Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397268.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_81.0, 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: 6219335
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 77647 characters in sequence are not A, C, G, or T
File 7 of 13
Found at i:3599265 original size:16 final size:16
Alignment explanation
Indices: 3599213--3599270 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 16
3599203 AAACGAAAAT
* *
3599213 AAAATATATAAGATTA
1 AAAATATATGACATTA
* *
3599229 TAATAATAGATGACAAT-
1 -AA-AATATATGACATTA
3599246 AAAATATATGACATTA
1 AAAATATATGACATTA
3599262 AAAATATAT
1 AAAATATAT
3599271 TTAAGAGATG
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
15 11 0.33
16 11 0.33
17 2 0.06
18 9 0.27
ACGTcount: A:0.59, C:0.03, G:0.07, T:0.31
Consensus pattern (16 bp):
AAAATATATGACATTA
Found at i:3599490 original size:15 final size:15
Alignment explanation
Indices: 3599470--3599526 Score: 60
Period size: 15 Copynumber: 3.8 Consensus size: 15
3599460 TTGTTTTCCC
*
3599470 TGCAATGACATTACT
1 TGCAATCACATTACT
** *
3599485 TGCAATCGTATTACC
1 TGCAATCACATTACT
*
3599500 TGCAATCACATTATT
1 TGCAATCACATTACT
*
3599515 TGTAATCACATT
1 TGCAATCACATT
3599527 GCATTGTAAA
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.37
Consensus pattern (15 bp):
TGCAATCACATTACT
Found at i:3605391 original size:22 final size:22
Alignment explanation
Indices: 3605363--3605406 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
3605353 CCAAATAAAC
*
3605363 AGGCAGATCATGTTGGTAGCCT
1 AGGCAGATCATGTTGCTAGCCT
3605385 AGGCAGATCATGTTGCTAGCCT
1 AGGCAGATCATGTTGCTAGCCT
3605407 GCTACCTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (22 bp):
AGGCAGATCATGTTGCTAGCCT
Found at i:3607943 original size:2 final size:2
Alignment explanation
Indices: 3607936--3607965 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3607926 AATGCAATGA
*
3607936 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3607966 CAATTATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:3608174 original size:2 final size:2
Alignment explanation
Indices: 3608167--3608193 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3608157 TAATGAAATA
3608167 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
3608194 CCAAAGGACT
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:3612060 original size:2 final size:2
Alignment explanation
Indices: 3612053--3612078 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3612043 TCCCGAGATA
3612053 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
3612079 TTGGTGCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3635795 original size:22 final size:21
Alignment explanation
Indices: 3635769--3635810 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3635759 TTTCTTTATC
3635769 TTTTC-TTATTTAATTTTTCTCA
1 TTTTCTTTATTT--TTTTTCTCA
3635791 TTTTCTTTATTTTTTTTCTC
1 TTTTCTTTATTTTTTTTCTC
3635811 TTCTCCCTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 5 0.26
23 6 0.32
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTCTTTATTTTTTTTCTCA
Found at i:3638288 original size:14 final size:15
Alignment explanation
Indices: 3638271--3638308 Score: 55
Period size: 13 Copynumber: 2.7 Consensus size: 15
3638261 TTTTGAACTT
3638271 TTTTTATTTT-TTTA
1 TTTTTATTTTATTTA
3638285 -TTTTATTTTATTTA
1 TTTTTATTTTATTTA
3638299 TTTTT-TTTTA
1 TTTTTATTTTA
3638309 AAAAAAAGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 9 0.41
14 9 0.41
15 4 0.18
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTTATTTTATTTA
Found at i:3638293 original size:18 final size:19
Alignment explanation
Indices: 3638272--3638308 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3638262 TTTGAACTTT
3638272 TTTTATTT-TTTTATTTTA
1 TTTTATTTATTTTATTTTA
*
3638290 TTTTATTTATTTTTTTTTA
1 TTTTATTTATTTTATTTTA
3638309 AAAAAAAGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (19 bp):
TTTTATTTATTTTATTTTA
Found at i:3638640 original size:31 final size:31
Alignment explanation
Indices: 3638605--3638965 Score: 169
Period size: 31 Copynumber: 11.7 Consensus size: 31
3638595 AATGCTCTCG
* *
3638605 TGCCAAGATAACTGGGCTTAAACATCTTGGA
1 TGCCAAGCTAATTGGGCTTAAACATCTTGGA
* * *
3638636 TGCC-AGCTAAATTGGGCTTAACCAACTTTG-
1 TGCCAAGCT-AATTGGGCTTAAACATCTTGGA
* * * *
3638666 TGCCAAGATAACTAGGCTTAAACATCTTAGA
1 TGCCAAGCTAATTGGGCTTAAACATCTTGGA
* *
3638697 TGCC-AGCTAAATTGGGCTTAAACAACTTTG-
1 TGCCAAGCT-AATTGGGCTTAAACATCTTGGA
** * ** **
3638727 TGCCAATATAACTAAGCTTAAATGTCTTGGA
1 TGCCAAGCTAATTGGGCTTAAACATCTTGGA
*
3638758 TGCC-AGCTAAATTGGGCTTAAAC-TCTTTTTG-
1 TGCCAAGCT-AATTGGGCTTAAACATC--TTGGA
* * *
3638789 TGCCAA-CGTAACTGGACTTAATACTTCTTGGA
1 TGCCAAGC-TAATTGGGCTTAA-ACATCTTGGA
* * * *
3638821 TG-CTAGCTAAATTAGGCTTAATCATCTTTG-
1 TGCCAAGCT-AATTGGGCTTAAACATCTTGGA
** *
3638851 TGCCAA-CGTAGCTAGGCTTAAACATCTTGGA
1 TGCCAAGC-TAATTGGGCTTAAACATCTTGGA
* * *
3638882 TG-CTAGCTAAATCGGGCTTAAAC-TCTTTTTG-
1 TGCCAAGCT-AATTGGGCTTAAACATC--TTGGA
* *
3638913 TGCCAA-CGTAATTGGACTTATACATCTTGGA
1 TGCCAAGC-TAATTGGGCTTAAACATCTTGGA
*
3638944 TGCC-AGTTAAATTGGGCTTAAA
1 TGCCAAGCT-AATTGGGCTTAAA
3638966 TATTTTTTTG
Statistics
Matches: 240, Mismatches: 61, Indels: 58
0.67 0.17 0.16
Matches are distributed among these distances:
30 78 0.32
31 133 0.55
32 27 0.11
33 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.32
Consensus pattern (31 bp):
TGCCAAGCTAATTGGGCTTAAACATCTTGGA
Found at i:3638851 original size:62 final size:62
Alignment explanation
Indices: 3638604--3640319 Score: 1004
Period size: 61 Copynumber: 27.9 Consensus size: 62
3638594 TAATGCTCTC
* * * *
3638604 GTGCCAA-GATAACTGGGCTTAA-ACATCTTGGATGCCAGCTAAATTGGGCTTAACCAACTTT
1 GTGCCAACG-TAACTGGACTTAATACTTCTTGGATGCCAGCTAAATTGGGCTTAATCATCTTT
* * * *
3638665 GTGCCAA-GATAACTAGG-CTTAA-ACATCTTAGATGCCAGCTAAATTGGGCTTAAACAACTTT
1 GTGCCAACG-TAACT-GGACTTAATACTTCTTGGATGCCAGCTAAATTGGGCTTAATCATCTTT
** * *
3638726 GTGCCAATATAACT-AAGCTTAA-A-TGTCTTGGATGCCAGCTAAATTGGGCTTAAACTC-TTTT
1 GTGCCAACGTAACTGGA-CTTAATACT-TCTTGGATGCCAGCTAAATTGGGCTT-AA-TCATCTT
3638787 T
62 T
* *
3638788 GTGCCAACGTAACTGGACTTAATACTTCTTGGATGCTAGCTAAATTAGGCTTAATCATCTTT
1 GTGCCAACGTAACTGGACTTAATACTTCTTGGATGCCAGCTAAATTGGGCTTAATCATCTTT
* * * * *
3638850 GTGCCAACGTAGCTAGG-CTTAA-ACATCTTGGATGCTAGCTAAATCGGGCTTAAACTC-TTTTT
1 GTGCCAACGTAACT-GGACTTAATACTTCTTGGATGCCAGCTAAATTGGGCTT-AA-TCATCTTT
* * * *
3638912 GTGCCAACGTAATTGGACTT-ATACATCTTGGATGCCAGTTAAATTGGGCTTAAAT-ATTTTTTT
1 GTGCCAACGTAACTGGACTTAATACTTCTTGGATGCCAGCTAAATTGGGCTT-AATCA--TCTTT
* ** * *
3638975 GTGCCAACGTAACTGGACTT-ATACTTCTTGGATGCCAGTTTGATTAGGCTTAAATCATTTTTT
1 GTGCCAACGTAACTGGACTTAATACTTCTTGGATGCCAGCTAAATTGGGCTT-AATCA-TCTTT
* * * * * * * * *
3639038 GTGCCAACATAATTGGACTT-ATTCTTCTTGGATTCTAGTTTAATTGGGCTTAAATCTTTTTTT
1 GTGCCAACGTAACTGGACTTAATACTTCTTGGATGCCAGCTAAATTGGGCTT-AATC-ATCTTT
** * * * * * *
3639101 GTGCTTACATAACCGGACTT-ATACTTCTTGGATGACAGTTTAATTGGGCTTAAAC-TCCTTTT
1 GTGCCAACGTAACTGGACTTAATACTTCTTGGATGCCAGCTAAATTGGGCTTAATCAT-C-TTT
* * * * *
3639163 GTGCCAACGTAACTGAACTT-ATACTCCTTGGATGCCAGTTTAATTGGGCTTAAACTC-TTTTT
1 GTGCCAACGTAACTGGACTTAATACTTCTTGGATGCCAGCTAAATTGGGCTT-AA-TCATCTTT
* * * *
3639225 GTGCCAACGTAATTGGACTT-ACACTCCTTGGATGCCAGCTAAATTGGGCTTAAACTC-TTTTT
1 GTGCCAACGTAACTGGACTTAATACTTCTTGGATGCCAGCTAAATTGGGCTT-AA-TCATCTTT
* * *
3639287 GTGCCAACGTAATTGGACTT-ATACTTCTTGGATGCCAGCTTAATTGGGCTTAAAGTC-TTTTT
1 GTGCCAACGTAACTGGACTTAATACTTCTTGGATGCCAGCTAAATTGGGCTT-AA-TCATCTTT
* * * ** * * *
3639349 GTGTCGACGTAACTGGACTT-ATACTTCTTGGATGCCAGATAAATTAAGTTTCATCATTTTT
1 GTGCCAACGTAACTGGACTTAATACTTCTTGGATGCCAGCTAAATTGGGCTTAATCATCTTT
** * * * *
3639410 GTGCCAATATAACT-GAGCTT-ATACATCTTGGATGCCAGTTTAATTGGGCTTAATCATTTTT
1 GTGCCAACGTAACTGGA-CTTAATACTTCTTGGATGCCAGCTAAATTGGGCTTAATCATCTTT
* * *
3639471 GTGCCAATGTAATTGGACTT-ATACTTCTTGGATGCCAG-T---TT-GACTT--T--T-TTT
1 GTGCCAACGTAACTGGACTTAATACTTCTTGGATGCCAGCTAAATTGGGCTTAATCATCTTT
** * * * *
3639522 GTGCCAACGTAGTTAGG-CTTAA-ACATCTTGGATGCTAGCTAAATTGGGC-TAA-CTTTTTT
1 GTGCCAACGTAACT-GGACTTAATACTTCTTGGATGCCAGCTAAATTGGGCTTAATCATCTTT
* * * * * *
3639581 GTGCCAACGTAGCTAGG-CTTAA-ACATT-TTAGATACTAGTTAAATTGGGCTTAATCAACTTT
1 GTGCCAACGTAACT-GGACTTAATAC-TTCTTGGATGCCAGCTAAATTGGGCTTAATCATCTTT
** * * * *
3639642 GTGCCAATATGACTAGG-CTTAA-ACGTCTTAGATGCCAACTAAATTGGGCTTAATCATCTTT
1 GTGCCAACGTAACT-GGACTTAATACTTCTTGGATGCCAGCTAAATTGGGCTTAATCATCTTT
** * * * **
3639703 GTGCCAATATAACTGGGCTT-ATACATCTTGGATGCCAGTTTTATTGGGCTTAAACTCAT-TTT
1 GTGCCAACGTAACTGGACTTAATACTTCTTGGATGCCAGCTAAATTGGGCTT-AA-TCATCTTT
* * * *
3639765 GTGCCAATGTAACTGGACTT-ATATTTCTTGGATGCCAACTAAATTGGGCTTTAAT-TTCTTT
1 GTGCCAACGTAACTGGACTTAATACTTCTTGGATGCCAGCTAAATTGGGC-TTAATCATCTTT
** * * * * * * *
3639826 GTGCCAATATAACTGGGCTTAA-ACGTCTTTTTG-TGCCAAC-ATAACTGGACTT-ATACTTCTT
1 GTGCCAACGTAACTGGACTTAATAC-T-TCTTGGATGCCAGCTA-AATTGGGCTTAAT-CATCTT
*
3639887 G
62 T
* *** * * * * * * * *
3639888 GATGCTAGTTTAATTGGGCTTAA-ACTCTTTTTG-TGCCAACGT-AATTAGACTT-ATACTTCTT
1 G-TGCCAACGTAACTGGACTTAATACT-TCTTGGATGCCAGC-TAAATTGGGCTTAAT-CATCTT
*
3639949 G
62 T
* * * * *
3639950 GATGCCAACTTAATTGGGCTTAA-ACTCTTTTTG-TGCCAATG-T-AATTGGGCTTATTAGGCTT
1 G-TGCCAACGTAACTGGACTTAATACT-TCTTGGATGCC-A-GCTAAATTGGGCTTA--A----T
*
3640011 AATCAATTT
56 CATC--TTT
* * * * * *
3640020 CGTGCCAACATAACTAGG-CTTAA-ACATCTTGGATGCTAGCTAAATTAGGCTTAATCAACCTT
1 -GTGCCAACGTAACT-GGACTTAATACTTCTTGGATGCCAGCTAAATTGGGCTTAATCATCTTT
** * * * *
3640082 GTGCCAATATAACTGGAGTTAA-ACGTCTTGGATGCCAGCTAAATTGGGCTTAATCAACTTC
1 GTGCCAACGTAACTGGACTTAATACTTCTTGGATGCCAGCTAAATTGGGCTTAATCATCTTT
* *
3640143 GTGCCAATC-TAACT-GAGCTTAAT--TATCTTGGATGCCAGGTAAATTGGGCTTAAAC-TCTTT
1 GTGCCAA-CGTAACTGGA-CTTAATACT-TCTTGGATGCCAGCTAAATTGGGCTTAATCATC-TT
3640203 T
62 T
* * * *
3640204 GAGCCAATGTAACTAGACTT-ATACTGCTCATGGATGCCAGCTAAATTGGGCTTAATCATCTTT
1 GTGCCAACGTAACTGGACTTAATACT--TCTTGGATGCCAGCTAAATTGGGCTTAATCATCTTT
* *
3640267 GTGCCAACGTAACTGGA-TTTATACATCTTGGATGCCAGCTAAATTGGGCTTAA
1 GTGCCAACGTAACTGGACTTAATACTTCTTGGATGCCAGCTAAATTGGGCTTAA
3640320 AACCTCTCAT
Statistics
Matches: 1380, Mismatches: 187, Indels: 176
0.79 0.11 0.10
Matches are distributed among these distances:
51 32 0.02
52 5 0.00
54 1 0.00
55 3 0.00
56 6 0.00
57 2 0.00
58 1 0.00
59 45 0.03
60 24 0.02
61 472 0.34
62 463 0.34
63 269 0.19
64 9 0.01
65 1 0.00
68 4 0.00
69 7 0.01
70 33 0.02
71 3 0.00
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (62 bp):
GTGCCAACGTAACTGGACTTAATACTTCTTGGATGCCAGCTAAATTGGGCTTAATCATCTTT
Found at i:3639011 original size:31 final size:31
Alignment explanation
Indices: 3638789--3639011 Score: 79
Period size: 31 Copynumber: 7.2 Consensus size: 31
3638779 ACTCTTTTTG
3638789 TGCCAACGTAACTGGACTTAATACTTCTTGGA
1 TGCCAACGTAACTGGACTT-ATACTTCTTGGA
* * * * *
3638821 TGCTAGC-TAAATTAGG-CTTA-ATCATCTTTG-
1 TGCCAACGT-AACT-GGACTTATA-CTTCTTGGA
* * *
3638851 TGCCAACGTAGCTAGG-CTTAAACATCTTGGA
1 TGCCAACGTAACT-GGACTTATACTTCTTGGA
* * * * * * *
3638882 TGCTAGC-TAAATCGGGCTTAAACTCTTTTTG-
1 TGCCAACGTAACT-GGACTTATACT-TCTTGGA
* *
3638913 TGCCAACGTAATTGGACTTATACATCTTGGA
1 TGCCAACGTAACTGGACTTATACTTCTTGGA
* * * * *
3638944 TGCC-A-GTTAAATTGGGCTTAAATATTTTTTTG-
1 TGCCAACG-T-AACTGGACTT--ATACTTCTTGGA
3638976 TGCCAACGTAACTGGACTTATACTTCTTGGA
1 TGCCAACGTAACTGGACTTATACTTCTTGGA
3639007 TGCCA
1 TGCCA
3639012 GTTTGATTAG
Statistics
Matches: 138, Mismatches: 36, Indels: 35
0.66 0.17 0.17
Matches are distributed among these distances:
29 1 0.01
30 41 0.30
31 53 0.38
32 31 0.22
33 11 0.08
34 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (31 bp):
TGCCAACGTAACTGGACTTATACTTCTTGGA
Found at i:3639199 original size:31 final size:31
Alignment explanation
Indices: 3639141--3639385 Score: 149
Period size: 31 Copynumber: 7.9 Consensus size: 31
3639131 GATGACAGTT
* *
3639141 TAATTGGGCTTAAACTCCTTTTG-TGCCAACG
1 TAATTGGACTTAAACTCC-TTGGATGCCAACG
* * * ***
3639172 TAACTGAACTTATACTCCTTGGATGCCAGTT
1 TAATTGGACTTAAACTCCTTGGATGCCAACG
* * *
3639203 TAATTGGGCTTAAACTCTTTTTG-TGCCAACG
1 TAATTGGACTTAAACTC-CTTGGATGCCAACG
* *
3639234 TAATTGGACTTACACTCCTTGGATGCCAGC-
1 TAATTGGACTTAAACTCCTTGGATGCCAACG
* * *
3639264 TAAATTGGGCTTAAACTCTTTTTG-TGCCAACG
1 T-AATTGGACTTAAACTC-CTTGGATGCCAACG
* * * *
3639296 TAATTGGACTTATACTTCTTGGATGCCAGCT
1 TAATTGGACTTAAACTCCTTGGATGCCAACG
* * * * * *
3639327 TAATTGGGCTTAAAGTCTTTTTG-TGTCGACG
1 TAATTGGACTTAAACTC-CTTGGATGCCAACG
* * *
3639358 TAACTGGACTTATACTTCTTGGATGCCA
1 TAATTGGACTTAAACTCCTTGGATGCCA
3639386 GATAAATTAA
Statistics
Matches: 152, Mismatches: 53, Indels: 18
0.68 0.24 0.08
Matches are distributed among these distances:
30 13 0.09
31 129 0.85
32 10 0.07
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (31 bp):
TAATTGGACTTAAACTCCTTGGATGCCAACG
Found at i:3639461 original size:31 final size:31
Alignment explanation
Indices: 3639426--3639511 Score: 95
Period size: 30 Copynumber: 2.8 Consensus size: 31
3639416 ATATAACTGA
3639426 GCTTATACATCTTGGATGCCAGTTTAATTGG
1 GCTTATACATCTTGGATGCCAGTTTAATTGG
* * * *
3639457 GCTTA-ATCATTTTTG-TGCCAATGTAATTGG
1 GCTTATA-CATCTTGGATGCCAGTTTAATTGG
* *
3639487 ACTTATACTTCTTGGATGCCAGTTT
1 GCTTATACATCTTGGATGCCAGTTT
3639512 GACTTTTTTT
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
30 23 0.55
31 19 0.45
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.42
Consensus pattern (31 bp):
GCTTATACATCTTGGATGCCAGTTTAATTGG
Found at i:3639484 original size:30 final size:30
Alignment explanation
Indices: 3639401--3639491 Score: 85
Period size: 30 Copynumber: 3.0 Consensus size: 30
3639391 ATTAAGTTTC
* *
3639401 ATCATTTTTGTGCCAATATAACTGAGCTT-
1 ATCATTTTTGTGCCAATATAATTGGGCTTA
* * * *
3639430 ATACATCTTGGATGCCAGTTTAATTGGGCTTA
1 AT-CATTTTTG-TGCCAATATAATTGGGCTTA
* *
3639462 ATCATTTTTGTGCCAATGTAATTGGACTTA
1 ATCATTTTTGTGCCAATATAATTGGGCTTA
3639492 TACTTCTTGG
Statistics
Matches: 48, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
29 2 0.04
30 23 0.48
31 21 0.44
32 2 0.04
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (30 bp):
ATCATTTTTGTGCCAATATAATTGGGCTTA
Found at i:3639663 original size:30 final size:30
Alignment explanation
Indices: 3639625--3639878 Score: 160
Period size: 31 Copynumber: 8.3 Consensus size: 30
3639615 CTAGTTAAAT
* *
3639625 TGGGCTTAATCAACTTTGTGCCAATATGAC
1 TGGGCTTAATCATCTTTGTGCCAATATAAC
* * * * *
3639655 TAGGCTTAAACGTCTTAGATGCCAACTA-AAT
1 TGGGCTTAATCATCTTTG-TGCCAA-TATAAC
3639686 TGGGCTTAATCATCTTTGTGCCAATATAAC
1 TGGGCTTAATCATCTTTGTGCCAATATAAC
* * * * *
3639716 TGGGCTT-ATACATCTTGGATGCCAGTTTTAT
1 TGGGCTTAAT-CATCTTTG-TGCCAATATAAC
*
3639747 TGGGCTTAAACTCAT-TTTGTGCCAATGTAAC
1 TGGGCTT-AA-TCATCTTTGTGCCAATATAAC
* * * *
3639778 TGGACTTATAT-TTCTTGGATGCCAACTA-AAT
1 TGGGCTTA-ATCATCTTTG-TGCCAA-TATAAC
*
3639809 TGGGCTTTAAT-TTCTTTGTGCCAATATAAC
1 TGGGC-TTAATCATCTTTGTGCCAATATAAC
* * *
3639839 TGGGCTTAAACGTCTTTTTGTGCCAACATAAC
1 TGGGCTTAATCATC--TTTGTGCCAATATAAC
*
3639871 TGGACTTA
1 TGGGCTTA
3639879 TACTTCTTGG
Statistics
Matches: 173, Mismatches: 34, Indels: 32
0.72 0.14 0.13
Matches are distributed among these distances:
29 11 0.06
30 55 0.32
31 71 0.41
32 31 0.18
33 4 0.02
34 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.37
Consensus pattern (30 bp):
TGGGCTTAATCATCTTTGTGCCAATATAAC
Found at i:3639887 original size:155 final size:156
Alignment explanation
Indices: 3639700--3640134 Score: 459
Period size: 155 Copynumber: 2.8 Consensus size: 156
3639690 CTTAATCATC
* * *
3639700 TTTGTGCCAATATAACTGGGCTTATACATCTTGGATGCCAGTTTTATTGGGCTTAAACTCATTTT
1 TTTGTGCCAACATAACTGGACTTATACATCTTGGATGCCAGTTTAATTGGGCTTAAACTCATTTT
* * * *
3639765 GTGCCAATGTAACTGGACTTATATTTCTTGGATGCCAACTAAATTGGGCTTTAA-T-TTCTTTGT
66 GTGCCAACGTAACTAGACTTATACTTCTTGGATGCCAACTAAATTGGGCTTAAACTCTT-TTTGT
3639828 GCCAATATAACTGGGCTTAAACGTCTT
130 GCCAATATAACTGGGCTTAAACGTCTT
* * *
3639855 TTTGTGCCAACATAACTGGACTTATACTTCTTGGATGCTAGTTTAATTGGGCTTAAACTCTTTTT
1 TTTGTGCCAACATAACTGGACTTATACATCTTGGATGCCAGTTTAATTGGGCTTAAACTCATTTT
* *
3639920 GTGCCAACGTAATTAGACTTATACTTCTTGGATGCCAACTTAATTGGGCTTAAACTCTTTTTGTG
66 GTGCCAACGTAACTAGACTTATACTTCTTGGATGCCAACTAAATTGGGCTTAAACTCTTTTTGTG
* * * *
3639985 CCAATGTAATTGGGCTTATTA-GGCTTAAT
131 CCAATATAACTGGGCTTA-AACGTC-T--T
* * * * *
3640014 CAATTTCGTGCCAACATAACTAGG-CTTAAACATCTTGGATGCTAGCTAAATTAGGCTT-AA-TC
1 ---TTT-GTGCCAACATAACT-GGACTTATACATCTTGGATGCCAGTTTAATTGGGCTTAAACTC
** ** * * * * *
3640076 AACCTTGTGCCAATATAACTGGAGTTAAACGTCTTGGATGCCAGCTAAATTGGGCTTAA
61 -ATTTTGTGCCAACGTAACTAGACTTATACTTCTTGGATGCCAACTAAATTGGGCTTAA
3640135 TCAACTTCGT
Statistics
Matches: 235, Mismatches: 33, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
155 107 0.46
156 25 0.11
157 4 0.02
159 1 0.00
161 2 0.01
162 51 0.22
163 43 0.18
164 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (156 bp):
TTTGTGCCAACATAACTGGACTTATACATCTTGGATGCCAGTTTAATTGGGCTTAAACTCATTTT
GTGCCAACGTAACTAGACTTATACTTCTTGGATGCCAACTAAATTGGGCTTAAACTCTTTTTGTG
CCAATATAACTGGGCTTAAACGTCTT
Found at i:3639903 original size:93 final size:93
Alignment explanation
Indices: 3639747--3639926 Score: 247
Period size: 93 Copynumber: 1.9 Consensus size: 93
3639737 CCAGTTTTAT
** *
3639747 TGGGCTTAAACTCATTTTGTGCCAATGTAACTGGACTTATATTTCTTGGATGCCAACTAAATTGG
1 TGGGCTTAAACTCATTTTGTGCCAACATAACTGGACTTATACTTCTTGGATGCCAACTAAATTGG
*
3639812 GCTTTAA-T-TTCTTTGTGCCAATATAAC
66 GCTTAAACTCTT-TTTGTGCCAATATAAC
* * ** *
3639839 TGGGCTTAAACGTCTTTTTGTGCCAACATAACTGGACTTATACTTCTTGGATGCTAGTTTAATTG
1 TGGGCTTAAAC-TCATTTTGTGCCAACATAACTGGACTTATACTTCTTGGATGCCAACTAAATTG
3639904 GGCTTAAACTCTTTTTGTGCCAA
65 GGCTTAAACTCTTTTTGTGCCAA
3639927 CGTAATTAGA
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
92 11 0.14
93 52 0.68
94 11 0.14
95 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.39
Consensus pattern (93 bp):
TGGGCTTAAACTCATTTTGTGCCAACATAACTGGACTTATACTTCTTGGATGCCAACTAAATTGG
GCTTAAACTCTTTTTGTGCCAATATAAC
Found at i:3639987 original size:31 final size:30
Alignment explanation
Indices: 3639674--3640002 Score: 166
Period size: 31 Copynumber: 10.7 Consensus size: 30
3639664 ACGTCTTAGA
* * * *
3639674 TGCCAACTAAATTGGGCTTAATCATCTTTG
1 TGCCAACTTAATTGGGCTTAAACTTTTTTG
* * * * *
3639704 TGCCAA-TATAACTGGGCTTATACATCTTGG
1 TGCCAACT-TAATTGGGCTTAAACTTTTTTG
** * *
3639734 ATGCCAGTTTTATTGGGCTTAAACTCATTTTG
1 -TGCCAACTTAATTGGGCTTAAACT-TTTTTG
* * * *
3639766 TGCCAA-TGTAACTGGACTTATA-TTTCTTGG
1 TGCCAACT-TAATTGGGCTTAAACTTT-TTTG
* *
3639796 ATGCCAACTAAATTGGGCTTTAA-TTTCTTTG
1 -TGCCAACTTAATTGGGCTTAAACTTT-TTTG
*
3639827 TGCCAA-TATAACTGGGCTTAAACGTCTTTTTG
1 TGCCAACT-TAATTGGGCTTAAAC-T-TTTTTG
* * * * * *
3639859 TGCCAACATAACTGGACTTATACTTCTTGG
1 TGCCAACTTAATTGGGCTTAAACTTTTTTG
* **
3639889 ATGCTAGTTTAATTGGGCTTAAACTCTTTTTG
1 -TGCCAACTTAATTGGGCTTAAACT-TTTTTG
* * * * * *
3639921 TGCCAACGTAATTAGACTTATACTTCTTGG
1 TGCCAACTTAATTGGGCTTAAACTTTTTTG
3639951 ATGCCAACTTAATTGGGCTTAAACTCTTTTTG
1 -TGCCAACTTAATTGGGCTTAAACT-TTTTTG
3639983 TGCCAA-TGTAATTGGGCTTA
1 TGCCAACT-TAATTGGGCTTA
3640003 TTAGGCTTAA
Statistics
Matches: 223, Mismatches: 58, Indels: 35
0.71 0.18 0.11
Matches are distributed among these distances:
29 3 0.01
30 54 0.24
31 127 0.57
32 37 0.17
33 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (30 bp):
TGCCAACTTAATTGGGCTTAAACTTTTTTG
Found at i:3640194 original size:31 final size:31
Alignment explanation
Indices: 3640036--3640319 Score: 101
Period size: 30 Copynumber: 9.2 Consensus size: 31
3640026 AACATAACTA
* * * *
3640036 GGCTTAAACATCTTGGATGCTAGCTAAATTA
1 GGCTTAATCATCTTGGATGCCAGATAAATTG
* *
3640067 GGCTTAATCAACCTT-G-TGCCA-ATATAACTG
1 GGCTTAATC-ATCTTGGATGCCAGATA-AATTG
* * *
3640097 GAG-TTAAACGTCTTGGATGCCAGCTAAATTG
1 G-GCTTAATCATCTTGGATGCCAGATAAATTG
* * * *
3640128 GGCTTAATCAACTTCG-TGCCA-ATCTAACTG
1 GGCTTAATCATCTTGGATGCCAGAT-AAATTG
* * *
3640158 AGCTTAATTATCTTGGATGCCAGGTAAATTG
1 GGCTTAATCATCTTGGATGCCAGATAAATTG
* * * * *
3640189 GGCTTAAAC-TCTTTTGA-GCCA-ATGTAACTA
1 GGCTTAATCATC-TTGGATGCCAGAT-AAATTG
* * *
3640219 GACTTATACTGC-TCATGGATGCCAGCTAAATTG
1 GGCTTA-A-T-CATCTTGGATGCCAGATAAATTG
* *
3640252 GGCTTAATCATCTTTG-TGCCA-ACGT-AACT-
1 GGCTTAATCATCTTGGATGCCAGA--TAAATTG
* * *
3640281 GGATTTATACATCTTGGATGCCAGCTAAATTG
1 GGCTTAAT-CATCTTGGATGCCAGATAAATTG
3640313 GGCTTAA
1 GGCTTAA
3640320 AACCTCTCAT
Statistics
Matches: 175, Mismatches: 53, Indels: 49
0.63 0.19 0.18
Matches are distributed among these distances:
29 13 0.07
30 67 0.38
31 63 0.36
32 16 0.09
33 15 0.09
34 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (31 bp):
GGCTTAATCATCTTGGATGCCAGATAAATTG
Found at i:3646292 original size:24 final size:26
Alignment explanation
Indices: 3646260--3646307 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
3646250 AACAACATGA
3646260 AATGATTGCATGTA-G-ATGAAATAT
1 AATGATTGCATGTATGCATGAAATAT
*
3646284 AATGTTTGCATGTATGCATGAAAT
1 AATGATTGCATGTATGCATGAAAT
3646308 GCTATGATGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 13 0.62
25 1 0.05
26 7 0.33
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.35
Consensus pattern (26 bp):
AATGATTGCATGTATGCATGAAATAT
Found at i:3649715 original size:22 final size:23
Alignment explanation
Indices: 3649672--3649715 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
3649662 TGCTGTTATT
* * *
3649672 CTTTTCTCTTTTTTCTTTTCTTC
1 CTTTTCTCTTTCTTATTCTCTTC
3649695 CTTTTC-CTTTCTTATTCTCTT
1 CTTTTCTCTTTCTTATTCTCTT
3649716 TGGCTGATCA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.70
Consensus pattern (23 bp):
CTTTTCTCTTTCTTATTCTCTTC
Found at i:3651577 original size:20 final size:21
Alignment explanation
Indices: 3651540--3651580 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
3651530 CTTATAATTT
3651540 TTCATTTTTAACTATTTATTA
1 TTCATTTTTAACTATTTATTA
3651561 TTCATTTTTAACT-TTTATTA
1 TTCATTTTTAACTATTTATTA
3651581 ATGAGAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.27, C:0.10, G:0.00, T:0.63
Consensus pattern (21 bp):
TTCATTTTTAACTATTTATTA
Found at i:3657602 original size:17 final size:17
Alignment explanation
Indices: 3657580--3657613 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3657570 TTTCAGATGT
3657580 TAAAATTAAAAA-AATAA
1 TAAAA-TAAAAAGAATAA
3657597 TAAAATAAAAAGAATAA
1 TAAAATAAAAAGAATAA
3657614 CTCTCAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (17 bp):
TAAAATAAAAAGAATAA
Found at i:3661197 original size:20 final size:21
Alignment explanation
Indices: 3661164--3661207 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
3661154 TTATTTATAT
3661164 AATATTTTTAATGT-TAAAAA
1 AATATTTTTAATGTATAAAAA
*
3661184 AATA-TTTTAGATGTATTAAAA
1 AATATTTTTA-ATGTATAAAAA
3661205 AAT
1 AAT
3661208 TAATAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 5 0.24
20 8 0.38
21 8 0.38
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (21 bp):
AATATTTTTAATGTATAAAAA
Found at i:3662090 original size:14 final size:15
Alignment explanation
Indices: 3662054--3662093 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
3662044 CCTAAAAATA
3662054 TTTGGAGGGAACTCT
1 TTTGGAGGGAACTCT
3662069 TTTGGAGGGAACT-T
1 TTTGGAGGGAACTCT
*
3662083 TTTTGAGGGAA
1 TTTGGAGGGAA
3662094 ATTGGCTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.23, C:0.07, G:0.35, T:0.35
Consensus pattern (15 bp):
TTTGGAGGGAACTCT
Found at i:3666547 original size:21 final size:21
Alignment explanation
Indices: 3666522--3666570 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
3666512 AAAAGCTTAC
3666522 ACAAGGGCCTTGTTCGAAGGT
1 ACAAGGGCCTTGTTCGAAGGT
3666543 ACAAGGGCCTTGTTCGAAGGT
1 ACAAGGGCCTTGTTCGAAGGT
3666564 ACAAGGG
1 ACAAGGG
3666571 GCCATATCGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.27, C:0.18, G:0.35, T:0.20
Consensus pattern (21 bp):
ACAAGGGCCTTGTTCGAAGGT
Found at i:3666580 original size:21 final size:21
Alignment explanation
Indices: 3666522--3666580 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
3666512 AAAAGCTTAC
* *
3666522 ACAAGGGCCTTGTTCGAAGGT
1 ACAAGGGCCATGATCGAAGGT
* *
3666543 ACAAGGGCCTTGTTCGAAGGT
1 ACAAGGGCCATGATCGAAGGT
3666564 ACAAGGGGCCAT-ATCGA
1 ACAA-GGGCCATGATCGA
3666581 GTGGTCAAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 29 0.83
22 6 0.17
ACGTcount: A:0.27, C:0.20, G:0.32, T:0.20
Consensus pattern (21 bp):
ACAAGGGCCATGATCGAAGGT
Found at i:3667206 original size:22 final size:22
Alignment explanation
Indices: 3667165--3667207 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3667155 CGACAAGCAC
* **
3667165 AGCAGGGGTGAGCGGCACGCAT
1 AGCAAGGGTGAGCGAAACGCAT
3667187 AGCAAGGGTGAGCGAAACGCA
1 AGCAAGGGTGAGCGAAACGCA
3667208 GACTCGCACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.21, G:0.42, T:0.07
Consensus pattern (22 bp):
AGCAAGGGTGAGCGAAACGCAT
Found at i:3667547 original size:14 final size:15
Alignment explanation
Indices: 3667509--3667548 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
3667499 CCTAAAAATG
*
3667509 TTTGGAGGGAATTAT
1 TTTGGAGGGAACTAT
*
3667524 TTTGGAGGGAACTCT
1 TTTGGAGGGAACTAT
3667539 TTT-GAGGGAA
1 TTTGGAGGGAA
3667549 ATTGGCTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.25, C:0.05, G:0.35, T:0.35
Consensus pattern (15 bp):
TTTGGAGGGAACTAT
Found at i:3672534 original size:22 final size:22
Alignment explanation
Indices: 3672510--3672551 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3672500 ATGAAAAATA
*
3672510 AAAATAT-AATTTTTTAAAAAG
1 AAAATATAAATTATTTAAAAAG
*
3672531 AAAATTTAAATTATTTAAAAA
1 AAAATATAAATTATTTAAAAA
3672552 ATTTAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
AAAATATAAATTATTTAAAAAG
Found at i:3674640 original size:29 final size:29
Alignment explanation
Indices: 3674584--3674637 Score: 85
Period size: 27 Copynumber: 1.9 Consensus size: 29
3674574 GATAAAGTTT
*
3674584 TTATTTAATTTTTTCTATTTATATTATTA
1 TTATTTAATTTTTTCAATTTATATTATTA
3674613 TTATTT-ATTTTTTCAA-TTATATTAT
1 TTATTTAATTTTTTCAATTTATATTAT
3674638 ATTTACTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 9 0.38
28 9 0.38
29 6 0.25
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.69
Consensus pattern (29 bp):
TTATTTAATTTTTTCAATTTATATTATTA
Found at i:3674790 original size:15 final size:16
Alignment explanation
Indices: 3674770--3674799 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3674760 TGTTTATGTG
3674770 AATTTT-ATTTTTAAT
1 AATTTTAATTTTTAAT
3674785 AATTTTAATTTTTAA
1 AATTTTAATTTTTAA
3674800 GATTTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
AATTTTAATTTTTAAT
Found at i:3675061 original size:28 final size:29
Alignment explanation
Indices: 3675007--3675066 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
3674997 GAAATTATTA
*
3675007 ATTTTGTATATCATATTTAACTATTTA-T
1 ATTTTATATATCATATTTAACTATTTAGT
* *
3675035 ATTTTATATATTATAGTTTAA-TCTTTAGT
1 ATTTTATATATCATA-TTTAACTATTTAGT
3675064 ATT
1 ATT
3675067 ATAAACTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 18 0.67
29 9 0.33
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (29 bp):
ATTTTATATATCATATTTAACTATTTAGT
Found at i:3676868 original size:19 final size:19
Alignment explanation
Indices: 3676844--3676881 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3676834 CCTCTCTAAT
3676844 TGTTGACCTAAGCTTTAGG
1 TGTTGACCTAAGCTTTAGG
3676863 TGTTGACCTAAGCTTTAGG
1 TGTTGACCTAAGCTTTAGG
3676882 CCCTACTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.16, G:0.26, T:0.37
Consensus pattern (19 bp):
TGTTGACCTAAGCTTTAGG
Found at i:3677397 original size:130 final size:131
Alignment explanation
Indices: 3677132--3677507 Score: 427
Period size: 130 Copynumber: 2.9 Consensus size: 131
3677122 TGAATCTAGA
* * * *
3677132 TTTTATTAGTATTTTCATTTTAAATTAAAATTAGGGTTGAGTGGTTGATTAAACTATTATATATA
1 TTTTATTAGTATTTTCATTTTAAATTAAAATTAAGATTAAGTGGTTAATTAAACTATTATATATA
* * * * ** * *
3677197 TGGTATTTAATTCTTGTATTCTTTCATGTTTAAGTCAATATCATACTAATATGCAAATGAATCCA
66 T-ATATTTAATTCTTATCTTCTTTCAGGTCCAAGTCAATATCATGCTAATATGCAAACGAATCCA
3677262 AG
130 AG
* * * *
3677264 TTTTATTAGTACTTTT-ATTTTGAATAAAAATTAAGATTAAGTGATTAATTAAAATATTATATAT
1 TTTTATTAGTA-TTTTCATTTTAAATTAAAATTAAGATTAAGTGGTTAATTAAACTATTATATAT
* * * *
3677328 A-ATATATAATTCTTATCTTCTTGCAGGTCCAAGTCAATATCATGCTAATATGCAAGCGAATTCA
65 ATATATTTAATTCTTATCTTCTTTCAGGTCCAAGTCAATATCATGCTAATATGCAAACGAATCCA
*
3677392 TG
130 AG
* * *
3677394 TTTTGTT-GCTATTTTCATTTTAAATTAAAATTAAGATTTAGTGGTTTATTAAACTATTATATAT
1 TTTTATTAG-TATTTTCATTTTAAATTAAAATTAAGATTAAGTGGTTAATTAAACTATTATATAT
* * **
3677458 ATAGTATTTAATTCTTA-CGTTTTTTTAGGTCCAAGTTTATATCATGCTAA
65 ATA-TATTTAATTCTTATC-TTCTTTCAGGTCCAAGTCAATATCATGCTAA
3677508 ATTGAAATTA
Statistics
Matches: 204, Mismatches: 34, Indels: 12
0.82 0.14 0.05
Matches are distributed among these distances:
129 5 0.02
130 103 0.50
131 2 0.01
132 90 0.44
133 4 0.02
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (131 bp):
TTTTATTAGTATTTTCATTTTAAATTAAAATTAAGATTAAGTGGTTAATTAAACTATTATATATA
TATATTTAATTCTTATCTTCTTTCAGGTCCAAGTCAATATCATGCTAATATGCAAACGAATCCAA
G
Found at i:3677502 original size:262 final size:254
Alignment explanation
Indices: 3676967--3677507 Score: 644
Period size: 262 Copynumber: 2.1 Consensus size: 254
3676957 ATGGTTTCTG
* * *
3676967 CAGGTCCAAG-CTAGTATCATGCTAATATGCAAGTGAATCCATGTTTTATTAATATTTTTATTTT
1 CAGGTCCAAGTCTA-TATCATGCTAATATGCAAATGAATCCAAGTTTTATTAATACTTTTATTTT
* * * * * *
3677031 GAATTAAAATTGAGATTAAGTAATTGATTAAAATATTATATAATAATATTTAATCCTGGCCTTTT
65 GAATAAAAATTAAGATTAAGTAATTAATTAAAATATTATATAATAATATATAATCCTGACCTTCT
* *
3677096 TGCAAGTTCAAGTCAATATCAGTAAATGAATCTAGATTTTATTAGTATTTTCATTTTAAATTAAA
130 TGCAAGTCCAAGTCAATATCAGTAAATGAAGCTAGATTTTATTAGTATTTTCATTTTAAATTAAA
* * *
3677161 ATTAGGGTTGAGTGGTTGATTAAACTATTATATATATGGTATTTAATTCTTGTATTCTTT
195 ATTAAGATTGAGTGGTTGATTAAACTATTATATATATAGTATTTAATTCTTGTATTCTTT
* ** * * *
3677221 CATGTTTAAGTCAATATCATACTAATATGCAAATGAATCCAAGTTTTATTAGTACTTTTATTTTG
1 CAGGTCCAAGTCTATATCATGCTAATATGCAAATGAATCCAAGTTTTATTAATACTTTTATTTTG
* * * *
3677286 AATAAAAATTAAGATTAAGTGATTAATTAAAATATTATAT-ATAATATATAATTCTTATCTTCTT
66 AATAAAAATTAAGATTAAGTAATTAATTAAAATATTATATAATAATATATAATCCTGACCTTCTT
* *
3677350 GCAGGTCCAAGTCAATATCATGCTAATATGCAAGCGAATTCATG-TTTTGTT-GCTATTTTCATT
131 GCAAGTCCAAGTCAATATCA-G-TAA-ATG-AAGC----T-A-GATTTTATTAG-TATTTTCATT
* *
3677413 TTAAATTAAAATTAAGATTTAGTGGTTTATTAAACTATTATATATATAGTATTTAATTCTTACGT
185 TTAAATTAAAATTAAGATTGAGTGGTTGATTAAACTATTATATATATAGTATTTAATTCTT--GT
3677478 -TT-TTT
248 ATTCTTT
* *
3677483 TAGGTCCAAGTTTATATCATGCTAA
1 CAGGTCCAAGTCTATATCATGCTAA
3677508 ATTGAAATTA
Statistics
Matches: 238, Mismatches: 35, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
253 36 0.15
254 90 0.38
255 5 0.02
256 3 0.01
257 3 0.01
261 2 0.01
262 94 0.39
263 3 0.01
264 2 0.01
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (254 bp):
CAGGTCCAAGTCTATATCATGCTAATATGCAAATGAATCCAAGTTTTATTAATACTTTTATTTTG
AATAAAAATTAAGATTAAGTAATTAATTAAAATATTATATAATAATATATAATCCTGACCTTCTT
GCAAGTCCAAGTCAATATCAGTAAATGAAGCTAGATTTTATTAGTATTTTCATTTTAAATTAAAA
TTAAGATTGAGTGGTTGATTAAACTATTATATATATAGTATTTAATTCTTGTATTCTTT
Found at i:3681810 original size:430 final size:427
Alignment explanation
Indices: 3680637--3681899 Score: 1667
Period size: 427 Copynumber: 2.9 Consensus size: 427
3680627 TTTCTTATTG
* *
3680637 GATAATATCTCCTGCATATTTGTGCTGATTCACATAGATTCCATATTGATTCCTTTTAACCTCTA
1 GATAATATCTCCTGCATATTTGTGCTGATTCACATAGATTTCATCTTGATTCCTTTTAACCTCTA
* * * * * * * *
3680702 ATCCTAAACAATAATGGAGGGTCTTCGGTCTTTTATTTTGAAACTAGTTTGGAAGTATATCTTAA
66 ACCCTAAA-AATAATGAAGGGTCCTAGGTCTTTTATTTTGAAACAAGTTTGGAAATATTTTTTAA
* **
3680767 ATTGTGTACATTTATCTCCATTATTCCCAACAAGTATAAGATCATCTACAAAGATTAATA-TTGT
130 ATTGTGTACATTTATCTCCATTATTCCCAACAAGTATAAGATCATCTACATAGATTAATACTACT
* * *
3680831 CAATAAACCATCCC-AGTATGAAAGTGTGAATAGTGAGTGATCCCATGGACTTTGTTTAAAACCA
195 -AAGAAACTATCCCTA-TATGAAAGTGTGAATAGTGAGTGATTCCATGGACTTTGTTTAAAACCA
* * * * *
3680895 TAATTAAGAAAAGAAATGGAGAGTTTTCCAAACCACTGTGGTGGTGCTAGTTTAAGTCCATATAA
258 TAATT-AGGAAAGAAGTGGAGAGTTTTCCAAACCATTGTGGTGGTGCTTGTTTGAGTCCATATAA
* ** * *
3680960 AGACTTATGTAGGTTACAAACTAGTGAATCATTATGAACTTCCATACCTTGAA-GAGGTTTTATG
322 AGACTTATGCAACTTACAAACTAGTGAATCATTAGGAACTTCCATACCTT-AAGGAGGTTTCATG
* * * * ** * *
3681024 AGTACTTTTTCATTGAGTTAGATTTTTGCGATCTACTTTTTT
386 AATACTTATTCATTGAGTTAGATCTCTGAAACCTACTTCTTT
* ** * *
3681066 GATAATATCTCCTGCATATTTATATTGATTCACATAG-TTTCCATCTTGATTCCTTTTAGCATCT
1 GATAATATCTCCTGCATATTTGTGCTGATTCACATAGATTT-CATCTTGATTCCTTTTAACCTCT
*
3681130 AACCCTAAAAATAATGCAAGGG-CCTAGGTTTTTTATTTTGAAACAAG-TTGGAAATATTTTTTA
65 AACCCTAAAAATAATG-AAGGGTCCTAGGTCTTTTATTTTGAAACAAGTTTGGAAATATTTTTTA
* * * *
3681193 AATTGTGTACATTTATCTCTATTATTCCCAACAAGTATAAGATCATCCACGTAGATTAATACTGC
129 AATTGTGTACATTTATCTCCATTATTCCCAACAAGTATAAGATCATCTACATAGATTAATACTAC
* * * *
3681258 TAAGAAATTATCCTTATATGAAAGTGCGAATAGTGAGTGA-TCCTATGGACTTTATTTAAAACCA
194 TAAGAAACTATCCCTATATGAAAGTGTGAATAGTGAGTGATTCC-ATGGACTTTGTTTAAAACCA
* * *
3681322 TAAATAAGAAGAGAAGTGGAGAGTTTTCCAAACCATTGTGGTGGTGCTTATTTGAGTCCATATAA
258 TAATTAGGAA-AGAAGTGGAGAGTTTTCCAAACCATTGTGGTGGTGCTTGTTTGAGTCCATATAA
* * *
3681387 TGACTTATGCAACTTACAAACTAGTGAGTCATTAGGAACTTCTATACCTTAAGGAGGTTTCATGA
322 AGACTTATGCAACTTACAAACTAGTGAATCATTAGGAACTTCCATACCTTAAGGAGGTTTCATGA
*
3681452 ATACTTATTCATTGAGTTGGATCTCTGAAACCTACTTCTTT
387 ATACTTATTCATTGAGTTAGATCTCTGAAACCTACTTCTTT
* * * *
3681493 GATAATATCTCTTTCATATTTGTGCTAATTCATATAGATTTCATCTTGATTCCTTTTAACCTCTA
1 GATAATATCTCCTGCATATTTGTGCTGATTCACATAGATTTCATCTTGATTCCTTTTAACCTCTA
* *
3681558 ACCCTAGAAAATAATGTAAGGGTCCTAGATCTTTTATTTTGAAACAAGTTTGAAAATATTTTTTA
66 ACCCTA-AAAATAATG-AAGGGTCCTAGGTCTTTTATTTTGAAACAAGTTTGGAAATATTTTTTA
* * * *
3681623 AATTGTGTACATTTATCTCCATTATTCCCGACAAGTATAAGATTATATACATAGATTAACACTAC
129 AATTGTGTACATTTATCTCCATTATTCCCAACAAGTATAAGATCATCTACATAGATTAATACTAC
* * * * *
3681688 TAAGAAGCTATCCCTATATGAAAGTGTGAATAGTGAGTGATTCCATTGACTTTGTTTGAGACTAT
194 TAAGAAACTATCCCTATATGAAAGTGTGAATAGTGAGTGATTCCATGGACTTTGTTTAAAACCAT
* * ** * *
3681753 AATTGAGGAAAGAAGTAGAAAGTTTTCCAAACCATTGTGGTAATGCTTGTGTGAGTCCATATAAG
259 AATT-AGGAAAGAAGTGGAGAGTTTTCCAAACCATTGTGGTGGTGCTTGTTTGAGTCCATATAAA
*
3681818 GACTTATGCAACTTACAAACTAGTGAATCATTAGGAACTTCCATACCTTGAGGAGGTTTCATGAA
323 GACTTATGCAACTTACAAACTAGTGAATCATTAGGAACTTCCATACCTTAAGGAGGTTTCATGAA
*
3681883 TACTTCTTCATTGAGTT
388 TACTTATTCATTGAGTT
3681900 CCCTATGTAA
Statistics
Matches: 724, Mismatches: 97, Indels: 25
0.86 0.11 0.03
Matches are distributed among these distances:
426 7 0.01
427 318 0.44
428 50 0.07
429 89 0.12
430 253 0.35
431 7 0.01
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (427 bp):
GATAATATCTCCTGCATATTTGTGCTGATTCACATAGATTTCATCTTGATTCCTTTTAACCTCTA
ACCCTAAAAATAATGAAGGGTCCTAGGTCTTTTATTTTGAAACAAGTTTGGAAATATTTTTTAAA
TTGTGTACATTTATCTCCATTATTCCCAACAAGTATAAGATCATCTACATAGATTAATACTACTA
AGAAACTATCCCTATATGAAAGTGTGAATAGTGAGTGATTCCATGGACTTTGTTTAAAACCATAA
TTAGGAAAGAAGTGGAGAGTTTTCCAAACCATTGTGGTGGTGCTTGTTTGAGTCCATATAAAGAC
TTATGCAACTTACAAACTAGTGAATCATTAGGAACTTCCATACCTTAAGGAGGTTTCATGAATAC
TTATTCATTGAGTTAGATCTCTGAAACCTACTTCTTT
Found at i:3683763 original size:6 final size:6
Alignment explanation
Indices: 3683752--3683793 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
3683742 AGACTTTCTT
*
3683752 AAAGTA AAAGTA AAAGTA AAA-TA AAAGGA AAA-TA AAAG-A AAA
1 AAAGTA AAAGTA AAAGTA AAAGTA AAAGTA AAAGTA AAAGTA AAA
3683794 TTACATAAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
5 13 0.41
6 19 0.59
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.12
Consensus pattern (6 bp):
AAAGTA
Found at i:3683776 original size:11 final size:11
Alignment explanation
Indices: 3683752--3683794 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
3683742 AGACTTTCTT
3683752 AAAGTAAAAGTA
1 AAAGTAAAA-TA
3683764 AAAGTAAAATA
1 AAAGTAAAATA
*
3683775 AAAGGAAAATA
1 AAAGTAAAATA
3683786 AAAG-AAAAT
1 AAAGTAAAAT
3683795 TACATAAGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
10 5 0.17
11 16 0.53
12 9 0.30
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (11 bp):
AAAGTAAAATA
Found at i:3689987 original size:21 final size:21
Alignment explanation
Indices: 3689929--3690003 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 21
3689919 AATGCAAAGG
*
3689929 AAGTTT-AAAACTAATTTAAAC
1 AAGTTTAAAAACT-ATTCAAAC
3689950 AAGTTTAAAAACTATTCAAAC
1 AAGTTTAAAAACTATTCAAAC
* * *
3689971 ATGTTTAACAA-TCATTCAAAG
1 AAGTTTAAAAACT-ATTCAAAC
*
3689992 AA-TTTCAAAACT
1 AAGTTTAAAAACT
3690004 TATTTGAGTA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
20 7 0.16
21 31 0.70
22 6 0.14
ACGTcount: A:0.49, C:0.13, G:0.05, T:0.32
Consensus pattern (21 bp):
AAGTTTAAAAACTATTCAAAC
Found at i:3690143 original size:21 final size:21
Alignment explanation
Indices: 3690079--3690166 Score: 88
Period size: 21 Copynumber: 4.1 Consensus size: 21
3690069 TTTAAAAACT
* *
3690079 ATTCACATAAGTTCAAAAACTC
1 ATTCAAATAAGTTCAAAGA-TC
* *
3690101 ATTCAAAGAACTTCCAAA-ATC
1 ATTCAAATAAGTT-CAAAGATC
3690122 ATTCAAATAAGTTCAAAGATC
1 ATTCAAATAAGTTCAAAGATC
* * *
3690143 ACTCAAACAAGTTCAAAGTTC
1 ATTCAAATAAGTTCAAAGATC
3690164 ATT
1 ATT
3690167 GAAACAATTT
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
20 4 0.07
21 36 0.65
22 11 0.20
23 4 0.07
ACGTcount: A:0.45, C:0.20, G:0.07, T:0.27
Consensus pattern (21 bp):
ATTCAAATAAGTTCAAAGATC
Found at i:3690648 original size:22 final size:23
Alignment explanation
Indices: 3690608--3690651 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
3690598 ATTTAATTTG
*
3690608 AATTTTAATAAATATATTTAAAA
1 AATTTTAATAAATAAATTTAAAA
3690631 AATTTTAA-AAATAAATTTAAA
1 AATTTTAATAAATAAATTTAAA
3690652 TTAAATGGGT
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
AATTTTAATAAATAAATTTAAAA
Found at i:3694044 original size:25 final size:25
Alignment explanation
Indices: 3694011--3694064 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
3694001 GATTAATAAT
*
3694011 ATTAATCTTCATGCAATAAATAAAC
1 ATTAATCTTCATACAATAAATAAAC
* * *
3694036 ATTAATCTTTATATAATGAATAAAC
1 ATTAATCTTCATACAATAAATAAAC
3694061 ATTA
1 ATTA
3694065 GTTTCAAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.48, C:0.11, G:0.04, T:0.37
Consensus pattern (25 bp):
ATTAATCTTCATACAATAAATAAAC
Found at i:3695173 original size:34 final size:32
Alignment explanation
Indices: 3695111--3695196 Score: 91
Period size: 32 Copynumber: 2.6 Consensus size: 32
3695101 NNNNNNNNNN
*
3695111 AAAATAAAATATATAATATAAAAAATTATATTAAA
1 AAAATAAAA-ATAAAATATAAAAAATTATA--AAA
* * *
3695146 AAAATAAAAATAAAATATAGAAGATTATAATA
1 AAAATAAAAATAAAATATAAAAAATTATAAAA
* *
3695178 AGAATGAAAATAAAATATA
1 AAAATAAAAATAAAATATA
3695197 TGAAATAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
32 19 0.42
34 17 0.38
35 9 0.20
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.27
Consensus pattern (32 bp):
AAAATAAAAATAAAATATAAAAAATTATAAAA
Found at i:3695203 original size:41 final size:36
Alignment explanation
Indices: 3695111--3695217 Score: 105
Period size: 34 Copynumber: 2.9 Consensus size: 36
3695101 NNNNNNNNNN
*
3695111 AAAATAAAATATAT-AATATAAAAAATTATATTAAA
1 AAAATAAAATATATAAATATAAAAAATTATATAAAA
* *
3695146 AAAATAAAA-ATA-AAATATAGAAGATTATAATAAGAA
1 AAAATAAAATATATAAATATAAAAAATTAT-ATAA-AA
*
3695182 TGAAAATAAAATATATGAA-ATAAAAAATATATATAA
1 --AAAATAAAATATATAAATATAAAAAAT-TATATAA
3695218 GAGATGATAT
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
34 16 0.28
35 12 0.21
36 2 0.03
38 9 0.16
39 14 0.24
40 5 0.09
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (36 bp):
AAAATAAAATATATAAATATAAAAAATTATATAAAA
Found at i:3695456 original size:15 final size:15
Alignment explanation
Indices: 3695413--3695471 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
3695403 TTATTTTCTC
*
3695413 TGCAATCACATTGCT
1 TGCAATCACATTACT
* *
3695428 TGCGATCACGTTACT
1 TGCAATCACATTACT
*
3695443 TGCAATCATATTACT
1 TGCAATCACATTACT
* *
3695458 TGTAATCAAATTAC
1 TGCAATCACATTAC
3695472 ATTATAAAGT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.36
Consensus pattern (15 bp):
TGCAATCACATTACT
Found at i:3700039 original size:143 final size:143
Alignment explanation
Indices: 3699784--3702570 Score: 2058
Period size: 143 Copynumber: 19.5 Consensus size: 143
3699774 GTATAATGAG
* * * * **
3699784 AGTAACTTTTTCAAAGTTCCAATGCTAATTACCATAGCAT-AA--TCT-TTTCATCTAGTTGATC
1 AGTAAATTTCTCAAAGTTTCAATGCTAATTACTATAGCATAAAGGT-TATTTCATCTCTTTGATC
* * * * * * * * * *
3699845 TGAATTTCTGTATCCAGAAACTCGAGGAAAATACCAAGATGGAGATGGAGAGGCTTTATGAAGAA
65 TGACTTTTTGTATCCAGAAACTCGAGGAAGAGAACAAGGTCGAGATCGAGAGGCTTTGTAAAGAA
* *
3699910 AATAATGCACATAG
130 AATGATGCACATAA
* * * * *
3699924 AGTAAATTTCTCAAAATTTCTATACTAATTA-TAATAGCATAAGGGTTATTTCAACTCTTTGATC
1 AGTAAATTTCTCAAAGTTTCAATGCTAATTACT-ATAGCATAAAGGTTATTTCATCTCTTTGATC
* * * * *
3699988 TGACTTTTTGTATTCAGAAACTCGAGGCAGAGAATAAGGTCAAGATTGAGAGGCTTTGTAAAG-A
65 TGACTTTTTGTATCCAGAAACTCGAGGAAGAGAACAAGGTCGAGATCGAGAGGCTTTGTAAAGAA
*
3700052 AATCGACGCAC-TCAA
130 AAT-GATGCACAT-AA
* * *
3700067 AGTAAATTTCTCAAAGTTTCAATGCTAATTACTATAGCATAAAAGTTATTTCATTTATTTGATCT
1 AGTAAATTTCTCAAAGTTTCAATGCTAATTACTATAGCATAAAGGTTATTTCATCTCTTTGATCT
* * * * * * *
3700132 GATTTTTTGTGTCCAGAAACTCGAAGAAGAGAATAAGGTCGAAATCGAAAGGCTTCGTAAAGAAA
66 GACTTTTTGTATCCAGAAACTCGAGGAAGAGAACAAGGTCGAGATCGAGAGGCTTTGTAAAGAAA
3700197 ATGATGCACATAA
131 ATGATGCACATAA
** * ** ** * *
3700210 AGTAAATTTCTTGAAGTTCCAATTTTAATTACTATAATATAAAAGTTATTTCATCTTTTTGATCT
1 AGTAAATTTCTCAAAGTTTCAATGCTAATTACTATAGCATAAAGGTTATTTCATCTCTTTGATCT
* * * * * * **
3700275 GACTTTTTGTGTCCAGAAACTAGAGGAAAAGAACAAGATTGAGATCGAGAGGCTTTGCAAACTAA
66 GACTTTTTGTATCCAGAAACTCGAGGAAGAGAACAAGGTCGAGATCGAGAGGCTTTGTAAAGAAA
*
3700340 ATGATGGACATAA
131 ATGATGCACATAA
* *** * *
3700353 AGTAAATTTCTCAAAGTTTCAATGCTAATTGCTATAGCATGGTGGTTATTTCATATCTTTGATAT
1 AGTAAATTTCTCAAAGTTTCAATGCTAATTACTATAGCATAAAGGTTATTTCATCTCTTTGATCT
** * * * * * *
3700418 GACTCCTTGTGTCCAGAAACTTGAGGAAGAGAACAATGTC-ACGATTGAAAGGCTTCGTAAAGAA
66 GACTTTTTGTATCCAGAAACTCGAGGAAGAGAACAAGGTCGA-GATCGAGAGGCTTTGTAAAGAA
3700482 AATGATGCACATAA
130 AATGATGCACATAA
* * * ** *
3700496 AGTAAATTTCTCAAAATTTTAATGTTAATTACTATATAATAAAGGTTATTTCATCTCTTTGATAT
1 AGTAAATTTCTCAAAGTTTCAATGCTAATTACTATAGCATAAAGGTTATTTCATCTCTTTGATCT
* * * * *
3700561 GACTTTTTGTGTCCAGAGACTCGAGGAAGAGAACAAGATTGAGATCAAGAGGCTTCT-TAAAGAA
66 GACTTTTTGTATCCAGAAACTCGAGGAAGAGAACAAGGTCGAGATCGAGAGGCTT-TGTAAAGAA
3700625 AATGATGCACATAA
130 AATGATGCACATAA
* * * ** *
3700639 AGTAAATTTCTTAAAGTTTCAATTCTAATTACTATA-AAGTAAAGGTTACCTCATCTCTTTGATT
1 AGTAAATTTCTCAAAGTTTCAATGCTAATTACTATAGCA-TAAAGGTTATTTCATCTCTTTGATC
* * ** * ** * * * * *
3700703 TGACTTTCTATATTTAGGAACTCGAAAAAGAG-ACAAAGGTCAAGGTGGAGAGG-TTTCTTCAAG
65 TGACTTTTTGTATCCAGAAACTCGAGGAAGAGAAC-AAGGTCGAGATCGAGAGGCTTT-GTAAAG
* *
3700766 AAAGTAATGCACATAA
128 AAAATGATGCACATAA
* * * * * * *
3700782 AGTAAGTTTCTCAAAATTCCAATGCTAATGACTATAGCATAAAGATTATTTCATCTCCTTGATAT
1 AGTAAATTTCTCAAAGTTTCAATGCTAATTACTATAGCATAAAGGTTATTTCATCTCTTTGATCT
* * * * * *
3700847 GATTTTTTGTATCTAGGAACTTGAGGAAGA-AACCAAGGTCAAGATCGAGAGGCTTCGTAAAGAA
66 GACTTTTTGTATCCAGAAACTCGAGGAAGAGAA-CAAGGTCGAGATCGAGAGGCTTTGTAAAGAA
**
3700911 AATGATGCATTTAA
130 AATGATGCACATAA
* * * * *
3700925 AGTAAATTTCTCAAAG-TTCTAAGGCTATTTACTATTGCATAAAAGTTACTTCATCT-TTTGATC
1 AGTAAATTTCTCAAAGTTTC-AATGCTAATTACTATAGCATAAAGGTTATTTCATCTCTTTGATC
* * * * * * * * *
3700988 TAACTCTTCGTATCTAGAAACTTGAGGAAGAGAACAAGATCGAGATTGAGAGGCTTCGAAAAGAA
65 TGACTTTTTGTATCCAGAAACTCGAGGAAGAGAACAAGGTCGAGATCGAGAGGCTTTGTAAAGAA
***
3701053 AATGATGTGTATAA
130 AATGATGCACATAA
* * * * * * *
3701067 AGTAAA-TTCTCAAAGTTCCAATGCTAATTA-TCATAGCATTATGGTTATTTCACCTTTTTAATA
1 AGTAAATTTCTCAAAGTTTCAATGCTAATTACT-ATAGCATAAAGGTTATTTCATCTCTTTGATC
* * * ** * * ** *
3701130 TGGCTTTTTATGTCCAGAAACTCGAGGAAGAGATTAAGATCGAGATCAAGAGGCTTCATGAAGAA
65 TGACTTTTTGTATCCAGAAACTCGAGGAAGAGAACAAGGTCGAGATCGAGAGGCTTTGTAAAGAA
*
3701195 AATGATGCATATAA
130 AATGATGCACATAA
* **
3701209 AGTAAATTTCTCAAAGTTTCAATGCTAATTACTATAGCATAAAGGTTATTTTATCTCCATGATCT
1 AGTAAATTTCTCAAAGTTTCAATGCTAATTACTATAGCATAAAGGTTATTTCATCTCTTTGATCT
* * * * * * * *
3701274 AACATTATG-AGTCCAGAAACTGGAGGAAGAGAACAAGGTTGAGATTGAGAGGCTTCGTCAAGAA
66 GACTTTTTGTA-TCCAGAAACTCGAGGAAGAGAACAAGGTCGAGATCGAGAGGCTTTGTAAAGAA
3701338 AATGATGCACATAA
130 AATGATGCACATAA
* * * * * **
3701352 GGTAAATTTCTCTAAGTTCCAATGCCAATTACTAAATTATAAAGGTTATTTCAT-TCTTTTGA-C
1 AGTAAATTTCTCAAAGTTTCAATGCTAATTACTATAGCATAAAGGTTATTTCATCTC-TTTGATC
* * * * * * ** * *
3701415 TTGACTTTTTATGTCTAGGAACTTGAGAAAGAG-ACGAACATCGAGATCAAGAGGATTCT-TAAA
65 -TGACTTTTTGTATCCAGAAACTCGAGGAAGAGAAC-AAGGTCGAGATCGAGAGGCTT-TGTAAA
3701478 GAAAATGATGCACATAA
127 GAAAATGATGCACATAA
* * *
3701495 AGTAAATTTCTCAAAATTTCAATGCTAATTACTATAGCATAAATGTTATTTCATCTCTTAGATCT
1 AGTAAATTTCTCAAAGTTTCAATGCTAATTACTATAGCATAAAGGTTATTTCATCTCTTTGATCT
* * * * * * * * *
3701560 AACTTTCTGTGT-CAGGAACTTGA-GAAGAAAACCAAGGTCGAGATGGAAAGG-TTTCTTAAAGA
66 GACTTTTTGTATCCAGAAACTCGAGGAAGAGAA-CAAGGTCGAGATCGAGAGGCTTT-GTAAAGA
3701622 AAATGATGCACATAA
129 AAATGATGCACATAA
* * * * *
3701637 AGTAAATTTCTCAAAGTTCCAATGTTAATTACTATAGTATAAAGATTATTTCATCTCTTTGATTT
1 AGTAAATTTCTCAAAGTTTCAATGCTAATTACTATAGCATAAAGGTTATTTCATCTCTTTGATCT
* * * * * *
3701702 GACTTTTTTTGTGTCCAGAAACTCGAGGAAGAAAACAAGATCGAGATTGAGAGACTTCGTAAAGA
66 GAC--TTTTTGTATCCAGAAACTCGAGGAAGAGAACAAGGTCGAGATCGAGAGGCTTTGTAAAGA
*
3701767 AAATGATGCACACAA
129 AAATGATGCACATAA
* * * * * * * *
3701782 AGTAATTTTCTCAAAGTTACAATGGTCATTACTATAGCTTAAAGGCTATTTCAT-TTTTGTGATT
1 AGTAAATTTCTCAAAGTTTCAATGCTAATTACTATAGCATAAAGGTTATTTCATCTCTT-TGATC
* * * * ** * * *
3701846 TGACTTTTTGTGTCTAGAAACT-GCAGGAAAAGACCAAGGTTAAGATCAAAAGGCTTCGTAAAGA
65 TGACTTTTTGTATCCAGAAACTCG-AGGAAGAGAACAAGGTCGAGATCGAGAGGCTTTGTAAAGA
* *
3701910 AAATGACGCACATCA
129 AAATGATGCACATAA
* * *
3701925 AGTAAAATTT-TCAAAGTTTCAATGCTAATTACTATAGCATAAAGATTATTTCATTATATGACTA
1 AGT-AAATTTCTCAAAGTTTCAATGCTAATTACTATAGCATAAAGGTTATTTC---ATCT--CTT
* * * * * *
3701989 TGATATGACTTTTTGTGTCCAGAAACTCAAGGAAGAGAACAAGATTGAGATCGAGAGGCTTCGTA
60 TGATCTGACTTTTTGTATCCAGAAACTCGAGGAAGAGAACAAGGTCGAGATCGAGAGGCTTTGTA
* *
3702054 AAAAAAATGATGCACATGA
125 AAGAAAATGATGCACATAA
* * * * * * * ** * * * *
3702073 AGTAAATTTTTTAATGATGCAATACTAATTACTATAACCCAAAGGTTATTGCCTCTCTTTAATTT
1 AGTAAATTTCTCAAAGTTTCAATGCTAATTACTATAGCATAAAGGTTATTTCATCTCTTTGATCT
* * * * * * * * * *
3702138 GACTTTTTGTTTCTAGAAACTC-ATGGAAAATACCAAGATCAAGAT-GAAAAGGCTTCGTGAAGA
66 GACTTTTTGTATCCAGAAACTCGA-GGAAGAGAACAAGGTCGAGATCG-AGAGGCTTTGTAAAGA
** * *
3702201 AAGGGATGCAAATAG
129 AAATGATGCACATAA
* * * * ** * * * * * * *
3702216 GGTAAACTTCTCAAA-CTCCTAATATTTAGTATTATGGCATAAAGGTTATTTTATCTGTTTGATA
1 AGTAAATTTCTCAAAGTTTC-AATGCTAATTACTATAGCATAAAGGTTATTTCATCTCTTTGATC
* * ** *** * * * *
3702280 TGA-TTTCTTGTATACAG-AATTTAATGGAAGAGATGGAGATCGAGAT-GAAGGGGCTTTATAAC
65 TGACTTT-TTGTATCCAGAAACTCGA-GGAAGAGAACAAGGTCGAGATCG-AGAGGCTTTGTAAA
* * * * *
3702342 GGAATTGATACATATCA
127 GAAAATGATGCACATAA
* * * * * ** * * *
3702359 AGTAAATTTCGCATCA-TTTGAATACTAATTATTATAATATAAAAAGTTATTTTATGTCTTTGAT
1 AGTAAATTTCTCA-AAGTTTCAATGCTAATTACTATAGCAT-AAAGGTTATTTCATCTCTTTGAT
* * * ** * * ** *
3702423 CTAATTTTTTGTGTCCAGAAA-TTTATGGAAGAG-ACTAAGATTGAGAT-GCAGAATCTTCGTAA
64 CTGACTTTTTGTATCCAGAAACTCGA-GGAAGAGAAC-AAGGTCGAGATCG-AGAGGCTTTGTAA
*
3702485 AGAAAAT-ATTGCACATCA
126 AGAAAATGA-TGCACATAA
* * *
3702503 AGTAAATTACTCACAA--TTCGAATGCTAATTATTATA-CTATAAAGGTTATTTTATCTCTTTGA
1 AGTAAATTTCTCA-AAGTTTC-AATGCTAATTACTATAGC-ATAAAGGTTATTTCATCTCTTTGA
3702565 TCTGAC
63 TCTGAC
3702571 ATTCTATAAT
Statistics
Matches: 2093, Mismatches: 485, Indels: 135
0.77 0.18 0.05
Matches are distributed among these distances:
140 34 0.02
141 43 0.02
142 285 0.14
143 1367 0.65
144 132 0.06
145 106 0.05
146 12 0.01
147 7 0.00
148 106 0.05
149 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (143 bp):
AGTAAATTTCTCAAAGTTTCAATGCTAATTACTATAGCATAAAGGTTATTTCATCTCTTTGATCT
GACTTTTTGTATCCAGAAACTCGAGGAAGAGAACAAGGTCGAGATCGAGAGGCTTTGTAAAGAAA
ATGATGCACATAA
Found at i:3702258 original size:291 final size:291
Alignment explanation
Indices: 3701454--3702266 Score: 636
Period size: 291 Copynumber: 2.8 Consensus size: 291
3701444 AGAGACGAAC
* * * * * *
3701454 ATCGAGATCAAGAGGA-TTCTTAAAGAAAATGATGCACATAAAGTAAATTTCTCAAA-ATTTCAA
1 ATCGAGATCGAGA-GACTTCGTAAAAAAAATGATGCACACAAAGTAATTTTCTCAAAGA-TACAA
* * ** * * * * * * *
3701517 TGCTAATTACTATAGCATAAATGTTATTTCA-TCTCT-TAGATCTAACTTTCTGTGTC-AGGAAC
64 TACTAATTACTATAACCCAAAGGCTATTGCATTCT-TGTA-ATTTGACTTTTTGTGTCTAGAAAC
* * * ** * * * * * *
3701579 TTG-A-GAAGAAAACCAAGGTCGAGATGGAAAGGTTTCTTAAAGAAAATGATGCACATAAAGTAA
127 -TGCAGGAA-AAGACCAAGATCAAGATCAAAAGGCTTCGTAAAGAAAAGGACGCAAATCAAGTAA
* * ** * * * * *
3701642 ATTTCTCAAAGT-TCCAATGTTAATTACTATAGTATAAAGATTATTTC---ATCT--CTTTGATT
190 AATTCTCAAACTCT-CAATACTAAGTACTATAGCATAAAGATTATTTCATTATATGACTATGATA
*
3701701 TGACTTTTTTTGTGTCCAGAAACTCGAGGAAGAAAACAAG
254 TGAC--TTTTTGTGTCCAGAAACTCAAGGAAGAAAACAAG
* * * *
3701741 ATCGAGATTGAGAGACTTCGTAAAGAAAATGATGCACACAAAGTAATTTTCTCAAAGTTACAATG
1 ATCGAGATCGAGAGACTTCGTAAAAAAAATGATGCACACAAAGTAATTTTCTCAAAGATACAATA
* * * ** * * *
3701806 GTCATTACTATAGCTTAAAGGCTATTTCATTTTTGTGATTTGACTTTTTGTGTCTAGAAACTGCA
66 CTAATTACTATAACCCAAAGGCTATTGCATTCTTGTAATTTGACTTTTTGTGTCTAGAAACTGCA
* * * * *
3701871 GGAAAAGACCAAGGTTAAGATCAAAAGGCTTCGTAAAGAAAATGACGCACATCAAGTAAAATTTT
131 GGAAAAGACCAAGATCAAGATCAAAAGGCTTCGTAAAGAAAAGGACGCAAATCAAGTAAAATTCT
* * * *
3701936 CAAAGTTTCAATGCTAATTACTATAGCATAAAGATTATTTCATTATATGACTATGATATGACTTT
196 CAAACTCTCAATACTAAGTACTATAGCATAAAGATTATTTCATTATATGACTATGATATGACTTT
*
3702001 TTGTGTCCAGAAACTCAAGGAAGAGAACAAG
261 TTGTGTCCAGAAACTCAAGGAAGAAAACAAG
* * ** * * *
3702032 ATTGAGATCGAGAGGCTTCGTAAAAAAAATGATGCACATGAAGTAAATTTT-TTAATGATGCAAT
1 ATCGAGATCGAGAGACTTCGTAAAAAAAATGATGCACACAAAGT-AATTTTCTCAAAGATACAAT
* * *
3702096 ACTAATTACTATAACCCAAAGGTTATTGCCTCTCTT-TAATTTGACTTTTTGTTTCTAGAAACT-
65 ACTAATTACTATAACCCAAAGGCTATTGCAT-TCTTGTAATTTGACTTTTTGTGTCTAGAAACTG
* * * * * * *
3702159 CATGGAAAATACCAAGATCAAGATGAAAAGGCTTCGTGAAGAAAGGGATGCAAAT-AGGGTAAAC
129 CA-GGAAAAGACCAAGATCAAGATCAAAAGGCTTCGTAAAGAAAAGGACGCAAATCA-AGTAAAA
* * * * *
3702223 TTCTCAAACTC-CTAATATTTAGTATTATGGCATAAAGGTTATTT
192 TTCTCAAACTCTC-AATACTAAGTACTATAGCATAAAGATTATTT
3702267 TATCTGTTTG
Statistics
Matches: 429, Mismatches: 79, Indels: 32
0.79 0.15 0.06
Matches are distributed among these distances:
286 2 0.00
287 95 0.22
288 96 0.22
289 4 0.01
290 4 0.01
291 209 0.49
292 9 0.02
293 10 0.02
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.32
Consensus pattern (291 bp):
ATCGAGATCGAGAGACTTCGTAAAAAAAATGATGCACACAAAGTAATTTTCTCAAAGATACAATA
CTAATTACTATAACCCAAAGGCTATTGCATTCTTGTAATTTGACTTTTTGTGTCTAGAAACTGCA
GGAAAAGACCAAGATCAAGATCAAAAGGCTTCGTAAAGAAAAGGACGCAAATCAAGTAAAATTCT
CAAACTCTCAATACTAAGTACTATAGCATAAAGATTATTTCATTATATGACTATGATATGACTTT
TTGTGTCCAGAAACTCAAGGAAGAAAACAAG
Found at i:3704716 original size:16 final size:16
Alignment explanation
Indices: 3704695--3704728 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3704685 TAATTATTCA
*
3704695 AAATCTGAAAACATTT
1 AAATCTAAAAACATTT
*
3704711 AAATCTAAAAAGATTT
1 AAATCTAAAAACATTT
3704727 AA
1 AA
3704729 TTTTGAAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.09, G:0.06, T:0.29
Consensus pattern (16 bp):
AAATCTAAAAACATTT
Found at i:3714511 original size:37 final size:36
Alignment explanation
Indices: 3714421--3714511 Score: 101
Period size: 37 Copynumber: 2.4 Consensus size: 36
3714411 TCCTTCACTT
* * * *
3714421 TTTTTTTATTTCCTCTCTTTTTAGAGTTTTTTTCTTC
1 TTTTGTTATTT-CTTTCTTTTCAAAGTTTTTTTCTTC
* *
3714458 TTTTGTTGCTTCCTTTCTTTTCAAAGTTTTTTTCTTC
1 TTTTGTT-ATTTCTTTCTTTTCAAAGTTTTTTTCTTC
3714495 TTTTAGTTATTTCTTTC
1 TTTT-GTTATTTCTTTC
3714512 CCTTGTTTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
37 39 0.89
38 5 0.11
ACGTcount: A:0.09, C:0.16, G:0.07, T:0.68
Consensus pattern (36 bp):
TTTTGTTATTTCTTTCTTTTCAAAGTTTTTTTCTTC
Found at i:3721643 original size:19 final size:19
Alignment explanation
Indices: 3721619--3721660 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
3721609 AAGTTTTCTC
*
3721619 AATTAGCATCTAGCTTTAA
1 AATTAGCATCAAGCTTTAA
*
3721638 AATTAGCATCAAGCTTTAT
1 AATTAGCATCAAGCTTTAA
3721657 AATT
1 AATT
3721661 GTCTCTTCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (19 bp):
AATTAGCATCAAGCTTTAA
Found at i:3725100 original size:31 final size:29
Alignment explanation
Indices: 3725064--3725131 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
3725054 TATTATGTGC
3725064 TAGTTATTATGGATATTCAATATATCTTGTT
1 TAGTTATTATGGATATT--ATATATCTTGTT
** * *
3725095 TAGTTACGATGGATGTTGTATATCTTGTT
1 TAGTTATTATGGATATTATATATCTTGTT
*
3725124 TAGCTATT
1 TAGTTATT
3725132 GTGTATGTTA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
29 16 0.53
31 14 0.47
ACGTcount: A:0.25, C:0.07, G:0.18, T:0.50
Consensus pattern (29 bp):
TAGTTATTATGGATATTATATATCTTGTT
Found at i:3728046 original size:142 final size:143
Alignment explanation
Indices: 3727869--3728130 Score: 413
Period size: 142 Copynumber: 1.8 Consensus size: 143
3727859 TATAACATTT
* * *
3727869 AAATGTAATTAATTAAAAGATTCCATGTACAAAATAACTAATAGAGTTTACAATTAATAGAATAA
1 AAATATAATTAATTAAAAGATTCAATGTACAAAATAACTAATAGAGTTCACAATTAATAGAATAA
* **
3727934 TTATTTTCGTAAAATAATTT-GTAAATT-AGTATTTTTATTAAAATAATATATTCAAATAACCCC
66 TTATTTTAGTAAAATAATTTACAAAATTGA-TATTTTTATTAAAATAATATATTCAAATAACCCC
3727997 TAAAACATTATGCC
130 TAAAACATTATGCC
* *
3728011 AAATATAATTAATTGAAAGATTCAATGTGA-AAAATAATTAATAGAGTTCACAATTAATAGAATA
1 AAATATAATTAATTAAAAGATTCAATGT-ACAAAATAACTAATAGAGTTCACAATTAATAGAATA
3728075 ATTATTTTAGTAAAATAATTTACAAAATTGATATTTTTATTAAAATAATATATTCA
65 ATTATTTTAGTAAAATAATTTACAAAATTGATATTTTTATTAAAATAATATATTCA
3728131 CATTTGAATA
Statistics
Matches: 109, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
142 77 0.71
143 31 0.28
144 1 0.01
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.37
Consensus pattern (143 bp):
AAATATAATTAATTAAAAGATTCAATGTACAAAATAACTAATAGAGTTCACAATTAATAGAATAA
TTATTTTAGTAAAATAATTTACAAAATTGATATTTTTATTAAAATAATATATTCAAATAACCCCT
AAAACATTATGCC
Found at i:3729374 original size:170 final size:165
Alignment explanation
Indices: 3729164--3729495 Score: 354
Period size: 170 Copynumber: 2.0 Consensus size: 165
3729154 TGATTAGATC
* *
3729164 ATAAATAAAACATTAATATATAAATGATCCATTATTAATATTCTAAATTAATTAT-A-ATT-TAT
1 ATAAATAAAACATTAATATATAAATGATCAATTATTAATATTATAAATTAATTATAATATTATAT
** *
3729226 -TAA-AAAT-TAAAATAAAATAAAATTTTAATTATATATAATAAAAAATAATATTT-TTAATTTA
66 GTAAGAAATATAAAATAAAATAAAATTTTAATTATATAT--TAAAAAATAATATTTAAAAATTAA
3729287 AAATGAATTAAAATTATTAATATTTTAATNNNNNNNNNNTTTAAATT
129 AAATGAATTAAAATTATTAATATTTTAAT----------TTTAAATT
* * * *
3729334 ATAAATAAAATATTAATCTTTAAATTATCAATTATTAATATTATAAATTAATTATAAATTATTAA
1 ATAAATAAAACATTAATATATAAATGATCAATTATTAATATTATAAATTAATTAT-AA-TATT-A
**
3729399 TATGTAAGAAATGAATAAAATAAAATAAAATTTTAATTATATATTTTAAAATAATATTTAAAAAT
63 TATGTAAGAAAT--ATAAAATAAAATAAAATTTTAATTATATATTAAAAAATAATATTTAAAAAT
*
3729464 TAAAAATTAATTAAAATTATTAATATTTTAAT
126 TAAAAATGAATTAAAATTATTAATATTTTAAT
3729496 CATAATAAAT
Statistics
Matches: 138, Mismatches: 12, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
170 49 0.36
172 1 0.01
174 3 0.02
176 3 0.02
177 3 0.02
178 4 0.03
179 13 0.09
180 33 0.24
181 29 0.21
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.42
Consensus pattern (165 bp):
ATAAATAAAACATTAATATATAAATGATCAATTATTAATATTATAAATTAATTATAATATTATAT
GTAAGAAATATAAAATAAAATAAAATTTTAATTATATATTAAAAAATAATATTTAAAAATTAAAA
ATGAATTAAAATTATTAATATTTTAATTTTAAATT
Found at i:3729419 original size:27 final size:27
Alignment explanation
Indices: 3729356--3729414 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
3729346 TTAATCTTTA
* * *
3729356 AATTATCAATTATTAATATTATAAATT
1 AATTATAAATTATTAATATTAGAAATG
3729383 AATTATAAATTATTAATATGTAAGAAATG
1 AATTATAAATTATTAATAT-T-AGAAATG
3729412 AAT
1 AAT
3729415 AAAATAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 18 0.67
28 1 0.04
29 8 0.30
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (27 bp):
AATTATAAATTATTAATATTAGAAATG
Found at i:3729528 original size:42 final size:41
Alignment explanation
Indices: 3729482--3729575 Score: 111
Period size: 42 Copynumber: 2.2 Consensus size: 41
3729472 AATTAAAATT
3729482 ATTAATATTTT-AATCATAATAAAT-TTAAATTATAAATAAAAG
1 ATTAATATTTTCAA--AT-ATAAATATTAAATTATAAATAAAAG
* * *
3729524 ATTAATATTTTCAAATATTAATGATTATATTATAAATAAAAT
1 ATTAATATTTTCAAATATAAAT-ATTAAATTATAAATAAAAG
3729566 ATTAATATTT
1 ATTAATATTT
3729576 AAATTATCAA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
40 5 0.11
41 2 0.04
42 37 0.80
43 2 0.04
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (41 bp):
ATTAATATTTTCAAATATAAATATTAAATTATAAATAAAAG
Found at i:3729556 original size:179 final size:180
Alignment explanation
Indices: 3729233--3729560 Score: 412
Period size: 179 Copynumber: 1.8 Consensus size: 180
3729223 TATTAAAAAT
** *
3729233 TAAAATAAAATAAAATTTTAATTATATATAATAAAAAATAATATTTTTAATTTAAAATGAATTAA
1 TAAAATAAAATAAAATTTTAATTATATAT-ATAAAAAATAATATTTAAAATTAAAAATGAATTAA
********** *
3729298 AATTATTAATATTTTAATNNNNNNNNNNTTTAAATTATAAATAAAATATTAATCTTTAAATTATC
65 AATTATTAATATTTTAATACATAATAAATTTAAATTATAAATAAAAGATTAATCTTTAAATTATC
*
3729363 AATTATTAATATTATAAATTAATTATAAATTATTAATATGTAAGAAATGAA
130 AATGATTAATATTATAAATTAATTATAAATTATTAATATGTAAGAAATGAA
** *
3729414 TAAAATAAAATAAAATTTTAATTATATAT-TTTAAAATAATATTTAAAAATTAAAAATTAATTAA
1 TAAAATAAAATAAAATTTTAATTATATATATAAAAAATAATATTT-AAAATTAAAAATGAATTAA
*
3729478 AATTATTAATATTTTAAT-CATAATAAATTTAAATTATAAATAAAAGATTAATATTTTCAAA-TA
65 AATTATTAATATTTTAATACATAATAAATTTAAATTATAAATAAAAGATTAAT-CTTT-AAATTA
*
3729541 TTAATGATT-ATATTATAAAT
128 TCAATGATTAATATTATAAAT
3729561 AAAATATTAA
Statistics
Matches: 125, Mismatches: 19, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
179 48 0.38
180 45 0.36
181 32 0.26
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.42
Consensus pattern (180 bp):
TAAAATAAAATAAAATTTTAATTATATATATAAAAAATAATATTTAAAATTAAAAATGAATTAAA
ATTATTAATATTTTAATACATAATAAATTTAAATTATAAATAAAAGATTAATCTTTAAATTATCA
ATGATTAATATTATAAATTAATTATAAATTATTAATATGTAAGAAATGAA
Found at i:3730265 original size:16 final size:17
Alignment explanation
Indices: 3730239--3730273 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
3730229 TCATCAAATT
3730239 ATATCAATTTTATCTCA
1 ATATCAATTTTATCTCA
*
3730256 ATAT-AATTTTATTTCA
1 ATATCAATTTTATCTCA
3730272 AT
1 AT
3730274 CTTTCTAGTC
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:0.37, C:0.11, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATCAATTTTATCTCA
Found at i:3730332 original size:24 final size:24
Alignment explanation
Indices: 3730260--3730332 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 24
3730250 ATCTCAATAT
*
3730260 AATTTTATTTCAATCTTTCTAGTC
1 AATTTTATTTCAATCTTTATAGTC
*
3730284 AA-TTT-TCTC-AT-TATTATA-T-
1 AATTTTATTTCAATCT-TTATAGTC
* *
3730303 AGTTTTATTTCAATCTTTTTAGTC
1 AATTTTATTTCAATCTTTATAGTC
3730327 AATTTT
1 AATTTT
3730333 CTTATTTAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
19 1 0.03
20 5 0.14
21 9 0.25
22 9 0.25
23 5 0.14
24 7 0.19
ACGTcount: A:0.26, C:0.12, G:0.04, T:0.58
Consensus pattern (24 bp):
AATTTTATTTCAATCTTTATAGTC
Found at i:3736636 original size:25 final size:25
Alignment explanation
Indices: 3736608--3736659 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
3736598 AAAACAAATA
*
3736608 AACAATAAAATTATAAGTTTACAAC
1 AACAACAAAATTATAAGTTTACAAC
3736633 AACAACAAAATTATAAGTTTACAAC
1 AACAACAAAATTATAAGTTTACAAC
3736658 AA
1 AA
3736660 TCATTGTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.58, C:0.13, G:0.04, T:0.25
Consensus pattern (25 bp):
AACAACAAAATTATAAGTTTACAAC
Found at i:3736763 original size:15 final size:15
Alignment explanation
Indices: 3736745--3736782 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
3736735 ATATGTTATA
3736745 TTTATAATTAATAA-T
1 TTTATAATT-ATAATT
3736760 TTTATAAATTATAATT
1 TTTAT-AATTATAATT
3736776 TTTATAA
1 TTTATAA
3736783 CGTTAACACA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTATAATTATAATT
Found at i:3736778 original size:16 final size:16
Alignment explanation
Indices: 3736745--3736782 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
3736735 ATATGTTATA
3736745 TTTAT-AATTAATAAT
1 TTTATAAATTAATAAT
3736760 TTTATAAATT-ATAATT
1 TTTATAAATTAATAA-T
3736776 TTTATAA
1 TTTATAA
3736783 CGTTAACACA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTATAAATTAATAAT
Found at i:3752255 original size:18 final size:20
Alignment explanation
Indices: 3752232--3752268 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3752222 ATTCAACAAA
3752232 AAAATA-TT-TTTTAAAAAT
1 AAAATATTTATTTTAAAAAT
3752250 AAAATATTTATTTTAAAAA
1 AAAATATTTATTTTAAAAA
3752269 CTTAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 2 0.12
20 9 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AAAATATTTATTTTAAAAAT
Found at i:3754952 original size:22 final size:22
Alignment explanation
Indices: 3754924--3754968 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
3754914 TCACAGTGTT
3754924 TATTAATTTAAGCATCTTATTG
1 TATTAATTTAAGCATCTTATTG
3754946 TATTAATTTAAGCATCTTATTG
1 TATTAATTTAAGCATCTTATTG
3754968 T
1 T
3754969 CAATACGACG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.09, G:0.09, T:0.51
Consensus pattern (22 bp):
TATTAATTTAAGCATCTTATTG
Found at i:3766136 original size:219 final size:219
Alignment explanation
Indices: 3765750--3766410 Score: 928
Period size: 219 Copynumber: 3.0 Consensus size: 219
3765740 TATGACGAAG
* * * * * * * *
3765750 CTGCCAGGACGATGTATGGGGAAAATGCCATACTAAATATGCCTCATATTTCGGGTTTTGACTCA
1 CTGCCTGGACGATGGATGGTGAAAATGCAATACTGAATATGCCTCATGTTTCAGATTTTGACTCA
* * * * * * **
3765815 GTTGCAACTACTTCACACGCGTTTTCGGAGGCTACTACTTGTGCTGCTTCTAACTCCACGACTGT
66 GTTACAATTACTTCACCCGTGTTTTCGGAGGCAACCACTTGTGCTGCTTCTAACTCCGTGACTGT
* * * * *
3765880 G-CCAATGAACTTTGAAATTTGTGGAACAGATGTGGATGGTGAAGGTGAACCACGTTGGATGAAT
131 GTCCAGT-AACTCTGAAATTTGTGGAAGAGATGTGGATGGTGAAGGTGAACCAAGTAGGATGAAT
3765944 GTTGAATATACTGTGGATTCTGAAA
195 GTTGAATATACTGTGGATTCTGAAA
* * * *
3765969 CTGCCTGGACGATGGATGGTGAAAATGCGATGCTGATTATGCCTAATGTTTCAGATTTTGACTCA
1 CTGCCTGGACGATGGATGGTGAAAATGCAATACTGAATATGCCTCATGTTTCAGATTTTGACTCA
* * *
3766034 GTTACAATTACTTCACCCGTGTTCTCGGAGGCAACGACTTGTGCTGCTTCTAACTCCGTGACCGT
66 GTTACAATTACTTCACCCGTGTTTTCGGAGGCAACCACTTGTGCTGCTTCTAACTCCGTGACTGT
* *
3766099 GTCTAGTAACTCTGAAATTTGTGGAAGAGACGTGGATGGTGAAGGTGAACCAAGTAGGATGAATG
131 GTCCAGTAACTCTGAAATTTGTGGAAGAGATGTGGATGGTGAAGGTGAACCAAGTAGGATGAATG
*
3766164 TTGAATACACTGTGGATTCTGAAA
196 TTGAATATACTGTGGATTCTGAAA
* *
3766188 CTACCTGGACGATGGATGGTGAAAATGCAATACTGAATATGCGTCATGTTTCAGATTTTGACTCA
1 CTGCCTGGACGATGGATGGTGAAAATGCAATACTGAATATGCCTCATGTTTCAGATTTTGACTCA
* * * *
3766253 GTTACAATTACCTCACCCGTGTTTTCGGAGGCAACCACTTCTGCTGCTTCTCACTCCGTGACTGC
66 GTTACAATTACTTCACCCGTGTTTTCGGAGGCAACCACTTGTGCTGCTTCTAACTCCGTGACTGT
* *
3766318 GTCGAGTAACTCTGAAATTTGTGGAAGAGATGTGGATGGTGAAGGTGAACCAAGTAAGATGAATG
131 GTCCAGTAACTCTGAAATTTGTGGAAGAGATGTGGATGGTGAAGGTGAACCAAGTAGGATGAATG
* * *
3766383 TTGAATATACCGTTGATTCTGAAG
196 TTGAATATACTGTGGATTCTGAAA
3766407 CTGC
1 CTGC
3766411 GACGACAAGT
Statistics
Matches: 391, Mismatches: 50, Indels: 2
0.88 0.11 0.00
Matches are distributed among these distances:
219 388 0.99
220 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (219 bp):
CTGCCTGGACGATGGATGGTGAAAATGCAATACTGAATATGCCTCATGTTTCAGATTTTGACTCA
GTTACAATTACTTCACCCGTGTTTTCGGAGGCAACCACTTGTGCTGCTTCTAACTCCGTGACTGT
GTCCAGTAACTCTGAAATTTGTGGAAGAGATGTGGATGGTGAAGGTGAACCAAGTAGGATGAATG
TTGAATATACTGTGGATTCTGAAA
Found at i:3768418 original size:3 final size:3
Alignment explanation
Indices: 3768410--3768447 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
3768400 TTTTCTCTCT
3768410 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
3768448 GAGTATTACT
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:3780156 original size:31 final size:31
Alignment explanation
Indices: 3780076--3780158 Score: 105
Period size: 31 Copynumber: 2.7 Consensus size: 31
3780066 GCTCGTGTAA
* *
3780076 TATAAAGTTTTGTTCAATGTAATCCCTACAC
1 TATAGAGTTTTGTTCAATTTAATCCCTACAC
* * *
3780107 TATAGAAG-TTTGTTCAATTTAATCCTTATAT
1 TATAG-AGTTTTGTTCAATTTAATCCCTACAC
3780138 TATAGAGTTTTGTTCAATTTA
1 TATAGAGTTTTGTTCAATTTA
3780159 GTCTCTATAC
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
30 2 0.04
31 41 0.91
32 2 0.04
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.46
Consensus pattern (31 bp):
TATAGAGTTTTGTTCAATTTAATCCCTACAC
Found at i:3781135 original size:23 final size:23
Alignment explanation
Indices: 3781062--3781127 Score: 80
Period size: 22 Copynumber: 2.9 Consensus size: 23
3781052 TAGGTGTTGT
* * *
3781062 ATGACTGGTTGATATGGCATTAC
1 ATGACTGATTGATAAGGTATTAC
* *
3781085 GTGACTAATTGAT-AGGTATTAC
1 ATGACTGATTGATAAGGTATTAC
3781107 ATGACTGATTGATAAGGTATT
1 ATGACTGATTGATAAGGTATT
3781128 GTGTGACTAG
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
22 18 0.51
23 17 0.49
ACGTcount: A:0.30, C:0.09, G:0.24, T:0.36
Consensus pattern (23 bp):
ATGACTGATTGATAAGGTATTAC
Found at i:3782484 original size:85 final size:85
Alignment explanation
Indices: 3782341--3782508 Score: 232
Period size: 85 Copynumber: 2.0 Consensus size: 85
3782331 GAGATGTTCA
* * *
3782341 TTTTATTGATGTTGCAAAATCCATTGGAGAGGTCATTAATGATCACGATACTTTCAAGGAGTTTG
1 TTTTATTGATGTTGCAAAATCCATTAGAGAGGTCATTAATGATAACGATACTTTCAAGGAATTTG
3782406 TTAAACTGAATGGTGATTCC
66 TTAAACTGAATGGTGATTCC
* * * * *
3782426 TTTTATTGTTGTTGCAAAATCTATTAGAGAGG-CGATTAATGA-AAGTGGTAGTTTCAAGGAATT
1 TTTTATTGATGTTGCAAAATCCATTAGAGAGGTC-ATTAATGATAA-CGATACTTTCAAGGAATT
3782489 TGTTAAACTGAATGGTGATT
64 TGTTAAACTGAATGGTGATT
3782509 GGGACCTTGA
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
84 2 0.03
85 71 0.97
ACGTcount: A:0.30, C:0.10, G:0.23, T:0.38
Consensus pattern (85 bp):
TTTTATTGATGTTGCAAAATCCATTAGAGAGGTCATTAATGATAACGATACTTTCAAGGAATTTG
TTAAACTGAATGGTGATTCC
Found at i:3787111 original size:50 final size:49
Alignment explanation
Indices: 3787052--3787198 Score: 231
Period size: 50 Copynumber: 2.9 Consensus size: 49
3787042 AATTCTTAAC
* *
3787052 TTTTCAACTTCAATGTCAGAGTATAACAATAAGACTGGAAGCCCAAACAT
1 TTTTCAACTTCAGTGT-AGAATATAACAATAAGACTGGAAGCCCAAACAT
* *
3787102 TTTTCAACTTCAGTGTAAGAATATAACAACAGGACTGGAAGCCCAAACAT
1 TTTTCAACTTCAGTGT-AGAATATAACAATAAGACTGGAAGCCCAAACAT
3787152 TTTTCAACTTCAGTGTACGAATATAACAATAAGACTGGAAGCCCAAA
1 TTTTCAACTTCAGTGTA-GAATATAACAATAAGACTGGAAGCCCAAA
3787199 TATTAATTAG
Statistics
Matches: 89, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
49 1 0.01
50 88 0.99
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (49 bp):
TTTTCAACTTCAGTGTAGAATATAACAATAAGACTGGAAGCCCAAACAT
Found at i:3788322 original size:15 final size:15
Alignment explanation
Indices: 3788284--3788332 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
3788274 CTTCTCTCTT
* *
3788284 AAATGTTTTAGAGGG
1 AAATATTTTGGAGGG
3788299 AAATATTTTGGAGGG
1 AAATATTTTGGAGGG
* * *
3788314 AACTCTTTTGGAGAG
1 AAATATTTTGGAGGG
3788329 AAAT
1 AAAT
3788333 TGGCTATAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.35, C:0.04, G:0.29, T:0.33
Consensus pattern (15 bp):
AAATATTTTGGAGGG
Found at i:3789001 original size:13 final size:13
Alignment explanation
Indices: 3788983--3789007 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3788973 TTATATTTGG
3788983 TATCAGGTTCTTA
1 TATCAGGTTCTTA
3788996 TATCAGGTTCTT
1 TATCAGGTTCTT
3789008 TTCCTTTGCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.48
Consensus pattern (13 bp):
TATCAGGTTCTTA
Found at i:3789579 original size:42 final size:42
Alignment explanation
Indices: 3789517--3789599 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
3789507 CAGCTTAGAG
* * * *
3789517 CTTTTATACAGGTGGCTGTTTTTGGATGCAGGGTAGATGGTA
1 CTTTTATACAGATGGCTGTTTTGGGATACAGGGTACATGGTA
* *
3789559 CTTTTGTACAGATGGTTGTTTTGGGATACAGGGTACATGGT
1 CTTTTATACAGATGGCTGTTTTGGGATACAGGGTACATGGT
3789600 GATTTGGTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.19, C:0.10, G:0.33, T:0.39
Consensus pattern (42 bp):
CTTTTATACAGATGGCTGTTTTGGGATACAGGGTACATGGTA
Found at i:3801274 original size:17 final size:16
Alignment explanation
Indices: 3801244--3801287 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 16
3801234 TTTTATTAAT
3801244 TATTTTTT-ATTTTTA
1 TATTTTTTAATTTTTA
3801259 TATTTGTTTAATTTTTA
1 TATTT-TTTAATTTTTA
3801276 TATATTTTTAAT
1 TAT-TTTTTAAT
3801288 ATAATAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 5 0.19
16 3 0.12
17 16 0.62
18 2 0.08
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (16 bp):
TATTTTTTAATTTTTA
Found at i:3803554 original size:12 final size:12
Alignment explanation
Indices: 3803537--3803561 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3803527 AGGCAACATT
3803537 AGTGGACTAATC
1 AGTGGACTAATC
3803549 AGTGGACTAATC
1 AGTGGACTAATC
3803561 A
1 A
3803562 TCCCTTCATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (12 bp):
AGTGGACTAATC
Found at i:3804054 original size:56 final size:56
Alignment explanation
Indices: 3803968--3804079 Score: 197
Period size: 56 Copynumber: 2.0 Consensus size: 56
3803958 GCTTCAATGC
*
3803968 GAGTAACTGCTGCATACCAAAAGCAAACTAATGCGAATGACAGAGTACTTAATTGT
1 GAGTAACTGCTACATACCAAAAGCAAACTAATGCGAATGACAGAGTACTTAATTGT
* *
3804024 GAGTAACTGCTACATAGCAAAAGCAAACTAATGTGAATGACAGAGTACTTAATTGT
1 GAGTAACTGCTACATACCAAAAGCAAACTAATGCGAATGACAGAGTACTTAATTGT
3804080 CATTCATTCT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (56 bp):
GAGTAACTGCTACATACCAAAAGCAAACTAATGCGAATGACAGAGTACTTAATTGT
Found at i:3806159 original size:20 final size:19
Alignment explanation
Indices: 3806134--3806178 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
3806124 ATTAATTAAA
*
3806134 TTTTTAGATCATTTTATATC
1 TTTTTACATCA-TTTATATC
* *
3806154 TTTTTACATGATTTATATT
1 TTTTTACATCATTTATATC
3806173 TTTTTA
1 TTTTTA
3806179 ATTCAACTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.24, C:0.07, G:0.04, T:0.64
Consensus pattern (19 bp):
TTTTTACATCATTTATATC
Found at i:3810395 original size:2 final size:2
Alignment explanation
Indices: 3810388--3810414 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3810378 GGTTAGTTTC
3810388 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
3810415 CTCTGAATTA
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:3812480 original size:26 final size:26
Alignment explanation
Indices: 3812425--3812499 Score: 84
Period size: 26 Copynumber: 3.0 Consensus size: 26
3812415 CAATAGTTTT
*
3812425 TTTTTTTAA-TATGACGTGTAACAAC
1 TTTTTTTAACTATGACGTGTAATAAC
* **
3812450 CTTTTTTAACTATGACGTGTAATATG
1 TTTTTTTAACTATGACGTGTAATAAC
*
3812476 TTTTTGT-AC-ATGACGTGTAATAAC
1 TTTTTTTAACTATGACGTGTAATAAC
3812500 CTAACCATGA
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
24 13 0.32
25 10 0.24
26 18 0.44
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (26 bp):
TTTTTTTAACTATGACGTGTAATAAC
Found at i:3824050 original size:28 final size:29
Alignment explanation
Indices: 3824005--3824059 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
3823995 TATGATTTAA
*
3824005 AATAAAAATATAATTATTTAATTAAATAT
1 AATAAAAATATAAATATTTAATTAAATAT
*
3824034 AATAAAAA-ATAAATATTTATTTAAAT
1 AATAAAAATATAAATATTTAATTAAAT
3824060 TTTTTTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 16 0.67
29 8 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (29 bp):
AATAAAAATATAAATATTTAATTAAATAT
Found at i:3824058 original size:12 final size:11
Alignment explanation
Indices: 3824043--3824093 Score: 54
Period size: 12 Copynumber: 4.7 Consensus size: 11
3824033 TAATAAAAAA
3824043 TAAATATTTATT
1 TAAATATTT-TT
3824055 TAAAT-TTTTT
1 TAAATATTTTT
3824065 TAAATA--TTT
1 TAAATATTTTT
*
3824074 TAAAGATTTTT
1 TAAATATTTTT
3824085 TCAAATATT
1 T-AAATATT
3824094 ATGCCACACA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
9 8 0.24
10 7 0.21
11 7 0.21
12 11 0.33
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (11 bp):
TAAATATTTTT
Found at i:3834004 original size:108 final size:108
Alignment explanation
Indices: 3833802--3834013 Score: 275
Period size: 108 Copynumber: 2.0 Consensus size: 108
3833792 TGCACAAACT
* * * *
3833802 ATCAAGGATATTAGGAACAACAAAAATAACATTAGAAAGAACCCAGCAAAAGCAAGAAAGTAGAG
1 ATCAAGGATACTAGGAACAACAAAAATAAAATTAGAAAGAACCCAACAAAAGCAAGAAAGTAAAG
* * *
3833867 AAAAGGAAAGTAAAGAAAGCATAAAATAGAGAAATGCAAACAA
66 AAAAGGAAAGAAAAGAAAGCAGAAAATAGAGAAAAGCAAACAA
* * * *
3833910 ATCAAGGATACTAGGGAACAACAAAAATAAAATTAGAAAGGACCCAATAATAG-TAGAAAGTAAA
1 ATCAAGGATACTA-GGAACAACAAAAATAAAATTAGAAAGAACCCAACAAAAGCAAGAAAGTAAA
* *
3833974 GAAAAGGAAGGCAAAAG-AAGTAGAAAATAGAGAAAAGCAA
65 GAAAAGGAAAG-AAAAGAAAGCAGAAAATAGAGAAAAGCAA
3834014 GAGGTGTGTT
Statistics
Matches: 89, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
108 51 0.57
109 38 0.43
ACGTcount: A:0.59, C:0.10, G:0.20, T:0.11
Consensus pattern (108 bp):
ATCAAGGATACTAGGAACAACAAAAATAAAATTAGAAAGAACCCAACAAAAGCAAGAAAGTAAAG
AAAAGGAAAGAAAAGAAAGCAGAAAATAGAGAAAAGCAAACAA
Found at i:3852309 original size:21 final size:21
Alignment explanation
Indices: 3852263--3852311 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
3852253 TGCTAATGTA
* *
3852263 TGCTATACATGTACTATTACT
1 TGCTTTACAGGTACTATTACT
3852284 TGCTTTACAGGTACTATTACT
1 TGCTTTACAGGTACTATTACT
3852305 TGCTTTA
1 TGCTTTA
3852312 GATTTTCTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.45
Consensus pattern (21 bp):
TGCTTTACAGGTACTATTACT
Found at i:3857697 original size:93 final size:93
Alignment explanation
Indices: 3857533--3857726 Score: 320
Period size: 93 Copynumber: 2.1 Consensus size: 93
3857523 AGAGTAAAAT
3857533 ATATATACTTAATTATTGAATCAAATACAACTCAATCAATAAATTAAGTCAATATTGATAAACAA
1 ATAT-TACTTAATTATTGAATCAAATACAACTCAATCAATAAATTAAGTCAATATTGATAAACAA
3857598 GATAAATAATAAATTTATTTTTAATATAA
65 GATAAATAATAAATTTATTTTTAATATAA
* * *
3857627 ATATTACTTAGTTATTGAATCAAA-AGCAATTCAGTCAATAAATTAAGTCAATATTGATAAAC-A
1 ATATTACTTAATTATTGAATCAAATA-CAACTCAATCAATAAATTAAGTCAATATTGATAAACAA
3857690 GAATAAATAATAAATTTATTTTTAATATAA
65 G-ATAAATAATAAATTTATTTTTAATATAA
3857720 ATATTAC
1 ATATTAC
3857727 CAGCTAATCA
Statistics
Matches: 95, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
92 3 0.03
93 88 0.93
94 4 0.04
ACGTcount: A:0.49, C:0.08, G:0.06, T:0.37
Consensus pattern (93 bp):
ATATTACTTAATTATTGAATCAAATACAACTCAATCAATAAATTAAGTCAATATTGATAAACAAG
ATAAATAATAAATTTATTTTTAATATAA
Found at i:3857980 original size:30 final size:30
Alignment explanation
Indices: 3857926--3857985 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
3857916 GTTATTCAAT
* *
3857926 TGAATAGAAATATAGTAAAAGTGTATTGAAC
1 TGAATAGAAACATAATAAAAGTGTA-TGAAC
*
3857957 TGAAT-GAAACATAATAAATGTGTATGAAC
1 TGAATAGAAACATAATAAAAGTGTATGAAC
3857986 AATATGTTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 5 0.19
30 16 0.62
31 5 0.19
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.28
Consensus pattern (30 bp):
TGAATAGAAACATAATAAAAGTGTATGAAC
Found at i:3861181 original size:2 final size:2
Alignment explanation
Indices: 3861174--3861214 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3861164 AAAAATCCTT
3861174 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3861215 GTTATGGAGC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3863820 original size:17 final size:17
Alignment explanation
Indices: 3863798--3863832 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3863788 TATGGTGGGA
3863798 TTTTCTTTGTATTTTTC
1 TTTTCTTTGTATTTTTC
* *
3863815 TTTTCTTTTTTTTTTTC
1 TTTTCTTTGTATTTTTC
3863832 T
1 T
3863833 CTATAATTTG
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:0.03, C:0.11, G:0.03, T:0.83
Consensus pattern (17 bp):
TTTTCTTTGTATTTTTC
Found at i:3864392 original size:21 final size:21
Alignment explanation
Indices: 3864349--3864392 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3864339 ATTTTTTTAT
*
3864349 ATTTTTATTATGTTTAATTAA
1 ATTTTTATTATGTTTAATCAA
*
3864370 ATTTTTTTTAT-TTTAAATCAA
1 ATTTTTATTATGTTT-AATCAA
3864391 AT
1 AT
3864393 ATATCTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (21 bp):
ATTTTTATTATGTTTAATCAA
Found at i:3864732 original size:2 final size:2
Alignment explanation
Indices: 3864725--3864754 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3864715 CTACAGATAA
*
3864725 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3864755 CTTGGGACCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3865923 original size:20 final size:19
Alignment explanation
Indices: 3865879--3865926 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
3865869 AATATGAAAA
3865879 TATTTAGTTTTTTTAATAGT
1 TATTTA-TTTTTTTAATAGT
*
3865899 GATTTATTTATTTTAATTA-T
1 TATTTATTT-TTTTAA-TAGT
3865919 TATTTATT
1 TATTTATT
3865927 ATTATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 3 0.12
20 19 0.79
21 2 0.08
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (19 bp):
TATTTATTTTTTTAATAGT
Found at i:3869692 original size:8 final size:8
Alignment explanation
Indices: 3869679--3869704 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
3869669 GTTACCTTGA
3869679 AATGTTTC
1 AATGTTTC
3869687 AATGTTTC
1 AATGTTTC
3869695 AATGTTTC
1 AATGTTTC
3869703 AA
1 AA
3869705 GATGCAAGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.46
Consensus pattern (8 bp):
AATGTTTC
Found at i:3875624 original size:866 final size:857
Alignment explanation
Indices: 3873951--3875679 Score: 2784
Period size: 866 Copynumber: 2.0 Consensus size: 857
3873941 ATCATTTGTC
*
3873951 ATTTTATAGTACATGACATGATATGCATGATGATATGATATAATGGCATGATTATTTTTCAACAT
1 ATTTTATAGTACATGACATGATATGCATGATGATATGATATAATGACATGATTATTTTTCAACAT
3874016 TTAACTCATCATCGCAACATTGTTTTGAGATATAAAATGATAAGTGATATTATAATTAATAATAA
66 TTAACTCATCATCGCAACATTGTTTTGAGATATAAAATGATAAGTGATATTATAATTAATAATAA
*
3874081 TTAATCGAATGTTAATGAAAAAAAAACTATTTGACTCAAAATAAAAATATTGTGATTTAATTGAA
131 TTAATCGAATGTTAATGAAAAAAAAACTATTTGACTCAAAATAAAAATATTATGATTTAATTGAA
*
3874146 CTCATAAAAAAAAAAATTTATTTAAATTTTTTAAAAATAATTTAGAAACCTTTTCAAGCATCGTA
196 CTCATAAAAAAAAAAATTTATTTAAATTTTTTAAAAATAATTTAGAAACCTTTTCAAGCATCATA
3874211 TGTCTATAATATAAAAAGAAAATTATTTATTAAGGGTGGGATATAAAAAATTGTTACATACTTAA
261 TGTCTATAATATAAAAAGAAAATTATTTATTAAGGGTGGGATATAAAAAATTGTTACATACTTAA
3874276 TTAAAATTATTAATNNNNNNNNNNGATAACTAAAAAGATTTATAATAATAAATATTTTAATCTCG
326 TTAAAATTATTAAT----------GATAACTAAAAAGATTTATAATAATAAATATTTTAATCTCG
* * *
3874341 ATAGTAGAATTTAATAATTCTACTAATTATATATAAAATAATAGTAAAAAGATTAAATCCTTTTA
381 ATAGTAAAATTTAATAATTCCACTAATTATACATAAAATAATAGTAAAAAGATTAAATCCTTTTA
*
3874406 TATTGAATGACTTCATAGTAAATTTTCTCAACATCCATGTGTACTACAATTTAAAAAAAAAAACA
446 TATTGAATGACTTCATAGTAAATTTTCTCAACATCCATGTATACTACAATTTAAAAAAAAAAACA
*
3874471 AAAAAGAAAACCAAATAATAAAAAAAATATCAATTAAACTAAACTAAACCTGCCTTCCCACCCAT
511 AAAAAGAAAACC-AATAATAAAAAAAATATCAATTAAACTAAACTAAACCTACCTTCCCACCCAT
* *
3874536 CTGCGACTCTTTCCATATTGAAAAAACCAAATCCGATCTCTCTCAAGAATCTTTCAGATTTGAAA
575 CTGCGACTCTTTCCATATTGAAAAAACCAAATCCGATCTCTCTCAAAAATCTTTCAGAATTGAAA
* *
3874601 TTCTTTTGTTGTATCATTAAAACCTACCTTCCAACCAATCCAGGACTTTGATTTTTCTCAAATTC
640 TTCTTTTGTTGTATCATTAAAACCTACATTCCAACCAATCCAGGACTCTGATTTTTCTCAAATTC
* * * * * *
3874666 GAAGATTTTTAAGAATAAAATTTCCATTTTTTTCTCAACAAAGCTTACTATCTTCTTATCTGTAT
705 GAAGATTTTTAAGAATAAAATATCCATATTTATCTCAACAAAACTTAATATCTTCTTATCCGTAT
*
3874731 CTTCTGTTTTATAATTAATTTTATATATTTAACCCTAGCCCAGCGTTTTCCCTTCGTTAATAATT
770 CTTCTGTTTTATAATTAATTTTATATATTTAACCCTAACCCAGCGTTTTCCCTTCGTTAATAATT
*
3874796 CTCAAAATTTTTCACTCATGGTT
835 CTCAAAAATTTTCACTCATGGTT
*
3874819 ATTTTATAGTACATGACATGATATGCATGATGATATGATATAATGACATGGTTATTTTTCAACAT
1 ATTTTATAGTACATGACATGATATGCATGATGATATGATATAATGACATGATTATTTTTCAACAT
********** *
3874884 TTAACTCATCATCGCAACATTNNNNNNNNNNATAAAATGATAAGTGGTATTATAATTAATAATAA
66 TTAACTCATCATCGCAACATTGTTTTGAGATATAAAATGATAAGTGATATTATAATTAATAATAA
* * *
3874949 TTAGTCGAATGTTAATG-ATAAAAAACTATTTGATTCAAAATAAAAATATTATGATTTAATTGAA
131 TTAATCGAATGTTAATGAAAAAAAAACTATTTGACTCAAAATAAAAATATTATGATTTAATTGAA
3875013 CTCATAAAAAAATAAAAATTTATTTAAATTTTTTAAAAATAATTTAGAAACCTTTTCAAGCATCA
196 CTCAT-AAAAAA-AAAAATTTATTTAAATTTTTTAAAAATAATTTAGAAACCTTTTCAAGCATCA
*
3875078 TATGTCTATAATATAAAAAGAAAATTATTTATTACGGGTGGGATATAAAAAATTGTTACATACTT
259 TATGTCTATAATATAAAAAGAAAATTATTTATTAAGGGTGGGATATAAAAAATTGTTACATACTT
3875143 AATTAAAATTATTAATNNNNNNNNNNGATAACTAAAAAGATTTATAATAATAAATATTTTAATCT
324 AATTAAAATTATTAAT----------GATAACTAAAAAGATTTATAATAATAAATATTTTAATCT
3875208 CGATAGTAAAATTTAATAATTCCACTAATTATACATAAAATAATAGTAAAAA-ATTAAATCCTTT
379 CGATAGTAAAATTTAATAATTCCACTAATTATACATAAAATAATAGTAAAAAGATTAAATCCTTT
3875272 TATATTGAATGACTTCATAGTAAATTTTCTCAACATCCATGTATACTACAATTTAGAAAAAAAAA
444 TATATTGAATGACTTCATAGTAAATTTTCTCAACATCCATGTATACTACAATTTA-AAAAAAAAA
* *
3875337 ACAACAAAGAAAACC-A-AATAAAAAAAATA-CTAATTAAACTAAACTAAACCTACTTTCCCACC
508 ACAAAAAAGAAAACCAATAATAAAAAAAATATC-AATTAAACTAAACTAAACCTACCTTCCCACC
* * *
3875399 CATCTGGGTCTCTTTCCATATTGAAAAAGCCAAATCCGATCTCTCTCAAAAATCTTTCAGAATTG
572 CATCTGCGACTCTTTCCATATTGAAAAAACCAAATCCGATCTCTCTCAAAAATCTTTCAGAATTG
* ** *
3875464 AAATTCTTTTGTTGTATCGTTAAAACCTGTATTCCAACTAATCCAGGACTCTGATTTTTCTCAAA
637 AAATTCTTTTGTTGTATCATTAAAACCTACATTCCAACCAATCCAGGACTCTGATTTTTCTCAAA
*
3875529 TTCGAAGATTTTTAAGGATAAAATATCCATATTTATCTCAACAAAACTTAATATCTTCTTATCCG
702 TTCGAAGATTTTTAAGAATAAAATATCCATATTTATCTCAACAAAACTTAATATCTTCTTATCCG
3875594 TATCTTCTGTTTTATAATTAATTTTATATATTTAACCCTAACCCAGCGTTTTCCCTTCGTTAATA
767 TATCTTCTGTTTTATAATTAATTTTATATATTTAACCCTAACCCAGCGTTTTCCCTTCGTTAATA
3875659 ATTCTCAAAAATTTTCACTCA
832 ATTCTCAAAAATTTTCACTCA
3875680 CCTTTCTGGC
Statistics
Matches: 811, Mismatches: 46, Indels: 10
0.94 0.05 0.01
Matches are distributed among these distances:
865 1 0.00
866 303 0.37
867 50 0.06
868 205 0.25
869 252 0.31
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.36
Consensus pattern (857 bp):
ATTTTATAGTACATGACATGATATGCATGATGATATGATATAATGACATGATTATTTTTCAACAT
TTAACTCATCATCGCAACATTGTTTTGAGATATAAAATGATAAGTGATATTATAATTAATAATAA
TTAATCGAATGTTAATGAAAAAAAAACTATTTGACTCAAAATAAAAATATTATGATTTAATTGAA
CTCATAAAAAAAAAAATTTATTTAAATTTTTTAAAAATAATTTAGAAACCTTTTCAAGCATCATA
TGTCTATAATATAAAAAGAAAATTATTTATTAAGGGTGGGATATAAAAAATTGTTACATACTTAA
TTAAAATTATTAATGATAACTAAAAAGATTTATAATAATAAATATTTTAATCTCGATAGTAAAAT
TTAATAATTCCACTAATTATACATAAAATAATAGTAAAAAGATTAAATCCTTTTATATTGAATGA
CTTCATAGTAAATTTTCTCAACATCCATGTATACTACAATTTAAAAAAAAAAACAAAAAAGAAAA
CCAATAATAAAAAAAATATCAATTAAACTAAACTAAACCTACCTTCCCACCCATCTGCGACTCTT
TCCATATTGAAAAAACCAAATCCGATCTCTCTCAAAAATCTTTCAGAATTGAAATTCTTTTGTTG
TATCATTAAAACCTACATTCCAACCAATCCAGGACTCTGATTTTTCTCAAATTCGAAGATTTTTA
AGAATAAAATATCCATATTTATCTCAACAAAACTTAATATCTTCTTATCCGTATCTTCTGTTTTA
TAATTAATTTTATATATTTAACCCTAACCCAGCGTTTTCCCTTCGTTAATAATTCTCAAAAATTT
TCACTCATGGTT
Found at i:3879058 original size:2 final size:2
Alignment explanation
Indices: 3879051--3879079 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3879041 GTAAGCTTTC
3879051 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
3879080 GTTTCTTCGC
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:3885033 original size:2 final size:2
Alignment explanation
Indices: 3885026--3885053 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3885016 CCCAACTAGT
3885026 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3885054 TCAAGCAATC
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3886747 original size:116 final size:115
Alignment explanation
Indices: 3886616--3887060 Score: 397
Period size: 116 Copynumber: 3.8 Consensus size: 115
3886606 TTCATGATTT
* * *
3886616 TTTTATTTTTTAAATATTAATAATGTATAATTTATTTACAATATTAATAACTGATCATTTAAATA
1 TTTTATTTTCTAAATATTAATAATTTATAATTTATTTAAAATATTAATAACTGATCATTTAAATA
*
3886681 ATAATATTTTATTTATAATTTAAATATTACTATGATTATTTATTTTTTAAA
66 ATAATATTTTATTTATAATTTAAATATTA-TATGATTATTTATTTTTTATA
* * *
3886732 TTTTATTTTCTAAATATTAATAATTTATAATTTATTTAAAATATTAATACCTGATTACTTAAATA
1 TTTTATTTTCTAAATATTAATAATTTATAATTTATTTAAAATATTAATAACTGATCATTTAAATA
* * *
3886797 TTAATATTTTATTTATAATTT--ATGTTATTATGATTGTTTATTTTTTATTTA
66 ATAATATTTTATTTATAATTTAAATATTA-TATGATTATTTATTTTTTA--TA
* * ** **
3886848 TTATATTTTGC-AAAAATTAATAATTTATAATTGATAATTT-AAATATTAATATTTTTTTTACGA
1 TTTTATTTT-CTAAATATTAATAATTTATAATT--T-ATTTAAAATATTAATA--ACTGAT-C-A
* * * *
3886911 TTT-AATCATTAACATTATAACATATTA-ATATATTAAATATTAT-T-ATTATTTATTTTTATTT
58 TTTAAAT-AATAATATT-T--TAT-TTATA-AT-TTAAATATTATATGATTATTTA-TTTT-TTA
3886972 TA
114 TA
* * * * *
3886974 TTTTA-TATGTAAATATTAATAATTTACAATTTATTTAAAATATTAATAATTAATCATTTAAAT-
1 TTTTATTTTCTAAATATTAATAATTTATAATTTATTTAAAATATTAATAACTGATCATTTAAATA
3887037 ATAAATATTTTATTTATAATTTAA
66 AT-AATATTTTATTTATAATTTAA
3887061 TCATTAATAT
Statistics
Matches: 268, Mismatches: 35, Indels: 54
0.75 0.10 0.15
Matches are distributed among these distances:
114 27 0.10
115 5 0.02
116 111 0.41
117 1 0.00
118 14 0.05
119 13 0.05
120 6 0.02
121 6 0.02
122 15 0.06
123 13 0.05
125 24 0.09
126 18 0.07
127 7 0.03
128 3 0.01
129 5 0.02
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.54
Consensus pattern (115 bp):
TTTTATTTTCTAAATATTAATAATTTATAATTTATTTAAAATATTAATAACTGATCATTTAAATA
ATAATATTTTATTTATAATTTAAATATTATATGATTATTTATTTTTTATA
Found at i:3887901 original size:23 final size:24
Alignment explanation
Indices: 3887857--3887902 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
3887847 ATGTGTTCTA
3887857 TCATATATTCTATCACATGTTTTG
1 TCATATATTCTATCACATGTTTTG
*
3887881 TCATATATTC-ATTACATGTTTT
1 TCATATATTCTATCACATGTTTT
3887903 ATTATGTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.26, C:0.15, G:0.07, T:0.52
Consensus pattern (24 bp):
TCATATATTCTATCACATGTTTTG
Found at i:3897281 original size:2 final size:2
Alignment explanation
Indices: 3897274--3897300 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3897264 TAACTTCATA
3897274 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
3897301 ACACACACAC
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:3899382 original size:33 final size:32
Alignment explanation
Indices: 3899345--3899417 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 32
3899335 AGGCTTCAGA
*
3899345 GGTAGAGGGA-ATGCAGACAGAGGAGGTTTTCGG
1 GGTAGAGGGAGAT-CAGACAGAGG-GGGTTTCGG
* *
3899378 GGTAGAGGTAGATCAGATAGAGGGGGTTTCGG
1 GGTAGAGGGAGATCAGACAGAGGGGGTTTCGG
*
3899410 GGTGGAGG
1 GGTAGAGG
3899418 TGATGGAGGC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 15 0.43
33 18 0.51
34 2 0.06
ACGTcount: A:0.25, C:0.07, G:0.49, T:0.19
Consensus pattern (32 bp):
GGTAGAGGGAGATCAGACAGAGGGGGTTTCGG
Found at i:3901922 original size:19 final size:20
Alignment explanation
Indices: 3901898--3901935 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3901888 ATTATCCAAA
*
3901898 GAAAAAG-GCTAAACAAAAG
1 GAAAAAGAGCAAAACAAAAG
3901917 GAAAAAGAGCAAAACAAAA
1 GAAAAAGAGCAAAACAAAA
3901936 TGGGGGGACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.68, C:0.11, G:0.18, T:0.03
Consensus pattern (20 bp):
GAAAAAGAGCAAAACAAAAG
Found at i:3908394 original size:9 final size:9
Alignment explanation
Indices: 3908380--3908411 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
3908370 AAAAGAACCT
3908380 TTTTTTTTG
1 TTTTTTTTG
3908389 TTTTTTTTG
1 TTTTTTTTG
3908398 TTTTTTTTG
1 TTTTTTTTG
3908407 TTTTT
1 TTTTT
3908412 CTCTCTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:3910601 original size:26 final size:26
Alignment explanation
Indices: 3910572--3910626 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
3910562 ATTTAAAATC
* **
3910572 AATAATTATAAAAACAGTTATAATAA
1 AATAATAATAAAAACAAATATAATAA
* *
3910598 AATAATAATAACATCAAATATAATAA
1 AATAATAATAAAAACAAATATAATAA
3910624 AAT
1 AAT
3910627 TTAGCATAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (26 bp):
AATAATAATAAAAACAAATATAATAA
Found at i:3915351 original size:84 final size:82
Alignment explanation
Indices: 3915201--3915370 Score: 186
Period size: 84 Copynumber: 2.0 Consensus size: 82
3915191 AGAAATAAGG
* * * *
3915201 TTTTTTAATAAAAGTCATTCAATGTAATTAAATTTTTTATTTACAAATGAAATATAAGGTATTAA
1 TTTTTTAATAAAAGTCATTCAATGTAATTAAATTTCTTATTTAAAAATGAAATATAACGTAATAA
*
3915266 TATTTGTAATGAAAAGAATA
66 TATTTATAAT--AAA-AATA
* * *
3915286 TTTTTT-ATGAAAGTCATTTAATGCT-ATTATAA-TTCTTATTTAAAAATGAAATA-AATCTTAA
1 TTTTTTAATAAAAGTCATTCAATG-TAATTA-AATTTCTTATTTAAAAATGAAATATAA-CGTAA
3915347 TAATATTTATAATAAAAATA
63 TAATATTTATAATAAAAATA
3915367 TTTT
1 TTTT
3915371 AGTGAAAGAG
Statistics
Matches: 74, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
81 8 0.11
82 3 0.04
83 2 0.03
84 52 0.70
85 9 0.12
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (82 bp):
TTTTTTAATAAAAGTCATTCAATGTAATTAAATTTCTTATTTAAAAATGAAATATAACGTAATAA
TATTTATAATAAAAATA
Found at i:3918675 original size:11 final size:11
Alignment explanation
Indices: 3918656--3918690 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
3918646 TTGAGTTACT
*
3918656 TCATTCATGCA
1 TCATGCATGCA
3918667 TCATGCATGCA
1 TCATGCATGCA
3918678 TCATGCATGCA
1 TCATGCATGCA
3918689 TC
1 TC
3918691 GTTCTCAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (11 bp):
TCATGCATGCA
Found at i:3921791 original size:28 final size:30
Alignment explanation
Indices: 3921759--3921825 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 30
3921749 ATAAAAGTTT
3921759 ATTTAATTTAAA-AT-ATAAAA-ATATAAAA
1 ATTTAATTTAAACATAATAAAAGA-ATAAAA
*
3921787 ATTTAA-TTAAACATAATAAAAGAATAAAT
1 ATTTAATTTAAACATAATAAAAGAATAAAA
3921816 ATTT-ATTTAA
1 ATTTAATTTAA
3921826 TTTTTTTTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
27 5 0.15
28 9 0.26
29 19 0.56
30 1 0.03
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (30 bp):
ATTTAATTTAAACATAATAAAAGAATAAAA
Found at i:3922473 original size:17 final size:18
Alignment explanation
Indices: 3922439--3922475 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
3922429 AAAAAATAAC
3922439 TTTAAAAGATAATATATT
1 TTTAAAAGATAATATATT
*
3922457 TTTAAAA-ATAATTTATT
1 TTTAAAAGATAATATATT
3922474 TT
1 TT
3922476 ATAATTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
TTTAAAAGATAATATATT
Found at i:3922748 original size:80 final size:81
Alignment explanation
Indices: 3922654--3922843 Score: 181
Period size: 81 Copynumber: 2.4 Consensus size: 81
3922644 TACTATTATT
* * *
3922654 ATTACATA-CTATGTACAAAAACATATTACAAATTCGGTT-GAAAAAAATATTATTGTTACACG-
1 ATTACATATC-ATGTACAAAAACATATTACAAATTAGATTAAAAAAAAATATTATTGTTACACGT
* *
3922716 CTATATTGAAAAAATATT
65 C-ATATTAAAAAAATATA
* * * * * * * * * *
3922734 ATTATATGTCATGTATAAACACATGTTACAAGTTATATTAAAAAAAAATATTTTTGTTATATGTC
1 ATTACATATCATGTACAAAAACATATTACAAATTAGATTAAAAAAAAATATTATTGTTACACGTC
*
3922799 ATGTTAAAAAAATATA
66 ATATTAAAAAAATATA
*
3922815 ATTACATATCATGCAC-AAAACATATTACA
1 ATTACATATCATGTACAAAAACATATTACA
3922844 TGTCAAACGG
Statistics
Matches: 85, Mismatches: 22, Indels: 6
0.75 0.19 0.05
Matches are distributed among these distances:
80 39 0.46
81 45 0.53
82 1 0.01
ACGTcount: A:0.46, C:0.11, G:0.08, T:0.35
Consensus pattern (81 bp):
ATTACATATCATGTACAAAAACATATTACAAATTAGATTAAAAAAAAATATTATTGTTACACGTC
ATATTAAAAAAATATA
Found at i:3925129 original size:51 final size:51
Alignment explanation
Indices: 3925024--3925169 Score: 143
Period size: 51 Copynumber: 2.8 Consensus size: 51
3925014 TAAAAAAAGT
* *
3925024 TATTACATATTATGTTAAAAAATAATATTATTATTACATGCTATATAAAAAAACA
1 TATTACAAATTATGTTGAAAAA-AATATTATTATTACATGC--TAT-AAAAAACA
*
3925079 TATTACAAATTATGTTGAAAAAAATATTATTATATGTCATGC-AT-AAAAACA
1 TATTACAAATTATGTTGAAAAAAATATTATTAT-T-ACATGCTATAAAAAACA
* * * * *
3925130 TGTTACAAGTTATATTGAAAAAAAATATTTTTGTTACATG
1 TATTACAAATTATGTTG-AAAAAAATATTATTATTACATG
3925170 TCATGTTGAA
Statistics
Matches: 79, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
50 4 0.05
51 22 0.28
52 14 0.18
53 2 0.03
54 11 0.14
55 21 0.27
56 5 0.06
ACGTcount: A:0.47, C:0.07, G:0.08, T:0.38
Consensus pattern (51 bp):
TATTACAAATTATGTTGAAAAAAATATTATTATTACATGCTATAAAAAACA
Found at i:3927053 original size:37 final size:36
Alignment explanation
Indices: 3927003--3927074 Score: 108
Period size: 37 Copynumber: 2.0 Consensus size: 36
3926993 TAATTTTGAT
* *
3927003 TAAAAATAGTTAATTAATCATTAATCAAAAATAAAAA
1 TAAAAATAGTTAATTAAACA-TAATAAAAAATAAAAA
*
3927040 TAAAAATATTTAATTAAACATAATAAAAAATAAAA
1 TAAAAATAGTTAATTAAACATAATAAAAAATAAAA
3927075 CTTTATTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 14 0.44
37 18 0.56
ACGTcount: A:0.65, C:0.04, G:0.01, T:0.29
Consensus pattern (36 bp):
TAAAAATAGTTAATTAAACATAATAAAAAATAAAAA
Found at i:3931377 original size:23 final size:23
Alignment explanation
Indices: 3931332--3931379 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
3931322 TAAATGAGCT
**
3931332 TATTTGTAAATAATTAATGAATA
1 TATTTGTAAATAATTAAAAAATA
*
3931355 TATTTGTAAATGATTAAAAAATA
1 TATTTGTAAATAATTAAAAAATA
3931378 TA
1 TA
3931380 AATCAGTCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (23 bp):
TATTTGTAAATAATTAAAAAATA
Found at i:3939468 original size:305 final size:314
Alignment explanation
Indices: 3938910--3939529 Score: 809
Period size: 305 Copynumber: 2.0 Consensus size: 314
3938900 GAGCCGGTCG
* * *
3938910 ACAACAAAAGGTTTTTGTACAATTTTTTAATGCTTTGTGCAAATTAATTTTTCTAATAACAGTGT
1 ACAACAAAAGGTTTTTGTACAATTTTTTAATGCTATGTGCAAATTAATGTTTCCAATAACAG-GT
* * * * * *
3938975 GCAATATTTAGGTTTTTGTAGAAACTTCATGATTACATAGGAAATTCCTGGTTTCTTTTATGTTT
65 GAAATATTTAGATTTTTATAGAAACTTCAAGATGACAAAGGAAATT-CTGGTTTCTTTTATGTTT
*
3939040 TTCTAGCAGGGTTTGTTTAAGAAGGCAATCTACTAGGTTTAAAGCCCAAAAACCAGAACTGACTG
129 TTCTAGCAGGGTTTGTTTAAGAAGGCAATCTACTAGGTTTAAAACCCAAAAACCAGAACTGACTG
** *
3939105 AAGATGCGTTTGTAGATGATACAAAATTTCTTGTTTCTTCTTCCTGTGATGATAAGGTGCATGAG
194 AAGATGCGTTTGTAGATGATACAAAATTTCTTGCATCTTCTTCCTGCGATGATAAGGTGCATGAG
*
3939170 AGTGG-C-C-T-TTCTGATTCATCAGTCAAAAAAGAACATGAAGAAGGAAGTACTA
259 AGTGGCCACATCTTCTCATTCATCAGTCAAAAAAGAACATGAAGAAGGAAGTACTA
* *
3939222 ACAACAAAAGGTTTTTGTACAATTTTTTATTGCTATGTGCAAATT-GTGTTTCCAATAACA-GTG
1 ACAACAAAAGGTTTTTGTACAATTTTTTAATGCTATGTGCAAATTAATGTTTCCAATAACAGGTG
*
3939285 AAATCTTTAGATTTTTATAGAAACTTCACAG-TGACAAAGGAAATT-TGTGTTT-TTTT-T-TTT
66 AAATATTTAGATTTTTATAGAAACTTCA-AGATGACAAAGGAAATTCTG-GTTTCTTTTATGTTT
* * * * * *
3939345 TTTTTGCAGGGTTTGTTTGAGAAGGCAATCTGCTAGGTTTAAAACCCAAGAACCGGAACTGACTG
129 TTCTAGCAGGGTTTGTTTAAGAAGGCAATCTACTAGGTTTAAAACCCAAAAACCAGAACTGACTG
* ** *
3939410 AAGATGTGTTTGATGTAGATGATACAGCATTTC-T-CAT-TTCTTCCTGCGATGATAAGGTGGAT
194 AAGATGCG-TT--TGTAGATGATACAAAATTTCTTGCATCTTCTTCCTGCGATGATAAGGTGCAT
*
3939472 GAGAGTGGCCCAACATCTTCTCATTCATTAGTCAAAAAAGAACATGAAGAAGGAAGTA
256 GAGAGTGG-CC-ACATCTTCTCATTCATCAGTCAAAAAAGAACATGAAGAAGGAAGTA
3939530 TCACCCCTAG
Statistics
Matches: 269, Mismatches: 28, Indels: 23
0.84 0.09 0.07
Matches are distributed among these distances:
305 99 0.37
306 4 0.01
307 8 0.03
308 22 0.08
309 40 0.15
310 2 0.01
311 51 0.19
312 43 0.16
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.35
Consensus pattern (314 bp):
ACAACAAAAGGTTTTTGTACAATTTTTTAATGCTATGTGCAAATTAATGTTTCCAATAACAGGTG
AAATATTTAGATTTTTATAGAAACTTCAAGATGACAAAGGAAATTCTGGTTTCTTTTATGTTTTT
CTAGCAGGGTTTGTTTAAGAAGGCAATCTACTAGGTTTAAAACCCAAAAACCAGAACTGACTGAA
GATGCGTTTGTAGATGATACAAAATTTCTTGCATCTTCTTCCTGCGATGATAAGGTGCATGAGAG
TGGCCACATCTTCTCATTCATCAGTCAAAAAAGAACATGAAGAAGGAAGTACTA
Found at i:3944997 original size:6 final size:6
Alignment explanation
Indices: 3944986--3945024 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
3944976 TGTCATTATA
3944986 TATATG TATATG TATATG TATATG TATATG -ATATG -ATAT
1 TATATG TATATG TATATG TATATG TATATG TATATG TATAT
3945025 CTTCGTTGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 9 0.27
6 24 0.73
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (6 bp):
TATATG
Found at i:3950874 original size:26 final size:26
Alignment explanation
Indices: 3950827--3950876 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
3950817 TCATGGCCTA
* * *
3950827 CAAGAAGGGAATTAAACTGAATTTAC
1 CAAGAAGGAAAATAAACAGAATTTAC
*
3950853 CAAGAAGGAAAATGAACAGAATTT
1 CAAGAAGGAAAATAAACAGAATTT
3950877 TTTATGGAGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.50, C:0.10, G:0.20, T:0.20
Consensus pattern (26 bp):
CAAGAAGGAAAATAAACAGAATTTAC
Found at i:3977670 original size:25 final size:24
Alignment explanation
Indices: 3977642--3977716 Score: 64
Period size: 25 Copynumber: 3.0 Consensus size: 24
3977632 ATTTCTAATT
3977642 TTTGCATTAAAATAATGTTAATGGC
1 TTTGCATTAAAATAATGTTAAT-GC
*
3977667 TTTGACATTGAAAATAAAAT-TATAAT-T
1 TTTG-CATT-AAAAT--AATGT-TAATGC
*
3977694 TTTGCAATAAAATAATGTTAATG
1 TTTGCATTAAAATAATGTTAATG
3977717 ATTATTTCTT
Statistics
Matches: 41, Mismatches: 2, Indels: 15
0.71 0.03 0.26
Matches are distributed among these distances:
23 7 0.17
24 1 0.02
25 9 0.22
26 7 0.17
27 9 0.22
28 1 0.02
29 7 0.17
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.40
Consensus pattern (24 bp):
TTTGCATTAAAATAATGTTAATGC
Found at i:3982215 original size:39 final size:39
Alignment explanation
Indices: 3982172--3982268 Score: 124
Period size: 39 Copynumber: 2.5 Consensus size: 39
3982162 TGGAAACTTG
* * *
3982172 GCGCTGCAGCGCTGGAGCTGCTGGAATGGG-CGTTTGGCA
1 GCGCTGCAGCACTGCAGCTGCTGGAA-GGGAAGTTTGGCA
* *
3982211 GCGCTGCAGCACTGTAGCTGCTGGAAGGGAAGTTTTGCA
1 GCGCTGCAGCACTGCAGCTGCTGGAAGGGAAGTTTGGCA
*
3982250 GTGCTGCAGCACTGCAGCT
1 GCGCTGCAGCACTGCAGCT
3982269 TCTGTTTCCA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
38 3 0.06
39 48 0.94
ACGTcount: A:0.16, C:0.24, G:0.38, T:0.22
Consensus pattern (39 bp):
GCGCTGCAGCACTGCAGCTGCTGGAAGGGAAGTTTGGCA
Found at i:3986121 original size:14 final size:14
Alignment explanation
Indices: 3986102--3986132 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3986092 ACTTTATTTA
3986102 TATTTGATATAATT
1 TATTTGATATAATT
*
3986116 TATTTGATGTAATT
1 TATTTGATATAATT
3986130 TAT
1 TAT
3986133 CTATTTGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.58
Consensus pattern (14 bp):
TATTTGATATAATT
Found at i:3986166 original size:12 final size:12
Alignment explanation
Indices: 3986149--3986191 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
3986139 GTAATATATT
*
3986149 TTTATTATTTAA
1 TTTATTAATTAA
3986161 TTTATTAATTAA
1 TTTATTAATTAA
* *
3986173 ATTATTAAATAA
1 TTTATTAATTAA
3986185 TATTATT
1 T-TTATT
3986192 GATAAAAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
12 21 0.81
13 5 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TTTATTAATTAA
Found at i:3989315 original size:33 final size:33
Alignment explanation
Indices: 3989249--3989315 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
3989239 ATATGTTACG
* *
3989249 TTATCATCAATTATGATATATTAGTATGGCATA
1 TTATCATCAATTATGATATATTAGCATGACATA
* * *
3989282 TTATTATCAATTATGATATGTTAGCATTACATA
1 TTATCATCAATTATGATATATTAGCATGACATA
3989315 T
1 T
3989316 CAGTGCGACG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.45
Consensus pattern (33 bp):
TTATCATCAATTATGATATATTAGCATGACATA
Found at i:3994294 original size:2 final size:2
Alignment explanation
Indices: 3994277--3994312 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
3994267 CAACTAAGCC
*
3994277 TA TA AA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3994313 NNNNNNNNNN
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3995669 original size:21 final size:20
Alignment explanation
Indices: 3995632--3995670 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3995622 GCCTTAGGAA
*
3995632 AAAAGAAGGAATTAGGAAGG
1 AAAAGAAGGAATAAGGAAGG
*
3995652 AAAAGAAGATAATAAGGAA
1 AAAAGAAG-GAATAAGGAA
3995671 ATTAGAACGG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.62, C:0.00, G:0.28, T:0.10
Consensus pattern (20 bp):
AAAAGAAGGAATAAGGAAGG
Done.