 AACTTTGACAAAATTACAC-TTTTGCCCCTA
** *
29195718 AACTTTTTCATAATTACACTTTTGCCCCTA
1 AACTTTGACAAAATTACACTTTTGCCCCTA
29195748 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.30, C:0.27, G:0.05, T:0.38
Consensus pattern (30 bp):
AACTTTGACAAAATTACACTTTTGCCCCTA
Found at i:29199279 original size:13 final size:13
Alignment explanation
Indices: 29199261--29199313 Score: 106
Period size: 13 Copynumber: 4.1 Consensus size: 13
29199251 GAAGCAATCG
29199261 CACACGGGCGTGT
1 CACACGGGCGTGT
29199274 CACACGGGCGTGT
1 CACACGGGCGTGT
29199287 CACACGGGCGTGT
1 CACACGGGCGTGT
29199300 CACACGGGCGTGT
1 CACACGGGCGTGT
29199313 C
1 C
29199314 CCTGTCGGGC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 40 1.00
ACGTcount: A:0.15, C:0.32, G:0.38, T:0.15
Consensus pattern (13 bp):
CACACGGGCGTGT
Found at i:29201642 original size:11 final size:11
Alignment explanation
Indices: 29201626--29201650 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
29201616 AATGAGTTAG
29201626 AAACCACTTTA
1 AAACCACTTTA
29201637 AAACCACTTTA
1 AAACCACTTTA
29201648 AAA
1 AAA
29201651 TAGTAGCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (11 bp):
AAACCACTTTA
Found at i:29202521 original size:21 final size:21
Alignment explanation
Indices: 29202493--29202574 Score: 94
Period size: 21 Copynumber: 3.9 Consensus size: 21
29202483 TTTTGGTGGA
29202493 TCAGCTCTTATGAGCTTCTGT
1 TCAGCTCTTATGAGCTTCTGT
* * * **
29202514 TTAGCTCTCACGAGCTTCAAT
1 TCAGCTCTTATGAGCTTCTGT
29202535 TCAGCTCTT-TCGAGCTTCTGT
1 TCAGCTCTTAT-GAGCTTCTGT
*
29202556 TCAACTCTTATGAGCTTCT
1 TCAGCTCTTATGAGCTTCT
29202575 ATTAGCATGA
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
21 47 0.98
22 1 0.02
ACGTcount: A:0.17, C:0.27, G:0.16, T:0.40
Consensus pattern (21 bp):
TCAGCTCTTATGAGCTTCTGT
Found at i:29202571 original size:42 final size:42
Alignment explanation
Indices: 29202493--29202573 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
29202483 TTTTGGTGGA
* *
29202493 TCAGCTCTTATGAGCTTCTGTTTAGCTCTCACGAGCTTCAAT
1 TCAGCTCTTATGAGCTTCTGTTCAACTCTCACGAGCTTCAAT
* *
29202535 TCAGCTCTT-TCGAGCTTCTGTTCAACTCTTATGAGCTTC
1 TCAGCTCTTAT-GAGCTTCTGTTCAACTCTCACGAGCTTC
29202574 TATTAGCATG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 1 0.03
42 33 0.97
ACGTcount: A:0.17, C:0.27, G:0.16, T:0.40
Consensus pattern (42 bp):
TCAGCTCTTATGAGCTTCTGTTCAACTCTCACGAGCTTCAAT
Found at i:29206371 original size:40 final size:40
Alignment explanation
Indices: 29206295--29206438 Score: 125
Period size: 40 Copynumber: 3.6 Consensus size: 40
29206285 TAACTCATTC
* *
29206295 AATGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACA
* *
29206335 AATGCCTTCGGGACTTAACCCGGA-ATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATATTA-AAACTCGCACA
* ** ** *
29206375 AAGGCCTTC-GGACCTTAGTCCGGATA-TAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGATATTA-AAAC-TCGCACA
*
29206416 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
29206439 CAGCATTCAA
Statistics
Matches: 88, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
39 6 0.07
40 70 0.80
41 12 0.14
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACA
Found at i:29211954 original size:25 final size:27
Alignment explanation
Indices: 29211920--29211974 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
29211910 CATTACAGTT
29211920 ATTTACCCTAT-GGG-GTATTTCGGTC
1 ATTTACCCTATGGGGTGTATTTCGGTC
29211945 ATTTACCCTATGGGGTGTATTTCGGTC
1 ATTTACCCTATGGGGTGTATTTCGGTC
29211972 ATT
1 ATT
29211975 ATTTTTCCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 11 0.39
26 3 0.11
27 14 0.50
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.42
Consensus pattern (27 bp):
ATTTACCCTATGGGGTGTATTTCGGTC
Found at i:29213522 original size:40 final size:40
Alignment explanation
Indices: 29213394--29213619 Score: 313
Period size: 40 Copynumber: 5.8 Consensus size: 40
29213384 CGGATATAGC
* *
29213394 ACTCGCTCAAATGCCTTCCGGACTTAGCCCGG-ATATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTA
**
29213434 GTTCGCACAAAT-CCTTCGGGACTTAGCCC-G-ATATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTA
29213472 ACTTC-CACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
1 AC-TCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
29213512 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
*
29213552 ACTCGCACAAATGCCTTCGGGACTTAG-CCGGAATTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
* *
29213591 ACTAGCACAGATGCCTTC-GGACTTAGCCC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCC
29213620 CGTTATCATC
Statistics
Matches: 171, Mismatches: 9, Indels: 13
0.89 0.05 0.07
Matches are distributed among these distances:
38 24 0.14
39 66 0.39
40 79 0.46
41 2 0.01
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
Found at i:29213613 original size:118 final size:118
Alignment explanation
Indices: 29213394--29213619 Score: 323
Period size: 118 Copynumber: 1.9 Consensus size: 118
29213384 CGGATATAGC
* **
29213394 ACTCGCTCAAATGCCTTCCGGACTTAGCCCGGATATAGTAGTTCGCACAAATCCTTCGGGACTTA
1 ACTCGCACAAATGCCTTCCGGACTTAGCCCGGATATAGTAACTCGCACAAATCCTTCGGGACTTA
*
29213459 GCCCGATATAGTAACTTCCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
66 GCCCGATATAGTAACTACCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
*
29213512 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGA-ATTAGTAACTCGCACAAATGCCTTCGGGACT
1 ACTCGCACAAATGCCTTCCGGACTTAGCCCGGATA-TAGTAACTCGCACAAAT-CCTTCGGGACT
* * * *
29213576 TAGCCGGA-ATTAGTCACTAGCACAGATGCCTTC-GGACTTAGCCC
64 TAGCCCGATA-TAGTAACTACCACAAATGCCTTCGGGACTTAGCCC
29213620 CGTTATCATC
Statistics
Matches: 96, Mismatches: 9, Indels: 6
0.86 0.08 0.05
Matches are distributed among these distances:
117 1 0.01
118 58 0.60
119 37 0.39
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (118 bp):
ACTCGCACAAATGCCTTCCGGACTTAGCCCGGATATAGTAACTCGCACAAATCCTTCGGGACTTA
GCCCGATATAGTAACTACCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
Found at i:29221473 original size:40 final size:40
Alignment explanation
Indices: 29221439--29221667 Score: 342
Period size: 40 Copynumber: 5.8 Consensus size: 40
29221429 GGATATAGCT
*
29221439 ACTCGCTCAAATGCCTTCGGGACTTAGCCCGG-ATATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTA
** *
29221479 GTTCGCACAAATGCCTTCGGGACTTAGCCTGG-ATATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTA
29221519 ACTTC-CACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
1 AC-TCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
29221559 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
*
29221599 ACTCGCACAAATGCCTTCGGGACTTAG-CCGGAATTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
*
29221638 ACTAGCAC-AATGCCTTCGGGACTTAGCCCG
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCG
29221668 TTATCATCCG
Statistics
Matches: 176, Mismatches: 9, Indels: 9
0.91 0.05 0.05
Matches are distributed among these distances:
38 18 0.10
39 23 0.13
40 131 0.74
41 4 0.02
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
Found at i:29225362 original size:43 final size:43
Alignment explanation
Indices: 29225310--29225437 Score: 175
Period size: 43 Copynumber: 3.0 Consensus size: 43
29225300 GGTTTAAACT
* * *
29225310 ATTGGCACTAAGTGTACGATAAAACTATAGCTTCGGGTAATTA
1 ATTGGCACTAAGTGTACGATACAATTATAGCTTCGGCTAATTA
* * * *
29225353 ATTTGCACTAAGTGTGCAATACAATTATAGCTACGGCTAATTA
1 ATTGGCACTAAGTGTACGATACAATTATAGCTTCGGCTAATTA
* *
29225396 ATTGGCACTAAGTGTTCGATACAATTATAGCTTCGGTTAATT
1 ATTGGCACTAAGTGTACGATACAATTATAGCTTCGGCTAATT
29225438 TGTGACACCC
Statistics
Matches: 73, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 73 1.00
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.34
Consensus pattern (43 bp):
ATTGGCACTAAGTGTACGATACAATTATAGCTTCGGCTAATTA
Found at i:29228044 original size:47 final size:47
Alignment explanation
Indices: 29227991--29228166 Score: 280
Period size: 47 Copynumber: 3.7 Consensus size: 47
29227981 TTAGGATTCT
29227991 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
29228038 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * *
29228085 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
29228132 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
29228167 TCCCGAAGGG
Statistics
Matches: 119, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 119 1.00
ACGTcount: A:0.32, C:0.08, G:0.31, T:0.28
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:29237808 original size:25 final size:25
Alignment explanation
Indices: 29237748--29237812 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 25
29237738 ATCATTTTTC
29237748 GCTCT-TTCGAGCT-ATGAATAGTAA
1 GCTCTATT-GAGCTGATGAATAGTAA
* * *
29237772 GCTCCACCTGAGCTGATGGATAGTAA
1 GCTCTA-TTGAGCTGATGAATAGTAA
29237798 GCTCTATTGAGCTGA
1 GCTCTATTGAGCTGA
29237813 AACGGTAAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
24 4 0.12
25 13 0.39
26 16 0.48
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (25 bp):
GCTCTATTGAGCTGATGAATAGTAA
Found at i:29237894 original size:24 final size:23
Alignment explanation
Indices: 29237793--29237894 Score: 109
Period size: 23 Copynumber: 4.4 Consensus size: 23
29237783 GCTGATGGAT
*
29237793 AGTAAGCTC-TATTGAGCTGAAAC
1 AGTAAGCTCATA-CGAGCTGAAAC
* * *
29237816 GGTAAACT-TTGACGAGCTGAAAC
1 AGTAAGCTCAT-ACGAGCTGAAAC
*
29237839 AGTATGCTCATACGAGCTGAAAC
1 AGTAAGCTCATACGAGCTGAAAC
*
29237862 AGTAAGCTCATACGAGCTGAGAAT
1 AGTAAGCTCATACGAGCTGA-AAC
29237886 AGTAAGCTC
1 AGTAAGCTC
29237895 TTAGGTAAGC
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
23 53 0.80
24 13 0.20
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.23
Consensus pattern (23 bp):
AGTAAGCTCATACGAGCTGAAAC
Found at i:29241547 original size:39 final size:39
Alignment explanation
Indices: 29241504--29241598 Score: 136
Period size: 39 Copynumber: 2.4 Consensus size: 39
29241494 TATATAATTA
* *
29241504 TACCCCTAATCGCACTTACATGCCCCTGTTGTACTTCGG
1 TACCCCTGATCGCACTTACATGCCCCTATTGTACTTCGG
* *
29241543 TACCCCTGATCGCACTTACGTGCCCGTATTGTACTTCGG
1 TACCCCTGATCGCACTTACATGCCCCTATTGTACTTCGG
* *
29241582 TACTCCTGATAGCACTT
1 TACCCCTGATCGCACTT
29241599 TTGAGCCGTG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.18, C:0.34, G:0.17, T:0.32
Consensus pattern (39 bp):
TACCCCTGATCGCACTTACATGCCCCTATTGTACTTCGG
Found at i:29246750 original size:16 final size:16
Alignment explanation
Indices: 29246729--29246764 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
29246719 TATGCTTGAA
29246729 AATACAGATTCCAGCC
1 AATACAGATTCCAGCC
29246745 AATACAGATTCCAGCC
1 AATACAGATTCCAGCC
29246761 AATA
1 AATA
29246765 GAAACTCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.42, C:0.28, G:0.11, T:0.19
Consensus pattern (16 bp):
AATACAGATTCCAGCC
Found at i:29253443 original size:19 final size:19
Alignment explanation
Indices: 29253412--29253483 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
29253402 AGATATATAA
29253412 ATTTTGTAATTTTTATAAA-T
1 ATTTTG-AATTTTTA-AAATT
29253432 ATTTTGAA-TTTTAAAATTT
1 ATTTTGAATTTTTAAAA-TT
29253451 ATTTTGAATTTTTGAAAATT
1 ATTTTGAATTTTT-AAAATT
*
29253471 ATTTTGTATTTTT
1 ATTTTGAATTTTT
29253484 TTGTTGAGAG
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
17 3 0.06
18 5 0.11
19 11 0.23
20 24 0.51
21 4 0.09
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (19 bp):
ATTTTGAATTTTTAAAATT
Found at i:29256841 original size:10 final size:10
Alignment explanation
Indices: 29256828--29256875 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
29256818 TTAATTTCAT
29256828 TTATCTTTAA
1 TTATCTTTAA
*
29256838 TTATATTTAA
1 TTATCTTTAA
*
29256848 TTATCTTTAT
1 TTATCTTTAA
*
29256858 TTAT-TTGTAT
1 TTATCTT-TAA
29256868 TTATCTTT
1 TTATCTTT
29256876 TAGAATTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
9 2 0.06
10 29 0.88
11 2 0.06
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (10 bp):
TTATCTTTAA
Done.