Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 54 of 226
Found at i:22052324 original size:27 final size:27
Alignment explanation
Indices: 22052277--22052328 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
22052267 AAATTTTTTT
*
22052277 ATTTACCAAAATATTATAAAAAAATTC
1 ATTTACCAAAATATTACAAAAAAATTC
*
22052304 ATTTATCAAAATA-TACCAAAAAAAT
1 ATTTACCAAAATATTA-CAAAAAAAT
22052329 AAAAAATAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 2 0.09
27 20 0.91
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.31
Consensus pattern (27 bp):
ATTTACCAAAATATTACAAAAAAATTC
Found at i:22052398 original size:27 final size:27
Alignment explanation
Indices: 22052367--22052426 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
22052357 GCCTGATCAG
* *
22052367 GCCAATCACATTGACGGCACTAAAGGT
1 GCCAAACACATTGACGGCACCAAAGGT
* * * *
22052394 GCCAAAGAGATTGGCGGCACCAATGGT
1 GCCAAACACATTGACGGCACCAAAGGT
22052421 GCCAAA
1 GCCAAA
22052427 AGACTAAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.25, G:0.27, T:0.15
Consensus pattern (27 bp):
GCCAAACACATTGACGGCACCAAAGGT
Found at i:22052955 original size:90 final size:88
Alignment explanation
Indices: 22052852--22053035 Score: 323
Period size: 90 Copynumber: 2.1 Consensus size: 88
22052842 ATTTGGGTTA
*
22052852 CATTTATGGGTGATCAGTTTTATTATTACTTCTGATTTTTCAATAAGGCATGTCTGGTATTTCTA
1 CATTTATGGGTGATCAGTTTTATTATTACTTCTGATTTTTCAATAAGGCATGCCTGGTATTTCTA
22052917 TTATTATTTTTAATTAGAATTCTCT
66 TTA-T-TTTTTAATTAGAATTCTCT
* *
22052942 CATTTATGGGTGATCAGTTTTATTATTACTTCTGGTTTTTCAATAAGGCATGCCTGGTATTTCTC
1 CATTTATGGGTGATCAGTTTTATTATTACTTCTGATTTTTCAATAAGGCATGCCTGGTATTTCTA
22053007 TTATTTTTTAATTAGAATTCTCT
66 TTATTTTTTAATTAGAATTCTCT
22053030 CATTTA
1 CATTTA
22053036 ATAACTCTAT
Statistics
Matches: 91, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
88 25 0.27
89 1 0.01
90 65 0.71
ACGTcount: A:0.23, C:0.12, G:0.14, T:0.51
Consensus pattern (88 bp):
CATTTATGGGTGATCAGTTTTATTATTACTTCTGATTTTTCAATAAGGCATGCCTGGTATTTCTA
TTATTTTTTAATTAGAATTCTCT
Found at i:22053128 original size:18 final size:18
Alignment explanation
Indices: 22053105--22053168 Score: 85
Period size: 18 Copynumber: 3.5 Consensus size: 18
22053095 TAAAATAGAG
22053105 TTATTAAATGAGAATAGT
1 TTATTAAATGAGAATAGT
* *
22053123 TTATTAAATTCA-AATAGAG
1 TTATTAAA-TGAGAATAG-T
22053142 TTATTAAATGAGAATAGT
1 TTATTAAATGAGAATAGT
22053160 TTATTAAAT
1 TTATTAAAT
22053169 TAAAATAGAG
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
18 24 0.62
19 15 0.38
ACGTcount: A:0.45, C:0.02, G:0.12, T:0.41
Consensus pattern (18 bp):
TTATTAAATGAGAATAGT
Found at i:22053138 original size:37 final size:37
Alignment explanation
Indices: 22053089--22053184 Score: 183
Period size: 37 Copynumber: 2.6 Consensus size: 37
22053079 ACTTGATTTT
22053089 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
1 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
*
22053126 TTAAATTCAAATAGAGTTATTAAATGAGAATAGTTTA
1 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
22053163 TTAAATTAAAATAGAGTTATTA
1 TTAAATTAAAATAGAGTTATTA
22053185 CTTAATTAGA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.48, C:0.01, G:0.12, T:0.39
Consensus pattern (37 bp):
TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
Found at i:22053175 original size:18 final size:19
Alignment explanation
Indices: 22053089--22053184 Score: 115
Period size: 19 Copynumber: 5.2 Consensus size: 19
22053079 ACTTGATTTT
22053089 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
* * *
22053108 TTAAATGAGAATAG-TTTA
1 TTAAATTAAAATAGAGTTA
*
22053126 TTAAATTCAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
* * *
22053145 TTAAATGAGAATAG-TTTA
1 TTAAATTAAAATAGAGTTA
22053163 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
22053182 TTA
1 TTA
22053185 CTTAATTAGA
Statistics
Matches: 61, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
18 29 0.48
19 32 0.52
ACGTcount: A:0.48, C:0.01, G:0.12, T:0.39
Consensus pattern (19 bp):
TTAAATTAAAATAGAGTTA
Found at i:22054267 original size:14 final size:13
Alignment explanation
Indices: 22054234--22054293 Score: 50
Period size: 14 Copynumber: 4.5 Consensus size: 13
22054224 GATAAATTGA
* *
22054234 AAAATTAAATATG
1 AAAATTAAGTATT
*
22054247 AATAATTAAGTGTT
1 AA-AATTAAGTATT
22054261 AGAAATTAAGTATT
1 A-AAATTAAGTATT
*
22054275 AAATTTAAGT-TAT
1 AAAATTAAGTAT-T
22054288 AAAATT
1 AAAATT
22054294 TGTTTGGTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
12 1 0.03
13 16 0.42
14 20 0.53
15 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (13 bp):
AAAATTAAGTATT
Found at i:22062359 original size:13 final size:13
Alignment explanation
Indices: 22062341--22062366 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
22062331 TCAAGATGAG
22062341 TTAGTCCAAAAAA
1 TTAGTCCAAAAAA
22062354 TTAGTCCAAAAAA
1 TTAGTCCAAAAAA
22062367 CTCGTGTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (13 bp):
TTAGTCCAAAAAA
Found at i:22062793 original size:14 final size:14
Alignment explanation
Indices: 22062774--22062823 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
22062764 ACAATGGCAT
22062774 ATAAATAATATAAA
1 ATAAATAATATAAA
**
22062788 ATAAATAA-ACGAA
1 ATAAATAATATAAA
*
22062801 ATGAATATATATAAA
1 ATAAATA-ATATAAA
22062816 A-AAATAAT
1 ATAAATAAT
22062824 CCATGACATG
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
13 11 0.39
14 13 0.46
15 4 0.14
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (14 bp):
ATAAATAATATAAA
Found at i:22063163 original size:57 final size:57
Alignment explanation
Indices: 22063072--22063179 Score: 137
Period size: 57 Copynumber: 1.9 Consensus size: 57
22063062 ATTTGAGCAT
* * ** * *
22063072 TTAAAAAAAAGAATAAATATACACATTTATATATATAAATGTA-AAAAAAACATTCG
1 TTAAAAAAAAAAATAAATACACACATACATATATACAAATATATAAAAAAACATTCG
*
22063128 TTAAAAAATAAAAATATATACACACATACATATATACAAATATATAAAAAAA
1 TTAAAAAA-AAAAATAAATACACACATACATATATACAAATATATAAAAAAA
22063180 TCGAAATTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
56 8 0.19
57 28 0.65
58 7 0.16
ACGTcount: A:0.62, C:0.08, G:0.03, T:0.27
Consensus pattern (57 bp):
TTAAAAAAAAAAATAAATACACACATACATATATACAAATATATAAAAAAACATTCG
Found at i:22065313 original size:40 final size:40
Alignment explanation
Indices: 22065269--22065351 Score: 157
Period size: 40 Copynumber: 2.1 Consensus size: 40
22065259 CCCATCGGAA
22065269 GACACCTTAAGAGAGCAGAGGCTCGAAGACACCCCAAACC
1 GACACCTTAAGAGAGCAGAGGCTCGAAGACACCCCAAACC
*
22065309 GACACCTTAAGAGAGCAGAGGCTCGAATACACCCCAAACC
1 GACACCTTAAGAGAGCAGAGGCTCGAAGACACCCCAAACC
22065349 GAC
1 GAC
22065352 TGAAATCAGC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.37, C:0.33, G:0.22, T:0.08
Consensus pattern (40 bp):
GACACCTTAAGAGAGCAGAGGCTCGAAGACACCCCAAACC
Found at i:22066722 original size:21 final size:21
Alignment explanation
Indices: 22066696--22066744 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
22066686 TTCAATAATT
22066696 GGCTTGGAGTTGTGA-TCTCGG
1 GGCTTGGAGTTGTGACT-TCGG
*
22066717 GGCTTGGAGTTGTGACTTTGG
1 GGCTTGGAGTTGTGACTTCGG
22066738 GGCTTGG
1 GGCTTGG
22066745 TGTCGCGACT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 25 0.96
22 1 0.04
ACGTcount: A:0.08, C:0.12, G:0.45, T:0.35
Consensus pattern (21 bp):
GGCTTGGAGTTGTGACTTCGG
Found at i:22066754 original size:21 final size:21
Alignment explanation
Indices: 22066715--22066756 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
22066705 TTGTGATCTC
* *
22066715 GGGGCTTGGAGTTGTGACTTT
1 GGGGCTTGGAGTCGCGACTTT
*
22066736 GGGGCTTGGTGTCGCGACTTT
1 GGGGCTTGGAGTCGCGACTTT
22066757 AACGACAAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.07, C:0.14, G:0.43, T:0.36
Consensus pattern (21 bp):
GGGGCTTGGAGTCGCGACTTT
Found at i:22068594 original size:3 final size:3
Alignment explanation
Indices: 22068586--22068615 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
22068576 AACGATACGG
*
22068586 TGA TGA TGA TGA TGA TGA TGA CGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
22068616 GAAAAGTTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.33, T:0.30
Consensus pattern (3 bp):
TGA
Found at i:22072547 original size:22 final size:22
Alignment explanation
Indices: 22072508--22072549 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
22072498 AGGATTGTAT
*
22072508 TTTTAAATAAATATTTTAAAGA
1 TTTTAAATAAATAGTTTAAAGA
22072530 TTTTAAATAAACT-GTTTAAA
1 TTTTAAATAAA-TAGTTTAAA
22072550 ACATAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (22 bp):
TTTTAAATAAATAGTTTAAAGA
Found at i:22072742 original size:14 final size:16
Alignment explanation
Indices: 22072723--22072755 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
22072713 AATATAATTT
22072723 TAAAAT-TTTAAA-GA
1 TAAAATATTTAAAGGA
22072737 TAAAATATTTAAAGGA
1 TAAAATATTTAAAGGA
22072753 TAA
1 TAA
22072756 TATTAAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 6 0.35
16 5 0.29
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (16 bp):
TAAAATATTTAAAGGA
Found at i:22075597 original size:2 final size:2
Alignment explanation
Indices: 22075590--22075623 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
22075580 NNNNNNNNNN
22075590 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
22075624 CTATTGCCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:22083850 original size:28 final size:27
Alignment explanation
Indices: 22083818--22083872 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
22083808 CTAACATCTT
22083818 CCATTCTACAATTCTTTATCTTTTAAAC
1 CCATTCTA-AATTCTTTATCTTTTAAAC
* **
22083846 CCATTTTAGTTTCTTTATCTTTTAAAC
1 CCATTCTAAATTCTTTATCTTTTAAAC
22083873 TTGGTTGAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 17 0.71
28 7 0.29
ACGTcount: A:0.25, C:0.22, G:0.02, T:0.51
Consensus pattern (27 bp):
CCATTCTAAATTCTTTATCTTTTAAAC
Found at i:22086287 original size:31 final size:32
Alignment explanation
Indices: 22086252--22086326 Score: 93
Period size: 30 Copynumber: 2.4 Consensus size: 32
22086242 TTTTTGGGGT
*
22086252 TTAATTTAAATTTTCT-AAAATTCTTAGGAG-C
1 TTAATTAAAATTTTCTAAAAATT-TTAGGAGCC
*
22086283 TTAA-TAAAATTTTTTAAAAATTTTAGGAGCC
1 TTAATTAAAATTTTCTAAAAATTTTAGGAGCC
*
22086314 TTACTTAAAATTT
1 TTAATTAAAATTT
22086327 CCAAAGATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
30 16 0.42
31 14 0.37
32 8 0.21
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (32 bp):
TTAATTAAAATTTTCTAAAAATTTTAGGAGCC
Found at i:22096567 original size:2 final size:2
Alignment explanation
Indices: 22096560--22096592 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
22096550 GAGTAACTTA
*
22096560 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22096593 AAACAAAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22102251 original size:41 final size:41
Alignment explanation
Indices: 22102201--22102284 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
22102191 AATCAGTATA
22102201 AAATTATAATTAACCTATATAATTTAAATACTAATTAATAC
1 AAATTATAATTAACCTATATAATTTAAATACTAATTAATAC
*
22102242 AAATTATAATTAACTTATATAATTTAAATACTAATTAATAC
1 AAATTATAATTAACCTATATAATTTAAATACTAATTAATAC
22102283 AA
1 AA
22102285 GCTTACTTGT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.39
Consensus pattern (41 bp):
AAATTATAATTAACCTATATAATTTAAATACTAATTAATAC
Found at i:22117373 original size:2 final size:2
Alignment explanation
Indices: 22117366--22117401 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
22117356 ATAAAACATA
22117366 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22117402 GCATGAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22124256 original size:23 final size:22
Alignment explanation
Indices: 22124212--22124256 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
22124202 TAATCAATTC
**
22124212 TAATCCCTATAAATATGTTATA
1 TAATCCCTATAAATATACTATA
*
22124234 TAATCTCCTATAAATCTACTATA
1 TAATC-CCTATAAATATACTATA
22124257 CAAATATTAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.40, C:0.18, G:0.02, T:0.40
Consensus pattern (22 bp):
TAATCCCTATAAATATACTATA
Found at i:22125515 original size:14 final size:14
Alignment explanation
Indices: 22125496--22125525 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
22125486 AAAAGTTTTG
22125496 AAAACATCAAAATC
1 AAAACATCAAAATC
22125510 AAAACATCAAAATC
1 AAAACATCAAAATC
22125524 AA
1 AA
22125526 TCTTTTTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.67, C:0.20, G:0.00, T:0.13
Consensus pattern (14 bp):
AAAACATCAAAATC
Found at i:22126363 original size:16 final size:16
Alignment explanation
Indices: 22126342--22126390 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
22126332 CGCTGTATTG
22126342 GAATAGAGGCGTAATA
1 GAATAGAGGCGTAATA
* *
22126358 GAATAGATGCGTAATG
1 GAATAGAGGCGTAATA
22126374 GAATAGAGGCGTAATA
1 GAATAGAGGCGTAATA
22126390 G
1 G
22126391 GTAATTCTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.41, C:0.06, G:0.33, T:0.20
Consensus pattern (16 bp):
GAATAGAGGCGTAATA
Found at i:22126456 original size:44 final size:46
Alignment explanation
Indices: 22126370--22126465 Score: 142
Period size: 44 Copynumber: 2.1 Consensus size: 46
22126360 ATAGATGCGT
* *
22126370 AATGGAATAGAGGCGTAATAGGTAATTCTTTTATTTGGTTGAATGG
1 AATGGAATACAGGCGTAATAGGTAATTCTTGTATTTGGTTGAATGG
* *
22126416 AATGGCATACAGGCGTAATA-GT-ATTCTTGTGTTTGGTTGAATGG
1 AATGGAATACAGGCGTAATAGGTAATTCTTGTATTTGGTTGAATGG
22126460 AATGGA
1 AATGGA
22126466 GGTGTAATAG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
44 25 0.56
45 2 0.04
46 18 0.40
ACGTcount: A:0.29, C:0.06, G:0.29, T:0.35
Consensus pattern (46 bp):
AATGGAATACAGGCGTAATAGGTAATTCTTGTATTTGGTTGAATGG
Found at i:22126674 original size:18 final size:17
Alignment explanation
Indices: 22126622--22126783 Score: 73
Period size: 18 Copynumber: 10.0 Consensus size: 17
22126612 TTATTATTAA
22126622 ATATAATTTAATAAAAAT
1 ATATAATTTAAT-AAAAT
*
22126640 ACATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
*
22126657 ATATGAATTTACTAAAAT
1 ATAT-AATTTAATAAAAT
* * *
22126675 -CATAATAT-ATAATACT
1 ATATAATTTAATAA-AAT
* *
22126691 ATAAAATATAATTTAAAAT
1 ATATAATTTAA--TAAAAT
* *
22126710 A-ATTA-TT-AT-TAA-
1 ATATAATTTAATAAAAT
22126722 ATATAATTTAATAAAA-
1 ATATAATTTAATAAAAT
*
22126738 A-AT-A-TT-AT-TAA-
1 ATATAATTTAATAAAAT
22126749 ATATAATTTAATAAAAAT
1 ATATAATTTAAT-AAAAT
*
22126767 ATATAATTTGATAAAAT
1 ATATAATTTAATAAAAT
22126784 TCTTAGTATT
Statistics
Matches: 108, Mismatches: 19, Indels: 35
0.67 0.12 0.22
Matches are distributed among these distances:
11 3 0.03
12 5 0.05
13 8 0.07
14 6 0.06
15 9 0.08
16 10 0.09
17 24 0.22
18 37 0.34
19 3 0.03
20 3 0.03
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:22126743 original size:27 final size:27
Alignment explanation
Indices: 22126685--22126770 Score: 120
Period size: 27 Copynumber: 3.2 Consensus size: 27
22126675 CATAATATAT
* * *
22126685 AATACTATAAAATATAATTTAA-AATA
1 AATATTATTAAATATAATTTAATAAAA
*
22126711 ATTATTATTAAATATAATTTAATAAAA
1 AATATTATTAAATATAATTTAATAAAA
22126738 AATATTATTAAATATAATTTAATAAAA
1 AATATTATTAAATATAATTTAATAAAA
22126765 ATATAT
1 A-ATAT
22126771 AATTTGATAA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
26 19 0.36
27 30 0.57
28 4 0.08
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (27 bp):
AATATTATTAAATATAATTTAATAAAA
Found at i:22126784 original size:28 final size:27
Alignment explanation
Indices: 22126644--22126784 Score: 88
Period size: 27 Copynumber: 5.1 Consensus size: 27
22126634 AAAAATACAT
* * *
22126644 AATTTAATAAAATATATGAATTTACTAA
1 AATTTAATAAAAAATAT-AATTAAATAA
* * * * *
22126672 AATCATAATATATAATACT-ATAAAATAT
1 AAT-TTAATAAAAAATA-TAATTAAATAA
* * * *
22126700 AATTTAA-AATAATTATTATTAAATAT
1 AATTTAATAAAAAATATAATTAAATAA
* *
22126726 AATTTAATAAAAAATATTATTAAATAT
1 AATTTAATAAAAAATATAATTAAATAA
**
22126753 AATTTAATAAAAATATATAATTTGATAA
1 AATTTAATAAAAA-ATATAATTAAATAA
22126781 AATT
1 AATT
22126785 CTTAGTATTA
Statistics
Matches: 88, Mismatches: 20, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
25 1 0.01
26 19 0.22
27 33 0.38
28 25 0.28
29 9 0.10
30 1 0.01
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.40
Consensus pattern (27 bp):
AATTTAATAAAAAATATAATTAAATAA
Found at i:22128922 original size:10 final size:10
Alignment explanation
Indices: 22128907--22128933 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
22128897 GTAGCATCTA
22128907 TAACAATGCT
1 TAACAATGCT
22128917 TAACAATGCT
1 TAACAATGCT
22128927 TAACAAT
1 TAACAAT
22128934 TAATAAACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.44, C:0.19, G:0.07, T:0.30
Consensus pattern (10 bp):
TAACAATGCT
Found at i:22141855 original size:37 final size:37
Alignment explanation
Indices: 22141778--22141866 Score: 99
Period size: 37 Copynumber: 2.4 Consensus size: 37
22141768 GCCACTCCGA
** *
22141778 CCACCCTGCACACCACTTATAGGTTATGATAAGCCTAT
1 CCACCCTGCACACCAC-TATAGGCCATGATAAGCCCAT
*
22141816 CCACCCTGCACACCAC-ATAGGACCATGATAGGCCCAT
1 CCACCCTGCACACCACTATAGG-CCATGATAAGCCCAT
* *
22141853 CCACTCTACACACC
1 CCACCCTGCACACC
22141867 GCGTAGTGGG
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
36 5 0.11
37 23 0.52
38 16 0.36
ACGTcount: A:0.29, C:0.39, G:0.12, T:0.19
Consensus pattern (37 bp):
CCACCCTGCACACCACTATAGGCCATGATAAGCCCAT
Found at i:22144513 original size:21 final size:21
Alignment explanation
Indices: 22144473--22144513 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
22144463 TGGAAATCTC
* * *
22144473 ACACGCCCGTGTGGCTAAGGG
1 ACACGACCGTGTGACCAAGGG
22144494 ACACGACCGTGTGACCAAGG
1 ACACGACCGTGTGACCAAGG
22144514 TATATGCCCG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.29, G:0.34, T:0.12
Consensus pattern (21 bp):
ACACGACCGTGTGACCAAGGG
Found at i:22152205 original size:21 final size:22
Alignment explanation
Indices: 22152163--22152205 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
22152153 ATTCTCTCAA
22152163 TAAAAGATAATAGACGAATGGT
1 TAAAAGATAATAGACGAATGGT
* *
22152185 TAAAATATAATA-ACTAATGGT
1 TAAAAGATAATAGACGAATGGT
22152206 AACTATTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.51, C:0.05, G:0.16, T:0.28
Consensus pattern (22 bp):
TAAAAGATAATAGACGAATGGT
Found at i:22155599 original size:31 final size:31
Alignment explanation
Indices: 22155564--22155626 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
22155554 GTTAACCAAG
22155564 AGTAAAGAATATGCTATATCCTTAAGAATCT
1 AGTAAAGAATATGCTATATCCTTAAGAATCT
22155595 AGTAAAGAATATGCTATATCCTTAAGAATCT
1 AGTAAAGAATATGCTATATCCTTAAGAATCT
22155626 A
1 A
22155627 TCATTAGTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.32
Consensus pattern (31 bp):
AGTAAAGAATATGCTATATCCTTAAGAATCT
Found at i:22159214 original size:13 final size:14
Alignment explanation
Indices: 22159180--22159211 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
22159170 AAGACATGTT
*
22159180 ATTTTAGTTAATGG
1 ATTTTAATTAATGG
22159194 ATTTTAATTAATGG
1 ATTTTAATTAATGG
22159208 ATTT
1 ATTT
22159212 AATGGCTACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.53
Consensus pattern (14 bp):
ATTTTAATTAATGG
Found at i:22167093 original size:2 final size:2
Alignment explanation
Indices: 22167062--22167106 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
22167052 CGATGAATAG
* * * *
22167062 AT AT AG AT AT AG AT AT AG AT AT AA AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22167104 AT A
1 AT A
22167107 AATCCATGAA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (2 bp):
AT
Found at i:22167106 original size:6 final size:6
Alignment explanation
Indices: 22167058--22167102 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
22167048 TCACCGATGA
* * *
22167058 ATAGAT ATAGAT ATAGAT ATAGAT ATAAAT ATATAT ATATAT ATA
1 ATAGAT ATAGAT ATAGAT ATAGAT ATAGAT ATAGAT ATAGAT ATA
22167103 TATAAATCCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (6 bp):
ATAGAT
Found at i:22168455 original size:75 final size:77
Alignment explanation
Indices: 22168327--22168473 Score: 253
Period size: 75 Copynumber: 1.9 Consensus size: 77
22168317 ATTGTACCAA
*
22168327 AAATATATTATACAAAATTTTAAGTTTAATTCAATCATTTGTATTTTAAAAAATAAATATATCA-
1 AAATATATTATACAAAATTTTAAGTTTAACTCAATCATTTGTATTTTAAAAAATAAATATATCAT
22168391 TTTATTATCATC
66 TTTATTATCATC
* *
22168403 AAATATA-TATACAAAATTTTAAGTTTGACTCAATTATTTGTATTTTAAAAAATAAATATATCAT
1 AAATATATTATACAAAATTTTAAGTTTAACTCAATCATTTGTATTTTAAAAAATAAATATATCAT
22168467 TTTATTA
66 TTTATTA
22168474 AGAAGTTAGA
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
75 53 0.79
76 14 0.21
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (77 bp):
AAATATATTATACAAAATTTTAAGTTTAACTCAATCATTTGTATTTTAAAAAATAAATATATCAT
TTTATTATCATC
Found at i:22170828 original size:47 final size:47
Alignment explanation
Indices: 22170777--22170871 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
22170767 ACCAGGAGTA
22170777 CTTCTTCCAACACGTTTCATGCATATATCAAGGAAGCCGCTTACATG
1 CTTCTTCCAACACGTTTCATGCATATATCAAGGAAGCCGCTTACATG
22170824 CTTCTTCCAACACGTTTCATGCATATATCAAGGAAGCCGCTTACATG
1 CTTCTTCCAACACGTTTCATGCATATATCAAGGAAGCCGCTTACATG
22170871 C
1 C
22170872 AGGCTCACTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.29
Consensus pattern (47 bp):
CTTCTTCCAACACGTTTCATGCATATATCAAGGAAGCCGCTTACATG
Found at i:22173845 original size:42 final size:42
Alignment explanation
Indices: 22173787--22173870 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
22173777 CTTTAGTAGG
* *
22173787 CGGTTCCTGGCTACCATCAGCCCCAAAATTCTCAACTTTACC
1 CGGTTCCTGACCACCATCAGCCCCAAAATTCTCAACTTTACC
* * * *
22173829 CGGTTCCTGACCACCATCTGCCTCAAATTTCTCATCTTTACC
1 CGGTTCCTGACCACCATCAGCCCCAAAATTCTCAACTTTACC
22173871 TAACTCAGCA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.21, C:0.38, G:0.11, T:0.30
Consensus pattern (42 bp):
CGGTTCCTGACCACCATCAGCCCCAAAATTCTCAACTTTACC
Found at i:22177442 original size:2 final size:2
Alignment explanation
Indices: 22177435--22177474 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
22177425 TGTTAAATCT
22177435 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
22177475 ATAACACGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:22182415 original size:33 final size:33
Alignment explanation
Indices: 22182366--22182463 Score: 117
Period size: 33 Copynumber: 3.0 Consensus size: 33
22182356 TGGAATGTTG
* *
22182366 TTTGCATCTGTATGGTATACTTTTTAAGTTACC
1 TTTGGATCTGTATGGTATGCTTTTTAAGTTACC
* * *
22182399 TTTGGATCTGTCTGGTATGCTTTTTATGTTA-T
1 TTTGGATCTGTATGGTATGCTTTTTAAGTTACC
* *
22182431 TTTTGATTCTGTATGATATGCTTTTTAAGTTAC
1 TTTGGA-TCTGTATGGTATGCTTTTTAAGTTAC
22182464 ATTGTCACAT
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
32 5 0.09
33 49 0.91
ACGTcount: A:0.18, C:0.11, G:0.17, T:0.53
Consensus pattern (33 bp):
TTTGGATCTGTATGGTATGCTTTTTAAGTTACC
Found at i:22183994 original size:19 final size:18
Alignment explanation
Indices: 22183957--22183995 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
22183947 TTTTCTTATT
* *
22183957 TTGAAAAAATAATAGAGA
1 TTGAAAAAAAAATAAAGA
22183975 TTGAAAAAAAAAGTAAAGA
1 TTGAAAAAAAAA-TAAAGA
22183994 TT
1 TT
22183996 AGGGTTGGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (18 bp):
TTGAAAAAAAAATAAAGA
Found at i:22189816 original size:16 final size:15
Alignment explanation
Indices: 22189791--22189820 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
22189781 CTTGGAACAG
22189791 TTTTTTTTTAATATT
1 TTTTTTTTTAATATT
22189806 TTTTATTTTTAATAT
1 TTTT-TTTTTAATAT
22189821 GGATGGATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTTTTTAATATT
Found at i:22197990 original size:16 final size:17
Alignment explanation
Indices: 22197964--22197999 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
22197954 TCTTAAACCT
22197964 TTTATATTTTTTTATAA
1 TTTATATTTTTTTATAA
22197981 TTTA-ATTTTTTTATAA
1 TTTATATTTTTTTATAA
22197997 TTT
1 TTT
22198000 TAAATTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTATATTTTTTTATAA
Found at i:22201720 original size:24 final size:24
Alignment explanation
Indices: 22201624--22201721 Score: 92
Period size: 24 Copynumber: 4.0 Consensus size: 24
22201614 AGTTACCCGT
22201624 TAAGCTCGCATGAGCTTTCTGATT-
1 TAAGCTCGCATGAGCTTTCTG-TTA
** *
22201648 TAAGCTCTTATGAGCTTCCTGTTA
1 TAAGCTCGCATGAGCTTTCTGTTA
* * *
22201672 TTAAGC-CTGGATAAGCTTTCCGTTA
1 -TAAGCTC-GCATGAGCTTTCTGTTA
*
22201697 TAAGCTCACATGAGCTTTCTGTTA
1 TAAGCTCGCATGAGCTTTCTGTTA
22201721 T
1 T
22201722 TTGGCTTGGA
Statistics
Matches: 58, Mismatches: 12, Indels: 8
0.74 0.15 0.10
Matches are distributed among these distances:
23 2 0.03
24 38 0.66
25 18 0.31
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.39
Consensus pattern (24 bp):
TAAGCTCGCATGAGCTTTCTGTTA
Found at i:22210775 original size:18 final size:18
Alignment explanation
Indices: 22210752--22210795 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
22210742 AAGTATTTCT
22210752 GAAAGTTTCACCTTGGAA
1 GAAAGTTTCACCTTGGAA
22210770 GAAAGTTTCACCTTGGAA
1 GAAAGTTTCACCTTGGAA
22210788 GAAAGTTT
1 GAAAGTTT
22210796 TTCGATTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.30
Consensus pattern (18 bp):
GAAAGTTTCACCTTGGAA
Found at i:22212708 original size:24 final size:24
Alignment explanation
Indices: 22212679--22212734 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
22212669 GAGTTATCTG
22212679 TTAAGCTCGCACGAGCTTTCTGAT
1 TTAAGCTCGCACGAGCTTTCTGAT
* *
22212703 TTAAGCTCGCATGTGCTTTCTGAT
1 TTAAGCTCGCACGAGCTTTCTGAT
22212727 TTAAGCTC
1 TTAAGCTC
22212735 TTATGAGCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.38
Consensus pattern (24 bp):
TTAAGCTCGCACGAGCTTTCTGAT
Found at i:22212744 original size:24 final size:24
Alignment explanation
Indices: 22212679--22212797 Score: 89
Period size: 24 Copynumber: 4.9 Consensus size: 24
22212669 GAGTTATCTG
* *
22212679 TTAAGCTCGCACGAGCTTTCTGAT
1 TTAAGCTCTCATGAGCTTTCTGAT
* *
22212703 TTAAGCTCGCATGTGCTTTCTGAT
1 TTAAGCTCTCATGAGCTTTCTGAT
* * *
22212727 TTAAGCTCTTATGAGCTTCCTGTT
1 TTAAGCTCTCATGAGCTTTCTGAT
* * **
22212751 ATTAAGC-CTGTATAAGC-TTCCCAT
1 -TTAAGCTCT-CATGAGCTTTCTGAT
*
22212775 TATAAGCTCACATGAGCTTTCTG
1 T-TAAGCTCTCATGAGCTTTCTG
22212798 TTATTTGGCT
Statistics
Matches: 73, Mismatches: 17, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
23 1 0.01
24 56 0.77
25 16 0.22
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.38
Consensus pattern (24 bp):
TTAAGCTCTCATGAGCTTTCTGAT
Found at i:22212777 original size:25 final size:25
Alignment explanation
Indices: 22212727--22212783 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
22212717 GCTTTCTGAT
* **
22212727 TTAAGCTCTTATGAGCTTCCTGTTA
1 TTAAGCTCTTATAAGCTTCCCATTA
22212752 TTAAGC-CTGTATAAGCTTCCCATTA
1 TTAAGCTCT-TATAAGCTTCCCATTA
22212777 -TAAGCTC
1 TTAAGCTC
22212784 ACATGAGCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 7 0.26
25 20 0.74
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.39
Consensus pattern (25 bp):
TTAAGCTCTTATAAGCTTCCCATTA
Found at i:22214381 original size:33 final size:33
Alignment explanation
Indices: 22214315--22214383 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
22214305 GAAGACAAAA
*
22214315 ACACTAGTAAAGGGTTTAGATTTTACGACGAAG
1 ACACTAGTAAAGGGTTTAGATTTGACGACGAAG
* * *
22214348 ACACTAGTAAATGGTTTAGATTTGATGATGAAG
1 ACACTAGTAAAGGGTTTAGATTTGACGACGAAG
22214381 ACA
1 ACA
22214384 TGTATCATGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29
Consensus pattern (33 bp):
ACACTAGTAAAGGGTTTAGATTTGACGACGAAG
Found at i:22215904 original size:13 final size:14
Alignment explanation
Indices: 22215886--22215919 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
22215876 AACAACCAAA
22215886 AACAATACTT-GTG
1 AACAATACTTCGTG
22215899 AACAATA-TTCGTG
1 AACAATACTTCGTG
22215912 AACAATAC
1 AACAATAC
22215920 CCATGAATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.11
13 17 0.89
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.26
Consensus pattern (14 bp):
AACAATACTTCGTG
Found at i:22220249 original size:87 final size:87
Alignment explanation
Indices: 22220103--22220284 Score: 346
Period size: 87 Copynumber: 2.1 Consensus size: 87
22220093 CTTCATTACA
22220103 ACTTCATCGACAGTGGAACCATTCTCCCCAAGGAACTCAACCTCAGTAGCCTTTCTTTTGGCAAT
1 ACTTCATCGACAGTGGAACCATTCTCCCCAAGGAACTCAACCTCAGTAGCCTTTCTTTTGGCAAT
*
22220168 GTCATGGCTTGGCGTCTCTTCG
66 GCCATGGCTTGGCGTCTCTTCG
22220190 ACTTCATCGACAGTGGAACCATTCTCCCCAAGGAACTCAACCTCAGTAGCCTTTCTTTTGGCAAT
1 ACTTCATCGACAGTGGAACCATTCTCCCCAAGGAACTCAACCTCAGTAGCCTTTCTTTTGGCAAT
*
22220255 GCCGTGGCTTGGCGTCTCTTCG
66 GCCATGGCTTGGCGTCTCTTCG
22220277 ACTTCATC
1 ACTTCATC
22220285 TTCCGAACTG
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
87 93 1.00
ACGTcount: A:0.20, C:0.31, G:0.19, T:0.30
Consensus pattern (87 bp):
ACTTCATCGACAGTGGAACCATTCTCCCCAAGGAACTCAACCTCAGTAGCCTTTCTTTTGGCAAT
GCCATGGCTTGGCGTCTCTTCG
Found at i:22224765 original size:27 final size:27
Alignment explanation
Indices: 22224735--22224788 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
22224725 GTTATTTTTC
22224735 AACGCATAGGTGAAAGATCGGATTGAA
1 AACGCATAGGTGAAAGATCGGATTGAA
* *
22224762 AACGCGTAGGTGAAAGATCTGATTGAA
1 AACGCATAGGTGAAAGATCGGATTGAA
22224789 GTTATCGTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.39, C:0.11, G:0.30, T:0.20
Consensus pattern (27 bp):
AACGCATAGGTGAAAGATCGGATTGAA
Found at i:22227708 original size:19 final size:21
Alignment explanation
Indices: 22227669--22227711 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
22227659 TTGATTGGCC
*
22227669 AAAATTATTAAGAATTATTTA
1 AAAATTATTAAGAACTATTTA
22227690 AAAATTA-TAA-AACTATTTA
1 AAAATTATTAAGAACTATTTA
22227709 AAA
1 AAA
22227712 TGAATAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.52
20 3 0.14
21 7 0.33
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
AAAATTATTAAGAACTATTTA
Found at i:22227782 original size:29 final size:28
Alignment explanation
Indices: 22227733--22227791 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
22227723 GCAAAATGTT
*
22227733 ATATAGAAAAATTAAAAATTATTTAAAA
1 ATATAGAAAAATTAAAAATTATTAAAAA
*
22227761 ATATA-AAAACATATAATAATTATTAAAAA
1 ATATAGAAAA-AT-TAAAAATTATTAAAAA
22227790 AT
1 AT
22227792 TTATAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 4 0.15
28 7 0.26
29 16 0.59
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (28 bp):
ATATAGAAAAATTAAAAATTATTAAAAA
Found at i:22228720 original size:9 final size:9
Alignment explanation
Indices: 22228708--22228811 Score: 120
Period size: 9 Copynumber: 11.4 Consensus size: 9
22228698 AAAATAAAAA
*
22228708 AATTTGGGT
1 AATTCGGGT
22228717 AATTCGGGT
1 AATTCGGGT
*
22228726 ATTTTTC-GGT
1 A--ATTCGGGT
* *
22228736 AATTCAGTT
1 AATTCGGGT
*
22228745 AATTCGGTT
1 AATTCGGGT
22228754 AATTCGGGT
1 AATTCGGGT
*
22228763 AATTCGGTT
1 AATTCGGGT
22228772 AATTCGGGT
1 AATTCGGGT
22228781 AATTCGGGT
1 AATTCGGGT
*
22228790 AATTCGGAT
1 AATTCGGGT
22228799 AATTCGGGT
1 AATTCGGGT
22228808 AATT
1 AATT
22228812 TTTAACCAAA
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
8 3 0.04
9 72 0.88
10 4 0.05
11 3 0.04
ACGTcount: A:0.24, C:0.10, G:0.26, T:0.40
Consensus pattern (9 bp):
AATTCGGGT
Found at i:22228988 original size:12 final size:12
Alignment explanation
Indices: 22228971--22228995 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
22228961 AGTAATTTCG
22228971 GGTCGGTTAACC
1 GGTCGGTTAACC
22228983 GGTCGGTTAACC
1 GGTCGGTTAACC
22228995 G
1 G
22228996 AATGAACACC
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:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:22234455 original size:32 final size:31
Alignment explanation
Indices: 22234418--22234499 Score: 119
Period size: 31 Copynumber: 2.6 Consensus size: 31
22234408 TAAACATTTC
* *
22234418 AAAATGGTCAAATAAGGGCCAAATCTTTTTTT
1 AAAATGCTCAAATAAGGGCCAAAT-TTTTTTA
*
22234450 AAAATGCTCAAATAAGGACCAAATTTTTTTA
1 AAAATGCTCAAATAAGGGCCAAATTTTTTTA
*
22234481 AAAATACTCAAATAAGGGC
1 AAAATGCTCAAATAAGGGC
22234500 TTTTCAAATG
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
31 23 0.51
32 22 0.49
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.29
Consensus pattern (31 bp):
AAAATGCTCAAATAAGGGCCAAATTTTTTTA
Found at i:22240370 original size:17 final size:16
Alignment explanation
Indices: 22240297--22240370 Score: 50
Period size: 16 Copynumber: 4.8 Consensus size: 16
22240287 TATTTAATAA
*
22240297 AATAATAAA-TTATTA
1 AATAATAAATTTATTT
*
22240312 ATATAATTAA-TTATTT
1 A-ATAATAAATTTATTT
22240328 CAAT-A-AAA-TTATTT
1 -AATAATAAATTTATTT
* *
22240342 AATATTACATTTATTTT
1 AATAATAAATTTA-TTT
22240359 AATAATAAATTT
1 AATAATAAATTT
22240371 TAACAGTAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
13 3 0.07
14 8 0.17
15 4 0.09
16 17 0.37
17 14 0.30
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (16 bp):
AATAATAAATTTATTT
Found at i:22240373 original size:30 final size:31
Alignment explanation
Indices: 22240297--22240373 Score: 77
Period size: 30 Copynumber: 2.5 Consensus size: 31
22240287 TATTTAATAA
*
22240297 AATAATAAATTATTAATATAATTAATTATTTC
1 AATAATAAATT-TTAATATAATCAATTATTTC
* * * *
22240329 AATAA-AATTATTTAATATTA-CATTTATTTT
1 AATAATAAAT-TTTAATATAATCAATTATTTC
22240359 AATAATAAATTTTAA
1 AATAATAAATTTTAA
22240374 CAGTAATAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
30 17 0.46
31 14 0.38
32 6 0.16
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (31 bp):
AATAATAAATTTTAATATAATCAATTATTTC
Found at i:22243115 original size:23 final size:23
Alignment explanation
Indices: 22243049--22243121 Score: 69
Period size: 25 Copynumber: 3.0 Consensus size: 23
22243039 ACAGCGTCCT
22243049 GTTATTAGCTC-TCATGAGCTTCCC
1 GTTA-TAGCTCTTCA-GAGCTTCCC
*
22243073 GTTATATGGTTCTTGC-GAGCTTCCC
1 GTTATA--GCTCTT-CAGAGCTTCCC
*
22243098 GTTATAGCTCTTCAGAGCATCCC
1 GTTATAGCTCTTCAGAGCTTCCC
22243121 G
1 G
22243122 ATAGGTTGTG
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
22 1 0.02
23 16 0.39
24 4 0.10
25 18 0.44
26 1 0.02
27 1 0.02
ACGTcount: A:0.16, C:0.27, G:0.21, T:0.36
Consensus pattern (23 bp):
GTTATAGCTCTTCAGAGCTTCCC
Found at i:22249009 original size:25 final size:25
Alignment explanation
Indices: 22248978--22249075 Score: 99
Period size: 25 Copynumber: 3.9 Consensus size: 25
22248968 AATCTCTTTC
* *
22248978 GAGCCATGTAACGGGAAGCTCATGT
1 GAGCCATATAACGGGAAGCTCATGA
* *
22249003 GAGCCATATAACGGGAAGCTCTTGC
1 GAGCCATATAACGGGAAGCTCATGA
* **
22249028 GAGCCA-ATTATCGGGAAGCTCCGGA
1 GAGCCATA-TAACGGGAAGCTCATGA
* *
22249053 GAGCCAAATAACGAGAAGCTCAT
1 GAGCCATATAACGGGAAGCTCAT
22249076 AAAAGCCAAT
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
24 1 0.02
25 58 0.97
26 1 0.02
ACGTcount: A:0.32, C:0.22, G:0.29, T:0.17
Consensus pattern (25 bp):
GAGCCATATAACGGGAAGCTCATGA
Found at i:22249046 original size:50 final size:50
Alignment explanation
Indices: 22248971--22249093 Score: 131
Period size: 50 Copynumber: 2.5 Consensus size: 50
22248961 AATCGAAAAT
* * * * * *
22248971 CTCTTTCGAGCC-ATGTAACGGGAAGCTCATGTGAGCCATATAACGGGAAG
1 CTCTTACGAGCCAAT-TATCGGGAAGCTCAGGAGAGCCAAATAACGAGAAG
* *
22249021 CTCTTGCGAGCCAATTATCGGGAAGCTCCGGAGAGCCAAATAACGAGAAG
1 CTCTTACGAGCCAATTATCGGGAAGCTCAGGAGAGCCAAATAACGAGAAG
* **
22249071 CTCATAAAAGCCAATTATCGGGA
1 CTCTTACGAGCCAATTATCGGGA
22249094 CACTCATAAG
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
50 59 0.97
51 2 0.03
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.20
Consensus pattern (50 bp):
CTCTTACGAGCCAATTATCGGGAAGCTCAGGAGAGCCAAATAACGAGAAG
Found at i:22250566 original size:7 final size:7
Alignment explanation
Indices: 22250556--22250580 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
22250546 TAAATTATAA
22250556 AAAAGTG
1 AAAAGTG
22250563 AAAAGTG
1 AAAAGTG
22250570 AAAAGTG
1 AAAAGTG
22250577 AAAA
1 AAAA
22250581 TATGGAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.12
Consensus pattern (7 bp):
AAAAGTG
Found at i:22251130 original size:23 final size:23
Alignment explanation
Indices: 22251104--22251166 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
22251094 CGTTATAATT
22251104 TGCACTTCGGTGCCCCTGACATA
1 TGCACTTCGGTGCCCCTGACATA
*
22251127 TGCAC-TCTGGTGCCCCTAACATA
1 TGCACTTC-GGTGCCCCTGACATA
**
22251150 -GCACTTATGTGCCCCTG
1 TGCACTTCGGTGCCCCTG
22251167 TTTATTCTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
22 14 0.41
23 20 0.59
ACGTcount: A:0.17, C:0.35, G:0.21, T:0.27
Consensus pattern (23 bp):
TGCACTTCGGTGCCCCTGACATA
Found at i:22256369 original size:12 final size:12
Alignment explanation
Indices: 22256352--22256378 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
22256342 ACCTAAGCGA
22256352 TTTTTTTATTTT
1 TTTTTTTATTTT
22256364 TTTTTTTATTTT
1 TTTTTTTATTTT
22256376 TTT
1 TTT
22256379 CTTTCACTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.00, G:0.00, T:0.93
Consensus pattern (12 bp):
TTTTTTTATTTT
Found at i:22256819 original size:17 final size:18
Alignment explanation
Indices: 22256788--22256821 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
22256778 TATTATATTT
*
22256788 ATCTATATATGCATATGC
1 ATCTATATATACATATGC
22256806 ATCT-TATATACATATG
1 ATCTATATATACATATG
22256822 TTACATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (18 bp):
ATCTATATATACATATGC
Found at i:22258358 original size:16 final size:16
Alignment explanation
Indices: 22258337--22258367 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
22258327 ACAATGACCC
*
22258337 AATACCTAAACAACCT
1 AATACCCAAACAACCT
22258353 AATACCCAAACAACC
1 AATACCCAAACAACC
22258368 CAACTAAACC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.35, G:0.00, T:0.13
Consensus pattern (16 bp):
AATACCCAAACAACCT
Found at i:22258379 original size:10 final size:10
Alignment explanation
Indices: 22258364--22258388 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
22258354 ATACCCAAAC
22258364 AACCCAACTA
1 AACCCAACTA
22258374 AACCCAACTA
1 AACCCAACTA
22258384 AACCC
1 AACCC
22258389 TAGCCCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.44, G:0.00, T:0.08
Consensus pattern (10 bp):
AACCCAACTA
Found at i:22258711 original size:6 final size:6
Alignment explanation
Indices: 22258700--22258746 Score: 60
Period size: 6 Copynumber: 7.7 Consensus size: 6
22258690 AAGGTAGTTG
*
22258700 TTTTAT TTTTAT TTATT-T TTTTCGT TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TT-TTAT TTTT-AT TTTTAT TTTTAT TTTTAT TTTT
22258747 TTAAAGCATA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
5 2 0.05
6 28 0.76
7 7 0.19
ACGTcount: A:0.13, C:0.02, G:0.02, T:0.83
Consensus pattern (6 bp):
TTTTAT
Found at i:22259508 original size:25 final size:25
Alignment explanation
Indices: 22259461--22259545 Score: 81
Period size: 25 Copynumber: 3.6 Consensus size: 25
22259451 AACTATTTAC
22259461 TTATTTATTTTAAA--CTT-TA-TA
1 TTATTTATTTTAAATTCTTCTATTA
*
22259482 TTATTTATTTTAAATTGTTCTATTA
1 TTATTTATTTTAAATTCTTCTATTA
* *
22259507 TTATTTATTTTAAGTTTTTC-ATATA
1 TTATTTATTTTAAATTCTTCTAT-TA
**
22259532 TTATCCATTTTAAA
1 TTATTTATTTTAAA
22259546 CTATTAAATG
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
21 14 0.26
23 2 0.04
24 4 0.08
25 33 0.62
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.61
Consensus pattern (25 bp):
TTATTTATTTTAAATTCTTCTATTA
Found at i:22259912 original size:16 final size:17
Alignment explanation
Indices: 22259893--22259925 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
22259883 TGTGCGGTCC
22259893 CTATTTT-CATTTTATT
1 CTATTTTACATTTTATT
*
22259909 CTATTTTACGTTTTATT
1 CTATTTTACATTTTATT
22259926 GTTACAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.18, C:0.12, G:0.03, T:0.67
Consensus pattern (17 bp):
CTATTTTACATTTTATT
Found at i:22263062 original size:114 final size:111
Alignment explanation
Indices: 22262641--22263062 Score: 297
Period size: 113 Copynumber: 3.7 Consensus size: 111
22262631 TTACCACAAT
* * * * * * * *
22262641 GCGCCGCTAAATCTCTTAACCAAAACGCTGTGTTTTCGTCTTGATGTATCTTAAAAGTAGTGGCG
1 GCGCCGCAAAATATCTTAACAAAAACGCAGCG-TTTGGTCTTGATGTAT-ATAAAATTAGTGGCG
* * * * * *** *
22262706 TTTACGCG-AAACGCCGTTAAAGGACAGTAATAGCGGCGCTTTTTGGAA
64 CTTATG-GTAAACGCCGGTAAAGAACAGTAATAGCGGCGATTCACGCAA
* * * * * * *
22262754 ACGCCGCAAAATAGCTTAACAAAAACGCAGAGTTTGGTCTTGAGGTATCTTAGAATTAGTGGCGT
1 GCGCCGCAAAATATCTTAACAAAAACGCAGCGTTTGGTCTTGATGTAT-ATAAAATTAGTGGCGC
* * * * * *
22262819 TTATAGGAAAACGCCGTTAAAGTACAGTAATAGCGGTGCTTCACGGAA
65 TTAT-GGTAAACGCCGGTAAAGAACAGTAATAGCGGCGATTCACGCAA
* * ** * * * * *
22262867 GCGCCGCAAACTATCTGAACCGAAACACATCGTTTTGGTCTTGATTTATACTACAACTAGTGGCG
1 GCGCCGCAAAATATCTTAACAAAAACGCAGCG-TTTGGTCTTGATGTATA-TAAAATTAGTGGCG
* * * * *** *
22262932 CATACGGTCAAACGCCGGTAAAGAATAGTATTAGCGGCGATTTGTGTCTA
64 CTTATGGT-AAACGCCGGTAAAGAACAGTAATAGCGGCGATTCACG-CAA
* *
22262982 GCGCCGCAAAATATCTTAACAAAAACGCAGCGTTGTGATCTTAATGTATATAAAATTAGTGGCGC
1 GCGCCGCAAAATATCTTAACAAAAACGCAGCGTT-TGGTCTTGATGTATATAAAATTAGTGGCGC
22263047 TTATGGTAAACCGCCG
65 TTATGGTAAA-CGCCG
22263063 CGAAAGATAT
Statistics
Matches: 242, Mismatches: 59, Indels: 15
0.77 0.19 0.05
Matches are distributed among these distances:
112 33 0.14
113 89 0.37
114 81 0.33
115 39 0.16
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (111 bp):
GCGCCGCAAAATATCTTAACAAAAACGCAGCGTTTGGTCTTGATGTATATAAAATTAGTGGCGCT
TATGGTAAACGCCGGTAAAGAACAGTAATAGCGGCGATTCACGCAA
Found at i:22263392 original size:115 final size:113
Alignment explanation
Indices: 22263126--22263393 Score: 250
Period size: 115 Copynumber: 2.3 Consensus size: 113
22263116 TTCGGCCTCG
* * * * * *
22263126 ATGTATAGTAGAATTAGTGGGGCTTAGTGAAACGCCGTTAAAGCATAGTATTAGCGGCGCTTGGA
1 ATGTATACTAAAATTAGTGGCGCTTTGTGAAACGCCGCTAAAGCATAGTATTAGCGGCGATTGGA
* * * *
22263191 TAAAAGCGCCACCAAATATCTGAACCAAAACGCATCCTTTTGGTATTG
66 TAAAAGCGCCACCAAATACCTGAAACAAAACGCAACCTTTTGGTATTA
** * * * *
22263239 ATGTATACTTGATTTAGTGGCGATTTCGGTAAAACGCCGCTAAAGCATAGTATTAGCGGCGATTT
1 ATGTATACTAAAATTAGTGGCGCTTT--GTGAAACGCCGCTAAAGCATAGTATTAGCGGCGATTG
* *** * * * * *
22263304 GTTGCTAGCGCCGCGACATACCAT-AAACAAAACGCAACGTTTTGGTCTTA
64 GATAAAAGCGCCACCAAATACC-TGAAACAAAACGCAACCTTTTGGTATTA
*
22263354 ATTTATACTAAAATTAGTGGCGCTTTGTTGAAAGCGCCGC
1 ATGTATACTAAAATTAGTGGCGCTTTG-TGAAA-CGCCGC
22263394 AAAATATCTT
Statistics
Matches: 121, Mismatches: 29, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
113 21 0.17
114 4 0.03
115 95 0.79
116 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (113 bp):
ATGTATACTAAAATTAGTGGCGCTTTGTGAAACGCCGCTAAAGCATAGTATTAGCGGCGATTGGA
TAAAAGCGCCACCAAATACCTGAAACAAAACGCAACCTTTTGGTATTA
Found at i:22263623 original size:90 final size:90
Alignment explanation
Indices: 22263472--22263675 Score: 383
Period size: 90 Copynumber: 2.3 Consensus size: 90
22263462 AATCATATTT
22263472 GGTTTA-GGTATAGGGTATTAGGGTTCATTATATAATGTTTAGTATTTTTGGATTACAGTGTAAA
1 GGTTTAGGGT-TAGGGTATTAGGGTTCATTATATAATGTTTAGTATTTTTGGATTACAGTGTAAA
22263536 GTTTAAAGTTTAGGGTTTACGATGTA
65 GTTTAAAGTTTAGGGTTTACGATGTA
*
22263562 GGTTTAGGGTTAGAGTATTAGGGTTCATTATATAATGTTTAGTATTTTTGGATTACAGTGTAAAG
1 GGTTTAGGGTTAGGGTATTAGGGTTCATTATATAATGTTTAGTATTTTTGGATTACAGTGTAAAG
22263627 TTTAAAGTTTAGGGTTTACGATGTA
66 TTTAAAGTTTAGGGTTTACGATGTA
22263652 GGTTTAGGGTTAGGGTATTAGGGT
1 GGTTTAGGGTTAGGGTATTAGGGT
22263676 GTTAATTTAG
Statistics
Matches: 111, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
90 108 0.97
91 3 0.03
ACGTcount: A:0.26, C:0.03, G:0.28, T:0.43
Consensus pattern (90 bp):
GGTTTAGGGTTAGGGTATTAGGGTTCATTATATAATGTTTAGTATTTTTGGATTACAGTGTAAAG
TTTAAAGTTTAGGGTTTACGATGTA
Found at i:22263674 original size:8 final size:7
Alignment explanation
Indices: 22263633--22263759 Score: 57
Period size: 7 Copynumber: 18.0 Consensus size: 7
22263623 AAAGTTTAAA
22263633 GTTTAGG
1 GTTTAGG
*
22263640 GTTTACG
1 GTTTAGG
* *
22263647 ATGTA-G
1 GTTTAGG
22263653 GTTTAGG
1 GTTTAGG
22263660 G-TTAGG
1 GTTTAGG
22263666 GTATTAGG
1 GT-TTAGG
22263674 GTGTTA--
1 GT-TTAGG
*
22263680 ATTTAGG
1 GTTTAGG
22263687 G-TTAGG
1 GTTTAGG
22263693 GTATTAGGG
1 GT-TTA-GG
*
22263702 TGTTTTGG
1 -GTTTAGG
*
22263710 GTTTAAG
1 GTTTAGG
22263717 GTTTAGG
1 GTTTAGG
* *
22263724 AGTCTGGG
1 -GTTTAGG
* *
22263732 GTATAAG
1 GTTTAGG
*
22263739 GTTTAAG
1 GTTTAGG
*
22263746 GTTTGGG
1 GTTTAGG
22263753 GTTTAGG
1 GTTTAGG
22263760 CTACTTTACT
Statistics
Matches: 89, Mismatches: 21, Indels: 20
0.68 0.16 0.15
Matches are distributed among these distances:
5 3 0.03
6 17 0.19
7 43 0.48
8 20 0.22
9 4 0.04
10 2 0.02
ACGTcount: A:0.19, C:0.02, G:0.39, T:0.40
Consensus pattern (7 bp):
GTTTAGG
Found at i:22263687 original size:27 final size:27
Alignment explanation
Indices: 22263654--22263705 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
22263644 ACGATGTAGG
22263654 TTTAGGGTTAGGGTATTAGGGTGTTAA
1 TTTAGGGTTAGGGTATTAGGGTGTTAA
22263681 TTTAGGGTTAGGGTATTAGGGTGTT
1 TTTAGGGTTAGGGTATTAGGGTGTT
22263706 TTGGGTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.19, C:0.00, G:0.38, T:0.42
Consensus pattern (27 bp):
TTTAGGGTTAGGGTATTAGGGTGTTAA
Found at i:22264912 original size:22 final size:22
Alignment explanation
Indices: 22264884--22264930 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
22264874 ACTATTCCGA
* *
22264884 TTAAATATGTAAGGTGTTTCTG
1 TTAAATAGGTAAGGCGTTTCTG
22264906 TTAAATAGGTAAGGCGTTTCTG
1 TTAAATAGGTAAGGCGTTTCTG
22264928 TTA
1 TTA
22264931 TTACAGCCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.28, C:0.06, G:0.23, T:0.43
Consensus pattern (22 bp):
TTAAATAGGTAAGGCGTTTCTG
Found at i:22265311 original size:36 final size:36
Alignment explanation
Indices: 22265269--22265384 Score: 114
Period size: 36 Copynumber: 3.2 Consensus size: 36
22265259 GTTGTTATGT
22265269 TCTGAAATATGCTTTGGATTTGAAATAATTTCTGAG
1 TCTGAAATATGCTTTGGATTTGAAATAATTTCTGAG
* ** * * *
22265305 TCTGAAATA--ATTTGTTTTTG--ATTATGTTGTTATG
1 TCTGAAATATGCTTTGGATTTGAAATAAT-TTCTGA-G
*
22265339 TTCTGAAATATGCTTTGGATTTGAAATAATTTCTGGG
1 -TCTGAAATATGCTTTGGATTTGAAATAATTTCTGAG
22265376 TCTGAAATA
1 TCTGAAATA
22265385 ATTTGTTTTT
Statistics
Matches: 60, Mismatches: 13, Indels: 14
0.69 0.15 0.16
Matches are distributed among these distances:
32 4 0.07
33 4 0.07
34 9 0.15
35 9 0.15
36 18 0.30
37 9 0.15
38 3 0.05
39 4 0.07
ACGTcount: A:0.28, C:0.07, G:0.19, T:0.46
Consensus pattern (36 bp):
TCTGAAATATGCTTTGGATTTGAAATAATTTCTGAG
Found at i:22265335 original size:71 final size:71
Alignment explanation
Indices: 22265236--22265436 Score: 368
Period size: 71 Copynumber: 2.8 Consensus size: 71
22265226 TGAGTGGATT
22265236 TGAAATAATTTGTTTTTGATTATGTTGTTATGTTCTGAAATATGCTTTGGATTTGAAATAATTTC
1 TGAAATAATTTGTTTTTGATTATGTTGTTATGTTCTGAAATATGCTTTGGATTTGAAATAATTTC
22265301 TGAGTC
66 TGAGTC
22265307 TGAAATAATTTGTTTTTGATTATGTTGTTATGTTCTGAAATATGCTTTGGATTTGAAATAATTTC
1 TGAAATAATTTGTTTTTGATTATGTTGTTATGTTCTGAAATATGCTTTGGATTTGAAATAATTTC
*
22265372 TGGGTC
66 TGAGTC
*
22265378 TGAAATAATTTGTTTTTGATTATGTTGTTATGTTCTGAATTATGCTTTGG-TTCTGAAAT
1 TGAAATAATTTGTTTTTGATTATGTTGTTATGTTCTGAAATATGCTTTGGATT-TGAAAT
22265437 CTGGATCTGG
Statistics
Matches: 127, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
70 2 0.02
71 125 0.98
ACGTcount: A:0.25, C:0.05, G:0.19, T:0.50
Consensus pattern (71 bp):
TGAAATAATTTGTTTTTGATTATGTTGTTATGTTCTGAAATATGCTTTGGATTTGAAATAATTTC
TGAGTC
Found at i:22265591 original size:14 final size:14
Alignment explanation
Indices: 22265572--22265601 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
22265562 ATAAAAGGTT
22265572 TTTAGTTAATCATC
1 TTTAGTTAATCATC
*
22265586 TTTAGTTAATCGTC
1 TTTAGTTAATCATC
22265600 TT
1 TT
22265602 GCTGTTCGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.13, G:0.10, T:0.53
Consensus pattern (14 bp):
TTTAGTTAATCATC
Found at i:22266222 original size:45 final size:43
Alignment explanation
Indices: 22266139--22266222 Score: 96
Period size: 45 Copynumber: 1.9 Consensus size: 43
22266129 AAATTTATAT
* * * * *
22266139 CTTACATTACTTAAATATATATTTTTAAGTATATTTTACATGA
1 CTTACATTACTTAAAAACATATTTTTAACTAAAATTTACATGA
*
22266182 CTTACATTACTTACTAAAACATATTTTTTACTAAAATTTAC
1 CTTACATTACTTA--AAAACATATTTTTAACTAAAATTTAC
22266223 TTGAATGAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
43 13 0.39
45 20 0.61
ACGTcount: A:0.38, C:0.13, G:0.02, T:0.46
Consensus pattern (43 bp):
CTTACATTACTTAAAAACATATTTTTAACTAAAATTTACATGA
Found at i:22266602 original size:9 final size:9
Alignment explanation
Indices: 22266579--22266731 Score: 67
Period size: 9 Copynumber: 17.9 Consensus size: 9
22266569 ATATATTCAT
22266579 TTACATAAC
1 TTACATAAC
22266588 --ACATAAC
1 TTACATAAC
22266595 TTACATAAC
1 TTACATAAC
* *
22266604 CTACTTAA-
1 TTACATAAC
*
22266612 -TATATAAC
1 TTACATAAC
*
22266620 TTGCATAAC
1 TTACATAAC
* *
22266629 TTAAATAAG
1 TTACATAAC
22266638 TTACATAA-
1 TTACATAAC
22266646 TAATACATAA-
1 T--TACATAAC
*
22266656 -TACACAAC
1 TTACATAAC
*
22266664 TTACAT--G
1 TTACATAAC
*
22266671 TGTAAATAA-
1 T-TACATAAC
*
22266680 -TACAGAAC
1 TTACATAAC
22266688 TTACATAAC
1 TTACATAAC
*
22266697 TTACATACC
1 TTACATAAC
* *
22266706 CTACATAAA
1 TTACATAAC
* *
22266715 TTAAATAAG
1 TTACATAAC
22266724 TTACATAA
1 TTACATAA
22266732 TAATACATAC
Statistics
Matches: 106, Mismatches: 25, Indels: 26
0.68 0.16 0.17
Matches are distributed among these distances:
7 24 0.23
8 5 0.05
9 70 0.66
10 7 0.07
ACGTcount: A:0.48, C:0.18, G:0.04, T:0.31
Consensus pattern (9 bp):
TTACATAAC
Found at i:22266710 original size:18 final size:17
Alignment explanation
Indices: 22266689--22266750 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 17
22266679 ATACAGAACT
22266689 TACATAACTTACATACCC
1 TACATAA-TTACATACCC
* ***
22266707 TACATAAATTAAATAAGT
1 TACAT-AATTACATACCC
22266725 TACATAATAATACATACCC
1 TACATAAT--TACATACCC
22266744 TACATAA
1 TACATAA
22266751 ATTAAATAAG
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
17 3 0.09
18 16 0.48
19 14 0.42
ACGTcount: A:0.48, C:0.21, G:0.02, T:0.29
Consensus pattern (17 bp):
TACATAATTACATACCC
Found at i:22266742 original size:37 final size:37
Alignment explanation
Indices: 22266698--22266771 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
22266688 TTACATAACT
22266698 TACATACCCTACATAAATTAAATAAGTTACATAATAA
1 TACATACCCTACATAAATTAAATAAGTTACATAATAA
*
22266735 TACATACCCTACATAAATTAAATAAGTTACATTATAA
1 TACATACCCTACATAAATTAAATAAGTTACATAATAA
22266772 GGTTTCTATA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.50, C:0.16, G:0.03, T:0.31
Consensus pattern (37 bp):
TACATACCCTACATAAATTAAATAAGTTACATAATAA
Found at i:22266804 original size:15 final size:15
Alignment explanation
Indices: 22266780--22266812 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
22266770 AAGGTTTCTA
*
22266780 TATTAGTATTAAATT
1 TATTACTATTAAATT
22266795 TATTACTATTAAATT
1 TATTACTATTAAATT
22266810 TAT
1 TAT
22266813 AAATAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (15 bp):
TATTACTATTAAATT
Found at i:22267144 original size:27 final size:25
Alignment explanation
Indices: 22267084--22267153 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 25
22267074 CAAAAAAAAA
* * *
22267084 ACTTACATAACTTAGATAATATCCT
1 ACTTACATAAATTAAATAATATCAT
* *
22267109 ACATA-ATAAATTACATAATAATACAT
1 ACTTACATAAATTAAATAAT-AT-CAT
22267135 ACTTACATAAATTAAATAA
1 ACTTACATAAATTAAATAA
22267154 GTTACATAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
24 12 0.33
25 6 0.17
26 6 0.17
27 12 0.33
ACGTcount: A:0.51, C:0.14, G:0.01, T:0.33
Consensus pattern (25 bp):
ACTTACATAAATTAAATAATATCAT
Found at i:22267178 original size:16 final size:16
Alignment explanation
Indices: 22267126--22267496 Score: 131
Period size: 16 Copynumber: 22.2 Consensus size: 16
22267116 AAATTACATA
*
22267126 ATAA-TACATACTTAC
1 ATAACTACATAATTAC
* *
22267141 ATAAATTAAATAAGTTAC
1 AT-AACTACATAA-TTAC
* *
22267159 ATAA-TACACAACTGAC
1 ATAACTACATAA-TTAC
22267175 ATAACTTACATAA-TAC
1 ATAAC-TACATAATTAC
*
22267191 ATAATTTACATAA-TAC
1 ATAA-CTACATAATTAC
*
22267207 ACAACTGACATAACTTAC
1 ATAACT-ACATAA-TTAC
22267225 ATAA-TACATAATTTAC
1 ATAACTACATAA-TTAC
* *
22267241 ATAA-TACACAACTGAC
1 ATAACTACATAA-TTAC
22267257 ATAACTTACATAA-TAC
1 ATAAC-TACATAATTAC
** *
22267273 ATATTTTACATCACTTAC
1 ATA-ACTACAT-AATTAC
*
22267291 ATAA-GACATAACTTAC
1 ATAACTACATAA-TTAC
* *
22267307 ATAAGTTTCATAA-TAC
1 ATAA-CTACATAATTAC
*
22267323 ACAACTGACATAACTTAC
1 ATAACT-ACATAA-TTAC
*
22267341 ATAA-TACATATTTTAC
1 ATAACTACATA-ATTAC
* *
22267357 ATCACTTACATAA-GAC
1 ATAAC-TACATAATTAC
*
22267373 ATAACTTACATAAGTTTC
1 ATAAC-TACATAA-TTAC
* *
22267391 ATAA-TACACAACTGAC
1 ATAACTACATAA-TTAC
22267407 ATAACTTACATAA-TAC
1 ATAAC-TACATAATTAC
* *
22267423 ACAACTTACATAAGTTTC
1 ATAAC-TACATAA-TTAC
* *
22267441 ATAA-GACACAACTTAC
1 ATAACTACATAA-TTAC
*
22267457 ATAGCTTACATAACTTAC
1 ATAAC-TACATAA-TTAC
*
22267475 ACAACTTACATAACTTAC
1 ATAAC-TACATAA-TTAC
22267493 ATAA
1 ATAA
22267497 TAAATAAGTT
Statistics
Matches: 269, Mismatches: 56, Indels: 59
0.70 0.15 0.15
Matches are distributed among these distances:
15 5 0.02
16 162 0.60
17 10 0.04
18 92 0.34
ACGTcount: A:0.46, C:0.20, G:0.04, T:0.30
Consensus pattern (16 bp):
ATAACTACATAATTAC
Found at i:22267201 original size:25 final size:25
Alignment explanation
Indices: 22267117--22267497 Score: 218
Period size: 25 Copynumber: 15.1 Consensus size: 25
22267107 CTACATAATA
22267117 AATTACATAATAATACAT-ACTTACAT
1 AATTACATAAT--TACATAACTTACAT
* *
22267143 AAATTAAATAAGTTACATAA--TACAC
1 -AATTACATAA-TTACATAACTTACAT
*
22267168 AACTGACATAACTTACATAA--TACAT
1 AA-TTACATAA-TTACATAACTTACAT
* *
22267193 AATTTACATAA-TACACAACTGACAT
1 AA-TTACATAATTACATAACTTACAT
*
22267218 AACTTACATAA-TACATAATTTACAT
1 AA-TTACATAATTACATAACTTACAT
* *
22267243 AA-TACACAACTGACATAACTTACAT
1 AATTACATAA-TTACATAACTTACAT
* *
22267268 AA-TACATATTTTACATCACTTACAT
1 AATTACATA-ATTACATAACTTACAT
* * *
22267293 AA-GACATAACTTACATAAGTTTCAT
1 AATTACATAA-TTACATAACTTACAT
* *
22267318 AA-TACACAACTGACATAACTTACAT
1 AATTACATAA-TTACATAACTTACAT
* *
22267343 AA-TACATATTTTACATCACTTACAT
1 AATTACATA-ATTACATAACTTACAT
* * *
22267368 AA-GACATAACTTACATAAGTTTCAT
1 AATTACATAA-TTACATAACTTACAT
* *
22267393 AA-TACACAACTGACATAACTTACAT
1 AATTACATAA-TTACATAACTTACAT
* * *
22267418 AA-TACACAACTTACATAAGTTTCAT
1 AATTACATAA-TTACATAACTTACAT
* * *
22267443 AA-GACACAACTTACATAGCTTACAT
1 AATTACATAA-TTACATAACTTACAT
*
22267468 AACTTACACAACTTACATAACTTACAT
1 AA-TTACATAA-TTACATAACTTACAT
22267495 AAT
1 AAT
22267498 AAATAAGTTA
Statistics
Matches: 287, Mismatches: 54, Indels: 27
0.78 0.15 0.07
Matches are distributed among these distances:
23 12 0.04
24 2 0.01
25 233 0.81
26 6 0.02
27 33 0.11
28 1 0.00
ACGTcount: A:0.46, C:0.20, G:0.03, T:0.30
Consensus pattern (25 bp):
AATTACATAATTACATAACTTACAT
Found at i:22267205 original size:41 final size:41
Alignment explanation
Indices: 22267131--22267435 Score: 315
Period size: 41 Copynumber: 7.8 Consensus size: 41
22267121 ACATAATAAT
* *
22267131 ACAT-ACTTACATAAATTAAATAAGTTACATAATACACAACTG
1 ACATAACTTACAT-AA-TACATAATTTACATAATACACAACTG
22267173 ACATAACTTACATAATACATAATTTACATAATACACAACTG
1 ACATAACTTACATAATACATAATTTACATAATACACAACTG
22267214 ACATAACTTACATAATACATAATTTACATAATACACAACTG
1 ACATAACTTACATAATACATAATTTACATAATACACAACTG
* * *
22267255 ACATAACTTACATAATACATATTTTACATCACTTACATAA--G
1 ACATAACTTACATAATACATAATTTACAT-A-ATACACAACTG
*
22267296 ACATAACTTAC---AT--A-AGTTT-CATAATACACAACTG
1 ACATAACTTACATAATACATAATTTACATAATACACAACTG
* * *
22267330 ACATAACTTACATAATACATATTTTACATCACTTACATAA--G
1 ACATAACTTACATAATACATAATTTACAT-A-ATACACAACTG
*
22267371 ACATAACTTAC---AT--A-AGTTT-CATAATACACAACTG
1 ACATAACTTACATAATACATAATTTACATAATACACAACTG
* *
22267405 ACATAACTTACATAATACACAACTTACATAA
1 ACATAACTTACATAATACATAATTTACATAA
22267436 GTTTCATAAG
Statistics
Matches: 224, Mismatches: 16, Indels: 47
0.78 0.06 0.16
Matches are distributed among these distances:
32 12 0.05
33 2 0.01
34 30 0.13
35 8 0.04
36 2 0.01
37 4 0.02
38 4 0.02
39 2 0.01
40 7 0.03
41 125 0.56
42 8 0.04
43 20 0.09
ACGTcount: A:0.47, C:0.20, G:0.03, T:0.30
Consensus pattern (41 bp):
ACATAACTTACATAATACATAATTTACATAATACACAACTG
Found at i:22267270 original size:75 final size:73
Alignment explanation
Indices: 22267223--22267498 Score: 369
Period size: 75 Copynumber: 3.7 Consensus size: 73
22267213 GACATAACTT
22267223 ACATAA-TACATAA-TTTACATAATACACAACTGACATAACTTACATAATACATATTTTACATCA
1 ACATAACTACATAAGTTT-CATAATACACAACTGACATAACTTACATAATACATA-TTTACATCA
22267286 CTTACATAAG
64 CTTACATAAG
22267296 ACATAACTTACATAAGTTTCATAATACACAACTGACATAACTTACATAATACATATTTTACATCA
1 ACATAAC-TACATAAGTTTCATAATACACAACTGACATAACTTACATAATACATA-TTTACATCA
22267361 CTTACATAAG
64 CTTACATAAG
* * *
22267371 ACATAACTTACATAAGTTTCATAATACACAACTGACATAACTTACATAATACACAACTTACATAA
1 ACATAAC-TACATAAGTTTCATAATACACAACTGACATAACTTACATAATACA-TATTTACATCA
* *
22267436 GTTTCATAAG
64 CTTACATAAG
* * *
22267446 ACACAACTTACAT-AGCTTACATAACTTACACAACTTACATAACTTACATAATA
1 ACATAAC-TACATAAG-TTTCATAA--TACACAACTGACATAACTTACATAATA
22267499 AATAAGTTAT
Statistics
Matches: 188, Mismatches: 8, Indels: 10
0.91 0.04 0.05
Matches are distributed among these distances:
73 6 0.03
74 2 0.01
75 150 0.80
76 4 0.02
77 26 0.14
ACGTcount: A:0.45, C:0.21, G:0.04, T:0.30
Consensus pattern (73 bp):
ACATAACTACATAAGTTTCATAATACACAACTGACATAACTTACATAATACATATTTACATCACT
TACATAAG
Found at i:22269850 original size:42 final size:42
Alignment explanation
Indices: 22269641--22269868 Score: 269
Period size: 42 Copynumber: 5.4 Consensus size: 42
22269631 TTACTTTTAA
* * * * *
22269641 TAAGCGCCGCTATAGAACATTA-CTTTTAGAGGCGCTTTCTTCC
1 TAAGCGCCGCTAAAGAACATGATC-TTTAGCGGCG-TTTTTTTC
* * *
22269684 AAAGCGTCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
* * *
22269726 AAAGCGCCGCTAAAGAACATGATCTTTAGGGGCGTTTCTTTC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
* *
22269768 TAAGTGCCGCTAAAGAGCATGATCTTTAGCGGCGTTTTTTTC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
* *
22269810 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCATTTTTTTATG
1 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGC-GTTTTTT-TC
*
22269854 TAAGCGCCGCAAAAG
1 TAAGCGCCGCTAAAG
22269869 TTAGTGACGT
Statistics
Matches: 162, Mismatches: 20, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
42 113 0.70
43 33 0.20
44 16 0.10
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (42 bp):
TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
Found at i:22272921 original size:24 final size:24
Alignment explanation
Indices: 22272889--22273016 Score: 238
Period size: 24 Copynumber: 5.3 Consensus size: 24
22272879 CAGAGAACAG
22272889 GAAGGTGGCAAGAGTACGACACAA
1 GAAGGTGGCAAGAGTACGACACAA
22272913 GAAGGTGGCAAGAGTACGACACAA
1 GAAGGTGGCAAGAGTACGACACAA
22272937 GAAGGTGGCAAGAGTACGACACAA
1 GAAGGTGGCAAGAGTACGACACAA
*
22272961 GAAGGTGGCAAGAGTAAGACACAA
1 GAAGGTGGCAAGAGTACGACACAA
*
22272985 GAAGGTGGCAAGAGTAGGACACAA
1 GAAGGTGGCAAGAGTACGACACAA
22273009 GAAGGTGG
1 GAAGGTGG
22273017 AAACAAGACT
Statistics
Matches: 102, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 102 1.00
ACGTcount: A:0.41, C:0.14, G:0.36, T:0.09
Consensus pattern (24 bp):
GAAGGTGGCAAGAGTACGACACAA
Found at i:22276782 original size:11 final size:13
Alignment explanation
Indices: 22276762--22276793 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
22276752 AATAAATTAA
22276762 TAAAATATCAT-T
1 TAAAATATCATAT
22276774 TAAAA-ATCATAT
1 TAAAATATCATAT
22276786 TAAAATAT
1 TAAAATAT
22276794 TAATAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATATCATAT
Found at i:22281569 original size:102 final size:101
Alignment explanation
Indices: 22281443--22281627 Score: 255
Period size: 101 Copynumber: 1.8 Consensus size: 101
22281433 ACCCGGTTCA
* * *
22281443 CATAGTAGACTGCACATAGTACTACAGATGTGACCATTTTCA-TCCAACACACGTAGTAGCCCGC
1 CATAGTAGACTGCACATAGTACTACACATGTGACC--TATCATTCCAACACACGTAGTAACCCGC
*
22281507 ACATATTACTACACACGTGATCGAAGCTATCTGGTACG
64 ACATAGTACTACACACGTGATCGAAGCTATCTGGTACG
* * *** *
22281545 CATAGTAGCCTGCACATAGTACTACACATGTGACCTATCATTTCGGTACACGTAGTAACCTGCAC
1 CATAGTAGACTGCACATAGTACTACACATGTGACCTATCATTCCAACACACGTAGTAACCCGCAC
22281610 ATAGTACTACACACGTGA
66 ATAGTACTACACACGTGA
22281628 CCTAGCAACT
Statistics
Matches: 72, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
100 4 0.06
101 35 0.49
102 33 0.46
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.25
Consensus pattern (101 bp):
CATAGTAGACTGCACATAGTACTACACATGTGACCTATCATTCCAACACACGTAGTAACCCGCAC
ATAGTACTACACACGTGATCGAAGCTATCTGGTACG
Found at i:22300250 original size:16 final size:17
Alignment explanation
Indices: 22300210--22300244 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
22300200 CAAAATCAAA
*
22300210 TTAAAATTTATTTTTAT
1 TTAATATTTATTTTTAT
22300227 TTAATATTT-TTTTTAT
1 TTAATATTTATTTTTAT
22300243 TT
1 TT
22300245 TTTATTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTAATATTTATTTTTAT
Found at i:22300900 original size:20 final size:20
Alignment explanation
Indices: 22300860--22300899 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
22300850 TTATGTATTA
22300860 TGTTCTTTTGAAATTCATTT
1 TGTTCTTTTGAAATTCATTT
22300880 TGTTACTTTT-AAATTC-TTT
1 TGTT-CTTTTGAAATTCATTT
22300899 T
1 T
22300900 TCAATGAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 10 0.53
21 5 0.26
ACGTcount: A:0.20, C:0.10, G:0.07, T:0.62
Consensus pattern (20 bp):
TGTTCTTTTGAAATTCATTT
Found at i:22301477 original size:30 final size:31
Alignment explanation
Indices: 22301432--22301493 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
22301422 TCAAATTTAT
*
22301432 GAATAGTCCCAGTACTTCACT-CAAGTTGTG
1 GAATAATCCCAGTACTTCACTCCAAGTTGTG
* **
22301462 GAATAATCCCTGTACTTTGCTCCAAGTTGTG
1 GAATAATCCCAGTACTTCACTCCAAGTTGTG
22301493 G
1 G
22301494 CACTACCCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 17 0.63
31 10 0.37
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (31 bp):
GAATAATCCCAGTACTTCACTCCAAGTTGTG
Found at i:22307546 original size:21 final size:21
Alignment explanation
Indices: 22307522--22307561 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
22307512 TAATGATGAC
22307522 ATTAATAATA-ATAATAATACT
1 ATTAATAATATA-AATAATACT
22307543 ATTAATAATATAAATAATA
1 ATTAATAATATAAATAATA
22307562 TTGCTACTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (21 bp):
ATTAATAATATAAATAATACT
Found at i:22307551 original size:24 final size:24
Alignment explanation
Indices: 22307524--22307583 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
22307514 ATGATGACAT
*
22307524 TAATAATAATAATAATACTATTAA
1 TAATAATAATAATAATACTACTAA
* *
22307548 TAAT-ATAAATAATATTGCTACTAA
1 TAATAAT-AATAATAATACTACTAA
*
22307572 TAATAAAAATAA
1 TAATAATAATAA
22307584 CGATAAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
23 2 0.07
24 27 0.90
25 1 0.03
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (24 bp):
TAATAATAATAATAATACTACTAA
Found at i:22307563 original size:18 final size:18
Alignment explanation
Indices: 22307474--22307552 Score: 54
Period size: 18 Copynumber: 4.4 Consensus size: 18
22307464 ATAGTAGTAG
* *
22307474 TAATAATAATAAAAGTAA
1 TAATAATAATAATATTAA
*
22307492 TAA-AAGTAATAATACT-A
1 TAATAA-TAATAATATTAA
* * * *
22307509 TAGTAATGATGACATTAA
1 TAATAATAATAATATTAA
* *
22307527 TAATAATAATAATACTAT
1 TAATAATAATAATATTAA
22307545 TAATAATA
1 TAATAATA
22307553 TAAATAATAT
Statistics
Matches: 45, Mismatches: 13, Indels: 6
0.70 0.20 0.09
Matches are distributed among these distances:
17 11 0.24
18 34 0.76
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (18 bp):
TAATAATAATAATATTAA
Found at i:22312865 original size:22 final size:22
Alignment explanation
Indices: 22312837--22312907 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
22312827 TAATTTCTCC
*
22312837 TTTCTTTCTTTCTCTTTTTCTT
1 TTTCTTTCTTTCTCTCTTTCTT
22312859 TTTCTTTCTTTC-C-CTTTCTGT
1 TTTCTTTCTTTCTCTCTTTCT-T
* * *
22312880 TTTCGTTTCTATCTCTGTTTATT
1 TTTC-TTTCTTTCTCTCTTTCTT
22312903 TTTCT
1 TTTCT
22312908 ATTTCTTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
20 5 0.12
21 6 0.15
22 20 0.49
23 6 0.15
24 4 0.10
ACGTcount: A:0.03, C:0.23, G:0.04, T:0.70
Consensus pattern (22 bp):
TTTCTTTCTTTCTCTCTTTCTT
Found at i:22312906 original size:18 final size:17
Alignment explanation
Indices: 22312885--22312918 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
22312875 TCTGTTTTCG
22312885 TTTCTATCTCTGTTTATT
1 TTTCTATCTCT-TTTATT
*
22312903 TTTCTATTTCTTTTAT
1 TTTCTATCTCTTTTAT
22312919 CTATTTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.12, C:0.15, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTCTATCTCTTTTATT
Found at i:22315342 original size:25 final size:25
Alignment explanation
Indices: 22315314--22315376 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
22315304 GAATTGGTAT
*
22315314 GCTCTCACGAGCTGTGAATCAATAA
1 GCTCTCACGAGCTGAGAATCAATAA
*
22315339 GCTCAT-ACGAGCTGAGAATCAGTAA
1 GCTC-TCACGAGCTGAGAATCAATAA
* *
22315364 GTTATCACGAGCT
1 GCTCTCACGAGCT
22315377 ACAAATTGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 1 0.03
25 30 0.94
26 1 0.03
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (25 bp):
GCTCTCACGAGCTGAGAATCAATAA
Found at i:22315593 original size:22 final size:23
Alignment explanation
Indices: 22315551--22315594 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
22315541 TATACAAAAC
* *
22315551 ACATATATATAATTCAATTTAAA
1 ACATATAAATAATACAATTTAAA
22315574 ACATATAAAT-ATACAATTTAA
1 ACATATAAATAATACAATTTAA
22315595 TTACACGAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (23 bp):
ACATATAAATAATACAATTTAAA
Found at i:22346554 original size:26 final size:27
Alignment explanation
Indices: 22346503--22346556 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
22346493 ACAGAATAGC
* *
22346503 AAAACGAAAACAGGGGAGAAAGGAAAG
1 AAAAAGAAAACAGGGAAGAAAGGAAAG
22346530 AAAAAGAAAA-AGGGAAGGAAA-GAAAG
1 AAAAAGAAAACAGGGAA-GAAAGGAAAG
22346556 A
1 A
22346557 GAATTTGGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 11 0.46
27 13 0.54
ACGTcount: A:0.65, C:0.04, G:0.31, T:0.00
Consensus pattern (27 bp):
AAAAAGAAAACAGGGAAGAAAGGAAAG
Found at i:22347458 original size:25 final size:24
Alignment explanation
Indices: 22347430--22347564 Score: 143
Period size: 25 Copynumber: 5.6 Consensus size: 24
22347420 ATTTTAGCGC
22347430 GCTCTCTGATTATTAGCACATCAGT
1 GCTCTCTG-TTATTAGCACATCAGT
* *
22347455 GCTCTCTGATTATTAGCACGTTAGT
1 GCTCTCTG-TTATTAGCACATCAGT
* **
22347480 GCTCTCTGATTACTAGCACGCCAGT
1 GCTCTCTG-TTATTAGCACATCAGT
*
22347505 GCTCTCTG-T-TTAGCACATCTGT
1 GCTCTCTGTTATTAGCACATCAGT
*
22347527 GCTCTCTG-TA-TAGCACTTCAGT
1 GCTCTCTGTTATTAGCACATCAGT
22347549 GCTCTCTGTTCATTAG
1 GCTCTCTGTT-ATTAG
22347565 TGCATAACAA
Statistics
Matches: 95, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
22 36 0.38
23 2 0.02
24 1 0.01
25 56 0.59
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.37
Consensus pattern (24 bp):
GCTCTCTGTTATTAGCACATCAGT
Found at i:22347528 original size:22 final size:22
Alignment explanation
Indices: 22347442--22347558 Score: 117
Period size: 22 Copynumber: 5.0 Consensus size: 22
22347432 TCTCTGATTA
22347442 TTAGCACATCAGTGCTCTCTGATT
1 TTAGCACATCAGTGCTCTCTG--T
* *
22347466 ATTAGCACGTTAGTGCTCTCTGAT
1 -TTAGCACATCAGTGCTCTCTG-T
**
22347490 TACTAGCACGCCAGTGCTCTCTGT
1 T--TAGCACATCAGTGCTCTCTGT
*
22347514 TTAGCACATCTGTGCTCTCTGT
1 TTAGCACATCAGTGCTCTCTGT
* *
22347536 ATAGCACTTCAGTGCTCTCTGT
1 TTAGCACATCAGTGCTCTCTGT
22347558 T
1 T
22347559 CATTAGTGCA
Statistics
Matches: 78, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
22 37 0.47
23 1 0.01
24 3 0.04
25 37 0.47
ACGTcount: A:0.18, C:0.26, G:0.19, T:0.37
Consensus pattern (22 bp):
TTAGCACATCAGTGCTCTCTGT
Found at i:22358101 original size:33 final size:32
Alignment explanation
Indices: 22358056--22358216 Score: 117
Period size: 33 Copynumber: 4.8 Consensus size: 32
22358046 ACATTCAAGG
* *
22358056 TGCCATAACCCAGTTATGGTCTTATCATCAGAA
1 TGCCATAGCCCAGCTATGGTCTTA-CATCAGAA
* *
22358089 TGCCATAGCCCAGCTATGGTCTTACATATAAACA
1 TGCCATAGCCCAGCTATGGTCTTACAT-CAGA-A
* * * * * * * *
22358123 CTGTCATGGTCCAACCATGGTCTTACGCTCATAG
1 -TGCCATAGCCCAGCTATGGTCTTAC-ATCAGAA
* *
22358157 TGCCATAACCCAGTTAAT-GTCTTATCATCAGAA
1 TGCCATAGCCCAGCT-ATGGTCTTA-CATCAGAA
*
22358190 TGCCATAGCCCAACTATGGTCTTACAT
1 TGCCATAGCCCAGCTATGGTCTTACAT
22358217 ATATATACTG
Statistics
Matches: 95, Mismatches: 26, Indels: 15
0.70 0.19 0.11
Matches are distributed among these distances:
32 8 0.08
33 60 0.63
34 4 0.04
35 22 0.23
36 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (32 bp):
TGCCATAGCCCAGCTATGGTCTTACATCAGAA
Found at i:22358188 original size:101 final size:101
Alignment explanation
Indices: 22357851--22358450 Score: 756
Period size: 101 Copynumber: 5.9 Consensus size: 101
22357841 TACATTCGTA
** * * * *
22357851 GTGCCATAAATCAGTTATGGTCTTATCATCAGAATGTCATAGCCTAGCTATGGTTTTACATATAA
1 GTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAACTATGGTCTTACATATAA
*
22357916 ACACTGCCATGGTCCAAACATGGTCTTACGTTCATA-
66 ACACTGCCATGGTCCAACCATGGTCTTACGTTCA-AG
* *
22357952 GTGTCATAACCCAGTTATGGTCTTATCATCAGAATGTCATAGCCCAACTATGGTCTTACATATAT
1 GTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAACTATGGTCTTACATATA-
* * * * ** *
22358017 ATATACTGCCACGATCTAACCATGACCTTACATTCAAG
65 A-ACACTGCCATGGTCCAACCATGGTCTTACGTTCAAG
*
22358055 GTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAGCTATGGTCTTACATATAA
1 GTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAACTATGGTCTTACATATAA
* *
22358120 ACACTGTCATGGTCCAACCATGGTCTTACGCTCATA-
66 ACACTGCCATGGTCCAACCATGGTCTTACGTTCA-AG
22358156 GTGCCATAACCCAGTTAAT-GTCTTATCATCAGAATGCCATAGCCCAACTATGGTCTTACATATA
1 GTGCCATAACCCAGTT-ATGGTCTTATCATCAGAATGCCATAGCCCAACTATGGTCTTACATATA
* * * * * ** *
22358220 TATACTGCCACGATCTAACCATGACCTTACATTCAAG
65 AACACTGCCATGGTCCAACCATGGTCTTACGTTCAAG
* ** *
22358257 GTGCCATAACCCAGTTATGGTCTTATCATTAGAATGCCATAGCCCAGGTATGGTCTTACATATAT
1 GTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAACTATGGTCTTACATATAA
* * **
22358322 ATATTGTTATGGTCCAACCATGGTCTTACGTTCAAG
66 ACACTGCCATGGTCCAACCATGGTCTTACGTTCAAG
* * * * * *
22358358 GTGCCATAATCCAGTTATGATCTTTTCATTAAAATGCCATAGCCCAACTATGGTCTTACATTTAA
1 GTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAACTATGGTCTTACATATAA
*
22358423 ACATTGCCATGGTCCAACCATGGTCTTA
66 ACACTGCCATGGTCCAACCATGGTCTTA
22358451 TCCATCAAAT
Statistics
Matches: 432, Mismatches: 60, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
100 3 0.01
101 336 0.78
102 6 0.01
103 87 0.20
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.31
Consensus pattern (101 bp):
GTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAACTATGGTCTTACATATAA
ACACTGCCATGGTCCAACCATGGTCTTACGTTCAAG
Found at i:22358190 original size:204 final size:203
Alignment explanation
Indices: 22357851--22358418 Score: 899
Period size: 202 Copynumber: 2.8 Consensus size: 203
22357841 TACATTCGTA
** * * *
22357851 GTGCCATAAATCAGTTATGGTCTTATCATCAGAATGTCATAGCCTAGCTATGGTTTTACATATAA
1 GTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAGCTATGGTCTTACATATAA
* * *
22357916 ACACTGCCATGGTCCAAACATGGTCTTACGTTCATAGTGTCATAACCCAGTTATGGTCTTATCAT
66 ACACTGTCATGGTCCAACCATGGTCTTACGTTCATAGTGCCATAACCCAGTTAT-GTCTTATCAT
*
22357981 CAGAATGTCATAGCCCAACTATGGTCTTACATATATATATACTGCCACGATCTAACCATGACCTT
130 CAGAATGCCATAGCCCAACTATGGTCTTACATATATATATACTGCCACGATCTAACCATGACCTT
22358046 ACATTCAAG
195 ACATTCAAG
22358055 GTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAGCTATGGTCTTACATATAA
1 GTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAGCTATGGTCTTACATATAA
*
22358120 ACACTGTCATGGTCCAACCATGGTCTTACGCTCATAGTGCCATAACCCAGTTAATGTCTTATCAT
66 ACACTGTCATGGTCCAACCATGGTCTTACGTTCATAGTGCCATAACCCAGTT-ATGTCTTATCAT
22358185 CAGAATGCCATAGCCCAACTATGGTCTTAC--ATATATATACTGCCACGATCTAACCATGACCTT
130 CAGAATGCCATAGCCCAACTATGGTCTTACATATATATATACTGCCACGATCTAACCATGACCTT
22358248 ACATTCAAG
195 ACATTCAAG
* * *
22358257 GTGCCATAACCCAGTTATGGTCTTATCATTAGAATGCCATAGCCCAGGTATGGTCTTACATATAT
1 GTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAGCTATGGTCTTACATATAA
* * * * *
22358322 ATATTGTTATGGTCCAACCATGGTCTTACGTTCA-AGGTGCCATAATCCAGTTATGATCTTTTCA
66 ACACTGTCATGGTCCAACCATGGTCTTACGTTCATA-GTGCCATAACCCAGTTATG-TCTTATCA
* *
22358386 TTAAAATGCCATAGCCCAACTATGGTCTTACAT
129 TCAGAATGCCATAGCCCAACTATGGTCTTACAT
22358419 TTAAACATTG
Statistics
Matches: 338, Mismatches: 21, Indels: 10
0.92 0.06 0.03
Matches are distributed among these distances:
201 4 0.01
202 185 0.55
204 147 0.43
205 2 0.01
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.31
Consensus pattern (203 bp):
GTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAGCTATGGTCTTACATATAA
ACACTGTCATGGTCCAACCATGGTCTTACGTTCATAGTGCCATAACCCAGTTATGTCTTATCATC
AGAATGCCATAGCCCAACTATGGTCTTACATATATATATACTGCCACGATCTAACCATGACCTTA
CATTCAAG
Found at i:22361124 original size:42 final size:42
Alignment explanation
Indices: 22361078--22361162 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 42
22361068 GCACAATTAT
* * * *
22361078 TTAAGCTTGCATGTGGAGCTTTACTGATACACAACTTGTCAC
1 TTAAGCTCGCATGGGGAGCTTCACTGATACACAACTTGCCAC
** * *
22361120 TTAAGCTCGTGTGGGGAGCTTCGCTGATACACAGCTTGCCAC
1 TTAAGCTCGCATGGGGAGCTTCACTGATACACAACTTGCCAC
22361162 T
1 T
22361163 GAAAATAGAG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.31
Consensus pattern (42 bp):
TTAAGCTCGCATGGGGAGCTTCACTGATACACAACTTGCCAC
Found at i:22374247 original size:18 final size:17
Alignment explanation
Indices: 22374207--22374247 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
22374197 AAATGTCTTC
22374207 CCAACACGGTTCATTCT
1 CCAACACGGTTCATTCT
**
22374224 TAAACACGGTTCCATTCT
1 CCAACACGGTT-CATTCT
22374242 CCAACA
1 CCAACA
22374248 TAATTGGTGG
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.29, C:0.34, G:0.10, T:0.27
Consensus pattern (17 bp):
CCAACACGGTTCATTCT
Found at i:22378322 original size:19 final size:19
Alignment explanation
Indices: 22378300--22378336 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
22378290 ATTAAAGTTA
22378300 TTAATTATA-ATTAATTAAG
1 TTAATTA-AGATTAATTAAG
22378319 TTAATTAAGATTAATTAA
1 TTAATTAAGATTAATTAA
22378337 TTATTAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 1 0.06
19 16 0.94
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (19 bp):
TTAATTAAGATTAATTAAG
Found at i:22378325 original size:23 final size:22
Alignment explanation
Indices: 22378294--22378339 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
22378284 ATTATGATTA
*
22378294 AAGTTATTAA-TTATAATTAATT
1 AAGTTATTAAGAT-TAATTAATT
22378316 AAGTTAATTAAGATTAATTAATT
1 AAGTT-ATTAAGATTAATTAATT
22378339 A
1 A
22378340 TTAATATAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 5 0.24
23 15 0.71
24 1 0.05
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.46
Consensus pattern (22 bp):
AAGTTATTAAGATTAATTAATT
Found at i:22382659 original size:24 final size:24
Alignment explanation
Indices: 22382632--22382682 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
22382622 TACTTGGGTA
*
22382632 ATTTGCCGTCAATTTATCATTTAC
1 ATTTGCCGTCAATTAATCATTTAC
** *
22382656 ATTTTTCGTCAATTAATCCTTTAC
1 ATTTGCCGTCAATTAATCATTTAC
22382680 ATT
1 ATT
22382683 AGTAGTGCCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.25, C:0.20, G:0.06, T:0.49
Consensus pattern (24 bp):
ATTTGCCGTCAATTAATCATTTAC
Found at i:22382744 original size:33 final size:33
Alignment explanation
Indices: 22382702--22382845 Score: 105
Period size: 33 Copynumber: 4.3 Consensus size: 33
22382692 ATAACCCAGT
*
22382702 TATGGTCTTATCATCAGAATGTCATAGCCCAAC
1 TATGGTCTTATCATCAAAATGTCATAGCCCAAC
* * *
22382735 TATGGTCTTAT-ATATAAACACTGTCATGGTCCAA-
1 TATGGTCTTATCAT-CAAA-A-TGTCATAGCCCAAC
* * * * * **
22382769 TCATGGTCTTA-CGTTCATAGTGCCATAACCCAGT
1 T-ATGGTCTTATC-ATCAAAATGTCATAGCCCAAC
* *
22382803 TATGGTCTTATCATCAAAATGTCATAGCCTAGC
1 TATGGTCTTATCATCAAAATGTCATAGCCCAAC
22382836 TATGGTCTTA
1 TATGGTCTTA
22382846 CATATAAACA
Statistics
Matches: 83, Mismatches: 20, Indels: 16
0.70 0.17 0.13
Matches are distributed among these distances:
32 2 0.02
33 54 0.65
34 4 0.05
35 22 0.27
36 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (33 bp):
TATGGTCTTATCATCAAAATGTCATAGCCCAAC
Found at i:22382863 original size:101 final size:101
Alignment explanation
Indices: 22382685--22382914 Score: 397
Period size: 101 Copynumber: 2.3 Consensus size: 101
22382675 TTTACATTAG
* *
22382685 TAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGTCATAGCCCAACTATGGTCTTATATAT
1 TAGTGCCATAACCCAGTTATGGTCTTATCATCAAAATGTCATAGCCCAACTATGGTCTTACATAT
* *
22382750 AAACACTGTCATGGTCCAATCATGGTCTTACGTTCA
66 AAACACTATCATGGTCCAACCATGGTCTTACGTTCA
* *
22382786 TAGTGCCATAACCCAGTTATGGTCTTATCATCAAAATGTCATAGCCTAGCTATGGTCTTACATAT
1 TAGTGCCATAACCCAGTTATGGTCTTATCATCAAAATGTCATAGCCCAACTATGGTCTTACATAT
22382851 AAACACTATCATGGTCCAACCATGGTCTTACGTTCA
66 AAACACTATCATGGTCCAACCATGGTCTTACGTTCA
*
22382887 TAGTGCCATAACCCAGTTATGGTATTAT
1 TAGTGCCATAACCCAGTTATGGTCTTAT
22382915 TCGCCAATTC
Statistics
Matches: 122, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
101 122 1.00
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.33
Consensus pattern (101 bp):
TAGTGCCATAACCCAGTTATGGTCTTATCATCAAAATGTCATAGCCCAACTATGGTCTTACATAT
AAACACTATCATGGTCCAACCATGGTCTTACGTTCA
Found at i:22384932 original size:42 final size:42
Alignment explanation
Indices: 22384873--22385158 Score: 346
Period size: 42 Copynumber: 6.8 Consensus size: 42
22384863 CACTTACAAA
* *
22384873 AAAAAACGCCGCTAAAGATCATGTTCTTTAACTGCGCTTAGG
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGG
22384915 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGG
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGG
* * * *
22384957 AAAAAACGCAGCAAAAGATCATGTTCTTTAGCGGCGTTTAGA
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGG
* *
22384999 AAAAAATGCCGCAAAAGATCATGTTCTTTAGCGGCGCTTAGG
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGG
* * * *
22385041 AAAAAACGTCGCTAAAGATCATGTTCTTTAGCGACGTTTTGG
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGG
* * * *
22385083 AAGAAAACGCCTCTAAA-AGTAATGTTCTATAGCGGCGCTT-GTT
1 AA-AAAACGCCGCTAAAGA-TCATGTTCTTTAGCGGCGCTTAG-G
*
22385126 CAAAAACGCCGCTAAA-AGT-AGTGTTCTTTAGCG
1 AAAAAACGCCGCTAAAGA-TCA-TGTTCTTTAGCG
22385159 TTAGCAGCGC
Statistics
Matches: 214, Mismatches: 26, Indels: 8
0.86 0.10 0.03
Matches are distributed among these distances:
41 1 0.00
42 183 0.86
43 30 0.14
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (42 bp):
AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGG
Done.