Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397258.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4.1, 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: 11097736
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 71999 characters in sequence are not A, C, G, or T
File 21 of 22
Found at i:10199934 original size:23 final size:23
Alignment explanation
Indices: 10199908--10199965 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
10199898 TATTGCATAG
**
10199908 TTTATTTTTAGGAGCATAAATAT
1 TTTATTTTTACAAGCATAAATAT
*
10199931 TTTATTTTTCCAAGCATAAATAT
1 TTTATTTTTACAAGCATAAATAT
10199954 TTGGTATTTTTA
1 TT--TATTTTTA
10199966 TTCTAAGACA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 22 0.76
25 7 0.24
ACGTcount: A:0.31, C:0.07, G:0.10, T:0.52
Consensus pattern (23 bp):
TTTATTTTTACAAGCATAAATAT
Found at i:10201545 original size:60 final size:60
Alignment explanation
Indices: 10201268--10201866 Score: 424
Period size: 60 Copynumber: 9.9 Consensus size: 60
10201258 GGAATTCCTT
* * * * * *
10201268 GACTTAATCTAAGCTCGATCTATTTCAAAATAGGTT-AGATTTGAAAAA-TTGAAATTTCTA
1 GACTTAATCTAGGCTTGACCTATCTCAAAACAAGTTCA-ATTT-AAAAATTTGAAATTTCTA
* ** * *
10201328 AACTTAATCTAGGCTCAACTTATC-CTAAAACAAGTTCAATTTTAAAAAATTGAAA-TTCTTA
1 GACTTAATCTAGGCTTGACCTATCTC-AAAACAAGTTCAA-TTTAAAAATTTGAAATTTC-TA
* * ** * * ** * * * *
10201389 GACTTAAT-TTGAGCTTTATATATGTCAAAACAAATTTGATTTAAATATTTAAAATTCCTTT
1 GACTTAATCTAG-GCTTGACCTATCTCAAAACAAGTTCAATTTAAAAATTTGAAATTTC-TA
* * * * * * *
10201450 GACTTAAT-TCAGACTCGATCTATCTAAAAAAAAGTTTAATTTAAAAAATTT-AAATTTCAA
1 GACTTAATCT-AGGCTTGACCTATCTCAAAACAAGTTCAATTT-AAAAATTTGAAATTTCTA
* * * *
10201510 GACTTAATATGGGCTTGACCTATTTCAAAACAAGTTCAACTTAAAAATTTGAAA-TTCTTA
1 GACTTAATCTAGGCTTGACCTATCTCAAAACAAGTTCAATTTAAAAATTTGAAATTTC-TA
* ** * * * * * *
10201570 GACTTAATTTAGGCTCAACGTATCTTAAAATAGGTTCAATTTAAAATTTTGAAATTCCTA
1 GACTTAATCTAGGCTTGACCTATCTCAAAACAAGTTCAATTTAAAAATTTGAAATTTCTA
* * * *
10201630 GACTTAATCTAGGTTTGACCTGTCTCAAAACAAGTTCGATTTAAAAATTTGAAATTCCTA
1 GACTTAATCTAGGCTTGACCTATCTCAAAACAAGTTCAATTTAAAAATTTGAAATTTCTA
* * * * ** * *
10201690 AACTTAATCTAGCCTTGGCCTATCTCAAAATAAGTTTGACTTAAAAATTTGAAATTTTTA
1 GACTTAATCTAGGCTTGACCTATCTCAAAACAAGTTCAATTTAAAAATTTGAAATTTCTA
* * * * ** *
10201750 CACTTGATCTAGGCTAGACCTATTTCAAAA-AAGGTTGTATTTAAAAATTTGAAATTTCTC
1 GACTTAATCTAGGCTTGACCTATCTCAAAACAA-GTTCAATTTAAAAATTTGAAATTTCTA
* * * * *
10201810 GACTTAATTTAGGCTCGATCTATCTCAAAACAGGTTCAATTTACAAAATTTTAAATT
1 GACTTAATCTAGGCTTGACCTATCTCAAAACAAGTTCAATTTA-AAAATTTGAAATT
10201867 CTTCTTTCAT
Statistics
Matches: 421, Mismatches: 101, Indels: 33
0.76 0.18 0.06
Matches are distributed among these distances:
59 14 0.03
60 306 0.73
61 92 0.22
62 9 0.02
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (60 bp):
GACTTAATCTAGGCTTGACCTATCTCAAAACAAGTTCAATTTAAAAATTTGAAATTTCTA
Found at i:10201737 original size:180 final size:179
Alignment explanation
Indices: 10201223--10201867 Score: 471
Period size: 180 Copynumber: 3.6 Consensus size: 179
10201213 TAAGTACTCA
* * ** * * * * *
10201223 ACCTAGTTCAAAATAGGTTTGATTATAACAATTTTGGAATTCCTTGACTTAATCTAAGCTCGATC
1 ACCTATTTCAAAAAAGGTTCAATT-TAA-AAATTTGAAATTCCTAGACTTAATCTAGGCTCGACC
* * * * * * * ** *
10201288 TATTTCAAAATAGGTT-AGATTTGAAAAATTGAAATTTCTAA-ACTTAATCTAGGCTCAACTTAT
64 TATCTCAAAACAAGTTCA-ATTT-AAAAATTTAAA-TTCCAAGACTTAATATAGCCTTGACCTAT
* * * * **
10201351 C-CTAAAACAAGTTCAATTTTAAAAAATTGAAATTCTTAGACTTAAT-TTGAGCTTT
126 CTC-AAAACAAGTTCAA-CTTAAAAATTTGAAATTCTTACACTTAATCTAG-GCTAG
** * * ** * * * * *
10201406 ATATATGTCAAAACAA-ATTTGATTTAAATATTTAAAATTCCTTTGACTTAAT-TCAGACTCGAT
1 ACCTATTTCAAAA-AAGGTTCAATTTAAAAATTTGAAATTCC-TAGACTTAATCT-AGGCTCGAC
* * * * * * *
10201469 CTATCTAAAAAAAAGTTTAATTTAAAAAATTTAAATTTCAAGACTTAATATGGGCTTGACCTATT
63 CTATCTCAAAACAAGTTCAATTT-AAAAATTTAAATTCCAAGACTTAATATAGCCTTGACCTATC
* *
10201534 TCAAAACAAGTTCAACTTAAAAATTTGAAATTCTTAGACTTAATTTAGGCTCA-
127 TCAAAACAAGTTCAACTTAAAAATTTGAAATTCTTACACTTAATCTAGGCT-AG
* * * * *
10201587 ACGTATCTT-AAAATAGGTTCAATTTAAAATTTTGAAATTCCTAGACTTAATCTAGGTTTGACCT
1 ACCTAT-TTCAAAAAAGGTTCAATTTAAAAATTTGAAATTCCTAGACTTAATCTAGGCTCGACCT
* * * *
10201651 GTCTCAAAACAAGTTCGATTTAAAAATTTGAAATTCCTAA-ACTTAATCTAGCCTTGGCCTATCT
65 ATCTCAAAACAAGTTCAATTTAAAAATTT-AAATTCC-AAGACTTAATATAGCCTTGACCTATCT
* ** * *
10201715 CAAAATAAGTTTGACTTAAAAATTTGAAATTTTTACACTTGATCTAGGCTAG
128 CAAAACAAGTTCAACTTAAAAATTTGAAATTCTTACACTTAATCTAGGCTAG
** * * * *
10201767 ACCTATTTCAAAAAAGGTTGTATTTAAAAATTTGAAATTTCTCGACTTAATTTAGGCTCGATCTA
1 ACCTATTTCAAAAAAGGTTCAATTTAAAAATTTGAAATTCCTAGACTTAATCTAGGCTCGACCTA
*
10201832 TCTCAAAACAGGTTCAATTTACAAAATTTTAAATTC
66 TCTCAAAACAAGTTCAATTTA-AAAA-TTTAAATTC
10201868 TTCTTTCATG
Statistics
Matches: 368, Mismatches: 77, Indels: 36
0.77 0.16 0.07
Matches are distributed among these distances:
179 11 0.03
180 170 0.46
181 85 0.23
182 83 0.23
183 18 0.05
184 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (179 bp):
ACCTATTTCAAAAAAGGTTCAATTTAAAAATTTGAAATTCCTAGACTTAATCTAGGCTCGACCTA
TCTCAAAACAAGTTCAATTTAAAAATTTAAATTCCAAGACTTAATATAGCCTTGACCTATCTCAA
AACAAGTTCAACTTAAAAATTTGAAATTCTTACACTTAATCTAGGCTAG
Found at i:10202689 original size:19 final size:19
Alignment explanation
Indices: 10202665--10202702 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
10202655 AGAGTCACGC
10202665 TAATTAGTTAAGCAGTTTG
1 TAATTAGTTAAGCAGTTTG
10202684 TAATTAGTTAAGCAGTTTG
1 TAATTAGTTAAGCAGTTTG
10202703 GTTAAACAGT
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:0.32, C:0.05, G:0.21, T:0.42
Consensus pattern (19 bp):
TAATTAGTTAAGCAGTTTG
Found at i:10209916 original size:28 final size:28
Alignment explanation
Indices: 10209884--10209948 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
10209874 GTAAGGGTTT
10209884 AAAGCTTGGGTTAGAAGCTTACCTTGTA
1 AAAGCTTGGGTTAGAAGCTTACCTTGTA
*
10209912 AAAGCTTGGGTTAGAAGCTTATCTTGTA
1 AAAGCTTGGGTTAGAAGCTTACCTTGTA
10209940 AAAGCTTGG
1 AAAGCTTGG
10209949 TGGAAGCTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.32
Consensus pattern (28 bp):
AAAGCTTGGGTTAGAAGCTTACCTTGTA
Found at i:10213759 original size:12 final size:10
Alignment explanation
Indices: 10213728--10213753 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
10213718 AACTAGCCTT
10213728 CAAGTCTCTC
1 CAAGTCTCTC
10213738 CAAGTCTCTC
1 CAAGTCTCTC
10213748 CAAGTC
1 CAAGTC
10213754 CTTCTCACCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.23, C:0.38, G:0.12, T:0.27
Consensus pattern (10 bp):
CAAGTCTCTC
Found at i:10219439 original size:8 final size:8
Alignment explanation
Indices: 10219426--10219480 Score: 69
Period size: 8 Copynumber: 7.0 Consensus size: 8
10219416 GTCTCTCCCC
10219426 TTCTTCCT
1 TTCTTCCT
10219434 TTCTTCCT
1 TTCTTCCT
10219442 TTC-T-CT
1 TTCTTCCT
**
10219448 TTCTTTTT
1 TTCTTCCT
10219456 TTCTTCCT
1 TTCTTCCT
10219464 TTCTTCCT
1 TTCTTCCT
10219472 TTGCTTCCT
1 TT-CTTCCT
10219481 AGCCGAATCT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
6 5 0.12
7 2 0.05
8 28 0.68
9 6 0.15
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.65
Consensus pattern (8 bp):
TTCTTCCT
Found at i:10219451 original size:22 final size:22
Alignment explanation
Indices: 10219426--10219467 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
10219416 GTCTCTCCCC
10219426 TTCTTCCTTTCTTCCTTTCTCT
1 TTCTTCCTTTCTTCCTTTCTCT
**
10219448 TTCTTTTTTTCTTCCTTTCT
1 TTCTTCCTTTCTTCCTTTCT
10219468 TCCTTTGCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (22 bp):
TTCTTCCTTTCTTCCTTTCTCT
Found at i:10225181 original size:23 final size:22
Alignment explanation
Indices: 10225137--10225182 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
10225127 ATTTTGCAAC
*
10225137 GAATATTATTTACAGATATGTT
1 GAATATTATTGACAGATATGTT
10225159 GAATATTAATTGACAGGAT-TGTT
1 GAATATT-ATTGACA-GATATGTT
10225182 G
1 G
10225183 CCTTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 7 0.33
23 11 0.52
24 3 0.14
ACGTcount: A:0.35, C:0.04, G:0.20, T:0.41
Consensus pattern (22 bp):
GAATATTATTGACAGATATGTT
Found at i:10225625 original size:4 final size:4
Alignment explanation
Indices: 10225612--10225642 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
10225602 AATTAGTCGT
10225612 TTTA -TTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
10225643 ATGACTTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:10228597 original size:23 final size:23
Alignment explanation
Indices: 10228547--10228602 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 23
10228537 TGTAAATAAA
* *
10228547 TAAATTAA-TATTTAAAATAATT
1 TAAATAAATTATTTAAAAAAATT
*
10228569 T--TTAAATTATTTAAAAAAATT
1 TAAATAAATTATTTAAAAAAATT
10228590 TAAATAAATTATT
1 TAAATAAATTATT
10228603 ATTCTATTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
20 3 0.11
21 14 0.52
22 1 0.04
23 9 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
TAAATAAATTATTTAAAAAAATT
Found at i:10229270 original size:20 final size:20
Alignment explanation
Indices: 10229234--10229271 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
10229224 AAAAGCATAC
*
10229234 AAATAATAAAATTTAAATTT
1 AAATAATAAAATATAAATTT
10229254 AAATAATCAAAA-ATAAAT
1 AAATAAT-AAAATATAAAT
10229272 ACCCAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (20 bp):
AAATAATAAAATATAAATTT
Found at i:10229290 original size:34 final size:34
Alignment explanation
Indices: 10229252--10229327 Score: 109
Period size: 34 Copynumber: 2.2 Consensus size: 34
10229242 AAATTTAAAT
10229252 TTAAATAATCAAAAATAAATACCCAAAT-ATCAAC
1 TTAAATAATCAAAAATAAATACCCAAATAAT-AAC
* **
10229286 TTAAATAATTAAAAATAAATATTCAAATAATAAC
1 TTAAATAATCAAAAATAAATACCCAAATAATAAC
10229320 TTAAATAA
1 TTAAATAA
10229328 CATTATAAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 36 0.95
35 2 0.05
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.29
Consensus pattern (34 bp):
TTAAATAATCAAAAATAAATACCCAAATAATAAC
Found at i:10235214 original size:12 final size:12
Alignment explanation
Indices: 10235197--10235231 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
10235187 GAATAGTTTC
10235197 TTGCTGCCTCAT
1 TTGCTGCCTCAT
10235209 TTGCTGCCTTC-T
1 TTGCTGCC-TCAT
10235221 TTGCTGCCTCA
1 TTGCTGCCTCA
10235232 AAAATCTCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.10
12 17 0.81
13 2 0.10
ACGTcount: A:0.06, C:0.34, G:0.17, T:0.43
Consensus pattern (12 bp):
TTGCTGCCTCAT
Found at i:10251816 original size:17 final size:16
Alignment explanation
Indices: 10251792--10251835 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 16
10251782 AGAAAAAGAA
10251792 AAAAGAAAAAAA-TAT
1 AAAAGAAAAAAACTAT
10251807 ATATAAGAAAGAAAACTAT
1 A-A-AAGAAA-AAAACTAT
10251826 AAAAGAAAAA
1 AAAAGAAAAA
10251836 TAAAACTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
15 1 0.04
16 3 0.12
17 12 0.48
18 5 0.20
19 4 0.16
ACGTcount: A:0.75, C:0.02, G:0.09, T:0.14
Consensus pattern (16 bp):
AAAAGAAAAAAACTAT
Found at i:10252365 original size:12 final size:12
Alignment explanation
Indices: 10252348--10252373 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
10252338 TTTTTTTATC
10252348 TTTTTGAATTTT
1 TTTTTGAATTTT
10252360 TTTTTGAATTTT
1 TTTTTGAATTTT
10252372 TT
1 TT
10252374 AGGGGGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (12 bp):
TTTTTGAATTTT
Found at i:10253897 original size:18 final size:19
Alignment explanation
Indices: 10253865--10253913 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
10253855 ACATTAACAT
*
10253865 AACATATTCATAATCAATA
1 AACATAATCATAATCAATA
*
10253884 AACATAATCA-AATCCATA
1 AACATAATCATAATCAATA
* *
10253902 AATATAAACATA
1 AACATAATCATA
10253914 TGACTGACTC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.57, C:0.16, G:0.00, T:0.27
Consensus pattern (19 bp):
AACATAATCATAATCAATA
Found at i:10255992 original size:20 final size:21
Alignment explanation
Indices: 10255949--10256002 Score: 83
Period size: 20 Copynumber: 2.6 Consensus size: 21
10255939 CTTTCTAATT
* *
10255949 GCCATCTATTGATAGATGGTA
1 GCCATTTATCGATAGATGGTA
10255970 GCCATTTATCGATAGAT-GTA
1 GCCATTTATCGATAGATGGTA
10255990 GCCATTTATCGAT
1 GCCATTTATCGAT
10256003 GGATCTGTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 16 0.52
21 15 0.48
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (21 bp):
GCCATTTATCGATAGATGGTA
Found at i:10261651 original size:24 final size:24
Alignment explanation
Indices: 10261620--10261669 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
10261610 AAGGATTAAC
10261620 TGTATGTTACTTTAAGCTGGAATT
1 TGTATGTTACTTTAAGCTGGAATT
*
10261644 TGTATGTTACTTTAAGTTGGAATT
1 TGTATGTTACTTTAAGCTGGAATT
10261668 TG
1 TG
10261670 AGTTAATTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.06, G:0.22, T:0.48
Consensus pattern (24 bp):
TGTATGTTACTTTAAGCTGGAATT
Found at i:10275334 original size:24 final size:24
Alignment explanation
Indices: 10275303--10275357 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
10275293 ATATAAAAAC
*
10275303 TAATAAACAATAA-CTAAATTAAGA
1 TAATAAAC-ATAAGCTAAATTAACA
* *
10275327 TAATAAACATAAGTTAAATTAACT
1 TAATAAACATAAGCTAAATTAACA
10275351 TAATAAA
1 TAATAAA
10275358 AACAAACTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 4 0.15
24 23 0.85
ACGTcount: A:0.60, C:0.07, G:0.04, T:0.29
Consensus pattern (24 bp):
TAATAAACATAAGCTAAATTAACA
Found at i:10275368 original size:24 final size:24
Alignment explanation
Indices: 10275314--10275369 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
10275304 AATAAACAAT
* * *
10275314 AACTAAATTAAGATAATAAACATA
1 AACTAAATTAACATAATAAAAACA
** *
10275338 AGTTAAATTAACTTAATAAAAACA
1 AACTAAATTAACATAATAAAAACA
10275362 AACTAAAT
1 AACTAAAT
10275370 AGAAAAATAA
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.61, C:0.09, G:0.04, T:0.27
Consensus pattern (24 bp):
AACTAAATTAACATAATAAAAACA
Found at i:10283336 original size:18 final size:18
Alignment explanation
Indices: 10283313--10283351 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
10283303 GCTTGAAGAA
*
10283313 AAAGAAG-AAGAAGACAAG
1 AAAGAAGCAA-AAGAAAAG
10283331 AAAGAAGCAAAAGAAAAG
1 AAAGAAGCAAAAGAAAAG
10283349 AAA
1 AAA
10283352 AAAAGTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.72, C:0.05, G:0.23, T:0.00
Consensus pattern (18 bp):
AAAGAAGCAAAAGAAAAG
Found at i:10291806 original size:74 final size:73
Alignment explanation
Indices: 10291635--10291830 Score: 218
Period size: 74 Copynumber: 2.7 Consensus size: 73
10291625 TGGCCGGTCC
* * * *
10291635 AGAAACAAAAAAGACTTAGTTGACCAAGAAGAATGGTTCGTTAACTAAGTGCTCACTACTAGAAA
1 AGAAACAAAAAAGACTTAGTCGACCAAGAAGAATGGTTAGTCAACTAAGTGCTCACTACCAGAAA
*
10291700 CTTCAATA
66 CTACAATA
* * * * *
10291708 AGAAAATAGAAAAATA-TTAATCGACCAAGAAGCATGGTTAGTCAACTAAGTGTTCACTACCAGA
1 AG-AAACA-AAAAAGACTTAGTCGACCAAGAAGAATGGTTAGTCAACTAAGTGCTCACTACCAGA
*
10291772 AACTAGAAGT-
64 AACTACAA-TA
* *
10291782 AGAAGACAAAAAAGACTTAGTCGACCAAAAAGTAT-GTTAGTCAACTAAG
1 AGAA-ACAAAAAAGACTTAGTCGACCAAGAAGAATGGTTAGTCAACTAAG
10291831 AGCACTCTGT
Statistics
Matches: 102, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
73 24 0.24
74 71 0.70
75 7 0.07
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.21
Consensus pattern (73 bp):
AGAAACAAAAAAGACTTAGTCGACCAAGAAGAATGGTTAGTCAACTAAGTGCTCACTACCAGAAA
CTACAATA
Found at i:10295083 original size:24 final size:24
Alignment explanation
Indices: 10295051--10295099 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
10295041 TAGTAAAACT
10295051 ACCTAGATCTTTAAGCTTTGGTGG
1 ACCTAGATCTTTAAGCTTTGGTGG
10295075 ACCTAGATCTTTAAGCTTTGGTGG
1 ACCTAGATCTTTAAGCTTTGGTGG
10295099 A
1 A
10295100 ATCTTATTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.37
Consensus pattern (24 bp):
ACCTAGATCTTTAAGCTTTGGTGG
Found at i:10298328 original size:43 final size:43
Alignment explanation
Indices: 10298267--10298348 Score: 155
Period size: 43 Copynumber: 1.9 Consensus size: 43
10298257 ATACATAGCC
*
10298267 AAATTAGGACACTTGCTTAATGAATTTAATTAATTGATTCCTA
1 AAATTAGGACACTTGCTTAATGAACTTAATTAATTGATTCCTA
10298310 AAATTAGGACACTTGCTTAATGAACTTAATTAATTGATT
1 AAATTAGGACACTTGCTTAATGAACTTAATTAATTGATT
10298349 TCGATAGACA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (43 bp):
AAATTAGGACACTTGCTTAATGAACTTAATTAATTGATTCCTA
Found at i:10320846 original size:43 final size:43
Alignment explanation
Indices: 10320776--10320903 Score: 161
Period size: 43 Copynumber: 3.0 Consensus size: 43
10320766 GTTTTAACTA
* *
10320776 GTTGTTTGGATATTTATTTTTAATTATTTAAGTTTATGTTGTT
1 GTTGTTTGGATATTTATATTTAGTTATTTAAGTTTATGTTGTT
* *
10320819 GTTGTTTGGATATTTGTATTTGGTTATTTAAGTTTATGTT-TT
1 GTTGTTTGGATATTTATATTTAGTTATTTAAGTTTATGTTGTT
* * * * *
10320861 -TTGTTTGGATCTTTTTGTTTAGTTACTTAAGTTTATGTCGTT
1 GTTGTTTGGATATTTATATTTAGTTATTTAAGTTTATGTTGTT
10320903 G
1 G
10320904 CAAGGATATT
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
41 33 0.45
42 4 0.05
43 36 0.49
ACGTcount: A:0.17, C:0.02, G:0.20, T:0.61
Consensus pattern (43 bp):
GTTGTTTGGATATTTATATTTAGTTATTTAAGTTTATGTTGTT
Found at i:10330796 original size:68 final size:68
Alignment explanation
Indices: 10330724--10330850 Score: 173
Period size: 68 Copynumber: 1.9 Consensus size: 68
10330714 TGAAATCTAC
** *
10330724 ATCATACACACTTTCTCATGGCATTCATCATGCATACTTAATCACCTCATATGGTATATGAAAAA
1 ATCATACACACAATCTCATGGCATACATCATGCATACTTAATCACCTCATATGGTATATGAAAAA
10330789 TGT
66 TGT
* * * * * *
10330792 ATCATATATACAATCTTATGGCATACATCATGCATATTTAATCATCTCCTATGGTATAT
1 ATCATACACACAATCTCATGGCATACATCATGCATACTTAATCACCTCATATGGTATAT
10330851 AGAATTTACA
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
68 50 1.00
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.36
Consensus pattern (68 bp):
ATCATACACACAATCTCATGGCATACATCATGCATACTTAATCACCTCATATGGTATATGAAAAA
TGT
Found at i:10330864 original size:68 final size:67
Alignment explanation
Indices: 10330741--10330880 Score: 183
Period size: 68 Copynumber: 2.1 Consensus size: 67
10330731 ACACTTTCTC
* *
10330741 ATGGCATTCATCATGCATACTTAATCACCTCATATGGTATATGAAAAATGTATCATATATACAAT
1 ATGGCATACATCATGCATACTTAATCACCTCATATGGTATAT-AAAAATGTATCATATACACAAT
10330806 CTT
65 CTT
* * * * *
10330809 ATGGCATACATCATGCATATTTAATCATCTCCTATGGTATAT-AGAATTTACATCATATACACAA
1 ATGGCATACATCATGCATACTTAATCACCTCATATGGTATATAAAAATGT--ATCATATACACAA
10330873 TCTT
64 TCTT
10330877 ATGG
1 ATGG
10330881 AATGTATCAT
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
66 5 0.08
68 58 0.92
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.36
Consensus pattern (67 bp):
ATGGCATACATCATGCATACTTAATCACCTCATATGGTATATAAAAATGTATCATATACACAATC
TT
Found at i:10331917 original size:21 final size:21
Alignment explanation
Indices: 10331895--10331968 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
10331885 AAATTATATT
*
10331895 GATACATTATGAACATGTATT
1 GATACATTATGAACATGTATC
* * *
10331916 GATAC-TTGAT-CATATGCATC
1 GATACATT-ATGAACATGTATC
*
10331936 GATACATTATAAACATGTATC
1 GATACATTATGAACATGTATC
*
10331957 AATACATT-TGAA
1 GATACATTATGAA
10331969 ACAGAATGCA
Statistics
Matches: 41, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
20 18 0.44
21 23 0.56
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (21 bp):
GATACATTATGAACATGTATC
Found at i:10332150 original size:17 final size:17
Alignment explanation
Indices: 10332128--10332174 Score: 69
Period size: 16 Copynumber: 2.8 Consensus size: 17
10332118 ATTTGGATTC
10332128 AATAAAAATATAAAAAA
1 AATAAAAATATAAAAAA
*
10332145 AATAAAAATAT-AAAAG
1 AATAAAAATATAAAAAA
*
10332161 AATCAAAATATAAA
1 AATAAAAATATAAA
10332175 TTTTGTTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 14 0.52
17 13 0.48
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (17 bp):
AATAAAAATATAAAAAA
Found at i:10334477 original size:21 final size:20
Alignment explanation
Indices: 10334447--10334485 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
10334437 TTAGATAAGC
10334447 AACTTAAATTGT-GTTTTGAA
1 AACTTAAATT-TAGTTTTGAA
10334467 AACTTGAAATTTAGTTTTG
1 AACTT-AAATTTAGTTTTG
10334486 TGAATGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.46
Consensus pattern (20 bp):
AACTTAAATTTAGTTTTGAA
Found at i:10354007 original size:31 final size:32
Alignment explanation
Indices: 10353972--10354040 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 32
10353962 ACCCCTATCA
* *
10353972 ACCTTGGGCCGGTAATGTTTG-ACCCCATGGC
1 ACCTTGGGCCGGAAATGTATGAACCCCATGGC
* *
10354003 ACCTTGGTCCGGAAATGTATGAACCCCATTGC
1 ACCTTGGGCCGGAAATGTATGAACCCCATGGC
10354035 ACCTTG
1 ACCTTG
10354041 TGCATTTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
31 18 0.55
32 15 0.45
ACGTcount: A:0.20, C:0.29, G:0.25, T:0.26
Consensus pattern (32 bp):
ACCTTGGGCCGGAAATGTATGAACCCCATGGC
Found at i:10354261 original size:68 final size:68
Alignment explanation
Indices: 10354170--10354353 Score: 199
Period size: 68 Copynumber: 2.7 Consensus size: 68
10354160 TATAACATCA
* * * **
10354170 ATCATACATACTTAATCATCTCATGTAGTATATGGAATCTACATCATACACACTTTCTCATGGCA
1 ATCATGCATACTTAATCACCTCATATAGTATATGGAATCTACATCATACACACAATCTCATGGCA
10354235 TTC
66 TTC
* * * * * * *
10354238 ATTATTCATACATAATCACCTCATATGGTATATGGAATTTGCATCATACACACAATCTTATGGCA
1 ATCATGCATACTTAATCACCTCATATAGTATATGGAATCTACATCATACACACAATCTCATGGCA
10354303 TTC
66 TTC
* * * * *
10354306 ATCATGCATACTTAATTATCTTATAT-GTTATATGAAATTTACATCATA
1 ATCATGCATACTTAATCACCTCATATAG-TATATGGAATCTACATCATA
10354354 TAAATAATTT
Statistics
Matches: 96, Mismatches: 19, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
67 1 0.01
68 95 0.99
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.38
Consensus pattern (68 bp):
ATCATGCATACTTAATCACCTCATATAGTATATGGAATCTACATCATACACACAATCTCATGGCA
TTC
Found at i:10354367 original size:68 final size:68
Alignment explanation
Indices: 10354170--10354378 Score: 193
Period size: 68 Copynumber: 3.1 Consensus size: 68
10354160 TATAACATCA
* * * * * * * * ** *
10354170 ATCATACATACTTAATCATCTCATGTAGTATATGGAATCTACATCATACACACTTTCTCATGGCA
1 ATCATGCATACATAATCACCTCATATGGTATATGAAATTTACATCATACAAACAATCTTATGGCA
10354235 TTC
66 TTC
* * * * *
10354238 ATTATTCATACATAATCACCTCATATGGTATATGGAATTTGCATCATACACACAATCTTATGGCA
1 ATCATGCATACATAATCACCTCATATGGTATATGAAATTTACATCATACAAACAATCTTATGGCA
10354303 TTC
66 TTC
* * * * * * * *
10354306 ATCATGCATACTTAATTATCTTATATGTTATATGAAATTTACATCATATAAATAATTTTATGGCA
1 ATCATGCATACATAATCACCTCATATGGTATATGAAATTTACATCATACAAACAATCTTATGGCA
*
10354371 TTT
66 TTC
10354374 ATCAT
1 ATCAT
10354379 ACCAAACATG
Statistics
Matches: 116, Mismatches: 25, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
68 116 1.00
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (68 bp):
ATCATGCATACATAATCACCTCATATGGTATATGAAATTTACATCATACAAACAATCTTATGGCA
TTC
Found at i:10355733 original size:21 final size:21
Alignment explanation
Indices: 10355707--10355746 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
10355697 AGATGATGAA
10355707 ATGTATAGATACATATAGGCC
1 ATGTATAGATACATATAGGCC
* *
10355728 ATGTATTGATACATTTAGG
1 ATGTATAGATACATATAGG
10355747 TTCTAGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (21 bp):
ATGTATAGATACATATAGGCC
Found at i:10363557 original size:14 final size:14
Alignment explanation
Indices: 10363538--10363564 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
10363528 ATTTTAGTGT
10363538 TTATATATATATAA
1 TTATATATATATAA
10363552 TTATATATATATA
1 TTATATATATATA
10363565 TATATCATAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTATATATATATAA
Found at i:10369121 original size:114 final size:114
Alignment explanation
Indices: 10368921--10369142 Score: 345
Period size: 114 Copynumber: 1.9 Consensus size: 114
10368911 GAATGGGAAT
* * * *
10368921 CATAGGCACTCATACATCTAAGTCATACAAGCTTGTAGATATAGTTCAGTAACTTTAAAAGTCAA
1 CATAGGCACTCATACACCTAAGTCATACAAGCTTATAGATATAGTTCAATAACTTCAAAAGTCAA
10368986 GCTTATAACTATGCAAGAACAAATATATGGGAGTTAAATCATTGATTCC
66 GCTTATAACTATGCAAGAACAAATATATGGGAGTTAAATCATTGATTCC
* * * **
10369035 CATAGGCACTCATATACCTAAGTTATACTAGCTTATAGATATAGTTCAATAACTTCAAGCGTCAA
1 CATAGGCACTCATACACCTAAGTCATACAAGCTTATAGATATAGTTCAATAACTTCAAAAGTCAA
* *
10369100 GCTTATAACTATGTAAGAACAAATGTATGGGAGTTAAATCATT
66 GCTTATAACTATGCAAGAACAAATATATGGGAGTTAAATCATT
10369143 TTAAGCGATT
Statistics
Matches: 97, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
114 97 1.00
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (114 bp):
CATAGGCACTCATACACCTAAGTCATACAAGCTTATAGATATAGTTCAATAACTTCAAAAGTCAA
GCTTATAACTATGCAAGAACAAATATATGGGAGTTAAATCATTGATTCC
Found at i:10376503 original size:15 final size:15
Alignment explanation
Indices: 10376483--10376513 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
10376473 TAAGTATGAA
10376483 ATGTGATTGAGATTG
1 ATGTGATTGAGATTG
10376498 ATGTGATTGAGATTG
1 ATGTGATTGAGATTG
10376513 A
1 A
10376514 GCTATCTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.32, T:0.39
Consensus pattern (15 bp):
ATGTGATTGAGATTG
Found at i:10380786 original size:18 final size:19
Alignment explanation
Indices: 10380763--10380805 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
10380753 AGGCGAAAGA
10380763 AATATTTTA-GAATAAAAT
1 AATATTTTATGAATAAAAT
*
10380781 AATATTTTATTAATAAAAT
1 AATATTTTATGAATAAAAT
10380800 AATATT
1 AATATT
10380806 ANNNNNNNNN
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
AATATTTTATGAATAAAAT
Found at i:10382630 original size:25 final size:24
Alignment explanation
Indices: 10382596--10382647 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
10382586 TAGTTTATGA
*
10382596 TATACGTGGCAAGGCCACGAGTTGT
1 TATACGTGGCAAGGCCACAAG-TGT
* *
10382621 TATATGTGGCTAGGCCACAAGTGT
1 TATACGTGGCAAGGCCACAAGTGT
10382645 TAT
1 TAT
10382648 TCGAGGTTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 6 0.25
25 18 0.75
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (24 bp):
TATACGTGGCAAGGCCACAAGTGT
Found at i:10386441 original size:13 final size:13
Alignment explanation
Indices: 10386423--10386458 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
10386413 CGACGTAATT
10386423 ATGTGGCACTGTC
1 ATGTGGCACTGTC
10386436 ATGTGGCACTGTC
1 ATGTGGCACTGTC
10386449 ATGTGGCACT
1 ATGTGGCACT
10386459 AATATGATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.17, C:0.22, G:0.31, T:0.31
Consensus pattern (13 bp):
ATGTGGCACTGTC
Found at i:10386736 original size:2 final size:2
Alignment explanation
Indices: 10386729--10386754 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10386719 TATGGTATTA
10386729 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
10386755 TCTTACTTGA
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:10403665 original size:23 final size:23
Alignment explanation
Indices: 10403592--10403665 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 23
10403582 TGGCGTCGTG
* *
10403592 GCACTCACTCTTTCA-TGGCTGCA
1 GCACCCACTCTTT-AGTGGTTGCA
* * * *
10403615 GCACCCATTCTGTCGTGGTTGTA
1 GCACCCACTCTTTAGTGGTTGCA
10403638 GCACCCACTCTTTAGTGGTTGCA
1 GCACCCACTCTTTAGTGGTTGCA
*
10403661 TCACC
1 GCACC
10403666 TAACTTGTTG
Statistics
Matches: 39, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.16, C:0.32, G:0.20, T:0.31
Consensus pattern (23 bp):
GCACCCACTCTTTAGTGGTTGCA
Found at i:10410382 original size:33 final size:33
Alignment explanation
Indices: 10410306--10410382 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 33
10410296 AACACTACAT
* * * *
10410306 CAGCATACCACATCATCATCTATTATGACGTGT
1 CAGCATGCCACATCAGCATCTATTATGACATGC
* *
10410339 CAGTAAGCCACATCAGCATCTATTATGACATGC
1 CAGCATGCCACATCAGCATCTATTATGACATGC
10410372 CAGCATGCCAC
1 CAGCATGCCAC
10410383 GTCAATGTCA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.31, C:0.30, G:0.14, T:0.25
Consensus pattern (33 bp):
CAGCATGCCACATCAGCATCTATTATGACATGC
Found at i:10419248 original size:239 final size:240
Alignment explanation
Indices: 10418865--10419347 Score: 677
Period size: 241 Copynumber: 2.0 Consensus size: 240
10418855 AAGAAGAAAA
10418865 AGAAGAAGACAAGAGAAAAGCCAAAGAGAGGAAGAAAAGCATTGCCTTGAAAGTAAGCACCCTTA
1 AGAAGAAGACAAGAGAAAAGCCAAAGAGAGGAAGAAAAGCATTGCCTTGAAAGTAAGCACCCTTA
** * *
10418930 AAGAAGAGCTAGAAAATCTACCATGTGACAACAATGAAGAGTTAGCCATGGTAGCTAGAAGATTT
66 AAGAAGAGCTAGAAAATCT--CATGCAACAACAATGAAGAGTTAGCCATGATAGCTAAAAGATTT
* * *
10418995 AGAAAGCTTATGGG-ATAGAGATAGAAGAATTACTAGGAAAAGTTATCAAAGAGATTAAGAGTCT
129 AGAAAGCTTATGGGAAAAGAGATAAAAGAATTACTAAGAAAAGTTATCAAAGAGATTAAGAGTCT
* **
10419059 TCATGGAAAGTAAAAAATAAAAAAGAACCTAACAAAAAGGATGATGT
194 TCATGGAAAGTAAAAAACAAAAAAGAACCTAACAAAAACAATGATGT
*
10419106 AGAAGAAGACAAGAGAAAAGCCAAAGAGAGGAAGAAAAGCATTGCCTTTGAAAGTAAGCACTCTT
1 AGAAGAAGACAAGAGAAAAGCCAAAGAGAGGAAGAAAAGCATTGCC-TTGAAAGTAAGCACCCTT
* * *
10419171 GAAA-AAGAGTTGGAAAATCT-ATGCAACGACAATGAAGAGTTAGCCATGATA-CTTAAAAGATT
65 -AAAGAAGAGCTAGAAAATCTCATGCAACAACAATGAAGAGTTAGCCATGATAGC-TAAAAGATT
* * * ** *
10419233 TAGAAAGTTTATGGGACAAAGAGATAAAAGACTTGCTAAGAAAAGTTATTGAAGAGATTAAGGGT
128 TAGAAAGCTTATGGGA-AAAGAGATAAAAGAATTACTAAGAAAAGTTATCAAAGAGATTAAGAGT
* * *
10419298 CTTCATGGAACGTTAGAAACAAAAAAGAACCTAACAAAAACAATGATGT
192 CTTCATGGAAAGTAAAAAACAAAAAAGAACCTAACAAAAACAATGATGT
10419347 A
1 A
10419348 ATATGTTTTG
Statistics
Matches: 214, Mismatches: 23, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
238 1 0.00
239 49 0.23
241 130 0.61
242 31 0.14
243 3 0.01
ACGTcount: A:0.47, C:0.11, G:0.22, T:0.19
Consensus pattern (240 bp):
AGAAGAAGACAAGAGAAAAGCCAAAGAGAGGAAGAAAAGCATTGCCTTGAAAGTAAGCACCCTTA
AAGAAGAGCTAGAAAATCTCATGCAACAACAATGAAGAGTTAGCCATGATAGCTAAAAGATTTAG
AAAGCTTATGGGAAAAGAGATAAAAGAATTACTAAGAAAAGTTATCAAAGAGATTAAGAGTCTTC
ATGGAAAGTAAAAAACAAAAAAGAACCTAACAAAAACAATGATGT
Found at i:10429255 original size:14 final size:14
Alignment explanation
Indices: 10429236--10429264 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
10429226 TAGTCATTCC
10429236 TAGGAGCCTTGTAG
1 TAGGAGCCTTGTAG
10429250 TAGGAGCCTTGTAG
1 TAGGAGCCTTGTAG
10429264 T
1 T
10429265 CGATCCTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.34, T:0.31
Consensus pattern (14 bp):
TAGGAGCCTTGTAG
Found at i:10429776 original size:36 final size:36
Alignment explanation
Indices: 10429664--10429820 Score: 102
Period size: 36 Copynumber: 4.4 Consensus size: 36
10429654 TTGAGCCTAG
* * * * *
10429664 TAAAAA-CCATTGTGAGGGTTATCGCTTGATTCCTT
1 TAAAAAGCCATTGTAAAGGTTATCACTTGATCCCAT
* * * * * *
10429699 TAAAAAGCCAATGTAAAAGTTACCACTTAATCTCGT
1 TAAAAAGCCATTGTAAAGGTTATCACTTGATCCCAT
* * * *
10429735 GAAAAAGCTATTGTAAGGGTTATCGCTTGATCCCAT
1 TAAAAAGCCATTGTAAAGGTTATCACTTGATCCCAT
* * * *
10429771 TAAAAAGCTGA-TGTAAAGGTCATCACTTTATCTCAT
1 TAAAAAGC-CATTGTAAAGGTTATCACTTGATCCCAT
* *
10429807 GAAAAAGCCGTTGT
1 TAAAAAGCCATTGT
10429821 GAGGGTCTGG
Statistics
Matches: 89, Mismatches: 30, Indels: 5
0.72 0.24 0.04
Matches are distributed among these distances:
35 6 0.07
36 82 0.92
37 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (36 bp):
TAAAAAGCCATTGTAAAGGTTATCACTTGATCCCAT
Found at i:10429826 original size:72 final size:72
Alignment explanation
Indices: 10429665--10429826 Score: 209
Period size: 72 Copynumber: 2.3 Consensus size: 72
10429655 TGAGCCTAGT
* * *
10429665 AAAAA-CCATTGTGAGGGTTATCGCTTGATTCCTTTAAAAAGCCAATGTAAAAGTTACCACTTAA
1 AAAAAGCCATTGTGAGGGTTATCGCTTGATCCCATTAAAAAGCCAATGTAAAAGTCACCACTTAA
*
10429729 TCTCGTG
66 TCTCATG
* * ** * * *
10429736 AAAAAGCTATTGTAAGGGTTATCGCTTGATCCCATTAAAAAGCTGATGTAAAGGTCATCACTTTA
1 AAAAAGCCATTGTGAGGGTTATCGCTTGATCCCATTAAAAAGCCAATGTAAAAGTCACCACTTAA
10429801 TCTCATG
66 TCTCATG
*
10429808 AAAAAGCCGTTGTGAGGGT
1 AAAAAGCCATTGTGAGGGT
10429827 CTGGTTGATC
Statistics
Matches: 76, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
71 5 0.07
72 71 0.93
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (72 bp):
AAAAAGCCATTGTGAGGGTTATCGCTTGATCCCATTAAAAAGCCAATGTAAAAGTCACCACTTAA
TCTCATG
Found at i:10431631 original size:18 final size:16
Alignment explanation
Indices: 10431608--10431655 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 16
10431598 ATGCATAATT
10431608 TTTATTTATATTTAAA
1 TTTATTTATATTTAAA
*
10431624 TATATATTTATGTTTAAA
1 T-T-TATTTATATTTAAA
10431642 TTTATTTATTATTT
1 TTTATTTA-TATTT
10431656 TTAATCTCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 7 0.26
17 6 0.22
18 14 0.52
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (16 bp):
TTTATTTATATTTAAA
Found at i:10433918 original size:342 final size:344
Alignment explanation
Indices: 10433211--10433972 Score: 893
Period size: 342 Copynumber: 2.2 Consensus size: 344
10433201 TATTTTATGT
* * * *
10433211 ATTTTTAATATAAATATATTAACTTTCTATTTTGTCTTTTAACATTACAAAAATTATAACTTATA
1 ATTTTAAATATAAATATATTTACTTTCTATTTTG--TGTTAACATTACAAAAATTATAACTCATA
* * * * *
10433276 AAACTATTAATTATAATACATATACCATCATTTATATAAACTTATAACATATATACTTAAGGAGA
64 AAATTATTAATTACAATACATATACCATCATTTATATAAACTTATAACATAAAAACTAAAGGAGA
* *
10433341 GCTTTTGAGATTAGAATAGTTTTCAAACCTAACTATTTTTTTTTAATTTCATGAAATTAAGAACA
129 GCTTGTGAGATTAGAATAGTTTGCAAACCTAACTATTTTTTTTTAATTTCATGAAATTAAGAACA
* * * * *
10433406 AATCCATATAGTTAGTTAAATTAATTCATGAAACTATTATTATTAATTGACTTGTAATGTCTTTC
194 AATCCATATAGTTAATAAAATTAATTAATGAAACTATGATTATTAATTGACTGGTAATGTCTTTC
* * * * **
10433471 AATATATATAGTTTATATATTGTGTTAATTTATAAGAAATATAATTACTATTATATATATATGTG
259 AATATATATACTTTATATATTGGGTTAATTTACAAGAAACATAATTACTATTATATATATAAATG
** *
10433536 GGTGTGTGTCTGTATATATAC
324 ACTGTGTGTCAGTATATATAC
* * * *
10433557 --TTTAGATATAAACATATTTACTTTCTATTTTGTGTTGATATTACAAAAATTATAACTCATAAA
1 ATTTTAAATATAAATATATTTACTTTCTATTTTGTGTTAACATTACAAAAATTATAACTCATAAA
* * ** * *
10433620 ATTATTAATTACAATATATATACCTTTTTTTGTATAAATTTATAACATAAAAATCTAAAGG-GAA
66 ATTATTAATTACAATACATATACCATCATTTATATAAACTTATAACATAAAAA-CTAAAGGAG-A
* * * ** * *
10433684 G-TTGTGAGATTAGAATAGTTTGGAAACTTAATTA-TTTTTTTTAATTT-ATTGTGATTGAGAAT
129 GCTTGTGAGATTAGAATAGTTTGCAAACCTAACTATTTTTTTTTAATTTCA-TGAAATTAAGAAC
* * *
10433746 AAA-CTTATTTAGTTAATAAAATTAATTAATGAAACTATGATTATTAATTGGCTGGTAATGTCTT
193 AAATC-CATATAGTTAATAAAATTAATTAATGAAACTATGATTATTAATTGACTGGTAATGTCTT
* *
10433810 TTAATATATATACTTTATATACATTGGGTTCATTTACAAGAAACATAATTACTATTATATATATT
257 TCAATATATATACTTTATAT--ATTGGGTTAATTTACAAGAAACATAATTACTATTATATATA-T
10433875 AAAAT-ACT-T-T-T-AGTATATATAC
319 -AAATGACTGTGTGTCAGTATATATAC
*
10433897 ATTTTAAATATAAATATATTTACTTTCTATTTTGTGTTAACATTACAAAAATTATTAC-CAATAA
1 ATTTTAAATATAAATATATTTACTTTCTATTTTGTGTTAACATTACAAAAATTATAACTC-ATAA
*
10433961 ATTTATTAATTA
65 AATTATTAATTA
10433973 TGTTTGAGAT
Statistics
Matches: 352, Mismatches: 53, Indels: 26
0.82 0.12 0.06
Matches are distributed among these distances:
340 12 0.03
341 96 0.27
342 166 0.47
343 46 0.13
344 30 0.09
345 2 0.01
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.44
Consensus pattern (344 bp):
ATTTTAAATATAAATATATTTACTTTCTATTTTGTGTTAACATTACAAAAATTATAACTCATAAA
ATTATTAATTACAATACATATACCATCATTTATATAAACTTATAACATAAAAACTAAAGGAGAGC
TTGTGAGATTAGAATAGTTTGCAAACCTAACTATTTTTTTTTAATTTCATGAAATTAAGAACAAA
TCCATATAGTTAATAAAATTAATTAATGAAACTATGATTATTAATTGACTGGTAATGTCTTTCAA
TATATATACTTTATATATTGGGTTAATTTACAAGAAACATAATTACTATTATATATATAAATGAC
TGTGTGTCAGTATATATAC
Found at i:10434006 original size:20 final size:20
Alignment explanation
Indices: 10433983--10434020 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
10433973 TGTTTGAGAT
10433983 ATTTAAATTTTATTATTTAA
1 ATTTAAATTTTATTATTTAA
10434003 ATTTAAATTTTATTATTT
1 ATTTAAATTTTATTATTT
10434021 GTGTGCTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
ATTTAAATTTTATTATTTAA
Found at i:10434432 original size:22 final size:23
Alignment explanation
Indices: 10434404--10434448 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
10434394 ATAAATGTAT
10434404 TTTAAATATTAAAATAA-AAATA
1 TTTAAATATTAAAATAATAAATA
*
10434426 TTTAAATATTTAAATAATAAATA
1 TTTAAATATTAAAATAATAAATA
10434449 ATACTATTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
TTTAAATATTAAAATAATAAATA
Found at i:10438458 original size:11 final size:11
Alignment explanation
Indices: 10438433--10438470 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
10438423 TTCTTCATAC
*
10438433 CTCTTTC-TAT
1 CTCTTTCTTTT
10438443 CTCTTTCTTTT
1 CTCTTTCTTTT
*
10438454 CTCTTTCTCTT
1 CTCTTTCTTTT
10438465 CTCTTT
1 CTCTTT
10438471 TGTCCCTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 7 0.28
11 18 0.72
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.66
Consensus pattern (11 bp):
CTCTTTCTTTT
Found at i:10442480 original size:20 final size:20
Alignment explanation
Indices: 10442443--10442480 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
10442433 CAAATTAAGG
* *
10442443 CAAATGTATTGATGCATTGC
1 CAAATGTATCGATACATTGC
10442463 CAAATGTATCGATACATT
1 CAAATGTATCGATACATT
10442481 AGAGAGGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (20 bp):
CAAATGTATCGATACATTGC
Found at i:10457367 original size:14 final size:15
Alignment explanation
Indices: 10457335--10457376 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 15
10457325 TTAACTATTT
10457335 TTAGTTATATTTTTAA
1 TTAGTT-TATTTTTAA
10457351 TTAGTTTATTTTT-A
1 TTAGTTTATTTTTAA
10457365 TTAAG-TTATTTT
1 TT-AGTTTATTTT
10457377 ATTTTATGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 10 0.40
15 9 0.36
16 6 0.24
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (15 bp):
TTAGTTTATTTTTAA
Found at i:10466101 original size:45 final size:45
Alignment explanation
Indices: 10466017--10466103 Score: 113
Period size: 45 Copynumber: 1.9 Consensus size: 45
10466007 AATGTGATTA
* *
10466017 CTAGGTATATGATTGTTGAGAATGTGATTATTGAAAATATAATTG
1 CTAGGTATATGATTATTGAGAATGTGATTACTGAAAATATAATTG
* * *
10466062 CTAGGTGTATGATTATT-AGAAATGTGATTGCTGAGAATATAA
1 CTAGGTATATGATTATTGAG-AATGTGATTACTGAAAATATAA
10466104 CTTTTCAACG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
44 2 0.06
45 34 0.94
ACGTcount: A:0.36, C:0.03, G:0.23, T:0.38
Consensus pattern (45 bp):
CTAGGTATATGATTATTGAGAATGTGATTACTGAAAATATAATTG
Found at i:10467044 original size:9 final size:9
Alignment explanation
Indices: 10467030--10467061 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
10467020 AAATAGGAAG
10467030 GAAGAAAGT
1 GAAGAAAGT
10467039 GAAGAAAGT
1 GAAGAAAGT
10467048 GAAGAAAGT
1 GAAGAAAGT
10467057 -AAGAA
1 GAAGAA
10467062 GAAGAAGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 5 0.22
9 18 0.78
ACGTcount: A:0.59, C:0.00, G:0.31, T:0.09
Consensus pattern (9 bp):
GAAGAAAGT
Found at i:10470679 original size:33 final size:32
Alignment explanation
Indices: 10470642--10470708 Score: 98
Period size: 33 Copynumber: 2.1 Consensus size: 32
10470632 ATTGTATAAG
*
10470642 GTTATAAGCAACGACATAAAAGTTCAACTTCAA
1 GTTATAAGCAACAACATAAAAGTTCAAC-TCAA
* *
10470675 GTTATAAGCAGCAACTTAAAAGTTCAACTCAA
1 GTTATAAGCAACAACATAAAAGTTCAACTCAA
10470707 GT
1 GT
10470709 ACAACTAGTC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
32 6 0.19
33 25 0.81
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.25
Consensus pattern (32 bp):
GTTATAAGCAACAACATAAAAGTTCAACTCAA
Found at i:10470722 original size:32 final size:32
Alignment explanation
Indices: 10470658--10470726 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 32
10470648 AGCAACGACA
*
10470658 TAAAAGTTCAACTTCAAGTTATAAGCAGCAAC
1 TAAAAGTTCAACTTCAAGTTACAAGCAGCAAC
10470690 TTAAAAGTTCAAC-TCAAG-TACAA-CTAGTCAAC
1 -TAAAAGTTCAACTTCAAGTTACAAGC-AG-CAAC
10470722 TAAAA
1 TAAAA
10470727 TCACCATACA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
30 1 0.03
31 11 0.33
32 9 0.27
33 12 0.36
ACGTcount: A:0.46, C:0.19, G:0.10, T:0.25
Consensus pattern (32 bp):
TAAAAGTTCAACTTCAAGTTACAAGCAGCAAC
Found at i:10474530 original size:15 final size:15
Alignment explanation
Indices: 10474497--10474539 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
10474487 AATTAAGTTA
10474497 TATTGTT-ATTTG-T
1 TATTGTTAATTTGTT
10474510 TATTGTTAATTTGTT
1 TATTGTTAATTTGTT
* *
10474525 TTTTGTTAATATGTT
1 TATTGTTAATTTGTT
10474540 AGATTTTAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 7 0.27
14 5 0.19
15 14 0.54
ACGTcount: A:0.19, C:0.00, G:0.14, T:0.67
Consensus pattern (15 bp):
TATTGTTAATTTGTT
Found at i:10474708 original size:24 final size:24
Alignment explanation
Indices: 10474654--10474710 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
10474644 ATGTCTATAC
*
10474654 ATATTA-TATTAATAATATACTTT
1 ATATTATTATTAATAATATACTTA
10474677 ATATTATTATTAATAGAT-TACATTA
1 ATATTATTATTAATA-ATATAC-TTA
10474702 ATA-TATTAT
1 ATATTATTAT
10474711 ACTAAATAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 6 0.20
24 17 0.57
25 7 0.23
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (24 bp):
ATATTATTATTAATAATATACTTA
Found at i:10475176 original size:26 final size:25
Alignment explanation
Indices: 10475142--10475206 Score: 76
Period size: 26 Copynumber: 2.6 Consensus size: 25
10475132 CAAAACAAAG
*
10475142 TATAGTATGTATAGTGTATTAAGAT
1 TATACTATGTATAGTGTATTAAGAT
* *
10475167 ATATACTATGCATAGTGTATTAATAT
1 -TATACTATGTATAGTGTATTAAGAT
* *
10475193 TTTACTATATATAG
1 TATACTATGTATAG
10475207 CTAATATATA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 11 0.33
26 22 0.67
ACGTcount: A:0.37, C:0.05, G:0.14, T:0.45
Consensus pattern (25 bp):
TATACTATGTATAGTGTATTAAGAT
Found at i:10475303 original size:20 final size:20
Alignment explanation
Indices: 10475263--10475303 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
10475253 ATATATATAC
* *
10475263 TATATAATAGTATATTGTTA
1 TATATAATAGTAAATTATTA
10475283 TATATAATAGTAAATTATTA
1 TATATAATAGTAAATTATTA
10475303 T
1 T
10475304 TGACTAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (20 bp):
TATATAATAGTAAATTATTA
Found at i:10475527 original size:8 final size:8
Alignment explanation
Indices: 10475455--10475511 Score: 55
Period size: 8 Copynumber: 7.0 Consensus size: 8
10475445 CTATAGTAAC
10475455 ATTAATAT
1 ATTAATAT
10475463 ATTAATAT
1 ATTAATAT
*
10475471 ATATAGTAT
1 AT-TAATAT
10475480 ATTAATA-
1 ATTAATAT
*
10475487 AGTTACTAT
1 A-TTAATAT
10475496 ATTAA-ATT
1 ATTAATA-T
10475504 ATTAATAT
1 ATTAATAT
10475512 TAGTTATATT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
7 2 0.05
8 29 0.73
9 9 0.22
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (8 bp):
ATTAATAT
Found at i:10475945 original size:2 final size:2
Alignment explanation
Indices: 10475938--10475962 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10475928 TCATTCATTC
10475938 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 A
10475963 CACACACACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10477975 original size:17 final size:17
Alignment explanation
Indices: 10477955--10477988 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
10477945 TTGACTTATG
*
10477955 TTTTTATGTCTTTGTTT
1 TTTTTATGTCTTGGTTT
*
10477972 TTTTTTTGTCTTGGTTT
1 TTTTTATGTCTTGGTTT
10477989 GCTGCTGATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.03, C:0.06, G:0.15, T:0.76
Consensus pattern (17 bp):
TTTTTATGTCTTGGTTT
Found at i:10478116 original size:58 final size:58
Alignment explanation
Indices: 10477986--10478116 Score: 154
Period size: 58 Copynumber: 2.3 Consensus size: 58
10477976 TTTGTCTTGG
* * * *
10477986 TTTGCTGCTGATGGAGTTCTGATTAGGGGATTATTGTTGTTTTGCATGTGTTGGGTGT
1 TTTGCTGCTGATGGAGTTCTGATTAGGGGATTACTATTATTTTGCATATGTTGGGTGT
* ** * * * *
10478044 TATGCTGCCCATGGAGTTTTGATTGGGGGATTACTATTATTTTTCCTATGTTGGGTGT
1 TTTGCTGCTGATGGAGTTCTGATTAGGGGATTACTATTATTTTGCATATGTTGGGTGT
*
10478102 TTTGCTGTTGATGGA
1 TTTGCTGCTGATGGA
10478117 CTTTGCACTT
Statistics
Matches: 58, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.14, C:0.09, G:0.31, T:0.46
Consensus pattern (58 bp):
TTTGCTGCTGATGGAGTTCTGATTAGGGGATTACTATTATTTTGCATATGTTGGGTGT
Found at i:10478796 original size:15 final size:15
Alignment explanation
Indices: 10478776--10478813 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
10478766 TTTTCTCAAC
10478776 AATCACATAACCTGT
1 AATCACATAACCTGT
10478791 AATCACATAACCTGT
1 AATCACATAACCTGT
10478806 AATCACAT
1 AATCACAT
10478814 TACTAACAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.42, C:0.26, G:0.05, T:0.26
Consensus pattern (15 bp):
AATCACATAACCTGT
Found at i:10486640 original size:2 final size:2
Alignment explanation
Indices: 10486633--10486660 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
10486623 ACATTTCGCT
10486633 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
10486661 CACACACACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10489877 original size:17 final size:17
Alignment explanation
Indices: 10489855--10489890 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
10489845 TTCAAAACAA
10489855 AAAGTTATTAATTAGTT
1 AAAGTTATTAATTAGTT
* *
10489872 AAAGTTGTTAATTGGTT
1 AAAGTTATTAATTAGTT
10489889 AA
1 AA
10489891 CATAGAGAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.17, T:0.44
Consensus pattern (17 bp):
AAAGTTATTAATTAGTT
Found at i:10498215 original size:25 final size:24
Alignment explanation
Indices: 10498171--10498217 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
10498161 AGTTTAGGAC
*
10498171 TTCAAATATTAGTTTGAATGTTCA
1 TTCAAATATTAGTTTAAATGTTCA
*
10498195 TTCAAATGTTAAGTTTAAATGTT
1 TTCAAATATT-AGTTTAAATGTT
10498218 GAGTATTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.47
Consensus pattern (24 bp):
TTCAAATATTAGTTTAAATGTTCA
Found at i:10505567 original size:20 final size:21
Alignment explanation
Indices: 10505528--10505567 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
10505518 TTAATTTTTA
* *
10505528 TATATTTTTAATATAATTAAT
1 TATATTATTAATAAAATTAAT
10505549 TATATTATT-ATAAAATTAA
1 TATATTATTAATAAAATTAA
10505568 GAGATCTATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TATATTATTAATAAAATTAAT
Found at i:10507984 original size:2 final size:2
Alignment explanation
Indices: 10507977--10508010 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
10507967 CAATATAGTG
10507977 GA GA GA 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 GA GA GA
10508011 ATTTTAGATT
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:10509531 original size:24 final size:24
Alignment explanation
Indices: 10509484--10509531 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
10509474 TTATAGTTGA
* *
10509484 CATGTCATGACATAGTAGGTTTGG
1 CATGCCATGACATAGTAGGATTGG
* *
10509508 CATGCCATGACATCGTATGATTGG
1 CATGCCATGACATAGTAGGATTGG
10509532 AGTGTCACGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (24 bp):
CATGCCATGACATAGTAGGATTGG
Found at i:10509728 original size:31 final size:31
Alignment explanation
Indices: 10509557--10509728 Score: 184
Period size: 31 Copynumber: 5.5 Consensus size: 31
10509547 CTTAGTGTTG
* * * * *
10509557 GTGTGTAACAACATTTGAGTTAGTAGGCTTA
1 GTGTGTAACAACATTTAACTTGGTATGCATA
* * *
10509588 GTGTGTAACGACACTTT-ACTTGATATGCTTA
1 GTGTGTAACAACA-TTTAACTTGGTATGCATA
* *
10509619 GTGTGTAACAACATTTTACTTGATATGCATA
1 GTGTGTAACAACATTTAACTTGGTATGCATA
*
10509650 GTGTGTAACAACATTTGACTTGGTATGCATA
1 GTGTGTAACAACATTTAACTTGGTATGCATA
** * * *
10509681 GTGTCCAATAAAATTTAACTTGGTATGCATG
1 GTGTGTAACAACATTTAACTTGGTATGCATA
10509712 GTGTGTAACAACATTTA
1 GTGTGTAACAACATTTA
10509729 TTTCTTTCTT
Statistics
Matches: 120, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
30 3 0.03
31 114 0.95
32 3 0.03
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (31 bp):
GTGTGTAACAACATTTAACTTGGTATGCATA
Found at i:10514567 original size:21 final size:22
Alignment explanation
Indices: 10514532--10514575 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
10514522 CTCTTAAAGT
10514532 AATTTAAAATAAAATAACCTAA
1 AATTTAAAATAAAATAACCTAA
* *
10514554 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACCTAA
10514575 A
1 A
10514576 TTAATCACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (22 bp):
AATTTAAAATAAAATAACCTAA
Found at i:10517019 original size:76 final size:76
Alignment explanation
Indices: 10516810--10517276 Score: 409
Period size: 76 Copynumber: 6.1 Consensus size: 76
10516800 GCGTGTTACT
* * * * ** * * *
10516810 CCATAACACTACAATGACTCAACTTCTCACCATTAGATGTCATCGACATCGAACAATTAGAGCAT
1 CCATAATACTACAATGACTCAGCGTGTCACCACAAGATGTCATCAACATCTAACAATTGGAGCAT
*
10516875 GGCATGTCACC
66 GGCTTGTCACC
** * * * * * * ** ** * *
10516886 TTATAATACTGCAACGATTCAGCGGGTCATCATAAGATGTTTTTGACATCTAGCAATTGGAGTAT
1 CCATAATACTACAATGACTCAGCGTGTCACCACAAGATGTCATCAACATCTAACAATTGGAGCAT
*
10516951 GGTTTGTCACC
66 GGCTTGTCACC
* * * * *
10516962 CCATAATATTGCAACGACTCAGCGTGTCACCACAAGATGTCATCAATATTTAACAATTGGAGCAT
1 CCATAATACTACAATGACTCAGCGTGTCACCACAAGATGTCATCAACATCTAACAATTGGAGCAT
* *
10517027 TGCGTGTCACC
66 GGCTTGTCACC
* * * *
10517038 CCATAATACTACAATGACTCAACATGTCACCATAAGATGTCATCAACATCTAACAATTGGAACGA
1 CCATAATACTACAATGACTCAGCGTGTCACCACAAGATGTCATCAACATCTAACAATTGGAGC-A
*
10517103 -GGCATGTCACC
65 TGGCTTGTCACC
* * * * *
10517114 CCACAATACTACAATGACTGA-CTGTGTCTCCACAAGATGTCATCGACATCTAACAATTGGAGCG
1 CCATAATACTACAATGACTCAGC-GTGTCACCACAAGATGTCATCAACATCTAACAATTGGAGCA
*
10517178 TGGTTTGTCACC
65 TGGCTTGTCACC
** * * ** * *
10517190 TTATAATATTGCAATGACTCAGCGTGTCACCACAAGATGTCATTGACATCTAACAATTAGAGCGT
1 CCATAATACTACAATGACTCAGCGTGTCACCACAAGATGTCATCAACATCTAACAATTGGAGCAT
*
10517255 -GATGTGTCACC
66 GGCT-TGTCACC
*
10517266 CTATAATACTA
1 CCATAATACTA
10517277 ACTTAATTCA
Statistics
Matches: 313, Mismatches: 73, Indels: 10
0.79 0.18 0.03
Matches are distributed among these distances:
75 3 0.01
76 308 0.98
77 2 0.01
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.27
Consensus pattern (76 bp):
CCATAATACTACAATGACTCAGCGTGTCACCACAAGATGTCATCAACATCTAACAATTGGAGCAT
GGCTTGTCACC
Found at i:10517214 original size:228 final size:227
Alignment explanation
Indices: 10516800--10517276 Score: 564
Period size: 228 Copynumber: 2.1 Consensus size: 227
10516790 TTGAAGGGTG
* * * * * *
10516800 GCGTGTTACTCCATAACACTACAATGACTCAACTTCTCACCATTAGATGTCATCGACATCGAACA
1 GCGTGTCACCCCATAATACTACAATGACTCAACATCTCACCATAAGATGTCATCAACATCGAACA
* ** * * * * ** *
10516865 ATTAGAGCATGGCATGTCACCTTATAATACTGCAACGATTCAGCGGGTCATCATAAGATGTTTTT
66 ATTAGAACATGGCATGTCACCCCACAATACTACAACGACTCAGCGGGTCATCACAAGATGTCATC
* *
10516930 GACATCTAGCAATTGGAGTATGGTTTGTCACCCCATAATATTGCAACGACTCAGCGTGTCACCAC
131 GACATCTAACAATTGGAGCATGGTTTGTCACCCCATAATATTGCAACGACTCAGCGTGTCACCAC
* * * *
10516995 AAGATGTCATCAATATTTAACAATTGGAGCATT
196 AAGATGTCATCAACATCTAACAATTAGAGC-GT
* *
10517028 GCGTGTCACCCCATAATACTACAATGACTCAACATGTCACCATAAGATGTCATCAACATCTAACA
1 GCGTGTCACCCCATAATACTACAATGACTCAACATCTCACCATAAGATGTCATCAACATCGAACA
* * * *
10517093 ATTGGAACGA-GGCATGTCACCCCACAATACTACAATGACTGA-CTGTGTC-TCCACAAGATGTC
66 ATTAGAAC-ATGGCATGTCACCCCACAATACTACAACGACTCAGC-GGGTCAT-CACAAGATGTC
* ** *
10517155 ATCGACATCTAACAATTGGAGCGTGGTTTGTCACCTTATAATATTGCAATGACTCAGCGTGTCAC
128 ATCGACATCTAACAATTGGAGCATGGTTTGTCACCCCATAATATTGCAACGACTCAGCGTGTCAC
**
10517220 CACAAGATGTCATTGACATCTAACAATTAGAGCGT
193 CACAAGATGTCATCAACATCTAACAATTAGAGCGT
* *
10517255 GATGTGTCACCCTATAATACTA
1 G-CGTGTCACCCCATAATACTA
10517277 ACTTAATTCA
Statistics
Matches: 209, Mismatches: 36, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
227 4 0.02
228 204 0.98
229 1 0.00
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (227 bp):
GCGTGTCACCCCATAATACTACAATGACTCAACATCTCACCATAAGATGTCATCAACATCGAACA
ATTAGAACATGGCATGTCACCCCACAATACTACAACGACTCAGCGGGTCATCACAAGATGTCATC
GACATCTAACAATTGGAGCATGGTTTGTCACCCCATAATATTGCAACGACTCAGCGTGTCACCAC
AAGATGTCATCAACATCTAACAATTAGAGCGT
Found at i:10517263 original size:152 final size:152
Alignment explanation
Indices: 10516810--10517276 Score: 477
Period size: 152 Copynumber: 3.1 Consensus size: 152
10516800 GCGTGTTACT
* * * * * ** * *
10516810 CCATAACACTACAATGACTCAACTTCTCACCATTAGATGTCATCGACATCGAACAATTAGAGCAT
1 CCATAATACTACAACGACTCAGCGTGTCACCACAAGATGTCATCGACATCTAACAATTGGAGCAT
* * * * ** *
10516875 GGCATGTCACCTTATAATACTGCAACGATTCAGCGGGTCATCATAAGATGTTTTTGACATCTAGC
66 GGCATGTCACCTTATAATACTGCAATGACTCAGCGTGTCACCATAAGATGTCATTGACATCTAAC
** *
10516940 AATTGGAGTATGGTTTGTCACC
131 AATTGGAGCGTGGTATGTCACC
* * * * *
10516962 CCATAATATTGCAACGACTCAGCGTGTCACCACAAGATGTCATCAATATTTAACAATTGGAGCAT
1 CCATAATACTACAACGACTCAGCGTGTCACCACAAGATGTCATCGACATCTAACAATTGGAGCAT
* * ** * * * **
10517027 TGCGTGTCACCCCATAATACTACAATGACTCAACATGTCACCATAAGATGTCATCAACATCTAAC
66 GGCATGTCACCTTATAATACTGCAATGACTCAGCGTGTCACCATAAGATGTCATTGACATCTAAC
* * *
10517092 AATTGGAACGAGGCATGTCACC
131 AATTGGAGCGTGGTATGTCACC
* * * * *
10517114 CCACAATACTACAATGACTGA-CTGTGTCTCCACAAGATGTCATCGACATCTAACAATTGGAGCG
1 CCATAATACTACAACGACTCAGC-GTGTCACCACAAGATGTCATCGACATCTAACAATTGGAGCA
** * *
10517178 TGGTTTGTCACCTTATAATATTGCAATGACTCAGCGTGTCACCACAAGATGTCATTGACATCTAA
65 TGGCATGTCACCTTATAATACTGCAATGACTCAGCGTGTCACCATAAGATGTCATTGACATCTAA
* * *
10517243 CAATTAGAGCGTGATGTGTCACC
130 CAATTGGAGCGTGGTATGTCACC
*
10517266 CTATAATACTA
1 CCATAATACTA
10517277 ACTTAATTCA
Statistics
Matches: 248, Mismatches: 66, Indels: 2
0.78 0.21 0.01
Matches are distributed among these distances:
151 1 0.00
152 247 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.27
Consensus pattern (152 bp):
CCATAATACTACAACGACTCAGCGTGTCACCACAAGATGTCATCGACATCTAACAATTGGAGCAT
GGCATGTCACCTTATAATACTGCAATGACTCAGCGTGTCACCATAAGATGTCATTGACATCTAAC
AATTGGAGCGTGGTATGTCACC
Found at i:10518022 original size:93 final size:95
Alignment explanation
Indices: 10517855--10518044 Score: 233
Period size: 93 Copynumber: 2.0 Consensus size: 95
10517845 TAAGACAACA
* * * * *
10517855 TACATTCTCAGACATTGTCTTTCGTATTAGACAGGTGCTACGTGTGTGACTGGTTTGTTTACAAG
1 TACATTCTCAAACATTGTCGTTCGTATTAGACAAGTGCTACGTGTGCGACTGGTTTGTCTACAAG
*
10517920 ATGAGCATGATTTCGATCATCGCACTAGTT
66 ATGAACATGATTTCGATCATCGCACTAGTT
* ** *
10517950 TACATTCTCAAACATTGT-GTTCGTATTGGACAAGTG-TTGGTGTGCGA-TCGGTTTGTCTGCAA
1 TACATTCTCAAACATTGTCGTTCGTATTAGACAAGTGCTACGTGTGCGACT-GGTTTGTCTACAA
* * *
10518012 GTTGAACATGATTTCGATCGTCGCACTTGTT
65 GATGAACATGATTTCGATCATCGCACTAGTT
10518043 TA
1 TA
10518045 GGCACCAATT
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
92 1 0.01
93 48 0.59
94 15 0.19
95 17 0.21
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.37
Consensus pattern (95 bp):
TACATTCTCAAACATTGTCGTTCGTATTAGACAAGTGCTACGTGTGCGACTGGTTTGTCTACAAG
ATGAACATGATTTCGATCATCGCACTAGTT
Found at i:10521017 original size:22 final size:23
Alignment explanation
Indices: 10520991--10521136 Score: 163
Period size: 22 Copynumber: 6.4 Consensus size: 23
10520981 TCAGTCATGT
10520991 TGTTACACGCCATGTTCAAAAAA
1 TGTTACACGCCATGTTCAAAAAA
* *
10521014 -GTTACACACCATGTTTAAAAAA
1 TGTTACACGCCATGTTCAAAAAA
*
10521036 TGTTACACGCCATATT-AAAAAA
1 TGTTACACGCCATGTTCAAAAAA
* * * *
10521058 TGCTACTCGCCATGTTC-ACACA
1 TGTTACACGCCATGTTCAAAAAA
* * *
10521080 TGTTACTCGCCATGTTCACAACA
1 TGTTACACGCCATGTTCAAAAAA
10521103 TGTTACACGCCATGTTCAATAAAAA
1 TGTTACACGCCATGTTC-A-AAAAA
10521128 TGTTACACG
1 TGTTACACG
10521137 TCATATACTA
Statistics
Matches: 103, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
22 58 0.56
23 32 0.31
24 1 0.01
25 12 0.12
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.28
Consensus pattern (23 bp):
TGTTACACGCCATGTTCAAAAAA
Found at i:10521042 original size:45 final size:45
Alignment explanation
Indices: 10520991--10521136 Score: 143
Period size: 45 Copynumber: 3.2 Consensus size: 45
10520981 TCAGTCATGT
*
10520991 TGTTACACGCCATGTTCAAAAAAGTTACACACCATGTTTAAAAAA
1 TGTTACACGCCATGTTCAAAAAAGTTACACGCCATGTTTAAAAAA
* * * * * *
10521036 TGTTACACGCCATATT-AAAAAATGCTACTCGCCATG-TTCACACA
1 TGTTACACGCCATGTTCAAAAAA-GTTACACGCCATGTTTAAAAAA
* * * *
10521080 TGTTACTCGCCATGTTCACAACATGTTACACGCCATGTTCAATAAAAA
1 TGTTACACGCCATGTTCA-AAAAAGTTACACGCCATGTT-TA-AAAAA
10521128 TGTTACACG
1 TGTTACACG
10521137 TCATATACTA
Statistics
Matches: 77, Mismatches: 18, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
44 25 0.32
45 37 0.48
46 4 0.05
48 11 0.14
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.28
Consensus pattern (45 bp):
TGTTACACGCCATGTTCAAAAAAGTTACACGCCATGTTTAAAAAA
Found at i:10521472 original size:63 final size:63
Alignment explanation
Indices: 10521373--10521496 Score: 194
Period size: 63 Copynumber: 2.0 Consensus size: 63
10521363 ACCACAATAC
* * *
10521373 AATGACGATGATGCTCAATAGAGAATTGACAGAGCTGATACAATTTAGAGAGCTAAGAGAGCT
1 AATGACGATGATGCTCAACAGAGAATTGACAGAGCTGATACAATTCAAAGAGCTAAGAGAGCT
* * *
10521436 AATGACGATGGTGCTCAACAGAGAGTTGACAGAGCTGATATAATTCAAAGAGCTAAGAGAG
1 AATGACGATGATGCTCAACAGAGAATTGACAGAGCTGATACAATTCAAAGAGCTAAGAGAG
10521497 TTGAGCGAGT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.40, C:0.13, G:0.27, T:0.21
Consensus pattern (63 bp):
AATGACGATGATGCTCAACAGAGAATTGACAGAGCTGATACAATTCAAAGAGCTAAGAGAGCT
Found at i:10526290 original size:35 final size:35
Alignment explanation
Indices: 10526180--10526302 Score: 133
Period size: 35 Copynumber: 3.5 Consensus size: 35
10526170 TTTAATTATT
* *
10526180 TAATTTAATCAATTAGGCCCAATAACTTGATTAAA
1 TAATTTAATCAATTAGGTCCAATAACTTTATTAAA
* ***
10526215 CAAATTTAATCAATTAGGTCCAATAAC-TTATTTGTT
1 -TAATTTAATCAATTAGGTCCAATAACTTTA-TTAAA
*
10526251 TAATTTAAT-AACTTAGGTCCAATGACTTTATTAAA
1 TAATTTAATCAA-TTAGGTCCAATAACTTTATTAAA
*
10526286 TAATTTAATGAATTAGG
1 TAATTTAATCAATTAGG
10526303 CACANNNNNN
Statistics
Matches: 72, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
34 2 0.03
35 39 0.54
36 31 0.43
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.39
Consensus pattern (35 bp):
TAATTTAATCAATTAGGTCCAATAACTTTATTAAA
Found at i:10533938 original size:83 final size:77
Alignment explanation
Indices: 10533851--10534054 Score: 223
Period size: 83 Copynumber: 2.6 Consensus size: 77
10533841 AACAATTTTT
*
10533851 TTTAACCATGGCGTGTAACATATTTTTGTACATGGCGTGCAATAACAGTATTTTCTTTTTCAACA
1 TTTAACCATGGCGTGTAACATATTTTTGTACATGGCGTGCAACAACAGTA-TTT-TTTTT-AACA
*
10533916 TGGCATGTAACAACC
63 TAGCATGTAACAACC
* * * * ** *
10533931 TTATTTAACCATGACATGTAACATATTTTGGTACATGGCCTATAACAATAGTATTTTTTTTAACA
1 ---TTTAACCATGGCGTGTAACATATTTTTGTACATGGCGTGCAACAACAGTATTTTTTTTAACA
**
10533996 TAGTGTGTAACAACC
63 TAGCATGTAACAACC
* *
10534011 --TAACCATGGCGTGTAACATGTTTTTATACATGGCGTGCAACAAC
1 TTTAACCATGGCGTGTAACATATTTTTGTACATGGCGTGCAACAAC
10534055 TTAGCCATAG
Statistics
Matches: 101, Mismatches: 20, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
75 35 0.35
80 16 0.16
81 5 0.05
82 3 0.03
83 42 0.42
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.36
Consensus pattern (77 bp):
TTTAACCATGGCGTGTAACATATTTTTGTACATGGCGTGCAACAACAGTATTTTTTTTAACATAG
CATGTAACAACC
Found at i:10534082 original size:66 final size:66
Alignment explanation
Indices: 10534004--10534128 Score: 196
Period size: 66 Copynumber: 1.9 Consensus size: 66
10533994 CATAGTGTGT
* *
10534004 AACAACCTAACCATGGCGTGTAACATGTTTTTATACATGGCGTGCAACAACTTAGCCATAGCATG
1 AACAACCTAACCATGGCGTGTAACACGTTTTTATACATGGCGTGCAACAACTTAACCATAGCATG
10534069 C
66 C
* * * *
10534070 AACAACTTAACCATGGCGTGTCACACGTTTTTGTACATGGCGTGTAACAACTTAACCAT
1 AACAACCTAACCATGGCGTGTAACACGTTTTTATACATGGCGTGCAACAACTTAACCAT
10534129 GGCGTTTAAC
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 53 1.00
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (66 bp):
AACAACCTAACCATGGCGTGTAACACGTTTTTATACATGGCGTGCAACAACTTAACCATAGCATG
C
Found at i:10534131 original size:21 final size:21
Alignment explanation
Indices: 10534000--10534139 Score: 79
Period size: 21 Copynumber: 6.4 Consensus size: 21
10533990 TTAACATAGT
*
10534000 GTGTAACAACCTAACCATGGC
1 GTGTAACAACTTAACCATGGC
**
10534021 GTGTAACATGTTTTTATA-CATGGC
1 GTGTAACA---ACTTA-ACCATGGC
* * *
10534045 GTGCAACAACTTAGCCATAGC
1 GTGTAACAACTTAACCATGGC
* *
10534066 ATGCAACAACTTAACCATGGC
1 GTGTAACAACTTAACCATGGC
* *
10534087 GTGTCAC-ACGTTTTTGTA-CATGGC
1 GTGTAACAAC----TT-AACCATGGC
10534111 GTGTAACAACTTAACCATGGC
1 GTGTAACAACTTAACCATGGC
*
10534132 GTTTAACA
1 GTGTAACA
10534140 TGTTTCTATA
Statistics
Matches: 89, Mismatches: 18, Indels: 24
0.68 0.14 0.18
Matches are distributed among these distances:
20 3 0.03
21 53 0.60
24 29 0.33
25 4 0.04
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (21 bp):
GTGTAACAACTTAACCATGGC
Found at i:10534161 original size:45 final size:45
Alignment explanation
Indices: 10534060--10534163 Score: 127
Period size: 45 Copynumber: 2.3 Consensus size: 45
10534050 ACAACTTAGC
* * * *
10534060 CATAGCATGCAACAACTTAACCATGGCGTGTCACACGTTTTTGTA
1 CATAGCATGTAACAACTTAACCATGGCGTGTAACACGTTTCTATA
* * * *
10534105 CATGGCGTGTAACAACTTAACCATGGCGTTTAACATGTTTCTATA
1 CATAGCATGTAACAACTTAACCATGGCGTGTAACACGTTTCTATA
*
10534150 CATAGTATGTAACA
1 CATAGCATGTAACA
10534164 TCATAGCATG
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (45 bp):
CATAGCATGTAACAACTTAACCATGGCGTGTAACACGTTTCTATA
Found at i:10535582 original size:20 final size:21
Alignment explanation
Indices: 10535544--10535582 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
10535534 TTTCACATTA
*
10535544 ATTATACAAATTTAGATATAT
1 ATTATACAAATTTAAATATAT
*
10535565 ATTAT-CAATTTTAAATAT
1 ATTATACAAATTTAAATAT
10535583 TTTTGAAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (21 bp):
ATTATACAAATTTAAATATAT
Found at i:10542768 original size:34 final size:34
Alignment explanation
Indices: 10542730--10542797 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
10542720 TGTTTAGTGA
10542730 ACTTGTTCTTTAACAAGCACTTACATATTATTCT
1 ACTTGTTCTTTAACAAGCACTTACATATTATTCT
*
10542764 ACTTGTTCTTTAACAAGCACTTACATGTTATTCT
1 ACTTGTTCTTTAACAAGCACTTACATATTATTCT
10542798 CAAATATCCC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.28, C:0.21, G:0.07, T:0.44
Consensus pattern (34 bp):
ACTTGTTCTTTAACAAGCACTTACATATTATTCT
Found at i:10543223 original size:11 final size:11
Alignment explanation
Indices: 10543207--10543237 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
10543197 TCACTTTGAA
10543207 CTTTTCTTTTT
1 CTTTTCTTTTT
10543218 CTTTTCTTTTT
1 CTTTTCTTTTT
10543229 -TTTTCTTTT
1 CTTTTCTTTT
10543238 CATCACAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
CTTTTCTTTTT
Found at i:10543233 original size:15 final size:16
Alignment explanation
Indices: 10543207--10543238 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
10543197 TCACTTTGAA
10543207 CTTTTCTTTTTCTTTT
1 CTTTTCTTTTTCTTTT
10543223 CTTTT-TTTTTCTTTT
1 CTTTTCTTTTTCTTTT
10543238 C
1 C
10543239 ATCACAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (16 bp):
CTTTTCTTTTTCTTTT
Found at i:10543969 original size:16 final size:18
Alignment explanation
Indices: 10543938--10543972 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
10543928 AAATAAAGTC
10543938 TCAACTTTCACAGAAAAA
1 TCAACTTTCACAGAAAAA
10543956 TCAAC-TTC-CAGAAAAA
1 TCAACTTTCACAGAAAAA
10543972 T
1 T
10543973 AATTCTCCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 3 0.18
18 5 0.29
ACGTcount: A:0.49, C:0.23, G:0.06, T:0.23
Consensus pattern (18 bp):
TCAACTTTCACAGAAAAA
Found at i:10563868 original size:32 final size:32
Alignment explanation
Indices: 10563816--10563883 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
10563806 ACTAAGTCGT
* * *
10563816 CTCTATCTCTGAACCCAGTTTCTGGCAGTAGG
1 CTCTATCTCTAAACCCAGTTTCTGGCAATAGC
* * *
10563848 CTCTGTCTCTAAACCTAGTTTTTGGCAATAGC
1 CTCTATCTCTAAACCCAGTTTCTGGCAATAGC
10563880 CTCT
1 CTCT
10563884 TAGTCAACTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (32 bp):
CTCTATCTCTAAACCCAGTTTCTGGCAATAGC
Found at i:10565780 original size:25 final size:25
Alignment explanation
Indices: 10565751--10565810 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
10565741 GTGGTTGTAA
* *
10565751 CCACGTATATCAACTCATGGCCTAG
1 CCACGTATAACAACTCATGACCTAG
* *
10565776 CCACGTATAACAACTCGTGACCTTG
1 CCACGTATAACAACTCATGACCTAG
10565801 CCACGTATAA
1 CCACGTATAA
10565811 TCATAAACCG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.30, C:0.32, G:0.15, T:0.23
Consensus pattern (25 bp):
CCACGTATAACAACTCATGACCTAG
Found at i:10569794 original size:17 final size:17
Alignment explanation
Indices: 10569772--10569804 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
10569762 GCTTTCATTT
*
10569772 TAATTTTTATATATATC
1 TAATTTCTATATATATC
10569789 TAATTTCTATATATAT
1 TAATTTCTATATATAT
10569805 ATATATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (17 bp):
TAATTTCTATATATATC
Found at i:10587994 original size:22 final size:22
Alignment explanation
Indices: 10587949--10587994 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
10587939 TGGATGATCC
* *
10587949 TAAAAATAAAACAACAATAAAA
1 TAAAAATAAAAAAACAAGAAAA
* *
10587971 TAAAAATAAAAAAATAAGATAA
1 TAAAAATAAAAAAACAAGAAAA
10587993 TA
1 TA
10587995 GAAAGAAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.17
Consensus pattern (22 bp):
TAAAAATAAAAAAACAAGAAAA
Found at i:10588053 original size:17 final size:17
Alignment explanation
Indices: 10588031--10588079 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
10588021 CATGATATCC
*
10588031 AAAATAAATATAAAAAT
1 AAAATAAAAATAAAAAT
** *
10588048 AAAATAACCATACAAAT
1 AAAATAAAAATAAAAAT
*
10588065 AATATAAAAATAAAA
1 AAAATAAAAATAAAA
10588080 TTTTAAATTA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.20
Consensus pattern (17 bp):
AAAATAAAAATAAAAAT
Found at i:10588528 original size:31 final size:32
Alignment explanation
Indices: 10588490--10588558 Score: 106
Period size: 31 Copynumber: 2.2 Consensus size: 32
10588480 TATTTTTTTT
*
10588490 TAAAAATATAATAATAGTAA-TTTT-AAATTAA
1 TAAAAATAT-ATAATAATAATTTTTAAAATTAA
10588521 TAAAAATATATAATAATAATTTTTAAAATTAA
1 TAAAAATATATAATAATAATTTTTAAAATTAA
10588553 TAAAAA
1 TAAAAA
10588559 GTAAAATTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
30 9 0.26
31 13 0.37
32 13 0.37
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (32 bp):
TAAAAATATATAATAATAATTTTTAAAATTAA
Found at i:10588537 original size:33 final size:31
Alignment explanation
Indices: 10588491--10588558 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 31
10588481 ATTTTTTTTT
10588491 AAAAATATAATAATAGTAATTTT-AAATTAATA
1 AAAAATATAATAATA--AATTTTAAAATTAATA
*
10588523 AAAATATATAATAATAATTTTTAAAATTAATA
1 AAAA-ATATAATAATAAATTTTAAAATTAATA
10588555 AAAA
1 AAAA
10588559 GTAAAATTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
31 5 0.15
32 17 0.52
33 11 0.33
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (31 bp):
AAAAATATAATAATAAATTTTAAAATTAATA
Found at i:10589161 original size:36 final size:36
Alignment explanation
Indices: 10589120--10589188 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
10589110 TTTTCAATAG
*
10589120 TCATAACTTTTTACATAAAAAAATATAATTTTTCAT
1 TCATAACTTTTTACATAAAAAAACATAATTTTTCAT
* * *
10589156 TCATAACTTTTTATATAAAGAGACATAATTTTT
1 TCATAACTTTTTACATAAAAAAACATAATTTTT
10589189 TATTTTTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.45
Consensus pattern (36 bp):
TCATAACTTTTTACATAAAAAAACATAATTTTTCAT
Found at i:10597996 original size:587 final size:586
Alignment explanation
Indices: 10596884--10598058 Score: 1917
Period size: 587 Copynumber: 2.0 Consensus size: 586
10596874 TGCACCATAC
* * *
10596884 TATGTGTTTTGTCGAGAGATTAGATGATAAAGTGATAATAATTATATAACAAGATTATACACTGA
1 TATGTGTCTTGTCGAGAGATTAAATGATAAAGTGATAATAATTATATAACAAGACTATACACTGA
*
10596949 AAGGATGAGTCAAACCACTAAGATTCTTCTCAACATTTGGGTAGTCATTACACATTTTAGATGTC
66 AAGGATGAGTCAAACCACTAAGATTCTTCTCAACATTTAGGTAGTCATTACACATTTTAGATGTC
* *
10597014 AATCTTCACTTATAAGTATGAATTAAGGGAATTGATGATGAATGCAAAGGAGTTTAATTAATCTA
131 AATCTTAACTTATAAATATGAATTAAGGGAATTGATGATGAATGCAAAGGAGTTTAATTAATCTA
10597079 GTCTTATTGTCAACATATTAGGAATCTAATGGTTCACATACATTAAAGAATATTGCTTGAGAATT
196 GTCTTATTGTCAACATATTAGGAATCTAATGGTTCACATACATTAAAGAATATTGCTTGAGAATT
* * ** *
10597144 TGCAAAGGCGTTAACAAAGTTGGACTTAATTGAAAAAAGTTAAAAATTTCAAGAAATTAATTGAA
261 TGAAAAAGCACTAACAAAGTTGGACTTAATTGAAAAAAGTTAAAAATTTCAAGAAATTAATTAAA
*
10597209 TGATTTTAATTAATCCTAAGGTAATTTTGTAATTAAAATAAAAGTCATGTAAATCCTACTAGGAT
326 TGATTTTAATTAATCCTAAGGTAATTTTGTAATTAAAATAAAAGTCATGCAAATCCTACTAGGAT
* *
10597274 TAGGATAAACTCGATTGCCTTTACATATTAGGCTTGTGTTGCACATTATGAGGTAGCAATTCATG
391 TAGGATAAACTCGATTGCCTTTAAATATTAGGCTTATGTTGCACATTATGAGGTAGCAATTCATG
10597339 GCTACAGTCAATCCACAAACAAAGAAATCCTAAGAGACTTGTGAAGAAATCGACAAAAAAGGTGA
456 GCTACAGTCAATCCACAAACAAAGAAATCCTAAGAGACTTGTGAAGAAATCGACAAAAAAGGTGA
*
10597404 AAGCCAGTGAGCCGACTTCATTTAACCCTATGAGCAATCGATTATTCTTCATTCTCCATTTCAAC
521 AAGCCAGTGA-CCGACTTCATTTAACCCTATGAACAATCGATTATTCTTCATTCTCCATTTCAAC
10597469 CA
585 CA
* *
10597471 TATGTGTCTTGTCGAGAGATTAAATGATAAATTGATAATAATTATATAACAAGGCTATACACTGA
1 TATGTGTCTTGTCGAGAGATTAAATGATAAAGTGATAATAATTATATAACAAGACTATACACTGA
* * *
10597536 AAGTATGAGTCAAACCACTAAGACTT-TTCTTAACATTTAGGTAGTCATTAGACATTTTTAGATG
66 AAGGATGAGTCAAACCACTAAGA-TTCTTCTCAACATTTAGGTAGTCATTACACA-TTTTAGATG
* * *
10597600 TTAGTCTTAACTTATAAATATGAATTAAGGGAATTGATGATGAATGCAAAGGAGTTTGATTAATC
129 TCAATCTTAACTTATAAATATGAATTAAGGGAATTGATGATGAATGCAAAGGAGTTTAATTAATC
* *
10597665 TAGT-TCTATTGTCAACATATTAGGAAT-TAATGGTTCACATATATTAAAGAATATTGTTTGAGA
194 TAGTCT-TATTGTCAACATATTAGGAATCTAATGGTTCACATACATTAAAGAATATTGCTTGAGA
* *
10597728 ATTTGAAAAAGCACTAACAAAGTTGGACTTAATT-AAAAGAAGTTAAAAATTTCAAGGACTTAAT
258 ATTTGAAAAAGCACTAACAAAGTTGGACTTAATTGAAAA-AAGTTAAAAATTTCAAGAAATTAAT
* * * * * *
10597792 TAAATGATTTTAATTAATCTTGAGTTAATTTTGTAATTAGAATAAAAGTTATGCAAATCCTATTA
322 TAAATGATTTTAATTAATCCTAAGGTAATTTTGTAATTAAAATAAAAGTCATGCAAATCCTACTA
10597857 GGATTAGGATAAACTCGATTGCCTTTAAATATTAGGCTTATGTTGCACATTATGAGGTAGCAATT
387 GGATTAGGATAAACTCGATTGCCTTTAAATATTAGGCTTATGTTGCACATTATGAGGTAGCAATT
* *
10597922 CATGGCTACAGTCAATCCACAAACAAGGAAATCCTAAGAGACTTGTGAAGAAATCGACAATAAAG
452 CATGGCTACAGTCAATCCACAAACAAAGAAATCCTAAGAGACTTGTGAAGAAATCGACAAAAAAG
* * * * *
10597987 GTGAAAGCCAGTGACTGACTTCTTTTAACCTTATGAACCATCGATTATTCTTCATTTTCCATTTC
517 GTGAAAGCCAGTGACCGACTTCATTTAACCCTATGAACAATCGATTATTCTTCATTCTCCATTTC
10598052 AACCA
582 AACCA
10598057 TA
1 TA
10598059 GTTTATTCTT
Statistics
Matches: 544, Mismatches: 40, Indels: 9
0.92 0.07 0.02
Matches are distributed among these distances:
586 56 0.10
587 392 0.72
588 96 0.18
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (586 bp):
TATGTGTCTTGTCGAGAGATTAAATGATAAAGTGATAATAATTATATAACAAGACTATACACTGA
AAGGATGAGTCAAACCACTAAGATTCTTCTCAACATTTAGGTAGTCATTACACATTTTAGATGTC
AATCTTAACTTATAAATATGAATTAAGGGAATTGATGATGAATGCAAAGGAGTTTAATTAATCTA
GTCTTATTGTCAACATATTAGGAATCTAATGGTTCACATACATTAAAGAATATTGCTTGAGAATT
TGAAAAAGCACTAACAAAGTTGGACTTAATTGAAAAAAGTTAAAAATTTCAAGAAATTAATTAAA
TGATTTTAATTAATCCTAAGGTAATTTTGTAATTAAAATAAAAGTCATGCAAATCCTACTAGGAT
TAGGATAAACTCGATTGCCTTTAAATATTAGGCTTATGTTGCACATTATGAGGTAGCAATTCATG
GCTACAGTCAATCCACAAACAAAGAAATCCTAAGAGACTTGTGAAGAAATCGACAAAAAAGGTGA
AAGCCAGTGACCGACTTCATTTAACCCTATGAACAATCGATTATTCTTCATTCTCCATTTCAACC
A
Found at i:10598146 original size:19 final size:19
Alignment explanation
Indices: 10598122--10598169 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
10598112 TTACGAAATA
10598122 ATTGACCAAAGCCCTATGT
1 ATTGACCAAAGCCCTATGT
10598141 ATTGACCAAAGCCCTATGT
1 ATTGACCAAAGCCCTATGT
10598160 ATTGACCAAA
1 ATTGACCAAA
10598170 AAAGAAGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (19 bp):
ATTGACCAAAGCCCTATGT
Found at i:10599459 original size:16 final size:15
Alignment explanation
Indices: 10599440--10599479 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
10599430 AACTAATTTT
*
10599440 TAAAACTACTAAAAAC
1 TAAAACAACT-AAAAC
10599456 TAAAACAACTAAAAC
1 TAAAACAACTAAAAC
10599471 TAATAACAA
1 TAA-AACAA
10599480 GAATCACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.65, C:0.17, G:0.00, T:0.17
Consensus pattern (15 bp):
TAAAACAACTAAAAC
Found at i:10610862 original size:36 final size:35
Alignment explanation
Indices: 10610753--10610876 Score: 167
Period size: 35 Copynumber: 3.5 Consensus size: 35
10610743 CTTAAGTTGT
* *
10610753 GCCTAATTCATTAAATTATTTAATTAAGTCATTGG
1 GCCTAATTAATTAAATTATTTAATTAAGTTATTGG
** *
10610788 GCCTAATTAATTAAATTAAATAATTAAGTTATTAG
1 GCCTAATTAATTAAATTATTTAATTAAGTTATTGG
* *
10610823 GCCTAATTAATTAAATTTGTTTAATCAAGTTATTGG
1 GCCTAATTAATTAAA-TTATTTAATTAAGTTATTGG
*
10610859 GCCTAATTGATTAAATTA
1 GCCTAATTAATTAAATTA
10610877 AACAATTAAG
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
35 47 0.62
36 29 0.38
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (35 bp):
GCCTAATTAATTAAATTATTTAATTAAGTTATTGG
Found at i:10610863 original size:71 final size:70
Alignment explanation
Indices: 10610753--10610889 Score: 211
Period size: 71 Copynumber: 1.9 Consensus size: 70
10610743 CTTAAGTTGT
* * *
10610753 GCCTAATTCATTAAATTATTTAATTAAGTCATTGGGCCTAATTAATTAAATTAAATAATTAAGTT
1 GCCTAATTAATTAAATTATTTAATCAAGTCATTGGGCCTAATTAATTAAATTAAACAATTAAGTT
10610818 ATTAG
66 ATTAG
* * *
10610823 GCCTAATTAATTAAATTTGTTTAATCAAGTTATTGGGCCTAATTGATTAAATTAAACAATTAAGT
1 GCCTAATTAATTAAA-TTATTTAATCAAGTCATTGGGCCTAATTAATTAAATTAAACAATTAAGT
10610888 TA
65 TA
10610890 ATTGAGCTTC
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
70 14 0.23
71 46 0.77
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (70 bp):
GCCTAATTAATTAAATTATTTAATCAAGTCATTGGGCCTAATTAATTAAATTAAACAATTAAGTT
ATTAG
Found at i:10613904 original size:3 final size:3
Alignment explanation
Indices: 10613896--10613938 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
10613886 TGTTGATAAA
10613896 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
10613939 ATTTTAGAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:10622369 original size:2 final size:2
Alignment explanation
Indices: 10622360--10622392 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
10622350 TATTAAAGTC
10622360 AT AT -T 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
10622393 TTACCTCTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:10622834 original size:23 final size:24
Alignment explanation
Indices: 10622798--10622844 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
10622788 AAAAATTGAT
* *
10622798 ATAATAATTTATTTATAATAAATA
1 ATAATAATTGATTTATAAAAAATA
*
10622822 ATAA-AATTGATTTTTAAAAAATA
1 ATAATAATTGATTTATAAAAAATA
10622845 TACGTCTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
ATAATAATTGATTTATAAAAAATA
Found at i:10626397 original size:12 final size:12
Alignment explanation
Indices: 10626372--10626418 Score: 71
Period size: 12 Copynumber: 4.0 Consensus size: 12
10626362 AGAGATTTTT
10626372 GAGGCAGC-AGA
1 GAGGCAGCAAGA
10626383 GAGGCAGCAAGA
1 GAGGCAGCAAGA
10626395 GAGGCAGCAA-A
1 GAGGCAGCAAGA
10626406 GGAGGCAGCAAGA
1 -GAGGCAGCAAGA
10626419 AACTATTCTG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 9 0.27
12 23 0.70
13 1 0.03
ACGTcount: A:0.40, C:0.17, G:0.43, T:0.00
Consensus pattern (12 bp):
GAGGCAGCAAGA
Found at i:10634455 original size:21 final size:22
Alignment explanation
Indices: 10634426--10634469 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
10634416 AAGTGATTAA
10634426 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
* *
10634447 TTTAGGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
10634469 T
1 T
10634470 ACTTTAAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:10635030 original size:12 final size:12
Alignment explanation
Indices: 10634999--10635045 Score: 71
Period size: 12 Copynumber: 4.0 Consensus size: 12
10634989 AGAGATTTTT
10634999 GAGGCAGCAAGA
1 GAGGCAGCAAGA
10635011 GA-GCAGCAAGA
1 GAGGCAGCAAGA
10635022 GAGGCAGCAA-A
1 GAGGCAGCAAGA
10635033 GGAGGCAGCAAGA
1 -GAGGCAGCAAGA
10635046 AACTATTCTG
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
11 12 0.38
12 19 0.59
13 1 0.03
ACGTcount: A:0.43, C:0.17, G:0.40, T:0.00
Consensus pattern (12 bp):
GAGGCAGCAAGA
Found at i:10636085 original size:27 final size:27
Alignment explanation
Indices: 10636048--10636123 Score: 125
Period size: 27 Copynumber: 2.8 Consensus size: 27
10636038 CCTTTGATTT
* *
10636048 TAAAAATTAGTCACGTAATTCCAATGCC
1 TAAAAA-TAGTCAAGTAATGCCAATGCC
10636076 TAAAAATAGTCAAGTAATGCCAATGCC
1 TAAAAATAGTCAAGTAATGCCAATGCC
10636103 TAAAAATAGTCAAGTAATGCC
1 TAAAAATAGTCAAGTAATGCC
10636124 TTAGTCACAC
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
27 40 0.87
28 6 0.13
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.25
Consensus pattern (27 bp):
TAAAAATAGTCAAGTAATGCCAATGCC
Found at i:10638321 original size:38 final size:38
Alignment explanation
Indices: 10638248--10638327 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 38
10638238 ATAGTAATAA
* * * *
10638248 AATGATTAAAAACCATTCACGCAATGCCTAAGTTATGT
1 AATGACTAAAAACCAGTCACACAATGCCTAAGTTATGC
**
10638286 AATGACTAAAAACCAGTCACACAATGCCTTTGTTATGC
1 AATGACTAAAAACCAGTCACACAATGCCTAAGTTATGC
10638324 AATG
1 AATG
10638328 CATATCAACT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.28
Consensus pattern (38 bp):
AATGACTAAAAACCAGTCACACAATGCCTAAGTTATGC
Found at i:10645527 original size:21 final size:22
Alignment explanation
Indices: 10645498--10645541 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
10645488 AAGTGATTAA
10645498 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
* *
10645519 TTTAGGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
10645541 T
1 T
10645542 ACTTTAAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:10645808 original size:55 final size:55
Alignment explanation
Indices: 10645724--10645834 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
10645714 ATCGAATTAT
10645724 AAGAAGAAGGGAAACAATGTTTATGTTCACCAATTGGCCCAGTTCTGATTGGATC
1 AAGAAGAAGGGAAACAATGTTTATGTTCACCAATTGGCCCAGTTCTGATTGGATC
10645779 AAGAAGAAGGGAAACAATGTTTATGTTCACCAATTGGCCCAGTTCTGATTGGATC
1 AAGAAGAAGGGAAACAATGTTTATGTTCACCAATTGGCCCAGTTCTGATTGGATC
10645834 A
1 A
10645835 TGGTCAAAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.27
Consensus pattern (55 bp):
AAGAAGAAGGGAAACAATGTTTATGTTCACCAATTGGCCCAGTTCTGATTGGATC
Found at i:10648957 original size:6 final size:6
Alignment explanation
Indices: 10648946--10648970 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
10648936 TTAATTAAAA
10648946 ATTTAT ATTTAT ATTTAT ATTTAT A
1 ATTTAT ATTTAT ATTTAT ATTTAT A
10648971 GATCATGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
ATTTAT
Found at i:10650080 original size:22 final size:22
Alignment explanation
Indices: 10650055--10650100 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
10650045 ATTTTGTACC
10650055 AAACTAATCACTATAAACTTAA
1 AAACTAATCACTATAAACTTAA
10650077 AAACTAATCACTATAAACTTAA
1 AAACTAATCACTATAAACTTAA
10650099 AA
1 AA
10650101 GTTACATCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.57, C:0.17, G:0.00, T:0.26
Consensus pattern (22 bp):
AAACTAATCACTATAAACTTAA
Found at i:10655276 original size:55 final size:55
Alignment explanation
Indices: 10655217--10655325 Score: 148
Period size: 55 Copynumber: 2.0 Consensus size: 55
10655207 GAGATTTGAT
* *
10655217 CAATTTTGTTAAGCAGCTGAAGTATATAA-TTACTAAACTATAAAAAAGGCTTAAC
1 CAATTTTGATAAGCAACTGAAGTATA-AATTTACTAAACTATAAAAAAGGCTTAAC
** * *
10655272 CAATTTTGATAAGCAACTGAAGTATAAATTTGTTAAACTATGAAAAAGGTTTAA
1 CAATTTTGATAAGCAACTGAAGTATAAATTTACTAAACTATAAAAAAGGCTTAA
10655326 TTGCTTTTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
54 2 0.04
55 45 0.96
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.32
Consensus pattern (55 bp):
CAATTTTGATAAGCAACTGAAGTATAAATTTACTAAACTATAAAAAAGGCTTAAC
Found at i:10655340 original size:55 final size:54
Alignment explanation
Indices: 10655217--10655354 Score: 134
Period size: 55 Copynumber: 2.5 Consensus size: 54
10655207 GAGATTTGAT
* *
10655217 CAATTTTGTTAAGCAGCTGAAGTATATAATTACTAAACTATAAAAAAGGCTTAAC
1 CAATTTTATTAAGCAACTGAAGTATA-AATTACTAAACTATAAAAAAGGCTTAAC
** * * *
10655272 CAATTTTGA-TAAGCAACTGAAGTATAAATTTGTTAAACTATGAAAAAGGTTTAAT
1 CAATTTT-ATTAAGCAACTGAAGTATAAA-TTACTAAACTATAAAAAAGGCTTAAC
*** * *
10655327 TGCTTTTATTAAGCAAGTGAACTATAAA
1 CAATTTTATTAAGCAACTGAAGTATAAA
10655355 GTTGGTATAC
Statistics
Matches: 68, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
54 3 0.04
55 65 0.96
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (54 bp):
CAATTTTATTAAGCAACTGAAGTATAAATTACTAAACTATAAAAAAGGCTTAAC
Done.