Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167915.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_18, 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: 20765110
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 90000 characters in sequence are not A, C, G, or T
File 54 of 117
Found at i:12235472 original size:21 final size:21
Alignment explanation
Indices: 12235417--12235474 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
12235407 TAAGTTCAAG
*
12235417 TTTAATTTATAATATTATTTAAT
1 TTTAATAT-TAAT-TTATTTAAT
*
12235440 TTATAA-AATAATTTATTTAAT
1 TT-TAATATTAATTTATTTAAT
12235461 TTTAATATTAATTT
1 TTTAATATTAATTT
12235475 TAAAAATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 3 0.10
21 18 0.60
22 4 0.13
23 2 0.07
24 3 0.10
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTAATATTAATTTATTTAAT
Found at i:12235779 original size:2 final size:2
Alignment explanation
Indices: 12235772--12235806 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
12235762 ATGCATATGA
12235772 AT AT AT 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 AT AT AT A
12235807 CTACTAAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12236690 original size:21 final size:23
Alignment explanation
Indices: 12236665--12236711 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 23
12236655 TTTTTCCATC
12236665 ATTTTTTA-TT-ATTTTTA-TTT
1 ATTTTTTAGTTAATTTTTATTTT
12236685 A-TTTTTAGTTAATTTTTATTTT
1 ATTTTTTAGTTAATTTTTATTTT
12236707 ATTTT
1 ATTTT
12236712 ATAAAAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
19 6 0.26
20 3 0.13
21 7 0.30
22 4 0.17
23 3 0.13
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (23 bp):
ATTTTTTAGTTAATTTTTATTTT
Found at i:12236710 original size:11 final size:10
Alignment explanation
Indices: 12236667--12236711 Score: 56
Period size: 11 Copynumber: 4.4 Consensus size: 10
12236657 TTTCCATCAT
12236667 TTTTTA-TTA
1 TTTTTATTTA
12236676 TTTTTATTTA
1 TTTTTATTTA
*
12236686 TTTTTAGTTAA
1 TTTTTA-TTTA
12236697 TTTTTATTTTA
1 TTTTTA-TTTA
12236708 TTTT
1 TTTT
12236712 ATAAAAAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
9 6 0.19
10 9 0.29
11 16 0.52
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (10 bp):
TTTTTATTTA
Found at i:12236712 original size:21 final size:19
Alignment explanation
Indices: 12236667--12236711 Score: 63
Period size: 22 Copynumber: 2.2 Consensus size: 19
12236657 TTTCCATCAT
12236667 TTTTTATTATTTTTATTTA
1 TTTTTATTATTTTTATTTA
12236686 TTTTTAGTTAATTTTTATTTTA
1 TTTTTA-TT-ATTTTTA-TTTA
12236708 TTTT
1 TTTT
12236712 ATAAAAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.26
20 2 0.09
21 7 0.30
22 8 0.35
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (19 bp):
TTTTTATTATTTTTATTTA
Found at i:12237781 original size:10 final size:10
Alignment explanation
Indices: 12237768--12237797 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
12237758 ATTGAGCTTT
12237768 TATATTTTAA
1 TATATTTTAA
12237778 TATATTTTAA
1 TATATTTTAA
12237788 T-TATTTTAA
1 TATATTTTAA
12237797 T
1 T
12237798 TGATAAAATA
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:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TATATTTTAA
Found at i:12239701 original size:6 final size:6
Alignment explanation
Indices: 12239690--12239743 Score: 81
Period size: 6 Copynumber: 8.8 Consensus size: 6
12239680 TAATTAATTT
* *
12239690 TAAAAA GTAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAGAGA TAAAAA
1 TAAAAA -TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
12239739 TAAAA
1 TAAAA
12239744 TTGGACTCTA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
6 37 0.86
7 6 0.14
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.17
Consensus pattern (6 bp):
TAAAAA
Found at i:12240269 original size:7 final size:7
Alignment explanation
Indices: 12240252--12240325 Score: 50
Period size: 7 Copynumber: 10.9 Consensus size: 7
12240242 TTTTTCAAAA
12240252 GTTTTTT
1 GTTTTTT
12240259 -TTTTTT
1 GTTTTTT
12240265 G--TTTT
1 GTTTTTT
*
12240270 G-GTTTT
1 GTTTTTT
*
12240276 ATTTTTT
1 GTTTTTT
*
12240283 GGTTTTT
1 GTTTTTT
12240290 GATTTTTT
1 G-TTTTTT
*
12240298 GTTTTTG
1 GTTTTTT
12240305 GTTTTGTT
1 GTTTT-TT
12240313 -TTTGTTT
1 GTTT-TTT
12240320 GTTTTT
1 GTTTTT
12240326 AAGAGTTGAA
Statistics
Matches: 53, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
5 5 0.09
6 10 0.19
7 27 0.51
8 11 0.21
ACGTcount: A:0.03, C:0.00, G:0.18, T:0.80
Consensus pattern (7 bp):
GTTTTTT
Found at i:12240282 original size:21 final size:20
Alignment explanation
Indices: 12240253--12240325 Score: 60
Period size: 19 Copynumber: 3.6 Consensus size: 20
12240243 TTTTCAAAAG
*
12240253 TTTTTTTTTTTTGTTTTG-G
1 TTTTTTTTTTTTGTTTTGAT
* *
12240272 TTTTATTTTTTGGTTTTTGAT
1 TTTTTTTTTTTTG-TTTTGAT
* *
12240293 TTTTTGTTTTTGGTTTTG-T
1 TTTTTTTTTTTTGTTTTGAT
12240312 TTTTGTTTGTTTTT
1 TTTT-TTT-TTTTT
12240326 AAGAGTTGAA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
19 16 0.37
20 12 0.28
21 15 0.35
ACGTcount: A:0.03, C:0.00, G:0.16, T:0.81
Consensus pattern (20 bp):
TTTTTTTTTTTTGTTTTGAT
Found at i:12240317 original size:6 final size:6
Alignment explanation
Indices: 12240254--12240319 Score: 62
Period size: 6 Copynumber: 10.5 Consensus size: 6
12240244 TTTCAAAAGT
* *
12240254 TTTTTT TTTTTG TTTTGG TTTTAT- TTTTTGG TTTTTG ATTTTTTG TTTTTG
1 TTTTTG TTTTTG TTTTTG TTTT-TG TTTTT-G TTTTTG --TTTTTG TTTTTG
*
12240305 GTTTTG TTTTTG TTT
1 TTTTTG TTTTTG TTT
12240320 GTTTTTAAGA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
5 1 0.02
6 38 0.76
7 5 0.10
8 6 0.12
ACGTcount: A:0.03, C:0.00, G:0.17, T:0.80
Consensus pattern (6 bp):
TTTTTG
Found at i:12240590 original size:35 final size:36
Alignment explanation
Indices: 12240516--12240670 Score: 117
Period size: 35 Copynumber: 4.4 Consensus size: 36
12240506 ACAAAGTTGC
* * * *
12240516 AAGTCAGAAAATAAAAACGACTG-GAATGAAACCAC
1 AAGTCAGAAAATAAAAATGACTGAGACTGAAGCCAT
12240551 AAGTCAGAAAATAAAAATGACTGAGACT-AAGCCAT
1 AAGTCAGAAAATAAAAATGACTGAGACTGAAGCCAT
* * * *
12240586 AAGTCA-AGGAATAACAATGACCGAGA-TGAAGTCAT
1 AAGTCAGA-AAATAAAAATGACTGAGACTGAAGCCAT
* * ** *
12240621 AACTAAGAAAATAAGGATGA-TCAGGAC-GAA-CTCAT
1 AAGTCAGAAAATAAAAATGACTGA-GACTGAAGC-CAT
12240656 AAGTCAGAAAATAAA
1 AAGTCAGAAAATAAA
12240671 GACCACTAAA
Statistics
Matches: 94, Mismatches: 19, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
34 3 0.03
35 87 0.93
36 4 0.04
ACGTcount: A:0.52, C:0.14, G:0.19, T:0.15
Consensus pattern (36 bp):
AAGTCAGAAAATAAAAATGACTGAGACTGAAGCCAT
Found at i:12240590 original size:70 final size:70
Alignment explanation
Indices: 12240516--12240723 Score: 154
Period size: 70 Copynumber: 3.0 Consensus size: 70
12240506 ACAAAGTTGC
* *
12240516 AAGTCAGAAAATAAAAACGACTGGAATGAAACCACAAGTCAGAAAATAAAAATGACTGAGACTAA
1 AAGTCAGAAAATAAAAACGACTAGAATGAAACCACAAGTAAGAAAATAAAAATGACTGAGACTAA
12240581 GCCAT
66 GCCAT
* * * * ** * * ** *
12240586 AAGTCA-AGGAATAACAATGAC-CGAGATGAAGTCATAACTAAGAAAATAAGGATGA-TCAGGAC
1 AAGTCAGA-AAATAAAAACGACTAGA-ATGAAACCACAAGTAAGAAAATAAAAATGACTGA-GAC
*
12240648 GAA-CTCAT
63 TAAGC-CAT
* * * * ** * *
12240656 AAGTCAGAAAATAAAGACCACTAAAAGGAAACTGCAAGTTAGAAAATAAAAATGACTGGGACTAA
1 AAGTCAGAAAATAAAAACGACTAGAATGAAACCACAAGTAAGAAAATAAAAATGACTGAGACTAA
12240721 GCC
66 GCC
12240724 GCAAGTCGAG
Statistics
Matches: 97, Mismatches: 33, Indels: 16
0.66 0.23 0.11
Matches are distributed among these distances:
69 6 0.06
70 87 0.90
71 4 0.04
ACGTcount: A:0.50, C:0.15, G:0.19, T:0.15
Consensus pattern (70 bp):
AAGTCAGAAAATAAAAACGACTAGAATGAAACCACAAGTAAGAAAATAAAAATGACTGAGACTAA
GCCAT
Found at i:12240772 original size:140 final size:140
Alignment explanation
Indices: 12240516--12240781 Score: 320
Period size: 140 Copynumber: 1.9 Consensus size: 140
12240506 ACAAAGTTGC
* ** *
12240516 AAGTCAGAAAATAAAAACGACTGGAATGAAACCACAAGTCAGAAAATAAAAATGACTGAGACTAA
1 AAGTCAGAAAATAAAAACCACTAAAAGGAAACCACAAGTCAGAAAATAAAAATGACTGAGACTAA
* * *
12240581 GCCATAAGTCAAGGAATAACAATGACCGAGATGAAGTCATAACTAAGAAAATAAGGATGATCAGG
66 GCCACAAGTCAAGGAATAACAATGACCGAGACGAAGTCATAACTAAGAAAATAAAGATGATCAGG
12240646 ACGAACTCAT
131 ACGAACTCAT
* ** * *
12240656 AAGTCAGAAAATAAAGACCACTAAAAGGAAACTGCAAGTTAGAAAATAAAAATGACTGGGACTAA
1 AAGTCAGAAAATAAAAACCACTAAAAGGAAACCACAAGTCAGAAAATAAAAATGACTGAGACTAA
* * * ** ** *
12240721 GCCGCAAGTCGAGGGATAA-AGATGATTGAGACGAAGTTGTAAGTCAA-AAAATAAAGATGAT
66 GCCACAAGTCAAGGAATAACA-ATGACCGAGACGAAGTCATAACT-AAGAAAATAAAGATGAT
12240782 TGGAACTAAA
Statistics
Matches: 104, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
139 1 0.01
140 101 0.97
141 2 0.02
ACGTcount: A:0.49, C:0.13, G:0.21, T:0.17
Consensus pattern (140 bp):
AAGTCAGAAAATAAAAACCACTAAAAGGAAACCACAAGTCAGAAAATAAAAATGACTGAGACTAA
GCCACAAGTCAAGGAATAACAATGACCGAGACGAAGTCATAACTAAGAAAATAAAGATGATCAGG
ACGAACTCAT
Found at i:12241244 original size:104 final size:103
Alignment explanation
Indices: 12240989--12241258 Score: 260
Period size: 104 Copynumber: 2.6 Consensus size: 103
12240979 AATACGATAG
* * * * *
12240989 GGACAAAACTGCAAGTCAAAAAATAAAAATAATAGGACTGAGTCATAAGTCAAGGAATTAAAATG
1 GGACTAAACTGCAAGTCAAAAAATAAAAATAATAGAACTAAGTCACAAGTCGAGGAA-TAAAATG
* * * * *
12241054 ATCAAGACAAAGTCGCAAGTTAGAAAATAGGGATAACTA
65 ACCAAAACAAAGTCACAAGTCAGAAAATAAGGATAACTA
* * * **
12241093 GGACTAAA-TCGCAAGTCAAAAAAT-AAAATTATTGAAATTAAACCACAAGTCGAGGAATAAAGA
1 GGACTAAACT-GCAAGTCAAAAAATAAAAATAATAG-AACTAAGTCACAAGTCGAGGAATAAA-A
* * * *
12241156 T-ACCAAAACGAAG-CTACAAGTCAGAAAATAAGGATGATTG
63 TGACCAAAACAAAGTC-ACAAGTCAGAAAATAAGGATAACTA
* * *
12241196 GGATTAAACTGCAAATCAAAAAATAAAAATAATCAGAACTAAGTCACAAATCGAGGAATAAAA
1 GGACTAAACTGCAAGTCAAAAAATAAAAATAAT-AGAACTAAGTCACAAGTCGAGGAATAAAA
12241259 ATGATAGGGA
Statistics
Matches: 132, Mismatches: 27, Indels: 15
0.76 0.16 0.09
Matches are distributed among these distances:
102 1 0.01
103 62 0.47
104 68 0.52
105 1 0.01
ACGTcount: A:0.52, C:0.13, G:0.17, T:0.18
Consensus pattern (103 bp):
GGACTAAACTGCAAGTCAAAAAATAAAAATAATAGAACTAAGTCACAAGTCGAGGAATAAAATGA
CCAAAACAAAGTCACAAGTCAGAAAATAAGGATAACTA
Found at i:12241376 original size:34 final size:35
Alignment explanation
Indices: 12241286--12241396 Score: 100
Period size: 35 Copynumber: 3.2 Consensus size: 35
12241276 GTAAGTTGAA
* * * ** *
12241286 AAATAAAGATAATCAGGACAAAGTTACAAGTCAAA
1 AAATAAAGATGACCAAGACAAAACTACAAGTCAAG
12241321 AAATAAAGATGACCAAGACAAAACTACAAGTCAAG
1 AAATAAAGATGACCAAGACAAAACTACAAGTCAAG
* * * * *
12241356 AAA-AAGGATGA-CTAGAACAAAGCCACAAGTTAAG
1 AAATAAAGATGACCAAG-ACAAAACTACAAGTCAAG
12241390 AAATAAA
1 AAATAAA
12241397 TACAATTAGG
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
33 3 0.05
34 25 0.40
35 34 0.55
ACGTcount: A:0.58, C:0.14, G:0.15, T:0.14
Consensus pattern (35 bp):
AAATAAAGATGACCAAGACAAAACTACAAGTCAAG
Found at i:12241395 original size:139 final size:139
Alignment explanation
Indices: 12241252--12241552 Score: 320
Period size: 139 Copynumber: 2.2 Consensus size: 139
12241242 CAAATCGAGG
* * * * * *
12241252 AATAAAAATGATAGGGATAAAGTTGTAAGTTGAAAAATAAAGATAATCAGGACAAAGTTACAAGT
1 AATAAATATGATAGGGATAAAGCTGCAAGTTGAAAAATAAAGACAATCAAGACAAAGTCACAAGT
* *
12241317 CAAAAAATAAAGATGACCAAGACAAAACTACAAGTCAAGAAA-AAGGATGACTAGAACAAAGCCA
66 C-AAAAACAAAGATGACCAAGACAAAACTACAAGTCAAGAAATAAAGATGACTAGAACAAAGCCA
12241381 CAAGTTA-AGA
130 CAAGTTAGA-A
** * * * * *
12241391 AATAAATACAATTA-GGATGAAGCTGCAAGTTGAGATATAAATACAATCAAGACAAAGTCGCAAG
1 AATAAATATGA-TAGGGATAAAGCTGCAAGTTGAAAAATAAAGACAATCAAGACAAAGTCACAAG
* * ** ** * * * *
12241455 TCAATAACAAGGATGACTGAGATTAAACTATAGGTCAAGAAATAAAGATGACTAGGACGAAGCCA
65 TCAAAAACAAAGATGACCAAGACAAAACTACAAGTCAAGAAATAAAGATGACTAGAACAAAGCCA
12241520 CAAGTTAGAA
130 CAAGTTAGAA
*
12241530 AATAAATATGATCGGGATAAAGC
1 AATAAATATGATAGGGATAAAGC
12241553 CATAAGTCAT
Statistics
Matches: 129, Mismatches: 29, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
138 32 0.25
139 94 0.73
140 3 0.02
ACGTcount: A:0.51, C:0.12, G:0.19, T:0.18
Consensus pattern (139 bp):
AATAAATATGATAGGGATAAAGCTGCAAGTTGAAAAATAAAGACAATCAAGACAAAGTCACAAGT
CAAAAACAAAGATGACCAAGACAAAACTACAAGTCAAGAAATAAAGATGACTAGAACAAAGCCAC
AAGTTAGAA
Found at i:12241511 original size:104 final size:104
Alignment explanation
Indices: 12241334--12241623 Score: 237
Period size: 104 Copynumber: 2.8 Consensus size: 104
12241324 TAAAGATGAC
* * * * * ** * * *
12241334 CAAGACAAAACTACAAGTCAAGAAAAAGGATGA-CTAGAACAAAGCCACAAGTTAAGAAATAAAT
1 CAAGACAAAGCCACAAGTCATGAACAAGGATGATCGAGATTAAA-CTACAAGTCAAGAAATAAAA
** * ** *
12241398 ACAATTAGGATGAAGCTGCAAGTT-GAGATATAAATACAAT
65 ATGACTAGGATGAAGCCACAAGTTAGA-AAATAAATACAAT
* * * *
12241438 CAAGACAAAGTCGCAAGTCAAT-AACAAGGATGA-CTGAGATTAAACTATAGGTCAAGAAATAAA
1 CAAGACAAAGCCACAAGTC-ATGAACAAGGATGATC-GAGATTAAACTACAAGTCAAGAAATAAA
* * **
12241501 GATGACTAGGACGAAGCCACAAGTTAGAAAATAAATATGAT
64 AATGACTAGGATGAAGCCACAAGTTAGAAAATAAATACAAT
** * * * *
12241542 CGGGATAAAGCCATAAGTCATGAACAAGGATGATCGAGATTGAGCTACAAGTCAAGAAATAAAAA
1 CAAGACAAAGCCACAAGTCATGAACAAGGATGATCGAGATTAAACTACAAGTCAAGAAATAAAAA
*
12241607 TGACTAAGATGAAGCCA
66 TGACTAGGATGAAGCCA
12241624 TGAGTCAAAA
Statistics
Matches: 145, Mismatches: 36, Indels: 10
0.76 0.19 0.05
Matches are distributed among these distances:
103 2 0.01
104 133 0.92
105 10 0.07
ACGTcount: A:0.49, C:0.14, G:0.20, T:0.18
Consensus pattern (104 bp):
CAAGACAAAGCCACAAGTCATGAACAAGGATGATCGAGATTAAACTACAAGTCAAGAAATAAAAA
TGACTAGGATGAAGCCACAAGTTAGAAAATAAATACAAT
Found at i:12241636 original size:104 final size:104
Alignment explanation
Indices: 12241452--12241644 Score: 246
Period size: 104 Copynumber: 1.9 Consensus size: 104
12241442 ACAAAGTCGC
* * * *
12241452 AAGTCAATAACAAGGATGACTGAGATTAAACTATAGGTCAAGAAATAAAGATGACTAGGACGAAG
1 AAGTCAATAACAAGGATGACTGAGATTAAACTACAAGTCAAGAAATAAAAATGACTAAGACGAAG
* * *
12241517 CCACAAGTTAGAAAATAAATATGATCGGGATAAAGCCAT
66 CCACAAGTCAAAAAATAAAGATGATCGGGATAAAGCCAT
* * *
12241556 AAGTC-ATGAACAAGGATGA-TCGAGATTGAGCTACAAGTCAAGAAATAAAAATGACTAAGATGA
1 AAGTCAAT-AACAAGGATGACT-GAGATTAAACTACAAGTCAAGAAATAAAAATGACTAAGACGA
**
12241619 AGCCATGAGTCAAAAAATAAAGATGA
64 AGCCACAAGTCAAAAAATAAAGATGA
12241645 CCACTAATAT
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
103 3 0.04
104 72 0.96
ACGTcount: A:0.48, C:0.12, G:0.21, T:0.19
Consensus pattern (104 bp):
AAGTCAATAACAAGGATGACTGAGATTAAACTACAAGTCAAGAAATAAAAATGACTAAGACGAAG
CCACAAGTCAAAAAATAAAGATGATCGGGATAAAGCCAT
Found at i:12241926 original size:22 final size:23
Alignment explanation
Indices: 12241901--12241955 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
12241891 ACTGATATGT
12241901 GCTTAG-GTGCCAACTAATCTGG
1 GCTTAGAGTGCCAACTAATCTGG
* *
12241923 GCTT-GAGTGTCAGCTAATCTGG
1 GCTTAGAGTGCCAACTAATCTGG
*
12241945 GCTTAAAGTGC
1 GCTTAGAGTGC
12241956 TAGCCAGCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 1 0.04
22 22 0.81
23 4 0.15
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (23 bp):
GCTTAGAGTGCCAACTAATCTGG
Found at i:12242107 original size:23 final size:23
Alignment explanation
Indices: 12242077--12242168 Score: 148
Period size: 23 Copynumber: 4.0 Consensus size: 23
12242067 TATCATTTGG
12242077 GTGCCAGCTAATCTAGGCTTAAA
1 GTGCCAGCTAATCTAGGCTTAAA
12242100 GTGCCAGCTAATCTAGGCTTAAA
1 GTGCCAGCTAATCTAGGCTTAAA
* *
12242123 GTGCCAGCTAATCTGGGCTTATA
1 GTGCCAGCTAATCTAGGCTTAAA
* *
12242146 GTGCCATCTAAACTAGGCTTAAA
1 GTGCCAGCTAATCTAGGCTTAAA
12242169 TCTCATCTTA
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 63 1.00
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (23 bp):
GTGCCAGCTAATCTAGGCTTAAA
Found at i:12243030 original size:27 final size:27
Alignment explanation
Indices: 12242992--12243059 Score: 127
Period size: 27 Copynumber: 2.5 Consensus size: 27
12242982 ATTTTTCACG
12242992 ATGCAAATATGAATATGAATACAAATA
1 ATGCAAATATGAATATGAATACAAATA
12243019 ATGCAAATATGAATATGAATACAAATA
1 ATGCAAATATGAATATGAATACAAATA
*
12243046 ATGCAAATACGAAT
1 ATGCAAATATGAAT
12243060 GTCTTTTTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.54, C:0.09, G:0.12, T:0.25
Consensus pattern (27 bp):
ATGCAAATATGAATATGAATACAAATA
Found at i:12251392 original size:21 final size:23
Alignment explanation
Indices: 12251367--12251413 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 23
12251357 ATTTTCCATC
12251367 ATTTTTTA-TT-ATTTTTA-TTT
1 ATTTTTTAGTTAATTTTTATTTT
12251387 A-TTTTTAGTTAATTTTTATTTT
1 ATTTTTTAGTTAATTTTTATTTT
12251409 ATTTT
1 ATTTT
12251414 ATAAAAAGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
19 6 0.26
20 3 0.13
21 7 0.30
22 4 0.17
23 3 0.13
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (23 bp):
ATTTTTTAGTTAATTTTTATTTT
Found at i:12251412 original size:11 final size:10
Alignment explanation
Indices: 12251369--12251413 Score: 56
Period size: 11 Copynumber: 4.4 Consensus size: 10
12251359 TTTCCATCAT
12251369 TTTTTA-TTA
1 TTTTTATTTA
12251378 TTTTTATTTA
1 TTTTTATTTA
*
12251388 TTTTTAGTTAA
1 TTTTTA-TTTA
12251399 TTTTTATTTTA
1 TTTTTA-TTTA
12251410 TTTT
1 TTTT
12251414 ATAAAAAGGG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
9 6 0.19
10 9 0.29
11 16 0.52
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (10 bp):
TTTTTATTTA
Found at i:12251414 original size:21 final size:19
Alignment explanation
Indices: 12251369--12251413 Score: 63
Period size: 22 Copynumber: 2.2 Consensus size: 19
12251359 TTTCCATCAT
12251369 TTTTTATTATTTTTATTTA
1 TTTTTATTATTTTTATTTA
12251388 TTTTTAGTTAATTTTTATTTTA
1 TTTTTA-TT-ATTTTTA-TTTA
12251410 TTTT
1 TTTT
12251414 ATAAAAAGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.26
20 2 0.09
21 7 0.30
22 8 0.35
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (19 bp):
TTTTTATTATTTTTATTTA
Found at i:12255375 original size:14 final size:13
Alignment explanation
Indices: 12255356--12255385 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
12255346 CTCATTTTGT
12255356 TAAAATAATAAATA
1 TAAAATAATAAA-A
12255370 TAAAATAATAAAA
1 TAAAATAATAAAA
12255383 TAA
1 TAA
12255386 TAAGAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
TAAAATAATAAAA
Found at i:12255380 original size:8 final size:8
Alignment explanation
Indices: 12255356--12255401 Score: 60
Period size: 8 Copynumber: 5.8 Consensus size: 8
12255346 CTCATTTTGT
12255356 TAAAATAA
1 TAAAATAA
12255364 T-AAAT-A
1 TAAAATAA
12255370 TAAAATAA
1 TAAAATAA
12255378 TAAAATAA
1 TAAAATAA
12255386 TAAGAAATAA
1 T-A-AAATAA
12255396 TAAAAT
1 TAAAAT
12255402 GAGATTTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
6 2 0.06
7 8 0.24
8 15 0.44
9 2 0.06
10 7 0.21
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (8 bp):
TAAAATAA
Found at i:12262945 original size:142 final size:144
Alignment explanation
Indices: 12262708--12263107 Score: 384
Period size: 142 Copynumber: 2.8 Consensus size: 144
12262698 TTAAAACACT
* * * * * * * ** * * *
12262708 AAAATCATGAAATATTATAACACTGAGATCTAGAAAGTTTC-TGAAAATCTAAGTTTGAGAATGC
1 AAAATCATGAAATATTATAAAATTAAGATCTAAAAAGTTTCATGAAAATTTCAGCTCCAAAAGGA
* *
12262772 CAAATTATGAAAATACCCTTATAAGGGTATTTTGGTAATTTTATACTTCTT-AGGTACCA-CTGT
66 CAAATTACGAAAATACCCTTATAAGGGTATTTT-GTAATTTTATACTTCTTCAGGTACCATC-AT
**
12262835 GATGTCAAATGTACCA
129 GATGTCAAATACACCA
* * * * * *
12262851 AAAATTATGAAATATTATGAAATTTAGATTTGAAAAGTTTCATGAAAA-TTCATGCT-CGAAA-G
1 AAAATCATGAAATATTATAAAATTAAGATCTAAAAAGTTTCATGAAAATTTCA-GCTCCAAAAGG
* * * * *
12262913 ATAAATTACGAAAATACCCTTATAAGGATATTTTGTAATTTCACACTT-TTCGAGGTACTATCAT
65 ACAAATTACGAAAATACCCTTATAAGGGTATTTTGTAATTTTATACTTCTTC-AGGTACCATCAT
* *
12262977 GATTTCAAATACACTA
129 GATGTCAAATACACCA
* * *
12262993 AAAATCATGAAATATTATAAAATTAAGATCTAAAAATTTTCATGAAAATTTGAGCTCCAAAAGGC
1 AAAATCATGAAATATTATAAAATTAAGATCTAAAAAGTTTCATGAAAATTTCAGCTCCAAAAGGA
* *
12263058 CAAATTACTAAAATATCCCTTA-AAGGGTATTTTAGTAATTTTGTACTTCT
66 CAAATTACGAAAATA-CCCTTATAAGGGTATTTT-GTAATTTTATACTTCT
12263108 CTTAATGCAA
Statistics
Matches: 205, Mismatches: 41, Indels: 19
0.77 0.15 0.07
Matches are distributed among these distances:
140 2 0.01
141 12 0.06
142 96 0.47
143 45 0.22
144 32 0.16
145 17 0.08
146 1 0.00
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.34
Consensus pattern (144 bp):
AAAATCATGAAATATTATAAAATTAAGATCTAAAAAGTTTCATGAAAATTTCAGCTCCAAAAGGA
CAAATTACGAAAATACCCTTATAAGGGTATTTTGTAATTTTATACTTCTTCAGGTACCATCATGA
TGTCAAATACACCA
Found at i:12263898 original size:50 final size:50
Alignment explanation
Indices: 12263805--12264224 Score: 436
Period size: 50 Copynumber: 8.3 Consensus size: 50
12263795 GCATTGAAGT
* * ** *
12263805 TTTAAAAGTTCTTGTTTGAAAATGACTTTCCCTAAACAAAGGCTTTGACAC
1 TTTAAAA-ATCTTGTTTGAAAATGGCTCCCCCTAAACAGAGGCTTTGACAC
* * *
12263856 TTTAAAAATTTTGTTTGAAAATGGCTCCCCCTCAACAGAGGCTTTGAAAC
1 TTTAAAAATCTTGTTTGAAAATGGCTCCCCCTAAACAGAGGCTTTGACAC
* * * * * *
12263906 TTTAAAAACCTTATTTGAAAATGGCTTCCTCTAAATAGAGGCTTTGACCC
1 TTTAAAAATCTTGTTTGAAAATGGCTCCCCCTAAACAGAGGCTTTGACAC
* * * * *
12263956 TTTAAAAAAAAAACTTGCTTGAAAATGGCTCTCCTTAAATAGAGGCTTTGACAC
1 TTT----AAAAATCTTGTTTGAAAATGGCTCCCCCTAAACAGAGGCTTTGACAC
* * * *
12264010 TTTAAAAAACTTGCTTGAAAATGGCTCCCCCTAAACAGAAGCTTTGACAA
1 TTTAAAAATCTTGTTTGAAAATGGCTCCCCCTAAACAGAGGCTTTGACAC
* * *
12264060 TTTAAAAAAACTTGTTTGAAAATGGCTCCCCCTAATA-A-AAGCTTTGAAAC
1 TTT-AAAAATCTTGTTTGAAAATGGCTCCCCCTAA-ACAGAGGCTTTGACAC
* *
12264110 TTTAAAAATCTTGTTT-AAAATGGCTCCCCCTAAACAGCA-GCTTTGAAAA
1 TTTAAAAATCTTGTTTGAAAATGGCTCCCCCTAAACAG-AGGCTTTGACAC
* * *
12264159 TTTAAAAATCTTATTTGAAAATGGCTCCCCCTAAATAG-GGCTTTAACAC
1 TTTAAAAATCTTGTTTGAAAATGGCTCCCCCTAAACAGAGGCTTTGACAC
*
12264208 TTTTAAAAATTTTGTTT
1 -TTTAAAAATCTTGTTT
12264225 TTCTTTTCTC
Statistics
Matches: 315, Mismatches: 42, Indels: 25
0.82 0.11 0.07
Matches are distributed among these distances:
47 1 0.00
48 18 0.06
49 43 0.14
50 172 0.55
51 38 0.12
52 1 0.00
54 42 0.13
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (50 bp):
TTTAAAAATCTTGTTTGAAAATGGCTCCCCCTAAACAGAGGCTTTGACAC
Found at i:12264012 original size:104 final size:100
Alignment explanation
Indices: 12263815--12264216 Score: 420
Period size: 104 Copynumber: 4.0 Consensus size: 100
12263805 TTTAAAAGTT
* ** * ** *
12263815 CTTGTTTGAAAATGACTTTCCCTAAACA-AAGGCTTTGACACTTT-AAAAATTTTGTTTGAAAAT
1 CTTGTTTGAAAATGGCTCCCCCTAAACAGAA-GCTTTGACAATTTAAAAAAACTTGCTTGAAAAT
* *
12263878 GGCTCCCCCTCAACAGAGGCTTTGAAACTTTAAAAAC
65 GGCTCCCCCT-AATAGAGGCTTTGAAACTTTAAAAAA
* * * * * **
12263915 CTTATTTGAAAATGGCTTCCTCTAAATAGAGGCTTTGACCCTTTAAAAAAAAAACTTGCTTGAAA
1 CTTGTTTGAAAATGGCTCCCCCTAAACAGAAGCTTTGACAATTT---AAAAAAACTTGCTTGAAA
* * *
12263980 ATGGCTCTCCTTAAATAGAGGCTTTGACACTTTAAAAAA
63 ATGGCTCCCCCT-AATAGAGGCTTTGAAACTTTAAAAAA
* *
12264019 CTTGCTTGAAAATGGCTCCCCCTAAACAGAAGCTTTGACAATTTAAAAAAACTTGTTTGAAAATG
1 CTTGTTTGAAAATGGCTCCCCCTAAACAGAAGCTTTGACAATTTAAAAAAACTTGCTTGAAAATG
* * *
12264084 GCTCCCCCTAATAAAAGCTTTGAAACTTTAAAAAT
66 GCTCCCCCTAATAGAGGCTTTGAAACTTTAAAAAA
* * * **
12264119 CTTGTTT-AAAATGGCTCCCCCTAAACAGCAGCTTTGAAAATTT-AAAAATCTTATTTGAAAATG
1 CTTGTTTGAAAATGGCTCCCCCTAAACAGAAGCTTTGACAATTTAAAAAAACTTGCTTGAAAATG
*
12264182 GCTCCCCCTAAATAG-GGCTTT-AACACTTTTAAAAA
66 GCTCCCCCT-AATAGAGGCTTTGAA-ACTTTAAAAAA
12264217 TTTTGTTTTT
Statistics
Matches: 255, Mismatches: 40, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
97 2 0.01
98 41 0.16
99 38 0.15
100 63 0.25
101 28 0.11
104 83 0.33
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.31
Consensus pattern (100 bp):
CTTGTTTGAAAATGGCTCCCCCTAAACAGAAGCTTTGACAATTTAAAAAAACTTGCTTGAAAATG
GCTCCCCCTAATAGAGGCTTTGAAACTTTAAAAAA
Found at i:12264104 original size:154 final size:149
Alignment explanation
Indices: 12263815--12264193 Score: 440
Period size: 154 Copynumber: 2.5 Consensus size: 149
12263805 TTTAAAAGTT
* * * *
12263815 CTTGTTTGAAAATGACTTTCCCTAAACAAAGGCTTTGACACTTTAAAAATTTTGTTTGAAAATGG
1 CTTG-TTGAAAATGGCTCTCCCTAAACAGAGGCTTTGACACTTTAAAAATCTTGTTTGAAAATGG
* * * * * *
12263880 CTCCCCCTCAACAGAGGCTTTGAAACTTTAAAAACCTTATTTGAAAATGGCTTCCTCTAAATAGA
65 CTCCCCCTAAACAGAAGCTTTGAAACTTTAAAAAACTTATTTGAAAATGGCTCCCCCTAAATAAA
* **
12263945 GGCTTTGACCCTTTAAAAAAAAAA
130 AGCTTTGAAACTTT----AAAAAA
* * * *
12263969 CTTGCTTGAAAATGGCTCTCCTTAAATAGAGGCTTTGACACTTTAAAAAACTTGCTTGAAAATGG
1 CTTG-TTGAAAATGGCTCTCCCTAAACAGAGGCTTTGACACTTTAAAAATCTTGTTTGAAAATGG
*
12264034 CTCCCCCTAAACAGAAGCTTTGACAA-TTTAAAAAAACTTGTTTGAAAATGGCTCCCCCT-AATA
65 CTCCCCCTAAACAGAAGCTTTGA-AACTTT-AAAAAACTTATTTGAAAATGGCTCCCCCTAAATA
*
12264097 AAAGCTTTGAAACTTTAAAAAT
128 AAAGCTTTGAAACTTTAAAAAA
* * * * *
12264119 CTTGTTTAAAATGGCTCCCCCTAAACAGCA-GCTTTGAAAATTTAAAAATCTTATTTGAAAATGG
1 CTTGTTGAAAATGGCTCTCCCTAAACAG-AGGCTTTGACACTTTAAAAATCTTGTTTGAAAATGG
12264183 CTCCCCCTAAA
65 CTCCCCCTAAA
12264194 TAGGGCTTTA
Statistics
Matches: 193, Mismatches: 29, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
149 60 0.31
150 10 0.05
154 96 0.50
155 27 0.14
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (149 bp):
CTTGTTGAAAATGGCTCTCCCTAAACAGAGGCTTTGACACTTTAAAAATCTTGTTTGAAAATGGC
TCCCCCTAAACAGAAGCTTTGAAACTTTAAAAAACTTATTTGAAAATGGCTCCCCCTAAATAAAA
GCTTTGAAACTTTAAAAAA
Found at i:12264427 original size:22 final size:23
Alignment explanation
Indices: 12264402--12264445 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
12264392 GAATATATTA
*
12264402 AATGTAATTCATG-AATGCAATG
1 AATGTAATACATGTAATGCAATG
12264424 AATGTAATACATGTAATGCAAT
1 AATGTAATACATGTAATGCAAT
12264446 TATTATTAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.32
Consensus pattern (23 bp):
AATGTAATACATGTAATGCAATG
Found at i:12265449 original size:175 final size:176
Alignment explanation
Indices: 12265258--12265602 Score: 541
Period size: 176 Copynumber: 2.0 Consensus size: 176
12265248 AATTTATCGA
* * * *
12265258 GTTTGGTAAGTCATCCCCATCCATCTTTGTCAAAATCAATGTTCCACCCAAAAAAGCCTTTTTGA
1 GTTTGGTAAGTCATCCCCATCCATCTCTATCAAAATCAATGCTCCACCCAAAAAAACCTTTTTGA
* * *
12265323 CTACATATA-ACCTTCTCAATTTGGCATCCA-TTTTTTTCAATTATCAAGCTGATTCAGAAGAAT
66 CTACATATAGACCCTCCCAATTTGGCATCCACTTTTCTT-AATTATCAAGCTGATTCAGAAGAAT
* *
12265386 TTTTTTTAAAACAAATTCTCCCTTACAGAAATGCCTAAATTTATAAG
130 TTTCTTTAAAACAAATTCTCCCTCACAGAAATGCCTAAATTTATAAG
* *
12265433 GTTTGGTAAGTCATCCCCATCCATCTCTATCAAGATCAATGCTCTACCCAAAAAAACCTTTTTGA
1 GTTTGGTAAGTCATCCCCATCCATCTCTATCAAAATCAATGCTCCACCCAAAAAAACCTTTTTGA
* *
12265498 CTATATATAGACCCTCCCAATTTGGTATCCACTTTTCTTAATTATCAAGCTGATTCAGAAGAATT
66 CTACATATAGACCCTCCCAATTTGGCATCCACTTTTCTTAATTATCAAGCTGATTCAGAAGAATT
*
12265563 TTCTTTAAAACCAATTCTCCCTCACAGAAATGCCTAAATT
131 TTCTTTAAAACAAATTCTCCCTCACAGAAATGCCTAAATT
12265603 GATCTCTTTT
Statistics
Matches: 154, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
175 67 0.44
176 81 0.53
177 6 0.04
ACGTcount: A:0.32, C:0.23, G:0.10, T:0.35
Consensus pattern (176 bp):
GTTTGGTAAGTCATCCCCATCCATCTCTATCAAAATCAATGCTCCACCCAAAAAAACCTTTTTGA
CTACATATAGACCCTCCCAATTTGGCATCCACTTTTCTTAATTATCAAGCTGATTCAGAAGAATT
TTCTTTAAAACAAATTCTCCCTCACAGAAATGCCTAAATTTATAAG
Found at i:12280074 original size:13 final size:13
Alignment explanation
Indices: 12280051--12280102 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 13
12280041 GGCTATTTCC
12280051 ATTAGTATTATTAT
1 ATTA-TATTATTAT
*
12280065 ATTATATTATTAG
1 ATTATATTATTAT
*
12280078 ATTATTTTATGTTATT
1 ATTATATTA--TTA-T
12280094 ATTATATTA
1 ATTATATTA
12280103 GAGTATAGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
13 16 0.52
14 4 0.13
15 3 0.10
16 8 0.26
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.60
Consensus pattern (13 bp):
ATTATATTATTAT
Found at i:12280087 original size:18 final size:18
Alignment explanation
Indices: 12280060--12280102 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
12280050 CATTAGTATT
12280060 ATTATATTATATTATTAG
1 ATTATATTATATTATTAG
* *
12280078 ATTATTTTATGTTATT--
1 ATTATATTATATTATTAG
12280094 ATTATATTA
1 ATTATATTA
12280103 GAGTATAGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 8 0.36
18 14 0.64
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (18 bp):
ATTATATTATATTATTAG
Found at i:12280149 original size:3 final size:3
Alignment explanation
Indices: 12280143--12280185 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
12280133 ATAGTAGTAG
* * *
12280143 TAT TAT TAT TAT TAT TAC TAC TAT TAC TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
12280186 TTAAAAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:12288789 original size:17 final size:17
Alignment explanation
Indices: 12288741--12288790 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 17
12288731 TAGTATTTTC
*
12288741 TTAGTTGGAAGTTAAAA
1 TTAGTTGGTAGTTAAAA
* *
12288758 TTAGTTAATGTAGTTAAAG
1 TTAGTT--GGTAGTTAAAA
12288777 TTAGTTGGTAGTTA
1 TTAGTTGGTAGTTA
12288791 GCTATTTAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
17 13 0.48
19 14 0.52
ACGTcount: A:0.34, C:0.00, G:0.24, T:0.42
Consensus pattern (17 bp):
TTAGTTGGTAGTTAAAA
Found at i:12289255 original size:3 final size:3
Alignment explanation
Indices: 12289247--12289272 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
12289237 TTATTTATTA
12289247 ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC AT
12289273 TTCTTTGTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:12290309 original size:13 final size:12
Alignment explanation
Indices: 12290280--12290308 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
12290270 TTTTTTGCAA
12290280 TTTTTAGTAAAT
1 TTTTTAGTAAAT
12290292 TTTTTAGTAAAT
1 TTTTTAGTAAAT
12290304 TTTTT
1 TTTTT
12290309 TTAATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.66
Consensus pattern (12 bp):
TTTTTAGTAAAT
Found at i:12295149 original size:33 final size:33
Alignment explanation
Indices: 12295103--12295264 Score: 116
Period size: 33 Copynumber: 4.9 Consensus size: 33
12295093 ATAACCTTTG
12295103 GTTAGAAG-AATCTTTCAAATACCA-CTACCTCTA
1 GTTA-AAGAAATCTTTCAAATACCATC-ACCTCTA
**
12295136 GTTAAAGAAATCTTTCAAATATTATCACCTCTA
1 GTTAAAGAAATCTTTCAAATACCATCACCTCTA
* ** * *
12295169 GTTAGAGAAAAT-TTTCAAATATTATCTCTTCTA
1 GTTAAAG-AAATCTTTCAAATACCATCACCTCTA
* * * *** *
12295202 GTTAGAGGAATTTTTCAAATATTGTCGCCTCTA
1 GTTAAAGAAATCTTTCAAATACCATCACCTCTA
* *
12295235 ATTAGAGAAATCTTTCAAAT-CTCATCACCT
1 GTTAAAGAAATCTTTCAAATAC-CATCACCT
12295265 TTGGATTAGA
Statistics
Matches: 108, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
32 6 0.06
33 97 0.90
34 5 0.05
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.36
Consensus pattern (33 bp):
GTTAAAGAAATCTTTCAAATACCATCACCTCTA
Found at i:12295363 original size:33 final size:33
Alignment explanation
Indices: 12295305--12295484 Score: 129
Period size: 33 Copynumber: 5.5 Consensus size: 33
12295295 AGCTTTTGGC
* ** *
12295305 TAAAAGAGTTTTTAAAGTGTTATAGCCTTTGAT
1 TAAAGGAGTTTTTAAAGTGCCATAGCCTCTGAT
* *
12295338 TAAAGGAGTTTTTAAAATGCCATAGCCTCTGGT
1 TAAAGGAGTTTTTAAAGTGCCATAGCCTCTGAT
*
12295371 T--A-GAGTTTTTAAAGT-CTCATAACCTCT-AGT
1 TAAAGGAGTTTTTAAAGTGC-CATAGCCTCTGA-T
* * * * ** * *
12295401 TAGATGTGTTTTTAAACTTTCATAGCCTTTGGT
1 TAAAGGAGTTTTTAAAGTGCCATAGCCTCTGAT
* *
12295434 TAAAGGAGTTTTTAAAGTGCCATAGTCTCTGGT
1 TAAAGGAGTTTTTAAAGTGCCATAGCCTCTGAT
*
12295467 TAGAA-GAGTTCTTAAAGT
1 TA-AAGGAGTTTTTAAAGT
12295485 CTCGTAGCTT
Statistics
Matches: 115, Mismatches: 24, Indels: 16
0.74 0.15 0.10
Matches are distributed among these distances:
29 1 0.01
30 23 0.20
31 1 0.01
32 1 0.01
33 87 0.76
34 2 0.02
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.39
Consensus pattern (33 bp):
TAAAGGAGTTTTTAAAGTGCCATAGCCTCTGAT
Found at i:12295500 original size:33 final size:33
Alignment explanation
Indices: 12295264--12295545 Score: 121
Period size: 33 Copynumber: 8.5 Consensus size: 33
12295254 TCTCATCACC
* *
12295264 TTTGGATTAGAAGAAGTTTAT-AAAGTCTTATAGCT
1 TTTGG-TTAGAAG-AGTTT-TCAAAGTATCATAGCT
* * * * * *
12295299 TTTGGCTAAAAGAGTTTTTAAAGTGTTATAGCC
1 TTTGGTTAGAAGAGTTTTCAAAGTATCATAGCT
* * * ** *
12295332 TTTGATTA-AAGGAGTTTTTAAAATGCCATAGCC
1 TTTGGTTAGAA-GAGTTTTCAAAGTATCATAGCT
* * * * *
12295365 TCTGGTT---AGAGTTTTTAAAGTCTCATAACC
1 TTTGGTTAGAAGAGTTTTCAAAGTATCATAGCT
* * * * * * * *
12295395 TCTAGTTAGATGTGTTTTTAAACTTTCATAGCC
1 TTTGGTTAGAAGAGTTTTCAAAGTATCATAGCT
* **
12295428 TTTGGTTA-AAGGAGTTTTTAAAGTGCCATAG-T
1 TTTGGTTAGAA-GAGTTTTCAAAGTATCATAGCT
* * *
12295460 CTCTGGTTAGAAGAGTTCTT-AAAGTCTCGTAGCT
1 -TTTGGTTAGAAGAGTT-TTCAAAGTATCATAGCT
*
12295494 TTTGGTTAGAAAAGCTTTTCAAAGTATCATAGCT
1 TTTGGTTAGAAGAG-TTTTCAAAGTATCATAGCT
*
12295528 TTTGGTTAGAGGAGTTTT
1 TTTGGTTAGAAGAGTTTT
12295546 TTAAAATTTA
Statistics
Matches: 196, Mismatches: 39, Indels: 26
0.75 0.15 0.10
Matches are distributed among these distances:
30 24 0.12
31 1 0.01
32 4 0.02
33 126 0.64
34 36 0.18
35 5 0.03
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (33 bp):
TTTGGTTAGAAGAGTTTTCAAAGTATCATAGCT
Found at i:12295705 original size:33 final size:32
Alignment explanation
Indices: 12295646--12295911 Score: 186
Period size: 33 Copynumber: 8.2 Consensus size: 32
12295636 ATTTTTTTTC
* *
12295646 TTTAAAGTGTCATAGCCTTTTA-TTAGAGGAGTT
1 TTTAAA-TGCCATAGCC-TCTAGTTAGAGGAGTT
* *
12295679 TTTGAAATGCCATAGCCTCTAGTTAGATGAGGT
1 TTT-AAATGCCATAGCCTCTAGTTAGAGGAGTT
* * *
12295712 TTTAAA-GTCTCATAGCTTCTGGTTAAAGGAGTT
1 TTTAAATG-C-CATAGCCTCTAGTTAGAGGAGTT
* * *
12295745 TTTAAAGTGCCATA-CCTTTTGGTTAGAAGAGTT
1 TTTAAA-TGCCATAGCC-TCTAGTTAGAGGAGTT
*
12295778 TTTAAA-GTCTCATAGCCTCTAGTTAGAAGAG--
1 TTTAAATG-C-CATAGCCTCTAGTTAGAGGAGTT
* ** * *
12295809 TTTAAGTTTCATTGCCTCTAGTTAGAAGAG-T
1 TTTAAATGCCATAGCCTCTAGTTAGAGGAGTT
* *
12295840 TTTAAAGTGCCATTGCCTCTAGTTAGAGAAGTT
1 TTTAAA-TGCCATAGCCTCTAGTTAGAGGAGTT
* * * *
12295873 TTTAAAGTACCATAGCCTTTGGTTAGAGGAATT
1 TTTAAA-TGCCATAGCCTCTAGTTAGAGGAGTT
12295906 TTTAAA
1 TTTAAA
12295912 GTCTATTGCC
Statistics
Matches: 189, Mismatches: 30, Indels: 28
0.77 0.12 0.11
Matches are distributed among these distances:
30 20 0.11
31 12 0.06
32 29 0.15
33 121 0.64
34 6 0.03
35 1 0.01
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.38
Consensus pattern (32 bp):
TTTAAATGCCATAGCCTCTAGTTAGAGGAGTT
Found at i:12295725 original size:66 final size:67
Alignment explanation
Indices: 12295646--12295924 Score: 240
Period size: 66 Copynumber: 4.3 Consensus size: 67
12295636 ATTTTTTTTC
* *
12295646 TTTAAAGTGTCATAGCCTTTTA-TTAGAGGAGTTTTTGAAA-TGCCATAGCCTCTAGTTAGATGA
1 TTTAAAGTCTCATAGCCTTTTAGTTAGAGGAGTTTTT-AAAGTGCCATAGCCTCTAGTTAGAAGA
12295709 GGT
65 GGT
* * * * *
12295712 TTTAAAGTCTCATAG-CTTCTGGTTAAAGGAGTTTTTAAAGTGCCATA-CCTTTTGGTTAGAAGA
1 TTTAAAGTCTCATAGCCTTTTAGTTAGAGGAGTTTTTAAAGTGCCATAGCC-TCTAGTTAGAAGA
*
12295775 GTT
65 GGT
* * ** *
12295778 TTTAAAGTCTCATAGCC-TCTAGTTAGAAGAG--TTT-AAGTTTCATTGCCTCTAGTTAGAAGA-
1 TTTAAAGTCTCATAGCCTTTTAGTTAGAGGAGTTTTTAAAGTGCCATAGCCTCTAGTTAGAAGAG
12295838 GT
66 GT
* * * * * * *
12295840 TTTAAAGTGC-CATTGCC-TCTAGTTAGAGAAGTTTTTAAAGTACCATAGCCTTTGGTTAGAGGA
1 TTTAAAGT-CTCATAGCCTTTTAGTTAGAGGAGTTTTTAAAGTGCCATAGCCTCTAGTTAGAAGA
**
12295903 ATT
65 GGT
*
12295906 TTTAAAGTCT-ATTGCCTTT
1 TTTAAAGTCTCATAGCCTTT
12295925 GGTTAGAAGA
Statistics
Matches: 173, Mismatches: 28, Indels: 24
0.77 0.12 0.11
Matches are distributed among these distances:
62 27 0.16
63 19 0.11
64 8 0.05
65 36 0.21
66 82 0.47
67 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (67 bp):
TTTAAAGTCTCATAGCCTTTTAGTTAGAGGAGTTTTTAAAGTGCCATAGCCTCTAGTTAGAAGAG
GT
Found at i:12295828 original size:30 final size:32
Alignment explanation
Indices: 12295693--12295940 Score: 181
Period size: 33 Copynumber: 7.7 Consensus size: 32
12295683 AAATGCCATA
* *
12295693 GCCTCTAGTTAGATGAGGTTTTAAAGTCTCATA
1 GCCTCTAGTTAGAAGA-GTTTTAAAGTCTCATT
* *
12295726 GCTTCTGGTTA-AAGGAGTTTTTAAAGTGC-CA-T
1 GCCTCTAGTTAGAA-GAG-TTTTAAAGT-CTCATT
* * * *
12295758 ACCTTTTGGTTAGAAGAGTTTTTAAAGTCTCATA
1 GCC-TCTAGTTAGAAGAG-TTTTAAAGTCTCATT
*
12295792 GCCTCTAGTTAGAAGAG-TTT-AAGTTTCATT
1 GCCTCTAGTTAGAAGAGTTTTAAAGTCTCATT
12295822 GCCTCTAGTTAGAAGAGTTTTAAAGTGC-CATT
1 GCCTCTAGTTAGAAGAGTTTTAAAGT-CTCATT
*
12295854 GCCTCTAGTTAG-AGAAGTTTTTAAAGTAC-CATA
1 GCCTCTAGTTAGAAG-AG-TTTTAAAGT-CTCATT
* * * *
12295887 GCCTTTGGTTAGAGGAATTTTTAAAGTCT-ATT
1 GCCTCTAGTTAGAAG-AGTTTTAAAGTCTCATT
* *
12295919 GCCTTTGGTTAGAAGAGGTTTT
1 GCCTCTAGTTAGAAGA-GTTTT
12295941 CAAGATCAGG
Statistics
Matches: 177, Mismatches: 23, Indels: 31
0.77 0.10 0.13
Matches are distributed among these distances:
30 25 0.14
31 9 0.05
32 47 0.27
33 88 0.50
34 8 0.05
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (32 bp):
GCCTCTAGTTAGAAGAGTTTTAAAGTCTCATT
Found at i:12295896 original size:128 final size:128
Alignment explanation
Indices: 12295693--12295935 Score: 330
Period size: 128 Copynumber: 1.9 Consensus size: 128
12295683 AAATGCCATA
* * * * *
12295693 GCCTCTAGTTAGATGAGGTTTTAAAGTCTCATAGCTTCTGGTTAAAGGAGTTTTTAAAGTGCCAT
1 GCCTCTAGTTAGAAGAGGTTTTAAAGTCTCATAGCCTCTAGTTAAAGAAGTTTTTAAAGTACCAT
*
12295758 ACCTTTTGGTTAGAAGAGTTTTTAAAGTCTCATAGCCTCTAGTTAGAAGAGTTTAAGTTTCATT
66 ACCTTTTGGTTAGAAGAATTTTTAAAGTCT-ATAGCCTCTAGTTAGAAGAGTTTAAGTTTCATT
* *
12295822 GCCTCTAGTTAGAAGA-GTTTTAAAGTGC-CATTGCCTCTAGTTAGAGAAGTTTTTAAAGTACCA
1 GCCTCTAGTTAGAAGAGGTTTTAAAGT-CTCATAGCCTCTAGTTAAAGAAGTTTTTAAAGTACCA
* * * *
12295885 TAGCC-TTTGGTTAGAGGAATTTTTAAAGTCTATTGCCTTTGGTTAGAAGAG
65 TA-CCTTTTGGTTAGAAGAATTTTTAAAGTCTATAGCCTCTAGTTAGAAGAG
12295936 GTTTTCAAGA
Statistics
Matches: 100, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
127 17 0.17
128 65 0.65
129 18 0.18
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (128 bp):
GCCTCTAGTTAGAAGAGGTTTTAAAGTCTCATAGCCTCTAGTTAAAGAAGTTTTTAAAGTACCAT
ACCTTTTGGTTAGAAGAATTTTTAAAGTCTATAGCCTCTAGTTAGAAGAGTTTAAGTTTCATT
Found at i:12296503 original size:13 final size:13
Alignment explanation
Indices: 12296460--12296503 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
12296450 TTTAAACTTT
12296460 TAAATTTTATTTA
1 TAAATTTTATTTA
*
12296473 TTAATTTATACTTT-
1 TAAATTT-TA-TTTA
12296487 TAAATTTTATTTA
1 TAAATTTTATTTA
12296500 TAAA
1 TAAA
12296504 ACCTTTGGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 3 0.12
13 12 0.46
14 8 0.31
15 3 0.12
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (13 bp):
TAAATTTTATTTA
Found at i:12296538 original size:3 final size:3
Alignment explanation
Indices: 12296518--12296561 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
12296508 TTGGGGTATA
* *
12296518 ATC ATT ATC ATT ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
12296562 TATTATTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.34, C:0.27, G:0.00, T:0.39
Consensus pattern (3 bp):
ATC
Found at i:12297709 original size:22 final size:24
Alignment explanation
Indices: 12297677--12297720 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
12297667 ATTTTTATTA
12297677 TTTTATGTTTATTT-TATGTGATT
1 TTTTATGTTTATTTGTATGTGATT
12297700 TTTTAT-TTTATTTGTATGTGA
1 TTTTATGTTTATTTGTATGTGA
12297721 ACTTTGTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.18, C:0.00, G:0.14, T:0.68
Consensus pattern (24 bp):
TTTTATGTTTATTTGTATGTGATT
Found at i:12298162 original size:95 final size:95
Alignment explanation
Indices: 12297955--12298171 Score: 226
Period size: 95 Copynumber: 2.3 Consensus size: 95
12297945 TGAAATAGTT
* ** * *
12297955 AGGAAAGAGTTAAAATATCAATTTTTCTTAAATTCTTTAAAAATAAAAATAAAATTTGGTATATA
1 AGGAAAAAGTTAAAATATCAATTTTTCTTAAATTCTTTAAAAATAAAAATAAAATAAGATAAATA
* *
12298020 AAATATGAAATAAATTTTGAAAAAATGCTA
66 AAATATAAAATAAATCTTGAAAAAATGCTA
** * * * *
12298050 AGGAAAAAGTTGGAATATCACTTTTTGC-TAAATTCTTTAAGACTAAGAATAAAATAAGATAAAT
1 AGGAAAAAGTTAAAATATCAATTTTT-CTTAAATTCTTTAAAAATAAAAATAAAATAAGATAAAT
12298114 AAAA-ATAAAATAAA-CTT-AAAAAATTTTGCTA
65 AAAATATAAAATAAATCTTGAAAAAA---TGCTA
* * *
12298145 GGGAAAATGTTAAAATATCAAGTTTTC
1 AGGAAAAAGTTAAAATATCAATTTTTC
12298172 CTTTCTTTAG
Statistics
Matches: 99, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
92 6 0.06
93 2 0.02
94 10 0.10
95 80 0.81
96 1 0.01
ACGTcount: A:0.50, C:0.06, G:0.11, T:0.33
Consensus pattern (95 bp):
AGGAAAAAGTTAAAATATCAATTTTTCTTAAATTCTTTAAAAATAAAAATAAAATAAGATAAATA
AAATATAAAATAAATCTTGAAAAAATGCTA
Found at i:12299074 original size:3 final size:3
Alignment explanation
Indices: 12299066--12299090 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12299056 AGGCAAAAGA
12299066 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
12299091 ATAGAGAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:12308004 original size:2 final size:2
Alignment explanation
Indices: 12307997--12308023 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12307987 AGCTTGGGGA
12307997 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 A
12308024 CTTGATATGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12311184 original size:50 final size:50
Alignment explanation
Indices: 12311109--12311207 Score: 173
Period size: 50 Copynumber: 2.0 Consensus size: 50
12311099 GTATAGATAG
12311109 TTTGTTTCATTCCTTCAGAAGGATATG-ATTTTTTTTTTAATTTTTTGCAA
1 TTTGTTTCATTCCTTCAGAAGGATATGAATTTTTTTTTT-ATTTTTTGCAA
*
12311159 TTTGTTTCATTCCTTCTGAAGGATATGAATTTTTTTTTTATTTTTTGCA
1 TTTGTTTCATTCCTTCAGAAGGATATGAATTTTTTTTTTATTTTTTGCA
12311208 GTTTATTTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
50 36 0.77
51 11 0.23
ACGTcount: A:0.20, C:0.10, G:0.12, T:0.58
Consensus pattern (50 bp):
TTTGTTTCATTCCTTCAGAAGGATATGAATTTTTTTTTTATTTTTTGCAA
Found at i:12312691 original size:16 final size:16
Alignment explanation
Indices: 12312663--12312717 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 16
12312653 AAGATAAATT
12312663 AAAAAAT-TATAAAAA
1 AAAAAATATATAAAAA
*
12312678 AAAACATATATAAAAA
1 AAAAAATATATAAAAA
12312694 ATTAAAAATATATAGAGAAA
1 A--AAAAATATATA-A-AAA
12312714 AAAA
1 AAAA
12312718 GAAGATTGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
15 6 0.18
16 9 0.27
18 13 0.39
19 1 0.03
20 4 0.12
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.20
Consensus pattern (16 bp):
AAAAAATATATAAAAA
Found at i:12312714 original size:20 final size:19
Alignment explanation
Indices: 12312658--12312707 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 19
12312648 TCATTAAGAT
*
12312658 AAATTAAAAAAT-TAT-AA
1 AAATTAAAACATATATAAA
12312675 AAA--AAAACATATATAAA
1 AAATTAAAACATATATAAA
12312692 AAATTAAAA-ATATATA
1 AAATTAAAACATATATA
12312708 GAGAAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 6 0.21
16 3 0.11
17 8 0.29
18 7 0.25
19 4 0.14
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (19 bp):
AAATTAAAACATATATAAA
Found at i:12314716 original size:4 final size:4
Alignment explanation
Indices: 12314707--12314775 Score: 56
Period size: 4 Copynumber: 17.8 Consensus size: 4
12314697 TATATTCATA
* * *
12314707 TAAT TAAT TAAT AAAT T-A- TAATT TAAT TAAA TAAT TAAT TAAT AAAT
1 TAAT TAAT TAAT TAAT TAAT TAA-T TAAT TAAT TAAT TAAT TAAT TAAT
*
12314754 T-A- TAATT TAAT TAAA TAAT TAA
1 TAAT TAA-T TAAT TAAT TAAT TAA
12314776 ACTCACATAC
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
2 2 0.04
3 4 0.08
4 39 0.76
5 6 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (4 bp):
TAAT
Found at i:12314735 original size:23 final size:26
Alignment explanation
Indices: 12314708--12314775 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 26
12314698 ATATTCATAT
12314708 AATTAATTAATAAATT-AT-AATT-T
1 AATTAATTAATAAATTAATAAATTAT
* *
12314731 AATTAAATAATTAATTAATAAATTAT
1 AATTAATTAATAAATTAATAAATTAT
12314757 AATTTAATTAA-ATAATTAA
1 AA-TTAATTAATA-AATTAA
12314776 ACTCACATAC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
23 14 0.39
24 2 0.06
25 4 0.11
26 3 0.08
27 13 0.36
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
AATTAATTAATAAATTAATAAATTAT
Found at i:12314741 original size:31 final size:31
Alignment explanation
Indices: 12314706--12314775 Score: 140
Period size: 31 Copynumber: 2.3 Consensus size: 31
12314696 TTATATTCAT
12314706 ATAATTAATTAATAAATTATAATTTAATTAA
1 ATAATTAATTAATAAATTATAATTTAATTAA
12314737 ATAATTAATTAATAAATTATAATTTAATTAA
1 ATAATTAATTAATAAATTATAATTTAATTAA
12314768 ATAATTAA
1 ATAATTAA
12314776 ACTCACATAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
ATAATTAATTAATAAATTATAATTTAATTAA
Found at i:12316417 original size:16 final size:18
Alignment explanation
Indices: 12316391--12316430 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
12316381 TATTTAATAA
*
12316391 ATATGTTAAA-TTTAAAT
1 ATATTTTAAATTTTAAAT
12316408 -TATTTTAAATTTTAAAT
1 ATATTTTAAATTTTAAAT
12316425 ATATTT
1 ATATTT
12316431 ATTCATAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 8 0.40
17 7 0.35
18 5 0.25
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (18 bp):
ATATTTTAAATTTTAAAT
Found at i:12316970 original size:2 final size:2
Alignment explanation
Indices: 12316963--12316991 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12316953 TAACGAGATA
12316963 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
12316992 AGTAAGATCC
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:12319896 original size:24 final size:25
Alignment explanation
Indices: 12319855--12319916 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 25
12319845 TAATTTACAC
* * *
12319855 AAAATTATCATACAAAAATTTTATA
1 AAAAATATCATGCAAAAATATTATA
*
12319880 AAAAATATCATGC-AAAATATTATC
1 AAAAATATCATGCAAAAATATTATA
*
12319904 ATAAATATCATGC
1 AAAAATATCATGC
12319917 TAATATAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 21 0.66
25 11 0.34
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.32
Consensus pattern (25 bp):
AAAAATATCATGCAAAAATATTATA
Found at i:12320112 original size:31 final size:32
Alignment explanation
Indices: 12320051--12320114 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 32
12320041 AATGATATGT
*
12320051 AATAAATCATGCAATTAAATTAGATCCATGCA
1 AATAAATCATGCAATTAAATTAAATCCATGCA
* *
12320083 AATAAATCATGTAA-TAAATTAAATTCATGCA
1 AATAAATCATGCAATTAAATTAAATCCATGCA
12320114 A
1 A
12320115 GATATCATAC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 16 0.55
32 13 0.45
ACGTcount: A:0.50, C:0.12, G:0.08, T:0.30
Consensus pattern (32 bp):
AATAAATCATGCAATTAAATTAAATCCATGCA
Found at i:12320307 original size:20 final size:20
Alignment explanation
Indices: 12320282--12320323 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
12320272 TAAGAAGGAT
12320282 ATAAAATAACT-GAAAATAAA
1 ATAAAA-AACTAGAAAATAAA
12320302 ATAAAAAACTAGAAAATAAA
1 ATAAAAAACTAGAAAATAAA
12320322 AT
1 AT
12320324 TACAGAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.71, C:0.05, G:0.05, T:0.19
Consensus pattern (20 bp):
ATAAAAAACTAGAAAATAAA
Found at i:12320343 original size:45 final size:45
Alignment explanation
Indices: 12320294--12320385 Score: 107
Period size: 45 Copynumber: 2.0 Consensus size: 45
12320284 AAAATAACTG
* *
12320294 AAAAT-AAAATAAAAAACTAGAAAATAAAATTACA-GAAAAAATAAA
1 AAAATCAAAAT-AAAAACTAGAAAATAAAATAAAATG-AAAAATAAA
* * *
12320339 AAAATCAAAATCAAAATTTGAAAATAAAATAAAATGAAAAATAAA
1 AAAATCAAAATAAAAACTAGAAAATAAAATAAAATGAAAAATAAA
12320384 AA
1 AA
12320386 CTTACGATCA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
45 34 0.85
46 6 0.15
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.17
Consensus pattern (45 bp):
AAAATCAAAATAAAAACTAGAAAATAAAATAAAATGAAAAATAAA
Found at i:12321646 original size:87 final size:85
Alignment explanation
Indices: 12321551--12321823 Score: 268
Period size: 86 Copynumber: 3.2 Consensus size: 85
12321541 CTTTTTAATA
* * * * * *
12321551 AAGGCTTTAAAACTTTTGGAGAATAAAATACTCCTTCTTAATAGAGGCCTTGAAACTTTTCAAAA
1 AAGGCTTTAAAACTTTTGAAAAATAAAATACT-ATTCCTACTAGAGGCTTTGAAACTTTT-AAAA
*
12321616 AATAAAATGCTCTCTC-TCAAC
64 AATAAAATGCTCTCCCTTCAAC
* * * * *
12321637 AGAGGCTTTAAAACTTTTCAAAAATAAAATGCTATCCCCACTAGAGGCTTTGAAACTTTTAGAAA
1 A-AGGCTTTAAAACTTTTGAAAAATAAAATACTATTCCTACTAGAGGCTTTGAAACTTTTAAAAA
* *
12321702 ACAAAATGCTCTCCCTTCATC
65 ATAAAATGCTCTCCCTTCAAC
* * * *
12321723 AATAGCTTTTGAAACTTTTGAAAAAT-AAATACTTTTCCTACTA-AGGCTTTGAAACTTTTTGAA
1 AA-GGC-TTTAAAACTTTTGAAAAATAAAATACTATTCCTACTAGAGGCTTTGAAAC-TTTTAAA
* *
12321786 AAATAAAATGCT-GCCCTT-ATC
63 AAATAAAATGCTCTCCCTTCAAC
12321807 GAAGGCTTTAAAACTTT
1 -AAGGCTTTAAAACTTT
12321824 CAAAAGTAAA
Statistics
Matches: 154, Mismatches: 27, Indels: 15
0.79 0.14 0.08
Matches are distributed among these distances:
83 10 0.06
84 5 0.03
85 37 0.24
86 58 0.38
87 44 0.29
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (85 bp):
AAGGCTTTAAAACTTTTGAAAAATAAAATACTATTCCTACTAGAGGCTTTGAAACTTTTAAAAAA
TAAAATGCTCTCCCTTCAAC
Found at i:12321693 original size:42 final size:42
Alignment explanation
Indices: 12321592--12321797 Score: 179
Period size: 42 Copynumber: 4.8 Consensus size: 42
12321582 TCCTTCTTAA
* *
12321592 TAGAGGCCTTGAAACTTTTCAAAAAATAAAATGCTCTCTCTCAAC
1 TAGAGGCTTTGAAACTTTTC-AAAAATAAAATGCTCTC-C-CCAC
* *
12321637 -AGAGGCTTTAAAACTTTTCAAAAATAAAATGCTATCCCCAC
1 TAGAGGCTTTGAAACTTTTCAAAAATAAAATGCTCTCCCCAC
*
12321678 TAGAGGCTTTGAAACTTTT-AGAAAACAAAATGCTCTCCCTTCATC
1 TAGAGGCTTTGAAACTTTTCA-AAAATAAAATGCTCTCCC--CA-C
* * * * * * *
12321723 AATA-GCTTTTGAAACTTTTGAAAAAT-AAATACTTTTCCTAC
1 TAGAGGC-TTTGAAACTTTTCAAAAATAAAATGCTCTCCCCAC
*
12321764 TA-AGGCTTTGAAACTTTTTGAAAAATAAAATGCT
1 TAGAGGCTTTGAAAC-TTTTCAAAAATAAAATGCT
12321798 GCCCTTATCG
Statistics
Matches: 135, Mismatches: 16, Indels: 23
0.78 0.09 0.13
Matches are distributed among these distances:
40 9 0.07
41 19 0.14
42 41 0.30
43 16 0.12
44 30 0.22
45 19 0.14
46 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.32
Consensus pattern (42 bp):
TAGAGGCTTTGAAACTTTTCAAAAATAAAATGCTCTCCCCAC
Found at i:12322202 original size:23 final size:22
Alignment explanation
Indices: 12322161--12322206 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 22
12322151 ATGAATGCCA
12322161 TGAATGAATGCAGTGAATGTAG
1 TGAATGAATGCAGTGAATGTAG
12322183 TGAATGCAATGCA-TGAAATGTAG
1 TGAATG-AATGCAGTG-AATGTAG
12322206 T
1 T
12322207 CATTTATCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.37, C:0.07, G:0.28, T:0.28
Consensus pattern (22 bp):
TGAATGAATGCAGTGAATGTAG
Found at i:12331220 original size:12 final size:12
Alignment explanation
Indices: 12331205--12331245 Score: 73
Period size: 12 Copynumber: 3.4 Consensus size: 12
12331195 ACCCGAACTT
12331205 GACCCCGAGCCC
1 GACCCCGAGCCC
12331217 GACCCCGAGCCC
1 GACCCCGAGCCC
*
12331229 GACCCCGATCCC
1 GACCCCGAGCCC
12331241 GACCC
1 GACCC
12331246 GATACTATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.17, C:0.59, G:0.22, T:0.02
Consensus pattern (12 bp):
GACCCCGAGCCC
Found at i:12331223 original size:6 final size:6
Alignment explanation
Indices: 12331205--12331245 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
12331195 ACCCGAACTT
* * *
12331205 GACCCC GAGCCC GACCCC GAGCCC GACCCC GATCCC GACCC
1 GACCCC GACCCC GACCCC GACCCC GACCCC GACCCC GACCC
12331246 GATACTATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.17, C:0.59, G:0.22, T:0.02
Consensus pattern (6 bp):
GACCCC
Found at i:12331316 original size:16 final size:16
Alignment explanation
Indices: 12331295--12331352 Score: 64
Period size: 16 Copynumber: 3.7 Consensus size: 16
12331285 ATTATTTTTT
*
12331295 AAATATAAATATTTAA
1 AAATATAAATATATAA
* *
12331311 AAATATCATTATATAA
1 AAATATAAATATATAA
* *
12331327 ATATATAAATATATAT
1 AAATATAAATATATAA
12331343 AAAT-TAAATA
1 AAATATAAATA
12331353 ATTATATAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
15 6 0.18
16 28 0.82
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATATAAATATATAA
Found at i:12331331 original size:8 final size:8
Alignment explanation
Indices: 12331297--12331341 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
12331287 TATTTTTTAA
12331297 ATATAAAT
1 ATATAAAT
* *
12331305 ATTTAAAA
1 ATATAAAT
* *
12331313 ATATCATT
1 ATATAAAT
12331321 ATATAAAT
1 ATATAAAT
12331329 ATATAAAT
1 ATATAAAT
12331337 ATATA
1 ATATA
12331342 TAAATTAAAT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (8 bp):
ATATAAAT
Found at i:12331352 original size:15 final size:17
Alignment explanation
Indices: 12331318--12331362 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
12331308 TAAAAATATC
*
12331318 ATTATATAAA-TATATAA
1 ATTATATAAATTAAAT-A
12331335 ATATATATAAATTAAATA
1 AT-TATATAAATTAAATA
12331353 ATTATATAAA
1 ATTATATAAA
12331363 AAATATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 10 0.40
18 11 0.44
19 4 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATTATATAAATTAAATA
Found at i:12331571 original size:20 final size:20
Alignment explanation
Indices: 12331548--12331586 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12331538 TAGTTTTATT
*
12331548 TAGAGTTTCGAGTTTACATA
1 TAGAGTTTAGAGTTTACATA
*
12331568 TAGAGTTTAGGGTTTACAT
1 TAGAGTTTAGAGTTTACAT
12331587 TTTAAGGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.08, G:0.23, T:0.41
Consensus pattern (20 bp):
TAGAGTTTAGAGTTTACATA
Found at i:12334306 original size:46 final size:46
Alignment explanation
Indices: 12334230--12334352 Score: 167
Period size: 46 Copynumber: 2.7 Consensus size: 46
12334220 GATCATTTGG
* * *
12334230 AAATGAATTTAAAAACTGCCTTT-AGCAAAGGCTCCATAACTTTTAA
1 AAATAAATTTAAAAACT-CCTTTAAGCAAAGGCTCAACAACTTTTAA
* * *
12334276 AAATAAATTTAAAAACTCATTTAAGTAAAGGCTCAACAACTTTTGA
1 AAATAAATTTAAAAACTCCTTTAAGCAAAGGCTCAACAACTTTTAA
*
12334322 AAATAAATTTAAAAACTCCTTTAAACAAAGG
1 AAATAAATTTAAAAACTCCTTTAAGCAAAGG
12334353 TTTAATGCCT
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
45 4 0.06
46 63 0.94
ACGTcount: A:0.47, C:0.15, G:0.09, T:0.29
Consensus pattern (46 bp):
AAATAAATTTAAAAACTCCTTTAAGCAAAGGCTCAACAACTTTTAA
Found at i:12334747 original size:81 final size:79
Alignment explanation
Indices: 12334581--12334996 Score: 261
Period size: 81 Copynumber: 5.2 Consensus size: 79
12334571 TGCTTAGAGG
* * * * * * * * *
12334581 TCTTAGGAAATAATTTAAAAATTTGAAGTTTTACTTGAAGATCTTGAAAATCCTTTAAAAATTTA
1 TCTTTGGAAATCATTTAAAAATCTAAAATTTTGCTTAAAGATCATGAAAATCATTT--AAATTTA
* * * *
12334646 AGATTTGGCTCTAAGG
64 AGATTTTGCCCAAAGA
* * ** *
12334662 TCTTTGGAAATCATTAAAAAATCTAAAATTTTGTTTGGAGGTCATGAAAATCATTTAAAATTTTA
1 TCTTTGGAAATCATTTAAAAATCTAAAATTTTGCTTAAAGATCATGAAAATCATTT-AAA-TTTA
12334727 AGATTTTGCCCAAAGA
64 AGATTTTGCCCAAAGA
* * * * *
12334743 TCTTTGAAAATC-TTTCAAAAATTTAAAATTTTGCCTT-AAGATC-TTAGAGATCATTTAGATTT
1 TCTTTGGAAATCATTT-AAAAATCTAAAATTTTG-CTTAAAGATCATGA-AAATCATTTAAATTT
*
12334805 AAGATTTTGCCCAAAGG
63 AAGATTTTGCCCAAAGA
* * * * * ** * * * * *
12334822 TTTTTGAAAATCTTTTAAAATTTTAAAGCTTTG-TCTATAGGTCATGGAGATCATTTAGATTTAA
1 TCTTTGGAAATCATTTAAAAATCTAAAATTTTGCT-TAAAGATCATGAAAATCATTTAAATTTAA
*
12334886 GATTTTTCCCAAA-A
65 GATTTTGCCCAAAGA
* ** * * *
12334900 GTCTTTTGAAATTGTTTAAACATCTAAAATTTTGCTCAAAGATCTTAGAAAATC-TTTCAAATTT
1 -TCTTTGGAAATCATTTAAAAATCTAAAATTTTGCTTAAAGATCAT-GAAAATCATTT-AAA-TT
* *
12334964 TAAAATTTTGCTCGAAAG-
62 TAAGATTTTGC-CCAAAGA
12334982 TCTTTGGAAATCATT
1 TCTTTGGAAATCATT
12334997 CAAACTTTTA
Statistics
Matches: 261, Mismatches: 59, Indels: 30
0.75 0.17 0.09
Matches are distributed among these distances:
77 1 0.00
78 1 0.00
79 109 0.42
80 22 0.08
81 122 0.47
82 6 0.02
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (79 bp):
TCTTTGGAAATCATTTAAAAATCTAAAATTTTGCTTAAAGATCATGAAAATCATTTAAATTTAAG
ATTTTGCCCAAAGA
Found at i:12334751 original size:41 final size:41
Alignment explanation
Indices: 12334618--12335015 Score: 187
Period size: 41 Copynumber: 9.9 Consensus size: 41
12334608 GTTTTACTTG
* * * * *
12334618 AAGATC-TTGAAAATCCTTTAAAAATTTAAGATTTGGCTCT
1 AAGATCTTTGAAAATCATTTAAAATTTTAAGATTTTGCCCA
* * * * * * ****
12334658 AAGGTCTTTGGAAATCATTAAAAAATCTAAAATTTTGTTTG
1 AAGATCTTTGAAAATCATTTAAAATTTTAAGATTTTGCCCA
* * *
12334699 GAGGTC-ATGAAAATCATTTAAAATTTTAAGATTTTGCCCA
1 AAGATCTTTGAAAATCATTTAAAATTTTAAGATTTTGCCCA
* * **
12334739 AAGATCTTTGAAAATC-TTTCAAAAATTTAAAATTTTGCCTT
1 AAGATCTTTGAAAATCATTT-AAAATTTTAAGATTTTGCCCA
* * *
12334780 AAGATCTTAG-AGATCATTT-AGA-TTTAAGATTTTGCCCA
1 AAGATCTTTGAAAATCATTTAAAATTTTAAGATTTTGCCCA
* * * * * *
12334818 AAGGTTTTTGAAAATCTTTTAAAATTTTAA-AGCTTTGTCTA
1 AAGATCTTTGAAAATCATTTAAAATTTTAAGA-TTTTGCCCA
* * * * * * *
12334859 TAGGTC-ATGGAGATCATTT-AGA-TTTAAGATTTTTCCCA
1 AAGATCTTTGAAAATCATTTAAAATTTTAAGATTTTGCCCA
** * * *
12334897 AA-AGTCTTTTG-AAATTGTTTAAACA-TCTAAAATTTTGCTCA
1 AAGA-TC-TTTGAAAATCATTTAAA-ATTTTAAGATTTTGCCCA
* * * *
12334938 AAGATCTTAGAAAATC-TTTCAAATTTTAAAATTTTGCTCGA
1 AAGATCTTTGAAAATCATTTAAAATTTTAAGATTTTGC-CCA
* * *
12334979 AAG-TCTTTGGAAATCATTCAAACTTTTAAGATTTTGC
1 AAGATCTTTGAAAATCATTTAAAATTTTAAGATTTTGC
12335016 TTGAAGGTCT
Statistics
Matches: 262, Mismatches: 77, Indels: 37
0.70 0.20 0.10
Matches are distributed among these distances:
38 33 0.13
39 19 0.07
40 85 0.32
41 124 0.47
42 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.40
Consensus pattern (41 bp):
AAGATCTTTGAAAATCATTTAAAATTTTAAGATTTTGCCCA
Found at i:12334833 original size:79 final size:77
Alignment explanation
Indices: 12334723--12334948 Score: 247
Period size: 79 Copynumber: 2.9 Consensus size: 77
12334713 CATTTAAAAT
* *
12334723 TTTAAGATTTTGCCCAAAGATCTTTGAAAATCTTTCAAAAATTTAAAATTTTGCCTTAAGATCTT
1 TTTAAGATTTTGCCCAAAGGTTTTTGAAAATCTTT-AAAAATTTAAAATTTTG-CTTAAGATCTT
12334788 AGAGATCATTTAGA
64 AGAGATCATTTAGA
* ** * *
12334802 TTTAAGATTTTGCCCAAAGGTTTTTGAAAATCTTTTAAAATTTTAAAGCTTTG-TCTATAGGTCA
1 TTTAAGATTTTGCCCAAAGGTTTTTGAAAATC-TTTAAAAATTTAAAATTTTGCT-TA-AGATCT
*
12334866 TGGAGATCATTTAGA
63 TAGAGATCATTTAGA
* * * * * * *
12334881 TTTAAGATTTTTCCCAAAAGTCTTTTGAAATTGTTTAAACATCTAAAATTTTGCTCAAAGATCTT
1 TTTAAGATTTTGCCCAAAGGT-TTTTGAAAATCTTTAAAAATTTAAAATTTTGCT-TAAGATCTT
12334946 AGA
64 AGA
12334949 AAATCTTTCA
Statistics
Matches: 121, Mismatches: 21, Indels: 10
0.80 0.14 0.07
Matches are distributed among these distances:
77 1 0.01
78 2 0.02
79 103 0.85
80 15 0.12
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.41
Consensus pattern (77 bp):
TTTAAGATTTTGCCCAAAGGTTTTTGAAAATCTTTAAAAATTTAAAATTTTGCTTAAGATCTTAG
AGATCATTTAGA
Found at i:12335026 original size:41 final size:40
Alignment explanation
Indices: 12334924--12335036 Score: 147
Period size: 41 Copynumber: 2.8 Consensus size: 40
12334914 TTTAAACATC
* * *
12334924 TAAAATTTTGCTC-AAAGATCTTAGAAAATCTTTCAAATTT
1 TAAAATTTTGCTCGAAAG-TCTTTGGAAATCATTCAAATTT
12334964 TAAAATTTTGCTCGAAAGTCTTTGGAAATCATTCAAACTTT
1 TAAAATTTTGCTCGAAAGTCTTTGGAAATCATTCAAA-TTT
* * *
12335005 TAAGATTTTGCTTGAAGGTCTTTGGAAATCAT
1 TAAAATTTTGCTCGAAAGTCTTTGGAAATCAT
12335037 GTTCTCATTC
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
40 29 0.45
41 36 0.55
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (40 bp):
TAAAATTTTGCTCGAAAGTCTTTGGAAATCATTCAAATTT
Found at i:12336570 original size:21 final size:22
Alignment explanation
Indices: 12336544--12336584 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
12336534 ACATTCATCT
12336544 TTTTTTTTC-CCTTTTCTTTTC
1 TTTTTTTTCTCCTTTTCTTTTC
*
12336565 TTTTTTTTCTCTTTTTCTTT
1 TTTTTTTTCTCCTTTTCTTT
12336585 ATTGATTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTTTTTTCTCCTTTTCTTTTC
Found at i:12337168 original size:37 final size:39
Alignment explanation
Indices: 12337094--12337169 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 39
12337084 TCTAAATGTA
*
12337094 TCCATTTTGCTTCTTAGTATGGAGAAGGTGATACTTAGT
1 TCCATTTTGCTTCATAGTATGGAGAAGGTGATACTTAGT
*
12337133 TCCATTTTG-TCTCATAGTAT-G-GAAGGTGATCCTTAGT
1 TCCATTTTGCT-TCATAGTATGGAGAAGGTGATACTTAGT
12337170 CAGAGTTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 15 0.44
38 2 0.06
39 17 0.50
ACGTcount: A:0.22, C:0.14, G:0.22, T:0.41
Consensus pattern (39 bp):
TCCATTTTGCTTCATAGTATGGAGAAGGTGATACTTAGT
Found at i:12337539 original size:13 final size:13
Alignment explanation
Indices: 12337504--12337541 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
12337494 ATTATTTGTC
12337504 CTTTTTTTTT-CT
1 CTTTTTTTTTACT
*
12337516 CACTTTTTTTTACT
1 C-TTTTTTTTTACT
12337530 CTTTTTTTTTAC
1 CTTTTTTTTTAC
12337542 ATATCCCCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 1 0.05
13 18 0.82
14 3 0.14
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (13 bp):
CTTTTTTTTTACT
Found at i:12339916 original size:28 final size:28
Alignment explanation
Indices: 12339885--12339942 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
12339875 TATCAAATCA
*
12339885 AACCTTATATCATTATCCATTATAAACT
1 AACCTTATATCATCATCCATTATAAACT
12339913 AACCTTATATCATCATCCATTATAAACT
1 AACCTTATATCATCATCCATTATAAACT
12339941 AA
1 AA
12339943 TAAGGCACAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.41, C:0.22, G:0.00, T:0.36
Consensus pattern (28 bp):
AACCTTATATCATCATCCATTATAAACT
Found at i:12341461 original size:26 final size:26
Alignment explanation
Indices: 12341432--12341493 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
12341422 TAAGGTTTAA
*
12341432 TTTAGGGTTTGGGTTTCACTTAAGGT
1 TTTAGGGTTTGGGTTTCACCTAAGGT
* *
12341458 TTTAAGGTTTGGGTTTCACCTAGGGT
1 TTTAGGGTTTGGGTTTCACCTAAGGT
12341484 TTTAGGGTTT
1 TTTAGGGTTT
12341494 CATTAGGATT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.15, C:0.08, G:0.31, T:0.47
Consensus pattern (26 bp):
TTTAGGGTTTGGGTTTCACCTAAGGT
Found at i:12341686 original size:14 final size:13
Alignment explanation
Indices: 12341649--12341703 Score: 51
Period size: 12 Copynumber: 4.2 Consensus size: 13
12341639 TAAAATTTTA
*
12341649 TTATTATTATTAT
1 TTATTTTTATTAT
* *
12341662 TGA-TATTATTAT
1 TTATTTTTATTAT
12341674 TTATCTTTTATTATT
1 TTAT-TTTTATTA-T
12341689 TTATTTTT-TTAT
1 TTATTTTTATTAT
12341701 TTA
1 TTA
12341704 ATAATTCTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
12 15 0.42
13 5 0.14
14 11 0.31
15 5 0.14
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (13 bp):
TTATTTTTATTAT
Found at i:12341700 original size:13 final size:15
Alignment explanation
Indices: 12341667--12341702 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
12341657 ATTATTGATA
12341667 TTATTA-TTTATCTT
1 TTATTATTTTATCTT
12341681 TTATTATTTTAT-TT
1 TTATTATTTTATCTT
12341695 TT-TTATTT
1 TTATTATTT
12341703 AATAATTCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.29
14 10 0.48
15 5 0.24
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (15 bp):
TTATTATTTTATCTT
Found at i:12343139 original size:120 final size:121
Alignment explanation
Indices: 12343005--12343247 Score: 416
Period size: 121 Copynumber: 2.0 Consensus size: 121
12342995 CTTCTGGTCC
* * * *
12343005 TCCTCTTTTTCC-TTTTTGCGAATGCCTCTTTAACGAAAGCCTGCCTTTTTCTTCTTTCTGCTTG
1 TCCTCTTTTTCCTTTTTTGAGAATGCCTCTCTAACGAAAGCCTCCCTGTTTCTTCTTTCTGCTTG
*
12343069 CTGCCAAGTTGTTCACATTCTTGATTTTTTCTAGTTCAGTTTTTTTGTTTTCTGCT
66 CTGCCAAGTTGTTCACATTCTTCATTTTTTCTAGTTCAGTTTTTTTGTTTTCTGCT
*
12343125 TCCTCTTTTTCCTTTTTTGAGAATGCCTCTCTCACGAAAGCCTCCCTGTTTCTTCTTTCTGCTTG
1 TCCTCTTTTTCCTTTTTTGAGAATGCCTCTCTAACGAAAGCCTCCCTGTTTCTTCTTTCTGCTTG
*
12343190 CTGCCCAGTTGTTCACATTCTTCATTTTTTCTAGTTCAGTTTTTTTGTTTTCTGCT
66 CTGCCAAGTTGTTCACATTCTTCATTTTTTCTAGTTCAGTTTTTTTGTTTTCTGCT
12343246 TC
1 TC
12343248 ACCCCTCGTC
Statistics
Matches: 115, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
120 12 0.10
121 103 0.90
ACGTcount: A:0.11, C:0.25, G:0.13, T:0.51
Consensus pattern (121 bp):
TCCTCTTTTTCCTTTTTTGAGAATGCCTCTCTAACGAAAGCCTCCCTGTTTCTTCTTTCTGCTTG
CTGCCAAGTTGTTCACATTCTTCATTTTTTCTAGTTCAGTTTTTTTGTTTTCTGCT
Found at i:12343778 original size:3 final size:3
Alignment explanation
Indices: 12343770--12343807 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
12343760 TTTATAGCCT
12343770 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
12343808 CGGCTTTATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:12345478 original size:45 final size:44
Alignment explanation
Indices: 12345429--12345515 Score: 129
Period size: 45 Copynumber: 2.0 Consensus size: 44
12345419 AGTTAAAATC
12345429 TACAAAATAAACAAATAAATTAGTACACATAAAAAAGTCATAAGA
1 TACAAAATAAACAAATAAATTAGTACACATAAAAAA-TCATAAGA
* * * *
12345474 TACAAAATAAACAAATAAGTTAGTGCATATGAAAAATCATAA
1 TACAAAATAAACAAATAAATTAGTACACATAAAAAATCATAA
12345516 ATAAAATCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
44 6 0.16
45 32 0.84
ACGTcount: A:0.60, C:0.10, G:0.08, T:0.22
Consensus pattern (44 bp):
TACAAAATAAACAAATAAATTAGTACACATAAAAAATCATAAGA
Found at i:12346248 original size:14 final size:14
Alignment explanation
Indices: 12346231--12346264 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
12346221 ATGAACAAAA
12346231 AAAAAAAACCATGC
1 AAAAAAAACCATGC
* *
12346245 AAAAATAATCATGC
1 AAAAAAAACCATGC
12346259 AAAAAA
1 AAAAAA
12346265 TATATAATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.68, C:0.15, G:0.06, T:0.12
Consensus pattern (14 bp):
AAAAAAAACCATGC
Found at i:12346495 original size:6 final size:6
Alignment explanation
Indices: 12346479--12346558 Score: 60
Period size: 6 Copynumber: 13.3 Consensus size: 6
12346469 ATATAAGAAG
* * *
12346479 AATAGAA AATAAA AATAAA AAT-AA TA-AAA AATAAA ATTAGAG AA-AAA
1 AATA-AA AATAAA AATAAA AATAAA AATAAA AATAAA AATA-AA AATAAA
*
12346526 ATTAAAA AATAAA AAT-AA AATAAAA AATAAA AA
1 AAT-AAA AATAAA AATAAA AAT-AAA AATAAA AA
12346559 CTTGTTATTA
Statistics
Matches: 58, Mismatches: 8, Indels: 15
0.72 0.10 0.19
Matches are distributed among these distances:
5 13 0.22
6 29 0.50
7 16 0.28
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (6 bp):
AATAAA
Found at i:12346496 original size:22 final size:22
Alignment explanation
Indices: 12346460--12346558 Score: 82
Period size: 22 Copynumber: 4.5 Consensus size: 22
12346450 ATAAAATATA
* * *
12346460 AAAAAAGAAATATAAGAAGAAT
1 AAAAAATAAAAATAAGAAAAAT
*
12346482 AGAAAATAAAAATAA-AAATAAT
1 AAAAAATAAAAATAAGAAA-AAT
*
12346504 AAAAAATAAAATTAGAGAAAAAATT
1 AAAAAATAAAAATA-AG-AAAAA-T
12346529 AAAAAATAAAAAT----AAAAT
1 AAAAAATAAAAATAAGAAAAAT
12346547 AAAAAATAAAAA
1 AAAAAATAAAAA
12346559 CTTGTTATTA
Statistics
Matches: 65, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
18 13 0.20
19 4 0.06
21 2 0.03
22 27 0.42
23 1 0.02
24 2 0.03
25 16 0.25
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (22 bp):
AAAAAATAAAAATAAGAAAAAT
Found at i:12346524 original size:17 final size:16
Alignment explanation
Indices: 12346489--12346551 Score: 63
Period size: 16 Copynumber: 3.7 Consensus size: 16
12346479 AATAGAAAAT
*
12346489 AAAAATAAAAATAATA
1 AAAAATAAAAATAAGA
*
12346505 AAAAATAAAATTAGAGA
1 AAAAATAAAAATA-AGA
*
12346522 AAAAATTAAAAAATAAAA
1 AAAAA-T-AAAAATAAGA
12346540 ATAAAATAAAAA
1 A-AAAATAAAAA
12346552 ATAAAAACTT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
16 12 0.31
17 12 0.31
18 5 0.13
19 10 0.26
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.17
Consensus pattern (16 bp):
AAAAATAAAAATAAGA
Found at i:12346534 original size:8 final size:7
Alignment explanation
Indices: 12346450--12346558 Score: 66
Period size: 7 Copynumber: 15.0 Consensus size: 7
12346440 TCATCATAAT
*
12346450 ATAAAAT
1 ATAAAAA
12346457 ATAAAAA
1 ATAAAAA
*
12346464 A-AGAAAT
1 ATA-AAAA
12346471 ATAAGAAGA
1 ATAA-AA-A
*
12346480 ATAGAAA
1 ATAAAAA
12346487 AT-AAAA
1 ATAAAAA
12346493 ATAAAAATA
1 AT-AAAA-A
12346502 ATAAAAA
1 ATAAAAA
12346509 ATAAAATTA
1 ATAAAA--A
*
12346518 GAGAAAAA
1 -ATAAAAA
12346526 ATTAAAAA
1 A-TAAAAA
12346534 AT-AAAA
1 ATAAAAA
12346540 AT--AAA
1 ATAAAAA
12346545 ATAAAAA
1 ATAAAAA
12346552 ATAAAAA
1 ATAAAAA
12346559 CTTGTTATTA
Statistics
Matches: 82, Mismatches: 7, Indels: 26
0.71 0.06 0.23
Matches are distributed among these distances:
5 5 0.06
6 12 0.15
7 34 0.41
8 19 0.23
9 7 0.09
10 5 0.06
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (7 bp):
ATAAAAA
Found at i:12354798 original size:18 final size:17
Alignment explanation
Indices: 12354777--12354815 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
12354767 AAATTTCAAC
*
12354777 TTTTGTATCAAGGTCCAA
1 TTTTGTATCAACGTCC-A
*
12354795 TTTTTTATCAACGTCCA
1 TTTTGTATCAACGTCCA
12354812 TTTT
1 TTTT
12354816 AATCTTGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.23, C:0.18, G:0.10, T:0.49
Consensus pattern (17 bp):
TTTTGTATCAACGTCCA
Found at i:12355024 original size:17 final size:18
Alignment explanation
Indices: 12354992--12355030 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
12354982 TTATTTTTCT
12354992 TTTTTATCATATTTATTA
1 TTTTTATCATATTTATTA
*
12355010 TTTTTATCTTA-TTATTA
1 TTTTTATCATATTTATTA
12355027 TTTT
1 TTTT
12355031 ATATTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTATCATATTTATTA
Found at i:12355031 original size:25 final size:25
Alignment explanation
Indices: 12354981--12355038 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
12354971 ACTAAAAAGG
* *
12354981 ATTATTTTTCTTTTTTATCATATTT
1 ATTATTTTTATTTATTATCATATTT
*
12355006 ATTATTTTTATCTTATTATTAT-TTT
1 ATTATTTTTAT-TTATTATCATATTT
12355031 A-TATTTTT
1 ATTATTTTT
12355039 TAGGGAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 7 0.24
25 14 0.48
26 8 0.28
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.72
Consensus pattern (25 bp):
ATTATTTTTATTTATTATCATATTT
Found at i:12357438 original size:22 final size:22
Alignment explanation
Indices: 12357397--12357445 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
12357387 ATTCGAGGAC
*
12357397 TTTTTTTTTTTTGGTTTTTT-A
1 TTTTTATTTTTTGGTTTTTTAA
*
12357418 TTTTTATTTTTTGATTTTTTTAA
1 TTTTTATTTTTTG-GTTTTTTAA
12357441 TTTTT
1 TTTTT
12357446 GAACTTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 12 0.50
22 6 0.25
23 6 0.25
ACGTcount: A:0.10, C:0.00, G:0.06, T:0.84
Consensus pattern (22 bp):
TTTTTATTTTTTGGTTTTTTAA
Found at i:12359071 original size:22 final size:22
Alignment explanation
Indices: 12359043--12359088 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
12359033 CTAAGCCAAT
12359043 AACTC-AACTAAAGAAATAAAAG
1 AACTCAAACTAAA-AAATAAAAG
*
12359065 AACTCAAAACTAAAAACTAAAAG
1 AACTC-AAACTAAAAAATAAAAG
12359088 A
1 A
12359089 GGTAAGAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 5 0.24
23 9 0.43
24 7 0.33
ACGTcount: A:0.65, C:0.15, G:0.07, T:0.13
Consensus pattern (22 bp):
AACTCAAACTAAAAAATAAAAG
Found at i:12361152 original size:19 final size:20
Alignment explanation
Indices: 12361130--12361170 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
12361120 AATACAAAAT
*
12361130 AAATCAAAATAAAATC-AAA
1 AAATAAAAATAAAATCGAAA
12361149 AAATAAAAATAAAATCGAAA
1 AAATAAAAATAAAATCGAAA
12361169 AA
1 AA
12361171 GGAAAACCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.15
Consensus pattern (20 bp):
AAATAAAAATAAAATCGAAA
Found at i:12361176 original size:19 final size:19
Alignment explanation
Indices: 12361135--12361176 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
12361125 AAAATAAATC
*
12361135 AAAATAAAATCAAAAAATA
1 AAAATAAAATCAAAAAAGA
*
12361154 AAAATAAAATCGAAAAAGGA
1 AAAATAAAATC-AAAAAAGA
12361174 AAA
1 AAA
12361177 CCTGTGATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.76, C:0.05, G:0.07, T:0.12
Consensus pattern (19 bp):
AAAATAAAATCAAAAAAGA
Found at i:12362005 original size:66 final size:66
Alignment explanation
Indices: 12361854--12362005 Score: 164
Period size: 66 Copynumber: 2.3 Consensus size: 66
12361844 GACTAGGACG
* * ** * * *
12361854 AAACTACGAGTCTAAAAGATAAAGTGACCAAAACTGAGTCAAGGTAAAAAACAAATGACTGTGAT
1 AAACCACGAGTCTAAAAAATAAAGCAACCAAAACTAAGTCAAGATAAAAAACAAATGACTGGGAT
12361919 A
66 A
** * **
12361920 AAACCATAAGTCTAAAAAATAAAGCAACCAAATCTAAGTCAAGATAAAAAATGAATGA-TCGGGA
1 AAACCACGAGTCTAAAAAATAAAGCAACCAAAACTAAGTCAAGATAAAAAACAAATGACT-GGGA
12361984 TA
65 TA
12361986 AAACCACGAGTC-AAGAAAAT
1 AAACCACGAGTCTAA-AAAAT
12362006 GATTTGGACT
Statistics
Matches: 70, Mismatches: 14, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
65 3 0.04
66 67 0.96
ACGTcount: A:0.53, C:0.14, G:0.16, T:0.17
Consensus pattern (66 bp):
AAACCACGAGTCTAAAAAATAAAGCAACCAAAACTAAGTCAAGATAAAAAACAAATGACTGGGAT
A
Found at i:12362146 original size:121 final size:120
Alignment explanation
Indices: 12361916--12362252 Score: 327
Period size: 121 Copynumber: 2.8 Consensus size: 120
12361906 AAATGACTGT
* * * * * * *
12361916 GATAAAACCATAAGTCTAAAAAATAAAGCAACCAAATCTAAGTCAAGATAAAAAATGAATGATCG
1 GATAAAACCACAAGTCTAAAAGATAAAGCAACCAGA-CTGAGTCAAGGTCAAAAATGAATGATAG
* * * * * *
12361981 GGATAAAACCACGAGTCAAGAAAATGATTTGGACTAAACCAAGATTGAATGACCAT
65 GGATGAAACCACGAGTCAAGAAAATGATCTGGACTAAACCAAGATCGAATAACAAG
* * * * *
12362037 GATGAAATCACAAGTCTAAAAGATAAAGCAACCAGGACTGAGTCGAGGTCAAAAATGAATAATTG
1 GATAAAACCACAAGTCTAAAAGATAAAGCAACCA-GACTGAGTCAAGGTCAAAAATGAATGATAG
* * *
12362102 GGATGAAACCATGAGTC-AGAAAGATGATCTGGAC-AGAGCTAAGATCGAATAACAAG
65 GGATGAAACCACGAGTCAAGAAA-ATGATCTGGACTA-AACCAAGATCGAATAACAAG
*** * * * *
12362158 GATAAAACCGTGAGTCCAAAAGATAAAGTAACCAGAATCGAGTCAAGGTCGAAAATGAATGATAG
1 GATAAAACCACAAGTCTAAAAGATAAAGCAACCAGACT-GAGTCAAGGTCAAAAATGAATGATAG
* * * *
12362223 GGATGAAATCGCGAGTTAAAAAAATGATCT
65 GGATGAAACCACGAGTCAAGAAAATGATCT
12362253 AGATTGAGCC
Statistics
Matches: 174, Mismatches: 37, Indels: 10
0.79 0.17 0.05
Matches are distributed among these distances:
120 9 0.05
121 160 0.92
122 5 0.03
ACGTcount: A:0.47, C:0.14, G:0.21, T:0.18
Consensus pattern (120 bp):
GATAAAACCACAAGTCTAAAAGATAAAGCAACCAGACTGAGTCAAGGTCAAAAATGAATGATAGG
GATGAAACCACGAGTCAAGAAAATGATCTGGACTAAACCAAGATCGAATAACAAG
Found at i:12363330 original size:25 final size:25
Alignment explanation
Indices: 12363300--12363349 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
12363290 TTCTCCTTCA
*
12363300 TTTTTTCTTTTTTTTTTTTTTTTTT
1 TTTTTTCTTTTTTTATTTTTTTTTT
12363325 TTTTTTCTTTTTTTATTTTTTTTTT
1 TTTTTTCTTTTTTTATTTTTTTTTT
12363350 CATTTCATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.02, C:0.04, G:0.00, T:0.94
Consensus pattern (25 bp):
TTTTTTCTTTTTTTATTTTTTTTTT
Found at i:12363362 original size:20 final size:19
Alignment explanation
Indices: 12363321--12363365 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
12363311 TTTTTTTTTT
** *
12363321 TTTTTTTTTTCTTTTTTTA
1 TTTTTTTTTTCTTTCATCA
12363340 TTTTTTTTTTCATTTCATCA
1 TTTTTTTTTTC-TTTCATCA
12363360 TTTTTT
1 TTTTTT
12363366 AAGAAAACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTTTTTTTCTTTCATCA
Found at i:12363365 original size:1 final size:1
Alignment explanation
Indices: 12363300--12363349 Score: 73
Period size: 1 Copynumber: 50.0 Consensus size: 1
12363290 TTCTCCTTCA
* * *
12363300 TTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTATTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
12363350 CATTTCATCA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.02, C:0.04, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:12366454 original size:37 final size:36
Alignment explanation
Indices: 12366383--12366454 Score: 83
Period size: 37 Copynumber: 2.0 Consensus size: 36
12366373 AAAAGAAAAG
* * *
12366383 GGTTAGTAAAAATACTATACAAAGACCACCATACAA
1 GGTTAGTAAAAATACTATACAAAAAACACAATACAA
*
12366419 GGTTAGTATACAAATA-TATACAAAAAAGACAATACA
1 GGTTAGTA-A-AAATACTATACAAAAAACACAATACA
12366455 TAGTATTACA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
36 8 0.27
37 17 0.57
38 5 0.17
ACGTcount: A:0.53, C:0.15, G:0.11, T:0.21
Consensus pattern (36 bp):
GGTTAGTAAAAATACTATACAAAAAACACAATACAA
Found at i:12367781 original size:19 final size:19
Alignment explanation
Indices: 12367759--12367805 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
12367749 AATATAAAAT
12367759 AAATAAAAATAAAATCAAA
1 AAATAAAAATAAAATCAAA
12367778 AAATAAAAATAAAATCAAA
1 AAATAAAAATAAAATCAAA
*
12367797 AAAGAAAAA
1 AAATAAAAA
12367806 CCTACGATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.81, C:0.04, G:0.02, T:0.13
Consensus pattern (19 bp):
AAATAAAAATAAAATCAAA
Found at i:12368697 original size:3 final size:3
Alignment explanation
Indices: 12368682--12368875 Score: 109
Period size: 3 Copynumber: 66.3 Consensus size: 3
12368672 CAATTAAAAA
* * * * *
12368682 AAT AAA AAT -AT AAT AAT AAT AAT AAT AAT AAT AAC AAC AAC AAC AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
12368729 AAT ACT AAT AACT -AT AGT AGT AGT AAT AGT AAT AAT AAT AAT AAT
1 AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* ** * * *
12368774 ATT AAT AAT AAT GGT AAT -AC AAT ATAT GAT AAT AAT -AC AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT
* * * *
12368817 AAT AGT AAT -GT AAT AAT AAT -AT AAT ATAT AAC ATCT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT A-AT AAT AAT AAT
12368862 -AT AAT AAT -AT AAT A
1 AAT AAT AAT AAT AAT A
12368876 TAGTATAGTC
Statistics
Matches: 148, Mismatches: 30, Indels: 26
0.73 0.15 0.13
Matches are distributed among these distances:
2 14 0.09
3 127 0.86
4 7 0.05
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:12372410 original size:17 final size:17
Alignment explanation
Indices: 12372390--12372506 Score: 58
Period size: 18 Copynumber: 6.6 Consensus size: 17
12372380 GATTCCAAAA
12372390 TCACAAAGATTCAAGAT
1 TCACAAAGATTCAAGAT
* *
12372407 TCACAATGATTCCAAAAGT
1 TCACAAAGATT-CAAGA-T
*
12372426 TCATAAATGATTCAAGATT
1 TCACAAA-GATTCAAGA-T
* *
12372445 TTA-AAAAATTTCAAGAT
1 TCACAAAGA-TTCAAGAT
** *
12372462 TCGTAAAGGTTTCAAGAT
1 TCACAAA-GATTCAAGAT
** *
12372480 TTGCAAAGTTTCAA-AT
1 TCACAAAGATTCAAGAT
*
12372496 TCACAAGGATT
1 TCACAAAGATT
12372507 TTCAGATTTG
Statistics
Matches: 76, Mismatches: 18, Indels: 13
0.71 0.17 0.12
Matches are distributed among these distances:
16 9 0.12
17 20 0.26
18 30 0.39
19 13 0.17
20 4 0.05
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.32
Consensus pattern (17 bp):
TCACAAAGATTCAAGAT
Found at i:12372416 original size:34 final size:36
Alignment explanation
Indices: 12372377--12372444 Score: 104
Period size: 34 Copynumber: 1.9 Consensus size: 36
12372367 AAAATTTTGT
12372377 AATGATTCCAAAA-TCACAAA-GATTCAAGATTCAC
1 AATGATTCCAAAAGTCACAAATGATTCAAGATTCAC
*
12372411 AATGATTCCAAAAGTTCATAAATGATTCAAGATT
1 AATGATTCCAAAAG-TCACAAATGATTCAAGATT
12372445 TTAAAAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
34 13 0.43
36 6 0.20
37 11 0.37
ACGTcount: A:0.46, C:0.16, G:0.10, T:0.28
Consensus pattern (36 bp):
AATGATTCCAAAAGTCACAAATGATTCAAGATTCAC
Found at i:12372573 original size:17 final size:17
Alignment explanation
Indices: 12372553--12372626 Score: 69
Period size: 17 Copynumber: 4.3 Consensus size: 17
12372543 TCAATTTTGT
*
12372553 AAGAATTTTAGGTTCGC
1 AAGAATTTGAGGTTCGC
*
12372570 AAGAATTATGAGATTCGC
1 AAGAATT-TGAGGTTCGC
* *
12372588 AATAA-TGGAGGATTCGC
1 AAGAATTTGAGG-TTCGC
* *
12372605 AAGAATTTCAAGTTCGC
1 AAGAATTTGAGGTTCGC
12372622 AAGAA
1 AAGAA
12372627 CACAAAGATT
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
16 3 0.07
17 27 0.60
18 15 0.33
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (17 bp):
AAGAATTTGAGGTTCGC
Found at i:12372672 original size:17 final size:17
Alignment explanation
Indices: 12372646--12372771 Score: 64
Period size: 17 Copynumber: 7.4 Consensus size: 17
12372636 TCGTAAAACT
12372646 TTTCAAATTTGCAAGAA
1 TTTCAAATTTGCAAGAA
* *
12372663 TTTCATATTTGCAATAA
1 TTTCAAATTTGCAAGAA
*
12372680 -TTCAAAGATT-CATAAGAA
1 TTTCAAA-TTTGC--AAGAA
**
12372698 -TTCAAATTTATAAGAA
1 TTTCAAATTTGCAAGAA
* * * *
12372714 TTTAAAGATTCGTAA-AGC
1 TTTCAA-ATTTGCAAGA-A
*
12372732 TTTCAGATTTGCAAGAA
1 TTTCAAATTTGCAAGAA
* *
12372749 TTTCAAGTTTACAAGAA
1 TTTCAAATTTGCAAGAA
12372766 -TTCAAA
1 TTTCAAA
12372772 GACTCACAAG
Statistics
Matches: 81, Mismatches: 20, Indels: 17
0.69 0.17 0.14
Matches are distributed among these distances:
16 16 0.20
17 44 0.54
18 21 0.26
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (17 bp):
TTTCAAATTTGCAAGAA
Found at i:12372751 original size:35 final size:34
Alignment explanation
Indices: 12372662--12372751 Score: 90
Period size: 34 Copynumber: 2.6 Consensus size: 34
12372652 ATTTGCAAGA
* * *
12372662 ATTTCATATTTGCAATAATTCAAAGATTCATAAG
1 ATTTCAAATTTGCAAGAATTTAAAGATTCATAAG
* ** *
12372696 AATTCAAATTTATAAGAATTTAAAGATTCGTAAAG
1 ATTTCAAATTTGCAAGAATTTAAAGATTCAT-AAG
* *
12372731 CTTTCAGATTTGCAAGAATTT
1 ATTTCAAATTTGCAAGAATTT
12372752 CAAGTTTACA
Statistics
Matches: 43, Mismatches: 12, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
34 24 0.56
35 19 0.44
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.38
Consensus pattern (34 bp):
ATTTCAAATTTGCAAGAATTTAAAGATTCATAAG
Found at i:12372799 original size:86 final size:87
Alignment explanation
Indices: 12372630--12372802 Score: 217
Period size: 86 Copynumber: 2.0 Consensus size: 87
12372620 GCAAGAACAC
* * * *
12372630 AAAGATTCGTAAAACTTTTCAAATTTGCAAGAATTTCATATTTGCAATAATTCAAAGATTCATAA
1 AAAGATTCGTAAAACTTTTCAAATTTGCAAGAATTTCATATTTACAAGAATTCAAAGACTCACAA
* **
12372695 GAATTCAAATTTATAAGAATTT
66 GAACTCAAATGGATAAGAATTT
* *
12372717 AAAGATTCGTAAAGC-TTTCAGATTTGCAAGAATTTCA-AGTTTACAAGAATTCAAAGACTCACA
1 AAAGATTCGTAAAACTTTTCAAATTTGCAAGAATTTCATA-TTTACAAGAATTCAAAGACTCACA
*
12372780 AGAACTCAGATAGGA-AAGAATTT
65 AGAACTCAAAT-GGATAAGAATTT
12372803 TAGTTTCGTA
Statistics
Matches: 74, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
85 1 0.01
86 58 0.78
87 15 0.20
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (87 bp):
AAAGATTCGTAAAACTTTTCAAATTTGCAAGAATTTCATATTTACAAGAATTCAAAGACTCACAA
GAACTCAAATGGATAAGAATTT
Found at i:12372977 original size:23 final size:23
Alignment explanation
Indices: 12372934--12373034 Score: 77
Period size: 23 Copynumber: 4.6 Consensus size: 23
12372924 ATTTCAAGGC
* *
12372934 TCACATTT-AAAA-TTCAAAGAT
1 TCACATTTGAAAATTTTAGAGAT
*
12372955 TCTCATTTGAAAATTTTAGAGAT
1 TCACATTTGAAAATTTTAGAGAT
** **
12372978 TTTCATTTGAAAAACTTAG-GTAT
1 TCACATTTGAAAATTTTAGAG-AT
* *
12373001 TCACA--TCAAAATTTTAAAGAT
1 TCACATTTGAAAATTTTAGAGAT
12373022 TCACATTTGAAAA
1 TCACATTTGAAAA
12373035 ACTTTAGTGT
Statistics
Matches: 61, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
21 22 0.36
22 6 0.10
23 33 0.54
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.38
Consensus pattern (23 bp):
TCACATTTGAAAATTTTAGAGAT
Found at i:12373014 original size:44 final size:45
Alignment explanation
Indices: 12372964--12373127 Score: 176
Period size: 43 Copynumber: 3.7 Consensus size: 45
12372954 TTCTCATTTG
*
12372964 AAAATTTTAGAGATTTTCATTTGAAAAAC-TTAGGTATTCACAT-C
1 AAAATTTTAAAGATTTTCATTTGAAAAACTTTAGGT-TTCACATCC
** *
12373008 AAAATTTTAAAGATTCACATTTGAAAAACTTTAGTGTTTTACATCC
1 AAAATTTTAAAGATTTTCATTTGAAAAACTTTAG-GTTTCACATCC
*
12373054 AAAATTTTAAAGA-TTT--TTCGAAAAACTTTATGGTTTCACATCC
1 AAAATTTTAAAGATTTTCATTTGAAAAACTTTA-GGTTTCACATCC
* * * **
12373097 AAAATTTCAAATATTCTCATTCAAAAAACTT
1 AAAATTTTAAAGATTTTCATTTGAAAAACTT
12373128 CAATGGTTAT
Statistics
Matches: 101, Mismatches: 12, Indels: 12
0.81 0.10 0.10
Matches are distributed among these distances:
43 34 0.34
44 29 0.29
45 11 0.11
46 27 0.27
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.38
Consensus pattern (45 bp):
AAAATTTTAAAGATTTTCATTTGAAAAACTTTAGGTTTCACATCC
Found at i:12380709 original size:16 final size:16
Alignment explanation
Indices: 12380679--12380711 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
12380669 TATTGTTAAA
12380679 CTATTATTCTTTTTTT
1 CTATTATTCTTTTTTT
*
12380695 CTATT-TTCTTATTTT
1 CTATTATTCTTTTTTT
12380710 CT
1 CT
12380712 CTCATCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (16 bp):
CTATTATTCTTTTTTT
Found at i:12380860 original size:5 final size:5
Alignment explanation
Indices: 12380850--12380882 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
12380840 TCCTTGATAA
*
12380850 TTTCT TTTCT TTTTT TTTCT TTTCT TTT-T TTTC
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTC
12380883 AAACTCAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (5 bp):
TTTCT
Found at i:12380870 original size:15 final size:15
Alignment explanation
Indices: 12380850--12380881 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
12380840 TCCTTGATAA
12380850 TTTCTTTTCTTTTTT
1 TTTCTTTTCTTTTTT
12380865 TTTCTTTTCTTTTTT
1 TTTCTTTTCTTTTTT
12380880 TT
1 TT
12380882 CAAACTCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (15 bp):
TTTCTTTTCTTTTTT
Found at i:12382879 original size:16 final size:17
Alignment explanation
Indices: 12382858--12382892 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
12382848 TGAAATTTTT
12382858 TTAAAAAAAA-TTAGAA
1 TTAAAAAAAATTTAGAA
12382874 TTAAAAAAAATTTAGAA
1 TTAAAAAAAATTTAGAA
12382891 TT
1 TT
12382893 TTTTAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (17 bp):
TTAAAAAAAATTTAGAA
Found at i:12382882 original size:17 final size:17
Alignment explanation
Indices: 12382860--12382892 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12382850 AAATTTTTTT
12382860 AAAAAAAATTAGAATTA
1 AAAAAAAATTAGAATTA
*
12382877 AAAAAAATTTAGAATT
1 AAAAAAAATTAGAATT
12382893 TTTTAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (17 bp):
AAAAAAAATTAGAATTA
Done.