Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167904.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_17, whole genome shotgun sequence
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: 21107920
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 100000 characters in sequence are not A, C, G, or T
File 26 of 121
Found at i:4586898 original size:22 final size:22
Alignment explanation
Indices: 4586873--4586917 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
4586863 TCTTTTTTAC
4586873 TTTGTTGGTTGAGTAATTTCAT
1 TTTGTTGGTTGAGTAATTTCAT
*
4586895 TTTGTTGGTTTAGTAATTTCAT
1 TTTGTTGGTTGAGTAATTTCAT
4586917 T
1 T
4586918 GTCATGTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.04, G:0.20, T:0.58
Consensus pattern (22 bp):
TTTGTTGGTTGAGTAATTTCAT
Found at i:4588577 original size:74 final size:74
Alignment explanation
Indices: 4588456--4588603 Score: 287
Period size: 74 Copynumber: 2.0 Consensus size: 74
4588446 GCCCGATGTT
4588456 GGGCATCCCGTTTCATTAAGATAATAACTTTGATCACTTTGGGATCAACTGAAGCTGTAGTAGTA
1 GGGCATCCCGTTTCATTAAGATAATAACTTTGATCACTTTGGGATCAACTGAAGCTGTAGTAGTA
4588521 CTGATTTTG
66 CTGATTTTG
*
4588530 GGGCATCCTGTTTCATTAAGATAATAACTTTGATCACTTTGGGATCAACTGAAGCTGTAGTAGTA
1 GGGCATCCCGTTTCATTAAGATAATAACTTTGATCACTTTGGGATCAACTGAAGCTGTAGTAGTA
4588595 CTGATTTTG
66 CTGATTTTG
4588604 AGGTCTCTTT
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.36
Consensus pattern (74 bp):
GGGCATCCCGTTTCATTAAGATAATAACTTTGATCACTTTGGGATCAACTGAAGCTGTAGTAGTA
CTGATTTTG
Found at i:4593246 original size:15 final size:16
Alignment explanation
Indices: 4593226--4593284 Score: 51
Period size: 15 Copynumber: 4.1 Consensus size: 16
4593216 TATTTTTATT
4593226 AATTAAAA-AATGAAA
1 AATTAAAACAATGAAA
*
4593241 AATTAAAACAAT---T
1 AATTAAAACAATGAAA
4593254 AA--AAAA-AATGAAA
1 AATTAAAACAATGAAA
*
4593267 AATTAAAACAATTAAA
1 AATTAAAACAATGAAA
4593283 AA
1 AA
4593285 AAATGAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 13
0.68 0.06 0.26
Matches are distributed among these distances:
10 3 0.09
11 4 0.12
13 4 0.12
15 12 0.35
16 11 0.32
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.20
Consensus pattern (16 bp):
AATTAAAACAATGAAA
Found at i:4593253 original size:9 final size:9
Alignment explanation
Indices: 4593241--4593283 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
4593231 AAAAATGAAA
4593241 AATTAAAAC
1 AATTAAAAC
*
4593250 AATTAAAAA
1 AATTAAAAC
* *
4593259 AAATGAAA-
1 AATTAAAAC
4593267 AATTAAAAC
1 AATTAAAAC
4593276 AATTAAAA
1 AATTAAAA
4593284 AAAATGAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
8 6 0.21
9 22 0.79
ACGTcount: A:0.72, C:0.05, G:0.02, T:0.21
Consensus pattern (9 bp):
AATTAAAAC
Found at i:4593265 original size:26 final size:26
Alignment explanation
Indices: 4593230--4593298 Score: 138
Period size: 26 Copynumber: 2.7 Consensus size: 26
4593220 TTTATTAATT
4593230 AAAAAATGAAAAATTAAAACAATTAA
1 AAAAAATGAAAAATTAAAACAATTAA
4593256 AAAAAATGAAAAATTAAAACAATTAA
1 AAAAAATGAAAAATTAAAACAATTAA
4593282 AAAAAATGAAAAATTAA
1 AAAAAATGAAAAATTAA
4593299 GTGGTTGGAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.74, C:0.03, G:0.04, T:0.19
Consensus pattern (26 bp):
AAAAAATGAAAAATTAAAACAATTAA
Found at i:4594975 original size:18 final size:18
Alignment explanation
Indices: 4594952--4594989 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
4594942 CCACATGCAA
*
4594952 TTGAATTCTCGAATTTTG
1 TTGAATTCTCAAATTTTG
4594970 TTGAATTCTCAAATTTTG
1 TTGAATTCTCAAATTTTG
4594988 TT
1 TT
4594990 TTGATTAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.11, G:0.13, T:0.53
Consensus pattern (18 bp):
TTGAATTCTCAAATTTTG
Found at i:4602407 original size:16 final size:15
Alignment explanation
Indices: 4602380--4602567 Score: 134
Period size: 15 Copynumber: 12.4 Consensus size: 15
4602370 AAAGCTTCGA
4602380 ATTTTAGGGTTTTGG
1 ATTTTAGGGTTTTGG
* *
4602395 ATTTTAGGGGTTTGA
1 ATTTTAGGGTTTTGG
* *
4602410 ATTTT-GGGGTATGG
1 ATTTTAGGGTTTTGG
* * *
4602424 ATTTAAAGG-TTGGG
1 ATTTTAGGGTTTTGG
4602438 ATTTTAGGGTTTTGG
1 ATTTTAGGGTTTTGG
*
4602453 ATTTTAGGGGTTTGG
1 ATTTTAGGGTTTTGG
* *
4602468 ATTTAAGGGTTTAAAGG
1 ATTTTAGGGTTT--TGG
*
4602485 -TTTTAGGGTTTCGG
1 ATTTTAGGGTTTTGG
4602499 ATTTAATAGGG-TTTGG
1 ATTT--TAGGGTTTTGG
* *
4602515 ATTTAAAGGATTTTGG
1 ATTT-TAGGGTTTTGG
*
4602531 ATTTTAGGGGTTTTAGA
1 ATTTTA-GGGTTTT-GG
**
4602548 ATCCTAGGGTTTTGG
1 ATTTTAGGGTTTTGG
4602563 -TTTTA
1 ATTTTA
4602568 AAAATTAAGG
Statistics
Matches: 135, Mismatches: 28, Indels: 21
0.73 0.15 0.11
Matches are distributed among these distances:
14 26 0.19
15 57 0.42
16 40 0.30
17 12 0.09
ACGTcount: A:0.20, C:0.02, G:0.32, T:0.46
Consensus pattern (15 bp):
ATTTTAGGGTTTTGG
Found at i:4602508 original size:17 final size:16
Alignment explanation
Indices: 4602416--4602534 Score: 64
Period size: 16 Copynumber: 7.8 Consensus size: 16
4602406 TTGAATTTTG
*
4602416 GGGTATGGATTTAA-A
1 GGGTTTGGATTTAATA
*
4602431 -GGTTGGGATTT--TA
1 GGGTTTGGATTTAATA
4602444 GGGTTTTGGATTT--TA
1 GGG-TTTGGATTTAATA
4602459 GGGGTTTGGATTT-A-A
1 -GGGTTTGGATTTAATA
4602474 GGGTTTAAAGG-TTT--TA
1 GGGTTT---GGATTTAATA
4602490 GGGTTTCGGATTTAATA
1 GGGTTT-GGATTTAATA
4602507 GGGTTTGGATTTAA-A
1 GGGTTTGGATTTAATA
*
4602522 GGATTTTGGATTT
1 GG-GTTTGGATTT
4602535 TAGGGGTTTT
Statistics
Matches: 86, Mismatches: 5, Indels: 25
0.74 0.04 0.22
Matches are distributed among these distances:
13 1 0.01
14 19 0.22
15 26 0.30
16 30 0.35
17 10 0.12
ACGTcount: A:0.22, C:0.01, G:0.34, T:0.44
Consensus pattern (16 bp):
GGGTTTGGATTTAATA
Found at i:4602845 original size:14 final size:14
Alignment explanation
Indices: 4602826--4602856 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
4602816 TTTTTAAGCA
4602826 TTTTTAATATATAT
1 TTTTTAATATATAT
4602840 TTTTTAATATATAT
1 TTTTTAATATATAT
4602854 TTT
1 TTT
4602857 ACTTATTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTTTAATATATAT
Found at i:4602957 original size:18 final size:17
Alignment explanation
Indices: 4602931--4602990 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
4602921 ATTATGCATA
*
4602931 AATATAAAAACTTAAAAT
1 AATA-AAAAAATTAAAAT
*
4602949 AATAAAAAAA-TAATAT
1 AATAAAAAAATTAAAAT
4602965 -ATAAAAAAATTAGAAA-
1 AATAAAAAAATTA-AAAT
*
4602981 ATTAAAAAAA
1 AATAAAAAAA
4602991 AAATTTTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
15 9 0.26
16 7 0.20
17 15 0.43
18 4 0.11
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (17 bp):
AATAAAAAAATTAAAAT
Found at i:4604046 original size:3 final size:3
Alignment explanation
Indices: 4604038--4604108 Score: 51
Period size: 3 Copynumber: 24.0 Consensus size: 3
4604028 CTATCTCCTT
*
4604038 TTA TTA TTA TTGA TTA TATA TT- TT- TTA -AA TATA TT- TTA TTA TTA
1 TTA TTA TTA TT-A TTA T-TA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
** *
4604082 TTA TTA TTA TTA AAA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
4604109 AACTGAAATA
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
2 7 0.13
3 39 0.72
4 8 0.15
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:4604504 original size:34 final size:35
Alignment explanation
Indices: 4604460--4604543 Score: 93
Period size: 34 Copynumber: 2.5 Consensus size: 35
4604450 AAATATCGAG
*
4604460 GATCAGGATTAAACTGCA-AACCAAAGAATAAAGA
1 GATCAAGATTAAACTGCAGAACCAAAGAATAAAGA
** *
4604494 GATCAAGATTAAA-T-CATGAATTACAGAATAAAGA
1 GATCAAGATTAAACTGCA-GAACCAAAGAATAAAGA
*
4604528 GATCGAGATTAAACTG
1 GATCAAGATTAAACTG
4604544 TGAGTCAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
32 2 0.05
33 1 0.02
34 37 0.90
35 1 0.02
ACGTcount: A:0.50, C:0.12, G:0.18, T:0.20
Consensus pattern (35 bp):
GATCAAGATTAAACTGCAGAACCAAAGAATAAAGA
Found at i:4604752 original size:134 final size:135
Alignment explanation
Indices: 4604522--4604808 Score: 378
Period size: 134 Copynumber: 2.1 Consensus size: 135
4604512 AATTACAGAA
* * * *
4604522 TAAAGAGATCGAGATTAAACTGTGAGTCAAAAAATGACGTTAACTTAGATCGAATCACAAGTCAG
1 TAAAGAGATCGGGATTAAACTGCGAATCAAAAAAT-A-GTTAACTTAGATCGAATCACAAGTAAG
* * * * * *
4604587 AAAATAAAGAGACCGGGATTAAACTATGAGTCAAAGGATAACAGCAATAGAGATTAAACTACGAT
64 AAAATAAAAAGACCAGGATTAAACCACGAGTCAAAGGATAACAACAATAGAGATTAAACTACGAC
*
4604652 TTTGACT
129 TTTGAAT
* * * * *
4604659 TAAAGAGATCGGGATTAAACTGCGAATCGAAGAAT-GTTAACTTGGATTGAATCATAAGTAAGAA
1 TAAAGAGATCGGGATTAAACTGCGAATCAAAAAATAGTTAACTTAGATCGAATCACAAGTAAGAA
* * *
4604723 AATAAAAAGATCAGGATTAAACCACGAGTCAGAGGATAACAACAATTGAGATTAAACTACGACTT
66 AATAAAAAGACCAGGATTAAACCACGAGTCAAAGGATAACAACAATAGAGATTAAACTACGACTT
4604788 TGAAT
131 TGAAT
4604793 TAAAGAGATCGGGATT
1 TAAAGAGATCGGGATT
4604809 GAACCGTGAA
Statistics
Matches: 131, Mismatches: 19, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
134 101 0.77
137 30 0.23
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.23
Consensus pattern (135 bp):
TAAAGAGATCGGGATTAAACTGCGAATCAAAAAATAGTTAACTTAGATCGAATCACAAGTAAGAA
AATAAAAAGACCAGGATTAAACCACGAGTCAAAGGATAACAACAATAGAGATTAAACTACGACTT
TGAAT
Found at i:4604858 original size:134 final size:132
Alignment explanation
Indices: 4604577--4604889 Score: 304
Period size: 134 Copynumber: 2.3 Consensus size: 132
4604567 TAGATCGAAT
* * * *
4604577 CACAAGTCAGAAAATAAAGAGACCGGGATTAAACTATGAGTCAAAGGATAACAGCAATAGAGATT
1 CACAAGT-AGAAAATAAAAAGA-CGGGATTAAACCACGAGTCAAAGGATAACAACAATAGAGATT
* * * * *** * *
4604642 AAACTACGATTTTGACTTAAAGAGATCGGGATTAAACTGCGAATCGAAGAATGTTAACTTGGATT
64 AAACTACGACTTTGAATTAAAGAGATCGGGATTAAACCGCGAATAGAAGAATAAAAAATGGGATT
* *
4604707 GAAT
129 AAAC
* * * *
4604711 CATAAGTAAGAAAATAAAAAGATCAGGATTAAACCACGAGTCAGAGGATAACAACAATTGAGATT
1 CACAAGT-AGAAAATAAAAAGA-CGGGATTAAACCACGAGTCAAAGGATAACAACAATAGAGATT
* *
4604776 AAACTACGACTTTGAATTAAAGAGATCGGGATTGAACCGTGAATTAG-AGAATAAAAAGATCGGG
64 AAACTACGACTTTGAATTAAAGAGATCGGGATTAAACCGCGAA-TAGAAGAATAAAAA-AT-GGG
4604840 ATTAAAC
126 ATTAAAC
* * *
4604847 CGCGAGTGAAAAAAATAAAAACGACTGGGATTAAACCACGAGT
1 CACAAGT--AGAAAATAAAAA-GAC-GGGATTAAACCACGAGT
4604890 TAAGAAAACT
Statistics
Matches: 145, Mismatches: 28, Indels: 8
0.80 0.15 0.04
Matches are distributed among these distances:
134 100 0.69
135 3 0.02
136 11 0.08
137 13 0.09
138 18 0.12
ACGTcount: A:0.45, C:0.13, G:0.21, T:0.21
Consensus pattern (132 bp):
CACAAGTAGAAAATAAAAAGACGGGATTAAACCACGAGTCAAAGGATAACAACAATAGAGATTAA
ACTACGACTTTGAATTAAAGAGATCGGGATTAAACCGCGAATAGAAGAATAAAAAATGGGATTAA
AC
Found at i:4604965 original size:74 final size:72
Alignment explanation
Indices: 4604869--4605045 Score: 180
Period size: 72 Copynumber: 2.4 Consensus size: 72
4604859 AAATAAAAAC
* * * *
4604869 GACTGGGATTAAACCACGAGTTAAGAAAACT-ATAGAAATGATCAG-GATTAAACCATAAG-TCA
1 GACTGGGACTAAACCGCAAGTT-AGAAAACTAAT-GAAATGA-CAGAGATTAAACCACAAGCT-A
4604931 AAGATTAAAGAT
62 AA-ATTAAAGAT
* * * *
4604943 GACTGGGACTAAACCGCAAGTTAGGAAATTAATGAAATGACCGAGATTAAACCACGAGCTAAAAT
1 GACTGGGACTAAACCGCAAGTTAGAAAACTAATGAAATGACAGAGATTAAACCACAAGCTAAAAT
4605008 TAAAGAT
66 TAAAGAT
* * * *
4605015 GACTAGGACTGAACCGCAAGTCAGGAAACTA
1 GACTGGGACTAAACCGCAAGTTAGAAAACTA
4605046 TATAAAACTG
Statistics
Matches: 88, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
72 38 0.43
73 28 0.32
74 22 0.25
ACGTcount: A:0.45, C:0.15, G:0.21, T:0.19
Consensus pattern (72 bp):
GACTGGGACTAAACCGCAAGTTAGAAAACTAATGAAATGACAGAGATTAAACCACAAGCTAAAAT
TAAAGAT
Found at i:4606093 original size:16 final size:16
Alignment explanation
Indices: 4606072--4606108 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
4606062 GAATCACTTC
4606072 TTTTATT-TTTTGTATT
1 TTTTATTATTTTGT-TT
4606088 TTTTATTATTTTGTTT
1 TTTTATTATTTTGTTT
4606104 TTTTA
1 TTTTA
4606109 AGCAAACTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.14, C:0.00, G:0.05, T:0.81
Consensus pattern (16 bp):
TTTTATTATTTTGTTT
Found at i:4617494 original size:15 final size:15
Alignment explanation
Indices: 4617476--4617589 Score: 97
Period size: 15 Copynumber: 7.6 Consensus size: 15
4617466 GAAGATTCGA
* *
4617476 ATTTTATGGTTTTGG
1 ATTTTAGGGGTTTGG
* *
4617491 ATTTTAGGGATTTTGA
1 ATTTTAGGG-GTTTGG
*
4617507 ATTTT-GGGGTCTGG
1 ATTTTAGGGGTTTGG
** *
4617521 A-TTTAAAGGTTGGG
1 ATTTTAGGGGTTTGG
* *
4617535 ATTTTAGGGTTTTGA
1 ATTTTAGGGGTTTGG
4617550 ATTTTAGGGGTTTGAG
1 ATTTTAGGGGTTTG-G
4617566 ATTTTAGGGGTTTGG
1 ATTTTAGGGGTTTGG
*
4617581 ATTTAAGGG
1 ATTTTAGGG
4617590 TTTTAAGGTT
Statistics
Matches: 78, Mismatches: 17, Indels: 8
0.76 0.17 0.08
Matches are distributed among these distances:
13 3 0.04
14 10 0.13
15 41 0.53
16 24 0.31
ACGTcount: A:0.19, C:0.01, G:0.33, T:0.46
Consensus pattern (15 bp):
ATTTTAGGGGTTTGG
Found at i:4617570 original size:59 final size:60
Alignment explanation
Indices: 4617476--4617591 Score: 164
Period size: 59 Copynumber: 1.9 Consensus size: 60
4617466 GAAGATTCGA
* * *
4617476 ATTTTATGGTTTTGGATTTTAGGGATTTTGAATTTT-GGGGTCTGGATTTAAAGGTTGGG
1 ATTTTAGGGTTTTGAATTTTAGGGAGTTTGAATTTTAGGGGTCTGGATTTAAAGGTTGGG
* *
4617535 ATTTTAGGGTTTTGAATTTTAGGG-GTTTGAGATTTTAGGGGTTTGGATTTAAGGGTT
1 ATTTTAGGGTTTTGAATTTTAGGGAGTTTGA-ATTTTAGGGGTCTGGATTTAAAGGTT
4617592 TTAAGGTTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
58 5 0.10
59 27 0.54
60 18 0.36
ACGTcount: A:0.19, C:0.01, G:0.33, T:0.47
Consensus pattern (60 bp):
ATTTTAGGGTTTTGAATTTTAGGGAGTTTGAATTTTAGGGGTCTGGATTTAAAGGTTGGG
Found at i:4617592 original size:14 final size:14
Alignment explanation
Indices: 4617513--4617592 Score: 61
Period size: 14 Copynumber: 5.4 Consensus size: 14
4617503 TTGAATTTTG
*
4617513 GGGTCTGGATTTAA
1 GGGTTTGGATTTAA
* * *
4617527 AGGTTGGGATTTTA
1 GGGTTTGGATTTAA
* *
4617541 GGGTTTTGAATTTTAG
1 GGG-TTTGGA-TTTAA
*
4617557 GGGTTTGAGATTTTAG
1 GGGTTTG-GA-TTTAA
4617573 GGGTTTGGATTTAA
1 GGGTTTGGATTTAA
4617587 GGGTTT
1 GGGTTT
4617593 TAAGGTTTTA
Statistics
Matches: 52, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
14 22 0.42
15 10 0.19
16 20 0.38
ACGTcount: A:0.19, C:0.01, G:0.36, T:0.44
Consensus pattern (14 bp):
GGGTTTGGATTTAA
Found at i:4617602 original size:31 final size:31
Alignment explanation
Indices: 4617534--4617648 Score: 86
Period size: 31 Copynumber: 3.5 Consensus size: 31
4617524 TAAAGGTTGG
* * *
4617534 GATTTTAGGGTTTTGAATTTTAGGGGTTTGA
1 GATTTTAGGGGTTTGAATTTAAGGGGTTTAA
* *
4617565 GATTTTAGGGGTTTGGATTTAAGGGTTTTAAGGTTTTA
1 GATTTTAGGGGTTTGAATTTAA-GG------GGTTTAA
* **
4617603 GATTTTAGAGGGTTTGAATTTAAGGGATTTTG
1 GATTTTAG-GGGTTTGAATTTAAGGGGTTTAA
4617635 GATTTTAGGGGTTT
1 GATTTTAGGGGTTT
4617649 TAGAATCCTA
Statistics
Matches: 69, Mismatches: 7, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
31 25 0.36
32 15 0.22
38 16 0.23
39 13 0.19
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.47
Consensus pattern (31 bp):
GATTTTAGGGGTTTGAATTTAAGGGGTTTAA
Found at i:4617616 original size:17 final size:17
Alignment explanation
Indices: 4617596--4617652 Score: 59
Period size: 16 Copynumber: 3.5 Consensus size: 17
4617586 AGGGTTTTAA
4617596 GGTTTTAGATTTTAGAG
1 GGTTTTAGATTTTAGAG
*
4617613 GG-TTT-GAATTTA-AG
1 GGTTTTAGATTTTAGAG
*
4617627 GGATTTTGGATTTTAG-G
1 GG-TTTTAGATTTTAGAG
4617644 GGTTTTAGA
1 GGTTTTAGA
4617653 ATCCTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
14 4 0.12
15 6 0.18
16 12 0.36
17 11 0.33
ACGTcount: A:0.23, C:0.00, G:0.32, T:0.46
Consensus pattern (17 bp):
GGTTTTAGATTTTAGAG
Found at i:4617616 original size:39 final size:39
Alignment explanation
Indices: 4617558--4617633 Score: 118
Period size: 39 Copynumber: 1.9 Consensus size: 39
4617548 GAATTTTAGG
*
4617558 GGTTTGAGATTTTAGGGGTTTGGATTTAAGGG-TTTTAA
1 GGTTTGAGATTTTAGGGGTTTGAATTTAAGGGATTTTAA
*
4617596 GGTTTTAGATTTTAGAGGGTTTGAATTTAAGGGATTTT
1 GGTTTGAGATTTTAG-GGGTTTGAATTTAAGGGATTTT
4617634 GGATTTTAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
38 14 0.41
39 16 0.47
40 4 0.12
ACGTcount: A:0.22, C:0.00, G:0.32, T:0.46
Consensus pattern (39 bp):
GGTTTGAGATTTTAGGGGTTTGAATTTAAGGGATTTTAA
Found at i:4617641 original size:39 final size:37
Alignment explanation
Indices: 4617558--4617642 Score: 109
Period size: 39 Copynumber: 2.2 Consensus size: 37
4617548 GAATTTTAGG
* *
4617558 GGTTTGAGATTTTAGGGGTTTGGATTTAAGGGTTTTAA
1 GGTTTTAGATTTTAGGGGTTTGAATTTAAGGGTTTT-A
4617596 GGTTTTAGATTTTAGAGGGTTTGAATTTAAGGGATTTT-
1 GGTTTTAGATTTTAG-GGGTTTGAATTTAAGGG-TTTTA
4617634 GGATTTTAG
1 GG-TTTTAG
4617643 GGGTTTTAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
38 16 0.38
39 22 0.52
40 4 0.10
ACGTcount: A:0.22, C:0.00, G:0.32, T:0.46
Consensus pattern (37 bp):
GGTTTTAGATTTTAGGGGTTTGAATTTAAGGGTTTTA
Found at i:4617666 original size:32 final size:30
Alignment explanation
Indices: 4617593--4617666 Score: 78
Period size: 32 Copynumber: 2.3 Consensus size: 30
4617583 TTAAGGGTTT
* *
4617593 TAAGGTTTTAGATTTTAGAGGGTTTGAATT
1 TAAGGTTTTGGATTTTAGAGGGTTTGAATC
4617623 TAAGGGATTTTGGATTTTAG-GGGTTTTAGAATCC
1 TAA-GG-TTTTGGATTTTAGAGGG-TTT-GAAT-C
4617657 TAAGGTTTTG
1 TAAGGTTTTG
4617667 TTTTAAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
30 3 0.08
31 5 0.14
32 20 0.54
33 6 0.16
34 3 0.08
ACGTcount: A:0.24, C:0.03, G:0.28, T:0.45
Consensus pattern (30 bp):
TAAGGTTTTGGATTTTAGAGGGTTTGAATC
Found at i:4617912 original size:3 final size:3
Alignment explanation
Indices: 4617904--4617933 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
4617894 AGTAATAAAA
4617904 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
4617934 TTAAGCATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:4619210 original size:18 final size:18
Alignment explanation
Indices: 4619189--4619227 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
4619179 TTAACGTATT
* * *
4619189 AATATTAAATTGAAATGA
1 AATAATAAATTCAAATAA
4619207 AATAATAAATTCAAATAA
1 AATAATAAATTCAAATAA
4619225 AAT
1 AAT
4619228 CGGTGTCTAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.31
Consensus pattern (18 bp):
AATAATAAATTCAAATAA
Found at i:4619775 original size:17 final size:16
Alignment explanation
Indices: 4619736--4619792 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 16
4619726 TTTTAATTTA
*
4619736 TATTTAAAT-AAATTCT
1 TATTTAAATAAAAGT-T
4619752 TACTTTAAATAAAAGATT
1 TA-TTTAAATAAAAG-TT
**
4619770 TATTTATTTAAAAGTT
1 TATTTAAATAAAAGTT
4619786 TATTTAA
1 TATTTAA
4619793 TTGTAAATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
16 10 0.29
17 17 0.50
18 6 0.18
19 1 0.03
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.49
Consensus pattern (16 bp):
TATTTAAATAAAAGTT
Found at i:4619818 original size:30 final size:29
Alignment explanation
Indices: 4619784--4619880 Score: 94
Period size: 30 Copynumber: 3.3 Consensus size: 29
4619774 TATTTAAAAG
4619784 TTTATTTAATTGTAAATTAAAGATTAAGTA
1 TTTATTTAATTGTAAATTAAA-ATTAAGTA
* * *
4619814 TTTATTTGATTATAAATTATAAATTATA-AA
1 TTTATTTAATTGTAAATTA-AAATTA-AGTA
4619844 TTTATTTGAA-TGT-AA-TAAAATATAAGTA
1 TTTATTT-AATTGTAAATTAAAAT-TAAGTA
4619872 TTTATTTAA
1 TTTATTTAA
4619881 ATAAAATGAT
Statistics
Matches: 56, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
27 7 0.12
28 12 0.21
29 2 0.04
30 31 0.55
31 4 0.07
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (29 bp):
TTTATTTAATTGTAAATTAAAATTAAGTA
Found at i:4620303 original size:9 final size:9
Alignment explanation
Indices: 4620291--4620320 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
4620281 CATATTTTAT
4620291 TAATTAAAA
1 TAATTAAAA
4620300 TAATTAAAA
1 TAATTAAAA
4620309 TATATTAAAA
1 TA-ATTAAAA
4620319 TA
1 TA
4620321 TAAAAATTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
TAATTAAAA
Found at i:4620317 original size:10 final size:10
Alignment explanation
Indices: 4620293--4620322 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
4620283 TATTTTATTA
4620293 ATTAAAATA-
1 ATTAAAATAT
4620302 ATTAAAATAT
1 ATTAAAATAT
4620312 ATTAAAATAT
1 ATTAAAATAT
4620322 A
1 A
4620323 AAAATTCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
ATTAAAATAT
Found at i:4621163 original size:18 final size:19
Alignment explanation
Indices: 4621140--4621183 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
4621130 TGTGAAAATT
4621140 TAAAAAAAA-TAAAAATCA
1 TAAAAAAAATTAAAAATCA
* *
4621158 TAAAAAAAATTTAAAATCG
1 TAAAAAAAATTAAAAATCA
4621177 TAAAAAA
1 TAAAAAA
4621184 TTTTGAGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.20
Consensus pattern (19 bp):
TAAAAAAAATTAAAAATCA
Found at i:4623757 original size:23 final size:23
Alignment explanation
Indices: 4623727--4623776 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
4623717 TTTCATAATG
4623727 AAATCACAAGTGATGATTTTCTT
1 AAATCACAAGTGATGATTTTCTT
4623750 AAATCACAAGTGATGATTTTCTT
1 AAATCACAAGTGATGATTTTCTT
4623773 AAAT
1 AAAT
4623777 GAAAAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (23 bp):
AAATCACAAGTGATGATTTTCTT
Found at i:4624406 original size:186 final size:186
Alignment explanation
Indices: 4624103--4624438 Score: 448
Period size: 186 Copynumber: 1.8 Consensus size: 186
4624093 TTGAAGATGA
* * *
4624103 AATTAAGAGAAAATAACAATTAGTGAATTTCTTGACTATTTTTAGGTAATGAATTTTTCTTAAAT
1 AATTAAGAGAAAATAACAAGTAGTGAATTTCTTGACTATTTTTAGATAATGAATTTTTCTAAAAT
* * * * *
4624168 TTTATCAAAAGTGTTTAGAGGATTTTGGAAAATTTTCATTAAAAGAAAATTTTATTTATTTTCTC
66 TTGATCAAAAGTGTTGAGAAGATTTTGGAAAATCTTCAATAAAAGAAAATTTTATTTATTTTCTC
*
4624233 A-TAACATTTAATATTTAATATTTAATAAATTTATAAGTAAGAACCTCTAATAATAG
131 ATTAA-ATTTAATAATTAATATTTAATAAATTTATAAGTAAGAACCTCTAATAATAG
* * * *
4624289 AATTAAGAGAAAATCATAAGTGGTGAATTTCTTGAC-ATTTTTTAGATGAA-GGATTGTTTCTAA
1 AATTAAGAGAAAATAACAAGTAGTGAATTTCTTGACTA-TTTTTAGAT-AATGAATT-TTTCTAA
* * *
4624352 AATTTGATCAAAATTGTTGGGAAGATTTT-GAGAAATCTTCAATAAAA-TAAATTTTATTTATTT
63 AATTTGATCAAAAGTGTTGAGAAGATTTTGGA-AAATCTTCAATAAAAGAAAATTTTATTTATTT
4624415 TCTCATTAAATTTAATAATTAATA
127 TCTCATTAAATTTAATAATTAATA
4624439 AGTTAGTAAA
Statistics
Matches: 129, Mismatches: 16, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
185 1 0.01
186 80 0.62
187 48 0.37
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.42
Consensus pattern (186 bp):
AATTAAGAGAAAATAACAAGTAGTGAATTTCTTGACTATTTTTAGATAATGAATTTTTCTAAAAT
TTGATCAAAAGTGTTGAGAAGATTTTGGAAAATCTTCAATAAAAGAAAATTTTATTTATTTTCTC
ATTAAATTTAATAATTAATATTTAATAAATTTATAAGTAAGAACCTCTAATAATAG
Found at i:4625273 original size:25 final size:25
Alignment explanation
Indices: 4625240--4625287 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
4625230 CATTGAAAAT
*
4625240 AATGGGTTTGGATGTTGAACTTTTC
1 AATGCGTTTGGATGTTGAACTTTTC
4625265 AATGCGTTTGGATGTTGAACTTT
1 AATGCGTTTGGATGTTGAACTTT
4625288 CTGATCAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.21, C:0.08, G:0.27, T:0.44
Consensus pattern (25 bp):
AATGCGTTTGGATGTTGAACTTTTC
Found at i:4628408 original size:30 final size:31
Alignment explanation
Indices: 4628372--4628434 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 31
4628362 ATCTTATATT
*
4628372 AAAATTAATTTTAAAATATAAATA-TTATAC
1 AAAATTAATTCTAAAATATAAATATTTATAC
* * *
4628402 AAAATTAATTCTGATATATAAGTATTTATAC
1 AAAATTAATTCTAAAATATAAATATTTATAC
4628433 AA
1 AA
4628435 TATCTTCAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 20 0.71
31 8 0.29
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (31 bp):
AAAATTAATTCTAAAATATAAATATTTATAC
Found at i:4637895 original size:8 final size:7
Alignment explanation
Indices: 4637882--4638204 Score: 100
Period size: 7 Copynumber: 45.4 Consensus size: 7
4637872 AAAACCAATC
4637882 AAACCCAT
1 AAACCC-T
4637890 AAACCCT
1 AAACCCT
*
4637897 AAAACC-
1 AAACCCT
*
4637903 -AACCAT
1 AAACCCT
*
4637909 AAACCTT
1 AAACCCT
4637916 AAACCCT
1 AAACCCT
*
4637923 AAA--AT
1 AAACCCT
4637928 AAACCCT
1 AAACCCT
4637935 AAACCCT
1 AAACCCT
*
4637942 AAAACC-
1 AAACCCT
*
4637948 AAAGCC-
1 AAACCCT
* *
4637954 AAAACCA
1 AAACCCT
4637961 AAACCCT
1 AAACCCT
4637968 AAACCCT
1 AAACCCT
4637975 AAAACCAACAT
1 -AAACC--C-T
*
4637986 CAAACCTT
1 -AAACCCT
* *
4637994 AAAACCA
1 AAACCCT
4638001 AAACCCT
1 AAACCCT
4638008 AAA-CCT
1 AAACCCT
*
4638014 -AACCTT
1 AAACCCT
*
4638020 AAAGCCT
1 AAACCCT
*
4638027 AAAACC-
1 AAACCCT
4638033 -AA-CCT
1 AAACCCT
4638038 CAAACCCT
1 -AAACCCT
** *
4638046 AAAATCA
1 AAACCCT
* *
4638053 AAATCAT
1 AAACCCT
4638060 AAACCCT
1 AAACCCT
4638067 AAACCAATCT
1 AAACC---CT
4638077 AAACCCT
1 AAACCCT
4638084 AAA-CC-
1 AAACCCT
4638089 AAACCCT
1 AAACCCT
*
4638096 AAACCTT
1 AAACCCT
*
4638103 AAAACC-
1 AAACCCT
*
4638109 -AACCCC
1 AAACCCT
4638115 AAACACCTT
1 AAAC-CC-T
4638124 AAACCCT
1 AAACCCT
*
4638131 AAAACCT
1 AAACCCT
4638138 AAAACCAATCT
1 -AAACC---CT
*
4638149 AAACCTTAT
1 AAACC--CT
*
4638158 AACAACCCC
1 -A-AACCCT
*
4638167 AAACCCC
1 AAACCCT
*
4638174 AAAACCT
1 AAACCCT
*
4638181 AAACCTT
1 AAACCCT
4638188 AAACCCT
1 AAACCCT
*
4638195 AAACACT
1 AAACCCT
4638202 AAA
1 AAA
4638205 AGATGTCGCT
Statistics
Matches: 236, Mismatches: 49, Indels: 61
0.68 0.14 0.18
Matches are distributed among these distances:
4 2 0.01
5 18 0.08
6 19 0.08
7 141 0.60
8 24 0.10
9 6 0.03
10 14 0.06
11 12 0.05
ACGTcount: A:0.50, C:0.35, G:0.01, T:0.14
Consensus pattern (7 bp):
AAACCCT
Found at i:4637910 original size:19 final size:19
Alignment explanation
Indices: 4637886--4638197 Score: 117
Period size: 19 Copynumber: 16.7 Consensus size: 19
4637876 CCAATCAAAC
4637886 CCATAAACCCTAAAACCAA
1 CCATAAACCCTAAAACCAA
* *
4637905 CCATAAACCTTAAACCCTAA
1 CCATAAACCCTAAAACC-AA
* *
4637925 -AATAAACCCTAAACCCTAAAA
1 CCATAAACCCTAAAACC---AA
*
4637946 CC--AAAGCC-AAAACCAAAA
1 CCATAAACCCTAAAACC--AA
*
4637964 CCCTAAACCCTAAAACCAA
1 CCATAAACCCTAAAACCAA
*
4637983 -CATCAAA-CCT-TAA--AA
1 CCAT-AAACCCTAAAACCAA
4637998 CCA-AAACCCT-AAACCTAA
1 CCATAAACCCTAAAACC-AA
* *
4638016 CCTTAAAGCCTAAAACCAA
1 CCATAAACCCTAAAACCAA
*
4638035 CC-TCAAACCCTAAAATCAAAA
1 CCAT-AAACCCTAAAA-C-CAA
*
4638056 TCATAAACCCT-AAACCAA
1 CCATAAACCCTAAAACCAA
*
4638074 TC-TAAACCCT-AAACCAAA
1 CCATAAACCCTAAAACC-AA
* *
4638092 CCCTAAACCTTAAAACCAA
1 CCATAAACCCTAAAACCAA
** *
4638111 CCCCAAACACCTTAAA-C--
1 CCATAAAC-CCTAAAACCAA
*
4638128 CC-TAAAACCTAAAACCAA
1 CCATAAACCCTAAAACCAA
* * *
4638146 TC-TAAACCTTATAA-CAA
1 CCATAAACCCTAAAACCAA
** *
4638163 CCCCAAACCCCAAAACCTAAA
1 CCATAAACCCTAAAACC--AA
*
4638184 CCTTAAACCCTAAA
1 CCATAAACCCTAAA
4638198 CACTAAAAGA
Statistics
Matches: 225, Mismatches: 38, Indels: 58
0.70 0.12 0.18
Matches are distributed among these distances:
14 3 0.01
15 13 0.06
16 6 0.03
17 21 0.09
18 41 0.18
19 78 0.35
20 31 0.14
21 31 0.14
22 1 0.00
ACGTcount: A:0.50, C:0.35, G:0.01, T:0.14
Consensus pattern (19 bp):
CCATAAACCCTAAAACCAA
Found at i:4637975 original size:40 final size:39
Alignment explanation
Indices: 4637882--4638012 Score: 112
Period size: 40 Copynumber: 3.3 Consensus size: 39
4637872 AAAACCAATC
*
4637882 AAACCCATAAACCCTAAAACC--AACCATAAACCTTAAACCCTA
1 AAACCC-TAAACCCTAAAACCAAAACC--AAACC-TAAAACC-A
*
4637924 AAA---TAAACCCTAAACCCTAAAACCAAAGCC-AAAACCA
1 AAACCCTAAACCCTAAAACC-AAAACCAAA-CCTAAAACCA
* *
4637961 AAACCCTAAACCCTAAAACCAACATCAAACCTTAAAACCA
1 AAACCCTAAACCCTAAAACCAAAACCAAACC-TAAAACCA
4638001 AAACCCTAAACC
1 AAACCCTAAACC
4638013 TAACCTTAAA
Statistics
Matches: 75, Mismatches: 5, Indels: 20
0.75 0.05 0.20
Matches are distributed among these distances:
37 4 0.05
38 20 0.27
39 10 0.13
40 34 0.45
41 4 0.05
42 3 0.04
ACGTcount: A:0.53, C:0.35, G:0.01, T:0.11
Consensus pattern (39 bp):
AAACCCTAAACCCTAAAACCAAAACCAAACCTAAAACCA
Found at i:4637977 original size:52 final size:52
Alignment explanation
Indices: 4637903--4638197 Score: 184
Period size: 52 Copynumber: 5.4 Consensus size: 52
4637893 CCCTAAAACC
* * *
4637903 AACCATAAACCTTAAACCCTAAAATAAACC-CTAAACCCTAAAACCAAAGCCAA
1 AACCA-AAACCCTAAACCCTAAAACAAACCTC-AAACCCTAAAACCAAACCCAA
* * * *
4637956 AACCAAAACCCTAAACCCTAAAACCAACATCAAACCTTAAAACCAAAACCCTA
1 AACCAAAACCCTAAACCCTAAAACAAACCTCAAACCCTAAAACC-AAACCCAA
* * * * * **
4638009 AACC-TAACCTTAAAGCCTAAAACCAACCTCAAACCCTAAAATCAAAATCATA
1 AACCAAAACCCTAAACCCTAAAACAAACCTCAAACCCTAAAACCAAACCCA-A
* * * *
4638061 AACCCTAAACCAATCTAAACCCTAAACCAAACC-CTAAACCTTAAAACCAACCCCAA
1 AA-CCAAAACC---CTAAACCCTAAAACAAACCTC-AAACCCTAAAACCAAACCCAA
* * * * *
4638117 ACACCTTAAACCCTAAAACCTAAAACCAATCT-AAACCTTATAACAACCCCAAACCCCAA
1 A-ACC-AAAACCCTAAACCCTAAAACAAACCTCAAACC--CTAA-AA--CCAAA-CCCAA
* *
4638176 AACCTAAACCTTAAACCCTAAA
1 AACCAAAACCCTAAACCCTAAA
4638198 CACTAAAAGA
Statistics
Matches: 190, Mismatches: 34, Indels: 32
0.74 0.13 0.12
Matches are distributed among these distances:
51 4 0.02
52 68 0.36
53 23 0.12
54 19 0.10
55 3 0.02
56 7 0.04
57 53 0.28
58 7 0.04
59 6 0.03
ACGTcount: A:0.50, C:0.35, G:0.01, T:0.14
Consensus pattern (52 bp):
AACCAAAACCCTAAACCCTAAAACAAACCTCAAACCCTAAAACCAAACCCAA
Found at i:4638034 original size:33 final size:33
Alignment explanation
Indices: 4637935--4638010 Score: 86
Period size: 33 Copynumber: 2.3 Consensus size: 33
4637925 AATAAACCCT
* *
4637935 AAACCCTAAAACCAA-AGCCAAAACC--AAAACCCT
1 AAACCCTAAAACCAACA-TC-AAACCTTAAAA-CCA
4637968 AAACCCTAAAACCAACATCAAACCTTAAAACCA
1 AAACCCTAAAACCAACATCAAACCTTAAAACCA
4638001 AAACCCTAAA
1 AAACCCTAAA
4638011 CCTAACCTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
32 5 0.13
33 28 0.74
34 5 0.13
ACGTcount: A:0.55, C:0.34, G:0.01, T:0.09
Consensus pattern (33 bp):
AAACCCTAAAACCAACATCAAACCTTAAAACCA
Found at i:4638043 original size:26 final size:26
Alignment explanation
Indices: 4637871--4638136 Score: 139
Period size: 26 Copynumber: 10.3 Consensus size: 26
4637861 CCCCAATCCT
4637871 TAAAACCAA--TCAAACCCATAAACCC
1 TAAAACCAACCTCAAACCC-TAAACCC
*
4637896 TAAAACCAACCAT-AAACCTTAAACCC
1 TAAAACCAACC-TCAAACCCTAAACCC
** *
4637922 TAAAATAAACC-CTAAACCCTAAAACC
1 TAAAACCAACCTC-AAACCCTAAACCC
* *
4637948 -AAAGCCAAAACC-AAAACCCTAAACCC
1 TAAAACC--AACCTCAAACCCTAAACCC
* * *
4637974 TAAAACCAACATCAAACCTTAAAACC
1 TAAAACCAACCTCAAACCCTAAACCC
* *
4638000 -AAAACCCTAAACCT--AACCTTAAAGCC
1 TAAAA-CC--AACCTCAAACCCTAAACCC
**
4638026 TAAAACCAACCTCAAACCCTAAAATC
1 TAAAACCAACCTCAAACCCTAAACCC
*
4638052 -AAAATC-A--T-AAACCCTAAACCAATC
1 TAAAACCAACCTCAAACCCTAAACC---C
* * *
4638076 TAAACCCTAAAC-CAAACCCTAAACCT
1 TAAAACC-AACCTCAAACCCTAAACCC
*
4638102 TAAAACCAACCCCAAACACCTTAAACCC
1 TAAAACCAACCTCAAAC-CC-TAAACCC
4638130 TAAAACC
1 TAAAACC
4638137 TAAAACCAAT
Statistics
Matches: 185, Mismatches: 29, Indels: 51
0.70 0.11 0.19
Matches are distributed among these distances:
21 10 0.05
22 1 0.01
24 7 0.04
25 31 0.17
26 85 0.46
27 21 0.11
28 18 0.10
29 12 0.06
ACGTcount: A:0.51, C:0.35, G:0.01, T:0.14
Consensus pattern (26 bp):
TAAAACCAACCTCAAACCCTAAACCC
Found at i:4638124 original size:21 final size:20
Alignment explanation
Indices: 4638084--4638126 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
4638074 TCTAAACCCT
*
4638084 AAACCAAACCCTAAACCTTA
1 AAACCAAACCCAAAACCTTA
*
4638104 AAACCAACCCCAAACACCTTA
1 AAACCAAACCCAAA-ACCTTA
4638125 AA
1 AA
4638127 CCCTAAAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.51, C:0.37, G:0.00, T:0.12
Consensus pattern (20 bp):
AAACCAAACCCAAAACCTTA
Found at i:4638164 original size:128 final size:129
Alignment explanation
Indices: 4637955--4638198 Score: 293
Period size: 128 Copynumber: 1.9 Consensus size: 129
4637945 ACCAAAGCCA
*
4637955 AAACCAAAACCCTAAACCCTAAAACCAACATCAAACCTTAAAACCAAAACCCTAAACCTAACCTT
1 AAACCAAAACCCTAAACCCTAAAACCAACACCAAACCTTAAAACCAAAACCCTAAACCTAACCTT
* * * *
4638020 AAAGCCTAAAACCAACCTCAAACCCTAAAATCAAAATCATAAACCCTAAACCAATCTAAACCCT
66 AAAGCCTAAAACCAACCCCAAACCCCAAAACCAAAACCATAAACCCTAAACCAATCTAAACCCT
* * *
4638084 AAACC-AAACCCTAAACCTTAAAACCAACCCCAAACACCTTAAACCCTAAAA-CCTAAAACC-AA
1 AAACCAAAACCCTAAACCCTAAAACCAACACC-AA-ACCTTAAAACC-AAAACCCT-AAACCTAA
* * * *
4638146 TC-TAAA-CCTTATAA-CAACCCCAAACCCCAAAACCTAAACCTTAAACCCTAAAC
62 CCTTAAAGCC-TAAAACCAACCCCAAACCCCAAAACCAAAACCATAAACCCTAAAC
4638199 ACTAAAAGAT
Statistics
Matches: 98, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
128 58 0.59
129 15 0.15
130 16 0.16
131 9 0.09
ACGTcount: A:0.50, C:0.36, G:0.00, T:0.14
Consensus pattern (129 bp):
AAACCAAAACCCTAAACCCTAAAACCAACACCAAACCTTAAAACCAAAACCCTAAACCTAACCTT
AAAGCCTAAAACCAACCCCAAACCCCAAAACCAAAACCATAAACCCTAAACCAATCTAAACCCT
Found at i:4638204 original size:14 final size:14
Alignment explanation
Indices: 4638059--4638105 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 14
4638049 ATCAAAATCA
4638059 TAAACCCTAAACCAAT
1 TAAACCCTAAACC--T
4638075 CTAAACCCTAAACC-
1 -TAAACCCTAAACCT
4638089 -AAACCCTAAACCT
1 TAAACCCTAAACCT
4638102 TAAA
1 TAAA
4638106 ACCAACCCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
12 12 0.43
14 3 0.11
17 13 0.46
ACGTcount: A:0.49, C:0.34, G:0.00, T:0.17
Consensus pattern (14 bp):
TAAACCCTAAACCT
Found at i:4646154 original size:160 final size:160
Alignment explanation
Indices: 4645760--4646223 Score: 765
Period size: 156 Copynumber: 2.9 Consensus size: 160
4645750 TTAAAATTTT
* * * *
4645760 ACCAAGTAGTTAGTTGTTGAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGA
1 ACCAAGTAATTAATTATCGAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGA
*
4645825 AAATTCCCTCACCTCAAGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCG
66 AAATTCCCTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCG
* *
4645890 GATTATTTAAAG----AAAAATCAAGATCA
131 GATTAATTAAAGAAAAAAAAATCAAAATCA
* *
4645916 ACCAATTAATTAATTATCGAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAAA
1 ACCAAGTAATTAATTATCGAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGA
*
4645981 AAATTCTCTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCG
66 AAATTCCCTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCG
4646046 GATTAATTAAAGAAAAAAAAATCAAAATCA
131 GATTAATTAAAGAAAAAAAAATCAAAATCA
* *
4646076 GCCAAGTAATTAATTATCGGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGA
1 ACCAAGTAATTAATTATCGAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGA
* *
4646141 AAATTCCCTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTTTACTTGTAGAGGCTCCGTCGTC
66 AAATTCCCTCACCTCAGGAGTATGCAAGAAAAACTACTG-TTTCACTTGCAGAGGCTCCGTCGTC
4646206 GGATTAATTAAAGAAAAA
130 GGATTAATTAAAGAAAAA
4646224 GGAAAAAAAA
Statistics
Matches: 286, Mismatches: 17, Indels: 5
0.93 0.06 0.02
Matches are distributed among these distances:
156 133 0.47
160 112 0.39
161 41 0.14
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (160 bp):
ACCAAGTAATTAATTATCGAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGA
AAATTCCCTCACCTCAGGAGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCG
GATTAATTAAAGAAAAAAAAATCAAAATCA
Found at i:4646261 original size:1 final size:1
Alignment explanation
Indices: 4646255--4646279 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
4646245 AATCAAAGTC
4646255 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
4646280 CCTGGAGCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:4646318 original size:15 final size:16
Alignment explanation
Indices: 4646287--4646341 Score: 69
Period size: 15 Copynumber: 3.5 Consensus size: 16
4646277 AAACCTGGAG
*
4646287 CGGCTCGGATCGCGGCT
1 CGGCTCGGCT-GCGGCT
*
4646304 CGGCTTGG-TGCGGCT
1 CGGCTCGGCTGCGGCT
4646319 CGGCTCGGCT-CGGCT
1 CGGCTCGGCTGCGGCT
4646334 CGGCTCGG
1 CGGCTCGG
4646342 AGGGGCTGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
15 26 0.74
16 2 0.06
17 7 0.20
ACGTcount: A:0.02, C:0.35, G:0.44, T:0.20
Consensus pattern (16 bp):
CGGCTCGGCTGCGGCT
Found at i:4646322 original size:5 final size:5
Alignment explanation
Indices: 4646299--4646341 Score: 61
Period size: 5 Copynumber: 8.6 Consensus size: 5
4646289 GCTCGGATCG
*
4646299 CGGCT CGGCT TGG-T GCGGCT CGGCT CGGCT CGGCT CGGCT CGG
1 CGGCT CGGCT CGGCT -CGGCT CGGCT CGGCT CGGCT CGGCT CGG
4646342 AGGGGCTGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 1 0.03
5 32 0.94
6 1 0.03
ACGTcount: A:0.00, C:0.35, G:0.44, T:0.21
Consensus pattern (5 bp):
CGGCT
Found at i:4646348 original size:15 final size:15
Alignment explanation
Indices: 4646287--4646348 Score: 61
Period size: 15 Copynumber: 4.0 Consensus size: 15
4646277 AAACCTGGAG
4646287 CGGCTCGGATCGCGGCT
1 CGGCTCGGA--GCGGCT
* *
4646304 CGGCTTGGTGCGGCT
1 CGGCTCGGAGCGGCT
**
4646319 CGGCTCGGCTCGGCT
1 CGGCTCGGAGCGGCT
*
4646334 CGGCTCGGAGGGGCT
1 CGGCTCGGAGCGGCT
4646349 GAAACGCGCG
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
15 30 0.81
17 7 0.19
ACGTcount: A:0.03, C:0.32, G:0.45, T:0.19
Consensus pattern (15 bp):
CGGCTCGGAGCGGCT
Found at i:4646590 original size:19 final size:19
Alignment explanation
Indices: 4646562--4646605 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
4646552 AACGCCGGTA
*
4646562 CCGGATTCTGGAAATTTCG
1 CCGGAATCTGGAAATTTCG
* *
4646581 TCGGAATCTGGGAATTTCG
1 CCGGAATCTGGAAATTTCG
4646600 CCGGAA
1 CCGGAA
4646606 ATTGGCCGGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (19 bp):
CCGGAATCTGGAAATTTCG
Found at i:4646715 original size:31 final size:31
Alignment explanation
Indices: 4646667--4646739 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
4646657 AAACTGGGTC
* * *
4646667 TGTCACCGGAAACTTC-AAAGTTCGTCGGAAT
1 TGTCGCCGGAAAATTCAAAAG-TCGCCGGAAT
4646698 TGTCGCCGGAAAATTCAAAAGTCGCCGGAAT
1 TGTCGCCGGAAAATTCAAAAGTCGCCGGAAT
* *
4646729 TTTCGTCGGAA
1 TGTCGCCGGAA
4646740 TCTGGAAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
31 32 0.89
32 4 0.11
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.25
Consensus pattern (31 bp):
TGTCGCCGGAAAATTCAAAAGTCGCCGGAAT
Found at i:4647072 original size:12 final size:12
Alignment explanation
Indices: 4647055--4647086 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
4647045 CTAGCCCTCC
4647055 AAAATAAAAATT
1 AAAATAAAAATT
4647067 AAAAT-AAAATT
1 AAAATAAAAATT
4647078 AAAA-AAAAA
1 AAAATAAAAA
4647087 AAATCTAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 14 0.74
12 5 0.26
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (12 bp):
AAAATAAAAATT
Found at i:4647335 original size:18 final size:18
Alignment explanation
Indices: 4647314--4647348 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
4647304 CACAAGAGAG
4647314 AAAAA-AAAATAATAAAAT
1 AAAAATAAAA-AATAAAAT
4647332 AAAAATAAAAAATAAAA
1 AAAAATAAAAAATAAAA
4647349 AATACGGGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (18 bp):
AAAAATAAAAAATAAAAT
Found at i:4647344 original size:7 final size:7
Alignment explanation
Indices: 4647317--4647352 Score: 56
Period size: 7 Copynumber: 5.1 Consensus size: 7
4647307 AAGAGAGAAA
4647317 AAAAAAT
1 AAAAAAT
4647324 AATAAAAT
1 AA-AAAAT
4647332 -AAAAAT
1 AAAAAAT
4647338 AAAAAAT
1 AAAAAAT
4647345 AAAAAAT
1 AAAAAAT
4647352 A
1 A
4647353 CGGGTAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 5 0.19
7 17 0.63
8 5 0.19
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (7 bp):
AAAAAAT
Found at i:4647407 original size:20 final size:20
Alignment explanation
Indices: 4647385--4647449 Score: 85
Period size: 20 Copynumber: 3.2 Consensus size: 20
4647375 TTGCCCATTT
* *
4647385 GGGCCAGGCCCAAATGATCT
1 GGGCCAGGCCCAATTGATCC
*
4647405 GGGTCAGGCCCAATTGATCC
1 GGGCCAGGCCCAATTGATCC
* *
4647425 GGGTCAAGCCCAATTGATCC
1 GGGCCAGGCCCAATTGATCC
4647445 GGGCC
1 GGGCC
4647450 CGGACCTGAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.22, C:0.31, G:0.31, T:0.17
Consensus pattern (20 bp):
GGGCCAGGCCCAATTGATCC
Found at i:4648904 original size:23 final size:23
Alignment explanation
Indices: 4648874--4648923 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
4648864 TTTCATAATG
4648874 AAATCACAAGTGATGATTTTCTT
1 AAATCACAAGTGATGATTTTCTT
4648897 AAATCACAAGTGATGATTTTCTT
1 AAATCACAAGTGATGATTTTCTT
4648920 AAAT
1 AAAT
4648924 GAAAAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (23 bp):
AAATCACAAGTGATGATTTTCTT
Found at i:4650500 original size:25 final size:25
Alignment explanation
Indices: 4650467--4650514 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
4650457 CATTGAAAAT
*
4650467 AATGGGTTTGGATGTTGAACTTTTC
1 AATGCGTTTGGATGTTGAACTTTTC
4650492 AATGCGTTTGGATGTTGAACTTT
1 AATGCGTTTGGATGTTGAACTTT
4650515 CTGATCAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.21, C:0.08, G:0.27, T:0.44
Consensus pattern (25 bp):
AATGCGTTTGGATGTTGAACTTTTC
Found at i:4650767 original size:163 final size:163
Alignment explanation
Indices: 4650497--4650826 Score: 633
Period size: 163 Copynumber: 2.0 Consensus size: 163
4650487 TTTTCAATGC
* *
4650497 GTTTGGATGTTGAACTTTCTGATCAAAGCAAGTCATCAAGCCAATAGGAATGTTACTTGACTGTG
1 GTTTGGATGTTGAACTTTCTGATCAAAGCAAGTCATCAAACCAATAGGAAAGTTACTTGACTGTG
*
4650562 CTTTGGATGCTCTGCTCAAACCCAATCCAGTTTTATCATGATTTTGTCTGCAGTTTTTCTACAGC
66 CTTTGGATGCTCTGCTCAAACCCAATCAAGTTTTATCATGATTTTGTCTGCAGTTTTTCTACAGC
4650627 TCTTGCCACTACTGCTTCTCGACTGGCTGGTGG
131 TCTTGCCACTACTGCTTCTCGACTGGCTGGTGG
4650660 GTTTGGATGTTGAACTTTCTGATCAAAGCAAGTCATCAAACCAATAGGAAAGTTACTTGACTGTG
1 GTTTGGATGTTGAACTTTCTGATCAAAGCAAGTCATCAAACCAATAGGAAAGTTACTTGACTGTG
4650725 CTTTGGATGCTCTGCTCAAACCCAATCAAGTTTTATCATGATTTTGTCTGCAGTTTTTCTACAGC
66 CTTTGGATGCTCTGCTCAAACCCAATCAAGTTTTATCATGATTTTGTCTGCAGTTTTTCTACAGC
4650790 TCTTGCCACTACTGCTTCTCGACTGGCTGGTGG
131 TCTTGCCACTACTGCTTCTCGACTGGCTGGTGG
4650823 GTTT
1 GTTT
4650827 TGTGAACAGC
Statistics
Matches: 164, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
163 164 1.00
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.36
Consensus pattern (163 bp):
GTTTGGATGTTGAACTTTCTGATCAAAGCAAGTCATCAAACCAATAGGAAAGTTACTTGACTGTG
CTTTGGATGCTCTGCTCAAACCCAATCAAGTTTTATCATGATTTTGTCTGCAGTTTTTCTACAGC
TCTTGCCACTACTGCTTCTCGACTGGCTGGTGG
Found at i:4653527 original size:31 final size:30
Alignment explanation
Indices: 4653451--4653527 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
4653441 GAGAGATATC
* * *
4653451 ATAAATCTTATATTAAAATTAATTTTAAAAT
1 ATAAATATTATA-CAAAATTAATTCTAAAAT
* *
4653482 ATAAATATTATACAAAATTAATTCTGATAT
1 ATAAATATTATACAAAATTAATTCTAAAAT
*
4653512 ATAAGTATTTATACAA
1 ATAAATA-TTATACAA
4653528 TATCTTCAAC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 20 0.51
31 19 0.49
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.42
Consensus pattern (30 bp):
ATAAATATTATACAAAATTAATTCTAAAAT
Found at i:4659681 original size:2 final size:2
Alignment explanation
Indices: 4659674--4659702 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4659664 AGCCTCATGA
4659674 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4659703 ATTGCCTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4662982 original size:7 final size:7
Alignment explanation
Indices: 4662970--4663167 Score: 52
Period size: 7 Copynumber: 28.7 Consensus size: 7
4662960 ACCTACTCTT
4662970 AAACCTA
1 AAACCTA
4662977 AAACCTA
1 AAACCTA
*
4662984 AAATCTA
1 AAACCTA
*
4662991 AATCCTA
1 AAACCTA
4662998 ACCCAATCCTTA
1 A---AA-CC-TA
4663010 AAACCAATCA
1 AAACC--T-A
*
4663020 AACCCATA
1 AAACC-TA
*
4663028 AACCCTA
1 AAACCTA
4663035 AAACC--
1 AAACCTA
4663040 -AACCATA
1 AAACC-TA
4663047 A-ACCTTA
1 AAACC-TA
*
4663054 AACCCTA
1 AAACCTA
4663061 AAA--TA
1 AAACCTA
4663066 A-ACCTA
1 AAACCTA
*
4663072 AACCCTA
1 AAACCTA
4663079 AAACC-A
1 AAACCTA
*
4663085 AAGCC-A
1 AAACCTA
4663091 AAACC-A
1 AAACCTA
4663097 AAACCCT-
1 AAA-CCTA
4663104 AAACCTA
1 AAACCTA
4663111 AAACC--
1 AAACCTA
* *
4663116 -AACATC
1 AAACCTA
4663122 AAACCTTA
1 AAACC-TA
*
4663130 AAACCAA
1 AAACCTA
4663137 AAACCT-
1 AAACCTA
4663143 AAACCT-
1 AAACCTA
4663149 -AACCTTA
1 AAACC-TA
*
4663156 AAGCCTA
1 AAACCTA
4663163 AAACC
1 AAACC
4663168 AACCTCAAAC
Statistics
Matches: 145, Mismatches: 21, Indels: 50
0.67 0.10 0.23
Matches are distributed among these distances:
4 8 0.06
5 7 0.05
6 27 0.19
7 68 0.47
8 19 0.13
9 5 0.03
10 6 0.04
11 2 0.01
12 3 0.02
ACGTcount: A:0.52, C:0.32, G:0.01, T:0.15
Consensus pattern (7 bp):
AAACCTA
Found at i:4663032 original size:8 final size:7
Alignment explanation
Indices: 4663019--4663339 Score: 73
Period size: 7 Copynumber: 45.4 Consensus size: 7
4663009 AAAACCAATC
4663019 AAACCCAT
1 AAACCC-T
4663027 AAACCCT
1 AAACCCT
*
4663034 AAAACC-
1 AAACCCT
*
4663040 -AACCAT
1 AAACCCT
*
4663046 AAACCTT
1 AAACCCT
4663053 AAACCCT
1 AAACCCT
*
4663060 AAA--AT
1 AAACCCT
4663065 AAA-CCT
1 AAACCCT
4663071 AAACCCT
1 AAACCCT
*
4663078 AAAACC-
1 AAACCCT
*
4663084 AAAGCC-
1 AAACCCT
* *
4663090 AAAACCA
1 AAACCCT
4663097 AAACCCT
1 AAACCCT
4663104 AAA-CCT
1 AAACCCT
4663110 AAAACCAACAT
1 -AAACC--C-T
*
4663121 CAAACCTT
1 -AAACCCT
* *
4663129 AAAACCA
1 AAACCCT
*
4663136 AAAACCT
1 AAACCCT
4663143 AAA-CCT
1 AAACCCT
*
4663149 -AACCTT
1 AAACCCT
*
4663155 AAAGCCT
1 AAACCCT
*
4663162 AAAACC-
1 AAACCCT
4663168 -AA-CCT
1 AAACCCT
4663173 CAAACCCT
1 -AAACCCT
** *
4663181 AAAATCA
1 AAACCCT
* *
4663188 AAATCAT
1 AAACCCT
4663195 AAACCCT
1 AAACCCT
4663202 AAACCAATCT
1 AAACC---CT
4663212 AAACCCT
1 AAACCCT
4663219 AAA-CC-
1 AAACCCT
4663224 AAACCCT
1 AAACCCT
*
4663231 AAACCTT
1 AAACCCT
*
4663238 AAAACC-
1 AAACCCT
*
4663244 -AACCCC
1 AAACCCT
4663250 AAACACCTT
1 AAAC-CC-T
4663259 AAACCCT
1 AAACCCT
*
4663266 AAAACCT
1 AAACCCT
4663273 AAAACCAATCT
1 -AAACC---CT
*
4663284 AAACCTTAT
1 AAACC--CT
*
4663293 AACAACCCC
1 -A-AACCCT
*
4663302 AAACCCC
1 AAACCCT
*
4663309 AAAACCT
1 AAACCCT
*
4663316 AAACCTT
1 AAACCCT
4663323 AAACCCT
1 AAACCCT
*
4663330 AAACACT
1 AAACCCT
4663337 AAA
1 AAA
4663340 AGATGTCGCT
Statistics
Matches: 234, Mismatches: 48, Indels: 63
0.68 0.14 0.18
Matches are distributed among these distances:
4 2 0.01
5 18 0.08
6 26 0.11
7 136 0.58
8 20 0.09
9 6 0.03
10 14 0.06
11 12 0.05
ACGTcount: A:0.51, C:0.34, G:0.01, T:0.14
Consensus pattern (7 bp):
AAACCCT
Found at i:4663060 original size:26 final size:26
Alignment explanation
Indices: 4663008--4663291 Score: 126
Period size: 26 Copynumber: 10.8 Consensus size: 26
4662998 ACCCAATCCT
* * * *
4663008 TAAAACCAATCA-AACCCATAAACCC
1 TAAAACCAACCATAAACCTTAAAACC
*
4663033 TAAAACCAACCATAAACCTTAAACCC
1 TAAAACCAACCATAAACCTTAAAACC
** *
4663059 TAAAATAAACC-TAAACCCTAAAACC
1 TAAAACCAACCATAAACCTTAAAACC
* *
4663084 -AAAGCCAAAACCA-AAACCCT-AAACC
1 TAAAACC--AACCATAAACCTTAAAACC
4663109 TAAAACCAA-CATCAAACCTTAAAACC
1 TAAAACCAACCAT-AAACCTTAAAACC
* *
4663135 AAAAACCTAAACC-T-AACCTTAAAGCC
1 TAAAACC--AACCATAAACCTTAAAACC
* *
4663161 TAAAACCAACC-TCAAACCCTAAAATC
1 TAAAACCAACCAT-AAACCTTAAAACC
* * *
4663187 -AAAATCATAAACCCTAAACCAATCTAAACCC
1 TAAAA-C--CAACCATAAACC--T-TAAAACC
*
4663218 T-AAACCAAACCCTAAACCTTAAAACC
1 TAAAACC-AACCATAAACCTTAAAACC
** * *
4663244 -AACCCCAAACACCTTAAACCCTAAAACC
1 TAAAACC--A-ACCATAAACCTTAAAACC
*
4663272 TAAAACCAATC-TAAACCTTA
1 TAAAACCAACCATAAACCTTA
4663292 TAACAACCCC
Statistics
Matches: 201, Mismatches: 32, Indels: 52
0.71 0.11 0.18
Matches are distributed among these distances:
23 2 0.01
24 10 0.05
25 46 0.23
26 85 0.42
27 4 0.02
28 28 0.14
29 17 0.08
30 1 0.00
31 8 0.04
ACGTcount: A:0.51, C:0.33, G:0.01, T:0.14
Consensus pattern (26 bp):
TAAAACCAACCATAAACCTTAAAACC
Found at i:4663073 original size:18 final size:19
Alignment explanation
Indices: 4663044--4663081 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
4663034 AAAACCAACC
4663044 ATAAACCTTAAACCCTAAA
1 ATAAACCTTAAACCCTAAA
4663063 ATAAACC-TAAACCCTAAA
1 ATAAACCTTAAACCCTAAA
4663081 A
1 A
4663082 CCAAAGCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.55, C:0.26, G:0.00, T:0.18
Consensus pattern (19 bp):
ATAAACCTTAAACCCTAAA
Found at i:4663108 original size:39 final size:38
Alignment explanation
Indices: 4663064--4663150 Score: 104
Period size: 39 Copynumber: 2.2 Consensus size: 38
4663054 AACCCTAAAA
* *
4663064 TAAACCTAAACCCTAAAACCAAAGCC-AAAACCAAAACCC
1 TAAACCTAAAACC-AAAACCAAA-CCTAAAACCAAAAACC
* *
4663103 TAAACCTAAAACCAACATCAAACCTTAAAACCAAAAACC
1 TAAACCTAAAACCAAAACCAAACC-TAAAACCAAAAACC
4663142 TAAACCTAA
1 TAAACCTAA
4663151 CCTTAAAGCC
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
37 2 0.05
38 7 0.17
39 33 0.79
ACGTcount: A:0.55, C:0.32, G:0.01, T:0.11
Consensus pattern (38 bp):
TAAACCTAAAACCAAAACCAAACCTAAAACCAAAAACC
Found at i:4663216 original size:17 final size:18
Alignment explanation
Indices: 4663189--4663225 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
4663179 CTAAAATCAA
4663189 AATCATAAACCCTAAACC
1 AATCATAAACCCTAAACC
4663207 AATC-TAAACCCTAAACC
1 AATCATAAACCCTAAACC
4663224 AA
1 AA
4663226 ACCCTAAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.51, C:0.32, G:0.00, T:0.16
Consensus pattern (18 bp):
AATCATAAACCCTAAACC
Found at i:4663259 original size:21 final size:20
Alignment explanation
Indices: 4663219--4663261 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
4663209 TCTAAACCCT
*
4663219 AAACCAAACCCTAAACCTTA
1 AAACCAAACCCAAAACCTTA
*
4663239 AAACCAACCCCAAACACCTTA
1 AAACCAAACCCAAA-ACCTTA
4663260 AA
1 AA
4663262 CCCTAAAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.51, C:0.37, G:0.00, T:0.12
Consensus pattern (20 bp):
AAACCAAACCCAAAACCTTA
Found at i:4663299 original size:128 final size:128
Alignment explanation
Indices: 4663091--4663333 Score: 298
Period size: 128 Copynumber: 1.9 Consensus size: 128
4663081 ACCAAAGCCA
*
4663091 AAACCAAAACCCTAAACCTAAAACCAACATCAAACCTTAAAACCAAAAACCTAAACCTAACCTTA
1 AAACCAAAACCCTAAACCTAAAACCAACACCAAACCTTAAAACCAAAAACCTAAACCTAACCTTA
* * * *
4663156 AAGCCTAAAACCAACCTCAAACCCTAAAATCAAAATCATAAACCCTAAACCAATCTAAACCCT
66 AAGCCTAAAACCAACCCCAAACCCCAAAACCAAAACCATAAACCCTAAACCAATCTAAACCCT
* * * *
4663219 AAACC-AAACCCTAAACCTTAAAACCAACCCCAAACACCTTAAACCCTAAAACCTAAAACC-AAT
1 AAACCAAAACCCTAAACC-TAAAACCAACACC-AA-ACCTTAAAACCAAAAACCT-AAACCTAAC
* * *
4663282 C-TAAA-CCTTATAA-CAACCCCAAACCCCAAAACCTAAACCTTAAACCCTAAAC
62 CTTAAAGCC-TAAAACCAACCCCAAACCCCAAAACCAAAACCATAAACCCTAAAC
4663334 ACTAAAAGAT
Statistics
Matches: 98, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
127 12 0.12
128 51 0.52
129 10 0.10
130 20 0.20
131 5 0.05
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.14
Consensus pattern (128 bp):
AAACCAAAACCCTAAACCTAAAACCAACACCAAACCTTAAAACCAAAAACCTAAACCTAACCTTA
AAGCCTAAAACCAACCCCAAACCCCAAAACCAAAACCATAAACCCTAAACCAATCTAAACCCT
Found at i:4663339 original size:14 final size:14
Alignment explanation
Indices: 4663194--4663240 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 14
4663184 ATCAAAATCA
4663194 TAAACCCTAAACCAAT
1 TAAACCCTAAACC--T
4663210 CTAAACCCTAAACC-
1 -TAAACCCTAAACCT
4663224 -AAACCCTAAACCT
1 TAAACCCTAAACCT
4663237 TAAA
1 TAAA
4663241 ACCAACCCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
12 12 0.43
14 3 0.11
17 13 0.46
ACGTcount: A:0.49, C:0.34, G:0.00, T:0.17
Consensus pattern (14 bp):
TAAACCCTAAACCT
Found at i:4675302 original size:35 final size:35
Alignment explanation
Indices: 4675245--4675417 Score: 105
Period size: 35 Copynumber: 4.9 Consensus size: 35
4675235 TTTTTTTTTT
* * * *
4675245 ACTTGTGGTTCAATCCTGGTCATCTTTAGTTTCTA
1 ACTTATGGTTCAGTCCCGGTCATCTTTATTTTCTA
**** * * *
4675280 ACTTATGGTTCAGTTTTTGTCATTTTTATTTTTTT
1 ACTTATGGTTCAGTCCCGGTCATCTTTATTTTCTA
* * *
4675315 ACTTATAGTTTAGTCCCGGTCATCTTTATTTTCAA
1 ACTTATGGTTCAGTCCCGGTCATCTTTATTTTCTA
* * ** *
4675350 ACTTAAGGTTCA-TCCCTAGTTGTTTTTATTTTCTA
1 ACTTATGGTTCAGTCCC-GGTCATCTTTATTTTCTA
** * * *
4675385 ACTTACAGTTCAATCCCAGTCATTTTTAGTTTT
1 ACTTATGGTTCAGTCCCGGTCATCTTTA-TTTT
4675418 TGACTTGCAG
Statistics
Matches: 104, Mismatches: 31, Indels: 5
0.74 0.22 0.04
Matches are distributed among these distances:
34 4 0.04
35 92 0.88
36 8 0.08
ACGTcount: A:0.20, C:0.17, G:0.12, T:0.51
Consensus pattern (35 bp):
ACTTATGGTTCAGTCCCGGTCATCTTTATTTTCTA
Found at i:4675429 original size:35 final size:34
Alignment explanation
Indices: 4675372--4675799 Score: 130
Period size: 35 Copynumber: 12.3 Consensus size: 34
4675362 TCCCTAGTTG
* *
4675372 TTTTTATTTTCTAACTTACAGTTCAATCCCAGTCA
1 TTTTTATTTT-TGACTTACAGTTCAATCCCAATCA
* *
4675407 TTTTTAGTTTTTGACTTGCAGTT-AATTCTCAATC-
1 TTTTTA-TTTTTGACTTACAGTTCAA-TCCCAATCA
* * * * *
4675441 GTTTTATTTTTTGACTTACGGTTCAATTCCAGTGA
1 TTTTTA-TTTTTGACTTACAGTTCAATCCCAATCA
* * ** **
4675476 TCTTTATTTTTTACTTATGGTTCAATCTTAATC-
1 TTTTTATTTTTGACTTACAGTTCAATCCCAATCA
** * * *
4675509 TCTTTTAGTTTTTGACTTATGGTTTAATTCGAATCA
1 T-TTTTA-TTTTTGACTTACAGTTCAATCCCAATCA
* * * * * *
4675545 TCTTTATTTTTTGACTTGCAATTCAGTCTCAGTCA
1 TTTTTA-TTTTTGACTTACAGTTCAATCCCAATCA
* * * * *
4675580 TTTTTATTTCTTGATTTACGGTTTAGTCCCGATCA
1 TTTTTATTT-TTGACTTACAGTTCAATCCCAATCA
* * * * * * * *
4675615 TATTTACTTTTTAACTTACAATTTAGTCTCAGTTA
1 TTTTTA-TTTTTGACTTACAGTTCAATCCCAATCA
* * * * **
4675650 TCTTTATTTTTTGACTTGC-GATTTAGTCCTTATCA
1 TTTTTA-TTTTTGACTTACAG-TTCAATCCCAATCA
* * * * *
4675685 TTTTTATTTTCTAACTTA-AGGTTTAGTCTCGATCA
1 TTTTTATTTT-TGACTTACA-GTTCAATCCCAATCA
** * * * *
4675720 TTTTTATTTTTTGACTTGTAATTCAAT-TCGATCT
1 TTTTTA-TTTTTGACTTACAGTTCAATCCCAATCA
** * *
4675754 TTTTTATTTTCTGACTTGTAGTTTAGTCCCAATCA
1 TTTTTATTTT-TGACTTACAGTTCAATCCCAATCA
*
4675789 TATTTATTTTT
1 TTTTTATTTTT
4675800 CAACTTGTGG
Statistics
Matches: 290, Mismatches: 86, Indels: 35
0.71 0.21 0.09
Matches are distributed among these distances:
33 5 0.02
34 82 0.28
35 189 0.65
36 14 0.05
ACGTcount: A:0.21, C:0.15, G:0.11, T:0.53
Consensus pattern (34 bp):
TTTTTATTTTTGACTTACAGTTCAATCCCAATCA
Found at i:4675486 original size:34 final size:34
Alignment explanation
Indices: 4675385--4675501 Score: 96
Period size: 34 Copynumber: 3.4 Consensus size: 34
4675375 TTATTTTCTA
* *
4675385 ACTTACAGTTCAATCCCAGTCATTTTTAGTTTTTG
1 ACTTACAGTTCAATTCCAGTGA-TTTTAGTTTTTG
* * *
4675420 ACTTGCAGTT-AATTCTCAATCG-TTTTATTTTTTG
1 ACTTACAGTTCAATTC-CAGT-GATTTTAGTTTTTG
* *
4675454 ACTTACGGTTCAATTCCAGTGATCTTTA-TTTTTT
1 ACTTACAGTTCAATTCCAGTGAT-TTTAGTTTTTG
**
4675488 ACTTATGGTTCAAT
1 ACTTACAGTTCAAT
4675502 CTTAATCTCT
Statistics
Matches: 67, Mismatches: 10, Indels: 11
0.76 0.11 0.12
Matches are distributed among these distances:
33 1 0.01
34 45 0.67
35 21 0.31
ACGTcount: A:0.22, C:0.17, G:0.12, T:0.49
Consensus pattern (34 bp):
ACTTACAGTTCAATTCCAGTGATTTTAGTTTTTG
Found at i:4675655 original size:105 final size:105
Alignment explanation
Indices: 4675544--4675736 Score: 264
Period size: 105 Copynumber: 1.8 Consensus size: 105
4675534 AATTCGAATC
* * *
4675544 ATCTTTATTTTTTGACTTGCAATTCAGT-CTCAGTCATTTTTA-TTTCTTGATTTACGGTTTAGT
1 ATCTTTATTTTTTGACTTGCAATTCAGTCCTCA-TCATTTTTATTTTC-TAACTTAAGGTTTAGT
4675607 CCCGATCATATTTACTTTTTAACTTACAATTTAGTCTCAGTT
64 CCCGATCATATTTACTTTTTAACTTACAATTTAGTCTCAGTT
* * * *
4675649 ATCTTTATTTTTTGACTTGCGATTTAGTCCTTATCATTTTTATTTTCTAACTTAAGGTTTAGTCT
1 ATCTTTATTTTTTGACTTGCAATTCAGTCCTCATCATTTTTATTTTCTAACTTAAGGTTTAGTCC
* * *
4675714 CGATCATTTTTATTTTTTGACTT
66 CGATCATATTTACTTTTTAACTT
4675737 GTAATTCAAT
Statistics
Matches: 76, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
105 69 0.91
106 7 0.09
ACGTcount: A:0.21, C:0.16, G:0.10, T:0.53
Consensus pattern (105 bp):
ATCTTTATTTTTTGACTTGCAATTCAGTCCTCATCATTTTTATTTTCTAACTTAAGGTTTAGTCC
CGATCATATTTACTTTTTAACTTACAATTTAGTCTCAGTT
Found at i:4675737 original size:70 final size:70
Alignment explanation
Indices: 4675541--4675737 Score: 211
Period size: 70 Copynumber: 2.8 Consensus size: 70
4675531 TTTAATTCGA
* * * * * * * * *
4675541 ATCATCTTTATTTTTTGACTTGCAATTCAGTCTCAGTCATTTTTATTTCTTGATTTACGGTTTAG
1 ATCATATTTACTTTTTAACTTACAATTTAGTCTCAGTCATTTTTATTTTTTGACTTGCGATTTAG
4675606 TCCCG
66 TCCCG
* *
4675611 ATCATATTTACTTTTTAACTTACAATTTAGTCTCAGTTATCTTTATTTTTTGACTTGCGATTTAG
1 ATCATATTTACTTTTTAACTTACAATTTAGTCTCAGTCATTTTTATTTTTTGACTTGCGATTTAG
**
4675676 TCCTT
66 TCCCG
* *
4675681 ATCATTTTTA-TTTTCTAACTTA-AGGTTTAGTCTC-GATCATTTTTATTTTTTGACTTG
1 ATCATATTTACTTTT-TAACTTACA-ATTTAGTCTCAG-TCATTTTTATTTTTTGACTTG
4675738 TAATTCAATT
Statistics
Matches: 107, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
69 6 0.06
70 101 0.94
ACGTcount: A:0.21, C:0.16, G:0.11, T:0.53
Consensus pattern (70 bp):
ATCATATTTACTTTTTAACTTACAATTTAGTCTCAGTCATTTTTATTTTTTGACTTGCGATTTAG
TCCCG
Found at i:4675969 original size:20 final size:18
Alignment explanation
Indices: 4675946--4676012 Score: 82
Period size: 20 Copynumber: 3.6 Consensus size: 18
4675936 AATGCCTTTA
4675946 AAAAACAAAAAATAAAAAGC
1 AAAAA-AAAAAATAAAAA-C
4675966 AAAAACAAAAAATAAAAA-
1 AAAAA-AAAAAATAAAAAC
* *
4675984 AAAAAAAACAACAAAAAC
1 AAAAAAAAAAATAAAAAC
4676002 AAAAAAAAAAA
1 AAAAAAAAAAA
4676013 ACACAAAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
17 10 0.23
18 15 0.35
20 18 0.42
ACGTcount: A:0.87, C:0.09, G:0.01, T:0.03
Consensus pattern (18 bp):
AAAAAAAAAAATAAAAAC
Found at i:4675976 original size:21 final size:20
Alignment explanation
Indices: 4675945--4676022 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 20
4675935 AAATGCCTTT
*
4675945 AAAAAACAAAAAATAAAAAG
1 AAAAAACAAAAAATAAAAAA
*
4675965 CAAAAACAAAAAATAAAAAAA
1 AAAAAACAAAAAAT-AAAAAA
*
4675986 AAAAAACAACAAAAACAAAAAA
1 AAAAAAC-A-AAAAATAAAAAA
4676008 AAAAAACACAAAAAT
1 AAAAAACA-AAAAAT
4676023 CTTTCAAGCT
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
20 13 0.26
21 18 0.36
22 14 0.28
23 5 0.10
ACGTcount: A:0.85, C:0.10, G:0.01, T:0.04
Consensus pattern (20 bp):
AAAAAACAAAAAATAAAAAA
Found at i:4676021 original size:1 final size:1
Alignment explanation
Indices: 4675945--4676013 Score: 57
Period size: 1 Copynumber: 69.0 Consensus size: 1
4675935 AAATGCCTTT
* * ** * * * * *
4675945 AAAAAACAAAAAATAAAAAGCAAAAACAAAAAATAAAAAAAAAAAAACAACAAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4676010 AAAA
1 AAAA
4676014 CACAAAAATC
Statistics
Matches: 51, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.87, C:0.09, G:0.01, T:0.03
Consensus pattern (1 bp):
A
Found at i:4676021 original size:13 final size:12
Alignment explanation
Indices: 4675945--4676012 Score: 75
Period size: 12 Copynumber: 5.5 Consensus size: 12
4675935 AAATGCCTTT
4675945 AAAAAACAAAAA
1 AAAAAACAAAAA
4675957 ATAAAAAGCAAAAA
1 A-AAAAA-CAAAAA
*
4675971 CAAAAAATAAAAA
1 -AAAAAACAAAAA
*
4675984 AAAAAA-AACAA
1 AAAAAACAAAAA
*
4675995 CAAAAACAAAAA
1 AAAAAACAAAAA
4676007 AAAAAA
1 AAAAAA
4676013 ACACAAAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
11 9 0.19
12 16 0.34
13 10 0.21
14 11 0.23
15 1 0.02
ACGTcount: A:0.87, C:0.09, G:0.01, T:0.03
Consensus pattern (12 bp):
AAAAAACAAAAA
Found at i:4676021 original size:30 final size:30
Alignment explanation
Indices: 4675946--4676013 Score: 93
Period size: 30 Copynumber: 2.2 Consensus size: 30
4675936 AATGCCTTTA
*
4675946 AAAAACAAAAAATAAAAAGCAAAAACAAAAAAT
1 AAAAA-AAAAAA-AACAA-CAAAAACAAAAAAT
4675979 AAAAAAAAAAAAACAACAAAAACAAAAAA-
1 AAAAAAAAAAAAACAACAAAAACAAAAAAT
4676008 AAAAAA
1 AAAAAA
4676014 CACAAAAATC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
29 6 0.18
30 13 0.38
31 4 0.12
32 6 0.18
33 5 0.15
ACGTcount: A:0.87, C:0.09, G:0.01, T:0.03
Consensus pattern (30 bp):
AAAAAAAAAAAAACAACAAAAACAAAAAAT
Found at i:4676890 original size:20 final size:20
Alignment explanation
Indices: 4676862--4676900 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4676852 TTAATTTTCT
*
4676862 TTATATGTTATTTTATTTAC
1 TTATATGTTACTTTATTTAC
* *
4676882 TTATTTGTTCCTTTATTTA
1 TTATATGTTACTTTATTTA
4676901 TTTGTCTATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.08, G:0.05, T:0.67
Consensus pattern (20 bp):
TTATATGTTACTTTATTTAC
Found at i:4678382 original size:21 final size:21
Alignment explanation
Indices: 4678356--4678414 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
4678346 TTGTCTATTT
4678356 TCATTCAT-T-TCATGTATCCAC
1 TCATTCATATATCAT-TAT-CAC
*
4678377 TCATTCATATATCATTATCAT
1 TCATTCATATATCATTATCAC
*
4678398 TCATTCATCATGTCATT
1 TCATTCAT-ATATCATT
4678415 GCATAATAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
21 18 0.55
22 11 0.33
23 4 0.12
ACGTcount: A:0.27, C:0.24, G:0.03, T:0.46
Consensus pattern (21 bp):
TCATTCATATATCATTATCAC
Found at i:4682326 original size:21 final size:21
Alignment explanation
Indices: 4682300--4682341 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
4682290 TGCATGATAA
4682300 AATATAAAGAA-AAAAGAAAAT
1 AATATAAA-AAGAAAAGAAAAT
*
4682321 AATATAAAAAGTAAAGAAAAT
1 AATATAAAAAGAAAAGAAAAT
4682342 GAAAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.17
Consensus pattern (21 bp):
AATATAAAAAGAAAAGAAAAT
Found at i:4682350 original size:21 final size:21
Alignment explanation
Indices: 4682312--4682352 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4682302 TATAAAGAAA
*
4682312 AAAGAAAATAATATAAAAAGT
1 AAAGAAAATAATAAAAAAAGT
*
4682333 AAAGAAAATGAAAAAAAAAA
1 AAAGAAAAT-AATAAAAAAA
4682353 ATGAAGCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (21 bp):
AAAGAAAATAATAAAAAAAGT
Found at i:4683253 original size:19 final size:20
Alignment explanation
Indices: 4683229--4683268 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
4683219 TTGACTTAAA
4683229 TTTTTGAT-AAAAAAAATTT
1 TTTTTGATCAAAAAAAATTT
*
4683248 TTTTTGATCAAATAAAATTT
1 TTTTTGATCAAAAAAAATTT
4683268 T
1 T
4683269 ACCTCAATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (20 bp):
TTTTTGATCAAAAAAAATTT
Found at i:4683415 original size:21 final size:21
Alignment explanation
Indices: 4683373--4683415 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
4683363 GTTAAGTTTA
* *
4683373 TAAAACCTTTAGGCATGATTT
1 TAAAACCTTTAGACATCATTT
* *
4683394 TAAAACCTTTAGATATCTTTT
1 TAAAACCTTTAGACATCATTT
4683415 T
1 T
4683416 TTTTTCTTTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (21 bp):
TAAAACCTTTAGACATCATTT
Found at i:4686315 original size:4 final size:4
Alignment explanation
Indices: 4686293--4686474 Score: 71
Period size: 4 Copynumber: 45.2 Consensus size: 4
4686283 CCTTTTGCAT
* * * *
4686293 TTTA TGTA TTT- TATTA TTTA TTTA -TTA TTACTA TTTA TTAA TATA TGTA
1 TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TT--TA TTTA TTTA TTTA TTTA
* * * *
4686342 TATC TTTA TTTA TTTA TTTA TTTA TTT- TTTC TGTTA -ATA TTTA TATGTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA T-T-TA
* * *
4686391 TTTTA TTTA TATA GTTA TATA TTTA -TTA TTATA TTATAA TTTA TTTA
1 -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT-TA TT-T-A TTTA TTTA
*
4686438 -TTA -TTA -TTA TTAA TGTT- TTATA TTT- TTT- TTTA TTTA T
1 TTTA TTTA TTTA TTTA T-TTA TT-TA TTTA TTTA TTTA TTTA T
4686475 CCTATAATAT
Statistics
Matches: 138, Mismatches: 21, Indels: 38
0.70 0.11 0.19
Matches are distributed among these distances:
3 28 0.20
4 83 0.60
5 16 0.12
6 10 0.07
7 1 0.01
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (4 bp):
TTTA
Found at i:4686327 original size:17 final size:16
Alignment explanation
Indices: 4686293--4686331 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
4686283 CCTTTTGCAT
* *
4686293 TTTATGTATTTTATTA
1 TTTATTTATTTTACTA
4686309 TTTATTTATTATTACTA
1 TTTATTTATT-TTACTA
4686326 TTTATT
1 TTTATT
4686332 AATATATGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (16 bp):
TTTATTTATTTTACTA
Found at i:4687019 original size:20 final size:21
Alignment explanation
Indices: 4686990--4687033 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
4686980 TTCTGGTGAA
* *
4686990 ATTTTCCAGATTTCGACG-AC
1 ATTTTCCAGAATCCGACGAAC
*
4687010 ATTTTTCAGAATCCGACGAAC
1 ATTTTCCAGAATCCGACGAAC
4687031 ATT
1 ATT
4687034 CCACCGGAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.34
Consensus pattern (21 bp):
ATTTTCCAGAATCCGACGAAC
Found at i:4687101 original size:18 final size:20
Alignment explanation
Indices: 4687059--4687102 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
4687049 AGCTTTTAGA
4687059 GAGAAGAGAGAGGAAAAAGG
1 GAGAAGAGAGAGGAAAAAGG
* *
4687079 AAGAAGAGAGA-G-AGAAGG
1 GAGAAGAGAGAGGAAAAAGG
4687097 GAGAAG
1 GAGAAG
4687103 GTTTCTATCG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 10 0.48
19 1 0.05
20 10 0.48
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (20 bp):
GAGAAGAGAGAGGAAAAAGG
Found at i:4687381 original size:23 final size:24
Alignment explanation
Indices: 4687355--4687403 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
4687345 TTTTTTTTTT
4687355 TTTGAATTTTTTTTAT-TTGTTTA
1 TTTGAATTTTTTTTATCTTGTTTA
** *
4687378 TTTGTTTTTTTTTTATCTTTTTTA
1 TTTGAATTTTTTTTATCTTGTTTA
4687402 TT
1 TT
4687404 GATTAGATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.12, C:0.02, G:0.06, T:0.80
Consensus pattern (24 bp):
TTTGAATTTTTTTTATCTTGTTTA
Found at i:4687448 original size:6 final size:6
Alignment explanation
Indices: 4687437--4687504 Score: 52
Period size: 6 Copynumber: 11.2 Consensus size: 6
4687427 TTCTTTTATC
* * *
4687437 TTATTT TTATTT TT-GTT TTACTT TTCTTT ATT-TTT TTATTT TTATTT
1 TTATTT TTATTT TTATTT TTATTT TTATTT -TTATTT TTATTT TTATTT
4687484 ATT-TTT TTATTAT TCTATTT T
1 -TTATTT TTATT-T T-TATTT T
4687505 CTTTAAACAA
Statistics
Matches: 51, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
5 8 0.16
6 31 0.61
7 8 0.16
8 4 0.08
ACGTcount: A:0.15, C:0.04, G:0.01, T:0.79
Consensus pattern (6 bp):
TTATTT
Found at i:4687455 original size:11 final size:10
Alignment explanation
Indices: 4687430--4687497 Score: 59
Period size: 10 Copynumber: 6.7 Consensus size: 10
4687420 TTTAATATTC
*
4687430 TTTTATCTTAT
1 TTTTAT-TTTT
4687441 TTTTATTTTT
1 TTTTATTTTT
*
4687451 GTTTTACTTTT
1 -TTTTATTTTT
*
4687462 CTTTA--TTT
1 TTTTATTTTT
4687470 TTTTATTTTT
1 TTTTATTTTT
*
4687480 ATTTATTTTT
1 TTTTATTTTT
4687490 TTATTATT
1 TT-TTATT
4687498 CTATTTTCTT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
8 7 0.15
10 20 0.43
11 20 0.43
ACGTcount: A:0.15, C:0.04, G:0.01, T:0.79
Consensus pattern (10 bp):
TTTTATTTTT
Found at i:4687471 original size:10 final size:9
Alignment explanation
Indices: 4687430--4687491 Score: 54
Period size: 11 Copynumber: 6.3 Consensus size: 9
4687420 TTTAATATTC
4687430 TTTTATCTTAT
1 TTTTAT-TT-T
4687441 TTTTATTTTT
1 TTTTA-TTTT
4687451 GTTTTACTTTT
1 -TTTTA-TTTT
*
4687462 CTTTA-TTT
1 TTTTATTTT
4687470 TTTTATTTT
1 TTTTATTTT
4687479 TATTTATTTT
1 T-TTTATTTT
4687489 TTT
1 TTT
4687492 ATTATTCTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
8 7 0.16
9 6 0.14
10 14 0.32
11 16 0.36
12 1 0.02
ACGTcount: A:0.13, C:0.05, G:0.02, T:0.81
Consensus pattern (9 bp):
TTTTATTTT
Found at i:4687491 original size:21 final size:21
Alignment explanation
Indices: 4687361--4687497 Score: 59
Period size: 21 Copynumber: 6.5 Consensus size: 21
4687351 TTTTTTTGAA
*
4687361 TTTTTTTTATTTGTTTATTTGTT
1 TTTTTTTTA-TT-TTTATTTATT
*
4687384 TTTTTTTTATCTTT-TTTATT
1 TTTTTTTTATTTTTATTTATT
* *** ** *
4687404 GATTAGATTAGGTTTATTTAAT
1 -TTTTTTTTATTTTTATTTATT
* *
4687426 ATTCTTTTATCTTATT-TTTATT
1 TTTTTTTTAT-TT-TTATTTATT
* * *
4687448 TTTGTTTTACTTTTCTTTA--
1 TTTTTTTTATTTTTATTTATT
4687467 -TTTTTTTATTTTTATTTATT
1 TTTTTTTTATTTTTATTTATT
*
4687487 TTTTTATTATT
1 TTTTTTTTATT
4687498 CTATTTTCTT
Statistics
Matches: 84, Mismatches: 22, Indels: 18
0.68 0.18 0.15
Matches are distributed among these distances:
18 15 0.18
20 7 0.08
21 32 0.38
22 19 0.23
23 11 0.13
ACGTcount: A:0.16, C:0.04, G:0.05, T:0.75
Consensus pattern (21 bp):
TTTTTTTTATTTTTATTTATT
Found at i:4687493 original size:18 final size:18
Alignment explanation
Indices: 4687437--4687494 Score: 82
Period size: 18 Copynumber: 3.3 Consensus size: 18
4687427 TTCTTTTATC
*
4687437 TTATTTTTATTT-TTGTT
1 TTATTTTTATTTATTTTT
* *
4687454 TTACTTTTCTTTATTTTT
1 TTATTTTTATTTATTTTT
4687472 TTATTTTTATTTATTTTT
1 TTATTTTTATTTATTTTT
4687490 TTATT
1 TTATT
4687495 ATTCTATTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
17 10 0.29
18 25 0.71
ACGTcount: A:0.14, C:0.03, G:0.02, T:0.81
Consensus pattern (18 bp):
TTATTTTTATTTATTTTT
Found at i:4687496 original size:29 final size:29
Alignment explanation
Indices: 4687440--4687504 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 29
4687430 TTTTATCTTA
*
4687440 TTTTTATTTTTGTTTTACTTTTCTTTATT
1 TTTTTATTTTTGATTTACTTTTCTTTATT
4687469 TTTTTATTTTT-ATTTA-TTTT-TTTATT
1 TTTTTATTTTTGATTTACTTTTCTTTATT
* *
4687495 ATTCTATTTT
1 TTTTTATTTT
4687505 CTTTAAACAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 14 0.42
27 4 0.12
28 4 0.12
29 11 0.33
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.80
Consensus pattern (29 bp):
TTTTTATTTTTGATTTACTTTTCTTTATT
Found at i:4687681 original size:59 final size:58
Alignment explanation
Indices: 4687514--4687865 Score: 453
Period size: 59 Copynumber: 5.9 Consensus size: 58
4687504 TCTTTAAACA
*
4687514 AAAATCAAAATTTCCAAAAAAAAAATATTTTTAGGGAAAAGTTAAAAGTATCAATTTTCCTT-
1 AAAATCAAAATTT-C---AAAAAAATATTTTTA-GGAAAAGTTGAAAGTATCAATTTTCCTTG
**
4687576 AGAAAT--AAATTTCAAAAAAAGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTG
1 A-AAATCAAAATTTCAAAAAAA-TATTTTT-AGGAAAAGTTGAAAGTATCAATTTTCCTTG
**
4687635 AAAATCAAAATTTTTAAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCCTTG
1 AAAATCAAAATTTCAAAAAAATATTTTTAGG-AAAAGTTGAAAGTATCAATTTTCCTTG
* *
4687694 AAAATCAAAATTTCTAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTT
1 AAAATCAAAATTTCAAAAAAATATTTTT-AGGAAAAGTTGAAAGTATCAATTTTCCTTG
*
4687753 AAAATCAAAATTTCCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTA
1 AAAATCAAAATTT-C-AAAAAAATATTTTTA-GGAAAAGTTGAAAGTATCAATTTTCCTTG
* *
4687814 AAAAT--AAATTTCCAAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTT
1 AAAATCAAAATTTCAAAAAAATATTTTTAG-GAAAAGTTGAAAGTATCAATTTT
4687866 TCCCACACAA
Statistics
Matches: 265, Mismatches: 13, Indels: 29
0.86 0.04 0.09
Matches are distributed among these distances:
56 1 0.00
57 43 0.16
58 40 0.15
59 106 0.40
60 18 0.07
61 52 0.20
62 1 0.00
63 4 0.02
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.34
Consensus pattern (58 bp):
AAAATCAAAATTTCAAAAAAATATTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTG
Found at i:4689806 original size:2 final size:2
Alignment explanation
Indices: 4689801--4689826 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4689791 TGTGTGTATG
4689801 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
4689827 ATAATAACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4690288 original size:2 final size:2
Alignment explanation
Indices: 4690283--4690315 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4690273 ACACACACAC
4690283 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4690316 GTTTTGATGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4698859 original size:2 final size:2
Alignment explanation
Indices: 4698852--4698879 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4698842 TTCTGTATCC
4698852 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4698880 TTGTTTTGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4700472 original size:24 final size:24
Alignment explanation
Indices: 4700445--4700490 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
4700435 ATAATGGATT
4700445 TATATTCAATATATTATCAATATG
1 TATATTCAATATATTATCAATATG
***
4700469 TATATTTTTTATATTATCAATA
1 TATATTCAATATATTATCAATA
4700491 AATAAAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (24 bp):
TATATTCAATATATTATCAATATG
Found at i:4703457 original size:28 final size:28
Alignment explanation
Indices: 4703418--4703483 Score: 77
Period size: 27 Copynumber: 2.4 Consensus size: 28
4703408 TGGTAATAGT
4703418 ATTTTA-TTTATTTTTATTGT-GTCAT-
1 ATTTTATTTTATTTTTATTGTAGTCATA
*
4703443 ATTACTTATTTTA-TTTTGTTGTAGTCATA
1 ATT--TTATTTTATTTTTATTGTAGTCATA
4703472 ATTTTATTTTAT
1 ATTTTATTTTAT
4703484 AATTTAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
25 3 0.09
27 19 0.56
28 9 0.26
29 3 0.09
ACGTcount: A:0.23, C:0.05, G:0.08, T:0.65
Consensus pattern (28 bp):
ATTTTATTTTATTTTTATTGTAGTCATA
Found at i:4703970 original size:15 final size:15
Alignment explanation
Indices: 4703950--4703980 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
4703940 TATAATCAAT
4703950 TAGCTAAATTTATAG
1 TAGCTAAATTTATAG
4703965 TAGCTAAATTTATAG
1 TAGCTAAATTTATAG
4703980 T
1 T
4703981 GTGGTTTAAG
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:0.39, C:0.06, G:0.13, T:0.42
Consensus pattern (15 bp):
TAGCTAAATTTATAG
Found at i:4707221 original size:18 final size:18
Alignment explanation
Indices: 4707190--4707242 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
4707180 ATTAGTAGTA
*
4707190 ATAT-TATATATATAAAT
1 ATATGTATATTTATAAAT
*
4707207 TTATGTATATTTATAAAT
1 ATATGTATATTTATAAAT
*
4707225 ATATTTATATTATATAAA
1 ATATGTATATT-TATAAA
4707243 AAATTTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 3 0.10
18 21 0.70
19 6 0.20
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
ATATGTATATTTATAAAT
Found at i:4707248 original size:18 final size:18
Alignment explanation
Indices: 4707193--4707248 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
4707183 AGTAGTAATA
* **
4707193 TTATATATATAAATTTAT
1 TTATATTTATAAATAAAT
* *
4707211 GTATATTTATAAATATAT
1 TTATATTTATAAATAAAT
4707229 TTATATTATATAAA-AAAT
1 TTATATT-TATAAATAAAT
4707247 TT
1 TT
4707249 TAAAATAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 26 0.81
19 6 0.19
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
TTATATTTATAAATAAAT
Found at i:4712197 original size:22 final size:22
Alignment explanation
Indices: 4712172--4712217 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
4712162 ATTAAAATAA
* *
4712172 AAATATATATTTTATTTTTATT
1 AAATATATATATAATTTTTATT
*
4712194 AAATTTATATATAATTTTTATT
1 AAATATATATATAATTTTTATT
4712216 AA
1 AA
4712218 TTTTAAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
AAATATATATATAATTTTTATT
Found at i:4714799 original size:36 final size:35
Alignment explanation
Indices: 4714743--4714811 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 35
4714733 CAATATAAAA
4714743 TAAATTATAATATAAGTATATTATATATATAATTT
1 TAAATTATAATATAAGTATATTATATATATAATTT
* * * *
4714778 TAAATTATTATATAAATTATATTGTATTTATAAT
1 TAAATTATAATAT-AAGTATATTATATATATAAT
4714812 ATATAATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 12 0.41
36 17 0.59
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (35 bp):
TAAATTATAATATAAGTATATTATATATATAATTT
Found at i:4715958 original size:30 final size:30
Alignment explanation
Indices: 4715924--4715981 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
4715914 TTATGACATG
4715924 AAAGCTACAT-TCATAACCACATGATTAGGT
1 AAAGCTACATATC-TAACCACATGATTAGGT
*
4715954 AAAGCTACATATCTAATCACATGATTAG
1 AAAGCTACATATCTAACCACATGATTAG
4715982 ACACCTGACA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 24 0.92
31 2 0.08
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (30 bp):
AAAGCTACATATCTAACCACATGATTAGGT
Found at i:4716330 original size:17 final size:17
Alignment explanation
Indices: 4716298--4716332 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
4716288 TTTCTGTAAA
*
4716298 TCAATAACTACGTTTCT
1 TCAATAACTACATTTCT
*
4716315 TCAATAACTATATTTCT
1 TCAATAACTACATTTCT
4716332 T
1 T
4716333 GTAAAAATGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.31, C:0.20, G:0.03, T:0.46
Consensus pattern (17 bp):
TCAATAACTACATTTCT
Found at i:4719175 original size:10 final size:10
Alignment explanation
Indices: 4719142--4719175 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
4719132 AAGATTGATC
4719142 AAAATTT-CA
1 AAAATTTCCA
4719151 AAAATTTTCCA
1 AAAA-TTTCCA
4719162 AAAATTTCCA
1 AAAATTTCCA
4719172 AAAA
1 AAAA
4719176 CTTTGTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 4 0.17
10 13 0.57
11 6 0.26
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (10 bp):
AAAATTTCCA
Found at i:4719632 original size:6 final size:6
Alignment explanation
Indices: 4719609--4719647 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
4719599 ATAGAATATC
4719609 TAAAGA TAAA-A -AAA-A TAAAGA TAAAGA TAAAGA TAAAGA
1 TAAAGA TAAAGA TAAAGA TAAAGA TAAAGA TAAAGA TAAAGA
4719648 GATAAACAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 4 0.13
5 4 0.13
6 23 0.74
ACGTcount: A:0.72, C:0.00, G:0.13, T:0.15
Consensus pattern (6 bp):
TAAAGA
Found at i:4720267 original size:16 final size:17
Alignment explanation
Indices: 4720246--4720280 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
4720236 TTTGAATTAA
*
4720246 TAAATTGCATTTTT-TT
1 TAAATTACATTTTTGTT
4720262 TAAATTACATTTTTGTT
1 TAAATTACATTTTTGTT
4720279 TA
1 TA
4720281 TACAAGTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.60
Consensus pattern (17 bp):
TAAATTACATTTTTGTT
Found at i:4721952 original size:22 final size:22
Alignment explanation
Indices: 4721927--4721972 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
4721917 GGGCTCCCAT
*
4721927 ATTTATC-TCATATTATGATTAA
1 ATTTATCAGCATATT-TGATTAA
*
4721949 ATTTATCAGCATATTTTATTAA
1 ATTTATCAGCATATTTGATTAA
4721971 AT
1 AT
4721973 ATTAAATCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.37, C:0.09, G:0.04, T:0.50
Consensus pattern (22 bp):
ATTTATCAGCATATTTGATTAA
Found at i:4722547 original size:20 final size:21
Alignment explanation
Indices: 4722509--4722547 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4722499 TTATATTGTG
4722509 ACATGTCAATATAAGATATGC
1 ACATGTCAATATAAGATATGC
4722530 ACATG-CAATAATAA-ATAT
1 ACATGTCAAT-ATAAGATAT
4722548 ATATACAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.49, C:0.13, G:0.10, T:0.28
Consensus pattern (21 bp):
ACATGTCAATATAAGATATGC
Found at i:4729789 original size:22 final size:22
Alignment explanation
Indices: 4729759--4729818 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
4729749 AATTAAAATA
*
4729759 AAATATATATTTTATTTTTATT
1 AAATTTATATTTTATTTTTATT
* *
4729781 AAATTTATA-TATAATTTTATT
1 AAATTTATATTTTATTTTTATT
* *
4729802 AATTTTAAATTATTATT
1 AAATTTATATT-TTATT
4729819 ATTTTTTTAT
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
21 17 0.59
22 9 0.31
23 3 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
AAATTTATATTTTATTTTTATT
Found at i:4729814 original size:26 final size:26
Alignment explanation
Indices: 4729761--4729828 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 26
4729751 TTAAAATAAA
*
4729761 ATATATATTTTATTTTTATTAAATTT
1 ATATATATTTTATTATTATTAAATTT
4729787 ATATATAATTTTATTAATT-TTAAA-TT
1 ATATAT-ATTTTATT-ATTATTAAATTT
*
4729813 AT-TATTATTTTTTTAT
1 ATATA-TATTTTATTAT
4729829 ATCATATCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
24 2 0.05
25 9 0.24
26 11 0.30
27 13 0.35
28 2 0.05
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (26 bp):
ATATATATTTTATTATTATTAAATTT
Found at i:4731140 original size:3 final size:3
Alignment explanation
Indices: 4731128--4731176 Score: 55
Period size: 3 Copynumber: 15.3 Consensus size: 3
4731118 ATCTTACAAA
4731128 AAT AAT -AT AAT AAT AAT AAT AAT AAT AAAT ATAT AAT ATAT AAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT A-AT AAT A-AT -AAT AAT
4731176 A
1 A
4731177 TACATATAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
2 2 0.05
3 28 0.68
4 10 0.24
5 1 0.02
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:4731177 original size:9 final size:9
Alignment explanation
Indices: 4731127--4731207 Score: 52
Period size: 8 Copynumber: 9.6 Consensus size: 9
4731117 TATCTTACAA
4731127 AAATAATAT
1 AAATAATAT
4731136 -AATAATA-
1 AAATAATAT
4731143 ATAATAATAAT
1 A-AATAAT-AT
4731154 AAAT-ATAT
1 AAATAATAT
4731162 -AAT-ATAT
1 AAATAATAT
4731169 AAATAATAT
1 AAATAATAT
*
4731178 ACAT-ATA-
1 AAATAATAT
* *
4731185 AATCTAATCT
1 AA-ATAATAT
4731195 AAATAA-AT
1 AAATAATAT
4731203 AAATA
1 AAATA
4731208 CAGATATACA
Statistics
Matches: 57, Mismatches: 6, Indels: 19
0.70 0.07 0.23
Matches are distributed among these distances:
7 8 0.14
8 22 0.39
9 20 0.35
10 6 0.11
11 1 0.02
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (9 bp):
AAATAATAT
Found at i:4731185 original size:11 final size:11
Alignment explanation
Indices: 4731129--4731185 Score: 57
Period size: 11 Copynumber: 5.4 Consensus size: 11
4731119 TCTTACAAAA
4731129 ATAATATA-AT
1 ATAATATATAT
4731139 AATAATA-ATA-
1 -ATAATATATAT
*
4731149 ATAATAAATAT
1 ATAATATATAT
*
4731160 ATAATATATAA
1 ATAATATATAT
*
4731171 ATAATATACAT
1 ATAATATATAT
4731182 ATAA
1 ATAA
4731186 ATCTAATCTA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
9 6 0.15
10 4 0.10
11 29 0.74
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (11 bp):
ATAATATATAT
Found at i:4731235 original size:15 final size:15
Alignment explanation
Indices: 4731129--4731240 Score: 60
Period size: 15 Copynumber: 7.6 Consensus size: 15
4731119 TCTTACAAAA
4731129 ATAAT-ATAAT-AAT
1 ATAATAATAATAAAT
4731142 AATAATAATAATAAAT
1 -ATAATAATAATAAAT
4731158 AT-ATAATATATAAAT
1 ATAATAATA-ATAAAT
4731173 A-ATATACAT-ATAAAT
1 ATA-ATA-ATAATAAAT
* *
4731188 CTAAT-CTAAATAAAT
1 ATAATAAT-AATAAAT
* * *
4731203 A-AATACA-GATATAC
1 ATAATA-ATAATAAAT
4731217 ATAATAATAATAAAT
1 ATAATAATAATAAAT
*
4731232 ATAAAAATA
1 ATAATAATA
4731241 CAAAGAAAAA
Statistics
Matches: 74, Mismatches: 11, Indels: 25
0.67 0.10 0.23
Matches are distributed among these distances:
13 1 0.01
14 20 0.27
15 44 0.59
16 7 0.09
17 2 0.03
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.32
Consensus pattern (15 bp):
ATAATAATAATAAAT
Done.