Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 75 of 310
Found at i:24007931 original size:23 final size:23
Alignment explanation
Indices: 24007882--24007935 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
24007872 TAAAATCGAT
* *
24007882 ATTATTATAAAATTGATGTTATT
1 ATTATTATAAAATTGATATTATC
* *
24007905 ATTATTATAAAATTGGTATTCTC
1 ATTATTATAAAATTGATATTATC
24007928 ATTATTAT
1 ATTATTAT
24007936 TGTAGTTGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (23 bp):
ATTATTATAAAATTGATATTATC
Found at i:24025068 original size:63 final size:63
Alignment explanation
Indices: 24024969--24025094 Score: 225
Period size: 63 Copynumber: 2.0 Consensus size: 63
24024959 CACACTTCAG
* *
24024969 ACTTCAAACTCTTTCTGTTTGGCCCATTTTACTATTTAAAAATAATCATAAATATTTAAAACA
1 ACTTCAAACTCTTTCAGTTTGGCCCATTTTACTATTTAAAAACAATCATAAATATTTAAAACA
*
24025032 ACTTCAAACTCTTTCAGTTTGGTCCATTTTACTATTTAAAAACAATCATAAATATTTAAAACA
1 ACTTCAAACTCTTTCAGTTTGGCCCATTTTACTATTTAAAAACAATCATAAATATTTAAAACA
24025095 TATACTTTAT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.39, C:0.17, G:0.05, T:0.39
Consensus pattern (63 bp):
ACTTCAAACTCTTTCAGTTTGGCCCATTTTACTATTTAAAAACAATCATAAATATTTAAAACA
Found at i:24026687 original size:21 final size:21
Alignment explanation
Indices: 24026622--24026687 Score: 69
Period size: 25 Copynumber: 3.0 Consensus size: 21
24026612 TATCCAACCA
*
24026622 AATAAATTTAATATCTAACAT
1 AATAAATTCAATATCTAACAT
* *
24026643 AATAAATTCAACAAGCTTAAAACAT
1 AATAAATTCAA-TATC-T--AACAT
24026668 AATAAATTCAATATCTAACA
1 AATAAATTCAATATCTAACA
24026688 AATTCAAGAC
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
21 14 0.39
22 2 0.06
23 2 0.06
24 2 0.06
25 16 0.44
ACGTcount: A:0.55, C:0.14, G:0.02, T:0.30
Consensus pattern (21 bp):
AATAAATTCAATATCTAACAT
Found at i:24026688 original size:32 final size:32
Alignment explanation
Indices: 24026661--24026721 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
24026651 CAACAAGCTT
* *
24026661 AAAACATAATAAATTCAATATCTAACAAATTC
1 AAAACATAATAAATTCAAAATCCAACAAATTC
* *
24026693 AAGACATAATAATTTCAAAATCCAACAAA
1 AAAACATAATAAATTCAAAATCCAACAAA
24026722 CTAAAATTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.57, C:0.16, G:0.02, T:0.25
Consensus pattern (32 bp):
AAAACATAATAAATTCAAAATCCAACAAATTC
Found at i:24030824 original size:36 final size:36
Alignment explanation
Indices: 24030777--24030875 Score: 198
Period size: 36 Copynumber: 2.8 Consensus size: 36
24030767 GGGTCTACAC
24030777 AAAAAAAGAACAAAACTTAAGACAACTTAAGACAAT
1 AAAAAAAGAACAAAACTTAAGACAACTTAAGACAAT
24030813 AAAAAAAGAACAAAACTTAAGACAACTTAAGACAAT
1 AAAAAAAGAACAAAACTTAAGACAACTTAAGACAAT
24030849 AAAAAAAGAACAAAACTTAAGACAACT
1 AAAAAAAGAACAAAACTTAAGACAACT
24030876 CATACAGTAT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 63 1.00
ACGTcount: A:0.65, C:0.14, G:0.08, T:0.13
Consensus pattern (36 bp):
AAAAAAAGAACAAAACTTAAGACAACTTAAGACAAT
Found at i:24031682 original size:25 final size:25
Alignment explanation
Indices: 24031635--24031685 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
24031625 AGTAACGAAC
**
24031635 AAGAAGAAAAAAAAAGAGTTTTAAA
1 AAGAAGAAAAAAAAAGAACTTTAAA
*
24031660 AAGAAGAAAAAAACAGAACTTTAAA
1 AAGAAGAAAAAAAAAGAACTTTAAA
24031685 A
1 A
24031686 TGAACATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.69, C:0.04, G:0.14, T:0.14
Consensus pattern (25 bp):
AAGAAGAAAAAAAAAGAACTTTAAA
Found at i:24043768 original size:56 final size:56
Alignment explanation
Indices: 24043687--24043800 Score: 201
Period size: 56 Copynumber: 2.0 Consensus size: 56
24043677 TTATTTTCAA
24043687 TCACAAGAATGGGTTAAAGAGATAAATTTACTGCCATGATGAGTACCGCACTATTT
1 TCACAAGAATGGGTTAAAGAGATAAATTTACTGCCATGATGAGTACCGCACTATTT
* * *
24043743 TCACAATAATGGGTTAAAGGGATAAATTTACTGCCATGATGAGTACTGCACTATTT
1 TCACAAGAATGGGTTAAAGAGATAAATTTACTGCCATGATGAGTACCGCACTATTT
24043799 TC
1 TC
24043801 CCACCAATCT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (56 bp):
TCACAAGAATGGGTTAAAGAGATAAATTTACTGCCATGATGAGTACCGCACTATTT
Found at i:24047106 original size:20 final size:21
Alignment explanation
Indices: 24047083--24047121 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
24047073 ATTACTTACC
*
24047083 ATAAACATTAA-AATTAAAAT
1 ATAAAAATTAATAATTAAAAT
24047103 ATAAAAATTAATAATTAAA
1 ATAAAAATTAATAATTAAA
24047122 TTCGGATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAAAAATTAATAATTAAAAT
Found at i:24047277 original size:23 final size:24
Alignment explanation
Indices: 24047223--24047277 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
24047213 TAGCTACGGA
24047223 AATTAAA-ACAATTAAAATTTATC
1 AATTAAATACAATTAAAATTTATC
24047246 AA-TACAATACAATT-AAATTT-TC
1 AATTA-AATACAATTAAAATTTATC
24047268 ACATTAAATA
1 A-ATTAAATA
24047278 TTTCAATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
22 5 0.18
23 15 0.54
24 8 0.29
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.35
Consensus pattern (24 bp):
AATTAAATACAATTAAAATTTATC
Found at i:24047809 original size:5 final size:5
Alignment explanation
Indices: 24047799--24047841 Score: 86
Period size: 5 Copynumber: 8.6 Consensus size: 5
24047789 TATTATTATA
24047799 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
24047842 TATTCTTAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:24047906 original size:19 final size:20
Alignment explanation
Indices: 24047869--24047907 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
24047859 TAGTATAATT
*
24047869 TATTATTTTATACATATGTA
1 TATTATTTTATACACATGTA
24047889 TATTATTTT-TACACATGTA
1 TATTATTTTATACACATGTA
24047908 AACACCAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.33, C:0.08, G:0.05, T:0.54
Consensus pattern (20 bp):
TATTATTTTATACACATGTA
Found at i:24048977 original size:325 final size:325
Alignment explanation
Indices: 24048383--24049022 Score: 955
Period size: 325 Copynumber: 2.0 Consensus size: 325
24048373 ATTTAATTCG
* * *
24048383 AGTGGCTAGAGGTACACATCCTGTTGATACAGTGATACAACGAGGGAATACGTAAGAAGATGTGG
1 AGTGGCTAGAAGTACACATCCTGTTGATACAGTGATACAACGAAGGAATACATAAGAAGATGTGG
* *
24048448 TGGAGCTAATGGAGGTCGGTTCACCCAATCGGAGTGGAGAGCCGAAGATTCCAAAGAGTGAAAGT
66 TGGAGCTAATGGAGGTCAGTTCACCCAATCGGAGTGGAGAGCCGAAGATTACAAAGAGTGAAAGT
* *
24048513 GGAGAAAGTATGAAGGCTAAGTGTTGAGGGTCAACTAGCAGAGTATAGGTAAGTATATCTCAGAG
131 GGAGAAAGTATGAAGGATAAGTGTTGAGGGTCAACTAGCAGAGTATAGGCAAGTATATCTCAGAG
* *
24048578 AGTCGATCAATTGATCATCGTTTTGGAGGCTATTTATGGGCAAGGTCCCATGTAGGATGATGTTA
196 AGTCGATCAATTGATCATCGTTTTGGAGGCTATTTATGGGCAAGGTCCCATGCAGGATGACGTTA
* **
24048643 ACGTGTTGAGCCCGTAACTAGGCCATCATTGTGGGACGTGTGGGGCGAATGTCTTCAATAGGACA
261 ACGTGTTGAGCCCGCAACTAGGCCATCATTGTGGGACGTGTAAGGCGAATGTCTTCAATAGGACA
* * * *
24048708 AGTGGCTAGAAGTACATA-CCTTGTTGATACATTGATACAATGAAGGAATACATAGGAAGATGTG
1 AGTGGCTAGAAGTACACATCC-TGTTGATACAGTGATACAACGAAGGAATACATAAGAAGATGTG
* **
24048772 GTGGAGCTAATGGAGGTCAGTTTACCCAATCAGG-GTGGAGAGTTGAAGATTACAAAGAGTGAAA
65 GTGGAGCTAATGGAGGTCAGTTCACCCAATC-GGAGTGGAGAGCCGAAGATTACAAAGAGTGAAA
*
24048836 GTGGAGAAAGTATGAAGGATAAGTGCTT-AGGGTCAACT-GACAGAGTGTAGGCAAGTATATCTC
129 GTGGAGAAAGTATGAAGGATAAGTG-TTGAGGGTCAACTAG-CAGAGTATAGGCAAGTATATCTC
* ** **
24048899 TGAGAGTCGATCCCTTGATCATCGTTTTGGAGGCTATTTATGGGCAAGGTCCTGTGCAGGATGAC
192 AGAGAGTCGATCAATTGATCATCGTTTTGGAGGCTATTTATGGGCAAGGTCCCATGCAGGATGAC
* * * *
24048964 GTTAACTTGTTGAGCCCGCAACTAGGCCATCATTGTTGGATGTGTAAGGTGAATGTCTT
257 GTTAACGTGTTGAGCCCGCAACTAGGCCATCATTGTGGGACGTGTAAGGCGAATGTCTT
24049023 TGATGGGATG
Statistics
Matches: 282, Mismatches: 29, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
324 3 0.01
325 275 0.98
326 4 0.01
ACGTcount: A:0.30, C:0.14, G:0.30, T:0.26
Consensus pattern (325 bp):
AGTGGCTAGAAGTACACATCCTGTTGATACAGTGATACAACGAAGGAATACATAAGAAGATGTGG
TGGAGCTAATGGAGGTCAGTTCACCCAATCGGAGTGGAGAGCCGAAGATTACAAAGAGTGAAAGT
GGAGAAAGTATGAAGGATAAGTGTTGAGGGTCAACTAGCAGAGTATAGGCAAGTATATCTCAGAG
AGTCGATCAATTGATCATCGTTTTGGAGGCTATTTATGGGCAAGGTCCCATGCAGGATGACGTTA
ACGTGTTGAGCCCGCAACTAGGCCATCATTGTGGGACGTGTAAGGCGAATGTCTTCAATAGGACA
Found at i:24054779 original size:23 final size:23
Alignment explanation
Indices: 24054749--24054796 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
24054739 TAGGGGACTT
24054749 TGGCATACAAGTCTTGAGACATA
1 TGGCATACAAGTCTTGAGACATA
24054772 TGGCATACAAGTCTTGAGACATA
1 TGGCATACAAGTCTTGAGACATA
24054795 TG
1 TG
24054797 ACACATGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (23 bp):
TGGCATACAAGTCTTGAGACATA
Found at i:24056829 original size:20 final size:19
Alignment explanation
Indices: 24056793--24056843 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
24056783 AAGGGCTATT
*
24056793 TTGTAAA-GTTGTAAAATAA
1 TTGTAAATG-TGTGAAATAA
24056812 GTTGTAAATGTGTGAAATAA
1 -TTGTAAATGTGTGAAATAA
24056832 TTG-AAAT-TGTGA
1 TTGTAAATGTGTGA
24056844 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:24058836 original size:24 final size:24
Alignment explanation
Indices: 24058809--24058879 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
24058799 ATCATAGAAA
24058809 GTGTACAT-TGGCACTATGTGTGCG
1 GTGTA-ATATGGCACTATGTGTGCG
*
24058833 GTGTAGTATGGCACTATGTGTGCG
1 GTGTAATATGGCACTATGTGTGCG
*
24058857 GAGTTGAATA--GCACTATGTGTGC
1 GTG-T-AATATGGCACTATGTGTGC
24058880 TGATTTGAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
23 1 0.02
24 36 0.88
25 1 0.02
26 3 0.07
ACGTcount: A:0.20, C:0.14, G:0.34, T:0.32
Consensus pattern (24 bp):
GTGTAATATGGCACTATGTGTGCG
Found at i:24058900 original size:26 final size:24
Alignment explanation
Indices: 24058819--24058889 Score: 88
Period size: 24 Copynumber: 3.0 Consensus size: 24
24058809 GTGTACATTG
* * * *
24058819 GCACTATGTGTGCGGTGTAGTATG
1 GCACTATGTGTGCGGAGTTGAATA
24058843 GCACTATGTGTGCGGAGTTGAATA
1 GCACTATGTGTGCGGAGTTGAATA
* *
24058867 GCACTATGTGTGCTGATTTGAAT
1 GCACTATGTGTGCGGAGTTGAAT
24058890 GTCAACATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.21, C:0.13, G:0.32, T:0.34
Consensus pattern (24 bp):
GCACTATGTGTGCGGAGTTGAATA
Found at i:24060352 original size:47 final size:44
Alignment explanation
Indices: 24060289--24060410 Score: 129
Period size: 47 Copynumber: 2.6 Consensus size: 44
24060279 TATGTGTGCT
* * *
24060289 AGTGTAAAACATGTCTGGGACATGCATGGGCTACATT-ATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGG-T--ATTGACGAGAGCC
*
24060335 AGTGTAAGACCATGTCTGGGACATGGCATCGGTATTGAGACGAGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGTATT--GACGAGAGCC
*
24060383 AGTGTAAGACATGTTTGGGACATGCATC
1 AGTGTAAGACATGTCTGGGACATGCATC
24060411 AGCCTTGAGA
Statistics
Matches: 66, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
45 3 0.05
46 13 0.20
47 28 0.42
48 22 0.33
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.25
Consensus pattern (44 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGTATTGACGAGAGCC
Found at i:24060391 original size:48 final size:48
Alignment explanation
Indices: 24060286--24060502 Score: 159
Period size: 48 Copynumber: 4.6 Consensus size: 48
24060276 TGATATGTGT
* ** *
24060286 GCTAGTGTAAAACATGTCTGGGACAT-GCATGGGC--T-ACATTATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGGCATCAGCATTGAGA-TA-GAGA
* * * *
24060332 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGTATTGAGA-CGAGA
1 GCTAGTGTAAGA-CATGTCTGGGACATGGCATCAGCATTGAGATAGAGA
* * * *
24060380 GCTAGTGTAAGACATGTTTGGGACAT-GCATCAGCCTTGAGATATACAA
1 GCTAGTGTAAGACATGTCTGGGACATGGCATCAGCATTGAGATAGA-GA
* * * *
24060428 GCTAGTGTAAGACTTGTCTGGGACATGGCGTCAGC-TT--GAT-GTGT
1 GCTAGTGTAAGACATGTCTGGGACATGGCATCAGCATTGAGATAGAGA
*
24060472 G-TCAGTGTAAGACCTGTCTGGGACATGGCAT
1 GCT-AGTGTAAGACATGTCTGGGACATGGCAT
24060503 TGACACCGAT
Statistics
Matches: 139, Mismatches: 23, Indels: 20
0.76 0.13 0.11
Matches are distributed among these distances:
43 1 0.01
44 27 0.19
46 25 0.18
47 28 0.20
48 48 0.35
49 7 0.05
50 1 0.01
51 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.26
Consensus pattern (48 bp):
GCTAGTGTAAGACATGTCTGGGACATGGCATCAGCATTGAGATAGAGA
Found at i:24060543 original size:49 final size:49
Alignment explanation
Indices: 24060326--24060604 Score: 166
Period size: 49 Copynumber: 5.8 Consensus size: 49
24060316 GGGCTACATT
* * *** *
24060326 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGTATTG--AG
1 ATGAAAGCCAGTGTAAGA-CTTGTCTGGGACATGGCATCGACCTCGATAG
* * * * * * * *
24060374 ACGAGAGCTAGTGTAAGACATGTTTGGGACAT-GCATC-AGCCTTGAGAT
1 ATGAAAGCCAGTGTAAGACTTGTCTGGGACATGGCATCGA-CCTCGATAG
* * * *
24060422 AT-ACAAGCTAGTGTAAGACTTGTCTGGGACATGGCGTC-AGCTTGAT-G
1 ATGA-AAGCCAGTGTAAGACTTGTCTGGGACATGGCATCGACCTCGATAG
* * * *
24060469 -TG--TGTCAGTGTAAGACCTGTCTGGGACATGGCATTGACAC-CGATAG
1 ATGAAAGCCAGTGTAAGACTTGTCTGGGACATGGCATCGAC-CTCGATAG
* * * * * * *
24060515 ATGAGAGCCAGTGTAAGACTTGTTTGGGACACGACATCGGCCTCGGTAT
1 ATGAAAGCCAGTGTAAGACTTGTCTGGGACATGGCATCGACCTCGATAG
* *
24060564 ATGAAAGTCAGTGTAAGACTTGTCTGGGAAATGGCATCGAC
1 ATGAAAGCCAGTGTAAGACTTGTCTGGGACATGGCATCGAC
24060605 TTTAATGTGC
Statistics
Matches: 178, Mismatches: 40, Indels: 25
0.73 0.16 0.10
Matches are distributed among these distances:
44 27 0.15
45 4 0.02
46 11 0.06
47 16 0.09
48 49 0.28
49 71 0.40
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (49 bp):
ATGAAAGCCAGTGTAAGACTTGTCTGGGACATGGCATCGACCTCGATAG
Found at i:24064116 original size:51 final size:51
Alignment explanation
Indices: 24064011--24064118 Score: 119
Period size: 51 Copynumber: 2.1 Consensus size: 51
24064001 CCAAGAATTG
* * * *
24064011 GTTCATATGAAATAACAGTTCTTACCAAATGACAGCTCATGCAAAGTAATA
1 GTTCATATGAAATAACAGTTCTTACCAAATAACAACTCATGCAAAATAACA
* * * * *
24064062 GTTCATATGAAATATCAGTT-TATATCGAATAACAATTCATTCAAAATAACA
1 GTTCATATGAAATAACAGTTCT-TACCAAATAACAACTCATGCAAAATAACA
24064113 GTTCAT
1 GTTCAT
24064119 GCTTCATCAT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
50 1 0.02
51 46 0.98
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.31
Consensus pattern (51 bp):
GTTCATATGAAATAACAGTTCTTACCAAATAACAACTCATGCAAAATAACA
Found at i:24070027 original size:19 final size:20
Alignment explanation
Indices: 24069989--24070027 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
24069979 TCACCATTCT
*
24069989 ATTGTTATTAGGCATTGAATA
1 ATTGTTATTA-GCATGGAATA
24070010 ATTGTTATT-GCATGGAAT
1 ATTGTTATTAGCATGGAAT
24070028 GTGCGATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
21 9 0.53
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.44
Consensus pattern (20 bp):
ATTGTTATTAGCATGGAATA
Found at i:24070213 original size:48 final size:49
Alignment explanation
Indices: 24070137--24070461 Score: 297
Period size: 48 Copynumber: 6.7 Consensus size: 49
24070127 GTTATTTGTG
*
24070137 GGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCAATATATGA
1 GGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTCAATATATGA
* * ** * **
24070186 GTC-AGTGTAAGATCATGTTTGAAACATGGCATCGGCAT-TGT-TATGA
1 GGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTCAATATATGA
* * ** * *
24070232 GAGCTAATGTAAGACCATGTCTATGACATGGCATCGACCTCAATATGTGA
1 G-GCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTCAATATATGA
* * * **
24070282 -GCTAGTGTAAGACCACGTTTGGAACATGGCATCGGCAT-TGT-TATGA
1 GGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTCAATATATGA
* * *
24070328 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCAATATGTAA
1 G-GCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTCAATATATGA
* * * *
24070378 GAC-AGTGTAAGACCATGTTTGGGACCTGGCATCGGCACT-GATACATGA
1 GGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGC-CTCAATATATGA
* * *
24070426 GAGCCAATGTAAGACCATGTCTGGGACATGGCATCG
1 G-GCTAGTGTAAGACCATGTTTGGGACATGGCATCG
24070462 ATATTTTACC
Statistics
Matches: 215, Mismatches: 50, Indels: 21
0.75 0.17 0.07
Matches are distributed among these distances:
46 10 0.05
47 3 0.01
48 158 0.73
49 8 0.04
50 36 0.17
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (49 bp):
GGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTCAATATATGA
Found at i:24070308 original size:96 final size:96
Alignment explanation
Indices: 24070138--24070462 Score: 456
Period size: 96 Copynumber: 3.4 Consensus size: 96
24070128 TTATTTGTGG
* * * *
24070138 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCAATATATGAG-TCAGTGTAAGATCAT
1 GCTAATGTAAGACCATGTCTGGGACATGGCATCGACCTCAATATGTGAGCT-AGTGTAAGACCAT
*
24070202 GTTTGAAACATGGCATCGGCATTGTTATGAGA
65 GTTTGGAACATGGCATCGGCATTGTTATGAGA
** *
24070234 GCTAATGTAAGACCATGTCTATGACATGGCATCGACCTCAATATGTGAGCTAGTGTAAGACCACG
1 GCTAATGTAAGACCATGTCTGGGACATGGCATCGACCTCAATATGTGAGCTAGTGTAAGACCATG
24070299 TTTGGAACATGGCATCGGCATTGTTATGAGA
66 TTTGGAACATGGCATCGGCATTGTTATGAGA
* * *
24070330 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCAATATGTAAGAC-AGTGTAAGACCAT
1 GCTAATGTAAGACCATGTCTGGGACATGGCATCGACCTCAATATGTGAG-CTAGTGTAAGACCAT
* * * *
24070394 GTTTGGGACCTGGCATCGGCACTGATACATGAGA
65 GTTTGGAACATGGCATCGGCATTG-T-TATGAGA
*
24070428 GCCAATGTAAGACCATGTCTGGGACATGGCATCGA
1 GCTAATGTAAGACCATGTCTGGGACATGGCATCGA
24070463 TATTTTACCC
Statistics
Matches: 204, Mismatches: 21, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
96 163 0.80
97 3 0.01
98 38 0.19
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (96 bp):
GCTAATGTAAGACCATGTCTGGGACATGGCATCGACCTCAATATGTGAGCTAGTGTAAGACCATG
TTTGGAACATGGCATCGGCATTGTTATGAGA
Found at i:24074449 original size:39 final size:39
Alignment explanation
Indices: 24074363--24074540 Score: 152
Period size: 39 Copynumber: 4.6 Consensus size: 39
24074353 ACTTGAAACC
* *
24074363 AATTACCAGCAC-AAGCCTGCGGGAATTTAAACCCGG-TAT
1 AATT-CCAGCACGAAGCCTGCGGGACTTT-AGCCCGGATAT
* * *
24074402 AATACCAGCTCGAAGCCTGCGGGACTTTAGCCCGGACAT
1 AATTCCAGCACGAAGCCTGCGGGACTTTAGCCCGGATAT
* * * *
24074441 ATTTCCAGCACGTAGCCTGC-GGATCTTAAGTCCGGATAT
1 AATTCCAGCACGAAGCCTGCGGGA-CTTTAGCCCGGATAT
* * *
24074480 AATTCCAGCAC-ATAGCCTGC-GGACCCTAAGTCCGGATAT
1 AATTCCAGCACGA-AGCCTGCGGGA-CTTTAGCCCGGATAT
24074519 AATTCCAGCAC-ATAGCCTGCGG
1 AATTCCAGCACGA-AGCCTGCGG
24074541 ACCCTAAGTC
Statistics
Matches: 118, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
38 15 0.13
39 102 0.86
40 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (39 bp):
AATTCCAGCACGAAGCCTGCGGGACTTTAGCCCGGATAT
Found at i:24074481 original size:78 final size:78
Alignment explanation
Indices: 24074395--24074558 Score: 199
Period size: 78 Copynumber: 2.1 Consensus size: 78
24074385 GAATTTAAAC
* * * * *
24074395 CCGG-TATAATACCAGCTCGA-AGCCTGCGGGA-CTTTAGCCCGGACATATTTCCAGCACGTAGC
1 CCGGATATAATACCAGCAC-ATAGCCTGC-GGACCCTAAGCCCGGACATAATTCCAGCACATAGC
* *
24074457 CTGCGGATCTTAAGT
64 CTGCGGACCCTAAGT
* * *
24074472 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATAATTCCAGCACATAGCCT
1 CCGGATATAATACCAGCACATAGCCTGCGGACCCTAAGCCCGGACATAATTCCAGCACATAGCCT
24074537 GCGGACCCTAAGT
66 GCGGACCCTAAGT
24074550 CCGGATATA
1 CCGGATATA
24074559 CATCACTGAA
Statistics
Matches: 74, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
77 8 0.11
78 66 0.89
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.22
Consensus pattern (78 bp):
CCGGATATAATACCAGCACATAGCCTGCGGACCCTAAGCCCGGACATAATTCCAGCACATAGCCT
GCGGACCCTAAGT
Found at i:24074541 original size:39 final size:39
Alignment explanation
Indices: 24074433--24074558 Score: 207
Period size: 39 Copynumber: 3.2 Consensus size: 39
24074423 GGACTTTAGC
* * * * *
24074433 CCGGACATATTTCCAGCACGTAGCCTGCGGATCTTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
24074472 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
24074511 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
24074550 CCGGATATA
1 CCGGATATA
24074559 CATCACTGAA
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 82 1.00
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.22
Consensus pattern (39 bp):
CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
Found at i:24082142 original size:78 final size:78
Alignment explanation
Indices: 24082060--24082219 Score: 189
Period size: 78 Copynumber: 2.1 Consensus size: 78
24082050 TTAAACCCGG
* * * * *
24082060 TATAATACCAGCTCGA-AGCCTGCGGGA-CTTTAGCCCAGACATATTTCCAGCACGTAGCCTGCG
1 TATAATACCAGCAC-ATAGCCTGC-GGACCCTAAGCCCAGACATAATTCCAGCACATAGCCTGCG
*
24082123 GACCTTAAGTCCGAA
64 GACCCTAAGTCCGAA
* * * *
24082138 TATAATTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATAATTCCAGCACATAGCCTGCGGA
1 TATAATACCAGCACATAGCCTGCGGACCCTAAGCCCAGACATAATTCCAGCACATAGCCTGCGGA
*
24082203 CCCTAAGTCCGGA
66 CCCTAAGTCCGAA
24082216 TATA
1 TATA
24082220 CATCACTGAA
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
77 4 0.06
78 65 0.94
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (78 bp):
TATAATACCAGCACATAGCCTGCGGACCCTAAGCCCAGACATAATTCCAGCACATAGCCTGCGGA
CCCTAAGTCCGAA
Found at i:24082147 original size:39 final size:39
Alignment explanation
Indices: 24082104--24082219 Score: 205
Period size: 39 Copynumber: 3.0 Consensus size: 39
24082094 CCAGACATAT
* * *
24082104 TTCCAGCACGTAGCCTGCGGACCTTAAGTCCGAATATAA
1 TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATAA
24082143 TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATAA
1 TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATAA
24082182 TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATA
1 TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATA
24082220 CATCACTGAA
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 74 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.22
Consensus pattern (39 bp):
TTCCAGCACATAGCCTGCGGACCCTAAGTCCGGATATAA
Found at i:24101174 original size:30 final size:30
Alignment explanation
Indices: 24101140--24101200 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
24101130 TTCCCGAGCC
24101140 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
* * *
24101170 TAGGGGCAAAATTGTAATTTTGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
24101200 T
1 T
24101201 GAGTTAAGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.39, C:0.07, G:0.25, T:0.30
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAAATATGCAAAAGTT
Found at i:24106029 original size:33 final size:33
Alignment explanation
Indices: 24105992--24106067 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 33
24105982 CAATCCCTCA
*
24105992 AACACACCGATACTCATAAGAGCTAA-TCCAACC
1 AACACACCAATACTCATAAGAGCTAACT-CAACC
** * * *
24106025 AACACATTAATGCTCATGAGAGTTAACTCAACC
1 AACACACCAATACTCATAAGAGCTAACTCAACC
24106058 AACACACCAA
1 AACACACCAA
24106068 ATGGAGTGTA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
33 33 0.97
34 1 0.03
ACGTcount: A:0.43, C:0.30, G:0.09, T:0.17
Consensus pattern (33 bp):
AACACACCAATACTCATAAGAGCTAACTCAACC
Found at i:24113347 original size:27 final size:27
Alignment explanation
Indices: 24113317--24113369 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
24113307 GAAGNNNNNN
24113317 CAGATATATGTGGCAAAGCCACCAGAT
1 CAGATATATGTGGCAAAGCCACCAGAT
* *
24113344 CAGATATTTGTGGCATAGCCACCAGA
1 CAGATATATGTGGCAAAGCCACCAGA
24113370 ACGCTTCCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.21
Consensus pattern (27 bp):
CAGATATATGTGGCAAAGCCACCAGAT
Found at i:24115021 original size:26 final size:26
Alignment explanation
Indices: 24114990--24115071 Score: 137
Period size: 26 Copynumber: 3.2 Consensus size: 26
24114980 TGAAATGCCC
24114990 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
* *
24115016 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAAACCATT
*
24115042 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
24115068 ATCA
1 ATCA
24115072 ATTTGTACCA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 52 1.00
ACGTcount: A:0.37, C:0.23, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Found at i:24117557 original size:36 final size:36
Alignment explanation
Indices: 24117510--24117587 Score: 88
Period size: 36 Copynumber: 2.2 Consensus size: 36
24117500 TTCCACAGTT
* *
24117510 TTGTTGTTATTT-CATTATTATATTGC-TACTCTTTTA
1 TTGTTATTATTTGCA-TATTATATAGCTTA-TCTTTTA
* *
24117546 TTGTTATTATTTGGATATTATATAGCTTATGTTTTA
1 TTGTTATTATTTGCATATTATATAGCTTATCTTTTA
24117582 TTGTTA
1 TTGTTA
24117588 ATGTTGCAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
36 33 0.92
37 3 0.08
ACGTcount: A:0.22, C:0.06, G:0.12, T:0.60
Consensus pattern (36 bp):
TTGTTATTATTTGCATATTATATAGCTTATCTTTTA
Found at i:24122690 original size:35 final size:35
Alignment explanation
Indices: 24122644--24122711 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
24122634 TTTGGGTTTT
24122644 TTACTTATATAATATAAAATAAATAAATAAAAATA
1 TTACTTATATAATATAAAATAAATAAATAAAAATA
24122679 TTACTTATATAATATAAAATAAATAAATAAAAA
1 TTACTTATATAATATAAAATAAATAAATAAAAA
24122712 ATACAAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (35 bp):
TTACTTATATAATATAAAATAAATAAATAAAAATA
Found at i:24122721 original size:15 final size:15
Alignment explanation
Indices: 24122654--24122714 Score: 50
Period size: 15 Copynumber: 3.7 Consensus size: 15
24122644 TTACTTATAT
*
24122654 AATATAAAATAAATA
1 AATAAAAAATAAATA
*
24122669 AATAAAAATATTACTTATA
1 AATAAAAA-A-TA--AATA
*
24122688 TAATATAAAATAAATA
1 -AATAAAAAATAAATA
24122704 AATAAAAAATA
1 AATAAAAAATA
24122715 CAAAAATGGC
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
15 17 0.47
16 4 0.11
17 2 0.06
18 2 0.06
19 4 0.11
20 7 0.19
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (15 bp):
AATAAAAAATAAATA
Found at i:24125298 original size:37 final size:39
Alignment explanation
Indices: 24125244--24125348 Score: 115
Period size: 37 Copynumber: 2.7 Consensus size: 39
24125234 TTCAAAAAAA
**
24125244 TAAAGTTGACACCCAGTGTCTCATCGGCTA-AACCGAAG
1 TAAAGTTGACACCCAGTGTCTCATCGAATATAACCGAAG
* * *
24125282 TAAA-TTGACACCCAGTGCCTCATTGAATATATCCGAAG
1 TAAAGTTGACACCCAGTGTCTCATCGAATATAACCGAAG
* *
24125320 TAATTATTTGACACCCAGTGTTTCATCGA
1 TAA--AGTTGACACCCAGTGTCTCATCGA
24125349 CTTGAAGTCG
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
37 21 0.38
38 14 0.25
40 1 0.02
41 19 0.35
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (39 bp):
TAAAGTTGACACCCAGTGTCTCATCGAATATAACCGAAG
Found at i:24125497 original size:11 final size:11
Alignment explanation
Indices: 24125481--24125529 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
24125471 ATTTAAATAA
24125481 TCAATATATAT
1 TCAATATATAT
24125492 TCAATATATAT
1 TCAATATATAT
24125503 ATCAAT-TCA-A-
1 -TCAATAT-ATAT
*
24125513 TCAATATAAAT
1 TCAATATATAT
24125524 TCAATA
1 TCAATA
24125530 AATTCATCAC
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
9 6 0.18
10 2 0.06
11 19 0.58
12 6 0.18
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (11 bp):
TCAATATATAT
Found at i:24125502 original size:13 final size:12
Alignment explanation
Indices: 24125480--24125508 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
24125470 AATTTAAATA
24125480 ATCAATATATAT
1 ATCAATATATAT
24125492 -TCAATATATAT
1 ATCAATATATAT
24125503 ATCAAT
1 ATCAAT
24125509 TCAATCAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.41
Consensus pattern (12 bp):
ATCAATATATAT
Found at i:24125510 original size:17 final size:14
Alignment explanation
Indices: 24125483--24125530 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 14
24125473 TTAAATAATC
*
24125483 AATATATATTCAAT
1 AATATAAATTCAAT
24125497 ATATATATCAATTCAAT
1 A-ATATA--AATTCAAT
24125514 CAATATAAATTCAAT
1 -AATATAAATTCAAT
24125529 AA
1 AA
24125531 ATTCATCACA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
14 3 0.10
15 13 0.45
17 12 0.41
18 1 0.03
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (14 bp):
AATATAAATTCAAT
Found at i:24125551 original size:24 final size:24
Alignment explanation
Indices: 24125506--24125552 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
24125496 TATATATATC
24125506 AATTCAATCAATATAAATTCAATA
1 AATTCAATCAATATAAATTCAATA
24125530 AATTC-ATCACATACTAAA-TCAAT
1 AATTCAATCA-ATA-TAAATTCAAT
24125553 TCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (24 bp):
AATTCAATCAATATAAATTCAATA
Found at i:24126329 original size:15 final size:15
Alignment explanation
Indices: 24126309--24126385 Score: 53
Period size: 15 Copynumber: 5.5 Consensus size: 15
24126299 TTAATTGTTT
24126309 TATTATTAT-ATAATA
1 TATTATTATAAT-ATA
24126324 TATTATTATAATATA
1 TATTATTATAATATA
*
24126339 TA-T-TTA-AATGT-
1 TATTATTATAATATA
*
24126350 TA--AGTA-AATATA
1 TATTATTATAATATA
*
24126362 TTTTATTATAATATA
1 TATTATTATAATATA
24126377 TATATATTA
1 TAT-TATTA
24126386 AATTTTACAT
Statistics
Matches: 49, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
11 8 0.16
12 5 0.10
13 3 0.06
14 4 0.08
15 22 0.45
16 7 0.14
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (15 bp):
TATTATTATAATATA
Found at i:24141750 original size:20 final size:21
Alignment explanation
Indices: 24141710--24141750 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
24141700 ACTTGTATAA
*
24141710 CTATAATCAAACATTCAAAAT
1 CTATAATCAAACATCCAAAAT
*
24141731 CTATCATCAAACA-CCAAAAT
1 CTATAATCAAACATCCAAAAT
24141751 ACTCATGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (21 bp):
CTATAATCAAACATCCAAAAT
Found at i:24145957 original size:10 final size:10
Alignment explanation
Indices: 24145891--24146007 Score: 84
Period size: 10 Copynumber: 11.7 Consensus size: 10
24145881 TCATGACTTT
24145891 TTAAATAATTA
1 TTAAA-AATTA
*
24145902 TAAAATAATTA
1 TTAAA-AATTA
24145913 TATAAAAA-TA
1 T-TAAAAATTA
*
24145923 ATATAAAA-TA
1 TTA-AAAATTA
24145933 TGTAAAAA-TA
1 T-TAAAAATTA
24145943 TTTAAAAATTA
1 -TTAAAAATTA
*
24145954 TT-AAGATTA
1 TTAAAAATTA
*
24145963 -TAAAAATAA
1 TTAAAAATTA
*
24145972 TTAAAAAATA
1 TTAAAAATTA
*
24145982 TT-AAATTTA
1 TTAAAAATTA
24145991 TTAAAAATTA
1 TTAAAAATTA
24146001 TTAAAAA
1 TTAAAAA
24146008 AAAGTCCCAA
Statistics
Matches: 86, Mismatches: 12, Indels: 17
0.75 0.10 0.15
Matches are distributed among these distances:
8 1 0.01
9 20 0.23
10 44 0.51
11 18 0.21
12 3 0.03
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (10 bp):
TTAAAAATTA
Found at i:24145966 original size:28 final size:29
Alignment explanation
Indices: 24145935--24146009 Score: 91
Period size: 28 Copynumber: 2.6 Consensus size: 29
24145925 ATAAAATATG
*
24145935 TAAAAATATTTAAAAATTATTAAGA-TTA-
1 TAAAAATATTTAAAAAATATTAA-ATTTAT
*
24145963 TAAAAATAATTAAAAAATATTAAATTTAT
1 TAAAAATATTTAAAAAATATTAAATTTAT
*
24145992 TAAAAATTATTAAAAAAA
1 TAAAAA-TATTTAAAAAA
24146010 AGTCCCAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
27 1 0.03
28 24 0.60
29 6 0.15
30 9 0.22
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (29 bp):
TAAAAATATTTAAAAAATATTAAATTTAT
Found at i:24146133 original size:10 final size:10
Alignment explanation
Indices: 24146080--24146172 Score: 55
Period size: 10 Copynumber: 9.2 Consensus size: 10
24146070 GGTTTTTAAT
*
24146080 AATTATTAAAC
1 AATTA-TAAAA
24146091 AATTATAAAA
1 AATTATAAAA
* **
24146101 GA-TATTTAA
1 AATTATAAAA
* * *
24146110 TATTATTAAT
1 AATTATAAAA
24146120 AATTATAAAA
1 AATTATAAAA
24146130 AATTATAAAAA
1 AATTAT-AAAA
24146141 AATT-TATAAA
1 AATTATA-AAA
* *
24146151 AAGTATTAAA
1 AATTATAAAA
*
24146161 AATAATAAAA
1 AATTATAAAA
24146171 AA
1 AA
24146173 GTAAAACATA
Statistics
Matches: 63, Mismatches: 15, Indels: 9
0.72 0.17 0.10
Matches are distributed among these distances:
9 7 0.11
10 42 0.67
11 14 0.22
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.34
Consensus pattern (10 bp):
AATTATAAAA
Found at i:24146441 original size:20 final size:20
Alignment explanation
Indices: 24146418--24146498 Score: 73
Period size: 20 Copynumber: 4.2 Consensus size: 20
24146408 TACTATGTTT
24146418 TTATAAATTTTAATAATTTA
1 TTATAAATTTTAATAATTTA
24146438 TTAT-AATTATTAATAATTTA
1 TTATAAATT-TTAATAATTTA
* *
24146458 --A-ATATTTTTATAATTTA
1 TTATAAATTTTAATAATTTA
*
24146475 CTTTATAAATTCTAATAA-TTA
1 --TTATAAATTTTAATAATTTA
24146496 TTA
1 TTA
24146499 AAACTATGTC
Statistics
Matches: 49, Mismatches: 5, Indels: 15
0.71 0.07 0.22
Matches are distributed among these distances:
17 10 0.20
18 4 0.08
19 7 0.14
20 15 0.31
21 4 0.08
22 9 0.18
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
TTATAAATTTTAATAATTTA
Found at i:24146611 original size:20 final size:19
Alignment explanation
Indices: 24146586--24146679 Score: 68
Period size: 20 Copynumber: 4.8 Consensus size: 19
24146576 TTTGGACGTG
24146586 AATTTTAATAATTATTAAAT
1 AATTTTAATAATT-TTAAAT
* *
24146606 AATTTT-ATCATTTTTTAAT
1 AATTTTAAT-AATTTTAAAT
** *
24146625 AAACTTAAT-ATTTT-TAT
1 AATTTTAATAATTTTAAAT
24146642 AATTATTAATCAATTTTAAAT
1 AATT-TTAAT-AATTTTAAAT
24146663 AATTTTATATATATTTT
1 AATTTTA-ATA-ATTTT
24146680 TGTAATTTTT
Statistics
Matches: 57, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
17 4 0.07
18 9 0.16
19 11 0.19
20 20 0.35
21 13 0.23
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (19 bp):
AATTTTAATAATTTTAAAT
Found at i:24146689 original size:21 final size:21
Alignment explanation
Indices: 24146661--24146707 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
24146651 TCAATTTTAA
24146661 ATAA-TTTTATATATATT-TTT
1 ATAATTTTTATATA-ATTCTTT
* *
24146681 GTAATTTTTCTATAATTCTTT
1 ATAATTTTTATATAATTCTTT
24146702 ATAATT
1 ATAATT
24146708 ATCTAAACAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (21 bp):
ATAATTTTTATATAATTCTTT
Found at i:24146704 original size:10 final size:10
Alignment explanation
Indices: 24146586--24146707 Score: 55
Period size: 10 Copynumber: 12.4 Consensus size: 10
24146576 TTTGGACGTG
24146586 AATTTTA-AT
1 AATTTTATAT
*
24146595 AATTATTAAAT
1 AATT-TTATAT
24146606 AATTTTATCAT
1 AATTTTAT-AT
*
24146617 -TTTTTA-AT
1 AATTTTATAT
**
24146625 AAACTTA-AT
1 AATTTTATAT
24146634 -ATTTT-TAT
1 AATTTTATAT
24146642 AATTATTA-AT
1 AATT-TTATAT
*
24146652 CAATTTTAAAT
1 -AATTTTATAT
24146663 AATTTTATAT
1 AATTTTATAT
*
24146673 ATATTTT-TGT
1 A-ATTTTATAT
*
24146683 AATTTTTCTAT
1 AA-TTTTATAT
24146694 AATTCTT-TAT
1 AATT-TTATAT
24146704 AATT
1 AATT
24146708 ATCTAAACAA
Statistics
Matches: 89, Mismatches: 10, Indels: 27
0.71 0.08 0.21
Matches are distributed among these distances:
8 7 0.08
9 13 0.15
10 44 0.49
11 25 0.28
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.57
Consensus pattern (10 bp):
AATTTTATAT
Found at i:24147835 original size:25 final size:25
Alignment explanation
Indices: 24147773--24147824 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
24147763 AAAAAGTCTA
*
24147773 AAGTATTAGTTTTCACATTTTAAGG
1 AAGTATTAATTTTCACATTTTAAGG
24147798 AAGTATTAATTTTCACATTTTAAGG
1 AAGTATTAATTTTCACATTTTAAGG
24147823 AA
1 AA
24147825 TTCTAATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.42
Consensus pattern (25 bp):
AAGTATTAATTTTCACATTTTAAGG
Found at i:24148552 original size:21 final size:20
Alignment explanation
Indices: 24148526--24148585 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
24148516 TTTAGATAAT
24148526 TATAAAAATTATAAAAAAACA
1 TATAAAAATTATAAAAAAA-A
* *
24148547 TATAAAAATAATTTAAAAATAA
1 TATAAAAAT--TATAAAAAAAA
*
24148569 T-TAAGAATTATAAAAAA
1 TATAAAAATTATAAAAAA
24148586 TTATTAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
19 7 0.22
21 15 0.47
22 2 0.06
23 8 0.25
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (20 bp):
TATAAAAATTATAAAAAAAA
Found at i:24148586 original size:20 final size:19
Alignment explanation
Indices: 24148530--24148597 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 19
24148520 GATAATTATA
24148530 AAAATTATAAAAAA-ACATAT
1 AAAATTATAAAAAATA-AT-T
* *
24148550 AAAAATAATTTAAAAATAATT
1 -AAAATTA-TAAAAAATAATT
*
24148571 AAGAATTATAAAAAATTATT
1 AA-AATTATAAAAAATAATT
24148591 AAAATTA
1 AAAATTA
24148598 AAATTTATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
19 5 0.13
20 14 0.36
21 11 0.28
22 8 0.21
23 1 0.03
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (19 bp):
AAAATTATAAAAAATAATT
Found at i:24154495 original size:29 final size:29
Alignment explanation
Indices: 24154436--24154496 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
24154426 GTTATAAAAT
* * * *
24154436 AAATTATGAATATTATTTTAAATTATTAA
1 AAATTATAAATATTATTTAAAAATATAAA
24154465 AAATTATAAGATATTA-TTAAAAATATAAA
1 AAATTATAA-ATATTATTTAAAAATATAAA
24154494 AAA
1 AAA
24154497 AGAGAGATTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 21 0.78
30 6 0.22
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.39
Consensus pattern (29 bp):
AAATTATAAATATTATTTAAAAATATAAA
Found at i:24154497 original size:30 final size:29
Alignment explanation
Indices: 24154428--24154497 Score: 70
Period size: 30 Copynumber: 2.3 Consensus size: 29
24154418 AAAAAAAAGT
* **
24154428 TATAAAATAAATTATGAATATTATTTTAAA
1 TATAAAA-AAATTATAAATATTATTAAAAA
*
24154458 T-TATTAAAAATTATAAGATATTATTAAAAA
1 TATA-AAAAAATTATAA-ATATTATTAAAAA
24154488 TATAAAAAAA
1 TATAAAAAAA
24154498 GAGAGATTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
29 10 0.31
30 20 0.62
31 2 0.06
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.39
Consensus pattern (29 bp):
TATAAAAAAATTATAAATATTATTAAAAA
Found at i:24154868 original size:76 final size:76
Alignment explanation
Indices: 24154738--24154890 Score: 279
Period size: 76 Copynumber: 2.0 Consensus size: 76
24154728 GAAAAGACAC
* * *
24154738 AAAGGATACGAATTCATAATATTTTTTTGGATGATACAACCAATAGCTTTGTGTCTCTTTTGTAC
1 AAAGGATACGAATTCATAATATTTTTTTAGACGATACAACCAATAGCTTCGTGTCTCTTTTGTAC
24154803 TAGTATTAATT
66 TAGTATTAATT
24154814 AAAGGATACGAATTCATAATATTTTTTTAGACGATACAACCAATAGCTTCGTGTCTCTTTTGTAC
1 AAAGGATACGAATTCATAATATTTTTTTAGACGATACAACCAATAGCTTCGTGTCTCTTTTGTAC
24154879 TAGTATTAATT
66 TAGTATTAATT
24154890 A
1 A
24154891 GTTCCCAATA
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 74 1.00
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.41
Consensus pattern (76 bp):
AAAGGATACGAATTCATAATATTTTTTTAGACGATACAACCAATAGCTTCGTGTCTCTTTTGTAC
TAGTATTAATT
Found at i:24155646 original size:5 final size:5
Alignment explanation
Indices: 24155636--24155667 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
24155626 TAATGAAGTT
24155636 AATAA AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AATAA AA
24155668 CAAATTTTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:24156809 original size:14 final size:14
Alignment explanation
Indices: 24156790--24156837 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
24156780 GTTTGTTAAC
24156790 TATTGTAAGCTACA
1 TATTGTAAGCTACA
** *
24156804 TATTGTTTGTTA-A
1 TATTGTAAGCTACA
24156817 CTATTGTAAGCTACA
1 -TATTGTAAGCTACA
24156832 TATTGT
1 TATTGT
24156838 TGTATTCAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
13 1 0.04
14 24 0.92
15 1 0.04
ACGTcount: A:0.29, C:0.10, G:0.15, T:0.46
Consensus pattern (14 bp):
TATTGTAAGCTACA
Found at i:24156812 original size:28 final size:28
Alignment explanation
Indices: 24156780--24156838 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
24156770 AATTTGAAAG
24156780 GTTTGTTAACTATTGTAAGCTACATATT
1 GTTTGTTAACTATTGTAAGCTACATATT
24156808 GTTTGTTAACTATTGTAAGCTACATATT
1 GTTTGTTAACTATTGTAAGCTACATATT
24156836 GTT
1 GTT
24156839 GTATTCAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.27, C:0.10, G:0.15, T:0.47
Consensus pattern (28 bp):
GTTTGTTAACTATTGTAAGCTACATATT
Found at i:24160694 original size:299 final size:298
Alignment explanation
Indices: 24160156--24160739 Score: 1078
Period size: 299 Copynumber: 2.0 Consensus size: 298
24160146 TCCCTCCTTC
* * * *
24160156 TTTTTTCTCTATTTGTAATTTCTTTCTCCAATATTTTTATCTATAACAAAGGTATTAGAGCCATT
1 TTTTTTCTATATTTGTAATTTCTTTCTCCAATATTTTAATCTATAACAAAGGTATCAGAGCAATT
* * *
24160221 GATCTTAGCTACGATTGATTTTAGAATGATGCTATCAAAGGAGGTGGTTGCTCAACTACTTGCTC
66 GATCTTAGCTACAATTGATTTCAGAATGATGCTATCAAAAGAGGTGGTTGCTCAACTACTTGCTC
24160286 AATTAGAGTCCAAAATCGATAGTTCTTTCGAGTGGTTGCAAAGTGGAACACAAAATGATCTTGAA
131 AATTAGAGTCCAAAATCGATAGTTCTTTCGAGTGGTTGCAAAGTGGAACACAAAATGATCTTGAA
24160351 AACTTTCACACAAAAGCAACTTTGGTGCTTAATCAAATGCTTGTGAGAATGGATGAGTTAGCCTA
196 AACTTTCACACAAAAGCAACTTTGGTGCTTAATCAAATGCTTGTGAGAATGGATGAGTTAGCCTA
24160416 TGATTTGCAGGTTAGTAAGGCATNTCTTCCTATCCTCCT
261 TGATTTGCAGGTTAGTAAGGCAT-TCTTCCTATCCTCCT
*
24160455 TTTTTTCTATATTTGTAATTTCTTTCTCGAATATTTTAATCTATAACAAAGGTATCAGAGCAATT
1 TTTTTTCTATATTTGTAATTTCTTTCTCCAATATTTTAATCTATAACAAAGGTATCAGAGCAATT
*
24160520 GATCTTAGTTACAATTGATTTCAGAATGATGCTATCAAAAGAGGTGGTTGCTCAACTACTTGCTC
66 GATCTTAGCTACAATTGATTTCAGAATGATGCTATCAAAAGAGGTGGTTGCTCAACTACTTGCTC
24160585 AATTAGAGTCCAAAATCGATAGTTCTTTCGAGTGGTTGCAAAGTGGAACACAAAATGATCTTGAA
131 AATTAGAGTCCAAAATCGATAGTTCTTTCGAGTGGTTGCAAAGTGGAACACAAAATGATCTTGAA
24160650 AACTTTCACACAAAAGCAACTTTGGTGCTTAATCAAATGCTTGTGAGAATGGATGAGTTAGCCTA
196 AACTTTCACACAAAAGCAACTTTGGTGCTTAATCAAATGCTTGTGAGAATGGATGAGTTAGCCTA
24160715 TGATTTGCAGGTTAGTAAGGCATTC
261 TGATTTGCAGGTTAGTAAGGCATTC
24160740 AACTCGAATA
Statistics
Matches: 276, Mismatches: 9, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
298 2 0.01
299 274 0.99
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.35
Consensus pattern (298 bp):
TTTTTTCTATATTTGTAATTTCTTTCTCCAATATTTTAATCTATAACAAAGGTATCAGAGCAATT
GATCTTAGCTACAATTGATTTCAGAATGATGCTATCAAAAGAGGTGGTTGCTCAACTACTTGCTC
AATTAGAGTCCAAAATCGATAGTTCTTTCGAGTGGTTGCAAAGTGGAACACAAAATGATCTTGAA
AACTTTCACACAAAAGCAACTTTGGTGCTTAATCAAATGCTTGTGAGAATGGATGAGTTAGCCTA
TGATTTGCAGGTTAGTAAGGCATTCTTCCTATCCTCCT
Found at i:24162013 original size:20 final size:21
Alignment explanation
Indices: 24161990--24162036 Score: 51
Period size: 23 Copynumber: 2.2 Consensus size: 21
24161980 TTATAATTAT
*
24161990 TAATAATTT-TAATTTTTTTA
1 TAATAATTTATAATTTTTTAA
*
24162010 TAATTTATTTTATAATTTTTTAA
1 TAA--TAATTTATAATTTTTTAA
24162033 TAAT
1 TAAT
24162037 TATTAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
20 3 0.14
21 1 0.05
22 5 0.23
23 13 0.59
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TAATAATTTATAATTTTTTAA
Found at i:24162022 original size:12 final size:11
Alignment explanation
Indices: 24161999--24162037 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
24161989 TTAATAATTT
24161999 TAATTTTTTTA
1 TAATTTTTTTA
24162010 TAATTTATTTTA
1 TAATTT-TTTTA
*
24162022 TAATTTTTTAA
1 TAATTTTTTTA
24162033 TAATT
1 TAATT
24162038 ATTAAAAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 15 0.58
12 11 0.42
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TAATTTTTTTA
Found at i:24165542 original size:9 final size:9
Alignment explanation
Indices: 24165526--24165568 Score: 77
Period size: 9 Copynumber: 4.8 Consensus size: 9
24165516 GGTATTTTTC
24165526 GGTAATTCG
1 GGTAATTCG
*
24165535 GTTAATTCG
1 GGTAATTCG
24165544 GGTAATTCG
1 GGTAATTCG
24165553 GGTAATTCG
1 GGTAATTCG
24165562 GGTAATT
1 GGTAATT
24165569 TTTAACCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.23, C:0.09, G:0.30, T:0.37
Consensus pattern (9 bp):
GGTAATTCG
Found at i:24168197 original size:78 final size:78
Alignment explanation
Indices: 24168068--24168223 Score: 303
Period size: 78 Copynumber: 2.0 Consensus size: 78
24168058 CAACAATTTA
24168068 GCAACATACTTTTGATAAGTTTAAGGAACTATGACCAGTCCCAAGCCAAATAGCAACGAAAATTT
1 GCAACATACTTTTGATAAGTTTAAGGAACTATGACCAGTCCCAAGCCAAATAGCAACGAAAATTT
24168133 CAACTAAAGGTCT
66 CAACTAAAGGTCT
*
24168146 GCAACTTACTTTTGATAAGTTTAAGGAACTATGACCAGTCCCAAGCCAAATAGCAACGAAAATTT
1 GCAACATACTTTTGATAAGTTTAAGGAACTATGACCAGTCCCAAGCCAAATAGCAACGAAAATTT
24168211 CAACTAAAGGTCT
66 CAACTAAAGGTCT
24168224 CACTTAACTA
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.39, C:0.21, G:0.15, T:0.25
Consensus pattern (78 bp):
GCAACATACTTTTGATAAGTTTAAGGAACTATGACCAGTCCCAAGCCAAATAGCAACGAAAATTT
CAACTAAAGGTCT
Found at i:24174872 original size:17 final size:17
Alignment explanation
Indices: 24174850--24174910 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
24174840 ATTGAATCAC
24174850 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
** * *
24174867 TACATAAGCCTTTGAATCAC
1 TACATAA---TTAAAAACAT
*
24174887 TACATAATTAAAAACTT
1 TACATAATTAAAAACAT
24174904 TACATAA
1 TACATAA
24174911 GTCTTGAAAT
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
17 19 0.59
20 13 0.41
ACGTcount: A:0.49, C:0.16, G:0.03, T:0.31
Consensus pattern (17 bp):
TACATAATTAAAAACAT
Found at i:24174891 original size:37 final size:37
Alignment explanation
Indices: 24174841--24174911 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
24174831 TGATTAAATA
24174841 TTGAATCACTACATAATTAAAAACATTACATAAGCCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGCCT
*
24174878 TTGAATCACTACATAATTAAAAACTTTACATAAG
1 TTGAATCACTACATAATTAAAAACATTACATAAG
24174912 TCTTGAAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.46, C:0.17, G:0.06, T:0.31
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAACATTACATAAGCCT
Found at i:24179060 original size:23 final size:23
Alignment explanation
Indices: 24179030--24179079 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
24179020 CTATATGGGA
*
24179030 TTACAAAATGAGTTTTCGTAAAC
1 TTACAAAATGAGTTTTCATAAAC
24179053 TTACAAAATGAGTTTTCATAAAC
1 TTACAAAATGAGTTTTCATAAAC
24179076 TTAC
1 TTAC
24179080 CCTTTTGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (23 bp):
TTACAAAATGAGTTTTCATAAAC
Found at i:24181927 original size:25 final size:22
Alignment explanation
Indices: 24181879--24181929 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 22
24181869 ATATGTATGA
*
24181879 AATA-TTAATATATGAATACTT
1 AATATTTAATATATGAATAATT
24181900 AATATTTAAGTATATGATATAATAT
1 AATATTTAA-TATATGA-ATAAT-T
24181925 AATAT
1 AATAT
24181930 GTTATTACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 4 0.16
22 4 0.16
23 7 0.28
24 4 0.16
25 6 0.24
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (22 bp):
AATATTTAATATATGAATAATT
Found at i:24181968 original size:11 final size:11
Alignment explanation
Indices: 24181938--24181975 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
24181928 ATGTTATTAC
**
24181938 AATAATAATTA
1 AATAATAAAGA
24181949 AATAATAAAGA
1 AATAATAAAGA
24181960 AATAATAAAGA
1 AATAATAAAGA
24181971 AATAA
1 AATAA
24181976 AAATAGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (11 bp):
AATAATAAAGA
Found at i:24184382 original size:181 final size:181
Alignment explanation
Indices: 24184078--24184440 Score: 645
Period size: 181 Copynumber: 2.0 Consensus size: 181
24184068 TGGCTGGCCG
24184078 TGTGATCTAAGTCAGAAATTTACACGGGGCTGGACACGGCCTGTGGCACAGGCGTGTCTATGGTC
1 TGTGATCTAAGTCAGAAATTTACACGGGGCTGGACACGGCCTGTGGCACAGGCGTGTCTATGGTC
*
24184143 ACACGAGCGTGTCCCTTGACCACATGAGCATGTTTGCCCTGCATCTAGGAAAATTTTTGAAATTT
66 ACACGAACGTGTCCCTTGACCACATGAGCATGTTTGCCCTGCATCTAGGAAAATTTTTGAAATTT
*
24184208 CACAAAAAATTTCTGAAGTACCCGATTTAGTCCCTGTTTGTTTCTAACATA
131 CACAAAAAATTTCTGAAGTACCCGATTTAGTCCCTATTTGTTTCTAACATA
*
24184259 TGTGATCTAAGTCAGAAATTTACACGGGGCTGGACACGGCCTGTGGTACAGGCGTGTCTATGGTC
1 TGTGATCTAAGTCAGAAATTTACACGGGGCTGGACACGGCCTGTGGCACAGGCGTGTCTATGGTC
* * *
24184324 ATACGAACGTGTCCCTTGACCACATGAGCATGTTTGCCTTGCATTTAGGAAAATTTTTGAAATTT
66 ACACGAACGTGTCCCTTGACCACATGAGCATGTTTGCCCTGCATCTAGGAAAATTTTTGAAATTT
* * *
24184389 CACGAAAAATTTTTGAAGTACCCGATTTATTCCCTATTTGTTTCTAACATA
131 CACAAAAAATTTCTGAAGTACCCGATTTAGTCCCTATTTGTTTCTAACATA
24184440 T
1 T
24184441 ATTTTGGGCC
Statistics
Matches: 173, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
181 173 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (181 bp):
TGTGATCTAAGTCAGAAATTTACACGGGGCTGGACACGGCCTGTGGCACAGGCGTGTCTATGGTC
ACACGAACGTGTCCCTTGACCACATGAGCATGTTTGCCCTGCATCTAGGAAAATTTTTGAAATTT
CACAAAAAATTTCTGAAGTACCCGATTTAGTCCCTATTTGTTTCTAACATA
Found at i:24188183 original size:18 final size:18
Alignment explanation
Indices: 24188160--24188194 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
24188150 TTAGGGTCTT
*
24188160 GACATATGTATGACACAA
1 GACATATATATGACACAA
*
24188178 GACATATATATGGCACA
1 GACATATATATGACACA
24188195 GATCCCATCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (18 bp):
GACATATATATGACACAA
Found at i:24189441 original size:18 final size:18
Alignment explanation
Indices: 24189415--24189450 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
24189405 CTTTACACCA
*
24189415 CATTATGGATGAACCACT
1 CATTATGGATAAACCACT
*
24189433 CATTGTGGATAAACCACT
1 CATTATGGATAAACCACT
24189451 AGTAATAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (18 bp):
CATTATGGATAAACCACT
Found at i:24189799 original size:34 final size:34
Alignment explanation
Indices: 24189703--24189799 Score: 99
Period size: 34 Copynumber: 2.8 Consensus size: 34
24189693 GTCAAGCTCA
* ** *
24189703 AACAGATCAATACAGTAGCATTTAATTATGTTTTT
1 AACAGATCAATACAATAGCAAATAA-TATGTTTAT
* *
24189738 AACAGAACAATACGATAGC-AATCAATATGTTTAT
1 AACAGATCAATACAATAGCAAAT-AATATGTTTAT
24189772 AACA-ATTCAATACAATAGCAAATAATAT
1 AACAGA-TCAATACAATAGCAAATAATAT
24189800 ACTTTTAATA
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
33 1 0.02
34 29 0.57
35 21 0.41
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (34 bp):
AACAGATCAATACAATAGCAAATAATATGTTTAT
Found at i:24190133 original size:28 final size:28
Alignment explanation
Indices: 24190070--24190141 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 28
24190060 AATATTTTAA
**
24190070 GTAAAATTGTAAAATTTGTAAAGTAGGG
1 GTAAAATTGTAAAATTTGTAAAACAGGG
* *
24190098 GACAAAATTGTAAAATTT-TAAAAACATGG
1 G-TAAAATTGTAAAATTTGT-AAAACAGGG
24190127 GTAAAATTGTAAAAT
1 GTAAAATTGTAAAAT
24190142 CTAAAAAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 15 0.41
29 22 0.59
ACGTcount: A:0.49, C:0.03, G:0.18, T:0.31
Consensus pattern (28 bp):
GTAAAATTGTAAAATTTGTAAAACAGGG
Found at i:24192142 original size:21 final size:22
Alignment explanation
Indices: 24192102--24192152 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
24192092 TGTATATACG
* *
24192102 TATATTTTATGTACATTATGTA
1 TATATTTTATATACATTATGCA
* *
24192124 TATATTTTA-ATATATTATGCG
1 TATATTTTATATACATTATGCA
24192145 TATATTTT
1 TATATTTT
24192153 GTTTTTTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.31, C:0.04, G:0.08, T:0.57
Consensus pattern (22 bp):
TATATTTTATATACATTATGCA
Found at i:24192761 original size:20 final size:23
Alignment explanation
Indices: 24192727--24192767 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
24192717 TACTAACGTA
24192727 TATATATACTATGTA-ATTTTAT
1 TATATATACTATGTACATTTTAT
24192749 TATAT-TACT-TGTACATTTT
1 TATATATACTATGTACATTTT
24192768 TATATACCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 9 0.50
22 5 0.28
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.56
Consensus pattern (23 bp):
TATATATACTATGTACATTTTAT
Found at i:24192773 original size:21 final size:21
Alignment explanation
Indices: 24192725--24192773 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
24192715 ATTACTAACG
24192725 TATATATATACTATGTAATTT
1 TATATATATACTATGTAATTT
24192746 TAT-TATATTACT-TGTACATTT
1 TATATATA-TACTATGTA-ATTT
24192767 T-TATATA
1 TATATATA
24192774 CCATGCATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (21 bp):
TATATATATACTATGTAATTT
Found at i:24208440 original size:42 final size:43
Alignment explanation
Indices: 24208244--24208456 Score: 144
Period size: 42 Copynumber: 5.0 Consensus size: 43
24208234 CTAGAATCAG
* * *
24208244 TGAATTCACCAGACCTTAATCCTCTAAGTAGTAGGGTAACAGGT
1 TGAATTCA-CAGACCTTAACCCCCTAAGCAGTAGGGTAACAGGT
* * * * * *
24208288 TGAATTTATAGATCTTAA-CCTCTAAGCAGTAGGGAAACAGAT
1 TGAATTCACAGACCTTAACCCCCTAAGCAGTAGGGTAACAGGT
* * * * ** * * * *
24208330 CGGAAGTGA-TGGGCTTCAACCCCCTAAGTAGTAGAGTAACAAGC
1 -TGAATTCACAGACCTT-AACCCCCTAAGCAGTAGGGTAACAGGT
** * **
24208374 CAAATTGACAGACCTTAAGTCCCTAAGCAGTAGGGTAACAGGT
1 TGAATTCACAGACCTTAACCCCCTAAGCAGTAGGGTAACAGGT
* *
24208417 TG-ATTCACAGATCTTAACCCCCTAAGCAGTAGGGAAACAG
1 TGAATTCACAGACCTTAACCCCCTAAGCAGTAGGGTAACAG
24208457 ATCAAAGGCG
Statistics
Matches: 127, Mismatches: 38, Indels: 10
0.73 0.22 0.06
Matches are distributed among these distances:
42 58 0.46
43 41 0.32
44 28 0.22
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.23
Consensus pattern (43 bp):
TGAATTCACAGACCTTAACCCCCTAAGCAGTAGGGTAACAGGT
Found at i:24208489 original size:129 final size:129
Alignment explanation
Indices: 24208253--24208492 Score: 342
Period size: 129 Copynumber: 1.9 Consensus size: 129
24208243 GTGAATTCAC
* * * *
24208253 CAGACCTTAATCCTCTAAGTAGTAGGGTAACAGGTTGAATTTATAGATCTTAACCTCTAAGCAGT
1 CAGACCTTAATCCTCTAAGCAGTAGGGTAACAGGTTGAATTCACAGATCTTAACCCCTAAGCAGT
* * *
24208318 AGGGAAACAGATCGGAAGTGATGGGCTTCAACCCCCTAAGTAGTAGAGTAACAAGCCAAATTGA
66 AGGGAAACAGATCGAAAGCGATGAGCTTCAACCCCCTAAGTAGTAGAGTAACAAGCCAAATTGA
24208382 CAGACCTTAAGTCC-CTAAGCAGTAGGGTAACAGGTTG-ATTCACAGATCTTAACCCCCTAAGCA
1 CAGACCTTAA-TCCTCTAAGCAGTAGGGTAACAGGTTGAATTCACAGATCTTAA-CCCCTAAGCA
* * *
24208445 GTAGGGAAACAGATC-AAAGGCGATGAGCTTTAACCCCTTGAGTAGTAG
64 GTAGGGAAACAGATCGAAA-GCGATGAGCTTCAACCCCCTAAGTAGTAG
24208493 GGTAGTAAGC
Statistics
Matches: 98, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
128 15 0.15
129 80 0.82
130 3 0.03
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (129 bp):
CAGACCTTAATCCTCTAAGCAGTAGGGTAACAGGTTGAATTCACAGATCTTAACCCCTAAGCAGT
AGGGAAACAGATCGAAAGCGATGAGCTTCAACCCCCTAAGTAGTAGAGTAACAAGCCAAATTGA
Found at i:24209694 original size:197 final size:195
Alignment explanation
Indices: 24209348--24209736 Score: 636
Period size: 197 Copynumber: 2.0 Consensus size: 195
24209338 GCTGGCGACG
* **
24209348 GAGACGCGGCAGAGGGCGGTGGTAGCTCGTCGGGACTTGACCGGACTTGGACCTGCAGAGGGAGA
1 GAGACGCGGCAGAGGGCGGTGGTAGCTCGCCGGGACCAGACCGGACTTGGACCTGCAGA-GGAGA
24209413 GAGCAAAGAAAAGTTTAATTTTTGATAGAAACAGACAACAAATGGGTAAAAAAGCAAGATTTTAA
65 GAGCAAAGAAAAGTTTAATTTTTGATAGAAACAGACAACAAATGGGTAAAAAAGCAAGATTTTAA
* * *
24209478 CTTATATAGATAATACAAAACGACGTCGTTTTGGTCAGCATCCATAAGCCCCAAAACGACGCCGT
130 CTTATATAAATAATACAAAACGACGTCATTTTGGTCAGCATCCATAAGCCCCAAAACAACGCCGT
24209543 NA
195 -A
* *
24209545 GAGATGCGGCGGAGGGCGGTGGTAGCTCGCCGGGACCAGACCGGACTTGGACCTGCAGA-GAGAG
1 GAGACGCGGCAGAGGGCGGTGGTAGCTCGCCGGGACCAGACCGGACTTGGACCTGCAGAGGAGAG
* *
24209609 AGCAAAGAAAATTTTAAATTTTTGTTAGAAACAGACAACAAATGGGTAAAAAAAGCAAGATTTTA
66 AGCAAAGAAAAGTTT-AATTTTTGATAGAAACAGACAACAAATGGGT-AAAAAAGCAAGATTTTA
*
24209674 ACTTATATAAATAATACAAAACGACGTCATTTTGGTCGGCATCCATAAGCCCCAAAACAACGC
129 ACTTATATAAATAATACAAAACGACGTCATTTTGGTCAGCATCCATAAGCCCCAAAACAACGC
24209737 TGTTTCGCCT
Statistics
Matches: 179, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
195 19 0.11
196 30 0.17
197 130 0.73
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.20
Consensus pattern (195 bp):
GAGACGCGGCAGAGGGCGGTGGTAGCTCGCCGGGACCAGACCGGACTTGGACCTGCAGAGGAGAG
AGCAAAGAAAAGTTTAATTTTTGATAGAAACAGACAACAAATGGGTAAAAAAGCAAGATTTTAAC
TTATATAAATAATACAAAACGACGTCATTTTGGTCAGCATCCATAAGCCCCAAAACAACGCCGTA
Found at i:24210419 original size:21 final size:22
Alignment explanation
Indices: 24210379--24210429 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
24210369 TTTATATACG
* *
24210379 TATATTTTATGTACATTATGTA
1 TATATTTTATATACATTATGCA
* *
24210401 TATATTTTA-ATATATTATGCG
1 TATATTTTATATACATTATGCA
24210422 TATATTTT
1 TATATTTT
24210430 GTTTTGTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.31, C:0.04, G:0.08, T:0.57
Consensus pattern (22 bp):
TATATTTTATATACATTATGCA
Found at i:24211038 original size:20 final size:23
Alignment explanation
Indices: 24211004--24211044 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
24210994 TACTAACGTA
24211004 TATATATACTATGTA-ATTTTAT
1 TATATATACTATGTACATTTTAT
24211026 TATAT-TACT-TGTACATTTT
1 TATATATACTATGTACATTTT
24211045 TATATACCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 9 0.50
22 5 0.28
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.56
Consensus pattern (23 bp):
TATATATACTATGTACATTTTAT
Found at i:24211050 original size:21 final size:21
Alignment explanation
Indices: 24211002--24211050 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
24210992 ATTACTAACG
24211002 TATATATATACTATGTAATTT
1 TATATATATACTATGTAATTT
24211023 TAT-TATATTACT-TGTACATTT
1 TATATATA-TACTATGTA-ATTT
24211044 T-TATATA
1 TATATATA
24211051 CCATGCATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (21 bp):
TATATATATACTATGTAATTT
Found at i:24212830 original size:19 final size:20
Alignment explanation
Indices: 24212806--24212848 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
24212796 TCAATTAAAT
*
24212806 AATATTTTTA-GTTATTTTA
1 AATATTTTTATATTATTTTA
*
24212825 AATATTTTTATATTATTTTC
1 AATATTTTTATATTATTTTA
24212845 AATA
1 AATA
24212849 CAAATTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (20 bp):
AATATTTTTATATTATTTTA
Found at i:24215173 original size:5 final size:5
Alignment explanation
Indices: 24215163--24215188 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
24215153 AGACAGCCCC
24215163 CTCTT CTCTT CTCTT CTCTT CTCTT C
1 CTCTT CTCTT CTCTT CTCTT CTCTT C
24215189 GCTTTAGCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (5 bp):
CTCTT
Found at i:24223722 original size:28 final size:28
Alignment explanation
Indices: 24223682--24223836 Score: 165
Period size: 28 Copynumber: 5.6 Consensus size: 28
24223672 AAAAATTTTC
*
24223682 TCGCACACTTAGTGCTCAATAACTGATT
1 TCGCACACTTAGTGCTCAATAACCGATT
* *
24223710 TCGCACACTTAGTGCTCGGAA-ATCCAATT
1 TCGCACACTTAGTGCTC--AATAACCGATT
* * * * *
24223739 T-GCACACTTAATGTTTAA-AACCAACT
1 TCGCACACTTAGTGCTCAATAACCGATT
* *
24223765 T-GCACACTCAGTGCTCAATGACCGATT
1 TCGCACACTTAGTGCTCAATAACCGATT
*
24223792 TCGCACACTTAGTGCTCAATGACCGATT
1 TCGCACACTTAGTGCTCAATAACCGATT
24223820 TCGCACACTTAGTGCTC
1 TCGCACACTTAGTGCTC
24223837 GGTATCAAAT
Statistics
Matches: 107, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
26 22 0.21
27 6 0.06
28 71 0.66
29 6 0.06
30 2 0.02
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (28 bp):
TCGCACACTTAGTGCTCAATAACCGATT
Found at i:24224004 original size:40 final size:40
Alignment explanation
Indices: 24223947--24224027 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
24223937 TATTCATCTC
24223947 ATTAATCACTGTCACACTCGGTTCTATCAATAATATATAT
1 ATTAATCACTGTCACACTCGGTTCTATCAATAATATATAT
*
24223987 ATTAATCACTGTTACACTCGGTTCTATCAATAATATATAT
1 ATTAATCACTGTCACACTCGGTTCTATCAATAATATATAT
24224027 A
1 A
24224028 CTTCCATTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.38
Consensus pattern (40 bp):
ATTAATCACTGTCACACTCGGTTCTATCAATAATATATAT
Found at i:24236000 original size:43 final size:43
Alignment explanation
Indices: 24235953--24236048 Score: 104
Period size: 43 Copynumber: 2.2 Consensus size: 43
24235943 CCCAGACGTG
* *
24235953 GTCTTACATGTAGTCAA-ATATCGATGCCATTGTCCCAGAGAAA
1 GTCTTACATGTAATCAATA-ATCGATGCCAGTGTCCCAGAGAAA
* ** * **
24235996 GTCTTACACGTAATCTCTAATCGATGCCAGTGTCCCAGATACG
1 GTCTTACATGTAATCAATAATCGATGCCAGTGTCCCAGAGAAA
24236039 GTCTTACATG
1 GTCTTACATG
24236049 ATATCTCAAG
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
43 42 0.98
44 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (43 bp):
GTCTTACATGTAATCAATAATCGATGCCAGTGTCCCAGAGAAA
Found at i:24236055 original size:43 final size:42
Alignment explanation
Indices: 24235972--24236067 Score: 113
Period size: 43 Copynumber: 2.2 Consensus size: 42
24235962 GTAGTCAAAT
*
24235972 ATCGATGCCATTGTCCCAGAGAAAGTCTTACACGTAATCTCTA
1 ATCGATGCCAGTGTCCCAGAGAAAGTCTTACACGTAATCTC-A
* ** *
24236015 ATCGATGCCAGTGTCCCAGATACGGTCTTACATG-ATATCTCA
1 ATCGATGCCAGTGTCCCAGAGAAAGTCTTACACGTA-ATCTCA
24236057 AGTCGATGCCA
1 A-TCGATGCCA
24236068 ACGTTCCAGA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
42 3 0.07
43 43 0.93
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (42 bp):
ATCGATGCCAGTGTCCCAGAGAAAGTCTTACACGTAATCTCA
Found at i:24240156 original size:18 final size:18
Alignment explanation
Indices: 24240133--24240169 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
24240123 CATGCAAATG
24240133 TATAAAAACAAAAAATAA
1 TATAAAAACAAAAAATAA
* *
24240151 TATAAAAATAACAAATAA
1 TATAAAAACAAAAAATAA
24240169 T
1 T
24240170 TTACGAGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (18 bp):
TATAAAAACAAAAAATAA
Found at i:24240557 original size:11 final size:12
Alignment explanation
Indices: 24240536--24240587 Score: 58
Period size: 11 Copynumber: 4.6 Consensus size: 12
24240526 ATAAATAGTT
*
24240536 TATAATAAAATGA
1 TATAAT-AAATAA
24240549 TAT-ATAAATAA
1 TATAATAAATAA
24240560 TATAATAAA-AA
1 TATAATAAATAA
24240571 -ATAA-AAATAA
1 TATAATAAATAA
24240581 TATAATA
1 TATAATA
24240588 TGTAATAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
9 3 0.09
10 6 0.18
11 14 0.41
12 8 0.24
13 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (12 bp):
TATAATAAATAA
Found at i:24240578 original size:21 final size:23
Alignment explanation
Indices: 24240536--24240587 Score: 72
Period size: 21 Copynumber: 2.3 Consensus size: 23
24240526 ATAAATAGTT
*
24240536 TATAATAAAATGATATATAAATAA
1 TATAATAAAA-GATATAAAAATAA
24240560 TATAATAAAA-A-ATAAAAATAA
1 TATAATAAAAGATATAAAAATAA
24240581 TATAATA
1 TATAATA
24240588 TGTAATAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 16 0.59
22 1 0.04
24 10 0.37
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (23 bp):
TATAATAAAAGATATAAAAATAA
Found at i:24241873 original size:15 final size:16
Alignment explanation
Indices: 24241853--24241882 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
24241843 TGTAAAGGAC
24241853 TTTTTA-TTATTTTTG
1 TTTTTATTTATTTTTG
24241868 TTTTTATTTATTTTT
1 TTTTTATTTATTTTT
24241883 CTATTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.83
Consensus pattern (16 bp):
TTTTTATTTATTTTTG
Found at i:24242282 original size:44 final size:44
Alignment explanation
Indices: 24242221--24242551 Score: 459
Period size: 44 Copynumber: 7.5 Consensus size: 44
24242211 CAAATGTCTG
* *
24242221 ATCTGCTATCTTCGATCTGCTCTTTGTCAATACAGAGACGTCAA
1 ATCTGCTATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
* * *
24242265 ATCTGCTATCCTGGATCTGCTCTCTGTCAATATAGAGACGCCAA
1 ATCTGCTATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
* *
24242309 ATCTGCTATAC-TCGATCTGTTTTCTGTCAATACAGAGACGCCAA
1 ATCTGCTAT-CTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
* *
24242353 ATCTGCTATCCTCGATCTGCTCTCTGTCAATACAGAGATGCCAA
1 ATCTGCTATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
* *
24242397 ATCTG-TCATCTTTGATCTGCTCTCTGTCAATACAGAGATGCCAA
1 ATCTGCT-ATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
* **
24242441 ATCTGTTATCTTCGATCTGCTCTCTAACAATACAGAGACGCCAA
1 ATCTGCTATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
* * * *
24242485 ATCTGTTATCTTCGATCTGTTCTCTGACAATACAGAGATGCCAA
1 ATCTGCTATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
*
24242529 ATCTGTTATCTTCGATCTGCTCT
1 ATCTGCTATCTTCGATCTGCTCT
24242552 TTGCCAAATC
Statistics
Matches: 261, Mismatches: 22, Indels: 8
0.90 0.08 0.03
Matches are distributed among these distances:
43 2 0.01
44 257 0.98
45 2 0.01
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.33
Consensus pattern (44 bp):
ATCTGCTATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAA
Found at i:24242458 original size:132 final size:132
Alignment explanation
Indices: 24242221--24242997 Score: 999
Period size: 132 Copynumber: 6.0 Consensus size: 132
24242211 CAAATGTCTG
* * * * * * *
24242221 ATCTGCTATCTTCGATCTGCTCTTTGTCAATACAGAGACGTCAAATCTGCTATCCTGGATCTGCT
1 ATCTGTTATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCTGTTATCTTCGATCTGCT
* * * * *
24242286 CTCTGTCAATATAGAGACGCCAAATCTGCTATAC-TCGATCTGTTTTCTGTCAATACAGAGACGC
66 CTCTGACAATACAGAGACGCCAAATCTGTTAT-CTTCGATCTGCTCTCTGTCAATACAGAGACGC
24242350 CAA
130 CAA
* * * * * *
24242353 ATCTGCTATCCTCGATCTGCTCTCTGTCAATACAGAGATGCCAAATCTGTCATCTTTGATCTGCT
1 ATCTGTTATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCTGTTATCTTCGATCTGCT
* * **
24242418 CTCTGTCAATACAGAGATGCCAAATCTGTTATCTTCGATCTGCTCTCTAACAATACAGAGACGCC
66 CTCTGACAATACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGTCAATACAGAGACGCC
24242483 AA
131 AA
* *
24242485 ATCTGTTATCTTCGATCTGTTCTCTGACAATACAGAGATGCCAAATCTGTTATCTTCGATCTGCT
1 ATCTGTTATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCTGTTATCTTCGATCTGCT
24242550 CT-T-----T--------GCCAAATCTGTTATCTTCGATCTGCTCTCTGTCAATACAGAGACGCC
66 CTCTGACAATACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGTCAATACAGAGACGCC
24242601 AA
131 AA
* *
24242603 ATCTGTTATCTTCGAGCTGCTCTCTGACAATACAGAGACGCCAAATCTGTTATATTCGATCTGCT
1 ATCTGTTATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCTGTTATCTTCGATCTGCT
* * * *
24242668 CTCTGACAATACAAATACGCCATATCTGTTATCTTCGATCTGCTCTCTGTTAATACAGAGACGCC
66 CTCTGACAATACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGTCAATACAGAGACGCC
24242733 AA
131 AA
* * *
24242735 ATCTGTTATCTTCGATCTGTTCTCTGACAATACAGAGACCCCAAATATGTTATCTTCGATCTGCT
1 ATCTGTTATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCTGTTATCTTCGATCTGCT
*
24242800 CTCTGACAATACAGAGACACCAAATCTGTTATCTTCGATCTGCTCTCTGTCAATACAGAGACGCC
66 CTCTGACAATACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGTCAATACAGAGACGCC
24242865 AA
131 AA
* * * * *
24242867 ATCTGTTATCTTCAATCTACTCTCTGACAATACAAAGACGCCAAATCTATTATCTTCAATCTGCT
1 ATCTGTTATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCTGTTATCTTCGATCTGCT
* * * * * * * * * *
24242932 CTCTAAAAATACAAAGACACCAAATCAGCTATCTTTGATCTGCTCTTTATCAATACAGAGATGCC
66 CTCTGACAATACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGTCAATACAGAGACGCC
24242997 A
131 A
24242998 GATTTGTCAC
Statistics
Matches: 574, Mismatches: 56, Indels: 30
0.87 0.08 0.05
Matches are distributed among these distances:
118 110 0.19
119 1 0.00
124 1 0.00
126 1 0.00
131 2 0.00
132 459 0.80
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (132 bp):
ATCTGTTATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCTGTTATCTTCGATCTGCT
CTCTGACAATACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCTCTGTCAATACAGAGACGCC
AA
Found at i:24242557 original size:30 final size:30
Alignment explanation
Indices: 24242523--24242581 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
24242513 AATACAGAGA
24242523 TGCCAAATCTGTTATCTTCGATCTGCTCTT
1 TGCCAAATCTGTTATCTTCGATCTGCTCTT
24242553 TGCCAAATCTGTTATCTTCGATCTGCTCT
1 TGCCAAATCTGTTATCTTCGATCTGCTCT
24242582 CTGTCAATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.17, C:0.27, G:0.14, T:0.42
Consensus pattern (30 bp):
TGCCAAATCTGTTATCTTCGATCTGCTCTT
Found at i:24242576 original size:74 final size:74
Alignment explanation
Indices: 24242480--24242625 Score: 256
Period size: 74 Copynumber: 2.0 Consensus size: 74
24242470 ATACAGAGAC
* * *
24242480 GCCAAATCTGTTATCTTCGATCTGTTCTCTGACAATACAGAGATGCCAAATCTGTTATCTTCGAT
1 GCCAAATCTGTTATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCTGTTATCTTCGAG
24242545 CTGCTCTTT
66 CTGCTCTTT
*
24242554 GCCAAATCTGTTATCTTCGATCTGCTCTCTGTCAATACAGAGACGCCAAATCTGTTATCTTCGAG
1 GCCAAATCTGTTATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCTGTTATCTTCGAG
24242619 CTGCTCT
66 CTGCTCT
24242626 CTGACAATAC
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
74 68 1.00
ACGTcount: A:0.23, C:0.26, G:0.16, T:0.36
Consensus pattern (74 bp):
GCCAAATCTGTTATCTTCGATCTGCTCTCTGACAATACAGAGACGCCAAATCTGTTATCTTCGAG
CTGCTCTTT
Found at i:24242604 original size:44 final size:44
Alignment explanation
Indices: 24242554--24242997 Score: 629
Period size: 44 Copynumber: 10.1 Consensus size: 44
24242544 TCTGCTCTTT
*
24242554 GCCAAATCTGTTATCTTCGATCTGCTCTCTGTCAATACAGAGAC
1 GCCAAATCTGTTATCTTCGATCTGCTCTCTGACAATACAGAGAC
*
24242598 GCCAAATCTGTTATCTTCGAGCTGCTCTCTGACAATACAGAGAC
1 GCCAAATCTGTTATCTTCGATCTGCTCTCTGACAATACAGAGAC
* * *
24242642 GCCAAATCTGTTATATTCGATCTGCTCTCTGACAATACAAATAC
1 GCCAAATCTGTTATCTTCGATCTGCTCTCTGACAATACAGAGAC
* **
24242686 GCCATATCTGTTATCTTCGATCTGCTCTCTGTTAATACAGAGAC
1 GCCAAATCTGTTATCTTCGATCTGCTCTCTGACAATACAGAGAC
*
24242730 GCCAAATCTGTTATCTTCGATCTGTTCTCTGACAATACAGAGAC
1 GCCAAATCTGTTATCTTCGATCTGCTCTCTGACAATACAGAGAC
* *
24242774 CCCAAATATGTTATCTTCGATCTGCTCTCTGACAATACAGAGAC
1 GCCAAATCTGTTATCTTCGATCTGCTCTCTGACAATACAGAGAC
* *
24242818 ACCAAATCTGTTATCTTCGATCTGCTCTCTGTCAATACAGAGAC
1 GCCAAATCTGTTATCTTCGATCTGCTCTCTGACAATACAGAGAC
* * *
24242862 GCCAAATCTGTTATCTTCAATCTACTCTCTGACAATACAAAGAC
1 GCCAAATCTGTTATCTTCGATCTGCTCTCTGACAATACAGAGAC
* * * * *
24242906 GCCAAATCTATTATCTTCAATCTGCTCTCTAAAAATACAAAGAC
1 GCCAAATCTGTTATCTTCGATCTGCTCTCTGACAATACAGAGAC
* * * * * *
24242950 ACCAAATCAGCTATCTTTGATCTGCTCT-TTATCAATACAGAGAT
1 GCCAAATCTGTTATCTTCGATCTGCTCTCTGA-CAATACAGAGAC
24242994 GCCA
1 GCCA
24242998 GATTTGTCAC
Statistics
Matches: 357, Mismatches: 42, Indels: 2
0.89 0.10 0.00
Matches are distributed among these distances:
43 2 0.01
44 355 0.99
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.31
Consensus pattern (44 bp):
GCCAAATCTGTTATCTTCGATCTGCTCTCTGACAATACAGAGAC
Found at i:24242651 original size:74 final size:74
Alignment explanation
Indices: 24242499--24242651 Score: 166
Period size: 74 Copynumber: 2.1 Consensus size: 74
24242489 GTTATCTTCG
* * * * * *
24242499 ATCTGTTCTCTGACAATACAGAGATGCCAAATCTGTTATCTTCGATCTGCTCTTTGCCAAATCTG
1 ATCTGCTCTCTGACAATACAGAGACGCCAAATCTGTTATCTTCGAGCTGCTCTCTGACAAATCAG
** ** *
24242564 TTATCTTCG
66 AGATCGCCA
*
24242573 ATCTGCTCTCTGTCAATACAGAGACGCCAAATCTGTTATCTTCGAGCTGCTCTCTGAC-AATACA
1 ATCTGCTCTCTGACAATACAGAGACGCCAAATCTGTTATCTTCGAGCTGCTCTCTGACAAAT-CA
24242637 GAGA-CGCCAA
65 GAGATCGCC-A
24242647 ATCTG
1 ATCTG
24242652 TTATATTCGA
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
73 5 0.08
74 60 0.92
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.32
Consensus pattern (74 bp):
ATCTGCTCTCTGACAATACAGAGACGCCAAATCTGTTATCTTCGAGCTGCTCTCTGACAAATCAG
AGATCGCCA
Found at i:24243906 original size:13 final size:13
Alignment explanation
Indices: 24243888--24243914 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
24243878 TGGCCTCTCC
24243888 ATTTTTATTTTTT
1 ATTTTTATTTTTT
24243901 ATTTTTATTTTTT
1 ATTTTTATTTTTT
24243914 A
1 A
24243915 GAAGTCTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (13 bp):
ATTTTTATTTTTT
Found at i:24254669 original size:18 final size:18
Alignment explanation
Indices: 24254646--24254682 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
24254636 CATGCAAACG
24254646 TATAAAAACAAAAAATAA
1 TATAAAAACAAAAAATAA
* *
24254664 TATAAAAATAACAAATAA
1 TATAAAAACAAAAAATAA
24254682 T
1 T
24254683 TTACGAGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (18 bp):
TATAAAAACAAAAAATAA
Found at i:24255071 original size:11 final size:12
Alignment explanation
Indices: 24255050--24255101 Score: 58
Period size: 11 Copynumber: 4.6 Consensus size: 12
24255040 ATAAATAGTT
*
24255050 TATAATAAAATGA
1 TATAAT-AAATAA
24255063 TAT-ATAAATAA
1 TATAATAAATAA
24255074 TATAATAAA-AA
1 TATAATAAATAA
24255085 -ATAA-AAATAA
1 TATAATAAATAA
24255095 TATAATA
1 TATAATA
24255102 TGTAATAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
9 3 0.09
10 6 0.18
11 14 0.41
12 8 0.24
13 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (12 bp):
TATAATAAATAA
Found at i:24255092 original size:21 final size:23
Alignment explanation
Indices: 24255050--24255101 Score: 72
Period size: 21 Copynumber: 2.3 Consensus size: 23
24255040 ATAAATAGTT
*
24255050 TATAATAAAATGATATATAAATAA
1 TATAATAAAA-GATATAAAAATAA
24255074 TATAATAAAA-A-ATAAAAATAA
1 TATAATAAAAGATATAAAAATAA
24255095 TATAATA
1 TATAATA
24255102 TGTAATAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 16 0.59
22 1 0.04
24 10 0.37
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (23 bp):
TATAATAAAAGATATAAAAATAA
Found at i:24256369 original size:15 final size:16
Alignment explanation
Indices: 24256349--24256378 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
24256339 TGTAAAGGAC
24256349 TTTTTA-TTATTTTTG
1 TTTTTATTTATTTTTG
24256364 TTTTTATTTATTTTT
1 TTTTTATTTATTTTT
24256379 CTATTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.83
Consensus pattern (16 bp):
TTTTTATTTATTTTTG
Found at i:24256385 original size:17 final size:16
Alignment explanation
Indices: 24256348--24256397 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
24256338 CTGTAAAGGA
24256348 CTTTTTA-TTATTTTT
1 CTTTTTATTTATTTTT
*
24256363 GTTTTTATTTATTTTT
1 CTTTTTATTTATTTTT
* *
24256379 CTATTTTTTTTCTTTTT
1 CT-TTTTATTTATTTTT
24256396 CT
1 CT
24256398 GGGCCGGGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
15 6 0.21
16 9 0.31
17 14 0.48
ACGTcount: A:0.10, C:0.08, G:0.02, T:0.80
Consensus pattern (16 bp):
CTTTTTATTTATTTTT
Found at i:24259713 original size:43 final size:43
Alignment explanation
Indices: 24259634--24259750 Score: 123
Period size: 43 Copynumber: 2.7 Consensus size: 43
24259624 TAAGCTCGTA
* **
24259634 CAATGCCAATGTCCCAGAC-GTGGTCTTACATGTAATCAA-ATAT
1 CAATGCCATTGTCCCAGACAG-GGTCTTACACATAATCAATA-AT
**
24259677 CAATGCCATTGTCCCAGACAGGGTCTTACACATAATCTCTAAT
1 CAATGCCATTGTCCCAGACAGGGTCTTACACATAATCAATAAT
* *
24259720 CGATGCCAGTT-TCCCAGACACGGTCTTACAC
1 CAATGCCA-TTGTCCCAGACAGGGTCTTACAC
24259751 GATATCTCAA
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
43 60 0.94
44 4 0.06
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.26
Consensus pattern (43 bp):
CAATGCCATTGTCCCAGACAGGGTCTTACACATAATCAATAAT
Found at i:24259758 original size:43 final size:43
Alignment explanation
Indices: 24259679--24259770 Score: 127
Period size: 43 Copynumber: 2.1 Consensus size: 43
24259669 TCAAATATCA
*
24259679 ATGCCATTGTCCCAGACAGGGTCTTACACATAATCTCTAA-TCG
1 ATGCCATTGTCCCAGACACGGTCTTACACATAATCTC-AAGTCG
24259722 ATGCCAGTT-TCCCAGACACGGTCTTACACGAT-ATCTCAAGTCG
1 ATGCCA-TTGTCCCAGACACGGTCTTACAC-ATAATCTCAAGTCG
24259765 ATGCCA
1 ATGCCA
24259771 AATCCCAGGC
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
42 2 0.04
43 39 0.87
44 4 0.09
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.26
Consensus pattern (43 bp):
ATGCCATTGTCCCAGACACGGTCTTACACATAATCTCAAGTCG
Found at i:24260415 original size:15 final size:15
Alignment explanation
Indices: 24260392--24260431 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
24260382 ATTCAAATAA
* *
24260392 AAAATATATTAACCC
1 AAAACATATCAACCC
24260407 AAAACATATCAACCC
1 AAAACATATCAACCC
24260422 AAAACATATC
1 AAAACATATC
24260432 TTTCATTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.55, C:0.25, G:0.00, T:0.20
Consensus pattern (15 bp):
AAAACATATCAACCC
Found at i:24262326 original size:42 final size:42
Alignment explanation
Indices: 24262267--24262351 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
24262257 TCACTGATCG
24262267 ACTAGTAGAGATGGGACCATACTGAATCCCAGATTTTTGCCA
1 ACTAGTAGAGATGGGACCATACTGAATCCCAGATTTTTGCCA
*
24262309 ACTAGTAGAGATGGGACCATAGTGAATCCCAGATTTTTGCCA
1 ACTAGTAGAGATGGGACCATACTGAATCCCAGATTTTTGCCA
24262351 A
1 A
24262352 TGAACACTAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (42 bp):
ACTAGTAGAGATGGGACCATACTGAATCCCAGATTTTTGCCA
Found at i:24262648 original size:24 final size:24
Alignment explanation
Indices: 24262609--24262657 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
24262599 TTTGAAGGAA
*
24262609 TTATTTTTGATACTAATAAATAAG
1 TTATTTTTAATACTAATAAATAAG
*
24262633 TTATTTTTAATTCTAATAAATAAG
1 TTATTTTTAATACTAATAAATAAG
24262657 T
1 T
24262658 CAAAAGCTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.49
Consensus pattern (24 bp):
TTATTTTTAATACTAATAAATAAG
Found at i:24272354 original size:40 final size:40
Alignment explanation
Indices: 24272249--24272394 Score: 181
Period size: 40 Copynumber: 3.6 Consensus size: 40
24272239 GCTACTCGTT
*
24272249 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
24272289 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
24272329 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
24272370 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
24272395 CATCATTCAA
Statistics
Matches: 93, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
39 3 0.03
40 77 0.83
41 13 0.14
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:24275658 original size:59 final size:58
Alignment explanation
Indices: 24275557--24275674 Score: 193
Period size: 59 Copynumber: 2.0 Consensus size: 58
24275547 AATCACTATA
24275557 TATCAAATCAAGCAATTTTGTTTTCCTTTTAACATTTGGGAAAGAGATTCTTGTAATT
1 TATCAAATCAAGCAATTTTGTTTTCCTTTTAACATTTGGGAAAGAGATTCTTGTAATT
* *
24275615 NTATCAAATCAAGCAATTTTGTTTTCCTTTTAACCTTAT-GGAAAGAGTTTCTTGTAATT
1 -TATCAAATCAAGCAATTTTGTTTTCCTTTTAACATT-TGGGAAAGAGATTCTTGTAATT
24275674 T
1 T
24275675 TAGTCAACAT
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
58 1 0.02
59 54 0.96
60 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.44
Consensus pattern (58 bp):
TATCAAATCAAGCAATTTTGTTTTCCTTTTAACATTTGGGAAAGAGATTCTTGTAATT
Found at i:24275894 original size:63 final size:62
Alignment explanation
Indices: 24275822--24275946 Score: 196
Period size: 63 Copynumber: 2.0 Consensus size: 62
24275812 GCAGAAATAG
*
24275822 TATTTTTATTCTTATTAATAATATTGAGTTTGAACATACTCTAATACATATACCATTTCCCT
1 TATTTTTATTCTTATTAATAATATTAAGTTTGAACATACTCTAATACATATACCATTTCCCT
* * * *
24275884 NTATTTTTATTCTTATTAATAATATTAAGTTTGAACATGCTTTCATACATATACCCTTTCCCT
1 -TATTTTTATTCTTATTAATAATATTAAGTTTGAACATACTCTAATACATATACCATTTCCCT
24275947 ACAAAAATTC
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.30, C:0.17, G:0.05, T:0.47
Consensus pattern (62 bp):
TATTTTTATTCTTATTAATAATATTAAGTTTGAACATACTCTAATACATATACCATTTCCCT
Found at i:24277163 original size:30 final size:30
Alignment explanation
Indices: 24277117--24277174 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
24277107 TAGGCACTTC
* * *
24277117 CACAAGGGTAATCCACACGTCCGTGTGTGA
1 CACAAGGGTAAGCCACACGCCCATGTGTGA
*
24277147 CACACGGGTAAGCCACACGCCCATGTGT
1 CACAAGGGTAAGCCACACGCCCATGTGT
24277175 CATGGCCGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.26, C:0.31, G:0.26, T:0.17
Consensus pattern (30 bp):
CACAAGGGTAAGCCACACGCCCATGTGTGA
Found at i:24281318 original size:43 final size:43
Alignment explanation
Indices: 24281222--24281389 Score: 162
Period size: 43 Copynumber: 3.9 Consensus size: 43
24281212 TTTATTTGAA
* **
24281222 AAAACGCCGCTAAAGATCATGACATTT-ACGGTACTTTTTCC-AC
1 AAAA-GCCGCTAAAGATCATGACCTTTAACGGCGC-TTTTCCTAC
*
24281265 AAACGCCGCTAAAGATCATGACCTTTAACGGCGCTTTTCCTAC
1 AAAAGCCGCTAAAGATCATGACCTTTAACGGCGCTTTTCCTAC
* * * * *
24281308 AAAAGACGCTAAAGATCATGACCTTCAGCGACGCTTTTTCTAC
1 AAAAGCCGCTAAAGATCATGACCTTTAACGGCGCTTTTCCTAC
* ** * *
24281351 AAACA-CCGCTAAAAATCACAACCTTTAGCAGCGCTTTTC
1 AAA-AGCCGCTAAAGATCATGACCTTTAACGGCGCTTTTC
24281390 TCAAAAACAC
Statistics
Matches: 104, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
42 27 0.26
43 76 0.73
44 1 0.01
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (43 bp):
AAAAGCCGCTAAAGATCATGACCTTTAACGGCGCTTTTCCTAC
Found at i:24281398 original size:43 final size:42
Alignment explanation
Indices: 24281221--24281414 Score: 146
Period size: 43 Copynumber: 4.5 Consensus size: 42
24281211 GTTTATTTGA
* * *
24281221 AAAAACGCCGCTAAAGATCATGACATTTA-CG-GTACTTTTTCC-
1 AAAAACACCGCTAAAAATCATGACCTTTAGCGCG--C-TTTTCCT
* * * *
24281263 ACAAACGCCGCTAAAGATCATGACCTTTAACGGCGCTTTTCCT
1 AAAAACACCGCTAAAAATCATGACCTTTAGC-GCGCTTTTCCT
* * * *
24281306 ACAAAAGA-CGCTAAAGATCATGACCTTCAGCGACGCTTTTTCT
1 A-AAAACACCGCTAAAAATCATGACCTTTAGCG-CGCTTTTCCT
* **
24281349 ACAAACACCGCTAAAAATCACAACCTTTAGCAGCGCTTTT-CT
1 AAAAACACCGCTAAAAATCATGACCTTTAGC-GCGCTTTTCCT
*
24281391 CAAAAACACCGCTAAAAGTCATGA
1 -AAAAACACCGCTAAAAATCATGA
24281415 AATTCAAAAA
Statistics
Matches: 125, Mismatches: 18, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
42 40 0.32
43 79 0.63
44 5 0.04
45 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.24
Consensus pattern (42 bp):
AAAAACACCGCTAAAAATCATGACCTTTAGCGCGCTTTTCCT
Found at i:24281404 original size:86 final size:85
Alignment explanation
Indices: 24281221--24281420 Score: 208
Period size: 86 Copynumber: 2.3 Consensus size: 85
24281211 GTTTATTTGA
* * ** * * **
24281221 AAAAACGCCGCTAAAGATCATGACATTTACGGTACTTTTTCCACAAACGCCGCTAAAGATCATGA
1 AAAAACACCGCTAAAGATCATGACATTCACGACACTTTTTCCACAAACACCGCTAAAAATCACAA
*
24281286 CCTTTAACGGCGCTTTTCCT
66 CCTTTAACAGCGCTTTTCCT
* * * *
24281306 ACAAAAGA-CGCTAAAGATCATGACCTTCAGCGACGCTTTTTCTACAAACACCGCTAAAAATCAC
1 A-AAAACACCGCTAAAGATCATGACATTCA-CGACACTTTTTCCACAAACACCGCTAAAAATCAC
*
24281370 AACCTTTAGCAGCGCTTTT-CT
64 AACCTTTAACAGCGCTTTTCCT
*
24281391 CAAAAACACCGCTAAA-AGTCATGAAATTCA
1 -AAAAACACCGCTAAAGA-TCATGACATTCA
24281421 AAAAAAATAT
Statistics
Matches: 93, Mismatches: 17, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
85 28 0.30
86 65 0.70
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.24
Consensus pattern (85 bp):
AAAAACACCGCTAAAGATCATGACATTCACGACACTTTTTCCACAAACACCGCTAAAAATCACAA
CCTTTAACAGCGCTTTTCCT
Found at i:24281675 original size:19 final size:19
Alignment explanation
Indices: 24281653--24281692 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
24281643 ATTTAGAATC
24281653 AAAACTAAAATAAATAATA
1 AAAACTAAAATAAATAATA
* * *
24281672 AAAATTAGATTAAATAATA
1 AAAACTAAAATAAATAATA
24281691 AA
1 AA
24281693 TATAAATGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.25
Consensus pattern (19 bp):
AAAACTAAAATAAATAATA
Found at i:24281698 original size:32 final size:33
Alignment explanation
Indices: 24281619--24281699 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 33
24281609 TCAAGTTATC
*
24281619 TTAAATATTAAAATAAA-AATAAAAATTTAGAA
1 TTAAATAATAAAATAAATAATAAAAATTTAGAA
* *
24281651 TCAAA-ACTAAAATAAATAATAAAAA-TTAG-A
1 TTAAATAATAAAATAAATAATAAAAATTTAGAA
24281681 TTAAATAATAAATATAAAT
1 TTAAATAATAAA-ATAAAT
24281700 GAAATAAAGA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
30 5 0.12
31 19 0.45
32 18 0.43
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (33 bp):
TTAAATAATAAAATAAATAATAAAAATTTAGAA
Found at i:24281706 original size:18 final size:18
Alignment explanation
Indices: 24281660--24281706 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
24281650 ATCAAAACTA
24281660 AAATAAATAATAAAAATT
1 AAATAAATAATAAAAATT
* *
24281678 AGATTAAATAATAAATA-T
1 A-AATAAATAATAAAAATT
24281696 AAATGAAATAA
1 AAAT-AAATAA
24281707 AGACTTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 2 0.08
18 9 0.38
19 13 0.54
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (18 bp):
AAATAAATAATAAAAATT
Found at i:24283476 original size:9 final size:9
Alignment explanation
Indices: 24283462--24283489 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
24283452 ATGGCAATCA
24283462 AGCATCATC
1 AGCATCATC
24283471 AGCATCATC
1 AGCATCATC
24283480 AGCATCATC
1 AGCATCATC
24283489 A
1 A
24283490 TTTTTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.36, C:0.32, G:0.11, T:0.21
Consensus pattern (9 bp):
AGCATCATC
Done.